Merge branch 'develop' into coupled_cluster

Author: EBB2675

CITATION.cff

@@ -0,0 +1,36 @@
+cff-version: 1.2.0
+title: NOMAD Simulations
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: José M.
+    family-names: Pizarro
+    orcid: 'https://orcid.org/0000-0002-6751-8192'
+  - given-names: Esma B.
+    family-names: Boydas
+    orcid: 'https://orcid.org/0009-0005-6729-4706'
+  - given-names: Nathan
+    family-names: Daelman
+    orcid: 'https://orcid.org/0000-0002-7647-1816'
+  - given-names: Alvin Noe
+    family-names: Ladines
+    orcid: 'https://orcid.org/0000-0003-0077-2097'
+  - given-names: Bernadette
+    family-names: Mohr
+    orcid: 'https://orcid.org/0000-0003-0903-0073'
+  - given-names: Joseph F.
+    family-names: Rudzinski
+    orcid: 'https://orcid.org/0000-0003-3403-640X'
+doi:
+repository-code: 'https://github.com/nomad-coe/nomad-simulations'
+url: 'https://nomad-coe.github.io/nomad-simulations/'
+abstract: >-
+  `nomad-simulations` is a plugin for the NOMAD software (https://zenodo.org/doi/10.5281/zenodo.8366162)
+  providing a common data standard and analysis tools for parsed Materials Science and Quantum Chemistry
+  simulations. This standard is used as a template and is populated by the many available NOMAD parsers to transform their
+  inputs / outputs into a structured data format. This plugin is community-driven, and users are encourage to
+  contribute towards providing Findable, Accessible, Interoperable, and Reusable (FAIR) data.
+
+license: Apache-2.0

README.md

@@ -2,19 +2,26 @@
 ![](https://coveralls.io/repos/github/nomad-coe/nomad-simulations/badge.svg?branch=develop)
 ![](https://img.shields.io/pypi/v/nomad-simulations)
 ![](https://img.shields.io/pypi/pyversions/nomad-simulations)
+[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/badge/latestdoi/744481756)
 
 
 
 # `nomad-simulations`
 
-This is a plugin for [NOMAD](https://nomad-lab.eu) which contains the base sections definitions for materials science simulations. This schema can be used at any prefered level by the user, it can be modified and extended, and we welcome external collaborators.
+The `nomad-simulations` is an open-source Python package for managing Materials Science simulation data. It is following the plugin architechture of [NOMAD](https://nomad-lab.eu). This package contains a set of section definitions (Python classes) with quantities (attributes) and methods defined to automate data extraction from different simulation codes. These section definitions can be used at any prefered level by the user, they can be modified and extended, and we welcome external collaborators.
+
+Read more in the [official documentation](https://nomad-coe.github.io/nomad-simulations/) page.
 
 
 ## Getting started
 
 `nomad-simulations` can be installed as a PyPI package using `pip`:
+
+> [!WARNING]
+> Unfortunately, the current plugin mechanism is not supported by the latest nomad-lab version on PyPI and therefore an index url pointing to the NOMAD Gitlab registry needs to be added.
+
 ```sh
-pip install nomad-simulations
+pip install nomad-simulations --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
 
@@ -48,6 +55,11 @@ The plugin is still under development. If you would like to contribute, install
 uv pip install -e '.[dev]'
 ```
 
+**Note:** If you do not use `uv`, you need to add the `--index-url` flag as in the PyPI command for installing the package:
+```sh
+pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+```
+
 
 ### Run the tests
 
@@ -138,7 +150,7 @@ Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/
 Modify the script under `/nomad/scripts/install_default_plugins.sh` and add the path to this repository pointing to the `@develop` branch:
 ```sh
 <other-content-in-install_default_plugins.sh...>
-pip install git+https://github.com/nomad-coe/nomad-simulations.git@develop
+git+https://github.com/nomad-coe/nomad-simulations.git@develop
 ```
 
 Then, go to your NOMAD folder, activate your NOMAD virtual environment and run:
@@ -160,6 +172,8 @@ plugins:
 **Note!**
 Once you modify your `nomad.yaml` file adding `include`, all the default plugins will be disconnected, so you will need to include them as well.
 
+## How to cite this work
+Pizarro, J.M., Boydas, E.B., Daelman, N., Ladines, A.N., Mohr, B. & Rudzinski, J.F., NOMAD Simulations [Computer software]. https://doi.org/xxxxx
 
 ## Main contributors
 | Name | E-mail     | Topics | Github profiles |

src/nomad_simulations/schema_packages/__init__.py

@@ -1,41 +1,23 @@
-#
-# 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.config.models.plugins import SchemaPackageEntryPoint
 from pydantic import Field
 
 
 class NOMADSimulationsEntryPoint(SchemaPackageEntryPoint):
     dos_energy_tolerance: float = Field(
         8.01088e-21,
-        description='Tolerance of the DOS energies in Joules to match the reference of energies in the DOS normalize function.',
+        description='Tolerance (in joules) of the DOS energies to match the reference of energies in the DOS normalize function.',
     )
     dos_intensities_threshold: float = Field(
         1e-8,
-        description='Threshold value at which the DOS intensities are considered non-zero.',
+        description='Threshold value (in joules^-1) at which the DOS intensities are considered non-zero.',
     )
     occupation_tolerance: float = Field(
         1e-3,
         description='Tolerance for the occupation of a eigenstate to be non-occupied.',
     )
     fermi_surface_tolerance: float = Field(
         1e-8,
-        description='Tolerance for energies to be close to the Fermi level and hence define the Fermi surface of a material.',
+        description='Tolerance (in joules) for energies to be close to the Fermi level and hence define the Fermi surface of a material.',
     )
     symmetry_tolerance: float = Field(
         0.1, description='Tolerance for the symmetry analyzer used from MatID.'
@@ -48,6 +30,10 @@ class NOMADSimulationsEntryPoint(SchemaPackageEntryPoint):
         64,
         description='Limite of the number of atoms in the unit cell to be treated for the system type classification from MatID to work. This is done to avoid overhead of the package.',
     )
+    equal_cell_positions_tolerance: float = Field(
+        1e-12,
+        description='Tolerance (in meters) for the cell positions to be considered equal.',
+    )
 
     def load(self):
         from nomad_simulations.schema_packages.general import m_package

src/nomad_simulations/schema_packages/atoms_state.py

@@ -1,21 +1,3 @@
-#
-# 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 typing import TYPE_CHECKING, Any, Optional, Union
 
 import ase

src/nomad_simulations/schema_packages/general.py

@@ -1,21 +1,3 @@
-#
-# 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 typing import TYPE_CHECKING
 
 if TYPE_CHECKING:

src/nomad_simulations/schema_packages/model_method.py

@@ -1,21 +1,3 @@
-#
-# 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
 from typing import TYPE_CHECKING, Optional
 

src/nomad_simulations/schema_packages/model_system.py

@@ -1,21 +1,3 @@
-#
-# 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
 from typing import TYPE_CHECKING, Optional
 
@@ -296,6 +278,46 @@ class Cell(GeometricSpace):
         """,
     )
 
+    def _check_positions(self, positions_1, positions_2) -> list:
+        # Check that all the `positions`` of `cell_1` match with the ones in `cell_2`
+        check_positions = []
+        for i1, pos1 in enumerate(positions_1):
+            for i2, pos2 in enumerate(positions_2):
+                if np.allclose(
+                    pos1, pos2, atol=configuration.equal_cell_positions_tolerance
+                ):
+                    check_positions.append([i1, i2])
+                    break
+        return check_positions
+
+    def is_equal_cell(self, other) -> bool:
+        """
+        Check if the cell is equal to an`other` cell by comparing the `positions`.
+        Args:
+            other: The other cell to compare with.
+        Returns:
+            bool: True if the cells are equal, False otherwise.
+        """
+        # TODO implement checks on `lattice_vectors` and other quantities to ensure the equality of primitive cells
+        if not isinstance(other, Cell):
+            return False
+
+        # If the `positions` are empty, return False
+        if self.positions is None or other.positions is None:
+            return False
+
+        # The `positions` should have the same length (same number of positions)
+        if len(self.positions) != len(other.positions):
+            return False
+        n_positions = len(self.positions)
+
+        check_positions = self._check_positions(
+            positions_1=self.positions, positions_2=other.positions
+        )
+        if len(check_positions) != n_positions:
+            return False
+        return True
+
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         super().normalize(archive, logger)
 
@@ -339,6 +361,36 @@ def __init__(self, m_def: 'Section' = None, m_context: 'Context' = None, **kwarg
         # Set the name of the section
         self.name = self.m_def.name
 
+    def is_equal_cell(self, other) -> bool:
+        """
+        Check if the atomic cell is equal to an`other` atomic cell by comparing the `positions` and
+        the `AtomsState[*].chemical_symbol`.
+        Args:
+            other: The other atomic cell to compare with.
+        Returns:
+            bool: True if the atomic cells are equal, False otherwise.
+        """
+        if not isinstance(other, AtomicCell):
+            return False
+
+        # Compare positions using the parent sections's `__eq__` method
+        if not super().is_equal_cell(other=other):
+            return False
+
+        # Check that the `chemical_symbol` of the atoms in `cell_1` match with the ones in `cell_2`
+        check_positions = self._check_positions(
+            positions_1=self.positions, positions_2=other.positions
+        )
+        try:
+            for atom in check_positions:
+                element_1 = self.atoms_state[atom[0]].chemical_symbol
+                element_2 = other.atoms_state[atom[1]].chemical_symbol
+                if element_1 != element_2:
+                    return False
+        except Exception:
+            return False
+        return True
+
     def to_ase_atoms(self, logger: 'BoundLogger') -> Optional[ase.Atoms]:
         """
         Generates an ASE Atoms object with the most basic information from the parsed `AtomicCell`

src/nomad_simulations/schema_packages/numerical_settings.py

@@ -1,21 +1,3 @@
-#
-# 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 itertools import accumulate, chain, tee
 from typing import TYPE_CHECKING, Optional, Union
 

src/nomad_simulations/schema_packages/outputs.py

@@ -1,21 +1,3 @@
-#
-# 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 typing import TYPE_CHECKING, Optional
 
 import numpy as np

src/nomad_simulations/schema_packages/physical_property.py

@@ -1,21 +1,3 @@
-#
-# 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 functools import wraps
 from typing import TYPE_CHECKING, Any, Optional