Added more parsers to NOMAD

.gitignore

@@ -55,3 +55,5 @@ TAGS
 
 lib/
 env/
+
+*.egg-info/*
\ No newline at end of file

parser/parser-fplo/FploCommon.py → fploparser/FploCommon.py

@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import setup_paths
 import calendar
 import json
 import os
@@ -53,13 +52,13 @@ def re_vec(name, units='', split="\s+"):
 
 # loading metadata from
 # nomad-meta-info/meta_info/nomad_meta_info/fplo.nomadmetainfo.json
-META_INFO = loadJsonFile(
-    filePath=os.path.normpath(os.path.join(
-        os.path.dirname(os.path.abspath(__file__)),
-        "../../../../nomad-meta-info/meta_info/nomad_meta_info/fplo.nomadmetainfo.json")),
-    dependencyLoader=None,
-    extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
-    uri=None)[0]
+# META_INFO = loadJsonFile(
+#     filePath=os.path.normpath(os.path.join(
+#         os.path.dirname(os.path.abspath(__file__)),
+#         "../../../../nomad-meta-info/meta_info/nomad_meta_info/fplo.nomadmetainfo.json")),
+#     dependencyLoader=None,
+#     extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
+#     uri=None)[0]
 
 PARSER_INFO_DEFAULT = {
   "name": "parser_fplo",

parser/parser-fplo/FploInputParser.py → fploparser/FploInputParser.py

@@ -25,15 +25,13 @@ This module is implemented as follows:
 TODO:
 4) transform AST to metaInfo backend calls
 """
-import setup_paths
 import re
 import sys
 import os
 import logging
 import json
-import FploCommon as FploC
+from . import FploCommon as FploC
 from nomadcore.match_highlighter import ANSI
-from nomadcore.parser_backend import JsonParseEventsWriterBackend
 from nomadcore.caching_backend import CachingLevel, ActiveBackend
 
 LOGGER = logging.getLogger(__name__)

fploparser/__init__.py

+from .parser_fplo_14 import FploParser
\ No newline at end of file

fploparser/metainfo/__init__.py

+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import fploparser.metainfo.fplo
+import nomad.datamodel.metainfo.common
+import nomad.datamodel.metainfo.public
+import nomad.datamodel.metainfo.general
+import fploparser.metainfo.fplo_temporaries
+import fploparser.metainfo.fplo_input_autogenerated
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['fploparser.metainfo.fplo'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['fploparser.metainfo.fplo_temporaries'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['fploparser.metainfo.fplo_input_autogenerated'].m_package)  # type: ignore

fploparser/metainfo/fplo.py

+import numpy as np            # pylint: disable=unused-import
+import typing                 # pylint: disable=unused-import
+from nomad.metainfo import (  # pylint: disable=unused-import
+    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+    Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+from nomad.datamodel.metainfo import common
+
+m_package = Package(
+    name='fplo_nomadmetainfo_json',
+    description='None',
+    a_legacy=LegacyDefinition(name='fplo.nomadmetainfo.json'))
+
+
+class section_run(public.section_run):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
+
+    x_fplo_program_version_sub = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO sub version
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_program_version_sub'))
+
+    x_fplo_program_compilation_options = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO compilation options
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_program_compilation_options'))
+
+
+class section_system(public.section_system):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
+
+    x_fplo_reciprocal_cell = Quantity(
+        type=np.dtype(np.float64),
+        shape=[3, 3],
+        unit='1 / meter',
+        description='''
+        Reciprocal Lattice vectors (in Cartesian coordinates). The first index runs over
+        the $x,y,z$ Cartesian coordinates, and the second index runs over the 3 lattice
+        vectors.
+        ''',
+        categories=[public.configuration_core],
+        a_legacy=LegacyDefinition(name='x_fplo_reciprocal_cell'))
+
+    x_fplo_atom_idx = Quantity(
+        type=np.dtype(np.int32),
+        shape=['number_of_atoms'],
+        description='''
+        FPLO-internal index for each atom
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_atom_idx'))
+
+    x_fplo_atom_wyckoff_idx = Quantity(
+        type=np.dtype(np.int32),
+        shape=['number_of_atoms'],
+        description='''
+        Wyckoff position index of each atom
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_atom_wyckoff_idx'))
+
+    x_fplo_atom_cpa_block = Quantity(
+        type=np.dtype(np.int32),
+        shape=['number_of_atoms'],
+        description='''
+        CPA block of each atom
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_atom_cpa_block'))
+
+    x_fplo_structure_type = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO structure type: Crystal/Molecule
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_structure_type'))
+
+
+class section_method(public.section_method):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+    x_fplo_xc_functional_number = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        FPLO number xc functional
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_xc_functional_number'))
+
+    x_fplo_xc_functional = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO notation of xc functional
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_xc_functional'))
+
+    x_fplo_dft_plus_u_projection_type = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO notation of DFT+U projection
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_projection_type'))
+
+    x_fplo_dft_plus_u_functional = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO notation of DFT+U functional
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_functional'))
+
+
+class section_dft_plus_u_orbital(common.section_dft_plus_u_orbital):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
+
+    x_fplo_dft_plus_u_orbital_element = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        FPLO: Atom/Orbital dependent DFT+U property: element
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_orbital_element'))
+
+    x_fplo_dft_plus_u_orbital_species = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        FPLO: Atom/Orbital dependent DFT+U property: species index
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_orbital_species'))
+
+    x_fplo_dft_plus_u_orbital_F0 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        FPLO: Atom/Orbital dependent DFT+U property: value F0
+        ''',
+        categories=[public.energy_value],
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_orbital_F0'))
+
+    x_fplo_dft_plus_u_orbital_F2 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        FPLO: Atom/Orbital dependent DFT+U property: value F2
+        ''',
+        categories=[public.energy_value],
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_orbital_F2'))
+
+    x_fplo_dft_plus_u_orbital_F4 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        FPLO: Atom/Orbital dependent DFT+U property: value F4
+        ''',
+        categories=[public.energy_value],
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_orbital_F4'))
+
+    x_fplo_dft_plus_u_orbital_F6 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        FPLO: Atom/Orbital dependent DFT+U property: value F6
+        ''',
+        categories=[public.energy_value],
+        a_legacy=LegacyDefinition(name='x_fplo_dft_plus_u_orbital_F6'))
+
+
+m_package.__init_metainfo__()

fploparser/metainfo/fplo_temporaries.py

+import numpy as np            # pylint: disable=unused-import
+import typing                 # pylint: disable=unused-import
+from nomad.metainfo import (  # pylint: disable=unused-import
+    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+    Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+
+m_package = Package(
+    name='fplo_temporaries_nomadmetainfo_json',
+    description='None',
+    a_legacy=LegacyDefinition(name='fplo.temporaries.nomadmetainfo.json'))
+
+
+class section_run(public.section_run):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
+
+    x_fplo_t_program_version_main = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        temporary: FPLO main version
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_program_version_main'))
+
+    x_fplo_t_program_version_release = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        temporary: FPLO release number
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_program_version_release'))
+
+    x_fplo_t_run_hosts = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        temporary: FPLO run hosts
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_run_hosts'))
+
+
+class section_system(public.section_system):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
+
+    x_fplo_t_vec_a_x = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for direct lattice vectors, x-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_vec_a_x'))
+
+    x_fplo_t_vec_a_y = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for direct lattice vectors, y-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_vec_a_y'))
+
+    x_fplo_t_vec_a_z = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for direct lattice vectors, z-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_vec_a_z'))
+
+    x_fplo_t_vec_b_x = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for reciprocal lattice vectors, x-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_vec_b_x'))
+
+    x_fplo_t_vec_b_y = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for reciprocal lattice vectors, y-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_vec_b_y'))
+
+    x_fplo_t_vec_b_z = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for reciprocal lattice vectors, z-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_vec_b_z'))
+
+    x_fplo_t_atom_positions_x = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for atom positions, x-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_positions_x'))
+
+    x_fplo_t_atom_positions_y = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for atom positions, y-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_positions_y'))
+
+    x_fplo_t_atom_positions_z = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for atom positions, z-component
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_positions_z'))
+
+    x_fplo_t_atom_idx = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO atom index
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_idx'))
+
+    x_fplo_t_atom_labels = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Temporary storage for FPLO atom labels
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_labels'))
+
+    x_fplo_t_atom_wyckoff_idx = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO Wyckoff position index of each atom
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_wyckoff_idx'))
+
+    x_fplo_t_atom_cpa_block = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO CPA block of each atom
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_atom_cpa_block'))
+
+
+class section_method(public.section_method):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+    x_fplo_t_relativity_method = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Temporary storage for FPLO relativistic method
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_relativity_method'))
+
+    x_fplo_t_dft_plus_u_species_subshell_species = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U species
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_species'))
+
+    x_fplo_t_dft_plus_u_species_subshell_element = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U element
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_element'))
+
+    x_fplo_t_dft_plus_u_species_subshell_subshell = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U (n,l)subshell
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_subshell'))
+
+    x_fplo_t_dft_plus_u_species_subshell_F0 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U F0
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_F0'))
+
+    x_fplo_t_dft_plus_u_species_subshell_F2 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U F2
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_F2'))
+
+    x_fplo_t_dft_plus_u_species_subshell_F4 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U F4
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_F4'))
+
+    x_fplo_t_dft_plus_u_species_subshell_F6 = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U F6
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_F6'))
+
+    x_fplo_t_dft_plus_u_species_subshell_U = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U U
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_U'))
+
+    x_fplo_t_dft_plus_u_species_subshell_J = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per species/(n,l)subshell DFT+U J
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_species_subshell_J'))
+
+    x_fplo_t_dft_plus_u_site_index = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per site DFT+U index
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_site_index'))
+
+    x_fplo_t_dft_plus_u_site_element = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Temporary storage for FPLO per site DFT+U element
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_site_element'))
+
+    x_fplo_t_dft_plus_u_site_species = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per site DFT+U species
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_site_species'))
+
+    x_fplo_t_dft_plus_u_site_subshell = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Temporary storage for FPLO per site DFT+U (n,l)subshell
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_site_subshell'))
+
+    x_fplo_t_dft_plus_u_site_ubi1 = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per site DFT+U ubi1
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_site_ubi1'))
+
+    x_fplo_t_dft_plus_u_site_ubi2 = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Temporary storage for FPLO per site DFT+U ubi2
+        ''',
+        a_legacy=LegacyDefinition(name='x_fplo_t_dft_plus_u_site_ubi2'))
+
+
+class section_scf_iteration(public.section_scf_iteration):
+
+    m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+    x_fplo_t_energy_reference_fermi_iteration = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule',
+        description='''
+        Temporary storage for FPLO Fermi energy in iteration
+        ''',
+        categories=[public.energy_type_reference, public.energy_value],
+        a_legacy=LegacyDefinition(name='x_fplo_t_energy_reference_fermi_iteration'))
+
+
+m_package.__init_metainfo__()

parser/parser-fplo/parser_fplo_14.py → fploparser/parser_fplo_14.py

@@ -13,7 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import setup_paths
 from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM, CachingLevel
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 import os
@@ -24,12 +23,12 @@ import logging
 import nomadcore.unit_conversion.unit_conversion as unit_conversion
 import math
 import numpy as np
-import FploCommon as FploC
+from . import FploCommon as FploC
 import calendar
 from nomadcore.parser_backend import valueForStrValue
-from FploCommon import RE_f, RE_i, cRE_f, cRE_i
+from .FploCommon import RE_f, RE_i, cRE_f, cRE_i
 from nomadcore.parser_backend import valueForStrValue
-import FploInputParser
+from . import FploInputParser
 
 
 LOGGER = logging.getLogger(__name__)
@@ -77,10 +76,10 @@ FPLO_DFT_PLUS_U_FUNCTIONAL = {
 
 class ParserFplo14(object):
     """main place to keep the parser status, open ancillary files,..."""
-    def __init__(self):
+    def __init__(self, metaInfoEnv):
         self.parserInfo = FploC.PARSER_INFO_DEFAULT.copy()
         self.cachingLevelForMetaName = {}
-        for name in FploC.META_INFO.infoKinds:
+        for name in metaInfoEnv.infoKinds:
             # set all temporaries to caching-only
             if name.startswith('x_fplo_t_'):
                 self.cachingLevelForMetaName[name] = CachingLevel.Cache
@@ -98,7 +97,7 @@ class ParserFplo14(object):
 
     def parse(self):
         self.coverageIgnore = re.compile(r"^(?:" + r"|".join(self.coverageIgnoreList) + r")$")
-        mainFunction(self.mainFileDescription(), FploC.META_INFO, self.parserInfo,
+        mainFunction(self.mainFileDescription(), metaInfoEnv, self.parserInfo,
                      cachingLevelForMetaName=self.cachingLevelForMetaName,
                      superContext=self)
 
@@ -695,6 +694,27 @@ class ParserFplo14(object):
                 backend.addValue(key, value)
         backend.closeSection(section_name, gIndex)
 
-if __name__ == "__main__":
-    parser = ParserFplo14()