Computer Lab: Difference between revisions
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==Basic Unix== | ==Basic Unix== | ||
*[https://wiki.physics.udel.edu/wiki_cmpb/images/6/67/LinuxIntro_2024.pdf Hands-on Linux Introduction] | *[https://wiki.physics.udel.edu/wiki_cmpb/images/6/67/LinuxIntro_2024.pdf Hands-on Linux Introduction] | ||
*How to submit parallel VASP jobs over | *How to submit parallel VASP jobs over 1 core of keldysh: | ||
<pre> | <pre> | ||
$ module load vasp | $ module load vasp | ||
$ mpirun -n | $ mpirun -n 1 vasp_std | ||
</pre> | </pre> | ||
*How to submit parallel openmx jobs over 16 cores of keldysh: | *How to submit parallel openmx jobs over 16 cores of keldysh: | ||
| Line 12: | Line 12: | ||
</pre> | </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. | 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== | ||
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
