From 61201e24a6606611c15252f719bfe06aafda97fb Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Wed, 24 Oct 2018 11:19:13 -0400
Subject: [PATCH] PuReMD-old: improve file I/O checks.
---
PuReMD/src/ffield.c | 6 +-
PuReMD/src/geo_tools.c | 20 +-
PuReMD/src/io_tools.c | 463 +++++++++++-------------------------
PuReMD/src/restart.c | 32 +--
PuReMD/src/torsion_angles.c | 2 +-
PuReMD/src/traj.c | 8 +-
6 files changed, 165 insertions(+), 366 deletions(-)
diff --git a/PuReMD/src/ffield.c b/PuReMD/src/ffield.c
index b05216bd..b25b8db4 100644
--- a/PuReMD/src/ffield.c
+++ b/PuReMD/src/ffield.c
@@ -43,11 +43,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
comm = MPI_COMM_WORLD;
/* open force field file */
- if ( (fp = fopen( ffield_file, "r" ) ) == NULL )
- {
- fprintf( stderr, "error opening the force filed file! terminating...\n" );
- MPI_Abort( comm, FILE_NOT_FOUND );
- }
+ fp = sfopen( ffield_file, "r", "Read_Force_Field::fp" );
s = (char*) malloc(sizeof(char) * MAX_LINE);
tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
diff --git a/PuReMD/src/geo_tools.c b/PuReMD/src/geo_tools.c
index c01f65cb..77e1f95b 100644
--- a/PuReMD/src/geo_tools.c
+++ b/PuReMD/src/geo_tools.c
@@ -81,11 +81,7 @@ char Read_Geo( char* geo_file, reax_system* system, control_params *control,
comm = MPI_COMM_WORLD;
/* open the geometry file */
- if ( (geo = fopen(geo_file, "r")) == NULL )
- {
- fprintf( stderr, "fopen: error opening the geo file! terminating...\n" );
- MPI_Abort( comm, FILE_NOT_FOUND );
- }
+ geo = sfopen( geo_file, "r", "Read_Geo::geo" );
/* read box information */
fscanf( geo, CUSTOM_BOXGEO_FORMAT,
@@ -140,7 +136,7 @@ char Read_Geo( char* geo_file, reax_system* system, control_params *control,
}
}
- fclose( geo );
+ sfclose( geo, "Read_Geo::geo" );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: finished reading the geo file\n", system->my_rank );
@@ -271,11 +267,7 @@ char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
comm = MPI_COMM_WORLD;
/* open pdb file */
- if ( (pdb = fopen(pdb_file, "r")) == NULL )
- {
- fprintf( stderr, "fopen: error opening the pdb file! terminating...\n" );
- MPI_Abort( comm, FILE_NOT_FOUND );
- }
+ pdb = sfopen( pdb_file, "r", "Read_PDB::pdb" );
/* allocate memory for tokenizing pdb lines */
if ( Allocate_Tokenizer_Space( &s, &s1, &tmp ) == FAILURE )
@@ -481,7 +473,7 @@ char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
return FAILURE;
}
- fclose( pdb );
+ sfclose( pdb, "Read_PDB::pdb" );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: finished reading the pdb file\n", system->my_rank );
@@ -550,7 +542,7 @@ char Write_PDB(reax_system* system, reax_list** bonds, simulation_data *data,
sprintf(fname, "%s-%d.pdb", control->sim_name, data->step);
- pdb = fopen(fname, "w");
+ pdb = sfopen( fname, "w", "Write_PDB::pdb" );
/*fprintf( pdb, PDB_CRYST1_FORMAT_O,
"CRYST1",
system->big_box.box_norms[0], system->big_box.box_norms[1],
@@ -601,7 +593,7 @@ char Write_PDB(reax_system* system, reax_list** bonds, simulation_data *data,
if ( me == MASTER_NODE)
{
fprintf( pdb, "%s", buffer );
- fclose( pdb );
+ sfclose( pdb, "Write_PDB::pdb" );
}
/* Writing connect information */
diff --git a/PuReMD/src/io_tools.c b/PuReMD/src/io_tools.c
index ef7a76c7..b22ef6bf 100644
--- a/PuReMD/src/io_tools.c
+++ b/PuReMD/src/io_tools.c
@@ -64,66 +64,45 @@ int Init_Output_Files( reax_system *system, control_params *control,
{
/* init out file */
sprintf( temp, "%s.out", control->sim_name );
- if ( (out_control->out = fopen( temp, "w" )) != NULL )
- {
+ out_control->out = sfopen( temp, "w", "Init_Output_Files" );
#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)" );
+ 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)" );
+ 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;
- }
+ fflush( out_control->out );
/* init potentials file */
sprintf( temp, "%s.pot", control->sim_name );
- if ( (out_control->pot = fopen( temp, "w" )) != NULL )
- {
+ out_control->pot = sfopen( temp, "w", "Init_Output_Files" );
#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" );
+ 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" );
+ 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;
- }
+ fflush( out_control->pot );
/* 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 %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s\n",
- "step", "total", "comm", "neighbors", "init", "bonded", "nonbonded",
- "CM", "CM Sort", "S iters", "Pre Comp", "Pre App", "S comm", "S allr",
- "S spmv", "S vec ops", "S orthog", "S tsolve" );
- fflush( out_control->log );
- }
- else
- {
- strcpy( msg, "init_out_controls: .log file could not be opened\n" );
- return FAILURE;
- }
+ out_control->log = sfopen( temp, "w", "Init_Output_Files" );
+ fprintf( out_control->log, "%-6s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s\n",
+ "step", "total", "comm", "neighbors", "init", "bonded", "nonbonded",
+ "CM", "CM Sort", "S iters", "Pre Comp", "Pre App", "S comm", "S allr",
+ "S spmv", "S vec ops", "S orthog", "S tsolve" );
+ fflush( out_control->log );
#endif
}
@@ -133,52 +112,31 @@ int Init_Output_Files( reax_system *system, control_params *control,
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;
- }
+ out_control->prs = sfopen( temp, "w", "Init_Output_Files" );
+ 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 );
}
/* init electric dipole moment analysis file */
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;
- }
+ out_control->dpl = sfopen( temp, "w", "Init_Output_Files" );
+ fprintf( out_control->dpl, "%6s%20s%30s",
+ "step", "molecule count", "avg dipole moment norm" );
+ fflush( out_control->dpl );
}
/* init diffusion coef analysis file */
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;
- }
+ out_control->drft = sfopen( temp, "w", "Init_Output_Files" );
+ fprintf( out_control->drft, "%7s%20s%20s\n",
+ "step", "type count", "avg disp^2" );
+ fflush( out_control->drft );
}
}
@@ -190,9 +148,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
/*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;
+ out_control->mol = sfopen( temp, "w", "Init_Output_Files" );
}
}
@@ -203,233 +159,121 @@ int Init_Output_Files( reax_system *system, control_params *control,
#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;
- }
+ out_control->ebond = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->elp = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->eov = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->eun = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->eval = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->ecoa = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->epen = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->etor = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->econ = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->ehb = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->evdw = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->ecou = sfopen( temp, "w", "Init_Output_Files" );
#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;
- }
+ out_control->fbo = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fdbo = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ Output_Files" )) == NULL )
/* 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;
- }
+ out_control->flp = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fov = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fun = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fang = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fcoa = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fpen = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->ftor = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fcon = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fhb = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fvdw = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fele = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->ftot = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->fcomp = sfopen( temp, "w", "Init_Output_Files" );
}
#endif
@@ -437,27 +281,15 @@ int Init_Output_Files( reax_system *system, control_params *control,
#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;
- }
+ out_control->flist = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->blist = sfopen( temp, "w", "Init_Output_Files" );
/* 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;
- }
+ out_control->nlist = sfopen( temp, "w", "Init_Output_Files" );
#endif
#endif
@@ -476,65 +308,68 @@ int Close_Output_Files( reax_system *system, control_params *control,
{
if ( out_control->energy_update_freq > 0 )
{
- fclose( out_control->out );
- fclose( out_control->pot );
+ sfclose( out_control->out, "Close_Output_Files" );
+ sfclose( out_control->pot, "Close_Output_Files" );
#if defined(LOG_PERFORMANCE)
- fclose( out_control->log );
+ sfclose( out_control->log, "Close_Output_Files" );
#endif
}
if ( control->ensemble == NPT || control->ensemble == iNPT ||
control->ensemble == sNPT )
- fclose( out_control->prs );
+ sfclose( out_control->prs, "Close_Output_Files" );
- if ( control->dipole_anal ) fclose( out_control->dpl );
- if ( control->diffusion_coef ) fclose( out_control->drft );
- if ( control->molecular_analysis ) fclose( out_control->mol );
+ if ( control->dipole_anal )
+ sfclose( out_control->dpl, "Close_Output_Files" );
+ if ( control->diffusion_coef )
+ sfclose( out_control->drft, "Close_Output_Files" );
+ if ( control->molecular_analysis )
+ sfclose( out_control->mol, "Close_Output_Files" );
}
#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 );
+ sfclose( out_control->ebond, "Close_Output_Files" );
+ sfclose( out_control->elp, "Close_Output_Files" );
+ sfclose( out_control->eov, "Close_Output_Files" );
+ sfclose( out_control->eun, "Close_Output_Files" );
+ sfclose( out_control->eval, "Close_Output_Files" );
+ sfclose( out_control->epen, "Close_Output_Files" );
+ sfclose( out_control->ecoa, "Close_Output_Files" );
+ sfclose( out_control->ehb, "Close_Output_Files" );
+ sfclose( out_control->etor, "Close_Output_Files" );
+ sfclose( out_control->econ, "Close_Output_Files" );
+ sfclose( out_control->evdw, "Close_Output_Files" );
+ sfclose( out_control->ecou, "Close_Output_Files" );
#endif
#ifdef TEST_FORCES
- fclose( out_control->fbo );
- fclose( out_control->fdbo );
+ sfclose( out_control->fbo, "Close_Output_Files" );
+ sfclose( out_control->fdbo, "Close_Output_Files" );
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 );
+ sfclose( out_control->fbond, "Close_Output_Files" );
+ sfclose( out_control->flp, "Close_Output_Files" );
+ sfclose( out_control->fov, "Close_Output_Files" );
+ sfclose( out_control->fun, "Close_Output_Files" );
+ sfclose( out_control->fang, "Close_Output_Files" );
+ sfclose( out_control->fcoa, "Close_Output_Files" );
+ sfclose( out_control->fpen, "Close_Output_Files" );
+ sfclose( out_control->ftor, "Close_Output_Files" );
+ sfclose( out_control->fcon, "Close_Output_Files" );
+ sfclose( out_control->fhb, "Close_Output_Files" );
+ sfclose( out_control->fvdw, "Close_Output_Files" );
+ sfclose( out_control->fele, "Close_Output_Files" );
+ sfclose( out_control->ftot, "Close_Output_Files" );
+ sfclose( out_control->fcomp, "Close_Output_Files" );
}
#endif
#if defined(PURE_REAX)
#if defined(TEST_FORCES) || defined(TEST_ENERGY)
- fclose( out_control->flist );
- fclose( out_control->blist );
- fclose( out_control->nlist );
+ sfclose( out_control->flist, "Close_Output_Files" );
+ sfclose( out_control->blist, "Close_Output_Files" );
+ sfclose( out_control->nlist, "Close_Output_Files" );
#endif
#endif
@@ -668,7 +503,7 @@ void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
char exch[3][10] = { "NONE", "NEAR_EXCH", "FULL_EXCH" };
sprintf( fname, "gcell_exchange_bounds%d", my_rank );
- f = fopen( fname, "w" );
+ f = sfopen( fname, "w", "Print_GCell_Exchange_Bounds" );
/* loop over neighbor processes */
for ( r[0] = -1; r[0] <= 1; ++r[0])
@@ -696,7 +531,7 @@ void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
nbr_pr->end_recv[2] );
}
- fclose(f);
+ sfclose( f, "Print_GCell_Exchange_Bounds" );
}
@@ -715,7 +550,7 @@ void Print_Native_GCells( reax_system *system )
};
sprintf( fname, "native_gcells.%d", system->my_rank );
- f = fopen( fname, "w" );
+ f = sfopen( fname, "w", "Print_Native_GCells" );
g = &(system->my_grid);
for ( i = g->native_str[0]; i < g->native_end[0]; i++ )
@@ -735,7 +570,7 @@ void Print_Native_GCells( reax_system *system )
fprintf( f, "\n" );
}
- fclose(f);
+ sfclose( f, "Print_Native_GCells" );
}
@@ -754,7 +589,7 @@ void Print_All_GCells( reax_system *system )
};
sprintf( fname, "all_gcells.%d", system->my_rank );
- f = fopen( fname, "w" );
+ f = sfopen( fname, "w", "Print_All_GCells" );
g = &(system->my_grid);
for ( i = 0; i < g->ncells[0]; i++ )
@@ -774,7 +609,7 @@ void Print_All_GCells( reax_system *system )
fprintf( f, "\n" );
}
- fclose(f);
+ sfclose( f, "Print_All_GCells" );
}
@@ -786,11 +621,7 @@ void Print_My_Atoms( reax_system *system, control_params *control, int step )
FILE *fh;
sprintf( fname, "%s.my_atoms.%d.%d", control->sim_name, step, 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 );
- }
+ fh = sfopen( fname, "w", "Print_My_Atoms" );
// fprintf( stderr, "p%d had %d atoms\n",
// system->my_rank, system->n );
@@ -803,7 +634,7 @@ void Print_My_Atoms( reax_system *system, control_params *control, int step )
system->my_atoms[i].x[1],
system->my_atoms[i].x[2] );
- fclose( fh );
+ sfclose( fh, "Print_My_Atoms" );
}
@@ -814,11 +645,7 @@ void Print_My_Ext_Atoms( reax_system *system )
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 );
- }
+ fh = sfopen( fname, "w", "Print_My_Ext_Atoms" );
// fprintf( stderr, "p%d had %d atoms\n",
// system->my_rank, system->n );
@@ -831,7 +658,7 @@ void Print_My_Ext_Atoms( reax_system *system )
system->my_atoms[i].x[1],
system->my_atoms[i].x[2] );
- fclose( fh );
+ sfclose( fh, "Print_My_Ext_Atoms" );
}
@@ -844,7 +671,7 @@ void Print_Far_Neighbors( reax_system *system, reax_list **lists,
reax_list *far_nbrs;
sprintf( fname, "%s.far_nbrs.%d", control->sim_name, system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_Far_Neighbors" );
far_nbrs = lists[FAR_NBRS];
natoms = system->N;
@@ -871,7 +698,7 @@ void Print_Far_Neighbors( reax_system *system, reax_list **lists,
}
}
- fclose( fout );
+ sfclose( fout, "Print_Far_Neighbors" );
}
@@ -891,7 +718,7 @@ void Print_Sparse_Matrix( reax_system *system, sparse_matrix *A )
void Print_Sparse_Matrix2( reax_system *system, sparse_matrix *A, char *fname )
{
int i, j;
- FILE *f = fopen( fname, "w" );
+ FILE *f = sfopen( fname, "w", "Print_Sparse_Matrix2" );
for ( i = 0; i < A->n; ++i )
for ( j = A->start[i]; j < A->end[i]; ++j )
@@ -900,7 +727,7 @@ void Print_Sparse_Matrix2( reax_system *system, sparse_matrix *A, char *fname )
system->my_atoms[A->entries[j].j].orig_id,
A->entries[j].val );
- fclose(f);
+ sfclose( f, "Print_Sparse_Matrix2" );
}
@@ -908,7 +735,7 @@ void Print_Symmetric_Sparse(reax_system *system, sparse_matrix *A, char *fname)
{
int i, j;
reax_atom *ai, *aj;
- FILE *f = fopen( fname, "w" );
+ FILE *f = sfopen( fname, "w", "Print_Symmetric_Sparse" );
for ( i = 0; i < A->n; ++i )
{
@@ -924,7 +751,7 @@ void Print_Symmetric_Sparse(reax_system *system, sparse_matrix *A, char *fname)
}
}
- fclose(f);
+ sfclose( f, "Print_Symmetric_Sparse" );
}
@@ -939,7 +766,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
// print rhs and init guesses for QEq
sprintf( fname, "%s.p%dstate%d", control->sim_name, system->my_rank, step );
- out = fopen( fname, "w" );
+ out = sfopen( fname, "w", "Print_Linear_System" );
for ( i = 0; i < system->n; i++ )
{
ai = &(system->my_atoms[i]);
@@ -948,7 +775,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
workspace->s[i], workspace->b_s[i],
workspace->t[i], workspace->b_t[i] );
}
- fclose( out );
+ sfclose( out, "Print_Linear_System" );
// print QEq coef matrix
sprintf( fname, "%s.p%dH%d", control->sim_name, system->my_rank, step );
@@ -956,7 +783,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
// print the incomplete H matrix
/*sprintf( fname, "%s.p%dHinc%d", control->sim_name, system->my_rank, step );
- out = fopen( fname, "w" );
+ out = sfopen( fname, "w", "Print_Linear_System" );
H = workspace->H;
for( i = 0; i < H->n; ++i ) {
ai = &(system->my_atoms[i]);
@@ -970,7 +797,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
aj->orig_id, ai->orig_id, H->entries[j].val );
}
}
- fclose( out );*/
+ sfclose( out, "Print_Linear_System" );*/
// print the L from incomplete cholesky decomposition
/*sprintf( fname, "%s.p%dL%d", control->sim_name, system->my_rank, step );
@@ -985,13 +812,13 @@ void Print_LinSys_Soln( reax_system *system, real *x, real *b_prm, real *b )
FILE *fout;
sprintf( fname, "qeq.%d.out", system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_LinSys_Soln" );
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 );
+ sfclose( fout, "Print_LinSys_Soln" );
}
@@ -1002,7 +829,7 @@ void Print_Charges( reax_system *system )
FILE *fout;
sprintf( fname, "q.%d.out", system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_Charges" );
for ( i = 0; i < system->n; ++i )
fprintf( fout, "%6d %10.7f %10.7f %10.7f\n",
@@ -1011,7 +838,7 @@ void Print_Charges( reax_system *system )
system->my_atoms[i].t[0],
system->my_atoms[i].q );
- fclose( fout );
+ sfclose( fout, "Print_Charges" );
}
@@ -1025,7 +852,7 @@ void Print_HBonds( reax_system *system, reax_list **lists,
reax_list *hbonds = lists[HBONDS];
sprintf( fname, "%s.hbonds.%d.%d", control->sim_name, step, system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_HBonds" );
for ( i = 0; i < system->numH; ++i )
{
@@ -1040,7 +867,7 @@ void Print_HBonds( reax_system *system, reax_list **lists,
}
}
- fclose( fout );
+ sfclose( fout, "Print_HBonds" );
}
@@ -1053,7 +880,7 @@ void Print_HBond_Indices( reax_system *system, reax_list **lists,
reax_list *hbonds = lists[HBONDS];
sprintf( fname, "%s.hbonds_indices.%d.%d", control->sim_name, step, system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_HBond_Indices" );
for ( i = 0; i < system->N; ++i )
{
@@ -1061,7 +888,7 @@ void Print_HBond_Indices( reax_system *system, reax_list **lists,
i, Start_Index(i, hbonds), End_Index(i, hbonds) );
}
- fclose( fout );
+ sfclose( fout, "Print_HBond_Indices" );
}
@@ -1076,7 +903,7 @@ void Print_Bonds( reax_system *system, reax_list **lists,
reax_list *bonds = lists[BONDS];
sprintf( fname, "%s.bonds.%d.%d", control->sim_name, step, system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_Bonds" );
for ( i = 0; i < system->N; ++i )
{
@@ -1093,7 +920,7 @@ void Print_Bonds( reax_system *system, reax_list **lists,
}
}
- fclose( fout );
+ sfclose( fout, "Print_Bonds" );
}
@@ -1105,7 +932,7 @@ int fn_qsort_intcmp( const void *a, const void *b )
void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
{
int i, j, id_i, id_j, nbr, pj;
- FILE *f = fopen( fname, "w" );
+ FILE *f = sfopen( fname, "w", "Print_Bond_List2" );
int temp[500];
int num = 0;
@@ -1156,7 +983,7 @@ void Print_Far_Neighbors_List_Adj_Format( reax_system *system,
FILE *fout;
sprintf( fname, "%s.far.%d.%d", control->sim_name, step, system->my_rank );
- fout = fopen( fname, "w" );
+ fout = sfopen( fname, "w", "Print_Far_Neighbors_Adj_Format" );
num_intrs = 0;
intrs = NULL;
@@ -1203,7 +1030,7 @@ void Print_Far_Neighbors_List_Adj_Format( reax_system *system,
free( intrs );
}
- fclose( fout );
+ sfclose( fout, "Print_Far_Neighbors_List_Adj_Format" );
}
void Output_Results( reax_system *system, control_params *control,
diff --git a/PuReMD/src/restart.c b/PuReMD/src/restart.c
index b687d82a..bdd2476f 100644
--- a/PuReMD/src/restart.c
+++ b/PuReMD/src/restart.c
@@ -49,11 +49,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
{
/* master handles the restart file */
sprintf( fname, "%s.res%d", control->sim_name, data->step );
- if ( (fres = fopen( fname, "wb" )) == NULL )
- {
- fprintf( stderr, "ERROR: can't open the restart file! terminating...\n" );
- MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
- }
+ fres = sfopen( fname, "wb", "Write_Binary_Restart" );
/* master can write the header by itself */
res_header.step = data->step;
@@ -108,7 +104,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
if ( me == MASTER_NODE )
{
fwrite( buffer, system->bigN, sizeof(restart_atom), fres );
- fclose( fres );
+ sfclose( fres, "Write_Binary_Restart" );
}
sfree(buffer, "buffer");
@@ -139,11 +135,7 @@ void Write_Restart( reax_system *system, control_params *control,
if ( me == MASTER_NODE )
{
sprintf( fname, "%s.res%d", control->sim_name, data->step );
- if ( (fres = fopen( fname, "w" )) == NULL )
- {
- fprintf( stderr, "ERROR: can't open the restart file! terminating...\n" );
- MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
- }
+ fres = sfopen( fname, "w", "Write_Restart" );
/* write the header - only master writes it */
fprintf( fres, RESTART_HEADER,
@@ -204,7 +196,7 @@ void Write_Restart( reax_system *system, control_params *control,
if ( me == MASTER_NODE )
{
fprintf( fres, "%s", buffer );
- fclose( fres );
+ sfclose( fres, "Write_Restart" );
}
sfree(buffer, "buffer");
sfree(line, "line");
@@ -250,11 +242,7 @@ void Read_Binary_Restart( char *res_file, reax_system *system,
comm = MPI_COMM_WORLD;
- if ( (fres = fopen(res_file, "rb")) == NULL )
- {
- fprintf( stderr, "ERROR: cannot open the restart file! terminating...\n" );
- MPI_Abort( comm, FILE_NOT_FOUND );
- }
+ fres = sfopen( res_file, "rb", "Read_Binary_Restart" );
/* first read the header lines */
fread(&res_header, sizeof(restart_header), 1, fres);
@@ -313,7 +301,7 @@ void Read_Binary_Restart( char *res_file, reax_system *system,
}
}
- fclose( fres );
+ sfclose( fres, "Read_Binary_Restart" );
data->step = data->prev_steps;
// nsteps is updated based on the number of steps in the previous run
@@ -368,11 +356,7 @@ void Read_Restart( char *res_file, reax_system *system,
comm = MPI_COMM_WORLD;
- if ( (fres = fopen(res_file, "r")) == NULL )
- {
- fprintf( stderr, "ERROR: cannot open the restart file! terminating...\n" );
- MPI_Abort( comm, FILE_NOT_FOUND );
- }
+ fres = sfopen( res_file, "r", "Read_Binary_Restart" );
s = (char*) malloc(sizeof(char) * MAX_LINE);
tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
@@ -464,7 +448,7 @@ void Read_Restart( char *res_file, reax_system *system,
top++;
}
}
- fclose( fres );
+ sfclose( fres, "Read_Restart" );
/* free memory allocations at the top */
for ( i = 0; i < MAX_TOKENS; i++ )
sfree( tmp[i], "tmp[i]" );
diff --git a/PuReMD/src/torsion_angles.c b/PuReMD/src/torsion_angles.c
index f915fdb8..8d9949da 100644
--- a/PuReMD/src/torsion_angles.c
+++ b/PuReMD/src/torsion_angles.c
@@ -197,7 +197,7 @@ void Torsion_Angles( reax_system *system, control_params *control,
// FILE *ftor;
// sprintf( fname, "tor%d.out", system->my_rank );
- // ftor = fopen( fname, "w" );
+ // ftor = sfopen( fname, "w", "Torsion_Angles" );
natoms = system->n;
diff --git a/PuReMD/src/traj.c b/PuReMD/src/traj.c
index d03a8289..e189c4fc 100644
--- a/PuReMD/src/traj.c
+++ b/PuReMD/src/traj.c
@@ -527,7 +527,7 @@ int Init_Traj( reax_system *system, control_params *control,
else if ( out_control->traj_method == REG_TRAJ)
{
if ( system->my_rank == MASTER_NODE )
- out_control->strj = fopen( fname, "w" );
+ out_control->strj = sfopen( fname, "w", "Init_Traj" );
}
else
{
@@ -538,7 +538,7 @@ int Init_Traj( reax_system *system, control_params *control,
if ( out_control->traj_method == REG_TRAJ)
{
if ( system->my_rank == MASTER_NODE )
- out_control->strj = fopen( fname, "w" );
+ out_control->strj = sfopen( fname, "w", "Init_Traj" );
}
else
{
@@ -1116,10 +1116,10 @@ int End_Traj( int my_rank, output_controls *out_control )
if ( out_control->traj_method == MPI_TRAJ )
MPI_File_close( &(out_control->trj) );
else if ( my_rank == MASTER_NODE )
- fclose( out_control->strj );
+ sfclose( out_control->strj, "End_Traj" );
#elif defined(LAMMPS_REAX)
if ( my_rank == MASTER_NODE )
- fclose( out_control->strj );
+ sfclose( out_control->strj, "End_Traj" );
#endif
sfree( out_control->buffer, "out_control->buffer" );
--
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