acom-music-box

A box/column model using MICM chemistry

Science Score: 85.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
6 of 15 committers (40.0%) from academic institutions
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Institutional organization owner
Organization ncar has institutional domain (ncar.ucar.edu)
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Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary

Keywords from Contributors

ode-solver atmospheric-chemistry atmospheric-modeling atmospheric-science standardization interpretability quantum-computing pde correlation hack

Last synced: 6 months ago · JSON representation ·

Repository

A box/column model using MICM chemistry

Basic Info

Host: GitHub
Owner: NCAR
License: apache-2.0
Language: Jupyter Notebook
Default Branch: main
Homepage: https://ncar.github.io/music-box/branch/main/
Size: 28.7 MB

Statistics

Stars: 35
Watchers: 9
Forks: 15
Open Issues: 17
Releases: 33

Created over 5 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

MusicBox

MusicBox: A MUSICA model for boxes and columns.

Installation

pip install acom_music_box

If you would like GPU support, you must first add the NVIDIA pypi index and then you can specify the gpu install option for music box.

pip install --upgrade setuptools pip wheel pip install nvidia-pyindex pip install acom_music_box[gpu]

Using the MusicBox API

MusicBox makes its chemical mechanism analysis and visualization available through a Python API. The following example works through solving a simple chemistry system. Please refer to the official documentation for further tutorials and examples. ```python

Import MusicBox, MusicBox conditions, and Musica mechanisms:

from acommusicbox import MusicBox, Conditions import musica.mechanism_configuration as mc

Define the chemical system of interest

MusicBox uses Musica (https://ncar.github.io/musica/index.html) to create specific chemical species and phases of interest for chemical mechanisms.

A = mc.Species(name="A") B = mc.Species(name="B") C = mc.Species(name="C")

species = {"A":A, "B":B, "C":C}

gas = mc.Phase(name="gas", species=list(species.values()))

Define a mechanism of interest

Through Musica, several different mechanisms can be explored to define reaction rates. Here, we use the Arrhenius equation as a simple example.

arr1 = mc.Arrhenius(name="A->B", A=4.0e-3, C=50,reactants=[species["A"]], products=[species["B"]], gas_phase=gas)

arr2 = mc.Arrhenius(name="B->C", A=1.2e-4, B=2.5, C=75, D=50, E=0.5, reactants=[species["B"]], products=[species["C"]], gas_phase=gas)

mechanism = mc.Mechanism(name="test_mechanism", species=list(species.values()),phases=[gas], reactions=[arr1, arr2])

Create a box model

To create a box model, including its mechanisms, conditions, length, time, and step times:

boxmodel = MusicBox() boxmodel.load_mechanism(mechanism)

In the box model, the initial set of conditions represent the starting environment for the reactions.

Both initial and evolving conditions are typically created alongside the creation of the box model:

boxmodel.initialconditions = Conditions(temperature=300.0, pressure=101000.0, species_concentrations={ "A": 1.0, "B": 3.0, "C": 5.0})

Evolving conditions represent a set of environmental and species values or rate constants that the box model should use at a specific time step.

The following adds an evolving condition to the model, the first float represents the time when the condition evolves:

boxmodel.addevolvingcondition(300.0,Conditions(temperature=290.0, pressure=100200.0, speciesconcentrations={"A": 1.0, "B": 3.0, "C": 10.0}))

boxmodel.boxmodeloptions.simulationlength = 20 # total simulation time boxmodel.boxmodeloptions.chemsteptime = 1 # time step for chemical reaction boxmodel.boxmodeloptions.outputsteptime = 4 # time step between each output

Solve your newly-created box model and view results:

df = box_model.solve() print(df)

To visualize specific results:

import matplotlib.pyplot as plt

df.plot(x='time.s', y=['CONC.A.mol m-3', 'CONC.B.mol m-3', 'CONC.C.mol m-3'], title='Concentration over time', ylabel='Concentration (mol m-3)', xlabel='Time (s)') plt.show()

```

Command line tool

MusicBox provides a command line tool that can run configurations as well as some pre-configured examples. Basic plotting can be done with matplotlib.

Checkout the command line options

music_box -h

Run an example. Notice that the output, in csv format, is printed to the terminal.

music_box -e Chapman

Output can be saved to a csv file (the default format) and printed to the terminal.

music_box -e Chapman -o output

Output can be saved to a csv file by specifying the .csv extension for Comma-Separated Values.

music_box -e Chapman -o output.csv

Output can be saved to a file as netcdf file by specifying the .nc file extension.

music_box -e Chapman -o output.nc

Output can be saved to a file in csv format when a filename is not specified. In this case a timestamped csv file is made.

music_box -e Chapman

You may also specify multiple output files with different formats, using the file extension.

music_box -e Analytical -o results.csv -o results.nc

You can also run your own configuration

music_box -c my_config.json

Plotting

Some basic plots can be made to show concentrations throughout the simulation using matplotlib.

music_box -e Chapman -o output.csv --plot O1D

You can also make multiple plots by specifying groupings of species

music_box -e TS1 --plot O3 --plot PAN,HF

Note that the windows may overlap each other

By default all plot units are in mol m-3. You can see a list of unit options to specify with --plot-output-unit

music_box -h

It is used like this

music_box -e TS1 --plot O3 --plot-output-unit "ppb"

Development and Contributing

For local development, install music-box as an editable installation:

pip install -e '.[dev]'

Tests

pytest

Owner

Name: NSF National Center for Atmospheric Research
Login: NCAR
Kind: organization
Location: Boulder, CO

Website: http://ncar.ucar.edu
Repositories: 934
Profile: https://github.com/NCAR

NSF NCAR is sponsored by the U.S. National Science Foundation and managed by the University Corporation for Atmospheric Research.

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it as below.
title: MusicBox
version: v2.9.1
authors:
  - family-names: Dawson
    given-names: Matthew
  - family-names: Shores
    given-names: Kyle
  - family-names: Conley
    given-names: Andrew
  - family-names: De la Garza
    given-names: Evan
  - family-names: Drury
    given-names: Walker
  - family-names: Garza
    given-names: Alexander
  - family-names: Fattig
    given-names: Brendan
  - family-names: Drews
    given-names: Carl
  - family-names: Thind
    given-names: Montek
  - family-names: Kiran
    given-names: Aditya
  - family-names: Winney
    given-names: Aidan
  - family-names: Pak
    given-names: Angela
license: Apache-2.0
url: "https://github.com/NCAR/music-box"

GitHub Events

Total

Create event: 62
Release event: 4
Issues event: 67
Watch event: 27
Delete event: 56
Member event: 4
Issue comment event: 162
Push event: 337
Pull request review comment event: 190
Pull request event: 119
Pull request review event: 241
Fork event: 5

Last Year

Create event: 62
Release event: 4
Issues event: 67
Watch event: 27
Delete event: 56
Member event: 4
Issue comment event: 162
Push event: 337
Pull request review comment event: 190
Pull request event: 119
Pull request review event: 241
Fork event: 5

Committers

Last synced: 9 months ago

All Time

Total Commits: 362
Total Committers: 15
Avg Commits per committer: 24.133
Development Distribution Score (DDS): 0.646

Past Year

Commits: 134
Committers: 10
Avg Commits per committer: 13.4
Development Distribution Score (DDS): 0.493

Top Committers

Name	Email	Commits
Matthew Dawson	m**n@u**u	128
Kyle Shores	k**4@g**m	94
s-omas	4****s	66
github-actions[bot]	4****]	31
Carl Drews	d**s@u**u	12
alexjamesgarza	1****a	6
Andrew Conley	a**y@u**u	5
Montek Thind	m**d@u**u	5
Jiwon Gim	j**m@u**u	5
matchaSamurai	9****3	3
GitHub Actions	a**s@g**m	3
Mudassir Chapra	3****0	1
Evan De la Garza	1****2	1
AshayV04	1****4	1
Matthew Dawson	m**n@m**u	1

Committer Domains (Top 20 + Academic)

ucar.edu: 5 modeling2.acom.ucar.edu: 1 github.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 137
Total pull requests: 219
Average time to close issues: 11 months
Average time to close pull requests: 6 days
Total issue authors: 13
Total pull request authors: 18
Average comments per issue: 0.76
Average comments per pull request: 0.8
Merged pull requests: 181
Bot issues: 0
Bot pull requests: 39

Past Year

Issues: 52
Pull requests: 120
Average time to close issues: 17 days
Average time to close pull requests: 2 days
Issue authors: 9
Pull request authors: 12
Average comments per issue: 0.58
Average comments per pull request: 1.1
Merged pull requests: 93
Bot issues: 0
Bot pull requests: 29

View more stats

Top Authors

Issue Authors

mattldawson (51)
K20shores (33)
AndrewJConley (16)
boulderdaze (10)
angelapak (7)
carl-drews (6)
aidan-winney (5)
marybarthbrock (2)
adityakiran1423 (2)
SancyW (2)
kkowalsk (1)
sjsprecious (1)
jolsolsen (1)

Pull Request Authors

K20shores (58)
mattldawson (44)
github-actions[bot] (39)
carl-drews (14)
aidan-winney (11)
s-omas (11)
angelapak (10)
montythind (6)
alexjamesgarza (6)
boulderdaze (6)
adityakiran1423 (3)
AndrewJConley (3)
DeeGrant (2)
AshayV04 (2)
eadlg2 (1)

Top Labels

Issue Labels

enhancement (46) documentation (19) bug (18) good first issue (7) question (5) help wanted (1) Stale (1) blocked (1)

Pull Request Labels

documentation (15) bug (4) enhancement (2) good first issue (1)

Packages

Total packages: 1
Total downloads:
- pypi 410 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 27
Total maintainers: 3

pypi.org: acom-music-box

An atmospheric chemistry box model. Powered by MUSICA.

Homepage: https://github.com/NCAR/music-box
Documentation: https://acom-music-box.readthedocs.io/
License: Apache Software License
Latest release: 2.9.1
published 8 months ago

Versions: 27
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 410 Last month

Rankings

Dependent packages count: 9.6%

Average: 36.4%

Dependent repos count: 63.2%

Maintainers (3)

musica boulderdaze kshores

Last synced: 6 months ago

Dependencies

.github/workflows/test.yml actions

actions/checkout v2 composite

Dockerfile docker

fedora 35 build

.github/workflows/publish-package.yml actions

actions/checkout v2 composite
docker/build-push-action v5 composite
docker/login-action f054a8b539a109f9f41c372932f1ae047eff08c9 composite
docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite

acom-music-box

Science Score: 85.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

MusicBox

Installation

Using the MusicBox API

Import MusicBox, MusicBox conditions, and Musica mechanisms:

Define the chemical system of interest

MusicBox uses Musica (https://ncar.github.io/musica/index.html) to create specific chemical species and phases of interest for chemical mechanisms.

Define a mechanism of interest

Through Musica, several different mechanisms can be explored to define reaction rates. Here, we use the Arrhenius equation as a simple example.

Create a box model

To create a box model, including its mechanisms, conditions, length, time, and step times:

In the box model, the initial set of conditions represent the starting environment for the reactions.

Both initial and evolving conditions are typically created alongside the creation of the box model:

Evolving conditions represent a set of environmental and species values or rate constants that the box model should use at a specific time step.

The following adds an evolving condition to the model, the first float represents the time when the condition evolves:

Solve your newly-created box model and view results:

To visualize specific results:

Command line tool

Plotting

Development and Contributing

Tests

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: acom-music-box

Rankings

Maintainers (3)

Dependencies