diff --git a/parser/parser-cp2k/cp2karser.egg-info/PKG-INFO b/parser/parser-cp2k/cp2karser.egg-info/PKG-INFO
new file mode 100644
index 0000000000000000000000000000000000000000..4733d8bdd5557572100ac7eaf494a6901e0193cb
--- /dev/null
+++ b/parser/parser-cp2k/cp2karser.egg-info/PKG-INFO
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: cp2karser
+Version: 0.1
+Summary: NoMaD parser implementation for CP2K
+Home-page: UNKNOWN
+Author: Lauri Himanen
+Author-email: lauri.himanen@gmail.com
+License: GPL3
+Description: UNKNOWN
+Platform: UNKNOWN
diff --git a/parser/parser-cp2k/cp2karser.egg-info/SOURCES.txt b/parser/parser-cp2k/cp2karser.egg-info/SOURCES.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2661e988366a716a00680bad1e363601b005c86
--- /dev/null
+++ b/parser/parser-cp2k/cp2karser.egg-info/SOURCES.txt
@@ -0,0 +1,10 @@
+setup.py
+cp2karser.egg-info/PKG-INFO
+cp2karser.egg-info/SOURCES.txt
+cp2karser.egg-info/dependency_links.txt
+cp2karser.egg-info/not-zip-safe
+cp2karser.egg-info/requires.txt
+cp2karser.egg-info/top_level.txt
+cp2kparser/__init__.py
+cp2kparser/__main__.py
+cp2kparser/scalainterface.py
\ No newline at end of file
diff --git a/parser/parser-cp2k/cp2karser.egg-info/dependency_links.txt b/parser/parser-cp2k/cp2karser.egg-info/dependency_links.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc
--- /dev/null
+++ b/parser/parser-cp2k/cp2karser.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/parser/parser-cp2k/cp2karser.egg-info/not-zip-safe b/parser/parser-cp2k/cp2karser.egg-info/not-zip-safe
new file mode 100644
index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc
--- /dev/null
+++ b/parser/parser-cp2k/cp2karser.egg-info/not-zip-safe
@@ -0,0 +1 @@
+
diff --git a/parser/parser-cp2k/cp2karser.egg-info/requires.txt b/parser/parser-cp2k/cp2karser.egg-info/requires.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b029f20d6692b303b91e128fc9ece5cc23f2cbd4
--- /dev/null
+++ b/parser/parser-cp2k/cp2karser.egg-info/requires.txt
@@ -0,0 +1,3 @@
+pint
+numpy
+ase
\ No newline at end of file
diff --git a/parser/parser-cp2k/cp2karser.egg-info/top_level.txt b/parser/parser-cp2k/cp2karser.egg-info/top_level.txt
new file mode 100644
index 0000000000000000000000000000000000000000..220915961d0ae656de630e7f4b069eea66770a61
--- /dev/null
+++ b/parser/parser-cp2k/cp2karser.egg-info/top_level.txt
@@ -0,0 +1 @@
+cp2kparser
diff --git a/parser/parser-cp2k/cp2kparser/__init__.py b/parser/parser-cp2k/cp2kparser/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..0a1233ac13e9e49e8a3e57dea359326879e2dd0a
--- /dev/null
+++ b/parser/parser-cp2k/cp2kparser/__init__.py
@@ -0,0 +1,2 @@
+import cp2kparser.utils.logconfig
+from cp2kparser.parsing.parser import CP2KParser
diff --git a/parser/parsercp2k/__main__.py b/parser/parser-cp2k/cp2kparser/__main__.py
similarity index 100%
rename from parser/parsercp2k/__main__.py
rename to parser/parser-cp2k/cp2kparser/__main__.py
diff --git a/parser/parsercp2k/parsing/__init__.py b/parser/parser-cp2k/cp2kparser/parsing/__init__.py
similarity index 100%
rename from parser/parsercp2k/parsing/__init__.py
rename to parser/parser-cp2k/cp2kparser/parsing/__init__.py
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/__init__.py b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/__init__.py
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/__init__.py
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/__init__.py
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/cp2k_input.xml b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/cp2k_input.xml
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/cp2k_input.xml
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/cp2k_input.xml
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/cp2k_input_tree.pickle b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/cp2k_input_tree.pickle
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/cp2k_input_tree.pickle
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/cp2k_input_tree.pickle
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/references.html b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/references.html
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/references.html
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/references.html
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/units.html b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/units.html
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/cp2k_262/units.html
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/cp2k_262/units.html
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/input_tree.py b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/input_tree.py
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/input_tree.py
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/input_tree.py
diff --git a/parser/parsercp2k/parsing/cp2kinputenginedata/xmlpreparser.py b/parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/xmlpreparser.py
similarity index 100%
rename from parser/parsercp2k/parsing/cp2kinputenginedata/xmlpreparser.py
rename to parser/parser-cp2k/cp2kparser/parsing/cp2kinputenginedata/xmlpreparser.py
diff --git a/parser/parsercp2k/parsing/csvparsing.py b/parser/parser-cp2k/cp2kparser/parsing/csvparsing.py
similarity index 100%
rename from parser/parsercp2k/parsing/csvparsing.py
rename to parser/parser-cp2k/cp2kparser/parsing/csvparsing.py
diff --git a/parser/parsercp2k/parsing/implementations.py b/parser/parser-cp2k/cp2kparser/parsing/implementations.py
similarity index 98%
rename from parser/parsercp2k/parsing/implementations.py
rename to parser/parser-cp2k/cp2kparser/parsing/implementations.py
index 9ea3cf6a97cee539421e831cc0d32691e7f489b7..7c4ccc8653685763ffced302d5c375357bc2b1b9 100644
--- a/parser/parsercp2k/parsing/implementations.py
+++ b/parser/parser-cp2k/cp2kparser/parsing/implementations.py
@@ -1,11 +1,11 @@
import re
import os
import logging
-from parsercp2k.parsing.csvparsing import CSVParser
-from parsercp2k.parsing.inputparsing import CP2KInputParser
-from parsercp2k.parsing.cp2kinputenginedata.input_tree import CP2KInput
-from parsercp2k.parsing.outputparsing import *
-from parsercp2k.utils.baseclasses import ParserImplementation
+from cp2kparser.parsing.csvparsing import CSVParser
+from cp2kparser.parsing.inputparsing import CP2KInputParser
+from cp2kparser.parsing.cp2kinputenginedata.input_tree import CP2KInput
+from cp2kparser.parsing.outputparsing import *
+from cp2kparser.utils.baseclasses import ParserImplementation
from nomadcore.coordinate_reader import CoordinateReader
logger = logging.getLogger(__name__)
diff --git a/parser/parsercp2k/parsing/inputparsing.py b/parser/parser-cp2k/cp2kparser/parsing/inputparsing.py
similarity index 100%
rename from parser/parsercp2k/parsing/inputparsing.py
rename to parser/parser-cp2k/cp2kparser/parsing/inputparsing.py
diff --git a/parser/parsercp2k/parsing/outputparsing.py b/parser/parser-cp2k/cp2kparser/parsing/outputparsing.py
similarity index 99%
rename from parser/parsercp2k/parsing/outputparsing.py
rename to parser/parser-cp2k/cp2kparser/parsing/outputparsing.py
index 6ae00584388515760916ba7ad5629d76c736719c..f051ef5e568de72d574067dc6ca61570e382f66d 100644
--- a/parser/parsercp2k/parsing/outputparsing.py
+++ b/parser/parser-cp2k/cp2kparser/parsing/outputparsing.py
@@ -204,7 +204,7 @@ class CP2KOutputParser262(object):
cell[1, :] = b_comp
cell[2, :] = c_comp
- backend.addArrayValues("cell", cell, unit="angstrom")
+ backend.addArrayValues("simulation_cell", cell, unit="angstrom")
# Get the number of atoms
numbers = section["cp2k_section_numbers"]
diff --git a/parser/parsercp2k/parser.py b/parser/parser-cp2k/cp2kparser/parsing/parser.py
similarity index 88%
rename from parser/parsercp2k/parser.py
rename to parser/parser-cp2k/cp2kparser/parsing/parser.py
index be9428e25e94078a46e24d0d3d89c6932789c1d4..36fca1009cd3f080f6356ecc9a664f8b4a972849 100644
--- a/parser/parsercp2k/parser.py
+++ b/parser/parser-cp2k/cp2kparser/parsing/parser.py
@@ -1,8 +1,7 @@
import re
import logging
-import parsercp2k.setup_paths
-from parsercp2k.utils.baseclasses import Parser
-from parsercp2k.parsing.implementations import *
+from cp2kparser.utils.baseclasses import Parser
+from cp2kparser.parsing.implementations import *
logger = logging.getLogger(__name__)
@@ -71,10 +70,3 @@ class CP2KParser(Parser):
the nomadtoolkit.
"""
return "cp2k.nomadmetainfo.json"
-
-
-#===============================================================================
-# This is what gets run when the scala layer calls for this parser
-if __name__ == "__main__":
- cp2kparser = CP2KParser()
- cp2kparser.scala_main_function()
diff --git a/parser/parser-cp2k/cp2kparser/scalainterface.py b/parser/parser-cp2k/cp2kparser/scalainterface.py
new file mode 100644
index 0000000000000000000000000000000000000000..bbb946a7101cae8e7689a95c57810b9e50225d56
--- /dev/null
+++ b/parser/parser-cp2k/cp2kparser/scalainterface.py
@@ -0,0 +1,37 @@
+"""
+This is the access point to the parser for the scala layer in the nomad project.
+"""
+import os
+from cp2kparser import CP2KParser
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+from nomadcore.simple_parser import mainFunction
+
+# 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.
+if __name__ == "__main__":
+ cp2kparser = CP2KParser()
+
+ # Get the outputparser class
+ outputparser = globals()["CP2KOutputParser{}".format("262")](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())))
+ metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath, dependencyLoader=None, extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS, uri=None)
+
+ # Parser info
+ parserInfo = {'name': 'cp2k-parser', 'version': '1.0'}
+
+ # Adjust caching of metadata
+ cachingLevelForMetaName = outputparser.cachingLevelForMetaName
+
+ # Supercontext is where the objet where the callback functions for
+ # section closing are found
+ superContext = outputparser
+
+ # Main file description is the SimpleParser tree
+ mainFileDescription = outputparser.outputstructure
+
+ # Use the main function from nomadcore
+ mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext=superContext, cachingLevelForMetaName=cachingLevelForMetaName, onClose={})
diff --git a/parser/parsercp2k/utils/__init__.py b/parser/parser-cp2k/cp2kparser/utils/__init__.py
similarity index 100%
rename from parser/parsercp2k/utils/__init__.py
rename to parser/parser-cp2k/cp2kparser/utils/__init__.py
diff --git a/parser/parsercp2k/utils/baseclasses.py b/parser/parser-cp2k/cp2kparser/utils/baseclasses.py
similarity index 89%
rename from parser/parsercp2k/utils/baseclasses.py
rename to parser/parser-cp2k/cp2kparser/utils/baseclasses.py
index c6a5450825438e26f303ca1473fab7c9f4454cdf..34aff6e42ad72334dd69cb042765d400ed20e9fc 100644
--- a/parser/parsercp2k/utils/baseclasses.py
+++ b/parser/parser-cp2k/cp2kparser/utils/baseclasses.py
@@ -3,11 +3,8 @@ import sys
import logging
import StringIO
from abc import ABCMeta, abstractmethod
-from parsercp2k.parsing.outputparsing import *
from nomadcore.simple_parser import SimpleParserBuilder, defaultParseFile, extractOnCloseTriggers
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel, ActiveBackend
-from nomadcore.simple_parser import mainFunction
logger = logging.getLogger(__name__)
@@ -16,8 +13,11 @@ class Parser(object):
"""A base class for nomad parsers.
Attributes:
- self.implementation: an object that actually does the parsing and is
+ implementation: an object that actually does the parsing and is
setup by this class based on the given contents.
+ parser_context: A wrapper class for all the parser related information.
+ This is contructed here and then passed onto the different
+ implementations.
"""
__metaclass__ = ABCMeta
parser_name = None
@@ -97,39 +97,12 @@ class Parser(object):
logger.error("No parser implementation has been setup.")
# Write the starting bracket
- self.backend.fileOut.write("[")
+ self.implementation.backend.fileOut.write("[")
self.implementation.parse()
# Write the ending bracket
- self.backend.fileOut.write("]\n")
-
- def scala_main_function(self):
- """This function gets called when the scala calls for a parser.
- """
-
- # Get the outputparser class
- outputparser = globals()["CP2KOutputParser{}".format("262")](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(self.get_metainfo_filename())))
- metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath, dependencyLoader=None, extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS, uri=None)
-
- # Parser info
- parserInfo = {'name': 'cp2k-parser', 'version': '1.0'}
-
- # Adjust caching of metadata
- cachingLevelForMetaName = outputparser.cachingLevelForMetaName
-
- # Supercontext is where the objet where the callback functions for
- # section closing are found
- superContext = outputparser
-
- # Main file description is the SimpleParser tree
- mainFileDescription = outputparser.outputstructure
-
- # Use the main function from nomadcore
- mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext=superContext, cachingLevelForMetaName=cachingLevelForMetaName, onClose={})
+ self.implementation.backend.fileOut.write("]\n")
#===============================================================================
diff --git a/parser/parsercp2k/utils/logconfig.py b/parser/parser-cp2k/cp2kparser/utils/logconfig.py
similarity index 100%
rename from parser/parsercp2k/utils/logconfig.py
rename to parser/parser-cp2k/cp2kparser/utils/logconfig.py
diff --git a/parser/parsercp2k/utils/testing.py b/parser/parser-cp2k/cp2kparser/utils/testing.py
similarity index 100%
rename from parser/parsercp2k/utils/testing.py
rename to parser/parser-cp2k/cp2kparser/utils/testing.py
diff --git a/parser/setup.py b/parser/parser-cp2k/setup.py
similarity index 91%
rename from parser/setup.py
rename to parser/parser-cp2k/setup.py
index 4282820cf99ac1d15b3935b5b2155c6275c0434d..03a5a1dec528a2f0155384f86e0d5e090cab80ea 100644
--- a/parser/setup.py
+++ b/parser/parser-cp2k/setup.py
@@ -5,7 +5,7 @@ from setuptools import setup, find_packages
def main():
# Start package setup
setup(
- name="parsercp2k",
+ name="cp2karser",
version="0.1",
include_package_data=True,
package_data={
@@ -15,7 +15,7 @@ def main():
author="Lauri Himanen",
author_email="lauri.himanen@gmail.com",
license="GPL3",
- packages=["parsercp2k"],
+ packages=["cp2kparser"],
install_requires=[
'pint',
'numpy',
diff --git a/parser/parsercp2k/__init__.py b/parser/parsercp2k/__init__.py
deleted file mode 100644
index 26705c5913af466df6a00563f5e0b30f72ff853c..0000000000000000000000000000000000000000
--- a/parser/parsercp2k/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-import parsercp2k.utils.logconfig
-from parsercp2k.parser import CP2KParser
diff --git a/parser/parsercp2k/parsing/autoparser.py b/parser/parsercp2k/parsing/autoparser.py
deleted file mode 100644
index bebecb473bc20c15284aed8e83cb140f5d4f58d8..0000000000000000000000000000000000000000
--- a/parser/parsercp2k/parsing/autoparser.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import sys
-import os
-import cStringIO
-from parsercp2k.implementation.cp2kparserversioner import CP2KParserVersioner
-from parsercp2k.generics.testing import get_parser
-
-
-#===============================================================================
-def parse_path(path, metainfo_to_keep=[], metainfo_to_skip=[], dump=False):
- """Generates a cp2k parser using the tools defined in testing.py and parses
- the contents in the given path
- """
- # If a dump is requested, the results will be saved to a file under the
- # current folder
- if dump:
- stream = cStringIO.StringIO()
- else:
- stream = sys.stdout
- parserbuilder = CP2KParserVersioner
- 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"))
- parser = get_parser(path, metainfopath, parserbuilder, metainfo_to_keep, metainfo_to_skip, stream)
- parser.parse()
-
- if dump:
- outputfile = open(path + "/parseroutput.json", "w")
- outputfile.write(stream.getvalue())
diff --git a/parser/parsercp2k/setup_paths.py b/parser/parsercp2k/setup_paths.py
deleted file mode 100644
index 89200e03930e073d5e934adb59df608663d89629..0000000000000000000000000000000000000000
--- a/parser/parsercp2k/setup_paths.py
+++ /dev/null
@@ -1,8 +0,0 @@
-import sys
-import os
-baseDir = os.path.dirname(os.path.abspath(__file__))
-commonDir = os.path.normpath(os.path.join(baseDir, "../../../../python-common/common/python"))
-
-if os.path.exists(commonDir):
- if not commonDir in sys.path:
- sys.path.insert(0, commonDir)