forked from lijiext/lammps
Implement GPU pair style lj/cut/tip4p/long/gpu
Source code, Makefiles and Install for GPU-accelerated TIP4P pair style. It is implemented as a part of the standard GPU package. The style is compatible with the standard lj/cut/tip4p/long. Also, this commit modifies "atom.h" just to add a getter for variable 'max_same'.
This commit is contained in:
parent
90729ebe25
commit
64bdc59623
|
@ -82,7 +82,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
|
|||
$(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
|
||||
|
||||
CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
|
||||
$(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
|
||||
|
@ -143,7 +144,8 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
|
|||
$(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
|
||||
$(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
|
||||
$(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
|
||||
$(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h \
|
||||
$(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long_cubin.h
|
||||
|
||||
all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
|
||||
|
||||
|
@ -297,6 +299,18 @@ $(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cubin.h $(OBJ_DI
|
|||
$(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long.cubin: lal_lj_tip4p_long.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_tip4p_long.cu
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long_cubin.h: $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long.cubin
|
||||
$(BIN2C) -c -n lj_tip4p_long $(OBJ_DIR)/lj_tip4p_long.cubin > $(OBJ_DIR)/lj_tip4p_long_cubin.h
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp $(OBJ_DIR)/lj_tip4p_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(CUDR) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
|
||||
$(CUDR) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul.cubin: lal_lj_coul.cu lal_precision.h lal_preprocessor.h
|
||||
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul.cu
|
||||
|
||||
|
|
|
@ -71,7 +71,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \
|
|||
$(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
|
||||
$(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
|
||||
$(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
|
||||
|
||||
KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
|
||||
$(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \
|
||||
|
@ -102,7 +103,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
|
|||
$(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \
|
||||
$(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/dipole_long_lj_cl.h \
|
||||
$(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/coul_long_cs_cl.h \
|
||||
$(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h
|
||||
$(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h \
|
||||
$(OBJ_DIR)/lj_tip4p_long_cl.h
|
||||
|
||||
|
||||
OCL_EXECS = $(BIN_DIR)/ocl_get_devices
|
||||
|
@ -202,6 +204,15 @@ $(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cl.h $(OBJ_DIR)
|
|||
$(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_tip4p_long_cl.h: lal_lj_tip4p_long.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_tip4p_long $(PRE1_H) lal_lj_tip4p_long.cu $(OBJ_DIR)/lj_tip4p_long_cl.h;
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lal_base_atomic.o
|
||||
$(OCL) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
|
||||
$(OCL) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
|
||||
|
||||
$(OBJ_DIR)/lj_coul_cl.h: lal_lj_coul.cu $(PRE1_H)
|
||||
$(BSH) ./geryon/file_to_cstr.sh lj_coul $(PRE1_H) lal_lj_coul.cu $(OBJ_DIR)/lj_coul_cl.h;
|
||||
|
||||
|
|
|
@ -0,0 +1,241 @@
|
|||
#if defined(USE_OPENCL)
|
||||
#include "lj_tip4p_long_cl.h"
|
||||
#elif defined(USE_CUDART)
|
||||
const char *lj_tip4p=0;
|
||||
#else
|
||||
#include "lj_tip4p_long_cubin.h"
|
||||
#endif
|
||||
|
||||
#include "lal_lj_tip4p_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
#define LJ_TIP4PLong_T LJ_TIP4PLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
LJ_TIP4PLong<numtyp, acctyp>::LJ_TIP4PLong(): BaseCharge<numtyp,acctyp>(), _allocated(false) {
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
LJ_TIP4PLong<numtyp, acctyp>::~LJ_TIP4PLong() {
|
||||
clear();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int LJ_TIP4PLong<numtyp, acctyp>::bytes_per_atom(const int max_nbors) const {
|
||||
return this->bytes_per_atom_atomic(max_nbors);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
|
||||
double **host_cutsq, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **host_offset,
|
||||
double *host_special_lj, const int nlocal,
|
||||
const int tH, const int tO,
|
||||
const double a, const double qd,
|
||||
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, const double host_cut_coulsqplus,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const double g_ewald, int* tag,
|
||||
int *map_array, int map_size,
|
||||
int *sametag, int max_same) {
|
||||
int success;
|
||||
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
|
||||
_screen,lj_tip4p_long,"k_lj_tip4p_long");
|
||||
if (success!=0)
|
||||
return success;
|
||||
k_pair_distrib.set_function(*this->pair_program,"k_lj_tip4p_long_distrib");
|
||||
|
||||
TypeH = tH;
|
||||
TypeO = tO;
|
||||
alpha = a;
|
||||
qdist = qd;
|
||||
|
||||
// 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);
|
||||
|
||||
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);
|
||||
|
||||
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);
|
||||
|
||||
force_comp.alloc(72*72, *(this->ucl_device), UCL_READ_WRITE);
|
||||
|
||||
_qqrd2e=qqrd2e;
|
||||
_g_ewald=g_ewald;
|
||||
cut_coulsq = host_cut_coulsq;
|
||||
cut_coulsqplus = host_cut_coulsqplus;
|
||||
|
||||
hneight.alloc(nall*4,*(this->ucl_device), UCL_READ_WRITE);
|
||||
m.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
|
||||
ansO.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
|
||||
|
||||
// Allocate a host write buffer for data initialization
|
||||
UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
|
||||
this->tag.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
|
||||
for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
|
||||
ucl_copy(this->tag, host_tag_write, nall, false);
|
||||
|
||||
//if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
|
||||
this->atom_sametag.alloc(nall, *(this->ucl_device), UCL_READ_WRITE);
|
||||
for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
|
||||
ucl_copy(this->atom_sametag, host_tag_write, nall, false);
|
||||
|
||||
if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
|
||||
this->map_array.alloc(map_size,*(this->ucl_device), UCL_READ_WRITE);
|
||||
for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
|
||||
ucl_copy(this->map_array, host_tag_write, map_size, false);
|
||||
|
||||
_allocated=true;
|
||||
this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+
|
||||
sp_lj.row_bytes() + hneight.row_bytes()+m.row_bytes()+
|
||||
this->tag.row_bytes()+this->atom_sametag.row_bytes() +
|
||||
this->map_array.row_bytes();
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void LJ_TIP4PLong<numtyp, acctyp>::clear() {
|
||||
if (!_allocated)
|
||||
return;
|
||||
_allocated=false;
|
||||
|
||||
lj1.clear();
|
||||
lj3.clear();
|
||||
sp_lj.clear();
|
||||
cutsq.clear();
|
||||
hneight.clear();
|
||||
m.clear();
|
||||
tag.clear();
|
||||
atom_sametag.clear();
|
||||
map_array.clear();
|
||||
ansO.clear();
|
||||
force_comp.clear();
|
||||
|
||||
k_pair_distrib.clear();
|
||||
|
||||
this->clear_atomic();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double LJ_TIP4PLong<numtyp, acctyp>::host_memory_usage() const {
|
||||
return this->host_memory_usage_atomic()+sizeof(LJ_TIP4PLong<numtyp,acctyp>);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Calculate energies, forces, and torques
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
|
||||
// Compute the block size and grid size to keep all cores busy
|
||||
const int BX=this->block_size();
|
||||
int eflag, vflag;
|
||||
if (_eflag)
|
||||
eflag=1;
|
||||
else
|
||||
eflag=0;
|
||||
|
||||
if (_vflag)
|
||||
vflag=1;
|
||||
else
|
||||
vflag=0;
|
||||
|
||||
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();
|
||||
|
||||
this->k_pair.set_size(GX,BX);
|
||||
if (vflag){
|
||||
this->ansO.resize(ainum*3);
|
||||
} else {
|
||||
this->ansO.resize(ainum);
|
||||
}
|
||||
this->ansO.zero();
|
||||
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->_threads_per_atom,
|
||||
&hneight, &m, &TypeO, &TypeH, &alpha,
|
||||
&this->atom->q, &cutsq, &_qqrd2e, &_g_ewald,
|
||||
&cut_coulsq, &cut_coulsqplus, &tag, &map_array,
|
||||
&atom_sametag, &this->ansO);
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
|
||||
this->k_pair_distrib.set_size(GX,BX);
|
||||
this->k_pair_distrib.run(&this->atom->x, &this->ans->force, &this->ans->engv, &eflag, &vflag,
|
||||
&ainum, &nbor_pitch, &this->_threads_per_atom,
|
||||
&hneight, &m, &TypeO, &TypeH, &alpha,
|
||||
&this->atom->q, &this->ansO);
|
||||
this->time_pair.stop();
|
||||
}
|
||||
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void LJ_TIP4PLong<numtyp, acctyp>::copy_relations_data(int **hn, double **newsite, int n,
|
||||
int* tag, int *map_array, int map_size, int *sametag, int max_same, int ago){
|
||||
int nall = n;
|
||||
const int hn_sz = n*4; // matrix size = col size * col number
|
||||
if(hn_sz > hneight.cols()){
|
||||
hneight.resize(hn_sz+1);
|
||||
}
|
||||
if (ago == 0)
|
||||
hneight.zero();
|
||||
if(n > m.cols()){
|
||||
m.resize(n+1);
|
||||
}
|
||||
m.zero();
|
||||
|
||||
UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
|
||||
if(this->tag.cols() < nall) this->tag.resize(nall);
|
||||
for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
|
||||
ucl_copy(this->tag, host_tag_write, nall, false);
|
||||
|
||||
if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
|
||||
if(this->atom_sametag.cols() < nall) this->atom_sametag.resize(nall);
|
||||
for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
|
||||
ucl_copy(this->atom_sametag, host_tag_write, nall, false);
|
||||
|
||||
if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
|
||||
if(this->map_array.cols() < map_size) this->map_array.resize(map_size);
|
||||
for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
|
||||
ucl_copy(this->map_array, host_tag_write, map_size, false);
|
||||
|
||||
host_tag_write.clear();
|
||||
}
|
||||
|
||||
template class LJ_TIP4PLong<PRECISION,ACC_PRECISION>;
|
|
@ -0,0 +1,518 @@
|
|||
#ifdef NV_KERNEL
|
||||
|
||||
#include "lal_aux_fun1.h"
|
||||
#ifndef _DOUBLE_DOUBLE
|
||||
texture<float4> pos_tex;
|
||||
texture<float> q_tex;
|
||||
#else
|
||||
texture<int4,1> pos_tex;
|
||||
texture<int2> q_tex;
|
||||
#endif
|
||||
|
||||
#else
|
||||
#define pos_tex x_
|
||||
#define q_tex q_
|
||||
#endif
|
||||
|
||||
ucl_inline int atom_mapping(const __global int *map, int glob){
|
||||
return map[glob];
|
||||
}
|
||||
|
||||
ucl_inline int closest_image(int i, int j, const __global int* sametag,
|
||||
const __global numtyp4 *restrict x_)
|
||||
{
|
||||
if (j < 0) return j;
|
||||
|
||||
numtyp4 xi; fetch4(xi,i,pos_tex); // = x[i];
|
||||
numtyp4 xj; fetch4(xj,j,pos_tex);
|
||||
|
||||
int closest = j;
|
||||
numtyp delx = xi.x - xj.x;
|
||||
numtyp dely = xi.y - xj.y;
|
||||
numtyp delz = xi.z - xj.z;
|
||||
numtyp rsqmin = delx*delx + dely*dely + delz*delz;
|
||||
numtyp rsq;
|
||||
|
||||
while (sametag[j] >= 0) {
|
||||
j = sametag[j];
|
||||
fetch4(xj,j,pos_tex);
|
||||
delx = xi.x - xj.x;
|
||||
dely = xi.y - xj.y;
|
||||
delz = xi.z - xj.z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
if (rsq < rsqmin) {
|
||||
rsqmin = rsq;
|
||||
closest = j;
|
||||
}
|
||||
}
|
||||
|
||||
return closest;
|
||||
}
|
||||
|
||||
ucl_inline void compute_newsite(int iO, int iH1, int iH2,
|
||||
__global numtyp4 *xM,
|
||||
numtyp alpha, const __global numtyp4 *restrict x_){
|
||||
numtyp4 xO; fetch4(xO,iO,pos_tex);
|
||||
numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
|
||||
numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
|
||||
|
||||
numtyp delx1 = xH1.x - xO.x;
|
||||
numtyp dely1 = xH1.y - xO.y;
|
||||
numtyp delz1 = xH1.z - xO.z;
|
||||
|
||||
numtyp delx2 = xH2.x - xO.x;
|
||||
numtyp dely2 = xH2.y - xO.y;
|
||||
numtyp delz2 = xH2.z - xO.z;
|
||||
|
||||
numtyp ap = alpha * (numtyp)0.5;
|
||||
|
||||
(*xM).x = xO.x + ap * (delx1 + delx2);
|
||||
(*xM).y = xO.y + ap * (dely1 + dely2);
|
||||
(*xM).z = xO.z + ap * (delz1 + delz2);
|
||||
}
|
||||
|
||||
__kernel void k_lj_tip4p_long_distrib(const __global numtyp4 *restrict x_,
|
||||
__global acctyp4 *restrict ans,
|
||||
__global acctyp *restrict engv,
|
||||
const int eflag, const int vflag, const int inum,
|
||||
const int nbor_pitch, const int t_per_atom,
|
||||
__global int *restrict hneigh,
|
||||
__global numtyp4 *restrict m,
|
||||
const int typeO, const int typeH,
|
||||
const numtyp alpha,
|
||||
const __global numtyp *restrict q_, const __global acctyp4 *restrict ansO) {
|
||||
int tid, ii, offset;
|
||||
atom_info(t_per_atom,ii,tid,offset);
|
||||
int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
|
||||
|
||||
acctyp4 f;
|
||||
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
|
||||
|
||||
if (i<inum) {
|
||||
numtyp4 ix; fetch4(ix,i,pos_tex);// = x_[i];
|
||||
int itype = ix.w;
|
||||
acctyp4 fM, vM;
|
||||
acctyp eM;
|
||||
if (itype == typeH) {
|
||||
int iO = hneigh[i*4];
|
||||
if (iO < inum) {
|
||||
fM = ansO[iO];
|
||||
f.x += fM.x * (acctyp)0.5 * alpha;
|
||||
f.y += fM.y * (acctyp)0.5 * alpha;
|
||||
f.z += fM.z * (acctyp)0.5 * alpha;
|
||||
if (vflag > 0) {
|
||||
vM = ansO[inum +iO];
|
||||
engv[inum*2 + i] += vM.x * (acctyp)0.5 * alpha;
|
||||
engv[inum*3 + i] += vM.y * (acctyp)0.5 * alpha;
|
||||
engv[inum*4 + i] += vM.z * (acctyp)0.5 * alpha;
|
||||
vM = ansO[inum*2+iO];
|
||||
engv[inum*5 + i] += vM.x * (acctyp)0.5 * alpha;
|
||||
engv[inum*6 + i] += vM.y * (acctyp)0.5 * alpha;
|
||||
engv[inum*7 + i] += vM.z * (acctyp)0.5 * alpha;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
fM = ansO[i];
|
||||
int iH1 = hneigh[i*4 ];
|
||||
int iH2 = hneigh[i*4+1];
|
||||
f.x += fM.x * (acctyp)(1 - alpha);
|
||||
f.y += fM.y * (acctyp)(1 - alpha);
|
||||
f.z += fM.z * (acctyp)(1 - alpha);
|
||||
if (eflag > 0) {
|
||||
eM = engv[i+inum];
|
||||
engv[inum+i] = eM*(acctyp)(1 - alpha);
|
||||
if (iH1 < inum) engv[inum+iH1] += eM * (acctyp)0.5 * alpha;
|
||||
if (iH2 < inum) engv[inum+iH2] += eM * (acctyp)0.5 * alpha;
|
||||
}
|
||||
if (vflag > 0) {
|
||||
vM = ansO[inum + i];
|
||||
engv[inum*2 + i] += vM.x * (acctyp)(1 - alpha);
|
||||
engv[inum*3 + i] += vM.y * (acctyp)(1 - alpha);
|
||||
engv[inum*4 + i] += vM.z * (acctyp)(1 - alpha);
|
||||
vM = ansO[inum*2 + i];
|
||||
engv[inum*5 + i] += vM.x * (acctyp)(1 - alpha);
|
||||
engv[inum*6 + i] += vM.y * (acctyp)(1 - alpha);
|
||||
engv[inum*7 + i] += vM.z * (acctyp)(1 - alpha);
|
||||
}
|
||||
}
|
||||
acctyp4 old=ans[i];
|
||||
old.x+=f.x;
|
||||
old.y+=f.y;
|
||||
old.z+=f.z;
|
||||
ans[i]=old;
|
||||
} // if ii
|
||||
}
|
||||
|
||||
__kernel void k_lj_tip4p_long(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,
|
||||
const __global int * dev_nbor,
|
||||
const __global int * dev_packed,
|
||||
__global acctyp4 *restrict ans,
|
||||
__global acctyp *restrict engv,
|
||||
const int eflag, const int vflag, const int inum,
|
||||
const int nbor_pitch, const int t_per_atom,
|
||||
__global int *restrict hneigh,
|
||||
__global numtyp4 *restrict m,
|
||||
const int typeO, const int typeH,
|
||||
const numtyp alpha,
|
||||
const __global numtyp *restrict q_,
|
||||
const __global numtyp *restrict cutsq,
|
||||
const numtyp qqrd2e, const numtyp g_ewald,
|
||||
const numtyp cut_coulsq, const numtyp cut_coulsqplus,
|
||||
const __global int *restrict tag, const __global int *restrict map,
|
||||
const __global int *restrict sametag, __global acctyp4 *restrict ansO) {
|
||||
int tid, ii, offset;
|
||||
atom_info(t_per_atom,ii,tid,offset);
|
||||
|
||||
acctyp energy = (acctyp)0;
|
||||
acctyp e_coul = (acctyp)0;
|
||||
acctyp4 f, fO;
|
||||
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
|
||||
fO.x=(acctyp)0; fO.y=(acctyp)0; fO.z=(acctyp)0;
|
||||
acctyp virial[6],vO[6];
|
||||
for (int i=0; i<6; i++) {
|
||||
virial[i]=(acctyp)0;
|
||||
vO[i]=(acctyp)0;
|
||||
}
|
||||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor, nbor_end;
|
||||
__local int n_stride;
|
||||
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;
|
||||
numtyp4 x1 = ix;
|
||||
|
||||
int non_local_oxy = 0;
|
||||
int iH1, iH2, iO;
|
||||
|
||||
if(itype == typeO) {
|
||||
iO = i;
|
||||
if (hneigh[i*4+2] != -1) {
|
||||
iH1 = atom_mapping(map, tag[i] + 1);
|
||||
iH2 = atom_mapping(map, tag[i] + 2);
|
||||
// set iH1,iH2 to closest image to O
|
||||
iH1 = closest_image(i, iH1, sametag, x_);
|
||||
iH2 = closest_image(i, iH2, sametag, x_);
|
||||
hneigh[ i*4 ] = iH1;
|
||||
hneigh[ i*4+1] = iH2;
|
||||
hneigh[ i*4+2] = -1;
|
||||
hneigh[iH1*4 ] = i;
|
||||
hneigh[iH1*4+1] += -1;
|
||||
hneigh[iH1*4+2] = -1;
|
||||
hneigh[iH2*4 ] = i;
|
||||
hneigh[iH2*4+1] += -1;
|
||||
hneigh[iH2*4+2] = -1;
|
||||
} else {
|
||||
iH1 = hneigh[i*4 ];
|
||||
iH2 = hneigh[i*4+1];
|
||||
}
|
||||
if(m[iO].w == 0) {
|
||||
compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
|
||||
m[iO].w = qtmp;
|
||||
}
|
||||
x1 = m[iO];
|
||||
} else {
|
||||
if (hneigh[i*4+2] != -1) {
|
||||
int iI, iH;
|
||||
iI = atom_mapping(map,tag[i] - 1);
|
||||
numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
|
||||
if (iIx.w == typeH) {
|
||||
iO = atom_mapping(map,tag[i] - 2);
|
||||
iO = closest_image(i, iO, sametag, x_);
|
||||
iH1 = closest_image(i, iI, sametag, x_);
|
||||
iH2 = i;
|
||||
} else if (iIx.w == typeO) {
|
||||
iH = atom_mapping(map, tag[i] + 1);
|
||||
iO = closest_image(i,iI,sametag, x_);
|
||||
iH1 = i;
|
||||
iH2 = closest_image(i,iH,sametag, x_);
|
||||
}
|
||||
|
||||
hneigh[iH1*4+0] = iO;
|
||||
hneigh[iH1*4+1] += -1;
|
||||
hneigh[iH1*4+2] = -1;
|
||||
|
||||
hneigh[iH2*4+0] = iO;
|
||||
hneigh[iH2*4+1] += -1;
|
||||
hneigh[iH2*4+2] = -1;
|
||||
|
||||
hneigh[iO*4+0] = iH1;
|
||||
hneigh[iO*4+1] = iH2;
|
||||
hneigh[iO*4+2] = -1;
|
||||
} else {
|
||||
iO = hneigh[i *4 ];
|
||||
iH1 = hneigh[iO*4 ];
|
||||
iH2 = hneigh[iO*4+1];
|
||||
}
|
||||
if (iO >= inum) {
|
||||
non_local_oxy = 1;
|
||||
if(m[iO].w == 0) {
|
||||
compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
|
||||
numtyp qO; fetch(qO,iO,q_tex);
|
||||
m[iO].w = qO;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
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 = (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) { // cut_ljsq
|
||||
numtyp r2inv = ucl_recip(rsq);
|
||||
numtyp r6inv = r2inv*r2inv*r2inv;
|
||||
numtyp forcelj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
|
||||
forcelj *= r2inv*factor_lj;
|
||||
|
||||
f.x += delx*forcelj;
|
||||
f.y += dely*forcelj;
|
||||
f.z += delz*forcelj;
|
||||
|
||||
if (eflag>0) {
|
||||
numtyp e = r6inv * (lj3[mtype].x*r6inv-lj3[mtype].y);
|
||||
energy += factor_lj * (e - lj3[mtype].z);
|
||||
}
|
||||
if (vflag>0) {
|
||||
virial[0] += delx*delx*forcelj;
|
||||
virial[1] += dely*dely*forcelj;
|
||||
virial[2] += delz*delz*forcelj;
|
||||
virial[3] += delx*dely*forcelj;
|
||||
virial[4] += delx*delz*forcelj;
|
||||
virial[5] += dely*delz*forcelj;
|
||||
}
|
||||
} // if LJ
|
||||
|
||||
if (rsq < cut_coulsqplus) { //cut_coulsqplus
|
||||
int jH1, jH2, jO;
|
||||
numtyp qj; fetch(qj,j,q_tex);
|
||||
numtyp4 x2 = jx;
|
||||
if(itype == typeO || jtype == typeO) {
|
||||
if (jtype == typeO) {
|
||||
jO = j;
|
||||
if (hneigh[j*4+2] != -1) {
|
||||
jH1 = atom_mapping(map,tag[j] + 1);
|
||||
jH2 = atom_mapping(map,tag[j] + 2);
|
||||
// set iH1,iH2 to closest image to O
|
||||
jH1 = closest_image(j, jH1, sametag, x_);
|
||||
jH2 = closest_image(j, jH2, sametag, x_);
|
||||
hneigh[j*4 ] = jH1;
|
||||
hneigh[j*4+1] = jH2;
|
||||
hneigh[j*4+2] = -1;
|
||||
hneigh[jH1*4 ] = j;
|
||||
hneigh[jH1*4+1] += -1;
|
||||
hneigh[jH1*4+2] = -1;
|
||||
hneigh[jH2*4 ] = j;
|
||||
hneigh[jH2*4+1] += -1;
|
||||
hneigh[jH2*4+2] = -1;
|
||||
} else {
|
||||
jH1 = hneigh[j*4 ];
|
||||
jH2 = hneigh[j*4+1];
|
||||
}
|
||||
if (m[j].w == 0) {
|
||||
compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
|
||||
m[j].w = qj;
|
||||
}
|
||||
x2 = m[j];
|
||||
}
|
||||
delx = x1.x-x2.x;
|
||||
dely = x1.y-x2.y;
|
||||
delz = x1.z-x2.z;
|
||||
rsq = delx*delx+dely*dely+delz*delz;
|
||||
}
|
||||
if (rsq < cut_coulsq) {
|
||||
numtyp r2inv = ucl_recip(rsq);
|
||||
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);
|
||||
numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
|
||||
numtyp prefactor = qj;
|
||||
prefactor *= qqrd2e*qtmp/r;
|
||||
numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
|
||||
|
||||
if (itype == typeH) {
|
||||
f.x += delx * force_coul;
|
||||
f.y += dely * force_coul;
|
||||
f.z += delz * force_coul;
|
||||
} else {
|
||||
fO.x += delx * force_coul;
|
||||
fO.y += dely * force_coul;
|
||||
fO.z += delz * force_coul;
|
||||
fO.w += -1;
|
||||
}
|
||||
if (eflag>0) {
|
||||
e_coul += prefactor*(_erfc-factor_coul);
|
||||
}
|
||||
if (vflag>0) {
|
||||
acctyp4 fd;
|
||||
fd.x = delx*force_coul;
|
||||
fd.y = dely*force_coul;
|
||||
fd.z = delz*force_coul;
|
||||
if (itype == typeH) {
|
||||
if (jtype == typeH){
|
||||
virial[0] += delx*fd.x;
|
||||
virial[1] += dely*fd.y;
|
||||
virial[2] += delz*fd.z;
|
||||
virial[3] += delx*fd.y;
|
||||
virial[4] += delx*fd.z;
|
||||
virial[5] += dely*fd.z;
|
||||
} else {
|
||||
numtyp cO = 1 - alpha, cH = 0.5*alpha;
|
||||
numtyp4 vdj;
|
||||
numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
|
||||
numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
|
||||
numtyp4 xjO; fetch4(xjO,jO,pos_tex);
|
||||
vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
|
||||
vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
|
||||
vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
|
||||
virial[0] += (ix.x - vdj.x)*fd.x;
|
||||
virial[1] += (ix.y - vdj.y)*fd.y;
|
||||
virial[2] += (ix.z - vdj.z)*fd.z;
|
||||
virial[3] += (ix.x - vdj.x)*fd.y;
|
||||
virial[4] += (ix.x - vdj.x)*fd.z;
|
||||
virial[5] += (ix.y - vdj.y)*fd.z;
|
||||
}
|
||||
} else {
|
||||
numtyp cO = 1 - alpha, cH = 0.5*alpha;
|
||||
numtyp4 vdi, vdj;
|
||||
numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
|
||||
numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
|
||||
numtyp4 xO; fetch4(xO,iO,pos_tex);
|
||||
vdi.x = xO.x*cO + xH1.x*cH + xH2.x*cH;
|
||||
vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
|
||||
vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
|
||||
if (jtype != typeH){
|
||||
numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
|
||||
numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
|
||||
numtyp4 xjO; fetch4(xjO,jO,pos_tex);
|
||||
vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
|
||||
vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
|
||||
vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
|
||||
} else vdj = jx;
|
||||
vO[0] += 0.5*(vdi.x - vdj.x)*fd.x;
|
||||
vO[1] += 0.5*(vdi.y - vdj.y)*fd.y;
|
||||
vO[2] += 0.5*(vdi.z - vdj.z)*fd.z;
|
||||
vO[3] += 0.5*(vdi.x - vdj.x)*fd.y;
|
||||
vO[4] += 0.5*(vdi.x - vdj.x)*fd.z;
|
||||
vO[5] += 0.5*(vdi.y - vdj.y)*fd.z;
|
||||
}
|
||||
}
|
||||
}
|
||||
if (non_local_oxy == 1) {
|
||||
if (iO == j) {
|
||||
x2 = ix;
|
||||
qj = qtmp;
|
||||
}
|
||||
numtyp4 x1m = m[iO];
|
||||
delx = x1m.x-x2.x;
|
||||
dely = x1m.y-x2.y;
|
||||
delz = x1m.z-x2.z;
|
||||
rsq = delx*delx+dely*dely+delz*delz;
|
||||
if (rsq < cut_coulsq) {
|
||||
numtyp r2inv = ucl_recip(rsq);
|
||||
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);
|
||||
numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
|
||||
numtyp prefactor = qj;
|
||||
prefactor *= qqrd2e*x1m.w/r;
|
||||
numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
|
||||
|
||||
numtyp cO = 1 - alpha, cH = 0.5*alpha;
|
||||
numtyp4 fd;
|
||||
fd.x = delx * force_coul * cH;
|
||||
fd.y = dely * force_coul * cH;
|
||||
fd.z = delz * force_coul * cH;
|
||||
|
||||
f.x += fd.x;
|
||||
f.y += fd.y;
|
||||
f.z += fd.z;
|
||||
|
||||
if (eflag>0) {
|
||||
e_coul += prefactor*(_erfc-factor_coul) * (acctyp)0.5 * alpha;
|
||||
}
|
||||
if (vflag>0) {
|
||||
numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
|
||||
numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
|
||||
numtyp4 xO; fetch4(xO,iO,pos_tex);
|
||||
|
||||
virial[0] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.x;
|
||||
virial[1] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.y;
|
||||
virial[2] += ((xO.z*cO + xH1.z*cH + xH2.z*cH) - x2.z) * fd.z;
|
||||
virial[3] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.y;
|
||||
virial[4] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.z;
|
||||
virial[5] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.z;
|
||||
}
|
||||
}
|
||||
}
|
||||
} // if cut_coulsqplus
|
||||
} // for nbor
|
||||
if (t_per_atom>1) {
|
||||
__local acctyp red_acc[6][BLOCK_PAIR];
|
||||
red_acc[0][tid]=fO.x;
|
||||
red_acc[1][tid]=fO.y;
|
||||
red_acc[2][tid]=fO.z;
|
||||
red_acc[3][tid]=fO.w;
|
||||
for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
|
||||
if (offset < s) {
|
||||
for (int r=0; r<4; r++)
|
||||
red_acc[r][tid] += red_acc[r][tid+s];
|
||||
}
|
||||
}
|
||||
fO.x=red_acc[0][tid];
|
||||
fO.y=red_acc[1][tid];
|
||||
fO.z=red_acc[2][tid];
|
||||
fO.w=red_acc[3][tid];
|
||||
if (vflag>0) {
|
||||
for (int r=0; r<6; r++) red_acc[r][tid]=vO[r];
|
||||
for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
|
||||
if (offset < s) {
|
||||
for (int r=0; r<6; r++)
|
||||
red_acc[r][tid] += red_acc[r][tid+s];
|
||||
}
|
||||
}
|
||||
for (int r=0; r<6; r++) vO[r]=red_acc[r][tid];
|
||||
}
|
||||
}
|
||||
if(offset == 0) {
|
||||
ansO[i] = fO;
|
||||
if (vflag>0) {
|
||||
ansO[inum + i].x = vO[0];
|
||||
ansO[inum + i].y = vO[1];
|
||||
ansO[inum + i].z = vO[2];
|
||||
ansO[inum*2 + i].x = vO[3];
|
||||
ansO[inum*2 + i].y = vO[4];
|
||||
ansO[inum*2 + i].z = vO[5];
|
||||
}
|
||||
}
|
||||
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
|
||||
vflag,ans,engv);
|
||||
} // if ii
|
||||
}
|
||||
|
||||
|
||||
__kernel void k_lj_tip4p_long_fast(){}
|
|
@ -0,0 +1,95 @@
|
|||
#ifndef LAL_LJ_TIP4P_LONG_H
|
||||
#define LAL_LJ_TIP4P_LONG_H
|
||||
|
||||
#include "lal_base_charge.h"
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class LJ_TIP4PLong : public BaseCharge<numtyp, acctyp> {
|
||||
public:
|
||||
LJ_TIP4PLong();
|
||||
~LJ_TIP4PLong();
|
||||
|
||||
/// 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 successfull
|
||||
* - -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_special_lj,
|
||||
const int nlocal, const int tH, const int tO,
|
||||
const double alpha, const double qdist,
|
||||
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, const double host_cut_coulsqplus,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const double g_ewald, int* tag,
|
||||
int *map_array, int map_size,
|
||||
int *sametag, int max_same);
|
||||
|
||||
/// 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;
|
||||
|
||||
/// Copy data which is easier to compute in LAMMPS_NS
|
||||
void copy_relations_data(int **hn, double **m, int n,int* tag, int *map_array, int map_size,
|
||||
int *sametag, int max_same, int ago);
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq_vdw
|
||||
UCL_D_Vec<numtyp4> lj1;
|
||||
/// lj3.x = lj3, lj3.y = lj4, lj3.z = offset
|
||||
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, _g_ewald;
|
||||
/// TIP4P water parameters
|
||||
int TypeO, TypeH;
|
||||
numtyp alpha, qdist;
|
||||
numtyp cut_coulsq, cut_coulsqplus;
|
||||
|
||||
UCL_D_Vec<int> hneight;
|
||||
UCL_D_Vec<numtyp4> m; // position and charge of virtual particle
|
||||
UCL_D_Vec<acctyp4> ansO; // force applied to virtual particle
|
||||
UCL_D_Vec<acctyp4> force_comp;
|
||||
|
||||
UCL_D_Vec<int> tag;
|
||||
UCL_D_Vec<int> map_array;
|
||||
UCL_D_Vec<int> atom_sametag;
|
||||
|
||||
UCL_Kernel k_pair_distrib;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
|
@ -0,0 +1,135 @@
|
|||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <cmath>
|
||||
|
||||
#include "lal_lj_tip4p_long.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
static LJ_TIP4PLong<PRECISION,ACC_PRECISION> LJTIP4PLMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3, double **host_lj4,
|
||||
double **offset, double *special_lj, const int inum,
|
||||
const int tH, const int tO,
|
||||
const double alpha, const double qdist,
|
||||
const int nall, const int max_nbors, const int maxspecial,
|
||||
const double cell_size, int &gpu_mode, FILE *screen,
|
||||
double **host_cut_ljsq,
|
||||
const double host_cut_coulsq, const double host_cut_coulsqplus,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const double g_ewald, int* tag,
|
||||
int *map_array, int map_size,
|
||||
int *sametag, int max_same) {
|
||||
LJTIP4PLMF.clear();
|
||||
gpu_mode=LJTIP4PLMF.device->gpu_mode();
|
||||
double gpu_split=LJTIP4PLMF.device->particle_split();
|
||||
int first_gpu=LJTIP4PLMF.device->first_device();
|
||||
int last_gpu=LJTIP4PLMF.device->last_device();
|
||||
int world_me=LJTIP4PLMF.device->world_me();
|
||||
int gpu_rank=LJTIP4PLMF.device->gpu_rank();
|
||||
int procs_per_gpu=LJTIP4PLMF.device->procs_per_gpu();
|
||||
|
||||
LJTIP4PLMF.device->init_message(screen,"lj/cut/tip4p/long/gpu",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (LJTIP4PLMF.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=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3,
|
||||
host_lj4, offset, special_lj, inum,
|
||||
tH, tO, alpha, qdist, nall, 300,
|
||||
maxspecial, cell_size, gpu_split, screen,
|
||||
host_cut_ljsq, host_cut_coulsq, host_cut_coulsqplus,
|
||||
host_special_coul, qqrd2e, g_ewald, tag,
|
||||
map_array, map_size,
|
||||
sametag, max_same);
|
||||
|
||||
LJTIP4PLMF.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=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
|
||||
offset, special_lj, inum,
|
||||
tH, tO, alpha, qdist, nall, 300, maxspecial,
|
||||
cell_size, gpu_split, screen, host_cut_ljsq,
|
||||
host_cut_coulsq, host_cut_coulsqplus,
|
||||
host_special_coul, qqrd2e, g_ewald,tag,
|
||||
map_array, map_size,
|
||||
sametag, max_same);
|
||||
|
||||
LJTIP4PLMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
LJTIP4PLMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
|
||||
|
||||
void ljtip4p_long_gpu_clear() {
|
||||
LJTIP4PLMF.clear();
|
||||
}
|
||||
|
||||
int ** ljtip4p_long_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 LJTIP4PLMF.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 ljtip4p_long_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) {
|
||||
LJTIP4PLMF.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 ljtip4p_long_gpu_bytes() {
|
||||
return LJTIP4PLMF.host_memory_usage();
|
||||
}
|
||||
|
||||
void ljtip4p_long_copy_molecule_data(int **hn, double **m, int n, int* tag,
|
||||
int *map_array, int map_size,
|
||||
int *sametag, int max_same, int ago){
|
||||
LJTIP4PLMF.copy_relations_data(hn, m, n, tag,map_array,map_size,sametag, max_same, ago);
|
||||
}
|
||||
|
||||
|
|
@ -143,6 +143,8 @@ action pair_ufm_gpu.cpp
|
|||
action pair_ufm_gpu.h
|
||||
action pair_lj_cut_dipole_long_gpu.cpp pair_lj_cut_dipole_long.cpp
|
||||
action pair_lj_cut_dipole_long_gpu.h pair_lj_cut_dipole_long.cpp
|
||||
action pair_lj_cut_tip4p_long_gpu.h
|
||||
action pair_lj_cut_tip4p_long_gpu.cpp
|
||||
|
||||
# edit 2 Makefile.package files to include/exclude package info
|
||||
|
||||
|
|
|
@ -0,0 +1,234 @@
|
|||
#include <cmath>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "pair_lj_cut_tip4p_long_gpu.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "integrate.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neigh_request.h"
|
||||
#include "universe.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "angle.h"
|
||||
#include "bond.h"
|
||||
#include "gpu_extra.h"
|
||||
|
||||
#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 ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3, double **host_lj4,
|
||||
double **offset, double *special_lj, const int nlocal,
|
||||
const int tH, const int tO, const double alpha, const double qdist,
|
||||
const int nall, const int max_nbors, const int maxspecial,
|
||||
const double cell_size, int &gpu_mode, FILE *screen,
|
||||
double **host_cut_ljsq, const double host_cut_coulsq,
|
||||
const double host_cut_coulsqplus,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const double g_ewald, int* tag,
|
||||
int *map_array, int map_size,
|
||||
int *sametag, int max_same);
|
||||
void ljtip4p_long_gpu_clear();
|
||||
int ** ljtip4p_long_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 ljtip4p_long_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 ljtip4p_long_gpu_bytes();
|
||||
void ljtip4p_long_copy_molecule_data(int **, double **, int, int* , int *, int, int *, int , int);
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
|
||||
: PairLJCutTIP4PLong(lmp), gpu_mode(GPU_FORCE)
|
||||
{
|
||||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
free all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutTIP4PLongGPU::~PairLJCutTIP4PLongGPU()
|
||||
{
|
||||
ljtip4p_long_gpu_clear();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongGPU::compute(int eflag, int vflag)
|
||||
{
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
int inum, host_start;
|
||||
|
||||
ljtip4p_long_copy_molecule_data(hneigh, newsite, nall, atom->tag,
|
||||
atom->get_map_array(), atom->get_map_size(),
|
||||
atom->sametag, atom->get_max_same(), neighbor->ago);
|
||||
|
||||
bool success = true;
|
||||
int *ilist, *numneigh, **firstneigh;
|
||||
if (gpu_mode != GPU_FORCE) {
|
||||
inum = atom->nlocal;
|
||||
firstneigh = ljtip4p_long_gpu_compute_n(neighbor->ago, inum, nall,
|
||||
atom->x, atom->type, domain->sublo,
|
||||
domain->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;
|
||||
ljtip4p_long_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 = MPI_Wtime();
|
||||
// cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
|
||||
// cpu_time = MPI_Wtime() - cpu_time;
|
||||
// }
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongGPU::init_style()
|
||||
{
|
||||
|
||||
cut_respa = NULL;
|
||||
if (atom->tag_enable == 0)
|
||||
error->all(FLERR,"Pair style lj/cut/tip4p/long/gpu requires atom IDs");
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,
|
||||
"Pair style lj/cut/tip4p/long/gpu requires atom attribute q");
|
||||
if (force->bond == NULL)
|
||||
error->all(FLERR,"Must use a bond style with TIP4P potential");
|
||||
if (force->angle == NULL)
|
||||
error->all(FLERR,"Must use an angle style with TIP4P potential");
|
||||
|
||||
if (atom->map_style == 2)
|
||||
error->all(FLERR,"GPU-accelerated lj/cut/tip4p/long currently requires map style 'array' (atom_modify map array)");
|
||||
|
||||
//PairLJCutCoulLong::init_style();
|
||||
// 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;
|
||||
|
||||
// insure use of KSpace long-range solver, set g_ewald
|
||||
if (force->kspace == NULL)
|
||||
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)
|
||||
maxspecial=atom->maxspecial;
|
||||
|
||||
// set alpha parameter
|
||||
double theta = force->angle->equilibrium_angle(typeA);
|
||||
double blen = force->bond->equilibrium_distance(typeB);
|
||||
alpha = qdist / (cos(0.5*theta) * blen);
|
||||
|
||||
cut_coulsq = cut_coul * cut_coul;
|
||||
double cut_coulsqplus = (cut_coul+qdist+blen) * (cut_coul+qdist+blen);
|
||||
if (maxcut < cut_coulsqplus) {
|
||||
cell_size = (cut_coul+qdist+blen) + neighbor->skin;
|
||||
}
|
||||
if (comm->cutghostuser < cell_size) {
|
||||
comm->cutghostuser = cell_size;
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Increasing communication cutoff for TIP4P GPU style");
|
||||
}
|
||||
|
||||
int success = ljtip4p_long_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
|
||||
offset, force->special_lj, atom->nlocal,
|
||||
typeH, typeO, alpha, qdist,
|
||||
atom->nlocal+atom->nghost, 300, maxspecial,
|
||||
cell_size, gpu_mode, screen, cut_ljsq,
|
||||
cut_coulsq, cut_coulsqplus,
|
||||
force->special_coul, force->qqrd2e,
|
||||
g_ewald,
|
||||
atom->tag,
|
||||
atom->get_map_array(), atom->get_map_size(),
|
||||
atom->sametag, atom->get_max_same());
|
||||
GPU_EXTRA::check_flag(success,error,world);
|
||||
if (gpu_mode == GPU_FORCE) {
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
neighbor->requests[irequest]->cut = 1;
|
||||
neighbor->requests[irequest]->cutoff = cut_coul+qdist+blen + neighbor->skin;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutTIP4PLongGPU::memory_usage()
|
||||
{
|
||||
double bytes = PairLJCutTIP4PLong::memory_usage();
|
||||
return bytes + ljtip4p_long_gpu_bytes();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
//void PairLJCutTIP4PLongGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
||||
// int *ilist, int *numneigh, int **firstneigh) {
|
||||
// error->all(FLERR,"PairLJCutTIP4PLongGPU::cpu_compute not implemented");
|
||||
//}
|
|
@ -0,0 +1,32 @@
|
|||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/tip4p/long/gpu,PairLJCutTIP4PLongGPU)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_TIP4P_LONG_GPU_H
|
||||
#define LMP_PAIR_LJ_TIP4P_LONG_GPU_H
|
||||
|
||||
#include "pair_lj_cut_tip4p_long.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutTIP4PLongGPU : public PairLJCutTIP4PLong {
|
||||
public:
|
||||
PairLJCutTIP4PLongGPU(LAMMPS *lmp);
|
||||
~PairLJCutTIP4PLongGPU();
|
||||
// void cpu_compute(int, int, int, int, int *, int *, int **);
|
||||
void compute(int, int);
|
||||
void init_style();
|
||||
double memory_usage();
|
||||
|
||||
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
|
||||
|
||||
private:
|
||||
int gpu_mode;
|
||||
double cpu_time;
|
||||
};
|
||||
|
||||
}
|
||||
#endif
|
||||
#endif
|
|
@ -287,6 +287,7 @@ class Atom : protected Pointers {
|
|||
|
||||
inline int* get_map_array() {return map_array;};
|
||||
inline int get_map_size() {return map_tag_max+1;};
|
||||
inline int get_max_same() {return max_same;};
|
||||
inline int get_map_maxarray() {return map_maxarray+1;};
|
||||
|
||||
bigint memory_usage();
|
||||
|
|
Loading…
Reference in New Issue