forked from lijiext/lammps
Added missing source files for born/coul/wolf/cs in the gpu library
This commit is contained in:
Trung Nguyen
parent
a9b794b2ab
commit
28504e91c0
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/***************************************************************************
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born_coul_wolf_cs.cpp
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-------------------
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Trung Dac Nguyen (Northwestern)
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Class for acceleration of the born/coul/wolf/cs pair style.
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__________________________________________________________________________
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This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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__________________________________________________________________________
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begin :
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email : ndactrung@gmail.com
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***************************************************************************/
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#ifdef USE_OPENCL
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#include "born_coul_wolf_cs_cl.h"
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#elif defined(USE_CUDART)
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const char *born_coul_wolf_cs=0;
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#else
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#include "born_coul_wolf_cs_cubin.h"
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#endif
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#include "lal_born_coul_wolf_cs.h"
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#include <cassert>
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using namespace LAMMPS_AL;
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#define BornCoulWolfCST BornCoulWolfCS<numtyp, acctyp>
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extern Device<PRECISION,ACC_PRECISION> device;
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template <class numtyp, class acctyp>
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int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_rhoinv,
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double **host_born1, double **host_born2, double **host_born3,
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double **host_a, double **host_c, double **host_d,
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double **host_sigma, double **host_offset,
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double *host_special_lj, const int nlocal,
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const int nall, const int max_nbors,
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const int maxspecial, const double cell_size,
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const double gpu_split, FILE *_screen,
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double **host_cut_ljsq, const double host_cut_coulsq,
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double *host_special_coul, const double qqrd2e,
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const double alf, const double e_shift, const double f_shift) {
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int success;
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success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
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_screen,born_coul_wolf_cs,"k_born_coul_wolf_cs");
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if (success!=0)
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return success;
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// If atom type constants fit in shared memory use fast kernel
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int lj_types=ntypes;
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this->shared_types=false;
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int max_shared_types=this->device->max_shared_types();
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if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
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lj_types=max_shared_types;
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this->shared_types=true;
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}
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this->_lj_types=lj_types;
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// Allocate a host write buffer for data initialization
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UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
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UCL_WRITE_ONLY);
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for (int i=0; i<lj_types*lj_types; i++)
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host_write[i]=0.0;
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this->coeff1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
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this->atom->type_pack4(ntypes,lj_types,this->coeff1,host_write,host_rhoinv,
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host_born1,host_born2,host_born3);
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this->coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
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this->atom->type_pack4(ntypes,lj_types,this->coeff2,host_write,host_a,host_c,
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host_d,host_offset);
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this->cutsq_sigma.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
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this->atom->type_pack4(ntypes,lj_types,this->cutsq_sigma,host_write,host_cutsq,
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host_cut_ljsq,host_sigma);
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this->sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
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for (int i=0; i<4; i++) {
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host_write[i]=host_special_lj[i];
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host_write[i+4]=host_special_coul[i];
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}
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ucl_copy(this->sp_lj,host_write,8,false);
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this->_cut_coulsq=host_cut_coulsq;
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this->_qqrd2e=qqrd2e;
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this->_alf=alf;
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this->_e_shift=e_shift;
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this->_f_shift=f_shift;
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this->_allocated=true;
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this->_max_bytes=this->coeff1.row_bytes()+this->coeff2.row_bytes()
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+this->cutsq_sigma.row_bytes()+this->sp_lj.row_bytes();
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return 0;
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}
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template class BornCoulWolfCS<PRECISION,ACC_PRECISION>;
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@ -0,0 +1,306 @@
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// **************************************************************************
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// born_coul_wolf_cs.cu
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// -------------------
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// Trung Dac Nguyen (Northwestern)
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//
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// Device code for acceleration of the born/coul/wolf/cs pair style
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//
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// __________________________________________________________________________
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// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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// __________________________________________________________________________
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//
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// begin :
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// email : ndactrung@gmail.com
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// ***************************************************************************/
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#ifdef NV_KERNEL
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#include "lal_aux_fun1.h"
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#ifndef _DOUBLE_DOUBLE
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texture<float4> pos_tex;
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texture<float> q_tex;
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#else
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texture<int4,1> pos_tex;
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texture<int2> q_tex;
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#endif
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#else
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#define pos_tex x_
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#define q_tex q_
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#endif
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#define EPSILON (acctyp)(1.0e-20)
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#define MY_PIS (acctyp)1.77245385090551602729
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__kernel void k_born_coul_wolf_cs(const __global numtyp4 *restrict x_,
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const __global numtyp4 *restrict coeff1,
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const __global numtyp4 *restrict coeff2,
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const int lj_types,
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const __global numtyp *restrict sp_lj_in,
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const __global int *dev_nbor,
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const __global int *dev_packed,
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__global acctyp4 *restrict ans,
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__global acctyp *restrict engv,
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const int eflag, const int vflag, const int inum,
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const int nbor_pitch,
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const __global numtyp *restrict q_,
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const __global numtyp4 *restrict cutsq_sigma,
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const numtyp cut_coulsq, const numtyp qqrd2e,
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const numtyp alf, const numtyp e_shift,
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const numtyp f_shift, const int t_per_atom) {
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int tid, ii, offset;
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atom_info(t_per_atom,ii,tid,offset);
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__local numtyp sp_lj[8];
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sp_lj[0]=sp_lj_in[0];
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sp_lj[1]=sp_lj_in[1];
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sp_lj[2]=sp_lj_in[2];
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sp_lj[3]=sp_lj_in[3];
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sp_lj[4]=sp_lj_in[4];
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sp_lj[5]=sp_lj_in[5];
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sp_lj[6]=sp_lj_in[6];
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sp_lj[7]=sp_lj_in[7];
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acctyp energy=(acctyp)0;
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acctyp e_coul=(acctyp)0;
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acctyp4 f;
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f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
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acctyp virial[6];
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for (int i=0; i<6; i++)
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virial[i]=(acctyp)0;
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if (ii<inum) {
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int nbor, nbor_end;
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int i, numj;
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__local int n_stride;
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nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
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n_stride,nbor_end,nbor);
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numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
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numtyp qtmp; fetch(qtmp,i,q_tex);
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int itype=ix.w;
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if (eflag>0) {
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acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) *
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qtmp*qtmp*qqrd2e/(acctyp)t_per_atom;
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e_coul += (acctyp)2.0*e_self;
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}
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for ( ; nbor<nbor_end; nbor+=n_stride) {
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int j=dev_packed[nbor];
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numtyp factor_lj, factor_coul;
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factor_lj = sp_lj[sbmask(j)];
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factor_coul = sp_lj[sbmask(j)+4];
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j &= NEIGHMASK;
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numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
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int jtype=jx.w;
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// Compute r12
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numtyp delx = ix.x-jx.x;
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numtyp dely = ix.y-jx.y;
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numtyp delz = ix.z-jx.z;
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numtyp rsq = delx*delx+dely*dely+delz*delz;
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int mtype=itype*lj_types+jtype;
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if (rsq<cutsq_sigma[mtype].x) { // cutsq
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rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
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acctyp r2inv = ucl_recip(rsq);
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numtyp forcecoul,forceborn,force,prefactor,rexp;
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acctyp v_sh,r6inv;
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if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq
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numtyp r = ucl_sqrt(rsq);
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rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x);
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r6inv = r2inv*r2inv*r2inv;
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forceborn = (coeff1[mtype].y*r*rexp - coeff1[mtype].z*r6inv
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+ coeff1[mtype].w*r2inv*r6inv)*factor_lj;
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} else forceborn = (numtyp)0.0;
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if (rsq < cut_coulsq) {
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numtyp r = ucl_rsqrt(r2inv);
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acctyp arij = alf * r;
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acctyp erfcd = ucl_exp(-arij*arij);
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fetch(prefactor,j,q_tex);
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prefactor *= qqrd2e * qtmp/r;
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const acctyp erfcc = erfc(arij);
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v_sh = (erfcc - e_shift*r)*prefactor;
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acctyp dvdrr = (erfcc/rsq + (numtyp)2.0*alf/MY_PIS * erfcd/r) + f_shift;
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forcecoul = prefactor * dvdrr*rsq;
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if (factor_coul < (numtyp)1.0) forcecoul -= ((numtyp)1.0-factor_coul)*prefactor;
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} else forcecoul = (numtyp)0.0;
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force = (forceborn + forcecoul) * r2inv;
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f.x+=delx*force;
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f.y+=dely*force;
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f.z+=delz*force;
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if (eflag>0) {
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if (rsq < cut_coulsq) {
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acctyp e=v_sh;
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if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
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e_coul += e;
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}
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if (rsq < cutsq_sigma[mtype].y) {
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numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv
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+ coeff2[mtype].z*r2inv*r6inv;
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energy+=factor_lj*(e-coeff2[mtype].w);
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}
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}
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if (vflag>0) {
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virial[0] += delx*delx*force;
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virial[1] += dely*dely*force;
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virial[2] += delz*delz*force;
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virial[3] += delx*dely*force;
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virial[4] += delx*delz*force;
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virial[5] += dely*delz*force;
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}
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}
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} // for nbor
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store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
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vflag,ans,engv);
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} // if ii
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}
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__kernel void k_born_coul_wolf_cs_fast(const __global numtyp4 *restrict x_,
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const __global numtyp4 *restrict coeff1_in,
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const __global numtyp4 *restrict coeff2_in,
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const __global numtyp *restrict sp_lj_in,
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const __global int *dev_nbor,
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const __global int *dev_packed,
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__global acctyp4 *restrict ans,
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__global acctyp *restrict engv,
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const int eflag, const int vflag, const int inum,
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const int nbor_pitch,
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const __global numtyp *restrict q_,
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const __global numtyp4 *restrict cutsq_sigma,
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const numtyp cut_coulsq, const numtyp qqrd2e,
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const numtyp alf, const numtyp e_shift,
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const numtyp f_shift, const int t_per_atom) {
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int tid, ii, offset;
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atom_info(t_per_atom,ii,tid,offset);
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__local numtyp4 coeff1[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
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__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
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__local numtyp sp_lj[8];
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if (tid<8)
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sp_lj[tid]=sp_lj_in[tid];
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if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
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coeff1[tid]=coeff1_in[tid];
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if (eflag>0)
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coeff2[tid]=coeff2_in[tid];
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}
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acctyp energy=(acctyp)0;
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acctyp e_coul=(acctyp)0;
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acctyp4 f;
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f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
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acctyp virial[6];
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for (int i=0; i<6; i++)
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virial[i]=(acctyp)0;
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__syncthreads();
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if (ii<inum) {
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int nbor, nbor_end;
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int i, numj;
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__local int n_stride;
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nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
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n_stride,nbor_end,nbor);
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numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
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numtyp qtmp; fetch(qtmp,i,q_tex);
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int iw=ix.w;
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int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
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if (eflag>0) {
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acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) *
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qtmp*qtmp*qqrd2e/(acctyp)t_per_atom;
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e_coul += (acctyp)2.0*e_self;
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}
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for ( ; nbor<nbor_end; nbor+=n_stride) {
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int j=dev_packed[nbor];
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numtyp factor_lj, factor_coul;
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factor_lj = sp_lj[sbmask(j)];
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factor_coul = sp_lj[sbmask(j)+4];
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j &= NEIGHMASK;
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numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
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int mtype=itype+jx.w;
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// Compute r12
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numtyp delx = ix.x-jx.x;
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numtyp dely = ix.y-jx.y;
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numtyp delz = ix.z-jx.z;
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acctyp rsq = delx*delx+dely*dely+delz*delz;
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if (rsq<cutsq_sigma[mtype].x) {
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rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
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acctyp r2inv = ucl_recip(rsq);
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numtyp forcecoul,forceborn,force,prefactor,rexp;
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acctyp v_sh,r6inv;
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if (rsq < cutsq_sigma[mtype].y) {
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r6inv = r2inv*r2inv*r2inv;
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numtyp r = ucl_sqrt(rsq);
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rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x);
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forceborn = (coeff1[mtype].y*r*rexp - coeff1[mtype].z*r6inv
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+ coeff1[mtype].w*r2inv*r6inv)*factor_lj;
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} else forceborn = (numtyp)0.0;
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if (rsq < cut_coulsq) {
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numtyp r = ucl_sqrt(rsq);
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acctyp arij = alf * r;
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acctyp erfcd = ucl_exp(-arij*arij);
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fetch(prefactor,j,q_tex);
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prefactor *= qqrd2e * qtmp/r;
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const acctyp erfcc = erfc(arij);
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v_sh = (erfcc - e_shift*r)*prefactor;
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acctyp dvdrr = (erfcc/rsq + (numtyp)2.0*alf/MY_PIS * erfcd/r) + f_shift;
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forcecoul = prefactor * dvdrr*rsq;
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if (factor_coul < (numtyp)1.0) forcecoul -= ((numtyp)1.0-factor_coul)*prefactor;
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} else forcecoul = (numtyp)0.0;
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force = (forceborn + forcecoul) * r2inv;
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f.x+=delx*force;
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f.y+=dely*force;
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f.z+=delz*force;
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if (eflag>0) {
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if (rsq < cut_coulsq) {
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acctyp e=v_sh;
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if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
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e_coul += e;
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}
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if (rsq < cutsq_sigma[mtype].y) {
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numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv
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+ coeff2[mtype].z*r2inv*r6inv;
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energy+=factor_lj*(e-coeff2[mtype].w);
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}
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}
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if (vflag>0) {
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virial[0] += delx*delx*force;
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virial[1] += dely*dely*force;
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virial[2] += delz*delz*force;
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virial[3] += delx*dely*force;
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virial[4] += delx*delz*force;
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virial[5] += dely*delz*force;
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}
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}
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} // for nbor
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store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
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vflag,ans,engv);
|
||||
} // if ii
|
||||
}
|
||||
|
||||
|
|
@ -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
|
||||
|
|
@ -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();
|
||||
}
|
||||
|
||||
|
||||
Loading…
Reference in New Issue