judftteam / aiida-spirit

AiiDA plugin for the spirit code

aiida-spirit

AiiDA plugin for the spirit code

Installation

pip install aiida-spirit # install aiida-spirit from pypi
verdi quicksetup  # better to set up a new profile
verdi plugin list aiida.calculations  # should now show your calclulation plugins

Usage

Here goes a complete example of how to submit a test calculation using this plugin.

A quick demo of how to submit a calculation (the spirit python API needs to be installed for this to work: pip install spirit):

verdi daemon start     # make sure the daemon is running
cd examples
./example_LLG.py       # run test calculation
verdi process list -a  # check record of calculation

Development

git clone https://github.com/JuDFTteam/aiida-spirit .
cd aiida-spirit
pip install -e .[pre-commit,testing]  # install extra dependencies
pre-commit install  # install pre-commit hooks
pytest -v  # discover and run all tests

Note that pytest -v will create a test database and profile which requires to find the pg_ctl command. If pg_ctl is not found you need to nake sure that postgres is installed and then add the localtion of pg_ctl to the PATH:

# add postgres path for pg_ctl to PATH
# this is an example for Postgres 9.6 installed on a mac
PATH="/Applications/Postgres.app/Contents/Versions/9.6/bin/:$PATH"
export PATH

Citation

If you use AiiDA-Spirit please cite the method paper

• P. Rüßmann, J. Ribas Sobreviela, M. Sallermann, M. Hoffmann, F. Rhiem, and S. Blügel, The AiiDA-Spirit Plugin for Automated Spin-Dynamics Simulations and Multi-Scale Modeling Based on First-Principles Calculations, Front. Mater. 9, 825043 (2022). doi: 10.3389/fmats.2022.825043,

and the latest code release

• P. Rüßmann, J. Ribas Sobreviela, M. Sallermann, M. Hoffmann, F. Rhiem, and S. Blügel. JuDFTteam/aiida-spirit. Zenodo. doi: 10.5281/zenodo.8070770.

License

The AiiDA-Spirit code is under the MIT license.

Contact

[email protected]

aiida-spirit's Issues

Create a tool to visualize the output spin structure

A tool is needed that allows to visualize the initial and final spin structures after the SpiritCalculation finished.
Maybe VFRendering is the right tool for this.

SpiritParser not properly implemented yet

The SpiritCalculation always terminates with exit code 100 (ERROR_MISSING_OUTPUT_FILES) because the SpiritParser is not properly implemented yet.

• The comparison to the expected list of files in

  aiida-spirit/aiida_spirit/parsers.py

  Line 45 in a928f18

  if not set(files_expected) <= set(files_retrieved):

  does not work properly
• no parsing is done but the template code from the cookiecutter is still present

Improve Spirit parser

So far the spirit parser only takes some basics. This should be improved. See also discussion in issue #4:

Other useful outputs might be:
For LLG (Dynamics) (meaning LLG with any solver that is not VP/LBFGS and direct_minimization=false)

Snapshots of the spin configuration at different time intervals

• Energies at different time intervals

For LLG (Minimization) (So we probably expect some metastable configurations)

• The profile/radius (thinking of Skyrmions)

• Topological charge

For GNEB

• The saddle point configuration/energies

• Energy barrier

For HTST

• All of the quantities in htst_info

• Eigenvalues/Eigenvectors (if non sparse calculation)

MC

• Critical temperatures (requires post processing, so maybe a bit out of scope)
• Ground state spin configuration (simulated annealing + final minimization with LLG) (How to control convergence?)

Improve Spirit parameters input

So far the parameters input node for a SpiritCalculation only accepts strings, e.g. {'llg_temperature': '50.0', 'external_field_normal': '0.0 0.0 1.0'}.

This should be generalized to work with numerical values and some type checking should be included to ensure consistency of the input (i.e. ensure that for vectors 3 values are given, warn when floats are used where integer are expected, ...).

Allow to use more than the LLG method in spirit

The run_spirit.py script that is created in the SpiritCalculation
https://github.com/JuDFTteam/aiida-spirit/blob/develop/aiida_spirit/calculations.py#L174
only works for LLG, the Depondt solver and may include the +z initialization of the spins.

This should be generalized to cover the other modes of spirit (MC, GNEB, HTST, MMF), solvers (HEUN, LBFGS_Atlas, LBFGS_OSO, RK4, SIB, VP, VP_OSO) and configurations (+/-z, random, pinning, skyrmion, hopfion, dw_skyrmion, spin_spiral, noise).

A reference for the differnet methods, solvers and configurations can be found in the spirit python API documentatoion.

The couplings file only takes Jij's and no DMI vectors yet

Writing the couplings.txt input of the spirit calculation in

aiida-spirit/aiida_spirit/calculations.py

Line 161 in a928f18

def write_couplings_file(self, folder):

only includes the Jij's. This should be extended to use also DMI vectors.