From a60a08840398c3f32eedeec7befc2aecc3028e67 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 6 Jul 2015 14:04:30 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13518
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/MANYBODY/pair_bop.cpp | 11218 +++++++++++++-----------------------
src/MANYBODY/pair_bop.h | 66 +-
2 files changed, 4029 insertions(+), 7255 deletions(-)
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 1017e58b47..5e916a9918 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -42,7 +42,6 @@
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
-#include "timer.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
@@ -50,10 +49,9 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include "math_special.h"
+#include "ctype.h"
using namespace LAMMPS_NS;
-using namespace MathSpecial;
#define MAXLINE 1024
#define EPSILON 1.0e-6
@@ -64,21 +62,19 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
one_coeff = 1;
- manybody_flag = 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;
- r1 = NULL;
sigma_beta0 = NULL;
pi_beta0 = NULL;
phi0 = NULL;
@@ -92,19 +88,21 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
sigma_delta = NULL;
sigma_c = NULL;
sigma_a = NULL;
- sigma_g0 = NULL;
- sigma_g1 = NULL;
- sigma_g2 = NULL;
- sigma_g3 = NULL;
- sigma_g4 = 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;
@@ -113,12 +111,7 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
repul = NULL;
dRepul = NULL;
itypeSigBk = NULL;
- nSigBk = NULL;
- sigB = NULL;
- sigB1 = NULL;
itypePiBk = NULL;
- nPiBk = NULL;
- piB = NULL;
pBetaS = NULL;
pBetaS1 = NULL;
pBetaS2 = NULL;
@@ -126,6 +119,13 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
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;
@@ -153,7 +153,14 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
setflag = NULL;
cutsq = NULL;
cutghost = NULL;
-
+ gfunc = NULL;
+ gfunc1 = NULL;
+ gfunc2 = NULL;
+ gfunc3 = NULL;
+ gfunc4 = NULL;
+ gfunc5 = NULL;
+ gfunc6 = NULL;
+ gpara = NULL;
ghostneigh = 1;
bt_sg=NULL;
bt_pi=NULL;
@@ -165,15 +172,24 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
PairBOP::~PairBOP()
{
+ int i;
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);
@@ -184,6 +200,13 @@ PairBOP::~PairBOP()
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);
@@ -205,59 +228,27 @@ PairBOP::~PairBOP()
memory->destroy(FsigBO4);
memory->destroy(FsigBO5);
memory->destroy(FsigBO6);
- if(table==0) {
- memory->destroy(pi_a);
- memory->destroy(pro_delta);
- memory->destroy(pi_delta);
- memory->destroy(pi_p);
- memory->destroy(pi_c);
- memory->destroy(sigma_r0);
- memory->destroy(pi_r0);
- memory->destroy(phi_r0);
- memory->destroy(sigma_rc);
- memory->destroy(pi_rc);
- memory->destroy(phi_rc);
- memory->destroy(r1);
- memory->destroy(sigma_beta0);
- memory->destroy(pi_beta0);
- memory->destroy(phi0);
- memory->destroy(sigma_n);
- memory->destroy(pi_n);
- memory->destroy(phi_m);
- memory->destroy(sigma_nc);
- memory->destroy(pi_nc);
- memory->destroy(phi_nc);
- memory->destroy(pro);
- memory->destroy(sigma_delta);
- memory->destroy(sigma_c);
- memory->destroy(sigma_a);
- memory->destroy(sigma_g0);
- memory->destroy(sigma_g1);
- memory->destroy(sigma_g2);
- memory->destroy(sigma_g3);
- memory->destroy(sigma_g4);
- memory->destroy(sigma_f);
- memory->destroy(sigma_k);
- memory->destroy(small3);
- }
- else {
- 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_g0);
- memory->destroy(sigma_g1);
- memory->destroy(sigma_g2);
- memory->destroy(sigma_f);
- memory->destroy(sigma_k);
- memory->destroy(small3);
- }
+ 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();
@@ -271,11 +262,11 @@ PairBOP::~PairBOP()
void PairBOP::compute(int eflag, int vflag)
{
- int ago,delay,every;
- int i,j,ii,jj,iij;
+ int ago,delay,every,pass;
+ int i,j,ii,jj,iij,i12;
int n,inum,temp_ij,ks;
- int itype,jtype;
- tagint i_tag,j_tag;
+ int nlisti;
+ int itype,jtype,i_tag,j_tag;
int *ilist,*iilist,*numneigh;
int **firstneigh;
double dpr1,ps;
@@ -284,16 +275,22 @@ void PairBOP::compute(int eflag, int vflag)
double betaS_ij,dBetaS_ij;
double betaP_ij,dBetaP_ij;
double repul_ij,dRepul_ij;
+ double value,dvalue;
double totE;
+ double fst[3];
+ double rcut_min;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
- tagint *tag = atom->tag;
+ int *tag = atom->tag;
int newton_pair = force->newton_pair;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
+ int timestep,cnt1;
+ MPI_Comm_rank(world,&me);
+ timestep = update->ntimestep;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -305,51 +302,39 @@ void PairBOP::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
- // BOP Neighbor lists must be updated every time
- // atoms are moved between processors
-
- if ((ago ==0)||bop_step==0||(ago>=delay&&(ago%every)==0)||(nall>maxnall))
- gneigh();
-
+ // 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
-
- if(otfly==0) theta();
- else theta_mod();
-
- // Calculate Sigma Bond-Order
-
- if(a_flag==1) {
- if (otfly==0) sigmaBo_noa();
- else sigmaBo_noa_otf();
- }
- else {
- if (otfly==0) sigmaBo();
- else sigmaBo_otf();
- }
-
- // Calculate Pi Bond-Order
-
- if (otfly==0) PiBo();
- else PiBo_otf();
-
n=0;
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];
- for(jj=0;jj<numneigh[i];jj++) {
+ nlisti=BOP_total[i];
+ for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
- j=iilist[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[n]
- -2.0*dBetaP[temp_ij]*piB[n])/rij[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];
@@ -359,11 +344,10 @@ void PairBOP::compute(int eflag, int vflag)
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[n]-2.0*betaP[temp_ij]*piB[n];
+ 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);
@@ -371,7 +355,6 @@ void PairBOP::compute(int eflag, int vflag)
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]);
}
- n++;
}
}
else {
@@ -408,8 +391,8 @@ void PairBOP::compute(int eflag, int vflag)
+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[n]
- -2.0*dBetaP_ij*piB[n])/r_ij;
+ 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];
@@ -423,7 +406,7 @@ void PairBOP::compute(int eflag, int vflag)
// add repulsive and bond order components to total energy
// (d) Eq. 1
- dE=-2.0*betaS_ij*sigB[n]-2.0*betaP_ij*piB[n];
+ 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);
@@ -431,13 +414,76 @@ void PairBOP::compute(int eflag, int vflag)
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,-ftmp1,-ftmp2,-ftmp3,
dis_ij[0],dis_ij[1],dis_ij[2]);
}
- n++;
}
}
}
}
}
-
+ 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;
}
@@ -452,8 +498,13 @@ void PairBOP::allocate()
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");
@@ -464,6 +515,13 @@ void PairBOP::allocate()
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");
@@ -493,21 +551,13 @@ void PairBOP::allocate()
void PairBOP::settings(int narg, char **arg)
{
- table = 0;
otfly = 1;
- a_flag = 0;
int iarg = 0;
while (iarg < narg) {
- if (strcmp(arg[iarg],"table") == 0) {
- table = 1;
- iarg++;
- } else if (strcmp(arg[iarg],"save") == 0) {
+ if (strcmp(arg[iarg],"save") == 0) {
otfly = 0;
iarg++;
- } else if (strcmp(arg[iarg],"sigmaoff") == 0) {
- a_flag = 1;
- iarg++;
} else error->all(FLERR,"Illegal pair_style command");
}
}
@@ -518,11 +568,12 @@ void PairBOP::settings(int narg, char **arg)
void PairBOP::coeff(int narg, char **arg)
{
- int i,j,n;
+ int i,j;
+ int n = atom->ntypes;
MPI_Comm_rank(world,&me);
- map = new int[atom->ntypes+1];
+ map = new int[n+1];
- if (narg < 3 + atom->ntypes)
+ if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// ensure I,J args are * *
@@ -531,9 +582,9 @@ void PairBOP::coeff(int narg, char **arg)
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;
@@ -541,42 +592,32 @@ void PairBOP::coeff(int narg, char **arg)
allocate_pi=0;
allocate_neigh=0;
update_list=0;
+ maxnall=0;
- if (table == 0) read_file(arg[2]);
- else read_table(arg[2]);
-
- if (table == 0) {
- setPbetaS();
- setPbetaP();
- setPrepul();
- setSign();
- }
+ 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],words[j]) == 0) break;
+ 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 (words) {
- for (i = 0; i < bop_types; i++) delete [] words[i];
- delete [] words;
+ 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++)
@@ -591,7 +632,6 @@ void PairBOP::coeff(int narg, char **arg)
setflag[i][j] = 1;
count++;
}
-
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
@@ -615,9 +655,7 @@ void PairBOP::init_style()
error->all(FLERR,str);
}
- // need a full neighbor list and neighbors of ghosts
-
- int irequest = neighbor->request(this,instance_me);
+ int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
@@ -637,11 +675,20 @@ double PairBOP::init_one(int i, int j)
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;
- 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];
+
+ 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];
+ }
}
/* ----------------------------------------------------------------------
@@ -654,59 +701,315 @@ double PairBOP::init_one(int i, int j)
void PairBOP::gneigh()
{
int i,ii;
+ int j,k,jj,kk;
+ int itype,jtype,i12;
+ int itag,jtag;
+ 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,rj2k1,rj1k2;
+ double **x = atom->x;
+ int *type = atom->type;
+ int *tag = atom->tag;
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];
- if(numneigh[i]>maxneigh) maxneigh=numneigh[i];
- } else {
+ if(ii<nlocal)
+ i= ilist[ii];
+ else
i=ii;
- if(numneigh[i]>maxneigh) maxneigh=numneigh[i];
+ 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;
- neigh_total+=numneigh[i];
+ 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+=numneigh[i]*(numneigh[i]-1)/2;
+ 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;
+ itag=tag[i];
+ iilist=firstneigh[i];
+ max_check=0;
+ max_check3=0;
+ for(jj=0;jj<numneigh[i];jj++) {
+ j=iilist[jj];
+ jtag=tag[j];
+ 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];
+ itag=tag[i];
+ max_check=0;
+ for(jj=0;jj<nlisti;jj++) {
+ temp_ij=BOP_index[i]+jj;
+ j=iilist[neigh_index[temp_ij]];
+ jtag=tag[j];
+ 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];
+ ps=rdr[i12];
+ ps=pBetaS1[i12][ks-1];
+ ps=pBetaS[i12][ks-1];
+ 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;
+ rj2k1=rj1k1*rij[temp_ij];
+ rj1k2=rj1k1*rij[temp_ik];
+ 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 i,j,k,ii,jj,kk;
int itype,jtype,i12;
int temp_ij,temp_ik,temp_ijk;
int n,nlocal,nall,ks;
+ int nlisti;
int *ilist,*numneigh;
int *iilist;
int **firstneigh;
+ int maxn,maxt;
double rj2,rk2,rsq,ps;
- double rj1k1,rj2k2;
+ double rj1k1,rj2k2,rj2k1,rj1k2;
double **x = atom->x;
int *type = atom->type;
@@ -727,11 +1030,13 @@ void PairBOP::theta()
itype = map[type[i]]+1;
iilist=firstneigh[i];
- for(jj=0;jj<numneigh[i];jj++) {
- j=iilist[jj];
+ maxt=0;
+ maxn=0;
+ 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)
@@ -748,20 +1053,28 @@ void PairBOP::theta()
+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])
+ if(rij[temp_ij]<=rcut[i12]) {
neigh_flag[temp_ij]=1;
+ maxt++;
+ }
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];
+ ps=rdr[i12];
+ ps=pBetaS1[i12][ks-1];
+ ps=pBetaS[i12][ks-1];
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];
+ 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
@@ -773,6 +1086,7 @@ void PairBOP::theta()
dRepul[temp_ij]=(pRepul6[i12][ks-1]*ps+pRepul5[i12][ks-1])*ps
+pRepul4[i12][ks-1];
}
+ if(maxt>maxn) maxn=maxt;
}
for (ii = 0; ii < nall; ii++) {
n=0;
@@ -781,11 +1095,12 @@ void PairBOP::theta()
else
i=ii;
iilist=firstneigh[i];
- for(jj=0;jj<numneigh[i];jj++) {
- j=iilist[jj];
+ 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<numneigh[i];kk++) {
+ for(kk=jj+1;kk<nlisti;kk++) {
if(cos_index[i]+n>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
@@ -797,6 +1112,9 @@ void PairBOP::theta()
rk2=rij[temp_ik]*rij[temp_ik];
rj1k1=rij[temp_ij]*rij[temp_ik];
rj2k2=rj1k1*rj1k1;
+ rj2k1=rj1k1*rij[temp_ij];
+ rj1k2=rj1k1*rij[temp_ik];
+ k=iilist[kk];
if(temp_ijk>=cos_total) {
error->one(FLERR,"Too many atom triplets for pair bop");
}
@@ -835,42 +1153,62 @@ void PairBOP::theta_mod()
/* The formulation differs slightly to avoid negative square roots
in the calculation of Sigma^(1/2) of (a) Eq. 6 and (b) Eq. 11 */
-void PairBOP::sigmaBo()
+/* ---------------------------------------------------------------------- */
+
+/* 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 n,i,j,k,kp,m,pp,kkp;
- int iij,ji,ki;
- int itmp,jtmp,ktmp,ltmp,mtmp;
- tagint i_tag,j_tag;
- int ngi,ngj,ngk,nglkp,ngli,nglj,ngl;
- int ngji,ngjk,nikj,ngki,ngkj,ngjkp;
- int ngkpk,ngkpj,ngkkp,nglk;
- int njik,nijk,nikkp,nkp,nijkp;
- int nkikp,njikp,nk0;
- int njkpk,nkjkp,njkkp;
+ int n,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;
+ int kpNeij,kpNeik,lp1;
int new1,new2,nlocal;
int inum,*ilist,*iilist,*jlist,*klist,*kplist;
int **firstneigh,*numneigh;
- int temp_ji,temp_ikp,temp_kkp;
int temp_ij,temp_ik,temp_jkp,temp_kk,temp_jk;
- int ang_ijkp,ang_ikkp,ang_jkpk,ang_kjkp;
- int ang_ijk,ang_ikj,ang_jikp,ang_jkkp;
- int ang_jik,ang_kikp;
+ 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 nsearch;
+ int kp_nsearch,nsearch;
int sig_flag,setting,ncmp,ks;
int itype,jtype,ktype,kptype;
- int bt_i,bt_j,bt_ij;
- int kp_index,same_ikp,same_jkp;
- int same_kkp;
+ 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,gmean0,gmean1,gmean2,ps;
- double gfactor1,gprime1,gsqprime;
+ double gfactor1,gprime1,gsqprime,factorsq;
double gfactorsq,gfactor2,gprime2;
double gfactorsq2,gsqprime2;
double gfactor3,gprime3,gfactor,rfactor;
@@ -878,478 +1216,951 @@ void PairBOP::sigmaBo()
double rfactor0,rfactorrt,rfactor1rt,rfactor1;
double rcm1,rcm2,gcm1,gcm2,gcm3;
double agpdpr1,agpdpr2,app1,app2,app3,app4;
- double dsigB1,dsigB2;
+ double dsigB1,dsigB2,xrun;
double part0,part1,part2,part3,part4;
double psign,bndtmp0,pp1;
double bndtmp1,bndtmp2,bndtmp3,bndtmp4,bndtmp5;
- double ftmp[3];
+ double dis_ij[3],rsq_ij,r_ij;
+ double betaS_ij,dBetaS_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 dis_kkp[3],rsq_kkp,r_kkp;
+ double betaS_kkp,dBetaS_kkp;
+ double betaP_kkp,dBetaP_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 tt1,tt2,tt3,tt4;
+
+ double ftmp[3],xtmp[3];
double **x = atom->x;
double **f = atom->f;
- tagint *tag = atom->tag;
+ int *tag = atom->tag;
int newton_pair = force->newton_pair;
int *type = atom->type;
-
+ int timestep=update->ntimestep;
nlocal = atom->nlocal;
- firstneigh = list->firstneigh;
- numneigh = list->numneigh;
+ int nall = nlocal + atom->nghost;
inum = list->inum;
ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+ MPI_Comm_rank(world,&me);
+
n=0;
-
-//loop over all local atoms
-
- if(nb_sg>16) {
- nb_sg=16;
- }
if(nb_sg==0) {
nb_sg=(maxneigh)*(maxneigh/2);
}
if(allocate_sigma) {
destroy_sigma();
}
+
create_sigma(nb_sg);
- for(itmp=0;itmp<inum;itmp++) {
+ sigB=0;
+ if(itmp<nlocal) {
i = ilist[itmp];
- i_tag=tag[i];
- itype = map[type[i]]+1;
-
-//j is loop over all neighbors of i
-
- for(jtmp=0;jtmp<numneigh[i];jtmp++) {
- temp_ij=BOP_index[i]+jtmp;
- if(neigh_flag[temp_ij]) {
- for(m=0;m<nb_sg;m++) {
- for(pp=0;pp<3;pp++) {
- bt_sg[m].dAA[pp]=0.0;
- bt_sg[m].dBB[pp]=0.0;
- bt_sg[m].dCC[pp]=0.0;
- bt_sg[m].dDD[pp]=0.0;
- bt_sg[m].dEE[pp]=0.0;
- bt_sg[m].dEE1[pp]=0.0;
- bt_sg[m].dFF[pp]=0.0;
- bt_sg[m].dAAC[pp]=0.0;
- bt_sg[m].dBBC[pp]=0.0;
- bt_sg[m].dCCC[pp]=0.0;
- bt_sg[m].dDDC[pp]=0.0;
- bt_sg[m].dEEC[pp]=0.0;
- bt_sg[m].dFFC[pp]=0.0;
- bt_sg[m].dGGC[pp]=0.0;
- bt_sg[m].dUT[pp]=0.0;
- bt_sg[m].dSigB1[pp]=0.0;
- bt_sg[m].dSigB[pp]=0.0;
- }
- bt_sg[m].i=-1;
- bt_sg[m].j=-1;
- bt_sg[m].temp=-1;
- }
- nb_t=0;
- iilist=firstneigh[i];
- j=iilist[jtmp];
- jlist=firstneigh[j];
- for(ki=0;ki<numneigh[j];ki++) {
- if(x[jlist[ki]][0]==x[i][0]) {
- if(x[jlist[ki]][1]==x[i][1]) {
- if(x[jlist[ki]][2]==x[i][2]) {
- break;
- }
- }
+ } else {
+ i=itmp;
+ }
+
+ i_tag=tag[i];
+ itype = map[type[i]]+1;
+
+ for(m=0;m<nb_sg;m++) {
+ for(pp=0;pp<3;pp++) {
+ bt_sg[m].dAA[pp]=0.0;
+ bt_sg[m].dBB[pp]=0.0;
+ bt_sg[m].dCC[pp]=0.0;
+ bt_sg[m].dDD[pp]=0.0;
+ bt_sg[m].dEE[pp]=0.0;
+ bt_sg[m].dEE1[pp]=0.0;
+ bt_sg[m].dFF[pp]=0.0;
+ bt_sg[m].dAAC[pp]=0.0;
+ bt_sg[m].dBBC[pp]=0.0;
+ bt_sg[m].dCCC[pp]=0.0;
+ bt_sg[m].dDDC[pp]=0.0;
+ bt_sg[m].dEEC[pp]=0.0;
+ bt_sg[m].dFFC[pp]=0.0;
+ bt_sg[m].dGGC[pp]=0.0;
+ bt_sg[m].dUT[pp]=0.0;
+ bt_sg[m].dSigB1[pp]=0.0;
+ bt_sg[m].dSigB[pp]=0.0;
+ }
+ 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;
}
}
- 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;
- for(ji=0;ji<numneigh[j];ji++) {
- temp_ji=BOP_index[j]+ji;
- if(x[jlist[ji]][0]==x[i][0]) {
- if(x[jlist[ji]][1]==x[i][1]) {
- if(x[jlist[ji]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- nSigBk[n]=0;
+ }
+ }
+ 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];
+ 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];
+ betaS_ij=betaS[temp_ij];
+ dBetaS_ij=dBetaS[temp_ij];
+ betaP_ij=betaP[temp_ij];
+ dBetaP_ij=dBetaP[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;
+ 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[temp_ij]*betaS[temp_ij];
+ FF=betaS_ij*betaS_ij;
//agpdpr1 is derivative of FF w.r.t. r_ij
- agpdpr1=2.0*betaS[temp_ij]*dBetaS[temp_ij]/rij[temp_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*disij[0][temp_ij];
- bt_sg[nb_ij].dFF[1]=agpdpr1*disij[1][temp_ij];
- bt_sg[nb_ij].dFF[2]=agpdpr1*disij[2][temp_ij];
+ 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
- for(ktmp=0;ktmp<numneigh[i];ktmp++) {
- temp_ik=BOP_index[i]+ktmp;
- if(neigh_flag[temp_ik]) {
- if(ktmp!=jtmp) {
- if(jtmp<ktmp) {
- njik=jtmp*(2*numneigh[i]-jtmp-1)/2+(ktmp-jtmp)-1;
- ngj=0;
- ngk=1;
- }
- else {
- njik=ktmp*(2*numneigh[i]-ktmp-1)/2+(jtmp-ktmp)-1;
- ngj=1;
- ngk=0;
- }
- k=iilist[ktmp];
- ktype = map[type[k]]+1;
+ 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
- klist=firstneigh[k];
- for(kNeii=0;kNeii<numneigh[k];kNeii++) {
- if(x[klist[kNeii]][0]==x[i][0]) {
- if(x[klist[kNeii]][1]==x[i][1]) {
- if(x[klist[kNeii]][2]==x[i][2]) {
- break;
- }
- }
- }
+ 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];
+ 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];
+ }
+ } 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(pass_ik==1) {
//find neighbor of i that is equal to k
- for(jNeik=0;jNeik<numneigh[j];jNeik++) {
- temp_jk=BOP_index[j]+jNeik;
- if(x[jlist[jNeik]][0]==x[k][0]) {
- if(x[jlist[jNeik]][1]==x[k][1]) {
- if(x[jlist[jNeik]][2]==x[k][2]) {
- break;
- }
- }
+ 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<numneigh[k];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;
- }
- }
+ 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[n];nsearch++) {
- ncmp=itypeSigBk[n][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;
- }
- }
+ }
+ }
+ 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[n]=nSigBk[n]+1;
- nk0=nSigBk[n]-1;
- itypeSigBk[n][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;
+ }
+ }
+ 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;
}
- 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;
+ else {
+ njik=ktmp*(2*nlisti-ktmp-1)/2+(jtmp-ktmp)-1;
+ ngj=1;
+ ngk=0;
}
- bt_sg[nb_jk].temp=temp_jk;
- bt_sg[nb_jk].i=j;
- bt_sg[nb_jk].j=k;
ang_jik=cos_index[i]+njik;
- gmean0=sigma_g0[jtype-1][itype-1][ktype-1];
- gmean1=sigma_g1[jtype-1][itype-1][ktype-1];
- gmean2=sigma_g2[jtype-1][itype-1][ktype-1];
- amean=cosAng[ang_jik];
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gfactorsq=gfactor1*gfactor1;
- gprime1=gmean1+2.0*gmean2*amean;
- gsqprime=2.0*gfactor1*gprime1;
+ 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[temp_ik]*betaS[temp_ik];
- CC=CC+gfactorsq*betaS[temp_ik]*betaS[temp_ik]*betaS[temp_ik]*betaS[temp_ik];
-
+ AA=AA+gfactorsq*betaS_ik*betaS_ik;
+
//agpdpr1 is derivative of AA w.r.t. Beta(rik)
-//agpdpr2 is derivative of CC 1st term w.r.t. Beta(rik)
//app1 is derivative of AA w.r.t. cos(theta_jik)
-//app2 is derivative of CC 1st term w.r.t. cos(theta_jik)
-
- agpdpr1=2.0*gfactorsq*betaS[temp_ik]*dBetaS[temp_ik]/rij[temp_ik];
- agpdpr1=2.0*betaS[temp_ik]*betaS[temp_ik]*agpdpr1;
- app1=betaS[temp_ik]*betaS[temp_ik]*gsqprime;
- app1=betaS[temp_ik]*betaS[temp_ik]*app1;
- bt_sg[nb_ij].dAA[0]+=
- app1*dcAng[ang_jik][0][ngj];
- bt_sg[nb_ij].dAA[1]+=
- app1*dcAng[ang_jik][1][ngj];
- bt_sg[nb_ij].dAA[2]+=
- app1*dcAng[ang_jik][2][ngj];
- bt_sg[nb_ij].dCC[0]+=
- app2*dcAng[ang_jik][0][ngj];
- bt_sg[nb_ij].dCC[1]+=
- app2*dcAng[ang_jik][1][ngj];
- bt_sg[nb_ij].dCC[2]+=
- app2*dcAng[ang_jik][2][ngj];
- bt_sg[nb_ik].dAA[0]+=
- app1*dcAng[ang_jik][0][ngk]
- +agpdpr1*disij[0][temp_ik];
- bt_sg[nb_ik].dAA[1]+=
- app1*dcAng[ang_jik][1][ngk]
- +agpdpr1*disij[1][temp_ik];
- bt_sg[nb_ik].dAA[2]+=
- app1*dcAng[ang_jik][2][ngk]
- +agpdpr1*disij[2][temp_ik];
- bt_sg[nb_ik].dCC[0]+=
- app2*dcAng[ang_jik][0][ngk]
- +agpdpr2*disij[0][temp_ik];
- bt_sg[nb_ik].dCC[1]+=
- app2*dcAng[ang_jik][1][ngk]
- +agpdpr2*disij[1][temp_ik];
- bt_sg[nb_ik].dCC[2]+=
- app2*dcAng[ang_jik][2][ngk]
- +agpdpr2*disij[2][temp_ik];
+
+ 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];
+ tt1=app1*dcA_jik[0][0];
+ tt2=app1*dcA_jik[0][1]+agpdpr1*dis_ik[0];
+
+ 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
-
- kp_index=0;
- for(ltmp=0;ltmp<numneigh[j];ltmp++) {
- temp_jkp=BOP_index[j]+ltmp;
- kp=jlist[ltmp];
- if(x[kp][0]==x[k][0]) {
- if(x[kp][1]==x[k][1]) {
- if(x[kp][2]==x[k][2]) {
- kp_index=1;
- break;
- }
+ 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(kp_index) {
+ }
+ if(same_kpk){
//loop over neighbors of k
- for(mtmp=0;mtmp<numneigh[k];mtmp++) {
- kp=klist[mtmp];
- if(x[kp][0]==x[j][0]) {
- if(x[kp][1]==x[j][1]) {
- if(x[kp][2]==x[j][2]) {
- break;
- }
+ 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(ki<ltmp) {
- nijk=ki*(2*numneigh[j]-ki-1)/2+(ltmp-ki)-1;
- ngji=0;
- ngjk=1;
- }
- else {
- nijk=ltmp*(2*numneigh[j]-ltmp-1)/2+(ki-ltmp)-1;
- ngji=1;
- ngjk=0;
+ }
+ 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];
+ 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_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];
+ betaP_jkp=betaP[temp_jkp];
+ dBetaP_jkp=dBetaP[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(kNeii<mtmp) {
- nikj=kNeii*(2*numneigh[k]-kNeii-1)/2+(mtmp-kNeii)-1;
- ngki=0;
- ngkj=1;
+ 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];
}
- else {
- nikj=mtmp*(2*numneigh[k]-mtmp-1)/2+(kNeii-mtmp)-1;
- ngki=1;
- ngkj=0;
+ 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];
+ }
}
- ang_ijk=cos_index[j]+nijk;
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng[ang_ijk];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[itype-1][ktype-1][jtype-1];
- gmean1=sigma_g1[itype-1][ktype-1][jtype-1];
- gmean2=sigma_g2[itype-1][ktype-1][jtype-1];
- ang_ikj=cos_index[k]+nikj;
- amean=cosAng[ang_ikj];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
gfactor=gfactor1*gfactor2*gfactor3;
- rfactor=betaS[temp_ik]*betaS[temp_jkp];
+ 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[temp_jkp]*dBetaS[temp_ik]/rij[temp_ik];
- rcm2=gfactor*betaS[temp_ik]*dBetaS[temp_jkp]/rij[temp_jkp];
+ 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*dcAng[ang_jik][0][ngj]
- -gcm2*dcAng[ang_ijk][0][ngji];
+ gcm1*dcA_jik[0][0]
+ -gcm2*dcA_ijk[0][0];
bt_sg[nb_ij].dEE1[1]+=
- gcm1*dcAng[ang_jik][1][ngj]
- -gcm2*dcAng[ang_ijk][1][ngji];
+ gcm1*dcA_jik[1][0]
+ -gcm2*dcA_ijk[1][0];
bt_sg[nb_ij].dEE1[2]+=
- gcm1*dcAng[ang_jik][2][ngj]
- -gcm2*dcAng[ang_ijk][2][ngji];
+ gcm1*dcA_jik[2][0]
+ -gcm2*dcA_ijk[2][0];
bt_sg[nb_ik].dEE1[0]+=
- gcm1*dcAng[ang_jik][0][ngk]
- +rcm1*disij[0][temp_ik]
- -gcm3*dcAng[ang_ikj][0][ngki];
+ gcm1*dcA_jik[0][1]
+ +rcm1*dis_ik[0]
+ -gcm3*dcA_ikj[0][0];
bt_sg[nb_ik].dEE1[1]+=
- gcm1*dcAng[ang_jik][1][ngk]
- +rcm1*disij[1][temp_ik]
- -gcm3*dcAng[ang_ikj][1][ngki];
+ gcm1*dcA_jik[1][1]
+ +rcm1*dis_ik[1]
+ -gcm3*dcA_ikj[1][0];
bt_sg[nb_ik].dEE1[2]+=
- gcm1*dcAng[ang_jik][2][ngk]
- +rcm1*disij[2][temp_ik]
- -gcm3*dcAng[ang_ikj][2][ngki];
+ gcm1*dcA_jik[2][1]
+ +rcm1*dis_ik[2]
+ -gcm3*dcA_ikj[2][0];
bt_sg[nb_jk].dEE1[0]+=
- gcm2*dcAng[ang_ijk][0][ngjk]
- +rcm2*disij[0][temp_jkp]
- -gcm3*dcAng[ang_ikj][0][ngkj];
+ gcm2*dcA_ijk[0][1]
+ +rcm2*dis_jkp[0]
+ -gcm3*dcA_ikj[0][1];
bt_sg[nb_jk].dEE1[1]+=
- gcm2*dcAng[ang_ijk][1][ngjk]
- +rcm2*disij[1][temp_jkp]
- -gcm3*dcAng[ang_ikj][1][ngkj];
+ gcm2*dcA_ijk[1][1]
+ +rcm2*dis_jkp[1]
+ -gcm3*dcA_ikj[1][1];
bt_sg[nb_jk].dEE1[2]+=
- gcm2*dcAng[ang_ijk][2][ngjk]
- +rcm2*disij[2][temp_jkp]
- -gcm3*dcAng[ang_ikj][2][ngkj];
+ 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
-
- for(ltmp=0;ltmp<ktmp;ltmp++) {
- if(ltmp!=jtmp) {
- temp_ikp=BOP_index[i]+ltmp;
- if(neigh_flag[temp_ikp]) {
- kp=iilist[ltmp];
- kptype = map[type[kp]]+1;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
+ 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];
+ 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];
+ }
+ } 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(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*numneigh[i]-jtmp-1)/2+(ltmp-jtmp)-1;
+ njikp=jtmp*(2*nlisti-jtmp-1)/2+(ltmp-jtmp)-1;
nglj=0;
ngl=1;
}
else {
- njikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(jtmp-ltmp)-1;
+ njikp=ltmp*(2*nlisti-ltmp-1)/2+(jtmp-ltmp)-1;
nglj=1;
ngl=0;
}
if(ktmp<ltmp) {
- nkikp=ktmp*(2*numneigh[i]-ktmp-1)/2+(ltmp-ktmp)-1;
+ nkikp=ktmp*(2*nlisti-ktmp-1)/2+(ltmp-ktmp)-1;
nglk=0;
nglkp=1;
}
else {
- nkikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(ktmp-ltmp)-1;
+ nkikp=ltmp*(2*nlisti-ltmp-1)/2+(ktmp-ltmp)-1;
nglk=1;
nglkp=0;
}
ang_jikp=cos_index[i]+njikp;
- 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;
- gmean0=sigma_g0[jtype-1][itype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][itype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][itype-1][kptype-1];
- amean=cosAng[ang_jikp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][itype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][itype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][itype-1][kptype-1];
+ 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;
- amean=cosAng[ang_kikp];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gfactor=gfactor1*gfactor2*gfactor3;
- rfactorrt=betaS[temp_ik]*betaS[temp_ikp];
- rfactor=rfactorrt*rfactorrt;
+ 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;
+ 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')
@@ -1357,4803 +2168,382 @@ void PairBOP::sigmaBo()
//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[temp_ikp]
- *dBetaS[temp_ik]/rij[temp_ik];
- agpdpr2=4.0*gfactor*rfactorrt*betaS[temp_ik]
- *dBetaS[temp_ikp]/rij[temp_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*dcAng[ang_jik][0][ngj]
- +app2*dcAng[ang_jikp][0][nglj];
- bt_sg[nb_ij].dCC[1]+=
- app1*dcAng[ang_jik][1][ngj]
- +app2*dcAng[ang_jikp][1][nglj];
- bt_sg[nb_ij].dCC[2]+=
- app1*dcAng[ang_jik][2][ngj]
- +app2*dcAng[ang_jikp][2][nglj];
- bt_sg[nb_ik].dCC[0]+=
- app1*dcAng[ang_jik][0][ngk]
- +app3*dcAng[ang_kikp][0][nglk]
- +agpdpr1*disij[0][temp_ik];
- bt_sg[nb_ik].dCC[1]+=
- app1*dcAng[ang_jik][1][ngk]
- +app3*dcAng[ang_kikp][1][nglk]
- +agpdpr1*disij[1][temp_ik];
- bt_sg[nb_ik].dCC[2]+=
- app1*dcAng[ang_jik][2][ngk]
- +app3*dcAng[ang_kikp][2][nglk]
- +agpdpr1*disij[2][temp_ik];
- bt_sg[nb_ikp].dCC[0]+=
- app2*dcAng[ang_jikp][0][ngl]
- +app3*dcAng[ang_kikp][0][nglkp]
- +agpdpr2*disij[0][temp_ikp];
- bt_sg[nb_ikp].dCC[1]+=
- app2*dcAng[ang_jikp][1][ngl]
- +app3*dcAng[ang_kikp][1][nglkp]
- +agpdpr2*disij[1][temp_ikp];
- bt_sg[nb_ikp].dCC[2]+=
- app2*dcAng[ang_jikp][2][ngl]
- +app3*dcAng[ang_kikp][2][nglkp]
- +agpdpr2*disij[2][temp_ikp];
- }
+ 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<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- if(neigh_flag[temp_kkp]) {
- kp=klist[ltmp];;
- 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;
- }
- }
+ 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(!same_ikp&&!same_jkp) {
- if(kNeii<ltmp) {
- nikkp=kNeii*(2*numneigh[k]-kNeii-1)/2+(ltmp-kNeii)-1;
- nglkp=1;
- ngli=0;
- }
- else {
- nikkp=ltmp*(2*numneigh[k]-ltmp-1)/2+(kNeii-ltmp)-1;
- nglkp=0;
- ngli=1;
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nkp=nSigBk[n]-1;
- itypeSigBk[n][nkp]=kp;
- }
- ang_ikkp=cos_index[k]+nikkp;
- 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;
- gmean0=sigma_g0[itype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[itype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[itype-1][ktype-1][kptype-1];
- amean=cosAng[ang_ikkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gfactorsq2=gfactor2*gfactor2;
- gsqprime2=2.0*gfactor2*gprime2;
- gfactor=gfactorsq*gfactorsq2;
- rfactorrt=betaS[temp_ik]*betaS[temp_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=2.0*gfactor*rfactorrt*betaS[temp_kkp]
- *dBetaS[temp_ik]/rij[temp_ik];
- agpdpr2=2.0*gfactor*rfactorrt*betaS[temp_ik]
- *dBetaS[temp_kkp]/rij[temp_kkp];
- app1=rfactor*gfactorsq2*gsqprime;
- app2=rfactor*gfactorsq*gsqprime2;
- bt_sg[nb_ij].dCC[0]+=
- app1*dcAng[ang_jik][0][ngj];
- bt_sg[nb_ij].dCC[1]+=
- app1*dcAng[ang_jik][1][ngj];
- bt_sg[nb_ij].dCC[2]+=
- app1*dcAng[ang_jik][2][ngj];
- bt_sg[nb_ik].dCC[0]+=
- app1*dcAng[ang_jik][0][ngk]
- +agpdpr1*disij[0][temp_ik]
- -app2*dcAng[ang_ikkp][0][ngli];
- bt_sg[nb_ik].dCC[1]+=
- app1*dcAng[ang_jik][1][ngk]
- +agpdpr1*disij[1][temp_ik]
- -app2*dcAng[ang_ikkp][1][ngli];
- bt_sg[nb_ik].dCC[2]+=
- app1*dcAng[ang_jik][2][ngk]
- +agpdpr1*disij[2][temp_ik]
- -app2*dcAng[ang_ikkp][2][ngli];
- bt_sg[nb_kkp].dCC[0]+=
- app2*dcAng[ang_ikkp][0][nglkp]
- +agpdpr2*disij[0][temp_kkp];
- bt_sg[nb_kkp].dCC[1]+=
- app2*dcAng[ang_ikkp][1][nglkp]
- +agpdpr2*disij[1][temp_kkp];
- bt_sg[nb_kkp].dCC[2]+=
- app2*dcAng[ang_ikkp][2][nglkp]
- +agpdpr2*disij[2][temp_kkp];
-
+ }
+ }
+ if(x[j][0]==x[kp][0]) {
+ if(x[j][1]==x[kp][1]) {
+ if(x[j][2]==x[kp][2]) {
+ same_jkp=1;
}
}
}
-
- //j and k are different neighbors of i and k' is a neighbor j not equal to k
-
- kplist=firstneigh[kp];
- for(ltmp=0;ltmp<numneigh[j];ltmp++) {
- sig_flag=0;
- temp_jkp=BOP_index[j]+ltmp;
- if(neigh_flag[temp_jkp]) {
- kp=jlist[ltmp];
- kptype = map[type[kp]]+1;
- same_jkp=0;
- same_kkp=0;
- for(kpNeij=0;kpNeij<numneigh[kp];kpNeij++) {
- 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];
+ betaP_kkp=((pBetaP3[ikkp][ks-1]*ps+pBetaP2[ikkp][ks-1])*ps
+ +pBetaP1[ikkp][ks-1])*ps+pBetaP[ikkp][ks-1];
+ dBetaP_kkp=(pBetaP6[ikkp][ks-1]*ps+pBetaP5[ikkp][ks-1])*ps
+ +pBetaP4[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];
+ betaP_kkp=betaP[temp_kkp];
+ dBetaP_kkp=dBetaP[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;
}
}
}
}
- for(kpNeik=0;kpNeik<numneigh[kp];kpNeik++) {
- if(x[k][0]==x[kp][0]) {
- if(x[k][1]==x[kp][1]) {
- if(x[k][2]==x[kp][2]) {
- same_kkp=1;
- 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];
}
- if(!same_kkp&&!same_jkp) {
- for(kNeikp=0;kNeikp<numneigh[k];kNeikp++) {
- temp_kkp=BOP_index[k]+kNeikp;
- kkp=klist[kNeikp];
- if(x[kkp][0]==x[kp][0]) {
- if(x[kkp][1]==x[kp][1]) {
- if(x[kkp][2]==x[kp][2]) {
- sig_flag=1;
- break;
- }
- }
- }
+
+ 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];
}
- if(sig_flag==1) {
- for(nsearch=0;nsearch<numneigh[kp];nsearch++) {
- ncmp=kplist[nsearch];
- 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(ji<ltmp) {
- nijkp=(ji)*numneigh[j]-(ji+1)*(ji+2)/2+ltmp;
- ngji=0;
- ngjkp=1;
- }
- else {
- nijkp=(ltmp)*numneigh[j]-(ltmp+1)*(ltmp+2)/2+ji;
- ngji=1;
- ngjkp=0;
- }
- if(kNeii<kNeikp) {
- nikkp=(kNeii)*numneigh[k]-(kNeii+1)*(kNeii+2)/2+kNeikp;
- ngki=0;
- ngkkp=1;
- }
- else {
- nikkp=(kNeikp)*numneigh[k]-(kNeikp+1)*(kNeikp+2)/2+kNeii;
- ngki=1;
- ngkkp=0;
- }
- if(kpNeij<kpNeik) {
- njkpk=(kpNeij)*numneigh[kp]-(kpNeij+1)*(kpNeij+2)/2+kpNeik;
- ngkpj=0;
- ngkpk=1;
- }
- else {
- njkpk=(kpNeik)*numneigh[kp]-(kpNeik+1)*(kpNeik+2)/2+kpNeij;
- ngkpj=1;
- ngkpk=0;
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nkp=nSigBk[n]-1;
- itypeSigBk[n][nkp]=kp;
- }
- ang_ijkp=cos_index[j]+nijkp;
- ang_ikkp=cos_index[k]+nikkp;
- ang_jkpk=cos_index[kp]+njkpk;
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[itype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[itype-1][jtype-1][kptype-1];
- amean=cosAng[ang_ijkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[itype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[itype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[itype-1][ktype-1][kptype-1];
- amean=cosAng[ang_ikkp];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[jtype-1][kptype-1][ktype-1];
- gmean1=sigma_g1[jtype-1][kptype-1][ktype-1];
- gmean2=sigma_g2[jtype-1][kptype-1][ktype-1];
- amean=cosAng[ang_jkpk];
- gfactor4=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime4=gmean1+2.0*gmean2*amean;
- gfactor=gfactor1*gfactor2*gfactor3*gfactor4;
- rfactor0=(betaS[temp_ik]+small2)*(betaS[temp_jkp]+small2)
- *(betaS[temp_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)
+ }
+ gfactorsq2=gfactor2*gfactor2;
+ gsqprime2=2.0*gfactor2*gprime2;
+ gfactor=gfactorsq*gfactorsq2;
+ rfactorrt=betaS_ik*betaS_kkp;
+ rfactor=rfactorrt*rfactorrt;
- EE=EE+gfactor*rfactor;
+//3rd CC is third term of Eq. 11 (c) for i atom
+//where j , k =neighbor of i & k' =neighbor of k
-//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)
+ 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=gfactor*drfactor*(betaS[temp_jkp]+small2)*(betaS[temp_kkp]
- +small2)*dBetaS[temp_ik]/rij[temp_ik];
- agpdpr2=gfactor*drfactor*(betaS[temp_ik]+small2)*(betaS[temp_kkp]
- +small2)*dBetaS[temp_jkp]/rij[temp_jkp];
- agpdpr3=gfactor*drfactor*(betaS[temp_ik]+small2)*(betaS[temp_jkp]
- +small2)*dBetaS[temp_kkp]/rij[temp_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*dcAng[ang_jik][0][ngj]
- -app2*dcAng[ang_ijkp][0][ngji];
- bt_sg[nb_ij].dEE[1]+=
- app1*dcAng[ang_jik][1][ngj]
- -app2*dcAng[ang_ijkp][1][ngji];
- bt_sg[nb_ij].dEE[2]+=
- app1*dcAng[ang_jik][2][ngj]
- -app2*dcAng[ang_ijkp][2][ngji];
- bt_sg[nb_ik].dEE[0]+=
- app1*dcAng[ang_jik][0][ngk]
- +agpdpr1*disij[0][temp_ik]
- -app3*dcAng[ang_ikkp][0][ngki];
- bt_sg[nb_ik].dEE[1]+=
- app1*dcAng[ang_jik][1][ngk]
- +agpdpr1*disij[1][temp_ik]
- -app3*dcAng[ang_ikkp][1][ngki];
- bt_sg[nb_ik].dEE[2]+=
- app1*dcAng[ang_jik][2][ngk]
- +agpdpr1*disij[2][temp_ik]
- -app3*dcAng[ang_ikkp][2][ngki];
- bt_sg[nb_jkp].dEE[0]+=
- app2*dcAng[ang_ijkp][0][ngjkp]
- +agpdpr2*disij[0][temp_jkp]
- -app4*dcAng[ang_jkpk][0][ngkpj];
- bt_sg[nb_jkp].dEE[1]+=
- app2*dcAng[ang_ijkp][1][ngjkp]
- +agpdpr2*disij[1][temp_jkp]
- -app4*dcAng[ang_jkpk][1][ngkpj];
- bt_sg[nb_jkp].dEE[2]+=
- app2*dcAng[ang_ijkp][2][ngjkp]
- +agpdpr2*disij[2][temp_jkp]
- -app4*dcAng[ang_jkpk][2][ngkpj];
- bt_sg[nb_kkp].dEE[0]+=
- app3*dcAng[ang_ikkp][0][ngkkp]
- +agpdpr3*disij[0][temp_kkp]
- -app4*dcAng[ang_jkpk][0][ngkpk];
- bt_sg[nb_kkp].dEE[1]+=
- app3*dcAng[ang_ikkp][1][ngkkp]
- +agpdpr3*disij[1][temp_kkp]
- -app4*dcAng[ang_jkpk][1][ngkpk];
- bt_sg[nb_kkp].dEE[2]+=
- app3*dcAng[ang_ikkp][2][ngkkp]
- +agpdpr3*disij[2][temp_kkp]
- -app4*dcAng[ang_jkpk][2][ngkpk];
- }
- }
+ 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 is a neighbor of i and k is a neighbor of j not equal to i
+//j and k are different neighbors of i and k' is a neighbor j not equal to k
- for(ktmp=0;ktmp<numneigh[j];ktmp++) {
- if(ktmp!=ji) {
- if(ktmp<ji) {
- njik=ktmp*(2*numneigh[j]-ktmp-1)/2+(ji-ktmp)-1;
- ngi=1;
- ngk=0;
- }
- else {
- njik=ji*(2*numneigh[j]-ji-1)/2+(ktmp-ji)-1;
- ngi=0;
- ngk=1;
- }
- temp_jk=BOP_index[j]+ktmp;
- if(neigh_flag[temp_jk]) {
- k=jlist[ktmp];
- ktype=map[type[k]]+1;
- klist=firstneigh[k];
-
- for(kNeij=0;kNeij<numneigh[k];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]) {
+ 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;
}
}
}
}
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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;
+ 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(sig_flag==0) {
- nSigBk[n]=nSigBk[n]+1;
- new1=nSigBk[n]-1;
- itypeSigBk[n][new1]=k;
- }
- ang_ijk=cos_index[j]+njik;
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng[ang_ijk];
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime1=gmean1+2.0*gmean2*amean;
- gfactorsq=gfactor1*gfactor1;
- gsqprime=2.0*gfactor1*gprime1;
- rfactor1rt=betaS[temp_jk]*betaS[temp_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;
- DD=DD+gfactorsq*rfactor1;
-
-//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[temp_jk]*dBetaS[temp_jk]/rij[temp_jk];
- app1=rfactor1rt*gsqprime;
- bt_sg[nb_ij].dBB[0]-=
- app1*dcAng[ang_ijk][0][ngi];
- bt_sg[nb_ij].dBB[1]-=
- app1*dcAng[ang_ijk][1][ngi];
- bt_sg[nb_ij].dBB[2]-=
- app1*dcAng[ang_ijk][2][ngi];
- bt_sg[nb_ij].dDD[0]-=
- app2*dcAng[ang_ijk][0][ngi];
- bt_sg[nb_ij].dDD[1]-=
- app2*dcAng[ang_ijk][1][ngi];
- bt_sg[nb_ij].dDD[2]-=
- app2*dcAng[ang_ijk][2][ngi];
- bt_sg[nb_jk].dBB[0]+=
- app1*dcAng[ang_ijk][0][ngk]
- +agpdpr1*disij[0][temp_jk];
- bt_sg[nb_jk].dBB[1]+=
- app1*dcAng[ang_ijk][1][ngk]
- +agpdpr1*disij[1][temp_jk];
- bt_sg[nb_jk].dBB[2]+=
- app1*dcAng[ang_ijk][2][ngk]
- +agpdpr1*disij[2][temp_jk];
- bt_sg[nb_jk].dDD[0]+=
- app2*dcAng[ang_ijk][0][ngk]
- +agpdpr2*disij[0][temp_jk];
- bt_sg[nb_jk].dDD[1]+=
- app2*dcAng[ang_ijk][1][ngk]
- +agpdpr2*disij[1][temp_jk];
- bt_sg[nb_jk].dDD[2]+=
- app2*dcAng[ang_ijk][2][ngk]
- +agpdpr2*disij[2][temp_jk];
-
-//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;
- if(neigh_flag[temp_jkp]) {
- kp=jlist[ltmp];
- kptype=map[type[kp]]+1;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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;
- }
- }
+ 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(ji<ltmp) {
- nijkp=ji*(2*numneigh[j]-ji-1)/2+(ltmp-ji)-1;
- ngli=0;
- ngl=1;
- }
- else {
- nijkp=ltmp*(2*numneigh[j]-ltmp-1)/2+(ji-ltmp)-1;
- ngli=1;
- ngl=0;
- }
- if(ktmp<ltmp) {
- nkjkp=ktmp*(2*numneigh[j]-ktmp-1)/2+(ltmp-ktmp)-1;
- ngjk=0;
- ngjkp=1;
- }
- else {
- nkjkp=ltmp*(2*numneigh[j]-ltmp-1)/2+(ktmp-ltmp)-1;
- ngjk=1;
- ngjkp=0;
- }
- ang_ijkp=cos_index[j]+nijkp;
- ang_kjkp=cos_index[j]+nkjkp;
- gmean0=sigma_g0[itype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[itype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[itype-1][jtype-1][kptype-1];
- amean=cosAng[ang_ijkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][jtype-1][kptype-1];
- amean=cosAng[ang_kjkp];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gfactor=gfactor1*gfactor2*gfactor3;
- rfactorrt=betaS[temp_jk]*betaS[temp_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[temp_jkp]
- *dBetaS[temp_jk]/rij[temp_jk];
- agpdpr2=4.0*gfactor*rfactorrt*betaS[temp_jk]
- *dBetaS[temp_jkp]/rij[temp_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*dcAng[ang_ijk][0][ngi]
- +app2*dcAng[ang_ijkp][0][ngli];
- bt_sg[nb_ij].dDD[1]-=
- app1*dcAng[ang_ijk][1][ngi]
- +app2*dcAng[ang_ijkp][1][ngli];
- bt_sg[nb_ij].dDD[2]-=
- app1*dcAng[ang_ijk][2][ngi]
- +app2*dcAng[ang_ijkp][2][ngli];
- bt_sg[nb_jk].dDD[0]+=
- app1*dcAng[ang_ijk][0][ngk]
- +app3*dcAng[ang_kjkp][0][ngjk]
- +agpdpr1*disij[0][temp_jk];
- bt_sg[nb_jk].dDD[1]+=
- app1*dcAng[ang_ijk][1][ngk]
- +app3*dcAng[ang_kjkp][1][ngjk]
- +agpdpr1*disij[1][temp_jk];
- bt_sg[nb_jk].dDD[2]+=
- app1*dcAng[ang_ijk][2][ngk]
- +app3*dcAng[ang_kjkp][2][ngjk]
- +agpdpr1*disij[2][temp_jk];
- bt_sg[nb_jkp].dDD[0]+=
- app2*dcAng[ang_ijkp][0][ngl]
- +app3*dcAng[ang_kjkp][0][ngjkp]
- +agpdpr2*disij[0][temp_jkp];
- bt_sg[nb_jkp].dDD[1]+=
- app2*dcAng[ang_ijkp][1][ngl]
- +app3*dcAng[ang_kjkp][1][ngjkp]
- +agpdpr2*disij[1][temp_jkp];
- bt_sg[nb_jkp].dDD[2]+=
- app2*dcAng[ang_ijkp][2][ngl]
- +app3*dcAng[ang_kjkp][2][ngjkp]
- +agpdpr2*disij[2][temp_jkp];
}
}
- }
-
-//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<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- if(neigh_flag[temp_kkp]) {
- kp=klist[ltmp];
- 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) {
- for(kNeij=0;kNeij<numneigh[k];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(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(kNeij<ltmp) {
- njkkp=kNeij*(2*numneigh[k]-kNeij-1)/2+(ltmp-kNeij)-1;
- nglkp=1;
- nglj=0;
- }
- else {
- njkkp=ltmp*(2*numneigh[k]-ltmp-1)/2+(kNeij-ltmp)-1;
- nglkp=0;
- nglj=1;
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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(x[ncmp][0]==x[k][0]) {
+ if(x[ncmp][1]==x[k][1]) {
+ if(x[ncmp][2]==x[k][2]) {
+ kpNeik=nsearch;
}
}
}
- if(sig_flag==0) {
- nSigBk[n]=nSigBk[n]+1;
- new2=nSigBk[n]-1;
- itypeSigBk[n][new2]=kp;
- }
- ang_jkkp=cos_index[k]+njkkp;
- 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;
- gmean0=sigma_g0[jtype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][ktype-1][kptype-1];
- amean=cosAng[ang_jkkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gfactorsq2=gfactor2*gfactor2;
- gsqprime2=2.0*gfactor2*gprime2;
- gfactor=gfactorsq*gfactorsq2;
- rfactorrt=betaS[temp_jk]*betaS[temp_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[temp_kkp]
- *dBetaS[temp_jk]/rij[temp_jk];
- agpdpr2=2.0*gfactor*rfactorrt*betaS[temp_jk]
- *dBetaS[temp_kkp]/rij[temp_kkp];
- app1=rfactor*gfactorsq2*gsqprime;
- app2=rfactor*gfactorsq*gsqprime2;
- bt_sg[nb_ij].dDD[0]-=
- app1*dcAng[ang_ijk][0][ngi];
- bt_sg[nb_ij].dDD[1]-=
- app1*dcAng[ang_ijk][1][ngi];
- bt_sg[nb_ij].dDD[2]-=
- app1*dcAng[ang_ijk][2][ngi];
- bt_sg[nb_jk].dDD[0]+=
- app1*dcAng[ang_ijk][0][ngk]
- +agpdpr1*disij[0][temp_jk]
- -app2*dcAng[ang_jkkp][0][nglj];
- bt_sg[nb_jk].dDD[1]+=
- app1*dcAng[ang_ijk][1][ngk]
- +agpdpr1*disij[1][temp_jk]
- -app2*dcAng[ang_jkkp][1][nglj];
- bt_sg[nb_jk].dDD[2]+=
- app1*dcAng[ang_ijk][2][ngk]
- +agpdpr1*disij[2][temp_jk]
- -app2*dcAng[ang_jkkp][2][nglj];
- bt_sg[nb_kkp].dDD[0]+=
- app2*dcAng[ang_jkkp][0][nglkp]
- +agpdpr2*disij[0][temp_kkp];
- bt_sg[nb_kkp].dDD[1]+=
- app2*dcAng[ang_jkkp][1][nglkp]
- +agpdpr2*disij[1][temp_kkp];
- bt_sg[nb_kkp].dDD[2]+=
- app2*dcAng[ang_jkkp][2][nglkp]
- +agpdpr2*disij[2][temp_kkp];
}
- }
- }
- }
- }
- }
-
- sig_flag=0;
- if(FF<=0.000001) {
- sigB[n]=0.0;
- sig_flag=1;
- }
- 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
-
- 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_i=bt_sg[m].i;
- bt_j=bt_sg[m].j;
- 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])
- +sigma_c[iij]*AAC+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[n]=psign*betaS[temp_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[temp_ij]
- *(1.0+sigma_a[iij]*GGC)*bndtmp*2.0*betaS[temp_ij]*(1.0
- +sigma_a[iij]*GGC)*(1.0+sigma_a[iij]*GGC);
- bndtmp1=bndtmp1*dBetaS[temp_ij]/rij[temp_ij];
- bndtmp2=psign*betaS[temp_ij]*(1.0+sigma_a[iij]*GGC)*bndtmp*sigma_c[iij];
- bndtmp3=psign*betaS[temp_ij]*(1.0+sigma_a[iij]*GGC)
- *bndtmp*sigma_c[iij]*sigma_a[iij];
- bndtmp4=psign*betaS[temp_ij]*(1.0+sigma_a[iij]*GGC)
- *bndtmp*sigma_c[iij]*sigma_a[iij]*(2.0+GGC);
- bndtmp5=sigma_a[iij]*psign*betaS[temp_ij]*bndtmp0
- +psign*betaS[temp_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*disij[0][temp_ij]
- +(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*disij[1][temp_ij]
- +(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*disij[2][temp_ij]
- +(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*disij[0][temp_ij]
- +(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*disij[1][temp_ij]
- +(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*disij[2][temp_ij]
- +(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)
-
- if(nb_t==0) {
- if(j>i) {
- bt_sg[0].dSigB1[0]=bndtmp1*disij[0][temp_ij];
- bt_sg[0].dSigB1[1]=bndtmp1*disij[1][temp_ij];
- bt_sg[0].dSigB1[2]=bndtmp1*disij[2][temp_ij];
- }
- else {
- bt_sg[0].dSigB1[0]=-bndtmp1*disij[0][temp_ij];
- bt_sg[0].dSigB1[1]=-bndtmp1*disij[1][temp_ij];
- bt_sg[0].dSigB1[2]=-bndtmp1*disij[2][temp_ij];
- }
- for(pp=0;pp<3;pp++) {
- bt_sg[0].dAA[pp]=0.0;
- bt_sg[0].dBB[pp]=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].dAAC[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].dSigB1[pp]=0.0;
- bt_sg[0].dSigB[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[n]*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];
- 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[n]=dsigB1*part2;
- pp1=2.0*betaS[temp_ij];
- 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_ij=bt_sg[m].temp;
- bt_i=bt_sg[m].i;
- bt_j=bt_sg[m].j;
- 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],disij[0][bt_ij],disij[1][bt_ij],disij[2][bt_ij]);
- }
- }
- }
- }
- n++;
- }
- }
- }
- }
- if(allocate_sigma)
- destroy_sigma();
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairBOP::sigmaBo_noa()
-{
- int nb_t,new_n_tot;
- int n,i,j,k,kp,m,pp;
- int iij,ji,ki;
- int itmp,jtmp,ktmp,ltmp,mtmp;
- tagint i_tag,j_tag;
- int ngi,ngj,ngk;
- int ngji,ngjk,nikj,ngki,ngkj;
- int njik,nijk,nikkp,nkp,nijkp;
- int nkikp,njikp,nk0,nkjkp,njkkp;
- int jNeik,kNeii,kNeij;
- int new1,new2,nlocal,nsearch;
- int inum,*ilist,*iilist,*jlist,*klist;
- int **firstneigh,*numneigh;
- int temp_ji,temp_ikp,temp_kkp;
- int temp_ij,temp_ik,temp_jkp,temp_kk,temp_jk;
- int ang_ijkp,ang_ikkp,ang_kjkp;
- int ang_ijk,ang_ikj,ang_jikp,ang_jkkp;
- int ang_jik,ang_kikp;
- int nb_ij,nb_ik,nb_jk;
- int sig_flag,setting,ncmp,ks;
- int itype,jtype,ktype,kptype;
- int bt_i,bt_j,bt_ij;
- int kp_index,same_ikp,same_jkp;
- double AA,BB,CC,DD,EE1,FF;
- double AAC,BBC,CCC,DDC,EEC;
- double UT,bndtmp;
- double amean,gmean0,gmean1,gmean2,ps;
- double gfactor1,gprime1,gsqprime;
- double gfactorsq,gfactor2,gprime2;
- double gfactorsq2;
- double gfactor3,gprime3,gfactor,rfactor;
- double rfactorrt,rfactor1rt,rfactor1;
- double rcm1,rcm2,gcm1,gcm2,gcm3;
- double agpdpr1,app1;
- double dsigB1,dsigB2;
- double part0,part1,part2,part3,part4;
- double psign,bndtmp0,pp1,bndtmp1,bndtmp2;
- double ftmp[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;
- firstneigh = list->firstneigh;
- numneigh = list->numneigh;
- inum = list->inum;
- ilist = list->ilist;
- n=0;
-
-//loop over all local atoms
-
- if(nb_sg>16) {
- nb_sg=16;
- }
- if(nb_sg==0) {
- nb_sg=(maxneigh)*(maxneigh/2);
- }
- if(allocate_sigma) {
- destroy_sigma();
- }
- create_sigma(nb_sg);
- for(itmp=0;itmp<inum;itmp++) {
- i = ilist[itmp];
- i_tag=tag[i];
- itype = map[type[i]]+1;
-
-//j is loop over all neighbors of i
-
- for(jtmp=0;jtmp<numneigh[i];jtmp++) {
- temp_ij=BOP_index[i]+jtmp;
- if(neigh_flag[temp_ij]) {
- for(m=0;m<nb_sg;m++) {
- for(pp=0;pp<3;pp++) {
- bt_sg[m].dAA[pp]=0.0;
- bt_sg[m].dBB[pp]=0.0;
- bt_sg[m].dEE1[pp]=0.0;
- bt_sg[m].dFF[pp]=0.0;
- bt_sg[m].dAAC[pp]=0.0;
- bt_sg[m].dSigB1[pp]=0.0;
- bt_sg[m].dSigB[pp]=0.0;
- }
- bt_sg[m].i=-1;
- bt_sg[m].j=-1;
- }
- nb_t=0;
- iilist=firstneigh[i];
- j=iilist[jtmp];
- jlist=firstneigh[j];
- for(ki=0;ki<numneigh[j];ki++) {
- if(x[jlist[ki]][0]==x[i][0]) {
- if(x[jlist[ki]][1]==x[i][1]) {
- if(x[jlist[ki]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- 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;
- for(ji=0;ji<numneigh[j];ji++) {
- temp_ji=BOP_index[j]+ji;
- if(x[jlist[ji]][0]==x[i][0]) {
- if(x[jlist[ji]][1]==x[i][1]) {
- if(x[jlist[ji]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- nSigBk[n]=0;
-
-//AA-EE1 are the components making up Eq. 30 (a)
-
- AA=0.0;
- BB=0.0;
- CC=0.0;
- DD=0.0;
- EE1=0.0;
-
-//FF is the Beta_sigma^2 term
-
- FF=betaS[temp_ij]*betaS[temp_ij];
-
-//agpdpr1 is derivative of FF w.r.t. r_ij
-
- agpdpr1=2.0*betaS[temp_ij]*dBetaS[temp_ij]/rij[temp_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*disij[0][temp_ij];
- bt_sg[nb_ij].dFF[1]=agpdpr1*disij[1][temp_ij];
- bt_sg[nb_ij].dFF[2]=agpdpr1*disij[2][temp_ij];
-
-//k is loop over all neighbors of i again with j neighbor of i
- for(ktmp=0;ktmp<numneigh[i];ktmp++) {
- temp_ik=BOP_index[i]+ktmp;
- if(neigh_flag[temp_ik]) {
- if(ktmp!=jtmp) {
- if(jtmp<ktmp) {
- njik=jtmp*(2*numneigh[i]-jtmp-1)/2+(ktmp-jtmp)-1;
- ngj=0;
- ngk=1;
- }
- else {
- njik=ktmp*(2*numneigh[i]-ktmp-1)/2+(jtmp-ktmp)-1;
- ngj=1;
- ngk=0;
- }
- k=iilist[ktmp];
- ktype = map[type[k]]+1;
-
-//find neighbor of k that is equal to i
-
- klist=firstneigh[k];
- for(kNeii=0;kNeii<numneigh[k];kNeii++) {
- if(x[klist[kNeii]][0]==x[i][0]) {
- if(x[klist[kNeii]][1]==x[i][1]) {
- if(x[klist[kNeii]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
-
-//find neighbor of i that is equal to k
-
- for(jNeik=0;jNeik<numneigh[j];jNeik++) {
- temp_jk=BOP_index[j]+jNeik;
- if(x[jlist[jNeik]][0]==x[k][0]) {
- if(x[jlist[jNeik]][1]==x[k][1]) {
- if(x[jlist[jNeik]][2]==x[k][2]) {
- break;
- }
- }
- }
- }
-
-//find neighbor of k that is equal to j
-
- for(kNeij=0;kNeij<numneigh[k];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;
- }
- }
- }
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nk0=nSigBk[n]-1;
- itypeSigBk[n][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;
- ang_jik=cos_index[i]+njik;
- if(ang_jik>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- gmean0=sigma_g0[jtype-1][itype-1][ktype-1];
- gmean1=sigma_g1[jtype-1][itype-1][ktype-1];
- gmean2=sigma_g2[jtype-1][itype-1][ktype-1];
- amean=cosAng[ang_jik];
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gfactorsq=gfactor1*gfactor1;
- gprime1=gmean1+2.0*gmean2*amean;
- 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[temp_ik]*betaS[temp_ik];
- CC=CC+gfactorsq*betaS[temp_ik]*betaS[temp_ik]*betaS[temp_ik]*betaS[temp_ik];
-//agpdpr1 is derivative of AA w.r.t. Beta(rik)
-//agpdpr2 is derivative of CC 1st term w.r.t. Beta(rik)
-//app1 is derivative of AA w.r.t. cos(theta_jik)
-//app2 is derivative of CC 1st term w.r.t. cos(theta_jik)
-
- agpdpr1=2.0*gfactorsq*betaS[temp_ik]*dBetaS[temp_ik]/rij[temp_ik];
- app1=betaS[temp_ik]*betaS[temp_ik]*gsqprime;
- bt_sg[nb_ij].dAA[0]+=
- app1*dcAng[ang_jik][0][ngj];
- bt_sg[nb_ij].dAA[1]+=
- app1*dcAng[ang_jik][1][ngj];
- bt_sg[nb_ij].dAA[2]+=
- app1*dcAng[ang_jik][2][ngj];
- bt_sg[nb_ik].dAA[0]+=
- app1*dcAng[ang_jik][0][ngk]
- +agpdpr1*disij[0][temp_ik];
- bt_sg[nb_ik].dAA[1]+=
- app1*dcAng[ang_jik][1][ngk]
- +agpdpr1*disij[1][temp_ik];
- bt_sg[nb_ik].dAA[2]+=
- app1*dcAng[ang_jik][2][ngk]
- +agpdpr1*disij[2][temp_ik];
-
-//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
-
- kp_index=0;
- for(ltmp=0;ltmp<numneigh[j];ltmp++) {
- temp_jkp=BOP_index[j]+ltmp;
- kp=jlist[ltmp];
- if(x[kp][0]==x[k][0]) {
- if(x[kp][1]==x[k][1]) {
- if(x[kp][2]==x[k][2]) {
- kp_index=1;
- break;
- }
- }
- }
- }
- if(kp_index) {
-
-//loop over neighbors of k
-
- for(mtmp=0;mtmp<numneigh[k];mtmp++) {
- kp=klist[mtmp];
- if(x[kp][0]==x[j][0]) {
- if(x[kp][1]==x[j][1]) {
- if(x[kp][2]==x[j][2]) {
- break;
- }
- }
- }
- }
- if(ki<ltmp) {
- nijk=ki*(2*numneigh[j]-ki-1)/2+(ltmp-ki)-1;
- ngji=0;
- ngjk=1;
- }
- else {
- nijk=ltmp*(2*numneigh[j]-ltmp-1)/2+(ki-ltmp)-1;
- ngji=1;
- ngjk=0;
- }
- if(kNeii<mtmp) {
- nikj=kNeii*(2*numneigh[k]-kNeii-1)/2+(mtmp-kNeii)-1;
- ngki=0;
- ngkj=1;
- }
- else {
- nikj=mtmp*(2*numneigh[k]-mtmp-1)/2+(kNeii-mtmp)-1;
- ngki=1;
- ngkj=0;
- }
- ang_ijk=cos_index[j]+nijk;
- if(ang_ijk>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng[ang_ijk];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[itype-1][ktype-1][jtype-1];
- gmean1=sigma_g1[itype-1][ktype-1][jtype-1];
- gmean2=sigma_g2[itype-1][ktype-1][jtype-1];
- ang_ikj=cos_index[k]+nikj;
- if(ang_ikj>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- amean=cosAng[ang_ikj];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gfactor=gfactor1*gfactor2*gfactor3;
- rfactor=betaS[temp_ik]*betaS[temp_jkp];
-
-//EE1 is (b) Eq. 12
-
- EE1=EE1+gfactor*rfactor;
-
-//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[temp_jkp]*dBetaS[temp_ik]/rij[temp_ik];
- rcm2=gfactor*betaS[temp_ik]*dBetaS[temp_jkp]/rij[temp_jkp];
- gcm1=rfactor*gprime1*gfactor2*gfactor3;
- gcm2=rfactor*gfactor1*gprime2*gfactor3;
- gcm3=rfactor*gfactor1*gfactor2*gprime3;
- bt_sg[nb_ij].dEE1[0]+=
- gcm1*dcAng[ang_jik][0][ngj]
- -gcm2*dcAng[ang_ijk][0][ngji];
- bt_sg[nb_ij].dEE1[1]+=
- gcm1*dcAng[ang_jik][1][ngj]
- -gcm2*dcAng[ang_ijk][1][ngji];
- bt_sg[nb_ij].dEE1[2]+=
- gcm1*dcAng[ang_jik][2][ngj]
- -gcm2*dcAng[ang_ijk][2][ngji];
- bt_sg[nb_ik].dEE1[0]+=
- gcm1*dcAng[ang_jik][0][ngk]
- +rcm1*disij[0][temp_ik]
- -gcm3*dcAng[ang_ikj][0][ngki];
- bt_sg[nb_ik].dEE1[1]+=
- gcm1*dcAng[ang_jik][1][ngk]
- +rcm1*disij[1][temp_ik]
- -gcm3*dcAng[ang_ikj][1][ngki];
- bt_sg[nb_ik].dEE1[2]+=
- gcm1*dcAng[ang_jik][2][ngk]
- +rcm1*disij[2][temp_ik]
- -gcm3*dcAng[ang_ikj][2][ngki];
- bt_sg[nb_jk].dEE1[0]+=
- gcm2*dcAng[ang_ijk][0][ngjk]
- +rcm2*disij[0][temp_jkp]
- -gcm3*dcAng[ang_ikj][0][ngkj];
- bt_sg[nb_jk].dEE1[1]+=
- gcm2*dcAng[ang_ijk][1][ngjk]
- +rcm2*disij[1][temp_jkp]
- -gcm3*dcAng[ang_ikj][1][ngkj];
- bt_sg[nb_jk].dEE1[2]+=
- gcm2*dcAng[ang_ijk][2][ngjk]
- +rcm2*disij[2][temp_jkp]
- -gcm3*dcAng[ang_ikj][2][ngkj];
- }
-
-// k and k' and j are all different neighbors of i
-
- for(ltmp=0;ltmp<ktmp;ltmp++) {
- if(ltmp!=jtmp) {
- temp_ikp=BOP_index[i]+ltmp;
- if(neigh_flag[temp_ikp]) {
- kp=iilist[ltmp];
- kptype = map[type[kp]]+1;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
- }
- }
- if(jtmp<ltmp) {
- njikp=jtmp*(2*numneigh[i]-jtmp-1)/2+(ltmp-jtmp)-1;
- } else {
- njikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(jtmp-ltmp)-1;
- }
- if(ktmp<ltmp) {
- nkikp=ktmp*(2*numneigh[i]-ktmp-1)/2+(ltmp-ktmp)-1;
- } else {
- nkikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(ktmp-ltmp)-1;
- }
- ang_jikp=cos_index[i]+njikp;
- if(ang_jikp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- gmean0=sigma_g0[jtype-1][itype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][itype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][itype-1][kptype-1];
- amean=cosAng[ang_jikp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][itype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][itype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][itype-1][kptype-1];
- ang_kikp=cos_index[i]+nkikp;
- if(ang_kikp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- amean=cosAng[ang_kikp];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gfactor=gfactor1*gfactor2*gfactor3;
- rfactorrt=betaS[temp_ik]*betaS[temp_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;
- }
- }
- }
-
-// j and k are different neighbors of i and k' is a neighbor k not equal to i
-
- for(ltmp=0;ltmp<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- if(neigh_flag[temp_kkp]) {
- kp=klist[ltmp];;
- 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(kNeii<ltmp) {
- nikkp=kNeii*(2*numneigh[k]-kNeii-1)/2+(ltmp-kNeii)-1;
- } else {
- nikkp=ltmp*(2*numneigh[k]-ltmp-1)/2+(kNeii-ltmp)-1;
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nkp=nSigBk[n]-1;
- itypeSigBk[n][nkp]=kp;
- }
- ang_ikkp=cos_index[k]+nikkp;
- if(ang_ikkp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- gmean0=sigma_g0[itype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[itype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[itype-1][ktype-1][kptype-1];
- amean=cosAng[ang_ikkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gfactorsq2=gfactor2*gfactor2;
- gfactor=gfactorsq*gfactorsq2;
- rfactorrt=betaS[temp_ik]*betaS[temp_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;
- }
- }
- }
- }
- }
- }
-
-//j is a neighbor of i and k is a neighbor of j not equal to i
-
- for(ktmp=0;ktmp<numneigh[j];ktmp++) {
- if(ktmp!=ji) {
- if(ktmp<ji) {
- njik=ktmp*(2*numneigh[j]-ktmp-1)/2+(ji-ktmp)-1;
- ngi=1;
- ngk=0;
- }
- else {
- njik=ji*(2*numneigh[j]-ji-1)/2+(ktmp-ji)-1;
- ngi=0;
- ngk=1;
- }
- temp_jk=BOP_index[j]+ktmp;
- if(neigh_flag[temp_jk]) {
- k=jlist[ktmp];
- ktype=map[type[k]]+1;
- klist=firstneigh[k];
-
- for(kNeij=0;kNeij<numneigh[k];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;
- }
- }
- }
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- new1=nSigBk[n]-1;
- itypeSigBk[n][new1]=k;
- }
- ang_ijk=cos_index[j]+njik;
- if(ang_ijk>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng[ang_ijk];
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime1=gmean1+2.0*gmean2*amean;
- gfactorsq=gfactor1*gfactor1;
- gsqprime=2.0*gfactor1*gprime1;
- rfactor1rt=betaS[temp_jk]*betaS[temp_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;
- DD=DD+gfactorsq*rfactor1;
-
-//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[temp_jk]*dBetaS[temp_jk]/rij[temp_jk];
- app1=rfactor1rt*gsqprime;
- bt_sg[nb_ij].dBB[0]-=
- app1*dcAng[ang_ijk][0][ngi];
- bt_sg[nb_ij].dBB[1]-=
- app1*dcAng[ang_ijk][1][ngi];
- bt_sg[nb_ij].dBB[2]-=
- app1*dcAng[ang_ijk][2][ngi];
- bt_sg[nb_jk].dBB[0]+=
- app1*dcAng[ang_ijk][0][ngk]
- +agpdpr1*disij[0][temp_jk];
- bt_sg[nb_jk].dBB[1]+=
- app1*dcAng[ang_ijk][1][ngk]
- +agpdpr1*disij[1][temp_jk];
- bt_sg[nb_jk].dBB[2]+=
- app1*dcAng[ang_ijk][2][ngk]
- +agpdpr1*disij[2][temp_jk];
-
-//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;
- if(neigh_flag[temp_jkp]) {
- kp=jlist[ltmp];
- kptype=map[type[kp]]+1;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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;
- }
- }
- }
- }
- if(ji<ltmp) {
- nijkp=ji*(2*numneigh[j]-ji-1)/2+(ltmp-ji)-1;
- } else {
- nijkp=ltmp*(2*numneigh[j]-ltmp-1)/2+(ji-ltmp)-1;
- }
- if(ktmp<ltmp) {
- nkjkp=ktmp*(2*numneigh[j]-ktmp-1)/2+(ltmp-ktmp)-1;
- ngjk=0;
- }
- else {
- nkjkp=ltmp*(2*numneigh[j]-ltmp-1)/2+(ktmp-ltmp)-1;
- ngjk=1;
- }
- ang_ijkp=cos_index[j]+nijkp;
- if(ang_ijkp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- ang_kjkp=cos_index[j]+nkjkp;
- if(ang_kjkp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- gmean0=sigma_g0[itype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[itype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[itype-1][jtype-1][kptype-1];
- amean=cosAng[ang_ijkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][jtype-1][kptype-1];
- amean=cosAng[ang_kjkp];
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gfactor=gfactor1*gfactor2*gfactor3;
- rfactorrt=betaS[temp_jk]*betaS[temp_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;
- }
- }
- }
-
-//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<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- if(neigh_flag[temp_kkp]) {
- kp=klist[ltmp];
- 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) {
- for(kNeij=0;kNeij<numneigh[k];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(kNeij<ltmp) {
- njkkp=kNeij*(2*numneigh[k]-kNeij-1)/2+(ltmp-kNeij)-1;
- } else {
- njkkp=ltmp*(2*numneigh[k]-ltmp-1)/2+(kNeij-ltmp)-1;
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- new2=nSigBk[n]-1;
- itypeSigBk[n][new2]=kp;
- }
- ang_jkkp=cos_index[k]+njkkp;
- if(ang_jkkp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- gmean0=sigma_g0[jtype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][ktype-1][kptype-1];
- amean=cosAng[ang_jkkp];
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gfactorsq2=gfactor2*gfactor2;
- gfactor=gfactorsq*gfactorsq2;
- rfactorrt=betaS[temp_jk]*betaS[temp_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;
- }
- }
- }
- }
- }
- }
-
- sig_flag=0;
- if(sig_flag==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
-
- EEC=(DDC-CCC)/(AAC+2.0*small1);
- for(m=0;m<nb_t;m++) {
- if((bt_sg[m].i>-1)&&(bt_sg[m].j>-1)) {
- bt_i=bt_sg[m].i;
- bt_j=bt_sg[m].j;
- 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];
- }
- }
- 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
-
- bndtmp=(FF+sigma_delta[iij]*sigma_delta[iij])
- +sigma_c[iij]*AAC+small4;
- psign=1.0;
- bndtmp0=1.0/sqrt(bndtmp);
- sigB1[n]=psign*betaS[temp_ij]*bndtmp0;
- bndtmp=-0.5*bndtmp0*bndtmp0*bndtmp0;
- bndtmp1=psign*bndtmp0+psign*betaS[temp_ij]
- *bndtmp*2.0*betaS[temp_ij];
- bndtmp1=bndtmp1*dBetaS[temp_ij]/rij[temp_ij];
- bndtmp2=psign*betaS[temp_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*disij[0][temp_ij]
- +(bndtmp2*bt_sg[m].dAAC[0]);
- bt_sg[m].dSigB1[1]=bndtmp1*disij[1][temp_ij]
- +(bndtmp2*bt_sg[m].dAAC[1]);
- bt_sg[m].dSigB1[2]=bndtmp1*disij[2][temp_ij]
- +(bndtmp2*bt_sg[m].dAAC[2]);
- setting=1;
- }
- else if(temp_kk==temp_ji&&setting==0) {
- bt_sg[m].dSigB1[0]=-bndtmp1*disij[0][temp_ij]
- +(bndtmp2*bt_sg[m].dAAC[0]);
- bt_sg[m].dSigB1[1]=-bndtmp1*disij[1][temp_ij]
- +(bndtmp2*bt_sg[m].dAAC[1]);
- bt_sg[m].dSigB1[2]=-bndtmp1*disij[2][temp_ij]
- +(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]);
- }
- }
- }
-
-//This loop is to ensure there is not an error for atoms with no neighbors (deposition)
-
- if(nb_t==0) {
- if(j>i) {
- bt_sg[0].dSigB1[0]=bndtmp1*disij[0][temp_ij];
- bt_sg[0].dSigB1[1]=bndtmp1*disij[1][temp_ij];
- bt_sg[0].dSigB1[2]=bndtmp1*disij[2][temp_ij];
- }
- else {
- bt_sg[0].dSigB1[0]=-bndtmp1*disij[0][temp_ij];
- bt_sg[0].dSigB1[1]=-bndtmp1*disij[1][temp_ij];
- bt_sg[0].dSigB1[2]=-bndtmp1*disij[2][temp_ij];
- }
- for(pp=0;pp<3;pp++) {
- bt_sg[0].dAA[pp]=0.0;
- bt_sg[0].dBB[pp]=0.0;
- bt_sg[0].dEE1[pp]=0.0;
- bt_sg[0].dFF[pp]=0.0;
- bt_sg[0].dAAC[pp]=0.0;
- bt_sg[0].dSigB[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[n]*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];
- 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[n]=dsigB1*part2;
- pp1=2.0*betaS[temp_ij];
- 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_ij=bt_sg[m].temp;
- bt_i=bt_sg[m].i;
- bt_j=bt_sg[m].j;
- 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],disij[0][bt_ij],disij[1][bt_ij],disij[2][bt_ij]);
- }
- }
- }
- }
- n++;
- }
- }
- }
- }
- destroy_sigma();
-}
-
-/* ---------------------------------------------------------------------- */
-
-/* The formulation differs slightly to avoid negative square roots
- in the calculation of Theta_pi,ij of (a) Eq. 36 and (b) Eq. 18 */
-
-void PairBOP::sigmaBo_otf()
-{
- int nb_t,new_n_tot;
- int n,i,j,k,kp,m,pp,kpj,kpk,kkp;
- int itmp,jtmp,ktmp,ltmp,mtmp;
- tagint i_tag,j_tag;
- int kp1,kp2,kp1type;
- int iij,iik,ijk,ikkp,ji,iikp,ijkp;
- int nkp;
- int nk0;
- int jNeik,kNeii,kNeij,kNeikp;
- int kpNeij,kpNeik;
- int new1,new2,nlocal;
- int inum,*ilist,*iilist,*jlist,*klist,*kplist;
- int **firstneigh,*numneigh;
- int temp_ij,temp_ik,temp_jkp,temp_kk,temp_jk;
- int temp_ji,temp_kkp;
- int temp_ikp;
- int nb_ij,nb_ik,nb_ikp;
- int nb_jk,nb_jkp,nb_kkp;
- int 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;
- double AA,BB,CC,DD,EE,EE1,FF;
- double AAC,BBC,CCC,DDC,EEC,FFC,GGC;
- double AACFF,UT,bndtmp,UTcom;
- double amean,gmean0,gmean1,gmean2,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;
- 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;
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- n=0;
- if(nb_sg==0) {
- nb_sg=(maxneigh)*(maxneigh/2);
- }
- if(allocate_sigma) {
- destroy_sigma();
- }
-
- create_sigma(nb_sg);
-
- for(itmp=0;itmp<inum;itmp++) {
- i = ilist[itmp];
- i_tag=tag[i];
- itype = map[type[i]]+1;
-
-//j is loop over all neighbors of i
-
- for(jtmp=0;jtmp<numneigh[i];jtmp++) {
- for(m=0;m<nb_sg;m++) {
- for(pp=0;pp<3;pp++) {
- bt_sg[m].dAA[pp]=0.0;
- bt_sg[m].dBB[pp]=0.0;
- bt_sg[m].dCC[pp]=0.0;
- bt_sg[m].dDD[pp]=0.0;
- bt_sg[m].dEE[pp]=0.0;
- bt_sg[m].dEE1[pp]=0.0;
- bt_sg[m].dFF[pp]=0.0;
- bt_sg[m].dAAC[pp]=0.0;
- bt_sg[m].dBBC[pp]=0.0;
- bt_sg[m].dCCC[pp]=0.0;
- bt_sg[m].dDDC[pp]=0.0;
- bt_sg[m].dEEC[pp]=0.0;
- bt_sg[m].dFFC[pp]=0.0;
- bt_sg[m].dGGC[pp]=0.0;
- bt_sg[m].dUT[pp]=0.0;
- bt_sg[m].dSigB1[pp]=0.0;
- bt_sg[m].dSigB[pp]=0.0;
- }
- 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;
- j=iilist[jtmp];
- 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;
- for(ji=0;ji<numneigh[j];ji++) {
- temp_ji=BOP_index[j]+ji;
- if(x[jlist[ji]][0]==x[i][0]) {
- if(x[jlist[ji]][1]==x[i][1]) {
- if(x[jlist[ji]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- 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];
- nSigBk[n]=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
-
- for(ktmp=0;ktmp<numneigh[i];ktmp++) {
- temp_ik=BOP_index[i]+ktmp;
- if(ktmp!=jtmp) {
- k=iilist[ktmp];
- 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
-
- for(kNeii=0;kNeii<numneigh[k];kNeii++) {
- if(x[klist[kNeii]][0]==x[i][0]) {
- if(x[klist[kNeii]][1]==x[i][1]) {
- if(x[klist[kNeii]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- 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]) {
- 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];
-
-//find neighbor of i that is equal to k
-
- for(jNeik=0;jNeik<numneigh[j];jNeik++) {
- temp_jk=BOP_index[j]+jNeik;
- if(x[jlist[jNeik]][0]==x[k][0]) {
- if(x[jlist[jNeik]][1]==x[k][1]) {
- if(x[jlist[jNeik]][2]==x[k][2]) {
- break;
- }
- }
- }
- }
-
-//find neighbor of k that is equal to j
-
- for(kNeij=0;kNeij<numneigh[k];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;
- }
- }
- }
- }
- 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);
-
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nk0=nSigBk[n]-1;
- itypeSigBk[n][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;
- 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);
- gmean0=sigma_g0[jtype-1][itype-1][ktype-1];
- gmean1=sigma_g1[jtype-1][itype-1][ktype-1];
- gmean2=sigma_g2[jtype-1][itype-1][ktype-1];
- amean=cosAng_jik;
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gfactorsq=gfactor1*gfactor1;
- gprime1=gmean1+2.0*gmean2*amean;
- 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;
- CC=CC+gfactorsq*betaS_ik*betaS_ik*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_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].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];
- 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
-
- same_kpk=0;
- for(ltmp=0;ltmp<numneigh[j];ltmp++) {
- temp_jkp=BOP_index[j]+ltmp;
- kp1=jlist[ltmp];
- 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<numneigh[k];mtmp++) {
- kp2=klist[mtmp];
- if(x[kp2][0]==x[k][0]) {
- if(x[kp2][1]==x[k][1]) {
- if(x[kp2][2]==x[k][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;
-
- 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]) {
- 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);
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng_ijk;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[itype-1][ktype-1][jtype-1];
- gmean1=sigma_g1[itype-1][ktype-1][jtype-1];
- gmean2=sigma_g2[itype-1][ktype-1][jtype-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);
- amean=cosAng_ikj;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- 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
-
- for(ltmp=0;ltmp<ktmp;ltmp++) {
- if(ltmp!=jtmp) {
- temp_ikp=BOP_index[i]+ltmp;
- kp=iilist[ltmp];;
- 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[n];nsearch++) {
- ncmp=itypeSigBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
- }
- }
- 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]) {
- 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];
- 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;
- gmean0=sigma_g0[jtype-1][itype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][itype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][itype-1][kptype-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);
- amean=cosAng_jikp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][itype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][itype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][itype-1][kptype-1];
- amean=cosAng_kikp;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- 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<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- kp=klist[ltmp];;
- 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;
- 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]) {
- 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];
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nkp=nSigBk[n]-1;
- itypeSigBk[n][nkp]=kp;
- }
- 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);
- 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;
- gmean0=sigma_g0[itype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[itype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[itype-1][ktype-1][kptype-1];
- amean=cosAng_ikkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- 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<numneigh[j];ltmp++) {
- sig_flag=0;
- temp_jkp=BOP_index[j]+ltmp;
- kp=jlist[ltmp];
- kptype = map[type[kp]]+1;
- kplist=firstneigh[kp];
-
- same_kkpk=0;
- same_jkpj=0;
-
- for(kpNeij=0;kpNeij<numneigh[kp];kpNeij++) {
- kpj=kplist[kpNeij];
- 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<numneigh[kp];kpNeik++) {
- kpk=kplist[kpNeik];
- 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<numneigh[k];kNeikp++) {
- temp_kkp=BOP_index[k]+kNeikp;
- kkp=kplist[kNeikp];
- 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<numneigh[kp];nsearch++) {
- ncmp=kplist[nsearch];
- 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;
-
- 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);
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nkp=nSigBk[n]-1;
- itypeSigBk[n][nkp]=kp;
- }
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[itype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[itype-1][jtype-1][kptype-1];
- amean=cosAng_ijkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[itype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[itype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[itype-1][ktype-1][kptype-1];
- amean=cosAng_ikkp;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[jtype-1][kptype-1][ktype-1];
- gmean1=sigma_g1[jtype-1][kptype-1][ktype-1];
- gmean2=sigma_g2[jtype-1][kptype-1][ktype-1];
- amean=cosAng_jkpk;
- gfactor4=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime4=gmean1+2.0*gmean2*amean;
- 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<numneigh[j];ktmp++) {
- if(ktmp!=ji) {
- temp_jk=BOP_index[j]+ktmp;
- k=jlist[ktmp];
- klist=firstneigh[k];
- ktype=map[type[k]]+1;
- for(kNeij=0;kNeij<numneigh[k];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[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- new1=nSigBk[n]-1;
- itypeSigBk[n][new1]=k;
- }
- 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]) {
- 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);
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng_ijk;
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime1=gmean1+2.0*gmean2*amean;
- 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;
- DD=DD+gfactorsq*rfactor1;
-
-//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;
- agpdpr2=2.0*rfactor1rt*agpdpr1;
- app1=rfactor1rt*gsqprime;
- app2=rfactor1rt*app1;
- 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_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].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];
- 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;
- kp=jlist[ltmp];
- 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[n];nsearch++) {
- ncmp=itypeSigBk[n][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;
- }
- }
- }
- }
- 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]) {
- 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);
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[itype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[itype-1][jtype-1][kptype-1];
- amean=cosAng_ijkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][jtype-1][kptype-1];
- amean=cosAng_kjkp;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- 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<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- kp=klist[ltmp];
- 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<numneigh[k];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;
- }
- }
- }
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- new2=nSigBk[n]-1;
- itypeSigBk[n][new2]=kp;
- }
- 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]) {
- 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);
- 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;
- gmean0=sigma_g0[jtype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][ktype-1][kptype-1];
- amean=cosAng_jkkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- 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[n]=0.0;
- sig_flag=1;
- }
- 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
-
- 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[n]=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)
-
- 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].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].dAAC[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].dSigB1[pp]=0.0;
- bt_sg[0].dSigB[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[n]*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];
- 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[n]=dsigB1*part2;
- pp1=2.0*betaS_ij;
- 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;
- 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]);
- }
- }
- }
- }
- n++;
- }
- }
- }
- }
- destroy_sigma();
-}
-
-/* ---------------------------------------------------------------------- */
-
-/* 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) */
-
-void PairBOP::sigmaBo_noa_otf()
-{
- int nb_t,new_n_tot;
- int n,i,j,k,kp,m,pp;
- int itmp,jtmp,ktmp,ltmp,mtmp;
- tagint i_tag,j_tag;
- int kp1,kp2,kp1type;
- int iij,iik,ijk,ikkp,ji,iikp,ijkp;
- int nkp;
- int nk0;
- int jNeik,kNeii,kNeij;
- int new1,new2,nlocal;
- int inum,*ilist,*iilist,*jlist,*klist;
- int **firstneigh,*numneigh;
- int temp_ij,temp_ik,temp_jkp,temp_kk,temp_jk;
- int temp_ji,temp_kkp;
- int nb_ij,nb_ik;
- int nb_jk,nb_jkp,nb_kkp;
- int nsearch;
- int sig_flag,setting,ncmp,ks;
- int itype,jtype,ktype,kptype;
- int bt_i,bt_j;
- int same_ikp,same_jkp,same_kpk;
- double AA,BB,CC,DD,EE1,FF;
- double AAC,BBC,CCC,DDC,EEC;
- double UT,bndtmp;
- double amean,gmean0,gmean1,gmean2,ps;
- double gfactor1,gprime1,gsqprime;
- double gfactorsq,gfactor2,gprime2;
- double gfactorsq2;
- double gfactor3,gprime3,gfactor,rfactor;
- double rfactorrt,rfactor1rt,rfactor1;
- double rcm1,rcm2,gcm1,gcm2,gcm3;
- double agpdpr1,app1;
- double dsigB1,dsigB2;
- double part0,part1,part2,part3,part4;
- double psign,bndtmp0,pp1;
- double bndtmp1,bndtmp2;
- 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;
- 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;
- double cosAng_jik,dcA_jik[3][2];
- double cosAng_jikp;
- double cosAng_kikp;
- double cosAng_ijk,dcA_ijk[3][2];
- double cosAng_ijkp;
- double cosAng_kjkp;
- double cosAng_ikj,dcA_ikj[3][2];
- double cosAng_ikkp;
- double cosAng_jkkp;
-
-
- 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;
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- n=0;
- if(nb_sg==0) {
- nb_sg=4;
- }
- if(allocate_sigma) {
- destroy_sigma();
- }
- create_sigma(nb_sg);
- for(itmp=0;itmp<inum;itmp++) {
-
- i = ilist[itmp];
- i_tag=tag[i];
- itype = map[type[i]]+1;
-
-//j is loop over all neighbors of i
-
- for(jtmp=0;jtmp<numneigh[i];jtmp++) {
- for(m=0;m<nb_sg;m++) {
- for(pp=0;pp<3;pp++) {
- bt_sg[m].dAA[pp]=0.0;
- bt_sg[m].dBB[pp]=0.0;
- bt_sg[m].dEE1[pp]=0.0;
- bt_sg[m].dFF[pp]=0.0;
- bt_sg[m].dAAC[pp]=0.0;
- bt_sg[m].dSigB1[pp]=0.0;
- bt_sg[m].dSigB[pp]=0.0;
- }
- bt_sg[m].i=-1;
- bt_sg[m].j=-1;
- }
- nb_t=0;
- iilist=firstneigh[i];
- temp_ij=BOP_index[i]+jtmp;
- j=iilist[jtmp];
- 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;
- for(ji=0;ji<numneigh[j];ji++) {
- temp_ji=BOP_index[j]+ji;
- if(x[jlist[ji]][0]==x[i][0]) {
- if(x[jlist[ji]][1]==x[i][1]) {
- if(x[jlist[ji]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- 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];
- nSigBk[n]=0;
-
-//AA-EE1 are the components making up Eq. 30 (a)
-
- AA=0.0;
- BB=0.0;
- CC=0.0;
- DD=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
-
- for(ktmp=0;ktmp<numneigh[i];ktmp++) {
- temp_ik=BOP_index[i]+ktmp;
- if(ktmp!=jtmp) {
- k=iilist[ktmp];
- 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
-
- for(kNeii=0;kNeii<numneigh[k];kNeii++) {
- if(x[klist[kNeii]][0]==x[i][0]) {
- if(x[klist[kNeii]][1]==x[i][1]) {
- if(x[klist[kNeii]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
- 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]) {
- 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];
-
-//find neighbor of i that is equal to k
-
- for(jNeik=0;jNeik<numneigh[j];jNeik++) {
- temp_jk=BOP_index[j]+jNeik;
- if(x[jlist[jNeik]][0]==x[k][0]) {
- if(x[jlist[jNeik]][1]==x[k][1]) {
- if(x[jlist[jNeik]][2]==x[k][2]) {
- break;
- }
- }
- }
- }
-
-//find neighbor of k that is equal to j
-
- for(kNeij=0;kNeij<numneigh[k];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;
- }
- }
- }
- }
- 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);
-
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nk0=nSigBk[n]-1;
- itypeSigBk[n][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;
- 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);
- gmean0=sigma_g0[jtype-1][itype-1][ktype-1];
- gmean1=sigma_g1[jtype-1][itype-1][ktype-1];
- gmean2=sigma_g2[jtype-1][itype-1][ktype-1];
- amean=cosAng_jik;
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gfactorsq=gfactor1*gfactor1;
- gprime1=gmean1+2.0*gmean2*amean;
- 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;
- CC=CC+gfactorsq*betaS_ik*betaS_ik*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];
-
-//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
-
- same_kpk=0;
- for(ltmp=0;ltmp<numneigh[j];ltmp++) {
- temp_jkp=BOP_index[j]+ltmp;
- kp1=jlist[ltmp];
- 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<numneigh[k];mtmp++) {
- kp2=klist[mtmp];
- if(x[kp2][0]==x[k][0]) {
- if(x[kp2][1]==x[k][1]) {
- if(x[kp2][2]==x[k][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;
-
- 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]) {
- 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);
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng_ijk;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[itype-1][ktype-1][jtype-1];
- gmean1=sigma_g1[itype-1][ktype-1][jtype-1];
- gmean2=sigma_g2[itype-1][ktype-1][jtype-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);
- amean=cosAng_ikj;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- 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
-
- for(ltmp=0;ltmp<ktmp;ltmp++) {
- if(ltmp!=jtmp) {
- kp=iilist[ltmp];;
- 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[n];nsearch++) {
- ncmp=itypeSigBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
- }
- }
- 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]) {
- 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];
- gmean0=sigma_g0[jtype-1][itype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][itype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][itype-1][kptype-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);
- cosAng_kikp=(dis_ik[0]*dis_ikp[0]+dis_ik[1]*dis_ikp[1]
- +dis_ik[2]*dis_ikp[2])/(r_ik*r_ikp);
- amean=cosAng_jikp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][itype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][itype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][itype-1][kptype-1];
- amean=cosAng_kikp;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- 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;
- }
- }
- }
-
-// j and k are different neighbors of i and k' is a neighbor k not equal to i
-
- for(ltmp=0;ltmp<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- kp=klist[ltmp];;
- 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;
- 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]) {
- 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];
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- nkp=nSigBk[n]-1;
- itypeSigBk[n][nkp]=kp;
- }
- cosAng_ikkp=(-dis_ik[0]*dis_kkp[0]-dis_ik[1]*dis_kkp[1]
- -dis_ik[2]*dis_kkp[2])/(r_ik*r_kkp);
- gmean0=sigma_g0[itype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[itype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[itype-1][ktype-1][kptype-1];
- amean=cosAng_ikkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gfactorsq2=gfactor2*gfactor2;
- 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;
- }
- }
- }
- }
- }
- }
-
-//j is a neighbor of i and k is a neighbor of j not equal to i
-
- for(ktmp=0;ktmp<numneigh[j];ktmp++) {
- if(ktmp!=ji) {
- temp_jk=BOP_index[j]+ktmp;
- k=jlist[ktmp];
- klist=firstneigh[k];
- ktype=map[type[k]]+1;
- for(kNeij=0;kNeij<numneigh[k];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[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- new1=nSigBk[n]-1;
- itypeSigBk[n][new1]=k;
- }
- 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]) {
- 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);
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][ktype-1];
- gmean1=sigma_g1[itype-1][jtype-1][ktype-1];
- gmean2=sigma_g2[itype-1][jtype-1][ktype-1];
- amean=cosAng_ijk;
- gfactor1=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime1=gmean1+2.0*gmean2*amean;
- 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;
- DD=DD+gfactorsq*rfactor1;
-
-//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];
-
-//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;
- kp=jlist[ltmp];
- 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[n];nsearch++) {
- ncmp=itypeSigBk[n][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;
- }
- }
- }
- }
- 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]) {
- 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);
- cosAng_kjkp=(dis_jk[0]*dis_jkp[0]+dis_jk[1]*dis_jkp[1]
- +dis_jk[2]*dis_jkp[2])/(r_jk*r_jkp);
- 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;
- gmean0=sigma_g0[itype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[itype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[itype-1][jtype-1][kptype-1];
- amean=cosAng_ijkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gmean0=sigma_g0[ktype-1][jtype-1][kptype-1];
- gmean1=sigma_g1[ktype-1][jtype-1][kptype-1];
- gmean2=sigma_g2[ktype-1][jtype-1][kptype-1];
- amean=cosAng_kjkp;
- gfactor3=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime3=gmean1+2.0*gmean2*amean;
- 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;
- }
- }
- }
-
-//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<numneigh[k];ltmp++) {
- temp_kkp=BOP_index[k]+ltmp;
- kp=klist[ltmp];
- 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<numneigh[k];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;
- }
- }
- }
- }
- sig_flag=0;
- for(nsearch=0;nsearch<nSigBk[n];nsearch++) {
- ncmp=itypeSigBk[n][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[n]=nSigBk[n]+1;
- new2=nSigBk[n]-1;
- itypeSigBk[n][new2]=kp;
- }
- 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]) {
+ 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];
+ 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];
+ 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)
@@ -6163,938 +2553,1381 @@ void PairBOP::sigmaBo_noa_otf()
ps=1.0;
betaS_kkp=((pBetaS3[ikkp][ks-1]*ps+pBetaS2[ikkp][ks-1])*ps
+pBetaS1[ikkp][ks-1])*ps+pBetaS[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);
- 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;
- gmean0=sigma_g0[jtype-1][ktype-1][kptype-1];
- gmean1=sigma_g1[jtype-1][ktype-1][kptype-1];
- gmean2=sigma_g2[jtype-1][ktype-1][kptype-1];
- amean=cosAng_jkkp;
- gfactor2=gmean0+gmean1*amean
- +gmean2*amean*amean;
- gprime2=gmean1+2.0*gmean2*amean;
- gfactorsq2=gfactor2*gfactor2;
- 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;
- }
- }
- }
- }
- }
- }
-
- sig_flag=0;
- if(FF<=0.000001) {
- sigB[n]=0.0;
- sig_flag=1;
- }
- 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
-
- EEC=(DDC-CCC)/(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];
- }
- }
- UT=EEC*FF+BBC+small3[iij];
- UT=1.0/sqrt(UT);
-
-// bndtmp is a slightly modified form of (a) Eq. 30 and (b) Eq. 8
-
- bndtmp=(FF+sigma_delta[iij]*sigma_delta[iij])
- +sigma_c[iij]*AAC+small4;
- psign=1.0;
- bndtmp0=1.0/sqrt(bndtmp);
- sigB1[n]=psign*betaS_ij*bndtmp0;
- bndtmp=-0.5*bndtmp0*bndtmp0*bndtmp0;
- bndtmp1=psign*bndtmp0+psign*betaS_ij
- *bndtmp*2.0*betaS_ij;
- bndtmp1=bndtmp1*dBetaS_ij/r_ij;
- bndtmp2=psign*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]);
- }
- }
- }
-
-//This loop is to ensure there is not an error for atoms with no neighbors (deposition)
-
- 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].dEE1[pp]=0.0;
- bt_sg[0].dFF[pp]=0.0;
- bt_sg[0].dAAC[pp]=0.0;
- bt_sg[0].dSigB[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[n]*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];
- 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[n]=dsigB1*part2;
- pp1=2.0*betaS_ij;
- 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;
- 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]);
- }
- }
- }
- }
- n++;
- }
- }
- }
- }
- destroy_sigma();
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairBOP::PiBo()
-{
- int new_n_tot;
- int i,j,k,kp,m,n,pp,nb_t;
- int iij,ji,ki;
- int nsearch,ncmp;
- tagint i_tag,j_tag;
- int njik,ngj,ngk,nglj,ngl,ngi;
- int nkjkp,nijkp,ngli,nkikp,njikp;
- int itmp,ltmp,jtmp,ktmp;
- int nlocal,pi_flag;
- int inum,*ilist,*iilist,*jlist;
- int **firstneigh,*numneigh;
- int itype,jtype;
- int temp_ij,temp_ik,temp_ikp;
- int temp_jk,temp_jkp;
- int ang_jikp,ang_kikp,ang_ijk;
- int ang_ijkp,ang_kjkp,ang_jik;
- int nb_ij,nb_ik,nb_jk,nb_ikp,nb_jkp;
- int bt_ij,bt_i,bt_j;
- 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,ftmp[3];
- double dPiB1,dPiB2,dPiB3,pp2;
- double **f = atom->f;
- double **x = atom->x;
- int *type = atom->type;
- tagint *tag = atom->tag;
- int newton_pair = force->newton_pair;
-
- nlocal = atom->nlocal;
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- n=0;
-
-// Loop over all local atoms for i
-
- if(nb_pi>16) {
- nb_pi=16;
- }
- if(nb_pi==0) {
- nb_pi=(maxneigh)*(maxneigh/2);
- }
- if(allocate_pi) {
- destroy_pi();
- }
- create_pi(nb_pi);
- for(itmp=0;itmp<inum;itmp++) {
- nb_t=0;
- i = ilist[itmp];
- itype = map[type[i]]+1;
- i_tag=tag[i];
-
-// j is a loop over all neighbors of i
-
- iilist=firstneigh[i];
- for(jtmp=0;jtmp<numneigh[i];jtmp++) {
- temp_ij=BOP_index[i]+jtmp;
- if(neigh_flag[temp_ij]) {
- 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;
- }
- j=iilist[jtmp];
- jlist=firstneigh[j];
- jtype=map[type[j]]+1;
- j_tag=tag[j];
- nb_t=0;
- ftmp[0]=0.0;
- ftmp[1]=0.0;
- ftmp[2]=0.0;
- 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;
- 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;
- AA=0.0;
- BB=0.0;
- nPiBk[n]=0;
- for(ji=0;ji<numneigh[j];ji++) {
- if(x[jlist[ji]][0]==x[i][0]) {
- if(x[jlist[ji]][1]==x[i][1]) {
- if(x[jlist[ji]][2]==x[i][2]) {
- break;
- }
- }
- }
- }
-
-// j and k are different neighbors of i
-
- for(ktmp=0;ktmp<numneigh[i];ktmp++) {
- if(ktmp!=jtmp) {
- temp_ik=BOP_index[i]+ktmp;
- if(neigh_flag[temp_ik]) {
- k=iilist[ktmp];
- if(jtmp<ktmp) {
- njik=jtmp*(2*numneigh[i]-jtmp-1)/2+(ktmp-jtmp)-1;
- ngj=0;
- ngk=1;
- }
- else {
- njik=ktmp*(2*numneigh[i]-ktmp-1)/2+(jtmp-ktmp)-1;
- ngj=1;
- ngk=0;
- }
- ang_jik=cos_index[i]+njik;
- if(ang_jik>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- 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[ang_jik]*cosAng[ang_jik];
- sinFactor=.5*(1.0-cosSq)*pi_p[itype-1]*betaS[temp_ik];
- cosFactor=.5*(1.0+cosSq)*betaP[temp_ik];
- betaCapSq1=pi_p[itype-1]*betaS[temp_ik]*betaS[temp_ik]-betaP[temp_ik]
- *betaP[temp_ik];
- dbetaCapSq1=2.0*pi_p[itype-1]*betaS[temp_ik]*dBetaS[temp_ik]
- -2.0*betaP[temp_ik]*dBetaP[temp_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[temp_ik]+cosFactor*betaP[temp_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[temp_ik]+2.0*cosFactor
- *dBetaP[temp_ik])/rij[temp_ik];
- app1=cosAng[ang_jik]*(-pi_p[itype-1]*betaS[temp_ik]*betaS[temp_ik]
- +betaP[temp_ik]*betaP[temp_ik]);
- app2=-(1.0-cosSq)*cosAng[ang_jik]*betaCapSq1*betaCapSq1;
- agpdpr2=.5*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*dbetaCapSq1/rij[temp_ik];
- itypePiBk[n][nPiBk[n]]=k;
- bt_pi[nb_ij].dAA[0]+=
- app1*dcAng[ang_jik][0][ngj];
- bt_pi[nb_ij].dAA[1]+=
- app1*dcAng[ang_jik][1][ngj];
- bt_pi[nb_ij].dAA[2]+=
- app1*dcAng[ang_jik][2][ngj];
- bt_pi[nb_ij].dBB[0]+=
- app2*dcAng[ang_jik][0][ngj];
- bt_pi[nb_ij].dBB[1]+=
- app2*dcAng[ang_jik][1][ngj];
- bt_pi[nb_ij].dBB[2]+=
- app2*dcAng[ang_jik][2][ngj];
- bt_pi[nb_ik].dAA[0]+=
- agpdpr1*disij[0][temp_ik]
- +app1*dcAng[ang_jik][0][ngk];
- bt_pi[nb_ik].dAA[1]+=
- agpdpr1*disij[1][temp_ik]
- +app1*dcAng[ang_jik][1][ngk];
- bt_pi[nb_ik].dAA[2]+=
- agpdpr1*disij[2][temp_ik]
- +app1*dcAng[ang_jik][2][ngk];
- bt_pi[nb_ik].dBB[0]+=
- app2*dcAng[ang_jik][0][ngk]
- +agpdpr2*disij[0][temp_ik];
- bt_pi[nb_ik].dBB[1]+=
- app2*dcAng[ang_jik][1][ngk]
- +agpdpr2*disij[1][temp_ik];
- bt_pi[nb_ik].dBB[2]+=
- app2*dcAng[ang_jik][2][ngk]
- +agpdpr2*disij[2][temp_ik];
-
-// 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;
- if(neigh_flag[temp_ikp]) {
- kp=iilist[ltmp];
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
- }
+ dBetaS_kkp=(pBetaS6[ikkp][ks-1]*ps+pBetaS5[ikkp][ks-1])*ps
+ +pBetaS4[ikkp][ks-1];
+ betaP_kkp=((pBetaP3[ikkp][ks-1]*ps+pBetaP2[ikkp][ks-1])*ps
+ +pBetaP1[ikkp][ks-1])*ps+pBetaP[ikkp][ks-1];
+ dBetaP_kkp=(pBetaP6[ikkp][ks-1]*ps+pBetaP5[ikkp][ks-1])*ps
+ +pBetaP4[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];
+ betaP_jkp=betaP[temp_jkp];
+ dBetaP_jkp=dBetaP[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];
+ betaP_kkp=betaP[temp_kkp];
+ dBetaP_kkp=dBetaP[temp_kkp];
+ if(ji<ltmp) {
+ nijkp=(ji)*nlistj-(ji+1)*(ji+2)/2+ltmp;
+ ngji=0;
+ ngjkp=1;
}
- nkikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(ktmp-ltmp)-1;
- if(jtmp<ltmp) {
- njikp=jtmp*(2*numneigh[i]-jtmp-1)/2+(ltmp-jtmp)-1;
- nglj=0;
- ngl=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 {
- njikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(jtmp-ltmp)-1;
- nglj=1;
- ngl=0;
+ nikkp=(kNeikp)*nlistk-(kNeikp+1)*(kNeikp+2)/2+kNeii;
+ ngki=1;
+ ngkkp=0;
}
- ang_jikp=cos_index[i]+njikp;
- if(ang_jikp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
+ if(kpNeij<kpNeik) {
+ njkpk=(kpNeij)*nlistkp-(kpNeij+1)*(kpNeij+2)/2+kpNeik;
+ ngkpj=0;
+ ngkpk=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;
+ else {
+ njkpk=(kpNeik)*nlistkp-(kpNeik+1)*(kpNeik+2)/2+kpNeij;
+ ngkpj=1;
+ ngkpk=0;
}
- bt_pi[nb_ikp].i=i;
- bt_pi[nb_ikp].j=kp;
- bt_pi[nb_ikp].temp=temp_ikp;
- ang_kikp=cos_index[i]+nkikp;
- if(ang_kikp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
+ 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;
+ }
+ }
}
- betaCapSq2=pi_p[itype-1]*betaS[temp_ikp]*betaS[temp_ikp]
- -betaP[temp_ikp]*betaP[temp_ikp];
- dbetaCapSq2=2.0*pi_p[itype-1]*betaS[temp_ikp]*dBetaS[temp_ikp]
- -2.0*betaP[temp_ikp]*dBetaP[temp_ikp];
- cosSq1=cosAng[ang_jikp]*cosAng[ang_jikp];
- angFactor=cosAng[ang_kikp]-cosAng[ang_jikp]*cosAng[ang_jik];
- angFactor1=4.0*angFactor;
- angFactor2=-angFactor1*cosAng[ang_jikp]
- +2.0*cosAng[ang_jik]*(1.0-cosSq1);
- angFactor3=-angFactor1*cosAng[ang_jik]
- +2.0*cosAng[ang_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;
+ }
+ 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)
-//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')
+ EE=EE+gfactor*rfactor;
- app1=betaCapSum*angFactor1;
- app2=betaCapSum*angFactor2;
- app3=betaCapSum*angFactor3;
- agpdpr1=.5*angFactor4*dbetaCapSq1*betaCapSq2/rij[temp_ik];
- agpdpr2=.5*angFactor4*betaCapSq1*dbetaCapSq2/rij[temp_ikp];
+//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)
- bt_pi[nb_ij].dBB[0]+=
- app2*dcAng[ang_jik][0][ngj]
- +app3*dcAng[ang_jikp][0][nglj];
- bt_pi[nb_ij].dBB[1]+=
- app2*dcAng[ang_jik][1][ngj]
- +app3*dcAng[ang_jikp][1][nglj];
- bt_pi[nb_ij].dBB[2]+=
- app2*dcAng[ang_jik][2][ngj]
- +app3*dcAng[ang_jikp][2][nglj];
- bt_pi[nb_ik].dBB[0]+=
- agpdpr1*disij[0][temp_ik]
- +app1*dcAng[ang_kikp][0][1]
- +app2*dcAng[ang_jik][0][ngk];
- bt_pi[nb_ik].dBB[1]+=
- agpdpr1*disij[1][temp_ik]
- +app1*dcAng[ang_kikp][1][1]
- +app2*dcAng[ang_jik][1][ngk];
- bt_pi[nb_ik].dBB[2]+=
- agpdpr1*disij[2][temp_ik]
- +app1*dcAng[ang_kikp][2][1]
- +app2*dcAng[ang_jik][2][ngk];
- bt_pi[nb_ikp].dBB[0]+=
- agpdpr2*disij[0][temp_ikp]
- +app1*dcAng[ang_kikp][0][0]
- +app3*dcAng[ang_jikp][0][ngl];
- bt_pi[nb_ikp].dBB[1]+=
- agpdpr2*disij[1][temp_ikp]
- +app1*dcAng[ang_kikp][1][0]
- +app3*dcAng[ang_jikp][1][ngl];
- bt_pi[nb_ikp].dBB[2]+=
- agpdpr2*disij[2][temp_ikp]
- +app1*dcAng[ang_kikp][2][0]
- +app3*dcAng[ang_jikp][2][ngl];
- }
+ 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];
}
}
- nPiBk[n]=nPiBk[n]+1;
}
}
}
-
-//j is a neighbor of i and k is a neighbor of j and equal to i
-
- for(ki=0;ki<numneigh[j];ki++) {
- k=jlist[ki];
- if(x[k][0]==x[i][0]) {
- if(x[k][1]==x[i][1]) {
- if(x[k][2]==x[i][2]) {
+ }
+ }
+//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;
}
}
}
}
-
-//j is a neighbor of i and k is a neighbor of j not equal to i
-
- for(ktmp=0;ktmp<numneigh[j];ktmp++) {
- if(ktmp!=ki) {
- temp_jk=BOP_index[j]+ktmp;
- if(neigh_flag[temp_jk]) {
- k=jlist[ktmp];
- pi_flag=0;
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][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[n][nPiBk[n]]=k;
- }
- if(ktmp<ki) {
- njik=ktmp*(2*numneigh[j]-ktmp-1)/2+(ki-ktmp)-1;
- ngi=1;
- ngk=0;
- }
- else {
- njik=ki*(2*numneigh[j]-ki-1)/2+(ktmp-ki)-1;
- ngi=0;
- ngk=1;
- }
- ang_ijk=cos_index[j]+njik;
- if(ang_ijk>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- 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;
+ 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;
}
- bt_pi[nb_jk].i=j;
- bt_pi[nb_jk].j=k;
- bt_pi[nb_jk].temp=temp_jk;
- cosSq=cosAng[ang_ijk]*cosAng[ang_ijk];
- sinFactor=.5*(1.0-cosSq)*pi_p[jtype-1]*betaS[temp_jk];
- cosFactor=.5*(1.0+cosSq)*betaP[temp_jk];
- betaCapSq1=pi_p[jtype-1]*betaS[temp_jk]*betaS[temp_jk]
- -betaP[temp_jk]*betaP[temp_jk];
- dbetaCapSq1=2.0*pi_p[jtype-1]*betaS[temp_jk]*dBetaS[temp_jk]
- -2.0*betaP[temp_jk]*dBetaP[temp_jk];
+ }
+ }
+ }
+ 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];
+ 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<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;
-//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
+//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
- AA=AA+sinFactor*betaS[temp_jk]+cosFactor*betaP[temp_jk];
- BB=BB+.25*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*betaCapSq1;
+ BB=BB+gfactorsq*rfactor1rt;
-//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)
+//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*sinFactor*dBetaS[temp_jk]+2.0*cosFactor
- *dBetaP[temp_jk])/rij[temp_jk];
- agpdpr2=.5*(1.0-cosSq)*(1.0-cosSq)*betaCapSq1*dbetaCapSq1/rij[temp_jk];
- app1=cosAng[ang_ijk]*(-pi_p[jtype-1]*betaS[temp_jk]*betaS[temp_jk]
- +betaP[temp_jk]*betaP[temp_jk]);
- app2=-(1.0-cosSq)*cosAng[ang_ijk]*betaCapSq1*betaCapSq1;
- bt_pi[nb_ij].dAA[0]-=
- app1*dcAng[ang_ijk][0][ngi];
- bt_pi[nb_ij].dAA[1]-=
- app1*dcAng[ang_ijk][1][ngi];
- bt_pi[nb_ij].dAA[2]-=
- app1*dcAng[ang_ijk][2][ngi];
- bt_pi[nb_ij].dBB[0]-=
- app2*dcAng[ang_ijk][0][ngi];
- bt_pi[nb_ij].dBB[1]-=
- app2*dcAng[ang_ijk][1][ngi];
- bt_pi[nb_ij].dBB[2]-=
- app2*dcAng[ang_ijk][2][ngi];
- bt_pi[nb_jk].dAA[0]+=
- agpdpr1*disij[0][temp_jk]
- +app1*dcAng[ang_ijk][0][ngk];
- bt_pi[nb_jk].dAA[1]+=
- agpdpr1*disij[1][temp_jk]
- +app1*dcAng[ang_ijk][1][ngk];
- bt_pi[nb_jk].dAA[2]+=
- agpdpr1*disij[2][temp_jk]
- +app1*dcAng[ang_ijk][2][ngk];
- bt_pi[nb_jk].dBB[0]+=
- app2*dcAng[ang_ijk][0][ngk]
- +agpdpr2*disij[0][temp_jk];
- bt_pi[nb_jk].dBB[1]+=
- app2*dcAng[ang_ijk][1][ngk]
- +agpdpr2*disij[1][temp_jk];
- bt_pi[nb_jk].dBB[2]+=
- app2*dcAng[ang_ijk][2][ngk]
- +agpdpr2*disij[2][temp_jk];
+ 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 and k and k' are different neighbors of j not equal to i
+//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!=ki) {
- temp_jkp=BOP_index[j]+ltmp;
- if(neigh_flag[temp_jkp]) {
- kp=jlist[ltmp];
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
+ 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;
}
}
- nkjkp=ltmp*(2*numneigh[j]-ltmp-1)/2+(ktmp-ltmp)-1;
- if(ki<ltmp) {
- nijkp=ki*(2*numneigh[j]-ki-1)/2+(ltmp-ki)-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];
+ if(ji<ltmp) {
+ nijkp=ji*(2*nlistj-ji-1)/2+(ltmp-ji)-1;
ngli=0;
ngl=1;
}
else {
- nijkp=ltmp*(2*numneigh[j]-ltmp-1)/2+(ki-ltmp)-1;
+ nijkp=ltmp*(2*nlistj-ltmp-1)/2+(ji-ltmp)-1;
ngli=1;
ngl=0;
}
- ang_ijkp=cos_index[j]+nijkp;
- if(ang_ijkp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
+ 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;
- if(ang_kjkp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
+ 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];
}
- 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;
+ }
+ 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];
}
- 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[temp_jkp]*betaS[temp_jkp]
- -betaP[temp_jkp]*betaP[temp_jkp];
- dbetaCapSq2=2.0*pi_p[jtype-1]*betaS[temp_jkp]*dBetaS[temp_jkp]
- -2.0*betaP[temp_jkp]*dBetaP[temp_jkp];
- cosSq1=cosAng[ang_ijkp]*cosAng[ang_ijkp];
- angFactor=cosAng[ang_kjkp]-cosAng[ang_ijkp]*cosAng[ang_ijk];
- angFactor1=4.0*angFactor;
- angFactor2=-angFactor1*cosAng[ang_ijkp]
- +2.0*cosAng[ang_ijk]*(1.0-cosSq1);
- angFactor3=-angFactor1*cosAng[ang_ijk]
- +2.0*cosAng[ang_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
+ }
+ 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
- BB=BB+betaCapSum*angFactor4;
+ 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)
-//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')
+ 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];
+
+ }
+ }
+ }
- app1=betaCapSum*angFactor1;
- app2=betaCapSum*angFactor2;
- app3=betaCapSum*angFactor3;
- agpdpr1=.5*angFactor4*dbetaCapSq1*betaCapSq2/rij[temp_jk];
- agpdpr2=.5*angFactor4*betaCapSq1*dbetaCapSq2/rij[temp_jkp];
+//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
- bt_pi[nb_ij].dBB[0]-=
- app3*dcAng[ang_ijkp][0][ngli]
- +app2*dcAng[ang_ijk][0][ngi];
- bt_pi[nb_ij].dBB[1]-=
- app3*dcAng[ang_ijkp][1][ngli]
- +app2*dcAng[ang_ijk][1][ngi];
- bt_pi[nb_ij].dBB[2]-=
- app3*dcAng[ang_ijkp][2][ngli]
- +app2*dcAng[ang_ijk][2][ngi];
- bt_pi[nb_jk].dBB[0]+=
- agpdpr1*disij[0][temp_jk]
- +app1*dcAng[ang_kjkp][0][1]
- +app2*dcAng[ang_ijk][0][ngk];
- bt_pi[nb_jk].dBB[1]+=
- agpdpr1*disij[1][temp_jk]
- +app1*dcAng[ang_kjkp][1][1]
- +app2*dcAng[ang_ijk][1][ngk];
- bt_pi[nb_jk].dBB[2]+=
- agpdpr1*disij[2][temp_jk]
- +app1*dcAng[ang_kjkp][2][1]
- +app2*dcAng[ang_ijk][2][ngk];
- bt_pi[nb_jkp].dBB[0]+=
- agpdpr2*disij[0][temp_jkp]
- +app1*dcAng[ang_kjkp][0][0]
- +app3*dcAng[ang_ijkp][0][ngl];
- bt_pi[nb_jkp].dBB[1]+=
- agpdpr2*disij[1][temp_jkp]
- +app1*dcAng[ang_kjkp][1][0]
- +app3*dcAng[ang_ijkp][1][ngl];
- bt_pi[nb_jkp].dBB[2]+=
- agpdpr2*disij[2][temp_jkp]
- +app1*dcAng[ang_kjkp][2][0]
- +app3*dcAng[ang_ijkp][2][ngl];
+ 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;
}
}
}
-
-//j and k' are different neighbors of i and k is a neighbor of j not equal to i
-
- for(ltmp=0;ltmp<numneigh[i];ltmp++) {
- if(ltmp!=jtmp) {
- temp_ikp=BOP_index[i]+ltmp;
- if(neigh_flag[temp_ikp]) {
- kp=iilist[ltmp];
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][nsearch];
- if(x[ncmp][0]==x[kp][0]) {
- if(x[ncmp][1]==x[kp][1]) {
- if(x[ncmp][2]==x[kp][2]) {
- break;
- }
- }
+ 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;
}
}
- if(ltmp<jtmp) {
- njikp=ltmp*(2*numneigh[i]-ltmp-1)/2+(jtmp-ltmp)-1;
- ngl=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]) {
+ 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];
+ betaP_kkp=((pBetaP3[ikkp][ks-1]*ps+pBetaP2[ikkp][ks-1])*ps
+ +pBetaP1[ikkp][ks-1])*ps+pBetaP[ikkp][ks-1];
+ dBetaP_kkp=(pBetaP6[ikkp][ks-1]*ps+pBetaP5[ikkp][ks-1])*ps
+ +pBetaP4[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];
+ betaP_kkp=betaP[temp_kkp];
+ dBetaP_kkp=dBetaP[temp_kkp];
+ if(kNeij<ltmp) {
+ njkkp=kNeij*(2*nlistk-kNeij-1)/2+(ltmp-kNeij)-1;
+ nglkp=1;
nglj=0;
}
else {
- njikp=jtmp*(2*numneigh[i]-jtmp-1)/2+(ltmp-jtmp)-1;
- ngl=0;
+ njkkp=ltmp*(2*nlistk-ltmp-1)/2+(kNeij-ltmp)-1;
+ nglkp=0;
nglj=1;
}
- ang_jikp=cos_index[i]+njikp;
- if(ang_jikp>=cos_total) {
- error->one(FLERR,"Too many atom triplets for pair bop");
- }
- 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;
+ 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];
}
- 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[temp_ikp]*betaS[temp_ikp]
- -betaP[temp_ikp]*betaP[temp_ikp];
- dbetaCapSq2=2.0*pi_p[itype-1]*betaS[temp_ikp]*dBetaS[temp_ikp]
- -2.0*betaP[temp_ikp]*dBetaP[temp_ikp];
- dotV=(disij[0][temp_jk]*disij[0][temp_ikp]+disij[1][temp_jk]
- *disij[1][temp_ikp]+disij[2][temp_jk]*disij[2][temp_ikp])
- /(rij[temp_jk]*rij[temp_ikp]);
- cosSq1=cosAng[ang_jikp]*cosAng[ang_jikp];
- angFactor=dotV+cosAng[ang_jikp]*cosAng[ang_ijk];
- angRfactor=4.0*angFactor*dotV;
- dAngR1=-angRfactor/rij[temp_jk];
- dAngR2=-angRfactor/rij[temp_ikp];
- angFactor1=4.0*angFactor*cosAng[ang_jikp]
- +2.0*cosAng[ang_ijk]*(1.0-cosSq1);
- angFactor2=4.0*angFactor*cosAng[ang_ijk]
- +2.0*cosAng[ang_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;
+ }
+ 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
-//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)
+ 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)
- app1=betaCapSum*angFactor1;
- app2=betaCapSum*angFactor2;
- agpdpr1=(.5*angFactor3*dbetaCapSq1*betaCapSq2
- +betaCapSum*dAngR1)/rij[temp_jk];
- agpdpr2=(.5*angFactor3*betaCapSq1*dbetaCapSq2
- +betaCapSum*dAngR2)/rij[temp_ikp];
- agpdpr3=4.0*betaCapSum*angFactor/(rij[temp_ikp]*rij[temp_jk]);
+ 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];
- bt_pi[nb_ij].dBB[0]+=
- +app2*dcAng[ang_jikp][0][ngl]
- -app1*dcAng[ang_ijk][0][ngi];
- bt_pi[nb_ij].dBB[1]+=
- +app2*dcAng[ang_jikp][1][ngl]
- -app1*dcAng[ang_ijk][1][ngi];
- bt_pi[nb_ij].dBB[2]+=
- +app2*dcAng[ang_jikp][2][ngl]
- -app1*dcAng[ang_ijk][2][ngi];
- bt_pi[nb_ikp].dBB[0]+=
- agpdpr2*disij[0][temp_ikp]
- +agpdpr3*disij[0][temp_jk]
- +app2*dcAng[ang_jikp][0][nglj];
- bt_pi[nb_ikp].dBB[1]+=
- agpdpr2*disij[1][temp_ikp]
- +agpdpr3*disij[1][temp_jk]
- +app2*dcAng[ang_jikp][1][nglj];
- bt_pi[nb_ikp].dBB[2]+=
- agpdpr2*disij[2][temp_ikp]
- +agpdpr3*disij[2][temp_jk]
- +app2*dcAng[ang_jikp][2][nglj];
- bt_pi[nb_jk].dBB[0]+=
- agpdpr1*disij[0][temp_jk]
- +agpdpr3*disij[0][temp_ikp]
- +app1*dcAng[ang_ijk][0][ngk];
- bt_pi[nb_jk].dBB[1]+=
- agpdpr1*disij[1][temp_jk]
- +agpdpr3*disij[1][temp_ikp]
- +app1*dcAng[ang_ijk][1][ngk];
- bt_pi[nb_jk].dBB[2]+=
- agpdpr1*disij[2][temp_jk]
- +agpdpr3*disij[2][temp_ikp]
- +app1*dcAng[ang_ijk][2][ngk];
- }
}
}
- if(pi_flag==0)
- nPiBk[n]=nPiBk[n]+1;
}
}
- }
- CC=betaP[temp_ij]*betaP[temp_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 is similary formulation to (a) Eq. 36 and (b) Eq. 18
-
- piB[n]=(ABrtR1+ABrtR2)*pi_a[iij]*betaP[temp_ij];
- dPiB1=-.5*(cube(ABrtR1)+cube(ABrtR2))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
- dPiB2=.25*BBrtR*(cube(ABrtR2)-cube(ABrtR1))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
- dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(cube(ABrtR1)+cube(ABrtR2))*pi_a[iij]
- *betaP[temp_ij]*betaP[temp_ij])*dBetaP[temp_ij]/rij[temp_ij];
- n++;
- pp2=2.0*betaP[temp_ij];
- for(m=0;m<nb_t;m++) {
- bt_ij=bt_pi[m].temp;
- bt_i=bt_pi[m].i;
- bt_j=bt_pi[m].j;
+ }
+ }
+ }
+
+ 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++) {
- 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];
+ 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],disij[0][bt_ij],disij[1][bt_ij],disij[2][bt_ij]);
+ ,ftmp[2],xtmp[0],xtmp[1],xtmp[2]);
}
}
- for(pp=0;pp<3;pp++) {
- ftmp[pp]=pp2*dPiB3*disij[pp][temp_ij];
- 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],disij[0][temp_ij],disij[1][temp_ij],disij[2][temp_ij]);
- }
}
}
}
+ }
}
- destroy_pi();
+ return(sigB);
+ destroy_sigma();
}
/* ---------------------------------------------------------------------- */
-void PairBOP::PiBo_otf()
+/* 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 itmp,ltmp,jtmp,ktmp;
+ int i_tag,j_tag;
+ int ltmp,ktmp;
int pi_flag,ks;
int nlocal;
int inum,*ilist,*iilist,*jlist;
@@ -7104,10 +3937,23 @@ void PairBOP::PiBo_otf()
int temp_jk,temp_jkp;
int nb_ij,nb_ik,nb_jk,nb_ikp,nb_jkp;
int bt_i,bt_j;
- double AA,BB,CC;
+ 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_ijkpi,ang_kjkp;
+ int ang_ijkp;
+ int ni_ij,ni_ji,ni_ik,ni_ikp;
+ int ni_ki,ni_jk,ni_jkp;
+ int temp_ji,temp_ki;
+ int nlistj,nlisti,nlistk;
+ double AA,BB,CC,DD,EE,FF;
double cosSq,sinFactor,cosFactor;
double cosSq1,dotV,BBrt,AB1,AB2;
- double BBrtR,ABrtR1,ABrtR2;
+ double BBrtR,ABrtR,ABrtR1,ABrtR2;
double angFactor,angFactor1,angFactor2;
double angFactor3,angFactor4,angRfactor;
double dAngR1,dAngR2,agpdpr3;
@@ -7145,9 +3991,11 @@ void PairBOP::PiBo_otf()
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
- tagint *tag = atom->tag;
+ int *tag = atom->tag;
nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+
numneigh = list->numneigh;
firstneigh = list->firstneigh;
inum = list->inum;
@@ -7166,17 +4014,13 @@ void PairBOP::PiBo_otf()
destroy_pi();
}
create_pi(nb_pi);
-
- for(itmp=0;itmp<inum;itmp++) {
- nb_t=0;
+ piB=0;
i = ilist[itmp];
- itype = map[type[i]]+1;
i_tag=tag[i];
+ itype = map[type[i]]+1;
// j is a loop over all neighbors of i
-
iilist=firstneigh[i];
- for(jtmp=0;jtmp<numneigh[i];jtmp++) {
for(m=0;m<nb_pi;m++) {
for(pp=0;pp<3;pp++) {
bt_pi[m].dAA[pp]=0.0;
@@ -7186,12 +4030,13 @@ void PairBOP::PiBo_otf()
bt_pi[m].i=-1;
bt_pi[m].j=-1;
}
+ nb_t=0;
temp_ij=BOP_index[i]+jtmp;
- j=iilist[jtmp];
+ ni_ij=neigh_index[temp_ij];
+ j=iilist[ni_ij];
jlist=firstneigh[j];
- jtype=map[type[j]]+1;
j_tag=tag[j];
- nb_t=0;
+ jtype=map[type[j]]+1;
ftmp[0]=0.0;
ftmp[1]=0.0;
ftmp[2]=0.0;
@@ -7202,13 +4047,20 @@ void PairBOP::PiBo_otf()
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[n]=0;
- for(ji=0;ji<numneigh[j];ji++) {
- if(x[jlist[ji]][0]==x[i][0]) {
- if(x[jlist[ji]][1]==x[i][1]) {
- if(x[jlist[ji]][2]==x[i][2]) {
+ 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;
}
}
@@ -7224,32 +4076,53 @@ void PairBOP::PiBo_otf()
bt_pi[nb_ij].i=i;
bt_pi[nb_ij].j=j;
bt_pi[nb_ij].temp=temp_ij;
- 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;
- 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];
+ 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
- for(ktmp=0;ktmp<numneigh[i];ktmp++) {
+ 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;
- k=iilist[ktmp];
+ ni_ik=neigh_index[temp_ik];
+ k=iilist[ni_ik];
ktype=map[type[k]]+1;
if(itype==ktype)
iik=itype-1;
@@ -7257,43 +4130,79 @@ void PairBOP::PiBo_otf()
iik=itype*bop_types-itype*(itype+1)/2+ktype-1;
else
iik=ktype*bop_types-ktype*(ktype+1)/2+itype-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]) {
- 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);
+ 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) {
@@ -7314,7 +4223,6 @@ void PairBOP::PiBo_otf()
//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;
@@ -7329,7 +4237,7 @@ void PairBOP::PiBo_otf()
+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[n][nPiBk[n]]=k;
+ itypePiBk[nPiBk]=k;
bt_pi[nb_ij].dAA[0]+=
app1*dcA_jik[0][0];
bt_pi[nb_ij].dAA[1]+=
@@ -7366,10 +4274,11 @@ void PairBOP::PiBo_otf()
for(ltmp=0;ltmp<ktmp;ltmp++) {
if(ltmp!=jtmp) {
temp_ikp=BOP_index[i]+ltmp;
- kp=iilist[ltmp];
+ ni_ikp=neigh_index[temp_ikp];
+ kp=iilist[ni_ikp];
kptype=map[type[kp]]+1;
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][nsearch];
+ 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]) {
@@ -7384,57 +4293,102 @@ void PairBOP::PiBo_otf()
iikp=itype*bop_types-itype*(itype+1)/2+kptype-1;
else
iikp=kptype*bop_types-kptype*(kptype+1)/2+itype-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]) {
- 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);
+ 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) {
@@ -7462,7 +4416,6 @@ void PairBOP::PiBo_otf()
//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')
@@ -7507,18 +4460,20 @@ void PairBOP::PiBo_otf()
agpdpr2*dis_ikp[2]
+app1*dcA_kikp[2][1]
+app3*dcA_jikp[2][1];
- }
}
}
- nPiBk[n]=nPiBk[n]+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<numneigh[j];ki++) {
- k=jlist[ki];
+ 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]) {
@@ -7529,15 +4484,15 @@ void PairBOP::PiBo_otf()
}
//j is a neighbor of i and k is a neighbor of j not equal to i
-
- for(ktmp=0;ktmp<numneigh[j];ktmp++) {
+ for(ktmp=0;ktmp<nlistj;ktmp++) {
if(ktmp!=ki) {
temp_jk=BOP_index[j]+ktmp;
- k=jlist[ktmp];
+ ni_jk=neigh_index[temp_jk];
+ k=jlist[ni_jk];
ktype=map[type[k]]+1;
pi_flag=0;
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][nsearch];
+ 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]) {
@@ -7548,7 +4503,7 @@ void PairBOP::PiBo_otf()
}
}
if(pi_flag==0) {
- itypePiBk[n][nPiBk[n]]=k;
+ itypePiBk[nPiBk]=k;
}
if(jtype==ktype)
ijk=jtype-1;
@@ -7556,43 +4511,79 @@ void PairBOP::PiBo_otf()
ijk=jtype*bop_types-jtype*(jtype+1)/2+ktype-1;
else
ijk=ktype*bop_types-ktype*(ktype+1)/2+jtype-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]) {
- 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);
+ 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) {
@@ -7646,94 +4637,140 @@ void PairBOP::PiBo_otf()
+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;
- kp=jlist[ltmp];
- kptype=map[type[kp]]+1;
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][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;
- 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]) {
- 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);
+ +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) {
@@ -7741,26 +4778,26 @@ void PairBOP::PiBo_otf()
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;
-
+ 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;
+ 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)
@@ -7768,57 +4805,58 @@ void PairBOP::PiBo_otf()
//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];
+ 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<numneigh[i];ltmp++) {
+ for(ltmp=0;ltmp<nlisti;ltmp++) {
if(ltmp!=jtmp) {
temp_ikp=BOP_index[i]+ltmp;
- kp=iilist[ltmp];
+ ni_ikp=neigh_index[temp_ikp];
+ kp=iilist[ni_ikp];
kptype=map[type[kp]]+1;
- for(nsearch=0;nsearch<nPiBk[n];nsearch++) {
- ncmp=itypePiBk[n][nsearch];
+ 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]) {
@@ -7833,43 +4871,79 @@ void PairBOP::PiBo_otf()
iikp=itype*bop_types-itype*(itype+1)/2+kptype-1;
else
iikp=kptype*bop_types-kptype*(kptype+1)/2+itype-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]) {
- 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);
+ 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) {
@@ -7938,353 +5012,169 @@ void PairBOP::PiBo_otf()
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[n]=nPiBk[n]+1;
- }
- }
- }
- 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 is similary formulation to (a) Eq. 36 and (b) Eq. 18
-
- piB[n]=(ABrtR1+ABrtR2)*pi_a[iij]*betaP_ij;
- dPiB1=-.5*(cube(ABrtR1)+cube(ABrtR2))*pi_c[iij]*pi_a[iij]*betaP_ij;
- dPiB2=.25*BBrtR*(cube(ABrtR2)-cube(ABrtR1))*pi_c[iij]*pi_a[iij]*betaP_ij;
- dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(cube(ABrtR1)+cube(ABrtR2))*pi_a[iij]
- *betaP_ij*betaP_ij)*dBetaP_ij/r_ij;
- 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;
- 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();
-}
-
-/* ----------------------------------------------------------------------
- read BOP potential file
-------------------------------------------------------------------------- */
-
-void PairBOP::read_file(char *filename)
-{
- int i,j,k;
- int ij,ii,jj;
- int buf1;
- int n;
- double buf2;
- char s[MAXLINE];
- char buf[2];
-
- MPI_Comm_rank(world,&me);
-
- // read file on proc 0
-
- rcore=0.1;
-
- 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);
- }
-
- // read parameters
-
- fgets(s,MAXLINE,fp);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%d",&bop_types);
- fclose(fp);
- npairs=bop_types*(bop_types+1)/2;
- }
-
- MPI_Bcast(&bop_types,1,MPI_INT,0,world);
- MPI_Bcast(&npairs,1,MPI_INT,0,world);
- allocate();
- 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(sigma_r0,npairs,"BOP:sigma_r0");
- memory->create(pi_r0,npairs,"BOP:pi_r0");
- memory->create(phi_r0,npairs,"BOP:phi_r0");
- memory->create(sigma_rc,npairs,"BOP:sigma_rc");
- memory->create(pi_rc,npairs,"BOP:pi_rc");
- memory->create(phi_rc,npairs,"BOP:phi_rc");
- memory->create(r1,npairs,"BOP:r1");
- memory->create(sigma_beta0,npairs,"BOP:sigma_beta0");
- memory->create(pi_beta0,npairs,"BOP:pi_beta0");
- memory->create(phi0,npairs,"BOP:phi0");
- memory->create(sigma_n,npairs,"BOP:sigma_n");
- memory->create(pi_n,npairs,"BOP:pi_n");
- memory->create(phi_m,npairs,"BOP:phi_m");
- memory->create(sigma_nc,npairs,"BOP:sigma_nc");
- memory->create(pi_nc,npairs,"BOP:pi_nc");
- memory->create(phi_nc,npairs,"BOP:phi_nc");
- 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_g0,bop_types
- ,bop_types,bop_types,"BOP:sigma_g0");
- memory->create(sigma_g1,bop_types
- ,bop_types,bop_types,"BOP:sigma_g1");
- memory->create(sigma_g2,bop_types
- ,bop_types,bop_types,"BOP:sigma_g2");
- memory->create(sigma_g3,bop_types
- ,bop_types,bop_types,"BOP:sigma_g3");
- memory->create(sigma_g4,bop_types
- ,bop_types,bop_types,"BOP:sigma_g4");
- memory->create(sigma_f,npairs,"BOP:sigma_f");
- memory->create(sigma_k,npairs,"BOP:sigma_k");
- memory->create(small3,npairs,"BOP:small3");
-
- if (me == 0) {
- words = new char*[bop_types];
- for(i=0;i<bop_types;i++) words[i]=NULL;
- 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);
- fgets(s,MAXLINE,fp);
- for(i=0;i<bop_types;i++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%d %lf %s",&buf1,&buf2,buf);
- n= strlen(buf)+1;
- words[i] = new char[n];
- strcpy(words[i],buf);
- }
- fgets(s,MAXLINE,fp);
- fgets(s,MAXLINE,fp);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g,&small4
- ,&small5,&small6,&small7);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%d%lf%lf",&ncutoff,&rbig,&rsmall);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%d",&which,&alpha,&nfunc);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&alpha1,&beta1,&gamma1);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf",&alpha2,&beta2);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf",&alpha3,&beta3);
- fgets(s,MAXLINE,fp);
- fgets(s,MAXLINE,fp);
- for(i=0;i<bop_types;i++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&pro[i],&pro_delta[i],&pi_p[i]);
- }
- fgets(s,MAXLINE,fp);
- fgets(s,MAXLINE,fp);
- cutmax=0;
-
- for(i=0;i<bop_types;i++) {
- ii=i+1;
- for(j=i;j<bop_types;j++) {
- jj=j+1;
- 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;
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf%lf",&sigma_r0[ij],&sigma_rc[ij],&r1[ij],&rcut[ij]);
- if(rcut[ij]>cutmax)
- cutmax=rcut[ij];
- pi_r0[ij]=sigma_r0[ij];
- phi_r0[ij]=sigma_r0[ij];
- pi_rc[ij]=sigma_rc[ij];
- phi_rc[ij]=sigma_rc[ij];
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&phi_m[ij],&sigma_n[ij],&sigma_nc[ij]);
- pi_n[ij]=sigma_n[ij];
- pi_nc[ij]=sigma_nc[ij];
- phi_nc[ij]=sigma_nc[ij];
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&phi0[ij],&sigma_beta0[ij],&pi_beta0[ij]);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&sigma_a[ij],&sigma_c[ij],&sigma_delta[ij]);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&pi_a[ij],&pi_c[ij],&pi_delta[ij]);
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&sigma_f[ij],&sigma_k[ij],&small3[ij]);
- }
- }
- fgets(s,MAXLINE,fp);
- fgets(s,MAXLINE,fp);
- for(i=0;i<bop_types;i++) {
- for(j=0;j<bop_types;j++) {
- for(k=j;k<bop_types;k++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lf%lf%lf",&sigma_g0[j][i][k],&sigma_g1[j][i][k]
- ,&sigma_g2[j][i][k]);
- sigma_g0[k][i][j]=sigma_g0[j][i][k];
- sigma_g1[k][i][j]=sigma_g1[j][i][k];
- sigma_g2[k][i][j]=sigma_g2[j][i][k];
+ 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]);
+ }
+ }
}
}
- }
- for(i=0;i<npairs;i++) {
- dr[i]=rcut[i]/(nr-1.0);
- rdr[i]=1.0/dr[i];
- }
- fclose(fp);
- }
- 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(&ncutoff,1,MPI_INT,0,world);
- MPI_Bcast(&rbig,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rsmall,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&which,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&nfunc,1,MPI_INT,0,world);
- MPI_Bcast(&alpha1,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&beta1,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&gamma1,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha2,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&beta2,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha3,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&beta3,1,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(&sigma_r0[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_rc[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&r1[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&rcut[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&cutmax,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&pi_r0[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&phi_r0[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&pi_rc[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&phi_rc[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&phi_m[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_n[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_nc[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&pi_n[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&pi_nc[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&phi_nc[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&phi0[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_beta0[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&pi_beta0[0],npairs,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(&sigma_g0[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_g1[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_g2[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_g3[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_g4[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&dr[0],npairs,MPI_DOUBLE,0,world);
- MPI_Bcast(&rdr[0],npairs,MPI_DOUBLE,0,world);
+ return(piB);
+ destroy_pi();
}
+/* ----------------------------------------------------------------------
+ read BOP potential file
+------------------------------------------------------------------------- */
+
/* ---------------------------------------------------------------------- */
void PairBOP::read_table(char *filename)
{
- int i,j,k,n;
- int buf1;
+ 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);
+ FILE *fp = fopen(filename,"r");
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);
- words = new char*[bop_types];
- for(i=0;i<bop_types;i++) words[i]=NULL;
+ 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;
- words[i] = new char[n];
- strcpy(words[i],buf);
+ elements[i] = new char[n];
+ strcpy(elements[i],buf);
}
+ nws=0;
+ ws=1;
fgets(s,MAXLINE,fp);
- sscanf(s,"%d %d",&nr,&nBOt);
+ 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");
@@ -8295,19 +5185,21 @@ void PairBOP::read_table(char *filename)
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_g0,bop_types
- ,bop_types,bop_types,"BOP:sigma_g0");
- memory->create(sigma_g1,bop_types
- ,bop_types,bop_types,"BOP:sigma_g1");
- memory->create(sigma_g2,bop_types
- ,bop_types,bop_types,"BOP:sigma_g2");
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);
+ FILE *fp = fopen(filename,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open BOP potential file %s",filename);
@@ -8334,14 +5226,81 @@ void PairBOP::read_table(char *filename)
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) {
+ sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
+ } else {
+ 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<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",&sigma_g0[i][j][k],&sigma_g1[i][j][k],&sigma_g2[i][j][k]);
- }
for(i=0;i<npairs;i++) {
for(j=0;j<nr;j++) {
fgets(s,MAXLINE,fp);
@@ -8383,12 +5342,45 @@ void PairBOP::read_table(char *filename)
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]);
@@ -8406,6 +5398,10 @@ void PairBOP::read_table(char *filename)
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;
@@ -8413,6 +5409,8 @@ void PairBOP::read_table(char *filename)
+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])
@@ -8431,6 +5429,10 @@ void PairBOP::read_table(char *filename)
-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])
@@ -8444,6 +5446,8 @@ void PairBOP::read_table(char *filename)
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++) {
@@ -8456,6 +5460,9 @@ void PairBOP::read_table(char *filename)
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;
@@ -8463,10 +5470,68 @@ void PairBOP::read_table(char *filename)
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 {
+ if(nws==3) {
+ for(n=0;n<npower+1;n++) {
+ gpara[j][i][k][n]=gpara[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);
@@ -8480,6 +5545,9 @@ void PairBOP::read_table(char *filename)
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);
@@ -8490,11 +5558,10 @@ void PairBOP::read_table(char *filename)
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(&sigma_g0[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_g1[0][0][0],bop_types*bop_types*bop_types,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_g2[0][0][0],bop_types*bop_types*bop_types,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);
@@ -8509,6 +5576,13 @@ void PairBOP::read_table(char *filename)
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);
@@ -8523,359 +5597,16 @@ void PairBOP::read_table(char *filename)
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);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairBOP::setPbetaS()
-{
- int i,j,k;
- double r,value,dvalue;
-
- for(i=0;i<npairs;i++) {
- for(j=0;j<nr;j++) {
- r=(double)j*dr[i];
- if(r<rcore)
- r=rcore;
- if(ncutoff==3) {
- if(r>=rcut[i])
- pBetaS[i][j]=0.0;
- else if(r<=r1[i]) {
- value=betaSfunc(i,r);
- dvalue=dBetaSfunc(i,r,value,1.0);
- pBetaS[i][j]=value;
- }
- else {
- value=betaSfunc(i,r1[i]);
- dvalue=dBetaSfunc(i,r1[i],value,1.0);
- pBetaS[i][j]=-(r-rcut[i])*(r-rcut[i])*(value*(2.0*r-3.0*r1[i]+rcut[i])
- -dvalue*(r-r1[i])*(r1[i]-rcut[i]))/((r1[i]-rcut[i])
- *(r1[i]-rcut[i])*(r1[i]-rcut[i]));
- }
- }
- else {
- if(r>=rcut[i])
- pBetaS[i][j]=0.0;
- else {
- value=betaSfunc(i,r);
- dvalue=dBetaSfunc(i,r,value,0.0);
- pBetaS[i][j]=value*cutoff(r1[i],rcut[i],ncutoff,r);
- }
- }
- }
- pBetaS[i][nr-1]=0.0;
- 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];
-
- 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;
- }
- 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]);
- }
- pBetaS2[i][nr-1]=0.0;
- pBetaS3[i][nr-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];
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairBOP::setPbetaP()
-{
- int i,j,k;
- double r,value,dvalue;
-
- for(i=0;i<npairs;i++) {
- for(j=0;j<nr;j++) {
- r=(double)j*dr[i];
- if(r<rcore)
- r=rcore;
- if(ncutoff==3) {
- if(r>=rcut[i])
- pBetaP[i][j]=0.0;
- else if(r<=r1[i]) {
- value=betaPfunc(i,r);
- dvalue=dBetaPfunc(i,r,value,0.0);
- pBetaP[i][j]=value;
- }
- else {
- value=betaPfunc(i,r1[i]);
- dvalue=dBetaPfunc(i,r1[i],value,1.0);
- pBetaP[i][j]=-(r-rcut[i])*(r-rcut[i])*(value*(2.0*r-3.0*r1[i]
- +rcut[i])-dvalue*(r-r1[1])*(r1[i]-rcut[i]))/((r1[i]-rcut[i])
- *(r1[i]-rcut[i])*(r1[i]-rcut[i]));
- }
- }
- else {
- if(r>=rcut[i])
- pBetaP[i][j]=0.0;
- else {
- value=betaPfunc(i,r);
- dvalue=dBetaPfunc(i,r,value,0.0);
- pBetaP[i][j]=value*cutoff(r1[i],rcut[i],ncutoff,r);
- }
- }
- }
- pBetaP[i][nr-1]=0.0;
- 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];
- for(k=2;k<nr-2;k++)
- pBetaP1[i][k]=((pBetaP[i][k-2]-pBetaP[i][k+2])+8.0*(pBetaP[i][k+1]
- -pBetaP[i][k-1]))/12.0;
- for(k=0;k<nr-1;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]);
- }
- pBetaP2[i][nr-1]=0.0;
- pBetaP3[i][nr-1]=0.0;
- for(k=0;k<nr;k++) {
- 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];
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairBOP::setPrepul()
-{
- int i,j,k;
- double r,value,dvalue;
-
- for(i=0;i<npairs;i++) {
- for(j=0;j<nr;j++) {
- r=(double)j*dr[i];
- if(r<rcore)
- r=rcore;
- if(ncutoff==3) {
- if(r>=rcut[i])
- pRepul[i][j]=0.0;
- else if(r<=r1[i]) {
- value=repulfunc(i,r);
- dvalue=dRepulfunc(i,r,value,0.0);
- pRepul[i][j]=value;
- }
- else {
- value=repulfunc(i,r1[i]);
- dvalue=dRepulfunc(i,r1[i],value,1.0);
- pRepul[i][j]=-(r-rcut[i])*(r-rcut[i])*(value*(2.0*r-3.0*r1[i]+rcut[i])
- -dvalue*(r-r1[i])*(r1[i]-rcut[i]))/((r1[i]-rcut[i])
- *(r1[i]-rcut[i])*(r1[i]-rcut[i]));
- }
- }
- else {
- if(r>=rcut[i])
- pRepul[i][j]=0.0;
- else {
- value=repulfunc(i,r);
- dvalue=dRepulfunc(i,r,value,0.0);
- pRepul[i][j]=value*cutoff(r1[i],rcut[i],ncutoff,r);
- }
- }
- }
- pRepul[i][nr-1]=0.0;
- 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];
- for(k=2;k<nr-2;k++)
- pRepul1[i][k]=((pRepul[i][k-2]-pRepul[i][k+2])+8.0*(pRepul[i][k+1]
- -pRepul[i][k-1]))/12.0;
- for(k=0;k<nr-1;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]);
- }
- pRepul2[i][nr-1]=0.0;
- pRepul3[i][nr-1]=0.0;
- for(k=0;k<nr;k++) {
- 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];
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairBOP::betaSfunc(int i,double r)
-{
- double temp_value;
-
- if(nfunc==1) {
- temp_value=pow(sigma_r0[i]/r,sigma_n[i])*exp(sigma_n[i]*pow(sigma_r0[i]
- /sigma_rc[i],sigma_nc[i])-sigma_n[i]*pow(r/sigma_rc[i],sigma_nc[i]));
- temp_value=sigma_beta0[i]*temp_value;
- }
- if(nfunc==2)
- temp_value=sigma_beta0[i]*exp(-sigma_n[i]*r);
- if(nfunc==3)
- temp_value=sigma_beta0[i]/pow(r,sigma_n[i]);
- return(temp_value);
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairBOP::dBetaSfunc(int i,double r,double value,double dmore)
-{
- double temp_dvalue;
-
- if(nfunc==1)
- if(dmore==1.0)
- temp_dvalue=-sigma_n[i]*value/r*(1.0+sigma_nc[i]
- *pow(r/sigma_rc[i],sigma_nc[i]));
- if(nfunc==2)
- if(dmore==1.0)
- temp_dvalue=-sigma_n[i]*value;
- if(nfunc==3)
- if(dmore==1.0)
- temp_dvalue=-sigma_n[i]*value/r;
- return(temp_dvalue);
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairBOP::betaPfunc(int i,double r)
-{
- double temp_value;
-
- if(nfunc==1) {
- temp_value=pow(pi_r0[i]/r,pi_n[i])*exp(pi_n[i]*pow(pi_r0[i]
- /pi_rc[i],pi_nc[i])-pi_n[i]*pow(r/pi_rc[i],pi_nc[i]));
- temp_value=pi_beta0[i]*temp_value;
- }
- if(nfunc==2)
- temp_value=pi_beta0[i]*exp(-pi_n[i]*r);
- if(nfunc==3)
- temp_value=pi_beta0[i]/pow(r,pi_n[i]);
- return(temp_value);
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairBOP::dBetaPfunc(int i,double r,double value,double dmore)
-{
- double temp_dvalue;
-
- if(nfunc==1)
- if(dmore==1.0)
- temp_dvalue=-pi_n[i]*value/r*(1.0+pi_nc[i]*pow(r/pi_rc[i],pi_nc[i]));
- if(nfunc==2)
- if(dmore==1.0)
- temp_dvalue=-pi_n[i]*value;
- if(nfunc==3)
- if(dmore==1.0)
- temp_dvalue=-pi_n[i]*value/r;
- return(temp_dvalue);
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairBOP::repulfunc(int i,double r)
-{
- double temp_value;
-
- if(nfunc==1) {
- temp_value=pow(phi_r0[i]/r,phi_m[i])*exp(phi_m[i]*pow(phi_r0[i]/phi_rc[i]
- ,phi_nc[i])-phi_m[i]*pow(r/phi_rc[i],phi_nc[i]));
- temp_value=phi0[i]*temp_value;
- }
- if(nfunc==2)
- temp_value=phi0[i]*exp(-phi_m[i]*r);
- if(nfunc==3)
- temp_value=phi0[i]/pow(r,phi_m[i]);
- return(temp_value);
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairBOP::dRepulfunc(int i,double r,double value,double dmore)
-{
- double temp_dvalue;
-
- if(nfunc==1)
- if(dmore==1.0)
- temp_dvalue=-phi_m[i]*value/r*(1.0+phi_nc[i]*pow(r/phi_rc[i],phi_nc[i]));
- if(nfunc==2)
- if(dmore==1.0)
- temp_dvalue=-phi_m[i]*value;
- if(nfunc==3)
- if(dmore==1.0)
- temp_dvalue=-phi_m[i]*value/r;
- return(temp_dvalue);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairBOP::setSign()
-{
- int i,j,k;
- double y0,tmp,xBO,fth,cs,bigF;
- double epsilon,fsigma1,slope,sat;
-
- dBO=1.0/(nBOt-1.0);
- rdBO=1.0/dBO;
- for(i=0;i<npairs;i++) {
- for(j=0;j<nBOt;j++) {
- xBO=(double)j*dBO;
- if(which==1.0) {
- fth=0.0;
- if(xBO>alpha)
- fth=4.0/3.0*(xBO-alpha);
- if(sigma_f[i]<=fth)
- FsigBO[i][j]=2.0*sigma_f[i];
- else if(sigma_f[i]>=1.0-fth)
- FsigBO[i][j]=2.0*(1.0-sigma_f[i]);
- else {
- cs=0.0;
- if(xBO<alpha)
- cs=32.0*(alpha-xBO);
- bigF=(sigma_f[i]*(1.0-sigma_f[i])-fth*(1.0-fth))/square(1.0-2.0*fth);
- FsigBO[i][j]=2.0*fth+2.0*bigF*(1.0-2.0*fth)*(1.0+bigF*(1.0-cs*bigF));
- }
- }
- else if(which==2.0) {
- epsilon=0.0000000001;
- fsigma1=sigma_f[i];
- if(fsigma1>0.5)
- fsigma1=1.0-fsigma1;
- y0=alpha1*pow(fsigma1,beta1)*pow(0.5-fsigma1,gamma1);
- slope=(1.0-exp(-alpha2*pow(fsigma1,beta2)))/(1.0-exp(-alpha2*pow(0.5,beta2)));
- sat=alpha3*fsigma1+beta3;
- tmp=y0+slope*xBO+sat;
- FsigBO[i][j]=(tmp-sqrt(tmp*tmp-4.0*(-epsilon*sqrt(1.0+slope*slope)
- +y0*sat+slope*sat*xBO)))/2.0;
- }
- }
- 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];
- for(k=2;k<nBOt-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<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]);
- }
- FsigBO2[i][nBOt-1]=0.0;
- FsigBO3[i][nBOt-1]=0.0;
- 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){
+ 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);
}
}
@@ -8914,10 +5645,20 @@ double PairBOP::memory_usage()
// 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
@@ -8940,6 +5681,20 @@ double PairBOP::memory_usage()
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
@@ -8983,21 +5738,13 @@ double PairBOP::memory_usage()
// FsigBO6
bytes += npairs * nr * sizeof (double);
// itypeSigBk
- bytes += neigh_total *neigh_ct* sizeof(int);
-// nSigBk
- bytes += neigh_total * sizeof(int);
-// sigB
- bytes += neigh_total * sizeof(int);
-// sigB1
- bytes += neigh_total * sizeof(int);
-// nPiBk
- bytes += neigh_total * sizeof(int);
-// piB
- bytes += neigh_total * sizeof(int);
+ bytes += neigh_ct* sizeof(int);
// itypePiBk
- bytes += neigh_total *neigh_ct* sizeof(int);
+ 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);
@@ -9024,8 +5771,8 @@ double PairBOP::memory_usage()
}
// pi_a
bytes += npairs * sizeof(double);
-// pro_delta
- bytes += npairs * sizeof(double);
+// pro
+ bytes += bop_types * sizeof(double);
// pi_delta
bytes += npairs * sizeof(double);
// pi_p
@@ -9045,7 +5792,7 @@ double PairBOP::memory_usage()
// pi_a
bytes += npairs * sizeof(double);
// pro_delta
- bytes += npairs * sizeof(double);
+ bytes += bop_types * sizeof(double);
// pi_delta
bytes += npairs * sizeof(double);
// pi_p
@@ -9084,24 +5831,12 @@ double PairBOP::memory_usage()
bytes += npairs * sizeof(double);
// phi_nc
bytes += npairs * sizeof(double);
-// pro
- bytes += npairs * sizeof(double);
// sigma_delta
bytes += npairs * sizeof(double);
// sigma_c
bytes += npairs * sizeof(double);
// sigma_a
bytes += npairs * sizeof(double);
-// sigma_g0
- bytes += bop_types * bop_types *bop_types * sizeof(double);
-// sigma_g1
- bytes += bop_types * bop_types *bop_types * sizeof(double);
-// sigma_g2
- bytes += bop_types * bop_types *bop_types * sizeof(double);
-// sigma_g3
- bytes += bop_types * bop_types *bop_types * sizeof(double);
-// sigma_g4
- bytes += bop_types * bop_types *bop_types * sizeof(double);
// sigma_f
bytes += npairs * sizeof(double);
// sigma_k
@@ -9112,7 +5847,24 @@ double PairBOP::memory_usage()
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;
}
@@ -9120,23 +5872,25 @@ double PairBOP::memory_usage()
void PairBOP::memory_theta_create()
{
+ int nlocal,nghost,nall;
+
+ nlocal = atom->nlocal;
+ nghost = atom->nghost;
+ nall = nlocal + nghost;
if(maxneigh<8)
neigh_ct=(maxneigh-1)*(maxneigh-1)*(maxneigh-1);
else
- neigh_ct=(maxneigh-1)*(maxneigh-1);
- memory->create(itypeSigBk,neigh_total
- ,neigh_ct,"itypeSigBk");
- memory->create(nSigBk,neigh_total,"nSigBk");
- memory->create(sigB,neigh_total,"sigB");
- memory->create(sigB1,neigh_total,"sigB1");
- memory->create(itypePiBk,neigh_total
- ,neigh_ct,"itypePiBk");
- memory->create(nPiBk,neigh_total,"nPiBk");
- memory->create(piB,neigh_total,"piB");
+ neigh_ct=(maxneigh-1)*(maxneigh-1)*(maxneigh-1);
+ if(neigh_ct<0) neigh_ct=0;
+ 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*2,3,2,"BOP:dcAng");
+ 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");
@@ -9153,23 +5907,25 @@ void PairBOP::memory_theta_create()
void PairBOP::memory_theta_grow()
{
+ int nlocal,nghost,nall;
+
+ nlocal = atom->nlocal;
+ nghost = atom->nghost;
+ nall = nlocal + nghost;
if(maxneigh<8)
neigh_ct=(maxneigh-1)*(maxneigh-1)*(maxneigh-1);
else
- neigh_ct=(maxneigh-1)*(maxneigh-1);
- memory->grow(itypeSigBk,neigh_total
- ,neigh_ct,"itypeSigBk");
- memory->grow(nSigBk,neigh_total,"nSigBk");
- memory->grow(sigB,neigh_total,"sigB");
- memory->grow(sigB1,neigh_total,"sigB1");
- memory->grow(itypePiBk,neigh_total
- ,neigh_ct,"itypePiBk");
- memory->grow(nPiBk,neigh_total,"nPiBk");
- memory->grow(piB,neigh_total,"piB");
+ neigh_ct=(maxneigh-1)*(maxneigh-1)*(maxneigh-1);
+ if(neigh_ct<0) neigh_ct=0;
+ 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*2,3,2,"BOP:dcAng");
+ 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");
@@ -9188,13 +5944,11 @@ void PairBOP::memory_theta_destroy()
{
memory->destroy(itypeSigBk);
- memory->destroy(nSigBk);
- memory->destroy(sigB);
- memory->destroy(sigB1);
memory->destroy(itypePiBk);
- memory->destroy(nPiBk);
- memory->destroy(piB);
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);
diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h
index 483884a936..ed8d1fdc27 100644
--- a/src/MANYBODY/pair_bop.h
+++ b/src/MANYBODY/pair_bop.h
@@ -1,4 +1,4 @@
-/* -*- c++ -*- ----------------------------------------------------------
+/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@@ -26,6 +26,7 @@ PairStyle(bop,PairBOP)
#define LMP_PAIR_BOP_H
#include "pair.h"
+#include "time.h"
#include "update.h"
namespace LAMMPS_NS {
@@ -44,23 +45,40 @@ class PairBOP : public Pair {
private:
int me;
int maxneigh; // maximum size of neighbor list on this processor
+ int maxneigh3; // maximum size of neighbor list on this processor
int update_list; // check for changing maximum size of neighbor list
+ int maxbopn; // maximum size of bop neighbor list for allocation
int maxnall; // maximum size of bop neighbor list for allocation
int *map; // mapping from atom types to elements
- int nr; // increments for the BOP potential
+ int nelements; // # of unique elments
+ int nr; // increments for the BOP pair potential
+ int ntheta; // increments for the angle function
+ int npower; // power of the angular function
int nBOt; // second BO increments
int bop_types; // number of elments in potential
int npairs; // number of element pairs
+ char **elements; // names of unique elements
+ int ***elem2param;
+ int nparams;
int bop_step;
int allocate_pi;
int allocate_sigma;
int allocate_neigh;
int nb_pi,nb_sg;
+ int ago1;
+// int cnt1;
int *BOP_index; // index for neighbor list position
+ int *BOP_total; // index for neighbor list position
+ int *BOP_index3; // index for neighbor list position
+ int *BOP_total3; // index for neighbor list position
+ int *neigh_index; // index for neighbor list position
+ int *neigh_index3; // index for neighbor list position
int neigh_total; // total number of neighbors stored
+ int neigh_total3; // total number of neighbors stored
int *cos_index; // index for neighbor cosine if not using on the fly
int *neigh_flag; // index for neighbor cosine if not using on the fly
+ int *neigh_flag3; // index for neighbor cosine if not using on the fly
int cos_total; // number of cosines stored if not using on the fly
int neigh_ct; // limit for large arrays
@@ -73,9 +91,8 @@ class PairBOP : public Pair {
double *sigma_rc,*pi_rc,*phi_rc,*r1,*sigma_beta0;
double *pi_beta0,*phi0,*sigma_n,*pi_n,*phi_m;
double *sigma_nc,*pi_nc,*phi_nc;
- double *pro,*sigma_delta,*sigma_c,*sigma_a;
- double ***sigma_g0,***sigma_g1,***sigma_g2,***sigma_g3;
- double ***sigma_g4,*sigma_f,*sigma_k,*small3;
+ double *pro,*sigma_delta,*sigma_c,*sigma_a;
+ double *sigma_f,*sigma_k,*small3;
double small1,small2,small3g,small4,small5,small6,small7;
double which,alpha,alpha1,beta1,gamma1,alpha2,beta2,alpha3;
double beta3,rsmall,rbig,rcore;
@@ -87,18 +104,16 @@ class PairBOP : public Pair {
//on the fly will slow down calculations
//but requires less memory on = 1, off=0
- int table; //determines the method for reading in
- //potential parameters a preset table
- //or generate the tables using a spline
-
/* Neigh variables */
- double *rcut,*dr,*rdr;
+ double *rcut,*rcut3,*dr,*rdr,*dr3,*rdr3;
+ double *rcutsq,*rcutsq3;
double **disij,*rij;
+ double rcutall,rctroot;
/*Triple variables */
- double *cosAng,***dcAng;
+ double *cosAng,***dcosAng,***dcAng;
/*Double variables */
@@ -107,15 +122,15 @@ class PairBOP : public Pair {
/*Sigma variables */
- int **itypeSigBk,*nSigBk;
- double *sigB;
- double *sigB1;
+ int *itypeSigBk,nSigBk;
+ double sigB,sigB_0;
+ double sigB1;
/*Pi variables */
- int **itypePiBk,*nPiBk;
- double *piB;
+ int *itypePiBk,nPiBk;
+ double piB,piB_0;
/*Grids1 variables */
@@ -132,6 +147,14 @@ class PairBOP : public Pair {
double **pRepul,**pRepul1,**pRepul2,**pRepul3;
double **pRepul4,**pRepul5,**pRepul6;
+ double **pLong,**pLong1,**pLong2,**pLong3;
+ double **pLong4,**pLong5,**pLong6;
+
+ double ****gfunc,****gpara;
+ double ****gfunc1,****gfunc2,****gfunc3;
+ double ****gfunc4,****gfunc5,****gfunc6;
+ double dtheta,rdtheta;
+
/*Grids4 variables */
double **FsigBO,**FsigBO1,**FsigBO2,**FsigBO3;
@@ -182,24 +205,21 @@ class PairBOP : public Pair {
void gneigh();
void theta();
void theta_mod();
- void sigmaBo();
- void PiBo();
- void sigmaBo_otf();
- void PiBo_otf();
- void sigmaBo_noa();
- void sigmaBo_noa_otf();
+ double sigmaBo(int, int);
+ double PiBo(int, int);
void memory_theta_create();
void memory_theta_destroy();
void memory_theta_grow();
double cutoff(double, double, int, double);
+/*
double betaSfunc(int, double);
double dBetaSfunc(int, double, double, double);
double betaPfunc(int, double);
double dBetaPfunc(int, double, double, double);
double repulfunc(int, double);
double dRepulfunc(int, double, double, double);
+*/
- void read_file(char *);
void read_table(char *);
void allocate();
void create_pi(int);
--
GitLab