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reaxc_init_md_omp.cpp
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Fri, Sep 13, 05:36

reaxc_init_md_omp.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
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 "pair_reaxc_omp.h"
#include "reaxc_init_md_omp.h"
#include "reaxc_allocate.h"
#include "reaxc_forces.h"
#include "reaxc_forces_omp.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_reset_tools.h"
#include "reaxc_system_props.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
#include "omp.h"
// Functions definedd in reaxc_init_md.cpp
extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*);
extern int Init_System(reax_system*, control_params*, char*);
extern int Init_Simulation_Data(reax_system*, control_params*, simulation_data*, char*);
extern int Init_Workspace(reax_system*, control_params*, storage*, MPI_Comm, char*);
/* ---------------------------------------------------------------------- */
int Init_ListsOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
int TWICE = 2;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS ));
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
int nthreads = control->nthreads;
reax_list *bonds = (*lists)+BONDS;
for (i = 0; i < bonds->num_intrs; ++i)
bonds->select.bond_list[i].bo_data.CdboReduction =
(double*) smalloc(sizeof(double)*nthreads, "CdboReduction", comm);
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
free( hb_top );
free( bond_top );
return SUCCESS;
}
/* ---------------------------------------------------------------------- */
// The only difference with the MPI-only function is calls to Init_ListsOMP and Init_Force_FunctionsOMP().
void InitializeOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data, MPI_Comm comm )
{
char msg[MAX_STR];
if( Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE ) {
fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
system->my_rank );
fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
if( Init_System(system, control, msg) == FAILURE ){
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
if( Init_Simulation_Data( system, control, data, msg ) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d:init_workspace: not enough memory\n",
system->my_rank );
fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
if( Init_ListsOMP( system, control, data, workspace, lists, mpi_data, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
if( Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: could not open output files! terminating...\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
if( control->tabulate ) {
if( Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
}
Init_Force_FunctionsOMP( control );
}

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