260 lines
7.9 KiB
C++
260 lines
7.9 KiB
C++
/*----------------------------------------------------------------------
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PuReMD - Purdue ReaxFF Molecular Dynamics Program
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Copyright (2010) Purdue University
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Hasan Metin Aktulga, hmaktulga@lbl.gov
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Joseph Fogarty, jcfogart@mail.usf.edu
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Sagar Pandit, pandit@usf.edu
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Ananth Y Grama, ayg@cs.purdue.edu
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Please cite the related publication:
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H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
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"Parallel Reactive Molecular Dynamics: Numerical Methods and
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Algorithmic Techniques", Parallel Computing, in press.
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This program is free software; you can redistribute it and/or
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modify it under the terms of the GNU General Public License as
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published by the Free Software Foundation; either version 2 of
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the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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See the GNU General Public License for more details:
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<http://www.gnu.org/licenses/>.
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----------------------------------------------------------------------*/
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#include "reaxc_init_md.h"
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#include <mpi.h>
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#include <cmath>
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#include <cstdlib>
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#include <cstring>
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#include "reaxc_defs.h"
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#include "reaxc_allocate.h"
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#include "reaxc_forces.h"
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#include "reaxc_io_tools.h"
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#include "reaxc_list.h"
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#include "reaxc_lookup.h"
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#include "reaxc_reset_tools.h"
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#include "reaxc_tool_box.h"
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#include "error.h"
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int Init_System( reax_system *system, control_params *control, char * /*msg*/ )
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{
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int i;
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reax_atom *atom;
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int mincap = system->mincap;
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double safezone = system->safezone;
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double saferzone = system->saferzone;
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// determine the local and total capacity
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system->local_cap = MAX( (int)(system->n * safezone), mincap);
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system->total_cap = MAX( (int)(system->N * safezone), mincap);
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/* estimate numH and Hcap */
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system->numH = 0;
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if (control->hbond_cut > 0)
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for( i = 0; i < system->n; ++i ) {
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atom = &(system->my_atoms[i]);
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if (system->reax_param.sbp[ atom->type ].p_hbond == 1 && atom->type >= 0)
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atom->Hindex = system->numH++;
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else atom->Hindex = -1;
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}
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system->Hcap = (int)(MAX( system->numH * saferzone, mincap ));
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return SUCCESS;
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}
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int Init_Simulation_Data( reax_system *system, control_params *control,
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simulation_data *data, char * /*msg*/ )
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{
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Reset_Simulation_Data( data, control->virial );
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/* initialize the timer(s) */
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if (system->my_rank == MASTER_NODE) {
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data->timing.start = Get_Time( );
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}
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data->step = data->prev_steps = 0;
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return SUCCESS;
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}
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void Init_Taper( control_params *control, storage *workspace )
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{
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double d1, d7;
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double swa, swa2, swa3;
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double swb, swb2, swb3;
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swa = control->nonb_low;
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swb = control->nonb_cut;
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if (fabs( swa ) > 0.01 && control->me == 0)
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control->error_ptr->warning( FLERR, "Non-zero lower Taper-radius cutoff" );
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if (swb < 0) {
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control->error_ptr->all(FLERR,"Negative upper Taper-radius cutoff");
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}
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else if( swb < 5 && control->me == 0) {
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char errmsg[256];
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snprintf(errmsg, 256, "Very low Taper-radius cutoff: %f", swb );
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control->error_ptr->warning( FLERR, errmsg );
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}
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d1 = swb - swa;
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d7 = pow( d1, 7.0 );
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swa2 = SQR( swa );
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swa3 = CUBE( swa );
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swb2 = SQR( swb );
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swb3 = CUBE( swb );
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workspace->Tap[7] = 20.0 / d7;
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workspace->Tap[6] = -70.0 * (swa + swb) / d7;
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workspace->Tap[5] = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7;
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workspace->Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3 ) / d7;
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workspace->Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;
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workspace->Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7;
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workspace->Tap[1] = 140.0 * swa3 * swb3 / d7;
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workspace->Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 -
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7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
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}
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int Init_Workspace( reax_system *system, control_params *control,
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storage *workspace, char *msg )
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{
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int ret;
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ret = Allocate_Workspace( system, control, workspace,
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system->local_cap, system->total_cap, msg );
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if (ret != SUCCESS)
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return ret;
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memset( &(workspace->realloc), 0, sizeof(reallocate_data) );
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Reset_Workspace( system, workspace );
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/* Initialize the Taper function */
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Init_Taper( control, workspace);
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return SUCCESS;
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}
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/************** setup communication data structures **************/
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int Init_MPI_Datatypes( reax_system *system, storage * /*workspace*/,
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mpi_datatypes *mpi_data, MPI_Comm comm, char * /*msg*/ )
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{
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/* setup the world */
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mpi_data->world = comm;
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MPI_Comm_size( comm, &(system->wsize) );
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return SUCCESS;
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}
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int Init_Lists( reax_system *system, control_params *control,
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simulation_data * /*data*/, storage * /*workspace*/, reax_list **lists,
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mpi_datatypes * /*mpi_data*/, char * /*msg*/ )
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{
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int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
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int *hb_top, *bond_top;
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int mincap = system->mincap;
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double safezone = system->safezone;
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double saferzone = system->saferzone;
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bond_top = (int*) calloc( system->total_cap, sizeof(int) );
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hb_top = (int*) calloc( system->local_cap, sizeof(int) );
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Estimate_Storages( system, control, lists,
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&Htop, hb_top, bond_top, &num_3body);
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if (control->hbond_cut > 0) {
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/* init H indexes */
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total_hbonds = 0;
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for( i = 0; i < system->n; ++i ) {
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system->my_atoms[i].num_hbonds = hb_top[i];
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total_hbonds += hb_top[i];
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}
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total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds));
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if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
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*lists+HBONDS ) ) {
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control->error_ptr->one(FLERR, "Not enough space for hbonds list.");
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}
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(*lists+HBONDS)->error_ptr = system->error_ptr;
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}
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total_bonds = 0;
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for( i = 0; i < system->N; ++i ) {
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system->my_atoms[i].num_bonds = bond_top[i];
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total_bonds += bond_top[i];
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}
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bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS ));
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if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
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*lists+BONDS ) ) {
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control->error_ptr->one(FLERR, "Not enough space for bonds list.");
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}
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(*lists+BONDS)->error_ptr = system->error_ptr;
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/* 3bodies list */
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cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
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if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
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*lists+THREE_BODIES ) ){
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control->error_ptr->one(FLERR,"Problem in initializing angles list.");
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}
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(*lists+THREE_BODIES)->error_ptr = system->error_ptr;
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free( hb_top );
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free( bond_top );
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return SUCCESS;
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}
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void Initialize( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, output_controls *out_control,
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mpi_datatypes *mpi_data, MPI_Comm comm )
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{
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char msg[MAX_STR];
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if (Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE) {
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control->error_ptr->one(FLERR,"Could not create datatypes");
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}
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if (Init_System(system, control, msg) == FAILURE) {
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control->error_ptr->one(FLERR,"System could not be initialized");
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}
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if (Init_Simulation_Data( system, control, data, msg ) == FAILURE) {
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control->error_ptr->one(FLERR,"Sim_data could not be initialized");
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}
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if (Init_Workspace( system, control, workspace, msg ) ==
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FAILURE) {
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control->error_ptr->one(FLERR,"Workspace could not be initialized");
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}
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if (Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
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FAILURE) {
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control->error_ptr->one(FLERR,"Lists could not be initialized");
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}
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if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
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control->error_ptr->one(FLERR,"Could not open output files");
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}
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if (control->tabulate) {
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if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) {
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control->error_ptr->one(FLERR,"Lookup table could not be created");
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}
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}
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Init_Force_Functions( control );
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}
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