GettingStarted en - cmsi/MateriAppsLive GitHub Wiki

MateriApps LIVE! / Getting Started

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Application Software installed in MateriApps LIVE!

Please refer to "Applications and Tools in MateriApps LIVE!"

How to start MateriApps LIVE!

MateriApps LIVE! can be used by importing MateriApps LIVE! virtual hard-disk image (OVA) into VirtualBox and boot on virtual machine [How to Start]

How to use MateriApps LIVE! Applications

In this document, we explain how to run AkaiKKR, ALPS, BSA, CONQUEST, DCore, DDMRG, DSQSS, HPhi, LAMMPS, mVMC, OCTA, OpenMX, Quantum ESPRESSO, RESPACK, SALMON, SMASH, TeNeS, xTAPP & TAPIOCA.

AkaiKKR (formerly called Machikaneyama2002)

  1. Example (Co)

    1. Copy /usr/share/akaikkr/in.

       cp -rp /usr/share/akaikkr/in .

    2. Make out and data directories

       mkdir out data

    3. Run AkaiKKR

       specx < in/co

For more detailed information, please look at "AkaiKKR Information" in MateriApp LIVE! wiki.

ALPS

  1. Tutorials: Sample files are available in /usr/share/alps/tutorials
  2. Example (Tutorial MC-02 Calculating magnetic susceptibilities by the classical MC and looper QMC codes)

    1. Copy tutorial files

       cp -rp /usr/share/alps/tutorials/mc-02-susceptibilities .
 cd mc-02-susceptibilities

    2. Execute Python scripts

       python3 tutorial2a.py
 python3 tutorial2b.py
 python3 tutorial2c.py
 python3 tutorial2d.py
 python3 tutorial2full.py

      At the end of each Python script, calculation results will be plotted. The Python scripts finishes after closing the window by clicking the top-right 'X' mark. By executing the last script, all the results will be plotted in one figure.

      boot

For more detailed information, please look at "ALPS Information" in MateriApp LIVE! wiki.

BSA

  1. Tutorials: Sample files are available in /usr/share/bsa/Sample

  2. Example

     new_bfss /usr/share/bsa/Sample/Ising-square-Binder.dat 1 0.42 1 0.9 1 0.1 > test.op 2>test.log
 new_bfss -c /usr/share/bsa/Sample/Ising-square-Binder.dat 1 0.42 1 0.9 1 0.1 > test_mc.op 2>test_mc.log

For more detailed information, please look at BSA Official Page.

CONQUEST

  1. Sample files are available in /usr/share/conquest/check

  2. Example

     cp -rp /usr/share/conquest/check .
 cd check
 Conquest

  3. Compare Conquest_out with Conquest_out.ref

For more detailed information, please look at MateriApps CONQUEST Page.

DCore

  1. Tutorials: Sample files are available in /usr/share/doc/dcore/doc/tutorial

  2. Example

     cp -rp /usr/share/dcore/tutorial/square .
 cd square
 dcore_pre dmft_square.ini
 dcore dmft_square.ini --np 1
 dcore_check dmft_square.ini
 dcore_post dmft_square.ini --np 1
 cd post
 gnuplot -persistent square_akw.gp

For more detailed information, please look at MateriApps DCore Page.

DDMRG (Dynamical DMRG)

  1. Tutorials: Sample files are available in /usr/share/ddmrg/example

  2. Example

     cp -rp /usr/share/ddmrg/example .
 cd example
 DDMRG

For more detailed information, please look at DDMRG Official Page.

DSQSS

  1. Tutorials: Sample files are available in /usr/share/dsqss/samples

  2. Example

     cp -rp /usr/share/dsqss/samples .
 cd samples/dla/01_spindimer
 dla_pre std.toml
 dla param.in
 cat sample.log | grep ene

For more detailed information, please look at "DSQSS Information" in MateriApp LIVE! wiki.

HPhi

  1. Tutorials: Sample files are available in /usr/share/hphi/samples

  2. Example: Solve spin dimer by the full diagonalization method

     cp -rp /usr/share/hphi/samples .
 cd samples/tutorial_1.1
 HPhi -s stan1.in

For more detailed information, please look at MateriApps HPhi Page.

LAMMPS

  1. Tutorials: Sample files are available in /usr/share/lammps/examples

  2. Example: NaCl using the EIM potential

     mkdir eim
 cp /usr/share/lammps/examples/eim/* eim
 cd eim
 lmp -in in.eim

For more detailed information, please look at MateriApps LAMMPS Page.

mVMC

  1. Tutorials: Sample files are available in /usr/share/mvmc/sample

  2. Example: Antiferromagnetic S=1/2 Heisenberg chain

     cp -rp /usr/share/mvmc/samples/Standard/Spin/HeisenbergChain .
 cd HeisenbergChain
 vmc -s StdFace.def

For more detailed information, please look at MateriApps mVMC Page.

OCTA

  1. Tutorials: Sample files are available in /usr/share/octa/tutorial

  2. Example: Sushi calculation of polymer blend interface

    1. Copy an input file and execute Sushi

       cp /usr/share/octa/tutorial/sushi/Input/interface_uin.udf .
 sushi -Iinterface_uin.udf

    2. Plot by using Gourmet

       gourmet interface_uot.pdf

      Move the slide bar at the bottom and change "Step" to 1. Right-click on the "SUSHIOutput" folder and select "Plot 1D field ...". Click "OK" in the parameter panel.

For more detailed information, please look at MateriApps OCTA Page.

OpenMX

  1. Tutorial: Sample files are available in /usr/share/openmx/work/.

  2. Example

    1. Make a directory for execution and copy an input file

        mkdir openmx
  cp /usr/share/openmx/work/Methane.dat openmx
  cd openmx

    2. Run OpenMX

        openmx Methane.dat

    3. Check of execution results

      Please compare the results with those on http://www.openmx-square.org/openmx_man3.7/node16.html.

Quantum ESPRESSO

  1. Tutorial: Sample files are available in /usr/share/espresso/examples

  2. Example

     cp -rp /usr/share/espresso/examples .
 cd examples/PW/examples/example01
 ./run_example

For more detailed information, please look at MateriApps Quantum ESPRESSO Page.

RESPACK

  1. Tutorial: Sample files are available in /usr/share/respack/sample.

  2. Example

     cp -rp /usr/share/respack/sample/xtapp/Al.fcc.6x6x6 .
 cd Al.fcc.6x6x6
 sh Al.sh

For more detailed information, please look at MateriApps RESPACK Page.

SALMON

  1. Tutorial: Sample files are available in /usr/share/salmon/samples.

  2. Example

     cp -rp /usr/share/salmon/samples .
 cd samples/exercise_01_C2H2_gs
 salmon < C2H2_gs.inp

For more detailed information, please look at MateriApps SALMON Page.

SMASH

  1. Tutorial: Sample files are available in /usr/share/smash/example.

  2. Example

    In the following example, the Hartree-Fock energy calculation of Anthracene (C14H10) with the 6-31G basis set and the visualization of its HOMO and LUMO are performed. The smash-vtk-generator file attached in SMASH and open source software ParaView are required for visualization.

    1. Generate a directory for execution and copy the input file.

        mkdir smash
  cd smash
  cp /usr/share/smash/example/anthracene.inp .

    2. Exectute SMASH.

        smash < anthracene.inp > anthracene.out

      After the execution, two files are generated, the output file "anthracene.out" and the checkpoint file "anthracene.chk". The output file can be seen as a text file, which shows the computational conditions, atomic coordinates, basis functions, SCF processes, MO energies, and MO coefficients.

    3. Generate vtk files for HOMO and LUMO (anthracene-HOMO.vtk and anthracene-LUMO.vtk).

        smash-vtk-generator anthracene.chk anthracene-HOMO.vtk MO HOMO
  smash-vtk-generator anthracene.chk anthracene-LUMO.vtk MO LUMO

    4. Bottom right menu > Education > ParView Client

    5. Select Load State from File menu and open the /usr/share/smash/visual/mo-view.pvsm file.

    6. Open the anthracene-HOMO.vtk file, and you can see the contour map of HOMO.

    7. To display LUMO, open the anthracene-LUMO.vtk file after opening the /usr/share/smash/visual/mo-view.pvsm file.

For more detailed information, please look at "SMASH Information" in MateriApps LIVE! Wiki.

TeNeS

  1. Tutorial: Sample files are available in /usr/share/tenes/sample.

  2. Example

     cp -rp /usr/share/tenes/sample .
 cd sample/01_transverse_field_ising
 python3 tutorial_example.py
 python3 tutorial_read.py

For more detailed information, please look at MateriApps TeNeS Page.

xTAPP & TAPIOCA

  1. Sample files are available in the following directories
    • xTAPP samples: /usr/share/xtapp/sample
    • TAPIOCA samples: /usr/share/tapioca/sample
  2. Examples

    1. Make directory for execution

       mkdir $HOME/xtapp

    2. Copy sample shell scripts

       cp /usr/share/xtapp/check/* $HOME/xtapp
 cd $HOME/xtapp

    3. Example 1: simulation of silicon Execute si.sh

       sh si.sh

    4. Example 2: simulation of alpha-quarts Execute quartz.sh

       sh quartz.sh

    5. Execution of TAPIOCA Type 'tapioca' in the terminal or execute from bottom-left menu (MateriApps > Tapioca).

      boot

For more detailed information, "Information of xTAPP & TAPIOCA" in MateriApp LIVE! wiki.