Merge pull request mantidproject#20544 from dymkowsk/AbinsGaussianFix

Abins gaussian fix
liquidmet · Sep 22, 2017 · 5b5c5a7 · 5b5c5a7
2 parents abf70ef + 77c655f
commit 5b5c5a7
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Showing 16 changed files with 73 additions and 32 deletions.
diff --git a/Framework/PythonInterface/plugins/algorithms/Abins.py b/Framework/PythonInterface/plugins/algorithms/Abins.py
@@ -58,7 +58,7 @@ def PyInit(self):
         self.declareProperty(FileProperty("PhononFile", "",
                              action=FileAction.Load,
                              direction=Direction.Input,
-                             extensions=["phonon", "out", "outmol", "log"]),
+                             extensions=["phonon", "out", "outmol", "log", "LOG"]),
                              doc="File with the data from a phonon calculation.")
 
         self.declareProperty(FileProperty("ExperimentalFile", "",
@@ -610,7 +610,7 @@ def _validate_dft_file_extension(self, filename_full_path=None, expected_file_ex
 
         # check  extension of a file
         found_filename_ext = os.path.splitext(filename_full_path)[1]
-        if found_filename_ext != expected_file_extension:
+        if found_filename_ext.lower() != expected_file_extension:
             return dict(Invalid=True,
                         Comment=msg_err + "Output from DFT program " + dft_program + " is expected." +
                                           " The expected extension of file is ." + expected_file_extension +

diff --git a/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN.LOG.md5 b/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN.LOG.md5
@@ -0,0 +1 @@
+03c06bc4afe62ae6e224fcb2e2d525c8
diff --git a/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_atomic_displacements_data_0.txt.md5 b/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_atomic_displacements_data_0.txt.md5
@@ -0,0 +1 @@
+8558dff4ff22e0e087220639b6e7acbc
diff --git a/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_data.txt.md5 b/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_data.txt.md5
@@ -0,0 +1 @@
+2032778ae20e60af1de825be6248aff3
diff --git a/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN.LOG.md5 b/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN.LOG.md5
@@ -0,0 +1 @@
+149d08e3ec152b17663792ef7f3bf59b
diff --git a/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_atomic_displacements_data_0.txt.md5 b/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_atomic_displacements_data_0.txt.md5
@@ -0,0 +1 @@
+b102805ec68153e4279ff4546ee92a5b
diff --git a/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_data.txt.md5 b/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_data.txt.md5
@@ -0,0 +1 @@
+ee3349c525b6601afc84643acc49fdc8
diff --git a/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN.log.md5 b/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN.log.md5
@@ -0,0 +1 @@
+689a5221e1843b715ddf4430dc692026
diff --git a/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_atomic_displacements_data_0.txt.md5 b/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_atomic_displacements_data_0.txt.md5
@@ -0,0 +1 @@
+98450f7b27e05c8a50232f2ffb85ec03
diff --git a/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_data.txt.md5 b/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_data.txt.md5
@@ -0,0 +1 @@
+26850832776754a46affe765b25ca483
diff --git a/scripts/AbinsModules/GeneralLoadDFTTester.py b/scripts/AbinsModules/GeneralLoadDFTTester.py
@@ -61,17 +61,27 @@ def _check_reader_data(self, correct_data=None, data=None, filename=None, extens
         self.assertEqual(correct_data["attributes"]["advanced_parameters"], data["attributes"]["advanced_parameters"])
         self.assertEqual(correct_data["attributes"]["hash"], data["attributes"]["hash"])
         self.assertEqual(correct_data["attributes"]["DFT_program"], data["attributes"]["DFT_program"])
-        self.assertEqual(AbinsModules.AbinsTestHelpers.find_file(filename + "." + extension),
-                         data["attributes"]["filename"])
+
+        try:
+            self.assertEqual(AbinsModules.AbinsTestHelpers.find_file(filename + "." + extension),
+                             data["attributes"]["filename"])
+        except AssertionError:
+            self.assertEqual(AbinsModules.AbinsTestHelpers.find_file(filename + "." + extension.upper()),
+                             data["attributes"]["filename"])
 
         # check datasets
         self.assertEqual(True, np.allclose(correct_data["datasets"]["unit_cell"], data["datasets"]["unit_cell"]))
 
-    def _check_loader_data(self, correct_data=None, input_dft_filename=None, extension=None):
+    def _check_loader_data(self, correct_data=None, input_dft_filename=None, extension=None, loader=None):
+
+        try:
+            read_filename = AbinsModules.AbinsTestHelpers.find_file(input_dft_filename + "." + extension)
+            dft_loader = loader(input_dft_filename=read_filename)
+        except ValueError:
+            read_filename = AbinsModules.AbinsTestHelpers.find_file(input_dft_filename + "." + extension.upper())
+            dft_loader = loader(input_dft_filename=read_filename)
 
-        loader = AbinsModules.LoadDMOL3(
-            input_dft_filename=AbinsModules.AbinsTestHelpers.find_file(input_dft_filename + "." + extension))
-        loaded_data = loader.load_formatted_data().extract()
+        loaded_data = dft_loader.load_formatted_data().extract()
 
         # k points
         correct_items = correct_data["datasets"]["k_points_data"]
@@ -96,7 +106,7 @@ def _check_loader_data(self, correct_data=None, input_dft_filename=None, extensi
             self.assertEqual(True, np.allclose(np.array(correct_atoms["atom_%s" % item]["coord"]),
                                                atoms["atom_%s" % item]["coord"]))
 
-    def _check(self, name=None, loader=None):
+    def check(self, name=None, loader=None):
 
         extension = self._loaders_extensions[str(loader)]
 
@@ -110,7 +120,7 @@ def _check(self, name=None, loader=None):
         self._check_reader_data(correct_data=correct_data, data=data, filename=name, extension=extension)
 
         # check loaded data
-        self._check_loader_data(correct_data=correct_data, input_dft_filename=name, extension=extension)
+        self._check_loader_data(correct_data=correct_data, input_dft_filename=name, extension=extension, loader=loader)
 
     def _read_dft(self, loader=None, filename=None, extension=None):
         """
@@ -120,13 +130,17 @@ def _read_dft(self, loader=None, filename=None, extension=None):
         :returns: phonon data
         """
         # 1) Read data
-        filename = AbinsModules.AbinsTestHelpers.find_file(filename=filename + "." + extension)
-        dft_reader = loader(input_dft_filename=filename)
+        try:
+            read_filename = AbinsModules.AbinsTestHelpers.find_file(filename=filename + "." + extension)
+            ab_initio_reader = loader(input_dft_filename=read_filename)
+        except ValueError:
+            read_filename = AbinsModules.AbinsTestHelpers.find_file(filename=filename + "." + extension.upper())
+            ab_initio_reader = loader(input_dft_filename=read_filename)
 
-        data = self._get_reader_data(dft_reader=dft_reader)
+        data = self._get_reader_data(dft_reader=ab_initio_reader)
 
         # test validData method
-        self.assertEqual(True, dft_reader._clerk._valid_hash())
+        self.assertEqual(True, ab_initio_reader._clerk._valid_hash())
 
         return data
 

diff --git a/scripts/AbinsModules/LoadGAUSSIAN.py b/scripts/AbinsModules/LoadGAUSSIAN.py
@@ -7,7 +7,7 @@
 
 class LoadGAUSSIAN(AbinsModules.GeneralDFTProgram):
     """
-    Class for loading GAUSSIAN DFT vibrational data.
+    Class for loading GAUSSIAN ab initio vibrational data.
     """
     def __init__(self, input_dft_filename):
         """
@@ -160,11 +160,12 @@ def _read_atomic_disp_block(self, file_obj=None, disp=None):
         :param file_obj: file object from which we read
         :param disp: list with x coordinates which we update [num_freq, num_atoms, dim]
         """
-        sub_block_start = "Atom AN      X      Y      Z        X      Y      Z        X      Y      Z"
+        sub_block_start = "X      Y      Z        X      Y      Z        X      Y      Z"
         self._parser.find_first(file_obj=file_obj, msg=sub_block_start)
 
         num_atom = 0
-        line_size = len(sub_block_start.split())
+        #   Atom  AN      X      Y      Z        X      Y      Z        X      Y      Z
+        line_size = len(sub_block_start.split()) + 2
         freq_per_line = sub_block_start.count("X")
 
         l = file_obj.readline().split()

diff --git a/scripts/test/AbinsLoadCASTEPTest.py b/scripts/test/AbinsLoadCASTEPTest.py
@@ -27,23 +27,23 @@ def tearDown(self):
     _gamma_sum = "squaricn_sum_LoadCASTEP"
 
     def test_gamma_sum_correction(self):
-        self._check(name=self._gamma_sum, loader=AbinsModules.LoadCASTEP)
+        self.check(name=self._gamma_sum, loader=AbinsModules.LoadCASTEP)
 
     # ===================================================================================
     # |     Use case: Gamma point calculation and no sum correction for Gamma point     |
     # ===================================================================================
     _gamma_no_sum = "squaricn_no_sum_LoadCASTEP"
 
     def test_gamma_no_sum_correction(self):
-        self._check(name=self._gamma_no_sum, loader=AbinsModules.LoadCASTEP)
+        self.check(name=self._gamma_no_sum, loader=AbinsModules.LoadCASTEP)
 
     # ===================================================================================
     # | Use case: more than one k-point and sum correction       |
     # ===================================================================================
     _many_k_sum = "Si2-phonon_LoadCASTEP"
 
     def test_sum_correction_single_crystal(self):
-        self._check(name=self._many_k_sum, loader=AbinsModules.LoadCASTEP)
+        self.check(name=self._many_k_sum, loader=AbinsModules.LoadCASTEP)
 
     # ===================================================================================
     # |   Use case: more than one k-point without sum correction                        |
@@ -52,7 +52,7 @@ def test_sum_correction_single_crystal(self):
     _many_k_no_sum = "Si2-sc_LoadCASTEP"
 
     def test_no_sum_correction_single_crystal(self):
-        self._check(name=self._many_k_no_sum, loader=AbinsModules.LoadCASTEP)
+        self.check(name=self._many_k_no_sum, loader=AbinsModules.LoadCASTEP)
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/scripts/test/AbinsLoadCRYSTALTest.py b/scripts/test/AbinsLoadCRYSTALTest.py
@@ -28,15 +28,15 @@ def tearDown(self):
     _phonon_dispersion_v2 = "MgO-222-DISP_LoadCRYSTAL"
 
     def test_gamma_crystal(self):
-        self._check(name=self._gamma_crystal, loader=AbinsModules.LoadCRYSTAL)
-        self._check(name=self._set_crystal, loader=AbinsModules.LoadCRYSTAL)
+        self.check(name=self._gamma_crystal, loader=AbinsModules.LoadCRYSTAL)
+        self.check(name=self._set_crystal, loader=AbinsModules.LoadCRYSTAL)
 
     def test_molecule(self):
-        self._check(name=self._molecule, loader=AbinsModules.LoadCRYSTAL)
+        self.check(name=self._molecule, loader=AbinsModules.LoadCRYSTAL)
 
     def test_phonon_dispersion_crystal(self):
-        self._check(name=self._phonon_dispersion_v1, loader=AbinsModules.LoadCRYSTAL)
-        self._check(name=self._phonon_dispersion_v2, loader=AbinsModules.LoadCRYSTAL)
+        self.check(name=self._phonon_dispersion_v1, loader=AbinsModules.LoadCRYSTAL)
+        self.check(name=self._phonon_dispersion_v2, loader=AbinsModules.LoadCRYSTAL)
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/scripts/test/AbinsLoadDMOL3Test.py b/scripts/test/AbinsLoadDMOL3Test.py
@@ -17,8 +17,8 @@ def tearDown(self):
     _gamma_no_h_dmol3 = "Na2SiF6_LoadDMOL3"
 
     def test_gamma_dmol3(self):
-        self._check(name=self._gamma_dmol3, loader=AbinsModules.LoadDMOL3)
-        self._check(name=self._gamma_no_h_dmol3, loader=AbinsModules.LoadDMOL3)
+        self.check(name=self._gamma_dmol3, loader=AbinsModules.LoadDMOL3)
+        self.check(name=self._gamma_no_h_dmol3, loader=AbinsModules.LoadDMOL3)
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/scripts/test/AbinsLoadGAUSSIANTest.py b/scripts/test/AbinsLoadGAUSSIANTest.py
@@ -11,12 +11,29 @@ def tearDown(self):
 
         #  *************************** USE CASES ********************************************
     # ===================================================================================
-    # | Use cases: molecular calculation for GAUSSIAN                                    |
+    # | Use cases: molecular calculation for GAUSSIAN03 Hartree Fock, Unix              |
     # ===================================================================================
-    _molecule_gaussian = "C6H5Cl-LoadGAUSSIAN"
+    _gaussian_system1 = "C6H5Cl_LoadGAUSSIAN"
+
+    def test_gaussian_1(self):
+        self.check(name=self._gaussian_system1, loader=AbinsModules.LoadGAUSSIAN)
+
+    # ===================================================================================
+    # | Use cases: molecular calculation for GAUSSIAN03 DFT, Win                        |
+    # ===================================================================================
+    _gaussian_system2 = "BENZENE4_g03_win_LoadGAUSSIAN"
+
+    def test_gaussian_2(self):
+        self.check(name=self._gaussian_system2, loader=AbinsModules.LoadGAUSSIAN)
+
+    # ===================================================================================
+    # | Use cases: molecular calculation for GAUSSIAN09 DFT, Win                        |
+    # ===================================================================================
+    _gaussian_system3 = "BENZENE4_g09_win_LoadGAUSSIAN"
+
+    def test_gaussian_3(self):
+        self.check(name=self._gaussian_system3, loader=AbinsModules.LoadGAUSSIAN)
 
-    def test_molecule_gaussian(self):
-        self._check(name=self._molecule_gaussian, loader=AbinsModules.LoadGAUSSIAN)
 
 if __name__ == '__main__':
     unittest.main()