Núria López and Group

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New members start here

• 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)

• 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 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: 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) [pdf] [ppt]

• How to do Born-Oppenheimer Molecular Dynamics in VASP (by Rodrigo)

• Managing large reaction networks (by Rodrigo)

• How to calculate the C6 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 [1]

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

• If the results are from the "OHPERA" project: ref. 01071010-OHPERA or the "SUPERVAL" project: Ref. 101115456

• If the results (or the money) are from the AGAUR - SGR project: XXXXXXX and EDISON project: Ref. 2023 CLIMA 00105

Physical Properties

Inorganic Crystal Structure Database – ICSD

• Cohesive Energies:

Cohesive Energies data in a pdf document: [2]

• Platinum Group Metals properties

Lots of data on metals and alloys: [3] [4]

• Crystal structures:

Wyckoff's Crystal Structures, vol. 1 [5]

Crystal Lattice-structures: [6]

American Mineralogist Crystal Structure Database: [7]

Crystal lattice prototypes [8]

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: [9]

• Energy Conversion

Add it to your bookmarks!: [10]

[11](Only corrected to one decimal place!)

• SciHub --- banned by ICIQ as from February 2023

To «read» those papers to which we have no access: [12] The rest are not working: [13][14][15][16]

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: [17] [18]

• Overleaf Licence

Ask someone in the group for access.

Useful Readings

List of very useful papers

• Fundamentals of Plane Wave calculations: [19]

• Test on functionals: [20]

• CI-NEB: [21]

• d-band model: [22]

• Ab initio thermodynamics: [23] [24]-broken [25]

• Universality and related concepts: [26]-broken [27]-broken [28]

• Linear-scaling relationships: [29] [30]-broken

• Bronsted-Evans-Polanyi relationships: [31]

• Sabatier contour plots: [32]-broken

• Bayesian: [33]-broken

• Concepts of Modern Catalysis And Kinetics: [34]-broken

• Computational scaling [35]

• New functional [36]

• Ten Tips for Capturing Figures with Captions: [37]

• Advances in Density-Functional Calculations for Materials Modeling: [38]

• So You Want to Be a Research Scientist: [39]

• The role of computational results databases in accelerating the discovery of catalysts: [40]

• The care and maintenance of your adviser: [41]

• Tips for structuring your papers: [42] [43] [44]

• The 11-step guide to running effective meetings: [45]

• Best practices in machine learning for chemistry: [46]

Videos

• Dr. Eng Lim Goh presents: Prediction - Use Science or History? [47]

• Interesting video on scientific writing: [48]

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 @TheorHetCatICIQ

• ioChem-BD Twitter: @ioChem_BD

• LinkedIn (managed by Núria V.) https://www.linkedin.com/in/computational-groups-iciq-09936661/