Input and Output files

Input

There are two required input files to run a simulation with mcdust, setup.par and prepocs.opt. The details are each file are explained below.

Input file 1: `setup.par`

This is the file to specify the simulation parameters. The parameters to be entered in the file are written below

number_of_particles_per_cell  - Number of particles in a cell
number_of_radial_zones  -  Number of radial grids
number_of_vertical_zones -  Number of vertical grids
steps_between_outputs  - Number of iterations between outputs
time_between_outputs_[yrs] - time interval between outputs
maximum_time_of_simulation_[yrs]  - simulation time in yrs
minimum_radius_[AU] - inner radial boundary of the simulation in AU
maximum_radius_[AU] - outer radial boundary of the simulation in AU
monomer_radius_[cm] - radius of the particle monomers in cm
material_density_[g/cm3] - internal density of the particles in g/cm3
dmmax  -  mass optimization value for grouped collisions
evaporation_radius_[AU] - radius inside which particles will not be tracked anymore
dust_to_gas_ratio - the dust to gas ratio in the disk
fragmentation_velocity_[cm/s] - fragmentation velocity of the particles
alpha - the alpha turbulence value to specifiy the strength of the turbulence in the disk
sigma_gas_[g/cm2] - gas surface density at 1 AU
temperature_[K]  - temperature in K at 1 AU
erosion_mass_ratio - mass ratio condition to trigger erosion
data_directory - directory name to write the data

If the values for the parameters are not specified in the setup.par file, the default values will be taken as specified in the parameters.F90 file. New parameters can also be added to the simulation via the parameters.F90 file.

Input file 2: `preprocs.opt`

This file specifies the regions of the code to be compiled based on compiler options. The current compiler options are listed:

VERTICALMODEL: activate this to setup a 1D vertical model
TRANSPORT: activate dust transport
VERTSETTLING: activate vertical settling of particles
RADRIFT: activate radial drift of particles
COLLISIONS: activate dust coagulation
EROSION: activate erosion as a collision outcome
AUXDATA: write timestep data
RESTART: continue a simulation from a snapshot

Comment or uncomment the options with # in the file based on the setup of the run.

Output

The output files are of the HDF5 file format with the extension .h5. Each snapshot has its own file and can accessed in outputs/ directory.

Each data file contains the properties of all representative particles (called as swarms). The properties that are stored in the default version are given below:

ID number of swarm
mass of the representative particle in grams
cylindrical radius in AU (distance from the central star)
height above midplane in AU
Stokes Number of the representative particle
Radial velocity v_r of the representative particle in cm/s
Vertical velocity v_z of the representative particle in cm/s

Teh data file contains the snapshot time of the data file in the group times` where the snapshot time (in years) is stored in the :code:`timesout dataset. Each data file also contains the mass of a swarm (in g) and the output number of the file as metadata.

The metadata of the code can be accessed using the h5dump command as shown in the example below.

h5dump -H data/swarms-00000.h5

The output of the command shows the metadata of the file swarms-00000.h5

HDF5 "swarms-00000.h5" {
GROUP "/" {
ATTRIBUTE "author" {
    DATATYPE  H5T_STRING {
        STRSIZE 20;
        STRPAD H5T_STR_NULLTERM;
        CSET H5T_CSET_ASCII;
        CTYPE H5T_C_S1;
    }
    DATASPACE  SCALAR
}
ATTRIBUTE "code" {
    DATATYPE  H5T_STRING {
        STRSIZE 9;
        STRPAD H5T_STR_NULLTERM;
        CSET H5T_CSET_ASCII;
        CTYPE H5T_C_S1;
    }
    DATASPACE  SCALAR
}
ATTRIBUTE "mass_of_swarm" {
    DATATYPE  H5T_IEEE_F32LE
    DATASPACE  SCALAR
}
ATTRIBUTE "output_number" {
    DATATYPE  H5T_IEEE_F32LE
    DATASPACE  SCALAR
}
GROUP "swarms" {
    DATASET "swarmsout" {
        DATATYPE  H5T_COMPOUND {
            H5T_STD_I32LE "id_number";
            H5T_IEEE_F64LE "mass_of_a_particle_[g]";
            H5T_IEEE_F64LE "cylindrical_radius_[AU]";
            H5T_IEEE_F64LE "height_above_midplane_[AU]";
            H5T_IEEE_F64LE "Stokes_number";
            H5T_IEEE_F64LE "Radial_velocity_v_r_[cm/s]";
            H5T_IEEE_F64LE "Vertical_velocity_v_z_[cm/s]";
        }
        DATASPACE  SIMPLE { ( 1, 1048576 ) / ( H5S_UNLIMITED, 1048576 ) }
    }
}
GROUP "times" {
    DATASET "timesout" {
        DATATYPE  H5T_IEEE_F64LE
        DATASPACE  SIMPLE { ( 1 ) / ( H5S_UNLIMITED ) }
    }
}
}

To add new properties to the data, one can modify the hdf5output.F90 file.

There are also more files that can be written out for auxilliary data. timesout.dat contains the snapshot times [in yr] of the output files in plain text format. timestep.dat contains the advection timestep [in yr] for each iteration. Writing these files can be turned on/off using the AUXDATA`preprocessor directive in :code:`preprocs.opt as described in the section Input File 2.

Input and Output files

Input

Input file 1: setup.par

Input file 2: preprocs.opt

Output

Input file 1: `setup.par`

Input file 2: `preprocs.opt`