Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/MANYBODY/pair_bop.cpp
5fb8bad60e5dlammm-master-deprecated

Last Change
Raw File

pair_bop.cpp
View Options

/* ----------------------------------------------------------------------
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: D.K. Ward (donward@sandia.gov) and X.W. Zhou (Sandia)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
The formulation for this work follows (a) D.G. Pettifor, et al., Mat.
Sci. and Eng. A365, 2-13, (2004);(b) D.A. Murdick, et al., Phys.
Rev. B 73, 045206 (2006);(c) D.G. Pettifor and I.I. Oleinik., Phys
Rev. Lett. 84, 4124 (2000); (d) D.K. Ward, et al., Phys. Rev. B 85,
115206 (2012).
Copyright (2012) Sandia Corporation. Under the terms of Contract DE-
AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
rights in this software.
pairbop v 1.0 comes with no warranty of any kind. pairbop v 1.0 is a
copyrighted code that is distributed free-of-charge, under the terms
of the GNU Public License (GPL). See "Open-Source
Rules"_http://lammps.sandia.gov/open_source.html
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <mpi.h>
#include "pair_bop.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include <ctype.h>
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define EPSILON 1.0e-6
/* ---------------------------------------------------------------------- */
PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
one_coeff = 1;
manybody_flag = 1;
ghostneigh = 1;
map = NULL;
pi_a = NULL;
pro_delta = NULL;
pi_delta = NULL;
pi_p = NULL;
pi_c = NULL;
r1 = NULL;
sigma_r0 = NULL;
pi_r0 = NULL;
phi_r0 = NULL;
sigma_rc = NULL;
pi_rc = NULL;
phi_rc = NULL;
sigma_beta0 = NULL;
pi_beta0 = NULL;
phi0 = NULL;
sigma_n = NULL;
pi_n = NULL;
phi_m = NULL;
sigma_nc = NULL;
pi_nc = NULL;
phi_nc = NULL;
pro = NULL;
sigma_delta = NULL;
sigma_c = NULL;
sigma_a = NULL;
sigma_f = NULL;
sigma_k = NULL;
small3 = NULL;
rcut = NULL;
rcut3 = NULL;
rcutsq = NULL;
rcutsq3 = NULL;
dr = NULL;
rdr = NULL;
dr3 = NULL;
rdr3 = NULL;
disij = NULL;
rij = NULL;
neigh_index = NULL;
neigh_index3 = NULL;
cosAng = NULL;
betaS = NULL;
dBetaS = NULL;
betaP = NULL;
dBetaP = NULL;
repul = NULL;
dRepul = NULL;
itypeSigBk = NULL;
itypePiBk = NULL;
pBetaS = NULL;
pBetaS1 = NULL;
pBetaS2 = NULL;
pBetaS3 = NULL;
pBetaS4 = NULL;
pBetaS5 = NULL;
pBetaS6 = NULL;
pLong = NULL;
pLong1 = NULL;
pLong2 = NULL;
pLong3 = NULL;
pLong4 = NULL;
pLong5 = NULL;
pLong6 = NULL;
pBetaP = NULL;
pBetaP1 = NULL;
pBetaP2 = NULL;
pBetaP3 = NULL;
pBetaP4 = NULL;
pBetaP5 = NULL;
pBetaP6 = NULL;
pRepul = NULL;
pRepul1 = NULL;
pRepul2 = NULL;
pRepul3 = NULL;
pRepul4 = NULL;
pRepul5 = NULL;
pRepul6 = NULL;
FsigBO = NULL;
FsigBO1 = NULL;
FsigBO2 = NULL;
FsigBO3 = NULL;
FsigBO4 = NULL;
FsigBO5 = NULL;
FsigBO6 = NULL;
rcmin = NULL;
rcmax = NULL;
rcmaxp = NULL;
setflag = NULL;
cutsq = NULL;
cutghost = NULL;
gfunc = NULL;
gfunc1 = NULL;
gfunc2 = NULL;
gfunc3 = NULL;
gfunc4 = NULL;
gfunc5 = NULL;
gfunc6 = NULL;
gpara = NULL;
bt_sg=NULL;
bt_pi=NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairBOP::~PairBOP()
{
if(allocated) {
memory_theta_destroy();
if (otfly==0) memory->destroy(cos_index);
delete [] map;
memory->destroy(BOP_index);
memory->destroy(BOP_total);
memory->destroy(BOP_index3);
memory->destroy(BOP_total3);
memory->destroy(rcut);
memory->destroy(rcut3);
memory->destroy(rcutsq);
memory->destroy(rcutsq3);
memory->destroy(dr);
memory->destroy(rdr);
memory->destroy(dr3);
memory->destroy(rdr3);
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cutghost);
memory->destroy(pBetaS);
memory->destroy(pBetaS1);
memory->destroy(pBetaS2);
memory->destroy(pBetaS3);
memory->destroy(pBetaS4);
memory->destroy(pBetaS5);
memory->destroy(pBetaS6);
memory->destroy(pLong);
memory->destroy(pLong1);
memory->destroy(pLong2);
memory->destroy(pLong3);
memory->destroy(pLong4);
memory->destroy(pLong5);
memory->destroy(pLong6);
memory->destroy(pBetaP);
memory->destroy(pBetaP1);
memory->destroy(pBetaP2);
memory->destroy(pBetaP3);
memory->destroy(pBetaP4);
memory->destroy(pBetaP5);
memory->destroy(pBetaP6);
memory->destroy(pRepul);
memory->destroy(pRepul1);
memory->destroy(pRepul2);
memory->destroy(pRepul3);
memory->destroy(pRepul4);
memory->destroy(pRepul5);
memory->destroy(pRepul6);
memory->destroy(FsigBO);
memory->destroy(FsigBO1);
memory->destroy(FsigBO2);
memory->destroy(FsigBO3);
memory->destroy(FsigBO4);
memory->destroy(FsigBO5);
memory->destroy(FsigBO6);
memory->destroy(pi_a);
memory->destroy(pro_delta);
memory->destroy(pi_delta);
memory->destroy(pi_p);
memory->destroy(pi_c);
memory->destroy(r1);
memory->destroy(pro);
memory->destroy(sigma_delta);
memory->destroy(sigma_c);
memory->destroy(sigma_a);
memory->destroy(sigma_f);
memory->destroy(sigma_k);
memory->destroy(small3);
memory->destroy(gfunc);
memory->destroy(gfunc1);
memory->destroy(gfunc2);
memory->destroy(gfunc3);
memory->destroy(gfunc4);
memory->destroy(gfunc5);
memory->destroy(gfunc6);
memory->destroy(gpara);
}
if(allocate_sigma) {
destroy_sigma();
}
if(allocate_pi) {
destroy_pi();
}
}
/* ---------------------------------------------------------------------- */
void PairBOP::compute(int eflag, int vflag)
{
int pass;
int i,j,ii,jj,iij,i12;
int inum,temp_ij,ks;
int nlisti;
int itype,jtype;
tagint i_tag,j_tag;
int *ilist,*iilist;
int **firstneigh;
double dpr1,ps;
double ftmp1,ftmp2,ftmp3,dE;
double dis_ij[3],rsq_ij,r_ij;
double betaS_ij,dBetaS_ij;
double betaP_ij,dBetaP_ij;
double repul_ij,dRepul_ij;
double value,dvalue;
double totE;
double rcut_min;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int cnt1;
MPI_Comm_rank(world,&me);
inum = list->inum;
ilist = list->ilist;
firstneigh = list->firstneigh;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// BOP Neighbor lists must be updated every timestep
maxnall=nall;
gneigh();
// For non on the fly calculations cos and derivatives
// are calculated in advance and stored
totE=0;
piB_0=0;
sigB_0=0;
for (ii = 0; ii < inum; ii++) {
i=ilist[ii];
f[i][0]=0;
f[i][1]=0;
f[i][2]=0;
}
for (ii = 0; ii < inum; ii++) {
i=ilist[ii];
i_tag=tag[i];
itype=map[type[i]]+1;
iilist=firstneigh[i];
nlisti=BOP_total[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
j_tag=tag[j];
jtype=map[type[j]]+1;
if(j_tag>=i_tag) {
sigB_0=sigmaBo(ii,jj);
piB_0=PiBo(ii,jj);
if(otfly==0) {
if(neigh_flag[temp_ij]) {
dpr1=(dRepul[temp_ij]-2.0*dBetaS[temp_ij]*sigB_0
-2.0*dBetaP[temp_ij]*piB_0)/rij[temp_ij];
ftmp1=dpr1*disij[0][temp_ij];
ftmp2=dpr1*disij[1][temp_ij];
ftmp3=dpr1*disij[2][temp_ij];
f[i][0]=f[i][0]+ftmp1;
f[i][1]=f[i][1]+ftmp2;
f[i][2]=f[i][2]+ftmp3;
f[j][0]=f[j][0]-ftmp1;
f[j][1]=f[j][1]-ftmp2;
f[j][2]=f[j][2]-ftmp3;
// add repulsive and bond order components to total energy
// (d) Eq.1
dE=-2.0*betaS[temp_ij]*sigB_0-2.0*betaP[temp_ij]*piB_0;
totE+=dE+repul[temp_ij];
if(evflag) {
ev_tally_full(i,repul[temp_ij],dE,0.0,0.0,0.0,0.0);
ev_tally_full(j,repul[temp_ij],dE,0.0,0.0,0.0,0.0);
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,-ftmp1,-ftmp2,-ftmp3,
disij[0][temp_ij],disij[1][temp_ij],disij[2][temp_ij]);
}
}
}
else {
if(itype==jtype)
iij=itype-1;
else if(itype<jtype)
iij=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
iij=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
dis_ij[0]=x[j][0]-x[i][0];
dis_ij[1]=x[j][1]-x[i][1];
dis_ij[2]=x[j][2]-x[i][2];
rsq_ij=dis_ij[0]*dis_ij[0]
+dis_ij[1]*dis_ij[1]
+dis_ij[2]*dis_ij[2];
r_ij=sqrt(rsq_ij);
if(r_ij<=rcut[iij]) {
ps=r_ij*rdr[iij]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ij=((pBetaS3[iij][ks-1]*ps+pBetaS2[iij][ks-1])*ps
+pBetaS1[iij][ks-1])*ps+pBetaS[iij][ks-1];
dBetaS_ij=(pBetaS6[iij][ks-1]*ps+pBetaS5[iij][ks-1])*ps
+pBetaS4[iij][ks-1];
betaP_ij=((pBetaP3[iij][ks-1]*ps+pBetaP2[iij][ks-1])*ps
+pBetaP1[iij][ks-1])*ps+pBetaP[iij][ks-1];
dBetaP_ij=(pBetaP6[iij][ks-1]*ps+pBetaP5[iij][ks-1])*ps
+pBetaP4[iij][ks-1];
repul_ij=((pRepul3[iij][ks-1]*ps+pRepul2[iij][ks-1])*ps
+pRepul1[iij][ks-1])*ps+pRepul[iij][ks-1];
dRepul_ij=(pRepul6[iij][ks-1]*ps+pRepul5[iij][ks-1])*ps
+pRepul4[iij][ks-1];
dpr1=(dRepul_ij-2.0*dBetaS_ij*sigB_0
-2.0*dBetaP_ij*piB_0)/r_ij;
ftmp1=dpr1*dis_ij[0];
ftmp2=dpr1*dis_ij[1];
ftmp3=dpr1*dis_ij[2];
f[i][0]=f[i][0]+ftmp1;
f[i][1]=f[i][1]+ftmp2;
f[i][2]=f[i][2]+ftmp3;
f[j][0]=f[j][0]-ftmp1;
f[j][1]=f[j][1]-ftmp2;
f[j][2]=f[j][2]-ftmp3;
// add repulsive and bond order components to total energy
// (d) Eq. 1
dE=-2.0*betaS_ij*sigB_0-2.0*betaP_ij*piB_0;
totE+=dE+repul_ij;
if(evflag) {
ev_tally_full(i,repul_ij,dE,0.0,0.0,0.0,0.0);
ev_tally_full(j,repul_ij,dE,0.0,0.0,0.0,0.0);
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,-ftmp1,-ftmp2,-ftmp3,
dis_ij[0],dis_ij[1],dis_ij[2]);
}
}
}
}
}
}
cnt1=0;
rcut_min=10000;
for (ii = 0; ii < inum; ii++) {
i=ilist[ii];
i_tag=tag[i];
itype=map[type[i]]+1;
iilist=firstneigh[i];
nlisti=BOP_total3[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index3[i]+jj;
j=iilist[neigh_index3[temp_ij]];
j_tag=tag[j];
if(i_tag < j_tag) {
jtype=map[type[j]]+1;
pass=0;
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
i12=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
i12=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
dis_ij[0]=x[j][0]-x[i][0];
dis_ij[1]=x[j][1]-x[i][1];
dis_ij[2]=x[j][2]-x[i][2];
r_ij=sqrt(dis_ij[0]*dis_ij[0]+dis_ij[1]*dis_ij[1]+dis_ij[2]*dis_ij[2]);
if(r_ij<rcut_min) {
rcut_min=r_ij;
}
if(r_ij<=rcut3[i12])
pass=1;
if(pass==1) {
ps=r_ij*rdr3[i12]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
value=((pLong3[i12][ks-1]*ps+pLong2[i12][ks-1])*ps+
pLong1[i12][ks-1])*ps+pLong[i12][ks-1];
if(value<=0.0) value=pLong[i12][ks-1];
dvalue=(pLong6[i12][ks-1]*ps+
pLong5[i12][ks-1])*ps+pLong4[i12][ks-1];
dpr1=-dvalue/r_ij;
ftmp1=dpr1*dis_ij[0];
ftmp2=dpr1*dis_ij[1];
ftmp3=dpr1*dis_ij[2];
f[i][0]=f[i][0]+ftmp1;
f[i][1]=f[i][1]+ftmp2;
f[i][2]=f[i][2]+ftmp3;
f[j][0]=f[j][0]-ftmp1;
f[j][1]=f[j][1]-ftmp2;
f[j][2]=f[j][2]-ftmp3;
totE=totE-value;
if(evflag) {
ev_tally_full(i,0,-value,0.0,0.0,0.0,0.0);
ev_tally_full(j,0,-value,0.0,0.0,0.0,0.0);
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,-ftmp1,-ftmp2,-ftmp3,
dis_ij[0],dis_ij[1],dis_ij[2]);
}
cnt1++;
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
bop_step = 1;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBOP::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(rcut,npairs,"BOP:rcut");
memory->create(rcut3,npairs,"BOP:rcut3");
memory->create(rcutsq,npairs,"BOP:rcutsq");
memory->create(rcutsq3,npairs,"BOP:rcutsq3");
memory->create(dr,npairs,"BOP:dr");
memory->create(rdr,npairs,"BOP:dr");
memory->create(dr3,npairs,"BOP:dr");
memory->create(rdr3,npairs,"BOP:dr");
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cutghost,n+1,n+1,"pair:cutghost");
memory->create(pBetaS,npairs,nr,"BOP:pBetaS");
memory->create(pBetaS1,npairs,nr,"BOP:pBetaS1");
memory->create(pBetaS2,npairs,nr,"BOP:pBetaS2");
memory->create(pBetaS3,npairs,nr,"BOP:pBetaS3");
memory->create(pBetaS4,npairs,nr,"BOP:pBetaS4");
memory->create(pBetaS5,npairs,nr,"BOP:pBetaS5");
memory->create(pBetaS6,npairs,nr,"BOP:pBetaS6");
memory->create(pLong,npairs,nr,"BOP:pLong");
memory->create(pLong1,npairs,nr,"BOP:pLong");
memory->create(pLong2,npairs,nr,"BOP:pLong");
memory->create(pLong3,npairs,nr,"BOP:pLong");
memory->create(pLong4,npairs,nr,"BOP:pLong");
memory->create(pLong5,npairs,nr,"BOP:pLong");
memory->create(pLong6,npairs,nr,"BOP:pLong");
memory->create(pBetaP,npairs,nr,"BOP:pBetaP");
memory->create(pBetaP1,npairs,nr,"BOP:pBetaP1");
memory->create(pBetaP2,npairs,nr,"BOP:pBetaP2");
memory->create(pBetaP3,npairs,nr,"BOP:pBetaP3");
memory->create(pBetaP4,npairs,nr,"BOP:pBetaP4");
memory->create(pBetaP5,npairs,nr,"BOP:pBetaP5");
memory->create(pBetaP6,npairs,nr,"BOP:pBetaP6");
memory->create(pRepul,npairs,nr,"BOP:pRepul");
memory->create(pRepul1,npairs,nr,"BOP:pRepul1");
memory->create(pRepul2,npairs,nr,"BOP:pRepul2");
memory->create(pRepul3,npairs,nr,"BOP:pRepul3");
memory->create(pRepul4,npairs,nr,"BOP:pRepul4");
memory->create(pRepul5,npairs,nr,"BOP:pRepul5");
memory->create(pRepul6,npairs,nr,"BOP:pRepul6");
memory->create(FsigBO,npairs,nBOt,"BOP:FsigBO");
memory->create(FsigBO1,npairs,nBOt,"BOP:FsigBO1");
memory->create(FsigBO2,npairs,nBOt,"BOP:FsigBO2");
memory->create(FsigBO3,npairs,nBOt,"BOP:FsigBO3");
memory->create(FsigBO4,npairs,nBOt,"BOP:FsigBO4");
memory->create(FsigBO5,npairs,nBOt,"BOP:FsigBO5");
memory->create(FsigBO6,npairs,nBOt,"BOP:FsigBO6");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBOP::settings(int narg, char **arg)
{
otfly = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"save") == 0) {
otfly = 0;
iarg++;
} else error->all(FLERR,"Illegal pair_style command");
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs(Updated: D.K. Ward 05/06/10)
------------------------------------------------------------------------- */
void PairBOP::coeff(int narg, char **arg)
{
int i,j;
int n = atom->ntypes;
MPI_Comm_rank(world,&me);
map = new int[n+1];
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// ensure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read the potential file
nr=2000;
nBOt=2000;
ntheta=2000;
bop_step=0;
nb_pi=0;
nb_sg=0;
allocate_sigma=0;
allocate_pi=0;
allocate_neigh=0;
update_list=0;
maxnall=0;
read_table(arg[2]);
// match element names to BOP word types
if (me == 0) {
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < bop_types; j++) {
if (strcmp(arg[i],elements[j]) == 0) break;
}
map[i-2] = j;
}
}
MPI_Bcast(&map[1],atom->ntypes,MPI_INT,0,world);
if (me == 0) {
if (elements) {
for (i = 0; i < bop_types; i++) delete [] elements[i];
delete [] elements;
}
}
// 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 PairBOP::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style BOP requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style BOP requires newton pair on");
// check that user sets comm->cutghostuser to 3x the max BOP cutoff
if (comm->cutghostuser < 3.0*cutmax - EPSILON) {
char str[128];
sprintf(str,"Pair style bop requires comm ghost cutoff "
"at least 3x larger than %g",cutmax);
error->all(FLERR,str);
}
// need a full neighbor list and neighbors of ghosts
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
}
/* ---------------------------------------------------------------------- */
double PairBOP::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
int ii = map[i]+1;
int jj = map[j]+1;
int ij;
if (ii==jj) ij=ii-1;
else if (ii<jj) ij=ii*bop_types-ii*(ii+1)/2+jj-1;
else ij=jj*bop_types-jj*(jj+1)/2+ii-1;
if(rcut[ij]>rcut3[ij]) {
cutghost[i][j] = rcut[ij];
cutghost[j][i] = cutghost[i][j];
cutsq[i][j] = rcut[ij]*rcut[ij];
cutsq[j][i] = cutsq[i][j];
return rcut[ij];
} else {
cutghost[i][j] = rcut3[ij];
cutghost[j][i] = cutghost[i][j];
cutsq[i][j] = rcut3[ij]*rcut3[ij];
cutsq[j][i] = cutsq[i][j];
return rcut3[ij];
}
}
/* ----------------------------------------------------------------------
create BOP neighbor list from main neighbor list
BOP neighbor list stores neighbors of ghost atoms
BOP requires neighbor's of k if k is a neighbor of
j and j is a neighbor of i
------------------------------------------------------------------------- */
void PairBOP::gneigh()
{
int i,ii;
int j,jj,kk;
int itype,jtype,i12;
int temp_ij,temp_ik,temp_ijk;
int n,ks,max_check,neigh_t;
int max_check3;
int nlisti;
int *ilist,*numneigh;
int *iilist;
int **firstneigh;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double dis[3],r;
double rj2,rk2,rsq,ps;
double rj1k1,rj2k2;
double **x = atom->x;
int *type = atom->type;
if(allocate_neigh==0) {
memory->create (BOP_index,nall,"BOP_index");
memory->create (BOP_index3,nall,"BOP_index3");
memory->create (BOP_total,nall,"BOP_total");
memory->create (BOP_total3,nall,"BOP_total");
if (otfly==0) memory->create (cos_index,nall,"cos_index");
allocate_neigh=1;
}
else {
memory->grow (BOP_index,nall,"BOP_index");
memory->grow (BOP_index3,nall,"BOP_index3");
memory->grow (BOP_total,nall,"BOP_total");
memory->grow (BOP_total3,nall,"BOP_total3");
if (otfly==0) memory->grow (cos_index,nall,"cos_index");
allocate_neigh=1;
}
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
if(bop_step==0) {
maxneigh=0;
maxneigh3=0;
maxnall=0;
}
neigh_total=0;
neigh_total3=0;
cos_total=0;
for (ii = 0; ii < nall; ii++) {
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
itype = map[type[i]]+1;
iilist=firstneigh[i];
max_check=0;
max_check3=0;
for(jj=0;jj<numneigh[i];jj++) {
j=iilist[jj];
jtype = map[type[j]]+1;
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
i12=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
i12=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
if(i12>=npairs) {
error->one(FLERR,"Too many atom pairs for pair bop");
}
dis[0]=x[j][0]-x[i][0];
dis[1]=x[j][1]-x[i][1];
dis[2]=x[j][2]-x[i][2];
rsq=dis[0]*dis[0]
+dis[1]*dis[1]
+dis[2]*dis[2];
r=sqrt(rsq);
if(r<=rcut[i12]) {
max_check++;
}
if(r<=rcut3[i12]) {
max_check3++;
}
}
BOP_index[i]=neigh_total;
BOP_index3[i]=neigh_total3;
BOP_total[i]=max_check;
BOP_total3[i]=max_check3;
neigh_total+=max_check;
neigh_total3+=max_check3;
if(max_check>maxneigh||max_check3>maxneigh3){
maxneigh=max_check;
maxneigh3=max_check3;
}
if(otfly==0) {
cos_index[i]=cos_total;
cos_total+=max_check*(max_check-1)/2;
}
}
maxnall=nall;
if(update_list!=0)
memory_theta_grow();
else
memory_theta_create();
neigh_t=0;
for (ii = 0; ii < nall; ii++) {
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
itype = map[type[i]]+1;
iilist=firstneigh[i];
max_check=0;
max_check3=0;
for(jj=0;jj<numneigh[i];jj++) {
j=iilist[jj];
jtype = map[type[j]]+1;
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
i12=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
i12=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
if(i12>=npairs) {
error->one(FLERR,"Too many atom pairs for pair bop");
}
dis[0]=x[j][0]-x[i][0];
dis[1]=x[j][1]-x[i][1];
dis[2]=x[j][2]-x[i][2];
rsq=dis[0]*dis[0]
+dis[1]*dis[1]
+dis[2]*dis[2];
r=sqrt(rsq);
if(r<=rcut[i12]) {
temp_ij=BOP_index[i]+max_check;
if(i==0) {
}
neigh_index[temp_ij]=jj;
neigh_flag[temp_ij]=1;
max_check++;
}
if(r<=rcut3[i12]) {
temp_ij=BOP_index3[i]+max_check3;
neigh_index3[temp_ij]=jj;
neigh_flag3[temp_ij]=1;
max_check3++;
}
}
}
if(otfly==0) {
for (ii = 0; ii < nall; ii++) {
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
itype = map[type[i]]+1;
iilist=firstneigh[i];
nlisti=BOP_total[i];
max_check=0;
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
if(temp_ij>=neigh_total) {
}
if(temp_ij<0) {
}
jtype = map[type[j]]+1;
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
i12=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
i12=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
if(i12>=npairs) {
error->one(FLERR,"Too many atom pairs for pair bop");
}
disij[0][temp_ij]=x[j][0]-x[i][0];
disij[1][temp_ij]=x[j][1]-x[i][1];
disij[2][temp_ij]=x[j][2]-x[i][2];
rsq=disij[0][temp_ij]*disij[0][temp_ij]
+disij[1][temp_ij]*disij[1][temp_ij]
+disij[2][temp_ij]*disij[2][temp_ij];
rij[temp_ij]=sqrt(rsq);
if(rij[temp_ij]<=rcut[i12]) {
max_check++;
}
else
neigh_flag[temp_ij]=0;
}
}
neigh_t+=max_check;
for (ii = 0; ii < nall; ii++) {
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
itype = map[type[i]]+1;
iilist=firstneigh[i];
nlisti=BOP_total[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
jtype = map[type[j]]+1;
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
i12=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
i12=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
if(i12>=npairs) {
error->one(FLERR,"Too many atom pairs for pair bop");
}
ps=rij[temp_ij]*rdr[i12]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS[temp_ij]=((pBetaS3[i12][ks-1]*ps+pBetaS2[i12][ks-1])*ps+pBetaS1[i12][ks-1])*ps+pBetaS[i12][ks-1];
dBetaS[temp_ij]=(pBetaS6[i12][ks-1]*ps+pBetaS5[i12][ks-1])*ps
+pBetaS4[i12][ks-1];
betaP[temp_ij]=((pBetaP3[i12][ks-1]*ps+pBetaP2[i12][ks-1])*ps
+pBetaP1[i12][ks-1])*ps+pBetaP[i12][ks-1];
dBetaP[temp_ij]=(pBetaP6[i12][ks-1]*ps+pBetaP5[i12][ks-1])*ps
+pBetaP4[i12][ks-1];
repul[temp_ij]=((pRepul3[i12][ks-1]*ps+pRepul2[i12][ks-1])*ps
+pRepul1[i12][ks-1])*ps+pRepul[i12][ks-1];
dRepul[temp_ij]=(pRepul6[i12][ks-1]*ps+pRepul5[i12][ks-1])*ps
+pRepul4[i12][ks-1];
}
}
for (ii = 0; ii < nall; ii++) {
n=0;
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
iilist=firstneigh[i];
nlisti=BOP_total[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
rj2=rij[temp_ij]*rij[temp_ij];
for(kk=jj+1;kk<nlisti;kk++) {
if(cos_index[i]+n>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
temp_ik=BOP_index[i]+kk;
temp_ijk=cos_index[i]+n;
if(temp_ijk>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
rk2=rij[temp_ik]*rij[temp_ik];
rj1k1=rij[temp_ij]*rij[temp_ik];
rj2k2=rj1k1*rj1k1;
if(temp_ijk>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
cosAng[temp_ijk]=(disij[0][temp_ij]*disij[0][temp_ik]+disij[1][temp_ij]
*disij[1][temp_ik]+disij[2][temp_ij]*disij[2][temp_ik])/rj1k1;
dcAng[temp_ijk][0][0]=(disij[0][temp_ik]*rj1k1-cosAng[temp_ijk]
*disij[0][temp_ij]*rk2)/(rj2k2);
dcAng[temp_ijk][1][0]=(disij[1][temp_ik]*rj1k1-cosAng[temp_ijk]
*disij[1][temp_ij]*rk2)/(rj2k2);
dcAng[temp_ijk][2][0]=(disij[2][temp_ik]*rj1k1-cosAng[temp_ijk]
*disij[2][temp_ij]*rk2)/(rj2k2);
dcAng[temp_ijk][0][1]=(disij[0][temp_ij]*rj1k1-cosAng[temp_ijk]
*disij[0][temp_ik]*rj2)/(rj2k2);
dcAng[temp_ijk][1][1]=(disij[1][temp_ij]*rj1k1-cosAng[temp_ijk]
*disij[1][temp_ik]*rj2)/(rj2k2);
dcAng[temp_ijk][2][1]=(disij[2][temp_ij]*rj1k1-cosAng[temp_ijk]
*disij[2][temp_ik]*rj2)/(rj2k2);
n++;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairBOP::theta()
{
int i,j,ii,jj,kk;
int itype,jtype,i12;
int temp_ij,temp_ik,temp_ijk;
int n,nlocal,nall,ks;
int nlisti;
int *ilist;
int *iilist;
int **firstneigh;
double rj2,rk2,rsq,ps;
double rj1k1,rj2k2;
double **x = atom->x;
int *type = atom->type;
nlocal = atom->nlocal;
nall = nlocal+atom->nghost;
ilist = list->ilist;
firstneigh = list->firstneigh;
if(update_list!=0)
memory_theta_grow();
else
memory_theta_create();
for (ii = 0; ii < nall; ii++) {
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
itype = map[type[i]]+1;
iilist=firstneigh[i];
nlisti=BOP_total[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
jtype = map[type[j]]+1;
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
i12=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
i12=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
if(i12>=npairs) {
error->one(FLERR,"Too many atom pairs for pair bop");
}
disij[0][temp_ij]=x[j][0]-x[i][0];
disij[1][temp_ij]=x[j][1]-x[i][1];
disij[2][temp_ij]=x[j][2]-x[i][2];
rsq=disij[0][temp_ij]*disij[0][temp_ij]
+disij[1][temp_ij]*disij[1][temp_ij]
+disij[2][temp_ij]*disij[2][temp_ij];
rij[temp_ij]=sqrt(rsq);
if(rij[temp_ij]<=rcut[i12])
neigh_flag[temp_ij]=1;
else
neigh_flag[temp_ij]=0;
if(rij[temp_ij]<=rcut3[i12])
neigh_flag3[temp_ij]=1;
else
neigh_flag3[temp_ij]=0;
ps=rij[temp_ij]*rdr[i12]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS[temp_ij]=((pBetaS3[i12][ks-1]*ps+pBetaS2[i12][ks-1])*ps+pBetaS1[i12][ks-1])*ps+pBetaS[i12][ks-1];
dBetaS[temp_ij]=(pBetaS6[i12][ks-1]*ps+pBetaS5[i12][ks-1])*ps
+pBetaS4[i12][ks-1];
betaP[temp_ij]=((pBetaP3[i12][ks-1]*ps+pBetaP2[i12][ks-1])*ps
+pBetaP1[i12][ks-1])*ps+pBetaP[i12][ks-1];
dBetaP[temp_ij]=(pBetaP6[i12][ks-1]*ps+pBetaP5[i12][ks-1])*ps
+pBetaP4[i12][ks-1];
repul[temp_ij]=((pRepul3[i12][ks-1]*ps+pRepul2[i12][ks-1])*ps
+pRepul1[i12][ks-1])*ps+pRepul[i12][ks-1];
dRepul[temp_ij]=(pRepul6[i12][ks-1]*ps+pRepul5[i12][ks-1])*ps
+pRepul4[i12][ks-1];
}
}
for (ii = 0; ii < nall; ii++) {
n=0;
if(ii<nlocal)
i= ilist[ii];
else
i=ii;
iilist=firstneigh[i];
nlisti=BOP_total[i];
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
rj2=rij[temp_ij]*rij[temp_ij];
for(kk=jj+1;kk<nlisti;kk++) {
if(cos_index[i]+n>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
temp_ik=BOP_index[i]+kk;
temp_ijk=cos_index[i]+n;
if(temp_ijk>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
rk2=rij[temp_ik]*rij[temp_ik];
rj1k1=rij[temp_ij]*rij[temp_ik];
rj2k2=rj1k1*rj1k1;
if(temp_ijk>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
cosAng[temp_ijk]=(disij[0][temp_ij]*disij[0][temp_ik]+disij[1][temp_ij]
*disij[1][temp_ik]+disij[2][temp_ij]*disij[2][temp_ik])/rj1k1;
dcAng[temp_ijk][0][0]=(disij[0][temp_ik]*rj1k1-cosAng[temp_ijk]
*disij[0][temp_ij]*rk2)/(rj2k2);
dcAng[temp_ijk][1][0]=(disij[1][temp_ik]*rj1k1-cosAng[temp_ijk]
*disij[1][temp_ij]*rk2)/(rj2k2);
dcAng[temp_ijk][2][0]=(disij[2][temp_ik]*rj1k1-cosAng[temp_ijk]
*disij[2][temp_ij]*rk2)/(rj2k2);
dcAng[temp_ijk][0][1]=(disij[0][temp_ij]*rj1k1-cosAng[temp_ijk]
*disij[0][temp_ik]*rj2)/(rj2k2);
dcAng[temp_ijk][1][1]=(disij[1][temp_ij]*rj1k1-cosAng[temp_ijk]
*disij[1][temp_ik]*rj2)/(rj2k2);
dcAng[temp_ijk][2][1]=(disij[2][temp_ij]*rj1k1-cosAng[temp_ijk]
*disij[2][temp_ik]*rj2)/(rj2k2);
n++;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairBOP::theta_mod()
{
if(update_list!=0)
memory_theta_grow();
else
memory_theta_create();
}
/* ---------------------------------------------------------------------- */
/* The formulation differs slightly to avoid negative square roots
in the calculation of Sigma^(1/2) of (a) Eq. 6 and (b) Eq. 11 */
/* ---------------------------------------------------------------------- */
/* The formulation differs slightly to avoid negative square roots
in the calculation of Theta_pi,ij of (a) Eq. 36 and (b) Eq. 18 */
double PairBOP::sigmaBo(int itmp, int jtmp)
{
int nb_t,new_n_tot;
int i,j,k,kp,m,pp,kpj,kpk,kkp;
int ktmp,ltmp,mtmp;
int i_tag,j_tag;
int kp1,kp2,kp1type;
int iij,iik,ijk,ikkp,ji,iikp,ijkp;
int nkp,nk0;
int jNeik,kNeii,kNeij,kNeikp;
int kpNeij,kpNeik,lp1;
int new1,new2,nlocal;
int *ilist,*iilist,*jlist,*klist,*kplist;
int **firstneigh;
int temp_ij,temp_ik,temp_jkp,temp_kk,temp_jk;
int temp_ji,temp_kpj,temp_kkp;
int temp_ikp,temp_kpk;
int nb_ij,nb_ik,nb_ikp;
int nb_jk,nb_jkp,nb_kkp;
int kp_nsearch,nsearch;
int sig_flag,setting,ncmp,ks;
int itype,jtype,ktype,kptype;
int bt_i,bt_j;
int same_ikp,same_jkp,same_kpk;
int same_jkpj,same_kkpk;
int pass_ij,pass_ik,pass_jk;
int pass_jkp,pass_ikp,pass_kkp;
int njik,ngj,ngk;
int nijk,ngji,ngjk;
int nikj,ngki,ngkj;
int njikp,nglj,ngl;
int nkikp,nglk,nglkp;
int nikkp,ngli,nijkp;
int ngkkp,njkpk,ngkpj;
int ngjkp,ngkpk,ngi;
int nkjkp,njkkp;
int ang_ijk,ang_jik,ang_ikj;
int ang_jikp,ang_kikp,ang_ikkp;
int ang_ijkp,ang_jkpk,ang_kjkp;
int ang_jkkp;
int ni_ij,ni_ji,ni_ik;
int ni_jk,ni_ikN,ni_kj;
int ni_jkp,ni_kpj,ni_ikp,ni_kkp;
int ni_kpk,ni_kpnsearch;
int temp_ikN,temp_kj;
int nlisti,nlistj,nlistk,nlistkp;
double AA,BB,CC,DD,EE,EE1,FF;
double AAC,BBC,CCC,DDC,EEC,FFC,GGC;
double AACFF,UT,bndtmp,UTcom;
double amean,ps;
double gfactor1,gprime1,gsqprime;
double gfactorsq,gfactor2,gprime2;
double gfactorsq2,gsqprime2;
double gfactor3,gprime3,gfactor,rfactor;
double drfactor,gfactor4,gprime4,agpdpr3;
double rfactor0,rfactorrt,rfactor1rt,rfactor1;
double rcm1,rcm2,gcm1,gcm2,gcm3;
double agpdpr1,agpdpr2,app1,app2,app3,app4;
double dsigB1,dsigB2,xrun;
double part0,part1,part2,part3,part4;
double psign,bndtmp0,pp1;
double bndtmp1,bndtmp2,bndtmp3,bndtmp4,bndtmp5;
double dis_ij[3],rsq_ij,r_ij;
double betaS_ij,dBetaS_ij;
double dis_ik[3],rsq_ik,r_ik;
double betaS_ik,dBetaS_ik;
double dis_ikp[3],rsq_ikp,r_ikp;
double betaS_ikp,dBetaS_ikp;
double dis_jk[3],rsq_jk,r_jk;
double betaS_jk,dBetaS_jk;
double dis_jkp[3],rsq_jkp,r_jkp;
double betaS_jkp,dBetaS_jkp;
double dis_kkp[3],rsq_kkp,r_kkp;
double betaS_kkp,dBetaS_kkp;
double cosAng_jik,dcA_jik[3][2];
double cosAng_jikp,dcA_jikp[3][2];
double cosAng_kikp,dcA_kikp[3][2];
double cosAng_ijk,dcA_ijk[3][2];
double cosAng_ijkp,dcA_ijkp[3][2];
double cosAng_kjkp,dcA_kjkp[3][2];
double cosAng_ikj,dcA_ikj[3][2];
double cosAng_ikkp,dcA_ikkp[3][2];
double cosAng_jkkp,dcA_jkkp[3][2];
double cosAng_jkpk,dcA_jkpk[3][2];
double ftmp[3],xtmp[3];
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int *type = atom->type;
nlocal = atom->nlocal;
ilist = list->ilist;
firstneigh = list->firstneigh;
MPI_Comm_rank(world,&me);
if(nb_sg==0) {
nb_sg=(maxneigh)*(maxneigh/2);
}
if(allocate_sigma) {
destroy_sigma();
}
create_sigma(nb_sg);
sigB=0;
if(itmp<nlocal) {
i = ilist[itmp];
} else {
i=itmp;
}
i_tag=tag[i];
itype = map[type[i]]+1;
memset(bt_sg,0,sizeof(struct B_SG)*nb_sg);
for(m=0;m<nb_sg;m++) {
bt_sg[m].i=-1;
bt_sg[m].j=-1;
bt_sg[m].temp=-1;
}
nb_t=0;
iilist=firstneigh[i];
temp_ij=BOP_index[i]+jtmp;
ni_ij=neigh_index[temp_ij];
j=iilist[ni_ij];
jlist=firstneigh[j];
j_tag=tag[j];
jtype = map[type[j]]+1;
nb_ij=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_ij].temp=temp_ij;
bt_sg[nb_ij].i=i;
bt_sg[nb_ij].j=j;
if(j_tag>=i_tag) {
if(itype==jtype)
iij=itype-1;
else if(itype<jtype)
iij=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
iij=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
nlistj=BOP_total[j];
for(ji=0;ji<nlistj;ji++) {
temp_ji=BOP_index[j]+ji;
ni_ji=neigh_index[temp_ji];
if(x[jlist[ni_ji]][0]==x[i][0]) {
if(x[jlist[ni_ji]][1]==x[i][1]) {
if(x[jlist[ni_ji]][2]==x[i][2]) {
break;
}
}
}
}
pass_ij=0;
if(otfly==1) {
dis_ij[0]=x[j][0]-x[i][0];
dis_ij[1]=x[j][1]-x[i][1];
dis_ij[2]=x[j][2]-x[i][2];
rsq_ij=dis_ij[0]*dis_ij[0]
+dis_ij[1]*dis_ij[1]
+dis_ij[2]*dis_ij[2];
r_ij=sqrt(rsq_ij);
if(r_ij<rcut[iij]) {
pass_ij=1;
ps=r_ij*rdr[iij]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ij=((pBetaS3[iij][ks-1]*ps+pBetaS2[iij][ks-1])*ps
+pBetaS1[iij][ks-1])*ps+pBetaS[iij][ks-1];
dBetaS_ij=(pBetaS6[iij][ks-1]*ps+pBetaS5[iij][ks-1])*ps
+pBetaS4[iij][ks-1];
}
} else {
if(neigh_flag[temp_ij]) {
pass_ij=1;
dis_ij[0]=disij[0][temp_ij];
dis_ij[1]=disij[1][temp_ij];
dis_ij[2]=disij[2][temp_ij];
r_ij=rij[temp_ij];
betaS_ij=betaS[temp_ij];
dBetaS_ij=dBetaS[temp_ij];
}
}
if(pass_ij==1) {
nSigBk=0;
//AA-EE1 are the components making up Eq. 30 (a)
AA=0.0;
BB=0.0;
CC=0.0;
DD=0.0;
EE=0.0;
EE1=0.0;
//FF is the Beta_sigma^2 term
FF=betaS_ij*betaS_ij;
//agpdpr1 is derivative of FF w.r.t. r_ij
agpdpr1=2.0*betaS_ij*dBetaS_ij/r_ij;
//dXX derivatives are taken with respect to all pairs contributing to the energy
//nb_ij is derivative w.r.t. ij pair
bt_sg[nb_ij].dFF[0]=agpdpr1*dis_ij[0];
bt_sg[nb_ij].dFF[1]=agpdpr1*dis_ij[1];
bt_sg[nb_ij].dFF[2]=agpdpr1*dis_ij[2];
//k is loop over all neighbors of i again with j neighbor of i
nlisti=BOP_total[i];
for(ktmp=0;ktmp<nlisti;ktmp++) {
temp_ik=BOP_index[i]+ktmp;
ni_ik=neigh_index[temp_ik];
if(ktmp!=jtmp) {
k=iilist[ni_ik];
klist=firstneigh[k];
ktype = map[type[k]]+1;
if(itype==ktype)
iik=itype-1;
else if(itype<ktype)
iik=itype*bop_types-itype*(itype+1)/2+ktype-1;
else
iik=ktype*bop_types-ktype*(ktype+1)/2+itype-1;
//find neighbor of k that is equal to i
nlistk=BOP_total[k];
for(kNeii=0;kNeii<nlistk;kNeii++) {
temp_ikN=BOP_index[k]+kNeii;
ni_ikN=neigh_index[temp_ikN];
if(x[klist[ni_ikN]][0]==x[i][0]) {
if(x[klist[ni_ikN]][1]==x[i][1]) {
if(x[klist[ni_ikN]][2]==x[i][2]) {
break;
}
}
}
}
pass_ik=0;
if(otfly==1) {
dis_ik[0]=x[k][0]-x[i][0];
dis_ik[1]=x[k][1]-x[i][1];
dis_ik[2]=x[k][2]-x[i][2];
rsq_ik=dis_ik[0]*dis_ik[0]
+dis_ik[1]*dis_ik[1]
+dis_ik[2]*dis_ik[2];
r_ik=sqrt(rsq_ik);
if(r_ik<=rcut[iik]) {
pass_ik=1;
ps=r_ik*rdr[iik]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ik=((pBetaS3[iik][ks-1]*ps+pBetaS2[iik][ks-1])*ps
+pBetaS1[iik][ks-1])*ps+pBetaS[iik][ks-1];
dBetaS_ik=(pBetaS6[iik][ks-1]*ps+pBetaS5[iik][ks-1])*ps
+pBetaS4[iik][ks-1];
}
} else {
if(neigh_flag[temp_ik]) {
pass_ik=1;
dis_ik[0]=disij[0][temp_ik];
dis_ik[1]=disij[1][temp_ik];
dis_ik[2]=disij[2][temp_ik];
r_ik=rij[temp_ik];
betaS_ik=betaS[temp_ik];
dBetaS_ik=dBetaS[temp_ik];
}
}
if(pass_ik==1) {
//find neighbor of i that is equal to k
nlistj=BOP_total[j];
for(jNeik=0;jNeik<nlistj;jNeik++) {
temp_jk=BOP_index[j]+jNeik;
ni_jk=neigh_index[temp_jk];
if(x[jlist[ni_jk]][0]==x[k][0]) {
if(x[jlist[ni_jk]][1]==x[k][1]) {
if(x[jlist[ni_jk]][2]==x[k][2]) {
break;
}
}
}
}
//find neighbor of k that is equal to j
for(kNeij=0;kNeij<nlistk;kNeij++) {
temp_kj=BOP_index[k]+kNeij;
ni_kj=neigh_index[temp_kj];
if(x[klist[ni_kj]][0]==x[j][0]) {
if(x[klist[ni_kj]][1]==x[j][1]) {
if(x[klist[ni_kj]][2]==x[j][2]) {
break;
}
}
}
}
pass_jk=0;
if(otfly==1) {
dis_jk[0]=x[k][0]-x[j][0];
dis_jk[1]=x[k][1]-x[j][1];
dis_jk[2]=x[k][2]-x[j][2];
rsq_jk=dis_jk[0]*dis_jk[0]
+dis_jk[1]*dis_jk[1]
+dis_jk[2]*dis_jk[2];
r_jk=sqrt(rsq_jk);
} else {
if(neigh_flag[temp_jk]) {
pass_jk=1;
dis_jk[0]=disij[0][temp_jk];
dis_jk[1]=disij[1][temp_jk];
dis_jk[2]=disij[2][temp_jk];
r_jk=rij[temp_jk];
}
}
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[k][0]) {
if(x[ncmp][1]==x[k][1]) {
if(x[ncmp][2]==x[k][2]) {
nk0=nsearch;
sig_flag=1;
break;
}
}
}
}
if(sig_flag==0) {
nSigBk=nSigBk+1;
nk0=nSigBk-1;
itypeSigBk[nk0]=k;
}
nb_ik=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_ik].temp=temp_ik;
bt_sg[nb_ik].i=i;
bt_sg[nb_ik].j=k;
nb_jk=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_jk].temp=temp_jk;
bt_sg[nb_jk].i=j;
bt_sg[nb_jk].j=k;
if(otfly==1) {
cosAng_jik=(dis_ij[0]*dis_ik[0]+dis_ij[1]*dis_ik[1]
+dis_ij[2]*dis_ik[2])/(r_ij*r_ik);
dcA_jik[0][0]=(dis_ik[0]*r_ij*r_ik-cosAng_jik
*dis_ij[0]*r_ik*r_ik)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[1][0]=(dis_ik[1]*r_ij*r_ik-cosAng_jik
*dis_ij[1]*r_ik*r_ik)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[2][0]=(dis_ik[2]*r_ij*r_ik-cosAng_jik
*dis_ij[2]*r_ik*r_ik)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[0][1]=(dis_ij[0]*r_ij*r_ik-cosAng_jik
*dis_ik[0]*r_ij*r_ij)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[1][1]=(dis_ij[1]*r_ij*r_ik-cosAng_jik
*dis_ik[1]*r_ij*r_ij)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[2][1]=(dis_ij[2]*r_ij*r_ik-cosAng_jik
*dis_ik[2]*r_ij*r_ij)/(r_ij*r_ij*r_ik*r_ik);
} else {
if(ktmp!=jtmp) {
if(jtmp<ktmp) {
njik=jtmp*(2*nlisti-jtmp-1)/2+(ktmp-jtmp)-1;
ngj=0;
ngk=1;
}
else {
njik=ktmp*(2*nlisti-ktmp-1)/2+(jtmp-ktmp)-1;
ngj=1;
ngk=0;
}
ang_jik=cos_index[i]+njik;
cosAng_jik=cosAng[ang_jik];
dcA_jik[0][0]=dcAng[ang_jik][0][ngj];
dcA_jik[1][0]=dcAng[ang_jik][1][ngj];
dcA_jik[2][0]=dcAng[ang_jik][2][ngj];
dcA_jik[0][1]=dcAng[ang_jik][0][ngk];
dcA_jik[1][1]=dcAng[ang_jik][1][ngk];
dcA_jik[2][1]=dcAng[ang_jik][2][ngk];
}
}
amean=cosAng_jik;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor1=((gfunc3[jtype][itype][ktype][ks]*ps+
gfunc2[jtype][itype][ktype][ks])*ps+
gfunc1[jtype][itype][ktype][ks])*ps+
gfunc[jtype][itype][ktype][ks];
gprime1=(gfunc6[jtype][itype][ktype][ks]*ps+
gfunc5[jtype][itype][ktype][ks])*ps+
gfunc4[jtype][itype][ktype][ks];
} else {
gfactor1=gpara[jtype-1][itype-1][ktype-1][0];
gprime1=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime1=gprime1+(double)(lp1)*xrun*gpara[jtype-1][itype-1][ktype-1][lp1];
xrun=xrun*amean;
gfactor1=gfactor1+xrun*gpara[jtype-1][itype-1][ktype-1][lp1];
}
}
gfactorsq=gfactor1*gfactor1;
gsqprime=2.0*gfactor1*gprime1;
//AA is Eq. 34 (a) or Eq. 10 (c) for the i atom
//1st CC is Eq. 11 (c) for i atom where j & k=neighbor of i
AA=AA+gfactorsq*betaS_ik*betaS_ik;
//agpdpr1 is derivative of AA w.r.t. Beta(rik)
//app1 is derivative of AA w.r.t. cos(theta_jik)
agpdpr1=2.0*gfactorsq*betaS_ik*dBetaS_ik/r_ik;
app1=betaS_ik*betaS_ik*gsqprime;
bt_sg[nb_ij].dAA[0]+=
app1*dcA_jik[0][0];
bt_sg[nb_ij].dAA[1]+=
app1*dcA_jik[1][0];
bt_sg[nb_ij].dAA[2]+=
app1*dcA_jik[2][0];
bt_sg[nb_ik].dAA[0]+=
app1*dcA_jik[0][1]
+agpdpr1*dis_ik[0];
bt_sg[nb_ik].dAA[1]+=
app1*dcA_jik[1][1]
+agpdpr1*dis_ik[1];
bt_sg[nb_ik].dAA[2]+=
app1*dcA_jik[2][1]
+agpdpr1*dis_ik[2];
if(sigma_a[iij]!=0.0) {
CC=CC+gfactorsq*betaS_ik*betaS_ik*betaS_ik*betaS_ik;
agpdpr2=2.0*betaS_ik*betaS_ik*agpdpr1;
app2=betaS_ik*betaS_ik*app1;
bt_sg[nb_ij].dCC[0]+=
app2*dcA_jik[0][0];
bt_sg[nb_ij].dCC[1]+=
app2*dcA_jik[1][0];
bt_sg[nb_ij].dCC[2]+=
app2*dcA_jik[2][0];
bt_sg[nb_ik].dCC[0]+=
app2*dcA_jik[0][1]
+agpdpr2*dis_ik[0];
bt_sg[nb_ik].dCC[1]+=
app2*dcA_jik[1][1]
+agpdpr2*dis_ik[1];
bt_sg[nb_ik].dCC[2]+=
app2*dcA_jik[2][1]
+agpdpr2*dis_ik[2];
}
//k' is loop over neighbors all neighbors of j with k a neighbor
//of i and j a neighbor of i and determine which k' is k
if(sigma_f[iij]!=0.5&&sigma_k[iij]!=0.0) {
same_kpk=0;
for(ltmp=0;ltmp<nlistj;ltmp++) {
temp_jkp=BOP_index[j]+ltmp;
ni_jkp=neigh_index[temp_jkp];
kp1=jlist[ni_jkp];
kp1type=map[type[kp1]]+1;
if(x[kp1][0]==x[k][0]) {
if(x[kp1][1]==x[k][1]) {
if(x[kp1][2]==x[k][2]) {
same_kpk=1;
break;
}
}
}
}
if(same_kpk){
//loop over neighbors of k
for(mtmp=0;mtmp<nlistk;mtmp++) {
temp_kpj=BOP_index[k]+mtmp;
ni_kpj=neigh_index[temp_kpj];
kp2=klist[ni_kpj];
if(x[kp2][0]==x[j][0]) {
if(x[kp2][1]==x[j][1]) {
if(x[kp2][2]==x[j][2]) {
break;
}
}
}
}
if(jtype==ktype)
ijk=jtype-1;
else if(jtype < ktype)
ijk=jtype*bop_types-jtype*(jtype+1)/2+ktype-1;
else
ijk=ktype*bop_types-ktype*(ktype+1)/2+jtype-1;
if(jtype==kp1type)
ijkp=jtype-1;
else if(jtype<kp1type)
ijkp=jtype*bop_types-jtype*(jtype+1)/2+kp1type-1;
else
ijkp=kp1type*bop_types-kp1type*(kp1type+1)/2+jtype-1;
pass_jkp=0;
if(otfly==1) {
dis_jkp[0]=x[kp1][0]-x[j][0];
dis_jkp[1]=x[kp1][1]-x[j][1];
dis_jkp[2]=x[kp1][2]-x[j][2];
rsq_jkp=dis_jkp[0]*dis_jkp[0]
+dis_jkp[1]*dis_jkp[1]
+dis_jkp[2]*dis_jkp[2];
r_jkp=sqrt(rsq_jkp);
if(r_jkp<=rcut[ijkp]) {
pass_jkp=1;
ps=r_jkp*rdr[ijkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_jkp=((pBetaS3[ijkp][ks-1]*ps+pBetaS2[ijkp][ks-1])*ps
+pBetaS1[ijkp][ks-1])*ps+pBetaS[ijkp][ks-1];
dBetaS_jkp=(pBetaS6[ijkp][ks-1]*ps+pBetaS5[ijkp][ks-1])*ps
+pBetaS4[ijkp][ks-1];
cosAng_ijk=(-dis_ij[0]*dis_jk[0]-dis_ij[1]*dis_jk[1]
-dis_ij[2]*dis_jk[2])/(r_ij*r_jk);
dcA_ijk[0][0]=(dis_jk[0]*r_ij*r_jk-cosAng_ijk
*-dis_ij[0]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[1][0]=(dis_jk[1]*r_ij*r_jk-cosAng_ijk
*-dis_ij[1]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][0]=(dis_jk[2]*r_ij*r_jk-cosAng_ijk
*-dis_ij[2]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[0][1]=(-dis_ij[0]*r_ij*r_jk-cosAng_ijk
*dis_jk[0]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[1][1]=(-dis_ij[1]*r_ij*r_jk-cosAng_ijk
*dis_jk[1]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][1]=(-dis_ij[2]*r_ij*r_jk-cosAng_ijk
*dis_jk[2]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
}
} else {
if(neigh_flag[temp_jkp]) {
pass_jkp=1;
dis_jkp[0]=disij[0][temp_jkp];
dis_jkp[1]=disij[1][temp_jkp];
dis_jkp[2]=disij[2][temp_jkp];
r_jkp=rij[temp_jkp];
betaS_jkp=betaS[temp_jkp];
dBetaS_jkp=dBetaS[temp_jkp];
if(ji<ltmp) {
nijk=ji*(2*nlistj-ji-1)/2+(ltmp-ji)-1;
ngji=0;
ngjk=1;
}
else {
nijk=ltmp*(2*nlistj-ltmp-1)/2+(ji-ltmp)-1;
ngji=1;
ngjk=0;
}
ang_ijk=cos_index[j]+nijk;
cosAng_ijk=cosAng[ang_ijk];
dcA_ijk[0][0]=dcAng[ang_ijk][0][ngji];
dcA_ijk[1][0]=dcAng[ang_ijk][1][ngji];
dcA_ijk[2][0]=dcAng[ang_ijk][2][ngji];
dcA_ijk[0][1]=dcAng[ang_ijk][0][ngjk];
dcA_ijk[1][1]=dcAng[ang_ijk][1][ngjk];
dcA_ijk[2][1]=dcAng[ang_ijk][2][ngjk];
}
}
if(pass_jkp==1) {
amean=cosAng_ijk;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor2=((gfunc3[itype][jtype][ktype][ks]*ps+
gfunc2[itype][jtype][ktype][ks])*ps+
gfunc1[itype][jtype][ktype][ks])*ps+
gfunc[itype][jtype][ktype][ks];
gprime2=(gfunc6[itype][jtype][ktype][ks]*ps+
gfunc5[itype][jtype][ktype][ks])*ps+
gfunc4[itype][jtype][ktype][ks];
} else {
gfactor2=gpara[itype-1][jtype-1][ktype-1][0];
gprime2=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime2=gprime2+(lp1)*xrun*gpara[itype-1][jtype-1][ktype-1][lp1];
xrun=xrun*amean;
gfactor2=gfactor2+xrun*gpara[itype-1][jtype-1][ktype-1][lp1];
}
}
if(otfly==1) {
cosAng_ikj=(dis_ik[0]*dis_jk[0]+dis_ik[1]*dis_jk[1]
+dis_ik[2]*dis_jk[2])/(r_ik*r_jk);
dcA_ikj[0][0]=(-dis_jk[0]*r_ik*r_jk-cosAng_ikj
*-dis_ik[0]*r_jk*r_jk)/(r_ik*r_ik*r_jk*r_jk);
dcA_ikj[1][0]=(-dis_jk[1]*r_ik*r_jk-cosAng_ikj
*-dis_ik[1]*r_jk*r_jk)/(r_ik*r_ik*r_jk*r_jk);
dcA_ikj[2][0]=(-dis_jk[2]*r_ik*r_jk-cosAng_ikj
*-dis_ik[2]*r_jk*r_jk)/(r_ik*r_ik*r_jk*r_jk);
dcA_ikj[0][1]=(-dis_ik[0]*r_ik*r_jk-cosAng_ikj
*-dis_jk[0]*r_ik*r_ik)/(r_ik*r_ik*r_jk*r_jk);
dcA_ikj[1][1]=(-dis_ik[1]*r_ik*r_jk-cosAng_ikj
*-dis_jk[1]*r_ik*r_ik)/(r_ik*r_ik*r_jk*r_jk);
dcA_ikj[2][1]=(-dis_ik[2]*r_ik*r_jk-cosAng_ikj
*-dis_jk[2]*r_ik*r_ik)/(r_ik*r_ik*r_jk*r_jk);
} else {
if(kNeii<mtmp) {
nikj=kNeii*(2*nlistk-kNeii-1)/2+(mtmp-kNeii)-1;
ngki=0;
ngkj=1;
}
else {
nikj=mtmp*(2*nlistk-mtmp-1)/2+(kNeii-mtmp)-1;
ngki=1;
ngkj=0;
}
ang_ikj=cos_index[k]+nikj;
cosAng_ikj=cosAng[ang_ikj];
dcA_ikj[0][0]=dcAng[ang_ikj][0][ngki];
dcA_ikj[1][0]=dcAng[ang_ikj][1][ngki];
dcA_ikj[2][0]=dcAng[ang_ikj][2][ngki];
dcA_ikj[0][1]=dcAng[ang_ikj][0][ngkj];
dcA_ikj[1][1]=dcAng[ang_ikj][1][ngkj];
dcA_ikj[2][1]=dcAng[ang_ikj][2][ngkj];
}
amean=cosAng_ikj;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor3=((gfunc3[itype][jtype][jtype][ks]*ps+
gfunc2[itype][ktype][jtype][ks])*ps+
gfunc1[itype][ktype][jtype][ks])*ps+
gfunc[itype][ktype][jtype][ks];
gprime3=(gfunc6[itype][ktype][jtype][ks]*ps+
gfunc5[itype][ktype][jtype][ks])*ps+
gfunc4[itype][ktype][jtype][ks];
} else {
gfactor3=gpara[itype-1][ktype-1][jtype-1][0];
gprime3=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime3=gprime3+(lp1)*xrun*gpara[itype-1][ktype-1][jtype-1][lp1];
xrun=xrun*amean;
gfactor3=gfactor3+xrun*gpara[itype-1][ktype-1][jtype-1][lp1];
}
}
gfactor=gfactor1*gfactor2*gfactor3;
rfactor=betaS_ik*betaS_jkp;
//EE1 is (b) Eq. 12
EE1=EE1+gfactor*rfactor;
//rcm1 is derivative of EE1 w.r.t Beta(r_ik)
//rcm2 is derivative of EE1 w.r.t Beta(r_jk')
//gcm1 is derivative of EE1 w.r.t cos(theta_jik)
//gcm2 is derivative of EE1 w.r.t cos(theta_ijk)
//gcm3 is derivative of EE1 w.r.t cos(theta_ikj)
rcm1=gfactor*betaS_jkp*dBetaS_ik/r_ik;
rcm2=gfactor*betaS_ik*dBetaS_jkp/r_jkp;
gcm1=rfactor*gprime1*gfactor2*gfactor3;
gcm2=rfactor*gfactor1*gprime2*gfactor3;
gcm3=rfactor*gfactor1*gfactor2*gprime3;
bt_sg[nb_ij].dEE1[0]+=
gcm1*dcA_jik[0][0]
-gcm2*dcA_ijk[0][0];
bt_sg[nb_ij].dEE1[1]+=
gcm1*dcA_jik[1][0]
-gcm2*dcA_ijk[1][0];
bt_sg[nb_ij].dEE1[2]+=
gcm1*dcA_jik[2][0]
-gcm2*dcA_ijk[2][0];
bt_sg[nb_ik].dEE1[0]+=
gcm1*dcA_jik[0][1]
+rcm1*dis_ik[0]
-gcm3*dcA_ikj[0][0];
bt_sg[nb_ik].dEE1[1]+=
gcm1*dcA_jik[1][1]
+rcm1*dis_ik[1]
-gcm3*dcA_ikj[1][0];
bt_sg[nb_ik].dEE1[2]+=
gcm1*dcA_jik[2][1]
+rcm1*dis_ik[2]
-gcm3*dcA_ikj[2][0];
bt_sg[nb_jk].dEE1[0]+=
gcm2*dcA_ijk[0][1]
+rcm2*dis_jkp[0]
-gcm3*dcA_ikj[0][1];
bt_sg[nb_jk].dEE1[1]+=
gcm2*dcA_ijk[1][1]
+rcm2*dis_jkp[1]
-gcm3*dcA_ikj[1][1];
bt_sg[nb_jk].dEE1[2]+=
gcm2*dcA_ijk[2][1]
+rcm2*dis_jkp[2]
-gcm3*dcA_ikj[2][1];
}
}
}
// k and k' and j are all different neighbors of i
if(sigma_a[iij]!=0) {
for(ltmp=0;ltmp<ktmp;ltmp++) {
if(ltmp!=jtmp) {
temp_ikp=BOP_index[i]+ltmp;
ni_ikp=neigh_index[temp_ikp];
kp=iilist[ni_ikp];
kptype = map[type[kp]]+1;
if(itype==kptype)
iikp=itype-1;
else if(itype<kptype)
iikp=itype*bop_types-itype*(itype+1)/2+kptype-1;
else
iikp=kptype*bop_types-kptype*(kptype+1)/2+itype-1;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
break;
}
}
}
}
pass_ikp=0;
if(otfly==1) {
dis_ikp[0]=x[kp][0]-x[i][0];
dis_ikp[1]=x[kp][1]-x[i][1];
dis_ikp[2]=x[kp][2]-x[i][2];
rsq_ikp=dis_ikp[0]*dis_ikp[0]
+dis_ikp[1]*dis_ikp[1]
+dis_ikp[2]*dis_ikp[2];
r_ikp=sqrt(rsq_ikp);
if(r_ikp<=rcut[iikp]) {
pass_ikp=1;
ps=r_ikp*rdr[iikp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ikp=((pBetaS3[iikp][ks-1]*ps+pBetaS2[iikp][ks-1])*ps
+pBetaS1[iikp][ks-1])*ps+pBetaS[iikp][ks-1];
dBetaS_ikp=(pBetaS6[iikp][ks-1]*ps+pBetaS5[iikp][ks-1])*ps
+pBetaS4[iikp][ks-1];
}
} else {
if(neigh_flag[temp_ikp]) {
pass_ikp=1;
dis_ikp[0]=disij[0][temp_ikp];
dis_ikp[1]=disij[1][temp_ikp];
dis_ikp[2]=disij[2][temp_ikp];
r_ikp=rij[temp_ikp];
betaS_ikp=betaS[temp_ikp];
dBetaS_ikp=dBetaS[temp_ikp];
}
}
if(pass_ikp==1) {
nb_ikp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_ikp].temp=temp_ikp;
bt_sg[nb_ikp].i=i;
bt_sg[nb_ikp].j=kp;
if(otfly==1) {
cosAng_jikp=(dis_ij[0]*dis_ikp[0]+dis_ij[1]*dis_ikp[1]
+dis_ij[2]*dis_ikp[2])/(r_ij*r_ikp);
dcA_jikp[0][0]=(dis_ikp[0]*r_ij*r_ikp-cosAng_jikp
*dis_ij[0]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[1][0]=(dis_ikp[1]*r_ij*r_ikp-cosAng_jikp
*dis_ij[1]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[2][0]=(dis_ikp[2]*r_ij*r_ikp-cosAng_jikp
*dis_ij[2]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[0][1]=(dis_ij[0]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[0]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[1][1]=(dis_ij[1]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[1]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[2][1]=(dis_ij[2]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[2]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
cosAng_kikp=(dis_ik[0]*dis_ikp[0]+dis_ik[1]*dis_ikp[1]
+dis_ik[2]*dis_ikp[2])/(r_ik*r_ikp);
dcA_kikp[0][0]=(dis_ikp[0]*r_ik*r_ikp-cosAng_kikp
*dis_ik[0]*r_ikp*r_ikp)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[1][0]=(dis_ikp[1]*r_ik*r_ikp-cosAng_kikp
*dis_ik[1]*r_ikp*r_ikp)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[2][0]=(dis_ikp[2]*r_ik*r_ikp-cosAng_kikp
*dis_ik[2]*r_ikp*r_ikp)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[0][1]=(dis_ik[0]*r_ik*r_ikp-cosAng_kikp
*dis_ikp[0]*r_ik*r_ik)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[1][1]=(dis_ik[1]*r_ik*r_ikp-cosAng_kikp
*dis_ikp[1]*r_ik*r_ik)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[2][1]=(dis_ik[2]*r_ik*r_ikp-cosAng_kikp
*dis_ikp[2]*r_ik*r_ik)/(r_ik*r_ik*r_ikp*r_ikp);
} else {
if(jtmp<ltmp) {
njikp=jtmp*(2*nlisti-jtmp-1)/2+(ltmp-jtmp)-1;
nglj=0;
ngl=1;
}
else {
njikp=ltmp*(2*nlisti-ltmp-1)/2+(jtmp-ltmp)-1;
nglj=1;
ngl=0;
}
if(ktmp<ltmp) {
nkikp=ktmp*(2*nlisti-ktmp-1)/2+(ltmp-ktmp)-1;
nglk=0;
nglkp=1;
}
else {
nkikp=ltmp*(2*nlisti-ltmp-1)/2+(ktmp-ltmp)-1;
nglk=1;
nglkp=0;
}
ang_jikp=cos_index[i]+njikp;
cosAng_jikp=cosAng[ang_jikp];
dcA_jikp[0][0]=dcAng[ang_jikp][0][nglj];
dcA_jikp[1][0]=dcAng[ang_jikp][1][nglj];
dcA_jikp[2][0]=dcAng[ang_jikp][2][nglj];
dcA_jikp[0][1]=dcAng[ang_jikp][0][ngl];
dcA_jikp[1][1]=dcAng[ang_jikp][1][ngl];
dcA_jikp[2][1]=dcAng[ang_jikp][2][ngl];
ang_kikp=cos_index[i]+nkikp;
cosAng_kikp=cosAng[ang_jikp];
dcA_kikp[0][0]=dcAng[ang_kikp][0][nglk];
dcA_kikp[1][0]=dcAng[ang_kikp][1][nglk];
dcA_kikp[2][0]=dcAng[ang_kikp][2][nglk];
dcA_kikp[0][1]=dcAng[ang_kikp][0][nglkp];
dcA_kikp[1][1]=dcAng[ang_kikp][1][nglkp];
dcA_kikp[2][1]=dcAng[ang_kikp][2][nglkp];
}
amean=cosAng_jikp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor2=((gfunc3[jtype][itype][kptype][ks]*ps+
gfunc2[jtype][itype][kptype][ks])*ps+
gfunc1[jtype][itype][kptype][ks])*ps+
gfunc[jtype][itype][kptype][ks];
gprime2=(gfunc6[jtype][itype][kptype][ks]*ps+
gfunc5[jtype][itype][kptype][ks])*ps+
gfunc4[jtype][itype][kptype][ks];
} else {
gfactor2=gpara[jtype-1][itype-1][kptype-1][0];
gprime2=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime2=gprime2+(lp1)*xrun*gpara[jtype-1][itype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor2=gfactor2+xrun*gpara[jtype-1][itype-1][kptype-1][lp1];
}
}
amean=cosAng_kikp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor3=((gfunc3[ktype][itype][kptype][ks]*ps+
gfunc2[ktype][itype][kptype][ks])*ps+
gfunc1[ktype][itype][kptype][ks])*ps+
gfunc[ktype][itype][kptype][ks];
gprime3=(gfunc6[ktype][itype][kptype][ks]*ps+
gfunc5[ktype][itype][kptype][ks])*ps+
gfunc4[ktype][itype][kptype][ks];
} else {
gfactor3=gpara[ktype-1][itype-1][kptype-1][0];
gprime3=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime3=gprime3+(lp1)*xrun*gpara[ktype-1][itype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor3=gfactor3+xrun*gpara[ktype-1][itype-1][kptype-1][lp1];
}
}
gfactor=gfactor1*gfactor2*gfactor3;
rfactorrt=betaS_ik*betaS_ikp;
rfactor=rfactorrt*rfactorrt;
//2nd CC is second term of Eq. 11 (c) for i atom where j , k & k' =neighbor of i
CC=CC+2.0*gfactor*rfactor;
//agpdpr1 is derivative of CC 2nd term w.r.t. Beta(r_ik)
//agpdpr2 is derivative of CC 2nd term w.r.t. Beta(r_ik')
//app1 is derivative of CC 2nd term w.r.t. cos(theta_jik)
//app2 is derivative of CC 2nd term w.r.t. cos(theta_jik')
//app3 is derivative of CC 2nd term w.r.t. cos(theta_kik')
agpdpr1=4.0*gfactor*rfactorrt*betaS_ikp
*dBetaS_ik/r_ik;
agpdpr2=4.0*gfactor*rfactorrt*betaS_ik
*dBetaS_ikp/r_ikp;
app1=2.0*rfactor*gfactor2*gfactor3*gprime1;
app2=2.0*rfactor*gfactor1*gfactor3*gprime2;
app3=2.0*rfactor*gfactor1*gfactor2*gprime3;
bt_sg[nb_ij].dCC[0]+=
app1*dcA_jik[0][0]
+app2*dcA_jikp[0][0];
bt_sg[nb_ij].dCC[1]+=
app1*dcA_jik[1][0]
+app2*dcA_jikp[1][0];
bt_sg[nb_ij].dCC[2]+=
app1*dcA_jik[2][0]
+app2*dcA_jikp[2][0];
bt_sg[nb_ik].dCC[0]+=
app1*dcA_jik[0][1]
+app3*dcA_kikp[0][0]
+agpdpr1*dis_ik[0];
bt_sg[nb_ik].dCC[1]+=
app1*dcA_jik[1][1]
+app3*dcA_kikp[1][0]
+agpdpr1*dis_ik[1];
bt_sg[nb_ik].dCC[2]+=
app1*dcA_jik[2][1]
+app3*dcA_kikp[2][0]
+agpdpr1*dis_ik[2];
bt_sg[nb_ikp].dCC[0]=
app2*dcA_jikp[0][1]
+app3*dcA_kikp[0][1]
+agpdpr2*dis_ikp[0];
bt_sg[nb_ikp].dCC[1]=
app2*dcA_jikp[1][1]
+app3*dcA_kikp[1][1]
+agpdpr2*dis_ikp[1];
bt_sg[nb_ikp].dCC[2]=
app2*dcA_jikp[2][1]
+app3*dcA_kikp[2][1]
+agpdpr2*dis_ikp[2];
}
}
}
// j and k are different neighbors of i and k' is a neighbor k not equal to i
for(ltmp=0;ltmp<nlistk;ltmp++) {
temp_kkp=BOP_index[k]+ltmp;
ni_kkp=neigh_index[temp_ik];
kp=klist[ni_kkp];;
kptype = map[type[kp]]+1;
same_ikp=0;
same_jkp=0;
if(x[i][0]==x[kp][0]) {
if(x[i][1]==x[kp][1]) {
if(x[i][2]==x[kp][2]) {
same_ikp=1;
}
}
}
if(x[j][0]==x[kp][0]) {
if(x[j][1]==x[kp][1]) {
if(x[j][2]==x[kp][2]) {
same_jkp=1;
}
}
}
if(!same_ikp&&!same_jkp) {
if(ktype==kptype)
ikkp=ktype-1;
else if(ktype<kptype)
ikkp=ktype*bop_types-ktype*(ktype+1)/2+kptype-1;
else
ikkp=kptype*bop_types-kptype*(kptype+1)/2+ktype-1;
pass_kkp=0;
if(otfly==1) {
dis_kkp[0]=x[kp][0]-x[k][0];
dis_kkp[1]=x[kp][1]-x[k][1];
dis_kkp[2]=x[kp][2]-x[k][2];
rsq_kkp=dis_kkp[0]*dis_kkp[0]
+dis_kkp[1]*dis_kkp[1]
+dis_kkp[2]*dis_kkp[2];
r_kkp=sqrt(rsq_kkp);
if(r_kkp<=rcut[ikkp]) {
pass_kkp=1;
ps=r_kkp*rdr[ikkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_kkp=((pBetaS3[ikkp][ks-1]*ps+pBetaS2[ikkp][ks-1])*ps
+pBetaS1[ikkp][ks-1])*ps+pBetaS[ikkp][ks-1];
dBetaS_kkp=(pBetaS6[ikkp][ks-1]*ps+pBetaS5[ikkp][ks-1])*ps
+pBetaS4[ikkp][ks-1];
}
} else {
if(neigh_flag[temp_kkp]) {
pass_kkp=1;
dis_kkp[0]=disij[0][temp_kkp];
dis_kkp[1]=disij[1][temp_kkp];
dis_kkp[2]=disij[2][temp_kkp];
r_kkp=rij[temp_kkp];
betaS_kkp=betaS[temp_kkp];
dBetaS_kkp=dBetaS[temp_kkp];
}
}
if(pass_kkp==1) {
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
sig_flag=1;
nkp=nsearch;
break;
}
}
}
}
if(sig_flag==0) {
nSigBk=nSigBk+1;
nkp=nSigBk-1;
itypeSigBk[nkp]=kp;
}
if(otfly==1) {
cosAng_ikkp=(-dis_ik[0]*dis_kkp[0]-dis_ik[1]*dis_kkp[1]
-dis_ik[2]*dis_kkp[2])/(r_ik*r_kkp);
dcA_ikkp[0][0]=(dis_kkp[0]*r_ik*r_kkp-cosAng_ikkp
*-dis_ik[0]*r_kkp*r_kkp)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[1][0]=(dis_kkp[1]*r_ik*r_kkp-cosAng_ikkp
*-dis_ik[1]*r_kkp*r_kkp)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[2][0]=(dis_kkp[2]*r_ik*r_kkp-cosAng_ikkp
*-dis_ik[2]*r_kkp*r_kkp)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[0][1]=(-dis_ik[0]*r_ik*r_kkp-cosAng_ikkp
*dis_kkp[0]*r_ik*r_ik)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[1][1]=(-dis_ik[1]*r_ik*r_kkp-cosAng_ikkp
*dis_kkp[1]*r_ik*r_ik)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[2][1]=(-dis_ik[2]*r_ik*r_kkp-cosAng_ikkp
*dis_kkp[2]*r_ik*r_ik)/(r_ik*r_ik*r_kkp*r_kkp);
} else {
if(kNeii<ltmp) {
nikkp=kNeii*(2*nlistk-kNeii-1)/2+(ltmp-kNeii)-1;
nglkp=1;
ngli=0;
}
else {
nikkp=ltmp*(2*nlistk-ltmp-1)/2+(kNeii-ltmp)-1;
nglkp=0;
ngli=1;
}
ang_ikkp=cos_index[i]+nikkp;
cosAng_ikkp=cosAng[ang_ikkp];
dcA_ikkp[0][0]=dcAng[ang_ikkp][0][nglkp];
dcA_ikkp[1][0]=dcAng[ang_ikkp][1][nglkp];
dcA_ikkp[2][0]=dcAng[ang_ikkp][2][nglkp];
dcA_ikkp[0][1]=dcAng[ang_ikkp][0][ngli];
dcA_ikkp[1][1]=dcAng[ang_ikkp][1][ngli];
dcA_ikkp[2][1]=dcAng[ang_ikkp][2][ngli];
}
nb_kkp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_kkp].temp=temp_kkp;
bt_sg[nb_kkp].i=k;
bt_sg[nb_kkp].j=kp;
amean=cosAng_ikkp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor2=((gfunc3[itype][ktype][kptype][ks]*ps+
gfunc2[itype][ktype][kptype][ks])*ps+
gfunc1[itype][ktype][kptype][ks])*ps+
gfunc[itype][ktype][kptype][ks];
gprime2=(gfunc6[itype][ktype][kptype][ks]*ps+
gfunc5[itype][ktype][kptype][ks])*ps+
gfunc4[itype][ktype][kptype][ks];
} else {
gfactor2=gpara[itype-1][ktype-1][kptype-1][0];
gprime2=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime2=gprime2+(lp1)*xrun*gpara[itype-1][ktype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor2=gfactor2+xrun*gpara[itype-1][ktype-1][kptype-1][lp1];
}
}
gfactorsq2=gfactor2*gfactor2;
gsqprime2=2.0*gfactor2*gprime2;
gfactor=gfactorsq*gfactorsq2;
rfactorrt=betaS_ik*betaS_kkp;
rfactor=rfactorrt*rfactorrt;
//3rd CC is third term of Eq. 11 (c) for i atom
//where j , k =neighbor of i & k' =neighbor of k
CC=CC+gfactor*rfactor;
//agpdpr1 is derivative of CC 3rd term w.r.t. Beta(r_ik)
//agpdpr2 is derivative of CC 3rd term w.r.t. Beta(r_kk')
//app1 is derivative of CC 3rd term w.r.t. cos(theta_jik)
//app2 is derivative of CC 3rd term w.r.t. cos(theta_ikk')
agpdpr1=2.0*gfactor*rfactorrt*betaS_kkp
*dBetaS_ik/r_ik;
agpdpr2=2.0*gfactor*rfactorrt*betaS_ik
*dBetaS_kkp/r_kkp;
app1=rfactor*gfactorsq2*gsqprime;
app2=rfactor*gfactorsq*gsqprime2;
bt_sg[nb_ij].dCC[0]+=
app1*dcA_jik[0][0];
bt_sg[nb_ij].dCC[1]+=
app1*dcA_jik[1][0];
bt_sg[nb_ij].dCC[2]+=
app1*dcA_jik[2][0];
bt_sg[nb_ik].dCC[0]+=
app1*dcA_jik[0][1]
+agpdpr1*dis_ik[0]
-app2*dcA_ikkp[0][0];
bt_sg[nb_ik].dCC[1]+=
app1*dcA_jik[1][1]
+agpdpr1*dis_ik[1]
-app2*dcA_ikkp[1][0];
bt_sg[nb_ik].dCC[2]+=
app1*dcA_jik[2][1]
+agpdpr1*dis_ik[2]
-app2*dcA_ikkp[2][0];
bt_sg[nb_kkp].dCC[0]+=
app2*dcA_ikkp[0][1]
+agpdpr2*dis_kkp[0];
bt_sg[nb_kkp].dCC[1]+=
app2*dcA_ikkp[1][1]
+agpdpr2*dis_kkp[1];
bt_sg[nb_kkp].dCC[2]+=
app2*dcA_ikkp[2][1]
+agpdpr2*dis_kkp[2];
}
}
}
//j and k are different neighbors of i and k' is a neighbor j not equal to k
for(ltmp=0;ltmp<nlistj;ltmp++) {
sig_flag=0;
temp_jkp=BOP_index[j]+ltmp;
ni_jkp=neigh_index[temp_jkp];
kp=jlist[ni_jkp];
kptype = map[type[kp]]+1;
kplist=firstneigh[kp];
same_kkpk=0;
same_jkpj=0;
nlistkp=BOP_total[kp];
for(kpNeij=0;kpNeij<nlistkp;kpNeij++) {
temp_kpj=BOP_index[kp]+kpNeij;
ni_kpj=neigh_index[temp_kpj];
kpj=kplist[ni_kpj];
if(x[j][0]==x[kpj][0]) {
if(x[j][1]==x[kpj][1]) {
if(x[j][2]==x[kpj][2]) {
same_jkpj=1;
break;
}
}
}
}
for(kpNeik=0;kpNeik<nlistkp;kpNeik++) {
temp_kpk=BOP_index[kp]+kpNeik;
ni_kpk=neigh_index[temp_kpk];
kpk=kplist[ni_kpk];
if(x[k][0]==x[kpk][0]) {
if(x[k][1]==x[kpk][1]) {
if(x[k][2]==x[kpk][2]) {
same_kkpk=1;
break;
}
}
}
}
if(!same_jkpj&&!same_kkpk) {
same_kkpk=0;
for(kNeikp=0;kNeikp<nlistk;kNeikp++) {
temp_kkp=BOP_index[k]+kNeikp;
ni_kkp=neigh_index[temp_kkp];
kkp=kplist[ni_kkp];
if(x[kp][0]==x[kkp][0]) {
if(x[kp][1]==x[kkp][1]) {
if(x[kp][2]==x[kkp][2]) {
sig_flag=1;
break;
}
}
}
}
if(sig_flag==1) {
for(nsearch=0;nsearch<nlistkp;nsearch++) {
kp_nsearch=BOP_index[kp]+nsearch;
ni_kpnsearch=neigh_index[kp_nsearch];
ncmp=kplist[ni_kpnsearch];
if(x[ncmp][0]==x[j][0]) {
if(x[ncmp][1]==x[j][1]) {
if(x[ncmp][2]==x[j][2]) {
kpNeij=nsearch;
}
}
}
if(x[ncmp][0]==x[k][0]) {
if(x[ncmp][1]==x[k][1]) {
if(x[ncmp][2]==x[k][2]) {
kpNeik=nsearch;
}
}
}
}
if(jtype==kptype)
ijkp=jtype-1;
else if(jtype<kptype)
ijkp=jtype*bop_types-jtype*(jtype+1)/2+kptype-1;
else
ijkp=kptype*bop_types-kptype*(kptype+1)/2+jtype-1;
if(ktype==kptype)
ikkp=ktype-1;
else if(ktype<kptype)
ikkp=ktype*bop_types-ktype*(ktype+1)/2+kptype-1;
else
ikkp=kptype*bop_types-kptype*(kptype+1)/2+ktype-1;
if(otfly==1) {
dis_jkp[0]=x[kp][0]-x[j][0];
dis_jkp[1]=x[kp][1]-x[j][1];
dis_jkp[2]=x[kp][2]-x[j][2];
rsq_jkp=dis_jkp[0]*dis_jkp[0]
+dis_jkp[1]*dis_jkp[1]
+dis_jkp[2]*dis_jkp[2];
r_jkp=sqrt(rsq_jkp);
ps=r_jkp*rdr[ijkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_jkp=((pBetaS3[ijkp][ks-1]*ps+pBetaS2[ijkp][ks-1])*ps
+pBetaS1[ijkp][ks-1])*ps+pBetaS[ijkp][ks-1];
dBetaS_jkp=(pBetaS6[ijkp][ks-1]*ps+pBetaS5[ijkp][ks-1])*ps
+pBetaS4[ijkp][ks-1];
dis_kkp[0]=x[kp][0]-x[k][0];
dis_kkp[1]=x[kp][1]-x[k][1];
dis_kkp[2]=x[kp][2]-x[k][2];
rsq_kkp=dis_kkp[0]*dis_kkp[0]
+dis_kkp[1]*dis_kkp[1]
+dis_kkp[2]*dis_kkp[2];
r_kkp=sqrt(rsq_kkp);
ps=r_kkp*rdr[ikkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_kkp=((pBetaS3[ikkp][ks-1]*ps+pBetaS2[ikkp][ks-1])*ps
+pBetaS1[ikkp][ks-1])*ps+pBetaS[ikkp][ks-1];
dBetaS_kkp=(pBetaS6[ikkp][ks-1]*ps+pBetaS5[ikkp][ks-1])*ps
+pBetaS4[ikkp][ks-1];
cosAng_ijkp=(-dis_ij[0]*dis_jkp[0]-dis_ij[1]*dis_jkp[1]
-dis_ij[2]*dis_jkp[2])/(r_ij*r_jkp);
dcA_ijkp[0][0]=(dis_jkp[0]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[0]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[1][0]=(dis_jkp[1]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[1]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[2][0]=(dis_jkp[2]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[2]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[0][1]=(-dis_ij[0]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[0]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[1][1]=(-dis_ij[1]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[1]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[2][1]=(-dis_ij[2]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[2]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
cosAng_ikkp=(-dis_ik[0]*dis_kkp[0]-dis_ik[1]*dis_kkp[1]
-dis_ik[2]*dis_kkp[2])/(r_ik*r_kkp);
dcA_ikkp[0][0]=(dis_kkp[0]*r_ik*r_kkp-cosAng_ikkp
*-dis_ik[0]*r_kkp*r_kkp)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[1][0]=(dis_kkp[1]*r_ik*r_kkp-cosAng_ikkp
*-dis_ik[1]*r_kkp*r_kkp)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[2][0]=(dis_kkp[2]*r_ik*r_kkp-cosAng_ikkp
*-dis_ik[2]*r_kkp*r_kkp)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[0][1]=(-dis_ik[0]*r_ik*r_kkp-cosAng_ikkp
*dis_kkp[0]*r_ik*r_ik)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[1][1]=(-dis_ik[1]*r_ik*r_kkp-cosAng_ikkp
*dis_kkp[1]*r_ik*r_ik)/(r_ik*r_ik*r_kkp*r_kkp);
dcA_ikkp[2][1]=(-dis_ik[2]*r_ik*r_kkp-cosAng_ikkp
*dis_kkp[2]*r_ik*r_ik)/(r_ik*r_ik*r_kkp*r_kkp);
cosAng_jkpk=(dis_jkp[0]*dis_kkp[0]+dis_jkp[1]*dis_kkp[1]
+dis_jkp[2]*dis_kkp[2])/(r_jkp*r_kkp);
dcA_jkpk[0][0]=(-dis_kkp[0]*r_jkp*r_kkp-cosAng_jkpk
*-dis_jkp[0]*r_kkp*r_kkp)/(r_jkp*r_jkp*r_kkp*r_kkp);
dcA_jkpk[1][0]=(-dis_kkp[1]*r_jkp*r_kkp-cosAng_jkpk
*-dis_jkp[1]*r_kkp*r_kkp)/(r_jkp*r_jkp*r_kkp*r_kkp);
dcA_jkpk[2][0]=(-dis_kkp[2]*r_jkp*r_kkp-cosAng_jkpk
*-dis_jkp[2]*r_kkp*r_kkp)/(r_jkp*r_jkp*r_kkp*r_kkp);
dcA_jkpk[0][1]=(-dis_jkp[0]*r_jkp*r_kkp-cosAng_jkpk
*-dis_kkp[0]*r_jkp*r_jkp)/(r_jkp*r_jkp*r_kkp*r_kkp);
dcA_jkpk[1][1]=(-dis_jkp[1]*r_jkp*r_kkp-cosAng_jkpk
*-dis_kkp[1]*r_jkp*r_jkp)/(r_jkp*r_jkp*r_kkp*r_kkp);
dcA_jkpk[2][1]=(-dis_jkp[2]*r_jkp*r_kkp-cosAng_jkpk
*-dis_kkp[2]*r_jkp*r_jkp)/(r_jkp*r_jkp*r_kkp*r_kkp);
} else {
dis_jkp[0]=disij[0][temp_jkp];
dis_jkp[1]=disij[1][temp_jkp];
dis_jkp[2]=disij[2][temp_jkp];
r_jkp=rij[temp_jkp];
betaS_jkp=betaS[temp_jkp];
dBetaS_jkp=dBetaS[temp_jkp];
dis_kkp[0]=disij[0][temp_kkp];
dis_kkp[1]=disij[1][temp_kkp];
dis_kkp[2]=disij[2][temp_kkp];
r_kkp=rij[temp_kkp];
betaS_kkp=betaS[temp_kkp];
dBetaS_kkp=dBetaS[temp_kkp];
if(ji<ltmp) {
nijkp=(ji)*nlistj-(ji+1)*(ji+2)/2+ltmp;
ngji=0;
ngjkp=1;
}
else {
nijkp=(ltmp)*nlistj-(ltmp+1)*(ltmp+2)/2+ji;
ngji=1;
ngjkp=0;
}
if(kNeii<kNeikp) {
nikkp=(kNeii)*nlistk-(kNeii+1)*(kNeii+2)/2+kNeikp;
ngki=0;
ngkkp=1;
}
else {
nikkp=(kNeikp)*nlistk-(kNeikp+1)*(kNeikp+2)/2+kNeii;
ngki=1;
ngkkp=0;
}
if(kpNeij<kpNeik) {
njkpk=(kpNeij)*nlistkp-(kpNeij+1)*(kpNeij+2)/2+kpNeik;
ngkpj=0;
ngkpk=1;
}
else {
njkpk=(kpNeik)*nlistkp-(kpNeik+1)*(kpNeik+2)/2+kpNeij;
ngkpj=1;
ngkpk=0;
}
ang_ijkp=cos_index[j]+nijkp;
ang_ikkp=cos_index[k]+nikkp;
ang_jkpk=cos_index[kp]+njkpk;
cosAng_ijkp=cosAng[ang_ijkp];
dcA_ijkp[0][0]=dcAng[ang_ijkp][0][ngji];
dcA_ijkp[1][0]=dcAng[ang_ijkp][1][ngji];
dcA_ijkp[2][0]=dcAng[ang_ijkp][2][ngji];
dcA_ijkp[0][1]=dcAng[ang_ijkp][0][ngjkp];
dcA_ijkp[1][1]=dcAng[ang_ijkp][1][ngjkp];
dcA_ijkp[2][1]=dcAng[ang_ijkp][2][ngjkp];
cosAng_ikkp=cosAng[ang_ikkp];
dcA_ikkp[0][0]=dcAng[ang_ikkp][0][ngki];
dcA_ikkp[1][0]=dcAng[ang_ikkp][1][ngki];
dcA_ikkp[2][0]=dcAng[ang_ikkp][2][ngki];
dcA_ikkp[0][1]=dcAng[ang_ikkp][0][ngkkp];
dcA_ikkp[1][1]=dcAng[ang_ikkp][1][ngkkp];
dcA_ikkp[2][1]=dcAng[ang_ikkp][2][ngkkp];
cosAng_jkpk=cosAng[ang_jkpk];
dcA_jkpk[0][0]=dcAng[ang_jkpk][0][ngkpj];
dcA_jkpk[1][0]=dcAng[ang_jkpk][1][ngkpj];
dcA_jkpk[2][0]=dcAng[ang_jkpk][2][ngkpj];
dcA_jkpk[0][1]=dcAng[ang_jkpk][0][ngkpk];
dcA_jkpk[1][1]=dcAng[ang_jkpk][1][ngkpk];
dcA_jkpk[2][1]=dcAng[ang_jkpk][2][ngkpk];
}
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
nkp=nsearch;
sig_flag=1;
break;
}
}
}
}
if(sig_flag==0) {
nSigBk=nSigBk+1;
nkp=nSigBk-1;
itypeSigBk[nkp]=kp;
}
temp_kpk=BOP_index[kp]+kpNeik;
nb_jkp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_jkp].temp=temp_jkp;
bt_sg[nb_jkp].i=j;
bt_sg[nb_jkp].j=kp;
nb_kkp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_kkp].temp=temp_kkp;
bt_sg[nb_kkp].i=k;
bt_sg[nb_kkp].j=kp;
amean=cosAng_ijkp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor2=((gfunc3[itype][jtype][kptype][ks]*ps+
gfunc2[itype][jtype][kptype][ks])*ps+
gfunc1[itype][jtype][kptype][ks])*ps+
gfunc[itype][jtype][kptype][ks];
gprime2=(gfunc6[itype][jtype][kptype][ks]*ps+
gfunc5[itype][jtype][kptype][ks])*ps+
gfunc4[itype][jtype][kptype][ks];
} else {
gfactor2=gpara[itype-1][jtype-1][kptype-1][0];
gprime2=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime2=gprime2+(lp1)*xrun*gpara[itype-1][jtype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor2=gfactor2+xrun*gpara[itype-1][jtype-1][kptype-1][lp1];
}
}
amean=cosAng_ikkp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor3=((gfunc3[itype][ktype][kptype][ks]*ps+
gfunc2[itype][ktype][kptype][ks])*ps+
gfunc1[itype][ktype][kptype][ks])*ps+
gfunc[itype][ktype][kptype][ks];
gprime3=(gfunc6[itype][ktype][kptype][ks]*ps+
gfunc5[itype][ktype][kptype][ks])*ps+
gfunc4[itype][ktype][kptype][ks];
} else {
gfactor3=gpara[itype-1][ktype-1][kptype-1][0];
gprime3=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime3=gprime3+(lp1)*xrun*gpara[itype-1][ktype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor3=gfactor3+xrun*gpara[itype-1][ktype-1][kptype-1][lp1];
}
}
amean=cosAng_jkpk;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor4=((gfunc3[jtype][kptype][ktype][ks]*ps+
gfunc2[jtype][kptype][ktype][ks])*ps+
gfunc1[jtype][kptype][ktype][ks])*ps+
gfunc[jtype][kptype][ktype][ks];
gprime4=(gfunc6[jtype][kptype][ktype][ks]*ps+
gfunc5[jtype][kptype][ktype][ks])*ps+
gfunc4[jtype][kptype][ktype][ks];
} else {
gfactor4=gpara[jtype-1][kptype-1][ktype-1][0];
gprime4=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime4=gprime4+(lp1)*xrun*gpara[jtype-1][kptype-1][ktype-1][lp1];
xrun=xrun*amean;
gfactor4=gfactor4+xrun*gpara[jtype-1][kptype-1][ktype-1][lp1];
}
}
gfactor=gfactor1*gfactor2*gfactor3*gfactor4;
rfactor0=(betaS_ik+small2)*(betaS_jkp+small2)
*(betaS_kkp+small2);
rfactor=pow(rfactor0,2.0/3.0);
drfactor=2.0/3.0*pow(rfactor0,-1.0/3.0);
//EE is Eq. 25(notes)
EE=EE+gfactor*rfactor;
//agpdpr1 is derivative of agpdpr1 w.r.t. Beta(r_ik)
//agpdpr2 is derivative of agpdpr1 w.r.t. Beta(r_jk')
//agpdpr3 is derivative of agpdpr1 w.r.t. Beta(r_kk')
//app1 is derivative of agpdpr1 w.r.t. cos(theta_jik)
//app2 is derivative of agpdpr1 w.r.t. cos(theta_ijk')
//app3 is derivative of agpdpr1 w.r.t. cos(theta_ikk')
//app4 is derivative of agpdpr1 w.r.t. cos(theta_jk'k)
agpdpr1=gfactor*drfactor*(betaS_jkp+small2)*(betaS_kkp
+small2)*dBetaS_ik/r_ik;
agpdpr2=gfactor*drfactor*(betaS_ik+small2)*(betaS_kkp
+small2)*dBetaS_jkp/r_jkp;
agpdpr3=gfactor*drfactor*(betaS_ik+small2)*(betaS_jkp
+small2)*dBetaS_kkp/r_kkp;
app1=rfactor*gfactor2*gfactor3*gfactor4*gprime1;
app2=rfactor*gfactor1*gfactor3*gfactor4*gprime2;
app3=rfactor*gfactor1*gfactor2*gfactor4*gprime3;
app4=rfactor*gfactor1*gfactor2*gfactor3*gprime4;
bt_sg[nb_ij].dEE[0]+=
app1*dcA_jik[0][0]
-app2*dcA_ijkp[0][0];
bt_sg[nb_ij].dEE[1]+=
app1*dcA_jik[1][0]
-app2*dcA_ijkp[1][0];
bt_sg[nb_ij].dEE[2]+=
app1*dcA_jik[2][0]
-app2*dcA_ijkp[2][0];
bt_sg[nb_ik].dEE[0]+=
app1*dcA_jik[0][1]
+agpdpr1*dis_ik[0]
-app3*dcA_ikkp[0][0];
bt_sg[nb_ik].dEE[1]+=
app1*dcA_jik[1][1]
+agpdpr1*dis_ik[1]
-app3*dcA_ikkp[1][0];
bt_sg[nb_ik].dEE[2]+=
app1*dcA_jik[2][1]
+agpdpr1*dis_ik[2]
-app3*dcA_ikkp[2][0];
bt_sg[nb_jkp].dEE[0]+=
app2*dcA_ijkp[0][1]
+agpdpr2*dis_jkp[0]
-app4*dcA_jkpk[0][0];
bt_sg[nb_jkp].dEE[1]+=
app2*dcA_ijkp[1][1]
+agpdpr2*dis_jkp[1]
-app4*dcA_jkpk[1][0];
bt_sg[nb_jkp].dEE[2]+=
app2*dcA_ijkp[2][1]
+agpdpr2*dis_jkp[2]
-app4*dcA_jkpk[2][0];
bt_sg[nb_kkp].dEE[0]+=
app3*dcA_ikkp[0][1]
+agpdpr3*dis_kkp[0]
-app4*dcA_jkpk[0][1];
bt_sg[nb_kkp].dEE[1]+=
app3*dcA_ikkp[1][1]
+agpdpr3*dis_kkp[1]
-app4*dcA_jkpk[1][1];
bt_sg[nb_kkp].dEE[2]+=
app3*dcA_ikkp[2][1]
+agpdpr3*dis_kkp[2]
-app4*dcA_jkpk[2][1];
}
}
}
}
}
}
}
//j is a neighbor of i and k is a neighbor of j not equal to i
for(ktmp=0;ktmp<nlistj;ktmp++) {
if(ktmp!=ji) {
temp_jk=BOP_index[j]+ktmp;
ni_jk=neigh_index[temp_jk];
k=jlist[ni_jk];
klist=firstneigh[k];
ktype=map[type[k]]+1;
nlistk=BOP_total[k];
for(kNeij=0;kNeij<nlistk;kNeij++) {
if(x[klist[kNeij]][0]==x[j][0]) {
if(x[klist[kNeij]][1]==x[j][1]) {
if(x[klist[kNeij]][2]==x[j][2]) {
break;
}
}
}
}
if(jtype==ktype)
ijk=jtype-1;
else if(jtype<ktype)
ijk=jtype*bop_types-jtype*(jtype+1)/2+ktype-1;
else
ijk=ktype*bop_types-ktype*(ktype+1)/2+jtype-1;
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[k][0]) {
if(x[ncmp][1]==x[k][1]) {
if(x[ncmp][2]==x[k][2]) {
new1=nsearch;
sig_flag=1;
break;
}
}
}
}
if(sig_flag==0) {
nSigBk=nSigBk+1;
new1=nSigBk-1;
itypeSigBk[new1]=k;
}
pass_jk=0;
if(otfly==1) {
dis_jk[0]=x[k][0]-x[j][0];
dis_jk[1]=x[k][1]-x[j][1];
dis_jk[2]=x[k][2]-x[j][2];
rsq_jk=dis_jk[0]*dis_jk[0]
+dis_jk[1]*dis_jk[1]
+dis_jk[2]*dis_jk[2];
r_jk=sqrt(rsq_jk);
if(r_jk<=rcut[ijk]) {
pass_jk=1;
ps=r_jk*rdr[ijk]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_jk=((pBetaS3[ijk][ks-1]*ps+pBetaS2[ijk][ks-1])*ps
+pBetaS1[ijk][ks-1])*ps+pBetaS[ijk][ks-1];
dBetaS_jk=(pBetaS6[ijk][ks-1]*ps+pBetaS5[ijk][ks-1])*ps
+pBetaS4[ijk][ks-1];
cosAng_ijk=(-dis_ij[0]*dis_jk[0]-dis_ij[1]*dis_jk[1]
-dis_ij[2]*dis_jk[2])/(r_ij*r_jk);
dcA_ijk[0][0]=(dis_jk[0]*r_ij*r_jk-cosAng_ijk
*-dis_ij[0]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[1][0]=(dis_jk[1]*r_ij*r_jk-cosAng_ijk
*-dis_ij[1]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][0]=(dis_jk[2]*r_ij*r_jk-cosAng_ijk
*-dis_ij[2]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[0][1]=(-dis_ij[0]*r_ij*r_jk-cosAng_ijk
*dis_jk[0]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[1][1]=(-dis_ij[1]*r_ij*r_jk-cosAng_ijk
*dis_jk[1]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][1]=(-dis_ij[2]*r_ij*r_jk-cosAng_ijk
*dis_jk[2]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
}
} else {
if(neigh_flag[temp_jk]) {
pass_jk=1;
dis_jk[0]=disij[0][temp_jk];
dis_jk[1]=disij[1][temp_jk];
dis_jk[2]=disij[2][temp_jk];
r_jk=rij[temp_jk];
betaS_jk=betaS[temp_jk];
dBetaS_jk=dBetaS[temp_jk];
if(ktmp<ji) {
nijk=ktmp*(2*nlistj-ktmp-1)/2+(ji-ktmp)-1;
ngi=1;
ngk=0;
}
else {
nijk=ji*(2*nlistj-ji-1)/2+(ktmp-ji)-1;
ngi=0;
ngk=1;
}
ang_ijk=cos_index[j]+nijk;
cosAng_ijk=cosAng[ang_ijk];
dcA_ijk[0][0]=dcAng[ang_ijk][0][ngi];
dcA_ijk[1][0]=dcAng[ang_ijk][1][ngi];
dcA_ijk[2][0]=dcAng[ang_ijk][2][ngi];
dcA_ijk[0][1]=dcAng[ang_ijk][0][ngk];
dcA_ijk[1][1]=dcAng[ang_ijk][1][ngk];
dcA_ijk[2][1]=dcAng[ang_ijk][2][ngk];
}
}
if(pass_jk==1) {
nb_jk=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_jk].temp=temp_jk;
bt_sg[nb_jk].i=j;
bt_sg[nb_jk].j=k;
amean=cosAng_ijk;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor1=((gfunc3[itype][jtype][ktype][ks]*ps+
gfunc2[itype][jtype][ktype][ks])*ps+
gfunc1[itype][jtype][ktype][ks])*ps+
gfunc[itype][jtype][ktype][ks];
gprime1=(gfunc6[itype][jtype][ktype][ks]*ps+
gfunc5[itype][jtype][ktype][ks])*ps+
gfunc4[itype][jtype][ktype][ks];
} else {
gfactor1=gpara[itype-1][jtype-1][ktype-1][0];
gprime1=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime1=gprime1+(lp1)*xrun*gpara[itype-1][jtype-1][ktype-1][lp1];
xrun=xrun*amean;
gfactor1=gfactor1+xrun*gpara[itype-1][jtype-1][ktype-1][lp1];
}
}
gfactorsq=gfactor1*gfactor1;
gsqprime=2.0*gfactor1*gprime1;
rfactor1rt=betaS_jk*betaS_jk;
rfactor1=rfactor1rt*rfactor1rt;
//BB is Eq. 34 (a) or Eq. 10 (c) for the j atom
//1st DD is Eq. 11 (c) for j atom where i & k=neighbor of j
BB=BB+gfactorsq*rfactor1rt;
//agpdpr1 is derivative of BB w.r.t. Beta(r_jk)
//app1 is derivative of BB w.r.t. cos(theta_ijk)
agpdpr1=2.0*gfactorsq*betaS_jk*dBetaS_jk/r_jk;
app1=rfactor1rt*gsqprime;
bt_sg[nb_ij].dBB[0]-=
app1*dcA_ijk[0][0];
bt_sg[nb_ij].dBB[1]-=
app1*dcA_ijk[1][0];
bt_sg[nb_ij].dBB[2]-=
app1*dcA_ijk[2][0];
bt_sg[nb_jk].dBB[0]+=
app1*dcA_ijk[0][1]
+agpdpr1*dis_jk[0];
bt_sg[nb_jk].dBB[1]+=
app1*dcA_ijk[1][1]
+agpdpr1*dis_jk[1];
bt_sg[nb_jk].dBB[2]+=
app1*dcA_ijk[2][1]
+agpdpr1*dis_jk[2];
if(sigma_a[iij]!=0) {
app2=rfactor1rt*app1;
agpdpr2=2.0*rfactor1rt*agpdpr1;
DD=DD+gfactorsq*rfactor1;
bt_sg[nb_ij].dDD[0]-=
app2*dcA_ijk[0][0];
bt_sg[nb_ij].dDD[1]-=
app2*dcA_ijk[1][0];
bt_sg[nb_ij].dDD[2]-=
app2*dcA_ijk[2][0];
bt_sg[nb_jk].dDD[0]+=
app2*dcA_ijk[0][1]
+agpdpr2*dis_jk[0];
bt_sg[nb_jk].dDD[1]+=
app2*dcA_ijk[1][1]
+agpdpr2*dis_jk[1];
bt_sg[nb_jk].dDD[2]+=
app2*dcA_ijk[2][1]
+agpdpr2*dis_jk[2];
//j is a neighbor of i, k and k' prime different neighbors of j not equal to i
for(ltmp=0;ltmp<ktmp;ltmp++) {
if(ltmp!=ji) {
temp_jkp=BOP_index[j]+ltmp;
ni_jkp=neigh_index[temp_jkp];
kp=jlist[ni_jkp];
kptype=map[type[kp]]+1;
if(jtype==kptype)
ijkp=jtype-1;
else if(jtype<kptype)
ijkp=jtype*bop_types-jtype*(jtype+1)/2+kptype-1;
else
ijkp=kptype*bop_types-kptype*(kptype+1)/2+jtype-1;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
new2=nsearch;
break;
}
}
}
}
pass_jkp=0;
if(otfly==1) {
dis_jkp[0]=x[kp][0]-x[j][0];
dis_jkp[1]=x[kp][1]-x[j][1];
dis_jkp[2]=x[kp][2]-x[j][2];
rsq_jkp=dis_jkp[0]*dis_jkp[0]
+dis_jkp[1]*dis_jkp[1]
+dis_jkp[2]*dis_jkp[2];
r_jkp=sqrt(rsq_jkp);
if(r_jkp<=rcut[ijkp]) {
pass_jkp=1;
ps=r_jkp*rdr[ijkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_jkp=((pBetaS3[ijkp][ks-1]*ps+pBetaS2[ijkp][ks-1])*ps
+pBetaS1[ijkp][ks-1])*ps+pBetaS[ijkp][ks-1];
dBetaS_jkp=(pBetaS6[ijkp][ks-1]*ps+pBetaS5[ijkp][ks-1])*ps
+pBetaS4[ijkp][ks-1];
cosAng_ijkp=(-dis_ij[0]*dis_jkp[0]-dis_ij[1]*dis_jkp[1]
-dis_ij[2]*dis_jkp[2])/(r_ij*r_jkp);
dcA_ijkp[0][0]=(dis_jkp[0]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[0]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[1][0]=(dis_jkp[1]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[1]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[2][0]=(dis_jkp[2]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[2]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[0][1]=(-dis_ij[0]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[0]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[1][1]=(-dis_ij[1]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[1]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[2][1]=(-dis_ij[2]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[2]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
cosAng_kjkp=(dis_jk[0]*dis_jkp[0]+dis_jk[1]*dis_jkp[1]
+dis_jk[2]*dis_jkp[2])/(r_jk*r_jkp);
dcA_kjkp[0][0]=(dis_jkp[0]*r_jk*r_jkp-cosAng_kjkp
*dis_jk[0]*r_jkp*r_jkp)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[1][0]=(dis_jkp[1]*r_jk*r_jkp-cosAng_kjkp
*dis_jk[1]*r_jkp*r_jkp)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[2][0]=(dis_jkp[2]*r_jk*r_jkp-cosAng_kjkp
*dis_jk[2]*r_jkp*r_jkp)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[0][1]=(dis_jk[0]*r_jk*r_jkp-cosAng_kjkp
*dis_jkp[0]*r_jk*r_jk)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[1][1]=(dis_jk[1]*r_jk*r_jkp-cosAng_kjkp
*dis_jkp[1]*r_jk*r_jk)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[2][1]=(dis_jk[2]*r_jk*r_jkp-cosAng_kjkp
*dis_jkp[2]*r_jk*r_jk)/(r_jk*r_jk*r_jkp*r_jkp);
}
} else {
if(neigh_flag[temp_jkp]) {
pass_jkp=1;
dis_jkp[0]=disij[0][temp_jkp];
dis_jkp[1]=disij[1][temp_jkp];
dis_jkp[2]=disij[2][temp_jkp];
r_jkp=rij[temp_jkp];
betaS_jkp=betaS[temp_jkp];
dBetaS_jkp=dBetaS[temp_jkp];
if(ji<ltmp) {
nijkp=ji*(2*nlistj-ji-1)/2+(ltmp-ji)-1;
ngli=0;
ngl=1;
}
else {
nijkp=ltmp*(2*nlistj-ltmp-1)/2+(ji-ltmp)-1;
ngli=1;
ngl=0;
}
if(ktmp<ltmp) {
nkjkp=ktmp*(2*nlistj-ktmp-1)/2+(ltmp-ktmp)-1;
ngjk=0;
ngjkp=1;
}
else {
nkjkp=ltmp*(2*nlistj-ltmp-1)/2+(ktmp-ltmp)-1;
ngjk=1;
ngjkp=0;
}
ang_ijkp=cos_index[j]+nijkp;
cosAng_ijkp=cosAng[ang_ijkp];
dcA_ijkp[0][0]=dcAng[ang_ijkp][0][ngli];
dcA_ijkp[1][0]=dcAng[ang_ijkp][1][ngli];
dcA_ijkp[2][0]=dcAng[ang_ijkp][2][ngli];
dcA_ijkp[0][1]=dcAng[ang_ijkp][0][ngl];
dcA_ijkp[1][1]=dcAng[ang_ijkp][1][ngl];
dcA_ijkp[2][1]=dcAng[ang_ijkp][2][ngl];
ang_kjkp=cos_index[j]+nkjkp;
cosAng_kjkp=cosAng[ang_kjkp];
dcA_kjkp[0][0]=dcAng[ang_kjkp][0][ngjk];
dcA_kjkp[1][0]=dcAng[ang_kjkp][1][ngjk];
dcA_kjkp[2][0]=dcAng[ang_kjkp][2][ngjk];
dcA_kjkp[0][1]=dcAng[ang_kjkp][0][ngjkp];
dcA_kjkp[1][1]=dcAng[ang_kjkp][1][ngjkp];
dcA_kjkp[2][1]=dcAng[ang_kjkp][2][ngjkp];
}
}
if(pass_jkp==1) {
nb_jkp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_jkp].temp=temp_jkp;
bt_sg[nb_jkp].i=j;
bt_sg[nb_jkp].j=kp;
amean=cosAng_ijkp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor2=((gfunc3[itype][jtype][kptype][ks]*ps+
gfunc2[itype][jtype][kptype][ks])*ps+
gfunc1[itype][jtype][kptype][ks])*ps+
gfunc[itype][jtype][kptype][ks];
gprime2=(gfunc6[itype][jtype][kptype][ks]*ps+
gfunc5[itype][jtype][kptype][ks])*ps+
gfunc4[itype][jtype][kptype][ks];
} else {
gfactor2=gpara[itype-1][jtype-1][kptype-1][0];
gprime2=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime2=gprime2+(lp1)*xrun*gpara[itype-1][jtype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor2=gfactor2+xrun*gpara[itype-1][jtype-1][kptype-1][lp1];
}
}
amean=cosAng_kjkp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor3=((gfunc3[ktype][jtype][kptype][ks]*ps+
gfunc2[ktype][jtype][kptype][ks])*ps+
gfunc1[ktype][jtype][kptype][ks])*ps+
gfunc[ktype][jtype][kptype][ks];
gprime3=(gfunc6[ktype][jtype][kptype][ks]*ps+
gfunc5[ktype][jtype][kptype][ks])*ps+
gfunc4[ktype][jtype][kptype][ks];
} else {
gfactor3=gpara[ktype-1][jtype-1][kptype-1][0];
gprime3=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime3=gprime3+(lp1)*xrun*gpara[ktype-1][jtype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor3=gfactor3+xrun*gpara[ktype-1][jtype-1][kptype-1][lp1];
}
}
gfactor=gfactor1*gfactor2*gfactor3;
rfactorrt=betaS_jk*betaS_jkp;
rfactor=rfactorrt*rfactorrt;
//2nd DD is Eq. 11 (c) for j atom where i , k & k'=neighbor of j
DD=DD+2.0*gfactor*rfactor;
//agpdpr1 is derivative of DD w.r.t. Beta(r_jk)
//agpdpr2 is derivative of DD w.r.t. Beta(r_jk')
//app1 is derivative of DD w.r.t. cos(theta_ijk)
//app2 is derivative of DD w.r.t. cos(theta_ijkp)
//app3 is derivative of DD w.r.t. cos(theta_kjkp)
agpdpr1=4.0*gfactor*rfactorrt*betaS_jkp
*dBetaS_jk/r_jk;
agpdpr2=4.0*gfactor*rfactorrt*betaS_jk
*dBetaS_jkp/r_jkp;
app1=2.0*rfactor*gfactor2*gfactor3*gprime1;
app2=2.0*rfactor*gfactor1*gfactor3*gprime2;
app3=2.0*rfactor*gfactor1*gfactor2*gprime3;
bt_sg[nb_ij].dDD[0]-=
app1*dcA_ijk[0][0]
+app2*dcA_ijkp[0][0];
bt_sg[nb_ij].dDD[1]-=
app1*dcA_ijk[1][0]
+app2*dcA_ijkp[1][0];
bt_sg[nb_ij].dDD[2]-=
app1*dcA_ijk[2][0]
+app2*dcA_ijkp[2][0];
bt_sg[nb_jk].dDD[0]+=
app1*dcA_ijk[0][1]
+app3*dcA_kjkp[0][0]
+agpdpr1*dis_jk[0];
bt_sg[nb_jk].dDD[1]+=
app1*dcA_ijk[1][1]
+app3*dcA_kjkp[1][0]
+agpdpr1*dis_jk[1];
bt_sg[nb_jk].dDD[2]+=
app1*dcA_ijk[2][1]
+app3*dcA_kjkp[2][0]
+agpdpr1*dis_jk[2];
bt_sg[nb_jkp].dDD[0]+=
app2*dcA_ijkp[0][1]
+app3*dcA_kjkp[0][1]
+agpdpr2*dis_jkp[0];
bt_sg[nb_jkp].dDD[1]+=
app2*dcA_ijkp[1][1]
+app3*dcA_kjkp[1][1]
+agpdpr2*dis_jkp[1];
bt_sg[nb_jkp].dDD[2]+=
app2*dcA_ijkp[2][1]
+app3*dcA_kjkp[2][1]
+agpdpr2*dis_jkp[2];
}
}
}
//j is a neighbor of i, k is a neighbor of j not equal to i and k'
//is a neighbor of k not equal to j or i
for(ltmp=0;ltmp<nlistk;ltmp++) {
temp_kkp=BOP_index[k]+ltmp;
ni_kkp=neigh_index[temp_kkp];
kp=klist[ni_kkp];
kptype=map[type[kp]]+1;
same_ikp=0;
same_jkp=0;
if(x[i][0]==x[kp][0]) {
if(x[i][1]==x[kp][1]) {
if(x[i][2]==x[kp][2]) {
same_ikp=1;
}
}
}
if(x[j][0]==x[kp][0]) {
if(x[j][1]==x[kp][1]) {
if(x[j][2]==x[kp][2]) {
same_jkp=1;
}
}
}
if(!same_ikp&&!same_jkp) {
if(ktype==kptype)
ikkp=ktype-1;
else if(ktype<kptype)
ikkp=ktype*bop_types-ktype*(ktype+1)/2+kptype-1;
else
ikkp=kptype*bop_types-kptype*(kptype+1)/2+ktype-1;
for(kNeij=0;kNeij<nlistk;kNeij++) {
temp_kj=BOP_index[k]+kNeij;
ni_kj=neigh_index[temp_kj];
if(x[klist[ni_kj]][0]==x[j][0]) {
if(x[klist[ni_kj]][1]==x[j][1]) {
if(x[klist[ni_kj]][2]==x[j][2]) {
break;
}
}
}
}
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
new2=nsearch;
sig_flag=1;
break;
}
}
}
}
if(sig_flag==0) {
nSigBk=nSigBk+1;
new2=nSigBk-1;
itypeSigBk[new2]=kp;
}
pass_kkp=0;
if(otfly==1) {
dis_kkp[0]=x[kp][0]-x[k][0];
dis_kkp[1]=x[kp][1]-x[k][1];
dis_kkp[2]=x[kp][2]-x[k][2];
rsq_kkp=dis_kkp[0]*dis_kkp[0]
+dis_kkp[1]*dis_kkp[1]
+dis_kkp[2]*dis_kkp[2];
r_kkp=sqrt(rsq_kkp);
if(r_kkp<=rcut[ikkp]) {
pass_kkp=1;
ps=r_kkp*rdr[ikkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_kkp=((pBetaS3[ikkp][ks-1]*ps+pBetaS2[ikkp][ks-1])*ps
+pBetaS1[ikkp][ks-1])*ps+pBetaS[ikkp][ks-1];
dBetaS_kkp=(pBetaS6[ikkp][ks-1]*ps+pBetaS5[ikkp][ks-1])*ps
+pBetaS4[ikkp][ks-1];
cosAng_jkkp=(-dis_jk[0]*dis_kkp[0]-dis_jk[1]*dis_kkp[1]
-dis_jk[2]*dis_kkp[2])/(r_jk*r_kkp);
dcA_jkkp[0][0]=(dis_kkp[0]*r_jk*r_kkp-cosAng_jkkp
*-dis_jk[0]*r_kkp*r_kkp)/(r_jk*r_jk*r_kkp*r_kkp);
dcA_jkkp[1][0]=(dis_kkp[1]*r_jk*r_kkp-cosAng_jkkp
*-dis_jk[1]*r_kkp*r_kkp)/(r_jk*r_jk*r_kkp*r_kkp);
dcA_jkkp[2][0]=(dis_kkp[2]*r_jk*r_kkp-cosAng_jkkp
*-dis_jk[2]*r_kkp*r_kkp)/(r_jk*r_jk*r_kkp*r_kkp);
dcA_jkkp[0][1]=(-dis_jk[0]*r_jk*r_kkp-cosAng_jkkp
*dis_kkp[0]*r_jk*r_jk)/(r_jk*r_jk*r_kkp*r_kkp);
dcA_jkkp[1][1]=(-dis_jk[1]*r_jk*r_kkp-cosAng_jkkp
*dis_kkp[1]*r_jk*r_jk)/(r_jk*r_jk*r_kkp*r_kkp);
dcA_jkkp[2][1]=(-dis_jk[2]*r_jk*r_kkp-cosAng_jkkp
*dis_kkp[2]*r_jk*r_jk)/(r_jk*r_jk*r_kkp*r_kkp);
}
} else {
if(neigh_flag[temp_kkp]) {
pass_kkp=1;
dis_kkp[0]=disij[0][temp_kkp];
dis_kkp[1]=disij[1][temp_kkp];
dis_kkp[2]=disij[2][temp_kkp];
r_kkp=rij[temp_kkp];
betaS_kkp=betaS[temp_kkp];
dBetaS_kkp=dBetaS[temp_kkp];
if(kNeij<ltmp) {
njkkp=kNeij*(2*nlistk-kNeij-1)/2+(ltmp-kNeij)-1;
nglkp=1;
nglj=0;
}
else {
njkkp=ltmp*(2*nlistk-ltmp-1)/2+(kNeij-ltmp)-1;
nglkp=0;
nglj=1;
}
ang_jkkp=cos_index[k]+njkkp;
cosAng_jkkp=cosAng[ang_jkkp];
dcA_jkkp[0][0]=dcAng[ang_jkkp][0][nglj];
dcA_jkkp[1][0]=dcAng[ang_jkkp][1][nglj];
dcA_jkkp[2][0]=dcAng[ang_jkkp][2][nglj];
dcA_jkkp[0][1]=dcAng[ang_jkkp][0][nglkp];
dcA_jkkp[1][1]=dcAng[ang_jkkp][1][nglkp];
dcA_jkkp[2][1]=dcAng[ang_jkkp][2][nglkp];
}
}
if(pass_kkp==1) {
nb_kkp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
bt_sg[nb_kkp].temp=temp_kkp;
bt_sg[nb_kkp].i=k;
bt_sg[nb_kkp].j=kp;
amean=cosAng_jkkp;
if(amean<-1.0) amean=-1.0;
if(npower<=2) {
ps=(amean-1.0)*rdtheta+1.0;
ks=(int)ps;
if(ntheta-1<ks)
ks=ntheta-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
ks=ks-1;
gfactor2=((gfunc3[jtype][ktype][kptype][ks]*ps+
gfunc2[jtype][ktype][kptype][ks])*ps+
gfunc1[jtype][ktype][kptype][ks])*ps+
gfunc[jtype][ktype][kptype][ks];
gprime2=(gfunc6[jtype][ktype][kptype][ks]*ps+
gfunc5[jtype][ktype][kptype][ks])*ps+
gfunc4[jtype][ktype][kptype][ks];
} else {
gfactor2=gpara[jtype-1][ktype-1][kptype-1][0];
gprime2=0.0;
xrun=1.0;
for(lp1=1;lp1<npower+1;lp1++) {
gprime2=gprime2+(lp1)*xrun*gpara[jtype-1][ktype-1][kptype-1][lp1];
xrun=xrun*amean;
gfactor2=gfactor2+xrun*gpara[jtype-1][ktype-1][kptype-1][lp1];
}
}
gfactorsq2=gfactor2*gfactor2;
gsqprime2=2.0*gfactor2*gprime2;
gfactor=gfactorsq*gfactorsq2;
rfactorrt=betaS_jk*betaS_kkp;
rfactor=rfactorrt*rfactorrt;
//3rd DD is Eq. 11 (c) for j atom where i & k=neighbor of j & k'=neighbor of k
DD=DD+gfactor*rfactor;
//agpdpr1 is derivative of DD 3rd term w.r.t. Beta(r_jk)
//agpdpr2 is derivative of DD 3rd term w.r.t. Beta(r_kk')
//app1 is derivative of DD 3rd term w.r.t. cos(theta_ijk)
//app2 is derivative of DD 3rd term w.r.t. cos(theta_jkkp)
agpdpr1=2.0*gfactor*rfactorrt*betaS_kkp
*dBetaS_jk/r_jk;
agpdpr2=2.0*gfactor*rfactorrt*betaS_jk
*dBetaS_kkp/r_kkp;
app1=rfactor*gfactorsq2*gsqprime;
app2=rfactor*gfactorsq*gsqprime2;
bt_sg[nb_ij].dDD[0]-=
app1*dcA_ijk[0][0];
bt_sg[nb_ij].dDD[1]-=
app1*dcA_ijk[1][0];
bt_sg[nb_ij].dDD[2]-=
app1*dcA_ijk[2][0];
bt_sg[nb_jk].dDD[0]+=
app1*dcA_ijk[0][1]
+agpdpr1*dis_jk[0]
-app2*dcA_jkkp[0][0];
bt_sg[nb_jk].dDD[1]+=
app1*dcA_ijk[1][1]
+agpdpr1*dis_jk[1]
-app2*dcA_jkkp[1][0];
bt_sg[nb_jk].dDD[2]+=
app1*dcA_ijk[2][1]
+agpdpr1*dis_jk[2]
-app2*dcA_jkkp[2][0];
bt_sg[nb_kkp].dDD[0]+=
app2*dcA_jkkp[0][1]
+agpdpr2*dis_kkp[0];
bt_sg[nb_kkp].dDD[1]+=
app2*dcA_jkkp[1][1]
+agpdpr2*dis_kkp[1];
bt_sg[nb_kkp].dDD[2]+=
app2*dcA_jkkp[2][1]
+agpdpr2*dis_kkp[2];
}
}
}
}
}
}
}
sig_flag=0;
if(FF<=0.000001) {
sigB=0.0;
sig_flag=1;
}
if(sig_flag==0){
if(sigma_a[iij]==0){
if(sig_flag==0) {
if(AA<0.0)
AA=0.0;
if(BB<0.0)
BB=0.0;
AAC=AA+BB;
for(m=0;m<nb_t;m++) {
if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
bt_sg[m].dAAC[0]=bt_sg[m].dAA[0]
+bt_sg[m].dBB[0];
bt_sg[m].dAAC[1]=bt_sg[m].dAA[1]
+bt_sg[m].dBB[1];
bt_sg[m].dAAC[2]=bt_sg[m].dAA[2]
+bt_sg[m].dBB[2];
}
}
bndtmp=(FF+sigma_delta[iij]*sigma_delta[iij]+sigma_c[iij]*AAC+small4);
bndtmp0=1.0/sqrt(bndtmp);
sigB1=betaS_ij*bndtmp0;
bndtmp=-0.5*bndtmp0*bndtmp0*bndtmp0;
bndtmp1=bndtmp0+betaS_ij*bndtmp*2.0*betaS_ij;
bndtmp1=bndtmp1*dBetaS_ij/r_ij;
bndtmp2=betaS_ij*bndtmp*sigma_c[iij];
setting=0;
for(m=0;m<nb_t;m++) {
if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
temp_kk=bt_sg[m].temp;
if(temp_kk==temp_ij&&setting==0) {
bt_sg[m].dSigB1[0]=bndtmp1*dis_ij[0]
+bndtmp2*bt_sg[m].dAAC[0];
bt_sg[m].dSigB1[1]=bndtmp1*dis_ij[1]
+bndtmp2*bt_sg[m].dAAC[1];
bt_sg[m].dSigB1[2]=bndtmp1*dis_ij[2]
+bndtmp2*bt_sg[m].dAAC[2];
setting=1;
}
else if(temp_kk==temp_ji&&setting==0) {
bt_sg[m].dSigB1[0]=-bndtmp1*dis_ij[0]
+bndtmp2*bt_sg[m].dAAC[0];
bt_sg[m].dSigB1[1]=-bndtmp1*dis_ij[1]
+bndtmp2*bt_sg[m].dAAC[1];
bt_sg[m].dSigB1[2]=-bndtmp1*dis_ij[2]
+bndtmp2*bt_sg[m].dAAC[2];
setting=1;
}
else {
bt_sg[m].dSigB1[0]=bndtmp2*bt_sg[m].dAAC[0];
bt_sg[m].dSigB1[1]=bndtmp2*bt_sg[m].dAAC[1];
bt_sg[m].dSigB1[2]=bndtmp2*bt_sg[m].dAAC[2];
}
}
}
}
} else {
if(sig_flag==0) {
if(AA<0.0)
AA=0.0;
if(BB<0.0)
BB=0.0;
if(CC<0.0)
CC=0.0;
if(DD<0.0)
DD=0.0;
// AA and BB are the representations of (a) Eq. 34 and (b) Eq. 9
// for atoms i and j respectively
AAC=AA+BB;
BBC=AA*BB;
CCC=AA*AA+BB*BB;
DDC=CC+DD;
//EEC is a modified form of (a) Eq. 33
if(DDC<CCC) DDC=CCC;
EEC=(DDC-CCC)/(AAC+2.0*small1);
AACFF=1.0/(AAC+2.0*small1);
for(m=0;m<nb_t;m++) {
if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
bt_sg[m].dAAC[0]=bt_sg[m].dAA[0]
+bt_sg[m].dBB[0];
bt_sg[m].dAAC[1]=bt_sg[m].dAA[1]
+bt_sg[m].dBB[1];
bt_sg[m].dAAC[2]=bt_sg[m].dAA[2]
+bt_sg[m].dBB[2];
bt_sg[m].dBBC[0]=bt_sg[m].dAA[0]*BB
+AA*bt_sg[m].dBB[0];
bt_sg[m].dBBC[1]=bt_sg[m].dAA[1]*BB
+AA*bt_sg[m].dBB[1];
bt_sg[m].dBBC[2]=bt_sg[m].dAA[2]*BB
+AA*bt_sg[m].dBB[2];
bt_sg[m].dCCC[0]=2.0*AA*bt_sg[m].dAA[0]
+2.0*BB*bt_sg[m].dBB[0];
bt_sg[m].dCCC[1]=2.0*AA*bt_sg[m].dAA[1]
+2.0*BB*bt_sg[m].dBB[1];
bt_sg[m].dCCC[2]=2.0*AA*bt_sg[m].dAA[2]
+2.0*BB*bt_sg[m].dBB[2];
bt_sg[m].dDDC[0]=bt_sg[m].dCC[0]
+bt_sg[m].dDD[0];
bt_sg[m].dDDC[1]=bt_sg[m].dCC[1]
+bt_sg[m].dDD[1];
bt_sg[m].dDDC[2]=bt_sg[m].dCC[2]
+bt_sg[m].dDD[2];
bt_sg[m].dEEC[0]=(bt_sg[m].dDDC[0]
-bt_sg[m].dCCC[0]
-EEC*bt_sg[m].dAAC[0])*AACFF;
bt_sg[m].dEEC[1]=(bt_sg[m].dDDC[1]
-bt_sg[m].dCCC[1]
-EEC*bt_sg[m].dAAC[1])*AACFF;
bt_sg[m].dEEC[2]=(bt_sg[m].dDDC[2]
-bt_sg[m].dCCC[2]
-EEC*bt_sg[m].dAAC[2])*AACFF;
}
}
UT=EEC*FF+BBC+small3[iij];
UT=1.0/sqrt(UT);
// FFC is slightly modified form of (a) Eq. 31
// GGC is slightly modified form of (a) Eq. 32
// bndtmp is a slightly modified form of (a) Eq. 30 and (b) Eq. 8
FFC=BBC*UT;
GGC=EEC*UT;
bndtmp=(FF+sigma_delta[iij]*sigma_delta[iij])*(1.0+sigma_a[iij]*GGC)
*(1.0+sigma_a[iij]*GGC)+sigma_c[iij]*(AAC+sigma_a[iij]*EE
+sigma_a[iij]*FFC*(2.0+GGC))+small4;
UTcom=-0.5*UT*UT*UT;
for(m=0;m<nb_t;m++) {
if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
bt_sg[m].dUT[0]=UTcom*(bt_sg[m].dEEC[0]*FF
+EEC*bt_sg[m].dFF[0]+bt_sg[m].dBBC[0]);
bt_sg[m].dUT[1]=UTcom*(bt_sg[m].dEEC[1]*FF
+EEC*bt_sg[m].dFF[1]+bt_sg[m].dBBC[1]);
bt_sg[m].dUT[2]=UTcom*(bt_sg[m].dEEC[2]*FF
+EEC*bt_sg[m].dFF[2]+bt_sg[m].dBBC[2]);
bt_sg[m].dFFC[0]=bt_sg[m].dBBC[0]*UT
+BBC*bt_sg[m].dUT[0];
bt_sg[m].dFFC[1]=bt_sg[m].dBBC[1]*UT
+BBC*bt_sg[m].dUT[1];
bt_sg[m].dFFC[2]=bt_sg[m].dBBC[2]*UT
+BBC*bt_sg[m].dUT[2];
bt_sg[m].dGGC[0]=bt_sg[m].dEEC[0]*UT
+EEC*bt_sg[m].dUT[0];
bt_sg[m].dGGC[1]=bt_sg[m].dEEC[1]*UT
+EEC*bt_sg[m].dUT[1];
bt_sg[m].dGGC[2]=bt_sg[m].dEEC[2]*UT
+EEC*bt_sg[m].dUT[2];
}
}
psign=1.0;
if(1.0+sigma_a[iij]*GGC<0.0)
psign=-1.0;
bndtmp0=1.0/sqrt(bndtmp);
sigB1=psign*betaS_ij*(1.0+sigma_a[iij]*GGC)*bndtmp0;
bndtmp=-0.5*bndtmp0*bndtmp0*bndtmp0;
bndtmp1=psign*(1.0+sigma_a[iij]*GGC)*bndtmp0+psign*betaS_ij
*(1.0+sigma_a[iij]*GGC)*bndtmp*2.0*betaS_ij*(1.0
+sigma_a[iij]*GGC)*(1.0+sigma_a[iij]*GGC);
bndtmp1=bndtmp1*dBetaS_ij/r_ij;
bndtmp2=psign*betaS_ij*(1.0+sigma_a[iij]*GGC)*bndtmp*sigma_c[iij];
bndtmp3=psign*betaS_ij*(1.0+sigma_a[iij]*GGC)
*bndtmp*sigma_c[iij]*sigma_a[iij];
bndtmp4=psign*betaS_ij*(1.0+sigma_a[iij]*GGC)
*bndtmp*sigma_c[iij]*sigma_a[iij]*(2.0+GGC);
bndtmp5=sigma_a[iij]*psign*betaS_ij*bndtmp0
+psign*betaS_ij*(1.0+sigma_a[iij]*GGC)*bndtmp
*(2.0*(FF+sigma_delta[iij]*sigma_delta[iij])*(1.0
+sigma_a[iij]*GGC)*sigma_a[iij]+sigma_c[iij]*sigma_a[iij]*FFC);
setting=0;
for(m=0;m<nb_t;m++) {
if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
temp_kk=bt_sg[m].temp;
if(temp_kk==temp_ij&&setting==0) {
bt_sg[m].dSigB1[0]=bndtmp1*dis_ij[0]
+(bndtmp2*bt_sg[m].dAAC[0]
+bndtmp3*bt_sg[m].dEE[0]
+bndtmp4*bt_sg[m].dFFC[0]
+bndtmp5*bt_sg[m].dGGC[0]);
bt_sg[m].dSigB1[1]=bndtmp1*dis_ij[1]
+(bndtmp2*bt_sg[m].dAAC[1]
+bndtmp3*bt_sg[m].dEE[1]
+bndtmp4*bt_sg[m].dFFC[1]
+bndtmp5*bt_sg[m].dGGC[1]);
bt_sg[m].dSigB1[2]=bndtmp1*dis_ij[2]
+(bndtmp2*bt_sg[m].dAAC[2]
+bndtmp3*bt_sg[m].dEE[2]
+bndtmp4*bt_sg[m].dFFC[2]
+bndtmp5*bt_sg[m].dGGC[2]);
setting=1;
}
else if(temp_kk==temp_ji&&setting==0) {
bt_sg[m].dSigB1[0]=-bndtmp1*dis_ij[0]
+(bndtmp2*bt_sg[m].dAAC[0]
+bndtmp3*bt_sg[m].dEE[0]
+bndtmp4*bt_sg[m].dFFC[0]
+bndtmp5*bt_sg[m].dGGC[0]);
bt_sg[m].dSigB1[1]=-bndtmp1*dis_ij[1]
+(bndtmp2*bt_sg[m].dAAC[1]
+bndtmp3*bt_sg[m].dEE[1]
+bndtmp4*bt_sg[m].dFFC[1]
+bndtmp5*bt_sg[m].dGGC[1]);
bt_sg[m].dSigB1[2]=-bndtmp1*dis_ij[2]
+(bndtmp2*bt_sg[m].dAAC[2]
+bndtmp3*bt_sg[m].dEE[2]
+bndtmp4*bt_sg[m].dFFC[2]
+bndtmp5*bt_sg[m].dGGC[2]);
setting=1;
}
else {
bt_sg[m].dSigB1[0]=(bndtmp2*bt_sg[m].dAAC[0]
+bndtmp3*bt_sg[m].dEE[0]
+bndtmp4*bt_sg[m].dFFC[0]
+bndtmp5*bt_sg[m].dGGC[0]);
bt_sg[m].dSigB1[1]=(bndtmp2*bt_sg[m].dAAC[1]
+bndtmp3*bt_sg[m].dEE[1]
+bndtmp4*bt_sg[m].dFFC[1]
+bndtmp5*bt_sg[m].dGGC[1]);
bt_sg[m].dSigB1[2]=(bndtmp2*bt_sg[m].dAAC[2]
+bndtmp3*bt_sg[m].dEE[2]
+bndtmp4*bt_sg[m].dFFC[2]
+bndtmp5*bt_sg[m].dGGC[2]);
}
}
}
}
}
//This loop is to ensure there is not an error for atoms with no neighbors (deposition)
// sigB is the final expression for (a) Eq. 6 and (b) Eq. 11
if(nb_t==0) {
if(j>i) {
bt_sg[0].dSigB1[0]=bndtmp1*dis_ij[0];
bt_sg[0].dSigB1[1]=bndtmp1*dis_ij[1];
bt_sg[0].dSigB1[2]=bndtmp1*dis_ij[2];
}
else {
bt_sg[0].dSigB1[0]=-bndtmp1*dis_ij[0];
bt_sg[0].dSigB1[1]=-bndtmp1*dis_ij[1];
bt_sg[0].dSigB1[2]=-bndtmp1*dis_ij[2];
}
for(pp=0;pp<3;pp++) {
bt_sg[0].dAA[pp]=0.0;
bt_sg[0].dBB[pp]=0.0;
bt_sg[0].dAAC[pp]=0.0;
bt_sg[0].dSigB1[pp]=0.0;
bt_sg[0].dSigB[pp]=0.0;
if(sigma_f[iij]!=0.5&&sigma_k[iij]!=0.0) {
bt_sg[0].dCC[pp]=0.0;
bt_sg[0].dDD[pp]=0.0;
bt_sg[0].dEE[pp]=0.0;
bt_sg[0].dEE1[pp]=0.0;
bt_sg[0].dFF[pp]=0.0;
bt_sg[0].dBBC[pp]=0.0;
bt_sg[0].dCCC[pp]=0.0;
bt_sg[0].dDDC[pp]=0.0;
bt_sg[0].dEEC[pp]=0.0;
bt_sg[0].dFFC[pp]=0.0;
bt_sg[0].dGGC[pp]=0.0;
bt_sg[0].dUT[pp]=0.0;
}
}
bt_sg[0].i=i;
bt_sg[0].j=j;
bt_sg[0].temp=temp_ij;
nb_t++;
if(nb_t>nb_sg) {
new_n_tot=nb_sg+maxneigh;
grow_sigma(nb_sg,new_n_tot);
nb_sg=new_n_tot;
}
}
ps=sigB1*rdBO+1.0;
ks=(int)ps;
if(nBOt-1<ks)
ks=nBOt-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
dsigB1=((FsigBO3[iij][ks-1]*ps+FsigBO2[iij][ks-1])*ps
+FsigBO1[iij][ks-1])*ps+FsigBO[iij][ks-1];
dsigB2=(FsigBO6[iij][ks-1]*ps+FsigBO5[iij][ks-1])*ps+FsigBO4[iij][ks-1];
for(m=0;m<nb_t;m++) {
if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
temp_kk=bt_sg[m].temp;
bt_i=bt_sg[m].i;
bt_j=bt_sg[m].j;
if(sigma_f[iij]==0.5&&sigma_k[iij]==0.0) {
sigB=dsigB1;
pp1=2.0*betaS_ij;
for(pp=0;pp<3;pp++) {
bt_sg[m].dSigB[pp]=dsigB2*bt_sg[m].dSigB1[pp];
}
for(pp=0;pp<3;pp++) {
ftmp[pp]=pp1*bt_sg[m].dSigB[pp];
f[bt_i][pp]-=ftmp[pp];
f[bt_j][pp]+=ftmp[pp];
}
if(evflag) {
ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0,ftmp[0],ftmp[1]
,ftmp[2],xtmp[0],xtmp[1],xtmp[2]);
}
} else {
part0=(FF+0.5*AAC+small5);
part1=(sigma_f[iij]-0.5)*sigma_k[iij];
part2=1.0-part1*EE1/part0;
part3=dsigB1*part1/part0;
part4=part3/part0*EE1;
// sigB is the final expression for (a) Eq. 6 and (b) Eq. 11
sigB=dsigB1*part2;
pp1=2.0*betaS_ij;
xtmp[0]=x[bt_j][0]-x[bt_i][0];
xtmp[1]=x[bt_j][1]-x[bt_i][1];
xtmp[2]=x[bt_j][2]-x[bt_i][2];
for(pp=0;pp<3;pp++) {
bt_sg[m].dSigB[pp]=dsigB2*part2*bt_sg[m].dSigB1[pp]
-part3*bt_sg[m].dEE1[pp]
+part4*(bt_sg[m].dFF[pp]
+0.5*bt_sg[m].dAAC[pp]);
}
for(pp=0;pp<3;pp++) {
ftmp[pp]=pp1*bt_sg[m].dSigB[pp];
f[bt_i][pp]-=ftmp[pp];
f[bt_j][pp]+=ftmp[pp];
}
if(evflag) {
ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0,ftmp[0],ftmp[1]
,ftmp[2],xtmp[0],xtmp[1],xtmp[2]);
}
}
}
}
}
}
}
return(sigB);
}
/* ---------------------------------------------------------------------- */
/* The formulation differs slightly to avoid negative square roots
in the calculation of Theta_pi,ij of (a) Eq. 36 and (b) Eq. 18
see (d) */
/* ---------------------------------------------------------------------- */
double PairBOP::PiBo(int itmp, int jtmp)
{
int new_n_tot;
int i,j,k,kp,m,n,pp,nb_t;
int iij,iik,iikp,ji,ki,ijkp,ijk;
int nsearch,ncmp;
tagint i_tag,j_tag;
int ltmp,ktmp;
int pi_flag,ks;
int nlocal;
int *ilist,*iilist,*jlist;
int **firstneigh;
int itype,jtype,ktype,kptype;
int temp_ij,temp_ik,temp_ikp;
int temp_jk,temp_jkp;
int nb_ij,nb_ik,nb_jk,nb_ikp,nb_jkp;
int bt_i,bt_j;
int pass_ij,pass_ik,pass_ikp;
int pass_jkp,pass_jk;
int njik,ngj,ngk;
int nkikp,njikp,nglj;
int ngl,ngi,nkjkp;
int nijkp,ngli,nijk;
int ang_jik,ang_jikp,ang_kikp;
int ang_ijk,ang_ijkp,ang_kjkp;
int ni_ij,ni_ji,ni_ik,ni_ikp;
int ni_ki,ni_jk,ni_jkp;
int temp_ji,temp_ki;
int nlistj,nlisti;
double AA,BB,CC;
double cosSq,sinFactor,cosFactor;
double cosSq1,dotV,BBrt,AB1,AB2;
double BBrtR,ABrtR1,ABrtR2;
double angFactor,angFactor1,angFactor2;
double angFactor3,angFactor4,angRfactor;
double dAngR1,dAngR2,agpdpr3;
double agpdpr1,agpdpr2,app1,app2,app3;
double betaCapSq1,dbetaCapSq1;
double betaCapSq2,dbetaCapSq2;
double betaCapSum,ps;
double ftmp[3],xtmp[3];
double dPiB1,dPiB2,dPiB3,pp2;
double dis_ij[3],rsq_ij,r_ij;
double betaP_ij,dBetaP_ij;
double dis_ik[3],rsq_ik,r_ik;
double betaS_ik,dBetaS_ik;
double betaP_ik,dBetaP_ik;
double dis_ikp[3],rsq_ikp,r_ikp;
double betaS_ikp,dBetaS_ikp;
double betaP_ikp,dBetaP_ikp;
double dis_jk[3],rsq_jk,r_jk;
double betaS_jk,dBetaS_jk;
double betaP_jk,dBetaP_jk;
double dis_jkp[3],rsq_jkp,r_jkp;
double betaS_jkp,dBetaS_jkp;
double betaP_jkp,dBetaP_jkp;
double cosAng_jik,dcA_jik[3][2];
double cosAng_jikp,dcA_jikp[3][2];
double cosAng_kikp,dcA_kikp[3][2];
double cosAng_ijk,dcA_ijk[3][2];
double cosAng_ijkp,dcA_ijkp[3][2];
double cosAng_kjkp,dcA_kjkp[3][2];
int newton_pair = force->newton_pair;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
tagint *tag = atom->tag;
nlocal = atom->nlocal;
firstneigh = list->firstneigh;
ilist = list->ilist;
n=0;
if(nb_pi>16) {
nb_pi=16;
}
if(nb_pi==0) {
nb_pi=(maxneigh)*(maxneigh/2);
}
// Loop over all local atoms for i
if(allocate_pi) {
destroy_pi();
}
create_pi(nb_pi);
piB=0;
i = ilist[itmp];
i_tag=tag[i];
itype = map[type[i]]+1;
// j is a loop over all neighbors of i
iilist=firstneigh[i];
for(m=0;m<nb_pi;m++) {
for(pp=0;pp<3;pp++) {
bt_pi[m].dAA[pp]=0.0;
bt_pi[m].dBB[pp]=0.0;
bt_pi[m].dPiB[pp]=0.0;
}
bt_pi[m].i=-1;
bt_pi[m].j=-1;
}
nb_t=0;
temp_ij=BOP_index[i]+jtmp;
ni_ij=neigh_index[temp_ij];
j=iilist[ni_ij];
jlist=firstneigh[j];
j_tag=tag[j];
jtype=map[type[j]]+1;
ftmp[0]=0.0;
ftmp[1]=0.0;
ftmp[2]=0.0;
if(j_tag>=i_tag) {
if(itype==jtype)
iij=itype-1;
else if(itype<jtype)
iij=itype*bop_types-itype*(itype+1)/2+jtype-1;
else
iij=jtype*bop_types-jtype*(jtype+1)/2+itype-1;
if(pi_a[iij]==0) {
nPiBk=0;
piB=0;
} else {
AA=0.0;
BB=0.0;
nPiBk=0;
nlistj=BOP_total[j];
for(ji=0;ji<nlistj;ji++) {
temp_ji=BOP_index[j]+ji;
ni_ji=neigh_index[temp_ji];
if(x[jlist[ni_ji]][0]==x[i][0]) {
if(x[jlist[ni_ji]][1]==x[i][1]) {
if(x[jlist[ni_ji]][2]==x[i][2]) {
break;
}
}
}
}
nb_ij=nb_t;
nb_t++;
if(nb_t>nb_pi) {
new_n_tot=nb_pi+maxneigh;
grow_pi(nb_pi,new_n_tot);
nb_pi=new_n_tot;
}
bt_pi[nb_ij].i=i;
bt_pi[nb_ij].j=j;
bt_pi[nb_ij].temp=temp_ij;
pass_ij=0;
if(otfly==1) {
dis_ij[0]=x[j][0]-x[i][0];
dis_ij[1]=x[j][1]-x[i][1];
dis_ij[2]=x[j][2]-x[i][2];
rsq_ij=dis_ij[0]*dis_ij[0]
+dis_ij[1]*dis_ij[1]
+dis_ij[2]*dis_ij[2];
r_ij=sqrt(rsq_ij);
if(r_ij<=rcut[iij]) {
pass_ij=1;
ps=r_ij*rdr[iij]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaP_ij=((pBetaP3[iij][ks-1]*ps+pBetaP2[iij][ks-1])*ps
+pBetaP1[iij][ks-1])*ps+pBetaP[iij][ks-1];
dBetaP_ij=(pBetaP6[iij][ks-1]*ps+pBetaP5[iij][ks-1])*ps
+pBetaP4[iij][ks-1];
}
} else {
if(neigh_flag[temp_ij]) {
pass_ij=1;
dis_ij[0]=disij[0][temp_ij];
dis_ij[1]=disij[1][temp_ij];
dis_ij[2]=disij[2][temp_ij];
r_ij=rij[temp_ij];
betaP_ij=betaP[temp_ij];
dBetaP_ij=dBetaP[temp_ij];
}
}
// j and k are different neighbors of i
AA=0.0;
BB=0.0;
if(pass_ij==1) {
nPiBk=0;
nlisti=BOP_total[i];
for(ktmp=0;ktmp<nlisti;ktmp++) {
if(ktmp!=jtmp) {
temp_ik=BOP_index[i]+ktmp;
ni_ik=neigh_index[temp_ik];
k=iilist[ni_ik];
ktype=map[type[k]]+1;
if(itype==ktype)
iik=itype-1;
else if(itype<ktype)
iik=itype*bop_types-itype*(itype+1)/2+ktype-1;
else
iik=ktype*bop_types-ktype*(ktype+1)/2+itype-1;
pass_ik=0;
if(otfly==1) {
dis_ik[0]=x[k][0]-x[i][0];
dis_ik[1]=x[k][1]-x[i][1];
dis_ik[2]=x[k][2]-x[i][2];
rsq_ik=dis_ik[0]*dis_ik[0]
+dis_ik[1]*dis_ik[1]
+dis_ik[2]*dis_ik[2];
r_ik=sqrt(rsq_ik);
if(r_ik<=rcut[iik]) {
pass_ik=1;
ps=r_ik*rdr[iik]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ik=((pBetaS3[iik][ks-1]*ps+pBetaS2[iik][ks-1])*ps
+pBetaS1[iik][ks-1])*ps+pBetaS[iik][ks-1];
dBetaS_ik=(pBetaS6[iik][ks-1]*ps+pBetaS5[iik][ks-1])*ps
+pBetaS4[iik][ks-1];
betaP_ik=((pBetaP3[iik][ks-1]*ps+pBetaP2[iik][ks-1])*ps
+pBetaP1[iik][ks-1])*ps+pBetaP[iik][ks-1];
dBetaP_ik=(pBetaP6[iik][ks-1]*ps+pBetaP5[iik][ks-1])*ps
+pBetaP4[iik][ks-1];
cosAng_jik=(dis_ij[0]*dis_ik[0]+dis_ij[1]*dis_ik[1]
+dis_ij[2]*dis_ik[2])/(r_ij*r_ik);
dcA_jik[0][0]=(dis_ik[0]*r_ij*r_ik-cosAng_jik
*dis_ij[0]*r_ik*r_ik)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[1][0]=(dis_ik[1]*r_ij*r_ik-cosAng_jik
*dis_ij[1]*r_ik*r_ik)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[2][0]=(dis_ik[2]*r_ij*r_ik-cosAng_jik
*dis_ij[2]*r_ik*r_ik)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[0][1]=(dis_ij[0]*r_ij*r_ik-cosAng_jik
*dis_ik[0]*r_ij*r_ij)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[1][1]=(dis_ij[1]*r_ij*r_ik-cosAng_jik
*dis_ik[1]*r_ij*r_ij)/(r_ij*r_ij*r_ik*r_ik);
dcA_jik[2][1]=(dis_ij[2]*r_ij*r_ik-cosAng_jik
*dis_ik[2]*r_ij*r_ij)/(r_ij*r_ij*r_ik*r_ik);
}
} else {
if(neigh_flag[temp_ik]) {
pass_ik=1;
dis_ik[0]=disij[0][temp_ik];
dis_ik[1]=disij[1][temp_ik];
dis_ik[2]=disij[2][temp_ik];
r_ik=rij[temp_ik];
betaS_ik=betaS[temp_ik];
dBetaS_ik=dBetaS[temp_ik];
betaP_ik=betaP[temp_ik];
dBetaP_ik=dBetaP[temp_ik];
if(jtmp<ktmp) {
njik=jtmp*(2*nlisti-jtmp-1)/2+(ktmp-jtmp)-1;
ngj=0;
ngk=1;
}
else {
njik=ktmp*(2*nlisti-ktmp-1)/2+(jtmp-ktmp)-1;
ngj=1;
ngk=0;
}
ang_jik=cos_index[i]+njik;
cosAng_jik=cosAng[ang_jik];
dcA_jik[0][0]=dcAng[ang_jik][0][ngj];
dcA_jik[1][0]=dcAng[ang_jik][1][ngj];
dcA_jik[2][0]=dcAng[ang_jik][2][ngj];
dcA_jik[0][1]=dcAng[ang_jik][0][ngk];
dcA_jik[1][1]=dcAng[ang_jik][1][ngk];
dcA_jik[2][1]=dcAng[ang_jik][2][ngk];
}
}
if(pass_ik==1) {
nb_ik=nb_t;
nb_t++;
if(nb_t>nb_pi) {
new_n_tot=nb_pi+maxneigh;
grow_pi(nb_pi,new_n_tot);
nb_pi=new_n_tot;
}
bt_pi[nb_ik].i=i;
bt_pi[nb_ik].j=k;
bt_pi[nb_ik].temp=temp_ik;
cosSq=cosAng_jik*cosAng_jik;
sinFactor=.5*(1.0-cosSq)*pi_p[itype-1]*betaS_ik;
cosFactor=.5*(1.0+cosSq)*betaP_ik;
betaCapSq1=pi_p[itype-1]*betaS_ik*betaS_ik-betaP_ik
*betaP_ik;
dbetaCapSq1=2.0*pi_p[itype-1]*betaS_ik*dBetaS_ik
-2.0*betaP_ik*dBetaP_ik;
//AA is Eq. 37 (a) and Eq. 19 (b) or i atoms
//1st BB is first term of Eq. 38 (a) where j and k =neighbors i
AA=AA+sinFactor*betaS_ik+cosFactor*betaP_ik;
BB=BB+.25*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*betaCapSq1;
//agpdpr1 is derivative of AA w.r.t. for atom i w.r.t. Beta(r_ik)
//agpdpr2 is derivative of BB w.r.t. for atom i w.r.t. Beta(r_ik)
//app1 is derivative of AA w.r.t. for atom i w.r.t. cos(theta_jik)
//app2 is derivative of BB w.r.t. for atom i w.r.t. cos(theta_jik)
agpdpr1=(2.0*sinFactor*dBetaS_ik+2.0*cosFactor
*dBetaP_ik)/r_ik;
app1=cosAng_jik*(-pi_p[itype-1]*betaS_ik*betaS_ik
+betaP_ik*betaP_ik);
app2=-(1.0-cosSq)*cosAng_jik*betaCapSq1*betaCapSq1;
agpdpr2=.5*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*dbetaCapSq1/r_ik;
itypePiBk[nPiBk]=k;
bt_pi[nb_ij].dAA[0]+=
app1*dcA_jik[0][0];
bt_pi[nb_ij].dAA[1]+=
app1*dcA_jik[1][0];
bt_pi[nb_ij].dAA[2]+=
app1*dcA_jik[2][0];
bt_pi[nb_ij].dBB[0]+=
app2*dcA_jik[0][0];
bt_pi[nb_ij].dBB[1]+=
app2*dcA_jik[1][0];
bt_pi[nb_ij].dBB[2]+=
app2*dcA_jik[2][0];
bt_pi[nb_ik].dAA[0]+=
agpdpr1*dis_ik[0]
+app1*dcA_jik[0][1];
bt_pi[nb_ik].dAA[1]+=
agpdpr1*dis_ik[1]
+app1*dcA_jik[1][1];
bt_pi[nb_ik].dAA[2]+=
agpdpr1*dis_ik[2]
+app1*dcA_jik[2][1];
bt_pi[nb_ik].dBB[0]+=
app2*dcA_jik[0][1]
+agpdpr2*dis_ik[0];
bt_pi[nb_ik].dBB[1]+=
app2*dcA_jik[1][1]
+agpdpr2*dis_ik[1];
bt_pi[nb_ik].dBB[2]+=
app2*dcA_jik[2][1]
+agpdpr2*dis_ik[2];
// j and k and k' are different neighbors of i
for(ltmp=0;ltmp<ktmp;ltmp++) {
if(ltmp!=jtmp) {
temp_ikp=BOP_index[i]+ltmp;
ni_ikp=neigh_index[temp_ikp];
kp=iilist[ni_ikp];
kptype=map[type[kp]]+1;
for(nsearch=0;nsearch<nPiBk;nsearch++) {
ncmp=itypePiBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
break;
}
}
}
}
if(itype==kptype)
iikp=itype-1;
else if(itype<kptype)
iikp=itype*bop_types-itype*(itype+1)/2+kptype-1;
else
iikp=kptype*bop_types-kptype*(kptype+1)/2+itype-1;
pass_ikp=0;
if(otfly==1) {
dis_ikp[0]=x[kp][0]-x[i][0];
dis_ikp[1]=x[kp][1]-x[i][1];
dis_ikp[2]=x[kp][2]-x[i][2];
rsq_ikp=dis_ikp[0]*dis_ikp[0]
+dis_ikp[1]*dis_ikp[1]
+dis_ikp[2]*dis_ikp[2];
r_ikp=sqrt(rsq_ikp);
if(r_ikp<=rcut[iikp]) {
pass_ikp=1;
ps=r_ikp*rdr[iikp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ikp=((pBetaS3[iikp][ks-1]*ps+pBetaS2[iikp][ks-1])*ps
+pBetaS1[iikp][ks-1])*ps+pBetaS[iikp][ks-1];
dBetaS_ikp=(pBetaS6[iikp][ks-1]*ps+pBetaS5[iikp][ks-1])*ps
+pBetaS4[iikp][ks-1];
betaP_ikp=((pBetaP3[iikp][ks-1]*ps+pBetaP2[iikp][ks-1])*ps
+pBetaP1[iikp][ks-1])*ps+pBetaP[iikp][ks-1];
dBetaP_ikp=(pBetaP6[iikp][ks-1]*ps+pBetaP5[iikp][ks-1])*ps
+pBetaP4[iikp][ks-1];
cosAng_jikp=(dis_ij[0]*dis_ikp[0]+dis_ij[1]*dis_ikp[1]
+dis_ij[2]*dis_ikp[2])/(r_ij*r_ikp);
dcA_jikp[0][0]=(dis_ikp[0]*r_ij*r_ikp-cosAng_jikp
*dis_ij[0]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[1][0]=(dis_ikp[1]*r_ij*r_ikp-cosAng_jikp
*dis_ij[1]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[2][0]=(dis_ikp[2]*r_ij*r_ikp-cosAng_jikp
*dis_ij[2]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[0][1]=(dis_ij[0]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[0]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[1][1]=(dis_ij[1]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[1]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[2][1]=(dis_ij[2]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[2]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
cosAng_kikp=(dis_ik[0]*dis_ikp[0]+dis_ik[1]*dis_ikp[1]
+dis_ik[2]*dis_ikp[2])/(r_ik*r_ikp);
dcA_kikp[0][0]=(dis_ikp[0]*r_ik*r_ikp-cosAng_kikp
*dis_ik[0]*r_ikp*r_ikp)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[1][0]=(dis_ikp[1]*r_ik*r_ikp-cosAng_kikp
*dis_ik[1]*r_ikp*r_ikp)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[2][0]=(dis_ikp[2]*r_ik*r_ikp-cosAng_kikp
*dis_ik[2]*r_ikp*r_ikp)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[0][1]=(dis_ik[0]*r_ik*r_ikp-cosAng_kikp
*dis_ikp[0]*r_ik*r_ik)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[1][1]=(dis_ik[1]*r_ik*r_ikp-cosAng_kikp
*dis_ikp[1]*r_ik*r_ik)/(r_ik*r_ik*r_ikp*r_ikp);
dcA_kikp[2][1]=(dis_ik[2]*r_ik*r_ikp-cosAng_kikp
*dis_ikp[2]*r_ik*r_ik)/(r_ik*r_ik*r_ikp*r_ikp);
}
} else {
if(neigh_flag[temp_ikp]) {
pass_ikp=1;
dis_ikp[0]=disij[0][temp_ikp];
dis_ikp[1]=disij[1][temp_ikp];
dis_ikp[2]=disij[2][temp_ikp];
r_ikp=rij[temp_ikp];
betaS_ikp=betaS[temp_ikp];
dBetaS_ikp=dBetaS[temp_ikp];
betaP_ikp=betaP[temp_ikp];
dBetaP_ikp=dBetaP[temp_ikp];
nkikp=ltmp*(2*nlisti-ltmp-1)/2+(ktmp-ltmp)-1;
if(jtmp<ltmp) {
njikp=jtmp*(2*nlisti-jtmp-1)/2+(ltmp-jtmp)-1;
nglj=0;
ngl=1;
}
else {
njikp=ltmp*(2*nlisti-ltmp-1)/2+(jtmp-ltmp)-1;
nglj=1;
ngl=0;
}
ang_jikp=cos_index[i]+njikp;
cosAng_jikp=cosAng[ang_jikp];
dcA_jikp[0][0]=dcAng[ang_jikp][0][nglj];
dcA_jikp[1][0]=dcAng[ang_jikp][1][nglj];
dcA_jikp[2][0]=dcAng[ang_jikp][2][nglj];
dcA_jikp[0][1]=dcAng[ang_jikp][0][ngl];
dcA_jikp[1][1]=dcAng[ang_jikp][1][ngl];
dcA_jikp[2][1]=dcAng[ang_jikp][2][ngl];
ang_kikp=cos_index[i]+nkikp;
cosAng_kikp=cosAng[ang_kikp];
dcA_kikp[0][0]=dcAng[ang_kikp][0][1];
dcA_kikp[1][0]=dcAng[ang_kikp][1][1];
dcA_kikp[2][0]=dcAng[ang_kikp][2][1];
dcA_kikp[0][1]=dcAng[ang_kikp][0][0];
dcA_kikp[1][1]=dcAng[ang_kikp][1][0];
dcA_kikp[2][1]=dcAng[ang_kikp][2][0];
}
}
if(pass_ikp==1) {
nb_ikp=nb_t;
nb_t++;
if(nb_t>nb_pi) {
new_n_tot=nb_pi+maxneigh;
grow_pi(nb_pi,new_n_tot);
nb_pi=new_n_tot;
}
bt_pi[nb_ikp].i=i;
bt_pi[nb_ikp].j=kp;
bt_pi[nb_ikp].temp=temp_ikp;
betaCapSq2=pi_p[itype-1]*betaS_ikp*betaS_ikp
-betaP_ikp*betaP_ikp;
dbetaCapSq2=2.0*pi_p[itype-1]*betaS_ikp*dBetaS_ikp
-2.0*betaP_ikp*dBetaP_ikp;
cosSq1=cosAng_jikp*cosAng_jikp;
angFactor=cosAng_kikp-cosAng_jikp*cosAng_jik;
angFactor1=4.0*angFactor;
angFactor2=-angFactor1*cosAng_jikp
+2.0*cosAng_jik*(1.0-cosSq1);
angFactor3=-angFactor1*cosAng_jik
+2.0*cosAng_jikp*(1.0-cosSq);
angFactor4=2.0*angFactor*angFactor-(1.0-cosSq)*(1.0-cosSq1);
betaCapSum=.5*betaCapSq1*betaCapSq2;
//2nd BB is third term of Eq. 38 (a) where j , k and k'=neighbors i
BB=BB+betaCapSum*angFactor4;
//agpdpr1 is derivative of BB w.r.t. for atom i w.r.t. Beta(r_ik)
//agpdpr2 is derivative of BB w.r.t. for atom i w.r.t. Beta(r_ik')
//app1 is derivative of BB 3rd term w.r.t. cos(theta_kik')
//app2 is derivative of BB 3rd term w.r.t. cos(theta_jik)
//app3 is derivative of BB 3rd term w.r.t. cos(theta_jik')
app1=betaCapSum*angFactor1;
app2=betaCapSum*angFactor2;
app3=betaCapSum*angFactor3;
agpdpr1=.5*angFactor4*dbetaCapSq1*betaCapSq2/r_ik;
agpdpr2=.5*angFactor4*betaCapSq1*dbetaCapSq2/r_ikp;
bt_pi[nb_ij].dBB[0]+=
app2*dcA_jik[0][0]
+app3*dcA_jikp[0][0];
bt_pi[nb_ij].dBB[1]+=
app2*dcA_jik[1][0]
+app3*dcA_jikp[1][0];
bt_pi[nb_ij].dBB[2]+=
app2*dcA_jik[2][0]
+app3*dcA_jikp[2][0];
bt_pi[nb_ik].dBB[0]+=
agpdpr1*dis_ik[0]
+app1*dcA_kikp[0][0]
+app2*dcA_jik[0][1];
bt_pi[nb_ik].dBB[1]+=
agpdpr1*dis_ik[1]
+app1*dcA_kikp[1][0]
+app2*dcA_jik[1][1];
bt_pi[nb_ik].dBB[2]+=
agpdpr1*dis_ik[2]
+app1*dcA_kikp[2][0]
+app2*dcA_jik[2][1];
bt_pi[nb_ikp].dBB[0]+=
agpdpr2*dis_ikp[0]
+app1*dcA_kikp[0][1]
+app3*dcA_jikp[0][1];
bt_pi[nb_ikp].dBB[1]+=
agpdpr2*dis_ikp[1]
+app1*dcA_kikp[1][1]
+app3*dcA_jikp[1][1];
bt_pi[nb_ikp].dBB[2]+=
agpdpr2*dis_ikp[2]
+app1*dcA_kikp[2][1]
+app3*dcA_jikp[2][1];
}
}
}
nPiBk=nPiBk+1;
}
}
}
//j is a neighbor of i and k is a neighbor of j and equal to i
for(ki=0;ki<nlistj;ki++) {
temp_ki=BOP_index[j]+ki;
ni_ki=neigh_index[temp_ki];
k=jlist[ni_ki];
if(x[k][0]==x[i][0]) {
if(x[k][1]==x[i][1]) {
if(x[k][2]==x[i][2]) {
break;
}
}
}
}
//j is a neighbor of i and k is a neighbor of j not equal to i
for(ktmp=0;ktmp<nlistj;ktmp++) {
if(ktmp!=ki) {
temp_jk=BOP_index[j]+ktmp;
ni_jk=neigh_index[temp_jk];
k=jlist[ni_jk];
ktype=map[type[k]]+1;
pi_flag=0;
for(nsearch=0;nsearch<nPiBk;nsearch++) {
ncmp=itypePiBk[nsearch];
if(x[ncmp][0]==x[k][0]) {
if(x[ncmp][1]==x[k][1]) {
if(x[ncmp][2]==x[k][2]) {
pi_flag=1;
break;
}
}
}
}
if(pi_flag==0) {
itypePiBk[nPiBk]=k;
}
if(jtype==ktype)
ijk=jtype-1;
else if(jtype<ktype)
ijk=jtype*bop_types-jtype*(jtype+1)/2+ktype-1;
else
ijk=ktype*bop_types-ktype*(ktype+1)/2+jtype-1;
pass_jk=0;
if(otfly==1) {
dis_jk[0]=x[k][0]-x[j][0];
dis_jk[1]=x[k][1]-x[j][1];
dis_jk[2]=x[k][2]-x[j][2];
rsq_jk=dis_jk[0]*dis_jk[0]
+dis_jk[1]*dis_jk[1]
+dis_jk[2]*dis_jk[2];
r_jk=sqrt(rsq_jk);
if(r_jk<=rcut[ijk]) {
pass_jk=1;
ps=r_jk*rdr[ijk]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_jk=((pBetaS3[ijk][ks-1]*ps+pBetaS2[ijk][ks-1])*ps
+pBetaS1[ijk][ks-1])*ps+pBetaS[ijk][ks-1];
dBetaS_jk=(pBetaS6[ijk][ks-1]*ps+pBetaS5[ijk][ks-1])*ps
+pBetaS4[ijk][ks-1];
betaP_jk=((pBetaP3[ijk][ks-1]*ps+pBetaP2[ijk][ks-1])*ps
+pBetaP1[ijk][ks-1])*ps+pBetaP[ijk][ks-1];
dBetaP_jk=(pBetaP6[ijk][ks-1]*ps+pBetaP5[ijk][ks-1])*ps
+pBetaP4[ijk][ks-1];
cosAng_ijk=(-dis_ij[0]*dis_jk[0]-dis_ij[1]*dis_jk[1]
-dis_ij[2]*dis_jk[2])/(r_ij*r_jk);
dcA_ijk[0][0]=(dis_jk[0]*r_ij*r_jk-cosAng_ijk
*-dis_ij[0]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[1][0]=(dis_jk[1]*r_ij*r_jk-cosAng_ijk
*-dis_ij[1]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][0]=(dis_jk[2]*r_ij*r_jk-cosAng_ijk
*-dis_ij[2]*r_jk*r_jk)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[0][1]=(-dis_ij[0]*r_ij*r_jk-cosAng_ijk
*dis_jk[0]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[1][1]=(-dis_ij[1]*r_ij*r_jk-cosAng_ijk
*dis_jk[1]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][1]=(-dis_ij[2]*r_ij*r_jk-cosAng_ijk
*dis_jk[2]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
}
} else {
if(neigh_flag[temp_jk]) {
pass_jk=1;
dis_jk[0]=disij[0][temp_jk];
dis_jk[1]=disij[1][temp_jk];
dis_jk[2]=disij[2][temp_jk];
r_jk=rij[temp_jk];
betaS_jk=betaS[temp_jk];
dBetaS_jk=dBetaS[temp_jk];
betaP_jk=betaP[temp_jk];
dBetaP_jk=dBetaP[temp_jk];
if(ktmp<ki) {
nijk=ktmp*(2*nlistj-ktmp-1)/2+(ki-ktmp)-1;
ngi=1;
ngk=0;
}
else {
nijk=ki*(2*nlistj-ki-1)/2+(ktmp-ki)-1;
ngi=0;
ngk=1;
}
ang_ijk=cos_index[j]+nijk;
cosAng_ijk=cosAng[ang_ijk];
dcA_ijk[0][0]=dcAng[ang_ijk][0][ngi];
dcA_ijk[1][0]=dcAng[ang_ijk][1][ngi];
dcA_ijk[2][0]=dcAng[ang_ijk][2][ngi];
dcA_ijk[0][1]=dcAng[ang_ijk][0][ngk];
dcA_ijk[1][1]=dcAng[ang_ijk][1][ngk];
dcA_ijk[2][1]=dcAng[ang_ijk][2][ngk];
}
}
if(pass_jk==1) {
nb_jk=nb_t;
nb_t++;
if(nb_t>nb_pi) {
new_n_tot=nb_pi+maxneigh;
grow_pi(nb_pi,new_n_tot);
nb_pi=new_n_tot;
}
bt_pi[nb_jk].i=j;
bt_pi[nb_jk].j=k;
bt_pi[nb_jk].temp=temp_jk;
cosSq=cosAng_ijk*cosAng_ijk;
sinFactor=.5*(1.0-cosSq)*pi_p[jtype-1]*betaS_jk;
cosFactor=.5*(1.0+cosSq)*betaP_jk;
betaCapSq1=pi_p[jtype-1]*betaS_jk*betaS_jk
-betaP_jk*betaP_jk;
dbetaCapSq1=2.0*pi_p[jtype-1]*betaS_jk*dBetaS_jk
-2.0*betaP_jk*dBetaP_jk;
//AA is Eq. 37 (a) and Eq. 19 (b) for j atoms
//3rd BB is 2nd term of Eq. 38 (a) where i and k =neighbors j
AA=AA+sinFactor*betaS_jk+cosFactor*betaP_jk;
BB=BB+.25*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*betaCapSq1;
agpdpr1=(2.0*sinFactor*dBetaS_jk+2.0*cosFactor
*dBetaP_jk)/r_jk;
//agpdpr1 is derivative of AA for atom j w.r.t. Beta(r_jk)
//agpdpr2 is derivative of BB for atom j w.r.t. Beta(r_jk)
//app1 is derivative of AA for j atom w.r.t. cos(theta_ijk)
//app2 is derivative of BB 2nd term w.r.t. cos(theta_ijk)
agpdpr2=.5*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*dbetaCapSq1/r_jk;
app1=cosAng_ijk*(-pi_p[jtype-1]*betaS_jk*betaS_jk
+betaP_jk*betaP_jk);
app2=-(1.0-cosSq)*cosAng_ijk*betaCapSq1*betaCapSq1;
bt_pi[nb_ij].dAA[0]-=
app1*dcA_ijk[0][0];
bt_pi[nb_ij].dAA[1]-=
app1*dcA_ijk[1][0];
bt_pi[nb_ij].dAA[2]-=
app1*dcA_ijk[2][0];
bt_pi[nb_ij].dBB[0]-=
app2*dcA_ijk[0][0];
bt_pi[nb_ij].dBB[1]-=
app2*dcA_ijk[1][0];
bt_pi[nb_ij].dBB[2]-=
app2*dcA_ijk[2][0];
bt_pi[nb_jk].dAA[0]+=
agpdpr1*dis_jk[0]
+app1*dcA_ijk[0][1];
bt_pi[nb_jk].dAA[1]+=
agpdpr1*dis_jk[1]
+app1*dcA_ijk[1][1];
bt_pi[nb_jk].dAA[2]+=
agpdpr1*dis_jk[2]
+app1*dcA_ijk[2][1];
bt_pi[nb_jk].dBB[0]+=
app2*dcA_ijk[0][1]
+agpdpr2*dis_jk[0];
bt_pi[nb_jk].dBB[1]+=
app2*dcA_ijk[1][1]
+agpdpr2*dis_jk[1];
bt_pi[nb_jk].dBB[2]+=
app2*dcA_ijk[2][1]
+agpdpr2*dis_jk[2];
//j is a neighbor of i and k and k' are different neighbors of j not equal to i
for(ltmp=0;ltmp<ktmp;ltmp++) {
if(ltmp!=ki) {
temp_jkp=BOP_index[j]+ltmp;
ni_jkp=neigh_index[temp_jkp];
kp=jlist[ni_jkp];
kptype=map[type[kp]]+1;
for(nsearch=0;nsearch<nPiBk;nsearch++) {
ncmp=itypePiBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
break;
}
}
}
}
if(jtype==kptype)
ijkp=jtype-1;
else if(jtype<kptype)
ijkp=jtype*bop_types-jtype*(jtype+1)/2+kptype-1;
else
ijkp=kptype*bop_types-kptype*(kptype+1)/2+jtype-1;
pass_jkp=0;
if(otfly==1) {
dis_jkp[0]=x[kp][0]-x[j][0];
dis_jkp[1]=x[kp][1]-x[j][1];
dis_jkp[2]=x[kp][2]-x[j][2];
rsq_jkp=dis_jkp[0]*dis_jkp[0]
+dis_jkp[1]*dis_jkp[1]
+dis_jkp[2]*dis_jkp[2];
r_jkp=sqrt(rsq_jkp);
if(r_jkp<=rcut[ijkp]) {
pass_jkp=1;
ps=r_jkp*rdr[ijkp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_jkp=((pBetaS3[ijkp][ks-1]*ps+pBetaS2[ijkp][ks-1])*ps
+pBetaS1[ijkp][ks-1])*ps+pBetaS[ijkp][ks-1];
dBetaS_jkp=(pBetaS6[ijkp][ks-1]*ps+pBetaS5[ijkp][ks-1])*ps
+pBetaS4[ijkp][ks-1];
betaP_jkp=((pBetaP3[ijkp][ks-1]*ps+pBetaP2[ijkp][ks-1])*ps
+pBetaP1[ijkp][ks-1])*ps+pBetaP[ijkp][ks-1];
dBetaP_jkp=(pBetaP6[ijkp][ks-1]*ps+pBetaP5[ijkp][ks-1])*ps
+pBetaP4[ijkp][ks-1];
cosAng_ijkp=(-dis_ij[0]*dis_jkp[0]-dis_ij[1]*dis_jkp[1]
-dis_ij[2]*dis_jkp[2])/(r_ij*r_jkp);
dcA_ijkp[0][0]=(dis_jkp[0]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[0]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[1][0]=(dis_jkp[1]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[1]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[2][0]=(dis_jkp[2]*r_ij*r_jkp-cosAng_ijkp
*-dis_ij[2]*r_jkp*r_jkp)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[0][1]=(-dis_ij[0]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[0]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[1][1]=(-dis_ij[1]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[1]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
dcA_ijkp[2][1]=(-dis_ij[2]*r_ij*r_jkp-cosAng_ijkp
*dis_jkp[2]*r_ij*r_ij)/(r_ij*r_ij*r_jkp*r_jkp);
cosAng_kjkp=(dis_jk[0]*dis_jkp[0]+dis_jk[1]*dis_jkp[1]
+dis_jk[2]*dis_jkp[2])/(r_jk*r_jkp);
dcA_kjkp[0][0]=(dis_jkp[0]*r_jk*r_jkp-cosAng_kjkp
*dis_jk[0]*r_jkp*r_jkp)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[1][0]=(dis_jkp[1]*r_jk*r_jkp-cosAng_kjkp
*dis_jk[1]*r_jkp*r_jkp)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[2][0]=(dis_jkp[2]*r_jk*r_jkp-cosAng_kjkp
*dis_jk[2]*r_jkp*r_jkp)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[0][1]=(dis_jk[0]*r_jk*r_jkp-cosAng_kjkp
*dis_jkp[0]*r_jk*r_jk)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[1][1]=(dis_jk[1]*r_jk*r_jkp-cosAng_kjkp
*dis_jkp[1]*r_jk*r_jk)/(r_jk*r_jk*r_jkp*r_jkp);
dcA_kjkp[2][1]=(dis_jk[2]*r_jk*r_jkp-cosAng_kjkp
*dis_jkp[2]*r_jk*r_jk)/(r_jk*r_jk*r_jkp*r_jkp);
}
} else {
if(neigh_flag[temp_jkp]) {
pass_jkp=1;
dis_jkp[0]=disij[0][temp_jkp];
dis_jkp[1]=disij[1][temp_jkp];
dis_jkp[2]=disij[2][temp_jkp];
r_jkp=rij[temp_jkp];
betaS_jkp=betaS[temp_jkp];
dBetaS_jkp=dBetaS[temp_jkp];
betaP_jkp=betaP[temp_jkp];
dBetaP_jkp=dBetaP[temp_jkp];
nkjkp=ltmp*(2*nlistj-ltmp-1)/2+(ktmp-ltmp)-1;
if(ki<ltmp) {
nijkp=ki*(2*nlistj-ki-1)/2+(ltmp-ki)-1;
ngli=0;
ngl=1;
}
else {
nijkp=ltmp*(2*nlistj-ltmp-1)/2+(ki-ltmp)-1;
ngli=1;
ngl=0;
}
ang_ijkp=cos_index[j]+nijkp;
cosAng_ijkp=cosAng[ang_ijkp];
dcA_ijkp[0][0]=dcAng[ang_ijkp][0][ngli];
dcA_ijkp[1][0]=dcAng[ang_ijkp][1][ngli];
dcA_ijkp[2][0]=dcAng[ang_ijkp][2][ngli];
dcA_ijkp[0][1]=dcAng[ang_ijkp][0][ngl];
dcA_ijkp[1][1]=dcAng[ang_ijkp][1][ngl];
dcA_ijkp[2][1]=dcAng[ang_ijkp][2][ngl];
ang_kjkp=cos_index[j]+nkjkp;
cosAng_kjkp=cosAng[ang_kjkp];
dcA_kjkp[0][0]=dcAng[ang_kjkp][0][1];
dcA_kjkp[1][0]=dcAng[ang_kjkp][1][1];
dcA_kjkp[2][0]=dcAng[ang_kjkp][2][1];
dcA_kjkp[0][1]=dcAng[ang_kjkp][0][0];
dcA_kjkp[1][1]=dcAng[ang_kjkp][1][0];
dcA_kjkp[2][1]=dcAng[ang_kjkp][2][0];
}
}
if(pass_jkp) {
nb_jkp=nb_t;
nb_t++;
if(nb_t>nb_pi) {
new_n_tot=nb_pi+maxneigh;
grow_pi(nb_pi,new_n_tot);
nb_pi=new_n_tot;
}
bt_pi[nb_jkp].i=j;
bt_pi[nb_jkp].j=kp;
bt_pi[nb_jkp].temp=temp_jkp;
betaCapSq2=pi_p[jtype-1]*betaS_jkp*betaS_jkp
-betaP_jkp*betaP_jkp;
dbetaCapSq2=2.0*pi_p[jtype-1]*betaS_jkp*dBetaS_jkp
-2.0*betaP_jkp*dBetaP_jkp;
cosSq1=cosAng_ijkp*cosAng_ijkp;
angFactor=cosAng_kjkp-cosAng_ijkp*cosAng_ijk;
angFactor1=4.0*angFactor;
angFactor2=-angFactor1*cosAng_ijkp
+2.0*cosAng_ijk*(1.0-cosSq1);
angFactor3=-angFactor1*cosAng_ijk
+2.0*cosAng_ijkp*(1.0-cosSq);
angFactor4=2.0*angFactor*angFactor-(1.0-cosSq)*(1.0-cosSq1);
betaCapSum=.5*betaCapSq1*betaCapSq2;
//4th BB is 4th term of Eq. 38 (a) where i , k and k' =neighbors j
BB=BB+betaCapSum*angFactor4;
//app1 is derivative of BB 4th term w.r.t. cos(theta_kjk')
//app2 is derivative of BB 4th term w.r.t. cos(theta_ijk)
//app3 is derivative of BB 4th term w.r.t. cos(theta_ijk')
//agpdpr1 is derivative of BB 4th term for atom j w.r.t. Beta(r_jk)
//agpdpr2 is derivative of BB 4th term for atom j w.r.t. Beta(r_jk')
app1=betaCapSum*angFactor1;
app2=betaCapSum*angFactor2;
app3=betaCapSum*angFactor3;
agpdpr1=.5*angFactor4*dbetaCapSq1*betaCapSq2/r_jk;
agpdpr2=.5*angFactor4*betaCapSq1*dbetaCapSq2/r_jkp;
bt_pi[nb_ij].dBB[0]-=
app3*dcA_ijkp[0][0]
+app2*dcA_ijk[0][0];
bt_pi[nb_ij].dBB[1]-=
app3*dcA_ijkp[1][0]
+app2*dcA_ijk[1][0];
bt_pi[nb_ij].dBB[2]-=
app3*dcA_ijkp[2][0]
+app2*dcA_ijk[2][0];
bt_pi[nb_jk].dBB[0]+=
agpdpr1*dis_jk[0]
+app1*dcA_kjkp[0][0]
+app2*dcA_ijk[0][1];
bt_pi[nb_jk].dBB[1]+=
agpdpr1*dis_jk[1]
+app1*dcA_kjkp[1][0]
+app2*dcA_ijk[1][1];
bt_pi[nb_jk].dBB[2]+=
agpdpr1*dis_jk[2]
+app1*dcA_kjkp[2][0]
+app2*dcA_ijk[2][1];
bt_pi[nb_jkp].dBB[0]+=
agpdpr2*dis_jkp[0]
+app1*dcA_kjkp[0][1]
+app3*dcA_ijkp[0][1];
bt_pi[nb_jkp].dBB[1]+=
agpdpr2*dis_jkp[1]
+app1*dcA_kjkp[1][1]
+app3*dcA_ijkp[1][1];
bt_pi[nb_jkp].dBB[2]+=
agpdpr2*dis_jkp[2]
+app1*dcA_kjkp[2][1]
+app3*dcA_ijkp[2][1];
}
}
}
//j and k' are different neighbors of i and k is a neighbor of j not equal to i
for(ltmp=0;ltmp<nlisti;ltmp++) {
if(ltmp!=jtmp) {
temp_ikp=BOP_index[i]+ltmp;
ni_ikp=neigh_index[temp_ikp];
kp=iilist[ni_ikp];
kptype=map[type[kp]]+1;
for(nsearch=0;nsearch<nPiBk;nsearch++) {
ncmp=itypePiBk[nsearch];
if(x[ncmp][0]==x[kp][0]) {
if(x[ncmp][1]==x[kp][1]) {
if(x[ncmp][2]==x[kp][2]) {
break;
}
}
}
}
if(itype==kptype)
iikp=itype-1;
else if(itype<kptype)
iikp=itype*bop_types-itype*(itype+1)/2+kptype-1;
else
iikp=kptype*bop_types-kptype*(kptype+1)/2+itype-1;
pass_ikp=0;
if(otfly==1) {
dis_ikp[0]=x[kp][0]-x[i][0];
dis_ikp[1]=x[kp][1]-x[i][1];
dis_ikp[2]=x[kp][2]-x[i][2];
rsq_ikp=dis_ikp[0]*dis_ikp[0]
+dis_ikp[1]*dis_ikp[1]
+dis_ikp[2]*dis_ikp[2];
r_ikp=sqrt(rsq_ikp);
if(r_ikp<=rcut[iikp]) {
pass_ikp=1;
ps=r_ikp*rdr[iikp]+1.0;
ks=(int)ps;
if(nr-1<ks)
ks=nr-1;
ps=ps-ks;
if(ps>1.0)
ps=1.0;
betaS_ikp=((pBetaS3[iikp][ks-1]*ps+pBetaS2[iikp][ks-1])*ps
+pBetaS1[iikp][ks-1])*ps+pBetaS[iikp][ks-1];
dBetaS_ikp=(pBetaS6[iikp][ks-1]*ps+pBetaS5[iikp][ks-1])*ps
+pBetaS4[iikp][ks-1];
betaP_ikp=((pBetaP3[iikp][ks-1]*ps+pBetaP2[iikp][ks-1])*ps
+pBetaP1[iikp][ks-1])*ps+pBetaP[iikp][ks-1];
dBetaP_ikp=(pBetaP6[iikp][ks-1]*ps+pBetaP5[iikp][ks-1])*ps
+pBetaP4[iikp][ks-1];
cosAng_jikp=(dis_ij[0]*dis_ikp[0]+dis_ij[1]*dis_ikp[1]
+dis_ij[2]*dis_ikp[2])/(r_ij*r_ikp);
dcA_jikp[0][0]=(dis_ikp[0]*r_ij*r_ikp-cosAng_jikp
*dis_ij[0]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[1][0]=(dis_ikp[1]*r_ij*r_ikp-cosAng_jikp
*dis_ij[1]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[2][0]=(dis_ikp[2]*r_ij*r_ikp-cosAng_jikp
*dis_ij[2]*r_ikp*r_ikp)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[0][1]=(dis_ij[0]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[0]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[1][1]=(dis_ij[1]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[1]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
dcA_jikp[2][1]=(dis_ij[2]*r_ij*r_ikp-cosAng_jikp
*dis_ikp[2]*r_ij*r_ij)/(r_ij*r_ij*r_ikp*r_ikp);
}
} else {
if(neigh_flag[temp_ikp]) {
pass_ikp=1;
dis_ikp[0]=disij[0][temp_ikp];
dis_ikp[1]=disij[1][temp_ikp];
dis_ikp[2]=disij[2][temp_ikp];
r_ikp=rij[temp_ikp];
betaS_ikp=betaS[temp_ikp];
dBetaS_ikp=dBetaS[temp_ikp];
betaP_ikp=betaP[temp_ikp];
dBetaP_ikp=dBetaP[temp_ikp];
if(ltmp<jtmp) {
njikp=ltmp*(2*nlisti-ltmp-1)/2+(jtmp-ltmp)-1;
ngl=1;
nglj=0;
}
else {
njikp=jtmp*(2*nlisti-jtmp-1)/2+(ltmp-jtmp)-1;
ngl=0;
nglj=1;
}
ang_jikp=cos_index[i]+njikp;
cosAng_jikp=cosAng[ang_jikp];
dcA_jikp[0][0]=dcAng[ang_jikp][0][ngl];
dcA_jikp[1][0]=dcAng[ang_jikp][1][ngl];
dcA_jikp[2][0]=dcAng[ang_jikp][2][ngl];
dcA_jikp[0][1]=dcAng[ang_jikp][0][nglj];
dcA_jikp[1][1]=dcAng[ang_jikp][1][nglj];
dcA_jikp[2][1]=dcAng[ang_jikp][2][nglj];
}
}
if(pass_ikp==1) {
nb_ikp=nb_t;
nb_t++;
if(nb_t>nb_pi) {
new_n_tot=nb_pi+maxneigh;
grow_pi(nb_pi,new_n_tot);
nb_pi=new_n_tot;
}
bt_pi[nb_ikp].i=i;
bt_pi[nb_ikp].j=kp;
bt_pi[nb_ikp].temp=temp_ikp;
betaCapSq2=pi_p[itype-1]*betaS_ikp*betaS_ikp
-betaP_ikp*betaP_ikp;
dbetaCapSq2=2.0*pi_p[itype-1]*betaS_ikp*dBetaS_ikp
-2.0*betaP_ikp*dBetaP_ikp;
dotV=(dis_jk[0]*dis_ikp[0]+dis_jk[1]
*dis_ikp[1]+dis_jk[2]*dis_ikp[2])
/(r_jk*r_ikp);
cosSq1=cosAng_jikp*cosAng_jikp;
angFactor=dotV+cosAng_jikp*cosAng_ijk;
angRfactor=4.0*angFactor*dotV;
dAngR1=-angRfactor/r_jk;
dAngR2=-angRfactor/r_ikp;
angFactor1=4.0*angFactor*cosAng_jikp
+2.0*cosAng_ijk*(1.0-cosSq1);
angFactor2=4.0*angFactor*cosAng_ijk
+2.0*cosAng_jikp*(1.0-cosSq);
angFactor3=2.0*angFactor*angFactor-(1.0-cosSq)*(1.0-cosSq1);
betaCapSum=.5*betaCapSq1*betaCapSq2;
//5th BB is 5th term of Eq. 38 (a) Eq. 21 (b) where i , k and k' =neighbors j
BB=BB+betaCapSum*angFactor3;
//app1 is derivative of BB 5th term w.r.t. cos(theta_ijk)
//app2 is derivative of BB 5th term w.r.t. cos(theta_jik')
//agpdpr1 is derivative of BB 5th term for atom j w.r.t. Beta(r_jk)
//agpdpr2 is derivative of BB 5th term for atom j w.r.t. Beta(r_ik')
//agpdpr3 is derivative of BB 5th term for atom j w.r.t. dot(r_ik',r_ij)
app1=betaCapSum*angFactor1;
app2=betaCapSum*angFactor2;
agpdpr1=(.5*angFactor3*dbetaCapSq1*betaCapSq2
+betaCapSum*dAngR1)/r_jk;
agpdpr2=(.5*angFactor3*betaCapSq1*dbetaCapSq2
+betaCapSum*dAngR2)/r_ikp;
agpdpr3=4.0*betaCapSum*angFactor/(r_ikp*r_jk);
bt_pi[nb_ij].dBB[0]+=
+app2*dcA_jikp[0][0]
-app1*dcA_ijk[0][0];
bt_pi[nb_ij].dBB[1]+=
+app2*dcA_jikp[1][0]
-app1*dcA_ijk[1][0];
bt_pi[nb_ij].dBB[2]+=
+app2*dcA_jikp[2][0]
-app1*dcA_ijk[2][0];
bt_pi[nb_ikp].dBB[0]+=
agpdpr2*dis_ikp[0]
+agpdpr3*dis_jk[0]
+app2*dcA_jikp[0][1];
bt_pi[nb_ikp].dBB[1]+=
agpdpr2*dis_ikp[1]
+agpdpr3*dis_jk[1]
+app2*dcA_jikp[1][1];
bt_pi[nb_ikp].dBB[2]+=
agpdpr2*dis_ikp[2]
+agpdpr3*dis_jk[2]
+app2*dcA_jikp[2][1];
bt_pi[nb_jk].dBB[0]+=
agpdpr1*dis_jk[0]
+agpdpr3*dis_ikp[0]
+app1*dcA_ijk[0][1];
bt_pi[nb_jk].dBB[1]+=
agpdpr1*dis_jk[1]
+agpdpr3*dis_ikp[1]
+app1*dcA_ijk[1][1];
bt_pi[nb_jk].dBB[2]+=
agpdpr1*dis_jk[2]
+agpdpr3*dis_ikp[2]
+app1*dcA_ijk[2][1];
}
}
}
if(pi_flag==0)
nPiBk=nPiBk+1;
}
}
}
n++;
pp2=2.0*betaP_ij;
for(m=0;m<nb_t;m++) {
bt_i=bt_pi[m].i;
bt_j=bt_pi[m].j;
CC=betaP_ij*betaP_ij+pi_delta[iij]*pi_delta[iij];
BBrt=sqrt(BB+small6);
AB1=CC+pi_c[iij]*(AA+BBrt)+small7;
AB2=CC+pi_c[iij]*(AA-BBrt+sqrt(small6))+small7;
BBrtR=1.0/BBrt;
ABrtR1=1.0/sqrt(AB1);
ABrtR2=1.0/sqrt(AB2);
piB=(ABrtR1+ABrtR2)*pi_a[iij]*betaP_ij;
dPiB1=-.5*(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_c[iij]*pi_a[iij]*betaP_ij;
dPiB2=.25*BBrtR*(pow(ABrtR2,3)-pow(ABrtR1,3))*pi_c[iij]*pi_a[iij]*betaP_ij;
dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_a[iij]
*betaP_ij*betaP_ij)*dBetaP_ij/r_ij;
xtmp[0]=x[bt_j][0]-x[bt_i][0];
xtmp[1]=x[bt_j][1]-x[bt_i][1];
xtmp[2]=x[bt_j][2]-x[bt_i][2];
for(pp=0;pp<3;pp++) {
bt_pi[m].dPiB[pp]=
+dPiB1*bt_pi[m].dAA[pp]
+dPiB2*bt_pi[m].dBB[pp];
ftmp[pp]=pp2*bt_pi[m].dPiB[pp];
f[bt_i][pp]-=ftmp[pp];
f[bt_j][pp]+=ftmp[pp];
}
if(evflag) {
ev_tally_xyz(bt_i,bt_j,nlocal,newton_pair,0.0,0.0,ftmp[0],ftmp[1]
,ftmp[2],xtmp[0],xtmp[1],xtmp[2]);
}
}
for(pp=0;pp<3;pp++) {
ftmp[pp]=pp2*dPiB3*dis_ij[pp];
f[i][pp]-=ftmp[pp];
f[j][pp]+=ftmp[pp];
}
if(evflag) {
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,ftmp[0],ftmp[1]
,ftmp[2],dis_ij[0],dis_ij[1],dis_ij[2]);
}
}
}
}
destroy_pi();
return(piB);
}
/* ----------------------------------------------------------------------
read BOP potential file
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void PairBOP::read_table(char *filename)
{
int i,j,k,n,m;
int buf1,pass;
int nws,ws;
double buf2;
char s[MAXLINE],buf[2];
MPI_Comm_rank(world,&me);
if (me == 0) {
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str);
}
fgets(s,MAXLINE,fp); // skip first comment line
fgets(s,MAXLINE,fp);
sscanf(s,"%d",&bop_types);
elements = new char*[bop_types];
for(i=0;i<bop_types;i++) elements[i]=NULL;
for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp);
nws=0;
ws=1;
for(j=0;j<strlen(s);j++) {
if(ws==1) {
if(isspace(s[j])) {
ws=1;
} else {
ws=0;
}
} else {
if(isspace(s[j])) {
ws=1;
nws++;
} else {
ws=0;
}
}
}
if(nws!=3){
error->all(FLERR,"Incorrect table format check for element types");
}
sscanf(s,"%d %lf %s",&buf1,&buf2,buf);
n= strlen(buf)+1;
elements[i] = new char[n];
strcpy(elements[i],buf);
}
nws=0;
ws=1;
fgets(s,MAXLINE,fp);
for(j=0;j<strlen(s);j++) {
if(ws==1) {
if(isspace(s[j])) {
ws=1;
} else {
ws=0;
}
} else {
if(isspace(s[j])) {
ws=1;
nws++;
} else {
ws=0;
}
}
}
if(nws==3) {
sscanf(s,"%d %d %d",&nr,&ntheta,&nBOt);
npower=2;
if(ntheta<=10) npower=ntheta;
}
else {
sscanf(s,"%d %d",&nr,&nBOt);
ntheta=0;
npower=3;
}
fclose(fp);
npairs=bop_types*(bop_types+1)/2;
}
MPI_Bcast(&nr,1,MPI_INT,0,world);
MPI_Bcast(&nBOt,1,MPI_INT,0,world);
MPI_Bcast(&ntheta,1,MPI_INT,0,world);
MPI_Bcast(&bop_types,1,MPI_INT,0,world);
MPI_Bcast(&npairs,1,MPI_INT,0,world);
MPI_Bcast(&npower,1,MPI_INT,0,world);
memory->create(pi_a,npairs,"BOP:pi_a");
memory->create(pro_delta,bop_types,"BOP:pro_delta");
memory->create(pi_delta,npairs,"BOP:pi_delta");
memory->create(pi_p,bop_types,"BOP:pi_p");
memory->create(pi_c,npairs,"BOP:pi_c");
memory->create(r1,npairs,"BOP:r1");
memory->create(pro,bop_types,"BOP:pro");
memory->create(sigma_delta,npairs,"BOP:sigma_delta");
memory->create(sigma_c,npairs,"BOP:sigma_c");
memory->create(sigma_a,npairs,"BOP:sigma_a");
memory->create(sigma_f,npairs,"BOP:sigma_f");
memory->create(sigma_k,npairs,"BOP:sigma_k");
memory->create(small3,npairs,"BOP:small3");
memory->create(gfunc,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc");
memory->create(gfunc1,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc1");
memory->create(gfunc2,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc2");
memory->create(gfunc3,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc3");
memory->create(gfunc4,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc4");
memory->create(gfunc5,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc5");
memory->create(gfunc6,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc6");
memory->create(gpara,bop_types,bop_types,bop_types,npower+1,"BOP:gpara");
allocate();
if (me == 0) {
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str);
}
fgets(s,MAXLINE,fp); // skip first comment line
for(i=0;i<bop_types+2;i++) {
fgets(s,MAXLINE,fp);
}
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g
,&small4,&small5,&small6,&small7);
for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf",&pi_p[i]);
}
cutmax=0;
for(i=0;i<npairs;i++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf",&rcut[i]);
if(rcut[i]>cutmax)
cutmax=rcut[i];
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
}
if(nws==3) {
for(i=0;i<bop_types;i++)
for(j=0;j<bop_types;j++)
for(k=j;k<bop_types;k++) {
if(npower<=2) {
for(m=0;m<ntheta;m++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1]
,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]);
n+=4;
}
} else {
if(npower==3) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]);
}
else if(npower==4) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
}
else if(npower==5) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf",&gpara[j][i][k][5]);
}
else if(npower==6) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]);
}
else if(npower==7) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]);
}
else if(npower==8) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]);
}
else if(npower==9) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
}
else if(npower==10) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
fgets(s,MAXLINE,fp);
sscanf(s,"%lf",&gpara[j][i][k][10]);
}
}
}
} else {
for(i=0;i<bop_types;i++)
for(j=0;j<bop_types;j++)
for(k=0;k<bop_types;k++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf",&gpara[i][j][k][0],&gpara[i][j][k][1],&gpara[i][j][k][2]);
gpara[j][i][k][3]=0;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&pRepul[i][j],&pRepul[i][j+1]
,&pRepul[i][j+2],&pRepul[i][j+3],&pRepul[i][j+4]);
j+=4;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&pBetaS[i][j],&pBetaS[i][j+1]
,&pBetaS[i][j+2],&pBetaS[i][j+3],&pBetaS[i][j+4]);
j+=4;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&pBetaP[i][j],&pBetaP[i][j+1]
,&pBetaP[i][j+2],&pBetaP[i][j+3],&pBetaP[i][j+4]);
j+=4;
}
}
for(i=0;i<npairs;i++) {
for(j=0;j<nBOt;j++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&FsigBO[i][j],&FsigBO[i][j+1]
,&FsigBO[i][j+2],&FsigBO[i][j+3],&FsigBO[i][j+4]);
j+=4;
}
}
for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf",&pro_delta[i]);
}
for(i=0;i<bop_types;i++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf",&pro[i]);
}
for(i=0;i<npairs;i++) {
rcut3[i]=0.0;
}
pass=0;
i=0;
if(nws==3) {
while(fgets(s,MAXLINE,fp)!=NULL&&i<npairs) {
sscanf(s,"%lf",&rcut3[i]);
pass=1;
i++;
}
if(pass==1) {
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
j+=4;
}
}
}
}
rcutall=0.0;
for(i=0;i<npairs;i++) {
if(rcut[i]>rcutall)
rcutall=rcut[i];
if(rcut3[i]>rcutall)
rcutall=rcut3[i];
rcutsq[i]=rcut[i]*rcut[i];
rcutsq3[i]=rcut3[i]*rcut3[i];
dr[i]=rcut[i]/((double)nr-1.0);
rdr[i]=1.0/dr[i];
dr3[i]=rcut3[i]/((double)nr-1.0);
rdr3[i]=1.0/dr3[i];
}
rctroot=rcutall;
dtheta=2.0/((double)ntheta-1.0);
rdtheta=1.0/dtheta;
dBO=1.0/((double)nBOt-1.0);
rdBO=1.0/(double)dBO;
for(i=0;i<npairs;i++) {
pBetaS1[i][0]=pBetaS[i][1]-pBetaS[i][0];
pBetaS1[i][1]=0.5*(pBetaS[i][2]-pBetaS[i][0]);
pBetaS1[i][nr-2]=0.5*(pBetaS[i][nr-1]-pBetaS[i][nr-3]);
pBetaS1[i][nr-1]=pBetaS[i][nr-1]-pBetaS[i][nr-2];
pBetaP1[i][0]=pBetaP[i][1]-pBetaP[i][0];
pBetaP1[i][1]=0.5*(pBetaP[i][2]-pBetaP[i][0]);
pBetaP1[i][nr-2]=0.5*(pBetaP[i][nr-1]-pBetaP[i][nr-3]);
pBetaP1[i][nr-1]=pBetaP[i][nr-1]-pBetaP[i][nr-2];
pRepul1[i][0]=pRepul[i][1]-pRepul[i][0];
pRepul1[i][1]=0.5*(pRepul[i][2]-pRepul[i][0]);
pRepul1[i][nr-2]=0.5*(pRepul[i][nr-1]-pRepul[i][nr-3]);
pRepul1[i][nr-1]=pRepul[i][nr-1]-pRepul[i][nr-2];
FsigBO1[i][0]=FsigBO[i][1]-FsigBO[i][0];
FsigBO1[i][1]=0.5*(FsigBO[i][2]-FsigBO[i][0]);
FsigBO1[i][nBOt-2]=0.5*(FsigBO[i][nBOt-1]-FsigBO[i][nBOt-3]);
FsigBO1[i][nBOt-1]=FsigBO[i][nBOt-1]-FsigBO[i][nBOt-2];
pLong1[i][0]=pLong[i][1]-pLong[i][0];
pLong1[i][1]=0.5*(pLong[i][2]-pLong[i][0]);
pLong1[i][nBOt-2]=0.5*(pLong[i][nr-1]-pLong[i][nr-3]);
pLong1[i][nBOt-1]=pLong[i][nr-1]-pLong[i][nr-2];
for(k=2;k<nr-2;k++) {
pBetaS1[i][k]=((pBetaS[i][k-2]-pBetaS[i][k+2])
+8.0*(pBetaS[i][k+1]-pBetaS[i][k-1]))/12.0;
pBetaP1[i][k]=((pBetaP[i][k-2]-pBetaP[i][k+2])
+8.0*(pBetaP[i][k+1]-pBetaP[i][k-1]))/12.0;
pRepul1[i][k]=((pRepul[i][k-2]-pRepul[i][k+2])
+8.0*(pRepul[i][k+1]-pRepul[i][k-1]))/12.0;
pLong1[i][k]=((pLong[i][k-2]-pLong[i][k+2])
+8.0*(pLong[i][k+1]-pLong[i][k-1]))/12.0;
}
for(k=2;k<nr-2;k++) {
FsigBO1[i][k]=((FsigBO[i][k-2]-FsigBO[i][k+2])
+8.0*(FsigBO[i][k+1]-FsigBO[i][k-1]))/12.0;
}
for(k=0;k<nr-1;k++) {
pBetaS2[i][k]=3.0*(pBetaS[i][k+1]-pBetaS[i][k])
-2.0*pBetaS1[i][k]-pBetaS1[i][k+1];
pBetaS3[i][k]=pBetaS1[i][k]+pBetaS1[i][k+1]
-2.0*(pBetaS[i][k+1]-pBetaS[i][k]);
pBetaP2[i][k]=3.0*(pBetaP[i][k+1]-pBetaP[i][k])
-2.0*pBetaP1[i][k]-pBetaP1[i][k+1];
pBetaP3[i][k]=pBetaP1[i][k]+pBetaP1[i][k+1]
-2.0*(pBetaP[i][k+1]-pBetaP[i][k]);
pRepul2[i][k]=3.0*(pRepul[i][k+1]-pRepul[i][k])
-2.0*pRepul1[i][k]-pRepul1[i][k+1];
pRepul3[i][k]=pRepul1[i][k]+pRepul1[i][k+1]
-2.0*(pRepul[i][k+1]-pRepul[i][k]);
pLong2[i][k]=3.0*(pLong[i][k+1]-pLong[i][k])
-2.0*pLong1[i][k]-pLong1[i][k+1];
pLong3[i][k]=pLong1[i][k]+pLong1[i][k+1]
-2.0*(pLong[i][k+1]-pLong[i][k]);
}
for(k=0;k<nBOt-1;k++) {
FsigBO2[i][k]=3.0*(FsigBO[i][k+1]-FsigBO[i][k])
-2.0*FsigBO1[i][k]-FsigBO1[i][k+1];
FsigBO3[i][k]=FsigBO1[i][k]+FsigBO1[i][k+1]
-2.0*(FsigBO[i][k+1]-FsigBO[i][k]);
}
pBetaS2[i][nr-1]=0.0;
pBetaS3[i][nr-1]=0.0;
pBetaP2[i][nr-1]=0.0;
pBetaP3[i][nr-1]=0.0;
pRepul2[i][nr-1]=0.0;
pRepul3[i][nr-1]=0.0;
pLong2[i][nr-1]=0.0;
pLong3[i][nr-1]=0.0;
FsigBO2[i][nBOt-1]=0.0;
FsigBO3[i][nBOt-1]=0.0;
for(k=0;k<nr;k++) {
pBetaS4[i][k]=pBetaS1[i][k]/dr[i];
pBetaS5[i][k]=2.0*pBetaS2[i][k]/dr[i];
pBetaS6[i][k]=3.0*pBetaS3[i][k]/dr[i];
pBetaP4[i][k]=pBetaP1[i][k]/dr[i];
pBetaP5[i][k]=2.0*pBetaP2[i][k]/dr[i];
pBetaP6[i][k]=3.0*pBetaP3[i][k]/dr[i];
pRepul4[i][k]=pRepul1[i][k]/dr[i];
pRepul5[i][k]=2.0*pRepul2[i][k]/dr[i];
pRepul6[i][k]=3.0*pRepul3[i][k]/dr[i];
pLong4[i][k]=pLong1[i][k]/dr3[i];
pLong5[i][k]=2.0*pLong2[i][k]/dr3[i];
pLong6[i][k]=3.0*pLong3[i][k]/dr3[i];
}
for(k=0;k<nBOt;k++) {
FsigBO4[i][k]=FsigBO1[i][k]/dBO;
FsigBO5[i][k]=2.0*FsigBO2[i][k]/dBO;
FsigBO6[i][k]=3.0*FsigBO3[i][k]/dBO;
}
}
if(npower<=2) {
for(i=0;i<bop_types;i++) {
for(j=0;j<bop_types;j++) {
for(k=j;k<bop_types;k++) {
gfunc1[j][i][k][0]=gfunc[j][i][k][1]-gfunc[j][i][k][0];
gfunc1[j][i][k][1]=0.5*(gfunc[j][i][k][2]-gfunc[j][i][k][0]);
gfunc1[j][i][k][ntheta-2]=0.5*(gfunc[j][i][k][ntheta-1]-gfunc[j][i][k][ntheta-3]);
gfunc1[j][i][k][ntheta-1]=0.5*(gfunc[j][i][k][ntheta-1]-gfunc[j][i][k][ntheta-2]);
for(m=2;m<ntheta-2;m++) {
gfunc1[j][i][k][m]=((gfunc[j][i][k][m-2]-gfunc[j][i][k][m+2])+
8.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m+1]-gfunc[j][i][k][m-1]))/12.0;
}
for(m=0;m<ntheta-1;m++) {
gfunc2[j][i][k][m]=3.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m])-
2.0*gfunc1[j][i][k][m]-gfunc1[j][i][k][m+1];
gfunc3[j][i][k][m]=gfunc1[j][i][k][m]+gfunc1[j][i][k][m+1]-
2.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m]);
}
gfunc2[j][i][k][ntheta-1]=0.0;
gfunc3[j][i][k][ntheta-1]=0.0;
for(m=0;m<ntheta;m++) {
gfunc4[j][i][k][ntheta-1]=gfunc1[j][i][k][m]/dtheta;
gfunc5[j][i][k][ntheta-1]=2.0*gfunc2[j][i][k][m]/dtheta;
gfunc6[j][i][k][ntheta-1]=3.0*gfunc3[j][i][k][m]/dtheta;
}
}
}
}
}
for(i=0;i<bop_types;i++) {
for(j=0;j<bop_types;j++) {
for(k=0;k<j;k++) {
if(npower<=2) {
for(n=0;n<ntheta;n++) {
gfunc[j][i][k][n]=gfunc[k][i][j][n];
gfunc1[j][i][k][n]=gfunc1[k][i][j][n];
gfunc2[j][i][k][n]=gfunc2[k][i][j][n];
gfunc3[j][i][k][n]=gfunc3[k][i][j][n];
gfunc4[j][i][k][n]=gfunc4[k][i][j][n];
gfunc5[j][i][k][n]=gfunc5[k][i][j][n];
gfunc6[j][i][k][n]=gfunc6[k][i][j][n];
}
} else {
for(n=0;n<npower+1;n++) {
gpara[j][i][k][n]=gpara[k][i][j][n];
}
}
}
}
}
fclose(fp);
}
MPI_Bcast(&rdBO,1,MPI_DOUBLE,0,world);
MPI_Bcast(&dBO,1,MPI_DOUBLE,0,world);
MPI_Bcast(&rdtheta,1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta,1,MPI_DOUBLE,0,world);
MPI_Bcast(&bop_types,1,MPI_INT,0,world);
MPI_Bcast(&small1,1,MPI_DOUBLE,0,world);
MPI_Bcast(&small2,1,MPI_DOUBLE,0,world);
MPI_Bcast(&small3g,1,MPI_DOUBLE,0,world);
MPI_Bcast(&small4,1,MPI_DOUBLE,0,world);
MPI_Bcast(&small5,1,MPI_DOUBLE,0,world);
MPI_Bcast(&small6,1,MPI_DOUBLE,0,world);
MPI_Bcast(&small7,1,MPI_DOUBLE,0,world);
MPI_Bcast(&pro[0],bop_types,MPI_DOUBLE,0,world);
MPI_Bcast(&pro_delta[0],bop_types,MPI_DOUBLE,0,world);
MPI_Bcast(&pi_p[0],bop_types,MPI_DOUBLE,0,world);
MPI_Bcast(&r1[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&rcut[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&rcut3[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&rcutsq[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&rcutsq3[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&cutmax,1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_a[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_c[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_delta[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&pi_a[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&pi_c[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&pi_delta[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_f[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_k[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&small3[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&dr[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&rdr[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&dr3[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&rdr3[0],npairs,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS1[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS2[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS3[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS4[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS5[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaS6[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP1[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP2[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP3[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP4[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP5[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pBetaP6[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong1[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong2[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong3[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong4[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong5[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pLong6[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul1[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul2[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul3[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul4[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul5[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&pRepul6[0][0],npairs*nr,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO1[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO2[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO3[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO4[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO5[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
MPI_Bcast(&FsigBO6[0][0],npairs*nBOt,MPI_DOUBLE,0,world);
if(npower<=2){
MPI_Bcast(&gfunc[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
MPI_Bcast(&gfunc1[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
MPI_Bcast(&gfunc2[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
MPI_Bcast(&gfunc3[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
MPI_Bcast(&gfunc4[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
MPI_Bcast(&gfunc5[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
MPI_Bcast(&gfunc6[0][0][0][0],bop_types*bop_types*bop_types*ntheta,MPI_DOUBLE,0,world);
} else {
MPI_Bcast(&gpara[0][0][0][0],bop_types*bop_types*bop_types*(npower+1),MPI_DOUBLE,0,world);
}
}
/* ---------------------------------------------------------------------- */
double PairBOP::cutoff(double rp,double vrcut,int mode,double r)
{
double tmp,tmp_beta,tmp_alpha,cut_store;
if(mode==1) {
tmp=(rsmall-rbig)*(r-rp)/(vrcut-rp)+rbig;
cut_store=(erfc(tmp)-erfc(rsmall))/(erfc(rbig)-erfc(rsmall));
}
else {
tmp_beta=log(log(rbig)/log(rsmall))/log(rp/vrcut);
tmp_alpha=-log(rbig)/pow(rp,tmp_beta);
cut_store=(exp(-tmp_alpha*pow(r,tmp_beta))-exp(-tmp_alpha*pow(vrcut
,tmp_beta)))/(exp(-tmp_alpha*pow(rp,tmp_beta))-exp(-tmp_alpha
*pow(vrcut,tmp_beta)));
}
return(cut_store);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairBOP::memory_usage()
{
int nlocal,nghost,nall;
int n = atom->ntypes;
nlocal = atom->nlocal;
nghost = atom->nghost;
nall = nlocal + nghost;
double bytes = 0.0;
// rcut
bytes += npairs * sizeof (double);
// rcut3
bytes += npairs * sizeof (double);
// rcutsq
bytes += npairs * sizeof (double);
// rcutsq3
bytes += npairs * sizeof (double);
// dr
bytes += npairs * sizeof (double);
// rdr
bytes += npairs * sizeof (double);
// dr3
bytes += npairs * sizeof (double);
// rdr3
bytes += npairs * sizeof (double);
// setflag
bytes += (n+1) * (n+1) * sizeof (int);
// cutsq
bytes += (n+1) * (n+1) * sizeof (double);
// cutghost
bytes += (n+1) * (n+1) * sizeof (double);
// cutghost
bytes += (n+1) * (n+1) * sizeof (double);
// pBetaS
bytes += npairs * nr * sizeof (double);
// pBetaS1
bytes += npairs * nr * sizeof (double);
// pBetaS2
bytes += npairs * nr * sizeof (double);
// pBetaS3
bytes += npairs * nr * sizeof (double);
// pBetaS4
bytes += npairs * nr * sizeof (double);
// pBetaS5
bytes += npairs * nr * sizeof (double);
// pBetaS6
bytes += npairs * nr * sizeof (double);
// pLong
bytes += npairs * nr * sizeof (double);
// pLong1
bytes += npairs * nr * sizeof (double);
// pLong2
bytes += npairs * nr * sizeof (double);
// pLong3
bytes += npairs * nr * sizeof (double);
// pLong4
bytes += npairs * nr * sizeof (double);
// pLong5
bytes += npairs * nr * sizeof (double);
// pLong6
bytes += npairs * nr * sizeof (double);
// pBetaP
bytes += npairs * nr * sizeof (double);
// pBetaP1
bytes += npairs * nr * sizeof (double);
// pBetaP2
bytes += npairs * nr * sizeof (double);
// pBetaP3
bytes += npairs * nr * sizeof (double);
// pBetaP4
bytes += npairs * nr * sizeof (double);
// pBetaP5
bytes += npairs * nr * sizeof (double);
// pBetaP6
bytes += npairs * nr * sizeof (double);
// pRepul
bytes += npairs * nr * sizeof (double);
// pRepul1
bytes += npairs * nr * sizeof (double);
// pRepul2
bytes += npairs * nr * sizeof (double);
// pRepul3
bytes += npairs * nr * sizeof (double);
// pRepul4
bytes += npairs * nr * sizeof (double);
// pRepul5
bytes += npairs * nr * sizeof (double);
// pRepul6
bytes += npairs * nr * sizeof (double);
// FsigBO
bytes += npairs * nr * sizeof (double);
// FsigBO1
bytes += npairs * nr * sizeof (double);
// FsigBO2
bytes += npairs * nr * sizeof (double);
// FsigBO3
bytes += npairs * nr * sizeof (double);
// FsigBO4
bytes += npairs * nr * sizeof (double);
// FsigBO5
bytes += npairs * nr * sizeof (double);
// FsigBO6
bytes += npairs * nr * sizeof (double);
// itypeSigBk
bytes += neigh_ct* sizeof(int);
// itypePiBk
bytes += neigh_ct* sizeof(int);
// BOP_index
bytes += nall * sizeof(double);
// BOP_total
bytes += nall * sizeof(double);
if(otfly==0) {
// cosAng
bytes += cos_total* sizeof(double);
// dcAng
bytes += cos_total * 3 * 2 * sizeof(double);
// disij
bytes += neigh_total * 3 * sizeof(double);
// rij
bytes += neigh_total * sizeof(double);
// betaS
bytes += neigh_total * sizeof(double);
// dBetaS
bytes += neigh_total * sizeof(double);
// betaP
bytes += neigh_total * sizeof(double);
// dBetaP
bytes += neigh_total * sizeof(double);
// repul
bytes += neigh_total * sizeof(double);
// dRepul
bytes += neigh_total * sizeof(double);
// cos_index
bytes += nall * sizeof(double);
}
// pi_a
bytes += npairs * sizeof(double);
// pro
bytes += bop_types * sizeof(double);
// pi_delta
bytes += npairs * sizeof(double);
// pi_p
bytes += npairs * sizeof(double);
// pi_c
bytes += npairs * sizeof(double);
// sigma_r0
bytes += npairs * sizeof(double);
// pi_r0
bytes += npairs * sizeof(double);
// phi_r0
bytes += npairs * sizeof(double);
// sigma_rc
bytes += npairs * sizeof(double);
// pi_rc
bytes += npairs * sizeof(double);
// pi_a
bytes += npairs * sizeof(double);
// pro_delta
bytes += bop_types * sizeof(double);
// pi_delta
bytes += npairs * sizeof(double);
// pi_p
bytes += npairs * sizeof(double);
// pi_c
bytes += npairs * sizeof(double);
// sigma_r0
bytes += npairs * sizeof(double);
// pi_r0
bytes += npairs * sizeof(double);
// phi_r0
bytes += npairs * sizeof(double);
// sigma_rc
bytes += npairs * sizeof(double);
// pi_rc
bytes += npairs * sizeof(double);
// phi_rc
bytes += npairs * sizeof(double);
// r1
bytes += npairs * sizeof(double);
// sigma_beta0
bytes += npairs * sizeof(double);
// pi_beta0
bytes += npairs * sizeof(double);
// phi0
bytes += npairs * sizeof(double);
// sigma_n
bytes += npairs * sizeof(double);
// pi_n
bytes += npairs * sizeof(double);
// phi_m
bytes += npairs * sizeof(double);
// sigma_nc
bytes += npairs * sizeof(double);
// pi_nc
bytes += npairs * sizeof(double);
// phi_nc
bytes += npairs * sizeof(double);
// sigma_delta
bytes += npairs * sizeof(double);
// sigma_c
bytes += npairs * sizeof(double);
// sigma_a
bytes += npairs * sizeof(double);
// sigma_f
bytes += npairs * sizeof(double);
// sigma_k
bytes += npairs * sizeof(double);
// small3
bytes += npairs * sizeof(double);
// bt_pi
bytes += maxneigh*(maxneigh/2) *sizeof(B_PI);
// bt_sigma
bytes += maxneigh*(maxneigh/2) *sizeof(B_SG);
if(npower<=2) {
// gfunc
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
// gfunc1
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
// gfunc2
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
// gfunc3
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
// gfunc4
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
// gfunc5
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
// gfunc6
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
} else {
bytes += bop_types*bop_types*bop_types*npower+1 *sizeof(double);
}
return bytes;
}
/* ---------------------------------------------------------------------- */
void PairBOP::memory_theta_create()
{
neigh_ct=(maxneigh-1)*(maxneigh-1)*(maxneigh-1);
if(neigh_ct<1) neigh_ct=1;
memory->create(itypeSigBk,neigh_ct,"itypeSigBk");
memory->create(itypePiBk,neigh_ct,"itypePiBk");
memory->create(neigh_flag,neigh_total,"neigh_flag");
memory->create(neigh_flag3,neigh_total3,"neigh_flag3");
memory->create(neigh_index,neigh_total,"neigh_index");
memory->create(neigh_index3,neigh_total3,"neigh_index3");
if(otfly==0) {
memory->create(cosAng,cos_total,"BOP:cosAng");
memory->create(dcAng,cos_total,3,2,"BOP:dcAng");
memory->create(disij,3,neigh_total,"disij");
memory->create(rij,neigh_total,"rij");
memory->create(betaS,neigh_total,"betaS");
memory->create(dBetaS,neigh_total,"dBetaS");
memory->create(betaP,neigh_total,"betaP");
memory->create(dBetaP,neigh_total,"dBetaP");
memory->create(repul,neigh_total,"repul");
memory->create(dRepul,neigh_total,"dRepul");
}
update_list=1;
}
/* ---------------------------------------------------------------------- */
void PairBOP::memory_theta_grow()
{
neigh_ct=(maxneigh-1)*(maxneigh-1)*(maxneigh-1);
if(neigh_ct<1) neigh_ct=1;
memory->grow(itypeSigBk,neigh_ct,"itypeSigBk");
memory->grow(itypePiBk,neigh_ct,"itypePiBk");
memory->grow(neigh_flag,neigh_total,"neigh_flag");
memory->grow(neigh_flag3,neigh_total3,"neigh_flag3");
memory->grow(neigh_index,neigh_total,"neigh_index");
memory->grow(neigh_index3,neigh_total3,"neigh_index3");
if(otfly==0) {
memory->grow(cosAng,cos_total,"BOP:cosAng");
memory->grow(dcAng,cos_total,3,2,"BOP:dcAng");
memory->grow(disij,3,neigh_total,"disij");
memory->grow(rij,neigh_total,"rij");
memory->grow(betaS,neigh_total,"betaS");
memory->grow(dBetaS,neigh_total,"dBetaS");
memory->grow(betaP,neigh_total,"betaP");
memory->grow(dBetaP,neigh_total,"dBetaP");
memory->grow(repul,neigh_total,"repul");
memory->grow(dRepul,neigh_total,"dRepul");
}
update_list=1;
}
/* ---------------------------------------------------------------------- */
void PairBOP::memory_theta_destroy()
{
memory->destroy(itypeSigBk);
memory->destroy(itypePiBk);
memory->destroy(neigh_flag);
memory->destroy(neigh_flag3);
memory->destroy(neigh_index);
memory->destroy(neigh_index3);
if(otfly==0) {
memory->destroy(cosAng);
memory->destroy(dcAng);
memory->destroy(disij);
memory->destroy(rij);
memory->destroy(betaS);
memory->destroy(dBetaS);
memory->destroy(betaP);
memory->destroy(dBetaP);
memory->destroy(repul);
memory->destroy(dRepul);
}
update_list=0;
}
/* ---------------------------------------------------------------------- */
void PairBOP::create_pi(int n_tot)
{
bt_pi = (B_PI *) memory->smalloc(n_tot*sizeof(B_PI),"BOP:bt_pi");
allocate_pi=1;
}
void PairBOP::create_sigma(int n_tot)
{
bt_sg = (B_SG *) memory->smalloc(n_tot*sizeof(B_SG),"BOP:bt_sg");
allocate_sigma=1;
}
void PairBOP::destroy_pi()
{
memory->destroy(bt_pi);
allocate_pi=0;
}
void PairBOP::destroy_sigma()
{
memory->destroy(bt_sg);
allocate_sigma=0;
}
/* ---------------------------------------------------------------------- */
void PairBOP::grow_pi(int n1, int n2)
{
int i,j;
B_PI *bt_temp;
bt_temp = (B_PI *) memory->smalloc(n1*sizeof(B_PI),"BOP:b_temp");
for(i=0;i<n1;i++) {
bt_temp[i].temp = bt_pi[i].temp;
bt_temp[i].i = bt_pi[i].i;
bt_temp[i].j = bt_pi[i].j;
for(j=0;j<3;j++) {
bt_temp[i].dAA[j] = bt_pi[i].dAA[j];
bt_temp[i].dBB[j] = bt_pi[i].dBB[j];
bt_temp[i].dPiB[j] = bt_pi[i].dPiB[j];
}
}
memory->destroy(bt_pi);
bt_pi=NULL;
bt_pi = (B_PI *) memory->smalloc(n2*sizeof(B_PI),"BOP:bt_pi");
for(i=0;i<n1;i++) {
bt_pi[i].temp = bt_temp[i].temp;
bt_pi[i].i = bt_temp[i].i;
bt_pi[i].j = bt_temp[i].j;
for(j=0;j<3;j++) {
bt_pi[i].dAA[j] = bt_temp[i].dAA[j];
bt_pi[i].dBB[j] = bt_temp[i].dBB[j];
bt_pi[i].dPiB[j] = bt_temp[i].dPiB[j];
}
}
for(i=n1;i<n2;i++) {
bt_pi[i].i = -1;
bt_pi[i].j = -1;
for(j=0;j<3;j++) {
bt_pi[i].dAA[j] = 0.0;
bt_pi[i].dBB[j] = 0.0;
bt_pi[i].dPiB[j] = 0.0;
}
}
memory->destroy(bt_temp);
}
/* ---------------------------------------------------------------------- */
void PairBOP::grow_sigma(int n1,int n2)
{
int i,j;
B_SG *bt_temp;
bt_temp = (B_SG *) memory->smalloc(n1*sizeof(B_SG),"BOP:bt_temp");
for(i=0;i<n1;i++) {
bt_temp[i].temp = bt_sg[i].temp;
bt_temp[i].i = bt_sg[i].i;
bt_temp[i].j = bt_sg[i].j;
for(j=0;j<3;j++) {
bt_temp[i].dAA[j] = bt_sg[i].dAA[j];
bt_temp[i].dBB[j] = bt_sg[i].dBB[j];
bt_temp[i].dCC[j] = bt_sg[i].dCC[j];
bt_temp[i].dDD[j] = bt_sg[i].dDD[j];
bt_temp[i].dEE[j] = bt_sg[i].dEE[j];
bt_temp[i].dEE1[j] = bt_sg[i].dEE1[j];
bt_temp[i].dFF[j] = bt_sg[i].dFF[j];
bt_temp[i].dAAC[j] = bt_sg[i].dAAC[j];
bt_temp[i].dBBC[j] = bt_sg[i].dBBC[j];
bt_temp[i].dCCC[j] = bt_sg[i].dCCC[j];
bt_temp[i].dDDC[j] = bt_sg[i].dDDC[j];
bt_temp[i].dEEC[j] = bt_sg[i].dEEC[j];
bt_temp[i].dFFC[j] = bt_sg[i].dFFC[j];
bt_temp[i].dGGC[j] = bt_sg[i].dGGC[j];
bt_temp[i].dUT[j] = bt_sg[i].dUT[j];
bt_temp[i].dSigB1[j] = bt_sg[i].dSigB1[j];
bt_temp[i].dSigB[j] = bt_sg[i].dSigB[j];
}
}
memory->destroy(bt_sg);
bt_sg=NULL;
bt_sg = (B_SG *) memory->smalloc(n2*sizeof(B_SG),"BOP:bt_sg");
for(i=0;i<n1;i++) {
bt_sg[i].temp = bt_temp[i].temp;
bt_sg[i].i = bt_temp[i].i;
bt_sg[i].j = bt_temp[i].j;
for(j=0;j<3;j++) {
bt_sg[i].dAA[j] = bt_temp[i].dAA[j];
bt_sg[i].dBB[j] = bt_temp[i].dBB[j];
bt_sg[i].dCC[j] = bt_temp[i].dCC[j];
bt_sg[i].dDD[j] = bt_temp[i].dDD[j];
bt_sg[i].dEE[j] = bt_temp[i].dEE[j];
bt_sg[i].dEE1[j] = bt_temp[i].dEE1[j];
bt_sg[i].dFF[j] = bt_temp[i].dFF[j];
bt_sg[i].dAAC[j] = bt_temp[i].dAAC[j];
bt_sg[i].dBBC[j] = bt_temp[i].dBBC[j];
bt_sg[i].dCCC[j] = bt_temp[i].dCCC[j];
bt_sg[i].dDDC[j] = bt_temp[i].dDDC[j];
bt_sg[i].dEEC[j] = bt_temp[i].dEEC[j];
bt_sg[i].dFFC[j] = bt_temp[i].dFFC[j];
bt_sg[i].dGGC[j] = bt_temp[i].dGGC[j];
bt_sg[i].dUT[j] = bt_temp[i].dUT[j];
bt_sg[i].dSigB1[j] = bt_temp[i].dSigB1[j];
bt_sg[i].dSigB[j] = bt_temp[i].dSigB[j];
}
}
for(i=n1;i<n2;i++) {
bt_sg[i].i = -1;
bt_sg[i].j = -1;
for(j=0;j<3;j++) {
bt_sg[i].dAA[j] = 0.0;
bt_sg[i].dBB[j] = 0.0;
bt_sg[i].dCC[j] = 0.0;
bt_sg[i].dDD[j] = 0.0;
bt_sg[i].dEE[j] = 0.0;
bt_sg[i].dEE1[j] = 0.0;
bt_sg[i].dFF[j] = 0.0;
bt_sg[i].dAAC[j] = 0.0;
bt_sg[i].dBBC[j] = 0.0;
bt_sg[i].dCCC[j] = 0.0;
bt_sg[i].dDDC[j] = 0.0;
bt_sg[i].dEEC[j] = 0.0;
bt_sg[i].dFFC[j] = 0.0;
bt_sg[i].dGGC[j] = 0.0;
bt_sg[i].dUT[j] = 0.0;
bt_sg[i].dSigB1[j] = 0.0;
bt_sg[i].dSigB[j] = 0.0;
}
}
memory->destroy(bt_temp);
}
c4science · Help