From cf669ba9fc1b130f461736fabb9dc79bb88ee1cd Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Wed, 3 Mar 2021 15:20:19 -0500
Subject: [PATCH] sPuReMD: fix geo_tools parsers not recognizing element types
with 2 character names.
---
sPuReMD/src/geo_tools.c | 19 ++++++++++++++++++-
1 file changed, 18 insertions(+), 1 deletion(-)
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index f01e1e4a..03037f48 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -26,6 +26,8 @@
#include "tool_box.h"
#include "vector.h"
+#include <ctype.h>
+
// CUSTOM_BOXGEO: BOXGEO box_x box_y box_z angle1 angle2 angle3
#define CUSTOM_BOXGEO_FORMAT " %s %lf %lf %lf %lf %lf %lf"
@@ -286,7 +288,7 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
simulation_data *data, static_storage *workspace )
{
FILE *geo;
- int i, n, serial, top;
+ int i, j, n, serial, top;
rvec x;
char element[3], name[9];
reax_atom *atom;
@@ -314,6 +316,13 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
{
fscanf( geo, CUSTOM_ATOM_FORMAT,
&serial, element, name, &x[0], &x[1], &x[2] );
+
+ for ( j = 0; j < sizeof(element) - 1; ++j )
+ {
+ element[j] = toupper( element[j] );
+ }
+ element[sizeof(element) - 1] = '\0';
+
Fit_to_Periodic_Box( &system->box, x );
#if defined(DEBUG_FOCUS)
@@ -470,6 +479,10 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
workspace->orig_id[top] = pdb_serial;
Trim_Spaces( element, sizeof(element) );
+ for ( i = 0; i < sizeof(element) - 1; ++i )
+ {
+ element[i] = toupper( element[i] );
+ }
atom->type = Get_Atom_Type( &system->reax_param, element, sizeof(element) );
strncpy( atom->name, atom_name, sizeof(atom->name) - 1 );
atom->name[sizeof(atom->name) - 1] = '\0';
@@ -745,6 +758,10 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
sizeof(system->atoms[atom_cnt].name) - 1 );
system->atoms[atom_cnt].name[sizeof(system->atoms[atom_cnt].name) - 1] = '\0';
Trim_Spaces( element, sizeof(element) );
+ for ( i = 0; i < sizeof(element) - 1; ++i )
+ {
+ element[i] = toupper( element[i] );
+ }
system->atoms[atom_cnt].type =
Get_Atom_Type( &system->reax_param, element, sizeof(element) );
--
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