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lammps/src/MANYBODY/pair_polymorphic.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: Reese Jones, Xiaowang Zhou (SNL)
This modifies from pair_tersoff.cpp by Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_polymorphic.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairPolymorphic::PairPolymorphic(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
one_coeff = 1;
nelements = 0;
elements = NULL;
pairParameters = NULL;
tripletParameters = NULL;
elem2param = NULL;
elem3param = NULL;
map = NULL;
epsilon = 0.0;
neighsize = 0;
firstneighV = NULL;
firstneighW = NULL;
firstneighW1 = NULL;
delxV = NULL;
delyV = NULL;
delzV = NULL;
drV = NULL;
delxW = NULL;
delyW = NULL;
delzW = NULL;
drW = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairPolymorphic::~PairPolymorphic()
{
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] match;
memory->destroy(pairParameters);
memory->destroy(tripletParameters);
memory->destroy(elem2param);
memory->destroy(elem3param);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
delete [] firstneighV;
delete [] firstneighW;
delete [] firstneighW1;
delete [] delxV;
delete [] delyV;
delete [] delzV;
delete [] drV;
delete [] delxW;
delete [] delyW;
delete [] delzW;
delete [] drW;
}
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::compute(int eflag, int vflag)
{
tagint itag,jtag;
int i,j,k,ii,jj,kk,kk1,inum,jnum;
int itype,jtype,ktype;
int iparam_ii,iparam_jj,iparam_kk,iparam_ij,iparam_ik,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r0,r1,r2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double zeta_ij,prefactor,wfac,pfac,gfac,fa,fa_d,bij,bij_d;
double costheta;
int *ilist,*jlist,*numneigh,**firstneigh;
double emb;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = vflag_atom = 0;
double **x = atom->x;
double **f = atom->f;
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;
// 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];
jlist = firstneigh[i];
jnum = numneigh[i];
if (neighsize < jnum) {
delete [] firstneighV;
delete [] delxV;
delete [] delyV;
delete [] delzV;
delete [] drV;
delete [] firstneighW;
delete [] delxW;
delete [] delyW;
delete [] delzW;
delete [] drW;
delete [] firstneighW1;
neighsize = jnum + 20;
firstneighV = new int[neighsize];
delxV = new double[neighsize];
delyV = new double[neighsize];
delzV = new double[neighsize];
drV = new double[neighsize];
firstneighW = new int[neighsize];
delxW = new double[neighsize];
delyW = new double[neighsize];
delzW = new double[neighsize];
drW = new double[neighsize];
firstneighW1 = new int[neighsize];
}
if (eta) {
iparam_ii = elem2param[itype][itype];
PairParameters & p = pairParameters[iparam_ii];
emb = (p.F)->get_vmax();
}
numneighV = -1;
numneighW = -1;
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 >= cutmaxsq) continue;
r0 = sqrt(rsq);
iparam_ij = elem2param[itype][jtype];
PairParameters & p = pairParameters[iparam_ij];
// do not include the neighbor if get_vmax() <= epsilon because the function is near zero
if (eta) {
if (emb > epsilon) {
iparam_jj = elem2param[jtype][jtype];
PairParameters & q = pairParameters[iparam_jj];
if (rsq < (q.W)->get_xmaxsq() && (q.W)->get_vmax() > epsilon) {
numneighW = numneighW + 1;
firstneighW[numneighW] = j;
delxW[numneighW] = delx;
delyW[numneighW] = dely;
delzW[numneighW] = delz;
drW[numneighW] = r0;
}
}
} else {
if ((p.F)->get_vmax() > epsilon) {
if (rsq < (p.V)->get_xmaxsq() && (p.V)->get_vmax() > epsilon) {
numneighV = numneighV + 1;
firstneighV[numneighV] = j;
delxV[numneighV] = delx;
delyV[numneighV] = dely;
delzV[numneighV] = delz;
drV[numneighV] = r0;
}
if (rsq < (p.W)->get_xmaxsq() && (p.W)->get_vmax() > epsilon) {
numneighW = numneighW + 1;
firstneighW[numneighW] = j;
delxW[numneighW] = delx;
delyW[numneighW] = dely;
delzW[numneighW] = delz;
drW[numneighW] = r0;
}
}
}
// two-body interactions, skip half of them
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;
}
if (rsq >= (p.U)->get_xmaxsq() || (p.U)->get_vmax() <= epsilon) continue;
(p.U)->value(r0,evdwl,eflag,fpair,1);
fpair = -fpair/r0;
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);
}
if (eta) {
if (emb > epsilon) {
iparam_ii = elem2param[itype][itype];
PairParameters & p = pairParameters[iparam_ii];
// accumulate bondorder zeta for each i-j interaction via loop over k
zeta_ij = 0.0;
for (kk = 0; kk <= numneighW; kk++) {
k = firstneighW[kk];
ktype = map[type[k]];
iparam_kk = elem2param[ktype][ktype];
PairParameters & q = pairParameters[iparam_kk];
(q.W)->value(drW[kk],wfac,1,fpair,0);
zeta_ij += wfac;
}
// pairwise force due to zeta
(p.F)->value(zeta_ij,bij,1,bij_d,1);
prefactor = 0.5* bij_d;
if (eflag) evdwl = -0.5*bij;
if (evflag) ev_tally(i,i,nlocal,newton_pair,evdwl,0.0,0.0,delx,dely,delz);
// attractive term via loop over k
for (kk = 0; kk <= numneighW; kk++) {
k = firstneighW[kk];
ktype = map[type[k]];
delr2[0] = -delxW[kk];
delr2[1] = -delyW[kk];
delr2[2] = -delzW[kk];
iparam_kk = elem2param[ktype][ktype];
PairParameters & q = pairParameters[iparam_kk];
(q.W)->value(drW[kk],wfac,0,fpair,1);
fpair = -prefactor*fpair/drW[kk];
f[i][0] += delr2[0]*fpair;
f[i][1] += delr2[1]*fpair;
f[i][2] += delr2[2]*fpair;
f[k][0] -= delr2[0]*fpair;
f[k][1] -= delr2[1]*fpair;
f[k][2] -= delr2[2]*fpair;
if (vflag_atom) v_tally2(i, k, -fpair, delr2);
}
}
} else {
for (jj = 0; jj <= numneighV; jj++) {
j = firstneighV[jj];
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype];
PairParameters & p = pairParameters[iparam_ij];
delr1[0] = -delxV[jj];
delr1[1] = -delyV[jj];
delr1[2] = -delzV[jj];
r1 = drV[jj];
// accumulate bondorder zeta for each i-j interaction via loop over k
zeta_ij = 0.0;
numneighW1 = -1;
for (kk = 0; kk <= numneighW; kk++) {
k = firstneighW[kk];
if (j == k) continue;
ktype = map[type[k]];
iparam_ijk = elem3param[jtype][itype][ktype];
TripletParameters & trip = tripletParameters[iparam_ijk];
if ((trip.G)->get_vmax() <= epsilon) continue;
numneighW1 = numneighW1 + 1;
firstneighW1[numneighW1] = kk;
delr2[0] = -delxW[kk];
delr2[1] = -delyW[kk];
delr2[2] = -delzW[kk];
r2 = drW[kk];
costheta = (delr1[0]*delr2[0] + delr1[1]*delr2[1] +
delr1[2]*delr2[2]) / (r1*r2);
iparam_ik = elem2param[itype][ktype];
PairParameters & q = pairParameters[iparam_ik];
(q.W)->value(r2,wfac,1,fpair,0);
(q.P)->value(r1-(p.xi)*r2,pfac,1,fpair,0);
(trip.G)->value(costheta,gfac,1,fpair,0);
zeta_ij += wfac*pfac*gfac;
}
// pairwise force due to zeta
(p.V)->value(r1,fa,1,fa_d,1);
(p.F)->value(zeta_ij,bij,1,bij_d,1);
fpair = -0.5*bij*fa_d / r1;
prefactor = 0.5* fa * bij_d;
if (eflag) evdwl = -0.5*bij*fa;
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
for (kk1 = 0; kk1 <= numneighW1; kk1++) {
kk = firstneighW1[kk1];
k = firstneighW[kk];
ktype = map[type[k]];
iparam_ijk = elem3param[jtype][itype][ktype];
TripletParameters & trip = tripletParameters[iparam_ijk];
delr2[0] = -delxW[kk];
delr2[1] = -delyW[kk];
delr2[2] = -delzW[kk];
r2 = drW[kk];
iparam_ik = elem2param[itype][ktype];
PairParameters & q = pairParameters[iparam_ik];
attractive(&q,&trip,prefactor,r1,r2,delr1,delr2,fi,fj,fk);
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::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];
neighsize = 40;
firstneighV = new int[neighsize];
delxV = new double[neighsize];
delyV = new double[neighsize];
delzV = new double[neighsize];
drV = new double[neighsize];
firstneighW = new int[neighsize];
delxW = new double[neighsize];
delyW = new double[neighsize];
delzW = new double[neighsize];
drW = new double[neighsize];
firstneighW1 = new int[neighsize];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPolymorphic::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPolymorphic::coeff(int narg, char **arg)
{
int i,j,n;
if (!allocated) allocate();
if (narg == 4 + atom->ntypes) {
narg--;
epsilon = atof(arg[narg]);
} else 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();
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
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 PairPolymorphic::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style polymorphic requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style polymorphic requires newton pair on");
// need a full neighbor list
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPolymorphic::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::read_file(char *file)
{
char line[MAXLINE],*ptr;
int n;
// open file on proc 0
FILE *fp=NULL;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open polymorphic potential file %s",file);
error->one(FLERR,str);
}
// move past comments to first data line
fgets(line,MAXLINE,fp);
while (line == strchr(line,'#')) fgets(line,MAXLINE,fp);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
ptr = strtok(line," \t\n\r\f"); // 1st line, 1st token
int ntypes = atoi(ptr);
if (ntypes != nelements)
error->all(FLERR,"Incorrect number of elements in potential file");
match = new int[nelements];
ptr = strtok(NULL," \t\n\r\f"); // 1st line, 2nd token
eta = (atoi(ptr)>0) ? true:false;
// map the elements in the potential file to LAMMPS atom types
for (int i = 0; i < nelements; i++) {
if (comm->me == 0) {
fgets(line,MAXLINE,fp);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
ptr = strtok(line," \t\n\r\f"); // 1st token
ptr = strtok(NULL," \t\n\r\f"); // 2st token
ptr = strtok(NULL," \t\n\r\f"); // 3st token
int j;
for (j = 0; j < nelements; j++) {
if (strcmp(ptr,elements[j]) == 0) break;
}
if (j == nelements)
error->all(FLERR,"Element not defined in potential file");
match[i] = j;
}
// sizes
if (comm->me == 0) {
fgets(line,MAXLINE,fp);
n = strlen(line) + 1;
}
// Note: the format of this line has changed between the
// 2015-06-06 and 2015-12-09 versions of the pair style.
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
nr = ng = nx = 0;
ptr = strtok(line," \t\n\r\f"); // 1st token
if (ptr) nr = atoi(ptr);
ptr = strtok(NULL," \t\n\r\f"); // 2nd token
if (ptr) ng = atoi(ptr);
ptr = strtok(NULL," \t\n\r\f"); // 3rd token
if (ptr) nx = atoi(ptr);
ptr = strtok(NULL," \t\n\r\f"); // 4th token
if (ptr) maxX = atof(ptr);
if (ptr == NULL)
error->all(FLERR,"Potential file incompatible with this pair style version");
if ((ng == 0) || (nr == 0) || (nx == 0))
error->all(FLERR,"Error reading potential file header");
npair = nelements*(nelements+1)/2;
ntriple = nelements*nelements*nelements;
pairParameters = (PairParameters*)
memory->srealloc(pairParameters,npair*sizeof(PairParameters),
"pair:pairParameters");
tripletParameters = (TripletParameters*)
memory->srealloc(tripletParameters,ntriple*sizeof(TripletParameters),
"pair:tripletParameters");
// cutoffs
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
fgets(line,MAXLINE,fp);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
ptr = strtok(line," \t\n\r\f"); // 1st token
p.cut = atof(ptr);
p.cutsq = p.cut*p.cut;
ptr = strtok(NULL," \t\n\r\f"); // 2nd token
p.xi = (atoi(ptr)>0) ? true:false;
}
// set cutmax to max of all params
cutmax = 0.0;
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
if (p.cut > cutmax) cutmax = p.cut;
}
cutmaxsq = cutmax*cutmax;
// start reading tabular functions
double * singletable = new double[nr];
for (int i = 0; i < npair; i++) { // U
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
grab(fp,nr,singletable);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.U = new tabularFunction(nr,0.0,p.cut);
(p.U)->set_values(nr,0.0,p.cut,singletable,epsilon);
}
for (int i = 0; i < npair; i++) { // V
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
grab(fp,nr,singletable);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.V = new tabularFunction(nr,0.0,p.cut);
(p.V)->set_values(nr,0.0,p.cut,singletable,epsilon);
}
for (int i = 0; i < npair; i++) { // W
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
grab(fp,nr,singletable);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.W = new tabularFunction(nr,0.0,p.cut);
(p.W)->set_values(nr,0.0,p.cut,singletable,epsilon);
}
for (int i = 0; i < npair; i++) { // P
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
grab(fp,nr,singletable);
}
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.P = new tabularFunction(nr,-cutmax,cutmax);
(p.P)->set_values(nr,-cutmax,cutmax,singletable,epsilon);
}
delete[] singletable;
singletable = new double[ng];
for (int i = 0; i < ntriple; i++) { // G
TripletParameters & p = tripletParameters[i];
if (comm->me == 0) {
grab(fp,ng,singletable);
}
MPI_Bcast(singletable,ng,MPI_DOUBLE,0,world);
p.G = new tabularFunction(ng,-1.0,1.0);
(p.G)->set_values(ng,-1.0,1.0,singletable,epsilon);
}
delete[] singletable;
singletable = new double[nx];
for (int i = 0; i < npair; i++) { // F
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
grab(fp,nx,singletable);
}
MPI_Bcast(singletable,nx,MPI_DOUBLE,0,world);
p.F = new tabularFunction(nx,0.0,maxX);
(p.F)->set_values(nx,0.0,maxX,singletable,epsilon);
}
delete[] singletable;
if (comm->me == 0) {
fclose(fp);
}
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::setup_params()
{
int i,j,k,n;
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,"pair:elem2param");
memory->destroy(elem3param);
memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param");
// map atom pair to parameter index
n = 0;
for (i = 0; i < nelements; i++) {
elem2param[match[i]][match[i]] = n;
n++;
}
for (i = 0; i < nelements-1; i++) {
for (j = i+1; j < nelements; j++) {
elem2param[match[i]][match[j]] = n;
elem2param[match[j]][match[i]] = n;
n++;
}
}
// map atom triplet to parameter index
n = 0;
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
elem3param[match[i]][match[j]][match[k]] = n;
n++;
}
// for debugging, call write_tables() to check the tabular functions
// if (comm->me == 0) {
// write_tables(51);
// errorX->all(FLERR,"Test potential tables");
// }
}
/* ----------------------------------------------------------------------
attractive term
------------------------------------------------------------------------- */
void PairPolymorphic::attractive(PairParameters *p, TripletParameters *trip,
double prefactor, double rij, double rik,
double *delrij, double *delrik,
double *fi, double *fj, double *fk)
{
double rij_hat[3],rik_hat[3];
double rijinv,rikinv;
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,p,trip);
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::ters_zetaterm_d(double prefactor,
double *rij_hat, double rij,
double *rik_hat, double rik,
double *dri, double *drj, double *drk,
PairParameters *p, TripletParameters *trip)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta;
double dcosdri[3],dcosdrj[3],dcosdrk[3];
cos_theta = vec3_dot(rij_hat,rik_hat);
(p->W)->value(rik,fc,1,dfc,1);
(p->P)->value(rij-(p->xi)*rik,ex_delr,1,ex_delr_d,1);
(trip->G)->value(cos_theta,gijk,1,gijk_d,1);
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);
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 PairPolymorphic::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);
}
/* ----------------------------------------------------------------------
* grab n values from file fp and put them in list
* values can be several to a line
* only called by proc 0
* ------------------------------------------------------------------------- */
void PairPolymorphic::grab(FILE *fp, int n, double *list)
{
char *ptr;
char line[MAXLINE];
int i = 0;
while (i < n) {
fgets(line,MAXLINE,fp);
ptr = strtok(line," \t\n\r\f");
list[i++] = atof(ptr);
while ((ptr = strtok(NULL," \t\n\r\f")))
list[i++] = atof(ptr);
}
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::write_tables(int npts)
{
char tag[6] = "";
if (comm->me != 0) sprintf(tag,"%d",comm->me);
FILE* fp = NULL;
double xmin,xmax,x,uf,vf,wf,pf,gf,ff,ufp,vfp,wfp,pfp,gfp,ffp;
char line[MAXLINE];
for (int i = 0; i < nelements; i++) {
for (int j = 0; j < nelements; j++) {
strcpy(line,elements[i]);
strcat(line,elements[j]);
strcat(line,"_UVW");
strcat(line,tag);
fp = fopen(line, "w");
int iparam_ij = elem2param[i][j];
PairParameters & pair = pairParameters[iparam_ij];
xmin = (pair.U)->get_xmin();
xmax = (pair.U)->get_xmax();
double xl = xmax - xmin;
xmin = xmin - 0.5*xl;
xmax = xmax + 0.5*xl;
for (int k = 0; k < npts; k++) {
x = xmin + (xmax-xmin) * k / (npts-1);
(pair.U)->value(x, uf, 1, ufp, 1);
(pair.V)->value(x, vf, 1, vfp, 1);
(pair.W)->value(x, wf, 1, wfp, 1);
fprintf(fp,"%12.4f %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f \n",x,uf,vf,wf,ufp,vfp,wfp);
}
fclose(fp);
}
}
for (int i = 0; i < nelements; i++) {
for (int j = 0; j < nelements; j++) {
strcpy(line,elements[i]);
strcat(line,elements[j]);
strcat(line,"_P");
strcat(line,tag);
fp = fopen(line, "w");
int iparam_ij = elem2param[i][j];
PairParameters & pair = pairParameters[iparam_ij];
xmin = (pair.P)->get_xmin();
xmax = (pair.P)->get_xmax();
double xl = xmax - xmin;
xmin = xmin - 0.5*xl;
xmax = xmax + 0.5*xl;
for (int k = 0; k < npts; k++) {
x = xmin + (xmax-xmin) * k / (npts-1);
(pair.P)->value(x, pf, 1, pfp, 1);
fprintf(fp,"%12.4f %12.4f %12.4f \n",x,pf,pfp);
}
fclose(fp);
}
}
for (int i = 0; i < nelements; i++) {
for (int j = 0; j < nelements; j++) {
for (int k = 0; k < nelements; k++) {
strcpy(line,elements[i]);
strcat(line,elements[j]);
strcat(line,elements[k]);
strcat(line,"_G");
strcat(line,tag);
fp = fopen(line, "w");
int iparam_ij = elem3param[i][j][k];
TripletParameters & pair = tripletParameters[iparam_ij];
xmin = (pair.G)->get_xmin();
xmax = (pair.G)->get_xmax();
for (int n = 0; n < npts; n++) {
x = xmin + (xmax-xmin) * n / (npts-1);
(pair.G)->value(x, gf, 1, gfp, 1);
fprintf(fp,"%12.4f %12.4f %12.4f \n",x,gf,gfp);
}
fclose(fp);
}
}
}
for (int i = 0; i < nelements; i++) {
for (int j = 0; j < nelements; j++) {
strcpy(line,elements[i]);
strcat(line,elements[j]);
strcat(line,"_F");
strcat(line,tag);
fp = fopen(line, "w");
int iparam_ij = elem2param[i][j];
PairParameters & pair = pairParameters[iparam_ij];
xmin = (pair.F)->get_xmin();
xmax = (pair.F)->get_xmax();
double xl = xmax - xmin;
xmin = xmin - 0.5*xl;
xmax = xmax + 0.5*xl;
for (int k = 0; k < npts; k++) {
x = xmin + (xmax-xmin) * k / (npts-1);
(pair.F)->value(x, ff, 1, ffp, 1);
fprintf(fp,"%12.4f %12.4f %12.4f \n",x,ff,ffp);
}
fclose(fp);
}
}
}
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