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go back to [[Main Page]], [[Group Pages]], [[Scripts_for_VASP]], [[VASP_beginners]] =New members start here= * '''[[VASP beginners|Checklist for VASP beginners]]''' (''by Federico and Rodrigo'') * '''[[Your first project]]''' (''by Rodrigo and Federico'') * '''[[Linux for beginners]]''' (''in prep'' but, meanwhile, Núria V. has books in PDF) * '''[[Steps in case tekla2 fails]]''' (''by S. Morandi'') * '''[[The Morandi-Loveday method]]''' (''Oliver Rosca'') =Calculations= ==Calculations with VASP== AI has entered the field of computational chemistry. VASP will die very soon ehehehehe. * '''[[Scripts for VASP]]''' * VASP has four input files: '''[[INCAR]]''', '''POSCAR''', '''[[KPOINTS]]''', and '''[[POTCAR]]'''. Follow the links to learn the set-up. * '''[[Hybrid functionals]]''' (''by Franziska'') * '''[[INCAR#DFT+U|DFT+U]]'''. Also see [[DFT+U]] (''by Max''). * How to perform a calculation using the [[VASP-MGCM (solvation module)]] (''by Miquel and Yecheng'') * '''[[STM calculation with VASP]]''' (''by Bob'') ==Calculations with Quantum Espresso== * [[Scripts for QE]] (''by Bob'') * [[Hybrid_functionals#Quantum_Espresso|Hybrid functionals in Quantum Espresso]] (''by Franziska'') * '''[[Self-consistent U determination]]''' by linear response approach (''by Franziska, in edition'') ==Calculations with CPMD== * [[Scripts for CPMD]] (Car-Parinello Molecular Dynamics) (''by Bob'') =Procedures= * How to [[Mount_MareNostrum_folders]] in your local computers. (''by Qiang and Rodrigo'') * How to simulate [[XPS]]. (''by Nathan, Rodrigo, Javier, and Edvin'') * How to simulate an [[EXAFS]]. (''by Edvin and Rodrigo'') * How to prepare a [[Microkinetic model]]. (''by Rodrigo, Albert, and Santiago'') * How to do a [[Kinetic Monte Carlo]] (KMC). (''by Albert'') * How to use the [[Bayesian Machine Scientist]] (BMS). (''by Sergio'') * How to do a [[Principal Component Analysis]] (PCA) in Python and Maple. (''by Jordi'') * How to find the lattice parameter with the [[Birch-Murnaghan fitting]] procedure (''by Franziska'') * How to find the proper POTIM for a [[IBRION=3 bulk optimization]] (''by Federico'') * How to construct a Surface from a Bulk with [[Materials Studio]]: [[Database bulk to surface builder | bulk-surface]] * How to make easily a Nudged Elastic Band Method ([[NEB]]). * How to 1. find the transition state using ''Improved Dimer Method'' (IDM) and 2. sample the path with ''Intrinsic Reaction Coordinate'' (IRC) [http://aliga.iciq.es/wiki/index.php/Image:2011-03-30-IDM-IRC.pdf [pdf]] [http://aliga.iciq.es/wiki/index.php/Image:2011-03-30-IDM-IRC.tgz [ppt]] * How to do [[INCAR#Ab-Initio_Molecular_Dynamics|Born-Oppenheimer Molecular Dynamics in VASP]] (''by Rodrigo'') * [[Managing large reaction networks]] (''by Rodrigo'') * How to calculate the [[C6 parameters|''C''6 parameters]] for Metals fcc and hcp (''by Neyvis'') * How to plot the [[molecular electrostatic potential]] (MEP) using VMD. * How to make a [[Pourbaix diagram]], code attached (''by Yecheng'') * How to calculate [[workfunctions]] (''by Nathan and Franziska'') * [[Tips to work remotely from Windows]] (''by Diego'') * [[Command line rendering of chemical structures in Blender]] (by ''Albert'' and ''Edvin'') * Sharing Latex projects on [[Overleaf]] (by ''Franziska'') * Using [[bibtex]] in Latex. * How to write a [[reply to reviewers]]. * Selecting [[Colour codes]] * [[Creating a booklet]] * Painting excel cells according to their values [http://aliga.iciq.es/wiki/index.php/Image:Gerard.pdf] =Acknowledgements in your papers, presentations (slides) and posters= * If the results are from the "Ministerio" project or your salary is funded by them: PID2024-157556OB-I00 “Artificial Intelligence for the Simulation of Materials in Energy (ANIMATE)” -------- also for posters! You also need to add a logo to your posters [[Image:MICIU EU+AEI (nou PID 2025 NL).jpg]] * If the results are from the "OHPERA" project: ref. 01071010-OHPERA or the "SUPERVAL" project: Ref. 101115456 [[Image: EU-OHPERA&SUPERVAL.png]] * If the results (or the money) are from the AGAUR - SGR project: XXXXXXX and EDISON project: Ref. 2023 CLIMA 00105 [[Image: AGAUR.png]] =Physical Properties= Inorganic Crystal Structure Database – [[ICSD]] *'''Cohesive Energies:''' Cohesive Energies data in a pdf document: [http://aliga.iciq.es/wiki/index.php/Image:Cohesive_Energies.pdf] *''' Platinum Group Metals properties ''' Lots of data on metals and alloys: [http://www.platinummetalsreview.com/jmpgm/index.jsp] [http://www.crct.polymtl.ca/FACT/documentation/SGTE/SGTE_Figs.htm] *'''Crystal structures:''' Wyckoff's Crystal Structures, vol. 1 [http://aliga.iciq.es/wiki/index.php/Image:CrystalStructures_Wyckoff_vol1.pdf] Crystal Lattice-structures: [http://cst-www.nrl.navy.mil/lattice/] American Mineralogist Crystal Structure Database: [http://rruff.geo.arizona.edu/AMS/amcsd.php] Crystal lattice prototypes [http://cst-www.nrl.navy.mil/lattice/] [[Rutile]] related structures *''' Own database on Crystal structures:''' Calculated [[Cell parameters]] for some transition and noble metals. Calculated [[Cell parameters rutile-anatase]] for some rutile and anatase structures. =Tools= *'''MatWeb Conversions''' A useful unit converter: [http://www.matweb.com/tools/conversion.asp] *'''Energy Conversion''' Add it to your bookmarks!: [http://wild.life.nctu.edu.tw/class/common/energy-unit-conv-table.html] [http://www.colby.edu/chemistry/PChem/Hartree.html](Only corrected to one decimal place!) *'''SciHub''' --- banned by ICIQ as from February 2023 To «read» those papers to which we have no access: [http://sci-hub.tw/] The rest are not working: [http://80.82.77.83/][https://sci-hub.la/][https://sci-hub.hk/][https://sci-hub.tv/] It currently works only when accessed via a Russian-based proxy server, otherwise you'll see "temporarily closed. download archived papers at libgen.org" message *'''Electronic book database''' To download technical books and print them for your personal use: [http://gen.lib.rus.ec/] [http://en.bookfi.org/] *'''Overleaf Licence''' Ask someone in the group for access. =Useful Readings= ''' List of very useful papers ''' * Fundamentals of Plane Wave calculations: [http://prola.aps.org/abstract/RMP/v64/i4/p1045_1 ] * Test on functionals: [http://prola.aps.org/abstract/PRB/v59/i11/p7413_1] * CI-NEB: [http://theory.cm.utexas.edu/vtsttools/neb.html#climbing-image] * d-band model: [http://prola.aps.org/abstract/PRL/v76/i12/p2141_1] * Ab initio thermodynamics: [http://prl.aps.org/abstract/PRL/v84/i16/p3650_1] [http://sfx.urv.cat/urv/cgi/core/sfxresolver.cgi?tmp_ctx_svc_id=1&tmp_ctx_obj_id=1&service_id=1000000000000460&request_id=624284&rft.year=2003&rft.volume=118&rft.issue=24&rft.spage=11179]-broken [http://prb.aps.org/abstract/PRB/v67/i8/e085410] * Universality and related concepts: [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHJ-4C4BK02-2&_user=1517337&_coverDate=05%2F15%2F2004&_alid=685117810&_rdoc=8&_fmt=full&_orig=search&_cdi=6852&_sort=d&_docanchor=&view=c&_ct=29&_acct=C000053456&_version=1&_urlVersion=0&_userid=1517337&md5=18bed248f00f637918096b4132a79e66]-broken [http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PRLTAO000099000001016105000001&idtype=cvips]-broken [http://pubs.acs.org/cgi-bin/article.cgi/jacsat/2001/123/i34/pdf/ja010963d.pdf] * Linear-scaling relationships: [http://prl.aps.org/abstract/PRL/v99/i1/e016105] [http://www3.interscience.wiley.com/journal/119163499/abstract]-broken * Bronsted-Evans-Polanyi relationships: [http://www.sciencedirect.com/science/article/pii/S0021951704001010] * Sabatier contour plots: [http://www3.interscience.wiley.com/journal/119230116/abstract]-broken * Bayesian: [http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PRLTAO000095000021216401000001&idtype=cvips]-broken * Concepts of Modern Catalysis And Kinetics: [http://www.catalysis.nl/kica/]-broken * Computational scaling [http://aliga.iciq.es/wiki/index.php/Image:Computational_scaling.pdf] * New functional [http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.2535.html] * Ten Tips for Capturing Figures with Captions: [https://pubs.acs.org/doi/10.1021/acsenergylett.9b00253] * Advances in Density-Functional Calculations for Materials Modeling: [https://www-annualreviews-org.sabidi.urv.cat/doi/pdf/10.1146/annurev-matsci-070218-010143] * So You Want to Be a Research Scientist: [https://medium.com/s/story/so-you-want-to-be-a-research-scientist-363c075d3d4c] * The role of computational results databases in accelerating the discovery of catalysts: [https://www.nature.com/articles/s41929-018-0176-4.epdf?author_access_token=wd9p--hqh5AzTjOTKdU05NRgN0jAjWel9jnR3ZoTv0MxBw5NFQv3CUqFzx3nWubbwoq1x1G7DGlpNykdKUr52Omeo9H_4bsIEuGYkxJ8x6H6fKk6h1K1ocfTfqklwcmO17pBTQc1E9VF6hqlyT0b8w%3D%3D] * The care and maintenance of your adviser: [https://www.nature.com/naturejobs/2011/110127/pdf/nj7331-570a.pdf?utm_content=buffer62a8a&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer&foxtrotcallback=true&error=cookies_not_supported&code=7874ce4c-7164-42c3-a08c-07354598c102] * Tips for structuring your papers: [https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005619&type=printable] [https://acsoncampus.acs.org/wp-content/uploads/2017/11/manuscript-tips-poster-newlogo-FINAL.pdf?utm_source=Twitter&utm_medium=Social&utm_campaign=Campus&hootPostID=e5b2f8b828ada54ef8db7fa8954eda0f] [https://threadreaderapp.com/thread/1111773593656918016.html] * The 11-step guide to running effective meetings: [https://www.nature.com/articles/d41586-019-02295-z?utm_source=twt_nnc&utm_medium=social&utm_campaign=naturenews&sf216635458=1] * Best practices in machine learning for chemistry: [https://www.nature.com/articles/s41557-021-00716-z] '''Videos''' * Dr. Eng Lim Goh presents: Prediction - Use Science or History? [https://www.youtube.com/watch?v=qbqfEocsvkI&feature=youtu.be] * Interesting video on scientific writing: [https://www.ibiology.org/professional-development/making-scientific-writing-painless/] ''' Thesis Submission''' * Things to keep in mind when you prepare your [[PhD Thesis]] * For when you cannot decide where to go to lunch [[lunch_rand]] '''Presentations''' [[Talks and Posters]] from group members =(Old) Group Guidelines= [[Who's in charge of what]] [[Know-how in the group]] [[Policy on Business Travels (conferences, etc.)]] [[Settlement of expenses at ICIQ- 2019]] =Social Media= * [[Photos (people, cluster etc)]] * Twitter [https://twitter.com/theorhetcaticiq @TheorHetCatICIQ] * ioChem-BD Twitter: [https://twitter.com/ioChem_BD @ioChem_BD] * LinkedIn (managed by Núria V.) https://www.linkedin.com/in/computational-groups-iciq-09936661/
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