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2a9c607da1dfbc3e023bee7c3d6bfce0737dd2b2
lammps/src/MANYBODY/pair_polymorphic.cpp
Axel Kohlmeyer 2a9c607da1 fix typo
2015-08-14 22:46:45 -04:00

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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 authors: Xiaowang Zhou, Reese Jones (SNL)
Based on pair_tersoff 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;
}
/* ----------------------------------------------------------------------
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;
memory->destroy(pairParameters);
memory->destroy(tripletParameters);
memory->destroy(elem2param);
memory->destroy(elem3param);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] type_map;
}
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::compute(int eflag, int vflag)
{
tagint itag,jtag;
int i,j,k,ii,jj,kk,inum,jnum;
int iel,jel,kel,iparam_ij,iparam_ik,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2,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;
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];
iel = type_map[type[i]];
if (iel < 0) continue;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// two-body interactions, skip half of them
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;
}
jel = type_map[type[j]];
if (jel < 0) continue;
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[iel][jel];
PairParameters & p = pairParameters[iparam_ij];
if (rsq > p.cutsq) continue;
r0 = sqrt(rsq);
if (eflag) evdwl = (p.U)->value(r0);
fpair = (p.U)->derivative(r0);
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) {
iparam_ij = elem2param[iel][iel];
PairParameters & p = pairParameters[iparam_ij];
// accumulate bondorder zeta for each i-j interaction via loop over k
zeta_ij = 0.0;
for (kk = 0; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
kel = type_map[type[k]];
if (kel < 0) continue;
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
iparam_ik = elem2param[kel][kel];
PairParameters & q = pairParameters[iparam_ik];
if (rsq2 > q.cutsq) continue;
r2 = sqrt(rsq2);
wfac = (q.W)->value(r2);
zeta_ij += wfac;
}
// pairwise force due to zeta
bij = (p.F)->value(zeta_ij);
bij_d = (p.F)->derivative(zeta_ij);
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,-delr1[0],-delr1[1],-delr1[2]);
// attractive term via loop over k
for (kk = 0; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
kel = type_map[type[k]];
if (kel < 0) continue;
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
iparam_ik = elem2param[kel][kel];
PairParameters & q = pairParameters[iparam_ik];
if (rsq2 > q.cutsq) continue;
r2 = sqrt(rsq2);
fpair = (q.W)->derivative(r2);
fpair = -prefactor*fpair/r2;
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 {
// three-body interactions
// skip immediately if I-J is not within cutoff
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jel = type_map[type[j]];
if (jel < 0) continue;
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
iparam_ij = elem2param[iel][jel];
PairParameters & p = pairParameters[iparam_ij];
if (rsq1 > p.cutsq) continue;
r1 = sqrt(rsq1);
// accumulate bondorder zeta for each i-j interaction via loop over k
zeta_ij = 0.0;
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
kel = type_map[type[k]];
if (kel < 0) continue;
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
iparam_ik = elem2param[iel][kel];
PairParameters & q = pairParameters[iparam_ik];
if (rsq2 > q.cutsq) continue;
r2 = sqrt(rsq2);
costheta = (delr1[0]*delr2[0] + delr1[1]*delr2[1] +
delr1[2]*delr2[2]) / (r1*r2);
iparam_ijk = elem3param[jel][iel][kel];
TripletParameters & trip = tripletParameters[iparam_ijk];
wfac= (q.W)->value(r2);
pfac= (q.P)->value(r1-(p.xi)*r2);
gfac= (trip.G)->value(costheta);
zeta_ij += wfac*pfac*gfac;
}
// pairwise force due to zeta
fa = (p.V)->value(r1);
fa_d = (p.V)->derivative(r1);
bij = (p.F)->value(zeta_ij);
bij_d = (p.F)->derivative(zeta_ij);
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 (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
kel = type_map[type[k]];
if (kel < 0) continue;
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
iparam_ik = elem2param[iel][kel];
PairParameters & q = pairParameters[iparam_ik];
if (rsq2 > q.cutsq) continue;
r2 = sqrt(rsq2);
iparam_ijk = elem3param[jel][iel][kel];
TripletParameters & trip = tripletParameters[iparam_ijk];
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");
type_map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPolymorphic::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
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::setup()
{
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, as read from potential file
n = 0;
for (i = 0; i < nelements; i++) { // note self first
elem2param[i][i] = n;
n++;
}
for (i = 0; i < nelements; i++)
for (j = i+1; j < nelements; j++) {
elem2param[i][j] = n;
elem2param[j][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[i][j][k] = n;
n++;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPolymorphic::coeff(int narg, char **arg)
{
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 type_map atom types to elements in potential file
int ntypes = atom->ntypes;
// type_map = atom type to element in potential file
if (type_map) { delete [] type_map; }
type_map = new int[ntypes+1];
for (int i = 0; i < ntypes+1; i++) {
type_map[i] = -1;
}
// elements = list of requested element names (ntypes long)
char** elements = new char*[ntypes];
for (int i = 0; i < ntypes; i++) { elements[i] = NULL; }
// parse and store
for (int i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") != 0) {
int n = strlen(arg[i]) + 1;
elements[i-3] = new char[n];
strcpy(elements[i-3],arg[i]);
}
}
// read potential file and initialize potential parameters
read_file(arg[2],elements);
setup();
if (elements)
for (int i = 0; i < ntypes; i++)
if (elements[i]) delete [] elements[i];
delete [] elements;
// clear setflag since coeff() called once with I,J = * *
int 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 type_mapped to elements
int count = 0;
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
if ((type_map[i] > -1) && (type_map[j] > -1)) {
setflag[i][j] = 1;
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::read_file(char *file, char** elements)
{
char line[MAXLINE],*ptr, ftype[MAXLINE];
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 : nelements
nelements = atoi(ptr); // number of elements in potential file
ptr = strtok(NULL," \t\n\r\f"); // 1st line, 2nd token : indicator eta
eta = (atoi(ptr)>0) ? true:false;
if (comm->me == 0) { printf("%d elements in: %s,",nelements,file); }
// type_map the elements in the potential file to LAMMPS atom types
for (int i = 0; i < nelements; i++) {
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token atomic number
ptr = strtok(NULL," \t\n\r\f"); // 2st token atomic mass
ptr = strtok(NULL," \t\n\r\f"); // 3st token atomic symbol
if (comm->me == 0) { printf(" %s",ptr); }
int j = 0;
for (j = 0; j < atom->ntypes; j++) {
if (elements[j] && strcmp(ptr,elements[j]) == 0) {
type_map[j+1] = i;
if (comm->me == 0) { printf("=%d ",j+1); }
break;
}
}
if (j == nelements)
error->all(FLERR,"Element not defined in potential file");
}
if (comm->me == 0) { printf("\n"); }
// size
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");
// pairwise cutoffs
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token: cutoff
p.cut = atof(ptr);
p.cutsq = p.cut*p.cut;
ptr = strtok(NULL," \t\n\r\f"); // 2nd token: indicator xi
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;
}
// start reading functions
for (int i = 0; i < npair; i++) { // U
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
p.U = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // V
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
p.V = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // W
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
p.W = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // P
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
p.P = create_function(ftype,fp);
}
for (int i = 0; i < ntriple; i++) { // G
TripletParameters & p = tripletParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
p.G = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // F
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
p.F = create_function(ftype,fp);
}
if (comm->me == 0) { fclose(fp); }
}
/* ---------------------------------------------------------------------- */
C1function * PairPolymorphic::create_function(char* ftype, FILE* fp)
{
char * ptr;
if (strcmp(ftype,"spline")==0) { // N, min, max, values
C1tabularFunction * f = new C1tabularFunction();
ptr = strtok(NULL," \t\n\r\f");
int n = atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
double xmin = atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
double xmax = atof(ptr);
double * table = new double[n];
read_array(fp,n,table);
f->set_values(n,xmin,xmax,table);
delete [] table;
return f;
}
else if (strcmp(ftype,"constant") == 0) {
ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
return new C1constant(c);
}
else if (strcmp(ftype,"exponential") == 0) {
ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
double lambda = atof(ptr);
return new C1exponential(c,lambda);
}
else if (strcmp(ftype,"sine") == 0) {
ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
double w = atof(ptr);
return new C1sine(c,w);
}
else if (strcmp(ftype,"cosine") == 0) {
ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
ptr = strtok(NULL," \t\n\r\f");
double w = atof(ptr);
return new C1cosine(c,w);
}
else { error->all(FLERR,"unknown function type"); }
return NULL;
}
/* ---------------------------------------------------------------------- */
void PairPolymorphic::read_line(FILE *fp, char *line)
{
int n = 0;
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);
}
void PairPolymorphic::read_array(FILE *fp, int n, double *list)
{
if (comm->me == 0) {
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);
}
}
MPI_Bcast(list,n,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
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);
fc = (p->W)->value(rik);
dfc = (p->W)->derivative(rik);
ex_delr = (p->P)->value(rij-(p->xi)*rik);
ex_delr_d = (p->P)->derivative(rij-(p->xi)*rik);
gijk = (trip->G)->value(cos_theta);
gijk_d = (trip->G)->derivative(cos_theta);
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);
}
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