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psitools

This is a Python package named psitools. It implements numerical methods and driver routines for solving the linear stability problem of the Polydispserse Streaming Instability (Paardekooper et al. 2020,Paardekooper et al. 2021; McNally et al. 2021).

Zenodo record for all versions 10.5281/zenodo.4305344

Please cite the Zenodo record and appropriate papers if you use psitools in a publication.

Figure: A colorized PSI dispersion relation map in the complex plane, showing the poles and branch cuts in a case for a growing size resonance mode.

Contents

  • psitools/: package source
    • psitools/complex_roots_mpi.py: MPI driver for evaluating the PSI dispersion relation
    • psitools/direct.py: Direct PSI eigensolver
    • psitools/direct_mpi.py: MPI driver for direct PSI eigensolver
    • psitools/monodisperse_si: mSI eigensolver
    • psitools/power_bump.py: PB dust distribution
    • psitools/psi_mode.py: The root-finder PSI eigenvalue solver
    • psitools/psi_mode_mpi.py: MPI driver for psi_mode
    • psitools/psi_grid_refine.py: MPI based grid-refinement eigenvalue mapper using psi_mode
    • psitools/tanhsinh.py: TanhSinh quadrature implementation
    • psitools/taus_gridding.py: Gridding functions for direct solver
    • psitools/terminalvelocitysolver.py: Terminal velocity approximation PSI eigensolver
    • psitools/test_*: pytest tests, provides functional examples
  • psitools_examples/: Some additional usage examples
  • anaconda_environments/: Anaconda Python environment specification with required packages
  • .circleci/ CircleCI based test setup for the GitHub repo.

Testing

The package includes tests built with pytest. There are several tags for selecting tests:

  • mpi: Tests to run with pytest-mpi
  • slow: Tests which take too long to use in the CI autotest

One way to run functional tests, using the included conda specification:

$ conda env create -f anaconda_environments/STE_environment.yml
$ conda activate STE

Then install psitools, by directing pip (not system pip, the one inside the above environment) to the location of the setup.py:

$ pip install -e ~/path/to/repo

Before trying to run tests, deactivate and reactivate the conda environment:

$ conda deactivate
$ conda activate STE

Then try pytest:

$ pytest -m "not mpi" path/to/psitools-public

To do the MPI tests, run under MPI with pytest-mpi, which you will probably need to install via pip. pytest-mpi in the current version has repeated output, but something should eventually show up.

$ mpirun -np 5 python -m pytest --pyargs psitools --with-mpi path/to/psitools-public

To run a specific test, do something like:

$ mpirun -np 4 python -m pytest --pyargs psitools --with-mpi \
    -s -k "test_psi_grid_refine_0" path/to/psitools-public

Or, testing with a virtualenv, do something like:

$ python -m venv --system-site-packages test-psitools/
$ . test-psitools/bin/activate
$ pip install -e ~/path/to/repo
$ deactivate
$ . test-psitools/bin/activate

And continue as before.

Authors / Contributors:

Papers

Polydisperse streaming instability - I. Tightly coupled particles and the terminal velocity approximation
Paardekooper, Sijme-Jan; McNally, Colin P.; Lovascio, Francesco
Monthly Notices of the Royal Astronomical Society, Volume 499, Issue 3, pp.4223-4238, 2020
DOI: 10.1093/mnras/staa3162
ADS: 2020MNRAS.499.4223P
arXiv:2010.01145

Polydisperse Streaming Instability II. Methods for solving the linear stability problem 
Paardekooper, Sijme-Jan; McNally, Colin P.; Lovascio, Francesco
Monthly Notices of the Royal Astronomical Society, Volume 502, Issue 2, pp.1579-1595, 2021
DOI: 10.1093/mnras/stab111 
ADS: 2021arXiv210104763P
arXiv:2101.04763

Polydisperse Streaming Instability III. Dust evolution encourages fast instability
McNally, Colin P.; Lovascio, Francesco; Paardekooper, Sijme-Jan
Monthly Notices of the Royal Astronomical Society, Volume 502, Issue 1, pp.1469-1486, 2021
DOI: 10.1093/mnras/stab112
ADS: 2021arXiv210104761M
arXiv:2101.04763

License

Copyright 2020 Colin McNally, Sijme-Jan Paardekooper, Francesco Lovascio

This file is part of psitools.

psitools is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

psitools is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with psitools. If not, see https://www.gnu.org/licenses/.