Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F70059616
dihedral_opls_intel.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
Fri, Jul 5, 02:12
Size
12 KB
Mime Type
text/x-c++
Expires
Sun, Jul 7, 02:12 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
18784794
Attached To
rLAMMPS lammps
dihedral_opls_intel.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: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include "dihedral_opls_intel.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "error.h"
#include "suffix.h"
using namespace LAMMPS_NS;
#define PTOLERANCE (flt_t)1.05
#define MTOLERANCE (flt_t)-1.05
#define SMALL2 (flt_t)0.000001
#define INVSMALL (flt_t)1000.0
#define SMALLER2 (flt_t)0.0000000001
#define INVSMALLER (flt_t)100000.0
typedef struct { int a,b,c,d,t; } int5_t;
/* ---------------------------------------------------------------------- */
DihedralOPLSIntel::DihedralOPLSIntel(class LAMMPS *lmp)
: DihedralOPLS(lmp)
{
suffix_flag |= Suffix::INTEL;
}
/* ---------------------------------------------------------------------- */
void DihedralOPLSIntel::compute(int eflag, int vflag)
{
#ifdef _LMP_INTEL_OFFLOAD
if (_use_base) {
DihedralOPLS::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 DihedralOPLSIntel::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 DihedralOPLSIntel::eval(const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc)
{
const int inum = neighbor->ndihedrallist;
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 oedihedral, ov0, ov1, ov2, ov3, ov4, ov5;
if (EVFLAG) {
if (EFLAG)
oedihedral = (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(+:oedihedral,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 dihedrallist =
(int5_t *) neighbor->dihedrallist[0];
acc_t sedihedral, sv0, sv1, sv2, sv3, sv4, sv5;
if (EVFLAG) {
if (EFLAG)
sedihedral = (acc_t)0.0;
if (vflag) {
sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0;
}
}
for (int n = nfrom; n < nto; n++) {
const int i1 = dihedrallist[n].a;
const int i2 = dihedrallist[n].b;
const int i3 = dihedrallist[n].c;
const int i4 = dihedrallist[n].d;
const int type = dihedrallist[n].t;
// 1st bond
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;
// 2nd bond
const flt_t vb2xm = x[i2].x - x[i3].x;
const flt_t vb2ym = x[i2].y - x[i3].y;
const flt_t vb2zm = x[i2].z - x[i3].z;
// 3rd bond
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;
// 1-4
const flt_t delx = x[i1].x - x[i4].x;
const flt_t dely = x[i1].y - x[i4].y;
const flt_t delz = x[i1].z - x[i4].z;
// c0 calculation
// 1st and 2nd angle
const flt_t b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
const flt_t rb1 = (flt_t)1.0 / sqrt(b1mag2);
const flt_t sb1 = (flt_t)1.0 / b1mag2;
const flt_t b2mag2 = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
const flt_t rb2 = (flt_t)1.0 / sqrt(b2mag2);
const flt_t sb2 = (flt_t)1.0 / b2mag2;
const flt_t b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
const flt_t rb3 = (flt_t)1.0 / sqrt(b3mag2);
const flt_t sb3 = (flt_t)1.0 / b3mag2;
const flt_t c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
flt_t ctmp = -vb1x*vb2xm - vb1y*vb2ym - vb1z*vb2zm;
const flt_t r12c1 = rb1 * rb2;
const flt_t c1mag = ctmp * r12c1;
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
const flt_t r12c2 = rb2 * rb3;
const flt_t c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
flt_t sin2 = MAX((flt_t)1.0 - c1mag*c1mag,(flt_t)0.0);
flt_t sc1 = (flt_t)1.0/sqrt(sin2);
if (sin2 < SMALL2) sc1 = INVSMALL;
sin2 = MAX((flt_t)1.0 - c2mag*c2mag,(flt_t)0.0);
flt_t sc2 = (flt_t)1.0/sqrt(sin2);
if (sin2 < SMALL2) sc2 = INVSMALL;
const flt_t s1 = sc1 * sc1;
const flt_t s2 = sc2 * sc2;
flt_t s12 = sc1 * sc2;
flt_t c = (c0 + c1mag*c2mag) * s12;
const flt_t cx = vb1z*vb2ym - vb1y*vb2zm;
const flt_t cy = vb1x*vb2zm - vb1z*vb2xm;
const flt_t cz = vb1y*vb2xm - vb1x*vb2ym;
const flt_t cmag = (flt_t)1.0/sqrt(cx*cx + cy*cy + cz*cz);
const flt_t dx = (cx*vb3x + cy*vb3y + cz*vb3z)*cmag*rb3;
// error check
if (c > PTOLERANCE || c < MTOLERANCE) {
int me = comm->me;
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,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);
}
}
if (c > (flt_t)1.0) c = (flt_t)1.0;
if (c < (flt_t)-1.0) c = (flt_t)-1.0;
// force & energy
// p = sum (i=1,4) k_i * (1 + (-1)**(i+1)*cos(i*phi) )
// pd = dp/dc
const flt_t cossq = c * c;
const flt_t sinsq = (flt_t)1.0 - cossq;
flt_t siinv = (flt_t)1.0/sqrt(sinsq);
if (sinsq < SMALLER2 ) siinv = INVSMALLER;
if (dx < (flt_t)0.0) siinv = -siinv;
const flt_t cos_2phi = cossq - sinsq;
const flt_t sin_2phim = (flt_t)2.0 * c;
const flt_t cos_3phi = (flt_t)2.0 * c * cos_2phi - c;
const flt_t sin_3phim = (flt_t)2.0 * cos_2phi + (flt_t)1.0;
const flt_t cos_4phi = (flt_t)2.0 * cos_2phi * cos_2phi - (flt_t)1.0;
const flt_t sin_4phim = (flt_t)2.0 * cos_2phi * sin_2phim;
flt_t p, pd;
p = fc.bp[type].k1*((flt_t)1.0 + c) +
fc.bp[type].k2*((flt_t)1.0 - cos_2phi) +
fc.bp[type].k3*((flt_t)1.0 + cos_3phi) +
fc.bp[type].k4*((flt_t)1.0 - cos_4phi) ;
pd = fc.bp[type].k1 -
(flt_t)2.0 * fc.bp[type].k2 * sin_2phim +
(flt_t)3.0 * fc.bp[type].k3 * sin_3phim -
(flt_t)4.0 * fc.bp[type].k4 * sin_4phim;
flt_t edihed;
if (EFLAG) edihed = p;
const flt_t a = pd;
c = c * a;
s12 = s12 * a;
const flt_t a11 = c*sb1*s1;
const flt_t a22 = -sb2 * ((flt_t)2.0*c0*s12 - c*(s1+s2));
const flt_t a33 = c*sb3*s2;
const flt_t a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
const flt_t a13 = -rb1*rb3*s12;
const flt_t a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
const flt_t sx2 = a12*vb1x - a22*vb2xm + a23*vb3x;
const flt_t sy2 = a12*vb1y - a22*vb2ym + a23*vb3y;
const flt_t sz2 = a12*vb1z - a22*vb2zm + a23*vb3z;
const flt_t f1x = a11*vb1x - a12*vb2xm + a13*vb3x;
const flt_t f1y = a11*vb1y - a12*vb2ym + a13*vb3y;
const flt_t f1z = a11*vb1z - a12*vb2zm + a13*vb3z;
const flt_t f2x = -sx2 - f1x;
const flt_t f2y = -sy2 - f1y;
const flt_t f2z = -sz2 - f1z;
const flt_t f4x = a13*vb1x - a23*vb2xm + a33*vb3x;
const flt_t f4y = a13*vb1y - a23*vb2ym + a33*vb3y;
const flt_t f4z = a13*vb1z - a23*vb2zm + a33*vb3z;
const flt_t f3x = sx2 - f4x;
const flt_t f3y = sy2 - f4y;
const flt_t f3z = sz2 - f4z;
if (EVFLAG) {
IP_PRE_ev_tally_dihed(EFLAG, eatom, vflag, edihed, i1, i2, i3, i4, f1x,
f1y, f1z, f3x, f3y, f3z, f4x, f4y, f4z, vb1x,
vb1y, vb1z, -vb2xm, -vb2ym, -vb2zm, vb3x, vb3y,
vb3z, sedihedral, f, NEWTON_BOND, nlocal,
sv0, sv1, sv2, sv3, sv4, sv5);
}
{
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;
}
}
} // for n
if (EVFLAG) {
if (EFLAG) oedihedral += sedihedral;
if (vflag) {
ov0 += sv0; ov1 += sv1; ov2 += sv2; ov3 += sv3; ov4 += sv4; ov5 += sv5;
}
}
} // omp parallel
if (EVFLAG) {
if (EFLAG) energy += oedihedral;
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 DihedralOPLSIntel::init_style()
{
DihedralOPLS::init_style();
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 DihedralOPLSIntel::pack_force_const(ForceConst<flt_t> &fc,
IntelBuffers<flt_t,acc_t> *buffers)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
fc.bp[i].k1 = k1[i];
fc.bp[i].k2 = k2[i];
fc.bp[i].k3 = k3[i];
fc.bp[i].k4 = k4[i];
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t>
void DihedralOPLSIntel::ForceConst<flt_t>::set_ntypes(const int nbondtypes,
Memory *memory) {
if (nbondtypes != _nbondtypes) {
if (_nbondtypes > 0)
_memory->destroy(bp);
if (nbondtypes > 0)
_memory->create(bp,nbondtypes,"dihedralcharmmintel.bp");
}
_nbondtypes = nbondtypes;
_memory = memory;
}
Event Timeline
Log In to Comment