sssp verify scripts

This repository store the pseudopotential files as input for SSSP verification and the scripts to run the verification.

Command to run

Batch launching precheck or standard verification of pseudos in a folder:

╰$ for FILE in _sssp_pbe/<element>/*.upf; do
echo $FILE && python run_verify.py --mode <precheck/standard> --computer mr32 -- $FILE
done

Database maintainance

The prototype database is folder sssp_db which contains json files store the results of outputs and bands/band structure information. We use the following way to properly maintain the database and its version.

Everytime there are result changes like new pseudo verification results or updated verification results need to publish. Running bumpver to bump db version in sssp_db/version.txt. Modify the sssp_db/CHANGELOG with information of changes.
Running python pre_and_post_process/extract_output.py without arguments. It will generate sssp_db.tar.gz.
push to main with commit info the the DB version is updated.

Soft link pseudos to the files of every element

In the root path of repository run:

python ./pre_and_post_process/link_pseudos.py N pbe

to soft link all N pseudopotentials to _sssp_pbe folder.

Computer to run

To make things easy and clean, to avoid caching issue that bands workchain of standard that may use precheck calcjob which may be cleaned and fail. I'll try to sure the precheck and standard are run on different machine/account. The principles are

precheck verification first go to imxgesrv1
if precheck on eiger (mr0 if not mentioned), then standard should use another account. mr0/mr32 or mr32/mr0

Pseudopotential libraries

Lanthanides

Lanthanides pseudopotentials are triky since the lanthanides contain f state which is hard to precisely describe in DFT.

ATOMPAW

The latest version of ATOMPAW is 4.2.0.0 which ... SCAN

The La and Ce run on Wentzcovich sinec these two can not generated with latest version.

ONCVPSP

SG15 inputs, some (list them) may failed to generate

PSLibrary

The PSLibrary pseudopotentials are gerenated by using ld1.x. I use inputs file from PSLibrary and re-generate pseudopotentials using docker image pspgen/ld1:0.1.0. ld1.x in the image is compiled from Quantum-Espresso v6.3-MAX with gfortran7 and lapack the in package.

The libraries re-generated are PBE and PBEsol with inputs:

PAW/HIGH from https://github.com/dalcorso/pslibrary/blob/master/paw_ps_high.job
US/HIGH from https://github.com/dalcorso/pslibrary/blob/master/us_ps_high.job
PAW/LOW from
US/LOW from
PAW/0.x from https://github.com/dalcorso/pslibrary/blob/master/paw_ps_collection.job
US/0.x from https://github.com/dalcorso/pslibrary/blob/master/us_ps_collection.job

The 0.x PPs have been tested in some cases and no error has been reported so far. The PPs that were in pslibrary.0.1 (See PSLibrary ChangeLog file) have been tested extensively

Notes

Cs.paw.z_9.ld1.psl.v1.0.0-low.upf: manually set z=9 and modified z since -5 in UPF.
Cs.us.z_9.ld1.psl.v1.0.0-low.upf: manually set z=9 and modified z since -5 in UPF.

Name convention of pseudopotential UPF file

The filename (it is easy to be done by using rename command of linux and script psp_fn_z_set.ipynb) will be used to deduct the label name when submit the verification. The naming conventios is: <element>.<psp_type>.z_<enum>.<tool>.<library>.<version>.<extra>.upf

element: the element of pseudopotential.
psp_type: nc for norm-conserving, us for ultra-solf and paw for paw pseudopotentials
enum: is the number of valence electrons
tool: is the tool used for pseudopotential generation
    oncvpsp4: ONCVPSP code version 4.0.1
    oncvpsp3: this is where the dojo from version 3.3.0
    ld1: used to generate PSlibrary
    uspp: Vanderbilt code used to generate GBRV library
    atompaw: ATOMPAW code for jth and wentzcovitch
library: is the pseudopotential library, we will run on: 
    dojo for PSEUDO-DOJO norm-conserving pseudos
    jth for ATOMPAW paw pseudos from pseudo-dojo webpage
    sg15 for SG15 pseudopotestials re-generated with oncvpsp 4.0.1
    psl for PSLibrary pseudos
    gbrv for ultrasoft pseudos of GBRV library by Vanderbilt
    wentzcovitch for lanthanides by wentzcovith, comment: legacy is downloaded, new is generated with same inputs but on ATOMPAW 4.2.0.0
version: is for version of pseudopotential. `v0` for no version specified.
extra: in the extra information related to pseudos that can be used to distingish the small distinctien.

Acknowledgements

The SSSP is a verification effort, but it is very important to give credit to the different authors that have generated the pseudopotential libraries that are tested here, and to the original methodological developments that underlie the generation of these pseudopotential tables and datasets. Citations can e.g. be taken from this list (contact us if we need to add more), appropriately for the libraries, methods, and datasets used. Please make an effort to acknowledge these and to ensure reproducibility of your calculations by listing/citing all pseudopotentials used.

VERIFICATION

SSSP: G. Prandini, A. Marrazzo, I. E. Castelli, N. Mounet and N. Marzari, npj Computational Materials 4, 72 (2018). WEB: http://materialscloud.org/sssp.
K. Lejaeghere et al., Science 351 (6280), 1415 (2016). DOI: 10.1126/science.aad3000, WEB: http://molmod.ugent.be/deltacodesdft. An open-access copy is available from Cottenier's page.
https://github.com/aiidateam/aiida-sssp-workflow

LIBRARIES

GBRV: K. F. Garrity, J. W. Bennett, K. M. Rabe, and D. Vanderbilt, Comput. Mater. Sci. 81, 446 (2014). DOI: 10.1016/j.commatsci.2013.08.053, WEB: http://www.physics.rutgers.edu/gbrv, LICENSE: GNU General Public License (version 3).
SG15: M. Schlipf and F. Gygi, Comp. Phys. Comm. 196, 36 (2015). DOI: 10.1016/j.cpc.2015.05.011, WEB: http://www.quantum-simulation.org/potentials/sg15_oncv, LICENSE: Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0).
Goedecker: A. Willand, Y. O. Kvashnin, L. Genovese, A. Vázquez-Mayagoitia, A. K. Deb, A. Sadeghi, T. Deutsch, and S. Goedecker, J. Chem. Phys. 138, 104109 (2013). DOI: 10.1063/1.4793260, WEB: http://bigdft.org/Wiki/index.php?title=New_Soft-Accurate_NLCC_pseudopotentials, LICENSE: Creative Commons Attribution 3.0 Unported License (CC BY 3.0).
Pslibrary 0.3.1: E. Küçükbenli et al., arXiv:1404.3015. WEB: http://theossrv1.epfl.ch/Main/Pseudopotentials, LICENSE: GNU General Public License (version 2 or later).
Pslibrary 1.0.0: A. Dal Corso, Comput. Mater. Sci. 95, 337 (2014). DOI: 10.1016/j.commatsci.2014.07.043, WEB: http://www.quantum-espresso.org/pseudopotentials, LICENSE: GNU General Public License (version 2 or later).
RE Wentzcovitch: M. Topsakal and R. M. Wentzcovitch, Comput. Mater. Sci. 95, 263 (2014). DOI: 10.1016/j.commatsci.2014.07.030, WEB: http://www.mineralscloud.com/resources/repaw/index.shtml.
Pseudo Dojo: M.J. van Setten, M. Giantomassi, E. Bousquet, M.J. Verstraete, D.R. Hamann, X. Gonze, G.-M. Rignanese, Comp. Phys. Comm. 226, 39 (2018). DOI: 10.1016/j.cpc.2018.01.012, WEB: http://www.pseudo-dojo.org/.

METHODS

Ultrasoft pseudopotentials: D. Vanderbilt, Phys. Rev. B 41, 7892(R) (1990). DOI: 10.1103/PhysRevB.41.7892, WEB: http://physics.rutgers.edu/~dhv/uspp.
Projector-augmented wave (PAW) method: P. E. Blöchl, Phys. Rev. B 50, 17953 (1994). DOI: 10.1103/PhysRevB.50.17953.
Norm conserving, multiple projectors pseudopotentials: D. R. Hamann, Phys. Rev. B 88, 085117 (2013). DOI: 10.1103/PhysRevB.88.085117, WEB: http://www.mat-simresearch.com.
Separable dual-space Gaussian pseudopotentials: S. Goedecker, M. Teter, J. Hutter, Phys. Rev. B 54, 1703 (1996). DOI: 10.1103/PhysRevB.54.1703, WEB: http://cp2k.web.psi.ch/potentials.

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