Better documentation.

cp2kparser/generics/nomadparser.py

@@ -3,13 +3,29 @@
 import json
 import os
 import time
+from abc import ABCMeta, abstractmethod
 from cp2kparser.generics.util import *
 
 
 #===============================================================================
 class NomadParser(object):
     """The base class for a NoMaD parser.
+
+    This class should be inherited by the python based parsers. It provides
+    general utility methods and a single interface for input and output.
+
+    The utilities that this class provides and the inherited classes should NOT
+    do:
+        - Converting results to JSON
+        - Converting units to SI
+        - Timing
+        - Caching of results
+        - Providing file contents, sizes and handles
+
+    This class also defines some absract methods that each parser must
+    implement.
     """
+    __metaclass__ = ABCMeta
 
     def __init__(self, input_json_string):
         self.input_json_string = input_json_string
@@ -27,7 +43,10 @@ class NomadParser(object):
         self.results = {}
 
     def get_file_contents(self, file_id):
-
+        """Get the contents for the file with the given id. Uses cached result
+        if available. Does not cache files that are bigger than a certain
+        limit.
+        """
         cache_limit = 10000
         contents = self.file_contents.get(file_id)
         if not contents:
@@ -39,7 +58,9 @@ class NomadParser(object):
         return contents
 
     def get_file_size(self, file_id):
-
+        """Get the size of a file with the given id. Uses cached result
+        if available.
+        """
         size = self.file_sizes.get(file_id)
         if not size:
             fh = self.file_handles[file_id]
@@ -49,10 +70,11 @@ class NomadParser(object):
         return size
 
     def get_file_handle(self, file_id):
-
+        """Get the handle for a file with the given id. Uses cached result
+        if available.
+        """
         handle = self.file_handles.get(file_id)
         if not handle:
-
             path = self.file_ids[file_id]
             try:
                 handle = open(path, "r")
@@ -64,7 +86,8 @@ class NomadParser(object):
         return handle
 
     def analyse_input_json(self):
-
+        """Analyze the JSON given as input.
+        """
         # Try to decode
         self.input_json_object = json.loads(self.input_json_string)
 
@@ -80,17 +103,6 @@ class NomadParser(object):
 
         # See if the metainfos exist
 
-    def setup_version(self):
-        """Setup a correct implementation for this version of CP2K.
-        """
-        pass
-
-    def determine_file_ids(self):
-        """If the files have not been given an id, try to determine the
-        correct ids by looking at the input file, contents and file extensions.
-        """
-        pass
-
     def get_quantity(self, name):
         """Given a unique quantity id which is present in the metainfo
         declaration, parses the corresponding quantity (if available) and
@@ -122,16 +134,30 @@ class NomadParser(object):
         print_debug("Elapsed time: {} ms".format((stop-start)*1000))
         return result
 
+    @abstractmethod
+    def setup_version(self):
+        """Setup a correct implementation for this version.
+        """
+        pass
+
+    @abstractmethod
+    def determine_file_ids(self):
+        """If the files have not been given an id, try to determine the
+        correct ids by looking at the input file, contents and file extensions.
+        """
+        pass
+
+    @abstractmethod
     def parse_quantity(self, name):
-        """Override this function in an actual implementation"""
+        """Parse a quantity from the given files."""
         pass
 
+    @abstractmethod
     def check_quantity_availability(self, name):
         """Check quantity availability.
-
           -Check the list of available quantities declared in interface.
           -Check if the run type actually produces the quantity
           -Check if the quantity is allowed by the 'metainfoToKeep' and
           'metainfoToSkip'
         """
-        return True
+        pass

cp2kparser/implementation/parser.py

@@ -13,7 +13,8 @@ from cp2kparser.engines.cp2kinputengine import CP2KInputEngine
 
 #===============================================================================
 class CP2KParser(NomadParser):
-    """The interface to a NoMaD CP2K parser.
+    """The interface for a NoMaD CP2K parser. All parsing actions will go
+    through this class.
     """
 
     def __init__(self, input_json_string):
@@ -167,9 +168,11 @@ class CP2KImplementation(object):
         xc_shortcut = self.inputengine.get_subsection("FORCE_EVAL/DFT/XC/XC_FUNCTIONAL").get_parameter()
 
         return {
+                'B3LYP': "HYB_GGA_XC_B3LYP",
+                'BEEFVDW': "",
+                'BLYP': "",
                 'PADE': "LDA_XC_TETER93",
                 'PBE': "GGA_X_PBE",
-                'B3LYP': "HYB_GGA_XC_B3LYP",
         }.get(xc_shortcut, None)
 
     def particle_forces(self):