Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/KOKKOS/angle_charmm_kokkos.cpp
f4dc6a4f6d33lammm-master-deprecated

Last Change
Raw File

angle_charmm_kokkos.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_charmm_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
template<class DeviceType>
AngleCharmmKokkos<DeviceType>::AngleCharmmKokkos(LAMMPS *lmp) : AngleCharmm(lmp)
{
atomKK = (AtomKokkos *) atom;
neighborKK = (NeighborKokkos *) neighbor;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
AngleCharmmKokkos<DeviceType>::~AngleCharmmKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void AngleCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
// reallocate per-atom arrays if necessary
if (eflag_atom) {
if(k_eatom.dimension_0()<maxeatom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.d_view;
}
}
if (vflag_atom) {
if(k_vatom.dimension_0()<maxvatom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
d_vatom = k_vatom.d_view;
}
}
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
else atomKK->modified(execution_space,F_MASK);
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
neighborKK->k_anglelist.template sync<DeviceType>();
anglelist = neighborKK->k_anglelist.view<DeviceType>();
int nanglelist = neighborKK->nanglelist;
nlocal = atom->nlocal;
newton_bond = force->newton_bond;
copymode = 1;
// loop over neighbors of my atoms
EV_FLOAT ev;
if (evflag) {
if (newton_bond) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleCharmmCompute<1,1> >(0,nanglelist),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleCharmmCompute<0,1> >(0,nanglelist),*this,ev);
}
} else {
if (newton_bond) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleCharmmCompute<1,0> >(0,nanglelist),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleCharmmCompute<0,0> >(0,nanglelist),*this);
}
}
DeviceType::fence();
if (eflag_global) energy += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
virial[1] += ev.v[1];
virial[2] += ev.v[2];
virial[3] += ev.v[3];
virial[4] += ev.v[4];
virial[5] += ev.v[5];
}
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
copymode = 0;
}
template<class DeviceType>
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void AngleCharmmKokkos<DeviceType>::operator()(TagAngleCharmmCompute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
const int i1 = anglelist(n,0);
const int i2 = anglelist(n,1);
const int i3 = anglelist(n,2);
const int type = anglelist(n,3);
// 1st bond
const F_FLOAT delx1 = x(i1,0) - x(i2,0);
const F_FLOAT dely1 = x(i1,1) - x(i2,1);
const F_FLOAT delz1 = x(i1,2) - x(i2,2);
const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
const F_FLOAT r1 = sqrt(rsq1);
// 2nd bond
const F_FLOAT delx2 = x(i3,0) - x(i2,0);
const F_FLOAT dely2 = x(i3,1) - x(i2,1);
const F_FLOAT delz2 = x(i3,2) - x(i2,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT r2 = sqrt(rsq2);
// Urey-Bradley bond
const F_FLOAT delxUB = x(i3,0) - x(i1,0);
const F_FLOAT delyUB = x(i3,1) - x(i1,1);
const F_FLOAT delzUB = x(i3,2) - x(i1,2);
const F_FLOAT rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;
const F_FLOAT rUB = sqrt(rsqUB);
// Urey-Bradley force & energy
const F_FLOAT dr = rUB - d_r_ub[type];
const F_FLOAT rk = d_k_ub[type] * dr;
F_FLOAT forceUB = 0.0;
if (rUB > 0.0) forceUB = -2.0*rk/rUB;
E_FLOAT eangle = 0.0;
if (eflag) eangle = rk*dr;
// angle (cos and sin)
F_FLOAT c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
F_FLOAT s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// harmonic force & energy
const F_FLOAT dtheta = acos(c) - d_theta0[type];
const F_FLOAT tk = d_k[type] * dtheta;
if (eflag) eangle += tk*dtheta;
const F_FLOAT a = -2.0 * tk * s;
const F_FLOAT a11 = a*c / rsq1;
const F_FLOAT a12 = -a / (r1*r2);
const F_FLOAT a22 = a*c / rsq2;
F_FLOAT f1[3],f3[3];
f1[0] = a11*delx1 + a12*delx2 - delxUB*forceUB;
f1[1] = a11*dely1 + a12*dely2 - delyUB*forceUB;
f1[2] = a11*delz1 + a12*delz2 - delzUB*forceUB;
f3[0] = a22*delx2 + a12*delx1 + delxUB*forceUB;
f3[1] = a22*dely2 + a12*dely1 + delyUB*forceUB;
f3[2] = a22*delz2 + a12*delz1 + delzUB*forceUB;
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f(i1,0) += f1[0];
f(i1,1) += f1[1];
f(i1,2) += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f(i2,0) -= f1[0] + f3[0];
f(i2,1) -= f1[1] + f3[1];
f(i2,2) -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f(i3,0) += f3[0];
f(i3,1) += f3[1];
f(i3,2) += f3[2];
}
if (EVFLAG) ev_tally(ev,i1,i2,i3,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
}
template<class DeviceType>
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void AngleCharmmKokkos<DeviceType>::operator()(TagAngleCharmmCompute<NEWTON_BOND,EVFLAG>, const int &n) const {
EV_FLOAT ev;
this->template operator()<NEWTON_BOND,EVFLAG>(TagAngleCharmmCompute<NEWTON_BOND,EVFLAG>(), n, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void AngleCharmmKokkos<DeviceType>::allocate()
{
AngleCharmm::allocate();
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
template<class DeviceType>
void AngleCharmmKokkos<DeviceType>::coeff(int narg, char **arg)
{
AngleCharmm::coeff(narg, arg);
int n = atom->nangletypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("AngleCharmm::k",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_theta0("AngleCharmm::theta0",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_k_ub("AngleCharmm::k_ub",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_r_ub("AngleCharmm::r_ub",n+1);
d_k = k_k.d_view;
d_theta0 = k_theta0.d_view;
d_k_ub = k_k_ub.d_view;
d_r_ub = k_r_ub.d_view;
for (int i = 1; i <= n; i++) {
k_k.h_view[i] = k[i];
k_theta0.h_view[i] = theta0[i];
k_k_ub.h_view[i] = k_ub[i];
k_r_ub.h_view[i] = r_ub[i];
}
k_k.template modify<LMPHostType>();
k_theta0.template modify<LMPHostType>();
k_k_ub.template modify<LMPHostType>();
k_r_ub.template modify<LMPHostType>();
k_k.template sync<DeviceType>();
k_theta0.template sync<DeviceType>();
k_k_ub.template sync<DeviceType>();
k_r_ub.template sync<DeviceType>();
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3
------------------------------------------------------------------------- */
template<class DeviceType>
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void AngleCharmmKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const int j, const int k,
F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3,
const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1,
const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const
{
E_FLOAT eanglethird;
F_FLOAT v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) ev.evdwl += eangle;
else {
eanglethird = THIRD*eangle;
if (i < nlocal) ev.evdwl += eanglethird;
if (j < nlocal) ev.evdwl += eanglethird;
if (k < nlocal) ev.evdwl += eanglethird;
}
}
if (eflag_atom) {
eanglethird = THIRD*eangle;
if (newton_bond || i < nlocal) d_eatom[i] += eanglethird;
if (newton_bond || j < nlocal) d_eatom[j] += eanglethird;
if (newton_bond || k < nlocal) d_eatom[k] += eanglethird;
}
}
if (vflag_either) {
v[0] = delx1*f1[0] + delx2*f3[0];
v[1] = dely1*f1[1] + dely2*f3[1];
v[2] = delz1*f1[2] + delz2*f3[2];
v[3] = delx1*f1[1] + delx2*f3[1];
v[4] = delx1*f1[2] + delx2*f3[2];
v[5] = dely1*f1[2] + dely2*f3[2];
if (vflag_global) {
if (newton_bond) {
ev.v[0] += v[0];
ev.v[1] += v[1];
ev.v[2] += v[2];
ev.v[3] += v[3];
ev.v[4] += v[4];
ev.v[5] += v[5];
} else {
if (i < nlocal) {
ev.v[0] += THIRD*v[0];
ev.v[1] += THIRD*v[1];
ev.v[2] += THIRD*v[2];
ev.v[3] += THIRD*v[3];
ev.v[4] += THIRD*v[4];
ev.v[5] += THIRD*v[5];
}
if (j < nlocal) {
ev.v[0] += THIRD*v[0];
ev.v[1] += THIRD*v[1];
ev.v[2] += THIRD*v[2];
ev.v[3] += THIRD*v[3];
ev.v[4] += THIRD*v[4];
ev.v[5] += THIRD*v[5];
}
if (k < nlocal) {
ev.v[0] += THIRD*v[0];
ev.v[1] += THIRD*v[1];
ev.v[2] += THIRD*v[2];
ev.v[3] += THIRD*v[3];
ev.v[4] += THIRD*v[4];
ev.v[5] += THIRD*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
d_vatom(i,0) += THIRD*v[0];
d_vatom(i,1) += THIRD*v[1];
d_vatom(i,2) += THIRD*v[2];
d_vatom(i,3) += THIRD*v[3];
d_vatom(i,4) += THIRD*v[4];
d_vatom(i,5) += THIRD*v[5];
}
if (newton_bond || j < nlocal) {
d_vatom(j,0) += THIRD*v[0];
d_vatom(j,1) += THIRD*v[1];
d_vatom(j,2) += THIRD*v[2];
d_vatom(j,3) += THIRD*v[3];
d_vatom(j,4) += THIRD*v[4];
d_vatom(j,5) += THIRD*v[5];
}
if (newton_bond || k < nlocal) {
d_vatom(k,0) += THIRD*v[0];
d_vatom(k,1) += THIRD*v[1];
d_vatom(k,2) += THIRD*v[2];
d_vatom(k,3) += THIRD*v[3];
d_vatom(k,4) += THIRD*v[4];
d_vatom(k,5) += THIRD*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class AngleCharmmKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class AngleCharmmKokkos<LMPHostType>;
#endif
}
c4science · Help