ChemWiki - User contributions [en]

Nano Electrochemistry Group

2023-09-28T14:33:42Z

Rea19:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
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 [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| 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.

===[[Run CRYSTALs on Imperial CX1]]===
Written by:[[Contributors| Huanyu ]]

Intructions on how to submit a CRYSTAL job on CX1

===[[Compile CP2Kv9.1 on Imperial CX1]]===
Written by:[[Contributors| Margherita ]]

==Reaction Dynamics==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Transport calculations using SMEAGOL]]===
Written by:[[Contributors| 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]]===
Written by:[[Contributors| 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.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| 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.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

written by [[Contributors| Clotilde Cucinotta]]

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

===[[Analysing AIMD runs with MATLAB in-house suit|Analysing AIMD runs with MATLAB in-house suit]]===
Written by:[[Contributors| Rashid ]]

Tutorial for generating crystal structure and surface with Python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==General DFT tutorials==
===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Machine Learning Potentials==

===[[Building ML potentials with AML|Building ML potentials with AML]]===
Written by:[[Contributors#Anthony| Anthony]]

Tutorial for building ML potentials with AML.
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

== Becoming an Efficient Research Scientist ==

===[[Writing a Project Proposal]]===
Written by:[[Contributors| Nicholas Harrison ]]

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.html CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis_sets.html CRYSTAL basis set database] - Paramaterised and tested for solid state calculations
* [https://www.basissetexchange.org/ Basis Set Exchange] - Note that this site usually contains very diffuse basis sets for quantum chemmistry, which might cause problems for solid state calculations.
* [https://vallico.net/mike_towler/crystal.html Mike Towler's basis set] - Parameterised around early 2000s
* [https://crysplot.crystalsolutions.eu/ CRYSPLOT] - A web-based visualisation tool
* [https://gitlab.com/bmgcsc/dl-visualize-v3 DLV3] - A visualisation tool
* [https://crystal-code-tools.github.io/CRYSTALpytools/ CRYSTALpytools] - A python-based toolbox for CRYSTAL inputs and outputs.
More information is available in [https://www.crystal.unito.it/documentation.html CRYSTAL23 official site].

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Analysing AIMD runs with MATLAB in-house suit

2023-09-28T14:33:27Z

Rea19: Created page with "https://gitlab.doc.ic.ac.uk/rgc/ccg_molsimanalysis"

https://gitlab.doc.ic.ac.uk/rgc/ccg_molsimanalysis

Nano Electrochemistry Group

2023-01-23T21:26:23Z

Rea19: /* Reaction Dynamics */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
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 [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| 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.

==Reaction Dynamics==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| 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.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| 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.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

===[[Analysing AIMD runs with MATLAB in-house suit]]===
Written by:[[Contributors| Rashid ]]

Tutorial for generating crystal structure and surface with Python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/CRYSTALpy CRYSTALpy: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2023-01-23T21:25:49Z

Rea19: /* Reaction Dynamics */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
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 [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| 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.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| 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.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| 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.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

===[[Analysing AIMD runs with MATLAB in-house suit]]===
Written by:[[Contributors| Rashid ]]

Tutorial for generating crystal structure and surface with Python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/CRYSTALpy CRYSTALpy: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2023-01-23T21:24:52Z

Rea19: /* Reaction Dynamics */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
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 [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| 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.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| 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.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| 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.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

===[[Analysing AIMD runs with MATLAB in-house suit]]===
Written by:[[Contributors| Rashid ]]

Tutorial for generating crystal structure and surface with Python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/CRYSTALpy CRYSTALpy: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Contributors

2023-01-23T21:17:34Z

Rea19:

====Huanyu Zhou====

====Fei Gao====

====Chris Ahart====
[[File:ChrisAhartProfile.png|frameless|bottom|200px|Chris Ahart]]

Postdoc August 2022 - present.
====Frederik====

====Paolo====

====Songyuan====

====Margherita Buraschi====
[[File:Margherita Buraschi photo.jpg|frameless|bottom|200px|Margherita Buraschi]]

PhD July 2020-present. In her PhD, Margherita is investigating the charge transfer properties of electrochemical nanojunctions (ECNJs) by means of computational studies. ECNJs are three-terminal functional devices of interest for the field of molecular electronics <ref> Huang et al., Chem. Soc. Rev., '''44''', 889-901 (2015) </ref> as they present the same functionality of common electronic units but at the molecular scale. Many factors define the conductance of ECNJs; amongst these factors are the structure of the functional unit, the type of metal as well as the EC transformations occurring in solutions. In order to obtain an atomistic understanding of all these factors and their effects on the overall conductance of the junction, ab initio molecular dynamics under bias and an explicit open‐boundary description of the electrons are performed during this project. To this end, the hair-probes formalism <ref> Horsfield, Boleininger, D'Agosta, Iyer, Thong, Todorov and White, Phys. Rev. B, '''94''', 075118 (2016) </ref><ref>Zauchner, Horsfield and Todorov, Physical Review B, '''97''', 045116 (2018) </ref>, an open‐boundary formalism suitable to describe multi-terminal EC systems, is being interfaced within the DFT scheme implemented in the CP2K computational package <ref>Kühne et al., The Journal of Chemical Physics, '''152'''(19), 194103 (2020) </ref>.
====Rashid Al-Heidous====
[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]

====Zehui Duan====
[[File:Zehui Duan photo.jpg|frameless|bottom|200px|Zehui Duan]]

MRes Oct 2020-present. Using density functional theory (DFT) as implemented in CP2K code, Zehui is investigating the thermodynamics of the CO<sub>2</sub> reduction reaction (CO2RR), to guide the rational design for dual-atom catalysts (DAC) with both high efficiency and good selectivity.

====Lorraine Wang====
[[File:Lorraine Wang photo.jpg|frameless|bottom|200px|Lorraine Wang]]

MRes Oct 2020-presnt. In her MRes project, Lorraine is studying dual-metal-atom catalysts (DAC) by means of density functional theory (DFT) as implemented in CP2K code. Dual-metal-atom catalysts with synergistic effect <ref>X. Zhu, J. Yan, M. Gu, T. Liu, Y. Dai, Y. Gu and Y. Li, J. Phys. Chem. Lett., '''10''', [tel:7760–7766 7760–7766] (2019) </ref> between the two metal atoms can enhance the catalytic oxygen reduction reaction (ORR). They usually consist of a substrate (doped graphene layers) and anchored metal atoms. Using DFT simulations implemented within the CP2K code can help to build a fundamental understanding of the structure. By studying the thermodynamics of various patterns, we can propose a thermodynamically favourable pathway of DAC synthesis. In the future, the project can further extend to study catalysts phase stability, catalytic performance and kinetics with more complexed models.

====Kalman====

====Felix====

====Luke====

Contributors

2023-01-23T21:15:42Z

Rea19:

Huanyu Zho

Fei Gao

====Chris Ahart====
[[File:ChrisAhartProfile.png|frameless|bottom|200px|Chris Ahart]]

Postdoc August 2022 - present.
====Frederik====

====Paolo====

====Songyuan====

====Margherita Buraschi====
[[File:Margherita Buraschi photo.jpg|frameless|bottom|200px|Margherita Buraschi]]

PhD July 2020-present. In her PhD, Margherita is investigating the charge transfer properties of electrochemical nanojunctions (ECNJs) by means of computational studies. ECNJs are three-terminal functional devices of interest for the field of molecular electronics <ref> Huang et al., Chem. Soc. Rev., '''44''', 889-901 (2015) </ref> as they present the same functionality of common electronic units but at the molecular scale. Many factors define the conductance of ECNJs; amongst these factors are the structure of the functional unit, the type of metal as well as the EC transformations occurring in solutions. In order to obtain an atomistic understanding of all these factors and their effects on the overall conductance of the junction, ab initio molecular dynamics under bias and an explicit open‐boundary description of the electrons are performed during this project. To this end, the hair-probes formalism <ref> Horsfield, Boleininger, D'Agosta, Iyer, Thong, Todorov and White, Phys. Rev. B, '''94''', 075118 (2016) </ref><ref>Zauchner, Horsfield and Todorov, Physical Review B, '''97''', 045116 (2018) </ref>, an open‐boundary formalism suitable to describe multi-terminal EC systems, is being interfaced within the DFT scheme implemented in the CP2K computational package <ref>Kühne et al., The Journal of Chemical Physics, '''152'''(19), 194103 (2020) </ref>.
====Rashid Al-Heidous====
[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]

====Zehui Duan====
[[File:Zehui Duan photo.jpg|frameless|bottom|200px|Zehui Duan]]

MRes Oct 2020-present. Using density functional theory (DFT) as implemented in CP2K code, Zehui is investigating the thermodynamics of the CO<sub>2</sub> reduction reaction (CO2RR), to guide the rational design for dual-atom catalysts (DAC) with both high efficiency and good selectivity.

====Lorraine Wang====
[[File:Lorraine Wang photo.jpg|frameless|bottom|200px|Lorraine Wang]]

MRes Oct 2020-presnt. In her MRes project, Lorraine is studying dual-metal-atom catalysts (DAC) by means of density functional theory (DFT) as implemented in CP2K code. Dual-metal-atom catalysts with synergistic effect <ref>X. Zhu, J. Yan, M. Gu, T. Liu, Y. Dai, Y. Gu and Y. Li, J. Phys. Chem. Lett., '''10''', [tel:7760–7766 7760–7766] (2019) </ref> between the two metal atoms can enhance the catalytic oxygen reduction reaction (ORR). They usually consist of a substrate (doped graphene layers) and anchored metal atoms. Using DFT simulations implemented within the CP2K code can help to build a fundamental understanding of the structure. By studying the thermodynamics of various patterns, we can propose a thermodynamically favourable pathway of DAC synthesis. In the future, the project can further extend to study catalysts phase stability, catalytic performance and kinetics with more complexed models.

====Kalman====

====Felix====

====Luke====

Nano Electrochemistry Group

2022-11-04T10:31:42Z

Rea19:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
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 [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| 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 exaplme);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| 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.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/crystal_functions crystal_functions: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2021-06-11T16:02:26Z

Rea19: /* Available Tutorials */

Nano Electrochemistry Group

2021-06-11T16:01:15Z

Rea19: /* Calculation of radial average (Kalman) */

Nano Electrochemistry Group

2021-06-11T16:00:42Z

Rea19: /* Dimers in gas phase (Frederik) */

Nano Electrochemistry Group

2021-06-11T16:00:11Z

Rea19: /* Surface analysis (Songyuan) */

Nano Electrochemistry Group

2021-06-11T15:58:05Z

Rea19: /* Optimizing parameters for metallic surfaces (Margherita) */

Nano Electrochemistry Group

2021-06-11T15:57:24Z

Rea19: /* Available Tutorials */

Nano Electrochemistry Group

2021-06-11T13:28:58Z

Rea19: /* Available Tutorials */

Nano Electrochemistry Group

2021-06-11T12:59:18Z

Rea19: /* How to run on ARCHER2 (Songyuan) */

How to run on ARCHER2 (Songyuan)

2021-06-11T12:59:07Z

Rea19: Rea19 moved page How to run on ARCHER2 (Songyuan) to How to run on ARCHER 2: Change title

#REDIRECT [[How to run on ARCHER 2]]

How to run on ARCHER 2

2021-06-11T12:59:07Z

Rea19: Rea19 moved page How to run on ARCHER2 (Songyuan) to How to run on ARCHER 2: Change title

This is a document for Research Group Cucinotta and Research Group Harrison guiding you through the setups for EPCC ARCHER2 and perform CP2K calculations there:[[File:Picture 1-Songyuan ARCHER2-.png|thumb|200px|Sample script 1.]]
#If you wish to perform calculation on ARCHER2 in the group, typically it means you have a fairly large system to compute, and your calculation may not proceed or proceed very slowly on CX1. You then may consult your group leader, Dr. Cucinotta, for permission to switch to run on ARCHER2;
#A budget will be applied as an annual basis. Currently, the budget we (RGC) are using is: e05-surfin-clo (not exclusive);
#You will need to apply for an ARCHER2 account at SAFE: https://safe.epcc.ed.ac.uk/. The details for registering on SAFE could be found here: https://epcced.github.io/safe-docs/safe-for-users/#register. For accessing ARCHER2, you will need to generate a SSH keypair;
#If you are an UNIX (Mac or so) user, the SSH keypair generation scheme is:
##Open your terminal window and type: ssh-keygen -t rsa;
##And the SSH keypair will be generated;
##You will be asked to setup a password for your SSH keypair. A kind reminder, a keypair with a password is definitely more secure; however, if your SSH keypair has a password, then every time when you login to ARCHER2, you will need to type in two passwords, one for your ARCHER2 account and one for your keypair.
##If you want to visualize your keypair, you will find them in a hidden directory. To view the hidden directory, press command+shift+.;
#Copy your public SSH key to SAFE and do not share your private key to anyone;[[File:Picture 2-Songyuan ARCHER2-.png|thumb|200px|Sample script 2.]]
#Then you should be able to login to ARCHER2. You will need to use the initial password for ARCHER2 provided by SAFE and then the first time you login, you will setup a new password.
#ARCHER2 is different from CX1. In CX1, you will be performing your calculation and saving your results in the same directory, the home directory. However, on ARCHER2, you will be submitting your calculation on a different directory, called the work directory, and then after you finish your calculations, move the data to home for permanent (not really, if anyone promise you anything you have is permanent, slap the person’s face) storage. So, the first wise thing to do is to check the access of the two directories. For example, your home directory will have the path: /home/e05/e05/[your username] and your work directory will have a path: /work/e05/e05/[your username].
#Job scripts:
##You will be using CP2K/8.1 version, the latest version of CP2K. Check the CP2K website for some keywords’ changes (Sample script 1).
##If your calculation will involve hybrid functional calculations, things turns to be tricker. Luckily, someone has already resolved the problem for you. This is what you need to do:
###Unfortunately, unlike ARCHER, ARCHER2 has not opened the “large memory” queue yet. So you will need to find a way of tuning the nodes and cores to balance the memory.
###The first thing you will need to do is to increase the number of nodes. For example, a given system, if you perform GGA calculation, you may only need 4 nodes; however, a hybrid calculation will at least demand a multiplication of 4 to 6 of the nodes.
###Switch cp2k.popt to cp2k.psmp;
###If you still have memory issues, then, decrease the number of tasks per node and increase the cpus per task. This should solve your problem (Sample script 2).
#Finally, if you are a loyal user of PBS instead of slurm, and you find using the slurm command for submitting jobs and checking status cumbersome; you may setup something to allow you use “qstat”, “qsub”; most importantly, if you do not want to cd into your work directory every time, it is also helpful to setup an alias for change directory into work directory. However, I will leave this up to you and will not iterate it here. Best of luck and always have fun.

Nano Electrochemistry Group

2021-06-11T12:58:15Z

Rea19: /* How to run on ARCHER2 (Songyuan) Contributors */

Nano Electrochemistry Group

2021-06-11T12:57:51Z

Rea19: /* Available Tutorials */

Nano Electrochemistry Group

2021-06-11T12:56:37Z

Rea19: /* Available Tutorials */

Nano Electrochemistry Group

2021-06-11T12:52:57Z

Rea19: /* How to run on ARCHER2 (Songyuan) Contributors */

Nano Electrochemistry Group

2021-06-11T12:52:24Z

Rea19: /* How to run on ARCHER2 (Songyuan) Contributors */

Nano Electrochemistry Group

2021-06-11T12:51:25Z

Rea19: /* How to run on ARCHER2 (Songyuan) Contributors */

Nano Electrochemistry Group

2021-06-11T12:48:55Z

Rea19: /* How to run on ARCHER2 (Songyuan)Contributors */

Nano Electrochemistry Group

2021-06-11T12:48:34Z

Rea19: /* How to run on ARCHER2 (Songyuan)Nano Electrochemistry Group/Contributors */

Nano Electrochemistry Group/Contributors

2021-06-11T12:48:15Z

Rea19: Rea19 moved page Nano Electrochemistry Group/Contributors to Contributors: Change title

#REDIRECT [[Contributors]]

Contributors

2021-06-11T12:48:15Z

Rea19: Rea19 moved page Nano Electrochemistry Group/Contributors to Contributors: Change title

====Frederik====

====Paolo====

====Songyuan====

====Margherita====

[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]
====Rashid Al-Heidous====

====Kalman====

====Felix====

====Luke====

Nano Electrochemistry Group

2021-06-11T12:47:12Z

Rea19: /* How to run on ARCHER2 (Songyuan)Contributors */

Nano Electrochemistry Group

2021-06-11T12:46:42Z

Rea19:

Contributors

2021-06-11T12:42:17Z

Rea19:

Contributors

2021-06-11T12:41:44Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]
====Rashid Al-Heidous====

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T12:41:30Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]
=====Rashid Al-Heidous=====

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T12:41:12Z

Rea19:

Contributors

2021-06-11T12:40:48Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]
==Rashid Al-Heidous==

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T12:40:12Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]
===Rashid===

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T12:39:48Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|frameless|bottm|200px|Rashid Al-Heidous]]
===Rashid===

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T12:39:20Z

Rea19:

Contributors

2021-06-11T12:37:20Z

Rea19:

Contributors

2021-06-11T12:36:22Z

Rea19:

Contributors

2021-06-11T12:04:44Z

Rea19:

Contributors

2021-06-11T12:03:05Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|right|thumb|200px|]]
===Rashid===

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T11:57:08Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

[[File:Rashid Personal Photo.jpeg|thumb|200px|]]
===Rashid===

===Kalman===

===Felix===

===Luke===

File:Rashid Personal Photo.jpeg

2021-06-11T11:52:19Z

Rea19:

Contributors

2021-06-11T11:46:26Z

Rea19:

===Frederik===

===Paolo===

===Songyuan===

===Margherita===

===Rashid===

===Kalman===

===Felix===

===Luke===

Contributors

2021-06-11T11:45:01Z

Rea19:

===Songyuan===

===Margherita===

===Frederik===

===Kalman===

===Paolo===

===Felix===

===Luke===

Contributors

2021-06-09T16:47:20Z

Rea19: Created page with "===Songyuan=== ===Margherita==="

===Songyuan===

===Margherita===

Nano Electrochemistry Group

2021-06-09T14:49:12Z

Rea19:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

==Research focus of the group==

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==Available Tutorials==
This section provides a series of tutorials designed to help with the computational modelling of electrochemical system. The tools described in each tutorial can be found in the linked gitlub repository [https://gitlab.doc.ic.ac.uk/rgc].

===[[How to run on ARCHER2 (Songyuan)]]===

===[[Lammps and plumed|Lammps and plumed (Frederik)]]===
Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces (Margherita)]]===
Tutorial for optimising parameters for metallic surfaces using CP2K.

===Surface analysis (Songyuan)===

===[[Dimers in gas phase|Dimers in gas phase (Frederik)]]===
Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average (Kalman)]]===
Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces (Paolo)]]===

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors (Felix)]]===
Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons (Luke)]]===
Tutorial for the simulation of hard carbon?.

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md How to install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Reference Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);
*…

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*How to install;
*Reading inputs and outputs (commented files and examples);
*…

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==

===[http://www.ks.uiuc.edu/Research/vmd/ VMD]===
*Read and visualize trajectory files
*…

===[http://www.xcrysden.org/ Xcrysden]===

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2021-06-09T14:25:38Z

Rea19:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

==Research focus of the group==

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==Available Tutorials==
This section provides a series of tutorials designed to help with the computational modelling of electrochemical system. The tools described in each tutorial can be found in the linked gitlub repository [https://gitlab.doc.ic.ac.uk/rgc].

{{Drop down list|Name=List1|Value1=[[How to run on ARCHER2 (Songyuan)]]|Value2=[[Lammps and plumed|Lammps and plumed (Frederik)]]|Value3=[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces (Margherita)]]|Value4=[[Surface analysis (Songyuan)]]|Value5=[[Dimers in gas phase|Dimers in gas phase (Frederik)]] |Value6= [[Calculation of radial average|Calculation of radial average (Kalman)]] |Value7= [[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces (Paolo)]] |Value8= [[Memristors|Simulation of Memristors (Felix)]] }}

===[[How to run on ARCHER2 (Songyuan)]]===

===[[Lammps and plumed|Lammps and plumed (Frederik)]]===
Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces (Margherita)]]===
Tutorial for optimising parameters for metallic surfaces using CP2K.

===Surface analysis (Songyuan)===

===[[Dimers in gas phase|Dimers in gas phase (Frederik)]]===
Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average (Kalman)]]===
Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces (Paolo)]]===

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors (Felix)]]===
Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons (Luke)]]===
Tutorial for the simulation of hard carbon?.

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md How to install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Reference Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);
*…

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*How to install;
*Reading inputs and outputs (commented files and examples);
*…

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==

===[http://www.ks.uiuc.edu/Research/vmd/ VMD]===
*Read and visualize trajectory files
*…

===[http://www.xcrysden.org/ Xcrysden]===

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2021-05-27T15:11:18Z

Rea19:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

==Research focus of the group==

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==Available Tutorials==
This section provides a series of tutorials designed to help with the computational modelling of electrochemical system. The tools described in each tutorial can be found in the linked gitlub repository [https://gitlab.doc.ic.ac.uk/rgc].

===[[How to run on ARCHER2 (Songyuan)]]===

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces (Margherita)]]===
Tutorial for optimising parameters for metallic surfaces using CP2K.

===Surface analysis (Songyuan)===

===[[Dimers in gas phase|Dimers in gas phase (Frederik)]]===
Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average (Kalman)]]===
Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces (Paolo)]]===

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors (Felix)]]===
Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons (Luke)]]===
Tutorial for the simulation of hard carbon?.

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md How to install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Reference Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);
*…

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*How to install;
*Reading inputs and outputs (commented files and examples);
*…

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==

===[http://www.ks.uiuc.edu/Research/vmd/ VMD]===
*Read and visualize trajectory files
*…

===[http://www.xcrysden.org/ Xcrysden]===

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>