jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'github/master' into add-ECO-DF

This commit is contained in:
Axel Kohlmeyer 2020-06-09 14:55:40 -04:00
parent 89fb194f51 719936580a
commit bb5b931d78
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
105 changed files with 20786 additions and 2028 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
cmake/CMakeLists.txt
View File

@ -32,6 +32,12 @@ endif()
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
# make sure LIBRARY_PATH is set if environment variable is set
if (DEFINED ENV{LIBRARY_PATH})
list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
endif()
include(LAMMPSUtils)
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)

13
cmake/Modules/Packages/GPU.cmake
View File

@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if (GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
"Please run\n"
" make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
"to remove\n"
"########################################################################")
endif()
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@ -79,7 +90,7 @@ if(GPU_API STREQUAL "CUDA")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}

4
doc/src/Build_extras.rst
View File

@ -132,6 +132,10 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`

1
doc/src/Commands_all.rst
View File

@ -94,6 +94,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`package <package>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`prd <prd>`

3
doc/src/fix_orient.rst
View File

@ -6,6 +6,9 @@ fix orient/fcc command
fix orient/bcc command
======================
Syntax
""""""
.. parsed-literal::
fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1

3
doc/src/fix_poems.rst
View File

@ -3,7 +3,8 @@
fix poems command
=================
Syntax:
Syntax
""""""
.. parsed-literal::

3
doc/src/fix_rhok.rst
View File

@ -3,6 +3,9 @@
fix rhok command
================
Syntax
""""""
.. parsed-literal::
fix ID group-ID rhok nx ny nz K a

4
doc/src/pair_lubricate.rst
View File

@ -28,7 +28,9 @@ Syntax
* flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
* flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
**Examples:** (all assume radius = 1)
Examples
""""""""
(all assume radius = 1)
.. code-block:: LAMMPS

4
doc/src/pair_lubricateU.rst
View File

@ -22,7 +22,9 @@ Syntax
* flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
* flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
**Examples:** (all assume radius = 1)
Examples
""""""""
(all assume radius = 1)
.. code-block:: LAMMPS

3
doc/src/special_bonds.rst
View File

@ -28,7 +28,8 @@ Syntax
*angle* value = *yes* or *no*
*dihedral* value = *yes* or *no*
Examples:
Examples
""""""""
.. code-block:: LAMMPS

17
src/GPU/pair_eam_alloy_gpu.cpp
View File

@ -374,15 +374,12 @@ void PairEAMAlloyGPU::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -398,8 +395,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -415,18 +411,17 @@ void PairEAMAlloyGPU::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(file->nr, &file->rhor[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

17
src/GPU/pair_eam_fs_gpu.cpp
View File

@ -374,15 +374,12 @@ void PairEAMFSGPU::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -398,8 +395,7 @@ void PairEAMFSGPU::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -415,21 +411,20 @@ void PairEAMFSGPU::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
for (int j = 0; j < file->nelements; j++) {
reader.next_dvector(file->nr, &file->rhor[i][j][1]);
reader.next_dvector(&file->rhor[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

5
src/KIM/kim_init.cpp
View File

@ -57,6 +57,8 @@
------------------------------------------------------------------------- */
#include "kim_init.h"
#include "fix_store_kim.h"
#include "kim_units.h"
#include <cstring>
#include <string>
#include <sstream>
@ -71,8 +73,7 @@
#include "input.h"
#include "variable.h"
#include "citeme.h"
#include "fix_store_kim.h"
#include "kim_units.h"
#include "utils.h"
extern "C" {
#include "KIM_SimulatorHeaders.h"

17
src/KOKKOS/pair_eam_alloy_kokkos.cpp
View File

@ -988,15 +988,12 @@ void PairEAMAlloyKokkos<DeviceType>::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -1012,8 +1009,7 @@ void PairEAMAlloyKokkos<DeviceType>::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -1029,18 +1025,17 @@ void PairEAMAlloyKokkos<DeviceType>::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(file->nr, &file->rhor[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

17
src/KOKKOS/pair_eam_fs_kokkos.cpp
View File

@ -988,15 +988,12 @@ void PairEAMFSKokkos<DeviceType>::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -1012,8 +1009,7 @@ void PairEAMFSKokkos<DeviceType>::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -1029,21 +1025,20 @@ void PairEAMFSKokkos<DeviceType>::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
for (int j = 0; j < file->nelements; j++) {
reader.next_dvector(file->nr, &file->rhor[i][j][1]);
reader.next_dvector(&file->rhor[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

21
src/MANYBODY/pair_adp.cpp
View File

@ -546,15 +546,12 @@ void PairADP::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "ADP");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -570,8 +567,7 @@ void PairADP::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -589,30 +585,29 @@ void PairADP::read_file(char *filename)
memory->create(file->w2r, file->nelements, file->nelements, file->nr + 1, "pair:w2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(file->nr, &file->rhor[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->u2r[i][j][1]);
reader.next_dvector(&file->u2r[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->w2r[i][j][1]);
reader.next_dvector(&file->w2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

711
src/MANYBODY/pair_airebo.cpp
View File

@ -35,11 +35,13 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
#define MAXLINE 1024
#define TOL 1.0e-9
#define PGDELTA 1
@ -3331,9 +3333,6 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
void PairAIREBO::read_file(char *filename)
{
int i,j,k,l,limit;
char s[MAXLINE];
// REBO Parameters (AIREBO)
double rcmin_CC,rcmin_CH,rcmin_HH,rcmax_CC,rcmax_CH,
@ -3357,562 +3356,298 @@ void PairAIREBO::read_file(char *filename)
double epsilonM_CC,epsilonM_CH,epsilonM_HH,alphaM_CC,alphaM_CH,alphaM_HH;
double reqM_CC,reqM_CH,reqM_HH;
MPI_Comm_rank(world,&me);
// read file on proc 0
int cerror = 0;
int numpar = 0;
FILE *fp = NULL;
if (comm->me == 0) {
std::string potential_name;
std::string header;
switch (variant) {
case AIREBO:
potential_name = "AIREBO";
header = "# AIREBO ";
break;
if (me == 0) {
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
switch (variant) {
case REBO_2:
potential_name = "REBO2";
header = "# REBO2 ";
break;
case AIREBO:
snprintf(str,128,"Cannot open AIREBO potential file %s",filename);
break;
case AIREBO_M:
potential_name = "Cannot open AIREBO-M";
header = "# AIREBO-M ";
break;
case REBO_2:
snprintf(str,128,"Cannot open REBO2 potential file %s",filename);
break;
case AIREBO_M:
snprintf(str,128,"Cannot open AIREBO-M potential file %s",filename);
break;
default:
snprintf(str,128,"Unknown REBO style variant %d",variant);
}
error->one(FLERR,str);
default:
error->one(FLERR, fmt::format("Unknown REBO style variant {}",variant));
}
PotentialFileReader reader(lmp, filename, potential_name);
reader.ignore_comments(false);
// skip initial comment line and check for potential file style identifier comment
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
reader.skip_line();
char * line = reader.next_line();
if (((variant == AIREBO) && (strncmp(s,"# AIREBO ",9) != 0))
|| ((variant == REBO_2) && (strncmp(s,"# REBO2 ",8) != 0))
|| ((variant == AIREBO_M) && (strncmp(s,"# AIREBO-M ",11) != 0))) {
error->one(FLERR,"Potential file does not match AIREBO/REBO style variant");
if (std::string(line).find(header) == std::string::npos) {
error->one(FLERR, fmt::format("Potential file does not match AIREBO/REBO style variant: {}: {}", header, line));
}
// skip remaining comments
while (1) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (s[0] != '#') break;
}
reader.ignore_comments(true);
// read parameters
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmin_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmin_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmin_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmax_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmax_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmax_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmaxp_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmaxp_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcmaxp_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&smin)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Nmin)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Nmax)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&NCmin)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&NCmax)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Q_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Q_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Q_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&alpha_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&alpha_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&alpha_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&A_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&A_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&A_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_CC1)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_CC2)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_CC3)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_CH1)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_CH2)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_CH3)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_HH1)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_HH2)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&BIJc_HH3)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_CC1)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_CC2)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_CC3)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_CH1)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_CH2)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_CH3)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_HH1)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_HH2)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Beta_HH3)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rho_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rho_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rho_HH)) ++cerror;
std::vector<double*> params {
&rcmin_CC,
&rcmin_CH,
&rcmin_HH,
&rcmax_CC,
&rcmax_CH,
&rcmax_HH,
&rcmaxp_CC,
&rcmaxp_CH,
&rcmaxp_HH,
&smin,
&Nmin,
&Nmax,
&NCmin,
&NCmax,
&Q_CC,
&Q_CH,
&Q_HH,
&alpha_CC,
&alpha_CH,
&alpha_HH,
&A_CC,
&A_CH,
&A_HH,
&BIJc_CC1,
&BIJc_CC2,
&BIJc_CC3,
&BIJc_CH1,
&BIJc_CH2,
&BIJc_CH3,
&BIJc_HH1,
&BIJc_HH2,
&BIJc_HH3,
&Beta_CC1,
&Beta_CC2,
&Beta_CC3,
&Beta_CH1,
&Beta_CH2,
&Beta_CH3,
&Beta_HH1,
&Beta_HH2,
&Beta_HH3,
&rho_CC,
&rho_CH,
&rho_HH,
// LJ parameters
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcLJmin_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcLJmin_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcLJmin_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcLJmax_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcLJmax_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&rcLJmax_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&bLJmin_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&bLJmin_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&bLJmin_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&bLJmax_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&bLJmax_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&bLJmax_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilon_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilon_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilon_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&sigma_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&sigma_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&sigma_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilonT_CCCC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilonT_CCCH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilonT_HCCH)) ++cerror;
// LJ parameters
&rcLJmin_CC,
&rcLJmin_CH,
&rcLJmin_HH,
&rcLJmax_CC,
&rcLJmax_CH,
&rcLJmax_HH,
&bLJmin_CC,
&bLJmin_CH,
&bLJmin_HH,
&bLJmax_CC,
&bLJmax_CH,
&bLJmax_HH,
&epsilon_CC,
&epsilon_CH,
&epsilon_HH,
&sigma_CC,
&sigma_CH,
&sigma_HH,
&epsilonT_CCCC,
&epsilonT_CCCH,
&epsilonT_HCCH
};
if (morseflag) {
// lines for reading in MORSE parameters from CH.airebo_m file
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilonM_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilonM_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&epsilonM_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&alphaM_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&alphaM_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&alphaM_HH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&reqM_CC)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&reqM_CH)) ++cerror;
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&reqM_HH)) ++cerror;
params.push_back(&epsilonM_CC);
params.push_back(&epsilonM_CH);
params.push_back(&epsilonM_HH);
params.push_back(&alphaM_CC);
params.push_back(&alphaM_CH);
params.push_back(&alphaM_HH);
params.push_back(&reqM_CC);
params.push_back(&reqM_CH);
params.push_back(&reqM_HH);
}
}
std::string current_section;
// check for errors parsing global parameters
try {
/////////////////////////////////////////////////////////////////////////
// global parameters
current_section = "global parameters";
MPI_Bcast(&cerror,1,MPI_INT,0,world);
if (cerror > 0) {
char msg[128];
snprintf(msg,128,"Could not parse %d of %d parameters from file %s",
cerror,numpar,filename);
error->all(FLERR,msg);
}
cerror = numpar = 0;
if (me == 0) {
// gC spline
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
// number-1 = # of domains for the spline
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit; i++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&gCdom[i])) ++cerror;
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < limit-1; i++) {
for (j = 0; j < 6; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&gC1[i][j])) ++cerror;
for(int i = 0; i < params.size(); i++) {
*params[i] = reader.next_double();
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < limit-1; i++) {
for (j = 0; j < 6; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&gC2[i][j])) ++cerror;
/////////////////////////////////////////////////////////////////////////
// gC spline
current_section = "gC spline";
// number-1 = # of domains for the spline
int limit = reader.next_int();
reader.next_dvector(gCdom, limit);
for (int i = 0; i < limit-1; i++) {
reader.next_dvector(&gC1[i][0], 6);
}
}
// gH spline
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit; i++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&gHdom[i])) ++cerror;
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < limit-1; i++) {
for (j = 0; j < 6; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&gH[i][j])) ++cerror;
for (int i = 0; i < limit-1; i++) {
reader.next_dvector(&gC2[i][0], 6);
}
}
// pCC spline
/////////////////////////////////////////////////////////////////////////
// gH spline
current_section = "gH spline";
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
limit = reader.next_int();
reader.next_dvector(gHdom, limit);
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/2; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&pCCdom[i][j])) ++cerror;
for (int i = 0; i < limit-1; i++) {
reader.next_dvector(&gH[i][0], 6);
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < (int) pCCdom[0][1]; i++) {
for (j = 0; j < (int) pCCdom[1][1]; j++) {
for (k = 0; k < 16; k++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&pCC[i][j][k])) ++cerror;
/////////////////////////////////////////////////////////////////////////
// pCC spline
current_section = "pCC spline";
limit = reader.next_int();
for (int i = 0; i < limit/2; i++) {
reader.next_dvector(&pCCdom[i][0], limit/2);
}
for (int i = 0; i < (int) pCCdom[0][1]; i++) {
for (int j = 0; j < (int) pCCdom[1][1]; j++) {
reader.next_dvector(&pCC[i][j][0], 16);
}
}
}
// pCH spline
/////////////////////////////////////////////////////////////////////////
// pCH spline
current_section = "pCH spline";
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
limit = reader.next_int();
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/2; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&pCHdom[i][j])) ++cerror;
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < (int) pCHdom[0][1]; i++) {
for (j = 0; j < (int) pCHdom[1][1]; j++) {
for (k = 0; k < 16; k++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&pCH[i][j][k])) ++cerror;
for (int i = 0; i < limit/2; i++) {
for (int j = 0; j < limit/2; j++) {
pCHdom[i][j] = reader.next_double();
}
}
}
// piCC cpline
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&piCCdom[i][j])) ++cerror;
for (int i = 0; i < (int) pCHdom[0][1]; i++) {
for (int j = 0; j < (int) pCHdom[1][1]; j++) {
reader.next_dvector(&pCH[i][j][0], 16);
}
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < (int) piCCdom[0][1]; i++) {
for (j = 0; j < (int) piCCdom[1][1]; j++) {
for (k = 0; k < (int) piCCdom[2][1]; k++) {
for (l = 0; l < 64; l = l+1) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&piCC[i][j][k][l])) ++cerror;
/////////////////////////////////////////////////////////////////////////
// piCC spline
current_section = "piCC spline";
limit = reader.next_int();
for (int i = 0; i < limit/2; i++) {
for (int j = 0; j < limit/3; j++) {
piCCdom[i][j] = reader.next_double();
}
}
for (int i = 0; i < (int) piCCdom[0][1]; i++) {
for (int j = 0; j < (int) piCCdom[1][1]; j++) {
for (int k = 0; k < (int) piCCdom[2][1]; k++) {
reader.next_dvector(&piCC[i][j][k][0], 64);
}
}
}
}
// piCH spline
/////////////////////////////////////////////////////////////////////////
// piCH spline
current_section = "piCH spline";
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
limit = reader.next_int();
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&piCHdom[i][j])) ++cerror;
for (int i = 0; i < limit/2; i++) {
for (int j = 0; j < limit/3; j++) {
piCHdom[i][j] = reader.next_double();
}
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < (int) piCHdom[0][1]; i++) {
for (j = 0; j < (int) piCHdom[1][1]; j++) {
for (k = 0; k < (int) piCHdom[2][1]; k++) {
for (l = 0; l < 64; l = l+1) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&piCH[i][j][k][l])) ++cerror;
for (int i = 0; i < (int) piCHdom[0][1]; i++) {
for (int j = 0; j < (int) piCHdom[1][1]; j++) {
for (int k = 0; k < (int) piCHdom[2][1]; k++) {
reader.next_dvector(&piCH[i][j][k][0], 64);
}
}
}
}
// piHH spline
/////////////////////////////////////////////////////////////////////////
// piHH spline
current_section = "piHH spline";
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
limit = reader.next_int();
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&piHHdom[i][j])) ++cerror;
for (int i = 0; i < limit/2; i++) {
for (int j = 0; j < limit/3; j++) {
piHHdom[i][j] = reader.next_double();
}
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < (int) piHHdom[0][1]; i++) {
for (j = 0; j < (int) piHHdom[1][1]; j++) {
for (k = 0; k < (int) piHHdom[2][1]; k++) {
for (l = 0; l < 64; l = l+1) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&piHH[i][j][k][l])) ++cerror;
for (int i = 0; i < (int) piHHdom[0][1]; i++) {
for (int j = 0; j < (int) piHHdom[1][1]; j++) {
for (int k = 0; k < (int) piHHdom[2][1]; k++) {
reader.next_dvector(&piHH[i][j][k][0], 64);
}
}
}
}
// Tij spline
/////////////////////////////////////////////////////////////////////////
// Tij spline
current_section = "Tij spline";
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
limit = reader.next_int();
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%d",&limit)) ++cerror;
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Tijdom[i][j])) ++cerror;
for (int i = 0; i < limit/2; i++) {
for (int j = 0; j < limit/3; j++) {
Tijdom[i][j] = reader.next_double();
}
}
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for (i = 0; i < (int) Tijdom[0][1]; i++) {
for (j = 0; j < (int) Tijdom[1][1]; j++) {
for (k = 0; k < (int) Tijdom[2][1]; k++) {
for (l = 0; l < 64; l = l+1) {
++numpar;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
if (1 != sscanf(s,"%lg",&Tijc[i][j][k][l])) ++cerror;
for (int i = 0; i < (int) Tijdom[0][1]; i++) {
for (int j = 0; j < (int) Tijdom[1][1]; j++) {
for (int k = 0; k < (int) Tijdom[2][1]; k++) {
reader.next_dvector(&Tijc[i][j][k][0], 64);
}
}
}
} catch (TokenizerException & e) {
std::string msg = fmt::format("ERROR reading {} section in {} file\n"
"REASON: {}\n",
current_section, potential_name, e.what());
error->one(FLERR, msg);
} catch (FileReaderException & fre) {
error->one(FLERR, fre.what());
std::string msg = fmt::format("ERROR reading {} section in {} file\n"
"REASON: {}\n",
current_section, potential_name, fre.what());
error->one(FLERR, msg);
}
fclose(fp);
}
// check for errors parsing spline data
MPI_Bcast(&cerror,1,MPI_INT,0,world);
if (cerror > 0) {
char msg[128];
snprintf(msg,128,"Could not parse %d of %d spline data from file %s",
cerror,numpar,filename);
error->all(FLERR,msg);
}
// store read-in values in arrays
if (me == 0) {
// store read-in values in arrays
// REBO

2
src/MANYBODY/pair_airebo.h
View File

@ -42,7 +42,7 @@ class PairAIREBO : public Pair {
protected:
int *map; // 0 (C), 1 (H), or -1 (NULL) for each type
int me,variant;
int variant;
int ljflag,torflag; // 0/1 if LJ/Morse,torsion terms included
int morseflag; // 1 if Morse instead of LJ for non-bonded

753
src/MANYBODY/pair_bop.cpp
View File

@ -46,10 +46,11 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define EPSILON 1.0e-6
/* ---------------------------------------------------------------------- */
@ -294,7 +295,6 @@ void PairBOP::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int cnt1;
MPI_Comm_rank(world,&me);
inum = list->inum;
ilist = list->ilist;
@ -616,7 +616,6 @@ void PairBOP::coeff(int narg, char **arg)
{
int i,j;
int n = atom->ntypes;
MPI_Comm_rank(world,&me);
delete[] map;
map = new int[n+1];
@ -645,7 +644,7 @@ void PairBOP::coeff(int narg, char **arg)
read_table(arg[2]);
// match element names to BOP word types
if (me == 0) {
if (comm->me == 0) {
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
@ -659,7 +658,7 @@ void PairBOP::coeff(int narg, char **arg)
}
MPI_Bcast(&map[1],atom->ntypes,MPI_INT,0,world);
if (me == 0) {
if (comm->me == 0) {
if (elements) {
for (i = 0; i < bop_types; i++) delete [] elements[i];
delete [] elements;
@ -1137,7 +1136,6 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
nlocal = atom->nlocal;
ilist = list->ilist;
firstneigh = list->firstneigh;
MPI_Comm_rank(world,&me);
if(nb_sg==0) {
nb_sg=(maxneigh)*(maxneigh/2);
@ -4873,101 +4871,11 @@ double PairBOP::PiBo(int itmp, int jtmp)
}
/* ----------------------------------------------------------------------
read BOP potential file
allocate BOP tables
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void _noopt PairBOP::read_table(char *filename)
void PairBOP::allocate_tables()
{
int i,j,k,n,m;
int buf1,pass;
int nws,ws;
double buf2;
char s[MAXLINE],buf[2];
MPI_Comm_rank(world,&me);
if (me == 0) {
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str);
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%d",&bop_types);
elements = new char*[bop_types];
for(i=0;i<bop_types;i++) elements[i]=NULL;
for(i=0;i<bop_types;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
nws=0;
ws=1;
for(j=0;j<(int)strlen(s);j++) {
if(ws==1) {
if(isspace(s[j])) {
ws=1;
} else {
ws=0;
}
} else {
if(isspace(s[j])) {
ws=1;
nws++;
} else {
ws=0;
}
}
}
if(nws!=3){
error->all(FLERR,"Incorrect table format check for element types");
}
sscanf(s,"%d %lf %s",&buf1,&buf2,buf);
n= strlen(buf)+1;
elements[i] = new char[n];
strcpy(elements[i],buf);
}
nws=0;
ws=1;
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
for(j=0;j<(int)strlen(s);j++) {
if(ws==1) {
if(isspace(s[j])) {
ws=1;
} else {
ws=0;
}
} else {
if(isspace(s[j])) {
ws=1;
nws++;
} else {
ws=0;
}
}
}
if (nws==3) {
sscanf(s,"%d %d %d",&nr,&ntheta,&nBOt);
npower=2;
if(ntheta<=10) npower=ntheta;
} else if (nws==2) {
sscanf(s,"%d %d",&nr,&nBOt);
ntheta=0;
npower=3;
} else {
error->one(FLERR,"Unsupported BOP potential file format");
}
fclose(fp);
npairs=bop_types*(bop_types+1)/2;
}
MPI_Bcast(&nr,1,MPI_INT,0,world);
MPI_Bcast(&nBOt,1,MPI_INT,0,world);
MPI_Bcast(&ntheta,1,MPI_INT,0,world);
MPI_Bcast(&bop_types,1,MPI_INT,0,world);
MPI_Bcast(&npairs,1,MPI_INT,0,world);
MPI_Bcast(&npower,1,MPI_INT,0,world);
memory->destroy(pi_a);
memory->destroy(pro_delta);
memory->destroy(pi_delta);
@ -5011,334 +4919,347 @@ void _noopt PairBOP::read_table(char *filename)
memory->create(gfunc5,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc5");
memory->create(gfunc6,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc6");
memory->create(gpara,bop_types,bop_types,bop_types,npower+1,"BOP:gpara");
}
allocate();
if (me == 0) {
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str);
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line
for(i=0;i<bop_types+2;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
}
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g
,&small4,&small5,&small6,&small7);
for(i=0;i<bop_types;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&pi_p[i]);
}
cutmax=0;
for(i=0;i<npairs;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&rcut[i]);
if(rcut[i]>cutmax)
cutmax=rcut[i];
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
}
if(nws==3) {
for(i=0;i<bop_types;i++)
for(j=0;j<bop_types;j++)
for(k=j;k<bop_types;k++) {
if(npower<=2) {
for(m=0;m<ntheta;m++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1]
,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]);
n+=4;
/* ----------------------------------------------------------------------
read BOP potential file
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void _noopt PairBOP::read_table(char *filename)
{
if (comm->me == 0) {
try {
PotentialFileReader reader(lmp, filename, "BOP");
bop_types = reader.next_int();
elements = new char*[bop_types];
for(int i=0; i < bop_types; i++) {
ValueTokenizer values = reader.next_values(3);
values.next_int();
values.next_double();
std::string name = values.next_string();
elements[i] = new char[name.length()+1];
strcpy(elements[i], name.c_str());
}
ValueTokenizer values = reader.next_values(2);
int format = values.count();
switch(format) {
case 3:
nr = values.next_int();
ntheta = values.next_int();
nBOt = values.next_int();
if(ntheta <= 10)
npower = ntheta;
else
npower = 2;
break;
case 2:
nr = values.next_int();
nBOt = values.next_int();
ntheta = 0;
npower = 3;
break;
default:
error->one(FLERR,"Unsupported BOP potential file format");
}
npairs = bop_types*(bop_types+1)/2;
allocate_tables();
allocate();
values = reader.next_values(7);
small1 = values.next_double();
small2 = values.next_double();
small3g = values.next_double();
small4 = values.next_double();
small5 = values.next_double();
small6 = values.next_double();
small7 = values.next_double();
for(int i = 0; i < bop_types; i++) {
pi_p[i] = reader.next_double();
}
cutmax = 0.0;
for(int i = 0; i < npairs; i++) {
rcut[i] = reader.next_double();
if (rcut[i] > cutmax)
cutmax = rcut[i];
values = reader.next_values(4);
sigma_c[i] = values.next_double();
sigma_a[i] = values.next_double();
pi_c[i] = values.next_double();
pi_a[i] = values.next_double();
values = reader.next_values(2);
sigma_delta[i] = values.next_double();
pi_delta[i] = values.next_double();
values = reader.next_values(3);
sigma_f[i] = values.next_double();
sigma_k[i] = values.next_double();
small3[i] = values.next_double();
}
if(format == 3) {
for(int i = 0; i < bop_types; i++)
for(int j = 0; j < bop_types; j++)
for(int k = j; k < bop_types; k++) {
if(npower <= 2) {
reader.next_dvector(&gfunc[j][i][k][0], ntheta);
} else {
reader.next_dvector(&gpara[j][i][k][0], npower+1);
}
}
} else {
for(int i = 0; i < bop_types; i++)
for(int j = 0; j < bop_types; j++)
for(int k = 0; k < bop_types; k++) {
reader.next_dvector(&gpara[i][j][k][0], 3);
gpara[j][i][k][3] = 0;
}
}
for(int i = 0; i < npairs; i++) {
reader.next_dvector(&pRepul[i][0], nr);
}
for(int i = 0; i < npairs; i++) {
reader.next_dvector(&pBetaS[i][0], nr);
}
for(int i = 0; i < npairs; i++) {
reader.next_dvector(&pBetaP[i][0], nr);
}
for(int i = 0; i < npairs; i++) {
reader.next_dvector(&FsigBO[i][0], nBOt);
}
for(int i = 0; i < bop_types; i++) {
pro_delta[i] = reader.next_double();
}
for(int i = 0; i < bop_types; i++) {
pro[i] = reader.next_double();
}
for(int i=0;i<npairs;i++) {
rcut3[i]=0.0;
}
if(format == 3) {
for(int i = 0; i < npairs; i++) {
rcut3[i] = reader.next_double();
}
for(int i = 0; i < npairs; i++) {
reader.next_dvector(&pLong[i][0], nr);
}
}
rcutall=0.0;
for(int i=0; i < npairs; i++) {
if(rcut[i]>rcutall)
rcutall=rcut[i];
if(rcut3[i]>rcutall)
rcutall=rcut3[i];
rcutsq[i]=rcut[i]*rcut[i];
dr[i]=rcut[i]/((double)nr-1.0);
rdr[i]=1.0/dr[i];
if (format == 3) {
rcutsq3[i]=rcut3[i]*rcut3[i];
dr3[i]=rcut3[i]/((double)nr-1.0);
rdr3[i]=1.0/dr3[i];
}
}
rctroot=rcutall;
dtheta=2.0/((double)ntheta-1.0);
rdtheta=1.0/dtheta;
dBO=1.0/((double)nBOt-1.0);
rdBO=1.0/(double)dBO;
for (int i = 0; i < npairs; i++) {
pBetaS1[i][0]=pBetaS[i][1]-pBetaS[i][0];
pBetaS1[i][1]=0.5*(pBetaS[i][2]-pBetaS[i][0]);
pBetaS1[i][nr-2]=0.5*(pBetaS[i][nr-1]-pBetaS[i][nr-3]);
pBetaS1[i][nr-1]=pBetaS[i][nr-1]-pBetaS[i][nr-2];
pBetaP1[i][0]=pBetaP[i][1]-pBetaP[i][0];
pBetaP1[i][1]=0.5*(pBetaP[i][2]-pBetaP[i][0]);
pBetaP1[i][nr-2]=0.5*(pBetaP[i][nr-1]-pBetaP[i][nr-3]);
pBetaP1[i][nr-1]=pBetaP[i][nr-1]-pBetaP[i][nr-2];
pRepul1[i][0]=pRepul[i][1]-pRepul[i][0];
pRepul1[i][1]=0.5*(pRepul[i][2]-pRepul[i][0]);
pRepul1[i][nr-2]=0.5*(pRepul[i][nr-1]-pRepul[i][nr-3]);
pRepul1[i][nr-1]=pRepul[i][nr-1]-pRepul[i][nr-2];
FsigBO1[i][0]=FsigBO[i][1]-FsigBO[i][0];
FsigBO1[i][1]=0.5*(FsigBO[i][2]-FsigBO[i][0]);
FsigBO1[i][nBOt-2]=0.5*(FsigBO[i][nBOt-1]-FsigBO[i][nBOt-3]);
FsigBO1[i][nBOt-1]=FsigBO[i][nBOt-1]-FsigBO[i][nBOt-2];
pLong1[i][0]=pLong[i][1]-pLong[i][0];
pLong1[i][1]=0.5*(pLong[i][2]-pLong[i][0]);
pLong1[i][nBOt-2]=0.5*(pLong[i][nr-1]-pLong[i][nr-3]);
pLong1[i][nBOt-1]=pLong[i][nr-1]-pLong[i][nr-2];
for (int k = 2; k < nr-2; k++) {
pBetaS1[i][k]=((pBetaS[i][k-2]-pBetaS[i][k+2])
+8.0*(pBetaS[i][k+1]-pBetaS[i][k-1]))/12.0;
pBetaP1[i][k]=((pBetaP[i][k-2]-pBetaP[i][k+2])
+8.0*(pBetaP[i][k+1]-pBetaP[i][k-1]))/12.0;
pRepul1[i][k]=((pRepul[i][k-2]-pRepul[i][k+2])
+8.0*(pRepul[i][k+1]-pRepul[i][k-1]))/12.0;
pLong1[i][k]=((pLong[i][k-2]-pLong[i][k+2])
+8.0*(pLong[i][k+1]-pLong[i][k-1]))/12.0;
}
for (int k=2; k < nr-2; k++) {
FsigBO1[i][k]=((FsigBO[i][k-2]-FsigBO[i][k+2])
+8.0*(FsigBO[i][k+1]-FsigBO[i][k-1]))/12.0;
}
for (int k = 0; k < nr-1; k++) {
pBetaS2[i][k]=3.0*(pBetaS[i][k+1]-pBetaS[i][k])
-2.0*pBetaS1[i][k]-pBetaS1[i][k+1];
pBetaS3[i][k]=pBetaS1[i][k]+pBetaS1[i][k+1]
-2.0*(pBetaS[i][k+1]-pBetaS[i][k]);
pBetaP2[i][k]=3.0*(pBetaP[i][k+1]-pBetaP[i][k])
-2.0*pBetaP1[i][k]-pBetaP1[i][k+1];
pBetaP3[i][k]=pBetaP1[i][k]+pBetaP1[i][k+1]
-2.0*(pBetaP[i][k+1]-pBetaP[i][k]);
pRepul2[i][k]=3.0*(pRepul[i][k+1]-pRepul[i][k])
-2.0*pRepul1[i][k]-pRepul1[i][k+1];
pRepul3[i][k]=pRepul1[i][k]+pRepul1[i][k+1]
-2.0*(pRepul[i][k+1]-pRepul[i][k]);
pLong2[i][k]=3.0*(pLong[i][k+1]-pLong[i][k])
-2.0*pLong1[i][k]-pLong1[i][k+1];
pLong3[i][k]=pLong1[i][k]+pLong1[i][k+1]
-2.0*(pLong[i][k+1]-pLong[i][k]);
}
for (int k = 0; k < nBOt-1; k++) {
FsigBO2[i][k]=3.0*(FsigBO[i][k+1]-FsigBO[i][k])
-2.0*FsigBO1[i][k]-FsigBO1[i][k+1];
FsigBO3[i][k]=FsigBO1[i][k]+FsigBO1[i][k+1]
-2.0*(FsigBO[i][k+1]-FsigBO[i][k]);
}
pBetaS2[i][nr-1]=0.0;
pBetaS3[i][nr-1]=0.0;
pBetaP2[i][nr-1]=0.0;
pBetaP3[i][nr-1]=0.0;
pRepul2[i][nr-1]=0.0;
pRepul3[i][nr-1]=0.0;
pLong2[i][nr-1]=0.0;
pLong3[i][nr-1]=0.0;
FsigBO2[i][nBOt-1]=0.0;
FsigBO3[i][nBOt-1]=0.0;
for (int k=0; k < nr; k++) {
pBetaS4[i][k]=pBetaS1[i][k]/dr[i];
pBetaS5[i][k]=2.0*pBetaS2[i][k]/dr[i];
pBetaS6[i][k]=3.0*pBetaS3[i][k]/dr[i];
pBetaP4[i][k]=pBetaP1[i][k]/dr[i];
pBetaP5[i][k]=2.0*pBetaP2[i][k]/dr[i];
pBetaP6[i][k]=3.0*pBetaP3[i][k]/dr[i];
pRepul4[i][k]=pRepul1[i][k]/dr[i];
pRepul5[i][k]=2.0*pRepul2[i][k]/dr[i];
pRepul6[i][k]=3.0*pRepul3[i][k]/dr[i];
if (format == 3) {
pLong4[i][k]=pLong1[i][k]/dr3[i];
pLong5[i][k]=2.0*pLong2[i][k]/dr3[i];
pLong6[i][k]=3.0*pLong3[i][k]/dr3[i];
}
}
for (int k=0; k < nBOt; k++) {
FsigBO4[i][k]=FsigBO1[i][k]/dBO;
FsigBO5[i][k]=2.0*FsigBO2[i][k]/dBO;
FsigBO6[i][k]=3.0*FsigBO3[i][k]/dBO;
}
}
if (npower <= 2) {
for (int i = 0; i < bop_types; i++) {
for (int j = 0; j < bop_types; j++) {
for (int k = j; k < bop_types; k++) {
gfunc1[j][i][k][0] = gfunc[j][i][k][1] - gfunc[j][i][k][0];
gfunc1[j][i][k][1] = 0.5 * (gfunc[j][i][k][2] - gfunc[j][i][k][0]);
gfunc1[j][i][k][ntheta - 2] = 0.5 * (gfunc[j][i][k][ntheta - 1] - gfunc[j][i][k][ntheta - 3]);
gfunc1[j][i][k][ntheta - 1] = 0.5 * (gfunc[j][i][k][ntheta - 1] - gfunc[j][i][k][ntheta - 2]);
for (int m = 2; m < ntheta - 2; m++) {
gfunc1[j][i][k][m] = ((gfunc[j][i][k][m - 2] - gfunc[j][i][k][m + 2]) +
8.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m + 1] - gfunc[j][i][k][m - 1])) /
12.0;
}
for (int m = 0; m < ntheta - 1; m++) {
gfunc2[j][i][k][m] = 3.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m]) -
2.0 * gfunc1[j][i][k][m] - gfunc1[j][i][k][m + 1];
gfunc3[j][i][k][m] = gfunc1[j][i][k][m] + gfunc1[j][i][k][m + 1] -
2.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m]);
}
gfunc2[j][i][k][ntheta - 1] = 0.0;
gfunc3[j][i][k][ntheta - 1] = 0.0;
for (int m = 0; m < ntheta; m++) {
gfunc4[j][i][k][ntheta - 1] = gfunc1[j][i][k][m] / dtheta;
gfunc5[j][i][k][ntheta - 1] = 2.0 * gfunc2[j][i][k][m] / dtheta;
gfunc6[j][i][k][ntheta - 1] = 3.0 * gfunc3[j][i][k][m] / dtheta;
}
}
}
}
}
for (int i = 0; i < bop_types; i++) {
for (int j = 0; j < bop_types; j++) {
for (int k = 0; k < j; k++) {
if (npower <= 2) {
for (int n = 0; n < ntheta; n++) {
gfunc[j][i][k][n] = gfunc[k][i][j][n];
gfunc1[j][i][k][n] = gfunc1[k][i][j][n];
gfunc2[j][i][k][n] = gfunc2[k][i][j][n];
gfunc3[j][i][k][n] = gfunc3[k][i][j][n];
gfunc4[j][i][k][n] = gfunc4[k][i][j][n];
gfunc5[j][i][k][n] = gfunc5[k][i][j][n];
gfunc6[j][i][k][n] = gfunc6[k][i][j][n];
}
} else {
if(npower==3) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]);
for (int n = 0; n < npower + 1; n++) {
gpara[j][i][k][n] = gpara[k][i][j][n];
}
else if(npower==4) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
}
else if(npower==5) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&gpara[j][i][k][5]);
}
else if(npower==6) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]);
}
else if(npower==7) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]);
}
else if(npower==8) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]);
}
else if(npower==9) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
}
else if(npower==10) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&gpara[j][i][k][10]);
}
}
}
} else {
for(i=0;i<bop_types;i++)
for(j=0;j<bop_types;j++)
for(k=0;k<bop_types;k++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf",&gpara[i][j][k][0],&gpara[i][j][k][1],&gpara[i][j][k][2]);
gpara[j][i][k][3]=0;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pRepul[i][j],&pRepul[i][j+1]
,&pRepul[i][j+2],&pRepul[i][j+3],&pRepul[i][j+4]);
j+=4;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pBetaS[i][j],&pBetaS[i][j+1]
,&pBetaS[i][j+2],&pBetaS[i][j+3],&pBetaS[i][j+4]);
j+=4;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&pBetaP[i][j],&pBetaP[i][j+1]
,&pBetaP[i][j+2],&pBetaP[i][j+3],&pBetaP[i][j+4]);
j+=4;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nBOt;j++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf%lf%lf%lf%lf",&FsigBO[i][j],&FsigBO[i][j+1]
,&FsigBO[i][j+2],&FsigBO[i][j+3],&FsigBO[i][j+4]);
j+=4;
}
}
for(i=0;i<bop_types;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&pro_delta[i]);
}
for(i=0;i<bop_types;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&pro[i]);
}
for(i=0;i<npairs;i++) {
rcut3[i]=0.0;
}
pass=0;
i=0;
if(nws==3) {
for(i=0;i<npairs;i++) {
utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
sscanf(s,"%lf",&rcut3[i]);
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
pass=0;
while(fgets(s,MAXLINE,fp)!=NULL&&pass==0) {
sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
j+=4;
pass=1;
}
}
}
}
rcutall=0.0;
for(i=0;i<npairs;i++) {
if(rcut[i]>rcutall)
rcutall=rcut[i];
if(rcut3[i]>rcutall)
rcutall=rcut3[i];
rcutsq[i]=rcut[i]*rcut[i];
dr[i]=rcut[i]/((double)nr-1.0);
rdr[i]=1.0/dr[i];
if (nws==3) {
rcutsq3[i]=rcut3[i]*rcut3[i];
dr3[i]=rcut3[i]/((double)nr-1.0);
rdr3[i]=1.0/dr3[i];
}
}
rctroot=rcutall;
dtheta=2.0/((double)ntheta-1.0);
rdtheta=1.0/dtheta;
dBO=1.0/((double)nBOt-1.0);
rdBO=1.0/(double)dBO;
for(i=0;i<npairs;i++) {
pBetaS1[i][0]=pBetaS[i][1]-pBetaS[i][0];
pBetaS1[i][1]=0.5*(pBetaS[i][2]-pBetaS[i][0]);
pBetaS1[i][nr-2]=0.5*(pBetaS[i][nr-1]-pBetaS[i][nr-3]);
pBetaS1[i][nr-1]=pBetaS[i][nr-1]-pBetaS[i][nr-2];
pBetaP1[i][0]=pBetaP[i][1]-pBetaP[i][0];
pBetaP1[i][1]=0.5*(pBetaP[i][2]-pBetaP[i][0]);
pBetaP1[i][nr-2]=0.5*(pBetaP[i][nr-1]-pBetaP[i][nr-3]);
pBetaP1[i][nr-1]=pBetaP[i][nr-1]-pBetaP[i][nr-2];
pRepul1[i][0]=pRepul[i][1]-pRepul[i][0];
pRepul1[i][1]=0.5*(pRepul[i][2]-pRepul[i][0]);
pRepul1[i][nr-2]=0.5*(pRepul[i][nr-1]-pRepul[i][nr-3]);
pRepul1[i][nr-1]=pRepul[i][nr-1]-pRepul[i][nr-2];
FsigBO1[i][0]=FsigBO[i][1]-FsigBO[i][0];
FsigBO1[i][1]=0.5*(FsigBO[i][2]-FsigBO[i][0]);
FsigBO1[i][nBOt-2]=0.5*(FsigBO[i][nBOt-1]-FsigBO[i][nBOt-3]);
FsigBO1[i][nBOt-1]=FsigBO[i][nBOt-1]-FsigBO[i][nBOt-2];
pLong1[i][0]=pLong[i][1]-pLong[i][0];
pLong1[i][1]=0.5*(pLong[i][2]-pLong[i][0]);
pLong1[i][nBOt-2]=0.5*(pLong[i][nr-1]-pLong[i][nr-3]);
pLong1[i][nBOt-1]=pLong[i][nr-1]-pLong[i][nr-2];
for(k=2;k<nr-2;k++) {
pBetaS1[i][k]=((pBetaS[i][k-2]-pBetaS[i][k+2])
+8.0*(pBetaS[i][k+1]-pBetaS[i][k-1]))/12.0;
pBetaP1[i][k]=((pBetaP[i][k-2]-pBetaP[i][k+2])
+8.0*(pBetaP[i][k+1]-pBetaP[i][k-1]))/12.0;
pRepul1[i][k]=((pRepul[i][k-2]-pRepul[i][k+2])
+8.0*(pRepul[i][k+1]-pRepul[i][k-1]))/12.0;
pLong1[i][k]=((pLong[i][k-2]-pLong[i][k+2])
+8.0*(pLong[i][k+1]-pLong[i][k-1]))/12.0;
}
for(k=2;k<nr-2;k++) {
FsigBO1[i][k]=((FsigBO[i][k-2]-FsigBO[i][k+2])
+8.0*(FsigBO[i][k+1]-FsigBO[i][k-1]))/12.0;
}
for(k=0;k<nr-1;k++) {
pBetaS2[i][k]=3.0*(pBetaS[i][k+1]-pBetaS[i][k])
-2.0*pBetaS1[i][k]-pBetaS1[i][k+1];
pBetaS3[i][k]=pBetaS1[i][k]+pBetaS1[i][k+1]
-2.0*(pBetaS[i][k+1]-pBetaS[i][k]);
pBetaP2[i][k]=3.0*(pBetaP[i][k+1]-pBetaP[i][k])
-2.0*pBetaP1[i][k]-pBetaP1[i][k+1];
pBetaP3[i][k]=pBetaP1[i][k]+pBetaP1[i][k+1]
-2.0*(pBetaP[i][k+1]-pBetaP[i][k]);
pRepul2[i][k]=3.0*(pRepul[i][k+1]-pRepul[i][k])
-2.0*pRepul1[i][k]-pRepul1[i][k+1];
pRepul3[i][k]=pRepul1[i][k]+pRepul1[i][k+1]
-2.0*(pRepul[i][k+1]-pRepul[i][k]);
pLong2[i][k]=3.0*(pLong[i][k+1]-pLong[i][k])
-2.0*pLong1[i][k]-pLong1[i][k+1];
pLong3[i][k]=pLong1[i][k]+pLong1[i][k+1]
-2.0*(pLong[i][k+1]-pLong[i][k]);
}
for(k=0;k<nBOt-1;k++) {
FsigBO2[i][k]=3.0*(FsigBO[i][k+1]-FsigBO[i][k])
-2.0*FsigBO1[i][k]-FsigBO1[i][k+1];
FsigBO3[i][k]=FsigBO1[i][k]+FsigBO1[i][k+1]
-2.0*(FsigBO[i][k+1]-FsigBO[i][k]);
}
pBetaS2[i][nr-1]=0.0;
pBetaS3[i][nr-1]=0.0;
pBetaP2[i][nr-1]=0.0;
pBetaP3[i][nr-1]=0.0;
pRepul2[i][nr-1]=0.0;
pRepul3[i][nr-1]=0.0;
pLong2[i][nr-1]=0.0;
pLong3[i][nr-1]=0.0;
FsigBO2[i][nBOt-1]=0.0;
FsigBO3[i][nBOt-1]=0.0;
for(k=0;k<nr;k++) {
pBetaS4[i][k]=pBetaS1[i][k]/dr[i];
pBetaS5[i][k]=2.0*pBetaS2[i][k]/dr[i];
pBetaS6[i][k]=3.0*pBetaS3[i][k]/dr[i];
pBetaP4[i][k]=pBetaP1[i][k]/dr[i];
pBetaP5[i][k]=2.0*pBetaP2[i][k]/dr[i];
pBetaP6[i][k]=3.0*pBetaP3[i][k]/dr[i];
pRepul4[i][k]=pRepul1[i][k]/dr[i];
pRepul5[i][k]=2.0*pRepul2[i][k]/dr[i];
pRepul6[i][k]=3.0*pRepul3[i][k]/dr[i];
if (nws==3) {
pLong4[i][k]=pLong1[i][k]/dr3[i];
pLong5[i][k]=2.0*pLong2[i][k]/dr3[i];
pLong6[i][k]=3.0*pLong3[i][k]/dr3[i];
}
}
for(k=0;k<nBOt;k++) {
FsigBO4[i][k]=FsigBO1[i][k]/dBO;
FsigBO5[i][k]=2.0*FsigBO2[i][k]/dBO;
FsigBO6[i][k]=3.0*FsigBO3[i][k]/dBO;
}
}
if(npower<=2) {
for(i=0;i<bop_types;i++) {
for(j=0;j<bop_types;j++) {
for(k=j;k<bop_types;k++) {
gfunc1[j][i][k][0]=gfunc[j][i][k][1]-gfunc[j][i][k][0];
gfunc1[j][i][k][1]=0.5*(gfunc[j][i][k][2]-gfunc[j][i][k][0]);
gfunc1[j][i][k][ntheta-2]=0.5*(gfunc[j][i][k][ntheta-1]-gfunc[j][i][k][ntheta-3]);
gfunc1[j][i][k][ntheta-1]=0.5*(gfunc[j][i][k][ntheta-1]-gfunc[j][i][k][ntheta-2]);
for(m=2;m<ntheta-2;m++) {
gfunc1[j][i][k][m]=((gfunc[j][i][k][m-2]-gfunc[j][i][k][m+2])+
8.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m+1]-gfunc[j][i][k][m-1]))/12.0;
}
for(m=0;m<ntheta-1;m++) {
gfunc2[j][i][k][m]=3.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m])-
2.0*gfunc1[j][i][k][m]-gfunc1[j][i][k][m+1];
gfunc3[j][i][k][m]=gfunc1[j][i][k][m]+gfunc1[j][i][k][m+1]-
2.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m]);
}
gfunc2[j][i][k][ntheta-1]=0.0;
gfunc3[j][i][k][ntheta-1]=0.0;
for(m=0;m<ntheta;m++) {
gfunc4[j][i][k][ntheta-1]=gfunc1[j][i][k][m]/dtheta;
gfunc5[j][i][k][ntheta-1]=2.0*gfunc2[j][i][k][m]/dtheta;
gfunc6[j][i][k][ntheta-1]=3.0*gfunc3[j][i][k][m]/dtheta;
}
}
}
}
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
} catch (FileReaderException & fre) {
error->one(FLERR, fre.what());
}
for(i=0;i<bop_types;i++) {
for(j=0;j<bop_types;j++) {
for(k=0;k<j;k++) {
if(npower<=2) {
for(n=0;n<ntheta;n++) {
gfunc[j][i][k][n]=gfunc[k][i][j][n];
gfunc1[j][i][k][n]=gfunc1[k][i][j][n];
gfunc2[j][i][k][n]=gfunc2[k][i][j][n];
gfunc3[j][i][k][n]=gfunc3[k][i][j][n];
gfunc4[j][i][k][n]=gfunc4[k][i][j][n];
gfunc5[j][i][k][n]=gfunc5[k][i][j][n];
gfunc6[j][i][k][n]=gfunc6[k][i][j][n];
}
} else {
for(n=0;n<npower+1;n++) {
gpara[j][i][k][n]=gpara[k][i][j][n];
}
}
}
}
}
fclose(fp);
}
MPI_Bcast(&nr,1,MPI_INT,0,world);
MPI_Bcast(&nBOt,1,MPI_INT,0,world);
MPI_Bcast(&ntheta,1,MPI_INT,0,world);
MPI_Bcast(&bop_types,1,MPI_INT,0,world);
MPI_Bcast(&npairs,1,MPI_INT,0,world);
MPI_Bcast(&npower,1,MPI_INT,0,world);
if (comm->me != 0){
allocate_tables();
allocate();
}
MPI_Bcast(&rdBO,1,MPI_DOUBLE,0,world);
MPI_Bcast(&dBO,1,MPI_DOUBLE,0,world);
MPI_Bcast(&rdtheta,1,MPI_DOUBLE,0,world);

2
src/MANYBODY/pair_bop.h
View File

@ -41,7 +41,6 @@ class PairBOP : public Pair {
double memory_usage();
private:
int me;
int maxneigh; // maximum size of neighbor list on this processor
int maxneigh3; // maximum size of neighbor list on this processor
int update_list; // check for changing maximum size of neighbor list
@ -207,6 +206,7 @@ class PairBOP : public Pair {
void read_table(char *);
void allocate();
void allocate_tables();
void create_pi(int);
void create_sigma(int);
void destroy_pi();

2
src/MANYBODY/pair_comb.cpp
View File

@ -594,7 +594,7 @@ void PairComb::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line," \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

109
src/MANYBODY/pair_comb3.cpp
View File

@ -312,84 +312,45 @@ double PairComb3::init_one(int i, int j)
void PairComb3::read_lib()
{
const unsigned int MAXLIB = 1024;
int i,j,k,l,m;
int ii,jj,kk,ll,mm,iii;
char s[MAXLIB];
// open library file on proc 0
if (comm->me == 0) {
const char filename[] = "lib.comb3";
FILE *fp = force->open_potential(filename);
if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file");
try {
// read and store at the same time
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
ValueTokenizer values(s, " \t\n\r\f");
ccutoff[0] = values.next_double();
ccutoff[1] = values.next_double();
ccutoff[2] = values.next_double();
ccutoff[3] = values.next_double();
ccutoff[4] = values.next_double();
ccutoff[5] = values.next_double();
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
ch_a[0] = values.next_double();
ch_a[1] = values.next_double();
ch_a[2] = values.next_double();
ch_a[3] = values.next_double();
ch_a[4] = values.next_double();
ch_a[5] = values.next_double();
ch_a[6] = values.next_double();
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
PotentialFileReader reader(lmp, "lib.comb3", "COMB3");
reader.next_dvector(ccutoff, 6);
reader.next_dvector(ch_a, 7);
ValueTokenizer values = reader.next_values(3);
nsplpcn = values.next_int();
nsplrad = values.next_int();
nspltor = values.next_int();
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(3);
maxx = values.next_int();
maxy = values.next_int();
maxz = values.next_int();
utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(3);
maxxc = values.next_int();
maxyc = values.next_int();
maxconj = values.next_int();
for (l = 0; l < nsplpcn; l++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(3);
values.skip(1);
maxxcn[l] = values.next_int();
vmaxxcn[l] = values.next_double();
dvmaxxcn[l] = values.next_double();
}
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
ntab = values.next_int();
ntab = reader.next_int();
for (i = 0; i < (ntab + 1); i++){
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(4);
values.skip(1);
pang[i] = values.next_double();
dpang[i] = values.next_double();
ddpang[i] = values.next_double();
@ -399,8 +360,7 @@ void PairComb3::read_lib()
for (i = 0; i < (maxx + 1); i++)
for (j = 0; j < (maxy + 1); j++)
for (k = 0; k < (maxz + 1); k++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(8);
ll = values.next_int() - 1;
ii = values.next_int();
@ -416,8 +376,7 @@ void PairComb3::read_lib()
for (i = 0; i < maxx; i++)
for (j = 0; j < maxy; j++)
for (k = 0; k < maxz; k++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(4);
ll = values.next_int()-1;
ii = values.next_int();
@ -425,13 +384,8 @@ void PairComb3::read_lib()
kk = values.next_int();
for(iii = 0; iii < 2; iii++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
for(m = 0; m < 32 ; m++) {
mm = iii*32 + m;
pcn_cubs[ll][ii][jj][kk][mm] = values.next_double();
}
mm = iii*32;
reader.next_dvector(&pcn_cubs[ll][ii][jj][kk][mm], 32);
}
}
@ -439,8 +393,7 @@ void PairComb3::read_lib()
for (i = 0; i < (maxxc + 1); i++)
for (j = 0; j < (maxyc + 1); j++)
for (k = 0; k < maxconj; k++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(8);
ll = values.next_int() - 1;
ii = values.next_int();
@ -456,8 +409,7 @@ void PairComb3::read_lib()
for (i = 0; i < maxxc; i++)
for (j = 0; j < maxyc; j++)
for (k = 0; k < (maxconj - 1); k++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(4);
ll = values.next_int() - 1;
ii = values.next_int();
@ -465,13 +417,8 @@ void PairComb3::read_lib()
kk = values.next_int() - 1;
for (iii = 0; iii < 2; iii++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
for(m = 0; m < 32 ; m++){
mm = iii * 32 + m;
rad_spl[ll][ii][jj][kk][mm] = values.next_double();
}
mm = iii * 32;
reader.next_dvector(&rad_spl[ll][ii][jj][kk][mm], 32);
}
}
@ -479,8 +426,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(8);
ll = values.next_int() - 1;
ii = values.next_int();
@ -496,26 +442,21 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
values = reader.next_values(4);
ll = values.next_int() - 1;
ii = values.next_int();
jj = values.next_int();
kk = values.next_int() - 1;
for(iii=0; iii<2; iii++) {
utils::sfgets(FLERR, s, MAXLIB, fp, filename, error);
values = ValueTokenizer(s, " \t\n\r\f");
for (m = 0; m < 32 ; m++){
mm=iii*32+m;
tor_spl[ll][ii][jj][kk][mm] = values.next_double();
}
mm=iii*32;
reader.next_dvector(&tor_spl[ll][ii][jj][kk][mm], 32);
}
}
fclose(fp);
} catch (FileReaderException & fre) {
error->one(FLERR, fre.what());
} catch (TokenizerException & e) {
fclose(fp);
error->one(FLERR, e.what());
}
}
@ -594,7 +535,7 @@ void PairComb3::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

12
src/MANYBODY/pair_eam.cpp
View File

@ -473,13 +473,11 @@ void PairEAM::read_file(char *filename)
reader.skip_line();
line = reader.next_line(2);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(2);
values.next_int(); // ignore
file->mass = values.next_double();
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -493,9 +491,9 @@ void PairEAM::read_file(char *filename)
memory->create(file->rhor, (file->nr+1), "pair:rhor");
memory->create(file->zr, (file->nr+1), "pair:zr");
reader.next_dvector(file->nrho, &file->frho[1]);
reader.next_dvector(file->nr, &file->zr[1]);
reader.next_dvector(file->nr, &file->rhor[1]);
reader.next_dvector(&file->frho[1], file->nrho);
reader.next_dvector(&file->zr[1], file->nr);
reader.next_dvector(&file->rhor[1], file->nr);
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}

17
src/MANYBODY/pair_eam_alloy.cpp
View File

@ -122,15 +122,12 @@ void PairEAMAlloy::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -146,8 +143,7 @@ void PairEAMAlloy::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -163,18 +159,17 @@ void PairEAMAlloy::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(file->nr, &file->rhor[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

2
src/MANYBODY/pair_eam_cd.cpp
View File

@ -514,7 +514,7 @@ void PairEAMCD::read_h_coeff(char *filename)
strcpy(line, nextline);
}
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
int degree = values.next_int();
nhcoeff = degree+1;

15
src/MANYBODY/pair_eam_fs.cpp
View File

@ -129,8 +129,7 @@ void PairEAMFS::read_file(char *filename)
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -146,8 +145,7 @@ void PairEAMFS::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -163,21 +161,20 @@ void PairEAMFS::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
for (int j = 0; j < file->nelements; j++) {
reader.next_dvector(file->nr, &file->rhor[i][j][1]);
reader.next_dvector(&file->rhor[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

7
src/MANYBODY/pair_eim.cpp
View File

@ -29,6 +29,7 @@
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
@ -1059,9 +1060,7 @@ EIMPotentialFileReader::EIMPotentialFileReader(LAMMPS * lmp, const std::string &
FILE * fp = force->open_potential(filename.c_str());
if (fp == NULL) {
char str[128];
snprintf(str, 128, "cannot open EIM potential file %s", filename.c_str());
error->one(FLERR, str);
error->one(FLERR, fmt::format("cannot open EIM potential file {}", filename));
}
parse(fp);
@ -1141,7 +1140,7 @@ void EIMPotentialFileReader::parse(FILE * fp)
bool found_global = false;
while((line = next_line(fp))) {
ValueTokenizer values(line, " \t\r\n\f");
ValueTokenizer values(line);
std::string type = values.next_string();
if (type == "global:") {

2
src/MANYBODY/pair_gw.cpp
View File

@ -380,7 +380,7 @@ void PairGW::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_gw_zbl.cpp
View File

@ -75,7 +75,7 @@ void PairGWZBL::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_nb3b_harmonic.cpp
View File

@ -296,7 +296,7 @@ void PairNb3bHarmonic::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

28
src/MANYBODY/pair_polymorphic.cpp
View File

@ -571,8 +571,7 @@ void PairPolymorphic::read_file(char *file)
try {
reader = new PotentialFileReader(lmp, file, "polymorphic");
char * line = reader->next_line(2);
ValueTokenizer values(line);
ValueTokenizer values = reader->next_values(2);
int ntypes = values.next_int();
@ -585,8 +584,7 @@ void PairPolymorphic::read_file(char *file)
match = new int[nelements];
for (int i = 0; i < nelements; i++) {
line = reader->next_line(3);
values = ValueTokenizer(line);
values = reader->next_values(3);
values.next_double(); // atomic number
values.next_double(); // atomic mass
std::string name = values.next_string();
@ -602,9 +600,8 @@ void PairPolymorphic::read_file(char *file)
// sizes
// Note: the format of this line has changed between the
// 2015-06-06 and 2015-12-09 versions of the pair style.
line = reader->next_line(4);
try {
values = ValueTokenizer(line);
values = reader->next_values(4);
nr = ng = nx = 0;
nr = values.next_int();
ng = values.next_int();
@ -625,8 +622,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
line = reader->next_line(2);
values = ValueTokenizer(line);
values = reader->next_values(2);
p.cut = values.next_double();
p.cutsq = p.cut*p.cut;
p.xi = values.next_double();
@ -658,7 +654,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < npair; i++) { // U
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(nr, singletable);
reader->next_dvector(singletable, nr);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.U = new tabularFunction(nr,0.0,p.cut);
@ -667,7 +663,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < npair; i++) { // V
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(nr, singletable);
reader->next_dvector(singletable, nr);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.V = new tabularFunction(nr,0.0,p.cut);
@ -676,7 +672,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < npair; i++) { // W
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(nr, singletable);
reader->next_dvector(singletable, nr);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.W = new tabularFunction(nr,0.0,p.cut);
@ -693,7 +689,7 @@ void PairPolymorphic::read_file(char *file)
if (eta != 3) {
for (int j = 0; j < nelements; j++) { // P
if (comm->me == 0) {
reader->next_dvector(nr, singletable);
reader->next_dvector(singletable, nr);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
for (int i = 0; i < nelements; i++) {
@ -705,7 +701,7 @@ void PairPolymorphic::read_file(char *file)
for (int j = 0; j < nelements-1; j++) { // P
for (int k = j+1; k < nelements; k++) {
if (comm->me == 0) {
reader->next_dvector(nr, singletable);
reader->next_dvector(singletable, nr);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
for (int i = 0; i < nelements; i++) {
@ -723,7 +719,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < ntriple; i++) { // P
TripletParameters & p = tripletParameters[i];
if (comm->me == 0) {
reader->next_dvector(nr, singletable);
reader->next_dvector(singletable, nr);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.P = new tabularFunction(nr,-cutmax,cutmax);
@ -735,7 +731,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < ntriple; i++) { // G
TripletParameters & p = tripletParameters[i];
if (comm->me == 0) {
reader->next_dvector(ng, singletable);
reader->next_dvector(singletable, ng);
}
MPI_Bcast(singletable,ng,MPI_DOUBLE,0,world);
p.G = new tabularFunction(ng,-1.0,1.0);
@ -746,7 +742,7 @@ void PairPolymorphic::read_file(char *file)
for (int i = 0; i < npair; i++) { // F
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(nx, singletable);
reader->next_dvector(singletable, nx);
}
MPI_Bcast(singletable,nx,MPI_DOUBLE,0,world);
p.F = new tabularFunction(nx,0.0,maxX);

2
src/MANYBODY/pair_sw.cpp
View File

@ -360,7 +360,7 @@ void PairSW::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_tersoff.cpp
View File

@ -405,7 +405,7 @@ void PairTersoff::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_tersoff_mod.cpp
View File

@ -58,7 +58,7 @@ void PairTersoffMOD::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_tersoff_mod_c.cpp
View File

@ -49,7 +49,7 @@ void PairTersoffMODC::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_tersoff_zbl.cpp
View File

@ -76,7 +76,7 @@ void PairTersoffZBL::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

2
src/MANYBODY/pair_vashishta.cpp
View File

@ -366,7 +366,7 @@ void PairVashishta::read_file(char *file)
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line, " \t\n\r\f");
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();

105
src/MOLECULE/angle_table.cpp
View File

@ -29,14 +29,15 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "utils.h"
#include "tokenizer.h"
#include "table_file_reader.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace MathConst;
enum{LINEAR,SPLINE};
#define MAXLINE 1024
#define SMALL 0.001
#define TINY 1.E-10
@ -381,61 +382,45 @@ void AngleTable::free_table(Table *tb)
void AngleTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
TableFileReader reader(lmp, file, "angle");
// open file
char * line = reader.find_section_start(keyword);
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword
utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line);
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++)
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
if (!line) {
error->one(FLERR,"Did not find keyword in table file");
}
// read args on 2nd line of section
// allocate table arrays for file values
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
param_extract(tb,line);
memory->create(tb->afile,tb->ninput,"angle:afile");
memory->create(tb->efile,tb->ninput,"angle:efile");
memory->create(tb->ffile,tb->ninput,"angle:ffile");
line = reader.next_line();
param_extract(tb, line);
memory->create(tb->afile, tb->ninput, "angle:afile");
memory->create(tb->efile, tb->ninput, "angle:efile");
memory->create(tb->ffile, tb->ninput, "angle:ffile");
// read a,e,f table values from file
int cerror = 0;
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
if (3 != sscanf(line,"%*d %lg %lg %lg",
&tb->afile[i],&tb->efile[i],&tb->ffile[i])) ++cerror;
line = reader.next_line(4);
try {
ValueTokenizer values(line);
values.next_int();
tb->afile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
} catch (TokenizerException & e) {
++cerror;
}
}
fclose(fp);
// warn if data was read incompletely, e.g. columns were missing
if (cerror) {
char str[128];
sprintf(str,"%d of %d lines in table were incomplete or could not be"
" parsed completely",cerror,tb->ninput);
error->warning(FLERR,str);
std::string str = fmt::format("{} of {} lines in table were incomplete or could not be parsed completely", cerror, tb->ninput);
error->warning(FLERR,str.c_str());
}
}
@ -521,26 +506,28 @@ void AngleTable::param_extract(Table *tb, char *line)
tb->fpflag = 0;
tb->theta0 = MY_PI;
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
} else if (strcmp(word,"FP") == 0) {
tb->fpflag = 1;
word = strtok(NULL," \t\n\r\f");
tb->fplo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->fphi = atof(word);
tb->fplo *= (180.0/MY_PI)*(180.0/MY_PI);
tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI);
} else if (strcmp(word,"EQ") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->theta0 = atof(word)/180.0*MY_PI;
} else {
error->one(FLERR,"Invalid keyword in angle table parameters");
try {
ValueTokenizer values(line);
while (values.has_next()) {
std::string word = values.next_string();
if (word == "N") {
tb->ninput = values.next_int();
} else if (word == "FP") {
tb->fpflag = 1;
tb->fplo = values.next_double();
tb->fphi = values.next_double();
tb->fplo *= (180.0/MY_PI)*(180.0/MY_PI);
tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI);
} else if (word == "EQ") {
tb->theta0 = values.next_double()/180.0*MY_PI;
} else {
error->one(FLERR,"Invalid keyword in angle table parameters");
}
}
word = strtok(NULL," \t\n\r\f");
} catch(TokenizerException & e) {
error->one(FLERR, e.what());
}
if (tb->ninput == 0) error->one(FLERR,"Angle table parameters did not set N");

99
src/MOLECULE/bond_table.cpp
View File

@ -27,12 +27,14 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "table_file_reader.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
enum{NONE,LINEAR,SPLINE};
#define MAXLINE 1024
#define BIGNUM 1.0e300
/* ---------------------------------------------------------------------- */
@ -307,38 +309,19 @@ void BondTable::free_table(Table *tb)
void BondTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
TableFileReader reader(lmp, file, "bond");
double emin = BIGNUM;
// open file
char * line = reader.find_section_start(keyword);
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword
utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line);
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++)
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
if (!line) {
error->one(FLERR,"Did not find keyword in table file");
}
// read args on 2nd line of section
// allocate table arrays for file values
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
line = reader.next_line();
param_extract(tb,line);
memory->create(tb->rfile,tb->ninput,"bond:rfile");
memory->create(tb->efile,tb->ninput,"bond:efile");
@ -349,18 +332,24 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
int cerror = 0;
int r0idx = -1;
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
if (NULL == fgets(line,MAXLINE,fp))
error->one(FLERR,"Premature end of file in bond table");
if (3 != sscanf(line,"%*d %lg %lg %lg",
&tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror;
line = reader.next_line(4);
try {
ValueTokenizer values(line);
values.next_int();
tb->rfile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
} catch (TokenizerException & e) {
++cerror;
}
if (tb->efile[i] < emin) {
emin = tb->efile[i];
r0idx = i;
}
}
fclose(fp);
// infer r0 from minimum of potential, if not given explicitly
@ -389,19 +378,15 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
}
if (ferror) {
char str[128];
sprintf(str,"%d of %d force values in table are inconsistent with -dE/dr.\n"
" Should only be flagged at inflection points",ferror,tb->ninput);
error->warning(FLERR,str);
error->warning(FLERR, fmt::format("{} of {} force values in table are inconsistent with -dE/dr.\n"
" Should only be flagged at inflection points",ferror,tb->ninput));
}
// warn if data was read incompletely, e.g. columns were missing
if (cerror) {
char str[128];
sprintf(str,"%d of %d lines in table were incomplete or could not be"
" parsed completely",cerror,tb->ninput);
error->warning(FLERR,str);
error->warning(FLERR, fmt::format("{} of {} lines in table were incomplete or could not be"
" parsed completely",cerror,tb->ninput));
}
}
@ -488,24 +473,26 @@ void BondTable::param_extract(Table *tb, char *line)
tb->fpflag = 0;
tb->r0 = 0.0;
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
} else if (strcmp(word,"FP") == 0) {
tb->fpflag = 1;
word = strtok(NULL," \t\n\r\f");
tb->fplo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->fphi = atof(word);
} else if (strcmp(word,"EQ") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->r0 = atof(word);
} else {
error->one(FLERR,"Invalid keyword in bond table parameters");
try {
ValueTokenizer values(line);
while (values.has_next()) {
std::string word = values.next_string();
if (word == "N") {
tb->ninput = values.next_int();
} else if (word == "FP") {
tb->fpflag = 1;
tb->fplo = values.next_double();
tb->fphi = values.next_double();
} else if (word == "EQ") {
tb->r0 = values.next_double();
} else {
error->one(FLERR,"Invalid keyword in bond table parameters");
}
}
word = strtok(NULL," \t\n\r\f");
} catch(TokenizerException & e) {
error->one(FLERR, e.what());
}
if (tb->ninput == 0) error->one(FLERR,"Bond table parameters did not set N");

2
src/RIGID/fix_rigid_small.cpp
View File

@ -2489,7 +2489,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
buf = buffer;
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::count_words(buf);
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != ATTRIBUTE_PERBODY)

4
src/SNAP/pair_snap.cpp
View File

@ -568,7 +568,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
nwords = utils::count_words(line);
nwords = utils::trim_and_count_words(line);
if (nwords != 3)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
@ -610,7 +610,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
nwords = utils::count_words(line);
nwords = utils::trim_and_count_words(line);
if (nwords != 1)
error->all(FLERR,"Incorrect format in SNAP coefficient file");

2
src/SPIN/neb_spin.cpp
View File

@ -441,7 +441,7 @@ void NEBSpin::readfile(char *file, int flag)
buf = buffer;
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::count_words(buf);
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != ATTRIBUTE_PERLINE)

17
src/USER-INTEL/pair_eam_alloy_intel.cpp
View File

@ -122,15 +122,12 @@ void PairEAMAlloyIntel::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -146,8 +143,7 @@ void PairEAMAlloyIntel::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -163,18 +159,17 @@ void PairEAMAlloyIntel::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(file->nr, &file->rhor[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

17
src/USER-INTEL/pair_eam_fs_intel.cpp
View File

@ -122,15 +122,12 @@ void PairEAMFSIntel::read_file(char *filename)
PotentialFileReader reader(lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -146,8 +143,7 @@ void PairEAMFSIntel::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -163,21 +159,20 @@ void PairEAMFSIntel::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
for (int j = 0; j < file->nelements; j++) {
reader.next_dvector(file->nr, &file->rhor[i][j][1]);
reader.next_dvector(&file->rhor[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

168
src/USER-MISC/dihedral_table.cpp
View File

@ -36,6 +36,9 @@
#include "utils.h"
#include "dihedral_table.h"
#include "utils.h"
#include "tokenizer.h"
#include "table_file_reader.h"
#include "fmt/format.h"
#include "math_const.h"
#include "math_extra.h"
@ -458,8 +461,7 @@ static double Phi(double const *x1, //array holding x,y,z coords atom 1
DihedralTable::DihedralTable(LAMMPS *lmp) : Dihedral(lmp)
{
ntables = 0;
tables = NULL;
checkU_fname = checkF_fname = NULL;
tables = nullptr;
}
/* ---------------------------------------------------------------------- */
@ -468,8 +470,6 @@ DihedralTable::~DihedralTable()
{
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
memory->sfree(checkU_fname);
memory->sfree(checkF_fname);
if (allocated) {
memory->destroy(setflag);
@ -832,13 +832,13 @@ void DihedralTable::coeff(int narg, char **arg)
string err_msg;
err_msg = string("Invalid dihedral table length (")
+ string(arg[2]) + string(").");
error->one(FLERR,err_msg.c_str());
error->one(FLERR,err_msg);
}
else if ((tb->ninput == 2) && (tabstyle == SPLINE)) {
string err_msg;
err_msg = string("Invalid dihedral spline table length. (Try linear)\n (")
+ string(arg[2]) + string(").");
error->one(FLERR,err_msg.c_str());
error->one(FLERR,err_msg);
}
// check for monotonicity
@ -851,7 +851,7 @@ void DihedralTable::coeff(int narg, char **arg)
string(arg[2]) + string(", ")+i_str.str()+string("th entry)");
if (i==0)
err_msg += string("\n(This is probably a mistake with your table format.)\n");
error->all(FLERR,err_msg.c_str());
error->all(FLERR,err_msg);
}
}
@ -863,7 +863,7 @@ void DihedralTable::coeff(int narg, char **arg)
string err_msg;
err_msg = string("Dihedral table angle range must be < 360 degrees (")
+string(arg[2]) + string(").");
error->all(FLERR,err_msg.c_str());
error->all(FLERR,err_msg);
}
}
else {
@ -871,7 +871,7 @@ void DihedralTable::coeff(int narg, char **arg)
string err_msg;
err_msg = string("Dihedral table angle range must be < 2*PI radians (")
+ string(arg[2]) + string(").");
error->all(FLERR,err_msg.c_str());
error->all(FLERR,err_msg);
}
}
@ -940,7 +940,7 @@ void DihedralTable::coeff(int narg, char **arg)
// Optional: allow the user to print out the interpolated spline tables
if (me == 0) {
if (checkU_fname && (strlen(checkU_fname) != 0))
if (!checkU_fname.empty())
{
ofstream checkU_file;
checkU_file.open(checkU_fname, ios::out);
@ -953,7 +953,7 @@ void DihedralTable::coeff(int narg, char **arg)
}
checkU_file.close();
}
if (checkF_fname && (strlen(checkF_fname) != 0))
if (!checkF_fname.empty())
{
ofstream checkF_file;
checkF_file.open(checkF_fname, ios::out);
@ -1084,42 +1084,21 @@ void DihedralTable::free_table(Table *tb)
/* ----------------------------------------------------------------------
read table file, only called by proc 0
------------------------------------------------------------------------- */
static const int MAXLINE=2048;
void DihedralTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
TableFileReader reader(lmp, file, "dihedral");
// open file
char * line = reader.find_section_start(keyword);
FILE *fp = force->open_potential(file);
if (fp == NULL) {
string err_msg = string("Cannot open file ") + string(file);
error->one(FLERR,err_msg.c_str());
if (!line) {
error->one(FLERR,"Did not find keyword in table file");
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL) {
string err_msg=string("Did not find keyword \"")
+string(keyword)+string("\" in dihedral table file.");
error->one(FLERR, err_msg.c_str());
}
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword
utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line);
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++)
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
}
// read args on 2nd line of section
// allocate table arrays for file values
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
line = reader.next_line();
param_extract(tb,line);
memory->create(tb->phifile,tb->ninput,"dihedral:phifile");
memory->create(tb->efile,tb->ninput,"dihedral:efile");
@ -1127,41 +1106,24 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
// read a,e,f table values from file
int itmp;
for (int i = 0; i < tb->ninput; i++) {
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
// Skip blank lines and delete text following a '#' character
char *pe = strchr(line, '#');
if (pe != NULL) *pe = '\0'; //terminate string at '#' character
char *pc = line;
while ((*pc != '\0') && isspace(*pc))
pc++;
if (*pc != '\0') { //If line is not a blank line
stringstream line_ss(line);
try {
if (tb->f_unspecified) {
line_ss >> itmp;
line_ss >> tb->phifile[i];
line_ss >> tb->efile[i];
ValueTokenizer values = reader.next_values(3);
values.next_int();
tb->phifile[i] = values.next_double();
tb->efile[i] = values.next_double();
} else {
line_ss >> itmp;
line_ss >> tb->phifile[i];
line_ss >> tb->efile[i];
line_ss >> tb->ffile[i];
ValueTokenizer values = reader.next_values(4);
values.next_int();
tb->phifile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
}
if (! line_ss) {
stringstream err_msg;
err_msg << "Read error in table "<< keyword<<", near line "<<i+1<<"\n"
<< " (Check to make sure the number of columns is correct.)";
if ((! tb->f_unspecified) && (i==0))
err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
error->one(FLERR, err_msg.str().c_str());
}
} else //if it is a blank line, then skip it.
i--;
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
} //for (int i = 0; (i < tb->ninput) && fp; i++) {
fclose(fp);
}
/* ----------------------------------------------------------------------
@ -1252,7 +1214,7 @@ void DihedralTable::spline_table(Table *tb)
if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) {
string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n");
error->all(FLERR,msg.c_str());
error->all(FLERR, msg);
}
} // check for consistency if (! tb->f_unspecified)
@ -1353,44 +1315,40 @@ void DihedralTable::param_extract(Table *tb, char *line)
tb->f_unspecified = false; //default
tb->use_degrees = true; //default
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
try {
ValueTokenizer values(line);
while (values.has_next()) {
std::string word = values.next_string();
if (word == "N") {
tb->ninput = values.next_int();
}
else if (word == "NOF") {
tb->f_unspecified = true;
}
else if ((word == "DEGREES") || (word == "degrees")) {
tb->use_degrees = true;
}
else if ((word == "RADIANS") || (word == "radians")) {
tb->use_degrees = false;
}
else if (word == "CHECKU") {
checkU_fname = values.next_string();
}
else if (word == "CHECKF") {
checkF_fname = values.next_string();
}
// COMMENTING OUT: equilibrium angles are not supported
//else if (word == "EQ") {
// tb->theta0 = values.next_double();
//}
else {
string err_msg = fmt::format("Invalid keyword in dihedral angle table parameters ({})", word);
error->one(FLERR,err_msg);
}
}
else if (strcmp(word,"NOF") == 0) {
tb->f_unspecified = true;
}
else if ((strcmp(word,"DEGREES") == 0) || (strcmp(word,"degrees") == 0)) {
tb->use_degrees = true;
}
else if ((strcmp(word,"RADIANS") == 0) || (strcmp(word,"radians") == 0)) {
tb->use_degrees = false;
}
else if (strcmp(word,"CHECKU") == 0) {
word = strtok(NULL," \t\n\r\f");
memory->sfree(checkU_fname);
memory->create(checkU_fname,strlen(word)+1,"dihedral_table:checkU");
strcpy(checkU_fname, word);
}
else if (strcmp(word,"CHECKF") == 0) {
word = strtok(NULL," \t\n\r\f");
memory->sfree(checkF_fname);
memory->create(checkF_fname,strlen(word)+1,"dihedral_table:checkF");
strcpy(checkF_fname, word);
}
// COMMENTING OUT: equilibrium angles are not supported
//else if (strcmp(word,"EQ") == 0) {
// word = strtok(NULL," \t\n\r\f");
// tb->theta0 = atof(word);
//}
else {
string err_msg("Invalid keyword in dihedral angle table parameters");
err_msg += string(" (") + string(word) + string(")");
error->one(FLERR,err_msg.c_str());
}
word = strtok(NULL," \t\n\r\f");
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
if (tb->ninput == 0)

5
src/USER-MISC/dihedral_table.h
View File

@ -24,6 +24,7 @@ DihedralStyle(table,DihedralTable)
#ifndef LMP_DIHEDRAL_TABLE_H
#define LMP_DIHEDRAL_TABLE_H
#include "dihedral.h"
#include <string>
namespace LAMMPS_NS {
@ -43,8 +44,8 @@ class DihedralTable : public Dihedral {
protected:
int tabstyle,tablength;
// double *phi0; <- equilibrium angles not supported
char *checkU_fname;
char *checkF_fname;
std::string checkU_fname;
std::string checkF_fname;
struct Table {
int ninput;

16
src/USER-MISC/dihedral_table_cut.cpp
View File

@ -824,13 +824,13 @@ void DihedralTableCut::coeff(int narg, char **arg)
string err_msg;
err_msg = string("Invalid dihedral table length (")
+ string(arg[5]) + string(").");
error->one(FLERR,err_msg.c_str());
error->one(FLERR,err_msg);
}
else if ((tb->ninput == 2) && (tabstyle == SPLINE)) {
string err_msg;
err_msg = string("Invalid dihedral spline table length. (Try linear)\n (")
+ string(arg[5]) + string(").");
error->one(FLERR,err_msg.c_str());
error->one(FLERR,err_msg);
}
// check for monotonicity
@ -843,7 +843,7 @@ void DihedralTableCut::coeff(int narg, char **arg)
string(arg[5]) + string(", ")+i_str.str()+string("th entry)");
if (i==0)
err_msg += string("\n(This is probably a mistake with your table format.)\n");
error->all(FLERR,err_msg.c_str());
error->all(FLERR,err_msg);
}
}
@ -855,7 +855,7 @@ void DihedralTableCut::coeff(int narg, char **arg)
string err_msg;
err_msg = string("Dihedral table angle range must be < 360 degrees (")
+string(arg[5]) + string(").");
error->all(FLERR,err_msg.c_str());
error->all(FLERR,err_msg);
}
}
else {
@ -863,7 +863,7 @@ void DihedralTableCut::coeff(int narg, char **arg)
string err_msg;
err_msg = string("Dihedral table angle range must be < 2*PI radians (")
+ string(arg[5]) + string(").");
error->all(FLERR,err_msg.c_str());
error->all(FLERR,err_msg);
}
}
@ -1081,7 +1081,7 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword)
FILE *fp = force->open_potential(file);
if (fp == NULL) {
string err_msg = string("Cannot open file ") + string(file);
error->one(FLERR,err_msg.c_str());
error->one(FLERR,err_msg);
}
// loop until section found with matching keyword
@ -1090,7 +1090,7 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword)
if (fgets(line,MAXLINE,fp) == NULL) {
string err_msg=string("Did not find keyword \"")
+string(keyword)+string("\" in dihedral table file.");
error->one(FLERR, err_msg.c_str());
error->one(FLERR, err_msg);
}
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
@ -1376,7 +1376,7 @@ void DihedralTableCut::param_extract(Table *tb, char *line)
else {
string err_msg("Invalid keyword in dihedral angle table parameters");
err_msg += string(" (") + string(word) + string(")");
error->one(FLERR,err_msg.c_str());
error->one(FLERR, err_msg);
}
word = strtok(NULL," \t\n\r\f");
}

17
src/USER-OMP/pair_eam_alloy_omp.cpp
View File

@ -122,15 +122,12 @@ void PairEAMAlloyOMP::read_file(char *filename)
PotentialFileReader reader(PairEAM::lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -146,8 +143,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -163,18 +159,17 @@ void PairEAMAlloyOMP::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(file->nr, &file->rhor[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

17
src/USER-OMP/pair_eam_fs_omp.cpp
View File

@ -122,15 +122,12 @@ void PairEAMFSOMP::read_file(char *filename)
PotentialFileReader reader(PairEAM::lmp, filename, "EAM");
try {
char * line = nullptr;
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
line = reader.next_line(1);
ValueTokenizer values(line);
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if (values.count() != file->nelements + 1)
@ -146,8 +143,7 @@ void PairEAMFSOMP::read_file(char *filename)
//
line = reader.next_line(5);
values = ValueTokenizer(line);
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
@ -163,21 +159,20 @@ void PairEAMFSOMP::read_file(char *filename)
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
for (int i = 0; i < file->nelements; i++) {
line = reader.next_line(2);
values = ValueTokenizer(line);
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(file->nrho, &file->frho[i][1]);
reader.next_dvector(&file->frho[i][1], file->nrho);
for (int j = 0; j < file->nelements; j++) {
reader.next_dvector(file->nr, &file->rhor[i][j][1]);
reader.next_dvector(&file->rhor[i][j][1], file->nr);
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
reader.next_dvector(&file->z2r[i][j][1], file->nr);
}
}
} catch (TokenizerException & e) {

217
src/USER-OMP/pair_tersoff_zbl_omp.cpp
View File

@ -31,6 +31,8 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "math_const.h"
#include "math_special.h"
@ -38,7 +40,6 @@ using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#define MAXLINE 1024
#define DELTA 4
/* ----------------------------------------------------------------------
@ -84,152 +85,108 @@ PairTersoffZBLOMP::PairTersoffZBLOMP(LAMMPS *lmp) : PairTersoffOMP(lmp)
void PairTersoffZBLOMP::read_file(char *file)
{
int params_per_line = 21;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
params = nullptr;
nparams = maxparam = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
PotentialFileReader reader(PairTersoff::lmp, file, "Tersoff");
char * line;
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line);
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
std::string iname = values.next_string();
std::string jname = values.next_string();
std::string kname = values.next_string();
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next entry in file
int ielement, jelement, kelement;
// strip comment, skip line if blank
for (ielement = 0; ielement < nelements; ielement++)
if (iname == elements[ielement]) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (jname == elements[jelement]) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (kname == elements[kelement]) break;
if (kelement == nelements) continue;
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
// load up parameter settings and error check their values
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = values.next_double();
params[nparams].gamma = values.next_double();
params[nparams].lam3 = values.next_double();
params[nparams].c = values.next_double();
params[nparams].d = values.next_double();
params[nparams].h = values.next_double();
params[nparams].powern = values.next_double();
params[nparams].beta = values.next_double();
params[nparams].lam2 = values.next_double();
params[nparams].bigb = values.next_double();
params[nparams].bigr = values.next_double();
params[nparams].bigd = values.next_double();
params[nparams].lam1 = values.next_double();
params[nparams].biga = values.next_double();
params[nparams].Z_i = values.next_double();
params[nparams].Z_j = values.next_double();
params[nparams].ZBLcut = values.next_double();
params[nparams].ZBLexpscale = values.next_double();
params[nparams].powermint = int(params[nparams].powerm);
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
// currently only allow m exponent of 1 or 3
if (params[nparams].c < 0.0 ||
params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 ||
params[nparams].beta < 0.0 ||
params[nparams].lam2 < 0.0 ||
params[nparams].bigb < 0.0 ||
params[nparams].bigr < 0.0 ||
params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].lam1 < 0.0 ||
params[nparams].biga < 0.0 ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 &&
params[nparams].powermint != 1) ||
params[nparams].gamma < 0.0 ||
params[nparams].Z_i < 1.0 ||
params[nparams].Z_j < 1.0 ||
params[nparams].ZBLcut < 0.0 ||
params[nparams].ZBLexpscale < 0.0)
error->one(FLERR,"Illegal Tersoff parameter");
nparams++;
}
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in Tersoff potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = atof(words[3]);
params[nparams].gamma = atof(words[4]);
params[nparams].lam3 = atof(words[5]);
params[nparams].c = atof(words[6]);
params[nparams].d = atof(words[7]);
params[nparams].h = atof(words[8]);
params[nparams].powern = atof(words[9]);
params[nparams].beta = atof(words[10]);
params[nparams].lam2 = atof(words[11]);
params[nparams].bigb = atof(words[12]);
params[nparams].bigr = atof(words[13]);
params[nparams].bigd = atof(words[14]);
params[nparams].lam1 = atof(words[15]);
params[nparams].biga = atof(words[16]);
params[nparams].Z_i = atof(words[17]);
params[nparams].Z_j = atof(words[18]);
params[nparams].ZBLcut = atof(words[19]);
params[nparams].ZBLexpscale = atof(words[20]);
// currently only allow m exponent of 1 or 3
params[nparams].powermint = int(params[nparams].powerm);
if (params[nparams].c < 0.0 ||
params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 ||
params[nparams].beta < 0.0 ||
params[nparams].lam2 < 0.0 ||
params[nparams].bigb < 0.0 ||
params[nparams].bigr < 0.0 ||
params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].lam1 < 0.0 ||
params[nparams].biga < 0.0 ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 &&
params[nparams].powermint != 1) ||
params[nparams].gamma < 0.0 ||
params[nparams].Z_i < 1.0 ||
params[nparams].Z_j < 1.0 ||
params[nparams].ZBLcut < 0.0 ||
params[nparams].ZBLexpscale < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
}
delete [] words;
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
if(comm->me != 0) {
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
}
MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
}
/* ---------------------------------------------------------------------- */

2
src/USER-PLUMED/fix_plumed.cpp
View File

@ -82,6 +82,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. "
"Only Plumed 2.4.x, 2.5.x, and 2.6.x are tested and supported.");
#if !defined(MPI_STUBS)
// If the -partition option is activated then enable
// inter-partition communication
@ -108,7 +109,6 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
// whereas if partitions are not defined then world is equal to
// MPI_COMM_WORLD.
#if !defined(MPI_STUBS)
// plumed does not know about LAMMPS using the MPI STUBS library and will
// fail if this is called under these circumstances
p->cmd("setMPIComm",&world);

204
src/USER-QTB/fix_qbmsst.cpp
View File

@ -21,6 +21,7 @@
#include <cmath>
#include <cstring>
#include <cstdlib>
#include <string>
#include "atom.h"
#include "force.h"
#include "update.h"
@ -34,6 +35,7 @@
#include "kspace.h"
#include "math_const.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -98,58 +100,71 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"q") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
qmass = atof(arg[iarg+1]); if (qmass < 0.0) error->all(FLERR,"Fix qbmsst qmass must be >= 0.0");
qmass = force->numeric(FLERR,arg[iarg+1]);
if (qmass < 0.0) error->all(FLERR,"Fix qbmsst qmass must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
mu = atof(arg[iarg+1]); if (mu < 0.0) error->all(FLERR,"Fix qbmsst mu must be >= 0.0");
mu = force->numeric(FLERR,arg[iarg+1]);
if (mu < 0.0) error->all(FLERR,"Fix qbmsst mu must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"p0") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
p0 = atof(arg[iarg+1]); if (p0 < 0.0) error->all(FLERR,"Fix qbmsst p0 must be >= 0.0");
p0 = force->numeric(FLERR,arg[iarg+1]);
if (p0 < 0.0) error->all(FLERR,"Fix qbmsst p0 must be >= 0.0");
p0_set = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"v0") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
v0 = atof(arg[iarg+1]); if (v0 < 0.0) error->all(FLERR,"Fix qbmsst v0 must be >= 0.0");
v0 = force->numeric(FLERR,arg[iarg+1]);
if (v0 < 0.0) error->all(FLERR,"Fix qbmsst v0 must be >= 0.0");
v0_set = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"e0") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
e0 = atof(arg[iarg+1]);
e0 = force->numeric(FLERR,arg[iarg+1]);
e0_set = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"tscale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
tscale = atof(arg[iarg+1]); if (tscale < 0.0 || tscale > 1.0) error->all(FLERR,"Fix qbmsst tscale must satisfy 0 <= tscale < 1");
tscale = force->numeric(FLERR,arg[iarg+1]);
if (tscale < 0.0 || tscale > 1.0) error->all(FLERR,"Fix qbmsst tscale must satisfy 0 <= tscale < 1");
iarg += 2;
} else if (strcmp(arg[iarg],"damp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
t_period = atof(arg[iarg+1]); if (t_period <= 0.0) error->all(FLERR,"Fix qbmsst damp must be > 0.0"); fric_coef = 1/t_period;
t_period = force->numeric(FLERR,arg[iarg+1]);
if (t_period <= 0.0) error->all(FLERR,"Fix qbmsst damp must be > 0.0");
fric_coef = 1/t_period;
iarg += 2;
} else if (strcmp(arg[iarg],"seed") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
seed = atof(arg[iarg+1]); if (seed <= 0) error->all(FLERR,"Fix qbmsst seed must be a positive integer");
seed = force->inumeric(FLERR,arg[iarg+1]);
if (seed <= 0) error->all(FLERR,"Fix qbmsst seed must be a positive integer");
iarg += 2;
} else if (strcmp(arg[iarg],"f_max") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
f_max = atof(arg[iarg+1]); if (f_max <= 0) error->all(FLERR,"Fix qbmsst f_max must be > 0.0");
f_max = force->numeric(FLERR,arg[iarg+1]);
if (f_max <= 0) error->all(FLERR,"Fix qbmsst f_max must be > 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"N_f") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
N_f = atof(arg[iarg+1]); if (N_f <= 0) error->all(FLERR,"Fix qbmsst N_f must be a positive integer");
N_f = force->inumeric(FLERR,arg[iarg+1]);
if (N_f <= 0) error->all(FLERR,"Fix qbmsst N_f must be a positive integer");
iarg += 2;
} else if (strcmp(arg[iarg],"eta") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
eta = atof(arg[iarg+1]); if (eta <= 0) error->all(FLERR,"Fix qbmsst eta must be >= 0.0");
eta = force->numeric(FLERR,arg[iarg+1]);
if (eta <= 0) error->all(FLERR,"Fix qbmsst eta must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"beta") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
beta = atof(arg[iarg+1]); if (beta <= 0) error->all(FLERR,"Fix qbmsst beta must be a positive integer");
beta = force->inumeric(FLERR,arg[iarg+1]);
if (beta <= 0) error->all(FLERR,"Fix qbmsst beta must be a positive integer");
iarg += 2;
} else if (strcmp(arg[iarg],"T_init") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
t_init = atof(arg[iarg+1]); if (t_init <= 0) error->all(FLERR,"Fix qbmsst T_init must be >= 0.0");
t_init = force->numeric(FLERR,arg[iarg+1]);
if (t_init <= 0) error->all(FLERR,"Fix qbmsst T_init must be >= 0.0");
iarg += 2;
} else error->all(FLERR,"Illegal fix qbmsst command");
}
@ -157,48 +172,32 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
// check for periodicity in controlled dimensions
if (domain->nonperiodic) error->all(FLERR,"Fix qbmsst requires a periodic box");
maxexchange = 6*N_f+3;
// comments
if (comm->me == 0) {
if (screen) {
fprintf(screen,"QBMSST parameters:\n");
if (direction == 0) fprintf(screen," Shock in x direction\n");
else if (direction == 1) fprintf(screen," Shock in y direction\n");
else if (direction == 2) fprintf(screen," Shock in z direction\n");
std::string msg = "QBMSST parameters:\n";
fprintf(screen," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(screen," Shock velocity = %12.5e\n", velocity);
fprintf(screen," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
if (direction == 0) msg += " Shock in x direction\n";
else if (direction == 1) msg += " Shock in y direction\n";
else if (direction == 2) msg += " Shock in z direction\n";
if (p0_set)
fprintf(screen," Initial pressure specified to be %12.5e\n", p0);
else fprintf(screen," Initial pressure calculated on first step\n");
if (v0_set)
fprintf(screen," Initial volume specified to be %12.5e\n", v0);
else fprintf(screen," Initial volume calculated on first step\n");
if (e0_set)
fprintf(screen," Initial energy specified to be %12.5e\n", e0);
else fprintf(screen," Initial energy calculated on first step\n");
}
if (logfile) {
fprintf(logfile,"QBMSST parameters:\n");
if (direction == 0) fprintf(logfile," Shock in x direction\n");
else if (direction == 1) fprintf(logfile," Shock in y direction\n");
else if (direction == 2) fprintf(logfile," Shock in z direction\n");
msg += fmt::format(" Cell mass-like parameter qmass "
"(units of mass^2/length^4) = {:12.5e}\n", qmass);
msg += fmt::format(" Shock velocity = {:12.5e}\n", velocity);
msg += fmt::format(" Artificial viscosity (units of "
"mass/length/time) = {:12.5e}\n", mu);
fprintf(logfile," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(logfile," Shock velocity = %12.5e\n", velocity);
fprintf(logfile," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
if (p0_set)
fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
else fprintf(logfile," Initial pressure calculated on first step\n");
if (v0_set)
fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
else fprintf(logfile," Initial volume calculated on first step\n");
if (e0_set)
fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
else fprintf(logfile," Initial energy calculated on first step\n");
}
if (p0_set)
msg += fmt::format(" Initial pressure specified to be {:12.5e}\n", p0);
else msg += " Initial pressure calculated on first step\n";
if (v0_set)
msg += fmt::format(" Initial volume specified to be {:12.5e}\n", v0);
else msg += " Initial volume calculated on first step\n";
if (e0_set)
msg += fmt::format(" Initial energy specified to be {:12.5e}\n", e0);
else msg += " Initial energy calculated on first step\n";
utils::logmesg(lmp,msg);
}
// create a new compute temp style
@ -363,14 +362,17 @@ void FixQBMSST::init()
//set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}}
if (int(1.0/(2*f_max*dtv)) == 0) {
if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n");
if (comm->me == 0) error->warning(FLERR,"Either f_max is too high or the time step "
"is too big, setting f_max to be 1/timestep!\n");
h_timestep=dtv;
alpha=1;
} else {
alpha=int(1.0/(2*f_max*dtv));
h_timestep=alpha*dtv;
}
if (comm->me == 0) printf ("The effective maximum frequncy is now %f inverse time unit with alpha value as %d!\n", 0.5/h_timestep, alpha);
if (comm->me == 0 && screen)
fmt::print(screen,"The effective maximum frequency is now {} inverse time unit "
"with alpha value as {}!\n", 0.5/h_timestep, alpha);
//gfactor is the random force \sqrt{\frac{2\gamma{}m_{i}}{\alpha*\delta{}t}}, \sqrt{12} makes the random array variance equal to unit.
for (int i = 1; i <= atom->ntypes; i++) {
@ -432,20 +434,16 @@ void FixQBMSST::setup(int /*vflag*/)
if ( v0_set == 0 ) {
v0 = compute_vol();
v0_set = 1;
if (comm->me == 0) {
if ( screen ) fprintf(screen,"Fix QBMSST v0 = %12.5e\n", v0);
if ( logfile ) fprintf(logfile,"Fix QBMSST v0 = %12.5e\n", v0);
}
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Fix QBMSST v0 = {:12.5e}\n", v0));
}
if ( p0_set == 0 ) {
p0 = p_current[direction];
p0_set = 1;
if ( comm->me == 0 ) {
if ( screen ) fprintf(screen,"Fix QBMSST p0 = %12.5e\n", p0);
if ( logfile ) fprintf(logfile,"Fix QBMSST p0 = %12.5e\n", p0);
}
if ( comm->me == 0 )
utils::logmesg(lmp,fmt::format("Fix QBMSST p0 = {:12.5e}\n", p0));
}
if ( e0_set == 0 ) {
@ -453,11 +451,8 @@ void FixQBMSST::setup(int /*vflag*/)
e0_set = 1;
old_eavg = e0;
if ( comm->me == 0 ) {
if ( screen ) fprintf(screen,"Fix QBMSST e0 = to be %12.5e\n",e0);
if ( logfile ) fprintf(logfile,"Fix QBMSST e0 = to be %12.5e\n",e0);
}
if ( comm->me == 0 )
utils::logmesg(lmp,fmt::format("Fix QBMSST e0 = to be {:12.5e}\n",e0));
}
temperature->compute_vector();
@ -476,16 +471,10 @@ void FixQBMSST::setup(int /*vflag*/)
omega[direction]=-1*sqrt(fac1);
double fac2 = omega[direction]/v0;
if ( comm->me == 0 && tscale != 1.0) {
if ( screen )
fprintf(screen,"Fix QBMSST initial strain rate of %12.5e established "
"by reducing temperature by factor of %12.5e\n",
fac2,tscale);
if ( logfile )
fprintf(logfile,"Fix QBMSST initial strain rate of %12.5e established "
"by reducing temperature by factor of %12.5e\n",
fac2,tscale);
}
if ( comm->me == 0 && tscale != 1.0)
utils::logmesg(lmp,fmt::format("Fix QBMSST initial strain rate of {:12.5e} "
"established by reducing temperature by "
"factor of {:12.5e}\n",fac2,tscale));
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & groupbit) {
for (int k = 0; k < 3; k++ ) {
@ -531,30 +520,31 @@ void FixQBMSST::initial_integrate(int /*vflag*/)
// decide if the qtb temperature need to be updated or not
if (counter_l == 0) {
t_current -= dtv*fric_coef*eta*beta*(old_eavg-e0)/(3*ntotal*boltz);
old_eavg = 0;//clear old energy average
if (t_current < 0.0) t_current=0;
if (t_current > 0.0) {
old_eavg = 0;//clear old energy average
// load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H
for (int k = 0; k < 2*N_f; k++) {
double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
if(k == N_f) {
omega_H[k]=sqrt(force->boltz * t_current);
} else {
double energy_k= force->hplanck * fabs(f_k);
omega_H[k]=sqrt( energy_k * (0.5+1.0/( exp(energy_k/(force->boltz * t_current)) - 1.0 )) );
omega_H[k]*=alpha*sin((k-N_f)*MY_PI/(2*alpha*N_f))/sin((k-N_f)*MY_PI/(2*N_f));
}
}
// construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right)
for (int n = 0; n < 2*N_f; n++) {
time_H[n] = 0;
double t_n=(n-N_f);
// load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H
for (int k = 0; k < 2*N_f; k++) {
double omega_k=(k-N_f)*MY_PI/N_f;
time_H[n] += omega_H[k]*(cos(omega_k*t_n));
double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
if(k == N_f) {
omega_H[k]=sqrt(force->boltz * t_current);
} else {
double energy_k= force->hplanck * fabs(f_k);
omega_H[k]=sqrt( energy_k * (0.5+1.0/( exp(energy_k/(force->boltz * t_current)) - 1.0 )) );
omega_H[k]*=alpha*sin((k-N_f)*MY_PI/(2*alpha*N_f))/sin((k-N_f)*MY_PI/(2*N_f));
}
}
// construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right)
for (int n = 0; n < 2*N_f; n++) {
time_H[n] = 0;
double t_n=(n-N_f);
for (int k = 0; k < 2*N_f; k++) {
double omega_k=(k-N_f)*MY_PI/N_f;
time_H[n] += omega_H[k]*(cos(omega_k*t_n));
}
time_H[n]/=(2.0*N_f);
}
time_H[n]/=(2.0*N_f);
}
}
@ -1170,11 +1160,12 @@ void FixQBMSST::copy_arrays(int i, int j, int /*delflag*/)
------------------------------------------------------------------------- */
int FixQBMSST::pack_exchange(int i, double *buf)
{
for (int m = 0; m < 2*N_f; m++) buf[m] = random_array_0[i][m];
for (int m = 0; m < 2*N_f; m++) buf[m+2*N_f] = random_array_1[i][m];
for (int m = 0; m < 2*N_f; m++) buf[m+4*N_f] = random_array_2[i][m];
for (int m = 0; m < 3; m++) buf[m+6*N_f] = fran[i][m];
return 6*N_f+3;
int n = 0;
for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_0[i][m];
for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_1[i][m];
for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_2[i][m];
for (int m = 0; m < 3; m++) buf[n++] = fran[i][m];
return n;
}
/* ----------------------------------------------------------------------
@ -1182,9 +1173,10 @@ int FixQBMSST::pack_exchange(int i, double *buf)
------------------------------------------------------------------------- */
int FixQBMSST::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[m];
for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[m+2*N_f];
for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[m+4*N_f];
for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[m+6*N_f];
return 6*N_f+3;
int n = 0;
for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[n++];
for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[n++];
for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[n++];
for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[n++];
return n;
}

52
src/USER-QTB/fix_qtb.cpp
View File

@ -32,6 +32,8 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -62,27 +64,34 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command");
t_target = atof(arg[iarg+1]); if (t_target < 0.0) error->all(FLERR,"Fix qtb temp must be >= 0.0");
t_target = force->numeric(FLERR,arg[iarg+1]);
if (t_target < 0.0) error->all(FLERR,"Fix qtb temp must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"damp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command");
t_period = atof(arg[iarg+1]); if (t_period <= 0.0) error->all(FLERR,"Fix qtb damp must be > 0.0"); fric_coef = 1/t_period;
t_period = force->numeric(FLERR,arg[iarg+1]);
if (t_period <= 0.0) error->all(FLERR,"Fix qtb damp must be > 0.0"); fric_coef = 1/t_period;
iarg += 2;
} else if (strcmp(arg[iarg],"seed") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command");
seed = atof(arg[iarg+1]); if (seed <= 0) error->all(FLERR,"Illegal fix qtb command");
seed = force->inumeric(FLERR,arg[iarg+1]);
if (seed <= 0) error->all(FLERR,"Illegal fix qtb command");
iarg += 2;
} else if (strcmp(arg[iarg],"f_max") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command");
f_max = atof(arg[iarg+1]); if (f_max <= 0) error->all(FLERR,"Illegal fix qtb command");
f_max = force->numeric(FLERR,arg[iarg+1]);
if (f_max <= 0) error->all(FLERR,"Illegal fix qtb command");
iarg += 2;
} else if (strcmp(arg[iarg],"N_f") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command");
N_f = atof(arg[iarg+1]); if (N_f <= 0) error->all(FLERR,"Illegal fix qtb command");
N_f = force->inumeric(FLERR,arg[iarg+1]);
if (N_f <= 0) error->all(FLERR,"Illegal fix qtb command");
iarg += 2;
} else error->all(FLERR,"Illegal fix qtb command");
}
maxexchange = 6*N_f+3;
// allocate qtb
gfactor1 = NULL;
gfactor3 = NULL;
@ -105,10 +114,6 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) :
// allocate random-arrays and fran
grow_arrays(atom->nmax);
atom->add_callback(0);
// memory->create(random_array_0,atom->nmax+300,2*N_f,"qtb:random_array_0");
// memory->create(random_array_1,atom->nmax+300,2*N_f,"qtb:random_array_1");
// memory->create(random_array_2,atom->nmax+300,2*N_f,"qtb:random_array_2");
// memory->create(fran,atom->nmax+300,3,"qtb:fran");
// allocate omega_H and time_H
memory->create(omega_H,2*N_f,"qtb:omega_H");
@ -160,14 +165,17 @@ void FixQTB::init()
//set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}}
if (int(1.0/(2*f_max*dtv)) == 0) {
if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n");
if (comm->me == 0) error->warning(FLERR,"Either f_max is too high or the time step "
"is too big, setting f_max to be 1/timestep!\n");
h_timestep=dtv;
alpha=1;
} else {
alpha=int(1.0/(2*f_max*dtv));
h_timestep=alpha*dtv;
}
if (comm->me == 0) printf ("The effective maximum frequncy is now %f inverse time unit with alpha value as %d!\n", 0.5/h_timestep, alpha);
if (comm->me == 0 && screen)
fmt::print(screen,"The effective maximum frequency is now {} inverse time unit "
"with alpha value as {}!\n", 0.5/h_timestep, alpha);
// set force prefactors
if (!atom->rmass) {
@ -404,11 +412,12 @@ void FixQTB::copy_arrays(int i, int j, int /*delflag*/)
------------------------------------------------------------------------- */
int FixQTB::pack_exchange(int i, double *buf)
{
for (int m = 0; m < 2*N_f; m++) buf[m] = random_array_0[i][m];
for (int m = 0; m < 2*N_f; m++) buf[m+2*N_f] = random_array_1[i][m];
for (int m = 0; m < 2*N_f; m++) buf[m+4*N_f] = random_array_2[i][m];
for (int m = 0; m < 3; m++) buf[m+6*N_f] = fran[i][m];
return 6*N_f+3;
int n = 0;
for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_0[i][m];
for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_1[i][m];
for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_2[i][m];
for (int m = 0; m < 3; m++) buf[n++] = fran[i][m];
return n;
}
/* ----------------------------------------------------------------------
@ -416,9 +425,10 @@ int FixQTB::pack_exchange(int i, double *buf)
------------------------------------------------------------------------- */
int FixQTB::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[m];
for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[m+2*N_f];
for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[m+4*N_f];
for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[m+6*N_f];
return 6*N_f+3;
int n = 0;
for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[n++];
for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[n++];
for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[n++];
for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[n++];
return n;
}

27
src/USER-QTB/fix_qtb.h
View File

@ -47,22 +47,23 @@ class FixQTB : public Fix {
private:
// qtb parameters
int counter_mu; // counter l and mu
double t_period, fric_coef; // friction coefficient
int seed; // seed for the random number generator
double f_max; // frequency cutoff
int N_f; // number of frequency grid
double t_target; // target qtb temperature
int counter_mu; // counter l and mu
double t_period, fric_coef; // friction coefficient
int seed; // seed for the random number generator
double f_max; // frequency cutoff
int N_f; // number of frequency grid
double t_target; // target qtb temperature
char *id_temp;
class Compute *temperature;
double h_timestep; // time step to update the random forces
int alpha; // number of time steps to update the random forces
class RanMars *random; // random number generator
double *gfactor1,*gfactor3; // factors of frictions and random forces
double *omega_H,*time_H; // H gives the desired power spectrum
double **random_array_0, **random_array_1, **random_array_2; // random number arrays give independence between atoms and directions
double h_timestep; // time step to update the random forces
int alpha; // number of time steps to update the random forces
class RanMars *random; // random number generator
double *gfactor1,*gfactor3; // factors of frictions and random forces
double *omega_H,*time_H; // H gives the desired power spectrum
// random number arrays give independence between atoms and directions
double **random_array_0, **random_array_1, **random_array_2;
int nlevels_respa;
double **fran, fsum[3], fsumall[3]; // random forces and their sums
double **fran, fsum[3], fsumall[3]; // random forces and their sums
};
}

26
src/USER-REAXC/reaxc_ffield.cpp
View File

@ -337,6 +337,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
if ((c < 10) || (j < 0) || (k < 0))
control->error_ptr->all(FLERR, "Inconsistent force field file");
if (j < reax->num_atom_types && k < reax->num_atom_types) {
@ -361,6 +363,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
/* line 2 */
fgets(s,MAX_LINE,fp);
c=Tokenize(s,&tmp);
if (c < 8)
control->error_ptr->all(FLERR, "Inconsistent force field file");
val = atof(tmp[0]); reax->tbp[j][k].p_be2 = val;
reax->tbp[k][j].p_be2 = val;
@ -491,6 +495,9 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
if ((c < (lgflag ? 9 : 8)) || (j < 0) || (k < 0))
control->error_ptr->all(FLERR, "Inconsistent force field file");
if (j < reax->num_atom_types && k < reax->num_atom_types) {
val = atof(tmp[2]);
if (val > 0.0) {
@ -528,10 +535,12 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
reax->tbp[k][j].r_pp = val;
}
val = atof(tmp[8]);
if (val >= 0.0) {
reax->tbp[j][k].lgcij = val;
reax->tbp[k][j].lgcij = val;
if (lgflag) {
val = atof(tmp[8]);
if (val >= 0.0) {
reax->tbp[j][k].lgcij = val;
reax->tbp[k][j].lgcij = val;
}
}
}
}
@ -552,6 +561,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
m = atoi(tmp[2]) - 1;
if ((c < 10) || (j < 0) || (k < 0) || (m < 0))
control->error_ptr->all(FLERR, "Inconsistent force field file");
if (j < reax->num_atom_types && k < reax->num_atom_types &&
m < reax->num_atom_types) {
@ -611,6 +622,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
k = atoi(tmp[1]) - 1;
m = atoi(tmp[2]) - 1;
n = atoi(tmp[3]) - 1;
if ((c < 9) || (k < 0) || (m < 0))
control->error_ptr->all(FLERR, "Inconsistent force field file");
if (j >= 0 && n >= 0) { // this means the entry is not in compact form
if (j < reax->num_atom_types && k < reax->num_atom_types &&
@ -667,8 +680,6 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
}
}
/* next line is number of hydrogen bond params and some comments */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
@ -686,7 +697,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
m = atoi(tmp[2]) - 1;
if ((c < 7) || (j < 0) || (k < 0) || (m < 0))
control->error_ptr->all(FLERR, "Inconsistent force field file");
if (j < reax->num_atom_types && m < reax->num_atom_types) {
val = atof(tmp[3]);

8
src/atom.cpp
View File

@ -48,8 +48,6 @@ using namespace MathConst;
#define DELTA_PERATOM 64
#define EPSILON 1.0e-6
enum{DOUBLE,INT,BIGINT};
/* ---------------------------------------------------------------------- */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
@ -1086,7 +1084,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::count_words(buf);
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
@ -1236,7 +1234,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::count_words(buf);
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != avec->size_data_vel)
@ -1588,7 +1586,7 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::count_words(buf);
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != avec_bonus->size_data_bonus)

1
src/atom.h
View File

@ -24,6 +24,7 @@ class Atom : protected Pointers {
public:
char *atom_style;
class AtomVec *avec;
enum{DOUBLE,INT,BIGINT};
// atom counts

166
src/atom_vec.cpp
View File

@ -33,8 +33,6 @@ using namespace MathConst;
#define DELTA 16384
#define DELTA_BONUS 8192
enum{DOUBLE,INT,BIGINT};
/* ---------------------------------------------------------------------- */
AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
@ -214,7 +212,7 @@ void AtomVec::grow(int n)
datatype = mgrow.datatype[i];
cols = mgrow.cols[i];
const int nthreads = threads[i] ? comm->nthreads : 1;
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0)
memory->grow(*((double **) pdata),nmax*nthreads,"atom:dvec");
else if (cols > 0)
@ -223,7 +221,7 @@ void AtomVec::grow(int n)
maxcols = *(mgrow.maxcols[i]);
memory->grow(*((double ***) pdata),nmax*nthreads,maxcols,"atom:darray");
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0)
memory->grow(*((int **) pdata),nmax*nthreads,"atom:ivec");
else if (cols > 0)
@ -232,14 +230,14 @@ void AtomVec::grow(int n)
maxcols = *(mgrow.maxcols[i]);
memory->grow(*((int ***) pdata),nmax*nthreads,maxcols,"atom:iarray");
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0)
memory->grow(*((bigint **) pdata),nmax*nthreads,"atom:bvec");
else if (cols > 0)
memory->grow(*((bigint ***) pdata),nmax*nthreads,cols,"atom:barray");
else {
maxcols = *(mgrow.maxcols[i]);
memory->grow(*((int ***) pdata),nmax*nthreads,maxcols,"atom:barray");
memory->grow(*((bigint ***) pdata),nmax*nthreads,maxcols,"atom:barray");
}
}
}
@ -275,7 +273,7 @@ void AtomVec::copy(int i, int j, int delflag)
pdata = mcopy.pdata[n];
datatype = mcopy.datatype[n];
cols = mcopy.cols[n];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
vec[j] = vec[i];
@ -292,7 +290,7 @@ void AtomVec::copy(int i, int j, int delflag)
for (m = 0; m < ncols; m++)
array[j][m] = array[i][m];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
vec[j] = vec[i];
@ -309,7 +307,7 @@ void AtomVec::copy(int i, int j, int delflag)
for (m = 0; m < ncols; m++)
array[j][m] = array[i][m];
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
vec[j] = vec[i];
@ -377,7 +375,7 @@ int AtomVec::pack_comm(int n, int *list, double *buf,
pdata = mcomm.pdata[nn];
datatype = mcomm.datatype[nn];
cols = mcomm.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = 0; i < n; i++) {
@ -392,7 +390,7 @@ int AtomVec::pack_comm(int n, int *list, double *buf,
buf[m++] = array[j][mm];
}
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = 0; i < n; i++) {
@ -407,7 +405,7 @@ int AtomVec::pack_comm(int n, int *list, double *buf,
buf[m++] = ubuf(array[j][mm]).d;
}
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = 0; i < n; i++) {
@ -498,7 +496,7 @@ int AtomVec::pack_comm_vel(int n, int *list, double *buf,
pdata = mcomm_vel.pdata[nn];
datatype = mcomm_vel.datatype[nn];
cols = mcomm_vel.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = 0; i < n; i++) {
@ -513,7 +511,7 @@ int AtomVec::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = array[j][mm];
}
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = 0; i < n; i++) {
@ -528,7 +526,7 @@ int AtomVec::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = ubuf(array[j][mm]).d;
}
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = 0; i < n; i++) {
@ -572,7 +570,7 @@ void AtomVec::unpack_comm(int n, int first, double *buf)
pdata = mcomm.pdata[nn];
datatype = mcomm.datatype[nn];
cols = mcomm.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = first; i < last; i++)
@ -583,7 +581,7 @@ void AtomVec::unpack_comm(int n, int first, double *buf)
for (mm = 0; mm < cols; mm++)
array[i][mm] = buf[m++];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = first; i < last; i++)
@ -594,7 +592,7 @@ void AtomVec::unpack_comm(int n, int first, double *buf)
for (mm = 0; mm < cols; mm++)
array[i][mm] = (int) ubuf(buf[m++]).i;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = first; i < last; i++)
@ -635,7 +633,7 @@ void AtomVec::unpack_comm_vel(int n, int first, double *buf)
pdata = mcomm_vel.pdata[nn];
datatype = mcomm_vel.datatype[nn];
cols = mcomm_vel.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = first; i < last; i++)
@ -646,18 +644,18 @@ void AtomVec::unpack_comm_vel(int n, int first, double *buf)
for (mm = 0; mm < cols; mm++)
array[i][mm] = buf[m++];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = first; i < last; i++)
vec[i] = ubuf(buf[m++]).i;
vec[i] = (int) ubuf(buf[m++]).i;
} else {
int **array = *((int ***) pdata);
for (i = first; i < last; i++)
for (mm = 0; mm < cols; mm++)
array[i][mm] = (int) ubuf(buf[m++]).i;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = first; i < last; i++)
@ -695,7 +693,7 @@ int AtomVec::pack_reverse(int n, int first, double *buf)
pdata = mreverse.pdata[nn];
datatype = mreverse.datatype[nn];
cols = mreverse.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = first; i < last; i++) {
@ -708,7 +706,7 @@ int AtomVec::pack_reverse(int n, int first, double *buf)
buf[m++] = array[i][mm];
}
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = first; i < last; i++) {
@ -721,7 +719,7 @@ int AtomVec::pack_reverse(int n, int first, double *buf)
buf[m++] = ubuf(array[i][mm]).d;
}
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = first; i < last; i++) {
@ -761,7 +759,7 @@ void AtomVec::unpack_reverse(int n, int *list, double *buf)
pdata = mreverse.pdata[nn];
datatype = mreverse.datatype[nn];
cols = mreverse.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = 0; i < n; i++) {
@ -776,34 +774,34 @@ void AtomVec::unpack_reverse(int n, int *list, double *buf)
array[j][mm] += buf[m++];
}
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = 0; i < n; i++) {
j = list[i];
vec[j] += buf[m++];
vec[j] += (int) ubuf(buf[m++]).i;
}
} else {
int **array = *((int ***) pdata);
for (i = 0; i < n; i++) {
j = list[i];
for (mm = 0; mm < cols; mm++)
array[j][mm] += buf[m++];
array[j][mm] += (int) ubuf(buf[m++]).i;
}
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = 0; i < n; i++) {
j = list[i];
vec[j] += buf[m++];
vec[j] += (bigint) ubuf(buf[m++]).i;
}
} else {
bigint **array = *((bigint ***) pdata);
for (i = 0; i < n; i++) {
j = list[i];
for (mm = 0; mm < cols; mm++)
array[j][mm] += buf[m++];
array[j][mm] += (bigint) ubuf(buf[m++]).i;
}
}
}
@ -856,7 +854,7 @@ int AtomVec::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc)
pdata = mborder.pdata[nn];
datatype = mborder.datatype[nn];
cols = mborder.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = 0; i < n; i++) {
@ -871,7 +869,7 @@ int AtomVec::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc)
buf[m++] = array[j][mm];
}
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = 0; i < n; i++) {
@ -886,7 +884,7 @@ int AtomVec::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc)
buf[m++] = ubuf(array[j][mm]).d;
}
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = 0; i < n; i++) {
@ -990,7 +988,7 @@ int AtomVec::pack_border_vel(int n, int *list, double *buf,
pdata = mborder_vel.pdata[nn];
datatype = mborder_vel.datatype[nn];
cols = mborder_vel.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = 0; i < n; i++) {
@ -1005,7 +1003,7 @@ int AtomVec::pack_border_vel(int n, int *list, double *buf,
buf[m++] = array[j][mm];
}
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = 0; i < n; i++) {
@ -1020,7 +1018,7 @@ int AtomVec::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(array[j][mm]).d;
}
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = 0; i < n; i++) {
@ -1072,7 +1070,7 @@ void AtomVec::unpack_border(int n, int first, double *buf)
pdata = mborder.pdata[nn];
datatype = mborder.datatype[nn];
cols = mborder.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = first; i < last; i++)
@ -1083,7 +1081,7 @@ void AtomVec::unpack_border(int n, int first, double *buf)
for (mm = 0; mm < cols; mm++)
array[i][mm] = buf[m++];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = first; i < last; i++)
@ -1094,7 +1092,7 @@ void AtomVec::unpack_border(int n, int first, double *buf)
for (mm = 0; mm < cols; mm++)
array[i][mm] = (int) ubuf(buf[m++]).i;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = first; i < last; i++)
@ -1144,7 +1142,7 @@ void AtomVec::unpack_border_vel(int n, int first, double *buf)
pdata = mborder_vel.pdata[nn];
datatype = mborder_vel.datatype[nn];
cols = mborder_vel.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
for (i = first; i < last; i++)
@ -1155,18 +1153,18 @@ void AtomVec::unpack_border_vel(int n, int first, double *buf)
for (mm = 0; mm < cols; mm++)
array[i][mm] = buf[m++];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
for (i = first; i < last; i++)
vec[i] = ubuf(buf[m++]).i;
vec[i] = (int) ubuf(buf[m++]).i;
} else {
int **array = *((int ***) pdata);
for (i = first; i < last; i++)
for (mm = 0; mm < cols; mm++)
array[i][mm] = (int) ubuf(buf[m++]).i;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
for (i = first; i < last; i++)
@ -1216,7 +1214,7 @@ int AtomVec::pack_exchange(int i, double *buf)
pdata = mexchange.pdata[nn];
datatype = mexchange.datatype[nn];
cols = mexchange.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
buf[m++] = vec[i];
@ -1233,7 +1231,7 @@ int AtomVec::pack_exchange(int i, double *buf)
for (mm = 0; mm < ncols; mm++)
buf[m++] = array[i][mm];
}
} if (datatype == INT) {
} if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
buf[m++] = ubuf(vec[i]).d;
@ -1250,7 +1248,7 @@ int AtomVec::pack_exchange(int i, double *buf)
for (mm = 0; mm < ncols; mm++)
buf[m++] = ubuf(array[i][mm]).d;
}
} if (datatype == BIGINT) {
} if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
buf[m++] = ubuf(vec[i]).d;
@ -1308,7 +1306,7 @@ int AtomVec::unpack_exchange(double *buf)
pdata = mexchange.pdata[nn];
datatype = mexchange.datatype[nn];
cols = mexchange.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
vec[nlocal] = buf[m++];
@ -1325,10 +1323,10 @@ int AtomVec::unpack_exchange(double *buf)
for (mm = 0; mm < ncols; mm++)
array[nlocal][mm] = buf[m++];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
vec[nlocal] = ubuf(buf[m++]).i;
vec[nlocal] = (int) ubuf(buf[m++]).i;
} else if (cols > 0) {
int **array = *((int ***) pdata);
for (mm = 0; mm < cols; mm++)
@ -1342,7 +1340,7 @@ int AtomVec::unpack_exchange(double *buf)
for (mm = 0; mm < ncols; mm++)
array[nlocal][mm] = (int) ubuf(buf[m++]).i;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
vec[nlocal] = (bigint) ubuf(buf[m++]).i;
@ -1450,7 +1448,7 @@ int AtomVec::pack_restart(int i, double *buf)
pdata = mrestart.pdata[nn];
datatype = mrestart.datatype[nn];
cols = mrestart.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
buf[m++] = vec[i];
@ -1467,7 +1465,7 @@ int AtomVec::pack_restart(int i, double *buf)
for (mm = 0; mm < ncols; mm++)
buf[m++] = array[i][mm];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
buf[m++] = ubuf(vec[i]).d;
@ -1484,7 +1482,7 @@ int AtomVec::pack_restart(int i, double *buf)
for (mm = 0; mm < ncols; mm++)
buf[m++] = ubuf(array[i][mm]).d;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
buf[m++] = ubuf(vec[i]).d;
@ -1551,7 +1549,7 @@ int AtomVec::unpack_restart(double *buf)
pdata = mrestart.pdata[nn];
datatype = mrestart.datatype[nn];
cols = mrestart.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
vec[nlocal] = buf[m++];
@ -1568,10 +1566,10 @@ int AtomVec::unpack_restart(double *buf)
for (mm = 0; mm < ncols; mm++)
array[nlocal][mm] = buf[m++];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
vec[nlocal] = ubuf(buf[m++]).i;
vec[nlocal] = (int) ubuf(buf[m++]).i;
} else if (cols > 0) {
int **array = *((int ***) pdata);
for (mm = 0; mm < cols; mm++)
@ -1585,7 +1583,7 @@ int AtomVec::unpack_restart(double *buf)
for (mm = 0; mm < ncols; mm++)
array[nlocal][mm] = (int) ubuf(buf[m++]).i;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
vec[nlocal] = (bigint) ubuf(buf[m++]).i;
@ -1594,7 +1592,7 @@ int AtomVec::unpack_restart(double *buf)
for (mm = 0; mm < cols; mm++)
array[nlocal][mm] = (bigint) ubuf(buf[m++]).i;
} else {
int **array = *((int ***) pdata);
bigint **array = *((bigint ***) pdata);
collength = mexchange.collength[nn];
plength = mexchange.plength[nn];
if (collength) ncols = (*((int ***) plength))[nlocal][collength-1];
@ -1654,7 +1652,7 @@ void AtomVec::create_atom(int itype, double *coord)
pdata = mcreate.pdata[n];
datatype = mcreate.datatype[n];
cols = mcreate.cols[n];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
vec[nlocal] = 0.0;
@ -1663,7 +1661,7 @@ void AtomVec::create_atom(int itype, double *coord)
for (m = 0; m < cols; m++)
array[nlocal][m] = 0.0;
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
vec[nlocal] = 0;
@ -1672,7 +1670,7 @@ void AtomVec::create_atom(int itype, double *coord)
for (m = 0; m < cols; m++)
array[nlocal][m] = 0;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
vec[nlocal] = 0;
@ -1718,7 +1716,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values)
pdata = mdata_atom.pdata[n];
datatype = mdata_atom.datatype[n];
cols = mdata_atom.cols[n];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
vec[nlocal] = utils::numeric(FLERR,values[ivalue++],true,lmp);
@ -1731,7 +1729,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values)
for (m = 0; m < cols; m++)
array[nlocal][m] = utils::numeric(FLERR,values[ivalue++],true,lmp);
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
vec[nlocal] = utils::inumeric(FLERR,values[ivalue++],true,lmp);
@ -1740,7 +1738,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values)
for (m = 0; m < cols; m++)
array[nlocal][m] = utils::inumeric(FLERR,values[ivalue++],true,lmp);
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
vec[nlocal] = utils::bnumeric(FLERR,values[ivalue++],true,lmp);
@ -1788,7 +1786,7 @@ void AtomVec::pack_data(double **buf)
pdata = mdata_atom.pdata[n];
datatype = mdata_atom.datatype[n];
cols = mdata_atom.cols[n];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
buf[i][j++] = vec[i];
@ -1797,7 +1795,7 @@ void AtomVec::pack_data(double **buf)
for (m = 0; m < cols; m++)
buf[i][j++] = array[i][m];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
buf[i][j++] = ubuf(vec[i]).d;
@ -1806,7 +1804,7 @@ void AtomVec::pack_data(double **buf)
for (m = 0; m < cols; m++)
buf[i][j++] = ubuf(array[i][m]).d;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
buf[i][j++] = ubuf(vec[i]).d;
@ -1844,21 +1842,21 @@ void AtomVec::write_data(FILE *fp, int n, double **buf)
for (nn = 1; nn < ndata_atom; nn++) {
datatype = mdata_atom.datatype[nn];
cols = mdata_atom.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
fprintf(fp," %-1.16e",buf[i][j++]);
} else {
for (m = 0; m < cols; m++)
fprintf(fp," %-1.16e",buf[i][j++]);
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
fprintf(fp," %d",(int) ubuf(buf[i][j++]).i);
} else {
for (m = 0; m < cols; m++)
fprintf(fp," %d",(int) ubuf(buf[i][j++]).i);
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
fmt::print(fp," {}",(bigint) ubuf(buf[i][j++]).i);
} else {
@ -1895,7 +1893,7 @@ void AtomVec::data_vel(int ilocal, char **values)
pdata = mdata_vel.pdata[n];
datatype = mdata_vel.datatype[n];
cols = mdata_vel.cols[n];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
vec[ilocal] = utils::numeric(FLERR,values[ivalue++],true,lmp);
@ -1904,7 +1902,7 @@ void AtomVec::data_vel(int ilocal, char **values)
for (m = 0; m < cols; m++)
array[ilocal][m] = utils::numeric(FLERR,values[ivalue++],true,lmp);
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
vec[ilocal] = utils::inumeric(FLERR,values[ivalue++],true,lmp);
@ -1913,7 +1911,7 @@ void AtomVec::data_vel(int ilocal, char **values)
for (m = 0; m < cols; m++)
array[ilocal][m] = utils::inumeric(FLERR,values[ivalue++],true,lmp);
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
vec[ilocal] = utils::bnumeric(FLERR,values[ivalue++],true,lmp);
@ -1944,7 +1942,7 @@ void AtomVec::pack_vel(double **buf)
pdata = mdata_vel.pdata[n];
datatype = mdata_vel.datatype[n];
cols = mdata_vel.cols[n];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
double *vec = *((double **) pdata);
buf[i][j++] = vec[i];
@ -1953,7 +1951,7 @@ void AtomVec::pack_vel(double **buf)
for (m = 0; m < cols; m++)
buf[i][j++] = array[i][m];
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
int *vec = *((int **) pdata);
buf[i][j++] = ubuf(vec[i]).d;
@ -1962,7 +1960,7 @@ void AtomVec::pack_vel(double **buf)
for (m = 0; m < cols; m++)
buf[i][j++] = ubuf(array[i][m]).d;
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
buf[i][j++] = ubuf(vec[i]).d;
@ -1992,21 +1990,21 @@ void AtomVec::write_vel(FILE *fp, int n, double **buf)
for (nn = 1; nn < ndata_vel; nn++) {
datatype = mdata_vel.datatype[nn];
cols = mdata_vel.cols[nn];
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
fprintf(fp," %-1.16e",buf[i][j++]);
} else {
for (m = 0; m < cols; m++)
fprintf(fp," %-1.16e",buf[i][j++]);
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
fprintf(fp," %d",(int) ubuf(buf[i][j++]).i);
} else {
for (m = 0; m < cols; m++)
fprintf(fp," %d",(int) ubuf(buf[i][j++]).i);
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
fmt::print(fp," {}",(bigint) ubuf(buf[i][j++]).i);
} else {
@ -2290,7 +2288,7 @@ bigint AtomVec::memory_usage()
datatype = mgrow.datatype[i];
cols = mgrow.cols[i];
const int nthreads = threads[i] ? comm->nthreads : 1;
if (datatype == DOUBLE) {
if (datatype == Atom::DOUBLE) {
if (cols == 0) {
bytes += memory->usage(*((double **) pdata),nmax*nthreads);
} else if (cols > 0) {
@ -2299,7 +2297,7 @@ bigint AtomVec::memory_usage()
maxcols = *(mgrow.maxcols[i]);
bytes += memory->usage(*((double ***) pdata),nmax*nthreads,maxcols);
}
} else if (datatype == INT) {
} else if (datatype == Atom::INT) {
if (cols == 0) {
bytes += memory->usage(*((int **) pdata),nmax*nthreads);
} else if (cols > 0) {
@ -2308,7 +2306,7 @@ bigint AtomVec::memory_usage()
maxcols = *(mgrow.maxcols[i]);
bytes += memory->usage(*((int ***) pdata),nmax*nthreads,maxcols);
}
} else if (datatype == BIGINT) {
} else if (datatype == Atom::BIGINT) {
if (cols == 0) {
bytes += memory->usage(*((bigint **) pdata),nmax*nthreads);
} else if (cols > 0) {

6
src/comm.cpp
View File

@ -258,10 +258,8 @@ void Comm::init_exchange()
int onefix;
maxexchange_fix = 0;
for (int i = 0; i < nfix; i++) {
onefix = fix[i]->maxexchange;
maxexchange_fix = MAX(maxexchange_fix,onefix);
}
for (int i = 0; i < nfix; i++)
maxexchange_fix += fix[i]->maxexchange;
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;

2
src/fix_property_atom.cpp
View File

@ -219,7 +219,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::count_words(buf);
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != nvalue+1)

4
src/fix_tmd.cpp
View File

@ -446,12 +446,12 @@ void FixTMD::readfile(char *file)
zprd = hi - lo;
bufptr = next + 1;
continue;
} else if (utils::count_words(bufptr) == 4) {
} else if (utils::trim_and_count_words(bufptr) == 4) {
if (xprd >= 0.0 || yprd >= 0.0 || zprd >= 0.0)
error->all(FLERR,"Incorrect format in TMD target file");
imageflag = 0;
firstline = 0;
} else if (utils::count_words(bufptr) == 7) {
} else if (utils::trim_and_count_words(bufptr) == 7) {
if (xprd < 0.0 || yprd < 0.0 || zprd < 0.0)
error->all(FLERR,"Incorrect format in TMD target file");
imageflag = 1;

101
src/force.cpp
View File

@ -1012,102 +1012,19 @@ tagint Force::tnumeric(const char *file, int line, char *str)
FILE *Force::open_potential(const char *name)
{
FILE *fp;
std::string filepath = utils::get_potential_file_path(name);
std::string date;
if (name == NULL) return NULL;
if(!filepath.empty()) {
date = utils::get_potential_date(filepath, "potential");
// attempt to open file directly
// if successful, return ptr
fp = fopen(name,"r");
if (fp) {
if (comm->me == 0) potential_date(fp,name);
rewind(fp);
return fp;
}
// try the environment variable directory
const char *path = getenv("LAMMPS_POTENTIALS");
if (path == NULL) return NULL;
const char *pot = potential_name(name);
if (pot == NULL) return NULL;
size_t len1 = strlen(path);
size_t len2 = strlen(pot);
char *newpath = new char[len1+len2+2];
strcpy(newpath,path);
#if defined(_WIN32)
newpath[len1] = '\\';
newpath[len1+1] = 0;
#else
newpath[len1] = '/';
newpath[len1+1] = 0;
#endif
strcat(newpath,pot);
fp = fopen(newpath,"r");
if (fp) {
if (comm->me == 0) potential_date(fp,name);
rewind(fp);
}
delete [] newpath;
return fp;
}
/* ----------------------------------------------------------------------
strip off leading part of path, return just the filename
------------------------------------------------------------------------- */
const char *Force::potential_name(const char *path)
{
const char *pot;
if (path == NULL) return NULL;
#if defined(_WIN32)
// skip over the disk drive part of windows pathnames
if (isalpha(path[0]) && path[1] == ':')
path += 2;
#endif
for (pot = path; *path != '\0'; ++path) {
#if defined(_WIN32)
if ((*path == '\\') || (*path == '/')) pot = path + 1;
#else
if (*path == '/') pot = path + 1;
#endif
}
return pot;
}
/* ----------------------------------------------------------------------
read first line of potential file
if has DATE field, print following word
------------------------------------------------------------------------- */
void Force::potential_date(FILE *fp, const char *name)
{
char line[MAXLINE];
char *ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) return;
char *word;
word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"DATE:") == 0) {
word = strtok(NULL," \t\n\r\f");
if (word == NULL) return;
utils::logmesg(lmp,fmt::format("Reading potential "
"file {} with DATE: {}",name,word));
return;
if(!date.empty()) {
utils::logmesg(lmp, fmt::format("Reading potential file {} "
"with DATE: {}\n", name, date));
}
word = strtok(NULL," \t\n\r\f");
return fopen(filepath.c_str(), "r");
}
return nullptr;
}
/* ----------------------------------------------------------------------

2
src/force.h
View File

@ -136,8 +136,6 @@ class Force : protected Pointers {
tagint tnumeric(const char *, int, char *);
FILE *open_potential(const char *);
const char *potential_name(const char *);
void potential_date(FILE *, const char *);
bigint memory_usage();

2
src/molecule.cpp
View File

@ -1402,7 +1402,7 @@ void Molecule::body(int flag, int pflag, char *line)
while (nword < nparam) {
readline(line);
ncount = utils::count_words(line);
ncount = utils::trim_and_count_words(line);
if (ncount == 0)
error->one(FLERR,"Too few values in body section of molecule file");
if (nword+ncount > nparam)

108
src/pair_table.cpp
View File

@ -28,12 +28,14 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "table_file_reader.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
enum{NONE,RLINEAR,RSQ,BMP};
#define MAXLINE 1024
#define EPSILONR 1.0e-6
/* ---------------------------------------------------------------------- */
@ -356,37 +358,18 @@ double PairTable::init_one(int i, int j)
void PairTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
TableFileReader reader(lmp, file, "pair");
// open file
char * line = reader.find_section_start(keyword);
FILE *fp = force->open_potential(file);
if (fp == NULL) {
std::string str("Cannot open file ");
str += file;
error->one(FLERR,str.c_str());
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword
utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
param_extract(tb,line);
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
for (int i = 0; i < tb->ninput; i++)
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
if (!line) {
error->one(FLERR,"Did not find keyword in table file");
}
// read args on 2nd line of section
// allocate table arrays for file values
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
line = reader.next_line();
param_extract(tb,line);
memory->create(tb->rfile,tb->ninput,"pair:rfile");
memory->create(tb->efile,tb->ninput,"pair:efile");
@ -407,19 +390,25 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
// if rflag set, compute r
// if rflag not set, use r from file
int itmp;
double rfile,rnew;
union_int_float_t rsq_lookup;
int rerror = 0;
int cerror = 0;
utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
if (NULL == fgets(line,MAXLINE,fp))
error->one(FLERR,"Premature end of file in pair table");
if (4 != sscanf(line,"%d %lg %lg %lg",
&itmp,&rfile,&tb->efile[i],&tb->ffile[i])) ++cerror;
line = reader.next_line(4);
try {
ValueTokenizer values(line);
values.next_int();
rfile = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
} catch (TokenizerException & e) {
++cerror;
}
rnew = rfile;
if (tb->rflag == RLINEAR)
@ -443,10 +432,6 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
tb->rfile[i] = rnew;
}
// close file
fclose(fp);
// warn if force != dE/dr at any point that is not an inflection point
// check via secant approximation to dE/dr
// skip two end points since do not have surrounding secants
@ -477,10 +462,9 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
}
if (ferror) {
char str[128];
sprintf(str,"%d of %d force values in table are inconsistent with -dE/dr.\n"
" Should only be flagged at inflection points",ferror,tb->ninput);
error->warning(FLERR,str);
std::string str = fmt::format("{} of {} force values in table are inconsistent with -dE/dr.\n"
" Should only be flagged at inflection points",ferror,tb->ninput);
error->warning(FLERR,str.c_str());
}
// warn if re-computed distance values differ from file values
@ -573,31 +557,29 @@ void PairTable::param_extract(Table *tb, char *line)
tb->rflag = NONE;
tb->fpflag = 0;
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
} else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0 ||
strcmp(word,"BITMAP") == 0) {
if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP;
word = strtok(NULL," \t\n\r\f");
tb->rlo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->rhi = atof(word);
} else if (strcmp(word,"FPRIME") == 0) {
tb->fpflag = 1;
word = strtok(NULL," \t\n\r\f");
tb->fplo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->fphi = atof(word);
} else {
printf("WORD: %s\n",word);
error->one(FLERR,"Invalid keyword in pair table parameters");
try {
ValueTokenizer values(line);
while (values.has_next()) {
std::string word = values.next_string();
if (word == "N") {
tb->ninput = values.next_int();
} else if ((word == "R") || (word == "RSQ") || (word == "BITMAP")) {
if (word == "R") tb->rflag = RLINEAR;
else if (word == "RSQ") tb->rflag = RSQ;
else if (word == "BITMAP") tb->rflag = BMP;
tb->rlo = values.next_double();
tb->rhi = values.next_double();
} else if (word == "FPRIME") {
tb->fpflag = 1;
tb->fplo = values.next_double();
tb->fphi = values.next_double();
} else {
error->one(FLERR,fmt::format("Invalid keyword {} in pair table parameters", word).c_str());
}
}
word = strtok(NULL," \t\n\r\f");
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
if (tb->ninput == 0) error->one(FLERR,"Pair table parameters did not set N");

180
src/potential_file_reader.cpp
View File

@ -30,91 +30,129 @@ using namespace LAMMPS_NS;
PotentialFileReader::PotentialFileReader(LAMMPS *lmp,
const std::string &filename,
const std::string &potential_name) : Pointers(lmp), filename(filename) {
const std::string &potential_name) :
Pointers(lmp),
reader(nullptr),
filename(filename),
filetype(potential_name + " potential")
{
if (comm->me != 0) {
error->one(FLERR, "PotentialFileReader should only be called by proc 0!");
error->one(FLERR, "FileReader should only be called by proc 0!");
}
fp = force->open_potential(filename.c_str());
if (fp == NULL)
error->one(FLERR,fmt::format("Cannot open {} potential file {}: {}",
potential_name, filename, utils::getsyserror()));
try {
reader = open_potential(filename);
if(!reader) {
error->one(FLERR, fmt::format("cannot open {} potential file {}", potential_name, filename));
}
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
}
PotentialFileReader::~PotentialFileReader() {
fclose(fp);
delete reader;
}
void PotentialFileReader::ignore_comments(bool value) {
reader->ignore_comments = value;
}
void PotentialFileReader::skip_line() {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr)
error->one(FLERR,fmt::format("Missing line in {} potential file!",
potential_name));
try {
reader->skip_line();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
}
char *PotentialFileReader::next_line(int nparams) {
// concatenate lines until have nparams words
int n = 0;
int nwords = 0;
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
return nullptr;
try {
return reader->next_line(nparams);
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
// strip comment
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords > 0) {
n = strlen(line);
}
while(nwords < nparams) {
char *ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) {
// EOF
if (nwords > 0 && nwords < nparams)
error->one(FLERR,fmt::format("Incorrect format in {} potential "
"file! {}/{} parameters",
potential_name, nwords, nparams));
return nullptr;
}
// strip comment
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
// skip line if blank
if (nwords > 0) {
n = strlen(line);
}
}
return line;
return nullptr;
}
void PotentialFileReader::next_dvector(int n, double * list) {
int i = 0;
while (i < n) {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
if (i < n)
error->one(FLERR,fmt::format("Incorrect format in {} potential file! "
"{}/{} values", potential_name, i, n));
}
ValueTokenizer values(line);
while(values.has_next()) {
list[i++] = values.next_double();
}
void PotentialFileReader::next_dvector(double * list, int n) {
try {
return reader->next_dvector(list, n);
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
}
ValueTokenizer PotentialFileReader::next_values(int nparams, const std::string & seperators) {
try {
return reader->next_values(nparams, seperators);
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return ValueTokenizer("");
}
double PotentialFileReader::next_double() {
try {
char * line = reader->next_line(1);
return ValueTokenizer(line).next_double();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return 0.0;
}
int PotentialFileReader::next_int() {
try {
char * line = reader->next_line(1);
return ValueTokenizer(line).next_int();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return 0;
}
tagint PotentialFileReader::next_tagint() {
try {
char * line = reader->next_line(1);
return ValueTokenizer(line).next_tagint();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return 0;
}
bigint PotentialFileReader::next_bigint() {
try {
char * line = reader->next_line(1);
return ValueTokenizer(line).next_bigint();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return 0;
}
std::string PotentialFileReader::next_string() {
try {
char * line = reader->next_line(1);
return ValueTokenizer(line).next_string();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return "";
}
TextFileReader * PotentialFileReader::open_potential(const std::string& path) {
std::string filepath = utils::get_potential_file_path(path);
std::string date;
if(!filepath.empty()) {
date = utils::get_potential_date(filepath, filetype);
if(!date.empty()) {
utils::logmesg(lmp, fmt::format("Reading potential file {} with DATE: {}", filename, date));
}
return new TextFileReader(filepath, filetype);
}
return nullptr;
}

27
src/potential_file_reader.h
View File

@ -21,23 +21,36 @@
#include <string>
#include "pointers.h"
#include "tokenizer.h"
#include "text_file_reader.h"
namespace LAMMPS_NS
{
class PotentialFileReader : protected Pointers {
std::string potential_name;
protected:
TextFileReader * reader;
std::string filename;
static const int MAXLINE = 1024;
char line[MAXLINE];
FILE *fp;
std::string filetype;
TextFileReader * open_potential(const std::string& path);
public:
PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name);
~PotentialFileReader();
virtual ~PotentialFileReader();
void ignore_comments(bool value);
void skip_line();
char * next_line(int nparams);
void next_dvector(int n, double * list);
char * next_line(int nparams = 0);
void next_dvector(double * list, int n);
ValueTokenizer next_values(int nparams, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS);
// convenience functions
double next_double();
int next_int();
tagint next_tagint();
bigint next_bigint();
std::string next_string();
};
} // namespace LAMMPS_NS

4
src/read_data.cpp
View File

@ -1661,7 +1661,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
while (nword < ninteger) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
ncount = utils::count_words(&buffer[m]);
ncount = utils::trim_and_count_words(&buffer[m]);
if (ncount == 0)
error->one(FLERR,"Too few values in body lines in data file");
nword += ncount;
@ -1675,7 +1675,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
while (nword < ndouble) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
ncount = utils::count_words(&buffer[m]);
ncount = utils::trim_and_count_words(&buffer[m]);
if (ncount == 0)
error->one(FLERR,"Too few values in body lines in data file");
nword += ncount;

2
src/reader_native.cpp
View File

@ -162,7 +162,7 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
char *labelline = &line[strlen("ITEM: ATOMS ")];
nwords = utils::count_words(labelline);
nwords = utils::trim_and_count_words(labelline);
char **labels = new char*[nwords];
labels[0] = strtok(labelline," \t\n\r\f");
if (labels[0] == NULL) {

51
src/table_file_reader.cpp Normal file
View File

@ -0,0 +1,51 @@
/* -*- 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: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include "lammps.h"
#include "error.h"
#include "table_file_reader.h"
#include "utils.h"
#include "tokenizer.h"
#include "fmt/format.h"
#include <cstring>
using namespace LAMMPS_NS;
TableFileReader::TableFileReader(LAMMPS *lmp,
const std::string &filename,
const std::string &type) :
PotentialFileReader(lmp, filename, type + " table")
{
}
TableFileReader::~TableFileReader() {
}
char * TableFileReader::find_section_start(const std::string & keyword) {
char * line = nullptr;
while (line = reader->next_line()) {
ValueTokenizer values(line);
std::string word = values.next_string();
if (word == keyword) {
// matching keyword
return line;
}
}
return nullptr;
}

35
src/table_file_reader.h Normal file
View File

@ -0,0 +1,35 @@
/* -*- 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: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifndef LMP_TABLE_FILE_READER_H
#define LMP_TABLE_FILE_READER_H
#include "potential_file_reader.h"
namespace LAMMPS_NS
{
class TableFileReader : public PotentialFileReader {
public:
TableFileReader(class LAMMPS *lmp, const std::string &filename, const std::string & type);
virtual ~TableFileReader();
char * find_section_start(const std::string & keyword);
};
} // namespace LAMMPS_NS
#endif

121
src/text_file_reader.cpp Normal file
View File

@ -0,0 +1,121 @@
/* -*- 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: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include "lammps.h"
#include "force.h"
#include "error.h"
#include "comm.h"
#include "utils.h"
#include "text_file_reader.h"
#include "tokenizer.h"
#include "fmt/format.h"
#include <cstring>
using namespace LAMMPS_NS;
TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype)
: filename(filename), filetype(filetype), ignore_comments(true)
{
fp = fopen(filename.c_str(), "r");
if (fp == nullptr) {
throw FileReaderException(fmt::format("cannot open {} file {}", filetype, filename));
}
}
TextFileReader::~TextFileReader() {
fclose(fp);
}
void TextFileReader::skip_line() {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
throw EOFException(fmt::format("Missing line in {} file!", filetype));
}
}
char *TextFileReader::next_line(int nparams) {
// concatenate lines until have nparams words
int n = 0;
int nwords = 0;
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
return nullptr;
}
// strip comment
if (ignore_comments && (ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords > 0) {
n = strlen(line);
}
while(nwords == 0 || nwords < nparams) {
char *ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) {
// EOF
if (nwords > 0 && nwords < nparams) {
throw EOFException(fmt::format("Incorrect format in {} file! {}/{} parameters", filetype, nwords, nparams));
}
return nullptr;
}
// strip comment
if (ignore_comments && (ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
// skip line if blank
if (nwords > 0) {
n = strlen(line);
}
}
return line;
}
void TextFileReader::next_dvector(double * list, int n) {
int i = 0;
while (i < n) {
char *ptr = next_line();
if (ptr == nullptr) {
// EOF
if (i < n) {
throw FileReaderException(fmt::format("Incorrect format in {} file! {}/{} values", filetype, i, n));
}
}
ValueTokenizer values(line);
while(values.has_next()) {
list[i++] = values.next_double();
}
}
}
ValueTokenizer TextFileReader::next_values(int nparams, const std::string & seperators) {
return ValueTokenizer(next_line(nparams), seperators);
}

70
src/text_file_reader.h Normal file
View File

@ -0,0 +1,70 @@
/* -*- 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: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifndef LMP_TEXT_FILE_READER_H
#define LMP_TEXT_FILE_READER_H
#include <cstdio>
#include <string>
#include <exception>
#include "tokenizer.h"
namespace LAMMPS_NS
{
class TextFileReader {
std::string filename;
std::string filetype;
static const int MAXLINE = 1024;
char line[MAXLINE];
FILE *fp;
public:
bool ignore_comments;
TextFileReader(const std::string &filename, const std::string &filetype);
~TextFileReader();
void skip_line();
char * next_line(int nparams = 0);
void next_dvector(double * list, int n);
ValueTokenizer next_values(int nparams, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS);
};
class FileReaderException : public std::exception {
std::string message;
public:
FileReaderException(const std::string & msg) : message(msg) {
}
~FileReaderException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
class EOFException : public FileReaderException {
public:
EOFException(const std::string & msg) : FileReaderException(msg) {
}
};
} // namespace LAMMPS_NS
#endif

2
src/thermo.cpp
View File

@ -160,7 +160,7 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
// allocate per-field memory
// process line of keywords
nfield_initial = utils::count_words(line);
nfield_initial = utils::trim_and_count_words(line);
allocate();
parse_fields(line);

14
src/tokenizer.cpp
View File

@ -37,6 +37,12 @@ Tokenizer::Tokenizer(const std::string & str, const std::string & seperators) {
} while(end != std::string::npos);
}
Tokenizer::Tokenizer(const Tokenizer & rhs) : tokens(rhs.tokens) {
}
Tokenizer::Tokenizer(Tokenizer && rhs) : tokens(std::move(rhs.tokens)) {
}
Tokenizer::iterator Tokenizer::begin() {
return tokens.begin();
}
@ -66,6 +72,14 @@ ValueTokenizer::ValueTokenizer(const std::string & str, const std::string & sepe
current = tokens.begin();
}
ValueTokenizer::ValueTokenizer(const ValueTokenizer & rhs) : tokens(rhs.tokens) {
current = tokens.begin();
}
ValueTokenizer::ValueTokenizer(ValueTokenizer && rhs) : tokens(std::move(rhs.tokens)) {
current = tokens.begin();
}
bool ValueTokenizer::has_next() const {
return current != tokens.cend();
}

14
src/tokenizer.h
View File

@ -25,13 +25,19 @@
namespace LAMMPS_NS {
#define TOKENIZER_DEFAULT_SEPERATORS " \t\r\n\f"
class Tokenizer {
std::vector<std::string> tokens;
public:
typedef std::vector<std::string>::iterator iterator;
typedef std::vector<std::string>::const_iterator const_iterator;
Tokenizer(const std::string & str, const std::string & seperators = " \t\r\n\f");
Tokenizer(const std::string & str, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS);
Tokenizer(Tokenizer &&);
Tokenizer(const Tokenizer &);
Tokenizer& operator=(const Tokenizer&) = default;
Tokenizer& operator=(Tokenizer&&) = default;
iterator begin();
iterator end();
@ -72,7 +78,11 @@ class ValueTokenizer {
Tokenizer tokens;
Tokenizer::const_iterator current;
public:
ValueTokenizer(const std::string & str, const std::string & seperators = " \t\r\n\f");
ValueTokenizer(const std::string & str, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS);
ValueTokenizer(const ValueTokenizer &);
ValueTokenizer(ValueTokenizer &&);
ValueTokenizer& operator=(const ValueTokenizer&) = default;
ValueTokenizer& operator=(ValueTokenizer&&) = default;
std::string next_string();
tagint next_tagint();

111
src/utils.cpp
View File

@ -18,6 +18,7 @@
#include "lammps.h"
#include "error.h"
#include "tokenizer.h"
#include "text_file_reader.h"
#include "fmt/format.h"
#if defined(__linux__)
@ -364,14 +365,22 @@ std::string utils::trim_comment(const std::string & line) {
}
/* ----------------------------------------------------------------------
Trim comment from string and return number of words
Return number of words
------------------------------------------------------------------------- */
size_t utils::count_words(const std::string & text, const std::string & seperators) {
Tokenizer words(utils::trim_comment(text), seperators);
ValueTokenizer words(text, seperators);
return words.count();
}
/* ----------------------------------------------------------------------
Trim comment from string and return number of words
------------------------------------------------------------------------- */
size_t utils::trim_and_count_words(const std::string & text, const std::string & seperators) {
return utils::count_words(utils::trim_comment(text), seperators);
}
/* ----------------------------------------------------------------------
Return whether string is a valid integer number
------------------------------------------------------------------------- */
@ -406,6 +415,104 @@ bool utils::is_double(const std::string & str) {
return true;
}
/* ----------------------------------------------------------------------
strip off leading part of path, return just the filename
------------------------------------------------------------------------- */
std::string utils::path_basename(const std::string & path) {
#if defined(_WIN32)
size_t start = path.find_last_of('/\\');
#else
size_t start = path.find_last_of('/');
#endif
if (start == std::string::npos) {
start = 0;
} else {
start += 1;
}
return path.substr(start);
}
/* ----------------------------------------------------------------------
join two paths
------------------------------------------------------------------------- */
std::string utils::path_join(const std::string & a, const std::string & b) {
#if defined(_WIN32)
return fmt::format("{}\\{}", a, b);
#else
return fmt::format("{}/{}", a, b);
#endif
}
/* ----------------------------------------------------------------------
try to open file for reading
------------------------------------------------------------------------- */
bool utils::file_is_readable(const std::string & path) {
FILE * fp = fopen(path.c_str(), "r");
if(fp) {
fclose(fp);
return true;
}
return false;
}
/* ----------------------------------------------------------------------
try to find potential file as specified by name
search current directory and the LAMMPS_POTENTIALS directory if
specified
------------------------------------------------------------------------- */
std::string utils::get_potential_file_path(const std::string& path) {
std::string filepath = path;
std::string filename = utils::path_basename(path);
if(utils::file_is_readable(filepath)) {
return filepath;
} else {
// try the environment variable directory
const char *path = getenv("LAMMPS_POTENTIALS");
if (path != nullptr){
std::string pot = utils::path_basename(filepath);
filepath = utils::path_join(path, pot);
if (utils::file_is_readable(filepath)) {
return filepath;
}
}
}
return "";
}
/* ----------------------------------------------------------------------
read first line of potential file
if has DATE field, print following word
------------------------------------------------------------------------- */
std::string utils::get_potential_date(const std::string & path, const std::string & potential_name) {
TextFileReader reader(path, potential_name);
reader.ignore_comments = false;
char * line = nullptr;
while (line = reader.next_line()) {
ValueTokenizer values(line);
while (values.has_next()) {
std::string word = values.next_string();
if (word == "DATE:") {
if (values.has_next()) {
std::string date = values.next_string();
return date;
}
}
}
}
return "";
}
/* ------------------------------------------------------------------ */
extern "C" {

48
src/utils.h
View File

@ -150,13 +150,21 @@ namespace LAMMPS_NS {
*/
std::string trim_comment(const std::string & line);
/**
* \brief Count words in string
* \param text string that should be searched
* \param seperators string containing characters that will be treated as whitespace
* \return number of words found
*/
size_t count_words(const std::string & text, const std::string & seperators = " \t\r\n\f");
/**
* \brief Count words in a single line, trim anything from '#' onward
* \param text string that should be trimmed and searched
* \param seperators string containing characters that will be treated as whitespace
* \return number of words found
*/
size_t count_words(const std::string & text, const std::string & seperators = " \t\r\n\f");
size_t trim_and_count_words(const std::string & text, const std::string & seperators = " \t\r\n\f");
/**
* \brief Check if string can be converted to valid integer
@ -171,6 +179,44 @@ namespace LAMMPS_NS {
* \return true, if string contains valid floating-point number, false otherwise
*/
bool is_double(const std::string & str);
/**
* \brief Strip off leading part of path, return just the filename
* \param path file path
* \return file name
*/
std::string path_basename(const std::string & path);
/**
* \brief Join two paths
* \param a first path
* \param b second path
* \return combined path
*/
std::string path_join(const std::string & a, const std::string & b);
/**
* \brief Check if file exists and is readable
* \param path file path
* \return true if file exists and is readable
*/
bool file_is_readable(const std::string & path);
/**
* \brief Determine full path of potential file
* If file is not found in current directory, search LAMMPS_POTENTIALS folder
* \param path file path
* \return full path to potential file
*/
std::string get_potential_file_path(const std::string& path);
/**
* \brief Read potential file and return DATE field if it is present
* \param path file path
* \param potential_name name of potential that is being read
* \return DATE field if present
*/
std::string get_potential_date(const std::string & path, const std::string & potential_name);
}
}

36
tools/singularity/centos7.def
View File

@ -11,9 +11,43 @@ From: centos:7
hdf5-devel python36-virtualenv python36-pip python-pip \
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant \
blas-devel lapack-devel libyaml-devel
blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel
yum clean all
# we need to reset any module variables
# inherited from the host.
unset __LMOD_REF_COUNT__LMFILES_
unset __LMOD_REF_COUNT_PATH
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
unset __LMOD_REF_COUNT_MANPATH
unset __LMOD_REF_COUNT_MODULEPATH
unset __LMOD_REF_COUNT_LOADEDMODULES
unset _LMFILES_
unset MODULEPATH
unset MODULESHOME
unset MODULEPATH_ROOT
unset LOADEDMODULES
unset LMOD_SYSTEM_DEFAULT_MODULES
# load MPI by default
. /etc/profile
module load mpi
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.0
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
tar -xzf plumed.tar.gz
cd plumed-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF

36
tools/singularity/centos8.def
View File

@ -16,9 +16,43 @@ From: centos:8
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
blas-devel lapack-devel libyaml-devel
blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel
dnf clean all
# we need to reset any module variables
# inherited from the host.
unset __LMOD_REF_COUNT__LMFILES_
unset __LMOD_REF_COUNT_PATH
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
unset __LMOD_REF_COUNT_MANPATH
unset __LMOD_REF_COUNT_MODULEPATH
unset __LMOD_REF_COUNT_LOADEDMODULES
unset _LMFILES_
unset MODULEPATH
unset MODULESHOME
unset MODULEPATH_ROOT
unset LOADEDMODULES
unset LMOD_SYSTEM_DEFAULT_MODULES
# load MPI by default
. /etc/profile
module load mpi
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.0
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
tar -xzf plumed.tar.gz
cd plumed-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF

22
tools/singularity/fedora32_mingw.def
View File

@ -35,9 +35,29 @@ From: fedora:32
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
blas-devel lapack-devel libyaml-devel
blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel
dnf clean all
# enable Lmod and load MPI
source /usr/share/lmod/lmod/init/profile
module purge
module load mpi
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.0
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
tar -xzf plumed.tar.gz
cd plumed-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF

22
tools/singularity/ubuntu18.04.def
View File

@ -4,6 +4,9 @@ From: ubuntu:18.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
@ -66,11 +69,28 @@ From: ubuntu:18.04
wget \
xxd \
valgrind \
gdb
gdb \
libkim-api-dev \
openkim-models
# clean cache
rm -rf /var/lib/apt/lists/*
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.0
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
tar -xzf plumed.tar.gz
cd plumed-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
# mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF

24
tools/singularity/ubuntu20.04.def
View File

@ -4,6 +4,9 @@ From: ubuntu:20.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
@ -62,11 +65,28 @@ From: ubuntu:20.04
wget \
xxd \
valgrind \
gdb
gdb \
libkim-api-dev \
openkim-models
# clean cache
rm -rf /var/lib/apt/lists/*
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.0
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
tar -xzf plumed.tar.gz
cd plumed-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
# mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
@ -75,10 +95,10 @@ PS1="[ubuntu20.04:\u@\h] \W> "
EOF
chmod 755 $CUSTOM_PROMPT_ENV
%environment
LC_ALL=C
export LC_ALL
export PATH=/usr/lib/ccache:$PATH
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="tcp,self"
# do not warn about unused components as this messes up testing

2
unittest/force-styles/angle_style.cpp
View File

@ -288,7 +288,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// equilibrium angle
std::stringstream eqstr;
eqstr << lmp->atom->nangletypes;
for (std::size_t i=0; i < lmp->atom->nangletypes; ++i) {
for (int i=0; i < lmp->atom->nangletypes; ++i) {
eqstr << " " << lmp->force->angle->equilibrium_angle(i+1);
}
writer.emit("equilibrium", eqstr.str());

2
unittest/force-styles/bond_style.cpp
View File

@ -288,7 +288,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
// equilibrium distance
std::stringstream eqstr;
eqstr << lmp->atom->nbondtypes;
for (std::size_t i=0; i < lmp->atom->nbondtypes; ++i) {
for (int i=0; i < lmp->atom->nbondtypes; ++i) {
eqstr << " " << lmp->force->bond->equilibrium_distance(i+1);
}
writer.emit("equilibrium", eqstr.str());

89
unittest/force-styles/tests/atomic-pair-table_bitmap.yaml Normal file
View File

@ -0,0 +1,89 @@
---
lammps_version: 2 Jun 2020
date_generated: Tue Jun 2 16:53:15 202
epsilon: 5e-13
prerequisites: ! |
pair table
pre_commands: ! ""
post_commands: ! ""
input_file: in.metal
pair_style: table bitmap 10
pair_coeff: ! |
* * ${input_dir}/pair_table_bitmap.txt beck_1_1
extract: ! ""
natoms: 32
init_vdwl: 1.66863069929167
init_coul: 0
init_stress: ! |2-
6.1952827280949752e+00 6.0616458078803026e+00 5.8879068387604203e+00 2.0730193733654706e-01 -2.1217457971568116e-02 -8.9424946009241696e-02
init_forces: ! |2
1 1.3462021756359327e-02 6.5546484939056501e-02 1.4239378405106444e-02
2 -2.2007228833976065e-02 -7.7589845112095546e-02 4.8902697347770523e-02
3 -3.8360617077969741e-02 1.9000610721085417e-01 -4.8543675419659094e-02
4 2.0909689528763566e-02 -9.9051714348463316e-03 -5.2627007649843807e-02
5 5.6017317782444738e-02 1.4268372317778771e-01 3.5492113737546842e-02
6 4.1557359610043018e-02 2.9641106441236388e-02 -6.9666505508374872e-03
7 -6.4166646403998925e-02 8.9315602328966931e-02 -1.0227283854625933e-02
8 -6.8596281778498247e-02 -6.0833941051629016e-02 4.4682109809175953e-02
9 1.4368972530624599e-02 -5.5197060731424975e-02 -2.8201433919835286e-02
10 -3.2703871825595171e-02 -1.4474456554468246e-01 -1.1516819202560430e-01
11 -4.0405247666710227e-02 -5.0409352470214198e-02 4.2972316829875207e-02
12 3.0916743299077298e-02 -8.8133140512779831e-02 -3.9753798941002949e-03
13 -1.8590365196257386e-02 2.4575364499331190e-02 -4.7077193181172067e-02
14 5.6675408248286062e-02 -1.8711344187186302e-02 7.0130262965183210e-02
15 -3.1926591760213181e-02 3.1641397846490678e-02 -2.8162923341260547e-02
16 1.1005724174097668e-01 -9.1797768313712017e-02 3.7455099430156756e-02
17 4.3878459411519591e-02 1.3059623784047278e-01 -1.6097155896137277e-03
18 -1.4777439020699670e-01 -3.5658427272011572e-02 -7.0718736029538459e-02
19 -1.5580794194082498e-01 -8.1567700677555310e-02 3.7488943756308291e-02
20 2.4266515940572463e-02 1.9762354212930246e-02 -3.4097639624214998e-02
21 1.6277874455848959e-01 5.0800476849828920e-02 4.3314810824989737e-03
22 2.9893704848344602e-03 -8.1978960608305021e-02 -1.1775536941431530e-02
23 4.6993698780955703e-02 1.2309490227999968e-01 -8.0573799329662799e-02
24 1.2797425247184574e-01 9.4738372709908938e-02 8.3761735780926952e-02
25 6.9930077496344431e-02 4.2200999537168552e-03 -4.6754566887666743e-02
26 -5.1872497435892714e-02 -1.5107287052733298e-01 1.2864569803094950e-01
27 4.6175201131873622e-02 -4.7147053051923900e-03 -2.1152042044204553e-04
28 1.1139415424523944e-02 5.7577179243740957e-02 7.3714500884676210e-02
29 4.8901565126232033e-02 1.0736209516268529e-01 -3.2125425217601846e-03
30 -4.2584465166652936e-02 -3.0054615946788474e-02 -8.4428957096643942e-02
31 -2.0649926244740491e-02 -1.1590442114762316e-01 7.4794527710849712e-02
32 -1.9354598378544019e-01 -6.3287613853627508e-02 -2.2278111493111191e-02
run_vdwl: 1.66741314145205
run_coul: 0
run_stress: ! |2-
6.1931374572792954e+00 6.0579168006450157e+00 5.8831944925174655e+00 2.0546568651742717e-01 -2.2310825568610582e-02 -9.0786598388712531e-02
run_forces: ! |2
1 1.0245582840443836e-02 6.5151854710940468e-02 1.3361955389177321e-02
2 -2.2314027604621318e-02 -7.7535528641419729e-02 4.9002169116395371e-02
3 -3.9051836443840873e-02 1.8729640241706769e-01 -5.0368800191922920e-02
4 2.1556848319449432e-02 -9.6560257281038397e-03 -5.2226270227499996e-02
5 5.5692513794487093e-02 1.4100131039803696e-01 3.6433829498680612e-02
6 4.2104114940438239e-02 2.9061099461956740e-02 -8.0757486645345530e-03
7 -6.4974396400004103e-02 9.0834827653364231e-02 -1.1497303228903639e-02
8 -6.9891945210390563e-02 -6.1365585968288172e-02 4.5058971443054034e-02
9 1.5494788785065767e-02 -5.6313873741252601e-02 -2.9239516346795842e-02
10 -3.0025791257554668e-02 -1.4356984394446920e-01 -1.1248096343757182e-01
11 -4.0162199915935268e-02 -5.1244062549941558e-02 4.2120428458812920e-02
12 3.2219067015055440e-02 -8.8023947653775636e-02 -4.0000605662452050e-03
13 -1.9322021317182518e-02 2.3705996957186400e-02 -4.6458078927757253e-02
14 5.7515188139881337e-02 -1.5720861856457415e-02 6.8903466211661560e-02
15 -3.1550376834563972e-02 3.2004964657920229e-02 -2.7509931415147928e-02
16 1.0690614440695038e-01 -9.0850865144888507e-02 3.6425761956666795e-02
17 4.4576246121271583e-02 1.3023640557355332e-01 -7.6587762084134013e-04
18 -1.4790335009012934e-01 -3.4561193108141076e-02 -7.1476252590456105e-02
19 -1.5517474793926253e-01 -8.1735148865468926e-02 3.6534263240961207e-02
20 2.3564800733902859e-02 2.0130469558539449e-02 -3.4093822740206496e-02
21 1.6267868459547039e-01 4.8910520011812009e-02 4.9415963505101621e-03
22 3.9143651683370253e-03 -8.1172695145679000e-02 -1.0834230526190378e-02
23 4.9870311913370033e-02 1.2420611623040828e-01 -7.7833840076172459e-02
24 1.2773385871506515e-01 9.4431969129075782e-02 8.4509868356579518e-02
25 7.0376169719190279e-02 4.4792786930559310e-03 -4.6803763947891978e-02
26 -5.0364526911511179e-02 -1.4929711058338557e-01 1.2850817811267942e-01
27 4.6472580366719141e-02 -4.1923069078539394e-03 -1.3401923595724521e-03
28 1.1441857387906706e-02 5.8173904345736008e-02 7.3370361778840071e-02
29 4.7811159682183739e-02 1.0733827504367408e-01 -1.9879309433676450e-03
30 -4.2511930547412778e-02 -2.9916695214642831e-02 -8.4066745720912481e-02
31 -2.1952102296720562e-02 -1.1662029578060293e-01 7.4721379144302519e-02
32 -1.9497502987605872e-01 -6.5187354007956666e-02 -2.2832899526331281e-02
...

91
unittest/force-styles/tests/atomic-pair-table_linear.yaml Normal file
View File

@ -0,0 +1,91 @@
---
lammps_version: 2 Jun 2020
date_generated: Tue Jun 2 16:46:19 202
epsilon: 5e-13
prerequisites: ! |
pair table
pre_commands: ! ""
post_commands: ! ""
input_file: in.metal
pair_style: table linear 10000
pair_coeff: ! |
1 1 ${input_dir}/pair_table_beck.txt beck_1_1
1 2 ${input_dir}/pair_table_beck.txt beck_1_1
2 2 ${input_dir}/pair_table_beck.txt beck_2_2
extract: ! ""
natoms: 32
init_vdwl: 1.66849758741132
init_coul: 0
init_stress: ! |2-
6.1946715433684973e+00 6.0610621944595691e+00 5.8874237884568794e+00 2.0726669272562587e-01 -2.1210093847498168e-02 -8.9416411707758034e-02
init_forces: ! |2
1 1.3461768519573423e-02 6.5534109919214642e-02 1.4238046153935983e-02
2 -2.2001532385230976e-02 -7.7578110900587721e-02 4.8895494306522291e-02
3 -3.8355274675308998e-02 1.8998944460354011e-01 -4.8534579158997129e-02
4 2.0908450525723498e-02 -9.9065259851936448e-03 -5.2618638347233404e-02
5 5.6008845819212463e-02 1.4266708026293753e-01 3.5487913450023841e-02
6 4.1552575164020243e-02 2.9642511828555394e-02 -6.9641129743398126e-03
7 -6.4155910069342403e-02 8.9302215279040434e-02 -1.0225629221330955e-02
8 -6.8587774765165088e-02 -6.0829429175094735e-02 4.4680410492059397e-02
9 1.4366115666253289e-02 -5.5193010436797592e-02 -2.8199868469874739e-02
10 -3.2696772118295803e-02 -1.4472907530040827e-01 -1.1516096653547711e-01
11 -4.0401292979786972e-02 -5.0403260261100417e-02 4.2969363549390502e-02
12 3.0908963526062479e-02 -8.8120722839359025e-02 -3.9792237714215200e-03
13 -1.8590586442952396e-02 2.4570524680954029e-02 -4.7073976129125013e-02
14 5.6668681846789561e-02 -1.8708035295572849e-02 7.0129732306455847e-02
15 -3.1927433330968973e-02 3.1638369787962112e-02 -2.8162497777685959e-02
16 1.1004266778296544e-01 -9.1785066871052839e-02 3.7455063670217288e-02
17 4.3874209968260171e-02 1.3058176120978526e-01 -1.6077990215935685e-03
18 -1.4775183032052960e-01 -3.5651338364660598e-02 -7.0714213256030112e-02
19 -1.5579450123857666e-01 -8.1557435871161682e-02 3.7491976413329374e-02
20 2.4262106793077946e-02 1.9762251986969553e-02 -3.4094105051678786e-02
21 1.6276246770534447e-01 5.0791644250007900e-02 4.3248360141969555e-03
22 2.9904687035853137e-03 -8.1967139210456882e-02 -1.1772377300447360e-02
23 4.6987794141318706e-02 1.2308604930197996e-01 -8.0566882858205235e-02
24 1.2795930744437653e-01 9.4726737159825200e-02 8.3749152147737538e-02
25 6.9925482162420033e-02 4.2199513301063160e-03 -4.6743912320864334e-02
26 -5.1856917641538880e-02 -1.5105261662137287e-01 1.2862943385759271e-01
27 4.6163997109484788e-02 -4.7144533487617334e-03 -2.0769859565411553e-04
28 1.1137606033726113e-02 5.7570749823347561e-02 7.3702486316706894e-02
29 4.8892603764312044e-02 1.0734444862695605e-01 -3.2133899506260749e-03
30 -4.2587368463202192e-02 -3.0047436022746527e-02 -8.4421201266270535e-02
31 -2.0646231349659299e-02 -1.1590205379082782e-01 7.4785818423894770e-02
32 -1.9352068689594826e-01 -6.3282139756026798e-02 -2.2278655095207611e-02
run_vdwl: 1.66727802356891
run_coul: 0
run_stress: ! |2-
6.1925738027578641e+00 6.0573149352705613e+00 5.8826519662480035e+00 2.0544288354756310e-01 -2.2314569036134008e-02 -9.0767397150969681e-02
run_forces: ! |2
1 1.0239417972012135e-02 6.5143936411888370e-02 1.3356763777998637e-02
2 -2.2314835701632570e-02 -7.7524477122967728e-02 4.8999346575662309e-02
3 -3.9043638693828556e-02 1.8727196361074283e-01 -5.0358906369839446e-02
4 2.1555046910191538e-02 -9.6562479880345862e-03 -5.2220025740068080e-02
5 5.5684458879600447e-02 1.4098102798381096e-01 3.6430504994586173e-02
6 4.2104147709418713e-02 2.9055058600247489e-02 -8.0778112152718948e-03
7 -6.4963866924303920e-02 9.0824824870264262e-02 -1.1492621439859574e-02
8 -6.9888106386663568e-02 -6.1362238801327997e-02 4.5061669154972568e-02
9 1.5493057273285156e-02 -5.6307006366398599e-02 -2.9234755420043165e-02
10 -3.0006706586658188e-02 -1.4355133290296190e-01 -1.1246538976169368e-01
11 -4.0156699765253455e-02 -5.1238883202820718e-02 4.2112202625462891e-02
12 3.2215165580774301e-02 -8.8013396380619557e-02 -4.0047290710007333e-03
13 -1.9322767417550984e-02 2.3711197649086194e-02 -4.6454058795633212e-02
14 5.7508424194302507e-02 -1.5717730349026085e-02 6.8892268883266869e-02
15 -3.1552192265302363e-02 3.2002449140037137e-02 -2.7508481800674743e-02
16 1.0688955089657577e-01 -9.0842508916126788e-02 3.6418887829925486e-02
17 4.4577236329712736e-02 1.3022532646095397e-01 -7.5825494000398793e-04
18 -1.4789247023417521e-01 -3.4554869410601124e-02 -7.1472651306375229e-02
19 -1.5516659799350990e-01 -8.1733259734237992e-02 3.6528023380248152e-02
20 2.3565292501585497e-02 2.0131963706666492e-02 -3.4090460756558867e-02
21 1.6266349958385409e-01 4.8905943278807026e-02 4.9357951969207243e-03
22 3.9108463662172284e-03 -8.1159914942901146e-02 -1.0833213112554453e-02
23 4.9862761614696910e-02 1.2418695431753196e-01 -7.7818580582703634e-02
24 1.2773299190190621e-01 9.4426552636226180e-02 8.4500013220674824e-02
25 7.0366190135544543e-02 4.4772942266913711e-03 -4.6793931216364631e-02
26 -5.0367407305875939e-02 -1.4928033291926532e-01 1.2849353197675831e-01
27 4.6468146723438429e-02 -4.1892634838488693e-03 -1.3380548635599163e-03
28 1.1447706368862415e-02 5.8175438626723523e-02 7.3359635688296038e-02
29 4.7807434863290775e-02 1.0732112842460283e-01 -1.9886348252873588e-03
30 -4.2515720470887731e-02 -2.9914625470396135e-02 -8.4056579797267661e-02
31 -2.1956047762899965e-02 -1.1661348485300055e-01 7.4709459326432123e-02
32 -1.9494431829672756e-01 -6.5181487099745139e-02 -2.2830961616444944e-02
...

91
unittest/force-styles/tests/atomic-pair-table_lookup.yaml Normal file
View File

@ -0,0 +1,91 @@
---
lammps_version: 2 Jun 2020
date_generated: Tue Jun 2 16:45:40 202
epsilon: 5e-13
prerequisites: ! |
pair table
pre_commands: ! ""
post_commands: ! ""
input_file: in.metal
pair_style: table lookup 10000
pair_coeff: ! |
1 1 ${input_dir}/pair_table_beck.txt beck_1_1
1 2 ${input_dir}/pair_table_beck.txt beck_1_1
2 2 ${input_dir}/pair_table_beck.txt beck_2_2
extract: ! ""
natoms: 32
init_vdwl: 1.66822081098814
init_coul: 0
init_stress: ! |2-
6.1925708391090373e+00 6.0607873158796632e+00 5.8866502515961283e+00 2.0635047994864009e-01 -2.2304749096038870e-02 -8.9977381381968910e-02
init_forces: ! |2
1 1.3652870615947011e-02 6.5292578314726832e-02 1.4401786849082793e-02
2 -2.2075986500789631e-02 -7.7530344175629484e-02 4.8918295738716797e-02
3 -3.8548065982306853e-02 1.9049129535293563e-01 -4.8497042796395010e-02
4 2.0883993795891603e-02 -9.8004460881346168e-03 -5.2544284235507610e-02
5 5.6473535558532267e-02 1.4259381967545881e-01 3.5283580728998398e-02
6 4.1436803654676703e-02 2.9757415671595559e-02 -6.9441568265177812e-03
7 -6.4342009716857218e-02 8.9407090045572943e-02 -1.0076354375758356e-02
8 -6.8438588566627351e-02 -6.0719143235589357e-02 4.4375134570496459e-02
9 1.4267631647248345e-02 -5.5225493516036783e-02 -2.8235579582748780e-02
10 -3.2874735468490235e-02 -1.4496018410464423e-01 -1.1522122672190530e-01
11 -4.0439244564162688e-02 -5.0797057909291822e-02 4.2990522799705479e-02
12 3.1118238818285009e-02 -8.8117800460577142e-02 -4.0963549347812021e-03
13 -1.8421701898180837e-02 2.4603479320682679e-02 -4.6953330610188748e-02
14 5.6779946032995847e-02 -1.8997405137617097e-02 7.0084749782857475e-02
15 -3.1872432338948091e-02 3.1520110382368773e-02 -2.8177989701802592e-02
16 1.1013395678084995e-01 -9.1707318824236786e-02 3.7083770573599802e-02
17 4.3975078896704253e-02 1.3054106752514974e-01 -1.5760211066586478e-03
18 -1.4753246799540981e-01 -3.5398540009504140e-02 -7.0784984645480470e-02
19 -1.5562703896771166e-01 -8.1533158870799177e-02 3.7998367628389429e-02
20 2.4120555351187806e-02 1.9895957059386932e-02 -3.4031571261011077e-02
21 1.6241181372756625e-01 5.0567395846590979e-02 4.0311135803611352e-03
22 3.0847862699784918e-03 -8.2082703890837161e-02 -1.1813933267531539e-02
23 4.6631319964723403e-02 1.2294704911631910e-01 -8.0759997950587623e-02
24 1.2784615418643658e-01 9.4570579283427048e-02 8.4136049252381967e-02
25 6.9854637188683621e-02 4.3796329364953045e-03 -4.6383679169275639e-02
26 -5.1672371161515490e-02 -1.5093773642419464e-01 1.2890155107784523e-01
27 4.6418514479134469e-02 -4.8647715941130543e-03 -3.3400893593061448e-04
28 1.0837875140475392e-02 5.7768778789330170e-02 7.3335429938361563e-02
29 4.8424486534314935e-02 1.0705191088477574e-01 -3.4221430692390835e-03
30 -4.2678491461167409e-02 -3.0167096740169222e-02 -8.4323491798094938e-02
31 -2.0446963122925290e-02 -1.1577119295225209e-01 7.4834425292344492e-02
32 -1.9338210089853922e-01 -6.2777766271189708e-02 -2.2198626823726184e-02
run_vdwl: 1.66790120138923
run_coul: 0
run_stress: ! |2-
6.1954399052539300e+00 6.0597796933663810e+00 5.8839846490596770e+00 2.0464958122047128e-01 -2.2990948428733799e-02 -9.0561388880444543e-02
run_forces: ! |2
1 1.0357196419898495e-02 6.5372257333873959e-02 1.3514409758410917e-02
2 -2.2518946587964585e-02 -7.7700478129363010e-02 4.8980708027650338e-02
3 -3.9187350884245992e-02 1.8746598368586515e-01 -5.0095509280450985e-02
4 2.1505122391926864e-02 -9.8121998835355474e-03 -5.2197325168546041e-02
5 5.6368397082486393e-02 1.4115837375527868e-01 3.6749677569935905e-02
6 4.2042380520510882e-02 2.9049092654418140e-02 -8.0059207630978693e-03
7 -6.5262053410956963e-02 9.1189712395790753e-02 -1.1162106417995799e-02
8 -6.9823982763573419e-02 -6.1642359327017858e-02 4.5148186601411129e-02
9 1.5581717631005403e-02 -5.6464988109373171e-02 -2.9179373549110328e-02
10 -2.9936010364121191e-02 -1.4403347574591194e-01 -1.1249323547874966e-01
11 -4.0279718641423851e-02 -5.1267663186455890e-02 4.2308426648069226e-02
12 3.2548290765190446e-02 -8.8360090934889973e-02 -4.1059424850670304e-03
13 -1.9100876563736404e-02 2.3923943182546592e-02 -4.6654992572323889e-02
14 5.7003886104469645e-02 -1.5977942426948746e-02 6.9080947733147463e-02
15 -3.1419200863690128e-02 3.2134894708585104e-02 -2.7460582419399034e-02
16 1.0678077169426231e-01 -9.0718758218836820e-02 3.6086450730476470e-02
17 4.4432206292973897e-02 1.3053785119638170e-01 -8.8349832217821166e-04
18 -1.4847693210486995e-01 -3.4770804844180284e-02 -7.1598050906370336e-02
19 -1.5584406172770648e-01 -8.1902850262455335e-02 3.6401901739187829e-02
20 2.3632828687886766e-02 2.0210640568054113e-02 -3.3962375402201296e-02
21 1.6251200328353549e-01 4.8509762572667509e-02 4.6262805117567836e-03
22 3.9297251786593766e-03 -8.1271664355599668e-02 -1.0814196256901271e-02
23 4.9681279655079395e-02 1.2435597457773782e-01 -7.8146336899556537e-02
24 1.2830345267622284e-01 9.4849763681645619e-02 8.4755594763442382e-02
25 7.0574066259719931e-02 4.7738855789510749e-03 -4.6746928071330643e-02
26 -5.0012323977413009e-02 -1.4919205052782003e-01 1.2835423785227032e-01
27 4.6693855278230161e-02 -4.3926905018267671e-03 -1.5097765818073844e-03
28 1.1103730609808571e-02 5.8020761280684265e-02 7.3177666578219974e-02
29 4.8063412527103180e-02 1.0769074559895483e-01 -1.8637969627234715e-03
30 -4.2307197338881525e-02 -2.9602719505751475e-02 -8.4192072289735478e-02
31 -2.2008710097816863e-02 -1.1651727431063712e-01 7.4819836125210509e-02
32 -1.9493695773256986e-01 -6.5615632500831411e-02 -2.2932304811643992e-02
...

91
unittest/force-styles/tests/atomic-pair-table_spline.yaml Normal file
View File

@ -0,0 +1,91 @@
---
lammps_version: 2 Jun 2020
date_generated: Tue Jun 2 16:47:29 202
epsilon: 5e-13
prerequisites: ! |
pair table
pre_commands: ! ""
post_commands: ! ""
input_file: in.metal
pair_style: table spline 10000
pair_coeff: ! |
1 1 ${input_dir}/pair_table_beck.txt beck_1_1
1 2 ${input_dir}/pair_table_beck.txt beck_1_1
2 2 ${input_dir}/pair_table_beck.txt beck_2_2
extract: ! ""
natoms: 32
init_vdwl: 1.66849237317226
init_coul: 0
init_stress: ! |2-
6.1946491697735437e+00 6.0610401365658024e+00 5.8874025724620429e+00 2.0726580316940962e-01 -2.1210361695457737e-02 -8.9415208770840096e-02
init_forces: ! |2
1 1.3461900166603218e-02 6.5533756921056424e-02 1.4237872357245411e-02
2 -2.2001295274018444e-02 -7.7577892895343906e-02 4.8895379860549121e-02
3 -3.8355321598214184e-02 1.8998901399717005e-01 -4.8534413942792565e-02
4 2.0908396793481509e-02 -9.9066117521727070e-03 -5.2618403012712124e-02
5 5.6008413316644114e-02 1.4266663667152152e-01 3.5487859843299545e-02
6 4.1552391358114872e-02 2.9642295673519448e-02 -6.9640527234652461e-03
7 -6.4155546133542837e-02 8.9301753561023003e-02 -1.0225594515349757e-02
8 -6.8587453028246703e-02 -6.0829070542048190e-02 4.4680193619080481e-02
9 1.4366068063822880e-02 -5.5192738935146854e-02 -2.8199665411938767e-02
10 -3.2697019980711756e-02 -1.4472840813665638e-01 -1.1516072254520793e-01
11 -4.0401272804121854e-02 -5.0402863668631913e-02 4.2969197904076183e-02
12 3.0908680631425673e-02 -8.8120244487072494e-02 -3.9791730686956463e-03
13 -1.8590573588915013e-02 2.4570208722629043e-02 -4.7073683697064536e-02
14 5.6668374919472228e-02 -1.8707913260279440e-02 7.0129358194749039e-02
15 -3.1927219149443416e-02 3.1638287874549260e-02 -2.8162304610562044e-02
16 1.1004228625210850e-01 -9.1784876878925489e-02 3.7455203664712555e-02
17 4.3874110434413707e-02 1.3058123184332987e-01 -1.6078470938548138e-03
18 -1.4775126775856298e-01 -3.5651201719208082e-02 -7.0713629953624360e-02
19 -1.5579381073821677e-01 -8.1556836647145553e-02 3.7492096227633373e-02
20 2.4262149455103726e-02 1.9762082500828778e-02 -3.4093995317030654e-02
21 1.6276229493138114e-01 5.0791551859706734e-02 4.3245301958938116e-03
22 2.9902891288209246e-03 -8.1966958449035843e-02 -1.1772410092696793e-02
23 4.6987757268038249e-02 1.2308546657800162e-01 -8.0566592682958557e-02
24 1.2795842291296708e-01 9.4726040785926641e-02 8.3748524809472952e-02
25 6.9925310941154381e-02 4.2197730528178625e-03 -4.6744097166442150e-02
26 -5.1856965388326640e-02 -1.5105237092347160e-01 1.2862892445018109e-01
27 4.6163842732722504e-02 -4.7145326827103505e-03 -2.0770802868259192e-04
28 1.1137379858917107e-02 5.7570783215990615e-02 7.3702487792676769e-02
29 4.8892657028303636e-02 1.0734409425986763e-01 -3.2134995127967849e-03
30 -4.2587398133307960e-02 -3.0047443784418228e-02 -8.4420705386072381e-02
31 -2.0646215207926085e-02 -1.1590108886476506e-01 7.4785520470549566e-02
32 -1.9351936740994052e-01 -6.3281923890906297e-02 -2.2278650628172247e-02
run_vdwl: 1.667273130413
run_coul: 0
run_stress: ! |2-
6.1925535687585693e+00 6.0572952105271769e+00 5.8826298841000604e+00 2.0544338949977917e-01 -2.2313078114848450e-02 -9.0766976514897041e-02
run_forces: ! |2
1 1.0239633061502058e-02 6.5143827221595174e-02 1.3356826587515483e-02
2 -2.2314719792140746e-02 -7.7524048417887792e-02 4.8999119168703323e-02
3 -3.9043356307568236e-02 1.8727112901323323e-01 -5.0358319574288206e-02
4 2.1555031522153656e-02 -9.6560578347078038e-03 -5.2219714561247452e-02
5 5.5684799810960112e-02 1.4098076857747269e-01 3.6430385068854737e-02
6 4.2103921190025241e-02 2.9054969033758940e-02 -8.0777612807259296e-03
7 -6.4964007703587665e-02 9.0824767825338215e-02 -1.1492723720965943e-02
8 -6.9887912879430303e-02 -6.1361831723537673e-02 4.5061147281770325e-02
9 1.5493100733112084e-02 -5.6306897360260899e-02 -2.9234346339233039e-02
10 -3.0007119234870205e-02 -1.4355108819988596e-01 -1.1246502096182201e-01
11 -4.0156584042997157e-02 -5.1238608709860869e-02 4.2111943089822509e-02
12 3.2215137999640264e-02 -8.8013573068877235e-02 -4.0049314316609446e-03
13 -1.9322692643690253e-02 2.3710729865779583e-02 -4.6453771618837091e-02
14 5.7508119522746703e-02 -1.5717550954823703e-02 6.8891636524075137e-02
15 -3.1551853579254628e-02 3.2002270904692251e-02 -2.7508263221790400e-02
16 1.0688913506500985e-01 -9.0842063672437995e-02 3.6419114766505958e-02
17 4.4576981599750799e-02 1.3022472720372444e-01 -7.5802573483000615e-04
18 -1.4789239369554841e-01 -3.4554795916705260e-02 -7.1472573328781749e-02
19 -1.5516657008010420e-01 -8.1733453599869749e-02 3.6527707427395764e-02
20 2.3565108550513952e-02 2.0131835710028016e-02 -3.4090223278000355e-02
21 1.6266310434046480e-01 4.8905845083266029e-02 4.9357148091662226e-03
22 3.9108125555495730e-03 -8.1159764595007206e-02 -1.0833146565530810e-02
23 4.9862133358188218e-02 1.2418637371342198e-01 -7.7818397024808514e-02
24 1.2773306535829987e-01 9.4426378198700950e-02 8.4499926668801975e-02
25 7.0365780658878857e-02 4.4772437288752168e-03 -4.6793953502009267e-02
26 -5.0367468278612715e-02 -1.4927976307827082e-01 1.2849283634143213e-01
27 4.6468158385616867e-02 -4.1893770730035470e-03 -1.3381218640924168e-03
28 1.1447647509745237e-02 5.8175457185785213e-02 7.3359279966104529e-02
29 4.7807504512594315e-02 1.0732100993527130e-01 -1.9887010850049803e-03
30 -4.2515398596597830e-02 -2.9914524234883048e-02 -8.4055979568242525e-02
31 -2.1955840630845491e-02 -1.1661294434426502e-01 7.4709133379083956e-02
32 -1.9494325826950429e-01 -6.5180990416658327e-02 -2.2830796417360581e-02
...

2
unittest/force-styles/tests/bond-gromos.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 17:49:16 202
epsilon: 2.5e-13
epsilon: 5e-13
prerequisites: ! |
atom full
bond gromos

2
unittest/force-styles/tests/bond-nonlinear.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Sat May 30 17:49:16 202
epsilon: 2.5e-13
epsilon: 5e-13
prerequisites: ! |
atom full
bond nonlinear

2
unittest/force-styles/tests/mol-pair-coul_cut.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Sun May 31 08:39:49 202
epsilon: 5e-14
epsilon: 1e-13
prerequisites: ! |
atom full
pair coul/cut

2
unittest/force-styles/tests/mol-pair-coul_dsf.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Sun May 31 08:50:20 202
epsilon: 1e-13
epsilon: 2e-13
prerequisites: ! |
atom full
pair coul/dsf

2
unittest/force-styles/tests/mol-pair-coul_wolf.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Sun May 31 09:23:33 202
epsilon: 1e-13
epsilon: 5e-13
prerequisites: ! |
atom full
pair coul/wolf

2
unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 5 May 2020
date_generated: Sun May 31 07:05:48 202
epsilon: 5e-14
epsilon: 2e-13
prerequisites: ! |
atom full
pair lj/charmm/coul/charmm/implicit

98
unittest/force-styles/tests/mol-pair-table.yaml Normal file
View File

@ -0,0 +1,98 @@
---
lammps_version: 2 Jun 2020
date_generated: Tue Jun 2 17:07:52 202
epsilon: 5e-14
prerequisites: ! |
atom full
pair table
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
pair_style: table linear 1000
pair_coeff: ! |
1 1 ${input_dir}/pair_table_lj_cut.txt lj_1_1
1 2 ${input_dir}/pair_table_lj_cut.txt lj_1_2
1 3 ${input_dir}/pair_table_lj_cut.txt lj_1_3
1 4 ${input_dir}/pair_table_lj_cut.txt lj_1_4
1 5 ${input_dir}/pair_table_lj_cut.txt lj_1_5
2 2 ${input_dir}/pair_table_lj_cut.txt lj_2_2
2 3 ${input_dir}/pair_table_lj_cut.txt lj_2_3
2 4 ${input_dir}/pair_table_lj_cut.txt lj_2_4
2 5 ${input_dir}/pair_table_lj_cut.txt lj_2_5
3 3 ${input_dir}/pair_table_lj_cut.txt lj_3_3
3 4 ${input_dir}/pair_table_lj_cut.txt lj_3_4
3 5 ${input_dir}/pair_table_lj_cut.txt lj_3_5
4 4 ${input_dir}/pair_table_lj_cut.txt lj_4_4
4 5 ${input_dir}/pair_table_lj_cut.txt lj_4_5
5 5 ${input_dir}/pair_table_lj_cut.txt lj_5_5
extract: ! ""
natoms: 29
init_vdwl: 756.641645798358
init_coul: 0
init_stress: ! |2-
2.2090340377185967e+03 2.2244453255747117e+03 4.7288126624664974e+03 -7.6403326905269398e+02 2.8082113929050504e+01 6.7633740837364439e+02
init_forces: ! |2
21 -7.4152834115258486e+01 -8.4097799952580075e+01 2.3159619440133380e+02
22 -1.1068613517882235e+02 -2.6823333923316500e+01 -1.7365467444566553e+02
23 1.8482904133388223e+02 1.1093264541659750e+02 -5.7930741636712071e+01
19 3.1933948922635905e-04 -2.3852967242197055e-04 1.7434557181616340e-03
18 -1.8861300062111192e-02 -3.3400052294502179e-02 3.0998859026254152e-02
20 -9.9899500683441750e-04 -1.0223083257768326e-03 3.6965867058990032e-04
28 -1.8537423924296499e+02 7.9666126830459447e+01 -1.2542634211727822e+02
4 -7.9160281367275722e+00 2.1475153087741110e+00 -5.6273386055724828e+00
10 5.3659703631942352e+02 -6.1638821121220133e+02 -1.8524754345847680e+02
11 -2.3998246191028687e+00 -6.0237447250432350e+00 -9.8493429965792298e+00
12 1.7521141359856628e+01 1.0629841850210417e+01 -7.9312291032117042e+00
14 -3.4254573458881881e+00 6.9454087271157916e-01 -8.8549490264531219e+00
3 -1.3601366655597215e+02 -3.8933969547126463e+02 -1.4673165295081574e+02
6 -8.3976623131970030e+02 9.7421656440040920e+02 1.1689035557011593e+03
7 5.9087836043818115e+01 -3.4067040950997404e+02 -1.7408617984623156e+03
15 -2.0812424842265748e-01 8.6236045287663003e+00 3.0626696691420956e+00
8 1.4404606696350953e+02 -1.1101530899074169e+02 3.9802209126866262e+02
9 8.1112222258717168e+01 8.7379022925008144e+01 3.5897466875849778e+02
16 4.6872469487658930e+02 -3.3472142759962014e+02 -1.2036108146826032e+03
17 -4.5876131348491481e+02 3.1932075524331395e+02 1.2202196485462191e+03
5 -2.5605507618514016e+00 -4.1184521759347588e+00 1.2369824594500452e+01
13 8.2458457495438626e+00 -3.2680411194697614e+00 -1.5173080370124606e-01
2 1.5875070222736517e+02 1.3063288077538610e+02 -1.8684429323195315e+02
1 -2.3000580006052314e+01 2.7192815329191200e+02 3.3414196848607327e+02
27 5.3953257632741014e+01 -2.3246330657484364e+02 9.3521822143445291e+01
29 1.3142887167232908e+02 1.5280375224826219e+02 3.1900088976429561e+01
24 3.6069363323679390e+01 -2.1770366344996296e+02 1.1410578468006614e+02
25 -1.5123846858732526e+02 2.4345575024648110e+01 -1.2714600914378309e+02
26 1.1515691479712817e+02 1.9334707687878640e+02 1.3017031466176082e+01
run_vdwl: 146.327829985032
run_coul: 0
run_stress: ! |2-
6.2914745307898283e+02 6.7439990734333583e+02 4.8382994180885322e+02 -3.2311602844067630e+02 -2.9168790037089135e+01 1.2280146536160866e+02
run_forces: ! |2
21 -9.8223704263420135e+00 -1.1937831142654984e+01 3.8747486275879332e+01
22 -1.8260879394786041e+01 -4.4231132834754163e+00 -2.9364817699370402e+01
23 2.8071936064676528e+01 1.6373759184425133e+01 -9.3702350107338450e+00
19 2.5604832046069535e-04 -2.4189898030892005e-04 1.6743691237745819e-03
18 -1.8054106711718410e-02 -3.1568964918282955e-02 2.9599553823736552e-02
20 -8.8390456832979493e-04 -9.1401459749508313e-04 3.6013486968785625e-04
28 -2.5002749675394742e+01 1.1546639020795190e+01 -1.6860888288423549e+01
4 -8.7521679338772564e+00 3.2350894298919783e+00 -6.3183019964749780e+00
10 6.3968310015089294e+01 -7.5154164336910185e+01 -7.5921779563234097e+01
11 -6.3974181801433527e+00 -8.2015044886741890e+00 -1.6623131445951760e+01
12 1.4375970778558539e+01 1.2183815698169100e+01 -8.2849268567516905e+00
14 -2.8220099744921270e+00 4.4312152330104282e-01 -7.1784838499077441e+00
3 -2.5170415829369691e+02 1.0807957243252388e+02 8.7902068634117185e+01
6 1.2021318256369948e+02 -1.0159989935597440e+02 -1.4455046866801038e+02
7 3.7064970613492512e+00 -1.0481522858827926e+01 -4.1617502928655071e+01
15 -4.0482676064288375e-01 8.2478176580999758e+00 3.1232194954592902e+00
8 -1.9012552812922401e+01 1.9341369900133493e+01 5.6061660162509632e+01
9 1.1002966844626583e+01 1.2955046425976752e+01 4.8964009756379951e+01
16 5.3215666467083004e+01 -6.8452018298715132e+01 1.6067414590921679e+01
17 -1.4543993736556850e+01 9.9518135650728148e+00 4.0557829246754260e+01
5 -1.7372909950509312e+00 -2.5663073053399832e+00 1.0327280945285382e+01
13 7.4327969687776196e+00 -2.8316539598264616e+00 -1.0441307986265116e-01
2 1.8402173670762625e+01 1.3899059683375182e+01 -2.2581973215530972e+01
1 1.3092386727121557e+01 8.0975258006863527e+01 6.0162717183582615e+01
27 3.0641658609965634e+00 -3.8727506359895912e+01 1.1409481341404170e+01
29 2.1946401102557179e+01 2.7187485766660277e+01 5.4471747925943950e+00
24 1.2590957134158188e+01 -3.6189602254037929e+01 2.3845923499083668e+01
25 -3.0061118850595161e+01 5.3993721695176697e+00 -2.5809444960387523e+01
26 1.7456807738003775e+01 3.0778628058022715e+01 1.9384675815059120e+00
...

2010
unittest/force-styles/tests/pair_table_beck.txt Normal file
View File

File diff suppressed because it is too large Load Diff

1029
unittest/force-styles/tests/pair_table_bitmap.txt Normal file
View File

File diff suppressed because it is too large Load Diff

15075
unittest/force-styles/tests/pair_table_lj_cut.txt Normal file
View File

File diff suppressed because it is too large Load Diff

13
unittest/formats/test_eim_potential_file_reader.cpp
View File

@ -1,3 +1,16 @@
/* ----------------------------------------------------------------------
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 "gmock/gmock.h"
#include "gtest/gtest.h"
#include "lammps.h"

Some files were not shown because too many files have changed in this diff Show More