Added missing source files for born/coul/wolf/cs in the gpu library

This commit is contained in:
Trung Nguyen 2018-06-20 15:08:24 -05:00
parent a9b794b2ab
commit 28504e91c0
4 changed files with 591 additions and 0 deletions

View File

@ -0,0 +1,97 @@
/***************************************************************************
born_coul_wolf_cs.cpp
-------------------
Trung Dac Nguyen (Northwestern)
Class for acceleration of the born/coul/wolf/cs pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndactrung@gmail.com
***************************************************************************/
#ifdef USE_OPENCL
#include "born_coul_wolf_cs_cl.h"
#elif defined(USE_CUDART)
const char *born_coul_wolf_cs=0;
#else
#include "born_coul_wolf_cs_cubin.h"
#endif
#include "lal_born_coul_wolf_cs.h"
#include <cassert>
using namespace LAMMPS_AL;
#define BornCoulWolfCST BornCoulWolfCS<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_rhoinv,
double **host_born1, double **host_born2, double **host_born3,
double **host_a, double **host_c, double **host_d,
double **host_sigma, double **host_offset,
double *host_special_lj, const int nlocal,
const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *_screen,
double **host_cut_ljsq, const double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double alf, const double e_shift, const double f_shift) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
_screen,born_coul_wolf_cs,"k_born_coul_wolf_cs");
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
this->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;
this->shared_types=true;
}
this->_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;
this->coeff1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,this->coeff1,host_write,host_rhoinv,
host_born1,host_born2,host_born3);
this->coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,this->coeff2,host_write,host_a,host_c,
host_d,host_offset);
this->cutsq_sigma.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,this->cutsq_sigma,host_write,host_cutsq,
host_cut_ljsq,host_sigma);
this->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(this->sp_lj,host_write,8,false);
this->_cut_coulsq=host_cut_coulsq;
this->_qqrd2e=qqrd2e;
this->_alf=alf;
this->_e_shift=e_shift;
this->_f_shift=f_shift;
this->_allocated=true;
this->_max_bytes=this->coeff1.row_bytes()+this->coeff2.row_bytes()
+this->cutsq_sigma.row_bytes()+this->sp_lj.row_bytes();
return 0;
}
template class BornCoulWolfCS<PRECISION,ACC_PRECISION>;

View File

@ -0,0 +1,306 @@
// **************************************************************************
// born_coul_wolf_cs.cu
// -------------------
// Trung Dac Nguyen (Northwestern)
//
// Device code for acceleration of the born/coul/wolf/cs pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin :
// email : ndactrung@gmail.com
// ***************************************************************************/
#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
#define EPSILON (acctyp)(1.0e-20)
#define MY_PIS (acctyp)1.77245385090551602729
__kernel void k_born_coul_wolf_cs(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict coeff1,
const __global numtyp4 *restrict coeff2,
const int lj_types,
const __global numtyp *restrict sp_lj_in,
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 __global numtyp *restrict q_,
const __global numtyp4 *restrict cutsq_sigma,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp alf, const numtyp e_shift,
const numtyp f_shift, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_lj[8];
sp_lj[0]=sp_lj_in[0];
sp_lj[1]=sp_lj_in[1];
sp_lj[2]=sp_lj_in[2];
sp_lj[3]=sp_lj_in[3];
sp_lj[4]=sp_lj_in[4];
sp_lj[5]=sp_lj_in[5];
sp_lj[6]=sp_lj_in[6];
sp_lj[7]=sp_lj_in[7];
acctyp energy=(acctyp)0;
acctyp e_coul=(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;
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
__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;
if (eflag>0) {
acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) *
qtmp*qtmp*qqrd2e/(acctyp)t_per_atom;
e_coul += (acctyp)2.0*e_self;
}
for ( ; nbor<nbor_end; nbor+=n_stride) {
int j=dev_packed[nbor];
numtyp factor_lj, factor_coul;
factor_lj = sp_lj[sbmask(j)];
factor_coul = sp_lj[sbmask(j)+4];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<cutsq_sigma[mtype].x) { // cutsq
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
acctyp r2inv = ucl_recip(rsq);
numtyp forcecoul,forceborn,force,prefactor,rexp;
acctyp v_sh,r6inv;
if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq
numtyp r = ucl_sqrt(rsq);
rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x);
r6inv = r2inv*r2inv*r2inv;
forceborn = (coeff1[mtype].y*r*rexp - coeff1[mtype].z*r6inv
+ coeff1[mtype].w*r2inv*r6inv)*factor_lj;
} else forceborn = (numtyp)0.0;
if (rsq < cut_coulsq) {
numtyp r = ucl_rsqrt(r2inv);
acctyp arij = alf * r;
acctyp erfcd = ucl_exp(-arij*arij);
fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * qtmp/r;
const acctyp erfcc = erfc(arij);
v_sh = (erfcc - e_shift*r)*prefactor;
acctyp dvdrr = (erfcc/rsq + (numtyp)2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = prefactor * dvdrr*rsq;
if (factor_coul < (numtyp)1.0) forcecoul -= ((numtyp)1.0-factor_coul)*prefactor;
} else forcecoul = (numtyp)0.0;
force = (forceborn + forcecoul) * r2inv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (eflag>0) {
if (rsq < cut_coulsq) {
acctyp e=v_sh;
if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
e_coul += e;
}
if (rsq < cutsq_sigma[mtype].y) {
numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv
+ coeff2[mtype].z*r2inv*r6inv;
energy+=factor_lj*(e-coeff2[mtype].w);
}
}
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_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
} // if ii
}
__kernel void k_born_coul_wolf_cs_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict coeff1_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp *restrict sp_lj_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp4 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const __global numtyp4 *restrict cutsq_sigma,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp alf, const numtyp e_shift,
const numtyp f_shift, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp4 coeff1[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[8];
if (tid<8)
sp_lj[tid]=sp_lj_in[tid];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff1[tid]=coeff1_in[tid];
if (eflag>0)
coeff2[tid]=coeff2_in[tid];
}
acctyp energy=(acctyp)0;
acctyp e_coul=(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;
__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 iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
if (eflag>0) {
acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) *
qtmp*qtmp*qqrd2e/(acctyp)t_per_atom;
e_coul += (acctyp)2.0*e_self;
}
for ( ; nbor<nbor_end; nbor+=n_stride) {
int j=dev_packed[nbor];
numtyp factor_lj, factor_coul;
factor_lj = sp_lj[sbmask(j)];
factor_coul = sp_lj[sbmask(j)+4];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int mtype=itype+jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
acctyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_sigma[mtype].x) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
acctyp r2inv = ucl_recip(rsq);
numtyp forcecoul,forceborn,force,prefactor,rexp;
acctyp v_sh,r6inv;
if (rsq < cutsq_sigma[mtype].y) {
r6inv = r2inv*r2inv*r2inv;
numtyp r = ucl_sqrt(rsq);
rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x);
forceborn = (coeff1[mtype].y*r*rexp - coeff1[mtype].z*r6inv
+ coeff1[mtype].w*r2inv*r6inv)*factor_lj;
} else forceborn = (numtyp)0.0;
if (rsq < cut_coulsq) {
numtyp r = ucl_sqrt(rsq);
acctyp arij = alf * r;
acctyp erfcd = ucl_exp(-arij*arij);
fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * qtmp/r;
const acctyp erfcc = erfc(arij);
v_sh = (erfcc - e_shift*r)*prefactor;
acctyp dvdrr = (erfcc/rsq + (numtyp)2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = prefactor * dvdrr*rsq;
if (factor_coul < (numtyp)1.0) forcecoul -= ((numtyp)1.0-factor_coul)*prefactor;
} else forcecoul = (numtyp)0.0;
force = (forceborn + forcecoul) * r2inv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (eflag>0) {
if (rsq < cut_coulsq) {
acctyp e=v_sh;
if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
e_coul += e;
}
if (rsq < cutsq_sigma[mtype].y) {
numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv
+ coeff2[mtype].z*r2inv*r6inv;
energy+=factor_lj*(e-coeff2[mtype].w);
}
}
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_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
} // if ii
}

View File

@ -0,0 +1,54 @@
/***************************************************************************
born_coul_wolf_cs.h
-------------------
Trung Dac Nguyen (Northwestern)
Class for acceleration of the born/coul/wolf/cs pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_BORN_COUL_WOLF_CS_H
#define LAL_BORN_COUL_WOLF_CS_H
#include "lal_born_coul_wolf.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class BornCoulWolfCS : public BornCoulWolf<numtyp, acctyp> {
public:
BornCoulWolfCS() {}
~BornCoulWolfCS() {}
/// 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_rhoinv,
double **host_born1, double **host_born2, double **host_born3,
double **host_a, double **host_c, double **host_d,
double **host_sigma, double **host_offset, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen, double **host_cut_ljsq,
const double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double alf, const double e_shift,
const double f_shift);
};
}
#endif

View File

@ -0,0 +1,134 @@
/***************************************************************************
born_coul_wolf_cs_ext.cpp
-------------------
Trung Dac Nguyen (Northwestern)
Functions for LAMMPS access to born/coul/wolf/cs acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_born_coul_wolf_cs.h"
using namespace std;
using namespace LAMMPS_AL;
static BornCoulWolfCS<PRECISION,ACC_PRECISION> BornCWCST;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int borncwcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_born1, double **host_born2, double **host_born3,
double **host_a, double **host_c, double **host_d,
double **sigma, double **offset, double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double alf, const double e_shift, const double f_shift) {
BornCWCST.clear();
gpu_mode=BornCWCST.device->gpu_mode();
double gpu_split=BornCWCST.device->particle_split();
int first_gpu=BornCWCST.device->first_device();
int last_gpu=BornCWCST.device->last_device();
int world_me=BornCWCST.device->world_me();
int gpu_rank=BornCWCST.device->gpu_rank();
int procs_per_gpu=BornCWCST.device->procs_per_gpu();
BornCWCST.device->init_message(screen,"born/coul/wolf/cs",first_gpu,last_gpu);
bool message=false;
if (BornCWCST.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=BornCWCST.init(ntypes, cutsq, host_rhoinv, host_born1, host_born2,
host_born3, host_a, host_c, host_d, sigma,
offset, special_lj, inum, nall, 300,
maxspecial, cell_size, gpu_split, screen, host_cut_ljsq,
host_cut_coulsq, host_special_coul, qqrd2e,
alf, e_shift, f_shift);
BornCWCST.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=BornCWCST.init(ntypes, cutsq, host_rhoinv, host_born1, host_born2,
host_born3, host_a, host_c, host_d, sigma,
offset, special_lj, inum, nall, 300,
maxspecial, cell_size, gpu_split, screen, host_cut_ljsq,
host_cut_coulsq, host_special_coul, qqrd2e,
alf, e_shift, f_shift);
BornCWCST.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
BornCWCST.estimate_gpu_overhead();
return init_ok;
}
void borncwcs_gpu_clear() {
BornCWCST.clear();
}
int** borncwcs_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 BornCWCST.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 borncwcs_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) {
BornCWCST.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 borncwcs_gpu_bytes() {
return BornCWCST.host_memory_usage();
}