419 lines
12 KiB
C++
419 lines
12 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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: Stan Moore (SNL)
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------------------------------------------------------------------------- */
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#include "angle_harmonic_kokkos.h"
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#include "atom_kokkos.h"
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#include "atom_masks.h"
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#include "comm.h"
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#include "force.h"
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#include "math_const.h"
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#include "memory_kokkos.h"
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#include "neighbor_kokkos.h"
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#include <cmath>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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static constexpr double SMALL = 0.001;
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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AngleHarmonicKokkos<DeviceType>::AngleHarmonicKokkos(LAMMPS *lmp) : AngleHarmonic(lmp)
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{
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kokkosable = 1;
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atomKK = (AtomKokkos *) atom;
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neighborKK = (NeighborKokkos *) neighbor;
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execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
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datamask_read = X_MASK | F_MASK | ENERGY_MASK | VIRIAL_MASK;
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datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
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centroidstressflag = CENTROID_NOTAVAIL;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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AngleHarmonicKokkos<DeviceType>::~AngleHarmonicKokkos()
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{
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if (!copymode) {
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memoryKK->destroy_kokkos(k_eatom,eatom);
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memoryKK->destroy_kokkos(k_vatom,vatom);
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}
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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void AngleHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
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{
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eflag = eflag_in;
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vflag = vflag_in;
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ev_init(eflag,vflag,0);
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// reallocate per-atom arrays if necessary
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if (eflag_atom) {
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if ((int)k_eatom.extent(0) < maxeatom) {
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memoryKK->destroy_kokkos(k_eatom,eatom);
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memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
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d_eatom = k_eatom.template view<DeviceType>();
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} else Kokkos::deep_copy(d_eatom,0.0);
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}
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if (vflag_atom) {
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if ((int)k_vatom.extent(0) < maxvatom) {
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memoryKK->destroy_kokkos(k_vatom,vatom);
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memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"angle:vatom");
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d_vatom = k_vatom.template view<DeviceType>();
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} else Kokkos::deep_copy(d_vatom,0.0);
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}
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//atomKK->sync(execution_space,datamask_read);
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k_k.template sync<DeviceType>();
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k_theta0.template sync<DeviceType>();
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// if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
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// else atomKK->modified(execution_space,F_MASK);
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x = atomKK->k_x.template view<DeviceType>();
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f = atomKK->k_f.template view<DeviceType>();
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neighborKK->k_anglelist.template sync<DeviceType>();
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anglelist = neighborKK->k_anglelist.template view<DeviceType>();
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int nanglelist = neighborKK->nanglelist;
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nlocal = atom->nlocal;
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newton_bond = force->newton_bond;
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copymode = 1;
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// loop over neighbors of my atoms
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EV_FLOAT ev;
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if (evflag) {
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if (newton_bond) {
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Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<1,1> >(0,nanglelist),*this,ev);
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} else {
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Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<0,1> >(0,nanglelist),*this,ev);
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}
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} else {
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if (newton_bond) {
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Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<1,0> >(0,nanglelist),*this);
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} else {
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Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<0,0> >(0,nanglelist),*this);
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}
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}
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if (eflag_global) energy += ev.evdwl;
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if (vflag_global) {
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virial[0] += ev.v[0];
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virial[1] += ev.v[1];
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virial[2] += ev.v[2];
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virial[3] += ev.v[3];
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virial[4] += ev.v[4];
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virial[5] += ev.v[5];
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}
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if (eflag_atom) {
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k_eatom.template modify<DeviceType>();
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k_eatom.sync_host();
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}
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if (vflag_atom) {
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k_vatom.template modify<DeviceType>();
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k_vatom.sync_host();
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}
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copymode = 0;
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}
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template<class DeviceType>
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template<int NEWTON_BOND, int EVFLAG>
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KOKKOS_INLINE_FUNCTION
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void AngleHarmonicKokkos<DeviceType>::operator()(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
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// The f array is atomic
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Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > a_f = f;
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const int i1 = anglelist(n,0);
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const int i2 = anglelist(n,1);
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const int i3 = anglelist(n,2);
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const int type = anglelist(n,3);
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// 1st bond
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const F_FLOAT delx1 = x(i1,0) - x(i2,0);
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const F_FLOAT dely1 = x(i1,1) - x(i2,1);
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const F_FLOAT delz1 = x(i1,2) - x(i2,2);
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const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
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const F_FLOAT r1 = sqrt(rsq1);
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// 2nd bond
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const F_FLOAT delx2 = x(i3,0) - x(i2,0);
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const F_FLOAT dely2 = x(i3,1) - x(i2,1);
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const F_FLOAT delz2 = x(i3,2) - x(i2,2);
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const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
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const F_FLOAT r2 = sqrt(rsq2);
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// angle (cos and sin)
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F_FLOAT c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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F_FLOAT s = sqrt(1.0 - c*c);
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if (s < SMALL) s = SMALL;
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s = 1.0/s;
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// force & energy
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const F_FLOAT dtheta = acos(c) - d_theta0[type];
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const F_FLOAT tk = d_k[type] * dtheta;
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F_FLOAT eangle = 0.0;
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if (eflag) eangle = tk*dtheta;
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const F_FLOAT a = -2.0 * tk * s;
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const F_FLOAT a11 = a*c / rsq1;
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const F_FLOAT a12 = -a / (r1*r2);
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const F_FLOAT a22 = a*c / rsq2;
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F_FLOAT f1[3],f3[3];
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f1[0] = a11*delx1 + a12*delx2;
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f1[1] = a11*dely1 + a12*dely2;
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f1[2] = a11*delz1 + a12*delz2;
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f3[0] = a22*delx2 + a12*delx1;
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f3[1] = a22*dely2 + a12*dely1;
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f3[2] = a22*delz2 + a12*delz1;
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// apply force to each of 3 atoms
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if (NEWTON_BOND || i1 < nlocal) {
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a_f(i1,0) += f1[0];
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a_f(i1,1) += f1[1];
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a_f(i1,2) += f1[2];
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}
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if (NEWTON_BOND || i2 < nlocal) {
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a_f(i2,0) -= f1[0] + f3[0];
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a_f(i2,1) -= f1[1] + f3[1];
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a_f(i2,2) -= f1[2] + f3[2];
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}
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if (NEWTON_BOND || i3 < nlocal) {
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a_f(i3,0) += f3[0];
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a_f(i3,1) += f3[1];
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a_f(i3,2) += f3[2];
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}
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if (EVFLAG) ev_tally(ev,i1,i2,i3,eangle,f1,f3,
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delx1,dely1,delz1,delx2,dely2,delz2);
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}
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template<class DeviceType>
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template<int NEWTON_BOND, int EVFLAG>
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KOKKOS_INLINE_FUNCTION
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void AngleHarmonicKokkos<DeviceType>::operator()(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>, const int &n) const {
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EV_FLOAT ev;
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this->template operator()<NEWTON_BOND,EVFLAG>(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>(), n, ev);
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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void AngleHarmonicKokkos<DeviceType>::allocate()
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{
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AngleHarmonic::allocate();
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int n = atom->nangletypes;
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k_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleHarmonic::k",n+1);
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k_theta0 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleHarmonic::theta0",n+1);
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d_k = k_k.template view<DeviceType>();
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d_theta0 = k_theta0.template view<DeviceType>();
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more types
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------------------------------------------------------------------------- */
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template<class DeviceType>
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void AngleHarmonicKokkos<DeviceType>::coeff(int narg, char **arg)
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{
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AngleHarmonic::coeff(narg, arg);
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int n = atom->nangletypes;
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for (int i = 1; i <= n; i++) {
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k_k.h_view[i] = k[i];
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k_theta0.h_view[i] = theta0[i];
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}
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k_k.modify_host();
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k_theta0.modify_host();
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}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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template<class DeviceType>
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void AngleHarmonicKokkos<DeviceType>::read_restart(FILE *fp)
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{
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AngleHarmonic::read_restart(fp);
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int n = atom->nangletypes;
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for (int i = 1; i <= n; i++) {
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k_k.h_view[i] = k[i];
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k_theta0.h_view[i] = theta0[i];
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}
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k_k.modify_host();
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k_theta0.modify_host();
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}
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/* ----------------------------------------------------------------------
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tally energy and virial into global and per-atom accumulators
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virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3
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------------------------------------------------------------------------- */
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template<class DeviceType>
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//template<int NEWTON_BOND>
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KOKKOS_INLINE_FUNCTION
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void AngleHarmonicKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const int j, const int k,
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F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3,
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const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1,
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const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const
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{
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E_FLOAT eanglethird;
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F_FLOAT v[6];
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// The eatom and vatom arrays are atomic
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Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_eatom = k_eatom.template view<DeviceType>();
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Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_vatom = k_vatom.template view<DeviceType>();
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if (eflag_either) {
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if (eflag_global) {
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if (newton_bond) ev.evdwl += eangle;
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else {
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eanglethird = THIRD*eangle;
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if (i < nlocal) ev.evdwl += eanglethird;
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if (j < nlocal) ev.evdwl += eanglethird;
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if (k < nlocal) ev.evdwl += eanglethird;
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}
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}
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if (eflag_atom) {
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eanglethird = THIRD*eangle;
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if (newton_bond || i < nlocal) v_eatom[i] += eanglethird;
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if (newton_bond || j < nlocal) v_eatom[j] += eanglethird;
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if (newton_bond || k < nlocal) v_eatom[k] += eanglethird;
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}
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}
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if (vflag_either) {
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v[0] = delx1*f1[0] + delx2*f3[0];
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v[1] = dely1*f1[1] + dely2*f3[1];
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v[2] = delz1*f1[2] + delz2*f3[2];
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v[3] = delx1*f1[1] + delx2*f3[1];
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v[4] = delx1*f1[2] + delx2*f3[2];
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v[5] = dely1*f1[2] + dely2*f3[2];
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if (vflag_global) {
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if (newton_bond) {
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ev.v[0] += v[0];
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ev.v[1] += v[1];
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ev.v[2] += v[2];
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ev.v[3] += v[3];
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ev.v[4] += v[4];
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ev.v[5] += v[5];
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} else {
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if (i < nlocal) {
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ev.v[0] += THIRD*v[0];
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ev.v[1] += THIRD*v[1];
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ev.v[2] += THIRD*v[2];
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ev.v[3] += THIRD*v[3];
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ev.v[4] += THIRD*v[4];
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ev.v[5] += THIRD*v[5];
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}
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if (j < nlocal) {
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ev.v[0] += THIRD*v[0];
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ev.v[1] += THIRD*v[1];
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ev.v[2] += THIRD*v[2];
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ev.v[3] += THIRD*v[3];
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ev.v[4] += THIRD*v[4];
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ev.v[5] += THIRD*v[5];
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}
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if (k < nlocal) {
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ev.v[0] += THIRD*v[0];
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ev.v[1] += THIRD*v[1];
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ev.v[2] += THIRD*v[2];
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ev.v[3] += THIRD*v[3];
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ev.v[4] += THIRD*v[4];
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ev.v[5] += THIRD*v[5];
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}
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}
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}
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if (vflag_atom) {
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if (newton_bond || i < nlocal) {
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v_vatom(i,0) += THIRD*v[0];
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v_vatom(i,1) += THIRD*v[1];
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v_vatom(i,2) += THIRD*v[2];
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v_vatom(i,3) += THIRD*v[3];
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v_vatom(i,4) += THIRD*v[4];
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v_vatom(i,5) += THIRD*v[5];
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}
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if (newton_bond || j < nlocal) {
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v_vatom(j,0) += THIRD*v[0];
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v_vatom(j,1) += THIRD*v[1];
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v_vatom(j,2) += THIRD*v[2];
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v_vatom(j,3) += THIRD*v[3];
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v_vatom(j,4) += THIRD*v[4];
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v_vatom(j,5) += THIRD*v[5];
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}
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if (newton_bond || k < nlocal) {
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v_vatom(k,0) += THIRD*v[0];
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v_vatom(k,1) += THIRD*v[1];
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v_vatom(k,2) += THIRD*v[2];
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v_vatom(k,3) += THIRD*v[3];
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v_vatom(k,4) += THIRD*v[4];
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v_vatom(k,5) += THIRD*v[5];
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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namespace LAMMPS_NS {
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template class AngleHarmonicKokkos<LMPDeviceType>;
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#ifdef LMP_KOKKOS_GPU
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template class AngleHarmonicKokkos<LMPHostType>;
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#endif
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}
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