Merge pull request #1643 from ReactionMechanismGenerator/recursive_as…

…_dictionary

Recursive as dictionary

arkane/common.py

@@ -52,7 +52,7 @@
 from rmgpy.statmech.vibration import HarmonicOscillator
 from rmgpy.pdep.collision import SingleExponentialDown
 from rmgpy.transport import TransportData
-from rmgpy.thermo import NASA, Wilhoit
+from rmgpy.thermo import NASA, Wilhoit, ThermoData, NASAPolynomial
 from rmgpy.species import Species, TransitionState
 import rmgpy.constants as constants
 
@@ -180,16 +180,19 @@ def update_species_attributes(self, species=None):
                 self.energy_transfer_model = species.energyTransferModel
             if species.thermo is not None:
                 self.thermo = species.thermo.as_dict()
-                thermo_data = species.getThermoData()
-                h298 = thermo_data.getEnthalpy(298) / 4184.
-                s298 = thermo_data.getEntropy(298) / 4.184
-                cp = dict()
-                for t in [300, 400, 500, 600, 800, 1000, 1500, 2000, 2400]:
-                    temp_str = '{0} K'.format(t)
-                    cp[temp_str] = '{0:.2f}'.format(thermo_data.getHeatCapacity(t) / 4.184)
-                self.thermo_data = {'H298': '{0:.2f} kcal/mol'.format(h298),
-                                    'S298': '{0:.2f} cal/mol*K'.format(s298),
-                                    'Cp (cal/mol*K)': cp}
+                data = species.getThermoData()
+                h298 = data.getEnthalpy(298) / 4184.
+                s298 = data.getEntropy(298) / 4.184
+                temperatures = numpy.array([300, 400, 500, 600, 800, 1000, 1500, 2000, 2400])
+                cp = []
+                for t in temperatures:
+                    cp.append(data.getHeatCapacity(t) / 4.184)
+
+                self.thermo_data = ThermoData(H298=(h298, 'kcal/mol'),
+                                              S298=(s298, 'cal/(mol*K)'),
+                                              Tdata=(temperatures, 'K'),
+                                              Cpdata=(cp, 'cal/(mol*K)'),
+                                              )
 
     def update_xyz_string(self):
         """
@@ -228,21 +231,30 @@ def save_yaml(self, path):
             yaml.dump(data=self.as_dict(), stream=f)
         logging.debug('Dumping species {0} data as {1}'.format(self.label, filename))
 
-    def load_yaml(self, path, species, pdep=False):
+    def load_yaml(self, path, label=None, pdep=False):
         """
         Load the all statMech data from the .yml file in `path` into `species`
         `pdep` is a boolean specifying whether or not jobList includes a pressureDependentJob.
         """
-        logging.info('Loading statistical mechanics parameters for {0} from .yml file...'.format(species.label))
+        yml_file = os.path.basename(path)
+        if label:
+            logging.info('Loading statistical mechanics parameters for {0} from {1} file...'.format(label, yml_file))
+        else:
+            logging.info('Loading statistical mechanics parameters from {0} file...'.format(yml_file))
         with open(path, 'r') as f:
             data = yaml.safe_load(stream=f)
-        try:
-            if species.label != data['label']:
-                logging.debug('Found different labels for species: {0} in input file, and {1} in the .yml file. '
-                              'Using the label "{0}" for this species.'.format(species.label, data['label']))
-        except KeyError:
-            # Lacking label in the YAML file is strange, but accepted
-            logging.debug('Did not find label for species {0} in .yml file.'.format(species.label))
+        if label:
+            # First, warn the user if the label doesn't match
+            try:
+                if label != data['label']:
+                    logging.debug('Found different labels for species: {0} in input file, and {1} in the .yml file. '
+                                  'Using the label "{0}" for this species.'.format(label, data['label']))
+            except KeyError:
+                # Lacking label in the YAML file is strange, but accepted
+                logging.debug('Did not find label for species {0} in .yml file.'.format(label))
+
+            # Then, set the ArkaneSpecies label to the user supplied label
+            data['label'] = label
         try:
             class_name = data['class']
         except KeyError:
@@ -265,19 +277,32 @@ def load_yaml(self, path, species, pdep=False):
                       'SingleExponentialDown': SingleExponentialDown,
                       'Wilhoit': Wilhoit,
                       'NASA': NASA,
+                      'NASAPolynomial': NASAPolynomial,
+                      'ThermoData': ThermoData,
+                      'np_array': numpy.array,
                       }
         freq_data = None
         if 'imaginary_frequency' in data:
             freq_data = data['imaginary_frequency']
             del data['imaginary_frequency']
+        if not data['is_ts']:
+            if 'smiles' in data:
+                data['species'] = Species(SMILES=data['smiles'])
+            elif 'adjacency_list' in data:
+                data['species'] = Species().fromAdjacencyList(data['adjacency_list'])
+            elif 'inchi' in data:
+                data['species'] = Species(InChI=data['inchi'])
+            else:
+                raise ValueError('Cannot load ArkaneSpecies from YAML file {0}. Either `smiles`, `adjacency_list`, or '
+                                 'InChI must be specified'.format(path))
+            # Finally, set the species label so that the special attributes are updated properly
+            data['species'].label = data['label']
+
         self.make_object(data=data, class_dict=class_dict)
         if freq_data is not None:
             self.imaginary_frequency = ScalarQuantity()
-            self.imaginary_frequency.make_object(data=freq_data, class_dict=dict())
-        self.adjacency_list = data['adjacency_list'] if 'adjacency_list' in data else None
-        self.inchi = data['inchi'] if 'inchi' in data else None
-        self.smiles = data['smiles'] if 'smiles' in data else None
-        self.is_ts = data['is_ts'] if 'is_ts' in data else False
+            self.imaginary_frequency.make_object(data=freq_data, class_dict=class_dict)
+
         if pdep and not self.is_ts and (self.transport_data is None or self.energy_transfer_model is None):
             raise ValueError('Transport data and an energy transfer model must be given if pressure-dependent '
                              'calculations are requested. Check file {0}'.format(path))

arkane/commonTest.py

@@ -40,9 +40,10 @@
 
 import rmgpy
 import rmgpy.constants as constants
+from rmgpy.pdep.collision import SingleExponentialDown
 from rmgpy.species import Species, TransitionState
 from rmgpy.quantity import ScalarQuantity
-from rmgpy.thermo import NASA
+from rmgpy.thermo import NASA, ThermoData
 
 from arkane import Arkane, input
 from arkane.common import ArkaneSpecies, get_element_mass
@@ -334,25 +335,65 @@ def test_dump_yaml(self):
             job.execute(outputFile=self.dump_output_file)
         self.assertTrue(os.path.isfile(self.dump_yaml_file))
 
-    def test_load_yaml(self):
+    def test_create_and_load_yaml(self):
         """
         Test properly loading the ArkaneSpecies object and respective sub-objects
         """
-        jobList = self.arkane.loadInputFile(self.load_input_path)
+        # Create YAML file by running Arkane
+        jobList = self.arkane.loadInputFile(self.dump_input_path)
         for job in jobList:
-            job.execute(outputFile=self.load_output_file)
-        arkane_spc = jobList[0].arkane_species
+            job.execute(outputFile=self.dump_output_file)
+
+        # Load in newly created YAML file
+        arkane_spc_old = jobList[0].arkane_species
+        arkane_spc = ArkaneSpecies.__new__(ArkaneSpecies)
+        arkane_spc.load_yaml(path=os.path.join(self.dump_path, 'species', arkane_spc_old.label + '.yml'))
+
+        self.assertIsInstance(arkane_spc, ArkaneSpecies)  # checks make_object
+        self.assertIsInstance(arkane_spc.molecular_weight, ScalarQuantity)
+        self.assertIsInstance(arkane_spc.thermo, NASA)
+        self.assertNotEqual(arkane_spc.author, '')
+        self.assertEqual(arkane_spc.inchi, 'InChI=1S/C2H6/c1-2/h1-2H3')
+        self.assertEqual(arkane_spc.inchi_key, 'OTMSDBZUPAUEDD-UHFFFAOYSA-N')
+        self.assertEqual(arkane_spc.smiles, 'CC')
+        self.assertTrue('8 H u0 p0 c0 {2,S}' in arkane_spc.adjacency_list)
+        self.assertEqual(arkane_spc.label, 'C2H6')
+        self.assertEqual(arkane_spc.frequency_scale_factor, 1.00386)  # checks float conversion
+        self.assertFalse(arkane_spc.use_bond_corrections)
+        self.assertAlmostEqual(arkane_spc.conformer.modes[2].frequencies.value_si[0], 830.38202, 4)  # HarmonicOsc.
+        self.assertIsInstance(arkane_spc.energy_transfer_model, SingleExponentialDown)
+        self.assertFalse(arkane_spc.is_ts)
+        self.assertEqual(arkane_spc.level_of_theory, 'cbs-qb3')
+        self.assertIsInstance(arkane_spc.thermo_data, ThermoData)
+        self.assertTrue(arkane_spc.use_hindered_rotors)
+        self.assertTrue('C 7.54e-14 1.193e-13 5.52e-14' in arkane_spc.xyz)
+        self.assertIsInstance(arkane_spc.chemkin_thermo_string, str)
+
+    def test_load_existing_yaml(self):
+        """
+        Test that existing Arkane YAML files can still be loaded
+        """
+        # Load in YAML file
+        arkane_spc = ArkaneSpecies.__new__(ArkaneSpecies)
+        arkane_spc.load_yaml(path=os.path.join(self.load_path, 'C2H6.yml'))
+
         self.assertIsInstance(arkane_spc, ArkaneSpecies)  # checks make_object
         self.assertIsInstance(arkane_spc.molecular_weight, ScalarQuantity)
         self.assertIsInstance(arkane_spc.thermo, NASA)
         self.assertNotEqual(arkane_spc.author, '')
         self.assertEqual(arkane_spc.inchi, 'InChI=1S/C2H6/c1-2/h1-2H3')
+        self.assertEqual(arkane_spc.inchi_key, 'OTMSDBZUPAUEDD-UHFFFAOYSA-N')
         self.assertEqual(arkane_spc.smiles, 'CC')
         self.assertTrue('8 H u0 p0 c0 {2,S}' in arkane_spc.adjacency_list)
         self.assertEqual(arkane_spc.label, 'C2H6')
         self.assertEqual(arkane_spc.frequency_scale_factor, 0.99)  # checks float conversion
         self.assertFalse(arkane_spc.use_bond_corrections)
         self.assertAlmostEqual(arkane_spc.conformer.modes[2].frequencies.value_si[0], 818.91718, 4)  # HarmonicOsc.
+        self.assertIsInstance(arkane_spc.energy_transfer_model, SingleExponentialDown)
+        self.assertFalse(arkane_spc.is_ts)
+        self.assertTrue(arkane_spc.use_hindered_rotors)
+        self.assertTrue('C 7.54e-14 1.193e-13 5.52e-14' in arkane_spc.xyz)
+        self.assertIsInstance(arkane_spc.chemkin_thermo_string, str)
 
     @classmethod
     def tearDownClass(cls):

arkane/statmech.py

@@ -209,7 +209,7 @@ def load(self, pdep=False):
         is_ts = isinstance(self.species, TransitionState)
         _, file_extension = os.path.splitext(path)
         if file_extension in ['.yml', '.yaml']:
-            self.arkane_species.load_yaml(path=path, species=self.species, pdep=pdep)
+            self.arkane_species.load_yaml(path=path, label=self.species.label, pdep=pdep)
             self.species.conformer = self.arkane_species.conformer
             if is_ts:
                 self.species.frequency = self.arkane_species.imaginary_frequency

rmgpy/quantity.pxd

@@ -29,9 +29,11 @@ cimport numpy
 
 cpdef list NOT_IMPLEMENTED_UNITS
 
+from rmgpy.rmgobject cimport RMGObject
+
 ################################################################################
 
-cdef class Units(object):
+cdef class Units(RMGObject):
 
     cdef public str units
 
@@ -51,8 +53,6 @@ cdef class ScalarQuantity(Units):
 
     cpdef dict as_dict(self)
 
-    cpdef make_object(self, dict data, dict class_dict)
-
     cpdef str getUncertaintyType(self)
     cpdef     setUncertaintyType(self, str v)
 
@@ -72,8 +72,6 @@ cdef class ArrayQuantity(Units):
 
     cpdef dict as_dict(self)
 
-    cpdef make_object(self, dict data, dict class_dict)
-
     cpdef str getUncertaintyType(self)
     cpdef     setUncertaintyType(self, str v)
 

rmgpy/quantity.py

@@ -41,6 +41,7 @@
 
 import rmgpy.constants as constants
 from rmgpy.exceptions import QuantityError
+from rmgpy.rmgobject import RMGObject, expand_to_dict
 
 ################################################################################
 
@@ -70,7 +71,7 @@
 
 ################################################################################
 
-class Units(object):
+class Units(RMGObject):
     """
     The :class:`Units` class provides a representation of the units of a
     physical quantity. The attributes are:
@@ -227,19 +228,6 @@ def as_dict(self):
             output_dict['uncertainty'] = self.uncertainty
             output_dict['uncertaintyType'] = self.uncertaintyType
         return output_dict
-
-    def make_object(self, data, class_dict):
-        """
-        A helper function for YAML parsing
-        """
-        # the `class_dict` parameter isn't used here, it is passed by default when calling the `make_object()` methods
-        if 'units' in data:
-            self.units = data['units']
-        self.value = data['value']
-        if 'uncertaintyType' in data:
-            self.uncertaintyType = data['uncertaintyType']
-        if 'uncertainty' in data:
-            self.uncertainty = data['uncertainty']
 
     def copy(self):
         """
@@ -461,29 +449,16 @@ def as_dict(self):
         """
         output_dict = dict()
         output_dict['class'] = self.__class__.__name__
-        output_dict['value'] = self.value.tolist()
+        output_dict['value'] = expand_to_dict(self.value)
         if self.units != '':
             output_dict['units'] = self.units
         if self.uncertainty is not None and any([val != 0.0 for val in numpy.nditer(self.uncertainty)]):
             logging.info(self.uncertainty)
             logging.info(type(self.uncertainty))
-            output_dict['uncertainty'] = self.uncertainty.tolist()
+            output_dict['uncertainty'] = expand_to_dict(self.uncertainty)
             output_dict['uncertaintyType'] = self.uncertaintyType
         return output_dict
 
-    def make_object(self, data, class_dict):
-        """
-        A helper function for YAML parsing
-        """
-        # the `class_dict` parameter isn't used here, it is passed by default when calling the `make_object()` methods
-        if 'units' in data:
-            self.units = data['units']
-        self.value = data['value']
-        if 'uncertaintyType' in data:
-            self.uncertaintyType = data['uncertaintyType']
-        if 'uncertainty' in data:
-            self.uncertainty = data['uncertainty']
-
     def copy(self):
         """
         Return a copy of the quantity.