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Merge branch 'develop' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2024-10-05 01:53:22 -04:00
parent d29533447a 224468d946
commit 0cb64f8bf3
31 changed files with 1071 additions and 206 deletions
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2
doc/src/Commands_pair.rst
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@ -44,7 +44,7 @@ OPT.
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
* :doc:`born/gauss <pair_born_gauss>`
* :doc:`bpm/spring <pair_bpm_spring>`
* :doc:`brownian (o) <pair_brownian>`
* :doc:`brownian (ko) <pair_brownian>`
* :doc:`brownian/poly (o) <pair_brownian>`
* :doc:`buck (giko) <pair_buck>`
* :doc:`buck/coul/cut (giko) <pair_buck>`

3
doc/src/pair_brownian.rst
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@ -1,12 +1,13 @@
.. index:: pair_style brownian
.. index:: pair_style brownian/omp
.. index:: pair_style brownian/kk
.. index:: pair_style brownian/poly
.. index:: pair_style brownian/poly/omp
pair_style brownian command
===========================
Accelerator Variants: *brownian/omp*
Accelerator Variants: *brownian/omp*, *brownian/kk*
pair_style brownian/poly command
================================

2
src/COLLOID/pair_brownian.cpp
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@ -54,6 +54,8 @@ PairBrownian::PairBrownian(LAMMPS *lmp) : Pair(lmp)
PairBrownian::~PairBrownian()
{
if (copymode) return;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);

4
src/COLLOID/pair_brownian.h
View File

@ -31,7 +31,7 @@ class PairBrownian : public Pair {
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
double init_one(int, int) override;
virtual double init_one(int, int) override;
void init_style() override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
@ -55,7 +55,7 @@ class PairBrownian : public Pair {
class RanMars *random;
void set_3_orthogonal_vectors(double *, double *, double *);
void allocate();
virtual void allocate();
};
} // namespace LAMMPS_NS

2
src/KOKKOS/Install.sh
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@ -277,6 +277,8 @@ action npair_trim_kokkos.h
action pack_kokkos.h pack.h
action pair_adp_kokkos.cpp pair_adp.cpp
action pair_adp_kokkos.h pair_adp.h
action pair_brownian_kokkos.cpp pair_brownian.cpp
action pair_brownian_kokkos.h pair_brownian.h
action pair_buck_coul_cut_kokkos.cpp
action pair_buck_coul_cut_kokkos.h
action pair_buck_coul_long_kokkos.cpp pair_buck_coul_long.cpp

20
src/KOKKOS/compute_temp_deform_kokkos.cpp
View File

@ -190,10 +190,20 @@ void ComputeTempDeformKokkos<DeviceType>::operator()(TagComputeTempDeformVector<
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeTempDeformKokkos<DeviceType>::remove_bias_all()
{
atomKK->sync(execution_space,datamask_read);
remove_bias_all_kk();
atomKK->sync(Host,V_MASK);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeTempDeformKokkos<DeviceType>::remove_bias_all_kk()
{
atomKK->sync(execution_space,X_MASK|V_MASK);
v = atomKK->k_v.view<DeviceType>();
x = atomKK->k_x.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
@ -214,6 +224,8 @@ void ComputeTempDeformKokkos<DeviceType>::remove_bias_all()
copymode = 0;
domainKK->lamda2x(nlocal);
atomKK->modified(execution_space,V_MASK);
}
template<class DeviceType>
@ -230,18 +242,20 @@ void ComputeTempDeformKokkos<DeviceType>::operator()(TagComputeTempDeformRemoveB
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeTempDeformKokkos<DeviceType>::restore_bias_all()
{
atomKK->sync(execution_space,datamask_read);
atomKK->sync(execution_space,V_MASK);
v = atomKK->k_v.view<DeviceType>();
x = atomKK->k_x.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
int nlocal = atom->nlocal;
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagComputeTempDeformRestoreBias >(0,nlocal),*this);
copymode = 0;
atomKK->modified(execution_space,V_MASK);
}
template<class DeviceType>

1
src/KOKKOS/compute_temp_deform_kokkos.h
View File

@ -69,6 +69,7 @@ class ComputeTempDeformKokkos: public ComputeTempDeform {
double compute_scalar() override;
void compute_vector() override;
void remove_bias_all() override;
void remove_bias_all_kk() override;
void restore_bias_all() override;
template<int RMASS>

8
src/KOKKOS/fix_deform_kokkos.cpp
View File

@ -55,7 +55,11 @@ void FixDeformKokkos::pre_exchange()
void FixDeformKokkos::end_of_step()
{
atomKK->sync(Host,ALL_MASK);
if (remapflag == Domain::X_REMAP && rfix.size() > 0)
atomKK->sync(Host,ALL_MASK);
FixDeform::end_of_step();
atomKK->modified(Host,ALL_MASK);
if (remapflag == Domain::X_REMAP && rfix.size() > 0)
atomKK->modified(Host,ALL_MASK);
}

28
src/KOKKOS/fix_langevin_kokkos.cpp
View File

@ -86,7 +86,6 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = V_MASK | F_MASK | MASK_MASK | RMASS_MASK | TYPE_MASK;
datamask_modify = F_MASK;
}
/* ---------------------------------------------------------------------- */
@ -227,12 +226,16 @@ void FixLangevinKokkos<DeviceType>::post_force(int /*vflag*/)
// account for bias velocity
if (tbiasflag == BIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->compute_scalar();
temperature->remove_bias_all(); // modifies velocities
// if temeprature compute is kokkosized host-device comm won't be needed
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (temperature->kokkosable) {
temperature->compute_scalar();
temperature->remove_bias_all_kk();
} else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->compute_scalar();
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
// compute langevin force in parallel on the device
@ -526,10 +529,13 @@ void FixLangevinKokkos<DeviceType>::post_force(int /*vflag*/)
if (tbiasflag == BIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all(); // modifies velocities
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->restore_bias_all();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
// set modify flags for the views modified in post_force functor

74
src/KOKKOS/fix_nh_kokkos.cpp
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@ -80,7 +80,11 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
{
// tdof needed by compute_temp_target()
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t_current = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
tdof = temperature->dof;
// t_target is needed by NPH and NPT in compute_scalar()
@ -105,6 +109,7 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t0 = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (t0 < EPSILON)
error->all(FLERR,"Current temperature too close to zero, consider using ptemp keyword");
}
@ -117,6 +122,8 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t_current = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
tdof = temperature->dof;
if (pstat_flag) {
@ -194,9 +201,7 @@ void FixNHKokkos<DeviceType>::initial_integrate(int /*vflag*/)
if (pstat_flag) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
//atomKK->sync(pressure->execution_space,pressure->datamask_read);
//atomKK->modified(pressure->execution_space,pressure->datamask_modify);
atomKK->sync(pressure->execution_space,pressure->datamask_read);
if (pstyle == ISO) {
temperature->compute_scalar();
pressure->compute_scalar();
@ -204,6 +209,10 @@ void FixNHKokkos<DeviceType>::initial_integrate(int /*vflag*/)
temperature->compute_vector();
pressure->compute_vector();
}
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->modified(pressure->execution_space,pressure->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,pressure->datamask_modify);
couple();
pressure->addstep(update->ntimestep+1);
}
@ -250,6 +259,7 @@ void FixNHKokkos<DeviceType>::final_integrate()
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t_current = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
if (pstat_flag) nh_v_press();
@ -260,15 +270,24 @@ void FixNHKokkos<DeviceType>::final_integrate()
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t_current = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
tdof = temperature->dof;
if (pstat_flag) {
//atomKK->sync(pressure->execution_space,pressure->datamask_read);
//atomKK->modified(pressure->execution_space,pressure->datamask_modify);
if (pstyle == ISO) pressure->compute_scalar();
else {
if (pstyle == ISO) {
atomKK->sync(pressure->execution_space,pressure->datamask_read);
pressure->compute_scalar();
atomKK->modified(pressure->execution_space,pressure->datamask_modify);
atomKK->sync(execution_space,pressure->datamask_modify);
} else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
atomKK->sync(pressure->execution_space,pressure->datamask_read);
temperature->compute_vector();
pressure->compute_vector();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->modified(pressure->execution_space,pressure->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,pressure->datamask_modify);
}
couple();
pressure->addstep(update->ntimestep+1);
@ -480,9 +499,13 @@ void FixNHKokkos<DeviceType>::nh_v_press()
factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
if (which == BIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->remove_bias_all_kk();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
atomKK->sync(execution_space,V_MASK | MASK_MASK);
@ -497,11 +520,14 @@ void FixNHKokkos<DeviceType>::nh_v_press()
atomKK->modified(execution_space,V_MASK);
if (which == BIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->restore_bias_all();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
}
template<class DeviceType>
@ -617,9 +643,13 @@ void FixNHKokkos<DeviceType>::nh_v_temp()
if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst;
if (which == BIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->remove_bias_all_kk();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
atomKK->sync(execution_space,V_MASK | MASK_MASK);
@ -631,9 +661,13 @@ void FixNHKokkos<DeviceType>::nh_v_temp()
atomKK->modified(execution_space,V_MASK);
if (which == BIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->restore_bias_all();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
}

35
src/KOKKOS/fix_nvt_sllod_kokkos.cpp
View File

@ -68,6 +68,10 @@ FixNVTSllodKokkos<DeviceType>::FixNVTSllodKokkos(LAMMPS *lmp, int narg, char **a
this->modify->add_compute(fmt::format("{} {} temp/deform/kk",this->id_temp,this->group->names[this->igroup]));
this->tcomputeflag = 1;
this->nondeformbias = 0;
this->execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
this->datamask_read = EMPTY_MASK;
this->datamask_modify = EMPTY_MASK;
}
/* ---------------------------------------------------------------------- */
@ -114,6 +118,7 @@ void FixNVTSllodKokkos<DeviceType>::nh_v_temp()
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->compute_scalar();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
atomKK->sync(this->execution_space,this->temperature->datamask_modify);
}
v = atomKK->k_v.view<DeviceType>();
@ -130,9 +135,13 @@ void FixNVTSllodKokkos<DeviceType>::nh_v_temp()
vdelu = typename AT::t_v_array(Kokkos::NoInit("nvt/sllod/kk:vdelu"), atomKK->nmax);
if (!this->psllod_flag) {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->remove_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
if (this->temperature->kokkosable) this->temperature->remove_bias_all_kk();
else {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->remove_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
atomKK->sync(this->execution_space,this->temperature->datamask_modify);
}
}
atomKK->sync(this->execution_space,V_MASK | MASK_MASK);
@ -142,9 +151,13 @@ void FixNVTSllodKokkos<DeviceType>::nh_v_temp()
this->copymode = 0;
if (this->psllod_flag) {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->remove_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
if (this->temperature->kokkosable) this->temperature->remove_bias_all_kk();
else {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->remove_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
atomKK->sync(this->execution_space,this->temperature->datamask_modify);
}
}
atomKK->sync(this->execution_space,V_MASK | MASK_MASK);
@ -155,9 +168,13 @@ void FixNVTSllodKokkos<DeviceType>::nh_v_temp()
atomKK->modified(this->execution_space,V_MASK);
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->restore_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
if (this->temperature->kokkosable) this->temperature->restore_bias_all();
else {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->restore_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
atomKK->sync(this->execution_space,this->temperature->datamask_modify);
}
}
template<class DeviceType>

22
src/KOKKOS/fix_temp_berendsen_kokkos.cpp
View File

@ -97,10 +97,13 @@ void FixTempBerendsenKokkos<DeviceType>::end_of_step()
auto groupbit = this->groupbit;
if (which == NOBIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->remove_bias_all_kk();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
atomKK->sync(execution_space,V_MASK|MASK_MASK);
@ -116,10 +119,13 @@ void FixTempBerendsenKokkos<DeviceType>::end_of_step()
atomKK->modified(execution_space,V_MASK);
if (which == NOBIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->restore_bias_all();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
}
/* ---------------------------------------------------------------------- */

23
src/KOKKOS/fix_temp_rescale_kokkos.cpp
View File

@ -99,10 +99,13 @@ void FixTempRescaleKokkos<DeviceType>::end_of_step()
auto groupbit = this->groupbit;
if (which == NOBIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->remove_bias_all_kk();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->remove_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
atomKK->sync(execution_space,V_MASK|MASK_MASK);
@ -118,11 +121,13 @@ void FixTempRescaleKokkos<DeviceType>::end_of_step()
atomKK->modified(execution_space,V_MASK);
if (which == NOBIAS) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
if (temperature->kokkosable) temperature->restore_bias_all();
else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
temperature->restore_bias_all();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
atomKK->sync(execution_space,temperature->datamask_modify);
}
}
}
}

15
src/KOKKOS/kokkos.cpp
View File

@ -633,15 +633,24 @@ void KokkosLMP::accelerator(int narg, char **arg)
// set neighbor binsize, same as neigh_modify command
force->newton = force->newton_pair = force->newton_bond = newtonflag;
if (neigh_thread && newtonflag)
error->all(FLERR,"Must use KOKKOS package option 'newton off' with 'neigh/thread on'");
newton_check();
neighbor->binsize_user = binsize;
if (binsize <= 0.0) neighbor->binsizeflag = 0;
else neighbor->binsizeflag = 1;
}
/* ---------------------------------------------------------------------- */
void KokkosLMP::newton_check()
{
if (neighflag == FULL && force->newton)
error->all(FLERR,"Must use 'newton off' with KOKKOS package option 'neigh full'");
if (neigh_thread && force->newton)
error->all(FLERR,"Must use 'newton off' with KOKKOS package option 'neigh/thread on'");
}
/* ----------------------------------------------------------------------
called by Finish
------------------------------------------------------------------------- */

1
src/KOKKOS/kokkos.h
View File

@ -64,6 +64,7 @@ class KokkosLMP : protected Pointers {
static void initialize(const Kokkos::InitializationSettings&, Error *);
static void finalize();
void accelerator(int, char **);
void newton_check();
bigint neigh_count(int);
template<class DeviceType>

1
src/KOKKOS/npair_kokkos.cpp
View File

@ -1438,7 +1438,6 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeGPU(typename Kokkos::TeamP
for (int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
if (ibin == jbin) continue;
if (HalfNeigh && Newton && !Tri && (ibin == jbin)) continue;
bincount_current = c_bincount[jbin];

634
src/KOKKOS/pair_brownian_kokkos.cpp Normal file
View File

@ -0,0 +1,634 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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.
------------------------------------------------------------------------- */
#include "pair_brownian_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "domain_kokkos.h"
#include "error.h"
#include "fix.h"
#include "fix_wall.h"
#include "force.h"
#include "input.h"
#include "kokkos.h"
#include "math_const.h"
#include "math_special_kokkos.h"
#include "memory_kokkos.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include "variable.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecialKokkos;
// same as fix_wall.cpp
enum { EDGE, CONSTANT, VARIABLE };
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairBrownianKokkos<DeviceType>::PairBrownianKokkos(LAMMPS *lmp) : PairBrownian(lmp),
rand_pool(seed + comm->me)
{
respa_enable = 0;
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | TORQUE_MASK | TYPE_MASK | VIRIAL_MASK | RADIUS_MASK;
datamask_modify = F_MASK | TORQUE_MASK | VIRIAL_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairBrownianKokkos<DeviceType>::~PairBrownianKokkos()
{
if (copymode) return;
if (allocated) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_cut_inner,cut_inner);
memoryKK->destroy_kokkos(k_cutsq,cutsq);
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
template<class DeviceType>
void PairBrownianKokkos<DeviceType>::init_style()
{
PairBrownian::init_style();
// error if rRESPA with inner levels
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
// adjust neighbor list request for KOKKOS
neighflag = lmp->kokkos->neighflag;
auto request = neighbor->find_request(this);
request->set_kokkos_host(std::is_same_v<DeviceType,LMPHostType> &&
!std::is_same_v<DeviceType,LMPDeviceType>);
request->set_kokkos_device(std::is_same_v<DeviceType,LMPDeviceType>);
if (neighflag == FULL) request->enable_full();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairBrownianKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (neighflag == FULL) no_virial_fdotr_compute = 1;
ev_init(eflag,vflag,0);
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
double dims[3], wallcoord;
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2) { // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (int j = 0; j < 3; j++) dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)) {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++) {
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++) {
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->xstyle[m] == VARIABLE) {
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
} else
wallcoord = wallfix->coord0[m];
if (side == 0)
walllo[dim] = wallcoord;
else
wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++) dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0] * dims[1] * dims[2];
double vol_f = vol_P / vol_T;
if (flaglog == 0) {
R0 = 6 * MY_PI * mu * rad * (1.0 + 2.16 * vol_f);
RT0 = 8 * MY_PI * mu * cube(rad);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6 * MY_PI * mu * rad * (1.0 + 2.725 * vol_f - 6.583 * vol_f * vol_f);
RT0 = 8 * MY_PI * mu * cube(rad) * (1.0 + 0.749 * vol_f - 2.469 * vol_f * vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// scale factor for Brownian moments
prethermostat = sqrt(24.0 * force->boltz * t_target / update->dt);
prethermostat *= sqrt(force->vxmu2f / force->ftm2v / force->mvv2e);
// reallocate per-atom arrays if necessary
if (vflag_atom) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
atomKK->sync(execution_space,datamask_read);
k_cutsq.template sync<DeviceType>();
k_cut_inner.template sync<DeviceType>();
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
else atomKK->modified(execution_space,F_MASK | TORQUE_MASK);
x = atomKK->k_x.view<DeviceType>();
c_x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
torque = atomKK->k_torque.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
radius = atomKK->k_radius.view<DeviceType>();
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
vxmu2f = force->vxmu2f;
// loop over neighbors of my atoms
int inum = list->inum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
copymode = 1;
EV_FLOAT ev;
if (flagfld) { // FLAGFLD == 1
if (vflag_either) { // VFLAG == 1
if (neighflag == HALF) {
if (newton_pair) Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,1,1,1> >(0,inum),*this,ev);
else Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,0,1,1> >(0,inum),*this,ev);
} else if (neighflag == HALFTHREAD) {
if (newton_pair) Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,1,1,1> >(0,inum),*this,ev);
else Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,0,1,1> >(0,inum),*this,ev);
} else if (neighflag == FULL) {
if (newton_pair) Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,1,1,1> >(0,inum),*this,ev);
else Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,0,1,1> >(0,inum),*this,ev);
}
} else { // VFLAG==0
if (neighflag == HALF) {
if (newton_pair) Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,1,0,1> >(0,inum),*this);
else Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,0,0,1> >(0,inum),*this);
} else if (neighflag == HALFTHREAD) {
if (newton_pair) Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,1,0,1> >(0,inum),*this);
else Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,0,0,1> >(0,inum),*this);
} else if (neighflag == FULL) {
if (newton_pair) Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,1,0,1> >(0,inum),*this);
else Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,0,0,1> >(0,inum),*this);
}
}
} else { // FLAGFLD == 0
if (evflag) { // VFLAG== 1
if (neighflag == HALF) {
if (newton_pair) Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,1,1,0> >(0,inum),*this,ev);
else Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,0,1,0> >(0,inum),*this,ev);
} else if (neighflag == HALFTHREAD) {
if (newton_pair) Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,1,1,0> >(0,inum),*this,ev);
else Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,0,1,0> >(0,inum),*this,ev);
} else if (neighflag == FULL) {
if (newton_pair) Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,1,1,0> >(0,inum),*this,ev);
else Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,0,1,0> >(0,inum),*this,ev);
}
} else { // VFLAG == 0
if (neighflag == HALF) {
if (newton_pair) Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,1,0,0> >(0,inum),*this);
else Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALF,0,0,0> >(0,inum),*this);
} else if (neighflag == HALFTHREAD) {
if (newton_pair) Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,1,0,0> >(0,inum),*this);
else Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<HALFTHREAD,0,0,0> >(0,inum),*this);
} else if (neighflag == FULL) {
if (newton_pair) Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,1,0,0> >(0,inum),*this);
else Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairBrownianCompute<FULL,0,0,0> >(0,inum),*this);
}
}
}
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 (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
}
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int FLAGFLD>
KOKKOS_INLINE_FUNCTION
void PairBrownianKokkos<DeviceType>::operator()(TagPairBrownianCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,FLAGFLD>, const int ii, EV_FLOAT &ev) const {
// The f and torque arrays are atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_torque = torque;
rand_type rand_gen = rand_pool.get_state();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int itype = type[i];
const LMP_FLOAT radi = radius[i];
const int jnum = d_numneigh[i];
LMP_FLOAT a_sq, a_sh, a_pu;
LMP_FLOAT xl[3], p1[3], p2[3], p3[3];
F_FLOAT fx_i = 0.0;
F_FLOAT fy_i = 0.0;
F_FLOAT fz_i = 0.0;
F_FLOAT torquex_i = 0.0;
F_FLOAT torquey_i = 0.0;
F_FLOAT torquez_i = 0.0;
if (FLAGFLD) {
fx_i = prethermostat * sqrt(R0) * (rand_gen.drand() - 0.5);
fy_i = prethermostat * sqrt(R0) * (rand_gen.drand() - 0.5);
fz_i = prethermostat * sqrt(R0) * (rand_gen.drand() - 0.5);
if (flaglog) {
torquex_i = prethermostat * sqrt(RT0) * (rand_gen.drand() - 0.5);
torquey_i = prethermostat * sqrt(RT0) * (rand_gen.drand() - 0.5);
torquez_i = prethermostat * sqrt(RT0) * (rand_gen.drand() - 0.5);
}
}
if (flagHI) {
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const X_FLOAT rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
if(rsq < d_cutsq(itype,jtype)) {
const LMP_FLOAT r = sqrt(rsq);
// scalar resistances a_sq and a_sh
LMP_FLOAT h_sep = r - 2.0 * radi;
// if less than minimum gap, use minimum gap instead
if (r < d_cut_inner(itype,jtype)) h_sep = d_cut_inner(itype,jtype) - 2.0 * radi;
// scale h_sep by radi
h_sep = h_sep / radi;
if (flaglog) {
a_sq = 6.0 * MY_PI * mu * radi * (1.0 / 4.0 / h_sep + 9.0 / 40.0 * log(1.0 / h_sep));
a_sh = 6.0 * MY_PI * mu * radi * (1.0 / 6.0 * log(1.0 / h_sep));
a_pu = 8.0 * MY_PI * mu * cube(radi) * (3.0 / 160.0 * log(1.0 / h_sep));
} else
a_sq = 6.0 * MY_PI * mu * radi * (1.0 / 4.0 / h_sep);
// generate the Pairwise Brownian Force: a_sq
LMP_FLOAT Fbmag = prethermostat * sqrt(a_sq);
// generate a random number
LMP_FLOAT randr = rand_gen.drand() - 0.5;
// contribution due to Brownian motion
F_FLOAT fx = Fbmag * randr * delx / r;
F_FLOAT fy = Fbmag * randr * dely / r;
F_FLOAT fz = Fbmag * randr * delz / r;
// add terms due to a_sh
if (flaglog) {
// generate two orthogonal vectors to the line of centers
p1[0] = delx / r;
p1[1] = dely / r;
p1[2] = delz / r;
set_3_orthogonal_vectors(p1, p2, p3);
// magnitude
Fbmag = prethermostat * sqrt(a_sh);
// force in each of the two directions
randr = rand_gen.drand() - 0.5;
fx += Fbmag * randr * p2[0];
fy += Fbmag * randr * p2[1];
fz += Fbmag * randr * p2[2];
randr = rand_gen.drand() - 0.5;
fx += Fbmag * randr * p3[0];
fy += Fbmag * randr * p3[1];
fz += Fbmag * randr * p3[2];
}
// scale forces to appropriate units
fx = vxmu2f * fx;
fy = vxmu2f * fy;
fz = vxmu2f * fz;
// sum to total force
fx_i -= fx;
fy_i -= fy;
fz_i -= fz;
if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
a_f(j,0) += fx;
a_f(j,1) += fy;
a_f(j,2) += fz;
}
// torque due to the Brownian Force
if (flaglog) {
// location of the point of closest approach on I from its center
xl[0] = -delx / r * radi;
xl[1] = -dely / r * radi;
xl[2] = -delz / r * radi;
// torque = xl_cross_F
F_FLOAT tx = xl[1] * fz - xl[2] * fy;
F_FLOAT ty = xl[2] * fx - xl[0] * fz;
F_FLOAT tz = xl[0] * fy - xl[1] * fx;
// torque is same on both particles
torquex_i -= tx;
torquey_i -= ty;
torquez_i -= tz;
if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
a_torque(j,0) -= tx;
a_torque(j,1) -= ty;
a_torque(j,2) -= tz;
}
// torque due to a_pu
Fbmag = prethermostat * sqrt(a_pu);
// force in each direction
randr = rand_gen.drand() - 0.5;
tx = Fbmag * randr * p2[0];
ty = Fbmag * randr * p2[1];
tz = Fbmag * randr * p2[2];
randr = rand_gen.drand() - 0.5;
tx += Fbmag * randr * p3[0];
ty += Fbmag * randr * p3[1];
tz += Fbmag * randr * p3[2];
// torque has opposite sign on two particles
torquex_i -= tx;
torquey_i -= ty;
torquez_i -= tz;
if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
a_torque(j,0) += tx;
a_torque(j,1) += ty;
a_torque(j,2) += tz;
}
}
if (VFLAG)
ev_tally_xyz<NEIGHFLAG, NEWTON_PAIR>(ev, i, j, -fx, -fy, -fz, delx, dely, delz);
}
}
} // if(flagHI)
rand_pool.free_state(rand_gen);
a_f(i,0) += fx_i;
a_f(i,1) += fy_i;
a_f(i,2) += fz_i;
a_torque(i,0) += torquex_i;
a_torque(i,1) += torquey_i;
a_torque(i,2) += torquez_i;
}
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int FLAGFLD>
KOKKOS_INLINE_FUNCTION
void PairBrownianKokkos<DeviceType>::operator()(TagPairBrownianCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,FLAGFLD>, const int ii) const {
EV_FLOAT ev;
this->template operator()<NEIGHFLAG,NEWTON_PAIR,VFLAG,FLAGFLD>(TagPairBrownianCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,FLAGFLD>(), ii, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void PairBrownianKokkos<DeviceType>::ev_tally_xyz(EV_FLOAT & ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
{
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
const F_FLOAT v0 = delx*fx;
const F_FLOAT v1 = dely*fy;
const F_FLOAT v2 = delz*fz;
const F_FLOAT v3 = delx*fy;
const F_FLOAT v4 = delx*fz;
const F_FLOAT v5 = dely*fz;
if (vflag_global) {
if (NEIGHFLAG != FULL) {
if (NEWTON_PAIR) { // neigh half, newton on
ev.v[0] += v0;
ev.v[1] += v1;
ev.v[2] += v2;
ev.v[3] += v3;
ev.v[4] += v4;
ev.v[5] += v5;
} else { // neigh half, newton off
if (i < nlocal) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
if (j < nlocal) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
}
} else { //neigh full
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
}
if (vflag_atom) {
if (NEIGHFLAG == FULL || NEWTON_PAIR || i < nlocal) {
v_vatom(i,0) += 0.5*v0;
v_vatom(i,1) += 0.5*v1;
v_vatom(i,2) += 0.5*v2;
v_vatom(i,3) += 0.5*v3;
v_vatom(i,4) += 0.5*v4;
v_vatom(i,5) += 0.5*v5;
}
if (NEIGHFLAG != FULL && (NEWTON_PAIR || j < nlocal)) {
v_vatom(j,0) += 0.5*v0;
v_vatom(j,1) += 0.5*v1;
v_vatom(j,2) += 0.5*v2;
v_vatom(j,3) += 0.5*v3;
v_vatom(j,4) += 0.5*v4;
v_vatom(j,5) += 0.5*v5;
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
template<class DeviceType>
void PairBrownianKokkos<DeviceType>::allocate()
{
PairBrownian::allocate();
int n = atom->ntypes;
memory->destroy(cutsq);
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_inner);
memoryKK->create_kokkos(k_cut_inner,cut_inner,n+1,n+1,"pair:cut_inner");
d_cut_inner = k_cut_inner.template view<DeviceType>();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
template<class DeviceType>
void PairBrownianKokkos<DeviceType>::settings(int narg, char **arg)
{
if (narg != 7 && narg != 9) error->all(FLERR, "Illegal pair_style command");
PairBrownian::settings(narg,arg);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
template<class DeviceType>
double PairBrownianKokkos<DeviceType>::init_one(int i, int j)
{
double cutone = PairBrownian::init_one(i,j);
double cutinnerm = cut_inner[i][j];
k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
k_cutsq.template modify<LMPHostType>();
k_cut_inner.h_view(i,j) = k_cut_inner.h_view(j,i) = cutinnerm;
k_cut_inner.template modify<LMPHostType>();
return cutone;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
template<class DeviceType>
void PairBrownianKokkos<DeviceType>::coeff(int narg, char **arg)
{
PairBrownian::coeff(narg,arg);
}
namespace LAMMPS_NS {
template class PairBrownianKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class PairBrownianKokkos<LMPHostType>;
#endif
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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 PAIR_CLASS
// clang-format off
PairStyle(brownian/kk,PairBrownianKokkos<LMPDeviceType>);
PairStyle(brownian/kk/device,PairBrownianKokkos<LMPDeviceType>);
PairStyle(brownian/kk/host,PairBrownianKokkos<LMPHostType>);
// clang-format on
#else
// clang-format off
#ifndef LMP_PAIR_BROWNIAN_KOKKOS_H
#define LMP_PAIR_BROWNIAN_KOKKOS_H
#include "pair_brownian.h"
#include "pair_kokkos.h"
#include "kokkos_type.h"
#include "kokkos_base.h"
#include "Kokkos_Random.hpp"
#include "comm_kokkos.h"
namespace LAMMPS_NS {
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int FLAGFLD>
struct TagPairBrownianCompute {};
template<class DeviceType>
class PairBrownianKokkos : public PairBrownian, public KokkosBase {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
typedef EV_FLOAT value_type;
PairBrownianKokkos(class LAMMPS *);
~PairBrownianKokkos() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
void init_style() override;
double init_one(int, int) override;
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int FLAGFLD>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairBrownianCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,FLAGFLD>, const int, EV_FLOAT &ev) const;
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int FLAGFLD>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairBrownianCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,FLAGFLD>, const int) const;
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void ev_tally_xyz(EV_FLOAT &ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
protected:
typename AT::t_x_array_randomread x;
typename AT::t_x_array c_x;
typename AT::t_f_array f;
typename AT::t_f_array torque;
typename AT::t_int_1d_randomread type;
typename AT::t_float_1d_randomread radius;
DAT::tdual_virial_array k_vatom;
typename AT::t_virial_array d_vatom;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d_randomread d_ilist;
typename AT::t_int_1d_randomread d_numneigh;
int newton_pair;
double special_lj[4];
typename AT::tdual_ffloat_2d k_cutsq;
typename AT::t_ffloat_2d d_cutsq;
typename AT::tdual_ffloat_2d k_cut_inner;
typename AT::t_ffloat_2d d_cut_inner;
int neighflag;
int nlocal,nall,eflag,vflag;
LMP_FLOAT vxmu2f;
LMP_FLOAT prethermostat;
void allocate() override;
KOKKOS_INLINE_FUNCTION
void set_3_orthogonal_vectors(const double p1[3], double * const p2, double * const p3) const {
double norm;
int ix, iy, iz;
// find the index of maximum magnitude and store it in iz
if (fabs(p1[0]) > fabs(p1[1])) {
iz = 0;
ix = 1;
iy = 2;
} else {
iz = 1;
ix = 2;
iy = 0;
}
if (iz == 0) {
if (fabs(p1[0]) < fabs(p1[2])) {
iz = 2;
ix = 0;
iy = 1;
}
} else {
if (fabs(p1[1]) < fabs(p1[2])) {
iz = 2;
ix = 0;
iy = 1;
}
}
// set p2 arbitrarily such that it's orthogonal to p1
p2[ix] = 1.0;
p2[iy] = 1.0;
p2[iz] = -(p1[ix] * p2[ix] + p1[iy] * p2[iy]) / p1[iz];
// normalize p2
norm = sqrt(p2[0] * p2[0] + p2[1] * p2[1] + p2[2] * p2[2]);
p2[0] = p2[0] / norm;
p2[1] = p2[1] / norm;
p2[2] = p2[2] / norm;
// Set p3 by taking the cross product p3=p2xp1
p3[0] = p1[1] * p2[2] - p1[2] * p2[1];
p3[1] = p1[2] * p2[0] - p1[0] * p2[2];
p3[2] = p1[0] * p2[1] - p1[1] * p2[0];
};
friend void pair_virial_fdotr_compute<PairBrownianKokkos>(PairBrownianKokkos*);
Kokkos::Random_XorShift64_Pool<DeviceType> rand_pool;
typedef typename Kokkos::Random_XorShift64_Pool<DeviceType>::generator_type rand_type;
};
}
#endif
#endif

170
src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
View File

@ -168,13 +168,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == HALF) {
if (force->newton_pair) {
if (vflag_atom) {
if (shearupdate) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,2,1>>(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,2,0>>(0,inum),*this);
}
} else if (vflag_global) {
if (vflag_either) {
if (shearupdate) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,1,1>>(0,inum),*this, ev);
} else {
@ -188,13 +182,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
} else {
if (vflag_atom) {
if (shearupdate) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,2,1>>(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,2,0>>(0,inum),*this);
}
} else if (vflag_global) {
if (vflag_either) {
if (shearupdate) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,1,1>>(0,inum),*this, ev);
} else {
@ -210,13 +198,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
} else { // HALFTHREAD
if (force->newton_pair) {
if (vflag_atom) {
if (shearupdate) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,2,1>>(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,2,0>>(0,inum),*this);
}
} else if (vflag_global) {
if (vflag_either) {
if (shearupdate) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,1,1>>(0,inum),*this, ev);
} else {
@ -230,13 +212,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
} else {
if (vflag_atom) {
if (shearupdate) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,2,1>>(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,2,0>>(0,inum),*this);
}
} else if (vflag_global) {
if (vflag_either) {
if (shearupdate) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,1,1>>(0,inum),*this, ev);
} else {
@ -277,9 +253,9 @@ void PairGranHookeHistoryKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG, int SHEARUPDATE>
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int SHEARUPDATE>
KOKKOS_INLINE_FUNCTION
void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG,SHEARUPDATE>, const int ii, EV_FLOAT &ev) const {
void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,SHEARUPDATE>, const int ii, EV_FLOAT &ev) const {
// The f and torque arrays are atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
@ -466,10 +442,8 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
a_torque(j,2) -= jrad*tor3;
}
if (EVFLAG == 2)
ev_tally_xyz_atom<NEIGHFLAG, NEWTON_PAIR>(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz);
if (EVFLAG == 1)
ev_tally_xyz<NEWTON_PAIR>(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz);
if (VFLAG)
ev_tally_xyz<NEIGHFLAG, NEWTON_PAIR>(ev, i, j, fx, fy, fz, delx, dely, delz);
}
a_f(i,0) += fx_i;
@ -481,89 +455,75 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
}
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG, int SHEARUPDATE>
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int SHEARUPDATE>
KOKKOS_INLINE_FUNCTION
void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG,SHEARUPDATE>, const int ii) const {
void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,SHEARUPDATE>, const int ii) const {
EV_FLOAT ev;
this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG,SHEARUPDATE>(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG,SHEARUPDATE>(), ii, ev);
}
template<class DeviceType>
template<int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void PairGranHookeHistoryKokkos<DeviceType>::ev_tally_xyz(EV_FLOAT &ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
{
F_FLOAT v[6];
v[0] = delx*fx;
v[1] = dely*fy;
v[2] = delz*fz;
v[3] = delx*fy;
v[4] = delx*fz;
v[5] = dely*fz;
if (NEWTON_PAIR) {
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];
}
}
this->template operator()<NEIGHFLAG,NEWTON_PAIR,VFLAG,SHEARUPDATE>(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,SHEARUPDATE>(), ii, ev);
}
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void PairGranHookeHistoryKokkos<DeviceType>::ev_tally_xyz_atom(EV_FLOAT & /*ev*/, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
void PairGranHookeHistoryKokkos<DeviceType>::ev_tally_xyz(EV_FLOAT &ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
{
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
F_FLOAT v[6];
const F_FLOAT v0 = delx*fx;
const F_FLOAT v1 = dely*fy;
const F_FLOAT v2 = delz*fz;
const F_FLOAT v3 = delx*fy;
const F_FLOAT v4 = delx*fz;
const F_FLOAT v5 = dely*fz;
v[0] = delx*fx;
v[1] = dely*fy;
v[2] = delz*fz;
v[3] = delx*fy;
v[4] = delx*fz;
v[5] = dely*fz;
if (NEWTON_PAIR || i < nlocal) {
v_vatom(i,0) += 0.5*v[0];
v_vatom(i,1) += 0.5*v[1];
v_vatom(i,2) += 0.5*v[2];
v_vatom(i,3) += 0.5*v[3];
v_vatom(i,4) += 0.5*v[4];
v_vatom(i,5) += 0.5*v[5];
if (vflag_global) {
if (NEWTON_PAIR) { // neigh half, newton on
ev.v[0] += v0;
ev.v[1] += v1;
ev.v[2] += v2;
ev.v[3] += v3;
ev.v[4] += v4;
ev.v[5] += v5;
} else { // neigh half, newton off
if (i < nlocal) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
if (j < nlocal) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
}
}
if (NEWTON_PAIR || j < nlocal) {
v_vatom(j,0) += 0.5*v[0];
v_vatom(j,1) += 0.5*v[1];
v_vatom(j,2) += 0.5*v[2];
v_vatom(j,3) += 0.5*v[3];
v_vatom(j,4) += 0.5*v[4];
v_vatom(j,5) += 0.5*v[5];
if (vflag_atom) {
if (NEWTON_PAIR || i < nlocal) {
v_vatom(i,0) += 0.5*v0;
v_vatom(i,1) += 0.5*v1;
v_vatom(i,2) += 0.5*v2;
v_vatom(i,3) += 0.5*v3;
v_vatom(i,4) += 0.5*v4;
v_vatom(i,5) += 0.5*v5;
}
if (NEWTON_PAIR || j < nlocal) {
v_vatom(j,0) += 0.5*v0;
v_vatom(j,1) += 0.5*v1;
v_vatom(j,2) += 0.5*v2;
v_vatom(j,3) += 0.5*v3;
v_vatom(j,4) += 0.5*v4;
v_vatom(j,5) += 0.5*v5;
}
}
}

17
src/KOKKOS/pair_gran_hooke_history_kokkos.h
View File

@ -32,7 +32,7 @@ namespace LAMMPS_NS {
template <class DeviceType>
class FixNeighHistoryKokkos;
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG, int SHEARUPDATE>
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int SHEARUPDATE>
struct TagPairGranHookeHistoryCompute {};
template <class DeviceType>
@ -47,23 +47,18 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory {
void compute(int, int) override;
void init_style() override;
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG, int SHEARUPDATE>
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int SHEARUPDATE>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG,SHEARUPDATE>, const int, EV_FLOAT &ev) const;
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG, int SHEARUPDATE>
void operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,SHEARUPDATE>, const int, EV_FLOAT &ev) const;
template<int NEIGHFLAG, int NEWTON_PAIR, int VFLAG, int SHEARUPDATE>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG,SHEARUPDATE>, const int) const;
void operator()(TagPairGranHookeHistoryCompute<NEIGHFLAG,NEWTON_PAIR,VFLAG,SHEARUPDATE>, const int) const;
template<int NEWTON_PAIR>
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void ev_tally_xyz(EV_FLOAT &ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
protected:
typename AT::t_x_array_randomread x;

1
src/accelerator_kokkos.h
View File

@ -59,6 +59,7 @@ class KokkosLMP {
void accelerator(int, char **) {}
int neigh_list_kokkos(int) { return 0; }
int neigh_count(int) { return 0; }
void newton_check() {};
};
class AtomKokkos : public Atom {

1
src/comm.cpp
View File

@ -75,6 +75,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
maxexchange = maxexchange_atom = maxexchange_fix = 0;
maxexchange_fix_dynamic = 0;
bufextra = BUFEXTRA;
bufextra_max = bufextra;
grid2proc = nullptr;
xsplit = ysplit = zsplit = nullptr;

1
src/comm.h
View File

@ -140,6 +140,7 @@ class Comm : protected Pointers {
int maxexchange_fix; // static contribution to maxexchange from Fixes
int maxexchange_fix_dynamic; // 1 if a fix has a dynamic contribution
int bufextra; // augment send buf size for an exchange atom
int bufextra_max;
int gridflag; // option for creating 3d grid
int mapflag; // option for mapping procs to 3d grid

12
src/comm_brick.cpp
View File

@ -133,9 +133,11 @@ void CommBrick::init()
{
Comm::init();
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
if (bufextra > bufextra_max) {
grow_send(maxsend+bufextra,2);
bufextra_max = bufextra;
}
// memory for multi style communication
// allocate in setup
@ -672,9 +674,11 @@ void CommBrick::exchange()
// only need to reset if a fix can dynamically add to size of single atom
if (maxexchange_fix_dynamic) {
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
if (bufextra > bufextra_max) {
grow_send(maxsend+bufextra,2);
bufextra_max = bufextra;
}
}
// subbox bounds for orthogonal or triclinic

6
src/comm_tiled.cpp
View File

@ -943,9 +943,11 @@ void CommTiled::exchange()
// only need to reset if a fix can dynamically add to size of single atom
if (maxexchange_fix_dynamic) {
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
if (bufextra > bufextra_max) {
grow_send(maxsend+bufextra,2);
bufextra = bufextra_max;
}
}
// domain properties used in exchange method and methods it calls

1
src/compute.h
View File

@ -144,6 +144,7 @@ class Compute : protected Pointers {
virtual void remove_bias(int, double *) {}
virtual void remove_bias_thr(int, double *, double *) {}
virtual void remove_bias_all() {}
virtual void remove_bias_all_kk() {}
virtual void reapply_bias_all() {}
virtual void restore_bias(int, double *) {}
virtual void restore_bias_thr(int, double *, double *) {}

3
src/compute_temp_sphere.cpp
View File

@ -14,6 +14,7 @@
#include "compute_temp_sphere.h"
#include "atom.h"
#include "atom_masks.h"
#include "domain.h"
#include "error.h"
#include "force.h"
@ -76,6 +77,8 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
if (!atom->omega_flag) error->all(FLERR, "Compute temp/sphere requires atom attribute omega");
if (!atom->radius_flag) error->all(FLERR, "Compute temp/sphere requires atom attribute radius");
datamask_modify = ALL_MASK & ~X_MASK;
}
/* ---------------------------------------------------------------------- */

18
src/fix.h
View File

@ -216,17 +216,17 @@ class Fix : protected Pointers {
virtual int pack_reverse_comm(int, int, double *) { return 0; }
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual void reset_grid(){};
virtual void reset_grid() {};
virtual void pack_forward_grid(int, void *, int, int *){};
virtual void unpack_forward_grid(int, void *, int, int *){};
virtual void pack_reverse_grid(int, void *, int, int *){};
virtual void unpack_reverse_grid(int, void *, int, int *){};
virtual void pack_remap_grid(int, void *, int, int *){};
virtual void unpack_remap_grid(int, void *, int, int *){};
virtual void pack_forward_grid(int, void *, int, int *) {};
virtual void unpack_forward_grid(int, void *, int, int *) {};
virtual void pack_reverse_grid(int, void *, int, int *) {};
virtual void unpack_reverse_grid(int, void *, int, int *) {};
virtual void pack_remap_grid(int, void *, int, int *) {};
virtual void unpack_remap_grid(int, void *, int, int *) {};
virtual int unpack_read_grid(int, char *) { return 0; };
virtual void pack_write_grid(int, void *){};
virtual void unpack_write_grid(int, void *, int *){};
virtual void pack_write_grid(int, void *) {};
virtual void unpack_write_grid(int, void *, int *) {};
virtual int get_grid_by_name(const std::string &, int &) { return -1; };
virtual void *get_grid_by_index(int) { return nullptr; };

8
src/fix_balance.h
View File

@ -43,9 +43,9 @@ class FixBalance : public Fix {
int nevery, lbstyle, nitermax;
double thresh, stopthresh;
std::string bstr;
int wtflag; // 1 for weighted balancing
int sortflag; // 1 for sorting comm messages
int reportonly; // 1 if skipping rebalancing and only computing imbalance
int wtflag; // 1 for weighted balancing
int sortflag; // 1 for sorting comm messages
int reportonly; // 1 if skipping rebalancing and only computing imbalance
double imbnow; // current imbalance factor
double imbprev; // imbalance factor before last rebalancing
@ -53,7 +53,7 @@ class FixBalance : public Fix {
double maxloadperproc; // max load on any processor
int itercount; // iteration count of last call to Balance
int pending;
bigint lastbalance; // last timestep balancing was attempted
bigint lastbalance; // last timestep balancing was attempted
class Balance *balance;
class Irregular *irregular;

2
src/fix_bond_history.h
View File

@ -62,7 +62,7 @@ class FixBondHistory : public Fix {
// to enable quick look up
std::map<std::pair<tagint, tagint>, std::vector<double>> cached_histories;
int *setflag; // Set by BondBPM, which bond types are used
int *setflag; // Set by BondBPM, which bond types are used
double **bondstore;
int stored_flag;
int ndata;

2
src/input.cpp
View File

@ -1687,6 +1687,8 @@ void Input::newton()
if (newton_pair || newton_bond) force->newton = 1;
else force->newton = 0;
if (lmp->kokkos) lmp->kokkos->newton_check();
}
/* ---------------------------------------------------------------------- */