aiida-sssp-workflow 0.2.0b1

AiiDA plugin SSSP verification workflows

aiida-sssp-workflow

The aiida-sssp-workflow is an aiida plugin to run the verification for a given pseudopotential. The plugin contains workflows to verify the pseudopotential. It can:

1. evaluate the delta factor of the pseudopotential with respect to WIEN2K all-electrons results.
2. Converge test on varies of properties to give a recommended energy cutoff of the pseudopotential, include properties:
   1. Cohesive energy
   2. phonon frequencies
   3. pressure
   4. bands distance

The computational details to running the calculation

Input Structures:

• In Δ-factor calculation: most stable elemental system from Cottenier's work and rare-earth nitrides from Topsakal-Wentzkovitch work;
• Phonon, pressure, cohesive energy: Cottenier's structures (except SiF4 has been used for F because of convergence issues) and rare-earth nitrides; Use primitive cells.
• Bands: Cottenier's structures reduced to primitive cells (except SiF4 has been used for F because of convergence issues) and rare-earth nitrides. PwbandWorkflow will make a primitive cell for band calculation (Remember to turn off the relax step).

Parameters of Δ calculations

• wave function cutoffs: 200 Ry;
• dual = 8 (PAW/US), 4 (NC); Mn/Fe/Co have larger duals tested as well; 12 and 16. We have gone in a mode where we do not use the dual, but we use ECUTRHO and ECUTWFC. However, dual is still used in simply setting the ecutwfc/ecutrho pairs.
• k-points: 0.1A^-1;
• smearing (degauss): Marzari-Vanderbilt, 0.01 Ry;
• non spin-polarized calculations except Mn (antiferromagnetic), O and Cr (antiferromagnetic), Fe, Co, and Ni (ferromagnetic).

As for calculation of lanthenide, always increase nbnd to two times of the default number.

Parameters in phonon, pressure, cohesive energy calculations:

• k-points: 0.15A^-1
• smearing: Marzari-Vanderbilt, 0.01 Ry;
• k-points for the isolated atoms: 1x1x1;
• smearing for the isolated atoms: gaussian 0.01 Ry;
• unit cell for the isolated atoms: 12x12x12 Å with atom sit in [6.0, 6.0, 6.0] the middle of the cell;
• q-point: only calculate the phonon frequencies on Brillouin-Zone border q=(0.5, 0.5, 0.5).
• all calculations non-spin-polarized.

In isolate atom energy calculation of cohesive energy evaluation. As for lanthenide, increase nbnd to three times of the default number. Moreover, use more RAM(by increase num_machine to 4).

NOTE: PWscf writes in the output something called total energy. This is NOT the total energy when you have smearing; it’s the total free energy E-TS. PWscf also writes -TS, so one can get back the total energy E. In general (for a metal) E-TS should be used. For an atom instead the total energy should be used, since the -TS term is not really physical (it comes from the entropy of fractional occupations on the atom). Check with Nicola if you have atoms where -TS is different from zero. (http://theossrv1.epfl.ch/Main/ElectronicTemperature)

The convergence pattern for the phonons is calculated as:

• circle = (1/N * ∑i=1,N [ωi(cutoff) - ωi(200Ry)]2 / ωi(200Ry)2)1/2 * 100 (in percentage) and half error bar = Max |[ω(cutoff) - ω(200Ry)] / ω(200Ry)| * 100, if the highest frequency is more than 100 cm-1;
• circle = (1/N * ∑i=1,N [ωi(cutoff) - ωi(200Ry)]2)1/2 (absolute value) and half error bar = Max |ωi(cutoff) - ω(200Ry)|, if the highest frequency is less than 100 cm-1;
• N is the total number of frequencies;
• For some elements, we have neglected the first n frequencies in the summation above, because the frequencies are negative and/or with strong oscillations as function of the cutoff for all the considered pseudos). We have neglected the first four frequencies for H and I, 12 for N and Cl, 6 for O and SiF4 (which replaces F).

Bands calculations:

• k-points for the self-consistent calculation: 0.1; (can use cache one for the latter calculation)
• k-points for the bands calculation (as in, calculations of the eta and eta10 factors): uniform mesh 0.2 with no symmetry reduction, rather than high-symmetry path which is not determinant;
• smearing: Marzari-Vanderbilt, 0.01 Ry in scf calculation and Fermi-Dirac in bands distance calculation;
• all calculations non spin-polarized.

Repository contents

Features

More meta-info collection

SiF4 structure and its (V0, B0, B1) reference value

Re-generate the SiF4 structure start from the cif file from COD database. Detail inputs parameters are list below.

Pseudopotentials(SSSP-v1.1 precision)

• Si: Si.pbe-n-rrkjus_psl.1.0.0.UPF
• F: F.oncvpsp.upf

Pw relax and eos

pwscf parameters

'SYSTEM': {
    'degauss': 0.00735,
    'ecutrho': 1600,
    'ecutwfc': 200,
    'occupations': 'smearing',
    'smearing': 'marzari-vanderbilt',
},
'ELECTRONS': {
    'conv_thr': 1e-10,
},

EOS parameters

• seven points
• 0.02 interval

Publishing Releases

1. Create a release PR/commit to the develop branch, updating version number of aiida_sssp_workflow/__init__.py, setup.json and update CHANGELOG.md.
2. Fast-forward merge develop into the master branch
3. Create a release on GitHub (https://github.com/aiidateam/aiida-sssp-workflow/releases/new), pointing to the release commit on master, named v.X.Y.Z (identical to version in setup.json)
4. This will trigger the continuous-deployment GitHub workflow which, if all tests pass, will publish the package to PyPi. Check this has successfully completed in the GitHub Actions tab (https://github.com/aiidateam/aiida-sssp-workflow/actions).

(if the release fails, delete the release and tag)

License

MIT

Contact

[e-mail]