reaxc_traj.cpp
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Created: Fri, Jul 5, 20:13

reaxc_traj.cpp
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	/*----------------------------------------------------------------------
	PuReMD - Purdue ReaxFF Molecular Dynamics Program

	Copyright (2010) Purdue University
	Hasan Metin Aktulga, haktulga@cs.purdue.edu
	Joseph Fogarty, jcfogart@mail.usf.edu
	Sagar Pandit, pandit@usf.edu
	Ananth Y Grama, ayg@cs.purdue.edu

	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 "reaxc_types.h"
	#if defined(PURE_REAX)
	#include "traj.h"
	#include "list.h"
	#include "tool_box.h"
	#elif defined(LAMMPS_REAX)
	#include "reaxc_traj.h"
	#include "reaxc_list.h"
	#include "reaxc_tool_box.h"
	#endif


	#if defined(PURE_REAX)
	int Set_My_Trajectory_View( MPI_File trj, int offset, MPI_Datatype etype,
	MPI_Comm comm, int my_rank, int my_n, int big_n )
	{
	int my_disp;
	int length[3];
	MPI_Aint line_len;
	MPI_Aint disp[3];
	MPI_Datatype type[3];
	MPI_Datatype view;

	/* line length inferred from etype */
	MPI_Type_extent( etype, &line_len );
	line_len /= sizeof(char);

	/* determine where to start writing into the mpi file */
	my_disp = SumScan( my_n, my_rank, MASTER_NODE, comm );
	my_disp -= my_n;

	/* create atom_info_view */
	length[0] = 1;
	length[1] = my_n;
	length[2] = 1;
	disp[0] = 0;
	disp[1] = line_len * my_disp;
	disp[2] = line_len * big_n;
	type[0] = MPI_LB;
	type[1] = etype;
	type[2] = MPI_UB;

	MPI_Type_struct( 3, length, disp, type, &view );
	MPI_Type_commit( &view );

	MPI_File_set_view( trj, offset, etype, view, "native", MPI_INFO_NULL );

	return my_disp;
	}
	#endif


	int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
	MPI_Comm comm )
	{
	if( out_control->buffer_len > 0 )
	free( out_control->buffer );

	out_control->buffer_len = (int)(req_space*SAFE_ZONE);
	out_control->buffer = (char) malloc(out_control->buffer_lensizeof(char));
	if( out_control->buffer == NULL ) {
	fprintf( stderr,
	"insufficient memory for required buffer size %d. terminating!\n",
	(int) (req_space*SAFE_ZONE) );
	MPI_Abort( comm, INSUFFICIENT_MEMORY );
	}

	return SUCCESS;
	}


	void Write_Skip_Line( output_controls out_control, mpi_datatypes mpi_data,
	int my_rank, int skip, int num_section )
	{
	#if defined(PURE_REAX)
	MPI_Status status;

	if( out_control->traj_method == MPI_TRAJ ) {
	MPI_File_set_view( out_control->trj, out_control->trj_offset,
	mpi_data->header_line, mpi_data->header_line,
	"native", MPI_INFO_NULL );
	if( my_rank == MASTER_NODE ) {
	sprintf( out_control->line, INT2_LINE, "chars_to_skip_section:",
	skip, num_section );
	MPI_File_write( out_control->trj, out_control->line, 1,
	mpi_data->header_line, &status );
	}
	out_control->trj_offset += HEADER_LINE_LEN;
	}
	else {
	if( my_rank == MASTER_NODE )
	fprintf( out_control->strj, INT2_LINE,
	"chars_to_skip_section:", skip, num_section );
	}
	#elif defined(LAMMPS_REAX)
	if( my_rank == MASTER_NODE )
	fprintf( out_control->strj, INT2_LINE,
	"chars_to_skip_section:", skip, num_section );
	#endif

	}


	int Write_Header( reax_system system, control_params control,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	int num_hdr_lines, my_hdr_lines, buffer_req;
	MPI_Status status;
	char ensembles[ens_N][25] = { "NVE", "NVT", "fully flexible NPT",
	"semi isotropic NPT", "isotropic NPT" };
	char reposition[3][25] = { "fit to periodic box", "CoM to center of box",
	"CoM to origin" };
	char t_regime[3][25] = { "T-coupling only", "step-wise", "constant slope" };

	char traj_methods[TF_N][10] = { "custom", "xyz" };
	char atom_formats[8][40] = { "none", "invalid", "invalid", "invalid",
	"xyz_q",
	"xyz_q_fxfyfz",
	"xyz_q_vxvyvz",
	"detailed_atom_info" };
	char bond_formats[3][30] = { "none",
	"basic_bond_info",
	"detailed_bond_info" };
	char angle_formats[2][30] = { "none", "basic_angle_info" };

	/* set header lengths */
	num_hdr_lines = NUM_HEADER_LINES;
	my_hdr_lines = num_hdr_lines * ( system->my_rank == MASTER_NODE );
	buffer_req = my_hdr_lines * HEADER_LINE_LEN;
	if( buffer_req > out_control->buffer_len * DANGER_ZONE )
	Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );

	/* only the master node writes into trajectory header */
	if( system->my_rank == MASTER_NODE ) {
	/* clear the contents of line & buffer */
	out_control->line[0] = 0;
	out_control->buffer[0] = 0;

	/* to skip the header */
	sprintf( out_control->line, INT_LINE, "chars_to_skip_header:",
	(num_hdr_lines-1) * HEADER_LINE_LEN );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* general simulation info */
	sprintf( out_control->line, STR_LINE, "simulation_name:",
	out_control->traj_title );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "number_of_atoms:", system->bigN );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "ensemble_type:",
	ensembles[ control->ensemble ] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "number_of_steps:",
	control->nsteps );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "timestep_length_(in_fs):",
	control->dt * 1000 );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* restart info */
	sprintf( out_control->line, STR_LINE, "is_this_a_restart?:",
	(control->restart ? "yes" : "no") );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	//sprintf( out_control->line, STR_LINE, "restarted_from_file:",
	// (control->restart ? control->restart_from : "NA") );
	//strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	//sprintf( out_control->line, STR_LINE, "kept_restart_velocities?:",
	// (control->restart ? (control->random_vel ? "no":"yes"):"NA") );
	//strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "write_restart_files?:",
	((out_control->restart_freq > 0) ? "yes" : "no") );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "frequency_to_write_restarts:",
	out_control->restart_freq );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* preferences */
	sprintf( out_control->line, STR_LINE, "tabulate_long_range_intrs?:",
	(control->tabulate ? "yes" : "no") );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "table_size:", control->tabulate );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "restrict_bonds?:",
	(control->restrict_bonds ? "yes" : "no") );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "bond_restriction_length:",
	control->restrict_bonds );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "reposition_atoms?:",
	reposition[control->reposition_atoms] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "remove_CoM_velocity?:",
	(control->ensemble==NVE) ? 0 : control->remove_CoM_vel);
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );


	/* cut-off values */
	sprintf( out_control->line, REAL_LINE, "bonded_intr_dist_cutoff:",
	control->bond_cut );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "nonbonded_intr_dist_cutoff:",
	control->nonb_cut );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "hbond_dist_cutoff:",
	control->hbond_cut );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "reax_bond_threshold:",
	control->bo_cut );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "physical_bond_threshold:",
	control->bg_cut );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "valence_angle_threshold:",
	control->thb_cut );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, SCI_LINE, "QEq_tolerance:", control->q_err );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* temperature controls */
	sprintf( out_control->line, REAL_LINE, "initial_temperature:",
	control->T_init );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "target_temperature:",
	control->T_final );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "thermal_inertia:",
	control->Tau_T );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "temperature_regime:",
	t_regime[ control->T_mode ] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "temperature_change_rate_(K/ps):",
	control->T_rate / control->T_freq );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* pressure controls */
	sprintf( out_control->line, REAL3_LINE, "target_pressure_(GPa):",
	control->P[0], control->P[1], control->P[2] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL3_LINE, "virial_inertia:",
	control->Tau_P[0], control->Tau_P[1], control->Tau_P[2] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* trajectory */
	sprintf( out_control->line, INT_LINE, "energy_dumping_freq:",
	out_control->energy_update_freq );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "trajectory_dumping_freq:",
	out_control->write_steps );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "compress_trajectory_output?:",
	(out_control->traj_compress ? "yes" : "no") );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "trajectory_format:",
	traj_methods[ out_control->traj_method ] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "atom_info:",
	atom_formats[ out_control->atom_info ] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "bond_info:",
	bond_formats[ out_control->bond_info ] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, STR_LINE, "angle_info:",
	angle_formats[ out_control->angle_info ] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* analysis */
	//sprintf( out_control->line, STR_LINE, "molecular_analysis:",
	// (control->molec_anal ? "yes" : "no") );
	//strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, INT_LINE, "molecular_analysis_frequency:",
	control->molecular_analysis );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
	}

	/* dump out the buffer */
	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ) {
	out_control->trj_offset = 0;
	Set_My_Trajectory_View( out_control->trj,
	out_control->trj_offset, mpi_data->header_line,
	mpi_data->world, system->my_rank,
	my_hdr_lines, num_hdr_lines );
	MPI_File_write_all( out_control->trj, out_control->buffer,
	num_hdr_lines, mpi_data->header_line, &status );
	out_control->trj_offset = (num_hdr_lines) * HEADER_LINE_LEN;
	}
	else {
	if( system->my_rank == MASTER_NODE )
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	#elif defined(LAMMPS_REAX)
	if( system->my_rank == MASTER_NODE )
	fprintf( out_control->strj, "%s", out_control->buffer );
	#endif

	return SUCCESS;
	}


	int Write_Init_Desc( reax_system system, control_params control,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	int i, me, np, cnt, buffer_len, buffer_req;
	reax_atom *p_atom;
	//MPI_Request request;
	MPI_Status status;

	me = system->my_rank;
	np = system->wsize;

	/* skip info */
	Write_Skip_Line( out_control, mpi_data, me,
	system->bigN * INIT_DESC_LEN, system->bigN );

	if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE )
	buffer_req = system->bigN * INIT_DESC_LEN + 1;
	else buffer_req = system->n * INIT_DESC_LEN + 1;

	if( buffer_req > out_control->buffer_len * DANGER_ZONE )
	Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );

	out_control->line[0] = 0;
	out_control->buffer[0] = 0;
	for( i = 0; i < system->n; ++i ) {
	p_atom = &( system->my_atoms[i] );
	sprintf( out_control->line, INIT_DESC,
	p_atom->orig_id, p_atom->type, p_atom->name,
	system->reax_param.sbp[ p_atom->type ].mass );
	strncpy( out_control->buffer + i*INIT_DESC_LEN,
	out_control->line, INIT_DESC_LEN+1 );
	}

	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ) {
	Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
	mpi_data->init_desc_line, mpi_data->world,
	me, system->n, system->bigN );
	MPI_File_write( out_control->trj, out_control->buffer, system->n,
	mpi_data->init_desc_line, &status );
	out_control->trj_offset += system->bigN * INIT_DESC_LEN;
	}
	else{
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np * INIT_DESCS + me, mpi_data->world );
	else{
	buffer_len = system->n * INIT_DESC_LEN;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	}
	#elif defined(LAMMPS_REAX)
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np * INIT_DESCS + me, mpi_data->world );
	else{
	buffer_len = system->n * INIT_DESC_LEN;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	#endif

	return SUCCESS;
	}


	int Init_Traj( reax_system system, control_params control,
	output_controls out_control, mpi_datatypes mpi_data,
	char *msg )
	{
	char fname[MAX_STR];
	int atom_line_len[ NR_OPT_ATOM ] = { 0, 0, 0, 0,
	ATOM_BASIC_LEN, ATOM_wV_LEN,
	ATOM_wF_LEN, ATOM_FULL_LEN };
	int bond_line_len[ NR_OPT_BOND ] = { 0, BOND_BASIC_LEN, BOND_FULL_LEN };
	int angle_line_len[ NR_OPT_ANGLE ] = { 0, ANGLE_BASIC_LEN };

	/* generate trajectory name */
	sprintf( fname, "%s.trj", control->sim_name );

	/* how should I write atoms? */
	out_control->atom_line_len = atom_line_len[ out_control->atom_info ];
	out_control->write_atoms = ( out_control->atom_line_len ? 1 : 0 );
	/* bonds? */
	out_control->bond_line_len = bond_line_len[ out_control->bond_info ];
	out_control->write_bonds = ( out_control->bond_line_len ? 1 : 0 );
	/* angles? */
	out_control->angle_line_len = angle_line_len[ out_control->angle_info ];
	out_control->write_angles = ( out_control->angle_line_len ? 1 : 0 );

	/* allocate line & buffer space */
	out_control->line = (char*) calloc( MAX_TRJ_LINE_LEN + 1, sizeof(char) );
	out_control->buffer_len = 0;
	out_control->buffer = NULL;

	/* fprintf( stderr, "p%d: init_traj: atom_line_len = %d " \
	"bond_line_len = %d, angle_line_len = %d\n" \
	"max_line = %d, max_buffer_size = %d\n",
	system->my_rank, out_control->atom_line_len,
	out_control->bond_line_len, out_control->angle_line_len,
	MAX_TRJ_LINE_LEN, MAX_TRJ_BUFFER_SIZE ); */

	/* write trajectory header and atom info, if applicable */
	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ) {
	/* attemp to delete the file to get rid of remnants of previous runs */
	if( system->my_rank == MASTER_NODE ) {
	MPI_File_delete( fname, MPI_INFO_NULL );
	}

	/* open a fresh trajectory file */
	if( MPI_File_open( mpi_data->world, fname,
	MPI_MODE_CREATE \| MPI_MODE_WRONLY, MPI_INFO_NULL,
	&(out_control->trj) ) ) {
	strcpy( msg, "init_traj: unable to open trajectory file" );
	return FAILURE;
	}

	/* build the mpi structs for trajectory */
	/* header_line */
	MPI_Type_contiguous( HEADER_LINE_LEN, MPI_CHAR, &(mpi_data->header_line) );
	MPI_Type_commit( &(mpi_data->header_line) );
	/* init_desc_line */
	MPI_Type_contiguous( INIT_DESC_LEN, MPI_CHAR, &(mpi_data->init_desc_line) );
	MPI_Type_commit( &(mpi_data->init_desc_line) );
	/* atom */
	MPI_Type_contiguous( out_control->atom_line_len, MPI_CHAR,
	&(mpi_data->atom_line) );
	MPI_Type_commit( &(mpi_data->atom_line) );
	/* bonds */
	MPI_Type_contiguous( out_control->bond_line_len, MPI_CHAR,
	&(mpi_data->bond_line) );
	MPI_Type_commit( &(mpi_data->bond_line) );
	/* angles */
	MPI_Type_contiguous( out_control->angle_line_len, MPI_CHAR,
	&(mpi_data->angle_line) );
	MPI_Type_commit( &(mpi_data->angle_line) );
	}
	else if( out_control->traj_method == REG_TRAJ) {
	if( system->my_rank == MASTER_NODE )
	out_control->strj = fopen( fname, "w" );
	}
	else {
	strcpy( msg, "init_traj: unknown trajectory option" );
	return FAILURE;
	}
	#elif defined(LAMMPS_REAX)
	if( out_control->traj_method == REG_TRAJ) {
	if( system->my_rank == MASTER_NODE )
	out_control->strj = fopen( fname, "w" );
	}
	else {
	strcpy( msg, "init_traj: unknown trajectory option" );
	return FAILURE;
	}
	#endif


	#if defined(DEBUG_FOCUS)
	fprintf( stderr, "p%d: initiated trajectory\n", system->my_rank );
	#endif
	Write_Header( system, control, out_control, mpi_data );
	#if defined(DEBUG_FOCUS)
	fprintf( stderr, "p%d: header written\n", system->my_rank );
	#endif
	Write_Init_Desc( system, control, out_control, mpi_data );
	#if defined(DEBUG_FOCUS)
	fprintf( stderr, "p%d: atom descriptions written\n", system->my_rank );
	#endif

	return SUCCESS;
	}


	int Write_Frame_Header( reax_system system, control_params control,
	simulation_data data, output_controls out_control,
	mpi_datatypes *mpi_data )
	{
	int me, num_frm_hdr_lines, my_frm_hdr_lines, buffer_req;
	MPI_Status status;

	me = system->my_rank;
	/* frame header lengths */
	num_frm_hdr_lines = 22;
	my_frm_hdr_lines = num_frm_hdr_lines * ( me == MASTER_NODE );
	buffer_req = my_frm_hdr_lines * HEADER_LINE_LEN;
	if( buffer_req > out_control->buffer_len * DANGER_ZONE )
	Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );

	/* only the master node writes into trajectory header */
	if( me == MASTER_NODE ) {
	/* clear the contents of line & buffer */
	out_control->line[0] = 0;
	out_control->buffer[0] = 0;

	/* skip info */
	sprintf( out_control->line, INT_LINE, "chars_to_skip_frame_header:",
	(num_frm_hdr_lines - 1) * HEADER_LINE_LEN );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	/* step & time */
	sprintf( out_control->line, INT_LINE, "step:", data->step );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "time_in_ps:",
	data->step * control->dt );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );


	/* box info */
	sprintf( out_control->line, REAL_LINE, "volume:", system->big_box.V );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL3_LINE, "box_dimensions:",
	system->big_box.box_norms[0],
	system->big_box.box_norms[1],
	system->big_box.box_norms[2] );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL3_LINE,
	"coordinate_angles:", 90.0, 90.0, 90.0 );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );


	/* system T and P */
	sprintf( out_control->line, REAL_LINE, "temperature:", data->therm.T );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "pressure:",
	(control->ensemble==iNPT) ?
	data->iso_bar.P : data->flex_bar.P_scalar );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );


	/* energies */
	sprintf( out_control->line, REAL_LINE, "total_energy:",
	data->sys_en.e_tot );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "total_kinetic:",
	data->sys_en.e_kin );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "total_potential:",
	data->sys_en.e_pot );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "bond_energy:",
	data->sys_en.e_bond );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "atom_energy:",
	data->sys_en.e_ov + data->sys_en.e_un );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "lone_pair_energy:",
	data->sys_en.e_lp );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "valence_angle_energy:",
	data->sys_en.e_ang + data->sys_en.e_pen );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "3-body_conjugation:",
	data->sys_en.e_coa );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "hydrogen_bond_energy:",
	data->sys_en.e_hb );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "torsion_angle_energy:",
	data->sys_en.e_tor );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "4-body_conjugation:",
	data->sys_en.e_con );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "vdWaals_energy:",
	data->sys_en.e_vdW );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "electrostatics_energy:",
	data->sys_en.e_ele );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );

	sprintf( out_control->line, REAL_LINE, "polarization_energy:",
	data->sys_en.e_pol );
	strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
	}

	/* dump out the buffer */
	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ) {
	Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
	mpi_data->header_line, mpi_data->world,
	me, my_frm_hdr_lines, num_frm_hdr_lines );

	MPI_File_write_all(out_control->trj, out_control->buffer, my_frm_hdr_lines,
	mpi_data->header_line, &status);
	out_control->trj_offset += (num_frm_hdr_lines) * HEADER_LINE_LEN;
	}
	else {
	if( system->my_rank == MASTER_NODE )
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	#elif defined(LAMMPS_REAX)
	if( system->my_rank == MASTER_NODE )
	fprintf( out_control->strj, "%s", out_control->buffer );
	#endif

	return SUCCESS;
	}



	int Write_Atoms( reax_system system, control_params control,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	int i, me, np, line_len, buffer_len, buffer_req, cnt;
	MPI_Status status;
	reax_atom *p_atom;

	me = system->my_rank;
	np = system->wsize;
	line_len = out_control->atom_line_len;

	Write_Skip_Line( out_control, mpi_data, me,
	system->bigN*line_len, system->bigN );

	if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE )
	buffer_req = system->bigN * line_len + 1;
	else buffer_req = system->n * line_len + 1;

	if( buffer_req > out_control->buffer_len * DANGER_ZONE )
	Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );

	/* fill in buffer */
	out_control->line[0] = 0;
	out_control->buffer[0] = 0;
	for( i = 0; i < system->n; ++i ) {
	p_atom = &( system->my_atoms[i] );

	switch( out_control->atom_info ) {
	case OPT_ATOM_BASIC:
	sprintf( out_control->line, ATOM_BASIC,
	p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
	p_atom->q );
	break;
	case OPT_ATOM_wF:
	sprintf( out_control->line, ATOM_wF,
	p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
	p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q );
	break;
	case OPT_ATOM_wV:
	sprintf( out_control->line, ATOM_wV,
	p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
	p_atom->v[0], p_atom->v[1], p_atom->v[2], p_atom->q );
	break;
	case OPT_ATOM_FULL:
	sprintf( out_control->line, ATOM_FULL,
	p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
	p_atom->v[0], p_atom->v[1], p_atom->v[2],
	p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q );
	break;
	default:
	fprintf( stderr,
	"write_traj_atoms: unknown atom trajectroy format!\n");
	MPI_Abort( mpi_data->world, UNKNOWN_OPTION );
	}

	strncpy( out_control->buffer + i*line_len, out_control->line, line_len+1 );
	}

	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ) {
	Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
	mpi_data->atom_line, mpi_data->world,
	me, system->n, system->bigN );
	MPI_File_write( out_control->trj, out_control->buffer, system->n,
	mpi_data->atom_line, &status );
	out_control->trj_offset += (system->bigN) * out_control->atom_line_len;
	}
	else{
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np*ATOM_LINES+me, mpi_data->world );
	else{
	buffer_len = system->n * line_len;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	}
	#elif defined(LAMMPS_REAX)
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np*ATOM_LINES+me, mpi_data->world );
	else{
	buffer_len = system->n * line_len;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	#endif

	return SUCCESS;
	}


	int Write_Bonds(reax_system system, control_params control, reax_list *bonds,
	output_controls out_control, mpi_datatypes mpi_data)
	{
	int i, j, pj, me, np;
	int my_bonds, num_bonds;
	int line_len, buffer_len, buffer_req, cnt;
	MPI_Status status;
	bond_data *bo_ij;

	me = system->my_rank;
	np = system->wsize;
	line_len = out_control->bond_line_len;

	/* count the number of bonds I will write */
	my_bonds = 0;
	for( i=0; i < system->n; ++i )
	for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
	j = bonds->select.bond_list[pj].nbr;
	if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id &&
	bonds->select.bond_list[pj].bo_data.BO >= control->bg_cut )
	++my_bonds;
	}
	/* allreduce - total number of bonds */
	MPI_Allreduce( &my_bonds, &num_bonds, 1, MPI_INT, MPI_SUM, mpi_data->world );

	Write_Skip_Line( out_control, mpi_data, me, num_bonds*line_len, num_bonds );

	if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE )
	buffer_req = num_bonds * line_len + 1;
	else buffer_req = my_bonds * line_len + 1;

	if( buffer_req > out_control->buffer_len * DANGER_ZONE )
	Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );

	/* fill in the buffer */
	my_bonds = 0;
	out_control->line[0] = 0;
	out_control->buffer[0] = 0;
	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] );
	j = bo_ij->nbr;

	if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id &&
	bo_ij->bo_data.BO >= control->bg_cut ) {
	switch( out_control->bond_info ) {
	case OPT_BOND_BASIC:
	sprintf( out_control->line, BOND_BASIC,
	system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
	bo_ij->d, bo_ij->bo_data.BO );
	break;
	case OPT_BOND_FULL:
	sprintf( out_control->line, BOND_FULL,
	system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
	bo_ij->d, bo_ij->bo_data.BO, bo_ij->bo_data.BO_s,
	bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 );
	break;
	default:
	fprintf(stderr, "write_traj_bonds: FATAL! invalid bond_info option");
	MPI_Abort( mpi_data->world, UNKNOWN_OPTION );
	}

	strncpy( out_control->buffer + my_bonds*line_len,
	out_control->line, line_len+1 );
	++my_bonds;
	}
	}

	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ) {
	Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
	mpi_data->bond_line, mpi_data->world,
	me, my_bonds, num_bonds );
	MPI_File_write( out_control->trj, out_control->buffer, my_bonds,
	mpi_data->bond_line, &status );
	out_control->trj_offset += num_bonds * line_len;
	}
	else{
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np*BOND_LINES+me, mpi_data->world );
	else{
	buffer_len = my_bonds * line_len;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	}
	#elif defined(LAMMPS_REAX)
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np*BOND_LINES+me, mpi_data->world );
	else{
	buffer_len = my_bonds * line_len;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	#endif

	return SUCCESS;
	}


	int Write_Angles( reax_system system, control_params control,
	reax_list bonds, reax_list thb_intrs,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	int i, j, k, pi, pk, me, np;
	int my_angles, num_angles;
	int line_len, buffer_len, buffer_req, cnt;
	bond_data bo_ij, bo_jk;
	three_body_interaction_data *angle_ijk;
	MPI_Status status;

	me = system->my_rank;
	np = system->wsize;
	line_len = out_control->angle_line_len;

	/* count the number of valence angles I will output */
	my_angles = 0;
	for( j = 0; j < system->n; ++j )
	for( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi ) {
	bo_ij = &(bonds->select.bond_list[pi]);
	i = bo_ij->nbr;

	if( bo_ij->bo_data.BO >= control->bg_cut ) // physical j&i bond
	for( pk = Start_Index( pi, thb_intrs );
	pk < End_Index( pi, thb_intrs ); ++pk ) {
	angle_ijk = &(thb_intrs->select.three_body_list[pk]);
	k = angle_ijk->thb;
	bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]);

	if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id &&
	bo_jk->bo_data.BO >= control->bg_cut ) // physical j&k bond
	++my_angles;
	}
	}
	/* total number of valences */
	MPI_Allreduce(&my_angles, &num_angles, 1, MPI_INT, MPI_SUM, mpi_data->world);

	Write_Skip_Line( out_control, mpi_data, me, num_angles*line_len, num_angles );

	if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE )
	buffer_req = num_angles * line_len + 1;
	else buffer_req = my_angles * line_len + 1;

	if( buffer_req > out_control->buffer_len * DANGER_ZONE )
	Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );

	/* fill in the buffer */
	my_angles = 0;
	out_control->line[0] = 0;
	out_control->buffer[0] = 0;
	for( j = 0; j < system->n; ++j )
	for( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi ) {
	bo_ij = &(bonds->select.bond_list[pi]);
	i = bo_ij->nbr;

	if( bo_ij->bo_data.BO >= control->bg_cut ) // physical j&i bond
	for( pk = Start_Index( pi, thb_intrs );
	pk < End_Index( pi, thb_intrs ); ++pk ) {
	angle_ijk = &(thb_intrs->select.three_body_list[pk]);
	k = angle_ijk->thb;
	bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]);

	if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id &&
	bo_jk->bo_data.BO >= control->bg_cut ) { // physical j&k bond
	sprintf( out_control->line, ANGLE_BASIC,
	system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
	system->my_atoms[k].orig_id, RAD2DEG( angle_ijk->theta ) );

	strncpy( out_control->buffer + my_angles*line_len,
	out_control->line, line_len+1 );
	++my_angles;
	}
	}
	}

	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ ){
	Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
	mpi_data->angle_line, mpi_data->world,
	me, my_angles, num_angles );
	MPI_File_write( out_control->trj, out_control->buffer, my_angles,
	mpi_data->angle_line, &status );
	out_control->trj_offset += num_angles * line_len;
	}
	else{
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np*ANGLE_LINES+me, mpi_data->world );
	else{
	buffer_len = my_angles * line_len;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	}
	#elif defined(LAMMPS_REAX)
	if( me != MASTER_NODE )
	MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
	np*ANGLE_LINES+me, mpi_data->world );
	else{
	buffer_len = my_angles * line_len;
	for( i = 0; i < np; ++i )
	if( i != MASTER_NODE ) {
	MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
	MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
	MPI_Get_count( &status, MPI_CHAR, &cnt );
	buffer_len += cnt;
	}
	out_control->buffer[buffer_len] = 0;
	fprintf( out_control->strj, "%s", out_control->buffer );
	}
	#endif

	return SUCCESS;
	}


	int Append_Frame( reax_system system, control_params control,
	simulation_data data, reax_list *lists,
	output_controls out_control, mpi_datatypes mpi_data )
	{
	#if defined(DEBUG_FOCUS)
	fprintf( stderr, "p%d: appending frame %d\n", system->my_rank, data->step );
	#endif
	Write_Frame_Header( system, control, data, out_control, mpi_data );

	if( out_control->write_atoms )
	Write_Atoms( system, control, out_control, mpi_data );

	if( out_control->write_bonds )
	Write_Bonds( system, control, (*lists + BONDS), out_control, mpi_data );

	if( out_control->write_angles )
	Write_Angles( system, control, (lists + BONDS), (lists + THREE_BODIES),
	out_control, mpi_data );
	#if defined(DEBUG_FOCUS)
	fprintf( stderr, "p%d: appended frame %d\n", system->my_rank, data->step );
	#endif

	return SUCCESS;
	}


	int End_Traj( int my_rank, output_controls *out_control )
	{
	#if defined(PURE_REAX)
	if( out_control->traj_method == MPI_TRAJ )
	MPI_File_close( &(out_control->trj) );
	else if( my_rank == MASTER_NODE )
	fclose( out_control->strj );
	#elif defined(LAMMPS_REAX)
	if( my_rank == MASTER_NODE )
	fclose( out_control->strj );
	#endif

	free( out_control->buffer );
	free( out_control->line );

	return SUCCESS;
	}

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