reaxc_reset_tools.cpp
2686b7f830f8lammm-devel

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_reaxc.h"
			#include "reaxc_reset_tools.h"
			#include "reaxc_list.h"
			#include "reaxc_tool_box.h"
			#include "reaxc_vector.h"

			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 (atom->type < 0) continue;
			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 );
			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;
			}

			void Reset_Workspace( reax_system system, storage workspace )
			{
			memset( workspace->total_bond_order, 0, system->total_cap * sizeof( double ) );
			memset( workspace->dDeltap_self, 0, system->total_cap * sizeof( rvec ) );
			memset( workspace->CdDelta, 0, system->total_cap * sizeof( double ) );
			memset( workspace->f, 0, system->total_cap * sizeof( rvec ) );

			}


			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 );
			}
			}
			}

			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 );
			}
			}
			}
			}


			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 );

			}

lammps/src/USER-REAXC/reaxc_reset_tools.cpp2686b7f830f8lammm-devel

reaxc_reset_tools.cppView Options

lammps/src/USER-REAXC/reaxc_reset_tools.cpp
2686b7f830f8lammm-devel

reaxc_reset_tools.cpp
View Options