diff --git a/chimesFF/api/chimescalc_C.cpp b/chimesFF/api/chimescalc_C.cpp index 540d051..898bed0 100644 --- a/chimesFF/api/chimescalc_C.cpp +++ b/chimesFF/api/chimescalc_C.cpp @@ -105,6 +105,9 @@ void chimes_compute_2b_props(double rij, double dr[3], char *atype2b[2], double // convert all doubles, etc., from C to type vector for C++ // declare needed vectors for chimes vector dr_vec(3); + + chimes2BTmp chimes_tmp(chimes_ptr->poly_orders[0]) ; + dr_vec[0] = dr[0]; dr_vec[1] = dr[1]; dr_vec[2] = dr[2]; @@ -124,41 +127,29 @@ void chimes_compute_2b_props(double rij, double dr[3], char *atype2b[2], double } //type_vec[0] = chimes_ptr->atmtoidx[atype2b[0]]; //type_vec[1] = chimes_ptr->atmtoidx[atype2b[1]]; - vector >force_vec; - force_vec.resize(2,vector(3)); - force_vec[0][0] = &force[0][0]; - force_vec[0][1] = &force[0][1]; - force_vec[0][2] = &force[0][2]; - force_vec[1][0] = &force[1][0]; - force_vec[1][1] = &force[1][1]; - force_vec[1][2] = &force[1][2]; - vector stress_vec(9); - stress_vec[0] = &stress[0]; - stress_vec[1] = &stress[1]; - stress_vec[2] = &stress[2]; - stress_vec[3] = &stress[3]; - stress_vec[4] = &stress[4]; - stress_vec[5] = &stress[5]; - stress_vec[6] = &stress[6]; - stress_vec[7] = &stress[7]; - stress_vec[8] = &stress[8]; - chimes_ptr->compute_2B(rij, dr_vec, type_vec, force_vec, stress_vec, *epot); + vector force_vec(2*CHDIM,0.0) ;; + vector stress_vec(9,0.0); + + chimes_ptr->compute_2B(rij, dr_vec, type_vec, force_vec, stress_vec, *epot, chimes_tmp); + + // save forces and stress tensor components - force[0][0] = *force_vec[0][0]; - force[0][1] = *force_vec[0][1]; - force[0][2] = *force_vec[0][2]; - force[1][0] = *force_vec[1][0]; - force[1][1] = *force_vec[1][1]; - force[1][2] = *force_vec[1][2]; - stress[0] = *stress_vec[0]; - stress[1] = *stress_vec[1]; - stress[2] = *stress_vec[2]; - stress[3] = *stress_vec[3]; - stress[4] = *stress_vec[4]; - stress[5] = *stress_vec[5]; - stress[6] = *stress_vec[6]; - stress[7] = *stress_vec[7]; - stress[8] = *stress_vec[8]; + force[0][0] += force_vec[0*CHDIM+0]; + force[0][1] += force_vec[0*CHDIM+1]; + force[0][2] += force_vec[0*CHDIM+2]; + force[1][0] += force_vec[1*CHDIM+0]; + force[1][1] += force_vec[1*CHDIM+1]; + force[1][2] += force_vec[1*CHDIM+2]; + + stress[0] += stress_vec[0]; + stress[1] += stress_vec[1]; + stress[2] += stress_vec[2]; + stress[3] += stress_vec[3]; + stress[4] += stress_vec[4]; + stress[5] += stress_vec[5]; + stress[6] += stress_vec[6]; + stress[7] += stress_vec[7]; + stress[8] += stress_vec[8]; } void chimes_compute_3b_props(double dr_3b[3], double dist_3b[3][3], char *atype3b[3], double f3b[3][3], double stress[9], double *epot) { @@ -167,20 +158,24 @@ void chimes_compute_3b_props(double dr_3b[3], double dist_3b[3][3], char *atype3 dr_3b_vec[0] = dr_3b[0]; dr_3b_vec[1] = dr_3b[1]; dr_3b_vec[2] = dr_3b[2]; - vector< vector > dist_3b_vec(3, vector (3)); - dist_3b_vec[0][0] = dist_3b[0][0]; - dist_3b_vec[0][1] = dist_3b[0][1]; - dist_3b_vec[0][2] = dist_3b[0][2]; - dist_3b_vec[1][0] = dist_3b[1][0]; - dist_3b_vec[1][1] = dist_3b[1][1]; - dist_3b_vec[1][2] = dist_3b[1][2]; - dist_3b_vec[2][0] = dist_3b[2][0]; - dist_3b_vec[2][1] = dist_3b[2][1]; - dist_3b_vec[2][2] = dist_3b[2][2]; + + vector dist_3b_vec(CHDIM*3) ; + + dist_3b_vec[0*CHDIM+0] = dist_3b[0][0]; + dist_3b_vec[0*CHDIM+1] = dist_3b[0][1]; + dist_3b_vec[0*CHDIM+2] = dist_3b[0][2]; + dist_3b_vec[1*CHDIM+0] = dist_3b[1][0]; + dist_3b_vec[1*CHDIM+1] = dist_3b[1][1]; + dist_3b_vec[1*CHDIM+2] = dist_3b[1][2]; + dist_3b_vec[2*CHDIM+0] = dist_3b[2][0]; + dist_3b_vec[2*CHDIM+1] = dist_3b[2][1]; + dist_3b_vec[2*CHDIM+2] = dist_3b[2][2]; + vector type_3b_vec(3); type_3b_vec[0] = distance(chimes_ptr->atmtyps.begin(),find(chimes_ptr->atmtyps.begin(), chimes_ptr->atmtyps.end(), atype3b[0])); type_3b_vec[1] = distance(chimes_ptr->atmtyps.begin(),find(chimes_ptr->atmtyps.begin(), chimes_ptr->atmtyps.end(), atype3b[1])); type_3b_vec[2] = distance(chimes_ptr->atmtyps.begin(),find(chimes_ptr->atmtyps.begin(), chimes_ptr->atmtyps.end(), atype3b[2])); + for(int i=0; i<3; i++) { if (type_3b_vec[i] >= chimes_ptr->atmtyps.size()) @@ -192,50 +187,38 @@ void chimes_compute_3b_props(double dr_3b[3], double dist_3b[3][3], char *atype3 //type_3b_vec[0] = chimes_ptr->atmtoidx[atype3b[0]]; //type_3b_vec[1] = chimes_ptr->atmtoidx[atype3b[1]]; //type_3b_vec[2] = chimes_ptr->atmtoidx[atype3b[2]]; - vector >force_3b_vec; - force_3b_vec.resize(3,vector(3)); - force_3b_vec[0][0] = &f3b[0][0]; - force_3b_vec[0][1] = &f3b[0][1]; - force_3b_vec[0][2] = &f3b[0][2]; - force_3b_vec[1][0] = &f3b[1][0]; - force_3b_vec[1][1] = &f3b[1][1]; - force_3b_vec[1][2] = &f3b[1][2]; - force_3b_vec[2][0] = &f3b[2][0]; - force_3b_vec[2][1] = &f3b[2][1]; - force_3b_vec[2][2] = &f3b[2][2]; - vector stress_vec(9); - stress_vec[0] = &stress[0]; - stress_vec[1] = &stress[1]; - stress_vec[2] = &stress[2]; - stress_vec[3] = &stress[3]; - stress_vec[4] = &stress[4]; - stress_vec[5] = &stress[5]; - stress_vec[6] = &stress[6]; - stress_vec[7] = &stress[7]; - stress_vec[8] = &stress[8]; - chimes_ptr->compute_3B(dr_3b_vec, dist_3b_vec, type_3b_vec, force_3b_vec, stress_vec, *epot); + vector force_3b_vec(3*CHDIM, 0.0) ; + vector stress_vec(9,0.0); + chimes3BTmp chimes_tmp(chimes_ptr->poly_orders[1]) ; + + chimes_ptr->compute_3B(dr_3b_vec, dist_3b_vec, type_3b_vec, force_3b_vec, stress_vec, *epot, + chimes_tmp) ; + // save forces and stress tensor components - f3b[0][0] = *force_3b_vec[0][0]; - f3b[0][1] = *force_3b_vec[0][1]; - f3b[0][2] = *force_3b_vec[0][2]; - f3b[1][0] = *force_3b_vec[1][0]; - f3b[1][1] = *force_3b_vec[1][1]; - f3b[1][2] = *force_3b_vec[1][2]; - f3b[2][0] = *force_3b_vec[2][0]; - f3b[2][1] = *force_3b_vec[2][1]; - f3b[2][2] = *force_3b_vec[2][2]; - stress[0] = *stress_vec[0]; - stress[1] = *stress_vec[1]; - stress[2] = *stress_vec[2]; - stress[3] = *stress_vec[3]; - stress[4] = *stress_vec[4]; - stress[5] = *stress_vec[5]; - stress[6] = *stress_vec[6]; - stress[7] = *stress_vec[7]; - stress[8] = *stress_vec[8]; + + f3b[0][0] += force_3b_vec[0*CHDIM+0]; + f3b[0][1] += force_3b_vec[0*CHDIM+1]; + f3b[0][2] += force_3b_vec[0*CHDIM+2]; + f3b[1][0] += force_3b_vec[1*CHDIM+0]; + f3b[1][1] += force_3b_vec[1*CHDIM+1]; + f3b[1][2] += force_3b_vec[1*CHDIM+2]; + f3b[2][0] += force_3b_vec[2*CHDIM+0]; + f3b[2][1] += force_3b_vec[2*CHDIM+1]; + f3b[2][2] += force_3b_vec[2*CHDIM+2]; + + stress[0] += stress_vec[0]; + stress[1] += stress_vec[1]; + stress[2] += stress_vec[2]; + stress[3] += stress_vec[3]; + stress[4] += stress_vec[4]; + stress[5] += stress_vec[5]; + stress[6] += stress_vec[6]; + stress[7] += stress_vec[7]; + stress[8] += stress_vec[8]; } -void chimes_compute_4b_props(double dr_4b[6], double dist_4b[6][3], char *atype4b[4], double f4b[4][3], double stress[9], double *epot) { +void chimes_compute_4b_props(double dr_4b[6], double dist_4b[6][3], char *atype4b[4], double f4b[4][3], double stress[9], double *epot) +{ // convert all doubles, etc., from C to type vector for C++ vector dr_4b_vec(6); dr_4b_vec[0] = dr_4b[0]; @@ -244,25 +227,28 @@ void chimes_compute_4b_props(double dr_4b[6], double dist_4b[6][3], char *atype4 dr_4b_vec[3] = dr_4b[3]; dr_4b_vec[4] = dr_4b[4]; dr_4b_vec[5] = dr_4b[5]; - vector< vector > dist_4b_vec(6, vector (3)); - dist_4b_vec[0][0] = dist_4b[0][0]; - dist_4b_vec[0][1] = dist_4b[0][1]; - dist_4b_vec[0][2] = dist_4b[0][2]; - dist_4b_vec[1][0] = dist_4b[1][0]; - dist_4b_vec[1][1] = dist_4b[1][1]; - dist_4b_vec[1][2] = dist_4b[1][2]; - dist_4b_vec[2][0] = dist_4b[2][0]; - dist_4b_vec[2][1] = dist_4b[2][1]; - dist_4b_vec[2][2] = dist_4b[2][2]; - dist_4b_vec[3][0] = dist_4b[3][0]; - dist_4b_vec[3][1] = dist_4b[3][1]; - dist_4b_vec[3][2] = dist_4b[3][2]; - dist_4b_vec[4][0] = dist_4b[4][0]; - dist_4b_vec[4][1] = dist_4b[4][1]; - dist_4b_vec[4][2] = dist_4b[4][2]; - dist_4b_vec[5][0] = dist_4b[5][0]; - dist_4b_vec[5][1] = dist_4b[5][1]; - dist_4b_vec[5][2] = dist_4b[5][2]; + + vector dist_4b_vec(6*CHDIM); + + dist_4b_vec[0*CHDIM+0] = dist_4b[0][0]; + dist_4b_vec[0*CHDIM+1] = dist_4b[0][1]; + dist_4b_vec[0*CHDIM+2] = dist_4b[0][2]; + dist_4b_vec[1*CHDIM+0] = dist_4b[1][0]; + dist_4b_vec[1*CHDIM+1] = dist_4b[1][1]; + dist_4b_vec[1*CHDIM+2] = dist_4b[1][2]; + dist_4b_vec[2*CHDIM+0] = dist_4b[2][0]; + dist_4b_vec[2*CHDIM+1] = dist_4b[2][1]; + dist_4b_vec[2*CHDIM+2] = dist_4b[2][2]; + dist_4b_vec[3*CHDIM+0] = dist_4b[3][0]; + dist_4b_vec[3*CHDIM+1] = dist_4b[3][1]; + dist_4b_vec[3*CHDIM+2] = dist_4b[3][2]; + dist_4b_vec[4*CHDIM+0] = dist_4b[4][0]; + dist_4b_vec[4*CHDIM+1] = dist_4b[4][1]; + dist_4b_vec[4*CHDIM+2] = dist_4b[4][2]; + dist_4b_vec[5*CHDIM+0] = dist_4b[5][0]; + dist_4b_vec[5*CHDIM+1] = dist_4b[5][1]; + dist_4b_vec[5*CHDIM+2] = dist_4b[5][2]; + vector type_4b_vec(4); type_4b_vec[0] = distance(chimes_ptr->atmtyps.begin(),find(chimes_ptr->atmtyps.begin(), chimes_ptr->atmtyps.end(), atype4b[0])); type_4b_vec[1] = distance(chimes_ptr->atmtyps.begin(),find(chimes_ptr->atmtyps.begin(), chimes_ptr->atmtyps.end(), atype4b[1])); @@ -280,51 +266,41 @@ void chimes_compute_4b_props(double dr_4b[6], double dist_4b[6][3], char *atype4 //type_4b_vec[1] = chimes_ptr->atmtoidx[atype4b[1]]; //type_4b_vec[2] = chimes_ptr->atmtoidx[atype4b[2]]; //type_4b_vec[3] = chimes_ptr->atmtoidx[atype4b[3]]; - vector >force_4b_vec; - force_4b_vec.resize(4,vector(3)); - force_4b_vec[0][0] = &f4b[0][0]; - force_4b_vec[0][1] = &f4b[0][1]; - force_4b_vec[0][2] = &f4b[0][2]; - force_4b_vec[1][0] = &f4b[1][0]; - force_4b_vec[1][1] = &f4b[1][1]; - force_4b_vec[1][2] = &f4b[1][2]; - force_4b_vec[2][0] = &f4b[2][0]; - force_4b_vec[2][1] = &f4b[2][1]; - force_4b_vec[2][2] = &f4b[2][2]; - force_4b_vec[3][0] = &f4b[3][0]; - force_4b_vec[3][1] = &f4b[3][1]; - force_4b_vec[3][2] = &f4b[3][2]; - vector stress_vec(9); - stress_vec[0] = &stress[0]; - stress_vec[1] = &stress[1]; - stress_vec[2] = &stress[2]; - stress_vec[3] = &stress[3]; - stress_vec[4] = &stress[4]; - stress_vec[5] = &stress[5]; - stress_vec[6] = &stress[6]; - stress_vec[7] = &stress[7]; - stress_vec[8] = &stress[8]; - chimes_ptr->compute_4B(dr_4b_vec, dist_4b_vec, type_4b_vec, force_4b_vec, stress_vec, *epot); + + vector force_4b(4*CHDIM,0.0) ; + + // No auto-conversion from double[9] to vector. + vector stress_vec(9) ; + + for ( int j = 0 ; j < 9 ; j++ ) { + stress_vec[j] = stress[j] ; + } + + chimes4BTmp chimes_tmp(chimes_ptr->poly_orders[2]) ; + + chimes_ptr->compute_4B(dr_4b_vec, dist_4b_vec, type_4b_vec, force_4b, stress_vec, *epot, chimes_tmp); // save forces and stress tensor components - f4b[0][0] = *force_4b_vec[0][0]; - f4b[0][1] = *force_4b_vec[0][1]; - f4b[0][2] = *force_4b_vec[0][2]; - f4b[1][0] = *force_4b_vec[1][0]; - f4b[1][1] = *force_4b_vec[1][1]; - f4b[1][2] = *force_4b_vec[1][2]; - f4b[2][0] = *force_4b_vec[2][0]; - f4b[2][1] = *force_4b_vec[2][1]; - f4b[2][2] = *force_4b_vec[2][2]; - f4b[3][0] = *force_4b_vec[3][0]; - f4b[3][1] = *force_4b_vec[3][1]; - f4b[3][2] = *force_4b_vec[3][2]; - stress[0] = *stress_vec[0]; - stress[1] = *stress_vec[1]; - stress[2] = *stress_vec[2]; - stress[3] = *stress_vec[3]; - stress[4] = *stress_vec[4]; - stress[5] = *stress_vec[5]; - stress[6] = *stress_vec[6]; - stress[7] = *stress_vec[7]; - stress[8] = *stress_vec[8]; + + f4b[0][0] += force_4b[0*CHDIM+0]; + f4b[0][1] += force_4b[0*CHDIM+1]; + f4b[0][2] += force_4b[0*CHDIM+2]; + f4b[1][0] += force_4b[1*CHDIM+0]; + f4b[1][1] += force_4b[1*CHDIM+1]; + f4b[1][2] += force_4b[1*CHDIM+2]; + f4b[2][0] += force_4b[2*CHDIM+0]; + f4b[2][1] += force_4b[2*CHDIM+1]; + f4b[2][2] += force_4b[2*CHDIM+2]; + f4b[3][0] += force_4b[3*CHDIM+0]; + f4b[3][1] += force_4b[3*CHDIM+1]; + f4b[3][2] += force_4b[3*CHDIM+2]; + + stress[0] = stress_vec[0]; + stress[1] = stress_vec[1]; + stress[2] = stress_vec[2]; + stress[3] = stress_vec[3]; + stress[4] = stress_vec[4]; + stress[5] = stress_vec[5]; + stress[6] = stress_vec[6]; + stress[7] = stress_vec[7]; + stress[8] = stress_vec[8]; } diff --git a/chimesFF/examples/c/Makefile b/chimesFF/examples/c/Makefile index d6573d8..02ac753 100644 --- a/chimesFF/examples/c/Makefile +++ b/chimesFF/examples/c/Makefile @@ -1,34 +1,34 @@ CC_LOC = $(realpath .) -CXX=g++ -O3 -std=c++11 +CXX=g++ -O3 -std=c++11 CHIMESFF_SRC=$(CC_LOC)/../../src/chimesFF.cpp CHIMESFF_HDR=$(CC_LOC)/../../src/chimesFF.h chimesFF.o : $(CHIMESFF_SRC) $(CXX) -c $(CHIMESFF_SRC) - + WRAPPER_SRC=$(CC_LOC)/../../api/chimescalc_C.cpp WRAPPER_HDR=$(CC_LOC)/../../api/chimescalc_C.h - + chimescalc_C.o : $(WRAPPER_SRC) $(WRAPPER_HDR) $(CHIMESFF_SRC) $(CHIMESFF_HDR) $(CXX) -c $(WRAPPER_SRC) $(CHIMESFF_SRC) -I $(CC_LOC)/../../api/ -I $(CC_LOC)/../../src/ - + CC = gcc test_wrapper-C.o : main.c $(WRAPPER_SRC) $(WRAPPER_HDR) - $(CC) -c main.c -o test_wrapper-C.o -I $(CC_LOC)/../../api/ + $(CC) -c main.c -o test_wrapper-C.o -I $(CC_LOC)/../../api/ LINKS = chimesFF.o test_wrapper-C.o chimescalc_C.o - -test_wrapper-C : $(LINKS) - $(CXX) $(LINKS) -o chimescalc-test_direct-C - + +test_wrapper-C : $(LINKS) + $(CXX) $(LINKS) -o C_wrapper-direct_interface + clean: - rm -f *.o - + rm -f *.o + clean-all: - rm -f *.o + rm -f *.o rm -f chimescalc-test_direct-C all: diff --git a/chimesFF/examples/fortran/Makefile b/chimesFF/examples/fortran/Makefile index c27ec1a..2cbed01 100644 --- a/chimesFF/examples/fortran/Makefile +++ b/chimesFF/examples/fortran/Makefile @@ -7,20 +7,20 @@ CHIMESFF_HDR=$(FCC_LOC)/../../src/chimesFF.h chimesFF.o : $(CHIMESFF_SRC) $(CXX) -c $(CHIMESFF_SRC) - + CC_WRAPPER_SRC=$(FCC_LOC)/../../api/chimescalc_C.cpp CC_WRAPPER_HDR=$(FCC_LOC)/../../api/chimescalc_C.h - + chimescalc_C.o : $(CC_WRAPPER_SRC) $(CC_WRAPPER_HDR) $(CHIMESFF_SRC) $(CHIMESFF_HDR) - $(CXX) -c $(CC_WRAPPER_SRC) $(CHIMESFF_SRC) -I $(FCC_LOC)/../../api/ -I $(FCC_LOC)/../../src/ + $(CXX) -c $(CC_WRAPPER_SRC) $(CHIMESFF_SRC) -I $(FCC_LOC)/../../api/ -I $(FCC_LOC)/../../src/ FCC = gfortran -O3 -fPIC -std=f2003 FCC_WRAPPER_SRC=$(FCC_LOC)/../../api/chimescalc_F.F90 - + chimescalc_F.o chimescalc.mod : $(FCC_WRAPPER_SRC) $(FCC) -c $(FCC_WRAPPER_SRC) -o chimescalc_F.o - + main.o : main.F90 $(FCC) -c main.F90 -o main.o @@ -49,6 +49,6 @@ all: make chimesFF.o make chimescalc_C.o make chimescalc_F.o chimescalc.mod - make main.o + make main.o make test_wrapper-F #make clean diff --git a/chimesFF/examples/fortran/main.F90 b/chimesFF/examples/fortran/main.F90 index 7eab4bb..9a6f6d0 100644 --- a/chimesFF/examples/fortran/main.F90 +++ b/chimesFF/examples/fortran/main.F90 @@ -1,6 +1,6 @@ ! ChIMES Calculator ! Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried -! Contributing Author: Nir Goldman (2020) +! Contributing Author: Nir Goldman (2020) program test_F_api use chimescalc @@ -8,12 +8,12 @@ program test_F_api implicit none integer io_num double precision, parameter :: GPa = 6.9479 ! convert kcal/mol.A^3 to GPa - character(C_char), dimension(80) :: c_file + character(C_char), dimension(80) :: c_file character(C_char), dimension(80) :: dummy_var character(2000) :: coord_file, param_file CHARACTER ( len = 2000 ) :: wq_char integer :: i, j, k, l, natom - integer(C_int) :: rank + integer(C_int) :: rank real(C_double) :: lx, ly, lz, ldummy double precision :: vol real(C_double) :: stress(9) @@ -36,8 +36,8 @@ program test_F_api real(C_double) :: dr_3b(3), dist_3b(3,3) real(C_double) :: dr_4b(6), dist_4b(3,6) real(C_double) :: rij - type(C_ptr) :: c_rij - + type(C_ptr) :: c_rij + io_num = command_argument_count() if (io_num .lt. 2) then print*,"To run: ./test_F.x " @@ -91,22 +91,22 @@ program test_F_api do j = i+1, natom xij = xc(i) - xc(j) xij = xij - lx*nint(xij/lx) - dr(1) = xij + dr(1) = xij yij = yc(i) - yc(j) yij = yij - lx*nint(yij/ly) - dr(2) = yij + dr(2) = yij zij = zc(i) - zc(j) zij = zij - lx*nint(zij/lz) - dr(3) = zij + dr(3) = zij rij = sqrt(xij*xij + yij*yij + zij*zij) f2b(:,1) = ftot(:,i) f2b(:,2) = ftot(:,j) - + type1 = string2Cstring(atom_type(i)) type2 = string2Cstring(atom_type(j)) if (rij .le. rcut_2b) then ! f2b, stress tensor, epot are all cumulative - call f_chimes_compute_2b_props_fromf90(rij, dr, type1, & + call f_chimes_compute_2b_props_fromf90(rij, dr, type1, & & type2, f2b, stress, sys_ener) endif !save results back in ftot @@ -129,7 +129,7 @@ program test_F_api do k = j+1, natom ! compute relative coordinates and apply minimum image PBC ! order in chimesFF is ij, ik, jk - ! ij pairs + ! ij pairs xij = (xc(i) - xc(j)); xij = xij - lx*nint(xij/lx); yij = (yc(i) - yc(j)); @@ -151,7 +151,7 @@ program test_F_api dist_3b(2,2) = yik; dist_3b(3,2) = zik; dr_3b(2) = sqrt(xik*xik + yik*yik + zik*zik); - ! jk pairs + ! jk pairs xjk = (xc(j) - xc(k)); xjk = xjk - lx*nint(xjk/lx); yjk = (yc(j) - yc(k)); @@ -165,7 +165,7 @@ program test_F_api f3b(:,1) = ftot(:,i) f3b(:,2) = ftot(:,j) f3b(:,3) = ftot(:,k) - + type1 = string2Cstring(atom_type(i)) type2 = string2Cstring(atom_type(j)) type3 = string2Cstring(atom_type(k)) @@ -173,7 +173,7 @@ program test_F_api if (dr_3b(2) .le. rcut_3b) then if (dr_3b(3) .le. rcut_3b) then ! f2b, stress tensor, epot are all cumulative - call f_chimes_compute_3b_props_fromf90(dr_3b, dist_3b, type1, & + call f_chimes_compute_3b_props_fromf90(dr_3b, dist_3b, type1, & & type2, type3, f3b, stress, sys_ener) endif endif @@ -202,7 +202,7 @@ program test_F_api do l = k+1, natom ! compute relative coordinates and apply minimum image PBC ! order in chimesFF is: ij, ik, il, jk, jl, kl - ! ij pairs + ! ij pairs xij = (xc(i) - xc(j)); xij = xij - lx*nint(xij/lx); yij = (yc(i) - yc(j)); @@ -213,7 +213,7 @@ program test_F_api dist_4b(2,1) = yij; dist_4b(3,1) = zij; dr_4b(1) = sqrt(xij*xij + yij*yij + zij*zij); - ! ik pairs + ! ik pairs xik = (xc(i) - xc(k)); xik = xik - lx*nint(xik/lx); yik = (yc(i) - yc(k)); @@ -224,7 +224,7 @@ program test_F_api dist_4b(2,2) = yik; dist_4b(3,2) = zik; dr_4b(2) = sqrt(xik*xik + yik*yik + zik*zik); - ! il pairs + ! il pairs xil = (xc(i) - xc(l)); xil = xil - lx*nint(xil/lx); yil = (yc(i) - yc(l)); @@ -235,7 +235,7 @@ program test_F_api dist_4b(2,3) = yil; dist_4b(3,3) = zil; dr_4b(3) = sqrt(xil*xil + yil*yil + zil*zil); - ! jk pairs + ! jk pairs xjk = (xc(j) - xc(k)); xjk = xjk - lx*nint(xjk/lx); yjk = (yc(j) - yc(k)); @@ -246,7 +246,7 @@ program test_F_api dist_4b(2,4) = yjk; dist_4b(3,4) = zjk; dr_4b(4) = sqrt(xjk*xjk + yjk*yjk + zjk*zjk); - ! jl pairs + ! jl pairs xjl = (xc(j) - xc(l)); xjl = xjl - lx*nint(xjl/lx); yjl = (yc(j) - yc(l)); @@ -257,7 +257,7 @@ program test_F_api dist_4b(2,5) = yjl; dist_4b(3,5) = zjl; dr_4b(5) = sqrt(xjl*xjl + yjl*yjl + zjl*zjl); - ! kl pairs + ! kl pairs xkl = (xc(k) - xc(l)); xkl = xkl - lx*nint(xkl/lx); ykl = (yc(k) - yc(l)); @@ -284,7 +284,7 @@ program test_F_api if (dr_4b(5) .le. rcut_4b) then if (dr_4b(6) .le. rcut_4b) then ! f2b, stress tensor, epot are all cumulative - call f_chimes_compute_4b_props_fromf90(dr_4b, dist_4b, type1, & + call f_chimes_compute_4b_props_fromf90(dr_4b, dist_4b, type1, & & type2, type3, type4, f4b, stress, sys_ener) endif endif diff --git a/chimesFF/examples/python/Makefile b/chimesFF/examples/python/Makefile index c03e152..865ef2a 100644 --- a/chimesFF/examples/python/Makefile +++ b/chimesFF/examples/python/Makefile @@ -12,12 +12,12 @@ CC_WRAPPER_SRC=$(CC_LOC)/../../api/chimescalc_C.cpp CC_WRAPPER_HDR=$(CC_LOC)/../../api/chimescalc_C.h chimescalc_C.o : $(CC_WRAPPER_SRC) $(CC_WRAPPER_HDR) $(CHIMESFF_SRC) $(CHIMESFF_HDR) - $(CXX) -c $(CC_WRAPPER_SRC) $(CHIMESFF_SRC) -I $(CC_LOC)/../../api/ -I $(CC_LOC)/../../src/ - + $(CXX) -c $(CC_WRAPPER_SRC) $(CHIMESFF_SRC) -I $(CC_LOC)/../../api/ -I $(CC_LOC)/../../src/ + chimescalc_C.so: $(CXX) -shared -o libchimescalc-direct_dl.so chimescalc_C.o chimesFF.o - + clean: rm -f *.o diff --git a/chimesFF/examples/python/main.py b/chimesFF/examples/python/main.py index b8ec185..8ad66b5 100644 --- a/chimesFF/examples/python/main.py +++ b/chimesFF/examples/python/main.py @@ -66,7 +66,7 @@ def get_dist(lx,ly,lz,xrd,ycrd,zcrd,i,j): # Read the parameters -chimescalc_py.read_params(param_file) +wrapper_py.read_params(param_file) # Read the coordinates, set up the force, stress, and energy vars diff --git a/chimesFF/src/chimesFF.cpp b/chimesFF/src/chimesFF.cpp index 3cc57f4..a383273 100644 --- a/chimesFF/src/chimesFF.cpp +++ b/chimesFF/src/chimesFF.cpp @@ -1,7 +1,7 @@ -/* +/* ChIMES Calculator Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried - Contributing Author: Rebecca K. Lindsey (2020) + Contributing Author: Rebecca K. Lindsey (2020) */ #include @@ -17,16 +17,13 @@ using namespace std; -#include "chimesFF.h" - -static const double pi = 3.14159265359; - +#include "chimesFF.h" template int get_index(const vector & vec, const T & element) { auto it = find(vec.begin(), vec.end(), element); - + if (it != vec.end()) { return distance(vec.begin(), it); @@ -60,10 +57,10 @@ int get_index_if(const vector & vec, const T & element, vector & disq } cout << "chimesFF: " << "ERROR: Could not find element in vector: " << element << endl; - + for(int i=0; i & items) { // Break a line up into tokens based on space separators. // Returns the number of tokens parsed. - + string contents; stringstream sstream; // Strip comments beginining with ! or ## and terminal new line int pos = line.find('!'); - - if ( pos != string::npos ) + + if ( pos != string::npos ) line.erase(pos, line.length() - pos); pos = line.find("##"); - if ( pos != string::npos ) + if ( pos != string::npos ) line.erase(pos, line.length()-pos); pos = line.find('\n'); - if ( pos != string::npos ) + if ( pos != string::npos ) line.erase(pos, 1); sstream.str(line); - + items.clear(); - while ( sstream >> contents ) + while ( sstream >> contents ) items.push_back(contents); return items.size(); @@ -165,11 +165,11 @@ int chimesFF::split_line(string line, vector & items) string chimesFF::get_next_line(istream& str) { // Read a line and return it, with error checking. - + string line; getline(str, line); - + if ( ! str.good() ) { if (rank == 0) @@ -183,23 +183,23 @@ string chimesFF::get_next_line(istream& str) void chimesFF::read_parameters(string paramfile) { // Open the parameter file, run sanity checks - + ifstream param_file; param_file.open(paramfile.data()); - + if (rank == 0) cout << "chimesFF: " << "Reading parameters from file: " << paramfile << endl; - + if(!param_file.is_open()) { if (rank == 0) cout << "chimesFF: " << "ERROR: Cannot open parameter file: " << paramfile << endl; exit(0); } - + // Declare parsing variables - - + + bool found_end = false; string line; string tmp_str; @@ -207,7 +207,7 @@ void chimesFF::read_parameters(string paramfile) int tmp_no_items; int tmp_int; int no_pairs; - + // Check that this is actually a chebyshev parameter set while (!found_end) @@ -225,68 +225,68 @@ void chimesFF::read_parameters(string paramfile) } exit(0); } - + if(line.find("PAIRTYP: CHEBYSHEV") != string::npos) { tmp_no_items = split_line(line, tmp_str_items); - + if (tmp_no_items < 3) - { + { if (rank == 0) cout << "chimesFF: " << "ERROR: \"PAIRTYP: CHEBYSHEV\" line must at least contain the 2-body order" << endl; exit(0); } - + poly_orders.push_back(stoi(tmp_str_items[2])); - + if (tmp_no_items >= 4) poly_orders.push_back(stoi(tmp_str_items[3])); if (tmp_no_items >= 5) - poly_orders.push_back(stoi(tmp_str_items[4])); - + poly_orders.push_back(stoi(tmp_str_items[4])); + while (poly_orders.size() < 3) poly_orders.push_back(0); - + if (rank == 0) { cout << "chimesFF: " << "Using respective 2, 3, and 4-body orders of: " << poly_orders[0] << " " << poly_orders[1] << " " << poly_orders[2] << endl; - - cout << "chimesFF: " << "Note: Ignoring polynomial domain; assuming [-1,1]" << endl; + + cout << "chimesFF: " << "Note: Ignoring polynomial domain; assuming [-1,1]" << endl; } - - break; + + break; } } - + // If we've made it to here, then this should contain Chebyshev params. Rewind and start looking for general information - + param_file.seekg(0); - + found_end = false; - + while (!found_end) { line = get_next_line(param_file); - + if(line.find("ENDFILE") != string::npos) - break; - + break; + if(line.find("ATOM TYPES:") != string::npos) { tmp_no_items = split_line(line, tmp_str_items); - + natmtyps = stoi(tmp_str_items[2]); - + if (rank == 0) cout << "chimesFF: " << "Will consider " << natmtyps << " atom types:" << endl; - + energy_offsets.resize(natmtyps); - + for(int i=0; i 0) { int ntrips; int tmp_idx; - + // Read parameters - + param_file.seekg(0); - + found_end = false; - + while (!found_end) { line = get_next_line(param_file); - + if(line.find("ENDFILE") != string::npos) - break; - + break; + if(line.find("ATOM PAIR TRIPLETS:") != string::npos) { split_line(line, tmp_str_items); - + ntrips = stoi(tmp_str_items[3]); - + ncoeffs_3b .resize(ntrips); - chimes_3b_powers.resize(ntrips); + chimes_3b_powers.resize(ntrips); chimes_3b_params.resize(ntrips); chimes_3b_cutoff.resize(ntrips); - - - trip_params_atm_chems.resize(ntrips); + + + trip_params_atm_chems.resize(ntrips); trip_params_pair_typs.resize(ntrips); } - + if(line.find("TRIPLETTYPE PARAMS:") != string::npos) { vector tmp_int_vec(3); 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]); trip_params_atm_chems[tmp_int].push_back(tmp_str_items[4]); trip_params_atm_chems[tmp_int].push_back(tmp_str_items[5]); if (rank == 0) cout << "chimesFF: " << "Read 3B parameters for triplet: " << tmp_int << " " << trip_params_atm_chems[tmp_int][0] << " " << trip_params_atm_chems[tmp_int][1] << " " << trip_params_atm_chems[tmp_int][2] << endl; - + line = get_next_line(param_file); - + split_line(line, tmp_str_items); - + 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]); - - ncoeffs_3b[tmp_int] = stoi(tmp_str_items[7]); + + ncoeffs_3b[tmp_int] = stoi(tmp_str_items[7]); get_next_line(param_file); get_next_line(param_file); - + for(int i=0; i pair_name(3); vector cutoffval(3); - + for(int i=0; i disqualified(3,false); - + chimes_3b_cutoff[tmp_int][1][ get_index_if(trip_params_pair_typs[tmp_int], pair_name[0], disqualified) ] = cutoffval[0]; chimes_3b_cutoff[tmp_int][1][ get_index_if(trip_params_pair_typs[tmp_int], pair_name[1], disqualified) ] = cutoffval[1]; chimes_3b_cutoff[tmp_int][1][ get_index_if(trip_params_pair_typs[tmp_int], pair_name[2], disqualified) ] = cutoffval[2]; - + } } - + for(int i=0; i pair_name(3); vector cutoffval(3); @@ -883,48 +892,48 @@ void chimesFF::read_parameters(string paramfile) for(int i=0; i disqualified(3,false); - + chimes_3b_cutoff[tmp_int][0][ get_index_if(trip_params_pair_typs[tmp_int], pair_name[0], disqualified) ] = cutoffval[0]; chimes_3b_cutoff[tmp_int][0][ get_index_if(trip_params_pair_typs[tmp_int], pair_name[1], disqualified) ] = cutoffval[1]; chimes_3b_cutoff[tmp_int][0][ get_index_if(trip_params_pair_typs[tmp_int], pair_name[2], disqualified) ] = cutoffval[2]; - + } } - + for(int i=0; i 0) { int nquads; int tmp_idx; - + // Read parameters - + param_file.seekg(0); - + found_end = false; - + while (!found_end) { line = get_next_line(param_file); @@ -935,26 +944,26 @@ void chimesFF::read_parameters(string paramfile) if(line.find("ATOM PAIR QUADRUPLETS:") != string::npos) { split_line(line, tmp_str_items); - + nquads = stoi(tmp_str_items[3]); - - ncoeffs_4b .resize(nquads); - chimes_4b_powers.resize(nquads); - chimes_4b_params.resize(nquads); - chimes_4b_cutoff.resize(nquads); - - quad_params_atm_chems.resize(nquads); + + ncoeffs_4b .resize(nquads); + chimes_4b_powers.resize(nquads); + chimes_4b_params.resize(nquads); + chimes_4b_cutoff.resize(nquads); + + quad_params_atm_chems.resize(nquads); quad_params_pair_typs.resize(nquads); } - + if(line.find("QUADRUPLETYPE PARAMS:") != string::npos) { line = get_next_line(param_file); - + split_line(line, tmp_str_items); - + tmp_int = stoi(tmp_str_items[1]); - + quad_params_atm_chems[tmp_int].push_back(tmp_str_items[3]); quad_params_atm_chems[tmp_int].push_back(tmp_str_items[4]); quad_params_atm_chems[tmp_int].push_back(tmp_str_items[5]); @@ -962,82 +971,82 @@ void chimesFF::read_parameters(string paramfile) if (rank == 0) cout << "chimesFF: " << "Read 4B parameters for quadruplets: " << tmp_int << " " << quad_params_atm_chems[tmp_int][0] << " " << quad_params_atm_chems[tmp_int][1] << " " << quad_params_atm_chems[tmp_int][2] << " " << quad_params_atm_chems[tmp_int][3]<< endl; - + line = get_next_line(param_file); - + split_line(line, tmp_str_items); - + quad_params_pair_typs[tmp_int].push_back(tmp_str_items[1]); quad_params_pair_typs[tmp_int].push_back(tmp_str_items[2]); quad_params_pair_typs[tmp_int].push_back(tmp_str_items[3]); quad_params_pair_typs[tmp_int].push_back(tmp_str_items[4]); quad_params_pair_typs[tmp_int].push_back(tmp_str_items[5]); - quad_params_pair_typs[tmp_int].push_back(tmp_str_items[6]); - - ncoeffs_4b[tmp_int] = stoi(tmp_str_items[10]); + quad_params_pair_typs[tmp_int].push_back(tmp_str_items[6]); + + ncoeffs_4b[tmp_int] = stoi(tmp_str_items[10]); get_next_line(param_file); get_next_line(param_file); - + vector tmp_int_vec(6); - + for(int i=0; i pair_name(6); vector cutoffval(6); for(int i=0; i disqualified(6,false); - + chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[0], disqualified) ] = cutoffval[0]; chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[1], disqualified) ] = cutoffval[1]; - chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[2], disqualified) ] = cutoffval[2]; + chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[2], disqualified) ] = cutoffval[2]; chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[3], disqualified) ] = cutoffval[3]; chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[4], disqualified) ] = cutoffval[4]; chimes_4b_cutoff[tmp_int][1][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[5], disqualified) ] = cutoffval[5]; } } - + for(int i=0; i pair_name(6); vector cutoffval(6); @@ -1255,9 +1264,9 @@ void chimesFF::read_parameters(string paramfile) for(int i=0; i disqualified(6,false); - + chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[0], disqualified) ] = cutoffval[0]; chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[1], disqualified) ] = cutoffval[1]; - chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[2], disqualified) ] = cutoffval[2]; + chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[2], disqualified) ] = cutoffval[2]; chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[3], disqualified) ] = cutoffval[3]; chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[4], disqualified) ] = cutoffval[4]; - chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[5], disqualified) ] = cutoffval[5]; + chimes_4b_cutoff[tmp_int][0][ get_index_if(quad_params_pair_typs[tmp_int], pair_name[5], disqualified) ] = cutoffval[5]; } } - + for(int i=0; i &Tn, vector &Tnd, double dx, double x, int poly_order, double inner_cutoff, double exprlen, double dx_dr) { - // Currently assumes a Morse-style transformation has been requested - - // Sets the value of the Chebyshev polynomials (Tn) and their derivatives (Tnd). Tnd is the derivative - // with respect to the interatomic distance, not the transformed distance (x). - - // Do the Morse transformation - - double x_min = exp(-1*inner_cutoff/morse_var[pair_idx]); - double x_max = exp(-1*outer_cutoff/morse_var[pair_idx]); - - double x_avg = 0.5 * (x_max + x_min); - double x_diff = 0.5 * (x_max - x_min); - - x_diff *= -1.0; // Special for Morse style - - double exprlen = exp(-1*dx/morse_var[pair_idx]); - - double x = (exprlen - x_avg)/x_diff; - - if ( x < -1.0) - x = -1.0; - else if ( x > 1.0 ) - x = 1.0; - - // Generate Chebyshev polynomials by recursion. - // - // What we're doing here. Want to fit using Cheby polynomials of the 1st kinD[i]. "T_n(x)." - // We need to calculate the derivative of these polynomials. - // Derivatives are defined through use of Cheby polynomials of the 2nd kind "U_n(x)", as: - // - // d/dx[ T_n(x) = n * U_n-1(x)] - // - // So we need to first set up the 1st-kind polynomials ("Tn[]") - // Then, to compute the derivatives ("Tnd[]"), first set equal to the 2nd-kind, then multiply by n to get the der's - - // First two 1st-kind Chebys: - + // Sets the value of the Chebyshev polynomials (Tn) and their derivatives (Tnd) when dx is < inner_cutoff. + // Tnd is the derivative with respect to the interatomic distance, not the transformed distance (x). + // + // The derivative Tnd is continuously set to zero inside the cutoff. + // The exponential smoothing distance is set to ChimesFF::inner_smooth_distance. + // x, exprlen, and dx_dr are evaluated at the inner cutoff. + // + // dx is the pair distance, which is assumed to be less than inner_cutoff. Tn[0] = 1.0; Tn[1] = x; @@ -1349,199 +1329,51 @@ inline void chimesFF::set_cheby_polys(double *Tn, double *Tnd, const double dx, Tnd[0] = 1.0; Tnd[1] = 2.0 * x; - + // Use recursion to set up the higher n-value Tn and Tnd's - - for ( int i = 2; i <= poly_orders[bodiedness_idx]; i++ ) + for ( int i = 2; i <= poly_order; i++ ) { Tn[i] = 2.0 * x * Tn[i-1] - Tn[i-2]; Tnd[i] = 2.0 * x * Tnd[i-1] - Tnd[i-2]; } - + // Now multiply by n to convert Tnd's to actual derivatives of Tn - // The following dx_dr compuation assumes a Morse transformation - // DERIV_CONST is no longer used. (old way: dx_dr = DERIV_CONST*cheby_var_deriv(x_diff, rlen, ff_2body.LAMBDA, ff_2body.CHEBY_TYPE, exprlen);) - - double dx_dr = (-exprlen/morse_var[pair_idx])/x_diff; - - for ( int i = poly_orders[bodiedness_idx]; i >= 1; i-- ) + for ( int i = poly_order; i >= 1; i-- ) Tnd[i] = i * dx_dr * Tnd[i-1]; Tnd[0] = 0.0; + // Exponential damping of the derivative. + double damp_fac = exp( (dx-inner_cutoff) / inner_smooth_distance ) ; + + // Correct Tn outside of the range using the damping factor. + for ( int i = 0 ; i <= poly_order ; i++ ) + { + Tn[i] += inner_smooth_distance * (damp_fac-1.0) * Tnd[i] ; + Tnd[i] *= damp_fac ; + } } -inline void chimesFF::get_fcut(const double dx, const double outer_cutoff, double & fcut, double & fcutderiv) +inline double chimesFF::dr2_3B(const double *dr2, int i, int j, int k, int l) { + // Access the dr2 distance tensor for a 3 body interaction. + return(dr2[i*CHDIM*3*CHDIM + j*3*CHDIM + k*CHDIM + l]) ; +} - static double THRESH; - static double fcut0; - static double fcut0_deriv, fcut_deriv; - - if(fcut_type == "CUBIC") - { - fcut0 = (1.0 - dx/outer_cutoff); - fcut = pow(fcut0,3.0); - fcutderiv = pow(fcut0,2.0); - fcutderiv *= -1.0 * 3.0 /outer_cutoff; - - return; - } - - if(fcut_type=="TERSOFF") - { - - THRESH = outer_cutoff-fcut_var*outer_cutoff; - - - if (dx < THRESH) // Case 1: Our pair distance is less than the fcut kick-in distance - { - fcut = 1.0; - fcutderiv = 0.0; - } - else if (dx > outer_cutoff) // Case 2: Our pair distance is greater than the cutoff - { - fcut = 0.0; - fcutderiv = 0.0; - } - else // Case 3: We'll use our modified sin function - { - fcut0 = (dx-THRESH) / (outer_cutoff-THRESH) * pi + pi/2.0; - fcut0_deriv = pi / (outer_cutoff - THRESH); - - fcut = 0.5 + 0.5 * sin( fcut0 ); - fcutderiv = 0.5 * cos( fcut0 ) * fcut0_deriv; - } - return; - } -} - -inline void chimesFF::get_penalty(const double dx, const int & pair_idx, double & E_penalty, double & force_scalar) +inline double chimesFF::dr2_4B(const double *dr2, int i, int j, int k, int l) { - double r_penalty = 0.0; - - E_penalty = 0.0; - force_scalar = 1.0; - - if (dx - penalty_params[0] < chimes_2b_cutoff[pair_idx][0]) - - r_penalty = chimes_2b_cutoff[pair_idx][0] + penalty_params[0] - dx; - - 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) - { - 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; - } - } + // Access the dr2 distance tensor for a 4 body interaction. + return(dr2[i*CHDIM*6*CHDIM + j*6*CHDIM + k*CHDIM + l]) ; } -inline void chimesFF::build_atom_and_pair_mappers(const int natoms, const int npairs, const vector typ_idxs, const vector > & clu_params_pair_typs, const int & cluidx, vector & mapped_pair_idx) +inline void chimesFF::init_distance_tensor(double *dr2, const vector & dr, int npairs) { - // Generate permutations for atoms... all we are doing is permuting the possible indices for typ_idxs - - - // build a copy of the atom type vector for permuting - - static vector tmp_typ_idxs; - static int nelements; - - nelements = typ_idxs.size(); - tmp_typ_idxs.resize(nelements); - - for(int i=0; i > tmp_pairs; - tmp_pairs.resize(npairs,vector(2)); - static vector > runtime_pairs; - runtime_pairs.resize(npairs,vector(2)); - - int idx = 0; - - for(int i=0; i runtime_pair_typs(npairs); - - while ( true ) - { - // Check if the permutation leads to pair types that match the order specified by the force field type - - idx = 0; - - for(int i=0; i & dr, const vector typ_idxs, vector > force, vector stress, double & energy ) +// Overload for calls from LAMMPS +void chimesFF::compute_2B(const double dx, const vector & dr, const vector typ_idxs, vector & force, vector & stress, double & energy, chimes2BTmp &tmp) +{ + double dummy_force_scalar; + compute_2B(dx, dr, typ_idxs, force, stress, energy, tmp, dummy_force_scalar); +} +void chimesFF::compute_2B(const double dx, const vector & dr, const vector typ_idxs, vector & force, vector & stress, double & energy, chimes2BTmp &tmp, double & force_scalar_in) { // Compute 2b (input: 2 atoms or distances, corresponding types... outputs (updates) force, acceleration, energy, stress // // Input parameters: // // dx: Scalar (pair distance) - // dr: 1d-Array (pair distance: [x, y, and z-component]) + // dr: 1d-Array (pair distance: [x, y, and z-component]) // Force: [natoms in interaction set][x,y, and z-component] *note // Stress [sxx, sxy, sxz, syy, syz, szz] *note // Energy: Scalar; energy for interaction set + // Tmp: Temporary storage for calculation. + // Assumes atom indices start from zero // Assumes distances are atom_2 - atom_1 // - // *note: force's pointer vector of vectors elements must be dereferenced! - - static bool called_before = false; // Used to insure we only declare the Tn's and Tnd's one time - static double *Tn, *Tnd; // The Chebyshev polymonials and thier derivatives - static int pair_idx; - static double fcut; - static double fcutderiv; - static double dx_dr; - static double E_penalty; - static double force_scalar; - static double fpair_total; - static double deriv; - static double coeff_val; - - if (!called_before) // Set up 2-body polynomials - { - called_before = true; + // *note: force is a packed array of coordinates. - Tn = new double [poly_orders[0]+1]; - Tnd = new double [poly_orders[0]+1]; - } + int pair_idx; + double fcut; + double fcutderiv; + // tmp.resize(poly_orders[0]+1) ; + + // Use references for readability. + vector &Tn = tmp.Tn ; + vector &Tnd = tmp.Tnd ; + pair_idx = atom_int_pair_map[ typ_idxs[0]*natmtyps + typ_idxs[1] ]; if (dx >= chimes_2b_cutoff[pair_idx][1]) - return; + return; set_cheby_polys(Tn, Tnd, dx, pair_idx, chimes_2b_cutoff[pair_idx][0], chimes_2b_cutoff[pair_idx][1], 0); - + get_fcut(dx, chimes_2b_cutoff[pair_idx][1], fcut, fcutderiv); + double dx_inv = ( dx > 0.0 ) ? 1.0 / dx : 1e20 ; + for(int coeffs=0; coeffs 0.0 ) + if ( E_penalty > 0.0 ) { energy += E_penalty; - // Note: force_scalar is negative (LEF) 7/30/21. - *force[0][0] += force_scalar * dr[0]/ dx; - *force[0][1] += force_scalar * dr[1]/ dx; - *force[0][2] += force_scalar * dr[2]/ dx; - - *force[1][0] -= force_scalar * dr[0]/ dx; - *force[1][1] -= force_scalar * dr[1]/ dx; - *force[1][2] -= force_scalar * dr[2]/ dx; + force_scalar /= dx ; - // Update stress according to penalty force. (LEF) 07/30/21 - *stress[0] -= force_scalar / dx * dr[0] * dr[0]; // xx tensor component - *stress[1] -= force_scalar / dx * dr[0] * dr[1]; // xy tensor component - *stress[2] -= force_scalar / dx * dr[0] * dr[2]; // xz tensor component + // Note: force_scalar is negative (LEF) 7/30/21. + force[0*CHDIM+0] += force_scalar * dr[0]; + force[0*CHDIM+1] += force_scalar * dr[1]; + force[0*CHDIM+2] += force_scalar * dr[2]; - *stress[3] -= force_scalar / dx * dr[1] * dr[0]; // yx tensor component - *stress[4] -= force_scalar / dx * dr[1] * dr[1]; // yy tensor component - *stress[5] -= force_scalar / dx * dr[1] * dr[2]; // yz tensor component - - *stress[6] -= force_scalar / dx * dr[2] * dr[0]; // zx tensor component - *stress[7] -= force_scalar / dx * dr[2] * dr[1]; // zy tensor component - *stress[8] -= force_scalar / dx * dr[2] * dr[2]; // zz tensor component + force[1*CHDIM+0] -= force_scalar * dr[0]; + force[1*CHDIM+1] -= force_scalar * dr[1]; + force[1*CHDIM+2] -= force_scalar * dr[2]; + + // Update stress according to penalty force. (LEF) 07/30/21 + stress[0] -= force_scalar * dr[0] * dr[0]; // xx tensor component + stress[1] -= force_scalar * dr[0] * dr[1]; // xy tensor component + stress[2] -= force_scalar * dr[0] * dr[2]; // xz tensor component + stress[3] -= force_scalar * dr[1] * dr[1]; // yy tensor component + stress[4] -= force_scalar * dr[1] * dr[2]; // yz tensor component + stress[5] -= force_scalar * dr[2] * dr[2]; // zz tensor component } + + force_scalar_in = force_scalar; } -void chimesFF::compute_3B(const vector & dx, const vector > & dr, const vector & typ_idxs, vector > force, vector stress, double & energy ) +// Overload for calls from LAMMPS +void chimesFF::compute_3B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force, vector & stress, double & energy, chimes3BTmp &tmp) +{ + vector dummy_force_scalar(3); + compute_3B(dx, dr, typ_idxs, force, stress, energy, tmp, dummy_force_scalar); +} +void chimesFF::compute_3B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force, vector & stress, double & energy, chimes3BTmp &tmp, vector & force_scalar_in) { // Compute 3b (input: 3 atoms or distances, corresponding types... outputs (updates) force, acceleration, energy, stress // @@ -1675,184 +1509,203 @@ void chimesFF::compute_3B(const vector & dx, const vector // dx_ij: Scalar (pair distance) // dr_ij: 1d-Array (pair distance: [x, y, and z-component]) // Force: [natoms in interaction set][x,y, and z-component] *note - // Stress [sxx, sxy, sxz, syy, syz, szz] *note + // Stress [sxx, sxy, sxz, syy, syz, szz] // Energy: Scalar; energy for interaction set + // Tmp: Temporary storage for 3-body interactions. + // Assumes atom indices start from zero // Assumes distances are atom_2 - atom_1 // - // *note: force's pointer vector of vectors elements must be dereferenced! - - static int natoms = 3; // Number of atoms in an interaction set - static int npairs = natoms*(natoms-1)/2; // Number of pairs in an interaction set - - - static bool called_before = false; // Used to insure we only declare the Tn's and Tnd's one time - static double *Tn_ij, *Tn_ik, *Tn_jk; // The Chebyshev polymonials - static double *Tnd_ij, *Tnd_ik, *Tnd_jk; // The Chebyshev polymonial derivatives - - static vector fcut (npairs); - static vector fcutderiv(npairs); - static vector deriv (npairs); - - if (!called_before) // Set up 3-body polynomials + // *note: force and dr are packed vectors of coordinates. + + const int natoms = 3; // Number of atoms in an interaction set + const int npairs = natoms*(natoms-1)/2; // Number of pairs in an interaction set + + // tmp.resize(poly_orders[1]) ; + + vector &Tn_ij = tmp.Tn_ij ; + vector &Tn_ik = tmp.Tn_ik ; + vector &Tn_jk = tmp.Tn_jk ; // The Chebyshev polymonials + vector &Tnd_ij = tmp.Tnd_ij ; + vector &Tnd_ik = tmp.Tnd_ik ; + vector &Tnd_jk = tmp.Tnd_jk ; // The Chebyshev polymonial derivatives + + // Avoid allocating std::vector quantities. Heap memory allocation is slow on the GPU. + // fixed-length C arrays are allocated on the stack. + double fcut[npairs] ; + double fcutderiv[npairs] ; + double deriv[npairs]; + +#if DEBUG == 1 + if ( dr.size() != 9 ) { - called_before = true; - - Tn_ij = new double [poly_orders[1]+1]; - Tn_ik = new double [poly_orders[1]+1]; - Tn_jk = new double [poly_orders[1]+1]; - - Tnd_ij = new double [poly_orders[1]+1]; - Tnd_ik = new double [poly_orders[1]+1]; - Tnd_jk = new double [poly_orders[1]+1]; + cout << "Error: dr should have length = 9. Current length = " << dr.size() << endl ; + exit(0) ; } +#endif - int tripidx = atom_int_trip_map[typ_idxs[0]*natmtyps*natmtyps + typ_idxs[1]*natmtyps + typ_idxs[2]]; + + int type_idx = typ_idxs[0]*natmtyps*natmtyps + typ_idxs[1]*natmtyps + typ_idxs[2] ; + int tripidx = atom_int_trip_map[type_idx]; if(tripidx < 0) // Skipping an excluded interaction return; - - // Build maps for associating atoms/pairs with corresponding force field atom/pair - - vector mapped_pair_idx(npairs); // Will store the force field index for the atom type - - build_atom_and_pair_mappers(natoms, npairs, typ_idxs, trip_params_pair_typs, tripidx, mapped_pair_idx); - + // Check whether cutoffs are within allowed ranges - + vector & mapped_pair_idx = pair_int_trip_map[type_idx] ; + if (dx[0] >= chimes_3b_cutoff[ tripidx ][1][mapped_pair_idx[0]]) // ij - return; + return; if (dx[1] >= chimes_3b_cutoff[ tripidx ][1][mapped_pair_idx[1]]) // ik - return; + return; if (dx[2] >= chimes_3b_cutoff[ tripidx ][1][mapped_pair_idx[2]]) // jk - return; - + return; + // At this point, all distances are within allowed ranges. We can now proceed to the force/stress/energy calculation - vector dx_dummy(npairs); - - for (int i=0; i powers(npairs); - vector force_scalar(npairs); - + int powers[npairs] ; + double force_scalar[npairs] ; + for(int coeffs=0; coeffs & dx, const vector > & dr, const vector & typ_idxs, vector > force, vector stress, double & energy ) +void chimesFF::compute_4B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force, vector & stress, double & energy, chimes4BTmp &tmp) +{ + vector dummy_force_scalar(6); + compute_4B(dx, dr, typ_idxs, force, stress, energy, tmp, dummy_force_scalar); +} +void chimesFF::compute_4B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force, vector & stress, double & energy, chimes4BTmp &tmp, vector & force_scalar_in) { // Compute 3b (input: 3 atoms or distances, corresponding types... outputs (updates) force, acceleration, energy, stress // @@ -1861,275 +1714,313 @@ void chimesFF::compute_4B(const vector & dx, const vector // dx_ij: Scalar (pair distance) // dr_ij: 1d-Array (pair distance: [x, y, and z-component]) // Force: [natoms in interaction set][x,y, and z-component] *note - // Stress [sxx, sxy, sxz, syy, syz, szz] *note + // Stress [sxx, sxy, sxz, syy, syz, szz] // Energy: Scalar; energy for interaction set + // Tmp: Structure containing temporary data. // Assumes atom indices start from zero // Assumes distances are atom_2 - atom_1 // - // *note: force's pointer vector of vectors elements must be dereferenced! + // *note: force and dr are packed vectors of coordinates. - int natoms = 4; // Number of atoms in an interaction set - int npairs = natoms*(natoms-1)/2; // Number of pairs in an interaction set + const int natoms = 4; // Number of atoms in an interaction set + const int npairs = natoms*(natoms-1)/2; // Number of pairs in an interaction set - static bool called_before = false; // Used to insure we only declare the Tn's and Tnd's one time - static double *Tn_ij, *Tn_ik, *Tn_il, *Tn_jk, *Tn_jl, *Tn_kl; // The Chebyshev polymonials - static double *Tnd_ij, *Tnd_ik, *Tnd_il, *Tnd_jk, *Tnd_jl, *Tnd_kl; // The Chebyshev polymonial derivatives - vector fcut (npairs); - vector fcutderiv(npairs); - vector deriv (npairs); + double fcut[npairs] ; + double fcutderiv[npairs] ; + double deriv[npairs] ; + - if (!called_before) // Set up 4-body polynomials - { - called_before = true; - - Tn_ij = new double [poly_orders[2]+1]; - Tn_ik = new double [poly_orders[2]+1]; - Tn_il = new double [poly_orders[2]+1]; - Tn_jk = new double [poly_orders[2]+1]; - Tn_jl = new double [poly_orders[2]+1]; - Tn_kl = new double [poly_orders[2]+1]; - - Tnd_ij = new double [poly_orders[2]+1]; - Tnd_ik = new double [poly_orders[2]+1]; - Tnd_il = new double [poly_orders[2]+1]; - Tnd_jk = new double [poly_orders[2]+1]; - Tnd_jl = new double [poly_orders[2]+1]; - Tnd_kl = new double [poly_orders[2]+1]; +#if DEBUG == 1 + if ( force.size() != CHDIM * natoms ) { + cout << "Error: force vector had incorrect dimension of " << force.size() << endl ; + exit(1) ; } - - int quadidx = atom_int_quad_map[typ_idxs[0]*natmtyps*natmtyps*natmtyps + typ_idxs[1]*natmtyps*natmtyps + typ_idxs[2]*natmtyps + typ_idxs[3]]; +#endif + + vector &Tn_ij = tmp.Tn_ij ; + vector &Tn_ik = tmp.Tn_ik ; + vector &Tn_il = tmp.Tn_il ; + vector &Tn_jk = tmp.Tn_jk ; + vector &Tn_jl = tmp.Tn_jl ; + vector &Tn_kl = tmp.Tn_kl ; + + vector &Tnd_ij = tmp.Tnd_ij ; + vector &Tnd_ik = tmp.Tnd_ik ; + vector &Tnd_il = tmp.Tnd_il ; + vector &Tnd_jk = tmp.Tnd_jk ; + vector &Tnd_jl = tmp.Tnd_jl ; + vector &Tnd_kl = tmp.Tnd_kl ; + + int idx = typ_idxs[0]*natmtyps*natmtyps*natmtyps + + typ_idxs[1]*natmtyps*natmtyps + typ_idxs[2]*natmtyps + typ_idxs[3] ; + + int quadidx = atom_int_quad_map[idx] ; if(quadidx < 0) // Skipping an excluded interaction return; + vector & mapped_pair_idx = pair_int_quad_map[idx] ; - // Build maps for associating atoms/pairs with corresponding force field atom/pair - - vector mapped_pair_idx(npairs); // Will store the force field index for the atom type - - build_atom_and_pair_mappers(natoms, npairs, typ_idxs, quad_params_pair_typs, quadidx, mapped_pair_idx); - // Check whether cutoffs are within allowed ranges for(int i=0; i= chimes_4b_cutoff[ quadidx ][1][mapped_pair_idx[i]]) - return; + return; // At this point, all distances are within allowed ranges. We can now proceed to the force/stress/energy calculation - - vector dx_dummy(npairs); - - for (int i=0; i powers(npairs); - vector force_scalar(npairs); + int powers[npairs] ; + double force_scalar[npairs] ; for(int coeffs=0; coeffs > & cutoff_2b) { - int dim = chimes_2b_cutoff.size(); - - cutoff_2b.resize(dim); - - for (int i=0; i > > & cutoff_list) { - double max = cutoff_list[0][1][0]; - + double max = cutoff_list[0][1][0]; + for (int i=0; i max) @@ -2141,55 +2032,162 @@ double chimesFF::max_cutoff(int ntypes, vector > > & cutof double chimesFF::max_cutoff_2B(bool silent) { - double max = chimes_2b_cutoff[0][1]; - + double max = chimes_2b_cutoff[0][1]; + for (int i=0; i max) max = chimes_2b_cutoff[i][1]; - - if ((rank == 0)&&(!silent)) + + if ((rank == 0)&&(!silent)) cout << "chimesFF: " << "\t" << "Setting 2-body max cutoff to: " << max << endl; - - return max; + + return max; } double chimesFF::max_cutoff_3B(bool silent) { - + if (poly_orders[1] == 0) return 0.0; - + double max = max_cutoff(chimes_3b_cutoff.size(), chimes_3b_cutoff); - - if ((rank == 0)&&(!silent)) + + if ((rank == 0)&&(!silent)) cout << "chimesFF: " << "\t" << "Setting 3-body max cutoff to: " << max << endl; - + return max; - + } double chimesFF::max_cutoff_4B(bool silent) { if (poly_orders[2] == 0) return 0.0; - + double max = max_cutoff(chimes_4b_cutoff.size(), chimes_4b_cutoff); - - if ((rank == 0)&&(!silent)) + + if ((rank == 0)&&(!silent)) cout << "chimesFF: " << "\t" << "Setting 4-body max cutoff to: " << max << endl; - + return max; } void chimesFF::set_atomtypes(vector & type_list) { type_list.resize(natmtyps); - + for(int i=0;i pair_map(npairs) ; + vector typ_idxs(natoms) ; + + if ( atom_int_quad_map.size() == 0 ) return ; // No quads ! + + pair_int_quad_map.resize(natmtyps*natmtyps*natmtyps*natmtyps) ; + + + for ( int i = 0 ; i < natmtyps ; i++ ) + { + typ_idxs[0] = i ; + for ( int j = 0 ; j < natmtyps ; j++ ) + { + typ_idxs[1] = j ; + for ( int k = 0 ; k < natmtyps ; k++ ) + { + typ_idxs[2] = k ; + for ( int l = 0 ; l < natmtyps ; l++ ) + { + typ_idxs[3] = l ; + int idx = i*natmtyps*natmtyps*natmtyps + j*natmtyps*natmtyps + k*natmtyps + l ; + int quadidx = atom_int_quad_map[idx]; + + build_atom_and_pair_mappers(natoms, npairs, typ_idxs, quad_params_pair_typs[quadidx], pair_map); + + // Save for re-use in force evaluators. + if ( quadidx >= natmtyps * natmtyps * natmtyps * natmtyps ) + { + cout << "Error: quadidx out of range\n" ; + cout << "Quadidx = " << quadidx << endl ; + exit(1) ; + } + + // Note: The entire vector<> is copied and stored. + pair_int_quad_map[idx] = pair_map ; + } + } + } + } + for ( int i = 0 ; i < pair_int_quad_map.size() ; i++ ) + { + if ( pair_int_quad_map[i].size() == 0 ) + { + cout << "Error: Did not initialize pair_int_quad_map entry " << i << endl ; + } + } +} + +void chimesFF::build_pair_int_trip_map() +// Build the pair maps for all possible triplets. Moved build_atom_and_pair_mappers out of the compute_XX routines +// to support GPU environment without string operations. +// This must be called prior to force evaluation. +{ + const int natoms = 3 ; + const int npairs = natoms * (natoms-1) / 2 ; + vector pair_map(npairs) ; + vector typ_idxs(natoms) ; + + if ( atom_int_trip_map.size() == 0 ) return ; // No quads ! + + pair_int_trip_map.resize(natmtyps*natmtyps*natmtyps) ; + + for ( int i = 0 ; i < natmtyps ; i++ ) + { + typ_idxs[0] = i ; + for ( int j = 0 ; j < natmtyps ; j++ ) + { + typ_idxs[1] = j ; + for ( int k = 0 ; k < natmtyps ; k++ ) + { + typ_idxs[2] = k ; + int tripidx = atom_int_trip_map[i*natmtyps*natmtyps + j*natmtyps + k]; + + build_atom_and_pair_mappers(natoms, npairs, typ_idxs, trip_params_pair_typs[tripidx], pair_map); + + // Save for re-use in force evaluators. + if ( tripidx >= natmtyps * natmtyps * natmtyps * natmtyps ) + { + cout << "Error: tripidx out of range\n" ; + cout << "Tripidx = " << tripidx << endl ; + exit(1) ; + } + + // Note: The entire vector<> is copied and stored. + pair_int_trip_map[i*natmtyps*natmtyps + j*natmtyps + k] = pair_map ; + } + } + } + for ( int i = 0 ; i < pair_int_trip_map.size() ; i++ ) + { + if ( pair_int_trip_map[i].size() == 0 ) + { + cout << "Error: Did not initialize pair_int_trip_map entry " << i << endl ; + } + } + } + diff --git a/chimesFF/src/chimesFF.h b/chimesFF/src/chimesFF.h index 06ae40c..e6fcd75 100644 --- a/chimesFF/src/chimesFF.h +++ b/chimesFF/src/chimesFF.h @@ -1,16 +1,26 @@ /* ChIMES Calculator Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried - Contributing Author: Rebecca K. Lindsey (2020) + Contributing Author: Rebecca K. Lindsey (2020) */ #ifndef _chimesFF_h #define _chimesFF_h + #include +#include +#include +#include #include +#include +#include +#include +#include #include +#define pi 3.14159265359 + using namespace std; // Notes: @@ -19,154 +29,558 @@ using namespace std; // 2. Polynomials are hard-coded over the domain [-1,1] // 3. A cubic style cutoff is assumed, and Tersoff is the only other style considered (see get_fcut) + +#define CHDIM 3 // The number of spatial dimensions. +#define USE_DISTANCE_TENSOR 1 // Use tensor of distances in computing stresses. + +// Temporary storage for ChIMES interaction. +class chimes2BTmp +{ +public: + inline chimes2BTmp(int poly_order) ; + inline void resize(int poly_order) ; + vector Tn ; + vector Tnd ; +} ; + +inline chimes2BTmp::chimes2BTmp(int poly_order) : Tn(poly_order+1), Tnd(poly_order+1) +{ + ; +} + +inline void chimes2BTmp::resize(int poly_order) +{ + + if ( Tn.size() < poly_order + 1 ) + Tn.resize(poly_order+1) ; + + if ( Tnd.size() < poly_order + 1 ) + Tnd.resize(poly_order+1) ; +} + +class chimes3BTmp +{ +public: + inline chimes3BTmp(int poly_order) ; + inline void resize(int poly_order) ; + + vector Tn_ij, Tn_ik, Tn_jk; // The Chebyshev polymonials + vector Tnd_ij, Tnd_ik, Tnd_jk; // The Chebyshev polymonial derivatives + +} ; + +inline chimes3BTmp::chimes3BTmp(int poly_order) : Tn_ij(poly_order+1), Tn_ik(poly_order+1), Tn_jk(poly_order+1), + Tnd_ij(poly_order+1), Tnd_ik(poly_order+1), Tnd_jk(poly_order+1) +{ + ; +} + + +class chimes4BTmp +{ +public: + inline chimes4BTmp(int poly_order) ; + inline void resize(int poly_order) ; + + vector Tn_ij, Tn_ik, Tn_il, Tn_jk, Tn_jl, Tn_kl; // The Chebyshev polymonials + vector Tnd_ij,Tnd_ik, Tnd_il, Tnd_jk, Tnd_jl, Tnd_kl ; // The Chebyshev polymonial derivatives +} ; + +inline chimes4BTmp::chimes4BTmp(int poly_order) : Tn_ij(poly_order+1), Tn_ik(poly_order+1), Tn_il(poly_order+1), + Tn_jk(poly_order+1), Tn_jl(poly_order+1), Tn_kl(poly_order+1), + Tnd_ij(poly_order+1), Tnd_ik(poly_order+1), Tnd_il(poly_order+1), + Tnd_jk(poly_order+1), Tnd_jl(poly_order+1), Tnd_kl(poly_order+1) +{ + ; +} + +inline void chimes3BTmp::resize(int poly_order) +{ + + if ( Tn_ij.size() < poly_order + 1 ) + Tn_ij.resize(poly_order+1) ; + + if ( Tnd_ij.size() < poly_order + 1 ) + Tnd_ij.resize(poly_order+1) ; + + if ( Tn_ik.size() < poly_order + 1 ) + Tn_ik.resize(poly_order+1) ; + + if ( Tnd_ik.size() < poly_order + 1 ) + Tnd_ik.resize(poly_order+1) ; + + if ( Tn_jk.size() < poly_order + 1 ) + Tn_jk.resize(poly_order+1) ; + + if ( Tnd_jk.size() < poly_order + 1 ) + Tnd_jk.resize(poly_order+1) ; +} + +enum class fcutType +{ + CUBIC, + TERSOFF, +} ; + class chimesFF { - public: +public: - //////////////////////// - // General parameters - //////////////////////// - - int rank; // Used to prevent multiple cout statements when accessed from MPI - int natmtyps; // How many atom types are defined for this force field? + //////////////////////// + // General parameters + //////////////////////// + + int rank; // Used to prevent multiple cout statements when accessed from MPI + int natmtyps; // How many atom types are defined for this force field? - vector poly_orders; // [bodiedness-1]; i.e. 12 = 2-body only, 12th order; 12 5 = 2+3-body, 0 5 = 3-body only, 5th order - vector atmtyps; // Atom types - vector masses; // Atom masses - + vector poly_orders; // [bodiedness-1]; i.e. 12 = 2-body only, 12th order; 12 5 = 2+3-body, 0 5 = 3-body only, 5th order + vector atmtyps; // Atom types + vector masses; // Atom masses - //////////////////////// - // Functions - //////////////////////// + //////////////////////// + // Functions + //////////////////////// - chimesFF(); - ~chimesFF(); - - void init(int mpi_rank); + chimesFF(); + ~chimesFF(); - void read_parameters(string paramfile); + void init(int mpi_rank); - void compute_1B(const int typ_idx, double & energy ); + void read_parameters(string paramfile); - void compute_2B(const double dx, const vector & dr, const vector typ_idxs, vector > force, vector stress, double & energy ); + void compute_1B(const int typ_idx, double & energy ); - void compute_3B(const vector & dx, const vector > & dr, const vector & typ_idxs, vector > force, vector stress, double & energy ); + // 2+B compute functions overloaded with force_scalar_in var for compatibility with LAMMPS - void compute_4B(const vector & dx, const vector > & dr, const vector & typ_idxs, vector > force, vector stress, double & energy ); + void compute_2B(const double dx, const vector & dr, const vector typ_idxs, vector & force, vector & stress, double & energy, chimes2BTmp &tmp); + void compute_2B(const double dx, const vector & dr, const vector typ_idxs, vector & force, vector & stress, double & energy, chimes2BTmp &tmp, double & 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 - double max_cutoff_3B(bool silent = false); // Returns the largest 3B cutoff - double max_cutoff_4B(bool silent = false); // Returns the largest 4B cutoff - - void set_atomtypes(vector & type_list); - - int get_atom_pair_index(int pair_id); + void compute_3B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force,vector & stress, double & energy, chimes3BTmp &tmp); + void compute_3B(const vector & dx, const vector & dr, const vector & typ_idxs, vector & force,vector & stress, double & energy, chimes3BTmp &tmp, vector & force_scalar_in); + 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 - private: + double max_cutoff_2B(bool silent = false); // Returns the largest 2B cutoff + double max_cutoff_3B(bool silent = false); // Returns the largest 3B cutoff + double max_cutoff_4B(bool silent = false); // Returns the largest 4B cutoff + void set_atomtypes(vector & type_list); + + int get_atom_pair_index(int pair_id); + void build_pair_int_trip_map() ; + void build_pair_int_quad_map() ; + +private: - string xform_style; // Morse, direct, inverse, etc... - string fcut_type; // cutoff function style (tersoff/cubic) - double fcut_var; // tersoff distance (if fcut_type) - 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 + string xform_style; // Morse, direct, inverse, etc... + fcutType fcut_type; // cutoff function style (tersoff/cubic) + double fcut_var; // tersoff distance (if fcut_type) + double inner_smooth_distance ; // Used in smoothing the cutoff interaction. + 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 - // Names (chemical symbols for constituent atoms) .. handled differently for 2-body versus >2-body interactions + // Names (chemical symbols for constituent atoms) .. handled differently for 2-body versus >2-body interactions - vector pair_params_atm_chem_1; //[npairs]; // first atom in pair - vector pair_params_atm_chem_2; //[npairs]; // second atom in pair + vector pair_params_atm_chem_1; //[npairs]; // first atom in pair + vector pair_params_atm_chem_2; //[npairs]; // second atom in pair - vector > trip_params_atm_chems; //[ntrips][3] // Gives chemical symbol for each ATOM in the triplet (i.e. "Si") - vector > trip_params_pair_typs; //[ntrips][3] // Gives chemical symbols for each PAIR in the triplet (i.e. "SiO") + vector > trip_params_atm_chems; //[ntrips][3] // Gives chemical symbol for each ATOM in the triplet (i.e. "Si") + vector > trip_params_pair_typs; //[ntrips][3] // Gives chemical symbols for each PAIR in the triplet (i.e. "SiO") - vector > quad_params_atm_chems; //[quads][3] // Gives chemical symbol for each ATOM in the quadruplet (i.e. "Si") - vector > quad_params_pair_typs; //[quads][3] // Gives chemical symbols for each PAIR in the quadruplet (i.e. "SiO") + vector > quad_params_atm_chems; //[quads][3] // Gives chemical symbol for each ATOM in the quadruplet (i.e. "Si") + vector > quad_params_pair_typs; //[quads][3] // Gives chemical symbols for each PAIR in the quadruplet (i.e. "SiO") - int n_pair_maps; // Number of pair maps entries - int n_trip_maps; // Number of trip maps entries - int n_quad_maps; // Number of quad maps entries + int n_pair_maps; // Number of pair maps entries + int n_trip_maps; // Number of trip maps entries + int n_quad_maps; // Number of quad maps entries - int pair_type_idx; - int trip_type_idx; - int quad_type_idx; + int pair_type_idx; + int trip_type_idx; + int quad_type_idx; - //////////////////////// - // Definitions for pair, triplet, and quadruplet types - //////////////////////// + //////////////////////// + // Definitions for pair, triplet, and quadruplet types + //////////////////////// - // 2-body maps + // 2-body maps - vector atom_typ_pair_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives chemical symbol list (i.e. "SiO") - vector atom_idx_pair_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives correspoding parameter index (i.e. 5) - vector atom_int_pair_map; // [nmaps] "fast" maps, based on atom type index - vector atom_int_prpr_map; // [nmaps] "fast" maps, based on atom type index ... returns the "proper" pair type instead of an index + vector atom_typ_pair_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives chemical symbol list (i.e. "SiO") + vector atom_idx_pair_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives correspoding parameter index (i.e. 5) + vector atom_int_pair_map; // [nmaps] "fast" maps, based on atom type index + vector atom_int_prpr_map; // [nmaps] "fast" maps, based on atom type index ... returns the "proper" pair type instead of an index - // 3-body maps + // 3-body maps - vector atom_typ_trip_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives chemical symbol list (i.e. "SiOSiOOO") - vector atom_idx_trip_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives correspoding parameter index (i.e. 3) - vector atom_int_trip_map; // [nmaps] "fast" maps, based on atom type index // gives the correspoding parameter index (i.e. 3) for a unique integer built from type index of three atoms of arbitrary order + vector atom_typ_trip_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives chemical symbol list (i.e. "SiOSiOOO") + vector atom_idx_trip_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives correspoding parameter index (i.e. 3) + vector atom_int_trip_map; // [nmaps] "fast" maps, based on atom type index // gives the correspoding parameter index (i.e. 3) for a unique integer built from type index of three atoms of arbitrary order + vector > pair_int_trip_map ; // Gives the atom pair indices for an arbitrary triplet of atom types. - // 4-body maps + // 4-body maps - vector atom_typ_quad_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives chemical symbol list (i.e. "SiOSiOOO") - vector atom_idx_quad_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives correspoding parameter index (i.e. 3) - vector atom_int_quad_map; // [nmaps] "fast" maps, based on atom type index // gives the correspoding parameter index (i.e. 3) for a unique integer built from type index of four atoms of arbitrary order + vector atom_typ_quad_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives chemical symbol list (i.e. "SiOSiOOO") + vector atom_idx_quad_map; // [nmaps] "slow" maps, based on atom chemical symbol // Used to build int map -- gives correspoding parameter index (i.e. 3) + vector atom_int_quad_map; // [nmaps] "fast" maps, based on atom type index // gives the correspoding parameter index (i.e. 3) for a unique integer built from type index of four atoms of arbitrary order + vector > pair_int_quad_map ; // Gives the atom pair indices for an arbitrary quad of atom types. - //////////////////////// - // Polynomial parameters - //////////////////////// + //////////////////////// + // Polynomial parameters + //////////////////////// - // number of coefficients for the pair/triplet/quadruplet type + // number of coefficients for the pair/triplet/quadruplet type - vector ncoeffs_2b; // [npairs] + vector ncoeffs_2b; // [npairs] - vector > chimes_2b_pows; // [npairs][npowers] power for the coresponding parameter + vector > chimes_2b_pows; // [npairs][npowers] power for the coresponding parameter - vector > chimes_2b_params; // [npairs][npowers] 2-body polynomial coefficients - vector > chimes_2b_cutoff; // [npairs][2] inner and outer cutoff for pair + vector > chimes_2b_params; // [npairs][npowers] 2-body polynomial coefficients + vector > chimes_2b_cutoff; // [npairs][2] inner and outer cutoff for pair - vector ncoeffs_3b; // [ntrips] - vector > > chimes_3b_powers; // [ntrips][nparams][constit. pair] - vector > chimes_3b_params; // [ntrips][nparams] - vector > > chimes_3b_cutoff; // [ntrips][2][constit. pair] inner and outer cutoff for pair 1 + vector ncoeffs_3b; // [ntrips] + vector > > chimes_3b_powers; // [ntrips][nparams][constit. pair] + vector > chimes_3b_params; // [ntrips][nparams] + vector > > chimes_3b_cutoff; // [ntrips][2][constit. pair] inner and outer cutoff for pair 1 - vector ncoeffs_4b; // [nquads] - vector > > chimes_4b_powers; // [nquads][nparams][constit. pair] - vector > chimes_4b_params; // [nquads][nparams] - vector > > chimes_4b_cutoff; // [nquads][2][constit. pair] inner and outer cutoff for pair 1 + vector ncoeffs_4b; // [nquads] + vector > > chimes_4b_powers; // [nquads][nparams][constit. pair] + vector > chimes_4b_params; // [nquads][nparams] + vector > > chimes_4b_cutoff; // [nquads][2][constit. pair] inner and outer cutoff for pair 1 - // Tools for compute functions + // Tools for compute functions - inline void set_cheby_polys(double *Tn, double *Tnd, const double dx, const int pair_idx, const double inner_cutoff, const double outer_cutoff, const int bodiedness_idx); + inline void set_cheby_polys(vector &Tn, vector &Tnd, double dx, const int pair_idx, + const double inner_cutoff, const double outer_cutoff, const int bodiedness_idx) ; + + void set_polys_out_of_range(vector &Tn, vector &Tnd, double dx, double x, + int poly_order, double inner_cutoff, double exprlen, double dx_dr) ; + + inline void get_fcut(const double dx, const double outer_cutoff, double & fcut, double & fcutderiv); - inline void get_fcut(const double dx, const double outer_cutoff, double & fcut, double & fcutderiv); + inline void get_penalty(const double dx, const int & pair_idx, double & E_penalty, double & force_scalar); - inline void get_penalty(const double dx, const int & pair_idx, double & E_penalty, double & force_scalar); + inline void build_atom_and_pair_mappers(const int natoms, const int npairs, const vector & typ_idxs, + const vector & clu_params_atm_chems, vector & mapped_pair_idx); + + inline void build_atom_and_pair_mappers(const int natoms, const int npairs, const vector & typ_idxs, const vector & clu_params_atm_chems, + int *mapped_pair_idx); + + int get_proper_pair(string ty1, string ty2); - inline void build_atom_and_pair_mappers(const int natoms, const int npairs, const vector typ_idxs, const vector > & clu_params_atm_chems, const int & cluidx, vector & mapped_pair_idx); + double max_cutoff(int ntypes, vector > > & cutoff_list); - int get_proper_pair(string ty1, string ty2); + // Tools for reading the input file - double max_cutoff(int ntypes, vector > > & cutoff_list); + int split_line(string line, vector & items); - // Tools for reading the input file + string get_next_line(istream& str); - int split_line(string line, vector & items); + // Fun stuff - string get_next_line(istream& str); + void print_pretty_stuff(); + + inline double dr2_3B(const double *dr2, int i, int j, int k, int l) ; + inline double dr2_4B(const double *dr2, int i, int j, int k, int l) ; + inline void init_distance_tensor(double *dr2, const vector & dr, int natoms) ; +}; + + + +inline void chimesFF::get_fcut(const double dx, const double outer_cutoff, double & fcut, double & fcutderiv) +{ + + double fcut0; + double fcut0_deriv ; + + if(fcut_type == fcutType::CUBIC ) + { + fcut0 = (1.0 - dx/outer_cutoff); + fcut = pow(fcut0,3.0); + fcutderiv = pow(fcut0,2.0); + fcutderiv *= -1.0 * 3.0 /outer_cutoff; + + } + else if ( fcut_type == fcutType::TERSOFF ) + { + + double THRESH = outer_cutoff-fcut_var*outer_cutoff; + + + if (dx < THRESH) // Case 1: Our pair distance is less than the fcut kick-in distance + { + fcut = 1.0; + fcutderiv = 0.0; + } + else if (dx > outer_cutoff) // Case 2: Our pair distance is greater than the cutoff + { + fcut = 0.0; + fcutderiv = 0.0; + } + else // Case 3: We'll use our modified sin function + { + fcut0 = (dx-THRESH) / (outer_cutoff-THRESH) * pi + pi/2.0; + fcut0_deriv = pi / (outer_cutoff - THRESH); + + fcut = 0.5 + 0.5 * sin( fcut0 ); + fcutderiv = 0.5 * cos( fcut0 ) * fcut0_deriv; + } + } +} + +inline void chimesFF::get_penalty(const double dx, const int & pair_idx, double & E_penalty, double & force_scalar) +{ + double r_penalty = 0.0; + + E_penalty = 0.0; + force_scalar = 1.0; + + if (dx - penalty_params[0] < chimes_2b_cutoff[pair_idx][0]) - // Fun stuff + r_penalty = chimes_2b_cutoff[pair_idx][0] + penalty_params[0] - dx; - void print_pretty_stuff(); -}; + 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) + { + 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 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. +{ + build_atom_and_pair_mappers(natoms, npairs, typ_idxs, clu_params_pair_typs, mapped_pair_idx.data() ) ; +} + +inline void chimesFF::build_atom_and_pair_mappers(const int natoms, const int npairs, const vector & typ_idxs, + const vector & clu_params_pair_typs, + int *mapped_pair_idx) +{ + // Generate permutations for atoms... all we are doing is permuting the possible indices for typ_idxs + + + // build a copy of the atom type vector for permuting + + vector tmp_typ_idxs; + int nelements; + + nelements = typ_idxs.size(); + tmp_typ_idxs.resize(nelements); + + for(int i=0; i > tmp_pairs; + tmp_pairs.resize(npairs,vector(2)); + vector > runtime_pairs; + runtime_pairs.resize(npairs,vector(2)); + + int idx = 0; + + for(int i=0; i runtime_pair_typs(npairs); + + do + { + // Check if the permutation leads to pair types that match the order specified by the force field type + + idx = 0; + + for(int i=0; i &Tn, vector &Tnd, double dx, const int pair_idx, + const double inner_cutoff, const double outer_cutoff, const int bodiedness_idx) +{ + // Currently assumes a Morse-style transformation has been requested + + // Sets the value of the Chebyshev polynomials (Tn) and their derivatives (Tnd). Tnd is the derivative + // with respect to the interatomic distance, not the transformed distance (x). + + // Do the Morse transformation + + double x_min = exp(-1*inner_cutoff/morse_var[pair_idx]); + double x_max = exp(-1*outer_cutoff/morse_var[pair_idx]); + + double x_avg = 0.5 * (x_max + x_min); + double x_diff = 0.5 * (x_max - x_min); + + x_diff *= -1.0; // Special for Morse style + + + bool out_of_range ; + double dx_orig = dx ; + + // The case dx > outer_cutoff is not treated, because it is assumed that the outer smoothing + // function will be zero for dx > outer_cutoff. + if ( dx < inner_cutoff ) + { + out_of_range = true ; + dx = inner_cutoff ; + } + else + out_of_range = false ; + + double exprlen = exp(-1*dx/morse_var[pair_idx]); + double x = (exprlen - x_avg)/x_diff; + double dx_dr = (-exprlen/morse_var[pair_idx])/x_diff; + + if ( ! out_of_range ) + { + // Generate Chebyshev polynomials by recursion. + // + // What we're doing here. Want to fit using Cheby polynomials of the 1st kinD[i]. "T_n(x)." + // We need to calculate the derivative of these polynomials. + // Derivatives are defined through use of Cheby polynomials of the 2nd kind "U_n(x)", as: + // + // d/dx[ T_n(x) = n * U_n-1(x)] + // + // So we need to first set up the 1st-kind polynomials ("Tn[]") + // Then, to compute the derivatives ("Tnd[]"), first set equal to the 2nd-kind, then multiply by n to get the der's + + // First two 1st-kind Chebys: + + Tn[0] = 1.0; + Tn[1] = x; + + // Start the derivative setup. Set the first two 1st-kind Cheby's equal to the first two of the 2nd-kind + + Tnd[0] = 1.0; + Tnd[1] = 2.0 * x; + + // Use recursion to set up the higher n-value Tn and Tnd's + + for ( int i = 2; i <= poly_orders[bodiedness_idx]; i++ ) + { + Tn[i] = 2.0 * x * Tn[i-1] - Tn[i-2]; + Tnd[i] = 2.0 * x * Tnd[i-1] - Tnd[i-2]; + } + + // Now multiply by n to convert Tnd's to actual derivatives of Tn + + // The following dx_dr compuation assumes a Morse transformation + // DERIV_CONST is no longer used. (old way: dx_dr = DERIV_CONST*cheby_var_deriv(x_diff, rlen, ff_2body.LAMBDA, ff_2body.CHEBY_TYPE, exprlen);) + + for ( int i = poly_orders[bodiedness_idx]; i >= 1; i-- ) + Tnd[i] = i * dx_dr * Tnd[i-1]; + + Tnd[0] = 0.0; + } + else // out_of_range == true + { + cout << "Warning: An intermolecular distance less than the inner cutoff = " << inner_cutoff << " was found\n " ; + cout << " Distance = " << dx_orig << endl ; + + set_polys_out_of_range(Tn, Tnd, dx_orig, x, poly_orders[bodiedness_idx], inner_cutoff, exprlen, dx_dr) ; + } + +} #endif + + + + + + + + + + + + + + + + + + + + + + diff --git a/etc/lmp/etc/Makefile.mpi_chimes b/etc/lmp/etc/Makefile.mpi_chimes index a00fb4f..70d1624 100644 --- a/etc/lmp/etc/Makefile.mpi_chimes +++ b/etc/lmp/etc/Makefile.mpi_chimes @@ -7,18 +7,18 @@ SHELL = /bin/sh # specify flags and libraries needed for your compiler CC = mpiicpc -CCFLAGS = -O3 -std=c++11 -restrict -SHFLAGS = -fPIC -DEPFLAGS = -M +CCFLAGS = -O3 -std=c++11 -restrict +SHFLAGS = -fPIC +DEPFLAGS = -M LINK = mpiicpc -LINKFLAGS = -O3 -std=c++11 -LIB = -SIZE = size +LINKFLAGS = -O3 -std=c++11 +LIB = +SIZE = size -ARCHIVE = ar -ARFLAGS = -rc -SHLIBFLAGS = -shared +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL @@ -28,7 +28,7 @@ SHLIBFLAGS = -shared # LAMMPS ifdef settings # see possible settings in Section 3.5 of the manual -LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 # -DLAMMPS_CXX98 +LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 # -DLAMMPS_CXX98 # MPI library # see discussion in Section 3.4 of the manual @@ -42,7 +42,7 @@ LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 # -DLAMMPS_CXX98 MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I${I_MPI_ROOT}/include MPI_PATH = -L${I_MPI_ROOT}/lib -L${I_MPI_ROOT}/lib/release -MPI_LIB = +MPI_LIB = # FFT library # see discussion in Section 3.5.2 of manual @@ -51,9 +51,9 @@ MPI_LIB = # PATH = path for FFT library # LIB = name of FFT library -FFT_INC = -FFT_PATH = -FFT_LIB = +FFT_INC = +FFT_PATH = +FFT_LIB = # JPEG and/or PNG library # see discussion in Section 3.5.4 of manual @@ -62,9 +62,9 @@ FFT_LIB = # PATH = path(s) for JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library -JPG_INC = -JPG_PATH = -JPG_LIB = +JPG_INC = +JPG_PATH = +JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies diff --git a/etc/lmp/etc/pair.cpp b/etc/lmp/etc/pair.cpp index 5c14be9..0725684 100644 --- a/etc/lmp/etc/pair.cpp +++ b/etc/lmp/etc/pair.cpp @@ -1309,19 +1309,51 @@ void Pair::ev_tally4(int i, int j, int k, int m, double evdwl, do not make sense. Expects newton_pair = 1. ------------------------------------------------------------------------- */ - -void Pair::ev_tally_mb(double evdwl, double sxx, double sxy, double sxz, double syy, double syz, double szz) -{ - eng_vdwl += evdwl; - - virial[0] += sxx; - virial[1] += syy; - virial[2] += szz; - virial[3] += sxy; - virial[4] += sxz; - virial[5] += syz; + void Pair::ev_tally_mb(int npair, int atmpairidxlst[6][2], double evdwl, std::vectorfscalar, std::vector & dist, std::vector &dr) + { + double v[6]; - } + eng_vdwl += evdwl; // Note: Assume eflag_global alsways true and eflag atom always false + + if (vflag_either) // Note: Assume newton_pair always true for this pair type + { + for (int i=0; ifscalar, std::vector & dist, std::vector &dr); + // general child-class methods diff --git a/etc/lmp/install.sh b/etc/lmp/install.sh index 2f4fe84..e12a1da 100755 --- a/etc/lmp/install.sh +++ b/etc/lmp/install.sh @@ -34,9 +34,11 @@ cp etc/Makefile.mpi_chimes build/lammps_stable_29Oct2020/src/MAKE # load the intel (e.g., icc) module and run the the setvars.sh command, e.g. located at # /sw/pkgs/arc/intel/2022.1.2/setvars.sh --also avail for free -if [ ! -v hosttype ] ; then - echo "No hosttype specified" +if [ -z "$hosttype" ] ; then + echo "" + echo "WARNING: No hosttype specified" echo "Be sure to load modules/configure compilers by hand before running this script!" + echo "" elif [[ "$hosttype" == "LLNL-LC" ]] ; then source modfiles/LLNL-LC.mod elif [[ "$hosttype" == "UM-ARC" ]] ; then @@ -59,7 +61,10 @@ else fi -module list +echo "Detected hosttype: $hosttype" +if [ ! -z "$hasmod" ] ; then + module list +fi # Compile @@ -82,3 +87,4 @@ echo "Generated the following LAMMPS executable with ChIMES support:" echo "${loc}/exe/lmp_mpi_chimes" echo "See ${loc}/tests for usage examples" echo "" + diff --git a/etc/lmp/src/pair_chimes.cpp b/etc/lmp/src/pair_chimes.cpp index 9ee06aa..ac39d3e 100644 --- a/etc/lmp/src/pair_chimes.cpp +++ b/etc/lmp/src/pair_chimes.cpp @@ -71,16 +71,17 @@ PairCHIMES::PairCHIMES(LAMMPS *lmp) : Pair(lmp) // 2, 3, and 4-body vars for chimesFF access - dr .resize(3); - dr_3b .resize(3, std::vector(3)); - dr_4b .resize(6, std::vector(3)); + dr .resize(CHDIM); + dr_3b .resize(3*CHDIM); + dr_4b .resize(6*CHDIM); dist_3b.resize(3); dist_4b.resize(6); - - force_ptr_2b.resize(2,std::vector(3)); - force_ptr_3b.resize(3,std::vector(3)); - force_ptr_4b.resize(4,std::vector(3)); + + // CHDIM is the number of spatial dimensions (usually 3). + force_2b.resize(2*CHDIM); + force_3b.resize(3*CHDIM) ; + force_4b.resize(4*CHDIM) ; typ_idxs_2b.resize(2); typ_idxs_3b.resize(3); @@ -129,7 +130,11 @@ void PairCHIMES::coeff(int narg, char **arg) chimesFF_paramfile = arg[2]; 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() ; // Set special LAMMPS flags/cutoffs @@ -204,7 +209,7 @@ double PairCHIMES::init_one(int i, int j) return sqrt(cutsq[i][j]); } -double PairCHIMES::get_dist(int i, int j, vector & dr) +inline double PairCHIMES::get_dist(int i, int j, double *dr) { double **x = atom -> x; // Access to system coordinates @@ -214,10 +219,10 @@ double PairCHIMES::get_dist(int i, int j, vector & dr) return sqrt(dr[0]*dr[0] + dr[1]*dr[1] + dr[2]*dr[2]); } - -double PairCHIMES::get_dist(int i, int j) + +inline double PairCHIMES::get_dist(int i, int j) { - vector dummy_dr(3); + double dummy_dr[3] ; return get_dist(i,j, dummy_dr); } @@ -376,8 +381,14 @@ void PairCHIMES::compute(int eflag, int vflag) { // Vars for access to chimesFF compute_XB functions - std::vector stensor(9); // pointers to system stress tensor - std::vector stmp(9); // Dummy var to prevent chimesFF from directly modifying LAMMPS stress + std::vector stensor(6); // pointers to system stress tensor + + // 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]; // General LAMMPS compute vars @@ -420,6 +431,11 @@ void PairCHIMES::compute(int eflag, int vflag) 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]) ; + chimes3BTmp chimes_3btmp(chimes_calculator.poly_orders[1]) ; + chimes4BTmp chimes_4btmp(chimes_calculator.poly_orders[2]) ; + // Build the ChIMES many-body neighbor lists.. only do so when LAMMPS neighborlist has been updated if ( neighbor->ago == 0) @@ -440,12 +456,6 @@ void PairCHIMES::compute(int eflag, int vflag) // Compute 1- and 2-body interactions //////////////////////////////////////// - for (idx=0; idx<9; idx++) - { - stensor[idx] = &stmp[idx]; - *stensor[idx] = 0; - } - for (ii = 0; ii < inum; ii++) // Loop over the atoms owned by the current process { i = ilist[ii]; // Index of the current atom @@ -461,8 +471,8 @@ void PairCHIMES::compute(int eflag, int vflag) chimes_calculator.compute_1B(type[i]-1, energy); if(evflag) - ev_tally_mb(energy, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0); - + ev_tally_mb(0, atmidxlst, energy, fscalar, tmp_dist, tmp_dr); + // Now move on to two-body force, stress, and energy for (jj = 0; jj < jnum; jj++) // Loop over neighbors of i @@ -477,31 +487,39 @@ void PairCHIMES::compute(int eflag, int vflag) // Get distance using ghost atoms... don't need MIC since we're using ghost atoms - dist = get_dist(i,j,dr); + 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[1] = chimes_type[type[j]-1]; - - for (idx=0; idx<3; idx++) - { - force_ptr_2b[0][idx] = &f[i][idx]; - force_ptr_2b[1][idx] = &f[j][idx]; - } - + + // Using std::fill for maximum efficiency. + std::fill(force_2b.begin(), force_2b.end(), 0.0) ; + // Do the same for stress tensors - - for (idx=0; idx<9; idx++) - *stensor[idx] = 0; + std::fill(stensor.begin(), stensor.end(), 0.0) ; energy = 0.0; - chimes_calculator.compute_2B( dist, dr, typ_idxs_2b, force_ptr_2b, stensor, energy); + chimes_calculator.compute_2B( dist, dr, typ_idxs_2b, force_2b, stensor, energy, chimes_2btmp); + + for (idx=0; idx<3; idx++) + { + f[i][idx] += force_2b[0*CHDIM+idx] ; + f[j][idx] += force_2b[1*CHDIM+idx] ; + } // "Save"/tally up the energy and stresses to the global virial/energy data objects (see pair.cpp ~ line 1000) // Compute pressure, (in contrast to chimes_md) AFTER penalty has been added + if(vflag_atom) + { + atmidxlst[0][0] = i; + atmidxlst[0][1] = j; + } + tmp_dist [0] = dist; + if (evflag) - ev_tally_mb(energy, *stensor[0], *stensor[1], *stensor[2], *stensor[4], *stensor[5], *stensor[8]); + ev_tally_mb(2, atmidxlst, energy, fscalar, tmp_dist, dr); } } @@ -517,30 +535,40 @@ void PairCHIMES::compute(int eflag, int vflag) j = neighborlist_3mers[ii][1]; k = neighborlist_3mers[ii][2]; - dist_3b[0] = get_dist(i,j,dr_3b[0]); - dist_3b[1] = get_dist(i,k,dr_3b[1]); - dist_3b[2] = get_dist(j,k,dr_3b[2]); + dist_3b[0] = get_dist(i,j,&dr_3b[0*CHDIM]); + dist_3b[1] = get_dist(i,k,&dr_3b[1*CHDIM]); + dist_3b[2] = get_dist(j,k,&dr_3b[2*CHDIM]); typ_idxs_3b[0] = chimes_type[type[i]-1]; typ_idxs_3b[1] = chimes_type[type[j]-1]; typ_idxs_3b[2] = chimes_type[type[k]-1]; + std::fill(force_3b.begin(), force_3b.end(), 0.0) ; + std::fill(stensor.begin(), stensor.end(), 0.0) ; + + energy = 0.0 ; + + chimes_calculator.compute_3B( dist_3b, dr_3b, typ_idxs_3b, force_3b, stensor, energy, chimes_3btmp); + for (idx=0; idx<3; idx++) { - force_ptr_3b[0][idx] = &f[i][idx]; - force_ptr_3b[1][idx] = &f[j][idx]; - force_ptr_3b[2][idx] = &f[k][idx]; + f[i][idx] += force_3b[0*CHDIM+idx] ; + f[j][idx] += force_3b[1*CHDIM+idx] ; + f[k][idx] += force_3b[2*CHDIM+idx] ; } - for (idx=0; idx<9; idx++) - *stensor[idx] = 0; - - energy = 0; + if (vflag_atom) + { + atmidxlst[0][0] = i; + atmidxlst[0][1] = j; + atmidxlst[1][0] = i; + atmidxlst[1][1] = k; + atmidxlst[2][0] = j; + atmidxlst[2][1] = k; + } - chimes_calculator.compute_3B( dist_3b, dr_3b, typ_idxs_3b, force_ptr_3b, stensor, energy); - if (evflag) - ev_tally_mb(energy, *stensor[0], *stensor[1], *stensor[2], *stensor[4], *stensor[5], *stensor[8]); + ev_tally_mb(3, atmidxlst, energy, fscalar, dist_3b, dr_3b); } } @@ -557,38 +585,58 @@ void PairCHIMES::compute(int eflag, int vflag) k = neighborlist_4mers[ii][2]; l = neighborlist_4mers[ii][3]; - dist_4b[0] = get_dist(i,j,dr_4b[0]); - dist_4b[1] = get_dist(i,k,dr_4b[1]); - dist_4b[2] = get_dist(i,l,dr_4b[2]); - dist_4b[3] = get_dist(j,k,dr_4b[3]); - dist_4b[4] = get_dist(j,l,dr_4b[4]); - dist_4b[5] = get_dist(k,l,dr_4b[5]); + dist_4b[0] = get_dist(i,j,&dr_4b[0*CHDIM]); + dist_4b[1] = get_dist(i,k,&dr_4b[1*CHDIM]); + dist_4b[2] = get_dist(i,l,&dr_4b[2*CHDIM]); + dist_4b[3] = get_dist(j,k,&dr_4b[3*CHDIM]); + dist_4b[4] = get_dist(j,l,&dr_4b[4*CHDIM]); + dist_4b[5] = get_dist(k,l,&dr_4b[5*CHDIM]); typ_idxs_4b[0] = chimes_type[type[i]-1]; typ_idxs_4b[1] = chimes_type[type[j]-1]; typ_idxs_4b[2] = chimes_type[type[k]-1]; typ_idxs_4b[3] = chimes_type[type[l]-1]; + std::fill(force_4b.begin(), force_4b.end(), 0.0) ; + std::fill(stensor.begin(), stensor.end(), 0.0) ; + + energy = 0.0 ; + + chimes_calculator.compute_4B( dist_4b, dr_4b, typ_idxs_4b, force_4b, stensor, energy, chimes_4btmp); + for (idx=0; idx<3; idx++) { - force_ptr_4b[0][idx] = &f[i][idx]; - force_ptr_4b[1][idx] = &f[j][idx]; - force_ptr_4b[2][idx] = &f[k][idx]; - force_ptr_4b[3][idx] = &f[l][idx]; + f[i][idx] += force_4b[0*CHDIM+idx] ; + f[j][idx] += force_4b[1*CHDIM+idx] ; + f[k][idx] += force_4b[2*CHDIM+idx] ; + f[l][idx] += force_4b[3*CHDIM+idx] ; } - - for (idx=0; idx<9; idx++) - *stensor[idx] = 0; - - energy = 0; - chimes_calculator.compute_4B( dist_4b, dr_4b, typ_idxs_4b, force_ptr_4b, stensor, energy); - + if (vflag_atom) + { + atmidxlst[0][0] = i; + atmidxlst[0][1] = j; + atmidxlst[1][0] = i; + atmidxlst[1][1] = k; + atmidxlst[2][0] = i; + atmidxlst[2][1] = l; + atmidxlst[3][0] = j; + atmidxlst[3][1] = k; + atmidxlst[4][0] = j; + atmidxlst[4][1] = l; + atmidxlst[5][0] = k; + atmidxlst[5][1] = l; + } + if (evflag) - ev_tally_mb(energy, *stensor[0], *stensor[1], *stensor[2], *stensor[4], *stensor[5], *stensor[8]); + ev_tally_mb(4, atmidxlst, energy, fscalar, dist_4b, dr_4b); + } } +if (vflag_fdotr) + virial_fdotr_compute(); + return; } @@ -605,8 +653,8 @@ void PairCHIMES::set_chimes_type() chimes_type.push_back(j); nmatches++; } - } - } + } } + if (nmatches < atom->ntypes ) { diff --git a/etc/lmp/src/pair_chimes.h b/etc/lmp/src/pair_chimes.h index f6e480e..942415e 100644 --- a/etc/lmp/src/pair_chimes.h +++ b/etc/lmp/src/pair_chimes.h @@ -28,7 +28,7 @@ PairStyle(chimesFF,PairCHIMES); // PairStyle(key, class) #include "pair.h" #include "chimesFF.h" -#include +#include /* Functions required by LAMMPS: @@ -47,48 +47,48 @@ read_restart_settings read global settings from restart file single force and energy fo a single pairwise interaction between two atoms */ - + namespace LAMMPS_NS { - class PairCHIMES : public Pair + class PairCHIMES : public Pair { public: - + // Variable definitions - + chimesFF chimes_calculator; // chimesFF instance - + 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 double maxcut_3b; double maxcut_4b; - + 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; - + // 2-body vars for chimesFF access std::vector dr; - std::vector > dr_3b; - std::vector > dr_4b; + std::vector dr_3b; + std::vector dr_4b; double dist; - std::vector dist_3b; - std::vector dist_4b; + std::vector dist_3b; + std::vector dist_4b; - std::vector > force_ptr_2b; - std::vector > force_ptr_3b; - std::vector > force_ptr_4b; + std::vector force_2b; + std::vector force_3b; + std::vector force_4b; std::vector typ_idxs_2b; std::vector typ_idxs_3b; - std::vector typ_idxs_4b; + std::vector typ_idxs_4b; // Vars for neighlist construction @@ -96,36 +96,36 @@ namespace LAMMPS_NS std::vector tmp_4mer; // Constructor/Deconstructor - + PairCHIMES(class LAMMPS *); - + virtual ~PairCHIMES(); - + // Functions that have been written void settings(int narg, char **arg); - void init_style(); + void init_style(); void coeff(int narg, char **arg); void allocate(); - double init_one(int i, int j); + double init_one(int i, int j); void compute(int eflag, int vflag); void build_mb_neighlists(); - double get_dist(int i, int j, vector & dr); - double get_dist(int i, int j); + inline double get_dist(int i, int j, double* dr); + inline double get_dist(int i, int j); void set_chimes_type(); - // Functions I haven't worked on - - void write_restart(); - void read_restart(); - void write_restart_settings(); + // Functions I haven't worked on + + void write_restart(); + void read_restart(); + void write_restart_settings(); void read_restart_settings(); - void single(); + void single(); }; -} - +} + #endif #endif diff --git a/install.sh b/install.sh index f08f4e9..87e14e9 100755 --- a/install.sh +++ b/install.sh @@ -9,15 +9,18 @@ # # Otherwise, load necessary modules manually and execute with # -# ./install.sh +# ./install.sh # # Note that additional arguments can be specified, i.e.: # # ./install.sh +# Verbose is required for testing. + BUILD=`pwd`/build DEBUG=${1-0} # False (0) by default. PREFX=${2-$BUILD} # Empty by default +VERBOSE=${4-0} # Clean up previous installation, @@ -32,6 +35,11 @@ if [ -z "$hosttype" ] ; then echo "" elif [[ "$hosttype" == "LLNL-LC" ]] ; then source modfiles/LLNL-LC.mod + ICC=`which icc` + IFORT=`which ifort` + my_flags="$my_flags -DCMAKE_CXX_COMPILER=${ICC} -DCMAKE_Fortran_COMPILER=${IFORT} -DCMAKE_C_COMPILER=${ICC}" + my_flags="$my_flags -DCMAKE_CXX_FLAGS_RELEASE=\"-O3 -fno-alias -fno-fnalias -xhost\"" + elif [[ "$hosttype" == "UM-ARC" ]] ; then source modfiles/UM-ARC.mod elif [[ "$hosttype" == "JHU-ARCH" ]] ; then @@ -62,12 +70,14 @@ fi mkdir build cd build -# Generate cmake flags - -my_flags="" +if [[ $VERBOSE -eq 1 ]] ; then + my_flags="-DVERBOSE=1" +else + my_flags="-DVERBOSE=0" +fi if [ ! -z $PREFX ] ; then - my_flags="-DCMAKE_INSTALL_PREFIX=${PREFX}" + my_flags="-DCMAKE_INSTALL_PREFIX=${PREFX} $my_flags" fi if [ $DEBUG -eq 1 ] ;then diff --git a/modfiles/LLNL-LC.mod b/modfiles/LLNL-LC.mod index 590885e..237bf9b 100755 --- a/modfiles/LLNL-LC.mod +++ b/modfiles/LLNL-LC.mod @@ -1,3 +1,4 @@ module load cmake/3.21.1 module load intel/18.0.1 -module load impi/2018.0 +module load intel/2021.3 +#module load impi/2018.0 diff --git a/serial_interface/examples/c/Makefile b/serial_interface/examples/c/Makefile index 74216a2..961a5c7 100644 --- a/serial_interface/examples/c/Makefile +++ b/serial_interface/examples/c/Makefile @@ -1,4 +1,4 @@ -CXX = g++ -O3 -std=c++11 +CXX = g++ -O3 -std=c++11 CCOMP = gcc -O3 DEBUG = 1 @@ -15,8 +15,8 @@ SERIAL_LOC=$(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) +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 @@ -28,7 +28,7 @@ chimescalc_serial_C.o : $(WRAPPER_SRC) TEST_LOC=$(C_LOC) TEST_SRC=$(TEST_LOC)/main.c -main.o: $(TEST_SRC) +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 @@ -37,7 +37,7 @@ test-C: $(TEST_LNK) $(CXX) $(TEST_LNK) -o chimescalc-test_serial-C clean: - rm -f *.o + rm -f *.o clean-all: make clean diff --git a/serial_interface/examples/fortran/Makefile b/serial_interface/examples/fortran/Makefile index 1f09d6d..30cebe3 100644 --- a/serial_interface/examples/fortran/Makefile +++ b/serial_interface/examples/fortran/Makefile @@ -2,8 +2,9 @@ CXX = g++ -O3 -std=c++11 -fPIC FCC = gfortran -O3 -fPIC -std=f2003 -cpp # last flag allows processing of C-style pre-processor directives DEBUG = 1 +VERBOSE = 1 -#CCFLAGS = -fPIC -O3 -std=c++11 +#CCFLAGS = -fPIC -O3 -std=c++11 #FFLAGS = -O3 -fPIC #COMM1 = chimescalc_serial_F.o main.o @@ -20,7 +21,7 @@ SERIAL_LOC=$(F_LOC)/../../src SERIAL_SRC=$(SERIAL_LOC)/serial_chimes_interface.cpp SERIAL_HDR=$(SERIAL_LOC)/serial_chimes_interface.h -serial_chimes_interface.o : $(SERIAL_SRC) +serial_chimes_interface.o : $(SERIAL_SRC) $(CXX) -c $(SERIAL_SRC) -I $(SERIAL_LOC) -I $(chimescalc_LOC) WRAPPERC_LOC=$(F_LOC)/../../api @@ -59,7 +60,7 @@ test-F: $(LINKS) lib : chimesFF.o serial_chimes_interface.o chimescalc_serial_C.o ar rcs libchimescalc-fortran.a chimesFF.o serial_chimes_interface.o chimescalc_serial_C.o -clean: +clean: rm -f *.o *.mod clean-all: @@ -69,10 +70,11 @@ clean-all: all: make chimesFF.o - make serial_chimes_interface.o + make serial_chimes_interface.o make chimescalc_serial_C.o make chimescalc_serial_F.o chimescalc_serial.mod make main.o make test-F make lib make clean + diff --git a/serial_interface/examples/fortran/main.F90 b/serial_interface/examples/fortran/main.F90 index ba55ad0..5de6a57 100644 --- a/serial_interface/examples/fortran/main.F90 +++ b/serial_interface/examples/fortran/main.F90 @@ -1,6 +1,6 @@ ! ChIMES Calculator ! Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried -! Contributing Author: Nir Goldman (2020) +! Contributing Author: Nir Goldman (2020) program test_F_api use chimescalc_serial @@ -32,23 +32,23 @@ program test_F_api 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:" + 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) @@ -77,18 +77,18 @@ program test_F_api energy = 0d0 call f_set_chimes(small) - + print*,"fcheck-1" call f_init_chimes(trim(param_file) // c_null_char, 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 (natom, xc, yc, zc, stringPtr, ca, & @@ -109,7 +109,7 @@ program test_F_api print '(F15.6)',fy(i) print '(F15.6)',fz(i) enddo - + #if DEBUG==1 open (unit = 20, status = 'replace', file='debug.dat') @@ -120,12 +120,16 @@ program test_F_api 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) -#endif + +#endif end program diff --git a/serial_interface/examples/fortran08/Makefile b/serial_interface/examples/fortran08/Makefile index e475a79..f00cf3b 100644 --- a/serial_interface/examples/fortran08/Makefile +++ b/serial_interface/examples/fortran08/Makefile @@ -3,7 +3,7 @@ FCC = gfortran -std=f2008 -O2 -fPIC -cpp DEBUG = 1 -#CCFLAGS = -fPIC -O3 -std=c++11 +#CCFLAGS = -fPIC -O3 -std=c++11 #FFLAGS = -O3 -fPIC #COMM1 = chimescalc_serial_F.o main.o @@ -20,15 +20,15 @@ SERIAL_LOC=$(F_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) - +serial_chimes_interface.o : $(SERIAL_SRC) + $(CXX) -c $(SERIAL_SRC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) + WRAPPERC_LOC=$(F_LOC)/../../api WRAPPERC_SRC=$(WRAPPERC_LOC)/chimescalc_serial_C.cpp WRAPPERC_HDR=$(WRAPPERC_LOC)/chimescalc_serial_.h chimescalc_serial_C.o : $(WRAPPERC_SRC) - $(CXX) -c $(WRAPPERC_SRC) -I $(WRAPPERC_LOC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) + $(CXX) -c $(WRAPPERC_SRC) -I $(WRAPPERC_LOC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) WRAPPERF_LOC=$(F_LOC)/../../api WRAPPERF_SRC=$(WRAPPERF_LOC)/chimescalc_serial_F.f90 @@ -60,17 +60,17 @@ test-F: $(LINKS) lib : chimesFF.o serial_chimes_interface.o chimescalc_serial_C.o ar rcs libchimescalc-fortran08.a chimesFF.o serial_chimes_interface.o chimescalc_serial_C.o -clean: +clean: rm -f *.o *.mod - + clean-all: make clean rm -f chimescalc-test_serial-F08 rm -f libchimescalc-fortran08.a - + all: make chimesFF.o - make serial_chimes_interface.o + make serial_chimes_interface.o make chimescalc_serial_C.o make chimescalc_serial_F.o chimescalc_serial.mod make chimescalc_serial_F08.o chimes_serial08.mod @@ -78,3 +78,4 @@ all: make test-F make lib make clean + diff --git a/serial_interface/examples/python/Makefile b/serial_interface/examples/python/Makefile index f370f1a..e1328fe 100644 --- a/serial_interface/examples/python/Makefile +++ b/serial_interface/examples/python/Makefile @@ -14,25 +14,25 @@ CHIMESFF_HDR=$(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) +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) - - + $(CXX) -c $(WRAPPER_SRC) -I $(WRAPPER_LOC) -I $(SERIAL_LOC) -I $(CHIMESFF_LOC) + + chimescalc_serial_C.so: $(CXX) -shared -o libchimescalc-serial_dl.so chimescalc_serial_C.o serial_chimes_interface.o chimesFF.o - + clean: rm -f *.o diff --git a/serial_interface/examples/python/main.py b/serial_interface/examples/python/main.py index 4a5ff55..d9b8d1b 100644 --- a/serial_interface/examples/python/main.py +++ b/serial_interface/examples/python/main.py @@ -64,9 +64,9 @@ def str2bool(v): # Initialize the ChIMES calculator curr_path should be /.../usr/WS2/rlindsey/chimes_calculator-fork/serial_interface/tests/ -print("HERE:",os.getcwd) +print("CURR PATH:",curr_path) -chimescalc_serial_py.chimes_wrapper = chimescalc_serial_py.init_chimes_wrapper("libchimescalc_dl.so") +chimescalc_serial_py.chimes_wrapper = chimescalc_serial_py.init_chimes_wrapper(curr_path + "/libchimescalc_dl.so") chimescalc_serial_py.set_chimes(small) rank = 0 diff --git a/serial_interface/src/serial_chimes_interface.cpp b/serial_interface/src/serial_chimes_interface.cpp index 119eaa6..27d7538 100644 --- a/serial_interface/src/serial_chimes_interface.cpp +++ b/serial_interface/src/serial_chimes_interface.cpp @@ -1,7 +1,7 @@ -/* +/* ChIMES Calculator Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried - Contributing Author: Rebecca K. Lindsey (2020) + Contributing Author: Rebecca K. Lindsey (2020) */ #include @@ -20,38 +20,38 @@ using namespace std; double mag_a (const vector & a) { double mag = 0; - + for(int i=0; i & a, vector & unit) +void unit_a (const vector & a, vector & unit) { double mag = mag_a(a); unit.resize(a.size()); - + for(int i=0; i & a, const vector & b) { double dot = 0; - + if (a.size() != b.size()) { cout << "ERROR in a_dot_b: Vectors of different length!" << endl; exit(0); } - + for(int i=0; i & a, const vector & b) @@ -61,8 +61,8 @@ double angle_ab (const vector & a, const vector & b) ang /= mag_a(a); ang /= mag_a(b); - return acos(ang); -} + return acos(ang); +} void a_cross_b(const vector & a, const vector & b, vector & cross) { if( a.size() != b.size()) @@ -75,44 +75,44 @@ void a_cross_b(const vector & a, const vector & b, vector & cell_a,const vector & cell_b, const vector & cell_c, vector & hmat, vector & invr_hmat, int replicates) { - // Define the h-matrix (stores the cell vectors locally) - - hmat[0] = cell_a[0]*(replicates+1); hmat[3] = cell_a[1]*(replicates+1); hmat[6] = cell_a[2]*(replicates+1); - hmat[1] = cell_b[0]*(replicates+1); hmat[4] = cell_b[1]*(replicates+1); hmat[7] = cell_b[2]*(replicates+1); - hmat[2] = cell_c[0]*(replicates+1); hmat[5] = cell_c[1]*(replicates+1); hmat[8] = cell_c[2]*(replicates+1); - - // Determine the h-matrix inverse - - double hmat_det = hmat[0] * (hmat[4]*hmat[8] - hmat[5]*hmat[7]) - - hmat[1] * (hmat[3]*hmat[8] - hmat[5]*hmat[6]) - + hmat[2] * (hmat[3]*hmat[7] - hmat[4]*hmat[6]); - - vector tmp_vec(9); - - tmp_vec[0] = (hmat[4]*hmat[8] - hmat[5]*hmat[7]); tmp_vec[3] = -1 * (hmat[1]*hmat[8] - hmat[2]*hmat[7]); tmp_vec[6] = (hmat[1]*hmat[5] - hmat[2]*hmat[4]); - tmp_vec[1] = -1 * (hmat[3]*hmat[8] - hmat[5]*hmat[6]); tmp_vec[4] = (hmat[0]*hmat[8] - hmat[2]*hmat[6]); tmp_vec[7] = -1 * (hmat[0]*hmat[5] - hmat[2]*hmat[3]); - tmp_vec[2] = (hmat[3]*hmat[7] - hmat[4]*hmat[6]); tmp_vec[5] = -1 * (hmat[0]*hmat[7] - hmat[1]*hmat[6]); tmp_vec[8] = (hmat[0]*hmat[4] - hmat[1]*hmat[3]); - - invr_hmat[0] = tmp_vec[0]; invr_hmat[3] = tmp_vec[1]; invr_hmat[6] = tmp_vec[2]; - invr_hmat[1] = tmp_vec[3]; invr_hmat[4] = tmp_vec[4]; invr_hmat[7] = tmp_vec[5]; - invr_hmat[2] = tmp_vec[6]; invr_hmat[5] = tmp_vec[7]; invr_hmat[8] = tmp_vec[8]; - - invr_hmat[0] /= hmat_det; invr_hmat[3] /= hmat_det; invr_hmat[6] /= hmat_det; - invr_hmat[1] /= hmat_det; invr_hmat[4] /= hmat_det; invr_hmat[7] /= hmat_det; - invr_hmat[2] /= hmat_det; invr_hmat[5] /= hmat_det; invr_hmat[8] /= hmat_det; - + // Define the h-matrix (stores the cell vectors locally) + + hmat[0] = cell_a[0]*(replicates+1); hmat[3] = cell_a[1]*(replicates+1); hmat[6] = cell_a[2]*(replicates+1); + hmat[1] = cell_b[0]*(replicates+1); hmat[4] = cell_b[1]*(replicates+1); hmat[7] = cell_b[2]*(replicates+1); + hmat[2] = cell_c[0]*(replicates+1); hmat[5] = cell_c[1]*(replicates+1); hmat[8] = cell_c[2]*(replicates+1); + + // Determine the h-matrix inverse + + double hmat_det = hmat[0] * (hmat[4]*hmat[8] - hmat[5]*hmat[7]) + - hmat[1] * (hmat[3]*hmat[8] - hmat[5]*hmat[6]) + + hmat[2] * (hmat[3]*hmat[7] - hmat[4]*hmat[6]); + + vector tmp_vec(9); + + tmp_vec[0] = (hmat[4]*hmat[8] - hmat[5]*hmat[7]); tmp_vec[3] = -1 * (hmat[1]*hmat[8] - hmat[2]*hmat[7]); tmp_vec[6] = (hmat[1]*hmat[5] - hmat[2]*hmat[4]); + tmp_vec[1] = -1 * (hmat[3]*hmat[8] - hmat[5]*hmat[6]); tmp_vec[4] = (hmat[0]*hmat[8] - hmat[2]*hmat[6]); tmp_vec[7] = -1 * (hmat[0]*hmat[5] - hmat[2]*hmat[3]); + tmp_vec[2] = (hmat[3]*hmat[7] - hmat[4]*hmat[6]); tmp_vec[5] = -1 * (hmat[0]*hmat[7] - hmat[1]*hmat[6]); tmp_vec[8] = (hmat[0]*hmat[4] - hmat[1]*hmat[3]); + + invr_hmat[0] = tmp_vec[0]; invr_hmat[3] = tmp_vec[1]; invr_hmat[6] = tmp_vec[2]; + invr_hmat[1] = tmp_vec[3]; invr_hmat[4] = tmp_vec[4]; invr_hmat[7] = tmp_vec[5]; + invr_hmat[2] = tmp_vec[6]; invr_hmat[5] = tmp_vec[7]; invr_hmat[8] = tmp_vec[8]; + + invr_hmat[0] /= hmat_det; invr_hmat[3] /= hmat_det; invr_hmat[6] /= hmat_det; + invr_hmat[1] /= hmat_det; invr_hmat[4] /= hmat_det; invr_hmat[7] /= hmat_det; + invr_hmat[2] /= hmat_det; invr_hmat[5] /= hmat_det; invr_hmat[8] /= hmat_det; + } - - + + // simulation_system member functions simulation_system::simulation_system() @@ -129,7 +129,7 @@ void simulation_system::set_atomtyp_indices(vector & type_list) for(int i=0; i & type_list) break; } } - + if (sys_atmtyp_indices[i] == -1) { cout << "ERROR: Couldn't assign an atom type index for (index/type) " << sys_parent[i] << " " << sys_atmtyps[i] << endl; @@ -149,18 +149,18 @@ void simulation_system::set_atomtyp_indices(vector & type_list) void simulation_system::init(vector & atmtyps, vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in, double max_2b_cut, bool small) { - allow_replication = small; - max_cut = max_2b_cut; - static bool called_before = false; - + allow_replication = small; + max_cut = max_2b_cut; + static bool called_before = false; + ////////////////////////////////////////// // STEP 1: Copy the system ////////////////////////////////////////// - + n_atoms = x_in.size(); - + // Sanity checks - + if (n_atoms != y_in.size()) { cout << "ERROR: x and y coordinate vector lengths do not match!" << endl; @@ -171,213 +171,213 @@ void simulation_system::init(vector & atmtyps, vector & x_in, ve cout << "ERROR: x and z coordinate vector lengths do not match!" << endl; exit(0); } - + // Copy over the system - + n_ghost = n_atoms; - n_repl = n_atoms; - + n_repl = n_atoms; + sys_atmtyp_indices.resize(0); - + sys_x.resize(0); sys_y.resize(0); sys_z.resize(0); - + for (int a=0; a 0) - { + sys_rep_parent.push_back(a); // for replicates + } + + // Determine if system is large enough + + latcon_a = mag_a({cella_in[0], cella_in[1], cella_in[2]}); + latcon_b = mag_a({cellb_in[0], cellb_in[1], cellb_in[2]}); + latcon_c = mag_a({cellc_in[0], cellc_in[1], cellc_in[2]}); + + double min_latcon = latcon_a; + + if (latcon_b < min_latcon) + min_latcon = latcon_b; + if (latcon_c < min_latcon) + min_latcon = latcon_c; + + n_replicates = 0; + + if (allow_replication) + n_replicates = ceil(max_cut/min_latcon)-1; + + if (n_replicates > 0) + { if (!called_before) { called_before = true; // Avoid printing the number of replicates on each MD step (LEF). cout << "SerialchimesFF: " << "Replicating the system " << n_replicates << " times prior to generating ghost atoms" << endl; - + cout << "SerialchimesFF: " << "\t" << "Warning: At least one cell length is smaller than the ChIMES outer cutoff." << endl; cout << "SerialchimesFF: " << "\t" << "System will be replicated prior to ghost atom generation." << endl; cout << "SerialchimesFF: " << "\t" << "Results will only be correct for perfectly crystalline cells." << endl; cout << "SerialchimesFF: " << "\t" << "For any other case, system size should be increased." << endl; } - } - - set_hmat(cella_in, cellb_in, cellc_in, hmat, invr_hmat, 0); - - // Build the replicates - - double tmp_x, tmp_y, tmp_z; - - - for (int i=0; i<=n_replicates; i++) // x - { - for (int j=0; j<=n_replicates; j++) // y - { - for (int k=0; k<=n_replicates; k++) // z - { - if ((i==0)&&(j==0)&&(k==0)) - continue; - - for (int a=0; a tmp_cella(3); vector tmp_cellb(3); vector tmp_cellc(3); vector tmp_unit (3); vector tmp_cross(3); - - vector cella_in = {hmat[0], hmat[3], hmat[6]}; - vector cellb_in = {hmat[1], hmat[4], hmat[7]}; - vector cellc_in = {hmat[2], hmat[5], hmat[8]}; - - + + vector cella_in = {hmat[0], hmat[3], hmat[6]}; + vector cellb_in = {hmat[1], hmat[4], hmat[7]}; + vector cellc_in = {hmat[2], hmat[5], hmat[8]}; + + unit_a (cella_in, tmp_unit); a_cross_b(tmp_unit, cellb_in, tmp_cross); - + // Determine cell vectors for the rotated system - + tmp_cella[0] = mag_a(cella_in); tmp_cella[1] = 0; tmp_cella[2] = 0; @@ -389,106 +389,106 @@ void simulation_system::reorient() tmp_cellc[0] = a_dot_b(cellc_in,tmp_unit); tmp_cellc[1] = (a_dot_b(cellb_in,cellc_in) - tmp_cellb[0]*tmp_cellc[0]) / tmp_cellb[1]; tmp_cellc[2] = sqrt( mag_a(cellc_in)*mag_a(cellc_in) - tmp_cellc[0]*tmp_cellc[0] - tmp_cellc[1]*tmp_cellc[1]); - + // Determine the new cell h-matrix and its inverse - set_hmat({tmp_cella[0], tmp_cella[1], tmp_cella[2]}, {tmp_cellb[0], tmp_cellb[1], tmp_cellb[2]}, {tmp_cellc[0], tmp_cellc[1], tmp_cellc[2]}, hmat, invr_hmat, 0); + set_hmat({tmp_cella[0], tmp_cella[1], tmp_cella[2]}, {tmp_cellb[0], tmp_cellb[1], tmp_cellb[2]}, {tmp_cellc[0], tmp_cellc[1], tmp_cellc[2]}, hmat, invr_hmat, 0); - // Transform to the new nominally rotated cell + // Transform to the new nominally rotated cell for(int i=0; i tmp) - tmp = xy; - if (xz > tmp) - tmp = xz; - if (xy+xz> tmp) - tmp = xy+xz; - xhi += tmp; - - double yhi = hmat[4]; - if(yz > 0.0) - yhi += yz; - - double zhi = hmat[8]; - - extent_x = xhi - xlo; - extent_y = yhi - ylo; - extent_z = zhi - zlo; + } + + // Determine cell extents and volume for neighbor list constructions + + latcon_a = mag_a({hmat[0], hmat[3], hmat[6]}); + latcon_b = mag_a({hmat[1], hmat[4], hmat[7]}); + latcon_c = mag_a({hmat[2], hmat[5], hmat[8]}); + + cell_alpha = angle_ab({hmat[1], hmat[4], hmat[7]}, {hmat[2], hmat[5], hmat[8]}); + cell_beta = angle_ab({hmat[2], hmat[5], hmat[8]}, {hmat[0], hmat[3], hmat[6]}); + cell_gamma = angle_ab({hmat[0], hmat[3], hmat[6]}, {hmat[1], hmat[4], hmat[7]}); + + double cell_lx = latcon_a; + double xy = latcon_b * cos(cell_gamma); + if(abs(xy) < 1E-12) + xy = 0.0; + + double xz = latcon_c * cos(cell_beta ); + if(abs(xz) < 1E-12) + xz = 0.0; + + double cell_ly = sqrt(latcon_b *latcon_b - xy*xy); + + double yz = (latcon_b*latcon_c * cos(cell_alpha) -xy*xz)/cell_ly; + if(abs(yz) < 1E-12) + yz = 0.0; + + double cell_lz = sqrt( latcon_c*latcon_c - xz*xz -yz*yz); + double tmp; + + double xlo = 0.0; + if (xy < xlo) + xlo = xy; + if (xz < xlo) + xlo = xz; + if(xy+xz < xlo) + xlo = xy+xz; + + double ylo = 0.0; + if (yz< ylo) + ylo = yz; + double zlo = 0.0; + + double xhi = hmat[0]; + tmp = 0.0; + if (xy > tmp) + tmp = xy; + if (xz > tmp) + tmp = xz; + if (xy+xz> tmp) + tmp = xy+xz; + xhi += tmp; + + double yhi = hmat[4]; + if(yz > 0.0) + yhi += yz; + + double zhi = hmat[8]; + + extent_x = xhi - xlo; + extent_y = yhi - ylo; + extent_z = zhi - zlo; } void simulation_system::build_layered_system(vector & atmtyps, vector & poly_orders, double max_2b_cut, double max_3b_cut, double max_4b_cut) { - + // use smallest lattice length to determine number of ghost atom layers (n_layers) - + vector latdist = {latcon_a,latcon_b,latcon_c}; - - double lat_min = *min_element(latdist.begin(),latdist.end()); - - double eff_length = max_2b_cut*2.0; - + + double lat_min = *min_element(latdist.begin(),latdist.end()); + + double eff_length = max_2b_cut*2.0; + // n_layers is set to ensure that max 2b rcut is less than half smallest box length - + n_layers = ceil(eff_length/lat_min+1); - - double eff_lx = latcon_a * (2*n_layers + 1); + + double eff_lx = latcon_a * (2*n_layers + 1); double eff_ly = latcon_b * (2*n_layers + 1); double eff_lz = latcon_c * (2*n_layers + 1); - + if ((max_2b_cut>0.5*eff_lx)||(max_2b_cut>0.5*eff_ly)||(max_2b_cut>0.5*eff_lz)) { cout << "ERROR: Maximum 2b cutoff is greater than half at least one box length." << endl; @@ -499,7 +499,7 @@ void simulation_system::build_layered_system(vector & atmtyps, vector0) { if ((max_3b_cut>0.5*eff_lx)||(max_3b_cut>0.5*eff_ly)||(max_3b_cut>0.5*eff_lz)) @@ -538,33 +538,33 @@ void simulation_system::build_layered_system(vector & atmtyps, vector & atmtyps, vector & poly_orders, vector > & neighlist_2b, vector > & neighlist_3b, vector > & neighlist_4b, double max_2b_cut, double max_3b_cut, double max_4b_cut) { // Make the 2b neighbor lists - + neighlist_2b.resize(n_ghost); - - for (int i = 0; i < n_ghost; i++) - neighlist_2b[i].resize(0,0); - + + for (int i = 0; i < n_ghost; i++) + neighlist_2b[i].resize(0,0); + neighlist_3b.resize(0); neighlist_4b.resize(0); // Determine search distances double search_dist = max_2b_cut; - + if (max_3b_cut > search_dist) search_dist = max_3b_cut; if (max_4b_cut > search_dist) - search_dist = max_4b_cut; - + search_dist = max_4b_cut; + // Prepare bins - + int nbins_x = ceil((2 * n_layers+1) * extent_x/search_dist) + 2; int nbins_y = ceil((2 * n_layers+1) * extent_y/search_dist) + 2; - int nbins_z = ceil((2 * n_layers+1) * extent_z/search_dist) + 2; - + int nbins_z = ceil((2 * n_layers+1) * extent_z/search_dist) + 2; + int total_bins = nbins_x * nbins_y * nbins_z; - + vector > bin(total_bins); - for (int i=0; i().swap(bin[i]); - + int bin_x_idx, bin_y_idx, bin_z_idx, ibin; - // Populate bins + // Populate bins for(int i=0; i= total_bins ) + + if ( ibin >= total_bins ) { cout << "Error: ibin out of range\n"; cout << ibin << " " << total_bins << endl; exit(1); } - // Push the atom into the bin + // Push the atom into the bin bin[ibin].push_back(i); - + } // Generate neighbor lists on basis of bins - + for(int ai=0; ai & poly_orders, vector= total_bins) - { - cout << "Error: binning BIN_IDX out of range\n"; - cout << "BIN_IDX.X = " << i << "BIN_IDX.Y = " << j << "BIN_IDX.Z = " << k << endl; - exit(1); - } + if (ibin >= total_bins) + { + cout << "Error: binning BIN_IDX out of range\n"; + cout << "BIN_IDX.X = " << i << "BIN_IDX.Y = " << j << "BIN_IDX.Z = " << k << endl; + exit(1); + } ajend = bin[ibin].size(); - - for (int aj=0; aj tmp_3mer(3); vector tmp_4mer(4); - + int jj, kk, ll; - + double dist; double dist_ij, dist_ik, dist_il, dist_jk, dist_jl, dist_kl; - + for(int i=0; i= max_3b_cut) valid_3mer = false; if (dist_ij >= max_4b_cut) valid_4mer = false; - + if (!valid_3mer && !valid_4mer) continue; - + for(int k=0; k sys_parent[kk]) continue; - + dist_ik = get_dist(i,kk); // Check i/k distance - + if (dist_ik >= max_3b_cut) valid_3mer = false; if (dist_ik >= max_4b_cut) valid_4mer = false; - + dist_jk = get_dist(jj,kk); // Check j/k distance - + if (dist_jk >= max_3b_cut) valid_3mer = false; if (dist_jk >= max_4b_cut) - valid_4mer = false; - + valid_4mer = false; + if (!valid_3mer && !valid_4mer) { if(dist_ij sys_parent[ll]) - continue; + continue; if (sys_parent[kk] > sys_parent[ll]) - continue; + continue; if (get_dist(i ,ll) >= max_4b_cut) // Check i/l distance - continue; + continue; if (get_dist(jj,ll) >= max_4b_cut) // Check j/l distance - continue; + continue; if (get_dist(kk,ll) >= max_4b_cut) // Check k/l distance - continue; - - // If we're here then we have a valid 4-mer ... add it to the 4b neighbor list - + continue; + + // If we're here then we have a valid 4-mer ... add it to the 4b neighbor list + tmp_4mer[0] = i; tmp_4mer[1] = jj; tmp_4mer[2] = kk; tmp_4mer[3] = ll; - + if (valid_4mer) - neighlist_4b.push_back(tmp_4mer); - } + neighlist_4b.push_back(tmp_4mer); + } } } } @@ -822,128 +822,90 @@ void simulation_system::build_neigh_lists(vector & poly_orders, vector & rij) -{ - /* Orthorhombic way - rij[0] = sys_x[j] - sys_x[i]; - rij[1] = sys_y[j] - sys_y[i]; - rij[2] = sys_z[j] - sys_z[i]; - */ - - // Transform atoms to scaled space - - double inv_ix = invr_hmat[0]*sys_x[i] + invr_hmat[1]*sys_y[i] + invr_hmat[2]*sys_z[i]; - double inv_iy = invr_hmat[3]*sys_x[i] + invr_hmat[4]*sys_y[i] + invr_hmat[5]*sys_z[i]; - double inv_iz = invr_hmat[6]*sys_x[i] + invr_hmat[7]*sys_y[i] + invr_hmat[8]*sys_z[i]; - - double inv_jx = invr_hmat[0]*sys_x[j] + invr_hmat[1]*sys_y[j] + invr_hmat[2]*sys_z[j]; - double inv_jy = invr_hmat[3]*sys_x[j] + invr_hmat[4]*sys_y[j] + invr_hmat[5]*sys_z[j]; - double inv_jz = invr_hmat[6]*sys_x[j] + invr_hmat[7]*sys_y[j] + invr_hmat[8]*sys_z[j]; - - // Get the distance - - double dx = inv_jx - inv_ix; - double dy = inv_jy - inv_iy; - double dz = inv_jz - inv_iz; - - // Convert back to standard units - - rij[0] = hmat[0]*dx + hmat[1]*dy + hmat[2]*dz; - rij[1] = hmat[3]*dx + hmat[4]*dy + hmat[5]*dz; - rij[2] = hmat[6]*dx + hmat[7]*dy + hmat[8]*dz; - - return sqrt(rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]); - -} -double simulation_system::get_dist(int i,int j) -{ - vector rij(3); - - return get_dist(i,j,rij); -} void simulation_system::run_checks(const vector& max_cuts, vector&poly_orders) { - // Sanity check 1: Are the cell vectors long enough? - - for(int i=0;i 2*latcon_a * (2*n_layers + 1)) || - (max_cuts[i] > 2*latcon_b * (2*n_layers + 1)) || - (max_cuts[i] > 2*latcon_c * (2*n_layers + 1)) - ) - { - cout << "ERROR: Layered system is smaller than 2x the model " << i+2 <<"-body maximum outer cutoff." << endl; - cout << "Please report this error to the developers." << endl; - cout << "Model maximum cutoff: " << max_cuts[i] << endl; - cout << "Layered system lattice cosntant (a): " << latcon_a * (2*n_layers + 1) << endl; - cout << "Layered system lattice cosntant (b): " << latcon_b * (2*n_layers + 1) << endl; - cout << "Layered system lattice cosntant (c): " << latcon_c * (2*n_layers + 1) << endl; - exit(0); - - } - } - - - // Sanity check 2: Does the system have enough atoms? - - int bodiedness = 2; - if (poly_orders[1] > 0) - bodiedness++; - if (poly_orders[2] > 0) - bodiedness++; - - if (bodiedness > sys_x.size()) - { - cout << "ERROR: Layered system contains too few atoms." << endl; - cout << " Model bodiedness: " << bodiedness << endl; - cout << " No. atoms in layered system: " << sys_x.size() << endl; - exit(0); - } -} + // Sanity check 1: Are the cell vectors long enough? + + for(int i=0;i 2*latcon_a * (2*n_layers + 1)) || + (max_cuts[i] > 2*latcon_b * (2*n_layers + 1)) || + (max_cuts[i] > 2*latcon_c * (2*n_layers + 1)) + ) + { + cout << "ERROR: Layered system is smaller than 2x the model " << i+2 <<"-body maximum outer cutoff." << endl; + cout << "Please report this error to the developers." << endl; + cout << "Model maximum cutoff: " << max_cuts[i] << endl; + cout << "Layered system lattice constant (a): " << latcon_a * (2*n_layers + 1) << endl; + cout << "Layered system lattice constant (b): " << latcon_b * (2*n_layers + 1) << endl; + cout << "Layered system lattice constant (c): " << latcon_c * (2*n_layers + 1) << endl; + exit(0); + + } + } + + // Sanity check 2: Does the system have enough atoms? + + int bodiedness = 2; + if (poly_orders[1] > 0) + bodiedness++; + if (poly_orders[2] > 0) + bodiedness++; + + if (bodiedness > sys_x.size()) + { + cout << "ERROR: Layered system contains too few atoms." << endl; + cout << " Model bodiedness: " << bodiedness << endl; + cout << " No. atoms in layered system: " << sys_x.size() << endl; + exit(0); + } +} + // serial_chimes_interface member functions serial_chimes_interface::serial_chimes_interface(bool small) { - // For small systems, allow explicit replication prior to ghost atom construction - // This should ONLY be done for perfectly crystalline systems - - allow_replication = small; - + // For small systems, allow explicit replication prior to ghost atom construction + // This should ONLY be done for perfectly crystalline systems + + allow_replication = small; + // Initialize Pointers, etc for chimes calculator interfacing (2-body only for now) // To set up for many body calculations, see the LAMMPS implementation dist_3b.resize(3); dist_4b.resize(6); - + dr .resize(3); - dr_3b.resize(3,std::vector(3)); - dr_4b.resize(6,std::vector(3)); - + dr_3b.resize(3*3) ; + dr_4b.resize(6*3); + force_ptr_2b.resize(2,std::vector(3)); - force_ptr_3b.resize(3,std::vector(3)); - force_ptr_4b.resize(4,std::vector(3)); - + typ_idxs_2b.resize(2); typ_idxs_3b.resize(3); typ_idxs_4b.resize(4); - + max_2b_cut = 0.0; max_3b_cut = 0.0; max_4b_cut = 0.0; - + } serial_chimes_interface::~serial_chimes_interface() {} + void serial_chimes_interface::init_chimesFF(string chimesFF_paramfile, int rank) { // Initialize the chimesFF object, read parameters - + init(rank); read_parameters(chimesFF_paramfile); set_atomtypes(type_list); + build_pair_int_trip_map() ; + build_pair_int_quad_map() ; } void serial_chimes_interface::build_neigh_lists(vector & atmtyps, vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in) @@ -956,7 +918,7 @@ void serial_chimes_interface::build_neigh_lists(vector & atmtyps, vector } void serial_chimes_interface::calculate(vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in, vector & atmtyps, double & energy, vector > & force, vector & stress) -{ +{ // Read system, set up lattice constants/hmats // Determine the max outer cutoff (MUST be 2-body, based on ChIMES logic) @@ -965,29 +927,33 @@ void serial_chimes_interface::calculate(vector & x_in, vector & max_2b_cut = max_cutoff_2B(true) ; max_3b_cut = max_cutoff_3B(true) ; max_4b_cut = max_cutoff_4B(true) ; - - sys.init(atmtyps, x_in, y_in, z_in, cella_in, cellb_in, cellc_in, max_2b_cut, allow_replication); - + + vector stress_chimes(6,0.0) ; // Switch Chimes to a packed stressed tensor. + + sys.init(atmtyps, x_in, y_in, z_in, cella_in, cellb_in, cellc_in, max_2b_cut, allow_replication); + sys.build_layered_system(atmtyps,poly_orders, max_2b_cut, max_3b_cut, max_4b_cut); sys.set_atomtyp_indices(type_list); - + sys.run_checks({max_2b_cut,max_3b_cut,max_4b_cut},poly_orders); build_neigh_lists(atmtyps, x_in, y_in, z_in, cella_in, cellb_in, cellc_in); - + // Setup vars - + int ii, jj, kk, ll; - - vector stensor(9); - - for (int idx=0; idx<9; idx++) - stensor[idx] = &stress[idx]; - + + vector force_4b(4*CHDIM) ; + vector force_3b(3*CHDIM) ; + vector force_2b(2*CHDIM) ; + chimes2BTmp chimes_2btmp(poly_orders[0]) ; + chimes3BTmp chimes_3btmp(poly_orders[1]) ; + chimes4BTmp chimes_4btmp(poly_orders[2]) ; + //////////////////////// - // interate over 1- and 2b's + // interate over 1- and 2b's //////////////////////// for(int i=0; i & x_in, vector & jj = neighlist_2b[i][j]; dist = sys.get_dist(i,jj,dr); // Populates dr, which is passed by ref (overloaded) - + typ_idxs_2b[0] = sys.sys_atmtyp_indices[i ]; typ_idxs_2b[1] = sys.sys_atmtyp_indices[jj]; + + for (int idx=0; idx<2*CHDIM; idx++) { + force_2b[idx] = 0.0 ; + } + + compute_2B(dist, dr, typ_idxs_2b, force_2b, stress_chimes, energy, chimes_2btmp); for (int idx=0; idx<3; idx++) { - force_ptr_2b[0][idx] = &force[sys.sys_rep_parent[i] ][idx]; - force_ptr_2b[1][idx] = &force[sys.sys_rep_parent[sys.sys_parent[jj]]][idx]; + force[sys.sys_rep_parent[i]][idx] += force_2b[0*CHDIM+idx] ; + force[sys.sys_rep_parent[sys.sys_parent[jj]]][idx] += force_2b[1*CHDIM+idx] ; } - compute_2B(dist, dr, typ_idxs_2b, force_ptr_2b, stensor, energy); } } - + //////////////////////// - // interate over 3b's + // interate over 3b's //////////////////////// - + if (poly_orders[1] > 0 ) { for(int i=0; i & x_in, vector & ii = neighlist_3b[i][0]; jj = neighlist_3b[i][1]; kk = neighlist_3b[i][2]; - - dist_3b[0] = sys.get_dist(ii,jj,dr_3b[0]); - dist_3b[1] = sys.get_dist(ii,kk,dr_3b[1]); - dist_3b[2] = sys.get_dist(jj,kk,dr_3b[2]); - + + dist_3b[0] = sys.get_dist(ii,jj,&dr_3b[0]); + dist_3b[1] = sys.get_dist(ii,kk,&dr_3b[3]); + dist_3b[2] = sys.get_dist(jj,kk,&dr_3b[6]); + typ_idxs_3b[0] = sys.sys_atmtyp_indices[ii]; typ_idxs_3b[1] = sys.sys_atmtyp_indices[jj]; typ_idxs_3b[2] = sys.sys_atmtyp_indices[kk]; - - for (int idx=0; idx<3; idx++) + + for (int idx=0; idx<3*CHDIM; idx++) { - force_ptr_3b[0][idx] = &force[sys.sys_rep_parent[sys.sys_parent[ii]]][idx]; - force_ptr_3b[1][idx] = &force[sys.sys_rep_parent[sys.sys_parent[jj]]][idx]; - force_ptr_3b[2][idx] = &force[sys.sys_rep_parent[sys.sys_parent[kk]]][idx]; + force_3b[idx] = 0.0 ; + } + + compute_3B(dist_3b, dr_3b, typ_idxs_3b, force_3b, stress_chimes, energy, chimes_3btmp); + + for (int idx=0; idx<3; idx++) { + force[sys.sys_rep_parent[sys.sys_parent[ii]]][idx] += force_3b[0*CHDIM+idx] ; + force[sys.sys_rep_parent[sys.sys_parent[jj]]][idx] += force_3b[1*CHDIM+idx] ; + force[sys.sys_rep_parent[sys.sys_parent[kk]]][idx] += force_3b[2*CHDIM+idx] ; } - - compute_3B(dist_3b, dr_3b, typ_idxs_3b, force_ptr_3b, stensor, energy); - } } //////////////////////// - // interate over 4b's + // interate over 4b's //////////////////////// if (poly_orders[2] > 0 ) @@ -1056,40 +1030,65 @@ void serial_chimes_interface::calculate(vector & x_in, vector & jj = neighlist_4b[i][1]; kk = neighlist_4b[i][2]; ll = neighlist_4b[i][3]; - - dist_4b[0] = sys.get_dist(ii,jj,dr_4b[0]); - dist_4b[1] = sys.get_dist(ii,kk,dr_4b[1]); - dist_4b[2] = sys.get_dist(ii,ll,dr_4b[2]); - dist_4b[3] = sys.get_dist(jj,kk,dr_4b[3]); - dist_4b[4] = sys.get_dist(jj,ll,dr_4b[4]); - dist_4b[5] = sys.get_dist(kk,ll,dr_4b[5]); + + dist_4b[0] = sys.get_dist(ii,jj,&dr_4b[0*CHDIM]); + dist_4b[1] = sys.get_dist(ii,kk,&dr_4b[1*CHDIM]); + dist_4b[2] = sys.get_dist(ii,ll,&dr_4b[2*CHDIM]); + dist_4b[3] = sys.get_dist(jj,kk,&dr_4b[3*CHDIM]); + dist_4b[4] = sys.get_dist(jj,ll,&dr_4b[4*CHDIM]); + dist_4b[5] = sys.get_dist(kk,ll,&dr_4b[5*CHDIM]); typ_idxs_4b[0] = sys.sys_atmtyp_indices[ii]; typ_idxs_4b[1] = sys.sys_atmtyp_indices[jj]; typ_idxs_4b[2] = sys.sys_atmtyp_indices[kk]; - typ_idxs_4b[3] = sys.sys_atmtyp_indices[ll]; + typ_idxs_4b[3] = sys.sys_atmtyp_indices[ll]; + + for (int idx=0; idx<4*CHDIM; idx++) + { + force_4b[idx] = 0.0 ; + } + + compute_4B(dist_4b, dr_4b, typ_idxs_4b, force_4b, stress_chimes, energy, chimes_4btmp); for (int idx=0; idx<3; idx++) { - force_ptr_4b[0][idx] = &force[sys.sys_rep_parent[sys.sys_parent[ii]]][idx]; - force_ptr_4b[1][idx] = &force[sys.sys_rep_parent[sys.sys_parent[jj]]][idx]; - force_ptr_4b[2][idx] = &force[sys.sys_rep_parent[sys.sys_parent[kk]]][idx]; - force_ptr_4b[3][idx] = &force[sys.sys_rep_parent[sys.sys_parent[ll]]][idx]; - } - - compute_4B(dist_4b, dr_4b, typ_idxs_4b, force_ptr_4b, stensor, energy); - } + force[sys.sys_rep_parent[sys.sys_parent[ii]]][idx] += force_4b[0*CHDIM+idx] ; + force[sys.sys_rep_parent[sys.sys_parent[jj]]][idx] += force_4b[1*CHDIM+idx] ; + force[sys.sys_rep_parent[sys.sys_parent[kk]]][idx] += force_4b[2*CHDIM+idx] ; + force[sys.sys_rep_parent[sys.sys_parent[ll]]][idx] += force_4b[3*CHDIM+idx] ; + } + } } // Correct for use of replicates, if applicable - + energy /= pow(sys.n_replicates+1.0,3.0); //////////////////////// // Finish pressure calculation //////////////////////// + // Chimes calculates only unique elements of stress tensor. + stress[0] = stress_chimes[0] ; // xx + stress[1] = stress_chimes[1] ; // xy + stress[2] = stress_chimes[2] ; // xz + stress[3] = stress_chimes[1] ; // yx + stress[4] = stress_chimes[3] ; // yy + stress[5] = stress_chimes[4] ; // yz + stress[6] = stress_chimes[2] ; // zx + stress[7] = stress_chimes[4] ; // zy + stress[8] = stress_chimes[5] ; // zz + for (int idx=0; idx<9; idx++) - *stensor[idx] /= sys.vol; - + stress[idx] /= sys.vol; } + + + + + + + + + + diff --git a/serial_interface/src/serial_chimes_interface.h b/serial_interface/src/serial_chimes_interface.h index 02809cb..5325364 100644 --- a/serial_interface/src/serial_chimes_interface.h +++ b/serial_interface/src/serial_chimes_interface.h @@ -1,17 +1,17 @@ -/* +/* ChIMES Calculator Copyright (C) 2020 Rebecca K. Lindsey, Nir Goldman, and Laurence E. Fried - Contributing Author: Rebecca K. Lindsey (2020) + Contributing Author: Rebecca K. Lindsey (2020) */ /* ---------------------------------------------------------------------- -This class demonstrates how chimesFF{h,cpp} can be used to obtain the -stress tensor, energy, and per-atom forces for a given system. See +This class demonstrates how chimesFF{h,cpp} can be used to obtain the +stress tensor, energy, and per-atom forces for a given system. See main.cpp for a usage example. Notes: This class has been written for readability rather than speed. -Optimization and parallel distribution is recommended prior to use with +Optimization and parallel distribution is recommended prior to use with large systems. ---------------------------------------------------------------------- */ @@ -24,117 +24,224 @@ large systems. using namespace std; -#include "chimesFF.h" +#include "chimesFF.h" class simulation_system { - public: - - simulation_system(); - ~simulation_system(); - - double get_dist(int i,int j, vector & rij); - double get_dist(int i,int j); - - void init(vector & atmtyps, vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in, double max_2b_cut, bool small = false); - void set_atomtyp_indices(vector & type_list); - void copy(simulation_system & to); - void reorient(); - void build_layered_system(vector & atmtyps, vector & poly_orders, double max_2b_cut, double max_3b_cut, double max_4b_cut); - void build_neigh_lists(vector & poly_orders, vector > & neighlist_2b, vector > & neighlist_3b, vector > & neighlist_4b, double max_2b_cut, double max_3b_cut, double max_4b_cut); - void run_checks(const vector& max_cuts, vector&poly_orders); - - - bool allow_replication; // If true, replicates coordinates prior to calculation - - int n_replicates; // number of "real" replicate layers to make - int n_layers; // number of ghost layers to make - int n_atoms; // number of real atoms - int n_ghost; // number of real+ghost atoms - int n_repl; // "real" replicate atoms - handling of itty-bitty crystalline systems + public: + + simulation_system(); + ~simulation_system(); + + inline double get_dist(int i,int j, vector & rij); + inline double get_dist(int i,int j, double* rij); + inline double get_dist(int i,int j); + + void init(vector & atmtyps, vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in, double max_2b_cut, bool small = false); + void set_atomtyp_indices(vector & type_list); + void copy(simulation_system & to); + void reorient(); + void build_layered_system(vector & atmtyps, vector & poly_orders, double max_2b_cut, double max_3b_cut, double max_4b_cut); + void build_neigh_lists(vector & poly_orders, vector > & neighlist_2b, vector > & neighlist_3b, vector > & neighlist_4b, double max_2b_cut, double max_3b_cut, double max_4b_cut); + void run_checks(const vector& max_cuts, vector&poly_orders); + + + bool allow_replication; // If true, replicates coordinates prior to calculation + + int n_replicates; // number of "real" replicate layers to make + int n_layers; // number of ghost layers to make + int n_atoms; // number of real atoms + int n_ghost; // number of real+ghost atoms + int n_repl; // "real" replicate atoms - handling of itty-bitty crystalline systems double max_cut; - vector sys_atmtyp_indices; // Atom type indices for all (real+ghost) atoms - vector sys_atmtyps; // Chemical symbols for all (real+ghost) atoms - - vector sys_x; // System (i.e. ghost+real) x-coordinates - vector sys_y; // System (i.e. ghost+real) y-coordinates - vector sys_z; // System (i.e. ghost+real) z-coordinates - vector sys_parent; // Index of atom i's (replicant) parent - vector sys_rep_parent; // Replicant's parent atom - - double vol; // System volume - - private: - - vector hmat; // System h-matrix - vector invr_hmat; // Inverse h-matrix - - // Used by both sys and neigh coordinates - - double latcon_a; - double latcon_b; - double latcon_c; - - double cell_alpha; - double cell_beta; - double cell_gamma; - - // only used by neigh coordinates - - double extent_x; // Length of projection of the rotated cell a onto the x axis - double extent_y; // Length of projection of the rotated cell b onto the y axis - double extent_z; // Length of projection of the rotated cell c onto the z axis + vector sys_atmtyp_indices; // Atom type indices for all (real+ghost) atoms + vector sys_atmtyps; // Chemical symbols for all (real+ghost) atoms + + vector sys_x; // System (i.e. ghost+real) x-coordinates + vector sys_y; // System (i.e. ghost+real) y-coordinates + vector sys_z; // System (i.e. ghost+real) z-coordinates + vector sys_parent; // Index of atom i's (replicant) parent + vector sys_rep_parent; // Replicant's parent atom + + double vol; // System volume + + private: + + vector hmat; // System h-matrix + vector invr_hmat; // Inverse h-matrix + + // Used by both sys and neigh coordinates + + double latcon_a; + double latcon_b; + double latcon_c; + + double cell_alpha; + double cell_beta; + double cell_gamma; + + // only used by neigh coordinates + + double extent_x; // Length of projection of the rotated cell a onto the x axis + double extent_y; // Length of projection of the rotated cell b onto the y axis + double extent_z; // Length of projection of the rotated cell c onto the z axis }; class serial_chimes_interface : public chimesFF { public: - + serial_chimes_interface(bool small = true); ~serial_chimes_interface(); - - bool allow_replication; // If true, replicates coordinates prior to calculation + + bool allow_replication; // If true, replicates coordinates prior to calculation - void init_chimesFF(string chimesFF_paramfile, int rank); + void init_chimesFF(string chimesFF_paramfile, int rank); void calculate(vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in, vector & atmtyps, double & energy, vector > & force, vector & stress); private: - simulation_system sys; // Input system - simulation_system neigh; // Re-oriented ss + simulation_system sys; // Input system + simulation_system neigh; // Re-oriented ss + vector type_list; // A list of possible unique atom types and thier corresponding numerical index, per the parameter file - + double max_2b_cut; // Maximum 2-body outer cutoff double max_3b_cut; // Maximum 3-body outer cutoff double max_4b_cut; // Maximum 4-body outer cutoff - + vector > neighlist_2b; // [real atom index][list of real/ghost atom neighbors] vector > neighlist_3b; // [interaction set index][list of 3 atoms within interaction range] -- currently unused - vector > neighlist_4b; // [interaction set index][list of 4 atoms within interaction range] -- currently unused - + vector > neighlist_4b; // [interaction set index][list of 4 atoms within interaction range] -- currently unused + // Pointers, etc for chimes calculator interfacing (2-body only for now) // To set up for many body calculations, see the LAMMPS implementation - + double dist; vector dist_3b; vector dist_4b; - + vector dr; - vector > dr_3b; - vector > dr_4b; - + vector dr_3b; + vector dr_4b; + vector > force_ptr_2b; - vector > force_ptr_3b; - vector > force_ptr_4b; - + vector typ_idxs_2b; vector typ_idxs_3b; vector typ_idxs_4b; - void build_neigh_lists(vector & atmtyps, vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in); + + void build_neigh_lists(vector & atmtyps, vector & x_in, vector & y_in, vector & z_in, vector & cella_in, vector & cellb_in, vector & cellc_in); }; +inline double simulation_system::get_dist(int i,int j, vector & rij) +{ + /* Orthorhombic way + rij[0] = sys_x[j] - sys_x[i]; + rij[1] = sys_y[j] - sys_y[i]; + rij[2] = sys_z[j] - sys_z[i]; + */ + + // Transform atoms to scaled space + + double inv_ix = invr_hmat[0]*sys_x[i] + invr_hmat[1]*sys_y[i] + invr_hmat[2]*sys_z[i]; + double inv_iy = invr_hmat[3]*sys_x[i] + invr_hmat[4]*sys_y[i] + invr_hmat[5]*sys_z[i]; + double inv_iz = invr_hmat[6]*sys_x[i] + invr_hmat[7]*sys_y[i] + invr_hmat[8]*sys_z[i]; + + double inv_jx = invr_hmat[0]*sys_x[j] + invr_hmat[1]*sys_y[j] + invr_hmat[2]*sys_z[j]; + double inv_jy = invr_hmat[3]*sys_x[j] + invr_hmat[4]*sys_y[j] + invr_hmat[5]*sys_z[j]; + double inv_jz = invr_hmat[6]*sys_x[j] + invr_hmat[7]*sys_y[j] + invr_hmat[8]*sys_z[j]; + + // Get the distance + + double dx = inv_jx - inv_ix; + double dy = inv_jy - inv_iy; + double dz = inv_jz - inv_iz; + + // Convert back to standard units + + rij[0] = hmat[0]*dx + hmat[1]*dy + hmat[2]*dz; + rij[1] = hmat[3]*dx + hmat[4]*dy + hmat[5]*dz; + rij[2] = hmat[6]*dx + hmat[7]*dy + hmat[8]*dz; + + return sqrt(rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]); + +} + + +inline double simulation_system::get_dist(int i,int j, double *rij) +{ + /* Orthorhombic way + rij[0] = sys_x[j] - sys_x[i]; + rij[1] = sys_y[j] - sys_y[i]; + rij[2] = sys_z[j] - sys_z[i]; + */ + + // Transform atoms to scaled space + + double inv_ix = invr_hmat[0]*sys_x[i] + invr_hmat[1]*sys_y[i] + invr_hmat[2]*sys_z[i]; + double inv_iy = invr_hmat[3]*sys_x[i] + invr_hmat[4]*sys_y[i] + invr_hmat[5]*sys_z[i]; + double inv_iz = invr_hmat[6]*sys_x[i] + invr_hmat[7]*sys_y[i] + invr_hmat[8]*sys_z[i]; + + double inv_jx = invr_hmat[0]*sys_x[j] + invr_hmat[1]*sys_y[j] + invr_hmat[2]*sys_z[j]; + double inv_jy = invr_hmat[3]*sys_x[j] + invr_hmat[4]*sys_y[j] + invr_hmat[5]*sys_z[j]; + double inv_jz = invr_hmat[6]*sys_x[j] + invr_hmat[7]*sys_y[j] + invr_hmat[8]*sys_z[j]; + + // Get the distance + + double dx = inv_jx - inv_ix; + double dy = inv_jy - inv_iy; + double dz = inv_jz - inv_iz; + + // Convert back to standard units + + rij[0] = hmat[0]*dx + hmat[1]*dy + hmat[2]*dz; + rij[1] = hmat[3]*dx + hmat[4]*dy + hmat[5]*dz; + rij[2] = hmat[6]*dx + hmat[7]*dy + hmat[8]*dz; + + return sqrt(rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]); + +} + +inline double simulation_system::get_dist(int i,int j) +{ + vector rij(3); + + return get_dist(i,j,rij); +} + #endif + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/serial_interface/tests/configurations/H2O.1.50gcc_2000K_#000.xyz b/serial_interface/tests/configurations/H2O.1.50gcc_2000K_#000.xyz new file mode 100644 index 0000000..bc6e997 --- /dev/null +++ b/serial_interface/tests/configurations/H2O.1.50gcc_2000K_#000.xyz @@ -0,0 +1,98 @@ +96 +8.6091309 0.0 0.0 0.0 8.6091309 0.0 0.0 0.0 8.6091309 +O 1.55969485153113 6.71975868019533 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8.561669e+00 +-5.208791e+00 +-2.648388e+00 diff --git a/serial_interface/tests/force_fields/published_params.ambH2O.2+3b.cubic.txt b/serial_interface/tests/force_fields/published_params.ambH2O.2+3b.cubic.txt index 9cad62a..a4765ac 100644 --- a/serial_interface/tests/force_fields/published_params.ambH2O.2+3b.cubic.txt +++ b/serial_interface/tests/force_fields/published_params.ambH2O.2+3b.cubic.txt @@ -1,7 +1,12 @@ -! https://doi.org/10.1021/acs.jctc.8b00831 +! Date 2018-05-08 ! -! WARNING: This force field is only intended for use with water at 298 K and 1 gcc -! WARNING: This force field comes with no guarantees +! Number of variables = 228 +! Number of equations = 94698 +! RMS force error = 3.94572986152 +! max abs variable = 1937.65973238 +! SVD regularization factor = 6.667e-06 +! number of SVD fitting vars = 220 +! Bayesian Information Criterion = 262492.237516 ! USECOUL: false FITCOUL: false @@ -15,562 +20,568 @@ PAIRTYP: CHEBYSHEV 12 5 0 -1 1 ATOM TYPES: 2 # TYPEIDX # # ATM_TYP # # ATMCHRG # # ATMMASS # -0 O 0 15.999 -1 H 0 1.0079 +0 O 0 15.9994 +1 H 0 1.0079 ATOM PAIRS: 3 -!# PAIRIDX # # ATM_TY1 # # ATM_TY1 # # S_MINIM # # S_MAXIM # # S_DELTA # # CHBDIST # # MORSE_LAMBDA # - 0 O O 2.307 10.0 0.01 MORSE 2.71 - 1 H H 1.141 10.0 0.01 MORSE 1.60 - 2 O H 0.894 10.0 0.01 MORSE 0.098 +# PAIRIDX # # ATM_TY1 # # ATM_TY1 # # S_MINIM # # S_MAXIM # # S_DELTA # # CHBDIST # # MORSE_LAMBDA # + 0 O O 2.305 9.855 0.01 MORSE 2.71 + 1 H H 1.112 9.855 0.01 MORSE 1.6 + 2 O H 0.855 9.855 0.01 MORSE 0.98 FCUT TYPE: CUBIC -SPECIAL 3B S_MAXIM: ALL 8.0 - -PAIR CHEBYSHEV PENALTY DIST: 0.01 +PAIR CHEBYSHEV PENALTY DIST: 0.02 PAIR CHEBYSHEV PENALTY SCALING: 1E5 +SPECIAL 3B S_MAXIM: SPECIFIC 4 +OOOOOO OO OO OO 8.00000 8.00000 8.00000 +OHOHOO OO OH OH 8.00000 6.00000 6.00000 +HHOHOH OH OH HH 6.00000 6.00000 5.00000 +HHHHHH HH HH HH 5.00000 5.00000 5.00000 + ATOM PAIR TRIPLETS: 4 +ATOM PAIR QUADRUPLETS: 0 -PAIR CHEBYSHEV PARAMS +PAIR CHEBYSHEV PARAMS PAIRTYPE PARAMS: 0 O O -0 -98.925281763412116 -1 25.309142715463473 -2 -16.212555054461731 -3 28.633791411129074 -4 -17.524003510017643 -5 9.0282185288011121 -6 -6.4399791933309976 -7 4.8471799080772549 -8 -2.81355150713066 -9 1.4301771700037995 -10 -0.50849252074208728 -11 0.20353889428006389 +0 -53.556624854198326 +1 44.297635592188556 +2 -29.321010528215798 +3 31.449035378427439 +4 -19.492795470521102 +5 13.326839292940912 +6 -8.651987644355664 +7 5.7162864455259763 +8 -3.2446309927198982 +9 1.6785718538643519 +10 -0.51990334731577392 +11 0.068307729898379466 PAIRTYPE PARAMS: 1 H H -0 -4.8827385973300581 -1 -8.5776992763161068 -2 4.3052572433475795 -3 -0.18369965233920915 -4 -4.5871631730193148 -5 1.2078268447883667 -6 0.4184307638630127 -7 -0.13720933046654882 -8 0.19469247576171644 -9 -0.11914993758277015 -10 0.069002778677973331 -11 -0.095244724251307686 +0 4.1736140188269903 +1 -7.8037664658002965 +2 2.6532798116696563 +3 -2.7931165448201378 +4 0.36495953390967451 +5 -0.19059511837309784 +6 1.676668871098473 +7 -0.1035555555125407 +8 0.61117677806435933 +9 -0.22079692906183368 +10 0.058664887821561387 +11 -0.037841615220618574 PAIRTYPE PARAMS: 2 O H -0 -32.193981298293288 -1 -23.877215832499353 -2 16.031197154644715 -3 4.923346898316014 -4 1.3010761433587881 -5 -1.2105414800925378 -6 0.072262002945428172 -7 0.29930904508588507 -8 -0.20136142809512808 -9 0.1762418194708677 -10 -0.15369063392630294 -11 0.070130421012281563 +0 -27.039551873246658 +1 -14.453162352021685 +2 11.798274652347185 +3 8.7143307961532646 +4 1.4818743455340329 +5 1.1035242519562853 +6 -1.6631200488306002 +7 1.589405679728485 +8 -0.6484802365067992 +9 0.51194570281129403 +10 -0.18375661598401466 +11 0.1967545076124525 TRIPLET CHEBYSHEV PARAMS TRIPLETTYPE PARAMS: INDEX: 0 ATOMS: O O O PAIRS: OO OO OO UNIQUE: 30 TOTAL: 112 - index | powers | equiv index | param index | parameter - ---------------------------------------------------------------------------- - 0 0 1 1 0 0 1402.7969032897649 - 1 0 1 2 1 1 -1298.342369081754 - 2 0 1 3 2 2 419.8989065033868 - 3 0 1 4 3 3 -31.990290403269185 - 4 0 2 1 1 1 -1298.342369081754 - 5 0 2 2 5 4 1224.3326291384401 - 6 0 2 3 6 5 -307.76372034882547 - 7 0 2 4 7 6 122.2054412860679 - 8 0 3 1 2 2 419.8989065033868 - 9 0 3 2 6 5 -307.76372034882547 - 10 0 3 3 10 7 5.775377895161057 - 11 0 3 4 11 8 31.894042098338062 - 12 0 4 1 3 3 -31.990290403269185 - 13 0 4 2 7 6 122.2054412860679 - 14 0 4 3 11 8 31.894042098338062 - 15 0 4 4 15 9 82.284913240665929 - 16 1 0 1 0 0 1402.7969032897649 - 17 1 0 2 1 1 -1298.342369081754 - 18 1 0 3 2 2 419.8989065033868 - 19 1 0 4 3 3 -31.990290403269185 - 20 1 1 0 0 0 1402.7969032897649 - 21 1 1 1 21 10 -4531.7214293481593 - 22 1 1 2 22 11 3112.5285382688699 - 23 1 1 3 23 12 -861.39249941223591 - 24 1 1 4 24 13 10.479035926748963 - 25 1 2 0 1 1 -1298.342369081754 - 26 1 2 1 22 11 3112.5285382688699 - 27 1 2 2 27 14 -2068.7703047359728 - 28 1 2 3 28 15 384.6917757072041 - 29 1 2 4 29 16 -46.809491072254986 - 30 1 3 0 2 2 419.8989065033868 - 31 1 3 1 23 12 -861.39249941223591 - 32 1 3 2 28 15 384.6917757072041 - 33 1 3 3 33 17 121.96247566026466 - 34 1 3 4 34 18 -150.33324290659249 - 35 1 4 0 3 3 -31.990290403269185 - 36 1 4 1 24 13 10.479035926748963 - 37 1 4 2 29 16 -46.809491072254986 - 38 1 4 3 34 18 -150.33324290659249 - 39 1 4 4 39 19 -67.757251747991006 - 40 2 0 1 1 1 -1298.342369081754 - 41 2 0 2 5 4 1224.3326291384401 - 42 2 0 3 6 5 -307.76372034882547 - 43 2 0 4 7 6 122.2054412860679 - 44 2 1 0 1 1 -1298.342369081754 - 45 2 1 1 22 11 3112.5285382688699 - 46 2 1 2 27 14 -2068.7703047359728 - 47 2 1 3 28 15 384.6917757072041 - 48 2 1 4 29 16 -46.809491072254986 - 49 2 2 0 5 4 1224.3326291384401 - 50 2 2 1 27 14 -2068.7703047359728 - 51 2 2 2 51 20 1242.5400110990367 - 52 2 2 3 52 21 -72.42215310701431 - 53 2 2 4 53 22 116.70965861917142 - 54 2 3 0 6 5 -307.76372034882547 - 55 2 3 1 28 15 384.6917757072041 - 56 2 3 2 52 21 -72.42215310701431 - 57 2 3 3 57 23 -234.94274968324066 - 58 2 3 4 58 24 97.215913337815778 - 59 2 4 0 7 6 122.2054412860679 - 60 2 4 1 29 16 -46.809491072254986 - 61 2 4 2 53 22 116.70965861917142 - 62 2 4 3 58 24 97.215913337815778 - 63 2 4 4 63 25 92.994437060536782 - 64 3 0 1 2 2 419.8989065033868 - 65 3 0 2 6 5 -307.76372034882547 - 66 3 0 3 10 7 5.775377895161057 - 67 3 0 4 11 8 31.894042098338062 - 68 3 1 0 2 2 419.8989065033868 - 69 3 1 1 23 12 -861.39249941223591 - 70 3 1 2 28 15 384.6917757072041 - 71 3 1 3 33 17 121.96247566026466 - 72 3 1 4 34 18 -150.33324290659249 - 73 3 2 0 6 5 -307.76372034882547 - 74 3 2 1 28 15 384.6917757072041 - 75 3 2 2 52 21 -72.42215310701431 - 76 3 2 3 57 23 -234.94274968324066 - 77 3 2 4 58 24 97.215913337815778 - 78 3 3 0 10 7 5.775377895161057 - 79 3 3 1 33 17 121.96247566026466 - 80 3 3 2 57 23 -234.94274968324066 - 81 3 3 3 81 26 251.68018665623526 - 82 3 3 4 82 27 -128.23608197580796 - 83 3 4 0 11 8 31.894042098338062 - 84 3 4 1 34 18 -150.33324290659249 - 85 3 4 2 58 24 97.215913337815778 - 86 3 4 3 82 27 -128.23608197580796 - 87 3 4 4 87 28 -2.5445319466327021 - 88 4 0 1 3 3 -31.990290403269185 - 89 4 0 2 7 6 122.2054412860679 - 90 4 0 3 11 8 31.894042098338062 - 91 4 0 4 15 9 82.284913240665929 - 92 4 1 0 3 3 -31.990290403269185 - 93 4 1 1 24 13 10.479035926748963 - 94 4 1 2 29 16 -46.809491072254986 - 95 4 1 3 34 18 -150.33324290659249 - 96 4 1 4 39 19 -67.757251747991006 - 97 4 2 0 7 6 122.2054412860679 - 98 4 2 1 29 16 -46.809491072254986 - 99 4 2 2 53 22 116.70965861917142 - 100 4 2 3 58 24 97.215913337815778 - 101 4 2 4 63 25 92.994437060536782 - 102 4 3 0 11 8 31.894042098338062 - 103 4 3 1 34 18 -150.33324290659249 - 104 4 3 2 58 24 97.215913337815778 - 105 4 3 3 82 27 -128.23608197580796 - 106 4 3 4 87 28 -2.5445319466327021 - 107 4 4 0 15 9 82.284913240665929 - 108 4 4 1 39 19 -67.757251747991006 - 109 4 4 2 63 25 92.994437060536782 - 110 4 4 3 87 28 -2.5445319466327021 - 111 4 4 4 111 29 47.623528525465417 + index | powers | equiv index | param index | parameter + ---------------------------------------------------------------------------- + 0 0 1 1 0 0 237.71658259893007 + 1 0 1 2 1 1 -313.66361360195964 + 2 0 1 3 2 2 -0.87412943255556641 + 3 0 1 4 3 3 8.5738336110087943 + 4 0 2 1 1 1 -313.66361360195964 + 5 0 2 2 5 4 219.13574938938922 + 6 0 2 3 6 5 -48.916639808850221 + 7 0 2 4 7 6 47.485305436362509 + 8 0 3 1 2 2 -0.87412943255556641 + 9 0 3 2 6 5 -48.916639808850221 + 10 0 3 3 10 7 -59.522511859901911 + 11 0 3 4 11 8 20.914961024944958 + 12 0 4 1 3 3 8.5738336110087943 + 13 0 4 2 7 6 47.485305436362509 + 14 0 4 3 11 8 20.914961024944958 + 15 0 4 4 15 9 47.046110820529904 + 16 1 0 1 0 0 237.71658259893007 + 17 1 0 2 1 1 -313.66361360195964 + 18 1 0 3 2 2 -0.87412943255556641 + 19 1 0 4 3 3 8.5738336110087943 + 20 1 1 0 0 0 237.71658259893007 + 21 1 1 1 21 10 191.57912288040922 + 22 1 1 2 22 11 190.94565844371968 + 23 1 1 3 23 12 315.79799381873983 + 24 1 1 4 24 13 -26.523325933888287 + 25 1 2 0 1 1 -313.66361360195964 + 26 1 2 1 22 11 190.94565844371968 + 27 1 2 2 27 14 -222.42902465070807 + 28 1 2 3 28 15 -83.696733313968025 + 29 1 2 4 29 16 -45.598205237344409 + 30 1 3 0 2 2 -0.87412943255556641 + 31 1 3 1 23 12 315.79799381873983 + 32 1 3 2 28 15 -83.696733313968025 + 33 1 3 3 33 17 250.48627775143757 + 34 1 3 4 34 18 -84.839644220901562 + 35 1 4 0 3 3 8.5738336110087943 + 36 1 4 1 24 13 -26.523325933888287 + 37 1 4 2 29 16 -45.598205237344409 + 38 1 4 3 34 18 -84.839644220901562 + 39 1 4 4 39 19 -49.409061380898628 + 40 2 0 1 1 1 -313.66361360195964 + 41 2 0 2 5 4 219.13574938938922 + 42 2 0 3 6 5 -48.916639808850221 + 43 2 0 4 7 6 47.485305436362509 + 44 2 1 0 1 1 -313.66361360195964 + 45 2 1 1 22 11 190.94565844371968 + 46 2 1 2 27 14 -222.42902465070807 + 47 2 1 3 28 15 -83.696733313968025 + 48 2 1 4 29 16 -45.598205237344409 + 49 2 2 0 5 4 219.13574938938922 + 50 2 2 1 27 14 -222.42902465070807 + 51 2 2 2 51 20 86.547152862242683 + 52 2 2 3 52 21 21.763600413002322 + 53 2 2 4 53 22 127.80199528347426 + 54 2 3 0 6 5 -48.916639808850221 + 55 2 3 1 28 15 -83.696733313968025 + 56 2 3 2 52 21 21.763600413002322 + 57 2 3 3 57 23 -150.74243500273533 + 58 2 3 4 58 24 17.976891971302614 + 59 2 4 0 7 6 47.485305436362509 + 60 2 4 1 29 16 -45.598205237344409 + 61 2 4 2 53 22 127.80199528347426 + 62 2 4 3 58 24 17.976891971302614 + 63 2 4 4 63 25 74.796823929198865 + 64 3 0 1 2 2 -0.87412943255556641 + 65 3 0 2 6 5 -48.916639808850221 + 66 3 0 3 10 7 -59.522511859901911 + 67 3 0 4 11 8 20.914961024944958 + 68 3 1 0 2 2 -0.87412943255556641 + 69 3 1 1 23 12 315.79799381873983 + 70 3 1 2 28 15 -83.696733313968025 + 71 3 1 3 33 17 250.48627775143757 + 72 3 1 4 34 18 -84.839644220901562 + 73 3 2 0 6 5 -48.916639808850221 + 74 3 2 1 28 15 -83.696733313968025 + 75 3 2 2 52 21 21.763600413002322 + 76 3 2 3 57 23 -150.74243500273533 + 77 3 2 4 58 24 17.976891971302614 + 78 3 3 0 10 7 -59.522511859901911 + 79 3 3 1 33 17 250.48627775143757 + 80 3 3 2 57 23 -150.74243500273533 + 81 3 3 3 81 26 191.21315224577711 + 82 3 3 4 82 27 -68.126425456213269 + 83 3 4 0 11 8 20.914961024944958 + 84 3 4 1 34 18 -84.839644220901562 + 85 3 4 2 58 24 17.976891971302614 + 86 3 4 3 82 27 -68.126425456213269 + 87 3 4 4 87 28 -8.7435116592593616 + 88 4 0 1 3 3 8.5738336110087943 + 89 4 0 2 7 6 47.485305436362509 + 90 4 0 3 11 8 20.914961024944958 + 91 4 0 4 15 9 47.046110820529904 + 92 4 1 0 3 3 8.5738336110087943 + 93 4 1 1 24 13 -26.523325933888287 + 94 4 1 2 29 16 -45.598205237344409 + 95 4 1 3 34 18 -84.839644220901562 + 96 4 1 4 39 19 -49.409061380898628 + 97 4 2 0 7 6 47.485305436362509 + 98 4 2 1 29 16 -45.598205237344409 + 99 4 2 2 53 22 127.80199528347426 + 100 4 2 3 58 24 17.976891971302614 + 101 4 2 4 63 25 74.796823929198865 + 102 4 3 0 11 8 20.914961024944958 + 103 4 3 1 34 18 -84.839644220901562 + 104 4 3 2 58 24 17.976891971302614 + 105 4 3 3 82 27 -68.126425456213269 + 106 4 3 4 87 28 -8.7435116592593616 + 107 4 4 0 15 9 47.046110820529904 + 108 4 4 1 39 19 -49.409061380898628 + 109 4 4 2 63 25 74.796823929198865 + 110 4 4 3 87 28 -8.7435116592593616 + 111 4 4 4 111 29 30.778899919129898 TRIPLETTYPE PARAMS: INDEX: 1 ATOMS: O O H PAIRS: OO OH OH UNIQUE: 66 TOTAL: 112 - index | powers | equiv index | param index | parameter - ---------------------------------------------------------------------------- - 0 0 1 1 0 0 -446.79297018948137 - 1 0 1 2 1 1 -707.79681032701251 - 2 0 1 3 2 2 -529.80456335576662 - 3 0 1 4 3 3 -297.84996174620051 - 4 0 2 1 1 1 -707.79681032701251 - 5 0 2 2 5 4 -1517.4959514307366 - 6 0 2 3 6 5 -1271.6685347852756 - 7 0 2 4 7 6 -450.94409871913086 - 8 0 3 1 2 2 -529.80456335576662 - 9 0 3 2 6 5 -1271.6685347852756 - 10 0 3 3 10 7 -828.25013199126431 - 11 0 3 4 11 8 -200.01227009231752 - 12 0 4 1 3 3 -297.84996174620051 - 13 0 4 2 7 6 -450.94409871913086 - 14 0 4 3 11 8 -200.01227009231752 - 15 0 4 4 15 9 2.9932530506393782 - 16 1 0 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98 4 2 1 94 57 -73.939969070704038 - 99 4 2 2 99 60 -61.085033747616016 - 100 4 2 3 100 61 -57.199155029504112 - 101 4 2 4 101 62 -25.95042532655723 - 102 4 3 0 90 54 -17.225010197623746 - 103 4 3 1 95 58 -27.879060379470907 - 104 4 3 2 100 61 -57.199155029504112 - 105 4 3 3 105 63 -23.57341051416882 - 106 4 3 4 106 64 -5.0463617388539177 - 107 4 4 0 91 55 4.4009421084362579 - 108 4 4 1 96 59 -20.095074637293813 - 109 4 4 2 101 62 -25.95042532655723 - 110 4 4 3 106 64 -5.0463617388539177 - 111 4 4 4 111 65 3.5501714966011235 + index | powers | equiv index | param index | parameter + ---------------------------------------------------------------------------- + 0 0 1 1 0 0 286.9757004241668 + 1 0 1 2 1 1 -174.26761509668478 + 2 0 1 3 2 2 149.01863222227598 + 3 0 1 4 3 3 -298.73786230925157 + 4 0 2 1 1 1 -174.26761509668478 + 5 0 2 2 5 4 201.84826987346594 + 6 0 2 3 6 5 -271.33554157070017 + 7 0 2 4 7 6 -276.82304085283914 + 8 0 3 1 2 2 149.01863222227598 + 9 0 3 2 6 5 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16.78327991010859 + 92 4 1 0 88 52 -23.662692154686496 + 93 4 1 1 93 56 2.8278964931263033 + 94 4 1 2 94 57 107.9562224463551 + 95 4 1 3 95 58 107.86360951883316 + 96 4 1 4 96 59 -11.443306694072596 + 97 4 2 0 89 53 32.783510978942452 + 98 4 2 1 94 57 107.9562224463551 + 99 4 2 2 99 60 166.74320751688023 + 100 4 2 3 100 61 59.187736345695455 + 101 4 2 4 101 62 -11.821181537691796 + 102 4 3 0 90 54 36.863933352634618 + 103 4 3 1 95 58 107.86360951883316 + 104 4 3 2 100 61 59.187736345695455 + 105 4 3 3 105 63 31.221462299476009 + 106 4 3 4 106 64 -2.3704875149988105 + 107 4 4 0 91 55 16.78327991010859 + 108 4 4 1 96 59 -11.443306694072596 + 109 4 4 2 101 62 -11.821181537691796 + 110 4 4 3 106 64 -2.3704875149988105 + 111 4 4 4 111 65 3.1648523094746048 TRIPLETTYPE PARAMS: INDEX: 2 ATOMS: O H H PAIRS: OH OH HH UNIQUE: 66 TOTAL: 112 - index | powers | equiv index | param index | parameter + index | powers | equiv index | param index | parameter ---------------------------------------------------------------------------- - 0 0 1 1 0 0 47.878484975374505 - 1 0 1 2 1 1 -80.342864345293464 - 2 0 1 3 2 2 68.081274418441907 - 3 0 1 4 3 3 -19.154040887350888 - 4 0 2 1 4 4 9.1225134053641312 - 5 0 2 2 5 5 -29.273986289590269 - 6 0 2 3 6 6 5.0879620656454136 - 7 0 2 4 7 7 -5.7015848710999011 - 8 0 3 1 8 8 -6.185346677340064 - 9 0 3 2 9 9 9.211228291485412 - 10 0 3 3 10 10 -0.77955424973158927 - 11 0 3 4 11 11 7.5317409645885718 - 12 0 4 1 12 12 -5.5091258974179169 - 13 0 4 2 13 13 6.0913515052770757 - 14 0 4 3 14 14 -5.9765720737303205 - 15 0 4 4 15 15 -0.39376581369586205 - 16 1 0 1 0 0 47.878484975374505 - 17 1 0 2 1 1 -80.342864345293464 - 18 1 0 3 2 2 68.081274418441907 - 19 1 0 4 3 3 -19.154040887350888 - 20 1 1 0 20 16 96.061967203271649 - 21 1 1 1 21 17 38.369209387424306 - 22 1 1 2 22 18 -87.151823235715909 - 23 1 1 3 23 19 105.66493819767626 - 24 1 1 4 24 20 -16.142059365919259 - 25 1 2 0 25 21 -68.315106389820556 - 26 1 2 1 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54 2 3 0 54 41 12.403700073330693 - 55 2 3 1 55 42 -15.95005913589905 - 56 2 3 2 56 43 25.865124050529602 - 57 2 3 3 57 44 -7.8378809785989141 - 58 2 3 4 58 45 9.6251875302709671 - 59 2 4 0 59 46 13.193814029391053 - 60 2 4 1 60 47 -28.552839265792105 - 61 2 4 2 61 48 18.904182813446855 - 62 2 4 3 62 49 -13.05082232665219 - 63 2 4 4 63 50 3.1394648498635132 - 64 3 0 1 8 8 -6.185346677340064 - 65 3 0 2 9 9 9.211228291485412 - 66 3 0 3 10 10 -0.77955424973158927 - 67 3 0 4 11 11 7.5317409645885718 - 68 3 1 0 30 26 29.148075065149722 - 69 3 1 1 31 27 -25.4450895498642 - 70 3 1 2 32 28 37.152543089427937 - 71 3 1 3 33 29 -15.599015795357673 - 72 3 1 4 34 30 12.345294448480663 - 73 3 2 0 54 41 12.403700073330693 - 74 3 2 1 55 42 -15.95005913589905 - 75 3 2 2 56 43 25.865124050529602 - 76 3 2 3 57 44 -7.8378809785989141 - 77 3 2 4 58 45 9.6251875302709671 - 78 3 3 0 78 51 15.445172387101326 - 79 3 3 1 79 52 -10.28192657994768 - 80 3 3 2 80 53 16.523112879446167 - 81 3 3 3 81 54 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-164.03429601517055 + 80 3 3 2 80 53 159.82187976503624 + 81 3 3 3 81 54 -54.145934134072483 + 82 3 3 4 82 55 24.959307029096543 + 83 3 4 0 83 56 45.368093715887099 + 84 3 4 1 84 57 -85.174748206110749 + 85 3 4 2 85 58 39.40535636618489 + 86 3 4 3 86 59 -12.326333714453064 + 87 3 4 4 87 60 -0.55107675976186954 + 88 4 0 1 12 12 -49.732185105617873 + 89 4 0 2 13 13 25.662102578059802 + 90 4 0 3 14 14 -31.370814244667731 + 91 4 0 4 15 15 -5.0039815912244006 + 92 4 1 0 35 31 59.942550079124921 + 93 4 1 1 36 32 -130.24370455152163 + 94 4 1 2 37 33 78.00791016492488 + 95 4 1 3 38 34 -40.971453786832939 + 96 4 1 4 39 35 4.9476198118327854 + 97 4 2 0 59 46 50.647947948068648 + 98 4 2 1 60 47 -142.73959201970379 + 99 4 2 2 61 48 69.368135754890289 + 100 4 2 3 62 49 -54.319390905190978 + 101 4 2 4 63 50 4.9870885226851378 + 102 4 3 0 83 56 45.368093715887099 + 103 4 3 1 84 57 -85.174748206110749 + 104 4 3 2 85 58 39.40535636618489 + 105 4 3 3 86 59 -12.326333714453064 + 106 4 3 4 87 60 -0.55107675976186954 + 107 4 4 0 107 61 -36.944292472418809 + 108 4 4 1 108 62 54.303902189989373 + 109 4 4 2 109 63 -57.08290113431886 + 110 4 4 3 110 64 16.956341710156455 + 111 4 4 4 111 65 -17.917641191221655 TRIPLETTYPE PARAMS: - INDEX: 3 ATOMS: O O O -PAIRS: OO OO OO UNIQUE: 30 TOTAL: 112 - - index | powers | equiv index | param index | parameter + INDEX: 3 ATOMS: H H H +PAIRS: HH HH HH UNIQUE: 30 TOTAL: 112 + index | powers | equiv index | param index | parameter ---------------------------------------------------------------------------- - 0 0 1 1 0 0 1402.7969032897649 - 1 0 1 2 1 1 -1298.342369081754 - 2 0 1 3 2 2 419.8989065033868 - 3 0 1 4 3 3 -31.990290403269185 - 4 0 2 1 1 1 -1298.342369081754 - 5 0 2 2 5 4 1224.3326291384401 - 6 0 2 3 6 5 -307.76372034882547 - 7 0 2 4 7 6 122.2054412860679 - 8 0 3 1 2 2 419.8989065033868 - 9 0 3 2 6 5 -307.76372034882547 - 10 0 3 3 10 7 5.775377895161057 - 11 0 3 4 11 8 31.894042098338062 - 12 0 4 1 3 3 -31.990290403269185 - 13 0 4 2 7 6 122.2054412860679 - 14 0 4 3 11 8 31.894042098338062 - 15 0 4 4 15 9 82.284913240665929 - 16 1 0 1 0 0 1402.7969032897649 - 17 1 0 2 1 1 -1298.342369081754 - 18 1 0 3 2 2 419.8989065033868 - 19 1 0 4 3 3 -31.990290403269185 - 20 1 1 0 0 0 1402.7969032897649 - 21 1 1 1 21 10 -4531.7214293481593 - 22 1 1 2 22 11 3112.5285382688699 - 23 1 1 3 23 12 -861.39249941223591 - 24 1 1 4 24 13 10.479035926748963 - 25 1 2 0 1 1 -1298.342369081754 - 26 1 2 1 22 11 3112.5285382688699 - 27 1 2 2 27 14 -2068.7703047359728 - 28 1 2 3 28 15 384.6917757072041 - 29 1 2 4 29 16 -46.809491072254986 - 30 1 3 0 2 2 419.8989065033868 - 31 1 3 1 23 12 -861.39249941223591 - 32 1 3 2 28 15 384.6917757072041 - 33 1 3 3 33 17 121.96247566026466 - 34 1 3 4 34 18 -150.33324290659249 - 35 1 4 0 3 3 -31.990290403269185 - 36 1 4 1 24 13 10.479035926748963 - 37 1 4 2 29 16 -46.809491072254986 - 38 1 4 3 34 18 -150.33324290659249 - 39 1 4 4 39 19 -67.757251747991006 - 40 2 0 1 1 1 -1298.342369081754 - 41 2 0 2 5 4 1224.3326291384401 - 42 2 0 3 6 5 -307.76372034882547 - 43 2 0 4 7 6 122.2054412860679 - 44 2 1 0 1 1 -1298.342369081754 - 45 2 1 1 22 11 3112.5285382688699 - 46 2 1 2 27 14 -2068.7703047359728 - 47 2 1 3 28 15 384.6917757072041 - 48 2 1 4 29 16 -46.809491072254986 - 49 2 2 0 5 4 1224.3326291384401 - 50 2 2 1 27 14 -2068.7703047359728 - 51 2 2 2 51 20 1242.5400110990367 - 52 2 2 3 52 21 -72.42215310701431 - 53 2 2 4 53 22 116.70965861917142 - 54 2 3 0 6 5 -307.76372034882547 - 55 2 3 1 28 15 384.6917757072041 - 56 2 3 2 52 21 -72.42215310701431 - 57 2 3 3 57 23 -234.94274968324066 - 58 2 3 4 58 24 97.215913337815778 - 59 2 4 0 7 6 122.2054412860679 - 60 2 4 1 29 16 -46.809491072254986 - 61 2 4 2 53 22 116.70965861917142 - 62 2 4 3 58 24 97.215913337815778 - 63 2 4 4 63 25 92.994437060536782 - 64 3 0 1 2 2 419.8989065033868 - 65 3 0 2 6 5 -307.76372034882547 - 66 3 0 3 10 7 5.775377895161057 - 67 3 0 4 11 8 31.894042098338062 - 68 3 1 0 2 2 419.8989065033868 - 69 3 1 1 23 12 -861.39249941223591 - 70 3 1 2 28 15 384.6917757072041 - 71 3 1 3 33 17 121.96247566026466 - 72 3 1 4 34 18 -150.33324290659249 - 73 3 2 0 6 5 -307.76372034882547 - 74 3 2 1 28 15 384.6917757072041 - 75 3 2 2 52 21 -72.42215310701431 - 76 3 2 3 57 23 -234.94274968324066 - 77 3 2 4 58 24 97.215913337815778 - 78 3 3 0 10 7 5.775377895161057 - 79 3 3 1 33 17 121.96247566026466 - 80 3 3 2 57 23 -234.94274968324066 - 81 3 3 3 81 26 251.68018665623526 - 82 3 3 4 82 27 -128.23608197580796 - 83 3 4 0 11 8 31.894042098338062 - 84 3 4 1 34 18 -150.33324290659249 - 85 3 4 2 58 24 97.215913337815778 - 86 3 4 3 82 27 -128.23608197580796 - 87 3 4 4 87 28 -2.5445319466327021 - 88 4 0 1 3 3 -31.990290403269185 - 89 4 0 2 7 6 122.2054412860679 - 90 4 0 3 11 8 31.894042098338062 - 91 4 0 4 15 9 82.284913240665929 - 92 4 1 0 3 3 -31.990290403269185 - 93 4 1 1 24 13 10.479035926748963 - 94 4 1 2 29 16 -46.809491072254986 - 95 4 1 3 34 18 -150.33324290659249 - 96 4 1 4 39 19 -67.757251747991006 - 97 4 2 0 7 6 122.2054412860679 - 98 4 2 1 29 16 -46.809491072254986 - 99 4 2 2 53 22 116.70965861917142 - 100 4 2 3 58 24 97.215913337815778 - 101 4 2 4 63 25 92.994437060536782 - 102 4 3 0 11 8 31.894042098338062 - 103 4 3 1 34 18 -150.33324290659249 - 104 4 3 2 58 24 97.215913337815778 - 105 4 3 3 82 27 -128.23608197580796 - 106 4 3 4 87 28 -2.5445319466327021 - 107 4 4 0 15 9 82.284913240665929 - 108 4 4 1 39 19 -67.757251747991006 - 109 4 4 2 63 25 92.994437060536782 - 110 4 4 3 87 28 -2.5445319466327021 - 111 4 4 4 111 29 47.623528525465417 + 0 0 1 1 0 0 -80.612106183507279 + 1 0 1 2 1 1 -428.6094935743086 + 2 0 1 3 2 2 -19.563222782271623 + 3 0 1 4 3 3 -82.960696966176926 + 4 0 2 1 1 1 -428.6094935743086 + 5 0 2 2 5 4 690.60425716979637 + 6 0 2 3 6 5 -257.88307339988137 + 7 0 2 4 7 6 212.13541527176133 + 8 0 3 1 2 2 -19.563222782271623 + 9 0 3 2 6 5 -257.88307339988137 + 10 0 3 3 10 7 -2.1037306546466121 + 11 0 3 4 11 8 -36.171215540754147 + 12 0 4 1 3 3 -82.960696966176926 + 13 0 4 2 7 6 212.13541527176133 + 14 0 4 3 11 8 -36.171215540754147 + 15 0 4 4 15 9 79.484261000472145 + 16 1 0 1 0 0 -80.612106183507279 + 17 1 0 2 1 1 -428.6094935743086 + 18 1 0 3 2 2 -19.563222782271623 + 19 1 0 4 3 3 -82.960696966176926 + 20 1 1 0 0 0 -80.612106183507279 + 21 1 1 1 21 10 789.58940549028534 + 22 1 1 2 22 11 962.24369756030706 + 23 1 1 3 23 12 367.78618016621073 + 24 1 1 4 24 13 145.11473876380353 + 25 1 2 0 1 1 -428.6094935743086 + 26 1 2 1 22 11 962.24369756030706 + 27 1 2 2 27 14 -1698.2142915082584 + 28 1 2 3 28 15 366.94344262365308 + 29 1 2 4 29 16 -375.90657412187335 + 30 1 3 0 2 2 -19.563222782271623 + 31 1 3 1 23 12 367.78618016621073 + 32 1 3 2 28 15 366.94344262365308 + 33 1 3 3 33 17 181.9019030305507 + 34 1 3 4 34 18 1.4328353727085243 + 35 1 4 0 3 3 -82.960696966176926 + 36 1 4 1 24 13 145.11473876380353 + 37 1 4 2 29 16 -375.90657412187335 + 38 1 4 3 34 18 1.4328353727085243 + 39 1 4 4 39 19 -99.856035847534798 + 40 2 0 1 1 1 -428.6094935743086 + 41 2 0 2 5 4 690.60425716979637 + 42 2 0 3 6 5 -257.88307339988137 + 43 2 0 4 7 6 212.13541527176133 + 44 2 1 0 1 1 -428.6094935743086 + 45 2 1 1 22 11 962.24369756030706 + 46 2 1 2 27 14 -1698.2142915082584 + 47 2 1 3 28 15 366.94344262365308 + 48 2 1 4 29 16 -375.90657412187335 + 49 2 2 0 5 4 690.60425716979637 + 50 2 2 1 27 14 -1698.2142915082584 + 51 2 2 2 51 20 1937.6597323849069 + 52 2 2 3 52 21 -708.79559006139425 + 53 2 2 4 53 22 501.73124365828767 + 54 2 3 0 6 5 -257.88307339988137 + 55 2 3 1 28 15 366.94344262365308 + 56 2 3 2 52 21 -708.79559006139425 + 57 2 3 3 57 23 107.16643400696094 + 58 2 3 4 58 24 -134.40420717778383 + 59 2 4 0 7 6 212.13541527176133 + 60 2 4 1 29 16 -375.90657412187335 + 61 2 4 2 53 22 501.73124365828767 + 62 2 4 3 58 24 -134.40420717778383 + 63 2 4 4 63 25 146.68544318831596 + 64 3 0 1 2 2 -19.563222782271623 + 65 3 0 2 6 5 -257.88307339988137 + 66 3 0 3 10 7 -2.1037306546466121 + 67 3 0 4 11 8 -36.171215540754147 + 68 3 1 0 2 2 -19.563222782271623 + 69 3 1 1 23 12 367.78618016621073 + 70 3 1 2 28 15 366.94344262365308 + 71 3 1 3 33 17 181.9019030305507 + 72 3 1 4 34 18 1.4328353727085243 + 73 3 2 0 6 5 -257.88307339988137 + 74 3 2 1 28 15 366.94344262365308 + 75 3 2 2 52 21 -708.79559006139425 + 76 3 2 3 57 23 107.16643400696094 + 77 3 2 4 58 24 -134.40420717778383 + 78 3 3 0 10 7 -2.1037306546466121 + 79 3 3 1 33 17 181.9019030305507 + 80 3 3 2 57 23 107.16643400696094 + 81 3 3 3 81 26 113.74842418054462 + 82 3 3 4 82 27 -37.603841984124628 + 83 3 4 0 11 8 -36.171215540754147 + 84 3 4 1 34 18 1.4328353727085243 + 85 3 4 2 58 24 -134.40420717778383 + 86 3 4 3 82 27 -37.603841984124628 + 87 3 4 4 87 28 -24.341736153164845 + 88 4 0 1 3 3 -82.960696966176926 + 89 4 0 2 7 6 212.13541527176133 + 90 4 0 3 11 8 -36.171215540754147 + 91 4 0 4 15 9 79.484261000472145 + 92 4 1 0 3 3 -82.960696966176926 + 93 4 1 1 24 13 145.11473876380353 + 94 4 1 2 29 16 -375.90657412187335 + 95 4 1 3 34 18 1.4328353727085243 + 96 4 1 4 39 19 -99.856035847534798 + 97 4 2 0 7 6 212.13541527176133 + 98 4 2 1 29 16 -375.90657412187335 + 99 4 2 2 53 22 501.73124365828767 + 100 4 2 3 58 24 -134.40420717778383 + 101 4 2 4 63 25 146.68544318831596 + 102 4 3 0 11 8 -36.171215540754147 + 103 4 3 1 34 18 1.4328353727085243 + 104 4 3 2 58 24 -134.40420717778383 + 105 4 3 3 82 27 -37.603841984124628 + 106 4 3 4 87 28 -24.341736153164845 + 107 4 4 0 15 9 79.484261000472145 + 108 4 4 1 39 19 -99.856035847534798 + 109 4 4 2 63 25 146.68544318831596 + 110 4 4 3 87 28 -24.341736153164845 + 111 4 4 4 111 29 26.971459943445666 + +QUADRUPLET CHEBYSHEV PARAMS PAIRMAPS: 4 -0 OO -2 OH -2 HO 1 HH +2 HO +2 OH +0 OO TRIPMAPS: 8 -0 OOOOOO -1 OOOHOH -1 OHOOOH -1 OHOHOO -2 OHOHHH -2 OHHHOH -2 HHOHOH 3 HHHHHH +2 HHOHOH +2 OHHHOH +2 OHOHHH +1 OHOHOO +1 OHOOOH +1 OOOHOH +0 OOOOOO ENDFILE diff --git a/serial_interface/tests/force_fields/test_params.HN3.penalty.txt b/serial_interface/tests/force_fields/test_params.HN3.penalty.txt new file mode 100644 index 0000000..1b06451 --- /dev/null +++ b/serial_interface/tests/force_fields/test_params.HN3.penalty.txt @@ -0,0 +1,6730 @@ +! https://doi.org/10.26434/chemrxiv.12921734.v1 +! +! WARNING: This force field is only intended for modeling HN3 from 300 K/1 gcc to 4500 K/2 gcc +! WARNING: This force field comes with no guarantees +! +USECOUL: false +FITCOUL: false +USEPOVR: false +FITPOVR: false +USE3BCH: true +USE4BCH: true + +PAIRTYP: CHEBYSHEV 12 8 4 -1 1 + +ATOM TYPES: 2 + +# TYPEIDX # # ATM_TYP # # ATMCHRG # # ATMMASS # +0 N 0 14.0064 +1 H 0 1.0079 + +ATOM PAIRS: 3 + +# PAIRIDX # # ATM_TY1 # # ATM_TY1 # # S_MINIM # # S_MAXIM # # S_DELTA # # CHBDIST # # MORSE_LAMBDA # + 0 N N 0.793 8 0.1 MORSE 1.15 + 1 H H 0.451 8 0.1 MORSE 0.8 + 2 N H 0.666 8 0.1 MORSE 1 + +PAIR CHEBYSHEV PENALTY DIST: 0.1 +PAIR CHEBYSHEV PENALTY SCALING: 1.0E4 + +FCUT TYPE: TERSOFF 0.5 + +SPECIAL 3B S_MAXIM: ALL 5.0 + +SPECIAL 4B S_MAXIM: ALL 4.0 + +ATOM PAIR TRIPLETS: 4 +ATOM PAIR QUADRUPLETS: 5 + +PAIR CHEBYSHEV PARAMS + +PAIRTYPE PARAMS: 0 N N + +0 17.341009355697139 +1 57.774119773766508 +2 76.220068702688152 +3 40.597946713780949 +4 -3.0909502931424067 +5 -9.5683232884817837 +6 -1.3984465091198888 +7 -0.28488328353618581 +8 -0.21731959305168455 +9 0.15689095165962866 +10 0.056716863392651549 +11 0.21485998130982475 + +PAIRTYPE PARAMS: 1 H H + +0 12.50578869600136 +1 28.829120708867389 +2 24.29592797843474 +3 9.3511833776237072 +4 0.80954006894461727 +5 1.1087614096539125 +6 2.3088310395700096 +7 -0.17153647829749744 +8 0.03543659934099596 +9 0.50123027271182286 +10 -0.056263800428875528 +11 0.20387198131834489 + +PAIRTYPE PARAMS: 2 N H + +0 1.7014818861712635 +1 10.542458855813658 +2 13.624902173816118 +3 -1.9516175005010132 +4 -11.233817110914156 +5 -4.3082174789307697 +6 -0.18964765490322932 +7 -0.9210761937243932 +8 -0.15935020918687481 +9 0.26743967584871786 +10 0.034690942326356888 +11 0.0020823960544321014 + +TRIPLET CHEBYSHEV PARAMS + +TRIPLETTYPE PARAMS: + INDEX: 0 ATOMS: N N N +PAIRS: NN NN NN UNIQUE: -1 TOTAL: 390 + index | powers | equiv index | param index | parameter + ---------------------------------------------------------------------------- +0 0 1 1 0 0 0.39719983417608717 +1 1 0 1 0 0 0.39719983417608717 +2 1 1 0 0 0 0.39719983417608717 +3 0 1 2 3 1 -4.8464470189335707 +4 1 0 2 3 1 -4.8464470189335707 +5 0 2 1 3 1 -4.8464470189335707 +6 2 0 1 3 1 -4.8464470189335707 +7 1 2 0 3 1 -4.8464470189335707 +8 2 1 0 3 1 -4.8464470189335707 +9 0 1 3 9 2 -16.738045005908702 +10 1 0 3 9 2 -16.738045005908702 +11 0 3 1 9 2 -16.738045005908702 +12 3 0 1 9 2 -16.738045005908702 +13 1 3 0 9 2 -16.738045005908702 +14 3 1 0 9 2 -16.738045005908702 +15 0 1 4 15 3 -11.903591850467697 +16 1 0 4 15 3 -11.903591850467697 +17 0 4 1 15 3 -11.903591850467697 +18 4 0 1 15 3 -11.903591850467697 +19 1 4 0 15 3 -11.903591850467697 +20 4 1 0 15 3 -11.903591850467697 +21 0 1 6 27 5 -0.97567034287145049 +22 1 0 6 27 5 -0.97567034287145049 +23 0 6 1 27 5 -0.97567034287145049 +24 6 0 1 27 5 -0.97567034287145049 +25 1 6 0 27 5 -0.97567034287145049 +26 6 1 0 27 5 -0.97567034287145049 +27 0 2 2 39 7 47.18906005619997 +28 2 0 2 39 7 47.18906005619997 +29 2 2 0 39 7 47.18906005619997 +30 0 2 3 42 8 27.59647935554149 +31 2 0 3 42 8 27.59647935554149 +32 0 3 2 42 8 27.59647935554149 +33 3 0 2 42 8 27.59647935554149 +34 2 3 0 42 8 27.59647935554149 +35 3 2 0 42 8 27.59647935554149 +36 0 2 4 48 9 21.47485150512831 +37 2 0 4 48 9 21.47485150512831 +38 0 4 2 48 9 21.47485150512831 +39 4 0 2 48 9 21.47485150512831 +40 2 4 0 48 9 21.47485150512831 +41 4 2 0 48 9 21.47485150512831 +42 0 2 5 54 10 5.575463081302396 +43 2 0 5 54 10 5.575463081302396 +44 0 5 2 54 10 5.575463081302396 +45 5 0 2 54 10 5.575463081302396 +46 2 5 0 54 10 5.575463081302396 +47 5 2 0 54 10 5.575463081302396 +48 0 3 4 75 14 2.8197965862905536 +49 3 0 4 75 14 2.8197965862905536 +50 0 4 3 75 14 2.8197965862905536 +51 4 0 3 75 14 2.8197965862905536 +52 3 4 0 75 14 2.8197965862905536 +53 4 3 0 75 14 2.8197965862905536 +54 0 3 5 81 15 4.122528974391714 +55 3 0 5 81 15 4.122528974391714 +56 0 5 3 81 15 4.122528974391714 +57 5 0 3 81 15 4.122528974391714 +58 3 5 0 81 15 4.122528974391714 +59 5 3 0 81 15 4.122528974391714 +60 0 3 7 93 17 -0.13000869958014277 +61 3 0 7 93 17 -0.13000869958014277 +62 0 7 3 93 17 -0.13000869958014277 +63 7 0 3 93 17 -0.13000869958014277 +64 3 7 0 93 17 -0.13000869958014277 +65 7 3 0 93 17 -0.13000869958014277 +66 0 4 4 99 18 -16.971776604150286 +67 4 0 4 99 18 -16.971776604150286 +68 4 4 0 99 18 -16.971776604150286 +69 0 4 5 102 19 -13.739991709289244 +70 4 0 5 102 19 -13.739991709289244 +71 0 5 4 102 19 -13.739991709289244 +72 5 0 4 102 19 -13.739991709289244 +73 4 5 0 102 19 -13.739991709289244 +74 5 4 0 102 19 -13.739991709289244 +75 0 4 6 108 20 -1.4317385386448496 +76 4 0 6 108 20 -1.4317385386448496 +77 0 6 4 108 20 -1.4317385386448496 +78 6 0 4 108 20 -1.4317385386448496 +79 4 6 0 108 20 -1.4317385386448496 +80 6 4 0 108 20 -1.4317385386448496 +81 0 4 7 114 21 2.8768173619855886 +82 4 0 7 114 21 2.8768173619855886 +83 0 7 4 114 21 2.8768173619855886 +84 7 0 4 114 21 2.8768173619855886 +85 4 7 0 114 21 2.8768173619855886 +86 7 4 0 114 21 2.8768173619855886 +87 0 5 5 120 22 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0.21033722013442527 +848 3 2 2 0 3 3 3063 184 0.21033722013442527 +849 3 2 2 3 0 3 3063 184 0.21033722013442527 +850 2 2 3 3 3 0 3063 184 0.21033722013442527 +851 2 3 2 3 3 0 3063 184 0.21033722013442527 +852 3 3 2 0 2 3 3063 184 0.21033722013442527 +853 3 2 3 2 0 3 3063 184 0.21033722013442527 +854 3 3 2 0 3 2 3063 184 0.21033722013442527 +855 3 2 3 3 0 2 3063 184 0.21033722013442527 +856 2 3 3 2 3 0 3063 184 0.21033722013442527 +857 2 3 3 3 2 0 3063 184 0.21033722013442527 + + +PAIRMAPS: 4 +1 HH +2 HN +2 NH +0 NN + +TRIPMAPS: 8 +3 HHHHHH +2 HHNHNH +2 NHHHNH +2 NHNHHH +1 NHNHNN +1 NHNNNH +1 NNNHNH +0 NNNNNN + +QUADMAPS: 16 +4 HHHHHHHHHHHH +3 HHHHNHHHNHNH +3 HHNHHHNHHHNH +2 HHNHNHNHNHNN +3 NHHHHHNHNHHH +2 NHHHNHNHNNNH +2 NHNHHHNNNHNH +3 NHNHNHHHHHHH +1 NHNHNHNNNNNN +2 NHNHNNHHNHNH +2 NHNNNHNHHHNH +1 NHNNNNNHNHNN +2 NNNHNHNHNHHH +1 NNNHNNNHNNNH +1 NNNNNHNNNHNH +0 NNNNNNNNNNNN + +NO ENERGY OFFSETS: 2 +ENERGY OFFSET 1 -126.828700616 +ENERGY OFFSET 2 -59.0402284083 +ENDFILE diff --git a/serial_interface/tests/force_fields/test_params.h2o_2bcheby.txt b/serial_interface/tests/force_fields/test_params.h2o_2bcheby.txt new file mode 100644 index 0000000..ee656f3 --- /dev/null +++ b/serial_interface/tests/force_fields/test_params.h2o_2bcheby.txt @@ -0,0 +1,84 @@ +! Date 2021-06-09 +! +! Number of variables = 27 +! Number of equations = 28514 +! svd algorithm used +! eps (= args.eps*dmax) = 6.4810e-02 +! SVD regularization factor = 1.0000e-05 +! RMS force error = 1.1392e+01 +! max abs variable = 1.2402e+02 +! number of fitting vars = 25 +! Bayesian Information Criterion = 1.3900e+05 +! +USECOUL: false +FITCOUL: false +USE3BCH: false +USE4BCH: false + +PAIRTYP: CHEBYSHEV 8 0 0 -1 1 + +ATOM TYPES: 2 + +# TYPEIDX # # ATM_TYP # # ATMCHRG # # ATMMASS # +0 O 0.0 15.9994 +1 H 0.0 1.0079 + +ATOM PAIRS: 3 + +# PAIRIDX # # ATM_TY1 # # ATM_TY1 # # S_MINIM # # S_MAXIM # # CHBDIST # # MORSE_LAMBDA # + 0 O O 0.6 6 MORSE 1.25 + 1 H H 0.6 6 MORSE 1.25 + 2 O H 0.6 6 MORSE 1.25 + +FCUT TYPE: CUBIC + +ATOM PAIR TRIPLETS: 0 +ATOM PAIR QUADRUPLETS: 0 + +PAIR CHEBYSHEV PARAMS + +PAIRTYPE PARAMS: 0 O O + + 0 -1.2402135452659e+02 + 1 -1.2194250391651e+02 + 2 7.9233371953572e+01 + 3 9.3768161098852e+01 + 4 -3.2951551982120e+01 + 5 -1.0932950044247e+02 + 6 -5.0309959010988e+01 + 7 -1.9491633485732e+01 + +PAIRTYPE PARAMS: 1 H H + + 0 -2.1709290361960e+01 + 1 -9.7664540386521e+00 + 2 1.3757279364043e+01 + 3 3.6426444952133e+01 + 4 4.2229224485115e+01 + 5 3.6175513360451e+01 + 6 1.8620903475289e+01 + 7 6.0796989873361e+00 + +PAIRTYPE PARAMS: 2 O H + + 0 1.4732200706827e+01 + 1 4.4018649095207e+01 + 2 1.1438706910015e+01 + 3 8.9040002428182e+00 + 4 -1.9788436460739e+01 + 5 -6.0378477953627e+00 + 6 -8.8614335450873e+00 + 7 1.6158044249025e-01 + +TRIPLET CHEBYSHEV PARAMS + +QUADRUPLET CHEBYSHEV PARAMS + + +PAIRMAPS: 4 +1 HH +2 HO +2 OH +0 OO + +ENDFILE diff --git a/serial_interface/tests/run_tests.sh b/serial_interface/tests/run_tests.sh index 7978823..e1853a1 100755 --- a/serial_interface/tests/run_tests.sh +++ b/serial_interface/tests/run_tests.sh @@ -45,32 +45,32 @@ do # Do the compilation if [[ $compile == "MAKEFILE" ]]; then - + for i in $API_LIST # Cycle through APIs do - cd ../examples/${API[$i]} - + cd ../examples/${API[$i]} + echo "Compiling for API ${API[$i]}" echo "" if [[ "${API[$i]}" != "python" ]] ; then - + make all DEBUG=1 else make all cp libchimescalc-serial_dl.so ../../tests/libchimescalc_dl.so fi - + cd ../../tests - - done - + + done + elif [[ $compile == "CMAKE" ]] ; then - + cd ../../ ./install.sh 1 $PREFX # Set the debug flag true cp build/libchimescalc_dl.so serial_interface/tests - cd - + cd - else echo "Error: Unknown compilation method $compile" @@ -78,64 +78,64 @@ do echo "Check logic in run_test.sh" exit 0 fi - + # Run the tasks - + for i in $API_LIST # Cycle through APIs - do - + do + idx=1 for ((j=0;j /dev/null else ../examples/${API[$i]}/${EXE[$i]} force_fields/${FFS[$j]} configurations/$CFG ${OPTIONS[$j]} > /dev/null fi - - else + + else ${PYTH3} ../examples/${API[$i]}/${EXE[$i]} force_fields/${FFS[$j]} configurations/$CFG ${OPTIONS[$j]} ${LOC}/../api 1 > /dev/null fi # Compare results against expected results (expected_output/${FFS[$j]}.$CFG.dat) - + paste debug.dat expected_output/${FFS[$j]}.$CFG.dat > san.dat # Print findings - - ${PYTH3} compare.py san.dat + + ${PYTH3} compare.py san.dat if [[ $STYLE == "SHORT" ]] ; then break fi - + done - + echo " Test $idx of $NO_TESTS for API ${API[$i]} complete" let idx=idx+1 - + done done @@ -160,3 +160,4 @@ rm -f debug.dat san.dat *.so output_lib.xyzf cd ../../ ./uninstall.sh $PREFX +