MateriApps LIVE! / Getting Started

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The latest version of this document is available at https://github.com/cmsi/MateriAppsLive/wiki/GettingStarted-en

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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, DDMRG, DSQSS, feram, HPhi, LAMMPS, mVMC, OpenMX, Quantum ESPRESSO, RESPACK, SALMON, SMASH, 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 $HOME
      cd $HOME/mc-02-susceptibilities
      
    2. Execute Python scripts

      python tutorial2a.py
      python tutorial2b.py
      python tutorial2c.py
      python tutorial2d.py
      python 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.

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. How to run and Examples are available (in Japanese) in the DSQSS official wiki.
  2. For the simplest example, perform directed loop algorithm for S=1/2 antiferromagnetic Heisenberg dimer.

    1. Set up (local) Hamiltonian

      • S=1/2, J=-0.5 (antiferro), H=0 (zero field)
      • Due to the periodic boundary condition, let the interaction J be -0.5 instead of -1.0.

        $ hamgen_H 1 -0.5 0.0
        $ dla_alg
        
    2. Set up lattice (including inverse temperature)

      • D=1, L=2, beta=10.0

        $ lattgene 1 2 10.0
        
    3. Copy an input file from /usr/share/dsqss/samples/manual_run/qmc.inp.org

          $ cp /usr/share/dsqss/samples/manual_run/qmc.inp.org qmc.inp
      
    4. Perfome simulation

      $ dla qmc.inp
      
    5. Check calculated energy per site

      • Expectation value and statistical error will be obtained

        $ grep ene sample.log.000
        

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

feram

feram is a fast molecular dynamics (MD) simulator for ferroelectrics. More information is available at feram homepage http://loto.sourceforge.net/feram/.

  1. Examples are provided in /usr/share/feram/example/.
  2. feram command is placed in the search path. It can be executed as feram foo123.feram in LXTerminal.
  3. Example (hysteresis loop will be drawn after simulation for tens of minutes)

    cp -a /usr/share/feram/example/27example-BaTiO3-new-param-E_wave .
    cd 27example-BaTiO3-new-param-E_wave
    feram 360cos.feram 360sin.feram
    ./hysteresis.gp
    evince hysteresis.eps
    

HPhi

  1. Tutorials: Sample files are available in /usr/share/hphi/samples
  2. Example: Solve 4x4-square lattice S=1/2 antiferromagnetic Heisenberg model by the LOBCG method

    $ cp -rp /usr/share/hphi/samples/CG/Heisenberg .
    $ cd Heisenberg
    $ HPhi -s stan.in
    

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

LAMMPS

  1. Tutorials: Sample files are available in /usr/share/doc/lammps-doc/examples
  2. Example: NaCl using the EIM potential

    $ cp -rp /usr/share/doc/lammps-doc/examples/eim .
    $ cd eim
    $ gunzip *.gz
    $ lammps -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.

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/examples.
  2. Example

    $ cp -rp /usr/share/salmon/examples .
    $ cd examples/C2H2
    $ salmon.cpu < 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.

xTAPP & TAPIOCA

  1. Sample files are available in the following directories
  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.