Merge pull request #1685 from ReactionMechanismGenerator/arkane_absolute

Allow relative paths in Arkane statmech

arkane/commonTest.py

@@ -457,5 +457,7 @@ def test_get_mass(self):
         self.assertEquals(get_element_mass('Bk'), (247.0703073, 97))  # test a two-element array (no isotope data)
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/explorerTest.py

@@ -96,5 +96,7 @@ def test_job_rxns(self):
             self.assertIn(rxn, self.explorer_job.networks[0].path_reactions)
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/gaussianTest.py

@@ -165,5 +165,7 @@ def test_determine_qm_software(self):
         self.assertIsInstance(log, GaussianLog)
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/inputTest.py

@@ -256,6 +256,5 @@ def test_process_model_chemistry(self):
 
 ################################################################################
 
-
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/kineticsTest.py

@@ -94,5 +94,7 @@ def test_get_tlist_for_kineticsjob(self):
                                                                            inverse_tlist[-1] - inverse_tlist[-2]))
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/mainTest.py

@@ -112,5 +112,7 @@ def tearDownClass(cls):
                         shutil.rmtree(item_path)
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/molproTest.py

@@ -157,5 +157,7 @@ def test_get_t1_diagnostic(self):
         self.assertAlmostEqual(t1_diagnostic, 0.01152184)
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/pdepTest.py

@@ -133,3 +133,9 @@ def tearDown(cls):
         for f in files:
             if 'pdep_sa' not in f:
                 os.remove(os.path.join(settings['test_data.directory'], 'arkane', 'tst1', f))
+
+
+################################################################################
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/qchemTest.py

@@ -125,5 +125,7 @@ def test_load_co_modes_from_qchem_log(self):
         self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, HinderedRotor)]) == 0)
 
 
+################################################################################
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/statmech.py

@@ -317,13 +317,19 @@ def load(self, pdep=False, plot=False):
             except KeyError:
                 raise InputError('Model chemistry {0!r} not found in from dictionary of energy values in species file '
                                  '{1!r}.'.format(self.modelChemistry, path))
+        if not os.path.isfile(energy.path):
+            modified_energy_path = os.path.join(directory, energy.path)
+            if not os.path.isfile(modified_energy_path):
+                raise InputError('Could not find single point energy file for species {0} '
+                                 'in the specified path {1}'.format(self.species.label, energy.path))
+            else:
+                energy.path = modified_energy_path
         e0, e_electronic = None, None  # E0 = e_electronic + ZPE
         energy_log = None
         if isinstance(energy, Log) and type(energy).__name__ == 'Log':
-            energy_log = determine_qm_software(os.path.join(directory, energy.path))
+            energy_log = determine_qm_software(energy.path)
         elif isinstance(energy, Log) and type(energy).__name__ != 'Log':
             energy_log = energy
-            energy_log.path = os.path.join(directory, energy_log.path)
         elif isinstance(energy, float):
             e_electronic = energy
         elif isinstance(energy, tuple) and len(energy) == 2:
@@ -345,16 +351,26 @@ def load(self, pdep=False, plot=False):
             statmech_log = local_context['frequencies']
         except KeyError:
             raise InputError('Required attribute "frequencies" not found in species file {0!r}.'.format(path))
+        if not os.path.isfile(statmech_log.path):
+            modified_statmech_path = os.path.join(directory, statmech_log.path)
+            if not os.path.isfile(modified_statmech_path):
+                raise InputError('Could not find Arkane statmech file for species {0} '
+                                 'in the specified path {1}'.format(self.species.label, statmech_log.path))
+            else:
+                statmech_log.path = modified_statmech_path
         if isinstance(statmech_log, Log) and type(statmech_log).__name__ == 'Log':
-            statmech_log = determine_qm_software(os.path.join(directory, statmech_log.path))
-        else:
-            statmech_log.path = os.path.join(directory, statmech_log.path)
+            statmech_log = determine_qm_software(statmech_log.path)
         try:
             geom_log = local_context['geometry']
+            if not os.path.isfile(geom_log.path):
+                modified_geom_path = os.path.join(directory, geom_log.path)
+                if not os.path.isfile(modified_geom_path):
+                    raise InputError('Could not find Arkane statmech file for species {0} '
+                                     'in the specified path {1}'.format(self.species.label, geom_log.path))
+                else:
+                    geom_log.path = modified_geom_path
             if isinstance(geom_log, Log) and type(geom_log).__name__ == 'Log':
-                geom_log = determine_qm_software(os.path.join(directory, geom_log.path))
-            else:
-                geom_log.path = os.path.join(directory, geom_log.path)
+                geom_log = determine_qm_software(geom_log.path)
         except KeyError:
             geom_log = statmech_log
             logging.debug("Reading geometry from the specified frequencies file.")
@@ -517,9 +533,15 @@ def load(self, pdep=False, plot=False):
                         # the symmetry number will be derived from the scan
                         scan_log, pivots, top, fit = q
                     # Load the hindered rotor scan energies
+                    if not os.path.isfile(scan_log.path):
+                        modified_scan_path = os.path.join(directory, scan_log.path)
+                        if not os.path.isfile(modified_scan_path):
+                            raise InputError('Could not find scan energy file for species {0} '
+                                             'in the specified path {1}'.format(self.species.label, scan_log.path))
+                        else:
+                            scan_log.path = modified_scan_path
                     if isinstance(scan_log, Log) and type(scan_log).__name__ == 'Log':
-                        scan_log = determine_qm_software(os.path.join(directory, scan_log.path))
-                    scan_log.path = os.path.join(directory, scan_log.path)
+                        scan_log = determine_qm_software(scan_log.path)
                     if isinstance(scan_log, (GaussianLog, QChemLog)):
                         v_list, angle = scan_log.load_scan_energies()
                         try:

arkane/statmechTest.py

@@ -37,6 +37,7 @@
 
 import numpy as np
 
+from rmgpy.species import Species
 from rmgpy.exceptions import InputError
 
 from arkane import Arkane
@@ -153,6 +154,48 @@ def test_is_linear(self):
         self.assertFalse(is_linear(xyz8))
         self.assertFalse(is_linear(xyz10))
 
+    def test_specifying_absolute_file_paths(self):
+        """Test specifying absolute file paths of statmech files"""
+        h2o2_input = """#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+bonds = {{'H-O': 2, 'O-O': 1}}
+
+externalSymmetry = 2
+
+spinMultiplicity = 1
+
+opticalIsomers = 1
+
+energy = {{'b3lyp/6-311+g(3df,2p)': Log('{energy}')}}
+
+geometry = Log('{freq}')
+
+frequencies = Log('{freq}')
+
+rotors = [HinderedRotor(scanLog=Log('{scan}'), pivots=[1, 2], top=[1, 3], symmetry=1, fit='fourier')]
+
+"""
+        abs_arkane_path = os.path.abspath(os.path.dirname(__file__))  # this is the absolute path to `.../RMG-Py/arkane`
+        energy_path = os.path.join('arkane', 'data', 'H2O2', 'sp_a19032.out')
+        freq_path = os.path.join('arkane', 'data', 'H2O2', 'freq_a19031.out')
+        scan_path = os.path.join('arkane', 'data', 'H2O2', 'scan_a19034.out')
+        h2o2_input = h2o2_input.format(energy=energy_path, freq=freq_path, scan=scan_path)
+        h2o2_path = os.path.join(abs_arkane_path, 'data', 'H2O2', 'H2O2.py')
+        if not os.path.exists(os.path.dirname(h2o2_path)):
+            os.makedirs(os.path.dirname(h2o2_path))
+        with open(h2o2_path, 'w') as f:
+            f.write(h2o2_input)
+        h2o2 = Species(label='H2O2', smiles='OO')
+        self.assertIsNone(h2o2.conformer)
+        statmech_job = StatMechJob(species=h2o2, path=h2o2_path)
+        statmech_job.modelChemistry = 'b3lyp/6-311+g(3df,2p)'
+        statmech_job.load(pdep=False, plot=False)
+        self.assertAlmostEqual(h2o2.conformer.E0.value_si, -146031.49933673252)
+        os.remove(h2o2_path)
+
+
+################################################################################
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arkane/thermoTest.py

@@ -65,8 +65,8 @@ def test_element_count_from_conformer(self):
         element_count = self.thermo_job.element_count_from_conformer()
         self.assertEqual(element_count, {'H': 4, 'C': 2})
 
-################################################################################
 
+################################################################################
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))