A few bugfixes

ConfPrune.pyx

@@ -118,7 +118,7 @@ def AlignMolecules(mol1, mol2, atoms):
         atomnum = GetAtomNum(a)
         #w.append(GetAtomWeight(atomnum))
         w.append(1)
-    
+
     #move both molecules to origin
     mol1 = Move2Origin(mol1, w)
     mol2 = Move2Origin(mol2, w)
@@ -139,10 +139,10 @@ def AlignedRMS(mol1, mol2, atoms):
     mol1b = []
     mol2b = []
     for a in mol1:
-        mol1b.append([float(x) for x in a[1:]])
+        mol1b.append([float(x) for x in a])
 
     for a in mol2:
-        mol2b.append([float(x) for x in a[1:]])
+        mol2b.append([float(x) for x in a])
 
     (amol1, amol2, w) = AlignMolecules(mol1b, mol2b, atoms)
 

Gaussian.py

@@ -14,7 +14,6 @@
 import subprocess
 import os
 import time
-import glob
 
 
 def SetupNMRCalcs(Isomers, settings):
@@ -159,6 +158,8 @@ def Converged(Isomers):
 
 def RunNMRCalcs(Isomers, settings):
 
+    print('\nRunning Gaussian DFT NMR calculations locally...')
+
     jobdir = os.getcwd()
     os.chdir('nmr')
 
@@ -179,6 +180,8 @@ def RunNMRCalcs(Isomers, settings):
 
 def RunECalcs(Isomers, settings):
 
+    print('\nRunning Gaussian DFT energy calculations locally...')
+
     jobdir = os.getcwd()
     os.chdir('e')
 
@@ -197,6 +200,28 @@ def RunECalcs(Isomers, settings):
     return Isomers
 
 
+def RunOptCalcs(Isomers, settings):
+
+    print('\nRunning Gaussian DFT geometry optimizations locally...')
+
+    jobdir = os.getcwd()
+    os.chdir('opt')
+
+    GausJobs = []
+
+    for iso in Isomers:
+        GausJobs.extend([x for x in iso.OptInputFiles if (x[:-4] + '.out') not in iso.OptOutputFiles])
+
+    Completed = RunCalcs(GausJobs)
+
+    for iso in Isomers:
+        iso.OptOutputFiles.extend([x[:-4] + '.out' for x in iso.OptInputFiles if (x[:-4] + '.out') in Completed])
+
+    os.chdir(jobdir)
+
+    return Isomers
+
+
 def RunCalcs(GausJobs):
 
     NCompleted = 0
@@ -340,7 +365,7 @@ def ReadEnergies(Isomers, settings):
     else:
         os.chdir('nmr')
 
-    for iso in Isomers:
+    for i, iso in enumerate(Isomers):
 
         if 'e' in settings.Workflow:
             GOutpFiles = iso.EOutputFiles
@@ -349,7 +374,7 @@ def ReadEnergies(Isomers, settings):
         else:
             GOutpFiles = iso.NMROutputFiles
 
-        DFTenergies = []
+        DFTEnergies = []
         for GOutpFile in GOutpFiles:
             gausfile = open(GOutpFile, 'r')
             GOutp = gausfile.readlines()
@@ -361,7 +386,10 @@ def ReadEnergies(Isomers, settings):
                     end = line.index('A.U.')
                     energy = float(line[start + 4:end])
 
-            iso.DFTEnergies.append(energy)
+            #iso.DFTEnergies.append(energy)
+            DFTEnergies.append(energy)
+
+        Isomers[i].DFTEnergies = DFTEnergies
 
     os.chdir(jobdir)
     return Isomers

GaussianDarwin.py

@@ -18,6 +18,8 @@
 
 import Gaussian
 
+MaxConcurrentJobs = 160
+
 SetupNMRCalcs = Gaussian.SetupNMRCalcs
 
 SetupECalcs = Gaussian.SetupECalcs
@@ -102,7 +104,7 @@ def RunOptCalcs(Isomers, settings):
 
 def RunCalcs(GausJobs, settings):
 
-    MaxCon = settings.MaxConcurrentJobs
+    MaxCon = MaxConcurrentJobs
 
     if len(GausJobs) < MaxCon:
         if len(GausJobs) > 0: