ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

changed file names and added a lj12-5 function type in GPU pkg.

Browse Source
This commit is contained in:
yskmiyazaki
2022-07-08 18:04:04 +09:00
parent 311596fb4f
commit 116098022f
5 changed files with 75 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
src/GPU/Install.sh
View File

@ -121,10 +121,10 @@ action pair_lj_expand_coul_long_gpu.cpp pair_lj_expand_coul_long.cpp
action pair_lj_expand_coul_long_gpu.h pair_lj_expand_coul_long.cpp
action pair_lj_gromacs_gpu.cpp pair_lj_gromacs.cpp
action pair_lj_gromacs_gpu.h pair_lj_gromacs.h
action pair_lj_sdk_coul_long_gpu.cpp pair_lj_sdk_coul_long.cpp
action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp
action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp
action pair_lj_sdk_gpu.h pair_lj_sdk.cpp
action pair_lj_spica_coul_long_gpu.cpp pair_lj_spica_coul_long.cpp
action pair_lj_spica_coul_long_gpu.h pair_lj_spica_coul_long.cpp
action pair_lj_spica_gpu.cpp pair_lj_spica.cpp
action pair_lj_spica_gpu.h pair_lj_spica.cpp
action pair_mie_cut_gpu.cpp pair_mie_cut.cpp
action pair_mie_cut_gpu.h pair_mie_cut.h
action pair_morse_gpu.cpp

50
src/GPU/pair_lj_sdk_coul_long_gpu.cpp → src/GPU/pair_lj_spica_coul_long_gpu.cpp
View File

@ -15,7 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "pair_lj_sdk_coul_long_gpu.h"
#include "pair_lj_spica_coul_long_gpu.h"
#include "atom.h"
#include "domain.h"
@ -41,34 +41,34 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int sdkl_gpu_init(const int ntypes, double **cutsq, int **lj_type, double **host_lj1,
int spical_gpu_init(const int ntypes, double **cutsq, int **lj_type, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
void sdkl_gpu_clear();
int **sdkl_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
void spical_gpu_clear();
int **spical_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q, double *boxlo,
double *prd);
void sdkl_gpu_compute(const int ago, const int inum, const int nall, double **host_x,
void spical_gpu_compute(const int ago, const int inum, const int nall, double **host_x,
int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag,
const bool vflag, const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q, const int nlocal,
double *boxlo, double *prd);
double sdkl_gpu_bytes();
double spical_gpu_bytes();
#include "lj_sdk_common.h"
#include "lj_spica_common.h"
using namespace LJSDKParms;
using namespace LJSPICAParms;
/* ---------------------------------------------------------------------- */
PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
PairLJSDKCoulLong(lmp), gpu_mode(GPU_FORCE)
PairLJSPICACoulLongGPU::PairLJSPICACoulLongGPU(LAMMPS *lmp) :
PairLJSPICACoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
@ -81,14 +81,14 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
free all arrays
------------------------------------------------------------------------- */
PairLJSDKCoulLongGPU::~PairLJSDKCoulLongGPU()
PairLJSPICACoulLongGPU::~PairLJSPICACoulLongGPU()
{
sdkl_gpu_clear();
spical_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
void PairLJSPICACoulLongGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
@ -110,7 +110,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = sdkl_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi,
firstneigh = spical_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi,
atom->tag, atom->nspecial, atom->special, eflag, vflag,
eflag_atom, vflag_atom, host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo, domain->prd);
@ -119,7 +119,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sdkl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
spical_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
@ -142,9 +142,9 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJSDKCoulLongGPU::init_style()
void PairLJSPICACoulLongGPU::init_style()
{
if (!atom->q_flag) error->all(FLERR, "Pair style lj/sdk/coul/long/gpu requires atom attribute q");
if (!atom->q_flag) error->all(FLERR, "Pair style lj/spica/coul/long/gpu requires atom attribute q");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
@ -177,7 +177,7 @@ void PairLJSDKCoulLongGPU::init_style()
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
sdkl_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, force->special_lj,
spical_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, force->special_lj,
atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode,
screen, cut_ljsq, cut_coulsq, force->special_coul, force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success, error, world);
@ -187,15 +187,15 @@ void PairLJSDKCoulLongGPU::init_style()
/* ---------------------------------------------------------------------- */
double PairLJSDKCoulLongGPU::memory_usage()
double PairLJSPICACoulLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + sdkl_gpu_bytes();
return bytes + spical_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG>
void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh,
void PairLJSPICACoulLongGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh,
int **firstneigh)
{
int i, j, ii, jj;
@ -307,6 +307,14 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist, int *num
if (EFLAG)
evdwl =
r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
} else if (ljt == LJ12_5) {
const double r5inv = r2inv * r2inv * sqrt(r2inv);
const double r7inv = r5inv * r2inv;
forcelj = r5inv * (lj1[itype][jtype] * r7inv - lj2[itype][jtype]);
if (EFLAG)
evdwl =
r5inv * (lj3[itype][jtype] * r7inv - lj4[itype][jtype]) - offset[itype][jtype];
}
if (EFLAG) evdwl *= factor_lj;

15
src/GPU/pair_lj_sdk_coul_long_gpu.h → src/GPU/pair_lj_spica_coul_long_gpu.h
View File

@ -13,21 +13,22 @@
#ifdef PAIR_CLASS
// clang-format off
PairStyle(lj/sdk/coul/long/gpu,PairLJSDKCoulLongGPU);
PairStyle(lj/spica/coul/long/gpu,PairLJSPICACoulLongGPU);
PairStyle(lj/sdk/coul/long/gpu,PairLJSPICACoulLongGPU);
// clang-format on
#else
#ifndef LMP_PAIR_LJ_SDK_COUL_LONG_GPU_H
#define LMP_PAIR_LJ_SDK_COUL_LONG_GPU_H
#ifndef LMP_PAIR_LJ_SPICA_COUL_LONG_GPU_H
#define LMP_PAIR_LJ_SPICA_COUL_LONG_GPU_H
#include "pair_lj_sdk_coul_long.h"
#include "pair_lj_spica_coul_long.h"
namespace LAMMPS_NS {
class PairLJSDKCoulLongGPU : public PairLJSDKCoulLong {
class PairLJSPICACoulLongGPU : public PairLJSPICACoulLong {
public:
PairLJSDKCoulLongGPU(LAMMPS *lmp);
~PairLJSDKCoulLongGPU() override;
PairLJSPICACoulLongGPU(LAMMPS *lmp);
~PairLJSPICACoulLongGPU() override;
template <int, int> void cpu_compute(int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;

45
src/GPU/pair_lj_sdk_gpu.cpp → src/GPU/pair_lj_spica_gpu.cpp
View File

@ -15,7 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "pair_lj_sdk_gpu.h"
#include "pair_lj_spica_gpu.h"
#include "atom.h"
#include "domain.h"
@ -32,29 +32,29 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1,
int spica_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen);
void sdk_gpu_clear();
int **sdk_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
void spica_gpu_clear();
int **spica_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success);
void sdk_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type,
void spica_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start, const double cpu_time,
bool &success);
double sdk_gpu_bytes();
double spica_gpu_bytes();
#include "lj_sdk_common.h"
#include "lj_spica_common.h"
using namespace LJSDKParms;
using namespace LJSPICAParms;
/* ---------------------------------------------------------------------- */
PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
PairLJSPICAGPU::PairLJSPICAGPU(LAMMPS *lmp) : PairLJSPICA(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
@ -67,14 +67,14 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
free all arrays
------------------------------------------------------------------------- */
PairLJSDKGPU::~PairLJSDKGPU()
PairLJSPICAGPU::~PairLJSPICAGPU()
{
sdk_gpu_clear();
spica_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJSDKGPU::compute(int eflag, int vflag)
void PairLJSPICAGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
@ -97,7 +97,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
}
inum = atom->nlocal;
firstneigh =
sdk_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag,
spica_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag,
atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time, success);
} else {
@ -105,7 +105,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sdk_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
spica_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
@ -127,7 +127,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJSDKGPU::init_style()
void PairLJSPICAGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
@ -149,7 +149,7 @@ void PairLJSDKGPU::init_style()
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = sdk_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset,
int success = spica_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset,
force->special_lj, atom->nlocal, atom->nlocal + atom->nghost, mnf,
maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
@ -159,15 +159,15 @@ void PairLJSDKGPU::init_style()
/* ---------------------------------------------------------------------- */
double PairLJSDKGPU::memory_usage()
double PairLJSPICAGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + sdk_gpu_bytes();
return bytes + spica_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG>
void PairLJSDKGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, int **firstneigh)
void PairLJSPICAGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
@ -228,6 +228,13 @@ void PairLJSDKGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, i
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
} else if (ljt == LJ12_5) {
const double r5inv = r2inv * r2inv * sqrt(r2inv);
const double r7inv = r5inv * r2inv;
forcelj = r5inv * (lj1[itype][jtype] * r7inv - lj2[itype][jtype]);
if (EFLAG)
evdwl = r5inv * (lj3[itype][jtype] * r7inv - lj4[itype][jtype]) - offset[itype][jtype];
} else
continue;

15
src/GPU/pair_lj_sdk_gpu.h → src/GPU/pair_lj_spica_gpu.h
View File

@ -13,21 +13,22 @@
#ifdef PAIR_CLASS
// clang-format off
PairStyle(lj/sdk/gpu,PairLJSDKGPU);
PairStyle(lj/spica/gpu,PairLJSPICAGPU);
PairStyle(lj/sdk/gpu,PairLJSPICAGPU);
// clang-format on
#else
#ifndef LMP_PAIR_LJ_SDK_GPU_H
#define LMP_PAIR_LJ_SDK_GPU_H
#ifndef LMP_PAIR_LJ_SPICA_GPU_H
#define LMP_PAIR_LJ_SPICA_GPU_H
#include "pair_lj_sdk.h"
#include "pair_lj_spica.h"
namespace LAMMPS_NS {
class PairLJSDKGPU : public PairLJSDK {
class PairLJSPICAGPU : public PairLJSPICA {
public:
PairLJSDKGPU(LAMMPS *lmp);
~PairLJSDKGPU() override;
PairLJSPICAGPU(LAMMPS *lmp);
~PairLJSPICAGPU() override;
template <int, int> void cpu_compute(int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;