Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80929749
angle_charmm_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
Tue, Sep 3, 07:42
Size
9 KB
Mime Type
text/x-c++
Expires
Thu, Sep 5, 07:42 (1 d, 22 h)
Engine
blob
Format
Raw Data
Handle
20227731
Attached To
rLAMMPS lammps
angle_charmm_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 <math.h>
#include <stdlib.h>
#include "angle_charmm_intel.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "suffix.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL2 (flt_t)0.000001
#define INVSMALL (flt_t)1000.0
typedef struct { int a,b,c,t; } int4_t;
/* ---------------------------------------------------------------------- */
AngleCharmmIntel::AngleCharmmIntel(LAMMPS *lmp) : AngleCharmm(lmp)
{
suffix_flag |= Suffix::INTEL;
}
/* ---------------------------------------------------------------------- */
AngleCharmmIntel::~AngleCharmmIntel()
{
}
/* ---------------------------------------------------------------------- */
void AngleCharmmIntel::compute(int eflag, int vflag)
{
#ifdef _LMP_INTEL_OFFLOAD
if (_use_base) {
AngleCharmm::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 AngleCharmmIntel::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 AngleCharmmIntel::eval(const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc)
{
const int inum = neighbor->nanglelist;
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 oeangle, ov0, ov1, ov2, ov3, ov4, ov5;
if (EVFLAG) {
if (EFLAG)
oeangle = (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(+:oeangle,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 int4_t * _noalias const anglelist =
(int4_t *) neighbor->anglelist[0];
for (int n = nfrom; n < nto; n++) {
const int i1 = anglelist[n].a;
const int i2 = anglelist[n].b;
const int i3 = anglelist[n].c;
const int type = anglelist[n].t;
// 1st bond
const flt_t delx1 = x[i1].x - x[i2].x;
const flt_t dely1 = x[i1].y - x[i2].y;
const flt_t delz1 = x[i1].z - x[i2].z;
const flt_t rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
flt_t ir12 = (flt_t)1.0/sqrt(rsq1);
// 2nd bond
const flt_t delx2 = x[i3].x - x[i2].x;
const flt_t dely2 = x[i3].y - x[i2].y;
const flt_t delz2 = x[i3].z - x[i2].z;
const flt_t rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
ir12 *= (flt_t)1.0/sqrt(rsq2);
// Urey-Bradley bond
const flt_t delxUB = x[i3].x - x[i1].x;
const flt_t delyUB = x[i3].y - x[i1].y;
const flt_t delzUB = x[i3].z - x[i1].z;
const flt_t rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;
const flt_t irUB = (flt_t)1.0/sqrt(rsqUB);
// Urey-Bradley force & energy
const flt_t dr = (flt_t)1.0/irUB - fc.fc[type].r_ub;
const flt_t rk = fc.fc[type].k_ub * dr;
flt_t forceUB;
if (rsqUB > (flt_t)0.0) forceUB = (flt_t)-2.0*rk*irUB;
else forceUB = 0.0;
flt_t eangle;
if (EFLAG) eangle = rk*dr;
// angle (cos and sin)
flt_t c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c *= ir12;
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;
// harmonic force & energy
const flt_t dtheta = acos(c) - fc.fc[type].theta0;
const flt_t tk = fc.fc[type].k * dtheta;
if (EFLAG) eangle += tk*dtheta;
const flt_t a = (flt_t)-2.0 * tk * s;
const flt_t a11 = a*c / rsq1;
const flt_t a12 = -a * ir12;
const flt_t a22 = a*c / rsq2;
const flt_t f1x = a11*delx1 + a12*delx2 - delxUB*forceUB;
const flt_t f1y = a11*dely1 + a12*dely2 - delyUB*forceUB;
const flt_t f1z = a11*delz1 + a12*delz2 - delzUB*forceUB;
const flt_t f3x = a22*delx2 + a12*delx1 + delxUB*forceUB;
const flt_t f3y = a22*dely2 + a12*dely1 + delyUB*forceUB;
const flt_t f3z = a22*delz2 + a12*delz1 + delzUB*forceUB;
// apply force to each of 3 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 -= f1x + f3x;
f[i2].y -= f1y + f3y;
f[i2].z -= f1z + f3z;
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += f3x;
f[i3].y += f3y;
f[i3].z += f3z;
}
if (EVFLAG) {
IP_PRE_ev_tally_angle(EFLAG, eatom, vflag, eangle, i1, i2, i3,f1x,
f1y, f1z, f3x, f3y, f3z, delx1, dely1, delz1,
delx2, dely2, delz2, oeangle, f, NEWTON_BOND,
nlocal, ov0, ov1, ov2, ov3, ov4, ov5);
}
} // for n
} // omp parallel
if (EVFLAG) {
if (EFLAG)
energy += oeangle;
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 AngleCharmmIntel::init_style()
{
AngleCharmm::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 AngleCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
IntelBuffers<flt_t,acc_t> *buffers)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].theta0 = theta0[i];
fc.fc[i].k_ub = k_ub[i];
fc.fc[i].r_ub = r_ub[i];
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t>
void AngleCharmmIntel::ForceConst<flt_t>::set_ntypes(const int nangletypes,
Memory *memory) {
if (nangletypes != _nangletypes) {
if (_nangletypes > 0)
_memory->destroy(fc);
if (nangletypes > 0)
_memory->create(fc,nangletypes,"anglecharmmintel.fc");
}
_nangletypes = nangletypes;
_memory = memory;
}
Event Timeline
Log In to Comment