Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F64184582
dihedral_helix_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
Sat, May 25, 03:57
Size
7 KB
Mime Type
text/x-c++
Expires
Mon, May 27, 03:57 (2 d)
Engine
blob
Format
Raw Data
Handle
17840337
Attached To
rLAMMPS lammps
dihedral_helix_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 "dihedral_helix_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "error.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
DihedralHelixOMP::DihedralHelixOMP(class LAMMPS *lmp)
: DihedralHelix(lmp), ThrOMP(lmp,THR_DIHEDRAL)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void DihedralHelixOMP::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->ndihedrallist;
#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 (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 DihedralHelixOMP::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,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
double c2mag,sc1,sc2,s1,s12,c,pd,a,a11,a22;
double a33,a12,a13,a23,sx2,sy2,sz2;
double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
r12c1 = 1.0 / (b1mag*b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
r12c2 = 1.0 / (b2mag*b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - c1mag*c1mag,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - c2mag*c2mag,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag*c2mag) * s12;
cx = vb1y*vb2z - vb1z*vb2y;
cy = vb1z*vb2x - vb1x*vb2z;
cz = vb1x*vb2y - vb1y*vb2x;
cmag = sqrt(cx*cx + cy*cy + cz*cz);
dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me = comm->me;
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
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][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
phi = acos(c);
if (dx < 0.0) phi *= -1.0;
si = sin(phi);
if (fabs(si) < SMALLER) si = SMALLER;
siinv = 1.0/si;
pd = -aphi[type] + 3.0*bphi[type]*sin(3.0*phi)*siinv +
cphi[type]*sin(phi + MY_PI4)*siinv;
if (EFLAG) edihedral = aphi[type]*(1.0 - c) + bphi[type]*(1.0 + cos(3.0*phi)) +
cphi[type]*(1.0 + cos(phi + MY_PI4));
a = pd;
c = c * a;
s12 = s12 * a;
a11 = c*sb1*s1;
a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
a33 = c*sb3*s2;
a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
a13 = -rb1*rb3*s12;
a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
f3[0] = sx2 - f4[0];
f3[1] = sy2 - f4[1];
f3[2] = sz2 - f4[2];
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
Event Timeline
Log In to Comment