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 jobs over 16 cores of keldysh:
*How to submit parallel VASP jobs over 1 core of keldysh:
<pre>
<pre>
mpirun -np 16 openmx material.in > material.out
$ module load vasp
$ mpirun -n 1 vasp_std
</pre>
</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==
*[https://wiki.physics.udel.edu/wiki_cmpb/images/c/c3/Dft_hand_on_h2o_relaxation.pdf H<sub>2</sub>O relaxation using VASP]
* H<sub>2</sub>O relaxation using VASP: [[Media:Dft_hand_on_h2o_relaxation.pdf|PDF]], [[Media:H2O_relaxation.zip|files]]
*[https://wiki.physics.udel.edu/wiki_cmpb/images/e/e0/Dft_hand_on_h2o_vibration.pdf H<sub>2</sub>O vibration using VASP]
*H<sub>2</sub>O vibrations using VASP: [[Media:Dft_hand_on_h2o_vibration.pdf|PDF]], [[Media:H2O_vibration.zip|files]]
*[https://wiki.physics.udel.edu/wiki_cmpb/images/9/9a/Dft_hand_on_graphene.pdf Band structure of graphene]
*Band structure of graphene: [[Media:Dft_hand_on_graphene.pdf|PDF]], [[Media:Graphene_files.zip|files]]
*[https://wiki.physics.udel.edu/wiki_cmpb/images/6/6b/Dft_hand_on_nio.pdf Band structure of NiO]
*Band structure of NiO: [[Media:Dft_hand_on_nio.pdf|PDF]], [[Media:NiO_files.zip|files]]


==OpenMX input files==
==OpenMX input files==
*[https://pranabdas.github.io/openmx/silicon/  Band structure of Si]
*[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]
*[https://pranabdas.github.io/openmx/convergence Testing convergence in kinetic energy cutoff, k-grid density and lattice constant]
*[https://pranabdas.github.io/openmx/dft-u Density of states of NiO via DFT vs. DFT+ U]
 
==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

$ 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

VASP input files

OpenMX input files

Q-Chem input files

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