.. _integration: Adding Grackle to Your Simulation Code ====================================== The majority of this document follows the implementation of Grackle in a C++ simulation code. Full implementation examples for C, C++, and Fortran are also available in the Grackle source. See :ref:`examples` for more information. For a list of all available functions, see the :ref:`reference`. .. _examples: Example Executables ------------------- The grackle source code contains examples for C, C++, and Fortran codes. They are located in the **src/example** directory and provide examples of calling all of grackle's functions. * **c_example.c** - C example * **c_local_example.c** - C example using only :ref:`local_functions` * **cxx_example.C** - C++ example * **cxx_omp_example.C** - C++ example using OpenMP * **fortran_example.F** - Fortran example Once you have already installed the grackle library, you can build the examples by typing *make* and the name of the file without extension. For example, to build the C++ example, type: .. code-block:: bash $ make cxx_example To run the example, make sure to add the path to the directory containing the installed **libgrackle.so** to your LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH on Mac). Header Files ------------ Seven header files are installed with the grackle library. They are: * **grackle.h** - the primary header file, containing declarations for all the available functions and data structures. This is the only header file that needs to be included for C and C++ codes. * **grackle.def** - the header file to be used in Fortran codes. Only this file needs to be included. * **grackle_types.h** - defines the variable type :c:type:`gr_float`, the field structure :c:type:`grackle_field_data`, and the units structure :c:type:`code_units`. * **grackle_chemistry_data.h** - defines the :c:type:`chemistry_data` structure, which stores all Grackle run-time parameters and the :c:type:`chemistry_data_storage` structure, which stores all chemistry and cooling rate data. * **grackle_fortran_types.def** - similar to **grackle_types.h**, but used with Fortran codes. This defines the variable type :c:type:`R_PREC` as either real\*4 or real\*8. * **grackle_fortran_interface.def** - defines the Fortran interface, including the Fortran analogs of :c:type:`grackle_field_data`, :c:type:`code_units`, and :c:type:`grackle_chemistry_data`. * **grackle_macros.h** - contains some macros used internally. For C and C++ codes, the only source file that needs to be included in your simulation code is **grackle.h**. For Fortran, use **grackle.def**. Since Grackle is written in C, including **grackle.h** in a C++ code requires the *extern "C"* directive. .. code-block:: c++ extern "C" { #include } Data Types ---------- The grackle library provides a configurable variable type to control the precision of the baryon fields passed to the grackle functions. For C and C++ codes, this is :c:type:`gr_float`. For Fortran codes, this is :c:type:`R_PREC`. The precision of these types can be configured with the *precision* compile option. Compile with *precision-32* to make :c:type:`gr_float` and :c:type:`R_PREC` a 4 byte float (*float* for C/C++ and *real\*4* for Fortran). Compile with *precision-64* to make :c:type:`gr_float` and :c:type:`R_PREC` an 8 byte float (*double* for C/C++ and *real\*8* for Fortran). .. c:type:: gr_float Floating point type used for the baryon fields. This is of type *float* if compiled with *precision-32* and type double if compiled with *precision-64*. .. c:type:: R_PREC The Fortran analog of :c:type:`gr_float`. This is of type *real\*4* if compiled with *precision-32* and type *real\*8* if compiled with *precision-64*. Enabling Output --------------- By default, grackle will not print anything but error messages. However, a short summary of the running configuration can be printed by setting ``grackle_verbose`` to 1. In a parallel code, it is recommended that output only be enabled for the root process. .. code-block:: c++ // Enable output grackle_verbose = 1; .. _code-units: Code Units ---------- Many of the calculations involved in chemical reactions and radiative cooling include multiplications by density squared or even density cubed. With typical gas densities relevant to galaxy formation being of the order of one hydrogren atom per cubic centimeter (~10\ :sup:`-24` g/cm\ :sup:`3`, give or take a few orders of magnitude), it is easy to end up with significant roundoff or underflow errors when quantities are stored in CGS units. The :c:data:`code_units` structure contains conversions from code units to CGS such that a value passed to Grackle multiplied by the appropriate code unit gives that value in CGS units. Units for density, length, time, and the expansion factor must be set manually. Units for velocity are then set by calling :c:data:`set_velocity_units`. When using the proper frame (i.e., setting :c:data:`comoving_coordinates` to 0), :c:data:`a_units` (units for the expansion factor) must be set to 1.0. See below for recommendations on choosing appropriate units. .. c:type:: code_units This structure contains the following members. .. c:var:: int comoving_coordinates If set to 1, the incoming field data is assumed to be in the comoving frame. If set to 0, the incoming field data is assumed to be in the proper frame. .. c:var:: double density_units Conversion factor to be multiplied by density fields to return densities in proper g/cm\ :sup:`3`\. .. c:var:: double length_units Conversion factor to be multiplied by length variables to return lengths in proper cm. .. c:var:: double time_units Conversion factor to be multiplied by time variables to return times in s. .. c:var:: double velocity_units Conversion factor to be multiplied by velocities to return proper cm/s. This should be set units the :c:data:`set_velocity_units` function. Note, units of specific energy (i.e., conversion to erg/g) are then defined as :c:data:`velocity_units`\ :sup:`2` (velocity units squared). .. c:var:: double a_units Conversion factor to be multiplied by the expansion factor such that a\ :sub:`true`\ = a\ :sub:`code`\ * :c:data:`a_units`. When using proper coordinates, :c:data:`a_units` must be set to 1. .. c:var:: double a_value The current value of the expansion factor in units of :c:data:`a_units`. The conversion from redshift to expansion factor in code units is given by :c:data:`a_value` = 1 / (1 + z) / :c:data:`a_units`. If the simulation is not cosmological, :c:data:`a_value` should be set to 1. Note, if :c:data:`a_value` is set to something other than 1 in a non-cosmological simulation, all redshift dependent chemistry and cooling terms will be set corresponding to the redshift given. .. code-block:: c++ code_units my_units; my_units.comoving_coordinates = 0; // 1 if cosmological sim, 0 if not my_units.density_units = 1.67e-24; // 1 m_H/cc my_units.length_units = 3.086e21; // 1 kpc my_units.time_units = 3.15569e13; // 1 Myr my_units.a_units = 1.0; // units for the expansion factor my_units.a_value = 1. / (1. + current_redshift) / my_units.a_units; // set velocity units set_velocity_units(&my_units); Choosing Appropriate Units ^^^^^^^^^^^^^^^^^^^^^^^^^^ The main consideration when setting code units is to keep density, length, and time values close to 1. Reasonable values for density, length, and time units are the hydrogen mass in g, 1 kpc to 1 Mpc in cm, and 1 Myr to 1 Gyr in s. .. _comoving_coordinates: Comoving Coordinates ^^^^^^^^^^^^^^^^^^^^ For cosmological simulations, a comoving unit system is preferred, though not required, since it allows the densities to stay close to 1 as the universe expands. If :c:data:`comoving_coordinates` is set to 1, it is assumed that the fields being passed to the solver are in the comoving frame. Hence, the units must convert from code units in the **comoving** frame to CGS in the **proper** frame. If :c:data:`comoving_coordinates` is set to 0, it is assumed that the fields passed into the solver are in the proper frame. For an example of using comoving units, see the `cosmological unit system `__ in the `Enzo `_ code. As the unit system is designed to convert from the comoving to the proper frame, some of the values in the :c:data:`code_units` struct are expected to change with expansion factor (or redshift) while some others should remain constant. Units that should remain constant include :c:data:`time_units` and :c:data:`a_units`. Units that should vary are :c:data:`a_value` (obviously), :c:data:`length_units`, and :c:data:`density_units`. Moving forward in time, :c:data:`length_units` should be increasing proportional to :c:data:`a_value` and :c:data:`density_units` should be decreasing as :c:data:`a_value`:sup:`-3`. There are two important corollaries of the above behavior. First, the :c:data:`velocity_units` should remain constant. In comoving coordinates, velocity units are given by .. math:: VU = \frac{LU}{a\ TU}, where VU is :c:data:`velocity_units`, a is :c:data:`a_value`, and TU is :c:data:`time_units`. Second, the internal unit for the cooling rate (equivalent to [erg s\ :sup:`-1` cm\ :sup:`+3`]) should remain constant. The cooling unit (CU) is given by .. math:: CU = \frac{VU^2\ m_H^2}{DU\ a^3\ TU}, where DU is :c:data:`density_units` and m\ :sub:`H` is the hydrogen mass. The above definitions also hold for proper coordinates by setting a to 1. .. _setup_data-storage: Chemistry Data -------------- The main Grackle header file contains a structure of type :c:type:`chemistry_data` called ``grackle_data``, which contains all of the parameters that control the behavior of the solver. The routine, :c:func:`set_default_chemistry_parameters` is responsible for the initial setup of this structure and for setting of all the default parameter values. This function must be handed a pointer to an instance of :c:type:`chemistry_data`, which will then be attached to ``grackle_data``. The function will return an integer indicating success (1) or failure (0). After this, parameters can then be set to their desired values by accessing ``grackle_data``. See :ref:`parameters` for a full list of the available parameters. .. c:type:: chemistry_data This structure holds all grackle run-time parameters, which are listed in :ref:`parameters`. .. c:type:: chemistry_data_storage This structure holds all chemistry and cooling rate arrays. The user will not normally need to work directly with its internals. The functions described below (i.e., the :ref:`primary_functions`) make use of an internally stored instance of this type and, hence, will not encounter it. Users implementing the :ref:`local_functions` will have to store one of these. See the :ref:`c_local_example.c ` sample code for an example of this implementation. .. code-block:: c++ chemistry_data *my_grackle_data; my_grackle_data = new chemistry_data; if (set_default_chemistry_parameters(my_grackle_data) == 0) { fprintf(stderr, "Error in set_default_chemistry_parameters.\n"); } // Set parameter values for chemistry. // Now access the global copy of the chemistry_data struct (grackle_data). grackle_data->use_grackle = 1; // chemistry on grackle_data->with_radiative_cooling = 1; // cooling on grackle_data->primordial_chemistry = 3; // molecular network with H, He, D grackle_data->metal_cooling = 1; // metal cooling on grackle_data->UVbackground = 1; // UV background on grackle_data->grackle_data_file = "CloudyData_UVB=HM2012.h5"; // data file Once the desired parameters have been set, the chemistry and cooling rates must be initialized by calling :c:func:`initialize_chemistry_data` with a pointer to the :c:data:`code_units` struct created earlier. This function will return an integer indicating success (1) or failure (0). .. code-block:: c++ // Finally, initialize the chemistry object. if (initialize_chemistry_data(&my_units) == 0) { fprintf(stderr, "Error in initialize_chemistry_data.\n"); return 0; } The Grackle is now ready to be used. As an aside, see :ref:`dynamic-api` for a description of an alternative approach for configuring a :c:type:`chemistry_data` struct. This other approach may provide additional compatability with multiple versions of Grackle, and in some cases may facillitate less-verbose, easier-to-maintain code. .. _openmp: Running with OpenMP ------------------- As of version 2.2, Grackle can be run with OpenMP parallelism. To do this, the library must first be compiled with OpenMP support enabled by issuing the command, "make omp-on", before compiling. See :ref:`compiler-settings` for more information on how to change settings. For an example of how to compile your code with OpenMP, see the **cxx_omp_example.C** code example (:ref:`examples`). Once your code has been compiled with OpenMP enabled, the number of threads used can be controlled by setting the :c:data:`omp_nthreads` parameter, stored in the ``grackle_data`` struct. .. code-block:: c++ // 8 threads per process grackle_data->omp_nthreads = 8; If not set, this parameter will be set to the maximum number of threads possible, as determined by the system or as configured by setting the ``OMP_NUM_THREADS`` environment variable. Creating the Necessary Fields ----------------------------- As of version 3.0, the various density and energy fields are passed to Grackle's functions using a struct of type :c:data:`grackle_field_data`. The struct contains information about the size and shape of the field arrays and pointers to all field arrays. .. _density-note: Note on Density Fields ^^^^^^^^^^^^^^^^^^^^^^ All density fields provided to Grackle should be mass densities, i.e., the number density of a given species multiplied by its mass. The units should be such that the field value multiplied by :c:data:`density_units` results in a value with units of g/cm\ :sup:`3`. See :ref:`code-units` for further discussion of Grackle unit systems. .. _e-density-note: Note on the Electron Density Field ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ For largely historical reasons, the value of the electron density (provided in :c:data:`e_density`) should be the true value of the electron mass density multiplied by the ratio of the proton mass to the electron mass, i.e., :c:data:`e_density` = :math:`{\rho}`\ :sub:`e` * m\ :sub:`p` / m\ :sub:`e`, where :math:`{\rho}`\ :sub:`e` is the true electron mass density in :c:data:`density_units` (see :ref:`density-note`). .. c:type:: grackle_field_data This structure is used to pass field data to Grackle's functions. It contains the following members: .. c:var:: int grid_rank The active dimensions (not including ignored boundary zones) of the field arrays. .. c:var:: int* grid_dimension This should point to an array of size :c:data:`grid_rank`. This stores the size of the field arrays in each dimension. .. c:var:: int* grid_start This should point to an array of size :c:data:`grid_rank`. This stores the starting value in each dimension for the field data. This can be used to ignore boundary cells in grid data. .. c:var:: int* grid_end This should point to an array of size :c:data:`grid_rank`. This stores the end value in each dimension for the field data. This can be used to ignore boundary cells in grid data. .. c:var:: gr_float grid_dx This is the grid cell width in :c:data:`length_units`. This is currently used only in computing approximate H2 self-shielding when H2 is tracked (:c:data:`primordial_chemistry` >= 2) and :c:data:`H2_self_shielding` is set to 1. .. c:var:: gr_float* density Pointer to the gas density field array. .. c:var:: gr_float* HI_density Pointer to the HI density field array. Used when :c:data:`primordial_chemistry` is set to 1, 2, or 3. .. c:var:: gr_float* HII_density Pointer to the HII density field array. Used when :c:data:`primordial_chemistry` is set to 1, 2, or 3. .. c:var:: gr_float* HM_density Pointer to the H\ :sup:`-`\ density field array. Used when :c:data:`primordial_chemistry` is set to 2 or 3. .. c:var:: gr_float* HeI_density Pointer to the HeI density field array. Used when :c:data:`primordial_chemistry` is set to 1, 2, or 3. .. c:var:: gr_float* HeII_density Pointer to the HeII density field array. Used when :c:data:`primordial_chemistry` is set to 1, 2, or 3. .. c:var:: gr_float* HeIII_density Pointer to the HeIII density field array. Used when :c:data:`primordial_chemistry` is set to 1, 2, or 3. .. c:var:: gr_float* H2I_density Pointer to the H\ :sub:`2`\ density field array. Used when :c:data:`primordial_chemistry` is set to 2 or 3. .. c:var:: gr_float* H2II_density Pointer to the H\ :sub:`2`\ \ :sup:`+`\ density field array. Used when :c:data:`primordial_chemistry` is set to 2 or 3. .. c:var:: gr_float* DI_density Pointer to the DI density field array. Used when :c:data:`primordial_chemistry` is set to 3. .. c:var:: gr_float* DII_density Pointer to the DII density field array. Used when :c:data:`primordial_chemistry` is set to 3. .. c:var:: gr_float* HDI_density Pointer to the HD density field array. Used when :c:data:`primordial_chemistry` is set to 3. .. c:var:: gr_float* e_density Pointer to the electron density field array. Used when :c:data:`primordial_chemistry` is set to 1, 2, or 3. Note, the electron mass density should be scaled by the ratio of the proton mass to the electron mass. See :ref:`e-density-note` for more information. .. c:var:: gr_float* metal_density Pointer to the metal density field array. Used when :c:data:`metal_cooling` is set to 1. .. c:var:: gr_float* dust_density Pointer to the dust density field array. Used when :c:data:`use_dust_density_field` is set to 1. .. c:var:: gr_float* internal_energy Pointer to the internal energy field array. Internal energies should be in units of :c:data:`velocity_units`\ :sup:`2` (velocity units squared). This can be converted to and from a temperature by using the :c:data:`get_temperature_units` function. .. c:var:: gr_float* x_velocity Pointer to the x-velocity field array. Currently not used. .. c:var:: gr_float* y_velocity Pointer to the y-velocity field array. Currently not used. .. c:var:: gr_float* z_velocity Pointer to the z-velocity field array. Currently not used. .. c:var:: gr_float* volumetric_heating_rate Pointer to values containing volumetric heating rates. Rates should be in units of erg/s/cm\ :sup:`3`\. Used when :c:data:`use_volumetric_heating_rate` is set to 1. .. c:var:: gr_float* specific_heating_rate Pointer to values containing specific heating rates. Rates should be in units of erg/s/g. Used when :c:data:`use_specific_heating_rate` is set to 1. .. c:var:: gr_float* temperature_floor Pointer to values containing a temperature floor for each element in units of K. No chemistry or cooling calculations will be performed on an element with a temperature at or below the specified value. Used when :c:data:`use_temperature_floor` is set to 2. .. c:var:: gr_float *RT_heating_rate Pointer to the radiation transfer heating rate field. Rates should be in units of (erg/s/cm\ :sup:`3`\) / n\ :sub:`HI`\, where n\ :sub:`HI`\ is the neutral hydrogen number density. Heating rates for additional species are currently not yet supported. Used when :c:data:`use_radiative_transfer` is set to 1. .. c:var:: gr_float *RT_HI_ionization_rate Pointer to the HI photo-ionization rate field used with radiative transfer. Rates should be in units of 1/:c:data:`time_units`. Used when :c:data:`use_radiative_transfer` is set to 1. .. c:var:: gr_float *RT_HeI_ionization_rate Pointer to the HeI photo-ionization rate field used with radiative transfer. Rates should be in units of 1/:c:data:`time_units`. Used when :c:data:`use_radiative_transfer` is set to 1. .. c:var:: gr_float *RT_HeII_ionization_rate Pointer to the HeII photo-ionization rate field used with radiative transfer. Rates should be in units of 1/:c:data:`time_units`. Used when :c:data:`use_radiative_transfer` is set to 1. .. c:var:: gr_float *RT_H2_dissociation_rate Pointer to the H\ :sub:`2`\ photo-dissociation rate field used with radiative transfer. Rates should be in units of 1/:c:data:`time_units`. Used when :c:data:`use_radiative_transfer` is set to 1 and :c:data:`primordial_chemistry` is either 2 or 3. .. c:var:: gr_float *H2_self_shielding_length Pointer to a field containing lengths to be used for calculating molecular hydrogen column denisty for H2\ :sub:`2`\ self-shielding. Used when :c:data:`H2_self_shielding` is set to 2. Field data should be in :c:data:`length_units`. .. c:var:: gr_float *H2_custom_shielding_factor Pointer to a field containing attenuation factors to be multiplied with the H\ :sub:`2`\ dissociation rate. Used when the :c:data:`H2_custom_shielding` flag is set. .. c:var:: gr_float *isrf_habing Pointer to a field containing values of the strength of the insterstellar radiation field used in the calculation of dust heating. This is used when :c:data:`use_isrf_field` is set to 1. The units of this field should be the same as those of the :c:data:`interstellar_radiation_field` parameter. It is not necessary to attach a pointer to any field that you do not intend to use. .. code-block:: c++ // Create struct for storing grackle field data grackle_field_data my_fields; // Set grid dimension and size. // grid_start and grid_end are used to ignore ghost zones. int field_size = 1; my_fields.grid_rank = 3; my_fields.grid_dimension = new int[3]; my_fields.grid_start = new int[3]; my_fields.grid_end = new int[3]; my_fields.grid_dx = 1.0; // only matters if H2 self-shielding is used for (int i = 0;i < 3;i++) { my_fields.grid_dimension[i] = 1; my_fields.grid_start[i] = 0; my_fields.grid_end[i] = 0; } my_fields.grid_dimension[0] = field_size; my_fields.grid_end[0] = field_size - 1; // Set field arrays. my_fields.density = new gr_float[field_size]; my_fields.internal_energy = new gr_float[field_size]; my_fields.x_velocity = new gr_float[field_size]; my_fields.y_velocity = new gr_float[field_size]; my_fields.z_velocity = new gr_float[field_size]; // for primordial_chemistry >= 1 my_fields.HI_density = new gr_float[field_size]; my_fields.HII_density = new gr_float[field_size]; my_fields.HeI_density = new gr_float[field_size]; my_fields.HeII_density = new gr_float[field_size]; my_fields.HeIII_density = new gr_float[field_size]; my_fields.e_density = new gr_float[field_size]; // for primordial_chemistry >= 2 my_fields.HM_density = new gr_float[field_size]; my_fields.H2I_density = new gr_float[field_size]; my_fields.H2II_density = new gr_float[field_size]; // for primordial_chemistry >= 3 my_fields.DI_density = new gr_float[field_size]; my_fields.DII_density = new gr_float[field_size]; my_fields.HDI_density = new gr_float[field_size]; // for metal_cooling = 1 my_fields.metal_density = new gr_float[field_size]; // volumetric heating rate (provide in units [erg s^-1 cm^-3]) my_fields.volumetric_heating_rate = new gr_float[field_size]; // specific heating rate (provide in units [egs s^-1 g^-1] my_fields.specific_heating_rate = new gr_float[field_size]; // heating rate from radiative transfer calculations (provide in units [erg s^-1 cm^-3] my_fields.RT_heating_rate = new gr_float[field_size]; // HI ionization rate from radiative transfer calculations (provide in units of [ 1/time_units ] my_fields.RT_HI_ionization_rate = new gr_float[field_size]; // HeI ionization rate from radiative transfer calculations (provide in units of [1/time_units] my_fields.RT_HeI_ionization_rate = new gr_float[field_size]; // HeII ionization rate from radiative transfer calculations (provide in units of [1/time_units] my_fields.RT_HeII_ionization_rate = new gr_float[field_size]; // H2 dissociation rate from radiative transfer calculations (provide in units of [1/time_units] my_fields.RT_H2_dissociation_rate = new gr_float[field_size]; .. note:: The electron mass density should be scaled by the ratio of the proton mass to the electron mass such that the electron density in the code is the electron number density times the **proton** mass. .. _functions: Calling the Available Functions ------------------------------- There are six functions available, one to solve the chemistry and cooling and five others to calculate the cooling time, temperature, pressure, ratio of the specific heats (gamma), and dust temperature. The arguments required are the :c:data:`code_units` structure and the :c:data:`grackle_field_data` struct. For the chemistry solving routine, a timestep must also be given. For the four field calculator routines, the array to be filled with the field values must be created and passed as an argument as well. The examples below make use of Grackle's :ref:`primary_functions`, where the parameters and rate data are stored in instances of the :c:data:`chemistry_data` and :c:data:`chemistry_data_storage` structs declared in **grackle.h**. Alternatively, a set of :ref:`local_functions` require these structs to be provided as arguments, allowing for explicitly thread-safe code. Solve the Chemistry and Cooling ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: c++ // some timestep (one million years) double dt = 3.15e7 * 1e6 / my_units.time_units; if (solve_chemistry(&my_units, &my_fields, dt) == 0) { fprintf(stderr, "Error in solve_chemistry.\n"); return 0; } Calculating the Cooling Time ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: c++ gr_float *cooling_time; cooling_time = new gr_float[field_size]; if (calculate_cooling_time(&my_units, &my_fields, cooling_time) == 0) { fprintf(stderr, "Error in calculate_cooling_time.\n"); return 0; } Calculating the Temperature Field ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: c++ gr_float *temperature; temperature = new gr_float[field_size]; if (calculate_temperature(&my_units, &my_fields, temperature) == 0) { fprintf(stderr, "Error in calculate_temperature.\n"); return EXIT_FAILURE; } Calculating the Pressure Field ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: c++ gr_float *pressure; pressure = new gr_float[field_size]; if (calculate_pressure(&my_units, &my_fields, pressure) == 0) { fprintf(stderr, "Error in calculate_pressure.\n"); return EXIT_FAILURE; } Calculating the Gamma Field ^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: c++ gr_float *gamma; gamma = new gr_float[field_size]; if (calculate_gamma(&my_units, &my_fields, gamma) == 0) { fprintf(stderr, "Error in calculate_gamma.\n"); return EXIT_FAILURE; } Calculating the Dust Temperature Field ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: c++ gr_float *dust_temperature; dust_temperature = new gr_float[field_size]; if (calculate_dust_temperature(&my_units, &my_fields, dust_temperature) == 0) { fprintf(stderr, "Error in calculate_dust_temperature.\n"); return EXIT_FAILURE; } Clearing the memory ------------------- .. code-block:: c++ free_chemistry_data(); Grackle is using global structures and therefore the global structure ``grackle_rates`` needs also to be released. Querying library version information ------------------------------------ A struct of type :c:data:`grackle_version` is used to hold version information about the version of Grackle that is being used. The struct contains information about the version number and particular git revision. .. c:type:: grackle_version This structure is used to organize version information for the library. .. c:var:: const char* version Specifies the version of the library using this template: ``.(.)(.dev)``. In this template ````, ````, and ```` correspond to a major, minor, and micro version numbers (the micro version number is omitted if it's zero). The final section can specify a development version. For concreteness, some example versions are provided in increasing order: ``"3.0"``, ``"3.1"``, ``"3.1.1"``, ``"3.1.2"``, ``"3.2.dev1"``, ``"3.2.dev2"``, ``"3.2"``. .. c:var:: const char* branch Specifies the name of the git branch that the library was compiled from. .. c:var:: const char* revision Specifies the hash identifying the git commit that the library was compiled from. The :c:func:`get_grackle_version` function is used to retrieve a properly intialized :c:data:`grackle_version` object. The following code snippet illustrates how one might query and print this information: .. code-block:: c++ grackle_version gversion = get_grackle_version(); printf ("The Grackle Version: %s\n", gversion.version); printf ("Git Branch: %s\n", gversion.branch); printf ("Git Revision: %s\n", gversion.revision); .. _dynamic-api: Dynamic configuration of Chemistry Data --------------------------------------- The functions providing dynamic access to the fields of :c:data:`chemistry_data` are useful for maintaining backwards compatibility with older versions of Grackle (that also provide this API) as new fields get added to :c:data:`chemistry_data`. This is exemplified in the following scenario. Suppose Grackle is updated to have a new heating/cooling mechanism, and to allow users to control that mechanism two new fields are added to :c:data:`chemistry_data`: * an ``int`` field called ``use_fancy_feature`` * a ``double`` field called ``fancy_feature_param`` Now suppose a downstream simulation code, written in ``c`` or ``c++``, wanted to support configuration of this feature. In this scenario, imagine that we have a pointer to a :c:data:`chemistry_data` structure called ``my_grackle_data``. The obvious way to configure this feature is to include the following snippet in the simulation code: .. code-block:: c++ if (configure_fancy_feature) { my_grackle_data->use_fancy_feature = 1; my_grackle_data->fancy_feature_param = 5.0; // arbitrary value } However, inclusion of the above snippet will prevent the simulation code from compiling if the user has a version of Grackle installed in which :c:data:`chemistry_data` does not have the ``use_fancy_feature`` and ``fancy_feature_param`` fields. Consequently, such users will have to update Grackle. * This can be inconvenient when a user has no interest in using this new feature, but needs an unrelated feature/bugfix introduced to the code in a subsequent changeset * This is especially inconvenient if a user is prototying a new feature in a custom Grackle branch in which the :c:data:`chemistry_data` struct is missing these fields. The following snippet shows how the dynamic access API can be used in the same way for versions of Grackle that include these parameters, and don't set the features in cases .. code-block:: c++ if (configure_fancy_feature) { int* use_fancy_feature = local_chemistry_data_access_int( my_grackle_data, "use_fancy_feature" ); double* fancy_feature_param = local_chemistry_data_access_double( my_grackle_data, "fancy_feature_param" ); if ((use_fancy_feature == NULL) || (fancy_feature_param == NULL)){ fprintf(stderr, "Update grackle version to use fancy feature\n"); } else { *use_fancy_feature = 1; *fancy_feature_param = 5.0; } } There are a few points worth noting: * As the above snippets show, the dynamic api clearly produces more verbose code when configuring :c:data:`chemistry_data` field-by-field. However, in codes where users configure Grackle by specifying the name of fields in the :c:data:`chemistry_data` struct and the associated values in a parameter file, the dynamic API can facillitate MUCH less verbose code. Under certain implementations, it may not even be necessary to modify a simulation code to support newly-introduced grackle parameters. * The dynamic API is slower than configuring :c:data:`chemistry_data` in the classic approach. However, this shouldn't be an issue since :c:data:`chemistry_data` is usually just configured once when the simulation code starts up. * The highlighted functions can also be used in tandem with other functions described in :ref:`dynamic_api_functions` to simplify (de)serialization of :c:data:`chemistry_data`. * For completeness, the dynamic API also provides an analogous function for configuring string parameters.