Added modules for vibration and properties calculation, fixed issues with...

Added modules for vibration and properties calculation, fixed issues with global cache having uninitialized values, fixedissues with empty MD information.

parser/parser-cpmd/cpmdparser/parser.py

@@ -38,6 +38,8 @@ class CPMDParser(ParserInterface):
         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)|( BORN-OPPENHEIMER MOLECULAR DYNAMICS)")
+        regex_vib = re.compile(r" PERFORM A VIBRATIONAL ANALYSIS BY FINITE DIFFERENCES")
+        regex_prop = re.compile(r" CALCULATE SOME PROPERTIES")
         run_type = None
         n_lines = 1000
         version_id = None
@@ -68,6 +70,16 @@ class CPMDParser(ParserInterface):
                 if result_md:
                     run_type = CPMDRunType(module_name="mdparser", class_name="CPMDMDParser")
 
+                # Look for vibrational analysis
+                result_vib = regex_vib.match(line)
+                if result_vib:
+                    run_type = CPMDRunType(module_name="vibrationparser", class_name="CPMDVibrationParser")
+
+                # Look for properties calculation
+                result_prop = regex_prop.match(line)
+                if result_prop:
+                    run_type = CPMDRunType(module_name="propertiesparser", class_name="CPMDPropertiesParser")
+
         if version_id is None:
             msg = "Could not find a version specification from the given main file."
             logger.exception(msg)

parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py

@@ -30,6 +30,11 @@ class CPMDCommonParser(CommonParser):
         self.cache_service.add("ensemble_type")
         self.cache_service.add("time_step_ions")
 
+        self.cache_service.add("trajectory_range", False)
+        self.cache_service.add("trajectory_sample", False)
+        self.cache_service.add("print_freq", 1)
+        self.cache_service.add("configuration_periodic_dimensions", single=False, update=False)
+
     #===========================================================================
     # Common SimpleMatchers
     def header(self):

parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py

@@ -16,10 +16,6 @@ class CPMDInputParser(BasicParser):
         """
         super(CPMDInputParser, self).__init__(file_path, parser_context)
         self.input_tree = None
-        self.cache_service.add("trajectory_range", False)
-        self.cache_service.add("trajectory_sample", False)
-        self.cache_service.add("print_freq", 1)
-        self.cache_service.add("configuration_periodic_dimensions", single=False, update=False)
 
     def parse(self):
         self.setup_input_tree(self.parser_context.version_id)

parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py

@@ -247,14 +247,12 @@ class CPMDMDParser(MainHierarchicalParser):
             self.backend.closeSection("section_system", sys_id)
 
         # Push the summaries
+        if potential_energies:
             potential_energies = np.array(potential_energies)
             self.backend.addArrayValues("frame_sequence_potential_energy", potential_energies, unit="hartree")
+        if kinetic_energies:
             kinetic_energies = np.array(kinetic_energies)
             self.backend.addArrayValues("frame_sequence_kinetic_energy", kinetic_energies, unit="hartree")
-        conserved_quantities = np.array(conserved_quantities)
-        self.backend.addArrayValues("frame_sequence_conserved_quantity", conserved_quantities, unit="hartree")
-        temperatures = np.array(temperatures)
-        self.backend.addArrayValues("frame_sequence_temperature", temperatures, unit="K")
 
             # Push the statistics. CPMD prints some statistics at the end, but the
             # mean and std of kinetic energy are missing
@@ -263,3 +261,10 @@ class CPMDMDParser(MainHierarchicalParser):
             kin_std = np.sqrt(np.dot(kin_temp, kin_temp)/kinetic_energies.size)
             kin_temp = None
             self.backend.addArrayValues("frame_sequence_kinetic_energy_stats", np.array([kin_mean, kin_std]), unit="hartree")
+
+        if conserved_quantities:
+            conserved_quantities = np.array(conserved_quantities)
+            self.backend.addArrayValues("frame_sequence_conserved_quantity", conserved_quantities, unit="hartree")
+        if temperatures:
+            temperatures = np.array(temperatures)
+            self.backend.addArrayValues("frame_sequence_temperature", temperatures, unit="K")

parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py

+from __future__ import absolute_import
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.baseclasses import MainHierarchicalParser
+import numpy as np
+from .commonparser import CPMDCommonParser
+import re
+import logging
+LOGGER = logging.getLogger("nomad")
+
+
+#===============================================================================
+class CPMDPropertiesParser(MainHierarchicalParser):
+    """The main parser class that is called for all run types. Parses the CPMD
+    output file.
+    """
+    def __init__(self, file_path, parser_context):
+        """
+        """
+        super(CPMDPropertiesParser, self).__init__(file_path, parser_context)
+        self.setup_common_matcher(CPMDCommonParser(parser_context))
+        self.n_frames = 0
+        self.sampling_method_gid = None
+        self.frame_refs = []
+        self.energies = []
+
+        #=======================================================================
+        # Main structure
+        self.root_matcher = SM("",
+            forwardMatch=True,
+            sections=['section_run', "section_method"],
+            subMatchers=[
+                self.cm.header(),
+                self.cm.method(),
+                self.cm.atoms(),
+                self.cm.cell(),
+                self.cm.initialization(),
+                self.cm.footer(),
+            ]
+        )
+
+    #=======================================================================
+    # onClose triggers
+    def onClose_section_system(self, backend, gIndex, section):
+        self.cache_service.addArrayValues("atom_labels")
+        self.cache_service.addArrayValues("simulation_cell", unit="bohr")
+        self.cache_service.addValue("number_of_atoms")
+
+    #=======================================================================
+    # adHoc

parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py

+from __future__ import absolute_import
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.baseclasses import MainHierarchicalParser
+import numpy as np
+from .commonparser import CPMDCommonParser
+import re
+import logging
+LOGGER = logging.getLogger("nomad")
+
+
+#===============================================================================
+class CPMDVibrationParser(MainHierarchicalParser):
+    """The main parser class that is called for all run types. Parses the CPMD
+    output file.
+    """
+    def __init__(self, file_path, parser_context):
+        """
+        """
+        super(CPMDVibrationParser, self).__init__(file_path, parser_context)
+        self.setup_common_matcher(CPMDCommonParser(parser_context))
+        self.n_frames = 0
+        self.sampling_method_gid = None
+        self.frame_refs = []
+        self.energies = []
+
+        #=======================================================================
+        # Main structure
+        self.root_matcher = SM("",
+            forwardMatch=True,
+            sections=['section_run', "section_method"],
+            subMatchers=[
+                self.cm.header(),
+                self.cm.method(),
+                self.cm.atoms(),
+                self.cm.cell(),
+                self.cm.initialization(),
+                self.cm.footer(),
+            ]
+        )
+
+    #=======================================================================
+    # onClose triggers
+    def onClose_section_system(self, backend, gIndex, section):
+        self.cache_service.addArrayValues("atom_labels")
+        self.cache_service.addArrayValues("simulation_cell", unit="bohr")
+        self.cache_service.addValue("number_of_atoms")
+
+    #=======================================================================
+    # adHoc