RMG-Py v2.4.1 release

Author: mliu49

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))
@@ -347,7 +372,7 @@ def get_element_mass(input_element, isotope=None):
     else:
         # no specific isotope is required
         if len(mass_list[0]) == 2:
-            # isotop weight is unavailable, use the first entry
+            # isotope weight is unavailable, use the first entry
             mass = mass_list[0][1]
             logging.warn("Assuming isotop {0} is representative of element {1}".format(mass_list[0][0], symbol))
         else:

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
@@ -248,9 +249,9 @@ def testSpeciesStatmech(self):
         job.includeHinderedRotors = self.useHinderedRotors
         job.applyBondEnergyCorrections = self.useBondCorrections
         job.load()
-        self.assertTrue(isinstance(job.species.props['elementCounts'], dict))
-        self.assertEqual(job.species.props['elementCounts']['C'], 2)
-        self.assertEqual(job.species.props['elementCounts']['H'], 4)
+        self.assertTrue(isinstance(job.species.props['element_counts'], dict))
+        self.assertEqual(job.species.props['element_counts']['C'], 2)
+        self.assertEqual(job.species.props['element_counts']['H'], 4)
 
     def testSpeciesThermo(self):
         """Test thermo job execution for species from separate input file."""
@@ -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, 0.99*1.014)  # 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/encorr/__init__.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+initialize imports
+"""
+
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2019 Prof. William H. Green ([email protected]),           #
+# Prof. Richard H. West ([email protected]) and the RMG Team ([email protected])   #
+#                                                                             #
+# Permission is hereby granted, free of charge, to any person obtaining a     #
+# copy of this software and associated documentation files (the 'Software'),  #
+# to deal in the Software without restriction, including without limitation   #
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,    #
+# and/or sell copies of the Software, and to permit persons to whom the       #
+# Software is furnished to do so, subject to the following conditions:        #
+#                                                                             #
+# The above copyright notice and this permission notice shall be included in  #
+# all copies or substantial portions of the Software.                         #
+#                                                                             #
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,    #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER      #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING     #
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER         #
+# DEALINGS IN THE SOFTWARE.                                                   #
+#                                                                             #
+###############################################################################