asap parser

parser/parser-asap/parser.py

+from __future__ import division
+import os
+from contextlib import contextmanager
+import numpy as np
+from ase.data import chemical_symbols
+from ase.io.aff import affopen as Reader
+import setup_paths
+from nomadcore.unit_conversion.unit_conversion import convert_unit as cu
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+from nomadcore.parser_backend import JsonParseEventsWriterBackend
+
+
+@contextmanager
+def open_section(p, name):
+    gid = p.openSection(name)
+    yield
+    p.closeSection(name, gid)
+
+
+def c(value, unit=None):
+    """ Dummy function for unit conversion"""
+    return cu(value, unit)
+
+
+parser_info = {"name": "parser_asap", "version": "1.0"}
+path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
+        'gpaw.nomadmetainfo.json'
+metaInfoPath = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
+
+metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
+                                  dependencyLoader=None,
+                                  extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
+                                  uri=None)
+
+
+def parse(filename):
+    p = JsonParseEventsWriterBackend(metaInfoEnv)
+    o = open_section
+    r = Reader(filename)
+    p.startedParsingSession(filename, parser_info)
+
+    with o(p, 'section_run'):
+        p.addValue('program_name', 'ASAP')
+        p.addValue('program_version', '1.0.0')
+        with o(p, 'section_system'):
+            p.addArrayValues('simulation_cell', c(r.UnitCell, 'bohr'))
+            symbols = np.array([chemical_symbols[z] for z in r.AtomicNumbers])
+            p.addArrayValues('atom_labels', symbols)
+            p.addArrayValues('atom_positions', c(r.CartesianPositions, 'bohr'))
+            p.addArrayValues('configuration_periodic_dimensions',
+                             np.array(r.BoundaryConditions, bool))
+        with o(p, 'section_sampling_method'):
+            p.addValue('ensemble_type', 'NVE')
+        with o(p, 'section_frame_sequence'):
+            pass
+        with o(p, 'section_single_configuration_calculation'):
+            p.addRealValue('energy_total', c(r.Epot, 'hartree'))
+            p.addRealValue('energy_correction_entropy', c(r.S, 'hartree'))
+            if 'CartesianForces' in r:
+                p.addArrayValues('atom_forces_free',
+                                 c(r.CartesianForces, 'bohr/hartree'))
+            with o(p, 'section_method'):
+                pass
+                #p.addValue('x_asap_electronic_structure_method', 'EMT')
+    p.finishedParsingSession("ParseSuccess", None)
+
+if __name__ == '__main__':
+    import sys
+    filename = sys.argv[1]
+    parse(filename)

parser/parser-asap/setup_paths.py

+import sys, os, os.path
+baseDir = os.path.dirname(os.path.abspath(__file__))
+commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
+
+if not commonDir in sys.path:
+    sys.path.insert(0, commonDir)