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lammps/src/pair_lj_cut.cpp
Axel Kohlmeyer 2132b1d904 update developer reference text
2022-10-24 11:08:26 -04:00

705 lines
21 KiB
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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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "pair_lj_cut.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairLJCut::PairLJCut(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
born_matrix_enable = 1;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairLJCut::~PairLJCut()
{
if (copymode) return;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairLJCut::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, r2inv, r6inv, forcelj, 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]) {
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fpair = factor_lj * forcelj * r2inv;
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 = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute_inner()
{
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
double rsq, r2inv, r6inv, forcelj, factor_lj, rsw;
int *ilist, *jlist, *numneigh, **firstneigh;
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_inner;
ilist = list->ilist_inner;
numneigh = list->numneigh_inner;
firstneigh = list->firstneigh_inner;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on * cut_out_on;
double cut_out_off_sq = cut_out_off * cut_out_off;
// 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;
if (rsq < cut_out_off_sq) {
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fpair = factor_lj * forcelj * r2inv;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on) / cut_out_diff;
fpair *= 1.0 - rsw * rsw * (3.0 - 2.0 * rsw);
}
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;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute_middle()
{
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
double rsq, r2inv, r6inv, forcelj, factor_lj, rsw;
int *ilist, *jlist, *numneigh, **firstneigh;
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_middle;
ilist = list->ilist_middle;
numneigh = list->numneigh_middle;
firstneigh = list->firstneigh_middle;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
double cut_out_off = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_out_diff = cut_out_off - cut_out_on;
double cut_in_off_sq = cut_in_off * cut_in_off;
double cut_in_on_sq = cut_in_on * cut_in_on;
double cut_out_on_sq = cut_out_on * cut_out_on;
double cut_out_off_sq = cut_out_off * cut_out_off;
// 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;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fpair = factor_lj * forcelj * r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off) / cut_in_diff;
fpair *= rsw * rsw * (3.0 - 2.0 * rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on) / cut_out_diff;
fpair *= 1.0 + rsw * rsw * (2.0 * rsw - 3.0);
}
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;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute_outer(int eflag, int vflag)
{
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
double rsq, r2inv, r6inv, forcelj, factor_lj, rsw;
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;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off * cut_in_off;
double cut_in_on_sq = cut_in_on * cut_in_on;
// 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]) {
if (rsq > cut_in_off_sq) {
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fpair = factor_lj * forcelj * r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off) / cut_in_diff;
fpair *= rsw * rsw * (3.0 - 2.0 * rsw);
}
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) {
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
evdwl *= factor_lj;
}
if (vflag) {
if (rsq <= cut_in_off_sq) {
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fpair = factor_lj * forcelj * r2inv;
} else if (rsq < cut_in_on_sq)
fpair = factor_lj * forcelj * r2inv;
}
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCut::allocate()
{
allocated = 1;
int n = atom->ntypes + 1;
memory->create(setflag, n, n, "pair:setflag");
for (int i = 1; i < n; i++)
for (int j = i; j < n; j++) setflag[i][j] = 0;
memory->create(cutsq, n, n, "pair:cutsq");
memory->create(cut, n, n, "pair:cut");
memory->create(epsilon, n, n, "pair:epsilon");
memory->create(sigma, n, n, "pair:sigma");
memory->create(lj1, n, n, "pair:lj1");
memory->create(lj2, n, n, "pair:lj2");
memory->create(lj3, n, n, "pair:lj3");
memory->create(lj4, n, n, "pair:lj4");
memory->create(offset, n, n, "pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJCut::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR, "Illegal pair_style command");
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
// reset cutoffs that have been explicitly set
if (allocated) {
int i, j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJCut::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5) 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 epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
double sigma_one = utils::numeric(FLERR, arg[3], false, lmp);
double cut_one = cut_global;
if (narg == 5) cut_one = utils::numeric(FLERR, arg[4], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCut::init_style()
{
// request regular or rRESPA neighbor list
int list_style = NeighConst::REQ_DEFAULT;
if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) {
auto respa = dynamic_cast<Respa *>(update->integrate);
if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT;
if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL;
}
neighbor->add_request(this, list_style);
// set rRESPA cutoffs
if (utils::strmatch(update->integrate_style, "^respa") &&
(dynamic_cast<Respa *>(update->integrate))->level_inner >= 0)
cut_respa = (dynamic_cast<Respa *>(update->integrate))->cutoff;
else
cut_respa = nullptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
}
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
if (offset_flag && (cut[i][j] > 0.0)) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio, 12.0) - pow(ratio, 6.0));
} else
offset[i][j] = 0.0;
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
// check interior rRESPA cutoff
if (cut_respa && cut[i][j] < cut_respa[3])
error->all(FLERR, "Pair cutoff < Respa interior cutoff");
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2], all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count, all, 2, MPI_DOUBLE, MPI_SUM, world);
double sig2 = sigma[i][j] * sigma[i][j];
double sig6 = sig2 * sig2 * sig2;
double rc3 = cut[i][j] * cut[i][j] * cut[i][j];
double rc6 = rc3 * rc3;
double rc9 = rc3 * rc6;
double prefactor = 8.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 / (9.0 * rc9);
etail_ij = prefactor * (sig6 - 3.0 * rc6);
ptail_ij = 2.0 * prefactor * (2.0 * sig6 - 3.0 * rc6);
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCut::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(&epsilon[i][j], sizeof(double), 1, fp);
fwrite(&sigma[i][j], sizeof(double), 1, fp);
fwrite(&cut[i][j], sizeof(double), 1, fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCut::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, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCut::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);
fwrite(&tail_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCut::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (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);
utils::sfread(FLERR, &tail_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);
MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCut::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g %g\n", i, epsilon[i][i], sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCut::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\n", i, j, epsilon[i][j], sigma[i][j], cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj, double &fforce)
{
double r2inv, r6inv, forcelj, philj;
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
fforce = factor_lj * forcelj * r2inv;
philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
return factor_lj * philj;
}
/* ---------------------------------------------------------------------- */
void PairLJCut::born_matrix(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj, double &dupair,
double &du2pair)
{
double rinv, r2inv, r6inv, du, du2;
r2inv = 1.0 / rsq;
rinv = sqrt(r2inv);
r6inv = r2inv * r2inv * r2inv;
// Reminder: lj1 = 48*e*s^12, lj2 = 24*e*s^6
// so dupair = -forcelj/r = -fforce*r (forcelj from single method)
du = r6inv * rinv * (lj2[itype][jtype] - lj1[itype][jtype] * r6inv);
du2 = r6inv * r2inv * (13 * lj1[itype][jtype] * r6inv - 7 * lj2[itype][jtype]);
dupair = factor_lj * du;
du2pair = factor_lj * du2;
}
/* ---------------------------------------------------------------------- */
void *PairLJCut::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
if (strcmp(str, "sigma") == 0) return (void *) sigma;
return nullptr;
}
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