The CCMD (Coulomb Crystal Molecular Dynamics) code provides a framework for performing molecular dynamics simulations of trapped ion clouds.

Requires the Boost library for parsing the input file and generating images.

## Compiling

Running make in src/ compliles the executable in bin/linux

XCode project file in build/macosx

The ccmd executable expects one command-line argument: the directory in which to run. This directory needs to hold the input file named trap.info; all output files will be written to this directory, overwriting any previous files. This is done so that the output files are automatically documented by the input file that generated them.

An example input file is in the directory config.

All the parameters are stored in a text input file following the Boost info file format (see documentation at the [boost website][info_doc]), which is parsed as a property tree. The base branches are trap containing ion trap parameters, integrator containing integrator parameters, ionnumber containing the number of each type of ion in the simulation and iontype which defines the physical properties of the ions.

Note: the names in the input file are not case sensitive.

trap {
    vrf     300.0
    vend    2.0
    eta     0.244
    r0      3.5e-3
    z0      2.75e-3
    freq    3.85e6
    type    {
        name    digital
        tau     0.1
    }
}
integrator {
    stepsPerPeriod 20
    respasteps  50       ; Respa inner loop steps
    coolperiods 2000
    histperiods   200
}
image {
    makeimage   true
    scale       1; 2.5     ; Image scaling in pixels per micron
    blur        5.0     ; Blur radius in microns
    dof         50.0    ; Depth of field in microns
    nz          640     ; Number of pixels in z axis
    nx          480     ; Number of pixels in x axis
}
simulation {
    threads     0
    seed        -1
}
ionnumbers {
    Ca      100
    CaF     50
}
iontype {
    CaF {
        name        CalciumFluoride
        mass        59.0
        charge      1
    }
    Ca {
        name        Calcium
        mass        40.0
        charge      1
        lasercooled true
        beta        0.6
        heating     true
        recoil      0.01
        direction   0.5
    }
}

In the block trap

Ions are described as follows: a branch named ionnumbers lists one ion formula followed by the number of this ion in the simulation. We then look within the iontype branch for a sub-branch with the same name as each formula given in the ionnumbers branch. The physical properties of each ion in use is then loaded.

The definition is arranged in two parts with the number defined separately to allow the definition of ion physical properties to be easily copied and pasted between input files. There is no penalty for having more ions defined than used, the function only looks for definitions matching those listed in the ionnumbers branch.

The lasercooled and heating parameters are optional, and are taken as false if not specified (e.g. for CaF in the example below.) the other parameters marked optional require heating or cooling and are ignored if these are false.

           |   (**optional**)

seed | Seed for random number generator, use -1 to generate | automatically, or an integer to remove all randomness. recoil | Heating recoil factor (optional)

             | Coulomb force calculation. `respasteps = 1` is equivalent to
             | velocity Verlet algorithm.

coolperiods | Number of RF periods for equilibration (no data collected) histperiods | Number of RF periods to propagate while collecting data.

        | The total number of running threads will be this number plus one.
        | Zero performs all calculations in a single thread.

seed | Seed for random number generator. Set to -1 to pick seed from | system clock.