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improper_harmonic_intel.cpp
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Sun, Nov 10, 08:31

improper_harmonic_intel.cpp
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/* ----------------------------------------------------------------------
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: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "improper_harmonic_intel.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "suffix.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define PTOLERANCE (flt_t)1.05
#define MTOLERANCE (flt_t)-1.05
#define SMALL (flt_t)0.001
#define SMALL2 (flt_t)0.000001
#define INVSMALL (flt_t)1000.0
typedef struct { int a,b,c,d,t; } int5_t;
/* ---------------------------------------------------------------------- */
ImproperHarmonicIntel::ImproperHarmonicIntel(LAMMPS *lmp) :
ImproperHarmonic(lmp)
{
suffix_flag |= Suffix::INTEL;
}
/* ---------------------------------------------------------------------- */
ImproperHarmonicIntel::~ImproperHarmonicIntel()
{
}
/* ---------------------------------------------------------------------- */
void ImproperHarmonicIntel::compute(int eflag, int vflag)
{
#ifdef _LMP_INTEL_OFFLOAD
if (_use_base) {
ImproperHarmonic::compute(eflag, vflag);
return;
}
#endif
if (fix->precision() == FixIntel::PREC_MODE_MIXED)
compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
force_const_single);
else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
compute<double,double>(eflag, vflag, fix->get_double_buffers(),
force_const_double);
else
compute<float,float>(eflag, vflag, fix->get_single_buffers(),
force_const_single);
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void ImproperHarmonicIntel::compute(int eflag, int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
if (evflag) {
if (eflag) {
if (force->newton_bond)
eval<1,1,1>(vflag, buffers, fc);
else
eval<1,1,0>(vflag, buffers, fc);
} else {
if (force->newton_bond)
eval<1,0,1>(vflag, buffers, fc);
else
eval<1,0,0>(vflag, buffers, fc);
}
} else {
if (force->newton_bond)
eval<0,0,1>(vflag, buffers, fc);
else
eval<0,0,0>(vflag, buffers, fc);
}
}
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG, int NEWTON_BOND, class flt_t, class acc_t>
void ImproperHarmonicIntel::eval(const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc)
{
const int inum = neighbor->nimproperlist;
if (inum == 0) return;
ATOM_T * _noalias const x = buffers->get_x(0);
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
int f_stride;
if (NEWTON_BOND) f_stride = buffers->get_stride(nall);
else f_stride = buffers->get_stride(nlocal);
int tc;
FORCE_T * _noalias f_start;
acc_t * _noalias ev_global;
IP_PRE_get_buffers(0, buffers, fix, tc, f_start, ev_global);
const int nthreads = tc;
acc_t oeimproper, ov0, ov1, ov2, ov3, ov4, ov5;
if (EVFLAG) {
if (EFLAG)
oeimproper = (acc_t)0.0;
if (vflag) {
ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0.0;
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(f_start,f_stride,fc) \
reduction(+:oeimproper,ov0,ov1,ov2,ov3,ov4,ov5)
#endif
{
int nfrom, nto, tid;
IP_PRE_omp_range_id(nfrom, nto, tid, inum, nthreads);
FORCE_T * _noalias const f = f_start + (tid * f_stride);
if (fix->need_zero(tid))
memset(f, 0, f_stride * sizeof(FORCE_T));
const int5_t * _noalias const improperlist =
(int5_t *) neighbor->improperlist[0];
for (int n = nfrom; n < nto; n++) {
const int i1 = improperlist[n].a;
const int i2 = improperlist[n].b;
const int i3 = improperlist[n].c;
const int i4 = improperlist[n].d;
const int type = improperlist[n].t;
// geometry of 4-body
const flt_t vb1x = x[i1].x - x[i2].x;
const flt_t vb1y = x[i1].y - x[i2].y;
const flt_t vb1z = x[i1].z - x[i2].z;
const flt_t vb2x = x[i3].x - x[i2].x;
const flt_t vb2y = x[i3].y - x[i2].y;
const flt_t vb2z = x[i3].z - x[i2].z;
const flt_t vb3x = x[i4].x - x[i3].x;
const flt_t vb3y = x[i4].y - x[i3].y;
const flt_t vb3z = x[i4].z - x[i3].z;
flt_t ss1 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
flt_t ss2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
flt_t ss3 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
const flt_t r1 = (flt_t)1.0 / sqrt(ss1);
const flt_t r2 = (flt_t)1.0 / sqrt(ss2);
const flt_t r3 = (flt_t)1.0 / sqrt(ss3);
ss1 = (flt_t)1.0 / ss1;
ss2 = (flt_t)1.0 / ss2;
ss3 = (flt_t)1.0 / ss3;
// sin and cos of angle
const flt_t c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
const flt_t c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
const flt_t c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
flt_t s1 = 1.0 - c1*c1;
if (s1 < SMALL) s1 = SMALL;
flt_t s2 = (flt_t)1.0 - c2*c2;
if (s2 < SMALL) s2 = SMALL;
flt_t s12 = (flt_t)1.0 / sqrt(s1*s2);
s1 = (flt_t)1.0 / s1;
s2 = (flt_t)1.0 / s2;
flt_t c = (c1*c2 + c0) * s12;
// error check
if (c > PTOLERANCE || c < MTOLERANCE) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,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);
}
}
if (c > (flt_t)1.0) c = (flt_t)1.0;
if (c < (flt_t)-1.0) c = (flt_t)-1.0;
const flt_t sd = (flt_t)1.0 - c * c;
flt_t s = (flt_t)1.0 / sqrt(sd);
if (sd < SMALL2) s = INVSMALL;
// force & energy
const flt_t domega = acos(c) - fc.fc[type].chi;
flt_t a;
a = fc.fc[type].k * domega;
flt_t eimproper;
if (EFLAG) eimproper = a*domega;
a = -a * (flt_t)2.0 * s;
c = c * a;
s12 = s12 * a;
const flt_t a11 = c*ss1*s1;
const flt_t a22 = -ss2 * ((flt_t)2.0*c0*s12 - c*(s1+s2));
const flt_t a33 = c*ss3*s2;
const flt_t a12 = -r1*r2*(c1*c*s1 + c2*s12);
const flt_t a13 = -r1*r3*s12;
const flt_t a23 = r2*r3*(c2*c*s2 + c1*s12);
const flt_t sx2 = a22*vb2x + a23*vb3x + a12*vb1x;
const flt_t sy2 = a22*vb2y + a23*vb3y + a12*vb1y;
const flt_t sz2 = a22*vb2z + a23*vb3z + a12*vb1z;
const flt_t f1x = a12*vb2x + a13*vb3x + a11*vb1x;
const flt_t f1y = a12*vb2y + a13*vb3y + a11*vb1y;
const flt_t f1z = a12*vb2z + a13*vb3z + a11*vb1z;
const flt_t f2x = -sx2 - f1x;
const flt_t f2y = -sy2 - f1y;
const flt_t f2z = -sz2 - f1z;
const flt_t f4x = a23*vb2x + a33*vb3x + a13*vb1x;
const flt_t f4y = a23*vb2y + a33*vb3y + a13*vb1y;
const flt_t f4z = a23*vb2z + a33*vb3z + a13*vb1z;
const flt_t f3x = sx2 - f4x;
const flt_t f3y = sy2 - f4y;
const flt_t f3z = sz2 - f4z;
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += f1x;
f[i1].y += f1y;
f[i1].z += f1z;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x += f2x;
f[i2].y += f2y;
f[i2].z += f2z;
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += f3x;
f[i3].y += f3y;
f[i3].z += f3z;
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x += f4x;
f[i4].y += f4y;
f[i4].z += f4z;
}
if (EVFLAG) {
IP_PRE_ev_tally_dihed(EFLAG, eatom, vflag, eimproper, i1, i2, i3, i4,
f1x, f1y, f1z, f3x, f3y, f3z, f4x, f4y, f4z,
vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y,
vb3z, oeimproper, f, NEWTON_BOND, nlocal,
ov0, ov1, ov2, ov3, ov4, ov5);
}
} // for n
} // omp parallel
if (EVFLAG) {
if (EFLAG)
energy += oeimproper;
if (vflag) {
virial[0] += ov0; virial[1] += ov1; virial[2] += ov2;
virial[3] += ov3; virial[4] += ov4; virial[5] += ov5;
}
}
fix->set_reduce_flag();
}
/* ---------------------------------------------------------------------- */
void ImproperHarmonicIntel::init()
{
ImproperHarmonic::init();
int ifix = modify->find_fix("package_intel");
if (ifix < 0)
error->all(FLERR,
"The 'package intel' command is required for /intel styles");
fix = static_cast<FixIntel *>(modify->fix[ifix]);
#ifdef _LMP_INTEL_OFFLOAD
_use_base = 0;
if (fix->offload_balance() != 0.0) {
_use_base = 1;
return;
}
#endif
fix->bond_init_check();
if (fix->precision() == FixIntel::PREC_MODE_MIXED)
pack_force_const(force_const_single, fix->get_mixed_buffers());
else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
pack_force_const(force_const_double, fix->get_double_buffers());
else
pack_force_const(force_const_single, fix->get_single_buffers());
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void ImproperHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
IntelBuffers<flt_t,acc_t> *buffers)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].chi = chi[i];
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t>
void ImproperHarmonicIntel::ForceConst<flt_t>::set_ntypes(const int nimproper,
Memory *memory) {
if (nimproper != _nimpropertypes) {
if (_nimpropertypes > 0)
_memory->destroy(fc);
if (nimproper > 0)
_memory->create(fc,nimproper,"improperharmonicintel.fc");
}
_nimpropertypes = nimproper;
_memory = memory;
}

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