From 0652052ef33cf4c4974215816dd1a3d38df5d7cd Mon Sep 17 00:00:00 2001 From: Aron Walsh Date: Sun, 14 Jul 2024 22:06:47 +0100 Subject: [PATCH] Update codes.markdown Tidy up --- codes.markdown | 196 ++++++++++++++++++++++++++++++------------------- 1 file changed, 119 insertions(+), 77 deletions(-) diff --git a/codes.markdown b/codes.markdown index 0f75bbf..038a5cc 100644 --- a/codes.markdown +++ b/codes.markdown @@ -7,157 +7,199 @@ permalink: /codes/ 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)