Initial commit.

.gitignore

+# use glob syntax.
+syntax: glob
+*.ser
+*.class
+*~
+*.bak
+#*.off
+*.old
+*.pyc
+*.bk
+*.swp
+.DS_Store
+**/__pycache__
+
+# logging files
+detailed.log
+
+# eclipse conf file
+.settings
+.classpath
+.project
+.manager
+.scala_dependencies
+
+# idea
+.idea
+*.iml
+
+# building
+target
+build
+null
+tmp*
+temp*
+dist
+test-output
+build.log
+
+# other scm
+.svn
+.CVS
+.hg*
+
+# switch to regexp syntax.
+#  syntax: regexp
+#  ^\.pc/
+
+#SHITTY output not in target directory
+build.log
+
+#emacs TAGS
+TAGS
+
+lib/
+env/

.gitlab-ci.yml

+stages:
+  - test
+
+testing:
+  stage: test
+  script:
+    - cd .. && rm -rf nomad-lab-base
+    - git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
+    - cd nomad-lab-base
+    - git submodule foreach git checkout master
+    - git submodule foreach git pull
+    - sbt nwchem/test
+    - export PYTHONEXE=/labEnv/bin/python
+    - sbt nwchem/test
+  only:
+    - master
+  tags:
+    - test
+    - spec2

parser/parser-nwchem/nwchemparser/__init__.py

+from nwchemparser.parser import NWChemParser

parser/parser-nwchem/nwchemparser/parser.py

+from builtins import next
+from builtins import range
+import os
+import re
+import logging
+import importlib
+from nomadcore.baseclasses import ParserInterface
+logger = logging.getLogger("nomad")
+
+
+#===============================================================================
+class NWChemParser(ParserInterface):
+    """This class handles the initial setup before any parsing can happen. It
+    determines which version of NWChem was used to generate the output and then
+    sets up a correct main parser.
+
+    After the implementation has been setup, you can parse the files with
+    parse().
+    """
+    def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True):
+        super(NWChemParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
+
+    def setup_version(self):
+        """Setups the version by looking at the output file and the version
+        specified in it.
+        """
+        # Search for the NWChem version specification. The correct parser is
+        # initialized based on this information.
+        regex_version = re.compile("              Northwest Computational Chemistry Package \(NWChem\) (\d+\.\d+)")
+        n_lines = 1000
+        version_id = None
+        with open(self.parser_context.main_file, 'r') as outputfile:
+            for i_line in range(n_lines):
+                try:
+                    line = next(outputfile)
+                except StopIteration:
+                    break
+
+                # Look for version
+                result_version = regex_version.match(line)
+                if result_version:
+                    version_id = result_version.group(1).replace('.', '')
+
+        if version_id is None:
+            msg = "Could not find a version specification from the given main file."
+            logger.exception(msg)
+            raise RuntimeError(msg)
+
+        # Setup the root folder to the fileservice that is used to access files
+        dirpath, filename = os.path.split(self.parser_context.main_file)
+        dirpath = os.path.abspath(dirpath)
+        self.parser_context.file_service.setup_root_folder(dirpath)
+        self.parser_context.file_service.set_file_id(filename, "output")
+
+        # Setup the correct main parser based on the version id. If no match
+        # for the version is found, use the main parser for NWChem 6.6
+        self.setup_main_parser(version_id)
+
+    def get_metainfo_filename(self):
+        return "nwchem.nomadmetainfo.json"
+
+    def get_parser_info(self):
+        return {'name': 'nwchem-parser', 'version': '1.0'}
+
+    def setup_main_parser(self, version_id):
+        # Currently the version id is a pure integer, so it can directly be mapped
+        # into a package name.
+        base = "nwchemparser.versions.nwchem{}.mainparser".format(version_id)
+        parser_module = None
+        parser_class = None
+        try:
+            parser_module = importlib.import_module(base)
+        except ImportError:
+            logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for NWChem 6.6".format(version_id))
+            base = "nwchemparser.versions.nwchem66.mainparser"
+            try:
+                parser_module = importlib.import_module(base)
+            except ImportError:
+                logger.exception("Tried to default to the NWChem 6.6 implementation but could not find the correct module.")
+                raise
+        try:
+            parser_class = getattr(parser_module, "NWChemMainParser")
+        except AttributeError:
+            logger.exception("A parser class 'NWChemMainParser' could not be found in the module '[]'.".format(parser_module))
+            raise
+        self.main_parser = parser_class(self.parser_context.main_file, self.parser_context)

parser/parser-nwchem/nwchemparser/scalainterface.py

+"""
+This is the access point to the parser for the scala layer in the
+nomad project.
+"""
+from __future__ import absolute_import
+import sys
+import setup_paths
+from nomadcore.parser_backend import JsonParseEventsWriterBackend
+from cpmdparser import CPMDParser
+
+
+if __name__ == "__main__":
+
+    # Initialise the parser with the main filename and a JSON backend
+    main_file = sys.argv[1]
+    parser = CPMDParser(main_file, backend=JsonParseEventsWriterBackend)
+    parser.parse()

parser/parser-nwchem/nwchemparser/setup_paths.py

+"""
+Setups the python-common library 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-cpmd"))
+
+# 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 commonDir not in sys.path:
+    sys.path.insert(1, commonDir)
+    sys.path.insert(1, parserDir)

setup.py

+"""
+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, find_packages
+
+
+#===============================================================================
+def main():
+    # Start package setup
+    setup(
+        name="nwchemparser",
+        version="0.1",
+        description="NoMaD parser implementation for NWChem.",
+        author="Lauri Himanen",
+        author_email="lauri.himanen@aalto.fi",
+        license="GPL3",
+        package_dir={'': 'parser/parser-nwchem'},
+        packages=find_packages(),
+        install_requires=[
+            'pint',
+            'numpy',
+            'nomadcore',
+        ],
+    )
+
+# Run main function by default
+if __name__ == "__main__":
+    main()

src/main/scala/eu/nomad_lab/parsers/NWChemParser.scala

+package eu.nomad_lab.parsers
+
+import eu.{ nomad_lab => lab }
+import eu.nomad_lab.DefaultPythonInterpreter
+import org.{ json4s => jn }
+import scala.collection.breakOut
+
+object NWChemParser extends SimpleExternalParserGenerator(
+  name = "NWChemParser",
+  parserInfo = jn.JObject(
+    ("name" -> jn.JString("NWChemParser")) ::
+      ("parserId" -> jn.JString("NWChemParser" + lab.NWChemVersionInfo.version)) ::
+      ("versionInfo" -> jn.JObject(
+        ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
+          case (k, v) => k -> jn.JString(v.toString)
+        }(breakOut): List[(String, jn.JString)])) ::
+          (lab.NWChemVersionInfo.toMap.map {
+            case (key, value) =>
+              (key -> jn.JString(value.toString))
+          }(breakOut): List[(String, jn.JString)])
+      )) :: Nil
+  ),
+  mainFileTypes = Seq("text/.*"),
+  mainFileRe = """              Northwest Computational Chemistry Package \(NWChem\) \d+\.\d+
+              ------------------------------------------------------
+
+
+                    Environmental Molecular Sciences Laboratory
+                       Pacific Northwest National Laboratory
+                                Richland, WA 99352""".r,
+  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/nwchem/parser/parser-nwchem/nwchemparser/scalainterface.py",
+    "${mainFilePath}"),
+  cmdCwd = "${mainFilePath}/..",
+  resList = Seq(
+    "parser-nwchem/nwchemparser/__init__.py",
+    "parser-nwchem/nwchemparser/setup_paths.py",
+    "parser-nwchem/nwchemparser/parser.py",
+    "parser-nwchem/nwchemparser/scalainterface.py",
+    "parser-nwchem/nwchemparser/versions/__init__.py",
+    "parser-nwchem/nwchemparser/versions/nwchem66/__init__.py",
+    "parser-nwchem/nwchemparser/versions/nwchem66/mainparser.py",
+    "nomad_meta_info/public.nomadmetainfo.json",
+    "nomad_meta_info/common.nomadmetainfo.json",
+    "nomad_meta_info/meta_types.nomadmetainfo.json",
+    "nomad_meta_info/nwchem.nomadmetainfo.json"
+  ) ++ DefaultPythonInterpreter.commonFiles(),
+  dirMap = Map(
+    "parser-nwchem" -> "parsers/nwchem/parser/parser-nwchem",
+    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
+  ) ++ DefaultPythonInterpreter.commonDirMapping()
+)

src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala

+package eu.nomad_lab.parsers
+
+import org.specs2.mutable.Specification
+
+object NWChemParserSpec extends Specification {
+  "NWChemParserTest" >> {
+    "test with json-events" >> {
+      ParserRun.parse(NWChemParser, "parsers/nwchem/test/examples/single_point/output.out", "json-events") must_== ParseResult.ParseSuccess
+    }
+  }
+
+  "test single_point with json" >> {
+    ParserRun.parse(NWChemParser, "parsers/nwchem/test/examples/single_point/output.out", "json") must_== ParseResult.ParseSuccess
+  }
+
+  "test geo_opt with json" >> {
+    ParserRun.parse(NWChemParser, "parsers/nwchem/test/examples/geo_opt/output.out", "json") must_== ParseResult.ParseSuccess
+  }
+}

test/examples/geo_opt/input.nw

+title "WATER 6-311G* meta-GGA XC geometry"
+echo
+geometry units angstroms
+ O       0.0  0.0  0.0
+ H       0.0  0.0  1.0
+ H       0.0  1.0  0.0
+end
+basis
+ H library 6-311G*
+ O library 6-311G*
+end
+dft
+ iterations 50
+ print  kinetic_energy
+ xc xtpss03 ctpss03
+ decomp
+end
+task dft optimize

test/examples/single_point/input.nw

+title "WATER 6-311G* meta-GGA XC geometry"
+echo
+geometry units angstroms
+ O       0.00000000     0.00000000    -0.06392934
+ H       0.76924532     0.00000000     0.52693942
+ H       -0.76924532     0.00000000     0.52693942
+end
+basis
+ H library 6-311G*
+ O library 6-311G*
+end
+dft
+ iterations 50
+ print  kinetic_energy
+ xc xtpss03 ctpss03
+ decomp
+end
+task dft energy

test/unittests/README.md

+# Unit tests
+This directory contains unit tests to evaluate the correctness of the parser in
+a systematic way. Ideally each parsed metainfo should have at least one unit
+test, and if the resulting values are predetermined, the available values
+should all be tested individually. Also certain scenarios that should produce a
+parsing error should be tested.

test/unittests/nwchem_6.6/dft/energy/input.nw

+title "WATER 6-311G* meta-GGA XC geometry"
+echo
+geometry units angstroms
+ O       0.00000000     0.00000000    -0.06392934
+ H       0.76924532     0.00000000     0.52693942
+ H       -0.76924532     0.00000000     0.52693942
+end
+basis
+ H library 6-311G*
+ O library 6-311G*
+end
+dft
+ iterations 50
+ print  kinetic_energy
+ xc xtpss03 ctpss03
+ decomp
+end
+task dft energy

test/unittests/nwchem_6.6/dft/force/input.nw

+title "WATER 6-311G* meta-GGA XC geometry"
+echo
+geometry units angstroms
+ O       0.00000000     0.00000000    -0.06392934
+ H       0.76924532     0.00000000     0.52693942
+ H       -0.76924532     0.00000000     0.52693942
+end
+basis
+ H library 6-311G*
+ O library 6-311G*
+end
+dft
+ iterations 50
+ print  kinetic_energy
+ xc xtpss03 ctpss03
+ decomp
+end
+task dft gradient

test/unittests/nwchem_6.6/dft/geo_opt/input.nw

+title "WATER 6-311G* meta-GGA XC geometry"
+echo
+geometry units angstroms
+ O       0.0  0.0  0.0
+ H       0.0  0.0  1.0
+ H       0.0  1.0  0.0
+end
+basis
+ H library 6-311G*
+ O library 6-311G*
+end
+dft
+ iterations 50
+ print  kinetic_energy
+ xc xtpss03 ctpss03
+ decomp
+end
+task dft optimize