From 45100528adbaa9dcfd1dee3db13d837982dd8ae0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 08:54:53 -0400 Subject: [PATCH 01/75] Update pair_coul.rst --- doc/src/pair_coul.rst | 79 +++++++++++++++++++------------------------ 1 file changed, 35 insertions(+), 44 deletions(-) diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 4874bf044e..37193d752c 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -1,58 +1,55 @@ .. index:: pair_style coul/cut +.. index:: pair_style coul/cut/gpu +.. index:: pair_style coul/cut/kk +.. index:: pair_style coul/cut/omp +.. index:: pair_style coul/debye +.. index:: pair_style coul/debye/gpu +.. index:: pair_style coul/debye/kk +.. index:: pair_style coul/debye/omp +.. index:: pair_style coul/dsf +.. index:: pair_style coul/dsf/gpu +.. index:: pair_style coul/dsf/kk +.. index:: pair_style coul/dsf/omp +.. index:: pair_style coul/long +.. index:: pair_style coul/long/omp +.. index:: pair_style coul/long/kk +.. index:: pair_style coul/long/gpu +.. index:: pair_style coul/msm +.. index:: pair_style coul/msm/omp +.. index:: pair_style coul/streitz +.. index:: pair_style coul/wolf +.. index:: pair_style coul/wolf/kk +.. index:: pair_style coul/wolf/omp +.. index:: pair_style tip4p/cut +.. index:: pair_style tip4p/cut/omp +.. index:: pair_style tip4p/long +.. index:: pair_style tip4p/long/omp + pair_style coul/cut command =========================== -pair_style coul/cut/gpu command -=============================== - -pair_style coul/cut/kk command -============================== - -pair_style coul/cut/omp command -=============================== +Accelerator Variants: *coul/cut/gpu*, *coul/cut/kk*, *coul/cut/omp* pair_style coul/debye command ============================= -pair_style coul/debye/gpu command -================================= - -pair_style coul/debye/kk command -================================ - -pair_style coul/debye/omp command -================================= +Accelerator Variants: *coul/debye/gpu*, *coul/debye/kk*, *coul/debye/omp* pair_style coul/dsf command =========================== -pair_style coul/dsf/gpu command -=============================== - -pair_style coul/dsf/kk command -============================== - -pair_style coul/dsf/omp command -=============================== +Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp* pair_style coul/long command ============================ -pair_style coul/long/omp command -================================ - -pair_style coul/long/gpu command -================================ - -pair_style coul/long/kk command -=============================== +Accelerator Variants: *coul/long/omp*, *coul/long/kk*, *coul/long/gpu* pair_style coul/msm command =========================== -pair_style coul/msm/omp command -=============================== +Accelerator Variants: *coul/msm/omp* pair_style coul/streitz command =============================== @@ -60,23 +57,17 @@ pair_style coul/streitz command pair_style coul/wolf command ============================ -pair_style coul/wolf/kk command -=============================== - -pair_style coul/wolf/omp command -================================ +Accelerator Variants: *coul/wolf/kk*, *coul/wolf/omp* pair_style tip4p/cut command ============================ +Accelerator Variants: *tip4p/cut/omp* + pair_style tip4p/long command ============================= -pair_style tip4p/cut/omp command -================================ - -pair_style tip4p/long/omp command -================================= +Accelerator Variants: *tip4p/long/omp* Syntax """""" -- GitLab From 7e733913d798f7b8b0b2fe37db284619ed74f67a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:03:00 -0400 Subject: [PATCH 02/75] Update pair_fep_soft.rst --- doc/src/pair_fep_soft.rst | 61 +++++++++++++++++++++++---------------- 1 file changed, 36 insertions(+), 25 deletions(-) diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index bd38fe1ec9..be35f84508 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -1,64 +1,75 @@ .. index:: pair_style lj/cut/soft +.. index:: pair_style lj/cut/soft/omp +.. index:: pair_style lj/cut/coul/cut/soft +.. index:: pair_style lj/cut/coul/cut/soft/omp +.. index:: pair_style lj/cut/coul/long/soft +.. index:: pair_style lj/cut/coul/long/soft/omp +.. index:: pair_style lj/cut/tip4p/long/soft +.. index:: pair_style lj/cut/tip4p/long/soft/omp +.. index:: pair_style lj/charmm/coul/long/soft +.. index:: pair_style lj/charmm/coul/long/soft/omp +.. index:: pair_style lj/class2/soft +.. index:: pair_style lj/class2/coul/cut/soft +.. index:: pair_style lj/class2/coul/long/soft +.. index:: pair_style coul/cut/soft +.. index:: pair_style coul/cut/soft/omp +.. index:: pair_style coul/long/soft +.. index:: pair_style coul/long/soft/omp +.. index:: pair_style tip4p/long/soft +.. index:: pair_style tip4p/long/soft/omp +.. index:: pair_style morse/soft pair_style lj/cut/soft command ============================== -pair_style lj/cut/soft/omp command -================================== +Accelerator Styles: *lj/cut/soft/omp* pair_style lj/cut/coul/cut/soft command ======================================= -pair_style lj/cut/coul/cut/soft/omp command -=========================================== +Accelerator Styles: *lj/cut/coul/cut/soft/omp* pair_style lj/cut/coul/long/soft command ======================================== -pair_style lj/cut/coul/long/soft/omp command -============================================ +Accelerator Styles: *lj/cut/coul/long/soft/omp* pair_style lj/cut/tip4p/long/soft command -========================================== +========================================= -pair_style lj/cut/tip4p/long/soft/omp command -============================================== +Accelerator Styles: *lj/cut/tip4p/long/soft/omp* pair_style lj/charmm/coul/long/soft command -============================================ +=========================================== -pair_style lj/charmm/coul/long/soft/omp command -================================================ +Accelerator Styles: *lj/charmm/coul/long/soft/omp* pair_style lj/class2/soft command -================================== +================================= pair_style lj/class2/coul/cut/soft command -=========================================== +========================================== pair_style lj/class2/coul/long/soft command -============================================ +=========================================== pair_style coul/cut/soft command -================================= +================================ -pair_style coul/cut/soft/omp command -===================================== +Accelerator Styles: *coul/cut/soft/omp* pair_style coul/long/soft command -================================== +================================= -pair_style coul/long/soft/omp command -====================================== +Accelerator Styles: *coul/long/soft/omp* pair_style tip4p/long/soft command -=================================== +================================== -pair_style tip4p/long/soft/omp command -======================================= +Accelerator Styles: *tip4p/long/soft/omp* pair_style morse/soft command -============================== +============================= Syntax """""" -- GitLab From a9cf25db4cdff396b0ad5515da63fa4aa9314153 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:13:59 -0400 Subject: [PATCH 03/75] Update pair_eam.rst --- doc/src/pair_eam.rst | 64 +++++++++++++++----------------------------- 1 file changed, 22 insertions(+), 42 deletions(-) diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index c5f9b26435..56eed64d01 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -1,40 +1,33 @@ .. index:: pair_style eam +.. index:: pair_style eam/gpu +.. index:: pair_style eam/intel +.. index:: pair_style eam/kk +.. index:: pair_style eam/omp +.. index:: pair_style eam/opt +.. index:: pair_style eam/alloy +.. index:: pair_style eam/alloy/gpu +.. index:: pair_style eam/alloy/intel +.. index:: pair_style eam/alloy/kk +.. index:: pair_style eam/alloy/omp +.. index:: pair_style eam/alloy/opt +.. index:: pair_style eam/cd +.. index:: pair_style eam/cd/old +.. index:: pair_style eam/fs +.. index:: pair_style eam/fs/gpu +.. index:: pair_style eam/fs/intel +.. index:: pair_style eam/fs/kk +.. index:: pair_style eam/fs/omp +.. index:: pair_style eam/fs/opt pair_style eam command ====================== -pair_style eam/gpu command -========================== - -pair_style eam/intel command -============================ - -pair_style eam/kk command -========================= - -pair_style eam/omp command -========================== - -pair_style eam/opt command -========================== +Accelerator Styles: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* pair_style eam/alloy command ============================ -pair_style eam/alloy/gpu command -================================ - -pair_style eam/alloy/intel command -================================== - -pair_style eam/alloy/kk command -=============================== - -pair_style eam/alloy/omp command -================================ - -pair_style eam/alloy/opt command -================================ +Accelerator Styles: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* pair_style eam/cd command ========================= @@ -45,20 +38,7 @@ pair_style eam/cd/old command pair_style eam/fs command ========================= -pair_style eam/fs/gpu command -============================= - -pair_style eam/fs/intel command -=============================== - -pair_style eam/fs/kk command -============================ - -pair_style eam/fs/omp command -============================= - -pair_style eam/fs/opt command -============================= +Accelerator Styles: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* Syntax """""" -- GitLab From 77f803b366f7ca60fcb73d6a30e945d9bfda4b50 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:14:20 -0400 Subject: [PATCH 04/75] Update pair_charmm.rst --- doc/src/pair_charmm.rst | 49 +++++++++++++++++------------------------ 1 file changed, 20 insertions(+), 29 deletions(-) diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index 183311e34d..cef1b333fb 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -1,49 +1,40 @@ .. index:: pair_style lj/charmm/coul/charmm +.. index:: pair_style lj/charmm/coul/charmm/intel +.. index:: pair_style lj/charmm/coul/charmm/kk +.. index:: pair_style lj/charmm/coul/charmm/omp +.. index:: pair_style lj/charmm/coul/charmm/implicit +.. index:: pair_style lj/charmm/coul/charmm/implicit/kk +.. index:: pair_style lj/charmm/coul/charmm/implicit/omp +.. index:: pair_style lj/charmm/coul/long +.. index:: pair_style lj/charmm/coul/long/gpu +.. index:: pair_style lj/charmm/coul/long/intel +.. index:: pair_style lj/charmm/coul/long/kk +.. index:: pair_style lj/charmm/coul/long/opt +.. index:: pair_style lj/charmm/coul/long/omp +.. index:: pair_style lj/charmm/coul/msm +.. index:: pair_style lj/charmm/coul/msm/omp +.. index:: pair_style lj/charmmfsw/coul/charmmfsh +.. index:: pair_style lj/charmmfsw/coul/long pair_style lj/charmm/coul/charmm command ========================================= -pair_style lj/charmm/coul/charmm/intel command -=============================================== - -pair_style lj/charmm/coul/charmm/kk command -============================================ - -pair_style lj/charmm/coul/charmm/omp command -============================================= +Accelerator Styles: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* pair_style lj/charmm/coul/charmm/implicit command ================================================== -pair_style lj/charmm/coul/charmm/implicit/kk command -===================================================== - -pair_style lj/charmm/coul/charmm/implicit/omp command -====================================================== +Accelerator Styles: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* pair_style lj/charmm/coul/long command ======================================= -pair_style lj/charmm/coul/long/gpu command -=========================================== - -pair_style lj/charmm/coul/long/intel command -============================================= - -pair_style lj/charmm/coul/long/kk command -========================================== - -pair_style lj/charmm/coul/long/opt command -=========================================== - -pair_style lj/charmm/coul/long/omp command -=========================================== +Accelerator Styles: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* pair_style lj/charmm/coul/msm command ====================================== -pair_style lj/charmm/coul/msm/omp command -========================================== +Accelerator Styles: *lj/charmm/coul/msm/omp* pair_style lj/charmmfsw/coul/charmmfsh command =============================================== -- GitLab From dce7a39021ac99ddb6e4a85891417af9d8540fb7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:47:32 -0400 Subject: [PATCH 05/75] Update pair_buck.rst --- doc/src/pair_buck.rst | 56 ++++++++++++++++--------------------------- 1 file changed, 21 insertions(+), 35 deletions(-) diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index e8a1475ccb..6ff5f84fe2 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -1,55 +1,41 @@ .. index:: pair_style buck +.. index:: pair_style buck +.. index:: pair_style buck/gpu +.. index:: pair_style buck/intel +.. index:: pair_style buck/kk +.. index:: pair_style buck/omp +.. index:: pair_style buck/coul/cut +.. index:: pair_style buck/coul/cut/gpu +.. index:: pair_style buck/coul/cut/intel +.. index:: pair_style buck/coul/cut/kk +.. index:: pair_style buck/coul/cut/omp +.. index:: pair_style buck/coul/long +.. index:: pair_style buck/coul/long/gpu +.. index:: pair_style buck/coul/long/intel +.. index:: pair_style buck/coul/long/kk +.. index:: pair_style buck/coul/long/omp +.. index:: pair_style buck/coul/msm +.. index:: pair_style buck/coul/msm/omp pair_style buck command ======================== -pair_style buck/gpu command -============================ - -pair_style buck/intel command -============================== - -pair_style buck/kk command -=========================== - -pair_style buck/omp command -============================ +Accelerator Styles: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* pair_style buck/coul/cut command ================================= -pair_style buck/coul/cut/gpu command -===================================== - -pair_style buck/coul/cut/intel command -======================================= - -pair_style buck/coul/cut/kk command -==================================== - -pair_style buck/coul/cut/omp command -===================================== +Accelerator Styles: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* pair_style buck/coul/long command ================================== -pair_style buck/coul/long/gpu command -====================================== - -pair_style buck/coul/long/intel command -======================================== - -pair_style buck/coul/long/kk command -===================================== - -pair_style buck/coul/long/omp command -====================================== +Accelerator Styles: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* pair_style buck/coul/msm command ================================= -pair_style buck/coul/msm/omp command -===================================== +Accelerator Styles: *buck/coul/msm/omp* Syntax """""" -- GitLab From 7ae98ffae11ee3b75ea2bba13e89db49444f5d02 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:50:16 -0400 Subject: [PATCH 06/75] Update fix_rigid.rst --- doc/src/fix_rigid.rst | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index a143817303..8756e72db1 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -1,40 +1,49 @@ .. index:: fix rigid +.. index:: fix rigid/omp +.. index:: fix rigid/nve +.. index:: fix rigid/nve/omp +.. index:: fix rigid/nvt +.. index:: fix rigid/nvt/omp +.. index:: fix rigid/npt +.. index:: fix rigid/npt/omp +.. index:: fix rigid/nph +.. index:: fix rigid/nph/omp +.. index:: fix rigid/small +.. index:: fix rigid/small/omp +.. index:: fix rigid/nve/small +.. index:: fix rigid/nvt/small +.. index:: fix rigid/npt/small +.. index:: fix rigid/nph/small fix rigid command ================= -fix rigid/omp command -===================== +Accelerator Styles: *rigid/omp* fix rigid/nve command ===================== -fix rigid/nve/omp command -========================= +Accelerator Styles: *rigid/nve/omp* fix rigid/nvt command ===================== -fix rigid/nvt/omp command -========================= +Accelerator Styles: *rigid/nvt/omp* fix rigid/npt command ===================== -fix rigid/npt/omp command -========================= +Accelerator Styles: *rigid/npt/omp* fix rigid/nph command ===================== -fix rigid/nph/omp command -========================= +Accelerator Styles: *rigid/nph/omp* fix rigid/small command ======================= -fix rigid/small/omp command -=========================== +Accelerator Styles: *rigid/small/omp* fix rigid/nve/small command =========================== -- GitLab From a6a49d80b27a5b0f3c2acc1ef899e700a1b37adb Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:19:20 -0400 Subject: [PATCH 07/75] Update pair_sdk.rst --- doc/src/pair_sdk.rst | 26 +++++++++++--------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 501ce6cd85..02fed36130 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -1,31 +1,27 @@ .. index:: pair_style lj/sdk +.. index:: pair_style lj/sdk/gpu +.. index:: pair_style lj/sdk/kk +.. index:: pair_style lj/sdk/omp +.. index:: pair_style lj/sdk/coul/long +.. index:: pair_style lj/sdk/coul/long/gpu +.. index:: pair_style lj/sdk/coul/long/omp +.. index:: pair_style lj/sdk/coul/msm +.. index:: pair_style lj/sdk/coul/msm/omp pair_style lj/sdk command ========================= -pair_style lj/sdk/gpu command -============================= - -pair_style lj/sdk/kk command -============================ - -pair_style lj/sdk/omp command -============================= +Accelerator Styles: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* pair_style lj/sdk/coul/long command =================================== -pair_style lj/sdk/coul/long/gpu command -======================================= - -pair_style lj/sdk/coul/long/omp command -======================================= +Accelerator Styles: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* pair_style lj/sdk/coul/msm command ================================== -pair_style lj/sdk/coul/msm/omp command -====================================== +Accelerator Styles: *lj/sdk/coul/msm/omp* Syntax """""" -- GitLab From e5f1f58aab04cf013f277760981ae82e1a72d8f8 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:26:37 -0400 Subject: [PATCH 08/75] Update pair_born.rst --- doc/src/pair_born.rst | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 761b40b812..15ce4ac560 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -1,41 +1,40 @@ .. index:: pair_style born +.. index:: pair_style born/omp +.. index:: pair_style born/gpu +.. index:: pair_style born/coul/long +.. index:: pair_style born/coul/long/gpu +.. index:: pair_style born/coul/long/omp +.. index:: pair_style born/coul/msm +.. index:: pair_style born/coul/msm/omp +.. index:: pair_style born/coul/wolf +.. index:: pair_style born/coul/wolf/gpu +.. index:: pair_style born/coul/wolf/omp +.. index:: pair_style born/coul/dsf pair_style born command ======================= -pair_style born/omp command -=========================== - -pair_style born/gpu command -=========================== +Accelerator Styles: *born/omp*, *born/gpu* pair_style born/coul/long command ================================= -pair_style born/coul/long/gpu command -===================================== - -pair_style born/coul/long/omp command -===================================== +Accelerator Styles: *born/coul/long/gpu*, *born/coul/long/omp* pair_style born/coul/msm command ================================ -pair_style born/coul/msm/omp command -==================================== +Accelerator Styles: *born/coul/msm/omp* pair_style born/coul/wolf command ================================= -pair_style born/coul/wolf/gpu command -===================================== - -pair_style born/coul/wolf/omp command -===================================== +Accelerator Styles: *born/coul/wolf/gpu*, *born/coul/wolf/omp* pair_style born/coul/dsf command ================================ + Syntax """""" -- GitLab From 4d6be195eca30d8e3979059687e3cbf5dfa1942d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:29:29 -0400 Subject: [PATCH 09/75] Add utility to fixup doc headers --- doc/utils/fixup_headers.py | 63 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100755 doc/utils/fixup_headers.py diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py new file mode 100755 index 0000000000..9cb11e9cb5 --- /dev/null +++ b/doc/utils/fixup_headers.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python3 +# Utility script to fix headers in doc pages and generate "Accelerator Styles" portion +import shutil +import re +import argparse + +pattern = re.compile(r"^(fix|pair_style)\s+([a-zA-Z0-9/_]+)\s+command$") + +parser = argparse.ArgumentParser(description='Fixup headers in docs') +parser.add_argument('files', metavar='FILE', nargs='+', help='files to fix') +args = parser.parse_args() + +for orig_file in args.files: + command_type = "unknown" + styles = [] + headings = {} + new_file = f"{orig_file}.tmp" + + with open(orig_file, 'r') as reader, open(new_file, 'w') as writer: + for line in reader: + if line.startswith("Syntax"): + break + + m = pattern.match(line) + if m: + command_type = m.group(1) + style = m.group(2) + + styles.append(style) + + base_name = '/'.join(style.split('/')[0:-1]) + ext = style.split('/')[-1] + + if ext not in ('omp', 'intel', 'kk', 'gpu', 'opt'): + headings[style] = [] + else: + headings[base_name].append(style) + + # write new header + for s in styles: + print(f".. index:: {command_type} {s}", file=writer) + + print(file=writer) + + for s, variants in headings.items(): + header = f"{command_type} {s} command" + print(header, file=writer) + print("="*len(header), file=writer) + print(file=writer) + + if len(variants) > 0: + print("Accelerator Styles: ", end="", file=writer) + print(", ".join([f"*{v}*" for v in variants]), file=writer) + + print(file=writer) + + # write rest of reader + print(line, end="", file=writer) + for line in reader: + print(line, end="", file=writer) + + # override original file + shutil.move(new_file, orig_file) -- GitLab From 3a22f26e87b39a35dd2a1626b191fd80a7ccf027 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:29:46 -0400 Subject: [PATCH 10/75] Update pair_cs.rst --- doc/src/pair_cs.rst | 40 ++++++++++++++++++++++++++-------------- 1 file changed, 26 insertions(+), 14 deletions(-) diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 8efd49197d..ae5c29aa32 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -1,37 +1,49 @@ .. index:: pair_style born/coul/dsf/cs +.. index:: pair_style born/coul/long/cs +.. index:: pair_style born/coul/long/cs/gpu +.. index:: pair_style born/coul/wolf/cs +.. index:: pair_style born/coul/wolf/cs/gpu +.. index:: pair_style buck/coul/long/cs +.. index:: pair_style coul/long/cs +.. index:: pair_style coul/long/cs/gpu +.. index:: pair_style coul/wolf/cs +.. index:: pair_style lj/cut/coul/long/cs +.. index:: pair_style lj/class2/coul/long/cs pair_style born/coul/dsf/cs command -==================================== +=================================== + pair_style born/coul/long/cs command -===================================== +==================================== -pair_style born/coul/long/cs/gpu command -========================================= +Accelerator Styles: *born/coul/long/cs/gpu* pair_style born/coul/wolf/cs command -===================================== +==================================== -pair_style born/coul/wolf/cs/gpu command -========================================= +Accelerator Styles: *born/coul/wolf/cs/gpu* pair_style buck/coul/long/cs command -===================================== +==================================== + pair_style coul/long/cs command -================================ +=============================== -pair_style coul/long/cs/gpu command -==================================== +Accelerator Styles: *coul/long/cs/gpu* pair_style coul/wolf/cs command -================================ +=============================== + pair_style lj/cut/coul/long/cs command -======================================= +====================================== + pair_style lj/class2/coul/long/cs command -========================================== +========================================= + Syntax """""" -- GitLab From 49a6bf5e30b45b7c27228c2502d8e0174e990858 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:30:31 -0400 Subject: [PATCH 11/75] Update pair_class2.rst --- doc/src/pair_class2.rst | 34 +++++++++++++--------------------- 1 file changed, 13 insertions(+), 21 deletions(-) diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 66a696938f..6fcdd4f533 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -1,37 +1,29 @@ .. index:: pair_style lj/class2 +.. index:: pair_style lj/class2/gpu +.. index:: pair_style lj/class2/kk +.. index:: pair_style lj/class2/omp +.. index:: pair_style lj/class2/coul/cut +.. index:: pair_style lj/class2/coul/cut/kk +.. index:: pair_style lj/class2/coul/cut/omp +.. index:: pair_style lj/class2/coul/long +.. index:: pair_style lj/class2/coul/long/gpu +.. index:: pair_style lj/class2/coul/long/kk +.. index:: pair_style lj/class2/coul/long/omp pair_style lj/class2 command ============================ -pair_style lj/class2/gpu command -================================ - -pair_style lj/class2/kk command -=============================== - -pair_style lj/class2/omp command -================================ +Accelerator Styles: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* pair_style lj/class2/coul/cut command ===================================== -pair_style lj/class2/coul/cut/kk command -======================================== - -pair_style lj/class2/coul/cut/omp command -========================================= +Accelerator Styles: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* pair_style lj/class2/coul/long command ====================================== -pair_style lj/class2/coul/long/gpu command -========================================== - -pair_style lj/class2/coul/long/kk command -========================================= - -pair_style lj/class2/coul/long/omp command -========================================== +Accelerator Styles: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* Syntax """""" -- GitLab From 3c60a9e08e7d5b9e5abc82e15c8acf44e5bcecba Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:31:21 -0400 Subject: [PATCH 12/75] Update fix_nh.rst --- doc/src/fix_nh.rst | 34 +++++++++++++--------------------- 1 file changed, 13 insertions(+), 21 deletions(-) diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 64a3c3b061..3e23c46e61 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -1,37 +1,29 @@ .. index:: fix nvt +.. index:: fix nvt/intel +.. index:: fix nvt/kk +.. index:: fix nvt/omp +.. index:: fix npt +.. index:: fix npt/intel +.. index:: fix npt/kk +.. index:: fix npt/omp +.. index:: fix nph +.. index:: fix nph/kk +.. index:: fix nph/omp fix nvt command =============== -fix nvt/intel command -===================== - -fix nvt/kk command -================== - -fix nvt/omp command -=================== +Accelerator Styles: *nvt/intel*, *nvt/kk*, *nvt/omp* fix npt command =============== -fix npt/intel command -===================== - -fix npt/kk command -================== - -fix npt/omp command -=================== +Accelerator Styles: *npt/intel*, *npt/kk*, *npt/omp* fix nph command =============== -fix nph/kk command -================== - -fix nph/omp command -=================== +Accelerator Styles: *nph/kk*, *nph/omp* Syntax """""" -- GitLab From e4790331098575c57efccf5a17a19e7e4e027a51 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:51:47 -0400 Subject: [PATCH 13/75] Avoid breaking already fixed headers --- doc/utils/fixup_headers.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 9cb11e9cb5..7bdd11a607 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -4,6 +4,7 @@ import shutil import re import argparse +index_pattern = re.compile(r"^.. index:: (fix|pair_style)\s+([a-zA-Z0-9/_]+)$") pattern = re.compile(r"^(fix|pair_style)\s+([a-zA-Z0-9/_]+)\s+command$") parser = argparse.ArgumentParser(description='Fixup headers in docs') @@ -21,19 +22,25 @@ for orig_file in args.files: if line.startswith("Syntax"): break - m = pattern.match(line) + m = index_pattern.match(line) + + if not m: + m = pattern.match(line) + if m: command_type = m.group(1) style = m.group(2) - styles.append(style) + if style not in styles: + styles.append(style) base_name = '/'.join(style.split('/')[0:-1]) ext = style.split('/')[-1] if ext not in ('omp', 'intel', 'kk', 'gpu', 'opt'): - headings[style] = [] - else: + if style not in headings: + headings[style] = [] + elif style not in headings[base_name]: headings[base_name].append(style) # write new header @@ -49,7 +56,7 @@ for orig_file in args.files: print(file=writer) if len(variants) > 0: - print("Accelerator Styles: ", end="", file=writer) + print("Accelerator Variants: ", end="", file=writer) print(", ".join([f"*{v}*" for v in variants]), file=writer) print(file=writer) -- GitLab From e5e2abe44628ac8a5e0493bd5c0ff92057f801cb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 10:51:55 -0400 Subject: [PATCH 14/75] update include file policy file and policy for pointers.h special case --- doc/include-file-conventions.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index e3448cb8ce..ea4e07eb59 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -91,21 +91,21 @@ statements should follow the "include what you use" principle. Include files should be included in this order: * the header matching the implementation (`some_class.h` for file `some_class.cpp`) -* mpi.h -* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* mpi.h (only if needed) * LAMMPS local headers (preferably in alphabetical order) +* system and library headers (anything that is using angular brackets; C-library headers first, then C++) ### Special Cases and Exceptions #### pointers.h -The `pointer.h` header file also includes `cstdio`, `cstddef`, -`string`, `lmptype.h`, and `utils.h` (and through those indirectly - `stdint.h`, `intttypes.h`, cstdlib, and `climits`). +The `pointer.h` header file also includes (in this order) `lmptype.h`, +`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h` +and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`. This means any header including `pointers.h` can assume that `FILE`, -`NULL`, `INT_MAX` are defined, they may freely use std::string -and functions from the utils namespace without including the -corresponding header files. +`NULL`, `INT_MAX` are defined, and the may freely use the std::string +for arguments. Corresponding implementation files do not need to include +those headers. ## Tools -- GitLab From cc594c0613b263caf0d4549ee4cb6c7a3134774e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 10:52:10 -0400 Subject: [PATCH 15/75] include fmt/format.h into pointers.h --- src/pointers.h | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/pointers.h b/src/pointers.h index 4b91e009ac..04f682f045 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -21,13 +21,14 @@ #ifndef LMP_POINTERS_H #define LMP_POINTERS_H -#include "lmptype.h" // IWYU pragma: export -#include // IWYU pragma: export -#include // IWYU pragme: export -#include // IWYU pragma: export -#include // IWYU pragma: export -#include "lammps.h" // IWYU pragma: export -#include "utils.h" // IWYU pragma: export +#include "lmptype.h" // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragme: export +#include // IWYU pragma: export +#include // IWYU pragma: export +#include "lammps.h" // IWYU pragma: export +#include "utils.h" // IWYU pragma: export +#include "fmt/format.h" // IWYU pragma: export namespace LAMMPS_NS { -- GitLab From 09bc686f714ceaa3e3c372afcd9e71acf88b0330 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:55:04 -0400 Subject: [PATCH 16/75] Avoid extra newline --- doc/utils/fixup_headers.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 7bdd11a607..884511bd32 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -58,8 +58,7 @@ for orig_file in args.files: if len(variants) > 0: print("Accelerator Variants: ", end="", file=writer) print(", ".join([f"*{v}*" for v in variants]), file=writer) - - print(file=writer) + print(file=writer) # write rest of reader print(line, end="", file=writer) -- GitLab From 8d1a117b75482c8ea8358e3946dbe1dab6e0c8d2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:59:01 -0400 Subject: [PATCH 17/75] Apply header fix to all remaining pair styles docs --- doc/src/pair_adp.rst | 4 ++-- doc/src/pair_agni.rst | 6 ++--- doc/src/pair_airebo.rst | 26 +++++++++------------ doc/src/pair_beck.rst | 8 +++---- doc/src/pair_born.rst | 9 ++++--- doc/src/pair_brownian.rst | 9 +++---- doc/src/pair_buck.rst | 17 +++++++------- doc/src/pair_buck6d_coul_gauss.rst | 1 + doc/src/pair_buck_long.rst | 6 ++--- doc/src/pair_charmm.rst | 20 ++++++++-------- doc/src/pair_class2.rst | 6 ++--- doc/src/pair_coeff.rst | 4 ---- doc/src/pair_colloid.rst | 8 +++---- doc/src/pair_comb.rst | 5 ++-- doc/src/pair_coul.rst | 1 - doc/src/pair_coul_diel.rst | 4 ++-- doc/src/pair_coul_slater.rst | 5 ++++ doc/src/pair_cs.rst | 11 +++------ doc/src/pair_dipole.rst | 23 +++++++++--------- doc/src/pair_dpd.rst | 21 +++++++---------- doc/src/pair_dpd_fdt.rst | 5 ++-- doc/src/pair_eam.rst | 6 ++--- doc/src/pair_edip.rst | 5 ++-- doc/src/pair_eim.rst | 4 ++-- doc/src/pair_exp6_rx.rst | 4 ++-- doc/src/pair_fep_soft.rst | 16 ++++++------- doc/src/pair_gauss.rst | 13 +++++------ doc/src/pair_gayberne.rst | 12 ++++------ doc/src/pair_gran.rst | 18 +++++++------- doc/src/pair_gromacs.rst | 21 +++++++---------- doc/src/pair_gw.rst | 1 + doc/src/pair_hbond_dreiding.rst | 9 +++---- doc/src/pair_hybrid.rst | 9 +++---- doc/src/pair_lj.rst | 1 - doc/src/pair_lj96.rst | 8 +++---- doc/src/pair_lj_cubic.rst | 8 +++---- doc/src/pair_lj_cut_coul.rst | 2 +- doc/src/pair_lj_cut_tip4p.rst | 1 - doc/src/pair_lj_expand.rst | 17 ++++++-------- doc/src/pair_lj_long.rst | 17 ++++++-------- doc/src/pair_lj_smooth.rst | 4 ++-- doc/src/pair_lj_smooth_linear.rst | 4 ++-- doc/src/pair_lubricate.rst | 9 +++---- doc/src/pair_lubricateU.rst | 1 + doc/src/pair_mdf.rst | 2 ++ doc/src/pair_meam_spline.rst | 4 ++-- doc/src/pair_mesodpd.rst | 3 +++ doc/src/pair_mesont_tpm.rst | 2 +- doc/src/pair_mie.rst | 4 ++-- doc/src/pair_mm3_switch3_coulgauss_long.rst | 2 +- doc/src/pair_modify.rst | 4 ---- doc/src/pair_morse.rst | 21 +++++++---------- doc/src/pair_multi_lucy_rx.rst | 4 ++-- doc/src/pair_nm.rst | 18 +++++++------- doc/src/pair_oxdna.rst | 4 ++++ doc/src/pair_oxdna2.rst | 5 ++++ doc/src/pair_oxrna2.rst | 5 ++++ doc/src/pair_peri.rst | 11 +++++---- doc/src/pair_reaxc.rst | 8 +++---- doc/src/pair_resquared.rst | 8 +++---- doc/src/pair_sdk.rst | 6 ++--- doc/src/pair_smd_triangulated_surface.rst | 2 +- doc/src/pair_smd_ulsph.rst | 2 +- doc/src/pair_snap.rst | 4 ++-- doc/src/pair_soft.rst | 8 +++---- doc/src/pair_spin_dipole.rst | 1 + doc/src/pair_spin_magelec.rst | 2 +- doc/src/pair_style.rst | 4 ---- doc/src/pair_sw.rst | 16 ++++--------- doc/src/pair_table.rst | 12 ++++------ doc/src/pair_table_rx.rst | 4 ++-- doc/src/pair_tersoff.rst | 23 +++++++----------- doc/src/pair_tersoff_mod.rst | 19 +++++++-------- doc/src/pair_tersoff_zbl.rst | 12 ++++------ doc/src/pair_thole.rst | 5 ++-- doc/src/pair_ufm.rst | 12 ++++------ doc/src/pair_vashishta.rst | 17 ++++++-------- doc/src/pair_write.rst | 4 ---- doc/src/pair_yukawa.rst | 12 ++++------ doc/src/pair_yukawa_colloid.rst | 8 +++---- doc/src/pair_zbl.rst | 12 ++++------ 81 files changed, 305 insertions(+), 374 deletions(-) diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 7017549925..5eec0004bf 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -1,10 +1,10 @@ .. index:: pair_style adp +.. index:: pair_style adp/omp pair_style adp command ====================== -pair_style adp/omp command -========================== +Accelerator Variants: *adp/omp* Syntax """""" diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index ee69f40d80..087c39e8f9 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -1,10 +1,10 @@ .. index:: pair_style agni +.. index:: pair_style agni/omp pair_style agni command -======================== +======================= -pair_style agni/omp command -============================ +Accelerator Variants: *agni/omp* Syntax """""" diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index f3be0e85de..d631d0a3d0 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -1,31 +1,27 @@ .. index:: pair_style airebo +.. index:: pair_style airebo/intel +.. index:: pair_style airebo/omp +.. index:: pair_style airebo/morse +.. index:: pair_style airebo/morse/intel +.. index:: pair_style airebo/morse/omp +.. index:: pair_style rebo +.. index:: pair_style rebo/intel +.. index:: pair_style rebo/omp pair_style airebo command ========================= -pair_style airebo/intel command -=============================== - -pair_style airebo/omp command -============================= +Accelerator Variants: *airebo/intel*, *airebo/omp* pair_style airebo/morse command =============================== -pair_style airebo/morse/intel command -===================================== - -pair_style airebo/morse/omp command -=================================== +Accelerator Variants: *airebo/morse/intel*, *airebo/morse/omp* pair_style rebo command ======================= -pair_style rebo/intel command -============================= - -pair_style rebo/omp command -=========================== +Accelerator Variants: *rebo/intel*, *rebo/omp* Syntax """""" diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 0e63fe77ba..44bc317138 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -1,13 +1,11 @@ .. index:: pair_style beck +.. index:: pair_style beck/gpu +.. index:: pair_style beck/omp pair_style beck command ======================= -pair_style beck/gpu command -=========================== - -pair_style beck/omp command -=========================== +Accelerator Variants: *beck/gpu*, *beck/omp* Syntax """""" diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 15ce4ac560..65be948f82 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -14,27 +14,26 @@ pair_style born command ======================= -Accelerator Styles: *born/omp*, *born/gpu* +Accelerator Variants: *born/omp*, *born/gpu* pair_style born/coul/long command ================================= -Accelerator Styles: *born/coul/long/gpu*, *born/coul/long/omp* +Accelerator Variants: *born/coul/long/gpu*, *born/coul/long/omp* pair_style born/coul/msm command ================================ -Accelerator Styles: *born/coul/msm/omp* +Accelerator Variants: *born/coul/msm/omp* pair_style born/coul/wolf command ================================= -Accelerator Styles: *born/coul/wolf/gpu*, *born/coul/wolf/omp* +Accelerator Variants: *born/coul/wolf/gpu*, *born/coul/wolf/omp* pair_style born/coul/dsf command ================================ - Syntax """""" diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index ea311d603e..43c17c9087 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -1,16 +1,17 @@ .. index:: pair_style brownian +.. index:: pair_style brownian/omp +.. index:: pair_style brownian/poly +.. index:: pair_style brownian/poly/omp pair_style brownian command =========================== -pair_style brownian/omp command -================================ +Accelerator Variants: *brownian/omp* pair_style brownian/poly command ================================ -pair_style brownian/poly/omp command -==================================== +Accelerator Variants: *brownian/poly/omp* Syntax """""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 6ff5f84fe2..5f255ece39 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -1,5 +1,4 @@ .. index:: pair_style buck -.. index:: pair_style buck .. index:: pair_style buck/gpu .. index:: pair_style buck/intel .. index:: pair_style buck/kk @@ -18,24 +17,24 @@ .. index:: pair_style buck/coul/msm/omp pair_style buck command -======================== +======================= -Accelerator Styles: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* +Accelerator Variants: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* pair_style buck/coul/cut command -================================= +================================ -Accelerator Styles: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* +Accelerator Variants: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* pair_style buck/coul/long command -================================== +================================= -Accelerator Styles: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* +Accelerator Variants: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* pair_style buck/coul/msm command -================================= +================================ -Accelerator Styles: *buck/coul/msm/omp* +Accelerator Variants: *buck/coul/msm/omp* Syntax """""" diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 7d3e5b9a22..5f96a93fee 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -1,4 +1,5 @@ .. index:: pair_style buck6d/coul/gauss/dsf +.. index:: pair_style buck6d/coul/gauss/long pair_style buck6d/coul/gauss/dsf command ======================================== diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index c0dd81d78f..1883cee637 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -1,10 +1,10 @@ .. index:: pair_style buck/long/coul/long +.. index:: pair_style buck/long/coul/long/omp pair_style buck/long/coul/long command -======================================= +====================================== -pair_style buck/long/coul/long/omp command -=========================================== +Accelerator Variants: *buck/long/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index cef1b333fb..6d81266a35 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -17,30 +17,30 @@ .. index:: pair_style lj/charmmfsw/coul/long pair_style lj/charmm/coul/charmm command -========================================= +======================================== -Accelerator Styles: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* +Accelerator Variants: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* pair_style lj/charmm/coul/charmm/implicit command -================================================== +================================================= -Accelerator Styles: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* +Accelerator Variants: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* pair_style lj/charmm/coul/long command -======================================= +====================================== -Accelerator Styles: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* +Accelerator Variants: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* pair_style lj/charmm/coul/msm command -====================================== +===================================== -Accelerator Styles: *lj/charmm/coul/msm/omp* +Accelerator Variants: *lj/charmm/coul/msm/omp* pair_style lj/charmmfsw/coul/charmmfsh command -=============================================== +============================================== pair_style lj/charmmfsw/coul/long command -========================================== +========================================= Syntax """""" diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 6fcdd4f533..cfa085cc28 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -13,17 +13,17 @@ pair_style lj/class2 command ============================ -Accelerator Styles: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* +Accelerator Variants: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* pair_style lj/class2/coul/cut command ===================================== -Accelerator Styles: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* +Accelerator Variants: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* pair_style lj/class2/coul/long command ====================================== -Accelerator Styles: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* +Accelerator Variants: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index ea62d839ab..7c72bb5843 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -1,7 +1,3 @@ -.. index:: pair_coeff - -pair_coeff command -================== Syntax """""" diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 4bb82e9615..040bea2487 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -1,13 +1,11 @@ .. index:: pair_style colloid +.. index:: pair_style colloid/gpu +.. index:: pair_style colloid/omp pair_style colloid command ========================== -pair_style colloid/gpu command -============================== - -pair_style colloid/omp command -============================== +Accelerator Variants: *colloid/gpu*, *colloid/omp* Syntax """""" diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 441f982996..2e164d46fc 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -1,10 +1,11 @@ .. index:: pair_style comb +.. index:: pair_style comb/omp +.. index:: pair_style comb3 pair_style comb command ======================= -pair_style comb/omp command -=========================== +Accelerator Variants: *comb/omp* pair_style comb3 command ======================== diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 37193d752c..4def43647f 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -25,7 +25,6 @@ .. index:: pair_style tip4p/long .. index:: pair_style tip4p/long/omp - pair_style coul/cut command =========================== diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index e979ceef31..bcf0c48e4d 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -1,10 +1,10 @@ .. index:: pair_style coul/diel +.. index:: pair_style coul/diel/omp pair_style coul/diel command ============================ -pair_style coul/diel/omp command -================================ +Accelerator Variants: *coul/diel/omp* Syntax """""" diff --git a/doc/src/pair_coul_slater.rst b/doc/src/pair_coul_slater.rst index cc8e6f243c..a4d8b253b1 100644 --- a/doc/src/pair_coul_slater.rst +++ b/doc/src/pair_coul_slater.rst @@ -1,4 +1,9 @@ .. index:: pair_style coul/slater +.. index:: pair_style coul/slater/cut +.. index:: pair_style coul/slater/long + +pair_style coul/slater command +============================== pair_style coul/slater/cut command ================================== diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index ae5c29aa32..f41d840216 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -13,38 +13,33 @@ pair_style born/coul/dsf/cs command =================================== - pair_style born/coul/long/cs command ==================================== -Accelerator Styles: *born/coul/long/cs/gpu* +Accelerator Variants: *born/coul/long/cs/gpu* pair_style born/coul/wolf/cs command ==================================== -Accelerator Styles: *born/coul/wolf/cs/gpu* +Accelerator Variants: *born/coul/wolf/cs/gpu* pair_style buck/coul/long/cs command ==================================== - pair_style coul/long/cs command =============================== -Accelerator Styles: *coul/long/cs/gpu* +Accelerator Variants: *coul/long/cs/gpu* pair_style coul/wolf/cs command =============================== - pair_style lj/cut/coul/long/cs command ====================================== - pair_style lj/class2/coul/long/cs command ========================================= - Syntax """""" diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 21548be4f0..602c374d9f 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -1,28 +1,27 @@ .. index:: pair_style lj/cut/dipole/cut +.. index:: pair_style lj/cut/dipole/cut/gpu +.. index:: pair_style lj/cut/dipole/cut/omp +.. index:: pair_style lj/sf/dipole/sf +.. index:: pair_style lj/sf/dipole/sf/gpu +.. index:: pair_style lj/sf/dipole/sf/omp +.. index:: pair_style lj/cut/dipole/long +.. index:: pair_style lj/cut/dipole/long/gpu +.. index:: pair_style lj/long/dipole/long pair_style lj/cut/dipole/cut command ==================================== -pair_style lj/cut/dipole/cut/gpu command -======================================== - -pair_style lj/cut/dipole/cut/omp command -======================================== +Accelerator Variants: *lj/cut/dipole/cut/gpu*, *lj/cut/dipole/cut/omp* pair_style lj/sf/dipole/sf command ================================== -pair_style lj/sf/dipole/sf/gpu command -====================================== - -pair_style lj/sf/dipole/sf/omp command -====================================== +Accelerator Variants: *lj/sf/dipole/sf/gpu*, *lj/sf/dipole/sf/omp* pair_style lj/cut/dipole/long command ===================================== -pair_style lj/cut/dipole/long/gpu command -========================================= +Accelerator Variants: *lj/cut/dipole/long/gpu* pair_style lj/long/dipole/long command ====================================== diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 94c9fa9bea..d1d84407c4 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -1,25 +1,20 @@ .. index:: pair_style dpd +.. index:: pair_style dpd/gpu +.. index:: pair_style dpd/intel +.. index:: pair_style dpd/omp +.. index:: pair_style dpd/tstat +.. index:: pair_style dpd/tstat/gpu +.. index:: pair_style dpd/tstat/omp pair_style dpd command ====================== -pair_style dpd/gpu command -========================== - -pair_style dpd/intel command -============================ - -pair_style dpd/omp command -========================== +Accelerator Variants: *dpd/gpu*, *dpd/intel*, *dpd/omp* pair_style dpd/tstat command ============================ -pair_style dpd/tstat/gpu command -================================ - -pair_style dpd/tstat/omp command -================================ +Accelerator Variants: *dpd/tstat/gpu*, *dpd/tstat/omp* Syntax """""" diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index e0659a7b78..bb810b0fe6 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -1,4 +1,6 @@ .. index:: pair_style dpd/fdt +.. index:: pair_style dpd/fdt/energy +.. index:: pair_style dpd/fdt/energy/kk pair_style dpd/fdt command ========================== @@ -6,8 +8,7 @@ pair_style dpd/fdt command pair_style dpd/fdt/energy command ================================= -pair_style dpd/fdt/energy/kk command -==================================== +Accelerator Variants: *dpd/fdt/energy/kk* Syntax """""" diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 56eed64d01..690b387bad 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -22,12 +22,12 @@ pair_style eam command ====================== -Accelerator Styles: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* +Accelerator Variants: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* pair_style eam/alloy command ============================ -Accelerator Styles: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* +Accelerator Variants: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* pair_style eam/cd command ========================= @@ -38,7 +38,7 @@ pair_style eam/cd/old command pair_style eam/fs command ========================= -Accelerator Styles: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* +Accelerator Variants: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* Syntax """""" diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index d8e747ddf4..8f8d70f2f6 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -1,10 +1,11 @@ .. index:: pair_style edip +.. index:: pair_style edip/omp +.. index:: pair_style edip/multi pair_style edip command ======================= -pair_style edip/omp command -=========================== +Accelerator Variants: *edip/omp* pair_style edip/multi command ============================= diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index aef7dba3a4..8360dbab64 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -1,10 +1,10 @@ .. index:: pair_style eim +.. index:: pair_style eim/omp pair_style eim command ====================== -pair_style eim/omp command -========================== +Accelerator Variants: *eim/omp* Syntax """""" diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index d6fe4850ce..49a4c5436f 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style exp6/rx +.. index:: pair_style exp6/rx/kk pair_style exp6/rx command ========================== -pair_style exp6/rx/kk command -============================= +Accelerator Variants: *exp6/rx/kk* Syntax """""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index be35f84508..109ddfdf21 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -22,27 +22,27 @@ pair_style lj/cut/soft command ============================== -Accelerator Styles: *lj/cut/soft/omp* +Accelerator Variants: *lj/cut/soft/omp* pair_style lj/cut/coul/cut/soft command ======================================= -Accelerator Styles: *lj/cut/coul/cut/soft/omp* +Accelerator Variants: *lj/cut/coul/cut/soft/omp* pair_style lj/cut/coul/long/soft command ======================================== -Accelerator Styles: *lj/cut/coul/long/soft/omp* +Accelerator Variants: *lj/cut/coul/long/soft/omp* pair_style lj/cut/tip4p/long/soft command ========================================= -Accelerator Styles: *lj/cut/tip4p/long/soft/omp* +Accelerator Variants: *lj/cut/tip4p/long/soft/omp* pair_style lj/charmm/coul/long/soft command =========================================== -Accelerator Styles: *lj/charmm/coul/long/soft/omp* +Accelerator Variants: *lj/charmm/coul/long/soft/omp* pair_style lj/class2/soft command ================================= @@ -56,17 +56,17 @@ pair_style lj/class2/coul/long/soft command pair_style coul/cut/soft command ================================ -Accelerator Styles: *coul/cut/soft/omp* +Accelerator Variants: *coul/cut/soft/omp* pair_style coul/long/soft command ================================= -Accelerator Styles: *coul/long/soft/omp* +Accelerator Variants: *coul/long/soft/omp* pair_style tip4p/long/soft command ================================== -Accelerator Styles: *tip4p/long/soft/omp* +Accelerator Variants: *tip4p/long/soft/omp* pair_style morse/soft command ============================= diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 8c7ce74174..9b516cce7b 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -1,19 +1,18 @@ .. index:: pair_style gauss +.. index:: pair_style gauss/gpu +.. index:: pair_style gauss/omp +.. index:: pair_style gauss/cut +.. index:: pair_style gauss/cut/omp pair_style gauss command ======================== -pair_style gauss/gpu command -============================ - -pair_style gauss/omp command -============================ +Accelerator Variants: *gauss/gpu*, *gauss/omp* pair_style gauss/cut command ============================ -pair_style gauss/cut/omp command -================================ +Accelerator Variants: *gauss/cut/omp* Syntax """""" diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 1e8094feef..309e949f97 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -1,16 +1,12 @@ .. index:: pair_style gayberne +.. index:: pair_style gayberne/gpu +.. index:: pair_style gayberne/intel +.. index:: pair_style gayberne/omp pair_style gayberne command =========================== -pair_style gayberne/gpu command -=============================== - -pair_style gayberne/intel command -================================= - -pair_style gayberne/omp command -=============================== +Accelerator Variants: *gayberne/gpu*, *gayberne/intel*, *gayberne/omp* Syntax """""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 9aacfdfa31..d3f87839e8 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -1,25 +1,25 @@ .. index:: pair_style gran/hooke +.. index:: pair_style gran/hooke/omp +.. index:: pair_style gran/hooke/history +.. index:: pair_style gran/hooke/history/omp +.. index:: pair_style gran/hooke/history/kk +.. index:: pair_style gran/hertz/history +.. index:: pair_style gran/hertz/history/omp pair_style gran/hooke command ============================= -pair_style gran/hooke/omp command -================================= +Accelerator Variants: *gran/hooke/omp* pair_style gran/hooke/history command ===================================== -pair_style gran/hooke/history/omp command -========================================= - -pair_style gran/hooke/history/kk command -======================================== +Accelerator Variants: *gran/hooke/history/omp*, *gran/hooke/history/kk* pair_style gran/hertz/history command ===================================== -pair_style gran/hertz/history/omp command -========================================= +Accelerator Variants: *gran/hertz/history/omp* Syntax """""" diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index a4c065e24d..88cb4ce880 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -1,25 +1,20 @@ .. index:: pair_style lj/gromacs +.. index:: pair_style lj/gromacs/gpu +.. index:: pair_style lj/gromacs/kk +.. index:: pair_style lj/gromacs/omp +.. index:: pair_style lj/gromacs/coul/gromacs +.. index:: pair_style lj/gromacs/coul/gromacs/kk +.. index:: pair_style lj/gromacs/coul/gromacs/omp pair_style lj/gromacs command ============================= -pair_style lj/gromacs/gpu command -================================= - -pair_style lj/gromacs/kk command -================================ - -pair_style lj/gromacs/omp command -================================= +Accelerator Variants: *lj/gromacs/gpu*, *lj/gromacs/kk*, *lj/gromacs/omp* pair_style lj/gromacs/coul/gromacs command ========================================== -pair_style lj/gromacs/coul/gromacs/kk command -============================================= - -pair_style lj/gromacs/coul/gromacs/omp command -============================================== +Accelerator Variants: *lj/gromacs/coul/gromacs/kk*, *lj/gromacs/coul/gromacs/omp* Syntax """""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index 544d13df9b..d0a7e69b00 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -1,4 +1,5 @@ .. index:: pair_style gw +.. index:: pair_style gw/zbl pair_style gw command ===================== diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 0d821fa946..5e7183a348 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -1,16 +1,17 @@ .. index:: pair_style hbond/dreiding/lj +.. index:: pair_style hbond/dreiding/lj/omp +.. index:: pair_style hbond/dreiding/morse +.. index:: pair_style hbond/dreiding/morse/omp pair_style hbond/dreiding/lj command ==================================== -pair_style hbond/dreiding/lj/omp command -======================================== +Accelerator Variants: *hbond/dreiding/lj/omp* pair_style hbond/dreiding/morse command ======================================= -pair_style hbond/dreiding/morse/omp command -=========================================== +Accelerator Variants: *hbond/dreiding/morse/omp* Syntax """""" diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 924e19a8b3..558c326175 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -1,16 +1,17 @@ .. index:: pair_style hybrid +.. index:: pair_style hybrid/kk +.. index:: pair_style hybrid/overlay +.. index:: pair_style hybrid/overlay/kk pair_style hybrid command ========================= -pair_style hybrid/kk command -============================ +Accelerator Variants: *hybrid/kk* pair_style hybrid/overlay command ================================= -pair_style hybrid/overlay/kk command -==================================== +Accelerator Variants: *hybrid/overlay/kk* Syntax """""" diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index b8c5be3940..22f0d0dd37 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -5,7 +5,6 @@ .. index:: pair_style lj/cut/opt .. index:: pair_style lj/cut/omp - pair_style lj/cut command ========================= diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 7ea3c2c9c1..3f1172618b 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -1,13 +1,11 @@ .. index:: pair_style lj96/cut +.. index:: pair_style lj96/cut/gpu +.. index:: pair_style lj96/cut/omp pair_style lj96/cut command =========================== -pair_style lj96/cut/gpu command -=============================== - -pair_style lj96/cut/omp command -=============================== +Accelerator Variants: *lj96/cut/gpu*, *lj96/cut/omp* Syntax """""" diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index 800de20e6f..e220e6e67c 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -1,13 +1,11 @@ .. index:: pair_style lj/cubic +.. index:: pair_style lj/cubic/gpu +.. index:: pair_style lj/cubic/omp pair_style lj/cubic command =========================== -pair_style lj/cubic/gpu command -=============================== - -pair_style lj/cubic/omp command -=============================== +Accelerator Variants: *lj/cubic/gpu*, *lj/cubic/omp* Syntax """""" diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index ec34777d8d..f729c2016e 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -30,7 +30,7 @@ Accelerator Variants: *lj/cut/coul/cut/gpu*, *lj/cut/coul/cut/kk*, *lj/cut/coul/ pair_style lj/cut/coul/debye command ==================================== -Accelerator Variants: *lj/cut/coul/debye/gpu*, lj/cut/coul/debye/kk, *lj/cut/coul/debye/omp* +Accelerator Variants: *lj/cut/coul/debye/gpu*, *lj/cut/coul/debye/kk*, *lj/cut/coul/debye/omp* pair_style lj/cut/coul/dsf command ================================== diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 14e970a59e..4f55f3b14e 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -5,7 +5,6 @@ .. index:: pair_style lj/cut/tip4p/long/omp .. index:: pair_style lj/cut/tip4p/long/opt - pair_style lj/cut/tip4p/cut command =================================== diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 8defbc3635..4d619a67e2 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -1,22 +1,19 @@ .. index:: pair_style lj/expand +.. index:: pair_style lj/expand/gpu +.. index:: pair_style lj/expand/kk +.. index:: pair_style lj/expand/omp +.. index:: pair_style lj/expand/coul/long +.. index:: pair_style lj/expand/coul/long/gpu pair_style lj/expand command ============================ -pair_style lj/expand/gpu command -================================ - -pair_style lj/expand/kk command -=============================== - -pair_style lj/expand/omp command -================================ +Accelerator Variants: *lj/expand/gpu*, *lj/expand/kk*, *lj/expand/omp* pair_style lj/expand/coul/long command ====================================== -pair_style lj/expand/coul/long/gpu command -========================================== +Accelerator Variants: *lj/expand/coul/long/gpu* Syntax """""" diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index ff6d834ad6..3609d093d9 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -1,22 +1,19 @@ .. index:: pair_style lj/long/coul/long +.. index:: pair_style lj/long/coul/long/intel +.. index:: pair_style lj/long/coul/long/omp +.. index:: pair_style lj/long/coul/long/opt +.. index:: pair_style lj/long/tip4p/long +.. index:: pair_style lj/long/tip4p/long/omp pair_style lj/long/coul/long command ==================================== -pair_style lj/long/coul/long/intel command -========================================== - -pair_style lj/long/coul/long/omp command -======================================== - -pair_style lj/long/coul/long/opt command -======================================== +Accelerator Variants: *lj/long/coul/long/intel*, *lj/long/coul/long/omp*, *lj/long/coul/long/opt* pair_style lj/long/tip4p/long command ===================================== -pair_style lj/long/tip4p/long/omp command -========================================= +Accelerator Variants: *lj/long/tip4p/long/omp* Syntax """""" diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 3137a17f73..7ba12c89ba 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -1,10 +1,10 @@ .. index:: pair_style lj/smooth +.. index:: pair_style lj/smooth/omp pair_style lj/smooth command ============================ -pair_style lj/smooth/omp command -================================ +Accelerator Variants: *lj/smooth/omp* Syntax """""" diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 833a4f035d..b105fc4911 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -1,10 +1,10 @@ .. index:: pair_style lj/smooth/linear +.. index:: pair_style lj/smooth/linear/omp pair_style lj/smooth/linear command =================================== -pair_style lj/smooth/linear/omp command -======================================= +Accelerator Variants: *lj/smooth/linear/omp* Syntax """""" diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 711f2576b3..e83a16c80b 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -1,16 +1,17 @@ .. index:: pair_style lubricate +.. index:: pair_style lubricate/omp +.. index:: pair_style lubricate/poly +.. index:: pair_style lubricate/poly/omp pair_style lubricate command ============================ -pair_style lubricate/omp command -================================ +Accelerator Variants: *lubricate/omp* pair_style lubricate/poly command ================================= -pair_style lubricate/poly/omp command -===================================== +Accelerator Variants: *lubricate/poly/omp* Syntax """""" diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index f4224ede47..a9382556c5 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -1,4 +1,5 @@ .. index:: pair_style lubricateU +.. index:: pair_style lubricateU/poly pair_style lubricateU command ============================= diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 1b46c51220..84d312e47c 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -1,4 +1,6 @@ .. index:: pair_style lj/mdf +.. index:: pair_style buck/mdf +.. index:: pair_style lennard/mdf pair_style lj/mdf command ========================= diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index bbba66c2b5..b5c94385fa 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -1,10 +1,10 @@ .. index:: pair_style meam/spline +.. index:: pair_style meam/spline/omp pair_style meam/spline command ============================== -pair_style meam/spline/omp command -================================== +Accelerator Variants: *meam/spline/omp* Syntax """""" diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 093eb707ad..1efdfa8b45 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -1,4 +1,7 @@ .. index:: pair_style edpd +.. index:: pair_style mdpd +.. index:: pair_style mdpd/rhosum +.. index:: pair_style tdpd pair_style edpd command ======================= diff --git a/doc/src/pair_mesont_tpm.rst b/doc/src/pair_mesont_tpm.rst index f5b5789315..e26f16fba3 100644 --- a/doc/src/pair_mesont_tpm.rst +++ b/doc/src/pair_mesont_tpm.rst @@ -1,7 +1,7 @@ .. index:: pair_style mesont/tpm pair_style mesont/tpm command -============================== +============================= Syntax """""" diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index 469817ee5e..e1a34893c9 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -1,10 +1,10 @@ .. index:: pair_style mie/cut +.. index:: pair_style mie/cut/gpu pair_style mie/cut command ========================== -pair_style mie/cut/gpu command -============================== +Accelerator Variants: *mie/cut/gpu* Syntax """""" diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 2b7e9cb903..798df0bf7a 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -1,7 +1,7 @@ .. index:: pair_style mm3/switch3/coulgauss/long pair_style mm3/switch3/coulgauss/long command -============================================== +============================================= Syntax """""" diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index b8969c0131..21d0977047 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -1,7 +1,3 @@ -.. index:: pair_modify - -pair_modify command -=================== Syntax """""" diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 1c8e731bc1..5ede37a916 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -1,25 +1,20 @@ .. index:: pair_style morse +.. index:: pair_style morse/gpu +.. index:: pair_style morse/omp +.. index:: pair_style morse/opt +.. index:: pair_style morse/smooth/linear +.. index:: pair_style morse/smooth/linear/omp +.. index:: pair_style morse/kk pair_style morse command ======================== -pair_style morse/gpu command -============================ - -pair_style morse/omp command -============================ - -pair_style morse/opt command -============================ +Accelerator Variants: *morse/gpu*, *morse/omp*, *morse/opt*, *morse/kk* pair_style morse/smooth/linear command ====================================== -pair_style morse/smooth/linear/omp command -========================================== - -pair_style morse/kk command -=========================== +Accelerator Variants: *morse/smooth/linear/omp* Syntax """""" diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 42a2525195..f6e6652271 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style multi/lucy/rx +.. index:: pair_style multi/lucy/rx/kk pair_style multi/lucy/rx command ================================ -pair_style multi/lucy/rx/kk command -=================================== +Accelerator Variants: *multi/lucy/rx/kk* Syntax """""" diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index 7d7648cdc9..d38e21fd15 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -1,22 +1,24 @@ .. index:: pair_style nm/cut +.. index:: pair_style nm/cut/coul/cut +.. index:: pair_style nm/cut/coul/long +.. index:: pair_style nm/cut/omp +.. index:: pair_style nm/cut/coul/cut/omp +.. index:: pair_style nm/cut/coul/long/omp pair_style nm/cut command ========================= +Accelerator Variants: *nm/cut/omp* + pair_style nm/cut/coul/cut command ================================== +Accelerator Variants: *nm/cut/coul/cut/omp* + pair_style nm/cut/coul/long command =================================== -pair_style nm/cut/omp command -============================= - -pair_style nm/cut/coul/cut/omp command -====================================== - -pair_style nm/cut/coul/long/omp command -======================================= +Accelerator Variants: *nm/cut/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index c16e872ccf..4cc57868b4 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -1,4 +1,8 @@ .. index:: pair_style oxdna/excv +.. index:: pair_style oxdna/stk +.. index:: pair_style oxdna/hbond +.. index:: pair_style oxdna/xstk +.. index:: pair_style oxdna/coaxstk pair_style oxdna/excv command ============================= diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index f63bec6a7f..ee01f2f488 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -1,4 +1,9 @@ .. index:: pair_style oxdna2/excv +.. index:: pair_style oxdna2/stk +.. index:: pair_style oxdna2/hbond +.. index:: pair_style oxdna2/xstk +.. index:: pair_style oxdna2/coaxstk +.. index:: pair_style oxdna2/dh pair_style oxdna2/excv command ============================== diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 05fd27b4a0..831e4d9c4e 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -1,4 +1,9 @@ .. index:: pair_style oxrna2/excv +.. index:: pair_style oxrna2/stk +.. index:: pair_style oxrna2/hbond +.. index:: pair_style oxrna2/xstk +.. index:: pair_style oxrna2/coaxstk +.. index:: pair_style oxrna2/dh pair_style oxrna2/excv command ============================== diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index de487df9a3..2a1c7f6aa5 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -1,16 +1,19 @@ .. index:: pair_style peri/pmb +.. index:: pair_style peri/pmb/omp +.. index:: pair_style peri/lps +.. index:: pair_style peri/lps/omp +.. index:: pair_style peri/ves +.. index:: pair_style peri/eps pair_style peri/pmb command =========================== -pair_style peri/pmb/omp command -=============================== +Accelerator Variants: *peri/pmb/omp* pair_style peri/lps command =========================== -pair_style peri/lps/omp command -=============================== +Accelerator Variants: *peri/lps/omp* pair_style peri/ves command =========================== diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index 4d4368729e..13ff16d4d3 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -1,13 +1,11 @@ .. index:: pair_style reax/c +.. index:: pair_style reax/c/kk +.. index:: pair_style reax/c/omp pair_style reax/c command ========================= -pair_style reax/c/kk command -============================ - -pair_style reax/c/omp command -============================= +Accelerator Variants: *reax/c/kk*, *reax/c/omp* Syntax """""" diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 33b40f6776..448af410db 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -1,13 +1,11 @@ .. index:: pair_style resquared +.. index:: pair_style resquared/gpu +.. index:: pair_style resquared/omp pair_style resquared command ============================ -pair_style resquared/gpu command -================================ - -pair_style resquared/omp command -================================ +Accelerator Variants: *resquared/gpu*, *resquared/omp* Syntax """""" diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 02fed36130..541c53d37e 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -11,17 +11,17 @@ pair_style lj/sdk command ========================= -Accelerator Styles: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* +Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* pair_style lj/sdk/coul/long command =================================== -Accelerator Styles: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* +Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* pair_style lj/sdk/coul/msm command ================================== -Accelerator Styles: *lj/sdk/coul/msm/omp* +Accelerator Variants: *lj/sdk/coul/msm/omp* Syntax """""" diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 9dbd66dcd8..1e33254865 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -1,7 +1,7 @@ .. index:: pair_style smd/tri_surface pair_style smd/tri_surface command -=================================== +================================== Syntax """""" diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 6b3ee7f019..33946d4649 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -1,7 +1,7 @@ .. index:: pair_style smd/ulsph pair_style smd/ulsph command -============================= +============================ Syntax """""" diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 2ba2a9dd58..8aa10f5986 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -1,10 +1,10 @@ .. index:: pair_style snap +.. index:: pair_style snap/kk pair_style snap command ======================= -pair_style snap/kk command -========================== +Accelerator Variants: *snap/kk* Syntax """""" diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 294868f872..cc024cb6dd 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -1,13 +1,11 @@ .. index:: pair_style soft +.. index:: pair_style soft/gpu +.. index:: pair_style soft/omp pair_style soft command ======================= -pair_style soft/gpu command -=========================== - -pair_style soft/omp command -=========================== +Accelerator Variants: *soft/gpu*, *soft/omp* Syntax """""" diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index c86083f1e5..d1bbf3b699 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -1,4 +1,5 @@ .. index:: pair_style spin/dipole/cut +.. index:: pair_style spin/dipole/long pair_style spin/dipole/cut command ================================== diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 5ef01ad10c..1860ed4677 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -1,7 +1,7 @@ .. index:: pair_style spin/magelec pair_style spin/magelec command -================================ +=============================== Syntax """""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4feaeacad0..1b9ceaf0ee 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -1,7 +1,3 @@ -.. index:: pair_style - -pair_style command -================== Syntax """""" diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index b673f652aa..bea417ed3d 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -1,19 +1,13 @@ .. index:: pair_style sw +.. index:: pair_style sw/gpu +.. index:: pair_style sw/intel +.. index:: pair_style sw/kk +.. index:: pair_style sw/omp pair_style sw command ===================== -pair_style sw/gpu command -========================= - -pair_style sw/intel command -=========================== - -pair_style sw/kk command -======================== - -pair_style sw/omp command -========================= +Accelerator Variants: *sw/gpu*, *sw/intel*, *sw/kk*, *sw/omp* Syntax """""" diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 1a35cea7fd..39ed690551 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -1,16 +1,12 @@ .. index:: pair_style table +.. index:: pair_style table/gpu +.. index:: pair_style table/kk +.. index:: pair_style table/omp pair_style table command ======================== -pair_style table/gpu command -============================ - -pair_style table/kk command -=========================== - -pair_style table/omp command -============================ +Accelerator Variants: *table/gpu*, *table/kk*, *table/omp* Syntax """""" diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 5545da22ef..9d23a479a3 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style table/rx +.. index:: pair_style table/rx/kk pair_style table/rx command =========================== -pair_style table/rx/kk command -============================== +Accelerator Variants: *table/rx/kk* Syntax """""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 251e12c87a..d9e5d60cd9 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -1,25 +1,20 @@ .. index:: pair_style tersoff +.. index:: pair_style tersoff/table +.. index:: pair_style tersoff/gpu +.. index:: pair_style tersoff/intel +.. index:: pair_style tersoff/kk +.. index:: pair_style tersoff/omp +.. index:: pair_style tersoff/table/omp pair_style tersoff command ========================== -pair_style tersoff/table command -================================ - -pair_style tersoff/gpu command -============================== +Accelerator Variants: *tersoff/gpu*, *tersoff/intel*, *tersoff/kk*, *tersoff/omp* -pair_style tersoff/intel command +pair_style tersoff/table command ================================ -pair_style tersoff/kk command -============================= - -pair_style tersoff/omp command -============================== - -pair_style tersoff/table/omp command -==================================== +Accelerator Variants: *tersoff/table/omp* Syntax """""" diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 0426e65f14..7457541c18 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -1,22 +1,19 @@ .. index:: pair_style tersoff/mod +.. index:: pair_style tersoff/mod/c +.. index:: pair_style tersoff/mod/gpu +.. index:: pair_style tersoff/mod/kk +.. index:: pair_style tersoff/mod/omp +.. index:: pair_style tersoff/mod/c/omp pair_style tersoff/mod command ============================== +Accelerator Variants: *tersoff/mod/gpu*, *tersoff/mod/kk*, *tersoff/mod/omp* + pair_style tersoff/mod/c command ================================ -pair_style tersoff/mod/gpu command -================================== - -pair_style tersoff/mod/kk command -================================= - -pair_style tersoff/mod/omp command -================================== - -pair_style tersoff/mod/c/omp command -==================================== +Accelerator Variants: *tersoff/mod/c/omp* Syntax """""" diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index eff394d9a0..19e77ce8eb 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -1,16 +1,12 @@ .. index:: pair_style tersoff/zbl +.. index:: pair_style tersoff/zbl/gpu +.. index:: pair_style tersoff/zbl/kk +.. index:: pair_style tersoff/zbl/omp pair_style tersoff/zbl command ============================== -pair_style tersoff/zbl/gpu command -================================== - -pair_style tersoff/zbl/kk command -================================= - -pair_style tersoff/zbl/omp command -================================== +Accelerator Variants: *tersoff/zbl/gpu*, *tersoff/zbl/kk*, *tersoff/zbl/omp* Syntax """""" diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 9b05e06cee..a8cf8ee044 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -1,4 +1,6 @@ .. index:: pair_style thole +.. index:: pair_style lj/cut/thole/long +.. index:: pair_style lj/cut/thole/long/omp pair_style thole command ======================== @@ -6,8 +8,7 @@ pair_style thole command pair_style lj/cut/thole/long command ==================================== -pair_style lj/cut/thole/long/omp command -======================================== +Accelerator Variants: *lj/cut/thole/long/omp* Syntax """""" diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index d9b08aaea2..140bb75ee7 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -1,16 +1,12 @@ .. index:: pair_style ufm +.. index:: pair_style ufm/gpu +.. index:: pair_style ufm/omp +.. index:: pair_style ufm/opt pair_style ufm command ====================== -pair_style ufm/gpu command -========================== - -pair_style ufm/omp command -========================== - -pair_style ufm/opt command -========================== +Accelerator Variants: *ufm/gpu*, *ufm/omp*, *ufm/opt* Syntax """""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 0ad6cc3521..aef401ec7c 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -1,22 +1,19 @@ .. index:: pair_style vashishta +.. index:: pair_style vashishta/gpu +.. index:: pair_style vashishta/omp +.. index:: pair_style vashishta/kk +.. index:: pair_style vashishta/table +.. index:: pair_style vashishta/table/omp pair_style vashishta command ============================ -pair_style vashishta/gpu command -================================ - -pair_style vashishta/omp command -================================ - -pair_style vashishta/kk command -=============================== +Accelerator Variants: *vashishta/gpu*, *vashishta/omp*, *vashishta/kk* pair_style vashishta/table command ================================== -pair_style vashishta/table/omp command -====================================== +Accelerator Variants: *vashishta/table/omp* Syntax """""" diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 340c151226..80fb02b47d 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -1,7 +1,3 @@ -.. index:: pair_write - -pair_write command -================== Syntax """""" diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 079c19c3fd..057adbd60f 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -1,16 +1,12 @@ .. index:: pair_style yukawa +.. index:: pair_style yukawa/gpu +.. index:: pair_style yukawa/omp +.. index:: pair_style yukawa/kk pair_style yukawa command ========================= -pair_style yukawa/gpu command -============================= - -pair_style yukawa/omp command -============================= - -pair_style yukawa/kk command -============================ +Accelerator Variants: *yukawa/gpu*, *yukawa/omp*, *yukawa/kk* Syntax """""" diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 78977118a1..4d21d8e8c3 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -1,13 +1,11 @@ .. index:: pair_style yukawa/colloid +.. index:: pair_style yukawa/colloid/gpu +.. index:: pair_style yukawa/colloid/omp pair_style yukawa/colloid command ================================= -pair_style yukawa/colloid/gpu command -===================================== - -pair_style yukawa/colloid/omp command -===================================== +Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/omp* Syntax """""" diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 5c25697484..e01cbf45f2 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -1,16 +1,12 @@ .. index:: pair_style zbl +.. index:: pair_style zbl/gpu +.. index:: pair_style zbl/kk +.. index:: pair_style zbl/omp pair_style zbl command ====================== -pair_style zbl/gpu command -========================== - -pair_style zbl/kk command -========================= - -pair_style zbl/omp command -========================== +Accelerator Variants: *zbl/gpu*, *zbl/kk*, *zbl/omp* Syntax """""" -- GitLab From 98808fb5ff4823cd4dfeb53f5212998e9e7b782a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 11:04:08 -0400 Subject: [PATCH 18/75] Skip doc files that don't have common file structure --- doc/utils/fixup_headers.py | 41 ++++++++++++++++++++++---------------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 884511bd32..73b1fd3112 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 # Utility script to fix headers in doc pages and generate "Accelerator Styles" portion +import os import shutil import re import argparse @@ -16,10 +17,12 @@ for orig_file in args.files: styles = [] headings = {} new_file = f"{orig_file}.tmp" + found_syntax = False with open(orig_file, 'r') as reader, open(new_file, 'w') as writer: for line in reader: if line.startswith("Syntax"): + found_syntax = True break m = index_pattern.match(line) @@ -42,28 +45,32 @@ for orig_file in args.files: headings[style] = [] elif style not in headings[base_name]: headings[base_name].append(style) - - # write new header - for s in styles: - print(f".. index:: {command_type} {s}", file=writer) - print(file=writer) + if found_syntax: + # write new header + for s in styles: + print(f".. index:: {command_type} {s}", file=writer) - for s, variants in headings.items(): - header = f"{command_type} {s} command" - print(header, file=writer) - print("="*len(header), file=writer) print(file=writer) - if len(variants) > 0: - print("Accelerator Variants: ", end="", file=writer) - print(", ".join([f"*{v}*" for v in variants]), file=writer) + for s, variants in headings.items(): + header = f"{command_type} {s} command" + print(header, file=writer) + print("="*len(header), file=writer) print(file=writer) - # write rest of reader - print(line, end="", file=writer) - for line in reader: + if len(variants) > 0: + print("Accelerator Variants: ", end="", file=writer) + print(", ".join([f"*{v}*" for v in variants]), file=writer) + print(file=writer) + + # write rest of reader print(line, end="", file=writer) + for line in reader: + print(line, end="", file=writer) - # override original file - shutil.move(new_file, orig_file) + if found_syntax: + # override original file + shutil.move(new_file, orig_file) + else: + os.remove(new_file) -- GitLab From 0c88074525b40474ef8042ef4a3213548e8a63c2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 11:05:33 -0400 Subject: [PATCH 19/75] Apply header fix to all remaining fix styles docs --- doc/src/fix_ave_histo.rst | 1 + doc/src/fix_bond_create.rst | 1 + doc/src/fix_deform.rst | 4 ++-- doc/src/fix_dpd_energy.rst | 4 ++-- doc/src/fix_dpd_source.rst | 1 + doc/src/fix_drude_transform.rst | 1 + doc/src/fix_enforce2d.rst | 4 ++-- doc/src/fix_eos_table_rx.rst | 4 ++-- doc/src/fix_freeze.rst | 4 ++-- doc/src/fix_gravity.rst | 8 +++----- doc/src/fix_langevin.rst | 4 ++-- doc/src/fix_modify.rst | 4 ---- doc/src/fix_momentum.rst | 5 +++-- doc/src/fix_mvv_dpd.rst | 2 ++ doc/src/fix_nh.rst | 6 +++--- doc/src/fix_nh_eff.rst | 2 ++ doc/src/fix_nh_uef.rst | 1 + doc/src/fix_nph_asphere.rst | 4 ++-- doc/src/fix_nph_sphere.rst | 4 ++-- doc/src/fix_nphug.rst | 4 ++-- doc/src/fix_npt_asphere.rst | 4 ++-- doc/src/fix_npt_sphere.rst | 4 ++-- doc/src/fix_numdiff.rst | 2 +- doc/src/fix_nve.rst | 12 ++++-------- doc/src/fix_nve_asphere.rst | 4 ++-- doc/src/fix_nve_sphere.rst | 8 +++----- doc/src/fix_nvt_asphere.rst | 4 ++-- doc/src/fix_nvt_sllod.rst | 8 +++----- doc/src/fix_nvt_sphere.rst | 4 ++-- doc/src/fix_orient.rst | 1 + doc/src/fix_property_atom.rst | 4 ++-- doc/src/fix_qeq.rst | 4 ++++ doc/src/fix_qeq_comb.rst | 4 ++-- doc/src/fix_qeq_reax.rst | 8 +++----- doc/src/fix_reaxc_bonds.rst | 4 ++-- doc/src/fix_reaxc_species.rst | 4 ++-- doc/src/fix_rigid.rst | 12 ++++++------ doc/src/fix_rx.rst | 4 ++-- doc/src/fix_setforce.rst | 5 +++-- doc/src/fix_shake.rst | 1 + doc/src/fix_shardlow.rst | 4 ++-- doc/src/fix_smd_integrate_ulsph.rst | 2 +- doc/src/fix_sph.rst | 2 +- doc/src/fix_sph_stationary.rst | 2 +- doc/src/fix_temp_csvr.rst | 1 + doc/src/fix_ttm.rst | 1 + doc/src/fix_wall.rst | 9 +++++++-- doc/src/fix_wall_ees.rst | 1 + doc/src/fix_wall_reflect.rst | 4 ++-- 49 files changed, 102 insertions(+), 93 deletions(-) diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 7c4ef88fd6..d50112ac48 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -1,4 +1,5 @@ .. index:: fix ave/histo +.. index:: fix ave/histo/weight fix ave/histo command ===================== diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index d0c7fb985c..34f0d19f8d 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -1,4 +1,5 @@ .. index:: fix bond/create +.. index:: fix bond/create/angle fix bond/create command ======================= diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 70b15f0d79..999a88c4e7 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -1,10 +1,10 @@ .. index:: fix deform +.. index:: fix deform/kk fix deform command ================== -fix deform/kk command -===================== +Accelerator Variants: *deform/kk* Syntax """""" diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 6d510f1825..732f99b516 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -1,10 +1,10 @@ .. index:: fix dpd/energy +.. index:: fix dpd/energy/kk fix dpd/energy command ====================== -fix dpd/energy/kk command -========================= +Accelerator Variants: *dpd/energy/kk* Syntax """""" diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 4373645c84..29bbc92f78 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -1,4 +1,5 @@ .. index:: fix edpd/source +.. index:: fix tdpd/source fix edpd/source command ======================= diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index bda2d25b1f..792b041576 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -1,4 +1,5 @@ .. index:: fix drude/transform/direct +.. index:: fix drude/transform/inverse fix drude/transform/direct command ================================== diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index e92011cb11..7c6ef75089 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -1,10 +1,10 @@ .. index:: fix enforce2d +.. index:: fix enforce2d/kk fix enforce2d command ===================== -fix enforce2d/kk command -======================== +Accelerator Variants: *enforce2d/kk* Syntax """""" diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index bd13398e0a..56bde44d98 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -1,10 +1,10 @@ .. index:: fix eos/table/rx +.. index:: fix eos/table/rx/kk fix eos/table/rx command ======================== -fix eos/table/rx/kk command -=========================== +Accelerator Variants: *eos/table/rx/kk* Syntax """""" diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index f81954ff5d..a7370c7f44 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -1,10 +1,10 @@ .. index:: fix freeze +.. index:: fix freeze/kk fix freeze command ================== -fix freeze/kk command -===================== +Accelerator Variants: *freeze/kk* Syntax """""" diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 5f06f6d22a..a163eb4ab2 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -1,13 +1,11 @@ .. index:: fix gravity +.. index:: fix gravity/omp +.. index:: fix gravity/kk fix gravity command =================== -fix gravity/omp command -======================= - -fix gravity/kk command -====================== +Accelerator Variants: *gravity/omp*, *gravity/kk* Syntax """""" diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 80f4964242..e31434247f 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -1,10 +1,10 @@ .. index:: fix langevin +.. index:: fix langevin/kk fix langevin command ==================== -fix langevin/kk command -======================= +Accelerator Variants: *langevin/kk* Syntax """""" diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 604b63550c..d6454431c5 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -1,7 +1,3 @@ -.. index:: fix_modify - -fix_modify command -================== Syntax """""" diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index ca6e19005e..393a6a16cd 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -1,10 +1,11 @@ .. index:: fix momentum +.. index:: fix momentum/kk +.. index:: fix momentum/chunk fix momentum command ==================== -fix momentum/kk command -======================= +Accelerator Variants: *momentum/kk* fix momentum/chunk command ========================== diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index c7e9b64c96..d0df1bd0f9 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -1,4 +1,6 @@ .. index:: fix mvv/dpd +.. index:: fix mvv/edpd +.. index:: fix mvv/tdpd fix mvv/dpd command =================== diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 3e23c46e61..84b497dc3f 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -13,17 +13,17 @@ fix nvt command =============== -Accelerator Styles: *nvt/intel*, *nvt/kk*, *nvt/omp* +Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp* fix npt command =============== -Accelerator Styles: *npt/intel*, *npt/kk*, *npt/omp* +Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp* fix nph command =============== -Accelerator Styles: *nph/kk*, *nph/omp* +Accelerator Variants: *nph/kk*, *nph/omp* Syntax """""" diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 4d4d536ac2..3e54ed9765 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -1,4 +1,6 @@ .. index:: fix nvt/eff +.. index:: fix npt/eff +.. index:: fix nph/eff fix nvt/eff command =================== diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 272f84d520..1c1e7a11d2 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -1,4 +1,5 @@ .. index:: fix nvt/uef +.. index:: fix npt/uef fix nvt/uef command =================== diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 2e5dd16c8f..da0510492e 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nph/asphere +.. index:: fix nph/asphere/omp fix nph/asphere command ======================= -fix nph/asphere/omp command -=========================== +Accelerator Variants: *nph/asphere/omp* Syntax """""" diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index efa6ca38b5..4b76f7252f 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix nph/sphere +.. index:: fix nph/sphere/omp fix nph/sphere command ====================== -fix nph/sphere/omp command -========================== +Accelerator Variants: *nph/sphere/omp* Syntax """""" diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index c46e98fe3e..d55f435d43 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -1,10 +1,10 @@ .. index:: fix nphug +.. index:: fix nphug/omp fix nphug command ================= -fix nphug/omp command -===================== +Accelerator Variants: *nphug/omp* Syntax """""" diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index 5537365359..de2289a068 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix npt/asphere +.. index:: fix npt/asphere/omp fix npt/asphere command ======================= -fix npt/asphere/omp command -=========================== +Accelerator Variants: *npt/asphere/omp* Syntax """""" diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index 4e8188ac0c..7363375ff3 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix npt/sphere +.. index:: fix npt/sphere/omp fix npt/sphere command ====================== -fix npt/sphere/omp command -========================== +Accelerator Variants: *npt/sphere/omp* Syntax """""" diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst index 0c4f731ea0..22c1c59748 100644 --- a/doc/src/fix_numdiff.rst +++ b/doc/src/fix_numdiff.rst @@ -1,7 +1,7 @@ .. index:: fix numdiff fix numdiff command -==================== +=================== Syntax """""" diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index 0026d38e8c..71f8ec300f 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -1,16 +1,12 @@ .. index:: fix nve +.. index:: fix nve/intel +.. index:: fix nve/kk +.. index:: fix nve/omp fix nve command =============== -fix nve/intel command -===================== - -fix nve/kk command -================== - -fix nve/omp command -=================== +Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp* Syntax """""" diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index f1441fdd3c..af80460b32 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nve/asphere +.. index:: fix nve/asphere/intel fix nve/asphere command ======================= -fix nve/asphere/intel command -============================= +Accelerator Variants: *nve/asphere/intel* Syntax """""" diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 59d951782a..0230255b42 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -1,13 +1,11 @@ .. index:: fix nve/sphere +.. index:: fix nve/sphere/omp +.. index:: fix nve/sphere/kk fix nve/sphere command ====================== -fix nve/sphere/omp command -========================== - -fix nve/sphere/kk command -========================= +Accelerator Variants: *nve/sphere/omp*, *nve/sphere/kk* Syntax """""" diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index a08dae765c..bb4139d95f 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nvt/asphere +.. index:: fix nvt/asphere/omp fix nvt/asphere command ======================= -fix nvt/asphere/omp command -=========================== +Accelerator Variants: *nvt/asphere/omp* Syntax """""" diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index b5051b8692..ff9a4f0d12 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -1,13 +1,11 @@ .. index:: fix nvt/sllod +.. index:: fix nvt/sllod/intel +.. index:: fix nvt/sllod/omp fix nvt/sllod command ===================== -fix nvt/sllod/intel command -=========================== - -fix nvt/sllod/omp command -========================= +Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp* Syntax """""" diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index dd4cf9cb3f..8226328cea 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix nvt/sphere +.. index:: fix nvt/sphere/omp fix nvt/sphere command ====================== -fix nvt/sphere/omp command -========================== +Accelerator Variants: *nvt/sphere/omp* Syntax """""" diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 51edbd48ad..31aa6074d1 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -1,4 +1,5 @@ .. index:: fix orient/fcc +.. index:: fix orient/bcc fix orient/fcc command ====================== diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index eaf246c1a3..7e322777aa 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -1,10 +1,10 @@ .. index:: fix property/atom +.. index:: fix property/atom/kk fix property/atom command ========================= -fix property/atom/kk command -============================ +Accelerator Variants: *property/atom/kk* Syntax """""" diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index f656049e73..56fde059e8 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -1,4 +1,8 @@ .. index:: fix qeq/point +.. index:: fix qeq/shielded +.. index:: fix qeq/slater +.. index:: fix qeq/dynamic +.. index:: fix qeq/fire fix qeq/point command ===================== diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index f70ecb1dd5..74a97720dc 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -1,10 +1,10 @@ .. index:: fix qeq/comb +.. index:: fix qeq/comb/omp fix qeq/comb command ==================== -fix qeq/comb/omp command -======================== +Accelerator Variants: *qeq/comb/omp* Syntax """""" diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 0fd5e78578..47dca86401 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -1,13 +1,11 @@ .. index:: fix qeq/reax +.. index:: fix qeq/reax/kk +.. index:: fix qeq/reax/omp fix qeq/reax command ==================== -fix qeq/reax/kk command -======================= - -fix qeq/reax/omp command -======================== +Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp* Syntax """""" diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 52f0581929..2d0d2d18db 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -1,10 +1,10 @@ .. index:: fix reax/c/bonds +.. index:: fix reax/c/bonds/kk fix reax/c/bonds command ======================== -fix reax/c/bonds/kk command -=========================== +Accelerator Variants: *reax/c/bonds/kk* Syntax """""" diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 275086b52b..9935ecaa3a 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -1,10 +1,10 @@ .. index:: fix reax/c/species +.. index:: fix reax/c/species/kk fix reax/c/species command ========================== -fix reax/c/species/kk command -============================= +Accelerator Variants: *reax/c/species/kk* Syntax """""" diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 8756e72db1..efadc5dd13 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -18,32 +18,32 @@ fix rigid command ================= -Accelerator Styles: *rigid/omp* +Accelerator Variants: *rigid/omp* fix rigid/nve command ===================== -Accelerator Styles: *rigid/nve/omp* +Accelerator Variants: *rigid/nve/omp* fix rigid/nvt command ===================== -Accelerator Styles: *rigid/nvt/omp* +Accelerator Variants: *rigid/nvt/omp* fix rigid/npt command ===================== -Accelerator Styles: *rigid/npt/omp* +Accelerator Variants: *rigid/npt/omp* fix rigid/nph command ===================== -Accelerator Styles: *rigid/nph/omp* +Accelerator Variants: *rigid/nph/omp* fix rigid/small command ======================= -Accelerator Styles: *rigid/small/omp* +Accelerator Variants: *rigid/small/omp* fix rigid/nve/small command =========================== diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 7a3a95f069..c1a1d0950c 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -1,10 +1,10 @@ .. index:: fix rx +.. index:: fix rx/kk fix rx command ============== -fix rx/kk command -================= +Accelerator Variants: *rx/kk* Syntax """""" diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index b417b369e5..406826e5b9 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -1,10 +1,11 @@ .. index:: fix setforce +.. index:: fix setforce/kk +.. index:: fix setforce/spin fix setforce command ==================== -fix setforce/kk command -======================= +Accelerator Variants: *setforce/kk* fix setforce/spin command ========================= diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 5f720d86ea..eb7add7035 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -1,4 +1,5 @@ .. index:: fix shake +.. index:: fix rattle fix shake command ================= diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index 3c046dae74..f928044db7 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -1,10 +1,10 @@ .. index:: fix shardlow +.. index:: fix shardlow/kk fix shardlow command ==================== -fix shardlow/kk command -======================= +Accelerator Variants: *shardlow/kk* Syntax """""" diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index f7ba223965..5b4c117452 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -1,7 +1,7 @@ .. index:: fix smd/integrate_ulsph fix smd/integrate_ulsph command -================================ +=============================== Syntax """""" diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 1b482e0252..5ba752debb 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -1,7 +1,7 @@ .. index:: fix sph fix sph command -================ +=============== Syntax """""" diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index 5fa3f1d04d..c86a30b542 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -1,7 +1,7 @@ .. index:: fix sph/stationary fix sph/stationary command -=========================== +========================== Syntax """""" diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 10c92dc2f2..8faa6035cf 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -1,4 +1,5 @@ .. index:: fix temp/csvr +.. index:: fix temp/csld fix temp/csvr command ===================== diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 97cb0cd05b..24bc6f297f 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -1,4 +1,5 @@ .. index:: fix ttm +.. index:: fix ttm/mod fix ttm command =============== diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index d4120ca625..39ff879138 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -1,10 +1,15 @@ .. index:: fix wall/lj93 +.. index:: fix wall/lj93/kk +.. index:: fix wall/lj126 +.. index:: fix wall/lj1043 +.. index:: fix wall/colloid +.. index:: fix wall/harmonic +.. index:: fix wall/morse fix wall/lj93 command ===================== -fix wall/lj93/kk command -======================== +Accelerator Variants: *wall/lj93/kk* fix wall/lj126 command ====================== diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 79f96765f8..2bab8c6056 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -1,4 +1,5 @@ .. index:: fix wall/ees +.. index:: fix wall/region/ees fix wall/ees command ==================== diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 44cde8f3d5..4f014cc628 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -1,10 +1,10 @@ .. index:: fix wall/reflect +.. index:: fix wall/reflect/kk fix wall/reflect command ======================== -fix wall/reflect/kk command -=========================== +Accelerator Variants: *wall/reflect/kk* Syntax """""" -- GitLab From 84e922eff649bff8831d08d02d8a7ce67af55b16 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 11:55:53 -0400 Subject: [PATCH 20/75] Add other styles to fixup_header.py --- doc/utils/fixup_headers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 73b1fd3112..fb39c59434 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -5,8 +5,8 @@ import shutil import re import argparse -index_pattern = re.compile(r"^.. index:: (fix|pair_style)\s+([a-zA-Z0-9/_]+)$") -pattern = re.compile(r"^(fix|pair_style)\s+([a-zA-Z0-9/_]+)\s+command$") +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)$") +pattern = re.compile(r"^(compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)\s+command$") parser = argparse.ArgumentParser(description='Fixup headers in docs') parser.add_argument('files', metavar='FILE', nargs='+', help='files to fix') -- GitLab From 549bdd080ccdf65a586aada4d6b3c753b01e4e82 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:37:48 -0400 Subject: [PATCH 21/75] Add kspace_style to fixup_headers.py --- doc/utils/fixup_headers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index fb39c59434..c7fe57bc17 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -5,8 +5,8 @@ import shutil import re import argparse -index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)$") -pattern = re.compile(r"^(compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)\s+command$") +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$") +pattern = re.compile(r"^(compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)\s+command$") parser = argparse.ArgumentParser(description='Fixup headers in docs') parser.add_argument('files', metavar='FILE', nargs='+', help='files to fix') -- GitLab From 286d3866e3bc27bd27b136d2bf775d39b3fac7c5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:42:18 -0400 Subject: [PATCH 22/75] Add style index check in check-styles.py --- doc/utils/check-styles.py | 61 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 60 insertions(+), 1 deletion(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 603f312e9d..45876ea738 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -60,6 +60,7 @@ reader = {} region = {} total = 0 +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$") style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)") upper = re.compile("[A-Z]+") gpu = re.compile("(.+)/gpu$") @@ -70,6 +71,26 @@ omp = re.compile("(.+)/omp$") opt = re.compile("(.+)/opt$") removed = re.compile("(.*)Deprecated$") +def load_index_entries_in_file(path): + entries = [] + with open(path, 'r') as reader: + for line in reader: + m = index_pattern.match(line) + if m: + command_type = m.group(1) + style = m.group(2) + entries.append((command_type, style)) + return entries + +def load_index_entries(): + index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(), + 'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()} + rst_files = glob(os.path.join(doc_dir, '*.rst')) + for f in rst_files: + for command_type, style in load_index_entries_in_file(f): + index[command_type].add(style) + return index + def register_style(styles, name, info): if name in styles: for key, value in info.items(): @@ -112,6 +133,24 @@ def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set counter += 1 return counter +def check_style_index(name, styles, index): + counter = 0 + for style in styles: + if style not in index and not styles[style]['removed']: + print(f"{name} index entry {style} is missing") + counter += 1 + + for suffix in styles[style]: + if suffix == 'removed': continue + if suffix == 'kokkos': + suffix_style = f"{style}/kk" + else: + suffix_style = f"{style}/{suffix}" + if styles[style][suffix] and suffix_style not in index: + print(f"{name} index entry {suffix_style} is missing") + counter += 1 + return counter + for header in headers: if verbose: print("Checking ", header) with open(header) as f: @@ -207,6 +246,13 @@ Total number of styles (including suffixes): %d""" \ len(fix), len(improper), len(integrate), len(kspace), \ len(minimize), len(pair), len(reader), len(region), total)) +index = load_index_entries() + +total_index = 0 +for command_type, entries in index.items(): + total_index += len(entries) + +print("Total number of style index entries:", total_index) counter = 0 @@ -244,5 +290,18 @@ counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) Date: Wed, 2 Sep 2020 12:43:48 -0400 Subject: [PATCH 23/75] Update headers in angle_*.rst files --- doc/src/angle_charmm.rst | 12 ++++-------- doc/src/angle_class2.rst | 9 ++++----- doc/src/angle_coeff.rst | 4 ---- doc/src/angle_cosine.rst | 8 +++----- doc/src/angle_cosine_delta.rst | 4 ++-- doc/src/angle_cosine_periodic.rst | 4 ++-- doc/src/angle_cosine_shift.rst | 6 +++--- doc/src/angle_cosine_shift_exp.rst | 4 ++-- doc/src/angle_cosine_squared.rst | 4 ++-- doc/src/angle_cross.rst | 2 +- doc/src/angle_dipole.rst | 4 ++-- doc/src/angle_fourier.rst | 4 ++-- doc/src/angle_fourier_simple.rst | 4 ++-- doc/src/angle_harmonic.rst | 12 ++++-------- doc/src/angle_quartic.rst | 4 ++-- doc/src/angle_sdk.rst | 4 ++-- doc/src/angle_style.rst | 4 ---- doc/src/angle_table.rst | 4 ++-- 18 files changed, 39 insertions(+), 58 deletions(-) diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 8410f0f8c0..e557648d9f 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -1,16 +1,12 @@ .. index:: angle_style charmm +.. index:: angle_style charmm/intel +.. index:: angle_style charmm/kk +.. index:: angle_style charmm/omp angle_style charmm command ========================== -angle_style charmm/intel command -================================ - -angle_style charmm/kk command -============================= - -angle_style charmm/omp command -============================== +Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp* Syntax """""" diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index 7d2fdd5d66..bf0305055a 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -1,13 +1,12 @@ .. index:: angle_style class2 +.. index:: angle_style class2/kk +.. index:: angle_style class2/omp +.. index:: angle_style class2/p6 angle_style class2 command ========================== -angle_style class2/kk command -============================= - -angle_style class2/omp command -============================== +Accelerator Variants: *class2/kk*, *class2/omp* angle_style class2/p6 command ============================= diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 07048c1432..873212f3b5 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -1,7 +1,3 @@ -.. index:: angle_coeff - -angle_coeff command -=================== Syntax """""" diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index e39e68b2e1..aea144f7be 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -1,13 +1,11 @@ .. index:: angle_style cosine +.. index:: angle_style cosine/omp +.. index:: angle_style cosine/kk angle_style cosine command ========================== -angle_style cosine/omp command -============================== - -angle_style cosine/kk command -============================= +Accelerator Variants: *cosine/omp*, *cosine/kk* Syntax """""" diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 017b64f8b0..280e6ea2c4 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/delta +.. index:: angle_style cosine/delta/omp angle_style cosine/delta command ================================ -angle_style cosine/delta/omp command -==================================== +Accelerator Variants: *cosine/delta/omp* Syntax """""" diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index aff4ba2322..71c2caa3f0 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/periodic +.. index:: angle_style cosine/periodic/omp angle_style cosine/periodic command =================================== -angle_style cosine/periodic/omp command -======================================= +Accelerator Variants: *cosine/periodic/omp* Syntax """""" diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index 26603e48be..71bda194c7 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/shift +.. index:: angle_style cosine/shift/omp angle_style cosine/shift command -================================= +================================ -angle_style cosine/shift/omp command -==================================== +Accelerator Variants: *cosine/shift/omp* Syntax """""" diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index fbdb76aa45..4ae4928751 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/shift/exp +.. index:: angle_style cosine/shift/exp/omp angle_style cosine/shift/exp command ==================================== -angle_style cosine/shift/exp/omp command -======================================== +Accelerator Variants: *cosine/shift/exp/omp* Syntax """""" diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 49ddf59741..4a6a1debe9 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/squared +.. index:: angle_style cosine/squared/omp angle_style cosine/squared command ================================== -angle_style cosine/squared/omp command -====================================== +Accelerator Variants: *cosine/squared/omp* Syntax """""" diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 5769e756c3..3cd1884be0 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -1,7 +1,7 @@ .. index:: angle_style cross angle_style cross command -========================== +========================= Syntax """""" diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 3b4e4f5304..4dd8aadfb8 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -1,10 +1,10 @@ .. index:: angle_style dipole +.. index:: angle_style dipole/omp angle_style dipole command ========================== -angle_style dipole/omp command -============================== +Accelerator Variants: *dipole/omp* Syntax """""" diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index cbe6544271..231f45e808 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -1,10 +1,10 @@ .. index:: angle_style fourier +.. index:: angle_style fourier/omp angle_style fourier command =========================== -angle_style fourier/omp command -=============================== +Accelerator Variants: *fourier/omp* Syntax """""" diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index b36f69cbec..14b4bbcfe9 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -1,10 +1,10 @@ .. index:: angle_style fourier/simple +.. index:: angle_style fourier/simple/omp angle_style fourier/simple command ================================== -angle_style fourier/simple/omp command -====================================== +Accelerator Variants: *fourier/simple/omp* Syntax """""" diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index c6ad93c3ec..06cf1d460b 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -1,16 +1,12 @@ .. index:: angle_style harmonic +.. index:: angle_style harmonic/intel +.. index:: angle_style harmonic/kk +.. index:: angle_style harmonic/omp angle_style harmonic command ============================ -angle_style harmonic/intel command -================================== - -angle_style harmonic/kk command -=============================== - -angle_style harmonic/omp command -================================ +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 71297e60a0..7dfb4b2896 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -1,10 +1,10 @@ .. index:: angle_style quartic +.. index:: angle_style quartic/omp angle_style quartic command =========================== -angle_style quartic/omp command -=============================== +Accelerator Variants: *quartic/omp* Syntax """""" diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index f5583d5013..340a3e4de7 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -1,10 +1,10 @@ .. index:: angle_style sdk +.. index:: angle_style sdk/omp angle_style sdk command ======================= -angle_style sdk/omp command -=========================== +Accelerator Variants: *sdk/omp* Syntax """""" diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 91232a6b6c..ba991954ab 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -1,7 +1,3 @@ -.. index:: angle_style - -angle_style command -=================== Syntax """""" diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index d8d9476620..cad9f5a82f 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -1,10 +1,10 @@ .. index:: angle_style table +.. index:: angle_style table/omp angle_style table command ========================= -angle_style table/omp command -============================= +Accelerator Variants: *table/omp* Syntax """""" -- GitLab From 4e27c47f962fd247219084e0f33b1e177eab34ff Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:52:30 -0400 Subject: [PATCH 24/75] Undo lost headers --- doc/src/angle_coeff.rst | 4 ++++ doc/src/angle_style.rst | 4 ++++ doc/src/fix_modify.rst | 4 ++++ doc/src/pair_coeff.rst | 4 ++++ doc/src/pair_modify.rst | 4 ++++ doc/src/pair_style.rst | 4 ++++ doc/src/pair_write.rst | 4 ++++ doc/utils/fixup_headers.py | 2 +- 8 files changed, 29 insertions(+), 1 deletion(-) diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 873212f3b5..07048c1432 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -1,3 +1,7 @@ +.. index:: angle_coeff + +angle_coeff command +=================== Syntax """""" diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index ba991954ab..91232a6b6c 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -1,3 +1,7 @@ +.. index:: angle_style + +angle_style command +=================== Syntax """""" diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index d6454431c5..604b63550c 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -1,3 +1,7 @@ +.. index:: fix_modify + +fix_modify command +================== Syntax """""" diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 7c72bb5843..ea62d839ab 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -1,3 +1,7 @@ +.. index:: pair_coeff + +pair_coeff command +================== Syntax """""" diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 21d0977047..b8969c0131 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -1,3 +1,7 @@ +.. index:: pair_modify + +pair_modify command +=================== Syntax """""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1b9ceaf0ee..4feaeacad0 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -1,3 +1,7 @@ +.. index:: pair_style + +pair_style command +================== Syntax """""" diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 80fb02b47d..340c151226 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -1,3 +1,7 @@ +.. index:: pair_write + +pair_write command +================== Syntax """""" diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index c7fe57bc17..520bec104b 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -69,7 +69,7 @@ for orig_file in args.files: for line in reader: print(line, end="", file=writer) - if found_syntax: + if found_syntax and len(styles) > 0: # override original file shutil.move(new_file, orig_file) else: -- GitLab From f4d2523ce0aca1e2717d77121c49daad3211de09 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:55:18 -0400 Subject: [PATCH 25/75] Update headers in bond_*.rst files --- doc/src/bond_class2.rst | 8 +++----- doc/src/bond_fene.rst | 12 ++++-------- doc/src/bond_fene_expand.rst | 4 ++-- doc/src/bond_gromos.rst | 4 ++-- doc/src/bond_harmonic.rst | 12 ++++-------- doc/src/bond_harmonic_shift.rst | 4 ++-- doc/src/bond_harmonic_shift_cut.rst | 4 ++-- doc/src/bond_morse.rst | 4 ++-- doc/src/bond_nonlinear.rst | 4 ++-- doc/src/bond_oxdna.rst | 2 ++ doc/src/bond_quartic.rst | 4 ++-- doc/src/bond_special.rst | 2 +- doc/src/bond_table.rst | 4 ++-- 13 files changed, 30 insertions(+), 38 deletions(-) diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index 41eb2b4e50..aea503738f 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -1,13 +1,11 @@ .. index:: bond_style class2 +.. index:: bond_style class2/omp +.. index:: bond_style class2/kk bond_style class2 command ========================= -bond_style class2/omp command -============================= - -bond_style class2/kk command -============================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index 8ec117bf24..0c6a37ca62 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -1,16 +1,12 @@ .. index:: bond_style fene +.. index:: bond_style fene/intel +.. index:: bond_style fene/kk +.. index:: bond_style fene/omp bond_style fene command ======================= -bond_style fene/intel command -============================= - -bond_style fene/kk command -========================== - -bond_style fene/omp command -=========================== +Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp* Syntax """""" diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 5bcb409238..1be06561e9 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -1,10 +1,10 @@ .. index:: bond_style fene/expand +.. index:: bond_style fene/expand/omp bond_style fene/expand command ============================== -bond_style fene/expand/omp command -================================== +Accelerator Variants: *fene/expand/omp* Syntax """""" diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index f09e5761fe..d4eb958ebe 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -1,10 +1,10 @@ .. index:: bond_style gromos +.. index:: bond_style gromos/omp bond_style gromos command ========================= -bond_style gromos/omp command -============================= +Accelerator Variants: *gromos/omp* Syntax """""" diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index eaa1ee7986..e3320f2e19 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -1,16 +1,12 @@ .. index:: bond_style harmonic +.. index:: bond_style harmonic/intel +.. index:: bond_style harmonic/kk +.. index:: bond_style harmonic/omp bond_style harmonic command =========================== -bond_style harmonic/intel command -================================= - -bond_style harmonic/kk command -============================== - -bond_style harmonic/omp command -=============================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index c124bacf0f..469c370969 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -1,10 +1,10 @@ .. index:: bond_style harmonic/shift +.. index:: bond_style harmonic/shift/omp bond_style harmonic/shift command ================================= -bond_style harmonic/shift/omp command -===================================== +Accelerator Variants: *harmonic/shift/omp* Syntax """""" diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index e1b7e990d4..d0f44740b3 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -1,10 +1,10 @@ .. index:: bond_style harmonic/shift/cut +.. index:: bond_style harmonic/shift/cut/omp bond_style harmonic/shift/cut command ===================================== -bond_style harmonic/shift/cut/omp command -========================================= +Accelerator Variants: *harmonic/shift/cut/omp* Syntax """""" diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 64fc61298a..f096624ba0 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -1,10 +1,10 @@ .. index:: bond_style morse +.. index:: bond_style morse/omp bond_style morse command ======================== -bond_style morse/omp command -============================ +Accelerator Variants: *morse/omp* Syntax """""" diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 75ab4ad347..77271502ea 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -1,10 +1,10 @@ .. index:: bond_style nonlinear +.. index:: bond_style nonlinear/omp bond_style nonlinear command ============================ -bond_style nonlinear/omp command -================================ +Accelerator Variants: *nonlinear/omp* Syntax """""" diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index ada2f0e1ed..3f52424d49 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -1,4 +1,6 @@ .. index:: bond_style oxdna/fene +.. index:: bond_style oxdna2/fene +.. index:: bond_style oxrna2/fene bond_style oxdna/fene command ============================= diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index d54c19bbd4..8c5b363e54 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -1,10 +1,10 @@ .. index:: bond_style quartic +.. index:: bond_style quartic/omp bond_style quartic command ========================== -bond_style quartic/omp command -============================== +Accelerator Variants: *quartic/omp* Syntax """""" diff --git a/doc/src/bond_special.rst b/doc/src/bond_special.rst index bd93bb644c..d2423c9e23 100644 --- a/doc/src/bond_special.rst +++ b/doc/src/bond_special.rst @@ -1,7 +1,7 @@ .. index:: bond_style special bond_style special command -================================= +========================== Syntax """""" diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 9f8ebacef0..fedb50355d 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -1,10 +1,10 @@ .. index:: bond_style table +.. index:: bond_style table/omp bond_style table command ======================== -bond_style table/omp command -============================ +Accelerator Variants: *table/omp* Syntax """""" -- GitLab From d01c985febf27f31aeb058515c861ddd3ade151d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:56:24 -0400 Subject: [PATCH 26/75] Update headers in compute_*.rst files --- doc/src/compute_cluster_atom.rst | 2 ++ doc/src/compute_coord_atom.rst | 4 ++-- doc/src/compute_mesont.rst | 2 +- doc/src/compute_orientorder_atom.rst | 4 ++-- doc/src/compute_reduce.rst | 1 + doc/src/compute_smd_ulsph_effm.rst | 2 +- doc/src/compute_sna_atom.rst | 3 +++ doc/src/compute_sph_e_atom.rst | 2 +- doc/src/compute_sph_rho_atom.rst | 2 +- doc/src/compute_sph_t_atom.rst | 2 +- doc/src/compute_stress_atom.rst | 1 + doc/src/compute_stress_mop.rst | 1 + doc/src/compute_tally.rst | 4 ++++ doc/src/compute_temp.rst | 4 ++-- 14 files changed, 23 insertions(+), 11 deletions(-) diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index 77149306dc..ab47aed9b3 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -1,4 +1,6 @@ .. index:: compute cluster/atom +.. index:: compute fragment/atom +.. index:: compute aggregate/atom compute cluster/atom command ============================ diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index cbf879b8bd..f3c6f818af 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -1,10 +1,10 @@ .. index:: compute coord/atom +.. index:: compute coord/atom/kk compute coord/atom command ========================== -compute coord/atom/kk command -=================================== +Accelerator Variants: *coord/atom/kk* Syntax """""" diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index bf0ade16c1..44d6054e22 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -1,7 +1,7 @@ .. index:: compute mesont compute mesont command -========================== +====================== Syntax """""" diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index c8ab4d7b9b..2a36fb4cc0 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -1,10 +1,10 @@ .. index:: compute orientorder/atom +.. index:: compute orientorder/atom/kk compute orientorder/atom command ================================ -compute orientorder/atom/kk command -=================================== +Accelerator Variants: *orientorder/atom/kk* Syntax """""" diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index bf7d0dc28c..c7815305c0 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -1,4 +1,5 @@ .. index:: compute reduce +.. index:: compute reduce/region compute reduce command ====================== diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index e6d6b772a0..ff12f9cdac 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -1,7 +1,7 @@ .. index:: compute smd/ulsph/effm compute smd/ulsph/effm command -================================ +============================== Syntax """""" diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 7e74a1bd61..08b06a32ec 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -1,4 +1,7 @@ .. index:: compute sna/atom +.. index:: compute snad/atom +.. index:: compute snav/atom +.. index:: compute snap compute sna/atom command ======================== diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index 08378c7c99..17591257f2 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/e/atom compute sph/e/atom command -=========================== +========================== Syntax """""" diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index 975ebf996d..c422a5ecbb 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/rho/atom compute sph/rho/atom command -============================= +============================ Syntax """""" diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index 2f8ad12f45..922adfff58 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/t/atom compute sph/t/atom command -=========================== +========================== Syntax """""" diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 2bdab03bda..16afd49548 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -1,4 +1,5 @@ .. index:: compute stress/atom +.. index:: compute centroid/stress/atom compute stress/atom command =========================== diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 4d0d21cb87..f164a33c26 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -1,4 +1,5 @@ .. index:: compute stress/mop +.. index:: compute stress/mop/profile compute stress/mop command ========================== diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 281425763a..6487618516 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -1,4 +1,8 @@ .. index:: compute force/tally +.. index:: compute heat/flux/tally +.. index:: compute pe/tally +.. index:: compute pe/mol/tally +.. index:: compute stress/tally compute force/tally command =========================== diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index ac11aa155c..a82046367e 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -1,10 +1,10 @@ .. index:: compute temp +.. index:: compute temp/kk compute temp command ==================== -compute temp/kk command -======================= +Accelerator Variants: *temp/kk* Syntax """""" -- GitLab From a0c9c213fd3eded5a61b507a471148edae29e4db Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:57:44 -0400 Subject: [PATCH 27/75] Update headers in dihedral_*.rst files --- doc/src/dihedral_charmm.rst | 13 +++++-------- doc/src/dihedral_class2.rst | 8 +++----- doc/src/dihedral_cosine_shift_exp.rst | 4 ++-- doc/src/dihedral_fourier.rst | 8 +++----- doc/src/dihedral_harmonic.rst | 12 ++++-------- doc/src/dihedral_helix.rst | 4 ++-- doc/src/dihedral_multi_harmonic.rst | 4 ++-- doc/src/dihedral_nharmonic.rst | 6 +++--- doc/src/dihedral_opls.rst | 12 ++++-------- doc/src/dihedral_quadratic.rst | 4 ++-- doc/src/dihedral_table.rst | 4 ++-- doc/src/dihedral_zero.rst | 2 +- 12 files changed, 33 insertions(+), 48 deletions(-) diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index bbaaaf2dd4..9588cf8272 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -1,16 +1,13 @@ .. index:: dihedral_style charmm +.. index:: dihedral_style charmm/intel +.. index:: dihedral_style charmm/kk +.. index:: dihedral_style charmm/omp +.. index:: dihedral_style charmmfsw dihedral_style charmm command ============================= -dihedral_style charmm/intel command -=================================== - -dihedral_style charmm/kk command -================================ - -dihedral_style charmm/omp command -================================= +Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp* dihedral_style charmmfsw command ================================ diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index 907102a4f6..a98cf6b041 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -1,13 +1,11 @@ .. index:: dihedral_style class2 +.. index:: dihedral_style class2/omp +.. index:: dihedral_style class2/kk dihedral_style class2 command ============================= -dihedral_style class2/omp command -================================= - -dihedral_style class2/kk command -================================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 9648bc5387..1f0195df83 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style cosine/shift/exp +.. index:: dihedral_style cosine/shift/exp/omp dihedral_style cosine/shift/exp command ======================================= -dihedral_style cosine/shift/exp/omp command -=========================================== +Accelerator Variants: *cosine/shift/exp/omp* Syntax """""" diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index d795488107..f55011c902 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -1,13 +1,11 @@ .. index:: dihedral_style fourier +.. index:: dihedral_style fourier/intel +.. index:: dihedral_style fourier/omp dihedral_style fourier command ============================== -dihedral_style fourier/intel command -==================================== - -dihedral_style fourier/omp command -================================== +Accelerator Variants: *fourier/intel*, *fourier/omp* Syntax """""" diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index f6e9794d3e..0ee6339ea0 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -1,16 +1,12 @@ .. index:: dihedral_style harmonic +.. index:: dihedral_style harmonic/intel +.. index:: dihedral_style harmonic/kk +.. index:: dihedral_style harmonic/omp dihedral_style harmonic command =============================== -dihedral_style harmonic/intel command -===================================== - -dihedral_style harmonic/kk command -================================== - -dihedral_style harmonic/omp command -=================================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 58738dd7a7..89258cff35 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style helix +.. index:: dihedral_style helix/omp dihedral_style helix command ============================ -dihedral_style helix/omp command -================================ +Accelerator Variants: *helix/omp* Syntax """""" diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index c13d45863f..176d3815dc 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style multi/harmonic +.. index:: dihedral_style multi/harmonic/omp dihedral_style multi/harmonic command ===================================== -dihedral_style multi/harmonic/omp command -========================================= +Accelerator Variants: *multi/harmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index e2223382e2..2411903126 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style nharmonic +.. index:: dihedral_style nharmonic/omp dihedral_style nharmonic command -================================= +================================ -dihedral_style nharmonic/omp command -===================================== +Accelerator Variants: *nharmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index a2be0b5b2d..36b1897fce 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -1,16 +1,12 @@ .. index:: dihedral_style opls +.. index:: dihedral_style opls/intel +.. index:: dihedral_style opls/kk +.. index:: dihedral_style opls/omp dihedral_style opls command =========================== -dihedral_style opls/intel command -================================= - -dihedral_style opls/kk command -============================== - -dihedral_style opls/omp command -=============================== +Accelerator Variants: *opls/intel*, *opls/kk*, *opls/omp* Syntax """""" diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 9c4a707562..dbe680fc82 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style quadratic +.. index:: dihedral_style quadratic/omp dihedral_style quadratic command ================================ -dihedral_style quadratic/omp command -==================================== +Accelerator Variants: *quadratic/omp* Syntax """""" diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 9ed7249572..ff3e61baee 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style table +.. index:: dihedral_style table/omp dihedral_style table command ============================ -dihedral_style table/omp command -================================ +Accelerator Variants: *table/omp* Syntax """""" diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 3df68edfd5..0f481f917d 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -1,7 +1,7 @@ .. index:: dihedral_style zero dihedral_style zero command -============================ +=========================== Syntax """""" -- GitLab From c812bf7a91b6830e798af64c253307fdb39055a3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:03:03 -0400 Subject: [PATCH 28/75] Update headers in improper_*.rst files --- doc/src/improper_class2.rst | 8 +++----- doc/src/improper_cossq.rst | 4 ++-- doc/src/improper_cvff.rst | 8 +++----- doc/src/improper_fourier.rst | 4 ++-- doc/src/improper_harmonic.rst | 12 ++++-------- doc/src/improper_ring.rst | 4 ++-- doc/src/improper_umbrella.rst | 4 ++-- 7 files changed, 18 insertions(+), 26 deletions(-) diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index eb6b8eab2c..a84e92b090 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -1,13 +1,11 @@ .. index:: improper_style class2 +.. index:: improper_style class2/omp +.. index:: improper_style class2/kk improper_style class2 command ============================= -improper_style class2/omp command -================================= - -improper_style class2/kk command -================================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 70885acc28..a6281bc260 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -1,10 +1,10 @@ .. index:: improper_style cossq +.. index:: improper_style cossq/omp improper_style cossq command ============================ -improper_style cossq/omp command -================================ +Accelerator Variants: *cossq/omp* Syntax """""" diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index bde510c3f7..5bd7fdf911 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -1,13 +1,11 @@ .. index:: improper_style cvff +.. index:: improper_style cvff/intel +.. index:: improper_style cvff/omp improper_style cvff command =========================== -improper_style cvff/intel command -================================= - -improper_style cvff/omp command -=============================== +Accelerator Variants: *cvff/intel*, *cvff/omp* Syntax """""" diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 04ce9ba994..84ea97509d 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -1,10 +1,10 @@ .. index:: improper_style fourier +.. index:: improper_style fourier/omp improper_style fourier command ============================== -improper_style fourier/omp command -================================== +Accelerator Variants: *fourier/omp* Syntax """""" diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index e1b78d21db..4f21e48fa9 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -1,16 +1,12 @@ .. index:: improper_style harmonic +.. index:: improper_style harmonic/intel +.. index:: improper_style harmonic/kk +.. index:: improper_style harmonic/omp improper_style harmonic command =============================== -improper_style harmonic/intel command -===================================== - -improper_style harmonic/kk command -================================== - -improper_style harmonic/omp command -=================================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index df319396e2..d67c999714 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -1,10 +1,10 @@ .. index:: improper_style ring +.. index:: improper_style ring/omp improper_style ring command =========================== -improper_style ring/omp command -=============================== +Accelerator Variants: *ring/omp* Syntax """""" diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 10981248d9..5d4aa571e1 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -1,10 +1,10 @@ .. index:: improper_style umbrella +.. index:: improper_style umbrella/omp improper_style umbrella command =============================== -improper_style umbrella/omp command -=================================== +Accelerator Variants: *umbrella/omp* Syntax """""" -- GitLab From 28c90a6dea68474297a8b5a3f6eade78c6dfef71 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:40:24 -0400 Subject: [PATCH 29/75] Update index for kspace_style commands --- doc/src/kspace_style.rst | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 5b45b00353..59f5b7f27c 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -1,4 +1,30 @@ -.. index:: kspace_style +.. index:: kspace_style ewald +.. index:: kspace_style ewald/dipole +.. index:: kspace_style ewald/dipole/spin +.. index:: kspace_style ewald/disp +.. index:: kspace_style ewald/omp +.. index:: kspace_style pppm +.. index:: kspace_style pppm/kk +.. index:: kspace_style pppm/omp +.. index:: kspace_style pppm/gpu +.. index:: kspace_style pppm/intel +.. index:: kspace_style pppm/cg +.. index:: kspace_style pppm/dipole +.. index:: kspace_style pppm/dipole/spin +.. index:: kspace_style pppm/disp +.. index:: kspace_style pppm/disp/omp +.. index:: kspace_style pppm/disp/tip4p +.. index:: kspace_style pppm/disp/tip4p/omp +.. index:: kspace_style pppm/disp/intel +.. index:: kspace_style pppm/cg/omp +.. index:: kspace_style pppm/stagger +.. index:: kspace_style pppm/tip4p +.. index:: kspace_style pppm/tip4p/omp +.. index:: kspace_style msm +.. index:: kspace_style msm/omp +.. index:: kspace_style msm/cg +.. index:: kspace_style msm/cg/omp +.. index:: kspace_style scafacos kspace_style command ==================== -- GitLab From e519919caedd58a89976c2d1746f4c1a894ac72e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:48:11 -0400 Subject: [PATCH 30/75] Fix typo --- doc/src/fix_orient_eco.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_orient_eco.rst b/doc/src/fix_orient_eco.rst index bdfab21c9d..58ff38268f 100644 --- a/doc/src/fix_orient_eco.rst +++ b/doc/src/fix_orient_eco.rst @@ -1,4 +1,4 @@ -.. index:: fix orient/eco +.. index:: fix orient/eco fix orient/eco command ====================== -- GitLab From 515746063f7177c9d11165aebf5f57f8e59b97b0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:55:27 -0400 Subject: [PATCH 31/75] Fix copy&paste error --- doc/utils/check-styles.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 45876ea738..6dddab82c0 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -299,7 +299,7 @@ counter += check_style_index("fix", fix, index["fix"]) counter += check_style_index("angle_style", angle, index["angle_style"]) counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) -counter += check_style_index("improper_style", dihedral, index["improper_style"]) +counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) counter += check_style_index("pair_style", pair, index["pair_style"]) -- GitLab From 0f9c46235cec801d597f33bfb0772481613dbf1a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:56:17 -0400 Subject: [PATCH 32/75] Add missing index entries --- doc/src/fix_python_invoke.rst | 4 ++++ doc/src/pair_meamc.rst | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 94bad11f00..9ccb24cba1 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -1,5 +1,9 @@ +.. index:: fix python .. index:: fix python/invoke +fix python command +================== + fix python/invoke command ========================= diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 757c4c6712..5f6e3ae984 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -1,5 +1,9 @@ +.. index:: pair_style meam .. index:: pair_style meam/c +pair_style meam command +======================= + pair_style meam/c command ========================= -- GitLab From ac7129b3a920708ac3da73cdfbcae4885d303e83 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 14:02:53 -0400 Subject: [PATCH 33/75] Revert "Add missing index entries" These are intentionally left out from docs --- doc/src/fix_python_invoke.rst | 4 ---- doc/src/pair_meamc.rst | 4 ---- 2 files changed, 8 deletions(-) diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 9ccb24cba1..94bad11f00 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -1,9 +1,5 @@ -.. index:: fix python .. index:: fix python/invoke -fix python command -================== - fix python/invoke command ========================= diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 5f6e3ae984..757c4c6712 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -1,9 +1,5 @@ -.. index:: pair_style meam .. index:: pair_style meam/c -pair_style meam command -======================= - pair_style meam/c command ========================= -- GitLab From 8def5844c89ef4113ffed754562391f9273d704b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 14:06:35 -0400 Subject: [PATCH 34/75] Skip old styles in check-styles --- doc/utils/check-styles.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 6dddab82c0..f9a7d3e39a 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -133,10 +133,10 @@ def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set counter += 1 return counter -def check_style_index(name, styles, index): +def check_style_index(name, styles, index, skip=[]): counter = 0 for style in styles: - if style not in index and not styles[style]['removed']: + if style not in index and not styles[style]['removed'] and style not in skip: print(f"{name} index entry {style} is missing") counter += 1 @@ -146,7 +146,7 @@ def check_style_index(name, styles, index): suffix_style = f"{style}/kk" else: suffix_style = f"{style}/{suffix}" - if styles[style][suffix] and suffix_style not in index: + if styles[style][suffix] and suffix_style not in index and style not in skip: print(f"{name} index entry {suffix_style} is missing") counter += 1 return counter @@ -295,13 +295,13 @@ if counter: counter = 0 counter += check_style_index("compute", compute, index["compute"]) -counter += check_style_index("fix", fix, index["fix"]) +counter += check_style_index("fix", fix, index["fix"], skip=['python']) counter += check_style_index("angle_style", angle, index["angle_style"]) counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) -counter += check_style_index("pair_style", pair, index["pair_style"]) +counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam', 'lj/sf']) if counter: print(f"Found {counter} issue(s) with style index") -- GitLab From 6113169a473dc847b8f877855747c26e3c1b754c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 15:26:00 -0400 Subject: [PATCH 35/75] IWYU based include statement cleanup --- src/ASPHERE/compute_erotate_asphere.cpp | 2 +- src/ASPHERE/compute_temp_asphere.cpp | 2 +- src/ASPHERE/fix_nph_asphere.cpp | 2 +- src/ASPHERE/fix_npt_asphere.cpp | 2 +- src/ASPHERE/fix_nvt_asphere.cpp | 4 +-- src/ASPHERE/pair_gayberne.cpp | 4 +-- src/ASPHERE/pair_line_lj.cpp | 2 +- src/ASPHERE/pair_resquared.cpp | 4 +-- src/ASPHERE/pair_tri_lj.cpp | 2 +- src/BODY/compute_body_local.cpp | 2 +- src/BODY/compute_temp_body.cpp | 2 +- src/BODY/fix_nph_body.cpp | 4 +-- src/BODY/fix_npt_body.cpp | 4 +-- src/BODY/fix_nvt_body.cpp | 4 +-- src/BODY/pair_body_nparticle.cpp | 2 +- src/BODY/pair_body_rounded_polygon.cpp | 4 +-- src/BODY/pair_body_rounded_polyhedron.cpp | 4 +-- src/CLASS2/angle_class2.cpp | 4 +-- src/CLASS2/bond_class2.cpp | 4 +-- src/CLASS2/dihedral_class2.cpp | 6 ++-- src/CLASS2/improper_class2.cpp | 6 ++-- src/CLASS2/pair_lj_class2.cpp | 4 +-- src/CLASS2/pair_lj_class2_coul_cut.cpp | 4 +-- src/CLASS2/pair_lj_class2_coul_long.cpp | 4 +-- src/COLLOID/fix_wall_colloid.cpp | 2 +- src/COLLOID/pair_brownian.cpp | 4 +-- src/COLLOID/pair_brownian_poly.cpp | 2 +- src/COLLOID/pair_colloid.cpp | 4 +-- src/COLLOID/pair_lubricate.cpp | 4 +-- src/COLLOID/pair_lubricateU.cpp | 4 +-- src/COLLOID/pair_lubricateU_poly.cpp | 2 +- src/COLLOID/pair_lubricate_poly.cpp | 2 +- src/COMPRESS/dump_atom_gz.cpp | 4 +-- src/COMPRESS/dump_atom_zstd.cpp | 4 +-- src/COMPRESS/dump_cfg_gz.cpp | 4 +-- src/COMPRESS/dump_cfg_zstd.cpp | 4 +-- src/COMPRESS/dump_custom_gz.cpp | 4 +-- src/COMPRESS/dump_custom_zstd.cpp | 4 +-- src/COMPRESS/dump_local_gz.cpp | 4 +-- src/COMPRESS/dump_local_zstd.cpp | 4 +-- src/COMPRESS/dump_xyz_gz.cpp | 4 +-- src/COMPRESS/dump_xyz_zstd.cpp | 4 +-- src/CORESHELL/compute_temp_cs.cpp | 6 ++-- src/DIPOLE/atom_vec_dipole.cpp | 2 +- src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 4 +-- src/DIPOLE/pair_lj_cut_dipole_long.cpp | 4 +-- src/DIPOLE/pair_lj_long_dipole_long.cpp | 4 +-- src/GPU/fix_gpu.cpp | 4 +-- src/GPU/pair_beck_gpu.cpp | 2 +- src/GPU/pair_born_coul_long_cs_gpu.cpp | 2 +- src/GPU/pair_born_coul_long_gpu.cpp | 2 +- src/GPU/pair_born_coul_wolf_cs_gpu.cpp | 2 +- src/GPU/pair_born_coul_wolf_gpu.cpp | 2 +- src/GPU/pair_born_gpu.cpp | 2 +- src/GPU/pair_buck_coul_cut_gpu.cpp | 2 +- src/GPU/pair_buck_coul_long_gpu.cpp | 2 +- src/GPU/pair_buck_gpu.cpp | 2 +- src/GPU/pair_colloid_gpu.cpp | 2 +- src/GPU/pair_coul_cut_gpu.cpp | 2 +- src/GPU/pair_coul_debye_gpu.cpp | 2 +- src/GPU/pair_coul_dsf_gpu.cpp | 2 +- src/GPU/pair_coul_long_cs_gpu.cpp | 2 +- src/GPU/pair_coul_long_gpu.cpp | 2 +- src/GPU/pair_dpd_gpu.cpp | 2 +- src/GPU/pair_dpd_tstat_gpu.cpp | 2 +- src/GPU/pair_eam_alloy_gpu.cpp | 4 +-- src/GPU/pair_eam_fs_gpu.cpp | 4 +-- src/GPU/pair_eam_gpu.cpp | 2 +- src/GPU/pair_gauss_gpu.cpp | 2 +- src/GPU/pair_gayberne_gpu.cpp | 2 +- src/GPU/pair_lj96_cut_gpu.cpp | 2 +- src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_class2_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_class2_gpu.cpp | 2 +- src/GPU/pair_lj_cubic_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 2 +- src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_dipole_long_gpu.cpp | 2 +- src/GPU/pair_lj_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_tip4p_long_gpu.cpp | 2 +- src/GPU/pair_lj_expand_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_expand_gpu.cpp | 2 +- src/GPU/pair_lj_gromacs_gpu.cpp | 2 +- src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_sdk_gpu.cpp | 2 +- src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 2 +- src/GPU/pair_mie_cut_gpu.cpp | 2 +- src/GPU/pair_morse_gpu.cpp | 2 +- src/GPU/pair_resquared_gpu.cpp | 2 +- src/GPU/pair_soft_gpu.cpp | 2 +- src/GPU/pair_sw_gpu.cpp | 2 +- src/GPU/pair_table_gpu.cpp | 2 +- src/GPU/pair_tersoff_gpu.cpp | 2 +- src/GPU/pair_tersoff_mod_gpu.cpp | 2 +- src/GPU/pair_tersoff_zbl_gpu.cpp | 2 +- src/GPU/pair_ufm_gpu.cpp | 2 +- src/GPU/pair_vashishta_gpu.cpp | 2 +- src/GPU/pair_yukawa_colloid_gpu.cpp | 2 +- src/GPU/pair_yukawa_gpu.cpp | 2 +- src/GPU/pair_zbl_gpu.cpp | 2 +- src/GRANULAR/fix_freeze.cpp | 2 +- src/GRANULAR/fix_pour.cpp | 4 +-- src/GRANULAR/pair_gran_hooke_history.cpp | 6 ++-- src/GRANULAR/pair_granular.cpp | 6 ++-- src/KIM/pair_kim.cpp | 6 ++-- src/KIM/pair_kim.h | 2 +- src/KOKKOS/angle_charmm_kokkos.cpp | 2 +- src/KOKKOS/angle_class2_kokkos.cpp | 2 +- src/KOKKOS/angle_cosine_kokkos.cpp | 2 +- src/KOKKOS/angle_harmonic_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_angle_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_bond_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_charge_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_full_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2 +- src/KOKKOS/bond_class2_kokkos.cpp | 2 +- src/KOKKOS/bond_fene_kokkos.cpp | 2 +- src/KOKKOS/bond_harmonic_kokkos.cpp | 2 +- .../compute_orientorder_atom_kokkos.cpp | 2 +- src/KOKKOS/compute_temp_kokkos.cpp | 2 +- src/KOKKOS/dihedral_charmm_kokkos.cpp | 2 +- src/KOKKOS/dihedral_class2_kokkos.cpp | 2 +- src/KOKKOS/dihedral_harmonic_kokkos.cpp | 2 +- src/KOKKOS/dihedral_opls_kokkos.cpp | 2 +- src/KOKKOS/fix_deform_kokkos.cpp | 2 +- src/KOKKOS/fix_momentum_kokkos.cpp | 2 +- src/KOKKOS/fix_nh_kokkos.cpp | 2 +- src/KOKKOS/fix_property_atom_kokkos.cpp | 2 +- src/KOKKOS/fix_rx_kokkos.cpp | 2 +- src/KOKKOS/fix_shardlow_kokkos.cpp | 2 +- src/KOKKOS/fix_wall_reflect_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 +- src/KOKKOS/pair_exp6_rx_kokkos.cpp | 4 +-- src/KOKKOS/pair_hybrid_overlay_kokkos.cpp | 2 +- src/KOKKOS/pair_reaxc_kokkos.cpp | 2 +- src/KOKKOS/pair_table_rx_kokkos.cpp | 4 +-- src/KSPACE/fix_tune_kspace.cpp | 6 ++-- src/KSPACE/fix_tune_kspace.h | 2 +- src/KSPACE/pair_born_coul_long.cpp | 2 +- src/KSPACE/pair_buck_coul_long.cpp | 4 +-- src/KSPACE/pair_buck_long_coul_long.cpp | 4 +-- src/KSPACE/pair_coul_long.cpp | 4 +-- src/KSPACE/pair_lj_charmm_coul_long.cpp | 2 +- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 2 +- src/KSPACE/pair_lj_cut_coul_long.cpp | 4 +-- src/KSPACE/pair_lj_cut_tip4p_long.cpp | 4 +-- src/KSPACE/pair_lj_long_coul_long.cpp | 6 ++-- src/KSPACE/pair_lj_long_tip4p_long.cpp | 4 +-- src/KSPACE/pair_tip4p_long.cpp | 4 +-- src/MANYBODY/fix_qeq_comb.cpp | 6 ++-- src/MANYBODY/pair_adp.cpp | 6 ++-- src/MANYBODY/pair_airebo.cpp | 6 ++-- src/MANYBODY/pair_atm.cpp | 4 +-- src/MANYBODY/pair_bop.cpp | 6 ++-- src/MANYBODY/pair_comb.cpp | 6 ++-- src/MANYBODY/pair_comb3.cpp | 8 ++--- src/MANYBODY/pair_eam.cpp | 6 ++-- src/MANYBODY/pair_eam_alloy.cpp | 4 +-- src/MANYBODY/pair_eam_cd.cpp | 8 ++--- src/MANYBODY/pair_eam_fs.cpp | 4 +-- src/MANYBODY/pair_eim.cpp | 6 ++-- src/MANYBODY/pair_eim.h | 2 +- src/MANYBODY/pair_gw.cpp | 6 ++-- src/MANYBODY/pair_gw_zbl.cpp | 6 ++-- src/MANYBODY/pair_lcbop.cpp | 4 +-- src/MANYBODY/pair_nb3b_harmonic.cpp | 6 ++-- src/MANYBODY/pair_polymorphic.cpp | 6 ++-- src/MANYBODY/pair_sw.cpp | 6 ++-- src/MANYBODY/pair_tersoff.cpp | 6 ++-- src/MANYBODY/pair_tersoff_mod.cpp | 6 ++-- src/MANYBODY/pair_tersoff_mod_c.cpp | 6 ++-- src/MANYBODY/pair_tersoff_zbl.cpp | 6 ++-- src/MANYBODY/pair_vashishta.cpp | 6 ++-- src/MC/fix_atom_swap.cpp | 2 +- src/MC/fix_bond_break.cpp | 2 +- src/MC/fix_bond_create.cpp | 2 +- src/MC/fix_bond_swap.cpp | 2 +- src/MC/fix_gcmc.cpp | 2 +- src/MC/fix_tfmc.cpp | 2 +- src/MC/fix_widom.cpp | 2 +- src/MC/pair_dsmc.cpp | 6 ++-- src/MISC/compute_msd_nongauss.cpp | 2 +- src/MISC/compute_ti.cpp | 4 +-- src/MISC/dump_xtc.cpp | 2 +- src/MISC/fix_deposit.cpp | 4 +-- src/MISC/fix_efield.cpp | 2 +- src/MISC/fix_evaporate.cpp | 2 +- src/MISC/fix_gld.cpp | 2 +- src/MISC/fix_orient_bcc.cpp | 10 +++--- src/MISC/fix_orient_fcc.cpp | 10 +++--- src/MISC/fix_thermal_conductivity.cpp | 2 +- src/MISC/fix_ttm.cpp | 6 ++-- src/MISC/fix_viscosity.cpp | 2 +- src/MISC/pair_nm_cut.cpp | 4 +-- src/MISC/pair_nm_cut_coul_cut.cpp | 4 +-- src/MISC/pair_nm_cut_coul_long.cpp | 4 +-- src/MLIAP/compute_mliap.cpp | 2 +- src/MLIAP/compute_mliap.h | 2 +- src/MLIAP/pair_mliap.cpp | 4 +-- src/MOLECULE/angle_charmm.cpp | 4 +-- src/MOLECULE/angle_cosine.cpp | 4 +-- src/MOLECULE/angle_cosine_periodic.cpp | 4 +-- src/MOLECULE/angle_cosine_squared.cpp | 4 +-- src/MOLECULE/angle_harmonic.cpp | 4 +-- src/MOLECULE/angle_table.cpp | 8 ++--- src/MOLECULE/atom_vec_template.cpp | 2 +- src/MOLECULE/bond_fene.cpp | 6 ++-- src/MOLECULE/bond_fene_expand.cpp | 4 +-- src/MOLECULE/bond_gromos.cpp | 4 +-- src/MOLECULE/bond_harmonic.cpp | 4 +-- src/MOLECULE/bond_morse.cpp | 4 +-- src/MOLECULE/bond_nonlinear.cpp | 4 +-- src/MOLECULE/bond_quartic.cpp | 4 +-- src/MOLECULE/bond_table.cpp | 8 ++--- src/MOLECULE/dihedral_charmm.cpp | 4 +-- src/MOLECULE/dihedral_charmmfsw.cpp | 4 +-- src/MOLECULE/dihedral_harmonic.cpp | 4 +-- src/MOLECULE/dihedral_helix.cpp | 4 +-- src/MOLECULE/dihedral_multi_harmonic.cpp | 4 +-- src/MOLECULE/dihedral_opls.cpp | 4 +-- src/MOLECULE/fix_cmap.cpp | 8 ++--- src/MOLECULE/improper_cvff.cpp | 4 +-- src/MOLECULE/improper_harmonic.cpp | 4 +-- src/MOLECULE/improper_umbrella.cpp | 4 +-- src/MOLECULE/pair_hbond_dreiding_lj.cpp | 2 +- src/MOLECULE/pair_hbond_dreiding_morse.cpp | 2 +- src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 4 +-- .../pair_lj_charmmfsw_coul_charmmfsh.cpp | 4 +-- src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 4 +-- src/MOLECULE/pair_tip4p_cut.cpp | 4 +-- src/MPIIO/dump_atom_mpiio.cpp | 2 +- src/MPIIO/dump_cfg_mpiio.cpp | 2 +- src/MPIIO/dump_custom_mpiio.cpp | 2 +- src/MPIIO/dump_xyz_mpiio.cpp | 2 +- src/MSCG/fix_mscg.cpp | 4 +-- src/OPT/pair_eam_opt.cpp | 2 +- src/OPT/pair_lj_charmm_coul_long_opt.cpp | 2 +- src/OPT/pair_lj_cut_opt.cpp | 2 +- src/OPT/pair_morse_opt.cpp | 2 +- src/OPT/pair_ufm_opt.cpp | 2 +- src/PERI/fix_peri_neigh.cpp | 2 +- src/PERI/pair_peri_eps.cpp | 6 ++-- src/PERI/pair_peri_lps.cpp | 6 ++-- src/PERI/pair_peri_pmb.cpp | 6 ++-- src/PERI/pair_peri_ves.cpp | 6 ++-- src/POEMS/fix_poems.cpp | 8 ++--- src/PYTHON/pair_python.cpp | 2 +- src/QEQ/fix_qeq.cpp | 4 +-- src/QEQ/fix_qeq_dynamic.cpp | 4 +-- src/QEQ/fix_qeq_fire.cpp | 4 +-- src/QEQ/fix_qeq_slater.cpp | 2 +- src/REPLICA/compute_event_displace.cpp | 2 +- src/REPLICA/fix_hyper_global.cpp | 2 +- src/REPLICA/fix_hyper_local.cpp | 6 ++-- src/REPLICA/fix_neb.cpp | 4 +-- src/RIGID/fix_ehex.cpp | 2 +- src/RIGID/fix_rattle.cpp | 2 +- src/RIGID/fix_rigid.cpp | 8 ++--- src/RIGID/fix_rigid_nh_small.cpp | 2 +- src/RIGID/fix_rigid_small.cpp | 8 ++--- src/RIGID/fix_shake.cpp | 6 ++-- src/SHOCK/fix_append_atoms.cpp | 2 +- src/SHOCK/fix_msst.cpp | 6 ++-- src/SNAP/compute_sna_atom.cpp | 2 +- src/SNAP/compute_snad_atom.cpp | 2 +- src/SNAP/compute_snap.cpp | 2 +- src/SNAP/compute_snav_atom.cpp | 2 +- src/SNAP/pair_snap.cpp | 6 ++-- src/SPIN/compute_spin.cpp | 2 +- src/SPIN/fix_langevin_spin.cpp | 2 +- src/SPIN/fix_neb_spin.cpp | 2 +- src/SPIN/fix_precession_spin.cpp | 2 +- src/SPIN/pair_spin_dipole_cut.cpp | 4 +-- src/SPIN/pair_spin_dipole_long.cpp | 4 +-- src/SPIN/pair_spin_dmi.cpp | 4 +-- src/SPIN/pair_spin_exchange.cpp | 4 +-- src/SPIN/pair_spin_magelec.cpp | 4 +-- src/SPIN/pair_spin_neel.cpp | 4 +-- src/SRD/fix_srd.cpp | 2 +- src/SRD/fix_wall_srd.cpp | 2 +- src/USER-AWPMD/fix_nve_awpmd.cpp | 2 +- src/USER-AWPMD/pair_awpmd_cut.cpp | 4 +-- src/USER-BOCS/compute_pressure_bocs.cpp | 6 ++-- src/USER-BOCS/fix_bocs.cpp | 4 +-- src/USER-CGDNA/bond_oxdna_fene.cpp | 4 +-- src/USER-CGDNA/bond_oxrna2_fene.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 4 +-- src/USER-CGDNA/pair_oxdna2_dh.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_excv.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_hbond.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_stk.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_xstk.cpp | 4 +-- src/USER-CGDNA/pair_oxrna2_excv.cpp | 2 +- src/USER-CGDNA/pair_oxrna2_stk.cpp | 4 +-- src/USER-CGDNA/pair_oxrna2_xstk.cpp | 4 +-- src/USER-CGSDK/angle_sdk.cpp | 4 +-- src/USER-CGSDK/pair_lj_sdk.cpp | 4 +-- src/USER-CGSDK/pair_lj_sdk_coul_long.cpp | 4 +-- src/USER-COLVARS/fix_colvars.cpp | 6 ++-- src/USER-DIFFRACTION/compute_saed.cpp | 4 +-- src/USER-DIFFRACTION/compute_xrd.cpp | 4 +-- src/USER-DIFFRACTION/fix_saed_vtk.cpp | 2 +- src/USER-DPD/compute_dpd.cpp | 2 +- src/USER-DPD/fix_eos_table.cpp | 6 ++-- src/USER-DPD/fix_eos_table_rx.cpp | 6 ++-- src/USER-DPD/fix_rx.cpp | 6 ++-- src/USER-DPD/fix_shardlow.cpp | 4 +-- src/USER-DPD/pair_dpd_fdt.cpp | 4 +-- src/USER-DPD/pair_dpd_fdt_energy.cpp | 4 +-- src/USER-DPD/pair_exp6_rx.cpp | 6 ++-- src/USER-DPD/pair_multi_lucy.cpp | 8 ++--- src/USER-DPD/pair_multi_lucy_rx.cpp | 8 ++--- src/USER-DPD/pair_table_rx.cpp | 4 +-- src/USER-DRUDE/compute_temp_drude.cpp | 2 +- src/USER-DRUDE/fix_drude.cpp | 2 +- src/USER-DRUDE/fix_drude_transform.cpp | 2 +- src/USER-DRUDE/fix_langevin_drude.cpp | 2 +- src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 4 +-- src/USER-DRUDE/pair_thole.cpp | 4 +-- src/USER-EFF/compute_ke_atom_eff.cpp | 2 +- src/USER-EFF/compute_ke_eff.cpp | 4 +-- src/USER-EFF/compute_temp_deform_eff.cpp | 4 +-- src/USER-EFF/compute_temp_eff.cpp | 4 +-- src/USER-EFF/compute_temp_region_eff.cpp | 4 +-- src/USER-EFF/fix_langevin_eff.cpp | 4 +-- src/USER-EFF/fix_nh_eff.cpp | 2 +- src/USER-EFF/fix_nve_eff.cpp | 2 +- src/USER-EFF/fix_nvt_sllod_eff.cpp | 2 +- src/USER-EFF/fix_temp_rescale_eff.cpp | 2 +- src/USER-EFF/pair_eff_cut.cpp | 6 ++-- src/USER-FEP/compute_fep.cpp | 4 +-- src/USER-FEP/fix_adapt_fep.cpp | 2 +- src/USER-FEP/pair_coul_cut_soft.cpp | 4 +-- src/USER-FEP/pair_coul_long_soft.cpp | 4 +-- .../pair_lj_charmm_coul_long_soft.cpp | 4 +-- src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp | 4 +-- .../pair_lj_class2_coul_long_soft.cpp | 4 +-- src/USER-FEP/pair_lj_class2_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp | 4 +-- src/USER-FEP/pair_morse_soft.cpp | 4 +-- src/USER-FEP/pair_tip4p_long_soft.cpp | 4 +-- src/USER-H5MD/dump_h5md.cpp | 2 +- src/USER-INTEL/angle_charmm_intel.cpp | 2 +- src/USER-INTEL/angle_harmonic_intel.cpp | 2 +- src/USER-INTEL/bond_fene_intel.cpp | 2 +- src/USER-INTEL/bond_harmonic_intel.cpp | 2 +- src/USER-INTEL/dihedral_charmm_intel.cpp | 2 +- src/USER-INTEL/dihedral_fourier_intel.cpp | 2 +- src/USER-INTEL/dihedral_harmonic_intel.cpp | 2 +- src/USER-INTEL/dihedral_opls_intel.cpp | 2 +- src/USER-INTEL/fix_intel.cpp | 4 +-- src/USER-INTEL/improper_cvff_intel.cpp | 4 +-- src/USER-INTEL/improper_harmonic_intel.cpp | 4 +-- src/USER-INTEL/pair_airebo_intel.cpp | 2 +- src/USER-INTEL/pair_buck_coul_cut_intel.cpp | 2 +- src/USER-INTEL/pair_buck_coul_long_intel.cpp | 2 +- src/USER-INTEL/pair_eam_alloy_intel.cpp | 4 +-- src/USER-INTEL/pair_eam_fs_intel.cpp | 4 +-- src/USER-INTEL/pair_eam_intel.cpp | 2 +- src/USER-INTEL/pair_sw_intel.cpp | 2 +- src/USER-INTEL/pair_tersoff_intel.cpp | 2 +- src/USER-LB/fix_lb_fluid.cpp | 4 +-- src/USER-LB/fix_lb_momentum.cpp | 4 +-- src/USER-LB/fix_lb_pc.cpp | 2 +- src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 6 ++-- src/USER-MANIFOLD/fix_manifoldforce.cpp | 2 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 2 +- src/USER-MEAMC/pair_meamc.cpp | 10 +++--- src/USER-MEAMC/pair_meamc.h | 2 +- src/USER-MESODPD/atom_vec_edpd.cpp | 2 +- src/USER-MESODPD/atom_vec_tdpd.cpp | 2 +- src/USER-MESODPD/pair_edpd.cpp | 4 +-- src/USER-MESODPD/pair_mdpd.cpp | 4 +-- src/USER-MESODPD/pair_mdpd_rhosum.cpp | 2 +- src/USER-MESODPD/pair_tdpd.cpp | 2 +- src/USER-MESONT/compute_mesont.cpp | 2 +- src/USER-MESONT/pair_mesocnt.cpp | 8 ++--- src/USER-MESONT/pair_mesont_tpm.cpp | 4 +-- src/USER-MGPT/pair_mgpt.cpp | 4 +-- src/USER-MISC/angle_cosine_shift.cpp | 4 +-- src/USER-MISC/angle_cosine_shift_exp.cpp | 4 +-- src/USER-MISC/angle_dipole.cpp | 4 +-- src/USER-MISC/angle_fourier.cpp | 4 +-- src/USER-MISC/angle_fourier_simple.cpp | 4 +-- src/USER-MISC/angle_quartic.cpp | 4 +-- src/USER-MISC/bond_harmonic_shift.cpp | 4 +-- src/USER-MISC/bond_harmonic_shift_cut.cpp | 4 +-- src/USER-MISC/bond_special.cpp | 4 +-- src/USER-MISC/compute_cnp_atom.cpp | 2 +- src/USER-MISC/compute_hma.cpp | 2 +- src/USER-MISC/compute_momentum.cpp | 2 +- src/USER-MISC/compute_pressure_cylinder.cpp | 2 +- src/USER-MISC/compute_stress_mop.cpp | 2 +- src/USER-MISC/compute_stress_mop_profile.cpp | 2 +- src/USER-MISC/compute_temp_rotate.cpp | 2 +- src/USER-MISC/compute_viscosity_cos.cpp | 2 +- src/USER-MISC/dihedral_cosine_shift_exp.cpp | 4 +-- src/USER-MISC/dihedral_fourier.cpp | 4 +-- src/USER-MISC/dihedral_nharmonic.cpp | 4 +-- src/USER-MISC/dihedral_quadratic.cpp | 4 +-- src/USER-MISC/dihedral_spherical.cpp | 4 +-- src/USER-MISC/dihedral_table.cpp | 12 +++---- src/USER-MISC/dihedral_table.h | 2 +- src/USER-MISC/dihedral_table_cut.cpp | 8 ++--- src/USER-MISC/fix_addtorque.cpp | 2 +- src/USER-MISC/fix_ave_correlate_long.cpp | 4 +-- src/USER-MISC/fix_ffl.cpp | 2 +- src/USER-MISC/fix_filter_corotate.cpp | 4 +-- src/USER-MISC/fix_flow_gauss.cpp | 2 +- src/USER-MISC/fix_gle.cpp | 6 ++-- src/USER-MISC/fix_imd.cpp | 2 +- src/USER-MISC/fix_ipi.cpp | 4 +-- src/USER-MISC/fix_momentum_chunk.cpp | 4 +-- src/USER-MISC/fix_momentum_chunk.h | 2 +- src/USER-MISC/fix_npt_cauchy.cpp | 2 +- src/USER-MISC/fix_nvk.cpp | 2 +- src/USER-MISC/fix_orient_eco.cpp | 6 ++-- src/USER-MISC/fix_pafi.cpp | 8 ++--- src/USER-MISC/fix_pimd.cpp | 4 +-- src/USER-MISC/fix_propel_self.cpp | 2 +- src/USER-MISC/fix_rhok.cpp | 2 +- src/USER-MISC/fix_smd.cpp | 2 +- src/USER-MISC/fix_srp.cpp | 2 +- src/USER-MISC/fix_ti_spring.cpp | 2 +- src/USER-MISC/fix_ttm_mod.cpp | 6 ++-- src/USER-MISC/fix_wall_reflect_stochastic.cpp | 2 +- src/USER-MISC/fix_wall_region_ees.cpp | 2 +- src/USER-MISC/improper_cossq.cpp | 4 +-- src/USER-MISC/improper_distance.cpp | 4 +-- src/USER-MISC/improper_fourier.cpp | 4 +-- src/USER-MISC/improper_ring.cpp | 4 +-- src/USER-MISC/pair_agni.cpp | 6 ++-- src/USER-MISC/pair_buck_mdf.cpp | 4 +-- src/USER-MISC/pair_cosine_squared.cpp | 4 +-- src/USER-MISC/pair_coul_diel.cpp | 4 +-- src/USER-MISC/pair_coul_shield.cpp | 2 +- src/USER-MISC/pair_coul_slater_cut.cpp | 2 +- src/USER-MISC/pair_coul_slater_long.cpp | 4 +-- src/USER-MISC/pair_drip.cpp | 6 ++-- src/USER-MISC/pair_e3b.cpp | 2 +- src/USER-MISC/pair_edip.cpp | 6 ++-- src/USER-MISC/pair_edip_multi.cpp | 6 ++-- src/USER-MISC/pair_extep.cpp | 6 ++-- src/USER-MISC/pair_gauss_cut.cpp | 4 +-- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 6 ++-- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 6 ++-- src/USER-MISC/pair_kolmogorov_crespi_z.cpp | 6 ++-- src/USER-MISC/pair_lebedeva_z.cpp | 6 ++-- src/USER-MISC/pair_lennard_mdf.cpp | 4 +-- src/USER-MISC/pair_list.cpp | 4 +-- src/USER-MISC/pair_lj_expand_coul_long.cpp | 4 +-- src/USER-MISC/pair_lj_mdf.cpp | 4 +-- src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 4 +-- src/USER-MISC/pair_local_density.cpp | 8 ++--- src/USER-MISC/pair_meam_spline.cpp | 4 +-- src/USER-MISC/pair_meam_sw_spline.cpp | 4 +-- src/USER-MISC/pair_momb.cpp | 4 +-- src/USER-MISC/pair_morse_smooth_linear.cpp | 4 +-- src/USER-MISC/pair_srp.cpp | 6 ++-- src/USER-MISC/pair_tersoff_table.cpp | 6 ++-- src/USER-MOFFF/angle_class2_p6.cpp | 4 +-- src/USER-MOFFF/angle_cosine_buck6d.cpp | 4 +-- .../improper_inversion_harmonic.cpp | 4 +-- src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp | 2 +- .../pair_buck6d_coul_gauss_long.cpp | 4 +-- src/USER-MOLFILE/dump_molfile.cpp | 2 +- src/USER-NETCDF/dump_netcdf.cpp | 2 +- src/USER-NETCDF/dump_netcdf_mpiio.cpp | 2 +- src/USER-OMP/fix_nh_asphere_omp.cpp | 2 +- src/USER-OMP/fix_qeq_comb_omp.cpp | 2 +- src/USER-OMP/fix_qeq_reax_omp.cpp | 2 +- src/USER-OMP/fix_rigid_nh_omp.cpp | 2 +- src/USER-OMP/fix_rigid_omp.cpp | 2 +- src/USER-OMP/pair_eam_alloy_omp.cpp | 4 +-- src/USER-OMP/pair_eam_fs_omp.cpp | 4 +-- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 2 +- src/USER-OMP/pair_reaxc_omp.cpp | 2 +- src/USER-OMP/pair_tersoff_zbl_omp.cpp | 4 +-- src/USER-PHONON/fix_phonon.cpp | 2 +- src/USER-PLUMED/fix_plumed.cpp | 4 +-- src/USER-QMMM/fix_qmmm.cpp | 2 +- src/USER-QTB/fix_qbmsst.cpp | 10 +++--- src/USER-QTB/fix_qtb.cpp | 8 ++--- src/USER-QUIP/pair_quip.cpp | 4 +-- src/USER-REACTION/fix_bond_react.cpp | 6 ++-- src/USER-REAXC/fix_qeq_reax.cpp | 2 +- src/USER-REAXC/fix_reaxc_bonds.cpp | 2 +- src/USER-REAXC/fix_reaxc_species.cpp | 4 +-- src/USER-REAXC/pair_reaxc.cpp | 6 ++-- .../pair_sdpd_taitwater_isothermal.cpp | 2 +- src/USER-SMD/compute_smd_vol.cpp | 2 +- src/USER-SMD/fix_smd_adjust_dt.cpp | 4 +-- src/USER-SMD/fix_smd_setvel.cpp | 2 +- .../fix_smd_tlsph_reference_configuration.cpp | 2 +- src/USER-SMD/fix_smd_wall_surface.cpp | 4 +-- src/USER-SMD/pair_smd_hertz.cpp | 6 ++-- src/USER-SMD/pair_smd_tlsph.cpp | 4 +-- .../pair_smd_triangulated_surface.cpp | 6 ++-- src/USER-SMD/pair_smd_ulsph.cpp | 4 +-- src/USER-SMTBQ/pair_smtbq.cpp | 4 +-- src/USER-SPH/pair_sph_heatconduction.cpp | 2 +- src/USER-SPH/pair_sph_idealgas.cpp | 2 +- src/USER-SPH/pair_sph_lj.cpp | 2 +- src/USER-SPH/pair_sph_rhosum.cpp | 2 +- src/USER-SPH/pair_sph_taitwater.cpp | 2 +- src/USER-SPH/pair_sph_taitwater_morris.cpp | 2 +- src/USER-TALLY/compute_force_tally.cpp | 2 +- src/USER-TALLY/compute_heat_flux_tally.cpp | 2 +- src/USER-TALLY/compute_pe_mol_tally.cpp | 2 +- src/USER-TALLY/compute_pe_tally.cpp | 2 +- src/USER-TALLY/compute_stress_tally.cpp | 2 +- src/USER-VTK/dump_vtk.cpp | 2 +- src/USER-VTK/dump_vtk.h | 2 +- src/USER-YAFF/angle_cross.cpp | 4 +-- src/USER-YAFF/angle_mm3.cpp | 4 +-- src/USER-YAFF/bond_mm3.cpp | 4 +-- src/USER-YAFF/improper_distharm.cpp | 4 +-- src/USER-YAFF/improper_sqdistharm.cpp | 4 +-- .../pair_lj_switch3_coulgauss_long.cpp | 4 +-- .../pair_mm3_switch3_coulgauss_long.cpp | 4 +-- src/VORONOI/compute_voronoi_atom.cpp | 2 +- src/angle_deprecated.cpp | 2 -- src/angle_hybrid.cpp | 8 ++--- src/angle_zero.cpp | 7 ++-- src/atom.cpp | 27 +++++++-------- src/atom.h | 16 +++++---- src/atom_map.cpp | 7 ++-- src/atom_vec.cpp | 13 ++++--- src/atom_vec_body.cpp | 15 ++++---- src/atom_vec_ellipsoid.cpp | 12 +++---- src/atom_vec_hybrid.cpp | 6 ++-- src/atom_vec_line.cpp | 12 +++---- src/atom_vec_sphere.cpp | 9 ++--- src/atom_vec_tri.cpp | 14 ++++---- src/balance.cpp | 22 ++++++------ src/bond.cpp | 14 ++++---- src/bond_deprecated.cpp | 5 ++- src/bond_hybrid.cpp | 12 +++---- src/bond_zero.cpp | 9 +++-- src/change_box.cpp | 22 ++++++------ src/comm.cpp | 28 +++++++-------- src/comm_brick.cpp | 15 ++++---- src/comm_tiled.cpp | 17 +++++----- src/compute.cpp | 15 ++++---- src/compute_adf.cpp | 22 ++++++------ src/compute_aggregate_atom.cpp | 20 +++++------ src/compute_angle.cpp | 6 ++-- src/compute_angmom_chunk.cpp | 11 +++--- src/compute_bond.cpp | 6 ++-- src/compute_chunk_atom.cpp | 28 +++++++-------- src/compute_chunk_spread_atom.cpp | 15 ++++---- src/compute_cluster_atom.cpp | 20 +++++------ src/compute_cna_atom.cpp | 20 +++++------ src/compute_com_chunk.cpp | 11 +++--- src/compute_coord_atom.cpp | 23 +++++++------ src/compute_deprecated.cpp | 3 +- src/compute_dihedral.cpp | 6 ++-- src/compute_dipole_chunk.cpp | 13 +++---- src/compute_displace_atom.cpp | 17 +++++----- src/compute_erotate_sphere.cpp | 6 ++-- src/compute_fragment_atom.cpp | 14 ++++---- src/compute_global_atom.cpp | 14 ++++---- src/compute_group_group.cpp | 2 +- src/compute_gyration.cpp | 2 +- src/compute_gyration_chunk.cpp | 2 +- src/compute_heat_flux.cpp | 2 +- src/compute_improper.cpp | 2 +- src/compute_inertia_chunk.cpp | 2 +- src/compute_ke.cpp | 2 +- src/compute_msd.cpp | 6 ++-- src/compute_msd_chunk.cpp | 6 ++-- src/compute_omega_chunk.cpp | 2 +- src/compute_orientorder_atom.cpp | 22 ++++++------ src/compute_pair.cpp | 2 +- src/compute_pair_local.cpp | 19 ++++++----- src/compute_pe.cpp | 2 +- src/compute_pressure.cpp | 2 +- src/compute_property_chunk.cpp | 2 +- src/compute_rdf.cpp | 4 +-- src/compute_reduce.cpp | 6 ++-- src/compute_reduce.h | 2 +- src/compute_reduce_chunk.cpp | 6 ++-- src/compute_reduce_region.cpp | 2 +- src/compute_slice.cpp | 15 ++++---- src/compute_temp.cpp | 2 +- src/compute_temp_chunk.cpp | 2 +- src/compute_temp_com.cpp | 2 +- src/compute_temp_deform.cpp | 2 +- src/compute_temp_partial.cpp | 2 +- src/compute_temp_profile.cpp | 2 +- src/compute_temp_ramp.cpp | 2 +- src/compute_temp_region.cpp | 2 +- src/compute_temp_sphere.cpp | 2 +- src/compute_torque_chunk.cpp | 2 +- src/compute_vacf.cpp | 6 ++-- src/compute_vcm_chunk.cpp | 2 +- src/delete_atoms.cpp | 21 +++++------- src/delete_bonds.cpp | 13 +++---- src/deprecated.cpp | 3 +- src/dihedral_deprecated.cpp | 8 ++--- src/dihedral_hybrid.cpp | 4 +-- src/dihedral_zero.cpp | 8 ++--- src/displace_atoms.cpp | 34 +++++++++---------- src/domain.cpp | 30 ++++++++-------- src/domain.h | 4 +-- src/dump.cpp | 6 ++-- src/dump_custom.cpp | 21 +++++------- src/dump_deprecated.cpp | 3 +- src/dump_image.cpp | 4 +-- src/dump_local.cpp | 6 ++-- src/dump_movie.cpp | 2 +- src/fix_adapt.cpp | 4 +-- src/fix_addforce.cpp | 4 +-- src/fix_ave_atom.cpp | 4 +-- src/fix_ave_chunk.cpp | 8 ++--- src/fix_ave_correlate.cpp | 8 ++--- src/fix_ave_histo.cpp | 8 ++--- src/fix_ave_histo_weight.cpp | 2 +- src/fix_ave_time.cpp | 8 ++--- src/fix_aveforce.cpp | 2 +- src/fix_box_relax.cpp | 4 +-- src/fix_controller.cpp | 2 +- src/fix_deprecated.cpp | 4 +-- src/fix_drag.cpp | 2 +- src/fix_dt_reset.cpp | 2 +- src/fix_enforce2d.cpp | 2 +- src/fix_gravity.cpp | 2 +- src/fix_halt.cpp | 6 ++-- src/fix_heat.cpp | 2 +- src/fix_indent.cpp | 2 +- src/fix_langevin.cpp | 4 +-- src/fix_momentum.cpp | 2 +- src/fix_neigh_history.cpp | 2 +- src/fix_nph.cpp | 2 +- src/fix_nph_sphere.cpp | 2 +- src/fix_npt.cpp | 2 +- src/fix_npt_sphere.cpp | 2 +- src/fix_numdiff.cpp | 2 +- src/fix_nve_limit.cpp | 4 +-- src/fix_nvt.cpp | 4 +-- src/fix_nvt_sllod.cpp | 2 +- src/fix_nvt_sphere.cpp | 4 +-- src/fix_press_berendsen.cpp | 2 +- src/fix_print.cpp | 6 ++-- src/fix_property_atom.cpp | 6 ++-- src/fix_restrain.cpp | 4 +-- src/fix_setforce.cpp | 2 +- src/fix_spring_self.cpp | 2 +- src/fix_store_state.cpp | 2 +- src/fix_temp_berendsen.cpp | 4 +-- src/fix_temp_csld.cpp | 4 +-- src/fix_temp_csvr.cpp | 6 ++-- src/fix_temp_rescale.cpp | 4 +-- src/fix_tmd.cpp | 6 ++-- src/fix_vector.cpp | 2 +- src/fix_wall.cpp | 4 +-- src/fix_wall_region.cpp | 2 +- src/improper_deprecated.cpp | 4 +-- src/improper_hybrid.cpp | 4 +-- src/improper_zero.cpp | 2 +- src/lmptype.h | 8 ++--- src/pair_beck.cpp | 4 +-- src/pair_born.cpp | 4 +-- src/pair_born_coul_dsf.cpp | 4 +-- src/pair_born_coul_wolf.cpp | 4 +-- src/pair_buck.cpp | 4 +-- src/pair_buck_coul_cut.cpp | 4 +-- src/pair_coul_cut.cpp | 4 +-- src/pair_coul_debye.cpp | 4 +-- src/pair_coul_dsf.cpp | 4 +-- src/pair_coul_streitz.cpp | 8 ++--- src/pair_coul_wolf.cpp | 4 +-- src/pair_deprecated.cpp | 4 +-- src/pair_dpd.cpp | 4 +-- src/pair_dpd_tstat.cpp | 4 +-- src/pair_gauss.cpp | 4 +-- src/pair_hybrid.cpp | 6 ++-- src/pair_hybrid_overlay.cpp | 2 +- src/pair_lj96_cut.cpp | 4 +-- src/pair_lj_cubic.cpp | 4 +-- src/pair_lj_cut.cpp | 4 +-- src/pair_lj_cut_coul_cut.cpp | 4 +-- src/pair_lj_cut_coul_debye.cpp | 4 +-- src/pair_lj_cut_coul_dsf.cpp | 4 +-- src/pair_lj_cut_coul_wolf.cpp | 4 +-- src/pair_lj_expand.cpp | 4 +-- src/pair_lj_gromacs.cpp | 4 +-- src/pair_lj_gromacs_coul_gromacs.cpp | 4 +-- src/pair_lj_smooth.cpp | 4 +-- src/pair_lj_smooth_linear.cpp | 4 +-- src/pair_mie_cut.cpp | 4 +-- src/pair_morse.cpp | 4 +-- src/pair_soft.cpp | 4 +-- src/pair_table.cpp | 10 +++--- src/pair_ufm.cpp | 4 +-- src/pair_yukawa.cpp | 4 +-- src/pair_zbl.cpp | 2 +- src/pair_zero.cpp | 4 +-- src/region_deprecated.cpp | 4 +-- src/tokenizer.h | 7 ++-- 714 files changed, 1522 insertions(+), 1544 deletions(-) diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index 3cf23b87eb..945b91fbbd 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_asphere.h" -#include + #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 4350678bbd..889563f617 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_asphere.h" -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 0501ea1e8a..6d1727ce45 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -13,7 +13,7 @@ #include "fix_nph_asphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index f7f253f40b..064a20d55b 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -13,7 +13,7 @@ #include "fix_npt_asphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index e0275d4acf..d439d947bf 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -13,11 +13,11 @@ #include "fix_nvt_asphere.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 064e365dc1..89350dd00f 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gayberne.h" -#include + #include #include "math_extra.h" #include "atom.h" @@ -28,7 +28,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index a1c6477542..6397e77f5b 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -20,7 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index a25addaba4..81fb4d4b6c 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_resquared.h" -#include + #include #include "math_extra.h" #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 0f840dadf3..cf89cf9d33 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 915407db92..861ffbe4a7 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_body_local.h" -#include + #include #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 4cf9ac5009..18c301678a 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_body.h" -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 1e8cc88e7c..f198919ad8 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -17,11 +17,11 @@ #include "fix_nph_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 295777753f..23194bc8ca 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -17,11 +17,11 @@ #include "fix_npt_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 458ff1ab14..3cab4416b0 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -17,11 +17,11 @@ #include "fix_nvt_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index b3333d4715..ece23d9522 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -23,7 +23,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 9687c28613..fa5a8e57da 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polygon.h" -#include + #include #include #include "math_extra.h" @@ -34,7 +34,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index dfefc318af..d376ac759e 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -21,7 +21,7 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polyhedron.h" -#include + #include #include #include "atom.h" @@ -37,7 +37,7 @@ #include "error.h" #include "math_extra.h" #include "math_const.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 431479b489..eea43480e1 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_class2.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 2cd63eafcb..a97b06a3c7 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -17,7 +17,7 @@ #include #include "bond_class2.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 44d4902e4a..5be522f2c9 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 662459abb7..0b07a7d60c 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_class2.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 96b035f83b..bb1dfe0ab3 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -10,7 +10,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 9aca9f048a..8375043ed8 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 5c7c107d02..3b9ef8deaf 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 58593a99b1..61b52a6585 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_colloid.h" -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index d7b2dba14a..786be66c70 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_brownian.h" -#include + #include #include #include "atom.h" @@ -36,7 +36,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index c3eb4f28a5..9c2593ffb1 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_brownian_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 7552d123c3..f95645c613 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_colloid.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4f2a4455a3..867bb91979 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate.h" -#include + #include #include #include "atom.h" @@ -35,7 +35,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 4fb1611660..2df1ecaaa6 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricateU.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 7fd847671e..8483bb0f51 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricateU_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index e347441cf4..351757e09b 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 6c78ba7910..484175762e 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index a8da9a1a2c..a993f58809 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 2d48e02f3c..18f0fa56d7 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -16,10 +16,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 0f74e2550b..51819772f6 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 35a2d25a2a..fb2b121f7f 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index 395ba51fdc..d0f5335813 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index a346de3127..49a3c3bef2 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 3e658fd070..9393654dd6 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 79d2d20997..cc07b1ce61 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -14,10 +14,10 @@ #include "dump_xyz_gz.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 066609eebb..839e743654 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -20,10 +20,10 @@ #include "dump_xyz_zstd.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index d8f952551d..1b7eb1e43f 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "compute_temp_cs.h" -#include + #include -#include + #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -31,7 +31,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index b6895be301..66de360f6e 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -20,7 +20,7 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 8f91420043..25fed599db 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 73aa628296..67d2e0aa3c 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_long.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index f7c8251e79..86e143626d 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_dipole_long.h" -#include + #include #include #include "math_const.h" @@ -30,7 +30,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 0552d23cdb..15bc42c37e 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -13,7 +13,7 @@ #include "fix_gpu.h" #include -#include + #include "atom.h" #include "force.h" #include "pair.h" @@ -30,7 +30,7 @@ #include "neighbor.h" #include "citeme.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 28386f5fd5..86467f49c0 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_beck_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 8bc99a3d49..c27c670f2a 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_long_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index 5dd4c3421f..a2524909e5 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4ba28c25aa..cf54b72cf5 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_wolf_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index b5e0edea6d..e9aa951236 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_wolf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index a5e94389b6..5a5a6d2a36 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index 1a5479ea1d..de9f0d1eba 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index 221e178b57..41823fc27e 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 07107750e6..1f7abc06bc 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index a7cafbe75a..39737ab183 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_colloid_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index bacbdbb1a0..34a76c1dff 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 96be67a1fa..40fb359484 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_debye_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 244941c117..8c05d14aef 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_dsf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index bcbf7216e2..da59873dd2 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_long_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index fcfb20f3ce..185d3a7f94 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index a2e20d016c..d41be6d8c2 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_dpd_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 991c6d900f..33d7178faa 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_dpd_tstat_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 08ffaef978..4939537770 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -17,7 +17,7 @@ #include "pair_eam_alloy_gpu.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -29,7 +29,7 @@ #include "neigh_request.h" #include "gpu_extra.h" #include "domain.h" -#include "utils.h" + #include "suffix.h" #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index a82107749b..eb028bc778 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -17,7 +17,7 @@ #include "pair_eam_fs_gpu.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -30,7 +30,7 @@ #include "gpu_extra.h" #include "domain.h" #include "suffix.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 1aac379c35..3965f27c67 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_eam_gpu.h" #include #include -#include + #include #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index eb83d5af44..51d4851dc5 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_gauss_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 83b24f8774..451799027b 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_gayberne_gpu.h" #include #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 7b0d45a437..215998bc88 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj96_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index b08ad5e232..09ed178200 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_charmm_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index 46ecaea9b8..f6d671d95a 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_class2_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index a7ca661927..fbd6aea08c 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_class2_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 38f6e1f908..28e74d8f39 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cubic_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 54f0e92bd5..48770d2713 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index e7b1ac5002..45c3cc82a0 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_debye_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 5d1f4f70be..784c0e379d 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_dsf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index dff2ba28d4..2a9d431a42 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 2f965d6476..f5987c0ddf 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_msm_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 43c2a1e9b7..ac053037d8 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_dipole_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 9416ede516..7de9ae2aa6 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_dipole_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 27924361f2..5656c2e18d 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp index 7c1bb74158..2bd7420e72 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_lj_cut_tip4p_long_gpu.h" #include "atom.h" diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 54eb4d47e6..f13eea51e7 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_expand_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index 32c35420a2..bdfa30b965 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_expand_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index d7122cb5f3..6d6abdb40d 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_gromacs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index cd76bbd2e9..4054f08523 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sdk_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 5f07bdbb6c..2016d1db2c 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sdk_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index a9ddf81bf0..e6834298f3 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sf_dipole_sf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 4db07ab79e..60e6e935e8 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_mie_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index fc966f6533..a256f500ce 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_morse_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 0bcabb451c..ca70e3c337 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_resquared_gpu.h" #include #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 48a4f689ff..49c27f515d 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_soft_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 4c4502828d..d544534c9d 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_sw_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index 858a2107dc..4ac674aa94 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_table_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index d7b1ef5dd5..885dd73d9e 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 1b35045902..35edd9ea22 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_mod_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index ae50552f14..73251ee726 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_zbl_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 2b4cc2269f..fe6adfef12 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -20,7 +20,7 @@ #include "pair_ufm_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index ccd2773130..868b8de0c0 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_vashishta_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index c3439e3306..3c7b2f5ba7 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_yukawa_colloid_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index b9b9d6e0a4..8147609f45 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_yukawa_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index d0cbfa1d7c..0472d9b7c1 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -19,7 +19,7 @@ #include "lmptype.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 1df5c9d0a8..dd68aa032f 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_freeze.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 879f48e023..d449bb5614 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_pour.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index a8cd808411..68a7803f4b 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_gran_hooke_history.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 88a9fe36f0..ee0eb2ad77 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -18,10 +18,10 @@ ----------------------------------------------------------------------- */ #include "pair_granular.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -37,7 +37,7 @@ #include "error.h" #include "math_const.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 69586b55d6..3422f93f3a 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -56,8 +56,8 @@ ------------------------------------------------------------------------- */ #include "pair_kim.h" #include -#include -#include + + #include #include "atom.h" #include "comm.h" @@ -68,7 +68,7 @@ #include "update.h" #include "memory.h" #include "domain.h" -#include "utils.h" + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 1f2c8c8599..0361f2351e 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -65,7 +65,7 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" -#include + extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 288e5a475b..14850525ef 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_charmm_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index ebb016b31b..4406f51f83 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_class2_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 960988b3b5..7ba634cd13 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_cosine_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index bc08ff4b65..2e5831ef07 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_harmonic_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e9fee6d8f6..e9c101eb79 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 7a66dc753a..c76af73420 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 157f194125..47e77c33b3 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 8f468b8e46..183bdb94e4 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 5319744c22..b112605859 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 5d5833af07..89275c7067 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 0cc609f91c..34a246008d 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -20,7 +20,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index b0fca4e316..dceedc8e60 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -16,7 +16,7 @@ #include "comm_kokkos.h" #include "domain.h" #include "atom_masks.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 7832d6f9b0..6a4d94dc14 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index b1099d0fa6..569498f664 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "memory_kokkos.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 88504608f6..5481a41806 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -17,7 +17,7 @@ #include "bond_class2_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index e6aa27649f..9d2200dd90 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -17,7 +17,7 @@ #include "bond_fene_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index ee1b58c91f..9239a4191b 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -17,7 +17,7 @@ #include "bond_harmonic_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp index b17434d09a..7d635dbeb7 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp @@ -17,7 +17,7 @@ #include "compute_orientorder_atom_kokkos.h" #include -#include + #include #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 0e7fe25540..7e4d3ad6ae 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 0d8256f306..c25ab18c60 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_charmm_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 371af44e9a..df60ebd1e4 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_class2_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp index 408fa276e4..0acd61222e 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_harmonic_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 309d617f0a..70beae918a 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_opls_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 05eb1c22f6..5d8430d337 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -17,7 +17,7 @@ #include "fix_deform_kokkos.h" #include -#include + #include #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 9c9d6cb1cd..1821b6dadd 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_momentum_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 96e9663712..8cd58b0927 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -17,7 +17,7 @@ #include "fix_nh_kokkos.h" #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index ff374b885f..d6afae3ec2 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_property_atom_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 38968bdd35..18bc4225a7 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -27,7 +27,7 @@ #include "comm.h" #include "domain.h" #include "kokkos.h" -#include "utils.h" + #include // DBL_EPSILON diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 75964f4829..9be4321ff2 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -35,7 +35,7 @@ #include "fix_shardlow_kokkos.h" #include -#include + #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index a5bd6e6e6c..c581edb123 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 28cf65c8d8..280e47b771 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -29,7 +29,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index da49414892..a4828c00aa 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -29,7 +29,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 2e2c3ef04e..035bf87cec 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -17,7 +17,7 @@ #include "pair_exp6_rx_kokkos.h" #include -#include + #include #include "atom.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "neigh_request.h" #include "atom_kokkos.h" #include "kokkos.h" -#include "utils.h" + #ifdef _OPENMP #include diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index 1f2ad404bb..9c75f3abe8 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -17,7 +17,7 @@ #include "atom.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index d0fe11285a..bf8518e3c3 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -17,7 +17,7 @@ #include "pair_reaxc_kokkos.h" #include -#include + #include #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 26aa4373cc..09e38e6387 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_table_rx_kokkos.h" -#include + #include #include #include "kokkos.h" @@ -33,7 +33,7 @@ #include "kokkos_few.h" #include "kokkos.h" #include "modify.h" -#include "utils.h" + #include using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 45c8a35971..3288f15ff7 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -19,7 +19,7 @@ #include #include #include -#include + #include "comm.h" #include "update.h" #include "force.h" @@ -32,8 +32,8 @@ #include "neighbor.h" #include "modify.h" #include "compute.h" -#include "utils.h" -#include "fmt/format.h" + + #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 339f79626f..3e4db40344 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -21,7 +21,7 @@ FixStyle(tune/kspace,FixTuneKspace) #define LMP_FIX_TUNE_KSPACE_H #include "fix.h" -#include + namespace LAMMPS_NS { diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 4742e4c48c..a05a6a282b 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index f589dfaa90..8d15a6480a 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_long.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 3552e8bb86..a845ddd1d2 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_long_coul_long.h" -#include + #include #include #include "math_vector.h" @@ -31,7 +31,7 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 60187ce901..2520da2654 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index ff52720a08..261e93fbc9 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -29,7 +29,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index b10cdf2b08..9df9862c11 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index ef25055a76..7fd8a72559 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index 426ec00e55..a62c1bd55b 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 7b7a065e22..b6727c2c99 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_coul_long.h" -#include + #include #include #include "math_vector.h" @@ -33,8 +33,8 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index c71fee8206..8f17bda008 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index ee7d4fed1b..54973c69c2 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index b8bbba73da..54169d08d7 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_comb.h" -#include + #include #include #include "pair_comb.h" @@ -30,8 +30,8 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 74fd03e080..ff30ac7b1e 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_adp.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 6d783545f7..50b5b7d953 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -23,7 +23,7 @@ #include "pair_airebo.h" #include #include -#include + #include "atom.h" #include "neighbor.h" #include "force.h" @@ -34,10 +34,10 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index 60905fd2ff..2a69e70b81 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_atm.h" -#include + #include #include "atom.h" #include "citeme.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 5b080c9f0e..28389cb59f 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -36,7 +36,7 @@ #include #include #include -#include + #include "atom.h" #include "neighbor.h" #include "neigh_request.h" @@ -45,10 +45,10 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 6b8d4e428e..a27aaef4ab 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -19,9 +19,9 @@ ------------------------------------------------------------------------- */ #include "pair_comb.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -34,7 +34,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 385e3ca35d..eea2fca927 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_comb3.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,10 +33,10 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 159ba55a29..999384ea2f 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_eam.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 3e33d40ee4..193134c24c 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_eam_alloy.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 4f5041090f..dc36c73272 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_eam_cd.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -29,8 +29,8 @@ #include "memory.h" #include "error.h" #include "tokenizer.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index fbe6bee529..78d7f4646d 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_eam_fs.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index cdd928788b..a17947b7fe 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_eim.h" -#include + #include #include #include "atom.h" @@ -26,10 +26,10 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 1266ffd242..75f8ea6bea 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -21,7 +21,7 @@ PairStyle(eim,PairEIM) #define LMP_PAIR_EIM_H #include "pair.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 0928d14696..051c30f873 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_gw.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index 1a2bf5eb5d..dc33ab20a9 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_gw_zbl.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -27,7 +27,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 56ef70d8f9..d2e478b37d 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lcbop.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index dc537a7b58..0a197a1576 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_nb3b_harmonic.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 502580719a..4c8ebaf8ad 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_polymorphic.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index f6b5a803d2..da6f7c1623 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_sw.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -28,7 +28,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index c57740963f..95212b23ab 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,7 +28,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index d1ab6f2034..b02545fb2b 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index ff8916cdcd..325e9ac677 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod_c.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 141cb45964..4c967b4ebb 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_zbl.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -29,7 +29,7 @@ #include "error.h" #include "math_const.h" #include "math_special.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 815854a34b..63765234b3 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 53338f08dc..f786179aa4 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_atom_swap.h" -#include + #include #include #include diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 833a071694..8a7cd20b0f 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_break.h" -#include + #include #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 9603fc1583..a2c2eee2c5 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_create.h" -#include + #include #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 82b27d490f..270a497772 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_swap.h" -#include + #include #include #include "atom.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index f286ab6807..fc306696ed 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_gcmc.h" -#include + #include #include #include "atom.h" diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index cf327dc2e1..b855c0b79e 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_tfmc.h" -#include + #include #include #include diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 7f6f7ae1bd..a87ead64a7 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_widom.h" #include "atom.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 30c66a671f..c00f5dcbff 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dsmc.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "domain.h" #include "update.h" #include "random_mars.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index 6123bf49af..7f4e6b1f3c 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_msd_nongauss.h" -#include + #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index 286770017c..d8be8679c6 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_ti.h" -#include + #include #include "atom.h" #include "update.h" @@ -27,7 +27,7 @@ #include "input.h" #include "variable.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index fbd56b9096..9f2bbfe424 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -24,7 +24,7 @@ #include "dump_xtc.h" #include -#include + #include #include #include "domain.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 7d9766c57c..32e836f31d 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_deposit.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 0dc0be4947..bd2f9acfb9 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_efield.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 153de8851b..6396d139a0 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_evaporate.h" -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index c4ff1ebeba..75642b632f 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_gld.h" -#include + #include #include #include "atom.h" diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 3141f6496c..ab9a921d3e 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -21,9 +21,9 @@ #include "fix_orient_bcc.h" #include #include -#include -#include -#include + + + #include "atom.h" #include "update.h" #include "respa.h" @@ -36,8 +36,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index bcba14c355..bcbdcfabc5 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -18,9 +18,9 @@ #include "fix_orient_fcc.h" #include #include -#include -#include -#include + + + #include "atom.h" #include "update.h" #include "respa.h" @@ -33,8 +33,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index 7eec60be8b..115045db81 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_thermal_conductivity.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 24f988a76d..2d38f3c6c6 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_ttm.h" -#include + #include #include #include "atom.h" @@ -29,8 +29,8 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index b8c04132ea..9c021c5ca8 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_viscosity.h" -#include + #include #include #include "atom.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index e2e6f40857..4fc1fb0628 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index efc84f22b5..4a18680415 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_cut.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 79b1ebae66..576637c593 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_long.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MLIAP/compute_mliap.cpp b/src/MLIAP/compute_mliap.cpp index 134994f829..aad28c7bb1 100644 --- a/src/MLIAP/compute_mliap.cpp +++ b/src/MLIAP/compute_mliap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "mliap_data.h" #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" diff --git a/src/MLIAP/compute_mliap.h b/src/MLIAP/compute_mliap.h index 5602ace89b..1172111247 100644 --- a/src/MLIAP/compute_mliap.h +++ b/src/MLIAP/compute_mliap.h @@ -21,7 +21,7 @@ ComputeStyle(mliap,ComputeMLIAP) #define LMP_COMPUTE_MLIAP_H #include "compute.h" -#include + namespace LAMMPS_NS { diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp index f2e042141c..d74a1820cc 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/MLIAP/pair_mliap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include + #include -#include + #include #include "mliap_data.h" #include "mliap_model_linear.h" diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 117056ac58..6cd550384d 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_charmm.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 732843f412..0288a61d83 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 2ec59bfb1e..1a05edc20b 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index ac276511a2..5fb40b54c9 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 02bab37a8a..eb5e48ec9b 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 83e4485d48..100b75cb0a 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "angle_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,10 +28,10 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 97d4c865ba..514250d058 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -20,7 +20,7 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 9617894a9a..b2271d45fc 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_fene.h" -#include + #include #include #include "atom.h" @@ -22,8 +22,8 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index eec8c14872..676d5f6871 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_fene_expand.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 4e20a2711d..89b3830cb5 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_gromos.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 773a4ee12a..28100512a8 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 38d8d6a45f..49074e1cdc 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_morse.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 1733ffc670..63b640730a 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_nonlinear.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index c89ac552ae..c8d182e4ff 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_quartic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "pair.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 2724d4f20c..5cc91ceae0 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "bond_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,10 +26,10 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 71c9f586a3..11422e0820 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmm.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index d4956b42bd..408be8ef99 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmmfsw.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 403bafd23e..55e2f25006 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index ce31a12ed3..40e026c2f1 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_helix.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index a3c76b91ee..963304da80 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_multi_harmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 151986ca3f..fe05dc7c3d 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index ddf035070b..2de6dd4183 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -28,9 +28,9 @@ ------------------------------------------------------------------------- */ #include "fix_cmap.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -41,8 +41,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index d819642bb1..90cf3eee39 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_cvff.h" -#include + #include #include "atom.h" #include "comm.h" @@ -21,7 +21,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 2af1126876..6327ea8b06 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 1f2da63486..7b2c4e0b09 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_umbrella.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 69ea81a017..6d9c851422 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -30,7 +30,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 8d6dfc7d68..422da8d827 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -30,7 +30,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index f09f9a483a..dea6bd6251 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_charmm.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index e646392e0e..31083312a9 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmmfsw_coul_charmmfsh.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index b23195086c..b5ed255789 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index bea8acbcbc..8d8f5ec78e 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_cut.h" -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index 9d15e8b1a8..62d940af37 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_atom_mpiio.h" #include -#include + #include #include "domain.h" #include "update.h" diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index bca19e58c8..e05b7bf317 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_cfg_mpiio.h" #include -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 3f9c09738e..b623df82d0 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_custom_mpiio.h" #include -#include + #include #include "domain.h" #include "input.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index d1b2d5079a..139245e4b0 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_xyz_mpiio.h" #include -#include + #include #include "domain.h" #include "update.h" diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index 9c9e415be5..29d6d550e4 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_mscg.h" -#include + #include -#include + #include "mscg.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index e6b6fb72f4..82510e8177 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -21,7 +21,7 @@ #include "pair_eam_opt.h" #include -#include + #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index 3dc6bdb6b4..a7fbfb823a 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -20,7 +20,7 @@ #include "pair_lj_charmm_coul_long_opt.h" #include -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index 3b3a19a9e8..a31f521ecc 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_opt.h" -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index 1d2e226777..89d254ee04 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -20,7 +20,7 @@ #include "pair_morse_opt.h" #include -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index d824d82e6c..2cb5323745 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_ufm_opt.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 022eb0bab6..2950381197 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_peri_neigh.h" -#include + #include #include "pair_peri_lps.h" #include "pair_peri_ves.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 5e3a514b61..b3986e75fa 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_peri_eps.h" -#include + #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -33,7 +33,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index e73e2eff67..101a6d0bd9 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_peri_lps.h" -#include + #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index cf751885d6..c5f893dd32 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "pair_peri_pmb.h" -#include + #include #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -33,7 +33,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 138584123a..dca80cc6fd 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_peri_ves.h" -#include + #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "update.h" using namespace LAMMPS_NS; diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index b0b1287717..12dc59c286 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include "fix_poems.h" -#include + #include #include -#include + #include "workspace.h" #include "atom.h" #include "domain.h" @@ -34,8 +34,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index d0650bcb51..c59ba5eb5f 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -17,7 +17,7 @@ #include "pair_python.h" #include // IWYU pragma: keep -#include + #include #include "atom.h" #include "force.h" diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index ba4932a485..5cadce617f 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index a2cc683b56..7f50736b18 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_dynamic.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 265528a089..6dcc5e9cdc 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_fire.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 4f5369eb87..327a9c5b3a 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -17,7 +17,7 @@ #include "fix_qeq_slater.h" #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index e130f85f5f..d7abcb62b8 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_event_displace.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 16c37fcb77..f104d14c2f 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_hyper_global.h" -#include + #include #include #include "atom.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index 9e3ce9b00d..e57419022c 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_hyper_local.h" -#include + #include #include -#include + #include "atom.h" #include "update.h" #include "group.h" @@ -30,7 +30,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 93689eb7f9..76953b6c2c 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_neb.h" -#include + #include #include -#include + #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 03119d304e..03b79cc750 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include "fix_ehex.h" -#include + #include #include #include "atom.h" diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index ff31ab9755..436b2191ff 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_rattle.h" -#include + #include #include #include "atom.h" diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 761b957292..f74cce8233 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid.h" -#include + #include -#include + #include #include "math_extra.h" #include "atom.h" @@ -35,8 +35,8 @@ #include "memory.h" #include "error.h" #include "rigid_const.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5b75640549..d1204e2bbc 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nh_small.h" -#include + #include #include #include "math_extra.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 01dd9e889e..85cadc826e 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_small.h" -#include + #include -#include + #include #include #include "math_extra.h" @@ -39,8 +39,8 @@ #include "memory.h" #include "error.h" #include "rigid_const.h" -#include "utils.h" -#include "fmt/format.h" + + #include diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index d6603cd7b6..ee88f57341 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_shake.h" -#include + #include #include #include @@ -32,8 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index b5b586bc7f..509e45202c 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_append_atoms.h" -#include + #include #include #include "atom.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 986b1323e8..3930133221 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_msst.h" -#include + #include #include #include "atom.h" @@ -32,8 +32,8 @@ #include "domain.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index 1e85441d1f..37b82b86f0 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -13,7 +13,7 @@ #include "compute_sna_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 1376193070..bb546708b8 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -13,7 +13,7 @@ #include "compute_snad_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp index eb18b7274e..ca989a75b4 100644 --- a/src/SNAP/compute_snap.cpp +++ b/src/SNAP/compute_snap.cpp @@ -13,7 +13,7 @@ #include "compute_snap.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 066fc56c11..dd562cac5c 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -13,7 +13,7 @@ #include "compute_snav_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 48014592ed..cb1a71aa45 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "pair_snap.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "sna.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 94eff27f53..281100740a 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "compute_spin.h" -#include + #include #include #include "atom.h" diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 6df9dd4af2..82bf83ac10 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -34,7 +34,7 @@ #include "random_mars.h" #include "respa.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 110cfb58d8..0b2e86e465 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_neb_spin.h" -#include + #include #include #include "universe.h" diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 9a33f0d61d..cbb367e438 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_precession_spin.h" -#include + #include #include #include "atom.h" diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 5573d914b7..4da05c57cb 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dipole_cut.h" -#include + #include #include #include "atom.h" @@ -35,7 +35,7 @@ #include "modify.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 4188bb214c..605370f7f1 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dipole_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "modify.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index b4b3fcb6f5..0a5bde2c9f 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dmi.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index b82dca3dcc..a932aa5c54 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_exchange.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 50cd1fe54a..65a2904228 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_magelec.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 4468e157b4..ceb487d378 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_neel.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index ca0bdbac0a..688522c1bd 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_srd.h" -#include + #include #include #include "math_extra.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 8b9ea6fb79..461dc5f5ad 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_srd.h" -#include + #include #include "fix.h" #include "domain.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 2aa2e7680b..178f0f42de 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -22,7 +22,7 @@ #include "update.h" #include "respa.h" #include "error.h" -#include "utils.h" + #include "TCP/wpmd_split.h" diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 4d812852db..18704deb0b 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_awpmd_cut.h" -#include + #include #include #include @@ -32,7 +32,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "logexc.h" #include "vector_3.h" diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 39da9fc23b..4af2356e1a 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -16,10 +16,10 @@ #include "compute_pressure_bocs.h" -#include + #include #include -#include + #include "angle.h" #include "atom.h" @@ -28,7 +28,7 @@ #include "domain.h" #include "error.h" #include "fix.h" -#include "fmt/format.h" + #include "force.h" #include "improper.h" #include "kspace.h" diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index c61a37388b..6f7962c83f 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -17,7 +17,7 @@ #include "fix_bocs.h" #include -#include + #include #include @@ -29,7 +29,7 @@ #include "domain.h" #include "error.h" #include "fix_deform.h" -#include "fmt/format.h" + #include "force.h" #include "group.h" #include "irregular.h" diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index cc70f2fb31..c9540bf0c0 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "bond_oxdna_fene.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp index bdddccda87..152961f290 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "bond_oxrna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 32ee0ed145..60c1c8788f 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_coaxstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 04aaf82ccb..7d2c8aa2c2 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_dh.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 87f58857bb..17ba194030 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_coaxstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 22ed310003..33005046b7 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_excv.h" -#include + #include #include #include "mf_oxdna.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index df952d0ff2..88c5dc5e36 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_hbond.h" -#include + #include #include #include "mf_oxdna.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index fa9204ed86..bf52d61182 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_stk.h" -#include + #include #include #include @@ -26,7 +26,7 @@ #include "neighbor.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 7845451daf..87de92e0e0 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_xstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp index 3c0194d636..ec93ce592e 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp @@ -16,7 +16,7 @@ #include #include -#include + #include #include "pair_oxrna2_excv.h" diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index 1b6c577a19..d38ccb86ab 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -16,7 +16,7 @@ #include #include -#include + #include #include "pair_oxrna2_stk.h" #include "mf_oxdna.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp index 11c2f2b9b1..f3f65b695e 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxrna2_xstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index d535baeda5..6f97d2104f 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "angle_sdk.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "lj_sdk_common.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index cf478e85fb..8185e24876 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index cd02c7f9e1..42f1ff3ce7 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk_coul_long.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index f9e071a0b3..fc575c2e79 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -25,11 +25,11 @@ ------------------------------------------------------------------------- */ #include "fix_colvars.h" -#include -#include + + #include #include -#include + #include #include diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 5dd47b28bd..677bf62a25 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -17,9 +17,9 @@ #include "omp_compat.h" #include "compute_saed.h" -#include + #include -#include + #include #include "math_const.h" #include "compute_saed_consts.h" diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index e75546b548..0dac7aca5e 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -18,9 +18,9 @@ #include "omp_compat.h" #include "compute_xrd.h" -#include + #include -#include + #include #include "math_const.h" #include "compute_xrd_consts.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 0a018338a4..08833db224 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_saed_vtk.h" -#include + #include #include #include "update.h" diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 0ef7868164..97e12d5cb4 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_dpd.h" -#include + #include "atom.h" #include "update.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 69e5336945..7134eaca22 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table.h" -#include -#include + + #include #include "atom.h" #include "error.h" #include "force.h" #include "memory.h" -#include "utils.h" + #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index d728f7e987..c220d84a57 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table_rx.h" -#include -#include + + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "memory.h" #include "comm.h" #include "modify.h" -#include "utils.h" + #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index ced7283ef4..d974d12473 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_rx.h" -#include -#include + + #include #include #include // DBL_EPSILON @@ -31,7 +31,7 @@ #include "neigh_request.h" #include "math_special.h" #include "pair_dpd_fdt_energy.h" -#include "utils.h" + #include // std::vector<> #include // std::max diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 18c86976ac..e533140dd6 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -34,7 +34,7 @@ ------------------------------------------------------------------------- */ #include "fix_shardlow.h" -#include + #include #include #include @@ -54,7 +54,7 @@ #include "pair_dpd_fdt_energy.h" #include "npair_half_bin_newton_ssa.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 876d76a42f..c988f4205c 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_fdt.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "memory.h" #include "modify.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 3686bcb7e9..9231ab7ba3 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_fdt_energy.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "memory.h" #include "modify.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 839d22b50b..666a1b0ea9 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "pair_exp6_rx.h" -#include + #include -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "modify.h" #include "fix.h" diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index f9074d5c05..ceb5c78eaf 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -21,10 +21,10 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include + #include #include "math_const.h" -#include + #include #include "pair_multi_lucy.h" #include "atom.h" @@ -33,9 +33,9 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 90f6dc6170..d769d94783 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -21,10 +21,10 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include + #include #include "math_const.h" -#include + #include #include "pair_multi_lucy_rx.h" #include "atom.h" @@ -33,11 +33,11 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" #include "modify.h" #include "fix.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 56c3e28c46..f791107f1d 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_table_rx.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index a12c248680..b806b4434b 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_drude.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 080408459c..313ac249d7 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_drude.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 4128c508d6..bdccaaebc8 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -13,7 +13,7 @@ /** Fix Drude Transform ******************************************************/ #include "fix_drude_transform.h" -#include + #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index e865e9cd29..da74510821 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_drude.h" -#include + #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 875b4a9cba..461f972885 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_thole_long.h" -#include + #include #include #include "fix_drude.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "modify.h" #include "domain.h" diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 882fd047a9..281317c076 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_thole.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "fix.h" #include "fix_drude.h" #include "domain.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index c943366f1b..001e1d4c43 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "compute_ke_atom_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index 3e277fc66c..d1781b75f7 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include + + #include "compute_ke_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index dcf7e86234..90e25ca3c8 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include -#include + #include "compute_temp_deform_eff.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index e9295ea680..174f032b83 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "compute_temp_eff.h" -#include -#include + + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index b27699cde9..c95cf0de2d 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include -#include + #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index 5158d7c681..3966bc7b98 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include + #include -#include + #include "fix_langevin_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 034233732e..9fdbc6a0bf 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,7 +15,7 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index ea719c91c0..f32a45fd46 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "fix_nve_eff.h" #include "atom.h" #include "force.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 0ebbf04d64..02a463b3ba 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -13,7 +13,7 @@ #include #include -#include + #include "fix_nvt_sllod_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index e2163990bd..a013270049 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_temp_rescale_eff.h" #include "atom.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index b9b442ed2a..f4e7af6584 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include + #include -#include + #include #include "pair_eff_cut.h" #include "pair_eff_inline.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index 488a85fc20..ff1e303a30 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -18,7 +18,7 @@ #include "compute_fep.h" #include #include -#include + #include "comm.h" #include "update.h" #include "atom.h" @@ -34,7 +34,7 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index f88f2b6c40..2f97b5a0e3 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index fd5141525c..b0a099a56f 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 39e06ddd60..80173f3f0f 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index f9149c8fb8..e13b98329f 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index f1aa99b416..bfd5a630f6 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index 19c41f04cb..e027a30185 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index 3c1869da08..0cd1fc9e87 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 4a92a6fcef..a18256f98a 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 56cf31b9d3..4b3fae77b3 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 2ab677c454..786715d6c9 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_soft.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 35342f68d8..18f8db5021 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long_soft.h" -#include + #include #include #include "angle.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 904799e1d3..85a30a5414 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index fa130a9dc6..9578befd37 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long_soft.h" -#include + #include #include #include "angle.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 0c07e844cb..e9daf71867 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include #include "ch5md.h" diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index 9275e82f1c..b6e0b0dac5 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "angle_charmm_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 49a71038da..6d3deee9ba 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "angle_harmonic_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 5c58e7bf10..072800db42 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "bond_fene_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 8bf0a82218..1ddb424a7b 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "bond_harmonic_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp index 61fc1dfbd5..ddfa0c1228 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/USER-INTEL/dihedral_charmm_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_charmm_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index fb8051474e..cd62012255 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_fourier_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index f6c4ea0fde..dd8c3d98db 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_harmonic_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 79a8874a72..ef48f7e8ee 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_opls_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 7bd510b189..b3649be7c8 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -29,10 +29,10 @@ #include "timer.h" #include "universe.h" #include "update.h" -#include "utils.h" + #include -#include + #include #include diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 4562c63cdb..4dcdb34b69 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include -#include + #include "improper_cvff_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index fc5cf08c52..c63dfc9567 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include -#include + #include "improper_harmonic_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index c1e4a5374a..8b7ff71603 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -19,7 +19,7 @@ #pragma offload_attribute(push, target(mic)) #endif #include -#include + #include #include #include diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 4ad4398fbe..a67db0ad32 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_buck_coul_cut_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index 150cfd3ee0..d0cb1837c9 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_buck_coul_long_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 31430e4bf7..b979d2dcdf 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_alloy_intel.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index c5804922f6..a1c71d9c21 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_fs_intel.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 994f0d3910..d27a019532 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_eam_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 32afcbf8a9..b8ac84bc3c 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -26,7 +26,7 @@ #endif #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index 8784029320..75f5f85f2d 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_tersoff_intel.h" #include "atom.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 8ad3dbe33e..204a9c073b 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -18,8 +18,8 @@ #include "fix_lb_fluid.h" #include -#include -#include + + #include #include #include diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index 10fffed018..0a307790d5 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include "fix_lb_momentum.h" -#include -#include + + #include #include "atom.h" #include "group.h" diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index d61692419a..2c7e8dbf47 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -26,7 +26,7 @@ #include "domain.h" #include "fix_lb_fluid.h" #include "modify.h" -#include + #include "group.h" using namespace LAMMPS_NS; diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 9cc03591fa..f714e31719 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "fix_lb_rigid_pc_sphere.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" @@ -31,7 +31,7 @@ #include "memory.h" #include "error.h" #include "fix_lb_fluid.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 41074903bd..b016dd8ecb 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_manifoldforce.h" // For stuff -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 2baa2944ae..b3122a68d4 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -33,7 +33,7 @@ #include "fix_nve_manifold_rattle.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index f40df56c19..6f674c9f45 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_meamc.h" -#include -#include + + #include -#include + #include "meam.h" #include "atom.h" #include "force.h" @@ -29,8 +29,8 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index 21e44e7ff2..9cbda8f6ad 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -22,7 +22,7 @@ PairStyle(meam,PairMEAMC) #define LMP_PAIR_MEAMC_H #include "pair.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp index d08a626fad..c3fae823ea 100644 --- a/src/USER-MESODPD/atom_vec_edpd.cpp +++ b/src/USER-MESODPD/atom_vec_edpd.cpp @@ -21,7 +21,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/atom_vec_tdpd.cpp b/src/USER-MESODPD/atom_vec_tdpd.cpp index f50fe168d6..63b88f921d 100644 --- a/src/USER-MESODPD/atom_vec_tdpd.cpp +++ b/src/USER-MESODPD/atom_vec_tdpd.cpp @@ -16,7 +16,7 @@ #include "atom.h" #include "update.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp index 60a437a47c..9c2e74b882 100644 --- a/src/USER-MESODPD/pair_edpd.cpp +++ b/src/USER-MESODPD/pair_edpd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_edpd.h" -#include + #include #include #include @@ -31,7 +31,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_mdpd.cpp b/src/USER-MESODPD/pair_mdpd.cpp index 755008f443..88b6724a03 100644 --- a/src/USER-MESODPD/pair_mdpd.cpp +++ b/src/USER-MESODPD/pair_mdpd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_mdpd.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp index bfbc6f7c82..def61dea8f 100644 --- a/src/USER-MESODPD/pair_mdpd_rhosum.cpp +++ b/src/USER-MESODPD/pair_mdpd_rhosum.cpp @@ -29,7 +29,7 @@ #include "memory.h" #include "error.h" #include "neighbor.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_tdpd.cpp b/src/USER-MESODPD/pair_tdpd.cpp index face9221d9..65a518c07e 100644 --- a/src/USER-MESODPD/pair_tdpd.cpp +++ b/src/USER-MESODPD/pair_tdpd.cpp @@ -29,7 +29,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESONT/compute_mesont.cpp b/src/USER-MESONT/compute_mesont.cpp index 397b071a1b..96792c8988 100644 --- a/src/USER-MESONT/compute_mesont.cpp +++ b/src/USER-MESONT/compute_mesont.cpp @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace LAMMPS_NS; diff --git a/src/USER-MESONT/pair_mesocnt.cpp b/src/USER-MESONT/pair_mesocnt.cpp index 4af8a99d6f..96d53bd41a 100644 --- a/src/USER-MESONT/pair_mesocnt.cpp +++ b/src/USER-MESONT/pair_mesocnt.cpp @@ -20,9 +20,9 @@ #include #include -#include + #include -#include + #include "atom.h" #include "comm.h" @@ -33,8 +33,8 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-MESONT/pair_mesont_tpm.cpp b/src/USER-MESONT/pair_mesont_tpm.cpp index 9fb0f604c8..6d8c8126ae 100644 --- a/src/USER-MESONT/pair_mesont_tpm.cpp +++ b/src/USER-MESONT/pair_mesont_tpm.cpp @@ -16,7 +16,7 @@ #include "pair_mesont_tpm.h" #include "export_mesont.h" -#include + #include "atom.h" #include "comm.h" #include "force.h" @@ -29,7 +29,7 @@ #include #include #include -#include + #include #include #include diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index e7ab62608a..070e3cb61e 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "pair_mgpt.h" -#include + #include -#include + #include #include diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index 2ed1a85672..a986cb8322 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index fb1cc0a4e6..52bfe751f1 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 6e449fe472..336638f25d 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_dipole.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 5f34be8d65..907ee973bd 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_fourier.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index cddc07da90..8894f7b4c9 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index c84739ac91..93f45f9562 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_quartic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index dd2c1a1524..5889400b97 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_shift.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 2cbfa01c0a..86e6263f93 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_shift_cut.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_special.cpp b/src/USER-MISC/bond_special.cpp index ebbdcb1899..a956468497 100644 --- a/src/USER-MISC/bond_special.cpp +++ b/src/USER-MISC/bond_special.cpp @@ -14,7 +14,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "bond_special.h" #include "atom.h" @@ -25,7 +25,7 @@ #include "pair.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index fdce944034..52656ec9d6 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "compute_cnp_atom.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index ccecf43aaf..02c697a786 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -45,7 +45,7 @@ https://doi.org/10.1103/PhysRevE.92.043303 #include #include -#include + #include "compute_hma.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp index 541b52d9c0..f1c35993e3 100644 --- a/src/USER-MISC/compute_momentum.cpp +++ b/src/USER-MISC/compute_momentum.cpp @@ -1,6 +1,6 @@ #include "compute_momentum.h" -#include + #include "atom.h" #include "error.h" #include "update.h" diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 8346bd3410..6cf375dd19 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pressure_cylinder.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index 1e42a9df02..c733c929ba 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -16,7 +16,7 @@ --------------------------------------------------------------------------*/ #include "compute_stress_mop.h" -#include + #include #include diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 022840166f..323aee851e 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -16,7 +16,7 @@ --------------------------------------------------------------------------*/ #include "compute_stress_mop_profile.h" -#include + #include #include diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 94c6115186..c333357a93 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_rotate.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/USER-MISC/compute_viscosity_cos.cpp index 7311f991cc..12e1991d54 100644 --- a/src/USER-MISC/compute_viscosity_cos.cpp +++ b/src/USER-MISC/compute_viscosity_cos.cpp @@ -15,7 +15,7 @@ Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com) ------------------------------------------------------------------------- */ -#include + #include "compute_viscosity_cos.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 1b3afb13eb..7c131682fa 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_cosine_shift_exp.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index e897e58649..066447f92d 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_fourier.h" -#include + #include #include "atom.h" #include "comm.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index 0ff62320e4..bde8d84070 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_nharmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index d91c237838..deafc8391f 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_quadratic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 1cfb756127..a33452dbe1 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_spherical.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index 37410ba085..aebe468905 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,12 +17,12 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ -#include + #include #include -#include + #include -#include + #include // IWYU pragma: keep #include // IWYU pragma: keep @@ -33,12 +33,12 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "dihedral_table.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index 8a397b20f2..a8d1f8f8bb 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -24,7 +24,7 @@ DihedralStyle(table,DihedralTable) #ifndef LMP_DIHEDRAL_TABLE_H #define LMP_DIHEDRAL_TABLE_H #include "dihedral.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 2a5b46a4f1..f8a2f02596 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -17,12 +17,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_table_cut.h" -#include + #include #include -#include + #include -#include + #include // IWYU pragma: keep #include // IWYU pragma: keep @@ -35,7 +35,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 4583d76e09..ed796280e7 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_addtorque.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index abfa751d15..1f2022d520 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "fix_ave_correlate_long.h" -#include + #include -#include + #include #include #include "update.h" diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 4460c55183..fb111c1f27 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_ffl.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 18fd784861..86650cd50d 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_filter_corotate.h" -#include + #include #include #include -#include + #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 2463e18b40..23e61641d8 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_flow_gauss.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 30e62c7eb9..f4776c3d6c 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_gle.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -29,7 +29,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index af4a517269..4264126c26 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,7 +58,7 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include + #include #if defined(_MSC_VER) || defined(__MINGW32__) diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index b1d07eef41..b8045a9ff1 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_ipi.h" -#include + #include #include "atom.h" #include "force.h" @@ -45,7 +45,7 @@ using namespace FixConst; // socket interface #ifndef _WIN32 -#include + #include #include #include diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/USER-MISC/fix_momentum_chunk.cpp index 0ed5e1f877..3df632eb30 100644 --- a/src/USER-MISC/fix_momentum_chunk.cpp +++ b/src/USER-MISC/fix_momentum_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_momentum_chunk.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "error.h" #include "force.h" #include "modify.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_momentum_chunk.h b/src/USER-MISC/fix_momentum_chunk.h index 5e056f2494..5007e38c69 100644 --- a/src/USER-MISC/fix_momentum_chunk.h +++ b/src/USER-MISC/fix_momentum_chunk.h @@ -21,7 +21,7 @@ FixStyle(momentum/chunk,FixMomentumChunk) #define LMP_FIX_MOMENTUM_CHUNK_H #include "fix.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/USER-MISC/fix_npt_cauchy.cpp index 221886d388..9361d9ebd6 100644 --- a/src/USER-MISC/fix_npt_cauchy.cpp +++ b/src/USER-MISC/fix_npt_cauchy.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_npt_cauchy.h" #include "math_extra.h" diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 410a269f8c..f0fbddf18d 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_nvk.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index 4e97cac3f9..a9abf7baf7 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_orient_eco.h" -#include + #include #include #include "atom.h" @@ -33,8 +33,8 @@ #include "pair.h" #include "respa.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 33407aec44..222369f572 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -19,10 +19,10 @@ #include "fix_pafi.h" -#include + #include #include -#include + #include "math_extra.h" #include "atom.h" #include "force.h" @@ -35,9 +35,9 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 8de31f19b3..5be9bf162b 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------- */ #include "fix_pimd.h" -#include + #include #include -#include + #include "universe.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index 0a40177993..b17ee55f94 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -21,7 +21,7 @@ #include #include -#include + #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 612352aae1..0771122bfd 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -14,7 +14,7 @@ ------------------------------------------------------------------------- */ #include "fix_rhok.h" -#include + #include #include diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index d110637b3c..baee8a5699 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index d61e7f1ee1..1bd6957997 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_srp.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index ef7c4c0296..34c667a9e2 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "fix_ti_spring.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 8c37b19e8b..c12019528c 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_ttm_mod.h" -#include + #include #include #include "atom.h" @@ -32,8 +32,8 @@ #include "error.h" #include "citeme.h" #include "math_const.h" -#include "utils.h" -#include "fmt/format.h" + + #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index 8afc506804..7da818732e 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -18,7 +18,7 @@ #include "fix_wall_reflect_stochastic.h" #include -#include + #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 3a8323d58d..a8d6ea9424 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_region_ees.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 09cf7cf2c6..5714931215 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_cossq.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 8ea58b23b3..476cf8ab43 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_distance.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 3bdbc7bc68..85f7809a02 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_fourier.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 4102a250dd..c85e4850c8 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -37,7 +37,7 @@ ------------------------------------------------------------------------- */ #include "improper_ring.h" -#include + #include #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 764ccc587f..0a00c914c7 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_agni.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -31,7 +31,7 @@ #include "citeme.h" #include "math_special.h" #include "math_const.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 6a4575c6e4..9ef96f1188 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_mdf.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 8e400d23ed..57dd55c593 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -16,7 +16,7 @@ #include "pair_cosine_squared.h" #include -#include + #include #include "atom.h" #include "comm.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index 14fbd374b6..5a3e12f1a5 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_diel.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 883796de1b..44ab555b02 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -28,7 +28,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/USER-MISC/pair_coul_slater_cut.cpp index 194ff664b3..6b1af9a42f 100644 --- a/src/USER-MISC/pair_coul_slater_cut.cpp +++ b/src/USER-MISC/pair_coul_slater_cut.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_coul_slater_cut.h" #include "atom.h" diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/USER-MISC/pair_coul_slater_long.cpp index d801d0342f..0fbd56f811 100644 --- a/src/USER-MISC/pair_coul_slater_long.cpp +++ b/src/USER-MISC/pair_coul_slater_long.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_coul_slater_long.h" #include "atom.h" @@ -31,7 +31,7 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index cc890f8c94..7b56caa205 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_drip.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index 2b58e4b1f8..a7ed0fcaad 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_e3b.h" -#include + #include #include #include diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index bb9c742212..6ccaded35d 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------- */ #include "pair_edip.h" -#include + #include #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -35,7 +35,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index 90a3502eae..4a81a41a26 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_edip_multi.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -31,7 +31,7 @@ #include "memory.h" #include "error.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 8f8d539679..0db7f8739a 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_extep.h" -#include + #include -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 38d4c4d4c2..c9601c416e 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gauss_cut.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 62101d0e80..671dcb309d 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_ilp_graphene_hbn.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -34,7 +34,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index fb1da5dab8..9f986fa101 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -22,9 +22,9 @@ #include "pair_kolmogorov_crespi_full.h" #include -#include + #include -#include + #include "atom.h" #include "comm.h" #include "force.h" @@ -34,7 +34,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index f02423e952..7ce6f8652a 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "pair_kolmogorov_crespi_z.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index 5a84882cd9..b8f9e5c38f 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -23,9 +23,9 @@ ------------------------------------------------------------------------- */ #include "pair_lebedeva_z.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index 6faa599d2c..31d32db505 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lennard_mdf.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index c553e671cb..a93e0a81af 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_list.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index 20081fa1e1..92e869e58c 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand_coul_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index 22f20a690e..baa0e233f2 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_mdf.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index 6a92602683..ab845e69d5 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sf_dipole_sf.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "update.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 8ad9793f98..3b76bd8482 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -18,11 +18,11 @@ ------------------------------------------------------------------------- */ #include "pair_local_density.h" -#include + #include -#include + #include -#include + #include "atom.h" #include "force.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "error.h" #include "domain.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 6091b95837..4d9b3866b7 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -33,7 +33,7 @@ #include "pair_meam_spline.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -43,7 +43,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 34cbe82581..0a8aae233a 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -25,7 +25,7 @@ #include "pair_meam_sw_spline.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -35,7 +35,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 534f4acff5..d534284b57 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_momb.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 399723e0c5..9f895800df 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse_smooth_linear.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 9926318597..150895108e 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -26,9 +26,9 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ #include "pair_srp.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -44,7 +44,7 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "thermo.h" #include "output.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 4df172a001..1f5cfddff1 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -32,7 +32,7 @@ #include "force.h" #include "comm.h" #include "memory.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index aa56ababe1..7ef134405d 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_class2_p6.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 0f49882e83..1bede58751 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_buck6d.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 0ecc60ecc1..bbe6e48a35 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "improper_inversion_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 28fc955448..0de5423d30 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -29,7 +29,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 20bf7fa049..c6ba832fff 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck6d_coul_gauss_long.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index d9d8ec3c97..e0e92f9339 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dump_molfile.h" -#include + #include #include #include "domain.h" diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index bb85dfb784..f936de6d02 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -18,7 +18,7 @@ #if defined(LMP_HAS_NETCDF) #include -#include + #include #include #include "dump_netcdf.h" diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 8747bbea25..19b0632922 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -18,7 +18,7 @@ #if defined(LMP_HAS_PNETCDF) #include -#include + #include #include #include "dump_netcdf_mpiio.h" diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index 9c7317bebd..f097e93be2 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include #include "math_extra.h" #include "fix_nh_asphere_omp.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index b0573dfa97..5b2ee88420 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_comb_omp.h" -#include + #include #include #include "pair_comb.h" diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index a10d3127a9..ef0f918cbf 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -32,7 +32,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax_omp.h" -#include + #include #include "pair_reaxc.h" #include "atom.h" diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 63084fcc9e..f53fcf63bc 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include "fix_rigid_nh_omp.h" -#include + #include #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 9f78f6dc26..62f853d23b 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include "fix_rigid_omp.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index 3e0e423f3d..f0823204c0 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_alloy_omp.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 76e9840a5c..89590bb3e6 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_fs_omp.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 72a7d5f16a..fb579fb980 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -19,7 +19,7 @@ #include "pair_lj_cut_thole_long_omp.h" #include #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 73b1373fad..08efb73aab 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -34,7 +34,7 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_omp.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index 005cd427a9..d1d808307a 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -18,7 +18,7 @@ #include #include -#include + #include #include "pair_tersoff_zbl_omp.h" #include "atom.h" @@ -30,7 +30,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index 17325b062a..382eabe82d 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,7 +23,7 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include + #include #include #include "fix_phonon.h" diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index 3a52bbaaa1..b7a29c7bc9 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "atom.h" @@ -33,7 +33,7 @@ #include "compute.h" #include "modify.h" #include "pair.h" -#include "utils.h" + #include "timer.h" #include "plumed/wrapper/Plumed.h" diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index f1a34d9538..9f07030004 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (ICTP) ------------------------------------------------------------------------- */ -#include + #include #include "fix_qmmm.h" #include "atom.h" diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b590e1ae9a..034738023c 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_qbmsst.h" -#include + #include #include -#include -#include + + #include "atom.h" #include "force.h" #include "update.h" @@ -34,8 +34,8 @@ #include "error.h" #include "kspace.h" #include "math_const.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 80c0efddab..3f29229beb 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_qtb.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -32,8 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 64c56cb0e6..5511efe681 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -16,10 +16,10 @@ Aidan Thompson (Sandia, athomps@sandia.gov) ------------------------------------------------------------------------- */ -#include + #include #include -#include + #include #include "pair_quip.h" #include "atom.h" diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 99d016f1a0..0370d83fdc 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -16,10 +16,10 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ #include "fix_bond_react.h" -#include + #include #include -#include + #include "update.h" #include "modify.h" #include "respa.h" @@ -43,7 +43,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "error.h" #include "input.h" #include "variable.h" -#include "fmt/format.h" + #include "superpose3d.h" #include diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 433fd82bcd..4a61cfa03b 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax.h" -#include + #include #include #include "pair_reaxc.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 5c57fed261..c0ffd4c17e 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_bonds.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 74692f1c9b..ec03ab1808 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_species.h" -#include -#include + + #include #include "fix_ave_atom.h" #include "atom.h" diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index e0888e8514..c38257ae30 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc.h" -#include + #include -#include + #include #include #include "atom.h" @@ -39,7 +39,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "reaxc_defs.h" #include "reaxc_types.h" diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index b215e8d278..9d52ee2250 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -30,7 +30,7 @@ #include "error.h" #include "domain.h" #include "update.h" -#include "utils.h" + #ifndef USE_ZEST #include "random_mars.h" #endif diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index eb1f144275..5999dfaa5d 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include "compute_smd_vol.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index ab6dd5ef5c..b5dab3d3a1 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -23,8 +23,8 @@ ------------------------------------------------------------------------- */ #include "fix_smd_adjust_dt.h" -#include -#include + + #include "update.h" #include "force.h" #include "pair.h" diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 895e5b1a25..90589f3044 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -24,7 +24,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd_setvel.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index 4ade21a6fd..3e63de08f3 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -25,7 +25,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd_tlsph_reference_configuration.h" -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index ba3a324d56..c61fe14353 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_smd_wall_surface.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 67fda5f18d..8d3c06d5e6 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -27,9 +27,9 @@ ------------------------------------------------------------------------- */ #include "pair_smd_hertz.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" @@ -40,7 +40,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1ba4b37520..25301685a7 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -23,10 +23,10 @@ ------------------------------------------------------------------------- */ #include "pair_smd_tlsph.h" -#include + #include #include -#include + #include #include #include "fix_smd_tlsph_reference_configuration.h" diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index 9243883719..8ccba562e2 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -27,9 +27,9 @@ ------------------------------------------------------------------------- */ #include "pair_smd_triangulated_surface.h" -#include + #include -#include + #include #include #include "atom.h" @@ -41,7 +41,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index ecd0d5f4ec..e9cf256c3c 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -23,10 +23,10 @@ ------------------------------------------------------------------------- */ #include "pair_smd_ulsph.h" -#include + #include #include -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index f6ecd40bb6..875d254ac9 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -39,9 +39,9 @@ ------------------------------------------------------------------------- */ #include "pair_smtbq.h" -#include + #include -#include + #include #include #include diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 7bb06c14d9..fb8c928f2d 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -19,7 +19,7 @@ #include "error.h" #include "neigh_list.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index c80e2b4725..5480ff8e4c 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -19,7 +19,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 4004e41574..eb76d800c8 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -19,7 +19,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index c70cc7cd83..429d4199a4 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "update.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index 6455c1e8be..c0051201d0 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -20,7 +20,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 7a6188da69..497aea293b 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -20,7 +20,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 9d15fbc441..d010b004d5 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_force_tally.h" -#include + #include #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 350bc4b4b6..1a2dd36285 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_heat_flux_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index ce647a04c3..835d1e80bd 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe_mol_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index edfa49b1b1..ef7c13fed2 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 1ea096e286..2a0cbc8e4b 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_stress_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 72ed2640d8..59dba0d90d 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "dump_vtk.h" #include "atom.h" diff --git a/src/USER-VTK/dump_vtk.h b/src/USER-VTK/dump_vtk.h index e8de87f11c..b9db1f88cb 100644 --- a/src/USER-VTK/dump_vtk.h +++ b/src/USER-VTK/dump_vtk.h @@ -27,7 +27,7 @@ DumpStyle(vtk,DumpVTK) #include "dump_custom.h" #include #include -#include + #include #include diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 9c925d2365..c45af1d198 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cross.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 38a2cea3aa..34de772672 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_mm3.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index 39f238f1ab..f5d5fed946 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_mm3.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index e9b454bdb9..37039b27e4 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_distharm.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index af5086917a..ddc4d78c93 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_sqdistharm.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 2cbf01f7b7..98fd317794 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_switch3_coulgauss_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 52bcf20b9b..e1ee0e0b98 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_mm3_switch3_coulgauss_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index bda4299a68..be77b8457b 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_voronoi_atom.h" -#include + #include #include #include diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index fb3f90ec28..7c2426739d 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -16,12 +16,10 @@ ------------------------------------------------------------------------- */ #include "angle_deprecated.h" -#include #include "angle_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index d0a1d29e65..56590d6757 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "angle_hybrid.h" -#include -#include -#include + #include "atom.h" #include "neighbor.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index eb9cbf1ea2..e087b774e0 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "angle_zero.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom.cpp b/src/atom.cpp index f4c93db459..6fff15d11f 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,31 +12,28 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include -#include -#include -#include -#include -#include #include "style_atom.h" + #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "comm.h" -#include "neighbor.h" -#include "force.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "group.h" #include "input.h" -#include "variable.h" -#include "molecule.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "molecule.h" +#include "neighbor.h" +#include "update.h" +#include "variable.h" + +#include +#include #ifdef LMP_USER_INTEL #include "neigh_request.h" diff --git a/src/atom.h b/src/atom.h index 4dac15d758..21b9c06f8c 100644 --- a/src/atom.h +++ b/src/atom.h @@ -15,16 +15,20 @@ #define LMP_ATOM_H #include "pointers.h" + #include #include -#include namespace LAMMPS_NS { + // forward declaration + + class AtomVec; + class Atom : protected Pointers { public: char *atom_style; - class AtomVec *avec; + AtomVec *avec; enum{DOUBLE,INT,BIGINT}; // atom counts @@ -273,12 +277,12 @@ class Atom : protected Pointers { void add_peratom_vary(const char *, void *, int, int *, void *, int collength=0); void create_avec(const std::string &, int, char **, int); - virtual class AtomVec *new_avec(const std::string &, int, int &); + virtual AtomVec *new_avec(const std::string &, int, int &); void init(); void setup(); - class AtomVec *style_match(const char *); + AtomVec *style_match(const char *); void modify_params(int, char **); void tag_check(); void tag_extend(); @@ -296,8 +300,8 @@ class Atom : protected Pointers { void data_angles(int, char *, int *, tagint, int); void data_dihedrals(int, char *, int *, tagint, int); void data_impropers(int, char *, int *, tagint, int); - void data_bonus(int, char *, class AtomVec *, tagint); - void data_bodies(int, char *, class AtomVec *, tagint); + void data_bonus(int, char *, AtomVec *, tagint); + void data_bodies(int, char *, AtomVec *, tagint); void data_fix_compute_variable(int, int); virtual void allocate_type_arrays(); diff --git a/src/atom_map.cpp b/src/atom_map.cpp index c23aeec83c..02b97a1134 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include -#include + #include "comm.h" -#include "memory.h" #include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 261b068997..4a00e5852b 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -12,20 +12,19 @@ ------------------------------------------------------------------------- */ #include "atom_vec.h" -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" -#include "modify.h" +#include "error.h" #include "fix.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" #include "tokenizer.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 10cbb9c841..871f40084d 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "atom_vec_body.h" -#include -#include -#include "my_pool_chunk.h" #include "style_body.h" -#include "body.h" + #include "atom.h" -#include "domain.h" -#include "modify.h" +#include "body.h" +#include "error.h" #include "fix.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "my_pool_chunk.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index dc2760c5f9..c22111f48c 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "atom_vec_ellipsoid.h" -#include -#include "math_extra.h" + #include "atom.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index db593dcee0..5c37be4aa4 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid.h" -#include + #include "atom.h" #include "comm.h" -#include "memory.h" #include "error.h" #include "tokenizer.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index af768f9943..88dcb8c2fa 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "atom_vec_line.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 03f417b1d0..03412a11cc 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere.h" -#include + #include "atom.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" -#include "error.h" -#include "utils.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index d5b48b9540..e391a73215 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -12,18 +12,18 @@ ------------------------------------------------------------------------- */ #include "atom_vec_tri.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/balance.cpp b/src/balance.cpp index 168d7f59a4..af8d904812 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -19,28 +19,26 @@ // #define BALANCE_DEBUG 1 #include "balance.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "rcb.h" -#include "irregular.h" #include "domain.h" -#include "force.h" -#include "update.h" -#include "modify.h" +#include "error.h" #include "fix_store.h" #include "imbalance.h" #include "imbalance_group.h" -#include "imbalance_time.h" #include "imbalance_neigh.h" #include "imbalance_store.h" +#include "imbalance_time.h" #include "imbalance_var.h" +#include "irregular.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "rcb.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/bond.cpp b/src/bond.cpp index 12659fd8aa..1f953bbd19 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -12,20 +12,18 @@ ------------------------------------------------------------------------- */ #include "bond.h" -#include -#include -#include + #include "atom.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" +#include "memory.h" #include "neighbor.h" #include "suffix.h" -#include "atom_masks.h" -#include "memory.h" -#include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 0d91f73ea7..5422ab35f6 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "bond_deprecated.h" -#include + #include "bond_hybrid.h" #include "comm.h" -#include "force.h" #include "error.h" -#include "utils.h" +#include "force.h" using namespace LAMMPS_NS; diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 2fe9f7d388..b42683c300 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "bond_hybrid.h" -#include -#include -#include + #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 8053c5531d..71146ec4d6 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "bond_zero.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/change_box.cpp b/src/change_box.cpp index 5fe4eb8a06..1bd3fe733f 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -12,22 +12,20 @@ ------------------------------------------------------------------------- */ #include "change_box.h" -#include -#include -#include + #include "atom.h" -#include "modify.h" -#include "fix.h" -#include "domain.h" -#include "lattice.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "group.h" #include "irregular.h" +#include "lattice.h" +#include "modify.h" #include "output.h" -#include "group.h" -#include "error.h" -#include "force.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/comm.cpp b/src/comm.cpp index 7e603f2104..24a5d050d4 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -12,31 +12,29 @@ ------------------------------------------------------------------------- */ #include "comm.h" -#include -#include -#include -#include "universe.h" + +#include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "modify.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" #include "domain.h" -#include "output.h" #include "dump.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "group.h" -#include "procmap.h" #include "irregular.h" -#include "accelerator_kokkos.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "procmap.h" +#include "universe.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include #ifdef _OPENMP #include diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index c5ec8b35f4..37a4f0ae3d 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -16,19 +16,20 @@ ------------------------------------------------------------------------- */ #include "comm_brick.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "pair.h" -#include "domain.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" #include "error.h" +#include "fix.h" #include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 9f0169568d..48c9680d2f 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -17,19 +17,20 @@ ------------------------------------------------------------------------- */ #include "comm_tiled.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" -#include "pair.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute.cpp b/src/compute.cpp index 208b93730e..4cde9ff567 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -12,16 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute.h" -#include -#include + +#include "atom_masks.h" #include "domain.h" -#include "force.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" +#include "group.h" #include "memory.h" -#include "error.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index 0bd329079a..5d55f1fbbb 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "compute_adf.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "comm.h" -#include "utils.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6e28a94388..6b6f376b4c 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -16,23 +16,23 @@ ------------------------------------------------------------------------- */ #include "compute_aggregate_atom.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "pair.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "update.h" -#include "group.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index fc72a58453..e3e44efbbb 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_angle.h" -#include + #include "angle.h" -#include "update.h" -#include "force.h" #include "angle_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 05ea963b82..6c9f1d65a2 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_angmom_chunk.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 5cc947c764..503582bc65 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_bond.h" -#include + #include "bond.h" -#include "update.h" -#include "force.h" #include "bond_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index ae041c1997..d0044410d8 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -14,29 +14,27 @@ // NOTE: allow for bin center to be variables for sphere/cylinder #include "compute_chunk_atom.h" -#include -#include -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "force.h" +#include "comm.h" #include "domain.h" -#include "region.h" -#include "lattice.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_store.h" -#include "comm.h" #include "group.h" #include "input.h" -#include "variable.h" +#include "lattice.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 579b194b9f..953ae3a8cb 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute_chunk_spread_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "compute.h" #include "compute_chunk_atom.h" -#include "input.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 021665a647..8086ef3f41 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -12,22 +12,22 @@ ------------------------------------------------------------------------- */ #include "compute_cluster_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "update.h" -#include "group.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 8bbe2c15d0..e9b6f16990 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "compute_cna_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index c39911214c..8398311a05 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_com_chunk.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index be2f9c39bd..cb919d3a83 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -12,22 +12,23 @@ ------------------------------------------------------------------------- */ #include "compute_coord_atom.h" -#include -#include -#include "compute_orientorder_atom.h" + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "compute_orientorder_atom.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "group.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index 2419e5bc8b..4b7e3dae3c 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index e50903104a..8853887f18 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_dihedral.h" -#include -#include "update.h" -#include "force.h" + #include "dihedral.h" #include "dihedral_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 3790da2035..361ee36c18 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "compute_dipole_chunk.h" -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" #include "math_special.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index b20dd3bec3..4b194cfab1 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -12,19 +12,20 @@ ------------------------------------------------------------------------- */ #include "compute_displace_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "group.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix_store.h" +#include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 2a8588f061..447b28b51a 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_sphere.h" -#include + #include "atom.h" -#include "update.h" -#include "force.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index 664e2fa9ec..db003c93e7 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "compute_fragment_atom.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "modify.h" -#include "force.h" -#include "group.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index 0c0e34fa0c..b3e4f88bf3 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute_global_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index c8876daeef..ca0483fce9 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_group_group.h" -#include + #include #include #include "atom.h" diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index bce0c0de85..81876109c4 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_gyration.h" -#include + #include "update.h" #include "atom.h" #include "group.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 5677ce4b6a..ad0520bc01 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_gyration_chunk.h" -#include + #include #include #include "atom.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 7b607bd4db..15a17949eb 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_heat_flux.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 181771dcfb..3721dbfd48 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_improper.h" -#include + #include "update.h" #include "force.h" #include "improper.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index be980a08ee..65de1d7bb5 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_inertia_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index c6ba478dcb..e673f7fe53 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_ke.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 930f979bf0..d23c389ab6 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_msd.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "group.h" @@ -22,7 +22,7 @@ #include "modify.h" #include "fix_store.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index dda921ef42..b0e2520f99 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_msd_chunk.h" -#include + #include -#include + #include "atom.h" #include "group.h" #include "update.h" @@ -24,7 +24,7 @@ #include "fix_store.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 327c64493f..4151b2cdb8 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_omega_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index ade9f7615e..84ae20e92a 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -17,22 +17,22 @@ ------------------------------------------------------------------------- */ #include "compute_orientorder_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 054a50bed4..7ace5615a7 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pair.h" -#include + #include #include #include "update.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 2018d929f3..e41221f70b 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "compute_pair_local.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 379de0f9de..d9ed312328 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 4712c83461..b57b53f522 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pressure.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 579c7cae3f..c27cfc4096 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_property_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 920228e056..a28223b3a7 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_rdf.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "memory.h" #include "error.h" #include "comm.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index d4730c1de0..b024b4365c 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_reduce.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "domain.h" @@ -25,7 +25,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/compute_reduce.h b/src/compute_reduce.h index 9701f0e61e..00c1a9a6b9 100644 --- a/src/compute_reduce.h +++ b/src/compute_reduce.h @@ -20,7 +20,7 @@ ComputeStyle(reduce,ComputeReduce) #ifndef LMP_COMPUTE_REDUCE_H #define LMP_COMPUTE_REDUCE_H -#include "compute.h" +#include "compute.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index cd64c8cb1b..6e8aa48410 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_reduce_chunk.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "modify.h" @@ -25,7 +25,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 9074124a61..8153618a88 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_reduce_region.h" -#include + #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index 6ff462258f..ca4b735d6e 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_slice.h" -#include -#include -#include -#include "update.h" -#include "modify.h" + +#include "error.h" #include "fix.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 402b84bb4b..6af5d2b86c 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 6274ac4292..54f0529006 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index dc12e8f6db..f69eaadf2b 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_com.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 7d81a84bc4..b50962a2c6 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_deform.h" -#include + #include #include "domain.h" #include "atom.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index c78e830c95..85e51d2a5d 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_partial.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index c2ef1d5c11..eacca87e19 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_profile.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 187ea2454c..3874c1f286 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_ramp.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 4c0b925eb6..74955da421 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_region.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 786ef523ad..6ef3038d68 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_sphere.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 35eef8fe10..c0b648418b 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_torque_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index ec19137a0e..635c3e4161 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_vacf.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "group.h" #include "modify.h" #include "fix_store.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index b0a8dbeee7..6651110e77 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_vcm_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 7dcc4748e9..8baee645cf 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -12,33 +12,30 @@ ------------------------------------------------------------------------- */ #include "delete_atoms.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" -#include "molecule.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" #include "group.h" -#include "region.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" +#include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "random_mars.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "region.h" +#include #include -#include +#include using namespace LAMMPS_NS; diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index f08c94a273..b8ec5f7883 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -12,20 +12,17 @@ ------------------------------------------------------------------------- */ #include "delete_bonds.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "group.h" #include "special.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/deprecated.cpp b/src/deprecated.cpp index dc0ab400d4..ab9cc8cf44 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "deprecated.h" -#include + #include "comm.h" #include "error.h" #include "input.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 1709f7d3d7..91ef3e8e9e 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_deprecated.h" -#include -#include "dihedral_hybrid.h" + #include "comm.h" -#include "force.h" +#include "dihedral_hybrid.h" #include "error.h" -#include "utils.h" +#include "force.h" + using namespace LAMMPS_NS; diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 8f41b30d56..61e0fdc72a 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_hybrid.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 59167ca30e..9570590c09 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_zero.h" -#include + #include "atom.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index a30ac2c2b2..018288d470 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -12,30 +12,28 @@ ------------------------------------------------------------------------- */ #include "displace_atoms.h" -#include -#include -#include + #include "atom.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "comm.h" -#include "irregular.h" -#include "group.h" -#include "math_const.h" -#include "random_park.h" -#include "force.h" -#include "input.h" -#include "variable.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "input.h" +#include "irregular.h" +#include "lattice.h" +#include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "random_park.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/domain.cpp b/src/domain.cpp index 81de88d1ee..f54df1f382 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,30 +16,28 @@ ------------------------------------------------------------------------- */ #include "domain.h" -#include -#include -#include -#include -#include "style_region.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "kspace.h" -#include "update.h" -#include "modify.h" +#include "comm.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "region.h" +#include "force.h" +#include "kspace.h" #include "lattice.h" -#include "comm.h" +#include "memory.h" +#include "modify.h" +#include "molecule.h" #include "output.h" +#include "region.h" +#include "style_region.h" #include "thermo.h" #include "universe.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/domain.h b/src/domain.h index 58b935ce01..f3c8026e72 100644 --- a/src/domain.h +++ b/src/domain.h @@ -14,10 +14,10 @@ #ifndef LMP_DOMAIN_H #define LMP_DOMAIN_H +#include "pointers.h" + #include #include -#include -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump.cpp b/src/dump.cpp index 0698a84e81..ecb87b79fd 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -12,21 +12,21 @@ ------------------------------------------------------------------------- */ #include "dump.h" -#include -#include + #include "atom.h" #include "irregular.h" #include "update.h" #include "domain.h" #include "group.h" #include "output.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "compute.h" #include "memory.h" #include "error.h" +#include + using namespace LAMMPS_NS; #if defined(LMP_QSORT) diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 3b0594a2cb..167d88789c 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -12,25 +12,22 @@ ------------------------------------------------------------------------- */ #include "dump_custom.h" -#include -#include -#include + #include "atom.h" -#include "force.h" -#include "domain.h" -#include "region.h" -#include "group.h" -#include "input.h" -#include "modify.h" #include "compute.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_store.h" +#include "group.h" +#include "input.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "region.h" #include "update.h" #include "variable.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index 822bed7832..ed8336eebc 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "dump_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/dump_image.cpp b/src/dump_image.cpp index ea9fb612cb..96a338950b 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "dump_image.h" -#include + #include #include #include @@ -35,7 +35,7 @@ #include "math_extra.h" #include "error.h" #include "memory.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 666a7773bd..6f824e5559 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "dump_local.h" -#include + #include -#include + #include "modify.h" #include "fix.h" #include "compute.h" @@ -24,7 +24,7 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 4966310470..a37341a15c 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index c07b225f9d..dba4fde077 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -30,8 +30,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index d5c1bbef29..08025b8392 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_addforce.h" -#include + #include -#include + #include "atom.h" #include "atom_masks.h" #include "update.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index a8d78f14e7..838d2487b2 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_ave_atom.h" -#include + #include #include "atom.h" #include "update.h" @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index dd753ddc2d..18fb335279 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_chunk.h" -#include -#include + + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 293b7fc296..92a01932e7 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -18,8 +18,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_correlate.h" -#include -#include + + #include #include #include "update.h" @@ -30,8 +30,8 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 091ec19fff..790fb9a1d4 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_histo.h" -#include -#include + + #include #include #include "atom.h" @@ -25,8 +25,8 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 4b86681153..5e93df0313 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -15,7 +15,7 @@ Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ #include "fix_ave_histo_weight.h" -#include + #include #include "fix.h" #include "atom.h" diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 4cc8cc3d3d..e83a3f60f5 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_time.h" -#include -#include + + #include #include #include "update.h" @@ -28,8 +28,8 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index b5b2527e25..7b8dc28cb3 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_aveforce.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 39760e9479..5fd9ef190e 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -18,7 +18,7 @@ #include "fix_box_relax.h" #include #include -#include + #include "atom.h" #include "domain.h" #include "update.h" @@ -29,7 +29,7 @@ #include "compute.h" #include "error.h" #include "math_extra.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 4b12c393cb..190a8bcd7d 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_controller.h" -#include + #include #include "force.h" #include "update.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index d3ceb69ea0..877eac0524 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 5b74b75fcd..25e21c5ee1 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_drag.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 8fb4f0cdfc..360f0d2998 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_dt_reset.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 7dd8c08204..be2a74d81b 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -19,7 +19,7 @@ #include "modify.h" #include "respa.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 82b8311968..88ce2faaad 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_gravity.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index cf39ba61e2..39591cd5f1 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_halt.h" -#include + #include #include -#include + #include "update.h" #include "force.h" #include "input.h" @@ -26,7 +26,7 @@ #include "comm.h" #include "timer.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 7fbdd24b4c..e2eb399322 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_heat.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index dcddad95b2..f42e0a527b 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_indent.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 81c186c703..9d0b5f28f1 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin.h" -#include + #include #include #include "math_extra.h" @@ -38,7 +38,7 @@ #include "memory.h" #include "error.h" #include "group.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index c1056d2b16..4af2ed3961 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_momentum.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index d951a924fe..43415a6ef5 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_neigh_history.h" -#include + #include #include "my_page.h" #include "atom.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 9251ce384e..f4ff71d3a3 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -13,7 +13,7 @@ #include "fix_nph.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index cf2298f5f8..b49eb0c5c5 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -13,7 +13,7 @@ #include "fix_nph_sphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index 6949ead1d6..f6ec24991b 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -13,7 +13,7 @@ #include "fix_npt.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index e38d88fadd..1bd879c786 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -13,7 +13,7 @@ #include "fix_npt_sphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_numdiff.cpp b/src/fix_numdiff.cpp index f6d064b794..145d60e8df 100644 --- a/src/fix_numdiff.cpp +++ b/src/fix_numdiff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_numdiff.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 83a6af5d0c..ed79c6b21b 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_nve_limit.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "modify.h" #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 7868693b69..f7a53cf382 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -13,11 +13,11 @@ #include "fix_nvt.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index ccf7aaecaf..3cc88772d7 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -26,7 +26,7 @@ #include "fix_deform.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 40c3ba19e3..7c4159455f 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -13,11 +13,11 @@ #include "fix_nvt_sphere.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index a430130fe4..a90bf86c56 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -14,7 +14,7 @@ #include "fix_press_berendsen.h" #include #include -#include + #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 8964a9ba82..017ae48925 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_print.h" -#include + #include #include "update.h" #include "input.h" @@ -21,8 +21,8 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 374d0069fd..07108721c4 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_property_atom.h" -#include + #include #include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 305ee0ea26..4f675bf7bf 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_restrain.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 1a3158ed4c..329edbd6ef 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_setforce.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index fef7e2086c..112b675826 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_spring_self.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index 60a1a70037..e18317ba03 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_store_state.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 5016b8c343..ec2965d072 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -13,7 +13,7 @@ #include "fix_temp_berendsen.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "modify.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 5a7b9a04db..cf7e9e9fe2 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -17,7 +17,7 @@ #include "fix_temp_csld.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -31,7 +31,7 @@ #include "compute.h" #include "random_mars.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 72e4dd635d..c620905102 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_temp_csvr.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "compute.h" #include "random_mars.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index e575d72f7f..b5cb9c9a1b 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -13,7 +13,7 @@ #include "fix_temp_rescale.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "modify.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 98fb373075..12e36d890e 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_tmd.h" -#include + #include #include #include "atom.h" @@ -29,8 +29,8 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 48f14f5e2f..8af098d66f 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_vector.h" -#include + #include #include "update.h" #include "force.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 0c343938ab..e2237d074d 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall.h" -#include + #include #include "input.h" #include "variable.h" @@ -23,7 +23,7 @@ #include "respa.h" #include "error.h" #include "force.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index e60b3b4aad..76b2cd11fa 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_region.h" -#include + #include #include #include "atom.h" diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 0c1a45603e..431cc03997 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_deprecated.h" -#include + #include "improper_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index ce0f36539f..096e0c3614 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_hybrid.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index f269f8bf03..11c9257ec9 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/lmptype.h b/src/lmptype.h index e2e7a88a42..e0e081dd12 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -42,10 +42,10 @@ #define __STDC_FORMAT_MACROS #endif -#include -#include -#include -#include +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export // grrr - IBM Power6 does not provide this def in their system header files diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index a858f87910..87aa0bab5f 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_beck.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/pair_born.cpp b/src/pair_born.cpp index ca0ab9a17b..5b0d3a6562 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_born.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 1a6b12a345..e4617b5c4b 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_dsf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 4c51b0bb9f..30fe8fcde9 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 91071fccb1..1abdbcc68b 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 6141205db0..9fac17aede 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_cut.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index d19374b5d9..67c471a5e3 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 2a3def0d4f..2093718245 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_coul_debye.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 2f1a834060..ee124c7f59 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_dsf.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index efe8d46017..f98b84417a 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_coul_streitz.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -30,8 +30,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + #include "potential_file_reader.h" using namespace LAMMPS_NS; diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index e94c4abb73..e3079dcaf6 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 75cb7efcdf..046726892e 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "pair_deprecated.h" -#include + #include "pair_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 613ad90cc3..d0d9b98fc9 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd.h" -#include + #include #include "atom.h" #include "comm.h" @@ -27,7 +27,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 3f3f05f7f5..dd0e144953 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_tstat.h" -#include + #include #include "atom.h" #include "update.h" @@ -21,7 +21,7 @@ #include "comm.h" #include "random_mars.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index d8b8e36b8c..6732296764 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gauss.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 693ed7fa24..0b1882f12b 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -13,7 +13,7 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid.h" -#include + #include #include #include "atom.h" @@ -26,9 +26,9 @@ #include "memory.h" #include "error.h" #include "respa.h" -#include "utils.h" + #include "suffix.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index dc8ac65dd4..e85973ed6a 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -17,7 +17,7 @@ #include "atom.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index c60908e8cf..a4ba3b8585 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj96_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 833c954330..b6c91cafe2 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cubic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace PairLJCubicConstants; diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index fedf029fb8..bd42801f3b 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index a11de35c53..669d48c860 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index 2d4b0bbe98..3ddb898c8f 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_debye.h" -#include + #include #include "atom.h" #include "neigh_list.h" #include "force.h" #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index 2d9368a0ca..952a140039 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_dsf.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index c6fa33f03c..749cc9e6a9 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 1063d05672..3f711e2a15 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index b7e3516ec3..0818c60f31 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 37837b695f..005bc44061 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs_coul_gromacs.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 5c6bc671f9..a53d703b8b 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 14646f19f2..3697208d42 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth_linear.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index f838d96145..7447e143f7 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_mie_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index cbfaccab2c..efcc1aa811 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 4d3702313e..f3dd139b69 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 4aec954c38..1711465ffa 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_table.h" -#include + #include -#include + #include -#include + #include "atom.h" #include "force.h" #include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index fd700e9886..50cc87cf96 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_ufm.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index b746204892..6429492346 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa.h" -#include + #include #include "atom.h" #include "force.h" @@ -20,7 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index d78c156935..68c63c9806 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + // From J.F. Zeigler, J. P. Biersack and U. Littmark, // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index f08d919f83..b34e0b2b82 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_zero.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index afbe9e4189..137c167ab9 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "region_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/tokenizer.h b/src/tokenizer.h index eb19c4421b..2db9870866 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -18,10 +18,11 @@ #ifndef LMP_TOKENIZER_H #define LMP_TOKENIZER_H -#include -#include #include "lmptype.h" -#include + +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export namespace LAMMPS_NS { -- GitLab From 1421817276e3107042e0432b07e69a96b77bec94 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 17:54:29 -0400 Subject: [PATCH 36/75] remove redundant includes --- src/atom.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 6fff15d11f..ccd93401fb 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -14,8 +14,6 @@ #include "atom.h" #include "style_atom.h" -#include "atom_vec.h" -#include "atom_vec_ellipsoid.h" #include "comm.h" #include "compute.h" #include "domain.h" -- GitLab From d5027c125c5df6f73153ad735a64b4c610433637 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 17:54:57 -0400 Subject: [PATCH 37/75] rename fmt() macro to logfmt() to avoid clashes with fmtlib --- lib/awpmd/ivutils/include/logexc.h | 2 +- lib/awpmd/systems/interact/TCP/wpmd.cpp | 22 +- lib/awpmd/systems/interact/TCP/wpmd_split.cpp | 376 +++++++++--------- lib/awpmd/systems/interact/TCP/wpmd_split.h | 4 +- src/USER-AWPMD/pair_awpmd_cut.cpp | 4 +- 5 files changed, 204 insertions(+), 204 deletions(-) diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h index 80942f60bf..7bf6125bc6 100644 --- a/lib/awpmd/ivutils/include/logexc.h +++ b/lib/awpmd/ivutils/include/logexc.h @@ -273,7 +273,7 @@ public: }; /// format a string -const char *fmt(const char *format,...); +const char *logfmt(const char *format,...); /// macros with common usage #define LOGFATAL(code,text,lineinfo) ((lineinfo) ? ::message(vblFATAL,(code)," %s at %s:%d",(text),__FILE__,__LINE__) : \ diff --git a/lib/awpmd/systems/interact/TCP/wpmd.cpp b/lib/awpmd/systems/interact/TCP/wpmd.cpp index 1e53f3141c..660d7c21d7 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd.cpp +++ b/lib/awpmd/systems/interact/TCP/wpmd.cpp @@ -170,7 +170,7 @@ int AWPMD::set_pbc(const Vector_3P pcell, int pbc_){ int AWPMD::set_electrons(int s, int n, Vector_3P x, Vector_3P v, double* w, double* pw, double mass, double *q) { if(s < 0 || s > 1) - return LOGERR(-1,fmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO); norm_matrix_state[s] = NORM_UNDEFINED; nwp[s]=ne[s]=n; @@ -363,20 +363,20 @@ int AWPMD::interaction(int flag, Vector_3P fi, Vector_3P fe_x, //3. inverting the overlap matrix int info=0; if(nes){ - /*FILE *f1=fopen(fmt("matrO_%d.d",s),"wt"); + /*FILE *f1=fopen(logfmt("matrO_%d.d",s),"wt"); fileout(f1,Y[s],"%15g"); fclose(f1);8*/ - + ZPPTRF("L",&nes,Y[s].arr,&info); // analyze return code here if(info<0) - return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); + return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); ZPPTRI("L",&nes,Y[s].arr,&info); if(info<0) - return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); + return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); - - /*f1=fopen(fmt("matrY_%d.d",s),"wt"); + + /*f1=fopen(logfmt("matrY_%d.d",s),"wt"); fileout(f1,Y[s],"%15g"); fclose(f1);*/ } @@ -758,7 +758,7 @@ void AWPMD::norm_factorize(int s) { int nes8 = ne[s]*8, info; DGETRF(&nes8, &nes8, Norm[s].arr, &nes8, &ipiv[0], &info); if(info < 0) - LOGERR(info,fmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); + LOGERR(info,logfmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); norm_matrix_state[s] = NORM_FACTORIZED; } @@ -773,7 +773,7 @@ void AWPMD::norm_invert(int s) { DGETRI(&nes8, Norm[s].arr, &nes8, &ipiv[0], (double*)IDD.arr, &IDD_size, &info); // use IDD for work storage if(info < 0) - LOGERR(info,fmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); + LOGERR(info,logfmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); norm_matrix_state[s] = NORM_INVERTED; } @@ -829,7 +829,7 @@ int AWPMD::step(double dt){ //e gets current electronic coordinates int AWPMD::get_electrons(int spin, Vector_3P x, Vector_3P v, double* w, double* pw, double mass){ if(spin<0 || spin >1) - return -1; // invalid spin: return LOGERR(-1,fmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO); + return -1; // invalid spin: return LOGERR(-1,logfmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO); if(mass<0) mass=me; for(int i=0;i 1) - return LOGERR(-1,fmt("AWPMD_split.set_electrons: invaid spin setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD_split.set_electrons: invaid spin setting (%d)!",s),LINFO); // calculating the total n nvar[s]=0; @@ -68,22 +68,22 @@ int AWPMD_split::set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* norm_matrix_state[s] = NORM_UNDEFINED; ne[s]=nel; wp[s].resize(n); - + split_c[s].resize(n); split_c[s].assign(c,c+n); - - + + nspl[s].resize(nel); nspl[s].assign(splits,splits+nel); partition1[s].clear(); for(int i=0;i0){ // width PBC, keeping the width are within [0,Lextra] w[i]=fmod(w[i],Lextra); @@ -107,7 +107,7 @@ int AWPMD_split::set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* else qe[s].assign(nwp[s],-1); - + return 1; } @@ -121,40 +121,40 @@ void AWPMD_split::eterm_deriv(int ic1,int s1,int c1, int j1,int ic2,int s2, int cdouble ck(split_c[s2][ic2+k2][0],split_c[s2][ic2+k2][1]); int indw1=8*ic1, indw2=8*ic2; int indn1=(nvar[s1]/10)*8+2*ic1, indn2=(nvar[s2]/10)*8+2*ic2; - cdouble part_jk=conj(cj)*ck; + cdouble part_jk=conj(cj)*ck; int M= 1; //(j1==k2 ? 1 : 2); // over a_k_re - E_der[s2][indw2+8*k2]+= M*real(pref*part_jk*(o.da2_re()*v+o.I0*dv_ak)); + E_der[s2][indw2+8*k2]+= M*real(pref*part_jk*(o.da2_re()*v+o.I0*dv_ak)); // over a_k_im - E_der[s2][indw2+8*k2+1]+= M*real(pref*part_jk*(o.da2_im()*v+i_unit*o.I0*dv_ak)); + E_der[s2][indw2+8*k2+1]+= M*real(pref*part_jk*(o.da2_im()*v+i_unit*o.I0*dv_ak)); // over a_j_re - E_der[s1][indw1+8*j1]+= M*real(pref*part_jk*(o.da1_re()*v+o.I0*dv_aj_conj)); + E_der[s1][indw1+8*j1]+= M*real(pref*part_jk*(o.da1_re()*v+o.I0*dv_aj_conj)); // over a_j_im - E_der[s1][indw1+8*j1+1]+= M*real(pref*part_jk*(o.da1_im()*v-i_unit*o.I0*dv_aj_conj)); + E_der[s1][indw1+8*j1+1]+= M*real(pref*part_jk*(o.da1_im()*v-i_unit*o.I0*dv_aj_conj)); for(int i=0;i<3;i++){ // over b_k_re - E_der[s2][indw2+8*k2+2+2*i]+= M*real(pref*part_jk*(o.db2_re(i)*v+o.I0*dv_bk[i])); + E_der[s2][indw2+8*k2+2+2*i]+= M*real(pref*part_jk*(o.db2_re(i)*v+o.I0*dv_bk[i])); // over b_k_im - E_der[s2][indw2+8*k2+2+2*i+1]+= M*real(pref*part_jk*(o.db2_im(i)*v+i_unit*o.I0*dv_bk[i])); + E_der[s2][indw2+8*k2+2+2*i+1]+= M*real(pref*part_jk*(o.db2_im(i)*v+i_unit*o.I0*dv_bk[i])); // over b_j_re - E_der[s1][indw1+8*j1+2+2*i]+= M*real(pref*part_jk*(o.db1_re(i)*v+o.I0*dv_bj_conj[i])); + E_der[s1][indw1+8*j1+2+2*i]+= M*real(pref*part_jk*(o.db1_re(i)*v+o.I0*dv_bj_conj[i])); // over b_j_im - E_der[s1][indw1+8*j1+2+2*i+1]+= M*real(pref*part_jk*(o.db1_im(i)*v-i_unit*o.I0*dv_bj_conj[i])); + E_der[s1][indw1+8*j1+2+2*i+1]+= M*real(pref*part_jk*(o.db1_im(i)*v-i_unit*o.I0*dv_bj_conj[i])); } // over ck_re - E_der[s2][indn2+2*k2]+=M*real(pref*conj(cj)*o.I0*v); + E_der[s2][indn2+2*k2]+=M*real(pref*conj(cj)*o.I0*v); // over ck_im E_der[s2][indn2+2*k2+1]+=M*real(pref*i_unit*conj(cj)*o.I0*v); // over cj_re - E_der[s1][indn1+2*j1]+=M*real(pref*ck*o.I0*v); + E_der[s1][indn1+2*j1]+=M*real(pref*ck*o.I0*v); // over cj_im - E_der[s1][indn1+2*j1+1]+=M*real(-pref*i_unit*ck*o.I0*v); - + E_der[s1][indn1+2*j1+1]+=M*real(-pref*i_unit*ck*o.I0*v); + double t= -M*real(pref*part_jk*o.I0*v); // nonlocal terms: TODO: make a separate global loop for summation of nonlocal terms for(int j=0;j -mu, v -> -v !!! } - - + + for(int k1=j1+1;k1(E_der[s1].begin()+indw1,(double *)&fe_x[iv1+k1],(double *)&fe_p[iv1+k1],&fe_w[iv1+k1],&fe_pw[iv1+k1], 1./one_h); @@ -341,14 +341,14 @@ void AWPMD_split::get_el_forces(int flag, Vector_3P fe_x, ic1+=nspl[s1][c1]; // incrementing block1 wp address iv1+=nspl[s1][c1]; // incrementing global variable address } - } + } } } //e same as interaction, but using Hartee factorization (no antisymmetrization) -int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, +int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, Vector_3P fe_p, double *fe_w, double *fe_pw, Vector_2P fe_c){ - + // resize arrays if needed enum APPROX tmp=HARTREE; swap(tmp,approx); // do not need large matrices @@ -358,39 +358,39 @@ int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, // clearing forces clear_forces(flag,fi,fe_x,fe_p,fe_w,fe_pw,fe_c); // calculate block norms and (optionally) derivatives - calc_norms(flag); + calc_norms(flag); Eee = Ew = 0.; for(int s1=0;s1<2;s1++){ Ee[s1]=0.; Eei[s1]=0.; int ic1=0; // starting index of the wp for current electron - + for(int c1=0;c1 1) - return LOGERR(-1,fmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO); s_add=s; spl_add=0; return ne[s_add]; diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 18704deb0b..d492cd082d 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -237,7 +237,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) etmap[etag[i]].push_back(i); } else - error->all(FLERR,fmt("Invalid spin value (%d) for particle %d !",spin[i],i)); + error->all(FLERR,logfmt("Invalid spin value (%d) for particle %d !",spin[i],i)); } // ion force vector Vector_3 *fi=NULL; @@ -254,7 +254,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) for(size_t k=0;kall(FLERR,fmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i)); + error->all(FLERR,logfmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i)); double m= atom->mass ? atom->mass[type[i]] : force->e_mass; Vector_3 xx=Vector_3(x[i][0],x[i][1],x[i][2]); Vector_3 rv=m*Vector_3(v[i][0],v[i][1],v[i][2]); -- GitLab From 4a10111ceda7f4de0727f3dcefa9d9f0e94522d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:42:19 -0400 Subject: [PATCH 38/75] add iwyu target to CMake configuration --- cmake/CMakeLists.txt | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index cc4c1cc905..8fd862e857 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -249,6 +249,27 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") endif() endif() +####################################### +# add custom target for IWYU analysis +####################################### +set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") +mark_as_advanced(ENABLE_IWYU) +if(ENABLE_IWYU) + find_program(IWYU_EXE NAMES include-what-you-use iwyu) + find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) + if (IWYU_EXE AND IWYU_TOOL) + add_custom_target( + iwyu + ${IWYU_TOOL} -p ${CMAKE_BINARY_DIR} + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMENT "Running IWYU") + add_dependencies(iwyu lammps) + else() + message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" + "and the iwyu-tool/iwyu_tool script installed in your PATH") + endif() +endif() + set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") mark_as_advanced(ENABLE_SANITIZER) set(ENABLE_SANITIZER_VALUES none address leak thread undefined) @@ -293,7 +314,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) endif() endif() - find_package(JPEG QUIET) option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) if(WITH_JPEG) -- GitLab From 5e429b8212dea8f435da1944338f843a66b4e4f8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:42:41 -0400 Subject: [PATCH 39/75] update include conventions and refer to the new CMake build target --- doc/include-file-conventions.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index ea4e07eb59..87b9eba8df 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -93,7 +93,8 @@ Include files should be included in this order: * the header matching the implementation (`some_class.h` for file `some_class.cpp`) * mpi.h (only if needed) * LAMMPS local headers (preferably in alphabetical order) -* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* system and library headers (anything that is using angular brackets; preferably in alphabetical order) +* conditional include statements (i.e. anything bracketed with ifdefs) ### Special Cases and Exceptions @@ -111,12 +112,10 @@ those headers. The [Include What You Use tool](https://include-what-you-use.org/) can be used to provide supporting information about compliance with -the rules listed here. There are some limitations and the IWYU tool -may give incorrect advice. The tools is activated by setting the -CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the -path of the `include-what-you-use` command. When activated, the -tool will be run after each compilation and provide suggestions for -which include files should be added or removed. +the rules listed here. Through setting `-DENABLE_IWYU=on` when running +CMake, a custom build target is added that will enable recording +the compilation commands and then run the `iwyu_tool` using the +recorded compilation commands information when typing `make iwyu`. ## Legacy Code -- GitLab From b741a07a34f22f68c320e3f949d19e76cf092ef3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:43:03 -0400 Subject: [PATCH 40/75] document IWYU analysis custom build target --- doc/src/Build_development.rst | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index cd432dddcb..eebde77b4d 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -28,6 +28,40 @@ variable VERBOSE set to 1: ---------- +.. _iwyu_processing: + +Report missing and unneeded '#include' statements +------------------------------------------------- + +The conventions for how and when to use and order include statements in +LAMMPS are `documented in a separate file `_ +(also included in the source code distribution). To assist with following +these conventions one can use the `Include What You Use tool `_. +This is still under development and for large and complex projects like LAMMPS +there are some false positives, so suggested changes need to be verified manually. +It is recommended to use at least version 0.14, which has much fewer incorrect +reports than earlier versions. + +The necessary steps to generate the report can be enabled via a +CMake variable: + +.. code-block:: bash + + -D ENABLE_IWYU=value # value = no (default) or yes + +This will check if the required binary (include-what-you-use or iwyu) +and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can +be found in the path. The analysis can then be started with: + +.. code-block:: bash + + make iwyu + +This may first run some compilation, as the analysis is dependent +on recording all commands required to do the compilation. + +---------- + .. _sanitizer: Address, Undefined Behavior, and Thread Sanitizer Support -- GitLab From 79584c842dfa99127bc990903dd8cf13a635cc8d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:44:12 -0400 Subject: [PATCH 41/75] add false positive --- doc/utils/sphinx-config/false_positives.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a9f976c3fd..586e14da88 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1355,6 +1355,7 @@ iva Ivanov Ivector Iw +iwyu ixcm ixx Ixx -- GitLab From 4ba6a4f958e2e0cb864e310631a9c3d28b82aa1f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 21:43:20 -0400 Subject: [PATCH 42/75] have clang-style output for easier parsing in compilation mode in emacs --- cmake/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 8fd862e857..1d67bfde37 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -260,7 +260,7 @@ if(ENABLE_IWYU) if (IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu - ${IWYU_TOOL} -p ${CMAKE_BINARY_DIR} + ${IWYU_TOOL} -o clang -p ${CMAKE_BINARY_DIR} WORKING_DIRECTORY ${CMAKE_BINARY_DIR} COMMENT "Running IWYU") add_dependencies(iwyu lammps) -- GitLab From f88f4cd60e22a9e62994602221d38f177042fdb4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 21:44:04 -0400 Subject: [PATCH 43/75] more include file updates --- .../pair_lj_charmm_coul_charmm_intel.cpp | 8 +-- src/atom.cpp | 2 +- src/atom_vec_body.cpp | 2 +- src/atom_vec_hybrid.cpp | 4 +- src/create_atoms.cpp | 30 +++++------ src/create_bonds.cpp | 18 +++---- src/domain.cpp | 5 +- src/dump_local.cpp | 13 ++--- src/dump_movie.cpp | 4 +- src/error.cpp | 13 ++--- src/error.h | 1 - src/finish.cpp | 20 ++++---- src/fix.cpp | 11 ++-- src/fix_addforce.cpp | 15 +++--- src/fix_ave_atom.cpp | 11 ++-- src/fix_ave_correlate.cpp | 15 +++--- src/fix_ave_histo.cpp | 15 +++--- src/fix_ave_time.cpp | 15 +++--- src/fix_aveforce.cpp | 12 ++--- src/fix_controller.cpp | 10 ++-- src/fix_drag.cpp | 10 ++-- src/fix_external.cpp | 9 ++-- src/fix_gravity.cpp | 16 +++--- src/fix_group.cpp | 17 ++++--- src/fix_halt.cpp | 18 +++---- src/fix_indent.cpp | 14 ++--- src/fix_lineforce.cpp | 11 ++-- src/fix_momentum.cpp | 8 +-- src/fix_nh_sphere.cpp | 11 ++-- src/fix_nve_sphere.cpp | 11 ++-- src/fix_planeforce.cpp | 11 ++-- src/fix_print.cpp | 10 ++-- src/fix_read_restart.cpp | 2 +- src/fix_recenter.cpp | 15 +++--- src/fix_respa.cpp | 5 +- src/fix_setforce.cpp | 14 ++--- src/fix_spring.cpp | 13 ++--- src/fix_spring_chunk.cpp | 15 +++--- src/fix_spring_rg.cpp | 11 ++-- src/fix_spring_self.cpp | 10 ++-- src/fix_store.cpp | 7 +-- src/fix_store_state.cpp | 16 +++--- src/fix_vector.cpp | 12 ++--- src/fix_viscous.cpp | 9 ++-- src/fix_wall.cpp | 11 ++-- src/fix_wall_reflect.cpp | 13 ++--- src/fix_wall_region.cpp | 12 ++--- src/force.cpp | 34 ++++++------- src/force.h | 2 +- src/group.cpp | 31 +++++------ src/group.h | 2 +- src/image.cpp | 16 +++--- src/imbalance_group.cpp | 5 +- src/imbalance_neigh.cpp | 10 ++-- src/imbalance_store.cpp | 5 +- src/imbalance_time.cpp | 6 +-- src/imbalance_var.cpp | 10 ++-- src/improper_zero.cpp | 6 +-- src/info.cpp | 32 ++++++------ src/info.h | 2 +- src/input.cpp | 51 +++++++++---------- src/input.h | 2 +- src/irregular.cpp | 9 ++-- src/kspace.cpp | 18 +++---- src/kspace_deprecated.cpp | 3 +- src/lammps.cpp | 15 +++--- 66 files changed, 381 insertions(+), 413 deletions(-) diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index ff8a9869b7..2078e5277b 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -12,19 +12,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_charmm_coul_charmm_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "group.h" #include "memory.h" #include "modify.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" #include "suffix.h" + +#include +#include + using namespace LAMMPS_NS; #define LJ_T typename IntelBuffers::vec4_t diff --git a/src/atom.cpp b/src/atom.cpp index ccd93401fb..864c7af638 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #include "comm.h" #include "compute.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 871f40084d..608c803e20 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom_vec_body.h" -#include "style_body.h" +#include "style_body.h" // IWYU pragma: keep #include "atom.h" #include "body.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 5c37be4aa4..7a8c73570d 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -595,7 +595,7 @@ void AtomVecHybrid::build_styles() nallstyles = 0; #define ATOM_CLASS #define AtomStyle(key,Class) nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS @@ -609,7 +609,7 @@ void AtomVecHybrid::build_styles() allstyles[nallstyles] = new char[n]; \ strcpy(allstyles[nallstyles],#key); \ nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS } diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index b121edb5b2..7e84e9cce0 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -16,31 +16,27 @@ ------------------------------------------------------------------------- */ #include "create_atoms.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" -#include "irregular.h" -#include "modify.h" -#include "force.h" -#include "special.h" #include "domain.h" -#include "lattice.h" -#include "region.h" +#include "error.h" #include "input.h" -#include "variable.h" -#include "random_park.h" -#include "random_mars.h" -#include "math_extra.h" +#include "irregular.h" +#include "lattice.h" #include "math_const.h" -#include "error.h" +#include "math_extra.h" #include "memory.h" +#include "modify.h" +#include "molecule.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "special.h" +#include "variable.h" -#include -#include "utils.h" -#include "fmt/format.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 4261d9f766..9e3eb65801 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -18,21 +18,19 @@ ------------------------------------------------------------------------- */ #include "create_bonds.h" -#include -#include -#include + #include "atom.h" +#include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" -#include "comm.h" #include "group.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "special.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/domain.cpp b/src/domain.cpp index f54df1f382..984c735a20 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "domain.h" +#include "style_region.h" // IWYU pragma: keep #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,6 @@ #include "molecule.h" #include "output.h" #include "region.h" -#include "style_region.h" #include "thermo.h" #include "universe.h" #include "update.h" @@ -106,7 +106,8 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) #define REGION_CLASS #define RegionStyle(key,Class) \ (*region_map)[#key] = ®ion_creator; -#include "style_region.h" +#include "style_region.h" // IWYU pragma: keep + #undef RegionStyle #undef REGION_CLASS } diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 6f824e5559..a71166ec57 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -13,18 +13,15 @@ #include "dump_local.h" -#include - -#include "modify.h" -#include "fix.h" #include "compute.h" #include "domain.h" -#include "update.h" -#include "input.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include using namespace LAMMPS_NS; diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index a37341a15c..5f6d0b80d7 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "dump_movie.h" -#include + #include "comm.h" -#include "force.h" #include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/error.cpp b/src/error.cpp index 7458f816c0..0ea218887f 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -12,16 +12,11 @@ ------------------------------------------------------------------------- */ #include "error.h" -#include -#include -#include -#include -#include "universe.h" -#include "output.h" -#include "input.h" + #include "accelerator_kokkos.h" -#include "utils.h" -#include "fmt/format.h" +#include "input.h" +#include "output.h" +#include "universe.h" #if defined(LAMMPS_EXCEPTIONS) #include "update.h" diff --git a/src/error.h b/src/error.h index 40c1559464..dedebc4148 100644 --- a/src/error.h +++ b/src/error.h @@ -15,7 +15,6 @@ #define LMP_ERROR_H #include "pointers.h" -#include #ifdef LAMMPS_EXCEPTIONS #include "exceptions.h" diff --git a/src/finish.cpp b/src/finish.cpp index 51f886b5db..7990a3c141 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -12,28 +12,26 @@ ------------------------------------------------------------------------- */ #include "finish.h" -#include -#include -#include -#include + #include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" +#include "memory.h" #include "min.h" -#include "neighbor.h" +#include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" #include "timer.h" #include "universe.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include #ifdef LMP_USER_OMP #include "modify.h" diff --git a/src/fix.cpp b/src/fix.cpp index 549208a0ce..03313739a1 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix.h" -#include -#include + #include "atom.h" -#include "group.h" -#include "force.h" #include "atom_masks.h" -#include "memory.h" #include "error.h" +#include "group.h" +#include "memory.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index 08025b8392..0983728ea9 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -13,20 +13,19 @@ #include "fix_addforce.h" -#include - #include "atom.h" #include "atom_masks.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index 838d2487b2..da009c55d5 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -13,17 +13,16 @@ #include "fix_ave_atom.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 92a01932e7..031dfc26bf 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -19,19 +19,16 @@ #include "fix_ave_correlate.h" - -#include -#include -#include "update.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" - +#include "modify.h" +#include "update.h" +#include "variable.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 790fb9a1d4..3a9346498f 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -13,20 +13,17 @@ #include "fix_ave_histo.h" - -#include -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" - +#include "modify.h" +#include "update.h" +#include "variable.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index e83a3f60f5..9c493b9846 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -17,19 +17,16 @@ #include "fix_ave_time.h" - -#include -#include -#include "update.h" -#include "force.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" - +#include "modify.h" +#include "update.h" +#include "variable.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 7b8dc28cb3..00ec0d67ba 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -13,17 +13,17 @@ #include "fix_aveforce.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 190a8bcd7d..92fd42f3db 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -13,14 +13,14 @@ #include "fix_controller.h" -#include -#include "force.h" -#include "update.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 25e21c5ee1..2400014569 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -13,14 +13,14 @@ #include "fix_drag.h" -#include -#include #include "atom.h" -#include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 5d810ff38b..1db7e15295 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_external.h" -#include + #include "atom.h" -#include "update.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "memory.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 88ce2faaad..6dff937385 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -13,18 +13,18 @@ #include "fix_gravity.h" -#include -#include #include "atom.h" -#include "update.h" #include "domain.h" -#include "respa.h" -#include "modify.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "math_const.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 5e2a12c988..bb51fafa12 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -12,20 +12,21 @@ ------------------------------------------------------------------------- */ #include "fix_group.h" -#include -#include "group.h" -#include "update.h" + #include "atom.h" -#include "force.h" #include "comm.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "group.h" +#include "input.h" +#include "memory.h" #include "modify.h" +#include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 39591cd5f1..f8222e3ece 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -13,20 +13,18 @@ #include "fix_halt.h" -#include -#include - -#include "update.h" -#include "force.h" -#include "input.h" -#include "variable.h" #include "atom.h" -#include "neighbor.h" -#include "modify.h" #include "comm.h" -#include "timer.h" #include "error.h" +#include "input.h" +#include "modify.h" +#include "neighbor.h" +#include "timer.h" +#include "update.h" +#include "variable.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index f42e0a527b..ae58f27913 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -17,18 +17,18 @@ #include "fix_indent.h" -#include -#include #include "atom.h" -#include "input.h" -#include "variable.h" #include "domain.h" +#include "error.h" +#include "input.h" #include "lattice.h" -#include "update.h" #include "modify.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 0287c8c0db..cacec13302 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_lineforce.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 4af2ed3961..259099e07c 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -13,13 +13,13 @@ #include "fix_momentum.h" -#include -#include #include "atom.h" #include "domain.h" -#include "group.h" #include "error.h" -#include "force.h" +#include "group.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index 1ff3fc2d4d..d60798e007 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -16,15 +16,16 @@ ------------------------------------------------------------------------- */ #include "fix_nh_sphere.h" -#include -#include + #include "atom.h" -#include "atom_vec.h" +#include "domain.h" #include "error.h" #include "force.h" -#include "domain.h" -#include "math_vector.h" #include "math_extra.h" +#include "math_vector.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index c0fea17c2b..87fba3eca3 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "fix_nve_sphere.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "atom_vec.h" -#include "force.h" #include "error.h" -#include "math_vector.h" +#include "force.h" #include "math_extra.h" +#include "math_vector.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 9434a4b348..2e3bcadd69 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_planeforce.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 017ae48925..78fceea184 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -13,16 +13,14 @@ #include "fix_print.h" -#include -#include "update.h" +#include "error.h" #include "input.h" +#include "memory.h" #include "modify.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" - +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index c1c0150177..2e10b15ffa 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_read_restart.h" + #include "atom.h" #include "memory.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 8997e4b805..3f9eec9ee4 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -16,18 +16,19 @@ ------------------------------------------------------------------------- */ #include "fix_recenter.h" -#include -#include + #include "atom.h" -#include "group.h" -#include "update.h" +#include "comm.h" #include "domain.h" +#include "error.h" +#include "group.h" #include "lattice.h" #include "modify.h" -#include "comm.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 459b30c1b2..b116f8ccac 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_respa.h" -#include + #include "atom.h" -#include "force.h" #include "memory.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 329edbd6ef..229890c5df 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -13,18 +13,18 @@ #include "fix_setforce.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 1bd76f5c55..2d695add26 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -16,14 +16,15 @@ ------------------------------------------------------------------------- */ #include "fix_spring.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" -#include "force.h" -#include "group.h" #include "error.h" +#include "group.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 778a6f0c43..d8de88bd63 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "fix_spring_chunk.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "force.h" -#include "respa.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index e3ba935340..5715e7eb88 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -17,15 +17,16 @@ ------------------------------------------------------------------------- */ #include "fix_spring_rg.h" -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "group.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "group.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 112b675826..8e7b3eb925 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -17,14 +17,14 @@ #include "fix_spring_self.h" -#include #include "atom.h" -#include "update.h" #include "domain.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "memory.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 8ce94fb54a..3eb2075250 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_store.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index e18317ba03..fd4563b7ad 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -13,19 +13,19 @@ #include "fix_store_state.h" -#include #include "atom.h" -#include "domain.h" -#include "update.h" -#include "group.h" -#include "modify.h" #include "compute.h" +#include "domain.h" +#include "error.h" #include "fix.h" +#include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 8af098d66f..6bcdfe948e 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -13,15 +13,15 @@ #include "fix_vector.h" -#include -#include "update.h" -#include "force.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 7d532d832d..08649280d8 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_viscous.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index e2237d074d..cb822f1090 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -13,17 +13,16 @@ #include "fix_wall.h" -#include -#include "input.h" -#include "variable.h" #include "domain.h" +#include "error.h" +#include "input.h" #include "lattice.h" -#include "update.h" #include "modify.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 061083e55c..227ef66564 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect.h" -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "force.h" -#include "lattice.h" +#include "error.h" #include "input.h" +#include "lattice.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 76b2cd11fa..fc3735cfbf 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -13,16 +13,16 @@ #include "fix_wall_region.h" -#include -#include #include "atom.h" #include "domain.h" -#include "region.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" #include "math_const.h" +#include "region.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/force.cpp b/src/force.cpp index 10b82afabe..8eef7a4224 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -12,31 +12,29 @@ ------------------------------------------------------------------------- */ #include "force.h" -#include -#include -#include -#include -#include "style_bond.h" -#include "style_angle.h" -#include "style_dihedral.h" -#include "style_improper.h" -#include "style_pair.h" -#include "style_kspace.h" +#include "style_angle.h" // IWYU pragma: keep +#include "style_bond.h" // IWYU pragma: keep +#include "style_dihedral.h" // IWYU pragma: keep +#include "style_improper.h" // IWYU pragma: keep +#include "style_kspace.h" // IWYU pragma: keep +#include "style_pair.h" // IWYU pragma: keep + +#include "angle.h" #include "atom.h" -#include "comm.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" #include "bond.h" #include "bond_hybrid.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "error.h" #include "improper.h" #include "kspace.h" -#include "error.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "pair_hybrid_overlay.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/force.h b/src/force.h index d7824ea90e..999e9650aa 100644 --- a/src/force.h +++ b/src/force.h @@ -15,8 +15,8 @@ #define LMP_FORCE_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/group.cpp b/src/group.cpp index 2377f028bd..ee96c20f47 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -12,30 +12,27 @@ ------------------------------------------------------------------------- */ #include "group.h" -#include -#include -#include -#include -#include -#include "domain.h" + #include "atom.h" -#include "force.h" #include "comm.h" -#include "region.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "output.h" -#include "input.h" -#include "variable.h" +#include "domain.h" #include "dump.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "input.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "output.h" +#include "region.h" +#include "variable.h" +#include +#include #include +#include using namespace LAMMPS_NS; @@ -538,7 +535,7 @@ void Group::assign(int narg, char **arg) void Group::assign(const std::string &groupcmd) { - std::vector args = utils::split_words(groupcmd); + auto args = utils::split_words(groupcmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { diff --git a/src/group.h b/src/group.h index b9a5c27140..39c446d119 100644 --- a/src/group.h +++ b/src/group.h @@ -15,8 +15,8 @@ #define LMP_GROUP_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/image.cpp b/src/image.cpp index 56d9bc301a..755be587d8 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "image.h" -#include -#include -#include -#include -#include "math_extra.h" -#include "random_mars.h" -#include "math_const.h" + #include "error.h" -#include "force.h" +#include "math_const.h" +#include "math_extra.h" #include "memory.h" +#include "random_mars.h" + +#include +#include +#include #ifdef LAMMPS_JPEG #include diff --git a/src/imbalance_group.cpp b/src/imbalance_group.cpp index 72b1028791..b7be70dd25 100644 --- a/src/imbalance_group.cpp +++ b/src/imbalance_group.cpp @@ -12,12 +12,11 @@ ------------------------------------------------------------------------- */ #include "imbalance_group.h" + #include "atom.h" +#include "error.h" #include "force.h" #include "group.h" -#include "error.h" -#include -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 0beb62bdb4..70d5580b9c 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "imbalance_neigh.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "error.h" -#include "fmt/format.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 919d1f3f61..2661b57b25 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "imbalance_store.h" -#include + #include "atom.h" #include "error.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index 99e549e90e..438728ef3e 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "imbalance_time.h" -#include + #include "atom.h" -#include "force.h" -#include "timer.h" #include "error.h" -#include "fmt/format.h" +#include "timer.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index d1a76ed9f7..a2c940789e 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "imbalance_var.h" -#include -#include + #include "atom.h" +#include "error.h" #include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 11c9257ec9..3da38a890c 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_zero.h" -#include + #include "atom.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include using namespace LAMMPS_NS; diff --git a/src/info.cpp b/src/info.cpp index fbe43442f0..79ba9f7a45 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -17,39 +17,37 @@ ------------------------------------------------------------------------- */ #include "info.h" -#include -#include -#include -#include -#include -#include -#include + #include "accelerator_kokkos.h" +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" #include "compute.h" +#include "dihedral.h" #include "domain.h" #include "dump.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" #include "group.h" +#include "improper.h" #include "input.h" #include "modify.h" #include "neighbor.h" #include "output.h" +#include "pair.h" +#include "pair_hybrid.h" #include "region.h" #include "universe.h" -#include "variable.h" #include "update.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "variable.h" + +#include +#include +#include +#include +#include #ifdef _WIN32 #define PSAPI_VERSION 1 diff --git a/src/info.h b/src/info.h index 5a379eaa78..65690ab28e 100644 --- a/src/info.h +++ b/src/info.h @@ -21,7 +21,7 @@ CommandStyle(info,Info) #define LMP_INFO_H #include "pointers.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/input.cpp b/src/input.cpp index c74232648c..84abaf141f 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -12,45 +12,44 @@ ------------------------------------------------------------------------- */ #include "input.h" -#include -#include -#include -#include -#include -#include -#include -#include "style_command.h" -#include "universe.h" + +#include "accelerator_kokkos.h" +#include "angle.h" #include "atom.h" #include "atom_vec.h" +#include "bond.h" #include "comm.h" #include "comm_brick.h" #include "comm_tiled.h" -#include "group.h" -#include "domain.h" -#include "output.h" -#include "thermo.h" -#include "force.h" -#include "pair.h" -#include "min.h" -#include "modify.h" #include "compute.h" -#include "fix.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "neighbor.h" +#include "output.h" +#include "pair.h" #include "special.h" +#include "style_command.h" +#include "thermo.h" #include "timer.h" +#include "universe.h" +#include "update.h" #include "variable.h" -#include "accelerator_kokkos.h" -#include "error.h" -#include "memory.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include +#include +#include +#include #ifdef _WIN32 #include diff --git a/src/input.h b/src/input.h index 48caa13fde..b8ffb276f9 100644 --- a/src/input.h +++ b/src/input.h @@ -15,8 +15,8 @@ #define LMP_INPUT_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/irregular.cpp b/src/irregular.cpp index 2213b37d55..f6de6947bd 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "irregular.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" -#include "modify.h" +#include "domain.h" #include "fix.h" #include "memory.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; diff --git a/src/kspace.cpp b/src/kspace.cpp index 2485db67b8..e51cc54c97 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -12,21 +12,19 @@ ------------------------------------------------------------------------- */ #include "kspace.h" -#include -#include -#include -#include -#include + #include "atom.h" +#include "atom_masks.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "pair.h" #include "memory.h" -#include "atom_masks.h" -#include "error.h" +#include "pair.h" #include "suffix.h" -#include "domain.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 5dc2b50e2b..16e9ff6abb 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "kspace_deprecated.h" -#include + #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/lammps.cpp b/src/lammps.cpp index ded9d93167..b6c8450a4d 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -12,13 +12,7 @@ ------------------------------------------------------------------------- */ #include "lammps.h" -#include -#include -#include -#include -#include -#include -#include + #include "style_angle.h" // IWYU pragma: keep #include "style_atom.h" // IWYU pragma: keep #include "style_bond.h" // IWYU pragma: keep @@ -54,8 +48,11 @@ #include "version.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include +#include #include "lmpinstalledpkgs.h" #include "lmpgitversion.h" -- GitLab From 203e42073a08aa4e8b9efccd064af3b956b9a508 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:51:14 -0400 Subject: [PATCH 44/75] fix compilation error --- lib/awpmd/ivutils/src/logexc.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/awpmd/ivutils/src/logexc.cpp b/lib/awpmd/ivutils/src/logexc.cpp index d29745fda1..7e82af0f65 100644 --- a/lib/awpmd/ivutils/src/logexc.cpp +++ b/lib/awpmd/ivutils/src/logexc.cpp @@ -16,7 +16,7 @@ message_logger &message_logger::global(){ message_logger *message_logger::glogp=NULL; stdfile_logger default_log("",0,stdout,stderr,vblALLBAD|vblMESS1,vblFATAL,1); -const char *fmt(const char *format,...){ +const char *logfmt(const char *format,...){ va_list args; va_start(args,format); static char buff[1024]; -- GitLab From 71d111ccd9cd355d1a4d6fe3b59510919a12ddd1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:51:30 -0400 Subject: [PATCH 45/75] get rid of 'using namespace std;' --- src/info.cpp | 55 ++++++++++++++++++++++++++-------------------------- 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/src/info.cpp b/src/info.cpp index 79ba9f7a45..87161e9ca5 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -103,6 +103,8 @@ static const int STYLES = ATOM_STYLES | INTEGRATE_STYLES | MINIMIZE_STYLES | DUMP_STYLES | COMMAND_STYLES; } +using namespace LAMMPS_NS; + static const char *varstyles[] = { "index", "loop", "world", "universe", "uloop", "string", "getenv", "file", "atomfile", "format", "equal", "atom", "vector", "python", "internal", "(unknown)"}; @@ -114,17 +116,15 @@ static const char *commlayout[] = { "uniform", "nonuniform", "irregular" }; static const char bstyles[] = "pfsm"; -using namespace LAMMPS_NS; -using namespace std; - template -static void print_columns(FILE* fp, map * styles); +static void print_columns(FILE *fp, std::map *styles); template -static bool find_style(const LAMMPS * lmp, map * styles, const string & name, bool suffix_check); +static bool find_style(const LAMMPS *lmp, std::map *styles, + const std::string &name, bool suffix_check); template -static vector get_style_names(map * styles); +static std::vector get_style_names(std::map *styles); /* ---------------------------------------------------------------------- */ @@ -355,7 +355,7 @@ void Info::command(int narg, char **arg) if (flags & COMM) { int major,minor; - string version = get_mpi_info(major,minor); + std::string version = get_mpi_info(major,minor); fmt::print(out,"\nCommunication information:\n" "MPI library level: MPI v{}.{}\n" @@ -947,7 +947,7 @@ bool Info::is_defined(const char *category, const char *name) return false; } -bool Info::has_style(const string & category, const string & name) +bool Info::has_style(const std::string &category, const std::string &name) { if ( category == "atom" ) { return find_style(lmp, atom->avec_map, name, false); @@ -981,7 +981,7 @@ bool Info::has_style(const string & category, const string & name) return false; } -vector Info::get_available_styles(const string & category) +std::vector Info::get_available_styles(const std::string &category) { if ( category == "atom" ) { return get_style_names(atom->avec_map); @@ -1012,13 +1012,13 @@ vector Info::get_available_styles(const string & category) } else if( category == "command" ) { return get_style_names(input->command_map); } - return vector(); + return std::vector(); } template -static vector get_style_names(map * styles) +static std::vector get_style_names(std::map *styles) { - vector names; + std::vector names; names.reserve(styles->size()); for(auto const& kv : *styles) { @@ -1031,7 +1031,8 @@ static vector get_style_names(map * styles) } template -static bool find_style(const LAMMPS* lmp, map * styles, const string & name, bool suffix_check) +static bool find_style(const LAMMPS *lmp, std::map *styles, + const std::string &name, bool suffix_check) { if (styles->find(name) != styles->end()) { return true; @@ -1039,13 +1040,13 @@ static bool find_style(const LAMMPS* lmp, map * styles, const if (suffix_check && lmp->suffix_enable) { if (lmp->suffix) { - string name_w_suffix = name + "/" + lmp->suffix; + std::string name_w_suffix = name + "/" + lmp->suffix; if (find_style(lmp, styles, name_w_suffix, false)) { return true; } } if (lmp->suffix2) { - string name_w_suffix = name + "/" + lmp->suffix2; + std::string name_w_suffix = name + "/" + lmp->suffix2; if (find_style(lmp, styles, name_w_suffix, false)) { return true; } @@ -1055,7 +1056,7 @@ static bool find_style(const LAMMPS* lmp, map * styles, const } template -static void print_columns(FILE* fp, map * styles) +static void print_columns(FILE *fp, std::map *styles) { if (styles->empty()) { fprintf(fp, "\nNone"); @@ -1064,8 +1065,8 @@ static void print_columns(FILE* fp, map * styles) // std::map keys are already sorted int pos = 80; - for(typename map::iterator it = styles->begin(); it != styles->end(); ++it) { - const string & style_name = it->first; + for(typename std::map::iterator it = styles->begin(); it != styles->end(); ++it) { + const std::string &style_name = it->first; // skip "secret" styles if (isupper(style_name[0])) continue; @@ -1147,9 +1148,9 @@ bool Info::has_package(const char * package_name) { /* ---------------------------------------------------------------------- */ #define _INFOBUF_SIZE 256 -string Info::get_os_info() +std::string Info::get_os_info() { - string buf; + std::string buf; #if defined(_WIN32) DWORD fullversion,majorv,minorv,buildv=0; @@ -1189,9 +1190,9 @@ string Info::get_os_info() return buf; } -string Info::get_compiler_info() +std::string Info::get_compiler_info() { - string buf; + std::string buf; #if __clang__ buf = fmt::format("Clang C++ {}", __VERSION__); #elif __INTEL_COMPILER @@ -1206,7 +1207,7 @@ string Info::get_compiler_info() return buf; } -string Info::get_openmp_info() +std::string Info::get_openmp_info() { #if !defined(_OPENMP) @@ -1241,7 +1242,7 @@ string Info::get_openmp_info() #endif } -string Info::get_mpi_vendor() { +std::string Info::get_mpi_vendor() { #if defined(MPI_STUBS) return "MPI STUBS"; #elif defined(OPEN_MPI) @@ -1261,7 +1262,7 @@ string Info::get_mpi_vendor() { #endif } -string Info::get_mpi_info(int &major, int &minor) +std::string Info::get_mpi_info(int &major, int &minor) { int len; #if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS) @@ -1277,10 +1278,10 @@ string Info::get_mpi_info(int &major, int &minor) char *ptr = strchr(version+80,'\n'); if (ptr) *ptr = '\0'; } - return string(version); + return std::string(version); } -string Info::get_cxx_info() +std::string Info::get_cxx_info() { #if __cplusplus > 201703L return "newer than C++17"; -- GitLab From 7b8fe97a88eadbe8fd32d94ed0f9c043a71fe1c5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:51:42 -0400 Subject: [PATCH 46/75] remove trailing whitespace --- doc/src/Build_development.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index eebde77b4d..bed5f31a13 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -59,7 +59,7 @@ be found in the path. The analysis can then be started with: This may first run some compilation, as the analysis is dependent on recording all commands required to do the compilation. - + ---------- .. _sanitizer: -- GitLab From 45f80f4f067bae3c5b3c05c40b4c78aa61444e2e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:52:22 -0400 Subject: [PATCH 47/75] more include file updates found by iwyu --- src/atom.cpp | 1 + src/body.h | 2 +- src/compute_orientorder_atom.cpp | 1 - src/compute_pressure.cpp | 19 ++++++++-------- src/domain.h | 3 ++- src/lattice.cpp | 16 ++++++-------- src/library.cpp | 38 +++++++++++++++----------------- src/memory.cpp | 3 +-- src/min_cg.cpp | 7 +++--- src/min_fire_old.cpp | 9 ++++---- src/min_hftn.cpp | 9 ++++---- src/min_linesearch.cpp | 9 ++++---- src/min_quickmin.cpp | 9 ++++---- src/min_sd.cpp | 6 +++-- src/minimize.cpp | 8 +++---- src/modify.cpp | 24 ++++++++++---------- src/modify.h | 13 ++++++----- 17 files changed, 92 insertions(+), 85 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 864c7af638..90dce44764 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom.h" +#include "atom_vec.h" #include "style_atom.h" // IWYU pragma: keep #include "comm.h" diff --git a/src/body.h b/src/body.h index 1c742d3e65..c9c289792e 100644 --- a/src/body.h +++ b/src/body.h @@ -15,7 +15,7 @@ #define LMP_BODY_H #include "pointers.h" -#include "atom_vec_body.h" +#include "atom_vec_body.h" // IWYU pragma: keep namespace LAMMPS_NS { diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 84ae20e92a..7323b6ef01 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -36,7 +36,6 @@ using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; #ifdef DBL_EPSILON #define MY_EPSILON (10.0*DBL_EPSILON) diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index b57b53f522..90e4f9b39c 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -13,22 +13,23 @@ #include "compute_pressure.h" -#include +#include "angle.h" #include "atom.h" -#include "update.h" +#include "bond.h" +#include "dihedral.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "error.h" +#include "modify.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/domain.h b/src/domain.h index f3c8026e72..d807463bf3 100644 --- a/src/domain.h +++ b/src/domain.h @@ -20,6 +20,7 @@ #include namespace LAMMPS_NS { + class Region; class Domain : protected Pointers { public: @@ -90,7 +91,7 @@ class Domain : protected Pointers { int nregion; // # of defined Regions int maxregion; // max # list can hold - class Region **regions; // list of defined Regions + Region **regions; // list of defined Regions int copymode; enum{NO_REMAP,X_REMAP,V_REMAP}; diff --git a/src/lattice.cpp b/src/lattice.cpp index f41c32d239..68f3e7abe1 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -12,17 +12,15 @@ ------------------------------------------------------------------------- */ #include "lattice.h" -#include -#include -#include -#include "update.h" -#include "domain.h" + #include "comm.h" -#include "force.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "memory.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/library.cpp b/src/library.cpp index 30d52aefe5..3f37aecd7a 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -16,33 +16,31 @@ #include "library.h" #include -#include -#include -#include -#include -#include "universe.h" -#include "atom_vec.h" + #include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "compute.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "fix.h" +#include "fix_external.h" +#include "force.h" #include "group.h" +#include "info.h" #include "input.h" -#include "variable.h" +#include "memory.h" #include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "output.h" #include "thermo.h" -#include "compute.h" -#include "fix.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "info.h" -#include "fix_external.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" diff --git a/src/memory.cpp b/src/memory.cpp index 6211687a7a..bbbc233bbf 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "memory.h" -#include + #include "error.h" -#include "fmt/format.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) #ifndef LMP_INTEL_NO_TBB diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 46da4bfa5b..511b16cef8 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "min_cg.h" -#include -#include + #include "error.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_fire_old.cpp b/src/min_fire_old.cpp index bd76b2d1fc..6efd00a4b8 100644 --- a/src/min_fire_old.cpp +++ b/src/min_fire_old.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "min_fire_old.h" -#include -#include -#include "universe.h" + #include "atom.h" #include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 63432aab63..909f0b0689 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -18,17 +18,18 @@ ------------------------------------------------------------------------- */ #include "min_hftn.h" -#include -#include -#include + #include "atom.h" #include "error.h" #include "fix_minimize.h" #include "modify.h" #include "output.h" #include "pair.h" -#include "update.h" #include "timer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index a7a10dcd51..7226f61614 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -22,15 +22,16 @@ ------------------------------------------------------------------------- */ #include "min_linesearch.h" -#include -#include + #include "atom.h" -#include "modify.h" #include "fix_minimize.h" -#include "pair.h" +#include "modify.h" #include "output.h" +#include "pair.h" #include "thermo.h" +#include + using namespace LAMMPS_NS; // ALPHA_MAX = max alpha allowed to avoid long backtracks diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 5e7643bf3b..025e80b95d 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "min_quickmin.h" -#include -#include -#include "universe.h" + #include "atom.h" #include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index d973ec1c82..5868acbe48 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -12,11 +12,13 @@ ------------------------------------------------------------------------- */ #include "min_sd.h" -#include + #include "error.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/minimize.cpp b/src/minimize.cpp index 0146390763..451412ecc8 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "minimize.h" + #include "domain.h" -#include "update.h" -#include "min.h" +#include "error.h" #include "finish.h" +#include "min.h" #include "timer.h" -#include "error.h" -#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/modify.cpp b/src/modify.cpp index 96335946ae..c88d52b623 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -12,24 +12,24 @@ ------------------------------------------------------------------------- */ #include "modify.h" -#include -#include #include "style_compute.h" #include "style_fix.h" + #include "atom.h" #include "comm.h" -#include "fix.h" #include "compute.h" -#include "group.h" -#include "update.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "fix.h" +#include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -947,7 +947,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) void Modify::add_fix(const std::string &fixcmd, int trysuffix) { - std::vector args = utils::split_words(fixcmd); + auto args = utils::split_words(fixcmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { @@ -1249,7 +1249,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix) void Modify::add_compute(const std::string &computecmd, int trysuffix) { - std::vector args = utils::split_words(computecmd); + auto args = utils::split_words(computecmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { diff --git a/src/modify.h b/src/modify.h index 05eebc7e14..4c3db0a1b9 100644 --- a/src/modify.h +++ b/src/modify.h @@ -15,11 +15,14 @@ #define LMP_MODIFY_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { + class Compute; + class Fix; + class Modify : protected Pointers { friend class Info; friend class FixSRP; @@ -27,7 +30,6 @@ class Modify : protected Pointers { friend class RespaOMP; public: - int nfix,maxfix; int n_initial_integrate,n_post_integrate,n_pre_exchange; int n_pre_neighbor,n_post_neighbor; int n_pre_force,n_pre_reverse,n_post_force; @@ -41,11 +43,12 @@ class Modify : protected Pointers { int nfix_restart_global; // stored fix global info from restart file int nfix_restart_peratom; // stored fix peratom info from restart file - class Fix **fix; // list of fixes + int nfix,maxfix; + Fix **fix; // list of fixes int *fmask; // bit mask for when each fix is applied - int ncompute,maxcompute; // list of computes - class Compute **compute; + int ncompute,maxcompute; + Compute **compute; // list of computes Modify(class LAMMPS *); virtual ~Modify(); -- GitLab From 047c14d17c055118258013b85b0797d0bac1800e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 23:41:16 -0400 Subject: [PATCH 48/75] tweak iwyu target. generate file with custom mappings --- cmake/CMakeLists.txt | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 1d67bfde37..f541ad7025 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -260,10 +260,14 @@ if(ENABLE_IWYU) if (IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu - ${IWYU_TOOL} -o clang -p ${CMAKE_BINARY_DIR} - WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp COMMENT "Running IWYU") add_dependencies(iwyu lammps) + # generate file with additional mappings + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "[\n") + file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp + " { include: [ \"\", private, \"\", public ] },\n") + file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "]\n") else() message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" "and the iwyu-tool/iwyu_tool script installed in your PATH") -- GitLab From a4a1f7e8484ce075048428ad6dd2f869b49e5efe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 23:42:08 -0400 Subject: [PATCH 49/75] more IWYU cleanup --- src/force.cpp | 2 -- src/force.h | 42 +++++++++++++++++++-------------- src/imbalance_group.cpp | 1 - src/input.cpp | 2 -- src/min.cpp | 32 ++++++++++++------------- src/min_fire.cpp | 17 ++++++------- src/ntopo.cpp | 6 ++--- src/ntopo_angle_all.cpp | 4 ++-- src/ntopo_angle_partial.cpp | 4 ++-- src/ntopo_angle_template.cpp | 4 ++-- src/ntopo_bond_all.cpp | 4 ++-- src/ntopo_bond_partial.cpp | 4 ++-- src/ntopo_bond_template.cpp | 4 ++-- src/ntopo_dihedral_all.cpp | 4 ++-- src/ntopo_dihedral_partial.cpp | 4 ++-- src/ntopo_dihedral_template.cpp | 4 ++-- src/ntopo_improper_all.cpp | 4 ++-- src/ntopo_improper_partial.cpp | 4 ++-- src/ntopo_improper_template.cpp | 4 ++-- src/output.cpp | 28 ++++++++++------------ src/output.h | 6 +++-- src/pair.cpp | 30 +++++++++++------------ src/pair_coul_streitz.cpp | 17 +++++++------ src/pair_hybrid_overlay.cpp | 6 ++--- src/pair_zero.cpp | 3 +-- src/potential_file_reader.cpp | 14 ++++------- src/potential_file_reader.h | 5 ++-- src/procmap.cpp | 16 ++++++------- src/rcb.cpp | 5 ++-- src/read_data.cpp | 33 +++++++++++++------------- src/read_dump.cpp | 19 +++++++-------- src/read_restart.cpp | 33 +++++++++++++------------- src/reader.cpp | 6 ++--- src/reader_native.cpp | 12 ++++++---- src/reader_native.h | 3 +-- src/table_file_reader.cpp | 9 +++---- 36 files changed, 190 insertions(+), 205 deletions(-) diff --git a/src/force.cpp b/src/force.cpp index 8eef7a4224..701113d7ef 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -31,9 +31,7 @@ #include "pair.h" #include "pair_hybrid.h" #include "pair_hybrid_overlay.h" -#include "update.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/force.h b/src/force.h index 999e9650aa..1302e20f12 100644 --- a/src/force.h +++ b/src/force.h @@ -19,6 +19,12 @@ #include namespace LAMMPS_NS { + class Angle; + class Bond; + class Dihedral; + class Improper; + class KSpace; + class Pair; class Force : protected Pointers { public: @@ -47,23 +53,23 @@ class Force : protected Pointers { int newton,newton_pair,newton_bond; // Newton's 3rd law settings - class Pair *pair; + Pair *pair; char *pair_style; char *pair_restart; - class Bond *bond; + Bond *bond; char *bond_style; - class Angle *angle; + Angle *angle; char *angle_style; - class Dihedral *dihedral; + Dihedral *dihedral; char *dihedral_style; - class Improper *improper; + Improper *improper; char *improper_style; - class KSpace *kspace; + KSpace *kspace; char *kspace_style; typedef Pair *(*PairCreator)(LAMMPS *); @@ -102,29 +108,29 @@ class Force : protected Pointers { void setup(); void create_pair(const std::string &, int); - class Pair *new_pair(const std::string &, int, int &); - class Pair *pair_match(const std::string &, int, int nsub=0); + Pair *new_pair(const std::string &, int, int &); + Pair *pair_match(const std::string &, int, int nsub=0); char *pair_match_ptr(Pair *); void create_bond(const std::string &, int); - class Bond *new_bond(const std::string &, int, int &); - class Bond *bond_match(const std::string &); + Bond *new_bond(const std::string &, int, int &); + Bond *bond_match(const std::string &); void create_angle(const std::string &, int); - class Angle *new_angle(const std::string &, int, int &); - class Angle *angle_match(const std::string &); + Angle *new_angle(const std::string &, int, int &); + Angle *angle_match(const std::string &); void create_dihedral(const std::string &, int); - class Dihedral *new_dihedral(const std::string &, int, int &); - class Dihedral *dihedral_match(const std::string &); + Dihedral *new_dihedral(const std::string &, int, int &); + Dihedral *dihedral_match(const std::string &); void create_improper(const std::string &, int); - class Improper *new_improper(const std::string &, int, int &); - class Improper *improper_match(const std::string &); + Improper *new_improper(const std::string &, int, int &); + Improper *improper_match(const std::string &); void create_kspace(const std::string &, int); - class KSpace *new_kspace(const std::string &, int, int &); - class KSpace *kspace_match(const std::string &, int); + KSpace *new_kspace(const std::string &, int, int &); + KSpace *kspace_match(const std::string &, int); void store_style(char *&, const std::string &, int); void set_special(int, char **); diff --git a/src/imbalance_group.cpp b/src/imbalance_group.cpp index b7be70dd25..f604f150b5 100644 --- a/src/imbalance_group.cpp +++ b/src/imbalance_group.cpp @@ -15,7 +15,6 @@ #include "atom.h" #include "error.h" -#include "force.h" #include "group.h" using namespace LAMMPS_NS; diff --git a/src/input.cpp b/src/input.cpp index 84abaf141f..1cb7893871 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -25,7 +25,6 @@ #include "dihedral.h" #include "domain.h" #include "error.h" -#include "fix.h" #include "force.h" #include "group.h" #include "improper.h" @@ -44,7 +43,6 @@ #include "update.h" #include "variable.h" -#include #include #include #include diff --git a/src/min.cpp b/src/min.cpp index 0bf0445525..6bcb4b4e2e 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -20,32 +20,32 @@ ------------------------------------------------------------------------- */ #include "min.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" -#include "fix_minimize.h" #include "compute.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_minimize.h" +#include "force.h" #include "improper.h" #include "kspace.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" #include "timer.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 53bedfbb6c..b7225a1a5a 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -16,21 +16,18 @@ Erik Bitzek, FAU Erlangen-Nuernberg ------------------------------------------------------------------------- */ -#include #include "min_fire.h" -#include "universe.h" + #include "atom.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "variable.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "neighbor.h" -#include "comm.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index ca63b85328..d4ddcc7fc0 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "ntopo.h" -#include + #include "atom.h" -#include "neighbor.h" #include "comm.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 71521e6891..21ac894d92 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index c72073718e..583339ed11 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index d6303a0ad4..17e17ca462 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 9fac01bdba..20ec5aa290 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 138f8f4330..9b5914b2c8 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index a651715320..88a31460d9 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 81193605c1..bcfe8ce712 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 855fa800b6..31a78c5c48 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 06fac50400..0d2a9451e0 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index e839e9161b..53f229a86a 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index c4c6ec3177..8fc619c9e4 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 060ba173fd..bd19d5877c 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/output.cpp b/src/output.cpp index 16d2fa54a0..9b091f89a2 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -12,27 +12,25 @@ ------------------------------------------------------------------------- */ #include "output.h" -#include -#include -#include #include "style_dump.h" + #include "atom.h" -#include "neighbor.h" -#include "input.h" -#include "variable.h" #include "comm.h" -#include "update.h" -#include "group.h" #include "domain.h" -#include "thermo.h" -#include "modify.h" -#include "force.h" #include "dump.h" -#include "write_restart.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "thermo.h" +#include "update.h" +#include "variable.h" +#include "write_restart.h" + +#include using namespace LAMMPS_NS; diff --git a/src/output.h b/src/output.h index 1bf4128ee0..06be7b244a 100644 --- a/src/output.h +++ b/src/output.h @@ -15,11 +15,13 @@ #define LMP_OUTPUT_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { +class Dump; + class Output : protected Pointers { public: bigint next; // next timestep for any kind of output @@ -39,7 +41,7 @@ class Output : protected Pointers { bigint *last_dump; // last timestep each snapshot was output char **var_dump; // variable name for dump frequency int *ivar_dump; // variable index for dump frequency - class Dump **dump; // list of defined Dumps + Dump **dump; // list of defined Dumps int restart_flag; // 1 if any restart files are written int restart_flag_single; // 1 if single restart files are written diff --git a/src/pair.cpp b/src/pair.cpp index e003ef740a..d869bbe8d8 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -16,28 +16,26 @@ ------------------------------------------------------------------------- */ #include "pair.h" -#include -#include // IWYU pragma: keep -#include // IWYU pragma: keep -#include -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "compute.h" -#include "suffix.h" -#include "atom_masks.h" -#include "memory.h" #include "math_const.h" -#include "error.h" +#include "memory.h" +#include "neighbor.h" +#include "suffix.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include // IWYU pragma: keep +#include // IWYU pragma: keep +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index f98b84417a..e538275b3c 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -17,22 +17,21 @@ #include "pair_coul_streitz.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" - - +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index e85973ed6a..34c4cfe418 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid_overlay.h" -#include -#include + #include "atom.h" -#include "force.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index b34e0b2b82..976bb1ba33 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -17,13 +17,12 @@ #include "pair_zero.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index 62658a9ac5..a71d7944d6 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -15,17 +15,13 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "force.h" -#include "error.h" -#include "comm.h" #include "potential_file_reader.h" -#include "update.h" -#include "utils.h" -#include "tokenizer.h" -#include "fmt/format.h" -#include +#include "comm.h" +#include "error.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 9094d3957a..57aa827638 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -18,14 +18,13 @@ #ifndef LMP_POTENTIAL_FILE_READER_H #define LMP_POTENTIAL_FILE_READER_H -#include - #include "pointers.h" #include "tokenizer.h" -#include "text_file_reader.h" namespace LAMMPS_NS { + class TextFileReader; + class PotentialFileReader : protected Pointers { protected: TextFileReader *reader; diff --git a/src/procmap.cpp b/src/procmap.cpp index 1741e351fe..f80af9330e 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -16,18 +16,18 @@ ------------------------------------------------------------------------- */ #include "procmap.h" -#include -#include -#include -#include -#include -#include -#include "universe.h" + #include "comm.h" #include "domain.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" +#include "universe.h" + +#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/rcb.cpp b/src/rcb.cpp index 2cc70a2de9..03c99560b3 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "rcb.h" -#include -#include + #include "irregular.h" #include "memory.h" +#include + using namespace LAMMPS_NS; #define MYHUGE 1.0e30 diff --git a/src/read_data.cpp b/src/read_data.cpp index 7224ac89ea..7cdb768dd2 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -16,34 +16,33 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_data.h" -#include -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "molecule.h" -#include "group.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "domain.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" -#include "special.h" #include "irregular.h" -#include "error.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "molecule.h" +#include "pair.h" +#include "special.h" +#include "update.h" + +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/read_dump.cpp b/src/read_dump.cpp index fbafb4ca84..eb58d3e3ff 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -20,22 +20,19 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_dump.h" -#include -#include -#include -#include "reader.h" -#include "style_reader.h" + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "domain.h" #include "comm.h" -#include "force.h" -#include "irregular.h" +#include "domain.h" #include "error.h" +#include "irregular.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "reader.h" +#include "style_reader.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 157992bce3..dcab9f834c 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -12,31 +12,30 @@ ------------------------------------------------------------------------- */ #include "read_restart.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" +#include "bond.h" #include "comm.h" -#include "irregular.h" -#include "update.h" -#include "modify.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix_read_restart.h" -#include "group.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" +#include "irregular.h" +#include "memory.h" +#include "modify.h" +#include "mpiio.h" +#include "pair.h" #include "special.h" #include "universe.h" -#include "mpiio.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include #include "lmprestart.h" diff --git a/src/reader.cpp b/src/reader.cpp index 2a6e4bf90c..8230fa3ed3 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "reader.h" -#include + #include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 9b93c78000..8ebab4b349 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -12,13 +12,17 @@ ------------------------------------------------------------------------- */ #include "reader_native.h" -#include -#include + #include "atom.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" #include "tokenizer.h" +#include "utils.h" + +#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/reader_native.h b/src/reader_native.h index 6456dc275a..d1c8433016 100644 --- a/src/reader_native.h +++ b/src/reader_native.h @@ -23,9 +23,8 @@ ReaderStyle(native,ReaderNative) #define LMP_READER_NATIVE_H #include "reader.h" -#include + #include -#include namespace LAMMPS_NS { diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index 525db24961..917aea7d49 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -15,14 +15,11 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "error.h" #include "table_file_reader.h" -#include "utils.h" -#include "tokenizer.h" -#include "fmt/format.h" -#include +#include "error.h" +#include "text_file_reader.h" +#include "tokenizer.h" using namespace LAMMPS_NS; -- GitLab From 9925122cea69079293b3bb5789f9c6fdabdc452c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:22:09 -0400 Subject: [PATCH 50/75] more IWYU updates --- src/tokenizer.cpp | 4 +++- src/universe.cpp | 12 +++++------- src/update.cpp | 8 ++++---- src/update.h | 2 +- src/utils.cpp | 12 ++++++------ src/variable.cpp | 43 ++++++++++++++++++++----------------------- src/variable.h | 1 - src/velocity.cpp | 26 +++++++++++++------------- src/verlet.cpp | 24 ++++++++++++------------ src/write_coeff.cpp | 23 +++++++++++------------ src/write_data.h | 1 - src/write_dump.cpp | 11 ++++++----- src/write_restart.cpp | 34 ++++++++++++++++------------------ src/write_restart.h | 1 - 14 files changed, 97 insertions(+), 105 deletions(-) diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index eadff698cb..33a81db748 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -17,7 +17,9 @@ #include "tokenizer.h" #include "utils.h" -#include +#include +#include + #include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/universe.cpp b/src/universe.cpp index e920270c1e..acb5100337 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -12,16 +12,14 @@ ------------------------------------------------------------------------- */ #include "universe.h" -#include -#include -#include -#include -#include "version.h" + #include "error.h" #include "force.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "version.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/update.cpp b/src/update.cpp index a1c712c354..399584473c 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -15,8 +15,8 @@ #include #include "integrate.h" #include "min.h" -#include "style_integrate.h" -#include "style_minimize.h" +#include "style_integrate.h" // IWYU pragma: keep +#include "style_minimize.h" // IWYU pragma: keep #include "neighbor.h" #include "force.h" #include "modify.h" @@ -61,7 +61,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) #define INTEGRATE_CLASS #define IntegrateStyle(key,Class) \ (*integrate_map)[#key] = &integrate_creator; -#include "style_integrate.h" +#include "style_integrate.h" // IWYU pragma: keep #undef IntegrateStyle #undef INTEGRATE_CLASS @@ -70,7 +70,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) #define MINIMIZE_CLASS #define MinimizeStyle(key,Class) \ (*minimize_map)[#key] = &minimize_creator; -#include "style_minimize.h" +#include "style_minimize.h" // IWYU pragma: keep #undef MinimizeStyle #undef MINIMIZE_CLASS diff --git a/src/update.h b/src/update.h index e70325a498..558719f4cc 100644 --- a/src/update.h +++ b/src/update.h @@ -15,8 +15,8 @@ #define LMP_UPDATE_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/utils.cpp b/src/utils.cpp index 45bd629c19..c3a6d1e480 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -12,20 +12,20 @@ ------------------------------------------------------------------------- */ #include "utils.h" -#include -#include -#include -#include "lammps.h" + #include "comm.h" #include "compute.h" #include "error.h" #include "fix.h" #include "memory.h" #include "modify.h" -#include "tokenizer.h" #include "text_file_reader.h" +#include "tokenizer.h" #include "update.h" -#include "fmt/format.h" + +#include +#include +#include #if defined(__linux__) #include // for readlink diff --git a/src/variable.cpp b/src/variable.cpp index d16987984f..8d4416dfa7 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -12,36 +12,33 @@ ------------------------------------------------------------------------- */ #include "variable.h" -#include -#include -#include -#include -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "group.h" -#include "domain.h" #include "comm.h" -#include "region.h" -#include "modify.h" #include "compute.h" -#include "input.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_store.h" -#include "force.h" -#include "output.h" -#include "thermo.h" -#include "random_mars.h" -#include "math_const.h" +#include "group.h" +#include "info.h" +#include "input.h" #include "lmppython.h" +#include "math_const.h" #include "memory.h" -#include "info.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "output.h" +#include "random_mars.h" +#include "region.h" +#include "thermo.h" +#include "universe.h" +#include "update.h" + +#include +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/variable.h b/src/variable.h index f5ea11c0b4..efffacc7bb 100644 --- a/src/variable.h +++ b/src/variable.h @@ -15,7 +15,6 @@ #define LMP_VARIABLE_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 140a396926..eafa98cb7c 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -12,24 +12,24 @@ ------------------------------------------------------------------------- */ #include "velocity.h" -#include -#include + #include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" -#include "force.h" -#include "modify.h" -#include "fix.h" +#include "comm.h" #include "compute.h" #include "compute_temp.h" -#include "random_park.h" +#include "domain.h" +#include "error.h" +#include "fix.h" #include "group.h" -#include "comm.h" +#include "input.h" +#include "lattice.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "random_park.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/verlet.cpp b/src/verlet.cpp index 97c5f918b5..a7b9ba4c22 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -12,26 +12,26 @@ ------------------------------------------------------------------------- */ #include "verlet.h" -#include -#include -#include "neighbor.h" -#include "domain.h" -#include "comm.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" #include "timer.h" -#include "error.h" -#include "fmt/format.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 612f5bb123..121a2ed1fd 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -12,22 +12,21 @@ ------------------------------------------------------------------------- */ #include "write_coeff.h" -#include -#include -#include -#include -#include "pair.h" -#include "bond.h" + #include "angle.h" -#include "dihedral.h" -#include "improper.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "force.h" +#include "improper.h" +#include "pair.h" #include "universe.h" -#include "error.h" -#include "domain.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/write_data.h b/src/write_data.h index e94e7f5595..a4e71c9cda 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -21,7 +21,6 @@ CommandStyle(write_data,WriteData) #define LMP_WRITE_DATA_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 9b257b9ab0..56839a2f5e 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -16,15 +16,16 @@ ------------------------------------------------------------------------- */ #include "write_dump.h" -#include -#include #include "style_dump.h" + +#include "comm.h" #include "dump.h" #include "dump_image.h" -#include "comm.h" -#include "update.h" #include "error.h" -#include "utils.h" +#include "update.h" + +#include + using namespace LAMMPS_NS; diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 22e993c37c..256d7a377e 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -12,32 +12,30 @@ ------------------------------------------------------------------------- */ #include "write_restart.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" -#include "improper.h" -#include "update.h" -#include "neighbor.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "universe.h" -#include "comm.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "memory.h" +#include "modify.h" +#include "mpiio.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" -#include "mpiio.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" + +#include #include "lmprestart.h" diff --git a/src/write_restart.h b/src/write_restart.h index 5056f50636..a4a606482e 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -21,7 +21,6 @@ CommandStyle(write_restart,WriteRestart) #define LMP_WRITE_RESTART_H #include "pointers.h" -#include namespace LAMMPS_NS { -- GitLab From baa79bd1c453a90d1e958cc04105e5782b1fca24 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:22:28 -0400 Subject: [PATCH 51/75] add another iwyu-mapping entry --- cmake/CMakeLists.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f541ad7025..87c70e4483 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -267,6 +267,8 @@ if(ENABLE_IWYU) file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "[\n") file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp " { include: [ \"\", private, \"\", public ] },\n") + file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp + " { include: [ \"\", public, \"\", public ] },\n") file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "]\n") else() message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" -- GitLab From c2cf19bdd49e57398b41b5e9fa5e780b25c69d3d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:32:57 -0400 Subject: [PATCH 52/75] fixes for file readers --- src/MANYBODY/pair_airebo.cpp | 20 ++++++++++---------- src/MANYBODY/pair_bop.cpp | 20 ++++++++++---------- src/MANYBODY/pair_comb3.cpp | 19 +++++++++---------- src/MANYBODY/pair_sw.cpp | 12 ++++++------ src/MANYBODY/pair_tersoff.cpp | 23 +++++++++++------------ 5 files changed, 46 insertions(+), 48 deletions(-) diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 50b5b7d953..7ab2eaa27b 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -21,23 +21,23 @@ ------------------------------------------------------------------------- */ #include "pair_airebo.h" -#include -#include #include "atom.h" -#include "neighbor.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "my_page.h" +#include "error.h" +#include "force.h" #include "math_special.h" #include "memory.h" -#include "error.h" - -#include "tokenizer.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 28389cb59f..cf7268ab62 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -33,22 +33,22 @@ ------------------------------------------------------------------------- */ #include "pair_bop.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index eea2fca927..265d30c6f7 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -19,24 +19,23 @@ #include "pair_comb3.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "my_page.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "group.h" #include "math_const.h" #include "memory.h" -#include "error.h" - -#include "tokenizer.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index da6f7c1623..4e010d816c 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -17,20 +17,20 @@ #include "pair_sw.h" -#include - -#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" - -#include "tokenizer.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 95212b23ab..a654922182 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -17,23 +17,22 @@ #include "pair_tersoff.h" -#include - -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" -#include "potential_file_reader.h" - +#include "force.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; -- GitLab From c7c4297cfc45ececef10a927ad04c29f0e23c582 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:51:58 -0400 Subject: [PATCH 53/75] update include handling for commands --- src/neighbor.cpp | 47 +++++++++++++++++++-------------------- src/read_data.cpp | 1 - src/reader_native.cpp | 2 -- src/reader_xyz.cpp | 5 +++-- src/region.cpp | 15 +++++++------ src/region_block.cpp | 7 +++--- src/region_cone.cpp | 7 +++--- src/region_cylinder.cpp | 11 ++++----- src/region_intersect.cpp | 5 +++-- src/region_plane.cpp | 5 +++-- src/region_prism.cpp | 7 +++--- src/region_sphere.cpp | 11 ++++----- src/region_union.cpp | 5 +++-- src/replicate.cpp | 16 ++++++------- src/rerun.cpp | 13 ++++++----- src/reset_atom_ids.cpp | 16 ++++++------- src/reset_mol_ids.cpp | 12 +++++----- src/respa.cpp | 29 ++++++++++++------------ src/run.cpp | 13 ++++++----- src/set.cpp | 28 +++++++++++------------ src/special.cpp | 12 +++++----- src/table_file_reader.cpp | 1 - src/text_file_reader.cpp | 9 +++----- src/text_file_reader.h | 2 +- src/thermo.cpp | 41 +++++++++++++++++----------------- src/write_data.cpp | 28 +++++++++++------------ 26 files changed, 170 insertions(+), 178 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index c9b16f67a0..66ab92496a 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -16,38 +16,37 @@ ------------------------------------------------------------------------- */ #include "neighbor.h" -#include -#include -#include + +#include "atom.h" +#include "atom_vec.h" +#include "citeme.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "nbin.h" #include "neigh_list.h" #include "neigh_request.h" -#include "nbin.h" -#include "nstencil.h" #include "npair.h" +#include "nstencil.h" #include "ntopo.h" +#include "output.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "respa.h" #include "style_nbin.h" -#include "style_nstencil.h" #include "style_npair.h" +#include "style_nstencil.h" #include "style_ntopo.h" -#include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" #include "update.h" -#include "respa.h" -#include "output.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/read_data.cpp b/src/read_data.cpp index 7cdb768dd2..2a6801b3a5 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -40,7 +40,6 @@ #include "special.h" #include "update.h" -#include #include #include diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 8ebab4b349..8931c569ff 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -17,10 +17,8 @@ #include "error.h" #include "memory.h" #include "tokenizer.h" -#include "utils.h" #include -#include #include #include diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index ad8cb0cc6e..5350e01117 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "reader_xyz.h" -#include + #include "memory.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region.cpp b/src/region.cpp index 8a6ec3305a..15b6fee272 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -12,16 +12,17 @@ ------------------------------------------------------------------------- */ #include "region.h" -#include -#include -#include "update.h" + #include "domain.h" -#include "lattice.h" +#include "error.h" #include "input.h" -#include "variable.h" +#include "lattice.h" #include "math_extra.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_block.cpp b/src/region_block.cpp index e06c05d1a7..2204f2e6a4 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "region_block.h" -#include -#include "force.h" + #include "domain.h" -#include "math_extra.h" #include "error.h" +#include "math_extra.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 400fb07229..d669008e93 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include "region_cone.h" -#include -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index dc1584a96b..f7676a3d74 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "region_cylinder.h" -#include -#include -#include "update.h" + #include "domain.h" +#include "error.h" #include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 4096657d30..a61e2556b0 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "region_intersect.h" -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_plane.cpp b/src/region_plane.cpp index bf12f3cd91..4895c1f081 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -12,9 +12,10 @@ ------------------------------------------------------------------------- */ #include "region_plane.h" -#include + #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 5d7c5bce1f..af270cc47f 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include "region_prism.h" -#include + #include "domain.h" -#include "force.h" -#include "math_extra.h" #include "error.h" +#include "math_extra.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 44db951fde..4256af4213 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "region_sphere.h" -#include -#include -#include "update.h" + +#include "error.h" #include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_union.cpp b/src/region_union.cpp index 30f563df2c..677f1022f9 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "region_union.h" -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/replicate.cpp b/src/replicate.cpp index 9c915d08c0..374d7113b2 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -12,19 +12,17 @@ ------------------------------------------------------------------------- */ #include "replicate.h" -#include -#include + +#include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "domain.h" #include "comm.h" -#include "special.h" -#include "accelerator_kokkos.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "memory.h" +#include "special.h" + +#include using namespace LAMMPS_NS; diff --git a/src/rerun.cpp b/src/rerun.cpp index a63fd1ea55..51c0f6fdb2 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "rerun.h" -#include -#include "read_dump.h" + #include "domain.h" -#include "update.h" +#include "error.h" +#include "finish.h" #include "integrate.h" #include "modify.h" #include "output.h" -#include "finish.h" +#include "read_dump.h" #include "timer.h" -#include "error.h" -#include "force.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp index 526de60cba..0b7cf9879f 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atom_ids.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ #include "reset_atom_ids.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" -#include "modify.h" +#include "domain.h" +#include "error.h" #include "fix.h" -#include "special.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "special.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index a6cfb69185..0d9fe55e07 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -16,17 +16,15 @@ ------------------------------------------------------------------------- */ #include "reset_mol_ids.h" -#include + #include "atom.h" -#include "domain.h" #include "comm.h" -#include "group.h" -#include "modify.h" -#include "compute_fragment_atom.h" #include "compute_chunk_atom.h" -#include "utils.h" +#include "compute_fragment_atom.h" +#include "domain.h" #include "error.h" -#include "fmt/format.h" +#include "group.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/respa.cpp b/src/respa.cpp index 1dcc4b898a..c970c63a19 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -16,30 +16,29 @@ ------------------------------------------------------------------------- */ #include "respa.h" -#include -#include -#include "neighbor.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix.h" +#include "fix_respa.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" -#include "fix_respa.h" -#include "timer.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" #include "pair_hybrid.h" -#include "fmt/format.h" +#include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/run.cpp b/src/run.cpp index 91e2db5c6b..166955d6ac 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "run.h" -#include + #include "domain.h" -#include "update.h" -#include "force.h" +#include "error.h" +#include "finish.h" +#include "input.h" #include "integrate.h" #include "modify.h" #include "output.h" -#include "finish.h" -#include "input.h" #include "timer.h" -#include "error.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/set.cpp b/src/set.cpp index b4a82e5c72..3b2cd44ad0 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -12,32 +12,30 @@ ------------------------------------------------------------------------- */ #include "set.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" -#include "domain.h" -#include "region.h" -#include "group.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" +#include "group.h" #include "input.h" -#include "variable.h" -#include "random_park.h" -#include "random_mars.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" #include "modify.h" -#include "utils.h" -#include "fmt/format.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/special.cpp b/src/special.cpp index 3780fab5c0..eb74f534f7 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -12,18 +12,16 @@ ------------------------------------------------------------------------- */ #include "special.h" -#include + +#include "accelerator_kokkos.h" // IWYU pragma: export #include "atom.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "force.h" #include "comm.h" -#include "modify.h" #include "fix.h" -#include "accelerator_kokkos.h" // IWYU pragma: export -#include "atom_masks.h" +#include "force.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index 917aea7d49..50843c119e 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -17,7 +17,6 @@ #include "table_file_reader.h" -#include "error.h" #include "text_file_reader.h" #include "tokenizer.h" diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 1e1e5e2ec1..3c63bba5fb 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -15,14 +15,11 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "force.h" -#include "error.h" -#include "comm.h" -#include "utils.h" #include "text_file_reader.h" -#include "tokenizer.h" + #include "fmt/format.h" +#include "tokenizer.h" +#include "utils.h" #include diff --git a/src/text_file_reader.h b/src/text_file_reader.h index b64407701f..e74a285961 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -19,8 +19,8 @@ #define LMP_TEXT_FILE_READER_H #include -#include #include + #include "tokenizer.h" namespace LAMMPS_NS diff --git a/src/thermo.cpp b/src/thermo.cpp index 96de72b4ab..787b0cdda8 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -16,37 +16,36 @@ // before lmptype.h can set flags to insure it is done correctly #include "thermo.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" -#include "update.h" +#include "bond.h" #include "comm.h" +#include "compute.h" +#include "dihedral.h" #include "domain.h" -#include "universe.h" -#include "lattice.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "neighbor.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" +#include "input.h" #include "kspace.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "utils.h" -#include "fmt/format.h" #include "tokenizer.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/write_data.cpp b/src/write_data.cpp index d549d8bf77..53d277b723 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -12,29 +12,27 @@ ------------------------------------------------------------------------- */ #include "write_data.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "improper.h" -#include "update.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "domain.h" -#include "universe.h" -#include "comm.h" #include "output.h" +#include "pair.h" #include "thermo.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; -- GitLab From 55704368d0f0ccc785579b574707cfd1d9c6a57e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 01:45:05 -0400 Subject: [PATCH 54/75] include updates for commonly used packages --- src/BODY/body_nparticle.cpp | 15 ++++++------ src/BODY/body_rounded_polygon.cpp | 14 +++++------ src/BODY/body_rounded_polyhedron.cpp | 15 ++++++------ src/BODY/compute_body_local.cpp | 8 +++---- src/COLLOID/fix_wall_colloid.cpp | 1 - src/COMPRESS/dump_atom_zstd.cpp | 4 ++-- src/COMPRESS/dump_cfg_zstd.cpp | 6 ++--- src/COMPRESS/dump_custom_zstd.cpp | 4 ++-- src/COMPRESS/dump_xyz_zstd.cpp | 3 +-- src/DIPOLE/atom_vec_dipole.cpp | 9 ++----- src/KSPACE/ewald.cpp | 14 +++++------ src/KSPACE/ewald_dipole.cpp | 16 ++++++------- src/KSPACE/ewald_dipole_spin.cpp | 16 ++++++------- src/KSPACE/ewald_disp.cpp | 22 ++++++++--------- src/KSPACE/fft3d_wrap.cpp | 2 +- src/KSPACE/fix_tune_kspace.cpp | 18 +++++++------- src/KSPACE/gridcomm.cpp | 6 ++--- src/KSPACE/msm.cpp | 18 +++++++------- src/KSPACE/pppm.cpp | 27 ++++++++++----------- src/KSPACE/pppm_cg.cpp | 16 ++++++------- src/KSPACE/pppm_dipole_spin.cpp | 17 ++++++------- src/KSPACE/pppm_disp.cpp | 26 ++++++++++---------- src/KSPACE/remap_wrap.cpp | 2 +- src/MANYBODY/pair_bop.cpp | 1 - src/MANYBODY/pair_eam_alloy.cpp | 9 ++++--- src/MANYBODY/pair_eam_fs.cpp | 9 ++++--- src/MANYBODY/pair_eim.cpp | 14 +++++------ src/MANYBODY/pair_gw_zbl.cpp | 17 ++++++------- src/MANYBODY/pair_sw.cpp | 1 - src/MANYBODY/pair_tersoff.cpp | 1 - src/MANYBODY/pair_tersoff_mod.cpp | 13 ++++------ src/MANYBODY/pair_tersoff_mod_c.cpp | 13 ++++------ src/MANYBODY/pair_tersoff_zbl.cpp | 15 +++++------- src/MC/fix_widom.cpp | 36 +++++++++++++--------------- src/MC/pair_dsmc.cpp | 10 ++++---- src/MISC/fix_deposit.cpp | 21 ++++++++-------- src/MISC/fix_oneway.cpp | 5 ++-- src/MISC/fix_orient_bcc.cpp | 22 +++++++---------- src/MISC/fix_viscosity.cpp | 8 +++---- src/MLIAP/mliap_data.cpp | 21 +++++----------- src/MLIAP/mliap_descriptor.cpp | 5 ---- src/reader_native.cpp | 1 - 42 files changed, 214 insertions(+), 287 deletions(-) diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index a99c025e1f..e63d50f814 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -12,16 +12,15 @@ ------------------------------------------------------------------------- */ #include "body_nparticle.h" -#include -#include -#include "my_pool_chunk.h" -#include "math_extra.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" -#include "memory.h" +#include "atom_vec_body.h" #include "error.h" -#include "fmt/format.h" +#include "math_extra.h" +#include "memory.h" +#include "my_pool_chunk.h" + +#include using namespace LAMMPS_NS; diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 349ad957c2..c43484dca2 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polygon.h" -#include -#include -#include "my_pool_chunk.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" +#include "atom_vec_body.h" #include "domain.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "my_pool_chunk.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index cb84517b6f..18fd65c1dd 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polyhedron.h" -#include -#include -#include -#include "my_pool_chunk.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" +#include "atom_vec_body.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "my_pool_chunk.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 861ffbe4a7..cf570d71a3 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -13,14 +13,14 @@ #include "compute_body_local.h" -#include #include "atom.h" #include "atom_vec_body.h" #include "body.h" -#include "update.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 61b52a6585..ef5bfb72e1 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -19,7 +19,6 @@ #include #include "atom.h" -#include "atom_vec.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index a993f58809..8fb08db3c8 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -17,12 +17,12 @@ #ifdef LAMMPS_ZSTD -#include "dump_atom_zstd.h" #include "domain.h" +#include "dump_atom_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 51819772f6..5948a3f83e 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #ifdef LAMMPS_ZSTD -#include "dump_cfg_zstd.h" + #include "atom.h" #include "domain.h" +#include "dump_cfg_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include - using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index d0f5335813..c7ede3b38c 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -17,12 +17,12 @@ #ifdef LAMMPS_ZSTD -#include "dump_custom_zstd.h" #include "domain.h" +#include "dump_custom_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 839e743654..eb0600f34b 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -19,12 +19,11 @@ #include "dump_xyz_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) : diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 66de360f6e..4193b5c6a8 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -12,15 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_dipole.h" -#include + #include "atom.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "memory.h" -#include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 4aa95318db..6133df398f 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -19,19 +19,17 @@ ------------------------------------------------------------------------- */ #include "ewald.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "pair.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 1921b8dc55..33d21b416e 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "ewald_dipole.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index bdbb737de8..94cacd3a75 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -16,21 +16,19 @@ ------------------------------------------------------------------------- */ #include "ewald_dipole_spin.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index b616b2ae5d..546ac472c9 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -16,23 +16,21 @@ ------------------------------------------------------------------------- */ #include "ewald_disp.h" -#include -#include -#include -#include -#include "math_vector.h" -#include "math_const.h" -#include "math_special.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_special.h" +#include "math_vector.h" +#include "memory.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index 507b23d27d..d0e3a2b50c 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fft3d_wrap.h" -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 3288f15ff7..c205f9de05 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -16,24 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_tune_kspace.h" -#include -#include -#include #include "comm.h" -#include "update.h" +#include "compute.h" +#include "error.h" #include "force.h" #include "info.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "pair.h" -#include "error.h" -#include "memory.h" #include "timer.h" -#include "neighbor.h" -#include "modify.h" -#include "compute.h" - +#include "update.h" +#include +#include +#include #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index 4024670b9f..0f899d31cf 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "gridcomm.h" -#include + #include "comm.h" -#include "kspace.h" +#include "error.h" #include "irregular.h" +#include "kspace.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 00bdac53db..d0f4d38686 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "msm.h" -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "gridcomm.h" +#include "math_const.h" +#include "memory.h" #include "neighbor.h" -#include "force.h" #include "pair.h" -#include "domain.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 9ce8ded7dd..41ffec4f3b 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -19,28 +19,25 @@ ------------------------------------------------------------------------- */ #include "pppm.h" -#include -#include -#include -#include + +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" #include "gridcomm.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" #include "neighbor.h" -#include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" -#include "domain.h" -#include "fft3d_wrap.h" #include "remap_wrap.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" -#include "math_special.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index fa5235d6eb..b319014c78 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -16,20 +16,18 @@ ------------------------------------------------------------------------- */ #include "pppm_cg.h" -#include -#include -#include + #include "atom.h" -#include "gridcomm.h" #include "domain.h" #include "error.h" -#include "force.h" -#include "neighbor.h" -#include "memory.h" +#include "gridcomm.h" #include "math_const.h" +#include "memory.h" +#include "neighbor.h" #include "remap.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 4e33c11793..595c257331 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -16,22 +16,19 @@ ------------------------------------------------------------------------- */ #include "pppm_dipole_spin.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "gridcomm.h" +#include "math_const.h" +#include "memory.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index fba3f27938..a484751a81 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -17,26 +17,24 @@ ------------------------------------------------------------------------- */ #include "pppm_disp.h" -#include -#include -#include -#include -#include "math_const.h" + +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" #include "gridcomm.h" +#include "math_const.h" +#include "memory.h" #include "neighbor.h" -#include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" -#include "domain.h" -#include "fft3d_wrap.h" #include "remap_wrap.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 7929cd053c..4aaaa1329e 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "remap_wrap.h" -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index cf7268ab62..e7c2f64672 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -46,7 +46,6 @@ #include "text_file_reader.h" #include "tokenizer.h" -#include #include #include diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 193134c24c..d30f46aa36 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -17,15 +17,14 @@ #include "pair_eam_alloy.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 78d7f4646d..dd45d12da3 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -17,15 +17,14 @@ #include "pair_eam_fs.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index a17947b7fe..cb5a95faa2 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -17,19 +17,17 @@ #include "pair_eim.h" -#include -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" - +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include "tokenizer.h" -#include "potential_file_reader.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index dc33ab20a9..ee3bebda13 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -18,20 +18,17 @@ #include "pair_gw_zbl.h" -#include - -#include -#include "atom.h" -#include "update.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "math_const.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include -#include "math_const.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 4e010d816c..2deb45ac75 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -26,7 +26,6 @@ #include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" -#include "text_file_reader.h" #include "tokenizer.h" #include diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index a654922182..c08c722e5f 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -28,7 +28,6 @@ #include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" -#include "text_file_reader.h" #include "tokenizer.h" #include diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index b02545fb2b..ea40125ce4 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -18,19 +18,16 @@ #include "pair_tersoff_mod.h" -#include - -#include -#include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" - -#include "tokenizer.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 325e9ac677..6a6497afae 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -17,17 +17,14 @@ #include "pair_tersoff_mod_c.h" -#include - -#include -#include "atom.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 4c967b4ebb..fad89195b2 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -18,20 +18,17 @@ #include "pair_tersoff_zbl.h" -#include - -#include -#include "atom.h" -#include "update.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" #include "math_const.h" #include "math_special.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index a87ead64a7..d7fdf69b86 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -15,38 +15,36 @@ Contributing author: Evangelos Voyiatzis (Royal DSM) ------------------------------------------------------------------------- */ -#include - -#include #include "fix_widom.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_hybrid.h" -#include "molecule.h" -#include "update.h" -#include "modify.h" -#include "fix.h" +#include "bond.h" #include "comm.h" #include "compute.h" -#include "group.h" +#include "dihedral.h" #include "domain.h" -#include "region.h" -#include "random_park.h" +#include "error.h" +#include "fix.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "thermo.h" -#include "output.h" +#include "modify.h" +#include "molecule.h" #include "neighbor.h" -#include +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace std; using namespace LAMMPS_NS; diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index c00f5dcbff..588d57f324 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -17,18 +17,16 @@ #include "pair_dsmc.h" -#include -#include #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "domain.h" -#include "update.h" #include "random_mars.h" +#include "update.h" - +#include using namespace LAMMPS_NS; diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 32e836f31d..7ee6fce1b9 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -13,25 +13,24 @@ #include "fix_deposit.h" -#include -#include #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix.h" #include "lattice.h" -#include "region.h" -#include "random_park.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "molecule.h" +#include "random_park.h" +#include "region.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index d2bef7cb9b..1ca24a5906 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_oneway.h" -#include + #include "atom.h" #include "domain.h" #include "error.h" -#include "force.h" #include "region.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index ab9a921d3e..cc22a509ba 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -19,25 +19,21 @@ ------------------------------------------------------------------------- */ #include "fix_orient_bcc.h" -#include -#include - - #include "atom.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "citeme.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "math_const.h" -#include "citeme.h" #include "memory.h" -#include "error.h" - +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 9c021c5ca8..5dcd2d291d 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -18,13 +18,13 @@ #include "fix_viscosity.h" -#include -#include #include "atom.h" #include "domain.h" -#include "modify.h" #include "error.h" -#include "force.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MLIAP/mliap_data.cpp b/src/MLIAP/mliap_data.cpp index 7bffd8ec3b..28f9a988d8 100644 --- a/src/MLIAP/mliap_data.cpp +++ b/src/MLIAP/mliap_data.cpp @@ -11,24 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "mliap_data.h" -#include "mliap_model_linear.h" -#include "mliap_model_quadratic.h" -#include "mliap_descriptor_snap.h" -#include "compute_mliap.h" + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" #include "memory.h" -#include "error.h" +#include "mliap_descriptor.h" +#include "mliap_model.h" +#include "neigh_list.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_descriptor.cpp b/src/MLIAP/mliap_descriptor.cpp index d654b33008..63d4241e01 100644 --- a/src/MLIAP/mliap_descriptor.cpp +++ b/src/MLIAP/mliap_descriptor.cpp @@ -12,14 +12,9 @@ ------------------------------------------------------------------------- */ #include "mliap_descriptor.h" -#include "atom.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -#define MAXLINE 1024 -#define MAXWORD 3 /* ---------------------------------------------------------------------- */ diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 8931c569ff..19e53f3efe 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -20,7 +20,6 @@ #include #include -#include using namespace LAMMPS_NS; -- GitLab From 88ddfa4eb05d20786204c58a5ce43228881046b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 04:39:23 -0400 Subject: [PATCH 55/75] more IWYU cleanup in packages --- src/KIM/kim_init.cpp | 21 ++-- src/KIM/kim_interactions.cpp | 19 ++-- src/KIM/kim_param.cpp | 15 ++- src/KIM/kim_property.cpp | 15 +-- src/KIM/kim_query.cpp | 14 +-- src/KIM/kim_units.cpp | 2 + src/KIM/pair_kim.h | 1 - src/MLIAP/mliap_descriptor_snap.cpp | 19 ++-- src/MLIAP/mliap_model.cpp | 12 +- src/MLIAP/mliap_model_linear.h | 2 +- src/MLIAP/pair_mliap.cpp | 16 +-- src/MOLECULE/atom_vec_template.cpp | 9 +- src/MPIIO/dump_cfg_mpiio.cpp | 5 +- src/MPIIO/restart_mpiio.cpp | 3 +- src/PERI/atom_vec_peri.cpp | 7 +- src/PERI/pair_peri_eps.cpp | 20 ++-- src/PERI/pair_peri_lps.cpp | 19 ++-- src/PERI/pair_peri_pmb.cpp | 19 ++-- src/PERI/pair_peri_ves.cpp | 19 ++-- src/PYTHON/fix_python_invoke.cpp | 9 +- src/PYTHON/fix_python_move.cpp | 8 +- src/PYTHON/pair_python.cpp | 11 +- src/PYTHON/python_compat.h | 2 + src/PYTHON/python_impl.cpp | 14 +-- src/REPLICA/compute_event_displace.cpp | 8 +- src/REPLICA/fix_event_hyper.cpp | 1 + src/REPLICA/fix_neb.cpp | 19 ++-- src/REPLICA/hyper.cpp | 29 +++-- src/REPLICA/neb.cpp | 28 +++-- src/REPLICA/prd.cpp | 35 +++--- src/REPLICA/tad.cpp | 28 ++--- src/REPLICA/temper.cpp | 23 ++-- src/USER-CGDNA/bond_oxrna2_fene.cpp | 2 - src/USER-CGDNA/fix_nve_dotc_langevin.cpp | 13 ++- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 15 ++- src/USER-CGDNA/pair_oxdna2_dh.cpp | 13 +-- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 15 ++- src/USER-CGDNA/pair_oxdna_excv.cpp | 15 ++- src/USER-CGDNA/pair_oxdna_hbond.cpp | 15 ++- src/USER-CGDNA/pair_oxdna_xstk.cpp | 15 ++- src/USER-CGDNA/pair_oxrna2_excv.cpp | 4 +- src/USER-CGDNA/pair_oxrna2_stk.cpp | 22 ++-- src/USER-CGDNA/pair_oxrna2_xstk.cpp | 15 ++- src/USER-CGSDK/pair_lj_sdk.h | 1 - src/USER-MEAMC/meam_dens_init.cpp | 6 +- src/USER-MEAMC/meam_force.cpp | 5 +- src/USER-MEAMC/meam_funcs.cpp | 2 + src/USER-MEAMC/meam_impl.cpp | 4 +- src/USER-MEAMC/meam_setup_done.cpp | 6 +- src/USER-MEAMC/meam_setup_global.cpp | 2 + src/USER-MEAMC/meam_setup_param.cpp | 5 + src/USER-MISC/bond_special.cpp | 12 +- src/USER-MISC/bond_special.h | 1 - src/USER-MISC/compute_hma.cpp | 31 +++--- src/USER-MISC/compute_viscosity_cos.cpp | 5 +- src/USER-MISC/dihedral_spherical.cpp | 9 +- src/USER-MISC/dihedral_table.cpp | 105 ++++++------------ src/USER-MISC/fix_accelerate_cos.cpp | 8 +- src/USER-MISC/fix_ave_correlate_long.cpp | 19 ++-- src/USER-MISC/fix_electron_stopping.cpp | 19 ++-- src/USER-MISC/fix_flow_gauss.cpp | 10 +- src/USER-MISC/fix_imd.cpp | 7 +- src/USER-MISC/fix_momentum_chunk.cpp | 7 +- src/USER-MISC/fix_orient_eco.cpp | 6 +- src/USER-MISC/fix_pafi.cpp | 85 ++++++-------- src/USER-MISC/fix_propel_self.cpp | 16 +-- src/USER-MISC/fix_rhok.cpp | 11 +- src/USER-MISC/fix_smd.cpp | 10 +- src/USER-MISC/fix_srp.cpp | 16 +-- src/USER-MISC/fix_ti_spring.cpp | 12 +- src/USER-MISC/fix_wall_ees.cpp | 5 +- src/USER-MISC/fix_wall_reflect_stochastic.cpp | 10 +- src/USER-MISC/fix_wall_region_ees.cpp | 12 +- src/USER-MISC/pair_agni.cpp | 18 ++- src/USER-MISC/pair_cosine_squared.cpp | 13 +-- src/USER-MISC/pair_coul_slater_cut.cpp | 11 +- src/USER-MISC/pair_coul_slater_long.cpp | 16 +-- src/USER-MISC/pair_local_density.cpp | 18 ++- src/USER-MISC/temper_npt.cpp | 23 ++-- src/USER-SMD/atom_vec_smd.cpp | 5 +- src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 12 +- src/USER-SMD/compute_smd_tlsph_shape.cpp | 12 +- src/USER-SMD/compute_smd_tlsph_strain.cpp | 12 +- .../compute_smd_tlsph_strain_rate.cpp | 12 +- 84 files changed, 537 insertions(+), 658 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 5e3bd934a9..684108be71 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -57,24 +57,19 @@ ------------------------------------------------------------------------- */ #include "kim_init.h" -#include "fix_store_kim.h" -#include "kim_units.h" -#include -#include -#include -#include -#include "error.h" -#include "atom.h" + +#include "citeme.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix_store_kim.h" +#include "input.h" +#include "kim_units.h" #include "modify.h" -#include "update.h" #include "universe.h" -#include "input.h" #include "variable.h" -#include "citeme.h" -#include "utils.h" -#include "fmt/format.h" + +#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index a91c615d09..5f45dd34dc 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -57,23 +57,18 @@ ------------------------------------------------------------------------- */ #include "kim_interactions.h" -#include -#include -#include -#include -#include -#include "error.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix_store_kim.h" +#include "input.h" #include "modify.h" #include "update.h" -#include "universe.h" -#include "input.h" -#include "variable.h" -#include "utils.h" -#include "fix_store_kim.h" -#include "fmt/format.h" + +#include +#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index 6df8c075dc..ae4ca9b13d 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -56,19 +56,18 @@ ------------------------------------------------------------------------- */ #include "kim_param.h" -#include "fix_store_kim.h" -#include "pair_kim.h" -#include -#include -#include -#include + #include "comm.h" #include "error.h" +#include "fix_store_kim.h" +#include "force.h" #include "input.h" #include "modify.h" +#include "pair_kim.h" #include "variable.h" -#include "force.h" -#include "fmt/format.h" + +#include +#include extern "C" { diff --git a/src/KIM/kim_property.cpp b/src/KIM/kim_property.cpp index 643e0da47b..95a1274859 100644 --- a/src/KIM/kim_property.cpp +++ b/src/KIM/kim_property.cpp @@ -53,21 +53,18 @@ Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ -#if LMP_PYTHON -#define PY_SSIZE_T_CLEAN -#include -#endif - #include "kim_property.h" #include "comm.h" -#include "input.h" -#include "variable.h" -#include "utils.h" #include "error.h" +#include "input.h" #include "lmppython.h" +#include "variable.h" -#include +#if LMP_PYTHON +#define PY_SSIZE_T_CLEAN +#include // IWYU pragma: export +#endif using namespace LAMMPS_NS; diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 4a1db9450d..ec13210665 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -56,24 +56,22 @@ ------------------------------------------------------------------------- */ #include "kim_query.h" -#include "fix_store_kim.h" -#include -#include -#include -#include + #include "comm.h" #include "error.h" +#include "fix_store_kim.h" +#include "info.h" #include "input.h" #include "modify.h" #include "variable.h" #include "version.h" -#include "info.h" -#include "fmt/format.h" + +#include +#include #if defined(LMP_KIM_CURL) #include #include -#include #endif using namespace LAMMPS_NS; diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index c0c1aee07c..77dbad6f1d 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -57,6 +57,8 @@ #include #include #include +#include + using namespace std; namespace diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 0361f2351e..0c2e8d2684 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -66,7 +66,6 @@ PairStyle(kim,PairKIM) class KIM_API_model; #include "pair.h" - extern "C" { #include "KIM_SimulatorHeaders.h" } diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index fd1bf18330..5f0ee33c8c 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -12,20 +12,17 @@ ------------------------------------------------------------------------- */ #include "mliap_descriptor_snap.h" -#include "pair_mliap.h" -#include "mliap_data.h" -#include -#include -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "utils.h" -#include "sna.h" -#include "memory.h" #include "error.h" -#include "fmt/format.h" +#include "memory.h" +#include "mliap_data.h" +#include "pair_mliap.h" +#include "sna.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index b8ad1913a0..ac82a671d4 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -12,17 +12,13 @@ ------------------------------------------------------------------------- */ #include "mliap_model.h" -#include "pair_mliap.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "utils.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "fmt/format.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_model_linear.h b/src/MLIAP/mliap_model_linear.h index 67ba0985a2..326407faa8 100644 --- a/src/MLIAP/mliap_model_linear.h +++ b/src/MLIAP/mliap_model_linear.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class MLIAPModelLinear : public MLIAPModel { public: - MLIAPModelLinear(LAMMPS*, char* = NULL); + MLIAPModelLinear(LAMMPS*, char* = nullptr); ~MLIAPModelLinear(); virtual int get_nparams(); virtual int get_gamma_nnz(class MLIAPData*); diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp index d74a1820cc..4c6d906787 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/MLIAP/pair_mliap.cpp @@ -11,22 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_mliap.h" -#include - -#include #include "mliap_data.h" #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" #include "mliap_descriptor_snap.h" -#include "pair_mliap.h" + #include "atom.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" -#include "error.h" +#include "neigh_request.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 514250d058..ead8de7cb5 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -12,15 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_template.h" + #include "atom.h" -#include "molecule.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "memory.h" #include "error.h" - +#include "molecule.h" using namespace LAMMPS_NS; diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index e05b7bf317..6d5fc3da8e 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -17,15 +17,16 @@ #include "omp_compat.h" #include "dump_cfg_mpiio.h" -#include -#include #include "atom.h" #include "domain.h" #include "update.h" #include "memory.h" #include "error.h" +#include +#include + #ifdef LMP_USER_IO_TIMER #include #include diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 66c7d8a417..b2caa411e3 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "restart_mpiio.h" -#include -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 5ce74575ba..ada25431c8 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "atom_vec_peri.h" -#include -#include + #include "atom.h" #include "citeme.h" -#include "memory.h" #include "error.h" +#include +#include + using namespace LAMMPS_NS; static const char cite_peri_package[] = diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index b3986e75fa..0e5760ac8d 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -17,23 +17,21 @@ #include "pair_peri_eps.h" -#include -#include - #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "math_const.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 101a6d0bd9..b60f28d9f1 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -17,23 +17,20 @@ #include "pair_peri_lps.h" -#include -#include - #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" -#include "math_const.h" +#include using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index c5f893dd32..5d6973a915 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -17,23 +17,20 @@ #include "pair_peri_pmb.h" -#include -#include -#include - #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index dca80cc6fd..93c980702b 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -17,24 +17,21 @@ #include "pair_peri_ves.h" -#include -#include - #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" - +#include "neighbor.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 767c22c496..8966d9a9db 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_python_invoke.h" -#include // IWYU pragma: keep -#include -#include "force.h" -#include "update.h" + #include "error.h" #include "lmppython.h" #include "python_compat.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index be63b851a2..53bde5e804 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -16,12 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_python_move.h" -#include // IWYU pragma: keep -#include -#include "lmppython.h" + #include "error.h" +#include "lmppython.h" #include "python_compat.h" +#include +#include // IWYU pragma: export + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index c59ba5eb5f..074de2f39a 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -16,17 +16,18 @@ ------------------------------------------------------------------------- */ #include "pair_python.h" -#include // IWYU pragma: keep -#include #include "atom.h" +#include "error.h" #include "force.h" +#include "lmppython.h" #include "memory.h" -#include "update.h" #include "neigh_list.h" -#include "lmppython.h" -#include "error.h" #include "python_compat.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; diff --git a/src/PYTHON/python_compat.h b/src/PYTHON/python_compat.h index 175d797ffa..effac81cef 100644 --- a/src/PYTHON/python_compat.h +++ b/src/PYTHON/python_compat.h @@ -14,6 +14,8 @@ #ifndef LMP_PYTHON_COMPAT_H #define LMP_PYTHON_COMPAT_H +#include + // Wrap API changes between Python 2 and 3 using macros #if PY_MAJOR_VERSION == 2 #define PY_INT_FROM_LONG(X) PyInt_FromLong(X) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index b54abe28b0..cb35cba85a 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) + Contributing authors: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ #include "python_impl.h" -#include -#include -#include // IWYU pragma: keep -#include "force.h" + +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" #include "python_compat.h" +#include "variable.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index d7abcb62b8..531f488e60 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -17,15 +17,15 @@ #include "compute_event_displace.h" -#include #include "atom.h" #include "domain.h" -#include "modify.h" -#include "fix_event.h" #include "error.h" -#include "force.h" +#include "fix_event.h" +#include "modify.h" #include "update.h" +#include + using namespace LAMMPS_NS; #define INVOKED_SCALAR 1 diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index ddbe10adc9..ba784cc3e9 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_event_hyper.h" + #include "comm.h" #include "error.h" #include "update.h" diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 76953b6c2c..b2981afa01 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -18,21 +18,20 @@ #include "fix_neb.h" -#include -#include - -#include "universe.h" -#include "update.h" #include "atom.h" -#include "domain.h" #include "comm.h" -#include "modify.h" #include "compute.h" -#include "group.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "force.h" +#include "group.h" #include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 1e78326fbd..6c4cba4ab8 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -12,28 +12,25 @@ ------------------------------------------------------------------------- */ #include "hyper.h" -#include -#include -#include -#include "update.h" + +#include "compute_event_displace.h" #include "domain.h" -#include "region.h" +#include "dump.h" +#include "error.h" +#include "finish.h" +#include "fix_event_hyper.h" +#include "fix_hyper.h" #include "integrate.h" +#include "memory.h" #include "min.h" -#include "force.h" -#include "neighbor.h" #include "modify.h" -#include "compute_event_displace.h" -#include "fix_hyper.h" -#include "fix_event_hyper.h" +#include "neighbor.h" #include "output.h" -#include "dump.h" -#include "finish.h" +#include "region.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 34b5cf40fe..2d1dd6eea7 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -12,28 +12,26 @@ ------------------------------------------------------------------------- */ #include "neb.h" -#include -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "domain.h" #include "comm.h" -#include "min.h" -#include "modify.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" #include "fix_neb.h" +#include "math_const.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "math_const.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 796cf01681..cdb1eb9b02 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -16,32 +16,29 @@ ------------------------------------------------------------------------- */ #include "prd.h" -#include -#include -#include -#include "universe.h" -#include "update.h" + #include "atom.h" -#include "domain.h" -#include "region.h" #include "comm.h" -#include "velocity.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix_event_prd.h" #include "integrate.h" +#include "memory.h" #include "min.h" -#include "neighbor.h" #include "modify.h" -#include "compute.h" -#include "fix.h" -#include "fix_event_prd.h" -#include "force.h" -#include "random_park.h" -#include "random_mars.h" +#include "neighbor.h" #include "output.h" -#include "finish.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" +#include "velocity.h" + +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index fba753d602..db74b63c35 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -16,28 +16,28 @@ ------------------------------------------------------------------------- */ #include "tad.h" -#include -#include -#include -#include "universe.h" -#include "update.h" + #include "atom.h" +#include "compute.h" #include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix_event_tad.h" +#include "fix_store.h" +#include "force.h" #include "integrate.h" +#include "memory.h" #include "min.h" -#include "neighbor.h" #include "modify.h" #include "neb.h" -#include "compute.h" -#include "fix_event_tad.h" -#include "fix_store.h" -#include "force.h" +#include "neighbor.h" #include "output.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index a7ad4c068b..0cce389bf0 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -16,22 +16,23 @@ ------------------------------------------------------------------------- */ #include "temper.h" -#include -#include -#include "universe.h" -#include "domain.h" + #include "atom.h" -#include "update.h" -#include "integrate.h" -#include "modify.h" #include "compute.h" -#include "force.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" +#include "force.h" +#include "integrate.h" +#include "modify.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp index 152961f290..2dee1224d3 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp @@ -14,8 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include - #include "bond_oxrna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index 66871fa64e..17b1fb7b42 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -16,16 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_nve_dotc_langevin.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" -#include "update.h" #include "comm.h" -#include "random_mars.h" #include "error.h" +#include "math_extra.h" +#include "random_mars.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 60c1c8788f..662d55c590 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxdna2_coaxstk.h" -#include -#include -#include "mf_oxdna.h" #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 7d2c8aa2c2..f23ca4fbf7 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -16,18 +16,17 @@ #include "pair_oxdna2_dh.h" -#include -#include #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 17ba194030..f1d425a0b3 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxdna_coaxstk.h" -#include -#include -#include "mf_oxdna.h" #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 33005046b7..ad96186b6b 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -16,19 +16,18 @@ #include "pair_oxdna_excv.h" -#include -#include -#include "mf_oxdna.h" #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; using namespace MFOxdna; diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 88c5dc5e36..7987210d7a 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -16,19 +16,18 @@ #include "pair_oxdna_hbond.h" -#include -#include -#include "mf_oxdna.h" #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; using namespace MFOxdna; diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 87de92e0e0..1751499683 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxdna_xstk.h" -#include -#include -#include "mf_oxdna.h" #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp index ec93ce592e..af9fdaaaa1 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp @@ -14,11 +14,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_oxrna2_excv.h" #include -#include "pair_oxrna2_excv.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index d38ccb86ab..fd02946134 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -14,26 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_oxrna2_stk.h" -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neighbor.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp index f3f65b695e..673ef1c9a3 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxrna2_xstk.h" -#include -#include -#include "mf_oxdna.h" #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" +#include "mf_oxdna.h" +#include "neigh_list.h" -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/USER-CGSDK/pair_lj_sdk.h index ef0263c06b..11c123a72c 100644 --- a/src/USER-CGSDK/pair_lj_sdk.h +++ b/src/USER-CGSDK/pair_lj_sdk.h @@ -27,7 +27,6 @@ PairStyle(lj/sdk,PairLJSDK) #include "pair.h" namespace LAMMPS_NS { -class LAMMPS; class PairLJSDK : public Pair { public: diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 39e3ff9467..dcaa5866de 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,7 +1,9 @@ #include "meam.h" -#include -#include "memory.h" + #include "math_special.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 2b6832e155..df1f8f9a1d 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,11 +1,12 @@ #include "meam.h" + +#include "math_special.h" + #include #include -#include "math_special.h" using namespace LAMMPS_NS; - void MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl, double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh, diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 706075ffd0..0a632bc40a 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -16,7 +16,9 @@ ------------------------------------------------------------------------- */ #include "meam.h" + #include "math_special.h" + #include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index 0a0b95e14a..a546aa0c7f 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -16,9 +16,11 @@ ------------------------------------------------------------------------- */ #include "meam.h" -#include + #include "memory.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 25f1bb9e81..f493d9dcac 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,9 +1,11 @@ #include "meam.h" + +#include "math_special.h" +#include "memory.h" + #include #include #include -#include "math_special.h" -#include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 60264b87cb..c5f3115249 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,5 +1,7 @@ #include "meam.h" + #include + using namespace LAMMPS_NS; template diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp index f0e04ff1c0..ea76ee896c 100644 --- a/src/USER-MEAMC/meam_setup_param.cpp +++ b/src/USER-MEAMC/meam_setup_param.cpp @@ -1,5 +1,10 @@ + #include "meam.h" + +#include "math_const.h" #include +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/bond_special.cpp b/src/USER-MISC/bond_special.cpp index a956468497..87671655b1 100644 --- a/src/USER-MISC/bond_special.cpp +++ b/src/USER-MISC/bond_special.cpp @@ -13,19 +13,15 @@ Contributing Author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include - -#include #include "bond_special.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" #include "memory.h" -#include "error.h" - +#include "neighbor.h" +#include "pair.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_special.h b/src/USER-MISC/bond_special.h index 389990b1d7..d5e360ca53 100644 --- a/src/USER-MISC/bond_special.h +++ b/src/USER-MISC/bond_special.h @@ -22,7 +22,6 @@ BondStyle(special,BondSpecial) #ifndef LMP_BOND_SPECIAL_H #define LMP_BOND_SPECIAL_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index 02c697a786..f2ccf2694d 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -43,33 +43,30 @@ properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015 https://doi.org/10.1103/PhysRevE.92.043303 ------------------------------------------------------------------------- */ -#include -#include - #include "compute_hma.h" + +#include "angle.h" #include "atom.h" -#include "update.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "group.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_store.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "kspace.h" #include "memory.h" -#include "error.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_request.h" +#include "modify.h" #include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" -#include - +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/USER-MISC/compute_viscosity_cos.cpp index 12e1991d54..dae93a8d81 100644 --- a/src/USER-MISC/compute_viscosity_cos.cpp +++ b/src/USER-MISC/compute_viscosity_cos.cpp @@ -15,17 +15,18 @@ Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com) ------------------------------------------------------------------------- */ - #include "compute_viscosity_cos.h" + #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "comm.h" #include "group.h" #include "error.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index a33452dbe1..15bb458c48 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -19,20 +19,19 @@ #include "dihedral_spherical.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include -using namespace std; using namespace LAMMPS_NS; using namespace MathConst; using namespace MathExtra; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index aebe468905..91a8642b10 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,33 +17,24 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ - -#include -#include - -#include - -#include // IWYU pragma: keep -#include // IWYU pragma: keep +#include "dihedral_table.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "error.h" #include "force.h" +#include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" - -#include "dihedral_table.h" - -#include "tokenizer.h" +#include "neighbor.h" #include "table_file_reader.h" +#include "tokenizer.h" +#include +#include +#include // IWYU pragma: keep -#include "math_const.h" -#include "math_extra.h" - -using namespace std; using namespace LAMMPS_NS; using namespace MathConst; using namespace MathExtra; @@ -829,28 +820,20 @@ void DihedralTable::coeff(int narg, char **arg) // --- and resolve issues with periodicity --- if (tb->ninput < 2) { - string err_msg; - err_msg = string("Invalid dihedral table length (") - + string(arg[2]) + string(")."); - error->one(FLERR,err_msg); - } - else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { - string err_msg; - err_msg = string("Invalid dihedral spline table length. (Try linear)\n (") - + string(arg[2]) + string(")."); - error->one(FLERR,err_msg); + error->one(FLERR,fmt::format("Invalid dihedral table length ({}).", + arg[2])); + } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { + error->one(FLERR,fmt::format("Invalid dihedral spline table length. " + "(Try linear)\n ({}).",arg[2])); } // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { if (tb->phifile[i] >= tb->phifile[i+1]) { - stringstream i_str; - i_str << i+1; - string err_msg = - string("Dihedral table values are not increasing (") + - string(arg[2]) + string(", ")+i_str.str()+string("th entry)"); + auto err_msg = fmt::format("Dihedral table values are not increasing " + "({}, {}th entry)",arg[2],i+1); if (i==0) - err_msg += string("\n(This is probably a mistake with your table format.)\n"); + err_msg += std::string("\n(This is probably a mistake with your table format.)\n"); error->all(FLERR,err_msg); } } @@ -859,20 +842,13 @@ void DihedralTable::coeff(int narg, char **arg) double philo = tb->phifile[0]; double phihi = tb->phifile[tb->ninput-1]; if (tb->use_degrees) { - if ((phihi - philo) >= 360) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 360 degrees (") - +string(arg[2]) + string(")."); - error->all(FLERR,err_msg); - } - } - else { - if ((phihi - philo) >= MY_2PI) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 2*PI radians (") - + string(arg[2]) + string(")."); - error->all(FLERR,err_msg); - } + if ((phihi - philo) >= 360) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 " + "degrees ({}).",arg[2])); + } else { + if ((phihi - philo) >= MY_2PI) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI " + "radians ({}).",arg[2])); } // convert phi from degrees to radians @@ -940,10 +916,9 @@ void DihedralTable::coeff(int narg, char **arg) // Optional: allow the user to print out the interpolated spline tables if (me == 0) { - if (!checkU_fname.empty()) - { - ofstream checkU_file; - checkU_file.open(checkU_fname, ios::out); + if (!checkU_fname.empty()) { + std::ofstream checkU_file; + checkU_file.open(checkU_fname, std::ios::out); for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double u = tb->e[i]; @@ -953,12 +928,10 @@ void DihedralTable::coeff(int narg, char **arg) } checkU_file.close(); } - if (!checkF_fname.empty()) - { - ofstream checkF_file; - checkF_file.open(checkF_fname, ios::out); - for (int i=0; i < tablength; i++) - { + if (!checkF_fname.empty()) { + std::ofstream checkF_file; + checkF_file.open(checkF_fname, std::ios::out); + for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double f; if ((tabstyle == SPLINE) && (tb->f_unspecified)) { @@ -973,8 +946,7 @@ void DihedralTable::coeff(int narg, char **arg) // To be nice and report something, I do the same thing here.) cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi); f = -dU_dphi; - } - else + } else // Otherwise we calculated the tb->f[] array. Report its contents. f = tb->f[i]; if (tb->use_degrees) { @@ -991,8 +963,7 @@ void DihedralTable::coeff(int narg, char **arg) // store ptr to table in tabindex int count = 0; - for (int i = ilo; i <= ihi; i++) - { + for (int i = ilo; i <= ihi; i++) { tabindex[i] = ntables; //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported setflag[i] = 1; @@ -1213,7 +1184,7 @@ void DihedralTable::spline_table(Table *tb) } // for (int i=0; ininput; i++) if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) { - string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); + std::string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); error->all(FLERR, msg); } @@ -1319,7 +1290,7 @@ void DihedralTable::param_extract(Table *tb, char *line) ValueTokenizer values(line); while (values.has_next()) { - std::string word = values.next_string(); + auto word = values.next_string(); if (word == "N") { tb->ninput = values.next_int(); } @@ -1342,10 +1313,8 @@ void DihedralTable::param_extract(Table *tb, char *line) //else if (word == "EQ") { // tb->theta0 = values.next_double(); //} - else { - string err_msg = fmt::format("Invalid keyword in dihedral angle table parameters ({})", word); - error->one(FLERR,err_msg); - } + else error->one(FLERR,fmt::format("Invalid keyword in dihedral angle " + "table parameters ({})", word)); } } catch (TokenizerException & e) { error->one(FLERR, e.what()); diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/USER-MISC/fix_accelerate_cos.cpp index 17d6e9ad94..4e84b47ac3 100644 --- a/src/USER-MISC/fix_accelerate_cos.cpp +++ b/src/USER-MISC/fix_accelerate_cos.cpp @@ -16,15 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_accelerate_cos.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "region.h" -#include "respa.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" #include "force.h" #include "math_const.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index 1f2022d520..d92789f03f 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -23,19 +23,18 @@ #include "fix_ave_correlate_long.h" -#include - -#include -#include -#include "update.h" -#include "modify.h" +#include "citeme.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" -#include "citeme.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp index bf97066275..952ffe7584 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/USER-MISC/fix_electron_stopping.cpp @@ -17,21 +17,22 @@ ------------------------------------------------------------------------- */ #include "fix_electron_stopping.h" -#include -#include -#include "mpi.h" + #include "atom.h" -#include "update.h" +#include "comm.h" #include "domain.h" -#include "region.h" -#include "force.h" +#include "error.h" #include "fix.h" +#include "force.h" #include "memory.h" -#include "comm.h" -#include "error.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 23e61641d8..d603e37671 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -18,15 +18,15 @@ #include "fix_flow_gauss.h" -#include #include "atom.h" -#include "force.h" -#include "group.h" -#include "update.h" +#include "citeme.h" #include "domain.h" #include "error.h" -#include "citeme.h" +#include "group.h" #include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index 4264126c26..7c3fac9c33 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -48,16 +48,15 @@ negotiate an appropriate license for such distribution." ------------------------------------------------------------------------- */ #include "fix_imd.h" + #include "atom.h" #include "comm.h" -#include "update.h" -#include "respa.h" #include "domain.h" -#include "force.h" #include "error.h" #include "group.h" #include "memory.h" - +#include "respa.h" +#include "update.h" #include diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/USER-MISC/fix_momentum_chunk.cpp index 3df632eb30..fcd6d47922 100644 --- a/src/USER-MISC/fix_momentum_chunk.cpp +++ b/src/USER-MISC/fix_momentum_chunk.cpp @@ -13,18 +13,17 @@ #include "fix_momentum_chunk.h" -#include -#include #include "atom.h" #include "compute.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" #include "domain.h" -#include "group.h" #include "error.h" -#include "force.h" +#include "group.h" #include "modify.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index a9abf7baf7..5f1582d580 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -17,12 +17,9 @@ #include "fix_orient_eco.h" -#include -#include #include "atom.h" #include "citeme.h" #include "comm.h" -#include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -34,7 +31,8 @@ #include "respa.h" #include "update.h" - +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 222369f572..1ac0ffb188 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -20,24 +20,21 @@ #include "fix_pafi.h" -#include -#include - -#include "math_extra.h" #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "respa.h" +#include "citeme.h" #include "comm.h" #include "compute.h" -#include "random_mars.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "respa.h" +#include "update.h" -#include "citeme.h" - +#include +#include using namespace LAMMPS_NS; @@ -61,7 +58,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), random(NULL), computename(NULL), + Fix(lmp, narg, arg), computename(NULL), random(NULL), h(NULL), step_respa(NULL) { if (lmp->citeme) lmp->citeme->add(cite_fix_pafi_package); @@ -122,15 +119,15 @@ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : } force_flag = 0; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i=0; i<6; i++) { + for (int i=0; i<6; i++) { proj[i] = 0.0; proj_all[i] = 0.0; } - for(int i=0; i<5; i++) { + for (int i=0; i<5; i++) { results[i] = 0.0; results_all[i] = 0.0; } @@ -208,14 +205,14 @@ void FixPAFI::setup(int vflag) void FixPAFI::min_setup(int vflag) { - if( utils::strmatch(update->minimize_style,"^fire")==0 && + if (utils::strmatch(update->minimize_style,"^fire")==0 && utils::strmatch(update->minimize_style,"^quickmin")==0 ) error->all(FLERR,"fix pafi requires a damped dynamics minimizer"); min_post_force(vflag); } -void FixPAFI::post_force(int vflag) +void FixPAFI::post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; @@ -236,24 +233,20 @@ void FixPAFI::post_force(int vflag) PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - double xum=0.; - // proj 0,1,2 = f.n, v.n, h.n // proj 3,4,5 = psi, f.n**2, f*(1-psi) // c_v 0,1,2 = fxcom, fycom, fzcom etc - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } double deviation[3] = {0.,0.,0.}; - double fn; - force_flag=0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -293,7 +286,7 @@ void FixPAFI::post_force(int vflag) } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -345,7 +338,7 @@ void FixPAFI::post_force(int vflag) if (od_flag == 0) { for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit) { - if(rmass) mass_f = sqrt(rmass[i]); + if (rmass) mass_f = sqrt(rmass[i]); else mass_f = sqrt(mass[type[i]]); f[i][0] += -gamma * mass_f * mass_f * v[i][0]; @@ -361,7 +354,7 @@ void FixPAFI::post_force(int vflag) for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit) { - if(rmass) mass_f = sqrt(rmass[i]); + if (rmass) mass_f = sqrt(rmass[i]); else mass_f = sqrt(mass[type[i]]); f[i][0] += sqrtD * h[i][0] * mass_f; @@ -378,13 +371,12 @@ void FixPAFI::post_force(int vflag) }; -void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) +void FixPAFI::post_force_respa(int vflag, int ilevel, int /*iloop*/) { // set force to desired value on requested level, 0.0 on other levels if (ilevel == ilevel_respa) post_force(vflag); else { - double **x = atom->x; double **f = atom->f; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -396,38 +388,31 @@ void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) } }; -void FixPAFI::min_post_force(int vflag) +void FixPAFI::min_post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; double **f = atom->f; - double *rmass = atom->rmass; - double *mass = atom->mass; - int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - double xum=0.; - // proj 0,1,2 = f.n, v.n, h.n // proj 3,4,5 = psi, f.n**2, f*(1-psi) // c_v 0,1,2 = fxcom, fycom, fzcom etc - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } double deviation[3] = {0.,0.,0.}; - double fn; - force_flag=0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -464,7 +449,7 @@ void FixPAFI::min_post_force(int vflag) } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -519,7 +504,7 @@ double FixPAFI::compute_vector(int n) -void FixPAFI::initial_integrate(int vflag) +void FixPAFI::initial_integrate(int /*vflag*/) { double dtfm; @@ -539,11 +524,11 @@ void FixPAFI::initial_integrate(int vflag) PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } @@ -559,7 +544,7 @@ void FixPAFI::initial_integrate(int vflag) proj[1] += v[i][2] * path[i][5]; // v.n } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -651,11 +636,11 @@ void FixPAFI::final_integrate() PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } @@ -665,7 +650,7 @@ void FixPAFI::final_integrate() proj[0] += f[i][1] * path[i][4]; // f.n proj[0] += f[i][2] * path[i][5]; // f.n } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -710,7 +695,7 @@ void FixPAFI::final_integrate() /* ---------------------------------------------------------------------- */ -void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -724,7 +709,7 @@ void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixPAFI::final_integrate_respa(int ilevel, int iloop) +void FixPAFI::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index b17ee55f94..e17ef4652f 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -19,25 +19,15 @@ #include "fix_propel_self.h" -#include -#include - - #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "citeme.h" -#include "comm.h" #include "error.h" -#include "force.h" -#include "group.h" #include "math.h" #include "math_const.h" #include "math_extra.h" -#include "math_vector.h" -#include "modify.h" -#include "random_mars.h" -#include "respa.h" -#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 0771122bfd..b088a86661 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -15,17 +15,16 @@ #include "fix_rhok.h" -#include -#include - #include "atom.h" +#include "citeme.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "math_const.h" #include "respa.h" #include "update.h" -#include "citeme.h" -#include "math_const.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index baee8a5699..0dace284a9 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -18,16 +18,16 @@ #include "fix_smd.h" -#include -#include #include "atom.h" #include "comm.h" -#include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" #include "group.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index 1bd6957997..97bf1fb07b 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -17,18 +17,18 @@ #include "fix_srp.h" -#include -#include #include "atom.h" -#include "force.h" -#include "domain.h" -#include "modify.h" +#include "atom_vec.h" #include "comm.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "neighbor.h" -#include "atom_vec.h" +#include "force.h" +#include "memory.h" #include "modify.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 34c667a9e2..bc10b5284c 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -20,15 +20,15 @@ #include "fix_ti_spring.h" -#include #include "atom.h" -#include "update.h" +#include "citeme.h" #include "domain.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "citeme.h" -#include "force.h" +#include "memory.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index bd7e230472..c4be8b9f1b 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_wall_ees.h" -#include + #include "math_extra.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index 7da818732e..9a8454b017 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -17,19 +17,17 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect_stochastic.h" -#include #include "atom.h" #include "comm.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" #include "force.h" #include "lattice.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" -#include "error.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index a8d6ea9424..dfb11d6467 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -17,17 +17,17 @@ #include "fix_wall_region_ees.h" -#include -#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "domain.h" -#include "region.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" #include "math_extra.h" +#include "region.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 0a00c914c7..41f9bc9531 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -17,21 +17,19 @@ #include "pair_agni.h" -#include - -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" +#include "citeme.h" #include "comm.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "citeme.h" -#include "math_special.h" #include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 57dd55c593..1203cea5f2 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -15,22 +15,17 @@ ------------------------------------------------------------------------- */ #include "pair_cosine_squared.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/USER-MISC/pair_coul_slater_cut.cpp index 6b1af9a42f..5e799178c9 100644 --- a/src/USER-MISC/pair_coul_slater_cut.cpp +++ b/src/USER-MISC/pair_coul_slater_cut.cpp @@ -15,18 +15,15 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_coul_slater_cut.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/USER-MISC/pair_coul_slater_long.cpp index 0fbd56f811..0c94254f48 100644 --- a/src/USER-MISC/pair_coul_slater_long.cpp +++ b/src/USER-MISC/pair_coul_slater_long.cpp @@ -15,23 +15,19 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_coul_slater_long.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 3b76bd8482..f8b813ef0b 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -19,21 +19,17 @@ #include "pair_local_density.h" -#include - -#include - #include "atom.h" -#include "force.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" #include "error.h" -#include "domain.h" -#include "citeme.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index e4cab277c1..69f4559cac 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -18,22 +18,23 @@ ------------------------------------------------------------------------- */ #include "temper_npt.h" -#include -#include -#include "universe.h" -#include "domain.h" + #include "atom.h" -#include "update.h" -#include "integrate.h" -#include "modify.h" #include "compute.h" -#include "force.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" +#include "force.h" +#include "integrate.h" +#include "modify.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 670783a3d7..81a43ff7f3 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -23,9 +23,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_smd.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 09aeeea74a..81792355e0 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -23,14 +23,16 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_defgrad.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index ba1a9306ef..a3727871de 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -23,16 +23,18 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_shape.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index f0061bf7a1..db51ca4125 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -24,16 +24,18 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_strain.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp index 895a973f6a..577dc0e40f 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp @@ -23,17 +23,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_smd_tlsph_strain_rate.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace LAMMPS_NS; -- GitLab From 27203304d60f04fa26732b4a0071766e9809db8b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 09:47:48 -0400 Subject: [PATCH 56/75] USER-INTEL include handling cleanup --- src/USER-INTEL/improper_cvff_intel.cpp | 16 +++---- src/USER-INTEL/improper_harmonic_intel.cpp | 15 ++++--- src/USER-INTEL/npair_full_bin_ghost_intel.cpp | 10 ++--- src/USER-INTEL/npair_full_bin_intel.cpp | 7 ++- .../npair_half_bin_newton_intel.cpp | 7 ++- .../npair_half_bin_newton_tri_intel.cpp | 7 ++- .../npair_halffull_newton_intel.cpp | 10 ++--- src/USER-INTEL/npair_intel.h | 1 + src/USER-INTEL/npair_skip_intel.cpp | 12 +++-- src/USER-INTEL/pair_airebo_intel.cpp | 44 +++++++++---------- src/USER-INTEL/pair_airebo_morse_intel.cpp | 1 - src/USER-INTEL/pair_buck_intel.cpp | 16 +++---- src/USER-INTEL/pair_eam_alloy_intel.cpp | 12 +++-- src/USER-INTEL/pair_eam_fs_intel.cpp | 12 +++-- src/USER-INTEL/pair_eam_intel.cpp | 16 +++---- .../pair_lj_charmm_coul_charmm_intel.cpp | 1 + .../pair_lj_cut_coul_long_intel.cpp | 9 ++-- .../pair_lj_long_coul_long_intel.cpp | 9 +--- src/USER-INTEL/pair_sw_intel.cpp | 28 ++++++------ src/USER-INTEL/pppm_disp_intel.cpp | 12 ++--- src/USER-INTEL/pppm_intel.cpp | 13 +++--- 21 files changed, 119 insertions(+), 139 deletions(-) diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 4dcdb34b69..ba5ff79cd5 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include - #include "improper_cvff_intel.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index c63dfc9567..8da3c67022 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -15,22 +15,23 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "improper_harmonic_intel.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 00b032d495..bd4a95f774 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_ghost_intel.h" -#include "neighbor.h" -#include "nstencil.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" -#include "domain.h" -#include "molecule.h" #include "error.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/USER-INTEL/npair_full_bin_intel.cpp index 4ef84be75f..c4433ba16c 100644 --- a/src/USER-INTEL/npair_full_bin_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_intel.cpp index 799ba2b57b..55bac4cdb7 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp index 1f859cb5f1..d5384904e5 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_tri_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/USER-INTEL/npair_halffull_newton_intel.cpp index 8248f2257a..dd11802797 100644 --- a/src/USER-INTEL/npair_halffull_newton_intel.cpp +++ b/src/USER-INTEL/npair_halffull_newton_intel.cpp @@ -16,16 +16,14 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" +#include "error.h" #include "modify.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h index 6d4e01462f..e040a1d8f3 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/USER-INTEL/npair_intel.h @@ -15,6 +15,7 @@ #define LMP_NPAIR_INTEL_H #include "npair.h" +#include "domain.h" #include "fix_intel.h" #if defined(_OPENMP) diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/USER-INTEL/npair_skip_intel.cpp index fa202d5da1..df09829c86 100644 --- a/src/USER-INTEL/npair_skip_intel.cpp +++ b/src/USER-INTEL/npair_skip_intel.cpp @@ -16,17 +16,15 @@ ------------------------------------------------------------------------- */ #include "npair_skip_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" +#include "error.h" #include "modify.h" -#include "molecule.h" -#include "neigh_request.h" -#include "domain.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 8b7ff71603..6b576220fe 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -15,41 +15,37 @@ Contributing author: Markus Hohnerbach (RWTH) ------------------------------------------------------------------------- */ -#ifdef __INTEL_OFFLOAD -#pragma offload_attribute(push, target(mic)) -#endif -#include +#include "pair_airebo_intel.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" -#include -#include -#include -#include // requires C++-11 #include -#include -#include "lmptype.h" +#include +#include + #include "intel_preprocess.h" #include "intel_intrinsics_airebo.h" + #ifdef __INTEL_OFFLOAD #pragma offload_attribute(pop) #endif +#ifdef __INTEL_OFFLOAD +#pragma offload_attribute(push, target(mic)) +#endif + #if defined(_OPENMP) #include #endif -#include "pair_airebo_intel.h" -#include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "group.h" -#include "kspace.h" -#include "modify.h" -#include "suffix.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/USER-INTEL/pair_airebo_morse_intel.cpp index f68e299fa0..a99ab913ba 100644 --- a/src/USER-INTEL/pair_airebo_morse_intel.cpp +++ b/src/USER-INTEL/pair_airebo_morse_intel.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse_intel.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index b21ce13a34..bb5b44d260 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -15,20 +15,20 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include #include "pair_buck_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "group.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "error.h" #include "math_const.h" #include "memory.h" -#include "suffix.h" -#include "force.h" #include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index b979d2dcdf..084714daf4 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -15,18 +15,16 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_alloy_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index a1c71d9c21..8786c0d782 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -15,18 +15,16 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_fs_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index d27a019532..561621a388 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -15,22 +15,22 @@ Contributing authors: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_eam_intel.h" + #include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" #include "suffix.h" +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 2078e5277b..c8e4a3d0ef 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" #include "modify.h" diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index 243c7f577d..34ab97fd35 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -12,20 +12,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_coul_long_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "group.h" #include "kspace.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" + +#include + using namespace LAMMPS_NS; #define C_FORCE_T typename ForceConst::c_force_t diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp index 8b9670f419..533252d018 100644 --- a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp @@ -15,21 +15,16 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include #include "pair_lj_long_coul_long_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "group.h" -#include "kspace.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" - using namespace LAMMPS_NS; #define C_FORCE_T typename ForceConst::c_force_t diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index b8ac84bc3c..4ec2af40b0 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -17,6 +17,19 @@ #include "pair_sw_intel.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "neighbor.h" +#include "suffix.h" + +#include + #ifdef _LMP_INTEL_OFFLOAD #pragma offload_attribute(push,target(mic)) #endif @@ -25,21 +38,6 @@ #pragma offload_attribute(pop) #endif -#include - -#include -#include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "modify.h" -#include "suffix.h" #ifdef LMP_USE_AVXCD #include "intel_simd.h" diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 270299b4c5..1149c9b2c3 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -15,23 +15,23 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "pppm_disp_intel.h" + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "modify.h" -#include "fft3d_wrap.h" #include "gridcomm.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "modify.h" #include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index 26af974086..d596df4490 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -18,23 +18,24 @@ W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "pppm_intel.h" + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "modify.h" -#include "fft3d_wrap.h" #include "gridcomm.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "modify.h" #include "suffix.h" +#include +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; -- GitLab From f67bd8eb5d4ffd536052bd77917f253abd4c7c6c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 10:22:08 -0400 Subject: [PATCH 57/75] more KOKKOS, USER-OMP, and USER-INTEL include file cleanup --- src/KOKKOS/angle_charmm_kokkos.cpp | 9 +++-- src/KOKKOS/angle_class2_kokkos.cpp | 9 +++-- src/KOKKOS/angle_cosine_kokkos.cpp | 9 +++-- src/KOKKOS/angle_harmonic_kokkos.cpp | 9 +++-- src/KOKKOS/atom_kokkos.h | 2 +- src/KOKKOS/atom_vec_angle_kokkos.cpp | 8 ++--- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 8 ++--- src/KOKKOS/atom_vec_bond_kokkos.cpp | 8 ++--- src/KOKKOS/atom_vec_charge_kokkos.cpp | 8 ++--- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 11 ++++--- src/KOKKOS/atom_vec_kokkos.cpp | 4 +-- src/KOKKOS/atom_vec_kokkos.h | 3 +- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 8 ++--- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 11 +++---- src/KOKKOS/bond_class2_kokkos.cpp | 9 +++-- src/KOKKOS/bond_fene_kokkos.cpp | 10 +++--- src/KOKKOS/bond_harmonic_kokkos.cpp | 10 +++--- src/KOKKOS/comm_kokkos.cpp | 19 ++++++----- src/KOKKOS/comm_tiled_kokkos.cpp | 16 ++------- src/KOKKOS/compute_coord_atom_kokkos.cpp | 20 +++++------ .../compute_orientorder_atom_kokkos.cpp | 20 +++++------ src/KOKKOS/compute_temp_kokkos.cpp | 11 +++---- src/KOKKOS/dihedral_charmm_kokkos.cpp | 15 ++++----- src/KOKKOS/dihedral_class2_kokkos.cpp | 11 +++---- src/KOKKOS/dihedral_harmonic_kokkos.cpp | 11 +++---- src/KOKKOS/dihedral_opls_kokkos.cpp | 11 +++---- src/KOKKOS/domain_kokkos.h | 2 +- src/KOKKOS/fft3d_kokkos.cpp | 9 ++--- src/KOKKOS/fix_deform_kokkos.cpp | 21 ++++++------ src/KOKKOS/fix_gravity_kokkos.cpp | 9 ++--- src/KOKKOS/fix_langevin_kokkos.cpp | 17 +++++----- src/KOKKOS/fix_minimize_kokkos.cpp | 3 +- src/KOKKOS/fix_momentum_kokkos.cpp | 5 ++- src/KOKKOS/fix_neigh_history_kokkos.cpp | 4 +-- src/KOKKOS/fix_nh_kokkos.cpp | 27 +++++++-------- src/KOKKOS/fix_nph_kokkos.cpp | 4 ++- src/KOKKOS/fix_npt_kokkos.cpp | 4 ++- src/KOKKOS/fix_nve_kokkos.cpp | 11 +++---- src/KOKKOS/fix_nvt_kokkos.cpp | 6 ++-- src/KOKKOS/fix_property_atom_kokkos.cpp | 9 +++-- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 16 ++++----- src/KOKKOS/fix_reaxc_bonds_kokkos.cpp | 9 +++-- src/KOKKOS/fix_setforce_kokkos.cpp | 5 +-- src/KOKKOS/fix_wall_reflect_kokkos.cpp | 13 +++----- src/KOKKOS/gridcomm_kokkos.cpp | 9 +++-- src/KOKKOS/kokkos.cpp | 16 ++++----- src/KOKKOS/memory_kokkos.h | 2 +- src/KOKKOS/min_kokkos.cpp | 33 +++++++++---------- src/KOKKOS/min_linesearch_kokkos.cpp | 5 +-- src/KOKKOS/nbin_kokkos.cpp | 7 ++-- src/KOKKOS/neigh_bond_kokkos.cpp | 20 +++++------ src/KOKKOS/neigh_list_kokkos.cpp | 2 -- src/KOKKOS/neigh_list_kokkos.h | 3 +- src/KOKKOS/neighbor_kokkos.cpp | 23 ++++++------- src/KOKKOS/neighbor_kokkos.h | 3 +- src/KOKKOS/npair_halffull_kokkos.cpp | 11 +++---- src/KOKKOS/npair_skip_kokkos.cpp | 6 ++-- src/KOKKOS/pair_kokkos.h | 2 +- src/KOKKOS/pair_reaxc_kokkos.cpp | 16 ++++----- src/KOKKOS/pair_vashishta_kokkos.cpp | 21 ++++++------ src/KOKKOS/pppm_kokkos.cpp | 24 ++++++-------- src/KOKKOS/remap_kokkos.cpp | 6 ++-- src/USER-INTEL/angle_charmm_intel.cpp | 15 +++++---- src/USER-INTEL/angle_harmonic_intel.cpp | 15 +++++---- src/USER-INTEL/bond_fene_intel.cpp | 14 ++++---- src/USER-INTEL/bond_harmonic_intel.cpp | 15 +++++---- src/USER-INTEL/dihedral_fourier_intel.cpp | 16 ++++----- src/USER-INTEL/dihedral_harmonic_intel.cpp | 16 ++++----- src/USER-INTEL/dihedral_opls_intel.cpp | 16 ++++----- src/USER-INTEL/fix_intel.cpp | 9 +---- src/USER-INTEL/fix_nh_intel.cpp | 4 +-- src/USER-INTEL/fix_nve_asphere_intel.cpp | 10 +++--- src/USER-INTEL/fix_nvt_sllod_intel.cpp | 15 +++++---- src/USER-INTEL/intel_buffers.cpp | 2 +- src/USER-INTEL/nbin_intel.cpp | 6 ++-- src/USER-INTEL/npair_intel.cpp | 8 ++--- src/USER-OMP/reaxc_forces_omp.cpp | 11 ++++--- src/USER-OMP/reaxc_init_md_omp.cpp | 4 ++- src/USER-OMP/reaxc_multi_body_omp.cpp | 8 +++-- src/USER-OMP/reaxc_torsion_angles_omp.cpp | 4 ++- src/USER-OMP/reaxc_valence_angles_omp.cpp | 9 ++--- 81 files changed, 401 insertions(+), 449 deletions(-) diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 14850525ef..59ccac92ce 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 4406f51f83..bfa0f81a1d 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_class2_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 7ba634cd13..cf93bfbde5 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index 2e5831ef07..3a8878d222 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index ce480f6f9d..6eebbad661 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "atom.h" +#include "atom.h" // IWYU pragma: export #include "kokkos_type.h" #ifndef LMP_ATOM_KOKKOS_H diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e9c101eb79..662f09fe5a 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_angle_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" - +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index c76af73420..995985b29d 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_atomic_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" - +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 47e77c33b3..db56d58dff 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_bond_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" - +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 183bdb94e4..9846d2f4f8 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_charge_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" - +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 34a246008d..7c7f3c9826 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid_kokkos.h" -#include + #include "atom_kokkos.h" +#include "atom_masks.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "modify.h" +#include using namespace LAMMPS_NS; @@ -1177,7 +1178,7 @@ void AtomVecHybridKokkos::build_styles() allstyles[nallstyles] = new char[n]; \ strcpy(allstyles[nallstyles],#key); \ nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS } diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index dceedc8e60..9e39f53733 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "atom_masks.h" - using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index 7d8796b1ae..d414101966 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -14,7 +14,8 @@ #ifndef LMP_ATOM_VEC_KOKKOS_H #define LMP_ATOM_VEC_KOKKOS_H -#include "atom_vec.h" +#include "atom_vec.h" // IWYU pragma: export + #include "kokkos_type.h" #include diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 6a4d94dc14..7e3cdbf5e3 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_molecular_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" - +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 569498f664..6b62014e4a 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -12,27 +12,26 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere_kokkos.h" -#include -#include + #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" #include "memory.h" -#include "error.h" #include "memory_kokkos.h" +#include "modify.h" +#include using namespace LAMMPS_NS; +using namespace MathConst; #define DELTA 10 -static const double MY_PI = 3.14159265358979323846; // pi - /* ---------------------------------------------------------------------- */ AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 5481a41806..07712df203 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -16,16 +16,15 @@ ------------------------------------------------------------------------- */ #include "bond_class2_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index 9d2200dd90..1ee82476b2 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "bond_fene_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 9239a4191b..20b8778463 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -16,19 +16,17 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" -using namespace LAMMPS_NS; +#include +using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 8f865f6459..51ba6bbdb2 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -12,23 +12,24 @@ ------------------------------------------------------------------------- */ #include "comm_kokkos.h" -#include "kokkos.h" + #include "atom.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" #include "atom_vec_kokkos.h" +#include "compute.h" #include "domain.h" -#include "atom_masks.h" +#include "dump.h" #include "error.h" -#include "memory_kokkos.h" -#include "force.h" -#include "pair.h" #include "fix.h" -#include "compute.h" -#include "dump.h" -#include "output.h" -#include "modify.h" +#include "force.h" +#include "kokkos.h" #include "kokkos_base.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "output.h" +#include "pair.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index a29d9f63b3..88d3d1ac8c 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -12,22 +12,10 @@ ------------------------------------------------------------------------- */ #include "comm_tiled_kokkos.h" -#include -#include "comm_brick.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" -#include "output.h" -#include "dump.h" -#include "memory_kokkos.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/compute_coord_atom_kokkos.cpp b/src/KOKKOS/compute_coord_atom_kokkos.cpp index 90bd151b2d..c1f9324942 100644 --- a/src/KOKKOS/compute_coord_atom_kokkos.cpp +++ b/src/KOKKOS/compute_coord_atom_kokkos.cpp @@ -12,22 +12,18 @@ ------------------------------------------------------------------------- */ #include "compute_coord_atom_kokkos.h" -#include -#include -#include "compute_orientorder_atom_kokkos.h" + #include "atom_kokkos.h" -#include "update.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute_orientorder_atom_kokkos.h" +#include "error.h" +#include "memory_kokkos.h" #include "modify.h" -#include "neighbor_kokkos.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" -#include "group.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp index 7d635dbeb7..6e35dfd94f 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp @@ -16,23 +16,19 @@ ------------------------------------------------------------------------- */ #include "compute_orientorder_atom_kokkos.h" -#include -#include #include "atom_kokkos.h" -#include "update.h" -#include "modify.h" -#include "neighbor_kokkos.h" +#include "atom_masks.h" +#include "kokkos.h" +#include "math_const.h" +#include "memory_kokkos.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor_kokkos.h" #include "pair.h" -#include "comm.h" -#include "memory_kokkos.h" -#include "error.h" -#include "math_const.h" -#include "atom_masks.h" -#include "kokkos.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 7e4d3ad6ae..5e60d62be1 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -13,15 +13,14 @@ #include "compute_temp_kokkos.h" -#include #include "atom_kokkos.h" -#include "update.h" -#include "force.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" -#include "group.h" #include "error.h" -#include "atom_masks.h" +#include "force.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index c25ab18c60..88b5e1344d 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -16,19 +16,18 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmm_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" +#include "error.h" #include "force.h" -#include "pair.h" +#include "kokkos.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "kokkos.h" +#include "neighbor_kokkos.h" +#include "pair.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index df60ebd1e4..156a13c2ec 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2_kokkos.h" -#include #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp index 0acd61222e..d4855b10c1 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_harmonic_kokkos.h" -#include #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 70beae918a..42874936f9 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls_kokkos.h" -#include #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/domain_kokkos.h b/src/KOKKOS/domain_kokkos.h index eccc36a021..3bfdeb708b 100644 --- a/src/KOKKOS/domain_kokkos.h +++ b/src/KOKKOS/domain_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_DOMAIN_KOKKOS_H #define LMP_DOMAIN_KOKKOS_H -#include "domain.h" +#include "domain.h" // IWYU pragma: export #include "kokkos_type.h" #include "kokkos_few.h" diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index e49d780040..ff95998e4e 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -14,16 +14,13 @@ /* ---------------------------------------------------------------------- Contributing authors: Stan Moore (SNL), Sam Mish (U.C. Davis) ------------------------------------------------------------------------- */ - -#include -#include -#include -#include #include "fft3d_kokkos.h" -#include "remap_kokkos.h" + #include "error.h" #include "kokkos.h" +#include "remap_kokkos.h" +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 5d8430d337..87d860b5ae 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -16,23 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_deform_kokkos.h" -#include -#include #include "atom_kokkos.h" -#include "update.h" -#include "comm.h" -#include "irregular.h" +#include "atom_masks.h" #include "domain_kokkos.h" -#include "lattice.h" +#include "error.h" #include "force.h" -#include "modify.h" -#include "math_const.h" -#include "kspace.h" #include "input.h" +#include "irregular.h" +#include "kspace.h" +#include "math_const.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "atom_masks.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_gravity_kokkos.cpp b/src/KOKKOS/fix_gravity_kokkos.cpp index 4f8b57365e..7d413a1d57 100644 --- a/src/KOKKOS/fix_gravity_kokkos.cpp +++ b/src/KOKKOS/fix_gravity_kokkos.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_gravity_kokkos.h" + +#include "atom_kokkos.h" #include "atom_masks.h" -#include "modify.h" +#include "atom_vec.h" #include "input.h" -#include "variable.h" +#include "modify.h" #include "update.h" -#include "atom_kokkos.h" -#include "atom_vec.h" +#include "variable.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 44ae18f9a9..dadf9e4c8b 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -12,21 +12,22 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_kokkos.h" -#include -#include "atom_masks.h" + #include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute.h" +#include "error.h" #include "force.h" #include "group.h" -#include "update.h" -#include "error.h" +#include "input.h" #include "memory_kokkos.h" -#include "compute.h" -#include "comm.h" #include "modify.h" -#include "input.h" -#include "region.h" +#include "update.h" #include "variable.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp index e7b10dbb8e..13b9cb02a7 100644 --- a/src/KOKKOS/fix_minimize_kokkos.cpp +++ b/src/KOKKOS/fix_minimize_kokkos.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_minimize_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "domain.h" #include "memory_kokkos.h" -#include "atom_masks.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 1821b6dadd..be486bf752 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -13,16 +13,15 @@ #include "fix_momentum_kokkos.h" -#include #include "atom_kokkos.h" #include "atom_masks.h" -#include "domain.h" #include "domain_kokkos.h" #include "group.h" #include "error.h" -#include "force.h" #include "kokkos_few.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index a43c5ef458..d1f3f66327 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_neigh_history_kokkos.h" + #include "atom_kokkos.h" #include "error.h" #include "memory_kokkos.h" +#include "modify.h" #include "neigh_list_kokkos.h" #include "pair_kokkos.h" -#include "comm.h" -#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 8cd58b0927..a2985502bb 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -16,27 +16,24 @@ ------------------------------------------------------------------------- */ #include "fix_nh_kokkos.h" -#include -#include -#include "math_extra.h" #include "atom.h" -#include "force.h" -#include "group.h" +#include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor.h" -#include "irregular.h" -#include "modify.h" -#include "fix_deform.h" #include "compute.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "domain_kokkos.h" -#include "memory_kokkos.h" #include "error.h" -#include "atom_masks.h" -#include "atom_kokkos.h" +#include "fix_deform.h" +#include "force.h" +#include "irregular.h" +#include "kspace.h" +#include "memory_kokkos.h" +#include "neighbor.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index d667e29221..7efcb150bd 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nph_kokkos.h" -#include + #include "modify.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 47b3da4efe..5b73eee4d7 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_npt_kokkos.h" -#include + #include "modify.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index da0a326d5d..beabc55727 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_nve_kokkos.h" -#include -#include -#include "atom_masks.h" + #include "atom_kokkos.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" +#include "atom_masks.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 013095abc0..6e69582617 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_kokkos.h" -#include + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index d6afae3ec2..185e7445b2 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -13,13 +13,12 @@ #include "fix_property_atom_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "memory_kokkos.h" -#include "error.h" -#include "update.h" #include "atom_masks.h" +#include "error.h" +#include "memory_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 8c007586a9..eac044da28 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -17,21 +17,21 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax_kokkos.h" -#include -#include "kokkos.h" + #include "atom.h" -#include "atom_masks.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "kokkos.h" +#include "memory_kokkos.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" +#include "neighbor.h" #include "update.h" -#include "integrate.h" -#include "memory_kokkos.h" -#include "error.h" -#include "pair_reaxc_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 3a706ece83..f98ab0314c 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_bonds_kokkos.h" + #include "atom.h" -#include "pair_reaxc_kokkos.h" +#include "atom_masks.h" +#include "error.h" #include "force.h" -#include "compute.h" #include "memory_kokkos.h" -#include "error.h" -#include "reaxc_defs.h" -#include "atom_masks.h" +#include "pair_reaxc_kokkos.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index da516f5ba2..a11e8b4bd4 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_setforce_kokkos.h" -#include + #include "atom_kokkos.h" #include "update.h" #include "modify.h" @@ -24,7 +24,8 @@ #include "error.h" #include "atom_masks.h" #include "kokkos_base.h" -#include "region.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index c581edb123..046c97c12b 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -13,19 +13,14 @@ #include "fix_wall_reflect_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" +#include "atom_masks.h" #include "input.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" -#include "atom_masks.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 5f32c5b4ae..909e3c8544 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -12,14 +12,13 @@ ------------------------------------------------------------------------- */ #include "gridcomm_kokkos.h" -#include + #include "comm.h" -#include "kspace.h" #include "irregular.h" -#include "memory_kokkos.h" -#include "error.h" -#include "kokkos_base_fft.h" #include "kokkos.h" +#include "kokkos_base_fft.h" +#include "kspace.h" +#include "memory_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index b5e6174528..79fd0685b0 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -12,19 +12,17 @@ ------------------------------------------------------------------------- */ #include "kokkos.h" -#include -#include + +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neighbor_kokkos.h" + #include -#include #include #include #include -#include "lammps.h" -#include "force.h" -#include "neighbor_kokkos.h" -#include "neigh_list_kokkos.h" -#include "error.h" -#include "memory_kokkos.h" #ifdef KOKKOS_ENABLE_CUDA diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h index 39d30ac785..83e8b9ec7c 100644 --- a/src/KOKKOS/memory_kokkos.h +++ b/src/KOKKOS/memory_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_MEMORY_KOKKOS_H #define LMP_MEMORY_KOKKOS_H -#include "memory.h" +#include "memory.h" // IWYU pragma: export #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index e5f22411f6..032538fe60 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -16,32 +16,31 @@ ------------------------------------------------------------------------- */ #include "min_kokkos.h" -#include -#include -#include + +#include "angle.h" #include "atom_kokkos.h" -#include "atom_vec.h" -#include "domain.h" +#include "atom_masks.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" -#include "fix_minimize_kokkos.h" #include "compute.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_minimize_kokkos.h" +#include "force.h" #include "improper.h" +#include "kokkos.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "kokkos.h" -#include "atom_masks.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index cb07c7db86..3c94f07233 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "min_linesearch_kokkos.h" -#include -#include + #include "atom_kokkos.h" #include "modify.h" #include "fix_minimize_kokkos.h" @@ -27,6 +26,8 @@ #include "error.h" #include "atom_masks.h" +#include + using namespace LAMMPS_NS; // ALPHA_MAX = max alpha allowed to avoid long backtracks diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp index 89a69dc633..158a87796e 100644 --- a/src/KOKKOS/nbin_kokkos.cpp +++ b/src/KOKKOS/nbin_kokkos.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "nbin_kokkos.h" -#include "neighbor.h" + #include "atom_kokkos.h" -#include "group.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "update.h" -#include "error.h" -#include "atom_masks.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index bf9234e17c..021dcc7a1c 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -16,22 +16,22 @@ ------------------------------------------------------------------------- */ #include "neigh_bond_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "update.h" #include "domain_kokkos.h" -#include "output.h" -#include "thermo.h" -#include "memory_kokkos.h" #include "error.h" -#include "modify.h" #include "fix.h" -#include -#include "atom_masks.h" -#include "domain.h" +#include "force.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "output.h" +#include "thermo.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; #define BONDDELTA 10000 diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index 14591f8246..7db78e38d2 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "neigh_list_kokkos.h" -#include "atom.h" -#include "memory_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index edd775f7f9..8ae873036b 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -15,7 +15,8 @@ #define LMP_NEIGH_LIST_KOKKOS_H #include "pointers.h" -#include "neigh_list.h" + +#include "neigh_list.h" // IWYU pragma: export #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index 4d0cf7ea3a..b21a7cb1ee 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -12,25 +12,26 @@ ------------------------------------------------------------------------- */ #include "neighbor_kokkos.h" + +#include "angle.h" #include "atom_kokkos.h" -#include "pair.h" -#include "fix.h" -#include "neigh_request.h" -#include "memory_kokkos.h" -#include "update.h" #include "atom_masks.h" -#include "error.h" -#include "kokkos.h" -#include "force.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "improper.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "neigh_request.h" +#include "pair.h" #include "style_nbin.h" -#include "style_nstencil.h" #include "style_npair.h" +#include "style_nstencil.h" #include "style_ntopo.h" -#include "comm.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 3829502c0d..304fe8f1da 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -14,11 +14,10 @@ #ifndef LMP_NEIGHBOR_KOKKOS_H #define LMP_NEIGHBOR_KOKKOS_H -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: export #include "neigh_list_kokkos.h" #include "neigh_bond_kokkos.h" #include "kokkos_type.h" -#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/npair_halffull_kokkos.cpp b/src/KOKKOS/npair_halffull_kokkos.cpp index b109010935..ca9c14b29d 100644 --- a/src/KOKKOS/npair_halffull_kokkos.cpp +++ b/src/KOKKOS/npair_halffull_kokkos.cpp @@ -12,15 +12,14 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_kokkos.h" -#include "neighbor.h" -#include "neigh_list_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "molecule.h" #include "domain.h" -#include "my_page.h" -#include "error.h" -#include "atom_masks.h" +#include "neigh_list_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index 13080a9580..81f78844d3 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_kokkos.h" -#include "neigh_list_kokkos.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" +#include "neigh_list_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index ffafdf7f17..396a5f2d48 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -19,7 +19,7 @@ #define LMP_PAIR_KOKKOS_H #include "Kokkos_Macros.hpp" -#include "pair.h" +#include "pair.h" // IWYU pragma: export #include "neighbor_kokkos.h" #include "neigh_list_kokkos.h" #include "Kokkos_Vectorization.hpp" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index bf8518e3c3..3a7359df93 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -16,25 +16,23 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_kokkos.h" -#include -#include -#include "kokkos.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list_kokkos.h" +#include "kokkos.h" #include "math_const.h" #include "math_special.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neigh_request.h" +#include "neighbor.h" #include "reaxc_defs.h" #include "reaxc_lookup.h" #include "reaxc_tool_box.h" +#include + #define TEAMSIZE 128 diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index f5489c0e0c..b5dd43f12a 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -16,20 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta_kokkos.h" -#include -#include -#include "kokkos.h" -#include "pair_kokkos.h" + #include "atom_kokkos.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" +#include "atom_masks.h" #include "comm.h" -#include "memory_kokkos.h" -#include "neigh_list_kokkos.h" #include "error.h" -#include "atom_masks.h" +#include "force.h" +#include "kokkos.h" #include "math_const.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 2eea527947..4a795833fb 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -16,26 +16,22 @@ ------------------------------------------------------------------------- */ #include "pppm_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "comm.h" -#include "gridcomm_kokkos.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" +#include "atom_masks.h" #include "domain.h" -#include "fft3d_kokkos.h" -#include "remap_kokkos.h" -#include "memory_kokkos.h" #include "error.h" -#include "atom_masks.h" +#include "fft3d_kokkos.h" +#include "force.h" +#include "gridcomm_kokkos.h" #include "kokkos.h" -#include "utils.h" -#include "fmt/format.h" - #include "math_const.h" #include "math_special_kokkos.h" +#include "memory_kokkos.h" +#include "pair.h" +#include "remap_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index d496db05e2..af87ba3644 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "remap_kokkos.h" -#include "pack_kokkos.h" + #include "error.h" +#include "pack_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index b6e0b0dac5..7aad7f754a 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -15,20 +15,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - #include "angle_charmm_intel.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "modify.h" #include "math_const.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 6d3deee9ba..290f7320b1 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -15,20 +15,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - #include "angle_harmonic_intel.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "modify.h" #include "math_const.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 072800db42..6b458aeefb 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -15,19 +15,21 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "bond_fene_intel.h" + #include "atom.h" -#include "modify.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 1ddb424a7b..84d94b8f3d 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -15,19 +15,20 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - #include "bond_harmonic_intel.h" + #include "atom.h" -#include "modify.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index cd62012255..67b82b62bf 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "dihedral_fourier_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" +#include "suffix.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index dd8c3d98db..ea9bc33c57 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "dihedral_harmonic_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" +#include "suffix.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index ef48f7e8ee..fa8fd53def 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "dihedral_opls_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" +#include "suffix.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index b3649be7c8..eacbc7ddcc 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -16,8 +16,8 @@ Anupama Kurpad (Intel) - Host Affinitization ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_intel.h" + #include "comm.h" #include "error.h" #include "force.h" @@ -25,17 +25,10 @@ #include "neigh_request.h" #include "pair.h" #include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" -#include "timer.h" -#include "universe.h" #include "update.h" - #include -#include -#include - #ifdef _LMP_INTEL_OFFLOAD #ifndef INTEL_OFFLOAD_NOAFFINITY #include diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index a072e823a4..2122bfd370 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "fix_nh_intel.h" + #include "atom.h" -#include "compute.h" #include "domain.h" #include "error.h" #include "force.h" -#include "kspace.h" #include "memory.h" #include "modify.h" #include "neighbor.h" @@ -29,7 +28,6 @@ #include #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp index 7eeb8a1635..55e51227f4 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp @@ -15,18 +15,16 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere_intel.h" -#include "math_extra_intel.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" +#include "error.h" #include "force.h" +#include "math_extra_intel.h" +#include "memory.h" #include "neighbor.h" #include "update.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index f5a5dabfb1..4382542710 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -11,18 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod_intel.h" -#include "math_extra.h" + #include "atom.h" +#include "compute.h" #include "domain.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "compute.h" -#include "error.h" +#include "group.h" +#include "math_extra.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 04791dee78..dc5b0fad5a 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -12,8 +12,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "intel_buffers.h" + #include "force.h" #include "memory.h" diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 78c6246389..4a046bc845 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include "nbin_intel.h" + #include "atom.h" -#include "group.h" #include "comm.h" -#include "domain.h" +#include "error.h" +#include "group.h" #include "modify.h" #include "update.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index f7a233efc9..9aae0d27b7 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -15,13 +15,13 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" +#include "npair_intel.h" + #include "comm.h" #include "domain.h" -#include "timer.h" #include "modify.h" -#include "npair_intel.h" -#include "nstencil.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index ee4670fe59..ce38cb0544 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -26,13 +26,11 @@ . ----------------------------------------------------------------------*/ -#include "omp_compat.h" #include "reaxc_forces_omp.h" -#include -#include + #include "fix_omp.h" -#include "reaxc_defs.h" #include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" @@ -44,6 +42,11 @@ #include "reaxc_valence_angles_omp.h" #include "reaxc_vector.h" +#include +#include + +#include "omp_compat.h" + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index b0cf4a5fb8..fd216844eb 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -27,7 +27,7 @@ ----------------------------------------------------------------------*/ #include "reaxc_init_md_omp.h" -#include + #include "reaxc_defs.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" @@ -38,6 +38,8 @@ #include "error.h" #include "fmt/format.h" +#include + // Functions defined in reaxc_init_md.cpp extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); extern int Init_System(reax_system*, control_params*, char*); diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 5f4b6d4eb0..57c056fff7 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -27,14 +27,16 @@ ----------------------------------------------------------------------*/ #include "reaxc_multi_body_omp.h" -#include -#include + #include "fix_omp.h" -#include #include "pair_reaxc_omp.h" + #include "reaxc_defs.h" #include "reaxc_list.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index 68bacb7202..7d567b259c 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -27,7 +27,7 @@ ----------------------------------------------------------------------*/ #include "reaxc_torsion_angles_omp.h" -#include + #include "fix_omp.h" #include "pair_reaxc_omp.h" @@ -36,6 +36,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 104fadbbae..f9117d3a53 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -27,11 +27,10 @@ ----------------------------------------------------------------------*/ #include "reaxc_valence_angles_omp.h" -#include -#include -#include "pair_reaxc_omp.h" -#include "fix_omp.h" + #include "error.h" +#include "fix_omp.h" +#include "pair_reaxc_omp.h" #include "reaxc_defs.h" #include "reaxc_types.h" @@ -39,6 +38,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif -- GitLab From 05c7cfe59f09f76b3ce4ac22e98bde3df3969bde Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 11:16:32 -0400 Subject: [PATCH 58/75] more include updates for USER-OMP --- src/USER-OMP/ewald_omp.cpp | 12 ++++++------ src/USER-OMP/improper_fourier_omp.cpp | 12 +++++++----- src/USER-OMP/improper_ring_omp.cpp | 11 ++++++----- src/USER-OMP/msm_cg_omp.cpp | 17 +++++++---------- src/USER-OMP/msm_omp.cpp | 7 ++++--- src/USER-OMP/pppm_cg_omp.cpp | 14 ++++++++------ src/USER-OMP/pppm_disp_tip4p_omp.cpp | 13 ++++++++----- src/USER-OMP/pppm_omp.cpp | 10 +++++----- src/USER-OMP/pppm_tip4p_omp.cpp | 13 +++++++------ src/USER-OMP/respa_omp.cpp | 20 ++++++++++---------- src/USER-OMP/thr_data.h | 2 +- 11 files changed, 69 insertions(+), 62 deletions(-) diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index ec8d708da2..d5480d2a9f 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -15,18 +15,18 @@ Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "ewald_omp.h" -#include -#include + #include "atom.h" #include "comm.h" #include "force.h" -#include "memory.h" -#include "timer.h" #include "math_const.h" - +#include "memory.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index 0671bdc375..3763465e79 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -15,18 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "improper_fourier_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "neighbor.h" +#include "suffix.h" #include "timer.h" -#include "force.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define TOLERANCE 0.05 diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index 4ba67aab70..51ea5e5198 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,17 +15,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "improper_ring_omp.h" -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "timer.h" #include "force.h" #include "math_special.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 524850eb63..93904fd8f8 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,24 +16,21 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "msm_cg_omp.h" -#include -#include -#include -#include #include "atom.h" -#include "gridcomm.h" #include "domain.h" #include "error.h" #include "force.h" -#include "neighbor.h" +#include "gridcomm.h" #include "memory.h" +#include "neighbor.h" #include "thr_omp.h" -#include "timer.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 2689226725..783ebb40f1 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -15,14 +15,15 @@ Contributing authors: Axel Kohlmeyer (Temple U), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "msm_omp.h" -#include + #include "comm.h" #include "domain.h" #include "error.h" -#include "timer.h" +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 31098d2675..86997713ef 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,22 +15,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_cg_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index 7da4257e07..93b7a87a61 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,21 +15,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_disp_tip4p_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index e3e46f4de0..7065588526 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,19 +15,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 8bd9805f01..936f3cf31c 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,11 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_tip4p_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" @@ -27,12 +24,16 @@ #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index b5e5293aa4..b8d0af5c86 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,25 +15,25 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "respa_omp.h" -#include "neighbor.h" -#include "comm.h" + +#include "angle.h" #include "atom.h" -#include "domain.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "update.h" -#include "modify.h" -#include "error.h" -#include "timer.h" +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 4853d6dbbf..4b87357101 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,7 +18,7 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#include "timer.h" +#include "timer.h" // IWYU pragma: export namespace LAMMPS_NS { -- GitLab From 93d0358ebc5e91428bb686ace66713c0275bb4b6 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 3 Sep 2020 11:36:02 -0600 Subject: [PATCH 59/75] cmake: use static iwyu-extra-map.imp --- cmake/CMakeLists.txt | 9 +-------- cmake/iwyu/iwyu-extra-map.imp | 4 ++++ 2 files changed, 5 insertions(+), 8 deletions(-) create mode 100644 cmake/iwyu/iwyu-extra-map.imp diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 87c70e4483..9fff73f49e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -260,16 +260,9 @@ if(ENABLE_IWYU) if (IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu - ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp COMMENT "Running IWYU") add_dependencies(iwyu lammps) - # generate file with additional mappings - file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "[\n") - file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp - " { include: [ \"\", private, \"\", public ] },\n") - file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp - " { include: [ \"\", public, \"\", public ] },\n") - file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "]\n") else() message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" "and the iwyu-tool/iwyu_tool script installed in your PATH") diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp new file mode 100644 index 0000000000..8985998704 --- /dev/null +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -0,0 +1,4 @@ +[ + { include: [ "", private, "", public ] } + { include: [ "", public, "", public ] } +] -- GitLab From 390c6ba1061d5461995f905c78af7418c9dd368c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 15:28:07 -0400 Subject: [PATCH 60/75] rechecking some corefiles with IWYU after the many updates --- src/comm.cpp | 8 ++++---- src/finish.cpp | 6 +++--- src/group.cpp | 1 + src/lammps.cpp | 6 +++--- src/molecule.cpp | 15 +++++++-------- src/molecule.h | 2 +- src/output.cpp | 4 ++-- src/read_dump.cpp | 4 ++-- src/reader_native.cpp | 1 - src/reset_mol_ids.cpp | 2 ++ src/reset_mol_ids.h | 1 - src/timer.cpp | 8 +++----- src/universe.cpp | 1 - 13 files changed, 28 insertions(+), 31 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 24a5d050d4..7b351e12fc 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -14,20 +14,20 @@ #include "comm.h" #include "accelerator_kokkos.h" -#include "atom.h" +#include "atom.h" // IWYU pragma: keep #include "atom_vec.h" #include "bond.h" #include "compute.h" -#include "domain.h" +#include "domain.h" // IWYU pragma: keep #include "dump.h" #include "error.h" #include "fix.h" #include "force.h" #include "group.h" #include "irregular.h" -#include "memory.h" +#include "memory.h" // IWYU pragma: keep #include "modify.h" -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: keep #include "output.h" #include "pair.h" #include "procmap.h" diff --git a/src/finish.cpp b/src/finish.cpp index 7990a3c141..3bfe3a7bbf 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -20,13 +20,13 @@ #include "error.h" #include "force.h" #include "kspace.h" -#include "memory.h" +#include "memory.h" // IWYU pragma: keep #include "min.h" #include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" -#include "neighbor.h" -#include "timer.h" +#include "neighbor.h" // IWYU pragma: keep +#include "timer.h" // IWYU pragma: keep #include "universe.h" #include "update.h" diff --git a/src/group.cpp b/src/group.cpp index ee96c20f47..a2e20a6ab1 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -33,6 +33,7 @@ #include #include #include +#include using namespace LAMMPS_NS; diff --git a/src/lammps.cpp b/src/lammps.cpp index b6c8450a4d..4d643c327c 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -30,12 +30,12 @@ #include "universe.h" #include "input.h" #include "info.h" -#include "atom.h" +#include "atom.h" // IWYU pragma: keep #include "update.h" -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: keep #include "comm.h" #include "comm_brick.h" -#include "domain.h" +#include "domain.h" // IWYU pragma: keep #include "force.h" #include "modify.h" #include "group.h" diff --git a/src/molecule.cpp b/src/molecule.cpp index 18f5c38992..0d81f49a50 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -12,23 +12,22 @@ ------------------------------------------------------------------------- */ #include "molecule.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" -#include "force.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" #include "tokenizer.h" +#include +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 256 diff --git a/src/molecule.h b/src/molecule.h index d752be3f81..5a3fa5a327 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -15,7 +15,7 @@ #define LMP_ONE_MOLECULE_H #include "pointers.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/output.cpp b/src/output.cpp index 9b091f89a2..6c90198de4 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "output.h" -#include "style_dump.h" +#include "style_dump.h" // IWYU pragma: keep #include "atom.h" #include "comm.h" @@ -79,7 +79,7 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp) #define DUMP_CLASS #define DumpStyle(key,Class) \ (*dump_map)[#key] = &dump_creator; -#include "style_dump.h" +#include "style_dump.h" // IWYU pragma: keep #undef DumpStyle #undef DUMP_CLASS } diff --git a/src/read_dump.cpp b/src/read_dump.cpp index eb58d3e3ff..10218fe617 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -29,7 +29,7 @@ #include "irregular.h" #include "memory.h" #include "reader.h" -#include "style_reader.h" +#include "style_reader.h" // IWYU pragma: keep #include "update.h" #include @@ -243,7 +243,7 @@ void ReadDump::setup_reader(int narg, char **arg) for (int i = 0; i < nreader; i++) \ readers[i] = new Class(lmp); \ } -#include "style_reader.h" +#include "style_reader.h" // IWYU pragma: keep #undef READER_CLASS // unrecognized style diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 19e53f3efe..e0f0d7792b 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -13,7 +13,6 @@ #include "reader_native.h" -#include "atom.h" #include "error.h" #include "memory.h" #include "tokenizer.h" diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index 0d9fe55e07..ad2caad656 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -26,6 +26,8 @@ #include "group.h" #include "modify.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index 9d2dd24bc8..fbb6fceb03 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -21,7 +21,6 @@ CommandStyle(reset_mol_ids,ResetMolIDs) #define LMP_RESET_MOL_IDS_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/timer.cpp b/src/timer.cpp index b9124978a9..adf143b4ae 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -12,13 +12,11 @@ ------------------------------------------------------------------------- */ #include "timer.h" -#include -#include -#include + #include "comm.h" #include "error.h" -#include "force.h" -#include "utils.h" + +#include #ifdef _WIN32 #include diff --git a/src/universe.cpp b/src/universe.cpp index acb5100337..838313665e 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -14,7 +14,6 @@ #include "universe.h" #include "error.h" -#include "force.h" #include "memory.h" #include "version.h" -- GitLab From 508b49c976303738e812de845ae3d6c5623e65cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 00:45:41 -0400 Subject: [PATCH 61/75] add missing comma --- cmake/iwyu/iwyu-extra-map.imp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index 8985998704..8f6af087b4 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -1,4 +1,4 @@ [ - { include: [ "", private, "", public ] } - { include: [ "", public, "", public ] } + { include: [ "", private, "", public ] }, + { include: [ "", public, "", public ] }, ] -- GitLab From 2e0af2fdcead01067edf54f10af585b4b78f03ec Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 00:46:23 -0400 Subject: [PATCH 62/75] some more second pass cleanup --- src/KIM/kim_init.h | 1 - src/KIM/kim_interactions.h | 1 - src/KIM/kim_param.h | 1 - src/KIM/kim_query.h | 1 - src/KOKKOS/min_linesearch_kokkos.cpp | 7 +++---- src/KSPACE/pppm_dipole.cpp | 23 +++++++++------------ src/MANYBODY/pair_polymorphic.cpp | 19 ++++++++--------- src/MANYBODY/pair_polymorphic.h | 1 - src/MC/fix_widom.cpp | 1 - src/MC/fix_widom.h | 1 - src/MLIAP/mliap_data.cpp | 2 -- src/USER-MISC/fix_accelerate_cos.cpp | 2 ++ src/USER-MISC/fix_propel_self.cpp | 1 + src/USER-MISC/fix_wall_reflect_stochastic.h | 1 - src/USER-MISC/pair_local_density.cpp | 1 - src/potential_file_reader.h | 2 +- src/text_file_reader.h | 5 ++--- src/tokenizer.cpp | 4 ++-- 18 files changed, 30 insertions(+), 44 deletions(-) diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 3311d4e13d..8fa3247b22 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -66,7 +66,6 @@ CommandStyle(kim_init,KimInit) #define LMP_KIM_INIT_H #include "pointers.h" -#include // Forward declaration. typedef struct KIM_Model KIM_Model; diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h index 414c7b39d5..071e5b284f 100644 --- a/src/KIM/kim_interactions.h +++ b/src/KIM/kim_interactions.h @@ -66,7 +66,6 @@ CommandStyle(kim_interactions,KimInteractions) #define LMP_KIM_INTERACTIONS_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h index a4e26451f2..e4fc5ce59a 100644 --- a/src/KIM/kim_param.h +++ b/src/KIM/kim_param.h @@ -65,7 +65,6 @@ CommandStyle(kim_param, KimParam) #define LMP_KIM_PARAM_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 6888f911f4..e1c49ed71d 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -64,7 +64,6 @@ CommandStyle(kim_query,KimQuery) #define LMP_KIM_QUERY_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index 3c94f07233..4306a5bd3b 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -18,13 +18,12 @@ #include "min_linesearch_kokkos.h" #include "atom_kokkos.h" -#include "modify.h" +#include "atom_masks.h" +#include "error.h" #include "fix_minimize_kokkos.h" -#include "pair.h" #include "output.h" +#include "pair.h" #include "thermo.h" -#include "error.h" -#include "atom_masks.h" #include diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 1a87c81bee..1b7d325326 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -16,26 +16,23 @@ ------------------------------------------------------------------------- */ #include "pppm_dipole.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" #include "fft3d_wrap.h" -#include "remap_wrap.h" +#include "force.h" +#include "gridcomm.h" +#include "math_const.h" +#include "math_special.h" #include "memory.h" -#include "error.h" +#include "pair.h" +#include "remap_wrap.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" -#include "math_special.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 4c8ebaf8ad..0f7fd7a1c7 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -18,20 +18,19 @@ #include "pair_polymorphic.h" -#include - -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 18956699d7..2593905b22 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -22,7 +22,6 @@ PairStyle(polymorphic,PairPolymorphic) #include "pair.h" #include -#include namespace LAMMPS_NS { diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index d7fdf69b86..94b2481742 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -20,7 +20,6 @@ #include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "bond.h" #include "comm.h" #include "compute.h" diff --git a/src/MC/fix_widom.h b/src/MC/fix_widom.h index 05060e76ac..19102e4f4a 100644 --- a/src/MC/fix_widom.h +++ b/src/MC/fix_widom.h @@ -20,7 +20,6 @@ FixStyle(widom,FixWidom) #ifndef LMP_FIX_WIDOM_H #define LMP_FIX_WIDOM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MLIAP/mliap_data.cpp b/src/MLIAP/mliap_data.cpp index 28f9a988d8..a7e50012cb 100644 --- a/src/MLIAP/mliap_data.cpp +++ b/src/MLIAP/mliap_data.cpp @@ -19,8 +19,6 @@ #include "mliap_model.h" #include "neigh_list.h" -#include - using namespace LAMMPS_NS; MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in, diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/USER-MISC/fix_accelerate_cos.cpp index 4e84b47ac3..4c15685556 100644 --- a/src/USER-MISC/fix_accelerate_cos.cpp +++ b/src/USER-MISC/fix_accelerate_cos.cpp @@ -23,6 +23,8 @@ #include "force.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index e17ef4652f..522c2eb4a5 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -27,6 +27,7 @@ #include "math_extra.h" #include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.h b/src/USER-MISC/fix_wall_reflect_stochastic.h index 0568dc8ae5..558ad7d084 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.h +++ b/src/USER-MISC/fix_wall_reflect_stochastic.h @@ -20,7 +20,6 @@ FixStyle(wall/reflect/stochastic,FixWallReflectStochastic) #ifndef LMP_FIX_WALL_REFLECT_STOCHASTIC_H #define LMP_FIX_WALL_REFLECT_STOCHASTIC_H -#include "random_mars.h" #include "fix_wall_reflect.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index f8b813ef0b..404f6e2db1 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -28,7 +28,6 @@ #include "neigh_list.h" #include "neighbor.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 57aa827638..d3befca282 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -18,7 +18,7 @@ #ifndef LMP_POTENTIAL_FILE_READER_H #define LMP_POTENTIAL_FILE_READER_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export #include "tokenizer.h" namespace LAMMPS_NS diff --git a/src/text_file_reader.h b/src/text_file_reader.h index e74a285961..65af0a08d9 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -18,11 +18,10 @@ #ifndef LMP_TEXT_FILE_READER_H #define LMP_TEXT_FILE_READER_H -#include -#include - #include "tokenizer.h" +#include + namespace LAMMPS_NS { class TextFileReader { diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index 33a81db748..3b172181a2 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -17,11 +17,11 @@ #include "tokenizer.h" #include "utils.h" +#include "fmt/format.h" + #include #include -#include "fmt/format.h" - using namespace LAMMPS_NS; TokenizerException::TokenizerException(const std::string & msg, const std::string & token){ -- GitLab From d0691d0a5d7291379293e3a3b45671c5a21458ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 01:32:15 -0400 Subject: [PATCH 63/75] add mapping for Eigen3 includes --- cmake/iwyu/iwyu-extra-map.imp | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index 8f6af087b4..a6d88cf571 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -1,4 +1,5 @@ [ { include: [ "", private, "", public ] }, { include: [ "", public, "", public ] }, + { include: [ "@", private, "", public ] }, ] -- GitLab From fc3d9fee5e4aeae2dc6ba04d1ee5fce475b59581 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 01:32:52 -0400 Subject: [PATCH 64/75] more USER-OMP updates --- src/USER-OMP/angle_charmm_omp.cpp | 2 +- src/USER-OMP/angle_class2_omp.cpp | 2 +- src/USER-OMP/angle_cosine_delta_omp.cpp | 2 +- src/USER-OMP/angle_cosine_omp.cpp | 2 +- src/USER-OMP/angle_cosine_periodic_omp.cpp | 2 +- src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 2 +- src/USER-OMP/angle_cosine_shift_omp.cpp | 2 +- src/USER-OMP/angle_cosine_squared_omp.cpp | 2 +- src/USER-OMP/angle_dipole_omp.cpp | 2 +- src/USER-OMP/angle_fourier_omp.cpp | 2 +- src/USER-OMP/angle_fourier_simple_omp.cpp | 2 +- src/USER-OMP/angle_harmonic_omp.cpp | 2 +- src/USER-OMP/angle_quartic_omp.cpp | 2 +- src/USER-OMP/angle_sdk_omp.cpp | 2 +- src/USER-OMP/angle_table_omp.cpp | 2 +- src/USER-OMP/bond_class2_omp.cpp | 2 +- src/USER-OMP/bond_fene_expand_omp.cpp | 2 +- src/USER-OMP/bond_fene_omp.cpp | 2 +- src/USER-OMP/bond_gromos_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_omp.cpp | 2 +- src/USER-OMP/bond_morse_omp.cpp | 2 +- src/USER-OMP/bond_nonlinear_omp.cpp | 2 +- src/USER-OMP/bond_quartic_omp.cpp | 2 +- src/USER-OMP/bond_table_omp.cpp | 2 +- src/USER-OMP/dihedral_charmm_omp.cpp | 2 +- src/USER-OMP/dihedral_class2_omp.cpp | 2 +- src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp | 2 +- src/USER-OMP/dihedral_fourier_omp.cpp | 2 +- src/USER-OMP/dihedral_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_helix_omp.cpp | 2 +- src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_nharmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_opls_omp.cpp | 2 +- src/USER-OMP/dihedral_quadratic_omp.cpp | 2 +- src/USER-OMP/dihedral_table_omp.cpp | 2 +- src/USER-OMP/fix_omp.cpp | 9 ++++----- src/USER-OMP/fix_rigid_nh_omp.cpp | 2 +- src/USER-OMP/fix_rigid_small_omp.cpp | 2 +- src/USER-OMP/improper_class2_omp.cpp | 2 +- src/USER-OMP/improper_cossq_omp.cpp | 2 +- src/USER-OMP/improper_cvff_omp.cpp | 2 +- src/USER-OMP/improper_fourier_omp.cpp | 2 +- src/USER-OMP/improper_harmonic_omp.cpp | 2 +- src/USER-OMP/improper_umbrella_omp.cpp | 2 +- src/USER-OMP/msm_cg_omp.cpp | 3 +++ src/USER-OMP/pair_adp_omp.cpp | 10 +++++----- src/USER-OMP/pair_airebo_morse_omp.cpp | 2 -- src/USER-OMP/pair_airebo_omp.cpp | 10 +++++----- src/USER-OMP/pair_beck_omp.cpp | 2 +- src/USER-OMP/pair_born_coul_long_omp.cpp | 9 +++++---- src/USER-OMP/pair_born_coul_msm_omp.cpp | 10 ++++++---- src/USER-OMP/pair_born_coul_wolf_omp.cpp | 2 +- src/USER-OMP/pair_born_omp.cpp | 2 +- src/USER-OMP/pair_brownian_omp.cpp | 17 ++++++++--------- src/USER-OMP/pair_brownian_poly_omp.cpp | 16 ++++++++-------- src/USER-OMP/pair_buck_coul_long_omp.cpp | 9 +++++---- src/USER-OMP/pair_buck_coul_msm_omp.cpp | 10 ++++++---- src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 14 +++++++------- src/USER-OMP/pair_buck_omp.cpp | 2 +- src/USER-OMP/pair_colloid_omp.cpp | 11 ++++++----- src/USER-OMP/pair_comb_omp.cpp | 12 +++++++----- src/USER-OMP/pair_coul_cut_omp.cpp | 2 +- src/USER-OMP/pair_coul_debye_omp.cpp | 2 +- src/USER-OMP/pair_coul_dsf_omp.cpp | 2 +- src/USER-OMP/pair_coul_long_omp.cpp | 9 +++++---- src/USER-OMP/pair_coul_msm_omp.cpp | 10 ++++++---- src/USER-OMP/pair_coul_wolf_omp.cpp | 2 +- src/USER-OMP/pair_dpd_omp.cpp | 2 +- src/USER-OMP/pair_dpd_tstat_omp.cpp | 11 ++++++----- src/USER-OMP/pair_gauss_omp.cpp | 9 +++++---- src/USER-OMP/pair_gayberne_omp.cpp | 11 +++++------ src/USER-OMP/pair_lj96_cut_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 10 ++++++---- src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_class2_coul_long_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_class2_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_cubic_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp | 11 ++++++----- src/USER-OMP/pair_lj_cut_coul_long_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 10 ++++++---- src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_cut_omp.cpp | 7 +++---- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 2 +- src/USER-OMP/pair_lj_expand_omp.cpp | 9 +++++---- .../pair_lj_gromacs_coul_gromacs_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_gromacs_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 11 ++++++----- src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp | 15 ++++++++------- src/USER-OMP/pair_lj_smooth_linear_omp.cpp | 9 +++++---- src/USER-OMP/pair_lj_smooth_omp.cpp | 9 +++++---- src/USER-OMP/pair_lubricate_omp.cpp | 17 ++++++++--------- src/USER-OMP/pair_lubricate_poly_omp.cpp | 16 +++++++--------- src/USER-OMP/pair_morse_omp.cpp | 9 +++++---- src/USER-OMP/pair_reaxc_omp.cpp | 2 +- src/USER-OMP/pair_resquared_omp.cpp | 10 ++++------ src/USER-OMP/pair_soft_omp.cpp | 9 +++++---- src/USER-OMP/pair_table_omp.cpp | 8 +++----- src/USER-OMP/pair_ufm_omp.cpp | 9 +++++---- src/USER-OMP/pair_yukawa_colloid_omp.cpp | 9 +++++---- src/USER-OMP/pair_yukawa_omp.cpp | 9 +++++---- src/USER-OMP/pair_zbl_omp.cpp | 9 +++++---- src/USER-OMP/pppm_disp_omp.cpp | 13 +++++++------ src/USER-OMP/thr_omp.cpp | 2 +- 108 files changed, 328 insertions(+), 295 deletions(-) diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 6933afdcd9..abc23367b1 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index 09ee59d5af..b33b1c2e2f 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index ca5afe1449..0c209d3fe5 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 48fdd9ba60..cbeb10e08c 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index a0e45fe131..b59046031a 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "math_special.h" #include "suffix.h" diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 21019336b3..4870e6a3bb 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 1e6d712b62..bec65caf6d 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6df1e028a0..dced90a967 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index 26d8a7817e..cea707161f 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -23,7 +23,7 @@ #include "error.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b6ddea3ff9..ec9236902c 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 992acf7c99..774f06f809 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 0cfc6f95af..5c81e3cba4 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index a774edb8c4..d6e9285f11 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e0bc021f1b..45d6c83aa1 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -20,7 +20,7 @@ #include #include "atom.h" #include "neighbor.h" -#include "timer.h" + #include "comm.h" #include "force.h" #include "lj_sdk_common.h" diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index 1af60f85f6..f67d340176 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index 06edf46024..9c52bdb281 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index 5f3dd48841..38df4f50da 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index ebf5afdc57..5dde355a76 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index d4d2d25601..012737f77d 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index 9160ee7023..e8f17d5eae 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 7a6c616e4a..61a60fa995 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 19f0a08510..50b4ed98a7 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index 90318c8faf..51586370f5 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 809950f2b7..720d660eae 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index 0efaa10e37..bc1ae96ac9 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index f503bcab26..3ccc65441a 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index afd3071434..8454dc1004 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 49b8659e2f..cf65d735a6 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index cea22adf1b..5d9164d3b3 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 756931774a..be19a6d958 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index d1f511954e..3d51a4db43 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 5289fc2c62..5209fac23a 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index edf8a20899..a6e0ab66d6 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index bf51a01713..4604771912 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "update.h" #include "error.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 8814d3f3f0..ff0f6bb12b 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index e61c5f0d85..5ffb8d64f2 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "update.h" #include "error.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index bf5332a1c1..c18d5fb4c0 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -23,7 +23,7 @@ #include "domain.h" #include "neighbor.h" #include "force.h" -#include "timer.h" + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 47757c4ec3..f3c86a7746 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -16,7 +16,9 @@ OpenMP based threading support for LAMMPS ------------------------------------------------------------------------- */ -#include "omp_compat.h" +#include "fix_omp.h" +#include "thr_data.h" + #include "atom.h" #include "comm.h" #include "error.h" @@ -25,10 +27,6 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "timer.h" - -#include "fix_omp.h" -#include "thr_data.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -39,6 +37,7 @@ #include +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index f53fcf63bc..9038efec13 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -31,7 +31,7 @@ #include "kspace.h" #include "modify.h" #include "update.h" -#include "timer.h" + #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 227b0e1f8a..f720dd617e 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -24,7 +24,7 @@ #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" -#include "timer.h" + #if defined(_OPENMP) #include diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index 8927980951..05fc8e4475 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 72d76e8c42..e2a43c58c4 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index e9ff4bfc73..715819cfb9 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index 3763465e79..93dfb9bc99 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -23,7 +23,7 @@ #include "force.h" #include "neighbor.h" #include "suffix.h" -#include "timer.h" + #include "update.h" #include diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 8bef42bf23..6bb76871b2 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index bf466afb19..0c9befade6 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 93904fd8f8..c42aa8e0c1 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -31,6 +31,9 @@ #include #include "omp_compat.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 63a539c93c..97d94e5513 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -12,19 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_adp_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_airebo_morse_omp.cpp b/src/USER-OMP/pair_airebo_morse_omp.cpp index 5d5ac0b885..6977842af2 100644 --- a/src/USER-OMP/pair_airebo_morse_omp.cpp +++ b/src/USER-OMP/pair_airebo_morse_omp.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse_omp.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 25d6c35174..77dd874076 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -12,19 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_airebo_omp.h" + #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" +#include "math_special.h" #include "memory.h" #include "my_page.h" -#include "math_special.h" -#include "neighbor.h" #include "neigh_list.h" +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index bb41334153..01e33dc5c5 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_special.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp index 7f92ab6734..b410c998e1 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.cpp +++ b/src/USER-OMP/pair_born_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_born_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp index eec1765859..4adba396e8 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_born_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index ffa069ec4e..9bc6507c6a 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_const.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index aaac28d07c..e74f0139c1 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index ca28fa14bb..b7b82c3dac 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,26 +12,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_brownian_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" +#include "math_special.h" #include "neigh_list.h" +#include "random_mars.h" +#include "suffix.h" #include "update.h" #include "variable.h" -#include "random_mars.h" -#include "math_const.h" -#include "math_special.h" -#include "timer.h" -#include "fix_wall.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 939bc223eb..4d8b457281 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,25 +12,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_brownian_poly_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" +#include "math_special.h" #include "neigh_list.h" +#include "random_mars.h" +#include "suffix.h" #include "update.h" #include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "math_const.h" -#include "math_special.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp index 1be2b7272f..264073a07e 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp index b26243b19a..631a1ee61d 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index a2e34b9a1b..71b1540e8c 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -11,18 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - -#include "omp_compat.h" -#include -#include "math_vector.h" #include "pair_buck_long_coul_long_omp.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" #include "force.h" - +#include "math_vector.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index fc85d79c81..bddacaf5b5 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp index cce588f516..94325232fc 100644 --- a/src/USER-OMP/pair_colloid_omp.cpp +++ b/src/USER-OMP/pair_colloid_omp.cpp @@ -12,18 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_colloid_omp.h" + #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_special.h" - +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index 8912cbc243..9a0155d6d3 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -12,19 +12,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_comb_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "group.h" -#include "force.h" #include "memory.h" #include "my_page.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; #define MAXNEIGH 24 diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 69eb9ac0f3..57b821cb8b 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index c22f7340c4..1bb8676998 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index ddcc8dbeb0..3a8db45634 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp index 6c9b9d034d..92cb51f7a4 100644 --- a/src/USER-OMP/pair_coul_long_omp.cpp +++ b/src/USER-OMP/pair_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp index 32a657e286..e907d63eb1 100644 --- a/src/USER-OMP/pair_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index d0f6fdb125..71e8148a50 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_const.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index f3a1c29a70..6e3da77cbe 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "update.h" #include "random_mars.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp index 06e80274bd..823367109b 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.cpp +++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp @@ -12,18 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_dpd_tstat_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" #include "random_mars.h" - #include "suffix.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EPSILON 1.0e-10 diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp index 103a766614..3e5777e4ec 100644 --- a/src/USER-OMP/pair_gauss_omp.cpp +++ b/src/USER-OMP/pair_gauss_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gauss_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EPSILON 1.0e-10 diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp index f0fd60a309..991c72a9be 100644 --- a/src/USER-OMP/pair_gayberne_omp.cpp +++ b/src/USER-OMP/pair_gayberne_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gayberne_omp.h" -#include "math_extra.h" + #include "atom.h" -#include "comm.h" #include "atom_vec_ellipsoid.h" +#include "comm.h" #include "force.h" -#include "neighbor.h" +#include "math_extra.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp index adf0aac9b2..5aeec25d13 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.cpp +++ b/src/USER-OMP/pair_lj96_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj96_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp index 437bd183ed..56cf0a68dd 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp index 0000e63cda..a39ef0aa81 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp index 59a6841c9e..63fb4fe529 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp index 480e2adae0..f618f7f423 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp index 2b91e10cfa..39cc320e44 100644 --- a/src/USER-OMP/pair_lj_class2_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp index 778c25393d..27f6132491 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.cpp +++ b/src/USER-OMP/pair_lj_cubic_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cubic_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace PairLJCubicConstants; diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp index d560b803f1..2f46e0bfe7 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp index 79754e704b..82031f91ab 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_debye_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp index ec69a1a1ca..7ab6f31b3f 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_dsf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" - #include "suffix.h" -#include "math_const.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp index 618986389c..c7b6de8022 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp index 58e5cee0c2..0e6d11327a 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp index 7d5d25c39b..2cc915a435 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_dipole_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp index 3e7e92de21..2aa71026e3 100644 --- a/src/USER-OMP/pair_lj_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index fb579fb980..9296050173 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -32,7 +32,7 @@ #include "math_const.h" #include "error.h" #include "suffix.h" -#include "timer.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp index 70b5e436fa..89077ba6af 100644 --- a/src/USER-OMP/pair_lj_expand_omp.cpp +++ b/src/USER-OMP/pair_lj_expand_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_expand_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp index 0f0a8de2ff..26a6e979b4 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_gromacs_coul_gromacs_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp index ea2c9e8f55..3082091539 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_gromacs_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index e74f487129..d869d91d09 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_long_coul_long_omp.h" + #include "atom.h" #include "comm.h" -#include "math_vector.h" #include "force.h" -#include "neighbor.h" +#include "math_vector.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index 9c8de110d7..af24e93a41 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -12,20 +12,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_long_tip4p_long_omp.h" + #include "atom.h" -#include "domain.h" #include "comm.h" -#include "math_vector.h" -#include "force.h" -#include "neighbor.h" +#include "domain.h" #include "error.h" +#include "force.h" #include "memory.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp index 497c2c3a43..2c0c028189 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_smooth_linear_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp index bdb9b3141e..0b4ea4e5f8 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_smooth_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 9db4239587..827fae8e44 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -12,24 +12,23 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lubricate_omp.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" -#include "update.h" +#include "neighbor.h" +#include "suffix.h" #include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "fix_deform.h" -#include "math_const.h" -#include "suffix.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index dc143a3160..feb110194f 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,24 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_lubricate_poly_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" -#include "update.h" +#include "suffix.h" #include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "fix_deform.h" -#include "math_const.h" -#include "suffix.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp index 1f566dbd42..48687781ef 100644 --- a/src/USER-OMP/pair_morse_omp.cpp +++ b/src/USER-OMP/pair_morse_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_morse_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 08efb73aab..dfc1f428eb 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -48,7 +48,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "timer.h" + #include "reaxc_defs.h" #include "reaxc_types.h" diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp index 557d212531..689ff297e5 100644 --- a/src/USER-OMP/pair_resquared_omp.cpp +++ b/src/USER-OMP/pair_resquared_omp.cpp @@ -12,18 +12,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_resquared_omp.h" -#include "math_extra.h" + #include "atom.h" #include "comm.h" -#include "atom_vec_ellipsoid.h" #include "force.h" -#include "neighbor.h" +#include "math_extra.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp index 85425974cc..f733b5106f 100644 --- a/src/USER-OMP/pair_soft_omp.cpp +++ b/src/USER-OMP/pair_soft_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp index 2546bfdc9a..f5fbabccab 100644 --- a/src/USER-OMP/pair_table_omp.cpp +++ b/src/USER-OMP/pair_table_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_table_omp.h" + #include "atom.h" #include "comm.h" -#include "error.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp index 605d6dd2c6..e1c2ff457e 100644 --- a/src/USER-OMP/pair_ufm_omp.cpp +++ b/src/USER-OMP/pair_ufm_omp.cpp @@ -14,16 +14,17 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_ufm_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp index e6ac3fa9fb..227ec0744f 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp +++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_yukawa_colloid_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp index f222876cb5..347575e283 100644 --- a/src/USER-OMP/pair_yukawa_omp.cpp +++ b/src/USER-OMP/pair_yukawa_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_yukawa_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp index 284ebbf09c..9679a00b24 100644 --- a/src/USER-OMP/pair_zbl_omp.cpp +++ b/src/USER-OMP/pair_zbl_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_zbl_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace PairZBLConstants; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index aad77cffc7..96a2cc282e 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,23 +16,24 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_disp_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index c086f6d6b5..6e096defa8 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "modify.h" #include "neighbor.h" -#include "timer.h" + #include "thr_omp.h" -- GitLab From bb7447363cd00147c0b3288de48b3ec90d11a77b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 07:22:39 -0400 Subject: [PATCH 65/75] more include cleanup and IWYU tweaks --- src/KIM/kim_param.cpp | 1 - src/KIM/pair_kim.cpp | 13 ++++----- src/MISC/fix_orient_fcc.cpp | 22 ++++++--------- src/MLIAP/mliap_model.cpp | 1 - src/SPIN/min_spin.cpp | 16 +++++------ src/SPIN/min_spin_cg.cpp | 19 ++++++------- src/SPIN/min_spin_lbfgs.cpp | 18 ++++++------ src/SPIN/neb_spin.cpp | 29 +++++++++----------- src/SPIN/pair_spin_dipole_cut.cpp | 11 +++----- src/SPIN/pair_spin_dipole_long.cpp | 11 +++----- src/SPIN/pair_spin_dmi.cpp | 9 ++---- src/SPIN/pair_spin_exchange.cpp | 9 ++---- src/SPIN/pair_spin_magelec.cpp | 9 ++---- src/SPIN/pair_spin_neel.cpp | 9 ++---- src/SRD/fix_wall_srd.cpp | 12 ++++---- src/USER-ATC/fix_atc.cpp | 18 ++++-------- src/USER-ATC/fix_atc.h | 1 - src/USER-AWPMD/atom_vec_wavepacket.cpp | 5 ++-- src/USER-AWPMD/pair_awpmd_cut.cpp | 23 ++++++++-------- src/USER-BOCS/compute_pressure_bocs.cpp | 9 ++---- src/USER-COLVARS/fix_colvars.cpp | 15 ++++------ src/USER-COLVARS/fix_colvars.h | 1 - src/USER-COLVARS/group_ndx.cpp | 5 ++-- src/USER-COLVARS/ndx_group.cpp | 8 +++--- src/USER-DIFFRACTION/compute_saed.cpp | 18 ++++++------ src/USER-DIFFRACTION/compute_xrd.cpp | 18 ++++++------ src/USER-DIFFRACTION/fix_saed_vtk.cpp | 13 ++++----- src/USER-DPD/fix_eos_cv.cpp | 2 +- src/USER-DPD/fix_eos_table.cpp | 4 +-- src/USER-DPD/fix_shardlow.cpp | 23 ++++++++-------- src/USER-DPD/pair_dpd_fdt.cpp | 13 ++++----- src/USER-DPD/pair_dpd_fdt_energy.cpp | 13 ++++----- src/USER-EFF/atom_vec_electron.cpp | 5 ++-- src/USER-EFF/fix_nh_eff.cpp | 2 +- src/USER-MANIFOLD/fix_manifoldforce.cpp | 13 ++++----- src/USER-MANIFOLD/manifold_gaussian_bump.cpp | 2 ++ src/USER-MEAMC/meam.h | 16 ++++++++++- src/USER-MEAMC/meam_dens_final.cpp | 12 ++++++++ src/USER-MEAMC/meam_dens_init.cpp | 12 ++++++++ src/USER-MEAMC/meam_force.cpp | 12 ++++++++ src/USER-MEAMC/meam_setup_done.cpp | 12 ++++++++ src/USER-MEAMC/meam_setup_global.cpp | 12 ++++++++ src/USER-MEAMC/meam_setup_param.cpp | 12 ++++++++ src/USER-MESODPD/atom_vec_edpd.cpp | 9 ++---- src/USER-MESODPD/compute_tdpd_cc_atom.cpp | 11 ++++---- src/USER-MESODPD/fix_edpd_source.cpp | 7 +++-- src/USER-MESODPD/fix_tdpd_source.cpp | 7 +++-- src/USER-MESODPD/pair_mdpd_rhosum.cpp | 8 +++--- src/USER-MISC/fix_propel_self.cpp | 1 - 49 files changed, 282 insertions(+), 249 deletions(-) diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index ae4ca9b13d..6f4ac5cc21 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -57,7 +57,6 @@ #include "kim_param.h" -#include "comm.h" #include "error.h" #include "fix_store_kim.h" #include "force.h" diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 3422f93f3a..7ed70972c5 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -55,21 +55,20 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ #include "pair_kim.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "update.h" -#include "memory.h" -#include "domain.h" -#include "error.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index bcbdcfabc5..f391eab91e 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -16,25 +16,21 @@ ------------------------------------------------------------------------- */ #include "fix_orient_fcc.h" -#include -#include - - #include "atom.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "citeme.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "math_const.h" -#include "citeme.h" #include "memory.h" -#include "error.h" - +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index ac82a671d4..b731e1c9f8 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -13,7 +13,6 @@ #include "mliap_model.h" -#include "atom.h" #include "comm.h" #include "error.h" #include "memory.h" diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index df7fc71f8b..f36f11f2a9 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -18,17 +18,17 @@ ------------------------------------------------------------------------- */ #include "min_spin.h" -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "output.h" -#include "timer.h" #include "error.h" #include "math_const.h" +#include "output.h" +#include "timer.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index a658713d1b..4b8b745419 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -21,25 +21,22 @@ preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "min_spin_cg.h" -#include "universe.h" + #include "atom.h" #include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" +#include "math_const.h" +#include "memory.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "memory.h" -#include "modify.h" -#include "math_special.h" -#include "math_const.h" #include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index f92fc69e04..40029b7e71 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -21,24 +21,22 @@ preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "min_spin_lbfgs.h" + #include "atom.h" #include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" +#include "math_const.h" +#include "memory.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "memory.h" -#include "modify.h" -#include "math_special.h" -#include "math_const.h" #include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 96808b7f10..a89ca403ce 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -22,29 +22,26 @@ ------------------------------------------------------------------------- */ #include "neb_spin.h" -#include -#include -#include -#include -#include "citeme.h" -#include "force.h" -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "domain.h" +#include "citeme.h" #include "comm.h" -#include "min.h" -#include "modify.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" #include "fix_neb_spin.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 4da05c57cb..b27c9736b2 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -23,19 +23,16 @@ #include "pair_spin_dipole_cut.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "fix.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" -#include "modify.h" -#include "error.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 605370f7f1..d4b1b8e43e 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -18,20 +18,17 @@ #include "pair_spin_dipole_long.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "fix.h" +#include "error.h" #include "force.h" #include "kspace.h" #include "math_const.h" #include "memory.h" -#include "modify.h" -#include "error.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 0a5bde2c9f..e27f9fad7d 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -23,18 +23,15 @@ #include "pair_spin_dmi.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "fix.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index a932aa5c54..27da47dd0f 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -23,18 +23,15 @@ #include "pair_spin_exchange.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 65a2904228..2242cf985d 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -23,18 +23,15 @@ #include "pair_spin_magelec.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index ceb487d378..33ea904c0c 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -23,18 +23,15 @@ #include "pair_spin_neel.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 461dc5f5ad..8ffd764447 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -13,17 +13,17 @@ #include "fix_wall_srd.h" -#include -#include "fix.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix.h" #include "input.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" #include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index 2165132856..dd02676466 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -12,23 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_atc.h" -#include -#include -#include -#include "fix_nve.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "pointers.h" #include "comm.h" +#include "error.h" #include "group.h" +#include "neigh_request.h" +#include "neighbor.h" #include "ATC_Method.h" -#include "ATC_Transfer.h" #include "ATC_TransferKernel.h" #include "ATC_TransferPartitionOfUnity.h" #include "ATC_CouplingEnergy.h" @@ -37,6 +29,8 @@ #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; using std::string; diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h index 2512c658db..5bf26f6eaa 100644 --- a/src/USER-ATC/fix_atc.h +++ b/src/USER-ATC/fix_atc.h @@ -8,7 +8,6 @@ FixStyle(atc,FixATC) #define FIX_ATC_H #include "fix.h" -#include "pointers.h" // access to lammps pointers namespace ATC { class ATC_Method; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 0d11e983ad..46b239be08 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -16,9 +16,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_wavepacket.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index d492cd082d..5e23b7fc69 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -17,28 +17,29 @@ #include "pair_awpmd_cut.h" -#include -#include -#include -#include #include "atom.h" -#include "update.h" -#include "min.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" +#include "min.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" - +#include "neighbor.h" +#include "update.h" #include "logexc.h" #include "vector_3.h" #include "TCP/wpmd.h" #include "TCP/wpmd_split.h" +#include +#include +#include +#include +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 4af2356e1a..a4b8de84bd 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -16,11 +16,6 @@ #include "compute_pressure_bocs.h" - -#include -#include - - #include "angle.h" #include "atom.h" #include "bond.h" @@ -28,15 +23,15 @@ #include "domain.h" #include "error.h" #include "fix.h" - #include "force.h" #include "improper.h" #include "kspace.h" -#include "memory.h" #include "modify.h" #include "pair.h" #include "update.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index fc575c2e79..fcbfb58456 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -26,28 +26,25 @@ #include "fix_colvars.h" - -#include -#include - -#include -#include - #include "atom.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "respa.h" #include "universe.h" #include "update.h" -#include "citeme.h" #include "colvarproxy_lammps.h" #include "colvarmodule.h" +#include +#include +#include +#include + static const char colvars_pub[] = "fix colvars command:\n\n" "@Article{fiorin13,\n" diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index 2486446f35..fff61ce218 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" -#include class colvarproxy_lammps; diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 1e37e2de9c..07a8ac2d5c 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,12 +17,11 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "group.h" #include "error.h" +#include "group.h" using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index feab2f22b2..bab1592b1e 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,13 +17,13 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "group.h" #include "error.h" +#include "group.h" + +#include using namespace LAMMPS_NS; #define BUFLEN 4096 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 677bf62a25..d16fbf2876 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -15,23 +15,23 @@ Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "compute_saed.h" -#include - -#include -#include "math_const.h" -#include "compute_saed_consts.h" #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "update.h" +#include "compute_saed_consts.h" #include "domain.h" +#include "error.h" #include "group.h" -#include "citeme.h" +#include "math_const.h" #include "memory.h" -#include "error.h" +#include "update.h" +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index 0dac7aca5e..b48de49c81 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -16,23 +16,23 @@ Updated: 06/17/2015-2 ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "compute_xrd.h" - -#include - -#include -#include "math_const.h" #include "compute_xrd_consts.h" + #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "update.h" #include "domain.h" +#include "error.h" #include "group.h" -#include "citeme.h" +#include "math_const.h" #include "memory.h" -#include "error.h" +#include "update.h" +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 08833db224..39382264c4 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -18,17 +18,16 @@ #include "fix_saed_vtk.h" -#include -#include -#include "update.h" -#include "modify.h" #include "compute.h" #include "compute_saed.h" -#include "memory.h" -#include "error.h" -#include "force.h" #include "domain.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index bd0e334ffc..db9b877b1c 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_eos_cv.h" + #include "atom.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 7134eaca22..57cfe03dc8 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -17,13 +17,11 @@ #include "fix_eos_table.h" - -#include #include "atom.h" #include "error.h" -#include "force.h" #include "memory.h" +#include #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index e533140dd6..c4480a0373 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -35,26 +35,25 @@ #include "fix_shardlow.h" -#include -#include -#include #include "atom.h" -#include "force.h" -#include "update.h" -#include "error.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "npair.h" -#include "memory.h" -#include "domain.h" -#include "modify.h" +#include "npair_half_bin_newton_ssa.h" #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy.h" -#include "npair_half_bin_newton_ssa.h" -#include "citeme.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index c988f4205c..1d3d952e9f 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -17,20 +17,19 @@ #include "pair_dpd_fdt.h" -#include -#include #include "atom.h" #include "comm.h" -#include "update.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" #include "memory.h" #include "modify.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 9231ab7ba3..b843e4601a 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -17,20 +17,19 @@ #include "pair_dpd_fdt_energy.h" -#include -#include #include "atom.h" #include "comm.h" -#include "update.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" #include "memory.h" #include "modify.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 0912fb0498..65923d2e75 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_electron.h" -#include + #include "atom.h" #include "citeme.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 9fdbc6a0bf..d5b574510c 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -17,8 +17,8 @@ #include "fix_nh_eff.h" + #include "atom.h" -#include "atom_vec.h" #include "error.h" #include "domain.h" diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index b016dd8ecb..732ba0909e 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -13,16 +13,15 @@ #include "fix_manifoldforce.h" // For stuff -#include -#include "atom.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "force.h" - #include "manifold.h" #include "manifold_factory.h" // For constructing manifold +#include "atom.h" +#include "error.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp index b9b7ae7279..ef26999295 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp @@ -3,6 +3,8 @@ #include "comm.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index b4f8fd341b..b974ce5bc8 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,9 +1,23 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MEAM_H #define LMP_MEAM_H +#include "math_const.h" // IWYU pragma: export + #include #include -#include "math_const.h" #define maxelt 5 diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index fe9e74ca7c..02c461e6b7 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index dcaa5866de..7a5ee7a651 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include "math_special.h" diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index df1f8f9a1d..eba4f79ea9 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include "math_special.h" diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index f493d9dcac..ddbb40310c 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include "math_special.h" diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index c5f3115249..93b866a14f 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp index ea76ee896c..f2c44504de 100644 --- a/src/USER-MEAMC/meam_setup_param.cpp +++ b/src/USER-MEAMC/meam_setup_param.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp index c3fae823ea..1542c73604 100644 --- a/src/USER-MESODPD/atom_vec_edpd.cpp +++ b/src/USER-MESODPD/atom_vec_edpd.cpp @@ -12,16 +12,13 @@ ------------------------------------------------------------------------- */ #include "atom_vec_edpd.h" -#include + #include "atom.h" -#include "comm.h" -#include "domain.h" +#include "error.h" #include "modify.h" -#include "fix.h" #include "update.h" -#include "memory.h" -#include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp index bc02c93e1a..7e9d5eb29e 100644 --- a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp +++ b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp @@ -11,15 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_tdpd_cc_atom.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/fix_edpd_source.cpp b/src/USER-MESODPD/fix_edpd_source.cpp index 9d31e5f410..c84f2f29a2 100644 --- a/src/USER-MESODPD/fix_edpd_source.cpp +++ b/src/USER-MESODPD/fix_edpd_source.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_edpd_source.h" -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MESODPD/fix_tdpd_source.cpp b/src/USER-MESODPD/fix_tdpd_source.cpp index 7c19d78b1f..440c5055fb 100644 --- a/src/USER-MESODPD/fix_tdpd_source.cpp +++ b/src/USER-MESODPD/fix_tdpd_source.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_tdpd_source.h" -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp index def61dea8f..2f25177b0a 100644 --- a/src/USER-MESODPD/pair_mdpd_rhosum.cpp +++ b/src/USER-MESODPD/pair_mdpd_rhosum.cpp @@ -20,16 +20,16 @@ ------------------------------------------------------------------------- */ #include "pair_mdpd_rhosum.h" -#include + #include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "neighbor.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index 522c2eb4a5..1b0d780c69 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -22,7 +22,6 @@ #include "atom.h" #include "atom_vec_ellipsoid.h" #include "error.h" -#include "math.h" #include "math_const.h" #include "math_extra.h" -- GitLab From 63e5ca53ef2cec88c38f4742c45de6c2cf7d8d55 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:00:38 -0400 Subject: [PATCH 66/75] add iwyu mappings for gtest and gmock --- cmake/iwyu/iwyu-extra-map.imp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index a6d88cf571..c212cc56dd 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -2,4 +2,6 @@ { include: [ "", private, "", public ] }, { include: [ "", public, "", public ] }, { include: [ "@", private, "", public ] }, + { include: [ "@\"gtest/.*\"", private, "\"gtest/gtest.h\"", public ] }, + { include: [ "@\"gmock/.*\"", private, "\"gmock/gmock.h\"", public ] }, ] -- GitLab From 91a87b745f7567d074a6eff918db7e7133c85245 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:01:11 -0400 Subject: [PATCH 67/75] final second round IWYU cleanup --- src/USER-MOLFILE/molfile_interface.cpp | 4 +-- src/USER-MOLFILE/reader_molfile.cpp | 9 +++-- src/USER-OMP/fix_nh_asphere_omp.cpp | 10 ++---- src/USER-OMP/fix_rigid_nh_omp.cpp | 12 +++---- src/USER-OMP/pair_agni_omp.cpp | 18 +++++----- src/USER-OMP/pair_buck_coul_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 1 + src/USER-OMP/pair_coul_cut_soft_omp.cpp | 9 ++--- src/USER-OMP/pair_coul_diel_omp.cpp | 9 ++--- src/USER-OMP/pair_coul_long_soft_omp.cpp | 9 ++--- src/USER-OMP/pair_eam_alloy_omp.cpp | 12 +++---- src/USER-OMP/pair_eam_fs_omp.cpp | 12 +++---- src/USER-OMP/pair_eam_omp.cpp | 11 +++--- src/USER-OMP/pair_edip_omp.cpp | 9 +++-- src/USER-OMP/pair_eim_omp.cpp | 11 +++--- src/USER-OMP/pair_gauss_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp | 14 ++++---- .../pair_hbond_dreiding_morse_omp.cpp | 14 ++++---- ...air_lj_charmm_coul_charmm_implicit_omp.cpp | 7 ++-- .../pair_lj_charmm_coul_charmm_omp.cpp | 9 ++--- .../pair_lj_charmm_coul_long_soft_omp.cpp | 9 ++--- .../pair_lj_cut_coul_cut_soft_omp.cpp | 9 ++--- .../pair_lj_cut_coul_long_soft_omp.cpp | 9 ++--- src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp | 11 +++--- src/USER-OMP/pair_lj_cut_soft_omp.cpp | 7 ++-- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 12 +++---- src/USER-OMP/pair_lj_cut_thole_long_omp.h | 1 - src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 1 + src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp | 10 +++--- src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 10 +++--- src/USER-OMP/pair_lj_sdk_omp.cpp | 10 +++--- src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 9 ++--- src/USER-OMP/pair_lubricate_omp.cpp | 1 - src/USER-OMP/pair_meam_spline_omp.cpp | 13 ++++--- src/USER-OMP/pair_morse_smooth_linear_omp.cpp | 9 ++--- src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_nm_cut_coul_long_omp.cpp | 9 ++--- src/USER-OMP/pair_nm_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_peri_lps_omp.cpp | 18 +++++----- src/USER-OMP/pair_peri_pmb_omp.cpp | 16 ++++----- src/USER-OMP/pair_sw_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_mod_c_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_mod_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_table_omp.cpp | 11 +++--- src/USER-OMP/pair_tersoff_zbl_omp.cpp | 15 +++----- src/USER-OMP/pair_vashishta_omp.cpp | 8 ++--- src/USER-OMP/pair_vashishta_table_omp.cpp | 8 ++--- src/USER-OMP/reaxc_bond_orders_omp.cpp | 7 ++-- src/USER-OMP/reaxc_bond_orders_omp.h | 1 - src/USER-OMP/reaxc_forces_omp.cpp | 3 +- src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp | 7 ++-- src/USER-OMP/reaxc_init_md_omp.h | 2 ++ src/USER-OMP/reaxc_nonbonded_omp.cpp | 4 +-- src/USER-PHONON/dynamical_matrix.cpp | 23 ++++++------ src/USER-PHONON/third_order.cpp | 25 +++++++------ src/USER-PTM/ptm_deformation_gradient.h | 4 ++- src/USER-REACTION/fix_bond_react.cpp | 35 ++++++++++--------- .../pair_sdpd_taitwater_isothermal.cpp | 15 ++++---- .../fix_smd_move_triangulated_surface.cpp | 11 +++--- src/USER-SMD/fix_smd_setvel.cpp | 14 ++++---- src/USER-SMD/fix_smd_wall_surface.cpp | 13 ++++--- src/USER-SMD/pair_smd_ulsph.cpp | 20 +++++------ src/USER-SMD/smd_material_models.cpp | 5 +-- src/USER-SPH/atom_vec_sph.cpp | 5 +-- src/USER-SPH/pair_sph_rhosum.cpp | 9 +++-- 66 files changed, 321 insertions(+), 336 deletions(-) diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index 798beaee09..90a5781fff 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "molfile_interface.h" +#include "molfile_plugin.h" #include #include -#include #include #include #include @@ -31,8 +31,6 @@ #include #endif -#include "molfile_plugin.h" - #if vmdplugin_ABIVERSION < 16 #error "unsupported VMD molfile plugin ABI version" #endif diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 292a451a87..d26a4d4ba0 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "reader_molfile.h" -#include -#include +#include "molfile_interface.h" + #include "comm.h" -#include "memory.h" #include "error.h" - -#include "molfile_interface.h" #include "math_const.h" +#include "memory.h" +#include using namespace LAMMPS_NS; typedef MolfileInterface MFI; using namespace MathConst; diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index f097e93be2..26cad769ec 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -15,19 +15,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - -#include -#include "math_extra.h" #include "fix_nh_asphere_omp.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" #include "compute.h" -#include "group.h" -#include "memory.h" #include "error.h" +#include "math_extra.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 9038efec13..d56b633bd0 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -15,10 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_rigid_nh_omp.h" -#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -29,18 +27,20 @@ #include "error.h" #include "force.h" #include "kspace.h" +#include "math_const.h" +#include "math_extra.h" #include "modify.h" +#include "rigid_const.h" #include "update.h" +#include +#include +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "math_extra.h" -#include "math_const.h" -#include "rigid_const.h" - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index b61bf52e4e..de6903aab9 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -12,21 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include // requires C++-11 #include "pair_agni_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_special.h" #include "math_const.h" - +#include "math_special.h" +#include "neigh_list.h" #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp index 4154c1281c..1c433f8083 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index 71b1540e8c..00ab1c248c 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -21,6 +21,7 @@ #include "suffix.h" #include +#include #include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp index 89222903ec..f8b3a36e39 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp index 656cdc9421..62f2580426 100644 --- a/src/USER-OMP/pair_coul_diel_omp.cpp +++ b/src/USER-OMP/pair_coul_diel_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_diel_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp index ff3267fb38..28ba13d5cf 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index f0823204c0..c7559420bc 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -15,18 +15,16 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_alloy_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 89590bb3e6..66a7581c21 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -15,18 +15,16 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_fs_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 60ae65def5..e6ba299a4d 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_eam_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 0e59674b0e..864ff68f7a 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_edip_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" using namespace LAMMPS_NS; +#include + +#include "omp_compat.h" #define GRIDDENSITY 8000 #define GRIDSTART 0.1 diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp index 02b765a956..74b460a788 100644 --- a/src/USER-OMP/pair_eim_omp.cpp +++ b/src/USER-OMP/pair_eim_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_eim_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp index 6d5344701d..a453915738 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.cpp +++ b/src/USER-OMP/pair_gauss_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gauss_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp index bb8bbcc984..338eb52453 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp @@ -12,22 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_hbond_dreiding_lj_omp.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - #include "math_const.h" #include "math_special.h" - +#include "molecule.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp index 4ad3a8f057..5094d5c193 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp @@ -12,22 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_hbond_dreiding_morse_omp.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - #include "math_const.h" #include "math_special.h" - +#include "molecule.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index f357fd9068..3ff02b6109 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_charmm_implicit_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp index 55227e2e10..77caf63f18 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_charmm_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp index b32f108098..e19632dc7e 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp index 1c88600e7a..03f0852b06 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp index ce84ba01c3..6e804bd8ae 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp index 4111c5b22c..0e9a333121 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_wolf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" - #include "suffix.h" -#include "math_const.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp index 5064c4705e..406c5f41d9 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 9296050173..b921c8f1c1 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,25 +15,21 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_lj_cut_thole_long_omp.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "fix_drude.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" -#include "error.h" +#include "neigh_list.h" #include "suffix.h" +#include +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.h b/src/USER-OMP/pair_lj_cut_thole_long_omp.h index dc64c5c3a2..212f3c4e2e 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.h +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.h @@ -20,7 +20,6 @@ PairStyle(lj/cut/thole/long/omp,PairLJCutTholeLongOMP) #ifndef LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H #define LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H -#include "pair.h" #include "pair_lj_cut_thole_long.h" #include "thr_omp.h" diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index d869d91d09..cdd62ff96e 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -22,6 +22,7 @@ #include "suffix.h" #include +#include #include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp index 4ad082cde1..4a53f2c083 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp @@ -12,18 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_coul_long_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" -#include "lj_sdk_common.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp index 4871356b18..4b89375b5b 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp @@ -13,19 +13,19 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_coul_msm_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" -#include "lj_sdk_common.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp index 9f0671c61c..d5146c6798 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_omp.cpp @@ -13,18 +13,18 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" -#include "lj_sdk_common.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp index 1adaf93953..8828b40b98 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sf_dipole_sf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 827fae8e44..caf5a11124 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -22,7 +22,6 @@ #include "input.h" #include "math_const.h" #include "neigh_list.h" -#include "neighbor.h" #include "suffix.h" #include "variable.h" diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp index 19fb09dd7b..782371e843 100644 --- a/src/USER-OMP/pair_meam_spline_omp.cpp +++ b/src/USER-OMP/pair_meam_spline_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_meam_spline_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp index f2ab417028..220fb9481d 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp @@ -13,16 +13,17 @@ Most code borrowed from pair_morse_omp.cpp ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_morse_smooth_linear_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp index 4326434450..1cfe576a32 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp index 970b383f7e..d9e1231827 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp index a937668fdd..a232da1a90 100644 --- a/src/USER-OMP/pair_nm_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp index cf29b5cab8..9bf707ad91 100644 --- a/src/USER-OMP/pair_peri_lps_omp.cpp +++ b/src/USER-OMP/pair_peri_lps_omp.cpp @@ -12,24 +12,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_peri_lps_omp.h" -#include "fix.h" -#include "fix_peri_neigh.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_peri_neigh.h" #include "force.h" -#include "memory.h" #include "lattice.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp index 1990b46fe5..28df45b67f 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.cpp +++ b/src/USER-OMP/pair_peri_pmb_omp.cpp @@ -12,23 +12,23 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_peri_pmb_omp.h" -#include "fix.h" -#include "fix_peri_neigh.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_peri_neigh.h" #include "force.h" -#include "memory.h" #include "lattice.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index ebe501ff8e..c2eb4cb156 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_sw_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index 5e1e6b1b0e..83baa56e44 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -12,16 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_mod_c_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index aa90b88375..ab2f07322d 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -12,16 +12,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_mod_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index 34dbfb73b6..a367749978 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -12,17 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index a0a7f4c810..8321ad9d9f 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_table_omp.h" + #include "atom.h" #include "comm.h" -#include "error.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define GRIDSTART 0.1 diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index d1d808307a..7bb3814549 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -16,26 +16,19 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_tersoff_zbl_omp.h" -#include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" #include "memory.h" #include "error.h" - #include "tokenizer.h" #include "potential_file_reader.h" - #include "math_const.h" #include "math_special.h" + +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index 425a06c296..0637fe3dfc 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -12,17 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_vashishta_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index 36c86a8995..9650a57e72 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_vashishta_table_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index d581819e00..85a77370fa 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -27,8 +27,8 @@ ----------------------------------------------------------------------*/ #include "reaxc_bond_orders_omp.h" -#include -#include +#include "reaxc_bond_orders.h" + #include "fix_omp.h" #include "reaxc_defs.h" #include "pair_reaxc_omp.h" @@ -36,6 +36,9 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/USER-OMP/reaxc_bond_orders_omp.h index 36be3337ad..2027a8628e 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.h +++ b/src/USER-OMP/reaxc_bond_orders_omp.h @@ -30,7 +30,6 @@ #define __BOND_ORDERS_OMP_H_ #include "reaxc_types.h" -#include "reaxc_bond_orders.h" void Add_dBond_to_ForcesOMP( reax_system*, int, int, storage*, reax_list** ); void Add_dBond_to_Forces_NPTOMP( reax_system *system, int, int, diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index ce38cb0544..ad6ea35eb8 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -28,6 +28,7 @@ #include "reaxc_forces_omp.h" +#include "error.h" #include "fix_omp.h" #include "pair_reaxc_omp.h" #include "reaxc_defs.h" @@ -45,8 +46,6 @@ #include #include -#include "omp_compat.h" - #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 22d9df7702..029062470d 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -26,10 +26,8 @@ . ----------------------------------------------------------------------*/ -#include "omp_compat.h" #include "reaxc_hydrogen_bonds_omp.h" -#include -#include + #include "fix_omp.h" #include "pair_reaxc_omp.h" #include "reaxc_defs.h" @@ -38,6 +36,9 @@ #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_init_md_omp.h b/src/USER-OMP/reaxc_init_md_omp.h index 8416a768cf..45478ec632 100644 --- a/src/USER-OMP/reaxc_init_md_omp.h +++ b/src/USER-OMP/reaxc_init_md_omp.h @@ -31,6 +31,8 @@ #include "reaxc_types.h" +#include + void InitializeOMP( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); #endif diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index 564088880a..3c3ca12575 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -27,17 +27,17 @@ ----------------------------------------------------------------------*/ #include "pair_reaxc_omp.h" -#include "thr_data.h" #include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_nonbonded.h" #include "reaxc_nonbonded_omp.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index adfcf6adb5..238aa7c96e 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -2,28 +2,29 @@ // Created by charlie sievers on 6/21/18. // -#include -#include -#include #include "dynamical_matrix.h" + +#include "angle.h" #include "atom.h" -#include "domain.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" #include "error.h" -#include "group.h" +#include "finish.h" #include "force.h" -#include "memory.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "memory.h" #include "modify.h" #include "neighbor.h" #include "pair.h" #include "timer.h" -#include "finish.h" +#include "update.h" + +#include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index 6e09710833..e15b82fbab 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -3,29 +3,28 @@ // #include "third_order.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" -#include "domain.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" #include "error.h" -#include "group.h" +#include "finish.h" #include "force.h" -#include "memory.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "math_special.h" +#include "memory.h" #include "neighbor.h" #include "pair.h" #include "timer.h" -#include "finish.h" -#include "math_special.h" +#include "update.h" + +#include #include -#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h index 546efab437..6c686431f6 100644 --- a/src/USER-PTM/ptm_deformation_gradient.h +++ b/src/USER-PTM/ptm_deformation_gradient.h @@ -10,9 +10,11 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #ifndef PTM_DEFORMATION_GRADIENT_H #define PTM_DEFORMATION_GRADIENT_H -#include #include "ptm_constants.h" +#include +#include + namespace ptm { void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 0370d83fdc..5d57b74056 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -17,35 +17,36 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "fix_bond_react.h" -#include -#include - -#include "update.h" -#include "modify.h" -#include "respa.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" +#include "citeme.h" #include "comm.h" #include "domain.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "reset_mol_ids.h" -#include "molecule.h" +#include "error.h" +#include "force.h" #include "group.h" -#include "citeme.h" +#include "input.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "input.h" +#include "modify.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "random_mars.h" +#include "reset_mol_ids.h" +#include "respa.h" +#include "update.h" #include "variable.h" #include "superpose3d.h" +#include +#include +#include + #include using namespace LAMMPS_NS; diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index 9d52ee2250..bf2fc73b01 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -19,18 +19,19 @@ ------------------------------------------------------------------------- */ #include "pair_sdpd_taitwater_isothermal.h" -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include "update.h" +#include + #ifndef USE_ZEST #include "random_mars.h" #endif diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index 2aa6f980ed..e0e76a18fb 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -23,15 +23,16 @@ ------------------------------------------------------------------------- */ #include "fix_smd_move_triangulated_surface.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "update.h" #include "error.h" #include "math_const.h" +#include "update.h" + +#include +#include +#include using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 90589f3044..d3e71f0e50 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -25,17 +25,17 @@ #include "fix_smd_setvel.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "region.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index c61fe14353..10f248c39f 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -17,16 +17,15 @@ #include "fix_smd_wall_surface.h" -#include - -#include #include "atom.h" -#include "domain.h" -#include "force.h" +#include "atom_vec.h" #include "comm.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "atom_vec.h" +#include "memory.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index e9cf256c3c..3a6cdf5d2f 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -24,23 +24,21 @@ #include "pair_smd_ulsph.h" -#include -#include - -#include #include "atom.h" -#include "domain.h" -#include "force.h" -#include "update.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include "smd_kernels.h" #include "smd_material_models.h" #include "smd_math.h" -#include "smd_kernels.h" +#include "update.h" + +#include +#include using namespace SMD_Kernels; using namespace std; diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 096600df52..942b6a8cab 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -22,12 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "smd_material_models.h" + +#include "math_special.h" + #include #include -#include #include #include -#include "math_special.h" #include diff --git a/src/USER-SPH/atom_vec_sph.cpp b/src/USER-SPH/atom_vec_sph.cpp index 2811c57e6c..93ca2b60a7 100644 --- a/src/USER-SPH/atom_vec_sph.cpp +++ b/src/USER-SPH/atom_vec_sph.cpp @@ -12,9 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sph.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 429d4199a4..3d3065f839 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "pair_sph_rhosum.h" + #include "atom.h" -#include "force.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "neighbor.h" #include "update.h" -#include "domain.h" - using namespace LAMMPS_NS; -- GitLab From 2d802411e99ee55b1a392bf52e2a43a35e0cc916 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:03:53 -0400 Subject: [PATCH 68/75] remove pointless stringstream abuse --- src/USER-PHONON/third_order.cpp | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index e15b82fbab..e7997d6397 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -169,13 +169,11 @@ void ThirdOrder::options(int narg, char **arg) if (narg < 0) error->all(FLERR,"Illegal third_order command"); int iarg = 0; const char *filename = "third_order.dat"; - std::stringstream fss; while (iarg < narg) { if (strcmp(arg[iarg],"file") == 0) { if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command"); - fss << arg[iarg + 1]; - filename = fss.str().c_str(); + filename = arg[iarg + 1]; file_flag = 1; iarg += 2; } else if (strcmp(arg[iarg],"binary") == 0) { -- GitLab From d6ba95bed6b982df025cbb219a8adb985e0ef5f1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:05:59 -0400 Subject: [PATCH 69/75] minor tweaks --- src/MLIAP/compute_mliap.cpp | 1 - src/USER-OMP/pair_airebo_omp.cpp | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/MLIAP/compute_mliap.cpp b/src/MLIAP/compute_mliap.cpp index aad28c7bb1..956cb0196f 100644 --- a/src/MLIAP/compute_mliap.cpp +++ b/src/MLIAP/compute_mliap.cpp @@ -22,7 +22,6 @@ #include "update.h" #include "modify.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "force.h" #include "pair.h" diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 77dd874076..837734d6e4 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -21,6 +21,7 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" +#include "suffix.h" #include @@ -29,7 +30,6 @@ #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathSpecial; -- GitLab From f541647d44332b94a0133ebef721dd89e83b1560 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 09:23:20 -0400 Subject: [PATCH 70/75] some more IWYU tweaks --- src/fix_nh.h | 2 +- src/main.cpp | 4 +++- src/min.h | 2 +- src/neigh_list.h | 2 +- src/reader_xyz.cpp | 2 -- tools/msi2lmp/src/WriteDataFile.c | 1 - tools/msi2lmp/src/msi2lmp.c | 1 - tools/msi2lmp/src/msi2lmp.h | 2 +- 8 files changed, 7 insertions(+), 9 deletions(-) diff --git a/src/fix_nh.h b/src/fix_nh.h index 624b0c8bb4..f137ecbe55 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -14,7 +14,7 @@ #ifndef LMP_FIX_NH_H #define LMP_FIX_NH_H -#include "fix.h" +#include "fix.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/main.cpp b/src/main.cpp index 9fb084aaea..d705db4e5b 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -12,9 +12,11 @@ ------------------------------------------------------------------------- */ #include "lammps.h" -#include #include "input.h" +#include +#include + #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include #endif diff --git a/src/min.h b/src/min.h index b23c9b6670..1db196a55e 100644 --- a/src/min.h +++ b/src/min.h @@ -14,7 +14,7 @@ #ifndef LMP_MIN_H #define LMP_MIN_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/neigh_list.h b/src/neigh_list.h index 501188a724..c26b008136 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -14,7 +14,7 @@ #ifndef LMP_NEIGH_LIST_H #define LMP_NEIGH_LIST_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 5350e01117..8a2f7a3989 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -20,8 +20,6 @@ #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; #define MAXLINE 1024 // max line length in dump file diff --git a/tools/msi2lmp/src/WriteDataFile.c b/tools/msi2lmp/src/WriteDataFile.c index c03eba71c5..a6f1615809 100644 --- a/tools/msi2lmp/src/WriteDataFile.c +++ b/tools/msi2lmp/src/WriteDataFile.c @@ -3,7 +3,6 @@ */ #include "msi2lmp.h" -#include "Forcefield.h" #include diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index efc929639a..b5e9a96293 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -151,7 +151,6 @@ #include #include -#include /* global variables */ diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index c9b1984444..af7978d181 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -34,7 +34,7 @@ * compatibility with the obsolete LAMMPS version written in Fortran 90. */ -# include +#include /* IWYU pragma: export */ #define MSI2LMP_VERSION "v3.9.9 / 05 Nov 2018" -- GitLab From 255bf2f8fd1dbdc66e06a3132f18ff95dca56d96 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 09:41:57 -0400 Subject: [PATCH 71/75] update iwyu custom mapping file --- cmake/iwyu/iwyu-extra-map.imp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index c212cc56dd..4fadea73fb 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -2,6 +2,6 @@ { include: [ "", private, "", public ] }, { include: [ "", public, "", public ] }, { include: [ "@", private, "", public ] }, - { include: [ "@\"gtest/.*\"", private, "\"gtest/gtest.h\"", public ] }, - { include: [ "@\"gmock/.*\"", private, "\"gmock/gmock.h\"", public ] }, + { include: [ "@", private, "\"gtest/gtest.h\"", public ] }, + { include: [ "@", private, "\"gmock/gmock.h\"", public ] }, ] -- GitLab From f19ce32bf56aa81a3b488c2f6a6227b668bb7704 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 09:42:11 -0400 Subject: [PATCH 72/75] a few more small tweaks --- unittest/formats/test_atom_styles.cpp | 1 + unittest/formats/test_pair_unit_convert.cpp | 6 ++---- unittest/formats/test_potential_file_reader.cpp | 5 ++--- unittest/utils/test_fmtlib.cpp | 1 - unittest/utils/test_tokenizer.cpp | 1 + unittest/utils/test_utils.cpp | 2 +- 6 files changed, 7 insertions(+), 9 deletions(-) diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index a409f3547c..80ee3926c8 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -28,6 +28,7 @@ #include #include #include +#include #include #if !defined(_FORTIFY_SOURCE) || (_FORTIFY_SOURCE == 0) diff --git a/unittest/formats/test_pair_unit_convert.cpp b/unittest/formats/test_pair_unit_convert.cpp index 6c4b38397d..8571c7b442 100644 --- a/unittest/formats/test_pair_unit_convert.cpp +++ b/unittest/formats/test_pair_unit_convert.cpp @@ -15,17 +15,15 @@ #include "force.h" #include "info.h" #include "input.h" -#include "lammps.h" #include "output.h" #include "pair.h" #include "thermo.h" -#include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" -#include +#include #include -#include +#include // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index f5b298874f..aaa52b1142 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -13,7 +13,6 @@ #include "MANYBODY/pair_comb.h" #include "MANYBODY/pair_comb3.h" -#include "MANYBODY/pair_eim.h" #include "MANYBODY/pair_gw.h" #include "MANYBODY/pair_gw_zbl.h" #include "MANYBODY/pair_nb3b_harmonic.h" @@ -26,13 +25,13 @@ #include "USER-MISC/pair_tersoff_table.h" #include "info.h" #include "input.h" -#include "lammps.h" #include "potential_file_reader.h" -#include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include +#include +#include #include #if defined(OMPI_MAJOR_VERSION) diff --git a/unittest/utils/test_fmtlib.cpp b/unittest/utils/test_fmtlib.cpp index fd9a4a06a2..7233d0ab1a 100644 --- a/unittest/utils/test_fmtlib.cpp +++ b/unittest/utils/test_fmtlib.cpp @@ -16,7 +16,6 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" #include -#include using namespace LAMMPS_NS; using ::testing::Eq; diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 7cef3cead0..28656ef9c8 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" #include "tokenizer.h" #include "gmock/gmock.h" #include "gtest/gtest.h" diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 1a3ca9fa0c..a78830c9d1 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include #include -#include #include #include -- GitLab From 2b1e4749dd2ea7b45a1921f02ae588f19b655e89 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 11:39:38 -0400 Subject: [PATCH 73/75] first chunk of revised updates to the manual addressing link issues. --- doc/src/Build_basics.rst | 24 ++++++++++++------------ doc/src/Build_development.rst | 8 ++++---- doc/src/Build_extras.rst | 22 +++++++++++----------- doc/src/Build_link.rst | 8 ++++---- doc/src/Build_make.rst | 2 +- doc/src/Build_settings.rst | 5 +++-- doc/src/Build_windows.rst | 2 +- doc/src/Commands_removed.rst | 7 ++++++- doc/src/Errors_bugs.rst | 23 +++++++++++------------ doc/src/Errors_common.rst | 6 ++++-- doc/src/Examples.rst | 3 +-- doc/src/Howto.rst | 2 +- doc/src/Howto_2d.rst | 8 ++++---- doc/src/Howto_body.rst | 6 +++--- doc/src/Howto_chunk.rst | 3 ++- doc/src/Howto_drude.rst | 2 +- doc/src/Howto_drude2.rst | 4 ++-- doc/src/Howto_github.rst | 2 +- doc/src/Howto_spherical.rst | 2 +- doc/src/Howto_thermostat.rst | 31 ++++++++++++++++++++++++------- doc/src/Howto_viscosity.rst | 4 ++-- doc/src/Install_git.rst | 35 +++++++++++++++++------------------ doc/src/Install_patch.rst | 7 +++++-- doc/src/Intro_features.rst | 6 +++--- doc/src/Intro_nonfeatures.rst | 6 ++++-- doc/src/Intro_overview.rst | 2 +- doc/src/Intro_website.rst | 12 ++++++------ doc/src/Manual.rst | 5 ++++- doc/src/Modify.rst | 3 ++- doc/src/Modify_atom.rst | 4 ++-- doc/src/Modify_contribute.rst | 10 +++++----- doc/src/Modify_thermo.rst | 2 +- doc/src/Packages_details.rst | 34 ++++++++++++++++++---------------- doc/src/Packages_standard.rst | 2 +- doc/src/Run_basics.rst | 4 ++-- doc/src/Run_options.rst | 23 ++++++++++++----------- doc/src/Speed_bench.rst | 2 +- doc/src/Speed_kokkos.rst | 21 ++++++++++++++------- 38 files changed, 197 insertions(+), 155 deletions(-) diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index baace2e063..7548a8a6e9 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -115,12 +115,12 @@ self-installed MPICH or OpenMPI, so you should study the provided documentation to find out how to build and link with it. The majority of OpenMP (threading) support in LAMMPS is provided by the -``USER-OMP`` package; see the :doc:`Speed omp ` doc page for -details. The ``USER-INTEL`` package also includes OpenMP threading (it -is compatible with ``USER-OMP`` and will usually fall back on styles -from that package, if a ``USER-INTEL`` does not exist) and adds -vectorization support when compiled with compatible compilers, in -particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` +``USER-OMP`` package; see the :doc:`Speed_omp` +page for details. The ``USER-INTEL`` package also includes OpenMP +threading (it is compatible with ``USER-OMP`` and will usually fall +back on styles from that package, if a ``USER-INTEL`` does not exist) +and adds vectorization support when compiled with compatible compilers, +in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` package can be compiled to include OpenMP threading. In addition, there are a few commands in LAMMPS that have native OpenMP @@ -290,13 +290,13 @@ Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``): compiler that supports C++11; either as a binary package or through compiling from source. -If you build LAMMPS with any :doc:`accelerator packages -` included, there may be specific optimization flags +If you build LAMMPS with any :doc:`Speed_packages` included, there may +be specific compiler or linker flags that are either required or recommended to enable required features and to achieve optimal performance. You need to include these in the CCFLAGS and LINKFLAGS settings above. For details, see the individual -package doc pages listed on the :doc:`Speed packages ` -doc page. Or examine these files in the src/MAKE/OPTIONS directory. +package doc pages listed on the :doc:`Speed_packages` +page. Or examine these files in the src/MAKE/OPTIONS directory. They correspond to each of the 5 accelerator packages and their hardware variants: @@ -418,7 +418,7 @@ recommended to ensure the integrity of the system software installation. .. _debug: -Excluding or removing debug support +Including or removing debug support ----------------------------------- By default the compilation settings will include the *-g* flag which @@ -460,7 +460,7 @@ python packages are installed into that virtual environment via the pip tool. The actual translation is then done via make commands. .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html -.. _sphinx: https://sphinx-doc.org +.. _sphinx: https://www.sphinx-doc.org Documentation make option ^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index cd432dddcb..b8e4c8171b 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -37,14 +37,14 @@ Compilers such as GCC and Clang support generating instrumented binaries which use different sanitizer libraries to detect problems in the code during run-time. They can detect issues like: - - `memory leaks `_ + - `memory leaks `_ - `undefined behavior `_ - `data races `_ Please note that this kind of instrumentation usually comes with a performance hit (but much less than using tools like `Valgrind -`_ with a more low level approach). The to enable -these features additional compiler flags need to be added to the +`_ with a more low level approach). To enable +these features, additional compiler flags need to be added to the compilation and linking stages. This is done through setting the ``ENABLE_SANITIZER`` variable during configuration. Examples: @@ -77,7 +77,7 @@ error margin). The status of this automated testing can be viewed on The unit testing facility is integrated into the CMake build process of the LAMMPS source code distribution itself. It can be enabled by setting ``-D ENABLE_TESTING=on`` during the CMake configuration step. -It requires the `YAML `_ library and development +It requires the `PyYAML `_ library and development headers to compile and will download and compile a recent version of the `Googletest `_ C++ test framework for implementing the tests. diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index b72dd95046..9595849b58 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -234,11 +234,10 @@ command, you also need to have libcurl installed with the matching development headers and the curl-config tool. If you would like to use the :doc:`kim_property ` -command, you need to build LAMMPS with the Python 3.6 or later package -installed. See the :doc:`Python ` doc page for more info on building -LAMMPS with the version of Python on your system. -After successfully building LAMMPS with Python, you need to -install the kim-property Python package, which can be easily done using +command, you need to build LAMMPS with the PYTHON package installed +and linked to Python 3.6 or later. See the :ref:`PYTHON package build info ` +for more details on this. After successfully building LAMMPS with Python, you +also need to install the kim-property Python package, which can be easily done using *pip* as ``pip install kim-property``, or from the *conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in Conda. More detailed information is available at: @@ -812,10 +811,11 @@ a corresponding ``Makefile.lammps.machine`` file. PYTHON package --------------------------- -Building with the PYTHON package requires you have a Python shared -library available on your system, which needs to be a Python 2.7 -version or a Python 3.x version. See ``lib/python/README`` for more -details. +Building with the PYTHON package requires you have a the Python development +headers and library available on your system, which needs to be a Python 2.7 +version or a Python 3.x version. Since support for Python 2.x has ended, +using Python 3.x is strongly recommended. See ``lib/python/README`` for +additional details. CMake build ^^^^^^^^^^^ @@ -1095,7 +1095,7 @@ USER-PLUMED package Before building LAMMPS with this package, you must first build PLUMED. PLUMED can be built as part of the LAMMPS build or installed separately -from LAMMPS using the generic `plumed installation instructions `_. +from LAMMPS using the generic `PLUMED installation instructions `_. The USER-PLUMED package has been tested to work with Plumed versions 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations with a different version of the Plumed kernel. @@ -1262,7 +1262,7 @@ To build with this package, you must choose which hardware you want to build for, either x86 CPUs or Intel KNLs in offload mode. You should also typically :ref:`install the USER-OMP package `, as it can be used in tandem with the USER-INTEL package to good effect, as explained -on the :doc:`Speed intel ` doc page. +on the :doc:`Speed_intel` page. When using Intel compilers version 16.0 or later is required. You can also use the GNU or Clang compilers and they will provide performance diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index 914142b3ce..87899739bc 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -4,11 +4,11 @@ Link LAMMPS as a library to another code LAMMPS is designed as a library of C++ objects that can be integrated into other applications including Python scripts. The files ``src/library.cpp`` and ``src/library.h`` define a -C-style API for using LAMMPS as a library. See the :doc:`Howto -library ` page for a description of the interface -and how to use it for your needs. +C-style API for using LAMMPS as a library. See the +:doc:`Howto_library` page +for a description of the interface and how to use it for your needs. -The :doc:`Build basics ` doc page explains how to build +The :doc:`Build_basics` page explains how to build LAMMPS as either a shared or static library. This results in a file in the compilation folder called ``liblammps.a`` or ``liblammps_.a`` in case of building a static library. In case of a shared library diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index af5e319121..cd71fd46e6 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -37,7 +37,7 @@ enable (or "install") them first, as discussed on the :doc:`Build package ` doc page. If a packages requires (provided or external) libraries, you must configure and build those libraries **before** building LAMMPS itself and especially **before** enabling -such a package with ``make yes-``. Building :doc:`LAMMPS with +such a package with ``make yes-``. :doc:`Building LAMMPS with CMake ` can automate much of this for many types of machines, especially workstations, desktops, and laptops, so we suggest you try it first when building LAMMPS in those cases. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 859bec9889..21107b7203 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -6,7 +6,7 @@ explain how to do this for building both with CMake and make. * :ref:`C++11 standard compliance ` when building all of LAMMPS * :ref:`FFT library ` for use with the :doc:`kspace_style pppm ` command -* :ref:`Size of LAMMPS data types ` +* :ref:`Size of LAMMPS integer types ` * :ref:`Read or write compressed files ` * :ref:`Output of JPG and PNG files ` via the :doc:`dump image ` command * :ref:`Output of movie files ` via the :doc:`dump_movie ` command @@ -123,7 +123,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed to the screen at the end of a run when using the -:doc:`kspace_style pppm ` command. The :doc:`Run output ` +:doc:`kspace_style pppm ` command. The +:doc:`Screen and logfile output ` doc page gives more details. A more detailed (and time consuming) report of the FFT performance is generated with the :doc:`kspace_modify fftbench yes ` command. diff --git a/doc/src/Build_windows.rst b/doc/src/Build_windows.rst index 4aacea9dfa..2df3fdd24e 100644 --- a/doc/src/Build_windows.rst +++ b/doc/src/Build_windows.rst @@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu from within Windows and from there on, you can pretty much use that shell like you are running on an Ubuntu Linux machine (e.g. installing software via apt-get and more). For more details on that, please -see :doc:`this tutorial ` +see :doc:`this tutorial `. .. _gnu: diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index e137e39a08..1f6da57945 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -17,6 +17,11 @@ ways through the :doc:`compute chunk/atom ` command and then averaging is done using :doc:`fix ave/chunk `. Please refer to the :doc:`chunk HOWTO ` section for an overview. +Reset_ids command +----------------- + +The reset_ids command has been renamed to :doc:`reset_atom_ids `. + MEAM package ------------ @@ -27,7 +32,7 @@ which removes several restrictions (e.g. there can be multiple instances in hybrid pair styles) and allows for some optimizations leading to better performance. The new pair style :doc:`meam/c ` has the exact same syntax as the old "meam" pair style and thus pair style -:doc:`meam ` is an alias to the new style and backward +meam is an alias to the new style and backward compatibility of old inputs is preserved. REAX package diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index ff0b155795..d2714c86b1 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -6,23 +6,25 @@ the steps outlined below: * Check the `New features and bug fixes `_ section of the `LAMMPS WWW site - `_ to see if the bug has already been addressed in a patch. + `_ or the + `GitHub Releases page `_ to + see if the bug has already been addressed in a patch release. * Check that your issue can be reproduced with the latest development version of LAMMPS. * Check the manual carefully to verify that the unexpected behavior you are observing is indeed in conflict with the documentation - * Check the `GitHub Issue page `_ + * Check the `GitHub Issue page `_ if your issue has already been reported and if it is still open. - * Check the `GitHub Pull Requests page `_ - if there is already a fix for your bug pending. + * Check the `GitHub Pull Requests page `_ + to see if there is already a fix for your bug pending. * Check the `mailing list archives `_ to see if the issue has been discussed before. If none of these steps yields any useful information, please file a new -bug report on the `GitHub Issue page `_. The website will offer -you to select a suitable template with explanations and then you should -replace those explanations with the information that you can provide to -reproduce your issue. +bug report on the `GitHub Issue page `_. +The website will offer you to select a suitable template with explanations +and then you should replace those explanations with the information that +you can provide to reproduce your issue. The most useful thing you can do to help us verify and fix a bug is to isolate the problem. Run it on the smallest number of atoms and fewest @@ -33,7 +35,7 @@ Please avoid using binary restart files unless the issue requires it. In the latter case you should also include an input deck to quickly generate this restart from a data file or a simple additional input. This input deck can be used with tools like a debugger or `valgrind -`_ to further :doc:`debug the crash `. +`_ to further :doc:`debug the crash `. You may also send an email to the LAMMPS mailing list at "lammps-users at lists.sourceforge.net" describing the problem with the @@ -44,6 +46,3 @@ is overlooked and then forgotten. Issues on GitHub have to be explicitly closed, so that will *guarantee* that at least one LAMMPS developer will have looked at it. -.. _lws: https://lammps.sandia.gov -.. _gip: https://github.com/lammps/issues -.. _valgrind: https://valgrind.org diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 34567db385..4d4483efec 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -48,8 +48,10 @@ to see it on the screen. If you get an error like "Invalid ... style", with ... being fix, compute, pair, etc, it means that you mistyped the style name or that the command is part of an optional package which was not compiled into your executable. The list of -available styles in your executable can be listed by using :doc:`the -h command-line swith `. The installation and -compilation of optional packages is explained on the :doc:`Build packages ` doc page. +available styles in your executable can be listed by using +:doc:`the -h command-line switch `. The installation and +compilation of optional packages is explained on the +:doc:`Build packages ` doc page. For a given command, LAMMPS expects certain arguments in a specified order. If you mess this up, LAMMPS will often flag the error, but it diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index dc122f2c78..8a76dca66e 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the :doc:`dump image ` doc page. Animations of many of the examples can be viewed on the Movies section -of the `LAMMPS web site `_. +of the `LAMMPS web site `_. There are two kinds of sub-directories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run @@ -223,4 +223,3 @@ instructions. See the :doc:`Packages_details ` doc page for more info on specific USER packages. .. _openkim: https://openkim.org -.. _lws: https://lammps.sandia.gov diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 89c0ce9ffe..6d8f6e9054 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -3,7 +3,7 @@ Howto discussions These doc pages describe how to perform various tasks with LAMMPS, both for users and developers. The -`glossary `_ website page also lists MD +`glossary `_ website page also lists MD terminology with links to corresponding LAMMPS manual pages. The example input scripts included in the examples directory of the LAMMPS distribution and highlighted on the :doc:`Examples ` doc page diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index 1b4be32106..9cf76ac3b0 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -6,14 +6,14 @@ Use the :doc:`dimension ` command to specify a 2d simulation. Make the simulation box periodic in z via the :doc:`boundary ` command. This is the default. -If using the :doc:`create box ` command to define a +If using the :doc:`create_box ` command to define a simulation box, set the z dimensions narrow, but finite, so that the -create_atoms command will tile the 3d simulation box with a single z -plane of atoms - e.g. +:doc:`create_atoms ` command will fill the 3d simulation +box with a single z plane of atoms - e.g. .. code-block:: LAMMPS - :doc:`create box ` 1 -10 10 -10 10 -0.25 0.25 + create box 1 -10 10 -10 10 -0.25 0.25 If using the :doc:`read data ` command to read in a file of atom coordinates, set the "zlo zhi" values to be finite but narrow, diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 36e40a88bd..0c0a930221 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -32,9 +32,9 @@ thus how they can be used to compute pairwise body/body or bond/non-body (point particle) interactions. More details of each style are described below. -More styles may be added in the future. See the :doc:`Modify body -` doc page for details on how to add a new body style to -the code. +More styles may be added in the future. See the +:doc:`page on creating new body styles ` for details on +how to add a new body style to the code. ---------- diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index 75fb30815b..c0a7792448 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -198,7 +198,8 @@ explained on the :doc:`compute chunk/spread/atom ` co (7) An example for using one set of per-chunk values for molecule chunks, to create a second set of micelle-scale chunks (clustered -molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce ` command doc page. +molecules, due to hydrophobicity), is explained on the +:doc:`compute reduce/chunk ` command doc page. (8) An example for using one set of per-chunk values (dipole moment vectors) for molecule chunks, spreading the values to each atom in diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index 62659711c4..c866340e77 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -29,7 +29,7 @@ molecular systems (:ref:`Lamoureux and Roux `): to the total charge of the core atom). A detailed tutorial covering the usage of Drude induced dipoles in -LAMMPS is on the :doc:`Howto drude2e ` doc page. +LAMMPS is on the :doc:`here `. As with the core-shell model, the cores and Drude particles should appear in the data file as standard atoms. The same holds for the diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index cbdbc2d250..3dacf99dec 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -377,7 +377,7 @@ For our phenol example, the groups would be defined as Note that with the fixes *drude/transform*\ , it is not required to specify *comm_modify vel yes* because the fixes do it anyway (several times and for the forces also). To avoid the flying ice cube artifact -:ref:`(Lamoureux) `, where the atoms progressively freeze and the +:ref:`(Lamoureux and Roux) `, where the atoms progressively freeze and the center of mass of the whole system drifts faster and faster, the *fix momentum* can be used. For instance: @@ -456,7 +456,7 @@ NPT ensemble using Nose-Hoover thermostat: .. _Lamoureux2: -**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) +**(Lamoureux and Roux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) .. _Schroeder: diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 795af96e0a..63cb8945e8 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -20,7 +20,7 @@ work required by the LAMMPS developers. Consequently, creating a pull request will increase your chances to have your contribution included and will reduce the time until the integration is complete. For more information on the requirements to have your code included into LAMMPS -please see the :doc:`Modify contribute ` doc page. +please see :doc:`this page `. ---------- diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst index 7ca8a1b060..aa17e6ce21 100644 --- a/doc/src/Howto_spherical.rst +++ b/doc/src/Howto_spherical.rst @@ -114,7 +114,7 @@ will only rotate and experience torque if the force field computes such interactions. These are the various :doc:`pair styles ` that generate torque: * :doc:`pair_style gran/history ` -* :doc:`pair_style gran/hertzian ` +* :doc:`pair_style gran/hertz ` * :doc:`pair_style gran/no_history ` * :doc:`pair_style dipole/cut ` * :doc:`pair_style gayberne ` diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 77745efa57..7bddb1c89d 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -42,12 +42,12 @@ particles. DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of :doc:`fix langevin `. -Any of the thermostatting fixes can use :doc:`temperature computes ` that remove bias which has two -effects. First, the current calculated temperature, which is compared -to the requested target temperature, is calculated with the velocity -bias removed. Second, the thermostat adjusts only the thermal -temperature component of the particle's velocities, which are the -velocities with the bias removed. The removed bias is then added back +Any of the thermostatting fixes can be instructed to use custom temperature +computes that remove bias which has two effects: first, the current +calculated temperature, which is compared to the requested target temperature, +is calculated with the velocity bias removed; second, the thermostat adjusts +only the thermal temperature component of the particle's velocities, which are +the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the doc pages for the individual fixes and for the :doc:`fix_modify ` command for instructions on how to assign a temperature compute to a @@ -55,7 +55,24 @@ thermostatting fix. For example, you can apply a thermostat to only the x and z components of velocity by using it in conjunction with :doc:`compute temp/partial `. Of you could thermostat only the thermal temperature of a streaming flow of -particles without affecting the streaming velocity, by using :doc:`compute temp/profile `. +particles without affecting the streaming velocity, by using +:doc:`compute temp/profile `. + +Below is a list of some custom temperature computes that can be used like that: + +* :doc:`compute_temp_asphere` +* :doc:`compute_temp_body` +* :doc:`compute_temp_chunk` +* :doc:`compute_temp_com` +* :doc:`compute_temp_deform` +* :doc:`compute_temp_partial` +* :doc:`compute_temp_profile` +* :doc:`compute_temp_ramp` +* :doc:`compute_temp_region` +* :doc:`compute_temp_rotate` +* :doc:`compute_temp_sphere` + + .. note:: diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index 8c7eb91b12..cfe9497665 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -5,8 +5,8 @@ The shear viscosity eta of a fluid can be measured in at least 6 ways using various options in LAMMPS. See the examples/VISCOSITY directory for scripts that implement the 5 methods discussed here for a simple Lennard-Jones fluid model and 1 method for SPC/E water model. -Also, see the :doc:`Howto kappa ` doc page for an analogous discussion for -thermal conductivity. +Also, see the :doc:`page on calculating thermal conductivity ` +for an analogous discussion for thermal conductivity. Eta is a measure of the propensity of a fluid to transmit momentum in a direction perpendicular to the direction of velocity or momentum diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 2f6e8096dc..868f679dbc 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -46,20 +46,19 @@ between them at any time using "git checkout ".) Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with the exception, that the HTML documentation files are not included. They can be fetched -from the LAMMPS website by typing "make fetch" in the doc directory. +from the LAMMPS website by typing ``make fetch`` in the doc directory. Or they can be generated from the content provided in doc/src by -typing "make html" from the doc directory. +typing ``make html`` from the doc directory. After initial cloning, as bug fixes and new features are added to -LAMMPS, as listed on :doc:`this page `, you can stay -up-to-date by typing the following git commands from within the -"mylammps" directory: +LAMMPS you can stay up-to-date by typing the following git commands +from within the "mylammps" directory: .. code-block:: bash $ git checkout unstable # not needed if you always stay in this branch - $ git checkout stable # use one of the 3 checkout commands - $ git checkout master + $ git checkout stable # use one of these 3 checkout commands + $ git checkout master # to choose the branch to follow $ git pull Doing a "pull" will not change any files you have added to the LAMMPS @@ -70,8 +69,8 @@ repository file with your version of the file and tell you if there are any conflicts. See the git documentation for details. If you want to access a particular previous release version of LAMMPS, -you can instead "checkout" any version with a published tag. See the -output of "git tag -l" for the list of tags. The git command to do +you can instead "check out" any version with a published tag. See the +output of ``git tag -l`` for the list of tags. The git command to do this is as follows. .. code-block:: bash @@ -79,14 +78,14 @@ this is as follows. $ git checkout tagID Stable versions and what tagID to use for a particular stable version -are discussed on :doc:`this page `. Note that this command -will print some warnings, because in order to get back to the latest -revision and to be able to update with "git pull" again, you first -will need to first type "git checkout unstable" (or check out any -other desired branch). - -Once you have updated your local files with a "git pull" (or "git -checkout"), you still need to re-build LAMMPS if any source files have +are discussed on `this page `_. +Note that this command will print some warnings, because in order to get +back to the latest revision and to be able to update with ``git pull`` +again, you will need to do ``git checkout unstable`` (or +check out any other desired branch) first. + +Once you have updated your local files with a ``git pull`` (or ``git +checkout``), you still need to re-build LAMMPS if any source files have changed. To do this, you should cd to the src directory and type: .. code-block:: bash @@ -95,7 +94,7 @@ changed. To do this, you should cd to the src directory and type: $ make package-update # sync package files with src files $ make foo # re-build for your machine (mpi, serial, etc) -just as described on the :doc:`Install patch ` doc page, +just as described on the :doc:`Apply patch ` doc page, after a patch has been installed. .. warning:: diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index 3acd72753f..0bbd7bbf00 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -6,9 +6,12 @@ if you use git to track the LAMMPS development. Instructions for how to stay current are on the :doc:`Download the LAMMPS source with git ` page. -If you prefer to download a tarball, as described on the :doc:`Install git ` doc page, you can stay current by +If you prefer to download a tarball, as described on the +:doc:`tarball download ` page, you can stay current by downloading "patch files" when new patch releases are made. A link to -a patch file is posted on the `bug and feature page `_ of the LAMMPS website, along +a patch file is posted on the +`bugf fixes and new feature page `_ +of the LAMMPS website, along with a list of changed files and details about what is in the new patch release. This page explains how to apply the patch file to your local LAMMPS directory. diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index cff198da70..acf27455cf 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -181,7 +181,7 @@ Pre- and post-processing * A handful of pre- and post-processing tools are packaged with LAMMPS, some of which can convert input and output files to/from formats used - by other codes; see the :doc:`Toos ` doc page. + by other codes; see the :doc:`Tools ` doc page. * Our group has also written and released a separate toolkit called `Pizza.py `_ which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is @@ -197,7 +197,7 @@ Specialized features ---------------------------------- LAMMPS can be built with optional packages which implement a variety -of additional capabilities. See the :doc:`Packages ` doc +of additional capabilities. See the :doc:`Optional Packages ` page for details. These are LAMMPS capabilities which you may not think of as typical @@ -214,7 +214,7 @@ classical MD options: * Monte Carlo via :doc:`GCMC ` and :doc:`tfMC ` and :doc:`atom swapping ` * :doc:`path-integral molecular dynamics (PIMD) ` and :doc:`this as well ` * :doc:`Direct Simulation Monte Carlo ` for low-density fluids -* :doc:`Peridynamics mesoscale modeling ` +* :doc:`Peridynamics modeling ` * :doc:`Lattice Boltzmann fluid ` * :doc:`targeted ` and :doc:`steered ` molecular dynamics * :doc:`two-temperature electron model ` diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index fb41b9a054..a22a726bdc 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -66,8 +66,10 @@ Here are suggestions on how to perform these tasks: on-the-fly via its :doc:`dump image ` command and pass them to an external program, `FFmpeg `_ to generate movies from them. For high-quality, interactive visualization there are - many excellent and free tools available. See the `Other Codes page `_ page of the LAMMPS website for - visualization packages that can use LAMMPS output data. + many excellent and free tools available. See the + `Visualization Tools `_ page of the + LAMMPS website for + visualization packages that can process LAMMPS output data. * **Plotting:** See the next bullet about Pizza.py as well as the :doc:`Python ` doc page for examples of plotting LAMMPS output. Scripts provided with the *python* tool in the tools diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 776002354a..df6bfad33d 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -15,7 +15,7 @@ that supports the `MPI `_ message-passing library. This includes shared-memory boxes and distributed-memory clusters and supercomputers. -.. _mpi: http://www-unix.mcs.anl.gov/mpi +.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface .. _lws: https://lammps.sandia.gov LAMMPS is written in C++. Earlier versions were written in F77 and diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index 125d2e0f4c..7abc78e7e4 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -2,22 +2,22 @@ Additional website links ======================== The `LAMMPS website `_ has a variety of additional info about -LAMMPS, beyond what is in this manual. Some of the other pages in -this Intr are included in this list. +LAMMPS, beyond what is in this manual. Some other useful resources +available online are listed below. .. _lws: https://lammps.sandia.gov * `Brief intro and recently added significant features `_ -* `List of features `_ -* `List of non-features `_ +* `List of features `_ +* `List of non-features `_ * `Recent bug fixes and new features `_ * `Download info `_ * `GitHub site `_ * `SourceForge site `_ -* `LAMMPS open-source license `_ +* `LAMMPS open-source license `_ -* `Glossary of MD terms relevant to LAMMPS `_ +* `Glossary of terms relevant to LAMMPS `_ * `LAMMPS highlights with images `_ * `LAMMPS highlights with movies `_ * `Mail list `_ diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 2ec830a0b7..ba6c40b255 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -27,7 +27,10 @@ all LAMMPS development is coordinated. The content for this manual is part of the LAMMPS distribution. You can build a local copy of the Manual as HTML pages or a PDF file, by following the steps on the :doc:`Manual build ` doc page. -The manual is split into two parts: 1) User documentation and 2) Programmer documentation. +The manual is organized in two parts: +1) A :ref:`User documentation ` for how to install +and use LAMMPS and 2) a :ref:`Programmer documentation ` +for how to write programs using the LAMMPS library or how to modify LAMMPS. ---------- diff --git a/doc/src/Modify.rst b/doc/src/Modify.rst index fa45c4818e..2a727dfd0f 100644 --- a/doc/src/Modify.rst +++ b/doc/src/Modify.rst @@ -8,7 +8,8 @@ this. If you add a new feature to LAMMPS and think it will be of interest to general users, we encourage you to submit it for inclusion in LAMMPS -as a pull request on our `GitHub site `_, after reading the :doc:`Modify contribute ` doc page. +as a pull request on our `GitHub site `_, +after reading :doc:`this page `. .. toctree:: :maxdepth: 1 diff --git a/doc/src/Modify_atom.rst b/doc/src/Modify_atom.rst index 34a529020a..5c3a96789e 100644 --- a/doc/src/Modify_atom.rst +++ b/doc/src/Modify_atom.rst @@ -47,13 +47,13 @@ other strings. * - fields_comm - list of properties communicated to ghost atoms every step * - fields_comm_vel - - additional properties communicated if :doc:`comm_modify vel ` is used + - additional properties communicated if :doc:`comm_modify vel ` is used * - fields_reverse - list of properties summed from ghost atoms every step * - fields_border - list of properties communicated with ghost atoms every reneighboring step * - fields_border_vel - - additional properties communicated if :doc:`comm_modify vel ` is used + - additional properties communicated if :doc:`comm_modify vel ` is used * - fields_exchange - list of properties communicated when an atom migrates to another processor * - fields_restart diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 8bc320a9b0..27de36f30c 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -31,14 +31,14 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS you are working on. Only discussions related to LAMMPS development are tolerated, so this is **NOT** for people that look for help with compiling, installing, or using LAMMPS. Please contact the `lammps-users mailing -list `_ for those purposes instead. +list `_ for those purposes instead. How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core codebase, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical -requirements. Once you have prepared everything, see the :doc:`Using -GitHub with LAMMPS Howto ` doc page for instructions on +requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub +Tutorial ` page for instructions on how to submit your changes or new files through a GitHub pull request. If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level @@ -58,8 +58,8 @@ are listed and described on the :doc:`Packages details ` doc p Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See the `Open source `_ page on the LAMMPS -website for details. +used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license +` doc page for details. With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source diff --git a/doc/src/Modify_thermo.rst b/doc/src/Modify_thermo.rst index 564df9ec7a..ea09e30c1d 100644 --- a/doc/src/Modify_thermo.rst +++ b/doc/src/Modify_thermo.rst @@ -20,7 +20,7 @@ for output. Search for the word "customize" with references to "keyword" in thermo.cpp to see the several locations where code will need to be added. -Note that the :doc:`thermo_style custom ` command already allows +Note that the :doc:`thermo_style custom ` command already allows for thermo output of quantities calculated by :doc:`fixes `, :doc:`computes `, and :doc:`variables `. Thus, it may be simpler to compute what you wish via one of those constructs, than diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 3d21232a8f..1beeeff5b4 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -299,7 +299,8 @@ Dozens of pair styles and a version of the PPPM long-range Coulombic solver optimized for GPUs. All such styles have a "gpu" as a suffix in their style name. The GPU code can be compiled with either CUDA or OpenCL, however the OpenCL variants are no longer actively maintained -and only the CUDA versions are regularly tested. The :doc:`Speed gpu ` doc page gives details of what hardware and GPU +and only the CUDA versions are regularly tested. The +:doc:`Speed_gpu` page gives details of what hardware and GPU software is required on your system, and details on how to build and use this package. Its styles can be invoked at run time via the "-sf gpu" or "-suffix gpu" :doc:`command-line switches `. See @@ -318,8 +319,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * src/GPU: filenames -> commands * src/GPU/README * lib/gpu/README -* :doc:`Speed packages ` -* :doc:`Speed gpu ` +* :doc:`Accelerator packages ` +* :doc:`GPU package ` * :doc:`Section 2.6 -sf gpu ` * :doc:`Section 2.6 -pk gpu ` * :doc:`package gpu ` @@ -433,7 +434,7 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their -style name. The :doc:`Speed kokkos ` doc page gives +style name. The :doc:`KOKKOS package ` doc page gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf kk" or "-suffix kk" :doc:`command-line switches `. Also see the :ref:`GPU `, :ref:`OPT `, @@ -463,8 +464,8 @@ This package has :ref:`specific installation instructions ` on the :doc: * src/KOKKOS: filenames -> commands * src/KOKKOS/README * lib/kokkos/README -* :doc:`Speed packages ` -* :doc:`Speed kokkos ` +* :doc:`Accelerator packages ` +* :doc:`KOKKOS package ` * :doc:`Section 2.6 -k on ... ` * :doc:`Section 2.6 -sf kk ` * :doc:`Section 2.6 -pk kokkos ` @@ -665,7 +666,7 @@ A general interface for machine-learning interatomic potentials. **Install:** -To use this package, also the :ref:`SNAP package` needs to be installed. +To use this package, also the :ref:`SNAP package ` needs to be installed. **Author:** Aidan Thompson (Sandia). @@ -773,7 +774,7 @@ OPT package A handful of pair styles which are optimized for improved CPU performance on single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. The styles have an "opt" suffix in -their style name. The :doc:`Speed opt ` doc page gives +their style name. The :doc:`OPT package ` doc page gives details of how to build and use this package. Its styles can be invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches `. See also the :ref:`KOKKOS `, :ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which @@ -789,8 +790,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu **Supporting info:** * src/OPT: filenames -> commands -* :doc:`Speed packages ` -* :doc:`Speed opt ` +* :doc:`Accelerator packages ` +* :doc:`OPT package ` * :doc:`Section 2.6 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) * `Benchmarks page `_ of web site @@ -1541,7 +1542,8 @@ USER-INTEL package Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. The :doc:`Speed intel ` doc page gives details of what hardware and +All of them have an "intel" in their style name. The +:doc:`USER-INTEL package ` page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf intel" or "-suffix intel" :doc:`command-line switches `. Also see @@ -1567,8 +1569,8 @@ This package has :ref:`specific installation instructions ` on the : * src/USER-INTEL: filenames -> commands * src/USER-INTEL/README -* :doc:`Speed packages ` -* :doc:`Speed intel ` +* :doc:`Accelerator packages ` +* :doc:`USER-INTEL package ` * :doc:`Section 2.6 -sf intel ` * :doc:`Section 2.6 -pk intel ` * :doc:`package intel ` @@ -1915,7 +1917,7 @@ USER-OMP package Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace styles which are altered to enable threading on many-core CPUs via OpenMP directives. All of them have an "omp" in their style name. -The :doc:`Speed omp ` doc page gives details of what hardware +The :doc:`USER-OMP package ` page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf omp" or "-suffix omp" :doc:`command-line switches `. Also see @@ -1947,8 +1949,8 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-OMP: filenames -> commands * src/USER-OMP/README -* :doc:`Speed packages ` -* :doc:`Speed omp ` +* :doc:`Accelerator packages ` +* :doc:`USER-OMP package ` * :doc:`Section 2.6 -sf omp ` * :doc:`Section 2.6 -pk omp ` * :doc:`package omp ` diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index ca22515590..ab9be69ab3 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -37,7 +37,7 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style dipole/cut ` | dipole | no | +| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style lj/.../dipole ` | dipole | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index d02873a8be..35d5f829a0 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -27,11 +27,11 @@ executable itself can be placed elsewhere. As LAMMPS runs it prints info to the screen and a logfile named *log.lammps*\ . More info about output is given on the -:doc:`Run output ` doc page. +:doc:`screen and logfile output ` page. If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING -message and continue. See the :doc:`Errors ` doc page for a +message and continue. See the :doc:`Common Problems ` page for a discussion of the various kinds of errors LAMMPS can or can't detect, a list of all ERROR and WARNING messages, and what to do about them. diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 054ed66d57..f5435ec3a9 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -80,7 +80,7 @@ stdin. Explicitly enable or disable KOKKOS support, as provided by the KOKKOS package. Even if LAMMPS is built with this package, as described -in :doc:`Speed kokkos `, this switch must be set to enable +in the :doc:`the KOKKOS package page `, this switch must be set to enable running with KOKKOS-enabled styles the package provides. If the switch is not set (the default), LAMMPS will operate as if the KOKKOS package were not installed; i.e. you can run standard LAMMPS or with @@ -98,7 +98,8 @@ Either the full word or an abbreviation can be used for the keywords. Note that the keywords do not use a leading minus sign. I.e. the keyword is "t", not "-t". Also note that each of the keywords has a default setting. Examples of when to use these options and what -settings to use on different platforms is given on the :doc:`Speed kokkos ` doc page. +settings to use on different platforms is given on the :doc:`KOKKOS package ` +doc page. * d or device * g or gpus @@ -268,7 +269,7 @@ machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors. To run multiple independent simulations from one input script, using -multiple partitions, see the :doc:`Howto multiple ` doc +multiple partitions, see the :doc:`Howto multiple ` page. World- and universe-style :doc:`variables ` are useful in this context. @@ -326,7 +327,7 @@ cores within each node are ranked in a desired order. Or when using the :doc:`run_style verlet/split ` command with 2 partitions to insure that a specific Kspace processor (in the second partition) is matched up with a specific set of processors in the first partition. -See the :doc:`Speed tips ` doc page for more details. +See the :doc:`General tips ` page for more details. If the keyword *nth* is used with a setting *N*\ , then it means every Nth processor will be moved to the end of the ranking. This is useful @@ -385,7 +386,7 @@ implementations, either by environment variables that specify how to order physical processors, or by config files that specify what physical processors to assign to each MPI rank. The -reorder switch simply gives you a portable way to do this without relying on MPI -itself. See the :doc:`processors out ` command for how +itself. See the :doc:`processors file ` command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. @@ -523,10 +524,10 @@ lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style can be specified explicitly in your input script, e.g. pair_style lj/cut/gpu. If the -suffix switch is used the specified suffix (gpu,intel,kk,omp,opt) is automatically appended whenever your input -script command creates a new :doc:`atom `, -:doc:`pair `, :doc:`fix `, :doc:`compute `, or -:doc:`run ` style. If the variant version does not exist, -the standard version is created. +script command creates a new :doc:`atom style `, +:doc:`pair style `, :doc:`fix `, +:doc:`compute `, or :doc:`run style `. If the +variant version does not exist, the standard version is created. For the GPU package, using this command-line switch also invokes the default GPU settings, as if the command "package gpu 1" were used at @@ -579,8 +580,8 @@ index variable in the input script, since index variables cannot be re-defined. See the :doc:`variable ` command for more info on defining -index and other kinds of variables and the :doc:`Commands parse ` page for more info on using variables in -input scripts. +index and other kinds of variables and the :doc:`Parsing rules ` +page for more info on using variables in input scripts. .. note:: diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index 45b5b21d8a..66db03e360 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -38,7 +38,7 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI and bench/KEPLER directories have input files and scripts and instructions for running the same (or similar) problems using OpenMP or GPU or Xeon Phi acceleration options. See the README files in those directories and the -:doc:`Speed packages ` doc pages for instructions on how +:doc:`Accelerator packages ` pages for instructions on how to build LAMMPS and run on that kind of hardware. The bench/POTENTIALS directory has input files which correspond to the diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 3269564d21..5df53ec2cd 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -9,7 +9,7 @@ different back end languages such as CUDA, OpenMP, or Pthreads. The Kokkos library also provides data abstractions to adjust (at compile time) the memory layout of data structures like 2d and 3d arrays to optimize performance on different hardware. For more information on -Kokkos, see `GitHub `_. +Kokkos, see `the Kokkos GitHub page `_. The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles that use data structures and macros provided by the Kokkos @@ -20,20 +20,20 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions see the Kokkos `Wiki `_. -Kokkos currently provides support for 3 modes of execution (per MPI +Kokkos currently provides support for 4 modes of execution (per MPI task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP -(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA -GPUs). You choose the mode at build time to produce an executable -compatible with specific hardware. +(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA +GPUs) and HIP (for AMD GPUs). You choose the mode at build time to +produce an executable compatible with a specific hardware. -.. note:: +.. admonition:: NVIDIA CUDA support To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit software version 9.0 or later must be installed on your system. See the discussion for the :doc:`GPU package ` for details of how to check and do this. -.. note:: +.. admonition:: CUDA and MPI library compatibility Kokkos with CUDA currently implicitly assumes that the MPI library is CUDA-aware. This is not always the case, especially when using @@ -45,6 +45,13 @@ compatible with specific hardware. LAMMPS command line or by using the command :doc:`package kokkos cuda/aware off ` in the input file. +.. admonition:: AMD GPU support + + To build with Kokkos the HIPCC compiler from the AMD ROCm software + version 3.5 or later is required. Supporting this Kokkos mode in + LAMMPS is still work in progress. Please contact the LAMMPS developers + if you run into problems. + Building LAMMPS with the KOKKOS package """"""""""""""""""""""""""""""""""""""" -- GitLab From d0d3cee28da9ef9f97d9dc48a4081e175fe9d940 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 11:50:02 -0400 Subject: [PATCH 74/75] a few more cosmetic changes --- doc/src/Speed_measure.rst | 2 +- doc/src/Speed_omp.rst | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/doc/src/Speed_measure.rst b/doc/src/Speed_measure.rst index 686fdb6adc..1daf49f4c4 100644 --- a/doc/src/Speed_measure.rst +++ b/doc/src/Speed_measure.rst @@ -14,7 +14,7 @@ timings; you can simply extrapolate from short runs. For the set of runs, look at the timing data printed to the screen and log file at the end of each LAMMPS run. The -:doc:`Run_output ` doc page gives an overview. +:doc:`screen and logfile output ` page gives an overview. Running on one (or a few processors) should give a good estimate of the serial performance and what portions of the timestep are taking diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 3d3cb4daf1..f29e3743b4 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -86,7 +86,8 @@ USER-OMP style (in serial or parallel) with a single thread per MPI task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This is because many of the USER-OMP styles contain similar optimizations -to those used in the OPT package, described in :doc:`Section 5.3.5 `. +to those used in the OPT package, described in +:doc:`the OPT package ` doc page. With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be @@ -95,7 +96,8 @@ specific machine, paying attention to guidelines discussed in the next sub-section. A description of the multi-threading strategy used in the USER-OMP -package and some performance examples are `presented here `_ +package and some performance examples are +`presented here `_. Guidelines for best performance """"""""""""""""""""""""""""""" -- GitLab From 41a3e7c712504b62f953345ff67a548edfd76218 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 11:59:04 -0400 Subject: [PATCH 75/75] update a few links in the programmer guide --- doc/src/pg_developer.rst | 21 ++++++++++++++------- doc/src/pg_lib_add.rst | 2 +- doc/src/pg_python.rst | 8 ++++---- 3 files changed, 19 insertions(+), 12 deletions(-) diff --git a/doc/src/pg_developer.rst b/doc/src/pg_developer.rst index b6fb10e37b..d3f11d52c4 100644 --- a/doc/src/pg_developer.rst +++ b/doc/src/pg_developer.rst @@ -10,11 +10,14 @@ of time and requests from the LAMMPS user community. LAMMPS source files =================== -The source files of the LAMMPS code are distributed across two -directories of the distribution. The core of the code is located in the -``src`` folder and its sub-directories. Almost all of those are C++ files -(implementation files have a ``.cpp`` extension and and headers a -``.h``). A sizable number of these files are in the ``src`` directory +The source files of the LAMMPS code are found in two +directories of the distribution: ``src`` and ``lib``. +Most of the code is C++ but there are small numbers of files +in several other languages. + +The core of the code is located in the +``src`` folder and its sub-directories. +A sizable number of these files are in the ``src`` directory itself, but there are plenty of :doc:`packages `, which can be included or excluded when LAMMPS is built. See the :doc:`Include packages in build ` section of the manual for more @@ -25,7 +28,7 @@ enabled or disabled for a LAMMPS binary. The source files for each package are in all-uppercase sub-directories of the ``src`` folder, for example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS`` sub-directory is not a package but contains a dummy MPI library, that is -used when building a serial version of the code. the ``src/MAKE`` +used when building a serial version of the code. The ``src/MAKE`` directory contains makefiles with settings and flags for a variety of configuration and machines for the build process with traditional makefiles. @@ -39,7 +42,8 @@ or CUDA. These libraries are linked to during a LAMMPS build, if the corresponding package is installed. LAMMPS C++ source files almost always come in pairs, such as -``src/run.cpp`` and ``src/run.h``. The pair of files defines a C++ +``src/run.cpp`` (implementation file) and ``src/run.h`` (header file). +Each pair of files defines a C++ class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the :doc:`run ` command in a LAMMPS input script. As this example illustrates, source file and class names often have a @@ -48,6 +52,9 @@ Some source files and classes do not have a corresponding input script command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force` class. They are discussed in the next section. +A small number of C++ classes and utility functions are implemented with +only a ``.h`` file. Examples are the Pointer class and the mergesort function. + LAMMPS class topology ===================== diff --git a/doc/src/pg_lib_add.rst b/doc/src/pg_lib_add.rst index 139476c683..e58b6c2b73 100644 --- a/doc/src/pg_lib_add.rst +++ b/doc/src/pg_lib_add.rst @@ -12,7 +12,7 @@ there are now a few requirements for inclusion of changes. implement functionality that can already be achieved with the existing APIs. - All changes and additions should be documented with - `Doxygen `_ style comments and references + `Doxygen `_ style comments and references to those functions added to the corresponding files in the ``doc/src`` folder. - If possible, new unit tests to test those new features should diff --git a/doc/src/pg_python.rst b/doc/src/pg_python.rst index 72d07c5983..80e83d4638 100644 --- a/doc/src/pg_python.rst +++ b/doc/src/pg_python.rst @@ -14,7 +14,7 @@ There are multiple Python interface classes in the :py:mod:`lammps` module: - the :py:class:`lammps ` class. This is a wrapper around the C-library interface and its member functions try to replicate the - :doc:`C-library API ` closely. This is the most + :ref:`C-library API ` closely. This is the most feature-complete Python API. - the :py:class:`PyLammps ` class. This is a more high-level and more Python style class implemented on top of the @@ -63,7 +63,7 @@ MPI ranks after splitting the communicator. Here is a simple example: # explicitly close and delete LAMMPS instance (optional) lmp.close() -Same as with the :doc:`C library API ` this will use the +Same as with the :ref:`C library API ` this will use the ``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was compiled with. The :py:func:`lmp.close() ` call is optional since the LAMMPS class instance will also be deleted @@ -113,8 +113,8 @@ The ``lammps`` class API ************************ The :py:class:`lammps ` class is the core of the LAMMPS -Python interfaces. It is a wrapper around the :doc:`LAMMPS C library -API ` using the `Python ctypes module +Python interfaces. It is a wrapper around the :ref:`LAMMPS C library +API ` using the `Python ctypes module `_ and a shared library compiled from the LAMMPS sources code. The individual methods in this class try to closely follow the corresponding C functions. The handle -- GitLab