From 63cb88daae36d48ff148132cf1d3d382cbfb8bf4 Mon Sep 17 00:00:00 2001 From: Yaser Afshar Date: Tue, 29 Oct 2019 10:46:35 -0500 Subject: [PATCH 01/16] Printing the mutable parameters of the KIM portable models Calling 'kim_init' would report the mutable parameters of KIM portable models (PM) including parameter's name, data type, and extent. --- src/KIM/kim_init.cpp | 103 +++++++++++++++++++++++++++++++++++++------ src/KIM/kim_init.h | 14 +++--- 2 files changed, 99 insertions(+), 18 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index a4272caa01..1d3830c275 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -13,8 +13,9 @@ /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), - Ryan S. Elliott (UMN) - Ellad B. Tadmor (UMN) + Ryan S. Elliott (UMN), + Ellad B. Tadmor (UMN), + Yaser Afshar (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -77,6 +78,14 @@ extern "C" { #include "KIM_SimulatorHeaders.h" } +#ifdef SNUM +#undef SNUM +#endif + +#define SNUM(x) \ + static_cast(std::ostringstream() \ + << std::dec << x).str() + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -98,11 +107,13 @@ void KimInit::command(int narg, char **arg) } else unit_conversion_mode = false; char *model_units; - determine_model_type_and_units(model_name, user_units, &model_units); + KIM_Model *pkim = NULL; + + determine_model_type_and_units(model_name, user_units, &model_units, pkim); write_log_cite(model_name); - do_init(model_name, user_units, model_units); + do_init(model_name, user_units, model_units, pkim); } @@ -156,7 +167,8 @@ void get_kim_unit_names( } // namespace void KimInit::determine_model_type_and_units(char * model_name, char * user_units, - char ** model_units) + char ** model_units, + KIM_Model *&pkim) { KIM_LengthUnit lengthUnit; KIM_EnergyUnit energyUnit; @@ -183,7 +195,6 @@ void KimInit::determine_model_type_and_units(char * model_name, { get_kim_unit_names(user_units, lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, error); - KIM_Model * kim_MO; int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, lengthUnit, energyUnit, @@ -192,19 +203,19 @@ void KimInit::determine_model_type_and_units(char * model_name, timeUnit, model_name, &units_accepted, - &kim_MO); + &pkim); if (kim_error) error->all(FLERR,"Unable to load KIM Simulator Model."); model_type = MO; - KIM_Model_Destroy(&kim_MO); if (units_accepted) { *model_units = new char[strlen(user_units)+1]; strcpy(*model_units,user_units); return; } else if (unit_conversion_mode) { + KIM_Model_Destroy(&pkim); int const num_systems = 5; char const * const systems[num_systems] = {"metal", "real", "si", "cgs", "electron"}; @@ -219,15 +230,17 @@ void KimInit::determine_model_type_and_units(char * model_name, timeUnit, model_name, &units_accepted, - &kim_MO); - KIM_Model_Destroy(&kim_MO); + &pkim); if (units_accepted) { *model_units = new char[strlen(systems[i])+1]; strcpy(*model_units,systems[i]); return; } - } error->all(FLERR,"KIM Model does not support any lammps unit system"); + KIM_Model_Destroy(&pkim); + } + error->all(FLERR,"KIM Model does not support any lammps unit system"); } else { + KIM_Model_Destroy(&pkim); error->all(FLERR,"KIM Model does not support the requested unit system"); } } @@ -270,7 +283,7 @@ void KimInit::determine_model_type_and_units(char * model_name, /* ---------------------------------------------------------------------- */ -void KimInit::do_init(char *model_name, char *user_units, char *model_units) +void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM_Model *&pkim) { // create storage proxy fix. delete existing fix, if needed. @@ -358,6 +371,68 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units) // reset template map. KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); } + else if (model_type == MO) + { + int numberOfParameters; + KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters); + + std::string mesg = "\nThis model has "; + if (numberOfParameters) + { + KIM_DataType kim_DataType; + int extent; + char const *str_name = NULL; + char const *str_desc = NULL; + + mesg += SNUM(numberOfParameters); + mesg += " mutable parameters. \n"; + + int max_len(0); + for (int i = 0; i < numberOfParameters; ++i) + { + KIM_Model_GetParameterMetadata(pkim, i, &kim_DataType, + &extent, &str_name, &str_desc); + max_len = MAX(max_len, strlen(str_name)); + } + ++max_len; + mesg += "No. | Parameter name "; + for (int i = 18; i < max_len; ++i) + mesg += " "; + mesg += "| data type | extent\n"; + for (int i = 0; i < 8 + MAX(18, max_len); ++i) + mesg += "-"; + mesg += "-----------------------\n"; + for (int i = 0; i < numberOfParameters; ++i) + { + KIM_Model_GetParameterMetadata(pkim, i, &kim_DataType, + &extent, &str_name, &str_desc); + mesg += SNUM(i+1); + for (int j = SNUM(i+1).size(); j < 8; ++j) + mesg += " "; + mesg += "| "; + mesg += str_name; + for (int j = strlen(str_name) + 1; j < MAX(18, strlen(str_name) + 1); ++j) + mesg += " "; + mesg += "| \""; + mesg += KIM_DataType_ToString(kim_DataType); + if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) + mesg += "\" | "; + else + mesg += "\" | "; + mesg += SNUM(extent); + mesg += "\n"; + } + } + else + mesg += "No mutable parameters. \n"; + + KIM_Model_Destroy(&pkim); + + if (comm->me == 0) + { + input->write_echo(mesg.c_str()); + } + } // End output to log file kim_init_log_delimiter("end"); @@ -366,7 +441,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units) /* ---------------------------------------------------------------------- */ -void KimInit::kim_init_log_delimiter(std::string const begin_end) const +void KimInit::kim_init_log_delimiter(std::string const &begin_end) const { if (comm->me == 0) { std::string mesg; @@ -506,3 +581,5 @@ void KimInit::write_log_cite(char * model_name) KIM_Collections_Destroy(&coll); } + +#undef SNUM diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 2b5dc520c7..62c404212b 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -13,8 +13,9 @@ /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), - Ryan S. Elliott (UMN) - Ellad B. Tadmor (UMN) + Ryan S. Elliott (UMN), + Ellad B. Tadmor (UMN), + Yaser Afshar (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -67,6 +68,9 @@ CommandStyle(kim_init,KimInit) #include "pointers.h" #include +// Forward declaration. +class KIM_Model; + namespace LAMMPS_NS { class KimInit : protected Pointers { @@ -78,11 +82,11 @@ class KimInit : protected Pointers { model_type_enum model_type; bool unit_conversion_mode; - void determine_model_type_and_units(char *, char *, char **); + void determine_model_type_and_units(char *, char *, char **, KIM_Model *&); void write_log_cite(char *); - void do_init(char *, char *, char *); + void do_init(char *, char *, char *, KIM_Model *&); void do_variables(char*, char*); - void kim_init_log_delimiter(std::string const begin_end) const; + void kim_init_log_delimiter(std::string const &begin_end) const; }; } -- GitLab From 3cca4e0d2d76169b0d278c2ef41f8cafeb8da5ca Mon Sep 17 00:00:00 2001 From: Yaser Afshar Date: Tue, 29 Oct 2019 11:50:28 -0500 Subject: [PATCH 02/16] New capabilities for updating KIM portable models parameters 1. Add new capabilities within LAMMPS for setting parameters of the KIM portable models (PM). The current implementation extends the 'pair_coeff' command to modify the PM parameters. A series of additional parameters after the species list is the input to the modified command. Each set of the other setting is parameter name, range of array indices, and corresponding parameter values. 2. Add two getters to the PairKIM class to get the KIM_Model object, and the atom type list outside the 'pair_kim' command for ease of use and extension ability of a new 'kim_param' command. --- src/KIM/pair_kim.cpp | 164 +++++++++++++++++++++++++++++++++++++++++-- src/KIM/pair_kim.h | 9 +++ 2 files changed, 169 insertions(+), 4 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 43b444418a..e54c76397f 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -14,6 +14,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Ryan S. Elliott (UMinn) Axel Kohlmeyer (Temple U) + Yaser Afshar (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -57,6 +58,7 @@ #include #include #include +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -66,6 +68,7 @@ #include "update.h" #include "memory.h" #include "domain.h" +#include "utils.h" #include "error.h" using namespace LAMMPS_NS; @@ -330,6 +333,14 @@ void PairKIM::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ +#ifdef SNUM +#undef SNUM +#endif + +#define SNUM(x) \ + static_cast(std::ostringstream() \ + << std::dec << x).str() + void PairKIM::coeff(int narg, char **arg) { // This is called when "pair_coeff ..." is read from input @@ -339,7 +350,7 @@ void PairKIM::coeff(int narg, char **arg) if (!allocated) allocate(); - if (narg != 2 + atom->ntypes) + if (narg < 2 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); // insure I,J args are * * @@ -368,10 +379,10 @@ void PairKIM::coeff(int narg, char **arg) // Assume all species arguments are valid // errors will be detected by below - std::string atom_type_sym_list; + atom_type_list.clear(); lmps_num_unique_elements = 0; - for (i = 2; i < narg; i++) { - atom_type_sym_list += std::string(" ") + arg[i]; + for (i = 2; i < 2 + atom->ntypes; i++) { + atom_type_list += std::string(" ") + arg[i]; for (j = 0; j < lmps_num_unique_elements; j++) if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; lmps_map_species_to_unique[i-1] = j; @@ -421,8 +432,147 @@ void PairKIM::coeff(int narg, char **arg) error->all(FLERR, msg.c_str()); } } + // Set the new values for PM parameters + if (narg > 2 + atom->ntypes) { + // Get the number of mutable parameters in the kim model + int numberOfParameters(0); + KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters); + + if (!numberOfParameters) { + std::string msg("Incorrect args for pair coefficients \n"); + msg += "This model has No mutable parameters."; + error->all(FLERR, msg.c_str()); + } + + int kimerror; + + // Parameter name + char *paramname = NULL; + + for (int i = 2 + atom->ntypes; i < narg;) { + // Parameter name + if (i < narg) + paramname = arg[i++]; + else + break; + + // Find the requested parameter within the model parameters + int param_index; + KIM_DataType kim_DataType; + int extent; + char const *str_name = NULL; + char const *str_desc = NULL; + + for (param_index = 0; param_index < numberOfParameters; ++param_index) { + kimerror = KIM_Model_GetParameterMetadata(pkim, param_index, + &kim_DataType, &extent, &str_name, &str_desc); + if (kimerror) + error->all(FLERR,"KIM GetParameterMetadata returned error"); + + if (strcmp(paramname, str_name) == 0) break; + } + + if (param_index >= numberOfParameters) { + std::string msg("Wrong argument for pair coefficients.\n"); + msg += "This Model does not have the requested '"; + msg += paramname; + msg += "' parameter."; + error->all(FLERR, msg.c_str()); + } + + // Get the index_range for the requested parameter + int nlbound(0); + int nubound(0); + + if (i < narg) { + std::string argtostr(arg[i++]); + + // Check to see if the indices range contains only integer numbers & : + if (argtostr.find_first_not_of("0123456789:") != std::string::npos) { + std::string msg("Illegal index_range.\n"); + msg += "Expected integer parameter(s) instead of '"; + msg += argtostr; + msg += "' in index_range."; + error->all(FLERR, msg.c_str()); + } + + std::string::size_type npos = argtostr.find(':'); + if (npos != std::string::npos) { + argtostr[npos] = ' '; + std::stringstream str(argtostr); + str >> nlbound >> nubound; + if (nubound < 1 || nubound > extent || + nlbound < 1 || nlbound > nubound) { + std::string msg("Illegal index_range '"); + msg += SNUM(nlbound) + "-" + SNUM(nubound); + msg += "' for '"; + msg += paramname; + msg += "' parameter with extent of '"; + msg += SNUM(extent); + msg += "' ."; + error->all(FLERR, msg.c_str()); + } + } else { + std::stringstream str(argtostr); + str >> nlbound; + if (nlbound < 1 || nlbound > extent) { + std::string msg("Illegal index '"); + msg += SNUM(nlbound) + "' for '"; + msg += paramname; + msg += "' parameter with extent of '"; + msg += SNUM(extent); + msg += "' ."; + error->all(FLERR, msg.c_str()); + } + nubound = nlbound; + } + } else { + std::string msg = + "Wrong number of arguments for pair coefficients.\n"; + msg += "Index range after parameter name is mandatory."; + error->all(FLERR, msg.c_str()); + } + + // Parameter values + if (i + nubound - nlbound < narg) { + if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Double)) { + for (int j = 0; j < nubound - nlbound + 1; ++j) { + double const V = utils::numeric(FLERR, arg[i++], true, lmp); + kimerror = KIM_Model_SetParameterDouble(pkim, param_index, + nlbound - 1 + j, V); + if (kimerror) + error->all(FLERR, "KIM SetParameterDouble returned error."); + } + } else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) { + for (int j = 0; j < nubound - nlbound + 1; ++j) { + int const V = utils::inumeric(FLERR, arg[i++], true, lmp); + kimerror = KIM_Model_SetParameterInteger(pkim, param_index, + nlbound - 1 + j, V); + if (kimerror) + error->all(FLERR, "KIM SetParameterInteger returned error."); + } + } else + error->all(FLERR, "Wrong parameter type to update"); + } else { + std::string msg = + "Wrong number of variable values for pair coefficients.\n"; + msg += "'"; + msg += SNUM(nubound - nlbound + 1); + msg += "' values are requested for '"; + msg += paramname; + msg += "' parameter."; + error->all(FLERR, msg.c_str()); + } + } + + kimerror = KIM_Model_ClearThenRefresh(pkim); + if (kimerror) + error->all(FLERR, "KIM KIM_Model_ClearThenRefresh returned error"); + } } +#undef SNUM + /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ @@ -747,6 +897,7 @@ void PairKIM::kim_init() KIM_LANGUAGE_NAME_cpp, reinterpret_cast(get_neigh), reinterpret_cast(this)); + if (kimerror) error->all(FLERR,"Unable to set KIM call back pointer"); } @@ -778,6 +929,7 @@ void PairKIM::set_argument_pointers() reinterpret_cast(NULL)); } } + // Set KIM pointer appropriately for particalEnergy if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, KIM_SUPPORT_STATUS_required) @@ -1009,3 +1161,7 @@ void PairKIM::set_kim_model_has_flags() error->all(FLERR,"KIM Model requires unsupported compute callback"); } } + +KIM_Model *PairKIM::get_KIM_Model() { return pkim; } + +std::string PairKIM::get_atom_type_list() { return atom_type_list; } diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index aa33b9b271..1f2c8c8599 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -65,6 +65,7 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" +#include extern "C" { #include "KIM_SimulatorHeaders.h" @@ -88,6 +89,11 @@ class PairKIM : public Pair { virtual void unpack_reverse_comm(int, int*, double*); virtual double memory_usage(); + // Get the KIM_Model object + KIM_Model *get_KIM_Model(); + + // Get the atom type list + std::string get_atom_type_list(); protected: // (nearly) all bool flags are not initialized in constructor, but set // explicitly in the indicated function. All other data members are @@ -98,6 +104,9 @@ class PairKIM : public Pair { // values set in settings() char* kim_modelname; + // list of args that map atom species to KIM elements + std::string atom_type_list; + // values set in coeff() // values set in allocate(), called by coeff() -- GitLab From c8c92189b43cb8922631c26fe6e41811578630e9 Mon Sep 17 00:00:00 2001 From: Yaser Afshar Date: Tue, 29 Oct 2019 11:44:40 -0500 Subject: [PATCH 03/16] New capabilities for accessing KIM portable models parameters Add an ability within LAMMPS for getting/setting KIM portable models (PM) parameters. The assumption is that the model is already known (through 'kim_init') when calling the new command. 'kim_param get' gets the value of PM parameters, where the command input includes: parameter name, & location, or indices range, and the variable(s) name / variable name + split / list /explicit to return the value(s). 'kim_param get paramname index_range varname [s|split|list|explicit]' 'kim_param set' sets the value(s) of PM parameters, where the command input includes: parameter name, & location, or indices range, and the corresponding variable(s) value(s). 'kim_param set paramname index_range value(s)' NOTE: The varable_name is the name of the lammps variable in the lammps input script and can be used in other locations in the script. --- src/KIM/kim_param.cpp | 569 ++++++++++++++++++++++++++++++++++++++++++ src/KIM/kim_param.h | 100 ++++++++ 2 files changed, 669 insertions(+) create mode 100644 src/KIM/kim_param.cpp create mode 100644 src/KIM/kim_param.h diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp new file mode 100644 index 0000000000..f5a154f2d9 --- /dev/null +++ b/src/KIM/kim_param.cpp @@ -0,0 +1,569 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Yaser Afshar (UMN), + Ryan S. Elliott (UMN), + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#include "kim_param.h" +#include +#include +#include +#include +#include "comm.h" +#include "error.h" +#include "input.h" +#include "modify.h" +#include "variable.h" +#include "force.h" +#include "fix_store_kim.h" +#include "pair_kim.h" + +extern "C" +{ +#include "KIM_SimulatorHeaders.h" +} + +#ifdef SNUM +#undef SNUM +#endif + +#define SNUM(x) \ + static_cast(std::ostringstream() \ + << std::dec << x).str() + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +namespace +{ +void get_kim_unit_names( + char const *const system, + KIM_LengthUnit &lengthUnit, + KIM_EnergyUnit &energyUnit, + KIM_ChargeUnit &chargeUnit, + KIM_TemperatureUnit &temperatureUnit, + KIM_TimeUnit &timeUnit, + Error *error) +{ + if ((strcmp(system, "real") == 0)) { + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_kcal_mol; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(system, "metal") == 0)) { + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_eV; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_ps; + } else if ((strcmp(system, "si") == 0)) { + lengthUnit = KIM_LENGTH_UNIT_m; + energyUnit = KIM_ENERGY_UNIT_J; + chargeUnit = KIM_CHARGE_UNIT_C; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(system, "cgs") == 0)) { + lengthUnit = KIM_LENGTH_UNIT_cm; + energyUnit = KIM_ENERGY_UNIT_erg; + chargeUnit = KIM_CHARGE_UNIT_statC; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(system, "electron") == 0)) { + lengthUnit = KIM_LENGTH_UNIT_Bohr; + energyUnit = KIM_ENERGY_UNIT_Hartree; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(system, "lj") == 0)) { + error->all(FLERR, "LAMMPS unit_style lj not supported by KIM models"); + } else + error->all(FLERR, "Unknown unit_style"); +} +} // namespace + +/* ---------------------------------------------------------------------- */ + +KimParam::KimParam(LAMMPS *lmp) : Pointers(lmp) {} + +KimParam::~KimParam() {} + +void KimParam::command(int narg, char **arg) +{ + // kim_param is a command for + // getting/setting the value of a %KIM PM parameter + // + // kim_param get param_name index_range variables formatarg + // kim_param set param_name index_range values + + // kim_param get paramname 1 varname + // kim_param get paramname index_range varname_1, ..., varname_N + // kim_param get paramname index_range varname_base split + // kim_param get paramname index_range varname_base list + // kim_param set paramname index_range values + + if (narg < 4) + error->all(FLERR, "Illegal kim_param command"); + + kim_param_get = (strcmp(arg[0], "get") == 0); + kim_param_set = (strcmp(arg[0], "set") == 0); + + if (!kim_param_get && !kim_param_set) { + std::string msg("Incorrect arguments in kim_param command.\n"); + msg += "'kim_param get/set' is mandatory."; + error->all(FLERR, msg.c_str()); + } + + // Check if we called a kim_init command + // by finding fix STORE/KIM + // retrieve model name and model units. + + char *model_name; + char *model_units; + + bool isPortableModel(false); + + int const ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) { + FixStoreKIM *fix_store = reinterpret_cast(modify->fix[ifix]); + + KIM_SimulatorModel *simulatorModel = + reinterpret_cast( + fix_store->getptr("simulator_model")); + + isPortableModel = simulatorModel ? false : true; + if (!isPortableModel) + error->all(FLERR, "kim_param can only be used with a KIM Portable Model"); + + model_name = (char *)fix_store->getptr("model_name"); + model_units = (char *)fix_store->getptr("model_units"); + } + else + error->all(FLERR, "Must use 'kim_init' before 'kim_param'"); + + kim_param_log_delimiter("begin"); + + KIM_Model *pkim = NULL; + + std::string atom_type_list; + + int kim_error; + + bool isPairStyleAssigned = force->pair ? true : false; + if (isPairStyleAssigned) { + Pair *pair = force->pair_match("kim", 1, 0); + if (pair) { + PairKIM *pairKIM = reinterpret_cast(pair); + + pkim = pairKIM->get_KIM_Model(); + if (!pkim) + error->all(FLERR, "Unable to get the KIM Portable Model."); + + if (kim_param_set) { + atom_type_list = pairKIM->get_atom_type_list(); + if (atom_type_list.empty()) + error->all(FLERR, "The requested atom type list is empty."); + } + } else + error->all(FLERR, "Pair style is defined," + " but there is no match for kim style in lammps."); + } else { + if (kim_param_set) { + std::string msg("Wrong kim_param set command.\n"); + msg += "To set the new parameter values, pair style must be assigned.\n"; + msg += "Must use 'kim_interactions' or"; + msg += "'pair_style kim ' before 'kim_param set'"; + error->all(FLERR, msg.c_str()); + } else { + KIM_LengthUnit lengthUnit; + KIM_EnergyUnit energyUnit; + KIM_ChargeUnit chargeUnit; + KIM_TemperatureUnit temperatureUnit; + KIM_TimeUnit timeUnit; + + get_kim_unit_names(model_units, lengthUnit, energyUnit, + chargeUnit, temperatureUnit, timeUnit, + error); + + int units_accepted; + + kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, + lengthUnit, + energyUnit, + chargeUnit, + temperatureUnit, + timeUnit, + model_name, + &units_accepted, + &pkim); + if (kim_error) + error->all(FLERR, "Unable to create KIM Portable Model."); + } + } + + // Get the number of mutable parameters in the kim model + int numberOfParameters(0); + + KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters); + if (numberOfParameters) { + // Get the parameters + if (kim_param_get) { + // Parameter name + char *paramname = NULL; + // Variable name + char *varname = NULL; + + // Loop over all the arguments + for (int i = 1; i < narg;) { + // Parameter name + if (i < narg) + paramname = arg[i++]; + else + break; + + // Find the requested parameter within the model parameters + int param_index; + KIM_DataType kim_DataType; + int extent; + char const *str_name = NULL; + char const *str_desc = NULL; + + for (param_index = 0; param_index < numberOfParameters; ++param_index) { + kim_error = KIM_Model_GetParameterMetadata(pkim, param_index, + &kim_DataType, &extent, + &str_name, &str_desc); + if (kim_error) + error->all(FLERR, "KIM GetParameterMetadata returned error."); + + if (strcmp(paramname, str_name) == 0) + break; + } + + if (param_index >= numberOfParameters) { + std::string msg("Wrong argument in kim_param get command.\n"); + msg += "This Model does not have the requested '"; + msg += paramname; + msg += "' parameter."; + error->all(FLERR, msg.c_str()); + } + + // Get the index_range for the requested parameter + int nlbound(0); + int nubound(0); + + if (i < narg) { + std::string argtostr(arg[i++]); + + // Check to see if the indices range contains + // only integer numbers and/or range : + if (argtostr.find_first_not_of("0123456789:") != std::string::npos) { + std::string msg("Illegal index_range.\n"); + msg += "Expected integer parameter(s) instead of '"; + msg += argtostr; + msg += "' in index_range."; + error->all(FLERR, msg.c_str()); + } + + std::string::size_type npos = argtostr.find(':'); + if (npos != std::string::npos) { + argtostr[npos] = ' '; + std::stringstream str(argtostr); + str >> nlbound >> nubound; + if (nubound < 1 || nubound > extent || + nlbound < 1 || nlbound > nubound) { + std::string msg("Illegal index_range '"); + msg += SNUM(nlbound) + "-" + SNUM(nubound); + msg += "' for '"; + msg += paramname; + msg += "' parameter with extent of '"; + msg += SNUM(extent); + msg += "' ."; + error->all(FLERR, msg.c_str()); + } + } else { + std::stringstream str(argtostr); + str >> nlbound; + if (nlbound < 1 || nlbound > extent) { + std::string msg("Illegal index '"); + msg += SNUM(nlbound) + "' for parameter '"; + msg += paramname; + msg += "' with the extent of '"; + msg += SNUM(extent); + msg += "' ."; + error->all(FLERR, msg.c_str()); + } + nubound = nlbound; + } + } else { + std::string msg("Wrong number of arguments in "); + msg += "kim_param get command.\n"; + msg += "Index range after parameter name is mandatory."; + error->all(FLERR, msg.c_str()); + } + + int const nvars = nubound - nlbound + 1; + char **varsname = NULL; + + if (i < narg) { + // Get the variable/variable_base name + varname = arg[i++]; + } else { + std::string msg("Wrong number of arguments in "); + msg += "kim_param get command.\n"; + msg += "The LAMMPS variable name is mandatory."; + error->all(FLERR, msg.c_str()); + } + + // indicator flag for list request + bool list_requested(false); + + if (nvars > 1) { + if (i < narg) { + if (strcmp(arg[i], "split") == 0) { + varsname = new char *[nvars]; + for (int j = 0, k = nlbound; j < nvars; ++j, ++k) { + std::stringstream str; + str << varname << "_" << k; + varsname[j] = const_cast(str.str().c_str()); + } + } else if (strcmp(arg[i], "list") == 0) { + list_requested = true; + varsname = new char *[1]; + varsname[0] = varname; + // Default explicit (optional) formatarg + } else if (i - 1 + nvars < narg) { + varsname = new char *[nvars]; + --i; + for (int j = 0; j < nvars; ++j, ++i) + varsname[j] = arg[i]; + if (i < narg) { + if (strcmp(arg[i], "explicit") == 0) + ++i; + } + } else { + std::string msg("Wrong number of arguments in "); + msg += "kim_param get command.\n"; + msg += "The LAMMPS '"; + msg += SNUM(nvars); + msg += "' variable names or '"; + msg += varname; + msg += " split' is mandatory."; + error->all(FLERR, msg.c_str()); + } + } else { + std::string msg("Wrong number of arguments in "); + msg += "kim_param get command.\n"; + msg += "The LAMMPS '"; + msg += SNUM(nvars); + msg += "' variable names or '"; + msg += varname; + msg += " split/list' is mandatory."; + error->all(FLERR, msg.c_str()); + } + } else { + varsname = new char *[1]; + if (i < narg) + { + if (strcmp(arg[i], "split") == 0) + { + std::stringstream str; + str << varname << "_" << nlbound; + varsname[0] = const_cast(str.str().c_str()); + ++i; + } else { + if ((strcmp(arg[i], "list") == 0) || + (strcmp(arg[i], "explicit") == 0)) + ++i; + varsname[0] = varname; + } + } else { + varsname[0] = varname; + } + } + + char **varcmd = new char *[3]; + varcmd[1] = const_cast("string"); + + if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Double)) { + if (list_requested) { + std::stringstream str; + double V; + { + kim_error = KIM_Model_GetParameterDouble(pkim, param_index, + nlbound - 1, &V); + if (kim_error) + error->all(FLERR, "KIM GetParameterDouble returned error."); + str << V; + } + for (int j = 1; j < nvars; ++j) { + kim_error = KIM_Model_GetParameterDouble(pkim, param_index, + nlbound - 1 + j, &V); + if (kim_error) + error->all(FLERR, "KIM GetParameterDouble returned error."); + str << " " << V; + } + varcmd[0] = varsname[0]; + varcmd[2] = const_cast(str.str().c_str()); + input->variable->set(3, varcmd); + echo_var_assign(varcmd[0], varcmd[2]); + } else { + for (int j = 0; j < nvars; ++j) { + varcmd[0] = varsname[j]; + double V; + kim_error = KIM_Model_GetParameterDouble(pkim, param_index, + nlbound - 1 + j, &V); + if (kim_error) + error->all(FLERR, "KIM GetParameterDouble returned error."); + std::stringstream str; + str << V; + varcmd[2] = const_cast(str.str().c_str()); + input->variable->set(3, varcmd); + echo_var_assign(varcmd[0], varcmd[2]); + } + } + } else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) { + if (list_requested) { + std::stringstream str; + int V; + { + kim_error = KIM_Model_GetParameterInteger(pkim, param_index, + nlbound - 1, &V); + if (kim_error) + error->all(FLERR, "KIM GetParameterInteger returned error."); + str << V; + } + for (int j = 1; j < nvars; ++j) { + kim_error = KIM_Model_GetParameterInteger(pkim, param_index, + nlbound - 1 + j, &V); + if (kim_error) + error->all(FLERR, "KIM GetParameterInteger returned error."); + str << " " << V; + } + varcmd[0] = varsname[0]; + varcmd[2] = const_cast(str.str().c_str()); + input->variable->set(3, varcmd); + echo_var_assign(varcmd[0], varcmd[2]); + } else { + for (int j = 0; j < nvars; ++j) { + varcmd[0] = varsname[j]; + int V; + kim_error = KIM_Model_GetParameterInteger(pkim, param_index, + nlbound - 1 + j, &V); + if (kim_error) + error->all(FLERR, "KIM GetParameterInteger returned error."); + std::stringstream str; + str << V; + varcmd[2] = const_cast(str.str().c_str()); + input->variable->set(3, varcmd); + echo_var_assign(varcmd[0], varcmd[2]); + } + } + } else + error->all(FLERR, "Wrong parameter type."); + + delete[] varcmd; + delete[] varsname; + } // End of loop over all the arguments + // Set the parameters + } else { + std::string set_cmd("pair_coeff * * "); + set_cmd += atom_type_list; + for (int i = 1; i < narg; ++i) { + set_cmd += " "; + set_cmd += arg[i]; + } + input->one(set_cmd.c_str()); + } + } else + error->all(FLERR, "This model has No mutable parameters."); + + if (!isPairStyleAssigned) + KIM_Model_Destroy(&pkim); + + kim_param_log_delimiter("end"); +} + +/* ---------------------------------------------------------------------- */ + +void KimParam::kim_param_log_delimiter(std::string const &begin_end) const +{ + if (comm->me == 0) { + std::string msg; + if (begin_end == "begin") { + msg = "#=== BEGIN kim-param "; + msg += kim_param_get ? "get " : "set "; + msg += "=====================================\n"; + } else if (begin_end == "end") { + msg = "#=== END kim-param "; + msg += kim_param_get ? "get " : "set "; + msg += "=======================================\n\n"; + } + input->write_echo(msg.c_str()); + } +} + +/* ---------------------------------------------------------------------- */ + +void KimParam::echo_var_assign(std::string const &name, + std::string const &value) const +{ + if (comm->me == 0) { + std::string msg; + msg += "variable " + name + " string " + value + "\n"; + input->write_echo(msg.c_str()); + } +} + +#undef SNUM diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h new file mode 100644 index 0000000000..5a9298628d --- /dev/null +++ b/src/KIM/kim_param.h @@ -0,0 +1,100 @@ +/* -*- 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Yaser Afshar (UMN), + Ryan S. Elliott (UMN), + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(kim_param, KimParam) + +#else + +#ifndef LMP_KIM_PARAM_H +#define LMP_KIM_PARAM_H + +#include "pointers.h" +#include + +namespace LAMMPS_NS +{ + +class KimParam : protected Pointers +{ +public: + KimParam(class LAMMPS *lmp); + + ~KimParam(); + + void command(int, char **); + +private: + void kim_param_log_delimiter(std::string const &begin_end) const; + + void echo_var_assign(std::string const &name, std::string const &value) + const; + +private: + bool kim_param_get; + bool kim_param_set; +}; + +} // namespace LAMMPS_NS + +#endif // LMP_KIM_PARAM_H +#endif // COMMAND_CLASS + +/* ERROR/WARNING messages: + +*/ -- GitLab From 5ce8860dce20c05785e47a3a9c12fa63320deac7 Mon Sep 17 00:00:00 2001 From: Yaser Afshar Date: Thu, 24 Oct 2019 08:58:11 -0500 Subject: [PATCH 04/16] Updating the 'kim_query' default behavior and adding the 'list' setting Adding the 'list' setting of {formatarg} (default behavior or if {formatarg} is not specified), the result is returned as a space-separated list of values in {variable}. --- src/KIM/kim_query.cpp | 38 ++++++++++++++++++++++++++++---------- 1 file changed, 28 insertions(+), 10 deletions(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 8ceefeceaf..38ae57c25a 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -13,7 +13,8 @@ /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), - Ryan S. Elliott (UMN) + Ryan S. Elliott (UMN), + Yaser Afshar (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -105,15 +106,25 @@ void KimQuery::command(int narg, char **arg) model_name = (char *)fix_store->getptr("model_name"); } else error->all(FLERR,"Must use 'kim_init' before 'kim_query'"); - varname = arg[0]; bool split = false; if (0 == strcmp("split",arg[1])) { if (narg == 2) error->all(FLERR,"Illegal kim_query command"); + if (0 == strcmp("list",arg[2])) + error->all(FLERR,"Illegal kim_query command"); split = true; arg++; narg--; } + + // The “list” is the default setting + // the result is returned as a space-separated list of values in variable + if (0 == strcmp("list",arg[1])) { + if (narg == 2) error->all(FLERR,"Illegal kim_query command"); + if (split) error->all(FLERR,"Illegal kim_query command"); + arg++; + narg--; + } function = arg[1]; for (int i = 2; i < narg; ++i) { @@ -143,12 +154,13 @@ void KimQuery::command(int narg, char **arg) kim_query_log_delimiter("begin"); char **varcmd = new char*[3]; + varcmd[1] = (char *) "string"; + + std::stringstream ss(value); + std::string token; + if (split) { int counter = 1; - std::stringstream ss(value); - std::string token; - varcmd[1] = (char *) "string"; - while(std::getline(ss, token, ',')) { token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim @@ -161,11 +173,17 @@ void KimQuery::command(int narg, char **arg) } } else { varcmd[0] = varname; - varcmd[1] = (char *) "string"; - varcmd[2] = value; + std::string value_string; + while(std::getline(ss, token, ',')) { + token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim + token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim + if (value_string.size() && token.size()) + value_string += " "; + value_string += token; + } + varcmd[2] = const_cast(value_string.c_str());; input->variable->set(3,varcmd); - - echo_var_assign(varname, value); + echo_var_assign(varname, value_string); } kim_query_log_delimiter("end"); -- GitLab From 63cce391caac0109fca496b96aa3901958bc05dd Mon Sep 17 00:00:00 2001 From: Yaser Afshar Date: Thu, 24 Oct 2019 09:01:00 -0500 Subject: [PATCH 05/16] Adding the documentation for the new 'kim_param' command New documnetation is added and the whole document is checked and partly rewritten for clarity and errors are corrected Adding the word "Zm" to prevent the spelling error in document building check. --- doc/src/kim_commands.txt | 318 ++++++++++++++++++-- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 289 insertions(+), 30 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 47beb776a1..e50950eae7 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -9,21 +9,37 @@ kim_init command :h3 kim_interactions command :h3 kim_query command :h3 +kim_param command :h3 [Syntax:] kim_init model user_units unitarg kim_interactions typeargs -kim_query variable formatarg query_function queryargs :pre +kim_query variable formatarg query_function queryargs +kim_param get param_name index_range variables formatarg +kim_param set param_name index_range values +:pre -model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) -user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script -unitarg = {unit_conversion_mode} (optional) -typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping -variable = name of a (string style) variable where the result of the query is stored -formatarg = {split} (optional) -query_function = name of the OpenKIM web API query function to be used -queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul +:link(formatarg_options) +model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) :ulb,l +user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script :l +unitarg = {unit_conversion_mode} (optional) :l +typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping :l +variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command. :l +formatarg = {list, split, or explicit} (optional): :l +{list} = returns a single string with a list of space separated values + (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as + defined by the {variable} argument. \[default for {kim_query}\] +{split} = returns the values separately in new variables with names based + on the prefix specified in {variable} and a number appended to + indicate which element in the list of values is in the variable. +{explicit} = returns the values separately in one more more variable names + provided as arguments that preceed {formatarg}. \[default for {kim_param}\] :pre +query_function = name of the OpenKIM web API query function to be used :l +queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :l +param_name = name of a KIM portable model parameter :l +index_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements) :l +values = new value(s) to replace the current value(s) of a KIM portable model parameter :l,ule [Examples:] @@ -33,9 +49,12 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O -Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real +kim_init Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolventsPolymers__SM_039297821658_000 real kim_interactions fixed_types -kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] +kim_param get gamma 1 varGamma +kim_param set gamma 1 3.0 +:pre [Description:] @@ -75,6 +94,7 @@ Types of IMs in OpenKIM :h4 There are two types of IMs archived in OpenKIM: +:link(PM_type) The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/). The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol @@ -106,7 +126,7 @@ The URL for the Model Page is constructed from the https://openkim.org/id/extended_KIM_ID :pre -For example for the Stillinger-Weber potential +For example, for the Stillinger--Weber potential listed above the Model Page is located at: "https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 @@ -196,7 +216,8 @@ print "Cohesive Energy = $\{EcJ\} eV" The above script will end with an error in the {kim_init} line if the IM is changed to another potential for Al that does not work with {metal} -units. To address this {kim_init} offers the {unit_conversion_mode}. +units. To address this {kim_init} offers the {unit_conversion_mode} +as shown below. If unit conversion mode {is} active, then {kim_init} calls the LAMMPS "units"_units.html command to set the units to the IM's required or preferred units. Conversion factors between the IM's units and the {user_units} @@ -250,7 +271,7 @@ will work correctly for any IM for Al (KIM PM or SM) selected by the {kim_init} command. Care must be taken to apply unit conversion to dimensional variables read in -from a file. For example if a configuration of atoms is read in from a +from a file. For example, if a configuration of atoms is read in from a dump file using the "read_dump"_read_dump.html command, the following can be done to convert the box and all atomic positions to the correct units: @@ -349,14 +370,34 @@ not appear in the input script. Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5 The {kim_query} command performs a web query to retrieve the predictions -of the IM set by {kim_init} for material properties archived in -"OpenKIM"_https://openkim.org. The {kim_query} command must be preceded -by a {kim_init} command. The result of the query is stored in a -"string style variable"_variable.html, the name of which is given as the first -argument of the {kim_query command}. (For the case of multiple -return values, the optional {split} keyword can be used after the -variable name to separate the results into multiple variables; see -the "example"_#split_example below.) +of an IM set by {kim_init} for material properties archived in +"OpenKIM"_https://openkim.org. + +NOTE: The {kim_query} command must be preceded by a {kim_init} command. + +The syntax for the {kim_query} command is as follows: + +kim_query variable formatarg query_function queryargs +:pre + +The result of the query is stored in one or more +"string style variables"_variable.html as determined by the +optional {formatarg} argument "documented above"_#formatarg_options. +For the "list" setting of {formatarg} (or if {formatarg} is not +specified), the result is returned as a space-separated list of +values in {variable}. +The {formatarg} keyword "split" separates the result values into +individual variables of the form {prefix_I}, where {prefix} is set to the +{kim_query} {variable} argument and {I} ranges from 1 to the number of +returned values. The number and order of the returned values is determined +by the type of query performed. (Note that the "explicit" setting of +{formatarg} is not supported by {kim_query}.) + +NOTE: {kim_query} only supports queries that return a single result or +an array of values. More complex queries that return a JSON structure +are not currently supported. An attempt to use {kim_query} in such +cases will generate an error. + The second required argument {query_function} is the name of the query function to be called (e.g. {get_lattice_constant_cubic}). All following "arguments"_Commands_parse.html are parameters handed over to @@ -380,7 +421,7 @@ be provided to select the method of choice. See the "query documentation"_https://openkim.org/doc/repository/kim-query to see which methods are available for a given {query function}. -{kim_query} Usage Examples and Further Clarifications: :h6 +{kim_query} Usage Examples and Further Clarifications :h5 The data obtained by {kim_query} commands can be used as part of the setup or analysis phases of LAMMPS simulations. Some examples are given below. @@ -406,7 +447,6 @@ Note that in {unit_conversion_mode} the results obtained from a For example, in the above script, the lattice command would need to be changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". -:link(split_example) [Define an equilibrium hcp crystal] kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal @@ -421,12 +461,11 @@ lattice custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c In this case the {kim_query} returns two arguments (since the hexagonal close packed (hcp) structure has two independent lattice constants). -The default behavior of {kim_query} returns the result as a string -with the values separated by commas. The optional keyword {split} -separates the result values into individual variables of the form -{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument -and {I} ranges from 1 to the number of returned values. The number and order of -the returned values is determined by the type of query performed. +The {formatarg} keyword "split" places the two values into +the variables {latconst_1} and {latconst_2}. (These variables are +created if they do not already exist.) For convenience the variables +{a0} and {c0} are created in order to make the remainder of the +input script more readable. [Define a crystal at finite temperature accounting for thermal expansion] @@ -477,6 +516,225 @@ In order to give credit to Test developers, the number of times results from these programs are queried is tracked. No other information about the nature of the query or its source is recorded. +Accessing KIM Model Parameters from LAMMPS ({kim_param}) :h5 + +All IMs are functional forms containing a set of +parameters. The values of these parameters are typically +selected to best reproduce a training set of quantum mechanical +calculations or available experimental data. For example, a +Lennard-Jones potential intended to model argon might have the values of +its two parameters, epsilon and sigma, fit to the +dimer dissociation energy or thermodynamic properties at a critical point +of the phase diagram. + +Normally a user employing an IM should not modify its parameters since, +as noted above, these are selected to reproduce material properties. +However, there are cases where accessing and modifying IM parameters +is desired, such as for assessing uncertainty, fitting an IM, +or working with an ensemble of IMs. As explained "above"_#IM_types, +IMs archived in OpenKIM are either Portable Models (PMs) or +Simulator Models (SMs). KIM PMs are complete independent implementations +of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS. +Two different mechanisms are provided for accessing IM parameters in these +two cases: + +For a KIM PM, the {kim_param} command can be used to {get} and {set} the values of the PM's parameters as explained below. +For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible). :ul + +The {kim_param get} and {kim_param set} commands provide an interface +to access and change the parameters of a KIM PM that "publishes" its +parameters and makes them publicly available (see the +"KIM API documentation"_https://kim-api.readthedocs.io/en/devel/features.html +for details). + +NOTE: The {kim_param get/set} commands must be preceded by {kim_init}. +The {kim_param set} command must additionally be preceded by a +{kim_interactions} command (or alternatively by a {pair_style kim} +and {pair_coeff} commands). The {kim_param set} command may be used wherever a {pair_coeff} command may occur. + +The syntax for the {kim_param} command is as follows: + +kim_param get param_name index_range variable formatarg +kim_param set param_name index_range values +:pre + +Here, {param_name} is the name of a KIM PM parameter (which is published +by the PM and available for access). The specific string used to identify +a parameter is defined by the PM. For example, for the +"Stillinger--Weber (SW) potential in OpenKIM"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005, +the parameter names are {A, B, p, q, sigma, gamma, cutoff, lambda, costheta0}. + +NOTE: The list of all the parameters that a PM exposes for access/mutation are +automatically written to the lammps log file when {kim_init} is called. + +Each published parameter of a KIM PM takes the form of an array of +numerical values. The array can contain one element for a single-valued +parameter, or a set of values. For example, the +"multispecies SW potential for the Zn-Cd-Hg-S-Se-Te system"_https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 +has the same parameter names as the +"single-species SW potential"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005, +but each parameter array contains 21 entries that correspond to the parameter +values used for each pairwise combination of the model's six supported species +(this model does not have parameters specific to individual ternary +combinations of its supported species). + +The {index_range} argument may either be an integer referring to +a specific element within the array associated with the parameter +specified by {param_name}, or a pair of integers separated by a colon +that refer to a slice of this array. In both cases, one-based indexing is +used to refer to the entries of the array. + +The result of a {get} operation for a specific {index_range} is stored in +one or more "LAMMPS string style variables"_variable.html as determined +by the optional {formatarg} argument "documented above."_#formatarg_options +If not specified, the default for {formatarg} is "explicit" for the +{kim_param} command. + +For the case where the result is an array with multiple values +(i.e. {index_range} contains a range), the optional "split" or "explicit" +{formatarg} keywords can be used to separate the results into multiple +variables; see the examples below. +Multiple parameters can be retrieved with a single call to {kim_param get} +by repeating the argument list following {get}. + +For a {set} operation, the {values} argument contains the new value(s) +for the element(s) of the parameter specified by {index_range}. For the case +where multiple values are being set, {values} contains a set of values +separated by spaces. Multiple parameters can be set with a single call to +{kim_param set} by repeating the argument list following {set}. + +{kim_param} Usage Examples and Further Clarifications :h5 + +Examples of getting and setting KIM PM parameters with further +clarifications are provided below. + +[Getting a scalar parameter] + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal +... +kim_param get A 1 VARA +:pre + +In this case, the value of the SW {A} parameter is retrieved and placed +in the LAMMPS variable {VARA}. The variable {VARA} can be used +in the remainder of the input script in the same manner as any other +LAMMPS variable. + +[Getting multiple scalar parameters with a single call] + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal +... +kim_param get A 1 VARA B 1 VARB +:pre + +This retrieves the {A} and {B} parameters of the SW potential and stores +them in the LAMMPS variables {VARA} and {VARB}. + +[Getting a range of values from a parameter] + +There are several options when getting a range of values from a parameter +determined by the {formatarg} argument. + +kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal +... +kim_param get lambda 7:9 LAM_TeTe LAM_TeZn LAM_TeSe +:pre + +In this case, {formatarg} is not specified and therefore the default +"explicit" mode is used. (The behavior would be the same if the word +{explicit} were added after {LAM_TeSe}.) Elements 7, 8 and 9 of parameter +lambda retrieved by the {get} operation are placed in the LAMMPS variables +{LAM_TeTe}, {LAM_TeZn} and {LAM_TeSe}, respectively. + +NOTE: In the above example, elements 7--9 of the lambda parameter correspond +to Te-Te, Te-Zm and Te-Se interactions. This can be determined by visiting +the "model page for the specified potential"_https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 +and looking at its parameter file linked to at the bottom of the page +(file with .param ending) and consulting the README documentation +provided with the driver for the PM being used. A link to the driver +is provided at the top of the model page. + +kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal +... +kim_param get lambda 15:17 LAMS list +variable LAM_VALUE index $\{LAMS\} +label loop_on_lambda +... +... do something with current value of lambda +... +next LAM_VALUE +jump SELF loop_on_lambda +:pre + +In this case, the "list" mode of {formatarg} is used. +The result of the {get} operation is stored in the LAMMPS variable +{LAMS} as a string containing the three retrieved values separated +by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an +{index} variable to access the values one at a time within a loop +as shown in the example. At each iteration of the loop {LAM_VALUE} +contains the current value of lambda. + +kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal +... +kim_param get lambda 15:17 LAM split +:pre + +In this case, the "split" mode of {formatarg} is used. +The three values retrieved by the {get} operation are stored in +the three LAMMPS variables {LAM_15}, {LAM_16} and {LAM_17}. +The provided name "LAM" is used as prefix and the location in +the lambda array is appended to create the variable names. + +[Setting a scalar parameter] + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal +... +kim_interactions Si +kim_param set gamma 1 2.6 +:pre + +Here, the SW potential's gamma parameter is set to 2.6. Note that the {get} +and {set} commands work together, so that a {get} following a {set} +operation will return the new value that was set. For example: + +... +kim_interactions Si +kim_param get gamma 1 ORIG_GAMMA +kim_param set gamma 1 2.6 +kim_param get gamma 1 NEW_GAMMA +... +print "original gamma = $\{ORIG_GAMMA\}, new gamma = $\{NEW_GAMMA\}" +:pre + +Here, {ORIG_GAMMA} will contain the original gamma value for the SW +potential, while {NEW_GAMMA} will contain the value 2.6. + +[Setting multiple scalar parameters with a single call] + +kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal +... +kim_interactions Cd Te +variable VARG equal 2.6 +variable VARS equal 2.0951 +kim_param set gamma 1 $\{VARG\} sigma 3 $\{VARS\} +:pre + +In this case, the first element of the {gamma} parameter and +third element of the {sigma} parameter are set to 2.6 and 2.0951, +respectively. This example also shows how LAMMPS variables can +be used when setting parameters. + +[Setting a range of values of a parameter] + +kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal +... +kim_interactions Cd Te Zn Se Hg S +kim_param set sigma 2:6 2.35214 2.23869 2.04516 2.43269 1.80415 +:pre + +In this case, elements 2 through 6 of the parameter {sigma} +are set to the values 2.35214, 2.23869, 2.04516, 2.43269 and 1.80415 in +order. Citation of OpenKIM IMs :h4 diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index f145227f7a..1a3e947b22 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3150,3 +3150,4 @@ zx zy Zybin zz +Zm -- GitLab From 9e7ca428aade7fdfad8254c63833a390e2f983a7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 3 Nov 2019 10:57:18 -0500 Subject: [PATCH 06/16] whitespace cleanup: remove (evil) tabs --- src/BODY/body_rounded_polygon.cpp | 8 +- src/BODY/body_rounded_polyhedron.cpp | 4 +- src/CLASS2/pair_lj_class2.cpp | 20 +- src/CLASS2/pair_lj_class2_coul_long.cpp | 36 +-- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 144 ++++++------ src/KOKKOS/fix_enforce2d_kokkos.cpp | 4 +- src/KOKKOS/fix_neigh_history_kokkos.cpp | 44 ++-- src/KOKKOS/npair_kokkos.cpp | 216 +++++++++--------- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 148 ++++++------ src/KOKKOS/verlet_kokkos.cpp | 4 +- src/KSPACE/ewald_disp.cpp | 2 +- src/KSPACE/pppm_disp.cpp | 4 +- src/SPIN/atom_vec_spin.h | 12 +- src/SPIN/fix_langevin_spin.h | 16 +- src/SPIN/fix_neb_spin.h | 28 +-- src/SPIN/fix_nve_spin.cpp | 8 +- src/SPIN/fix_nve_spin.h | 36 +-- src/SPIN/fix_precession_spin.cpp | 8 +- src/SPIN/fix_precession_spin.h | 14 +- src/SPIN/min_spin.cpp | 6 +- src/SPIN/min_spin_cg.cpp | 12 +- src/SPIN/min_spin_cg.h | 30 +-- src/SPIN/min_spin_lbfgs.cpp | 8 +- src/SPIN/min_spin_lbfgs.h | 32 +-- src/SPIN/neb_spin.cpp | 112 ++++----- src/SPIN/pair_spin.h | 4 +- src/SPIN/pair_spin_dipole_cut.cpp | 42 ++-- src/SPIN/pair_spin_dipole_cut.h | 14 +- src/SPIN/pair_spin_dipole_long.h | 14 +- src/SPIN/pair_spin_dmi.h | 10 +- src/SPIN/pair_spin_exchange.h | 8 +- src/SPIN/pair_spin_magelec.h | 8 +- src/SPIN/pair_spin_neel.h | 12 +- src/USER-MISC/compute_hma.cpp | 2 +- src/USER-MISC/fix_bond_react.cpp | 12 +- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 14 +- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 28 +-- src/USER-MISC/pair_lj_expand_coul_long.cpp | 4 +- src/USER-MISC/pair_local_density.cpp | 88 +++---- src/USER-MISC/pair_local_density.h | 12 +- src/USER-OMP/reaxc_init_md_omp.cpp | 4 +- src/USER-REAXC/reaxc_ffield.cpp | 2 +- src/force.cpp | 6 +- src/min.h | 8 +- src/min_cg.cpp | 8 +- src/min_fire.cpp | 6 +- src/min_sd.cpp | 6 +- 47 files changed, 634 insertions(+), 634 deletions(-) diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index d60372781a..d855c5aea7 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -116,7 +116,7 @@ double BodyRoundedPolygon::enclosing_radius(struct AtomVecBody::Bonus *bonus) { int nvertices = bonus->ivalue[0]; if (nvertices == 1 || nvertices == 2) - return *(bonus->dvalue+3*nsub(bonus)+2); + return *(bonus->dvalue+3*nsub(bonus)+2); return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)); } @@ -126,7 +126,7 @@ double BodyRoundedPolygon::rounded_radius(struct AtomVecBody::Bonus *bonus) { int nvertices = bonus->ivalue[0]; if (nvertices == 1 || nvertices == 2) - return *(bonus->dvalue+3*nsub(bonus)+2+1); + return *(bonus->dvalue+3*nsub(bonus)+2+1); return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)+1); } @@ -156,7 +156,7 @@ int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus, ------------------------------------------------------------------------- */ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, - int *ifile, double *dfile) + int *ifile, double *dfile) { AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; @@ -327,7 +327,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, ------------------------------------------------------------------------- */ double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble, - int *ifile, double *dfile) + int *ifile, double *dfile) { int nsub = ifile[0]; if (nsub < 1) diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 49ec6f1d78..a82404ab15 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -134,7 +134,7 @@ double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus) { int nvertices = bonus->ivalue[0]; if (nvertices == 1 || nvertices == 2) - return *(bonus->dvalue+3*nsub(bonus)+2); + return *(bonus->dvalue+3*nsub(bonus)+2); return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + MAX_FACE_SIZE*nfaces(bonus)); } @@ -385,7 +385,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, ------------------------------------------------------------------------- */ double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble, - int *ifile, double *dfile) + int *ifile, double *dfile) { int nsub = ifile[0]; int ned = ifile[1]; diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 641ca67226..c930173864 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -188,8 +188,8 @@ void PairLJClass2::compute_inner() if (rsq < cut_out_off_sq) { r2inv = 1.0/rsq; - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; jtype = type[j]; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); @@ -268,8 +268,8 @@ void PairLJClass2::compute_middle() if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) { r2inv = 1.0/rsq; - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; jtype = type[j]; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); @@ -352,8 +352,8 @@ void PairLJClass2::compute_outer(int eflag, int vflag) if (rsq < cutsq[itype][jtype]) { if (rsq > cut_in_off_sq) { r2inv = 1.0/rsq; - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; @@ -374,8 +374,8 @@ void PairLJClass2::compute_outer(int eflag, int vflag) if (eflag) { r2inv = 1.0/rsq; - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) - offset[itype][jtype]; @@ -385,8 +385,8 @@ void PairLJClass2::compute_outer(int eflag, int vflag) if (vflag) { if (rsq <= cut_in_off_sq) { r2inv = 1.0/rsq; - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 5487878f27..c2b127fa58 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -262,8 +262,8 @@ void PairLJClass2CoulLong::compute_inner() jtype = type[j]; if (rsq < cut_ljsq[itype][jtype]) { - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); } else forcelj = 0.0; @@ -354,8 +354,8 @@ void PairLJClass2CoulLong::compute_middle() jtype = type[j]; if (rsq < cut_ljsq[itype][jtype]) { - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); } else forcelj = 0.0; @@ -487,9 +487,9 @@ void PairLJClass2CoulLong::compute_outer(int eflag, int vflag) } else forcecoul = 0.0; if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) { - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; - r6inv = r3inv*r3inv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; + r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); if (rsq < cut_in_on_sq) { rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; @@ -525,9 +525,9 @@ void PairLJClass2CoulLong::compute_outer(int eflag, int vflag) } else ecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; - r6inv = r3inv*r3inv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; + r6inv = r3inv*r3inv; evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) - offset[itype][jtype]; evdwl *= factor_lj; @@ -552,13 +552,13 @@ void PairLJClass2CoulLong::compute_outer(int eflag, int vflag) if (rsq <= cut_in_off_sq) { rinv = sqrt(r2inv); - r3inv = r2inv*rinv; - r6inv = r3inv*r3inv; + r3inv = r2inv*rinv; + r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); } else if (rsq <= cut_in_on_sq) { - rinv = sqrt(r2inv); - r3inv = r2inv*rinv; - r6inv = r3inv*r3inv; + rinv = sqrt(r2inv); + r3inv = r2inv*rinv; + r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); } fpair = (forcecoul + factor_lj*forcelj) * r2inv; @@ -672,14 +672,14 @@ void PairLJClass2CoulLong::init_style() if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } irequest = neighbor->request(this,instance_me); if (respa >= 1) { neighbor->requests[irequest]->respaouter = 1; - neighbor->requests[irequest]->respainner = 1; + neighbor->requests[irequest]->respainner = 1; } if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; @@ -690,7 +690,7 @@ void PairLJClass2CoulLong::init_style() if (strstr(update->integrate_style,"respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; - else cut_respa = NULL; + else cut_respa = NULL; // insure use of KSpace long-range solver, set g_ewald diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 7e217df2a6..67aaa32c21 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -247,13 +247,13 @@ struct AtomVecSphereKokkos_PackComm { _buf(i,2) = _x(j,2); } else { if (TRICLINIC == 0) { - _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; - _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; - _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; } else { - _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; - _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; - _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; } } _buf(i,3) = _radius(j); @@ -419,13 +419,13 @@ struct AtomVecSphereKokkos_PackCommVel { _buf(i,2) = _x(j,2); } else { if (TRICLINIC == 0) { - _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; - _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; - _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; } else { - _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; - _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; - _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; } } if (DEFORM_VREMAP == 0) { @@ -772,13 +772,13 @@ struct AtomVecSphereKokkos_PackCommSelf { _xw(i+_nfirst,2) = _x(j,2); } else { if (TRICLINIC == 0) { - _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd; - _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd; - _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd; + _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd; + _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd; + _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd; } else { - _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; - _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; - _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd; + _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd; } } _radius(i+_nfirst) = _radius(j); @@ -799,39 +799,39 @@ int AtomVecSphereKokkos::pack_comm_self( atomKK->modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK); if(pbc_flag) { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } } else { @@ -839,39 +839,39 @@ int AtomVecSphereKokkos::pack_comm_self( atomKK->modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK); if(pbc_flag) { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackCommSelf f( + struct AtomVecSphereKokkos_PackCommSelf f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - nfirst,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } } @@ -1037,7 +1037,7 @@ void AtomVecSphereKokkos::unpack_comm_vel_kokkos( /* ---------------------------------------------------------------------- */ int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int pbc_flag, int *pbc) { int i,j,m; double dx,dy,dz; @@ -1109,7 +1109,7 @@ int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ int AtomVecSphereKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int pbc_flag, int *pbc) { int i,j,m; double dx,dy,dz,dvx,dvy,dvz; @@ -1926,7 +1926,7 @@ struct AtomVecSphereKokkos_UnpackBorder { /* ---------------------------------------------------------------------- */ void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first, - const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { + const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { while (first+n >= nmax) grow(0); if(space==Host) { struct AtomVecSphereKokkos_UnpackBorder f(buf.view(), @@ -1943,7 +1943,7 @@ void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first, } atomKK->modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| - RADIUS_MASK|RMASS_MASK); + RADIUS_MASK|RMASS_MASK); } /* ---------------------------------------------------------------------- */ @@ -2053,7 +2053,7 @@ void AtomVecSphereKokkos::unpack_border_vel_kokkos( } atomKK->modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| - RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); } /* ---------------------------------------------------------------------- */ @@ -2496,7 +2496,7 @@ int AtomVecSphereKokkos::unpack_restart(double *buf) atomKK->modified(Host,X_MASK | TAG_MASK | TYPE_MASK | MASK_MASK | IMAGE_MASK | V_MASK | - RADIUS_MASK | RMASS_MASK | OMEGA_MASK); + RADIUS_MASK | RMASS_MASK | OMEGA_MASK); atom->nlocal++; return m; diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp index bf2a882539..205451d96f 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.cpp +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -34,10 +34,10 @@ FixEnforce2DKokkos::FixEnforce2DKokkos(LAMMPS *lmp, int narg, char * execution_space = ExecutionSpaceFromDevice::space; datamask_read = V_MASK | F_MASK | OMEGA_MASK | MASK_MASK - | TORQUE_MASK | ANGMOM_MASK; + | TORQUE_MASK | ANGMOM_MASK; datamask_modify = V_MASK | F_MASK | OMEGA_MASK - | TORQUE_MASK | ANGMOM_MASK; + | TORQUE_MASK | ANGMOM_MASK; } diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index 8cfe7111dd..7906d37cc3 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -122,21 +122,21 @@ void FixNeighHistoryKokkos::pre_exchange_item(const int &ii) const j &= NEIGHMASK; int m = Kokkos::atomic_fetch_add(&d_npartner[i],1); if (m < maxpartner) { - d_partner(i,m) = tag[j]; - for (int k = 0; k < dnum; k++) - d_valuepartner(i,dnum*m+k) = d_firstvalue(i,dnum*jj+k); + d_partner(i,m) = tag[j]; + for (int k = 0; k < dnum; k++) + d_valuepartner(i,dnum*m+k) = d_firstvalue(i,dnum*jj+k); } else { - d_resize() = 1; + d_resize() = 1; } if (j < nlocal_neigh) { - m = Kokkos::atomic_fetch_add(&d_npartner[j],1); - if (m < maxpartner) { - d_partner(j,m) = tag[i]; - for (int k = 0; k < dnum; k++) - d_valuepartner(j,dnum*m+k) = d_firstvalue(i,dnum*jj+k); - } else { - d_resize() = 1; - } + m = Kokkos::atomic_fetch_add(&d_npartner[j],1); + if (m < maxpartner) { + d_partner(j,m) = tag[i]; + for (int k = 0; k < dnum; k++) + d_valuepartner(j,dnum*m+k) = d_firstvalue(i,dnum*jj+k); + } else { + d_resize() = 1; + } } } } @@ -205,22 +205,22 @@ void FixNeighHistoryKokkos::post_neighbor_item(const int &ii) const if (rflag) { int jtag = tag(j); for (m = 0; m < np; m++) - if (d_partner(i, m) == jtag) break; + if (d_partner(i, m) == jtag) break; if (m < np) { - d_firstflag(i,jj) = 1; - for (int k = 0; k < dnum; k++) { - d_firstvalue(i, dnum*jj+k) = d_valuepartner(i, dnum*m+k); - } + d_firstflag(i,jj) = 1; + for (int k = 0; k < dnum; k++) { + d_firstvalue(i, dnum*jj+k) = d_valuepartner(i, dnum*m+k); + } } else { - d_firstflag(i,jj) = 0; - for (int k = 0; k < dnum; k++) { - d_firstvalue(i, dnum*jj+k) = 0; - } + d_firstflag(i,jj) = 0; + for (int k = 0; k < dnum; k++) { + d_firstvalue(i, dnum*jj+k) = 0; + } } } else { d_firstflag(i,jj) = 0; for (int k = 0; k < dnum; k++) { - d_firstvalue(i, dnum*jj+k) = 0; + d_firstvalue(i, dnum*jj+k) = 0; } } } diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 4daf4b84c5..5470001967 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -224,49 +224,49 @@ void NPairKokkos::build(NeighList *list_) Kokkos::parallel_for(nall, f); } else { if (newton_pair) { - if (SIZE) { - NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); + if (SIZE) { + NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); #ifdef KOKKOS_ENABLE_CUDA - if (ExecutionSpaceFromDevice::space == Device) - Kokkos::parallel_for(config, f); - else - Kokkos::parallel_for(nall, f); + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); #else - Kokkos::parallel_for(nall, f); + Kokkos::parallel_for(nall, f); #endif - } else { - NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); + } else { + NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); #ifdef KOKKOS_ENABLE_CUDA - if (ExecutionSpaceFromDevice::space == Device) - Kokkos::parallel_for(config, f); - else - Kokkos::parallel_for(nall, f); + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); #else - Kokkos::parallel_for(nall, f); + Kokkos::parallel_for(nall, f); #endif - } + } } else { - if (SIZE) { - NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); + if (SIZE) { + NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); #ifdef KOKKOS_ENABLE_CUDA - if (ExecutionSpaceFromDevice::space == Device) - Kokkos::parallel_for(config, f); - else - Kokkos::parallel_for(nall, f); + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); #else - Kokkos::parallel_for(nall, f); + Kokkos::parallel_for(nall, f); #endif - } else { - NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); + } else { + NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); #ifdef KOKKOS_ENABLE_CUDA - if (ExecutionSpaceFromDevice::space == Device) - Kokkos::parallel_for(config, f); - else - Kokkos::parallel_for(nall, f); + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); #else - Kokkos::parallel_for(nall, f); + Kokkos::parallel_for(nall, f); #endif - } + } } } Kokkos::deep_copy(h_scalars, d_scalars); @@ -871,8 +871,8 @@ void NeighborKokkosExecute:: if(rsq <= cutsq) { if(n:: if(HalfNeigh && !Newton && (j < i)) continue; if(!HalfNeigh && j==i) continue; if(Tri) { - if (x(j,2) < ztmp) continue; - if (x(j,2) == ztmp) { - if (x(j,1) < ytmp) continue; - if (x(j,1) == ytmp) { - if (x(j,0) < xtmp) continue; - if (x(j,0) == xtmp && j <= i) continue; - } - } + if (x(j,2) < ztmp) continue; + if (x(j,2) == ztmp) { + if (x(j,1) < ytmp) continue; + if (x(j,1) == ytmp) { + if (x(j,0) < xtmp) continue; + if (x(j,0) == xtmp && j <= i) continue; + } + } } if(exclude && exclusion(i,j,itype,jtype)) continue; @@ -911,11 +911,11 @@ void NeighborKokkosExecute:: const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); if(rsq <= cutsq) { - if(n::build_ItemSizeCuda(typename Kokkos::Team if(i >= 0 && i < nlocal) { #pragma unroll 4 for(int m = 0; m < bincount_current; m++) { - int j = other_id[m]; - const int jtype = other_x[m + 3 * atoms_per_bin]; + int j = other_id[m]; + const int jtype = other_x[m + 3 * atoms_per_bin]; - //for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists - if((j == i) || - (HalfNeigh && !Newton && (j < i)) || - (HalfNeigh && Newton && + //for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists + if((j == i) || + (HalfNeigh && !Newton && (j < i)) || + (HalfNeigh && Newton && ((j < i) || - ((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) || - (x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp))))) - ) continue; + ((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) || + (x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp))))) + ) continue; if(Tri) { if (x(j,2) < ztmp) continue; if (x(j,2) == ztmp) { @@ -1011,21 +1011,21 @@ void NeighborKokkosExecute::build_ItemSizeCuda(typename Kokkos::Team } } } - if(exclude && exclusion(i,j,itype,jtype)) continue; - const X_FLOAT delx = xtmp - other_x[m]; - const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin]; - const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin]; - const X_FLOAT rsq = delx * delx + dely * dely + delz * delz; - const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin]; - const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); - - if(rsq <= cutsq) { - if(n::build_ItemSizeCuda(typename Kokkos::Team int j = MY_II < bincount_current ? c_bins(jbin, MY_II) : -1; if(j >= 0) { - other_x[MY_II] = x(j, 0); - other_x[MY_II + atoms_per_bin] = x(j, 1); - other_x[MY_II + 2 * atoms_per_bin] = x(j, 2); - other_x[MY_II + 3 * atoms_per_bin] = type(j); - other_x[MY_II + 4 * atoms_per_bin] = radius(j); + other_x[MY_II] = x(j, 0); + other_x[MY_II + atoms_per_bin] = x(j, 1); + other_x[MY_II + 2 * atoms_per_bin] = x(j, 2); + other_x[MY_II + 3 * atoms_per_bin] = type(j); + other_x[MY_II + 4 * atoms_per_bin] = radius(j); } other_id[MY_II] = j; @@ -1054,40 +1054,40 @@ void NeighborKokkosExecute::build_ItemSizeCuda(typename Kokkos::Team if(i >= 0 && i < nlocal) { #pragma unroll 8 - for(int m = 0; m < bincount_current; m++) { - const int j = other_id[m]; - const int jtype = other_x[m + 3 * atoms_per_bin]; - - if(HalfNeigh && (j < i)) continue; - if(HalfNeigh && !Newton && (j < i)) continue; - if(!HalfNeigh && j==i) continue; - if(Tri) { - if (x(j,2) < ztmp) continue; - if (x(j,2) == ztmp) { - if (x(j,1) < ytmp) continue; - if (x(j,1) == ytmp) { - if (x(j,0) < xtmp) continue; - if (x(j,0) == xtmp && j <= i) continue; - } - } - } - if(exclude && exclusion(i,j,itype,jtype)) continue; - - const X_FLOAT delx = xtmp - other_x[m]; - const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin]; - const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin]; - const X_FLOAT rsq = delx * delx + dely * dely + delz * delz; - const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin]; - const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); - - if(rsq <= cutsq) { - if(n::compute(int eflag_in, int vflag_in) if (lmp->kokkos->neighflag == HALF) { if (force->newton_pair) { if (vflag_atom) { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } else if (vflag_global) { - if (shearupdate) { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } else { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } } else { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } } else { if (vflag_atom) { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } else if (vflag_global) { - if (shearupdate) { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } else { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } } else { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } } } else { // HALFTHREAD if (force->newton_pair) { if (vflag_atom) { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } else if (vflag_global) { - if (shearupdate) { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } else { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } } else { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } } else { if (vflag_atom) { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } else if (vflag_global) { - if (shearupdate) { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } else { - Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); - } + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } } else { - if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); - } + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } } } } @@ -408,7 +408,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC shear3 += vtr3*dt; } X_FLOAT shrmag = sqrt(shear1*shear1 + shear2*shear2 + - shear3*shear3); + shear3*shear3); // rotate shear displacements @@ -433,15 +433,15 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC if (fs > fn) { if (shrmag != 0.0) { - shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) - - meff*gammat*vtr1/kt; - shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) - - meff*gammat*vtr2/kt; - shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) - - meff*gammat*vtr3/kt; - fs1 *= fn/fs; - fs2 *= fn/fs; - fs3 *= fn/fs; + shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) - + meff*gammat*vtr1/kt; + shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) - + meff*gammat*vtr2/kt; + shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) - + meff*gammat*vtr3/kt; + fs1 *= fn/fs; + fs2 *= fn/fs; + fs3 *= fn/fs; } else fs1 = fs2 = fs3 = 0.0; } @@ -503,8 +503,8 @@ template template KOKKOS_INLINE_FUNCTION void PairGranHookeHistoryKokkos::ev_tally_xyz(EV_FLOAT &ev, int i, int j, - F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, - X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const { F_FLOAT v[6]; @@ -546,8 +546,8 @@ template template KOKKOS_INLINE_FUNCTION void PairGranHookeHistoryKokkos::ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j, - F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, - X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const { Kokkos::View::value> > v_vatom = k_vatom.view(); diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 23952b71d8..3367e97c6d 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -614,8 +614,8 @@ void VerletKokkos::force_clear() atomKK->modified(Device,F_MASK); if (torqueflag) { - Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); - atomKK->modified(Device,TORQUE_MASK); + Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); + atomKK->modified(Device,TORQUE_MASK); } } } diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index a24ee4203c..a7f0698c0c 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -131,7 +131,7 @@ void EwaldDisp::init() else if (ewald_mix==Pair::ARITHMETIC) { k = 2; break; } error->all(FLERR, "Unsupported mixing rule in kspace_style ewald/disp"); - break; + break; default: error->all(FLERR,"Unsupported order in kspace_style ewald/disp"); } diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index abc33b90fa..0d0d4c7eb2 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -320,8 +320,8 @@ void PPPMDisp::init() mixflag == 1) && mixflag!= 2) { k = 1; break; } else if (ewald_mix==Pair::ARITHMETIC && mixflag!=2) { k = 2; break; } else if (mixflag == 2) { k = 3; break; } - else error->all(FLERR,"Unsupported mixing rule in kspace_style pppm/disp"); - break; + else error->all(FLERR,"Unsupported mixing rule in kspace_style pppm/disp"); + break; default: sprintf(str, "Unsupported order in kspace_style " "pppm/disp, pair_style %s", force->pair_style); diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index 1f1c34df52..a31e57bb48 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -67,13 +67,13 @@ class AtomVecSpin : public AtomVec { tagint *tag; int *type,*mask; imageint *image; - double **x,**v,**f; // lattice quantities + double **x,**v,**f; // lattice quantities - // spin quantities - double **sp; // sp[i][0-2] direction of the spin i - // sp[i][3] atomic magnetic moment of the spin i - double **fm; // fm[i][0-2] direction of magnetic precession - double **fm_long; // storage of long-range spin prec. components + // spin quantities + double **sp; // sp[i][0-2] direction of the spin i + // sp[i][3] atomic magnetic moment of the spin i + double **fm; // fm[i][0-2] direction of magnetic precession + double **fm_long; // storage of long-range spin prec. components }; } diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index 5358438396..b581b70d34 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -32,17 +32,17 @@ class FixLangevinSpin : public Fix { void init(); void setup(int); void post_force_respa(int, int, int); - void add_tdamping(double spi[3], double fmi[3]); // add transverse damping - void add_temperature(double fmi[3]); // add temperature - int tdamp_flag, ldamp_flag, temp_flag; // damping and temperature flags + void add_tdamping(double spi[3], double fmi[3]); // add transverse damping + void add_temperature(double fmi[3]); // add temperature + int tdamp_flag, ldamp_flag, temp_flag; // damping and temperature flags protected: double *spi, *fmi; - double alpha_t; // transverse mag. damping - double dts; // magnetic timestep - double temp; // spin bath temperature - double D,sigma; // bath intensity var. - double gil_factor; // gilbert's prefactor + double alpha_t; // transverse mag. damping + double dts; // magnetic timestep + double temp; // spin bath temperature + double D,sigma; // bath intensity var. + double gil_factor; // gilbert's prefactor char *id_temp; class Compute *temperature; diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h index 7ac83ddce7..9646684a3a 100644 --- a/src/SPIN/fix_neb_spin.h +++ b/src/SPIN/fix_neb_spin.h @@ -60,20 +60,20 @@ class FixNEBSpin : public Fix { double **spprev,**spnext,**fmnext; double **springF; double **tangent; - double **xsend,**xrecv; // coords to send/recv to/from other replica - double **fsend,**frecv; // coords to send/recv to/from other replica - double **spsend,**sprecv; // sp to send/recv to/from other replica - double **fmsend,**fmrecv; // fm to send/recv to/from other replica - tagint *tagsend,*tagrecv; // ditto for atom IDs - - // info gathered from all procs in my replica - double **xsendall,**xrecvall; // coords to send/recv to/from other replica - double **fsendall,**frecvall; // force to send/recv to/from other replica - double **spsendall,**sprecvall; // sp to send/recv to/from other replica - double **fmsendall,**fmrecvall; // fm to send/recv to/from other replica - tagint *tagsendall,*tagrecvall; // ditto for atom IDs - - int *counts,*displacements; // used for MPI_Gather + double **xsend,**xrecv; // coords to send/recv to/from other replica + double **fsend,**frecv; // coords to send/recv to/from other replica + double **spsend,**sprecv; // sp to send/recv to/from other replica + double **fmsend,**fmrecv; // fm to send/recv to/from other replica + tagint *tagsend,*tagrecv; // ditto for atom IDs + + // info gathered from all procs in my replica + double **xsendall,**xrecvall; // coords to send/recv to/from other replica + double **fsendall,**frecvall; // force to send/recv to/from other replica + double **spsendall,**sprecvall; // sp to send/recv to/from other replica + double **fmsendall,**fmrecvall; // fm to send/recv to/from other replica + tagint *tagsendall,*tagrecvall; // ditto for atom IDs + + int *counts,*displacements; // used for MPI_Gather double geodesic_distance(double *, double *); void inter_replica_comm(); diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 9b4f1916ae..87546ba9da 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -307,7 +307,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/) ComputeInteractionsSpin(i); AdvanceSingleSpin(i); i = forward_stacks[i]; - } + } } } for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal @@ -318,7 +318,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/) ComputeInteractionsSpin(i); AdvanceSingleSpin(i); i = backward_stacks[i]; - } + } } } } else if (sector_flag == 0) { // serial seq. update @@ -360,7 +360,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/) ComputeInteractionsSpin(i); AdvanceSingleSpin(i); i = forward_stacks[i]; - } + } } } for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal @@ -371,7 +371,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/) ComputeInteractionsSpin(i); AdvanceSingleSpin(i); i = backward_stacks[i]; - } + } } } } else if (sector_flag == 0) { // serial seq. update diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 5871f721be..5aa6b8e4e4 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -34,30 +34,30 @@ friend class PairSpin; virtual void initial_integrate(int); virtual void final_integrate(); - void ComputeInteractionsSpin(int); // compute and advance single spin functions + void ComputeInteractionsSpin(int); // compute and advance single spin functions void AdvanceSingleSpin(int); - void sectoring(); // sectoring operation functions + void sectoring(); // sectoring operation functions int coords2sector(double *); void setup_pre_neighbor(); void pre_neighbor(); - int lattice_flag; // lattice_flag = 0 if spins only - // lattice_flag = 1 if spin-lattice calc. + int lattice_flag; // lattice_flag = 0 if spins only + // lattice_flag = 1 if spin-lattice calc. protected: - int sector_flag; // sector_flag = 0 if serial algorithm - // sector_flag = 1 if parallel algorithm + int sector_flag; // sector_flag = 0 if serial algorithm + // sector_flag = 1 if parallel algorithm - double dtv, dtf, dts; // velocity, force, and spin timesteps + double dtv, dtf, dts; // velocity, force, and spin timesteps - int nlocal_max; // max value of nlocal (for size of lists) + int nlocal_max; // max value of nlocal (for size of lists) - int pair_spin_flag; // magnetic pair flags - int long_spin_flag; // magnetic long-range flag - int precession_spin_flag; // magnetic precession flags - int maglangevin_flag; // magnetic langevin flags + int pair_spin_flag; // magnetic pair flags + int long_spin_flag; // magnetic long-range flag + int precession_spin_flag; // magnetic precession flags + int maglangevin_flag; // magnetic langevin flags int tdamp_flag, temp_flag; int setforce_spin_flag; @@ -69,9 +69,9 @@ friend class PairSpin; // pointers to magnetic pair styles - int npairs, npairspin; // # of pairs, and # of spin pairs + int npairs, npairspin; // # of pairs, and # of spin pairs class Pair *pair; - class PairSpin **spin_pairs; // vector of spin pairs + class PairSpin **spin_pairs; // vector of spin pairs // sectoring variables @@ -80,10 +80,10 @@ friend class PairSpin; // stacking variables for sectoring algorithm - int *stack_head; // index of first atom in backward_stacks - int *stack_foot; // index of first atom in forward_stacks - int *backward_stacks; // index of next atom in backward stack - int *forward_stacks; // index of next atom in forward stack + int *stack_head; // index of first atom in backward_stacks + int *stack_foot; // index of first atom in forward_stacks + int *backward_stacks; // index of next atom in backward stack + int *forward_stacks; // index of next atom in forward stack }; diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 3296b28228..97dbe7ba6f 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -236,7 +236,7 @@ void FixPrecessionSpin::post_force(int /* vflag */) if (varflag != CONSTANT) { modify->clearstep_compute(); modify->addstep_compute(update->ntimestep + 1); - set_magneticprecession(); // update mag. field if time-dep. + set_magneticprecession(); // update mag. field if time-dep. } int *mask = atom->mask; @@ -265,9 +265,9 @@ void FixPrecessionSpin::post_force(int /* vflag */) epreci -= compute_anisotropy_energy(spi); } - if (cubic_flag) { // compute cubic anisotropy - compute_cubic(spi,fmi); - epreci -= compute_cubic_energy(spi); + if (cubic_flag) { // compute cubic anisotropy + compute_cubic(spi,fmi); + epreci -= compute_cubic_energy(spi); } eprec += epreci; diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index 0037784a48..96d89e004e 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -54,7 +54,7 @@ class FixPrecessionSpin : public Fix { double compute_cubic_energy(double *); protected: - int style; // style of the magnetic precession + int style; // style of the magnetic precession double degree2rad; double hbar; @@ -72,19 +72,19 @@ class FixPrecessionSpin : public Fix { double H_field; double nhx, nhy, nhz; - double hx, hy, hz; // temp. force variables + double hx, hy, hz; // temp. force variables // magnetic anisotropy intensity and direction - double Ka; // aniso const. in eV - double Kah; // aniso const. in rad.THz + double Ka; // aniso const. in eV + double Kah; // aniso const. in rad.THz double nax, nay, naz; - double Kax, Kay, Kaz; // temp. force variables + double Kax, Kay, Kaz; // temp. force variables // cubic anisotropy intensity - double k1c,k2c; // cubic const. in eV - double k1ch,k2ch; // cubic const. in rad.THz + double k1c,k2c; // cubic const. in eV + double k1ch,k2ch; // cubic const. in rad.THz double nc1x,nc1y,nc1z; double nc2x,nc2y,nc2z; double nc3x,nc3y,nc3z; diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index 7315aca056..e39eb18744 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -165,9 +165,9 @@ int MinSpin::iterate(int maxiter) fmdotfm = fmsq = 0.0; if (update->ftol > 0.0) { - if (normstyle == MAX) fmsq = max_torque(); // max torque norm - else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm - else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm + if (normstyle == MAX) fmsq = max_torque(); // max torque norm + else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm + else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm else error->all(FLERR,"Illegal min_modify command"); fmdotfm = fmsq*fmsq; if (update->multireplica == 0) { diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index 95bbcf437b..9c8c814bc4 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -270,9 +270,9 @@ int MinSpinCG::iterate(int maxiter) fmdotfm = fmsq = 0.0; if (update->ftol > 0.0) { - if (normstyle == MAX) fmsq = max_torque(); // max torque norm - else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm - else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm + if (normstyle == MAX) fmsq = max_torque(); // max torque norm + else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm + else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm else error->all(FLERR,"Illegal min_modify command"); fmdotfm = fmsq*fmsq; if (update->multireplica == 0) { @@ -347,12 +347,12 @@ void MinSpinCG::calc_search_direction() factor = 0.0; - if (local_iter == 0 || local_iter % 5 == 0){ // steepest descent direction + if (local_iter == 0 || local_iter % 5 == 0){ // steepest descent direction for (int i = 0; i < 3 * nlocal; i++) { p_s[i] = -g_cur[i] * factor; g_old[i] = g_cur[i] * factor; } - } else { // conjugate direction + } else { // conjugate direction for (int i = 0; i < 3 * nlocal; i++) { g2old += g_old[i] * g_old[i]; g2 += g_cur[i] * g_cur[i]; @@ -394,7 +394,7 @@ void MinSpinCG::advance_spins() { int nlocal = atom->nlocal; double **sp = atom->sp; - double rot_mat[9]; // exponential of matrix made of search direction + double rot_mat[9]; // exponential of matrix made of search direction double s_new[3]; // loop on all spins on proc. diff --git a/src/SPIN/min_spin_cg.h b/src/SPIN/min_spin_cg.h index 0eed7a61e6..640721b8ef 100644 --- a/src/SPIN/min_spin_cg.h +++ b/src/SPIN/min_spin_cg.h @@ -35,21 +35,21 @@ class MinSpinCG: public Min { int iterate(int); private: - int local_iter; // for neb - int nlocal_max; // max value of nlocal (for size of lists) - int use_line_search; // use line search or not. - int ireplica,nreplica; // for neb - double dt; // global timestep - double dts; // spin timestep - double discrete_factor; // factor for spin timestep evaluation - double der_e_cur; // current derivative along search dir. - double der_e_pr; // previous derivative along search dir. - double *spvec; // variables for atomic dof, as 1d vector - double *fmvec; // variables for atomic dof, as 1d vector - double *g_old; // gradient vector at previous step - double *g_cur; // current gradient vector - double *p_s; // search direction vector - double **sp_copy; // copy of the spins + int local_iter; // for neb + int nlocal_max; // max value of nlocal (for size of lists) + int use_line_search; // use line search or not. + int ireplica,nreplica; // for neb + double dt; // global timestep + double dts; // spin timestep + double discrete_factor; // factor for spin timestep evaluation + double der_e_cur; // current derivative along search dir. + double der_e_pr; // previous derivative along search dir. + double *spvec; // variables for atomic dof, as 1d vector + double *fmvec; // variables for atomic dof, as 1d vector + double *g_old; // gradient vector at previous step + double *g_cur; // current gradient vector + double *p_s; // search direction vector + double **sp_copy; // copy of the spins void advance_spins(); void calc_gradient(); diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index f86bdd5d48..a1ee010f3f 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -285,9 +285,9 @@ int MinSpinLBFGS::iterate(int maxiter) fmdotfm = fmsq = 0.0; if (update->ftol > 0.0) { - if (normstyle == MAX) fmsq = max_torque(); // max torque norm - else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm - else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm + if (normstyle == MAX) fmsq = max_torque(); // max torque norm + else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm + else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm else error->all(FLERR,"Illegal min_modify command"); fmdotfm = fmsq*fmsq; if (update->multireplica == 0) { @@ -372,7 +372,7 @@ void MinSpinLBFGS::calc_search_direction() factor = 1.0; } - if (local_iter == 0){ // steepest descent direction + if (local_iter == 0){ // steepest descent direction //if no line search then calculate maximum rotation if (use_line_search == 0) diff --git a/src/SPIN/min_spin_lbfgs.h b/src/SPIN/min_spin_lbfgs.h index cead605b32..8b470b5d23 100644 --- a/src/SPIN/min_spin_lbfgs.h +++ b/src/SPIN/min_spin_lbfgs.h @@ -35,18 +35,18 @@ class MinSpinLBFGS: public Min { int iterate(int); private: - int local_iter; // for neb - int use_line_search; // use line search or not. - int nlocal_max; // max value of nlocal (for size of lists) - int ireplica,nreplica; // for neb - double der_e_cur; // current derivative along search dir. - double der_e_pr; // previous derivative along search dir. + int local_iter; // for neb + int use_line_search; // use line search or not. + int nlocal_max; // max value of nlocal (for size of lists) + int ireplica,nreplica; // for neb + double der_e_cur; // current derivative along search dir. + double der_e_pr; // previous derivative along search dir. double maxepsrot; - double *spvec; // variables for atomic dof, as 1d vector - double *fmvec; // variables for atomic dof, as 1d vector - double *g_old; // gradient vector at previous step - double *g_cur; // current gradient vector - double *p_s; // search direction vector + double *spvec; // variables for atomic dof, as 1d vector + double *fmvec; // variables for atomic dof, as 1d vector + double *g_old; // gradient vector at previous step + double *g_cur; // current gradient vector + double *p_s; // search direction vector void advance_spins(); void calc_gradient(); @@ -58,11 +58,11 @@ class MinSpinLBFGS: public Min { int adescent(double, double); double maximum_rotation(double *); - double *rho; // estimation of curvature - double **ds; // change in rotation matrix between two iterations, da - double **dy; // change in gradients between two iterations, dg - double **sp_copy; // copy of the spins - int num_mem; // number of stored steps + double *rho; // estimation of curvature + double **ds; // change in rotation matrix between two iterations, da + double **dy; // change in gradients between two iterations, dg + double **sp_copy; // copy of the spins + int num_mem; // number of stored steps bigint last_negative; }; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 559fd1cb49..075850d1af 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -179,7 +179,7 @@ void NEBSpin::run() update->whichflag = 2; update->etol = etol; - update->ftol = ttol; // update->ftol is a torque tolerance + update->ftol = ttol; // update->ftol is a torque tolerance update->multireplica = 1; lmp->init(); @@ -214,7 +214,7 @@ void NEBSpin::run() fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan DN0 ... GradVNdottan DNN\n"); + "GradV0dottan DN0 ... GradVNdottan DNN\n"); } else { fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " @@ -224,10 +224,10 @@ void NEBSpin::run() if (ulogfile) { if (verbose) { - fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " - "GradV0 GradV1 GradVc EBF EBR RDT " - "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan DN0 ... GradVNdottan DNN\n"); + fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN " + "GradV0dottan DN0 ... GradVNdottan DNN\n"); } else { fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " @@ -301,7 +301,7 @@ void NEBSpin::run() fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan DN0... GradVNdottan DNN\n"); + "GradV0dottan DN0... GradVNdottan DNN\n"); } else { fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc " @@ -311,10 +311,10 @@ void NEBSpin::run() } if (ulogfile) { if (verbose) { - fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " - "GradV0 GradV1 GradVc EBF EBR RDT " - "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan DN0 ... GradVNdottan DNN\n"); + fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " + "GradV0 GradV1 GradVc EBF EBR RDT " + "RD1 PE1 RD2 PE2 ... RDN PEN " + "GradV0dottan DN0 ... GradVNdottan DNN\n"); } else { fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc " @@ -472,8 +472,8 @@ void NEBSpin::readfile(char *file, int flag) m = atom->map(tag); if (m >= 0 && m < nlocal) { ncount++; - musp = atof(values[1]); - xx = atof(values[2]); + musp = atof(values[1]); + xx = atof(values[2]); yy = atof(values[3]); zz = atof(values[4]); spx = atof(values[5]); @@ -482,39 +482,39 @@ void NEBSpin::readfile(char *file, int flag) if (flag == 0) { - spinit[0] = sp[m][0]; - spinit[1] = sp[m][1]; - spinit[2] = sp[m][2]; - spfinal[0] = spx; - spfinal[1] = spy; - spfinal[2] = spz; - - // interpolate intermediate spin states - - sp[m][3] = musp; - if (fraction == 0.0) { - sp[m][0] = spinit[0]; - sp[m][1] = spinit[1]; - sp[m][2] = spinit[2]; - } else if (fraction == 1.0) { - sp[m][0] = spfinal[0]; - sp[m][1] = spfinal[1]; - sp[m][2] = spfinal[2]; - } else { + spinit[0] = sp[m][0]; + spinit[1] = sp[m][1]; + spinit[2] = sp[m][2]; + spfinal[0] = spx; + spfinal[1] = spy; + spfinal[2] = spz; + + // interpolate intermediate spin states + + sp[m][3] = musp; + if (fraction == 0.0) { + sp[m][0] = spinit[0]; + sp[m][1] = spinit[1]; + sp[m][2] = spinit[2]; + } else if (fraction == 1.0) { + sp[m][0] = spfinal[0]; + sp[m][1] = spfinal[1]; + sp[m][2] = spfinal[2]; + } else { temp_flag = initial_rotation(spinit,spfinal,fraction); rot_flag = MAX(temp_flag,rot_flag); - sp[m][0] = spfinal[0]; - sp[m][1] = spfinal[1]; - sp[m][2] = spfinal[2]; - } + sp[m][0] = spfinal[0]; + sp[m][1] = spfinal[1]; + sp[m][2] = spfinal[2]; + } } else { sp[m][3] = musp; - x[m][0] = xx; + x[m][0] = xx; x[m][1] = yy; x[m][2] = zz; - sp[m][0] = spx; - sp[m][1] = spy; - sp[m][2] = spz; + sp[m][0] = spx; + sp[m][1] = spy; + sp[m][2] = spz; } } @@ -602,24 +602,24 @@ int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction) // Rodrigues' formula breaks, needs to define another axis k if (knormsq == 0.0) { - if (sidotsf > 0.0) { // spins aligned and in same direction + if (sidotsf > 0.0) { // spins aligned and in same direction return 0; - } else if (sidotsf < 0.0) { // spins aligned and in opposite directions + } else if (sidotsf < 0.0) { // spins aligned and in opposite directions // defining a rotation axis // first guess, k = spi x [100] // second guess, k = spi x [010] if (spiy*spiy + spiz*spiz != 0.0) { // spin not along [100] - kx = 0.0; - ky = spiz; - kz = -spiy; - knormsq = ky*ky + kz*kz; + kx = 0.0; + ky = spiz; + kz = -spiy; + knormsq = ky*ky + kz*kz; } else if (spix*spix + spiz*spiz != 0.0) { // spin not along [010] - kx = -spiz; - ky = 0.0; - kz = spix; - knormsq = kx*kx + kz*kz; + kx = -spiz; + ky = 0.0; + kz = spix; + knormsq = kx*kx + kz*kz; } else error->all(FLERR,"Incorrect initial rotation operation"); rot_flag = 1; } @@ -822,9 +822,9 @@ void NEBSpin::print_status() for (int i = 0; i < nreplica; i++) fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]); if (verbose) { - for (int i = 0; i < nreplica-1; i++) - fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]); - fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); + for (int i = 0; i < nreplica-1; i++) + fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]); + fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); } fprintf(uscreen,"\n"); } @@ -838,9 +838,9 @@ void NEBSpin::print_status() for (int i = 0; i < nreplica; i++) fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]); if (verbose) { - for (int i = 0; i < nreplica-1; i++) - fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]); - fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); + for (int i = 0; i < nreplica-1; i++) + fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]); + fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); } fprintf(ulogfile,"\n"); fflush(ulogfile); diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 0111814c72..34f12d8d59 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -33,8 +33,8 @@ friend class FixNVESpin; virtual void compute_single_pair(int, double *) {} protected: - double hbar; // Planck constant (eV.ps.rad-1) - int lattice_flag; // flag for mech force computation + double hbar; // Planck constant (eV.ps.rad-1) + int lattice_flag; // flag for mech force computation virtual void allocate() {} }; diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 4ff90323f2..bae09689de 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -46,11 +46,11 @@ PairSpinDipoleCut::PairSpinDipoleCut(LAMMPS *lmp) : PairSpin(lmp) { spinflag = 1; - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) mub = 9.274e-4; // in A.Ang^2 mu_0 = 785.15; // in eV/Ang/A^2 mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV + //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } @@ -178,7 +178,7 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; inum = list->inum; ilist = list->ilist; @@ -228,36 +228,36 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) if (rsq < local_cut2) { r2inv = 1.0/rsq; - r3inv = r2inv*rinv; - - compute_dipolar(i,j,eij,fmi,spi,spj,r3inv); - if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv); + r3inv = r2inv*rinv; + + compute_dipolar(i,j,eij,fmi,spi,spj,r3inv); + if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv); } // force accumulation f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][1] += fi[1]; f[i][2] += fi[2]; fm[i][0] += fmi[0]; fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { - if (rsq <= local_cut2) { - evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); - evdwl *= hbar; - } + if (rsq <= local_cut2) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); + evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); } } @@ -277,7 +277,7 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) int k,locflag; int *type = atom->type; double **x = atom->x; - double **sp = atom->sp; + double **sp = atom->sp; numneigh = list->numneigh; firstneigh = list->firstneigh; @@ -427,7 +427,7 @@ void PairSpinDipoleCut::write_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); if (setflag[i][j]) { - fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); + fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); } } } @@ -450,10 +450,10 @@ void PairSpinDipoleCut::read_restart(FILE *fp) if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) { - utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error); - } - MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); + if (me == 0) { + utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error); + } + MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); } } } diff --git a/src/SPIN/pair_spin_dipole_cut.h b/src/SPIN/pair_spin_dipole_cut.h index f9159a629f..33f62d1633 100644 --- a/src/SPIN/pair_spin_dipole_cut.h +++ b/src/SPIN/pair_spin_dipole_cut.h @@ -49,16 +49,16 @@ class PairSpinDipoleCut : public PairSpin { void write_restart_settings(FILE *); void read_restart_settings(FILE *); - double cut_spin_long_global; // global long cutoff distance + double cut_spin_long_global; // global long cutoff distance protected: - double hbar; // reduced Planck's constant - double mub; // Bohr's magneton - double mu_0; // vacuum permeability - double mub2mu0; // prefactor for mech force - double mub2mu0hbinv; // prefactor for mag force + double hbar; // reduced Planck's constant + double mub; // Bohr's magneton + double mu_0; // vacuum permeability + double mub2mu0; // prefactor for mech force + double mub2mu0hbinv; // prefactor for mag force - double **cut_spin_long; // cutoff distance long + double **cut_spin_long; // cutoff distance long double g_ewald; int ewald_order; diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h index 1997cbbc55..56fd4c7126 100644 --- a/src/SPIN/pair_spin_dipole_long.h +++ b/src/SPIN/pair_spin_dipole_long.h @@ -50,16 +50,16 @@ class PairSpinDipoleLong : public PairSpin { void write_restart_settings(FILE *); void read_restart_settings(FILE *); - double cut_spin_long_global; // global long cutoff distance + double cut_spin_long_global; // global long cutoff distance protected: - double hbar; // reduced Planck's constant - double mub; // Bohr's magneton - double mu_0; // vacuum permeability - double mub2mu0; // prefactor for mech force - double mub2mu0hbinv; // prefactor for mag force + double hbar; // reduced Planck's constant + double mub; // Bohr's magneton + double mu_0; // vacuum permeability + double mub2mu0; // prefactor for mech force + double mub2mu0hbinv; // prefactor for mag force - double **cut_spin_long; // cutoff distance long + double **cut_spin_long; // cutoff distance long double g_ewald; int ewald_order; diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h index ac2aa387b3..01022623ec 100644 --- a/src/SPIN/pair_spin_dmi.h +++ b/src/SPIN/pair_spin_dmi.h @@ -44,13 +44,13 @@ class PairSpinDmi : public PairSpin { void write_restart_settings(FILE *); void read_restart_settings(FILE *); - double cut_spin_dmi_global; // short range pair cutoff + double cut_spin_dmi_global; // short range pair cutoff protected: - double **DM; // dmi coeff in eV - double **v_dmx, **v_dmy, **v_dmz; // dmi direction - double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction - double **cut_spin_dmi; // cutoff distance dmi + double **DM; // dmi coeff in eV + double **v_dmx, **v_dmy, **v_dmz; // dmi direction + double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction + double **cut_spin_dmi; // cutoff distance dmi void allocate(); }; diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h index 5feb99210f..19eafeb5ca 100644 --- a/src/SPIN/pair_spin_exchange.h +++ b/src/SPIN/pair_spin_exchange.h @@ -44,13 +44,13 @@ class PairSpinExchange : public PairSpin { void write_restart_settings(FILE *); void read_restart_settings(FILE *); - double cut_spin_exchange_global; // global exchange cutoff distance + double cut_spin_exchange_global; // global exchange cutoff distance protected: - double **J1_mag; // exchange coeffs in eV - double **J1_mech; // mech exchange coeffs in + double **J1_mag; // exchange coeffs in eV + double **J1_mech; // mech exchange coeffs in double **J2, **J3; // J1 in eV, J2 adim, J3 in Ang - double **cut_spin_exchange; // cutoff distance exchange + double **cut_spin_exchange; // cutoff distance exchange void allocate(); }; diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h index b9e820b1d1..4df0078bea 100644 --- a/src/SPIN/pair_spin_magelec.h +++ b/src/SPIN/pair_spin_magelec.h @@ -44,12 +44,12 @@ class PairSpinMagelec : public PairSpin { void write_restart_settings(FILE *); void read_restart_settings(FILE *); - double cut_spin_magelec_global; // global me cutoff + double cut_spin_magelec_global; // global me cutoff protected: - double **ME, **ME_mech; // magelec coeff in eV - double **v_mex, **v_mey, **v_mez; // magelec direction - double **cut_spin_magelec; // magelec cutoff distance + double **ME, **ME_mech; // magelec coeff in eV + double **v_mex, **v_mey, **v_mez; // magelec direction + double **cut_spin_magelec; // magelec cutoff distance void allocate(); }; diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h index 796d8b53f0..5261a7f746 100644 --- a/src/SPIN/pair_spin_neel.h +++ b/src/SPIN/pair_spin_neel.h @@ -44,17 +44,17 @@ class PairSpinNeel : public PairSpin { void write_restart_settings(FILE *); void read_restart_settings(FILE *); - double cut_spin_neel_global; // global neel cutoff distance + double cut_spin_neel_global; // global neel cutoff distance protected: // pseudo-dipolar and pseudo-quadrupolar coeff. - double **g1, **g1_mech; // neel coeffs gij - double **g2, **g3; // g1 in eV, g2 adim, g3 in Ang - double **q1, **q1_mech; // neel coeffs qij - double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang - double **cut_spin_neel; // cutoff distance exchange + double **g1, **g1_mech; // neel coeffs gij + double **g2, **g3; // g1 in eV, g2 adim, g3 in Ang + double **q1, **q1_mech; // neel coeffs qij + double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang + double **cut_spin_neel; // cutoff distance exchange void allocate(); }; diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index f1c2e9ba3a..56103a42b0 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -457,7 +457,7 @@ double ComputeHMA::virial_compute(int n) /* ---------------------------------------------------------------------- */ int ComputeHMA::pack_forward_comm(int n, int *list, double *buf, - int /* pbc_flag */, int * /* pbc */) + int /* pbc_flag */, int * /* pbc */) { int m = 0; for (int ii = 0; ii < n; ii++) { diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index bfa93e178c..33aab5b4ad 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -259,12 +259,12 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "probability seed must be positive"); iarg += 3; } else if (strcmp(arg[iarg],"max_rxn") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " - "'max_rxn' has too few arguments"); - max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]); - if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: " - "'max_rxn' cannot be negative"); - iarg += 2; + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'max_rxn' has too few arguments"); + max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]); + if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: " + "'max_rxn' cannot be negative"); + iarg += 2; } else if (strcmp(arg[iarg],"stabilize_steps") == 0) { if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword " "used without stabilization keyword"); diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index e09287ae23..9faa350468 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -523,7 +523,7 @@ void PairILPGrapheneHBN::calc_FvdW(int eflag, int /* vflag */) // derivatives fpair = -6.0*p.C6*r8inv/TSvdw + p.C6*p.d/p.seff*(TSvdw-1.0)*TSvdw2inv*r8inv*r; - fsum = fpair*Tap - Vilp*dTap/r; + fsum = fpair*Tap - Vilp*dTap/r; f[i][0] += fsum*delx; f[i][1] += fsum*dely; @@ -634,12 +634,12 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */) dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz; dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz; dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz; - fp1[0] = prodnorm1*normal[i][0]*fpair1; - fp1[1] = prodnorm1*normal[i][1]*fpair1; - fp1[2] = prodnorm1*normal[i][2]*fpair1; - fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1; - fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1; - fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1; + fp1[0] = prodnorm1*normal[i][0]*fpair1; + fp1[1] = prodnorm1*normal[i][1]*fpair1; + fp1[2] = prodnorm1*normal[i][2]*fpair1; + fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1; + fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1; + fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1; fkcx = (delx*fsum - fp1[0])*Tap - Vilp*dTap*delx/r; fkcy = (dely*fsum - fp1[1])*Tap - Vilp*dTap*dely/r; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 8ba3dc9db3..d0d8517550 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -519,11 +519,11 @@ void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int /* vflag */) dTap = calc_dTap(r,Rcut); } else {Tap = 1.0; dTap = 0.0;} - Vkc = -p.A*p.z06*r6inv; + Vkc = -p.A*p.z06*r6inv; // derivatives fpair = -6.0*p.A*p.z06*r8inv; - fsum = fpair*Tap - Vkc*dTap/r; + fsum = fpair*Tap - Vkc*dTap/r; f[i][0] += fsum*delx; f[i][1] += fsum*dely; @@ -607,11 +607,11 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */) r = sqrt(rsq); - // turn on/off taper function - if (tap_flag) { - Tap = calc_Tap(r,sqrt(cutsq[itype][jtype])); - dTap = calc_dTap(r,sqrt(cutsq[itype][jtype])); - } else {Tap = 1.0; dTap = 0.0;} + // turn on/off taper function + if (tap_flag) { + Tap = calc_Tap(r,sqrt(cutsq[itype][jtype])); + dTap = calc_dTap(r,sqrt(cutsq[itype][jtype])); + } else {Tap = 1.0; dTap = 0.0;} // Calculate the transverse distance prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz; @@ -626,7 +626,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */) sumC11 = (p.C2 + 2.0*p.C4*rho_ij)*p.delta2inv; frho_ij = exp1*sumC1; sumCff = 0.5*p.C + frho_ij; - Vkc = exp0*sumCff; + Vkc = exp0*sumCff; // derivatives fpair = p.lambda*exp0/r*sumCff; @@ -653,10 +653,10 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */) f[j][1] -= fkcy; f[j][2] -= fkcz; - // calculate the forces acted on the neighbors of atom i from atom j - KC_neighs_i = KC_firstneigh[i]; - for (kk = 0; kk < KC_numneigh[i]; kk++) { - k = KC_neighs_i[kk]; + // calculate the forces acted on the neighbors of atom i from atom j + KC_neighs_i = KC_firstneigh[i]; + for (kk = 0; kk < KC_numneigh[i]; kk++) { + k = KC_neighs_i[kk]; if (k == i) continue; // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz; @@ -672,7 +672,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */) delkj[1] = x[k][1] - x[j][1]; delkj[2] = x[k][2] - x[j][2]; if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]); - } + } if (eflag) { if (tap_flag) pvector[1] += evdwl = Tap*Vkc; @@ -790,7 +790,7 @@ void PairKolmogorovCrespiFull::calc_normal() memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal"); } - inum = list->inum; + inum = list->inum; ilist = list->ilist; //Calculate normals for (ii = 0; ii < inum; ii++) { diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index 957173bf7f..f52e427c18 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -786,9 +786,9 @@ double PairLJExpandCoulLong::init_one(int i, int j) (1.0/3.0 + 2.0*shift1/(4.0*rc1) + shift2/(5.0*rc2))/rc3); ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 * ((1.0/9.0 + 3.0*shift1/(10.0*rc1) + - 3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 - + 3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 - (1.0/3.0 + 3.0*shift1/(4.0*rc1) + - 3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3); + 3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3); } return cut; diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 97aa3dcaca..1e4ad3edf6 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -61,7 +61,7 @@ static const char cite_pair_local_density[] = PairLocalDensity::PairLocalDensity(LAMMPS *lmp) : Pair(lmp) { restartinfo = 0; - one_coeff = 1; + one_coeff = 1; single_enable = 1; // stuff read from tabulated file @@ -117,7 +117,7 @@ PairLocalDensity::~PairLocalDensity() memory->destroy(rho_min); memory->destroy(rho_max); - memory->destroy(delta_rho); + memory->destroy(delta_rho); memory->destroy(c0); memory->destroy(c2); memory->destroy(c4); @@ -144,7 +144,7 @@ void PairLocalDensity::compute(int eflag, int vflag) double p, *coeff; int *ilist,*jlist,*numneigh,**firstneigh; - phi = uLD = evdwl = fpair = rsqinv = 0.0; + phi = uLD = evdwl = fpair = rsqinv = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; @@ -180,11 +180,11 @@ void PairLocalDensity::compute(int eflag, int vflag) if (newton_pair) { m = nlocal + atom->nghost; for (k = 0; k < nLD; k++) { - for (i = 0; i < m; i++) { + for (i = 0; i < m; i++) { localrho[k][i] = 0.0; fp[k][i] = 0.0; } - } + } } else { for (k = 0; k < nLD; k++){ @@ -209,14 +209,14 @@ void PairLocalDensity::compute(int eflag, int vflag) for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - jtype = type[j]; + jtype = type[j]; // calculate distance-squared between i,j atom-types delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + rsq = delx*delx + dely*dely + delz*delz; // calculating LDs based on central and neigh filters @@ -239,7 +239,7 @@ void PairLocalDensity::compute(int eflag, int vflag) localrho[k][j] += (phi * b[k][itype]); } } - } + } } // communicate and sum LDs over all procs @@ -247,10 +247,10 @@ void PairLocalDensity::compute(int eflag, int vflag) // - for (ii = 0; ii < inum; ii++) { + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; itype = type[i]; - uLD = 0.0; + uLD = 0.0; for (k = 0; k < nLD; k++) { @@ -284,7 +284,7 @@ void PairLocalDensity::compute(int eflag, int vflag) if (eflag) { if (eflag_global) eng_vdwl += uLD; - if (eflag_atom) eatom[i] += uLD; + if (eflag_atom) eatom[i] += uLD; } } @@ -306,7 +306,7 @@ void PairLocalDensity::compute(int eflag, int vflag) jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; + j = jlist[jj]; j &= NEIGHMASK; jtype = type[j]; @@ -326,7 +326,7 @@ void PairLocalDensity::compute(int eflag, int vflag) dphi = rsq * (2.0*c2[k] + rsq * (4.0*c4[k] + 6.0*c6[k]*rsq)); fpair += -(a[k][itype]*b[k][jtype]*fp[k][i] + a[k][jtype]*b[k][itype]*fp[k][j]) * dphi; } - } + } fpair *= rsqinv; f[i][0] += delx*fpair; @@ -459,8 +459,8 @@ double PairLocalDensity::init_one(int /* i */, int /* j */) ---------------------------------------------------------------------------*/ double PairLocalDensity::single(int /* i */, int /* j */, int itype, int jtype, - double rsq, double /* factor_coul */, - double /* factor_lj */, double &fforce) + double rsq, double /* factor_coul */, + double /* factor_lj */, double &fforce) { int m, k, index; double rsqinv, p, uLD; @@ -473,7 +473,7 @@ double PairLocalDensity::single(int /* i */, int /* j */, int itype, int jtype, for (k = 0; k < nLD; k++) { LD[k][1] = 0.0; // itype:- 1 LD[k][2] = 0.0; // jtype:- 2 - } + } rsqinv = 1.0/rsq; for (k = 0; k < nLD; k++) { @@ -556,24 +556,24 @@ void PairLocalDensity::interpolate_cbspl(int n, double delta, { /* inputs: n number of interpolating points - - f array containing function values to - be interpolated; f[i] is the function - value corresponding to x[i] - ('x' refers to the independent var) - - delta difference in tabulated values of x + + f array containing function values to + be interpolated; f[i] is the function + value corresponding to x[i] + ('x' refers to the independent var) + + delta difference in tabulated values of x - outputs: (packaged as columns of the coeff matrix) - coeff_b coeffs of linear terms - coeff_c coeffs of quadratic terms - coeff_d coeffs of cubic terms + outputs: (packaged as columns of the coeff matrix) + coeff_b coeffs of linear terms + coeff_c coeffs of quadratic terms + coeff_d coeffs of cubic terms spline matrix that collects b,c,d - - other parameters: - fpa derivative of function at x=a - fpb derivative of function at x=b + + other parameters: + fpa derivative of function at x=a + fpb derivative of function at x=b */ double *dl, *dd, *du; @@ -684,12 +684,12 @@ void PairLocalDensity::parse_file(char *filename) { // broadcast number of LD potentials and number of (rho,frho) pairs if (me == 0) { - // first 2 comment lines ignored + // first 2 comment lines ignored utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); // extract number of potentials and number of (frho, rho) points - utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line, "%d %d", &nLD, &nrho); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); } @@ -711,9 +711,9 @@ void PairLocalDensity::parse_file(char *filename) { memory->create(delta_rho, nLD,"pairLD:delta_rho"); memory->create(ftmp, nrho*nLD, "pairLD:ftmp"); - // setting up central and neighbor atom filters + // setting up central and neighbor atom filters memory->create(a, nLD, atom->ntypes+1 , "pairLD:a"); - memory->create(b, nLD, atom->ntypes+1, "pairLD:b"); + memory->create(b, nLD, atom->ntypes+1, "pairLD:b"); if (me == 0) { for (n = 1; n <= atom->ntypes; n++){ for (k = 0; k < nLD; k++) { @@ -721,14 +721,14 @@ void PairLocalDensity::parse_file(char *filename) { b[k][n] = 0; } } - } + } // read file block by block if (me == 0) { for (k = 0; k < nLD; k++) { - // parse upper and lower cut values + // parse upper and lower cut values if (fgets(line,MAXLINE,fptr)==NULL) break; sscanf(line, "%lf %lf", &lowercut[k], &uppercut[k]); @@ -743,7 +743,7 @@ void PairLocalDensity::parse_file(char *filename) { // parse neighbor atom filter utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); tmp = strtok(line, " /t/n/r/f"); - while (tmp != NULL) { + while (tmp != NULL) { b[k][atoi(tmp)] = 1; tmp = strtok(NULL, " /t/n/r/f"); } @@ -778,7 +778,7 @@ void PairLocalDensity::parse_file(char *filename) { } } - // Broadcast all parsed arrays + // Broadcast all parsed arrays MPI_Bcast(&lowercut[0], nLD, MPI_DOUBLE, 0, world); MPI_Bcast(&uppercut[0], nLD, MPI_DOUBLE, 0, world); MPI_Bcast(&lowercutsq[0], nLD, MPI_DOUBLE, 0, world); @@ -818,16 +818,16 @@ void PairLocalDensity::parse_file(char *filename) { ------------------------------------------------------------------------- */ int PairLocalDensity::pack_comm(int n, int *list, double *buf, - int /* pbc_flag */, int * /* pbc */) { + int /* pbc_flag */, int * /* pbc */) { int i,j,k; - int m; + int m; m = 0; for (i = 0; i < n; i++) { j = list[i]; for (k = 0; k < nLD; k++) { buf[m++] = fp[k][j]; - } + } } return nLD; @@ -845,7 +845,7 @@ void PairLocalDensity::unpack_comm(int n, int first, double *buf) { for (k = 0; k < nLD; k++) { fp[k][i] = buf[m++]; } - } + } } /* ---------------------------------------------------------------------- */ @@ -876,7 +876,7 @@ void PairLocalDensity::unpack_reverse_comm(int n, int *list, double *buf) { j = list[i]; for (k = 0; k < nLD; k++) { localrho[k][j] += buf[m++]; - } + } } } diff --git a/src/USER-MISC/pair_local_density.h b/src/USER-MISC/pair_local_density.h index 77aab1399b..5e37376ece 100644 --- a/src/USER-MISC/pair_local_density.h +++ b/src/USER-MISC/pair_local_density.h @@ -72,13 +72,13 @@ class PairLocalDensity : public Pair { void allocate(); - // read tabulated input file - void parse_file(char *); + // read tabulated input file + void parse_file(char *); - // convert array to spline - void array2spline(); - - // cubic spline interpolation + // convert array to spline + void array2spline(); + + // cubic spline interpolation void interpolate_cbspl(int, double, double *, double **); }; diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index fce23c645f..66f1acf91c 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -46,8 +46,8 @@ extern int Init_Workspace(reax_system*, control_params*, storage*, char*); /* ---------------------------------------------------------------------- */ int Init_ListsOMP(reax_system *system, control_params *control, - simulation_data * /* data */, storage * /* workspace */, - reax_list **lists, mpi_datatypes * /* mpi_data */, char * /* msg */) + simulation_data * /* data */, storage * /* workspace */, + reax_list **lists, mpi_datatypes * /* mpi_data */, char * /* msg */) { int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; int *hb_top, *bond_top; diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index e3a6645fc2..a44c7d5cbd 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -154,7 +154,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity checks */ if (c == 2 && !lgflag) - control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); + control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); if (c < 9) { snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); diff --git a/src/force.cpp b/src/force.cpp index cc121a5f80..63d1fcbe31 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -204,17 +204,17 @@ void Force::init() if (!bond && (atom->nbonds > 0)) { error->warning(FLERR,"Bonds are defined but no bond style is set"); if ((special_lj[1] != 1.0) || (special_coul[1] != 1.0)) - error->warning(FLERR,"Likewise 1-2 special neighbor interactions != 1.0"); + error->warning(FLERR,"Likewise 1-2 special neighbor interactions != 1.0"); } if (!angle && (atom->nangles > 0)) { error->warning(FLERR,"Angles are defined but no angle style is set"); if ((special_lj[2] != 1.0) || (special_coul[2] != 1.0)) - error->warning(FLERR,"Likewise 1-3 special neighbor interactions != 1.0"); + error->warning(FLERR,"Likewise 1-3 special neighbor interactions != 1.0"); } if (!dihedral && (atom->ndihedrals > 0)) { error->warning(FLERR,"Dihedrals are defined but no dihedral style is set"); if ((special_lj[3] != 1.0) || (special_coul[3] != 1.0)) - error->warning(FLERR,"Likewise 1-4 special neighbor interactions != 1.0"); + error->warning(FLERR,"Likewise 1-4 special neighbor interactions != 1.0"); } if (!improper && (atom->nimpropers > 0)) error->warning(FLERR,"Impropers are defined but no improper style is set"); diff --git a/src/min.h b/src/min.h index 61f9ce0bda..6f3e10d048 100644 --- a/src/min.h +++ b/src/min.h @@ -64,11 +64,11 @@ class Min : protected Pointers { int virial_style; // compute virial explicitly or implicitly int external_force_clear; // clear forces locally or externally - double dmax; // max dist to move any atom in one step - int linestyle; // 0 = backtrack, 1 = quadratic, 2 = forcezero - // 3 = spin_cubic, 4 = spin_none + double dmax; // max dist to move any atom in one step + int linestyle; // 0 = backtrack, 1 = quadratic, 2 = forcezero + // 3 = spin_cubic, 4 = spin_none - int normstyle; // TWO, MAX or INF flag for force norm evaluation + int normstyle; // TWO, MAX or INF flag for force norm evaluation int nelist_global,nelist_atom; // # of PE,virial computes to check int nvlist_global,nvlist_atom; diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 80dde25f51..7b7046ea00 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -100,7 +100,7 @@ int MinCG::iterate(int maxiter) for (i = 0; i < n; i++) { dot[0] += fatom[i]*fatom[i]; dot[1] += fatom[i]*gatom[i]; - fmax = MAX(fmax,fatom[i]*fatom[i]); + fmax = MAX(fmax,fatom[i]*fatom[i]); } } MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world); @@ -111,13 +111,13 @@ int MinCG::iterate(int maxiter) } fmax = 0.0; - if (normstyle == MAX) { // max force norm + if (normstyle == MAX) { // max force norm fmax = fnorm_max(); if (fmax < update->ftol*update->ftol) return FTOL; - } else if (normstyle == INF) { // infinite force norm + } else if (normstyle == INF) { // infinite force norm fmax = fnorm_inf(); if (fmax < update->ftol*update->ftol) return FTOL; - } else if (normstyle == TWO) { // Euclidean force 2-norm + } else if (normstyle == TWO) { // Euclidean force 2-norm if (dotall[0] < update->ftol*update->ftol) return FTOL; } else error->all(FLERR,"Illegal min_modify command"); diff --git a/src/min_fire.cpp b/src/min_fire.cpp index b4b0f14534..3449f431c9 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -251,9 +251,9 @@ int MinFire::iterate(int maxiter) // sync across replicas if running multi-replica minimization if (update->ftol > 0.0) { - if (normstyle == MAX) fdotf = fnorm_max(); // max force norm - else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm - else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + if (normstyle == MAX) fdotf = fnorm_max(); // max force norm + else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm + else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm else error->all(FLERR,"Illegal min_modify command"); if (update->multireplica == 0) { if (fdotf < update->ftol*update->ftol) return FTOL; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 627a3b3cf3..b89682ab5c 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -78,9 +78,9 @@ int MinSD::iterate(int maxiter) // force tolerance criterion - if (normstyle == MAX) fdotf = fnorm_max(); // max force norm - else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm - else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + if (normstyle == MAX) fdotf = fnorm_max(); // max force norm + else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm + else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm else error->all(FLERR,"Illegal min_modify command"); if (fdotf < update->ftol*update->ftol) return FTOL; -- GitLab From b6b022b6107eeb06edcb9c0937e8e4691526ae84 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 3 Nov 2019 11:03:39 -0500 Subject: [PATCH 07/16] whitespace cleanup: remove trailing blanks --- src/CLASS2/pair_lj_class2_coul_long.cpp | 20 +- src/CLASS2/pair_lj_class2_coul_long.h | 2 +- src/KOKKOS/comm_kokkos.cpp | 2 +- src/KOKKOS/domain_kokkos.cpp | 6 +- src/KOKKOS/kokkos.cpp | 2 +- src/KOKKOS/npair_kokkos.cpp | 2 +- src/KOKKOS/pair_kokkos.h | 4 +- src/KOKKOS/pair_snap_kokkos_impl.h | 16 +- src/KOKKOS/sna_kokkos.h | 2 +- src/KOKKOS/sna_kokkos_impl.h | 30 +-- src/KSPACE/ewald_dipole.cpp | 22 +- src/KSPACE/ewald_dipole_spin.cpp | 26 +- src/KSPACE/ewald_dipole_spin.h | 6 +- src/KSPACE/pppm_dipole.cpp | 16 +- src/KSPACE/pppm_dipole.h | 2 +- src/KSPACE/pppm_dipole_spin.cpp | 8 +- src/KSPACE/pppm_dipole_spin.h | 4 +- src/MANYBODY/pair_airebo.cpp | 8 +- src/RIGID/rigid_const.h | 2 +- src/SNAP/pair_snap.cpp | 4 +- src/SNAP/sna.cpp | 40 +-- src/SNAP/sna.h | 4 +- src/SPIN/atom_vec_spin.h | 2 +- src/SPIN/fix_nve_spin.cpp | 2 +- src/SPIN/fix_precession_spin.cpp | 10 +- src/SPIN/fix_precession_spin.h | 4 +- src/SPIN/fix_setforce_spin.cpp | 2 +- src/SPIN/fix_setforce_spin.h | 2 +- src/SPIN/min_spin_cg.cpp | 26 +- src/SPIN/min_spin_lbfgs.cpp | 16 +- src/SPIN/pair_spin.cpp | 2 +- src/SPIN/pair_spin_dipole_cut.cpp | 88 +++---- src/SPIN/pair_spin_dipole_cut.h | 12 +- src/SPIN/pair_spin_dipole_long.cpp | 86 +++---- src/SPIN/pair_spin_dipole_long.h | 12 +- src/USER-CGDNA/pair_oxdna2_excv.cpp | 2 +- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 2 +- src/USER-CGDNA/pair_oxdna_excv.cpp | 2 +- src/USER-CGDNA/pair_oxdna_hbond.cpp | 2 +- src/USER-CGDNA/pair_oxdna_stk.cpp | 4 +- src/USER-MEAMC/meam_setup_done.cpp | 2 +- src/USER-MISC/compute_gyration_shape.cpp | 2 +- src/USER-MISC/compute_hma.cpp | 58 ++--- src/USER-MISC/compute_hma.h | 2 +- src/USER-MISC/pair_cosine_squared.cpp | 6 +- src/USER-MISC/pair_extep.cpp | 2 +- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 4 +- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 6 +- src/USER-MISC/pair_local_density.cpp | 230 +++++++++--------- src/USER-MISC/pair_local_density.h | 22 +- src/USER-MOLFILE/reader_molfile.cpp | 2 +- src/USER-PHONON/dynamical_matrix.cpp | 2 +- src/USER-PLUMED/fix_plumed.cpp | 2 +- src/USER-REAXC/reaxc_ffield.cpp | 2 +- .../pair_lj_switch3_coulgauss_long.cpp | 6 +- .../pair_mm3_switch3_coulgauss_long.cpp | 6 +- src/comm.cpp | 2 +- src/compute_bond_local.cpp | 2 +- src/compute_orientorder_atom.cpp | 10 +- src/fix_neigh_history.cpp | 4 +- src/input.h | 2 +- src/lammps.cpp | 2 +- src/min.cpp | 2 +- src/min.h | 6 +- src/min_cg.cpp | 4 +- src/neighbor.cpp | 6 +- src/read_data.cpp | 2 +- src/read_dump.cpp | 2 +- src/reader_native.cpp | 2 +- 69 files changed, 452 insertions(+), 452 deletions(-) diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index c2b127fa58..1544232e49 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -664,19 +664,19 @@ void PairLJClass2CoulLong::init_style() if (!atom->q_flag) error->all(FLERR, "Pair style lj/class2/coul/long requires atom attribute q"); - + // request regular or rRESPA neighbor list - + int irequest; int respa = 0; - + if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } - + irequest = neighbor->request(this,instance_me); - + if (respa >= 1) { neighbor->requests[irequest]->respaouter = 1; neighbor->requests[irequest]->respainner = 1; @@ -684,13 +684,13 @@ void PairLJClass2CoulLong::init_style() if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; cut_coulsq = cut_coul * cut_coul; - + // set rRESPA cutoffs - + if (strstr(update->integrate_style,"respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; - else cut_respa = NULL; + else cut_respa = NULL; // insure use of KSpace long-range solver, set g_ewald @@ -739,9 +739,9 @@ double PairLJClass2CoulLong::init_one(int i, int j) lj3[j][i] = lj3[i][j]; lj4[j][i] = lj4[i][j]; offset[j][i] = offset[i][j]; - + // check interior rRESPA cutoff - + if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3]) error->all(FLERR,"Pair cutoff < Respa interior cutoff"); diff --git a/src/CLASS2/pair_lj_class2_coul_long.h b/src/CLASS2/pair_lj_class2_coul_long.h index 50d7092541..7b68382295 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.h +++ b/src/CLASS2/pair_lj_class2_coul_long.h @@ -40,7 +40,7 @@ class PairLJClass2CoulLong : public Pair { void write_data(FILE *); void write_data_all(FILE *); double single(int, int, int, int, double, double, double, double &); - + void compute_inner(); void compute_middle(); void compute_outer(int, int); diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index d0bd978ae7..774d7040cc 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -210,7 +210,7 @@ void CommKokkos::forward_comm_device(int dummy) MPI_Send(k_buf_send.view().data(), n,MPI_DOUBLE,sendproc[iswap],0,world); } - + if (size_forward_recv[iswap]) { MPI_Wait(&request,MPI_STATUS_IGNORE); atomKK->modified(ExecutionSpaceFromDevice:: diff --git a/src/KOKKOS/domain_kokkos.cpp b/src/KOKKOS/domain_kokkos.cpp index 4cf3e6ab52..cb4eaddfec 100644 --- a/src/KOKKOS/domain_kokkos.cpp +++ b/src/KOKKOS/domain_kokkos.cpp @@ -340,11 +340,11 @@ struct DomainPBCFunctor { void DomainKokkos::pbc() { - + if (lmp->kokkos->exchange_comm_classic) { - + // reduce GPU data movement - + atomKK->sync(Host,X_MASK|V_MASK|MASK_MASK|IMAGE_MASK); Domain::pbc(); atomKK->modified(Host,X_MASK|V_MASK|MASK_MASK|IMAGE_MASK); diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 18dff991b2..720dd3b3b2 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -187,7 +187,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) binsize = 0.0; #ifdef KOKKOS_ENABLE_CUDA - cuda_aware_flag = 1; + cuda_aware_flag = 1; #else cuda_aware_flag = 0; #endif diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 5470001967..dc0efbc193 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -101,7 +101,7 @@ void NPairKokkos::copy_stencil_info() // copy stencil to device as it may have changed int maxstencil = ns->get_maxstencil(); - + if (maxstencil > k_stencil.extent(0)) k_stencil = DAT::tdual_int_1d("neighlist:stencil",maxstencil); for (int k = 0; k < maxstencil; k++) diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 9ca5d9578d..52a05b3991 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -293,7 +293,7 @@ struct PairComputeFunctor { const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; if(rsq < (STACKPARAMS?c.m_cutsq[itype][jtype]:c.d_cutsq(itype,jtype))) { - + const F_FLOAT fpair = factor_lj*c.template compute_fpair(rsq,i,j,itype,jtype); ftmp.x += delx*fpair; @@ -412,7 +412,7 @@ struct PairComputeFunctor { const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; if(rsq < (STACKPARAMS?c.m_cutsq[itype][jtype]:c.d_cutsq(itype,jtype))) { - + const F_FLOAT fpair = factor_lj*c.template compute_fpair(rsq,i,j,itype,jtype); fev_tmp.f[0] += delx*fpair; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 02c8554fa5..ef01ec5ea3 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -584,7 +584,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeDeidrj,const type const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size()); const int ninside = d_ninside(ii); if (jj >= ninside) return; - + my_sna.compute_deidrj(team,ii,jj); } @@ -619,9 +619,9 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeForce(ev,i,j, @@ -630,7 +630,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeForce::operator() (TagPairSNAPComputeForce::build_indexlist() for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - h_idxcg_block(j1,j2,j) = idxcg_count; + h_idxcg_block(j1,j2,j) = idxcg_count; for (int m1 = 0; m1 <= j1; m1++) for (int m2 = 0; m2 <= j2; m2++) idxcg_count++; @@ -98,9 +98,9 @@ void SNAKokkos::build_indexlist() auto h_idxu_block = Kokkos::create_mirror_view(idxu_block); int idxu_count = 0; - + for(int j = 0; j <= twojmax; j++) { - h_idxu_block[j] = idxu_count; + h_idxu_block[j] = idxu_count; for(int mb = 0; mb <= j; mb++) for(int ma = 0; ma <= j; ma++) idxu_count++; @@ -110,16 +110,16 @@ void SNAKokkos::build_indexlist() // index list for beta and B - int idxb_count = 0; + int idxb_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) if (j >= j1) idxb_count++; - + idxb_max = idxb_count; idxb = Kokkos::View("SNAKokkos::idxb",idxb_max); auto h_idxb = Kokkos::create_mirror_view(idxb); - + idxb_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) @@ -142,7 +142,7 @@ void SNAKokkos::build_indexlist() for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { if (j >= j1) { - h_idxb_block(j1,j2,j) = idxb_count; + h_idxb_block(j1,j2,j) = idxb_count; idxb_count++; } } @@ -158,19 +158,19 @@ void SNAKokkos::build_indexlist() for (int mb = 0; 2*mb <= j; mb++) for (int ma = 0; ma <= j; ma++) idxz_count++; - + idxz_max = idxz_count; idxz = Kokkos::View("SNAKokkos::idxz",idxz_max); auto h_idxz = Kokkos::create_mirror_view(idxz); idxz_block = Kokkos::View("SNAKokkos::idxz_block", jdim,jdim,jdim); auto h_idxz_block = Kokkos::create_mirror_view(idxz_block); - + idxz_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - h_idxz_block(j1,j2,j) = idxz_count; + h_idxz_block(j1,j2,j) = idxz_count; // find right beta(ii,jjb) entry // multiply and divide by j+1 factors @@ -226,7 +226,7 @@ void SNAKokkos::grow_rij(int newnatom, int newnmax) blist = t_sna_2d("sna:blist",natom,idxb_max); ulisttot = t_sna_2c("sna:ulisttot",natom,idxu_max); - if (!Kokkos::Impl::is_same::value) + if (!Kokkos::Impl::is_same::value) ulisttot_lr = t_sna_2c_lr("sna:ulisttot_lr",natom,idxu_max); zlist = t_sna_2c("sna:zlist",natom,idxz_max); @@ -306,7 +306,7 @@ void SNAKokkos::compute_zi(const int& iter) const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); - zlist(iatom,jjz).re = 0.0; + zlist(iatom,jjz).re = 0.0; zlist(iatom,jjz).im = 0.0; int jju1 = idxu_block[j1] + (j1+1)*mb1min; @@ -419,7 +419,7 @@ void SNAKokkos::compute_yi(int iter, if (j1 == j) { if (j2 == j) betaj = 3*beta(iatom,jjb); else betaj = 2*beta(iatom,jjb); - } else betaj = beta(iatom,jjb); + } else betaj = beta(iatom,jjb); } else if (j >= j2) { const int jjb = idxb_block(j,j2,j1); if (j2 == j) betaj = 2*beta(iatom,jjb)*(j1+1)/(j+1.0); @@ -1176,7 +1176,7 @@ void SNAKokkos::init_clebsch_gordan() factorial((j + cc2) / 2) * factorial((j - cc2) / 2) * (j + 1)); - + h_cglist[idxcg_count] = sum * dcg * sfaccg; idxcg_count++; } @@ -1278,7 +1278,7 @@ double SNAKokkos::memory_usage() if (!Kokkos::Impl::is_same::value) bytes += natom * idxu_max * sizeof(double) * 2; // ulisttot_lr bytes += natom * idxu_max * 3 * sizeof(double) * 2; // dulist - + bytes += natom * idxz_max * sizeof(double) * 2; // zlist bytes += natom * idxb_max * sizeof(double); // blist bytes += natom * idxu_max * sizeof(double) * 2; // ylist diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index a003ce91fd..1939742bfc 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -167,7 +167,7 @@ void EwaldDipole::init() NewtonSolve(g_ewald,cutoff,natoms,xprd*yprd*zprd,mu2); if (g_ewald_new > 0.0) g_ewald = g_ewald_new; else error->warning(FLERR,"Ewald/disp Newton solver failed, " - "using old method to estimate g_ewald"); + "using old method to estimate g_ewald"); } // setup EwaldDipole coefficients so can print stats @@ -246,7 +246,7 @@ void EwaldDipole::setup() double err; kxmax = 1; kymax = 1; - kzmax = 1; + kzmax = 1; // set kmax in 3 directions to respect accuracy @@ -462,7 +462,7 @@ void EwaldDipole::compute(int eflag, int vflag) vc[k][4] += vcik[4] = -(partial_peratom * mu[i][0] * eg[k][2]); vc[k][5] += vcik[5] = -(partial_peratom * mu[i][1] * eg[k][2]); - // taking re-part of struct_fact x exp(i*k*ri) + // taking re-part of struct_fact x exp(i*k*ri) // (for per-atom energy and virial calc.) if (evflag_atom) { @@ -653,12 +653,12 @@ void EwaldDipole::eik_dot_r() muz = mu[i][2]; // dir 1: (0,l,m) - mudotk = (muy*l*unitk[1] + muz*m*unitk[2]); + mudotk = (muy*l*unitk[1] + muz*m*unitk[2]); cstr1 += mudotk*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]); sstr1 += mudotk*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]); // dir 2: (0,l,-m) - mudotk = (muy*l*unitk[1] - muz*m*unitk[2]); + mudotk = (muy*l*unitk[1] - muz*m*unitk[2]); cstr2 += mudotk*(cs[l][1][i]*cs[m][2][i]+sn[l][1][i]*sn[m][2][i]); sstr2 += mudotk*(sn[l][1][i]*cs[m][2][i]-cs[l][1][i]*sn[m][2][i]); } @@ -685,12 +685,12 @@ void EwaldDipole::eik_dot_r() muz = mu[i][2]; // dir 1: (k,0,m) - mudotk = (mux*k*unitk[0] + muz*m*unitk[2]); + mudotk = (mux*k*unitk[0] + muz*m*unitk[2]); cstr1 += mudotk*(cs[k][0][i]*cs[m][2][i]-sn[k][0][i]*sn[m][2][i]); sstr1 += mudotk*(sn[k][0][i]*cs[m][2][i]+cs[k][0][i]*sn[m][2][i]); // dir 2: (k,0,-m) - mudotk = (mux*k*unitk[0] - muz*m*unitk[2]); + mudotk = (mux*k*unitk[0] - muz*m*unitk[2]); cstr2 += mudotk*(cs[k][0][i]*cs[m][2][i]+sn[k][0][i]*sn[m][2][i]); sstr2 += mudotk*(sn[k][0][i]*cs[m][2][i]-cs[k][0][i]*sn[m][2][i]); } @@ -724,28 +724,28 @@ void EwaldDipole::eik_dot_r() muz = mu[i][2]; // dir 1: (k,l,m) - mudotk = (mux*k*unitk[0] + muy*l*unitk[1] + muz*m*unitk[2]); + mudotk = (mux*k*unitk[0] + muy*l*unitk[1] + muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr1 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr1 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); // dir 2: (k,-l,m) - mudotk = (mux*k*unitk[0] - muy*l*unitk[1] + muz*m*unitk[2]); + mudotk = (mux*k*unitk[0] - muy*l*unitk[1] + muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr2 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr2 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); // dir 3: (k,l,-m) - mudotk = (mux*k*unitk[0] + muy*l*unitk[1] - muz*m*unitk[2]); + mudotk = (mux*k*unitk[0] + muy*l*unitk[1] - muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr3 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr3 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); // dir 4: (k,-l,-m) - mudotk = (mux*k*unitk[0] - muy*l*unitk[1] - muz*m*unitk[2]); + mudotk = (mux*k*unitk[0] - muy*l*unitk[1] - muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr4 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index 531f4cdec5..82832f6e4c 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -36,7 +36,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -EwaldDipoleSpin::EwaldDipoleSpin(LAMMPS *lmp) : +EwaldDipoleSpin::EwaldDipoleSpin(LAMMPS *lmp) : EwaldDipole(lmp) { dipoleflag = 0; @@ -157,7 +157,7 @@ void EwaldDipoleSpin::init() NewtonSolve(g_ewald,cutoff,natoms,xprd*yprd*zprd,mu2); if (g_ewald_new > 0.0) g_ewald = g_ewald_new; else error->warning(FLERR,"Ewald/disp Newton solver failed, " - "using old method to estimate g_ewald"); + "using old method to estimate g_ewald"); } // setup EwaldDipoleSpin coefficients so can print stats @@ -236,7 +236,7 @@ void EwaldDipoleSpin::setup() double err; kxmax = 1; kymax = 1; - kzmax = 1; + kzmax = 1; // set kmax in 3 directions to respect accuracy @@ -440,7 +440,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) vc[k][4] += vcik[4] = -(partial_peratom * spx * eg[k][2]); vc[k][5] += vcik[5] = -(partial_peratom * spy * eg[k][2]); - // taking re-part of struct_fact x exp(i*k*ri) + // taking re-part of struct_fact x exp(i*k*ri) // (for per-atom energy and virial calc.) if (evflag_atom) { @@ -639,12 +639,12 @@ void EwaldDipoleSpin::eik_dot_r() spz = sp[i][2]*sp[i][3]; // dir 1: (0,l,m) - mudotk = (spy*l*unitk[1] + spz*m*unitk[2]); + mudotk = (spy*l*unitk[1] + spz*m*unitk[2]); cstr1 += mudotk*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]); sstr1 += mudotk*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]); // dir 2: (0,l,-m) - mudotk = (spy*l*unitk[1] - spz*m*unitk[2]); + mudotk = (spy*l*unitk[1] - spz*m*unitk[2]); cstr2 += mudotk*(cs[l][1][i]*cs[m][2][i]+sn[l][1][i]*sn[m][2][i]); sstr2 += mudotk*(sn[l][1][i]*cs[m][2][i]-cs[l][1][i]*sn[m][2][i]); } @@ -671,12 +671,12 @@ void EwaldDipoleSpin::eik_dot_r() spz = sp[i][2]*sp[i][3]; // dir 1: (k,0,m) - mudotk = (spx*k*unitk[0] + spz*m*unitk[2]); + mudotk = (spx*k*unitk[0] + spz*m*unitk[2]); cstr1 += mudotk*(cs[k][0][i]*cs[m][2][i]-sn[k][0][i]*sn[m][2][i]); sstr1 += mudotk*(sn[k][0][i]*cs[m][2][i]+cs[k][0][i]*sn[m][2][i]); // dir 2: (k,0,-m) - mudotk = (spx*k*unitk[0] - spz*m*unitk[2]); + mudotk = (spx*k*unitk[0] - spz*m*unitk[2]); cstr2 += mudotk*(cs[k][0][i]*cs[m][2][i]+sn[k][0][i]*sn[m][2][i]); sstr2 += mudotk*(sn[k][0][i]*cs[m][2][i]-cs[k][0][i]*sn[m][2][i]); } @@ -710,28 +710,28 @@ void EwaldDipoleSpin::eik_dot_r() spz = sp[i][2]*sp[i][3]; // dir 1: (k,l,m) - mudotk = (spx*k*unitk[0] + spy*l*unitk[1] + spz*m*unitk[2]); + mudotk = (spx*k*unitk[0] + spy*l*unitk[1] + spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr1 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr1 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); // dir 2: (k,-l,m) - mudotk = (spx*k*unitk[0] - spy*l*unitk[1] + spz*m*unitk[2]); + mudotk = (spx*k*unitk[0] - spy*l*unitk[1] + spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr2 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr2 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); // dir 3: (k,l,-m) - mudotk = (spx*k*unitk[0] + spy*l*unitk[1] - spz*m*unitk[2]); + mudotk = (spx*k*unitk[0] + spy*l*unitk[1] - spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr3 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr3 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); // dir 4: (k,-l,-m) - mudotk = (spx*k*unitk[0] - spy*l*unitk[1] - spz*m*unitk[2]); + mudotk = (spx*k*unitk[0] - spy*l*unitk[1] - spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr4 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); @@ -768,7 +768,7 @@ void EwaldDipoleSpin::slabcorr() double spz; int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { spz = sp[i][2]*sp[i][3]; spin += spz; } diff --git a/src/KSPACE/ewald_dipole_spin.h b/src/KSPACE/ewald_dipole_spin.h index 20852c08c1..32c7ddb5f1 100644 --- a/src/KSPACE/ewald_dipole_spin.h +++ b/src/KSPACE/ewald_dipole_spin.h @@ -33,13 +33,13 @@ class EwaldDipoleSpin : public EwaldDipole { void compute(int, int); protected: - double hbar; // reduced Planck's constant - double mub; // Bohr's magneton + double hbar; // reduced Planck's constant + double mub; // Bohr's magneton double mu_0; // vacuum permeability double mub2mu0; // prefactor for mech force double mub2mu0hbinv; // prefactor for mag force - void spsum_musq(); + void spsum_musq(); virtual void eik_dot_r(); void slabcorr(); diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 5d69ca27b6..40d0c1ac73 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -58,19 +58,19 @@ enum{FORWARD_MU,FORWARD_MU_PERATOM}; /* ---------------------------------------------------------------------- */ PPPMDipole::PPPMDipole(LAMMPS *lmp) : PPPM(lmp), - densityx_brick_dipole(NULL), densityy_brick_dipole(NULL), + densityx_brick_dipole(NULL), densityy_brick_dipole(NULL), densityz_brick_dipole(NULL), vdxx_brick_dipole(NULL), vdyy_brick_dipole(NULL), vdzz_brick_dipole(NULL), vdxy_brick_dipole(NULL), vdxz_brick_dipole(NULL), vdyz_brick_dipole(NULL), ux_brick_dipole(NULL), uy_brick_dipole(NULL), uz_brick_dipole(NULL), v0x_brick_dipole(NULL), v1x_brick_dipole(NULL), - v2x_brick_dipole(NULL), v3x_brick_dipole(NULL), v4x_brick_dipole(NULL), - v5x_brick_dipole(NULL), v0y_brick_dipole(NULL), v1y_brick_dipole(NULL), - v2y_brick_dipole(NULL), v3y_brick_dipole(NULL), v4y_brick_dipole(NULL), - v5y_brick_dipole(NULL), v0z_brick_dipole(NULL), v1z_brick_dipole(NULL), - v2z_brick_dipole(NULL), v3z_brick_dipole(NULL), v4z_brick_dipole(NULL), - v5z_brick_dipole(NULL), work3(NULL), work4(NULL), - densityx_fft_dipole(NULL), densityy_fft_dipole(NULL), + v2x_brick_dipole(NULL), v3x_brick_dipole(NULL), v4x_brick_dipole(NULL), + v5x_brick_dipole(NULL), v0y_brick_dipole(NULL), v1y_brick_dipole(NULL), + v2y_brick_dipole(NULL), v3y_brick_dipole(NULL), v4y_brick_dipole(NULL), + v5y_brick_dipole(NULL), v0z_brick_dipole(NULL), v1z_brick_dipole(NULL), + v2z_brick_dipole(NULL), v3z_brick_dipole(NULL), v4z_brick_dipole(NULL), + v5z_brick_dipole(NULL), work3(NULL), work4(NULL), + densityx_fft_dipole(NULL), densityy_fft_dipole(NULL), densityz_fft_dipole(NULL) { dipoleflag = 1; diff --git a/src/KSPACE/pppm_dipole.h b/src/KSPACE/pppm_dipole.h index d06919644b..a767f8b4c2 100644 --- a/src/KSPACE/pppm_dipole.h +++ b/src/KSPACE/pppm_dipole.h @@ -38,7 +38,7 @@ class PPPMDipole : public PPPM { protected: void set_grid_global(); - double newton_raphson_f(); + double newton_raphson_f(); void allocate(); void allocate_peratom(); diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 38757ced21..7f7745eb3e 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -52,7 +52,7 @@ enum{FORWARD_MU,FORWARD_MU_PERATOM}; /* ---------------------------------------------------------------------- */ -PPPMDipoleSpin::PPPMDipoleSpin(LAMMPS *lmp) : +PPPMDipoleSpin::PPPMDipoleSpin(LAMMPS *lmp) : PPPMDipole(lmp) { dipoleflag = 0; @@ -147,7 +147,7 @@ void PPPMDipoleSpin::init() // kspace TIP4P not yet supported // qdist = offset only for TIP4P fictitious charge - qdist = 0.0; + qdist = 0.0; if (tip4pflag) error->all(FLERR,"Cannot yet use TIP4P with PPPMDipoleSpin"); @@ -668,7 +668,7 @@ void PPPMDipoleSpin::slabcorr() double spz; int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { spz = sp[i][2]*sp[i][3]; spin += spz; } @@ -729,7 +729,7 @@ void PPPMDipoleSpin::spsum_spsq() spsqsum_local += spx*spx + spy*spy + spz*spz; } - // store results into pppm_dipole quantities + // store results into pppm_dipole quantities MPI_Allreduce(&spsum_local,&musum,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&spsqsum_local,&musqsum,1,MPI_DOUBLE,MPI_SUM,world); diff --git a/src/KSPACE/pppm_dipole_spin.h b/src/KSPACE/pppm_dipole_spin.h index 2b4a989d5c..fe88fc75ce 100644 --- a/src/KSPACE/pppm_dipole_spin.h +++ b/src/KSPACE/pppm_dipole_spin.h @@ -32,8 +32,8 @@ class PPPMDipoleSpin : public PPPMDipole { void compute(int, int); protected: - double hbar; // reduced Planck's constant - double mub; // Bohr's magneton + double hbar; // reduced Planck's constant + double mub; // Bohr's magneton double mu_0; // vacuum permeability double mub2mu0; // prefactor for mech force double mub2mu0hbinv; // prefactor for mag force diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 7cdffa7ea9..1d9dd18887 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -3638,9 +3638,9 @@ void PairAIREBO::read_file(char *filename) utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (1 != sscanf(s,"%lg",&reqM_HH)) ++cerror; } - + } - + // check for errors parsing global parameters MPI_Bcast(&cerror,1,MPI_INT,0,world); @@ -3654,7 +3654,7 @@ void PairAIREBO::read_file(char *filename) cerror = numpar = 0; if (me == 0) { - + // gC spline utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); @@ -3899,7 +3899,7 @@ void PairAIREBO::read_file(char *filename) fclose(fp); } - + // check for errors parsing spline data MPI_Bcast(&cerror,1,MPI_INT,0,world); diff --git a/src/RIGID/rigid_const.h b/src/RIGID/rigid_const.h index 14db517fcd..3aae988197 100644 --- a/src/RIGID/rigid_const.h +++ b/src/RIGID/rigid_const.h @@ -32,7 +32,7 @@ namespace LAMMPS_NS { ANGMOM = 1<<7, TORQUE = 1<<8 }; - + static const double TOLERANCE = 1.0e-6; static const double EPSILON = 1.0e-7; static const double BIG = 1.0e20; diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 133f0e414b..6f7cf54659 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -108,7 +108,7 @@ void PairSNAP::compute(int eflag, int vflag) // compute dE_i/dB_i = beta_i for all i in list - if (quadraticflag || eflag) + if (quadraticflag || eflag) compute_bispectrum(); compute_beta(); @@ -165,7 +165,7 @@ void PairSNAP::compute(int eflag, int vflag) snaptr->compute_ui(ninside); // for neighbors of I within cutoff: - // compute Fij = dEi/dRj = -dEi/dRi + // compute Fij = dEi/dRj = -dEi/dRi // add to Fi, subtract from Fj snaptr->compute_yi(beta[ii]); diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 9e8768c477..99834635b7 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -171,7 +171,7 @@ void SNA::build_indexlist() for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - idxcg_block[j1][j2][j] = idxcg_count; + idxcg_block[j1][j2][j] = idxcg_count; for (int m1 = 0; m1 <= j1; m1++) for (int m2 = 0; m2 <= j2; m2++) idxcg_count++; @@ -185,9 +185,9 @@ void SNA::build_indexlist() "sna:idxu_block"); int idxu_count = 0; - + for(int j = 0; j <= twojmax; j++) { - idxu_block[j] = idxu_count; + idxu_block[j] = idxu_count; for(int mb = 0; mb <= j; mb++) for(int ma = 0; ma <= j; ma++) idxu_count++; @@ -196,15 +196,15 @@ void SNA::build_indexlist() // index list for beta and B - int idxb_count = 0; + int idxb_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) if (j >= j1) idxb_count++; - + idxb_max = idxb_count; idxb = new SNA_BINDICES[idxb_max]; - + idxb_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) @@ -225,7 +225,7 @@ void SNA::build_indexlist() for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { if (j >= j1) { - idxb_block[j1][j2][j] = idxb_count; + idxb_block[j1][j2][j] = idxb_count; idxb_count++; } } @@ -240,18 +240,18 @@ void SNA::build_indexlist() for (int mb = 0; 2*mb <= j; mb++) for (int ma = 0; ma <= j; ma++) idxz_count++; - + idxz_max = idxz_count; idxz = new SNA_ZINDICES[idxz_max]; - + memory->create(idxz_block, jdim, jdim, jdim, "sna:idxz_block"); - + idxz_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { - idxz_block[j1][j2][j] = idxz_count; + idxz_block[j1][j2][j] = idxz_count; // find right beta[jjb] entry // multiply and divide by j+1 factors @@ -481,7 +481,7 @@ void SNA::compute_yi(const double* beta) if (j1 == j) { if (j2 == j) betaj = 3*beta[jjb]; else betaj = 2*beta[jjb]; - } else betaj = beta[jjb]; + } else betaj = beta[jjb]; } else if (j >= j2) { const int jjb = idxb_block[j][j2][j1]; if (j2 == j) betaj = 2*beta[jjb]*(j1+1)/(j+1.0); @@ -549,7 +549,7 @@ void SNA::compute_deidrj(double* dedr) double jjjmambyarray_i = ylist_i[jju]; for(int k = 0; k < 3; k++) - dedr[k] += + dedr[k] += (dudr_r[k] * jjjmambyarray_r + dudr_i[k] * jjjmambyarray_i)*0.5; jju++; @@ -588,24 +588,24 @@ void SNA::compute_bi() double sumzu = 0.0; for (int mb = 0; 2*mb < j; mb++) for (int ma = 0; ma <= j; ma++) { - sumzu += ulisttot_r[jju]*zlist_r[jjz] + + sumzu += ulisttot_r[jju]*zlist_r[jjz] + ulisttot_i[jju]*zlist_i[jjz]; jjz++; jju++; - } // end loop over ma, mb + } // end loop over ma, mb // For j even, handle middle column if (j%2 == 0) { int mb = j/2; for(int ma = 0; ma < mb; ma++) { - sumzu += ulisttot_r[jju]*zlist_r[jjz] + + sumzu += ulisttot_r[jju]*zlist_r[jjz] + ulisttot_i[jju]*zlist_i[jjz]; jjz++; jju++; } - sumzu += 0.5*(ulisttot_r[jju]*zlist_r[jjz] + + sumzu += 0.5*(ulisttot_r[jju]*zlist_r[jjz] + ulisttot_i[jju]*zlist_i[jjz]); } // end if jeven @@ -1485,7 +1485,7 @@ void SNA::init_clebsch_gordan() factorial((j - j2 + aa2) / 2 + z) * factorial((j - j1 - bb2) / 2 + z)); } - + cc2 = 2 * m - j; dcg = deltacg(j1, j2, j); sfaccg = sqrt(factorial((j1 + aa2) / 2) * @@ -1495,7 +1495,7 @@ void SNA::init_clebsch_gordan() factorial((j + cc2) / 2) * factorial((j - cc2) / 2) * (j + 1)); - + cglist[idxcg_count] = sum * dcg * sfaccg; idxcg_count++; } @@ -1519,7 +1519,7 @@ void SNA::print_clebsch_gordan() for (int j1 = 0; j1 <= twojmax; j1++) for (int j2 = 0; j2 <= j1; j2++) if (j1-j2 <= j && j1+j2 >= j && (j1+j2+j)%2 == 0) { - int idxcg_count = idxcg_block[j1][j2][j]; + int idxcg_count = idxcg_block[j1][j2][j]; for (int m1 = 0; m1 <= j1; m1++) { aa2 = 2*m1-j1; for (int m2 = 0; m2 <= j2; m2++) { diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h index 5ea65fd84b..16d3338277 100644 --- a/src/SNAP/sna.h +++ b/src/SNAP/sna.h @@ -81,8 +81,8 @@ private: int idxcg_max, idxu_max, idxz_max, idxb_max; double** rootpqarray; - double* cglist; - int*** idxcg_block; + double* cglist; + int*** idxcg_block; double* ulisttot_r, * ulisttot_i; double** ulist_r_ij, ** ulist_i_ij; diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index a31e57bb48..6ce2c9dc7d 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -68,7 +68,7 @@ class AtomVecSpin : public AtomVec { int *type,*mask; imageint *image; double **x,**v,**f; // lattice quantities - + // spin quantities double **sp; // sp[i][0-2] direction of the spin i // sp[i][3] atomic magnetic moment of the spin i diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 87546ba9da..462a359d99 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -247,7 +247,7 @@ void FixNVESpin::init() locksetforcespin = (FixSetForceSpin *) modify->fix[iforce]; } } - + // setting the sector variables/lists nsectors = 0; diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 97dbe7ba6f..e1f24e36c2 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -126,7 +126,7 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm nay *= inorm; naz *= inorm; } - + if (cubic_flag) { inorm = 1.0/sqrt(nc1x*nc1x + nc1y*nc1y + nc1z*nc1z); nc1x *= inorm; @@ -244,7 +244,7 @@ void FixPrecessionSpin::post_force(int /* vflag */) double **sp = atom->sp; const int nlocal = atom->nlocal; double spi[3], fmi[3], epreci; - + eflag = 0; eprec = 0.0; for (int i = 0; i < nlocal; i++) { @@ -317,7 +317,7 @@ double FixPrecessionSpin::compute_anisotropy_energy(double spi[3]) double energy = 0.0; double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2]; energy = Ka*scalar*scalar; - return energy; + return energy; } /* ---------------------------------------------------------------------- */ @@ -391,11 +391,11 @@ void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3]) six1 = 2.0*skx*sky2*skz2; six2 = 2.0*sky*skx2*skz2; six3 = 2.0*skz*skx2*sky2; - + sixx = k2ch*(nc1x*six1 + nc2x*six2 + nc3x*six3); sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3); sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3); - + fmi[0] += fourx + sixx; fmi[1] += foury + sixy; fmi[2] += fourz + sixz; diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index 96d89e004e..6ece653ca7 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -42,7 +42,7 @@ class FixPrecessionSpin : public Fix { int zeeman_flag, aniso_flag, cubic_flag; void compute_single_precession(int, double *, double *); void compute_zeeman(int, double *); - + // uniaxial aniso calculations void compute_anisotropy(double *, double *); @@ -52,7 +52,7 @@ class FixPrecessionSpin : public Fix { void compute_cubic(double *, double *); double compute_cubic_energy(double *); - + protected: int style; // style of the magnetic precession diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index e36a9d260d..ec738b7522 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -140,7 +140,7 @@ void FixSetForceSpin::single_setforce_spin(int i, double fmi[3]) foriginal[0] = foriginal[1] = foriginal[2] = 0.0; force_flag = 0; - + // constant force if (varflag == CONSTANT) { diff --git a/src/SPIN/fix_setforce_spin.h b/src/SPIN/fix_setforce_spin.h index a836911d85..1c5ce54dd3 100644 --- a/src/SPIN/fix_setforce_spin.h +++ b/src/SPIN/fix_setforce_spin.h @@ -29,7 +29,7 @@ class FixSetForceSpin : public FixSetForce { FixSetForceSpin(class LAMMPS *, int, char **); virtual void post_force(int); void post_force_respa(int, int, int); - void single_setforce_spin(int, double *); + void single_setforce_spin(int, double *); }; } diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index 9c8c814bc4..8815ad89db 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -16,8 +16,8 @@ Julien Tranchida (SNL) Please cite the related publication: - Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust - Algorithm for the Minimisation of the Energy of Spin Systems. arXiv + Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust + Algorithm for the Minimisation of the Energy of Spin Systems. arXiv preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ @@ -105,7 +105,7 @@ void MinSpinCG::init() error->warning(FLERR,"Line search incompatible gneb"); // set back use_line_search to 0 if more than one replica - + if (linestyle == 3 && nreplica == 1){ use_line_search = 1; } @@ -201,10 +201,10 @@ int MinSpinCG::iterate(int maxiter) if (timer->check_timeout(niter)) return TIMEOUT; - + ntimestep = ++update->ntimestep; niter++; - + // optimize timestep accross processes / replicas // need a force calculation for timestep optimization @@ -249,7 +249,7 @@ int MinSpinCG::iterate(int maxiter) // energy tolerance criterion // only check after DELAYSTEP elapsed since velocties reset to 0 // sync across replicas if running multi-replica minimization - + if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { if (update->multireplica == 0) { if (fabs(ecurrent-eprevious) < @@ -365,7 +365,7 @@ void MinSpinCG::calc_search_direction() MPI_Allreduce(&g2old,&g2old_global,1,MPI_DOUBLE,MPI_SUM,world); // Sum over all replicas. Good for GNEB. - + if (nreplica > 1) { g2 = g2_global * factor; g2old = g2old_global * factor; @@ -374,9 +374,9 @@ void MinSpinCG::calc_search_direction() } if (fabs(g2_global) < 1.0e-60) beta = 0.0; else beta = g2_global / g2old_global; - + // calculate conjugate direction - + for (int i = 0; i < 3 * nlocal; i++) { p_s[i] = (beta * p_s[i] - g_cur[i]) * factor; g_old[i] = g_cur[i] * factor; @@ -401,9 +401,9 @@ void MinSpinCG::advance_spins() for (int i = 0; i < nlocal; i++) { rodrigues_rotation(p_s + 3 * i, rot_mat); - + // rotate spins - + vm3(rot_mat, sp[i], s_new); for (int j = 0; j < 3; j++) sp[i][j] = s_new[j]; } @@ -414,7 +414,7 @@ void MinSpinCG::advance_spins() (R. Murray, Z. Li, and S. Shankar Sastry, A Mathematical Introduction to Robotic Manipulation (1994), p. 28 and 30). - + upp_tr - vector x, y, z so that one calculate U = exp(A) with A= [[0, x, y], [-x, 0, z], @@ -431,7 +431,7 @@ void MinSpinCG::rodrigues_rotation(const double *upp_tr, double *out) fabs(upp_tr[2]) < 1.0e-40){ // if upp_tr is zero, return unity matrix - + for(int k = 0; k < 3; k++){ for(int m = 0; m < 3; m++){ if (m == k) out[3 * k + m] = 1.0; diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index a1ee010f3f..7f6d7692cd 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -16,8 +16,8 @@ Julien Tranchida (SNL) Please cite the related publication: - Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust - Algorithm for the Minimisation of the Energy of Spin Systems. arXiv + Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust + Algorithm for the Minimisation of the Energy of Spin Systems. arXiv preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ @@ -213,10 +213,10 @@ int MinSpinLBFGS::iterate(int maxiter) if (timer->check_timeout(niter)) return TIMEOUT; - + ntimestep = ++update->ntimestep; niter++; - + // optimize timestep accross processes / replicas // need a force calculation for timestep optimization @@ -264,7 +264,7 @@ int MinSpinLBFGS::iterate(int maxiter) // energy tolerance criterion // only check after DELAYSTEP elapsed since velocties reset to 0 // sync across replicas if running multi-replica minimization - + if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { if (update->multireplica == 0) { if (fabs(ecurrent-eprevious) < @@ -526,9 +526,9 @@ void MinSpinLBFGS::advance_spins() for (int i = 0; i < nlocal; i++) { rodrigues_rotation(p_s + 3 * i, rot_mat); - + // rotate spins - + vm3(rot_mat, sp[i], s_new); for (int j = 0; j < 3; j++) sp[i][j] = s_new[j]; } @@ -539,7 +539,7 @@ void MinSpinLBFGS::advance_spins() (R. Murray, Z. Li, and S. Shankar Sastry, A Mathematical Introduction to Robotic Manipulation (1994), p. 28 and 30). - + upp_tr - vector x, y, z so that one calculate U = exp(A) with A= [[0, x, y], [-x, 0, z], diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index d956729e60..f167e3455c 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -82,7 +82,7 @@ void PairSpin::init_style() bool have_fix = ((modify->find_fix_by_style("^nve/spin") != -1) || (modify->find_fix_by_style("^neb/spin") != -1)); - + if (!have_fix && (comm->me == 0)) error->warning(FLERR,"Using spin pair style without nve/spin or neb/spin"); diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index bae09689de..a393fe7021 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -76,9 +76,9 @@ void PairSpinDipoleCut::settings(int narg, char **arg) PairSpin::settings(narg,arg); cut_spin_long_global = force->numeric(FLERR,arg[0]); - + // reset cutoffs that have been explicitly set - + if (allocated) { int i,j; for (i = 1; i <= atom->ntypes; i++) { @@ -99,10 +99,10 @@ void PairSpinDipoleCut::settings(int narg, char **arg) void PairSpinDipoleCut::coeff(int narg, char **arg) { if (!allocated) allocate(); - - if (narg != 3) + + if (narg != 3) error->all(FLERR,"Incorrect args in pair_style command"); - + int ilo,ihi,jlo,jhi; force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); @@ -128,9 +128,9 @@ void PairSpinDipoleCut::coeff(int narg, char **arg) double PairSpinDipoleCut::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - + cut_spin_long[j][i] = cut_spin_long[i][j]; - + return cut_spin_long_global; } @@ -163,8 +163,8 @@ void *PairSpinDipoleCut::extract(const char *str, int &dim) void PairSpinDipoleCut::compute(int eflag, int vflag) { - int i,j,ii,jj,inum,jnum,itype,jtype; - int *ilist,*jlist,*numneigh,**firstneigh; + int i,j,ii,jj,inum,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; double rinv,r2inv,r3inv,rsq,local_cut2,evdwl,ecoul; double xi[3],rij[3],eij[3],spi[4],spj[4],fi[3],fmi[3]; @@ -172,13 +172,13 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = 0; - int *type = atom->type; - int nlocal = atom->nlocal; + int *type = atom->type; + int nlocal = atom->nlocal; int newton_pair = force->newton_pair; double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; inum = list->inum; ilist = list->ilist; @@ -194,9 +194,9 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) xi[1] = x[i][1]; xi[2] = x[i][2]; jlist = firstneigh[i]; - jnum = numneigh[i]; - spi[0] = sp[i][0]; - spi[1] = sp[i][1]; + jnum = numneigh[i]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; spi[2] = sp[i][2]; spi[3] = sp[i][3]; itype = type[i]; @@ -206,15 +206,15 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) j &= NEIGHMASK; jtype = type[j]; - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - spj[3] = sp[j][3]; + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + spj[3] = sp[j][3]; evdwl = 0.0; fi[0] = fi[1] = fi[2] = 0.0; fmi[0] = fmi[1] = fmi[2] = 0.0; - + rij[0] = x[j][0] - xi[0]; rij[1] = x[j][1] - xi[1]; rij[2] = x[j][2] - xi[2]; @@ -229,23 +229,23 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) if (rsq < local_cut2) { r2inv = 1.0/rsq; r3inv = r2inv*rinv; - + compute_dipolar(i,j,eij,fmi,spi,spj,r3inv); if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv); } // force accumulation - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; fm[i][0] += fmi[0]; fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } @@ -269,21 +269,21 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) { - int j,jnum,itype,jtype,ntypes; - int *jlist,*numneigh,**firstneigh; + int j,jnum,itype,jtype,ntypes; + int *jlist,*numneigh,**firstneigh; double rsq,rinv,r2inv,r3inv,local_cut2; double xi[3],rij[3],eij[3],spi[4],spj[4]; int k,locflag; - int *type = atom->type; + int *type = atom->type; double **x = atom->x; - double **sp = atom->sp; + double **sp = atom->sp; numneigh = list->numneigh; firstneigh = list->firstneigh; // check if interaction applies to type of ii - + itype = type[ii]; ntypes = atom->ntypes; locflag = 0; @@ -307,28 +307,28 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) // if interaction applies to type ii, // locflag = 1 and compute pair interaction - + if (locflag == 1) { xi[0] = x[ii][0]; xi[1] = x[ii][1]; xi[2] = x[ii][2]; - spi[0] = sp[ii][0]; - spi[1] = sp[ii][1]; + spi[0] = sp[ii][0]; + spi[1] = sp[ii][1]; spi[2] = sp[ii][2]; spi[3] = sp[ii][3]; jlist = firstneigh[ii]; - jnum = numneigh[ii]; - + jnum = numneigh[ii]; + for (int jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; jtype = type[j]; - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - spj[3] = sp[j][3]; + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + spj[3] = sp[j][3]; rij[0] = x[j][0] - xi[0]; rij[1] = x[j][1] - xi[1]; @@ -344,9 +344,9 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) if (rsq < local_cut2) { r2inv = 1.0/rsq; r3inv = r2inv*rinv; - + // compute dipolar interaction - + compute_dipolar(ii,j,eij,fmi,spi,spj,r3inv); } } @@ -357,7 +357,7 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) compute dipolar interaction between spins i and j ------------------------------------------------------------------------- */ -void PairSpinDipoleCut::compute_dipolar(int /* i */, int /* j */, double eij[3], +void PairSpinDipoleCut::compute_dipolar(int /* i */, int /* j */, double eij[3], double fmi[3], double spi[4], double spj[4], double r3inv) { double sjdotr; @@ -373,7 +373,7 @@ void PairSpinDipoleCut::compute_dipolar(int /* i */, int /* j */, double eij[3], } /* ---------------------------------------------------------------------- - compute the mechanical force due to the dipolar interaction between + compute the mechanical force due to the dipolar interaction between atom i and atom j ------------------------------------------------------------------------- */ @@ -387,7 +387,7 @@ void PairSpinDipoleCut::compute_dipolar_mech(int /* i */, int /* j */, double ei sisj = spi[0]*spj[0] + spi[1]*spj[1] + spi[2]*spj[2]; sieij = spi[0]*eij[0] + spi[1]*eij[1] + spi[2]*eij[2]; sjeij = spj[0]*eij[0] + spj[1]*eij[1] + spj[2]*eij[2]; - + bij = sisj - 5.0*sieij*sjeij; pre = 3.0*mub2mu0*gigjri4; diff --git a/src/SPIN/pair_spin_dipole_cut.h b/src/SPIN/pair_spin_dipole_cut.h index 33f62d1633..3adceaf1c7 100644 --- a/src/SPIN/pair_spin_dipole_cut.h +++ b/src/SPIN/pair_spin_dipole_cut.h @@ -34,22 +34,22 @@ class PairSpinDipoleCut : public PairSpin { void settings(int, char **); void coeff(int, char **); double init_one(int, int); - void *extract(const char *, int &); - + void *extract(const char *, int &); + void compute(int, int); void compute_single_pair(int, double *); - void compute_dipolar(int, int, double *, double *, double *, + void compute_dipolar(int, int, double *, double *, double *, double *, double); - void compute_dipolar_mech(int, int, double *, double *, double *, + void compute_dipolar_mech(int, int, double *, double *, double *, double *, double); void write_restart(FILE *); void read_restart(FILE *); void write_restart_settings(FILE *); void read_restart_settings(FILE *); - - double cut_spin_long_global; // global long cutoff distance + + double cut_spin_long_global; // global long cutoff distance protected: double hbar; // reduced Planck's constant diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 3805eb3291..356f73a809 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -81,9 +81,9 @@ void PairSpinDipoleLong::settings(int narg, char **arg) PairSpin::settings(narg,arg); cut_spin_long_global = force->numeric(FLERR,arg[0]); - + // reset cutoffs that have been explicitly set - + if (allocated) { int i,j; for (i = 1; i <= atom->ntypes; i++) { @@ -103,10 +103,10 @@ void PairSpinDipoleLong::settings(int narg, char **arg) void PairSpinDipoleLong::coeff(int narg, char **arg) { if (!allocated) allocate(); - + if (narg != 3) error->all(FLERR,"Incorrect args in pair_style command"); - + int ilo,ihi,jlo,jhi; force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); @@ -148,9 +148,9 @@ void PairSpinDipoleLong::init_style() double PairSpinDipoleLong::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - + cut_spin_long[j][i] = cut_spin_long[i][j]; - + return cut_spin_long_global; } @@ -183,7 +183,7 @@ void *PairSpinDipoleLong::extract(const char *str, int &dim) void PairSpinDipoleLong::compute(int eflag, int vflag) { - int i,j,ii,jj,inum,jnum,itype,jtype; + int i,j,ii,jj,inum,jnum,itype,jtype; double r,rinv,r2inv,rsq; double grij,expm2,t,erfc; double evdwl,ecoul; @@ -193,7 +193,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) double fi[3],fmi[3]; double local_cut2; double pre1,pre2,pre3; - int *ilist,*jlist,*numneigh,**firstneigh; + int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); @@ -202,9 +202,9 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; - int *type = atom->type; - int nlocal = atom->nlocal; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; int newton_pair = force->newton_pair; inum = list->inum; @@ -225,9 +225,9 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) xi[1] = x[i][1]; xi[2] = x[i][2]; jlist = firstneigh[i]; - jnum = numneigh[i]; - spi[0] = sp[i][0]; - spi[1] = sp[i][1]; + jnum = numneigh[i]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; spi[2] = sp[i][2]; spi[3] = sp[i][3]; itype = type[i]; @@ -237,17 +237,17 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) j &= NEIGHMASK; jtype = type[j]; - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - spj[3] = sp[j][3]; + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + spj[3] = sp[j][3]; evdwl = 0.0; fi[0] = fi[1] = fi[2] = 0.0; fmi[0] = fmi[1] = fmi[2] = 0.0; bij[0] = bij[1] = bij[2] = bij[3] = 0.0; - + rij[0] = x[j][0] - xi[0]; rij[1] = x[j][1] - xi[1]; rij[2] = x[j][2] - xi[2]; @@ -279,22 +279,22 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) // force accumulation - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { if (rsq <= local_cut2) { - evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + + evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]; evdwl *= hbar; } @@ -314,21 +314,21 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) { - int j,jj,jnum,itype,jtype,ntypes; + int j,jj,jnum,itype,jtype,ntypes; int k,locflag; - int *jlist,*numneigh,**firstneigh; + int *jlist,*numneigh,**firstneigh; double r,rinv,r2inv,rsq,grij,expm2,t,erfc; double local_cut2,pre1,pre2,pre3; double bij[4],xi[3],rij[3],eij[3],spi[4],spj[4]; - int *type = atom->type; + int *type = atom->type; double **x = atom->x; - double **sp = atom->sp; + double **sp = atom->sp; double **fm_long = atom->fm_long; numneigh = list->numneigh; firstneigh = list->firstneigh; - + // check if interaction applies to type of ii itype = type[ii]; @@ -362,16 +362,16 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) // computation of the exchange interaction // loop over neighbors of atom i - + xi[0] = x[ii][0]; xi[1] = x[ii][1]; xi[2] = x[ii][2]; - spi[0] = sp[ii][0]; - spi[1] = sp[ii][1]; + spi[0] = sp[ii][0]; + spi[1] = sp[ii][1]; spi[2] = sp[ii][2]; spi[3] = sp[ii][3]; jlist = firstneigh[ii]; - jnum = numneigh[ii]; + jnum = numneigh[ii]; //itype = type[i]; for (jj = 0; jj < jnum; jj++) { @@ -379,14 +379,14 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) j &= NEIGHMASK; jtype = type[j]; - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - spj[3] = sp[j][3]; + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + spj[3] = sp[j][3]; fmi[0] = fmi[1] = fmi[2] = 0.0; bij[0] = bij[1] = bij[2] = bij[3] = 0.0; - + rij[0] = x[j][0] - xi[0]; rij[1] = x[j][1] - xi[1]; rij[2] = x[j][2] - xi[2]; @@ -417,7 +417,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) } // adding the kspace components to fm - + fmi[0] += fm_long[ii][0]; fmi[1] += fm_long[ii][1]; fmi[2] += fm_long[ii][2]; @@ -428,7 +428,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) compute dipolar interaction between spins i and j ------------------------------------------------------------------------- */ -void PairSpinDipoleLong::compute_long(int /* i */, int /* j */, double eij[3], +void PairSpinDipoleLong::compute_long(int /* i */, int /* j */, double eij[3], double bij[4], double fmi[3], double spi[4], double spj[4]) { double sjeij,pre; @@ -447,7 +447,7 @@ void PairSpinDipoleLong::compute_long(int /* i */, int /* j */, double eij[3], } /* ---------------------------------------------------------------------- - compute the mechanical force due to the dipolar interaction between + compute the mechanical force due to the dipolar interaction between atom i and atom j ------------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h index 56fd4c7126..1ec30cdb93 100644 --- a/src/SPIN/pair_spin_dipole_long.h +++ b/src/SPIN/pair_spin_dipole_long.h @@ -35,22 +35,22 @@ class PairSpinDipoleLong : public PairSpin { void coeff(int, char **); void init_style(); double init_one(int, int); - void *extract(const char *, int &); - + void *extract(const char *, int &); + void compute(int, int); void compute_single_pair(int, double *); - void compute_long(int, int, double *, double *, double *, + void compute_long(int, int, double *, double *, double *, double *, double *); - void compute_long_mech(int, int, double *, double *, double *, + void compute_long_mech(int, int, double *, double *, double *, double *, double *); void write_restart(FILE *); void read_restart(FILE *); void write_restart_settings(FILE *); void read_restart_settings(FILE *); - - double cut_spin_long_global; // global long cutoff distance + + double cut_spin_long_global; // global long cutoff distance protected: double hbar; // reduced Planck's constant diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index d8a263676f..dd0f6c9d68 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -35,7 +35,7 @@ PairOxdna2Excv::~PairOxdna2Excv() /* ---------------------------------------------------------------------- compute vector COM-excluded volume interaction sites in oxDNA2 ------------------------------------------------------------------------- */ -void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], +void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], double rs[3], double rb[3]) { double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index f0777fcdbd..750c6c022d 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -59,7 +59,7 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk() memory->destroy(cut_cxst_hi); memory->destroy(cut_cxst_lc); memory->destroy(cut_cxst_hc); - memory->destroy(cutsq_cxst_hc); + memory->destroy(cutsq_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 8506f5e3d1..e8e2fad020 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -86,7 +86,7 @@ PairOxdnaExcv::~PairOxdnaExcv() /* ---------------------------------------------------------------------- compute vector COM-excluded volume interaction sites in oxDNA ------------------------------------------------------------------------- */ -void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], +void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], double /*e3*/[3], double rs[3], double rb[3]) { double d_cs=-0.4, d_cb=+0.4; diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 9e4bb1c273..26042339ea 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -42,7 +42,7 @@ PairOxdnaHbond::PairOxdnaHbond(LAMMPS *lmp) : Pair(lmp) // sequence-specific base-pairing strength // A:0 C:1 G:2 T:3, 5'- [i][j] -3' - + alpha_hb[0][0] = 1.00000; alpha_hb[0][1] = 1.00000; alpha_hb[0][2] = 1.00000; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 9db554366b..4d1c4a7101 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -43,7 +43,7 @@ PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp) // sequence-specific stacking strength // A:0 C:1 G:2 T:3, 5'- [i][j] -3' - eta_st[0][0] = 1.11960; + eta_st[0][0] = 1.11960; eta_st[0][1] = 1.00852; eta_st[0][2] = 0.96950; eta_st[0][3] = 0.99632; @@ -121,7 +121,7 @@ PairOxdnaStk::~PairOxdnaStk() tally energy and virial into global and per-atom accumulators NOTE: Although this is a pair style interaction, the algorithm below - follows the virial incrementation of the bond style. This is because + follows the virial incrementation of the bond style. This is because the bond topology is used in the main compute loop. ------------------------------------------------------------------------- */ diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 7000eac6ae..37bfce5873 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -454,7 +454,7 @@ MEAM::phi_meam(double r, int a, int b) F1 = embedding(this->A_meam[a], this->Ec_meam[a][a], rhobar1, dF); F2 = embedding(this->A_meam[b], this->Ec_meam[b][b], rhobar2, dF); - + // compute Rose function, I.16 Eu = erose(r, this->re_meam[a][b], this->alpha_meam[a][b], this->Ec_meam[a][b], this->repuls_meam[a][b], diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp index 8c660cfb9e..aef5ef91a3 100644 --- a/src/USER-MISC/compute_gyration_shape.cpp +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -39,7 +39,7 @@ ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) : extscalar = 0; extvector = 0; - // ID of compute gyration + // ID of compute gyration int n = strlen(arg[3]) + 1; id_gyration = new char[n]; strcpy(id_gyration,arg[3]); diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index 56103a42b0..f552126f4f 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -78,21 +78,21 @@ using namespace LAMMPS_NS; ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), id_temp(NULL), deltaR(NULL) { - if (narg < 4) error->all(FLERR,"Illegal compute hma command"); + if (narg < 4) error->all(FLERR,"Illegal compute hma command"); if (igroup) error->all(FLERR,"Compute hma must use group all"); - if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");} + if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");} else { - int n = strlen(arg[3]) + 1; - id_temp = new char[n]; - strcpy(id_temp,arg[3]); + int n = strlen(arg[3]) + 1; + id_temp = new char[n]; + strcpy(id_temp,arg[3]); } - - create_attribute = 1; - extscalar = 1; - timeflag = 1; - // (from compute displace/atom) create a new fix STORE style - // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE + create_attribute = 1; + extscalar = 1; + timeflag = 1; + + // (from compute displace/atom) create a new fix STORE style + // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE // our new fix's group = same as compute group int n = strlen(id) + strlen("_COMPUTE_STORE") + 1; @@ -100,30 +100,30 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : strcpy(id_fix,id); strcat(id_fix,"_COMPUTE_STORE"); - char **newarg = new char*[6]; + char **newarg = new char*[6]; newarg[0] = id_fix; newarg[1] = group->names[igroup]; - newarg[2] = (char *) "STORE"; + newarg[2] = (char *) "STORE"; newarg[3] = (char *) "peratom"; newarg[4] = (char *) "1"; newarg[5] = (char *) "3"; - modify->add_fix(6,newarg); - fix = (FixStore *) modify->fix[modify->nfix-1]; - - delete [] newarg; + modify->add_fix(6,newarg); + fix = (FixStore *) modify->fix[modify->nfix-1]; + + delete [] newarg; // calculate xu,yu,zu for fix store array // skip if reset from restart file - if (fix->restart_reset) fix->restart_reset = 0; + if (fix->restart_reset) fix->restart_reset = 0; else { - double **xoriginal = fix->astore; + double **xoriginal = fix->astore; double **x = atom->x; imageint *image = atom->image; int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) - domain->unmap(x[i],image[i],xoriginal[i]); + domain->unmap(x[i],image[i],xoriginal[i]); } vector_flag = 1; @@ -175,7 +175,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : memory->create(vector, size_vector, "hma:vector"); if (computeU>-1 || computeCv>-1) { - peflag = 1; + peflag = 1; } if (computeP>-1) { pressflag = 1; @@ -209,9 +209,9 @@ void ComputeHMA::init() { } int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->compute = 1; - neighbor->requests[irequest]->occasional = 1; + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; } void ComputeHMA::init_list(int /* id */, NeighList *ptr) @@ -224,22 +224,22 @@ void ComputeHMA::setup() int dummy=0; int ifix = modify->find_fix(id_temp); if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID"); - double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy); + double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy); if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID"); - finaltemp = * temperat; + finaltemp = * temperat; // set fix which stores original atom coords int ifix2 = modify->find_fix(id_fix); if (ifix2 < 0) error->all(FLERR,"Could not find hma store fix ID"); - fix = (FixStore *) modify->fix[ifix2]; + fix = (FixStore *) modify->fix[ifix2]; } /* ---------------------------------------------------------------------- */ void ComputeHMA::compute_vector() { - invoked_vector = update->ntimestep; + invoked_vector = update->ntimestep; // grow deltaR array if necessary if (comm_forward>0 && atom->nmax > nmax) { @@ -257,7 +257,7 @@ void ComputeHMA::compute_vector() int nlocal = atom->nlocal; double *h = domain->h; - double xprd = domain->xprd; + double xprd = domain->xprd; double yprd = domain->yprd; double zprd = domain->zprd; diff --git a/src/USER-MISC/compute_hma.h b/src/USER-MISC/compute_hma.h index 233e8bbe57..5fc1130c8b 100644 --- a/src/USER-MISC/compute_hma.h +++ b/src/USER-MISC/compute_hma.h @@ -64,4 +64,4 @@ class ComputeHMA : public Compute { #endif #endif - + diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index ffa8a6603c..7c0cb3372d 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -125,7 +125,7 @@ void PairCosineSquared::coeff(int narg, char **arg) { if (narg < 4 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)"); - + if (!allocated) allocate(); @@ -459,7 +459,7 @@ double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype, double &fforce) { double r, r2inv, r6inv, cosone, force, energy; - + r = sqrt(rsq); if (r <= sigma[itype][jtype]) { @@ -478,7 +478,7 @@ double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype, } } else { cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype])); - force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) * + force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) * sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]) / r; energy = -epsilon[itype][jtype]*cosone*cosone; } diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 8507fd49f6..f7670d30b5 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -757,7 +757,7 @@ void PairExTeP::read_file(char *file) // skip line if it is a leftover from the previous section, // which can be identified by having 3 elements (instead of 2) // as first words. - + if (isupper(words[0][0]) && isupper(words[1][0]) && isupper(words[2][0])) continue; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 9faa350468..e998abf005 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -442,7 +442,7 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag) if (vflag_fdotr) virial_fdotr_compute(); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- van der Waals forces and energy ------------------------------------------------------------------------- */ @@ -540,7 +540,7 @@ void PairILPGrapheneHBN::calc_FvdW(int eflag, int /* vflag */) } } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- Repulsive forces and energy ------------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index d0d8517550..eea0b1261c 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -444,7 +444,7 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) if (vflag_fdotr) virial_fdotr_compute(); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- van der Waals forces and energy ------------------------------------------------------------------------- */ @@ -540,7 +540,7 @@ void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int /* vflag */) } } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- Repulsive forces and energy ------------------------------------------------------------------------- */ @@ -790,7 +790,7 @@ void PairKolmogorovCrespiFull::calc_normal() memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal"); } - inum = list->inum; + inum = list->inum; ilist = list->ilist; //Calculate normals for (ii = 0; ii < inum; ii++) { diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 1e4ad3edf6..8ad9793f98 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -61,9 +61,9 @@ static const char cite_pair_local_density[] = PairLocalDensity::PairLocalDensity(LAMMPS *lmp) : Pair(lmp) { restartinfo = 0; - one_coeff = 1; + one_coeff = 1; single_enable = 1; - + // stuff read from tabulated file nLD = 0; nrho = 0; @@ -81,14 +81,14 @@ PairLocalDensity::PairLocalDensity(LAMMPS *lmp) : Pair(lmp) lowercutsq = NULL; frho = NULL; rho = NULL; - + // splined arrays frho_spline = NULL; - + // per-atom arrays nmax = 0; fp = NULL; - localrho = NULL; + localrho = NULL; // set comm size needed by this pair comm_forward = 1; @@ -114,10 +114,10 @@ PairLocalDensity::~PairLocalDensity() } memory->destroy(frho_spline); - - memory->destroy(rho_min); + + memory->destroy(rho_min); memory->destroy(rho_max); - memory->destroy(delta_rho); + memory->destroy(delta_rho); memory->destroy(c0); memory->destroy(c2); memory->destroy(c4); @@ -137,37 +137,37 @@ PairLocalDensity::~PairLocalDensity() void PairLocalDensity::compute(int eflag, int vflag) { - + int i,j,ii,jj,m,k,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double rsqinv, phi, uLD, dphi, evdwl,fpair; double p, *coeff; int *ilist,*jlist,*numneigh,**firstneigh; - phi = uLD = evdwl = fpair = rsqinv = 0.0; + phi = uLD = evdwl = fpair = rsqinv = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; /* localrho = LD at each atom fp = derivative of embedding energy at each atom for each LD potential - uLD = embedding energy of each atom due to each LD potential*/ - + uLD = embedding energy of each atom due to each LD potential*/ + // grow LD and fp arrays if necessary // need to be atom->nmax in length - + if (atom->nmax > nmax) { memory->destroy(localrho); memory->destroy(fp); - nmax = atom->nmax; + nmax = atom->nmax; memory->create(localrho, nLD, nmax, "pairLD:localrho"); memory->create(fp, nLD, nmax, "pairLD:fp"); } - double **x = atom->x; + double **x = atom->x; double **f = atom->f; - int *type = atom->type; - int nlocal = atom->nlocal; + int *type = atom->type; + int nlocal = atom->nlocal; int newton_pair = force->newton_pair; inum = list->inum; @@ -179,13 +179,13 @@ void PairLocalDensity::compute(int eflag, int vflag) if (newton_pair) { m = nlocal + atom->nghost; - for (k = 0; k < nLD; k++) { - for (i = 0; i < m; i++) { + for (k = 0; k < nLD; k++) { + for (i = 0; i < m; i++) { localrho[k][i] = 0.0; fp[k][i] = 0.0; } - } - } + } + } else { for (k = 0; k < nLD; k++){ for (i = 0; i < nlocal; i++) { @@ -196,7 +196,7 @@ void PairLocalDensity::compute(int eflag, int vflag) } // loop over neighs of central atoms and types of LDs - + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; xtmp = x[i][0]; @@ -205,19 +205,19 @@ void PairLocalDensity::compute(int eflag, int vflag) itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; - + for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - jtype = type[j]; + jtype = type[j]; // calculate distance-squared between i,j atom-types - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - + rsq = delx*delx + dely*dely + delz*delz; + // calculating LDs based on central and neigh filters for (k = 0; k < nLD; k++) { @@ -230,36 +230,36 @@ void PairLocalDensity::compute(int eflag, int vflag) else { phi = c0[k] + rsq * (c2[k] + rsq * (c4[k] + c6[k]*rsq)); } - localrho[k][i] += (phi * b[k][jtype]); - - /*checking for both i,j is necessary + localrho[k][i] += (phi * b[k][jtype]); + + /*checking for both i,j is necessary since a half neighbor list is processed.*/ - + if (newton_pair || jreverse_comm_pair(this); - // + // - for (ii = 0; ii < inum; ii++) { + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; itype = type[i]; - uLD = 0.0; + uLD = 0.0; for (k = 0; k < nLD; k++) { - /*skip over this loop if the LD potential + /*skip over this loop if the LD potential is not intendend for central atomtype */ - if (!(a[k][itype])) continue; - + if (!(a[k][itype])) continue; + // linear extrapolation at rho_min and rho_max - + if (localrho[k][i] <= rho_min[k]) { coeff = frho_spline[k][0]; fp[k][i] = coeff[2]; @@ -284,14 +284,14 @@ void PairLocalDensity::compute(int eflag, int vflag) if (eflag) { if (eflag_global) eng_vdwl += uLD; - if (eflag_atom) eatom[i] += uLD; + if (eflag_atom) eatom[i] += uLD; } } // communicate LD and fp to all procs comm->forward_comm_pair(this); - + // compute forces on each atom // loop over neighbors of my atoms @@ -306,7 +306,7 @@ void PairLocalDensity::compute(int eflag, int vflag) jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; + j = jlist[jj]; j &= NEIGHMASK; jtype = type[j]; @@ -316,19 +316,19 @@ void PairLocalDensity::compute(int eflag, int vflag) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - - // calculate force between two atoms + + // calculate force between two atoms fpair = 0.0; if (rsq < cutforcesq) { // global cutoff check rsqinv = 1.0/rsq; for (k = 0; k < nLD; k++) { if (rsq >= lowercutsq[k] && rsq < uppercutsq[k]) { dphi = rsq * (2.0*c2[k] + rsq * (4.0*c4[k] + 6.0*c6[k]*rsq)); - fpair += -(a[k][itype]*b[k][jtype]*fp[k][i] + a[k][jtype]*b[k][itype]*fp[k][j]) * dphi; + fpair += -(a[k][itype]*b[k][jtype]*fp[k][i] + a[k][jtype]*b[k][itype]*fp[k][j]) * dphi; } - } - fpair *= rsqinv; - + } + fpair *= rsqinv; + f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; @@ -337,19 +337,19 @@ void PairLocalDensity::compute(int eflag, int vflag) f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; } - - /*eng_vdwl has already been completely built, + + /*eng_vdwl has already been completely built, so no need to add anything here*/ - + if (eflag) evdwl = 0.0; - + if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fpair,delx,dely,delz); } } } - + if (vflag_fdotr) virial_fdotr_compute(); } @@ -362,7 +362,7 @@ void PairLocalDensity::allocate() { allocated = 1; int n = atom->ntypes; - + memory->create(cutsq,n+1,n+1,"pair:cutsq"); memory->create(setflag,n+1,n+1,"pair:setflag"); @@ -430,7 +430,7 @@ void PairLocalDensity::init_style() // request half neighbor list array2spline(); - + // half neighbor request neighbor->request(this); } @@ -446,7 +446,7 @@ double PairLocalDensity::init_one(int /* i */, int /* j */) cutmax = 0.0; for (int k = 0; k < nLD; k++) cutmax = MAX(cutmax,uppercut[k]); - + cutforcesq = cutmax*cutmax; return cutmax; @@ -454,7 +454,7 @@ double PairLocalDensity::init_one(int /* i */, int /* j */) /*-------------------------------------------------------------------------- - pair_write functionality for this pair style that gives just a snap-shot + pair_write functionality for this pair style that gives just a snap-shot of the LD potential without doing an actual MD run ---------------------------------------------------------------------------*/ @@ -473,7 +473,7 @@ double PairLocalDensity::single(int /* i */, int /* j */, int itype, int jtype, for (k = 0; k < nLD; k++) { LD[k][1] = 0.0; // itype:- 1 LD[k][2] = 0.0; // jtype:- 2 - } + } rsqinv = 1.0/rsq; for (k = 0; k < nLD; k++) { @@ -487,13 +487,13 @@ double PairLocalDensity::single(int /* i */, int /* j */, int itype, int jtype, phi = c0[k] + rsq * (c2[k] + rsq * (c4[k] + c6[k]*rsq)); } LD[k][1] += (phi * b[k][jtype]); - LD[k][2] += (phi * b[k][itype]); + LD[k][2] += (phi * b[k][itype]); } for (k = 0; k < nLD; k++) { if (a[k][itype]) index = 1; if (a[k][jtype]) index = 2; - + if (LD[k][index] <= rho_min[k]) { coeff = frho_spline[k][0]; dFdrho = coeff[2]; @@ -545,43 +545,43 @@ void PairLocalDensity::array2spline() { } -/* ---------------------------------------------------------------------- - (one-dimensional) cubic spline interpolation sub-routine, - which determines the coeffs for a clamped cubic spline +/* ---------------------------------------------------------------------- + (one-dimensional) cubic spline interpolation sub-routine, + which determines the coeffs for a clamped cubic spline given tabulated data ------------------------------------------------------------------------*/ -void PairLocalDensity::interpolate_cbspl(int n, double delta, - double *f, double **spline) +void PairLocalDensity::interpolate_cbspl(int n, double delta, + double *f, double **spline) { /* inputs: n number of interpolating points - + f array containing function values to be interpolated; f[i] is the function value corresponding to x[i] ('x' refers to the independent var) - + delta difference in tabulated values of x - + outputs: (packaged as columns of the coeff matrix) coeff_b coeffs of linear terms coeff_c coeffs of quadratic terms coeff_d coeffs of cubic terms spline matrix that collects b,c,d - - + + other parameters: fpa derivative of function at x=a fpb derivative of function at x=b */ - + double *dl, *dd, *du; double *coeff_b, *coeff_c, *coeff_d; double fpa, fpb; int i; - + coeff_b = new double [n]; coeff_c = new double [n]; coeff_d = new double [n]; @@ -598,11 +598,11 @@ void PairLocalDensity::interpolate_cbspl(int n, double delta, // set slopes at beginning and end fpa = 0.; fpb = 0.; - + for ( i = 0; i < n-1; i++ ) { dl[i] = du[i] = delta; } - + dd[0] = 2.0 * delta; dd[n-1] = 2.0 * delta; coeff_c[0] = ( 3.0 / delta ) * ( f[1] - f[0] ) - 3.0 * fpa; @@ -612,20 +612,20 @@ void PairLocalDensity::interpolate_cbspl(int n, double delta, coeff_c[i+1] = ( 3.0 / delta ) * ( f[i+2] - f[i+1] ) - ( 3.0 / delta ) * ( f[i+1] - f[i] ); } - + // tridiagonal solver for ( i = 0; i < n-1; i++ ) { du[i] /= dd[i]; dd[i+1] -= dl[i]*du[i]; } - + coeff_c[0] /= dd[0]; for ( i = 1; i < n; i++ ) coeff_c[i] = ( coeff_c[i] - dl[i-1] * coeff_c[i-1] ) / dd[i]; - + for ( i = n-2; i >= 0; i-- ) coeff_c[i] -= coeff_c[i+1] * du[i]; - + for ( i = 0; i < n-1; i++ ) { coeff_d[i] = ( coeff_c[i+1] - coeff_c[i] ) / ( 3.0 * delta ); coeff_b[i] = ( f[i+1] - f[i] ) / delta - delta * ( coeff_c[i+1] + 2.0*coeff_c[i] ) / 3.0; @@ -648,7 +648,7 @@ void PairLocalDensity::interpolate_cbspl(int n, double delta, spline[i][1] = 2.0*spline[i][4]/delta; spline[i][0] = 3.0*spline[i][3]/delta; } - + delete [] coeff_b; delete [] coeff_c; delete [] coeff_d; @@ -662,7 +662,7 @@ void PairLocalDensity::interpolate_cbspl(int n, double delta, ------------------------------------------------------------------------- */ void PairLocalDensity::parse_file(char *filename) { - + int k, n; int me = comm->me; FILE *fptr; @@ -680,23 +680,23 @@ void PairLocalDensity::parse_file(char *filename) { } double *ftmp; // tmp var to extract the complete 2D frho array from file - + // broadcast number of LD potentials and number of (rho,frho) pairs if (me == 0) { - - // first 2 comment lines ignored + + // first 2 comment lines ignored utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); - + // extract number of potentials and number of (frho, rho) points - utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line, "%d %d", &nLD, &nrho); utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); } MPI_Bcast(&nLD,1,MPI_INT,0,world); MPI_Bcast(&nrho,1,MPI_INT,0,world); - + // setting up all arrays to be read from files and broadcasted memory->create(uppercut, nLD, "pairLD:uppercut"); memory->create(lowercut, nLD, "pairLD:lowercut"); @@ -706,14 +706,14 @@ void PairLocalDensity::parse_file(char *filename) { memory->create(c2, nLD, "pairLD:c2"); memory->create(c4, nLD, "pairLD:c4"); memory->create(c6, nLD, "pairLD:c6"); - memory->create(rho_min, nLD, "pairLD:rho_min"); + memory->create(rho_min, nLD, "pairLD:rho_min"); memory->create(rho_max, nLD, "pairLD:rho_max"); memory->create(delta_rho, nLD,"pairLD:delta_rho"); memory->create(ftmp, nrho*nLD, "pairLD:ftmp"); - - // setting up central and neighbor atom filters + + // setting up central and neighbor atom filters memory->create(a, nLD, atom->ntypes+1 , "pairLD:a"); - memory->create(b, nLD, atom->ntypes+1, "pairLD:b"); + memory->create(b, nLD, atom->ntypes+1, "pairLD:b"); if (me == 0) { for (n = 1; n <= atom->ntypes; n++){ for (k = 0; k < nLD; k++) { @@ -721,17 +721,17 @@ void PairLocalDensity::parse_file(char *filename) { b[k][n] = 0; } } - } - + } + // read file block by block - + if (me == 0) { for (k = 0; k < nLD; k++) { - - // parse upper and lower cut values + + // parse upper and lower cut values if (fgets(line,MAXLINE,fptr)==NULL) break; sscanf(line, "%lf %lf", &lowercut[k], &uppercut[k]); - + // parse and broadcast central atom filter utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); char *tmp = strtok(line, " /t/n/r/f"); @@ -739,27 +739,27 @@ void PairLocalDensity::parse_file(char *filename) { a[k][atoi(tmp)] = 1; tmp = strtok(NULL, " /t/n/r/f"); } - + // parse neighbor atom filter utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); tmp = strtok(line, " /t/n/r/f"); - while (tmp != NULL) { + while (tmp != NULL) { b[k][atoi(tmp)] = 1; tmp = strtok(NULL, " /t/n/r/f"); } - + // parse min, max and delta rho values utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); sscanf(line, "%lf %lf %lf", &rho_min[k], &rho_max[k], &delta_rho[k]); // recompute delta_rho from scratch for precision delta_rho[k] = (rho_max[k] - rho_min[k]) / (nrho - 1); - + // parse tabulated frho values from each line into temporary array - for (n = 0; n < nrho; n++) { + for (n = 0; n < nrho; n++) { utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line, "%lf", &ftmp[k*nrho + n]); } - + // ignore blank line at the end of every block utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); @@ -778,7 +778,7 @@ void PairLocalDensity::parse_file(char *filename) { } } - // Broadcast all parsed arrays + // Broadcast all parsed arrays MPI_Bcast(&lowercut[0], nLD, MPI_DOUBLE, 0, world); MPI_Bcast(&uppercut[0], nLD, MPI_DOUBLE, 0, world); MPI_Bcast(&lowercutsq[0], nLD, MPI_DOUBLE, 0, world); @@ -800,8 +800,8 @@ void PairLocalDensity::parse_file(char *filename) { // set up rho and frho arrays memory->create(rho, nLD, nrho, "pairLD:rho"); - memory->create(frho, nLD, nrho, "pairLD:frho"); - + memory->create(frho, nLD, nrho, "pairLD:frho"); + for (k = 0; k < nLD; k++) { for (n = 0; n < nrho; n++) { rho[k][n] = rho_min[k] + n*delta_rho[k]; @@ -812,7 +812,7 @@ void PairLocalDensity::parse_file(char *filename) { // delete temporary array memory->destroy(ftmp); } - + /* ---------------------------------------------------------------------- communication routines ------------------------------------------------------------------------- */ @@ -820,16 +820,16 @@ void PairLocalDensity::parse_file(char *filename) { int PairLocalDensity::pack_comm(int n, int *list, double *buf, int /* pbc_flag */, int * /* pbc */) { int i,j,k; - int m; + int m; m = 0; for (i = 0; i < n; i++) { - j = list[i]; + j = list[i]; for (k = 0; k < nLD; k++) { - buf[m++] = fp[k][j]; - } + buf[m++] = fp[k][j]; + } } - + return nLD; } @@ -838,14 +838,14 @@ int PairLocalDensity::pack_comm(int n, int *list, double *buf, void PairLocalDensity::unpack_comm(int n, int first, double *buf) { int i,k,m,last; - + m = 0; last = first + n; for (i = first; i < last; i++) { for (k = 0; k < nLD; k++) { fp[k][i] = buf[m++]; } - } + } } /* ---------------------------------------------------------------------- */ @@ -876,7 +876,7 @@ void PairLocalDensity::unpack_reverse_comm(int n, int *list, double *buf) { j = list[i]; for (k = 0; k < nLD; k++) { localrho[k][j] += buf[m++]; - } + } } } diff --git a/src/USER-MISC/pair_local_density.h b/src/USER-MISC/pair_local_density.h index 5e37376ece..e999352680 100644 --- a/src/USER-MISC/pair_local_density.h +++ b/src/USER-MISC/pair_local_density.h @@ -13,8 +13,8 @@ pair_LocalDensity written by: Tanmoy Sanyal and M. Scott Shell from UC Santa Barbara David Rosenberger: TU Darmstadt --------------------------------------------------------------------------*/ - +-------------------------------------------------------------------------*/ + #ifdef PAIR_CLASS @@ -40,7 +40,7 @@ class PairLocalDensity : public Pair { void init_style(); double init_one(int, int); double single(int, int, int, int, double, double, double, double &); - + virtual int pack_comm(int, int *, double *, int, int *); virtual void unpack_comm(int, int, double *); int pack_reverse_comm(int, int, double *); @@ -51,7 +51,7 @@ class PairLocalDensity : public Pair { protected: //------------------------------------------------------------------------ //This information is read from the tabulated input file - + int nLD, nrho; // number of LD types int **a, **b; // central and neigh atom filters double *uppercut, *lowercut; // upper and lower cutoffs @@ -59,25 +59,25 @@ class PairLocalDensity : public Pair { double *c0, *c2, *c4, *c6; // coeffs for indicator function double *rho_min, *rho_max, *delta_rho; // min, max & grid-size for LDs double **rho, **frho; // LD and LD function tables - + //------------------------------------------------------------------------ - + double ***frho_spline; // splined LD potentials double cutmax; // max cutoff for all elements double cutforcesq; // square of global upper cutoff - + int nmax; // max size of per-atom arrays double **localrho; // per-atom LD double **fp; // per-atom LD potential function derivative - + void allocate(); - + // read tabulated input file void parse_file(char *); - + // convert array to spline void array2spline(); - + // cubic spline interpolation void interpolate_cbspl(int, double, double *, double **); }; diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 5cff56753b..292a451a87 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -282,7 +282,7 @@ bigint ReaderMolfile::read_header(double box[3][3], int &boxinfo, int &triclinic } // if no field info requested, just return - + if (!fieldinfo) return natoms; memory->create(fieldindex,nfield,"read_dump:fieldindex"); diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index fe266fba76..1495219124 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -259,7 +259,7 @@ void DynamicalMatrix::calculateMatrix() fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount); fprintf(screen," Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) ); } - + // emit dynlen rows of dimalpha*dynlen*dimbeta elements update->nsteps = 0; diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index c75a48f9b4..b02de2af0d 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -411,7 +411,7 @@ void FixPlumed::post_force(int /* vflag */) // pass all pointers to plumed: p->cmd("setStep",&step); - int plumedStopCondition=0; + int plumedStopCondition=0; p->cmd("setStopFlag",&plumedStopCondition); p->cmd("setPositions",&atom->x[0][0]); p->cmd("setBox",&box[0][0]); diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index a44c7d5cbd..c8e097eb1c 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -154,7 +154,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity checks */ if (c == 2 && !lgflag) - control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); + control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); if (c < 9) { snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 77a25db7cc..022b93a0d2 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -133,7 +133,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) if (rsq < cutsq[itype][jtype]) { r2inv = 1.0/rsq; - + if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) { r = sqrt(rsq); @@ -202,7 +202,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) if (r>cut_lj[itype][jtype]-truncw) { trx = (cut_lj[itype][jtype]-r)*truncwi; tr = trx*trx*(3.0-2.0*trx); - ftr = 6.0*trx*(1.0-trx)*r*truncwi; + ftr = 6.0*trx*(1.0-trx)*r*truncwi; forcelj = forcelj*tr + evdwl*ftr; evdwl *= tr; } @@ -683,7 +683,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, if (r>cut_lj[itype][jtype]-truncw) { trx = (cut_lj[itype][jtype]-r)*truncwi; tr = trx*trx*(3.0-2.0*trx); - ftr = 6.0*trx*(1.0-trx)*r*truncwi; + ftr = 6.0*trx*(1.0-trx)*r*truncwi; forcelj = forcelj*tr + evdwl*ftr; evdwl *= tr; } diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 3a4a49c880..6b0466cd6d 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -133,7 +133,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag) if (rsq < cutsq[itype][jtype]) { r2inv = 1.0/rsq; - + if (rsq < cut_coulsq) { if (!ncoultablebits || rsq <= tabinnersq) { r = sqrt(rsq); @@ -204,7 +204,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag) if (r>cut_lj[itype][jtype]-truncw) { trx = (cut_lj[itype][jtype]-r)*truncwi; tr = trx*trx*(3.0-2.0*trx); - ftr = 6.0*trx*(1.0-trx)*r*truncwi; + ftr = 6.0*trx*(1.0-trx)*r*truncwi; forcelj = forcelj*tr + evdwl*ftr; evdwl *= tr; } @@ -683,7 +683,7 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, if (r>cut_lj[itype][jtype]-truncw) { trx = (cut_lj[itype][jtype]-r)*truncwi; tr = trx*trx*(3.0-2.0*trx); - ftr = 6.0*trx*(1.0-trx)*r*truncwi; + ftr = 6.0*trx*(1.0-trx)*r*truncwi; forcelj = forcelj*tr + evdwl*ftr; evdwl *= tr; } diff --git a/src/comm.cpp b/src/comm.cpp index fa6790e0ec..9a577c0e4f 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -673,7 +673,7 @@ double Comm::get_comm_cutoff() // cutoff was given and no pair style present. Otherwise print a // warning, if the estimated bond based cutoff is larger than what // is currently used. - + if (!force->pair && (cutghostuser == 0.0)) { maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff); } else { diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index e14f188e62..010e8db627 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -130,7 +130,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : singleflag = 0; velflag = 0; for (int i = 0; i < nvalues; i++) { - if (bstyle[i] == ENGPOT || bstyle[i] == FORCE || bstyle[i] == FX || + if (bstyle[i] == ENGPOT || bstyle[i] == FORCE || bstyle[i] == FX || bstyle[i] == FY || bstyle[i] == FZ) singleflag = 1; if (bstyle[i] == VELVIB || bstyle[i] == OMEGA || bstyle[i] == ENGTRANS || bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1; diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 0a78356127..dcb104fc3a 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -493,7 +493,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, } // calculate Q_l - // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values + // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values int jj = 0; for (int il = 0; il < nqlist; il++) { @@ -505,7 +505,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, qn[jj++] = qnormfac * sqrt(qm_sum); } - // TODO: + // TODO: // 1. [done]Need to allocate extra memory in qnarray[] for this option // 2. [done]Need to add keyword option // 3. [done]Need to caclulate Clebsch-Gordan/Wigner 3j coefficients @@ -673,7 +673,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan() for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { bb2 = m2 - l; m = aa2 + bb2 + l; - + sum = 0.0; for (int z = MAX(0, MAX(-aa2, bb2)); z <= MIN(l, MIN(l - aa2, l + bb2)); z++) { @@ -686,7 +686,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan() factorial(aa2 + z) * factorial(-bb2 + z)); } - + cc2 = m - l; sfaccg = sqrt(factorial(l + aa2) * factorial(l - aa2) * @@ -695,7 +695,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan() factorial(l + cc2) * factorial(l - cc2) * (2*l + 1)); - + sfac1 = factorial(3*l + 1); sfac2 = factorial(l); dcg = sqrt(sfac2*sfac2*sfac2 / sfac1); diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 673e2b1c06..86865ba316 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -407,7 +407,7 @@ void FixNeighHistory::pre_exchange_newton() m = npartner[j]++; partner[j][m] = tag[i]; jvalues = &valuepartner[j][dnum*m]; - if (pair->nondefault_history_transfer) + if (pair->nondefault_history_transfer) pair->transfer_history(onevalues,jvalues); else for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n]; } @@ -521,7 +521,7 @@ void FixNeighHistory::pre_exchange_no_newton() m = npartner[j]++; partner[j][m] = tag[i]; jvalues = &valuepartner[j][dnum*m]; - if (pair->nondefault_history_transfer) + if (pair->nondefault_history_transfer) pair->transfer_history(onevalues, jvalues); else for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n]; } diff --git a/src/input.h b/src/input.h index 4b274c17a9..b4df0f0160 100644 --- a/src/input.h +++ b/src/input.h @@ -39,7 +39,7 @@ class Input : protected Pointers { // substitute for variables in a string int expand_args(int, char **, int, char **&); // expand args due to wildcard void write_echo(const char *); // send text to active echo file pointers - + protected: char *command; // ptr to current command int echo_screen; // 0 = no, 1 = yes diff --git a/src/lammps.cpp b/src/lammps.cpp index b3f420b03d..a2d405855d 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -1013,7 +1013,7 @@ void _noopt LAMMPS::init_pkg_lists() #undef REGION_CLASS } -bool LAMMPS::is_installed_pkg(const char *pkg) +bool LAMMPS::is_installed_pkg(const char *pkg) { for (int i=0; installed_packages[i] != NULL; ++i) if (strcmp(installed_packages[i],pkg) == 0) return true; diff --git a/src/min.cpp b/src/min.cpp index 5721d5ab3e..3b60f2c2e6 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -898,7 +898,7 @@ double Min::total_torque() MPI_Allreduce(&ftotsqone,&ftotsqall,1,MPI_DOUBLE,MPI_SUM,world); // multiply it by hbar so that units are in eV - + return sqrt(ftotsqall) * hbar; } diff --git a/src/min.h b/src/min.h index 6f3e10d048..874c7b773d 100644 --- a/src/min.h +++ b/src/min.h @@ -47,8 +47,8 @@ class Min : protected Pointers { // methods for spin minimizers double total_torque(); - double inf_torque(); - double max_torque(); + double inf_torque(); + double max_torque(); virtual void init_style() {} virtual void setup_style() = 0; @@ -65,7 +65,7 @@ class Min : protected Pointers { int external_force_clear; // clear forces locally or externally double dmax; // max dist to move any atom in one step - int linestyle; // 0 = backtrack, 1 = quadratic, 2 = forcezero + int linestyle; // 0 = backtrack, 1 = quadratic, 2 = forcezero // 3 = spin_cubic, 4 = spin_none int normstyle; // TWO, MAX or INF flag for force norm evaluation diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 7b7046ea00..c2c9c1318e 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -91,7 +91,7 @@ int MinCG::iterate(int maxiter) dot[0] += fvec[i]*fvec[i]; dot[1] += fvec[i]*g[i]; } - + if (nextra_atom) for (m = 0; m < nextra_atom; m++) { fatom = fextra_atom[m]; @@ -119,7 +119,7 @@ int MinCG::iterate(int maxiter) if (fmax < update->ftol*update->ftol) return FTOL; } else if (normstyle == TWO) { // Euclidean force 2-norm if (dotall[0] < update->ftol*update->ftol) return FTOL; - } else error->all(FLERR,"Illegal min_modify command"); + } else error->all(FLERR,"Illegal min_modify command"); // update new search direction h from new f = -Grad(x) and old g // this is Polak-Ribieri formulation diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 2c77a13258..eceb34c437 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1941,7 +1941,7 @@ int Neighbor::decide() conservative shrink procedure: compute distance each of 8 corners of box has moved since last reneighbor reduce skin distance by sum of 2 largest of the 8 values - if reduced skin distance is negative, set to zero + if reduced skin distance is negative, set to zero new trigger = 1/2 of reduced skin distance for orthogonal box, only need 2 lo/hi corners for triclinic, need all 8 corners since deformations can displace all 8 @@ -1963,7 +1963,7 @@ int Neighbor::check_distance() delz = bboxhi[2] - boxhi_hold[2]; delta2 = sqrt(delx*delx + dely*dely + delz*delz); delta = 0.5 * (skin - (delta1+delta2)); - if (delta < 0.0) delta = 0.0; + if (delta < 0.0) delta = 0.0; deltasq = delta*delta; } else { domain->box_corners(); @@ -1977,7 +1977,7 @@ int Neighbor::check_distance() else if (delta > delta2) delta2 = delta; } delta = 0.5 * (skin - (delta1+delta2)); - if (delta < 0.0) delta = 0.0; + if (delta < 0.0) delta = 0.0; deltasq = delta*delta; } } else deltasq = triggersq; diff --git a/src/read_data.cpp b/src/read_data.cpp index 1208ab4b43..d558b87633 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -2151,7 +2151,7 @@ void ReadData::parse_coeffs(char *line, const char *addstr, // to avoid segfaults on empty lines if (narg == 0) return; - + if (noffset) { int value = force->inumeric(FLERR,arg[0]); sprintf(argoffset1,"%d",value+offset); diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 7316a2f5cd..dd9395c092 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -503,7 +503,7 @@ void ReadDump::header(int fieldinfo) yhi = box[1][1]; zlo = box[2][0]; zhi = box[2][1]; - + if (triclinic_snap) { xy = box[0][2]; xz = box[1][2]; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index a4b188be5f..da2c97bbe5 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -113,7 +113,7 @@ void ReaderNative::skip() only called by proc 0 ------------------------------------------------------------------------- */ -bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, +bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, int fieldinfo, int nfield, int *fieldtype, char **fieldlabel, int scaleflag, int wrapflag, int &fieldflag, -- GitLab From 7ec1dccbe0d9a5f3b6339d1d8c08c34471a6e123 Mon Sep 17 00:00:00 2001 From: marian-code Date: Tue, 5 Nov 2019 14:57:44 +0100 Subject: [PATCH 08/16] wrong cmake option for QUIP QUIP cmake option for specifying library path should be QUIP_LIBRARY not QUIP_LIBRARIES --- doc/rst/Build_extras.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/rst/Build_extras.rst b/doc/rst/Build_extras.rst index 1b5fa1672f..49e3d5c801 100644 --- a/doc/rst/Build_extras.rst +++ b/doc/rst/Build_extras.rst @@ -1254,7 +1254,7 @@ lib/quip/README file for details on how to do this. .. parsed-literal:: - -D QUIP_LIBRARIES=path # path to libquip.a (only needed if a custom location) + -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) CMake will not download and build the QUIP library. But once you have done that, a CMake build of LAMMPS with "-D PKG\_USER-QUIP=yes" should -- GitLab From ae4764e61481aadeb54d2a92a53833dfb8c963a3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 5 Nov 2019 11:03:25 -0500 Subject: [PATCH 09/16] address pair match issue with multiple hybrid substyles in exclusion settings --- src/neighbor.cpp | 30 +++++++++++++++++++++++++++--- src/pair_hybrid.h | 1 + 2 files changed, 28 insertions(+), 3 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 2c77a13258..05259c86e0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -34,6 +34,7 @@ #include "comm.h" #include "force.h" #include "pair.h" +#include "pair_hybrid.h" #include "domain.h" #include "group.h" #include "modify.h" @@ -374,9 +375,32 @@ void Neighbor::init() special_flag[3] = 1; else special_flag[3] = 2; - if (force->kspace || force->pair_match("coul/wolf",0) || - force->pair_match("coul/dsf",0) || force->pair_match("thole",0)) - special_flag[1] = special_flag[2] = special_flag[3] = 2; + // We cannot remove special neighbors with kspace or kspace-like pair styles + // as the exclusion needs to remove the full coulomb and not the damped interaction. + // Special treatment is required for hybrid pair styles since Force::pair_match() + // will only return a non-NULL pointer if there is only one substyle of the kind. + + if (force->kspace) { + special_flag[1] = special_flag[2] = special_flag[3] = 2; + } else { + PairHybrid *ph = reinterpret_cast(force->pair_match("^hybrid",0)); + if (ph) { + int flag=0; + for (int isub=0; isub < ph->nstyles; ++isub) { + if (force->pair_match("coul/wolf",0,isub) + || force->pair_match("coul/dsf",0,isub) + || force->pair_match("thole",0,isub)) + ++flag; + } + if (flag) + special_flag[1] = special_flag[2] = special_flag[3] = 2; + } else { + if (force->pair_match("coul/wolf",0) + || force->pair_match("coul/dsf",0) + || force->pair_match("thole",0)) + special_flag[1] = special_flag[2] = special_flag[3] = 2; + } + } // maxwt = max multiplicative factor on atom indices stored in neigh list diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 61e961ddcb..7717d1fd51 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -29,6 +29,7 @@ class PairHybrid : public Pair { friend class FixIntel; friend class FixOMP; friend class Force; + friend class Neighbor; friend class Respa; friend class Info; friend class PairDeprecated; -- GitLab From 74dade3ccb388d36cf10e416a0cc6e6d9070e9ea Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 14:01:48 -0500 Subject: [PATCH 10/16] Change doc folder src -> txt, rst -> src --- doc/Makefile | 25 +++++++++--------- doc/{rst => src}/.gitignore | 0 doc/{rst => src}/Build.rst | 0 doc/{rst => src}/Build_basics.rst | 0 doc/{rst => src}/Build_cmake.rst | 0 doc/{rst => src}/Build_development.rst | 0 doc/{rst => src}/Build_extras.rst | 0 doc/{rst => src}/Build_link.rst | 0 doc/{rst => src}/Build_make.rst | 0 doc/{rst => src}/Build_package.rst | 0 doc/{rst => 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doc/{src => txt}/special_bonds.txt (100%) rename doc/{src => txt}/suffix.txt (100%) rename doc/{src => txt}/tad.txt (100%) rename doc/{src => txt}/temper.txt (100%) rename doc/{src => txt}/temper_grem.txt (100%) rename doc/{src => txt}/temper_npt.txt (100%) rename doc/{src => txt}/thermo.txt (100%) rename doc/{src => txt}/thermo_modify.txt (100%) rename doc/{src => txt}/thermo_style.txt (100%) rename doc/{src => txt}/third_order.txt (100%) rename doc/{src => txt}/timer.txt (100%) rename doc/{src => txt}/timestep.txt (100%) rename doc/{src => txt}/uncompute.txt (100%) rename doc/{src => txt}/undump.txt (100%) rename doc/{src => txt}/unfix.txt (100%) rename doc/{src => txt}/units.txt (100%) rename doc/{src => txt}/variable.txt (100%) rename doc/{src => txt}/velocity.txt (100%) rename doc/{src => txt}/write_coeff.txt (100%) rename doc/{src => txt}/write_data.txt (100%) rename doc/{src => txt}/write_dump.txt (100%) rename doc/{src => txt}/write_restart.txt (100%) diff --git a/doc/Makefile b/doc/Makefile index fc5e930121..5dcb070f4f 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -1,11 +1,12 @@ # Makefile for LAMMPS documentation SHELL = /bin/bash -BUILDDIR = ${PWD} -RSTDIR = $(BUILDDIR)/rst +BUILDDIR = ${CURDIR} +RSTDIR = $(BUILDDIR)/src +TXTDIR = $(BUILDDIR)/txt VENV = $(BUILDDIR)/docenv TXT2RST = $(VENV)/bin/txt2rst -ANCHORCHECK = $(VENV)/bin/doc_anchor_check +ANCHORCHECK = $(VENV)/bin/rst_anchor_check PYTHON = $(shell which python3) VIRTUALENV = virtualenv @@ -27,8 +28,8 @@ HAS_VIRTUALENV = YES endif SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') -SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt)) -OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) +SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt)) +OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst) .PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check @@ -53,7 +54,7 @@ clean-all: clean rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees clean: - rm -rf $(RSTDIR)/{Eqs,JPG,*.rst} html epub latex + rm -rf html epub latex rm -rf spelling clean-spelling: @@ -64,12 +65,10 @@ rst: clean $(OBJECTS) $(ANCHORCHECK) html: $(OBJECTS) $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ - cp -r src/JPG $(RSTDIR)/ ;\ - cp -r src/Eqs $(RSTDIR)/ ;\ sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ echo "############################################" ;\ - doc_anchor_check src/*.txt ;\ - env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\ + rst_anchor_check src/*.rst ;\ + env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ echo "############################################" ;\ deactivate ;\ ) @@ -89,7 +88,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt @(\ . $(VENV)/bin/activate ;\ pip install sphinxcontrib-spelling ;\ - cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\ + cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\ sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\ deactivate ;\ ) @@ -126,7 +125,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK) . $(VENV)/bin/activate ;\ sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ echo "############################################" ;\ - doc_anchor_check src/*.txt ;\ + rst_anchor_check src/*.rst ;\ echo "############################################" ;\ deactivate ;\ ) @@ -163,7 +162,7 @@ fetch: anchor_check : $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ - doc_anchor_check src/*.txt ;\ + rst_anchor_check src/*.txt ;\ deactivate ;\ ) diff --git a/doc/rst/.gitignore b/doc/src/.gitignore similarity index 100% rename from doc/rst/.gitignore rename to doc/src/.gitignore diff --git a/doc/rst/Build.rst b/doc/src/Build.rst 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a/doc/rst/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst similarity index 100% rename from doc/rst/compute_edpd_temp_atom.rst rename to doc/src/compute_edpd_temp_atom.rst diff --git a/doc/rst/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst similarity index 100% rename from doc/rst/compute_entropy_atom.rst rename to doc/src/compute_entropy_atom.rst diff --git a/doc/rst/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst similarity index 100% rename from doc/rst/compute_erotate_asphere.rst rename to doc/src/compute_erotate_asphere.rst diff --git a/doc/rst/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst similarity index 100% rename from doc/rst/compute_erotate_rigid.rst rename to doc/src/compute_erotate_rigid.rst diff --git a/doc/rst/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst similarity index 100% rename from doc/rst/compute_erotate_sphere.rst rename to doc/src/compute_erotate_sphere.rst diff --git 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to doc/txt/compute_bond.txt diff --git a/doc/src/compute_bond_local.txt b/doc/txt/compute_bond_local.txt similarity index 100% rename from doc/src/compute_bond_local.txt rename to doc/txt/compute_bond_local.txt diff --git a/doc/src/compute_centro_atom.txt b/doc/txt/compute_centro_atom.txt similarity index 100% rename from doc/src/compute_centro_atom.txt rename to doc/txt/compute_centro_atom.txt diff --git a/doc/src/compute_chunk_atom.txt b/doc/txt/compute_chunk_atom.txt similarity index 100% rename from doc/src/compute_chunk_atom.txt rename to doc/txt/compute_chunk_atom.txt diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/txt/compute_chunk_spread_atom.txt similarity index 100% rename from doc/src/compute_chunk_spread_atom.txt rename to doc/txt/compute_chunk_spread_atom.txt diff --git a/doc/src/compute_cluster_atom.txt b/doc/txt/compute_cluster_atom.txt similarity index 100% rename from doc/src/compute_cluster_atom.txt rename to doc/txt/compute_cluster_atom.txt diff --git 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doc/src/compute_coord_atom.txt rename to doc/txt/compute_coord_atom.txt diff --git a/doc/src/compute_damage_atom.txt b/doc/txt/compute_damage_atom.txt similarity index 100% rename from doc/src/compute_damage_atom.txt rename to doc/txt/compute_damage_atom.txt diff --git a/doc/src/compute_dihedral.txt b/doc/txt/compute_dihedral.txt similarity index 100% rename from doc/src/compute_dihedral.txt rename to doc/txt/compute_dihedral.txt diff --git a/doc/src/compute_dihedral_local.txt b/doc/txt/compute_dihedral_local.txt similarity index 100% rename from doc/src/compute_dihedral_local.txt rename to doc/txt/compute_dihedral_local.txt diff --git a/doc/src/compute_dilatation_atom.txt b/doc/txt/compute_dilatation_atom.txt similarity index 100% rename from doc/src/compute_dilatation_atom.txt rename to doc/txt/compute_dilatation_atom.txt diff --git a/doc/src/compute_dipole_chunk.txt b/doc/txt/compute_dipole_chunk.txt similarity index 100% rename from doc/src/compute_dipole_chunk.txt rename to 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a/doc/src/compute_fep.txt b/doc/txt/compute_fep.txt similarity index 100% rename from doc/src/compute_fep.txt rename to doc/txt/compute_fep.txt diff --git a/doc/src/compute_global_atom.txt b/doc/txt/compute_global_atom.txt similarity index 100% rename from doc/src/compute_global_atom.txt rename to doc/txt/compute_global_atom.txt diff --git a/doc/src/compute_group_group.txt b/doc/txt/compute_group_group.txt similarity index 100% rename from doc/src/compute_group_group.txt rename to doc/txt/compute_group_group.txt diff --git a/doc/src/compute_gyration.txt b/doc/txt/compute_gyration.txt similarity index 100% rename from doc/src/compute_gyration.txt rename to doc/txt/compute_gyration.txt diff --git a/doc/src/compute_gyration_chunk.txt b/doc/txt/compute_gyration_chunk.txt similarity index 100% rename from doc/src/compute_gyration_chunk.txt rename to doc/txt/compute_gyration_chunk.txt diff --git a/doc/src/compute_gyration_shape.txt b/doc/txt/compute_gyration_shape.txt similarity index 100% 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a/doc/src/compute_msd.txt b/doc/txt/compute_msd.txt similarity index 100% rename from doc/src/compute_msd.txt rename to doc/txt/compute_msd.txt diff --git a/doc/src/compute_msd_chunk.txt b/doc/txt/compute_msd_chunk.txt similarity index 100% rename from doc/src/compute_msd_chunk.txt rename to doc/txt/compute_msd_chunk.txt diff --git a/doc/src/compute_msd_nongauss.txt b/doc/txt/compute_msd_nongauss.txt similarity index 100% rename from doc/src/compute_msd_nongauss.txt rename to doc/txt/compute_msd_nongauss.txt diff --git a/doc/src/compute_omega_chunk.txt b/doc/txt/compute_omega_chunk.txt similarity index 100% rename from doc/src/compute_omega_chunk.txt rename to doc/txt/compute_omega_chunk.txt diff --git a/doc/src/compute_orientorder_atom.txt b/doc/txt/compute_orientorder_atom.txt similarity index 100% rename from doc/src/compute_orientorder_atom.txt rename to doc/txt/compute_orientorder_atom.txt diff --git a/doc/src/compute_pair.txt b/doc/txt/compute_pair.txt similarity index 100% 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a/doc/src/compute_ptm_atom.txt b/doc/txt/compute_ptm_atom.txt similarity index 100% rename from doc/src/compute_ptm_atom.txt rename to doc/txt/compute_ptm_atom.txt diff --git a/doc/src/compute_rdf.txt b/doc/txt/compute_rdf.txt similarity index 100% rename from doc/src/compute_rdf.txt rename to doc/txt/compute_rdf.txt diff --git a/doc/src/compute_reduce.txt b/doc/txt/compute_reduce.txt similarity index 100% rename from doc/src/compute_reduce.txt rename to doc/txt/compute_reduce.txt diff --git a/doc/src/compute_reduce_chunk.txt b/doc/txt/compute_reduce_chunk.txt similarity index 100% rename from doc/src/compute_reduce_chunk.txt rename to doc/txt/compute_reduce_chunk.txt diff --git a/doc/src/compute_rigid_local.txt b/doc/txt/compute_rigid_local.txt similarity index 100% rename from doc/src/compute_rigid_local.txt rename to doc/txt/compute_rigid_local.txt diff --git a/doc/src/compute_saed.txt b/doc/txt/compute_saed.txt similarity index 100% rename from doc/src/compute_saed.txt rename to 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b/doc/txt/pair_nb3b_harmonic.txt similarity index 100% rename from doc/src/pair_nb3b_harmonic.txt rename to doc/txt/pair_nb3b_harmonic.txt diff --git a/doc/src/pair_nm.txt b/doc/txt/pair_nm.txt similarity index 100% rename from doc/src/pair_nm.txt rename to doc/txt/pair_nm.txt diff --git a/doc/src/pair_none.txt b/doc/txt/pair_none.txt similarity index 100% rename from doc/src/pair_none.txt rename to doc/txt/pair_none.txt diff --git a/doc/src/pair_oxdna.txt b/doc/txt/pair_oxdna.txt similarity index 100% rename from doc/src/pair_oxdna.txt rename to doc/txt/pair_oxdna.txt diff --git a/doc/src/pair_oxdna2.txt b/doc/txt/pair_oxdna2.txt similarity index 100% rename from doc/src/pair_oxdna2.txt rename to doc/txt/pair_oxdna2.txt diff --git a/doc/src/pair_peri.txt b/doc/txt/pair_peri.txt similarity index 100% rename from doc/src/pair_peri.txt rename to doc/txt/pair_peri.txt diff --git a/doc/src/pair_polymorphic.txt b/doc/txt/pair_polymorphic.txt similarity index 100% rename from doc/src/pair_polymorphic.txt rename to doc/txt/pair_polymorphic.txt diff --git a/doc/src/pair_python.txt b/doc/txt/pair_python.txt similarity index 100% rename from doc/src/pair_python.txt rename to doc/txt/pair_python.txt diff --git a/doc/src/pair_quip.txt b/doc/txt/pair_quip.txt similarity index 100% rename from doc/src/pair_quip.txt rename to doc/txt/pair_quip.txt diff --git a/doc/src/pair_reaxc.txt b/doc/txt/pair_reaxc.txt similarity index 100% rename from doc/src/pair_reaxc.txt rename to doc/txt/pair_reaxc.txt diff --git a/doc/src/pair_resquared.txt b/doc/txt/pair_resquared.txt similarity index 100% rename from doc/src/pair_resquared.txt rename to doc/txt/pair_resquared.txt diff --git a/doc/src/pair_sdk.txt b/doc/txt/pair_sdk.txt similarity index 100% rename from doc/src/pair_sdk.txt rename to doc/txt/pair_sdk.txt diff --git a/doc/src/pair_sdpd_taitwater_isothermal.txt b/doc/txt/pair_sdpd_taitwater_isothermal.txt similarity index 100% rename from doc/src/pair_sdpd_taitwater_isothermal.txt rename to doc/txt/pair_sdpd_taitwater_isothermal.txt diff --git a/doc/src/pair_smd_hertz.txt b/doc/txt/pair_smd_hertz.txt similarity index 100% rename from doc/src/pair_smd_hertz.txt rename to doc/txt/pair_smd_hertz.txt diff --git a/doc/src/pair_smd_tlsph.txt b/doc/txt/pair_smd_tlsph.txt similarity index 100% rename from doc/src/pair_smd_tlsph.txt rename to doc/txt/pair_smd_tlsph.txt diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/txt/pair_smd_triangulated_surface.txt similarity index 100% rename from doc/src/pair_smd_triangulated_surface.txt rename to doc/txt/pair_smd_triangulated_surface.txt diff --git a/doc/src/pair_smd_ulsph.txt b/doc/txt/pair_smd_ulsph.txt similarity index 100% rename from doc/src/pair_smd_ulsph.txt rename to doc/txt/pair_smd_ulsph.txt diff --git a/doc/src/pair_smtbq.txt b/doc/txt/pair_smtbq.txt similarity index 100% rename from doc/src/pair_smtbq.txt rename to doc/txt/pair_smtbq.txt diff --git a/doc/src/pair_snap.txt b/doc/txt/pair_snap.txt similarity index 100% rename from doc/src/pair_snap.txt rename to doc/txt/pair_snap.txt diff --git a/doc/src/pair_soft.txt b/doc/txt/pair_soft.txt similarity index 100% rename from doc/src/pair_soft.txt rename to doc/txt/pair_soft.txt diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/txt/pair_sph_heatconduction.txt similarity index 100% rename from doc/src/pair_sph_heatconduction.txt rename to doc/txt/pair_sph_heatconduction.txt diff --git a/doc/src/pair_sph_idealgas.txt b/doc/txt/pair_sph_idealgas.txt similarity index 100% rename from doc/src/pair_sph_idealgas.txt rename to doc/txt/pair_sph_idealgas.txt diff --git a/doc/src/pair_sph_lj.txt b/doc/txt/pair_sph_lj.txt similarity index 100% rename from doc/src/pair_sph_lj.txt rename to doc/txt/pair_sph_lj.txt diff --git a/doc/src/pair_sph_rhosum.txt b/doc/txt/pair_sph_rhosum.txt similarity index 100% rename from doc/src/pair_sph_rhosum.txt rename to doc/txt/pair_sph_rhosum.txt diff --git a/doc/src/pair_sph_taitwater.txt b/doc/txt/pair_sph_taitwater.txt similarity index 100% rename from doc/src/pair_sph_taitwater.txt rename to doc/txt/pair_sph_taitwater.txt diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/txt/pair_sph_taitwater_morris.txt similarity index 100% rename from doc/src/pair_sph_taitwater_morris.txt rename to doc/txt/pair_sph_taitwater_morris.txt diff --git a/doc/src/pair_spin_dipole.txt b/doc/txt/pair_spin_dipole.txt similarity index 100% rename from doc/src/pair_spin_dipole.txt rename to doc/txt/pair_spin_dipole.txt diff --git a/doc/src/pair_spin_dmi.txt b/doc/txt/pair_spin_dmi.txt similarity index 100% rename from doc/src/pair_spin_dmi.txt rename to doc/txt/pair_spin_dmi.txt diff --git a/doc/src/pair_spin_exchange.txt b/doc/txt/pair_spin_exchange.txt similarity index 100% rename from doc/src/pair_spin_exchange.txt rename to doc/txt/pair_spin_exchange.txt diff --git a/doc/src/pair_spin_magelec.txt b/doc/txt/pair_spin_magelec.txt similarity index 100% rename from doc/src/pair_spin_magelec.txt rename to doc/txt/pair_spin_magelec.txt diff --git a/doc/src/pair_spin_neel.txt b/doc/txt/pair_spin_neel.txt similarity index 100% rename from doc/src/pair_spin_neel.txt rename to doc/txt/pair_spin_neel.txt diff --git a/doc/src/pair_srp.txt b/doc/txt/pair_srp.txt similarity index 100% rename from doc/src/pair_srp.txt rename to doc/txt/pair_srp.txt diff --git a/doc/src/pair_style.txt b/doc/txt/pair_style.txt similarity index 100% rename from doc/src/pair_style.txt rename to doc/txt/pair_style.txt diff --git a/doc/src/pair_sw.txt b/doc/txt/pair_sw.txt similarity index 100% rename from doc/src/pair_sw.txt rename to doc/txt/pair_sw.txt diff --git a/doc/src/pair_table.txt b/doc/txt/pair_table.txt similarity index 100% rename from doc/src/pair_table.txt rename to doc/txt/pair_table.txt diff --git a/doc/src/pair_table_rx.txt b/doc/txt/pair_table_rx.txt similarity index 100% rename from doc/src/pair_table_rx.txt rename to doc/txt/pair_table_rx.txt diff --git a/doc/src/pair_tersoff.txt b/doc/txt/pair_tersoff.txt similarity index 100% rename from doc/src/pair_tersoff.txt rename to doc/txt/pair_tersoff.txt diff --git a/doc/src/pair_tersoff_mod.txt b/doc/txt/pair_tersoff_mod.txt similarity index 100% rename from doc/src/pair_tersoff_mod.txt rename to doc/txt/pair_tersoff_mod.txt diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/txt/pair_tersoff_zbl.txt similarity index 100% rename from doc/src/pair_tersoff_zbl.txt rename to doc/txt/pair_tersoff_zbl.txt diff --git a/doc/src/pair_thole.txt b/doc/txt/pair_thole.txt similarity index 100% rename from doc/src/pair_thole.txt rename to doc/txt/pair_thole.txt diff --git a/doc/src/pair_tri_lj.txt b/doc/txt/pair_tri_lj.txt similarity index 100% rename from doc/src/pair_tri_lj.txt rename to doc/txt/pair_tri_lj.txt diff --git a/doc/src/pair_ufm.txt b/doc/txt/pair_ufm.txt similarity index 100% rename from doc/src/pair_ufm.txt rename to doc/txt/pair_ufm.txt diff --git a/doc/src/pair_vashishta.txt b/doc/txt/pair_vashishta.txt similarity index 100% rename from doc/src/pair_vashishta.txt rename to doc/txt/pair_vashishta.txt diff --git a/doc/src/pair_write.txt b/doc/txt/pair_write.txt similarity index 100% rename from doc/src/pair_write.txt rename to doc/txt/pair_write.txt diff --git a/doc/src/pair_yukawa.txt b/doc/txt/pair_yukawa.txt similarity index 100% rename from doc/src/pair_yukawa.txt rename to doc/txt/pair_yukawa.txt diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/txt/pair_yukawa_colloid.txt similarity index 100% rename from doc/src/pair_yukawa_colloid.txt rename to doc/txt/pair_yukawa_colloid.txt diff --git a/doc/src/pair_zbl.txt b/doc/txt/pair_zbl.txt similarity index 100% rename from doc/src/pair_zbl.txt rename to doc/txt/pair_zbl.txt diff --git a/doc/src/pair_zero.txt b/doc/txt/pair_zero.txt similarity index 100% rename from doc/src/pair_zero.txt rename to doc/txt/pair_zero.txt diff --git a/doc/src/pairs.txt b/doc/txt/pairs.txt similarity index 100% rename from doc/src/pairs.txt rename to doc/txt/pairs.txt diff --git a/doc/src/partition.txt b/doc/txt/partition.txt similarity index 100% rename from doc/src/partition.txt rename to doc/txt/partition.txt diff --git a/doc/src/prd.txt b/doc/txt/prd.txt similarity index 100% rename from doc/src/prd.txt rename to doc/txt/prd.txt diff --git a/doc/src/print.txt b/doc/txt/print.txt similarity index 100% rename from doc/src/print.txt rename to doc/txt/print.txt diff --git a/doc/src/processors.txt b/doc/txt/processors.txt similarity index 100% rename from doc/src/processors.txt rename to doc/txt/processors.txt diff --git a/doc/src/python.txt b/doc/txt/python.txt similarity index 100% rename from doc/src/python.txt rename to doc/txt/python.txt diff --git a/doc/src/quit.txt b/doc/txt/quit.txt similarity index 100% rename from doc/src/quit.txt rename to doc/txt/quit.txt diff --git a/doc/src/read_data.txt b/doc/txt/read_data.txt similarity index 100% rename from doc/src/read_data.txt rename to doc/txt/read_data.txt diff --git a/doc/src/read_dump.txt b/doc/txt/read_dump.txt similarity index 100% rename from doc/src/read_dump.txt rename to doc/txt/read_dump.txt diff --git a/doc/src/read_restart.txt b/doc/txt/read_restart.txt similarity index 100% rename from doc/src/read_restart.txt rename to doc/txt/read_restart.txt diff --git a/doc/src/region.txt b/doc/txt/region.txt similarity index 100% rename from doc/src/region.txt rename to doc/txt/region.txt diff --git a/doc/src/replicate.txt b/doc/txt/replicate.txt similarity index 100% rename from doc/src/replicate.txt rename to doc/txt/replicate.txt diff --git a/doc/src/rerun.txt b/doc/txt/rerun.txt similarity index 100% rename from doc/src/rerun.txt rename to doc/txt/rerun.txt diff --git a/doc/src/reset_ids.txt b/doc/txt/reset_ids.txt similarity index 100% rename from doc/src/reset_ids.txt rename to doc/txt/reset_ids.txt diff --git a/doc/src/reset_timestep.txt b/doc/txt/reset_timestep.txt similarity index 100% rename from doc/src/reset_timestep.txt rename to doc/txt/reset_timestep.txt diff --git a/doc/src/restart.txt b/doc/txt/restart.txt similarity index 100% rename from doc/src/restart.txt rename to doc/txt/restart.txt diff --git a/doc/src/run.txt b/doc/txt/run.txt similarity index 100% rename from doc/src/run.txt rename to doc/txt/run.txt diff --git a/doc/src/run_style.txt b/doc/txt/run_style.txt similarity index 100% rename from doc/src/run_style.txt rename to doc/txt/run_style.txt diff --git a/doc/src/server.txt b/doc/txt/server.txt similarity index 100% rename from doc/src/server.txt rename to doc/txt/server.txt diff --git a/doc/src/server_mc.txt b/doc/txt/server_mc.txt similarity index 100% rename from doc/src/server_mc.txt rename to doc/txt/server_mc.txt diff --git a/doc/src/server_md.txt b/doc/txt/server_md.txt similarity index 100% rename from doc/src/server_md.txt rename to doc/txt/server_md.txt diff --git a/doc/src/set.txt b/doc/txt/set.txt similarity index 100% rename from doc/src/set.txt rename to doc/txt/set.txt diff --git a/doc/src/shell.txt b/doc/txt/shell.txt similarity index 100% rename from doc/src/shell.txt rename to doc/txt/shell.txt diff --git a/doc/src/special_bonds.txt b/doc/txt/special_bonds.txt similarity index 100% rename from doc/src/special_bonds.txt rename to doc/txt/special_bonds.txt diff --git a/doc/src/suffix.txt b/doc/txt/suffix.txt similarity index 100% rename from doc/src/suffix.txt rename to doc/txt/suffix.txt diff --git a/doc/src/tad.txt b/doc/txt/tad.txt similarity index 100% rename from doc/src/tad.txt rename to doc/txt/tad.txt diff --git a/doc/src/temper.txt b/doc/txt/temper.txt similarity index 100% rename from doc/src/temper.txt rename to doc/txt/temper.txt diff --git a/doc/src/temper_grem.txt b/doc/txt/temper_grem.txt similarity index 100% rename from doc/src/temper_grem.txt rename to doc/txt/temper_grem.txt diff --git a/doc/src/temper_npt.txt b/doc/txt/temper_npt.txt similarity index 100% rename from doc/src/temper_npt.txt rename to doc/txt/temper_npt.txt diff --git a/doc/src/thermo.txt b/doc/txt/thermo.txt similarity index 100% rename from doc/src/thermo.txt rename to doc/txt/thermo.txt diff --git a/doc/src/thermo_modify.txt b/doc/txt/thermo_modify.txt similarity index 100% rename from doc/src/thermo_modify.txt rename to doc/txt/thermo_modify.txt diff --git a/doc/src/thermo_style.txt b/doc/txt/thermo_style.txt similarity index 100% rename from doc/src/thermo_style.txt rename to doc/txt/thermo_style.txt diff --git a/doc/src/third_order.txt b/doc/txt/third_order.txt similarity index 100% rename from doc/src/third_order.txt rename to doc/txt/third_order.txt diff --git a/doc/src/timer.txt b/doc/txt/timer.txt similarity index 100% rename from doc/src/timer.txt rename to doc/txt/timer.txt diff --git a/doc/src/timestep.txt b/doc/txt/timestep.txt similarity index 100% rename from doc/src/timestep.txt rename to doc/txt/timestep.txt diff --git a/doc/src/uncompute.txt b/doc/txt/uncompute.txt similarity index 100% rename from doc/src/uncompute.txt rename to doc/txt/uncompute.txt diff --git a/doc/src/undump.txt b/doc/txt/undump.txt similarity index 100% rename from doc/src/undump.txt rename to doc/txt/undump.txt diff --git a/doc/src/unfix.txt b/doc/txt/unfix.txt similarity index 100% rename from doc/src/unfix.txt rename to doc/txt/unfix.txt diff --git a/doc/src/units.txt b/doc/txt/units.txt similarity index 100% rename from doc/src/units.txt rename to doc/txt/units.txt diff --git a/doc/src/variable.txt b/doc/txt/variable.txt similarity index 100% rename from doc/src/variable.txt rename to doc/txt/variable.txt diff --git a/doc/src/velocity.txt b/doc/txt/velocity.txt similarity index 100% rename from doc/src/velocity.txt rename to doc/txt/velocity.txt diff --git a/doc/src/write_coeff.txt b/doc/txt/write_coeff.txt similarity index 100% rename from doc/src/write_coeff.txt rename to doc/txt/write_coeff.txt diff --git a/doc/src/write_data.txt b/doc/txt/write_data.txt similarity index 100% rename from doc/src/write_data.txt rename to doc/txt/write_data.txt diff --git a/doc/src/write_dump.txt b/doc/txt/write_dump.txt similarity index 100% rename from doc/src/write_dump.txt rename to doc/txt/write_dump.txt diff --git a/doc/src/write_restart.txt b/doc/txt/write_restart.txt similarity index 100% rename from doc/src/write_restart.txt rename to doc/txt/write_restart.txt -- GitLab From 423a3bb99f9f8f294670c2f5a0f2516b3cd0c190 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 14:22:17 -0500 Subject: [PATCH 11/16] Add initial version of updated tools from #1533 --- .../lammpsdoc/eqImg2mathjaxInline.py | 238 ++++++++++++++++++ .../converters/lammpsdoc/rst_anchor_check.py | 64 +++++ doc/utils/converters/setup.py | 2 +- 3 files changed, 303 insertions(+), 1 deletion(-) create mode 100644 doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py create mode 100644 doc/utils/converters/lammpsdoc/rst_anchor_check.py diff --git a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py new file mode 100644 index 0000000000..6db83da7fd --- /dev/null +++ b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py @@ -0,0 +1,238 @@ +#! /usr/bin/env python3 +# LAMMPS Documentation Utilities +# +# Scan for duplicate anchor labels in documentation files +# +# Copyright (C) 2019 E. Anne Gunn +# Based largely on doc_anchor_check.py by Richard Berger +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +import argparse +import os +import re +import sys + + +# We only want to replace image lines where image is +# pulled from Eqs subfolder +image_pattern = re.compile(r'.*image:: Eqs/(.*)\.jpg') +tex_eq_pattern = re.compile(r'\$\$') +latex_begin_eq_pattern = re.compile(r'\\begin{equation}') +latex_end_eq_pattern = re.compile(r'\\end{equation}') +latex_begin_eqArray_pattern = re.compile(r'\\begin{eqnarray\*}') +latex_end_eqArray_pattern = re.compile(r'\\end{eqnarray\*}') + +imageMarker = ">>>image was here" +image_marker_pattern = re.compile(r'>>>image was here') +align_pattern = re.compile(r'.*:align: center') + +modifiedFileFolder = "src/modifiedRst/" +# Since this is a proof of concept implementation, +# skip any rst files that are known to cause problems +skipFileList = ["pair_tersoff_zbl.rst"] + +runReport = { +} + + +def checkForEquationStart(texLine): + eqType = None + texMatch = tex_eq_pattern.match(texLine) + if texMatch: + eqType = "texMatch" + else: + eqMatch = latex_begin_eq_pattern.match(texLine) + if eqMatch: + eqType = "eqMatch" + else: + eqArrayMatch = latex_begin_eqArray_pattern.match(texLine) + if eqArrayMatch: + eqType = "eqArrayMatch" + return eqType + + +def checkForEquationEnd(texLine, eqType): + endPattern = tex_eq_pattern + if eqType == "texMatch": + endPattern = tex_eq_pattern + elif eqType == "eqMatch": + endPattern = latex_end_eq_pattern + elif eqType == "eqArrayMatch": + endPattern = latex_end_eqArray_pattern + else: + print("***error: unexpected eqType %s, will look for tex delimiter" % eqType) + + endMatch = endPattern.match(texLine) + endFound = endMatch is not None + if endFound: + print("found pattern end, line: %s" % texLine) + return endFound + + +def startMathjax(): + mathjaxLines = [] + mathjaxLines.append(".. math::\n\n") + return mathjaxLines + + +def endMathjax(mathjaxLines): + mathjaxLines.append("\n") + mathjaxLines.append("%s\n" % imageMarker) + return mathjaxLines + + +def processFile(filename): + print("in processFile for filename: %s" % filename) + imageCount = 0 + + modifiedFileLines = [] + doWriteModifiedFile = False + with open(filename, 'rt') as f: + for line_number, line in enumerate(f): + m = image_pattern.match(line) + if m: + fileroot = m.group(1) + print("fileroot: {0}".format(fileroot)) + imageCount += 1 + texFilename = "src/Eqs/{0}.tex".format(fileroot) + print("will try to open %s" % texFilename) + eqType = None + eqLines = [] + try: + with open(texFilename, 'rt', encoding='utf-8') as t: + print("%s file opened ok" % texFilename) + eqLines = startMathjax() + try: + for dummy, texLine in enumerate(t): + #print(texLine) + if eqType == None: + eqType = checkForEquationStart(texLine) + if eqType != None: + print("equation type: {0}".format(eqType)) + else: + endFound = checkForEquationEnd(texLine, eqType) + if endFound != True: + eqLines.append(texLine) + else: + eqType = None + eqLines = endMathjax(eqLines) + print("Equation lines will be:") + print("-----------------------------") + print(*eqLines, sep="\n") + print("-----------------------------") + except UnicodeDecodeError: + print("UnicodeDecodeError reading file file %s, image markup will be left in place" % texFilename) + break + except EnvironmentError: + error = "could not open source tex file {0}, line: {1}".format(texFilename, line) + print(error) + print("image markup will be left in place") + if filename not in runReport: + runReport[filename] = [] + runReport[filename].append(error) + # put the image line we could not replace back into the output + eqLines.append(line) + if len(eqLines) > 0: + modifiedFileLines.extend(eqLines) + doWriteModifiedFile = True + eqLines = [] + else: + # not an equation line, so simply queue it up for output as is + modifiedFileLines.append(line) + if doWriteModifiedFile: + #print(*modifiedFileLines, sep="\n") + print("modifiedFileLines has %d lines before align center cleanup" % len(modifiedFileLines)) + # First, go through the file and pull out the lines where there is + # now an image file marker followed by an align center directive + deleteLines = [] + for lineNumber, line in enumerate(modifiedFileLines): + m = image_marker_pattern.match(line) + if m: + print("found image marker in line %d" % lineNumber) + n = align_pattern.match(modifiedFileLines[lineNumber+1]) + if n: + print("found align center") + deleteLines.append(lineNumber) + deleteLines.append(lineNumber+1) + #When deleting, always work from the back of the list to the front + for lineNumber in reversed(deleteLines): + print(lineNumber) + del modifiedFileLines[lineNumber] + print("modifiedFileLines has %d lines after align center cleanup" % len(modifiedFileLines)) + # Now we can actually write out the new contents + try: + if not os.path.exists(modifiedFileFolder): + os.makedirs(modifiedFileFolder) + nameParts = filename.split("/") + filenamePos = len(nameParts) - 1 + modFilePath = "{0}{1}".format(modifiedFileFolder, nameParts[filenamePos]) + modRst = open(modFilePath, "w") + for rstLine in modifiedFileLines: + modRst.write(rstLine) + modRst.close() + except OSError: + print('Error: Creating directory. ' + modifiedFileFolder) + return imageCount + + +def main(): + fileCount = 0 + totalImageCount = 0 + + parser = argparse.ArgumentParser(description='replace image markup in rst files with inline mathjax markup from .txt source of images') + parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') + parsed_args = parser.parse_args() + + # TODO: make originalRst folder and copy src/*.rst files into it + + # Because we may decide to add files to the skip list between runs, + # if we have more than one file to process, + # remove the modified file folder so we don't end up with + # zombie modifications + if len(parsed_args.files) > 1: + for outputFile in os.listdir(modifiedFileFolder): + filePath = os.path.join(modifiedFileFolder, outputFile) + try: + if os.path.isfile(filePath): + os.unlink(filePath) + except Exception as e: + print(e) + sys.exit(1) + + for filename in parsed_args.files: + doSkip = False + for skipName in skipFileList: + if filename.find(skipName) != -1: + print("skipping file: %s" % filename) + doSkip = True + runReport[filename] = ["skipped based on skipFileList"] + break + if not doSkip: + fileCount += 1 + ic = processFile(filename) + totalImageCount += ic + + print("============================================") + print("Processed %d rst files." % fileCount) + print("Found %d image lines." % totalImageCount) + + for fileKey in runReport: + print("--------------------------------------------") + print("run report for %s:" % fileKey) + print(*runReport[fileKey], sep="\n") + + print("============================================") + +if __name__ == "__main__": + main() diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py new file mode 100644 index 0000000000..9c097e7d0e --- /dev/null +++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py @@ -0,0 +1,64 @@ +#! /usr/bin/env python3 +# LAMMPS Documentation Utilities +# +# Scan for duplicate anchor labels in documentation files +# +# Copyright (C) 2017 Richard Berger +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +import re +import sys +import argparse + +def main(): + parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files') + parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') + parsed_args = parser.parse_args() + + anchor_pattern = re.compile(r'^\.\. _(.*):$') + anchors = {} + + for filename in parsed_args.files: + #print("filename: %s" % filename) + with open(filename, 'rt') as f: + for line_number, line in enumerate(f): + m = anchor_pattern.match(line) + if m: + label = m.group(1) + #print("found label: %s" % label) + if label in anchors: + anchors[label].append((filename, line_number+1)) + else: + anchors[label] = [(filename, line_number+1)] + + print("found %d anchor labels" % len(anchors)) + + count = 0 + + for label in sorted(anchors.keys()): + if len(anchors[label]) > 1: + print(label) + count += 1 + for filename, line_number in anchors[label]: + print(" - %s:%d" % (filename, line_number)) + + + if count > 0: + print("Found %d anchor label errors." % count) + sys.exit(1) + else: + print("No anchor label errors.") + +if __name__ == "__main__": + main() diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py index f4656a7f69..d85669bcc1 100644 --- a/doc/utils/converters/setup.py +++ b/doc/utils/converters/setup.py @@ -13,6 +13,6 @@ setup(name='LAMMPS Documentation Utilities', entry_points = { "console_scripts": ['txt2html = lammpsdoc.txt2html:main', 'txt2rst = lammpsdoc.txt2rst:main', - 'doc_anchor_check = lammpsdoc.doc_anchor_check:main '] + 'rst_anchor_check = lammpsdoc.rst_anchor_check:main '] }, ) -- GitLab From 5e6694f3bcda89237fe8cb96903abfdd81413df2 Mon Sep 17 00:00:00 2001 From: Anne Gunn Date: Fri, 21 Jun 2019 08:34:32 -0600 Subject: [PATCH 12/16] Re-enabled conversion of equations arrays. Disabled works even worse --- .../lammpsdoc/eqImg2mathjaxInline.py | 41 +++++++++++++------ 1 file changed, 29 insertions(+), 12 deletions(-) diff --git a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py index 6db83da7fd..353eed8b6e 100644 --- a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py +++ b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py @@ -21,6 +21,7 @@ import argparse import os import re +import shutil import sys @@ -37,7 +38,8 @@ imageMarker = ">>>image was here" image_marker_pattern = re.compile(r'>>>image was here') align_pattern = re.compile(r'.*:align: center') -modifiedFileFolder = "src/modifiedRst/" +modifiedRstFolder = "src/modifiedRst/" +safeRstFolder = "src/safeRst/" # Since this is a proof of concept implementation, # skip any rst files that are known to cause problems skipFileList = ["pair_tersoff_zbl.rst"] @@ -151,7 +153,13 @@ def processFile(filename): # not an equation line, so simply queue it up for output as is modifiedFileLines.append(line) if doWriteModifiedFile: - #print(*modifiedFileLines, sep="\n") + # We're going to write out a modified file, so first copy the original rst + # file into the original file folder. + nameParts = filename.split("/") + filenamePos = len(nameParts) - 1 + safeFilePath = "{0}{1}".format(safeRstFolder, nameParts[filenamePos]) + shutil.copyfile(filename, safeFilePath) + print("modifiedFileLines has %d lines before align center cleanup" % len(modifiedFileLines)) # First, go through the file and pull out the lines where there is # now an image file marker followed by an align center directive @@ -172,17 +180,13 @@ def processFile(filename): print("modifiedFileLines has %d lines after align center cleanup" % len(modifiedFileLines)) # Now we can actually write out the new contents try: - if not os.path.exists(modifiedFileFolder): - os.makedirs(modifiedFileFolder) - nameParts = filename.split("/") - filenamePos = len(nameParts) - 1 - modFilePath = "{0}{1}".format(modifiedFileFolder, nameParts[filenamePos]) + modFilePath = "{0}{1}".format(modifiedRstFolder, nameParts[filenamePos]) modRst = open(modFilePath, "w") for rstLine in modifiedFileLines: modRst.write(rstLine) modRst.close() except OSError: - print('Error: Creating directory. ' + modifiedFileFolder) + print('Error: Creating directory. ' + modifiedRstFolder) return imageCount @@ -193,16 +197,28 @@ def main(): parser = argparse.ArgumentParser(description='replace image markup in rst files with inline mathjax markup from .txt source of images') parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') parsed_args = parser.parse_args() + print(parsed_args) - # TODO: make originalRst folder and copy src/*.rst files into it + if not os.path.exists(safeRstFolder): + os.makedirs(safeRstFolder) + if not os.path.exists(modifiedRstFolder): + os.makedirs(modifiedRstFolder) # Because we may decide to add files to the skip list between runs, # if we have more than one file to process, - # remove the modified file folder so we don't end up with + # files from both original and modified folders # zombie modifications if len(parsed_args.files) > 1: - for outputFile in os.listdir(modifiedFileFolder): - filePath = os.path.join(modifiedFileFolder, outputFile) + for outputFile in os.listdir(modifiedRstFolder): + filePath = os.path.join(modifiedRstFolder, outputFile) + try: + if os.path.isfile(filePath): + os.unlink(filePath) + except Exception as e: + print(e) + sys.exit(1) + for safeFile in os.listdir(safeRstFolder): + filePath = os.path.join(safeRstFolder, safeFile) try: if os.path.isfile(filePath): os.unlink(filePath) @@ -211,6 +227,7 @@ def main(): sys.exit(1) for filename in parsed_args.files: + print("filename: %s" % filename) doSkip = False for skipName in skipFileList: if filename.find(skipName) != -1: -- GitLab From c756e472aeab235f7ea7e939b45dba5abccddb73 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 15:34:57 -0500 Subject: [PATCH 13/16] Remove Manual.txt and use variable for version --- doc/src/Manual.rst | 4 +- doc/txt/Manual.txt | 124 --------------------------------------------- 2 files changed, 2 insertions(+), 126 deletions(-) delete mode 100644 doc/txt/Manual.txt diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index c5485271e1..dd67a13427 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -1,8 +1,8 @@ LAMMPS Documentation #################### -30 Oct 2019 version -******************* +|version| version +***************** :doc:`What is a LAMMPS version? ` diff --git a/doc/txt/Manual.txt b/doc/txt/Manual.txt deleted file mode 100644 index 041a481547..0000000000 --- a/doc/txt/Manual.txt +++ /dev/null @@ -1,124 +0,0 @@ - - -LAMMPS Users Manual - - - - - - - -

- - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html#comm) - -:line - -LAMMPS Documentation :c,h1 -30 Oct 2019 version :c,h2 - -"What is a LAMMPS version?"_Manual_version.html - -LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. - -LAMMPS is a classical molecular dynamics simulation code with a focus -on materials modeling. It was designed to run efficiently on parallel -computers. It was developed originally at Sandia National -Laboratories, a US Department of Energy facility. The majority of -funding for LAMMPS has come from the US Department of Energy (DOE). -LAMMPS is an open-source code, distributed freely under the terms of -the GNU Public License (GPL). - -The "LAMMPS website"_lws has a variety of information about the code. -It includes links to an on-line version of this manual, a "mailing -list"_http://lammps.sandia.gov/mail.html where users can post -questions, and a "GitHub site"_https://github.com/lammps/lammps where -all LAMMPS development is coordinated. - -:line - -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 "Manual build"_Manual_build.html doc page. -There is also a "Developer.pdf"_Developer.pdf document which gives -a brief description of the basic code structure of LAMMPS. - -:line - -Once you are familiar with LAMMPS, you may want to bookmark "this -page"_Commands.html since it gives quick access to a doc page for -every LAMMPS command. - - - - -"Introduction"_Intro.html :olb,l -"Install LAMMPS"_Install.html :l -"Build LAMMPS"_Build.html :l -"Run LAMMPS"_Run_head.html :l -"Commands"_Commands.html :l -"Optional packages"_Packages.html :l -"Accelerate performance"_Speed.html :l -"How-to discussions"_Howto.html :l -"Example scripts"_Examples.html :l -"Auxiliary tools"_Tools.html :l -"Modify & extend LAMMPS"_Modify.html :l -"Use Python with LAMMPS"_Python_head.html :l -"Errors"_Errors.html :l -"Building the LAMMPS manual"_Manual_build.html :l -:ole - - - - -- GitLab From c3e52c3c8cced95f63fcf87b14c1e96aec362175 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 15:48:00 -0500 Subject: [PATCH 14/16] Use globs for style lists --- doc/src/angles.rst | 24 +----- doc/src/bonds.rst | 19 +---- doc/src/computes.rst | 131 +---------------------------- doc/src/dihedrals.rst | 34 +------- doc/src/fixes.rst | 184 +--------------------------------------- doc/src/impropers.rst | 17 +--- doc/src/pairs.rst | 125 +-------------------------- doc/txt/angles.txt | 30 ------- doc/txt/bonds.txt | 25 ------ doc/txt/dihedrals.txt | 40 --------- doc/txt/fixes.txt | 190 ------------------------------------------ doc/txt/pairs.txt | 131 ----------------------------- 12 files changed, 14 insertions(+), 936 deletions(-) delete mode 100644 doc/txt/angles.txt delete mode 100644 doc/txt/bonds.txt delete mode 100644 doc/txt/dihedrals.txt delete mode 100644 doc/txt/fixes.txt delete mode 100644 doc/txt/pairs.txt diff --git a/doc/src/angles.rst b/doc/src/angles.rst index 84a8fad6a8..79c52a5525 100644 --- a/doc/src/angles.rst +++ b/doc/src/angles.rst @@ -4,26 +4,6 @@ Angle Styles .. toctree:: :maxdepth: 1 + :glob: - angle_charmm - angle_class2 - angle_cosine - angle_cosine_buck6d - angle_cosine_delta - angle_cosine_periodic - angle_cosine_shift - angle_cosine_shift_exp - angle_cosine_squared - angle_cross - angle_dipole - angle_fourier - angle_fourier_simple - angle_harmonic - angle_hybrid - angle_mm3 - angle_none - angle_quartic - angle_sdk - angle_table - angle_zero - + angle_* diff --git a/doc/src/bonds.rst b/doc/src/bonds.rst index 55c9702171..3019e0c177 100644 --- a/doc/src/bonds.rst +++ b/doc/src/bonds.rst @@ -4,21 +4,6 @@ Bond Styles .. toctree:: :maxdepth: 1 + :glob: - bond_class2 - bond_fene - bond_fene_expand - bond_gromos - bond_harmonic - bond_harmonic_shift - bond_harmonic_shift_cut - bond_hybrid - bond_mm3 - bond_morse - bond_none - bond_nonlinear - bond_oxdna - bond_quartic - bond_table - bond_zero - + bond_* diff --git a/doc/src/computes.rst b/doc/src/computes.rst index 1bb603f39c..1c1819a444 100644 --- a/doc/src/computes.rst +++ b/doc/src/computes.rst @@ -4,133 +4,6 @@ Computes .. toctree:: :maxdepth: 1 + :glob: - compute_ackland_atom - compute_adf - compute_angle - compute_angle_local - compute_angmom_chunk - compute_basal_atom - compute_body_local - compute_bond - compute_bond_local - compute_centro_atom - compute_chunk_atom - compute_chunk_spread_atom - compute_cluster_atom - compute_cna_atom - compute_cnp_atom - compute_com - compute_com_chunk - compute_contact_atom - compute_coord_atom - compute_damage_atom - compute_dihedral - compute_dihedral_local - compute_dilatation_atom - compute_dipole_chunk - compute_displace_atom - compute_dpd - compute_dpd_atom - compute_edpd_temp_atom - compute_entropy_atom - compute_erotate_asphere - compute_erotate_rigid - compute_erotate_sphere - compute_erotate_sphere_atom - compute_event_displace - compute_fep - compute_global_atom - compute_group_group - compute_gyration - compute_gyration_chunk - compute_gyration_shape - compute_heat_flux - compute_hexorder_atom - compute_hma - compute_improper - compute_improper_local - compute_inertia_chunk - compute_ke - compute_ke_atom - compute_ke_atom_eff - compute_ke_eff - compute_ke_rigid - compute_meso_e_atom - compute_meso_rho_atom - compute_meso_t_atom - compute_momentum - compute_msd - compute_msd_chunk - compute_msd_nongauss - compute_omega_chunk - compute_orientorder_atom - compute_pair - compute_pair_local - compute_pe - compute_pe_atom - compute_plasticity_atom - compute_pressure - compute_pressure_cylinder - compute_pressure_uef - compute_property_atom - compute_property_chunk - compute_property_local - compute_ptm_atom - compute_rdf - compute_reduce - compute_reduce_chunk - compute_rigid_local - compute_saed - compute_slice - compute_smd_contact_radius - compute_smd_damage - compute_smd_hourglass_error - compute_smd_internal_energy - compute_smd_plastic_strain - compute_smd_plastic_strain_rate - compute_smd_rho - compute_smd_tlsph_defgrad - compute_smd_tlsph_dt - compute_smd_tlsph_num_neighs - compute_smd_tlsph_shape - compute_smd_tlsph_strain - compute_smd_tlsph_strain_rate - compute_smd_tlsph_stress - compute_smd_triangle_vertices - compute_smd_ulsph_num_neighs - compute_smd_ulsph_strain - compute_smd_ulsph_strain_rate - compute_smd_ulsph_stress - compute_smd_vol - compute_sna_atom - compute_spin - compute_stress_atom - compute_stress_mop - compute_tally - compute_tdpd_cc_atom - compute_temp - compute_temp_asphere - compute_temp_body - compute_temp_chunk - compute_temp_com - compute_temp_cs - compute_temp_deform - compute_temp_deform_eff - compute_temp_drude - compute_temp_eff - compute_temp_partial - compute_temp_profile - compute_temp_ramp - compute_temp_region - compute_temp_region_eff - compute_temp_rotate - compute_temp_sphere - compute_temp_uef - compute_ti - compute_torque_chunk - compute_vacf - compute_vcm_chunk - compute_voronoi_atom - compute_xrd - + compute_* diff --git a/doc/src/dihedrals.rst b/doc/src/dihedrals.rst index e14399fcb6..bab913f1c2 100644 --- a/doc/src/dihedrals.rst +++ b/doc/src/dihedrals.rst @@ -4,36 +4,6 @@ Dihedral Styles .. toctree:: :maxdepth: 1 + :glob: - dihedral_charmm - dihedral_class2 - dihedral_cosine_shift_exp - dihedral_fourier - dihedral_harmonic - dihedral_helix - dihedral_hybrid - dihedral_multi_harmonic - dihedral_nharmonic - dihedral_none - dihedral_opls - dihedral_quadratic - dihedral_spherical - dihedral_table - dihedral_table_cut - dihedral_zero - dihedral_charmm - dihedral_class2 - dihedral_cosine_shift_exp - dihedral_fourier - dihedral_harmonic - dihedral_helix - dihedral_hybrid - dihedral_multi_harmonic - dihedral_nharmonic - dihedral_none - dihedral_opls - dihedral_quadratic - dihedral_spherical - dihedral_table - dihedral_zero - + dihedral_* diff --git a/doc/src/fixes.rst b/doc/src/fixes.rst index 3678fcc853..5a85738c45 100644 --- a/doc/src/fixes.rst +++ b/doc/src/fixes.rst @@ -4,186 +4,6 @@ Fixes .. toctree:: :maxdepth: 1 + :glob: - fix_adapt - fix_adapt_fep - fix_addforce - fix_addtorque - fix_append_atoms - fix_atc - fix_atom_swap - fix_ave_atom - fix_ave_chunk - fix_ave_correlate - fix_ave_correlate_long - fix_ave_histo - fix_ave_time - fix_aveforce - fix_balance - fix_bocs - fix_bond_break - fix_bond_create - fix_bond_swap - fix_bond_react - fix_box_relax - fix_client_md - fix_cmap - fix_colvars - fix_controller - fix_deform - fix_deposit - fix_drag - fix_drude - fix_drude_transform - fix_dpd_energy - fix_dpd_source - fix_dt_reset - fix_efield - fix_ehex - fix_electron_stopping - fix_enforce2d - fix_eos_cv - fix_eos_table - fix_eos_table_rx - fix_evaporate - fix_external - fix_ffl - fix_filter_corotate - fix_flow_gauss - fix_freeze - fix_gcmc - fix_gld - fix_gle - fix_gravity - fix_grem - fix_halt - fix_heat - fix_hyper_global - fix_hyper_local - fix_imd - fix_indent - fix_ipi - fix_langevin - fix_langevin_drude - fix_langevin_eff - fix_langevin_spin - fix_latte - fix_lb_fluid - fix_lb_momentum - fix_lb_pc - fix_lb_rigid_pc_sphere - fix_lb_viscous - fix_lineforce - fix_manifoldforce - fix_meso - fix_meso_move - fix_meso_stationary - fix_momentum - fix_move - fix_mscg - fix_msst - fix_mvv_dpd - fix_neb - fix_neb_spin - fix_nh - fix_nh_eff - fix_nh_uef - fix_nph_asphere - fix_nph_body - fix_nph_sphere - fix_nphug - fix_npt_asphere - fix_npt_body - fix_npt_sphere - fix_nve - fix_nve_asphere - fix_nve_asphere_noforce - fix_nve_awpmd - fix_nve_body - fix_nve_dot - fix_nve_dotc_langevin - fix_nve_eff - fix_nve_limit - fix_nve_line - fix_nve_manifold_rattle - fix_nve_noforce - fix_nve_sphere - fix_nve_spin - fix_nve_tri - fix_nvk - fix_nvt_asphere - fix_nvt_body - fix_nvt_manifold_rattle - fix_nvt_sllod - fix_nvt_sllod_eff - fix_nvt_sphere - fix_oneway - fix_orient - fix_phonon - fix_pimd - fix_planeforce - fix_plumed - fix_poems - fix_pour - fix_precession_spin - fix_press_berendsen - fix_print - fix_property_atom - fix_python_invoke - fix_python_move - fix_qbmsst - fix_qeq - fix_qeq_comb - fix_qeq_reax - fix_qmmm - fix_qtb - fix_reaxc_bonds - fix_reaxc_species - fix_recenter - fix_restrain - fix_rhok - fix_rigid - fix_rigid_meso - fix_rx - fix_saed_vtk - fix_setforce - fix_shake - fix_shardlow - fix_smd - fix_smd_adjust_dt - fix_smd_integrate_tlsph - fix_smd_integrate_ulsph - fix_smd_move_triangulated_surface - fix_smd_setvel - fix_smd_wall_surface - fix_spring - fix_spring_chunk - fix_spring_rg - fix_spring_self - fix_srd - fix_store_force - fix_store_state - fix_temp_berendsen - fix_temp_csvr - fix_temp_rescale - fix_temp_rescale_eff - fix_tfmc - fix_thermal_conductivity - fix_ti_spring - fix_tmd - fix_ttm - fix_tune_kspace - fix_vector - fix_viscosity - fix_viscous - fix_wall - fix_wall_body_polygon - fix_wall_body_polyhedron - fix_wall_ees - fix_wall_gran - fix_wall_gran_region - fix_wall_piston - fix_wall_reflect - fix_wall_region - fix_wall_srd - + fix_* diff --git a/doc/src/impropers.rst b/doc/src/impropers.rst index c524004fc4..93b4776d2c 100644 --- a/doc/src/impropers.rst +++ b/doc/src/impropers.rst @@ -4,19 +4,6 @@ Improper Styles .. toctree:: :maxdepth: 1 + :glob: - improper_class2 - improper_cossq - improper_cvff - improper_distance - improper_distharm - improper_fourier - improper_harmonic - improper_hybrid - improper_inversion_harmonic - improper_none - improper_ring - improper_umbrella - improper_sqdistharm - improper_zero - + improper_* diff --git a/doc/src/pairs.rst b/doc/src/pairs.rst index 9124013161..4fdf2b2c69 100644 --- a/doc/src/pairs.rst +++ b/doc/src/pairs.rst @@ -4,127 +4,6 @@ Pair Styles .. toctree:: :maxdepth: 1 + :glob: - pair_adp - pair_agni - pair_airebo - pair_atm - pair_awpmd - pair_beck - pair_body_nparticle - pair_body_rounded_polygon - pair_body_rounded_polyhedron - pair_bop - pair_born - pair_brownian - pair_buck - pair_buck_long - pair_buck6d_coul_gauss - pair_charmm - pair_class2 - pair_colloid - pair_comb - pair_cosine_squared - pair_coul - pair_coul_diel - pair_coul_shield - pair_cs - pair_dipole - pair_dpd - pair_dpd_fdt - pair_drip - pair_dsmc - pair_e3b - pair_eam - pair_edip - pair_eff - pair_eim - pair_exp6_rx - pair_extep - pair_fep_soft - pair_gauss - pair_gayberne - pair_gran - pair_granular - pair_gromacs - pair_gw - pair_hbond_dreiding - pair_hybrid - pair_ilp_graphene_hbn - pair_kim - pair_kolmogorov_crespi_full - pair_kolmogorov_crespi_z - pair_lcbop - pair_lebedeva_z - pair_line_lj - pair_list - pair_lj - pair_lj96 - pair_lj_cubic - pair_lj_expand - pair_lj_long - pair_lj_smooth - pair_lj_smooth_linear - pair_lj_switch3_coulgauss - pair_local_density - pair_lubricate - pair_lubricateU - pair_mdf - pair_meamc - pair_meam_spline - pair_meam_sw_spline - pair_meso - pair_mgpt - pair_mie - pair_mm3_switch3_coulgauss - pair_momb - pair_morse - pair_multi_lucy - pair_multi_lucy_rx - pair_nb3b_harmonic - pair_nm - pair_none - pair_oxdna - pair_oxdna2 - pair_peri - pair_polymorphic - pair_python - pair_quip - pair_reaxc - pair_resquared - pair_sdk - pair_sdpd_taitwater_isothermal - pair_smd_hertz - pair_smd_tlsph - pair_smd_triangulated_surface - pair_smd_ulsph - pair_smtbq - pair_snap - pair_soft - pair_sph_heatconduction - pair_sph_idealgas - pair_sph_lj - pair_sph_rhosum - pair_sph_taitwater - pair_sph_taitwater_morris - pair_spin_dipole - pair_spin_dmi - pair_spin_exchange - pair_spin_magelec - pair_spin_neel - pair_srp - pair_sw - pair_table - pair_table_rx - pair_tersoff - pair_tersoff_mod - pair_tersoff_zbl - pair_thole - pair_tri_lj - pair_ufm - pair_vashishta - pair_yukawa - pair_yukawa_colloid - pair_zbl - pair_zero - + pair_* diff --git a/doc/txt/angles.txt b/doc/txt/angles.txt deleted file mode 100644 index 3d8a47b2eb..0000000000 --- a/doc/txt/angles.txt +++ /dev/null @@ -1,30 +0,0 @@ -Angle Styles :h1 - - diff --git a/doc/txt/bonds.txt b/doc/txt/bonds.txt deleted file mode 100644 index 48896e711c..0000000000 --- a/doc/txt/bonds.txt +++ /dev/null @@ -1,25 +0,0 @@ -Bond Styles :h1 - - diff --git a/doc/txt/dihedrals.txt b/doc/txt/dihedrals.txt deleted file mode 100644 index a862bf50a0..0000000000 --- a/doc/txt/dihedrals.txt +++ /dev/null @@ -1,40 +0,0 @@ -Dihedral Styles :h1 - - diff --git a/doc/txt/fixes.txt b/doc/txt/fixes.txt deleted file mode 100644 index d966b9a225..0000000000 --- a/doc/txt/fixes.txt +++ /dev/null @@ -1,190 +0,0 @@ -Fixes :h1 - - diff --git a/doc/txt/pairs.txt b/doc/txt/pairs.txt deleted file mode 100644 index 1f8f130e48..0000000000 --- a/doc/txt/pairs.txt +++ /dev/null @@ -1,131 +0,0 @@ -Pair Styles :h1 - - -- GitLab From 729eabd77146592763f3dd3ad4234cb428905c49 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 6 Nov 2019 08:32:07 -0500 Subject: [PATCH 15/16] make QUIP_LIBRARY setting consistent and backport change to .rst file only --- doc/rst/Build_extras.rst | 2 +- doc/src/Build_extras.txt | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/rst/Build_extras.rst b/doc/rst/Build_extras.rst index 49e3d5c801..6162940015 100644 --- a/doc/rst/Build_extras.rst +++ b/doc/rst/Build_extras.rst @@ -1258,7 +1258,7 @@ lib/quip/README file for details on how to do this. CMake will not download and build the QUIP library. But once you have done that, a CMake build of LAMMPS with "-D PKG\_USER-QUIP=yes" should -work. Set QUIP\_LIBRARIES if CMake cannot find the QUIP library. +work. Set QUIP\_LIBRARY if CMake cannot find the QUIP library. **Traditional make**\ : diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index b315e244c5..114aeda7af 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -1034,11 +1034,11 @@ lib/quip/README file for details on how to do this. [CMake build]: --D QUIP_LIBRARIES=path # path to libquip.a (only needed if a custom location) :pre +-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) :pre CMake will not download and build the QUIP library. But once you have done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should -work. Set QUIP_LIBRARIES if CMake cannot find the QUIP library. +work. Set QUIP_LIBRARY if CMake cannot find the QUIP library. [Traditional make]: -- GitLab From 2fd9a2790263c5641540efd8b0e6d47f1dc9abdd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 6 Nov 2019 08:33:05 -0500 Subject: [PATCH 16/16] update kim_commands.rst from .txt file --- doc/rst/kim_commands.rst | 352 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 326 insertions(+), 26 deletions(-) diff --git a/doc/rst/kim_commands.rst b/doc/rst/kim_commands.rst index e9393200d7..9f0b5a6775 100644 --- a/doc/rst/kim_commands.rst +++ b/doc/rst/kim_commands.rst @@ -9,6 +9,9 @@ kim\_interactions command kim\_query command ================== +kim\_param command +================== + Syntax """""" @@ -18,15 +21,36 @@ Syntax kim_init model user_units unitarg kim_interactions typeargs kim_query variable formatarg query_function queryargs + kim_param get param_name index_range variables formatarg + kim_param set param_name index_range values + +.. _formatarg\_options: + + * model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) * user\_units = the LAMMPS :doc:`units ` style assumed in the LAMMPS input script * unitarg = *unit\_conversion\_mode* (optional) * typeargs = atom type to species mapping (one entry per atom type) or *fixed\_types* for models with a preset fixed mapping -* variable = name of a (string style) variable where the result of the query is stored -* formatarg = *split* (optional) +* variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command. +* formatarg = *list, split, or explicit* (optional): + + .. parsed-literal:: + + *list* = returns a single string with a list of space separated values + (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as + defined by the *variable* argument. [default for *kim_query*] + *split* = returns the values separately in new variables with names based + on the prefix specified in *variable* and a number appended to + indicate which element in the list of values is in the variable. + *explicit* = returns the values separately in one more more variable names + provided as arguments that preceed *formatarg*\ . [default for *kim_param*] + * query\_function = name of the OpenKIM web API query function to be used * queryargs = a series of *keyword=value* pairs that represent the web query; supported keywords depend on the query function +* param\_name = name of a KIM portable model parameter +* index\_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements) +* values = new value(s) to replace the current value(s) of a KIM portable model parameter Examples """""""" @@ -39,9 +63,11 @@ Examples kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O - Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real + kim_init Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolventsPolymers__SM_039297821658_000 real kim_interactions fixed_types kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"] + kim_param get gamma 1 varGamma + kim_param set gamma 1 3.0 Description """"""""""" @@ -90,6 +116,10 @@ Types of IMs in OpenKIM There are two types of IMs archived in OpenKIM: +.. _PM\_type: + + + 1. The first type is called a *KIM Portable Model* (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface (`KIM API `_) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see `complete list of supported codes `_). 2. The second type is called a *KIM Simulator Model* (SM). A KIM SM is an IM that is implemented natively within a simulation code (\ *simulator*\ ) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. @@ -126,7 +156,7 @@ The URL for the Model Page is constructed from the https://openkim.org/id/extended_KIM_ID -For example for the Stillinger-Weber potential +For example, for the Stillinger--Weber potential listed above the Model Page is located at: @@ -224,7 +254,8 @@ potential for Al: The above script will end with an error in the *kim\_init* line if the IM is changed to another potential for Al that does not work with *metal* -units. To address this *kim\_init* offers the *unit\_conversion\_mode*. +units. To address this *kim\_init* offers the *unit\_conversion\_mode* +as shown below. If unit conversion mode *is* active, then *kim\_init* calls the LAMMPS :doc:`units ` command to set the units to the IM's required or preferred units. Conversion factors between the IM's units and the *user\_units* @@ -284,7 +315,7 @@ will work correctly for any IM for Al (KIM PM or SM) selected by the *kim\_init* command. Care must be taken to apply unit conversion to dimensional variables read in -from a file. For example if a configuration of atoms is read in from a +from a file. For example, if a configuration of atoms is read in from a dump file using the :doc:`read\_dump ` command, the following can be done to convert the box and all atomic positions to the correct units: @@ -408,14 +439,40 @@ Using OpenKIM Web Queries in LAMMPS (*kim\_query*) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The *kim\_query* command performs a web query to retrieve the predictions -of the IM set by *kim\_init* for material properties archived in -`OpenKIM `_. The *kim\_query* command must be preceded -by a *kim\_init* command. The result of the query is stored in a -:doc:`string style variable `, the name of which is given as the first -argument of the *kim\_query command*. (For the case of multiple -return values, the optional *split* keyword can be used after the -variable name to separate the results into multiple variables; see -the :ref:`example ` below.) +of an IM set by *kim\_init* for material properties archived in +`OpenKIM `_. + +.. note:: + + The *kim\_query* command must be preceded by a *kim\_init* command. + +The syntax for the *kim\_query* command is as follows: + + +.. parsed-literal:: + + kim_query variable formatarg query_function queryargs + +The result of the query is stored in one or more +:doc:`string style variables ` as determined by the +optional *formatarg* argument :ref:`documented above `. +For the "list" setting of *formatarg* (or if *formatarg* is not +specified), the result is returned as a space-separated list of +values in *variable*\ . +The *formatarg* keyword "split" separates the result values into +individual variables of the form *prefix\_I*, where *prefix* is set to the +*kim\_query* *variable* argument and *I* ranges from 1 to the number of +returned values. The number and order of the returned values is determined +by the type of query performed. (Note that the "explicit" setting of +*formatarg* is not supported by *kim\_query*.) + +.. note:: + + *kim\_query* only supports queries that return a single result or + an array of values. More complex queries that return a JSON structure + are not currently supported. An attempt to use *kim\_query* in such + cases will generate an error. + The second required argument *query\_function* is the name of the query function to be called (e.g. *get\_lattice\_constant\_cubic*). All following :doc:`arguments ` are parameters handed over to @@ -443,8 +500,8 @@ is available on the OpenKIM webpage at `query documentation `_ to see which methods are available for a given *query function*\ . -*kim\_query* Usage Examples and Further Clarifications: -""""""""""""""""""""""""""""""""""""""""""""""""""""""" +*kim\_query* Usage Examples and Further Clarifications +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The data obtained by *kim\_query* commands can be used as part of the setup or analysis phases of LAMMPS simulations. Some examples are given below. @@ -473,10 +530,6 @@ Note that in *unit\_conversion\_mode* the results obtained from a For example, in the above script, the lattice command would need to be changed to: "lattice fcc ${a0}\*${\_u_distance}". -.. _split\_example: - - - **Define an equilibrium hcp crystal** @@ -494,12 +547,11 @@ changed to: "lattice fcc ${a0}\*${\_u_distance}". In this case the *kim\_query* returns two arguments (since the hexagonal close packed (hcp) structure has two independent lattice constants). -The default behavior of *kim\_query* returns the result as a string -with the values separated by commas. The optional keyword *split* -separates the result values into individual variables of the form -*prefix\_I*, where *prefix* is set to the the *kim\_query* *variable* argument -and *I* ranges from 1 to the number of returned values. The number and order of -the returned values is determined by the type of query performed. +The *formatarg* keyword "split" places the two values into +the variables *latconst\_1* and *latconst\_2*. (These variables are +created if they do not already exist.) For convenience the variables +*a0* and *c0* are created in order to make the remainder of the +input script more readable. **Define a crystal at finite temperature accounting for thermal expansion** @@ -560,6 +612,254 @@ ideal fcc cohesive energy of the atoms in the system obtained from from these programs are queried is tracked. No other information about the nature of the query or its source is recorded. +Accessing KIM Model Parameters from LAMMPS (*kim\_param*) +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +All IMs are functional forms containing a set of +parameters. The values of these parameters are typically +selected to best reproduce a training set of quantum mechanical +calculations or available experimental data. For example, a +Lennard-Jones potential intended to model argon might have the values of +its two parameters, epsilon and sigma, fit to the +dimer dissociation energy or thermodynamic properties at a critical point +of the phase diagram. + +Normally a user employing an IM should not modify its parameters since, +as noted above, these are selected to reproduce material properties. +However, there are cases where accessing and modifying IM parameters +is desired, such as for assessing uncertainty, fitting an IM, +or working with an ensemble of IMs. As explained :ref:`above `, +IMs archived in OpenKIM are either Portable Models (PMs) or +Simulator Models (SMs). KIM PMs are complete independent implementations +of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS. +Two different mechanisms are provided for accessing IM parameters in these +two cases: + +* For a KIM PM, the *kim\_param* command can be used to *get* and *set* the values of the PM's parameters as explained below. +* For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible). + +The *kim\_param get* and *kim\_param set* commands provide an interface +to access and change the parameters of a KIM PM that "publishes" its +parameters and makes them publicly available (see the +`KIM API documentation `_ +for details). + +.. note:: + + The *kim\_param get/set* commands must be preceded by *kim\_init*. + The *kim\_param set* command must additionally be preceded by a + *kim\_interactions* command (or alternatively by a *pair\_style kim* + and *pair\_coeff* commands). The *kim\_param set* command may be used wherever a *pair\_coeff* command may occur. + +The syntax for the *kim\_param* command is as follows: + + +.. parsed-literal:: + + kim_param get param_name index_range variable formatarg + kim_param set param_name index_range values + +Here, *param\_name* is the name of a KIM PM parameter (which is published +by the PM and available for access). The specific string used to identify +a parameter is defined by the PM. For example, for the +`Stillinger--Weber (SW) potential in OpenKIM `_, +the parameter names are *A, B, p, q, sigma, gamma, cutoff, lambda, costheta0*\ . + +.. note:: + + The list of all the parameters that a PM exposes for access/mutation are + automatically written to the lammps log file when *kim\_init* is called. + +Each published parameter of a KIM PM takes the form of an array of +numerical values. The array can contain one element for a single-valued +parameter, or a set of values. For example, the +`multispecies SW potential for the Zn-Cd-Hg-S-Se-Te system `_ +has the same parameter names as the +`single-species SW potential `_, +but each parameter array contains 21 entries that correspond to the parameter +values used for each pairwise combination of the model's six supported species +(this model does not have parameters specific to individual ternary +combinations of its supported species). + +The *index\_range* argument may either be an integer referring to +a specific element within the array associated with the parameter +specified by *param\_name*, or a pair of integers separated by a colon +that refer to a slice of this array. In both cases, one-based indexing is +used to refer to the entries of the array. + +The result of a *get* operation for a specific *index\_range* is stored in +one or more :doc:`LAMMPS string style variables ` as determined +by the optional *formatarg* argument :ref:`documented above. ` +If not specified, the default for *formatarg* is "explicit" for the +*kim\_param* command. + +For the case where the result is an array with multiple values +(i.e. *index\_range* contains a range), the optional "split" or "explicit" +*formatarg* keywords can be used to separate the results into multiple +variables; see the examples below. +Multiple parameters can be retrieved with a single call to *kim\_param get* +by repeating the argument list following *get*\ . + +For a *set* operation, the *values* argument contains the new value(s) +for the element(s) of the parameter specified by *index\_range*. For the case +where multiple values are being set, *values* contains a set of values +separated by spaces. Multiple parameters can be set with a single call to +*kim\_param set* by repeating the argument list following *set*\ . + +*kim\_param* Usage Examples and Further Clarifications +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Examples of getting and setting KIM PM parameters with further +clarifications are provided below. + +**Getting a scalar parameter** + + +.. parsed-literal:: + + kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal + ... + kim_param get A 1 VARA + +In this case, the value of the SW *A* parameter is retrieved and placed +in the LAMMPS variable *VARA*\ . The variable *VARA* can be used +in the remainder of the input script in the same manner as any other +LAMMPS variable. + +**Getting multiple scalar parameters with a single call** + + +.. parsed-literal:: + + kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal + ... + kim_param get A 1 VARA B 1 VARB + +This retrieves the *A* and *B* parameters of the SW potential and stores +them in the LAMMPS variables *VARA* and *VARB*\ . + +**Getting a range of values from a parameter** + +There are several options when getting a range of values from a parameter +determined by the *formatarg* argument. + + +.. parsed-literal:: + + kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal + ... + kim_param get lambda 7:9 LAM_TeTe LAM_TeZn LAM_TeSe + +In this case, *formatarg* is not specified and therefore the default +"explicit" mode is used. (The behavior would be the same if the word +*explicit* were added after *LAM\_TeSe*.) Elements 7, 8 and 9 of parameter +lambda retrieved by the *get* operation are placed in the LAMMPS variables +*LAM\_TeTe*, *LAM\_TeZn* and *LAM\_TeSe*, respectively. + +.. note:: + + In the above example, elements 7--9 of the lambda parameter correspond + to Te-Te, Te-Zm and Te-Se interactions. This can be determined by visiting + the `model page for the specified potential `_ + and looking at its parameter file linked to at the bottom of the page + (file with .param ending) and consulting the README documentation + provided with the driver for the PM being used. A link to the driver + is provided at the top of the model page. + + +.. parsed-literal:: + + kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal + ... + kim_param get lambda 15:17 LAMS list + variable LAM_VALUE index ${LAMS} + label loop_on_lambda + ... + ... do something with current value of lambda + ... + next LAM_VALUE + jump SELF loop_on_lambda + +In this case, the "list" mode of *formatarg* is used. +The result of the *get* operation is stored in the LAMMPS variable +*LAMS* as a string containing the three retrieved values separated +by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an +*index* variable to access the values one at a time within a loop +as shown in the example. At each iteration of the loop *LAM\_VALUE* +contains the current value of lambda. + + +.. parsed-literal:: + + kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal + ... + kim_param get lambda 15:17 LAM split + +In this case, the "split" mode of *formatarg* is used. +The three values retrieved by the *get* operation are stored in +the three LAMMPS variables *LAM\_15*, *LAM\_16* and *LAM\_17*. +The provided name "LAM" is used as prefix and the location in +the lambda array is appended to create the variable names. + +**Setting a scalar parameter** + + +.. parsed-literal:: + + kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal + ... + kim_interactions Si + kim_param set gamma 1 2.6 + +Here, the SW potential's gamma parameter is set to 2.6. Note that the *get* +and *set* commands work together, so that a *get* following a *set* +operation will return the new value that was set. For example: + + +.. parsed-literal:: + + ... + kim_interactions Si + kim_param get gamma 1 ORIG_GAMMA + kim_param set gamma 1 2.6 + kim_param get gamma 1 NEW_GAMMA + ... + print "original gamma = ${ORIG_GAMMA}, new gamma = ${NEW_GAMMA}" + +Here, *ORIG\_GAMMA* will contain the original gamma value for the SW +potential, while *NEW\_GAMMA* will contain the value 2.6. + +**Setting multiple scalar parameters with a single call** + + +.. parsed-literal:: + + kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal + ... + kim_interactions Cd Te + variable VARG equal 2.6 + variable VARS equal 2.0951 + kim_param set gamma 1 ${VARG} sigma 3 ${VARS} + +In this case, the first element of the *gamma* parameter and +third element of the *sigma* parameter are set to 2.6 and 2.0951, +respectively. This example also shows how LAMMPS variables can +be used when setting parameters. + +**Setting a range of values of a parameter** + + +.. parsed-literal:: + + kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal + ... + kim_interactions Cd Te Zn Se Hg S + kim_param set sigma 2:6 2.35214 2.23869 2.04516 2.43269 1.80415 + +In this case, elements 2 through 6 of the parameter *sigma* +are set to the values 2.35214, 2.23869, 2.04516, 2.43269 and 1.80415 in +order. + Citation of OpenKIM IMs ----------------------- -- GitLab