Introduction to VESTA and VMD
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
1
We need to transfer some tutorial files. Please do the following from your terminal.
mkdir ~/day2
# ( if you didn't do it before )
cd ~/day2 scp -r
[email protected]:/day2-material/* . ( first enter “yes”, then enter “qaz” as password when prompted.) (or you can download them from https://sites.google.com/site/asesma2015/tutorials )
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
2
Why do we need good paper figures ??
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
3
In order to explain your research in the form of a paper, you should be able to make good “paper figures” !!!
http://journals.aps.org/prl/pdf/10.1103/PhysRevLett.108.126103
ASESMA 2015
“Introduction to VESTA and VMD”
http://journals.aps.org/prb/pdf/10.1103/PhysRevB.80.155453 Prepared by Mehmet Topsakal.
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Mg(1-0.125)Fe0.125SiO4 (same .xsf file is visualized in Xcrysden and VESTA)
Xcrysden cannot produce good figures as VESTA ASESMA 2015
“Introduction to VESTA and VMD”
VESTA output is more suitable for paper figures !! You can modify view according to your needs. Prepared by Mehmet Topsakal.
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Xcrysden is still very useful. You can directly open Quantum Espresso input and output files (like scf.in and scf.out) with Xcrysden. You need to convert QE files to .xsf format in order to open them with VESTA.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
6
How do we obtain VESTA ?
VESTA can be downloaded from: http://jp-minerals.org/vesta/en/ It works on Windows and mac It is completely FREE !!!
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
7
Installation of VESTA Left-click here type “terminal” here
As we did yesterday, please open terminal and do the followings: cd wget http://www.geocities.jp/kmo_mma/crystal/download/VESTA-x86_64.tar.bz2
tar -xvjf VESTA-x86_64.tar.bz2 cp $HOME/.bashrc $HOME/.bashrc.saved echo 'alias VESTA=$HOME/VESTA-x86_64/VESTA $1' >> $HOME/.bashrc source $HOME/.bashrc
after you do these, you should be able to run VESTA by typing VESTA & Note: If you are using 32 bit Linux, you should download 32 bit version of VESTA (VESTA-i686.tar.bz2). ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
8
Using VESTA View angle buttons
rotation buttons
translation buttons
zoom buttons
Visualization area Bond length measurement Bond angle measurement Dihedral angle measurement
Style box
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
9
[ VESTA exercise-1 - Graphene nanoribbon ]
Please do these from terminal:
Using these buttons, practice rotating, shifting, zooming.
cd cd day2 VESTA graphene-nanoribbon.xsf &
ASESMA 2015
“Introduction to VESTA and VMD”
Try to obtain these views
Prepared by Mehmet Topsakal.
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tip: Enabling antialiasing improves the figure quality (but may decrease performance)
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
11
From Objects box, you can add atom labels, hide/select same atoms, please practice them.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
12
From Properties box, you can change many visualization options. please practice them. Here set color of C atoms to blue, H atoms to red and increase ball radius and try to obtain the version on the right.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
13
From Edit>Bonds menu, you can add bonds. please practice them.
By setting like here, try to obtain view on the right
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
14
From Boundary box, you can increase the periodicity. please practice.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
15
Here you can measure bond lengths and angles please practice. please measure other bond lengths and angles.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
16
[ VESTA exercise-2 - LaCoO3 ]
Please do these from terminal:
cd cd day2 VESTA LaCoO3.xsf &
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
17
Please examine the structure using these buttons.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
18
From Bonds menu, add bonds
Set like these and try to obtain image on the right
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
19
By selecting Polyhedra, you can get Co-O octahedra ASESMA 2015
Octahedras can be very useful to understand structure
From Properties and Boundary features, try to obtain this view.
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
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By selecting and hitting “Delete” on keyboard, you can remove atoms that you don't want to see.
select and delete
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
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Exporting figures as png
ASESMA 2015
“Introduction to VESTA and VMD”
From File menu, select “Export Raster Image” and save as LaCoO3.png
Prepared by Mehmet Topsakal.
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[ VESTA exercise-3 - Si charge density ]
Please do these from terminal:
cd cd day2 VESTA si.rho.xsf &
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
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By using wireframe style and increasing boundary ranges, you can improve charge density views.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
24
In this part, first select 3 Si atoms using selection button and Shift-key on keyboard.
ASESMA 2015
“Introduction to VESTA and VMD”
Go to “2D Data Display” section
Prepared by Mehmet Topsakal.
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Click on “Slice” and select “Calculate the best plane..” option
Here is the Si-Si bonds !!! ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
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Part-2 VMD
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
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Download page for VMD http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Similar to VESTA, VMD is free. But in order to download it, you need to register first. VMD is installed on workshop computers. You just need to enter vmd from terminal
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
28
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
29
VMD can open .xsf files as VESTA cd cd day2 vmd graphene-nanoribbon.xsf &
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
30
From Graphics>Representation menu, you can play with many visualization options. When you select, CPK as Drawing method, you should get this. Play with other options and familiarize yourself with VMD.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
31
In practice, you should be able to repeat Exampe-2 and Example-3 of VESTA part. You just need to replace VESTA with vmd while loading xsf files.
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
32
(optional) We provide various structures. You can practice using VESTA and VMD with them. From terminal, type:
ASESMA 2015
VESTA MgO.xsf &
vmd MgO.xsf &
VESTA STO-primitive.xsf &
vmd STO-primitive.xsf &
VESTA TbPc2-molecule.xsf &
vmd TbPc2-molecule.xsf &
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
33
Thank you for your attention [If you completely did this tutorial, you should be an expert on VESTA , right ?]
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
34
ASESMA 2015
“Introduction to VESTA and VMD”
Prepared by Mehmet Topsakal.
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