PyPartMC 0.7.1__cp311-cp311-macosx_14_0_arm64.whl → 1.3.6__cp311-cp311-macosx_14_0_arm64.whl
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- PyPartMC/__init__.py +48 -16
- {PyPartMC-0.7.1.dist-info → PyPartMC-1.3.6.dist-info}/METADATA +109 -86
- PyPartMC-1.3.6.dist-info/RECORD +7 -0
- PyPartMC-1.3.6.dist-info/WHEEL +5 -0
- _PyPartMC.cpython-311-darwin.so +0 -0
- PyPartMC-0.7.1.dist-info/RECORD +0 -7
- PyPartMC-0.7.1.dist-info/WHEEL +0 -5
- {PyPartMC-0.7.1.dist-info → PyPartMC-1.3.6.dist-info}/LICENSE +0 -0
- {PyPartMC-0.7.1.dist-info → PyPartMC-1.3.6.dist-info}/top_level.txt +0 -0
PyPartMC/__init__.py
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"""
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.. include::../README.md
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"""
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# pylint: disable=invalid-name,wrong-import-position
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import os
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from collections import namedtuple
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""
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def __generate_si():
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prefixes = {
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"T": 1e12,
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"G": 1e9,
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"M": 1e6,
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"k": 1e3,
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"h": 1e2,
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"da": 1e1,
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"": 1e0,
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"d": 1e-1,
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"c": 1e-2,
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"m": 1e-3,
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"u": 1e-6,
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"n": 1e-9,
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"p": 1e-12,
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}
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units = {
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"m": 1e0,
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"g": 1e-3,
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"s": 1e0,
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"K": 1e0,
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"Pa": 1e0,
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"mol": 1e0,
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"W": 1e0,
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"J": 1e0,
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"N": 1e0,
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}
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return namedtuple("SI", [prefix + unit for prefix in prefixes for unit in units])(
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**{
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prefix_k + unit_k: prefix_v * unit_v
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for prefix_k, prefix_v in prefixes.items()
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for unit_k, unit_v in units.items()
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}
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)
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si = __generate_si()
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""" a utility namedtuple aimed at clrifying physics-related code by providing
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SI-prefix-aware unit multipliers, resulting in e.g.: `p = 1000 * si.hPa`
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notation. Note: no dimensional analysis is done! """
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with __build_extension_env():
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import _PyPartMC
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from _PyPartMC import *
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from _PyPartMC import __all__
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from _PyPartMC import __all__ as _PyPartMC_all # pylint: disable=no-name-in-module
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from _PyPartMC import __version__, __versions_of_build_time_dependencies__
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__all__ = tuple([*_PyPartMC_all, "si"])
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Metadata-Version: 2.1
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Name: PyPartMC
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Version:
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Version: 1.3.6
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Summary: Python interface to PartMC
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Author:
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Author-email:
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Author: PyPartMC team (see https://github.com/open-atmos/PyPartMC/graphs/contributors)
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Author-email: nriemer@illinois.edu
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License: GPL-3.0
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Project-URL: Tracker, https://github.com/open-atmos/PyPartMC/issues
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Project-URL: Documentation, https://open-atmos.github.io/PyPartMC
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License-File: LICENSE
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Requires-Dist: numpy
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Provides-Extra: tests
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Requires-Dist: pytest
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Requires-Dist: pytest-order
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Requires-Dist: fastcore
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Requires-Dist: ghapi
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Requires-Dist: pytest; extra == "tests"
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Requires-Dist: pytest-order; extra == "tests"
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Requires-Dist: fastcore!=1.5.8; extra == "tests"
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Requires-Dist: ghapi; extra == "tests"
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Requires-Dist: scipy; extra == "tests"
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PyPartMC is a Python interface to [PartMC](https://lagrange.mechse.illinois.edu/partmc/),
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a particle-resolved Monte-Carlo code for atmospheric aerosol simulation.
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PyPartMC is implemented in C++ and it also constitutes a C++ API to the PartMC Fortran internals.
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The Python API can facilitate using PartMC from other environments - see, e.g., Julia
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The Python API can facilitate using PartMC from other environments - see, e.g., Julia and Matlab examples below.
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For an outline of the project, rationale, architecture, and features, refer to: [D'Aquino et al.,
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For an outline of the project, rationale, architecture, and features, refer to: [D'Aquino et al., 2024 (SoftwareX)](https://doi.org/10.1016/j.softx.2023.101613) (please cite if PyPartMC is used in your research).
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For a list of talks and other relevant resources, please see [project Wiki](https://github.com/open-atmos/PyPartMC/wiki/).
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If interested in contributing to PyPartMC, please have a look a the [notes for developers](https://github.com/open-atmos/PyPartMC/tree/main/CONTRIBUTING.md).
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[](https://asr.science.energy.gov/)
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[](https://asr.science.energy.gov/) [](https://www.ncn.gov.pl/?language=en)
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[](https://www.gnu.org/licenses/gpl-3.0.html)
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[](https://atmos.illinois.edu/)
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[](https://open-atmos.github.io/PyPartMC/)
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[](https://github.com/open-atmos/PyPartMC/actions)
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[](https://open-atmos.github.io/PyPartMC/)
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[](https://doi.org/10.5281/zenodo.7662635)
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[](https://pypi.org/p/PyPartMC)
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## TL;DR (try in a Jupyter notebook)
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```
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#### Jupyter notebooks with examples
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Note: clicking the badges below redirects to cloud-computing platforms. The mybinder.org links allow anonymous execution, Google Colab requires logging in with a Google account, ARM JupyerHub requires logging in with an ARM account (and directing Jupyter to a particular notebook within the `examples` folder).
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- Urban plume scenario demo (as in [PartMC](https://github.com/compdyn/partmc/tree/master/scenarios/1_urban_plume)):
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[](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb)
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- Urban plume scenario demo (as in [PartMC](https://github.com/compdyn/partmc/tree/master/scenarios/1_urban_plume)):
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[](https://github.com/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb)
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[](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb)
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[](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/particle_simulation.ipynb)
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[](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=)
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- Dry-Wet Particle Size Equilibration with PartMC and PySDM:
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[](https://github.com/open-atmos/PyPartMC/blob/main/examples/lognorm_ex.ipynb)
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[](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/lognorm_ex.ipynb)
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[](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/lognorm_ex.ipynb)
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[](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=)
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[](https://mybinder.org/v2/gh/open-atmos/PyPartMC/main?urlpath=voila%2Frender%2Fexamples%2Flognorm_ex.ipynb)
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- Simulation output processing example (loading from netCDF files using PyPartMC):
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[](https://github.com/open-atmos/PyPartMC/blob/main/examples/process_simulation_output.ipynb)
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[](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/process_simulation_output.ipynb)
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[](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/process_simulation_output.ipynb)
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[](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=)
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- Optical properties calculation using external Python package ([PyMieScatt](https://pymiescatt.readthedocs.io/en/latest/)):
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[](https://github.com/open-atmos/PyPartMC/blob/main/examples/mie_optical.ipynb)
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[](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/mie_optical.ipynb)
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[](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/mie_optical.ipynb)
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[](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=)
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- Cloud parcel example featuring supersaturation-evolution-coupled CCN activation and drop growth:
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[](https://github.com/open-atmos/PyPartMC/blob/main/examples/cloud_parcel.ipynb)
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[](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/cloud_parcel.ipynb)
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[](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/cloud_parcel.ipynb)
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[](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=)
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## Features
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- ships with [a set of examples](https://github.com/open-atmos/PyPartMC/tree/main/examples) maintained in a form of Jupyter notebooks
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- Pythonic API (but retaining PartMC jargon) incl. Python GC deallocation of Fortran objects
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- specification of parameters using native Python datatypes (lists, dicts) in place of PartMC spec files
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- code snippets in README depicting how to use PyPartMC from Julia (also executed on CI)
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- code snippets in README depicting how to use PyPartMC from Julia and Matlab (also executed on CI)
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- auto-generated [API docs on the web](https://open-atmos.github.io/PyPartMC/)
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- support for [de]serialization of selected wrapped structures using JSON
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- based on [unmodified PartMC code](https://github.com/open-atmos/PyPartMC/tree/main/gitmodules)
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## Usage examples
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The listings below depict how the identical task of randomly sampling particles from an aerosol size distribution in PartMC can be
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done in different programming languages.
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For a Fortran equivalent of the Python and
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For a Fortran equivalent of the Python, Julia and Matlab programs below, see the [`readme_fortran` folder](https://github.com/open-atmos/PyPartMC/tree/main/readme_fortran).
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#### Python
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```
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#### Julia (using [PyCall.jl](https://github.com/JuliaPy/PyCall.jl))
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print(aero_state.masses()'aero_state.num_concs, "# kg/m3")
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```
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#### Matlab (using [Matlab's built-in Python interface](https://www.mathworks.com/help/matlab/python-language.html))
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notes (see the [PyPartMC Matlab CI workflow](https://github.com/open-atmos/PyPartMC/blob/main/.github/workflows/readme_listings.yml) for an example on how to achieve it on Ubuntu 20):
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- Matlab ships with convenience copies of C, C++ and Fortran runtime libraries which are `dlopened()` by default; one way to make PyPartMC OK with it is to [pip-]install by compiling from source using the very same version of GCC that Matlab borrowed these libraries from (e.g., [GCC 9 for Matlab R2022a, etc](https://www.mathworks.com/support/requirements/supported-compilers-linux.html));
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- Matlab needs to [use the same Python interpretter/venv](https://www.mathworks.com/support/requirements/python-compatibility.html) as the pip invocation used to install PyPartMC;
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- a single-line `pybind11_builtins.py` file with just `pybind11_type=type` inside needs to be placed within Matlab's `PYTHONPATH` to sort out a [Matlab-pybind11 incompatibility](https://github.com/pybind/pybind11/issues/3945).
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````Matlab
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ppmc = py.importlib.import_module('PyPartMC');
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si = py.importlib.import_module('PyPartMC').si;
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aero_data = ppmc.AeroData(py.tuple({ ...
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py.dict(pyargs("OC", py.tuple({1000 * si.kg/si.m^3, 0, 1e-3 * si.kg/si.mol, 0.001}))), ...
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py.dict(pyargs("BC", py.tuple({1800 * si.kg/si.m^3, 0, 1e-3 * si.kg/si.mol, 0}))) ...
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}));
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aero_dist = ppmc.AeroDist(aero_data, py.tuple({ ...
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py.dict(pyargs( ...
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"mass_frac", py.tuple({py.dict(pyargs("OC", py.tuple({1})))}), ...
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"diam_type", "geometric", ...
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"num_conc", 3200 / si.cm^3, ...
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"geom_mean_diam", 8.64 * si.nm, ...
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"log10_geom_std_dev", .28 ...
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)) ...
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)), ...
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py.dict(pyargs( ...
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"diesel", py.dict(pyargs( ...
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"mass_frac", py.tuple({ ...
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py.dict(pyargs("OC", py.tuple({.3}))), ...
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py.dict(pyargs("BC", py.tuple({.7}))), ...
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}), ...
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)) ...
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)) ...
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}));
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n_part = 100;
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aero_state = ppmc.AeroState(aero_data, n_part, "nummass_source");
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aero_state.dist_sample(aero_dist);
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masses = cell(aero_state.masses());
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num_concs = cell(aero_state.num_concs);
|
|
244
|
+
fprintf('%g # kg/m3\n', dot([masses{:}], [num_concs{:}]))
|
|
245
|
+
````
|
|
246
|
+
|
|
177
247
|
#### usage in other projects
|
|
178
248
|
|
|
179
249
|
PyPartMC is used within the [test workflow of the PySDM project](https://github.com/atmos-cloud-sim-uj/PySDM/tree/main/tests/smoke_tests/box/partmc).
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|
180
250
|
|
|
181
|
-
##
|
|
182
|
-
|
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183
|
-
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184
|
-
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185
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-
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186
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-
- C (SUNDIALS, netCDF), C++ (pybind11, ...) and Fortran (PartMC, CAMP, netCDF-fortran) dependencies are linked through [git submodules](https://github.com/open-atmos/PyPartMC/blob/main/.gitmodules)
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187
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-
- MOSAIC dependency is optionally linked through setting the environmental variable `MOSAIC_HOME`
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188
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-
- a [drop-in replacement of the PartMC spec file routines](https://github.com/open-atmos/PyPartMC/blob/main/src/fake_spec_file.F90) is used for i/o from/to JSON
|
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189
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-
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190
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-
## Implementation architecture
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-
|
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-
```mermaid
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-
flowchart TD
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|
-
subgraph J ["Julia"]
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195
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-
julia_user_code["Julia user code"] --> PyCall.jl
|
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196
|
-
end
|
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197
|
-
subgraph P ["Python"]
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198
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-
PyCall.jl --> PyPartMC
|
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199
|
-
python_user_code -.-> NumPy
|
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200
|
-
python_user_code["Python user code"] ---> PyPartMC["pubind11-generated PyPartMC module"]
|
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201
|
-
end
|
|
202
|
-
subgraph Cpp ["C++"]
|
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203
|
-
cpp_user_code["C++ user code"] ----> ppmc_cpp
|
|
204
|
-
PyPartMC --> ppmc_cpp["PyPartMC-C++"]
|
|
205
|
-
ppmc_cpp --> pybind11_json
|
|
206
|
-
pybind11_json ---> nlohmann::JSON
|
|
207
|
-
fake_spec_file_cpp --> nlohmann::JSON
|
|
208
|
-
end
|
|
209
|
-
subgraph C ["C"]
|
|
210
|
-
fake_spec_file_c --> fake_spec_file_cpp["SpecFile-C++"]
|
|
211
|
-
ppmc_cpp --> ppmc_c["PyPartMC-C"]
|
|
212
|
-
netCDF-C
|
|
213
|
-
SUNDIALS
|
|
214
|
-
camp_c["CAMP C code"]
|
|
215
|
-
end
|
|
216
|
-
subgraph Fortran ["Fortran"]
|
|
217
|
-
PartMC -....-> MOSAIC
|
|
218
|
-
ppmc_c --> ppmc_f["PyPartMC-F"]
|
|
219
|
-
ppmc_f ---> PartMC
|
|
220
|
-
PartMC --> netCDF-F
|
|
221
|
-
netCDF-F --> netCDF-C
|
|
222
|
-
PartMC --> SUNDIALS
|
|
223
|
-
PartMC ---> camp_f
|
|
224
|
-
camp_f["CAMP"] --> camp_c
|
|
225
|
-
PartMC ----> fake_spec_file_f[SpecFile-F]
|
|
226
|
-
fake_spec_file_f --> fake_spec_file_c["SpecFile-C"]
|
|
227
|
-
end
|
|
228
|
-
|
|
229
|
-
style PartMC fill:#7ae7ff,stroke-width:2px,color:#2B2B2B
|
|
251
|
+
## FAQ
|
|
252
|
+
- Q: How to install PyPartMC with MOSAIC enabled?
|
|
253
|
+
A: Installation can be done using `pip`, however, `pip` needs to be instructed not to use binary packages available at pypi.org but rather to compile from source (pip will download the source from pip.org), and the path to compiled MOSAIC library needs to be provided at compile-time; the following command should convey it:
|
|
254
|
+
```bash
|
|
255
|
+
MOSAIC_HOME=<<PATH_TO_MOSAIC_LIB>> pip install --force-reinstall --no-binary=PyPartMC PyPartMC
|
|
230
256
|
```
|
|
231
257
|
|
|
232
|
-
## FAQ
|
|
233
258
|
- Q: Why `pip install PyPartMC` triggers compilation on my brand new Apple machine, while it quickly downloads and installs binary packages when executed on older Macs, Windows or Linux?
|
|
234
|
-
A: We are
|
|
259
|
+
A: We are providing binary wheels on PyPI for Apple-silicon (arm64) machines for selected macOS version made available by Github. In case the macOS version you are using is newer, compilation from source is triggered.
|
|
235
260
|
|
|
236
261
|
- Q: Why some of the constructors expect data to be passed as **lists of single-entry dictionaries** instead of multi-element dictionaries?
|
|
237
262
|
A: This is intentional and related with PartMC relying on the order of elements within spec-file input; while Python dictionaries preserve ordering (insertion order), JSON format does not, and we intend to make these data structures safe to be [de]serialized using JSON.
|
|
238
263
|
|
|
264
|
+
- Q: How to check the version of PartMC that PyPartMC was compiled against?
|
|
265
|
+
A: Version numbers of compile-time dependencies of PyPartMC, including PartMC, can be accessed as follows:
|
|
266
|
+
```Python
|
|
267
|
+
import PyPartMC
|
|
268
|
+
PyPartMC.__versions_of_build_time_dependencies__['PartMC']
|
|
269
|
+
```
|
|
270
|
+
|
|
271
|
+
- Q: Why m4 and perl are required at compile time?
|
|
272
|
+
A: PyPartMC includes parts of netCDF and HDF5 codebases which depend on m4 and perl, respectively, for generating source files before compilation.
|
|
273
|
+
|
|
239
274
|
## Troubleshooting
|
|
240
275
|
|
|
241
276
|
#### Common installation issues
|
|
@@ -254,24 +289,12 @@ Could not find NC_M4 using the following names: m4, m4.exe
|
|
|
254
289
|
```
|
|
255
290
|
Try installing `m4` (e.g., using [MSYS2](https://packages.msys2.org/package/m4?repo=msys&variant=x86_64) on Windows).
|
|
256
291
|
|
|
257
|
-
## Notes for developers
|
|
258
|
-
#### How to debug
|
|
259
|
-
```sh
|
|
260
|
-
git clone --recursive git+https://github.com/open-atmos/PyPartMC.git
|
|
261
|
-
cd PyPartMC
|
|
262
|
-
DEBUG=1 VERBOSE=1 pip --verbose install -e .
|
|
263
|
-
gdb python
|
|
264
|
-
(gdb) run -m pytest -s -vv -We -p no:unraisableexception tests
|
|
265
|
-
```
|
|
266
|
-
#### Pre-commit hooks
|
|
267
|
-
PyPartMC codebase benefits from Pylint, Black and isort code analysis (which are all part of the CI workflows where we also use pre-commit hooks. The pre-commit hooks can be run locally, and then the resultant changes need to be staged before committing. To set up the hooks locally, install pre-commit via `pip install pre-commit` and set up the git hooks via `pre-commit install` (this needs to be done every time you clone the project). To run all pre-commit hooks, run `pre-commit run --all-files`. The `.pre-commit-config.yaml` file can be modified in case new hooks are to be added or existing ones need to be altered.
|
|
268
|
-
|
|
269
292
|
## Credits
|
|
270
293
|
|
|
271
294
|
#### PyPartMC:
|
|
272
295
|
|
|
273
296
|
authors: [PyPartMC developers](https://github.com/open-atmos/PyPartMC/graphs/contributors)
|
|
274
|
-
funding: [US Department of Energy Atmospheric System Research programme](https://asr.science.energy.gov/)
|
|
297
|
+
funding: [US Department of Energy Atmospheric System Research programme](https://asr.science.energy.gov/), [Polish National Science Centre](https://ncn.gov.pl/en)
|
|
275
298
|
copyright: [University of Illinois at Urbana-Champaign](https://atmos.illinois.edu/)
|
|
276
299
|
licence: [GPL v3](https://www.gnu.org/licenses/gpl-3.0.en.html)
|
|
277
300
|
|
|
@@ -0,0 +1,7 @@
|
|
|
1
|
+
_PyPartMC.cpython-311-darwin.so,sha256=PlgK4xEGPvnCymGfkSx2mNjQ_P5Q7hcj2igLpWSWD5E,7690960
|
|
2
|
+
PyPartMC/__init__.py,sha256=VAqwePpJZEFJ7YieM1GbUvfluRhUyWXciP89pY9xIH4,2217
|
|
3
|
+
PyPartMC-1.3.6.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
|
|
4
|
+
PyPartMC-1.3.6.dist-info/METADATA,sha256=8VrL8W2i2SupJBy_VIYUncaGGu92F-8tSdZ76HShRbs,19059
|
|
5
|
+
PyPartMC-1.3.6.dist-info/WHEEL,sha256=Q7p5oqHZOZAXAiIGnjR5HFR_GU55bmirdQn4LwDE4jM,114
|
|
6
|
+
PyPartMC-1.3.6.dist-info/top_level.txt,sha256=PJxy22pTnxcBhqrb6r4AIL32rkxA61gzw7ohlzybgSM,19
|
|
7
|
+
PyPartMC-1.3.6.dist-info/RECORD,,
|
_PyPartMC.cpython-311-darwin.so
CHANGED
|
Binary file
|
PyPartMC-0.7.1.dist-info/RECORD
DELETED
|
@@ -1,7 +0,0 @@
|
|
|
1
|
-
_PyPartMC.cpython-311-darwin.so,sha256=fN-r3Ghib_4Tacl3ZdLfR2aBjUrv8R5jeDLxWZoG8Jk,3609504
|
|
2
|
-
PyPartMC/__init__.py,sha256=x4i-ZXpn25wXmkfhYD3h8u0Ylf5RLosn-r7CUuHzh1U,1372
|
|
3
|
-
PyPartMC-0.7.1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
|
|
4
|
-
PyPartMC-0.7.1.dist-info/METADATA,sha256=5CnIGOJWBsnei-qjZSe_IDOb8ALsvjByytxQDZncy74,14695
|
|
5
|
-
PyPartMC-0.7.1.dist-info/WHEEL,sha256=HWYX263JeAjyVv057HbcELWrJCfjqgjaP_5I-d5jo6M,110
|
|
6
|
-
PyPartMC-0.7.1.dist-info/top_level.txt,sha256=PJxy22pTnxcBhqrb6r4AIL32rkxA61gzw7ohlzybgSM,19
|
|
7
|
-
PyPartMC-0.7.1.dist-info/RECORD,,
|
PyPartMC-0.7.1.dist-info/WHEEL
DELETED
|
File without changes
|
|
File without changes
|