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pair_sw_gen.cpp
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pair_sw_gen.cpp
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, [email protected]
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: PotC / Markus Hoehnerbach (RWTH Aachen)
------------------------------------------------------------------------- */
#include "pair_sw_gen.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <fenv.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairSwGen::PairSwGen(LAMMPS *lmp) : Pair(lmp) {
manybody_flag = 1;
one_coeff = 1;
single_enable = 0;
restartinfo = 0;
ghostneigh = 1;
}
/* ---------------------------------------------------------------------- */
PairSwGen::~PairSwGen() {
if (copymode) return;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(type_map);
memory->destroy(cutghost);
memory->destroy(param_A);
memory->destroy(param_a);
memory->destroy(param_B);
memory->destroy(param_p);
memory->destroy(param_q);
memory->destroy(param_epsilon);
memory->destroy(param_sigma);
memory->destroy(param_gamma);
memory->destroy(param_lambda);
memory->destroy(param_cos_theta0);
}
}
/* ---------------------------------------------------------------------- */
void PairSwGen::compute(int eflag, int vflag) {
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
int inum = list->inum;
int *ilist = list->ilist;
tagint *tag = atom->tag;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
double i_a_2 = 0.0;
double i_a_98 = 0.0;
for (int i_i_3 = 0; i_i_3 < nlocal; i_i_3++) {
double i_px_4 = x[i_i_3][0];
double i_py_4 = x[i_i_3][1];
double i_pz_4 = x[i_i_3][2];
int i_ty_4 = type[i_i_3];
double i_fx_4 = 0.0;
double i_fy_4 = 0.0;
double i_fz_4 = 0.0;
double i_a_5 = 0.0;
int listnum_i_snlist_227 = 0;
int listentry_i_snlist_227[neighbor->oneatom];
for (int i_scounter_228 = 0; i_scounter_228 < numneigh[i_i_3]; i_scounter_228++) {
int i_satom_229 = firstneigh[i_i_3][i_scounter_228];
double i_dx_229 = i_px_4 - x[i_satom_229][0];
double i_dy_229 = i_py_4 - x[i_satom_229][1];
double i_dz_229 = i_pz_4 - x[i_satom_229][2];
if ((i_dx_229 * i_dx_229 + i_dy_229 * i_dy_229 + i_dz_229 * i_dz_229) > cutsq[i_ty_4][type[i_satom_229]]) continue;
listentry_i_snlist_227[listnum_i_snlist_227++] = i_satom_229;
}
for (int i_i_6 = 0; i_i_6 < listnum_i_snlist_227; i_i_6++) {
int i_a_7 = listentry_i_snlist_227[i_i_6];
int i = i_i_3;
int j = i_a_7;
tagint itag = tag[i];
tagint jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue;
if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
}
int i_ty_8 = type[i_a_7];
double i_dx_9 = i_px_4 - x[i_a_7][0];
double i_dy_9 = i_py_4 - x[i_a_7][1];
double i_dz_9 = i_pz_4 - x[i_a_7][2];
double i_rsq_9 = i_dx_9 * i_dx_9 + i_dy_9 * i_dy_9 + i_dz_9 * i_dz_9;
double i_param_11 = param_sigma[i_ty_4][i_ty_8];
double i_mul_val_12 = param_a[i_ty_4][i_ty_8] * i_param_11;
if (i_rsq_9 > (i_mul_val_12 * i_mul_val_12)) continue;
double i_r_13 = sqrt(i_rsq_9);
double i_param_15 = param_A[i_ty_4][i_ty_8];
double i_param_16 = param_epsilon[i_ty_4][i_ty_8];
double i_param_17 = param_B[i_ty_4][i_ty_8];
double i_recip_20 = 1 / ((double) i_r_13);
double i_mul_val_19 = i_param_11 * i_recip_20;
double i_param_21 = param_p[i_ty_4][i_ty_8];
double i_param_27 = param_q[i_ty_4][i_ty_8];
double i_recip_36 = 1 / ((double) (i_r_13 - i_mul_val_12));
double i_bultin_37 = exp(i_param_11 * i_recip_36);
double i_mul_adj_40 = i_bultin_37 * i_param_15 * i_param_16;
double i_builtin_adj_81 = (i_param_17 * pow(i_mul_val_19, i_param_21) - pow(i_mul_val_19, i_param_27)) * i_bultin_37 * i_param_15 * i_param_16;
double i_adj_by_r_97 = (i_mul_adj_40 * i_param_11 * i_param_27 * i_recip_20 * i_recip_20 * pow(i_mul_val_19, (i_param_27 - 1)) - i_mul_adj_40 * i_param_11 * i_param_17 * i_param_21 * i_recip_20 * i_recip_20 * pow(i_mul_val_19, (i_param_21 - 1)) - i_builtin_adj_81 * i_param_11 * i_recip_36 * i_recip_36) * i_recip_20;
i_fx_4 += - i_adj_by_r_97 * i_dx_9;
i_fy_4 += - i_adj_by_r_97 * i_dy_9;
i_fz_4 += - i_adj_by_r_97 * i_dz_9;
i_a_5 += i_builtin_adj_81;
f[i_a_7][0] += i_adj_by_r_97 * i_dx_9;
f[i_a_7][1] += i_adj_by_r_97 * i_dy_9;
f[i_a_7][2] += i_adj_by_r_97 * i_dz_9;
}
i_a_2 += i_a_5;
f[i_i_3][0] += i_fx_4;
f[i_i_3][1] += i_fy_4;
f[i_i_3][2] += i_fz_4;
double i_fx_100 = 0.0;
double i_fy_100 = 0.0;
double i_fz_100 = 0.0;
double i_a_101 = 0.0;
for (int i_i_102 = 0; i_i_102 < listnum_i_snlist_227; i_i_102++) {
int i_a_103 = listentry_i_snlist_227[i_i_102];
double i_px_104 = x[i_a_103][0];
double i_py_104 = x[i_a_103][1];
double i_pz_104 = x[i_a_103][2];
int i_ty_104 = type[i_a_103];
double i_dx_105 = i_px_4 - i_px_104;
double i_dy_105 = i_py_4 - i_py_104;
double i_dz_105 = i_pz_4 - i_pz_104;
double i_rsq_105 = i_dx_105 * i_dx_105 + i_dy_105 * i_dy_105 + i_dz_105 * i_dz_105;
double i_param_107 = param_sigma[i_ty_4][i_ty_104];
double i_mul_val_108 = param_a[i_ty_4][i_ty_104] * i_param_107;
if (i_rsq_105 > (i_mul_val_108 * i_mul_val_108)) continue;
double i_fx_104 = 0.0;
double i_fy_104 = 0.0;
double i_fz_104 = 0.0;
double i_a_109 = 0.0;
double i_r_117 = sqrt(i_rsq_105);
double i_recip_a_124 = 1 / ((double) i_r_117);
double i_param_127 = param_epsilon[i_ty_4][i_ty_104];
double i_param_132 = param_gamma[i_ty_4][i_ty_104];
double i_recip_139 = 1 / ((double) (i_r_117 - i_mul_val_108));
double i_bultin_140 = exp(i_param_107 * i_param_132 * i_recip_139);
for (int i_i_110 = 1 + i_i_102; i_i_110 < listnum_i_snlist_227; i_i_110++) {
int i_a_111 = listentry_i_snlist_227[i_i_110];
double i_px_112 = x[i_a_111][0];
double i_py_112 = x[i_a_111][1];
double i_pz_112 = x[i_a_111][2];
int i_ty_112 = type[i_a_111];
double i_dx_113 = i_px_4 - i_px_112;
double i_dy_113 = i_py_4 - i_py_112;
double i_dz_113 = i_pz_4 - i_pz_112;
double i_rsq_113 = i_dx_113 * i_dx_113 + i_dy_113 * i_dy_113 + i_dz_113 * i_dz_113;
double i_param_115 = param_sigma[i_ty_4][i_ty_112];
double i_mul_val_116 = param_a[i_ty_4][i_ty_112] * i_param_115;
if (i_rsq_113 > (i_mul_val_116 * i_mul_val_116)) continue;
double i_r_119 = sqrt(i_rsq_113);
double i_dx_123 = i_px_104 - i_px_112;
double i_dy_123 = i_py_104 - i_py_112;
double i_dz_123 = i_pz_104 - i_pz_112;
double i_recip_b_124 = 1 / ((double) i_r_119);
double i_cos_124 = (i_dx_105 * i_dx_113 + i_dy_105 * i_dy_113 + i_dz_105 * i_dz_113) * i_recip_a_124 * i_recip_b_124;
double i_param_126 = param_lambda[i_ty_4][i_ty_104][i_ty_112];
double i_v_130 = i_cos_124 - param_cos_theta0[i_ty_4][i_ty_104][i_ty_112];
double i_v_131 = i_v_130 * i_v_130;
double i_param_141 = param_gamma[i_ty_4][i_ty_112];
double i_recip_148 = 1 / ((double) (i_r_119 - i_mul_val_116));
double i_bultin_149 = exp(i_param_115 * i_param_141 * i_recip_148);
double i_builtin_adj_198 = i_bultin_140 * i_bultin_149 * i_param_126 * i_param_127 * i_v_131;
double i_adj_by_r_216 = - i_bultin_140 * i_bultin_149 * i_param_107 * i_param_126 * i_param_127 * i_param_132 * i_recip_139 * i_recip_139 * i_recip_a_124 * i_v_131;
i_fx_100 += - i_adj_by_r_216 * i_dx_105;
i_fy_100 += - i_adj_by_r_216 * i_dy_105;
i_fz_100 += - i_adj_by_r_216 * i_dz_105;
i_fx_104 += i_adj_by_r_216 * i_dx_105;
i_fy_104 += i_adj_by_r_216 * i_dy_105;
i_fz_104 += i_adj_by_r_216 * i_dz_105;
double i_adj_by_r_218 = - i_builtin_adj_198 * i_param_115 * i_param_141 * i_recip_148 * i_recip_148 * i_recip_b_124;
i_fx_100 += - i_adj_by_r_218 * i_dx_113;
i_fy_100 += - i_adj_by_r_218 * i_dy_113;
i_fz_100 += - i_adj_by_r_218 * i_dz_113;
double i_adj_acos_223 = 2 * i_bultin_140 * i_bultin_149 * i_param_126 * i_param_127 * i_v_130;
double i_adj_by_r_224 = (i_recip_b_124 - i_cos_124 * i_recip_a_124) * i_adj_acos_223 * i_recip_a_124;
i_fx_100 += - i_adj_by_r_224 * i_dx_105;
i_fy_100 += - i_adj_by_r_224 * i_dy_105;
i_fz_100 += - i_adj_by_r_224 * i_dz_105;
i_fx_104 += i_adj_by_r_224 * i_dx_105;
i_fy_104 += i_adj_by_r_224 * i_dy_105;
i_fz_104 += i_adj_by_r_224 * i_dz_105;
double i_adj_by_r_225 = (i_recip_a_124 - i_cos_124 * i_recip_b_124) * i_adj_acos_223 * i_recip_b_124;
i_fx_100 += - i_adj_by_r_225 * i_dx_113;
i_fy_100 += - i_adj_by_r_225 * i_dy_113;
i_fz_100 += - i_adj_by_r_225 * i_dz_113;
double i_adj_by_r_226 = - i_adj_acos_223 * i_recip_a_124 * i_recip_b_124;
i_fx_104 += - i_adj_by_r_226 * i_dx_123;
i_fy_104 += - i_adj_by_r_226 * i_dy_123;
i_fz_104 += - i_adj_by_r_226 * i_dz_123;
i_a_109 += i_builtin_adj_198;
f[i_a_111][0] += i_adj_by_r_218 * i_dx_113 + i_adj_by_r_225 * i_dx_113 + i_adj_by_r_226 * i_dx_123;
f[i_a_111][1] += i_adj_by_r_218 * i_dy_113 + i_adj_by_r_225 * i_dy_113 + i_adj_by_r_226 * i_dy_123;
f[i_a_111][2] += i_adj_by_r_218 * i_dz_113 + i_adj_by_r_225 * i_dz_113 + i_adj_by_r_226 * i_dz_123;
}
i_a_101 += i_a_109;
f[i_a_103][0] += i_fx_104;
f[i_a_103][1] += i_fy_104;
f[i_a_103][2] += i_fz_104;
}
i_a_98 += i_a_101;
f[i_i_3][0] += i_fx_100;
f[i_i_3][1] += i_fy_100;
f[i_i_3][2] += i_fz_100;
}
eng_vdwl += i_a_2;
eng_vdwl += i_a_98;
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairSwGen::init_style() {
if (force->newton_pair == 0)
error->all(FLERR, "Pair style sw/gen requires atom IDs");
if (atom->tag_enable == 0)
error->all(FLERR, "Pair style sw/gen requires newton pair on");
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
}
/* ---------------------------------------------------------------------- */
void PairSwGen::allocate() {
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n+1, n+1, "pair:setflag");
memory->create(type_map, n+1, "pair:typemap");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq, n+1, n+1, "pair:cutsq");
memory->create(cutghost, n+1, n+1, "pair:cutghost");
memory->create(param_A, n+1, n+1, "pair:A");
memory->create(param_a, n+1, n+1, "pair:a");
memory->create(param_B, n+1, n+1, "pair:B");
memory->create(param_p, n+1, n+1, "pair:p");
memory->create(param_q, n+1, n+1, "pair:q");
memory->create(param_epsilon, n+1, n+1, "pair:epsilon");
memory->create(param_sigma, n+1, n+1, "pair:sigma");
memory->create(param_gamma, n+1, n+1, "pair:gamma");
memory->create(param_lambda, n+1, n+1, n+1, "pair:lambda");
memory->create(param_cos_theta0, n+1, n+1, n+1, "pair:cos_theta0");
}
/* ---------------------------------------------------------------------- */
double PairSwGen::init_one(int i, int j) {
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
cutghost[i][j] = cutmax;
cutghost[j][i] = cutmax;
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairSwGen::settings(int narg, char **arg) {
if (narg != 1) error->all(FLERR, "Illegal pair_style command");
cutmax = atof(arg[0]);
}
/* ---------------------------------------------------------------------- */
void PairSwGen::coeff(int narg, char **arg) {
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0], "*") != 0 || strcmp(arg[1], "*") != 0)
error->all(FLERR, "Incorrect args for pair coefficients");
for (int i = 3; i < narg; i++) {
}
char * file = arg[2];
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str, "Cannot open potential file %s",file);
error->one(FLERR,str);
}
}
const int MAXLINE = 1024; char line[MAXLINE],*ptr;
int n, eof = 0;
const int MAX_WORDS = 128;
char * words[MAX_WORDS] = {0};
int next_word = 0;
int read_header = 0; // 0 = read data, 1 = read header
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
char *word = strtok(line," \t\n\r\f");
while (word) {
if (next_word > MAX_WORDS) error->all(FLERR, "Too many words in line.");
free(words[next_word]);
words[next_word] = strdup(word);
int is_header = isalpha(words[next_word][0]);
if ((read_header == 0) && is_header) {
file_process_line(next_word, words, arg + 3 - 1);
if (next_word != 0) {
words[0] = words[next_word];
words[next_word] = NULL;
}
next_word = 0;
read_header = 1;
} else read_header = is_header;
next_word += 1;
word = strtok(NULL, " \t\n\r\f");
}
}
file_process_line(next_word, words, arg + 3 - 1);
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if ((strcmp("NULL", arg[i + 3 - 1]) != 0) && (strcmp("NULL", arg[j + 3 - 1]) != 0)) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ---------------------------------------------------------------------- */
void PairSwGen::file_process_line(int narg, char **arg, char **coeff_arg) {
if (narg == 0) return;
const char * SPLINE_PREFIX = "spline:";
if (strncmp(arg[0], SPLINE_PREFIX, strlen(SPLINE_PREFIX)) == 0) {
return;
}
int num_header = 0;
while (isalpha(arg[num_header][0])) num_header += 1;
if (2 == num_header) {
for (int i_0 = 1; i_0 <= this->atom->ntypes; i_0++) {
if (strcmp(coeff_arg[i_0], arg[0]) != 0) continue;
for (int i_1 = 1; i_1 <= this->atom->ntypes; i_1++) {
if (strcmp(coeff_arg[i_1], arg[1]) != 0) continue;
this->param_A[i_0][i_1] = atof(arg[2]);
this->param_a[i_0][i_1] = atof(arg[3]);
this->param_B[i_0][i_1] = atof(arg[4]);
this->param_p[i_0][i_1] = atof(arg[5]);
this->param_q[i_0][i_1] = atof(arg[6]);
this->param_epsilon[i_0][i_1] = atof(arg[7]);
this->param_sigma[i_0][i_1] = atof(arg[8]);
this->param_gamma[i_0][i_1] = atof(arg[9]);
}
}
return;
}
if (3 == num_header) {
for (int i_0 = 1; i_0 <= this->atom->ntypes; i_0++) {
if (strcmp(coeff_arg[i_0], arg[0]) != 0) continue;
for (int i_1 = 1; i_1 <= this->atom->ntypes; i_1++) {
if (strcmp(coeff_arg[i_1], arg[1]) != 0) continue;
for (int i_2 = 1; i_2 <= this->atom->ntypes; i_2++) {
if (strcmp(coeff_arg[i_2], arg[2]) != 0) continue;
this->param_lambda[i_0][i_1][i_2] = atof(arg[3]);
this->param_cos_theta0[i_0][i_1][i_2] = atof(arg[4]);
}
}
}
return;
}
error->all(FLERR, "Could not process file input.");
}