Núria López and Group
go back to Main Page, Group Pages, Scripts_for_VASP, VASP_beginners
New members start here[edit]
- 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[edit]
Calculations with VASP[edit]
AI has entered the field of computational chemistry. VASP will die very soon ehehehehe.
- VASP has four input files: INCAR, POSCAR, KPOINTS, and POTCAR. Follow the links to learn the set-up.
- Hybrid functionals (by Franziska)
- 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[edit]
- 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[edit]
- Scripts for CPMD (Car-Parinello Molecular Dynamics) (by Bob)
Procedures[edit]
- 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
- Painting excel cells according to their values [1]
Acknowledgements in your papers, presentations (slides) and posters[edit]
- 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 .jpg)
- 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[edit]
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[edit]
- 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[edit]
List of very useful papers
- Fundamentals of Plane Wave calculations: [19]
- Test on functionals: [20]
- CI-NEB: [21]
- d-band model: [22]
- 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]
- 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[edit]
Policy on Business Travels (conferences, etc.)
Settlement of expenses at ICIQ- 2019
Social Media[edit]
- Twitter @TheorHetCatICIQ
- ioChem-BD Twitter: @ioChem_BD
- LinkedIn (managed by Núria V.) https://www.linkedin.com/in/computational-groups-iciq-09936661/