3c329d1707
removed are: - DOS/Windows text format carriage return characters (^M) - tabs replaced with spaces (tabs are evil!!) - trailing whitespace
453 lines
14 KiB
C++
453 lines
14 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: W. Michael Brown (Intel)
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <math.h>
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#include "dihedral_opls_intel.h"
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#include "atom.h"
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#include "comm.h"
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#include "memory.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "force.h"
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#include "pair.h"
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#include "update.h"
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#include "error.h"
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#include "suffix.h"
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using namespace LAMMPS_NS;
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#define PTOLERANCE (flt_t)1.05
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#define MTOLERANCE (flt_t)-1.05
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#define SMALL2 (flt_t)0.000001
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#define INVSMALL (flt_t)1000.0
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#define SMALLER2 (flt_t)0.0000000001
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#define INVSMALLER (flt_t)100000.0
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typedef struct { int a,b,c,d,t; } int5_t;
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/* ---------------------------------------------------------------------- */
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DihedralOPLSIntel::DihedralOPLSIntel(class LAMMPS *lmp)
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: DihedralOPLS(lmp)
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{
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suffix_flag |= Suffix::INTEL;
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}
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/* ---------------------------------------------------------------------- */
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void DihedralOPLSIntel::compute(int eflag, int vflag)
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{
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#ifdef _LMP_INTEL_OFFLOAD
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if (_use_base) {
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DihedralOPLS::compute(eflag, vflag);
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return;
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}
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#endif
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if (fix->precision() == FixIntel::PREC_MODE_MIXED)
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compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
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force_const_single);
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else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
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compute<double,double>(eflag, vflag, fix->get_double_buffers(),
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force_const_double);
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else
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compute<float,float>(eflag, vflag, fix->get_single_buffers(),
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force_const_single);
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}
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/* ---------------------------------------------------------------------- */
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template <class flt_t, class acc_t>
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void DihedralOPLSIntel::compute(int eflag, int vflag,
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IntelBuffers<flt_t,acc_t> *buffers,
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const ForceConst<flt_t> &fc)
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{
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if (eflag || vflag) {
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ev_setup(eflag,vflag);
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} else evflag = 0;
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if (evflag) {
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if (vflag && !eflag) {
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if (force->newton_bond)
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eval<0,1,1>(vflag, buffers, fc);
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else
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eval<0,1,0>(vflag, buffers, fc);
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} else {
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if (force->newton_bond)
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eval<1,1,1>(vflag, buffers, fc);
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else
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eval<1,1,0>(vflag, buffers, fc);
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}
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} else {
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if (force->newton_bond)
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eval<0,0,1>(vflag, buffers, fc);
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else
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eval<0,0,0>(vflag, buffers, fc);
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}
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}
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template <int EFLAG, int VFLAG, int NEWTON_BOND, class flt_t, class acc_t>
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void DihedralOPLSIntel::eval(const int vflag,
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IntelBuffers<flt_t,acc_t> *buffers,
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const ForceConst<flt_t> &fc)
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{
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const int inum = neighbor->ndihedrallist;
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if (inum == 0) return;
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ATOM_T * _noalias const x = buffers->get_x(0);
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const int nlocal = atom->nlocal;
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const int nall = nlocal + atom->nghost;
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int f_stride;
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if (NEWTON_BOND) f_stride = buffers->get_stride(nall);
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else f_stride = buffers->get_stride(nlocal);
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int tc;
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FORCE_T * _noalias f_start;
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acc_t * _noalias ev_global;
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IP_PRE_get_buffers(0, buffers, fix, tc, f_start, ev_global);
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const int nthreads = tc;
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acc_t oedihedral, ov0, ov1, ov2, ov3, ov4, ov5;
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if (EFLAG) oedihedral = (acc_t)0.0;
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if (VFLAG && vflag) {
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ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0.0;
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}
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#if defined(_OPENMP)
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#pragma omp parallel default(none) \
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shared(f_start,f_stride,fc) \
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reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5)
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#endif
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{
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int nfrom, npl, nto, tid;
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#ifdef LMP_INTEL_USE_SIMDOFF
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IP_PRE_omp_range_id(nfrom, nto, tid, inum, nthreads);
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#else
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IP_PRE_omp_stride_id(nfrom, npl, nto, tid, inum, nthreads);
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#endif
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FORCE_T * _noalias const f = f_start + (tid * f_stride);
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if (fix->need_zero(tid))
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memset(f, 0, f_stride * sizeof(FORCE_T));
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const int5_t * _noalias const dihedrallist =
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(int5_t *) neighbor->dihedrallist[0];
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#ifdef LMP_INTEL_USE_SIMDOFF
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acc_t sedihedral, sv0, sv1, sv2, sv3, sv4, sv5;
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if (EFLAG) sedihedral = (acc_t)0.0;
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if (VFLAG && vflag) {
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sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0.0;
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}
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#pragma simd reduction(+:sedihedral, sv0, sv1, sv2, sv3, sv4, sv5)
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for (int n = nfrom; n < nto; n ++) {
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#else
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for (int n = nfrom; n < nto; n += npl) {
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#endif
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const int i1 = dihedrallist[n].a;
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const int i2 = dihedrallist[n].b;
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const int i3 = dihedrallist[n].c;
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const int i4 = dihedrallist[n].d;
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const int type = dihedrallist[n].t;
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// 1st bond
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const flt_t vb1x = x[i1].x - x[i2].x;
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const flt_t vb1y = x[i1].y - x[i2].y;
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const flt_t vb1z = x[i1].z - x[i2].z;
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// 2nd bond
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const flt_t vb2xm = x[i2].x - x[i3].x;
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const flt_t vb2ym = x[i2].y - x[i3].y;
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const flt_t vb2zm = x[i2].z - x[i3].z;
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// 3rd bond
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const flt_t vb3x = x[i4].x - x[i3].x;
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const flt_t vb3y = x[i4].y - x[i3].y;
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const flt_t vb3z = x[i4].z - x[i3].z;
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// 1-4
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const flt_t delx = x[i1].x - x[i4].x;
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const flt_t dely = x[i1].y - x[i4].y;
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const flt_t delz = x[i1].z - x[i4].z;
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// c0 calculation
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// 1st and 2nd angle
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const flt_t b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
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const flt_t rb1 = (flt_t)1.0 / sqrt(b1mag2);
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const flt_t sb1 = (flt_t)1.0 / b1mag2;
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const flt_t b2mag2 = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
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const flt_t rb2 = (flt_t)1.0 / sqrt(b2mag2);
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const flt_t sb2 = (flt_t)1.0 / b2mag2;
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const flt_t b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
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const flt_t rb3 = (flt_t)1.0 / sqrt(b3mag2);
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const flt_t sb3 = (flt_t)1.0 / b3mag2;
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const flt_t c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
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flt_t ctmp = -vb1x*vb2xm - vb1y*vb2ym - vb1z*vb2zm;
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const flt_t r12c1 = rb1 * rb2;
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const flt_t c1mag = ctmp * r12c1;
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ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
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const flt_t r12c2 = rb2 * rb3;
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const flt_t c2mag = ctmp * r12c2;
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// cos and sin of 2 angles and final c
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flt_t sin2 = MAX((flt_t)1.0 - c1mag*c1mag,(flt_t)0.0);
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flt_t sc1 = (flt_t)1.0/sqrt(sin2);
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if (sin2 < SMALL2) sc1 = INVSMALL;
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sin2 = MAX((flt_t)1.0 - c2mag*c2mag,(flt_t)0.0);
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flt_t sc2 = (flt_t)1.0/sqrt(sin2);
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if (sin2 < SMALL2) sc2 = INVSMALL;
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const flt_t s1 = sc1 * sc1;
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const flt_t s2 = sc2 * sc2;
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flt_t s12 = sc1 * sc2;
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flt_t c = (c0 + c1mag*c2mag) * s12;
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const flt_t cx = vb1z*vb2ym - vb1y*vb2zm;
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const flt_t cy = vb1x*vb2zm - vb1z*vb2xm;
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const flt_t cz = vb1y*vb2xm - vb1x*vb2ym;
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const flt_t cmag = (flt_t)1.0/sqrt(cx*cx + cy*cy + cz*cz);
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const flt_t dx = (cx*vb3x + cy*vb3y + cz*vb3z)*cmag*rb3;
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// error check
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#ifndef LMP_INTEL_USE_SIMDOFF
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if (c > PTOLERANCE || c < MTOLERANCE) {
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int me = comm->me;
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if (screen) {
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char str[128];
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sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " "
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TAGINT_FORMAT " " TAGINT_FORMAT " "
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TAGINT_FORMAT " " TAGINT_FORMAT,
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me,tid,update->ntimestep,
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atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
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error->warning(FLERR,str,0);
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fprintf(screen," 1st atom: %d %g %g %g\n",
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me,x[i1].x,x[i1].y,x[i1].z);
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fprintf(screen," 2nd atom: %d %g %g %g\n",
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me,x[i2].x,x[i2].y,x[i2].z);
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fprintf(screen," 3rd atom: %d %g %g %g\n",
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me,x[i3].x,x[i3].y,x[i3].z);
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fprintf(screen," 4th atom: %d %g %g %g\n",
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me,x[i4].x,x[i4].y,x[i4].z);
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}
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}
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#endif
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if (c > (flt_t)1.0) c = (flt_t)1.0;
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if (c < (flt_t)-1.0) c = (flt_t)-1.0;
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// force & energy
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// p = sum (i=1,4) k_i * (1 + (-1)**(i+1)*cos(i*phi) )
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// pd = dp/dc
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const flt_t cossq = c * c;
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const flt_t sinsq = (flt_t)1.0 - cossq;
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flt_t siinv = (flt_t)1.0/sqrt(sinsq);
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if (sinsq < SMALLER2 ) siinv = INVSMALLER;
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if (dx < (flt_t)0.0) siinv = -siinv;
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const flt_t cos_2phi = cossq - sinsq;
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const flt_t sin_2phim = (flt_t)2.0 * c;
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const flt_t cos_3phi = (flt_t)2.0 * c * cos_2phi - c;
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const flt_t sin_3phim = (flt_t)2.0 * cos_2phi + (flt_t)1.0;
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const flt_t cos_4phi = (flt_t)2.0 * cos_2phi * cos_2phi - (flt_t)1.0;
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const flt_t sin_4phim = (flt_t)2.0 * cos_2phi * sin_2phim;
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flt_t p, pd;
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p = fc.bp[type].k1*((flt_t)1.0 + c) +
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fc.bp[type].k2*((flt_t)1.0 - cos_2phi) +
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fc.bp[type].k3*((flt_t)1.0 + cos_3phi) +
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fc.bp[type].k4*((flt_t)1.0 - cos_4phi) ;
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pd = fc.bp[type].k1 -
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(flt_t)2.0 * fc.bp[type].k2 * sin_2phim +
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(flt_t)3.0 * fc.bp[type].k3 * sin_3phim -
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(flt_t)4.0 * fc.bp[type].k4 * sin_4phim;
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flt_t edihed;
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if (EFLAG) edihed = p;
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const flt_t a = pd;
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c = c * a;
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s12 = s12 * a;
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const flt_t a11 = c*sb1*s1;
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const flt_t a22 = -sb2 * ((flt_t)2.0*c0*s12 - c*(s1+s2));
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const flt_t a33 = c*sb3*s2;
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const flt_t a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
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const flt_t a13 = -rb1*rb3*s12;
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const flt_t a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
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const flt_t sx2 = a12*vb1x - a22*vb2xm + a23*vb3x;
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const flt_t sy2 = a12*vb1y - a22*vb2ym + a23*vb3y;
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const flt_t sz2 = a12*vb1z - a22*vb2zm + a23*vb3z;
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const flt_t f1x = a11*vb1x - a12*vb2xm + a13*vb3x;
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const flt_t f1y = a11*vb1y - a12*vb2ym + a13*vb3y;
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const flt_t f1z = a11*vb1z - a12*vb2zm + a13*vb3z;
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const flt_t f2x = -sx2 - f1x;
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const flt_t f2y = -sy2 - f1y;
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const flt_t f2z = -sz2 - f1z;
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const flt_t f4x = a13*vb1x - a23*vb2xm + a33*vb3x;
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const flt_t f4y = a13*vb1y - a23*vb2ym + a33*vb3y;
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const flt_t f4z = a13*vb1z - a23*vb2zm + a33*vb3z;
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const flt_t f3x = sx2 - f4x;
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const flt_t f3y = sy2 - f4y;
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const flt_t f3z = sz2 - f4z;
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if (EFLAG || VFLAG) {
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#ifdef LMP_INTEL_USE_SIMDOFF
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IP_PRE_ev_tally_dihed(EFLAG, VFLAG, eatom, vflag, edihed, i1, i2, i3,
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i4, f1x, f1y, f1z, f3x, f3y, f3z, f4x, f4y, f4z,
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vb1x, vb1y, vb1z, -vb2xm, -vb2ym, -vb2zm, vb3x,
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vb3y, vb3z, sedihedral, f, NEWTON_BOND, nlocal,
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sv0, sv1, sv2, sv3, sv4, sv5);
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#else
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IP_PRE_ev_tally_dihed(EFLAG, VFLAG, eatom, vflag, edihed, i1, i2, i3,
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i4, f1x, f1y, f1z, f3x, f3y, f3z, f4x, f4y, f4z,
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vb1x, vb1y, vb1z, -vb2xm, -vb2ym, -vb2zm, vb3x,
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vb3y, vb3z, oedihedral, f, NEWTON_BOND, nlocal,
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ov0, ov1, ov2, ov3, ov4, ov5);
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#endif
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}
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#ifdef LMP_INTEL_USE_SIMDOFF
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#pragma simdoff
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#endif
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{
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if (NEWTON_BOND || i1 < nlocal) {
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f[i1].x += f1x;
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f[i1].y += f1y;
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f[i1].z += f1z;
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}
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if (NEWTON_BOND || i2 < nlocal) {
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f[i2].x += f2x;
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f[i2].y += f2y;
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f[i2].z += f2z;
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}
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if (NEWTON_BOND || i3 < nlocal) {
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f[i3].x += f3x;
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f[i3].y += f3y;
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f[i3].z += f3z;
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}
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if (NEWTON_BOND || i4 < nlocal) {
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f[i4].x += f4x;
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f[i4].y += f4y;
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f[i4].z += f4z;
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}
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}
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} // for n
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#ifdef LMP_INTEL_USE_SIMDOFF
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if (EFLAG) oedihedral += sedihedral;
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if (VFLAG && vflag) {
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ov0 += sv0; ov1 += sv1; ov2 += sv2;
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ov3 += sv3; ov4 += sv4; ov5 += sv5;
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}
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#endif
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} // omp parallel
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if (EFLAG) energy += oedihedral;
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if (VFLAG && vflag) {
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virial[0] += ov0; virial[1] += ov1; virial[2] += ov2;
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virial[3] += ov3; virial[4] += ov4; virial[5] += ov5;
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}
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fix->set_reduce_flag();
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}
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/* ---------------------------------------------------------------------- */
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void DihedralOPLSIntel::init_style()
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{
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DihedralOPLS::init_style();
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int ifix = modify->find_fix("package_intel");
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if (ifix < 0)
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error->all(FLERR,
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"The 'package intel' command is required for /intel styles");
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fix = static_cast<FixIntel *>(modify->fix[ifix]);
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#ifdef _LMP_INTEL_OFFLOAD
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_use_base = 0;
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if (fix->offload_balance() != 0.0) {
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_use_base = 1;
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return;
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}
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#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;
|
|
}
|