ChemWiki - User contributions [en]

Third year simulation experiment/Files to download

2021-10-22T11:13:29Z

Prestucc: /* Connecting to the Virtual Machine */ correct wrong password

'''<big><span style="color:blue; ">This is the first section of the third year simulation experiment. You can return to the introduction page, [[Third year simulation experiment]], or jump ahead to the next section, [[Third year simulation experiment/Introduction to molecular dynamics simulation|Introduction to molecular dynamics simulation]].</span></big>'''

All of the simulations that you run in this experiment are going to be performed in Virtual Machines (VM). Before the beginning of your lab session, you should have received an invitation email to register/connect to the VM.

'''The small-scale simulations that we will perform in this experiment should not be too long a few minutes. '''

In each section of the exercise, we have tried to provide a number of mathematical and/or research exercises that you should attempt while you are waiting for the simulations in that section to be completed. You can also use this time to write your report on the previous sections!

In this first section, we will teach you how to login to the Virtual Machines and submit an example simulation. While you wait for that example to complete, you can move on to the next section and read about the theory of molecular dynamics simulations

==Connecting to the Virtual Machine==

You will be using a Microsoft Azure Lab Virtual Machine (VM) to access the software needed for the lab.

: 1. You will receive an invitation email, before your session starts, with the subject Register for Lab - IC_Chemistry_UK.
: 2. Follow the link to 'Register for the lab' in the email which will direct you to the Azure Lab Services page.
: 3. On the web page, you should see a box corresponding to the VM shared with you. In the bottom left, slide the toggle from left to right to start the VM (It may take some time to start running).
: 4. Once running, at the bottom right of the box, click the computer-style icon next to the three vertical dots.
A file with the extension rdp will be downloaded: IC_Chemistry_UK.rdp. Follow the instructions for your operating service below to use the file:

'''Windows'''

:: a. Navigate to where the file has downloaded and double click on the file to open.

'''Linux'''

:: a. Open a terminal window and through the terminal, go to the location where the file has downloaded.
:: b. Type the command: <pre> remmina IC_Chemistry_UK.rdp </pre> to run the file.

'''Mac'''

:: a. Download and install the Microsoft Remote Desktop app for Mac OS.
:: b. Open the Microsoft Remote Desktop app
:: c. On the top toolbar bar, click on the cog icon and then select Import from RDP file..
:: d. Navigate and select the downloaded rdp file.
:: e. There should now be an 'IC_Chemistry_UK' PC showing, double click on this to initialise.

: 5. You should be asked to Accept Certificate?, select Yes.
: 6. You will be asked to Enter authentication credentials:
:: a. Change the username into "chemistry" by removing "~/".
:: b. Enter Imperial2122 as the password.
The VM should now launch and you will be taken to a Windows desktop where you should be able to see the LAMMPS icon on the desktop. Double click this to launch.

If you have any problems with accessing the VM then let a demonstrator know.



==Getting the files for the experiment==

You can download all of the files that you will need for this experiment [https://imperialcollegelondon.box.com/s/mjxn9zxl67y10pgn8wkwlin05hmyqdsn from this address]. You should copy the folder '''ImperialChem-Year3SimExpt1415-master''' to a location of your choice. It contains a number of subfolders — one for each section of the experiment. Every subsequent page of this lab manual will begin with a line telling you which folder contains the necessary files, like this one:

<big>'''THE FILES THAT YOU NEED FOR THIS SECTION ARE FOUND IN THE "Intro" SUBFOLDER'''.</big>

Have a look in the '''"Intro"''' folder now. It contains a file called '''melt_crystal.in''', which you should open with a text editor (like Notepad++ or VSCode which you can find on Software Hub. VSCode is also on the Virtual Machines). This file is called an "input script", and it controls how the simulation software operates. We will perform all of our simulations with a software package called [http://lammps.sandia.gov LAMMPS]. Over the course of the experiment, you will learn what all of the commands in this file mean. The [https://lammps.sandia.gov/doc/Commands.html LAMMPS manual] contains a lot of valuable information about each of the commands, if you don't understand one of them or want to look up what some parameter means you can look it up there. To make life easier, we put "further info" links in the wiki. For now, we are going to use this file to run a few trial simulations.

'''<big><span style="color:blue; ">This is the first section of the third year simulation experiment. You can return to the introduction page, [[Third year simulation experiment]], or jump ahead to the next section, [[Third year simulation experiment/Introduction to molecular dynamics simulation|Introduction to molecular dynamics simulation]].</span></big>'''

Nano Electrochemistry Group

2021-01-15T14:16:05Z

Prestucc: /* Adsorption of molecule on surfaces (Paolo) */ add small description for my tutorial

''Nano Electrochemistry Group''
==Research focus of the group==

==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].

===[[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?.

==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===

==Molecular visualizers==

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

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

===Others===

==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===

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

Adsorption of molecule on surfaces

2021-01-11T11:36:06Z

Prestucc: Create new page from scratch

The adsorption is the process of adhesion of any atom, ion or molecule from a generic phase (such as gas, liquid or solid) to a surface. This is a surface phenomenon and it is strictly related to the surface energy of a specific material: differently from a bulk structure, the surface atoms are under-coordinated, thus enabling the attraction of adsorbent. The adsorption of molecules can be divided in two main categories: physisorption, which is usually related to weak van der Waals interaction, and chemisorption, in which covalent bonding arises between the surface and the adsorbate. With this definition, chemisorption is usually stronger than physisorption.

Adsorption is present in a variety of natural processes and is involved in many research field (such as physics, chemistry and biology). Moreover, it is of paramount importance in many industrial and technological applications such as the creation heterogeneous catalysts, the addition of lubricant additives in base oils, the use of molecular inhibitors to reduce corrosion, and so on.

In the following sections, you will find a quick guide on how to compute the adsorption energy of molecules on a generic surface. This guide is completely independent on the code you are using, so it can be used as a general overview.

== Creating the surface ==

The first step in computing the adsorption energy is to create the proper surface on which you will adsorb the molecule. This choice depends on the system you want to study. Usually, you have to choose the proper surface orientation (i.e., the proper Miller index, such as (100) or (111)) and model the system using a supercell with a specific number of layers and in-plane size of the surface (such as 1x1 or 2x2). In this way, you can change the coverage of your adsorbate, check if this can affect the adsorption energy and analyse different configurations useful for your study. Moreover, depending on the code you are using, you could add also a vacuum region along the vertical direction in order to avoid the self interaction of the system with its replicas (when periodic boundary conditions are applied).

== Select the proper adsorption site ==

After you have decided which surface you want to use in your system, you have to choose the adsorption sites of your molecule. In principle, you can put your molecule in any point of the surface. However, it is well known that a surface has specific high symmetry points in which usually the adsorption of atoms and molecule reach a minimum (or a maximum). This is due to the fact that the surface atoms in these specific points have a higher (or lower) coordination, thus favouring a higher (or lower) adsorption of the molecule.

[[File:H2O on Al 100.png|thumb|400px|Adsorption of a water molecule on a Al(100) surface in different adsorption sites.]]

In the picture, you can see an example of a water molecule adsorbed on an aluminium (100) surface. As you can see, there are 3 high symmetry points in this surface. When you change the position of the water molecule over the surface, you can find different values of the adsorption energy, which can give you some hints of the nature of the adsorption process. If you don’t have any previous knowledge of which is the most favourable adsorption site, you can run separate calculations in order to find it.

To detect the high symmetry points of a surface, you can check the literature since these points have been already identify for any possible surface orientation and add manually the molecule over a specific site. Another possible approach is to use computational codes that can automatically check where are these points in a specific surface and that can add automatically the molecule over the surface. To do that, you can use the adsorption code written in python which is present in the repository.

== Computing the adsorption energy ==

Once you have completed the previous steps, you can run the calculation and optimise (i.e., find the structure with the minimum energy) of you adsorbed system. To compute the adsorption energy <math>E_{ads}</math>, you can simply use the following formula:

:<math>E_{ads} = \frac{E_{tot} - n E_a - E_{surf}}{n},</math>

where <math>E_{tot}</math> is the energy of the surface covered by <math>n</math> molecules, <math>E_a</math> is the energy of the isolated molecule and <math>E_{surf}</math> is the energy of the isolated surface. Therefore, to compute properly the adsorption energy, you should run 3 separate calculation: the first one in which you compute the energy of the complete system with the adsorbed molecule over the surface, and the following two with the calculation of the energy of the isolated surface and the isolated molecule. You can notice that when you use this formula, the adsorption will be energetically favourable when it is lower than 0.

== References ==

File:H2O on Al 100.png

2021-01-11T11:28:26Z

Prestucc: Adsorption of a water molecule on a Al(100) surface in different adsorption sites.

Adsorption of a water molecule on a Al(100) surface in different adsorption sites.

Nano Electrochemistry Group

2021-01-11T11:25:21Z

Prestucc: /* Adsorption of molecule on surfaces (Paolo) */ create blank page

''Nano Electrochemistry Group''
==Research focus of the group==

==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].

===[[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)]]===

===[[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?.

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
#[[CP2K_Tutorial|CP2K TUTORIAL]]
#How to install CP2K
#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===

==Molecular visualizers==

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

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

===Others===

==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===

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

Nano Electrochemistry Group

2021-01-11T11:24:33Z

Prestucc: change page formatting

''Nano Electrochemistry Group''
==Research focus of the group==

==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].

===[[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 (Paolo)===

===[[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?.

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
#[[CP2K_Tutorial|CP2K TUTORIAL]]
#How to install CP2K
#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===

==Molecular visualizers==

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

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

===Others===

==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===

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