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Added vashishta GPU package for NVidia

This commit is contained in:
Anders Hafreager 2017-06-14 10:24:16 +02:00
parent 286d4f2743
commit eeff0b8633
8 changed files with 1606 additions and 0 deletions
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14
lib/gpu/Nvidia.makefile
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@ -63,6 +63,7 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
$(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \
$(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \
$(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \
$(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \
$(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \
$(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \
$(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \
@ -117,6 +118,7 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
$(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye_cubin.h \
$(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf_cubin.h \
$(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw_cubin.h \
$(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta_cubin.h \
$(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck_cubin.h \
$(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie_cubin.h \
$(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft_cubin.h \
@ -613,6 +615,18 @@ $(OBJ_DIR)/lal_coul_dsf.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf.cpp $(OBJ_DIR)/c
$(OBJ_DIR)/lal_coul_dsf_ext.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf_ext.cpp lal_base_charge.h
$(CUDR) -o $@ -c lal_coul_dsf_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/vashishta.cubin: lal_vashishta.cu lal_precision.h lal_preprocessor.h
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_vashishta.cu
$(OBJ_DIR)/vashishta_cubin.h: $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta.cubin
$(BIN2C) -c -n vashishta $(OBJ_DIR)/vashishta.cubin > $(OBJ_DIR)/vashishta_cubin.h
$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cubin.h $(OBJ_DIR)/lal_base_three.o
$(CUDR) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h
$(CUDR) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/sw.cubin: lal_sw.cu lal_precision.h lal_preprocessor.h
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_sw.cu

283
lib/gpu/lal_vashishta.cpp Normal file
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@ -0,0 +1,283 @@
/***************************************************************************
vashishta.cpp
-------------------
Anders Hafreager (UiO)
Class for acceleration of the vashishta pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : Mon June 12, 2017
email : andershaf@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "vashishta_cl.h"
#elif defined(USE_CUDART)
const char *vashishta=0;
#else
#include "vashishta_cubin.h"
#endif
#include "lal_vashishta.h"
#include <cassert>
using namespace LAMMPS_AL;
#define VashishtaT Vashishta<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
VashishtaT::Vashishta() : BaseThree<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
VashishtaT::~Vashishta() {
clear();
}
template <class numtyp, class acctyp>
int VashishtaT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int VashishtaT::init(const int ntypes, const int nlocal, const int nall, const int max_nbors,
const double cell_size, const double gpu_split, FILE *_screen,
int* host_map, const int nelements, int*** host_elem2param, const int nparams,
const double* cutsq, const double* r0,
const double* gamma, const double* eta,
const double* lam1inv, const double* lam4inv,
const double* zizj, const double* mbigd,
const double* dvrc, const double* big6w,
const double* heta, const double* bigh,
const double* bigw, const double* c0,
const double* costheta, const double* bigb,
const double* big2b, const double* bigc)
{
int success;
success=this->init_three(nlocal,nall,max_nbors,0,cell_size,gpu_split,
_screen,vashishta,"k_vashishta","k_vashishta_three_center",
"k_vashishta_three_end");
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;
_nparams = nparams;
_nelements = nelements;
UCL_H_Vec<numtyp4> dview(nparams,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<nparams; i++) {
dview[i].x=(numtyp)0;
dview[i].y=(numtyp)0;
dview[i].z=(numtyp)0;
dview[i].w=(numtyp)0;
}
// pack coefficients into arrays
param1.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<nparams; i++) {
dview[i].x=static_cast<numtyp>(eta[i]);
dview[i].y=static_cast<numtyp>(lam1inv[i]);
dview[i].z=static_cast<numtyp>(lam4inv[i]);
dview[i].w=static_cast<numtyp>(zizj[i]);
}
ucl_copy(param1,dview,false);
param1_tex.get_texture(*(this->pair_program),"param1_tex");
param1_tex.bind_float(param1,4);
param2.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<nparams; i++) {
dview[i].x=static_cast<numtyp>(mbigd[i]);
dview[i].y=static_cast<numtyp>(dvrc[i]);
dview[i].z=static_cast<numtyp>(big6w[i]);
dview[i].w=static_cast<numtyp>(heta[i]);
}
ucl_copy(param2,dview,false);
param2_tex.get_texture(*(this->pair_program),"param2_tex");
param2_tex.bind_float(param2,4);
param3.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<nparams; i++) {
dview[i].x=static_cast<numtyp>(bigh[i]);
dview[i].y=static_cast<numtyp>(bigw[i]);
dview[i].z=static_cast<numtyp>(dvrc[i]);
dview[i].w=static_cast<numtyp>(c0[i]);
}
ucl_copy(param3,dview,false);
param3_tex.get_texture(*(this->pair_program),"param3_tex");
param3_tex.bind_float(param3,4);
param4.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<nparams; i++) {
double r0sq = r0[i]*r0[i]-1e-4; // TODO: should we have the 1e-4?
dview[i].x=static_cast<numtyp>(r0sq);
dview[i].y=static_cast<numtyp>(gamma[i]);
dview[i].z=static_cast<numtyp>(cutsq[i]);
dview[i].w=static_cast<numtyp>(r0[i]);
}
ucl_copy(param4,dview,false);
param4_tex.get_texture(*(this->pair_program),"param4_tex");
param4_tex.bind_float(param4,4);
param5.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<nparams; i++) {
dview[i].x=static_cast<numtyp>(bigc[i]);
dview[i].y=static_cast<numtyp>(costheta[i]);
dview[i].z=static_cast<numtyp>(bigb[i]);
dview[i].w=static_cast<numtyp>(big2b[i]);
}
ucl_copy(param5,dview,false);
param5_tex.get_texture(*(this->pair_program),"param5_tex");
param5_tex.bind_float(param5,4);
UCL_H_Vec<int> dview_elem2param(nelements*nelements*nelements,
*(this->ucl_device), UCL_WRITE_ONLY);
elem2param.alloc(nelements*nelements*nelements,*(this->ucl_device),
UCL_READ_ONLY);
for (int i = 0; i < nelements; i++)
for (int j = 0; j < nelements; j++)
for (int k = 0; k < nelements; k++) {
int idx = i*nelements*nelements+j*nelements+k;
dview_elem2param[idx] = host_elem2param[i][j][k];
}
ucl_copy(elem2param,dview_elem2param,false);
UCL_H_Vec<int> dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY);
for (int i = 0; i < ntypes; i++)
dview_map[i] = host_map[i];
map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY);
ucl_copy(map,dview_map,false);
_allocated=true;
this->_max_bytes=param1.row_bytes()+param2.row_bytes()+param3.row_bytes()+param4.row_bytes()+param5.row_bytes()+
map.row_bytes()+elem2param.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void VashishtaT::clear() {
if (!_allocated)
return;
_allocated=false;
param1.clear();
param2.clear();
param3.clear();
param4.clear();
param5.clear();
map.clear();
elem2param.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double VashishtaT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(Vashishta<numtyp,acctyp>);
}
#define KTHREADS this->_threads_per_atom
#define JTHREADS this->_threads_per_atom
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) {
// Compute the block size and grid size to keep all cores busy
int BX=this->block_pair();
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)));
// this->_nbor_data == nbor->dev_packed for gpu_nbor == 0 and tpa > 1
// this->_nbor_data == nbor->dev_nbor for gpu_nbor == 1 or tpa == 1
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &param1, &param2, &param3, &param4, &param5,
&map, &elem2param, &_nelements,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv,
&eflag, &vflag, &ainum, &nbor_pitch,
&this->_threads_per_atom);
BX=this->block_size();
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/(KTHREADS*JTHREADS))));
this->k_three_center.set_size(GX,BX);
this->k_three_center.run(&this->atom->x, &param1, &param2, &param3, &param4, &param5,
&map, &elem2param, &_nelements,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom, &evatom);
Answer<numtyp,acctyp> *end_ans;
#ifdef THREE_CONCURRENT
end_ans=this->ans2;
#else
end_ans=this->ans;
#endif
if (evatom!=0) {
this->k_three_end_vatom.set_size(GX,BX);
this->k_three_end_vatom.run(&this->atom->x, &param1, &param2, &param3, &param4, &param5,
&map, &elem2param, &_nelements,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->nbor->dev_acc,
&end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor);
} else {
this->k_three_end.set_size(GX,BX);
this->k_three_end.run(&this->atom->x, &param1, &param2, &param3, &param4, &param5,
&map, &elem2param, &_nelements,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->nbor->dev_acc,
&end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor);
}
this->time_pair.stop();
}
template class Vashishta<PRECISION,ACC_PRECISION>;

744
lib/gpu/lal_vashishta.cu Normal file
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@ -0,0 +1,744 @@
// **************************************************************************
// vashishta.cu
// -------------------
// Anders Hafreager (UiO)
//
// Device code for acceleration of the vashishta pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : Mon June 12, 2017
// email : andershaf@gmail.com
// ***************************************************************************/
#ifdef NV_KERNEL
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
texture<float4> pos_tex;
texture<float4> param1_tex;
texture<float4> param2_tex;
texture<float4> param3_tex;
texture<float4> param4_tex;
texture<float4> param5_tex;
#else
texture<int4,1> pos_tex;
texture<int4> param1_tex;
texture<int4> param2_tex;
texture<int4> param3_tex;
texture<int4> param4_tex;
texture<int4> param5_tex;
#endif
#else
#define pos_tex x_
#define param1_tex param1
#define param2_tex param2
#define param3_tex param3
#define param3_tex param4
#define param3_tex param5
#endif
#define THIRD (numtyp)0.66666666666666666667
//#define THREE_CONCURRENT
#if (ARCH < 300)
#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom, offset, \
eflag, vflag, ans, engv) \
if (t_per_atom>1) { \
__local acctyp red_acc[6][BLOCK_ELLIPSE]; \
red_acc[0][tid]=f.x; \
red_acc[1][tid]=f.y; \
red_acc[2][tid]=f.z; \
red_acc[3][tid]=energy; \
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]; \
} \
} \
f.x=red_acc[0][tid]; \
f.y=red_acc[1][tid]; \
f.z=red_acc[2][tid]; \
energy=red_acc[3][tid]; \
if (vflag>0) { \
for (int r=0; r<6; r++) \
red_acc[r][tid]=virial[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++) \
virial[r]=red_acc[r][tid]; \
} \
} \
if (offset==0) { \
int ei=ii; \
if (eflag>0) { \
engv[ei]+=energy*(acctyp)0.5; \
ei+=inum; \
} \
if (vflag>0) { \
for (int i=0; i<6; i++) { \
engv[ei]+=virial[i]*(acctyp)0.5; \
ei+=inum; \
} \
} \
acctyp4 old=ans[ii]; \
old.x+=f.x; \
old.y+=f.y; \
old.z+=f.z; \
ans[ii]=old; \
}
#else
#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom, offset, \
eflag, vflag, ans, engv) \
if (t_per_atom>1) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
f.x += shfl_xor(f.x, s, t_per_atom); \
f.y += shfl_xor(f.y, s, t_per_atom); \
f.z += shfl_xor(f.z, s, t_per_atom); \
energy += shfl_xor(energy, s, t_per_atom); \
} \
if (vflag>0) { \
for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
for (int r=0; r<6; r++) \
virial[r] += shfl_xor(virial[r], s, t_per_atom); \
} \
} \
} \
if (offset==0) { \
int ei=ii; \
if (eflag>0) { \
engv[ei]+=energy*(acctyp)0.5; \
ei+=inum; \
} \
if (vflag>0) { \
for (int i=0; i<6; i++) { \
engv[ei]+=virial[i]*(acctyp)0.5; \
ei+=inum; \
} \
} \
acctyp4 old=ans[ii]; \
old.x+=f.x; \
old.y+=f.y; \
old.z+=f.z; \
ans[ii]=old; \
}
#endif
__kernel void k_vashishta(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict param1,
const __global numtyp4 *restrict param2,
const __global numtyp4 *restrict param3,
const __global numtyp4 *restrict param4,
const __global numtyp4 *restrict param5,
const __global int *restrict map,
const __global int *restrict elem2param,
const int nelements,
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) {
__local int n_stride;
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp virial[6];
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];
int itype=ix.w;
itype=map[itype];
for ( ; nbor<nbor_end; nbor+=n_stride) {
int j=dev_packed[nbor];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
jtype=map[jtype];
int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
// 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<param4[ijparam].z) { // cutsq = param4[ijparam].z
numtyp4 param1_ijparam; fetch4(param1_ijparam,ijparam,param1_tex);
numtyp param1_eta=param1_ijparam.x;
numtyp param1_lam1inv=param1_ijparam.y;
numtyp param1_lam4inv=param1_ijparam.z;
numtyp param1_zizj=param1_ijparam.w;
numtyp4 param2_ijparam; fetch4(param2_ijparam,ijparam,param2_tex);
numtyp param2_mbigd=param2_ijparam.x;
numtyp param2_dvrc =param2_ijparam.y;
numtyp param2_big6w=param2_ijparam.z;
numtyp param2_heta =param2_ijparam.w;
numtyp4 param3_ijparam; fetch4(param3_ijparam,ijparam,param3_tex);
numtyp param3_bigh=param3_ijparam.x;
numtyp param3_bigw=param3_ijparam.y;
numtyp param3_dvrc=param3_ijparam.z;
numtyp param3_c0 =param3_ijparam.w;
numtyp r=sqrt(rsq);
numtyp rinvsq=1.0/rsq;
numtyp r4inv = rinvsq*rinvsq;
numtyp r6inv = rinvsq*r4inv;
numtyp reta = pow(r,-param1_eta);
numtyp lam1r = r*param1_lam1inv;
numtyp lam4r = r*param1_lam4inv;
numtyp vc2 = param1_zizj * exp(-lam1r)/r;
numtyp vc3 = param2_mbigd * r4inv*exp(-lam4r);
numtyp force = (param2_dvrc*r
- (4.0*vc3 + lam4r*vc3+param2_big6w*r6inv
- param2_heta*reta - vc2 - lam1r*vc2)
) * rinvsq;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (eflag>0)
energy += (param3_bigh*reta+vc2-vc3-param3_bigw*r6inv-r*param3_dvrc+param3_c0);
if (vflag>0) {
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
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
} // if ii
}
#define threebody(delr1x, delr1y, delr1z, eflag, energy) \
{ \
numtyp r1 = ucl_sqrt(rsq1); \
numtyp rinvsq1 = ucl_recip(rsq1); \
numtyp rainv1 = ucl_recip(r1 - param_r0_ij); \
numtyp gsrainv1 = param_gamma_ij * rainv1; \
numtyp gsrainvsq1 = gsrainv1*rainv1/r1; \
numtyp expgsrainv1 = ucl_exp(gsrainv1); \
\
numtyp r2 = ucl_sqrt(rsq2); \
numtyp rinvsq2 = ucl_recip(rsq2); \
numtyp rainv2 = ucl_recip(r2 - param_r0_ik); \
numtyp gsrainv2 = param_gamma_ik * rainv2; \
numtyp gsrainvsq2 = gsrainv2*rainv2/r2; \
numtyp expgsrainv2 = ucl_exp(gsrainv2); \
\
numtyp rinv12 = ucl_recip(r1*r2); \
numtyp cs = (delr1x*delr2x + delr1y*delr2y + delr1z*delr2z) * rinv12; \
numtyp delcs = cs - param_costheta_ijk; \
numtyp delcssq = delcs*delcs; \
numtyp pcsinv = param_bigc_ijk*delcssq+1.0; \
numtyp pcsinvsq = pcsinv*pcsinv; \
numtyp pcs = delcssq/pcsinv; \
\
numtyp facexp = expgsrainv1*expgsrainv2; \
\
numtyp facrad = param_bigb_ijk * facexp*pcs; \
numtyp frad1 = facrad*gsrainvsq1; \
numtyp frad2 = facrad*gsrainvsq2; \
numtyp facang = param_big2b_ijk * facexp*delcs/pcsinvsq; \
numtyp facang12 = rinv12*facang; \
numtyp csfacang = cs*facang; \
numtyp csfac1 = rinvsq1*csfacang; \
\
fjx = delr1x*(frad1+csfac1)-delr2x*facang12; \
fjy = delr1y*(frad1+csfac1)-delr2y*facang12; \
fjz = delr1z*(frad1+csfac1)-delr2z*facang12; \
\
numtyp csfac2 = rinvsq2*csfacang; \
\
fkx = delr2x*(frad2+csfac2)-delr1x*facang12; \
fky = delr2y*(frad2+csfac2)-delr1y*facang12; \
fkz = delr2z*(frad2+csfac2)-delr1z*facang12; \
\
if (eflag>0) \
energy+=facrad; \
if (vflag>0) { \
virial[0] += delr1x*fjx + delr2x*fkx; \
virial[1] += delr1y*fjy + delr2y*fky; \
virial[2] += delr1z*fjz + delr2z*fkz; \
virial[3] += delr1x*fjy + delr2x*fky; \
virial[4] += delr1x*fjz + delr2x*fkz; \
virial[5] += delr1y*fjz + delr2y*fkz; \
} \
}
#define threebody_half(delr1x, delr1y, delr1z) \
{ \
numtyp r1 = ucl_sqrt(rsq1); \
numtyp rinvsq1 = ucl_recip(rsq1); \
numtyp rainv1 = ucl_recip(r1 - param_r0_ij); \
numtyp gsrainv1 = param_gamma_ij * rainv1; \
numtyp gsrainvsq1 = gsrainv1*rainv1/r1; \
numtyp expgsrainv1 = ucl_exp(gsrainv1); \
\
numtyp r2 = ucl_sqrt(rsq2); \
numtyp rainv2 = ucl_recip(r2 - param_r0_ik); \
numtyp gsrainv2 = param_gamma_ik * rainv2; \
numtyp expgsrainv2 = ucl_exp(gsrainv2); \
\
numtyp rinv12 = ucl_recip(r1*r2); \
numtyp cs = (delr1x*delr2x + delr1y*delr2y + delr1z*delr2z) * rinv12; \
numtyp delcs = cs - param_costheta_ijk; \
numtyp delcssq = delcs*delcs; \
numtyp pcsinv = param_bigc_ijk*delcssq+1.0; \
numtyp pcsinvsq = pcsinv*pcsinv; \
numtyp pcs = delcssq/pcsinv; \
\
numtyp facexp = expgsrainv1*expgsrainv2; \
\
numtyp facrad = param_bigb_ijk * facexp*pcs; \
numtyp frad1 = facrad*gsrainvsq1; \
numtyp facang = param_big2b_ijk * facexp*delcs/pcsinvsq; \
numtyp facang12 = rinv12*facang; \
numtyp csfacang = cs*facang; \
numtyp csfac1 = rinvsq1*csfacang; \
\
fjx = delr1x*(frad1+csfac1)-delr2x*facang12; \
fjy = delr1y*(frad1+csfac1)-delr2y*facang12; \
fjz = delr1z*(frad1+csfac1)-delr2z*facang12; \
}
__kernel void k_vashishta_three_center(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict param1,
const __global numtyp4 *restrict param2,
const __global numtyp4 *restrict param3,
const __global numtyp4 *restrict param4,
const __global numtyp4 *restrict param5,
const __global int *restrict map,
const __global int *restrict elem2param,
const int nelements,
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, const int evatom) {
__local int tpa_sq, n_stride;
tpa_sq=fast_mul(t_per_atom,t_per_atom);
numtyp param_gamma_ij, param_r0sq_ij, param_r0_ij, param_gamma_ik, param_r0sq_ik, param_r0_ik;
numtyp param_costheta_ijk, param_bigc_ijk, param_bigb_ijk, param_big2b_ijk;
int tid, ii, offset;
atom_info(tpa_sq,ii,tid,offset);
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(acctyp)0;
__syncthreads();
if (ii<inum) {
int i, numj, nbor_j, nbor_end;
int offset_j=offset/t_per_atom;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
n_stride,nbor_end,nbor_j);
int offset_k=tid & (t_per_atom-1);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
itype=map[itype];
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
jtype=map[jtype];
// Compute r12
numtyp delr1x = jx.x-ix.x;
numtyp delr1y = jx.y-ix.y;
numtyp delr1z = jx.z-ix.z;
numtyp rsq1 = delr1x*delr1x+delr1y*delr1y+delr1z*delr1z;
int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
numtyp4 param4_ijparam; fetch4(param4_ijparam,ijparam,param4_tex);
param_r0sq_ij=param4_ijparam.x;
if (rsq1 > param_r0sq_ij) continue;
param_gamma_ij=param4_ijparam.y;
param_r0_ij=param4_ijparam.w;
int nbor_k=nbor_j-offset_j+offset_k;
if (nbor_k<=nbor_j)
nbor_k+=n_stride;
for ( ; nbor_k<nbor_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
k &= NEIGHMASK;
numtyp4 kx; fetch4(kx,k,pos_tex);
int ktype=kx.w;
ktype=map[ktype];
int ikparam=elem2param[itype*nelements*nelements+ktype*nelements+ktype];
numtyp4 param4_ikparam; fetch4(param4_ikparam,ikparam,param4_tex);
numtyp delr2x = kx.x-ix.x;
numtyp delr2y = kx.y-ix.y;
numtyp delr2z = kx.z-ix.z;
numtyp rsq2 = delr2x*delr2x + delr2y*delr2y + delr2z*delr2z;
param_r0sq_ik=param4_ikparam.x;
if (rsq2 < param_r0sq_ik) {
param_gamma_ik=param4_ikparam.y;
param_r0_ik=param4_ikparam.w;
int ijkparam=elem2param[itype*nelements*nelements+jtype*nelements+ktype];
numtyp4 param5_ijkparam; fetch4(param5_ijkparam,ijkparam,param5_tex);
param_bigc_ijk=param5_ijkparam.x;
param_bigb_ijk=param5_ijkparam.z;
param_big2b_ijk=param5_ijkparam.w;
param_costheta_ijk=param5_ijkparam.y;
numtyp fjx, fjy, fjz, fkx, fky, fkz;
threebody(delr1x,delr1y,delr1z,eflag,energy);
f.x -= fjx + fkx;
f.y -= fjy + fky;
f.z -= fjz + fkz;
}
}
} // for nbor
numtyp pre;
if (evatom==1)
pre=THIRD;
else
pre=(numtyp)2.0;
energy*=pre;
for (int i=0; i<6; i++)
virial[i]*=pre;
store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
eflag,vflag,ans,engv);
} // if ii
}
__kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict param1,
const __global numtyp4 *restrict param2,
const __global numtyp4 *restrict param3,
const __global numtyp4 *restrict param4,
const __global numtyp4 *restrict param5,
const __global int *restrict map,
const __global int *restrict elem2param,
const int nelements,
const __global int * dev_nbor,
const __global int * dev_packed,
const __global int * dev_acc,
__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, const int gpu_nbor) {
__local int tpa_sq, n_stride;
tpa_sq=fast_mul(t_per_atom,t_per_atom);
numtyp param_gamma_ij, param_r0sq_ij, param_r0_ij, param_gamma_ik, param_r0sq_ik, param_r0_ik;
numtyp param_costheta_ijk, param_bigc_ijk, param_bigb_ijk, param_big2b_ijk;
int tid, ii, offset;
atom_info(tpa_sq,ii,tid,offset);
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(acctyp)0;
__syncthreads();
if (ii<inum) {
int i, numj, nbor_j, nbor_end, k_end;
int offset_j=offset/t_per_atom;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
n_stride,nbor_end,nbor_j);
int offset_k=tid & (t_per_atom-1);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
itype=map[itype];
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
jtype=map[jtype];
// Compute r12
numtyp delr1x = ix.x-jx.x;
numtyp delr1y = ix.y-jx.y;
numtyp delr1z = ix.z-jx.z;
numtyp rsq1 = delr1x*delr1x+delr1y*delr1y+delr1z*delr1z;
int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
numtyp4 param4_ijparam; fetch4(param4_ijparam,ijparam,param4_tex);
param_r0sq_ij = param4_ijparam.x;
if (rsq1 > param_r0sq_ij) continue;
param_gamma_ij=param4_ijparam.y;
param_r0_ij = param4_ijparam.w;
int nbor_k,numk;
if (dev_nbor==dev_packed) {
if (gpu_nbor) nbor_k=j+nbor_pitch;
else nbor_k=dev_acc[j]+nbor_pitch;
numk=dev_nbor[nbor_k];
nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1);
k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1));
nbor_k+=offset_k;
} else {
nbor_k=dev_acc[j]+nbor_pitch;
numk=dev_nbor[nbor_k];
nbor_k+=nbor_pitch;
nbor_k=dev_nbor[nbor_k];
k_end=nbor_k+numk;
nbor_k+=offset_k;
}
for ( ; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
k &= NEIGHMASK;
if (k == i) continue;
numtyp4 kx; fetch4(kx,k,pos_tex);
int ktype=kx.w;
ktype=map[ktype];
int ikparam=elem2param[jtype*nelements*nelements+ktype*nelements+ktype]; //jk
numtyp delr2x = kx.x - jx.x;
numtyp delr2y = kx.y - jx.y;
numtyp delr2z = kx.z - jx.z;
numtyp rsq2 = delr2x*delr2x + delr2y*delr2y + delr2z*delr2z;
numtyp4 param4_ikparam; fetch4(param4_ikparam,ikparam,param4_tex);
param_r0sq_ik=param4_ikparam.x;
if (rsq2 < param_r0sq_ik) {
param_gamma_ik=param4_ikparam.y;
param_r0_ik=param4_ikparam.w;
int ijkparam=elem2param[jtype*nelements*nelements+itype*nelements+ktype]; //jik
numtyp4 param5_ijkparam; fetch4(param5_ijkparam,ijkparam,param5_tex);
param_bigc_ijk=param5_ijkparam.x;
param_costheta_ijk=param5_ijkparam.y;
param_bigb_ijk=param5_ijkparam.z;
param_big2b_ijk=param5_ijkparam.w;
numtyp fjx, fjy, fjz;
//if (evatom==0) {
threebody_half(delr1x,delr1y,delr1z);
//} else {
// numtyp fkx, fky, fkz;
// threebody(delr1x,delr1y,delr1z,eflag,energy);
//}
f.x += fjx;
f.y += fjy;
f.z += fjz;
}
}
} // for nbor
#ifdef THREE_CONCURRENT
store_answers(f,energy,virial,ii,inum,tid,tpa_sq,offset,
eflag,vflag,ans,engv);
#else
store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
eflag,vflag,ans,engv);
#endif
} // if ii
}
__kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict param1,
const __global numtyp4 *restrict param2,
const __global numtyp4 *restrict param3,
const __global numtyp4 *restrict param4,
const __global numtyp4 *restrict param5,
const __global int *restrict map,
const __global int *restrict elem2param,
const int nelements,
const __global int * dev_nbor,
const __global int * dev_packed,
const __global int * dev_acc,
__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, const int gpu_nbor) {
__local int tpa_sq, n_stride;
tpa_sq=fast_mul(t_per_atom,t_per_atom);
numtyp param_gamma_ij, param_r0sq_ij, param_r0_ij, param_gamma_ik, param_r0sq_ik, param_r0_ik;
numtyp param_costheta_ijk, param_bigc_ijk, param_bigb_ijk, param_big2b_ijk;
int tid, ii, offset;
atom_info(tpa_sq,ii,tid,offset);
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(acctyp)0;
__syncthreads();
if (ii<inum) {
int i, numj, nbor_j, nbor_end, k_end;
int offset_j=offset/t_per_atom;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
n_stride,nbor_end,nbor_j);
int offset_k=tid & (t_per_atom-1);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
itype=map[itype];
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
jtype=map[jtype];
// Compute r12
numtyp delr1x = ix.x-jx.x;
numtyp delr1y = ix.y-jx.y;
numtyp delr1z = ix.z-jx.z;
numtyp rsq1 = delr1x*delr1x+delr1y*delr1y+delr1z*delr1z;
int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
numtyp4 param4_ijparam; fetch4(param4_ijparam,ijparam,param4_tex);
param_r0sq_ij=param4_ijparam.x;
if (rsq1 > param_r0sq_ij) continue;
param_gamma_ij=param4_ijparam.y;
param_r0_ij=param4_ijparam.w;
int nbor_k,numk;
if (dev_nbor==dev_packed) {
if (gpu_nbor) nbor_k=j+nbor_pitch;
else nbor_k=dev_acc[j]+nbor_pitch;
numk=dev_nbor[nbor_k];
nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1);
k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1));
nbor_k+=offset_k;
} else {
nbor_k=dev_acc[j]+nbor_pitch;
numk=dev_nbor[nbor_k];
nbor_k+=nbor_pitch;
nbor_k=dev_nbor[nbor_k];
k_end=nbor_k+numk;
nbor_k+=offset_k;
}
for ( ; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
k &= NEIGHMASK;
if (k == i) continue;
numtyp4 kx; fetch4(kx,k,pos_tex);
int ktype=kx.w;
ktype=map[ktype];
int ikparam=elem2param[jtype*nelements*nelements+ktype*nelements+ktype]; // jk
numtyp4 param4_ikparam; fetch4(param4_ikparam,ikparam,param4_tex);
numtyp delr2x = kx.x - jx.x;
numtyp delr2y = kx.y - jx.y;
numtyp delr2z = kx.z - jx.z;
numtyp rsq2 = delr2x*delr2x + delr2y*delr2y + delr2z*delr2z;
param_r0sq_ik=param4_ikparam.x;
if (rsq2 < param_r0sq_ik) {
param_gamma_ik=param4_ikparam.y;
param_r0_ik=param4_ikparam.w;
int ijkparam=elem2param[jtype*nelements*nelements+itype*nelements+ktype]; // jik
numtyp4 param5_ijkparam; fetch4(param5_ijkparam,ijkparam,param5_tex);
param_bigc_ijk=param5_ijkparam.x;
param_costheta_ijk=param5_ijkparam.y;
param_bigb_ijk=param5_ijkparam.z;
param_big2b_ijk=param5_ijkparam.w;
numtyp fjx, fjy, fjz, fkx, fky, fkz;
threebody(delr1x,delr1y,delr1z,eflag,energy);
f.x += fjx;
f.y += fjy;
f.z += fjz;
}
}
} // for nbor
energy*=THIRD;
for (int i=0; i<6; i++)
virial[i]*=THIRD;
#ifdef THREE_CONCURRENT
store_answers(f,energy,virial,ii,inum,tid,tpa_sq,offset,
eflag,vflag,ans,engv);
#else
store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
eflag,vflag,ans,engv);
#endif
} // if ii
}

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/***************************************************************************
vashishta.h
-------------------
Anders Hafreager (UiO9)
Class for acceleration of the vashishta pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : Mon June 12, 2017
email : andershaf@gmail.com
***************************************************************************/
#ifndef LAL_VASHISHTA_H
#define LAL_VASHISHTA_H
#include "lal_base_three.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class Vashishta : public BaseThree<numtyp, acctyp> {
public:
Vashishta();
~Vashishta();
/// 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, const int nlocal, const int nall, const int max_nbors,
const double cell_size, const double gpu_split, FILE *screen,
int* host_map, const int nelements, int*** host_elem2param, const int nparams,
const double* cutsq, const double* r0,
const double* gamma, const double* eta,
const double* lam1inv, const double* lam4inv,
const double* zizj, const double* mbigd,
const double* dvrc, const double* big6w,
const double* heta, const double* bigh,
const double* bigw, const double* c0,
const double* costheta, const double* bigb,
const double* big2b, const double* bigc);
/// 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 --------------------------
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// param1.x = eta, param1.y = lam1inv, param1.z = lam4inv, param1.w = zizj
UCL_D_Vec<numtyp4> param1;
/// param2.x = mbigd, param2.y = dvrc, param2.z = big6w, param2.w = heta
UCL_D_Vec<numtyp4> param2;
/// param3.x = bigh, param3.y = bigw, param3.z = dvrc, param3.w = c0
UCL_D_Vec<numtyp4> param3;
/// param4.x = r0sq, param4.y = gamma, param4.z = cutsq, param4.w = r0
UCL_D_Vec<numtyp4> param4;
/// param5.x = bigc, param5.y = costheta, param5.z = bigb, param5.w = big2b
UCL_D_Vec<numtyp4> param5;
UCL_D_Vec<int> elem2param;
UCL_D_Vec<int> map;
int _nparams,_nelements;
UCL_Texture param1_tex, param2_tex, param3_tex, param4_tex, param5_tex;
private:
bool _allocated;
void loop(const bool _eflag, const bool _vflag, const int evatom);
};
}
#endif

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/***************************************************************************
vashishta_ext.cpp
-------------------
Anders Hafreager (UiO)
Class for acceleration of the vashishta pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : Mon June 12, 2017
email : andershaf@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <math.h>
#include "lal_vashishta.h"
#include <iostream>
using namespace std;
using namespace std;
using namespace LAMMPS_AL;
static Vashishta<PRECISION,ACC_PRECISION> VashishtaMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int vashishta_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors,
const double cell_size, int &gpu_mode, FILE *screen,
int* host_map, const int nelements, int*** host_elem2param, const int nparams,
const double* cutsq, const double* r0,
const double* gamma, const double* eta,
const double* lam1inv, const double* lam4inv,
const double* zizj, const double* mbigd,
const double* dvrc, const double* big6w,
const double* heta, const double* bigh,
const double* bigw, const double* c0,
const double* costheta, const double* bigb,
const double* big2b, const double* bigc) {
VashishtaMF.clear();
gpu_mode=VashishtaMF.device->gpu_mode();
double gpu_split=VashishtaMF.device->particle_split();
int first_gpu=VashishtaMF.device->first_device();
int last_gpu=VashishtaMF.device->last_device();
int world_me=VashishtaMF.device->world_me();
int gpu_rank=VashishtaMF.device->gpu_rank();
int procs_per_gpu=VashishtaMF.device->procs_per_gpu();
// disable host/device split for now
if (gpu_split != 1.0)
return -8;
VashishtaMF.device->init_message(screen,"vashishta/gpu",first_gpu,last_gpu);
bool message=false;
if (VashishtaMF.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=VashishtaMF.init(ntypes, inum, nall, 500, cell_size, gpu_split, screen,
host_map, nelements, host_elem2param, nparams,
cutsq, r0, gamma, eta, lam1inv,
lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw,
c0, costheta, bigb, big2b, bigc);
VashishtaMF.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=VashishtaMF.init(ntypes, inum, nall, 500, cell_size, gpu_split, screen,
host_map, nelements, host_elem2param, nparams,
cutsq, r0, gamma, eta, lam1inv,
lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw,
c0, costheta, bigb, big2b, bigc);
VashishtaMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
VashishtaMF.estimate_gpu_overhead();
cout << "Seems like this was ok!" << endl;
return init_ok;
}
void vashishta_gpu_clear() {
VashishtaMF.clear();
}
int ** vashishta_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) {
return VashishtaMF.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);
}
void vashishta_gpu_compute(const int ago, const int nlocal, const int nall,
const int nlist, 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) {
VashishtaMF.compute(ago,nlocal,nall,nlist,host_x,host_type,ilist,numj,
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
}
double vashishta_gpu_bytes() {
return VashishtaMF.host_memory_usage();
}

2
src/GPU/Install.sh
View File

@ -113,6 +113,8 @@ action pair_soft_gpu.cpp
action pair_soft_gpu.h
action pair_sw_gpu.cpp pair_sw.cpp
action pair_sw_gpu.h pair_sw.h
action pair_vashishta_gpu.cpp pair_vashishta.cpp
action pair_vashishta_gpu.h pair_vashishta.h
action pair_table_gpu.cpp pair_table.cpp
action pair_table_gpu.h pair_table.cpp
action pair_tersoff_gpu.cpp pair_tersoff.cpp

258
src/GPU/pair_vashishta_gpu.cpp Normal file
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@ -0,0 +1,258 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Anders Hafreager (UiO)
------------------------------------------------------------------------- */
#include <limits>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_vashishta_gpu.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
#include "gpu_extra.h"
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int vashishta_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors,
const double cell_size, int &gpu_mode, FILE *screen,
int* host_map, const int nelements, int*** host_elem2param, const int nparams,
const double* cutsq, const double* r0,
const double* gamma, const double* eta,
const double* lam1inv, const double* lam4inv,
const double* zizj, const double* mbigd,
const double* dvrc, const double* big6w,
const double* heta, const double* bigh,
const double* bigw, const double* c0,
const double* costheta, const double* bigb,
const double* big2b, const double* bigc);
void vashishta_gpu_clear();
int ** vashishta_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
void vashishta_gpu_compute(const int ago, const int nloc, const int nall, const int ln,
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 vashishta_gpu_bytes();
extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
double **vatom, double *virial, double &ecoul);
/* ---------------------------------------------------------------------- */
PairVashishtaGPU::PairVashishtaGPU(LAMMPS *lmp) : PairVashishta(lmp), gpu_mode(GPU_FORCE)
{
cpu_time = 0.0;
reinitflag = 0;
gpu_allocated = false;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
cutghost = NULL;
ghostneigh = 1;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairVashishtaGPU::~PairVashishtaGPU()
{
vashishta_gpu_clear();
if (allocated)
memory->destroy(cutghost);
}
/* ---------------------------------------------------------------------- */
void PairVashishtaGPU::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;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = vashishta_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);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
vashishta_gpu_compute(neighbor->ago, inum, nall, inum+list->gnum,
atom->x, atom->type, ilist, numneigh, firstneigh, eflag,
vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
}
/* ---------------------------------------------------------------------- */
void PairVashishtaGPU::allocate()
{
if(!allocated) {
PairVashishta::allocate();
}
int n = atom->ntypes;
memory->create(cutghost,n+1,n+1,"pair:cutghost");
gpu_allocated = true;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairVashishtaGPU::init_style()
{
double cell_size = cutmax + neighbor->skin;
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style vashishta/gpu requires atom IDs");
if (force->newton_pair != 0)
error->all(FLERR,"Pair style vashishta/gpu requires newton pair off");
double *cutsq, *r0, *r0eps, *gamma, *eta;
double *lam1inv, *lam4inv, *zizj, *mbigd;
double *dvrc, *big6w, *heta, *bigh;
double *bigw, *c0, *costheta, *bigb;
double *big2b, *bigc;
cutsq = r0 = gamma = eta = NULL;
lam1inv = lam4inv = zizj = mbigd = NULL;
dvrc = big6w = heta = bigh = NULL;
bigw = c0 = costheta = bigb = NULL;
big2b = bigc = NULL;
memory->create(cutsq,nparams,"pair:cutsq");
memory->create(r0,nparams,"pair:r0");
memory->create(gamma,nparams,"pair:gamma");
memory->create(eta,nparams,"pair:eta");
memory->create(lam1inv,nparams,"pair:lam1inv");
memory->create(lam4inv,nparams,"pair:lam4inv");
memory->create(zizj,nparams,"pair:zizj");
memory->create(mbigd,nparams,"pair:mbigd");
memory->create(dvrc,nparams,"pair:dvrc");
memory->create(big6w,nparams,"pair:big6w");
memory->create(heta,nparams,"pair:heta");
memory->create(bigh,nparams,"pair:bigh");
memory->create(bigw,nparams,"pair:bigw");
memory->create(c0,nparams,"pair:c0");
memory->create(costheta,nparams,"pair:costheta");
memory->create(bigb,nparams,"pair:bigb");
memory->create(big2b,nparams,"pair:big2b");
memory->create(bigc,nparams,"pair:bigc");
for (int i = 0; i < nparams; i++) {
cutsq[i] = params[i].cutsq;
r0[i] = params[i].r0;
gamma[i] = params[i].gamma;
eta[i] = params[i].eta;
lam1inv[i] = params[i].lam1inv;
lam4inv[i] = params[i].lam4inv;
zizj[i] = params[i].zizj;
mbigd[i] = params[i].mbigd;
dvrc[i] = params[i].dvrc;
big6w[i] = params[i].big6w;
heta[i] = params[i].heta;
bigh[i] = params[i].bigh;
bigw[i] = params[i].bigw;
c0[i] = params[i].c0;
costheta[i] = params[i].costheta;
bigb[i] = params[i].bigb;
big2b[i] = params[i].big2b;
bigc[i] = params[i].bigc;
}
int success = vashishta_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, 500,
cell_size, gpu_mode, screen, map, nelements,
elem2param, nparams, cutsq, r0, gamma, eta, lam1inv,
lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw,
c0, costheta, bigb, big2b, bigc);
memory->destroy(cutsq);
memory->destroy(r0);
memory->destroy(gamma);
memory->destroy(eta);
memory->destroy(lam1inv);
memory->destroy(lam4inv);
memory->destroy(zizj);
memory->destroy(mbigd);
memory->destroy(dvrc);
memory->destroy(big6w);
memory->destroy(heta);
memory->destroy(bigh);
memory->destroy(bigw);
memory->destroy(c0);
memory->destroy(costheta);
memory->destroy(bigb);
memory->destroy(big2b);
memory->destroy(bigc);
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]->ghost = 1;
}
if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) )
comm->cutghostuser=2.0*cutmax + neighbor->skin;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairVashishtaGPU::init_one(int i, int j)
{
if(!gpu_allocated) {
allocate();
}
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
cutghost[i][j] = cutmax;
cutghost[j][i] = cutmax;
return cutmax;
}

69
src/GPU/pair_vashishta_gpu.h Normal file
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@ -0,0 +1,69 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(vashishta/gpu,PairVashishtaGPU)
#else
#ifndef LMP_PAIR_VASHISHTA_GPU_H
#define LMP_PAIR_VASHISHTA_GPU_H
#include "pair_vashishta.h"
namespace LAMMPS_NS {
class PairVashishtaGPU : public PairVashishta {
public:
PairVashishtaGPU(class LAMMPS *);
~PairVashishtaGPU();
void compute(int, int);
double init_one(int, int);
void init_style();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
protected:
void allocate();
int gpu_allocated;
int gpu_mode;
double cpu_time;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Pair style vashishta/gpu requires atom IDs
This is a requirement to use this potential.
E: Pair style vashishta/gpu requires newton pair off
See the newton command. This is a restriction to use this potential.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/