From 78dac2f42140d319f8bf02efff318e27def95e04 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Mon, 10 May 2021 16:12:12 -0400
Subject: [PATCH] sPuReMD: fix bug for BGF files if no CRYSTX line supplied
(simulation box dimensions).
---
sPuReMD/src/geo_tools.c | 56 +++++++++++++++++++++++++----------------
1 file changed, 34 insertions(+), 22 deletions(-)
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 03037f48..3b361e20 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -689,6 +689,40 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
atom_cnt = 0;
token_cnt = 0;
+ while ( fgets( line, MAX_LINE, bgf ) )
+ {
+ /* read new line and tokenize it */
+ strncpy( backup, line, MAX_LINE - 1 );
+ backup[MAX_LINE - 1] = '\0';
+ token_cnt = Tokenize( line, &tokens, MAX_TOKEN_LEN );
+
+ if ( strncmp( tokens[0], "CRYSTX", 6 ) == 0 )
+ {
+ sscanf( backup, BGF_CRYSTX_FORMAT, descriptor,
+ s_a, s_b, s_c, s_alpha, s_beta, s_gamma );
+
+ /* compute full volume tensor from the angles */
+ Setup_Box( sstrtod( s_a, __FILE__, __LINE__ ),
+ sstrtod( s_b, __FILE__, __LINE__ ),
+ sstrtod( s_c, __FILE__, __LINE__ ),
+ sstrtod( s_alpha, __FILE__, __LINE__ ),
+ sstrtod( s_beta, __FILE__, __LINE__ ),
+ sstrtod( s_gamma, __FILE__, __LINE__ ),
+ &system->box );
+
+ crystx_found = TRUE;
+ break;
+ }
+ }
+
+ if ( crystx_found == FALSE )
+ {
+ fprintf( stderr, "[ERROR] improperly formatted BGF file (no CRYSTX keyword found). Terminating...\n" );
+ exit( INVALID_INPUT );
+ }
+
+ fseek( bgf, 0, SEEK_SET );
+
while ( fgets( line, MAX_LINE, bgf ) )
{
/* read new line and tokenize it */
@@ -777,22 +811,6 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
atom_cnt++;
}
- else if ( strncmp( tokens[0], "CRYSTX", 6 ) == 0 )
- {
- sscanf( backup, BGF_CRYSTX_FORMAT, descriptor,
- s_a, s_b, s_c, s_alpha, s_beta, s_gamma );
-
- /* compute full volume tensor from the angles */
- Setup_Box( sstrtod( s_a, __FILE__, __LINE__ ),
- sstrtod( s_b, __FILE__, __LINE__ ),
- sstrtod( s_c, __FILE__, __LINE__ ),
- sstrtod( s_alpha, __FILE__, __LINE__ ),
- sstrtod( s_beta, __FILE__, __LINE__ ),
- sstrtod( s_gamma, __FILE__, __LINE__ ),
- &system->box );
-
- crystx_found = TRUE;
- }
else if ( strncmp( tokens[0], "CONECT", 6 ) == 0 )
{
if ( control->restrict_bonds )
@@ -835,12 +853,6 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
exit( INVALID_INPUT );
}
- if ( crystx_found == FALSE )
- {
- fprintf( stderr, "[ERROR] improperly formatted BGF file (no CRYSTX keyword found). Terminating...\n" );
- exit( INVALID_INPUT );
- }
-
Deallocate_Tokenizer_Space( &line, &backup, &tokens, MAX_TOKENS );
sfclose( bgf, "Read_BGF::bgf" );
--
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