Added profiling tools, disabled CP2K input information loading for now.

parser/parser-cp2k/cp2kparser/parsing/versions/cp2k262/implementation.py

@@ -2,7 +2,7 @@ import re
 import os
 import logging
 from cp2kparser.parsing.csvparsing import CSVParser
-from .inputparsing import CP2KInputParser
+# from .inputparsing import CP2KInputParser
 from .outputparser import CP2KOutputParser
 # from cp2kparser.parsing.cp2kinputenginedata.input_tree import CP2KInput
 from cp2kparser.utils.baseclasses import ParserImplementation
@@ -23,14 +23,14 @@ class CP2KImplementation(ParserImplementation):
         # know the version id.
         self.csvengine = CSVParser(self)
         self.atomsengine = CoordinateReader()
-        self.inputparser = CP2KInputParser()
-        self.inputparser.setup_version(self.version_id)
+        # self.inputparser = CP2KInputParser()
+        # self.inputparser.setup_version(self.version_id)
         self.input_tree = None
         self.extended_input = None
 
         self.determine_file_ids_pre_setup()
-        self.input_preprocessor()
-        self.determine_file_ids_post_setup()
+        # self.input_preprocessor()
+        # self.determine_file_ids_post_setup()
 
     def determine_file_ids_pre_setup(self):
         """Resolve the input and output files based on extension and the
@@ -151,71 +151,71 @@ class CP2KImplementation(ParserImplementation):
             input_variables_replaced.append(new_line)
 
         self.extended_input = '\n'.join(input_variables_replaced)
-        self.input_tree = self.inputparser.parse(self.extended_input)
+        # self.input_tree = self.inputparser.parse(self.extended_input)
 
-    def determine_file_ids_post_setup(self):
-        """Determines the file id's after the CP2K verion has been set
-        up. This includes force files, coordinate files, cell files, etc.
-        """
-        # Determine the presence of force file
-        force_path = self.input_tree.get_keyword("FORCE_EVAL/PRINT/FORCES/FILENAME")
-        project_name = self.input_tree.get_keyword("GLOBAL/PROJECT_NAME")
-        if force_path is not None and force_path != "__STD_OUT__":
-
-            # The force path is not typically exactly as written in input
-            if force_path.startswith("="):
-                logger.debug("Using single force file.")
-                force_path = force_path[1:]
-            elif re.match(r".?/", force_path):
-                logger.debug("Using separate force file for each step.")
-                force_path = "{}-1_0.xyz".format(force_path)
-            else:
-                logger.debug("Using separate force file for each step.")
-                force_path = "{}-{}-1_0.xyz".format(project_name, force_path)
-            force_path = os.path.basename(force_path)
-
-            # Check against the given files
-            file_path = self.search_file(force_path)
-            self.file_storage.setup_file_id(file_path, "forces")
-
-        # Determine the presence of an initial coordinate file
-        init_coord_file = self.input_tree.get_keyword("FORCE_EVAL/SUBSYS/TOPOLOGY/COORD_FILE_NAME")
-        if init_coord_file is not None:
-            logger.debug("Initial coordinate file found.")
-            # Check against the given files
-            file_path = self.search_file(init_coord_file)
-            self.file_storage.setup_file_id(file_path, "initial_coordinates")
-
-        # Determine the presence of a trajectory file
-        traj_file = self.input_tree.get_keyword("MOTION/PRINT/TRAJECTORY/FILENAME")
-        if traj_file is not None and traj_file != "__STD_OUT__":
-            file_format = self.input_tree.get_keyword("MOTION/PRINT/TRAJECTORY/FORMAT")
-            extension = {
-                "PDB": "pdb",
-                "XYZ": "xyz",
-                "XMOL": "xyz",
-                "ATOMIC": "xyz",
-                "DCD": "dcd",
-            }[file_format]
-            logger.debug("Trajectory file found.")
-            normalized_path = self.normalize_cp2k_path(traj_file, extension, "pos")
-            file_path = self.search_file(normalized_path)
-            self.file_storage.setup_file_id(file_path, "trajectory")
-
-        # Determine the presence of a cell output file
-        cell_motion_file = self.input_tree.get_keyword("MOTION/PRINT/CELL/FILENAME")
-        if cell_motion_file is not None:
-            logger.debug("Cell file found.")
-            extension = "cell"
-            normalized_path = self.normalize_cp2k_path(cell_motion_file, extension)
-            file_path = self.search_file(normalized_path)
-            self.file_storage.setup_file_id(file_path, "cell_output")
-
-        # Determine the presence of a cell input file
-        cell_input_file = self.input_tree.get_keyword("FORCE_EVAL/SUBSYS/CELL/CELL_FILE_NAME")
-        if cell_input_file is not None:
-            file_path = self.search_file(cell_input_file)
-            self.file_storage.setup_file_id(file_path, "cell_input")
+    # def determine_file_ids_post_setup(self):
+        # """Determines the file id's after the CP2K verion has been set
+        # up. This includes force files, coordinate files, cell files, etc.
+        # """
+        # # Determine the presence of force file
+        # force_path = self.input_tree.get_keyword("FORCE_EVAL/PRINT/FORCES/FILENAME")
+        # project_name = self.input_tree.get_keyword("GLOBAL/PROJECT_NAME")
+        # if force_path is not None and force_path != "__STD_OUT__":
+
+            # # The force path is not typically exactly as written in input
+            # if force_path.startswith("="):
+                # logger.debug("Using single force file.")
+                # force_path = force_path[1:]
+            # elif re.match(r".?/", force_path):
+                # logger.debug("Using separate force file for each step.")
+                # force_path = "{}-1_0.xyz".format(force_path)
+            # else:
+                # logger.debug("Using separate force file for each step.")
+                # force_path = "{}-{}-1_0.xyz".format(project_name, force_path)
+            # force_path = os.path.basename(force_path)
+
+            # # Check against the given files
+            # file_path = self.search_file(force_path)
+            # self.file_storage.setup_file_id(file_path, "forces")
+
+        # # Determine the presence of an initial coordinate file
+        # init_coord_file = self.input_tree.get_keyword("FORCE_EVAL/SUBSYS/TOPOLOGY/COORD_FILE_NAME")
+        # if init_coord_file is not None:
+            # logger.debug("Initial coordinate file found.")
+            # # Check against the given files
+            # file_path = self.search_file(init_coord_file)
+            # self.file_storage.setup_file_id(file_path, "initial_coordinates")
+
+        # # Determine the presence of a trajectory file
+        # traj_file = self.input_tree.get_keyword("MOTION/PRINT/TRAJECTORY/FILENAME")
+        # if traj_file is not None and traj_file != "__STD_OUT__":
+            # file_format = self.input_tree.get_keyword("MOTION/PRINT/TRAJECTORY/FORMAT")
+            # extension = {
+                # "PDB": "pdb",
+                # "XYZ": "xyz",
+                # "XMOL": "xyz",
+                # "ATOMIC": "xyz",
+                # "DCD": "dcd",
+            # }[file_format]
+            # logger.debug("Trajectory file found.")
+            # normalized_path = self.normalize_cp2k_path(traj_file, extension, "pos")
+            # file_path = self.search_file(normalized_path)
+            # self.file_storage.setup_file_id(file_path, "trajectory")
+
+        # # Determine the presence of a cell output file
+        # cell_motion_file = self.input_tree.get_keyword("MOTION/PRINT/CELL/FILENAME")
+        # if cell_motion_file is not None:
+            # logger.debug("Cell file found.")
+            # extension = "cell"
+            # normalized_path = self.normalize_cp2k_path(cell_motion_file, extension)
+            # file_path = self.search_file(normalized_path)
+            # self.file_storage.setup_file_id(file_path, "cell_output")
+
+        # # Determine the presence of a cell input file
+        # cell_input_file = self.input_tree.get_keyword("FORCE_EVAL/SUBSYS/CELL/CELL_FILE_NAME")
+        # if cell_input_file is not None:
+            # file_path = self.search_file(cell_input_file)
+            # self.file_storage.setup_file_id(file_path, "cell_input")
 
     def normalize_cp2k_path(self, path, extension, name=""):
         """The paths in CP2K input can be given in many ways. This function

parser/parser-cp2k/cp2kparser/utils/baseclasses.py

@@ -393,7 +393,7 @@ class MainParser(HierarchicalParser):
         process just override this method.
         """
         # Initialize the parser builder
-        parserBuilder = SimpleParserBuilder(self.root_matcher, self.backend.metaInfoEnv(), self.metainfo_to_keep)
+        parserBuilder = SimpleParserBuilder(self.root_matcher, self.backend.metaInfoEnv(), self.metainfo_to_keep, units=self.parser_context.units)
 
         # Verify the metainfo
         if not parserBuilder.verifyMetaInfo(sys.stderr):
@@ -416,6 +416,7 @@ class MainParser(HierarchicalParser):
             defaultSectionCachingLevel=self.default_section_caching_level,
             onClose=onClose,
             superBackend=self.backend)
+        self.caching_backend.units = self.parser_context.units
 
         # Compile the SimpleMatcher tree
         parserBuilder.compile()
@@ -451,9 +452,10 @@ class MainParser(HierarchicalParser):
 class ParserContext(object):
     """Contains everything needed to instantiate a parser implementation.
     """
-    def __init__(self, files=None, metainfo_to_keep=None, backend=None, version_id=None, main_file=None):
+    def __init__(self, files=None, metainfo_to_keep=None, backend=None, version_id=None, main_file=None, units=None):
         self.files = files
         self.version_id = version_id
         self.metainfo_to_keep = metainfo_to_keep
         self.backend = backend
         self.main_file = main_file
+        self.units = units

test/unittests/cp2k_2.6.2/run_tests.py

@@ -40,6 +40,8 @@ def get_result(folder, metaname):
 
 #===============================================================================
 class TestXCFunctional(unittest.TestCase):
+    """Tests that the XC functionals can be properly parsed.
+    """
 
     def test_pade(self):
         xc = get_result("XC_functional/pade", "XC_functional")
@@ -59,10 +61,12 @@ class TestXCFunctional(unittest.TestCase):
 
 
 #===============================================================================
-class TestSectionSingleConfigurationCalculation(unittest.TestCase):
+class TestEnergyForce(unittest.TestCase):
+    """Tests for a CP2K calculation with RUN_TYPE ENERGY_FORCE.
+    """
 
     def setUp(self):
-        self.results = get_results("section_single_configuration_calculation", "section_single_configuration_calculation")
+        self.results = get_results("energy_force", "section_run")
 
     def test_energy_total_scf_iteration(self):
         energy_total = self.results["energy_total_scf_iteration"]
@@ -91,13 +95,6 @@ class TestSectionSingleConfigurationCalculation(unittest.TestCase):
         )
         self.assertTrue(np.array_equal(atomic_forces, expected_result))
 
-
-#===============================================================================
-class TestSectionSystemDescription(unittest.TestCase):
-
-    def setUp(self):
-        self.results = get_results("section_system_description", "section_system_description")
-
     def test_atom_label(self):
         atom_labels = self.results["atom_label"]
         expected_labels = np.array(8*["Si"])
@@ -130,7 +127,6 @@ if __name__ == '__main__':
 
     suites = []
     suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
-    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSectionSingleConfigurationCalculation))
-    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSectionSystemDescription))
+    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
     alltests = unittest.TestSuite(suites)
     unittest.TextTestRunner(verbosity=0).run(alltests)