Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79669213
improper_cossq_omp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Aug 27, 16:04
Size
7 KB
Mime Type
text/x-c++
Expires
Thu, Aug 29, 16:04 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
20218536
Attached To
rLAMMPS lammps
improper_cossq_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_cossq_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
/* ---------------------------------------------------------------------- */
ImproperCossqOMP::ImproperCossqOMP(class LAMMPS *lmp)
: ImproperCossq(lmp), ThrOMP(lmp,THR_IMPROPER)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void ImproperCossqOMP::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);
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);
}
}
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double rjisq, rji, rlksq, rlk, cosphi, angfac;
double cjiji, clkji, clklk, cfact1, cfact2, cfact3;
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;
/* separation vector between i1 and i2, (i2-i1) */
vb1x = x[i2].x - x[i1].x;
vb1y = x[i2].y - x[i1].y;
vb1z = x[i2].z - x[i1].z;
rjisq = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z ;
rji = sqrt(rjisq);
/* separation vector between i2 and i3 (i3-i2) */
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
/* separation vector between i3 and i4, (i4-i3) */
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
rlksq = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z ;
rlk = sqrt(rlksq);
cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk);
/* Check that cos(phi) is in the correct limits. */
if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE)) {
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);
}
/* Apply corrections to round-off errors. */
if (cosphi > 1.0) cosphi -= SMALL;
if (cosphi < -1.0) cosphi += SMALL;
/* Calculate the angle: */
double torangle = acos(cosphi);
cosphi = cos(torangle - chi[type]);
if (EFLAG) eimproper = 0.5 * k[type] * cosphi * cosphi;
/*
printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
printf("The cosine of the angle: %-1.16e.\n", cosphi);
printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
*/
/* Work out forces. */
angfac = - k[type] * cosphi;
cjiji = rjisq;
clklk = rlksq;
/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
/*CFACT1 = CLKLK * CJIJI
CFACT1 = SQRT(CFACT1)
CFACT1 = ANGFAC / CFACT1*/
cfact1 = angfac / sqrt(clklk * cjiji);
/*CFACT2 = CLKJI / CLKLK*/
cfact2 = clkji / clklk;
/*CFACT3 = CLKJI / CJIJI*/
cfact3 = clkji / cjiji;
/*FIX = -RXLK + CFACT3 * RXJI
FIY = -RYLK + CFACT3 * RYJI
FIZ = -RZLK + CFACT3 * RZJI*/
f1[0] = - vb3x + cfact3 * vb1x;
f1[1] = - vb3y + cfact3 * vb1y;
f1[2] = - vb3z + cfact3 * vb1z;
/*FJX = -FIX
FJY = -FIY
FJZ = -FIZ*/
f2[0] = - f1[0];
f2[1] = - f1[1];
f2[2] = - f1[2];
/*FKX = CFACT2 * RXLK - RXJI
FKY = CFACT2 * RYLK - RYJI
FKZ = CFACT2 * RZLK - RZJI*/
f3[0] = cfact2 * vb3x - vb1x;
f3[1] = cfact2 * vb3y - vb1y;
f3[2] = cfact2 * vb3z - vb1z;
/*FLX = -FKX
FLY = -FKY
FLZ = -FKZ*/
f4[0] = - f3[0];
f4[1] = - f3[1];
f4[2] = - f3[2];
/*FIX = FIX * CFACT1
FIY = FIY * CFACT1
FIZ = FIZ * CFACT1*/
f1[0] *= cfact1;
f1[1] *= cfact1;
f1[2] *= cfact1;
/*FJX = FJX * CFACT1
FJY = FJY * CFACT1
FJZ = FJZ * CFACT1*/
f2[0] *= cfact1;
f2[1] *= cfact1;
f2[2] *= cfact1;
/*FKX = FKX * CFACT1
FKY = FKY * CFACT1
FKZ = FKZ * CFACT1*/
f3[0] *= cfact1;
f3[1] *= cfact1;
f3[2] *= cfact1;
/*FLX = FLX * CFACT1
FLY = FLY * CFACT1
FLZ = FLZ * CFACT1*/
f4[0] *= cfact1;
f4[1] *= cfact1;
f4[2] *= cfact1;
/* Apply force to each of 4 atoms */
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
-vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
}
Event Timeline
Log In to Comment