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Merge pull request #4009 from ndtrung81/gpu-updates-Dec23

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GPU package updates Dec 2023
This commit is contained in:
Axel Kohlmeyer
2023-12-13 11:59:10 -05:00
committed by GitHub
parent 98feaa00cb 569c23a1e6
commit 0c4a1cb21d
71 changed files with 9239 additions and 44 deletions
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4
cmake/Modules/Packages/GPU.cmake
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@ -151,10 +151,10 @@ if(GPU_API STREQUAL "CUDA")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)

11
cmake/presets/gpu-cuda.cmake Normal file
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@ -0,0 +1,11 @@
# preset that enables GPU and selects CUDA API
set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
set(GPU_PREC "mixed" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

16
doc/src/Commands_pair.rst
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@ -87,7 +87,7 @@ OPT.
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/slater/cut <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/slater/long (g) <pair_coul_slater>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/tt <pair_coul_tt>`
@ -110,7 +110,7 @@ OPT.
* :doc:`eam/he <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd <pair_mesodpd>`
* :doc:`edpd (g) <pair_mesodpd>`
* :doc:`eff/cut <pair_eff>`
* :doc:`eim (o) <pair_eim>`
* :doc:`exp6/rx (k) <pair_exp6_rx>`
@ -158,14 +158,14 @@ OPT.
* :doc:`lj/cut (gikot) <pair_lj>`
* :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/cut/soft (go) <pair_fep_soft>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long/cs <pair_cs>`
* :doc:`lj/cut/coul/long/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/long/soft (go) <pair_fep_soft>`
* :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
@ -202,7 +202,7 @@ OPT.
* :doc:`lubricate/poly (o) <pair_lubricate>`
* :doc:`lubricateU <pair_lubricateU>`
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_mesodpd>`
* :doc:`mdpd (g) <pair_mesodpd>`
* :doc:`mdpd/rhosum <pair_mesodpd>`
* :doc:`meam (k) <pair_meam>`
* :doc:`meam/ms (k) <pair_meam>`
@ -268,11 +268,11 @@ OPT.
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj <pair_sph_lj>`
* :doc:`sph/lj (g) <pair_sph_lj>`
* :doc:`sph/rhosum <pair_sph_rhosum>`
* :doc:`sph/taitwater <pair_sph_taitwater>`
* :doc:`sph/taitwater (g) <pair_sph_taitwater>`
* :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
* :doc:`spin/dipole/cut <pair_spin_dipole>`
* :doc:`spin/dipole/long <pair_spin_dipole>`

3
doc/src/pair_coul_slater.rst
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@ -1,6 +1,7 @@
.. index:: pair_style coul/slater
.. index:: pair_style coul/slater/cut
.. index:: pair_style coul/slater/long
.. index:: pair_style coul/slater/long/gpu
pair_style coul/slater command
==============================
@ -11,6 +12,8 @@ pair_style coul/slater/cut command
pair_style coul/slater/long command
===================================
Accelerator Variants: *coul/slater/long/gpu*
Syntax
""""""

6
doc/src/pair_fep_soft.rst
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@ -1,8 +1,10 @@
.. index:: pair_style lj/cut/soft
.. index:: pair_style lj/cut/soft/omp
.. index:: pair_style lj/cut/coul/cut/soft
.. index:: pair_style lj/cut/coul/cut/soft/gpu
.. index:: pair_style lj/cut/coul/cut/soft/omp
.. index:: pair_style lj/cut/coul/long/soft
.. index:: pair_style lj/cut/coul/long/soft/gpu
.. index:: pair_style lj/cut/coul/long/soft/omp
.. index:: pair_style lj/cut/tip4p/long/soft
.. index:: pair_style lj/cut/tip4p/long/soft/omp
@ -27,12 +29,12 @@ Accelerator Variants: *lj/cut/soft/omp*
pair_style lj/cut/coul/cut/soft command
=======================================
Accelerator Variants: *lj/cut/coul/cut/soft/omp*
Accelerator Variants: *lj/cut/coul/cut/soft/gpu*, *lj/cut/coul/cut/soft/omp*
pair_style lj/cut/coul/long/soft command
========================================
Accelerator Variants: *lj/cut/coul/long/soft/omp*
Accelerator Variants: *lj/cut/coul/long/soft/gpu*, *lj/cut/coul/long/soft/omp*
pair_style lj/cut/tip4p/long/soft command
=========================================

6
doc/src/pair_mesodpd.rst
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@ -1,14 +1,20 @@
.. index:: pair_style edpd
.. index:: pair_style edpd/gpu
.. index:: pair_style mdpd
.. index:: pair_style mdpd/gpu
.. index:: pair_style mdpd/rhosum
.. index:: pair_style tdpd
pair_style edpd command
=======================
Accelerator Variants: *edpd/gpu*
pair_style mdpd command
=======================
Accelerator Variants: *mdpd/gpu*
pair_style mdpd/rhosum command
==============================

3
doc/src/pair_sph_heatconduction.rst
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@ -1,8 +1,11 @@
.. index:: pair_style sph/heatconduction
.. index:: pair_style sph/heatconduction/gpu
pair_style sph/heatconduction command
=====================================
Accelerator Variants: *sph/heatconduction/gpu*
Syntax
""""""

3
doc/src/pair_sph_lj.rst
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@ -1,8 +1,11 @@
.. index:: pair_style sph/lj
.. index:: pair_style sph/lj/gpu
pair_style sph/lj command
=========================
Accelerator Variants: *sph/lj/gpu*
Syntax
""""""

3
doc/src/pair_sph_taitwater.rst
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@ -1,8 +1,11 @@
.. index:: pair_style sph/taitwater
.. index:: pair_style sph/taitwater/gpu
pair_style sph/taitwater command
================================
Accelerator Variants: *sph/taitwater/gpu*
Syntax
""""""

1
examples/PACKAGES/dpd-meso/mdpd/in.mdpd
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@ -16,6 +16,7 @@ neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
comm_modify vel yes
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd

2
lib/gpu/Makefile.linux_multi
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@ -65,7 +65,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC -allow-unsupported-compiler
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC -std=c++11
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias

2
lib/gpu/geryon/ocl_mat.h
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@ -54,6 +54,6 @@ namespace ucl_opencl {
#include "ucl_print.h"
#undef UCL_PRINT_ALLOW
} // namespace ucl_cudart
} // namespace ucl_opencl
#endif

8
lib/gpu/lal_amoeba.cpp
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@ -281,13 +281,7 @@ int AmoebaT::polar_real(const int eflag, const int vflag) {
const int BX=this->block_size();
const int GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
/*
const int cus = this->device->gpu->cus();
while (GX < cus && GX > 1) {
BX /= 2;
GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
}
*/
this->time_pair.start();
// Build the short neighbor list if not done yet

6
lib/gpu/lal_base_dpd.cpp
View File

@ -56,7 +56,8 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program,
const char *k_name, const int onetype) {
const char *k_name, const int onetype,
const int extra_fields) {
screen=_screen;
int gpu_nbor=0;
@ -75,7 +76,8 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
bool charge = false;
bool rot = false;
bool vel = true;
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel);
_extra_fields = extra_fields;
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel,_extra_fields/4);
if (success!=0)
return success;

5
lib/gpu/lal_base_dpd.h
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@ -53,7 +53,7 @@ class BaseDPD {
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const void *pair_program, const char *k_name,
const int onetype=0);
const int onetype=0, const int extra_fields=0);
/// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead();
@ -167,7 +167,6 @@ class BaseDPD {
/// Atom Data
Atom<numtyp,acctyp> *atom;
// ------------------------ FORCE/ENERGY DATA -----------------------
Answer<numtyp,acctyp> *ans;
@ -199,7 +198,7 @@ class BaseDPD {
protected:
bool _compiled;
int _block_size, _threads_per_atom, _onetype;
int _block_size, _threads_per_atom, _onetype, _extra_fields;
double _max_bytes, _max_an_bytes;
double _gpu_overhead, _driver_overhead;
UCL_D_Vec<int> *_nbor_data;

362
lib/gpu/lal_base_sph.cpp Normal file
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@ -0,0 +1,362 @@
/***************************************************************************
base_sph.cpp
-------------------
Trung Nguyen (U Chicago)
Base class for SPH pair styles needing per-particle data for position,
velocity, and type.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include "lal_base_sph.h"
namespace LAMMPS_AL {
#define BaseSPHT BaseSPH<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
template <class numtyp, class acctyp>
BaseSPHT::BaseSPH() : _compiled(false), _max_bytes(0) {
device=&global_device;
ans=new Answer<numtyp,acctyp>();
nbor=new Neighbor();
pair_program=nullptr;
ucl_device=nullptr;
#if defined(LAL_OCL_EV_JIT)
pair_program_noev=nullptr;
#endif
}
template <class numtyp, class acctyp>
BaseSPHT::~BaseSPH() {
delete ans;
delete nbor;
k_pair_fast.clear();
k_pair.clear();
if (pair_program) delete pair_program;
#if defined(LAL_OCL_EV_JIT)
k_pair_noev.clear();
if (pair_program_noev) delete pair_program_noev;
#endif
}
template <class numtyp, class acctyp>
int BaseSPHT::bytes_per_atom_atomic(const int max_nbors) const {
return device->atom.bytes_per_atom()+ans->bytes_per_atom()+
nbor->bytes_per_atom(max_nbors);
}
template <class numtyp, class acctyp>
int BaseSPHT::init_atomic(const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program,
const char *k_name, const int onetype,
const int extra_fields) {
screen=_screen;
int gpu_nbor=0;
if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_NEIGH)
gpu_nbor=1;
else if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_HYB_NEIGH)
gpu_nbor=2;
int _gpu_host=0;
int host_nlocal=hd_balancer.first_host_count(nlocal,gpu_split,gpu_nbor);
if (host_nlocal>0)
_gpu_host=1;
_threads_per_atom=device->threads_per_atom();
bool charge = false;
bool rot = false;
bool vel = true;
_extra_fields = extra_fields;
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel,_extra_fields/4);
if (success!=0)
return success;
if (ucl_device!=device->gpu) _compiled=false;
ucl_device=device->gpu;
atom=&device->atom;
_block_size=device->pair_block_size();
compile_kernels(*ucl_device,pair_program,k_name,onetype);
if (_threads_per_atom>1 && gpu_nbor==0) {
nbor->packing(true);
_nbor_data=&(nbor->dev_packed);
} else
_nbor_data=&(nbor->dev_nbor);
success = device->init_nbor(nbor,nlocal,host_nlocal,nall,maxspecial,_gpu_host,
max_nbors,cell_size,false,_threads_per_atom);
if (success!=0)
return success;
// Initialize host-device load balancer
hd_balancer.init(device,gpu_nbor,gpu_split);
// Initialize timers for the selected GPU
time_pair.init(*ucl_device);
time_pair.zero();
pos_tex.bind_float(atom->x,4);
vel_tex.bind_float(atom->v,4);
_max_an_bytes=ans->gpu_bytes()+nbor->gpu_bytes();
return success;
}
template <class numtyp, class acctyp>
void BaseSPHT::estimate_gpu_overhead() {
device->estimate_gpu_overhead(1,_gpu_overhead,_driver_overhead);
}
template <class numtyp, class acctyp>
void BaseSPHT::clear_atomic() {
// Output any timing information
acc_timers();
double avg_split=hd_balancer.all_avg_split();
_gpu_overhead*=hd_balancer.timestep();
_driver_overhead*=hd_balancer.timestep();
device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
_gpu_overhead,_driver_overhead,_threads_per_atom,screen);
time_pair.clear();
hd_balancer.clear();
nbor->clear();
ans->clear();
}
// ---------------------------------------------------------------------------
// Copy neighbor list from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int * BaseSPHT::reset_nbors(const int nall, const int inum, int *ilist,
int *numj, int **firstneigh, bool &success) {
success=true;
int mn=nbor->max_nbor_loop(inum,numj,ilist);
resize_atom(inum,nall,success);
resize_local(inum,mn,success);
if (!success)
return nullptr;
nbor->get_host(inum,ilist,numj,firstneigh,block_size());
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
if (bytes>_max_an_bytes)
_max_an_bytes=bytes;
return ilist;
}
// ---------------------------------------------------------------------------
// Build neighbor list on device
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
inline void BaseSPHT::build_nbor_list(const int inum, const int host_inum,
const int nall, double **host_x,
int *host_type, double *sublo,
double *subhi, tagint *tag,
int **nspecial, tagint **special,
bool &success) {
success=true;
resize_atom(inum,nall,success);
resize_local(inum,host_inum,nbor->max_nbors(),success);
if (!success)
return;
atom->cast_copy_x(host_x,host_type);
int mn;
nbor->build_nbor_list(host_x, inum, host_inum, nall, *atom, sublo, subhi,
tag, nspecial, special, success, mn, ans->error_flag);
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
if (bytes>_max_an_bytes)
_max_an_bytes=bytes;
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then calculate forces, virials,..
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void BaseSPHT::compute(const int f_ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const int nlocal) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
else if (eflag_in) eflag=1;
else eflag=0;
if (vatom) vflag=2;
else if (vflag_in) vflag=1;
else vflag=0;
#ifdef LAL_NO_BLOCK_REDUCE
if (eflag) eflag=2;
if (vflag) vflag=2;
#endif
set_kernel(eflag,vflag);
if (inum_full==0) {
host_start=0;
// Make sure textures are correct if realloc by a different hybrid style
resize_atom(0,nall,success);
zero_timers();
return;
}
int ago=hd_balancer.ago_first(f_ago);
int inum=hd_balancer.balance(ago,inum_full,cpu_time);
ans->inum(inum);
host_start=inum;
if (ago==0) {
reset_nbors(nall, inum, ilist, numj, firstneigh, success);
if (!success)
return;
}
atom->cast_x_data(host_x,host_type);
atom->cast_v_data(host_v,tag);
hd_balancer.start_timer();
atom->add_x_data(host_x,host_type);
atom->add_v_data(host_v,tag);
const int red_blocks=loop(eflag,vflag);
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,ilist,red_blocks);
device->add_ans_object(ans);
hd_balancer.stop_timer();
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary and then compute forces, virials, energies
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseSPHT::compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time, bool &success,
double **host_v) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
else if (eflag_in) eflag=1;
else eflag=0;
if (vatom) vflag=2;
else if (vflag_in) vflag=1;
else vflag=0;
#ifdef LAL_NO_BLOCK_REDUCE
if (eflag) eflag=2;
if (vflag) vflag=2;
#endif
set_kernel(eflag,vflag);
if (inum_full==0) {
host_start=0;
// Make sure textures are correct if realloc by a different hybrid style
resize_atom(0,nall,success);
zero_timers();
return nullptr;
}
hd_balancer.balance(cpu_time);
int inum=hd_balancer.get_gpu_count(ago,inum_full);
ans->inum(inum);
host_start=inum;
// Build neighbor list on GPU if necessary
if (ago==0) {
build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
sublo, subhi, tag, nspecial, special, success);
if (!success)
return nullptr;
atom->cast_v_data(host_v,tag);
hd_balancer.start_timer();
} else {
atom->cast_x_data(host_x,host_type);
atom->cast_v_data(host_v,tag);
hd_balancer.start_timer();
atom->add_x_data(host_x,host_type);
}
atom->add_v_data(host_v,tag);
*ilist=nbor->host_ilist.begin();
*jnum=nbor->host_acc.begin();
const int red_blocks=loop(eflag,vflag);
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
device->add_ans_object(ans);
hd_balancer.stop_timer();
return nbor->host_jlist.begin()-host_start;
}
template <class numtyp, class acctyp>
double BaseSPHT::host_memory_usage_atomic() const {
return device->atom.host_memory_usage()+nbor->host_memory_usage()+
4*sizeof(numtyp)+sizeof(BaseSPH<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void BaseSPHT::compile_kernels(UCL_Device &dev, const void *pair_str,
const char *kname, const int onetype) {
if (_compiled && _onetype==onetype)
return;
_onetype=onetype;
std::string s_fast=std::string(kname)+"_fast";
if (pair_program) delete pair_program;
pair_program=new UCL_Program(dev);
std::string oclstring = device->compile_string()+" -DEVFLAG=1";
if (_onetype) oclstring+=" -DONETYPE="+device->toa(_onetype);
pair_program->load_string(pair_str,oclstring.c_str(),nullptr,screen);
k_pair_fast.set_function(*pair_program,s_fast.c_str());
k_pair.set_function(*pair_program,kname);
pos_tex.get_texture(*pair_program,"pos_tex");
vel_tex.get_texture(*pair_program,"vel_tex");
#if defined(LAL_OCL_EV_JIT)
oclstring = device->compile_string()+" -DEVFLAG=0";
if (_onetype) oclstring+=" -DONETYPE="+device->toa(_onetype);
if (pair_program_noev) delete pair_program_noev;
pair_program_noev=new UCL_Program(dev);
pair_program_noev->load_string(pair_str,oclstring.c_str(),nullptr,screen);
k_pair_noev.set_function(*pair_program_noev,s_fast.c_str());
#else
k_pair_sel = &k_pair_fast;
#endif
_compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size);
#if defined(LAL_OCL_EV_JIT)
mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size));
#endif
if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz;
device->set_simd_size(mx_subgroup_sz);
}
#endif
}
template class BaseSPH<PRECISION,ACC_PRECISION>;
}

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/***************************************************************************
base_sph.h
-------------------
Trung Nguyen (U Chicago)
Base class for SPH pair styles needing per-particle data for position,
velocity, and type.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_BASE_SPH_H
#define LAL_BASE_DPD_H
#include "lal_device.h"
#include "lal_balance.h"
#include "mpi.h"
#ifdef USE_OPENCL
#include "geryon/ocl_texture.h"
#elif defined(USE_HIP)
#include "geryon/hip_texture.h"
#else
#include "geryon/nvd_texture.h"
#endif
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class BaseSPH {
public:
BaseSPH();
virtual ~BaseSPH();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
* \param k_name name for the kernel for force calculation
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init_atomic(const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const void *pair_program, const char *k_name,
const int onetype=0, const int extra_fields=0);
/// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead();
/// Check if there is enough storage for atom arrays and realloc if not
/** \param success set to false if insufficient memory **/
inline void resize_atom(const int inum, const int nall, bool &success) {
if (atom->resize(nall, success)) {
pos_tex.bind_float(atom->x,4);
vel_tex.bind_float(atom->v,4);
}
ans->resize(inum,success);
}
/// Check if there is enough storage for neighbors and realloc if not
/** \param nlocal number of particles whose nbors must be stored on device
* \param host_inum number of particles whose nbors need to copied to host
* \param current maximum number of neighbors
* \note olist_size=total number of local particles **/
inline void resize_local(const int inum, const int max_nbors, bool &success) {
nbor->resize(inum,max_nbors,success);
}
/// Check if there is enough storage for neighbors and realloc if not
/** \param nlocal number of particles whose nbors must be stored on device
* \param host_inum number of particles whose nbors need to copied to host
* \param current maximum number of neighbors
* \note host_inum is 0 if the host is performing neighboring
* \note nlocal+host_inum=total number local particles
* \note olist_size=0 **/
inline void resize_local(const int inum, const int host_inum,
const int max_nbors, bool &success) {
nbor->resize(inum,host_inum,max_nbors,success);
}
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear_atomic();
/// Returns memory usage on device per atom
int bytes_per_atom_atomic(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage_atomic() const;
/// Accumulate timers
inline void acc_timers() {
if (device->time_device()) {
nbor->acc_timers(screen);
time_pair.add_to_total();
atom->acc_timers();
ans->acc_timers();
}
}
/// Zero timers
inline void zero_timers() {
time_pair.zero();
atom->zero_timers();
ans->zero_timers();
}
/// Copy neighbor list from host
int * reset_nbors(const int nall, const int inum, int *ilist, int *numj,
int **firstneigh, bool &success);
/// Build neighbor list on device
void build_nbor_list(const int inum, const int host_inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, bool &success);
/// Pair loop with host neighboring
void compute(const int f_ago, const int inum_full, 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, tagint *tag,
double **v, const int nlocal);
/// Pair loop with device neighboring
int** compute(const int ago, const int inum_full, 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 **numj, const double cpu_time, bool &success,
double **v);
// -------------------------- DEVICE DATA -------------------------
/// Device Properties and Atom and Neighbor storage
Device<numtyp,acctyp> *device;
/// Geryon device
UCL_Device *ucl_device;
/// Device Timers
UCL_Timer time_pair;
/// Host device load balancer
Balance<numtyp,acctyp> hd_balancer;
/// LAMMPS pointer for screen output
FILE *screen;
// --------------------------- ATOM DATA --------------------------
/// Atom Data
Atom<numtyp,acctyp> *atom;
// ------------------------ FORCE/ENERGY DATA -----------------------
Answer<numtyp,acctyp> *ans;
// --------------------------- NBOR DATA ----------------------------
/// Neighbor data
Neighbor *nbor;
// ------------------------- DEVICE KERNELS -------------------------
UCL_Program *pair_program, *pair_program_noev;
UCL_Kernel k_pair_fast, k_pair, k_pair_noev, *k_pair_sel;
inline int block_size() { return _block_size; }
inline void set_kernel(const int eflag, const int vflag) {
#if defined(LAL_OCL_EV_JIT)
if (eflag || vflag) k_pair_sel = &k_pair_fast;
else k_pair_sel = &k_pair_noev;
#endif
}
// --------------------------- TEXTURES -----------------------------
UCL_Texture pos_tex;
UCL_Texture vel_tex;
// ------------------------- COMMON VARS ----------------------------
protected:
bool _compiled;
int _block_size, _threads_per_atom, _onetype, _extra_fields;
double _max_bytes, _max_an_bytes;
double _gpu_overhead, _driver_overhead;
UCL_D_Vec<int> *_nbor_data;
void compile_kernels(UCL_Device &dev, const void *pair_string,
const char *k, const int onetype);
virtual int loop(const int eflag, const int vflag) = 0;
};
}
#endif

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/***************************************************************************
coul_slater_long_ext.cpp
------------------------
Trung Nguyen (U Chicago)
Class for acceleration of the coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "coul_slater_long_cl.h"
#elif defined(USE_CUDART)
const char *coul_slater_long=0;
#else
#include "coul_slater_long_cubin.h"
#endif
#include "lal_coul_slater_long.h"
#include <cassert>
namespace LAMMPS_AL {
#define CoulSlaterLongT CoulSlaterLong<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> pair_gpu_device;
template <class numtyp, class acctyp>
CoulSlaterLongT::CoulSlaterLong() : BaseCharge<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
CoulSlaterLongT::~CoulSlaterLong() {
clear();
}
template <class numtyp, class acctyp>
int CoulSlaterLongT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int CoulSlaterLongT::init(const int ntypes, double **host_scale,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *_screen,
const double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, double lamda) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,coul_slater_long,"k_coul_slater_long");
if (success!=0)
return success;
int lj_types=ntypes;
shared_types=false;
int max_shared_types=this->device->max_shared_types();
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
scale.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,scale,host_write,host_scale);
sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<4; i++) {
host_write[i]=host_special_coul[i];
}
ucl_copy(sp_cl,host_write,4,false);
_cut_coulsq=host_cut_coulsq;
_qqrd2e=qqrd2e;
_g_ewald=g_ewald;
_lamda=lamda;
_allocated=true;
this->_max_bytes=scale.row_bytes()+sp_cl.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void CoulSlaterLongT::reinit(const int ntypes, double **host_scale) {
UCL_H_Vec<numtyp> hscale(_lj_types*_lj_types,*(this->ucl_device),
UCL_WRITE_ONLY);
this->atom->type_pack1(ntypes,_lj_types,scale,hscale,host_scale);
}
template <class numtyp, class acctyp>
void CoulSlaterLongT::clear() {
if (!_allocated)
return;
_allocated=false;
scale.clear();
sp_cl.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double CoulSlaterLongT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(CoulSlaterLong<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int CoulSlaterLongT::loop(const int eflag, const int vflag) {
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &scale, &sp_cl,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv,
&eflag, &vflag, &ainum, &nbor_pitch,
&this->atom->q, &_cut_coulsq, &_qqrd2e, &_g_ewald,
&_lamda, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &scale, &_lj_types, &sp_cl,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->q, &_cut_coulsq,
&_qqrd2e, &_g_ewald, &_lamda, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template class CoulSlaterLong<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// coul_slater_long.cu
// -------------------
// Trung Nguyen (U Chicago)
//
// Device code for acceleration of the coul/slater/long pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( q_tex,float);
#else
_texture_2d( pos_tex,int4);
_texture( q_tex,int2);
#endif
#else
#define pos_tex x_
#define q_tex q_
#endif
__kernel void k_coul_slater_long(const __global numtyp4 *restrict x_,
const __global numtyp *restrict scale,
const int lj_types,
const __global numtyp *restrict sp_cl_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_cl[4];
int n_stride;
local_allocate_store_charge();
sp_cl[0]=sp_cl_in[0];
sp_cl[1]=sp_cl_in[1];
sp_cl[2]=sp_cl_in[2];
sp_cl[3]=sp_cl_in[3];
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, virial[6];
if (EVFLAG) {
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp qtmp; fetch(qtmp,i,q_tex);
numtyp lamdainv = ucl_recip(lamda);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq < cut_coulsq) {
numtyp r2inv=ucl_recip(rsq);
numtyp force, prefactor, _erfc;
numtyp r = ucl_rsqrt(r2inv);
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
fetch(prefactor,j,q_tex);
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
force = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force *= r2inv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
acctyp energy;
if (EVFLAG) energy=(acctyp)0.0;
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}
__kernel void k_coul_slater_long_fast(const __global numtyp4 *restrict x_,
const __global numtyp *restrict scale_in,
const __global numtyp *restrict sp_cl_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp scale[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_cl[4];
int n_stride;
local_allocate_store_charge();
if (tid<4)
sp_cl[tid]=sp_cl_in[tid];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES)
scale[tid]=scale_in[tid];
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, virial[6];
if (EVFLAG) {
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
__syncthreads();
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
numtyp qtmp; fetch(qtmp,i,q_tex);
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
numtyp lamdainv = ucl_recip(lamda);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int mtype=itype+jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq < cut_coulsq) {
numtyp r2inv=ucl_recip(rsq);
numtyp force, prefactor, _erfc;
numtyp r = ucl_rsqrt(r2inv);
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * scale[mtype] * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
force = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force *= r2inv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
acctyp energy;
if (EVFLAG) energy=(acctyp)0.0;
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}

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/***************************************************************************
coul_slater_long.h
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_Coul_Slater_Long_H
#define LAL_Coul_Slater_Long_H
#include "lal_base_charge.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class CoulSlaterLong : public BaseCharge<numtyp, acctyp> {
public:
CoulSlaterLong();
~CoulSlaterLong();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **scale,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, const double lamda);
/// Send updated coeffs from host to device (to be compatible with fix adapt)
void reinit(const int ntypes, double **scale);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
// --------------------------- TYPE DATA --------------------------
/// scale
UCL_D_Vec<numtyp> scale;
/// Special Coul values [0-3]
UCL_D_Vec<numtyp> sp_cl;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
numtyp _cut_coulsq, _qqrd2e, _g_ewald, _lamda;
protected:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

145
lib/gpu/lal_coul_slater_long_ext.cpp Normal file
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@ -0,0 +1,145 @@
/***************************************************************************
coul_slater_long_ext.cpp
------------------------
Trung Nguyen (U Chicago)
Functions for LAMMPS access to coul/slater/long acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_coul_slater_long.h"
using namespace std;
using namespace LAMMPS_AL;
static CoulSlaterLong<PRECISION,ACC_PRECISION> CSLMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int csl_gpu_init(const int ntypes, double **host_scale,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, const double lamda) {
CSLMF.clear();
gpu_mode=CSLMF.device->gpu_mode();
double gpu_split=CSLMF.device->particle_split();
int first_gpu=CSLMF.device->first_device();
int last_gpu=CSLMF.device->last_device();
int world_me=CSLMF.device->world_me();
int gpu_rank=CSLMF.device->gpu_rank();
int procs_per_gpu=CSLMF.device->procs_per_gpu();
CSLMF.device->init_message(screen,"coul/slater/long",first_gpu,last_gpu);
bool message=false;
if (CSLMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=CSLMF.init(ntypes, host_scale, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_coulsq,
host_special_coul, qqrd2e, g_ewald, lamda);
CSLMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=CSLMF.init(ntypes, host_scale, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_coulsq,
host_special_coul, qqrd2e, g_ewald, lamda);
CSLMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
CSLMF.estimate_gpu_overhead();
return init_ok;
}
// ---------------------------------------------------------------------------
// Copy updated coeffs from host to device
// ---------------------------------------------------------------------------
void csl_gpu_reinit(const int ntypes, double **host_scale) {
int world_me=CSLMF.device->world_me();
int gpu_rank=CSLMF.device->gpu_rank();
int procs_per_gpu=CSLMF.device->procs_per_gpu();
if (world_me==0)
CSLMF.reinit(ntypes, host_scale);
CSLMF.device->world_barrier();
for (int i=0; i<procs_per_gpu; i++) {
if (gpu_rank==i && world_me!=0)
CSLMF.reinit(ntypes, host_scale);
CSLMF.device->serialize_init();
}
}
void csl_gpu_clear() {
CSLMF.clear();
}
int** csl_gpu_compute_n(const int ago, const int inum_full,
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) {
return CSLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_q, boxlo, prd);
}
void csl_gpu_compute(const int ago, const int inum_full, 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) {
CSLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,
host_q,nlocal,boxlo,prd);
}
double csl_gpu_bytes() {
return CSLMF.host_memory_usage();
}

38
lib/gpu/lal_device.cpp
View File

@ -364,6 +364,12 @@ int DeviceT::init_device(MPI_Comm /*world*/, MPI_Comm replica, const int ngpu,
} else
_neighbor_shared.setup_auto_cell_size(false,_user_cell_size,_simd_size);
#ifndef LAL_USE_OLD_NEIGHBOR
_use_old_nbor_build = 0;
#else
_use_old_nbor_build = 1;
#endif
return flag;
}
@ -510,9 +516,13 @@ int DeviceT::init(Answer<numtyp,acctyp> &ans, const bool charge,
gpu_nbor=1;
else if (_gpu_mode==Device<numtyp,acctyp>::GPU_HYB_NEIGH)
gpu_nbor=2;
// NOTE: enforce the hybrid mode (binning on the CPU)
// when not using sorting on the device
#if !defined(USE_CUDPP) && !defined(USE_HIP_DEVICE_SORT)
if (gpu_nbor==1) gpu_nbor=2;
#endif
// or when the device supports subgroups
#ifndef LAL_USE_OLD_NEIGHBOR
if (gpu_nbor==1) gpu_nbor=2;
#endif
@ -886,19 +896,31 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer<numtyp,acctyp> &ans,
}
if (times[5] > 0.0)
fprintf(screen,"Device Overhead: %.4f s.\n",times[5]/_replica_size);
fprintf(screen,"Average split: %.4f.\n",avg_split);
fprintf(screen,"Lanes / atom: %d.\n",threads_per_atom);
fprintf(screen,"Vector width: %d.\n", simd_size());
fprintf(screen,"Prefetch mode: ");
if (_nbor_prefetch==2) fprintf(screen,"Intrinsics.\n");
else if (_nbor_prefetch==1) fprintf(screen,"API.\n");
else fprintf(screen,"None.\n");
fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
if (nbor.gpu_nbor()==2)
fprintf(screen,"CPU Neighbor: %.4f s.\n",times[8]/_replica_size);
fprintf(screen,"CPU Cast/Pack: %.4f s.\n",times[4]/_replica_size);
fprintf(screen,"CPU Driver_Time: %.4f s.\n",times[6]/_replica_size);
fprintf(screen,"CPU Idle_Time: %.4f s.\n",times[7]/_replica_size);
fprintf(screen,"Average split: %.4f.\n",avg_split);
fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
fprintf(screen,"Prefetch mode: ");
if (_nbor_prefetch==2) fprintf(screen,"Intrinsics.\n");
else if (_nbor_prefetch==1) fprintf(screen,"API.\n");
else fprintf(screen,"None.\n");
fprintf(screen,"Vector width: %d.\n", simd_size());
fprintf(screen,"Lanes / atom: %d.\n",threads_per_atom);
fprintf(screen,"Pair block: %d.\n",_block_pair);
fprintf(screen,"Neigh block: %d.\n",_block_nbor_build);
if (nbor.gpu_nbor()==2) {
fprintf(screen,"Neigh mode: Hybrid (binning on host)");
if (_use_old_nbor_build == 1) fprintf(screen," - legacy\n");
else fprintf(screen," with subgroup support\n");
} else if (nbor.gpu_nbor()==1) {
fprintf(screen,"Neigh mode: Device");
if (_use_old_nbor_build == 1) fprintf(screen," - legacy\n");
else fprintf(screen," - with subgroup support\n");
} else if (nbor.gpu_nbor()==0)
fprintf(screen,"Neigh mode: Host\n");
fprintf(screen,"-------------------------------------");
fprintf(screen,"--------------------------------\n\n");

1
lib/gpu/lal_device.h
View File

@ -347,6 +347,7 @@ class Device {
int _pppm_block, _block_nbor_build, _block_cell_2d, _block_cell_id;
int _max_shared_types, _max_bio_shared_types, _pppm_max_spline;
int _nbor_prefetch;
int _use_old_nbor_build;
UCL_Program *dev_program;
UCL_Kernel k_zero, k_info;

285
lib/gpu/lal_edpd.cpp Normal file
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@ -0,0 +1,285 @@
/***************************************************************************
edpd.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the edpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "edpd_cl.h"
#elif defined(USE_CUDART)
const char *edpd=0;
#else
#include "edpd_cubin.h"
#endif
#include "lal_edpd.h"
#include <cassert>
namespace LAMMPS_AL {
#define EDPDT EDPD<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
EDPDT::EDPD() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
_max_q_size = 0;
}
template <class numtyp, class acctyp>
EDPDT::~EDPD() {
clear();
}
template <class numtyp, class acctyp>
int EDPDT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int EDPDT::init(const int ntypes,
double **host_cutsq, double **host_a0,
double **host_gamma, double **host_cut,
double **host_power, double **host_kappa,
double **host_powerT, double **host_cutT,
double ***host_sc, double ***host_kc, double *host_mass,
double *host_special_lj,
const int power_flag, const int kappa_flag,
const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// T and cv
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,edpd,"k_edpd",onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma,
host_cut);
coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff2,host_write,host_power,host_kappa,
host_powerT,host_cutT);
UCL_H_Vec<numtyp> dview_mass(ntypes, *(this->ucl_device), UCL_WRITE_ONLY);
for (int i = 0; i < ntypes; i++)
dview_mass[i] = host_mass[i];
mass.alloc(ntypes,*(this->ucl_device), UCL_READ_ONLY);
ucl_copy(mass,dview_mass,false);
if (host_sc) {
UCL_H_Vec<numtyp4> dview(lj_types*lj_types,*(this->ucl_device),UCL_WRITE_ONLY);;
sc.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
int n = 0;
for (int i = 1; i < ntypes; i++)
for (int j = 1; j < ntypes; j++) {
dview[n].x = host_sc[i][j][0];
dview[n].y = host_sc[i][j][1];
dview[n].z = host_sc[i][j][2];
dview[n].w = host_sc[i][j][3];
n++;
}
ucl_copy(sc,dview,false);
}
if (host_kc) {
UCL_H_Vec<numtyp4> dview(lj_types*lj_types,*(this->ucl_device),UCL_WRITE_ONLY);;
kc.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
int n = 0;
for (int i = 1; i < ntypes; i++)
for (int j = 1; j < ntypes; j++) {
dview[n].x = host_kc[i][j][0];
dview[n].y = host_kc[i][j][1];
dview[n].z = host_kc[i][j][2];
dview[n].w = host_kc[i][j][3];
n++;
}
ucl_copy(kc,dview,false);
}
UCL_H_Vec<numtyp> host_rsq(lj_types*lj_types,*(this->ucl_device),
UCL_WRITE_ONLY);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,cutsq,host_rsq,host_cutsq);
double special_sqrt[4];
special_sqrt[0] = sqrt(host_special_lj[0]);
special_sqrt[1] = sqrt(host_special_lj[1]);
special_sqrt[2] = sqrt(host_special_lj[2]);
special_sqrt[3] = sqrt(host_special_lj[3]);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(special_sqrt,4,*(this->ucl_device));
ucl_copy(sp_sqrt,dview,false);
_power_flag = power_flag;
_kappa_flag = kappa_flag;
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_max_q_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
Q.alloc(_max_q_size,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_allocated=true;
this->_max_bytes=coeff.row_bytes()+coeff2.row_bytes()+Q.row_bytes()+
sc.row_bytes()+kc.row_bytes()+mass.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes()+sp_sqrt.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void EDPDT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
coeff2.clear();
sc.clear();
kc.clear();
Q.clear();
mass.clear();
cutsq.clear();
sp_lj.clear();
sp_sqrt.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double EDPDT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(EDPD<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void EDPDT::update_flux(void **flux_ptr) {
*flux_ptr=Q.host.begin();
Q.update_host(_max_q_size,false);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int EDPDT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// Resize Q array if necessary
if (nall > _max_q_size) {
_max_q_size=static_cast<int>(static_cast<double>(nall)*1.10);
Q.resize(_max_q_size);
}
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = edpd_temp[i];
v.y = edpd_cv[i];
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &coeff2, &mass,
&sc, &kc, &sp_lj, &sp_sqrt, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &Q, &eflag, &vflag,
&_power_flag, &_kappa_flag, &ainum, &nbor_pitch,
&this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &coeff2, &mass,
&sc, &kc, &_lj_types, &sp_lj, &sp_sqrt,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &Q, &eflag, &vflag,
&_power_flag, &_kappa_flag, &ainum, &nbor_pitch,
&this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void EDPDT::get_extra_data(double *host_T, double *host_cv) {
edpd_temp = host_T;
edpd_cv = host_cv;
}
template class EDPD<PRECISION,ACC_PRECISION>;
}

619
lib/gpu/lal_edpd.cu Normal file
View File

@ -0,0 +1,619 @@
// **************************************************************************
// edpd.cu
// -------------------
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the edpd pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#define EPSILON (numtyp)1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
#if (SHUFFLE_AVAIL == 0)
#define store_heatflux(Qi, ii, inum, tid, t_per_atom, offset, Q) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add1(t_per_atom, red_acc, offset, tid, Qi); \
} \
if (offset==0 && ii<inum) { \
Q[ii]=Qi; \
}
#else
#define store_heatflux(Qi, ii, inum, tid, t_per_atom, offset, Q) \
if (t_per_atom>1) { \
simd_reduce_add1(t_per_atom,Qi); \
} \
if (offset==0 && ii<inum) { \
Q[ii]=Qi; \
}
#endif
#define MIN(A,B) ((A) < (B) ? (A) : (B))
#define MAX(A,B) ((A) < (B) ? (B) : (A))
// note the change in coeff: coeff.x = a0, coeff.y = gamma, coeff.z = cut (no sigma)
__kernel void k_edpd(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp4 *restrict coeff2,
const __global numtyp *restrict mass,
const __global numtyp4 *restrict sc,
const __global numtyp4 *restrict kc,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global numtyp *restrict sp_sqrt,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp *restrict Q,
const int eflag, const int vflag,
const int power_flag, const int kappa_flag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp Qi = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp mass_itype = mass[itype];
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp4 Tcvi = extra[i];
numtyp Ti = Tcvi.x;
numtyp cvi = Tcvi.y;
numtyp factor_dpd;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<cutsq[mtype]) {
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp vijeij = dot*rinv;
const numtyp coeffx=coeff[mtype].x; // a0[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // gamma[itype][jtype]
const numtyp coeffz=coeff[mtype].z; // cut[itype][jtype]
const numtyp4 Tcvj = extra[j];
numtyp Tj = Tcvj.x;
numtyp cvj = Tcvj.y;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
numtyp T_ij=(numtyp)0.5*(Ti+Tj);
numtyp4 T_pow;
T_pow.x = T_ij - (numtyp)1.0;
T_pow.y = T_pow.x*T_pow.x;
T_pow.z = T_pow.x*T_pow.y;
T_pow.w = T_pow.x*T_pow.z;
numtyp coeff2x = coeff2[mtype].x; //power[itype][jtype]
numtyp coeff2y = coeff2[mtype].y; //kappa[itype][jtype]
numtyp coeff2z = coeff2[mtype].z; //powerT[itype][jtype]
numtyp coeff2w = coeff2[mtype].w; //cutT[itype][jtype]
numtyp power_d = coeff2x;
if (power_flag) {
numtyp factor = (numtyp)1.0;
factor += sc[mtype].x*T_pow.x + sc[mtype].y*T_pow.y +
sc[mtype].z*T_pow.z + sc[mtype].w*T_pow.w;
power_d *= factor;
}
power_d = MAX((numtyp)0.01,power_d);
numtyp wc = (numtyp)1.0 - r/coeffz; // cut[itype][jtype]
wc = MAX((numtyp)0.0,MIN((numtyp)1.0,wc));
numtyp wr = ucl_pow(wc, (numtyp)0.5*power_d);
numtyp kboltz = (numtyp)1.0;
numtyp GammaIJ = coeffy; // gamma[itype][jtype]
numtyp SigmaIJ = (numtyp)4.0*GammaIJ*kboltz*Ti*Tj/(Ti+Tj);
SigmaIJ = ucl_sqrt(SigmaIJ);
numtyp force = coeffx*T_ij*wc; // a0[itype][jtype]
force -= GammaIJ *wr*wr *dot*rinv;
force += SigmaIJ * wr *randnum * dtinvsqrt;
force *= factor_dpd*rinv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// heat transfer
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
numtyp randnumT = (numtyp)0;
saru(tag1, tag2, seed+tag1+tag2, timestep, randnumT); // randomT->gaussian();
randnumT = MAX((numtyp)-5.0,MIN(randnum,(numtyp)5.0));
numtyp kappaT = coeff2y; // kappa[itype][jtype]
if (kappa_flag) {
numtyp factor = (numtyp)1.0;
factor += kc[mtype].x*T_pow.x + kc[mtype].y*T_pow.y +
kc[mtype].z*T_pow.z + kc[mtype].w*T_pow.w;
kappaT *= factor;
}
numtyp kij = cvi*cvj*kappaT * T_ij*T_ij;
numtyp alphaij = ucl_sqrt((numtyp)2.0*kboltz*kij);
numtyp dQc = kij * wrT*wrT * (Tj - Ti)/(Ti*Tj);
numtyp dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass_itype ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cvi+cvj);
numtyp dQr = alphaij * wrT * dtinvsqrt * randnumT;
Qi += (dQc + dQd + dQr );
}
if (EVFLAG && eflag) {
numtyp e = (numtyp)0.5*coeffx*T_ij*coeffz * wc*wc;
energy+=factor_dpd*e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
store_heatflux(Qi,ii,inum,tid,t_per_atom,offset,Q);
}
__kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp *restrict mass,
const __global numtyp4 *restrict sc_in,
const __global numtyp4 *restrict kc_in,
const __global numtyp *restrict sp_lj_in,
const __global numtyp *restrict sp_sqrt_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp *restrict Q,
const int eflag, const int vflag,
const int power_flag, const int kappa_flag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 sc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 kc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
coeff2[tid]=coeff2_in[tid];
sc[tid]=sc_in[tid];
kc[tid]=kc_in[tid];
}
__syncthreads();
#else
const numtyp coeffx=coeff_in[ONETYPE].x; // a0[itype][jtype]
const numtyp coeffy=coeff_in[ONETYPE].y; // gamma[itype][jtype]
const numtyp coeffz=coeff_in[ONETYPE].z; // cut[itype][jtype]
const numtyp coeff2x=coeff2_in[ONETYPE].x; // power[itype][jtype]
const numtyp coeff2y=coeff2_in[ONETYPE].y; // kappa[itype][jtype]
const numtyp coeff2z=coeff2_in[ONETYPE].z; // powerT[itype][jtype]
const numtyp coeff2w=coeff2_in[ONETYPE].w; // cutT[itype][jtype]
const numtyp cutsq_p=cutsq[ONETYPE];
const numtyp scx=sc_in[ONETYPE].x;
const numtyp scy=sc_in[ONETYPE].y;
const numtyp scz=sc_in[ONETYPE].z;
const numtyp scw=sc_in[ONETYPE].w;
const numtyp kcx=kc_in[ONETYPE].x;
const numtyp kcy=kc_in[ONETYPE].y;
const numtyp kcz=kc_in[ONETYPE].z;
const numtyp kcw=kc_in[ONETYPE].w;
#endif
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp Qi = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
numtyp mass_itype = mass[iw];
#ifndef ONETYPE
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp4 Tcvi = extra[i];
numtyp Ti = Tcvi.x;
numtyp cvi = Tcvi.y;
#ifndef ONETYPE
numtyp factor_dpd;
#endif
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
factor_dpd = sp_lj[sbmask(j)];
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=cutsq[mtype];
#endif
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp vijeij = dot*rinv;
#ifndef ONETYPE
const numtyp coeffx=coeff[mtype].x; // a0[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // gamma[itype][jtype]
const numtyp coeffz=coeff[mtype].z; // cut[itype][jtype]
const numtyp coeff2x=coeff2[mtype].x; // power[itype][jtype]
const numtyp coeff2y=coeff2[mtype].y; // kappa[itype][jtype]
const numtyp coeff2z=coeff2[mtype].z; // powerT[itype][jtype]
const numtyp coeff2w=coeff2[mtype].w; // cutT[itype][jtype]
const numtyp scx = sc[mtype].x;
const numtyp scy = sc[mtype].y;
const numtyp scz = sc[mtype].z;
const numtyp scw = sc[mtype].w;
const numtyp kcx = kc[mtype].x;
const numtyp kcy = kc[mtype].y;
const numtyp kcz = kc[mtype].z;
const numtyp kcw = kc[mtype].w;
#endif
const numtyp4 Tcvj = extra[j];
numtyp Tj = Tcvj.x;
numtyp cvj = Tcvj.y;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
numtyp T_ij=(numtyp)0.5*(Ti+Tj);
numtyp4 T_pow;
T_pow.x = T_ij - (numtyp)1.0;
T_pow.y = T_pow.x*T_pow.x;
T_pow.z = T_pow.x*T_pow.y;
T_pow.w = T_pow.x*T_pow.z;
numtyp power_d = coeff2x; // power[itype][jtype]
if (power_flag) {
numtyp factor = (numtyp)1.0;
factor += scx*T_pow.x + scy*T_pow.y + scz*T_pow.z + scw*T_pow.w;
power_d *= factor;
}
power_d = MAX((numtyp)0.01,power_d);
numtyp wc = (numtyp)1.0 - r/coeffz; // cut[itype][jtype]
wc = MAX((numtyp)0.0,MIN((numtyp)1.0,wc));
numtyp wr = ucl_pow((numtyp)wc, (numtyp)0.5*power_d);
numtyp kboltz = (numtyp)1.0;
numtyp GammaIJ = coeffy; // gamma[itype][jtype]
numtyp SigmaIJ = (numtyp)4.0*GammaIJ*kboltz*Ti*Tj/(Ti+Tj);
SigmaIJ = ucl_sqrt(SigmaIJ);
numtyp force = coeffx*T_ij*wc; // a0[itype][jtype]
force -= GammaIJ *wr*wr *dot*rinv;
force += SigmaIJ* wr *randnum * dtinvsqrt;
#ifndef ONETYPE
force *= factor_dpd*rinv;
#else
force *= rinv;
#endif
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// heat transfer
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
numtyp randnumT = (numtyp)0;
saru(tag1, tag2, seed+tag1+tag2, timestep, randnumT); // randomT->gaussian();
randnumT = MAX((numtyp)-5.0,MIN(randnum,(numtyp)5.0));
numtyp kappaT = coeff2y; // kappa[itype][jtype]
if (kappa_flag) {
numtyp factor = (numtyp)1.0;
factor += kcx*T_pow.x + kcy*T_pow.y + kcz*T_pow.z + kcw*T_pow.w;
kappaT *= factor;
}
numtyp kij = cvi*cvj*kappaT * T_ij*T_ij;
numtyp alphaij = ucl_sqrt((numtyp)2.0*kboltz*kij);
numtyp dQc = kij * wrT*wrT * (Tj - Ti )/(Ti*Tj);
numtyp dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass_itype ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cvi+cvj);
numtyp dQr = alphaij * wrT * dtinvsqrt * randnumT;
Qi += (dQc + dQd + dQr );
}
if (EVFLAG && eflag) {
numtyp e = (numtyp)0.5*coeffx*T_ij*coeffz * wc*wc;
#ifndef ONETYPE
energy+=factor_dpd*e;
#else
energy+=e;
#endif
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv);
store_heatflux(Qi,ii,inum,tid,t_per_atom,offset,Q);
}

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lib/gpu/lal_edpd.h Normal file
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/***************************************************************************
edpd.h
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the edpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_EDPD_H
#define LAL_EDPD_H
#include "lal_base_dpd.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class EDPD : public BaseDPD<numtyp, acctyp> {
public:
EDPD();
~EDPD();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq, double **host_a0,
double **host_gamma, double **host_cut, double **host_power,
double **host_kappa, double **host_powerT, double **host_cutT,
double ***host_sc, double ***host_kc, double *host_mass,
double *host_special_lj, const int power_flag, const int kappa_flag,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, const double gpu_split,
FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
void get_extra_data(double *host_T, double *host_cv);
/// copy Q (flux) from device to host
void update_flux(void **flux_ptr);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = a0, coeff.y = gamma, coeff.z = cut
UCL_D_Vec<numtyp4> coeff;
/// coeff2.x = power, coeff2.y = kappa, coeff2.z = powerT, coeff2.w = cutT
UCL_D_Vec<numtyp4> coeff2;
UCL_D_Vec<numtyp4> kc, sc;
UCL_D_Vec<numtyp> cutsq;
/// per-type array
UCL_D_Vec<numtyp> mass;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Per-atom arrays
UCL_Vector<acctyp,acctyp> Q;
int _max_q_size;
int _power_flag, _kappa_flag;
/// pointer to host data
double *edpd_temp, *edpd_cv;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

142
lib/gpu/lal_edpd_ext.cpp Normal file
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@ -0,0 +1,142 @@
/***************************************************************************
edpd_ext.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to edpd acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_edpd.h"
using namespace std;
using namespace LAMMPS_AL;
static EDPD<PRECISION,ACC_PRECISION> EDPDMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int edpd_gpu_init(const int ntypes, double **cutsq, double **host_a0,
double **host_gamma, double **host_cut, double **host_power,
double **host_kappa, double **host_powerT, double **host_cutT,
double ***host_sc, double ***host_kc, double *host_mass,
double *special_lj, const int power_flag, const int kappa_flag,
const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
EDPDMF.clear();
gpu_mode=EDPDMF.device->gpu_mode();
double gpu_split=EDPDMF.device->particle_split();
int first_gpu=EDPDMF.device->first_device();
int last_gpu=EDPDMF.device->last_device();
int world_me=EDPDMF.device->world_me();
int gpu_rank=EDPDMF.device->gpu_rank();
int procs_per_gpu=EDPDMF.device->procs_per_gpu();
EDPDMF.device->init_message(screen,"edpd",first_gpu,last_gpu);
bool message=false;
if (EDPDMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=EDPDMF.init(ntypes, cutsq, host_a0, host_gamma, host_cut,
host_power, host_kappa, host_powerT,
host_cutT, host_sc, host_kc, host_mass,
special_lj, power_flag, kappa_flag,
inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
EDPDMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=EDPDMF.init(ntypes, cutsq, host_a0, host_gamma, host_cut,
host_power, host_kappa, host_powerT, host_cutT,
host_sc, host_kc, host_mass,
special_lj, power_flag, kappa_flag,
inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
EDPDMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
EDPDMF.estimate_gpu_overhead();
return init_ok;
}
void edpd_gpu_clear() {
EDPDMF.clear();
}
int ** edpd_gpu_compute_n(const int ago, const int inum_full, 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_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
return EDPDMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
}
void edpd_gpu_compute(const int ago, const int inum_full, 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, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
EDPDMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void edpd_gpu_get_extra_data(double *host_T, double *host_cv) {
EDPDMF.get_extra_data(host_T, host_cv);
}
void edpd_gpu_update_flux(void **flux_ptr) {
EDPDMF.update_flux(flux_ptr);
}
double edpd_gpu_bytes() {
return EDPDMF.host_memory_usage();
}

8
lib/gpu/lal_hippo.cpp
View File

@ -603,13 +603,7 @@ int HippoT::polar_real(const int eflag, const int vflag) {
const int BX=this->block_size();
const int GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
/*
const int cus = this->device->gpu->cus();
while (GX < cus && GX > 1) {
BX /= 2;
GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
}
*/
this->time_pair.start();
// Build the short neighbor list if not done yet

2
lib/gpu/lal_lj_coul_long.h
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@ -78,7 +78,7 @@ class LJCoulLong : public BaseCharge<numtyp, acctyp> {
numtyp _cut_coulsq, _qqrd2e, _g_ewald;
private:
protected:
bool _allocated;
int loop(const int eflag, const int vflag);
};

174
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@ -0,0 +1,174 @@
/***************************************************************************
lj_coul_long_soft.cpp
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the lj/cut/coul/long/soft pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "lj_coul_long_soft_cl.h"
#elif defined(USE_CUDART)
const char *lj_coul_long_soft=0;
#else
#include "lj_coul_long_soft_cubin.h"
#endif
#include "lal_lj_coul_long_soft.h"
#include <cassert>
namespace LAMMPS_AL {
#define LJCoulLongSoftT LJCoulLongSoft<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
LJCoulLongSoftT::LJCoulLongSoft() : BaseCharge<numtyp,acctyp>(),
_allocated(false) {
}
template <class numtyp, class acctyp>
LJCoulLongSoftT::~LJCoulLongSoft() {
clear();
}
template <class numtyp, class acctyp>
int LJCoulLongSoftT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int LJCoulLongSoftT::init(const int ntypes,
double **host_cutsq, double **host_lj1,
double **host_lj2, double **host_lj3,
double **host_lj4, double **host_offset, double **host_epsilon,
double *host_special_lj, const int nlocal,
const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *_screen,
double **host_cut_ljsq, const double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
_screen,lj_coul_long_soft,"k_lj_coul_long_soft");
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
int max_shared_types=this->device->max_shared_types();
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
host_cutsq, host_cut_ljsq);
lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
host_offset, host_epsilon);
sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<4; i++) {
host_write[i]=host_special_lj[i];
host_write[i+4]=host_special_coul[i];
}
ucl_copy(sp_lj,host_write,8,false);
_cut_coulsq=host_cut_coulsq;
_qqrd2e=qqrd2e;
_g_ewald=g_ewald;
_allocated=true;
this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+sp_lj.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void LJCoulLongSoftT::reinit(const int ntypes, double **host_cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **host_offset, double **host_epsilon, double **host_cut_ljsq) {
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(_lj_types*_lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<_lj_types*_lj_types; i++)
host_write[i]=0.0;
this->atom->type_pack4(ntypes,_lj_types,lj1,host_write,host_lj1,host_lj2,
host_cutsq, host_cut_ljsq);
this->atom->type_pack4(ntypes,_lj_types,lj3,host_write,host_lj3,host_lj4,
host_offset, host_epsilon);
}
template <class numtyp, class acctyp>
void LJCoulLongSoftT::clear() {
if (!_allocated)
return;
_allocated=false;
lj1.clear();
lj3.clear();
sp_lj.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double LJCoulLongSoftT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(LJCoulLongSoft<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int LJCoulLongSoftT::loop(const int eflag, const int vflag) {
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &lj1, &lj3, &sp_lj,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag,
&vflag, &ainum, &nbor_pitch, &this->atom->q,
&_cut_coulsq, &_qqrd2e, &_g_ewald,
&this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &lj1, &lj3,
&_lj_types, &sp_lj, &this->nbor->dev_nbor,
&this->_nbor_data->begin(), &this->ans->force,
&this->ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->atom->q, &_cut_coulsq,
&_qqrd2e, &_g_ewald, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template class LJCoulLongSoft<PRECISION,ACC_PRECISION>;
}

290
lib/gpu/lal_lj_coul_long_soft.cu Normal file
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@ -0,0 +1,290 @@
// **************************************************************************
// lj_coul_long_soft.cu
// -------------------
// Trung Nguyen (U Chicago)
//
// Device code for acceleration of the lj/cut/coul/long/soft pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin :
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( q_tex,float);
#else
_texture_2d( pos_tex,int4);
_texture( q_tex,int2);
#endif
#else
#define pos_tex x_
#define q_tex q_
#endif
__kernel void k_lj_coul_long_soft(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1,
const __global numtyp4 *restrict lj3,
const int lj_types,
const __global numtyp *restrict sp_lj_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp g_ewald, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_lj[8];
int n_stride;
local_allocate_store_charge();
sp_lj[0]=sp_lj_in[0];
sp_lj[1]=sp_lj_in[1];
sp_lj[2]=sp_lj_in[2];
sp_lj[3]=sp_lj_in[3];
sp_lj[4]=sp_lj_in[4];
sp_lj[5]=sp_lj_in[5];
sp_lj[6]=sp_lj_in[6];
sp_lj[7]=sp_lj_in[7];
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, e_coul, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
numtyp qtmp; fetch(qtmp,i,q_tex);
int itype=ix.w;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_lj, factor_coul;
factor_lj = sp_lj[sbmask(j)];
factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<lj1[mtype].z) {
numtyp r2inv=ucl_recip(rsq);
numtyp forcecoul, force_lj, force, prefactor, _erfc;
numtyp denc, denlj, r4sig6;
if (rsq < lj1[mtype].w) {
r4sig6 = rsq*rsq / lj1[mtype].y;
denlj = lj3[mtype].x + rsq*r4sig6;
force_lj = lj1[mtype].x * lj3[mtype].w *
((numtyp)48.0*r4sig6/(denlj*denlj*denlj) - (numtyp)24.0*r4sig6/(denlj*denlj));
} else
force_lj = (numtyp)0.0;
if (rsq < cut_coulsq) {
numtyp r = ucl_rsqrt(r2inv);
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
fetch(prefactor,j,q_tex);
denc = ucl_sqrt(lj3[mtype].y + rsq);
prefactor *= qqrd2e * lj1[mtype].x * qtmp / (denc*denc*denc);
forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2-factor_coul);
} else
forcecoul = (numtyp)0.0;
force = factor_lj * force_lj + forcecoul;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
if (rsq < cut_coulsq) {
prefactor *= (denc*denc);
e_coul += prefactor*(_erfc-factor_coul);
}
if (rsq < lj1[mtype].w) {
numtyp e= lj1[mtype].x * (numtyp)4.0 * lj3[mtype].w *
((numtyp)1.0/(denlj*denlj) - (numtyp)1.0/denlj);
energy+=factor_lj*(e-lj3[mtype].z);
}
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}
__kernel void k_lj_coul_long_soft_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1_in,
const __global numtyp4 *restrict lj3_in,
const __global numtyp *restrict sp_lj_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp *restrict q_,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp g_ewald, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp4 lj1[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 lj3[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[8];
int n_stride;
local_allocate_store_charge();
if (tid<8)
sp_lj[tid]=sp_lj_in[tid];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
lj1[tid]=lj1_in[tid];
if (EVFLAG && eflag)
lj3[tid]=lj3_in[tid];
}
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, e_coul, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
__syncthreads();
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
numtyp qtmp; fetch(qtmp,i,q_tex);
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_lj, factor_coul;
factor_lj = sp_lj[sbmask(j)];
factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int mtype=itype+jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<lj1[mtype].z) {
numtyp forcecoul, force_lj, force, prefactor, _erfc;
numtyp denc, denlj, r4sig6;
if (rsq < lj1[mtype].w) {
r4sig6 = rsq*rsq / lj1[mtype].y;
denlj = lj3[mtype].x + rsq*r4sig6;
force_lj = lj1[mtype].x * lj3[mtype].w *
((numtyp)48.0*r4sig6/(denlj*denlj*denlj) - (numtyp)24.0*r4sig6/(denlj*denlj));
} else
force_lj = (numtyp)0.0;
if (rsq < cut_coulsq) {
numtyp r = ucl_sqrt(rsq);
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
fetch(prefactor,j,q_tex);
denc = ucl_sqrt(lj3[mtype].y + rsq);
prefactor *= qqrd2e * lj1[mtype].x * qtmp / (denc*denc*denc);
forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2-factor_coul);
} else
forcecoul = (numtyp)0.0;
force = forcecoul + factor_lj*force_lj;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
if (rsq < cut_coulsq) {
prefactor *= (denc*denc);
e_coul += prefactor*(_erfc-factor_coul);
}
if (rsq < lj1[mtype].w) {
numtyp e= lj1[mtype].x * (numtyp)4.0 * lj3[mtype].w *
((numtyp)1.0/(denlj*denlj) - (numtyp)1.0/denlj);
energy+=factor_lj*(e-lj3[mtype].z);
}
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}

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/***************************************************************************
lj_coul_long_soft.h
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the lj/cut/coul/long/soft pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_LJ_COUL_LONG_SOFT_H
#define LAL_LJ_COUL_LONG_SOFT_H
#include "lal_base_charge.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class LJCoulLongSoft : public BaseCharge<numtyp, acctyp> {
public:
LJCoulLongSoft();
~LJCoulLongSoft();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **host_offset, double **host_epsilon, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen, double **host_cut_ljsq,
const double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
/// Send updated coeffs from host to device (to be compatible with fix adapt)
void reinit(const int ntypes, double **host_cutsq,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **host_offset, double **host_epsilon, double **host_cut_ljsq);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
// --------------------------- TYPE DATA --------------------------
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cutsq_vdw
UCL_D_Vec<numtyp4> lj1;
/// lj3.x = lj3, lj3.y = lj4, lj3.z = offset, lj3.w = epsilon
UCL_D_Vec<numtyp4> lj3;
/// Special LJ values [0-3] and Special Coul values [4-7]
UCL_D_Vec<numtyp> sp_lj;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
numtyp _cut_coulsq, _qqrd2e, _g_ewald;
protected:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
lj_coul_long_soft_ext.cpp
-------------------------
Trung Nguyen (U Chicago)
Functions for LAMMPS access to lj/cut/coul/long/soft acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_lj_coul_long_soft.h"
using namespace std;
using namespace LAMMPS_AL;
static LJCoulLongSoft<PRECISION,ACC_PRECISION> LJCLSMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int ljcls_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double **epsilon, double *special_lj, const int inum,
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) {
LJCLSMF.clear();
gpu_mode=LJCLSMF.device->gpu_mode();
double gpu_split=LJCLSMF.device->particle_split();
int first_gpu=LJCLSMF.device->first_device();
int last_gpu=LJCLSMF.device->last_device();
int world_me=LJCLSMF.device->world_me();
int gpu_rank=LJCLSMF.device->gpu_rank();
int procs_per_gpu=LJCLSMF.device->procs_per_gpu();
LJCLSMF.device->init_message(screen,"lj/cut/coul/long/soft",first_gpu,last_gpu);
bool message=false;
if (LJCLSMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=LJCLSMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
offset, epsilon, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_ljsq,
host_cut_coulsq, host_special_coul, qqrd2e, g_ewald);
LJCLSMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=LJCLSMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
offset, epsilon, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_ljsq,
host_cut_coulsq, host_special_coul, qqrd2e, g_ewald);
LJCLSMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
LJCLSMF.estimate_gpu_overhead();
return init_ok;
}
// ---------------------------------------------------------------------------
// Copy updated coeffs from host to device
// ---------------------------------------------------------------------------
void ljcls_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double **epsilon, double **host_cut_ljsq) {
int world_me=LJCLSMF.device->world_me();
int gpu_rank=LJCLSMF.device->gpu_rank();
int procs_per_gpu=LJCLSMF.device->procs_per_gpu();
if (world_me==0)
LJCLSMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
offset, epsilon, host_cut_ljsq);
LJCLSMF.device->world_barrier();
for (int i=0; i<procs_per_gpu; i++) {
if (gpu_rank==i && world_me!=0)
LJCLSMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
offset, epsilon, host_cut_ljsq);
LJCLSMF.device->gpu_barrier();
}
}
void ljcls_gpu_clear() {
LJCLSMF.clear();
}
int** ljcls_gpu_compute_n(const int ago, const int inum_full,
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) {
return LJCLSMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_q, boxlo, prd);
}
void ljcls_gpu_compute(const int ago, const int inum_full, 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) {
LJCLSMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,
host_q,nlocal,boxlo,prd);
}
double ljcls_gpu_bytes() {
return LJCLSMF.host_memory_usage();
}

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/***************************************************************************
lj_coul_soft.cpp
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the lj/cut/coul/cut/soft pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndtrung@uchicago.edu
***************************************************************************/
#if defined(USE_OPENCL)
#include "lj_coul_soft_cl.h"
#elif defined(USE_CUDART)
const char *lj_coul_soft=0;
#else
#include "lj_coul_soft_cubin.h"
#endif
#include "lal_lj_coul_soft.h"
#include <cassert>
namespace LAMMPS_AL {
#define LJCoulSoftT LJCoulSoft<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
LJCoulSoftT::LJCoulSoft() : BaseCharge<numtyp,acctyp>(),
_allocated(false) {
}
template <class numtyp, class acctyp>
LJCoulSoftT::~LJCoulSoft() {
clear();
}
template <class numtyp, class acctyp>
int LJCoulSoftT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int LJCoulSoftT::init(const int ntypes,
double **host_cutsq, double **host_lj1,
double **host_lj2, double **host_lj3,
double **host_lj4, double **host_offset, double **host_epsilon,
double *host_special_lj, const int nlocal,
const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *_screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
_screen,lj_coul_soft,"k_lj_coul_soft");
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
int max_shared_types=this->device->max_shared_types();
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
host_cut_ljsq, host_cut_coulsq);
lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
host_offset, host_epsilon);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq);
sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<4; i++) {
host_write[i]=host_special_lj[i];
host_write[i+4]=host_special_coul[i];
}
ucl_copy(sp_lj,host_write,8,false);
_qqrd2e=qqrd2e;
_allocated=true;
this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+
sp_lj.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void LJCoulSoftT::clear() {
if (!_allocated)
return;
_allocated=false;
lj1.clear();
lj3.clear();
cutsq.clear();
sp_lj.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double LJCoulSoftT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(LJCoulSoft<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int LJCoulSoftT::loop(const int eflag, const int vflag) {
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &lj1, &lj3, &sp_lj,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag,
&vflag, &ainum, &nbor_pitch, &this->atom->q,
&cutsq, &_qqrd2e, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &lj1, &lj3, &_lj_types, &sp_lj,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv,
&eflag, &vflag, &ainum, &nbor_pitch, &this->atom->q,
&cutsq, &_qqrd2e, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template class LJCoulSoft<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// lj_coul_soft.cu
// -------------------
// Trung Nguyen (U Chicago)
//
// Device code for acceleration of the lj/coul/cut/soft pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin :
// email : ndtrung@uchicago.edu
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( q_tex,float);
#else
_texture_2d( pos_tex,int4);
_texture( q_tex,int2);
#endif
#else
#define pos_tex x_
#define q_tex q_
#endif
__kernel void k_lj_coul_soft(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1,
const __global numtyp4 *restrict lj3,
const int lj_types,
const __global numtyp *restrict sp_lj_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const __global numtyp *restrict cutsq,
const numtyp qqrd2e, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_lj[8];
int n_stride;
local_allocate_store_charge();
sp_lj[0]=sp_lj_in[0];
sp_lj[1]=sp_lj_in[1];
sp_lj[2]=sp_lj_in[2];
sp_lj[3]=sp_lj_in[3];
sp_lj[4]=sp_lj_in[4];
sp_lj[5]=sp_lj_in[5];
sp_lj[6]=sp_lj_in[6];
sp_lj[7]=sp_lj_in[7];
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, e_coul, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
numtyp qtmp; fetch(qtmp,i,q_tex);
int itype=ix.w;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_lj, factor_coul;
factor_lj = sp_lj[sbmask(j)];
factor_coul = sp_lj[sbmask(j)+4];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<cutsq[mtype]) {
numtyp forcecoul, force_lj, force;
numtyp r4sig6, denlj, denc;
if (rsq < lj1[mtype].z) {
r4sig6 = rsq*rsq / lj1[mtype].y;
denlj = lj3[mtype].x + rsq*r4sig6;
force_lj = lj1[mtype].x * lj3[mtype].w *
((numtyp)48.0*r4sig6/(denlj*denlj*denlj) - (numtyp)24.0*r4sig6/(denlj*denlj));
force_lj *= factor_lj;
} else
force_lj = (numtyp)0.0;
if (rsq < lj1[mtype].w) {
fetch(forcecoul,j,q_tex);
denc = sqrt(lj3[mtype].y + rsq);
forcecoul *= qqrd2e * lj1[mtype].x * qtmp / (denc*denc*denc);
forcecoul *= factor_coul;
} else
forcecoul = (numtyp)0.0;
force = force_lj + forcecoul;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
if (rsq < lj1[mtype].w) {
e_coul += forcecoul*(denc*denc);
}
if (rsq < lj1[mtype].z) {
numtyp e = lj1[mtype].x * (numtyp)4.0 * lj3[mtype].w *
((numtyp)1.0/(denlj*denlj) - (numtyp)1.0/denlj);
energy+=factor_lj*(e-lj3[mtype].z);
}
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}
__kernel void k_lj_coul_soft_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1_in,
const __global numtyp4 *restrict lj3_in,
const __global numtyp *restrict sp_lj_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const __global numtyp *restrict _cutsq,
const numtyp qqrd2e, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp4 lj1[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 lj3[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[8];
int n_stride;
local_allocate_store_charge();
if (tid<8)
sp_lj[tid]=sp_lj_in[tid];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
lj1[tid]=lj1_in[tid];
cutsq[tid]=_cutsq[tid];
if (EVFLAG && eflag)
lj3[tid]=lj3_in[tid];
}
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, e_coul, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
__syncthreads();
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
numtyp qtmp; fetch(qtmp,i,q_tex);
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
for ( ; nbor<nbor_end; nbor+=n_stride) {
int j=dev_packed[nbor];
numtyp factor_lj, factor_coul;
factor_lj = sp_lj[sbmask(j)];
factor_coul = sp_lj[sbmask(j)+4];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int mtype=itype+jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq[mtype]) {
numtyp forcecoul, force_lj, force;
numtyp r4sig6, denlj, denc;
if (rsq < lj1[mtype].z) { // cut_ljsq[itype][jtype]
r4sig6 = rsq*rsq / lj1[mtype].y;
denlj = lj3[mtype].x + rsq*r4sig6;
force_lj = lj1[mtype].x * lj3[mtype].w *
((numtyp)48.0*r4sig6/(denlj*denlj*denlj) - (numtyp)24.0*r4sig6/(denlj*denlj));
force_lj *= factor_lj;
} else
force_lj = (numtyp)0.0;
if (rsq < lj1[mtype].w) { // cut_coulsq[itype][jtype]
fetch(forcecoul,j,q_tex);
denc = sqrt(lj3[mtype].y + rsq);
forcecoul *= qqrd2e * lj1[mtype].x * qtmp / (denc*denc*denc);
forcecoul *= factor_coul;
} else
forcecoul = (numtyp)0.0;
force = force_lj + forcecoul;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
if (rsq < lj1[mtype].w) {
e_coul += forcecoul*(denc*denc);
}
if (rsq < lj1[mtype].z) {
numtyp e = lj1[mtype].x * (numtyp)4.0 * lj3[mtype].w *
((numtyp)1.0/(denlj*denlj) - (numtyp)1.0/denlj);
energy+=factor_lj*(e-lj3[mtype].z);
}
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}

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/***************************************************************************
lj_coul_soft.h
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the lj/cut/coul/cut/soft pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndtrung@uchicago.edu
***************************************************************************/
#ifndef LAL_LJ_COUL_SOFT_H
#define LAL_LJ_COUL_SOFT_H
#include "lal_base_charge.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class LJCoulSoft : public BaseCharge<numtyp, acctyp> {
public:
LJCoulSoft();
~LJCoulSoft();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **host_offset, double **host_epsilon, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen, double **host_cut_ljsq,
double **host_cut_coulsq, double *host_special_coul,
const double qqrd2e);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
// --------------------------- TYPE DATA --------------------------
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq_vdw, lj1.w = cutsq_coul
UCL_D_Vec<numtyp4> lj1;
/// lj3.x = lj3, lj3.y = lj4, lj3.z = offset, lj3.w = epsilon
UCL_D_Vec<numtyp4> lj3;
/// cutsq
UCL_D_Vec<numtyp> cutsq;
/// Special LJ values [0-3] and Special Coul values [4-7]
UCL_D_Vec<numtyp> sp_lj;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
numtyp _qqrd2e;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
lj_coul_soft_ext.cpp
-------------------
Trung Nguyen (U Chicago)
Functions for LAMMPS access to lj/cut/coul/cut/soft acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndtrung@uchicago.edu
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_lj_coul_soft.h"
using namespace std;
using namespace LAMMPS_AL;
static LJCoulSoft<PRECISION,ACC_PRECISION> LJCSMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int ljcs_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double **epsilon, double *special_lj, const int inum,
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) {
LJCSMF.clear();
gpu_mode=LJCSMF.device->gpu_mode();
double gpu_split=LJCSMF.device->particle_split();
int first_gpu=LJCSMF.device->first_device();
int last_gpu=LJCSMF.device->last_device();
int world_me=LJCSMF.device->world_me();
int gpu_rank=LJCSMF.device->gpu_rank();
int procs_per_gpu=LJCSMF.device->procs_per_gpu();
LJCSMF.device->init_message(screen,"lj/cut/coul/cut/soft",first_gpu,last_gpu);
bool message=false;
if (LJCSMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=LJCSMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3,
host_lj4, offset, epsilon, special_lj, inum, nall, max_nbors,
maxspecial, cell_size, gpu_split, screen, host_cut_ljsq,
host_cut_coulsq, host_special_coul, qqrd2e);
LJCSMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=LJCSMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
offset, epsilon, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_ljsq,
host_cut_coulsq, host_special_coul, qqrd2e);
LJCSMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
LJCSMF.estimate_gpu_overhead();
return init_ok;
}
void ljcs_gpu_clear() {
LJCSMF.clear();
}
int** ljcs_gpu_compute_n(const int ago, const int inum_full,
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) {
return LJCSMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_q, boxlo, prd);
}
void ljcs_gpu_compute(const int ago, const int inum_full, 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) {
LJCSMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,firstneigh,eflag,
vflag,eatom,vatom,host_start,cpu_time,success,host_q,
nlocal,boxlo,prd);
}
double ljcs_gpu_bytes() {
return LJCSMF.host_memory_usage();
}

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/***************************************************************************
mdpd.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the mdpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "mdpd_cl.h"
#elif defined(USE_CUDART)
const char *mdpd=0;
#else
#include "mdpd_cubin.h"
#endif
#include "lal_mdpd.h"
#include <cassert>
namespace LAMMPS_AL {
#define MDPDT MDPD<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
MDPDT::MDPD() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
MDPDT::~MDPD() {
clear();
}
template <class numtyp, class acctyp>
int MDPDT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int MDPDT::init(const int ntypes,
double **host_cutsq, double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma,
double **host_cut, double **host_cut_r,
double *host_special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// rho
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,mdpd,"k_mdpd",onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_A_att,host_B_rep,
host_gamma,host_sigma);
coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff2,host_write,host_cut,host_cut_r,
host_cutsq);
UCL_H_Vec<numtyp> host_rsq(lj_types*lj_types,*(this->ucl_device),
UCL_WRITE_ONLY);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,cutsq,host_rsq,host_cutsq);
double special_sqrt[4];
special_sqrt[0] = sqrt(host_special_lj[0]);
special_sqrt[1] = sqrt(host_special_lj[1]);
special_sqrt[2] = sqrt(host_special_lj[2]);
special_sqrt[3] = sqrt(host_special_lj[3]);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(special_sqrt,4,*(this->ucl_device));
ucl_copy(sp_sqrt,dview,false);
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+coeff2.row_bytes()+cutsq.row_bytes()+
sp_lj.row_bytes()+sp_sqrt.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void MDPDT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
coeff2.clear();
cutsq.clear();
sp_lj.clear();
sp_sqrt.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double MDPDT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(MDPD<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int MDPDT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = mdpd_rho[i];
v.y = 0;
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &coeff2,
&sp_lj, &sp_sqrt, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &coeff2,
&_lj_types, &sp_lj, &sp_sqrt, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void MDPDT::get_extra_data(double *host_rho) {
mdpd_rho = host_rho;
}
template class MDPD<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// mdpd.cu
// -------------------
// Trung Dac Nguyen (ORNL)
//
// Device code for acceleration of the mdpd pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : December 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#define EPSILON (numtyp)1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
#define MIN(A,B) ((A) < (B) ? (A) : (B))
#define MAX(A,B) ((A) < (B) ? (B) : (A))
// coeff.x = A_att, coeff.y = B_rep, coeff.z = gamma, coeff.w = sigma
// coeff2.x = cut, coeff2.y = cut_r, coeff2.z = cutsq
__kernel void k_mdpd(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp4 *restrict coeff2,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global numtyp *restrict sp_sqrt,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp rhoi = extra[i].x;
numtyp factor_dpd, factor_sqrt;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<coeff2[mtype].z) { // cutsq[itype][jtype]
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp A_attij = coeff[mtype].x;
numtyp B_repij = coeff[mtype].y;
numtyp gammaij = coeff[mtype].z;
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
numtyp wc = (numtyp)1.0 - r/cutij;
numtyp wc_r = (numtyp)1.0 - r/cut_rij;
wc_r = MAX(wc_r,(numtyp)0.0);
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = A_att * wc + B_rep*(rhoi+rhoj)*wc_r
// drag force = -gamma * wr^2 * (delx dot delv) / r
// random force = sigma * wr * rnd * dtinvsqrt;
numtyp force = A_attij*wc + B_repij*(rhoi+rhoj)*wc_r;
force -= gammaij*wr*wr*dot*rinv;
force += sigmaij*wr*randnum*dtinvsqrt;
force *= factor_dpd*rinv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*A_attij*cutij * wr*wr + (numtyp)0.5*B_repij*cut_rij*(rhoi+rhoj)*wc_r*wc_r;
energy+=factor_dpd*e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}
__kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp *restrict sp_lj_in,
const __global numtyp *restrict sp_sqrt_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
coeff2[tid]=coeff2_in[tid];
}
__syncthreads();
#else
const numtyp A_attij=coeff_in[ONETYPE].x;
const numtyp B_repij=coeff_in[ONETYPE].y;
const numtyp gammaij=coeff_in[ONETYPE].z;
const numtyp sigmaij=coeff_in[ONETYPE].w;
const numtyp cutij=coeff2_in[ONETYPE].x;
const numtyp cut_rij=coeff2_in[ONETYPE].y;
const numtyp cutsqij=coeff2_in[ONETYPE].z;
const numtyp cutsq_p=cutsq[ONETYPE];
#endif
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
#ifndef ONETYPE
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp rhoi = extra[i].x;
#ifndef ONETYPE
numtyp factor_dpd;
#endif
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
factor_dpd = sp_lj[sbmask(j)];
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=cutsq[mtype];
#endif
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
#ifndef ONETYPE
numtyp A_attij = coeff[mtype].x;
numtyp B_repij = coeff[mtype].y;
numtyp gammaij = coeff[mtype].z;
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
#endif
numtyp wc = (numtyp)1.0 - r/cutij;
numtyp wc_r = (numtyp)1.0 - r/cut_rij;
wc_r = MAX(wc_r,(numtyp)0.0);
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = A_att * wc + B_rep*(rhoi+rhoj)*wc_r
// drag force = -gamma * wr^2 * (delx dot delv) / r
// random force = sigma * wr * rnd * dtinvsqrt;
numtyp force = A_attij*wc + B_repij*(rhoi+rhoj)*wc_r;
force -= gammaij*wr*wr*dot*rinv;
force += sigmaij*wr*randnum*dtinvsqrt;
#ifndef ONETYPE
force *= factor_dpd*rinv;
#else
force*=rinv;
#endif
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*A_attij*cutij * wr*wr + (numtyp)0.5*B_repij*cut_rij*(rhoi+rhoj)*wc_r*wc_r;
#ifndef ONETYPE
energy+=factor_dpd*e;
#else
energy+=e;
#endif
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}

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/***************************************************************************
mdpd.h
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the mdpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_MDPD_H
#define LAL_MDPD_H
#include "lal_base_dpd.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class MDPD : public BaseDPD<numtyp, acctyp> {
public:
MDPD();
~MDPD();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq,
double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma,
double **host_cut, double **host_cut_r, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, const double gpu_split,
FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
void get_extra_data(double *host_rho);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = A_att, coeff.x = B_rep, coeff.z = gamma, coeff.w = sigma
UCL_D_Vec<numtyp4> coeff;
/// coeff2.x = cut, coeff2.y = cut_r, coeff2.z = cutsq
UCL_D_Vec<numtyp4> coeff2;
UCL_D_Vec<numtyp> cutsq;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// pointer to host data
double *mdpd_rho;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

133
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/***************************************************************************
mdpd_ext.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to mdpd acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_mdpd.h"
using namespace std;
using namespace LAMMPS_AL;
static MDPD<PRECISION,ACC_PRECISION> MDPDMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int mdpd_gpu_init(const int ntypes, double **cutsq,
double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma,
double **host_cut, double **host_cut_r,
double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
MDPDMF.clear();
gpu_mode=MDPDMF.device->gpu_mode();
double gpu_split=MDPDMF.device->particle_split();
int first_gpu=MDPDMF.device->first_device();
int last_gpu=MDPDMF.device->last_device();
int world_me=MDPDMF.device->world_me();
int gpu_rank=MDPDMF.device->gpu_rank();
int procs_per_gpu=MDPDMF.device->procs_per_gpu();
MDPDMF.device->init_message(screen,"mdpd",first_gpu,last_gpu);
bool message=false;
if (MDPDMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=MDPDMF.init(ntypes, cutsq, host_A_att, host_B_rep, host_gamma, host_sigma,
host_cut, host_cut_r, special_lj, inum, nall, max_nbors,
maxspecial, cell_size, gpu_split, screen);
MDPDMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=MDPDMF.init(ntypes, cutsq, host_A_att, host_B_rep, host_gamma, host_sigma,
host_cut, host_cut_r, special_lj, inum, nall, max_nbors,
maxspecial, cell_size, gpu_split, screen);
MDPDMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
MDPDMF.estimate_gpu_overhead();
return init_ok;
}
void mdpd_gpu_clear() {
MDPDMF.clear();
}
int ** mdpd_gpu_compute_n(const int ago, const int inum_full, 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_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
return MDPDMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
}
void mdpd_gpu_compute(const int ago, const int inum_full, 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, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
MDPDMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void mdpd_gpu_get_extra_data(double *host_rho) {
MDPDMF.get_extra_data(host_rho);
}
double mdpd_gpu_bytes() {
return MDPDMF.host_memory_usage();
}

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/***************************************************************************
sph_heatconduction.cpp
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the sph_heatconduction pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "sph_heatconduction_cl.h"
#elif defined(USE_CUDART)
const char *sph_heatconduction=0;
#else
#include "sph_heatconduction_cubin.h"
#endif
#include "lal_sph_heatconduction.h"
#include <cassert>
namespace LAMMPS_AL {
#define SPHHeatConductionT SPHHeatConduction<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
SPHHeatConductionT::SPHHeatConduction() : BaseSPH<numtyp,acctyp>(), _allocated(false) {
_max_dE_size = 0;
}
template <class numtyp, class acctyp>
SPHHeatConductionT::~SPHHeatConduction() {
clear();
}
template <class numtyp, class acctyp>
int SPHHeatConductionT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int SPHHeatConductionT::init(const int ntypes,
double **host_cutsq, double **host_cut,
double **host_alpha, double* host_mass,
const int dimension, double *host_special_lj,
const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// rho, esph
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,sph_heatconduction,"k_sph_heatconduction",
onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_alpha,
host_cut, host_cutsq);
UCL_H_Vec<numtyp> dview_mass(ntypes, *(this->ucl_device), UCL_WRITE_ONLY);
for (int i = 0; i < ntypes; i++)
dview_mass[i] = host_mass[i];
mass.alloc(ntypes,*(this->ucl_device), UCL_READ_ONLY);
ucl_copy(mass,dview_mass,false);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_max_dE_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
dE.alloc(_max_dE_size,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_dimension = dimension;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+dE.row_bytes()+sp_lj.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void SPHHeatConductionT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
mass.clear();
dE.clear();
sp_lj.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double SPHHeatConductionT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(SPHHeatConduction<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void SPHHeatConductionT::update_dE(void **dE_ptr) {
*dE_ptr=dE.host.begin();
dE.update_host(_max_dE_size,false);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int SPHHeatConductionT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// Resize dE array if necessary
if (nall > _max_dE_size) {
_max_dE_size=static_cast<int>(static_cast<double>(nall)*1.10);
dE.resize(_max_dE_size);
}
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = rho[i];
v.y = esph[i];
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &mass, &sp_lj,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &dE, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &_dimension, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &mass,
&_lj_types, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &dE, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &_dimension, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void SPHHeatConductionT::get_extra_data(double *host_rho, double *host_esph) {
rho = host_rho;
esph = host_esph;
}
template class SPHHeatConduction<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// sph_heatconduction.cu
// ---------------------
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the sph/heatconduction pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#if (SHUFFLE_AVAIL == 0)
#define store_dE(dEacc, ii, inum, tid, t_per_atom, offset, dE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add1(t_per_atom, red_acc, offset, tid, dEacc); \
} \
if (offset==0 && ii<inum) { \
dE[ii]=dEacc; \
}
#else
#define store_drhoE(dEacc, ii, inum, tid, t_per_atom, offset, dE) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
dEacc += shfl_down(dEacc, s, t_per_atom); \
} \
} \
if (offset==0 && ii<inum) { \
dE[ii]=dEacc; \
}
#endif
/* ------------------------------------------------------------------------ */
__kernel void k_sph_heatconduction(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp *restrict mass,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp *restrict dE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp dEacc = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp mass_itype = mass[itype];
const numtyp4 extrai = extra[i];
numtyp rhoi = extrai.x;
numtyp esphi = extrai.y;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<coeff[mtype].z) { // cutsq[itype][jtype]
numtyp mass_jtype = mass[jtype];
const numtyp coeffx=coeff[mtype].x; // alpha[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // cut[itype][jtype]
const numtyp4 extraj = extra[j];
numtyp rhoj = extraj.x;
numtyp esphj = extraj.y;
numtyp h = coeffy; // cut[itype][jtype]
numtyp ih = ucl_recip(h); // (numtyp)1.0 / h;
numtyp ihsq = ih * ih;
numtyp wfd = h - ucl_sqrt(rsq);
if (dimension == 3) {
// Lucy Kernel, 3d
wfd = (numtyp)-25.066903536973515383 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// total thermal energy increment
numtyp D = coeffx; // alpha[itype][jtype] diffusion coefficient
numtyp deltaE = (numtyp)2.0 * mass_itype * mass_jtype / (mass_itype + mass_jtype);
deltaE *= (rhoi + rhoj) / (rhoi * rhoj);
deltaE *= D * (esphi - esphj) * wfd;
// change in thermal energy, desph[i]
dEacc += deltaE;
}
} // for nbor
} // if ii
store_drhoE(dEacc,ii,inum,tid,t_per_atom,offset,dE);
}
__kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp *restrict mass,
const __global numtyp *restrict sp_lj_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp *restrict dE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
}
__syncthreads();
#else
const numtyp coeffx=coeff_in[ONETYPE].x; // alpha[itype][jtype]
const numtyp coeffy=coeff_in[ONETYPE].y; // cut[itype][jtype]
const numtyp cutsq_p=coeff_in[ONETYPE].z; // cutsq[itype][jtype]
#endif
int n_stride;
local_allocate_store_pair();
acctyp dEacc = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
numtyp mass_itype = mass[iw];
#ifndef ONETYPE
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
const numtyp4 extrai = extra[i];
numtyp rhoi = extrai.x;
numtyp esphi = extrai.y;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype = jx.w;
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=coeff[mtype].z;
#endif
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
numtyp mass_jtype = mass[jtype];
#ifndef ONETYPE
const numtyp coeffx=coeff[mtype].x; // alpha[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // cut[itype][jtype]
#endif
const numtyp4 extraj = extra[j];
numtyp rhoj = extraj.x;
numtyp esphj = extraj.y;
numtyp h = coeffy; // cut[itype][jtype]
numtyp ih = ih = ucl_recip(h); // (numtyp)1.0 / h;
numtyp ihsq = ih * ih;
numtyp wfd = h - ucl_sqrt(rsq);
if (dimension == 3) {
// Lucy Kernel, 3d
wfd = (numtyp)-25.066903536973515383 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// total thermal energy increment
numtyp D = coeffx; // alpha[itype][jtype] diffusion coefficient
numtyp deltaE = (numtyp)2.0 * mass_itype * mass_jtype / (mass_itype + mass_jtype);
deltaE *= (rhoi + rhoj) / (rhoi * rhoj);
deltaE *= D * (esphi - esphj) * wfd;
// change in thermal energy, desph[i]
dEacc += deltaE;
}
} // for nbor
} // if ii
store_drhoE(dEacc,ii,inum,tid,t_per_atom,offset,dE);
}

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/***************************************************************************
sph_heatconduction.h
--------------------
Trung Nguyen (U Chicago)
Class for acceleration of the sph heatconduction pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_SPH_LJ_H
#define LAL_SPH_LJ_H
#include "lal_base_sph.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class SPHHeatConduction : public BaseSPH<numtyp, acctyp> {
public:
SPHHeatConduction();
~SPHHeatConduction();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq,
double** host_cut, double **host_alpha, double *host_mass,
const int dimension, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
void get_extra_data(double *host_rho, double *host_esph);
/// copy desph from device to host
void update_dE(void **dE_ptr);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = alpha, coeff.y = cut, coeff.z = cutsq
UCL_D_Vec<numtyp4> coeff;
/// per-type coeffs
UCL_D_Vec<numtyp> mass;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Per-atom arrays
UCL_Vector<acctyp,acctyp> dE;
int _max_dE_size;
int _dimension;
/// pointer to host data
double *rho, *esph, *cv;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
sph_heatconduction_ext.cpp
--------------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to sph/heatconduction acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_sph_heatconduction.h"
using namespace std;
using namespace LAMMPS_AL;
static SPHHeatConduction<PRECISION,ACC_PRECISION> SPHHeatConductionMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int sph_heatconduction_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_alpha, double* host_mass, const int dimension,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
SPHHeatConductionMF.clear();
gpu_mode=SPHHeatConductionMF.device->gpu_mode();
double gpu_split=SPHHeatConductionMF.device->particle_split();
int first_gpu=SPHHeatConductionMF.device->first_device();
int last_gpu=SPHHeatConductionMF.device->last_device();
int world_me=SPHHeatConductionMF.device->world_me();
int gpu_rank=SPHHeatConductionMF.device->gpu_rank();
int procs_per_gpu=SPHHeatConductionMF.device->procs_per_gpu();
SPHHeatConductionMF.device->init_message(screen,"sph_heatconduction",first_gpu,last_gpu);
bool message=false;
if (SPHHeatConductionMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=SPHHeatConductionMF.init(ntypes, cutsq, host_cut, host_alpha, host_mass,
dimension, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
SPHHeatConductionMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=SPHHeatConductionMF.init(ntypes, cutsq, host_cut, host_alpha, host_mass,
dimension, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
SPHHeatConductionMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
SPHHeatConductionMF.estimate_gpu_overhead();
return init_ok;
}
void sph_heatconduction_gpu_clear() {
SPHHeatConductionMF.clear();
}
int ** sph_heatconduction_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *host_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_v) {
return SPHHeatConductionMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, host_tag, nspecial, special, eflag, vflag,
eatom, vatom, host_start, ilist, jnum, cpu_time, success,
host_v);
}
void sph_heatconduction_gpu_compute(const int ago, const int inum_full, 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, tagint *host_tag,
double **host_v, const int nlocal) {
SPHHeatConductionMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
}
void sph_heatconduction_gpu_get_extra_data(double *host_rho, double *host_esph) {
SPHHeatConductionMF.get_extra_data(host_rho, host_esph);
}
void sph_heatconduction_gpu_update_dE(void **dE_ptr) {
SPHHeatConductionMF.update_dE(dE_ptr);
}
double sph_heatconduction_gpu_bytes() {
return SPHHeatConductionMF.host_memory_usage();
}

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/***************************************************************************
sph_lj.cpp
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the sph_lj pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "sph_lj_cl.h"
#elif defined(USE_CUDART)
const char *sph_lj=0;
#else
#include "sph_lj_cubin.h"
#endif
#include "lal_sph_lj.h"
#include <cassert>
namespace LAMMPS_AL {
#define SPHLJT SPHLJ<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
SPHLJT::SPHLJ() : BaseSPH<numtyp,acctyp>(), _allocated(false) {
_max_drhoE_size = 0;
}
template <class numtyp, class acctyp>
SPHLJT::~SPHLJ() {
clear();
}
template <class numtyp, class acctyp>
int SPHLJT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int SPHLJT::init(const int ntypes,
double **host_cutsq, double **host_cut,
double **host_viscosity, double* host_mass,
const int dimension, double *host_special_lj,
const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// rho, cv
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,sph_lj,"k_sph_lj",onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_viscosity,
host_cut, host_cutsq);
UCL_H_Vec<numtyp> dview_mass(ntypes, *(this->ucl_device), UCL_WRITE_ONLY);
for (int i = 0; i < ntypes; i++)
dview_mass[i] = host_mass[i];
mass.alloc(ntypes,*(this->ucl_device), UCL_READ_ONLY);
ucl_copy(mass,dview_mass,false);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_max_drhoE_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
drhoE.alloc(_max_drhoE_size*2,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_dimension = dimension;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+drhoE.row_bytes()+sp_lj.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void SPHLJT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
mass.clear();
drhoE.clear();
sp_lj.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double SPHLJT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(SPHLJ<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void SPHLJT::update_drhoE(void **drhoE_ptr) {
*drhoE_ptr=drhoE.host.begin();
drhoE.update_host(_max_drhoE_size*2,false);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int SPHLJT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// Resize drhoE array if necessary
if (nall > _max_drhoE_size) {
_max_drhoE_size=static_cast<int>(static_cast<double>(nall)*1.10);
drhoE.resize(_max_drhoE_size*2);
}
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = rho[i];
v.y = esph[i];
v.z = cv[i];
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &mass, &sp_lj,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &drhoE, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &_dimension, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &mass,
&_lj_types, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &drhoE, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &_dimension, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void SPHLJT::get_extra_data(double *host_rho, double *host_esph, double *host_cv) {
rho = host_rho;
esph = host_esph;
cv = host_cv;
}
template class SPHLJ<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// sph_lj.cu
// -------------------
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the sph/lj pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#if (SHUFFLE_AVAIL == 0)
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add2(t_per_atom, red_acc, offset, tid, \
drhoEacc.x, drhoEacc.y); \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
}
#else
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
drhoEacc.x += shfl_down(drhoEacc.x, s, t_per_atom); \
drhoEacc.y += shfl_down(drhoEacc.y, s, t_per_atom); \
} \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
}
#endif
/* ------------------------------------------------------------------------ */
/* Lennard-Jones EOS,
Francis H. Ree
"Analytic representation of thermodynamic data for the Lennard‐Jones fluid",
Journal of Chemical Physics 73 pp. 5401-5403 (1980)
return p = pc[0], c = pc[1]
*/
ucl_inline void LJEOS2(const numtyp rho, const numtyp e, const numtyp cv, numtyp pc[2])
{
numtyp T = e/cv;
numtyp beta = ucl_recip(T); // (numtyp)1.0 / T;
numtyp beta_sqrt = ucl_sqrt(beta);
numtyp x = rho * ucl_sqrt(beta_sqrt);
numtyp xsq = x * x;
numtyp xpow3 = xsq * x;
numtyp xpow4 = xsq * xsq;
/* differential of Helmholtz free energy w.r.t. x */
numtyp diff_A_NkT = (numtyp)3.629 + (numtyp)7.264*x -
beta*((numtyp)3.492 - (numtyp)18.698*x + (numtyp)35.505*xsq - (numtyp)31.816*xpow3 +
(numtyp)11.195*xpow4) - beta_sqrt*((numtyp)5.369 + (numtyp)13.16*x +
(numtyp)18.525*xsq - (numtyp)17.076*xpow3 + (numtyp)9.32*xpow4) +
(numtyp)10.4925*xsq + (numtyp)11.46*xpow3 + (numtyp)2.176*xpow4*xpow4*x;
/* differential of Helmholtz free energy w.r.t. x^2 */
numtyp d2A_dx2 = (numtyp)7.264 + (numtyp)20.985*x +
beta*((numtyp)18.698 - (numtyp)71.01*x + (numtyp)95.448*xsq - (numtyp)44.78*xpow3) -
beta_sqrt*((numtyp)13.16 + (numtyp)37.05*x - (numtyp)51.228*xsq + (numtyp)37.28*xpow3) +
(numtyp)34.38*xsq + (numtyp)19.584*xpow4*xpow4;
// p = rho k T * (1 + rho * d(A/(NkT))/drho)
// dx/drho = rho/x
pc[0] = rho * T * ((numtyp)1.0 + diff_A_NkT * x); // pressure
numtyp csq = T * ((numtyp)1.0 + (numtyp)2.0 * diff_A_NkT * x + d2A_dx2 * x * x); // soundspeed squared
if (csq > (numtyp)0.0) {
pc[1] = ucl_sqrt(csq); // soundspeed
} else {
pc[1] = (numtyp)0.0;
}
}
__kernel void k_sph_lj(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp *restrict mass,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp mass_itype = mass[itype];
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
const numtyp4 extrai = extra[i];
numtyp rhoi = extrai.x;
numtyp esphi = extrai.y;
numtyp cvi = extrai.z;
// compute pressure of particle i with LJ EOS
numtyp fci[2];
LJEOS2(rhoi, esphi, cvi, fci);
numtyp fi = fci[0];
numtyp ci = fci[1];
fi /= (rhoi * rhoi);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<coeff[mtype].z) { // cutsq[itype][jtype]
numtyp mass_jtype = mass[jtype];
const numtyp coeffx=coeff[mtype].x; // viscosity[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // cut[itype][jtype]
const numtyp4 extraj = extra[j];
numtyp rhoj = extraj.x;
numtyp esphj = extraj.y;
numtyp cvj = extraj.z;
numtyp h = coeffy; // cut[itype][jtype]
numtyp ih = ucl_recip(h); // (numtyp)1.0 / h;
numtyp ihsq = ih * ih;
numtyp ihcub = ihsq * ih;
numtyp wfd = h - ucl_sqrt(rsq);
if (dimension == 3) {
// Lucy Kernel, 3d
wfd = (numtyp)-25.066903536973515383 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// function call to LJ EOS
numtyp fcj[2];
LJEOS2(rhoj, esphj, cvj, fcj);
numtyp fj = fcj[0];
numtyp cj = fcj[1];
fj /= (rhoj * rhoj);
// apply long-range correction to model a LJ fluid with cutoff
// this implies that the modelled LJ fluid has cutoff == SPH cutoff
numtyp lrc = (numtyp)-11.1701 * (ihcub * ihcub * ihcub - (numtyp)1.5 * ihcub);
fi += lrc;
fj += lrc;
// dot product of velocity delta and distance vector
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp delVdotDelR = delx*delvx + dely*delvy + delz*delvz;
// artificial viscosity (Monaghan 1992)
numtyp fvisc = (numtyp)0;
if (delVdotDelR < (numtyp)0) {
numtyp mu = h * delVdotDelR / (rsq + (numtyp)0.01 * h * h);
fvisc = -coeffx * (ci + cj) * mu / (rhoi + rhoj); // viscosity[itype][jtype]
}
// total pair force & thermal energy increment
numtyp force = -mass_itype * mass_jtype * (fi + fj + fvisc) * wfd;
numtyp deltaE = (numtyp)-0.5 * force * delVdotDelR;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// and change in density, drho[i]
drhoEacc.x += mass_jtype * delVdotDelR * wfd;
// change in thermal energy, desph[i]
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
}
__kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp *restrict mass,
const __global numtyp *restrict sp_lj_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
}
__syncthreads();
#else
const numtyp coeffx=coeff_in[ONETYPE].x; // viscosity[itype][jtype]
const numtyp coeffy=coeff_in[ONETYPE].y; // cut[itype][jtype]
const numtyp cutsq_p=coeff_in[ONETYPE].z; // cutsq[itype][jtype]
#endif
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
numtyp mass_itype = mass[iw];
#ifndef ONETYPE
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
const numtyp4 extrai = extra[i];
numtyp rhoi = extrai.x;
numtyp esphi = extrai.y;
numtyp cvi = extrai.z;
// compute pressure of particle i with LJ EOS
numtyp fci[2];
LJEOS2(rhoi, esphi, cvi, fci);
numtyp fi = fci[0];
numtyp ci = fci[1];
fi /= (rhoi * rhoi);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype = jx.w;
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=coeff[mtype].z; // cutsq[itype][jtype];
#endif
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
numtyp mass_jtype = mass[jtype];
#ifndef ONETYPE
const numtyp coeffx=coeff[mtype].x; // viscosity[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // cut[itype][jtype]
#endif
const numtyp4 extraj = extra[j];
numtyp rhoj = extraj.x;
numtyp esphj = extraj.y;
numtyp cvj = extraj.z;
numtyp h = coeffy; // cut[itype][jtype]
numtyp ih = ucl_recip(h); // (numtyp)1.0 / h;
numtyp ihsq = ih * ih;
numtyp ihcub = ihsq * ih;
numtyp wfd = h - ucl_sqrt(rsq);
if (dimension == 3) {
// Lucy Kernel, 3d
wfd = (numtyp)-25.066903536973515383 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// function call to LJ EOS
numtyp fcj[2];
LJEOS2(rhoj, esphj, cvj, fcj);
numtyp fj = fcj[0];
numtyp cj = fcj[1];
fj /= (rhoj * rhoj);
// apply long-range correction to model a LJ fluid with cutoff
// this implies that the modelled LJ fluid has cutoff == SPH cutoff
numtyp lrc = (numtyp)-11.1701 * (ihcub * ihcub * ihcub - (numtyp)1.5 * ihcub);
fi += lrc;
fj += lrc;
// dot product of velocity delta and distance vector
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp delVdotDelR = delx*delvx + dely*delvy + delz*delvz;
// artificial viscosity (Monaghan 1992)
numtyp fvisc = (numtyp)0;
if (delVdotDelR < (numtyp)0) {
numtyp mu = h * delVdotDelR / (rsq + (numtyp)0.01 * h * h);
fvisc = -coeffx * (ci + cj) * mu / (rhoi + rhoj); // viscosity[itype][jtype]
}
// total pair force & thermal energy increment
numtyp force = -mass_itype * mass_jtype * (fi + fj + fvisc) * wfd;
numtyp deltaE = (numtyp)-0.5 * force * delVdotDelR;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// and change in density, drho[i]
drhoEacc.x += mass_jtype * delVdotDelR * wfd;
// change in thermal energy, desph[i]
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
}

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/***************************************************************************
sph_lj.h
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the sph lj pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_SPH_LJ_H
#define LAL_SPH_LJ_H
#include "lal_base_sph.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class SPHLJ : public BaseSPH<numtyp, acctyp> {
public:
SPHLJ();
~SPHLJ();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq,
double** host_cut, double **host_viscosity, double *host_mass,
const int dimension,
double *host_special_lj, const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, const double gpu_split,
FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
void get_extra_data(double *host_rho, double *host_esph,
double *host_cv);
/// copy drho and desph from device to host
void update_drhoE(void **drhoE_ptr);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = viscosity, coeff.y = cut, coeff.z = cutsq
UCL_D_Vec<numtyp4> coeff;
/// per-type coeffs
UCL_D_Vec<numtyp> mass;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Per-atom arrays
UCL_Vector<acctyp,acctyp> drhoE;
int _max_drhoE_size;
int _dimension;
/// pointer to host data
double *rho, *esph, *cv;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
sph_lj_ext.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to sph/lj acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_sph_lj.h"
using namespace std;
using namespace LAMMPS_AL;
static SPHLJ<PRECISION,ACC_PRECISION> SPHLJMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int sph_lj_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_viscosity, double* host_mass, const int dimension,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
SPHLJMF.clear();
gpu_mode=SPHLJMF.device->gpu_mode();
double gpu_split=SPHLJMF.device->particle_split();
int first_gpu=SPHLJMF.device->first_device();
int last_gpu=SPHLJMF.device->last_device();
int world_me=SPHLJMF.device->world_me();
int gpu_rank=SPHLJMF.device->gpu_rank();
int procs_per_gpu=SPHLJMF.device->procs_per_gpu();
SPHLJMF.device->init_message(screen,"sph_lj",first_gpu,last_gpu);
bool message=false;
if (SPHLJMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=SPHLJMF.init(ntypes, cutsq, host_cut, host_viscosity, host_mass,
dimension, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
SPHLJMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=SPHLJMF.init(ntypes, cutsq, host_cut, host_viscosity, host_mass,
dimension, special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
SPHLJMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
SPHLJMF.estimate_gpu_overhead();
return init_ok;
}
void sph_lj_gpu_clear() {
SPHLJMF.clear();
}
int ** sph_lj_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *host_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_v) {
return SPHLJMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, host_tag, nspecial, special, eflag, vflag,
eatom, vatom, host_start, ilist, jnum, cpu_time, success,
host_v);
}
void sph_lj_gpu_compute(const int ago, const int inum_full, 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, tagint *host_tag,
double **host_v, const int nlocal) {
SPHLJMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
}
void sph_lj_gpu_get_extra_data(double *host_rho, double *host_esph, double *host_cv) {
SPHLJMF.get_extra_data(host_rho, host_esph, host_cv);
}
void sph_lj_gpu_update_drhoE(void **drhoE_ptr) {
SPHLJMF.update_drhoE(drhoE_ptr);
}
double sph_lj_gpu_bytes() {
return SPHLJMF.host_memory_usage();
}

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/***************************************************************************
sph_taitwater.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the sph/taitwater pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "sph_taitwater_cl.h"
#elif defined(USE_CUDART)
const char *sph_taitwater=0;
#else
#include "sph_taitwater_cubin.h"
#endif
#include "lal_sph_taitwater.h"
#include <cassert>
namespace LAMMPS_AL {
#define SPHTaitwaterT SPHTaitwater<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
SPHTaitwaterT::SPHTaitwater() : BaseSPH<numtyp,acctyp>(), _allocated(false) {
_max_drhoE_size = 0;
}
template <class numtyp, class acctyp>
SPHTaitwaterT::~SPHTaitwater() {
clear();
}
template <class numtyp, class acctyp>
int SPHTaitwaterT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int SPHTaitwaterT::init(const int ntypes, double **host_cutsq,
double **host_cut, double **host_viscosity,
double* host_mass, double* host_rho0,
double* host_soundspeed, double* host_B, const int dimension,
double *host_special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// rho
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,sph_taitwater,"k_sph_taitwater",
onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_viscosity,
host_cut, host_cutsq);
UCL_H_Vec<numtyp4> dview_coeff2(ntypes, *(this->ucl_device), UCL_WRITE_ONLY);
for (int i = 0; i < ntypes; i++) {
dview_coeff2[i].x = host_mass[i];
dview_coeff2[i].y = host_rho0[i];
dview_coeff2[i].z = host_soundspeed[i];
dview_coeff2[i].w = host_B[i];
}
coeff2.alloc(ntypes,*(this->ucl_device), UCL_READ_ONLY);
ucl_copy(coeff2,dview_coeff2,false);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_max_drhoE_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
drhoE.alloc(_max_drhoE_size*2,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_dimension = dimension;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+coeff2.row_bytes()+drhoE.row_bytes()+sp_lj.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void SPHTaitwaterT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
coeff2.clear();
drhoE.clear();
sp_lj.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double SPHTaitwaterT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(SPHTaitwater<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void SPHTaitwaterT::update_drhoE(void **drhoE_ptr) {
*drhoE_ptr=drhoE.host.begin();
drhoE.update_host(_max_drhoE_size*2,false);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int SPHTaitwaterT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// Resize drhoE array if necessary
if (nall > _max_drhoE_size) {
_max_drhoE_size=static_cast<int>(static_cast<double>(nall)*1.10);
drhoE.resize(_max_drhoE_size*2);
}
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = rho[i];
v.y = 0;
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &coeff2, &sp_lj,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &drhoE, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &_dimension, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &coeff2,
&_lj_types, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &drhoE, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &_dimension, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void SPHTaitwaterT::get_extra_data(double *host_rho) {
rho = host_rho;
}
template class SPHTaitwater<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// sph_taitwater.cu
// -------------------
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the sph/taitwater pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#if (SHUFFLE_AVAIL == 0)
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add2(t_per_atom, red_acc, offset, tid, \
drhoEacc.x, drhoEacc.y); \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
}
#else
#define store_drhoE(drhoEacc, ii, inum, tid, t_per_atom, offset, drhoE) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
drhoEacc.x += shfl_down(drhoEacc.x, s, t_per_atom); \
drhoEacc.y += shfl_down(drhoEacc.y, s, t_per_atom); \
} \
} \
if (offset==0 && ii<inum) { \
drhoE[ii]=drhoEacc; \
}
#endif
__kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp4 *restrict coeff2,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp mass_itype = coeff2[itype].x;
numtyp rho0_itype = coeff2[itype].y;
numtyp soundspeed_itype = coeff2[itype].z;
numtyp B_itype = coeff2[itype].w;
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
const numtyp4 extrai = extra[i];
numtyp rhoi = extrai.x;
// compute pressure of atom i with Tait EOS
numtyp tmp = rhoi / rho0_itype;
numtyp fi = tmp * tmp * tmp;
fi = B_itype * (fi * fi * tmp - (numtyp)1.0);
fi /= (rhoi * rhoi);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<coeff[mtype].z) { // cutsq[itype][jtype]
const numtyp coeffx=coeff[mtype].x; // viscosity[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // cut[itype][jtype]
numtyp mass_jtype = coeff2[jtype].x;
numtyp rho0_jtype = coeff2[jtype].y;
numtyp soundspeed_jtype = coeff2[jtype].z;
numtyp B_jtype = coeff2[jtype].w;
const numtyp4 extraj = extra[j];
numtyp rhoj = extraj.x;
numtyp h = coeffy; // cut[itype][jtype]
numtyp ih = ucl_recip(h); // (numtyp)1.0 / h;
numtyp ihsq = ih * ih;
numtyp wfd = h - ucl_sqrt(rsq);
if (dimension == 3) {
// Lucy Kernel, 3d
wfd = (numtyp)-25.066903536973515383 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// compute pressure of atom j with Tait EOS
numtyp tmp = rhoj / rho0_jtype;
numtyp fj = tmp * tmp * tmp;
fj = B_jtype * (fj * fj * tmp - (numtyp)1.0);
fj /= (rhoj * rhoj);
// dot product of velocity delta and distance vector
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp delVdotDelR = delx*delvx + dely*delvy + delz*delvz;
// artificial viscosity (Monaghan 1992)
numtyp fvisc = (numtyp)0;
if (delVdotDelR < (numtyp)0) {
numtyp mu = h * delVdotDelR / (rsq + (numtyp)0.01 * h * h);
fvisc = -coeffx * (soundspeed_itype
+ soundspeed_jtype) * mu / (rhoi + rhoj);
}
// total pair force & thermal energy increment
numtyp force = -mass_itype * mass_jtype * (fi + fj + fvisc) * wfd;
numtyp deltaE = (numtyp)-0.5 * force * delVdotDelR;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// and change in density, drho[i]
drhoEacc.x += mass_jtype* delVdotDelR * wfd;
// change in thermal energy, desph[i]
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
}
__kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp *restrict sp_lj_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp2 *restrict drhoE,
const int eflag, const int vflag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const int dimension, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES];
if (tid<MAX_SHARED_TYPES) {
coeff2[tid] = coeff2_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
}
__syncthreads();
#else
const numtyp coeffx=coeff_in[ONETYPE].x; // viscosity[itype][jtype]
const numtyp coeffy=coeff_in[ONETYPE].y; // cut[itype][jtype]
const numtyp cutsq_p=coeff_in[ONETYPE].z; // cutsq[itype][jtype]
#endif
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp2 drhoEacc;
drhoEacc.x = drhoEacc.x = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
numtyp mass_itype = coeff2[iw].x;
numtyp rho0_itype = coeff2[iw].y;
numtyp soundspeed_itype = coeff2[iw].z;
numtyp B_itype = coeff2[iw].w;
#ifndef ONETYPE
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
const numtyp4 extrai = extra[i];
numtyp rhoi = extrai.x;
// compute pressure of atom i with Tait EOS
numtyp tmp = rhoi / rho0_itype;
numtyp fi = tmp * tmp * tmp;
fi = B_itype * (fi * fi * tmp - (numtyp)1.0);
fi /= (rhoi * rhoi);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=coeff[mtype].z;
#endif
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
#ifndef ONETYPE
const numtyp coeffx=coeff[mtype].x; // viscosity[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // cut[itype][jtype]
#endif
numtyp mass_jtype = coeff2[jtype].x;
numtyp rho0_jtype = coeff2[jtype].y;
numtyp soundspeed_jtype = coeff2[jtype].z;
numtyp B_jtype = coeff2[jtype].w;
const numtyp4 extraj = extra[j];
numtyp rhoj = extraj.x;
numtyp h = coeffy; // cut[itype][jtype]
numtyp ih = ucl_recip(h); // (numtyp)1.0 / h;
numtyp ihsq = ih * ih;
numtyp wfd = h - ucl_sqrt(rsq);
if (dimension == 3) {
// Lucy Kernel, 3d
wfd = (numtyp)-25.066903536973515383 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// compute pressure of atom j with Tait EOS
numtyp tmp = rhoj / rho0_jtype;
numtyp fj = tmp * tmp * tmp;
fj = B_jtype * (fj * fj * tmp - (numtyp)1.0);
fj /= (rhoj * rhoj);
// dot product of velocity delta and distance vector
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp delVdotDelR = delx*delvx + dely*delvy + delz*delvz;
// artificial viscosity (Monaghan 1992)
numtyp fvisc = (numtyp)0;
if (delVdotDelR < (numtyp)0) {
numtyp mu = h * delVdotDelR / (rsq + (numtyp)0.01 * h * h);
fvisc = -coeffx * (soundspeed_itype
+ soundspeed_jtype) * mu / (rhoi + rhoj);
}
// total pair force & thermal energy increment
numtyp force = -mass_itype * mass_jtype * (fi + fj + fvisc) * wfd;
numtyp deltaE = (numtyp)-0.5 * force * delVdotDelR;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// and change in density
drhoEacc.x += mass_jtype * delVdotDelR * wfd;
// change in thermal energy
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv);
store_drhoE(drhoEacc,ii,inum,tid,t_per_atom,offset,drhoE);
}

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/***************************************************************************
sph_taitwater.h
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the sph/taitwater pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_SPH_TAITWATER_H
#define LAL_SPH_TAITWATER_H
#include "lal_base_sph.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class SPHTaitwater : public BaseSPH<numtyp, acctyp> {
public:
SPHTaitwater();
~SPHTaitwater();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq,
double** host_cut, double **host_viscosity, double *host_mass,
double* host_rho0, double* host_soundspeed, double* host_B,
const int dimension, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
void get_extra_data(double *host_rho);
/// copy drho and desph from device to host
void update_drhoE(void **drhoE_ptr);
// --------------------------- TYPE DATA --------------------------
/// per-pair coeffs: coeff.x = viscosity, coeff.y = cut, coeff.z = cutsq
UCL_D_Vec<numtyp4> coeff;
/// per-type coeffs
UCL_D_Vec<numtyp4> coeff2;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Per-atom arrays
UCL_Vector<acctyp,acctyp> drhoE;
int _max_drhoE_size;
int _dimension;
/// pointer to host data
double *rho;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
sph_taitwater_ext.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to sph taitwater acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_sph_taitwater.h"
using namespace std;
using namespace LAMMPS_AL;
static SPHTaitwater<PRECISION,ACC_PRECISION> SPHTaitwaterMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int sph_taitwater_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_viscosity, double* host_mass,
double* host_rho0, double* host_soundspeed, double* host_B,
const int dimension, double *special_lj,
const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
SPHTaitwaterMF.clear();
gpu_mode=SPHTaitwaterMF.device->gpu_mode();
double gpu_split=SPHTaitwaterMF.device->particle_split();
int first_gpu=SPHTaitwaterMF.device->first_device();
int last_gpu=SPHTaitwaterMF.device->last_device();
int world_me=SPHTaitwaterMF.device->world_me();
int gpu_rank=SPHTaitwaterMF.device->gpu_rank();
int procs_per_gpu=SPHTaitwaterMF.device->procs_per_gpu();
SPHTaitwaterMF.device->init_message(screen,"sph_taitwater",first_gpu,last_gpu);
bool message=false;
if (SPHTaitwaterMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=SPHTaitwaterMF.init(ntypes, cutsq, host_cut, host_viscosity, host_mass,
host_rho0, host_soundspeed, host_B, dimension,
special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
SPHTaitwaterMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=SPHTaitwaterMF.init(ntypes, cutsq, host_cut, host_viscosity, host_mass,
host_rho0, host_soundspeed, host_B, dimension,
special_lj, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
SPHTaitwaterMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
SPHTaitwaterMF.estimate_gpu_overhead();
return init_ok;
}
void sph_taitwater_gpu_clear() {
SPHTaitwaterMF.clear();
}
int ** sph_taitwater_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *host_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_v) {
return SPHTaitwaterMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, host_tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v);
}
void sph_taitwater_gpu_compute(const int ago, const int inum_full, 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, tagint *host_tag,
double **host_v, const int nlocal) {
SPHTaitwaterMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
}
void sph_taitwater_gpu_get_extra_data(double *host_rho) {
SPHTaitwaterMF.get_extra_data(host_rho);
}
void sph_taitwater_gpu_update_drhoE(void **drhoE_ptr) {
SPHTaitwaterMF.update_drhoE(drhoE_ptr);
}
double sph_taitwater_gpu_bytes() {
return SPHTaitwaterMF.host_memory_usage();
}

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_coul_slater_long_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "kspace.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int csl_gpu_init(const int ntypes, double **scale, 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_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, const double lamda);
void csl_gpu_reinit(const int ntypes, double **scale);
void csl_gpu_clear();
int **csl_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 csl_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 csl_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairCoulSlaterLongGPU::PairCoulSlaterLongGPU(LAMMPS *lmp) : PairCoulSlaterLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairCoulSlaterLongGPU::~PairCoulSlaterLongGPU()
{
csl_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairCoulSlaterLongGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = csl_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);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
csl_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);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulSlaterLongGPU::init_style()
{
if (!atom->q_flag) error->all(FLERR, "Pair style coul/slater/long/gpu requires atom attribute q");
// Call init_one calculation make sure scale is correct
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { init_one(i, j); }
}
}
double cell_size = cut_coul + neighbor->skin;
cut_coulsq = cut_coul * cut_coul;
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = csl_gpu_init(atom->ntypes + 1, scale, atom->nlocal, atom->nlocal + atom->nghost, mnf,
maxspecial, cell_size, gpu_mode, screen, cut_coulsq,
force->special_coul, force->qqrd2e, g_ewald, lamda);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
void PairCoulSlaterLongGPU::reinit()
{
Pair::reinit();
csl_gpu_reinit(atom->ntypes + 1, scale);
}
/* ---------------------------------------------------------------------- */
double PairCoulSlaterLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + csl_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairCoulSlaterLongGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum;
double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, ecoul, fpair;
double r, r2inv, forcecoul, factor_coul;
double grij, expm2, prefactor, t, erfc;
int *jlist;
double rsq;
ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
double *special_coul = force->special_coul;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
double slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
fpair = forcecoul * r2inv;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
} else
ecoul = 0.0;
}
if (evflag) ev_tally_full(i, 0.0, ecoul, fpair, delx, dely, delz);
}
}
}
}

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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(coul/slater/long/gpu,PairCoulSlaterLongGPU);
// clang-format on
#else
#ifndef LMP_PAIR_COUL_SLATER_LONG_GPU_H
#define LMP_PAIR_COUL_SLATER_LONG_GPU_H
#include "pair_coul_slater_long.h"
namespace LAMMPS_NS {
class PairCoulSlaterLongGPU : public PairCoulSlaterLong {
public:
PairCoulSlaterLongGPU(LAMMPS *lmp);
~PairCoulSlaterLongGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
void reinit() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_edpd_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int edpd_gpu_init(const int ntypes, double **cutsq, double **host_a0, double **host_gamma,
double **host_cut, double **host_power, double **host_kappa,
double **host_powerT, double** host_cutT, double*** host_sc, double ***host_kc,
double *host_mass, double *special_lj, const int power_flag, const int kappa_flag,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen);
void edpd_gpu_clear();
int **edpd_gpu_compute_n(const int ago, const int inum_full, 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_v,
const double dtinvsqrt, const int seed, const int timestep, double *boxlo,
double *prd);
void edpd_gpu_compute(const int ago, const int inum_full, 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, tagint *tag, double **host_v,
const double dtinvsqrt, const int seed, const int timestep, const int nlocal,
double *boxlo, double *prd);
void edpd_gpu_get_extra_data(double *host_T, double *host_cv);
void edpd_gpu_update_flux(void **flux_ptr);
double edpd_gpu_bytes();
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairEDPDGPU::PairEDPDGPU(LAMMPS *lmp) : PairEDPD(lmp), gpu_mode(GPU_FORCE)
{
flux_pinned = nullptr;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairEDPDGPU::~PairEDPDGPU()
{
edpd_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairEDPDGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0 / sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *T = atom->edpd_temp;
double *cv = atom->edpd_cv;
edpd_gpu_get_extra_data(T, cv);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = edpd_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->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
edpd_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->tag,
atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo, domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
// get the heat flux from device
double *Q = atom->edpd_flux;
edpd_gpu_update_flux(&flux_pinned);
int nlocal = atom->nlocal;
if (acc_float) {
auto flux_ptr = (float *)flux_pinned;
for (int i = 0; i < nlocal; i++)
Q[i] = flux_ptr[i];
} else {
auto flux_ptr = (double *)flux_pinned;
for (int i = 0; i < nlocal; i++)
Q[i] = flux_ptr[i];
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEDPDGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
edpd_gpu_init(atom->ntypes + 1, cutsq, a0, gamma, cut, power, kappa,
powerT, cutT, sc, kc, atom->mass, force->special_lj,
power_flag, kappa_flag, atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
acc_float = Info::has_accelerator_feature("GPU", "precision", "single");
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairEDPDGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + edpd_gpu_bytes();
}

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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(edpd/gpu,PairEDPDGPU);
// clang-format on
#else
#ifndef LMP_PAIR_EDPD_GPU_H
#define LMP_PAIR_EDPD_GPU_H
#include "pair_edpd.h"
namespace LAMMPS_NS {
class PairEDPDGPU : public PairEDPD {
public:
PairEDPDGPU(LAMMPS *lmp);
~PairEDPDGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
void *flux_pinned;
bool acc_float;
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_lj_cut_coul_cut_soft_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int ljcs_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset, double **epsilon, 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);
void ljcs_gpu_clear();
int **ljcs_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 ljcs_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 ljcs_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairLJCutCoulCutSoftGPU::PairLJCutCoulCutSoftGPU(LAMMPS *lmp) :
PairLJCutCoulCutSoft(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutCoulCutSoftGPU::~PairLJCutCoulCutSoftGPU()
{
ljcs_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutSoftGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = ljcs_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);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljcs_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);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulCutSoftGPU::init_style()
{
if (!atom->q_flag) error->all(FLERR, "Pair style lj/cut/coul/cut/soft/gpu requires atom attribute q");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i, j);
cut *= cut;
if (cut > maxcut) maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
ljcs_gpu_init(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, epsilon, 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);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulCutSoftGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + ljcs_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutSoftGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum, itype, jtype;
double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair;
double forcecoul, forcelj, factor_coul, factor_lj;
double denc, denlj, r4sig6;
int *jlist;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
if (rsq < cut_coulsq[itype][jtype]) {
denc = sqrt(lj4[itype][jtype] + rsq);
forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
fpair = factor_coul*forcecoul + factor_lj*forcelj;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
else
ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else
evdwl = 0.0;
}
if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz);
}
}
}
}

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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(lj/cut/coul/cut/soft/gpu,PairLJCutCoulCutSoftGPU);
// clang-format on
#else
#ifndef LMP_PAIR_LJ_CUT_COUL_CUT_SOFT_GPU_H
#define LMP_PAIR_LJ_CUT_COUL_CUT_SOFT_GPU_H
#include "pair_lj_cut_coul_cut_soft.h"
namespace LAMMPS_NS {
class PairLJCutCoulCutSoftGPU : public PairLJCutCoulCutSoft {
public:
PairLJCutCoulCutSoftGPU(LAMMPS *lmp);
~PairLJCutCoulCutSoftGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_lj_cut_coul_long_soft_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "kspace.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int ljcls_gpu_init(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset, double **epsilon, 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 ljcls_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset, double **epsilon,
double **host_lj_cutsq);
void ljcls_gpu_clear();
int **ljcls_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 ljcls_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 ljcls_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongSoftGPU::PairLJCutCoulLongSoftGPU(LAMMPS *lmp) :
PairLJCutCoulLongSoft(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutCoulLongSoftGPU::~PairLJCutCoulLongSoftGPU()
{
ljcls_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongSoftGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = ljcls_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);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljcls_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);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulLongSoftGPU::init_style()
{
cut_respa = nullptr;
if (!atom->q_flag) error->all(FLERR, "Pair style lj/cut/coul/long/soft/gpu requires atom attribute q");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i, j);
cut *= cut;
if (cut > maxcut) maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
cut_coulsq = cut_coul * cut_coul;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables(cut_coul, cut_respa);
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
ljcls_gpu_init(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, epsilon, 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);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongSoftGPU::reinit()
{
Pair::reinit();
ljcls_gpu_reinit(atom->ntypes + 1, cutsq, lj1, lj2, lj3, lj4, offset, epsilon, cut_ljsq);
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulLongSoftGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + ljcls_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongSoftGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum, itype, jtype;
double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair;
double r, r2inv, forcecoul, forcelj, factor_coul, factor_lj;
double denc, denlj, r4sig6;
double grij, expm2, prefactor, t, erfc;
int *jlist;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij * grij);
t = 1.0 / (1.0 + EWALD_P * grij);
erfc = t * (A1 + t * (A2 + t * (A3 + t * (A4 + t * A5)))) * expm2;
denc = sqrt(lj4[itype][jtype] + rsq);
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
forcecoul = prefactor * (erfc + EWALD_F * grij * expm2);
if (factor_coul < 1.0) forcecoul -= (1.0 - factor_coul) * prefactor;
} else
forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else
forcelj = 0.0;
fpair = (forcecoul + factor_lj * forcelj) * r2inv;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (eflag) {
if (rsq < cut_coulsq) {
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
ecoul = prefactor*erfc;
} else
ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else
evdwl = 0.0;
}
if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz);
}
}
}
}

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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(lj/cut/coul/long/soft/gpu,PairLJCutCoulLongSoftGPU);
// clang-format on
#else
#ifndef LMP_PAIR_LJ_CUT_COUL_LONG_SOFT_GPU_H
#define LMP_PAIR_LJ_CUT_COUL_LONG_SOFT_GPU_H
#include "pair_lj_cut_coul_long_soft.h"
namespace LAMMPS_NS {
class PairLJCutCoulLongSoftGPU : public PairLJCutCoulLongSoft {
public:
PairLJCutCoulLongSoftGPU(LAMMPS *lmp);
~PairLJCutCoulLongSoftGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
void reinit() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_mdpd_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int mdpd_gpu_init(const int ntypes, double **cutsq, double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma, double **host_cut, double **host_cut_r,
double *special_lj, const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen);
void mdpd_gpu_clear();
int **mdpd_gpu_compute_n(const int ago, const int inum_full, 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_v,
const double dtinvsqrt, const int seed, const int timestep, double *boxlo,
double *prd);
void mdpd_gpu_compute(const int ago, const int inum_full, 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, tagint *tag, double **host_v,
const double dtinvsqrt, const int seed, const int timestep, const int nlocal,
double *boxlo, double *prd);
void mdpd_gpu_get_extra_data(double *host_rho);
double mdpd_gpu_bytes();
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairMDPDGPU::PairMDPDGPU(LAMMPS *lmp) : PairMDPD(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairMDPDGPU::~PairMDPDGPU()
{
mdpd_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairMDPDGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0 / sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *rho = atom->rho;
mdpd_gpu_get_extra_data(rho);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = mdpd_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->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
mdpd_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->tag,
atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo, domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairMDPDGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
mdpd_gpu_init(atom->ntypes + 1, cutsq, A_att, B_rep, gamma, sigma,
cut, cut_r, force->special_lj,
atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairMDPDGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + mdpd_gpu_bytes();
}

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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(mdpd/gpu,PairMDPDGPU);
// clang-format on
#else
#ifndef LMP_PAIR_MDPD_GPU_H
#define LMP_PAIR_MDPD_GPU_H
#include "pair_mdpd.h"
namespace LAMMPS_NS {
class PairMDPDGPU : public PairMDPD {
public:
PairMDPDGPU(LAMMPS *lmp);
~PairMDPDGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_sph_heatconduction_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int sph_heatconduction_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_alpha, double* host_mass,
const int dimension, double *special_lj,
const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void sph_heatconduction_gpu_clear();
int **sph_heatconduction_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *host_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_v);
void sph_heatconduction_gpu_compute(const int ago, const int inum_full, 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, tagint *host_tag,
double **host_v, const int nlocal);
void sph_heatconduction_gpu_get_extra_data(double *host_rho, double *host_esph);
void sph_heatconduction_gpu_update_dE(void **dE_ptr);
double sph_heatconduction_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairSPHHeatConductionGPU::PairSPHHeatConductionGPU(LAMMPS *lmp) :
PairSPHHeatConduction(lmp), gpu_mode(GPU_FORCE)
{
dE_pinned = nullptr;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairSPHHeatConductionGPU::~PairSPHHeatConductionGPU()
{
sph_heatconduction_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairSPHHeatConductionGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *rho = atom->rho;
double *esph = atom->esph;
sph_heatconduction_gpu_get_extra_data(rho, esph);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = sph_heatconduction_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->v);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sph_heatconduction_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->tag, atom->v, atom->nlocal);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
// get the drho and dE from device
double *desph = atom->desph;
sph_heatconduction_gpu_update_dE(&dE_pinned);
int nlocal = atom->nlocal;
if (acc_float) {
auto dE_ptr = (float *)dE_pinned;
for (int i = 0; i < nlocal; i++) {
desph[i] = dE_ptr[i];
}
} else {
auto dE_ptr = (double *)dE_pinned;
for (int i = 0; i < nlocal; i++) {
desph[i] = dE_ptr[i];
}
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairSPHHeatConductionGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
sph_heatconduction_gpu_init(atom->ntypes + 1, cutsq, cut, alpha, atom->mass,
domain->dimension, force->special_lj, atom->nlocal,
atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
acc_float = Info::has_accelerator_feature("GPU", "precision", "single");
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairSPHHeatConductionGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + sph_heatconduction_gpu_bytes();
}

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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(sph/heatconduction/gpu,PairSPHHeatConductionGPU);
// clang-format on
#else
#ifndef LMP_PAIR_SPH_HEATCONDUCTION_GPU_H
#define LMP_PAIR_SPH_HEATCONDUCTION_GPU_H
#include "pair_sph_heatconduction.h"
namespace LAMMPS_NS {
class PairSPHHeatConductionGPU : public PairSPHHeatConduction {
public:
PairSPHHeatConductionGPU(LAMMPS *lmp);
~PairSPHHeatConductionGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
void *dE_pinned;
bool acc_float;
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_sph_lj_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int sph_lj_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_viscosity, double* host_mass,
const int dimension, double *special_lj,
const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void sph_lj_gpu_clear();
int **sph_lj_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *host_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_v);
void sph_lj_gpu_compute(const int ago, const int inum_full, 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, tagint *host_tag,
double **host_v, const int nlocal);
void sph_lj_gpu_get_extra_data(double *host_rho, double *host_esph,
double *host_cv);
void sph_lj_gpu_update_drhoE(void **drhoE_ptr);
double sph_lj_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairSPHLJGPU::PairSPHLJGPU(LAMMPS *lmp) : PairSPHLJ(lmp), gpu_mode(GPU_FORCE)
{
drhoE_pinned = nullptr;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairSPHLJGPU::~PairSPHLJGPU()
{
sph_lj_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairSPHLJGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *rho = atom->rho;
double *esph = atom->esph;
double *cv = atom->cv;
sph_lj_gpu_get_extra_data(rho, esph, cv);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = sph_lj_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->v);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sph_lj_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->tag, atom->v, atom->nlocal);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
// get the drho and dE from device
double *drho = atom->drho;
double *desph = atom->desph;
sph_lj_gpu_update_drhoE(&drhoE_pinned);
int nlocal = atom->nlocal;
if (acc_float) {
auto drhoE_ptr = (float *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
} else {
auto drhoE_ptr = (double *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairSPHLJGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
sph_lj_gpu_init(atom->ntypes + 1, cutsq, cut, viscosity, atom->mass,
domain->dimension, force->special_lj, atom->nlocal,
atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
acc_float = Info::has_accelerator_feature("GPU", "precision", "single");
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairSPHLJGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + sph_lj_gpu_bytes();
}

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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(sph/lj/gpu,PairSPHLJGPU);
// clang-format on
#else
#ifndef LMP_PAIR_SPH_LJ_GPU_H
#define LMP_PAIR_SPH_LJ_GPU_H
#include "pair_sph_lj.h"
namespace LAMMPS_NS {
class PairSPHLJGPU : public PairSPHLJ {
public:
PairSPHLJGPU(LAMMPS *lmp);
~PairSPHLJGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
void *drhoE_pinned;
bool acc_float;
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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src/GPU/pair_sph_taitwater_gpu.cpp Normal file
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_sph_taitwater_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int sph_taitwater_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_viscosity, double* host_mass, double* host_rho0,
double* host_soundspeed, double* host_B, const int dimension,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void sph_taitwater_gpu_clear();
int **sph_taitwater_gpu_compute_n(const int ago, const int inum_full, 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_v);
void sph_taitwater_gpu_compute(const int ago, const int inum_full, 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, tagint *tag,
double **host_v, const int nlocal);
void sph_taitwater_gpu_get_extra_data(double *host_rho);
void sph_taitwater_gpu_update_drhoE(void **drhoE_ptr);
double sph_taitwater_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairSPHTaitwaterGPU::PairSPHTaitwaterGPU(LAMMPS *lmp) : PairSPHTaitwater(lmp), gpu_mode(GPU_FORCE)
{
drhoE_pinned = nullptr;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairSPHTaitwaterGPU::~PairSPHTaitwaterGPU()
{
sph_taitwater_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairSPHTaitwaterGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *rho = atom->rho;
sph_taitwater_gpu_get_extra_data(rho);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = sph_taitwater_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->v);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sph_taitwater_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->tag, atom->v, atom->nlocal);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
// get the drho and dE from device
double *drho = atom->drho;
double *desph = atom->desph;
sph_taitwater_gpu_update_drhoE(&drhoE_pinned);
int nlocal = atom->nlocal;
if (acc_float) {
auto drhoE_ptr = (float *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
} else {
auto drhoE_ptr = (double *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairSPHTaitwaterGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
sph_taitwater_gpu_init(atom->ntypes + 1, cutsq, cut, viscosity, atom->mass,
rho0, soundspeed, B, domain->dimension, force->special_lj,
atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
acc_float = Info::has_accelerator_feature("GPU", "precision", "single");
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairSPHTaitwaterGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + sph_taitwater_gpu_bytes();
}

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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(sph/taitwater/gpu,PairSPHTaitwaterGPU);
// clang-format on
#else
#ifndef LMP_PAIR_SPH_TAITWATER_GPU_H
#define LMP_PAIR_SPH_TAITWATER_GPU_H
#include "pair_sph_taitwater.h"
namespace LAMMPS_NS {
class PairSPHTaitwaterGPU : public PairSPHTaitwater {
public:
PairSPHTaitwaterGPU(LAMMPS *lmp);
~PairSPHTaitwaterGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
void *drhoE_pinned;
bool acc_float;
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

2
unittest/force-styles/tests/mol-pair-coul_slater_long.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 23 Jun 2022
date_generated: Thu Jul 7 09:00:39 2022
epsilon: 2e-13
epsilon: 1e-12
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/mol-pair-lj_cut_coul_long_soft.yaml
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---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:31 2022
epsilon: 5e-12
epsilon: 7.5e-12
skip_tests:
prerequisites: ! |
atom full