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reaxc_control.cpp
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Sat, Nov 2, 01:13

reaxc_control.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"
#if defined(PURE_REAX)
#include "control.h"
#include "tool_box.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_control.h"
#include "reaxc_tool_box.h"
#endif
char Read_Control_File( char *control_file, control_params* control,
output_controls *out_control )
{
FILE *fp;
char *s, **tmp;
int c,i,ival;
real val;
/* open control file */
if ( (fp = fopen( control_file, "r" ) ) == NULL ) {
fprintf( stderr, "error opening the control file! terminating...\n" );
MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
}
/* assign default values */
strcpy( control->sim_name, "simulate" );
control->ensemble = NVE;
control->nsteps = 0;
control->dt = 0.25;
control->nprocs = 1;
control->procs_by_dim[0] = 1;
control->procs_by_dim[1] = 1;
control->procs_by_dim[2] = 1;
control->geo_format = 1;
control->restart = 0;
out_control->restart_format = WRITE_BINARY;
out_control->restart_freq = 0;
control->reposition_atoms = 0;
control->restrict_bonds = 0;
control->remove_CoM_vel = 25;
out_control->debug_level = 0;
out_control->energy_update_freq = 0;
control->reneighbor = 1;
control->vlist_cut = control->nonb_cut;
control->bond_cut = 5.0;
control->bg_cut = 0.3;
control->thb_cut = 0.001;
control->hbond_cut = 0.0;
control->tabulate = 0;
control->qeq_freq = 1;
control->q_err = 1e-6;
control->refactor = 100;
control->droptol = 1e-2;;
control->T_init = 0.;
control->T_final = 300.;
control->Tau_T = 500.0;
control->T_mode = 0;
control->T_rate = 1.;
control->T_freq = 1.;
control->P[0] = control->P[1] = control->P[2] = 0.000101325;
control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] = 500.0;
control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] = 500.0;
control->compressibility = 1.0;
control->press_mode = 0;
control->virial = 0;
out_control->write_steps = 0;
out_control->traj_compress = 0;
out_control->traj_method = REG_TRAJ;
strcpy( out_control->traj_title, "default_title" );
out_control->atom_info = 0;
out_control->bond_info = 0;
out_control->angle_info = 0;
control->molecular_analysis = 0;
control->dipole_anal = 0;
control->freq_dipole_anal = 0;
control->diffusion_coef = 0;
control->freq_diffusion_coef = 0;
control->restrict_type = 0;
/* memory allocations */
s = (char*) malloc(sizeof(char)*MAX_LINE);
tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
for (i=0; i < MAX_TOKENS; i++)
tmp[i] = (char*) malloc(sizeof(char)*MAX_LINE);
/* read control parameters file */
while (!feof(fp)) {
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
//fprintf( stderr, "%s\n", s );
if( strcmp(tmp[0], "simulation_name") == 0 ) {
strcpy( control->sim_name, tmp[1] );
}
else if( strcmp(tmp[0], "ensemble_type") == 0 ) {
ival = atoi(tmp[1]);
control->ensemble = ival;
if( ival == iNPT || ival ==sNPT || ival == NPT )
control->virial = 1;
}
else if( strcmp(tmp[0], "nsteps") == 0 ) {
ival = atoi(tmp[1]);
control->nsteps = ival;
}
else if( strcmp(tmp[0], "dt") == 0) {
val = atof(tmp[1]);
control->dt = val * 1.e-3; // convert dt from fs to ps!
}
else if( strcmp(tmp[0], "proc_by_dim") == 0 ) {
ival = atoi(tmp[1]);
control->procs_by_dim[0] = ival;
ival = atoi(tmp[2]);
control->procs_by_dim[1] = ival;
ival = atoi(tmp[3]);
control->procs_by_dim[2] = ival;
control->nprocs = control->procs_by_dim[0]*control->procs_by_dim[1]*
control->procs_by_dim[2];
}
//else if( strcmp(tmp[0], "restart") == 0 ) {
// ival = atoi(tmp[1]);
// control->restart = ival;
//}
//else if( strcmp(tmp[0], "restart_from") == 0 ) {
// strcpy( control->restart_from, tmp[1] );
//}
else if( strcmp(tmp[0], "random_vel") == 0 ) {
ival = atoi(tmp[1]);
control->random_vel = ival;
}
else if( strcmp(tmp[0], "restart_format") == 0 ) {
ival = atoi(tmp[1]);
out_control->restart_format = ival;
}
else if( strcmp(tmp[0], "restart_freq") == 0 ) {
ival = atoi(tmp[1]);
out_control->restart_freq = ival;
}
else if( strcmp(tmp[0], "reposition_atoms") == 0 ) {
ival = atoi(tmp[1]);
control->reposition_atoms = ival;
}
else if( strcmp(tmp[0], "restrict_bonds") == 0 ) {
ival = atoi( tmp[1] );
control->restrict_bonds = ival;
}
else if( strcmp(tmp[0], "remove_CoM_vel") == 0 ) {
ival = atoi(tmp[1]);
control->remove_CoM_vel = ival;
}
else if( strcmp(tmp[0], "debug_level") == 0 ) {
ival = atoi(tmp[1]);
out_control->debug_level = ival;
}
else if( strcmp(tmp[0], "energy_update_freq") == 0 ) {
ival = atoi(tmp[1]);
out_control->energy_update_freq = ival;
}
else if( strcmp(tmp[0], "reneighbor") == 0 ) {
ival = atoi( tmp[1] );
control->reneighbor = ival;
}
else if( strcmp(tmp[0], "vlist_buffer") == 0 ) {
val = atof(tmp[1]);
control->vlist_cut= val + control->nonb_cut;
}
else if( strcmp(tmp[0], "nbrhood_cutoff") == 0 ) {
val = atof(tmp[1]);
control->bond_cut = val;
}
else if( strcmp(tmp[0], "bond_graph_cutoff") == 0 ) {
val = atof(tmp[1]);
control->bg_cut = val;
}
else if( strcmp(tmp[0], "thb_cutoff") == 0 ) {
val = atof(tmp[1]);
control->thb_cut = val;
}
else if( strcmp(tmp[0], "hbond_cutoff") == 0 ) {
val = atof( tmp[1] );
control->hbond_cut = val;
}
else if( strcmp(tmp[0], "ghost_cutoff") == 0 ) {
val = atof(tmp[1]);
control->user_ghost_cut = val;
}
else if( strcmp(tmp[0], "tabulate_long_range") == 0 ) {
ival = atoi( tmp[1] );
control->tabulate = ival;
}
else if( strcmp(tmp[0], "qeq_freq") == 0 ) {
ival = atoi( tmp[1] );
control->qeq_freq = ival;
}
else if( strcmp(tmp[0], "q_err") == 0 ) {
val = atof( tmp[1] );
control->q_err = val;
}
else if( strcmp(tmp[0], "ilu_refactor") == 0 ) {
ival = atoi( tmp[1] );
control->refactor = ival;
}
else if( strcmp(tmp[0], "ilu_droptol") == 0 ) {
val = atof( tmp[1] );
control->droptol = val;
}
else if( strcmp(tmp[0], "temp_init") == 0 ) {
val = atof(tmp[1]);
control->T_init = val;
if( control->T_init < 0.1 )
control->T_init = 0.1;
}
else if( strcmp(tmp[0], "temp_final") == 0 ) {
val = atof(tmp[1]);
control->T_final = val;
if( control->T_final < 0.1 )
control->T_final = 0.1;
}
else if( strcmp(tmp[0], "t_mass") == 0 ) {
val = atof(tmp[1]);
control->Tau_T = val * 1.e-3; // convert t_mass from fs to ps
}
else if( strcmp(tmp[0], "t_mode") == 0 ) {
ival = atoi(tmp[1]);
control->T_mode = ival;
}
else if( strcmp(tmp[0], "t_rate") == 0 ) {
val = atof(tmp[1]);
control->T_rate = val;
}
else if( strcmp(tmp[0], "t_freq") == 0 ) {
val = atof(tmp[1]);
control->T_freq = val;
}
else if( strcmp(tmp[0], "pressure") == 0 ) {
if( control->ensemble == iNPT ) {
control->P[0] = control->P[1] = control->P[2] = atof(tmp[1]);
}
else if( control->ensemble == sNPT ) {
control->P[0] = atof(tmp[1]);
control->P[1] = atof(tmp[2]);
control->P[2] = atof(tmp[3]);
}
}
else if( strcmp(tmp[0], "p_mass") == 0 ) {
// convert p_mass from fs to ps
if( control->ensemble == iNPT ) {
control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] =
atof(tmp[1]) * 1.e-3;
}
else if( control->ensemble == sNPT ) {
control->Tau_P[0] = atof(tmp[1]) * 1.e-3;
control->Tau_P[1] = atof(tmp[2]) * 1.e-3;
control->Tau_P[2] = atof(tmp[3]) * 1.e-3;
}
}
else if( strcmp(tmp[0], "pt_mass") == 0 ) {
val = atof(tmp[1]);
control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] =
val * 1.e-3; // convert pt_mass from fs to ps
}
else if( strcmp(tmp[0], "compress") == 0 ) {
val = atof(tmp[1]);
control->compressibility = val;
}
else if( strcmp(tmp[0], "press_mode") == 0 ) {
ival = atoi(tmp[1]);
control->press_mode = ival;
}
else if( strcmp(tmp[0], "geo_format") == 0 ) {
ival = atoi( tmp[1] );
control->geo_format = ival;
}
else if( strcmp(tmp[0], "write_freq") == 0 ) {
ival = atoi(tmp[1]);
out_control->write_steps = ival;
}
else if( strcmp(tmp[0], "traj_compress") == 0 ) {
ival = atoi(tmp[1]);
out_control->traj_compress = ival;
}
else if( strcmp(tmp[0], "traj_method") == 0 ) {
ival = atoi(tmp[1]);
out_control->traj_method = ival;
}
else if( strcmp(tmp[0], "traj_title") == 0 ) {
strcpy( out_control->traj_title, tmp[1] );
}
else if( strcmp(tmp[0], "atom_info") == 0 ) {
ival = atoi(tmp[1]);
out_control->atom_info += ival * 4;
}
else if( strcmp(tmp[0], "atom_velocities") == 0 ) {
ival = atoi(tmp[1]);
out_control->atom_info += ival * 2;
}
else if( strcmp(tmp[0], "atom_forces") == 0 ) {
ival = atoi(tmp[1]);
out_control->atom_info += ival * 1;
}
else if( strcmp(tmp[0], "bond_info") == 0 ) {
ival = atoi(tmp[1]);
out_control->bond_info = ival;
}
else if( strcmp(tmp[0], "angle_info") == 0 ) {
ival = atoi(tmp[1]);
out_control->angle_info = ival;
}
else if( strcmp(tmp[0], "molecular_analysis") == 0 ) {
ival = atoi(tmp[1]);
control->molecular_analysis = ival;
}
else if( strcmp(tmp[0], "ignore") == 0 ) {
control->num_ignored = atoi(tmp[1]);
for( i = 0; i < control->num_ignored; ++i )
control->ignore[atoi(tmp[i+2])] = 1;
}
else if( strcmp(tmp[0], "dipole_anal") == 0 ) {
ival = atoi(tmp[1]);
control->dipole_anal = ival;
}
else if( strcmp(tmp[0], "freq_dipole_anal") == 0 ) {
ival = atoi(tmp[1]);
control->freq_dipole_anal = ival;
}
else if( strcmp(tmp[0], "diffusion_coef") == 0 ) {
ival = atoi(tmp[1]);
control->diffusion_coef = ival;
}
else if( strcmp(tmp[0], "freq_diffusion_coef") == 0 ) {
ival = atoi(tmp[1]);
control->freq_diffusion_coef = ival;
}
else if( strcmp(tmp[0], "restrict_type") == 0 ) {
ival = atoi(tmp[1]);
control->restrict_type = ival;
}
else {
fprintf( stderr, "WARNING: unknown parameter %s\n", tmp[0] );
MPI_Abort( MPI_COMM_WORLD, 15 );
}
}
/* determine target T */
if( control->T_mode == 0 )
control->T = control->T_final;
else control->T = control->T_init;
/* free memory allocations at the top */
for( i = 0; i < MAX_TOKENS; i++ )
free( tmp[i] );
free( tmp );
free( s );
// fprintf( stderr,"%d %d %10.5f %d %10.5f %10.5f\n",
// control->ensemble, control->nsteps, control->dt,
// control->tabulate, control->T, control->P );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "control file read\n" );
#endif
return SUCCESS;
}

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