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891c284754ed45c6ab94c67a5c86cf0848a434d0
lammps/src/EXTRA-PAIR/pair_born_gauss.cpp
Axel Kohlmeyer 891c284754 avoid static code analysis warnings
2023-04-08 16:38:39 -04:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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: Axel Kohlmeyer, Temple University, akohlmey@gmail.com
#include "pair_born_gauss.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairBornGauss::PairBornGauss(LAMMPS *lmp) :
Pair(lmp), cut(nullptr), biga0(nullptr), alpha(nullptr), biga1(nullptr), beta(nullptr),
r0(nullptr), offset(nullptr)
{
single_enable = 1;
respa_enable = 0;
writedata = 1;
cut_global = 0.0;
}
/* ---------------------------------------------------------------------- */
PairBornGauss::~PairBornGauss()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(biga0);
memory->destroy(alpha);
memory->destroy(biga1);
memory->destroy(beta);
memory->destroy(r0);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairBornGauss::compute(int eflag, int vflag)
{
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
double rsq, r, dr, aexp, bexp, factor_lj;
int *ilist, *jlist, *numneigh, **firstneigh;
evdwl = 0.0;
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
dr = r - r0[itype][jtype];
aexp = biga0[itype][jtype] * exp(-alpha[itype][jtype] * r);
bexp = biga1[itype][jtype] * exp(-beta[itype][jtype] * dr * dr);
fpair = alpha[itype][jtype] * aexp;
fpair -= 2.0 * beta[itype][jtype] * dr * bexp;
fpair *= factor_lj / r;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx * fpair;
f[j][1] -= dely * fpair;
f[j][2] -= delz * fpair;
}
if (eflag) evdwl = factor_lj * (aexp - bexp - offset[itype][jtype]);
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBornGauss::allocate()
{
allocated = 1;
int np1 = atom->ntypes + 1;
memory->create(setflag, np1, np1, "pair:setflag");
for (int i = 1; i < np1; i++)
for (int j = i; j < np1; j++) setflag[i][j] = 0;
memory->create(cutsq, np1, np1, "pair:cutsq");
memory->create(cut, np1, np1, "pair:cut");
memory->create(biga0, np1, np1, "pair:biga0");
memory->create(alpha, np1, np1, "pair:alpha");
memory->create(biga1, np1, np1, "pair:biga1");
memory->create(beta, np1, np1, "pair:beta");
memory->create(r0, np1, np1, "pair:r0");
memory->create(offset, np1, np1, "pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBornGauss::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR, "Pair style bond/gauss must have exactly one argument");
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
// reset per-type pair cutoffs that have been explicitly set previously
if (allocated) {
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBornGauss::coeff(int narg, char **arg)
{
if (narg < 7 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
double biga0_one = utils::numeric(FLERR, arg[2], false, lmp);
double alpha_one = utils::numeric(FLERR, arg[3], false, lmp);
double biga1_one = utils::numeric(FLERR, arg[4], false, lmp);
double beta_one = utils::numeric(FLERR, arg[5], false, lmp);
double r0_one = utils::numeric(FLERR, arg[6], false, lmp);
double cut_one = cut_global;
if (narg == 10) cut_one = utils::numeric(FLERR, arg[7], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
biga0[i][j] = biga0_one;
alpha[i][j] = alpha_one;
biga1[i][j] = biga1_one;
beta[i][j] = beta_one;
r0[i][j] = r0_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBornGauss::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
if (offset_flag) {
double dr = cut[i][j] - r0[i][j];
offset[i][j] =
biga0[i][j] * exp(-alpha[i][j] * cut[i][j]) - biga1[i][j] * exp(-beta[i][j] * dr * dr);
} else
offset[i][j] = 0.0;
biga0[j][i] = biga0[i][j];
alpha[j][i] = alpha[i][j];
biga1[j][i] = biga1[i][j];
beta[j][i] = beta[i][j];
r0[j][i] = r0[i][j];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBornGauss::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i, j;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) {
fwrite(&biga0[i][j], sizeof(double), 1, fp);
fwrite(&alpha[i][j], sizeof(double), 1, fp);
fwrite(&biga1[i][j], sizeof(double), 1, fp);
fwrite(&beta[i][j], sizeof(double), 1, fp);
fwrite(&r0[i][j], sizeof(double), 1, fp);
fwrite(&cut[i][j], sizeof(double), 1, fp);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBornGauss::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR, &biga0[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &alpha[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &biga1[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &beta[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&biga0[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&alpha[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&biga1[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&beta[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBornGauss::write_restart_settings(FILE *fp)
{
fwrite(&cut_global, sizeof(double), 1, fp);
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBornGauss::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairBornGauss::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp, "%d %g %g %g %g %g\n", i, biga0[i][i], alpha[i][i], biga1[i][i], beta[i][i],
r0[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairBornGauss::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, biga0[i][j], alpha[i][j], biga1[i][j],
beta[i][j], r0[i][j], cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairBornGauss::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj, double &fforce)
{
double r, dr, aexp, bexp;
r = sqrt(rsq);
dr = r - r0[itype][jtype];
aexp = biga0[itype][jtype] * exp(-alpha[itype][jtype] * r);
bexp = biga1[itype][jtype] * exp(-beta[itype][jtype] * dr * dr);
fforce = factor_lj * (alpha[itype][jtype] * aexp - 2.0 * dr * beta[itype][jtype] * bexp) / r;
return factor_lj * (aexp - bexp - offset[itype][jtype]);
}
/* ---------------------------------------------------------------------- */
void *PairBornGauss::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str, "biga0") == 0) return (void *) biga0;
if (strcmp(str, "biga1") == 0) return (void *) biga1;
if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr;
}
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