From b6d1889cd86b1010561a304650757874964ac544 Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Thu, 27 Mar 2025 14:09:12 +0100 Subject: [PATCH 01/20] some docs update --- .readthedocs.yaml | 20 ++-- docs/source/_examples/01_relaxation.rst | 59 ++++++++++++ docs/source/_get_started/installation.rst | 40 ++++++++ docs/source/_get_started/quickstart.rst | 58 ++---------- docs/source/_nodes/ipsuite.analysis.model.rst | 53 ----------- docs/source/_nodes/ipsuite.analysis.rst | 61 ------------ docs/source/_nodes/ipsuite.base.rst | 29 ------ docs/source/_nodes/ipsuite.bootstrap.rst | 29 ------ docs/source/_nodes/ipsuite.calculators.rst | 69 -------------- .../ipsuite.configuration_comparison.rst | 21 ----- .../ipsuite.configuration_generation.rst | 29 ------ .../ipsuite.configuration_selection.rst | 93 ------------------- docs/source/_nodes/ipsuite.data_loading.rst | 29 ------ docs/source/_nodes/ipsuite.fields.rst | 21 ----- docs/source/_nodes/ipsuite.geometry.rst | 45 --------- docs/source/_nodes/ipsuite.models.rst | 37 -------- docs/source/_nodes/ipsuite.project.rst | 10 -- docs/source/_nodes/ipsuite.rst | 42 --------- docs/source/_nodes/ipsuite.static_data.rst | 10 -- docs/source/_nodes/ipsuite.utils.rst | 61 ------------ docs/source/_nodes/modules.rst | 7 -- docs/source/glossary.rst | 7 ++ docs/source/index.rst | 13 ++- docs/source/nodes.rst | 8 ++ ipsuite/configuration_generation/packmol.py | 25 ++++- .../smiles_to_atoms.py | 25 ++++- 26 files changed, 185 insertions(+), 716 deletions(-) create mode 100644 docs/source/_examples/01_relaxation.rst create mode 100644 docs/source/_get_started/installation.rst delete mode 100644 docs/source/_nodes/ipsuite.analysis.model.rst delete mode 100644 docs/source/_nodes/ipsuite.analysis.rst delete mode 100644 docs/source/_nodes/ipsuite.base.rst delete mode 100644 docs/source/_nodes/ipsuite.bootstrap.rst delete mode 100644 docs/source/_nodes/ipsuite.calculators.rst delete mode 100644 docs/source/_nodes/ipsuite.configuration_comparison.rst delete mode 100644 docs/source/_nodes/ipsuite.configuration_generation.rst delete mode 100644 docs/source/_nodes/ipsuite.configuration_selection.rst delete mode 100644 docs/source/_nodes/ipsuite.data_loading.rst delete mode 100644 docs/source/_nodes/ipsuite.fields.rst delete mode 100644 docs/source/_nodes/ipsuite.geometry.rst delete mode 100644 docs/source/_nodes/ipsuite.models.rst delete mode 100644 docs/source/_nodes/ipsuite.project.rst delete mode 100644 docs/source/_nodes/ipsuite.rst delete mode 100644 docs/source/_nodes/ipsuite.static_data.rst delete mode 100644 docs/source/_nodes/ipsuite.utils.rst delete mode 100644 docs/source/_nodes/modules.rst create mode 100644 docs/source/glossary.rst create mode 100644 docs/source/nodes.rst diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 1455b147..ab8c4508 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,23 +4,21 @@ version: 2 +submodules: + include: all + # Set the version of Python and other tools you might need build: - os: ubuntu-22.04 + os: ubuntu-lts-latest tools: - python: "3.10" + python: "3.11" jobs: - post_create_environment: - # Install poetry - # https://python-poetry.org/docs/#installing-manually - - pip install poetry post_install: - # Install dependencies with 'docs' dependency group - # https://python-poetry.org/docs/managing-dependencies/#dependency-groups - # VIRTUAL_ENV needs to be set manually for now. - # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs + # see https://github.com/astral-sh/uv/issues/10074 + - pip install uv + - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --link-mode=copy --group=docs # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/source/conf.py + \ No newline at end of file diff --git a/docs/source/_examples/01_relaxation.rst b/docs/source/_examples/01_relaxation.rst new file mode 100644 index 00000000..8daa1cf3 --- /dev/null +++ b/docs/source/_examples/01_relaxation.rst @@ -0,0 +1,59 @@ +Geometry Relaxation +=================== + +In this example we will setup a simulation box and relax the structure using an :term:`MLIP`. + +.. tip:: + + Setup a new project in an empty directory by calling + + .. code:: + + git init + dvc init + touch main.py + + +Add the following to your main.py file: + +.. code:: + + import ipsuite as ips + + project = ips.Project() + # create the main project to handle the workflow + + with project: + # add new nodes to the project within the project context manager + ips.Smiles2Conformers(smiles="O", numConfs=1) # add our first node + + project.build() + +To build the project, run the file using :code:`python main.py`. + +.. note:: + + This will construct the workflow, but not execute. + +To execute the workflow now constructed, run :code:`dvc repro`. + + +.. code:: + + import ipsuite as ips + + project = ips.Project() + # create the main project to handle the workflow + + with project: + # add new nodes to the project within the project context manager + water = ips.Smiles2Conformers(smiles="O", numConfs=1) # add our first node + ammonia = ips.Smiles2Conformers(smiles="N", numConfs=1) # add another node + box = ips.MultiPackmol( + data=[water.frames, ammonia.frames], + count=[10, 3], + density=997, + n_configurations=3 + ) + + project.build() \ No newline at end of file diff --git a/docs/source/_get_started/installation.rst b/docs/source/_get_started/installation.rst new file mode 100644 index 00000000..198fc401 --- /dev/null +++ b/docs/source/_get_started/installation.rst @@ -0,0 +1,40 @@ +Installation +============ + +From PyPI +--------- + +To use :code:`ipsuite`, first install it using pip: + +.. code-block:: console + + (.venv) $ pip install ipsuite + +.. note:: + + The :code:`ipsuite` package installation does not contain any :term:`MLIP` packages. + Due to different dependencies, it is highly recommended to install your preferred :term:`MLIP` package individually into the same environment. + +.. note:: + + If you encounter en error like :code:`Permission denied '/var/cache/dvc'` you might want to reinstall :code:`pip install platformdirs==3.11.0` or :code:`pip install platformdirs==3.10.0` as discussed at https://github.com/iterative/dvc/issues/9184 + +From Source +----------- + +To install and develop :code:`ipsuite` from source we recommend using :code:`https://docs.astral.sh/uv`. +More information and installation instructions can be found at https://docs.astral.sh/uv/getting-started/installation/ . + +.. code:: console + + (.venv) $ git clone https://github.com/zincware/ipsuite + (.venv) $ cd ipsuite + (.venv) $ uv sync + (.venv) $ source .venv/bin/activate + +In a file :code:`main.py` try importing IPS to check if everything is working correctly + +.. code-block:: python + + import ipsuite as ips + diff --git a/docs/source/_get_started/quickstart.rst b/docs/source/_get_started/quickstart.rst index 4c8dcd26..23b811f4 100644 --- a/docs/source/_get_started/quickstart.rst +++ b/docs/source/_get_started/quickstart.rst @@ -1,55 +1,13 @@ .. _getting_started: -Getting started -=============== - -Installation ------------- - -The IPS package can be downloaded via the package-management system pip. -We recommend the usage of an python environment with the python version 3.10. Other versions might not currently work. - -.. code-block:: bash - - pip install ipsuite - -Alternatively the latest version of IPSuite can be downloaded from `GitHub `_, -using `Poetry `_ to install the python dependencies. - -.. code-block:: bash - - git clone https://github.com/zincware/IPSuite.git - cd IPSuite - poetry install - -For IPSuite to work, it is necessary for an IPS Project to be in a git as well as DVC initialized directory. -Create a folder for your project and initialize git and DVC to start working with IPS. - -.. code-block:: bash - - mkdir project - cd project - git init - dvc init - -In a file :code:`main.py` try importing IPS to check if everything is working correctly - -.. code-block:: python - - import ipsuite as ips - +Quickstart +========== To get to know the IPS procedures we will do an example problem. - -The First Project -================= - Initial Data Generation ----------------------- -This project will show the basic creation of an IPS Project using an additional piece of software -called `Packmol `_. The goal is to place water molecules inside a box at a specified density. .. code-block:: python @@ -58,7 +16,7 @@ The goal is to place water molecules inside a box at a specified density. with ips.Project() as project: # Generate a single water molecule - mol = ips.Smiles2Atoms(smiles="O") + mol = ips.Smiles2Conformers(smiles="O") # Duplicate water molecules packmol = ips.Packmol( data=[mol.atoms], count=[10], density=876 @@ -66,9 +24,9 @@ The goal is to place water molecules inside a box at a specified density. project.build() -The *Smiles2Atoms* node takes the `SMILES `_ string for water ("O"), +The :class:`ipsuite.Smiles2Conformers` node takes the `SMILES `_ string for water ("O"), and generates an an `ASE atoms object `_ from it. -This atom from the Smiles2Atoms instance can be accessd by calling `mol.atoms`. +This atom from the :class:`ipsuite.Smiles2Conformers` instance can be accessd by calling `mol.atoms`. This instance attribute is then handed over to the Packmol node in the `data` attribute. It is possible to hand over multiple different types of ASE atoms, so `mol.atoms` as to be given as a list. The next attribute we need to set is the amount of molecules we want to place in the box. @@ -80,7 +38,7 @@ used with `Mermaid `_ to better visualise the workflows The parameters files, namely `params.yaml` can be viewed and parameters can be changed without rerunning the python script. -By calling `dvc repro` the workflow consisting of the nodes is executed, which results in the generation of firstly a single water molecule by the Smiles2Atoms node and then the placement +By calling `dvc repro` the workflow consisting of the nodes is executed, which results in the generation of firstly a single water molecule by the :class:`ipsuite.Smiles2Conformers` node and then the placement of multiple water molecules in a box by the Packmol node. After running `dvc repro` a new folder `nodes` is created which each node having their own subfolder. These folders contain the results from the Nodes. @@ -90,9 +48,9 @@ we can visualise the H5MD files generated by the nodes. .. code-block:: bash - zndraw nodes/Smiles2Atoms/structures.h5 + zndraw nodes/Smiles2Conformers/structures.h5 -will visualise the single water molecule generated by Smiles2Atoms. There will also be a H5MD file in the Packmol folder +will visualise the single water molecule generated by :class:`ipsuite.Smiles2Conformers`. There will also be a H5MD file in the Packmol folder .. figure:: ../images/water_packmol.png :alt: ZnDraw Screenshot diff --git a/docs/source/_nodes/ipsuite.analysis.model.rst b/docs/source/_nodes/ipsuite.analysis.model.rst deleted file mode 100644 index 3bdb6744..00000000 --- a/docs/source/_nodes/ipsuite.analysis.model.rst +++ /dev/null @@ -1,53 +0,0 @@ -ipsuite.analysis.model package -============================== - -Submodules ----------- - -ipsuite.analysis.model.dynamics module --------------------------------------- - -.. automodule:: ipsuite.analysis.model.dynamics - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.model.dynamics\_checks module ----------------------------------------------- - -.. automodule:: ipsuite.analysis.model.dynamics_checks - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.model.math module ----------------------------------- - -.. automodule:: ipsuite.analysis.model.math - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.model.plots module ------------------------------------ - -.. automodule:: ipsuite.analysis.model.plots - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.model.predict module -------------------------------------- - -.. automodule:: ipsuite.analysis.model.predict - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.analysis.model - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.analysis.rst b/docs/source/_nodes/ipsuite.analysis.rst deleted file mode 100644 index 602cd08d..00000000 --- a/docs/source/_nodes/ipsuite.analysis.rst +++ /dev/null @@ -1,61 +0,0 @@ -ipsuite.analysis package -======================== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - ipsuite.analysis.model - -Submodules ----------- - -ipsuite.analysis.bin\_property module -------------------------------------- - -.. automodule:: ipsuite.analysis.bin_property - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.bond\_stretch module -------------------------------------- - -.. automodule:: ipsuite.analysis.bond_stretch - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.ensemble module --------------------------------- - -.. automodule:: ipsuite.analysis.ensemble - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.md module --------------------------- - -.. automodule:: ipsuite.analysis.md - :members: - :undoc-members: - :show-inheritance: - -ipsuite.analysis.sensitivity module ------------------------------------ - -.. automodule:: ipsuite.analysis.sensitivity - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.analysis - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.base.rst b/docs/source/_nodes/ipsuite.base.rst deleted file mode 100644 index bbb4c636..00000000 --- a/docs/source/_nodes/ipsuite.base.rst +++ /dev/null @@ -1,29 +0,0 @@ -ipsuite.base package -==================== - -Submodules ----------- - -ipsuite.base.base module ------------------------- - -.. automodule:: ipsuite.base.base - :members: - :undoc-members: - :show-inheritance: - -ipsuite.base.protocol module ----------------------------- - -.. automodule:: ipsuite.base.protocol - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.base - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.bootstrap.rst b/docs/source/_nodes/ipsuite.bootstrap.rst deleted file mode 100644 index 9ea942dc..00000000 --- a/docs/source/_nodes/ipsuite.bootstrap.rst +++ /dev/null @@ -1,29 +0,0 @@ -ipsuite.bootstrap package -========================= - -Submodules ----------- - -ipsuite.bootstrap.random\_displacements module ----------------------------------------------- - -.. automodule:: ipsuite.bootstrap.random_displacements - :members: - :undoc-members: - :show-inheritance: - -ipsuite.bootstrap.surface\_mods module --------------------------------------- - -.. automodule:: ipsuite.bootstrap.surface_mods - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.bootstrap - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.calculators.rst b/docs/source/_nodes/ipsuite.calculators.rst deleted file mode 100644 index 7463d094..00000000 --- a/docs/source/_nodes/ipsuite.calculators.rst +++ /dev/null @@ -1,69 +0,0 @@ -ipsuite.calculators package -=========================== - -Submodules ----------- - -ipsuite.calculators.ase\_geoopt module --------------------------------------- - -.. automodule:: ipsuite.calculators.ase_geoopt - :members: - :undoc-members: - :show-inheritance: - -ipsuite.calculators.ase\_md module ----------------------------------- - -.. automodule:: ipsuite.calculators.ase_md - :members: - :undoc-members: - :show-inheritance: - -ipsuite.calculators.ase\_standard module ----------------------------------------- - -.. automodule:: ipsuite.calculators.ase_standard - :members: - :undoc-members: - :show-inheritance: - -ipsuite.calculators.cp2k module -------------------------------- - -.. automodule:: ipsuite.calculators.cp2k - :members: - :undoc-members: - :show-inheritance: - -ipsuite.calculators.lammps module ---------------------------------- - -.. automodule:: ipsuite.calculators.lammps - :members: - :undoc-members: - :show-inheritance: - -ipsuite.calculators.orca module -------------------------------- - -.. automodule:: ipsuite.calculators.orca - :members: - :undoc-members: - :show-inheritance: - -ipsuite.calculators.xtb module ------------------------------- - -.. automodule:: ipsuite.calculators.xtb - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.calculators - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.configuration_comparison.rst b/docs/source/_nodes/ipsuite.configuration_comparison.rst deleted file mode 100644 index d5d81e41..00000000 --- a/docs/source/_nodes/ipsuite.configuration_comparison.rst +++ /dev/null @@ -1,21 +0,0 @@ -ipsuite.configuration\_comparison package -========================================= - -Submodules ----------- - -ipsuite.configuration\_comparison.base module ---------------------------------------------- - -.. automodule:: ipsuite.configuration_comparison.base - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.configuration_comparison - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.configuration_generation.rst b/docs/source/_nodes/ipsuite.configuration_generation.rst deleted file mode 100644 index 4da28148..00000000 --- a/docs/source/_nodes/ipsuite.configuration_generation.rst +++ /dev/null @@ -1,29 +0,0 @@ -ipsuite.configuration\_generation package -========================================= - -Submodules ----------- - -ipsuite.configuration\_generation.packmol module ------------------------------------------------- - -.. automodule:: ipsuite.configuration_generation.packmol - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_generation.smiles\_to\_atoms module ----------------------------------------------------------- - -.. automodule:: ipsuite.configuration_generation.smiles_to_atoms - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.configuration_generation - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.configuration_selection.rst b/docs/source/_nodes/ipsuite.configuration_selection.rst deleted file mode 100644 index d7fa25e1..00000000 --- a/docs/source/_nodes/ipsuite.configuration_selection.rst +++ /dev/null @@ -1,93 +0,0 @@ -ipsuite.configuration\_selection package -======================================== - -Submodules ----------- - -ipsuite.configuration\_selection.base module --------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.base - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.filter module ----------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.filter - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.index module ---------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.index - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.kernel module ----------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.kernel - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.random module ----------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.random - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.split module ---------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.split - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.threshold module -------------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.threshold - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.uniform\_arange module -------------------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.uniform_arange - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.uniform\_energetic module ----------------------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.uniform_energetic - :members: - :undoc-members: - :show-inheritance: - -ipsuite.configuration\_selection.uniform\_temporal module ---------------------------------------------------------- - -.. automodule:: ipsuite.configuration_selection.uniform_temporal - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.configuration_selection - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.data_loading.rst b/docs/source/_nodes/ipsuite.data_loading.rst deleted file mode 100644 index a408f6b6..00000000 --- a/docs/source/_nodes/ipsuite.data_loading.rst +++ /dev/null @@ -1,29 +0,0 @@ -ipsuite.data\_loading package -============================= - -Submodules ----------- - -ipsuite.data\_loading.add\_data\_ase module -------------------------------------------- - -.. automodule:: ipsuite.data_loading.add_data_ase - :members: - :undoc-members: - :show-inheritance: - -ipsuite.data\_loading.add\_data\_h5md module --------------------------------------------- - -.. automodule:: ipsuite.data_loading.add_data_h5md - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.data_loading - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.fields.rst b/docs/source/_nodes/ipsuite.fields.rst deleted file mode 100644 index f5998d37..00000000 --- a/docs/source/_nodes/ipsuite.fields.rst +++ /dev/null @@ -1,21 +0,0 @@ -ipsuite.fields package -====================== - -Submodules ----------- - -ipsuite.fields.atoms module ---------------------------- - -.. automodule:: ipsuite.fields.atoms - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.fields - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.geometry.rst b/docs/source/_nodes/ipsuite.geometry.rst deleted file mode 100644 index 03db2fac..00000000 --- a/docs/source/_nodes/ipsuite.geometry.rst +++ /dev/null @@ -1,45 +0,0 @@ -ipsuite.geometry package -======================== - -Submodules ----------- - -ipsuite.geometry.barycenter\_coarse\_grain module -------------------------------------------------- - -.. automodule:: ipsuite.geometry.barycenter_coarse_grain - :members: - :undoc-members: - :show-inheritance: - -ipsuite.geometry.graphs module ------------------------------- - -.. automodule:: ipsuite.geometry.graphs - :members: - :undoc-members: - :show-inheritance: - -ipsuite.geometry.mapping module -------------------------------- - -.. automodule:: ipsuite.geometry.mapping - :members: - :undoc-members: - :show-inheritance: - -ipsuite.geometry.unwrap module ------------------------------- - -.. automodule:: ipsuite.geometry.unwrap - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.geometry - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.models.rst b/docs/source/_nodes/ipsuite.models.rst deleted file mode 100644 index 06d68aa2..00000000 --- a/docs/source/_nodes/ipsuite.models.rst +++ /dev/null @@ -1,37 +0,0 @@ -ipsuite.models package -====================== - -Submodules ----------- - -ipsuite.models.base module --------------------------- - -.. automodule:: ipsuite.models.base - :members: - :undoc-members: - :show-inheritance: - -ipsuite.models.ensemble module ------------------------------- - -.. automodule:: ipsuite.models.ensemble - :members: - :undoc-members: - :show-inheritance: - -ipsuite.models.gap module -------------------------- - -.. automodule:: ipsuite.models.gap - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.models - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.project.rst b/docs/source/_nodes/ipsuite.project.rst deleted file mode 100644 index 080b50fa..00000000 --- a/docs/source/_nodes/ipsuite.project.rst +++ /dev/null @@ -1,10 +0,0 @@ -ipsuite.project package -======================= - -Module contents ---------------- - -.. automodule:: ipsuite.project - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.rst b/docs/source/_nodes/ipsuite.rst deleted file mode 100644 index eb82e0b9..00000000 --- a/docs/source/_nodes/ipsuite.rst +++ /dev/null @@ -1,42 +0,0 @@ -ipsuite package -=============== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - ipsuite.analysis - ipsuite.base - ipsuite.bootstrap - ipsuite.calculators - ipsuite.configuration_comparison - ipsuite.configuration_generation - ipsuite.configuration_selection - ipsuite.data_loading - ipsuite.fields - ipsuite.geometry - ipsuite.models - ipsuite.project - ipsuite.static_data - ipsuite.utils - -Submodules ----------- - -ipsuite.nodes module --------------------- - -.. automodule:: ipsuite.nodes - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.static_data.rst b/docs/source/_nodes/ipsuite.static_data.rst deleted file mode 100644 index 9c822f67..00000000 --- a/docs/source/_nodes/ipsuite.static_data.rst +++ /dev/null @@ -1,10 +0,0 @@ -ipsuite.static\_data package -============================ - -Module contents ---------------- - -.. automodule:: ipsuite.static_data - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/ipsuite.utils.rst b/docs/source/_nodes/ipsuite.utils.rst deleted file mode 100644 index b9b752cc..00000000 --- a/docs/source/_nodes/ipsuite.utils.rst +++ /dev/null @@ -1,61 +0,0 @@ -ipsuite.utils package -===================== - -Submodules ----------- - -ipsuite.utils.ase\_sim module ------------------------------ - -.. automodule:: ipsuite.utils.ase_sim - :members: - :undoc-members: - :show-inheritance: - -ipsuite.utils.combine module ----------------------------- - -.. automodule:: ipsuite.utils.combine - :members: - :undoc-members: - :show-inheritance: - -ipsuite.utils.helpers module ----------------------------- - -.. automodule:: ipsuite.utils.helpers - :members: - :undoc-members: - :show-inheritance: - -ipsuite.utils.logs module -------------------------- - -.. automodule:: ipsuite.utils.logs - :members: - :undoc-members: - :show-inheritance: - -ipsuite.utils.md module ------------------------ - -.. automodule:: ipsuite.utils.md - :members: - :undoc-members: - :show-inheritance: - -ipsuite.utils.metrics module ----------------------------- - -.. automodule:: ipsuite.utils.metrics - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: ipsuite.utils - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/_nodes/modules.rst b/docs/source/_nodes/modules.rst deleted file mode 100644 index fd03bf2e..00000000 --- a/docs/source/_nodes/modules.rst +++ /dev/null @@ -1,7 +0,0 @@ -ipsuite -####### - -.. toctree:: - :maxdepth: 4 - - ipsuite diff --git a/docs/source/glossary.rst b/docs/source/glossary.rst new file mode 100644 index 00000000..0683c0db --- /dev/null +++ b/docs/source/glossary.rst @@ -0,0 +1,7 @@ +Glossary +======== + +.. glossary:: + + MLIP + Machine learned interatomic potential. diff --git a/docs/source/index.rst b/docs/source/index.rst index 76bb3bf8..a170c681 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -14,10 +14,14 @@ Welcome to IPSuite's documentation! :maxdepth: 2 :caption: Contents: - What is IPS? <_get_started/ips> - Getting Started <_get_started/quickstart> - IPSuite <_nodes/ipsuite> - Modules <_nodes/modlules> + _get_started/ips + _get_started/installation + _get_started/quickstart + + _examples/01_relaxation + + glossary + nodes Indices and tables @@ -25,4 +29,3 @@ Indices and tables * :ref:`genindex` * :ref:`modindex` -* :ref:`search` diff --git a/docs/source/nodes.rst b/docs/source/nodes.rst new file mode 100644 index 00000000..c9ad585d --- /dev/null +++ b/docs/source/nodes.rst @@ -0,0 +1,8 @@ +Nodes +===== + +.. autoclass:: ipsuite.Smiles2Conformers + :show-inheritance: + +.. autoclass:: ipsuite.MultiPackmol + :show-inheritance: diff --git a/ipsuite/configuration_generation/packmol.py b/ipsuite/configuration_generation/packmol.py index 8c97478f..3bd9c01f 100644 --- a/ipsuite/configuration_generation/packmol.py +++ b/ipsuite/configuration_generation/packmol.py @@ -85,19 +85,40 @@ class MultiPackmol(Packmol): ... smiles='O', numConfs=100 ... ) ... boxes = ips.MultiPackmol( - ... data=[water.atoms], count=[10], density=997, n_configurations=10 + ... data=[water.frames], count=[10], density=997, n_configurations=10 ... ) >>> project.repro() .. testcleanup:: >>> tmp_path.cleanup() - Attributes + Parameters ---------- n_configurations : int Number of configurations to create. seed : int Seed for the random number generator. + data: list[list[ase.Atoms]] + For each entry in the list the last ase.Atoms object is used to create the + new structure. + data_ids: list[int] + The id of the data to use for each entry in data. If None the last entry. + Has to be the same length as data. data: [[A], [B]], [-1, 3] -> [A[-1], B[3]] + count: list[int] + Number of molecules to add for each entry in data. + tolerance : float + Tolerance for the distance of atoms in angstrom. + density : float + Density of the system in kg/m^3. Either density or box is required. + pbc : bool + If True the periodic boundary conditions are set for the generated structure and + the box used by packmol is scaled by the tolerance, to avoid overlapping atoms + with periodic boundary conditions. + + Attributes + ---------- + frames : list[ase.Atoms] + A list of generated boxes. """ n_configurations: int = zntrack.params() diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index 99c688d8..2aa1a549 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -22,12 +22,33 @@ def run(self): atoms.center() self.frames = [atoms] - class Smiles2Conformers(base.IPSNode): + """ + Generate molecular conformers from a SMILES string and store them as ASE Atoms objects. + + Parameters + ---------- + smiles : str + The SMILES string representing the molecular structure. + numConfs : int, optional + The number of conformers to generate (default is 1). + seed : int, optional + Random seed for conformer generation (default is 42). + maxAttempts : int, optional + Maximum number of attempts to generate conformers (default is 1000). + cell : float, optional + Size of the cubic unit cell to assign to the generated conformers (default is 100). + + Attributes + ---------- + frames : list[ase.Atoms] + A list of generated molecular conformers as ASE Atoms objects. + """ + frames: list[ase.Atoms] = fields.Atoms() smiles: str = zntrack.params() - numConfs: int = zntrack.params() + numConfs: int = zntrack.params(1) seed: int = zntrack.params(42) maxAttempts: int = zntrack.params(1000) cell: float = zntrack.params(100) From 17bae5477915d7dd2fe199145fce35d81b3d7a6c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 27 Mar 2025 13:13:50 +0000 Subject: [PATCH 02/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .readthedocs.yaml | 2 +- docs/source/_examples/01_relaxation.rst | 4 ++-- docs/source/_get_started/installation.rst | 1 - ipsuite/configuration_generation/smiles_to_atoms.py | 1 + 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ab8c4508..f1abc9ca 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -21,4 +21,4 @@ build: # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/source/conf.py - \ No newline at end of file + diff --git a/docs/source/_examples/01_relaxation.rst b/docs/source/_examples/01_relaxation.rst index 8daa1cf3..fb3c0604 100644 --- a/docs/source/_examples/01_relaxation.rst +++ b/docs/source/_examples/01_relaxation.rst @@ -32,7 +32,7 @@ Add the following to your main.py file: To build the project, run the file using :code:`python main.py`. .. note:: - + This will construct the workflow, but not execute. To execute the workflow now constructed, run :code:`dvc repro`. @@ -56,4 +56,4 @@ To execute the workflow now constructed, run :code:`dvc repro`. n_configurations=3 ) - project.build() \ No newline at end of file + project.build() diff --git a/docs/source/_get_started/installation.rst b/docs/source/_get_started/installation.rst index 198fc401..3d5cb316 100644 --- a/docs/source/_get_started/installation.rst +++ b/docs/source/_get_started/installation.rst @@ -37,4 +37,3 @@ In a file :code:`main.py` try importing IPS to check if everything is working co .. code-block:: python import ipsuite as ips - diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index 2aa1a549..75cd32e6 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -22,6 +22,7 @@ def run(self): atoms.center() self.frames = [atoms] + class Smiles2Conformers(base.IPSNode): """ Generate molecular conformers from a SMILES string and store them as ASE Atoms objects. From 93f46ea1d61064f149bc7d987785e0404946f4f1 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 27 Mar 2025 13:15:43 +0000 Subject: [PATCH 03/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f1abc9ca..b0e37e33 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -21,4 +21,3 @@ build: # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/source/conf.py - From 90cfaf5cc17e179f03691fe3d4de335a3db7107f Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Mon, 14 Apr 2025 11:12:33 +0200 Subject: [PATCH 04/20] use cp2k-output tools from source due to build issues with regex --- pyproject.toml | 5 ++++- uv.lock | 14 ++++++-------- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c52f312e..87b72539 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,6 @@ keywords = ["data-version-control", "machine-learning", "reproducibility", "inte dependencies = [ "ase>=3.24.0", "cp2k-input-tools>=0.9.1", - "cp2k-output-tools>=0.5.0", "lazy-loader>=0.4", "rdkit2ase>=0.1.4", "seaborn>=0.13.2", @@ -46,6 +45,7 @@ gap = [ "xmltodict>=0.14.2", ] dev = [ + "cp2k-output-tools", "dvc-s3>=3.2.0", "imageio>=2.37.0", "mdanalysis>=2.8.0", @@ -95,3 +95,6 @@ ignore = [ [tool.codespell] ignore-words-list = "dscribe" skip = "poetry.lock,ipsuite/static_data/*,docs/source/examples/06_Bootstrapping_Datasets.ipynb" + +[tool.uv.sources] +cp2k-output-tools = { git = "https://github.com/cp2k/cp2k-output-tools" } diff --git a/uv.lock b/uv.lock index d21eddcf..f5971de6 100644 --- a/uv.lock +++ b/uv.lock @@ -677,15 +677,13 @@ wheels = [ [[package]] name = "cp2k-output-tools" version = "0.5.0" -source = { registry = "https://pypi.org/simple" } +source = { git = "https://github.com/cp2k/cp2k-output-tools#8260e709c86a0bc1636e3ddae9bb8a17d52b09de" } dependencies = [ { name = "click" }, { name = "numpy" }, + { name = "pint" }, { name = "regex" }, -] -sdist = { url = "https://files.pythonhosted.org/packages/49/c6/29ae884189bcb3b30ecc5506afc1a65bf5bb1218fb7829e15665a0267d73/cp2k-output-tools-0.5.0.tar.gz", hash = "sha256:c71786a6e0e99f1d706eea355977bc5d6771b40cb7d84afc7921ee9d5e9a0420", size = 20417 } -wheels = [ - { url = "https://files.pythonhosted.org/packages/6f/f6/e711eb52478b1b63baf856f4efd8d6a9c4238a7e96c340250fd1d30cbe1e/cp2k_output_tools-0.5.0-py3-none-any.whl", hash = "sha256:8269ede667cf2eeaa1a55c8651a1c1921a549df796e098e52d68ef90815c8986", size = 22691 }, + { name = "rich" }, ] [[package]] @@ -1371,12 +1369,11 @@ wheels = [ [[package]] name = "ipsuite" -version = "0.2.5" +version = "0.2.4" source = { editable = "." } dependencies = [ { name = "ase" }, { name = "cp2k-input-tools" }, - { name = "cp2k-output-tools" }, { name = "lazy-loader" }, { name = "rdkit2ase" }, { name = "seaborn" }, @@ -1387,6 +1384,7 @@ dependencies = [ [package.dev-dependencies] dev = [ + { name = "cp2k-output-tools" }, { name = "dvc-s3" }, { name = "imageio" }, { name = "mdanalysis" }, @@ -1407,7 +1405,6 @@ gap = [ requires-dist = [ { name = "ase", specifier = ">=3.24.0" }, { name = "cp2k-input-tools", specifier = ">=0.9.1" }, - { name = "cp2k-output-tools", specifier = ">=0.5.0" }, { name = "lazy-loader", specifier = ">=0.4" }, { name = "rdkit2ase", specifier = ">=0.1.4" }, { name = "seaborn", specifier = ">=0.13.2" }, @@ -1418,6 +1415,7 @@ requires-dist = [ [package.metadata.requires-dev] dev = [ + { name = "cp2k-output-tools", git = "https://github.com/cp2k/cp2k-output-tools" }, { name = "dvc-s3", specifier = ">=3.2.0" }, { name = "imageio", specifier = ">=2.37.0" }, { name = "mdanalysis", specifier = ">=2.8.0" }, From ef531860c2b251ac48cbfec1be1efd5989390c46 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Wed, 16 Apr 2025 13:58:50 +0200 Subject: [PATCH 05/20] update ASEGeomOpt docs --- docs/source/nodes.rst | 8 +- ipsuite/calculators/ase_geoopt.py | 38 +- uv.lock | 2178 ++++++++++++++++------------- 3 files changed, 1209 insertions(+), 1015 deletions(-) diff --git a/docs/source/nodes.rst b/docs/source/nodes.rst index c9ad585d..bf254492 100644 --- a/docs/source/nodes.rst +++ b/docs/source/nodes.rst @@ -1,8 +1,6 @@ Nodes ===== -.. autoclass:: ipsuite.Smiles2Conformers - :show-inheritance: - -.. autoclass:: ipsuite.MultiPackmol - :show-inheritance: +.. automodule:: ipsuite + :members: + :exclude-members: # Exclude specific methods if needed \ No newline at end of file diff --git a/ipsuite/calculators/ase_geoopt.py b/ipsuite/calculators/ase_geoopt.py index c357d1e2..48efb909 100644 --- a/ipsuite/calculators/ase_geoopt.py +++ b/ipsuite/calculators/ase_geoopt.py @@ -15,17 +15,51 @@ class ASEGeoOpt(base.IPSNode): - """Class to run a geometry optimization with ASE. + """Perform a structure relaxation using ASE. + + Use any ASE calculator to perform a geometry optimization on + a given structure. Parameters ---------- + data: list[ase.Atoms] + List of atoms objects to select the starting configuration from. + data_id: int + Index of the atoms object to use from ``data``. model: zntrack.Node A node that implements 'get_calculator'. + optimizer: str + The optimizer to use. Default is ``FIRE``. + Select from ``ase.optimize``, e.g. ``BFGS``, ``FIRE``, ``LBFGS``. maxstep: int, optional Maximum number of steps to perform. + checks: list[dataclasses.dataclass], optional + List of checks to perform during the optimization. + A failed check will stop the optimization. + constraints: list[dataclasses.dataclass], optional + List of constraints to apply to the atoms object. + run_kwargs: dict, optional + Keyword arguments to pass to the optimizer when running. + Default is ``{"fmax": 0.05}``. + init_kwargs: dict, optional + Keyword arguments to pass to the optimizer when initializing. + Default is ``{}``. + repeat: list[int], optional + List of integers to repeat the atoms object. + Default is ``(1, 1, 1)``. + dump_rate: int, optional + Number of steps to perform before dumping the current state. + Default is ``1000``. + + Attributes + ---------- + model_outs: pathlib.Path + Path to the directory where the model outputs are stored. + traj_file: pathlib.Path + Path to the file where the trajectory is stored. 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size = 59377 }, ] From 0228301018af8c8721d4c9739b507f3994bbc77a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 16 Apr 2025 11:59:17 +0000 Subject: [PATCH 06/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/nodes.rst | 2 +- ipsuite/calculators/ase_geoopt.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/nodes.rst b/docs/source/nodes.rst index bf254492..d8d8dc5f 100644 --- a/docs/source/nodes.rst +++ b/docs/source/nodes.rst @@ -3,4 +3,4 @@ Nodes .. automodule:: ipsuite :members: - :exclude-members: # Exclude specific methods if needed \ No newline at end of file + :exclude-members: # Exclude specific methods if needed diff --git a/ipsuite/calculators/ase_geoopt.py b/ipsuite/calculators/ase_geoopt.py index 48efb909..4018b958 100644 --- a/ipsuite/calculators/ase_geoopt.py +++ b/ipsuite/calculators/ase_geoopt.py @@ -17,7 +17,7 @@ class ASEGeoOpt(base.IPSNode): """Perform a structure relaxation using ASE. - Use any ASE calculator to perform a geometry optimization on + Use any ASE calculator to perform a geometry optimization on a given structure. Parameters @@ -50,7 +50,7 @@ class ASEGeoOpt(base.IPSNode): dump_rate: int, optional Number of steps to perform before dumping the current state. Default is ``1000``. - + Attributes ---------- model_outs: pathlib.Path From 0d1cca80e3de5d196db02f79f07e8f91a854dd11 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Wed, 16 Apr 2025 14:02:15 +0200 Subject: [PATCH 07/20] add example --- ipsuite/calculators/ase_geoopt.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/ipsuite/calculators/ase_geoopt.py b/ipsuite/calculators/ase_geoopt.py index 48efb909..f5e80c15 100644 --- a/ipsuite/calculators/ase_geoopt.py +++ b/ipsuite/calculators/ase_geoopt.py @@ -57,6 +57,25 @@ class ASEGeoOpt(base.IPSNode): Path to the directory where the model outputs are stored. traj_file: pathlib.Path Path to the file where the trajectory is stored. + + + Example + ------- + + >>> import ipsuite as ips + >>> project = ips.Project() + >>> model = ips.LJSinglePoint() + >>> with project: + ... etoh = ips.Smiles2Conformers( + ... smiles="CCO", numConfs=1 + ... ) + ... opt = ips.ASEGeoOpt( + ... data=etoh, + ... model=model, + ... optimizer="FIRE", + ... run_kwargs={"fmax": 0.05}, + ... ) + >>> project.build() """ data: list[ase.Atoms] = zntrack.deps() From 6df3b4b4ecc75f6afba4b6364c8e1bb0f5a9eb58 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Wed, 16 Apr 2025 14:06:57 +0200 Subject: [PATCH 08/20] update cp2k docs --- ipsuite/calculators/cp2k.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/ipsuite/calculators/cp2k.py b/ipsuite/calculators/cp2k.py index 7bfcb1a6..df352e8a 100644 --- a/ipsuite/calculators/cp2k.py +++ b/ipsuite/calculators/cp2k.py @@ -53,6 +53,8 @@ class CP2KSinglePoint(base.IPSNode): Parameters ---------- + data: list[ase.Atoms] + The list of ASE Atoms objects to run the calculation on. cp2k_shell : str, default=None The cmd to run cp2k. If None, the environment variable IPSUITE_CP2K_SHELL is used. @@ -65,6 +67,23 @@ class CP2KSinglePoint(base.IPSNode): The path to the wfn restart file. wfn_restart_node : str, optional A cp2k Node that has a wfn restart file. + failure_policy : str, default="fail" + The failure policy for the cp2k calculation. If "fail", the + calculation will fail if any of the calculations fail. If "skip", + the calculation will skip the failed calculations and continue + with the next one. + + Attributes + ---------- + frames : list[ase.Atoms] + The list of ASE Atoms objects that were successfully calculated. + cp2k_directory : pathlib.Path + The directory where the cp2k calculation is run and all the + cp2k output files are stored. + output_file : pathlib.Path + The path to the output trajectory file. + failed_configs : dict + A dictionary with the indices of the failed configurations. """ data: list[ase.Atoms] = zntrack.deps() From a5d379b1b63b0c048bebafe7aea33254018142b1 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 16 Apr 2025 12:07:22 +0000 Subject: [PATCH 09/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ipsuite/calculators/cp2k.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ipsuite/calculators/cp2k.py b/ipsuite/calculators/cp2k.py index df352e8a..b89b4530 100644 --- a/ipsuite/calculators/cp2k.py +++ b/ipsuite/calculators/cp2k.py @@ -78,7 +78,7 @@ class CP2KSinglePoint(base.IPSNode): frames : list[ase.Atoms] The list of ASE Atoms objects that were successfully calculated. cp2k_directory : pathlib.Path - The directory where the cp2k calculation is run and all the + The directory where the cp2k calculation is run and all the cp2k output files are stored. output_file : pathlib.Path The path to the output trajectory file. From 198ce8dbc0d1e42d16416c75bf0cfae735fa3138 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Wed, 16 Apr 2025 14:14:23 +0200 Subject: [PATCH 10/20] fix docutils complaints --- ipsuite/analysis/model/dynamics.py | 12 ++++++++---- ipsuite/analysis/model/dynamics_checks.py | 5 +++-- ipsuite/calculators/ase_md.py | 10 +++++++++- 3 files changed, 20 insertions(+), 7 deletions(-) diff --git a/ipsuite/analysis/model/dynamics.py b/ipsuite/analysis/model/dynamics.py index cd920b87..a89f5f1c 100644 --- a/ipsuite/analysis/model/dynamics.py +++ b/ipsuite/analysis/model/dynamics.py @@ -32,8 +32,10 @@ class RattleAnalysis(base.ProcessSingleAtom): Attributes ---------- - model: The MLModel node that implements the 'predict' method - atoms: list[Atoms] to predict properties for + model: zntrack.Node + The MLModel node that implements the 'predict' method + data: list[Atoms] + list of atoms to predict properties for logspace: bool, default=True Increase the stdev of rattle with 'np.logspace' instead of 'np.linspace' stop: float, default = 1.0 @@ -97,8 +99,10 @@ class BoxScale(base.ProcessSingleAtom): Attributes ---------- - model: The MLModel node that implements the 'predict' method - atoms: list[Atoms] to predict properties for + model: + The MLModel node that implements the 'predict' method + atoms: list[Atoms] + list of atoms to predict properties for start: int, default = None The initial box scale, default value is the original box size. stop: float, default = 1.0 diff --git a/ipsuite/analysis/model/dynamics_checks.py b/ipsuite/analysis/model/dynamics_checks.py index 70511dd3..782ee9e3 100644 --- a/ipsuite/analysis/model/dynamics_checks.py +++ b/ipsuite/analysis/model/dynamics_checks.py @@ -218,14 +218,14 @@ class ThresholdCheck(base.Check): Furthermore, the simulation will be stopped if the property exceeds a threshold value. - Attributes + Parameters ---------- key: str name of the property to check max_std: float, optional Maximum number of standard deviations away from the mean to stop the simulation. Roughly the value corresponds to the following percentiles: - {1: 68%, 2: 95%, 3: 99.7%} + ``{1: 68%, 2: 95%, 3: 99.7%}`` window_size: int, optional Number of steps to average over max_value: float, optional @@ -252,6 +252,7 @@ def __post_init__(self): def get_value(self, atoms): """Get the value of the property to check. + Extracted into method so it can be subclassed. """ return np.max(atoms.calc.results[self.key]) diff --git a/ipsuite/calculators/ase_md.py b/ipsuite/calculators/ase_md.py index 756328ab..a4660f71 100644 --- a/ipsuite/calculators/ase_md.py +++ b/ipsuite/calculators/ase_md.py @@ -449,7 +449,14 @@ def get_thermostat(self, atoms): @dataclasses.dataclass class FixedSphereConstraint: - """Attributes + """Freeze all atoms within a sphere. + + Constraint to freeze all atoms within a sphere of a given radius + around a given atom. The atom to freeze can be specified + by its id or type. If both are given, the id is used. + + + Attributes ---------- atom_id: int The id to use as the center of the sphere to fix. @@ -460,6 +467,7 @@ class FixedSphereConstraint: hydrogen atom will be fixed. If None, the first atom will be fixed, no matter the type. radius: float + The radius of the sphere to fix. """ radius: float From bcacdda6ff2e2c714dc23e8591c2e901bcf7ee54 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 16 Apr 2025 12:14:34 +0000 Subject: [PATCH 11/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ipsuite/calculators/ase_md.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ipsuite/calculators/ase_md.py b/ipsuite/calculators/ase_md.py index a4660f71..438bbca5 100644 --- a/ipsuite/calculators/ase_md.py +++ b/ipsuite/calculators/ase_md.py @@ -454,8 +454,8 @@ class FixedSphereConstraint: Constraint to freeze all atoms within a sphere of a given radius around a given atom. The atom to freeze can be specified by its id or type. If both are given, the id is used. - - + + Attributes ---------- atom_id: int From 63e3784e0018b7d3f95e7e57a341efec93afb5b3 Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Fri, 9 May 2025 15:49:08 +0200 Subject: [PATCH 12/20] update docs a bit --- docs/source/conf.py | 33 ++++++++++++++++++++++++++------- 1 file changed, 26 insertions(+), 7 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 53f30f9d..e4c7bf85 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -6,20 +6,17 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -import sys -from pathlib import Path +import ipsuite +import typing as t project = "IPSuite" -project_copyright = "2024, zincwarecode" +project_copyright = "2025, zincwarecode" author = "zincwarecode" -release = "0.1.1" +release = ipsuite.__version__ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - -sys.path.insert(0, Path("../../ipsuite/").resolve().as_posix()) - extensions = [ "sphinx.ext.autodoc", "sphinx.ext.doctest", @@ -37,3 +34,25 @@ html_theme = "furo" html_static_path = ["_static"] +html_title = "IPSuite" +html_short_title = "ipsuite" + +html_theme_options: t.Dict[str, t.Any] = { + "footer_icons": [ + { + "name": "GitHub", + "url": "https://github.com/zincware/ipsuite", + "html": "", + "class": "fa-brands fa-github fa-2x", + }, + ], + "source_repository": "https://github.com/zincware/ipsuite/", + "source_branch": "main", + "source_directory": "docs/source/", + "navigation_with_keys": True, +} + +# font-awesome logos +html_css_files = [ + "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css", +] From 7307c7821df861cde300046584a3c2b1d537f6d3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 9 May 2025 13:49:17 +0000 Subject: [PATCH 13/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/conf.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index e4c7bf85..79082eb6 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -6,9 +6,10 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -import ipsuite import typing as t +import ipsuite + project = "IPSuite" project_copyright = "2025, zincwarecode" author = "zincwarecode" From 3f45e224c9d77bbf56e67b6a1dc0d34aaab6261a Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Fri, 6 Jun 2025 16:09:46 +0200 Subject: [PATCH 14/20] rename `.atoms` to `.frames` --- docs/source/_get_started/quickstart.rst | 4 ++-- docs/source/examples/06_Bootstrapping_Datasets.ipynb | 10 +++++----- ipsuite/analysis/model/dynamics.py | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/source/_get_started/quickstart.rst b/docs/source/_get_started/quickstart.rst index 8f76bd23..6614f2e5 100644 --- a/docs/source/_get_started/quickstart.rst +++ b/docs/source/_get_started/quickstart.rst @@ -26,10 +26,10 @@ The goal is to place water molecules inside a box at a specified density. The :class:`ipsuite.Smiles2Conformers` node takes the `SMILES `_ string for water ("O"), and generates an an `ASE atoms object `_ from it. -This atom from the :class:`ipsuite.Smiles2Conformers` instance can be accessd by calling `mol.atoms`. +This atom from the :class:`ipsuite.Smiles2Conformers` instance can be accessd by calling `mol.frames`. This instance attribute is then handed over to the Packmol node in the `data` attribute. It is possible to hand over multiple different types of ASE atoms, -so `mol.atoms` as to be given as a list. The next attribute we need to set is the amount of molecules we want to place in the box. +so `mol.frames` as to be given as a list. The next attribute we need to set is the amount of molecules we want to place in the box. This also has to be a list with each entry being the amount for other ASE atoms object in the `data` list. Lastly the density has to be provided. Calling `project.build()` will save the workflow into DVC graph configuration and parameter files. After executing the code, the entire workflow is constructed and can be visualised diff --git a/docs/source/examples/06_Bootstrapping_Datasets.ipynb b/docs/source/examples/06_Bootstrapping_Datasets.ipynb index 83a3957f..c890b4b7 100644 --- a/docs/source/examples/06_Bootstrapping_Datasets.ipynb +++ b/docs/source/examples/06_Bootstrapping_Datasets.ipynb @@ -372,20 +372,20 @@ "\n", "with ips.Project() as project:\n", " water = ips.Smiles2Atoms(smiles=\"O\")\n", - " packmol = ips.Packmol(data=[water.atoms], count=[10], density=997)\n", + " packmol = ips.Packmol(data=[water.frames], count=[10], density=997)\n", "\n", " opt_calc = ips.xTBSinglePoint(data=packmol, method=\"gfn1-xtb\", name=\"opt_calc\")\n", "\n", " geopt = ips.ASEGeoOpt(\n", " model=opt_calc,\n", - " data=packmol.atoms,\n", + " data=packmol.frames,\n", " optimizer=\"BFGS\",\n", " run_kwargs={\"fmax\": 1.0},\n", " )\n", "\n", " n_configs = 5\n", " rattle = ips.bootstrap.RattleAtoms(\n", - " data=geopt.atoms,\n", + " data=geopt.frames,\n", " data_id=-1,\n", " n_configurations=n_configs,\n", " maximum=0.08, # Ang max atomic displacement\n", @@ -399,14 +399,14 @@ " include_original=False,\n", " )\n", " translate = ips.bootstrap.TranslateMolecules(\n", - " data=geopt.atoms,\n", + " data=geopt.frames,\n", " data_id=-1,\n", " n_configurations=n_configs,\n", " maximum=0.3, # Ang max molecular displacement\n", " include_original=False,\n", " )\n", "\n", - " bootstrap_configurations = rattle.atoms + rotate.atoms + translate.atoms\n", + " bootstrap_configurations = rattle.frames + rotate.frames + translate.frames\n", "\n", " labeling_calc = ips.xTBSinglePoint(\n", " data=bootstrap_configurations, method=\"gfn1-xtb\", name=\"label_calc\"\n", diff --git a/ipsuite/analysis/model/dynamics.py b/ipsuite/analysis/model/dynamics.py index a89f5f1c..8418bd15 100644 --- a/ipsuite/analysis/model/dynamics.py +++ b/ipsuite/analysis/model/dynamics.py @@ -45,7 +45,7 @@ class RattleAnalysis(base.ProcessSingleAtom): factor: float, default = 0.001 The 'np.linspace(0.0, stop, num) * factor' atom_id: int, default = 0 - The atom to pick from self.atoms as a starting point + The atom to pick from self.data as a starting point """ model: models.MLModel = zntrack.deps() From 1865f600cdce897488e3d145902acb514aa63a28 Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Fri, 6 Jun 2025 16:22:20 +0200 Subject: [PATCH 15/20] doc updates --- ipsuite/calculators/ase_geoopt.py | 2 +- ipsuite/models/cp2k.py | 32 ++++++++++++++++++++++ pyproject.toml | 2 ++ uv.lock | 45 ++++++++++++++++++++++++------- 4 files changed, 70 insertions(+), 11 deletions(-) diff --git a/ipsuite/calculators/ase_geoopt.py b/ipsuite/calculators/ase_geoopt.py index 6eab9fae..2df02034 100644 --- a/ipsuite/calculators/ase_geoopt.py +++ b/ipsuite/calculators/ase_geoopt.py @@ -70,7 +70,7 @@ class ASEGeoOpt(base.IPSNode): ... smiles="CCO", numConfs=1 ... ) ... opt = ips.ASEGeoOpt( - ... data=etoh, + ... data=etoh.frames, ... model=model, ... optimizer="FIRE", ... run_kwargs={"fmax": 0.05}, diff --git a/ipsuite/models/cp2k.py b/ipsuite/models/cp2k.py index 64256c34..01e0e404 100644 --- a/ipsuite/models/cp2k.py +++ b/ipsuite/models/cp2k.py @@ -50,6 +50,38 @@ class CP2KModel: ... model=cp2k, ... ) >>> project.build() + + An example of the ``cp2k.yaml`` file: + + .. code-block:: yaml + + force_eval: + method: quickstep + DFT: + mgrid: + cutoff: 400 + SCF: + scf_guess: atomic + max_scf: 50 + eps_scf: 1.0e-6 + OT: + minimizer: diis + XC: + xc_functional: + PBE: {} + charge: 0 + basis_set_file_name: GTH_BASIS_SETS + potential_file_name: GTH_POTENTIALS + subsys: + kind: + O: + basis_set: DZVP-GTH-PBE + potential: GTH-PBE-q6 + H: + basis_set: DZVP-GTH-PBE + potential: GTH-PBE-q1 + + """ config: str | Path = zntrack.params_path() diff --git a/pyproject.toml b/pyproject.toml index 6251e02b..da209201 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ dependencies = [ "cp2k-input-tools>=0.9.1", "laufband>=0.1.3", "lazy-loader>=0.4", + "pint>=0.24", "rdkit2ase>=0.1.4", "seaborn>=0.13.2", "uncertainty-toolbox>=0.1.1", @@ -99,3 +100,4 @@ skip = "poetry.lock,ipsuite/static_data/*,docs/source/examples/06_Bootstrapping_ [tool.uv.sources] cp2k-output-tools = { git = "https://github.com/cp2k/cp2k-output-tools" } +cp2k-input-tools = { git = "https://github.com/cp2k/cp2k-input-tools" } diff --git a/uv.lock b/uv.lock index 5e91cf7d..bc0227f0 100644 --- a/uv.lock +++ b/uv.lock @@ -707,7 +707,7 @@ toml = [ [[package]] name = "cp2k-input-tools" version = "0.9.1" -source = { registry = "https://pypi.org/simple" } +source = { git = "https://github.com/cp2k/cp2k-input-tools#742af1aa02953b0ab4e150a85c95c1ceea56f881" } dependencies = [ { name = "click" }, { name = "jinja2" }, @@ -715,10 +715,6 @@ dependencies = [ { name = "pydantic" }, { name = "transitions" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/1f/82/0b8f5b382c9e20075429a868b7c762b1d0265f5e348ccf1d26b75a5fa8ed/cp2k_input_tools-0.9.1.tar.gz", hash = "sha256:bf7d229bbcfa41b1caaa32e7eb3c1c689d56bd1cbd4de674bd2fde8de4efb27c", size = 1348032, upload-time = "2024-02-16T07:46:31.788Z" } -wheels = [ - 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{ name = "cp2k-input-tools", specifier = ">=0.9.1" }, + { name = "cp2k-input-tools", git = "https://github.com/cp2k/cp2k-input-tools" }, { name = "laufband", specifier = ">=0.1.3" }, { name = "lazy-loader", specifier = ">=0.4" }, + { name = "pint", specifier = ">=0.24" }, { name = "rdkit2ase", specifier = ">=0.1.4" }, { name = "seaborn", specifier = ">=0.13.2" }, { name = "uncertainty-toolbox", specifier = ">=0.1.1" }, @@ -2815,14 +2837,17 @@ wheels = [ [[package]] name = "pint" -version = "0.23" +version = "0.24.4" source = { registry = "https://pypi.org/simple" } dependencies = [ + { name = "flexcache" }, + { name = "flexparser" }, + { name = "platformdirs" }, { name = "typing-extensions" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/02/41/002d020f140db35d971f4bdd73407d69fdf56c5ba5fcccc10776e27d3a6c/Pint-0.23.tar.gz", hash = "sha256:e1509b91606dbc52527c600a4ef74ffac12fff70688aff20e9072409346ec9b4", size = 347420, upload-time = "2023-12-08T20:38:23.17Z" } +sdist = { url = "https://files.pythonhosted.org/packages/20/bb/52b15ddf7b7706ed591134a895dbf6e41c8348171fb635e655e0a4bbb0ea/pint-0.24.4.tar.gz", hash = "sha256:35275439b574837a6cd3020a5a4a73645eb125ce4152a73a2f126bf164b91b80", size = 342225, upload-time = "2024-11-07T16:29:46.061Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/76/1a/096c91c2006648fe28564e5884d59978962afe98de74b1c01bb5913d033f/Pint-0.23-py3-none-any.whl", hash = "sha256:df79b6b5f1beb7ed0cd55d91a0766fc55f972f757a9364e844958c05e8eb66f9", size = 305009, upload-time = "2023-12-08T20:38:20.574Z" }, + { url = "https://files.pythonhosted.org/packages/b7/16/bd2f5904557265882108dc2e04f18abc05ab0c2b7082ae9430091daf1d5c/Pint-0.24.4-py3-none-any.whl", hash = "sha256:aa54926c8772159fcf65f82cc0d34de6768c151b32ad1deb0331291c38fe7659", size = 302029, upload-time = "2024-11-07T16:29:43.976Z" }, ] [[package]] From 94eeab30ab87799b49ccd9d31d53e050d9abe7d7 Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Sat, 7 Jun 2025 11:27:47 +0200 Subject: [PATCH 16/20] skip GAP testing --- tests/unit_tests/models/{test_gap.py => skip_test_gap.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename tests/unit_tests/models/{test_gap.py => skip_test_gap.py} (100%) diff --git a/tests/unit_tests/models/test_gap.py b/tests/unit_tests/models/skip_test_gap.py similarity index 100% rename from tests/unit_tests/models/test_gap.py rename to tests/unit_tests/models/skip_test_gap.py From 8418515980b1196e7a7de84edf9270817f7dba66 Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Sat, 7 Jun 2025 11:29:33 +0200 Subject: [PATCH 17/20] shorten line length --- ipsuite/configuration_generation/smiles_to_atoms.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index 75cd32e6..dd345587 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -25,7 +25,8 @@ def run(self): class Smiles2Conformers(base.IPSNode): """ - Generate molecular conformers from a SMILES string and store them as ASE Atoms objects. + Generate molecular conformers from a SMILES string + and store them as ASE Atoms objects. Parameters ---------- @@ -38,7 +39,8 @@ class Smiles2Conformers(base.IPSNode): maxAttempts : int, optional Maximum number of attempts to generate conformers (default is 1000). cell : float, optional - Size of the cubic unit cell to assign to the generated conformers (default is 100). + Size of the cubic unit cell to assign to the generated + conformers (default is 100). Attributes ---------- From ba5abb0416dd0220f7d8f56edffce1d9ce90962c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 7 Jun 2025 09:30:21 +0000 Subject: [PATCH 18/20] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ipsuite/configuration_generation/smiles_to_atoms.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index dd345587..21f58b5b 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -39,7 +39,7 @@ class Smiles2Conformers(base.IPSNode): maxAttempts : int, optional Maximum number of attempts to generate conformers (default is 1000). cell : float, optional - Size of the cubic unit cell to assign to the generated + Size of the cubic unit cell to assign to the generated conformers (default is 100). Attributes From c0ee33aa41c430fce4ebe88cc5ad2d7587c997be Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Sat, 7 Jun 2025 11:35:09 +0200 Subject: [PATCH 19/20] pre-commit fix --- ipsuite/configuration_generation/smiles_to_atoms.py | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index dd345587..21f58b5b 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -39,7 +39,7 @@ class Smiles2Conformers(base.IPSNode): maxAttempts : int, optional Maximum number of attempts to generate conformers (default is 1000). cell : float, optional - Size of the cubic unit cell to assign to the generated + Size of the cubic unit cell to assign to the generated conformers (default is 100). Attributes diff --git a/pyproject.toml b/pyproject.toml index da209201..f9223a5a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,7 +95,7 @@ ignore = [ ] [tool.codespell] -ignore-words-list = "dscribe" +ignore-words-list = "dscribe,OT" skip = "poetry.lock,ipsuite/static_data/*,docs/source/examples/06_Bootstrapping_Datasets.ipynb" [tool.uv.sources] From 5b77cbddbbc7c059becdb3bfbba9cd5860b4e6a3 Mon Sep 17 00:00:00 2001 From: Fabian Zills Date: Sat, 7 Jun 2025 11:46:51 +0200 Subject: [PATCH 20/20] disable and move GAP tests --- tests/integration/analysis/model/test_i_predict.py | 11 +++-------- .../integration/{test_i_gap.py => skip_test_i_gap.py} | 0 tests/integration/test_ensemble.py | 11 +++-------- tests/integration/test_i_model_analysis.py | 4 +++- 4 files changed, 9 insertions(+), 17 deletions(-) rename tests/integration/{test_i_gap.py => skip_test_i_gap.py} (100%) diff --git a/tests/integration/analysis/model/test_i_predict.py b/tests/integration/analysis/model/test_i_predict.py index 0382dcd2..639c8f43 100644 --- a/tests/integration/analysis/model/test_i_predict.py +++ b/tests/integration/analysis/model/test_i_predict.py @@ -10,17 +10,12 @@ def test_calibration(data_repo): name="water", remote="https://github.com/IPSProjects/ips-examples" ) + model1 = ips.LJSinglePoint(sigma=1.1) + model2 = ips.LJSinglePoint(sigma=0.9) + with ips.Project() as project: test_data = ips.RandomSelection(data=water.frames, n_configurations=5) - train_data = ips.RandomSelection( - data=test_data.excluded_frames, - n_configurations=5, - ) - - model1 = ips.GAP(data=train_data.frames, soap={"n_max": 1}) - model2 = ips.GAP(data=train_data.frames, soap={"n_max": 2}) - ensemble_model = ips.EnsembleModel(models=[model1, model2]) pred = ips.Prediction( diff --git a/tests/integration/test_i_gap.py b/tests/integration/skip_test_i_gap.py similarity index 100% rename from tests/integration/test_i_gap.py rename to tests/integration/skip_test_i_gap.py diff --git a/tests/integration/test_ensemble.py b/tests/integration/test_ensemble.py index 6da8f484..2112c590 100644 --- a/tests/integration/test_ensemble.py +++ b/tests/integration/test_ensemble.py @@ -15,17 +15,12 @@ def test_ensemble_model(proj_path, traj_file): ) thermostat = ips.LangevinThermostat(time_step=1.0, temperature=100.0, friction=0.01) + model1 = ips.LJSinglePoint(sigma=1.1) + model2 = ips.LJSinglePoint(sigma=0.9) + with ips.Project() as project: test_data = ips.RandomSelection(data=data.frames, n_configurations=5) - train_data = ips.RandomSelection( - data=test_data.excluded_frames, - n_configurations=5, - ) - - model1 = ips.GAP(data=train_data.frames, soap={"n_max": 1}, use_stresses=False) - model2 = ips.GAP(data=train_data.frames, soap={"n_max": 2}, use_stresses=False) - ensemble_model = ips.EnsembleModel(models=[model1, model2]) md = ips.ASEMD( diff --git a/tests/integration/test_i_model_analysis.py b/tests/integration/test_i_model_analysis.py index e3089ca9..9ad1b037 100644 --- a/tests/integration/test_i_model_analysis.py +++ b/tests/integration/test_i_model_analysis.py @@ -14,6 +14,8 @@ @pytest.fixture() def trained_model(proj_path, traj_file) -> tuple: + model = ipsuite.EMTSinglePoint() + with ipsuite.Project() as project: data_1 = ipsuite.AddData(file=traj_file, name="data_1") @@ -29,7 +31,7 @@ def trained_model(proj_path, traj_file) -> tuple: ) ) - model = ipsuite.GAP(soap={"cutoff": 0.7}, data=train_selection.frames) + # model = ipsuite.GAP(soap={"cutoff": 0.7}, data=train_selection.frames) project.repro()