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https://github.com/trixi-framework/krome.jl

KROME.jl is a lightweight Julia wrapper for KROME, a Fortran library for including chemistry and microphysics in astrophysics simulations.
https://github.com/trixi-framework/krome.jl

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KROME.jl is a lightweight Julia wrapper for KROME, a Fortran library for including chemistry and microphysics in astrophysics simulations.

Host: GitHub
URL: https://github.com/trixi-framework/krome.jl
Owner: trixi-framework
License: mit
Created: 2021-02-01T13:45:58.000Z (almost 4 years ago)
Default Branch: main
Last Pushed: 2024-03-24T16:00:35.000Z (9 months ago)
Last Synced: 2024-04-24T19:12:02.609Z (8 months ago)
Language: Julia
Homepage:
Size: 85 KB
Stars: 3
Watchers: 7
Forks: 0
Open Issues: 7
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Security: SECURITY.md

Awesome Lists containing this project

README

        # KROME.jl

[![Build Status](https://github.com/trixi-framework/KROME.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/KROME.jl/actions?query=workflow%3ACI)

[![Coveralls](https://coveralls.io/repos/github/trixi-framework/KROME.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/KROME.jl?branch=main)

[![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)

**KROME.jl** is a Julia package that wraps [KROME](http://kromepackage.org), a

Fortran library for including chemistry and microphysics in astrophysics

simulations.

**NOTE: This package is in its early stages and still highly experimental!

        Some things might not work yet, and implementation details may change

        at any time without warning.**

## Prerequisites

The following programs and tools must be available in the `PATH` such that they

can be called by the Julia process while building the package:

* Python 3 (`python3`)

* `make`

* GNU Fortran compiler (`gfortran`)

Also note that KROME has primarily been developed for Linux, but also works on

macOS. Both OS are automatically tested with KROME.jl. Windows is not supported

by KROME.

## Installation

If you have not yet installed Julia, please [follow the instructions for your

operating system](https://julialang.org/downloads/platform/). KROMEjl works

with Julia v1.5.

You can then install KROME.jl by executing

```shell

julia -e 'using Pkg; Pkg.add("KROME")'

```

By default, this will build the KROME library with the `hello` test activated,

i.e., passing `-test=hello` to the KROME preprocessing script. However, usually

you will want to pass your own network file and possibly other options to KROME

during preprocessing. This can be achieved via the environment variable

`JULIA_KROME_CUSTOM_ARGS`, which accepts a `;`-separated list of arguments that

will be passed to the `krome` preprocessor. For example, to provide a custom

network file while disabling the recombinations check, you can run the build

command above with

```shell

JULIA_KROME_CUSTOM_ARGS="-n;abs/path/to/react_skynet" julia -e 'using Pkg; Pkg.build("KROME")'

```

Please note that you have to specify the *absolute* path to the network file.

Next to the arguments to the `krome` preprocessing script, you can also

configure which Python 3 executable to use by setting the environment variable

`JULIA_KROME_PYTHON3_EXEC` to its full path. Furthermore, you can disable

compiler optimizations for the KROME library by setting the environment variable

`JULIA_KROME_OPTIMIZED_BUILD` to something other than `true`. By default,

optimizations are enabled.

## Usage

Have a look at the examples in [examples/](examples/) to find out how to use

KROME.jl. Right now there are two examples available.

### test_hello

To run this example, start Julia and execute the following:

```julia

julia> using KROME

julia> include(joinpath(KROME.examples_dir(), "test_hello", "test_hello.jl"));

julia> test_hello()

```

This will print out the abundancies as the chemical network evolves in time. To

store the results in a file, e.g., `test_hello.txt`, change the last line of the

snippet above to

```julia

julia> open("test_hello.txt", "w+") do io; test_hello(io); end

```

### av-slab-benchmark

To run this example, you first need to build KROME.jl with a different network

file by executing

```shell

KROME_NETWORK_FILE=$(julia -e 'using KROME; println(joinpath(KROME.examples_dir(), "av-slab-benchmark", "react_chnet5"))') \

  JULIA_KROME_CUSTOM_ARGS="-n;$KROME_NETWORK_FILE;-noRecCheck" \

  julia -e 'using Pkg; Pkg.build("KROME")'

```

The command

```shell

julia -e 'using KROME; println(joinpath(KROME.examples_dir(), "av-slab-benchmark", "react_chnet5"))'

```

is used here to obtain the path to the chemical network file from the

corresponding example directory of the KROME.jl package.

After re-building KROME.jl successfully, start Julia and execute the following:

```julia

julia> using KROME

julia> include(joinpath(KROME.examples_dir(), "av-slab-benchmark", "av_slab.jl"))

julia> av_slab()

```

This will start the example and printing the chemical network updates as they

are computed. Note that this example takes a minute or two to fully run through.

## Authors

KROME.jl was initiated by

[Michael Schlottke-Lakemper](https://www.mi.uni-koeln.de/NumSim/schlottke-lakemper)

(University of Cologne, Germany).

The [KROME](http://kromepackage.org) package itself is developed and maintained by

Tommaso Grassi, Stefano Bovino, and many others.

## License and contributing

KROME.jl is licensed under the MIT license (see [LICENSE.md](LICENSE.md)).

The [KROME](http://kromepackage.org) package itself is licensed under the GNU

General Public License, version 3.