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توضیحات

High throughput analysis of interfaces using VASP and Materials Project tools

ویژگی	مقدار
سیستم عامل	OS Independent
نام فایل	MPInterfaces-2020.6.19
نام	MPInterfaces
نسخه کتابخانه	2020.6.19
نگهدارنده	['Venkata Surya Chaitanya Kolluru, Joshua T. Paul']
ایمیل نگهدارنده	['kvs.chaitanya@ufl.edu,joshuapaul@ufl.edu']
نویسنده	Kiran Mathew, Joshua J. Gabriel, Michael Ashton, Arunima K. Singh, Joshua T. Paul, Seve G. Monahan, Richard G. Hennig, Venkata Surya Chaitanya Kolluru
ایمیل نویسنده	joshgabriel92@gmail.com, kmathew@lbl.gov, ashtonmv@gmail.com,kvs.chaitanya@ufl.edu,joshuapaul@ufl.edu
آدرس صفحه اصلی	https://github.com/henniggroup/MPInterfaces
آدرس اینترنتی	https://pypi.org/project/MPInterfaces/
مجوز	MIT

.. image:: https://travis-ci.org/henniggroup/MPInterfaces.svg?branch=master .. image:: https://codecov.io/gh/henniggroup/MPInterfaces/coverage.svg?branch=master MPinterfaces is a python package that enables high throughput Density Functional Theory(DFT) analysis of arbitrary material interfaces(two dimensional materials, hetero-structure, ligand capped nanoparticles and surfaces in the presence of solvents) using VASP_, VASPsol_, LAMMPS_, materialsproject_ database as well as their open source tools_ and a little bit of ase_. .. _materialsproject: https://github.com/materialsproject .. _VASPsol: https://github.com/henniggroup/VASPsol .. _VASP: http://www.vasp.at/ .. _tools: https://github.com/materialsproject .. _LAMMPS: http://lammps.sandia.gov/ .. _ase: https://wiki.fysik.dtu.dk/ase/ .. image:: https://github.com/henniggroup/MPInterfaces/blob/master/docs/mpinterfaces-logo.png :width: 75 % :align: center Installation ============== Prepping - Setting up Virtual Environments with Miniconda =========================================================== We recommend setting up virtual environment using Miniconda which can be installed according to their instructions from https://conda.io/miniconda.html Note for SuperComputer Clusters with Linux OS: ============================================== HiperGator2 and other linux based supercomputing clusters have shared modules one of which are the C++ modules under gcc. This needs to be loaded before any of the aforementioned gcc/5.2.0 has all the shared libraries required for a successful installation. Do the following on HiperGator2 before you create the Miniconda environment: $ module purge $ module load gcc/5.2.0 Follow the following steps to set up virtual environment using Miniconda $ conda create -n name_of_your_environment python=3.6 On Mac OS and Linux $ source activate name_of_your_environment $ conda install numpy scipy matplotlib ipython On Windows: $ activate name_of_your_environment $ conda install numpy scipy matplotlib ipython Installing Pymatgen ==================== $ conda install -c matsci pymatgen Note: You will need to have C++ libraries properly installed for the package to install correctly on Windows. Note: If this does not work, see http://pymatgen.org/#getting-pymatgen Installing MPInterfaces from GitHub ===================================== If you would like to get the latest updates, or develop and contribute we recommend getting the bleeding edge copy from the github repository. If you already have a local copy, steps 1 and 2 of the following instructions can be skipped. Just do a "git pull" from the MPInterfaces folder and go to step 3(if the local copy was installed in the develop mode this step can be skipped too). Note: on using virtual environments on your own machine, we recommend to use Miniconda. 1. Clone the latest version from github - git clone https://github.com/henniggroup/MPInterfaces.git 2. cd MPInterfaces 3. python setup.py install(or develop) 4. Copy the mpint_config.yaml file from config_files/mpint_config.yaml to ~/mpint_config.yaml and update the file so that you at least have the following environment variables : - MAPI_KEY=the_key_obtained_from_materialsproject - PMG_VASP_PSP_DIR=path_to_vasp_potcar_files For teaching and demo purposes, we recommend using Microsoft Azure notebooks, an example of which is at https://notebooks.azure.com/JoshGabriel92/libraries/PourbaixCourse which contains two notebooks that illustrate installing pymatgen and pyhull for on the fly data science tutorials. We have one notebook FeOH_Example.ipynb for Pourbaix diagrams and an MPInterfacesDemo that illustrate other features of the MPInterfaces code with more to come. Installing MPInterfaces from PyPI ================================== Once you have a nicely prepped virtual environment with miniconda and you do not seek to do extensive code development/contributions, we recommend installing from PyPI with: $ pip install MPInterfaces_Latest Documentation ============== A very minimal documentation is avaiable at http://henniggroup.github.io/MPInterfaces/ and work is underway to improve it. Usage ========== We use pymatgen tools for all structure manipulation tasks, so it would be a good idea to start from here: http://pymatgen.org/#using-pymatgen The examples folder contain some sample scripts that demonstrate the usage of mpinterfaces as well as materialsproject packages. For basic usage please see **docs/usage.rst**. Cite ====== If you use MPInterfaces for your work, please cite the paper: mpinterfaces-paper_ .. _mpinterfaces-paper: http://www.sciencedirect.com/science/article/pii/S0927025616302440 License ======= MPInterfaces is released under the MIT License.:: Copyright (c) 2014-2017 Henniggroup Cornell/University of Florida & NIST Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Contributing ============= We try to follow the coding style used by pymatgen(PEP8): http://pymatgen.org/contributing.html#coding-guidelines Authors ========= Kiran Mathew Joshua Gabriel Michael Ashton Arunima Singh Joshua T. Paul Venkata Surya Chaitanya Kolluru Seve G. Monahan Richard G. Hennig How to cite =========== DOI for the MPInterfaces Github repository: .. image:: https://zenodo.org/badge/37893482.svg :target: https://doi.org/10.5281/zenodo.2554262 BibTex entry for the Github repository and the publication:: @misc{MPInterface, title = {MPInterfaces - Python package for high throughput analysis of materials interfaces}, author = {K. Mathew and J. J. Gabriel and M. Ashton and A. K. Singh and J. T. Paul and S. G. Monahan and R. G. Hennig}, year = 2018, publisher = {GitHub}, journal = {GitHub repository}, howpublished = {\url{https://github.com/henniggroup/MPInterfaces}}, url = {https://github.com/henniggroup/MPInterfaces}, doi = {10.5281/zenodo.2554262} } @article{Mathew2016, title = {MPInterfaces: A Materials Project based Python tool for high-throughput computational screening of interfacial systems}, author = {K. Mathew and A. K. Singh and J. J. Gabriel and K. Choudhary and S. B. Sinnott and A. V. Davydov and F. Tavazza and R. G. Hennig", year = 2016, journal = {Comp. Mater. Sci.}, volume = 122, pages = {183 - 190}, doi = {10.1016/j.commatsci.2016.05.020} }

نیازمندی

مقدار	نام
>=1.4.0	FireWorks
>=1.0.1	custodian
>=0.5.1	pymatgen-db
>=3.11.0	ase
-	six
>=1.5.3	pyhull
-	seaborn
-	pyyaml
-	nose
-	openbabel
-	pybel
>=1.3.1	sphinx
>=0.1.8	sphinx-rtd-theme
-	fabric

نحوه نصب

نصب پکیج whl MPInterfaces-2020.6.19:

pip install MPInterfaces-2020.6.19.whl

نصب پکیج tar.gz MPInterfaces-2020.6.19:

pip install MPInterfaces-2020.6.19.tar.gz