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dihedral_charmm_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 "dihedral_charmm_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 SMALL (flt_t)0.001
typedef struct { int a,b,c,d,t; } int5_t;
/* ---------------------------------------------------------------------- */
DihedralCharmmIntel::DihedralCharmmIntel(class LAMMPS *lmp)
: DihedralCharmm(lmp)
{
suffix_flag |= Suffix::INTEL;
}
/* ---------------------------------------------------------------------- */
void DihedralCharmmIntel::compute(int eflag, int vflag)
{
#ifdef _LMP_INTEL_OFFLOAD
if (_use_base) {
DihedralCharmm::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 DihedralCharmmIntel::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;
// insure pair->ev_tally() will use 1-4 virial contribution
if (weightflag && vflag_global == 2)
force->pair->vflag_either = force->pair->vflag_global = 1;
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 DihedralCharmmIntel::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);
flt_t * _noalias const q = buffers->get_q(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;
acc_t oevdwl, oecoul, opv0, opv1, opv2, opv3, opv4, opv5;
if (EVFLAG) {
if (EFLAG)
oevdwl = oecoul = oedihedral = (acc_t)0.0;
if (vflag) {
ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0.0;
opv0 = opv1 = opv2 = opv3 = opv4 = opv5 = (acc_t)0.0;
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(f_start,f_stride,fc) \
reduction(+:oevdwl,oecoul,oedihedral,ov0,ov1,ov2,ov3,ov4,ov5, \
opv0,opv1,opv2,opv3,opv4,opv5)
#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];
const flt_t qqrd2e = force->qqrd2e;
acc_t sedihedral, sv0, sv1, sv2, sv3, sv4, sv5;
acc_t sevdwl, secoul, spv0, spv1, spv2, spv3, spv4, spv5;
if (EVFLAG) {
if (EFLAG)
sevdwl = secoul = sedihedral = (acc_t)0.0;
if (vflag) {
sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0;
spv0 = spv1 = spv2 = spv3 = spv4 = spv5 = (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;
const int itype = x[i1].w;
// 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;
const int jtype = x[i4].w;
// 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;
// c,s calculation
const flt_t ax = vb1y*vb2zm - vb1z*vb2ym;
const flt_t ay = vb1z*vb2xm - vb1x*vb2zm;
const flt_t az = vb1x*vb2ym - vb1y*vb2xm;
const flt_t bx = vb3y*vb2zm - vb3z*vb2ym;
const flt_t by = vb3z*vb2xm - vb3x*vb2zm;
const flt_t bz = vb3x*vb2ym - vb3y*vb2xm;
const flt_t rasq = ax*ax + ay*ay + az*az;
const flt_t rbsq = bx*bx + by*by + bz*bz;
const flt_t rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
const flt_t rg = sqrt(rgsq);
flt_t rginv, ra2inv, rb2inv;
rginv = ra2inv = rb2inv = (flt_t)0.0;
if (rg > 0) rginv = (flt_t)1.0/rg;
if (rasq > 0) ra2inv = (flt_t)1.0/rasq;
if (rbsq > 0) rb2inv = (flt_t)1.0/rbsq;
const flt_t rabinv = sqrt(ra2inv*rb2inv);
flt_t c = (ax*bx + ay*by + az*bz)*rabinv;
const flt_t s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
// 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;
const flt_t tcos_shift = fc.bp[type].cos_shift;
const flt_t tsin_shift = fc.bp[type].sin_shift;
const flt_t tk = fc.bp[type].k;
const int m = fc.bp[type].multiplicity;
flt_t p = (flt_t)1.0;
flt_t ddf1, df1;
ddf1 = df1 = (flt_t)0.0;
for (int i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
}
p = p*tcos_shift + df1*tsin_shift;
df1 = df1*tcos_shift - ddf1*tsin_shift;
df1 *= -m;
p += (flt_t)1.0;
if (m == 0) {
p = (flt_t)1.0 + tcos_shift;
df1 = (flt_t)0.0;
}
const flt_t fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
const flt_t hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
const flt_t fga = fg*ra2inv*rginv;
const flt_t hgb = hg*rb2inv*rginv;
const flt_t gaa = -ra2inv*rg;
const flt_t gbb = rb2inv*rg;
const flt_t dtfx = gaa*ax;
const flt_t dtfy = gaa*ay;
const flt_t dtfz = gaa*az;
const flt_t dtgx = fga*ax - hgb*bx;
const flt_t dtgy = fga*ay - hgb*by;
const flt_t dtgz = fga*az - hgb*bz;
const flt_t dthx = gbb*bx;
const flt_t dthy = gbb*by;
const flt_t dthz = gbb*bz;
const flt_t df = -tk * df1;
const flt_t sx2 = df*dtgx;
const flt_t sy2 = df*dtgy;
const flt_t sz2 = df*dtgz;
flt_t f1x = df*dtfx;
flt_t f1y = df*dtfy;
flt_t f1z = df*dtfz;
const flt_t f2x = sx2 - f1x;
const flt_t f2y = sy2 - f1y;
const flt_t f2z = sz2 - f1z;
flt_t f4x = df*dthx;
flt_t f4y = df*dthy;
flt_t f4z = df*dthz;
const flt_t f3x = -sx2 - f4x;
const flt_t f3y = -sy2 - f4y;
const flt_t f3z = -sz2 - f4z;
if (EVFLAG) {
flt_t deng;
if (EFLAG) deng = tk * p;
IP_PRE_ev_tally_dihed(EFLAG, eatom, vflag, deng, 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 || 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;
}
}
// 1-4 LJ and Coulomb interactions
// tally energy/virial in pair, using newton_bond as newton flag
const flt_t tweight = fc.weight[type];
const flt_t rsq = delx*delx + dely*dely + delz*delz;
const flt_t r2inv = (flt_t)1.0/rsq;
const flt_t r6inv = r2inv*r2inv*r2inv;
flt_t forcecoul;
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
else forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
const flt_t forcelj = r6inv * (fc.ljp[itype][jtype].lj1*r6inv -
fc.ljp[itype][jtype].lj2);
const flt_t fpair = tweight * (forcelj+forcecoul)*r2inv;
if (NEWTON_BOND || i1 < nlocal) {
f1x += delx*fpair;
f1y += dely*fpair;
f1z += delz*fpair;
}
if (NEWTON_BOND || i4 < nlocal) {
f4x -= delx*fpair;
f4y -= dely*fpair;
f4z -= delz*fpair;
}
if (EVFLAG) {
flt_t ev_pre = (flt_t)0;
if (NEWTON_BOND || i1 < nlocal)
ev_pre += (flt_t)0.5;
if (NEWTON_BOND || i4 < nlocal)
ev_pre += (flt_t)0.5;
if (EFLAG) {
flt_t ecoul, evdwl;
ecoul = tweight * forcecoul;
evdwl = tweight * r6inv * (fc.ljp[itype][jtype].lj3*r6inv -
fc.ljp[itype][jtype].lj4);
secoul += ev_pre * ecoul;
sevdwl += ev_pre * evdwl;
if (eatom) {
evdwl *= (flt_t)0.5;
evdwl += (flt_t)0.5 * ecoul;
if (NEWTON_BOND || i1 < nlocal)
f[i1].w += evdwl;
if (NEWTON_BOND || i4 < nlocal)
f[i4].w += evdwl;
}
}
if (vflag) {
spv0 += ev_pre * delx * delx * fpair;
spv1 += ev_pre * dely * dely * fpair;
spv2 += ev_pre * delz * delz * fpair;
spv3 += ev_pre * delx * dely * fpair;
spv4 += ev_pre * delx * delz * fpair;
spv5 += ev_pre * dely * delz * fpair;
}
}
// 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 || i4 < nlocal) {
f[i4].x += f4x;
f[i4].y += f4y;
f[i4].z += f4z;
}
}
} // for n
if (EVFLAG) {
if (EFLAG) {
oedihedral += sedihedral;
oecoul += secoul;
oevdwl += sevdwl;
}
if (vflag) {
ov0 += sv0; ov1 += sv1; ov2 += sv2; ov3 += sv3; ov4 += sv4; ov5 += sv5;
opv0 += spv0; opv1 += spv1; opv2 += spv2;
opv3 += spv3; opv4 += spv4; opv5 += spv5;
}
}
} // omp parallel
if (EVFLAG) {
if (EFLAG) {
energy += oedihedral;
force->pair->eng_vdwl += oevdwl;
force->pair->eng_coul += oecoul;
}
if (vflag) {
virial[0] += ov0; virial[1] += ov1; virial[2] += ov2;
virial[3] += ov3; virial[4] += ov4; virial[5] += ov5;
force->pair->virial[0] += opv0;
force->pair->virial[1] += opv1;
force->pair->virial[2] += opv2;
force->pair->virial[3] += opv3;
force->pair->virial[4] += opv4;
force->pair->virial[5] += opv5;
}
}
fix->set_reduce_flag();
}
/* ---------------------------------------------------------------------- */
void DihedralCharmmIntel::init_style()
{
DihedralCharmm::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 DihedralCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
IntelBuffers<flt_t,acc_t> *buffers)
{
const int tp1 = atom->ntypes + 1;
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(tp1,bp1,memory);
buffers->set_ntypes(tp1);
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
fc.ljp[i][j].lj1 = lj14_1[i][j];
fc.ljp[i][j].lj2 = lj14_2[i][j];
fc.ljp[i][j].lj3 = lj14_3[i][j];
fc.ljp[i][j].lj4 = lj14_4[i][j];
}
}
for (int i = 0; i < bp1; i++) {
fc.bp[i].multiplicity = multiplicity[i];
fc.bp[i].cos_shift = cos_shift[i];
fc.bp[i].sin_shift = sin_shift[i];
fc.bp[i].k = k[i];
fc.weight[i] = weight[i];
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t>
void DihedralCharmmIntel::ForceConst<flt_t>::set_ntypes(const int npairtypes,
const int nbondtypes,
Memory *memory) {
if (npairtypes != _npairtypes) {
if (_npairtypes > 0)
_memory->destroy(ljp);
if (npairtypes > 0)
memory->create(ljp,npairtypes,npairtypes,"fc.ljp");
}
if (nbondtypes != _nbondtypes) {
if (_nbondtypes > 0) {
_memory->destroy(bp);
_memory->destroy(weight);
}
if (nbondtypes > 0) {
_memory->create(bp,nbondtypes,"dihedralcharmmintel.bp");
_memory->create(weight,nbondtypes,"dihedralcharmmintel.weight");
}
}
_npairtypes = npairtypes;
_nbondtypes = nbondtypes;
_memory = memory;
}

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