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pair_comb.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, 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: Tzu-Ray Shan (U Florida, present: tnshan@sandia.gov)
LAMMPS implementation of the Charge-optimized many-body (COMB) potential
based on the HELL MD program (Prof Simon Phillpot, UF, sphil@mse.ufl.edu)
and Aidan Thompson's Tersoff code in LAMMPS
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_comb.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "group.h"
#include "update.h"
#include "my_page.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
#define PGDELTA 1
#define MAXNEIGH 24
/* ---------------------------------------------------------------------- */
PairComb::PairComb(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
nmax = 0;
NCo = NULL;
bbij = NULL;
map = NULL;
esm = NULL;
nelements = 0;
elements = NULL;
nparams = 0;
maxparam = 0;
params = NULL;
elem2param = NULL;
intype = NULL;
fafb = NULL;
dfafb = NULL;
ddfafb = NULL;
phin = NULL;
dphin = NULL;
erpaw = NULL;
sht_num = NULL;
sht_first = NULL;
ipage = NULL;
pgsize = oneatom = 0;
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairComb::~PairComb()
{
memory->destroy(NCo);
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
memory->sfree(params);
memory->destroy(elem2param);
memory->destroy(intype);
memory->destroy(fafb);
memory->destroy(dfafb);
memory->destroy(ddfafb);
memory->destroy(phin);
memory->destroy(dphin);
memory->destroy(erpaw);
memory->destroy(bbij);
memory->destroy(sht_num);
memory->sfree(sht_first);
delete [] ipage;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
delete [] esm;
}
}
/* ---------------------------------------------------------------------- */
void PairComb::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,iparam_i;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double zeta_ij,prefactor;
int *ilist,*jlist,*numneigh,**firstneigh;
int mr1,mr2,mr3;
int rsc,inty;
double elp_ij,filp[3],fjlp[3],fklp[3];
double iq,jq;
double yaself;
double potal,fac11,fac11e;
double vionij,fvionij,sr1,sr2,sr3,Eov,Fov;
int sht_jnum, *sht_jlist, nj;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = vflag_atom = 0;
// Build short range neighbor list
Short_neigh();
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
yaself = vionij = fvionij = Eov = Fov = 0.0;
// self energy correction term: potal
potal_calc(potal,fac11,fac11e);
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
iq = q[i];
NCo[i] = 0;
nj = 0;
iparam_i = elem2param[itype][itype][itype];
// self energy, only on i atom
yaself = self(&params[iparam_i],iq,potal);
if (evflag) ev_tally(i,i,nlocal,0,yaself,0.0,0.0,0.0,0.0,0.0);
// two-body interactions (long and short repulsive)
jlist = firstneigh[i];
jnum = numneigh[i];
sht_jlist = sht_first[i];
sht_jnum = sht_num[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) 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;
}
// Qj calculates 2-body Coulombic
jtype = map[type[j]];
jq = q[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
iparam_ij = elem2param[itype][jtype][jtype];
// long range q-dependent
if (rsq > params[iparam_ij].lcutsq) continue;
inty = intype[itype][jtype];
// polynomial three-point interpolation
tri_point(rsq, mr1, mr2, mr3, sr1, sr2, sr3, itype);
// 1/r energy and forces
direct(inty,mr1,mr2,mr3,rsq,sr1,sr2,sr3,iq,jq,
potal,fac11,fac11e,vionij,fvionij);
// field correction to self energy
field(&params[iparam_ij],rsq,iq,jq,vionij,fvionij);
// polarization field
// sums up long range forces
f[i][0] += delx*fvionij;
f[i][1] += dely*fvionij;
f[i][2] += delz*fvionij;
f[j][0] -= delx*fvionij;
f[j][1] -= dely*fvionij;
f[j][2] -= delz*fvionij;
if (evflag)
ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// short range q-independent
if (rsq > params[iparam_ij].cutsq) continue;
repulsive(&params[iparam_ij],rsq,fpair,eflag,evdwl,iq,jq);
// repulsion is pure two-body, sums up pair repulsive forces
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
// accumulate coordination number information
if (cor_flag) {
for (jj = 0; jj < sht_jnum; jj++) {
j = sht_jlist[jj];
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
if(params[iparam_ij].hfocor > 0.0 ) {
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = vec3_dot(delr1,delr1);
if (rsq1 > params[iparam_ij].cutsq) continue;
NCo[i] += 1;
}
}
}
// three-body interactions
// half i-j loop
for (jj = 0; jj < sht_jnum; jj++) {
j = sht_jlist[jj];
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
// this Qj for q-dependent BSi
jq = q[j];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = vec3_dot(delr1,delr1);
if (rsq1 > params[iparam_ij].cutsq) continue;
nj ++;
// accumulate bondorder zeta for each i-j interaction via loop over k
zeta_ij = 0.0;
cuo_flag1 = 0; cuo_flag2 = 0;
for (kk = 0; kk < sht_jnum; kk++) {
k = sht_jlist[kk];
if (j == k) continue;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = vec3_dot(delr2,delr2);
if (rsq2 > params[iparam_ijk].cutsq) continue;
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,delr1,delr2);
if (params[iparam_ijk].hfocor == -2.0) cuo_flag1 = 1;
if (params[iparam_ijk].hfocor == -1.0) cuo_flag2 = 1;
}
if (cuo_flag1 && cuo_flag2) cuo_flag = 1;
else cuo_flag = 0;
force_zeta(&params[iparam_ij],eflag,i,nj,rsq1,zeta_ij,
iq,jq,fpair,prefactor,evdwl);
// over-coordination correction for HfO2
if (cor_flag && NCo[i] != 0)
Over_cor(&params[iparam_ij],rsq1,NCo[i],Eov, Fov);
evdwl += Eov;
fpair += Fov;
f[i][0] += delr1[0]*fpair;
f[i][1] += delr1[1]*fpair;
f[i][2] += delr1[2]*fpair;
f[j][0] -= delr1[0]*fpair;
f[j][1] -= delr1[1]*fpair;
f[j][2] -= delr1[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
// attractive term via loop over k (3-body forces)
for (kk = 0; kk < sht_jnum; kk++) {
k = sht_jlist[kk];
if (j == k) continue;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = vec3_dot(delr2,delr2);
if (rsq2 > params[iparam_ijk].cutsq) continue;
for (rsc = 0; rsc < 3; rsc++)
fi[rsc] = fj[rsc] = fk[rsc] = 0.0;
attractive(&params[iparam_ijk],prefactor,
rsq1,rsq2,delr1,delr2,fi,fj,fk);
// 3-body LP and BB correction and forces
elp_ij = elp(&params[iparam_ijk],rsq1,rsq2,delr1,delr2);
flp(&params[iparam_ijk],rsq1,rsq2,delr1,delr2,filp,fjlp,fklp);
for (rsc = 0; rsc < 3; rsc++) {
fi[rsc] += filp[rsc];
fj[rsc] += fjlp[rsc];
fk[rsc] += fklp[rsc];
}
for (rsc = 0; rsc < 3; rsc++) {
f[i][rsc] += fi[rsc];
f[j][rsc] += fj[rsc];
f[k][rsc] += fk[rsc];
}
if (evflag)
ev_tally(i,j,nlocal,newton_pair,elp_ij,0.0,0.0,0.0,0.0,0.0);
if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
}
if (cuo_flag) params[iparam_i].cutsq *= 0.65;
}
cuo_flag = 0;
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairComb::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
esm = new double[n];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairComb::settings(int narg, char **arg)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairComb::coeff(int narg, char **arg)
{
int i,j,n;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
// read potential file and initialize potential parameters
read_file(arg[2]);
setup_params();
n = atom->ntypes;
// generate streitz-mintmire direct 1/r energy look-up table
if (comm->me == 0 && screen) fprintf(screen,"Pair COMB:\n");
if (comm->me == 0 && screen)
fprintf(screen," generating Coulomb integral lookup table ...\n");
sm_table();
if (cor_flag && comm->me == 0 && screen)
fprintf(screen," will apply over-coordination correction ...\n");
if (!cor_flag&& comm->me == 0 && screen)
fprintf(screen," will not apply over-coordination correction ...\n");
// clear setflag since coeff() called once with I,J = * *
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairComb::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style COMB requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style COMB requires newton pair on");
if (!atom->q_flag)
error->all(FLERR,"Pair style COMB requires atom attribute q");
// ptr to QEQ fix
//for (i = 0; i < modify->nfix; i++)
// if (strcmp(modify->fix[i]->style,"qeq") == 0) break;
//if (i < modify->nfix) fixqeq = (FixQEQ *) modify->fix[i];
//else fixqeq = NULL;
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// local Comb neighbor list
// create pages if first time or if neighbor pgsize/oneatom has changed
int create = 0;
if (ipage == NULL) 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);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairComb::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairComb::read_file(char *file)
{
int params_per_line = 49;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
nparams = 0;
maxparam = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open COMB potential file %s",file);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
}
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in COMB potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = atof(words[3]);
params[nparams].c = atof(words[4]);
params[nparams].d = atof(words[5]);
params[nparams].h = atof(words[6]);
params[nparams].powern = atof(words[7]);
params[nparams].beta = atof(words[8]);
params[nparams].lam21 = atof(words[9]);
params[nparams].lam22 = atof(words[10]);
params[nparams].bigb1 = atof(words[11]);
params[nparams].bigb2 = atof(words[12]);
params[nparams].bigr = atof(words[13]);
params[nparams].bigd = atof(words[14]);
params[nparams].lam11 = atof(words[15]);
params[nparams].lam12 = atof(words[16]);
params[nparams].biga1 = atof(words[17]);
params[nparams].biga2 = atof(words[18]);
params[nparams].plp1 = atof(words[19]);
params[nparams].plp3 = atof(words[20]);
params[nparams].plp6 = atof(words[21]);
params[nparams].a123 = atof(words[22]);
params[nparams].aconf= atof(words[23]);
params[nparams].addrep = atof(words[24]);
params[nparams].romigb = atof(words[25]);
params[nparams].romigc = atof(words[26]);
params[nparams].romigd = atof(words[27]);
params[nparams].romiga = atof(words[28]);
params[nparams].QL1 = atof(words[29]);
params[nparams].QU1 = atof(words[30]);
params[nparams].DL1 = atof(words[31]);
params[nparams].DU1 = atof(words[32]);
params[nparams].QL2 = atof(words[33]);
params[nparams].QU2 = atof(words[34]);
params[nparams].DL2 = atof(words[35]);
params[nparams].DU2 = atof(words[36]);
params[nparams].chi = atof(words[37]);
params[nparams].dj = atof(words[38]);
params[nparams].dk = atof(words[39]);
params[nparams].dl = atof(words[40]);
params[nparams].dm = atof(words[41]);
params[nparams].esm1 = atof(words[42]);
params[nparams].cmn1 = atof(words[43]);
params[nparams].cml1 = atof(words[44]);
params[nparams].cmn2 = atof(words[45]);
params[nparams].cml2 = atof(words[46]);
params[nparams].coulcut = atof(words[47]);
params[nparams].hfocor = atof(words[48]);
params[nparams].powermint = int(params[nparams].powerm);
// parameter sanity checks
if (params[nparams].lam11 < 0.0 || params[nparams].lam12 < 0.0 ||
params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
params[nparams].lam21 < 0.0 || params[nparams].lam22 < 0.0 ||
params[nparams].bigb1< 0.0 || params[nparams].bigb2< 0.0 ||
params[nparams].biga1< 0.0 || params[nparams].biga2< 0.0 ||
params[nparams].bigr < 0.0 || params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
params[nparams].plp1 < 0.0 || params[nparams].plp3 < 0.0 ||
params[nparams].plp6 < 0.0 ||
params[nparams].a123 > 360.0 || params[nparams].aconf < 0.0 ||
params[nparams].addrep < 0.0 || params[nparams].romigb < 0.0 ||
params[nparams].romigc < 0.0 || params[nparams].romigd < 0.0 ||
params[nparams].romiga < 0.0 ||
params[nparams].QL1 > 0.0 || params[nparams].QU1 < 0.0 ||
params[nparams].DL1 < 0.0 || params[nparams].DU1 > 0.0 ||
params[nparams].QL2 > 0.0 || params[nparams].QU2 < 0.0 ||
params[nparams].DL2 < 0.0 || params[nparams].DU2 > 0.0 ||
params[nparams].chi < 0.0 ||
// params[nparams].dj < 0.0 || params[nparams].dk < 0.0 ||
// params[nparams].dl < 0.0 || params[nparams].dm < 0.0 ||
params[nparams].esm1 < 0.0)
error->all(FLERR,"Illegal COMB parameter");
if (params[nparams].lam11 < params[nparams].lam21 ||
params[nparams].lam12 < params[nparams].lam22 ||
params[nparams].biga1< params[nparams].bigb1 ||
params[nparams].biga2< params[nparams].bigb2)
error->all(FLERR,"Illegal COMB parameter");
nparams++;
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairComb::setup_params()
{
int i,j,k,m,n;
// set elem2param for all element triplet combinations
// must be a single exact match to lines read from file
// do not allow for ACB in place of ABC
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j][k] = n;
}
// compute parameter values derived from inputs
for (m = 0; m < nparams; m++) {
params[m].cut = params[m].bigr + params[m].bigd;
params[m].cutsq = params[m].cut*params[m].cut;
params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
params[m].c3 = 1.0/params[m].c2;
params[m].c4 = 1.0/params[m].c1;
params[m].rlm1 = 0.5*(params[m].lam11+params[m].lam12)*params[m].romigc;
params[m].rlm2 = 0.5*(params[m].lam21+params[m].lam22)*params[m].romigd;
params[m].Qo1 = (params[m].QU1+params[m].QL1)/2.0; // (A22)
params[m].dQ1 = (params[m].QU1-params[m].QL1)/2.0; // (A21)
params[m].aB1 = 1.0 /
(1.0-pow(fabs(params[m].Qo1/params[m].dQ1),10.0)); // (A20)
params[m].bB1 = pow(fabs(params[m].aB1),0.1)/params[m].dQ1; // (A19)
params[m].nD1 = log(params[m].DU1/(params[m].DU1-params[m].DL1))/
log(params[m].QU1/(params[m].QU1-params[m].QL1));
params[m].bD1 = (pow((params[m].DL1-params[m].DU1),(1.0/params[m].nD1)))/
(params[m].QU1-params[m].QL1);
params[m].Qo2 = (params[m].QU2+params[m].QL2)/2.0; // (A22)
params[m].dQ2 = (params[m].QU2-params[m].QL2)/2.0; // (A21)
params[m].aB2 = 1.0 /
(1.0-pow(fabs(params[m].Qo2/params[m].dQ2),10.0)); // (A20)
params[m].bB2 = pow(fabs(params[m].aB2),0.1)/params[m].dQ2; // (A19)
params[m].nD2 = log(params[m].DU2/(params[m].DU2-params[m].DL2))/
log(params[m].QU2/(params[m].QU2-params[m].QL2));
params[m].bD2 = (pow((params[m].DL2-params[m].DU2),(1.0/params[m].nD2)))/
(params[m].QU2-params[m].QL2);
params[m].lcut = params[m].coulcut;
params[m].lcutsq = params[m].lcut*params[m].lcut;
params[m].gamma = 1.0; // for the change in pair_comb.h
}
// set cutmax to max of all params
cutmax = cutmin = 0.0;
cor_flag = 0;
for (m = 0; m < nparams; m++) {
if (params[m].cut > cutmax) cutmax = params[m].cut;
if (params[m].lcut > cutmax) cutmax = params[m].lcut;
if (params[m].cutsq > cutmin) cutmin = params[m].cutsq+0.2;
if (params[m].hfocor > 0.0001) cor_flag = 1;
}
}
/* ---------------------------------------------------------------------- */
void PairComb::repulsive(Param *param, double rsq, double &fforce,
int eflag, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,tmp_exp,Di,Dj;
double bigA,Asi,Asj,vrcs,fvrcs,fforce_tmp;
double rslp,rslp2,rslp4,arr1,arr2,fc2j,fc3j,fcp2j,fcp3j;
double romi = param->addrep;
double rrcs = param->bigr + param->bigd;
r = sqrt(rsq);
if (r > rrcs) return ;
tmp_fc = comb_fc(r,param);
tmp_fc_d = comb_fc_d(r,param);
tmp_exp = exp(-param->rlm1 * r);
arr1 = 2.22850; arr2 = 1.89350;
fc2j = comb_fc2(r);
fc3j = comb_fc3(r);
fcp2j = comb_fc2_d(r);
fcp3j = comb_fc3_d(r);
Di = param->DU1 + pow(fabs(param->bD1*(param->QU1-iq)),param->nD1);
Dj = param->DU2 + pow(fabs(param->bD2*(param->QU2-jq)),param->nD2);
Asi = param->biga1 * exp(param->lam11*Di);
Asj = param->biga2 * exp(param->lam12*Dj);
if ( Asi > 0.0 && Asj > 0.0 )
bigA = sqrt(Asi*Asj)*param->romiga;
else
bigA = 0.0;
fforce = -bigA * tmp_exp * (tmp_fc_d - tmp_fc*param->rlm1) / r;
// additional repulsion for TiO2 and HfO2 (switch by cor_flag)
vrcs = 0.0; fvrcs = 0.0;
if (romi > 0.0) {
if (!cor_flag) {
vrcs = romi * pow((1.0-r/rrcs),2.0);
fvrcs= romi * 2.0 * (r/rrcs-1.0)/rrcs; }
else if (cor_flag) {
rslp = ((arr1-r)/(arr1-arr2));
rslp2 = rslp * rslp; rslp4 = rslp2 * rslp2;
vrcs = fc2j * fc3j * romi * ((50.0*rslp4-30.0*rslp2+4.50))/8.0;
fvrcs = fcp2j*fcp3j*romi*rslp*(-25.0*rslp2+7.50)/(arr1-arr2);
}
fforce_tmp = fforce*vrcs - (tmp_fc * bigA * tmp_exp * fvrcs);
fforce += fforce_tmp;
}
// eng = repulsive energy
if (eflag) eng = (tmp_fc * bigA * tmp_exp)*(1.0+vrcs);
}
/* ---------------------------------------------------------------------- */
double PairComb::zeta(Param *param, double rsqij, double rsqik,
double *delrij, double *delrik)
{
double rij,rik,costheta,arg,ex_delr;
rij = sqrt(rsqij);
if (rij > param->bigr+param->bigd) return 0.0;
rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
if (param->powermint == 3) arg = pow(param->rlm2 * (rij-rik),3.0);
else arg = param->rlm2 * (rij-rik);
if (arg > 69.0776) ex_delr = 1.e30;
else if (arg < -69.0776) ex_delr = 0.0;
else ex_delr = exp(arg);
return comb_fc(rik,param) * comb_gijk(costheta,param) * ex_delr;
}
/* ----------------------------------------------------------------------
Legendre polynomial bond angle correction to energy
------------------------------------------------------------------------- */
double PairComb::elp(Param *param, double rsqij, double rsqik,
double *delrij, double *delrik)
{
if (param->aconf > 1.0e-6 || param->plp1 > 1.0e-6 ||
param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
double rij,rik,costheta,lp1,lp3,lp6;
double rmu,rmu2,comtt,fcj,fck;
double pplp1 = param->plp1, pplp3 = param->plp3, pplp6 = param->plp6;
double c123 = cos(param->a123*MY_PI/180.0);
// cos(theta) of the i-j-k
// cutoff function of rik
rij = sqrt(rsqij);
rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
fcj = comb_fc(rij,param);
fck = comb_fc(rik,param);
rmu = costheta;
// Legendre Polynomial functions
if (param->plp1 > 1.0e-6 || param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
rmu2 = rmu*rmu;
lp1 = rmu; lp3 = 0.5*(5.0*rmu2*rmu-3.0*rmu);
lp6 = (231.0*rmu2*rmu2*rmu2-315.0*rmu2*rmu2+105.0*rmu2-5.0)/16.0;
comtt = pplp1*lp1 + pplp3*lp3 + pplp6*lp6;
} else comtt = 0.0;
// bond-bending terms
if (param->aconf>1e-4) {
if (param->hfocor >= 0.0)
comtt += param->aconf *(rmu-c123)*(rmu-c123);
else if (param->hfocor < 0.0)
comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
}
return 0.5 * fcj * fck * comtt;
}
return 0.0;
}
/* ----------------------------------------------------------------------
Legendre polynomial bond angle correction to forces
------------------------------------------------------------------------- */
void PairComb::flp(Param *param, double rsqij, double rsqik,
double *delrij, double *delrik, double *drilp,
double *drjlp, double *drklp)
{
double ffj1,ffj2,ffk1,ffk2;
ffj1 = 0.0; ffj2 = 0.0; ffk1 = 0.0; ffk2 = 0.0;
if (param->aconf > 1.0e-4 || param->plp1 > 1.0e-6 ||
param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
double rij,rik,costheta,lp1,lp1_d,lp3,lp3_d,lp6,lp6_d;
double rmu,rmu2,comtt,comtt_d,com4k,com5,fcj,fck,fck_d;
double pplp1 = param->plp1;
double pplp3 = param->plp3;
double pplp6 = param->plp6;
double c123 = cos(param->a123*MY_PI/180.0);
// fck_d = derivative of cutoff function
rij = sqrt(rsqij); rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
fcj = comb_fc(rij,param);
fck = comb_fc(rik,param);
fck_d = comb_fc_d(rik,param);
rmu = costheta;
// Legendre Polynomial functions and derivatives
if (param->plp1 > 1.0e-6 || param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
rmu2 = rmu*rmu;
lp1 = rmu; lp3 = (2.5*rmu2*rmu-1.5*rmu);
lp6 = (231.0*rmu2*rmu2*rmu2-315.0*rmu2*rmu2+105.0*rmu2-5.0)/16.0;
lp1_d = 1.0;lp3_d = (7.5*rmu2-1.5);
lp6_d = (1386.0*rmu2*rmu2*rmu-1260.0*rmu2*rmu+210.0)/16.0;
comtt = pplp1*lp1 + pplp3*lp3 + pplp6*lp6;
comtt_d = pplp1*lp1_d + pplp3*lp3_d + pplp6*lp6_d;
} else {
comtt = 0.0;
comtt_d = 0.0;
}
// bond-bending terms derivatives
if (param->aconf > 1.0e-4) {
if (param->hfocor >= 0.0) {
comtt += param->aconf *(rmu-c123)*(rmu-c123);
comtt_d += 2.0*param->aconf*(rmu-c123);
} else if (param->hfocor < 0.0) {
comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
comtt_d += -2.0*param->aconf*(rmu-c123);
}
}
com4k = 2.0 * fcj * fck_d * comtt;
com5 = fcj * fck * comtt_d;
ffj1 =-0.5*(com5/(rij*rik));
ffj2 = 0.5*(com5*rmu/rsqij);
ffk1 = ffj1;
ffk2 = 0.5*(-com4k/rik+com5*rmu/rsqik);
} else {
ffj1 = 0.0; ffj2 = 0.0;
ffk1 = 0.0; ffk2 = 0.0;
}
// j-atom
vec3_scale(ffj1,delrik,drjlp); // (k,x[],y[]), y[]=k*x[]
vec3_scaleadd(ffj2,delrij,drjlp,drjlp); // (k,x[],y[],z[]), z[]=k*x[]+y[]
// k-atom
vec3_scale(ffk1,delrij,drklp);
vec3_scaleadd(ffk2,delrik,drklp,drklp);
// i-atom
vec3_add(drjlp,drklp,drilp); // (x[],y[],z[]), z[]=x[]+y[]
vec3_scale(-1.0,drilp,drilp);
}
/* ---------------------------------------------------------------------- */
void PairComb::force_zeta(Param *param, int eflag, int i, int j, double rsq,
double zeta_ij, double iq, double jq, double &fforce,
double &prefactor, double &eng)
{
double r,fa,fa_d,bij;
r = sqrt(rsq);
if (r > param->bigr+param->bigd) return;
fa = comb_fa(r,param,iq,jq);
fa_d = comb_fa_d(r,param,iq,jq);
bij = comb_bij(zeta_ij,param);
bbij[i][j] = bij;
// force
fforce = 0.5*bij*fa_d / r;
prefactor = -0.5*fa * comb_bij_d(zeta_ij,param);
// eng = attractive energy
if (eflag) eng = 0.5*bij*fa;
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fc(double r, Param *param)
{
double comb_R = param->bigr;
double comb_D = param->bigd;
if (r < comb_R-comb_D) return 1.0;
if (r > comb_R+comb_D) return 0.0;
return 0.5*(1.0 - sin(MY_PI2*(r - comb_R)/comb_D));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fc_d(double r, Param *param)
{
double comb_R = param->bigr;
double comb_D = param->bigd;
if (r < comb_R-comb_D) return 0.0;
if (r > comb_R+comb_D) return 0.0;
return -(MY_PI4/comb_D) * cos(MY_PI2*(r - comb_R)/comb_D);
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fc2(double r)
{
double comb_R = 1.89350;
double comb_D = comb_R + 0.050;
if (r < comb_R) return 0.0;
if (r > comb_D) return 1.0;
return 0.5*(1.0 + cos(MY_PI*(r - comb_R)/(comb_D-comb_R)));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fc2_d(double r)
{
double comb_R = 1.89350;
double comb_D = comb_R + 0.050;
if (r < comb_R) return 0.0;
if (r > comb_D) return 0.0;
return -(MY_PI2/(comb_D-comb_R)) * sin(MY_PI*(r - comb_R)/(comb_D-comb_R));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fc3(double r)
{
double comb_R = 2.51350;
double comb_D = comb_R + 0.050;
if (r < comb_R) return 1.0;
if (r > comb_D) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(r - comb_R)/(comb_D-comb_R)));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fc3_d(double r)
{
double comb_R = 2.51350;
double comb_D = comb_R + 0.050;
if (r < comb_R) return 0.0;
if (r > comb_D) return 0.0;
return -(MY_PI2/(comb_D-comb_R)) * sin(MY_PI*(r - comb_R)/(comb_D-comb_R));
}
/* ---------------------------------------------------------------------- */
double PairComb::self(Param *param, double qi, double selfpot)
{
double self_tmp, cmin, cmax, qmin, qmax;
double s1=param->chi, s2=param->dj, s3=param->dk, s4=param->dl, s5=param->dm;
self_tmp = 0.0;
qmin = param->QL1*0.90;
qmax = param->QU1*0.90;
cmin = cmax = 1000.0;
self_tmp = qi*(s1+qi*(s2+selfpot+qi*(s3+qi*(s4+qi*qi*s5))));
if (qi < qmin) self_tmp += cmin * pow((qi-qmin),4.0);
if (qi > qmax) self_tmp += cmax * pow((qi-qmax),4.0);
return self_tmp;
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fa(double r, Param *param, double iq, double jq)
{
double bigB,Bsi,Bsj;
double qi,qj,Di,Dj;
if (r > param->bigr + param->bigd) return 0.0;
qi = iq; qj = jq;
Di = Dj = Bsi = Bsj = bigB = 0.0;
Di = param->DU1 + pow(fabs(param->bD1*(param->QU1-qi)),param->nD1);
Dj = param->DU2 + pow(fabs(param->bD2*(param->QU2-qj)),param->nD2);
Bsi = param->bigb1 * exp(param->lam21*Di)*
(param->aB1-fabs(pow(param->bB1*(qi-param->Qo1),10.0)));
Bsj = param->bigb2 * exp(param->lam22*Dj)*
(param->aB2-fabs(pow(param->bB2*(qj-param->Qo2),10.0)));
if (Bsi > 0.0 && Bsj > 0.0) bigB = sqrt(Bsi*Bsj)*param->romigb;
else bigB = 0.0;
return -bigB * exp(-param->rlm2 * r) * comb_fc(r,param);
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_fa_d(double r, Param *param, double iq, double jq)
{
double bigB,Bsi,Bsj;
double qi,qj,Di,Dj;
if (r > param->bigr + param->bigd) return 0.0;
qi = iq; qj = jq;
Di = Dj = Bsi = Bsj = bigB = 0.0;
Di = param->DU1 + pow(fabs(param->bD1*(param->QU1-qi)),param->nD1);
Dj = param->DU2 + pow(fabs(param->bD2*(param->QU2-qj)),param->nD2);
Bsi = param->bigb1 * exp(param->lam21*Di)*
(param->aB1-fabs(pow(param->bB1*(qi-param->Qo1),10.0)));
Bsj = param->bigb2 * exp(param->lam22*Dj)*
(param->aB2-fabs(pow(param->bB2*(qj-param->Qo2),10.0)));
if (Bsi > 0.0 && Bsj > 0.0) bigB = sqrt(Bsi*Bsj)*param->romigb;
else bigB = 0.0;
return bigB * exp(-param->rlm2 * r) *
(param->rlm2 * comb_fc(r,param) - comb_fc_d(r,param));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_bij(double zeta, Param *param)
{
double tmp = param->beta * zeta;
if (tmp > param->c1) return 1.0/sqrt(tmp);
if (tmp > param->c2)
return (1.0 - pow(tmp,-1.0*param->powern) / (2.0*param->powern))/sqrt(tmp);
if (tmp < param->c4) return 1.0;
if (tmp < param->c3)
return 1.0 - pow(tmp,param->powern)/(2.0*param->powern);
return pow(1.0 + pow(tmp,param->powern), -1.0/(2.0*param->powern));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_bij_d(double zeta, Param *param)
{
double tmp = param->beta * zeta;
if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
if (tmp > param->c2)
return param->beta * (-0.5*pow(tmp,-1.5) *
// error in negligible 2nd term fixed 9/30/2015
// (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
(1.0 - (1.0 + 1.0/(2.0*param->powern)) *
pow(tmp,-param->powern)));
if (tmp < param->c4) return 0.0;
if (tmp < param->c3)
return -0.5*param->beta * pow(tmp,param->powern-1.0);
double tmp_n = pow(tmp,param->powern);
return -0.5 * pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern)))*tmp_n / zeta;
}
/* ---------------------------------------------------------------------- */
void PairComb::attractive(Param *param, double prefactor,
double rsqij, double rsqik,
double *delrij, double *delrik,
double *fi, double *fj, double *fk)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
comb_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,param);
}
/* ---------------------------------------------------------------------- */
void PairComb::comb_zetaterm_d(double prefactor, double *rij_hat, double rij,
double *rik_hat, double rik, double *dri,
double *drj, double *drk, Param *param)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
double dcosdri[3],dcosdrj[3],dcosdrk[3];
fc = comb_fc(rik,param);
dfc = comb_fc_d(rik,param);
if (param->powermint == 3) tmp = pow(param->rlm2 * (rij-rik),3.0);
else tmp = param->rlm2 * (rij-rik);
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp); // ex_delr is Ygexp
if (param->powermint == 3)
ex_delr_d = 3.0*pow(param->rlm2,3.0) * pow(rij-rik,2.0)*ex_delr; // com3
else ex_delr_d = param->rlm2 * ex_delr; // com3
cos_theta = vec3_dot(rij_hat,rik_hat);
gijk = comb_gijk(cos_theta,param);
gijk_d = comb_gijk_d(cos_theta,param);
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
// compute the derivative wrt Ri
// dri = -dfc*gijk*ex_delr*rik_hat;
// dri += fc*gijk_d*ex_delr*dcosdri;
// dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
// (k,x[],y[]), y[]=k*x[]
// (k,x[],y[],z[]), z[]=k*x[]+y[]
vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
vec3_scale(prefactor,dri,dri);
// compute the derivative wrt Rj
// drj = fc*gijk_d*ex_delr*dcosdrj;
// drj += fc*gijk*ex_delr_d*rij_hat;
vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
vec3_scale(prefactor,drj,drj);
// compute the derivative wrt Rk
// drk = dfc*gijk*ex_delr*rik_hat;
// drk += fc*gijk_d*ex_delr*dcosdrk;
// drk += -fc*gijk*ex_delr_d*rik_hat;
vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
vec3_scale(prefactor,drk,drk);
}
/* ---------------------------------------------------------------------- */
void PairComb::costheta_d(double *rij_hat, double rij,
double *rik_hat, double rik,
double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
double cos_theta = vec3_dot(rij_hat,rik_hat);
vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
vec3_scale(1.0/rij,drj,drj);
vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
vec3_scale(1.0/rik,drk,drk);
vec3_add(drj,drk,dri);
vec3_scale(-1.0,dri,dri);
}
/* ---------------------------------------------------------------------- */
void PairComb::sm_table()
{
int i,j,k,m,nntypes,ncoul;
int inty, itype, jtype;
int iparam_i, iparam_ij, iparam_ji;
double r,dra,drin,rc,z,zr,zrc,ea,eb,ea3,eb3,alf;
double exp2er,exp2ersh,fafash,dfafash,F1,dF1,ddF1,E1,E2,E3,E4;
double exp2ear,exp2ebr,exp2earsh,exp2ebrsh,fafbsh,dfafbsh;
int n = atom->ntypes;
int nmax = atom->nmax;
dra = 0.001; // lookup table step size
drin = 0.1; // starting distance of 1/r
rc = cutmax;
alf = 0.20;
nntypes = int((n+1)*n/2); // interaction types
ncoul = int((rc-drin)/dra)+1;
// allocate arrays
memory->create(intype,n,n,"pair:intype");
memory->create(fafb,ncoul,nntypes,"pair:fafb");
memory->create(dfafb,ncoul,nntypes,"pair:dfafb");
memory->create(ddfafb,ncoul,nntypes,"pair:ddfafb");
memory->create(phin,ncoul,nntypes,"pair:phin");
memory->create(dphin,ncoul,nntypes,"pair:dphin");
memory->create(erpaw,25000,2,"pair:erpaw");
memory->create(NCo,nmax,"pair:NCo");
memory->create(bbij,nmax,MAXNEIGH,"pair:bbij");
memory->create(sht_num,nmax,"pair:sht_num");
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),"pair:sht_first");
// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
m = 0; k = n;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (j == i) {
intype[i][j] = m;
m += 1;
} else if (j != i && j > i) {
intype[i][j] = k;
k += 1;
} else if (j != i && j < i) {
intype[i][j] = intype[j][i];
}
}
}
// default arrays to zero
for (i = 0; i < ncoul; i ++) {
for (j = 0; j < nntypes; j ++) {
fafb[i][j] = 0.0;
dfafb[i][j] = 0.0;
ddfafb[i][j] = 0.0;
phin[i][j] = 0.0;
dphin[i][j] = 0.0;
}
}
// direct 1/r energy with Slater 1S orbital overlap
for (i = 0; i < n; i++) {
if (map[i+1] < 0) continue;
r = drin;
itype = params[map[i+1]].ielement;
iparam_i = elem2param[itype][itype][itype];
z = params[iparam_i].esm1;
if (comm->me == 0 && screen)
fprintf(screen," element[%d] = %-2s, z = %g\n",i+1,elements[map[i+1]],z);
for (j = 0; j < ncoul; j++) {
exp2er = exp(-2.0 * z * r);
phin[j][i] = 1.0 - exp2er * (1.0 + 2.0 * z * r * (1.0 + z * r));
dphin[j][i] = (4.0 * exp2er * z * z * z * r * r);
r += dra;
}
}
for (i = 0; i < n; i ++) {
if (map[i+1] < 0) continue;
for (j = 0; j < n; j ++) {
if (map[j+1] < 0) continue;
r = drin;
if (j == i) {
itype = params[map[i+1]].ielement;
inty = intype[itype][itype];
iparam_i = elem2param[itype][itype][itype];
z = params[iparam_i].esm1;
zrc = z * rc;
exp2ersh = exp(-2.0 * zrc);
fafash = -exp2ersh * (1.0 / rc +
z * (11.0/8.0 + 3.0/4.0*zrc + zrc*zrc/6.0));
dfafash = exp2ersh * (1.0/(rc*rc) + 2.0*z/rc +
z*z*(2.0 + 7.0/6.0*zrc + zrc*zrc/3.0));
for (k = 0; k < ncoul; k ++) {
zr = z * r;
exp2er = exp(-2.0*zr);
F1 = -exp2er * (1.0 / r +
z * (11.0/8.0 + 3.0/4.0*zr + zr*zr/6.0));
dF1 = exp2er * (1.0/(r*r) + 2.0*z/r +
z*z*(2.0 + 7.0/6.0*zr + zr*zr/3.0));
ddF1 = -exp2er * (2.0/(r*r*r) + 4.0*z/(r*r) -
z*z*z/3.0*(17.0/2.0 + 5.0*zr + 2.0*zr*zr));
fafb[k][inty] = F1-fafash-(r-rc)*dfafash;
dfafb[k][inty] = (dF1 - dfafash);
ddfafb[k][inty] = ddF1;
r += dra;
}
} else if (j != i) {
itype = params[map[i+1]].ielement;
jtype = params[map[j+1]].ielement;
inty = intype[itype][jtype];
iparam_ij = elem2param[itype][jtype][jtype];
ea = params[iparam_ij].esm1;
ea3 = ea*ea*ea;
iparam_ji = elem2param[jtype][itype][itype];
eb = params[iparam_ji].esm1;
eb3 = eb*eb*eb;
E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb));
E2 = eb*ea3*ea/((ea+eb)*(ea+eb)*(eb-ea)*(eb-ea));
E3 = (3.0*ea*ea*eb3*eb-eb3*eb3) /
((ea+eb)*(ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)*(ea-eb));
E4 = (3.0*eb*eb*ea3*ea-ea3*ea3) /
((ea+eb)*(ea+eb)*(ea+eb)*(eb-ea)*(eb-ea)*(eb-ea));
exp2earsh = exp(-2.0*ea*rc);
exp2ebrsh = exp(-2.0*eb*rc);
fafbsh = -exp2earsh*(E1 + E3/rc)-exp2ebrsh*(E2 + E4/rc);
dfafbsh =
exp2earsh*(2.0*ea*(E1+E3/rc)+E3/(rc*rc)) +
exp2ebrsh*(2.0*eb*(E2+E4/rc)+E4/(rc*rc));
for (k = 0; k < ncoul; k ++) {
exp2ear = exp(-2.0*ea*r);
exp2ebr = exp(-2.0*eb*r);
fafb[k][inty] =
- exp2ear*(E1+E3/r) - exp2ebr*(E2+E4/r)
- fafbsh - (r-rc) * dfafbsh;
dfafb[k][inty] = (exp2ear*(2.0*ea*(E1+E3/r) + E3/(r*r))
+ exp2ebr*(2.0*eb*(E2+E4/r) + E4/(r*r))- dfafbsh);
ddfafb[k][inty] = (- exp2ear*(E3/(r*r)*(1.0/r+2.0*ea/r+2.0/(r*r))
+ 2.0*ea*(E1+E3/r))-
exp2ebr*(E4/(r*r)
*(1.0/r+2.0*eb/r+2.0/(r*r)) +
2.0*eb*(E2+E4/r)));
r += dra;
}
}
}
}
for (i = 0; i < 25000; i ++) {
r = dra * i + drin;
erpaw[i][0] = erfc(r*alf);
erpaw[i][1] = exp(-r*r*alf*alf);
}
}
/* ---------------------------------------------------------------------- */
void PairComb::potal_calc(double &calc1, double &calc2, double &calc3)
{
double alf,rcoul,esucon;
int m;
rcoul = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].lcut > rcoul) rcoul = params[m].lcut;
alf = 0.20;
esucon = force->qqr2e;
calc2 = (erfc(rcoul*alf)/rcoul/rcoul+2.0*alf/MY_PIS*
exp(-alf*alf*rcoul*rcoul)/rcoul)*esucon/rcoul;
calc3 = (erfc(rcoul*alf)/rcoul)*esucon;
calc1 = -(alf/MY_PIS*esucon+calc3*0.5);
}
/* ---------------------------------------------------------------------- */
void PairComb::tri_point(double rsq, int &mr1, int &mr2,
int &mr3, double &sr1, double &sr2,
double &sr3, int &itype)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
rin = 0.10; dr = 0.0010;
r = sqrt(rsq);
if (r < rin + 2.0*dr) r = rin + 2.0*dr;
if (r > cutmax - 2.0*dr) r = cutmax - 2.0*dr;
rridr = (r-rin)/dr;
mr1 = int(rridr)-1;
dd = rridr - float(mr1);
if (dd > 0.5) mr1 += 1;
mr2 = mr1 + 1;
mr3 = mr2 + 1;
rr1 = float(mr1)*dr;
rridr = (r - rin - rr1)/dr;
rridr2 = rridr * rridr;
sr1 = (rridr2 - rridr) * 0.50;
sr2 = 1.0 - rridr2;
sr3 = (rridr2 + rridr) * 0.50;
}
/* ---------------------------------------------------------------------- */
void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq,
double sr1, double sr2, double sr3,
double iq, double jq,
double potal, double fac11, double fac11e,
double &pot_tmp, double &pot_d)
{
double r,erfcc,fafbn1,potij,sme2,esucon;
double r3,erfcd,dfafbn1,smf2,dvdrr,alf,alfdpi;
r = sqrt(rsq);
r3 = r * rsq;
alf = 0.20;
alfdpi = 2.0*alf/MY_PIS;
esucon = force->qqr2e;
pot_tmp = 0.0;
pot_d = 0.0;
// 1/r energy
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
fafbn1= sr1*fafb[mr1][inty] + sr2*fafb[mr2][inty] + sr3*fafb[mr3][inty];
potij = (erfcc/r * esucon - fac11e);
sme2 = potij + fafbn1 * esucon;
pot_tmp = 1.0 * iq * jq *sme2;
// 1/r force (wrt r)
erfcd = sr1*erpaw[mr1][1] + sr2*erpaw[mr2][1] + sr3*erpaw[mr3][1];
dfafbn1= sr1*dfafb[mr1][inty] + sr2*dfafb[mr2][inty] + sr3*dfafb[mr3][inty];
dvdrr = (erfcc/r3+alfdpi*erfcd/rsq)*esucon-fac11;
smf2 = dvdrr - dfafbn1 * esucon/r;
pot_d = 1.0 * iq * jq * smf2;
}
/* ---------------------------------------------------------------------- */
void PairComb::field(Param *param, double rsq, double iq,double jq,
double &vionij,double &fvionij)
{
double r,r5,r6,rc,rc5,rc6,rf5,drf6,smpn,smpl,rfx1,rfx2;
double cmi1,cmi2,cmj1,cmj2;
r = sqrt(rsq);
r5 = r*r*r*r*r;
r6 = r5 * r;
rc = param->lcut;
rc5 = rc*rc*rc*rc*rc;
rc6 = rc5 * rc;
cmi1 = param->cmn1;
cmi2 = param->cmn2;
cmj1 = param->cml1;
cmj2 = param->cml2;
rf5 = 1.0/r5 - 1.0/rc5 + 5.0*(r-rc)/rc6;
drf6 = 5.0/rc6 - 5.0/r6;
// field correction energy
smpn = rf5*jq*(cmi1+jq*cmi2);
smpl = rf5*iq*(cmj1+iq*cmj2);
vionij += 1.0 * (smpn + smpl);
// field correction force
rfx1 = jq*drf6*(cmi1+jq*cmi2)/r;
rfx2 = iq*drf6*(cmj1+iq*cmj2)/r;
fvionij -= 1.0 * (rfx1 + rfx2);
}
/* ---------------------------------------------------------------------- */
double PairComb::yasu_char(double *qf_fix, int &igroup)
{
int i,j,ii,jj,jnum;
int itype,jtype,iparam_i,iparam_ij;
tagint itag,jtag;
double xtmp,ytmp,ztmp;
double rsq1,delr1[3];
int *ilist,*jlist,*numneigh,**firstneigh;
double iq,jq,fqi,fqij,fqjj;
double potal,fac11,fac11e,sr1,sr2,sr3;
int mr1,mr2,mr3,inty,nj;
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
tagint *tag = atom->tag;
int inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
qf = qf_fix;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
qf[i] = 0.0;
}
// communicating charge force to all nodes, first forward then reverse
comm->forward_comm_pair(this);
// self energy correction term: potal
potal_calc(potal,fac11,fac11e);
// loop over full neighbor list of my atoms
fqi = fqij = fqjj = 0.0;
for (ii = 0; ii < inum; ii ++) {
i = ilist[ii];
itag = tag[i];
nj = 0;
if (mask[i] & groupbit) {
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
iq = q[i];
iparam_i = elem2param[itype][itype][itype];
// charge force from self energy
fqi = qfo_self(&params[iparam_i],iq,potal);
// two-body interactions
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) 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;
}
jtype = map[type[j]];
jq = q[j];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = vec3_dot(delr1,delr1);
iparam_ij = elem2param[itype][jtype][jtype];
// long range q-dependent
if (rsq1 > params[iparam_ij].lcutsq) continue;
inty = intype[itype][jtype];
// polynomial three-point interpolation
tri_point(rsq1,mr1,mr2,mr3,sr1,sr2,sr3,itype);
// 1/r charge forces
qfo_direct(inty,mr1,mr2,mr3,rsq1,sr1,sr2,sr3,fac11e,fqij);
fqi += jq * fqij; qf[j] += iq * fqij;
// field correction to self energy and charge force
qfo_field(&params[iparam_ij],rsq1,iq,jq,fqij,fqjj);
fqi += fqij;
qf[j] += fqjj;
}
// three-body interactions
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
jq = q[j];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = vec3_dot(delr1,delr1);
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq1 > params[iparam_ij].cutsq) continue;
nj ++;
// charge force in Aij and Bij
qfo_short(&params[iparam_ij],i,nj,rsq1,iq,jq,fqij,fqjj);
fqi += fqij; qf[j] += fqjj;
}
qf[i] += fqi;
}
}
comm->reverse_comm_pair(this);
// sum charge force on each node and return it
double eneg = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
eneg += qf[i];
}
MPI_Allreduce(&eneg,&enegtot,1,MPI_DOUBLE,MPI_SUM,world);
return enegtot;
}
/* ---------------------------------------------------------------------- */
double PairComb::qfo_self(Param *param, double qi, double selfpot)
{
double self_d,cmin,cmax,qmin,qmax;
double s1 = param->chi;
double s2 = param->dj;
double s3 = param->dk;
double s4 = param->dl;
double s5 = param->dm;
self_d = 0.0;
qmin = param->QL1*0.90;
qmax = param->QU1*0.90;
cmin = cmax = 1000.0;
self_d = s1+qi*(2.0*(s2+selfpot)+qi*(3.0*s3+qi*(4.0*s4+qi*qi*6.0*s5)));
if (qi < qmin) {
// char str[128];
// sprintf(str,"Pair COMB charge %.10f with force %.10f hit min barrier",
// qi,self_d);
// error->warning(FLERR,str,0);
self_d += 4.0 * cmin * pow((qi-qmin),3.0);
}
if (qi > qmax) {
// char str[128];
// sprintf(str,"Pair COMB charge %.10f with force %.10f hit max barrier",
// qi,self_d);
// error->warning(FLERR,str,0);
self_d += 4.0 * cmax * pow((qi-qmax),3.0);
}
return self_d;
}
/* ---------------------------------------------------------------------- */
void PairComb::qfo_direct(int inty, int mr1, int mr2, int mr3,
double rsq, double sr1, double sr2,
double sr3, double fac11e, double &fqij)
{
double r, erfcc, fafbn1, vm, esucon;
r = sqrt(rsq);
esucon=force->qqr2e;
// 1/r force (wrt q)
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
fafbn1= sr1*fafb[mr1][inty] + sr2*fafb[mr2][inty] + sr3*fafb[mr3][inty];
vm = (erfcc/r * esucon - fac11e);
fqij = 1.0 * (vm+esucon*fafbn1);
}
/* ---------------------------------------------------------------------- */
void PairComb::qfo_field(Param *param, double rsq,double iq,double jq,
double &fqij, double &fqjj)
{
double r,r5,rc,rc5,rc6;
double cmi1,cmi2,cmj1,cmj2,rf5;
fqij = fqjj = 0.0;
r = sqrt(rsq);
r5 = r*r*r*r*r;
rc = param->lcut;
rc5 = rc*rc*rc*rc*rc;
rc6 = rc5 * rc;
cmi1 = param->cmn1;
cmi2 = param->cmn2;
cmj1 = param->cml1;
cmj2 = param->cml2;
rf5 = 1.0/r5 - 1.0/rc5 + 5.0*(r-rc)/rc6;
// field correction charge force
fqij = 1.0 * rf5 * (cmj1 + 2.0 * iq * cmj2);
fqjj = 1.0 * rf5 * (cmi1 + 2.0 * jq * cmi2);
}
/* ---------------------------------------------------------------------- */
void PairComb::qfo_short(Param *param, int i, int j, double rsq,
double iq, double jq, double &fqij, double &fqjj)
{
double r,tmp_fc,tmp_exp1,tmp_exp2;
double Asi,Asj,vrcs;
double romi = param->addrep,rrcs = param->bigr + param->bigd;
double qi,qj,Di,Dj,Bsi,Bsj;
double QUchi,QOchi,QUchj,QOchj,YYDiqp,YYDjqp;
double YYAsiqp,YYAsjqp,YYBsiqp,YYBsjqp;
double caj,cbj,bij,cfqr,cfqs;
double romie = param->romiga;
double romib = param->romigb;
double ca1,ca2,ca3,ca4;
double rslp,rslp2,rslp4,arr1,arr2,fc2j,fc3j;
qi = iq; qj = jq; r = sqrt(rsq);
Di = Dj = Asi = Asj = Bsi = Bsj = 0.0;
QUchi = QOchi = QUchj = QOchj = YYDiqp = YYDjqp =0.0;
YYAsiqp = YYAsjqp = YYBsiqp = YYBsjqp = 0.0;
caj = cbj = vrcs = cfqr = cfqs = 0.0;
tmp_fc = comb_fc(r,param);
tmp_exp1 = exp(-param->rlm1 * r);
tmp_exp2 = exp(-param->rlm2 * r);
bij = bbij[i][j]; //comb_bij(zeta_ij,param);
arr1 = 2.22850; arr2 = 1.89350;
fc2j = comb_fc2(r);
fc3j = comb_fc3(r);
vrcs = 0.0;
if (romi > 0.0) {
if (!cor_flag) vrcs = romi * pow((1.0-r/rrcs),2.0);
else if (cor_flag) {
rslp = ((arr1-r)/(arr1-arr2));
rslp2 = rslp * rslp; rslp4 = rslp2 * rslp2;
vrcs = fc2j * fc3j * romi * ((50.0*rslp4-30.0*rslp2+4.50))/8.0;
}
}
Di = param->DU1 + pow(fabs(param->bD1*(param->QU1-qi)),param->nD1);
Dj = param->DU2 + pow(fabs(param->bD2*(param->QU2-qj)),param->nD2);
Asi = param->biga1 * exp(param->lam11*Di);
Asj = param->biga2 * exp(param->lam12*Dj);
Bsi = param->bigb1 * exp(param->lam21*Di)*
(param->aB1-fabs(pow(param->bB1*(qi-param->Qo1),10.0)));
Bsj = param->bigb2 * exp(param->lam22*Dj)*
(param->aB2-fabs(pow(param->bB2*(qj-param->Qo2),10.0)));
QUchi = (param->QU1-qi)*param->bD1;
QUchj = (param->QU2-qj)*param->bD2;
QOchi = (qi-param->Qo1)*param->bB1;
QOchj = (qj-param->Qo2)*param->bB2;
if (QUchi == 0.0) YYDiqp = 0.0;
else YYDiqp = -param->nD1 * QUchi * param->bD1 *
pow(fabs(QUchi),(param->nD1-2.0));
if (QUchj == 0.0) YYDjqp = 0.0;
else YYDjqp = -param->nD2 * QUchj * param->bD2 *
pow(fabs(QUchj),(param->nD2-2.0));
YYAsiqp = Asi * param->lam11 * YYDiqp;
YYAsjqp = Asj * param->lam12 * YYDjqp;
if (QOchi == 0.0)
YYBsiqp=Bsi*param->lam21*YYDiqp;
else
YYBsiqp=Bsi*param->lam21*YYDiqp-param->bigb1*exp(param->lam21*Di)*
10.0*QOchi*param->bB1*pow(fabs(QOchi),(10.0-2.0));
if (QOchj == 0.0)
YYBsjqp=Bsj*param->lam22*YYDjqp;
else
YYBsjqp=Bsj*param->lam22*YYDjqp-param->bigb2*exp(param->lam22*Dj)*
10.0*QOchj*param->bB2*pow(fabs(QOchj),(10.0-2.0));
if (Asi > 0.0 && Asj > 0.0) caj = 1.0/(2.0*sqrt(Asi*Asj)) * romie;
else caj = 0.0;
if (Bsi > 0.0 && Bsj > 0.0) cbj = 1.0/(2.0*sqrt(Bsi*Bsj)) * romib ;
else cbj = 0.0;
cfqr = 0.50 * tmp_fc * (1.0 + vrcs); // 0.5 b/c full atom loop
cfqs = -0.50 * tmp_fc * bij;
ca1 = Asj * caj * YYAsiqp;
ca2 = Bsj * cbj * YYBsiqp;
ca3 = Asi * caj * YYAsjqp;
ca4 = Bsi * cbj * YYBsjqp;
fqij = cfqr * tmp_exp1 * ca1;
fqij += cfqs * tmp_exp2 * ca2;
fqjj = cfqr * tmp_exp1 * ca3;
fqjj += cfqs * tmp_exp2 * ca4;
}
/* ---------------------------------------------------------------------- */
void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
double &Eov, double &Fov)
{
double ECo,BCo,tmp_fc,tmp_fc_d;
double r = sqrt(rsq1);
int NCon = NCoi - 7;
tmp_fc = comb_fc(r,param);
tmp_fc_d = comb_fc(r,param);
Eov = 0.0; Fov = 0.0;
ECo = param->hfocor;
BCo = 0.1;
if (NCon >= 0.20) {
Eov = tmp_fc * ECo * NCon/(1.0+exp(BCo*NCon));
Fov = -(tmp_fc_d*Eov + tmp_fc*ECo/(1.0+exp(BCo*NCon)) -
(tmp_fc*ECo*NCon*BCo*exp(BCo*NCon)) /
((1.0+exp(BCo*NCon))*(1.0+exp(BCo*NCon))));
Fov /= r;
}
}
/* ---------------------------------------------------------------------- */
int PairComb::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++] = qf[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairComb::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n ;
for (i = first; i < last; i++) qf[i] = buf[m++];
}
/* ---------------------------------------------------------------------- */
int PairComb::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++] = qf[i];
return m;
}
/* ---------------------------------------------------------------------- */
void PairComb::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
qf[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void PairComb::Short_neigh()
{
int nj;
int inum,jnum,i,j,ii,jj;
int *neighptrj,*ilist,*jlist,*numneigh;
int **firstneigh;
double xtmp,ytmp,ztmp,rsq,delrj[3];
double **x = atom->x;
if (atom->nmax > nmax) {
memory->sfree(sht_first);
nmax = atom->nmax;
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
"pair:sht_first");
memory->grow(sht_num,nmax,"pair:sht_num");
memory->grow(NCo,nmax,"pair:NCo");
memory->grow(bbij,nmax,MAXNEIGH,"pair:bbij");
}
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// create Comb neighbor list
ipage->reset();
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
nj = 0;
neighptrj = ipage->vget();
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;
delrj[0] = xtmp - x[j][0];
delrj[1] = ytmp - x[j][1];
delrj[2] = ztmp - x[j][2];
rsq = vec3_dot(delrj,delrj);
if (rsq > cutmin) continue;
neighptrj[nj++] = j;
}
sht_first[i] = neighptrj;
sht_num[i] = nj;
ipage->vgot(nj);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairComb::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
bytes += nmax * sizeof(int);
bytes += nmax * sizeof(int *);
for (int i = 0; i < comm->nthreads; i++)
bytes += ipage[i].size();
bytes += nmax * sizeof(int);
bytes += MAXNEIGH*nmax * sizeof(double);
return bytes;
}

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