[[https://storion.ru/|Back to Storion]] ====== Storion Lab knowledgebase ====== ===== Our Resources ===== ==== Internal Lab Resources ==== - [[res:magnus|Magnus cluster]] [[http://cest-cms-wiki.skoltech.ru/doku.php?id=start|Wiki]] - [[res:raz|Razor workstations]] - [[http://10.16.77.5:8005|Jupyter Notebook server]] - [[http://10.16.77.5|Apache Web-server]] - [[http://10.16.77.6:7113|Synology data storage]] - [[tbd|Windows 7 server]] - [[res:vpn|Our vpn server in Amsterdam]] /*=== Manuals === [[man:vpn|Connection to our vpn]]*/ ==== Internal Skoltech Resources ==== - [[res:arcuda|Arcuda]] - Pardus ==== Getting started ===== - [[start:term|Getting started with cluster]] - [[start:vasp|Getting started with VASP using terminal]] - [[start:siman|Getting started with SIMAN]] ===== Software ===== ==== Our Developed software ==== * [[soft:matsolver|Matsolver (Wiki)]] * [[soft:siman|SIMAN (Wiki)]] (a set of Python tools for high-througput DFT calculations and their analysis) * [[soft:gb|GB]] (C++ tool for construction of grain boundaries in metals) * [[soft:diffraction|Diffraction]] (C++ and Fortran tool for constructing theorectical electronogramms of crystal structures) === Friendly software === * [[https://github.com/dembart/BVlain|BVlain]]. Python tool for making bond valence analysis in crystal structures and determine percolation barriers of ionic conduction * [[https://github.com/dembart/ions|Ions]]. Python library made for studying percolation in ionic crystals === Other software === * [[https://atomsk.univ-lille.fr/doc/en/index.html| Atomsk ]] - a set of tools for structure manipulation useful in DFT calculations * [[https://github.com/zorkzou/UniMoVib| UniMoVib ]] A unified interface for molecular harmonic vibrational frequency calculations. (Vibrational analysis, partial hessian) ==== Simulation ==== * [[soft:vasp|VASP]] * [[soft:lammps|LAMMPS]] * [[https://engineering.purdue.edu/gekcogrp/software-projects/nemo5/|NEMO5 - electronic transport]] * [[soft:Gaussian|Gaussian]] * [[soft:Orca|Orca]] * [[https://www.quanty.org/documentation/tutorials/small_programs_a_quick_start/start| quanty]] - learn QM ==== Visualization ==== * [[vsoft:jmol|Jmol]] * [[vsoft:vesta|VESTA]] * [[vsoft:ovito|OVITO]] * [[vsoft:avogadro|Avogadro]] ===== Theory ===== * [[theory:dft|Density functional theory]] * [[theory:hubbard|Hubbard correction]] * [[theory:elastic|Elastic constants]] * [[theory:surface|Surface energies]] * [[theory:SOC|SOC]] * [[theory:TM|Transition metal oxides: Hubbard model, Jahn Teller, Spin-orbit coupling]] * [[theory:phonos|Phonons]] * [[theory:Liion|Li-ion Descriptors]] ===== Linux ===== ==== General ==== * [[linux:pdf|Working with pdf]] * [[linux:pdf|Working with text]] ==== Workload managers ==== * [[linux:slurm|SLURM]] * [[linux:torque|Torque]] ===== Python ===== * [[python:plt| Matplotlib]] * [[https://mendeleev.readthedocs.io/en/stable/index.html|Mendeleev table python]] * [[python:jupyter|How to setup Jupyter Notebook on Ubuntu]] ===== Github ===== * [[https://docs.google.com/document/d/155gRIQoltwF2VRnZPRgijCggj6VwbNH1nk3NM4RQ5dg/edit#heading=h.sm6fr4wlsxma|Our github help]] ===== Tutorials ===== * [[tut:void_vol|How to calculate the volume of a void]] * [[tut:pd|How to construct a phase diagram]] * [[tut:interface|How to create a supercell with interface]] * [[tut:gb|How to create a grain boundary]] * [[tut:pcm|How to perform a calculation with implicit solvent]] ===== Useful services ===== ==== Databases ==== * [[https://materialsproject.org/|MaterialsProject]] * [[http://crystalium.materialsvirtuallab.org/|Crystalium]] An Exploration of the Grain Boundaries, Surfaces, and Wulff shapes of the Elements by materialsvirtuallab * [[https://bg.imet-db.ru/Subst_Res.asp|Bandgap - Database on forbidden zones of solids]] * [[https://github.com/QingyangDong-qd220/BandgapDatabase1|Bandgap database]] Tools for extracting bandgap information from scientific documents and generating a database using ChemDataExtractor. * [[http://abulafia.mt.ic.ac.uk/shannon/ptable.php|Shannon radii]] * [[https://sites.google.com/site/zrftum/home/l/physical-properties/cohesive-energy-of-elements|Cohesive energy of elements]] * [[http://atomistry.com/|Energetic properties of elements]] * [[https://www.cryst.ehu.es/|Bilbao Crystallographic Server]] * [[https://paulingfile.com/|Pauling file]] phase diagrams + crystal structures + physical properties together in the world largest database for inorganic compounds * [[https://www.oqmd.org/|The Open Quantum Materials Database (OQMD)]] - The OQMD is a database of DFT calculated thermodynamic and structural properties of 1,022,603 materials, created in Chris Wolverton's group at Northwestern University. ==== Communities ==== * https://matsci.org/ ==== Calculators ==== * [[https://www.colby.edu/chemistry/PChem/Hartree.html|Energy Units Converter]] * [[https://www.iap.tuwien.ac.at/www/surface/chemical_potentials|Chemical potential calculator]] * [[https://ssd.phys.strath.ac.uk/resources/crystallography/crystallographic-direction-calculator/|Crystallographic calculator]] ==== Working with image ==== * Increase quality of image using Deep Convolutional Neural Networks [[https://waifu2x.udp.jp/index.ru.html|waifu2x]] * Get points from graph[[https://apps.automeris.io/wpd/|WebPlotDigitizer App]] [[https://automeris.io/WebPlotDigitizer/|Project Webpage]] * Get wonderfull colors for your plot[[https://coolors.co/|Pallete generator]] * Convert color format[[https://coding.tools/rgba-to-hex|RGBA2HEX]] ==== Glossary ==== * [[https://cccbdb.nist.gov/glossary.asp#6-31G|Glossary of Common Terms and Abbreviations in Quantum Chemistry]] ==== Telegram ==== * [[https://t.me/+FUtZHZ_xka8wMDMy|Sci Journal Club]] - Community in Telegram for sharing sci papers (write DOI - someone who has access send you a pdf) ==== Recommended textbooks ==== // **Li-ion batteries:**// - Handbook of Battery Materials, Edited by Claus Daniel and Jürgen O. Besenhard - Lithium Batteries Science and Technology. Edited by Gholam-Abbas Nazri, Gianfranco Pistoia ==== Recommended overviews ==== // **Battery topics:**// - Aksyonov, D. A., Boev, A. O., Fedotov, S. S., & Abakumov, A. M. (2023). Computational insights into ionic conductivity of transition metal electrode materials for metal-ion batteries-A review. Solid State Ionics, 393, 116170. - Aksyonov, D. A., & Nikitina, V. A. (2021). Charge transfer through interfaces in metal-ion intercalation systems. ==== English Communication for Scientists ==== https://www.nature.com/scitable/ebooks/english-communication-for-scientists-14053993/contents/ ==== Modeling groups in the world ==== Karsten Albe https://www.mawi.tu-darmstadt.de/mm/home_mm/index.en.jsp Shyue Ping Ong https://materialsvirtuallab.org/ Ceder https://ceder.berkeley.edu/ Persson https://perssongroup.lbl.gov/ Oganov https://uspex-team.org/en Anubhav Jain https://hackingmaterials.lbl.gov/