Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F78556795
reaxc_reset_tools.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Aug 21, 14:48
Size
7 KB
Mime Type
text/x-c
Expires
Fri, Aug 23, 14:48 (2 d)
Engine
blob
Format
Raw Data
Handle
19318533
Attached To
rLAMMPS lammps
reaxc_reset_tools.cpp
View Options
/*----------------------------------------------------------------------
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_reax_c.h"
#if defined(PURE_REAX)
#include "reset_tools.h"
#include "list.h"
#include "tool_box.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_reset_tools.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
#endif
void Reset_Atoms( reax_system* system, control_params *control )
{
int i;
reax_atom *atom;
system->numH = 0;
if( control->hbond_cut > 0 )
for( i = 0; i < system->n; ++i ) {
atom = &(system->my_atoms[i]);
if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
atom->Hindex = system->numH++;
else atom->Hindex = -1;
}
}
void Reset_Energies( energy_data *en )
{
en->e_bond = 0;
en->e_ov = 0;
en->e_un = 0;
en->e_lp = 0;
en->e_ang = 0;
en->e_pen = 0;
en->e_coa = 0;
en->e_hb = 0;
en->e_tor = 0;
en->e_con = 0;
en->e_vdW = 0;
en->e_ele = 0;
en->e_pol = 0;
en->e_pot = 0;
en->e_kin = 0;
en->e_tot = 0;
}
void Reset_Temperatures( simulation_data *data )
{
data->therm.T = 0;
}
void Reset_Pressures( simulation_data *data )
{
data->flex_bar.P_scalar = 0;
rtensor_MakeZero( data->flex_bar.P );
data->iso_bar.P = 0;
rvec_MakeZero( data->int_press );
rvec_MakeZero( data->my_ext_press );
rvec_MakeZero( data->ext_press );
}
void Reset_Simulation_Data( simulation_data* data, int virial )
{
Reset_Energies( &data->my_en );
Reset_Energies( &data->sys_en );
Reset_Temperatures( data );
//if( virial )
Reset_Pressures( data );
}
void Reset_Timing( reax_timing *rt )
{
rt->total = Get_Time();
rt->comm = 0;
rt->nbrs = 0;
rt->init_forces = 0;
rt->bonded = 0;
rt->nonb = 0;
rt->qEq = 0;
rt->s_matvecs = 0;
rt->t_matvecs = 0;
}
#ifdef TEST_FORCES
void Reset_Test_Forces( reax_system *system, storage *workspace )
{
memset( workspace->f_ele, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_vdw, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_bo, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_be, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_lp, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_ov, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_un, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_ang, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_coa, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_pen, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_hb, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_tor, 0, system->total_cap * sizeof(rvec) );
memset( workspace->f_con, 0, system->total_cap * sizeof(rvec) );
}
#endif
void Reset_Workspace( reax_system *system, storage *workspace )
{
memset( workspace->total_bond_order, 0, system->total_cap * sizeof( real ) );
memset( workspace->dDeltap_self, 0, system->total_cap * sizeof( rvec ) );
memset( workspace->CdDelta, 0, system->total_cap * sizeof( real ) );
memset( workspace->f, 0, system->total_cap * sizeof( rvec ) );
#ifdef TEST_FORCES
memset( workspace->dDelta, 0, sizeof(rvec) * system->total_cap );
Reset_Test_Forces( system, workspace );
#endif
}
void Reset_Grid( grid *g )
{
int i, j, k;
for( i = 0; i < g->ncells[0]; i++ )
for( j = 0; j < g->ncells[1]; j++ )
for( k = 0; k < g->ncells[2]; k++ ) {
g->cells[i][j][k].top = 0;
g->cells[i][j][k].str = 0;
g->cells[i][j][k].end = 0;
}
}
void Reset_Out_Buffers( mpi_out_data *out_buf, int n )
{
int i;
for( i = 0; i < n; ++i )
out_buf[i].cnt = 0;
}
void Reset_Neighbor_Lists( reax_system *system, control_params *control,
storage *workspace, reax_list **lists,
MPI_Comm comm )
{
int i, total_bonds, Hindex, total_hbonds;
reax_list *bonds, *hbonds;
/* bonds list */
if( system->N > 0 ){
bonds = (*lists) + BONDS;
total_bonds = 0;
/* reset start-end indexes */
for( i = 0; i < system->N; ++i ) {
Set_Start_Index( i, total_bonds, bonds );
Set_End_Index( i, total_bonds, bonds );
total_bonds += system->my_atoms[i].num_bonds;
}
/* is reallocation needed? */
if( total_bonds >= bonds->num_intrs * DANGER_ZONE ) {
workspace->realloc.bonds = 1;
if( total_bonds >= bonds->num_intrs ) {
fprintf(stderr,
"p%d: not enough space for bonds! total=%d allocated=%d\n",
system->my_rank, total_bonds, bonds->num_intrs );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
// fprintf( stderr, "p%d: n:%d num_intrs:%d num_H:%d\n",
// system->my_rank, hbonds->n, hbonds->num_intrs, workspace->num_H );
// MPI_Barrier( comm );
/* hbonds list */
if( control->hbond_cut > 0 && system->numH > 0 ) {
hbonds = (*lists) + HBONDS;
total_hbonds = 0;
/* reset start-end indexes */
for( i = 0; i < system->n; ++i ) {
Hindex = system->my_atoms[i].Hindex;
if( Hindex > -1 ) {
Set_Start_Index( Hindex, total_hbonds, hbonds );
Set_End_Index( Hindex, total_hbonds, hbonds );
total_hbonds += system->my_atoms[i].num_hbonds;
}
}
/* is reallocation needed? */
if( total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/ ) {
workspace->realloc.hbonds = 1;
if( total_hbonds >= hbonds->num_intrs ) {
fprintf(stderr,
"p%d: not enough space for hbonds! total=%d allocated=%d\n",
system->my_rank, total_hbonds, hbonds->num_intrs );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
// fprintf( stderr, "p%d: cleared hbonds\n", system->my_rank );
// MPI_Barrier( comm );
}
void Reset( reax_system *system, control_params *control, simulation_data *data,
storage *workspace, reax_list **lists, MPI_Comm comm )
{
Reset_Atoms( system, control );
Reset_Simulation_Data( data, control->virial );
Reset_Workspace( system, workspace );
Reset_Neighbor_Lists( system, control, workspace, lists, comm );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: reset done\n", system->my_rank, data->step );
MPI_Barrier( comm );
#endif
}
Event Timeline
Log In to Comment