diff --git a/README.md b/README.md index 821092d07c4d1ce8843a9494ba2c273b4a26cdbf..24a80b21a9dd44c2aa5025e0734a726fb95757e1 100644 --- a/README.md +++ b/README.md @@ -79,9 +79,10 @@ but can only test that the data is outputted in the correct format and according to some general rules. These tests cannot verify that the contents are correct. -In order to truly test the parser output, unit testing is needed. The unit -tests for this parser are located in **cpmd/test/unittests**. Unit tests provide one way -to test each parseable quantity and python has a very good [library for unit +In order to truly test the parser output, regression testing is needed. The +tests for this parser are located in +**/cpmd/parser/parser-cpmd/cpmdparser/regtest**. Tests provide one way to test +each parseable quantity and python has a very good [library for unit testing](https://docs.python.org/2/library/unittest.html). When the parser supports a new quantity it is quite fast to create unit tests for it. These tests will validate the parsing, and also easily detect bugs that may rise when diff --git a/parser/parser-cpmd/cpmdparser/parser.py b/parser/parser-cpmd/cpmdparser/parser.py index e7b7096ee571554a06e32e6b51d925e5b1553c31..de76da85b7652fb91829ad46b4c42935f50bf448 100644 --- a/parser/parser-cpmd/cpmdparser/parser.py +++ b/parser/parser-cpmd/cpmdparser/parser.py @@ -37,7 +37,7 @@ class CPMDParser(ParserInterface): regex_version = re.compile("\s+VERSION ([\d\.]+)") regex_single_point = re.compile(r" SINGLE POINT DENSITY OPTIMIZATION") regex_geo_opt = re.compile(r" OPTIMIZATION OF IONIC POSITIONS") - regex_md = re.compile(r" CAR-PARRINELLO MOLECULAR DYNAMICS") + regex_md = re.compile(r"( CAR-PARRINELLO MOLECULAR DYNAMICS)|( BORN-OPPENHEIMER MOLECULAR DYNAMICS)") run_type = None n_lines = 1000 version_id = None @@ -74,7 +74,7 @@ class CPMDParser(ParserInterface): raise RuntimeError(msg) if run_type is None: - msg = "Could not find a run type specification from the given main file." + msg = "Could not find a run type specification from the given main file at: {}".format(self.parser_context.main_file) logger.exception(msg) raise RuntimeError(msg) @@ -104,7 +104,7 @@ class CPMDParser(ParserInterface): parser_module = importlib.import_module(base) except ImportError: logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for CPMD 4.1".format(version_id)) - base = "cpmdparser.versions.cp2k41.{}".format(run_type.module_name) + base = "cpmdparser.versions.cpmd41.{}".format(run_type.module_name) try: parser_module = importlib.import_module(base) except ImportError: diff --git a/test/unittests/README.md b/parser/parser-cpmd/cpmdparser/regtest/README.md similarity index 100% rename from test/unittests/README.md rename to parser/parser-cpmd/cpmdparser/regtest/README.md diff --git a/test/unittests/cpmd_4.1/H_CVB_BLYP.psp b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_CVB_BLYP.psp similarity index 100% rename from test/unittests/cpmd_4.1/H_CVB_BLYP.psp rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_CVB_BLYP.psp diff --git a/test/unittests/cpmd_4.1/H_MT_LDA.psp b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_MT_LDA.psp similarity index 100% rename from test/unittests/cpmd_4.1/H_MT_LDA.psp rename to 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test/unittests/cpmd_4.1/periodicity/surface_yz/RESTART.1 rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/RESTART.1 diff --git a/test/unittests/cpmd_4.1/periodicity/surface_yz/input.inp b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/input.inp similarity index 100% rename from test/unittests/cpmd_4.1/periodicity/surface_yz/input.inp rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/input.inp diff --git a/test/unittests/cpmd_4.1/periodicity/surface_yz/output.out b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/output.out similarity index 100% rename from test/unittests/cpmd_4.1/periodicity/surface_yz/output.out rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/output.out diff --git a/test/unittests/cpmd_4.1/periodicity/surface_yz/run.sh b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/run.sh similarity index 100% rename from test/unittests/cpmd_4.1/periodicity/surface_yz/run.sh rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/surface_yz/run.sh diff --git a/test/unittests/cpmd_4.1/run_tests.py b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py similarity index 86% rename from test/unittests/cpmd_4.1/run_tests.py rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py index 1b0a7971632487874c57016afbe649eac99ee572..5775341a409125966be4f1555fa097ccd3ff9c49 100644 --- a/test/unittests/cpmd_4.1/run_tests.py +++ b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py @@ -238,42 +238,6 @@ class TestSinglePoint(unittest.TestCase): # multiplicity = self.results["spin_target_multiplicity"] # self.assertEqual(multiplicity, 1) - # def test_stress_tensor(self): - # result = self.results["stress_tensor"] - # expected_result = convert_unit( - # np.array([ - # [7.77640934, -0.00000098, -0.00000099], - # [-0.00000098, 7.77640935, -0.00000101], - # [-0.00000099, -0.00000101, 7.77640935], - # ]), - # "GPa" - # ) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_stress_tensor_eigenvalues(self): - # result = self.results["x_cp2k_stress_tensor_eigenvalues"] - # expected_result = convert_unit(np.array([7.77640735, 7.77641033, 7.77641036]), "GPa") - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_stress_tensor_eigenvectors(self): - # result = self.results["x_cp2k_stress_tensor_eigenvectors"] - # expected_result = np.array([ - # [0.57490332, -0.79965737, -0.17330395], - # [0.57753686, 0.54662171, -0.60634634], - # [0.57960102, 0.24850110, 0.77608624], - # ]) - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_stress_tensor_determinant(self): - # result = self.results["x_cp2k_stress_tensor_determinant"] - # expected_result = convert_unit(4.70259243E+02, "GPa^3") - # self.assertTrue(np.array_equal(result, expected_result)) - - # def test_stress_tensor_one_third_of_trace(self): - # result = self.results["x_cp2k_stress_tensor_one_third_of_trace"] - # expected_result = convert_unit(7.77640934E+00, "GPa") - # self.assertTrue(np.array_equal(result, expected_result)) - #=============================================================================== class TestGeoOpt(unittest.TestCase): @@ -793,32 +757,6 @@ class TestXCFunctional(unittest.TestCase): self.assertEqual(xc, "1*HYB_GGA_XC_HSE06") -# #=============================================================================== -# class TestErrors(unittest.TestCase): - # """Test misc. error stuations which may occur during the parsing. - # """ - # def test_no_file(self): - # self.assertRaises(IOError, get_result, "errors/no_file", "XC_functional") - - # def test_invalid_file(self): - # self.assertRaises(RuntimeError, get_result, "errors/invalid_file", "XC_functional") - - # def test_invalid_run_type(self): - # self.assertRaises(KeyError, get_result, "errors/invalid_run_type", "XC_functional") - - # def test_unknown_version(self): - # get_result("errors/unknown_version", "XC_functional") - - # def test_unknown_input_keyword(self): - # get_result("errors/unknown_input_keyword", "XC_functional") - - # def test_unknown_input_section(self): - # get_result("errors/unknown_input_section", "XC_functional") - - # def test_unknown_input_section_parameter(self): - # get_result("errors/unknown_input_section_parameter", "XC_functional") - - # #=============================================================================== # class TestSCFConvergence(unittest.TestCase): # """Tests whether the convergence status and number of SCF step can be @@ -834,65 +772,6 @@ class TestXCFunctional(unittest.TestCase): # self.assertFalse(result) -#=============================================================================== -# class TestSelfInteractionCorrectionMethod(unittest.TestCase): - # """Tests that the self-interaction correction can be properly parsed. - # """ - - # def test_no(self): - # sic = get_result("sic/no", "self_interaction_correction_method") - # self.assertEqual(sic, "") - - # def test_ad(self): - # sic = get_result("sic/ad", "self_interaction_correction_method") - # self.assertEqual(sic, "SIC_AD") - - # def test_explicit_orbitals(self): - # sic = get_result("sic/explicit_orbitals", "self_interaction_correction_method") - # self.assertEqual(sic, "SIC_EXPLICIT_ORBITALS") - - # def test_mauri_spz(self): - # sic = get_result("sic/mauri_spz", "self_interaction_correction_method") - # self.assertEqual(sic, "SIC_MAURI_SPZ") - - # def test_mauri_us(self): - # sic = get_result("sic/mauri_us", "self_interaction_correction_method") - # self.assertEqual(sic, "SIC_MAURI_US") - - -# #=============================================================================== -# class TestStressTensorMethods(unittest.TestCase): - # """Tests that the stress tensor can be properly parsed for different - # calculation methods. - # """ - # def test_none(self): - # get_results("stress_tensor/none", "section_stress_tensor") - - # def test_analytical(self): - # results = get_results("stress_tensor/analytical", ["stress_tensor_method", "stress_tensor"]) - # method = results["stress_tensor_method"] - # results["stress_tensor"] - # self.assertEqual(method, "Analytical") - - # def test_numerical(self): - # results = get_results("stress_tensor/numerical", ["stress_tensor_method", "stress_tensor"]) - # method = results["stress_tensor_method"] - # results["stress_tensor"] - # self.assertEqual(method, "Numerical") - - # def test_diagonal_analytical(self): - # results = get_results("stress_tensor/diagonal_analytical", ["stress_tensor_method", "stress_tensor"]) - # method = results["stress_tensor_method"] - # results["stress_tensor"] - # self.assertEqual(method, "Diagonal analytical") - - # def test_diagonal_numerical(self): - # results = get_results("stress_tensor/diagonal_numerical", ["stress_tensor_method", "stress_tensor"]) - # method = results["stress_tensor_method"] - # results["stress_tensor"] - # self.assertEqual(method, "Diagonal numerical") - - # # =============================================================================== # class TestGeoOptTrajFormats(unittest.TestCase): @@ -1107,25 +986,6 @@ class TestXCFunctional(unittest.TestCase): # self.assertTrue(np.array_equal(expected_cell_end, simulation_cell[-1,:,:])) -# #=============================================================================== -# class TestElectronicStructureMethod(unittest.TestCase): - - # def test_mp2(self): - # results = get_results("electronic_structure_method/mp2", "section_run") - # result = results["electronic_structure_method"] - # self.assertEqual(result, "MP2") - - # def test_dft_plus_u(self): - # results = get_results("electronic_structure_method/dft_plus_u", "section_run") - # result = results["electronic_structure_method"] - # self.assertEqual(result, "DFT+U") - - # def test_rpa(self): - # results = get_results("electronic_structure_method/rpa", "section_run") - # result = results["electronic_structure_method"] - # self.assertEqual(result, "RPA") - - #=============================================================================== if __name__ == '__main__': suites = [] diff --git a/test/unittests/cpmd_4.1/single_point/GEOMETRY b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/single_point/GEOMETRY similarity index 100% rename from test/unittests/cpmd_4.1/single_point/GEOMETRY rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/single_point/GEOMETRY diff --git a/test/unittests/cpmd_4.1/single_point/GEOMETRY.xyz b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/single_point/GEOMETRY.xyz similarity index 100% rename from test/unittests/cpmd_4.1/single_point/GEOMETRY.xyz rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/single_point/GEOMETRY.xyz diff --git a/test/unittests/cpmd_4.1/single_point/LATEST b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/single_point/LATEST 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b/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/run.sh similarity index 100% rename from test/unittests/cpmd_4.1/xc_functional/xlyp/run.sh rename to parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/run.sh diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py index a9034c977d77042ad833e6f3a351fb0e5e7059d5..dfed5c7fcdcf117bd85d47ac6d7c5a9fc7155b9f 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py @@ -1,6 +1,7 @@ import re import logging import datetime +import calendar import numpy as np from nomadcore.baseclasses import CommonParser from nomadcore.simple_parser import SimpleMatcher as SM @@ -53,7 +54,7 @@ class CPMDCommonParser(CommonParser): """Returns the simplematcher that parses informatio about the method used. Common to all run types. """ - return SM( "(?: SINGLE POINT DENSITY OPTIMIZATION)|(?: OPTIMIZATION OF IONIC POSITIONS)|(?: CAR-PARRINELLO MOLECULAR DYNAMICS)", + return SM( "(?: SINGLE POINT DENSITY OPTIMIZATION)|(?: OPTIMIZATION OF IONIC POSITIONS)|(?: CAR-PARRINELLO MOLECULAR DYNAMICS)|(?: BORN-OPPENHEIMER MOLECULAR DYNAMICS)", subMatchers=[ SM( " USING SEED", forwardMatch=True, @@ -231,9 +232,11 @@ class CPMDCommonParser(CommonParser): def onClose_x_cpmd_section_start_information(self, backend, gIndex, section): # Starting date and time start_datetime = section.get_latest_value("x_cpmd_start_datetime") - start_date_stamp, start_wall_time = self.timestamp_from_string(start_datetime) - backend.addValue("time_run_date_start", start_date_stamp) - backend.addValue("time_run_wall_start", start_wall_time) + timestamp = self.timestamp_from_string(start_datetime) + if timestamp: + start_date_stamp, start_wall_time = timestamp + backend.addValue("time_run_date_start", start_date_stamp) + backend.addValue("time_run_wall_start", start_wall_time) # Input file input_filename = section.get_latest_value("x_cpmd_input_filename") @@ -346,7 +349,6 @@ class CPMDCommonParser(CommonParser): while match: line = parser.fIn.readline() result = regex_compiled.match(line) - # print(line) if result: match = True @@ -393,16 +395,38 @@ class CPMDCommonParser(CommonParser): """Returns the seconds since epoch for the given date and the wall clock seconds for the given wall clock time. Assumes UTC timezone. """ - timestring = timestring.strip() - date, clock_time = timestring.split() - year, month, day = [int(x) for x in date.split("-")] - hour, minute, second, msec = [float(x) for x in re.split("[:.]", clock_time)] - - date_obj = datetime.datetime(year, month, day, tzinfo=UTCtzinfo()) - date_timestamp = (date_obj - datetime.datetime(1970, 1, 1, tzinfo=UTCtzinfo())).total_seconds() - - wall_time = hour*3600+minute*60+second+0.001*msec - return date_timestamp, wall_time + # The start datetime can be formatted in different ways. First we try + # to determine which way is used. + try: + timestring = timestring.strip() + splitted = timestring.split() + n_split = len(splitted) + if n_split == 2: + date, clock_time = timestring.split() + year, month, day = [int(x) for x in date.split("-")] + hour, minute, second, msec = [float(x) for x in re.split("[:.]", clock_time)] + + date_obj = datetime.datetime(year, month, day, tzinfo=UTCtzinfo()) + date_timestamp = (date_obj - datetime.datetime(1970, 1, 1, tzinfo=UTCtzinfo())).total_seconds() + + wall_time = hour*3600+minute*60+second+0.001*msec + elif n_split == 5: + weekday, month, day, clock_time, year = timestring.split() + year = int(year) + day = int(day) + hour, minute, second = [float(x) for x in re.split("[:]", clock_time)] + month_name_to_number = dict((v, k) for k, v in enumerate(calendar.month_abbr)) + month = month_name_to_number[month] + + date_obj = datetime.datetime(year, month, day, tzinfo=UTCtzinfo()) + date_timestamp = (date_obj - datetime.datetime(1970, 1, 1, tzinfo=UTCtzinfo())).total_seconds() + wall_time = hour*3600+minute*60+second + # If any sxception is encountered here, just return None as the + # datetime is not very crucial + except Exception: + return None + else: + return date_timestamp, wall_time def get_atom_number(self, symbol): """ Returns the atomic number when given the atomic symbol. diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py index b3264e8d64182fbcceb7d79c62966b97d1c3c562..6c5f2eea7110d13eaf4df7779f4a9144ca8e368b 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py @@ -102,9 +102,11 @@ class CPMDInputParser(BasicParser): # If keyword object found, place the options and save any # parameters that were found before if keyword_object is not None: + # print(keyword_object.name) if parameters: - old_keyword_object.parameters = "\n".join(parameters) - parameters = [] + if old_keyword_object is not None: + old_keyword_object.parameters = "\n".join(parameters) + parameters = [] options = splitted[i_match+1:] if options: options = " ".join(options) @@ -114,8 +116,9 @@ class CPMDInputParser(BasicParser): keyword_object.accessed = True old_keyword_object = keyword_object - # If no keyword was found, the line is a parameter line - if keyword_object is None: + # If no keyword was found, and a section is open, the line is a + # parameter line + if keyword_object is None and len(section_stack) != 0: parameters.append(line) def analyze_input(self): diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py index 2cdc631e4327c77b7f768418afe1fdb9977f0d55..e016d883218e59b495448b9be881f12999ea6d6d 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py @@ -100,9 +100,13 @@ class CPMDMDParser(MainHierarchicalParser): pot_std = section.get_latest_value("x_cpmd_density_functional_energy_std") self.parse_md() - backend.addArrayValues("frame_sequence_temperature_stats", np.array([temp_mean, temp_std]), unit="K") - backend.addArrayValues("frame_sequence_conserved_quantity_stats", np.array([cons_mean, cons_std]), unit="hartree") - backend.addArrayValues("frame_sequence_potential_energy_stats", np.array([pot_mean, pot_std]), unit="hartree") + + if temp_mean is not None and temp_std is not None: + backend.addArrayValues("frame_sequence_temperature_stats", np.array([temp_mean, temp_std]), unit="K") + if cons_mean is not None and cons_std is not None: + backend.addArrayValues("frame_sequence_conserved_quantity_stats", np.array([cons_mean, cons_std]), unit="hartree") + if pot_mean is not None and pot_std is not None: + backend.addArrayValues("frame_sequence_potential_energy_stats", np.array([pot_mean, pot_std]), unit="hartree") #======================================================================= # adHoc @@ -141,7 +145,9 @@ class CPMDMDParser(MainHierarchicalParser): trajectory_file_iterator = nomadcore.csvparsing.iread(self.trajectory_filepath, columns=range(7), n_conf=n_atoms) # Initialize the ENERGIES file iterator - energies_iterator = nomadcore.csvparsing.iread(self.energies_filepath, columns=range(8)) + energies_iterator = None + if self.energies_filepath is not None: + energies_iterator = nomadcore.csvparsing.iread(self.energies_filepath, columns=range(8)) # Start reading the frames i_frame = 0