forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14335 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
82d5d73bba
commit
704f170053
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/* ----------------------------------------------------------------------
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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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#include <string.h>
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#include <stdlib.h>
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#include "fix_setforce_kokkos.h"
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#include "atom_kokkos.h"
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#include "update.h"
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#include "modify.h"
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#include "domain.h"
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#include "region.h"
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#include "respa.h"
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#include "input.h"
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#include "variable.h"
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#include "memory.h"
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#include "error.h"
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#include "force.h"
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#include "atom_masks.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{NONE,CONSTANT,EQUAL,ATOM};
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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FixSetForceKokkos<DeviceType>::FixSetForceKokkos(LAMMPS *lmp, int narg, char **arg) :
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FixSetForce(lmp, narg, arg)
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{
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atomKK = (AtomKokkos *) atom;
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execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
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datamask_read = EMPTY_MASK;
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datamask_modify = EMPTY_MASK;
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memory->destroy(sforce);
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memory->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce");
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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FixSetForceKokkos<DeviceType>::~FixSetForceKokkos()
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{
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if (copymode) return;
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memory->destroy_kokkos(k_sforce,sforce);
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sforce = NULL;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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void FixSetForceKokkos<DeviceType>::init()
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{
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FixSetForce::init();
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if (strstr(update->integrate_style,"respa"))
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error->all(FLERR,"Cannot (yet) use respa with Kokkos");
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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void FixSetForceKokkos<DeviceType>::post_force(int vflag)
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{
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atomKK->sync(execution_space, X_MASK | F_MASK | MASK_MASK);
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x = atomKK->k_x.view<DeviceType>();
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f = atomKK->k_f.view<DeviceType>();
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mask = atomKK->k_mask.view<DeviceType>();
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int nlocal = atom->nlocal;
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// update region if necessary
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region = NULL;
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if (iregion >= 0) {
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region = domain->regions[iregion];
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region->prematch();
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d_match = DAT::t_int_1d("setforce:d_match",nlocal);
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region->match_all_kokkos(groupbit,d_match);
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}
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// reallocate sforce array if necessary
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if (varflag == ATOM && nlocal > maxatom) {
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maxatom = atom->nmax;
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memory->destroy_kokkos(k_sforce,sforce);
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memory->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce");
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}
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foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
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double_3 foriginal_kk;
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force_flag = 0;
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if (varflag == CONSTANT) {
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copymode = 1;
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Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixSetForceConstant>(0,nlocal),*this,foriginal_kk);
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DeviceType::fence();
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copymode = 0;
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// variable force, wrap with clear/add
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} else {
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atomKK->sync(Host,ALL_MASK); // this can be removed when variable class is ported to Kokkos
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modify->clearstep_compute();
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if (xstyle == EQUAL) xvalue = input->variable->compute_equal(xvar);
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else if (xstyle == ATOM)
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input->variable->compute_atom(xvar,igroup,&sforce[0][0],3,0);
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if (ystyle == EQUAL) yvalue = input->variable->compute_equal(yvar);
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else if (ystyle == ATOM)
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input->variable->compute_atom(yvar,igroup,&sforce[0][1],3,0);
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if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar);
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else if (zstyle == ATOM)
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input->variable->compute_atom(zvar,igroup,&sforce[0][2],3,0);
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modify->addstep_compute(update->ntimestep + 1);
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if (varflag == ATOM) { // this can be removed when variable class is ported to Kokkos
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k_sforce.modify<LMPHostType>();
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k_sforce.sync<DeviceType>();
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}
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copymode = 1;
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Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixSetForceNonConstant>(0,nlocal),*this,foriginal_kk);
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DeviceType::fence();
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copymode = 0;
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}
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atomKK->modified(execution_space, F_MASK);
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foriginal[0] = foriginal_kk.d0;
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foriginal[1] = foriginal_kk.d1;
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foriginal[2] = foriginal_kk.d2;
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}
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void FixSetForceKokkos<DeviceType>::operator()(TagFixSetForceConstant, const int &i, double_3& foriginal_kk) const {
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if (mask[i] & groupbit) {
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if (region && !d_match[i]) return;
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foriginal_kk.d0 += f(i,0);
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foriginal_kk.d1 += f(i,1);
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foriginal_kk.d2 += f(i,2);
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if (xstyle) f(i,0) = xvalue;
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if (ystyle) f(i,1) = yvalue;
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if (zstyle) f(i,2) = zvalue;
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}
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}
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void FixSetForceKokkos<DeviceType>::operator()(TagFixSetForceNonConstant, const int &i, double_3& foriginal_kk) const {
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if (mask[i] & groupbit) {
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if (region && !d_match[i]) return;
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foriginal_kk.d0 += f(i,0);
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foriginal_kk.d1 += f(i,1);
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foriginal_kk.d2 += f(i,2);
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if (xstyle == ATOM) f(i,0) = d_sforce(i,0);
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else if (xstyle) f(i,0) = xvalue;
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if (ystyle == ATOM) f(i,1) = d_sforce(i,1);
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else if (ystyle) f(i,1) = yvalue;
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if (zstyle == ATOM) f(i,2) = d_sforce(i,2);
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else if (zstyle) f(i,2) = zvalue;
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}
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}
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template class FixSetForceKokkos<LMPDeviceType>;
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#ifdef KOKKOS_HAVE_CUDA
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template class FixSetForceKokkos<LMPHostType>;
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#endif
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@ -0,0 +1,100 @@
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/* -*- 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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#ifdef FIX_CLASS
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FixStyle(setforce/kk,FixSetForceKokkos<LMPDeviceType>)
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FixStyle(setforce/kk/device,FixSetForceKokkos<LMPDeviceType>)
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FixStyle(setforce/kk/host,FixSetForceKokkos<LMPHostType>)
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#else
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#ifndef LMP_FIX_SET_FORCE_KOKKOS_H
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#define LMP_FIX_SET_FORCE_KOKKOS_H
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#include "fix_setforce.h"
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#include "region.h"
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#include "kokkos_type.h"
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namespace LAMMPS_NS {
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struct s_double_3 {
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double d0, d1, d2;
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KOKKOS_INLINE_FUNCTION
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s_double_3() {
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d0 = d1 = d2 = 0.0;
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}
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KOKKOS_INLINE_FUNCTION
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s_double_3& operator+=(const s_double_3 &rhs){
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d0 += rhs.d0;
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d1 += rhs.d1;
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d2 += rhs.d2;
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return *this;
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}
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KOKKOS_INLINE_FUNCTION
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volatile s_double_3& operator+=(const volatile s_double_3 &rhs) volatile {
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d0 += rhs.d0;
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d1 += rhs.d1;
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d2 += rhs.d2;
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return *this;
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}
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};
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typedef s_double_3 double_3;
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struct TagFixSetForceConstant{};
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struct TagFixSetForceNonConstant{};
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template<class DeviceType>
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class FixSetForceKokkos : public FixSetForce {
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public:
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typedef DeviceType device_type;
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typedef double_3 value_type;
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typedef ArrayTypes<DeviceType> AT;
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FixSetForceKokkos(class LAMMPS *, int, char **);
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~FixSetForceKokkos();
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void init();
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void post_force(int);
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KOKKOS_INLINE_FUNCTION
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void operator()(TagFixSetForceConstant, const int&, double_3&) const;
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KOKKOS_INLINE_FUNCTION
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void operator()(TagFixSetForceNonConstant, const int&, double_3&) const;
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private:
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DAT::tdual_ffloat_2d k_sforce;
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DAT::t_ffloat_2d_randomread d_sforce;
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DAT::t_int_1d d_match;
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typename AT::t_x_array_randomread x;
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typename AT::t_f_array f;
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typename AT::t_int_1d_randomread mask;
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Region* region;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Cannot (yet) use respa with Kokkos
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Self-explanatory.
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*/
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@ -0,0 +1,170 @@
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/* ----------------------------------------------------------------------
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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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|
|
||||||
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include <stdlib.h>
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#include <string.h>
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#include "region_block_kokkos.h"
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#include "domain.h"
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#include "force.h"
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#include "atom_kokkos.h"
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#include "atom_masks.h"
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using namespace LAMMPS_NS;
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#define BIG 1.0e20
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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RegBlockKokkos<DeviceType>::RegBlockKokkos(LAMMPS *lmp, int narg, char **arg) : RegBlock(lmp, narg, arg)
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{
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atomKK = (AtomKokkos*) atom;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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RegBlockKokkos<DeviceType>::~RegBlockKokkos()
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{
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}
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/* ----------------------------------------------------------------------
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inside = 1 if x,y,z is inside or on surface
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inside = 0 if x,y,z is outside and not on surface
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------------------------------------------------------------------------- */
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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int RegBlockKokkos<DeviceType>::inside(double x, double y, double z) const
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{
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if (x >= xlo && x <= xhi && y >= ylo && y <= yhi && z >= zlo && z <= zhi)
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return 1;
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return 0;
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}
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template<class DeviceType>
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void RegBlockKokkos<DeviceType>::match_all_kokkos(int groupbit_in, DAT::t_int_1d d_match_in)
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{
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groupbit = groupbit_in;
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d_match = d_match_in;
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atomKK->sync(Device, X_MASK | MASK_MASK);
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x = atomKK->k_x.view<DeviceType>();
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mask = atomKK->k_mask.view<DeviceType>();
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int nlocal = atom->nlocal;
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copymode = 1;
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Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagRegBlockMatchAll>(0,nlocal),*this);
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DeviceType::fence();
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copymode = 0;
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}
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||||||
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void RegBlockKokkos<DeviceType>::operator()(TagRegBlockMatchAll, const int &i) const {
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if (mask[i] & groupbit) {
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double x_tmp = x(i,0);
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double y_tmp = x(i,1);
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double z_tmp = x(i,2);
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d_match[i] = match(x_tmp,y_tmp,z_tmp);
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}
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}
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/* ----------------------------------------------------------------------
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determine if point x,y,z is a match to region volume
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XOR computes 0 if 2 args are the same, 1 if different
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note that inside() returns 1 for points on surface of region
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thus point on surface of exterior region will not match
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if region has variable shape, invoke shape_update() once per timestep
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if region is dynamic, apply inverse transform to x,y,z
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unmove first, then unrotate, so don't have to change rotation point
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caller is responsible for wrapping this call with
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||||||
|
modify->clearstep_compute() and modify->addstep_compute() if needed
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
template<class DeviceType>
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
int RegBlockKokkos<DeviceType>::match(double x, double y, double z) const
|
||||||
|
{
|
||||||
|
if (dynamic) inverse_transform(x,y,z);
|
||||||
|
return !(inside(x,y,z) ^ interior);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
transform a point x,y,z in moved space back to region space
|
||||||
|
undisplace first, then unrotate (around original P)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
template<class DeviceType>
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
void RegBlockKokkos<DeviceType>::inverse_transform(double &x, double &y, double &z) const
|
||||||
|
{
|
||||||
|
if (moveflag) {
|
||||||
|
x -= dx;
|
||||||
|
y -= dy;
|
||||||
|
z -= dz;
|
||||||
|
}
|
||||||
|
if (rotateflag) rotate(x,y,z,-theta);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
rotate x,y,z by angle via right-hand rule around point and runit normal
|
||||||
|
sign of angle determines whether rotating forward/backward in time
|
||||||
|
return updated x,y,z
|
||||||
|
R = vector axis of rotation
|
||||||
|
P = point = point to rotate around
|
||||||
|
R0 = runit = unit vector for R
|
||||||
|
X0 = x,y,z = initial coord of atom
|
||||||
|
D = X0 - P = vector from P to X0
|
||||||
|
C = (D dot R0) R0 = projection of D onto R, i.e. Dparallel
|
||||||
|
A = D - C = vector from R line to X0, i.e. Dperp
|
||||||
|
B = R0 cross A = vector perp to A in plane of rotation, same len as A
|
||||||
|
A,B define plane of circular rotation around R line
|
||||||
|
new x,y,z = P + C + A cos(angle) + B sin(angle)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
template<class DeviceType>
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
void RegBlockKokkos<DeviceType>::rotate(double &x, double &y, double &z, double angle) const
|
||||||
|
{
|
||||||
|
double a[3],b[3],c[3],d[3],disp[3];
|
||||||
|
|
||||||
|
double sine = sin(angle);
|
||||||
|
double cosine = cos(angle);
|
||||||
|
d[0] = x - point[0];
|
||||||
|
d[1] = y - point[1];
|
||||||
|
d[2] = z - point[2];
|
||||||
|
double x0dotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
|
||||||
|
c[0] = x0dotr * runit[0];
|
||||||
|
c[1] = x0dotr * runit[1];
|
||||||
|
c[2] = x0dotr * runit[2];
|
||||||
|
a[0] = d[0] - c[0];
|
||||||
|
a[1] = d[1] - c[1];
|
||||||
|
a[2] = d[2] - c[2];
|
||||||
|
b[0] = runit[1]*a[2] - runit[2]*a[1];
|
||||||
|
b[1] = runit[2]*a[0] - runit[0]*a[2];
|
||||||
|
b[2] = runit[0]*a[1] - runit[1]*a[0];
|
||||||
|
disp[0] = a[0]*cosine + b[0]*sine;
|
||||||
|
disp[1] = a[1]*cosine + b[1]*sine;
|
||||||
|
disp[2] = a[2]*cosine + b[2]*sine;
|
||||||
|
x = point[0] + c[0] + disp[0];
|
||||||
|
y = point[1] + c[1] + disp[1];
|
||||||
|
z = point[2] + c[2] + disp[2];
|
||||||
|
}
|
||||||
|
|
||||||
|
template class RegBlockKokkos<LMPDeviceType>;
|
||||||
|
#ifdef KOKKOS_HAVE_CUDA
|
||||||
|
template class RegBlockKokkos<LMPHostType>;
|
||||||
|
#endif
|
||||||
|
|
@ -0,0 +1,83 @@
|
||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef REGION_CLASS
|
||||||
|
|
||||||
|
RegionStyle(block/kk,RegBlockKokkos<LMPDeviceType>)
|
||||||
|
RegionStyle(block/kk/device,RegBlockKokkos<LMPDeviceType>)
|
||||||
|
RegionStyle(block/kk/host,RegBlockKokkos<LMPHostType>)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_REGION_BLOCK_KOKKOS_H
|
||||||
|
#define LMP_REGION_BLOCK_KOKKOS_H
|
||||||
|
|
||||||
|
#include "region_block.h"
|
||||||
|
#include "kokkos_type.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
struct TagRegBlockMatchAll{};
|
||||||
|
|
||||||
|
template<class DeviceType>
|
||||||
|
class RegBlockKokkos : public RegBlock {
|
||||||
|
friend class FixPour;
|
||||||
|
|
||||||
|
typedef DeviceType device_type;
|
||||||
|
typedef ArrayTypes<DeviceType> AT;
|
||||||
|
|
||||||
|
public:
|
||||||
|
RegBlockKokkos(class LAMMPS *, int, char **);
|
||||||
|
~RegBlockKokkos();
|
||||||
|
void match_all_kokkos(int, DAT::t_int_1d);
|
||||||
|
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
void operator()(TagRegBlockMatchAll, const int&) const;
|
||||||
|
|
||||||
|
private:
|
||||||
|
int groupbit;
|
||||||
|
DAT::t_int_1d d_match;
|
||||||
|
|
||||||
|
typename AT::t_x_array_randomread x;
|
||||||
|
typename AT::t_int_1d_randomread mask;
|
||||||
|
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
int inside(double, double, double) const;
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
int match(double, double, double) const;
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
void inverse_transform(double &, double &, double &) const;
|
||||||
|
KOKKOS_INLINE_FUNCTION
|
||||||
|
void rotate(double &, double &, double &, double) const;
|
||||||
|
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Cannot use region INF or EDGE when box does not exist
|
||||||
|
|
||||||
|
Regions that extend to the box boundaries can only be used after the
|
||||||
|
create_box command has been used.
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
*/
|
||||||
Loading…
Reference in New Issue