Nano Electrochemistry Group
(Redirected from NanoElectroChemistryGroup)
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [1].
Compiling Codes and Running Calculations on a HPC cluster
How to run on ARCHER 2
- by Songyuan
Imperial CX1: Instructions and basic concepts of parallel computing
- by Huanyu
- A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.
- by Huanyu
- About shared software hosted on RDS CMSG (For CMSG group members).
Compile CP2Kv9.1 on Imperial CX1
- by Margherita
Modelling and Visualising Materials
Modelling of Interfaces and Adsorption processes
Building structures with Pymatgen
- by Fei
- Tutorial for generating crystal structure and surface with Python.
ASE and materials modelling
- Currently left blank
Adsorption of molecule on surfaces
- by Paolo
- Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.
Error Evaluation during Simulations
CP2K: Optimizing parameters for metallic surfaces
- by Margherita
- Contents:
- Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and k-points grid;
- Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
- System: metallic surfaces (Platinum slab used as example);
- Computational package: CP2K.
CP2K: Simulation of Hard Carbons
- by Luke
- Tutorial for the simulation of hard carbon?
CRYSTAL: Convergence tests of critical parameters
- by Huanyu
- Tutorial for optimising simulation parameters using the DFT code CRYSTAL (LCAO-GTO basis set).
Quantum Espresso: Simulation of Memristors
- by Felix
- Tutorial for optimising simulation parameters using the DFT code QuantumEspresso (plane waves basis set). The simulated system is a ZnO surface.
Postprocessing
Analysing AIMD runs with MATLAB in-house suit
- by Rashid
Surface analysis
- by Songyuan
Calculation of radial average
- Kalman
- Tutorial for calculating the radial average ?.
Machine Learning Potentials
Building ML potentials with AML
- by Anthony
- Tutorial for building ML potentials with AML.
Activation Barriers
NEB Calculation
- Currently left blank
Metadynamics with Lammps and plumed
- by Frederik
- Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.
Methodologic developments
Potential control and current induced forces using CP2K+SMEAGOL
- by Chris
- Contents:
- How to run CP2K+SMEAGOL and SIESTA+SMEAGOL calculations
- How to exploit SMEAGOL parallelism
- System: Au nanojunctions
- Computational package: CP2K, SIESTA, SMEAGOL.
Converging magnetic systems in CP2K
- by Chris
- Contents:
- MULTIPLICITY keyword to calculate magnetic systems
- &BS section and MAGNETIZATION keyword to improve convergence
- System: Metallic bulk Ni and slab in vacuum
- Computational package: CP2K.
Running a HP-DFT calculation with CP2K
- by Margherita
- A tutorial to run a HP-DFT calculation using CP2K
Solving 1D Poisson equation
- by Remi Khatib
- Tutorial for the solution of the 1D Poisson equations given a distribution of point charges
Tutorials
Dimers in gas phase
- by Fredrik
- Tutorial for optimising dimers in the gas phase using Gaussian.
Trends in catalytic Activity
- by Clotilde Cucinotta
- Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.
Others
Becoming an Efficient Research Scientist
Writing a Project Proposal
Computational Tools
CP2K
- CP2K TUTORIAL;
- Download and install CP2K ;
- Manual;
- Useful HOWTOs;
- Reading inputs and outputs (commented files and examples);
QUANTUM ESPRESSO
- Download and install QUANTUM ESPRESSO;
- Useful Tutorials;
- Reading inputs and outputs (commented files and examples);
LAMMPS
CRYSTAL
- CRYSTAL Tutorial Project
- CRYSTAL basis set database - Paramaterised and tested for solid state calculations
- Basis Set Exchange - Note that this site usually contains very diffuse basis sets for quantum chemmistry, which might cause problems for solid state calculations.
- Mike Towler's basis set - Parameterised around early 2000s
- CRYSPLOT - A web-based visualisation tool
- CRYSTALpytools - A python-based toolbox for CRYSTAL inputs and outputs.
More information is available in CRYSTAL23 official site.