IPS2024Workshop
Exercise of DFT/OpenMX at the IPS2024 Workshop, May 31, 2024
- e-mail: ishii@cphys.s.kanazawa-u.ac.jp
最終更新時間:2024年05月29日 09時52分22秒
Practice Content
- ―――Preparation for Lecture (Software Installation)―――
We will use a band calculation program called OpenMX in this exercise session.
Please refer to the manual below.
http://www.openmx-square.org/openmx_man3.9/
Other Resources
- OpenMX viewer
http://www.openmx-square.org/viewer/index.html
- VESTA (crystal structure visualization software, cif, xyz, etc.)
http://jp-minerals.org/vesta/jp/
- XCrysDen
- Fermi Surface Database (University of Florida, Tight-binding approximation)
http://www.phys.ufl.edu/fermisurface/
- OpenMX Pseudopotentials and Pseudoatomic Orbital Database
http://www.jaist.ac.jp/~t-ozaki/vps_pao2013/
- Crystal Structure Database
http://www.crystallography.net/cod/
- Lattice Constants of Elements in the Periodic Table
https://periodictable.com/Properties/A/LatticeConstants.html
- Reference Files (Examples of inputs for substances inquired about)
Practice 1, Molecules
- Installation
- Copy the example input files
cp /usr/share/openmx/work .
- Operation Check
- Calculate the water (H2O) molecule
cd work
openmx H2O.dat
- Visualize the water molecule
After the calculation is complete, visualize h2o.md with xcrysden.
xcrysden --xyz h2o.md&
- H2 Molecule
- Copy H2O.dat to H2.dat
cp H2O.dat H2.dat
- Edit H2.dat with emacs or another editor
- 1. Change System.Name from h2o to h2
- 2. Change Species.Number from 2 to 1 and delete the line for oxygen (O)
(lines between <Definition.of.Atomic.Species and Definition.of.Atomic.Species>)
- 3. Change H7.0-s2p1 to H7.0-s1
- 4. Change Atoms.Number from 3 to 2
- 5. Delete the lines for oxygen O coordinates and electron numbers between <Atoms.SpeciesAndCoordinates and Atoms.SpeciesAndCoordinates> and change the previous sequence numbers of the hydrogen molecule from 2, 3 to 1, 2
- 6. Visualize h2.md with xcrysden
xcrysden --xyz h2.md&
- 7. Edit files with # attached to H2.dat and confirm that atomic positions have changed
- 8. Edit H2.dat# and change MD.Type from EF to Nomd
- 9. Perform the OpenMX calculation again with H2O.dat#
openmx H2O.dat#
- 10. After the calculation is complete, open h2.out and search for Chemi. Confirm that the energy levels (Eigenvalues) are displayed under the second Chemical potential
- 11. Visualize h2.tden.cube with xcrysden
Total Energy Dependence on Interatomic Distance for H2 Molecule
Change
MD.type EF
in H2.dat to
MD.type Nomd
Practice 2, Solids
- Diamond
openmx cdia.dat
- Band Diagram
bandgnu13 cdia.Band
Start gnuplot and load 'cdia.GNUBAND' to draw the band diagram.
mathematica
コードをコピーする
- Density of States
DosMain *.val *.vec
Plot cdia.Dos.Tetrahedron with gnuplot.
- Calculation of GaAs, etc.
Practice 3, Volume Optimization
- EvsLC, Alfcc (example files)
Alfcc-EvsLC.dat(25)
MateriApps Live
In the practice, we will use MateriAppsLive!
http://cmsi.github.io/MateriAppsLive/
which is a Linux OS pre-installed with computational materials science applications.
Please prepare the following before the lecture date.
Preparation:
Follow the instructions in "Using MateriApps LIVE! on VirtualBox"
https://github.com/cmsi/MateriAppsLive/wiki/Using-MateriApps-LIVE!-on-VirtualBox
to install it on your PC's VirtualBox.
Download the latest ova as of 2021/10/22 (2.57GB, so it will take time). Download MateriAppsLive-3.3-amd64.ova from the link below.
https://sourceforge.net/projects/materiappslive/files/
Refer to the following slides for guidance.
https://www.slideshare.net/cms_initiative/materiapps-live-154816291
Also, perform the operation check with the slides below.
https://www.slideshare.net/cms_initiative/materiapps-openmx
(Even if you cannot do it in advance, we will do it during the lecture.)
Note: In the practice, we will use a band calculation program called OpenMX.
Please refer to the Japanese manual below.
http://www.openmx-square.org/openmx_man3.9jp/
After Installation
Log in with
user
live
To enable the Japanese keyboard, type "setxkbmap -layout jp" in LXTerminal and press enter.
The example files that come with OpenMX are in /usr/share/openmx/work.
MateriApps Live (Old Information)
You can also use MateriAppsLive!
http://cmsi.github.io/MateriAppsLive/
which is a Linux OS pre-installed with computational materials science applications, on your own PC.
In that case, follow the instructions in "Using MateriApps LIVE! on VirtualBox"
https://github.com/cmsi/MateriAppsLive/wiki/Using-MateriApps-LIVE!-on-VirtualBox
to install it on your PC's VirtualBox.
Refer to the slides below as well.
https://www.slideshare.net/cms_initiative/materiapps-live-154816291
Also, refer to the slides below for the operation check.
https://www.slideshare.net/cms_initiative/materiapps-openmx
- Related Links
- To run it on Windows or Mac, install VirtualBox from the link below
→http://www.oracle.com/technetwork/jp/server-storage/virtualbox/overview/index.html
- Download the VirtualBox version of MateriApps LIVE!
→https://sourceforge.net/projects/materiappslive/files/Release-1.12/
To enable the Japanese keyboard, type "setxkbmap -layout jp" in LXTerminal and press enter.
The example files that come with OpenMX are in /usr/share/openmx/work.
OpenMX Manual
- English