reaxc_io_tools.cpp
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Created: Sun, Jul 13, 23:48

reaxc_io_tools.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_reax_c.h"
	#include "update.h"
	#if defined(PURE_REAX)
	#include "io_tools.h"
	#include "basic_comm.h"
	#include "list.h"
	#include "reset_tools.h"
	#include "system_props.h"
	#include "tool_box.h"
	#include "traj.h"
	#include "vector.h"
	#elif defined(LAMMPS_REAX)
	#include "reaxc_io_tools.h"
	#include "reaxc_basic_comm.h"
	#include "reaxc_list.h"
	#include "reaxc_reset_tools.h"
	#include "reaxc_system_props.h"
	#include "reaxc_tool_box.h"
	#include "reaxc_traj.h"
	#include "reaxc_vector.h"
	#endif

	print_interaction Print_Interactions[NUM_INTRS];

	/********************** initialize output controls **********************/
	int Init_Output_Files( reax_system system, control_params control,
	output_controls out_control, mpi_datatypes mpi_data,
	char *msg )
	{
	char temp[MAX_STR];
	int ret;

	if( out_control->write_steps > 0 ){
	ret = Init_Traj( system, control, out_control, mpi_data, msg );
	if( ret == FAILURE )
	return ret;
	}

	if( system->my_rank == MASTER_NODE ) {
	/* These files are written only by the master node */
	if( out_control->energy_update_freq > 0 ) {
	#if defined(PURE_REAX)
	/* init out file */
	sprintf( temp, "%s.out", control->sim_name );
	if( (out_control->out = fopen( temp, "w" )) != NULL ) {
	#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
	fprintf( out_control->out, "%-6s%14s%14s%14s%11s%13s%13s\n",
	"step", "total energy", "potential", "kinetic",
	"T(K)", "V(A^3)", "P(Gpa)" );
	#else
	fprintf( out_control->out, "%-6s%24s%24s%24s%13s%16s%13s\n",
	"step", "total energy", "potential", "kinetic",
	"T(K)", "V(A^3)", "P(GPa)" );
	#endif
	fflush( out_control->out );
	}
	else {
	strcpy( msg, "init_out_controls: .out file could not be opened\n" );
	return FAILURE;
	}
	#endif

	/* init potentials file */
	sprintf( temp, "%s.pot", control->sim_name );
	if( (out_control->pot = fopen( temp, "w" )) != NULL ) {
	#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
	fprintf( out_control->pot,
	"%-6s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s\n",
	"step", "ebond", "eatom", "elp",
	"eang", "ecoa", "ehb", "etor", "econj",
	"evdw","ecoul", "epol" );
	#else
	fprintf( out_control->pot,
	"%-6s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s\n",
	"step", "ebond", "eatom", "elp",
	"eang", "ecoa", "ehb", "etor", "econj",
	"evdw","ecoul", "epol" );
	#endif
	fflush( out_control->pot );
	}
	else {
	strcpy( msg, "init_out_controls: .pot file could not be opened\n" );
	return FAILURE;
	}

	/* init log file */
	#if defined(LOG_PERFORMANCE)
	sprintf( temp, "%s.log", control->sim_name );
	if( (out_control->log = fopen( temp, "w" )) != NULL ) {
	fprintf( out_control->log, "%6s%8s%8s%8s%8s%8s%8s%8s%8s\n",
	"step", "total", "comm", "nbrs", "init", "bonded", "nonb",
	"qeq", "matvecs" );
	fflush( out_control->log );
	}
	else {
	strcpy( msg, "init_out_controls: .log file could not be opened\n" );
	return FAILURE;
	}
	#endif
	}

	/* init pressure file */
	if( control->ensemble == NPT \|\|
	control->ensemble == iNPT \|\|
	control->ensemble == sNPT ) {
	sprintf( temp, "%s.prs", control->sim_name );
	if( (out_control->prs = fopen( temp, "w" )) != NULL ) {
	fprintf(out_control->prs,"%8s%13s%13s%13s%13s%13s%13s%13s\n",
	"step", "Pint/norm[x]", "Pint/norm[y]", "Pint/norm[z]",
	"Pext/Ptot[x]", "Pext/Ptot[y]", "Pext/Ptot[z]", "Pkin/V" );
	fflush( out_control->prs );
	}
	else {
	strcpy(msg,"init_out_controls: .prs file couldn't be opened\n");
	return FAILURE;
	}
	}

	/* init electric dipole moment analysis file */
	// not yet implemented in the parallel version!!!
	// if( control->dipole_anal ) {
	// sprintf( temp, "%s.dpl", control->sim_name );
	// if( (out_control->dpl = fopen( temp, "w" )) != NULL ) {
	// fprintf( out_control->dpl, "%6s%20s%30s",
	// "step", "molecule count", "avg dipole moment norm" );
	// fflush( out_control->dpl );
	// }
	// else {
	// strcpy(msg, "init_out_controls: .dpl file couldn't be opened\n");
	// return FAILURE;
	// }
	// }

	/* init diffusion coef analysis file */
	// not yet implemented in the parallel version!!!
	// if( control->diffusion_coef ) {
	// sprintf( temp, "%s.drft", control->sim_name );
	// if( (out_control->drft = fopen( temp, "w" )) != NULL ) {
	// fprintf( out_control->drft, "%7s%20s%20s\n",
	// "step", "type count", "avg disp^2" );
	// fflush( out_control->drft );
	// }
	// else {
	// strcpy(msg,"init_out_controls: .drft file couldn't be opened\n");
	// return FAILURE;
	// }
	// }
	}


	/* init molecular analysis file */
	/* proc0 opens this file and shares it with everyone.
	then all processors write into it in a round-robin
	fashion controlled by their rank */
	/*if( control->molecular_analysis ) {
	if( system->my_rank == MASTER_NODE ) {
	sprintf( temp, "%s.mol", control->sim_name );
	if( (out_control->mol = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"init_out_controls: .mol file could not be opened\n");
	return FAILURE;
	}
	}

	MPI_Bcast( &(out_control->mol), 1, MPI_LONG, 0, MPI_COMM_WORLD );
	}*/


	#ifdef TEST_ENERGY
	/* open bond energy file */
	sprintf( temp, "%s.ebond.%d", control->sim_name, system->my_rank );
	if( (out_control->ebond = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .ebond file couldn't be opened\n");
	return FAILURE;
	}

	/* open lone-pair energy file */
	sprintf( temp, "%s.elp.%d", control->sim_name, system->my_rank );
	if( (out_control->elp = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .elp file couldn't be opened\n");
	return FAILURE;
	}

	/* open overcoordination energy file */
	sprintf( temp, "%s.eov.%d", control->sim_name, system->my_rank );
	if( (out_control->eov = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .eov file couldn't be opened\n");
	return FAILURE;
	}

	/* open undercoordination energy file */
	sprintf( temp, "%s.eun.%d", control->sim_name, system->my_rank );
	if( (out_control->eun = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .eun file couldn't be opened\n");
	return FAILURE;
	}

	/* open angle energy file */
	sprintf( temp, "%s.eval.%d", control->sim_name, system->my_rank );
	if( (out_control->eval = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .eval file couldn't be opened\n");
	return FAILURE;
	}

	/* open coalition energy file */
	sprintf( temp, "%s.ecoa.%d", control->sim_name, system->my_rank );
	if( (out_control->ecoa = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .ecoa file couldn't be opened\n");
	return FAILURE;
	}

	/* open penalty energy file */
	sprintf( temp, "%s.epen.%d", control->sim_name, system->my_rank );
	if( (out_control->epen = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .epen file couldn't be opened\n");
	return FAILURE;
	}

	/* open torsion energy file */
	sprintf( temp, "%s.etor.%d", control->sim_name, system->my_rank );
	if( (out_control->etor = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .etor file couldn't be opened\n");
	return FAILURE;
	}

	/* open conjugation energy file */
	sprintf( temp, "%s.econ.%d", control->sim_name, system->my_rank );
	if( (out_control->econ = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .econ file couldn't be opened\n");
	return FAILURE;
	}

	/* open hydrogen bond energy file */
	sprintf( temp, "%s.ehb.%d", control->sim_name, system->my_rank );
	if( (out_control->ehb = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .ehb file couldn't be opened\n");
	return FAILURE;
	}

	/* open vdWaals energy file */
	sprintf( temp, "%s.evdw.%d", control->sim_name, system->my_rank );
	if( (out_control->evdw = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .evdw file couldn't be opened\n");
	return FAILURE;
	}

	/* open coulomb energy file */
	sprintf( temp, "%s.ecou.%d", control->sim_name, system->my_rank );
	if( (out_control->ecou = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .ecou file couldn't be opened\n");
	return FAILURE;
	}
	#endif


	#ifdef TEST_FORCES
	/* open bond orders file */
	sprintf( temp, "%s.fbo.%d", control->sim_name, system->my_rank );
	if( (out_control->fbo = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fbo file couldn't be opened\n");
	return FAILURE;
	}

	/* open bond orders derivatives file */
	sprintf( temp, "%s.fdbo.%d", control->sim_name, system->my_rank );
	if( (out_control->fdbo = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fdbo file couldn't be opened\n");
	return FAILURE;
	}

	/* produce a single force file - to be written by p0 */
	if( system->my_rank == MASTER_NODE ) {
	/* open bond forces file */
	sprintf( temp, "%s.fbond", control->sim_name );
	if( (out_control->fbond = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fbond file couldn't be opened\n");
	return FAILURE;
	}

	/* open lone-pair forces file */
	sprintf( temp, "%s.flp", control->sim_name );
	if( (out_control->flp = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .flp file couldn't be opened\n");
	return FAILURE;
	}

	/* open overcoordination forces file */
	sprintf( temp, "%s.fov", control->sim_name );
	if( (out_control->fov = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fov file couldn't be opened\n");
	return FAILURE;
	}

	/* open undercoordination forces file */
	sprintf( temp, "%s.fun", control->sim_name );
	if( (out_control->fun = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fun file couldn't be opened\n");
	return FAILURE;
	}

	/* open angle forces file */
	sprintf( temp, "%s.fang", control->sim_name );
	if( (out_control->fang = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fang file couldn't be opened\n");
	return FAILURE;
	}

	/* open coalition forces file */
	sprintf( temp, "%s.fcoa", control->sim_name );
	if( (out_control->fcoa = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fcoa file couldn't be opened\n");
	return FAILURE;
	}

	/* open penalty forces file */
	sprintf( temp, "%s.fpen", control->sim_name );
	if( (out_control->fpen = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fpen file couldn't be opened\n");
	return FAILURE;
	}

	/* open torsion forces file */
	sprintf( temp, "%s.ftor", control->sim_name );
	if( (out_control->ftor = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .ftor file couldn't be opened\n");
	return FAILURE;
	}

	/* open conjugation forces file */
	sprintf( temp, "%s.fcon", control->sim_name );
	if( (out_control->fcon = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fcon file couldn't be opened\n");
	return FAILURE;
	}

	/* open hydrogen bond forces file */
	sprintf( temp, "%s.fhb", control->sim_name );
	if( (out_control->fhb = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fhb file couldn't be opened\n");
	return FAILURE;
	}

	/* open vdw forces file */
	sprintf( temp, "%s.fvdw", control->sim_name );
	if( (out_control->fvdw = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fvdw file couldn't be opened\n");
	return FAILURE;
	}

	/* open nonbonded forces file */
	sprintf( temp, "%s.fele", control->sim_name );
	if( (out_control->fele = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fele file couldn't be opened\n");
	return FAILURE;
	}

	/* open total force file */
	sprintf( temp, "%s.ftot", control->sim_name );
	if( (out_control->ftot = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .ftot file couldn't be opened\n");
	return FAILURE;
	}

	/* open force comprison file */
	sprintf( temp, "%s.fcomp", control->sim_name );
	if( (out_control->fcomp = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .fcomp file couldn't be opened\n");
	return FAILURE;
	}
	}
	#endif

	#if defined(PURE_REAX)
	#if defined(TEST_FORCES) \|\| defined(TEST_ENERGY)
	/* open far neighbor list file */
	sprintf( temp, "%s.far_nbrs_list.%d", control->sim_name, system->my_rank );
	if( (out_control->flist = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .far_nbrs_list file couldn't be opened\n");
	return FAILURE;
	}

	/* open bond list file */
	sprintf( temp, "%s.bond_list.%d", control->sim_name, system->my_rank );
	if( (out_control->blist = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .bond_list file couldn't be opened\n");
	return FAILURE;
	}

	/* open near neighbor list file */
	sprintf( temp, "%s.near_nbrs_list.%d", control->sim_name, system->my_rank );
	if( (out_control->nlist = fopen( temp, "w" )) == NULL ) {
	strcpy(msg,"Init_Out_Files: .near_nbrs_list file couldn't be opened\n");
	return FAILURE;
	}
	#endif
	#endif

	return SUCCESS;
	}


	/********************** close output files **********************/
	int Close_Output_Files( reax_system system, control_params control,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	if( out_control->write_steps > 0 )
	End_Traj( system->my_rank, out_control );

	if( system->my_rank == MASTER_NODE ) {
	if( out_control->energy_update_freq > 0 ) {
	#if defined(PURE_REAX)
	fclose( out_control->out );
	#endif
	fclose( out_control->pot );
	#if defined(LOG_PERFORMANCE)
	fclose( out_control->log );
	#endif
	}

	if( control->ensemble == NPT \|\| control->ensemble == iNPT \|\|
	control->ensemble == sNPT )
	fclose( out_control->prs );

	// not yet implemented in the parallel version
	//if( control->dipole_anal ) fclose( out_control->dpl );
	//if( control->diffusion_coef ) fclose( out_control->drft );
	//if( control->molecular_analysis ) fclose( out_control->mol );
	}

	#ifdef TEST_ENERGY
	fclose( out_control->ebond );
	fclose( out_control->elp );
	fclose( out_control->eov );
	fclose( out_control->eun );
	fclose( out_control->eval );
	fclose( out_control->epen );
	fclose( out_control->ecoa );
	fclose( out_control->ehb );
	fclose( out_control->etor );
	fclose( out_control->econ );
	fclose( out_control->evdw );
	fclose( out_control->ecou );
	#endif

	#ifdef TEST_FORCES
	fclose( out_control->fbo );
	fclose( out_control->fdbo );

	if( system->my_rank == MASTER_NODE ) {
	fclose( out_control->fbond );
	fclose( out_control->flp );
	fclose( out_control->fov );
	fclose( out_control->fun );
	fclose( out_control->fang );
	fclose( out_control->fcoa );
	fclose( out_control->fpen );
	fclose( out_control->ftor );
	fclose( out_control->fcon );
	fclose( out_control->fhb );
	fclose( out_control->fvdw );
	fclose( out_control->fele );
	fclose( out_control->ftot );
	fclose( out_control->fcomp );
	}
	#endif

	#if defined(PURE_REAX)
	#if defined(TEST_FORCES) \|\| defined(TEST_ENERGY)
	fclose( out_control->flist );
	fclose( out_control->blist );
	fclose( out_control->nlist );
	#endif
	#endif

	return SUCCESS;
	}



	void Print_Box( simulation_box* box, char name, FILE out )
	{
	// int i, j;

	fprintf( out, "%s:\n", name );
	fprintf( out, "\tmin[%8.3f %8.3f %8.3f]\n",
	box->min[0], box->min[1], box->min[2] );
	fprintf( out, "\tmax[%8.3f %8.3f %8.3f]\n",
	box->max[0], box->max[1], box->max[2] );
	fprintf( out, "\tdims[%8.3f%8.3f%8.3f]\n",
	box->box_norms[0], box->box_norms[1], box->box_norms[2] );

	// fprintf( out, "box: {" );
	// for( i = 0; i < 3; ++i )
	// {
	// fprintf( out, "{" );
	// for( j = 0; j < 3; ++j )
	// fprintf( out, "%8.3f ", box->box[i][j] );
	// fprintf( out, "}" );
	// }
	// fprintf( out, "}\n" );

	// fprintf( out, "box_trans: {" );
	// for( i = 0; i < 3; ++i )
	// {
	// fprintf( out, "{" );
	// for( j = 0; j < 3; ++j )
	// fprintf( out, "%8.3f ", box->trans[i][j] );
	// fprintf( out, "}" );
	// }
	// fprintf( out, "}\n" );

	// fprintf( out, "box_trinv: {" );
	// for( i = 0; i < 3; ++i )
	// {
	// fprintf( out, "{" );
	// for( j = 0; j < 3; ++j )
	// fprintf( out, "%8.3f ", box->trans_inv[i][j] );
	// fprintf( out, "}" );
	// }
	// fprintf( out, "}\n" );
	}



	void Print_Grid( grid* g, FILE *out )
	{
	int x, y, z, gc_type;
	ivec gc_str;
	char gcell_type_text[10][12] =
	{ "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
	"NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" };

	fprintf( out, "\tnumber of grid cells: %d %d %d\n",
	g->ncells[0], g->ncells[1], g->ncells[2] );
	fprintf( out, "\tgcell lengths: %8.3f %8.3f %8.3f\n",
	g->cell_len[0], g->cell_len[1], g->cell_len[2] );
	fprintf( out, "\tinverses of gcell lengths: %8.3f %8.3f %8.3f\n",
	g->inv_len[0], g->inv_len[1], g->inv_len[2] );
	fprintf( out, "\t---------------------------------\n" );
	fprintf( out, "\tnumber of native gcells: %d %d %d\n",
	g->native_cells[0], g->native_cells[1], g->native_cells[2] );
	fprintf( out, "\tnative gcell span: %d-%d %d-%d %d-%d\n",
	g->native_str[0], g->native_end[0],
	g->native_str[1], g->native_end[1],
	g->native_str[2], g->native_end[2] );
	fprintf( out, "\t---------------------------------\n" );
	fprintf( out, "\tvlist gcell stretch: %d %d %d\n",
	g->vlist_span[0], g->vlist_span[1], g->vlist_span[2] );
	fprintf( out, "\tnonbonded nbrs gcell stretch: %d %d %d\n",
	g->nonb_span[0], g->nonb_span[1], g->nonb_span[2] );
	fprintf( out, "\tbonded nbrs gcell stretch: %d %d %d\n",
	g->bond_span[0], g->bond_span[1], g->bond_span[2] );
	fprintf( out, "\t---------------------------------\n" );
	fprintf( out, "\tghost gcell span: %d %d %d\n",
	g->ghost_span[0], g->ghost_span[1], g->ghost_span[2] );
	fprintf( out, "\tnonbonded ghost gcell span: %d %d %d\n",
	g->ghost_nonb_span[0],g->ghost_nonb_span[1],g->ghost_nonb_span[2]);
	fprintf(out, "\thbonded ghost gcell span: %d %d %d\n",
	g->ghost_hbond_span[0],g->ghost_hbond_span[1],g->ghost_hbond_span[2]);
	fprintf( out, "\tbonded ghost gcell span: %d %d %d\n",
	g->ghost_bond_span[0],g->ghost_bond_span[1],g->ghost_bond_span[2]);
	//fprintf(out, "\t---------------------------------\n" );
	//fprintf(out, "\tmax number of gcells at the boundary: %d\n", g->gcell_cap);
	fprintf( out, "\t---------------------------------\n" );

	fprintf( stderr, "GCELL MARKS:\n" );
	gc_type = g->cells[0][0][0].type;
	ivec_MakeZero( gc_str );

	x = y = z = 0;
	for( x = 0; x < g->ncells[0]; ++x )
	for( y = 0; y < g->ncells[1]; ++y )
	for( z = 0; z < g->ncells[2]; ++z )
	if( g->cells[x][y][z].type != gc_type ){
	fprintf( stderr,
	"\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n",
	gc_str[0], gc_str[1], gc_str[2], x, y, z,
	gc_type, gcell_type_text[gc_type] );
	gc_type = g->cells[x][y][z].type;
	gc_str[0] = x;
	gc_str[1] = y;
	gc_str[2] = z;
	}
	fprintf( stderr, "\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n",
	gc_str[0], gc_str[1], gc_str[2], x, y, z,
	gc_type, gcell_type_text[gc_type] );
	fprintf( out, "-------------------------------------\n" );
	}


	#if 0
	void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
	{
	ivec r;
	int nbr;
	neighbor_proc *nbr_pr;
	char fname[100];
	FILE *f;
	char exch[3][10] = { "NONE", "NEAR_EXCH", "FULL_EXCH" };

	sprintf( fname, "gcell_exchange_bounds%d", my_rank );
	f = fopen( fname, "w" );

	/* loop over neighbor processes */
	for( r[0] = -1; r[0] <= 1; ++r[0])
	for( r[1] = -1; r[1] <= 1; ++r[1] )
	for( r[2] = -1; r[2] <= 1; ++r[2] )
	if( r[0]!=0 \|\| r[1]!=0 \|\| r[2]!=0 ) {
	nbr_pr = &(my_nbrs[nbr]);

	fprintf( f, "p%-2d GCELL BOUNDARIES with r(%2d %2d %2d):\n",
	my_rank, r[0], r[1], r[2] );

	fprintf( f, "\tsend_type %s: send(%d %d %d) to (%d %d %d)\n",
	exch[nbr_pr->send_type],
	nbr_pr->str_send[0], nbr_pr->str_send[1],
	nbr_pr->str_send[2],
	nbr_pr->end_send[0], nbr_pr->end_send[1],
	nbr_pr->end_send[2] );

	fprintf( f, "\trecv_type %s: recv(%d %d %d) to (%d %d %d)\n",
	exch[nbr_pr->recv_type],
	nbr_pr->str_recv[0], nbr_pr->str_recv[1],
	nbr_pr->str_recv[2],
	nbr_pr->end_recv[0], nbr_pr->end_recv[1],
	nbr_pr->end_recv[2] );
	}

	fclose(f);
	}
	#endif



	void Print_Native_GCells( reax_system *system )
	{
	int i, j, k, l;
	char fname[100];
	FILE *f;
	grid *g;
	grid_cell *gc;
	char gcell_type_text[10][12] =
	{ "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
	"NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" };

	sprintf( fname, "native_gcells.%d", system->my_rank );
	f = fopen( fname, "w" );
	g = &(system->my_grid);

	for( i = g->native_str[0]; i < g->native_end[0]; i++ )
	for( j = g->native_str[1]; j < g->native_end[1]; j++ )
	for( k = g->native_str[2]; k < g->native_end[2]; k++ )
	{
	gc = &( g->cells[i][j][k] );

	fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n",
	system->my_rank, i, j, k,
	gc->type, gcell_type_text[gc->type] );

	fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end );

	for( l = gc->str; l < gc->end; ++l )
	fprintf( f, TAGINT_FORMAT, system->my_atoms[l].orig_id );
	fprintf( f, "\n" );
	}

	fclose(f);
	}



	void Print_All_GCells( reax_system *system )
	{
	int i, j, k, l;
	char fname[100];
	FILE *f;
	grid *g;
	grid_cell *gc;
	char gcell_type_text[10][12] =
	{ "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
	"NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" };

	sprintf( fname, "all_gcells.%d", system->my_rank );
	f = fopen( fname, "w" );
	g = &(system->my_grid);

	for( i = 0; i < g->ncells[0]; i++ )
	for( j = 0; j < g->ncells[1]; j++ )
	for( k = 0; k < g->ncells[2]; k++ )
	{
	gc = &( g->cells[i][j][k] );

	fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n",
	system->my_rank, i, j, k,
	gc->type, gcell_type_text[gc->type] );

	fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end );

	for( l = gc->str; l < gc->end; ++l )
	fprintf( f, TAGINT_FORMAT, system->my_atoms[l].orig_id );
	fprintf( f, "\n" );
	}

	fclose(f);
	}



	void Print_My_Atoms( reax_system *system )
	{
	int i;
	char fname[100];
	FILE *fh;

	sprintf( fname, "my_atoms.%d", system->my_rank );
	if( (fh = fopen( fname, "w" )) == NULL )
	{
	fprintf( stderr, "error in opening my_atoms file" );
	MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
	}

	// fprintf( stderr, "p%d had %d atoms\n",
	// system->my_rank, system->n );

	for( i = 0; i < system->n; ++i )
	fprintf( fh, "p%-2d %-5d %2d %24.15e%24.15e%24.15e\n",
	system->my_rank,
	system->my_atoms[i].orig_id, system->my_atoms[i].type,
	system->my_atoms[i].x[0],
	system->my_atoms[i].x[1],
	system->my_atoms[i].x[2] );

	fclose( fh );
	}


	void Print_My_Ext_Atoms( reax_system *system )
	{
	int i;
	char fname[100];
	FILE *fh;

	sprintf( fname, "my_ext_atoms.%d", system->my_rank );
	if( (fh = fopen( fname, "w" )) == NULL )
	{
	fprintf( stderr, "error in opening my_ext_atoms file" );
	MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
	}

	// fprintf( stderr, "p%d had %d atoms\n",
	// system->my_rank, system->n );

	for( i = 0; i < system->N; ++i )
	fprintf( fh, "p%-2d %-5d imprt%-5d %2d %24.15e%24.15e%24.15e\n",
	system->my_rank, system->my_atoms[i].orig_id,
	system->my_atoms[i].imprt_id, system->my_atoms[i].type,
	system->my_atoms[i].x[0],
	system->my_atoms[i].x[1],
	system->my_atoms[i].x[2] );

	fclose( fh );
	}


	void Print_Far_Neighbors( reax_system system, reax_list *lists,
	control_params *control )
	{
	char fname[100];
	int i, j, nbr, natoms;
	tagint id_i, id_j;
	FILE *fout;
	reax_list *far_nbrs;

	sprintf( fname, "%s.far_nbrs.%d", control->sim_name, system->my_rank );
	fout = fopen( fname, "w" );
	far_nbrs = (*lists) + FAR_NBRS;
	natoms = system->N;

	for( i = 0; i < natoms; ++i ) {
	id_i = system->my_atoms[i].orig_id;

	for( j = Start_Index(i,far_nbrs); j < End_Index(i,far_nbrs); ++j ) {
	nbr = far_nbrs->select.far_nbr_list[j].nbr;
	id_j = system->my_atoms[nbr].orig_id;

	fprintf( fout, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
	id_i, id_j, far_nbrs->select.far_nbr_list[j].d,
	far_nbrs->select.far_nbr_list[j].dvec[0],
	far_nbrs->select.far_nbr_list[j].dvec[1],
	far_nbrs->select.far_nbr_list[j].dvec[2] );

	fprintf( fout, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
	id_j, id_i, far_nbrs->select.far_nbr_list[j].d,
	-far_nbrs->select.far_nbr_list[j].dvec[0],
	-far_nbrs->select.far_nbr_list[j].dvec[1],
	-far_nbrs->select.far_nbr_list[j].dvec[2] );
	}
	}

	fclose( fout );
	}


	void Print_Sparse_Matrix( reax_system system, sparse_matrix A )
	{
	int i, j;

	for( i = 0; i < A->n; ++i )
	for( j = A->start[i]; j < A->end[i]; ++j )
	fprintf( stderr, "%d %d %.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[A->entries[j].j].orig_id,
	A->entries[j].val );
	}


	void Print_Sparse_Matrix2( reax_system system, sparse_matrix A, char *fname )
	{
	int i, j;
	FILE *f = fopen( fname, "w" );

	for( i = 0; i < A->n; ++i )
	for( j = A->start[i]; j < A->end[i]; ++j )
	fprintf( f, "%d %d %.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[A->entries[j].j].orig_id,
	A->entries[j].val );

	fclose(f);
	}


	void Print_Symmetric_Sparse(reax_system system, sparse_matrix A, char *fname)
	{
	int i, j;
	reax_atom ai, aj;
	FILE *f = fopen( fname, "w" );

	for( i = 0; i < A->n; ++i ) {
	ai = &(system->my_atoms[i]);
	for( j = A->start[i]; j < A->end[i]; ++j ) {
	aj = &(system->my_atoms[A->entries[j].j]);
	fprintf( f, "%d %d %.15e\n",
	ai->renumber, aj->renumber, A->entries[j].val );
	if( A->entries[j].j < system->n && ai->renumber != aj->renumber )
	fprintf( f, "%d %d %.15e\n",
	aj->renumber, ai->renumber, A->entries[j].val );
	}
	}

	fclose(f);
	}


	void Print_Linear_System( reax_system system, control_params control,
	storage *workspace, int step )
	{
	int i;
	char fname[100];
	reax_atom *ai;
	FILE *out;

	// print rhs and init guesses for QEq
	sprintf( fname, "%s.p%dstate%d", control->sim_name, system->my_rank, step );
	out = fopen( fname, "w" );
	for( i = 0; i < system->n; i++ ) {
	ai = &(system->my_atoms[i]);
	fprintf( out, "%6d%2d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
	ai->renumber, ai->type, ai->x[0], ai->x[1], ai->x[2],
	workspace->s[i], workspace->b_s[i],
	workspace->t[i], workspace->b_t[i] );
	}
	fclose( out );

	// print QEq coef matrix
	sprintf( fname, "%s.p%dH%d", control->sim_name, system->my_rank, step );
	Print_Symmetric_Sparse( system, workspace->H, fname );

	// print the incomplete H matrix
	/*sprintf( fname, "%s.p%dHinc%d", control->sim_name, system->my_rank, step );
	out = fopen( fname, "w" );
	H = workspace->H;
	for( i = 0; i < H->n; ++i ) {
	ai = &(system->my_atoms[i]);
	for( j = H->start[i]; j < H->end[i]; ++j )
	if( H->entries[j].j < system->n ) {
	aj = &(system->my_atoms[H->entries[j].j]);
	fprintf( out, "%d %d %.15e\n",
	ai->orig_id, aj->orig_id, H->entries[j].val );
	if( ai->orig_id != aj->orig_id )
	fprintf( out, "%d %d %.15e\n",
	aj->orig_id, ai->orig_id, H->entries[j].val );
	}
	}
	fclose( out );*/

	// print the L from incomplete cholesky decomposition
	/*sprintf( fname, "%s.p%dL%d", control->sim_name, system->my_rank, step );
	Print_Sparse_Matrix2( system, workspace->L, fname );*/
	}


	void Print_LinSys_Soln( reax_system system, real x, real b_prm, real b )
	{
	int i;
	char fname[100];
	FILE *fout;

	sprintf( fname, "qeq.%d.out", system->my_rank );
	fout = fopen( fname, "w" );

	for( i = 0; i < system->n; ++i )
	fprintf( fout, "%6d%10.4f%10.4f%10.4f\n",
	system->my_atoms[i].orig_id, x[i], b_prm[i], b[i] );

	fclose( fout );
	}


	void Print_Charges( reax_system *system )
	{
	int i;
	char fname[100];
	FILE *fout;

	sprintf( fname, "q.%d.out", system->my_rank );
	fout = fopen( fname, "w" );

	for( i = 0; i < system->n; ++i )
	fprintf( fout, "%6d %10.7f %10.7f %10.7f\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[i].s[0],
	system->my_atoms[i].t[0],
	system->my_atoms[i].q );

	fclose( fout );
	}


	void Print_Bonds( reax_system system, reax_list bonds, char *fname )
	{
	int i, j, pj;
	bond_data *pbond;
	bond_order_data *bo_ij;
	FILE *f = fopen( fname, "w" );

	for( i = 0; i < system->N; ++i )
	for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
	pbond = &(bonds->select.bond_list[pj]);
	bo_ij = &(pbond->bo_data);
	j = pbond->nbr;
	//fprintf( f, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
	// system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
	// pbond->d, bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
	fprintf( f, "%8d%8d %24.15f %24.15f\n",
	i, j,//system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
	pbond->d, bo_ij->BO );
	}

	fclose(f);
	}


	int fn_qsort_intcmp( const void a, const void b )
	{
	return( (int )a - (int )b );
	}

	void Print_Bond_List2( reax_system system, reax_list bonds, char *fname )
	{
	int i,j, nbr, pj;
	tagint id_i, id_j;
	FILE *f = fopen( fname, "w" );
	int temp[500];
	int num=0;

	for( i = 0; i < system->n; ++i ) {
	num=0;
	id_i = system->my_atoms[i].orig_id;
	fprintf( f, "%6d:", id_i);
	for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
	nbr = bonds->select.bond_list[pj].nbr;
	id_j = system->my_atoms[nbr].orig_id;
	if( id_i < id_j )
	temp[num++] = id_j;
	}

	qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
	for(j=0; j < num; j++)
	fprintf(f, "%6d", temp[j] );
	fprintf(f, "\n");
	}
	}


	void Print_Total_Force( reax_system system, simulation_data data,
	storage *workspace )
	{
	int i;

	fprintf( stderr, "step: %d\n", data->step );
	fprintf( stderr, "%6s\t%-38s\n", "atom", "atom.f[0,1,2]");

	for( i = 0; i < system->N; ++i )
	fprintf( stderr, "%6d %f %f %f\n",
	//"%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	workspace->f[i][0], workspace->f[i][1], workspace->f[i][2] );
	}

	void Output_Results( reax_system system, control_params control,
	simulation_data data, reax_list *lists,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	#if defined(LOG_PERFORMANCE)
	real t_elapsed, denom;
	#endif

	if((out_control->energy_update_freq > 0 &&
	data->step%out_control->energy_update_freq == 0) \|\|
	(out_control->write_steps > 0 &&
	data->step%out_control->write_steps == 0)){
	/* update system-wide energies */
	Compute_System_Energy( system, data, mpi_data->world );

	/* output energies */
	if( system->my_rank == MASTER_NODE &&
	out_control->energy_update_freq > 0 &&
	data->step % out_control->energy_update_freq == 0 ) {
	#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
	#if defined(PURE_REAX)
	fprintf( out_control->out,
	"%-6d%14.2f%14.2f%14.2f%11.2f%13.2f%13.5f\n",
	data->step, data->sys_en.e_tot, data->sys_en.e_pot,
	E_CONV * data->sys_en.e_kin, data->therm.T,
	system->big_box.V, data->iso_bar.P );
	fflush( out_control->out );
	#endif

	fprintf( out_control->pot,
	"%-6d%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f\n",
	data->step,
	data->sys_en.e_bond,
	data->sys_en.e_ov + data->sys_en.e_un, data->sys_en.e_lp,
	data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
	data->sys_en.e_hb,
	data->sys_en.e_tor, data->sys_en.e_con,
	data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
	fflush( out_control->pot );
	#else
	#if defined(PURE_REAX)
	fprintf( out_control->out,
	"%-6d%24.15e%24.15e%24.15e%13.5f%16.5f%13.5f\n",
	data->step, data->sys_en.e_tot, data->sys_en.e_pot,
	E_CONV * data->sys_en.e_kin, data->therm.T,
	system->big_box.V, data->iso_bar.P );
	fflush( out_control->out );
	#endif

	fprintf( out_control->pot,
	"%-6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
	data->step,
	data->sys_en.e_bond,
	data->sys_en.e_ov + data->sys_en.e_un, data->sys_en.e_lp,
	data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
	data->sys_en.e_hb,
	data->sys_en.e_tor, data->sys_en.e_con,
	data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
	fflush( out_control->pot );
	#endif //DEBUG

	#if defined(LOG_PERFORMANCE)
	t_elapsed = Get_Timing_Info( data->timing.total );
	if( data->step - data->prev_steps > 0 )
	denom = 1.0 / out_control->energy_update_freq;
	else denom = 1;

	fprintf( out_control->log, "%6d%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%6d\n",
	data->step,
	t_elapsed * denom,
	data->timing.comm * denom,
	data->timing.nbrs * denom,
	data->timing.init_forces * denom,
	data->timing.bonded * denom,
	data->timing.nonb * denom,
	data->timing.qEq * denom,
	(int)((data->timing.s_matvecs+data->timing.t_matvecs)*denom) );

	Reset_Timing( &(data->timing) );
	fflush( out_control->log );
	#endif //LOG_PERFORMANCE

	if( control->virial ){
	fprintf( out_control->prs,
	"%8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
	data->step,
	data->int_press[0], data->int_press[1], data->int_press[2],
	data->ext_press[0], data->ext_press[1], data->ext_press[2],
	data->kin_press );

	fprintf( out_control->prs,
	"%8s%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
	"",system->big_box.box_norms[0], system->big_box.box_norms[1],
	system->big_box.box_norms[2],
	data->tot_press[0], data->tot_press[1], data->tot_press[2],
	system->big_box.V );

	fflush( out_control->prs);
	}
	}

	/* write current frame */
	if( out_control->write_steps > 0 &&
	(data->step-data->prev_steps) % out_control->write_steps == 0 ) {
	Append_Frame( system, control, data, lists, out_control, mpi_data );
	}
	}

	#if defined(DEBUG)
	fprintf( stderr, "output_results... done\n" );
	#endif
	}


	#ifdef TEST_ENERGY
	void Debug_Marker_Bonded( output_controls *out_control, int step )
	{
	fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
	step, "atom1", "atom2", "bo", "ebond", "total" );
	fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
	step, "atom", "nlp", "elp", "total" );
	fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
	step, "atom", "eov", "total" );
	fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
	step, "atom", "eun", "total" );
	fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "atom3", "angle", "theta0",
	"bo(12)", "bo(23)", "eval", "total" );
	fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
	"epen", "total" );
	fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
	"ecoa", "total" );
	fprintf( out_control->ehb, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "atom3", "r(23)", "angle", "bo(12)",
	"ehb", "total" );
	fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "atom3", "atom4", "phi", "bo(23)",
	"etor", "total" );
	fprintf( out_control->econ,"step:%d\n%6s%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "atom3", "atom4",
	"phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
	}

	void Debug_Marker_Nonbonded( output_controls *out_control, int step )
	{
	fprintf( out_control->evdw, "step: %d\n%6s%6s%12s%12s%12s\n",
	step, "atom1", "atom2", "r12", "evdw", "total" );
	fprintf( out_control->ecou, "step: %d\n%6s%6s%12s%12s%12s%12s%12s\n",
	step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
	}

	#endif


	#ifdef TEST_FORCES
	void Dummy_Printer( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	}



	void Print_Bond_Orders( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i, pj, pk;
	bond_order_data *bo_ij;
	dbond_data *dbo_k;
	reax_list bonds = (lists) + BONDS;
	reax_list dBOs = (lists) + DBOS;

	/* bond orders */
	fprintf( out_control->fbo, "step: %d\n", data->step );
	fprintf( out_control->fbo, "%6s%6s%12s%12s%12s%12s%12s\n",
	"atom1", "atom2", "r_ij", "total_bo", "bo_s", "bo_p", "bo_pp" );

	for( i = 0; i < system->N; ++i )
	for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
	bo_ij = &(bonds->select.bond_list[pj].bo_data);
	fprintf( out_control->fbo,
	"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
	bonds->select.bond_list[pj].d,
	bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
	}


	/* derivatives of bond orders */
	fprintf( out_control->fdbo, "step: %d\n", data->step );
	fprintf( out_control->fdbo, "%6s%6s%6s%24s%24s%24s\n",
	"atom1", "atom2", "atom2", "dBO", "dBOpi", "dBOpi2" );
	for( i = 0; i < system->N; ++i )
	for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
	/* fprintf( out_control->fdbo, "%6d %6d\tstart: %6d\tend: %6d\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
	Start_Index( pj, dBOs ), End_Index( pj, dBOs ) ); */
	for( pk = Start_Index(pj, dBOs); pk < End_Index(pj, dBOs); ++pk ) {
	dbo_k = &(dBOs->select.dbo_list[pk]);
	fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
	system->my_atoms[dbo_k->wrt].orig_id,
	dbo_k->dBO[0], dbo_k->dBO[1], dbo_k->dBO[2] );

	fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
	system->my_atoms[dbo_k->wrt].orig_id,
	dbo_k->dBOpi[0], dbo_k->dBOpi[1], dbo_k->dBOpi[2] );

	fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
	system->my_atoms[dbo_k->wrt].orig_id,
	dbo_k->dBOpi2[0], dbo_k->dBOpi2[1], dbo_k->dBOpi2[2] );
	}
	}
	}


	void Print_Forces( FILE f, storage workspace, int N, int step )
	{
	int i;

	fprintf( f, "step: %d\n", step );
	for( i = 0; i < N; ++i )
	//fprintf( f, "%6d %23.15e %23.15e %23.15e\n",
	//fprintf( f, "%6d%12.6f%12.6f%12.6f\n",
	fprintf( f, "%6d %19.9e %19.9e %19.9e\n",
	workspace->id_all[i], workspace->f_all[i][0],
	workspace->f_all[i][1], workspace->f_all[i][2] );
	}


	void Print_Force_Files( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control,
	mpi_datatypes *mpi_data )
	{
	int i, d;

	Coll_ids_at_Master( system, workspace, mpi_data );

	Print_Bond_Orders( system, control, data, workspace, lists, out_control );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_be );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fbond, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_lp );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->flp, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_ov );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fov, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_un );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fun, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_ang );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fang, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_coa );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fcoa, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_pen );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fpen, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_tor );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->ftor, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_con );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fcon, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_hb );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fhb, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_vdw );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fvdw, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_ele );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fele, workspace, system->bigN, data->step );

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->ftot, workspace, system->bigN, data->step );

	for( i = 0; i < system->n; ++i ) {
	for( d = 0; d < 3; ++d )
	workspace->f_tot[i][d] = workspace->f_be[i][d] +
	workspace->f_lp[i][d]+workspace->f_ov[i][d]+workspace->f_un[i][d] +
	workspace->f_ang[i][d]+workspace->f_pen[i][d]+workspace->f_coa[i][d] +
	workspace->f_tor[i][d]+workspace->f_con[i][d] +
	workspace->f_vdw[i][d]+workspace->f_ele[i][d] +
	workspace->f_hb[i][d];
	}

	Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_tot );
	if( system->my_rank == MASTER_NODE )
	Print_Forces( out_control->fcomp, workspace, system->bigN, data->step );
	}
	#endif


	#if defined(TEST_FORCES) \|\| defined(TEST_ENERGY)

	void Print_Far_Neighbors_List( reax_system system, reax_list *lists,
	control_params control, simulation_data data,
	output_controls *out_control )
	{
	int i, j, nbr, natoms;
	tagint id_i, id_j;
	int num=0;
	int temp[500];
	reax_list *far_nbrs;

	far_nbrs = (*lists) + FAR_NBRS;
	fprintf( out_control->flist, "step: %d\n", data->step );
	fprintf( out_control->flist, "%6s\t%-38s\n", "atom", "Far_nbrs_list");


	natoms = system->n;
	for( i = 0; i < natoms; ++i ) {
	id_i = system->my_atoms[i].orig_id;
	fprintf( out_control->flist, "%6d:",id_i);
	num=0;

	for( j = Start_Index(i,far_nbrs); j < End_Index(i,far_nbrs); ++j ) {
	nbr = far_nbrs->select.far_nbr_list[j].nbr;
	id_j = system->my_atoms[nbr].orig_id;
	temp[num++] = id_j;
	}

	qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
	for(j=0; j < num; j++)
	fprintf(out_control->flist, "%6d",temp[j]);
	fprintf( out_control->flist, "\n");
	}
	}

	void Print_Bond_List( reax_system system, control_params control,
	simulation_data data, reax_list *lists,
	output_controls *out_control)
	{
	int i,j, nbr, pj;
	tagint id_i, id_j;
	reax_list bonds = (lists) + BONDS;

	int temp[500];
	int num=0;

	fprintf( out_control->blist, "step: %d\n", data->step );
	fprintf( out_control->blist, "%6s\t%-38s\n", "atom", "Bond_list");

	/* bond list */
	for( i = 0; i < system->n; ++i ) {
	num=0;
	id_i = system->my_atoms[i].orig_id;
	fprintf( out_control->blist, "%6d:", id_i);
	for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
	nbr = bonds->select.bond_list[pj].nbr;
	id_j = system->my_atoms[nbr].orig_id;
	if( id_i < id_j )
	temp[num++] = id_j;
	}

	qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
	for(j=0; j < num; j++)
	fprintf(out_control->blist, "%6d",temp[j]);
	fprintf(out_control->blist, "\n");
	}
	}


	#endif


	#ifdef OLD_VERSION
	void Print_Init_Atoms( reax_system system, storage workspace )
	{
	int i;

	fprintf( stderr, "p%d had %d atoms\n",
	system->my_rank, workspace->init_cnt );

	for( i = 0; i < workspace->init_cnt; ++i )
	fprintf( stderr, "p%d, atom%d: %d %s %8.3f %8.3f %8.3f\n",
	system->my_rank, i,
	workspace->init_atoms[i].type, workspace->init_atoms[i].name,
	workspace->init_atoms[i].x[0],
	workspace->init_atoms[i].x[1],
	workspace->init_atoms[i].x[2] );
	}
	#endif //OLD_VERSION


	/void Print_Bond_Forces( reax_system system, control_params *control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	fprintf( out_control->fbond, "step: %d\n", data->step );
	fprintf( out_control->fbond, "%6s%24s%24s%24s\n",
	"atom", "f_be[0]", "f_be[1]", "f_be[2]" );

	for( i = 0; i < system->bigN; ++i )
	fprintf(out_control->fbond, "%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	workspace->f_all[i][0], workspace->f_all[i][1],
	workspace->f_all[i][2]);
	}

	void Print_LonePair_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	fprintf( out_control->flp, "step: %d\n", data->step );
	fprintf( out_control->flp, "%6s%24s\n", "atom", "f_lonepair" );

	for( i = 0; i < system->bigN; ++i )
	fprintf(out_control->flp, "%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	workspace->f_all[i][0], workspace->f_all[i][1],
	workspace->f_all[i][2]);
	}


	void Print_OverCoor_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	fprintf( out_control->fov, "step: %d\n", data->step );
	fprintf( out_control->fov, "%6s%-38s%-38s%-38s\n",
	"atom","f_over[0]", "f_over[1]", "f_over[2]" );

	for( i = 0; i < system->bigN; ++i )
	fprintf( out_control->fov,
	"%6d %24.15e%24.15e%24.15e 0 0 0\n",
	system->my_atoms[i].orig_id,
	workspace->f_all[i][0], workspace->f_all[i][1],
	workspace->f_all[i][2] );
	}


	void Print_UnderCoor_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	fprintf( out_control->fun, "step: %d\n", data->step );
	fprintf( out_control->fun, "%6s%-38s%-38s%-38s\n",
	"atom","f_under[0]", "f_under[1]", "f_under[2]" );

	for( i = 0; i < system->bigN; ++i )
	fprintf( out_control->fun,
	"%6d %24.15e%24.15e%24.15e 0 0 0\n",
	system->my_atoms[i].orig_id,
	workspace->f_all[i][0], workspace->f_all[i][1],
	workspace->f_all[i][2] );
	}


	void Print_ValAngle_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int j;

	fprintf( out_control->f3body, "step: %d\n", data->step );
	fprintf( out_control->f3body, "%6s%-37s%-37s%-37s%-38s\n",
	"atom", "3-body total", "f_ang", "f_pen", "f_coa" );

	for( j = 0; j < system->N; ++j ){
	if( rvec_isZero(workspace->f_pen[j]) && rvec_isZero(workspace->f_coa[j]) )
	fprintf( out_control->f3body,
	"%6d %24.15e%24.15e%24.15e 0 0 0 0 0 0\n",
	system->my_atoms[j].orig_id,
	workspace->f_ang[j][0], workspace->f_ang[j][1],
	workspace->f_ang[j][2] );
	else if( rvec_isZero(workspace->f_coa[j]) )
	fprintf( out_control->f3body,
	"%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e " \
	"%24.15e%24.15e%24.15e\n",
	system->my_atoms[j].orig_id,
	workspace->f_ang[j][0] + workspace->f_pen[j][0],
	workspace->f_ang[j][1] + workspace->f_pen[j][1],
	workspace->f_ang[j][2] + workspace->f_pen[j][2],
	workspace->f_ang[j][0], workspace->f_ang[j][1],
	workspace->f_ang[j][2],
	workspace->f_pen[j][0], workspace->f_pen[j][1],
	workspace->f_pen[j][2] );
	else{
	fprintf( out_control->f3body, "%6d %24.15e%24.15e%24.15e ",
	system->my_atoms[j].orig_id,
	workspace->f_ang[j][0] + workspace->f_pen[j][0] +
	workspace->f_coa[j][0],
	workspace->f_ang[j][1] + workspace->f_pen[j][1] +
	workspace->f_coa[j][1],
	workspace->f_ang[j][2] + workspace->f_pen[j][2] +
	workspace->f_coa[j][2] );

	fprintf( out_control->f3body,
	"%24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
	"%24.15e%24.15e%24.15e\n",
	workspace->f_ang[j][0], workspace->f_ang[j][1],
	workspace->f_ang[j][2],
	workspace->f_pen[j][0], workspace->f_pen[j][1],
	workspace->f_pen[j][2],
	workspace->f_coa[j][0], workspace->f_coa[j][1],
	workspace->f_coa[j][2] );
	}
	}
	}


	void Print_Hydrogen_Bond_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control)
	{
	int j;

	fprintf( out_control->fhb, "step: %d\n", data->step );
	fprintf( out_control->fhb, "%6s\t%-38s\n", "atom", "f_hb[0,1,2]" );

	for( j = 0; j < system->N; ++j )
	fprintf(out_control->fhb, "%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[j].orig_id,
	workspace->f_hb[j][0],
	workspace->f_hb[j][1],
	workspace->f_hb[j][2] );
	}


	void Print_Four_Body_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int j;

	fprintf( out_control->f4body, "step: %d\n", data->step );
	fprintf( out_control->f4body, "%6s\t%-38s%-38s%-38s\n",
	"atom", "4-body total", "f_tor", "f_con" );

	for( j = 0; j < system->N; ++j ){
	if( !rvec_isZero( workspace->f_con[j] ) )
	fprintf( out_control->f4body,
	"%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
	"%24.15e%24.15e%24.15e\n",
	system->my_atoms[j].orig_id,
	workspace->f_tor[j][0] + workspace->f_con[j][0],
	workspace->f_tor[j][1] + workspace->f_con[j][1],
	workspace->f_tor[j][2] + workspace->f_con[j][2],
	workspace->f_tor[j][0], workspace->f_tor[j][1],
	workspace->f_tor[j][2],
	workspace->f_con[j][0], workspace->f_con[j][1],
	workspace->f_con[j][2] );
	else
	fprintf( out_control->f4body,
	"%6d %24.15e%24.15e%24.15e 0 0 0\n",
	system->my_atoms[j].orig_id, workspace->f_tor[j][0],
	workspace->f_tor[j][1], workspace->f_tor[j][2] );
	}

	}


	void Print_vdW_Coulomb_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	return;

	fprintf( out_control->fnonb, "step: %d\n", data->step );
	fprintf( out_control->fnonb, "%6s\t%-38s%-38s%-38s\n",
	"atom", "nonbonded_total[0,1,2]", "f_vdw[0,1,2]", "f_ele[0,1,2]" );

	for( i = 0; i < system->N; ++i )
	fprintf( out_control->fnonb,
	"%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	workspace->f_vdw[i][0] + workspace->f_ele[i][0],
	workspace->f_vdw[i][1] + workspace->f_ele[i][1],
	workspace->f_vdw[i][2] + workspace->f_ele[i][2],
	workspace->f_vdw[i][0],
	workspace->f_vdw[i][1],
	workspace->f_vdw[i][2],
	workspace->f_ele[i][0],
	workspace->f_ele[i][1],
	workspace->f_ele[i][2] );
	}


	void Print_Total_Force( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	return;

	fprintf( out_control->ftot, "step: %d\n", data->step );
	fprintf( out_control->ftot, "%6s\t%-38s\n", "atom", "atom.f[0,1,2]");

	for( i = 0; i < system->n; ++i )
	fprintf( out_control->ftot, "%6d%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[i].f[0],
	system->my_atoms[i].f[1],
	system->my_atoms[i].f[2] );
	}


	void Compare_Total_Forces( reax_system system, control_params control,
	simulation_data data, storage workspace,
	reax_list *lists, output_controls out_control )
	{
	int i;

	return;

	fprintf( out_control->ftot2, "step: %d\n", data->step );
	fprintf( out_control->ftot2, "%6s\t%-38s%-38s\n",
	"atom", "f_total[0,1,2]", "test_force_total[0,1,2]" );

	for( i = 0; i < system->N; ++i )
	fprintf( out_control->ftot2, "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
	system->my_atoms[i].orig_id,
	system->my_atoms[i].f[0],
	system->my_atoms[i].f[1],
	system->my_atoms[i].f[2],
	workspace->f_be[i][0] + workspace->f_lp[i][0] +
	workspace->f_ov[i][0] + workspace->f_un[i][0] +
	workspace->f_ang[i][0]+ workspace->f_pen[i][0]+
	workspace->f_coa[i][0]+ + workspace->f_hb[i][0] +
	workspace->f_tor[i][0] + workspace->f_con[i][0] +
	workspace->f_vdw[i][0] + workspace->f_ele[i][0],
	workspace->f_be[i][1] + workspace->f_lp[i][1] +
	workspace->f_ov[i][1] + workspace->f_un[i][1] +
	workspace->f_ang[i][1]+ workspace->f_pen[i][1]+
	workspace->f_coa[i][1]+ + workspace->f_hb[i][1] +
	workspace->f_tor[i][1] + workspace->f_con[i][1] +
	workspace->f_vdw[i][1] + workspace->f_ele[i][1],
	workspace->f_be[i][2] + workspace->f_lp[i][2] +
	workspace->f_ov[i][2] + workspace->f_un[i][2] +
	workspace->f_ang[i][2]+ workspace->f_pen[i][2] +
	workspace->f_coa[i][2]+ + workspace->f_hb[i][2] +
	workspace->f_tor[i][2] + workspace->f_con[i][2] +
	workspace->f_vdw[i][2] + workspace->f_ele[i][2] );
	}*/

	/*void Init_Force_Test_Functions( )
	{
	Print_Interactions[0] = Print_Bond_Orders;
	Print_Interactions[1] = Print_Bond_Forces;
	Print_Interactions[2] = Print_LonePair_Forces;
	Print_Interactions[3] = Print_OverUnderCoor_Forces;
	Print_Interactions[4] = Print_Three_Body_Forces;
	Print_Interactions[5] = Print_Four_Body_Forces;
	Print_Interactions[6] = Print_Hydrogen_Bond_Forces;
	Print_Interactions[7] = Print_vdW_Coulomb_Forces;
	Print_Interactions[8] = Print_Total_Force;
	Print_Interactions[9] = Compare_Total_Forces;
	}*/

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