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Build C-library

Build C-library

This template comes with a Makefile that lets the user to compile the library. Apart from specifying the CVODE_PATH, SUITESPARSE_PATH, DENGO_INSTALL_PATH, HDF5_PATH, there are additional options the user can choose. One can choose either the CVDLS which refers to the CVODE dense linear solver, or CVKLU which refers to the CVODE KLU Sparse solver. CVKLU is oftentimes preferred as it leverages the emptyness in the Jacobian matrix, and utilizes the SuiteSparse library to perform the newton iterations. DENGO_INSTALL_PATH is where the library will be installed. MAX_NCELLS determines how many cells would be batched together when the CVODE solver is invoked.

# Use the Dense Linear Solver interface (CVDLS)
#OPTIONS+= -DMAX_NCELLS=1
# Use the Sparse KLU direct solver
OPTIONS = -DCVKLU -DMAX_NCELLS=256

The Make script uses libtool to compile the files and build the libraries. The command Make would build and install the libraries. Now you have built a libdengo.so in your specified installed path, and you are ready to link it to your favorite program with the sample below, or checkout the Makefile:run_dengo.

$(CC) -o $@ $^ $(OPTIONS) -I$(DENGO_INSTALL_PATH)/include -I$(CVODE_PATH)/include -I$(INCLUDES_KLU) -I$(HDF5_PATH)/include -L$(HDF5_PATH)/lib -lhdf5_hl -lhdf5 -L$(DENGO_INSTALL_PATH)/lib -ldengo -lm

Main components that drives Dengo C-solver

In brief, similar to the example we shown before with the python RHS function, the C templates generate primarily solvers

  • _solver.h

  • _solver.C (major modules in Dengo)

  • _solver_main.h

  • _solver_main.C (example script to use the C library)

  • initialize_cvode_solver.C (wrapper function for the CVode library)

  • Makefile (to compile the dengo library libdengo.a)

An example usage of the built dengo library can be found in the {{solver_name}}_solver_main.C. The solver is accessed through

int simple_solve_chemistry_enzo( code_units *units, dengo_field_data *field_data, double dt );

This API follows closely the Grackle solver solver_chemistry which is tailored to work with Enzo simulations. dengo_field_data is a data structure that points to the respective abundance pointer {species.name}_density. It also informs the setup of the incoming grid. code_units informs the dengo solver how to convert from code_units into physical cgs units. dt is the delta time the user want to advance the system for. The structure definition taken from {{solver_name}}_solver.h are shown below. dengo_field_data.CoolingTime, dengo_field_data.MolecularWeight, dengo_field_data.temperature, dengo_field_data.Gamma, dengo_field_data.Pressure are not required inputs. User however needs to allocate space to these pointers if one want Dengo to compute these quantities alongside the chemical evolution. dengo_data_file points to the reaction rates hdf5 data for on-the-fly interpolations.

typedef struct dengo_field_data
{

  unsigned long int nstrip;
  unsigned long int ncells; 
  // let's just pass them passively through field_data
  double reltol;
  double floor_value;
  // This should be updated dynamically 
  // with dengo
  double *density;
  double *H_1_density;
  double *H_2_density;
  double *de_density;
  double *ge_density;
    
  double *CoolingTime;
  double *MolecularWeight;
  double *temperature;
  double *Gamma;
  double *Pressure;

  int *grid_start;
  int *grid_end;
  int *grid_dimension;

  const char *dengo_data_file;
  code_units *units;
} dengo_field_data;

typedef struct code_units
{

  int comoving_coordinates;
  double density_units;
  double length_units;
  double time_units;
  double velocity_units;
  double a_units;
  double a_value;

} code_units;

Conclusion

  1. We outlie how ChemicalNetwork.write_solver works.

  2. How to build the cython module from the templates generated.

  3. We also outline how the C-library can be built.

In the next chapter, we will outline the procedures needed to link hydrodynamical simulations like enzo to dengo.

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Threebody Reaction Example