Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-OMP/improper_class2_omp.cpp
354e20f43157efficient_neuronet

Last Change
Raw File

improper_class2_omp.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "improper_class2_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "error.h"
#include "suffix.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperClass2OMP::ImproperClass2OMP(class LAMMPS *lmp)
: ImproperClass2(lmp), ThrOMP(lmp,THR_IMPROPER)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void ImproperClass2OMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = neighbor->nimproperlist;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (inum > 0) {
if (evflag) {
if (eflag) {
if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
}
thr->timer(Timer::BOND);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,i3,i4,i,j,k,n,type;
double eimproper;
double delr[3][3],rmag[3],rinvmag[3],rmag2[3];
double theta[3],costheta[3],sintheta[3];
double cossqtheta[3],sinsqtheta[3],invstheta[3];
double rABxrCB[3],rDBxrAB[3],rCBxrDB[3];
double ddelr[3][4],dr[3][4][3],dinvr[3][4][3];
double dthetadr[3][4][3],dinvsth[3][4][3];
double dinv3r[4][3],dinvs3r[3][4][3];
double drCBxrDB[3],rCBxdrDB[3],drDBxrAB[3],rDBxdrAB[3];
double drABxrCB[3],rABxdrCB[3];
double dot1,dot2,dd[3];
double fdot[3][4][3],ftmp,invs3r[3],inv3r;
double t,tt1,tt3,sc1;
double dotCBDBAB,dotDBABCB,dotABCBDB;
double chi,deltachi,d2chi,cossin2;
double drAB[3][4][3],drCB[3][4][3],drDB[3][4][3];
double dchi[3][4][3],dtotalchi[4][3];
double schiABCD,chiABCD,schiCBDA,chiCBDA,schiDBAC,chiDBAC;
double fabcd[4][3];
eimproper = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
dthetadr[i][j][k] = 0.0;
drAB[i][j][k] = 0.0;
drCB[i][j][k] = 0.0;
drDB[i][j][k] = 0.0;
}
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
if (k0[type] == 0.0) continue;
// difference vectors
delr[0][0] = x[i1].x - x[i2].x;
delr[0][1] = x[i1].y - x[i2].y;
delr[0][2] = x[i1].z - x[i2].z;
delr[1][0] = x[i3].x - x[i2].x;
delr[1][1] = x[i3].y - x[i2].y;
delr[1][2] = x[i3].z - x[i2].z;
delr[2][0] = x[i4].x - x[i2].x;
delr[2][1] = x[i4].y - x[i2].y;
delr[2][2] = x[i4].z - x[i2].z;
// bond lengths and associated values
for (i = 0; i < 3; i++) {
rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
delr[i][2]*delr[i][2];
rmag[i] = sqrt(rmag2[i]);
rinvmag[i] = 1.0/rmag[i];
}
// angle ABC, CBD, ABD
costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
// angle error check
for (i = 0; i < 3; i++) {
if (costheta[i] == -1.0) {
int me = comm->me;
if (screen) {
char str[128];
sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me, thr->get_tid(),update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4].x,x[i4].y,x[i4].z);
}
}
}
for (i = 0; i < 3; i++) {
if (costheta[i] > 1.0) costheta[i] = 1.0;
if (costheta[i] < -1.0) costheta[i] = -1.0;
theta[i] = acos(costheta[i]);
cossqtheta[i] = costheta[i]*costheta[i];
sintheta[i] = sin(theta[i]);
invstheta[i] = 1.0/sintheta[i];
sinsqtheta[i] = sintheta[i]*sintheta[i];
}
// cross & dot products
cross(delr[0],delr[1],rABxrCB);
cross(delr[2],delr[0],rDBxrAB);
cross(delr[1],delr[2],rCBxrDB);
dotCBDBAB = dot(rCBxrDB,delr[0]);
dotDBABCB = dot(rDBxrAB,delr[1]);
dotABCBDB = dot(rABxrCB,delr[2]);
t = rmag[0] * rmag[1] * rmag[2];
inv3r = 1.0/t;
invs3r[0] = invstheta[1] * inv3r;
invs3r[1] = invstheta[2] * inv3r;
invs3r[2] = invstheta[0] * inv3r;
// chi ABCD, CBDA, DBAC
// final chi is average of three
schiABCD = dotCBDBAB * invs3r[0];
chiABCD = asin(schiABCD);
schiCBDA = dotDBABCB * invs3r[1];
chiCBDA = asin(schiCBDA);
schiDBAC = dotABCBDB * invs3r[2];
chiDBAC = asin(schiDBAC);
chi = (chiABCD + chiCBDA + chiDBAC) / 3.0;
deltachi = chi - chi0[type];
d2chi = deltachi * deltachi;
// energy
if (EFLAG) eimproper = k0[type]*d2chi;
// forces
// define d(delr)
// i = bond AB/CB/DB, j = atom A/B/C/D
ddelr[0][0] = 1.0;
ddelr[0][1] = -1.0;
ddelr[0][2] = 0.0;
ddelr[0][3] = 0.0;
ddelr[1][0] = 0.0;
ddelr[1][1] = -1.0;
ddelr[1][2] = 1.0;
ddelr[1][3] = 0.0;
ddelr[2][0] = 0.0;
ddelr[2][1] = -1.0;
ddelr[2][2] = 0.0;
ddelr[2][3] = 1.0;
// compute d(|r|)/dr and d(1/|r|)/dr for each direction, bond and atom
// define d(r) for each r
// i = bond AB/CB/DB, j = atom A/B/C/D, k = X/Y/Z
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
}
// compute d(1 / (|r_AB| * |r_CB| * |r_DB|) / dr
// i = atom A/B/C/D, j = X/Y/Z
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
rinvmag[0] * dinvr[2][i][j]) +
rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
// compute d(theta)/d(r) for 3 angles
// angleABC
tt1 = costheta[0] / rmag2[0];
tt3 = costheta[0] / rmag2[1];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[0]);
dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
// angleCBD
tt1 = costheta[1] / rmag2[1];
tt3 = costheta[1] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[1]);
dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]));
dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
// angleABD
tt1 = costheta[2] / rmag2[0];
tt3 = costheta[2] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[2]);
dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]));
dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
// compute d( 1 / sin(theta))/dr
// i = angle, j = atom, k = direction
for (i = 0; i < 3; i++) {
cossin2 = -costheta[i] / sinsqtheta[i];
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
}
// compute d(1 / sin(theta) * |r_AB| * |r_CB| * |r_DB|)/dr
// i = angle, j = atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
(inv3r * dinvsth[1][i][j]);
dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
(inv3r * dinvsth[2][i][j]);
dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
(inv3r * dinvsth[0][i][j]);
}
// drCB(i,j,k), etc
// i = vector X'/Y'/Z', j = atom A/B/C/D, k = direction X/Y/Z
for (i = 0; i < 3; i++) {
drCB[i][1][i] = -1.0;
drAB[i][1][i] = -1.0;
drDB[i][1][i] = -1.0;
drDB[i][3][i] = 1.0;
drCB[i][2][i] = 1.0;
drAB[i][0][i] = 1.0;
}
// d((r_CB x r_DB) dot r_AB)
// r_CB x d(r_DB)
// d(r_CB) x r_DB
// (r_CB x d(r_DB)) + (d(r_CB) x r_DB)
// (r_CB x d(r_DB)) + (d(r_CB) x r_DB) dot r_AB
// d(r_AB) dot (r_CB x r_DB)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[1],drDB[i][j],rCBxdrDB);
cross(drCB[i][j],delr[2],drCBxrDB);
for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
dot1 = dot(dd,delr[0]);
dot2 = dot(rCBxrDB,drAB[i][j]);
fdot[0][j][i] = dot1 + dot2;
}
// d((r_DB x r_AB) dot r_CB)
// r_DB x d(r_AB)
// d(r_DB) x r_AB
// (r_DB x d(r_AB)) + (d(r_DB) x r_AB)
// (r_DB x d(r_AB)) + (d(r_DB) x r_AB) dot r_CB
// d(r_CB) dot (r_DB x r_AB)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[2],drAB[i][j],rDBxdrAB);
cross(drDB[i][j],delr[0],drDBxrAB);
for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
dot1 = dot(dd,delr[1]);
dot2 = dot(rDBxrAB,drCB[i][j]);
fdot[1][j][i] = dot1 + dot2;
}
// d((r_AB x r_CB) dot r_DB)
// r_AB x d(r_CB)
// d(r_AB) x r_CB
// (r_AB x d(r_CB)) + (d(r_AB) x r_CB)
// (r_AB x d(r_CB)) + (d(r_AB) x r_CB) dot r_DB
// d(r_DB) dot (r_AB x r_CB)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[0],drCB[i][j],rABxdrCB);
cross(drAB[i][j],delr[1],drABxrCB);
for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
dot1 = dot(dd,delr[2]);
dot2 = dot(rABxrCB,drDB[i][j]);
fdot[2][j][i] = dot1 + dot2;
}
// force on each atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
ftmp = (fdot[0][i][j] * invs3r[0]) +
(dinvs3r[0][i][j] * dotCBDBAB);
dchi[0][i][j] = ftmp / cos(chiABCD);
ftmp = (fdot[1][i][j] * invs3r[1]) +
(dinvs3r[1][i][j] * dotDBABCB);
dchi[1][i][j] = ftmp / cos(chiCBDA);
ftmp = (fdot[2][i][j] * invs3r[2]) +
(dinvs3r[2][i][j] * dotABCBDB);
dchi[2][i][j] = ftmp / cos(chiDBAC);
dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
}
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += fabcd[0][0];
f[i1].y += fabcd[0][1];
f[i1].z += fabcd[0][2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x += fabcd[1][0];
f[i2].y += fabcd[1][1];
f[i2].z += fabcd[1][2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += fabcd[2][0];
f[i3].y += fabcd[2][1];
f[i3].z += fabcd[2][2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x += fabcd[3][0];
f[i4].y += fabcd[3][1];
f[i4].z += fabcd[3][2];
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,
fabcd[0],fabcd[2],fabcd[3],
delr[0][0],delr[0][1],delr[0][2],
delr[1][0],delr[1][1],delr[1][2],
delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
delr[2][2]-delr[1][2],thr);
}
// compute angle-angle interactions
angleangle_thr<EVFLAG, EFLAG, NEWTON_BOND>(nfrom,nto,thr);
}
/* ----------------------------------------------------------------------
angle-angle interactions within improper
------------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,i3,i4,i,j,k,n,type;
double eimproper;
double delxAB,delyAB,delzAB,rABmag2,rAB;
double delxBC,delyBC,delzBC,rBCmag2,rBC;
double delxBD,delyBD,delzBD,rBDmag2,rBD;
double costhABC,thetaABC,costhABD;
double thetaABD,costhCBD,thetaCBD,dthABC,dthCBD,dthABD;
double sc1,t1,t3,r12;
double dthetadr[3][4][3],fabcd[4][3];
eimproper = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
// difference vectors
delxAB = x[i1].x - x[i2].x;
delyAB = x[i1].y - x[i2].y;
delzAB = x[i1].z - x[i2].z;
delxBC = x[i3].x - x[i2].x;
delyBC = x[i3].y - x[i2].y;
delzBC = x[i3].z - x[i2].z;
delxBD = x[i4].x - x[i2].x;
delyBD = x[i4].y - x[i2].y;
delzBD = x[i4].z - x[i2].z;
// bond lengths
rABmag2 = delxAB*delxAB + delyAB*delyAB + delzAB*delzAB;
rAB = sqrt(rABmag2);
rBCmag2 = delxBC*delxBC + delyBC*delyBC + delzBC*delzBC;
rBC = sqrt(rBCmag2);
rBDmag2 = delxBD*delxBD + delyBD*delyBD + delzBD*delzBD;
rBD = sqrt(rBDmag2);
// angle ABC, ABD, CBD
costhABC = (delxAB*delxBC + delyAB*delyBC + delzAB*delzBC) / (rAB * rBC);
if (costhABC > 1.0) costhABC = 1.0;
if (costhABC < -1.0) costhABC = -1.0;
thetaABC = acos(costhABC);
costhABD = (delxAB*delxBD + delyAB*delyBD + delzAB*delzBD) / (rAB * rBD);
if (costhABD > 1.0) costhABD = 1.0;
if (costhABD < -1.0) costhABD = -1.0;
thetaABD = acos(costhABD);
costhCBD = (delxBC*delxBD + delyBC*delyBD + delzBC*delzBD) /(rBC * rBD);
if (costhCBD > 1.0) costhCBD = 1.0;
if (costhCBD < -1.0) costhCBD = -1.0;
thetaCBD = acos(costhCBD);
dthABC = thetaABC - aa_theta0_1[type];
dthABD = thetaABD - aa_theta0_2[type];
dthCBD = thetaCBD - aa_theta0_3[type];
// energy
if (EFLAG) eimproper = aa_k2[type] * dthABC * dthABD +
aa_k1[type] * dthABC * dthCBD +
aa_k3[type] * dthABD * dthCBD;
// d(theta)/d(r) array
// angle i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
// angle ABC
sc1 = sqrt(1.0/(1.0 - costhABC*costhABC));
t1 = costhABC / rABmag2;
t3 = costhABC / rBCmag2;
r12 = 1.0 / (rAB * rBC);
dthetadr[0][0][0] = sc1 * ((t1 * delxAB) - (delxBC * r12));
dthetadr[0][0][1] = sc1 * ((t1 * delyAB) - (delyBC * r12));
dthetadr[0][0][2] = sc1 * ((t1 * delzAB) - (delzBC * r12));
dthetadr[0][1][0] = sc1 * ((-t1 * delxAB) + (delxBC * r12) +
(-t3 * delxBC) + (delxAB * r12));
dthetadr[0][1][1] = sc1 * ((-t1 * delyAB) + (delyBC * r12) +
(-t3 * delyBC) + (delyAB * r12));
dthetadr[0][1][2] = sc1 * ((-t1 * delzAB) + (delzBC * r12) +
(-t3 * delzBC) + (delzAB * r12));
dthetadr[0][2][0] = sc1 * ((t3 * delxBC) - (delxAB * r12));
dthetadr[0][2][1] = sc1 * ((t3 * delyBC) - (delyAB * r12));
dthetadr[0][2][2] = sc1 * ((t3 * delzBC) - (delzAB * r12));
// angle CBD
sc1 = sqrt(1.0/(1.0 - costhCBD*costhCBD));
t1 = costhCBD / rBCmag2;
t3 = costhCBD / rBDmag2;
r12 = 1.0 / (rBC * rBD);
dthetadr[1][2][0] = sc1 * ((t1 * delxBC) - (delxBD * r12));
dthetadr[1][2][1] = sc1 * ((t1 * delyBC) - (delyBD * r12));
dthetadr[1][2][2] = sc1 * ((t1 * delzBC) - (delzBD * r12));
dthetadr[1][1][0] = sc1 * ((-t1 * delxBC) + (delxBD * r12) +
(-t3 * delxBD) + (delxBC * r12));
dthetadr[1][1][1] = sc1 * ((-t1 * delyBC) + (delyBD * r12) +
(-t3 * delyBD) + (delyBC * r12));
dthetadr[1][1][2] = sc1 * ((-t1 * delzBC) + (delzBD * r12) +
(-t3 * delzBD) + (delzBC * r12));
dthetadr[1][3][0] = sc1 * ((t3 * delxBD) - (delxBC * r12));
dthetadr[1][3][1] = sc1 * ((t3 * delyBD) - (delyBC * r12));
dthetadr[1][3][2] = sc1 * ((t3 * delzBD) - (delzBC * r12));
// angle ABD
sc1 = sqrt(1.0/(1.0 - costhABD*costhABD));
t1 = costhABD / rABmag2;
t3 = costhABD / rBDmag2;
r12 = 1.0 / (rAB * rBD);
dthetadr[2][0][0] = sc1 * ((t1 * delxAB) - (delxBD * r12));
dthetadr[2][0][1] = sc1 * ((t1 * delyAB) - (delyBD * r12));
dthetadr[2][0][2] = sc1 * ((t1 * delzAB) - (delzBD * r12));
dthetadr[2][1][0] = sc1 * ((-t1 * delxAB) + (delxBD * r12) +
(-t3 * delxBD) + (delxAB * r12));
dthetadr[2][1][1] = sc1 * ((-t1 * delyAB) + (delyBD * r12) +
(-t3 * delyBD) + (delyAB * r12));
dthetadr[2][1][2] = sc1 * ((-t1 * delzAB) + (delzBD * r12) +
(-t3 * delzBD) + (delzAB * r12));
dthetadr[2][3][0] = sc1 * ((t3 * delxBD) - (delxAB * r12));
dthetadr[2][3][1] = sc1 * ((t3 * delyBD) - (delyAB * r12));
dthetadr[2][3][2] = sc1 * ((t3 * delzBD) - (delzAB * r12));
// angleangle forces
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = -
((aa_k1[type] *
(dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
(aa_k2[type] *
(dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
(aa_k3[type] *
(dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += fabcd[0][0];
f[i1].y += fabcd[0][1];
f[i1].z += fabcd[0][2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x += fabcd[1][0];
f[i2].y += fabcd[1][1];
f[i2].z += fabcd[1][2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += fabcd[2][0];
f[i3].y += fabcd[2][1];
f[i3].z += fabcd[2][2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x += fabcd[3][0];
f[i4].y += fabcd[3][1];
f[i4].z += fabcd[3][2];
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,
fabcd[0],fabcd[2],fabcd[3],delxAB,delyAB,delzAB,
delxBC,delyBC,delzBC,delxBD,delyBD,delzBD,thr);
}
}
c4science · Help