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

• Exercise of DFT/OpenMX at the IPS2024 Workshop, May 31, 2024
  • Practice Content
  • Other Resources
  • Practice 1, Molecules
    • Total Energy Dependence on Interatomic Distance for H2 Molecule
  • Practice 2, Solids
  • Practice 3, Volume Optimization
  • MateriApps Live
  • After Installation
  • MateriApps Live (Old Information)
  • OpenMX Manual

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

http://www.xcrysden.org

• 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(16)

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

http://www.openmx-square.org/openmx_man3.9/index.html