Tools: fix geo_format for run_md_custom (geo file is mandatory, so the file...

Tools: fix geo_format for run_md_custom (geo file is mandatory, so the file type extension should always happen).

tools/run_sim.py

@@ -834,17 +834,14 @@ if __name__ == '__main__':
                     exit(-1)
 
         geo_base, geo_ext = path.splitext(args.geo_file[0])
-        if 'geo_format' in control_params_dict:
-            geo_format = control_params_dict['geo_format']
         # infer geometry file format by file extension
+        if geo_ext.lower() == '.pdb':
+            geo_format = ['1']
+        elif geo_ext.lower() == '.geo':
+            geo_format = ['0']
         else:
-            if geo_ext.lower() == '.pdb':
-                geo_format = ['1']
-            elif geo_ext.lower() == '.geo':
-                geo_format = ['0']
-            else:
-                print("[ERROR] unrecognized geometry format {0}. Terminating...".format(ext))
-                exit(-1)
+            print("[ERROR] unrecognized geometry format {0}. Terminating...".format(ext))
+            exit(-1)
 
         test_case = TestCase(geo_base, args.geo_file[0], args.ffield_file[0],
                 params=control_params_dict, geo_format=geo_format)