Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81316139
improper_fourier_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
Thu, Sep 5, 07:54
Size
7 KB
Mime Type
text/x-c++
Expires
Sat, Sep 7, 07:54 (1 d, 22 h)
Engine
blob
Format
Raw Data
Handle
20548857
Attached To
rLAMMPS lammps
improper_fourier_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_fourier_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
/* ---------------------------------------------------------------------- */
ImproperFourierOMP::ImproperFourierOMP(class LAMMPS *lmp)
: ImproperFourier(lmp), ThrOMP(lmp,THR_IMPROPER)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void ImproperFourierOMP::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 ImproperFourierOMP::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;
const double * const * const x = atom->x;
const int * const * const improperlist = neighbor->improperlist;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// 1st bond
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
// 2nd bond
vb2x = x[i3][0] - x[i1][0];
vb2y = x[i3][1] - x[i1][1];
vb2z = x[i3][2] - x[i1][2];
// 3rd bond
vb3x = x[i4][0] - x[i1][0];
vb3y = x[i4][1] - x[i1][1];
vb3z = x[i4][2] - x[i1][2];
add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i2,i3,i4,type,
vb1x,vb1y,vb1z,
vb2x,vb2y,vb2z,
vb3x,vb3y,vb3z,thr);
if ( all[type] ) {
add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i4,i2,i3,type,
vb3x,vb3y,vb3z,
vb1x,vb1y,vb1z,
vb2x,vb2y,vb2z,thr);
add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i3,i4,i2,type,
vb2x,vb2y,vb2z,
vb3x,vb3y,vb3z,
vb1x,vb1y,vb1z,thr);
}
}
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperFourierOMP::add1_thr(const int i1,const int i2,
const int i3,const int i4,
const int type,
const double &vb1x,
const double &vb1y,
const double &vb1z,
const double &vb2x,
const double &vb2y,
const double &vb2z,
const double &vb3x,
const double &vb3y,
const double &vb3z,
ThrData * const thr)
{
double eimproper,f1[3],f2[3],f3[3],f4[3];
double c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz;
double * const * const f = thr->get_f();
const int nlocal = atom->nlocal;
eimproper = 0.0;
// c0 calculation
// A = vb1 X vb2 is perpendicular to IJK plane
ax = vb1y*vb2z-vb1z*vb2y;
ay = vb1z*vb2x-vb1x*vb2z;
az = vb1x*vb2y-vb1y*vb2x;
ra2 = ax*ax+ay*ay+az*az;
rh2 = vb3x*vb3x+vb3y*vb3y+vb3z*vb3z;
ra = sqrt(ra2);
rh = sqrt(rh2);
if (ra < SMALL) ra = SMALL;
if (rh < SMALL) rh = SMALL;
rar = 1/ra;
rhr = 1/rh;
arx = ax*rar;
ary = ay*rar;
arz = az*rar;
hrx = vb3x*rhr;
hry = vb3y*rhr;
hrz = vb3z*rhr;
c = arx*hrx+ary*hry+arz*hrz;
// error check
if (c > 1.0 + TOLERANCE || c < (-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,atom->x[i1][0],atom->x[i1][1],atom->x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,atom->x[i2][0],atom->x[i2][1],atom->x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,atom->x[i3][0],atom->x[i3][1],atom->x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,atom->x[i4][0],atom->x[i4][1],atom->x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
cotphi = c/s;
projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
if (projhfg > 0.0) {
s *= -1.0;
cotphi *= -1.0;
}
// force and energy
// E = k ( C0 + C1 cos(w) + C2 cos(w)
c2 = 2.0*s*s-1.0;
if (EFLAG) eimproper = k[type]*(C0[type]+C1[type]*s+C2[type]*c2);
// dhax = diffrence between H and A in X direction, etc
a = k[type]*(C1[type]+4.0*C2[type]*s)*cotphi;
dhax = hrx-c*arx;
dhay = hry-c*ary;
dhaz = hrz-c*arz;
dahx = arx-c*hrx;
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
f1[2] = -(f2[2] + f3[2] + f4[2]);
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
}
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