Merge pull request #1521 from ReactionMechanismGenerator/mp_coord

Processing monoatomic species in Arkane/molpro
ReactionMechanismGenerator · Jan 3, 2019 · 99f712f · 99f712f
2 parents a70bd44 + bf04302
commit 99f712f
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/arkane/molpro.py b/arkane/molpro.py
@@ -66,7 +66,7 @@ def getNumberOfAtoms(self):
             # Automatically determine the number of atoms
             if 'ATOMIC COORDINATES' in line and Natoms == 0:
                 for i in range(4): line = f.readline()
-                while 'Bond lengths' not in line:
+                while 'Bond lengths' not in line and 'nuclear charge' not in line.lower():
                     Natoms += 1
                     line = f.readline()
             line = f.readline()
@@ -137,12 +137,13 @@ def loadGeometry(self):
         # Close file when finished
         f.close()
 
-        #If no optimized coordinates were found, uses the input geometry (for example if reading the geometry from a frequency file
+        # If no optimized coordinates were found, uses the input geometry
+        # (for example if reading the geometry from a frequency file)
         if coord == []:
             f = open(self.path, 'r')
             line = f.readline()
             while line != '':
-                if 'Atomic Coordinates' in line:
+                if 'atomic coordinates' in line.lower():
                     symbol = []; coord = []
                     for i in range(4):
                         line = f.readline()

diff --git a/arkane/statmech.py b/arkane/statmech.py
@@ -394,7 +394,11 @@ def load(self):
                                         atomEnergies=self.atomEnergies,
                                         applyAtomEnergyCorrections=self.applyAtomEnergyCorrections,
                                         applyBondEnergyCorrections=self.applyBondEnergyCorrections)
-            ZPE = statmechLog.loadZeroPointEnergy() * self.frequencyScaleFactor
+            if len(number) > 1:
+                ZPE = statmechLog.loadZeroPointEnergy() * self.frequencyScaleFactor
+            else:
+                # Monoatomic species don't have frequencies
+                ZPE = 0.0
             logging.debug('Corrected minimum energy is {0} J/mol'.format(E0))
             # The E0_withZPE at this stage contains the ZPE
             E0_withZPE = E0 + ZPE