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A selection of tools we use, some we like, and others we develop. Also see our [Github](https://github.com/WMD-group) and [Zenodo](https://zenodo.org/communities/wmd-group) groups.

# Journal of Open Source Software
* [CarrierCapture.jl: Anharmonic Carrier Capture](https://joss.theoj.org/papers/10.21105/joss.02102)

* [CarrierCapture.jl: anharmonic carrier capture](https://joss.theoj.org/papers/10.21105/joss.02102)
* [doped: Python toolkit for robust and repeatable charged defect supercell calculations](https://joss.theoj.org/papers/10.21105/joss.06433)
* [effmass: An Effective Mass Package](https://joss.theoj.org/papers/10.21105/joss.00797)
* [PyTASER: Simulating transient absorption spectroscopy (TAS) for crystals from first principles](https://joss.theoj.org/papers/10.21105/joss.05999)
* [ShakeNBreak: Navigating the Defect Configurational Landscape](https://joss.theoj.org/papers/6545bcc1a0439b16360ace684ac5aa25)
* [SMACT: Semiconducting Materials by Analogy and Chemical Theory](https://joss.theoj.org/papers/10.21105/joss.01361)
* [UnlockNN: Uncertainty Quantification for Neural Network Models of Chemical Systems](https://joss.theoj.org/papers/b00df538a159c4b6816ec24d4d1716fb)
* [effmass: an effective mass package](https://joss.theoj.org/papers/10.21105/joss.00797)
* [PyTASER: simulating transient absorption spectroscopy (TAS) for crystals from first principles](https://joss.theoj.org/papers/10.21105/joss.05999)
* [ShakeNBreak: navigating the defect configurational landscape](https://joss.theoj.org/papers/6545bcc1a0439b16360ace684ac5aa25)
* [SMACT: semiconducting materials by analogy and chemical theory](https://joss.theoj.org/papers/10.21105/joss.01361)
* [UnlockNN: uncertainty quantification for neural network models of chemical systems](https://joss.theoj.org/papers/b00df538a159c4b6816ec24d4d1716fb)

# Platforms and Toolkits

# Simulation Toolkits
* [AFLOW](http://www.aflowlib.org)
* [AiiDA](http://www.aiida.net) powers [Materials Cloud](https://www.materialscloud.org)
* [ASE](https://wiki.fysik.dtu.dk/ase/) powers [Computational Materials Repository](https://cmr.fysik.dtu.dk) with [Recipes](https://asr.readthedocs.io)
* [Atomate](https://github.com/hackingmaterials/atomate), [Atomate2](https://github.com/materialsproject/atomate2)
* [NOMAD](https://nomad-coe.eu)
* [Pymatgen](http://pymatgen.org) powers [Materials Project](https://materialsproject.org) and [Crystal Toolkit](https://next-gen.materialsproject.org/toolkit) with [Recipes](http://matgenb.materialsvirtuallab.org)
* [Atomate2](https://github.com/materialsproject/atomate2)
* [NOMAD](https://nomad-coe.eu)
* [Pymatgen](http://pymatgen.org) powers [Materials Project](https://materialsproject.org) and [Crystal Toolkit](https://next-gen.materialsproject.org/toolkit) with [Recipes](http://matgenb.materialsvirtuallab.org)

# Databases and Datasets

# Databases and Datasets
* [CoRE-MOF](https://zenodo.org/record/3370144), [QMOF](https://github.com/arosen93/QMOF),
* [CoRE-MOF](https://zenodo.org/record/3370144), [QMOF](https://github.com/arosen93/QMOF)
* [CoRE-COF](https://core-cof.github.io/CoRE-COF-Database), [Curated COFs](https://www.materialscloud.org/discover/curated-cofs), [ReDD-COFFEE](https://archive.materialscloud.org/record/2023.13)
* [Crystalium](http://crystalium.materialsvirtuallab.org)
* [Crystals.ai](https://crystals.ai)
* [Crystallography Open Database](http://www.crystallography.net/cod/)
* [Crystals.ai](https://crystals.ai)
* [Crystallography Open Database](http://www.crystallography.net/cod/)
* [CSD](https://www.psds.ac.uk/csd), [ICSD](https://www.psds.ac.uk/icsd)
* [Foundry-ML](https://foundry-ml.org)
* [HybriD3](https://materials.hybrid3.duke.edu)
* [HybriD3](https://materials.hybrid3.duke.edu) and [2D Metal Halide Perovskites](http://www.pdb.nmse-lab.ru)
* [MatNavi](https://mits.nims.go.jp/index_en.html)
* [MPDS](https://www.mpds.io)
* [NIST-Jarvis](https://jarvis.nist.gov)
* [Nomad Repository](https://nomad-coe.eu)
* [NREL Materials Database](https://materials.nrel.gov)
* [Open Quantum Materials Database](http://oqmd.org)
* [Optimade API](https://www.optimade.org)
* [2D Metal Halide Perovskites](http://www.pdb.nmse-lab.ru)
* [Optimade](https://www.optimade.org)

# Machine Learning Crystals
* [DScribe](https://singroup.github.io/dscribe), [MOFDScribe](https://github.com/kjappelbaum/mofdscribe)

* [CGCNN](https://github.com/txie-93/cgcnn) and [MEGNet](https://github.com/materialsvirtuallab/megnet)
* [DScribe](https://singroup.github.io/dscribe) and [MOFDScribe](https://github.com/kjappelbaum/mofdscribe)
* [Magpie](https://bitbucket.org/wolverton/magpie) built on [Weka](https://www.cs.waikato.ac.nz/ml/weka/) and [scikit-learn](http://scikit-learn.org)
* [Matbench](https://matbench.materialsproject.org) and [Matbench-discovery](https://matbench-discovery.materialsproject.org)
* [MatMiner](http://hackingmaterials.github.io/matminer) built on [scikit-learn](http://scikit-learn.org)
* [M2Hub](https://github.com/yuanqidu/M2Hub)
* [Sketch-Map](https://sketchmap.org)
* [SISSO](https://github.com/rouyang2017/SISSO)
* [Sketch-Map](https://sketchmap.org)

#### Machine Learning Force Fields

* [ACE](https://github.com/ACEsuit/ACE1.jl) and [MACE](https://github.com/ACEsuit/mace)
* [CGCNN](https://github.com/txie-93/cgcnn), [MatGL](https://github.com/materialsvirtuallab/matgl)
* [FLARE](https://github.com/mir-group/flare) and [Allegro](https://github.com/mir-group/allegro)
* [M3GNet](https://github.com/materialsvirtuallab/matgl), [CHGNet](https://github.com/CederGroupHub/chgnet)
* [ANI](https://github.com/isayev/ANI1_dataset)
* [DeepMD](https://github.com/deepmodeling/deepmd-kit)
* [FLARE](https://github.com/mir-group/flare), [NequIP](https://github.com/mir-group/nequip), and [Allegro](https://github.com/mir-group/allegro)
* [MatGL](https://github.com/materialsvirtuallab/matgl) and [CHGNet](https://github.com/CederGroupHub/chgnet)
* [PyXtal_FF](https://github.com/qzhu2017/pyxtal_ff)
* [SchNetPack](https://github.com/atomistic-machine-learning/schnetpack)

#### Compositional Descriptors and Models

* [Aviary](https://github.com/CompRhys/aviary) from [RooSt](https://github.com/CompRhys/roost)
* [Crabnet](https://github.com/anthony-wang/CrabNet)
* [ElementEmbeddings](https://github.com/WMD-group/ElementEmbeddings)
* [Element Movers Distance](https://github.com/lrcfmd/ElMD)
* [mat2vec](https://github.com/materialsintelligence/mat2vec)
* [RooSt](https://github.com/CompRhys/roost)
* [SkipAtom](https://github.com/lantunes/skipatom)

# Crystal Structure Prediction
* [AIRSS](https://www.mtg.msm.cam.ac.uk/Codes/AIRSS)
* [CALYPSO](http://www.calypso.cn)
* [p2ptrans](https://github.com/ftherrien/p2ptrans)
* [USPEX](http://uspex-team.org/en/uspex)

* [AIRSS](https://www.mtg.msm.cam.ac.uk/Codes/AIRSS)
* [CALYPSO](http://www.calypso.cn)
* [p2ptrans](https://github.com/ftherrien/p2ptrans)
* [PyXtal](https://github.com/qzhu2017/pyxtal)
* [USPEX](http://uspex-team.org/en/uspex)
* [XtalOpt](http://xtalopt.openmolecules.net)

# Structure Analysis

* [FINDSYM](https://stokes.byu.edu/iso/findsym.php)
* [PIEFACE](https://github.com/jcumby/PIEFACE)
* [Mercury](https://www.ccdc.cam.ac.uk/Community/csd-community/FreeMercury/)
* [PDynA](https://github.com/WMD-group/PDynA)
* [PLATON](http://www.cryst.chem.uu.nl/platon/)
* [pyTilting](https://dwang5.github.io/PyTiltingDoc)
* [spglib](http://spglib.github.io/spglib)
* [TOPOS](http://www.topospro.com)
* [VESTA](http://jp-minerals.org/vesta/en/)
* [Zeo++](http://www.zeoplusplus.org)

# Electronic Structure

* [ABINIT](https://www.abinit.org)
* [BigDFT](http://bigdft.org)
* [CP2K](https://www.cp2k.org)
* [ELK](http://elk.sourceforge.net)
* [FHI-AIMS](https://aimsclub.fhi-berlin.mpg.de)
* [GPAW](https://wiki.fysik.dtu.dk/gpaw/)
* [ORCA](https://orcaforum.kofo.mpg.de)
* [Quantum Espresso](https://www.quantum-espresso.org)
* [QUESTAAL](https://www.questaal.org)
* [QUESTAAL](https://www.questaal.org)
* [VASP](https://www.vasp.at)
* [WIEN2k](http://susi.theochem.tuwien.ac.at)
* [xTB](https://github.com/grimme-lab/xtb)

#### Processing Tools
* [AMSET](https://github.com/hackingmaterials/amset)
* [BAPT](https://github.com/utf/bapt)
* [ElectronicLatticeMatch](https://github.com/keeeto/ElectronicLatticeMatch)

* [AMSET](https://github.com/hackingmaterials/amset)
* [BAPT](https://github.com/utf/bapt)
* [BoltzTraP2](https://github.com/simonrh/boltztrap2)
* [Critic2](https://github.com/aoterodelaroza/critic2)
* [ElectronicLatticeMatch](https://github.com/keeeto/ElectronicLatticeMatch)
* [Galore](https://github.com/SMTG-UCL/galore)
* [iFermi](https://github.com/fermisurfaces/IFermi)
* [iFermi](https://github.com/fermisurfaces/IFermi)
* [kgrid](https://github.com/WMD-group/kgrid)
* [Lobster](http://www.cohp.de) and [LobsterPy](https://github.com/JaGeo/LobsterPy/tree/main)
* [Lobster](http://www.cohp.de) and [LobsterPy](https://github.com/JaGeo/LobsterPy)
* [Macrodensity](https://github.com/WMD-group/MacroDensity)
* [Packmol](https://m3g.github.io/packmol/)
* [SetupKpoints](https://github.com/keeeto/SetupKpoints)
* [PyProcar](https://github.com/romerogroup/pyprocar)
* [SetupKpoints](https://github.com/keeeto/SetupKpoints)
* [Sumo](https://github.com/SMTG-UCL/sumo)
* [Surfaxe](https://github.com/SMTG-UCL/surfaxe)
* [vaspup2.0](https://github.com/kavanase/vaspup2.0)
* [VASP-Examples](https://github.com/JMSkelton/VASP-Examples)
* [VASPpy](https://github.com/bjmorgan/vasppy)
* [VASPsol](https://github.com/henniggroup/VASPsol)
* [Z2Pack](http://z2pack.ethz.ch)

# Solar Energy
* [Perovskite crystal structures](https://github.com/WMD-group/hybrid-perovskites), [Disordered](https://github.com/jarvist/Disordered-MAPI-Phonons)
* [Driftfusion](https://github.com/barnesgroupICL/Driftfusion)
* [Eris](https://github.com/WMD-group/Eris)
* [vaspup2.0](https://github.com/kavanase/vaspup2.0)
* [VASP-Examples](https://github.com/JMSkelton/VASP-Examples)
* [VASPpy](https://github.com/bjmorgan/vasppy)
* [VASPsol](https://github.com/henniggroup/VASPsol)
* [Wannier90](http://www.wannier.org)
* [Z2Pack](http://z2pack.ethz.ch)

# Solar Energy

* [Driftfusion](https://github.com/barnesgroupICL/Driftfusion)
* [Eris](https://github.com/WMD-group/Eris)
* [Perovskite crystal structures](https://github.com/WMD-group/hybrid-perovskites), [Disordered](https://github.com/jarvist/Disordered-MAPI-Phonons)
* [PVlib](https://pvlib-python.readthedocs.io)
* [Solcore5](https://github.com/dalonsoa/solcore5)
* [Starrynight](https://github.com/WMD-group/StarryNight)
* [Solcore5](https://github.com/dalonsoa/solcore5)

# Phonons
* [Alamode](https://alamode.readthedocs.io)
* [Phonopy](https://atztogo.github.io/phonopy), [Phono3py](https://atztogo.github.io/phono3py)

* [Alamode](https://alamode.readthedocs.io)
* [Phonopy](https://atztogo.github.io/phonopy), [Phono3py](https://atztogo.github.io/phono3py)
* [TDEP](https://github.com/tdep-developers/tdep)

#### Processing Tools

* [ELATE](http://progs.coudert.name/elate)
* [IR and Raman spectra](https://github.com/JMSkelton/Phonopy-Spectroscopy)
* [Julia-Phonons](https://github.com/jarvist/Julia-Phonons)
* [IR and Raman spectra](https://github.com/JMSkelton/Phonopy-Spectroscopy)
* [Julia-Phonons](https://github.com/jarvist/Julia-Phonons)
* [Modemap](https://github.com/JMSkelton/ModeMap)
* [Phono3py-Power-Tools](https://github.com/skelton-group/Phono3py-Power-Tools)
* [PolaronMobility](https://github.com/jarvist/PolaronMobility.jl)
* [RVO](https://github.com/WMD-group/rvo)
* [Phono3py-Power-Tools](https://github.com/skelton-group/Phono3py-Power-Tools)
* [PolaronMobility](https://github.com/jarvist/PolaronMobility.jl)
* [RVO](https://github.com/WMD-group/rvo)

#### Animations

* [ASCII phonons](https://github.com/ajjackson/ascii-phonons)
* [Molecular crystal phonons](https://github.com/JMSkelton/MolecularCrystalPhononAnimation)
* [Phonon website](http://henriquemiranda.github.io/phononwebsite/phonon.html)
* [Phonon website](http://henriquemiranda.github.io/phononwebsite/phonon.html)

#### Datasets
* [Phonondb](https://github.com/atztogo/phonondb)

* [Phonondb](https://github.com/atztogo/phonondb)
* [Our Phonons](https://github.com/WMD-group/Phonons)
* [Phonon website](http://henriquemiranda.github.io/phononwebsite/phonon.html)
* [Phonon website](http://henriquemiranda.github.io/phononwebsite/phonon.html)

# Alloys and Solid Solutions
* [ATAT](https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/)
* [CASM](https://github.com/prisms-center/CASMcode)
* [icet](https://icet.materialsmodeling.org)
* [Transformer](https://github.com/JMSkelton/Transformer)
* [SOD](https://github.com/Grau-CrespoGroup/sod)
# Alloys and Solid Solutions

* [ATAT](https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/)
* [CASM](https://github.com/prisms-center/CASMcode)
* [icet](https://icet.materialsmodeling.org)
* [Transformer](https://github.com/JMSkelton/Transformer)
* [SOD](https://github.com/Grau-CrespoGroup/sod)

# Point Defects
* [CPLAP](https://github.com/jbuckeridge/cplap)
* [Doped](https://github.com/SMTG-UCL/doped)

* [CPLAP](https://github.com/jbuckeridge/cplap)
* [Doped](https://github.com/SMTG-UCL/doped) and [ShakeNBreak](https://github.com/SMTG-Bham/ShakeNBreak)
* [PyCDT](https://github.com/mbkumar/pycdt)
* [PyDefect](https://github.com/kumagai-group/pydefect)
* [PyLada](https://github.com/pylada/pylada-defects)
* [SC-FERMI](https://github.com/jbuckeridge/sc-fermi), [PY-SC-FERMI](https://github.com/bjmorgan/py-sc-fermi)
* [sxdefectalign](https://sxrepo.mpie.de/projects/sphinx-add-ons/files?sort=filename)
* [SC-FERMI](https://github.com/jbuckeridge/sc-fermi) and [PY-SC-FERMI](https://github.com/bjmorgan/py-sc-fermi)
* [sxdefectalign](https://sxrepo.mpie.de/projects/sphinx-add-ons/files?sort=filename)

# Python and Friends
* [Awesome Python Chemistry](https://github.com/lmmentel/awesome-python-chemistry)
* [Datacamp](https://www.datacamp.com)
* [DFT-Book](http://kitchingroup.cheme.cmu.edu/dft-book/dft.html)
* [Julia](https://julialang.org)
* [Jupyter Lab](https://jupyter.org)

* [Awesome Python Chemistry](https://github.com/lmmentel/awesome-python-chemistry)
* [Datacamp](https://www.datacamp.com)
* [DFT-Book](http://kitchingroup.cheme.cmu.edu/dft-book/dft.html)
* [Julia](https://julialang.org)
* [Jupyter Lab](https://jupyter.org)
* [Visual Studio Code](https://code.visualstudio.com)

# Publication Tools
* [doi2bib](http://www.doi2bib.org)
* [ffmpeg](https://www.ffmpeg.org)
* [imagemagik](https://www.imagemagick.org)
* [mhchem](https://ctan.org/pkg/mhchem?lang=en)

* [doi2bib](http://www.doi2bib.org)
* [ffmpeg](https://www.ffmpeg.org)
* [ImageMagick](https://www.imagemagick.org)
* [mhchem](https://ctan.org/pkg/mhchem?lang=en)
* [Overleaf](https://www.overleaf.com)
* [Zotero](https://www.zotero.org)

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