-
Daniel F Kortemeyer authored
Just removing now unnecessary printfs that clutter the code
Daniel F Kortemeyer authoredJust removing now unnecessary printfs that clutter the code
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forces.c 63.56 KiB
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "reax_types.h"
#include "index_utils.h"
#ifdef HAVE_CUDA
#include "cuda_forces.h"
#include "cuda_linear_solvers.h"
#include "cuda_neighbors.h"
//#include "cuda_bond_orders.h"
#include "validation.h"
#endif
#if defined(PURE_REAX)
#include "forces.h"
#include "bond_orders.h"
#include "bonds.h"
#include "basic_comm.h"
#include "hydrogen_bonds.h"
#include "io_tools.h"
#include "list.h"
#include "lookup.h"
#include "multi_body.h"
#include "nonbonded.h"
#include "qEq.h"
#include "tool_box.h"
#include "torsion_angles.h"
#include "valence_angles.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reax_forces.h"
#include "reax_bond_orders.h"
#include "reax_bonds.h"
#include "reax_basic_comm.h"
#include "reax_hydrogen_bonds.h"
#include "reax_io_tools.h"
#include "reax_list.h"
#include "reax_lookup.h"
#include "reax_multi_body.h"
#include "reax_nonbonded.h"
#include "reax_tool_box.h"
#include "reax_torsion_angles.h"
#include "reax_valence_angles.h"
#include "reax_vector.h"
#endif
interaction_function Interaction_Functions[NUM_INTRS];
#ifdef HAVE_CUDA
void Cuda_Total_Forces (reax_system *, control_params *, simulation_data *, storage *);void Cuda_Total_Forces_PURE (reax_system *, storage *);
#endif
void Dummy_Interaction( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
}
void Init_Force_Functions( control_params *control )
{
Interaction_Functions[0] = BO;
Interaction_Functions[1] = Bonds; //Dummy_Interaction;
Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction;
Interaction_Functions[3] = Valence_Angles; //Dummy_Interaction;
Interaction_Functions[4] = Torsion_Angles; //Dummy_Interaction;
if ( control->hbond_cut > 0 )
Interaction_Functions[5] = Hydrogen_Bonds;
else Interaction_Functions[5] = Dummy_Interaction;
Interaction_Functions[6] = Dummy_Interaction; //empty
Interaction_Functions[7] = Dummy_Interaction; //empty
Interaction_Functions[8] = Dummy_Interaction; //empty
Interaction_Functions[9] = Dummy_Interaction; //empty
}
void Compute_Bonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i;
/* Mark beginning of a new timestep in bonded energy files */
#if defined(TEST_ENERGY)
Debug_Marker_Bonded( out_control, data->step );
#endif
/* Implement all force calls as function pointers */
// for( i = 0; i < NUM_INTRS; i++ ) {
//#if defined(DEBUG)
// fprintf( stderr, "p%d: starting f%d\n", system->my_rank, i );
// MPI_Barrier( MPI_COMM_WORLD );
//#endif
// (Interaction_Functions[i])( system, control, data, workspace,
// lists, out_control );
//#if defined(DEBUG)
// fprintf( stderr, "p%d: f%d done\n", system->my_rank, i );
// MPI_Barrier( MPI_COMM_WORLD );
//#endif
// }
(Interaction_Functions[0])( system, control, data, workspace, lists, out_control );
(Interaction_Functions[1])( system, control, data, workspace, lists, out_control );
(Interaction_Functions[2])( system, control, data, workspace, lists, out_control );
(Interaction_Functions[3])( system, control, data, workspace, lists, out_control );
(Interaction_Functions[4])( system, control, data, workspace, lists, out_control );
(Interaction_Functions[5])( system, control, data, workspace, lists, out_control );
}
void Compute_NonBonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
/* Mark beginning of a new timestep in nonbonded energy files */
#if defined(TEST_ENERGY)
Debug_Marker_Nonbonded( out_control, data->step );
#endif
/* van der Waals and Coulomb interactions */
if ( control->tabulate == 0 )
vdW_Coulomb_Energy( system, control, data, workspace,
lists, out_control );
else
Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
lists, out_control );
#if defined(DEBUG)
fprintf( stderr, "p%d: nonbonded forces done\n", system->my_rank );
MPI_Barrier( MPI_COMM_WORLD );
#endif
}
/* this version of Compute_Total_Force computes forces from
coefficients accumulated by all interaction functions.
Saves enormous time & space! */
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, mpi_datatypes *mpi_data )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
for ( i = 0; i < system->N; ++i )
for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
if ( i < bonds->select.bond_list[pj].nbr )
{
if ( control->virial == 0 )
Add_dBond_to_Forces( i, pj, workspace, lists );
else
Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
}
//Print_Total_Force( system, data, workspace );
#if defined(PURE_REAX)
/* now all forces are computed to their partially-final values
based on the neighbors information each processor has had.
final values of force on each atom needs to be computed by adding up
all partially-final pieces */
Coll( system, mpi_data, workspace->f, mpi_data->mpi_rvec,
sizeof(rvec) / sizeof(void), rvec_unpacker );
for ( i = 0; i < system->n; ++i )
rvec_Copy( system->my_atoms[i].f, workspace->f[i] );
#if defined(TEST_FORCES)
Coll( system, mpi_data, workspace->f_ele, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_vdw, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_be, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_lp, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_ov, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_un, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_ang, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_coa, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_pen, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_hb, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_tor, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_con, mpi_data->mpi_rvec, rvec_unpacker);
#endif
#endif
}
#ifdef HAVE_CUDA
void Cuda_Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists, mpi_datatypes *mpi_data )
{
rvec *f = (rvec *) host_scratch;
memset (f, 0, sizeof (rvec) * system->N );
Cuda_Total_Forces (system, control, data, workspace);
#if defined(PURE_REAX)
/* now all forces are computed to their partially-final values
based on the neighbors information each processor has had.
final values of force on each atom needs to be computed by adding up
all partially-final pieces */
//MVAPICH2
get_from_device (f, dev_workspace->f, sizeof (rvec) * system->N , "total_force:f:get");
Coll( system, mpi_data, f, mpi_data->mpi_rvec,
sizeof(rvec) / sizeof(void), rvec_unpacker );
put_on_device (f, dev_workspace->f, sizeof (rvec) * system->N, "total_force:f:put" );
Cuda_Total_Forces_PURE (system, dev_workspace);
#endif
}
#endif
// Essentially no-cuda copies of cuda kernels, to be used only in the mpi-not-gpu version
////////////////////////
// HBOND ISSUE
void mpi_not_gpu_update_bonds (reax_atom *my_atoms,
reax_list bonds,
int n)
{
// int i = blockIdx.x * blockDim.x + threadIdx.x;
// if (i >= n) return;
int i;
for (i=0;i<n;i++){
my_atoms [i].num_bonds =
MAX(Num_Entries(i, &bonds) * 2, MIN_BONDS);
}
}
void mpi_not_gpu_update_hbonds (reax_atom *my_atoms,
reax_list hbonds,
int n)
{
int Hindex;
int i;
//int i = blockIdx.x * blockDim.x + threadIdx.x;
//if (i >= n) return;
for (i=0;i<n;i++){
Hindex = my_atoms[i].Hindex;
my_atoms [i].num_hbonds =
MAX(Num_Entries(Hindex, &hbonds) * SAFER_ZONE, MIN_HBONDS);
}
}
// Essentially a copy of cuda_validate_lists, but with all cuda-dependent kernels turned into serial versions
int MPI_Not_GPU_Validate_Lists (reax_system *system, storage *workspace, reax_list **lists, control_params *control,
int step, int n, int N, int numH )
{
int blocks;
int i, comp, Hindex;
int *index, *end_index;
reax_list *bonds, *hbonds;
reax_atom *my_atoms; reallocate_data *realloc;
realloc = &( workspace->realloc);
int max_sp_entries, num_hbonds, num_bonds;
int total_sp_entries;
//blocks = system->n / DEF_BLOCK_SIZE +
// ((system->n % DEF_BLOCK_SIZE == 0) ? 0 : 1);
//ker_update_bonds <<< blocks, DEF_BLOCK_SIZE >>>
// (system->d_my_atoms, *(*lists + BONDS),
// system->n);
//cudaThreadSynchronize ();
//cudaCheckError ();
mpi_not_gpu_update_bonds(system->my_atoms, *(*lists + BONDS),system->n);
////////////////////////
// HBOND ISSUE
//FIX - 4 - Added this check for hydrogen bond issue
if ((control->hbond_cut > 0) && (system->numH > 0)){
//ker_update_hbonds <<< blocks, DEF_BLOCK_SIZE >>>
// (system->d_my_atoms, *(*lists + HBONDS),
// system->n);
//cudaThreadSynchronize ();
//cudaCheckError ();
mpi_not_gpu_update_hbonds(system->my_atoms, *(*lists + HBONDS),system->n);
}
//validate sparse matrix entries.
//memset (host_scratch, 0, 2 * system->N * sizeof (int));
//index = (int *) host_scratch;
//end_index = index + system->N;
index = workspace->H.start;
end_index = workspace->H.end;
// immediately set these to host version since there is no device version.
//memcpy(index, workspace->H.start, system->N * sizeof (int));
//memcpy(end_index, workspace->H.end, system->N * sizeof (int));
// don't need these, everything is already at host
//copy_host_device (index, dev_workspace->H.start, system->N * sizeof (int),
// cudaMemcpyDeviceToHost, "sparse_matrix:start" );
//copy_host_device (end_index, dev_workspace->H.end, system->N * sizeof (int),
// cudaMemcpyDeviceToHost, "sparse_matrix:end" );
max_sp_entries = total_sp_entries = 0;
for (i = 0; i < n; i++ ){
//if (i < N-1)
// comp = index [i+1];
//else
// comp = dev_workspace->H.m;
total_sp_entries += end_index [i] - index[i];
if (end_index [i] - index[i] > system->max_sparse_entries) {
fprintf( stderr, "step%d-sparsemat-chk failed: i=%d start(i)=%d end(i)=%d \n",
step, i, index[i], end_index[i] );
return FAILURE;
} else if (end_index[i] >= workspace->H.m) {
//SUDHIR_FIX_SPARSE_MATRIX
//TODO move this carver //TODO move this carver
//TODO move this carver
fprintf (stderr, "p:%d - step%d-sparsemat-chk failed (exceed limits): i=%d start(i)=%d end(i)=%d \n",
system->my_rank, step, i, index[i], end_index[i]);
//TODO move this carver
//TODO move this carver
//TODO move this carver
return FAILURE;
} else {
if (max_sp_entries <= end_index[i] - index [i])
max_sp_entries = end_index[i] - index [i];
}
}
//if (max_sp_entries <= end_index[i] - index [i])
// max_sp_entries = end_index[i] - index [i];
//update the current step max_sp_entries;
realloc->Htop = max_sp_entries;
fprintf (stderr, "p:%d - MPI-Not-GPU Reallocate: Total H matrix entries: %d, cap: %d, used: %d \n",
system->my_rank, workspace->H.n, workspace->H.m, total_sp_entries);
if (total_sp_entries >= workspace->H.m) {
fprintf (stderr, "p:%d - **ran out of space for sparse matrix: step: %d, allocated: %d, used: %d \n",
system->my_rank, step, workspace->H.m, total_sp_entries);
return FAILURE;
}
//validate Bond list
if (N > 0) {
num_bonds = 0;
bonds = *lists + BONDS;
// memset (host_scratch, 0, 2 * bonds->n * sizeof (int));
// index = (int *) host_scratch;
// end_index = index + bonds->n;
index = bonds->index;
end_index = bonds->end_index;
// memcpy(index, bonds->index, bonds->n * sizeof (int));
// memcpy(end_index, bonds->end_index, bonds->n * sizeof (int));
/*
copy_host_device (index, bonds->index, bonds->n * sizeof (int),
cudaMemcpyDeviceToHost, "bonds:index");
copy_host_device (end_index, bonds->end_index, bonds->n * sizeof (int),
cudaMemcpyDeviceToHost, "bonds:end_index");
*/
/*
for (i = 0; i < N; i++) {
if (i < N-1)
comp = index [i+1];
else
comp = bonds->num_intrs;
if (end_index [i] > comp) {
fprintf( stderr, "step%d-bondchk failed: i=%d start(i)=%d end(i)=%d str(i+1)=%d\n",
step, i, index[i], end_index[i], comp );
return FAILURE;
}
num_bonds += MAX( (end_index[i] - index[i]) * 4, MIN_BONDS);
}
if (end_index[N-1] >= bonds->num_intrs) {
fprintf( stderr, "step%d-bondchk failed(end): i=N-1 start(i)=%d end(i)=%d num_intrs=%d\n",
step, index[N-1], end_index[N-1], bonds->num_intrs);
return FAILURE; }
num_bonds = MAX( num_bonds, MIN_CAP*MIN_BONDS );
//check the condition for reallocation
realloc->num_bonds = num_bonds;
*/
int max_bonds = 0;
for (i = 0; i < N; i++) {
if (end_index[i] - index[i] >= system->max_bonds) {
fprintf( stderr, "MPI-Not-GPU step%d-bondchk failed: i=%d start(i)=%d end(i)=%d max_bonds=%d\n",
step, i, index[i], end_index[i], system->max_bonds);
return FAILURE;
}
if (end_index[i] - index[i] >= max_bonds)
max_bonds = end_index[i] - index[i];
}
realloc->num_bonds = max_bonds;
}
//validate Hbonds list
num_hbonds = 0;
// FIX - 4 - added additional check here
if ((numH > 0) && (control->hbond_cut > 0)) {
hbonds = *lists + HBONDS;
memset (host_scratch, 0, 2 * hbonds->n * sizeof (int) + sizeof (reax_atom) * system->N);
index = (int *) host_scratch;
end_index = index + hbonds->n;
my_atoms = (reax_atom *)(end_index + hbonds->n);
/*
copy_host_device (index, hbonds->index, hbonds->n * sizeof (int),
cudaMemcpyDeviceToHost, "hbonds:index");
copy_host_device (end_index, hbonds->end_index, hbonds->n * sizeof (int),
cudaMemcpyDeviceToHost, "hbonds:end_index");
copy_host_device (my_atoms, system->d_my_atoms, system->N * sizeof (reax_atom),
cudaMemcpyDeviceToHost, "system:d_my_atoms");
*/
//fprintf (stderr, " Total local atoms: %d \n", n);
/*
for (i = 0; i < N-1; i++) {
Hindex = my_atoms [i].Hindex;
if (Hindex > -1)
comp = index [Hindex + 1];
else
comp = hbonds->num_intrs;
if (end_index [Hindex] > comp) {
fprintf(stderr,"step%d-atom:%d hbondchk failed: H=%d start(H)=%d end(H)=%d str(H+1)=%d\n",
step, i, Hindex, index[Hindex], end_index[Hindex], comp );
return FAILURE;
}
num_hbonds += MAX( (end_index [Hindex] - index [Hindex]) * 2, MIN_HBONDS * 2);
}
if (end_index [my_atoms[i].Hindex] > hbonds->num_intrs) {
fprintf(stderr,"step%d-atom:%d hbondchk failed: H=%d start(H)=%d end(H)=%d num_intrs=%d\n",
step, i, Hindex, index[Hindex], end_index[Hindex], hbonds->num_intrs);
return FAILURE;
}
num_hbonds += MIN( (end_index [my_atoms[i].Hindex] - index [my_atoms[i].Hindex]) * 2,
2 * MIN_HBONDS);
num_hbonds = MAX( num_hbonds, MIN_CAP*MIN_HBONDS );
realloc->num_hbonds = num_hbonds;
*/
int max_hbonds = 0;
for (i = 0; i < N; i++) {
if (end_index[i] - index[i] >= system->max_hbonds) { fprintf( stderr, "step%d-hbondchk failed: i=%d start(i)=%d end(i)=%d max_hbonds=%d\n",
step, i, index[i], end_index[i], system->max_hbonds);
return FAILURE;
}
if (end_index[i] - index[i] >= max_hbonds)
max_hbonds = end_index[i] - index[i];
}
realloc->num_hbonds = max_hbonds;
}
return SUCCESS;
}
/*
void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
int step, int n, int N, int numH )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
reallocate_data *realloc;
realloc = &(workspace->realloc);
// bond list
if ( N > 0 )
{
bonds = *lists + BONDS;
for ( i = 0; i < N; ++i )
{
if ( i < n )
system->my_atoms[i].num_bonds = MAX(Num_Entries(i, bonds) * 2, MIN_BONDS);
//if( End_Index(i, bonds) >= Start_Index(i+1, bonds)-2 )
//workspace->realloc.bonds = 1;
if ( i < N - 1 )
comp = Start_Index(i + 1, bonds);
else comp = bonds->num_intrs;
if ( End_Index(i, bonds) > comp )
{
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, i, End_Index(i, bonds), comp );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
}
// hbonds list
if ( numH > 0 )
{
hbonds = *lists + HBONDS;
for ( i = 0; i < n; ++i )
{
Hindex = system->my_atoms[i].Hindex;
if ( Hindex > -1 )
{
system->my_atoms[i].num_hbonds =
MAX( Num_Entries(Hindex, hbonds) * SAFER_ZONE, MIN_HBONDS );
*/
//if( Num_Entries(i, hbonds) >=
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
// workspace->realloc.hbonds = 1;
/*
//TODO
if ( Hindex < system->n - 1 )
comp = Start_Index(Hindex + 1, hbonds);
else comp = hbonds->num_intrs;
if ( End_Index(Hindex, hbonds) > comp )
{
fprintf(stderr, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
step, Hindex, End_Index(Hindex, hbonds), comp );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
}
}
}*/
void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
int step, int n, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
reallocate_data *realloc;
realloc = &(workspace->realloc);
/* bond list */
if ( N > 0 )
{
bonds = *lists + BONDS;
for ( i = 0; i < N; ++i )
{
// if( i < n ) - we need to update ghost estimates for delayed nbrings
system->my_atoms[i].num_bonds = MAX(Num_Entries(i, bonds) * 2, MIN_BONDS);
//if( End_Index(i, bonds) >= Start_Index(i+1, bonds)-2 )
//workspace->realloc.bonds = 1;
if ( i < N - 1 )
comp = Start_Index(i + 1, bonds);
else comp = bonds->num_intrs;
if ( End_Index(i, bonds) > comp )
{
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, i, End_Index(i, bonds), comp );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
/* hbonds list */
if ( numH > 0 )
{
hbonds = *lists + HBONDS;
for ( i = 0; i < n; ++i )
{
Hindex = system->my_atoms[i].Hindex;
if ( Hindex > -1 )
{
system->my_atoms[i].num_hbonds =
(int)(MAX( Num_Entries(Hindex, hbonds) * SAFER_ZONE, MIN_HBONDS ));
//if( Num_Entries(i, hbonds) >=
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
// workspace->realloc.hbonds = 1;
if ( Hindex < numH - 1 )
comp = Start_Index(Hindex + 1, hbonds);
else comp = hbonds->num_intrs;
if ( End_Index(Hindex, hbonds) > comp ) {
fprintf(stderr, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
step, Hindex, End_Index(Hindex, hbonds), comp );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
/*
if ( Hindex > -1 )
{
system->my_atoms[i].num_hbonds =
MAX( Num_Entries(Hindex, hbonds) * SAFER_ZONE, MIN_HBONDS );
*/
//if( Num_Entries(i, hbonds) >=
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
// workspace->realloc.hbonds = 1;
/*
//TODO
if ( Hindex < system->n - 1 )
comp = Start_Index(Hindex + 1, hbonds);
else comp = hbonds->num_intrs;
if ( End_Index(Hindex, hbonds) > comp )
{
fprintf(stderr, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
step, Hindex, End_Index(Hindex, hbonds), comp );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
*/
}
}
}
#if defined(OLD_VALIDATE)
void Validate_Lists( storage *workspace, reax_list **lists,
int step, int n, int N, int numH )
{
int i, flag;
reax_list *bonds, *hbonds;
reallocate_data *realloc;
realloc = &(workspace->realloc);
/* bond list */
if ( N > 0 )
{
flag = -1;
bonds = *lists + BONDS;
for ( i = 0; i < N - 1; ++i )
if ( End_Index(i, bonds) >= Start_Index(i + 1, bonds) - 2 )
{
workspace->realloc.bonds = 1;
if ( End_Index(i, bonds) > Start_Index(i + 1, bonds) )
flag = i;
}
if ( flag > -1 )
{
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, flag, End_Index(flag, bonds), Start_Index(flag + 1, bonds) );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
if ( End_Index(i, bonds) >= bonds->num_intrs - 2 ) {
workspace->realloc.bonds = 1;
if ( End_Index(i, bonds) > bonds->num_intrs )
{
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d bond_end=%d\n",
step, flag, End_Index(i, bonds), bonds->num_intrs );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
}
/* hbonds list */
if ( numH > 0 )
{
flag = -1;
hbonds = *lists + HBONDS;
for ( i = 0; i < numH - 1; ++i )
if ( Num_Entries(i, hbonds) >=
(Start_Index(i + 1, hbonds) - Start_Index(i, hbonds)) * 0.90/*DANGER_ZONE*/ )
{
workspace->realloc.hbonds = 1;
if ( End_Index(i, hbonds) > Start_Index(i + 1, hbonds) )
flag = i;
}
if ( flag > -1 )
{
fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, flag, End_Index(flag, hbonds), Start_Index(flag + 1, hbonds) );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
if ( Num_Entries(i, hbonds) >=
(hbonds->num_intrs - Start_Index(i, hbonds)) * 0.90/*DANGER_ZONE*/ )
{
workspace->realloc.hbonds = 1;
if ( End_Index(i, hbonds) > hbonds->num_intrs )
{
fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d hbondend=%d\n",
step, flag, End_Index(i, hbonds), hbonds->num_intrs );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
}
}
#endif
inline real Compute_H( real r, real gamma, real *ctap )
{
real taper, dr3gamij_1, dr3gamij_3;
taper = ctap[7] * r + ctap[6];
taper = taper * r + ctap[5];
taper = taper * r + ctap[4];
taper = taper * r + ctap[3];
taper = taper * r + ctap[2];
taper = taper * r + ctap[1];
taper = taper * r + ctap[0];
dr3gamij_1 = ( r * r * r + gamma );
dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
return taper * EV_to_KCALpMOL / dr3gamij_3;
}
inline real Compute_tabH( real r_ij, int ti, int tj, int num_atom_types )
{
int r, tmin, tmax; real val, dif, base;
LR_lookup_table *t;
tmin = MIN( ti, tj );
tmax = MAX( ti, tj );
//SUDHIR
//t = &( LR[tmin][tmax] );
t = &( LR[index_lr (tmin, tmax, num_atom_types)] );
/* cubic spline interpolation */
r = (int)(r_ij * t->inv_dx);
if ( r == 0 ) ++r;
base = (real)(r + 1) * t->dx;
dif = r_ij - base;
val = ((t->ele[r].d * dif + t->ele[r].c) * dif + t->ele[r].b) * dif +
t->ele[r].a;
val *= EV_to_KCALpMOL / C_ele;
return val;
}
void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int Htop, btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
real r_ij, cutoff;
sparse_matrix *H;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
//Print_List(*lists + BONDS);
for ( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for ( i = system->n; i < system->N; ++i )
{
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
//workspace->done_after[i] = Start_Index( i, far_nbrs );
}
H = &(workspace->H); //MATRIX CHANGES
H->n = system->n;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
for ( i = 0; i < system->N; ++i )
{
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds ); sbp_i = &(system->reax_param.sbp[type_i]);
if ( i < system->n )
{
local = 1;
cutoff = control->nonb_cut;
}
else
{
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if ( local )
{
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
if ( control->hbond_cut > 0 )
{
ihb = sbp_i->p_hbond;
if ( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
}
/* update i-j distance - check if j is within cutoff */
for ( pj = start_i; pj < end_i; ++pj )
{
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
//fprintf( stderr, "%d%d i=%d x_i: %f %f %f,j=%d x_j: %f %f %f, d=%f\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
// j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
if ( renbr )
{
if (nbr_pj->d <= cutoff)
flag = 1;
else flag = 0;
}
else
{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if ( nbr_pj->d <= SQR(cutoff) )
{
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else
{
flag = 0;
}
}
if ( flag )
{
type_j = atom_j->type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]); //SUDHIR
//twbp = &(system->reax_param.tbp[type_i][type_j]);
twbp = &(system->reax_param.tbp[ index_tbp (type_i, type_j, system->reax_param.num_atom_types)]);
if ( local )
{
/* H matrix entry */
if ( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq||1
{
H->entries[Htop].j = j;
//fprintf( stdout, "%d%d %d %d\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id) );
if ( control->tabulate == 0 )
H->entries[Htop].val = Compute_H(r_ij, twbp->gamma, workspace->Tap);
else
H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j, system->reax_param.num_atom_types);
++Htop;
}
/* hydrogen bond lists */
if ( control->hbond_cut > 0 && (ihb == 1 || ihb == 2) &&
nbr_pj->d <= control->hbond_cut )
{
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if ( ihb == 1 && jhb == 2 )
{
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if ( j < system->n && ihb == 2 && jhb == 1 )
{
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top + 1, hbonds );
++num_hbonds;
}
}
}
/* uncorrected bond orders */
if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) )
{
num_bonds += 2;
++btop_i;
if ( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if ( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
{
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//if( workspace->bond_mark[i] == 1000 )
// workspace->done_after[i] = pj;
}
//fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
// H->end[i] = Htop;
Set_End_Index( i, btop_i, bonds );
if ( local )
{
//printf("Htop: %d \n", Htop);
H->end[i] = Htop;
if ( ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
//fprintf( stderr, "after the first init loop\n" );
/*for( i = system->n; i < system->N; ++i )
if( workspace->bond_mark[i] > 3 ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
Set_End_Index(i, start_i, bonds );
}*/
/*for( i = system->n; i < system->N; ++i ) {
start_i = Start_Index(i, far_nbrs);
end_i = workspace->done_after[i];
if( workspace->bond_mark[i] >= 2 && start_i < end_i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
}
}*/
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
system->my_rank, data->step, Htop, num_bonds, num_hbonds );
MPI_Barrier( MPI_COMM_WORLD );
#endif#if defined( DEBUG )
// Print_Bonds( system, bonds, "debugbonds.out" );
// Print_Bond_List2( system, bonds, "pbonds.out" );
// Print_Sparse_Matrix( system, H );
/* for ( i = 0; i < H->n; ++i )
for ( j = H->start[i]; j < H->end[i]; ++j )
fprintf( stderr, "%d %d %.15e\n",
MIN(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
MAX(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
H->entries[j].val );*/
#endif
//Print_List(*lists + BONDS);
//reax_system *system, storage *workspace, reax_list **lists,
// int step, int n, int N, int numH )
/*
Validate_Lists( system, workspace, lists, control,
data->step, system->n, system->N, system->numH );*/
MPI_Not_GPU_Validate_Lists( system, workspace, lists, control,
data->step, system->n, system->N, system->numH );
}
void Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
real r_ij, cutoff;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
for ( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for ( i = system->n; i < system->N; ++i )
{
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
//workspace->done_after[i] = Start_Index( i, far_nbrs );
}
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
for ( i = 0; i < system->N; ++i )
{
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs); btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if ( i < system->n )
{
local = 1;
cutoff = MAX( control->hbond_cut, control->bond_cut );
}
else
{
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if ( local && control->hbond_cut > 0 )
{
ihb = sbp_i->p_hbond;
if ( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
/* update i-j distance - check if j is within cutoff */
for ( pj = start_i; pj < end_i; ++pj )
{
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if ( renbr )
{
if ( nbr_pj->d <= cutoff )
flag = 1;
else flag = 0;
}
else
{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if ( nbr_pj->d <= SQR(cutoff) )
{
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else
{
flag = 0;
}
}
if ( flag )
{
type_j = atom_j->type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
//SUDHIR
//twbp = &(system->reax_param.tbp[type_i][type_j]);
twbp = &(system->reax_param.tbp[index_tbp(type_i, type_j, system->reax_param.num_atom_types)]);
if ( local )
{
/* hydrogen bond lists */
if ( control->hbond_cut > 0 && (ihb == 1 || ihb == 2) &&
nbr_pj->d <= control->hbond_cut )
{
// fprintf( stderr, "%d %d\n", atom1, atom2 ); jhb = sbp_j->p_hbond;
if ( ihb == 1 && jhb == 2 )
{
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if ( j < system->n && ihb == 2 && jhb == 1 )
{
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top + 1, hbonds );
++num_hbonds;
}
}
}
/* uncorrected bond orders */
if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) )
{
num_bonds += 2;
++btop_i;
if ( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if ( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
{
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//if( workspace->bond_mark[i] == 1000 )
// workspace->done_after[i] = pj;
}
//fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
if ( local && ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
for ( i = system->n; i < system->N; ++i )
if ( workspace->bond_mark[i] > 3 )
{
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
Set_End_Index(i, start_i, bonds );
}
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: num_bonds = %d num_hbonds = %d\n",
system->my_rank, data->step, num_bonds, num_hbonds );
MPI_Barrier( MPI_COMM_WORLD );
#endif
#if defined( DEBUG )
Print_Bonds( system, bonds, "debugbonds.out" );
Print_Bond_List2( system, bonds, "pbonds.out" );#endif
MPI_Not_GPU_Validate_Lists( system, workspace, lists, control,
data->step, system->n, system->N, system->numH );
}
void Host_Estimate_Sparse_Matrix (reax_atom *my_atoms, control_params *control,
reax_list p_far_nbrs, int n, int N, int renbr, int *indices)
{
int i, j, pj;
int start_i, end_i;
int flag;
real cutoff;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
reax_list *far_nbrs = &( p_far_nbrs );
//i = blockIdx.x * blockDim.x + threadIdx.x;
//if (i >= N) return;
for (i=0;i<N;i++){
atom_i = &(my_atoms[i]);
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
cutoff = control->nonb_cut;
//++Htop;
if ( i < n)
indices [i] ++;
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(my_atoms[j]);
if( renbr ) {
if(nbr_pj->d <= cutoff)
flag = 1;
else flag = 0;
}
else {
if (i < j) {
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
} else {
nbr_pj->dvec[0] = atom_i->x[0] - atom_j->x[0];
nbr_pj->dvec[1] = atom_i->x[1] - atom_j->x[1];
nbr_pj->dvec[2] = atom_i->x[2] - atom_j->x[2];
}
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
//TODO
//TODO
//TODO
//if( nbr_pj->d <= (cutoff) ) {
if( nbr_pj->d <= SQR(cutoff) )
{
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else
{
flag = 0;
}
}
if( flag )
{
/* H matrix entry */
//if( j < n || atom_i->orig_id < atom_j->orig_id ) //++Htop;
// indices [i] ++;
//else if (j < n || atom_i->orig_id > atom_j->orig_id )
// indices [i] ++;
//if ((i < n) || (j < n))
// indices [i] ++;
//if ((i < n) && (i < j) && ((j < n) || atom_i->orig_id < atom_j->orig_id))
// indices [i] ++;
//if ( i >= n && j < n && atom_i->orig_id > atom_j->orig_id)
// indices [i] ++;
//else if ((i >=n) && (i > j) && ((j < n) || (atom_i->orig_id > atom_j->orig_id)))
// indices [i] ++;
//THIS IS THE HOST CONDITION
//if (i < n && i < j && ( j < n || atom_i->orig_id < atom_j->orig_id ))
//if (i < n && i < j && atom_i->orig_id < atom_j->orig_id && j >=n)
// indices [i] ++;
//THIS IS THE DEVICE CONDITION
//if ( i > j && i >= n && j < n && atom_j->orig_id < atom_i->orig_id)
// indices [i] ++;
//this is the working condition
if (i < j && i < n && ( j < n || atom_i->orig_id < atom_j->orig_id))
indices [i]++;
else if (i > j && i >= n && j < n && atom_j->orig_id < atom_i->orig_id)
indices [i] ++;
else if (i > j && i < n && ( j < n || atom_j->orig_id < atom_i->orig_id ))
indices [i] ++;
}
}
}
}
#ifdef HAVE_CUDA
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop,
int *hb_top, int *bond_top, int *num_3body )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb;
int local;
real cutoff;
real r_ij, r2;
real C12, C34, C56;
real BO, BO_s, BO_pi, BO_pi2;
reax_list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
*Htop = 0;
//printf("Hcap: %d \n", system->Hcap);
memset( hb_top, 0, sizeof(int) * system->Hcap );
memset( bond_top, 0, sizeof(int) * system->total_cap );
*num_3body = 0;
for ( i = 0; i < system->N; ++i )
{
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
sbp_i = &(system->reax_param.sbp[type_i]);
if ( i < system->n )
{ local = 1;
cutoff = control->nonb_cut;
++(*Htop);
ihb = sbp_i->p_hbond;
}
else
{
local = 0;
cutoff = control->bond_cut;
ihb = -1;
}
for ( pj = start_i; pj < end_i; ++pj )
{
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if (nbr_pj->d <= cutoff)
{
type_j = system->my_atoms[j].type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
//SUDHIR
//twbp = &(system->reax_param.tbp[type_i][type_j]);
twbp = &(system->reax_param.tbp[index_tbp (type_i, type_j, system->reax_param.num_atom_types)]);
if ( local )
{
if ( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
++(*Htop);
if ( control->hbond_cut > 0.1 && (ihb == 1 || ihb == 2) &&
nbr_pj->d <= control->hbond_cut )
{
jhb = sbp_j->p_hbond;
if ( ihb == 1 && jhb == 2 )
++hb_top[i];
else if ( j < system->n && ihb == 2 && jhb == 1 ){
++hb_top[j];
}
}
}
// uncorrected bond orders
if ( nbr_pj->d <= control->bond_cut )
{
r2 = SQR(r_ij);
if ( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0)
{
C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + control->bo_cut) * EXP( C12 );
}
else BO_s = C12 = 0.0;
if ( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0)
{
C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
BO_pi = EXP( C34 );
}
else BO_pi = C34 = 0.0;
if ( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0)
{
C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
BO_pi2 = EXP( C56 );
} else BO_pi2 = C56 = 0.0;
// Initially BO values are the uncorrected ones, page 1
BO = BO_s + BO_pi + BO_pi2;
if ( BO >= control->bo_cut )
{
++bond_top[i];
++bond_top[j];
}
}
}
}
}
fprintf (stderr, "HOST SPARSE MATRIX ENTRIES: %d \n", *Htop );
*Htop = MAX( *Htop * SAFE_ZONE, MIN_CAP * MIN_HENTRIES );
int hbond_count = 0;
for ( i = 0; i < system->n; ++i )
{
hbond_count += hb_top[i];
hb_top[i] = MAX( hb_top[i] * SAFER_ZONE, MIN_HBONDS );
}
fprintf (stderr, "HOST HBOND COUNT: %d \n", hbond_count);
int bond_count = 0;
for ( i = 0; i < system->N; ++i )
{
bond_count += bond_top[i];
*num_3body += SQR(bond_top[i]);
//if( i < system->n )
bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
//else bond_top[i] = MAX_BONDS;
}
fprintf (stderr, "HOST BOND COUNT: %d \n", bond_count);
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ estimate storages: Htop = %d, num_3body = %d\n",
system->my_rank, *Htop, *num_3body );
MPI_Barrier( MPI_COMM_WORLD );
#endif
}
#else
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop, int *hb_top,
int *bond_top, int *num_3body)
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb;
int local;
real cutoff;
real r_ij, r2;
real C12, C34, C56;
real BO, BO_s, BO_pi, BO_pi2;
reax_list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
*Htop = 0;
memset( hb_top, 0, sizeof(int) * system->local_cap ); memset( bond_top, 0, sizeof(int) * system->total_cap );
*num_3body = 0;
for ( i = 0; i < system->N; ++i )
{
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
sbp_i = &(system->reax_param.sbp[type_i]);
if ( i < system->n )
{
local = 1;
cutoff = control->nonb_cut;
++(*Htop);
ihb = sbp_i->p_hbond;
}
else
{
local = 0;
cutoff = control->bond_cut;
ihb = -1;
}
for ( pj = start_i; pj < end_i; ++pj )
{
//nbr_pj = &( far_nbrs->far_nbr_list[pj] );
nbr_pj = &( far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if (nbr_pj->d <= cutoff)
{
type_j = system->my_atoms[j].type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
//twbp = &(system->reax_param.tbp[type_i][type_j]);
twbp = &(system->reax_param.tbp[index_tbp (type_i, type_j, system->reax_param.num_atom_types)]);
if ( local )
{
if ( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
++(*Htop);
/* hydrogen bond lists */
if ( control->hbond_cut > 0.1 && (ihb == 1 || ihb == 2) &&
nbr_pj->d <= control->hbond_cut )
{
jhb = sbp_j->p_hbond;
if ( ihb == 1 && jhb == 2 )
++hb_top[i];
else if ( j < system->n && ihb == 2 && jhb == 1 )
++hb_top[j];
}
}
/* uncorrected bond orders */
if ( nbr_pj->d <= control->bond_cut )
{
r2 = SQR(r_ij);
if ( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0)
{
C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + control->bo_cut) * exp( C12 );
}
else BO_s = C12 = 0.0;
if ( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 );
BO_pi = exp( C34 );
}
else BO_pi = C34 = 0.0;
if ( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0)
{
C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 );
BO_pi2 = exp( C56 );
}
else BO_pi2 = C56 = 0.0;
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
if ( BO >= control->bo_cut )
{
++bond_top[i];
++bond_top[j];
}
}
}
}
}
*Htop = (int)(MAX( *Htop * SAFE_ZONE, MIN_CAP * MIN_HENTRIES ));
// Set max sparse entries, needed for first iteration of validate_list
system->max_sparse_entries = *Htop * SAFE_ZONE;
for ( i = 0; i < system->n; ++i )
hb_top[i] = (int)(MAX( hb_top[i] * SAFER_ZONE, MIN_HBONDS ));
for ( i = 0; i < system->N; ++i )
{
*num_3body += SQR(bond_top[i]);
//if( i < system->n )
bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
//else bond_top[i] = MAX_BONDS;
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ estimate storages: Htop = %d, num_3body = %d\n",
system->my_rank, *Htop, *num_3body );
MPI_Barrier( MPI_COMM_WORLD );
#endif
}
#endif
void Compute_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
int qeq_flag;
#if defined(LOG_PERFORMANCE)
real t_start = 0;
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
t_start = Get_Time( );
#endif
/********* init forces ************/
if ( control->qeq_freq && (data->step - data->prev_steps) % control->qeq_freq == 0 )
qeq_flag = 1;
else qeq_flag = 0;
if ( qeq_flag ) Init_Forces( system, control, data, workspace, lists, out_control );
else
Init_Forces_noQEq( system, control, data, workspace, lists, out_control );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.init_forces) );
#endif
/********* bonded interactions ************/
Compute_Bonded_Forces( system, control, data, workspace, lists, out_control );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: completed bonded\n",
system->my_rank, data->step );
MPI_Barrier( MPI_COMM_WORLD );
#endif
/**************** qeq ************************/
#if defined(PURE_REAX)
if ( qeq_flag )
QEq( system, control, data, workspace, out_control, mpi_data );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.qEq) );
#endif
#if defined(DEBUG_FOCUS)
fprintf(stderr, "p%d @ step%d: qeq completed\n", system->my_rank, data->step);
MPI_Barrier( MPI_COMM_WORLD );
#endif
#endif //PURE_REAX
/********* nonbonded interactions ************/
Compute_NonBonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.nonb) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
system->my_rank, data->step );
MPI_Barrier( MPI_COMM_WORLD );
#endif
/*********** total force ***************/
Compute_Total_Force( system, control, data, workspace, lists, mpi_data );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: total forces computed\n",
system->my_rank, data->step );
//Print_Total_Force( system, data, workspace );
MPI_Barrier( MPI_COMM_WORLD );
#endif
#if defined(TEST_FORCES)
Print_Force_Files( system, control, data, workspace,
lists, out_control, mpi_data );
#endif
}
#ifdef HAVE_CUDA
void Cuda_Compute_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
int qeq_flag, retVal = SUCCESS;
#if defined(LOG_PERFORMANCE)
real t_start = 0;
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
t_start = Get_Time( );
#endif
/********* init forces ************/
if ( control->qeq_freq && (data->step - data->prev_steps) % control->qeq_freq == 0 )
qeq_flag = 1;
else qeq_flag = 0;
if ( qeq_flag )
retVal = Cuda_Init_Forces( system, control, data, workspace, lists, out_control );
else
retVal = Cuda_Init_Forces_noQEq( system, control, data, workspace, lists, out_control );
if (retVal == FAILURE)
{
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
//validate_sparse_matrix (system, workspace);
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.init_forces) );
#endif
/********* bonded interactions ************/
retVal = Cuda_Compute_Bonded_Forces( system, control, data, workspace, lists, out_control );
if (retVal == FAILURE)
{
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: completed bonded\n",
system->my_rank, data->step );
MPI_Barrier( MPI_COMM_WORLD );
#endif
/**************** qeq ************************/
#if defined(PURE_REAX)
if ( qeq_flag )
Cuda_QEq( system, control, data, workspace, out_control, mpi_data );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.qEq) );
#endif
#if defined(DEBUG_FOCUS)
fprintf(stderr, "p%d @ step%d: qeq completed\n", system->my_rank, data->step);
MPI_Barrier( MPI_COMM_WORLD );
#endif
#endif //PURE_REAX
/********* nonbonded interactions ************/
Cuda_Compute_NonBonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.nonb) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
system->my_rank, data->step );
MPI_Barrier( MPI_COMM_WORLD );
#endif
/*********** total force ***************/
Cuda_Compute_Total_Force( system, control, data, workspace, lists, mpi_data );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( MPI_COMM_WORLD );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: total forces computed\n",
system->my_rank, data->step );
//Print_Total_Force( system, data, workspace );
MPI_Barrier( MPI_COMM_WORLD );
#endif
}
#endif
int validate_device (reax_system *system, simulation_data *data, storage *workspace, reax_list **lists )
{
int retval = FAILURE;
#ifdef __CUDA_DEBUG__
//retval |= validate_neighbors (system, lists);
//retval |= validate_sym_dbond_indices (system, workspace, lists);
//retval |= validate_hbonds (system, workspace, lists);
//retval |= validate_workspace (system, workspace);
//retval |= validate_bonds (system, workspace, lists);
//retval |= validate_three_bodies (system, workspace, lists );
retval |= validate_sparse_matrix (system, workspace);
//retval |= validate_data (system, data);
//retval |= validate_atoms (system, lists);
//analyze_hbonds (system, workspace, lists);
if (!retval) {
fprintf (stderr, "Results *DOES NOT* mattch between device and host \n");
}
#endif
return retval;
}