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lammps/src/INTERLAYER/pair_saip_metal.cpp
oywg11 51b45d6830 fix small format issues
2023-06-06 22:16:41 +08:00

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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: Wengen Ouyang (Wuhan University)
e-mail: w.g.ouyang at gmail dot com
This is a full version of the potential described in
[Ouyang et al., J. Chem. Theory Comput. 17, 7215-7223 (2021)]
------------------------------------------------------------------------- */
#include "pair_saip_metal.h"
#include "atom.h"
#include "citeme.h"
#include "error.h"
#include "force.h"
#include "interlayer_taper.h"
#include "neigh_list.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace InterLayer;
#define MAXLINE 1024
#define DELTA 4
#define PGDELTA 1
static const char cite_saip[] =
"saip/metal potential: doi:10.1021/acs.jctc.1c00622\n\n"
"@Article{Ouyang2021\n"
" author = {W. Ouyang and O. Hod and R. Guerra},\n"
" title = {Registry-Dependent Potential for Interfaces of Gold with Graphitic Systems},\n"
" journal = {J.~Chem.\\ Theory Comput.},\n"
" volume = 17,\n"
" pages = {7215--7223}\n"
" year = 2021,\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairSAIPMETAL::PairSAIPMETAL(LAMMPS *lmp) : PairILPGrapheneHBN(lmp)
{
variant = SAIP_METAL;
single_enable = 0;
if (lmp->citeme) lmp->citeme->add(cite_saip);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSAIPMETAL::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
error->all(FLERR, "Pair style saip/metal must be used as sub-style with hybrid/overlay");
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
}
/* ----------------------------------------------------------------------
Repulsive forces and energy
------------------------------------------------------------------------- */
void PairSAIPMETAL::calc_FRep(int eflag, int /* vflag */)
{
int i, j, ii, jj, inum, jnum, itype, jtype, k, kk;
double prodnorm1, fkcx, fkcy, fkcz, filp;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair, fpair1;
double rsq, r, Rcut, rhosq1, exp0, exp1, Tap, dTap, Vilp;
double frho1, Erep, fsum, rdsq1;
int *ilist, *jlist, *numneigh, **firstneigh;
int *ILP_neighs_i;
evdwl = 0.0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
double dprodnorm1[3] = {0.0, 0.0, 0.0};
double fp1[3] = {0.0, 0.0, 0.0};
double fprod1[3] = {0.0, 0.0, 0.0};
double delki[3] = {0.0, 0.0, 0.0};
double fk[3] = {0.0, 0.0, 0.0};
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
//calculate exp(-lambda*(r-z0))*[epsilon/2 + f(rho_ij)]
// loop over neighbors of owned 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];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
// only include the interaction between different layers
if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
int iparam_ij = elem2param[map[itype]][map[jtype]];
Param &p = params[iparam_ij];
r = sqrt(rsq);
// turn on/off taper function
if (tap_flag) {
Rcut = sqrt(cutsq[itype][jtype]);
Tap = calc_Tap(r, Rcut);
dTap = calc_dTap(r, Rcut);
} else {
Tap = 1.0;
dTap = 0.0;
}
// for atoms in bulk materials
if (strcmp(elements[map[itype]], "C") != 0 && strcmp(elements[map[itype]], "H") != 0 &&
strcmp(elements[map[itype]], "B") != 0 && strcmp(elements[map[itype]], "N") != 0) {
// Set ni along rij
exp0 = exp(-p.lambda * (r - p.z0));
frho1 = 1.0 * p.C;
Erep = 0.5 * p.epsilon + frho1;
Vilp = exp0 * Erep;
// derivatives
fpair = p.lambda * exp0 / r * Erep;
filp = fpair * Tap - Vilp * dTap / r;
fkcx = delx * filp;
fkcy = dely * filp;
fkcz = delz * filp;
f[i][0] += fkcx;
f[i][1] += fkcy;
f[i][2] += fkcz;
f[j][0] -= fkcx;
f[j][1] -= fkcy;
f[j][2] -= fkcz;
if (eflag) pvector[1] += evdwl = Tap * Vilp;
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, filp, delx, dely, delz);
} else { // for atoms in 2D materials
// Calculate the transverse distance
prodnorm1 = normal[i][0] * delx + normal[i][1] * dely + normal[i][2] * delz;
rhosq1 = rsq - prodnorm1 * prodnorm1; // rho_ij
rdsq1 = rhosq1 * p.delta2inv; // (rho_ij/delta)^2
// store exponents
exp0 = exp(-p.lambda * (r - p.z0));
exp1 = exp(-rdsq1);
frho1 = exp1 * p.C;
Erep = 0.5 * p.epsilon + frho1;
Vilp = exp0 * Erep;
// derivatives
fpair = p.lambda * exp0 / r * Erep;
fpair1 = 2.0 * exp0 * frho1 * p.delta2inv;
fsum = fpair + fpair1;
// derivatives of the product of rij and ni, the result is a vector
dprodnorm1[0] =
dnormdri[0][0][i] * delx + dnormdri[1][0][i] * dely + dnormdri[2][0][i] * delz;
dprodnorm1[1] =
dnormdri[0][1][i] * delx + dnormdri[1][1][i] * dely + dnormdri[2][1][i] * delz;
dprodnorm1[2] =
dnormdri[0][2][i] * delx + dnormdri[1][2][i] * dely + dnormdri[2][2][i] * delz;
fp1[0] = prodnorm1 * normal[i][0] * fpair1;
fp1[1] = prodnorm1 * normal[i][1] * fpair1;
fp1[2] = prodnorm1 * normal[i][2] * fpair1;
fprod1[0] = prodnorm1 * dprodnorm1[0] * fpair1;
fprod1[1] = prodnorm1 * dprodnorm1[1] * fpair1;
fprod1[2] = prodnorm1 * dprodnorm1[2] * fpair1;
fkcx = (delx * fsum - fp1[0]) * Tap - Vilp * dTap * delx / r;
fkcy = (dely * fsum - fp1[1]) * Tap - Vilp * dTap * dely / r;
fkcz = (delz * fsum - fp1[2]) * Tap - Vilp * dTap * delz / r;
f[i][0] += fkcx - fprod1[0] * Tap;
f[i][1] += fkcy - fprod1[1] * Tap;
f[i][2] += fkcz - fprod1[2] * Tap;
f[j][0] -= fkcx;
f[j][1] -= fkcy;
f[j][2] -= fkcz;
// calculate the forces acted on the neighbors of atom i from atom j
ILP_neighs_i = ILP_firstneigh[i];
for (kk = 0; kk < ILP_numneigh[i]; kk++) {
k = ILP_neighs_i[kk];
if (k == i) continue;
// derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
dprodnorm1[0] = dnormal[0][0][kk][i] * delx + dnormal[1][0][kk][i] * dely +
dnormal[2][0][kk][i] * delz;
dprodnorm1[1] = dnormal[0][1][kk][i] * delx + dnormal[1][1][kk][i] * dely +
dnormal[2][1][kk][i] * delz;
dprodnorm1[2] = dnormal[0][2][kk][i] * delx + dnormal[1][2][kk][i] * dely +
dnormal[2][2][kk][i] * delz;
fk[0] = (-prodnorm1 * dprodnorm1[0] * fpair1) * Tap;
fk[1] = (-prodnorm1 * dprodnorm1[1] * fpair1) * Tap;
fk[2] = (-prodnorm1 * dprodnorm1[2] * fpair1) * Tap;
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
delki[0] = x[k][0] - x[i][0];
delki[1] = x[k][1] - x[i][1];
delki[2] = x[k][2] - x[i][2];
if (evflag)
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0],
delki[1], delki[2]);
}
if (eflag) pvector[1] += evdwl = Tap * Vilp;
if (evflag)
ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fkcx, fkcy, fkcz, delx, dely, delz);
} // end of speration atoms for bulk materials
} // end of rsq < cutoff
} // loop over jj
} // loop over ii
}
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