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Merge branch 'master' into next_lammps_version

This commit is contained in:
Axel Kohlmeyer 2020-04-15 05:08:53 -04:00
parent 48c136b784 f5733ccd75
commit 3deece168e
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8 changed files with 692 additions and 57 deletions
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14
cmake/CMakeLists.txt
View File

@ -107,7 +107,7 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) 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 GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI 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 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-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-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) USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF) option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach() endforeach()
@ -362,7 +362,7 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
############################################## ##############################################
# add sources of enabled packages # add sources of enabled packages
############################################ ############################################
foreach(PKG ${DEFAULT_PACKAGES}) foreach(PKG ${STANDARD_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@ -390,7 +390,7 @@ foreach(PKG MPIIO)
endforeach() endforeach()
# dedicated check for entire contents of accelerator packages # dedicated check for entire contents of accelerator packages
foreach(PKG ${ACCEL_PACKAGES}) foreach(PKG ${SUFFIX_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@ -481,7 +481,7 @@ target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR})
###################################### ######################################
set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n") set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n") set(temp "${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) list(SORT temp_PKG_LIST)
foreach(PKG ${temp_PKG_LIST}) foreach(PKG ${temp_PKG_LIST})
if(PKG_${PKG}) if(PKG_${PKG})
@ -655,7 +655,7 @@ include(CodeCoverage)
############################################################################### ###############################################################################
# Print package summary # Print package summary
############################################################################### ###############################################################################
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG}) if(PKG_${PKG})
message(STATUS "Building package: ${PKG}") message(STATUS "Building package: ${PKG}")
endif() endif()

1
doc/src/Commands_pair.rst
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@ -131,6 +131,7 @@ OPT.
* :doc:`lj/class2/coul/cut (ko) <pair_class2>` * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>` * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
* :doc:`lj/class2/coul/long (gko) <pair_class2>` * :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/coul/long/soft <pair_fep_soft>`
* :doc:`lj/class2/soft <pair_fep_soft>` * :doc:`lj/class2/soft <pair_fep_soft>`
* :doc:`lj/cubic (go) <pair_lj_cubic>` * :doc:`lj/cubic (go) <pair_lj_cubic>`

9
doc/src/pair_cs.rst
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@ -30,6 +30,9 @@ pair_style coul/wolf/cs command
pair_style lj/cut/coul/long/cs command pair_style lj/cut/coul/long/cs command
======================================= =======================================
pair_style lj/class2/coul/long/cs command
==========================================
Syntax Syntax
"""""" """"""
@ -37,7 +40,7 @@ Syntax
pair_style style args 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 * args = list of arguments for a particular style
.. parsed-literal:: .. parsed-literal::
@ -64,6 +67,9 @@ Syntax
*lj/cut/coul/long/cs* args = cutoff (cutoff2) *lj/cut/coul/long/cs* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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 Examples
"""""""" """"""""
@ -115,6 +121,7 @@ the "/cs" in the name:
* :doc:`pair_style coul/long <pair_coul>` * :doc:`pair_style coul/long <pair_coul>`
* :doc:`pair_style coul/wolf <pair_coul>` * :doc:`pair_style coul/wolf <pair_coul>`
* :doc:`pair_style lj/cut/coul/long <pair_lj>` * :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 except that they correctly treat the special case where the distance
between two charged core and shell atoms in the same core/shell pair between two charged core and shell atoms in the same core/shell pair

87
doc/src/pair_style.rst
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@ -111,41 +111,41 @@ accelerated styles exist.
* :doc:`born <pair_born>` - Born-Mayer-Huggins potential * :doc:`born <pair_born>` - Born-Mayer-Huggins potential
* :doc:`born/coul/dsf <pair_born>` - Born with damped-shifted-force model * :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/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 <pair_born>` - Born with long-range Coulomb
* :doc:`born/coul/long/cs <pair_cs>` - Born with long-range Coulombics and core/shell * :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 Coulombics * :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb
* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulombics * :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb
* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulombics and core/shell model * :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 <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity * :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
* :doc:`buck <pair_buck>` - Buckingham potential * :doc:`buck <pair_buck>` - Buckingham potential
* :doc:`buck/coul/cut <pair_buck>` - Buckingham with cutoff Coulomb * :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 <pair_buck>` - Buckingham with long-range Coulomb
* :doc:`buck/coul/long/cs <pair_cs>` - Buckingham with long-range Coulombics and core/shell * :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 Coulombics * :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 Coulombics * :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:`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/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:`colloid <pair_colloid>` - integrated colloidal potential
* :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential * :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential
* :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential * :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
* :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential * :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential
* :doc:`coul/cut <pair_coul>` - cutoff Coulombic potential * :doc:`coul/cut <pair_coul>` - cutoff Coulomb potential
* :doc:`coul/cut/soft <pair_fep_soft>` - Coulombic potential with a soft core * :doc:`coul/cut/soft <pair_fep_soft>` - Coulomb potential with a soft core
* :doc:`coul/debye <pair_coul>` - cutoff Coulombic potential with Debye screening * :doc:`coul/debye <pair_coul>` - cutoff Coulomb potential with Debye screening
* :doc:`coul/diel <pair_coul_diel>` - Coulomb potential with dielectric permittivity * :doc:`coul/diel <pair_coul_diel>` - Coulomb potential with dielectric permittivity
* :doc:`coul/dsf <pair_coul>` - Coulombics with damped-shifted-force model * :doc:`coul/dsf <pair_coul>` - Coulomb with damped-shifted-force model
* :doc:`coul/long <pair_coul>` - long-range Coulombic potential * :doc:`coul/long <pair_coul>` - long-range Coulomb potential
* :doc:`coul/long/cs <pair_cs>` - long-range Coulombic potential and core/shell * :doc:`coul/long/cs <pair_cs>` - long-range Coulomb potential and core/shell
* :doc:`coul/long/soft <pair_fep_soft>` - long-range Coulombic potential with a soft core * :doc:`coul/long/soft <pair_fep_soft>` - long-range Coulomb potential with a soft core
* :doc:`coul/msm <pair_coul>` - long-range MSM Coulombics * :doc:`coul/msm <pair_coul>` - long-range MSM Coulomb
* :doc:`coul/slater/cut <pair_coul>` - smeared out Coulombics * :doc:`coul/slater/cut <pair_coul>` - smeared out Coulomb
* :doc:`coul/slater/long <pair_coul>` - long-range smeared out Coulombics * :doc:`coul/slater/long <pair_coul>` - long-range smeared out Coulomb
* :doc:`coul/shield <pair_coul_shield>` - Coulombics for boron nitride for use with :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` potential * :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>` - Coulombics via Streitz/Mintmire Slater orbitals * :doc:`coul/streitz <pair_coul>` - Coulomb via Streitz/Mintmire Slater orbitals
* :doc:`coul/wolf <pair_coul>` - Coulombics via Wolf potential * :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
* :doc:`coul/wolf/cs <pair_cs>` - ditto with core/shell adjustments * :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD) * :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure * :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 * :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/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 <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/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/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/charmmfsw/coul/long <pair_charmm>` - CHARMM with force switching and long-rnage Coulomb
* :doc:`lj/class2 <pair_class2>` - COMPASS (class 2) force field with no 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 <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/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 <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/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/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/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 <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/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/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/dsf <pair_lj>` - LJ with Coulomb via damped shifted forces
* :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulombics * :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulomb
* :doc:`lj/cut/coul/long/cs <pair_cs>` - ditto with core/shell adjustments * :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 Coulombics with a soft core * :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 Coulombics * :doc:`lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulomb
* :doc:`lj/cut/coul/wolf <pair_lj>` - LJ with Coulombics via Wolf potential * :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/cut <pair_dipole>` - point dipoles with cutoff
* :doc:`lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald * :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/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/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 <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/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 <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 <pair_gromacs>` - GROMACS-style Lennard-Jones potential
* :doc:`lj/gromacs/coul/gromacs <pair_gromacs>` - GROMACS-style LJ and Coulombic potential * :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 Coulombics * :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/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/mdf <pair_mdf>` - LJ potential with a taper function
* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining * :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/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 Coulombics via MSM * :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/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 <pair_lj_smooth>` - smoothed Lennard-Jones potential
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ 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:`nb3b/harmonic <pair_nb3b_harmonic>` - non-bonded 3-body harmonic potential
* :doc:`nm/cut <pair_nm>` - N-M 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/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/coaxstk <pair_oxdna>` -
* :doc:`oxdna/excv <pair_oxdna>` - * :doc:`oxdna/excv <pair_oxdna>` -
* :doc:`oxdna/hbond <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:`tersoff/zbl <pair_tersoff_zbl>` - Tersoff/ZBL 3-body potential
* :doc:`thole <pair_thole>` - Coulomb interactions with thole damping * :doc:`thole <pair_thole>` - Coulomb interactions with thole damping
* :doc:`tip4p/cut <pair_coul>` - Coulomb for TIP4P water w/out LJ * :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:`tip4p/long/soft <pair_fep_soft>` -
* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles * :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
* :doc:`ufm <pair_ufm>` - * :doc:`ufm <pair_ufm>` -

2
src/CORESHELL/Install.sh
View File

@ -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_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.cpp pair_lj_cut_coul_long.cpp
action pair_lj_cut_coul_long_cs.h pair_lj_cut_coul_long.h 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.cpp pair_born_coul_wolf.cpp
action pair_born_coul_wolf_cs.h pair_born_coul_wolf.h action pair_born_coul_wolf_cs.h pair_born_coul_wolf.h

561
src/CORESHELL/pair_lj_class2_coul_long_cs.cpp Normal file
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@ -0,0 +1,561 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "pair_lj_class2_coul_long_cs.h"
#include <cmath>
#include "atom.h"
#include "force.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
#define EWALD_F 1.12837917
#define EWALD_P 9.95473818e-1
#define B0 -0.1335096380159268
#define B1 -2.57839507e-1
#define B2 -1.37203639e-1
#define B3 -8.88822059e-3
#define B4 -5.80844129e-3
#define B5 1.14652755e-1
#define EPSILON 1.0e-20
#define EPS_EWALD 1.0e-6
#define EPS_EWALD_SQR 1.0e-12
/* ---------------------------------------------------------------------- */
PairLJClass2CoulLongCS::PairLJClass2CoulLongCS(LAMMPS *lmp) : PairLJClass2CoulLong(lmp)
{
ewaldflag = pppmflag = 1;
respa_enable = 0; // TODO: r-RESPA handling is inconsistent and thus disabled until fixed
writedata = 1;
ftable = NULL;
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongCS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double rsq,r,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj;
double grij,expm2,prefactor,t,erfc,u;
double factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
// When bonded parts are being calculated a minimal distance (EPS_EWALD)
// has to be added to the prefactor and erfc in order to make the
// used approximation functions for the Ewald correction valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
u = 1.0 - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = 1.0/(rsq + EPS_EWALD_SQR);
} else {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
u = 1.0 - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongCS::compute_inner()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double rsq,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double rsw;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum_inner;
ilist = list->ilist_inner;
numneigh = list->numneigh_inner;
firstneigh = list->firstneigh_inner;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongCS::compute_middle()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double rsq,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double rsw;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum_middle;
ilist = list->ilist_middle;
numneigh = list->numneigh_middle;
firstneigh = list->firstneigh_middle;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
double cut_out_off = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_out_diff = cut_out_off - cut_out_on;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongCS::compute_outer(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc,u;
double rsw;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
evdwl = ecoul = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
u = 1. - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
if (rsq > cut_in_off_sq) {
if (rsq < cut_in_on_sq) {
rsw = (r - cut_in_off)/cut_in_diff;
forcecoul += prefactor*rsw*rsw*(3.0 - 2.0*rsw);
if (factor_coul < 1.0)
forcecoul -=
(1.0-factor_coul)*prefactor*rsw*rsw*(3.0 - 2.0*rsw);
} else {
forcecoul += prefactor;
if (factor_coul < 1.0)
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) {
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;
forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
}
} else forcelj = 0.0;
fpair = (forcecoul + forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ptable[itable] + fraction*dptable[itable];
prefactor = qtmp*q[j] * table;
ecoul -= (1.0-factor_coul)*prefactor;
}
}
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (vflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
table = vtable[itable] + fraction*dvtable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ptable[itable] + fraction*dptable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq <= cut_in_off_sq) {
rinv = sqrt(r2inv);
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;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
}
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}

67
src/CORESHELL/pair_lj_class2_coul_long_cs.h Normal file
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@ -0,0 +1,67 @@
/* -*- 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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(lj/class2/coul/long/cs,PairLJClass2CoulLongCS)
#else
#ifndef LMP_PAIR_LJ_CLASS2_COUL_LONG_CS_H
#define LMP_PAIR_LJ_CLASS2_COUL_LONG_CS_H
#include "pair_lj_class2_coul_long.h"
namespace LAMMPS_NS {
class PairLJClass2CoulLongCS : public PairLJClass2CoulLong {
public:
PairLJClass2CoulLongCS(class LAMMPS *);
virtual void compute(int, int);
void compute_inner();
void compute_middle();
void compute_outer(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style lj/class2/coul/long requires atom attribute q
The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
No kspace style is defined.
E: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
*/

6
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
View File

@ -41,7 +41,7 @@ using namespace LAMMPS_NS;
PairLJCutCoulLongCS::PairLJCutCoulLongCS(LAMMPS *lmp) : PairLJCutCoulLong(lmp) PairLJCutCoulLongCS::PairLJCutCoulLongCS(LAMMPS *lmp) : PairLJCutCoulLong(lmp)
{ {
ewaldflag = pppmflag = 1; ewaldflag = pppmflag = 1;
respa_enable = 1; respa_enable = 0; // TODO: r-RESPA handling is inconsistent and thus disabled until fixed
writedata = 1; writedata = 1;
ftable = NULL; ftable = NULL;
qdist = 0.0; qdist = 0.0;
@ -173,7 +173,6 @@ void PairLJCutCoulLongCS::compute(int eflag, int vflag)
} }
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0; } else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) { if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype]; offset[itype][jtype];
@ -433,7 +432,6 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
jtype = type[j]; jtype = type[j];
if (rsq < cutsq[itype][jtype]) { if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq; r2inv = 1.0/rsq;
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
@ -444,7 +442,6 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
t = 1.0 / (1.0 + EWALD_P*grij); t = 1.0 / (1.0 + EWALD_P*grij);
u = 1. - t; u = 1. - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
//erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r; prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0); forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
if (rsq > cut_in_off_sq) { if (rsq > cut_in_off_sq) {
@ -543,7 +540,6 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
r6inv = r2inv*r2inv*r2inv; r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} }
fpair = (forcecoul + factor_lj*forcelj) * r2inv; fpair = (forcecoul + factor_lj*forcelj) * r2inv;
} }