Package: amof
aMOFaMOF is a python package consisting in a collection of tools to analyze Molecular Dynamics (MD) trajectories of amorphous Metal-Organic Frameworks (MOFs).FunctionalitiesGeneral-purpose MD toolboxThis package brings together a number of analyses that can be performed on every MD trajectory (not necessarily MOFs), heavily using both other python packages and non-python codes.
It can compute the following properties:Radial Distribution Functions (RDF), based onASAPBond-Angle DistributionsCoordination numbersMean Squared Displacement (MSD)Elastic constants from cell properties, and mechanical properties from elastic constants by callingELATEPore analysis by wrappingZeo++, reusing code frompysimmRing statistics by wrapping theRINGS codeThe backend for manipulating trajectories isASE, which areASE trajectoryobjects.Building units identification of aMOFsA module calledcoordinationallows the identification of the different building blocks of amorphous MOFs with anad hocapproach per MOF system.Only ZIF-4 is supported in the current release.This allows the computation of rings statistics of the metal-ligand network.This code is designed to be compatible withmolsys, and can be used to generate input files inmfpxformat.The detailed algorithm for ZIF-4 is presented in the supporting information of the paperChallenges in Molecular Dynamics of Amorphous ZIFs using Reactive Force Fields.InstallationPre-requisitesTo use theporeandringmodules,Zeo++and theRINGS codeneed to be installed and accessible in the system path.First download and follow the installation instructions on their respective websites (here for Zeo++andhere for RINGS).Then for Zeo++, create the following variable on your system:export ZEOpp_EXEC=/path/to/zeo++-0.3/networkFor RINGS, ensure that theringsbinary is in your path:export PATH=$PATH:/path/to/rings/binInstallation with pipaMOF can be installed from PyPI:pip install amofor directly from source:git clone https://github.com/coudertlab/amof.git
cd amof
pip install .Special care should be taken withAsap, which can only be installed ifnumpyis already installed and is thus not a default dependency.
To solve this, either installasapindependently (followingtheir installation guide), or first installnumpythen installamofwith therdfextra:pip install numpy
pip install amof[rdf]By default, graphical dependencies (used in theplotmodule) are not installed. To install them use thegraphicsextra:pip install amof[graphics]Installation with condaSupport for installing aMOF withcondais not included at the moment.
However,condacan be used to first install all dependencies before installingamofwithpip.conda install -c conda-forge ase=3.20.1 asap3 pandas numpy xarray=0.19.0 dask netCDF4 bottleneck ase asap3 joblib pymatgen hvplot atomman jupyter jupyterlab jupytext matplotlib networkx scipy plotly seaborn cairosvg pyarrow seleniumDocumentationA documentation is can easily be created withpdoc.Simply run (with pdoc installed):pdoc --html --output-dir path\to\docs path\to\amofUsageExamplesExamples analyses can be found in theexamplesfolder of this repository.CitationIf you use the python package in published results (paper, conference, etc.), please cite the first paper for which it was developed:Challenges in Molecular Dynamics of Amorphous ZIFs using Reactive Force Fields.