TBStudio parser (#154)

* Initial commit TBS parser

* Changed name from TBS to TBStudio

* Added tight binding studio parser

* parse SK method

* fix bugs

* fix bugs

* added program name

* Initial commit TBS parser

* Changed name from TBS to TBStudio

* Added tight binding studio parser

* parse SK method

* fix bugs

* fix bugs

* Added dft-to-tb workflow

* compatiblity with the newest version

* Initial commit TBS parser

* Changed name from TBS to TBStudio

* Added tight binding studio parser

* parse SK method

* fix bugs

* fix bugs

* added program name

* Initial commit TBS parser

* Changed name from TBS to TBStudio

* Added dft-to-tb workflow

* compatiblity with the newest version

* Fixed workflow import after rebasing

* fix bug

* refactor TightBinding to TB in tbstudio and wannier90

* parse sk integrals and orbitals

* fix parser and the model

* show the tight-binding band-structure and the dft band-structure in workflow

* fix the band-structures in workflow and SinglePoint

* added firstPrinciples-TB workflow

* added fermi level

* fixed Tight-Binding BZ

* Added the new workflow implementation

* Added a test for parser

* remove the middle parsed dictionary

* Harmonized the workflow name with the method name

* sec_atoms.labels is the correct atomic types
get the labels from atomic numbers using ase library

* correct the name of the tasks to be consistent

* test the labels instead of species

use units converter instead of multiplying by numbers

* add a default empty array for protection

* fix lint

* Added test tbstudio file

* Rafactor and Added error handling

* Remove unused import

* Fix Wannier90 method.tb

* fix ruff

---------

Co-authored-by: mohammad <[email protected]>

electronicparsers/tbstudio/__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 TBStudioParser

electronicparsers/tbstudio/__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.tbstudio import TBStudioParser
+
+if __name__ == "__main__":
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    TBStudioParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

electronicparsers/tbstudio/metainfo/__init__.py

@@ -0,0 +1,25 @@
+#
+# 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 nomad.metainfo import Environment
+
+from . import tbstudio
+
+
+m_env = Environment()
+m_env.m_add_sub_section(Environment.packages, tbstudio.m_package)

electronicparsers/tbstudio/metainfo/tbstudio.py

@@ -0,0 +1,27 @@
+#
+# 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 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
+)
+
+
+m_package = Package()

electronicparsers/tbstudio/nomad_plugin.yaml

@@ -0,0 +1,24 @@
+code_category: Atomistic code
+code_homepage: https://tight-binding.com/
+code_name: TBStudio
+metadata:
+  codeCategory: Atomistic code
+  codeLabel: TBStudio
+  codeLabelStyle: All in capitals
+  codeName: tbstudio
+  codeUrl: https://tight-binding.com/
+  parserDirName: dependencies/electronic/electronicparsers/tbstudio/
+  parserGitUrl: https://github.com/nomad-coe/electronic-parsers.git
+  parserSpecific: ''
+  preamble: ''
+  status: production
+  tableOfFiles: '| Input Filename | Description |
+
+    | --- | --- |
+
+    | `*.tbm` | **Mainfile**: output binary file |
+
+    '
+name: parsers/tbstudio
+parser_class_name: electronicparsers.tbstudio.parser.TBStudioParser
+python_package: electronicparsers.tbstudio