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Merge pull request #3031 from Iximiel/develop

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Second Moment Aproximation to the Tight Binding addes as pair style
This commit is contained in:
Axel Kohlmeyer
2022-04-28 22:32:38 -04:00
committed by GitHub
parent cb41e354b8 b76594e551
commit 6fb3cef39f
21 changed files with 3060 additions and 25 deletions
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4
src/.gitignore vendored
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@ -1537,6 +1537,10 @@
/pair_mgpt.h
/pair_morse_smooth_linear.cpp
/pair_morse_smooth_linear.h
/pair_smatb.cpp
/pair_smatb.h
/pair_smatb_single.cpp
/pair_smatb_single.h
/pair_smtbq.cpp
/pair_smtbq.h
/pair_vashishta*.cpp

3
src/MANYBODY/pair_eam.cpp
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@ -319,8 +319,7 @@ void PairEAM::compute(int eflag, int vflag)
}
if (eflag) evdwl = scale[itype][jtype]*phi;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

16
src/SMTBQ/README
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@ -1,16 +0,0 @@
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.
Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot
at ICB, Universite de Bourgogne and ICMMO, Universite Paris-Sud.
Contact emails: lammps@u-bourgogne.fr, nsalles33@gmail.com
This package is occasionally maintained.
See the doc page for the pair_style smtbq command to get started.
There are potential files for this potential in the potentials dir.
There are example scripts for using this package in
examples/PACKAGES/smtbq.

558
src/SMTBQ/pair_smatb.cpp Normal file
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@ -0,0 +1,558 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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: Daniele Rapetti (iximiel@gmail.com)
------------------------------------------------------------------------- */
#include "pair_smatb.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairSMATB::PairSMATB(LAMMPS *_lmp) :
Pair(_lmp), nmax(0), on_eb(nullptr), r0(nullptr), p(nullptr), A(nullptr), q(nullptr),
QSI(nullptr), cutOffStart(nullptr), cutOffEnd(nullptr), cutOffEnd2(nullptr), a3(nullptr),
a4(nullptr), a5(nullptr), x3(nullptr), x4(nullptr), x5(nullptr)
{
single_enable = 0; // 1 if single() routine exists
restartinfo = 1; // 1 if pair style writes restart info
respa_enable = 0; // 1 if inner/middle/outer rRESPA routines
one_coeff = 0; // 1 if allows only one coeff * * call
manybody_flag = 1; // 1 if a manybody potential
no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute()
writedata = 1; // 1 if writes coeffs to data file
ghostneigh = 0; // 1 if pair style needs neighbors of ghosts
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
PairSMATB::~PairSMATB()
{
if (copymode) { return; }
memory->destroy(on_eb);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(r0);
memory->destroy(p);
memory->destroy(A);
memory->destroy(q);
memory->destroy(QSI);
memory->destroy(cutOffStart);
memory->destroy(cutOffEnd);
memory->destroy(cutOffEnd2);
memory->destroy(a3);
memory->destroy(a4);
memory->destroy(a5);
memory->destroy(x5);
memory->destroy(x4);
memory->destroy(x3);
}
}
/* ---------------------------------------------------------------------- */
void PairSMATB::compute(int eflag, int vflag)
{
int i, j, ii, jj, jnum, itype, jtype;
double xtmp, ytmp, ztmp, del[3], fpair;
double dijsq, dij;
double espo, aexpp, qsiexpq, eb_i, Fb, Fr;
double polyval, polyval2, polyval3, polyval4, polyval5;
if (eflag || vflag) {
ev_setup(eflag, vflag);
eng_vdwl = 0;
} else {
evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
}
// grow on_eb array if necessary
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->grow(on_eb, nmax, "pair_smatb:on_eb");
}
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
// zero out on_eb
memset(on_eb, 0, nall * sizeof(double));
int inum = list->inum;
int *ilist = list->ilist;
int *jlist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// FIRST LOOP: CALCULATES the squared bonding energy and accumulate it in on_eb for each atom
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];
j &= NEIGHMASK;
jtype = type[j];
del[0] = xtmp - x[j][0];
del[1] = ytmp - x[j][1];
del[2] = ztmp - x[j][2];
dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2];
if (dijsq < cutOffEnd2[itype][jtype]) {
dij = sqrt(dijsq);
if (dij < cutOffStart[itype][jtype]) {
qsiexpq = (QSI[itype][jtype] * QSI[itype][jtype]) *
exp(2.0 * q[itype][jtype] * (1.0 - dij / r0[itype][jtype]));
} else {
polyval = dij - cutOffEnd[itype][jtype];
polyval3 = polyval * polyval * polyval;
polyval4 = polyval3 * polyval;
polyval5 = polyval4 * polyval;
qsiexpq = x5[itype][jtype] * polyval5 + x4[itype][jtype] * polyval4 +
x3[itype][jtype] * polyval3;
qsiexpq = qsiexpq * qsiexpq;
}
on_eb[i] += qsiexpq;
if (newton_pair) on_eb[j] += qsiexpq;
}
}
}
// communicate the squared bonding energy between the various bins
if (newton_pair) comm->reverse_comm(this);
// Support Loop: take the square root of the bonding energy and
// accumulate it in the energy accumulator if needed the store the
// reciprocal in on_eb in order to not do it in the SECOND LOOP
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
if (i < nlocal) {
eb_i = sqrt(on_eb[i]);
if (eb_i != 0.0) {
on_eb[i] = 1.0 / eb_i;
} else {
on_eb[i] = 0.0;
}
// if needed the bonding energy is accumulated:
if (eflag_either) {
if (eflag_atom) { eatom[i] -= eb_i; }
if (eflag_global) { eng_vdwl -= eb_i; }
}
}
}
// this communication stores the denominators in the ghosts atoms,
// this is needed because of how forces are calculated
comm->forward_comm(this);
// SECOND LOOP: given on_eb[i] calculates forces and energies
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];
j &= NEIGHMASK;
jtype = type[j];
del[0] = xtmp - x[j][0];
del[1] = ytmp - x[j][1];
del[2] = ztmp - x[j][2];
dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2];
if (dijsq < cutOffEnd2[itype][jtype]) {
dij = sqrt(dijsq);
if (dij < cutOffStart[itype][jtype]) {
espo = 1.0 - dij / r0[itype][jtype];
aexpp = exp(p[itype][jtype] * espo) * A[itype][jtype];
Fr = (2.0 * aexpp) * (p[itype][jtype] / r0[itype][jtype]);
qsiexpq = (QSI[itype][jtype] * QSI[itype][jtype]) * exp(2.0 * q[itype][jtype] * espo);
Fb = -qsiexpq * q[itype][jtype] / r0[itype][jtype];
} else {
polyval = dij - cutOffEnd[itype][jtype];
polyval2 = polyval * polyval;
polyval3 = polyval2 * polyval;
polyval4 = polyval3 * polyval;
polyval5 = polyval4 * polyval;
aexpp = a5[itype][jtype] * polyval5 + a4[itype][jtype] * polyval4 +
a3[itype][jtype] * polyval3;
Fr = -2.0 *
(5.0 * a5[itype][jtype] * polyval4 + 4.0 * a4[itype][jtype] * polyval3 +
3.0 * a3[itype][jtype] * polyval2);
qsiexpq = x5[itype][jtype] * polyval5 + x4[itype][jtype] * polyval4 +
x3[itype][jtype] * polyval3;
Fb = ((5.0 * x5[itype][jtype] * polyval4 + 4.0 * x4[itype][jtype] * polyval3 +
3.0 * x3[itype][jtype] * polyval2)) *
qsiexpq;
}
// calculates the module of the pair energy between i and j
fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij;
f[i][0] += del[0] * fpair;
f[i][1] += del[1] * fpair;
f[i][2] += del[2] * fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= del[0] * fpair;
f[j][1] -= del[1] * fpair;
f[j][2] -= del[2] * fpair;
}
if (evflag) {
ev_tally(i, j, nlocal, newton_pair, 2.0 * aexpp, 0.0, fpair, del[0], del[1], del[2]);
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSMATB::settings(int narg, char **)
{
if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options");
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairSMATB::allocate()
{
const int np1 = atom->ntypes + 1;
memory->create(setflag, np1, np1, "pair_smatb: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_smatb:cutsq");
memory->create(r0, np1, np1, "pair_smatb:r0");
memory->create(p, np1, np1, "pair_smatb:p");
memory->create(A, np1, np1, "pair_smatb:A");
memory->create(q, np1, np1, "pair_smatb:q");
memory->create(QSI, np1, np1, "pair_smatb:QSI");
memory->create(cutOffStart, np1, np1, "pair_smatb:cutOffStart");
memory->create(cutOffEnd, np1, np1, "pair_smatb:cutOffEnd");
memory->create(cutOffEnd2, np1, np1, "pair_smatb:cutOffEnd2");
memory->create(a3, np1, np1, "pair_smatb:a1");
memory->create(a4, np1, np1, "pair_smatb:a2");
memory->create(a5, np1, np1, "pair_smatb:a5");
memory->create(x3, np1, np1, "pair_smatb:x1");
memory->create(x4, np1, np1, "pair_smatb:x2");
memory->create(x5, np1, np1, "pair_smatb:x3");
allocated = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairSMATB::coeff(int narg, char **arg)
{
if (!allocated) { allocate(); }
if (narg != 9) utils::missing_cmd_args(FLERR, "pair_style smatb", error);
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 myr0 = utils::numeric(FLERR, arg[2], false, lmp);
double myp = utils::numeric(FLERR, arg[3], false, lmp);
double myq = utils::numeric(FLERR, arg[4], false, lmp);
double myA = utils::numeric(FLERR, arg[5], false, lmp);
double myQSI = utils::numeric(FLERR, arg[6], false, lmp);
double mycutOffStart = utils::numeric(FLERR, arg[7], false, lmp);
double mycutOffEnd = utils::numeric(FLERR, arg[8], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
r0[i][j] = myr0;
p[i][j] = myp;
A[i][j] = myA;
q[i][j] = myq;
QSI[i][j] = myQSI;
cutOffStart[i][j] = mycutOffStart;
cutOffEnd[i][j] = mycutOffEnd;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ------------------------------------------------------------------------ */
void PairSMATB::init_style()
{
if (force->newton_pair == 0) error->all(FLERR, "Pair style smatb requires newton pair on");
neighbor->add_request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairSMATB::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
///@todo implement smatb mixing rules
cutOffStart[i][j] = MIN(cutOffStart[i][i], cutOffStart[j][j]);
cutOffEnd[i][j] = MAX(cutOffEnd[i][i], cutOffEnd[j][j]);
error->all(FLERR, "All pair coeffs are not set");
}
double es = cutOffEnd[i][j] - cutOffStart[i][j];
double es2 = es * es;
double es3 = es2 * es;
// variables for poly for p and A
double expp = A[i][j] * exp(p[i][j] * (1. - cutOffStart[i][j] / r0[i][j]));
double ap = -1. / es3;
double bp = p[i][j] / (r0[i][j] * es2);
double cp = -(p[i][j] * p[i][j]) / (es * r0[i][j] * r0[i][j]);
a5[i][j] = expp * (12. * ap + 6. * bp + cp) / (2. * es2);
a4[i][j] = expp * (15. * ap + 7. * bp + cp) / es;
a3[i][j] = expp * (20. * ap + 8. * bp + cp) / 2.;
// variables for poly for q and qsi
double expq = QSI[i][j] * exp(q[i][j] * (1. - cutOffStart[i][j] / r0[i][j]));
double aq = -1 / es3;
double bq = q[i][j] / (es2 * r0[i][j]);
double cq = -(q[i][j] * q[i][j]) / (es * r0[i][j] * r0[i][j]);
x5[i][j] = expq * (12. * aq + 6. * bq + cq) / (2. * es2);
x4[i][j] = expq * (15. * aq + 7. * bq + cq) / es;
x3[i][j] = expq * (20. * aq + 8. * bq + cq) / 2.;
cutOffEnd2[i][j] = cutOffEnd[i][j] * cutOffEnd[i][j];
if (i != j) {
setflag[j][i] = 1;
cutOffEnd2[j][i] = cutOffEnd2[i][j];
r0[j][i] = r0[i][j];
p[j][i] = p[i][j];
q[j][i] = q[i][j];
A[j][i] = A[i][j];
QSI[j][i] = QSI[i][j];
cutOffStart[j][i] = cutOffStart[i][j];
cutOffEnd[j][i] = cutOffEnd[i][j];
a3[j][i] = a3[i][j];
a4[j][i] = a4[i][j];
a5[j][i] = a5[i][j];
x3[j][i] = x3[i][j];
x4[j][i] = x4[i][j];
x5[j][i] = x5[i][j];
}
return cutOffEnd[i][j];
}
/* ---------------------------------------------------------------------- */
int PairSMATB::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i, j, m;
m = 0;
for (i = 0; i < n; ++i) {
j = list[i];
buf[m++] = on_eb[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairSMATB::unpack_forward_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; ++i) { on_eb[i] = buf[m++]; }
}
/* ---------------------------------------------------------------------- */
int PairSMATB::pack_reverse_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; ++i) { buf[m++] = on_eb[i]; }
return m;
}
/* ---------------------------------------------------------------------- */
void PairSMATB::unpack_reverse_comm(int n, int *list, double *buf)
{
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
on_eb[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void PairSMATB::write_restart_settings(FILE *fp)
{
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
fwrite(&tail_flag, sizeof(int), 1, fp);
}
/* ---------------------------------------------------------------------- */
void PairSMATB::read_restart_settings(FILE *fp)
{
int me = comm->me;
size_t result;
if (me == 0) {
result = fread(&offset_flag, sizeof(int), 1, fp);
result = fread(&mix_flag, sizeof(int), 1, fp);
result = fread(&tail_flag, sizeof(int), 1, fp);
}
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);
}
/* ---------------------------------------------------------------------- */
void PairSMATB::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(&r0[i][j], sizeof(double), 1, fp);
fwrite(&p[i][j], sizeof(double), 1, fp);
fwrite(&q[i][j], sizeof(double), 1, fp);
fwrite(&A[i][j], sizeof(double), 1, fp);
fwrite(&QSI[i][j], sizeof(double), 1, fp);
fwrite(&cutOffStart[i][j], sizeof(double), 1, fp);
fwrite(&cutOffEnd[i][j], sizeof(double), 1, fp);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairSMATB::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
size_t result;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); }
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &p[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &q[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &A[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &QSI[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cutOffStart[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cutOffEnd[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&p[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&q[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&A[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&QSI[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cutOffStart[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cutOffEnd[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
/* ---------------------------------------------------------------------- */
void PairSMATB::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++) {
fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0[i][i], p[i][i], q[i][i], A[i][i], QSI[i][i],
cutOffStart[i][i], cutOffEnd[i][i]);
}
}
/* ---------------------------------------------------------------------- */
void PairSMATB::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 %g\n", i, j, r0[i][j], p[i][j], q[i][j], A[i][j],
QSI[i][j], cutOffStart[i][j], cutOffEnd[i][j]);
}
}
}

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src/SMTBQ/pair_smatb.h Normal file
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@ -0,0 +1,80 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This pair style is written by Daniele Rapetti (iximiel@gmail.com)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(smatb,PairSMATB);
// clang-format on
#else
#ifndef LMP_PAIR_SMATB_H
#define LMP_PAIR_SMATB_H
#include "pair.h"
namespace LAMMPS_NS {
class PairSMATB : public Pair {
public:
PairSMATB(class LAMMPS *);
~PairSMATB() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
int pack_forward_comm(int, int *, double *, int, int *) override;
void unpack_forward_comm(int, int, double *) override;
int pack_reverse_comm(int, int, double *) override;
void unpack_reverse_comm(int, int *, double *) override;
protected:
virtual void allocate();
// allocated size of per-atom arrays
int nmax;
//allocated to store up calculation values
double *on_eb;
// interaction radius, user-given
double **r0;
// parameters user-given
double **p;
double **A;
double **q;
double **QSI;
//extremes of the cut off, user given
double **cutOffStart;
double **cutOffEnd;
//squared cut off end, calculated
double **cutOffEnd2;
//polynomial for cutoff linking to zero: Ae^p substitution
double **a3;
double **a4;
double **a5;
//polynomial for cutoff linking to zero: QSIe^q substitution
double **x3;
double **x4;
double **x5;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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: Daniele Rapetti (iximiel@gmail.com)
------------------------------------------------------------------------- */
#include "pair_smatb_single.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairSMATBSingle::PairSMATBSingle(LAMMPS *_lmp) :
Pair(_lmp), nmax(0), on_eb(nullptr), r0(0), p(0), A(0), q(0), QSI(0), cutOffStart(0),
cutOffEnd(0), cutOffEnd2(0), a3(0), a4(0), a5(0), x3(0), x4(0), x5(0)
{
single_enable = 0; // 1 if single() routine exists
restartinfo = 1; // 1 if pair style writes restart info
respa_enable = 0; // 1 if inner/middle/outer rRESPA routines
one_coeff = 0; // 1 if allows only one coeff * * call
manybody_flag = 1; // 1 if a manybody potential
no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute()
writedata = 1; // 1 if writes coeffs to data file
ghostneigh = 0; // 1 if pair style needs neighbors of ghosts
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
PairSMATBSingle::~PairSMATBSingle()
{
if (copymode) { return; }
memory->destroy(on_eb);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::compute(int eflag, int vflag)
{
int i, j, ii, jj, jnum;
double xtmp, ytmp, ztmp, del[3], fpair;
double dijsq, dij;
double espo, aexpp, qsiexpq, eb_i, Fb, Fr;
double polyval, polyval2, polyval3, polyval4, polyval5;
if (eflag || vflag) {
ev_setup(eflag, vflag);
eng_vdwl = 0;
} else {
evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
}
// grow on_eb array if necessary
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->grow(on_eb, nmax, "pair_smatb:on_eb");
}
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
// zero out on_eb
memset(on_eb, 0, nall * sizeof(double));
int inum = list->inum;
int *ilist = list->ilist;
int *jlist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// FIRST LOOP: CALCULATES the squared bonding energy and accumulate it in on_eb for each atom
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; ++jj) {
j = jlist[jj];
j &= NEIGHMASK;
del[0] = xtmp - x[j][0];
del[1] = ytmp - x[j][1];
del[2] = ztmp - x[j][2];
dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2];
if (dijsq < cutOffEnd2) {
dij = sqrt(dijsq);
if (dij < cutOffStart) {
qsiexpq = (QSI * QSI) * exp(2.0 * q * (1.0 - dij / r0));
} else {
polyval = dij - cutOffEnd;
polyval3 = polyval * polyval * polyval;
polyval4 = polyval3 * polyval;
polyval5 = polyval4 * polyval;
qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3;
qsiexpq = qsiexpq * qsiexpq;
}
on_eb[i] += qsiexpq;
if (newton_pair) on_eb[j] += qsiexpq;
}
}
}
// communicate the squared bonding energy between the various bins
if (newton_pair) comm->reverse_comm(this);
// Support Loop: take the square root of the bonding energy and
// accumulate it in the energy accumulator if needed the store the
// reciprocal in on_eb in order to not do it in the SECOND LOOP
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
if (i < nlocal) {
eb_i = sqrt(on_eb[i]);
if (eb_i != 0.0) {
on_eb[i] = 1.0 / eb_i;
} else {
on_eb[i] = 0.0;
}
// if needed the bonding energy is accumulated:
if (eflag_either) {
if (eflag_atom) { eatom[i] -= eb_i; }
if (eflag_global) { eng_vdwl -= eb_i; }
}
}
}
// this communication stores the denominators in the ghosts atoms,
// this is needed because of how forces are calculated
comm->forward_comm(this);
// SECOND LOOP: given on_eb[i] calculates forces and energies
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
del[0] = xtmp - x[j][0];
del[1] = ytmp - x[j][1];
del[2] = ztmp - x[j][2];
dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2];
if (dijsq < cutOffEnd2) {
dij = sqrt(dijsq);
if (dij < cutOffStart) {
espo = 1.0 - dij / r0;
aexpp = exp(p * espo) * A;
Fr = (2.0 * aexpp) * (p / r0);
qsiexpq = (QSI * QSI) * exp(2.0 * q * espo);
Fb = -qsiexpq * q / r0;
} else {
polyval = dij - cutOffEnd;
polyval2 = polyval * polyval;
polyval3 = polyval2 * polyval;
polyval4 = polyval3 * polyval;
polyval5 = polyval4 * polyval;
aexpp = a5 * polyval5 + a4 * polyval4 + a3 * polyval3;
Fr = -2.0 * (5.0 * a5 * polyval4 + 4.0 * a4 * polyval3 + 3.0 * a3 * polyval2);
qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3;
Fb = ((5.0 * x5 * polyval4 + 4.0 * x4 * polyval3 + 3.0 * x3 * polyval2)) * qsiexpq;
}
// calculates the module of the pair energy between i and j
fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij;
f[i][0] += del[0] * fpair;
f[i][1] += del[1] * fpair;
f[i][2] += del[2] * fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= del[0] * fpair;
f[j][1] -= del[1] * fpair;
f[j][2] -= del[2] * fpair;
}
if (evflag) {
ev_tally(i, j, nlocal, newton_pair, 2.0 * aexpp, 0.0, fpair, del[0], del[1], del[2]);
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSMATBSingle::settings(int narg, char **)
{
if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb/single accepts no options");
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairSMATBSingle::allocate()
{
int n = atom->ntypes;
int natoms = atom->natoms;
memory->create(setflag, n + 1, n + 1, "pair_smatb:setflag");
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_smatb:cutsq");
allocated = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairSMATBSingle::coeff(int narg, char **arg)
{
if (!allocated) { allocate(); }
if (narg != 9) utils::missing_cmd_args(FLERR, "pair_style smatb/single", error);
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);
r0 = utils::numeric(FLERR, arg[2], false, lmp);
p = utils::numeric(FLERR, arg[3], false, lmp);
q = utils::numeric(FLERR, arg[4], false, lmp);
A = utils::numeric(FLERR, arg[5], false, lmp);
QSI = utils::numeric(FLERR, arg[6], false, lmp);
cutOffStart = utils::numeric(FLERR, arg[7], false, lmp);
cutOffEnd = utils::numeric(FLERR, arg[8], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ------------------------------------------------------------------------ */
void PairSMATBSingle::init_style()
{
if (force->newton_pair == 0) error->all(FLERR, "Pair style smatb/single requires newton pair on");
neighbor->add_request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairSMATBSingle::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
//calculating the polynomial linking to zero
double es = cutOffEnd - cutOffStart;
double es2 = es * es;
double es3 = es2 * es;
//variables for poly for p and A
double expp = A * exp(p * (1. - cutOffStart / r0));
double ap = -1. / es3;
double bp = p / (r0 * es2);
double cp = -(p * p) / (es * r0 * r0);
a5 = expp * (12. * ap + 6. * bp + cp) / (2. * es2);
a4 = expp * (15. * ap + 7. * bp + cp) / es;
a3 = expp * (20. * ap + 8. * bp + cp) / 2.;
//variables for poly for q and qsi
double expq = QSI * exp(q * (1. - cutOffStart / r0));
double aq = -1 / es3;
double bq = q / (es2 * r0);
double cq = -(q * q) / (es * r0 * r0);
x5 = expq * (12. * aq + 6. * bq + cq) / (2. * es2);
x4 = expq * (15. * aq + 7. * bq + cq) / es;
x3 = expq * (20. * aq + 8. * bq + cq) / 2.;
cutOffEnd2 = cutOffEnd * cutOffEnd;
if (i != j) {
setflag[j][i] = 1;
cutOffEnd2 = cutOffEnd2;
r0 = r0;
p = p;
q = q;
A = A;
QSI = QSI;
cutOffStart = cutOffStart;
cutOffEnd = cutOffEnd;
a3 = a3;
a4 = a4;
a5 = a5;
x3 = x3;
x4 = x4;
x5 = x5;
}
return cutOffEnd;
}
/* ---------------------------------------------------------------------- */
int PairSMATBSingle::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i, j, m;
m = 0;
for (i = 0; i < n; ++i) {
j = list[i];
buf[m++] = on_eb[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::unpack_forward_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; ++i) { on_eb[i] = buf[m++]; }
}
/* ---------------------------------------------------------------------- */
int PairSMATBSingle::pack_reverse_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; ++i) { buf[m++] = on_eb[i]; }
return m;
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::unpack_reverse_comm(int n, int *list, double *buf)
{
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
on_eb[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
//write binary data of this simulation:
void PairSMATBSingle::write_restart_settings(FILE *fp)
{
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
fwrite(&tail_flag, sizeof(int), 1, fp);
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::read_restart_settings(FILE *fp)
{
int me = comm->me;
size_t result;
if (me == 0) {
result = fread(&offset_flag, sizeof(int), 1, fp);
result = fread(&mix_flag, sizeof(int), 1, fp);
result = fread(&tail_flag, sizeof(int), 1, fp);
}
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);
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::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(&r0, sizeof(double), 1, fp);
fwrite(&p, sizeof(double), 1, fp);
fwrite(&q, sizeof(double), 1, fp);
fwrite(&A, sizeof(double), 1, fp);
fwrite(&QSI, sizeof(double), 1, fp);
fwrite(&cutOffStart, sizeof(double), 1, fp);
fwrite(&cutOffEnd, sizeof(double), 1, fp);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
size_t result;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); }
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR, &r0, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &p, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &q, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &A, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &QSI, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cutOffStart, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cutOffEnd, sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&r0, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&p, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&q, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&A, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&QSI, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cutOffStart, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cutOffEnd, 1, MPI_DOUBLE, 0, world);
}
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++) {
fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0, p, q, A, QSI, cutOffStart, cutOffEnd);
}
}
/* ---------------------------------------------------------------------- */
void PairSMATBSingle::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 %g\n", i, j, r0, p, q, A, QSI, cutOffStart, cutOffEnd);
}
}
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This pair style is written by Daniele Rapetti (iximiel@gmail.com)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(smatb/single,PairSMATBSingle);
// clang-format on
#else
#ifndef LMP_PAIR_SMATB_SINGLE_H
#define LMP_PAIR_SMATB_SINGLE_H
#include "pair.h"
namespace LAMMPS_NS {
class PairSMATBSingle : public Pair {
public:
PairSMATBSingle(class LAMMPS *);
~PairSMATBSingle() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
int pack_forward_comm(int, int *, double *, int, int *) override;
void unpack_forward_comm(int, int, double *) override;
int pack_reverse_comm(int, int, double *) override;
void unpack_reverse_comm(int, int *, double *) override;
protected:
virtual void allocate();
// allocated size of per-atom arrays
int nmax;
//allocated to store up calculation values
double *on_eb{nullptr};
// interaction radius, user-given
double r0;
// parameters user-given
double p;
double A;
double q;
double QSI;
//cut offs, user given
double cutOffStart;
double cutOffEnd;
//squared cut off end, calculated
double cutOffEnd2;
//polynomial for cutoff linking to zero: Ae^p substitution
double a3;
double a4;
double a5;
//polynomial for cutoff linking to zero: QSIe^q substitution
double x3;
double x4;
double x5;
};
} // namespace LAMMPS_NS
#endif
#endif