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atom.cpp
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atom.cpp
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/***************************************************************************
atom.cpp
-------------------
W. Michael Brown (ORNL)
Class for particle data management
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : brownw@ornl.gov
***************************************************************************/
#include "atom.h"
#define AtomT Atom<numtyp,acctyp>
template <class numtyp, class acctyp>
AtomT::Atom() : _compiled(false),_allocated(false),
_max_gpu_bytes(0) {
#ifndef USE_OPENCL
sort_config.op = CUDPP_ADD;
sort_config.datatype = CUDPP_UINT;
sort_config.algorithm = CUDPP_SORT_RADIX;
sort_config.options = CUDPP_OPTION_KEY_VALUE_PAIRS;
#endif
}
template <class numtyp, class acctyp>
int AtomT::bytes_per_atom() const {
int id_space=0;
if (_gpu_nbor)
id_space=2;
int bytes=4*sizeof(numtyp)+id_space;
if (_rot)
bytes+=4*sizeof(numtyp);
if (_charge)
bytes+=sizeof(numtyp);
return bytes;
}
template <class numtyp, class acctyp>
bool AtomT::alloc(const int nall) {
_max_atoms=static_cast<int>(static_cast<double>(nall)*1.10);
bool success=true;
// Ignore host/device transfers?
bool cpuview=false;
if (dev->device_type()==UCL_CPU)
cpuview=true;
// Allocate storage for CUDPP sort
#ifndef USE_OPENCL
if (_gpu_nbor) {
CUDPPResult result = cudppPlan(&sort_plan, sort_config, _max_atoms, 1, 0);
if (CUDPP_SUCCESS != result)
return false;
}
#endif
// -------------------------- Host allocations
// Get a host write only buffer
#ifdef GPU_CAST
success=success && (host_x_cast.alloc(_max_atoms*3,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
success=success && (host_type_cast.alloc(_max_atoms,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
#else
success=success && (host_x.alloc(_max_atoms*4,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
#endif
// Buffer for casting only if different precisions
if (_charge)
success=success && (host_q.alloc(_max_atoms,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
// Buffer for casting only if different precisions
if (_rot)
success=success && (host_quat.alloc(_max_atoms*4,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
// --------------------------- Device allocations
int gpu_bytes=0;
if (cpuview) {
#ifdef GPU_CAST
assert(0==1);
#else
dev_x.view(host_x);
#endif
if (_rot)
dev_quat.view(host_quat);
if (_charge)
dev_q.view(host_q);
} else {
#ifdef GPU_CAST
success=success && (UCL_SUCCESS==dev_x.alloc(_max_atoms*4,*dev));
success=success && (UCL_SUCCESS==
dev_x_cast.alloc(_max_atoms*3,*dev,UCL_READ_ONLY));
success=success && (UCL_SUCCESS==
dev_type_cast.alloc(_max_atoms,*dev,UCL_READ_ONLY));
gpu_bytes+=dev_x_cast.row_bytes()+dev_type_cast.row_bytes();
#else
success=success && (UCL_SUCCESS==
dev_x.alloc(_max_atoms*4,*dev,UCL_READ_ONLY));
#endif
if (_charge) {
success=success && (dev_q.alloc(_max_atoms,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
gpu_bytes+=dev_q.row_bytes();
}
if (_rot) {
success=success && (dev_quat.alloc(_max_atoms*4,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
gpu_bytes+=dev_quat.row_bytes();
}
}
if (_gpu_nbor) {
success=success && (dev_cell_id.alloc(_max_atoms,*dev)==UCL_SUCCESS);
success=success && (dev_particle_id.alloc(_max_atoms,*dev)==UCL_SUCCESS);
gpu_bytes+=dev_cell_id.row_bytes()+dev_particle_id.row_bytes();
if (_bonds) {
success=success && (dev_tag.alloc(_max_atoms,*dev)==UCL_SUCCESS);
gpu_bytes+=dev_tag.row_bytes();
}
}
gpu_bytes+=dev_x.row_bytes();
if (gpu_bytes>_max_gpu_bytes)
_max_gpu_bytes=gpu_bytes;
_allocated=true;
return success;
}
template <class numtyp, class acctyp>
bool AtomT::add_fields(const bool charge, const bool rot,
const bool gpu_nbor, const bool bonds) {
bool realloc=false;
if (charge && _charge==false) {
_charge=true;
realloc=true;
}
if (rot && _rot==false) {
_rot=true;
realloc=true;
}
if (gpu_nbor && _gpu_nbor==false) {
_gpu_nbor=true;
realloc=true;
}
if (bonds && _bonds==false) {
_bonds=true;
realloc=true;
}
if (realloc) {
_other=_charge || _rot;
int max_atoms=_max_atoms;
clear_resize();
return alloc(max_atoms);
}
return true;
}
template <class numtyp, class acctyp>
bool AtomT::init(const int nall, const bool charge, const bool rot,
UCL_Device &devi, const bool gpu_nbor,
const bool bonds) {
clear();
bool success=true;
_x_avail=false;
_q_avail=false;
_quat_avail=false;
_resized=false;
_gpu_nbor=gpu_nbor;
_bonds=bonds;
_charge=charge;
_rot=rot;
_other=_charge || _rot;
dev=&devi;
// Initialize atom and nbor data
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
// Initialize timers for the selected device
time_pos.init(*dev);
time_q.init(*dev);
time_quat.init(*dev);
time_pos.zero();
time_q.zero();
time_quat.zero();
_time_cast=0.0;
#ifdef GPU_CAST
compile_kernels(*dev);
#endif
return success && alloc(ef_nall);
}
template <class numtyp, class acctyp>
void AtomT::clear_resize() {
if (!_allocated)
return;
_allocated=false;
dev_x.clear();
if (_charge) {
dev_q.clear();
host_q.clear();
}
if (_rot) {
dev_quat.clear();
host_quat.clear();
}
#ifndef GPU_CAST
host_x.clear();
#else
host_x_cast.clear();
host_type_cast.clear();
#endif
dev_cell_id.clear();
dev_particle_id.clear();
dev_tag.clear();
#ifdef GPU_CAST
dev_x_cast.clear();
dev_type_cast.clear();
#endif
#ifndef USE_OPENCL
if (_gpu_nbor) cudppDestroyPlan(sort_plan);
#endif
}
template <class numtyp, class acctyp>
void AtomT::clear() {
_max_gpu_bytes=0;
if (!_allocated)
return;
time_pos.clear();
time_q.clear();
time_quat.clear();
clear_resize();
#ifdef GPU_CAST
if (_compiled) {
k_cast_x.clear();
delete atom_program;
_compiled=false;
}
#endif
}
template <class numtyp, class acctyp>
double AtomT::host_memory_usage() const {
int atom_bytes=4;
if (_charge)
atom_bytes+=1;
if (_rot)
atom_bytes+=4;
return _max_atoms*atom_bytes*sizeof(numtyp)+
sizeof(Atom<numtyp,acctyp>);
}
// Sort arrays for neighbor list calculation
template <class numtyp, class acctyp>
void AtomT::sort_neighbor(const int num_atoms) {
#ifndef USE_OPENCL
CUDPPResult result = cudppSort(sort_plan, (unsigned *)dev_cell_id.begin(),
(int *)dev_particle_id.begin(),
8*sizeof(unsigned), num_atoms);
if (CUDPP_SUCCESS != result) {
printf("Error in cudppSort\n");
NVD_GERYON_EXIT;
}
#endif
}
#ifdef GPU_CAST
#ifdef USE_OPENCL
#include "atom_cl.h"
#else
#include "atom_ptx.h"
#endif
template <class numtyp, class acctyp>
void AtomT::compile_kernels(UCL_Device &dev) {
atom_program=new UCL_Program(dev);
atom_program->load_string(atom,"");
k_cast_x.set_function(*atom_program,"kernel_cast_x");
_compiled=true;
}
#endif
template class Atom<PRECISION,ACC_PRECISION>;

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