wien2k: added in1 and in2 parsers

parser/parser-wien2k/wien2k_parser.py

@@ -4,7 +4,7 @@ from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
 from nomadcore.simple_parser import SimpleMatcher as SM
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 import os, sys, json
-import wien2k_parser_struct, wien2k_parser_in0, wien2k_parser_in1c,  wien2k_parser_in2c
+import wien2k_parser_struct, wien2k_parser_in0, wien2k_parser_in1c,  wien2k_parser_in2c, wien2k_parser_in1,  wien2k_parser_in2
 
 class Wien2kContext(object):
     """context for wien2k parser"""
@@ -81,6 +81,30 @@ class Wien2kContext(object):
             with open(fName) as fIn:
                 subParser.parseFile(fIn)
 
+        mainFile = self.parser.fIn.fIn.name
+        fName = mainFile[:-4] + ".in1"
+        if os.path.exists(fName):
+            subSuperContext = wien2k_parser_in1.Wien2kIn1Context()
+            subParser = AncillaryParser(
+                fileDescription = wien2k_parser_in1.buildIn1Matchers(),
+                parser = self.parser,
+                cachingLevelForMetaName = wien2k_parser_in1.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
+                superContext = subSuperContext)
+            with open(fName) as fIn:
+                subParser.parseFile(fIn)
+
+
+        mainFile = self.parser.fIn.fIn.name
+        fName = mainFile[:-4] + ".in2"
+        if os.path.exists(fName):
+            subSuperContext = wien2k_parser_in2.Wien2kIn2Context()
+            subParser = AncillaryParser(
+                fileDescription = wien2k_parser_in2.buildIn2Matchers(),
+                parser = self.parser,
+                cachingLevelForMetaName = wien2k_parser_in2.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
+                superContext = subSuperContext)
+            with open(fName) as fIn:
+                subParser.parseFile(fIn)
 
 # description of the input
 mainFileDescription = SM(

parser/parser-wien2k/wien2k_parser_in1.py

+from builtins import object
+import setup_paths
+from nomadcore.simple_parser import mainFunction, CachingLevel
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+import os, sys, json
+
+class Wien2kIn1Context(object):
+    """context for wien2k struct parser"""
+
+    def __init__(self):
+        self.parser = None
+
+    def initialize_values(self):
+        """allows to reset values if the same superContext is used to parse different files"""
+        pass
+
+    def startedParsing(self, path, parser):
+        """called when parsing starts"""
+        self.parser = parser
+        # allows to reset values if the same superContext is used to parse different files
+        self.initialize_values()
+
+
+# description of the input
+def buildIn1Matchers():
+    return SM(
+    name = 'root',
+    weak = True,
+    startReStr = "",
+        sections = ["section_run", "section_method"],
+    subMatchers = [
+#        SM(name = 'systemName',
+#          startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
+        SM(r"\s*(?P<x_wien2k_wf_switch>[\w*]+)\s*EF=[-+.0-9]*\s*\W*WFFIL, WFPRI, ENFIL, SUPWF\W"),
+        SM(r"\s*(?P<x_wien2k_rkmax>[0-9.]+)\s*[0-9]+\s*[0-9]+\s*\WR-..\WK-...; MAX \w*.*")
+#        SM(r"(?P<x_wien2k_calc_mode>.*)"),
+#        SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
+#        SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
+#           repeats=True,
+#           sections=["x_wien2k_section_equiv_atoms"],
+#           subMatchers=[
+#               SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
+#                  repeats=True
+#              ),
+#               SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
+#           ]
+#       )
+    ])
+
+def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
+    """Sets the caching level for the metadata.
+
+    Args:
+        metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
+        CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
+            This allows to run the parser without opening new sections.
+
+    Returns:
+        Dictionary with metaname as key and caching level as value.
+    """
+    # manually adjust caching of metadata
+    cachingLevelForMetaName = {
+                               'section_run': CachingLvl,
+                               'section_method': CachingLvl
+                              }
+    return cachingLevelForMetaName
+
+# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json

parser/parser-wien2k/wien2k_parser_in2.py

+from builtins import object
+import setup_paths
+from nomadcore.simple_parser import mainFunction, CachingLevel
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+import os, sys, json
+
+class Wien2kIn2Context(object):
+    """context for wien2k struct parser"""
+
+    def __init__(self):
+        self.parser = None
+
+    def initialize_values(self):
+        """allows to reset values if the same superContext is used to parse different files"""
+        pass
+
+    def startedParsing(self, path, parser):
+        """called when parsing starts"""
+        self.parser = parser
+        # allows to reset values if the same superContext is used to parse different files
+        self.initialize_values()
+
+
+# description of the input
+def buildIn2Matchers():
+    return SM(
+    name = 'root',
+    weak = True,
+    startReStr = "",
+        sections = ["section_run", "section_method"],
+    subMatchers = [
+#        SM(name = 'systemName',
+#          startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
+        SM(r"\s*(?P<x_wien2k_in2c_switch>[A-Z]+)\s*.*")
+#        SM(r"\s*(?P<x_wien2k_rkmax>[0-9.]+)\s*[0-9]+\s*[0-9]+\s*\WR-..\WK-...; MAX \w*.*")
+#        SM(r"(?P<x_wien2k_calc_mode>.*)"),
+#        SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
+#        SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
+#           repeats=True,
+#           sections=["x_wien2k_section_equiv_atoms"],
+#           subMatchers=[
+#               SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
+#                  repeats=True
+#              ),
+#               SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
+#           ]
+#       )
+    ])
+
+def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
+    """Sets the caching level for the metadata.
+
+    Args:
+        metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
+        CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
+            This allows to run the parser without opening new sections.
+
+    Returns:
+        Dictionary with metaname as key and caching level as value.
+    """
+    # manually adjust caching of metadata
+    cachingLevelForMetaName = {
+                               'section_run': CachingLvl,
+                               'section_method': CachingLvl
+                              }
+    return cachingLevelForMetaName
+
+# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json