Moved generateQMData to higher QMMolecule class along with minor modifications

Author: keceli

rmgpy/qm/gaussian.py

@@ -51,8 +51,7 @@ def run(self):
         # submits the input file to Gaussian
         process = Popen([self.executablePath, self.inputFilePath, self.outputFilePath])
         process.communicate()# necessary to wait for executable termination!
-        import time
-        time.sleep(1)
+        
         return self.verifyOutputFile()
 
     def verifyOutputFile(self):
@@ -185,28 +184,6 @@ def inputFileKeywords(self, attempt):
         """
         raise NotImplementedError("Should be defined by subclass, eg. GaussianMolPM3")
 
-    def generateQMData(self):
-        """
-        Calculate the QM data and return a QMData object.
-        """
-        self.createGeometry()
-        if self.verifyOutputFile():
-            logging.info("Found a successful output file already; using that.")
-        else:
-            success = False
-            for attempt in range(1, self.maxAttempts+1):
-                self.writeInputFile(attempt)
-                success = self.run()
-                if success:
-                    logging.info('Attempt {0} of {1} on species {2} succeeded.'.format(attempt, self.maxAttempts, self.molecule.toAugmentedInChI()))
-                    break
-            else:
-                logging.error('QM thermo calculation failed for {0}.'.format(self.molecule.toAugmentedInChI()))
-                return None
-        result = self.parse() # parsed in cclib
-        return result
-    
-
 
 class GaussianMolPM3(GaussianMol):
 
@@ -251,4 +228,4 @@ def inputFileKeywords(self, attempt):
         assert attempt <= self.maxAttempts
         if attempt > self.scriptAttempts:
             attempt -= self.scriptAttempts
-        return self.keywords[attempt-1]
+        return self.keywords[attempt-1]

rmgpy/qm/main.py

@@ -96,7 +96,7 @@ def __init__(self,
 
     def setDefaultOutputDirectory(self, outputDirectory):
         """
-        IF the fileStore or scratchDirectory are not already set, put them in here.
+        If the fileStore or scratchDirectory are not already set, put them in here.
         """
         if not self.settings.fileStore:
             self.settings.fileStore = os.path.join(outputDirectory, 'QMfiles')
@@ -124,7 +124,8 @@ def checkPaths(self):
         """
         self.settings.fileStore = os.path.expandvars(self.settings.fileStore) # to allow things like $HOME or $RMGpy
         self.settings.scratchDirectory = os.path.expandvars(self.settings.scratchDirectory)
-        for path in [self.settings.fileStore, self.settings.scratchDirectory]:
+#        for path in [self.settings.fileStore, self.settings.scratchDirectory]:
+        for path in [self.settings.fileStore]:
             if not os.path.exists(path):
                 logging.info("Creating directory %s for QM files."%os.path.abspath(path))
                 os.makedirs(path)
@@ -148,7 +149,7 @@ def getThermoData(self, molecule):
         mopacPM7: PM7, excludes computational results from training set, might be better or slightly worse compared to PM6
         gaussian: Only PM3 is available. 
         """
-        if self.settings.software == 'mopac':
+        if self.settings.software == 'mopac' or self.settings.software == 'mopacPM3':
             qm_molecule_calculator = rmgpy.qm.mopac.MopacMolPM3(molecule, self.settings)
             thermo0 = qm_molecule_calculator.generateThermoData()
         elif self.settings.software == 'mopacPM6':

rmgpy/qm/molecule.py

@@ -202,10 +202,27 @@ def createGeometry(self):
 
     def generateQMData(self):
         """
-        Calculate the QM data somehow and return a CCLibData object, or None if it fails.
+        Calculate the QM data and return a QMData object, or None if it fails.
         """
-        raise NotImplementedError("This should be defined in a subclass that inherits from QMMolecule")
-        return qmdata.QMData() or None
+        if self.verifyOutputFile():
+            logging.info("Found a successful output file already; using that.")
+            source = "QM {0} result file found from previous run.".format(self.__class__.__name__)
+        else:
+            self.createGeometry()
+            success = False
+            for attempt in range(1, self.maxAttempts+1):
+                self.writeInputFile(attempt)
+                logging.info('Trying {3} attempt {0} of {1} on molecule {2}.'.format(attempt, self.maxAttempts, self.molecule.toSMILES(), self.__class__.__name__))
+                success = self.run()
+                if success:
+                    source = "QM {0} calculation attempt {1}".format(self.__class__.__name__, attempt )
+                    break
+            else:
+                logging.error('QM thermo calculation failed for {0}.'.format(self.molecule.toAugmentedInChI()))
+                return None
+        result = self.parse() # parsed in cclib
+        result.source = source
+        return result # a CCLibData object
 
     def generateThermoData(self):
         """

rmgpy/qm/mopac.py

@@ -63,9 +63,7 @@ def run(self):
         # submits the input file to mopac
         process = Popen([self.executablePath, self.inputFilePath])
         process.communicate()# necessary to wait for executable termination!
-        #Wait for OS to flush the buffer to disk. There should be a better way
- #       import time
- #       time.sleep(1)
+    
         return self.verifyOutputFile()
 
     def verifyOutputFile(self):
@@ -88,7 +86,7 @@ def verifyOutputFile(self):
         if not os.path.exists(self.outputFilePath):
             logging.debug("Output file {0} does not (yet) exist.".format(self.outputFilePath))
             return False
-        
+    
         InChIMatch=False #flag (1 or 0) indicating whether the InChI in the file matches InChIaug this can only be 1 if InChIFound is also 1
         InChIFound=False #flag (1 or 0) indicating whether an InChI was found in the log file
 
@@ -195,31 +193,6 @@ def inputFileKeywords(self, attempt):
         """
         raise NotImplementedError("Should be defined by subclass, eg. MopacMolPM3")
 
-    def generateQMData(self):
-        """
-        Calculate the QM data and return a QMData object, or None if it fails.
-        """
-        if self.verifyOutputFile():
-            logging.info("Found a successful output file already; using that.")
-            source = "QM MOPAC result file found from previous run."
-        else:
-            self.createGeometry()
-            success = False
-            for attempt in range(1, self.maxAttempts+1):
-                self.writeInputFile(attempt)
-                logging.info('Trying {3} attempt {0} of {1} on molecule {2}.'.format(attempt, self.maxAttempts, self.molecule.toSMILES(), self.__class__.__name__))
-                success = self.run()
-                if success:
-                    source = "QM {0} calculation attempt {1}".format(self.__class__.__name__, attempt )
-                    break
-            else:
-                logging.error('QM thermo calculation failed for {0}.'.format(self.molecule.toAugmentedInChI()))
-                return None
-        result = self.parse() # parsed in cclib
-        result.source = source
-        return result # a CCLibData object
-
-
 class MopacMolPM3(MopacMol):
 
     #: Keywords that will be added at the top and bottom of the qm input file
@@ -368,4 +341,4 @@ def inputFileKeywords(self, attempt):
                 multiplicity_keys,
                 )
 
-        return top_keys, bottom_keys, polar_keys    
+        return top_keys, bottom_keys, polar_keys    

rmgpy/rmg/model.py

@@ -74,7 +74,7 @@ def makeThermoForSpecies(spec,qmValue=None):
         import cPickle, logging
         filename = scoop.shared.getConst('databaseFile')
         database_hash = scoop.shared.getConst('databaseHash')
-        logging.info('Loading database pickle2 file from {0!r} on worker {1}'.format(filename, scoop.WORKER_NAME.decode() ))
+        #logging.info('Loading database pickle2 file from {0!r} on worker {1}'.format(filename, scoop.WORKER_NAME.decode() ))
         f = open(filename, 'rb')
         __database = cPickle.load(f)
         f.close()