1038 lines
36 KiB
C++
1038 lines
36 KiB
C++
/***************************************************************************
|
|
base_amoeba.cpp
|
|
-------------------
|
|
Trung Dac Nguyen (Northwestern)
|
|
|
|
Base class for pair styles needing per-particle data for position,
|
|
charge, and type.
|
|
|
|
__________________________________________________________________________
|
|
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
|
__________________________________________________________________________
|
|
|
|
begin :
|
|
email : trung.nguyen@northwestern.edu
|
|
***************************************************************************/
|
|
|
|
#include "lal_base_amoeba.h"
|
|
|
|
namespace LAMMPS_AL {
|
|
#define BaseAmoebaT BaseAmoeba<numtyp, acctyp>
|
|
|
|
extern Device<PRECISION,ACC_PRECISION> global_device;
|
|
|
|
template <class numtyp, class acctyp>
|
|
BaseAmoebaT::BaseAmoeba() : _compiled(false), _max_bytes(0), short_nbor_polar_avail(false) {
|
|
device=&global_device;
|
|
ans=new Answer<numtyp,acctyp>();
|
|
nbor=new Neighbor();
|
|
pair_program=nullptr;
|
|
ucl_device=nullptr;
|
|
}
|
|
|
|
template <class numtyp, class acctyp>
|
|
BaseAmoebaT::~BaseAmoeba() {
|
|
delete ans;
|
|
delete nbor;
|
|
k_multipole.clear();
|
|
k_udirect2b.clear();
|
|
k_umutual2b.clear();
|
|
k_fphi_uind.clear();
|
|
k_fphi_mpole.clear();
|
|
k_polar.clear();
|
|
k_special15.clear();
|
|
k_short_nbor.clear();
|
|
|
|
#if 0 // !defined(USE_OPENCL) && !defined(USE_HIP)
|
|
if (fft_plan_created) cufftDestroy(plan);
|
|
#endif
|
|
|
|
if (pair_program) delete pair_program;
|
|
}
|
|
|
|
template <class numtyp, class acctyp>
|
|
int BaseAmoebaT::bytes_per_atom_atomic(const int max_nbors) const {
|
|
return device->atom.bytes_per_atom()+ans->bytes_per_atom()+
|
|
nbor->bytes_per_atom(max_nbors);
|
|
}
|
|
|
|
template <class numtyp, class acctyp>
|
|
int BaseAmoebaT::init_atomic(const int nlocal, const int nall,
|
|
const int max_nbors, const int maxspecial,
|
|
const int maxspecial15,
|
|
const double cell_size, const double gpu_split,
|
|
FILE *_screen, const void *pair_program,
|
|
const char *k_name_multipole,
|
|
const char *k_name_udirect2b,
|
|
const char *k_name_umutual2b,
|
|
const char *k_name_polar,
|
|
const char *k_name_fphi_uind,
|
|
const char *k_name_fphi_mpole,
|
|
const char *k_name_short_nbor,
|
|
const char* k_name_special15) {
|
|
screen=_screen;
|
|
|
|
int gpu_nbor=0;
|
|
if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_NEIGH)
|
|
gpu_nbor=1;
|
|
else if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_HYB_NEIGH)
|
|
gpu_nbor=2;
|
|
|
|
int _gpu_host=0;
|
|
int host_nlocal=hd_balancer.first_host_count(nlocal,gpu_split,gpu_nbor);
|
|
if (host_nlocal>0)
|
|
_gpu_host=1;
|
|
|
|
_threads_per_atom=device->threads_per_charge();
|
|
|
|
bool charge = true;
|
|
bool rot = false;
|
|
bool vel = false;
|
|
_extra_fields = 24; // round up to accomodate quadruples of numtyp values
|
|
// rpole 13; uind 3; uinp 3; amtype, amgroup; pval
|
|
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel,_extra_fields);
|
|
if (success!=0)
|
|
return success;
|
|
|
|
if (ucl_device!=device->gpu) _compiled=false;
|
|
|
|
ucl_device=device->gpu;
|
|
atom=&device->atom;
|
|
|
|
_block_size=device->pair_block_size();
|
|
_block_bio_size=device->block_bio_pair();
|
|
compile_kernels(*ucl_device,pair_program,k_name_multipole,
|
|
k_name_udirect2b, k_name_umutual2b,k_name_polar,
|
|
k_name_fphi_uind, k_name_fphi_mpole,
|
|
k_name_short_nbor, k_name_special15);
|
|
|
|
if (_threads_per_atom>1 && gpu_nbor==0) {
|
|
nbor->packing(true);
|
|
_nbor_data=&(nbor->dev_packed);
|
|
} else {
|
|
_nbor_data=&(nbor->dev_nbor);
|
|
}
|
|
|
|
bool alloc_packed=false;
|
|
success = device->init_nbor(nbor,nlocal,host_nlocal,nall,maxspecial,
|
|
_gpu_host,max_nbors,cell_size,alloc_packed,
|
|
_threads_per_atom);
|
|
if (success!=0)
|
|
return success;
|
|
|
|
// Initialize host-device load balancer
|
|
hd_balancer.init(device,gpu_nbor,gpu_split);
|
|
|
|
// Initialize timers for the selected GPU
|
|
time_pair.init(*ucl_device);
|
|
time_pair.zero();
|
|
|
|
pos_tex.bind_float(atom->x,4);
|
|
q_tex.bind_float(atom->q,1);
|
|
|
|
_max_an_bytes=ans->gpu_bytes()+nbor->gpu_bytes();
|
|
_maxspecial=maxspecial;
|
|
_maxspecial15=maxspecial15;
|
|
|
|
// allocate per-atom array tep
|
|
|
|
int ef_nall=nlocal; //nall;
|
|
if (ef_nall==0)
|
|
ef_nall=2000;
|
|
|
|
dev_short_nbor.alloc(ef_nall*(2+max_nbors),*(this->ucl_device),UCL_READ_WRITE);
|
|
|
|
_max_tep_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
|
|
_tep.alloc(_max_tep_size*4,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
|
|
|
|
_max_fieldp_size = _max_tep_size;
|
|
_fieldp.alloc(_max_fieldp_size*8,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
|
|
|
|
_max_thetai_size = 0;
|
|
|
|
_nmax = nall;
|
|
dev_nspecial15.alloc(nall,*(this->ucl_device),UCL_READ_ONLY);
|
|
dev_special15.alloc(_maxspecial15*nall,*(this->ucl_device),UCL_READ_ONLY);
|
|
dev_special15_t.alloc(nall*_maxspecial15,*(this->ucl_device),UCL_READ_ONLY);
|
|
|
|
fft_plan_created = false;
|
|
|
|
return success;
|
|
}
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::estimate_gpu_overhead(const int add_kernels) {
|
|
device->estimate_gpu_overhead(1+add_kernels,_gpu_overhead,_driver_overhead);
|
|
}
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::clear_atomic() {
|
|
// Output any timing information
|
|
acc_timers();
|
|
double avg_split=hd_balancer.all_avg_split();
|
|
_gpu_overhead*=hd_balancer.timestep();
|
|
_driver_overhead*=hd_balancer.timestep();
|
|
device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
|
|
_gpu_overhead,_driver_overhead,_threads_per_atom,screen);
|
|
|
|
time_pair.clear();
|
|
hd_balancer.clear();
|
|
|
|
dev_short_nbor.clear();
|
|
nbor->clear();
|
|
ans->clear();
|
|
|
|
_tep.clear();
|
|
_fieldp.clear();
|
|
_thetai1.clear();
|
|
_thetai2.clear();
|
|
_thetai3.clear();
|
|
_igrid.clear();
|
|
_fdip_phi1.clear();
|
|
_fdip_phi2.clear();
|
|
_fdip_sum_phi.clear();
|
|
_cgrid_brick.clear();
|
|
|
|
dev_nspecial15.clear();
|
|
dev_special15.clear();
|
|
dev_special15_t.clear();
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Copy neighbor list from host
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
int * BaseAmoebaT::reset_nbors(const int nall, const int inum, int *ilist,
|
|
int *numj, int **firstneigh, bool &success) {
|
|
success=true;
|
|
|
|
int mn=nbor->max_nbor_loop(inum,numj,ilist);
|
|
resize_atom(inum,nall,success);
|
|
resize_local(inum,mn,success);
|
|
if (!success)
|
|
return nullptr;
|
|
|
|
nbor->get_host(inum,ilist,numj,firstneigh,block_size());
|
|
|
|
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
|
|
if (bytes>_max_an_bytes)
|
|
_max_an_bytes=bytes;
|
|
|
|
return ilist;
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Build neighbor list on device
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
inline int BaseAmoebaT::build_nbor_list(const int inum, const int host_inum,
|
|
const int nall, double **host_x,
|
|
int *host_type, double *sublo,
|
|
double *subhi, tagint *tag,
|
|
int **nspecial, tagint **special,
|
|
int *nspecial15, tagint **special15,
|
|
bool &success) {
|
|
success=true;
|
|
resize_atom(inum,nall,success);
|
|
resize_local(inum,host_inum,nbor->max_nbors(),success);
|
|
if (!success)
|
|
return 0;
|
|
atom->cast_copy_x(host_x,host_type);
|
|
|
|
int mn;
|
|
nbor->build_nbor_list(host_x, inum, host_inum, nall, *atom, sublo, subhi,
|
|
tag, nspecial, special, success, mn, ans->error_flag);
|
|
|
|
// add one-five neighbors
|
|
|
|
if (_maxspecial15>0) {
|
|
UCL_H_Vec<int> view_nspecial15;
|
|
UCL_H_Vec<tagint> view_special15;
|
|
view_nspecial15.view(nspecial15,nall,*ucl_device);
|
|
view_special15.view(special15[0],nall*_maxspecial15,*ucl_device);
|
|
ucl_copy(dev_nspecial15,view_nspecial15,nall,false);
|
|
ucl_copy(dev_special15_t,view_special15,_maxspecial15*nall,false);
|
|
nbor->transpose(dev_special15, dev_special15_t, _maxspecial15, nall);
|
|
|
|
add_onefive_neighbors();
|
|
}
|
|
|
|
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
|
|
if (bytes>_max_an_bytes)
|
|
_max_an_bytes=bytes;
|
|
return mn;
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Copy nbor list from host if necessary and then calculate forces, virials
|
|
// for the polar real-space term
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_polar_real_host_nbor(const int f_ago, const int inum_full,
|
|
const int nall, double **host_x, int *host_type,
|
|
int *host_amtype, int *host_amgroup, double **host_rpole,
|
|
double **host_uind, double **host_uinp,
|
|
int *ilist, int *numj, int **firstneigh,
|
|
const bool eflag_in, const bool vflag_in,
|
|
const bool eatom, const bool vatom,
|
|
int &host_start, const double cpu_time,
|
|
bool &success, const double aewald, const double felec,
|
|
const double off2_polar, double *host_q, const int nlocal,
|
|
double *boxlo, double *prd, void **tep_ptr) {
|
|
acc_timers();
|
|
int eflag, vflag;
|
|
if (eatom) eflag=2;
|
|
else if (eflag_in) eflag=1;
|
|
else eflag=0;
|
|
if (vatom) vflag=2;
|
|
else if (vflag_in) vflag=1;
|
|
else vflag=0;
|
|
|
|
#ifdef LAL_NO_BLOCK_REDUCE
|
|
if (eflag) eflag=2;
|
|
if (vflag) vflag=2;
|
|
#endif
|
|
|
|
set_kernel(eflag,vflag);
|
|
|
|
// ------------------- Resize _tep array ------------------------
|
|
|
|
if (nall>_max_tep_size) {
|
|
_max_tep_size=static_cast<int>(static_cast<double>(nall)*1.10);
|
|
_tep.resize(_max_tep_size*4);
|
|
|
|
dev_nspecial15.clear();
|
|
dev_special15.clear();
|
|
dev_special15_t.clear();
|
|
dev_nspecial15.alloc(nall,*(this->ucl_device),UCL_READ_ONLY);
|
|
dev_special15.alloc(_maxspecial15*nall,*(this->ucl_device),UCL_READ_ONLY);
|
|
dev_special15_t.alloc(nall*_maxspecial15,*(this->ucl_device),UCL_READ_ONLY);
|
|
}
|
|
|
|
*tep_ptr=_tep.host.begin();
|
|
|
|
if (inum_full==0) {
|
|
host_start=0;
|
|
// Make sure textures are correct if realloc by a different hybrid style
|
|
resize_atom(0,nall,success);
|
|
zero_timers();
|
|
return;
|
|
}
|
|
|
|
int ago=hd_balancer.ago_first(f_ago);
|
|
int inum=hd_balancer.balance(ago,inum_full,cpu_time);
|
|
ans->inum(inum);
|
|
host_start=inum;
|
|
|
|
if (ago==0) {
|
|
reset_nbors(nall, inum, ilist, numj, firstneigh, success);
|
|
if (!success)
|
|
return;
|
|
}
|
|
|
|
// packing host arrays into host_extra
|
|
|
|
atom->cast_x_data(host_x,host_type);
|
|
atom->cast_q_data(host_q);
|
|
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp);
|
|
hd_balancer.start_timer();
|
|
atom->add_x_data(host_x,host_type);
|
|
atom->add_q_data();
|
|
atom->add_extra_data();
|
|
|
|
device->precompute(f_ago,nlocal,nall,host_x,host_type,success,host_q,
|
|
boxlo, prd);
|
|
|
|
_off2_polar = off2_polar;
|
|
_felec = felec;
|
|
const int red_blocks=polar_real(eflag,vflag);
|
|
|
|
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,ilist,red_blocks);
|
|
device->add_ans_object(ans);
|
|
hd_balancer.stop_timer();
|
|
|
|
// copy tep from device to host
|
|
|
|
_tep.update_host(_max_tep_size*4,false);
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Prepare for multiple kernel calls in a time step:
|
|
// - reallocate per-atom arrays, if needed
|
|
// - transfer extra data from host to device
|
|
// - build the full neighbor lists for use by different kernels
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall,
|
|
double **host_x, int *host_type, int *host_amtype,
|
|
int *host_amgroup, double **host_rpole,
|
|
double **host_uind, double **host_uinp, double *host_pval,
|
|
double *sublo, double *subhi, tagint *tag,
|
|
int **nspecial, tagint **special,
|
|
int *nspecial15, tagint **special15,
|
|
const bool eflag_in, const bool vflag_in,
|
|
const bool eatom, const bool vatom, int &host_start,
|
|
int **&ilist, int **&jnum, const double cpu_time,
|
|
bool &success, double *host_q, double *boxlo, double *prd) {
|
|
acc_timers();
|
|
if (eatom) _eflag=2;
|
|
else if (eflag_in) _eflag=1;
|
|
else _eflag=0;
|
|
if (vatom) _vflag=2;
|
|
else if (vflag_in) _vflag=1;
|
|
else _vflag=0;
|
|
|
|
#ifdef LAL_NO_BLOCK_REDUCE
|
|
if (_eflag) _eflag=2;
|
|
if (_vflag) _vflag=2;
|
|
#endif
|
|
|
|
set_kernel(_eflag,_vflag);
|
|
|
|
// ------------------- Resize 1-5 neighbor arrays ------------------------
|
|
|
|
if (nall>_nmax) {
|
|
_nmax = nall;
|
|
dev_nspecial15.clear();
|
|
dev_special15.clear();
|
|
dev_special15_t.clear();
|
|
dev_nspecial15.alloc(nall,*(this->ucl_device),UCL_READ_ONLY);
|
|
dev_special15.alloc(_maxspecial15*nall,*(this->ucl_device),UCL_READ_ONLY);
|
|
dev_special15_t.alloc(nall*_maxspecial15,*(this->ucl_device),UCL_READ_ONLY);
|
|
}
|
|
|
|
if (inum_full==0) {
|
|
host_start=0;
|
|
// Make sure textures are correct if realloc by a different hybrid style
|
|
resize_atom(0,nall,success);
|
|
zero_timers();
|
|
return nullptr;
|
|
}
|
|
|
|
hd_balancer.balance(cpu_time);
|
|
int inum=hd_balancer.get_gpu_count(ago,inum_full);
|
|
ans->inum(inum);
|
|
host_start=inum;
|
|
|
|
// Build neighbor list on GPU if necessary
|
|
if (ago==0) {
|
|
_max_nbors = build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
|
|
sublo, subhi, tag, nspecial, special, nspecial15, special15,
|
|
success);
|
|
if (!success)
|
|
return nullptr;
|
|
atom->cast_q_data(host_q);
|
|
hd_balancer.start_timer();
|
|
} else {
|
|
atom->cast_x_data(host_x,host_type);
|
|
atom->cast_q_data(host_q);
|
|
hd_balancer.start_timer();
|
|
atom->add_x_data(host_x,host_type);
|
|
}
|
|
atom->add_q_data();
|
|
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
|
|
atom->add_extra_data();
|
|
|
|
*ilist=nbor->host_ilist.begin();
|
|
*jnum=nbor->host_acc.begin();
|
|
|
|
// re-allocate dev_short_nbor if necessary
|
|
if (inum_full*(2+_max_nbors) > dev_short_nbor.cols()) {
|
|
int _nmax=static_cast<int>(static_cast<double>(inum_full)*1.10);
|
|
dev_short_nbor.resize((2+_max_nbors)*_nmax);
|
|
}
|
|
|
|
return nbor->host_jlist.begin()-host_start;
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Compute multipole real-space part
|
|
// precompute() should be already invoked before mem (re)allocation
|
|
// this is the first part in a time step done on the GPU for AMOEBA for now
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
|
|
const int nall, double **host_x,
|
|
int *host_type, int *host_amtype,
|
|
int *host_amgroup, double **host_rpole, double *host_pval,
|
|
double *sublo, double *subhi, tagint *tag,
|
|
int **nspecial, tagint **special,
|
|
int *nspecial15, tagint **special15,
|
|
const bool eflag_in, const bool vflag_in,
|
|
const bool eatom, const bool vatom,
|
|
int &host_start, int **ilist, int **jnum,
|
|
const double cpu_time, bool &success,
|
|
const double aewald, const double felec,
|
|
const double off2_mpole, double *host_q,
|
|
double *boxlo, double *prd, void **tep_ptr) {
|
|
// ------------------- Resize _tep array ------------------------
|
|
|
|
if (inum_full>_max_tep_size) {
|
|
_max_tep_size=static_cast<int>(static_cast<double>(inum_full)*1.10);
|
|
_tep.resize(_max_tep_size*4);
|
|
}
|
|
*tep_ptr=_tep.host.begin();
|
|
|
|
_off2_mpole = off2_mpole;
|
|
_felec = felec;
|
|
_aewald = aewald;
|
|
const int red_blocks=multipole_real(_eflag,_vflag);
|
|
|
|
// leave the answers (forces, energies and virial) on the device,
|
|
// only copy them back in the last kernel (polar_real)
|
|
//ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
|
|
//device->add_ans_object(ans);
|
|
|
|
hd_balancer.stop_timer();
|
|
|
|
// copy tep from device to host
|
|
|
|
_tep.update_host(_max_tep_size*4,false);
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Reneighbor on GPU if necessary, and then compute the direct real space part
|
|
// of the permanent field
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_udirect2b(int *host_amtype, int *host_amgroup, double **host_rpole,
|
|
double **host_uind, double **host_uinp, double *host_pval,
|
|
const double aewald, const double off2_polar,
|
|
void** fieldp_ptr) {
|
|
// all the necessary data arrays are already copied from host to device
|
|
|
|
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
|
|
atom->add_extra_data();
|
|
|
|
*fieldp_ptr=_fieldp.host.begin();
|
|
|
|
_off2_polar = off2_polar;
|
|
_aewald = aewald;
|
|
const int red_blocks=udirect2b(_eflag,_vflag);
|
|
|
|
// copy field and fieldp from device to host (_fieldp store both arrays, one after another)
|
|
|
|
_fieldp.update_host(_max_fieldp_size*8,false);
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Reneighbor on GPU if necessary, and then compute the direct real space part
|
|
// of the induced field
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_umutual2b(int *host_amtype, int *host_amgroup, double **host_rpole,
|
|
double **host_uind, double **host_uinp, double *host_pval,
|
|
const double aewald, const double off2_polar,
|
|
void** fieldp_ptr) {
|
|
// all the necessary data arrays are already copied from host to device
|
|
|
|
//cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
|
|
cast_extra_data(host_amtype, host_amgroup, nullptr, host_uind, host_uinp, nullptr);
|
|
atom->add_extra_data();
|
|
|
|
_off2_polar = off2_polar;
|
|
_aewald = aewald;
|
|
const int red_blocks=umutual2b(_eflag,_vflag);
|
|
|
|
// copy field and fieldp from device to host (_fieldp store both arrays, one after another)
|
|
// NOTE: move this step to update_fieldp() to delay device-host transfer
|
|
// *fieldp_ptr=_fieldp.host.begin();
|
|
// _fieldp.update_host(_max_fieldp_size*8,false);
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Prepare for umutual1() after bspline_fill() is done on host
|
|
// - reallocate per-atom arrays, thetai1, thetai2, thetai3, and igrid if needed
|
|
// host_thetai1, host_thetai2, host_thetai3 are allocated with nmax by bsordermax by 4
|
|
// host_igrid is allocated with nmax by 4
|
|
// - transfer extra data from host to device
|
|
// NOTE: can be re-used for fphi_mpole() (already allocate 2x grid points)
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::precompute_kspace(const int inum_full, const int bsorder,
|
|
double ***host_thetai1, double ***host_thetai2,
|
|
double ***host_thetai3, int** host_igrid,
|
|
const int nzlo_out, const int nzhi_out,
|
|
const int nylo_out, const int nyhi_out,
|
|
const int nxlo_out, const int nxhi_out) {
|
|
// update bsorder with that of the kspace solver
|
|
_bsorder = bsorder;
|
|
|
|
// allocate or resize per-atom arrays
|
|
// _max_thetai_size, _max_tep_size and _max_fieldp_size are essentially _nmax
|
|
// will be consolidated once all terms are ready
|
|
|
|
if (_max_thetai_size == 0) {
|
|
_max_thetai_size = static_cast<int>(static_cast<double>(inum_full)*1.10);
|
|
_thetai1.alloc(_max_thetai_size*bsorder,*(this->ucl_device),UCL_READ_ONLY);
|
|
_thetai2.alloc(_max_thetai_size*bsorder,*(this->ucl_device),UCL_READ_ONLY);
|
|
_thetai3.alloc(_max_thetai_size*bsorder,*(this->ucl_device),UCL_READ_ONLY);
|
|
_igrid.alloc(_max_thetai_size*4,*(this->ucl_device),UCL_WRITE_ONLY,UCL_READ_ONLY);
|
|
|
|
_fdip_phi1.alloc(_max_thetai_size*10,*(this->ucl_device),UCL_READ_WRITE);
|
|
_fdip_phi2.alloc(_max_thetai_size*10,*(this->ucl_device),UCL_READ_WRITE);
|
|
_fdip_sum_phi.alloc(_max_thetai_size*20,*(this->ucl_device),UCL_READ_WRITE);
|
|
} else {
|
|
if (_thetai1.cols()<_max_thetai_size*bsorder) {
|
|
_max_thetai_size=static_cast<int>(static_cast<double>(inum_full)*1.10);
|
|
_thetai1.resize(_max_thetai_size*bsorder);
|
|
_thetai2.resize(_max_thetai_size*bsorder);
|
|
_thetai3.resize(_max_thetai_size*bsorder);
|
|
_igrid.resize(_max_thetai_size*4);
|
|
|
|
_fdip_phi1.resize(_max_thetai_size*10);
|
|
_fdip_phi2.resize(_max_thetai_size*10);
|
|
_fdip_sum_phi.resize(_max_thetai_size*20);
|
|
}
|
|
}
|
|
|
|
// pack host data to device
|
|
|
|
for (int i = 0; i < inum_full; i++)
|
|
for (int j = 0; j < bsorder; j++) {
|
|
int idx = i*bsorder + j;
|
|
numtyp4 v;
|
|
v.x = host_thetai1[i][j][0];
|
|
v.y = host_thetai1[i][j][1];
|
|
v.z = host_thetai1[i][j][2];
|
|
v.w = host_thetai1[i][j][3];
|
|
_thetai1[idx] = v;
|
|
}
|
|
_thetai1.update_device(true);
|
|
|
|
for (int i = 0; i < inum_full; i++)
|
|
for (int j = 0; j < bsorder; j++) {
|
|
int idx = i*bsorder + j;
|
|
numtyp4 v;
|
|
v.x = host_thetai2[i][j][0];
|
|
v.y = host_thetai2[i][j][1];
|
|
v.z = host_thetai2[i][j][2];
|
|
v.w = host_thetai2[i][j][3];
|
|
_thetai2[idx] = v;
|
|
}
|
|
_thetai2.update_device(true);
|
|
|
|
for (int i = 0; i < inum_full; i++)
|
|
for (int j = 0; j < bsorder; j++) {
|
|
int idx = i*bsorder + j;
|
|
numtyp4 v;
|
|
v.x = host_thetai3[i][j][0];
|
|
v.y = host_thetai3[i][j][1];
|
|
v.z = host_thetai3[i][j][2];
|
|
v.w = host_thetai3[i][j][3];
|
|
_thetai3[idx] = v;
|
|
}
|
|
_thetai3.update_device(true);
|
|
|
|
for (int i = 0; i < inum_full; i++) {
|
|
int idx = i*4;
|
|
_igrid[idx+0] = host_igrid[i][0];
|
|
_igrid[idx+1] = host_igrid[i][1];
|
|
_igrid[idx+2] = host_igrid[i][2];
|
|
}
|
|
_igrid.update_device(true);
|
|
|
|
_nzlo_out = nzlo_out;
|
|
_nzhi_out = nzhi_out;
|
|
_nylo_out = nylo_out;
|
|
_nyhi_out = nyhi_out;
|
|
_nxlo_out = nxlo_out;
|
|
_nxhi_out = nxhi_out;
|
|
_ngridz = nzhi_out - nzlo_out + 1;
|
|
_ngridy = nyhi_out - nylo_out + 1;
|
|
_ngridx = nxhi_out - nxlo_out + 1;
|
|
_num_grid_points = _ngridx * _ngridy * _ngridz;
|
|
|
|
int numel = _num_grid_points;
|
|
if (_cgrid_brick.cols() == 0) {
|
|
_cgrid_brick.alloc(numel, *(this->ucl_device), UCL_READ_WRITE, UCL_READ_ONLY);
|
|
} else if (numel > _cgrid_brick.cols()) {
|
|
_cgrid_brick.resize(numel);
|
|
}
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// fphi_uind = induced potential from grid
|
|
// fphi_uind extracts the induced dipole potential from the particle mesh Ewald grid
|
|
// NOTE: host_grid_brick is from ic_kspace post_convolution()
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_fphi_uind(double ****host_grid_brick,
|
|
void **host_fdip_phi1,
|
|
void **host_fdip_phi2,
|
|
void **host_fdip_sum_phi)
|
|
{
|
|
// TODO: find out why this (dummy) host alloc helps the cgrid_brick update_device() work correcly
|
|
UCL_H_Vec<numtyp> hdummy;
|
|
hdummy.alloc(1, *(this->ucl_device), UCL_READ_ONLY);
|
|
|
|
int n = 0;
|
|
for (int iz = _nzlo_out; iz <= _nzhi_out; iz++)
|
|
for (int iy = _nylo_out; iy <= _nyhi_out; iy++)
|
|
for (int ix = _nxlo_out; ix <= _nxhi_out; ix++) {
|
|
numtyp2 v;
|
|
v.x = host_grid_brick[iz][iy][ix][0];
|
|
v.y = host_grid_brick[iz][iy][ix][1];
|
|
_cgrid_brick[n] = v;
|
|
n++;
|
|
}
|
|
_cgrid_brick.update_device(_num_grid_points, false);
|
|
|
|
const int red_blocks = fphi_uind();
|
|
|
|
_fdip_phi1.update_host(_max_thetai_size*10);
|
|
_fdip_phi2.update_host(_max_thetai_size*10);
|
|
_fdip_sum_phi.update_host(_max_thetai_size*20);
|
|
|
|
*host_fdip_phi1 = _fdip_phi1.host.begin();
|
|
*host_fdip_phi2 = _fdip_phi2.host.begin();
|
|
*host_fdip_sum_phi = _fdip_sum_phi.host.begin();
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Interpolate the potential from the PME grid
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
int BaseAmoebaT::fphi_uind() {
|
|
int ainum=ans->inum();
|
|
if (ainum == 0)
|
|
return 0;
|
|
|
|
int _nall=atom->nall();
|
|
int nbor_pitch=nbor->nbor_pitch();
|
|
|
|
// Compute the block size and grid size to keep all cores busy
|
|
const int BX=block_size();
|
|
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
|
|
|
|
time_pair.start();
|
|
int ngridxy = _ngridx * _ngridy;
|
|
k_fphi_uind.set_size(GX,BX);
|
|
k_fphi_uind.run(&_thetai1, &_thetai2, &_thetai3, &_igrid, &_cgrid_brick,
|
|
&_fdip_phi1, &_fdip_phi2, &_fdip_sum_phi, &_bsorder, &ainum,
|
|
&_nzlo_out, &_nylo_out, &_nxlo_out, &ngridxy, &_ngridx);
|
|
time_pair.stop();
|
|
|
|
return GX;
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// fphi_mpole = multipole potential from grid (limited to polar_kspace for now)
|
|
// fphi_mpole extracts the permanent multipole potential from
|
|
// the particle mesh Ewald grid
|
|
// NOTE: host_grid_brick is from p_kspace post_convolution()
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_fphi_mpole(double ***host_grid_brick, void **host_fphi, const double felec)
|
|
{
|
|
// TODO: grid brick[k][j][i] is a scalar
|
|
UCL_H_Vec<numtyp> hdummy;
|
|
hdummy.alloc(1, *(this->ucl_device), UCL_READ_ONLY);
|
|
|
|
int n = 0;
|
|
for (int iz = _nzlo_out; iz <= _nzhi_out; iz++)
|
|
for (int iy = _nylo_out; iy <= _nyhi_out; iy++)
|
|
for (int ix = _nxlo_out; ix <= _nxhi_out; ix++) {
|
|
numtyp2 v;
|
|
v.x = host_grid_brick[iz][iy][ix];
|
|
v.y = (numtyp)0;
|
|
_cgrid_brick[n] = v;
|
|
n++;
|
|
}
|
|
_cgrid_brick.update_device(_num_grid_points, false);
|
|
|
|
_felec = felec;
|
|
const int red_blocks = fphi_mpole();
|
|
|
|
_fdip_sum_phi.update_host(_max_thetai_size*20);
|
|
|
|
*host_fphi = _fdip_sum_phi.host.begin();
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Interpolate the potential from the PME grid
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
int BaseAmoebaT::fphi_mpole() {
|
|
int ainum=ans->inum();
|
|
if (ainum == 0)
|
|
return 0;
|
|
|
|
int _nall=atom->nall();
|
|
int nbor_pitch=nbor->nbor_pitch();
|
|
|
|
// Compute the block size and grid size to keep all cores busy
|
|
const int BX=block_size();
|
|
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
|
|
|
|
time_pair.start();
|
|
int ngridxy = _ngridx * _ngridy;
|
|
k_fphi_mpole.set_size(GX,BX);
|
|
k_fphi_mpole.run(&_thetai1, &_thetai2, &_thetai3, &_igrid, &_cgrid_brick,
|
|
&_fdip_sum_phi, &_bsorder, &ainum, &_felec,
|
|
&_nzlo_out, &_nylo_out, &_nxlo_out, &ngridxy, &_ngridx);
|
|
time_pair.stop();
|
|
|
|
return GX;
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Reneighbor on GPU if necessary, and then compute polar real-space
|
|
// ---------------------------------------------------------------------------
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_polar_real(int *host_amtype, int *host_amgroup,
|
|
double **host_rpole, double **host_uind,
|
|
double **host_uinp, double *host_pval,
|
|
const bool eflag_in, const bool vflag_in,
|
|
const bool eatom, const bool vatom,
|
|
const double aewald, const double felec,
|
|
const double off2_polar, void **tep_ptr) {
|
|
|
|
int** firstneigh = nullptr;
|
|
|
|
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
|
|
atom->add_extra_data();
|
|
|
|
*tep_ptr=_tep.host.begin();
|
|
|
|
_off2_polar = off2_polar;
|
|
_felec = felec;
|
|
_aewald = aewald;
|
|
const int red_blocks=polar_real(_eflag,_vflag);
|
|
|
|
// only copy answers (forces, energies and virial) back from the device
|
|
// in the last kernel (which is polar_real here)
|
|
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
|
|
device->add_ans_object(ans);
|
|
|
|
hd_balancer.stop_timer();
|
|
|
|
// copy tep from device to host
|
|
|
|
_tep.update_host(_max_tep_size*4,false);
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Return the memory bytes allocated on the host and device
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
double BaseAmoebaT::host_memory_usage_atomic() const {
|
|
return device->atom.host_memory_usage()+nbor->host_memory_usage()+
|
|
4*sizeof(numtyp)+sizeof(BaseAmoeba<numtyp,acctyp>);
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Setup the FFT plan: only placeholder for now
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::setup_fft(const int numel, const int element_type)
|
|
{
|
|
// TODO: setting up FFT plan based on the backend (cuFFT or hipFFT)
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Compute FFT on the device: only placeholder for now
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compute_fft1d(void* in, void* out, const int numel, const int mode)
|
|
{
|
|
// TODO: setting up FFT plan based on the backend (cuFFT or hipFFT)
|
|
#if 0 // !defined(USE_OPENCL) && !defined(USE_HIP)
|
|
if (fft_plan_created == false) {
|
|
int m = numel/2;
|
|
cufftPlan1d(&plan, m, CUFFT_Z2Z, 1);
|
|
fft_plan_created = true;
|
|
}
|
|
|
|
// n = number of double complex
|
|
int n = numel/2;
|
|
|
|
// copy the host array to the device (data)
|
|
UCL_Vector<cufftDoubleComplex,cufftDoubleComplex> data;
|
|
data.alloc(n, *(this->ucl_device), UCL_READ_WRITE, UCL_READ_WRITE);
|
|
int m = 0;
|
|
double* d_in = (double*)in;
|
|
for (int i = 0; i < n; i++) {
|
|
data[i].x = d_in[m];
|
|
data[i].y = d_in[m+1];
|
|
m += 2;
|
|
}
|
|
data.update_device(false);
|
|
|
|
// perform the in-place forward FFT
|
|
|
|
cufftResult result = cufftExecZ2Z(plan, (cufftDoubleComplex*)&data.device,
|
|
(cufftDoubleComplex*)&data.device, CUFFT_FORWARD);
|
|
if (result != CUFFT_SUCCESS) printf("failed cufft %d\n", result);
|
|
ucl_device->sync();
|
|
data.update_host(false);
|
|
|
|
// copy back the data to the host array
|
|
|
|
m = 0;
|
|
double* d_out = (double*)out;
|
|
for (int i = 0; i < n; i++) {
|
|
d_out[m] = data[i].x;
|
|
d_out[m+1] = data[i].y;
|
|
m += 2;
|
|
}
|
|
|
|
data.clear();
|
|
#endif
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Copy the extra data from host to device
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::cast_extra_data(int* amtype, int* amgroup, double** rpole,
|
|
double** uind, double** uinp, double* pval) {
|
|
// signal that we need to transfer extra data from the host
|
|
|
|
atom->extra_data_unavail();
|
|
|
|
int _nall=atom->nall();
|
|
numtyp *pextra=reinterpret_cast<numtyp*>(&(atom->extra[0]));
|
|
|
|
int n = 0;
|
|
int nstride = 4;
|
|
if (rpole) {
|
|
for (int i = 0; i < _nall; i++) {
|
|
int idx = n+i*nstride;
|
|
pextra[idx] = rpole[i][0];
|
|
pextra[idx+1] = rpole[i][1];
|
|
pextra[idx+2] = rpole[i][2];
|
|
pextra[idx+3] = rpole[i][3];
|
|
}
|
|
|
|
n += nstride*_nall;
|
|
for (int i = 0; i < _nall; i++) {
|
|
int idx = n+i*nstride;
|
|
pextra[idx] = rpole[i][4];
|
|
pextra[idx+1] = rpole[i][5];
|
|
pextra[idx+2] = rpole[i][6];
|
|
pextra[idx+3] = rpole[i][8];
|
|
}
|
|
|
|
n += nstride*_nall;
|
|
for (int i = 0; i < _nall; i++) {
|
|
int idx = n+i*nstride;
|
|
pextra[idx] = rpole[i][9];
|
|
pextra[idx+1] = rpole[i][12];
|
|
pextra[idx+2] = (numtyp)amtype[i];
|
|
pextra[idx+3] = (numtyp)amgroup[i];
|
|
}
|
|
} else {
|
|
n += 2*nstride*_nall;
|
|
}
|
|
|
|
n += nstride*_nall;
|
|
if (uind) {
|
|
for (int i = 0; i < _nall; i++) {
|
|
int idx = n+i*nstride;
|
|
pextra[idx] = uind[i][0];
|
|
pextra[idx+1] = uind[i][1];
|
|
pextra[idx+2] = uind[i][2];
|
|
}
|
|
}
|
|
|
|
n += nstride*_nall;
|
|
if (uinp) {
|
|
for (int i = 0; i < _nall; i++) {
|
|
int idx = n+i*nstride;
|
|
pextra[idx] = uinp[i][0];
|
|
pextra[idx+1] = uinp[i][1];
|
|
pextra[idx+2] = uinp[i][2];
|
|
}
|
|
}
|
|
|
|
n += nstride*_nall;
|
|
if (pval) {
|
|
for (int i = 0; i < _nall; i++) {
|
|
int idx = n+i*nstride;
|
|
pextra[idx] = pval[i];
|
|
}
|
|
}
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Compile (load) the kernel strings and set the kernels
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
void BaseAmoebaT::compile_kernels(UCL_Device &dev, const void *pair_str,
|
|
const char *kname_multipole,
|
|
const char *kname_udirect2b,
|
|
const char *kname_umutual2b,
|
|
const char *kname_polar,
|
|
const char *kname_fphi_uind,
|
|
const char *kname_fphi_mpole,
|
|
const char *kname_short_nbor,
|
|
const char* kname_special15) {
|
|
if (_compiled)
|
|
return;
|
|
|
|
if (pair_program) delete pair_program;
|
|
pair_program=new UCL_Program(dev);
|
|
std::string oclstring = device->compile_string()+" -DEVFLAG=1";
|
|
pair_program->load_string(pair_str, oclstring.c_str(),nullptr, screen);
|
|
|
|
k_multipole.set_function(*pair_program, kname_multipole);
|
|
k_udirect2b.set_function(*pair_program, kname_udirect2b);
|
|
k_umutual2b.set_function(*pair_program, kname_umutual2b);
|
|
k_polar.set_function(*pair_program, kname_polar);
|
|
k_fphi_uind.set_function(*pair_program, kname_fphi_uind);
|
|
k_fphi_mpole.set_function(*pair_program, kname_fphi_mpole);
|
|
k_short_nbor.set_function(*pair_program, kname_short_nbor);
|
|
k_special15.set_function(*pair_program, kname_special15);
|
|
pos_tex.get_texture(*pair_program, "pos_tex");
|
|
q_tex.get_texture(*pair_program, "q_tex");
|
|
|
|
_compiled=true;
|
|
|
|
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
|
|
if (dev.has_subgroup_support()) {
|
|
size_t mx_subgroup_sz = k_polar.max_subgroup_size(_block_size);
|
|
if (_threads_per_atom > mx_subgroup_sz)
|
|
_threads_per_atom = mx_subgroup_sz;
|
|
device->set_simd_size(mx_subgroup_sz);
|
|
}
|
|
#endif
|
|
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------
|
|
// Specify 1-5 neighbors from the current neighbor list
|
|
// ---------------------------------------------------------------------------
|
|
|
|
template <class numtyp, class acctyp>
|
|
int BaseAmoebaT::add_onefive_neighbors() {
|
|
// Compute the block size and grid size to keep all cores busy
|
|
const int BX=block_size();
|
|
int GX=static_cast<int>(ceil(static_cast<double>(ans->inum())/
|
|
(BX/_threads_per_atom)));
|
|
|
|
int _nall=atom->nall();
|
|
int ainum=ans->inum();
|
|
int nbor_pitch=nbor->nbor_pitch();
|
|
|
|
k_special15.set_size(GX,BX);
|
|
k_special15.run(&nbor->dev_nbor, &_nbor_data->begin(),
|
|
&atom->dev_tag, &dev_nspecial15, &dev_special15,
|
|
&ainum, &_nall, &nbor_pitch,
|
|
&_threads_per_atom);
|
|
|
|
return GX;
|
|
}
|
|
|
|
template class BaseAmoeba<PRECISION,ACC_PRECISION>;
|
|
}
|