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lammps/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
Axel Kohlmeyer 340207988c fix a couple more bugs like in 5246cedda6
2021-10-05 10:36:25 -04:00

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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: Wengen Ouyang (Tel Aviv University)
e-mail: w.g.ouyang at gmail dot com
This is a full version of the potential described in
[Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
The definition of normals are the same as that in
[Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
------------------------------------------------------------------------- */
#include "pair_ilp_graphene_hbn.h"
#include "atom.h"
#include "citeme.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "interlayer_taper.h"
#include "memory.h"
#include "my_page.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "tokenizer.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_ilp[] =
"ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848\n"
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
" journal = {Nano Letters},\n"
" volume = 18,\n"
" pages = {6009}\n"
" year = 2018,\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
{
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
centroidstressflag = CENTROID_NOTAVAIL;
unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
if (lmp->citeme) lmp->citeme->add(cite_ilp);
nextra = 2;
pvector = new double[nextra];
// initialize element to parameter maps
params = nullptr;
cutILPsq = nullptr;
nmax = 0;
maxlocal = 0;
ILP_numneigh = nullptr;
ILP_firstneigh = nullptr;
ipage = nullptr;
pgsize = oneatom = 0;
normal = nullptr;
dnormal = nullptr;
dnormdri = nullptr;
// always compute energy offset
offset_flag = 1;
// turn on the taper function by default
tap_flag = 1;
}
/* ---------------------------------------------------------------------- */
PairILPGrapheneHBN::~PairILPGrapheneHBN()
{
memory->destroy(ILP_numneigh);
memory->sfree(ILP_firstneigh);
delete[] ipage;
delete[] pvector;
memory->destroy(normal);
memory->destroy(dnormal);
memory->destroy(dnormdri);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(offset);
}
memory->destroy(elem2param);
memory->destroy(cutILPsq);
memory->sfree(params);
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::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(offset, n, n, "pair:offset");
map = new int[n];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::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 ilp/graphene/hbn 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);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::coeff(int narg, char **arg)
{
if (!allocated) allocate();
map_element2type(narg - 3, arg + 3);
read_file(arg[2]);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairILPGrapheneHBN::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
if (!offset_flag) error->all(FLERR, "Must use 'pair_modify shift yes' with this pair style");
if (offset_flag && (cut_global > 0.0)) {
int iparam_ij = elem2param[map[i]][map[j]];
Param &p = params[iparam_ij];
offset[i][j] =
-p.C6 * pow(1.0 / cut_global, 6) / (1.0 + exp(-p.d * (cut_global / p.seff - 1.0)));
} else
offset[i][j] = 0.0;
offset[j][i] = offset[i][j];
return cut_global;
}
/* ----------------------------------------------------------------------
read Interlayer potential file
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::read_file(char *filename)
{
memory->sfree(params);
params = nullptr;
nparams = maxparam = 0;
// open file on proc 0
if (comm->me == 0) {
PotentialFileReader reader(lmp, filename, "ilp/graphene/hbn", unit_convert_flag);
char *line;
// transparently convert units for supported conversions
int unit_convert = reader.get_unit_convert();
double conversion_factor = utils::get_conversion_factor(utils::ENERGY, unit_convert);
while ((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
ValueTokenizer values(line);
std::string iname = values.next_string();
std::string jname = values.next_string();
// ielement,jelement = 1st args
// if both args are in element list, then parse this line
// else skip to next entry in file
int ielement, jelement;
for (ielement = 0; ielement < nelements; ielement++)
if (iname == elements[ielement]) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (jname == elements[jelement]) break;
if (jelement == nelements) continue;
// expand storage, if needed
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
// make certain all addional allocated storage is initialized
// to avoid false positives when checking with valgrind
memset(params + nparams, 0, DELTA * sizeof(Param));
}
// load up parameter settings and error check their values
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].z0 = values.next_double();
params[nparams].alpha = values.next_double();
params[nparams].delta = values.next_double();
params[nparams].epsilon = values.next_double();
params[nparams].C = values.next_double();
params[nparams].d = values.next_double();
params[nparams].sR = values.next_double();
params[nparams].reff = values.next_double();
params[nparams].C6 = values.next_double();
// S provides a convenient scaling of all energies
params[nparams].S = values.next_double();
params[nparams].rcut = values.next_double();
} catch (TokenizerException &e) {
error->one(FLERR, e.what());
}
// energies in meV further scaled by S
// S = 43.3634 meV = 1 kcal/mol
double meV = 1e-3 * params[nparams].S;
if (unit_convert) meV *= conversion_factor;
params[nparams].C *= meV;
params[nparams].C6 *= meV;
params[nparams].epsilon *= meV;
// precompute some quantities
params[nparams].delta2inv = pow(params[nparams].delta, -2.0);
params[nparams].lambda = params[nparams].alpha / params[nparams].z0;
params[nparams].seff = params[nparams].sR * params[nparams].reff;
nparams++;
}
}
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
if (comm->me != 0) {
params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
}
MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
memory->destroy(elem2param);
memory->destroy(cutILPsq);
memory->create(elem2param, nelements, nelements, "pair:elem2param");
memory->create(cutILPsq, nelements, nelements, "pair:cutILPsq");
for (int i = 0; i < nelements; i++) {
for (int j = 0; j < nelements; j++) {
int n = -1;
for (int m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement) {
if (n >= 0) error->all(FLERR, "ILP potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR, "Potential file is missing an entry");
elem2param[i][j] = n;
cutILPsq[i][j] = params[n].rcut * params[n].rcut;
}
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR, "Pair style ilp/graphene/hbn requires newton pair on");
if (!atom->molecule_flag)
error->all(FLERR, "Pair style ilp/graphene/hbn requires atom attribute molecule");
// need a full neighbor list, including neighbors of ghosts
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
// local ILP neighbor list
// create pages if first time or if neighbor pgsize/oneatom has changed
int create = 0;
if (ipage == nullptr) create = 1;
if (pgsize != neighbor->pgsize) create = 1;
if (oneatom != neighbor->oneatom) create = 1;
if (create) {
delete[] ipage;
pgsize = neighbor->pgsize;
oneatom = neighbor->oneatom;
int nmypage = comm->nthreads;
ipage = new MyPage<int>[nmypage];
for (int i = 0; i < nmypage; i++) ipage[i].init(oneatom, pgsize, PGDELTA);
}
}
/* ---------------------------------------------------------------------- */
void PairILPGrapheneHBN::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
pvector[0] = pvector[1] = 0.0;
// Build full neighbor list
ILP_neigh();
// Calculate the normals and its derivatives
calc_normal();
// Calculate the van der Waals force and energy
calc_FvdW(eflag, vflag);
// Calculate the repulsive force and energy
calc_FRep(eflag, vflag);
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
van der Waals forces and energy
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::calc_FvdW(int eflag, int /* vflag */)
{
int i, j, ii, jj, inum, jnum, itype, jtype;
tagint itag, jtag;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
double rsq, r, Rcut, r2inv, r6inv, r8inv, Tap, dTap, Vilp, TSvdw, TSvdw2inv, fsum;
int *ilist, *jlist, *numneigh, **firstneigh;
evdwl = 0.0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
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];
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
jtag = tag[j];
// two-body interactions from full neighbor list, skip half of them
if (itag > jtag) {
if ((itag + jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag + jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
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);
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
r8inv = r6inv * r2inv;
// 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;
}
TSvdw = 1.0 + exp(-p.d * (r / p.seff - 1.0));
TSvdw2inv = pow(TSvdw, -2.0);
Vilp = -p.C6 * r6inv / TSvdw;
// derivatives
fpair = -6.0 * p.C6 * r8inv / TSvdw +
p.C6 * p.d / p.seff * (TSvdw - 1.0) * TSvdw2inv * r8inv * r;
fsum = fpair * Tap - Vilp * dTap / r;
f[i][0] += fsum * delx;
f[i][1] += fsum * dely;
f[i][2] += fsum * delz;
f[j][0] -= fsum * delx;
f[j][1] -= fsum * dely;
f[j][2] -= fsum * delz;
if (eflag) pvector[0] += evdwl = Vilp * Tap;
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fsum, delx, dely, delz);
}
}
}
}
/* ----------------------------------------------------------------------
Repulsive forces and energy
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
{
int i, j, ii, jj, inum, jnum, itype, jtype, k, kk;
double prodnorm1, fkcx, fkcy, fkcz;
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;
}
// 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, i, 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);
}
} // loop over jj
} // loop over ii
}
/* ----------------------------------------------------------------------
create ILP neighbor list from main neighbor list to calculate normals
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::ILP_neigh()
{
int i, j, ii, jj, n, allnum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
int *neighptr;
double **x = atom->x;
int *type = atom->type;
if (atom->nmax > maxlocal) {
maxlocal = atom->nmax;
memory->destroy(ILP_numneigh);
memory->sfree(ILP_firstneigh);
memory->create(ILP_numneigh, maxlocal, "ILPGrapheneHBN:numneigh");
ILP_firstneigh =
(int **) memory->smalloc(maxlocal * sizeof(int *), "ILPGrapheneHBN:firstneigh");
}
allnum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// store all ILP neighs of owned and ghost atoms
// scan full neighbor list of I
ipage->reset();
for (ii = 0; ii < allnum; ii++) {
i = ilist[ii];
n = 0;
neighptr = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = map[type[i]];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
if (rsq != 0 && rsq < cutILPsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) {
neighptr[n++] = j;
}
} // loop over jj
ILP_firstneigh[i] = neighptr;
ILP_numneigh[i] = n;
if (n > 3)
error->one(FLERR,
"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
}
}
/* ----------------------------------------------------------------------
Calculate the normals for each atom
------------------------------------------------------------------------- */
void PairILPGrapheneHBN::calc_normal()
{
int i, j, ii, jj, inum, jnum;
int cont, id, ip, m;
double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
int *ilist, *jlist;
double pv12[3], pv31[3], pv23[3], n1[3], dni[3], dnn[3][3], vet[3][3], dpvdri[3][3];
double dn1[3][3][3], dpv12[3][3][3], dpv23[3][3][3], dpv31[3][3][3];
double **x = atom->x;
// grow normal array if necessary
if (atom->nmax > nmax) {
memory->destroy(normal);
memory->destroy(dnormal);
memory->destroy(dnormdri);
nmax = atom->nmax;
memory->create(normal, nmax, 3, "ILPGrapheneHBN:normal");
memory->create(dnormdri, 3, 3, nmax, "ILPGrapheneHBN:dnormdri");
memory->create(dnormal, 3, 3, 3, nmax, "ILPGrapheneHBN:dnormal");
}
inum = list->inum;
ilist = list->ilist;
//Calculate normals
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
// Initialize the arrays
for (id = 0; id < 3; id++) {
pv12[id] = 0.0;
pv31[id] = 0.0;
pv23[id] = 0.0;
n1[id] = 0.0;
dni[id] = 0.0;
normal[i][id] = 0.0;
for (ip = 0; ip < 3; ip++) {
vet[ip][id] = 0.0;
dnn[ip][id] = 0.0;
dpvdri[ip][id] = 0.0;
dnormdri[ip][id][i] = 0.0;
for (m = 0; m < 3; m++) {
dpv12[ip][id][m] = 0.0;
dpv31[ip][id][m] = 0.0;
dpv23[ip][id][m] = 0.0;
dn1[ip][id][m] = 0.0;
dnormal[ip][id][m][i] = 0.0;
}
}
}
xtp = x[i][0];
ytp = x[i][1];
ztp = x[i][2];
cont = 0;
jlist = ILP_firstneigh[i];
jnum = ILP_numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = x[j][0] - xtp;
dely = x[j][1] - ytp;
delz = x[j][2] - ztp;
vet[cont][0] = delx;
vet[cont][1] = dely;
vet[cont][2] = delz;
cont++;
}
if (cont <= 1) {
normal[i][0] = 0.0;
normal[i][1] = 0.0;
normal[i][2] = 1.0;
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormdri[id][ip][i] = 0.0;
for (m = 0; m < 3; m++) { dnormal[id][ip][m][i] = 0.0; }
}
}
} else if (cont == 2) {
pv12[0] = vet[0][1] * vet[1][2] - vet[1][1] * vet[0][2];
pv12[1] = vet[0][2] * vet[1][0] - vet[1][2] * vet[0][0];
pv12[2] = vet[0][0] * vet[1][1] - vet[1][0] * vet[0][1];
// derivatives of pv12[0] to ri
dpvdri[0][0] = 0.0;
dpvdri[0][1] = vet[0][2] - vet[1][2];
dpvdri[0][2] = vet[1][1] - vet[0][1];
// derivatives of pv12[1] to ri
dpvdri[1][0] = vet[1][2] - vet[0][2];
dpvdri[1][1] = 0.0;
dpvdri[1][2] = vet[0][0] - vet[1][0];
// derivatives of pv12[2] to ri
dpvdri[2][0] = vet[0][1] - vet[1][1];
dpvdri[2][1] = vet[1][0] - vet[0][0];
dpvdri[2][2] = 0.0;
dpv12[0][0][0] = 0.0;
dpv12[0][1][0] = vet[1][2];
dpv12[0][2][0] = -vet[1][1];
dpv12[1][0][0] = -vet[1][2];
dpv12[1][1][0] = 0.0;
dpv12[1][2][0] = vet[1][0];
dpv12[2][0][0] = vet[1][1];
dpv12[2][1][0] = -vet[1][0];
dpv12[2][2][0] = 0.0;
// derivatives respect to the second neighbor, atom l
dpv12[0][0][1] = 0.0;
dpv12[0][1][1] = -vet[0][2];
dpv12[0][2][1] = vet[0][1];
dpv12[1][0][1] = vet[0][2];
dpv12[1][1][1] = 0.0;
dpv12[1][2][1] = -vet[0][0];
dpv12[2][0][1] = -vet[0][1];
dpv12[2][1][1] = vet[0][0];
dpv12[2][2][1] = 0.0;
// derivatives respect to the third neighbor, atom n
// derivatives of pv12 to rn is zero
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) { dpv12[id][ip][2] = 0.0; }
}
n1[0] = pv12[0];
n1[1] = pv12[1];
n1[2] = pv12[2];
// the magnitude of the normal vector
nn2 = n1[0] * n1[0] + n1[1] * n1[1] + n1[2] * n1[2];
nn = sqrt(nn2);
if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = n1[0] / nn;
normal[i][1] = n1[1] / nn;
normal[i][2] = n1[2] / nn;
// derivatives of nn, dnn:3x1 vector
dni[0] = (n1[0] * dpvdri[0][0] + n1[1] * dpvdri[1][0] + n1[2] * dpvdri[2][0]) / nn;
dni[1] = (n1[0] * dpvdri[0][1] + n1[1] * dpvdri[1][1] + n1[2] * dpvdri[2][1]) / nn;
dni[2] = (n1[0] * dpvdri[0][2] + n1[1] * dpvdri[1][2] + n1[2] * dpvdri[2][2]) / nn;
// derivatives of unit vector ni respect to ri, the result is 3x3 matrix
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormdri[id][ip][i] = dpvdri[id][ip] / nn - n1[id] * dni[ip] / nn2;
}
}
// derivatives of non-normalized normal vector, dn1:3x3x3 array
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
for (m = 0; m < 3; m++) { dn1[id][ip][m] = dpv12[id][ip][m]; }
}
}
// derivatives of nn, dnn:3x3 vector
// dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
// r[id][m]: the id's component of atom m
for (m = 0; m < 3; m++) {
for (id = 0; id < 3; id++) {
dnn[id][m] = (n1[0] * dn1[0][id][m] + n1[1] * dn1[1][id][m] + n1[2] * dn1[2][id][m]) / nn;
}
}
// dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
// for atom m, which is a neighbor atom of atom i, m=0,jnum-1
for (m = 0; m < 3; m++) {
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormal[id][ip][m][i] = dn1[id][ip][m] / nn - n1[id] * dnn[ip][m] / nn2;
}
}
}
}
//##############################################################################################
else if (cont == 3) {
pv12[0] = vet[0][1] * vet[1][2] - vet[1][1] * vet[0][2];
pv12[1] = vet[0][2] * vet[1][0] - vet[1][2] * vet[0][0];
pv12[2] = vet[0][0] * vet[1][1] - vet[1][0] * vet[0][1];
// derivatives respect to the first neighbor, atom k
dpv12[0][0][0] = 0.0;
dpv12[0][1][0] = vet[1][2];
dpv12[0][2][0] = -vet[1][1];
dpv12[1][0][0] = -vet[1][2];
dpv12[1][1][0] = 0.0;
dpv12[1][2][0] = vet[1][0];
dpv12[2][0][0] = vet[1][1];
dpv12[2][1][0] = -vet[1][0];
dpv12[2][2][0] = 0.0;
// derivatives respect to the second neighbor, atom l
dpv12[0][0][1] = 0.0;
dpv12[0][1][1] = -vet[0][2];
dpv12[0][2][1] = vet[0][1];
dpv12[1][0][1] = vet[0][2];
dpv12[1][1][1] = 0.0;
dpv12[1][2][1] = -vet[0][0];
dpv12[2][0][1] = -vet[0][1];
dpv12[2][1][1] = vet[0][0];
dpv12[2][2][1] = 0.0;
// derivatives respect to the third neighbor, atom n
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) { dpv12[id][ip][2] = 0.0; }
}
pv31[0] = vet[2][1] * vet[0][2] - vet[0][1] * vet[2][2];
pv31[1] = vet[2][2] * vet[0][0] - vet[0][2] * vet[2][0];
pv31[2] = vet[2][0] * vet[0][1] - vet[0][0] * vet[2][1];
// derivatives respect to the first neighbor, atom k
dpv31[0][0][0] = 0.0;
dpv31[0][1][0] = -vet[2][2];
dpv31[0][2][0] = vet[2][1];
dpv31[1][0][0] = vet[2][2];
dpv31[1][1][0] = 0.0;
dpv31[1][2][0] = -vet[2][0];
dpv31[2][0][0] = -vet[2][1];
dpv31[2][1][0] = vet[2][0];
dpv31[2][2][0] = 0.0;
// derivatives respect to the third neighbor, atom n
dpv31[0][0][2] = 0.0;
dpv31[0][1][2] = vet[0][2];
dpv31[0][2][2] = -vet[0][1];
dpv31[1][0][2] = -vet[0][2];
dpv31[1][1][2] = 0.0;
dpv31[1][2][2] = vet[0][0];
dpv31[2][0][2] = vet[0][1];
dpv31[2][1][2] = -vet[0][0];
dpv31[2][2][2] = 0.0;
// derivatives respect to the second neighbor, atom l
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) { dpv31[id][ip][1] = 0.0; }
}
pv23[0] = vet[1][1] * vet[2][2] - vet[2][1] * vet[1][2];
pv23[1] = vet[1][2] * vet[2][0] - vet[2][2] * vet[1][0];
pv23[2] = vet[1][0] * vet[2][1] - vet[2][0] * vet[1][1];
// derivatives respect to the second neighbor, atom k
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) { dpv23[id][ip][0] = 0.0; }
}
// derivatives respect to the second neighbor, atom l
dpv23[0][0][1] = 0.0;
dpv23[0][1][1] = vet[2][2];
dpv23[0][2][1] = -vet[2][1];
dpv23[1][0][1] = -vet[2][2];
dpv23[1][1][1] = 0.0;
dpv23[1][2][1] = vet[2][0];
dpv23[2][0][1] = vet[2][1];
dpv23[2][1][1] = -vet[2][0];
dpv23[2][2][1] = 0.0;
// derivatives respect to the third neighbor, atom n
dpv23[0][0][2] = 0.0;
dpv23[0][1][2] = -vet[1][2];
dpv23[0][2][2] = vet[1][1];
dpv23[1][0][2] = vet[1][2];
dpv23[1][1][2] = 0.0;
dpv23[1][2][2] = -vet[1][0];
dpv23[2][0][2] = -vet[1][1];
dpv23[2][1][2] = vet[1][0];
dpv23[2][2][2] = 0.0;
//############################################################################################
// average the normal vectors by using the 3 neighboring planes
n1[0] = (pv12[0] + pv31[0] + pv23[0]) / cont;
n1[1] = (pv12[1] + pv31[1] + pv23[1]) / cont;
n1[2] = (pv12[2] + pv31[2] + pv23[2]) / cont;
// the magnitude of the normal vector
nn2 = n1[0] * n1[0] + n1[1] * n1[1] + n1[2] * n1[2];
nn = sqrt(nn2);
if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = n1[0] / nn;
normal[i][1] = n1[1] / nn;
normal[i][2] = n1[2] / nn;
// for the central atoms, dnormdri is always zero
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) { dnormdri[id][ip][i] = 0.0; }
}
// derivatives of non-normalized normal vector, dn1:3x3x3 array
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
for (m = 0; m < 3; m++) {
dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m]) / cont;
}
}
}
// derivatives of nn, dnn:3x3 vector
// dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
// r[id][m]: the id's component of atom m
for (m = 0; m < 3; m++) {
for (id = 0; id < 3; id++) {
dnn[id][m] = (n1[0] * dn1[0][id][m] + n1[1] * dn1[1][id][m] + n1[2] * dn1[2][id][m]) / nn;
}
}
// dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
// for atom m, which is a neighbor atom of atom i, m=0,jnum-1
for (m = 0; m < 3; m++) {
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormal[id][ip][m][i] = dn1[id][ip][m] / nn - n1[id] * dnn[ip][m] / nn2;
}
}
}
} else {
error->one(FLERR, "There are too many neighbors for calculating normals");
}
//##############################################################################################
}
}
/* ---------------------------------------------------------------------- */
double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj, double &fforce)
{
double r, r2inv, r6inv, r8inv, forcelj, philj, fpair;
double Tap, dTap, Vilp, TSvdw, TSvdw2inv;
int iparam_ij = elem2param[map[itype]][map[jtype]];
Param &p = params[iparam_ij];
r = sqrt(rsq);
// turn on/off taper function
if (tap_flag) {
Tap = calc_Tap(r, sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r, sqrt(cutsq[itype][jtype]));
} else {
Tap = 1.0;
dTap = 0.0;
}
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
r8inv = r2inv * r6inv;
TSvdw = 1.0 + exp(-p.d * (r / p.seff - 1.0));
TSvdw2inv = pow(TSvdw, -2.0);
Vilp = -p.C6 * r6inv / TSvdw;
// derivatives
fpair = -6.0 * p.C6 * r8inv / TSvdw + p.d / p.seff * p.C6 * (TSvdw - 1.0) * r6inv * TSvdw2inv / r;
forcelj = fpair;
fforce = factor_lj * (forcelj * Tap - Vilp * dTap / r);
philj = Vilp * Tap;
return factor_lj * philj;
}
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