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‎docs/source/installation/dependencies.rst‎

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@@ -43,68 +43,87 @@ To deactivate the enviornment, simply run::
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conda install pip setuptools
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Computational chemistry software
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Required Software
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---------------------------------
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Computational chemistry software dependencies
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=============================================
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At the backend, MISPR uses:
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* `Gaussian <https://gaussian.com>`_ software to perform DFT calculations
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* `AmberTools <https://ambermd.org/AmberTools.php>`_ to generate GAFF parameters
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* `Schrödinger <https://www.schrodinger.com/>`_ (optional) to automatically generate
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OPLS2005 parameters
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* `LAMMPS <https://www.lammps.org/#gsc.tab=0>`_ to run MD simulations
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* `Packmol <https://m3g.github.io/packmol/download.shtml>`_ to
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create initial configurations for MD simulations. To install packmol,
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follow their `user guide <https://m3g.github.io/packmol/userguide.shtml>`_
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.. list-table::
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:widths: 20 40 40 20
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:header-rows: 1
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* - Software
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- License Type
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- Purpose
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- Installation
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* - `Gaussian <https://gaussian.com>`_
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- Commercial
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- Perform DFT calculations
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- License required
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* - `AmberTools <https://ambermd.org/AmberTools.php>`_
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- Open Source
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- Generate GAFF parameter
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- Direct download
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* - `LAMMPS <https://www.lammps.org>`_
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- Open Source
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- Run MD simulations
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- Direct download
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* - `Packmol <https://m3g.github.io/packmol/download.shtml>`_
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- Open Source
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- Build initial MD configurations
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- Follow `user guide <https://m3g.github.io/packmol/userguide.shtml>`_
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* - `Schrödinger <https://www.schrodinger.com/>`_
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- Commercial (Academic license available)
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- Generate OPLS2005 parameter (Optional)
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- License required
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Ensure that you have access to the executables of these software
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before using MISPR. Gaussian is a commercial software
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that requires a license while AmberTools, LAMMPS, and Packmol are open source.
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Schrödinger also requires a license, though academic licenses are available for university researchers.
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If Gaussian, AmberTools, Schrödinger and LAMMPS are already installed on HPC
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before using MISPR. If Gaussian, AmberTools, Schrödinger and LAMMPS are already installed on HPC
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machines, the user typically needs to load their corresponding modules
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before their use.
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Base Python libraries and dependencies
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---------------------------------
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* `pymatgen <https://pymatgen.org>`_: MISPR uses pymatgen for handling
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different molecule representations and i/o operations specific to
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Gaussian and LAMMPS. We have made changes to the pymatgen library to
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make it compatible with our needs in MISPR. These changes have not
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been merged yet with the main pymatgen library. Therefore, in order
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to use MISPR, you need to install the MolMD version of pymatgen by
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running the following commands in your ``|CODES_DIR|``::
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pip3 install pymatgen@git+https://github.com/molmd/pymatgen@molmd_fix_3-9#egg=pymatgen
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* `FireWorks <https://materialsproject.github.io/fireworks/>`_: MISPR
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uses FireWorks to design, manage, and execute workflows.
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Further details can be found in the `FireWorks documentation <https://materialsproject.github.io/fireworks/installation.html>`_.
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Python package dependencies
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============================
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.. list-table::
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:widths: 25 70 20
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:header-rows: 1
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* - Package
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- Purpose
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- Installation Command
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* - `pymatgen <https://pymatgen.org>`_
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- Molecule handling and I/O operations
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- ``pip3 install pymatgen@git+https://github.com/molmd/pymatgen@molmd_fix_3-9#egg=pymatgen``
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* - `OpenBabel <https://openbabel.org>`_
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- Used by pymatgen for molecule operations
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- ``conda install -c conda-forge openbabel=3.1.1``
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* - `FireWorks <https://materialsproject.github.io/fireworks/>`_
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- Workflow management and execution
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- Auto-installed with MISPR
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* - `custodian <https://materialsproject.github.io/custodian/>`_
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- Automatic Gaussian error handling and correction using predefined rules
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- Auto-installed with MISPR
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* - `MDPropTools <https://github.com/molmd/mdproptools>`_
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- Standalone, in-house package for analyzing MD outputs and trajectories
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- Auto-installed with MISPR
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.. note::
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.. important::
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We have made changes to the pymatgen library to
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make it compatible with our needs in MISPR. These changes have not
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been merged yet with the main pymatgen library. Therefore, in order
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to use MISPR, you need to install the MolMD version of pymatgen using
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the installation command shown in the table above.
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.. note::
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While FireWorks is used in MISPR for managing the DFT and MD
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workflows due to its many advantages, it takes some time to learn
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and get used to it.
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* `custodian <https://materialsproject.github.io/custodian/>`_: MISPR uses
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custodian for handling errors that occur during the simulations and
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correcting them according to predefined rules. We have contributed a Gaussian
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plug-in to the custodian library, and these changes have been merged with
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the main custodian library.
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* `OpenBabel <https://openbabel.org>`_ to handle molecule operations
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via pymatgen as an interface. You can install OpenBabel using conda::
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conda install -c conda-forge openbabel=3.1.1
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* `MDPropTools <https://github.com/molmd/mdproptools>`_: MISPR uses mdproptools, which is a standalone
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Python package we developed for analyzing molecular dynamics trajectories and
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output files.
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and get used to it. Further details can be found in the `FireWorks documentation <https://materialsproject.github.io/fireworks/installation.html>`_.
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.. note::
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FireWorks, custodian, and MDPropTools will be automatically installed as dependencies when you
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install MISPR. You don't need to install them separately.
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We have contributed a Gaussian plug-in to the custodian library, and these
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changes have been merged with the main custodian library.
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MongoDB
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-------------------------

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