Computer Lab: Difference between revisions
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==Basic Unix== | ==Basic Unix== | ||
*[https:// | *[https://wiki.physics.udel.edu/wiki_cmpb/images/6/67/LinuxIntro_2024.pdf Hands-on Linux Introduction] | ||
*How to submit parallel jobs | *How to submit parallel VASP jobs over 1 core of keldysh: | ||
<pre> | |||
$ module load vasp | |||
$ mpirun -n 1 vasp_std | |||
</pre> | |||
*How to submit parallel openmx jobs over 16 cores of keldysh: | |||
<pre> | |||
$ module load openmx | |||
$ mpirun -np 16 openmx material.dat -nt 4 > material.std | |||
</pre> | |||
Note that OpenMX has hybrid MPI/OpenMP parallelization, so nt specifies the number of threads in each process managed by MPI. If '-nt' is not specified, then the number of threads is set to 1, which corresponds to the flat MPI parallelization. | |||
==Databases== | |||
*[https://next-gen.materialsproject.org/ Materials Project] | |||
*[https://oqmd.org/ Open Quantum Materials Database] | |||
*[https://www.materialscloud.org/home Materials Cloud] | |||
*[https://www.aflowlib.org/ AFLOW] | |||
==Pre- and post-processing== | |||
*[https://wiki.fysik.dtu.dk/ase/ Atomistic Simulation Environment] | |||
*[https://www.sciencedirect.com/science/article/abs/pii/S0010465515003379 ''CellMatch'': Combining two unit cells into a common supercell with minimal strain] | |||
*[https://tb2j.readthedocs.io/en/latest/# TB2J for automatic computation of magnetic interaction parameters from OpenMX produced DFT Hamiltonian] | |||
==VASP input files== | ==VASP input files== | ||
*[[ | * H<sub>2</sub>O relaxation using VASP: [[Media:Dft_hand_on_h2o_relaxation.pdf|PDF]], [[Media:H2O_relaxation.zip|files]] | ||
*[[ | *H<sub>2</sub>O vibrations using VASP: [[Media:Dft_hand_on_h2o_vibration.pdf|PDF]], [[Media:H2O_vibration.zip|files]] | ||
*[[ | *Band structure of graphene: [[Media:Dft_hand_on_graphene.pdf|PDF]], [[Media:Graphene_files.zip|files]] | ||
*Band structure of NiO: [[Media:Dft_hand_on_nio.pdf|PDF]], [[Media:NiO_files.zip|files]] | |||
==OpenMX input files== | ==OpenMX input files== | ||
*[https://t-ozaki.issp.u-tokyo.ac.jp/lectures-2023/OpenMX-2.pdf Structure of OpenMX input files explained] | |||
*Silicon using OpenMX: [[Media:Hands-On.pdf|PDF]], [[Media:Si.zip|files]] | |||
*Magnons in Fe using OpenMX: [[Media:Hands-On-Fe.pdf|PDF]], [[Media:Fe.zip|files]] | |||
*NiO using OpenMX: [[Media:Hands-On-NiO.pdf|PDF]], [[Media:NiO.zip|files]] | |||
*[https://pranabdas.github.io/openmx/convergence Testing convergence in kinetic energy cutoff, k-grid density and lattice constant] | |||
==Q-Chem input files== | |||
*Molecules via Q-Chem: [[Media:q-chem-intro.pdf|PDF]], [[Media:Qchem_inputs.zip|files]]. | |||
Latest revision as of 11:59, 22 August 2024
Basic Unix
- Hands-on Linux Introduction
- How to submit parallel VASP jobs over 1 core of keldysh:
$ module load vasp $ mpirun -n 1 vasp_std
- How to submit parallel openmx jobs over 16 cores of keldysh:
$ module load openmx $ mpirun -np 16 openmx material.dat -nt 4 > material.std
Note that OpenMX has hybrid MPI/OpenMP parallelization, so nt specifies the number of threads in each process managed by MPI. If '-nt' is not specified, then the number of threads is set to 1, which corresponds to the flat MPI parallelization.
Databases
Pre- and post-processing
- Atomistic Simulation Environment
- CellMatch: Combining two unit cells into a common supercell with minimal strain
- TB2J for automatic computation of magnetic interaction parameters from OpenMX produced DFT Hamiltonian
VASP input files
- H2O relaxation using VASP: PDF, files
- H2O vibrations using VASP: PDF, files
- Band structure of graphene: PDF, files
- Band structure of NiO: PDF, files
OpenMX input files
- Structure of OpenMX input files explained
- Silicon using OpenMX: PDF, files
- Magnons in Fe using OpenMX: PDF, files
- NiO using OpenMX: PDF, files
- Testing convergence in kinetic energy cutoff, k-grid density and lattice constant
