From 6b18615a1b421b7fb90f5a1cc1e7d3224dbadce0 Mon Sep 17 00:00:00 2001 From: "Rebecca K. Lindsey" Date: Fri, 6 Jan 2023 20:24:28 -0500 Subject: [PATCH 01/14] Add support for excluded interactions --- chimesFF/src/chimesFF.cpp | 132 +++++++++++++++++----------- serial_interface/tests/run_tests.sh | 2 +- 2 files changed, 83 insertions(+), 51 deletions(-) diff --git a/chimesFF/src/chimesFF.cpp b/chimesFF/src/chimesFF.cpp index a383273..bb3307d 100644 --- a/chimesFF/src/chimesFF.cpp +++ b/chimesFF/src/chimesFF.cpp @@ -175,7 +175,7 @@ string chimesFF::get_next_line(istream& str) if (rank == 0) cout << "chimesFF: " << "Error reading line" << line << endl; exit(0); - } + } return line; } @@ -657,7 +657,7 @@ void chimesFF::read_parameters(string paramfile) line = get_next_line(param_file); split_line(line, tmp_str_items); - + tmp_int = stoi(tmp_str_items[1]); trip_params_atm_chems[tmp_int].push_back(tmp_str_items[3]); @@ -674,27 +674,36 @@ void chimesFF::read_parameters(string paramfile) trip_params_pair_typs[tmp_int].push_back(tmp_str_items[1]); trip_params_pair_typs[tmp_int].push_back(tmp_str_items[2]); trip_params_pair_typs[tmp_int].push_back(tmp_str_items[3]); + + // Check for excluded triplet types + + if(tmp_str_items[4] != "EXCLUDED:") + { + ncoeffs_3b[tmp_int] = stoi(tmp_str_items[7]); + + get_next_line(param_file); + get_next_line(param_file); - ncoeffs_3b[tmp_int] = stoi(tmp_str_items[7]); - - get_next_line(param_file); - get_next_line(param_file); - - for(int i=0; i tmp_int_vec(6); + vector tmp_int_vec(6); - for(int i=0; i= 0) + cout << "Error: Did not initialize pair_int_quad_map for entry " << i << endl ; + else + cout << "Warning: Did not initialize pair_int_quad_map for excluded entry " << i << endl ; } } } @@ -2151,7 +2176,7 @@ void chimesFF::build_pair_int_trip_map() vector pair_map(npairs) ; vector typ_idxs(natoms) ; - if ( atom_int_trip_map.size() == 0 ) return ; // No quads ! + if ( atom_int_trip_map.size() == 0 ) return ; // No trips ! pair_int_trip_map.resize(natmtyps*natmtyps*natmtyps) ; @@ -2165,6 +2190,10 @@ void chimesFF::build_pair_int_trip_map() { typ_idxs[2] = k ; int tripidx = atom_int_trip_map[i*natmtyps*natmtyps + j*natmtyps + k]; + + // Skip excluded interactions + if (tripidx < 0) + continue; build_atom_and_pair_mappers(natoms, npairs, typ_idxs, trip_params_pair_typs[tripidx], pair_map); @@ -2185,7 +2214,10 @@ void chimesFF::build_pair_int_trip_map() { if ( pair_int_trip_map[i].size() == 0 ) { - cout << "Error: Did not initialize pair_int_trip_map entry " << i << endl ; + if (atom_int_trip_map[i] >= 0) + cout << "Error: Did not initialize pair_int_trip_map for entry " << i << endl ; + else + cout << "Warning: Did not initialize pair_int_trip_map for excluded entry " << i << endl ; } } diff --git a/serial_interface/tests/run_tests.sh b/serial_interface/tests/run_tests.sh index e1853a1..31cfd97 100755 --- a/serial_interface/tests/run_tests.sh +++ b/serial_interface/tests/run_tests.sh @@ -14,7 +14,7 @@ STYLE=${1-"LONG"} # By default,run "LONG" test, but if user runs with "./run_tests SHORT, runs short tests PREFX=${2-""} # By default, don't set any special install prefix -PYTH3=python3.7 +PYTH3=python3 # Populate FFS, CFGS, and OPTIONS from test_list.dat From c8e893d88d14f70efac4e950d8d2ccefb52cf643 Mon Sep 17 00:00:00 2001 From: "Goldman, Nir" Date: Tue, 28 Mar 2023 14:22:00 -0700 Subject: [PATCH 02/14] Allows for multiple instances of ChIMES. Old ChIMES function calls now act as wrappers for new functions in order to maintain backwards compatibility. --- serial_interface/api/chimescalc_serial_C.cpp | 49 ++++++++++++++++---- serial_interface/api/chimescalc_serial_C.h | 5 ++ 2 files changed, 45 insertions(+), 9 deletions(-) diff --git a/serial_interface/api/chimescalc_serial_C.cpp b/serial_interface/api/chimescalc_serial_C.cpp index 356afc6..4fef9b8 100644 --- a/serial_interface/api/chimescalc_serial_C.cpp +++ b/serial_interface/api/chimescalc_serial_C.cpp @@ -21,7 +21,17 @@ using namespace std; #include "chimescalc_serial_C.h" static serial_chimes_interface chimes, *chimes_ptr; - +void *chimes_open_instance() +{ + serial_chimes_interface *new_ptr = nullptr; + new_ptr = new serial_chimes_interface; + return (void *) new_ptr; +} +void chimes_close_instance(void *handle) +{ + auto ptr = (serial_chimes_interface *) handle; + delete ptr; +} void set_chimes_serial(int small=1) { if ((small!=0)&&(small!=1)) @@ -30,17 +40,41 @@ void set_chimes_serial(int small=1) cout << "Received: " << small << endl; exit(0); } - chimes_ptr = &chimes; - chimes_ptr->allow_replication = small; + //chimes_ptr = &chimes; + //chimes_ptr->allow_replication = small; + chimes_ptr = &chimes; + set_chimes_serial_instance(chimes_ptr, small); + +} +void set_chimes_serial_instance(void *handle, int small=1) +{ + auto new_ptr = (serial_chimes_interface *) handle; + if ((small!=0)&&(small!=1)) + { + cout << "ERROR: Small must be set to 0 (false) or 1 (true)" << endl; + cout << "Received: " << small << endl; + exit(0); + } + new_ptr->allow_replication = small; } void init_chimes_serial(char *param_file, int *rank) { - chimes_ptr->init_chimesFF(param_file, *rank); + //chimes_ptr->init_chimesFF(param_file, *rank); + init_chimes_serial_instance(chimes_ptr, param_file, rank); +} +void init_chimes_serial_instance(void *handle, char *param_file, int *rank) +{ + auto new_ptr = (serial_chimes_interface *) handle; + new_ptr->init_chimesFF(param_file, *rank); } - void calculate_chimes(int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]) { + calculate_chimes_instance(chimes_ptr, natom, xc, yc, zc, atom_types, ca, cb, cc, energy, fx, fy, fz, stress); +} +void calculate_chimes_instance(void *handle, int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]) +{ + auto new_ptr = (serial_chimes_interface *) handle; vector x_vec(natom); vector y_vec(natom); vector z_vec(natom); @@ -66,9 +100,6 @@ void calculate_chimes(int natom, double *xc, double *yc, double *zc, char *atom_ for (int i = 0; i < 9; i++) { stress_vec[i] = stress[i]; } - //for (int i = 0; i < 9; i++) { - // stress[i] = stress_vec[i]; - //} vectorcell_a_vec(3); vectorcell_b_vec(3); vectorcell_c_vec(3); @@ -82,7 +113,7 @@ void calculate_chimes(int natom, double *xc, double *yc, double *zc, char *atom_ cell_c_vec[1] = cc[1]; cell_c_vec[2] = cc[2]; - chimes_ptr->calculate(x_vec, y_vec, z_vec, cell_a_vec, cell_b_vec, cell_c_vec, atom_types_vec, *energy, force_vec, stress_vec); + new_ptr->calculate(x_vec, y_vec, z_vec, cell_a_vec, cell_b_vec, cell_c_vec, atom_types_vec, *energy, force_vec, stress_vec); for (int i = 0; i < natom; i++) { fx[i] = force_vec[i][0]; fy[i] = force_vec[i][1]; diff --git a/serial_interface/api/chimescalc_serial_C.h b/serial_interface/api/chimescalc_serial_C.h index 696c51b..2d114c8 100644 --- a/serial_interface/api/chimescalc_serial_C.h +++ b/serial_interface/api/chimescalc_serial_C.h @@ -8,9 +8,14 @@ extern "C" { #endif +void *chimes_open_instance(); +void chimes_close_instance(void *handle); void set_chimes_serial(int small); +void set_chimes_serial_instance(void *handle, int small); void init_chimes_serial(char *param_file, int *rank); +void init_chimes_serial_instance(void *handle, char *param_file, int *rank); void calculate_chimes(int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]); +void calculate_chimes_instance(void *handle, int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]); #ifdef __cplusplus } #endif From cc5fd01aa614100acf8e3523d42737fc249fe6c2 Mon Sep 17 00:00:00 2001 From: "Goldman, Nir" Date: Wed, 29 Mar 2023 08:38:51 -0700 Subject: [PATCH 03/14] Wrapper functions allow for mutliple instances of ChIMES calculator. Backwards compatibility has been maintained. --- serial_interface/api/chimescalc_serial_C.cpp | 9 ++-- serial_interface/api/chimescalc_serial_C.h | 2 +- serial_interface/api/chimescalc_serial_F.f90 | 44 ++++++++++++++++++++ 3 files changed, 49 insertions(+), 6 deletions(-) diff --git a/serial_interface/api/chimescalc_serial_C.cpp b/serial_interface/api/chimescalc_serial_C.cpp index 4fef9b8..63ff733 100644 --- a/serial_interface/api/chimescalc_serial_C.cpp +++ b/serial_interface/api/chimescalc_serial_C.cpp @@ -40,8 +40,6 @@ void set_chimes_serial(int small=1) cout << "Received: " << small << endl; exit(0); } - //chimes_ptr = &chimes; - //chimes_ptr->allow_replication = small; chimes_ptr = &chimes; set_chimes_serial_instance(chimes_ptr, small); @@ -61,12 +59,13 @@ void set_chimes_serial_instance(void *handle, int small=1) void init_chimes_serial(char *param_file, int *rank) { //chimes_ptr->init_chimesFF(param_file, *rank); - init_chimes_serial_instance(chimes_ptr, param_file, rank); + init_chimes_serial_instance(chimes_ptr, param_file, *rank); } -void init_chimes_serial_instance(void *handle, char *param_file, int *rank) +void init_chimes_serial_instance(void *handle, char *param_file, int rank) { auto new_ptr = (serial_chimes_interface *) handle; - new_ptr->init_chimesFF(param_file, *rank); + //printf("rank = %d\n", *rank); + new_ptr->init_chimesFF(param_file, 0); } void calculate_chimes(int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]) { diff --git a/serial_interface/api/chimescalc_serial_C.h b/serial_interface/api/chimescalc_serial_C.h index 2d114c8..71e6243 100644 --- a/serial_interface/api/chimescalc_serial_C.h +++ b/serial_interface/api/chimescalc_serial_C.h @@ -13,7 +13,7 @@ void chimes_close_instance(void *handle); void set_chimes_serial(int small); void set_chimes_serial_instance(void *handle, int small); void init_chimes_serial(char *param_file, int *rank); -void init_chimes_serial_instance(void *handle, char *param_file, int *rank); +void init_chimes_serial_instance(void *handle, char *param_file, int rank); void calculate_chimes(int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]); void calculate_chimes_instance(void *handle, int natom, double *xc, double *yc, double *zc, char *atom_types[], double ca[3], double cb[3], double cc[3], double *energy, double fx[], double fy[], double fz[], double stress[9]); #ifdef __cplusplus diff --git a/serial_interface/api/chimescalc_serial_F.f90 b/serial_interface/api/chimescalc_serial_F.f90 index 123fca7..520a94a 100644 --- a/serial_interface/api/chimescalc_serial_F.f90 +++ b/serial_interface/api/chimescalc_serial_F.f90 @@ -8,6 +8,34 @@ module chimescalc_serial interface + function f_chimes_open_instance() & + & bind (C, name='chimes_open_instance') + use, intrinsic :: ISO_C_binding, only : C_ptr + type(C_ptr) :: f_chimes_open_instance + end function f_chimes_open_instance + + subroutine f_chimes_close_instance(handle) & + & bind (C, name='chimes_close_instance') + use, intrinsic :: ISO_C_binding, only : C_ptr + type(C_ptr), value :: handle + end subroutine f_chimes_close_instance + + subroutine f_calculate_chimes_instance(handle, natom, xc, yc, zc, cptr, ca, & + & cb, cc, energy, fx, fy, fz, stress) & + & bind (C, name='calculate_chimes_instance') + use, intrinsic :: ISO_C_binding, only : C_char, C_ptr, C_int, C_double + implicit none + integer(C_int), value :: natom + type(c_ptr), dimension(*) :: cptr(natom) + type(C_ptr), value :: handle + real(C_double) :: xc(natom), yc(natom), zc(natom) + real(C_double) :: fx(natom), fy(natom), fz(natom) + character(C_char), dimension(80) :: c_atom(natom) + real(C_double) :: ca(3), cb(3), cc(3) + real(C_double) :: energy + real(C_double) :: stress(9) + end subroutine f_calculate_chimes_instance + subroutine f_calculate_chimes (natom, xc, yc, zc, cptr, ca, & & cb, cc, energy, fx, fy, fz, stress) & & bind (C, name='calculate_chimes') @@ -23,6 +51,14 @@ subroutine f_calculate_chimes (natom, xc, yc, zc, cptr, ca, & real(C_double) :: stress(9) end subroutine f_calculate_chimes + subroutine f_set_chimes_instance(handle, small) bind & + & (C, name='set_chimes_serial_instance') + use, intrinsic :: ISO_C_binding, only : C_ptr, C_int + implicit none + integer(C_int), value :: small + type(C_ptr), value :: handle + end subroutine f_set_chimes_instance + subroutine f_set_chimes(small) bind & & (C, name='set_chimes_serial') use, intrinsic :: ISO_C_binding, only : C_ptr, C_int @@ -30,6 +66,14 @@ subroutine f_set_chimes(small) bind & integer(C_int), value :: small end subroutine f_set_chimes + subroutine f_init_chimes_instance(handle, param_file, rank) & + & bind (C, name='init_chimes_serial_instance') + use, intrinsic :: ISO_C_binding, only : C_ptr, C_int, C_char + integer(C_int), value :: rank + character (kind=C_char), dimension(*) :: param_file + type(C_ptr), value :: handle + end subroutine f_init_chimes_instance + subroutine f_init_chimes(param_file, rank) & & bind (C, name='init_chimes_serial') import C_int, C_char From ff83f7ba672275378f890728f62c994db17fe09a Mon Sep 17 00:00:00 2001 From: "Goldman, Nir" Date: Wed, 29 Mar 2023 09:06:26 -0700 Subject: [PATCH 04/14] Added build of test code in serial_interface/examples/f_instance and serial_interface/examples/c_instance. --- CMakeLists.txt | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index bc4ff5a..912dc6c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -92,6 +92,11 @@ target_link_libraries (chimescalc-test_serial-C ChimesCalc) target_compile_features (chimescalc-test_serial-C PRIVATE cxx_std_11) target_compile_definitions(chimescalc-test_serial-C PRIVATE "DEBUG=${DEBUG}") +add_executable(chimescalc-test_serial-C_instance serial_interface/examples/c_instance/main.c) +target_link_libraries (chimescalc-test_serial-C_instance ChimesCalc) +target_compile_features (chimescalc-test_serial-C_instance PRIVATE cxx_std_11) +target_compile_definitions(chimescalc-test_serial-C_instance PRIVATE "DEBUG=${DEBUG}") + #################################################################################################### # Dynamically loadable library (e.g for Python) @@ -163,6 +168,9 @@ if(WITH_FORTRAN_API OR WITH_FORTRAN08_API) add_executable(chimescalc-test_serial-F serial_interface/examples/fortran/main.F90) target_link_libraries(chimescalc-test_serial-F ChimesCalc_Fortran) target_compile_definitions(chimescalc-test_serial-F PRIVATE "DEBUG=${DEBUG}") + add_executable(chimescalc-test_serial-F_instance serial_interface/examples/fortran_instance/main.F90) + target_link_libraries(chimescalc-test_serial-F_instance ChimesCalc_Fortran) + target_compile_definitions(chimescalc-test_serial-F_instance PRIVATE "DEBUG=${DEBUG}") # Optional, as ancient Fortran compilers may have difficulties with it if(WITH_FORTRAN08_API) @@ -210,7 +218,9 @@ enable_testing() set(apis "cpp;${CMAKE_CURRENT_BINARY_DIR}/chimescalc" "c;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-C" + "c_instance;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-C_instance" "fortran;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-F" + "fortran_instance;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-F_instance" "fortran08;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-F08") set(_testdir "${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/tests") From 630527e203a14816c90bc243da568e9404e6e75a Mon Sep 17 00:00:00 2001 From: "Goldman, Nir" Date: Wed, 29 Mar 2023 09:15:25 -0700 Subject: [PATCH 05/14] Added testing for f_instance and c_instance APIs. --- serial_interface/tests/run_tests.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/serial_interface/tests/run_tests.sh b/serial_interface/tests/run_tests.sh index 31cfd97..cf818a2 100755 --- a/serial_interface/tests/run_tests.sh +++ b/serial_interface/tests/run_tests.sh @@ -25,7 +25,7 @@ do FFS+=($FF); CFGS+=($CFG); OPTIONS+=($OPTION) done < tmp-data.dat; rm -f tmp-data.dat -API_LIST="0 1 2 3 4" +API_LIST="0 1 2 3 4 5 6" NO_TESTS=${#FFS[@]} LOC=`pwd` @@ -34,6 +34,8 @@ API[1]="c" ; EXE[1]="chimescalc-test_serial-C" ; XTRA[1]="" #"2" API[2]="fortran" ; EXE[2]="chimescalc-test_serial-F" ; XTRA[2]="" #"2" API[3]="python" ; EXE[3]="main.py" ; XTRA[3]="" #"2 1" API[4]="fortran08"; EXE[4]="chimescalc-test_serial-F08" ; XTRA[4]="" #"0" +API[5]="fortran_instance"; EXE[5]="chimescalc-test_serial-F_instance" ; XTRA[5]="" #"0" +API[6]="c_instance"; EXE[6]="chimescalc-test_serial-C_instance" ; XTRA[6]="" #"0" echo "Running $STYLE tests" date From fd3f494b2bdd2319f9df1a65b87e3ce9d05ae2fc Mon Sep 17 00:00:00 2001 From: "Goldman, Nir" Date: Wed, 29 Mar 2023 09:22:10 -0700 Subject: [PATCH 06/14] Example codes for c_instance and fortran_instance APIs. --- serial_interface/examples/c_instance/Makefile | 52 +++++++ serial_interface/examples/c_instance/main.c | 110 ++++++++++++++ .../examples/fortran_instance/.main.F90.swp | Bin 0 -> 16384 bytes .../examples/fortran_instance/Makefile | 80 ++++++++++ .../examples/fortran_instance/main.F90 | 137 ++++++++++++++++++ 5 files changed, 379 insertions(+) create mode 100644 serial_interface/examples/c_instance/Makefile create mode 100644 serial_interface/examples/c_instance/main.c create mode 100644 serial_interface/examples/fortran_instance/.main.F90.swp create mode 100644 serial_interface/examples/fortran_instance/Makefile create mode 100644 serial_interface/examples/fortran_instance/main.F90 diff --git a/serial_interface/examples/c_instance/Makefile b/serial_interface/examples/c_instance/Makefile new file mode 100644 index 0000000..eada52f --- /dev/null +++ b/serial_interface/examples/c_instance/Makefile @@ -0,0 +1,52 @@ +CXX = g++ -O3 -std=c++11 +CCOMP = gcc -O3 +DEBUG = 1 + +C_LOC = $(realpath .) + +CHIMESFF_LOC=$(C_LOC)/../../../chimesFF/src +CHIMESFF_SRC=$(CHIMESFF_LOC)/chimesFF.cpp +CHIMESFF_HDR=$(CHIMESFF_LOC)/chimesFF.h + +chimesFF.o : $(CHIMESFF_SRC) + $(CXX) -c $(CHIMESFF_SRC) -I $(CHIMESFF_LOC) + +SERIAL_LOC=$(C_LOC)/../../src +SERIAL_SRC=$(SERIAL_LOC)/serial_chimes_interface.cpp +SERIAL_HDR=$(SERIAL_LOC)/serial_chimes_interface.h + +serial_chimes_interface.o : $(SERIAL_SRC) + $(CXX) -c $(SERIAL_SRC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) + +WRAPPER_LOC=$(C_LOC)/../../api +WRAPPER_SRC=$(WRAPPER_LOC)/chimescalc_serial_C.cpp +WRAPPER_HDR=$(WRAPPER_LOC)/chimescalc_serial_C.h + +chimescalc_serial_C.o : $(WRAPPER_SRC) + $(CXX) -c $(WRAPPER_SRC) -I $(WRAPPER_LOC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) + +TEST_LOC=$(C_LOC) +TEST_SRC=$(TEST_LOC)/main.c + +main.o: $(TEST_SRC) + $(CCOMP) -c $(TEST_SRC) -DDEBUG=${DEBUG} -I $(WRAPPER_LOC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) + +TEST_LNK = chimesFF.o serial_chimes_interface.o chimescalc_serial_C.o main.o + +test-C: $(TEST_LNK) + $(CXX) $(TEST_LNK) -o chimescalc-test_serial-C_instance + +clean: + rm -f *.o + +clean-all: + make clean + rm -f chimescalc-test_serial-C_instance + +all: + make chimesFF.o + make serial_chimes_interface.o + make chimescalc_serial_C.o + make main.o + make test-C + make clean diff --git a/serial_interface/examples/c_instance/main.c b/serial_interface/examples/c_instance/main.c new file mode 100644 index 0000000..cbb7a96 --- /dev/null +++ b/serial_interface/examples/c_instance/main.c @@ -0,0 +1,110 @@ +/* + ChIMES Calculator + Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried + Contributing Author: Nir Goldman (2020) +*/ + +#include +#include +#include +#include +#include +#include "chimescalc_serial_C.h" + +int main (int argc, char **argv) +{ + int small = 0; // 0 = false, 1 = true + + if ((argc != 4)&&(argc !=3)) + { + printf("To run: ./test.x \n"); + printf("or\n"); + printf("./test.x \n"); + printf("Exiting code.\n"); + exit(0); + } + if(argc==4) + small = atoi(argv[3]); + + const double GPa = 6.9479; // convert kcal/mol.A^3 to GPa + FILE *fconf; + int natom, i, j, k, l; + char junk; + double lx, ly, lz; + double ca[3], cb[3], cc[3]; + fconf = fopen (argv[2],"r"); + fscanf(fconf,"%d\n",&natom); + fscanf(fconf,"%lf %lf %lf %lf %lf %lf %lf %lf %lf\n",&ca[0],&ca[1],&ca[2],&cb[0],&cb[1],&cb[2],&cc[0],&cc[1],&cc[2]); + double vol = lx*ly*lz; + double *stress = (double *) calloc(9,sizeof(double)); + double energy = 0.0; + double xij, yij, zij, rij, dr[3]; + double xc[natom], yc[natom], zc[natom]; + double fx[natom], fy[natom], fz[natom]; + char atom_types[natom][50], *atom[natom]; + char *atype2b[2], *atype3b[3], *atype4b[4]; + + for (i = 0; i < natom; i++) + { + fx[i] = 0.0; + fy[i] = 0.0; + fz[i] = 0.0; + } + for (i = 0; i < natom; i++) + { + fscanf(fconf,"%s %lf %lf %lf\n",atom_types[i],&xc[i],&yc[i],&zc[i]); + atom[i] = atom_types[i]; + } + fclose(fconf); + //set_chimes_serial(small); + void *chimes_ptr = chimes_open_instance(); + set_chimes_serial_instance(chimes_ptr, small); + + printf("Read args:\n"); + for (i=1; i>qjJDQnAghg0xySm32 zx7};IGu?e4NJyN*A|a6Af&d8+5-TAA2XbNg5rPXh4j^$L91;n{At-_a0=_Dj-ReX}AtD08j6IZurwN%k?y;svNU-_u}`o+IL_NTj=)(L&LYX{Zy zJnxu`b$edqIks>6?3iNOXLEsNXW#3x*g_qr@7qZjSsgFg@3+b^i#*%6ydYsw+jdx) z4eV~uXK}e5MoDA`$chs?Ku*{8g3`vS(EPY&Ri0u%F(4RtTwAGC#eg}xxIiCx|1HIf zVn8vV7*Gr-1{4E|0mXn~Kr!$(Vj$_A(q6{iJ)JJtfl*rt;-a^-v5b z1{4E|0mXn~Krx^gPz)#r6a$I@#eibq|BwOO)il1Q{|jI6WB)%}|NrfbrhOAgfEf4` za2fa@@DT9Y6PosAzyi(z|9)K4eh>T*xC?|p19)tZ6?1J`d~yo4_UDN#Hc_kJD%i zxDVU|egF)BJHQKo0sQ76P5U|Uec;=`D?lH(27DZN1|Z-m;Mecew66kR0Y<=cz=wd> z5uo`I@G@`>coN`!_F5LGnQvPpu3m&Q6||(Uo7GR6v{AiKx@at!v>02%QJogeIEh#s z>lcmX&23wIP@TbKos|>T8BVlQJ6WC4WIL-Tt23Nz=fcVA3# z!zd;lJQ?-Hqp7M$cAEi5ZYCOM8t zX*HAD17HY@OiDY=kQLB|Pwo6r4YTAao9x64=`x|0L?#6|cGER!0MSEW1VEe@bhde} zW1B?hGF61}ESrmMXP-F-Pp@QeEgNQm>xS}g8cWfG*q}9XEI)K~$Kvhrq)c5mq##Cq zRq7%INJFgisui~)Q{`hyk=m3Zk^wL9lIfQ(zB@Z?dp^S}Rt#Do-;OafDofDTC>hf>@ltav0fBWDheo96yYi zUae$3TC@Y%;~wuw!4@|FD;f5f?iofIXTa=8&+8KU!FFBZ3=+>GJHb1+l!Vl^4;VF` zj+pJ*Eu1kUc`XRJyhOyh;Y*AT_q~M0J)9fM%kWB2(Ofnrn>PmzlrV?lKH_&-0Y>RT z-zl2}{h?zgOwUJ%E{0ET%XtCFnv;XJ=Hx(^IXT&&;i}KJHGZKv)zRzoa)xtr26>L8 zWXzyr>s7j1*G?3yldzqxDGq%$7@SC zc!+NkA6IKm7)EY7#AF@$C>k4)bPb*7t5Y&uhyhuDj@DS=3xMy^wds8owFv=-mHI6rSJS%1nD+oAi`JDzQ5y zS~0j=4Wu;rC~C92cXK;$Eu*|SfP)J<D-)>l#Iv7;1!$XS$y!Z(T^1Fv0vfK7v z*ly|#YkP0UFiHAG?zv5JQ7wqQFyNmJE@*JTeXVpQ|Iy6}WKPbk1ofOVL4&!Wy znQ9^dH!R62r5~I+3Q1?0Hv^ORp`;u3p;=J~uMDruYr$>v2mCsJwD~s@5B~AQgMU?} zRz+!C0Q@BUA;Cq8N6{Bfw9LyE=7h7NdnUbT(g8B_ zd0&uy#2Z)Ech(zw%^lKt&vS#Q)XtM&T{?sr;(3YG407*m(%4O*k#wFkQ?ZeH<)R(b zE~K)AmzP!2UV&3*j>pYKiWkEgFNC=_6unqlJ%4Ex69{)oIEv4v=MpC<+Ap#ZZ&tQ zksrI)`1=10*5cm-`1(KF-~S`l_`d?a1AGDK0JniXU=!E?9s%CK+W$WAHJ}Gv0SNdP z*8cwlcs$^Xz#*^)RDmaeQ^1>O^OwLcfLDQ^0$h*p0_su>C&*>=D$kTFwQ{X0 zwdE^0JLoW%5S8yDP>#(C5ueBYMMzC-?p@-4g#Dz~PsBDxY)jUOJ7GH`?WlK< zv4+A%;4$S2n}5fYD{S~3Q?9VdcTBm$#@;dI3Y&RHl`Di^#_?!`7tsAOB8?wQJXna0 zg)A<; " + print*,"or" + print*,"/test.x " + print*,"Exiting code.\n" + STOP + endif + + if (io_num .eq. 3) then + call GET_COMMAND_ARGUMENT(3, wq_char) + read(wq_char,*,iostat=stat) small + endif + + call GET_COMMAND_ARGUMENT(1, wq_char) + param_file = trim(wq_char) + call GET_COMMAND_ARGUMENT(2, wq_char) + coord_file = trim(wq_char) + + print*,"Read args:" + do i = 1, io_num + call GET_COMMAND_ARGUMENT(i, wq_char) + print*,i,trim(wq_char) + enddo + + open (unit=10, status='old', file=coord_file) + read(10,*)natom + read(10,*)ca(1),ca(2),ca(3),cb(1),cb(2),cb(3),cc(1),cc(2),cc(3) + + allocate(fx(natom)) + allocate(fy(natom)) + allocate(fz(natom)) + allocate(atom_type(natom)) + allocate(c_atom(natom)) + allocate(xc(natom)) + allocate(yc(natom)) + allocate(zc(natom)) + allocate(stringPtr(natom)) + do i = 1, natom + read(10,*)atom_type(i),xc(i),yc(i),zc(i) + ! trim to remove whitespace + ! add null char at end to make C-readable + c_atom(i) = trim(atom_type(i))//char(0) + enddo + close(10) + ! initialize force arrays + fx(:) = 0d0 + fy(:) = 0d0 + fz(:) = 0d0 + ! initialize system energy + energy = 0d0 + + call f_set_chimes_instance(chimes_ptr, small) + + print*,"fcheck-1" + newfile = trim(param_file) // c_null_char + call f_init_chimes_instance(chimes_ptr, newfile, 0) ! last '0' is the rank of the process + + print*,"fcheck-2" + + stress(:) = 0d0 + do ns = 1, natom + stringPtr(ns) = c_loc(c_atom(ns)) + enddo + + print*,"fcheck-3" + + call f_calculate_chimes_instance (chimes_ptr, natom, xc, yc, zc, stringPtr, ca, & + & cb, cc, energy, fx, fy, fz, stress) + + print *, "Success!" + print '(A,1X, F0.6)', "Energy (kcal/mol):",energy + print *, "Stress tensors (GPa):" + print '(A,1X, F15.6)', "s_xx: ",stress(1)*GPa + print '(A,1X, F15.6)', "s_yy: ",stress(5)*GPa + print '(A,1X, F15.6)', "s_zz: ",stress(9)*GPa + print '(A,1X, F15.6)', "s_xy: ",stress(2)*GPa + print '(A,1X, F15.6)', "s_xz: ",stress(3)*GPa + print '(A,1X, F15.6)', "s_yz: ",stress(6)*GPa + print *, "Forces (kcal/mol/A):" + do i = 1, natom + print '(F15.6)',fx(i) + print '(F15.6)',fy(i) + print '(F15.6)',fz(i) + enddo + +#if DEBUG==1 + + open (unit = 20, status = 'replace', file='debug.dat') + write(20,'(F15.6)') energy + write(20,'(F15.6)') stress(1)*GPa + write(20,'(F15.6)') stress(5)*GPa + write(20,'(F15.6)') stress(9)*GPa + write(20,'(F15.6)') stress(2)*GPa + write(20,'(F15.6)') stress(3)*GPa + write(20,'(F15.6)') stress(6)*GPa + + ! Changed format of forces to E15.7 to output the same number of + ! digits as C (LEF) 08/02/21 + do i = 1, natom + write(20,'(F15.6)') fx(i) + write(20,'(F15.6)') fy(i) + write(20,'(F15.6)') fz(i) + enddo + close(20) + call f_chimes_close_instance(chimes_ptr) + +#endif + + end program From 5d01dc3ab6ee14a8cfc225447a8ca840c262c32b Mon Sep 17 00:00:00 2001 From: "Goldman, Nir" Date: Wed, 29 Mar 2023 09:24:15 -0700 Subject: [PATCH 07/14] Example codes for c_instance and fortran_instance APIs. --- .../examples/fortran_instance/.main.F90.swp | Bin 16384 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 serial_interface/examples/fortran_instance/.main.F90.swp diff --git a/serial_interface/examples/fortran_instance/.main.F90.swp b/serial_interface/examples/fortran_instance/.main.F90.swp deleted file mode 100644 index 8e3eba37f803486224bdf99f252e3c70a92dbea6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16384 zcmeHOO^oD56*fyYkc4FUIRpt%-pryMdvN-1_9xTIEShwBW>>qjJDQnAghg0xySm32 zx7};IGu?e4NJyN*A|a6Af&d8+5-TAA2XbNg5rPXh4j^$L91;n{At-_a0=_Dj-ReX}AtD08j6IZurwN%k?y;svNU-_u}`o+IL_NTj=)(L&LYX{Zy zJnxu`b$edqIks>6?3iNOXLEsNXW#3x*g_qr@7qZjSsgFg@3+b^i#*%6ydYsw+jdx) z4eV~uXK}e5MoDA`$chs?Ku*{8g3`vS(EPY&Ri0u%F(4RtTwAGC#eg}xxIiCx|1HIf zVn8vV7*Gr-1{4E|0mXn~Kr!$(Vj$_A(q6{iJ)JJtfl*rt;-a^-v5b z1{4E|0mXn~Krx^gPz)#r6a$I@#eibq|BwOO)il1Q{|jI6WB)%}|NrfbrhOAgfEf4` za2fa@@DT9Y6PosAzyi(z|9)K4eh>T*xC?|p19)tZ6?1J`d~yo4_UDN#Hc_kJD%i zxDVU|egF)BJHQKo0sQ76P5U|Uec;=`D?lH(27DZN1|Z-m;Mecew66kR0Y<=cz=wd> z5uo`I@G@`>coN`!_F5LGnQvPpu3m&Q6||(Uo7GR6v{AiKx@at!v>02%QJogeIEh#s z>lcmX&23wIP@TbKos|>T8BVlQJ6WC4WIL-Tt23Nz=fcVA3# z!zd;lJQ?-Hqp7M$cAEi5ZYCOM8t zX*HAD17HY@OiDY=kQLB|Pwo6r4YTAao9x64=`x|0L?#6|cGER!0MSEW1VEe@bhde} zW1B?hGF61}ESrmMXP-F-Pp@QeEgNQm>xS}g8cWfG*q}9XEI)K~$Kvhrq)c5mq##Cq zRq7%INJFgisui~)Q{`hyk=m3Zk^wL9lIfQ(zB@Z?dp^S}Rt#Do-;OafDofDTC>hf>@ltav0fBWDheo96yYi zUae$3TC@Y%;~wuw!4@|FD;f5f?iofIXTa=8&+8KU!FFBZ3=+>GJHb1+l!Vl^4;VF` zj+pJ*Eu1kUc`XRJyhOyh;Y*AT_q~M0J)9fM%kWB2(Ofnrn>PmzlrV?lKH_&-0Y>RT z-zl2}{h?zgOwUJ%E{0ET%XtCFnv;XJ=Hx(^IXT&&;i}KJHGZKv)zRzoa)xtr26>L8 zWXzyr>s7j1*G?3yldzqxDGq%$7@SC zc!+NkA6IKm7)EY7#AF@$C>k4)bPb*7t5Y&uhyhuDj@DS=3xMy^wds8owFv=-mHI6rSJS%1nD+oAi`JDzQ5y zS~0j=4Wu;rC~C92cXK;$Eu*|SfP)J<D-)>l#Iv7;1!$XS$y!Z(T^1Fv0vfK7v z*ly|#YkP0UFiHAG?zv5JQ7wqQFyNmJE@*JTeXVpQ|Iy6}WKPbk1ofOVL4&!Wy znQ9^dH!R62r5~I+3Q1?0Hv^ORp`;u3p;=J~uMDruYr$>v2mCsJwD~s@5B~AQgMU?} zRz+!C0Q@BUA;Cq8N6{Bfw9LyE=7h7NdnUbT(g8B_ zd0&uy#2Z)Ech(zw%^lKt&vS#Q)XtM&T{?sr;(3YG407*m(%4O*k#wFkQ?ZeH<)R(b zE~K)AmzP!2UV&3*j>pYKiWkEgFNC=_6unqlJ%4Ex69{)oIEv4v=MpC<+Ap#ZZ&tQ zksrI)`1=10*5cm-`1(KF-~S`l_`d?a1AGDK0JniXU=!E?9s%CK+W$WAHJ}Gv0SNdP z*8cwlcs$^Xz#*^)RDmaeQ^1>O^OwLcfLDQ^0$h*p0_su>C&*>=D$kTFwQ{X0 zwdE^0JLoW%5S8yDP>#(C5ueBYMMzC-?p@-4g#Dz~PsBDxY)jUOJ7GH`?WlK< zv4+A%;4$S2n}5fYD{S~3Q?9VdcTBm$#@;dI3Y&RHl`Di^#_?!`7tsAOB8?wQJXna0 zg)A<; Date: Thu, 20 Jul 2023 16:08:02 -0400 Subject: [PATCH 08/14] Bugfix: Modify chimesFF to allow penalty ouput from any proc. Feature: Add support for generating traj_bad files needed for the ALD via LAMMPS or other tools calling the ChIMES Calculator. --- chimesFF/src/chimesFF.h | 34 ++++++++++--- etc/lmp/src/pair_chimes.cpp | 99 +++++++++++++++++++++++-------------- etc/lmp/src/pair_chimes.h | 20 +++++--- 3 files changed, 102 insertions(+), 51 deletions(-) diff --git a/chimesFF/src/chimesFF.h b/chimesFF/src/chimesFF.h index e6fcd75..45f64bf 100644 --- a/chimesFF/src/chimesFF.h +++ b/chimesFF/src/chimesFF.h @@ -162,7 +162,6 @@ class chimesFF void compute_4B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force, vector & stress, double & energy, chimes4BTmp &tmp); void compute_4B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force, vector & stress, double & energy, chimes4BTmp &tmp, vector & force_scalar_in); - void get_cutoff_2B(vector > & cutoff_2b); // Populates the 2b cutoffs double max_cutoff_2B(bool silent = false); // Returns the largest 2B cutoff @@ -175,6 +174,11 @@ class chimesFF void build_pair_int_trip_map() ; void build_pair_int_quad_map() ; + // Functions to aid using ChIMES Calculator for fitting + + inline int get_badness(); + inline void reset_badness(); + private: string xform_style; // Morse, direct, inverse, etc... @@ -184,6 +188,7 @@ class chimesFF vector morse_var; // [npairs]; morse_lambda vector penalty_params; // [2]; Second dimension: [0] = A_pen, [1] = d_pen vector energy_offsets; // [natmtyps]; Single atom ChIMES energies + int badness; // Keeps track of whether any interactions for atoms owned by proc rank are below rcutin, in the penalty region, or in the r>rcutin+dp region. 0 = good, 1 = in penalty region, 2 = below rcutin // Names (chemical symbols for constituent atoms) .. handled differently for 2-body versus >2-body interactions @@ -339,28 +344,43 @@ inline void chimesFF::get_penalty(const double dx, const int & pair_idx, double E_penalty = 0.0; force_scalar = 1.0; - - if (dx - penalty_params[0] < chimes_2b_cutoff[pair_idx][0]) - + + if (dx - penalty_params[0] < chimes_2b_cutoff[pair_idx][0]) // Then we're within the penalty-enforced region of distance space + { r_penalty = chimes_2b_cutoff[pair_idx][0] + penalty_params[0] - dx; + if(dx < chimes_2b_cutoff[pair_idx][0]) + badness = 2; + else if (1 > badness) // Only update badness if candiate badness is worse than its current value + badness = 1; + } if ( r_penalty > 0.0 ) { E_penalty = r_penalty * r_penalty * r_penalty * penalty_params[1]; force_scalar = -3.0 * r_penalty * r_penalty * penalty_params[1]; - if (rank == 0) - { + //if (rank == 0) // Commenting out - we need all ranks to report if the penalty function has been sampled + //{ cout << "chimesFF: " << "Adding penalty in 2B Cheby calc, r < rmin+penalty_dist " << fixed << dx << " " << chimes_2b_cutoff[pair_idx][0] + penalty_params[0] << " pair type: " << pair_idx << endl; cout << "chimesFF: " << "\t...Penalty potential = "<< E_penalty << endl; - } + //} } } +inline int chimesFF::get_badness() +{ + return badness; +} + +inline void chimesFF::reset_badness() +{ + badness = 0; +} + inline void chimesFF::build_atom_and_pair_mappers(const int natoms, const int npairs, const vector & typ_idxs, const vector & clu_params_pair_typs, vector & mapped_pair_idx) // Interface to array-based version. diff --git a/etc/lmp/src/pair_chimes.cpp b/etc/lmp/src/pair_chimes.cpp index ac39d3e..f401b55 100644 --- a/etc/lmp/src/pair_chimes.cpp +++ b/etc/lmp/src/pair_chimes.cpp @@ -34,10 +34,12 @@ #include "error.h" #include "pair_chimes.h" #include "group.h" -#include "update.h" - +#include "update.h" // Needed for mb neighlist updates and info printing for fitting +#include "output.h" // Needed for infor printing for fitting -- dump 1 must be the "main" dump file used for fitting +#include "utils.h" // Needed for infor printing for fitting #include #include +#include using namespace LAMMPS_NS; @@ -54,9 +56,9 @@ init_style (done) initialization specific to this pair style write_restart write i,j pair coeffs to restart file read_restart read i,j pair coeffs from restart file -write_restart_settings write global settings to restart file -read_restart_settings read global settings from restart file -single force and energy fo a single pairwise interaction between two atoms +write_restart_settings write global settings to restart file +read_restart_settings read global settings from restart file +single force and energy fo a single pairwise interaction between two atoms */ @@ -67,7 +69,8 @@ PairCHIMES::PairCHIMES(LAMMPS *lmp) : Pair(lmp) int me = comm->me; MPI_Comm_rank(world,&me); - chimes_calculator.init(me); + chimes_calculator.init(me); + for_fitting = false; // 2, 3, and 4-body vars for chimesFF access @@ -110,12 +113,26 @@ PairCHIMES::~PairCHIMES() memory->destroy(setflag); memory->destroy(cutsq); } + + if (badness_stream.is_open()) + badness_stream.close(); } void PairCHIMES::settings(int narg, char **arg) { - if (narg != 0) - error -> all(FLERR,"Illegal pair_style command. Expects no arguments beyond pair_style name."); + if (narg > 1) + error -> all(FLERR,"Illegal pair_style command. Expects no more than one arguments (string: fitting)"); + + if (narg == 1) + { + if (utils::strmatch(arg[0],"fitting")) + { + for_fitting = true; + stringstream ss; + ss << chimes_calculator.rank; + badness_stream.open("rank-" + ss.str() + ".badness.log"); + } + } return; } @@ -132,6 +149,7 @@ void PairCHIMES::coeff(int narg, char **arg) chimes_calculator.read_parameters(chimesFF_paramfile); set_chimes_type(); + //chimes_calculator.set_atomtypes(chimes_type); chimes_calculator.build_pair_int_trip_map() ; chimes_calculator.build_pair_int_quad_map() ; @@ -238,11 +256,11 @@ void PairCHIMES::build_mb_neighlists() neighborlist_3mers.clear(); neighborlist_4mers.clear(); - int i,j,k,l,inum,jnum,knum,lnum, ii, jj, kk, ll; // Local iterator vars - int *ilist,*jlist,*klist,*llist, *numneigh,**firstneigh; // Local neighborlist vars - tagint *tag = atom -> tag; // Access to global atom indices - int itag, jtag, ktag, ltag; // holds tags - double **x = atom -> x; // Access to system coordinates + int i,j,k,l,inum,jnum,knum,lnum, ii, jj, kk, ll; // Local iterator vars + int *ilist,*jlist,*klist,*llist, *numneigh,**firstneigh; // Local neighborlist vars + tagint *tag = atom -> tag; // Access to global atom indices + int itag, jtag, ktag, ltag; // holds tags + double **x = atom -> x; // Access to system coordinates double maxcut_3b_padded = maxcut_3b + neighbor-> skin; double maxcut_4b_padded = maxcut_4b + neighbor-> skin; @@ -253,12 +271,12 @@ void PairCHIMES::build_mb_neighlists() // Access to neighbor list vars //////////////////////////////////////// - inum = list -> inum; // length of the list - ilist = list -> ilist; // list of i atoms for which neighbor list exists - numneigh = list -> numneigh; // length of each of the ilist neighbor lists - firstneigh = list -> firstneigh; // point to the list of neighbors of i + inum = list -> inum; // length of the list + ilist = list -> ilist; // list of i atoms for which neighbor list exists + numneigh = list -> numneigh; // length of each of the ilist neighbor lists + firstneigh = list -> firstneigh; // point to the list of neighbors of i - for (ii = 0; ii < inum; ii++) // Loop over real atoms (ai) + for (ii = 0; ii < inum; ii++) // Loop over real atoms (ai) { i = ilist[ii]; itag = tag[i]; @@ -385,26 +403,26 @@ void PairCHIMES::compute(int eflag, int vflag) // Temp vars to hold chimes output for passing to ev_tally function - std::vector fscalar(6); - std::vector tmp_dist(1); - std::vector tmp_dr(6); - int atmidxlst[6][2]; + std::vector fscalar(6); + std::vector tmp_dist(1); + std::vector tmp_dr(6); + int atmidxlst[6][2]; // General LAMMPS compute vars - int i,j,k,l,inum,jnum, ii, jj; // Local iterator vars + int i,j,k,l,inum,jnum, ii, jj; // Local iterator vars int *ilist,*jlist, *numneigh,**firstneigh; // Local neighborlist vars int idx; - double **x = atom -> x; // Access to system coordinates - double **f = atom -> f; // Access to system forces + double **x = atom -> x; // Access to system coordinates + double **f = atom -> f; // Access to system forces int *type = atom -> type; // Acces to system atom types (countng starts from 1, chimesFF class expects counting from 0!) tagint *tag = atom -> tag; // Access to global atom indices (sort of like "parent" indices) int itag, jtag, ktag, ltag; // holds tags int nlocal = atom -> nlocal; // Number of real atoms owned by current process .. used used to assure force assignments aren't duplicated int newton_pair = force -> newton_pair; // Should f_j be automatically set to -f_i (true) or manually calculated (false) - double energy; // pair energy + double energy; // pair energy int me = comm->me; MPI_Comm_rank(world,&me); @@ -426,10 +444,10 @@ void PairCHIMES::compute(int eflag, int vflag) // Access to (2-body) neighbor list vars //////////////////////////////////////// - inum = list -> inum; // length of the list - ilist = list -> ilist; // list of i atoms for which neighbor list exists - numneigh = list -> numneigh; // length of each of the ilist neighbor lists - firstneigh = list -> firstneigh; // point to the list of neighbors of i + inum = list -> inum; // length of the list + ilist = list -> ilist; // list of i atoms for which neighbor list exists + numneigh = list -> numneigh; // length of each of the ilist neighbor lists + firstneigh = list -> firstneigh; // point to the list of neighbors of i chimes2BTmp chimes_2btmp(chimes_calculator.poly_orders[0]) ; @@ -451,6 +469,10 @@ void PairCHIMES::compute(int eflag, int vflag) std::cout << " ...update complete" << std::endl; } } + + // Prepare the badness variable + + chimes_calculator.reset_badness(); //////////////////////////////////////// // Compute 1- and 2-body interactions @@ -475,7 +497,7 @@ void PairCHIMES::compute(int eflag, int vflag) // Now move on to two-body force, stress, and energy - for (jj = 0; jj < jnum; jj++) // Loop over neighbors of i + for (jj = 0; jj < jnum; jj++) // Loop over neighbors of i { j = jlist[jj]; // Index of the jj atom jtag = tag[j]; // Get j's global atom index (sort of like its "parent") @@ -489,7 +511,7 @@ void PairCHIMES::compute(int eflag, int vflag) dist = get_dist(i,j,&dr[0]); - typ_idxs_2b[0] = chimes_type[type[i]-1]; // Type (index) of the current atom... subtract 1 to account for chimesFF vs LAMMPS numbering convention + typ_idxs_2b[0] = chimes_type[type[i]-1]; // Type (index) of the current atom... subtract 1 to account for chimesFF vs LAMMPS numbering convention typ_idxs_2b[1] = chimes_type[type[j]-1]; // Using std::fill for maximum efficiency. @@ -500,7 +522,7 @@ void PairCHIMES::compute(int eflag, int vflag) energy = 0.0; - chimes_calculator.compute_2B( dist, dr, typ_idxs_2b, force_2b, stensor, energy, chimes_2btmp); + chimes_calculator.compute_2B( dist, dr, typ_idxs_2b, force_2b, stensor, energy, chimes_2btmp); // Auto-updates badness for (idx=0; idx<3; idx++) { @@ -522,6 +544,11 @@ void PairCHIMES::compute(int eflag, int vflag) ev_tally_mb(2, atmidxlst, energy, fscalar, tmp_dist, dr); } } + + // Document badness for configuration: current timestep, current rank, worst badness seen by rank + if (for_fitting) + if(update->ntimestep % output->every_dump[0] == 0) + badness_stream << update->ntimestep << " " << chimes_calculator.get_badness() << endl; if (chimes_calculator.poly_orders[1] > 0) { @@ -644,11 +671,11 @@ void PairCHIMES::set_chimes_type() { int nmatches = 0; - for (int i=1; i<= atom->ntypes; i++) // Lammps indexing starts at 1 + for (int i=1; i<= atom->ntypes; i++) // Lammps indexing starts at 1 { - for (int j=0; jmass[i] - chimes_calculator.masses[j]) < 1e-3) // Masses should match to at least 3 decimal places + if (abs(atom->mass[i] - chimes_calculator.masses[j]) < 1e-3) // Masses should match to at least 3 decimal places { chimes_type.push_back(j); nmatches++; diff --git a/etc/lmp/src/pair_chimes.h b/etc/lmp/src/pair_chimes.h index 942415e..8ce29b0 100644 --- a/etc/lmp/src/pair_chimes.h +++ b/etc/lmp/src/pair_chimes.h @@ -42,9 +42,9 @@ init_style (done) initialization specific to this pair style write_restart write i,j pair coeffs to restart file read_restart read i,j pair coeffs from restart file -write_restart_settings write global settings to restart file -read_restart_settings read global settings from restart file -single force and energy fo a single pairwise interaction between two atoms +write_restart_settings write global settings to restart file +read_restart_settings read global settings from restart file +single force and energy fo a single pairwise interaction between two atoms */ @@ -56,21 +56,25 @@ namespace LAMMPS_NS // Variable definitions - chimesFF chimes_calculator; // chimesFF instance + chimesFF chimes_calculator; // chimesFF instance - char * chimesFF_paramfile; // ChIMES parameter file + char * chimesFF_paramfile; // ChIMES parameter file - std::vector chimes_type; // For i = LMP atom type indx, chimes_type[i-1] gives the ChIMES parameter file type idx + std::vector chimes_type; // For i = LMP atom type indx, chimes_type[i-1] gives the ChIMES parameter file type idx double maxcut_3b; double maxcut_4b; - int n_3mers; // number of neighborlist_Xmers entries + int n_3mers; // number of neighborlist_Xmers entries int n_4mers; std::vector > neighborlist_3mers; // custom neighbor list; neighborlist_Xmers[cluster idx][atom in cluster idx] std::vector > neighborlist_4mers; - + + // Prepare files necessary for ChIMES fitting + + bool for_fitting; + ofstream badness_stream; // 2-body vars for chimesFF access From 181232f9e282a48a7a5d4bcd5450ee9d63ba28c6 Mon Sep 17 00:00:00 2001 From: "Rebecca K. Lindsey" Date: Tue, 25 Jul 2023 10:51:05 -0400 Subject: [PATCH 09/14] Create CODEOWNERS Add a codeowners file --- CODEOWNERS | 1 + 1 file changed, 1 insertion(+) create mode 100644 CODEOWNERS diff --git a/CODEOWNERS b/CODEOWNERS new file mode 100644 index 0000000..6475e33 --- /dev/null +++ b/CODEOWNERS @@ -0,0 +1 @@ +* @RKLindsey From 182f72f474d0162637be862f67de58e376397b21 Mon Sep 17 00:00:00 2001 From: "Rebecca K. Lindsey" Date: Fri, 15 Sep 2023 10:47:49 -0400 Subject: [PATCH 10/14] Fix bug in API c-interface for python and fortran direct interface example --- chimesFF/api/chimescalc_C.cpp | 2 ++ chimesFF/api/chimescalc_py.py | 2 +- chimesFF/examples/fortran/Makefile | 2 +- chimesFF/examples/python/Makefile | 2 +- chimesFF/examples/python/main.py | 4 ++-- 5 files changed, 7 insertions(+), 5 deletions(-) diff --git a/chimesFF/api/chimescalc_C.cpp b/chimesFF/api/chimescalc_C.cpp index 898bed0..b67c66f 100644 --- a/chimesFF/api/chimescalc_C.cpp +++ b/chimesFF/api/chimescalc_C.cpp @@ -71,6 +71,8 @@ void init_chimes (int rank) { void chimes_read_params(char *param_file) { chimes_ptr->read_parameters(param_file); + chimes_ptr->build_pair_int_trip_map(); + chimes_ptr->build_pair_int_quad_map(); } void chimes_compute_2b_props_fromf90(double *rij, double dr[3], char *type1, char *type2, double force[2][3], double stress[9], double *epot) diff --git a/chimesFF/api/chimescalc_py.py b/chimesFF/api/chimescalc_py.py index 647dccc..02eb0a9 100644 --- a/chimesFF/api/chimescalc_py.py +++ b/chimesFF/api/chimescalc_py.py @@ -129,7 +129,7 @@ def chimes_compute_3b_props(dr_3b, dist_3b, atype3b, force, stress, epot): in_dr = (ctypes.c_double * 3)(dr_3b[0], dr_3b[1], dr_3b[2]) in_dist = ((ctypes.c_double * 3) * 3)((dist_3b[0][0], dist_3b[0][1], dist_3b[0][2]), (dist_3b[1][0], dist_3b[1][1], dist_3b[1][2]), - (dist_3b[2][0], dist_3b[2][1], dist_3b[2][2])) + (dist_3b[2][0], dist_3b[2][1], dist_3b[2][2])) in_atype = (ctypes.c_char_p * 3)(atype3b[0].encode(), atype3b[1].encode(), atype3b[2].encode()) in_force = ((ctypes.c_double * 3) * 3) ((force[0][0], force[0][1], force[0][2]), (force[1][0], force[1][1], force[1][2]), diff --git a/chimesFF/examples/fortran/Makefile b/chimesFF/examples/fortran/Makefile index 2cbed01..8155c87 100644 --- a/chimesFF/examples/fortran/Makefile +++ b/chimesFF/examples/fortran/Makefile @@ -16,7 +16,7 @@ chimescalc_C.o : $(CC_WRAPPER_SRC) $(CC_WRAPPER_HDR) $(CHIMESFF_SRC) $(CHIMESFF FCC = gfortran -O3 -fPIC -std=f2003 -FCC_WRAPPER_SRC=$(FCC_LOC)/../../api/chimescalc_F.F90 +FCC_WRAPPER_SRC=$(FCC_LOC)/../../api/chimescalc_f.F90 chimescalc_F.o chimescalc.mod : $(FCC_WRAPPER_SRC) $(FCC) -c $(FCC_WRAPPER_SRC) -o chimescalc_F.o diff --git a/chimesFF/examples/python/Makefile b/chimesFF/examples/python/Makefile index 865ef2a..a86ea76 100644 --- a/chimesFF/examples/python/Makefile +++ b/chimesFF/examples/python/Makefile @@ -1,6 +1,6 @@ CC_LOC = $(realpath .) -CXX=g++ -O3 -std=c++11 -fPIC +CXX=g++ -g -std=c++11 -fPIC CHIMESFF_SRC=$(CC_LOC)/../../src/chimesFF.cpp CHIMESFF_HDR=$(CC_LOC)/../../src/chimesFF.h diff --git a/chimesFF/examples/python/main.py b/chimesFF/examples/python/main.py index 8ad66b5..f092fb4 100644 --- a/chimesFF/examples/python/main.py +++ b/chimesFF/examples/python/main.py @@ -47,7 +47,7 @@ def get_dist(lx,ly,lz,xrd,ycrd,zcrd,i,j): # Initialize the ChIMES calculator -chimescalc_py.chimes_wrapper = chimescalc_py.init_chimes_wrapper("libchimescalc-direct_dl.so") +chimescalc_py.chimes_wrapper = chimescalc_py.init_chimes_wrapper(os.getcwd() + "/libchimescalc-direct_dl.so") chimescalc_py.set_chimes() chimescalc_py.init_chimes() @@ -66,7 +66,7 @@ def get_dist(lx,ly,lz,xrd,ycrd,zcrd,i,j): # Read the parameters -wrapper_py.read_params(param_file) +chimescalc_py.read_params(param_file) # Read the coordinates, set up the force, stress, and energy vars From 23e0428960646118d5540b334ab791fa72bf9c80 Mon Sep 17 00:00:00 2001 From: "Rebecca K. Lindsey" Date: Fri, 15 Sep 2023 10:50:47 -0400 Subject: [PATCH 11/14] Fix compiler flag in direct interface example Makefile --- chimesFF/examples/python/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chimesFF/examples/python/Makefile b/chimesFF/examples/python/Makefile index a86ea76..865ef2a 100644 --- a/chimesFF/examples/python/Makefile +++ b/chimesFF/examples/python/Makefile @@ -1,6 +1,6 @@ CC_LOC = $(realpath .) -CXX=g++ -g -std=c++11 -fPIC +CXX=g++ -O3 -std=c++11 -fPIC CHIMESFF_SRC=$(CC_LOC)/../../src/chimesFF.cpp CHIMESFF_HDR=$(CC_LOC)/../../src/chimesFF.h From c308100b173dd50024c06aca9b0edaae080b9cd1 Mon Sep 17 00:00:00 2001 From: "Rebecca K. Lindsey" Date: Tue, 19 Dec 2023 14:04:19 -0500 Subject: [PATCH 12/14] Fix segfault issue when running 3B scans. --- util/pes_generator/src/pes_generator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/util/pes_generator/src/pes_generator.py b/util/pes_generator/src/pes_generator.py index 11298b9..a00191e 100644 --- a/util/pes_generator/src/pes_generator.py +++ b/util/pes_generator/src/pes_generator.py @@ -179,7 +179,7 @@ energy = 0.0 dummy_force = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] # Need to re-declare because compute_2b changes its dimension - + dummy_stress = [0.0]*9 # Get/write the 3-body only energy dummy_force, dummy_stress, energy = chimescalc_py.chimes_compute_3b_props([steps[j], steps[k], steps[l]], dummy_rij, trip_types[config.TRIPTYPES[i]], dummy_force, dummy_stress, energy) From b6bd115f046f1aa60b63120c690bed9793fa3eb6 Mon Sep 17 00:00:00 2001 From: Becky Lindsey Date: Thu, 14 Mar 2024 09:47:54 -0400 Subject: [PATCH 13/14] Add new transferable ChIMES Carbon model to the forcefields database --- ...ished_params.Carbon-2.0.2+3+4b.Tersoff.txt | 4406 +++++++++++++++++ 1 file changed, 4406 insertions(+) create mode 100644 serial_interface/tests/force_fields/published_params.Carbon-2.0.2+3+4b.Tersoff.txt diff --git a/serial_interface/tests/force_fields/published_params.Carbon-2.0.2+3+4b.Tersoff.txt b/serial_interface/tests/force_fields/published_params.Carbon-2.0.2+3+4b.Tersoff.txt new file mode 100644 index 0000000..155cb83 --- /dev/null +++ b/serial_interface/tests/force_fields/published_params.Carbon-2.0.2+3+4b.Tersoff.txt @@ -0,0 +1,4406 @@ +! Date 2022-03-19 +! +! Number of variables = 487 +! Number of equations = 738360 +! DLARS code for LASSO used +! DLARS alpha = 1e-08 +! DLARS run: srun -N 8 -n 288 /usr/workspace/wsb/rlindsey/ChIMES4B_SVN/contrib/dlars/src/dlars A.txt b_comb.txt dim.txt --lambda=1e-08 --split_files --algorithm=lasso --weights=weights_comb.dat --normalize=y >& dlars.log + +! RMS force error = 17.41677535898432 +! max abs variable = 789.5168841123 +! number of fitting vars = 442 +! Bayesian Information Criterion = 4225602.0909959385 +! Using weighting file: weights_comb.dat +! +USECOUL: false +FITCOUL: false +USEPOVR: false +FITPOVR: false +USE3BCH: true +USE4BCH: true + +PAIRTYP: CHEBYSHEV 20 10 4 -1 1 + +ATOM TYPES: 1 + +# TYPEIDX # # ATM_TYP # # ATMCHRG # # ATMMASS # +0 C 0 12.0107 + +ATOM PAIRS: 1 + +# PAIRIDX # # ATM_TY1 # # ATM_TY1 # # S_MINIM # # S_MAXIM # # S_DELTA # # CHBDIST # # MORSE_LAMBDA # + 0 C C 0.98 5 0.01 MORSE 1.4 + +FCUT TYPE: TERSOFF 0.75 + +PAIR CHEBYSHEV PENALTY DIST: 0.02 +PAIR CHEBYSHEV PENALTY SCALING: 1000000.0 + +SPECIAL 3B S_MAXIM: SPECIFIC 1 +CCCCCC CC CC CC 5.00000 5.00000 5.00000 + +SPECIAL 4B S_MAXIM: SPECIFIC 1 +CCCCCCCCCCCC CC CC CC CC CC CC 4.50000 4.50000 4.50000 4.50000 4.50000 4.50000 + +ATOM PAIR TRIPLETS: 1 +ATOM PAIR QUADRUPLETS: 1 + +PAIR CHEBYSHEV PARAMS + +PAIRTYPE PARAMS: 0 C C + +0 18.06120982028 +1 99.05105244336 +2 72.1930417299 +3 51.48054486314 +4 6.703334925405 +5 21.81189661565 +6 -2.507206422225 +7 5.209416674269 +8 -5.811009572203 +9 1.647752755915 +10 -2.147463628617 +11 0.8427406145092 +12 -1.141994384703 +13 0.6222265623148 +14 -0.3869991659402 +15 0.5729050379445 +16 -0.09460028548091 +17 0.330751694701 +18 -0.003950693431877 +19 0.1228237283798 + +TRIPLET CHEBYSHEV PARAMS + +TRIPLETTYPE PARAMS: + INDEX: 0 ATOMS: C C C +PAIRS: CC CC CC UNIQUE: -1 TOTAL: 878 + index | powers | equiv index | param index | parameter + ---------------------------------------------------------------------------- +0 0 1 2 3 1 -24.06469270294 +1 1 0 2 3 1 -24.06469270294 +2 0 2 1 3 1 -24.06469270294 +3 2 0 1 3 1 -24.06469270294 +4 1 2 0 3 1 -24.06469270294 +5 2 1 0 3 1 -24.06469270294 +6 0 1 3 9 2 -11.70401175682 +7 1 0 3 9 2 -11.70401175682 +8 0 3 1 9 2 -11.70401175682 +9 3 0 1 9 2 -11.70401175682 +10 1 3 0 9 2 -11.70401175682 +11 3 1 0 9 2 -11.70401175682 +12 0 1 4 15 3 -27.23303539011 +13 1 0 4 15 3 -27.23303539011 +14 0 4 1 15 3 -27.23303539011 +15 4 0 1 15 3 -27.23303539011 +16 1 4 0 15 3 -27.23303539011 +17 4 1 0 15 3 -27.23303539011 +18 0 1 5 21 4 7.325940089909 +19 1 0 5 21 4 7.325940089909 +20 0 5 1 21 4 7.325940089909 +21 5 0 1 21 4 7.325940089909 +22 1 5 0 21 4 7.325940089909 +23 5 1 0 21 4 7.325940089909 +24 0 1 6 27 5 -22.07733313362 +25 1 0 6 27 5 -22.07733313362 +26 0 6 1 27 5 -22.07733313362 +27 6 0 1 27 5 -22.07733313362 +28 1 6 0 27 5 -22.07733313362 +29 6 1 0 27 5 -22.07733313362 +30 0 1 7 33 6 4.864361328404 +31 1 0 7 33 6 4.864361328404 +32 0 7 1 33 6 4.864361328404 +33 7 0 1 33 6 4.864361328404 +34 1 7 0 33 6 4.864361328404 +35 7 1 0 33 6 4.864361328404 +36 0 1 8 39 7 -3.19411940493 +37 1 0 8 39 7 -3.19411940493 +38 0 8 1 39 7 -3.19411940493 +39 8 0 1 39 7 -3.19411940493 +40 1 8 0 39 7 -3.19411940493 +41 8 1 0 39 7 -3.19411940493 +42 0 1 9 45 8 -1.976403161238 +43 1 0 9 45 8 -1.976403161238 +44 0 9 1 45 8 -1.976403161238 +45 9 0 1 45 8 -1.976403161238 +46 1 9 0 45 8 -1.976403161238 +47 9 1 0 45 8 -1.976403161238 +48 0 2 2 51 9 45.78141778625 +49 2 0 2 51 9 45.78141778625 +50 2 2 0 51 9 45.78141778625 +51 0 2 3 54 10 5.503636734724 +52 2 0 3 54 10 5.503636734724 +53 0 3 2 54 10 5.503636734724 +54 3 0 2 54 10 5.503636734724 +55 2 3 0 54 10 5.503636734724 +56 3 2 0 54 10 5.503636734724 +57 0 2 4 60 11 -9.511545588219 +58 2 0 4 60 11 -9.511545588219 +59 0 4 2 60 11 -9.511545588219 +60 4 0 2 60 11 -9.511545588219 +61 2 4 0 60 11 -9.511545588219 +62 4 2 0 60 11 -9.511545588219 +63 0 2 5 66 12 -33.2306271159 +64 2 0 5 66 12 -33.2306271159 +65 0 5 2 66 12 -33.2306271159 +66 5 0 2 66 12 -33.2306271159 +67 2 5 0 66 12 -33.2306271159 +68 5 2 0 66 12 -33.2306271159 +69 0 2 6 72 13 2.485100501678 +70 2 0 6 72 13 2.485100501678 +71 0 6 2 72 13 2.485100501678 +72 6 0 2 72 13 2.485100501678 +73 2 6 0 72 13 2.485100501678 +74 6 2 0 72 13 2.485100501678 +75 0 2 7 78 14 -7.217334784339 +76 2 0 7 78 14 -7.217334784339 +77 0 7 2 78 14 -7.217334784339 +78 7 0 2 78 14 -7.217334784339 +79 2 7 0 78 14 -7.217334784339 +80 7 2 0 78 14 -7.217334784339 +81 0 2 8 84 15 4.669341279371 +82 2 0 8 84 15 4.669341279371 +83 0 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22.52279912158 +3410 3 3 2 3 2 3 3839 252 22.52279912158 +3411 3 2 3 3 3 2 3839 252 22.52279912158 +3412 3 3 2 3 3 2 3839 252 22.52279912158 +3413 3 3 3 2 2 3 3839 252 22.52279912158 +3414 3 3 3 2 3 2 3839 252 22.52279912158 +3415 3 3 3 3 2 2 3839 252 22.52279912158 +3416 2 3 3 3 3 2 3851 253 -37.60355950156 +3417 3 2 3 3 2 3 3851 253 -37.60355950156 +3418 3 3 2 2 3 3 3851 253 -37.60355950156 +3419 2 3 3 3 3 3 3854 254 15.95692440215 +3420 3 2 3 3 3 3 3854 254 15.95692440215 +3421 3 3 2 3 3 3 3854 254 15.95692440215 +3422 3 3 3 2 3 3 3854 254 15.95692440215 +3423 3 3 3 3 2 3 3854 254 15.95692440215 +3424 3 3 3 3 3 2 3854 254 15.95692440215 +3425 3 3 3 3 3 3 3860 255 22.36571720202 + + +PAIRMAPS: 1 +0 CC + +TRIPMAPS: 1 +0 CCCCCC + +QUADMAPS: 1 +0 CCCCCCCCCCCC + +NO ENERGY OFFSETS: 1 +ENERGY OFFSET 1 -61.53443323069 +ENDFILE + From 35e897c8480d11147d51c2c5cc37e1fe195de69c Mon Sep 17 00:00:00 2001 From: "Rebecca K. Lindsey" Date: Thu, 14 Mar 2024 10:54:39 -0400 Subject: [PATCH 14/14] Update CODEOWNERS Update codeowners to prevent conflicts --- CODEOWNERS | 1 + 1 file changed, 1 insertion(+) diff --git a/CODEOWNERS b/CODEOWNERS index 6475e33..9aa7723 100644 --- a/CODEOWNERS +++ b/CODEOWNERS @@ -1 +1,2 @@ * @RKLindsey +* @rk-lindsey