Scala integration should now be possible. Added test folder. Updated README.md.

README.md

 # CP2K NoMaD Parser
+This is the parser for [CP2K](https://www.cp2k.org/).
+It is part of the [NOMAD Laboratory](http://nomad-lab.eu).
 
-# QuickStart
-- Clone repository
+#Installation
 
-    ```shell
+## Within NOMAD
+When used within the NOMAD Laboratory, this parser will be available as a
+submodule of the nomad-lab-base repository. You can download the base repository
+with the command:
+
+```sh
+    git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
+```
+
+And the installation will be done according to the instruction found in
+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-lab-base/wikis/how-to-write-a-parser#shell-commands
+
+## Standalone Installation
+The parser is also available as a standalone package within the repository:
+
+```sh
     git clone git@gitlab.mpcdf.mpg.de:nomad-lab/parser-cp2k.git
-    ```
+```
 
-- Run setup by running the setup.py script. For local, user specific install
-  without sudo permissions use (omit --user for a system-wide install):
+If used in this standalone mode you can use the installation script
+parser-cp2k/parser/parser-cp2k/setup.py with the folllowing command
 
-    ```shell
+```sh
     python setup.py install --user
-    ```
-
-# Structure
-Currently the python package is divided the following subpackages:
-- utils: Generic utility classes and base classes
-- parsing: The classes that actually define the parser functionality.
+```
+
+After the local install the parser will be available to python import under the name
+'cp2kparser'.
+
+# Usage
+
+## Within NOMAD
+The scala layer can access the parser throught the scalainterface.py file.
+
+## Standalone
+The parser can be used in a python only standalone mode with a separate
+'nomadtoolkit' package. In this local mode the parser can be like this:
+
+```python
+    from nomadtoolkit import Analyzer
+    from cp2kparser import CP2KParser
+
+    # Initialize the contents and the parser you want to use.
+    paths = "/home/lauri/Dropbox/nomad-dev/parser-cp2k/parser/parser-cp2k/cp2kparser/tests/cp2k_2.6.2/functionals/lda"
+    parser = CP2KParser(contents=paths)
+
+    # Initialize the analyzer. The analyzer will initialize the parser with a local
+    # backend so that the results will be available as a python dictionary.
+    analyzer = Analyzer(parser)
+    results = analyzer.parse()
+    cell = results["simulation_cell"]
+    n_atoms = results["number_of_atoms"]
+    atom_position = results["atom_position"]
+    atom_label = results["atom_label"]
+
+    print cell.value
+    print n_atoms.value
+    print atom_position.value
+    print atom_label.value
+```
+
+This standalone python-only mode is primarily for people who want to easily
+access the parser without the need to setup the whole "NOMAD Stack". It is also
+used when running unit tests. The nomadtoolkit package is currently used by the
+developer only and is thus not available through gitlab.
 
 # Tools and Methods
 

parser/parser-cp2k/cp2kparser/scalainterface.py

 """
 This is the access point to the parser for the scala layer in the nomad project.
 """
+import setup_paths
 import os
 from cp2kparser import CP2KParser
 from cp2kparser.parsing.versions.cp2k262.outputparser import CP2KOutputParser
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 from nomadcore.simple_parser import mainFunction
 
-# This is what should be called by the scala layer to run the parser. Currently
+# This is what gets run when the scala layer calls for this parser. Currently
 # only the outputparser is used because the scala layer doesn't support
 # auxiliary files. Also the version identification is skipped and the structure
 # used in CP2K 2.6.2 is assumed.
@@ -19,7 +20,7 @@ if __name__ == "__main__":
     outputparser = CP2KOutputParser(None, None)
 
     # Setup the metainfos
-    metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../../nomad-meta-info/meta_info/nomad_meta_info/{}".format(cp2kparser.get_metainfo_filename())))
+    metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../../nomad-meta-info/meta_info/nomad_meta_info/cp2k.nomadmetainfo.json"))
     metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath, dependencyLoader=None, extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS, uri=None)
 
     # Parser info

parser/parser-cp2k/cp2kparser/setup_paths.py

+"""
+Setups the python-common lirary in the PYTHONPATH system variable.
+"""
+import sys
+import os
+import os.path
+
+baseDir = os.path.dirname(os.path.abspath(__file__))
+commonDir = os.path.normpath(os.path.join(baseDir, "../../../../../python-common/common/python"))
+parserDir = os.path.normpath(os.path.join(baseDir, "../../parser-cp2k"))
+
+# Using sys.path.insert(1, ...) instead of sys.path.insert(0, ...) based on
+# this discusssion:
+# http://stackoverflow.com/questions/10095037/why-use-sys-path-appendpath-instead-of-sys-path-insert1-path
+if not commonDir in sys.path:
+    sys.path.insert(1, commonDir)
+    sys.path.insert(1, parserDir)

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

@@ -372,6 +372,14 @@ class FileParser(object):
         """
         return self.root_matcher.allMetaNames()
 
+    def startedParsing(self, fInName, parser):
+        """Function is called when the parsing starts.
+
+        Get compiled parser.
+        Later one can compile a parser for parsing an external file.
+        """
+        self.parser = parser
+
 
 #===============================================================================
 class ParserContext(object):

parser/parser-cp2k/setup.py

-from setuptools import setup, find_packages
+"""
+This is a setup script for installing the parser locally on python path with
+all the required dependencies. Used mainly for local testing.
+"""
+from setuptools import setup
 
 
 #===============================================================================
 def main():
     # Start package setup
     setup(
-        name="cp2karser",
+        name="cp2kparser",
         version="0.1",
         include_package_data=True,
         package_data={
@@ -19,7 +23,6 @@ def main():
         install_requires=[
             'pint',
             'numpy',
-            'ase'
         ],
         zip_safe=False
     )

test/examples/Si_bulk_energy_force.inp

+&GLOBAL
+  PROJECT Si_bulk8
+  RUN_TYPE ENERGY_FORCE
+  PRINT_LEVEL MEDIUM
+&END GLOBAL
+&FORCE_EVAL
+  METHOD Quickstep
+  &SUBSYS
+    &KIND Si
+      ELEMENT   Si
+      BASIS_SET DZVP-GTH-PADE
+      POTENTIAL GTH-PADE-q4
+    &END KIND
+    &CELL
+      A     5.430697500    0.000000000    0.000000000
+      B     0.000000000    5.430697500    0.000000000
+      C     0.000000000    0.000000000    5.430697500
+    &END CELL
+    &COORD
+      Si    0.000000000    0.000000000    0.000000000
+      Si    0.000000000    2.715348700    2.715348700
+      Si    2.715348700    2.715348700    0.000000000
+      Si    2.715348700    0.000000000    2.715348700
+      Si    4.073023100    1.357674400    4.073023100
+      Si    1.357674400    1.357674400    1.357674400
+      Si    1.357674400    4.073023100    4.073023100
+      Si    4.073023100    4.073023100    1.357674400
+    &END COORD
+  &END SUBSYS
+  &DFT
+    BASIS_SET_FILE_NAME  BASIS_SET
+    POTENTIAL_FILE_NAME  GTH_POTENTIALS
+    &QS
+      EPS_DEFAULT 1.0E-10
+    &END QS
+    &MGRID
+      NGRIDS 4
+      CUTOFF 300
+      REL_CUTOFF 60
+    &END MGRID
+    &XC
+      &XC_FUNCTIONAL PADE
+      &END XC_FUNCTIONAL
+    &END XC
+    &SCF
+      SCF_GUESS ATOMIC
+      EPS_SCF 1.0E-7
+      MAX_SCF 300
+      &DIAGONALIZATION  ON
+        ALGORITHM STANDARD
+      &END DIAGONALIZATION
+      &MIXING  T
+        METHOD BROYDEN_MIXING
+        ALPHA 0.4
+        NBROYDEN 8
+      &END MIXING
+    &END SCF
+  &END DFT
+  &PRINT
+    &FORCES ON
+    &END FORCES
+  &END PRINT
+&END FORCE_EVAL