jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add files from Ray Shan for Kokkos version of class2 angle, bond, etc.

This commit is contained in:
Stan Moore 2017-02-15 12:29:52 -07:00
parent cb982f2f28
commit 69a8e19dc5
9 changed files with 3341 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
src/KOKKOS/Install.sh
View File

@ -35,6 +35,8 @@ touch ../memory.h
action angle_charmm_kokkos.cpp angle_charmm.cpp
action angle_charmm_kokkos.h angle_charmm.h
action angle_class2_kokkos.cpp angle_class2.cpp
action angle_class2_kokkos.h angle_class2.h
action angle_harmonic_kokkos.cpp angle_harmonic.cpp
action angle_harmonic_kokkos.h angle_harmonic.h
action atom_kokkos.cpp
@ -53,6 +55,8 @@ action atom_vec_kokkos.cpp
action atom_vec_kokkos.h
action atom_vec_molecular_kokkos.cpp atom_vec_molecular.cpp
action atom_vec_molecular_kokkos.h atom_vec_molecular.h
action bond_class2_kokkos.cpp bond_class2.cpp
action bond_class2_kokkos.h bond_class2.h
action bond_fene_kokkos.cpp bond_fene.cpp
action bond_fene_kokkos.h bond_fene.h
action bond_harmonic_kokkos.cpp bond_harmonic.cpp
@ -65,6 +69,8 @@ action compute_temp_kokkos.cpp
action compute_temp_kokkos.h
action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp
action dihedral_charmm_kokkos.h dihedral_charmm.h
action dihedral_class2_kokkos.cpp dihedral_class2.cpp
action dihedral_class2_kokkos.h dihedral_class2.h
action dihedral_opls_kokkos.cpp dihedral_opls.cpp
action dihedral_opls_kokkos.h dihedral_opls.h
action domain_kokkos.cpp
@ -97,6 +103,8 @@ action fix_wall_reflect_kokkos.cpp
action fix_wall_reflect_kokkos.h
action gridcomm_kokkos.cpp gridcomm.cpp
action gridcomm_kokkos.h gridcomm.h
action improper_class2_kokkos.cpp improper_class2.cpp
action improper_class2_kokkos.h improper_class2.h
action improper_harmonic_kokkos.cpp improper_harmonic.cpp
action improper_harmonic_kokkos.h improper_harmonic.h
action kokkos.cpp

526
src/KOKKOS/angle_class2_kokkos.cpp Normal file
View File

@ -0,0 +1,526 @@
/* ----------------------------------------------------------------------
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: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_class2_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>
AngleClass2Kokkos<DeviceType>::AngleClass2Kokkos(LAMMPS *lmp) : AngleClass2(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>
AngleClass2Kokkos<DeviceType>::~AngleClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void AngleClass2Kokkos<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) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
//atomKK->sync(execution_space,datamask_read);
//if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
//else atomKK->modified(execution_space,F_MASK);
k_theta0.template sync<DeviceType>();
k_k2.template sync<DeviceType>();
k_k3.template sync<DeviceType>();
k_k4.template sync<DeviceType>();
k_bb_k.template sync<DeviceType>();
k_bb_r1.template sync<DeviceType>();
k_bb_r2.template sync<DeviceType>();
k_ba_k1.template sync<DeviceType>();
k_ba_k2.template sync<DeviceType>();
k_ba_r1.template sync<DeviceType>();
k_ba_r2.template sync<DeviceType>();
k_setflag.template sync<DeviceType>();
k_setflag_a.template sync<DeviceType>();
k_setflag_bb.template sync<DeviceType>();
k_setflag_ba.template sync<DeviceType>();
x = atomKK->k_x.template view<DeviceType>();
f = atomKK->k_f.template view<DeviceType>();
neighborKK->k_anglelist.template sync<DeviceType>();
anglelist = neighborKK->k_anglelist.template 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, TagAngleClass2Compute<1,1> >(0,nanglelist),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleClass2Compute<0,1> >(0,nanglelist),*this,ev);
}
} else {
if (newton_bond) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleClass2Compute<1,0> >(0,nanglelist),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleClass2Compute<0,0> >(0,nanglelist),*this);
}
}
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 AngleClass2Kokkos<DeviceType>::operator()(TagAngleClass2Compute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
// The f array is atomic
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > a_f = f;
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);
// 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;
// force & energy for angle term
const F_FLOAT dtheta = acos(c) - d_theta0[type];
const F_FLOAT dtheta2 = dtheta*dtheta;
const F_FLOAT dtheta3 = dtheta2*dtheta;
const F_FLOAT dtheta4 = dtheta3*dtheta;
const F_FLOAT de_angle = 2.0*d_k2[type]*dtheta + 3.0*d_k3[type]*dtheta2 + 4.0*d_k4[type]*dtheta3;
const F_FLOAT a = -de_angle*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;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
F_FLOAT eangle = 0.0;
if (eflag) eangle = d_k2[type]*dtheta2 + d_k3[type]*dtheta3 + d_k4[type]*dtheta4;
// force & energy for bond-bond term
const F_FLOAT dr1 = r1 - d_bb_r1[type];
const F_FLOAT dr2 = r2 - d_bb_r2[type];
const F_FLOAT tk1 = d_bb_k[type] * dr1;
const F_FLOAT tk2 = d_bb_k[type] * dr2;
f1[0] -= delx1*tk2/r1;
f1[1] -= dely1*tk2/r1;
f1[2] -= delz1*tk2/r1;
f3[0] -= delx2*tk1/r2;
f3[1] -= dely2*tk1/r2;
f3[2] -= delz2*tk1/r2;
if (eflag) eangle += d_bb_k[type]*dr1*dr2;
// force & energy for bond-angle term
const F_FLOAT aa1 = s * dr1 * d_ba_k1[type];
const F_FLOAT aa2 = s * dr2 * d_ba_k2[type];
F_FLOAT aa11 = aa1 * c / rsq1;
F_FLOAT aa12 = -aa1 / (r1 * r2);
F_FLOAT aa21 = aa2 * c / rsq1;
F_FLOAT aa22 = -aa2 / (r1 * r2);
const F_FLOAT vx11 = (aa11 * delx1) + (aa12 * delx2);
const F_FLOAT vx12 = (aa21 * delx1) + (aa22 * delx2);
const F_FLOAT vy11 = (aa11 * dely1) + (aa12 * dely2);
const F_FLOAT vy12 = (aa21 * dely1) + (aa22 * dely2);
const F_FLOAT vz11 = (aa11 * delz1) + (aa12 * delz2);
const F_FLOAT vz12 = (aa21 * delz1) + (aa22 * delz2);
aa11 = aa1 * c / rsq2;
aa21 = aa2 * c / rsq2;
const F_FLOAT vx21 = (aa11 * delx2) + (aa12 * delx1);
const F_FLOAT vx22 = (aa21 * delx2) + (aa22 * delx1);
const F_FLOAT vy21 = (aa11 * dely2) + (aa12 * dely1);
const F_FLOAT vy22 = (aa21 * dely2) + (aa22 * dely1);
const F_FLOAT vz21 = (aa11 * delz2) + (aa12 * delz1);
const F_FLOAT vz22 = (aa21 * delz2) + (aa22 * delz1);
const F_FLOAT b1 = d_ba_k1[type] * dtheta / r1;
const F_FLOAT b2 = d_ba_k2[type] * dtheta / r2;
f1[0] -= vx11 + b1*delx1 + vx12;
f1[1] -= vy11 + b1*dely1 + vy12;
f1[2] -= vz11 + b1*delz1 + vz12;
f3[0] -= vx21 + b2*delx2 + vx22;
f3[1] -= vy21 + b2*dely2 + vy22;
f3[2] -= vz21 + b2*delz2 + vz22;
if (eflag) eangle += d_ba_k1[type]*dr1*dtheta + d_ba_k2[type]*dr2*dtheta;
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
a_f(i1,0) += f1[0];
a_f(i1,1) += f1[1];
a_f(i1,2) += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
a_f(i2,0) -= f1[0] + f3[0];
a_f(i2,1) -= f1[1] + f3[1];
a_f(i2,2) -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
a_f(i3,0) += f3[0];
a_f(i3,1) += f3[1];
a_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 AngleClass2Kokkos<DeviceType>::operator()(TagAngleClass2Compute<NEWTON_BOND,EVFLAG>, const int &n) const {
EV_FLOAT ev;
this->template operator()<NEWTON_BOND,EVFLAG>(TagAngleClass2Compute<NEWTON_BOND,EVFLAG>(), n, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void AngleClass2Kokkos<DeviceType>::allocate()
{
AngleClass2::allocate();
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
template<class DeviceType>
void AngleClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
{
AngleClass2::coeff(narg, arg);
int n = atom->nangletypes;
k_k2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::k2",n+1);
k_k3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::k3",n+1);
k_k4 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::k4",n+1);
k_bb_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::bb_k",n+1);
k_bb_r1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::bb_r1",n+1);
k_bb_r2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::bb_r2",n+1);
k_ba_k1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::ba_k1",n+1);
k_ba_k2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::ba_k2",n+1);
k_ba_r1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::ba_r1",n+1);
k_ba_r2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::ba_r2",n+1);
k_setflag = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag",n+1);
k_setflag_a = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_a",n+1);
k_setflag_bb = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_bb",n+1);
k_setflag_ba = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_ba",n+1);
k_theta0 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::theta0",n+1);
d_k2 = k_k2.template view<DeviceType>();
d_k3 = k_k3.template view<DeviceType>();
d_k4 = k_k4.template view<DeviceType>();
d_bb_k = k_bb_k.template view<DeviceType>();
d_bb_r1 = k_bb_r1.template view<DeviceType>();
d_bb_r2 = k_bb_r2.template view<DeviceType>();
d_ba_k1 = k_ba_k1.template view<DeviceType>();
d_ba_k2 = k_ba_k2.template view<DeviceType>();
d_ba_r1 = k_ba_r1.template view<DeviceType>();
d_ba_r2 = k_ba_r2.template view<DeviceType>();
d_ba_r2 = k_ba_r2.template view<DeviceType>();
d_setflag = k_setflag.template view<DeviceType>();
d_setflag_a = k_setflag_a.template view<DeviceType>();
d_setflag_bb = k_setflag_bb.template view<DeviceType>();
d_setflag_ba = k_setflag_ba.template view<DeviceType>();
d_theta0 = k_theta0.template view<DeviceType>();
//int n = atom->nangletypes;
for (int i = 1; i <= n; i++) {
k_k2.h_view[i] = k2[i];
k_k3.h_view[i] = k3[i];
k_k4.h_view[i] = k4[i];
k_bb_k.h_view[i] = bb_k[i];
k_bb_r1.h_view[i] = bb_r1[i];
k_bb_r2.h_view[i] = bb_r2[i];
k_ba_k1.h_view[i] = ba_k1[i];
k_ba_k2.h_view[i] = ba_k2[i];
k_ba_r1.h_view[i] = ba_r1[i];
k_ba_r2.h_view[i] = ba_r2[i];
k_setflag.h_view[i] = setflag[i];
k_setflag_a.h_view[i] = setflag_a[i];
k_setflag_bb.h_view[i] = setflag_bb[i];
k_setflag_ba.h_view[i] = setflag_ba[i];
k_theta0.h_view[i] = theta0[i];
}
k_k2.template modify<LMPHostType>();
k_k3.template modify<LMPHostType>();
k_k4.template modify<LMPHostType>();
k_bb_k.template modify<LMPHostType>();
k_bb_r1.template modify<LMPHostType>();
k_bb_r2.template modify<LMPHostType>();
k_ba_k1.template modify<LMPHostType>();
k_ba_k2.template modify<LMPHostType>();
k_ba_r1.template modify<LMPHostType>();
k_ba_r2.template modify<LMPHostType>();
k_setflag.template modify<LMPHostType>();
k_setflag_a.template modify<LMPHostType>();
k_setflag_bb.template modify<LMPHostType>();
k_setflag_ba.template modify<LMPHostType>();
k_theta0.template modify<LMPHostType>();
}
/* ----------------------------------------------------------------------
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 AngleClass2Kokkos<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];
// The eatom and vatom arrays are atomic
Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_eatom = k_eatom.template view<DeviceType>();
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_vatom = k_vatom.template view<DeviceType>();
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) v_eatom[i] += eanglethird;
if (newton_bond || j < nlocal) v_eatom[j] += eanglethird;
if (newton_bond || k < nlocal) v_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) {
v_vatom(i,0) += THIRD*v[0];
v_vatom(i,1) += THIRD*v[1];
v_vatom(i,2) += THIRD*v[2];
v_vatom(i,3) += THIRD*v[3];
v_vatom(i,4) += THIRD*v[4];
v_vatom(i,5) += THIRD*v[5];
}
if (newton_bond || j < nlocal) {
v_vatom(j,0) += THIRD*v[0];
v_vatom(j,1) += THIRD*v[1];
v_vatom(j,2) += THIRD*v[2];
v_vatom(j,3) += THIRD*v[3];
v_vatom(j,4) += THIRD*v[4];
v_vatom(j,5) += THIRD*v[5];
}
if (newton_bond || k < nlocal) {
v_vatom(k,0) += THIRD*v[0];
v_vatom(k,1) += THIRD*v[1];
v_vatom(k,2) += THIRD*v[2];
v_vatom(k,3) += THIRD*v[3];
v_vatom(k,4) += THIRD*v[4];
v_vatom(k,5) += THIRD*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class AngleClass2Kokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class AngleClass2Kokkos<LMPHostType>;
#endif
}

98
src/KOKKOS/angle_class2_kokkos.h Normal file
View File

@ -0,0 +1,98 @@
/* -*- 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 ANGLE_CLASS
AngleStyle(class2/kk,AngleClass2Kokkos<LMPDeviceType>)
AngleStyle(class2/kk/device,AngleClass2Kokkos<LMPDeviceType>)
AngleStyle(class2/kk/host,AngleClass2Kokkos<LMPHostType>)
#else
#ifndef LMP_ANGLE_CLASS2_KOKKOS_H
#define LMP_ANGLE_CLASS2_KOKKOS_H
#include "angle_class2.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
template<int NEWTON_BOND, int EVFLAG>
struct TagAngleClass2Compute{};
template<class DeviceType>
class AngleClass2Kokkos : public AngleClass2 {
public:
typedef DeviceType device_type;
typedef EV_FLOAT value_type;
AngleClass2Kokkos(class LAMMPS *);
virtual ~AngleClass2Kokkos();
virtual void compute(int, int);
virtual void coeff(int, char **);
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagAngleClass2Compute<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagAngleClass2Compute<NEWTON_BOND,EVFLAG>, const int&) const;
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void 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;
protected:
class NeighborKokkos *neighborKK;
typename ArrayTypes<DeviceType>::t_x_array_randomread x;
typename ArrayTypes<DeviceType>::t_f_array f;
typename ArrayTypes<DeviceType>::t_int_2d anglelist;
typename ArrayTypes<DeviceType>::tdual_efloat_1d k_eatom;
typename ArrayTypes<DeviceType>::tdual_virial_array k_vatom;
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
int nlocal,newton_bond;
int eflag,vflag;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_theta0;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_k2, k_k3, k_k4;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_bb_k, k_bb_r1, k_bb_r2;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_ba_k1, k_ba_k2, k_ba_r1, k_ba_r2;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_setflag, k_setflag_a, k_setflag_bb, k_setflag_ba;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_theta0;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_k2, d_k3, d_k4;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_bb_k, d_bb_r1, d_bb_r2;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_ba_k1, d_ba_k2, d_ba_r1, d_ba_r2;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_setflag, d_setflag_a, d_setflag_bb, d_setflag_ba;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

338
src/KOKKOS/bond_class2_kokkos.cpp Normal file
View File

@ -0,0 +1,338 @@
/* ----------------------------------------------------------------------
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: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_class2_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
template<class DeviceType>
BondClass2Kokkos<DeviceType>::BondClass2Kokkos(LAMMPS *lmp) : BondClass2(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>
BondClass2Kokkos<DeviceType>::~BondClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void BondClass2Kokkos<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.template view<DeviceType>();
f = atomKK->k_f.template view<DeviceType>();
neighborKK->k_bondlist.template sync<DeviceType>();
bondlist = neighborKK->k_bondlist.template view<DeviceType>();
int nbondlist = neighborKK->nbondlist;
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, TagBondClass2Compute<1,1> >(0,nbondlist),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagBondClass2Compute<0,1> >(0,nbondlist),*this,ev);
}
} else {
if (newton_bond) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagBondClass2Compute<1,0> >(0,nbondlist),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagBondClass2Compute<0,0> >(0,nbondlist),*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 BondClass2Kokkos<DeviceType>::operator()(TagBondClass2Compute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
const int i1 = bondlist(n,0);
const int i2 = bondlist(n,1);
const int type = bondlist(n,2);
const F_FLOAT delx = x(i1,0) - x(i2,0);
const F_FLOAT dely = x(i1,1) - x(i2,1);
const F_FLOAT delz = x(i1,2) - x(i2,2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
const F_FLOAT r = sqrt(rsq);
const F_FLOAT dr = r - d_r0[type];
const F_FLOAT dr2 = dr*dr;
const F_FLOAT dr3 = dr2*dr;
const F_FLOAT dr4 = dr3*dr;
// force & energy
F_FLOAT ebond, fbond, de_bond;
de_bond = 2.0*d_k2[type]*dr + 3.0*d_k3[type]*dr2 + 4.0*d_k4[type]*dr3;
if (r > 0.0) fbond = -de_bond/r;
else fbond = 0.0;
if (eflag) ebond = d_k2[type]*dr2 + d_k3[type]*dr3 + d_k4[type]*dr4;
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f(i1,0) += delx*fbond;
f(i1,1) += dely*fbond;
f(i1,2) += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f(i2,0) -= delx*fbond;
f(i2,1) -= dely*fbond;
f(i2,2) -= delz*fbond;
}
if (EVFLAG) ev_tally(ev,i1,i2,ebond,fbond,delx,dely,delz);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void BondClass2Kokkos<DeviceType>::operator()(TagBondClass2Compute<NEWTON_BOND,EVFLAG>, const int &n) const {
EV_FLOAT ev;
this->template operator()<NEWTON_BOND,EVFLAG>(TagBondClass2Compute<NEWTON_BOND,EVFLAG>(), n, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void BondClass2Kokkos<DeviceType>::allocate()
{
BondClass2::allocate();
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
template<class DeviceType>
void BondClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
{
BondClass2::coeff(narg, arg);
int n = atom->nbondtypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k2("BondClass2::k2",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_k3("BondClass2::k3",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_k4("BondClass2::k4",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_r0("BondClass2::r0",n+1);
d_k2 = k_k2.template view<DeviceType>();
d_k3 = k_k3.template view<DeviceType>();
d_k4 = k_k4.template view<DeviceType>();
d_r0 = k_r0.template view<DeviceType>();
for (int i = 1; i <= n; i++) {
k_k2.h_view[i] = k2[i];
k_k3.h_view[i] = k3[i];
k_k4.h_view[i] = k4[i];
k_r0.h_view[i] = r0[i];
}
k_k2.template modify<LMPHostType>();
k_k2.template sync<DeviceType>();
k_k3.template modify<LMPHostType>();
k_k3.template sync<DeviceType>();
k_k4.template modify<LMPHostType>();
k_k4.template sync<DeviceType>();
k_r0.template modify<LMPHostType>();
k_r0.template sync<DeviceType>();
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
------------------------------------------------------------------------- */
template<class DeviceType>
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void BondClass2Kokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j,
const F_FLOAT &ebond, const F_FLOAT &fbond, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const
{
E_FLOAT ebondhalf;
F_FLOAT v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) ev.evdwl += ebond;
else {
ebondhalf = 0.5*ebond;
if (i < nlocal) ev.evdwl += ebondhalf;
if (j < nlocal) ev.evdwl += ebondhalf;
}
}
if (eflag_atom) {
ebondhalf = 0.5*ebond;
if (newton_bond || i < nlocal) d_eatom[i] += ebondhalf;
if (newton_bond || j < nlocal) d_eatom[j] += ebondhalf;
}
}
if (vflag_either) {
v[0] = delx*delx*fbond;
v[1] = dely*dely*fbond;
v[2] = delz*delz*fbond;
v[3] = delx*dely*fbond;
v[4] = delx*delz*fbond;
v[5] = dely*delz*fbond;
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] += 0.5*v[0];
ev.v[1] += 0.5*v[1];
ev.v[2] += 0.5*v[2];
ev.v[3] += 0.5*v[3];
ev.v[4] += 0.5*v[4];
ev.v[5] += 0.5*v[5];
}
if (j < nlocal) {
ev.v[0] += 0.5*v[0];
ev.v[1] += 0.5*v[1];
ev.v[2] += 0.5*v[2];
ev.v[3] += 0.5*v[3];
ev.v[4] += 0.5*v[4];
ev.v[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
d_vatom(i,0) += 0.5*v[0];
d_vatom(i,1) += 0.5*v[1];
d_vatom(i,2) += 0.5*v[2];
d_vatom(i,3) += 0.5*v[3];
d_vatom(i,4) += 0.5*v[4];
d_vatom(i,5) += 0.5*v[5];
}
if (newton_bond || j < nlocal) {
d_vatom(j,0) += 0.5*v[0];
d_vatom(j,1) += 0.5*v[1];
d_vatom(j,2) += 0.5*v[2];
d_vatom(j,3) += 0.5*v[3];
d_vatom(j,4) += 0.5*v[4];
d_vatom(j,5) += 0.5*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class BondClass2Kokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class BondClass2Kokkos<LMPHostType>;
#endif
}

89
src/KOKKOS/bond_class2_kokkos.h Normal file
View File

@ -0,0 +1,89 @@
/* -*- 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 BOND_CLASS
BondStyle(class2/kk,BondClass2Kokkos<LMPDeviceType>)
BondStyle(class2/kk/device,BondClass2Kokkos<LMPDeviceType>)
BondStyle(class2/kk/host,BondClass2Kokkos<LMPHostType>)
#else
#ifndef LMP_BOND_CLASS2_KOKKOS_H
#define LMP_BOND_CLASS2_KOKKOS_H
#include "bond_class2.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
template<int NEWTON_BOND, int EVFLAG>
struct TagBondClass2Compute{};
template<class DeviceType>
class BondClass2Kokkos : public BondClass2 {
public:
typedef DeviceType device_type;
typedef EV_FLOAT value_type;
BondClass2Kokkos(class LAMMPS *);
virtual ~BondClass2Kokkos();
virtual void compute(int, int);
virtual void coeff(int, char **);
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagBondClass2Compute<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagBondClass2Compute<NEWTON_BOND,EVFLAG>, const int&) const;
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
const F_FLOAT &ebond, const F_FLOAT &fbond, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
protected:
class NeighborKokkos *neighborKK;
typedef ArrayTypes<DeviceType> AT;
typename AT::t_x_array_randomread x;
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typename AT::t_int_2d bondlist;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
int nlocal,newton_bond;
int eflag,vflag;
typename AT::t_ffloat_1d d_k2, d_k3, d_k4;
typename AT::t_ffloat_1d d_r0;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

965
src/KOKKOS/dihedral_class2_kokkos.cpp Normal file
View File

@ -0,0 +1,965 @@
/* ----------------------------------------------------------------------
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: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "dihedral_class2_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
#include "neighbor_kokkos.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
template<class DeviceType>
DihedralClass2Kokkos<DeviceType>::DihedralClass2Kokkos(LAMMPS *lmp) : DihedralClass2(lmp)
{
atomKK = (AtomKokkos *) atom;
neighborKK = (NeighborKokkos *) neighbor;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
k_warning_flag = DAT::tdual_int_scalar("Dihedral:warning_flag");
d_warning_flag = k_warning_flag.view<DeviceType>();
h_warning_flag = k_warning_flag.h_view;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
DihedralClass2Kokkos<DeviceType>::~DihedralClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void DihedralClass2Kokkos<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) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
d_eatom = k_eatom.d_view;
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
d_vatom = k_vatom.d_view;
}
atomKK->sync(execution_space,datamask_read);
k_k1.template sync<DeviceType>();
k_k2.template sync<DeviceType>();
k_k3.template sync<DeviceType>();
k_phi1.template sync<DeviceType>();
k_phi2.template sync<DeviceType>();
k_phi3.template sync<DeviceType>();
k_mbt_f1.template sync<DeviceType>();
k_mbt_f2.template sync<DeviceType>();
k_mbt_f3.template sync<DeviceType>();
k_mbt_r0.template sync<DeviceType>();
k_ebt_f1_1.template sync<DeviceType>();
k_ebt_f2_1.template sync<DeviceType>();
k_ebt_f3_1.template sync<DeviceType>();
k_ebt_r0_1.template sync<DeviceType>();
k_ebt_f1_2.template sync<DeviceType>();
k_ebt_f2_2.template sync<DeviceType>();
k_ebt_f3_2.template sync<DeviceType>();
k_ebt_r0_2.template sync<DeviceType>();
k_at_f1_1.template sync<DeviceType>();
k_at_f2_1.template sync<DeviceType>();
k_at_f3_1.template sync<DeviceType>();
k_at_f1_2.template sync<DeviceType>();
k_at_f2_2.template sync<DeviceType>();
k_at_f3_2.template sync<DeviceType>();
k_at_theta0_1.template sync<DeviceType>();
k_at_theta0_2.template sync<DeviceType>();
k_aat_k.template sync<DeviceType>();
k_aat_theta0_1.template sync<DeviceType>();
k_aat_theta0_2.template sync<DeviceType>();
k_bb13t_k.template sync<DeviceType>();
k_bb13t_r10.template sync<DeviceType>();
k_bb13t_r30.template sync<DeviceType>();
k_setflag_d.template sync<DeviceType>();
k_setflag_mbt.template sync<DeviceType>();
k_setflag_ebt.template sync<DeviceType>();
k_setflag_at.template sync<DeviceType>();
k_setflag_aat.template sync<DeviceType>();
k_setflag_bb13t.template sync<DeviceType>();
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_dihedrallist.template sync<DeviceType>();
dihedrallist = neighborKK->k_dihedrallist.view<DeviceType>();
int ndihedrallist = neighborKK->ndihedrallist;
nlocal = atom->nlocal;
newton_bond = force->newton_bond;
h_warning_flag() = 0;
k_warning_flag.template modify<LMPHostType>();
k_warning_flag.template sync<DeviceType>();
copymode = 1;
// loop over neighbors of my atoms
EV_FLOAT ev;
if (evflag) {
if (newton_bond) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<1,1> >(0,ndihedrallist),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<0,1> >(0,ndihedrallist),*this,ev);
}
} else {
if (newton_bond) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<1,0> >(0,ndihedrallist),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<0,0> >(0,ndihedrallist),*this);
}
}
DeviceType::fence();
// error check
k_warning_flag.template modify<DeviceType>();
k_warning_flag.template sync<LMPHostType>();
if (h_warning_flag())
error->warning(FLERR,"Dihedral problem",0);
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 DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
// The f array is atomic
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > a_f = f;
const int i1 = dihedrallist(n,0);
const int i2 = dihedrallist(n,1);
const int i3 = dihedrallist(n,2);
const int i4 = dihedrallist(n,3);
const int type = dihedrallist(n,4);
// 1st bond
const F_FLOAT vb1x = x(i1,0) - x(i2,0);
const F_FLOAT vb1y = x(i1,1) - x(i2,1);
const F_FLOAT vb1z = x(i1,2) - x(i2,2);
// 2nd bond
const F_FLOAT vb2x = x(i3,0) - x(i2,0);
const F_FLOAT vb2y = x(i3,1) - x(i2,1);
const F_FLOAT vb2z = x(i3,2) - x(i2,2);
const F_FLOAT vb2xm = -vb2x;
const F_FLOAT vb2ym = -vb2y;
const F_FLOAT vb2zm = -vb2z;
// 3rd bond
const F_FLOAT vb3x = x(i4,0) - x(i3,0);
const F_FLOAT vb3y = x(i4,1) - x(i3,1);
const F_FLOAT vb3z = x(i4,2) - x(i3,2);
// distance: c0 calculation
const F_FLOAT r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
const F_FLOAT r1 = sqrt(r1mag2);
const F_FLOAT r2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
const F_FLOAT r2 = sqrt(r2mag2);
const F_FLOAT r3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
const F_FLOAT r3 = sqrt(r3mag2);
const F_FLOAT sb1 = 1.0/r1mag2;
const F_FLOAT rb1 = 1.0/r1;
const F_FLOAT sb2 = 1.0/r2mag2;
const F_FLOAT rb2 = 1.0/r2;
const F_FLOAT sb3 = 1.0/r3mag2;
const F_FLOAT rb3 = 1.0/r3;
const F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
const F_FLOAT r12c1 = rb1*rb2;
const F_FLOAT r12c2 = rb2*rb3;
const F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
const F_FLOAT costh13 = c0;
const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
// cos and sin of 2 angles and final c
F_FLOAT sin2 = MAX(1.0 - costh12*costh12,0.0);
F_FLOAT sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - costh23*costh23,0.0);
F_FLOAT sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
const F_FLOAT s1 = sc1 * sc1;
const F_FLOAT s2 = sc2 * sc2;
const F_FLOAT s12 = sc1 * sc2;
F_FLOAT c = (c0 + costh12*costh23) * s12;
// error check
if ((c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) && !d_warning_flag())
Kokkos::atomic_fetch_add(&d_warning_flag(),1);
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
const F_FLOAT cosphi = c;
F_FLOAT phi = acos(c);
F_FLOAT sinphi = sqrt(1.0 - c*c);
sinphi = MAX(sinphi,SMALL);
// n123 = vb1 x vb2
const F_FLOAT n123x = vb1y*vb2z - vb1z*vb2y;
const F_FLOAT n123y = vb1z*vb2x - vb1x*vb2z;
const F_FLOAT n123z = vb1x*vb2y - vb1y*vb2x;
const F_FLOAT n123_dot_vb3 = n123x*vb3x + n123y*vb3y + n123z*vb3z;
if (n123_dot_vb3 > 0.0) {
phi = -phi;
sinphi = -sinphi;
}
const F_FLOAT a11 = -c*sb1*s1;
const F_FLOAT a22 = sb2 * (2.0*costh13*s12 - c*(s1+s2));
const F_FLOAT a33 = -c*sb3*s2;
const F_FLOAT a12 = r12c1 * (costh12*c*s1 + costh23*s12);
const F_FLOAT a13 = rb1*rb3*s12;
const F_FLOAT a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
const F_FLOAT sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
const F_FLOAT sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
const F_FLOAT sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
const F_FLOAT sy1 = a11*vb1y + a12*vb2y + a13*vb3y;
const F_FLOAT sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
const F_FLOAT sy12 = a13*vb1y + a23*vb2y + a33*vb3y;
const F_FLOAT sz1 = a11*vb1z + a12*vb2z + a13*vb3z;
const F_FLOAT sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
const F_FLOAT sz12 = a13*vb1z + a23*vb2z + a33*vb3z;
// set up d(cos(phi))/d(r) and dphi/dr arrays
F_FLOAT dcosphidr[4][3], dphidr[4][3];
dcosphidr[0][0] = -sx1;
dcosphidr[0][1] = -sy1;
dcosphidr[0][2] = -sz1;
dcosphidr[1][0] = sx2 + sx1;
dcosphidr[1][1] = sy2 + sy1;
dcosphidr[1][2] = sz2 + sz1;
dcosphidr[2][0] = sx12 - sx2;
dcosphidr[2][1] = sy12 - sy2;
dcosphidr[2][2] = sz12 - sz2;
dcosphidr[3][0] = -sx12;
dcosphidr[3][1] = -sy12;
dcosphidr[3][2] = -sz12;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
F_FLOAT edihedral = 0.0;
const F_FLOAT dphi1 = phi - d_phi1[type];
const F_FLOAT dphi2 = 2.0*phi - d_phi2[type];
const F_FLOAT dphi3 = 3.0*phi - d_phi3[type];
if (eflag) edihedral = d_k1[type]*(1.0 - cos(dphi1)) +
d_k2[type]*(1.0 - cos(dphi2)) +
d_k3[type]*(1.0 - cos(dphi3));
const F_FLOAT de_dihedral = d_k1[type]*sin(dphi1) + 2.0*d_k2[type]*sin(dphi2) +
3.0*d_k3[type]*sin(dphi3);
// torsion forces on all 4 atoms
F_FLOAT dbonddr[3][4][3], fabcd[4][3];
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (int i = 0; i < 3; i++)
for (int j = 0; j < 4; j++)
for (int k = 0; k < 3; k++)
dbonddr[i][j][k] = 0.0;
// bond1
dbonddr[0][0][0] = vb1x / r1;
dbonddr[0][0][1] = vb1y / r1;
dbonddr[0][0][2] = vb1z / r1;
dbonddr[0][1][0] = -vb1x / r1;
dbonddr[0][1][1] = -vb1y / r1;
dbonddr[0][1][2] = -vb1z / r1;
// bond2
dbonddr[1][1][0] = vb2x / r2;
dbonddr[1][1][1] = vb2y / r2;
dbonddr[1][1][2] = vb2z / r2;
dbonddr[1][2][0] = -vb2x / r2;
dbonddr[1][2][1] = -vb2y / r2;
dbonddr[1][2][2] = -vb2z / r2;
// bond3
dbonddr[2][2][0] = vb3x / r3;
dbonddr[2][2][1] = vb3y / r3;
dbonddr[2][2][2] = vb3z / r3;
dbonddr[2][3][0] = -vb3x / r3;
dbonddr[2][3][1] = -vb3y / r3;
dbonddr[2][3][2] = -vb3z / r3;
// set up d(theta)/d(r) array
// dthetadr(i,j,k) = angle i, atom j, coordinate k
F_FLOAT dthetadr[2][4][3];
for (int i = 0; i < 2; i++)
for (int j = 0; j < 4; j++)
for (int k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
const F_FLOAT t1 = costh12 / r1mag2;
const F_FLOAT t2 = costh23 / r2mag2;
const F_FLOAT t3 = costh12 / r2mag2;
const F_FLOAT t4 = costh23 / r3mag2;
// angle12
dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
(-t3 * vb2x) + (vb1x * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
(-t3 * vb2y) + (vb1y * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
(-t3 * vb2z) + (vb1z * r12c1));
dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
// angle23
dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
(t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
(t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
(t4 * vb3z) + (vb2z * r12c2));
dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
F_FLOAT cos2phi = cos(2.0*phi);
F_FLOAT cos3phi = cos(3.0*phi);
F_FLOAT bt1 = d_mbt_f1[type] * cosphi;
F_FLOAT bt2 = d_mbt_f2[type] * cos2phi;
F_FLOAT bt3 = d_mbt_f3[type] * cos3phi;
F_FLOAT sumbte = bt1 + bt2 + bt3;
F_FLOAT db = r2 - d_mbt_r0[type];
if (eflag) edihedral += db * sumbte;
// force on bond2
bt1 = -d_mbt_f1[type] * sinphi;
bt2 = -2.0 * d_mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * d_mbt_f3[type] * sin(3.0*phi);
F_FLOAT sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
bt1 = d_ebt_f1_1[type] * cosphi;
bt2 = d_ebt_f2_1[type] * cos2phi;
bt3 = d_ebt_f3_1[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r1 - d_ebt_r0_1[type];
if (eflag) edihedral += db * (bt1+bt2+bt3);
// force on bond1
bt1 = d_ebt_f1_1[type] * sinphi;
bt2 = 2.0 * d_ebt_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * d_ebt_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
bt1 = d_ebt_f1_2[type] * cosphi;
bt2 = d_ebt_f2_2[type] * cos2phi;
bt3 = d_ebt_f3_2[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r3 - d_ebt_r0_2[type];
if (eflag) edihedral += db * (bt1+bt2+bt3);
// force on bond3
bt1 = -d_ebt_f1_2[type] * sinphi;
bt2 = -2.0 * d_ebt_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * d_ebt_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
F_FLOAT at1 = d_at_f1_1[type] * cosphi;
F_FLOAT at2 = d_at_f2_1[type] * cos2phi;
F_FLOAT at3 = d_at_f3_1[type] * cos3phi;
sumbte = at1 + at2 + at3;
F_FLOAT da = acos(costh12) - d_at_theta0_1[type];
if (eflag) edihedral += da * (at1+at2+at3);
// force on angle1
bt1 = d_at_f1_1[type] * sinphi;
bt2 = 2.0 * d_at_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * d_at_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
at1 = d_at_f1_2[type] * cosphi;
at2 = d_at_f2_2[type] * cos2phi;
at3 = d_at_f3_2[type] * cos3phi;
sumbte = at1 + at2 + at3;
da = acos(costh23) - d_at_theta0_2[type];
if (eflag) edihedral += da * (at1+at2+at3);
// force on angle2
bt1 = -d_at_f1_2[type] * sinphi;
bt2 = -2.0 * d_at_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * d_at_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
const F_FLOAT da1 = acos(costh12) - d_aat_theta0_1[type];
const F_FLOAT da2 = acos(costh23) - d_aat_theta0_2[type];
if (eflag) edihedral += d_aat_k[type]*da1*da2*cosphi;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] -= d_aat_k[type] *
(cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
if (fabs(d_bb13t_k[type]) > SMALL) {
const F_FLOAT r1_0 = d_bb13t_r10[type];
const F_FLOAT r3_0 = d_bb13t_r30[type];
const F_FLOAT dr1 = r1 - r1_0;
const F_FLOAT dr2 = r3 - r3_0;
const F_FLOAT tk1 = -d_bb13t_k[type] * dr1 / r3;
const F_FLOAT tk2 = -d_bb13t_k[type] * dr2 / r1;
if (eflag) edihedral += d_bb13t_k[type]*dr1*dr2;
fabcd[0][0] += tk2 * vb1x;
fabcd[0][1] += tk2 * vb1y;
fabcd[0][2] += tk2 * vb1z;
fabcd[1][0] -= tk2 * vb1x;
fabcd[1][1] -= tk2 * vb1y;
fabcd[1][2] -= tk2 * vb1z;
fabcd[2][0] -= tk1 * vb3x;
fabcd[2][1] -= tk1 * vb3y;
fabcd[2][2] -= tk1 * vb3z;
fabcd[3][0] += tk1 * vb3x;
fabcd[3][1] += tk1 * vb3y;
fabcd[3][2] += tk1 * vb3z;
}
F_FLOAT f1[3],f2[3],f3[3],f4[3];
for (int i = 0; i < 3; i++) {
f1[i] = fabcd[0][i];
f2[i] = fabcd[1][i];
f3[i] = fabcd[2][i];
f4[i] = fabcd[3][i];
}
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
a_f(i1,0) += f1[0];
a_f(i1,1) += f1[1];
a_f(i1,2) += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
a_f(i2,0) += f2[0];
a_f(i2,1) += f2[1];
a_f(i2,2) += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
a_f(i3,0) += f3[0];
a_f(i3,1) += f3[1];
a_f(i3,2) += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
a_f(i4,0) += f4[0];
a_f(i4,1) += f4[1];
a_f(i4,2) += f4[2];
}
if (EVFLAG)
ev_tally(ev,i1,i2,i3,i4,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>, const int &n) const {
EV_FLOAT ev;
this->template operator()<NEWTON_BOND,EVFLAG>(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>(), n, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void DihedralClass2Kokkos<DeviceType>::allocate()
{
DihedralClass2::allocate();
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
template<class DeviceType>
void DihedralClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
{
DihedralClass2::coeff(narg, arg);
int n = atom->ndihedraltypes;
k_k1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::k1",n+1);
k_k2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::k2",n+1);
k_k3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::k3",n+1);
k_phi1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::phi1",n+1);
k_phi2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::phi2",n+1);
k_phi3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::phi3",n+1);
k_mbt_f1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_f1",n+1);
k_mbt_f2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_f2",n+1);
k_mbt_f3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_f3",n+1);
k_mbt_r0 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_r0",n+1);
k_ebt_f1_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f1_1",n+1);
k_ebt_f2_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f2_1",n+1);
k_ebt_f3_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f3_1",n+1);
k_ebt_r0_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_r0_1",n+1);
k_ebt_f1_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f1_2",n+1);
k_ebt_f2_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f2_2",n+1);
k_ebt_f3_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f3_2",n+1);
k_ebt_r0_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_r0_2",n+1);
k_at_f1_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f1_1",n+1);
k_at_f2_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f2_1",n+1);
k_at_f3_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f3_1",n+1);
k_at_f1_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f1_2",n+1);
k_at_f2_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f2_2",n+1);
k_at_f3_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f3_2",n+1);
k_at_theta0_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_theta0_1",n+1);
k_at_theta0_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_theta0_2",n+1);
k_aat_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::aat_k",n+1);
k_aat_theta0_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::aat_theta0_1",n+1);
k_aat_theta0_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::aat_theta0_2",n+1);
k_bb13t_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::bb13t_k",n+1);
k_bb13t_r10 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::bb13t_r10",n+1);
k_bb13t_r30 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::bb13t_r30",n+1);
k_setflag_d = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_d",n+1);
k_setflag_mbt = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_mbt",n+1);
k_setflag_ebt = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_ebt",n+1);
k_setflag_at = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_at",n+1);
k_setflag_aat = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_aat",n+1);
k_setflag_bb13t = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_bb13t",n+1);
d_k1 = k_k1.template view<DeviceType>();
d_k2 = k_k2.template view<DeviceType>();
d_k3 = k_k3.template view<DeviceType>();
d_phi1 = k_phi1.template view<DeviceType>();
d_phi2 = k_phi2.template view<DeviceType>();
d_phi3 = k_phi3.template view<DeviceType>();
d_mbt_f1 = k_mbt_f1.template view<DeviceType>();
d_mbt_f2 = k_mbt_f2.template view<DeviceType>();
d_mbt_f3 = k_mbt_f3.template view<DeviceType>();
d_mbt_r0 = k_mbt_r0.template view<DeviceType>();
d_ebt_f1_1 = k_ebt_f1_1.template view<DeviceType>();
d_ebt_f2_1 = k_ebt_f2_1.template view<DeviceType>();
d_ebt_f3_1 = k_ebt_f3_1.template view<DeviceType>();
d_ebt_r0_1 = k_ebt_r0_1.template view<DeviceType>();
d_ebt_f1_2 = k_ebt_f1_2.template view<DeviceType>();
d_ebt_f2_2 = k_ebt_f2_2.template view<DeviceType>();
d_ebt_f3_2 = k_ebt_f3_2.template view<DeviceType>();
d_ebt_r0_2 = k_ebt_r0_2.template view<DeviceType>();
d_at_f1_1 = k_at_f1_1.template view<DeviceType>();
d_at_f2_1 = k_at_f2_1.template view<DeviceType>();
d_at_f3_1 = k_at_f3_1.template view<DeviceType>();
d_at_f1_2 = k_at_f1_2.template view<DeviceType>();
d_at_f2_2 = k_at_f2_2.template view<DeviceType>();
d_at_f3_2 = k_at_f3_2.template view<DeviceType>();
d_at_theta0_1 = k_at_theta0_1.template view<DeviceType>();
d_at_theta0_2 = k_at_theta0_2.template view<DeviceType>();
d_aat_k = k_aat_k.template view<DeviceType>();
d_aat_theta0_1 = k_aat_theta0_1.template view<DeviceType>();
d_aat_theta0_2 = k_aat_theta0_2.template view<DeviceType>();
d_bb13t_k = k_bb13t_k.template view<DeviceType>();
d_bb13t_r10 = k_bb13t_r10.template view<DeviceType>();
d_bb13t_r30 = k_bb13t_r30.template view<DeviceType>();
d_setflag_d = k_setflag_d.template view<DeviceType>();
d_setflag_mbt = k_setflag_mbt.template view<DeviceType>();
d_setflag_ebt = k_setflag_ebt.template view<DeviceType>();
d_setflag_at = k_setflag_at.template view<DeviceType>();
d_setflag_aat = k_setflag_aat.template view<DeviceType>();
d_setflag_bb13t = k_setflag_bb13t.template view<DeviceType>();
for (int i = 1; i <= n; i++) {
k_k1.h_view[i] = k1[i];
k_k2.h_view[i] = k2[i];
k_k3.h_view[i] = k3[i];
k_phi1.h_view[i] = phi1[i];
k_phi2.h_view[i] = phi2[i];
k_phi3.h_view[i] = phi3[i];
k_mbt_f1.h_view[i] = mbt_f1[i];
k_mbt_f2.h_view[i] = mbt_f2[i];
k_mbt_f3.h_view[i] = mbt_f3[i];
k_mbt_r0.h_view[i] = mbt_r0[i];
k_ebt_f1_1.h_view[i] = ebt_f1_1[i];
k_ebt_f2_1.h_view[i] = ebt_f2_1[i];
k_ebt_f3_1.h_view[i] = ebt_f3_1[i];
k_ebt_r0_1.h_view[i] = ebt_r0_1[i];
k_ebt_f1_2.h_view[i] = ebt_f1_2[i];
k_ebt_f2_2.h_view[i] = ebt_f2_2[i];
k_ebt_f3_2.h_view[i] = ebt_f3_2[i];
k_ebt_r0_2.h_view[i] = ebt_r0_2[i];
k_at_f1_1.h_view[i] = at_f1_1[i];
k_at_f2_1.h_view[i] = at_f2_1[i];
k_at_f3_1.h_view[i] = at_f3_1[i];
k_at_f1_2.h_view[i] = at_f1_2[i];
k_at_f2_2.h_view[i] = at_f2_2[i];
k_at_f3_2.h_view[i] = at_f3_2[i];
k_at_theta0_1.h_view[i] = at_theta0_1[i];
k_at_theta0_2.h_view[i] = at_theta0_2[i];
k_aat_k.h_view[i] = aat_k[i];
k_aat_theta0_1.h_view[i] = aat_theta0_1[i];
k_aat_theta0_2.h_view[i] = aat_theta0_2[i];
k_bb13t_k.h_view[i] = bb13t_k[i];
k_bb13t_r10.h_view[i] = bb13t_r10[i];
k_bb13t_r30.h_view[i] = bb13t_r30[i];
k_setflag_d.h_view[i] = setflag_d[i];
k_setflag_mbt.h_view[i] = setflag_mbt[i];
k_setflag_ebt.h_view[i] = setflag_ebt[i];
k_setflag_at.h_view[i] = setflag_at[i];
k_setflag_aat.h_view[i] = setflag_aat[i];
k_setflag_bb13t.h_view[i] = setflag_bb13t[i];
}
k_k1.template modify<LMPHostType>();
k_k2.template modify<LMPHostType>();
k_k3.template modify<LMPHostType>();
k_phi1.template modify<LMPHostType>();
k_phi2.template modify<LMPHostType>();
k_phi3.template modify<LMPHostType>();
k_mbt_f1.template modify<LMPHostType>();
k_mbt_f2.template modify<LMPHostType>();
k_mbt_f3.template modify<LMPHostType>();
k_mbt_r0.template modify<LMPHostType>();
k_ebt_f1_1.template modify<LMPHostType>();
k_ebt_f2_1.template modify<LMPHostType>();
k_ebt_f3_1.template modify<LMPHostType>();
k_ebt_r0_1.template modify<LMPHostType>();
k_ebt_f1_2.template modify<LMPHostType>();
k_ebt_f2_2.template modify<LMPHostType>();
k_ebt_f3_2.template modify<LMPHostType>();
k_ebt_r0_2.template modify<LMPHostType>();
k_at_f1_1.template modify<LMPHostType>();
k_at_f2_1.template modify<LMPHostType>();
k_at_f3_1.template modify<LMPHostType>();
k_at_f1_2.template modify<LMPHostType>();
k_at_f2_2.template modify<LMPHostType>();
k_at_f3_2.template modify<LMPHostType>();
k_at_theta0_1.template modify<LMPHostType>();
k_at_theta0_2.template modify<LMPHostType>();
k_aat_k.template modify<LMPHostType>();
k_aat_theta0_1.template modify<LMPHostType>();
k_aat_theta0_2.template modify<LMPHostType>();
k_bb13t_k.template modify<LMPHostType>();
k_bb13t_r10.template modify<LMPHostType>();
k_bb13t_r30.template modify<LMPHostType>();
k_setflag_d.template modify<LMPHostType>();
k_setflag_mbt.template modify<LMPHostType>();
k_setflag_ebt.template modify<LMPHostType>();
k_setflag_at.template modify<LMPHostType>();
k_setflag_aat.template modify<LMPHostType>();
k_setflag_bb13t.template modify<LMPHostType>();
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
= vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
template<class DeviceType>
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void DihedralClass2Kokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i1, const int i2, const int i3, const int i4,
F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4,
const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z,
const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z,
const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const
{
E_FLOAT edihedralquarter;
F_FLOAT v[6];
// The eatom and vatom arrays are atomic
Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_eatom = k_eatom.view<DeviceType>();
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_vatom = k_vatom.view<DeviceType>();
if (eflag_either) {
if (eflag_global) {
if (newton_bond) ev.evdwl += edihedral;
else {
edihedralquarter = 0.25*edihedral;
if (i1 < nlocal) ev.evdwl += edihedralquarter;
if (i2 < nlocal) ev.evdwl += edihedralquarter;
if (i3 < nlocal) ev.evdwl += edihedralquarter;
if (i4 < nlocal) ev.evdwl += edihedralquarter;
}
}
if (eflag_atom) {
edihedralquarter = 0.25*edihedral;
if (newton_bond || i1 < nlocal) v_eatom[i1] += edihedralquarter;
if (newton_bond || i2 < nlocal) v_eatom[i2] += edihedralquarter;
if (newton_bond || i3 < nlocal) v_eatom[i3] += edihedralquarter;
if (newton_bond || i4 < nlocal) v_eatom[i4] += edihedralquarter;
}
}
if (vflag_either) {
v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0];
v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1];
v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2];
v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1];
v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2];
v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[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 (i1 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
if (i2 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
if (i3 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
if (i4 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i1 < nlocal) {
v_vatom(i1,0) += 0.25*v[0];
v_vatom(i1,1) += 0.25*v[1];
v_vatom(i1,2) += 0.25*v[2];
v_vatom(i1,3) += 0.25*v[3];
v_vatom(i1,4) += 0.25*v[4];
v_vatom(i1,5) += 0.25*v[5];
}
if (newton_bond || i2 < nlocal) {
v_vatom(i2,0) += 0.25*v[0];
v_vatom(i2,1) += 0.25*v[1];
v_vatom(i2,2) += 0.25*v[2];
v_vatom(i2,3) += 0.25*v[3];
v_vatom(i2,4) += 0.25*v[4];
v_vatom(i2,5) += 0.25*v[5];
}
if (newton_bond || i3 < nlocal) {
v_vatom(i3,0) += 0.25*v[0];
v_vatom(i3,1) += 0.25*v[1];
v_vatom(i3,2) += 0.25*v[2];
v_vatom(i3,3) += 0.25*v[3];
v_vatom(i3,4) += 0.25*v[4];
v_vatom(i3,5) += 0.25*v[5];
}
if (newton_bond || i4 < nlocal) {
v_vatom(i4,0) += 0.25*v[0];
v_vatom(i4,1) += 0.25*v[1];
v_vatom(i4,2) += 0.25*v[2];
v_vatom(i4,3) += 0.25*v[3];
v_vatom(i4,4) += 0.25*v[4];
v_vatom(i4,5) += 0.25*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class DihedralClass2Kokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class DihedralClass2Kokkos<LMPHostType>;
#endif
}

120
src/KOKKOS/dihedral_class2_kokkos.h Normal file
View File

@ -0,0 +1,120 @@
/* -*- 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 DIHEDRAL_CLASS
DihedralStyle(class2/kk,DihedralClass2Kokkos<LMPDeviceType>)
DihedralStyle(class2/kk/device,DihedralClass2Kokkos<LMPDeviceType>)
DihedralStyle(class2/kk/host,DihedralClass2Kokkos<LMPHostType>)
#else
#ifndef LMP_DIHEDRAL_CLASS2_KOKKOS_H
#define LMP_DIHEDRAL_CLASS2_KOKKOS_H
#include "dihedral_class2.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
template<int NEWTON_BOND, int EVFLAG>
struct TagDihedralClass2Compute{};
template<class DeviceType>
class DihedralClass2Kokkos : public DihedralClass2 {
public:
typedef DeviceType device_type;
typedef EV_FLOAT value_type;
typedef ArrayTypes<DeviceType> AT;
DihedralClass2Kokkos(class LAMMPS *);
virtual ~DihedralClass2Kokkos();
virtual void compute(int, int);
virtual void coeff(int, char **);
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>, const int&) const;
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void ev_tally(EV_FLOAT &ev, const int i1, const int i2, const int i3, const int i4,
F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4,
const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z,
const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z,
const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const;
protected:
class NeighborKokkos *neighborKK;
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_int_2d dihedrallist;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
DAT::t_efloat_1d d_eatom;
DAT::t_virial_array d_vatom;
int nlocal,newton_bond;
int eflag,vflag;
DAT::tdual_int_scalar k_warning_flag;
typename AT::t_int_scalar d_warning_flag;
HAT::t_int_scalar h_warning_flag;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_k2, k_k3, k_k1;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_phi1, k_phi2, k_phi3;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_mbt_f1, k_mbt_f2, k_mbt_f3, k_mbt_r0;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_ebt_f1_1, k_ebt_f2_1, k_ebt_f3_1, k_ebt_r0_1;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_ebt_f1_2, k_ebt_f2_2, k_ebt_f3_2, k_ebt_r0_2;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_at_f1_1, k_at_f2_1, k_at_f3_1, k_at_theta0_1;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_at_f1_2, k_at_f2_2, k_at_f3_2, k_at_theta0_2;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_aat_k, k_aat_theta0_1, k_aat_theta0_2;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_bb13t_k, k_bb13t_r10, k_bb13t_r30;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_setflag_d, k_setflag_mbt, k_setflag_ebt;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_setflag_at, k_setflag_aat, k_setflag_bb13t;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_k2, d_k3, d_k1;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_phi1, d_phi2, d_phi3;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_mbt_f1, d_mbt_f2, d_mbt_f3, d_mbt_r0;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_ebt_f1_1, d_ebt_f2_1, d_ebt_f3_1, d_ebt_r0_1;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_ebt_f1_2, d_ebt_f2_2, d_ebt_f3_2, d_ebt_r0_2;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_at_f1_1, d_at_f2_1, d_at_f3_1, d_at_theta0_1;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_at_f1_2, d_at_f2_2, d_at_f3_2, d_at_theta0_2;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_aat_k, d_aat_theta0_1, d_aat_theta0_2;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_bb13t_k, d_bb13t_r10, d_bb13t_r30;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_setflag_d, d_setflag_mbt, d_setflag_ebt;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_setflag_at, d_setflag_aat, d_setflag_bb13t;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
W: Dihedral problem
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.
*/

1082
src/KOKKOS/improper_class2_kokkos.cpp Normal file
View File

File diff suppressed because it is too large Load Diff

115
src/KOKKOS/improper_class2_kokkos.h Normal file
View File

@ -0,0 +1,115 @@
/* -*- 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 IMPROPER_CLASS
ImproperStyle(class2/kk,ImproperClass2Kokkos<LMPDeviceType>)
ImproperStyle(class2/kk/device,ImproperClass2Kokkos<LMPDeviceType>)
ImproperStyle(class2/kk/host,ImproperClass2Kokkos<LMPHostType>)
#else
#ifndef LMP_IMPROPER_CLASS2_KOKKOS_H
#define LMP_IMPROPER_CLASS2_KOKKOS_H
#include "improper_class2.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
template<int NEWTON_BOND, int EVFLAG>
struct TagImproperClass2Compute{};
template<int NEWTON_BOND, int EVFLAG>
struct TagImproperClass2AngleAngle{};
template<class DeviceType>
class ImproperClass2Kokkos : public ImproperClass2 {
public:
typedef DeviceType device_type;
typedef EV_FLOAT value_type;
typedef ArrayTypes<DeviceType> AT;
ImproperClass2Kokkos(class LAMMPS *);
virtual ~ImproperClass2Kokkos();
virtual void compute(int, int);
virtual void coeff(int, char **);
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagImproperClass2Compute<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagImproperClass2Compute<NEWTON_BOND,EVFLAG>, const int&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagImproperClass2AngleAngle<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagImproperClass2AngleAngle<NEWTON_BOND,EVFLAG>, const int&) const;
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void ev_tally(EV_FLOAT &ev, const int i1, const int i2, const int i3, const int i4,
F_FLOAT &eimproper, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4,
const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z,
const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z,
const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const;
protected:
class NeighborKokkos *neighborKK;
typename AT::t_x_array_randomread x;
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typename AT::t_int_2d improperlist;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
DAT::t_efloat_1d d_eatom;
DAT::t_virial_array d_vatom;
int nlocal,newton_bond;
int eflag,vflag;
DAT::tdual_int_scalar k_warning_flag;
typename AT::t_int_scalar d_warning_flag;
HAT::t_int_scalar h_warning_flag;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_k0,k_chi0;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_aa_k1,k_aa_k2,k_aa_k3,k_aa_theta0_1,k_aa_theta0_2,k_aa_theta0_3;
typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_setflag_i,k_setflag_aa,k_setflag;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_k0,d_chi0;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_aa_k1,d_aa_k2,d_aa_k3,d_aa_theta0_1,d_aa_theta0_2,d_aa_theta0_3;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_setflag_i,d_setflag_aa,d_setflag;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
W: Dihedral problem
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.
*/