Unverified Commit 3deece16 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into next_lammps_version

parents 48c136b7 f5733ccd

cmake/CMakeLists.txt

+7 −7
Original line number Diff line number Diff line
@@ -107,7 +107,7 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR}) 


option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)



set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE

set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE

  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ

  REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI

  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
@@ -116,8 +116,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE 
  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION

  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY

  USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)

set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)

foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})

set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)

foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})

  option(PKG_${PKG} "Build ${PKG} Package" OFF)

endforeach()
@@ -362,7 +362,7 @@ RegisterStyles(${LAMMPS_SOURCE_DIR}) 
##############################################

# add sources of enabled packages

############################################

foreach(PKG ${DEFAULT_PACKAGES})

foreach(PKG ${STANDARD_PACKAGES})

  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})



  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@@ -390,7 +390,7 @@ foreach(PKG MPIIO) 
endforeach()



# dedicated check for entire contents of accelerator packages

foreach(PKG ${ACCEL_PACKAGES})

foreach(PKG ${SUFFIX_PACKAGES})

  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})



  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@@ -481,7 +481,7 @@ target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR}) 
######################################

set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")

set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")

set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})

set(temp_PKG_LIST ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})

list(SORT temp_PKG_LIST)

foreach(PKG ${temp_PKG_LIST})

    if(PKG_${PKG})
@@ -655,7 +655,7 @@ include(CodeCoverage) 
###############################################################################

# Print package summary

###############################################################################

foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})

foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})

  if(PKG_${PKG})

    message(STATUS "Building package: ${PKG}")

  endif()

doc/src/Commands_pair.rst

+1 −0
Original line number Diff line number Diff line
@@ -131,6 +131,7 @@ OPT. 
   * :doc:`lj/class2/coul/cut (ko) <pair_class2>`

   * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`

   * :doc:`lj/class2/coul/long (gko) <pair_class2>`

   * :doc:`lj/class2/coul/long/cs <pair_cs>`

   * :doc:`lj/class2/coul/long/soft <pair_fep_soft>`

   * :doc:`lj/class2/soft <pair_fep_soft>`

   * :doc:`lj/cubic (go) <pair_lj_cubic>`

doc/src/pair_cs.rst

+8 −1
Original line number Diff line number Diff line
@@ -30,6 +30,9 @@ pair_style coul/wolf/cs command 
pair_style lj/cut/coul/long/cs command

=======================================



pair_style lj/class2/coul/long/cs command

==========================================



Syntax

""""""
@@ -37,7 +40,7 @@ Syntax 


   pair_style style args



* style = *born/coul/dsf/cs* or *born/coul/long/cs* or *born/coul/wolf/cs* or *buck/coul/long/cs* or *coul/long/cs* or *coul/wolf/cs* or *lj/cut/coul/long/cs*

* style = *born/coul/dsf/cs* or *born/coul/long/cs* or *born/coul/wolf/cs* or *buck/coul/long/cs* or *coul/long/cs* or *coul/wolf/cs* or *lj/cut/coul/long/cs* or *lj/class2/coul/long/cs*

* args = list of arguments for a particular style



.. parsed-literal::
@@ -64,6 +67,9 @@ Syntax 
     *lj/cut/coul/long/cs* args = cutoff (cutoff2)

       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)

       cutoff2 = global cutoff for Coulombic (optional) (distance units)

     *lj/class2/coul/long/cs* args = cutoff (cutoff2)

       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)

       cutoff2 = global cutoff for Coulombic (optional) (distance units)



Examples

""""""""
@@ -115,6 +121,7 @@ the "/cs" in the name: 
* :doc:`pair_style coul/long <pair_coul>`

* :doc:`pair_style coul/wolf <pair_coul>`

* :doc:`pair_style lj/cut/coul/long <pair_lj>`

* :doc:`pair_style lj/class2/coul/long <pair_class2>`



except that they correctly treat the special case where the distance

between two charged core and shell atoms in the same core/shell pair

doc/src/pair_style.rst

+44 −43
Original line number Diff line number Diff line
@@ -111,41 +111,41 @@ accelerated styles exist. 
* :doc:`born <pair_born>` - Born-Mayer-Huggins potential

* :doc:`born/coul/dsf <pair_born>` - Born with damped-shifted-force model

* :doc:`born/coul/dsf/cs <pair_cs>` - Born with damped-shifted-force and core/shell model

* :doc:`born/coul/long <pair_born>` - Born with long-range Coulombics

* :doc:`born/coul/long/cs <pair_cs>` - Born with long-range Coulombics and core/shell

* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulombics

* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulombics

* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulombics and core/shell model

* :doc:`born/coul/long <pair_born>` - Born with long-range Coulomb

* :doc:`born/coul/long/cs <pair_cs>` - Born with long-range Coulomb and core/shell

* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb

* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb

* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model

* :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics

* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity

* :doc:`buck <pair_buck>` - Buckingham potential

* :doc:`buck/coul/cut <pair_buck>` - Buckingham with cutoff Coulomb

* :doc:`buck/coul/long <pair_buck>` - Buckingham with long-range Coulombics

* :doc:`buck/coul/long/cs <pair_cs>` - Buckingham with long-range Coulombics and core/shell

* :doc:`buck/coul/msm <pair_buck>` - Buckingham with long-range MSM Coulombics

* :doc:`buck/long/coul/long <pair_buck_long>` - long-range Buckingham with long-range Coulombics

* :doc:`buck/coul/long <pair_buck>` - Buckingham with long-range Coulomb

* :doc:`buck/coul/long/cs <pair_cs>` - Buckingham with long-range Coulomb and core/shell

* :doc:`buck/coul/msm <pair_buck>` - Buckingham with long-range MSM Coulomb

* :doc:`buck/long/coul/long <pair_buck_long>` - long-range Buckingham with long-range Coulomb

* :doc:`buck/mdf <pair_mdf>` - Buckingham with a taper function

* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with damped-shift-force model

* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with long-range Coulombics

* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with long-range Coulomb

* :doc:`colloid <pair_colloid>` - integrated colloidal potential

* :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential

* :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential

* :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential

* :doc:`coul/cut <pair_coul>` - cutoff Coulombic potential

* :doc:`coul/cut/soft <pair_fep_soft>` - Coulombic potential with a soft core

* :doc:`coul/debye <pair_coul>` - cutoff Coulombic potential with Debye screening

* :doc:`coul/cut <pair_coul>` - cutoff Coulomb potential

* :doc:`coul/cut/soft <pair_fep_soft>` - Coulomb potential with a soft core

* :doc:`coul/debye <pair_coul>` - cutoff Coulomb potential with Debye screening

* :doc:`coul/diel <pair_coul_diel>` - Coulomb potential with dielectric permittivity

* :doc:`coul/dsf <pair_coul>` - Coulombics with damped-shifted-force model

* :doc:`coul/long <pair_coul>` - long-range Coulombic potential

* :doc:`coul/long/cs <pair_cs>` - long-range Coulombic potential and core/shell

* :doc:`coul/long/soft <pair_fep_soft>` - long-range Coulombic potential with a soft core

* :doc:`coul/msm <pair_coul>` - long-range MSM Coulombics

* :doc:`coul/slater/cut <pair_coul>` - smeared out Coulombics

* :doc:`coul/slater/long <pair_coul>` - long-range smeared out Coulombics

* :doc:`coul/shield <pair_coul_shield>` - Coulombics for boron nitride for use with :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` potential

* :doc:`coul/streitz <pair_coul>` - Coulombics via Streitz/Mintmire Slater orbitals

* :doc:`coul/wolf <pair_coul>` - Coulombics via Wolf potential

* :doc:`coul/wolf/cs <pair_cs>` - ditto with core/shell adjustments

* :doc:`coul/dsf <pair_coul>` - Coulomb with damped-shifted-force model

* :doc:`coul/long <pair_coul>` - long-range Coulomb potential

* :doc:`coul/long/cs <pair_cs>` - long-range Coulomb potential and core/shell

* :doc:`coul/long/soft <pair_fep_soft>` - long-range Coulomb potential with a soft core

* :doc:`coul/msm <pair_coul>` - long-range MSM Coulomb

* :doc:`coul/slater/cut <pair_coul>` - smeared out Coulomb

* :doc:`coul/slater/long <pair_coul>` - long-range smeared out Coulomb

* :doc:`coul/shield <pair_coul_shield>` - Coulomb for boron nitride for use with :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` potential

* :doc:`coul/streitz <pair_coul>` - Coulomb via Streitz/Mintmire Slater orbitals

* :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential

* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments

* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)

* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure

* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
@@ -189,44 +189,45 @@ accelerated styles exist. 
* :doc:`lj/charmm/coul/charmm/implicit <pair_charmm>` - CHARMM for implicit solvent

* :doc:`lj/charmm/coul/long <pair_charmm>` - CHARMM with long-range Coulomb

* :doc:`lj/charmm/coul/long/soft <pair_fep_soft>` - CHARMM with long-range Coulomb and a soft core

* :doc:`lj/charmm/coul/msm <pair_charmm>` - CHARMM with long-range MSM Coulombics

* :doc:`lj/charmm/coul/msm <pair_charmm>` - CHARMM with long-range MSM Coulomb

* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>` - CHARMM with force switching and shifting

* :doc:`lj/charmmfsw/coul/long <pair_charmm>` - CHARMM with force switching and long-rnage Coulombics

* :doc:`lj/class2 <pair_class2>` - COMPASS (class 2) force field with no Coulomb

* :doc:`lj/charmmfsw/coul/long <pair_charmm>` - CHARMM with force switching and long-rnage Coulomb

* :doc:`lj/class2 <pair_class2>` - COMPASS (class 2) force field without Coulomb

* :doc:`lj/class2/coul/cut <pair_class2>` - COMPASS with cutoff Coulomb

* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>` - COMPASS with cutoff Coulomb with a soft core

* :doc:`lj/class2/coul/long <pair_class2>` - COMPASS with long-range Coulomb

* :doc:`lj/class2/coul/long/cs <pair_cs>` - COMPASS with long-range Coulomb with core/shell adjustments

* :doc:`lj/class2/coul/long/soft <pair_fep_soft>` - COMPASS with long-range Coulomb with a soft core

* :doc:`lj/class2/soft <pair_fep_soft>` - COMPASS (class 2) force field with no Coulomb with a soft core

* :doc:`lj/cubic <pair_lj_cubic>` - LJ with cubic after inflection point

* :doc:`lj/cut <pair_lj>` - cutoff Lennard-Jones potential with no Coulomb

* :doc:`lj/cut <pair_lj>` - cutoff Lennard-Jones potential without Coulomb

* :doc:`lj/cut/coul/cut <pair_lj>` - LJ with cutoff Coulomb

* :doc:`lj/cut/coul/cut/soft <pair_fep_soft>` - LJ with cutoff Coulomb with a soft core

* :doc:`lj/cut/coul/debye <pair_lj>` - LJ with Debye screening added to Coulomb

* :doc:`lj/cut/coul/dsf <pair_lj>` - LJ with Coulombics via damped shifted forces

* :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulombics

* :doc:`lj/cut/coul/long/cs <pair_cs>` - ditto with core/shell adjustments

* :doc:`lj/cut/coul/long/soft <pair_fep_soft>` - LJ with long-range Coulombics with a soft core

* :doc:`lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulombics

* :doc:`lj/cut/coul/wolf <pair_lj>` - LJ with Coulombics via Wolf potential

* :doc:`lj/cut/coul/dsf <pair_lj>` - LJ with Coulomb via damped shifted forces

* :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulomb

* :doc:`lj/cut/coul/long/cs <pair_cs>` - LJ with long-range Coulomb with core/shell adjustments

* :doc:`lj/cut/coul/long/soft <pair_fep_soft>` - LJ with long-range Coulomb with a soft core

* :doc:`lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulomb

* :doc:`lj/cut/coul/wolf <pair_lj>` - LJ with Coulomb via Wolf potential

* :doc:`lj/cut/dipole/cut <pair_dipole>` - point dipoles with cutoff

* :doc:`lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald

* :doc:`lj/cut/soft <pair_fep_soft>` - LJ with a soft core

* :doc:`lj/cut/thole/long <pair_thole>` - LJ with Coulombics with thole damping

* :doc:`lj/cut/thole/long <pair_thole>` - LJ with Coulomb with thole damping

* :doc:`lj/cut/tip4p/cut <pair_lj>` - LJ with cutoff Coulomb for TIP4P water

* :doc:`lj/cut/tip4p/long <pair_lj>` - LJ with long-range Coulomb for TIP4P water

* :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` - LJ with cutoff Coulomb for TIP4P water with a soft core

* :doc:`lj/expand <pair_lj_expand>` - Lennard-Jones for variable size particles

* :doc:`lj/expand/coul/long <pair_lj_expand>` - Lennard-Jones for variable size particles with long-range Coulombics

* :doc:`lj/expand/coul/long <pair_lj_expand>` - Lennard-Jones for variable size particles with long-range Coulomb

* :doc:`lj/gromacs <pair_gromacs>` - GROMACS-style Lennard-Jones potential

* :doc:`lj/gromacs/coul/gromacs <pair_gromacs>` - GROMACS-style LJ and Coulombic potential

* :doc:`lj/long/coul/long <pair_lj_long>` - long-range LJ and long-range Coulombics

* :doc:`lj/gromacs/coul/gromacs <pair_gromacs>` - GROMACS-style LJ and Coulomb potential

* :doc:`lj/long/coul/long <pair_lj_long>` - long-range LJ and long-range Coulomb

* :doc:`lj/long/dipole/long <pair_dipole>` - long-range LJ and long-range point dipoles

* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulombics for TIP4P water

* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water

* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function

* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining

* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulombics

* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulombics via MSM

* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb

* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM

* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces

* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential

* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
@@ -255,7 +256,7 @@ accelerated styles exist. 
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>` - non-bonded 3-body harmonic potential

* :doc:`nm/cut <pair_nm>` - N-M potential

* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb

* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulombics

* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb

* :doc:`oxdna/coaxstk <pair_oxdna>` -

* :doc:`oxdna/excv <pair_oxdna>` -

* :doc:`oxdna/hbond <pair_oxdna>` -
@@ -315,7 +316,7 @@ accelerated styles exist. 
* :doc:`tersoff/zbl <pair_tersoff_zbl>` - Tersoff/ZBL 3-body potential

* :doc:`thole <pair_thole>` - Coulomb interactions with thole damping

* :doc:`tip4p/cut <pair_coul>` - Coulomb for TIP4P water w/out LJ

* :doc:`tip4p/long <pair_coul>` - long-range Coulombics for TIP4P water w/out LJ

* :doc:`tip4p/long <pair_coul>` - long-range Coulomb for TIP4P water w/out LJ

* :doc:`tip4p/long/soft <pair_fep_soft>` -

* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles

* :doc:`ufm <pair_ufm>` -

src/CORESHELL/Install.sh

+2 −0
Original line number Diff line number Diff line
@@ -41,6 +41,8 @@ action pair_coul_long_cs.cpp pair_coul_long.cpp 
action pair_coul_long_cs.h          pair_coul_long.h

action pair_lj_cut_coul_long_cs.cpp pair_lj_cut_coul_long.cpp

action pair_lj_cut_coul_long_cs.h   pair_lj_cut_coul_long.h

action pair_lj_class2_coul_long_cs.cpp pair_lj_class2_coul_long.cpp

action pair_lj_class2_coul_long_cs.h pair_lj_class2_coul_long.h



action pair_born_coul_wolf_cs.cpp   pair_born_coul_wolf.cpp

action pair_born_coul_wolf_cs.h     pair_born_coul_wolf.h

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