[santacruzgalaxy-list] Grackle proposal

[Matthew Turk]

Hi all,

On Wed, Mar 19, 2014 at 4:58 PM, Romain Teyssier
<romain.teyssier at gmail.com> wrote:
>
> I totally agree with the 3 routines that need to be used.
> Nothing else should be required on the code's side, except passing the required variables.
>
>
>> grackle_init_run()
>>     called once per simulation
>>
>
> The parameters that should be passed here are
> - some cosmological model parameters
> - UV background model (spectrum, reionization redshift...)
> - starting redshift to compute the initial temperature and ionisation state
>
>> grackle_init_step(aexp,...)
>>     called once per each time-step, uses the value of the scale
>>     factor and other parameters as needed
>
> In principle at this stage, only aexp is required for cosmo runs.
> For non cosmo runs, the cooling tables do not need to be modified.
>
>>
>> grackle_solve_chemistry(dt,den,tem,...)
>>     called for each resolution element one or more times per one
>>     global time-step, uses gas properties to update internal energy.
>>     Input gas properties may be required to have specific units and
>>     be of specific data type. It should internally sense if it
>>     runs within an OpenMP construct and support OpenMP
>>     parallelization.
>>
>
> I would rather give the possibility of passing an array of cell.
> Users could also set the array size to 1 to deal with cells one by one.
> The required information could be
> nH, T or Tovermu or specific energy, metallicity in some units, dt_hydro, ncell
> On output, Delta T or Delta Tovermu or Delta specific energy
> I suggest we use fixed units (cgs or mks) for all input and output variables.
>
> These 3 routines are the only one that the user should care about.
>

This is awfully similar to the existing API:

https://bitbucket.org/brittonsmith/grackle/src/642cd133535a2dd3c57626b768c7c8c107096ac7/src/clib/grackle.h?at=default

The only necessary functions, according to
http://grackle.readthedocs.org/en/latest/Integration.html , are:

initialize_chemistry_data
solve_chemistry or solve_chemistry for tabular data

Looking at the example (non-equilibrium) executable:

https://bitbucket.org/brittonsmith/grackle/src/642cd133535a2dd3c57626b768c7c8c107096ac7/src/example/example.C?at=default

those are the only *functional* routines.  Everything else is to
provide additional information, *not* to actually do any computation.
I think that we have actually met these standards.  All of the units
are provided so as the *avoid* any boilerplate -- but if you want to
supply in CGS, you can set the input unit conversions to 1.0.

To compute the equilibrium tables:

https://bitbucket.org/brittonsmith/grackle/src/642cd133535a2dd3c57626b768c7c8c107096ac7/src/example/table_example.C?at=default

it's even simpler.  The only *active* routine is called on line 120,
"solve_chemistry".  I am genuinely being earnest when I ask, from the
.h file linked above, which arguments to the functions would you like
to see removed?  I've included the full function signatures below.  If
you want to get *out* various things, you can utilize the other
functions -- like the cooling time function and so on.

-Matt

int initialize_chemistry_data(chemistry_data &my_chemistry,
                              code_units &my_units, gr_float a_value);

int solve_chemistry(chemistry_data &my_chemistry,
   code_units &my_units,
   gr_float a_value, gr_float dt_value,
   gr_int grid_rank, gr_int *grid_dimension,
   gr_int *grid_start, gr_int *grid_end,
   gr_float *density, gr_float *internal_energy,
   gr_float *x_velocity, gr_float *y_velocity, gr_float *z_velocity,
   gr_float *HI_density, gr_float *HII_density, gr_float *HM_density,
   gr_float *HeI_density, gr_float *HeII_density, gr_float *HeIII_density,
   gr_float *H2I_density, gr_float *H2II_density,
   gr_float *DI_density, gr_float *DII_density, gr_float *HDI_density,
   gr_float *e_density, gr_float *metal_density);

int solve_chemistry(chemistry_data &my_chemistry,
                    code_units &my_units,
                    gr_float a_value, gr_float dt_value,
                    gr_int grid_rank, gr_int *grid_dimension,
                    gr_int *grid_start, gr_int *grid_end,
                    gr_float *density, gr_float *internal_energy,
                    gr_float *x_velocity, gr_float *y_velocity,
gr_float *z_velocity,
                    gr_float *metal_density);

> Cheers,
> Romain
>
>
>
>> The API can also define its own data types with natutal conversion from
>> standard types, for example the following code should be valid:
>>
>> float f;
>> double d;
>> gr_float gr_f;
>>
>> gr_f = f;
>> gr_f = d;
>>
>> An analogous API should be provided for F77.
>>
>> Then in a code the API will be implemented as follows:
>>
>> Begin_code
>>
>>     grackle_init_run()
>>
>>     Loop_over_timesteps(aexp)
>>
>>         grackle_init_step(aexp,...)
>>
>> #pragma omp parallel loop
>>         Loop_over_resolution_elements(elem)
>>         {
>>              gr_float dt = code_time_step*time_unit;
>>              gr_float den = code_density(elem)*den_unit;
>>              gr_float tem = code_temperature(elem)*tem_unit;
>>              grackle_solve_chemistry(dt,den,tem,...)
>>         }
>>
>>     End_loop
>>
>> End_code
>>
>> Let's converge on the API, and then the Grackle team will be able to
>> write a couple of wrappers that will suit everyone.
>>
>> Given the wrappers, if Grackle is installed as an external library and
>> provides a proper Linus-style installer (that will handle all HDF5 and
>> other dependencies), then it should be trivial to integrate it in any code.
>>
>> Nick
>>
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