basic rspt parser

electronicparsers/__init__.py

@@ -911,6 +911,32 @@ def load(self):
     },
 )
 
+rspt_parser_entry_point = EntryPoint(
+    name='parsers/rspt',
+    aliases=['parsers/rspt'],
+    description='NOMAD parser for RSPt.',
+    python_package='electronicparsers.rspt',
+    mainfile_contents_re=r'MPI RSPT',
+    mainfile_name_re=r'.*out_last',
+    parser_class_name='electronicparsers.rspt.RSPtParser',
+    code_name='RSPT',
+    code_homepage='https://www.uu.se/en/department/physics-and-astronomy/research/materials-theory/code-development',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'RSPT',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'rspt',
+        'codeUrl': 'https://www.uu.se/en/department/physics-and-astronomy/research/materials-theory/code-development',
+        'parserDirName': 'dependencies/electronic/electronicparsers/rspt/',
+        'parserGitUrl': 'https://github.com/nomad-coe/electronic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
 siesta_parser_entry_point = EntryPoint(
     name='parsers/siesta',
     aliases=['parsers/siesta'],

electronicparsers/rspt/README.md

@@ -0,0 +1,10 @@
+This is a very basic NOMAD parser for [RSPt](https://www.uu.se/en/department/physics-and-astronomy/research/materials-theory/code-development) with the following features:
+
+- identifies RSPt calculation as a file ending with `out_last` and with the header `MPI RSPT`,
+- reads the version number from the line `RSPt version number: <version>`
+- reads the method (DFT or DMFT) from the line `Initialization of the <method> code`
+- reads the temperature from the line `Readin: Setting the temperature to <temperature>` (needed for proper normalization of the DMFT method class)
+- reads the structure information from a cif file found in the same directory as the `out_last` file
+
+
+

electronicparsers/rspt/__init__.py

@@ -0,0 +1,19 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+from .parser import RSPtParser

electronicparsers/rspt/__main__.py

@@ -0,0 +1,31 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+import sys
+import json
+import logging
+
+from nomad.utils import configure_logging
+from nomad.datamodel import EntryArchive
+from electronicparsers.rspt import RSPtParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    RSPtParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

electronicparsers/rspt/metainfo/__init__.py

@@ -0,0 +1,18 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

electronicparsers/rspt/nomad_plugin.yaml

@@ -0,0 +1,18 @@
+code_category: Atomistic code
+code_homepage: https://www.uu.se/en/department/physics-and-astronomy/research/materials-theory/code-development
+code_name: RSPT
+metadata:
+  codeCategory: Atomistic code
+  codeLabel: RSPT
+  codeLabelStyle: all in capitals
+  codeName: rspt
+  codeUrl: https://www.uu.se/en/department/physics-and-astronomy/research/materials-theory/code-development
+  parserDirName: dependencies/electronic/electronicparsers/rspt/
+  parserGitUrl: https://github.com/nomad-coe/electronic-parsers.git
+  preamble: ''
+  status: production
+  tableOfFiles: ''
+name: parsers/rspt
+parser_class_name: electronicparsers.rspt.parser.RSPtParser
+python_package: electronicparsers.rspt
+plugin_source_code_url: https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/rspt

electronicparsers/rspt/parser.py

@@ -0,0 +1,134 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import re
+import os
+import numpy as np
+
+from simulationparsers.utils import BasicParser
+from nomad.units import ureg
+from nomad.utils import get_logger
+from nomad.parsing.file_parser import Quantity, TextParser, Parser
+from runschema.system import System, Atoms
+from runschema.calculation import Calculation
+from runschema.method import (
+    Method,
+    DFT,
+    Electronic,
+    DMFT,
+)
+from ase.io import read as ase_read
+from nomad.normalizing.common import nomad_atoms_from_ase_atoms
+
+
+class MethodParser(TextParser):
+    def __init__(self):
+        self.method = None
+        super().__init__(None)
+
+    def init_quantities(self):
+        self._quantities = [
+            Quantity(
+                'method',
+                r'\s*Initialization of the (\w+) code\s*\n',
+                comment='#',
+                repeats=True,
+            ),
+            Quantity(
+                'temperature',
+                r'\s*Readin: Setting the temperature to\s+([+-]?\d+\.\d+E[+-]?\d+)\s*\n',
+                comment='#',
+                repeats=False,
+            ),
+        ]
+
+
+class RSPtParser(Parser):
+    def __init__(self, **kwargs) -> None:
+        self._method_parser = MethodParser()
+        super().__init__(**kwargs)
+
+        self._parser = BasicParser(
+            'RSPt',
+            program_version=r'RSPt version number:\s*rspt\.(\d+\.\d+)',
+        )
+
+    def parse(self, mainfile, archive, logger=None):
+        logger = logger if logger is not None else get_logger(__name__)
+        self._method_parser.logger = logger
+        self._method_parser.mainfile = mainfile
+        self.mainfile = mainfile
+        self._maindir = os.path.dirname(self.mainfile)
+        self._auxillary_files = os.listdir(self._maindir)
+
+        self._parser.parse(mainfile, archive, logger=None)
+
+        # PARSE METHOD
+        method = self._method_parser.get('method', '')
+        temperature = self._method_parser.get('temperature', None)
+        # TODO - check rspt units - inverse T has temp units?
+        temperature = temperature * ureg.kelvin if temperature else None
+        inverse_temperature = (
+            1.0 / (ureg.boltzmann_constant * temperature) if temperature else None
+        )
+        if all(m.upper() == 'DFT' for m in method):
+            archive.run[0].method.append(
+                Method(dft=DFT(), electronic=Electronic(method='DFT'))
+            )
+        elif all(m.upper() == 'DMFT' for m in method):
+            archive.run[0].method.append(
+                Method(dmft=DMFT(inverse_temperature=inverse_temperature))
+            )
+        else:
+            logger.warning(
+                'RSPtParser method not recognized, or multiple distinct methods found.'
+            )
+
+        # PARSE SYSTEM
+        cif_files = [f for f in self._auxillary_files if f.endswith('.cif')]
+        if cif_files:
+            if len(cif_files) > 1:
+                self.logger.warning(
+                    'RSPtParser found multiple CIF files, using the first one found.'
+                )
+            ase_atoms = ase_read(f'{self._maindir}/{cif_files[0]}', format='cif')
+            nomad_atoms = nomad_atoms_from_ase_atoms(ase_atoms)
+            archive.run[0].system.append(
+                System(
+                    atoms=Atoms(
+                        atomic_numbers=nomad_atoms.atomic_numbers,
+                        species=nomad_atoms.species,
+                        labels=nomad_atoms.labels,
+                        positions=nomad_atoms.positions,
+                        lattice_vectors=nomad_atoms.lattice_vectors,
+                        periodic=nomad_atoms.periodic,
+                    ),
+                )
+            )
+
+        # PARSE CALCULATION
+        sec_method = archive.run[0].method[0] if archive.run[0].method else None
+        sec_system = archive.run[0].system[0] if archive.run[0].system else None
+        archive.run[0].calculation.append(
+            Calculation(
+                system_ref=sec_system,
+                method_ref=sec_method,
+                temperature=temperature,
+            )
+        )

pyproject.toml

@@ -127,6 +127,7 @@ psi4parser = "electronicparsers:psi4_parser_entry_point"
 qballparser = "electronicparsers:qball_parser_entry_point"
 qboxparser = "electronicparsers:qbox_parser_entry_point"
 quantumespressoparser = "electronicparsers:quantumespresso_parser_entry_point"
+rspt = "electronicparsers:rspt_parser_entry_point"
 siestaparser = "electronicparsers:siesta_parser_entry_point"
 soliddmftparser = "electronicparsers:soliddmft_parser_entry_point"
 tbstudioparser = "electronicparsers:tbstudio_parser_entry_point"