Nucleating Dust Code in C++
nuDustC++ is used to calculate the dust neclation and destruction in gaseous systems.
All Units are in CGS
Required: OpenMP, MPI, Boost, SunDials, Plog. This build uses cmake.
Plog is a header only package. Running cmake fetches Plog, but it can also be aquired by:
git clone git@github.com:SergiusTheBest/plog.gitIf using conda, install boost as:
conda install conda-forge::boostFurther documentation and installation of Boost can be found at:
On MacOS using HomeBrew, run:
brew install sundialsInstallation instructions for sundials can be found at:
https://computing.llnl.gov/projects/sundials/faq#inst
In order to build nuDustC++, go to the head of the git repository (nuDustC/) and run:
$> mkdir build;
$> cd build;
$> cmake .. ;
$> make;To build nuDustC++ in release mode to run faster, instead of the above, run:
$> mkdir build;
$> cd build;
$> cmake -DCMAKE_BUILD_TYPE=Release .. ;
$> make;Run nuDustc with
$> ./nudust++ -c data/inputs/test_config.iniYou may need to add the paths of the packages to LD_LIBRARY_PATH. If using conda nuDustC++ can then be run by:
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:~/miniconda3/lib ./nudust++ -c data/inputs/test_config.iniOr specifying the paths to the packages and libraries in LD_LIBRARY_PATH.
The default had OpenMP (NUDUSTC_ENABLE_OPENMP) and MPI (NUDUSTC_ENABLE_MPI) areturned on and sundials (NUDUSTC_USE_SUNDIALS) are turned off. This can be edited in the CMakeLists.txt file.
If using MPI, run with
$> mpirun -N 'n' ./nudust++ -c /data/inputs/test_config.txtwhere 'n' is the number of processors.
Required: Config file. This lists the various input information such as data files, integration parameters, and calculation options.
ode_dt_0: Initial timestep for integration.
ode_abs_err: The Solver's absolute error.
ode_rel_err: The Solver's relative error.
ode_dt_min: The minimum allowed timestep.
de_dt_max: The maximum allowed timestep.
sizeDist_file: This describes the size distribution for the model. Each cell has one line. Each line is an array of size distribtuions of grain species in the order specified in the header line.
environment_file: This contains the trajectory data for each timestep. The time is specified on a single line. Below, each cell's is describe in a single line: cell_ID, temperature (K), volume(cm^3), density(g/cm^3), pressure (Ba), velocity (cm/s), radius (cm).
network_file: This includes the chemical network of grain reactions. Each grain species takes up one line in order: reactants, "->", products, "|", key species, Gibb's free energy 'A' term (A/10^4 K), Gibb's free energy 'B' term, surface energy of the condensate (ergs/cm^2), radius of condensate (angstroms).
abundance_file: This lists the names of gas species in the header. Each cell has one line listing: cell ID, number density for each gas species.
shock_file: This contains information on a shock. Each cell has one line: cell ID, the time of the shock, the shock temperature, the shock velocity.
size_dist_min_rad_exponent_cm: The exponent of the left edge of the distribtuion.
size_dist_max_rad_exponent_cm: The exponent of the right edge of the distribtion.
number_of_size_bins: The number of size bins.
do_destruction: 1, if doing destruction, 0 if no destruction.
do_nucleation: 1, if soind nucleation, 0 if no nucleation.
If both are set to '1', both destruction and nucleation are calculated.
io_dump_n_steps : Number of cycles until a dump file is updated.
io_restart_n_steps: Number of cycles until a restart file is updated.
pile_up_factor: This is used to calculate the increase in density when a shock passes through. The density if multiplied by this number.
shock_velo: This is the velocity of the shock that will be applied to all cells.
shock_temp: This is the temperature of the shock that will be applied to all cells.
sim_start_time: This is the time of the shock. It is used to calculate the change in volume, assuming homologous expansion.
mod_number: This specifies the model used in order to differentiate multiple runs.
There are 5 main calculation paths including destruction or nucleation calculations. Destruction has 2 main branches based on if the user is specifying shock values or reading them in from a file.
Nucleation & Destruction With User Input Shock Temperature & Velocity Required Input Files: Hydrodynamical Trajectory file (Time, Temperature, Volumes, Density, Pressure, Velocity), Abundance File, & Network File, Shock Velocity, Shock Temperature, Shock Time, Pile up factor, Size Distribution File or Size Parameters
Nucleation & Destruction With Shock Times and Velocities from a file Required Input Files: Hydrodynamical Trajectory file (Time, Temperature, Volumes, Density, Pressure, Velocity), Abundance File, & Network File, Shock Velocity, Shock Temperature, Shock Time, Pile up factor, Size Distribution File or Size Parameters
Nucleation Required Input Files: Hydrodynamical Trajectory file (Time, Temperature, Volumes, Density), Abundance File, & Network File, Size Distribution File or Size Parameters
Destruction With Shock Times and Velocities from a file Required Input Files: Shock File (Cell #, Time, Shock Temperature, Shock Velocity), Size Distribution File or Size Parameters, Abundance File, & Network File
Destruction With User Input Shock Temperature & Velocity Required Input Files: Shock Velocity, Shock Temperature, Shock Time, Pile up factor, Size Distribution File or Size Parameters, Abundance File, & Network File
The integrator is setup in src/cell.cpp in the solve() funtion. nuDustC++ comes defaulted with a runge-kutta doPri 5 integrator. Additional information on the available integrators offered by Boost can be found at:
https://www.boost.org/doc/libs/1_78_0/libs/numeric/odeint/doc/html/index.html
nuDustC++ currently uses a makima 1-D interpolator. The interpolator is defined in include/cell.h in the 'cell' class declaration. Additional interpolators offered by Boost can be found at:
https://www.boost.org/doc/libs/1_78_0/libs/math/doc/html/interpolation.html
To run a test of nudustc++,
./nudustc++ -c data/inputs/test_config.ininuDustC++ should complete the test run in under a minute in release mode. If it doesn't, try changing the configuration file to output data after more cycles by changing io_dump_n_steps and io_restart_n_steps. This will produce data files in the build directory's "output/" directory and restart data in the "restart/" directory.
nuDustC++ automatically checks for restart files when creating each cell. If a restart file is found, that data is loaded into the cell object. If no restart file is found, the cell is initialized with data from the input files. Make sure the same config file used to start the run is selected when restarting.
If the compiler cannot find required packages or libraries, make sure LD_LIBRARY_PATH is up to date and points to the location of each package or library.
MPI issuse: make sure you have the installed location of MPI in your path. You might need to change CMakeLists.txt depending on your MPI build.
Ensure the configuration file points to the accessible location of each input file and contains the necessary parameters for the calculation path.
Boost Math errors: Some older versions of Boost might not work the Gauss Kronrod Quadrature. We haven't checked any builds older than 1.78.0. If you get math errors, try updating Boost.
If you use nuDustC++ and need help, submit an issue to the nuDustC++ repository. If you'd like to contribute, just fork and submit a pull request. One of the developers will review your PR.
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