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The latest version of this document is available at https://github.com/cmsi/MateriAppsLive/wiki/GettingStarted-en
Feel free to ask in MateriApps LIVE! Users Forum
Please refer to "Applications and Tools in 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]
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.
Example (Co)
Copy /usr/share/akaikkr/in.
cp -rp /usr/share/akaikkr/in .
Make out and data directories
mkdir out data
Run AkaiKKR
specx < in/co
For more detailed information, please look at "AkaiKKR Information" in MateriApp LIVE! wiki.
Example (Tutorial MC-02 Calculating magnetic susceptibilities by the classical MC and looper QMC codes)
Copy tutorial files
cp -rp /usr/share/alps/tutorials/mc-02-susceptibilities $HOME
cd $HOME/mc-02-susceptibilities
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.
For more detailed information, please look at "ALPS Information" in MateriApp LIVE! wiki.
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.
Example
$ cp -rp /usr/share/ddmrg/example .
$ cd example
$ DDMRG
For more detailed information, please look at DDMRG Official Page.
For the simplest example, perform directed loop algorithm for S=1/2 antiferromagnetic Heisenberg dimer.
Set up (local) Hamiltonian
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
Set up lattice (including inverse temperature)
D=1, L=2, beta=10.0
$ lattgene 1 2 10.0
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
Perfome simulation
$ dla qmc.inp
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 is a fast molecular dynamics (MD) simulator for ferroelectrics. More information is available at feram homepage http://loto.sourceforge.net/feram/.
feram
command is placed in the search path. It can be executed as feram foo123.feram
in LXTerminal.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
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.
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.
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.
Example
Make a directory for execution and copy an input file
mkdir openmx
cp /usr/share/openmx/work/Methane.dat openmx
cd openmx
Run OpenMX
openmx Methane.dat
Check of execution results
Please compare the results with those on http://www.openmx-square.org/openmx_man3.7/node16.html.
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.
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.
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.
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.
Generate a directory for execution and copy the input file.
mkdir smash
cd smash
cp /usr/share/smash/example/anthracene.inp .
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.
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
For more detailed information, please look at "SMASH Information" in MateriApps LIVE! Wiki.
Examples
Make directory for execution
mkdir $HOME/xtapp
Copy sample shell scripts
cp /usr/share/xtapp/check/* $HOME/xtapp
cd $HOME/xtapp
Example 1: simulation of silicon Execute si.sh
sh si.sh
Example 2: simulation of alpha-quarts Execute quartz.sh
sh quartz.sh
Execution of TAPIOCA Type 'tapioca' in the terminal or execute from bottom-left menu (MateriApps > Tapioca).
For more detailed information, "Information of xTAPP & TAPIOCA" in MateriApp LIVE! wiki.