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dsvatunek · Apr 27, 2020 · 2c595d0 · 2c595d0
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/DIAS_inputparser.py b/DIAS_inputparser.py
@@ -277,13 +277,16 @@ def get_irc(file):
 	structures.xyz.append(np.array([x.split()[3:] for x in raw_coordinates]))
 	structures.atoms = [x.split()[1] for x in raw_coordinates]
 	structures.atoms = [periodic_table[int(x)] for x in structures.atoms]
-	# find everything except the TS structure
-	regex = r'---------------------------------------------------------------------((?:(?!---------------------------------------------------------------------).)*?)---------------------------------------------------------------------(?:(?!---------------------------------------------------------------------).)*?Delta-x\ Convergence\ Met'
-	for match in re.finditer(regex, file_contents, re.IGNORECASE|re.DOTALL):
+	# find everything except the TS structure for normal run
+	regex2 = r'---------------------------------------------------------------------((?:(?!---------------------------------------------------------------------).)*?)---------------------------------------------------------------------(?:(?!---------------------------------------------------------------------).)*?Delta-x\ Convergence\ Met'
+	for match in re.finditer(regex2, file_contents, re.IGNORECASE|re.DOTALL):
 		raw_coordinates = match.group(1).strip().split("\n")
 		structures.xyz.append(np.array([x.split()[3:] for x in raw_coordinates]))
-
-
+	# find everything except the TS structure for #p
+	regex3 = r'(?:(CURRENT).+?)(?:---------------------------------------------------------------------)(?:.*?(---------------------------------------------------------------------))(.*?)(?:(---------------------------------------------------------------------))'	
+	for match in re.finditer(regex3, file_contents, re.DOTALL):
+		raw_coordinates = match.group(3).strip().split("\n")
+		structures.xyz.append(np.array([x.split()[2:] for x in raw_coordinates]))
 	for i in range(len(structures.xyz)):
 		structures.xyz[i] = structures.xyz[i].astype(float)	
 	structures.title = [str(x) for x in range(len(structures.xyz))]

diff --git a/autoDIAS.py b/autoDIAS.py
@@ -11,7 +11,7 @@
 						Download the newest version from:
 					   https://github.com/dsvatunek/autoDIAS
 					   
-					 Please cite. DOI: 10.26434/chemrxiv.7789940
+					 Please cite. DOI: 10.1002/jcc.26023
 *****************************************************************************************				   
 
 Python wrapper for several computational chemistry software packages to automatically