IonSim.jl

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a simple tool for simulating trapped ion systems

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- - format-check.yml
  - TagBot.yml
  - test.yml
- format.sh
- - _include_species.jl
  - be9.jl
  - ca40.jl
  - mg25.jl
  - yb171.jl
- analyticfunctions.jl
- chambers.jl
- constants.jl
- hamiltonians.jl
- ions.jl
- IonSim.jl
- iontraps.jl
- lasers.jl
- operators.jl
- timeevolution.jl
- vibrationalmodes.jl
- runtests.jl
- runtests.sh
- test_analytic_functions.jl
- test_chambers.jl
- test_constants.jl
- test_dynamics.jl
- test_hamiltonians.jl
- test_ion_traps.jl
- test_ions.jl
- test_lasers.jl
- test_load_LinearChain_fromyaml.yaml
- test_load_LinearChain_fromyaml_broken.yaml
- test_operators.jl
- test_time_evolution.jl
- test_vibrational_modes.jl
.gitignore
.JuliaFormatter.toml
LICENSE.md
Project.toml
README.md

// repository documentation

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[![test status](https://github.com/HaeffnerLab/IonSim.jl/actions/workflows/test.yml/badge.svg)](https://github.com/HaeffnerLab/IonSim.jl/actions/workflows/test.yml)
[![codecov][codecov-badge]][codecov-url]
[![License: MIT][license-badge]][license-url]

A simple tool, built on top of [QuantumOptics.jl](https://qojulia.org/), for simulating the dynamics of a configuration of
trapped ions interacting with laser light.

**IonSim.jl** primarily performs two jobs:
1. Keeps track of the physical parameters necessary for describing the system.
2. Using these parameters, constructs a function that quickly computes the system's Hamiltonian as a function of time.

The functional form of the Hamiltonian can then be used as input to any of the solvers implemented in
[`QuantumOptics.timeevolution`](https://qojulia.org/documentation/timeevolution/timeevolution/). For more information see:

+ Main code: [https://github.com/HaeffnerLab/IonSim.jl/tree/master/src](https://github.com/HaeffnerLab/IonSim.jl/tree/master/src)
+ Documentation: [https://docs.ionsim.org](https://docs.ionsim.org)
+ Examples: [https://examples.ionsim.org](https://examples.ionsim.org)
+ Benchmarks: (coming soon)

If you have an idea for how to improve IonSim, need some help getting things working or have any other IonSim-related questions feel free to open a GitHub issue.

## How to use

1. Install Julia ([instructions here](https://julialang.org/downloads/)).
2. Open up a Terminal session and fire up the [Julia REPL](https://docs.julialang.org/en/v1/stdlib/REPL/#The-Julia-REPL-1) with
```bash
$ julia
```
(*If using Windows it's easier to start a REPL with the julia executable available after installation.*)

3. Now run
```julia
julia> using Pkg
julia> Pkg.add("IonSim")
julia> Pkg.add("IJulia")
```
The last line adds Jupyter compatibility, so you'll have the option to start a Julia kernel from Jupyter notebook. This is the suggested way
to interact with IonSim.

### Updating IonSim

IonSim.jl is a work in progress. You can update your local code to the most recent version
with the following:

```julia
julia> using Pkg
julia> Pkg.update("IonSim")
```

### Extra Linux notes
* Extract the downloaded file
* copy to `/opt` with:

```bash
$ sudo cp -r julia-1.3.1 /opt/
```
(replacing `julia-1.3.1` with the appropriate version)
* then create a symbolic link in `/usr/local/bin` with
```bash
$ sudo ln -s /opt/julia-1.3.1/bin/julia /usr/local/bin/julia
```

## Development

If you want to run IonSim locally:
* Open up the Julia REPL
```bash
$ julia
```
* Open the package manager by pressing `]`
* Run the following:
```julia
pkg> dev IonSim
```
This will clone a version of this repo in `~/.julia/dev/IonSim/`. Then when you make changes to that repo, it will be immediately reflected when using Julia.

You can run tests with
```julia
pkg> test IonSim
```

Don't forget to format the code! `./scripts/format.sh`

To go back to the version in the registry, use
```julia
pkg> free IonSim
```

In order to update the IonSim.jl version that lives in the Julia general registry, change the version number in the Project.toml file, commit the changes and then add a comment to the commit that reads:
```
@JuliaRegistrator register
```

If you have any questions, please make a GitHub issue.

[license-url]: https://github.com/HaeffnerLab/IonSim.jl/blob/master/LICENSE.md
[license-badge]: https://img.shields.io/badge/License-MIT-green.svg

[codecov-url]: https://codecov.io/gh/HaeffnerLab/IonSim.jl
[codecov-badge]: https://codecov.io/gh/HaeffnerLab/IonSim.jl/branch/master/graph/badge.svg

[twitter-url]: https://twitter.com/Berkeley_ions
[twitter-badge]: https://img.shields.io/twitter/follow/Berkeley_ions.svg?style=social&label=@Berkeley_ions

[logo-url]: https://github.com/HaeffnerLab/IonSim.jl/blob/media/smallest_logo.png?raw=true

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