fix QChem for ZimmermanGroup#15 and fix the missing variable in se_gsm

Author: ms860309

pygsm/growing_string_methods/se_gsm.py

@@ -164,7 +164,7 @@ def go_gsm(self,max_iters=50,opt_steps=10,rtype=2):
 
         filename="opt_converged_{:03d}.xyz".format(self.ID)
         print(" Printing string to " + filename)
-        self.xyz_writer(filename,self.geometries,self.energies,self.gradrms,self.dEs)
+        self.xyz_writer(filename,self.geometries,self.energies,self.gradrmss,self.dEs)
         print("Finished GSM!")  
 
 

pygsm/level_of_theories/qchem.py

@@ -96,11 +96,11 @@ def run(self,geom,multiplicity,ad_idx,runtype='gradient'):
         #  Run the process
         output = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr = subprocess.PIPE).communicate()[0]
 
-        self.parse()
+        self.parse(qcscratch, multiplicity)
 
         return 
 
-    def parse(self):
+    def parse(self, qcscratch, multiplicity):
         # PARSE OUTPUT #
         if self.calc_grad:
             efilepath = qcscratch + '/string_{:03d}/{}.{}/GRAD'.format(self.ID,self.node_id,multiplicity)