From 2997aa122f64a365e7c90ddcb7d417823ddf421c Mon Sep 17 00:00:00 2001
From: Fawzi Mohamed <fawzi.mohamed@fhi-berlin.mpg.de>
Date: Sat, 26 Jan 2019 12:14:02 +0100
Subject: [PATCH] meta 2.0 changes
---
parser/parser-gaussian/parser_gaussian.py | 27 ++++++++++---------
.../eu/nomad_lab/parsers/GaussianParser.scala | 2 +-
2 files changed, 16 insertions(+), 13 deletions(-)
diff --git a/parser/parser-gaussian/parser_gaussian.py b/parser/parser-gaussian/parser_gaussian.py
index c2fc4c3..51f727b 100644
--- a/parser/parser-gaussian/parser_gaussian.py
+++ b/parser/parser-gaussian/parser_gaussian.py
@@ -133,7 +133,7 @@ mainFileDescription = SM(
SM(r"\s*NFock=\s*[0-9]+\s*Conv=(?P<x_gaussian_energy_error__hartree>[-+0-9EeDd.]+)\s*"),
SM(r"\s*KE=\s*(?P<x_gaussian_electronic_kinetic_energy__hartree>[-+0-9EeDd.]+)\s*"),
SM(r"\s*Annihilation of the first spin contaminant"),
- SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*(?P<spin_S2>[0-9.]+),\s*after\s*(?P<x_gaussian_after_annihilation_spin_S2>[0-9.]+)"),
+ SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*(?P<spin_s2>[0-9.]+),\s*after\s*(?P<x_gaussian_after_annihilation_spin_s2>[0-9.]+)"),
SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P<x_gaussian_perturbation_energy__hartree>[-+0-9D.]+)"),
]
),
@@ -343,7 +343,7 @@ mainFileDescription = SM(
subMatchers = [
SM(r"\s*Temperature\s*(?P<x_gaussian_temperature>[0-9.]+)\s*Kelvin.\s*Pressure\s*(?P<x_gaussian_pressure__atmosphere>[0-9.]+)\s*Atm."),
SM(r"\s*Principal axes and moments of inertia in atomic units:"),
- SM(r"\s*Eigenvalues --\s*(?P<x_gaussian_moment_of_inertia_X__amu_angstrom_angstrom>(\d+\.\d{5}))\s*?(?P<x_gaussian_moment_of_inertia_Y__amu_angstrom_angstrom>(\d+\.\d{5}))\s*?(?P<x_gaussian_moment_of_inertia_Z__amu_angstrom_angstrom>(\d+\.\d{5}))"),
+ SM(r"\s*Eigenvalues --\s*(?P<x_gaussian_moment_of_inertia_x__amu_angstrom_angstrom>(\d+\.\d{5}))\s*?(?P<x_gaussian_moment_of_inertia_y__amu_angstrom_angstrom>(\d+\.\d{5}))\s*?(?P<x_gaussian_moment_of_inertia_z__amu_angstrom_angstrom>(\d+\.\d{5}))"),
SM(r"\s*Zero-point correction=\s*(?P<x_gaussian_zero_point_energy__hartree>[0-9.]+)"),
SM(r"\s*Thermal correction to Energy=\s*(?P<x_gaussian_thermal_correction_energy__hartree>[0-9.]+)"),
SM(r"\s*Thermal correction to Enthalpy=\s*(?P<x_gaussian_thermal_correction_enthalpy__hartree>[0-9.]+)"),
@@ -474,8 +474,8 @@ class GaussianParserContext(object):
backend.addValue("sampling_method", sampling_method)
backend.closeSection("section_sampling_method", samplingGIndex)
frameSequenceGIndex = backend.openSection("section_frame_sequence")
- backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex)
- backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
+ backend.addValue("frame_sequence_to_sampling_method_ref", samplingGIndex)
+ backend.addArrayValues("frame_sequence_to_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex)
# reset all variables
self.initialize_values()
@@ -510,7 +510,10 @@ class GaussianParserContext(object):
atom_forces[i,0] = xForce[i]
atom_forces[i,1] = yForce[i]
atom_forces[i,2] = zForce[i]
- backend.addArrayValues("atom_forces_raw", atom_forces)
+ fId = backend.openSection('section_atom_forces')
+ backend.addValue('atom_forces_constraints', 'raw')
+ backend.addArrayValues("atom_forces", atom_forces)
+ backend.closeSection('section_atom_forces', fId)
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
self.singleConfCalcs.append(gIndex)
@@ -526,7 +529,7 @@ class GaussianParserContext(object):
# start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1
# write the references to section_method and section_system
- backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
+ backend.addValue('single_configuration_calculation_to_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)
def onClose_x_gaussian_section_geometry_optimization_info(self, backend, gIndex, section):
@@ -1325,11 +1328,11 @@ class GaussianParserContext(object):
for xcItem in xcList:
xcName = xcItem.get('name')
if xcName is not None:
- # write section and XC_functional_name
- gIndexTmp = backend.openSection('section_XC_functionals')
- backend.addValue('XC_functional_name', xcName)
- # write hybrid_xc_coeff for PBE1PBE into XC_functional_parameters
- backend.closeSection('section_XC_functionals', gIndexTmp)
+ # write section and xc_functional_name
+ gIndexTmp = backend.openSection('section_xc_functionals')
+ backend.addValue('xc_functional_name', xcName)
+ # write hybrid_xc_coeff for PBE1PBE into xc_functional_parameters
+ backend.closeSection('section_xc_functionals', gIndexTmp)
else:
logger.error("The dictionary for xc functional '%s' does not have the key 'name'. Please correct the dictionary xcDict in %s." % (xc[-1], os.path.basename(__file__)))
else:
@@ -1531,7 +1534,7 @@ cachingLevelForMetaName = {
"section_method": CachingLevel.Forward,
"x_gaussian_section_elstruc_method": CachingLevel.Forward,
"x_gaussian_electronic_structure_method": CachingLevel.ForwardAndCache,
- "XC_functional_name": CachingLevel.ForwardAndCache,
+ "xc_functional_name": CachingLevel.ForwardAndCache,
"basis_set_atom_centered_short_name": CachingLevel.Forward,
"x_gaussian_settings": CachingLevel.Cache,
"x_gaussian_settings_corrected": CachingLevel.ForwardAndCache,
diff --git a/src/main/scala/eu/nomad_lab/parsers/GaussianParser.scala b/src/main/scala/eu/nomad_lab/parsers/GaussianParser.scala
index c44db93..e39d082 100644
--- a/src/main/scala/eu/nomad_lab/parsers/GaussianParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/GaussianParser.scala
@@ -47,7 +47,7 @@ object GaussianParser extends SimpleExternalParserGenerator(
"parser-gaussian/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
- "nomad_meta_info/meta_types.nomadmetainfo.json",
+ "nomad_meta_info/meta.nomadmetainfo.json",
"nomad_meta_info/gaussian.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
--
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