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Add Kokkos version of angle_cosine

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This commit is contained in:
Stan Moore
2019-01-28 11:29:28 -07:00
parent fb30d2d078
commit 54b9a1335c
7 changed files with 492 additions and 5 deletions
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2
doc/src/Commands_bond.txt
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@ -61,7 +61,7 @@ OPT.
"charmm (iko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"class2/p6"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine (ko)"_angle_cosine.html,
"cosine/buck6d"_angle_cosine_buck6d.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,

1
doc/src/angle_cosine.txt
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@ -8,6 +8,7 @@
angle_style cosine command :h3
angle_style cosine/omp command :h3
angle_style cosine/kk command :h3
[Syntax:]

2
src/KOKKOS/Install.sh
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@ -49,6 +49,8 @@ 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_cosine_kokkos.cpp angle_cosine.cpp
action angle_cosine_kokkos.h angle_cosine.h
action angle_harmonic_kokkos.cpp angle_harmonic.cpp
action angle_harmonic_kokkos.h angle_harmonic.h
action atom_kokkos.cpp

394
src/KOKKOS/angle_cosine_kokkos.cpp Normal file
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@ -0,0 +1,394 @@
/* ----------------------------------------------------------------------
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 <cmath>
#include <cstdlib>
#include "angle_cosine_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_kokkos.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
template<class DeviceType>
AngleCosineKokkos<DeviceType>::AngleCosineKokkos(LAMMPS *lmp) : AngleCosine(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>
AngleCosineKokkos<DeviceType>::~AngleCosineKokkos()
{
if (!copymode) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void AngleCosineKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
//atomKK->sync(execution_space,datamask_read);
k_k.template sync<DeviceType>();
// 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_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, TagAngleCosineCompute<1,1> >(0,nanglelist),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<0,1> >(0,nanglelist),*this,ev);
}
} else {
if (newton_bond) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<1,0> >(0,nanglelist),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<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 AngleCosineKokkos<DeviceType>::operator()(TagAngleCosineCompute<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);
// c = cosine of angle
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;
// force & energy
F_FLOAT eangle = 0.0;
if (eflag) eangle = d_k[type]*(1.0+c);
const F_FLOAT a = d_k[type];
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;
// 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 AngleCosineKokkos<DeviceType>::operator()(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>, const int &n) const {
EV_FLOAT ev;
this->template operator()<NEWTON_BOND,EVFLAG>(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>(), n, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void AngleCosineKokkos<DeviceType>::allocate()
{
AngleCosine::allocate();
int n = atom->nangletypes;
k_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleCosine::k",n+1);
d_k = k_k.template view<DeviceType>();
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
template<class DeviceType>
void AngleCosineKokkos<DeviceType>::coeff(int narg, char **arg)
{
AngleCosine::coeff(narg, arg);
int n = atom->nangletypes;
for (int i = 1; i <= n; i++)
k_k.h_view[i] = k[i];
k_k.template modify<LMPHostType>();
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
template<class DeviceType>
void AngleCosineKokkos<DeviceType>::read_restart(FILE *fp)
{
AngleCosine::read_restart(fp);
int n = atom->nangletypes;
for (int i = 1; i <= n; i++)
k_k.h_view[i] = k[i];
k_k.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 AngleCosineKokkos<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 AngleCosineKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class AngleCosineKokkos<LMPHostType>;
#endif
}

90
src/KOKKOS/angle_cosine_kokkos.h Normal file
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@ -0,0 +1,90 @@
/* -*- 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(cosine/kk,AngleCosineKokkos<LMPDeviceType>)
AngleStyle(cosine/kk/device,AngleCosineKokkos<LMPDeviceType>)
AngleStyle(cosine/kk/host,AngleCosineKokkos<LMPHostType>)
#else
#ifndef LMP_ANGLE_COSINE_KOKKOS_H
#define LMP_ANGLE_COSINE_KOKKOS_H
#include "angle_cosine.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
template<int NEWTON_BOND, int EVFLAG>
struct TagAngleCosineCompute{};
template<class DeviceType>
class AngleCosineKokkos : public AngleCosine {
public:
typedef DeviceType device_type;
typedef EV_FLOAT value_type;
AngleCosineKokkos(class LAMMPS *);
virtual ~AngleCosineKokkos();
void compute(int, int);
void coeff(int, char **);
void read_restart(FILE *);
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagAngleCosineCompute<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_k;
typename ArrayTypes<DeviceType>::t_ffloat_1d d_k;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

2
src/MOLECULE/angle_cosine.cpp
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@ -36,7 +36,7 @@ AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {}
AngleCosine::~AngleCosine()
{
if (allocated) {
if (allocated && !copymode) {
memory->destroy(setflag);
memory->destroy(k);
}

6
src/MOLECULE/angle_cosine.h
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@ -30,17 +30,17 @@ class AngleCosine : public Angle {
AngleCosine(class LAMMPS *);
virtual ~AngleCosine();
virtual void compute(int, int);
void coeff(int, char **);
virtual void coeff(int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual void read_restart(FILE *);
void write_data(FILE *);
double single(int, int, int, int);
protected:
double *k;
void allocate();
virtual void allocate();
};
}