From 04656a61aef394226bb62c38ce5129f5f9d72097 Mon Sep 17 00:00:00 2001 From: Fawzi Mohamed <fawzi.mohamed@fhi-berlin.mpg.de> Date: Sun, 27 Jan 2019 06:35:58 +0100 Subject: [PATCH] meta 2.0 changes --- parser/parser-mopac/parser_mopac.py | 8 +++++--- parser/parser-mopac/reader.py | 10 +++++----- src/main/scala/eu/nomad_lab/parsers/MopacParser.scala | 2 +- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/parser/parser-mopac/parser_mopac.py b/parser/parser-mopac/parser_mopac.py index 134f482..039921f 100644 --- a/parser/parser-mopac/parser_mopac.py +++ b/parser/parser-mopac/parser_mopac.py @@ -80,7 +80,7 @@ def parse(filename): with o(p, 'section_single_configuration_calculation'): p.addValue('single_configuration_calculation_to_system_ref', system_gid) - p.addValue('single_configuration_to_calculation_method_ref', + p.addValue('single_configuration_calculation_to_method_ref', method_gid) p.addRealValue('energy_total', c(r.energy_total, 'eV')) if 'x_mopac_fhof' in r: @@ -89,13 +89,15 @@ def parse(filename): p.addRealValue('electronic_kinetic_energy', c(r.electronic_kinetic_energy, 'eV')) if 'atom_forces' in r: + fId = p.openSection('section_atom_forces') p.addArrayValues('atom_forces', c(r.atom_forces, 'eV/angstrom')) + p.closeSection('section_atom_forces', fId) if 'energy_reference_highest_occupied' in r: p.addArrayValues('energy_reference_highest_occupied', c(r.energy_reference_highest_occupied, 'eV')) - if 'spin_S2' in r: - p.addRealValue('spin_S2', r.spin_S2) + if 'spin_s2' in r: + p.addRealValue('spin_s2', r.spin_s2) if 'time_calculation' in r: p.addRealValue('time_calculation', r.time_calculation) diff --git a/parser/parser-mopac/reader.py b/parser/parser-mopac/reader.py index 50f61d5..c1cac53 100644 --- a/parser/parser-mopac/reader.py +++ b/parser/parser-mopac/reader.py @@ -62,8 +62,8 @@ class Reader: re.compile(r"NO.\s*OF\s*ALPHA\s*ELECTRONS\s*=\s*(?P<n_alpha>[0-9]+)"), 'n_beta': re.compile(r"NO.\s*OF\s*BETA\s*ELECTRONS\s*=\s*(?P<n_beta>[0-9]+)"), - 'spin_S2': - re.compile(r"\(S\*\*2\)\s*=\s*(?P<spin_S2>[0-9.]+)"), + 'spin_s2': + re.compile(r"\(S\*\*2\)\s*=\s*(?P<spin_s2>[0-9.]+)"), 'time_calculation': re.compile(r"TOTAL\s*JOB\s*TIME:\s*(?P<time_calculation>[0-9.]+)\s*"), 'total_charge': @@ -200,10 +200,10 @@ class Reader: float)).reshape(1, 1, -1) self.data['eigenvalues_values'] = eigs - if self.data.get('spin_S2') is None: - m = re.search(self.restrs['spin_S2'], line) + if self.data.get('spin_s2') is None: + m = re.search(self.restrs['spin_s2'], line) if m: - self.data['spin_S2'] = float(m.group('spin_S2')) + self.data['spin_s2'] = float(m.group('spin_s2')) if self.data.get('time_calculation') is None: m = re.search(self.restrs['time_calculation'], line) diff --git a/src/main/scala/eu/nomad_lab/parsers/MopacParser.scala b/src/main/scala/eu/nomad_lab/parsers/MopacParser.scala index d9deba4..62f73ee 100644 --- a/src/main/scala/eu/nomad_lab/parsers/MopacParser.scala +++ b/src/main/scala/eu/nomad_lab/parsers/MopacParser.scala @@ -49,7 +49,7 @@ object MopacParser extends SimpleExternalParserGenerator( "parser-mopac/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/mopac.nomadmetainfo.json" ) ++ DefaultPythonInterpreter.commonFiles(), dirMap = Map( -- GitLab