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Commit 50659c85 authored by Mladen Ivkovic's avatar Mladen Ivkovic Committed by Matthieu Schaller
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fixed grackle compilation issue

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1 merge request!1522fixed grackle compilation issue
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doc/RTD/source/RadiativeTransfer/GEAR_RT.rst
+ 2
− 1
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......@@ -35,7 +35,8 @@ Compiling for GEAR RT
Please note that the current implementation is not (yet) as
advanced as the :ref:`GEAR subgrid model grackle cooling <gear_grackle_cooling>`,
and the parameters listed as available there are not applicable for the
grackle cooling in combination with GEAR RT.
grackle cooling in combination with GEAR RT. You can however follow the Grackle
installation instructions documented there.
......
doc/RTD/source/SubgridModels/GEAR/index.rst
+ 3
− 1
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......@@ -57,7 +57,7 @@ When starting a simulation without providing the different element fractions in
The code uses an iterative method in order to find the correct initial composition and this method can be tuned with two parameters. ``GrackleCooling:max_steps`` defines the maximal number of steps to reach the convergence and ``GrackleCooling:convergence_limit`` defines the tolerance in the relative error.
In order to compile SWIFT with Grackle, you need to provide the options ``with-chemistry=GEAR`` and ``with-grackle=$GRACKLE_ROOT``
where ``$GRACKLE_ROOT`` is the root of the install directory (not the ``lib``).
where ``$GRACKLE_ROOT`` is the root of the install directory (not the ``lib``).
You will need a Grackle version later than 3.1.1. To compile it, run
the following commands from the root directory of Grackle:
......@@ -65,6 +65,8 @@ the following commands from the root directory of Grackle:
Update the variables ``LOCAL_HDF5_INSTALL`` and ``MACH_INSTALL_PREFIX`` in
the file ``src/clib/Make.mach.linux-gnu``.
Finish with ``make machine-linux-gnu; make && make install``.
Note that we require the 64 bit float version of Grackle, which should be the default setting.
(The precision can be set while compiling grackle with ``make precision-64``).
If you encounter any problem, you can look at the `Grackle documentation <https://grackle.readthedocs.io/en/latest/>`_
You can now provide the path given for ``MACH_INSTALL_PREFIX`` to ``with-grackle``.
......
src/cooling/grackle/cooling.c
+ 53
− 39
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......@@ -159,6 +159,8 @@ void cooling_compute_equilibrium(
const struct cooling_function_data* restrict cooling,
const struct part* restrict p, struct xpart* restrict xp) {
/* TODO: this can fail spectacularly and needs to be replaced. */
/* get temporary data */
struct part p_tmp = *p;
struct cooling_function_data cooling_tmp = *cooling;
......@@ -227,9 +229,9 @@ void cooling_first_init_part(const struct phys_const* restrict phys_const,
/* primordial chemistry >= 1 */
xp->cooling_data.HI_frac = zero;
xp->cooling_data.HII_frac = grackle_data->HydrogenFractionByMass;
xp->cooling_data.HeI_frac = 1. - grackle_data->HydrogenFractionByMass;
xp->cooling_data.HeI_frac = zero;
xp->cooling_data.HeII_frac = zero;
xp->cooling_data.HeIII_frac = zero;
xp->cooling_data.HeIII_frac = 1. - grackle_data->HydrogenFractionByMass;
xp->cooling_data.e_frac = xp->cooling_data.HII_frac +
0.25 * xp->cooling_data.HeII_frac +
0.5 * xp->cooling_data.HeIII_frac;
......@@ -251,6 +253,7 @@ void cooling_first_init_part(const struct phys_const* restrict phys_const,
#endif // MODE >= 3
#if COOLING_GRACKLE_MODE > 0
/* TODO: this can fail spectacularly and needs to be replaced. */
cooling_compute_equilibrium(phys_const, us, hydro_props, cosmo, cooling, p,
xp);
#endif
......@@ -308,33 +311,35 @@ void cooling_print_backend(const struct cooling_function_data* cooling) {
*/
#if COOLING_GRACKLE_MODE > 0
void cooling_copy_to_grackle1(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
/* HI */
xp->cooling_data.HI_frac *= rho;
data->HI_density = &xp->cooling_data.HI_frac;
species_densities[0] = xp->cooling_data.HI_frac * rho;
data->HI_density = &species_densities[0];
/* HII */
xp->cooling_data.HII_frac *= rho;
data->HII_density = &xp->cooling_data.HII_frac;
species_densities[1] = xp->cooling_data.HII_frac * rho;
data->HII_density = &species_densities[1];
/* HeI */
xp->cooling_data.HeI_frac *= rho;
data->HeI_density = &xp->cooling_data.HeI_frac;
species_densities[2] = xp->cooling_data.HeI_frac * rho;
data->HeI_density = &species_densities[2];
/* HeII */
xp->cooling_data.HeII_frac *= rho;
data->HeII_density = &xp->cooling_data.HeII_frac;
species_densities[3] = xp->cooling_data.HeII_frac * rho;
data->HeII_density = &species_densities[3];
/* HeIII */
xp->cooling_data.HeIII_frac *= rho;
data->HeIII_density = &xp->cooling_data.HeIII_frac;
species_densities[4] = xp->cooling_data.HeIII_frac * rho;
data->HeIII_density = &species_densities[4];
/* HeII */
xp->cooling_data.e_frac *= rho;
data->e_density = &xp->cooling_data.e_frac;
species_densities[5] = xp->cooling_data.e_frac * rho;
data->e_density = &species_densities[5];
}
#else
void cooling_copy_to_grackle1(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
data->HI_density = NULL;
data->HII_density = NULL;
data->HeI_density = NULL;
......@@ -354,22 +359,24 @@ void cooling_copy_to_grackle1(grackle_field_data* data, const struct part* p,
*/
#if COOLING_GRACKLE_MODE > 1
void cooling_copy_to_grackle2(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
/* HM */
xp->cooling_data.HM_frac *= rho;
data->HM_density = &xp->cooling_data.HM_frac;
species_densities[6] = xp->cooling_data.HM_frac * rho;
data->HM_density = &species_densities[6]
/* H2I */
xp->cooling_data.H2I_frac *= rho;
data->H2I_density = &xp->cooling_data.H2I_frac;
/* H2I */
species_densities[7] = xp->cooling_data.H2I_frac * rho;
data->H2I_density = &species_densities[7];
/* H2II */
xp->cooling_data.H2II_frac *= rho;
data->H2II_density = &xp->cooling_data.H2II_frac;
species_densities[8] = xp->cooling_data.H2II_frac * rho;
data->H2II_density = &species_densities[8];
}
#else
void cooling_copy_to_grackle2(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
data->HM_density = NULL;
data->H2I_density = NULL;
data->H2II_density = NULL;
......@@ -386,22 +393,24 @@ void cooling_copy_to_grackle2(grackle_field_data* data, const struct part* p,
*/
#if COOLING_GRACKLE_MODE > 2
void cooling_copy_to_grackle3(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
/* DI */
xp->cooling_data.DI_frac *= rho;
data->DI_density = &xp->cooling_data.DI_frac;
species_densities[9] = xp->cooling_data.DI_frac * rho;
data->DI_density = &species_densities[9];
/* DII */
xp->cooling_data.DII_frac *= rho;
data->DII_density = &xp->cooling_data.DII_frac;
species_densities[10] = xp->cooling_data.DII_frac * rho;
data->DII_density = &species_densities[10];
/* HDI */
xp->cooling_data.HDI_frac *= rho;
data->HDI_density = &xp->cooling_data.HDI_frac;
species_densities[11] = xp->cooling_data.HDI_frac * rho;
data->HDI_density = &species_densities[11];
}
#else
void cooling_copy_to_grackle3(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
data->DI_density = NULL;
data->DII_density = NULL;
data->HDI_density = NULL;
......@@ -504,11 +513,12 @@ void cooling_copy_from_grackle3(grackle_field_data* data, const struct part* p,
* @param rho The particle density.
*/
void cooling_copy_to_grackle(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho) {
struct xpart* xp, gr_float rho,
gr_float species_densities[12]) {
cooling_copy_to_grackle1(data, p, xp, rho);
cooling_copy_to_grackle2(data, p, xp, rho);
cooling_copy_to_grackle3(data, p, xp, rho);
cooling_copy_to_grackle1(data, p, xp, rho, species_densities);
cooling_copy_to_grackle2(data, p, xp, rho, species_densities);
cooling_copy_to_grackle3(data, p, xp, rho, species_densities);
data->volumetric_heating_rate = NULL;
data->specific_heating_rate = NULL;
......@@ -620,6 +630,9 @@ gr_float cooling_new_energy(
gr_float energy = hydro_get_physical_internal_energy(p, xp, cosmo) +
dt_therm * hydro_get_physical_internal_energy_dt(p, cosmo);
energy = max(energy, hydro_props->minimal_internal_energy);
/* keep this array here so you can point to and from it in
* copy to/from grackle */
gr_float species_densities[12];
/* initialize density */
data.density = &density;
......@@ -633,7 +646,7 @@ gr_float cooling_new_energy(
data.z_velocity = NULL;
/* copy to grackle structure */
cooling_copy_to_grackle(&data, p, xp, density);
cooling_copy_to_grackle(&data, p, xp, density, species_densities);
/* Apply the self shielding if requested */
cooling_apply_self_shielding(cooling, &chemistry_grackle, p, cosmo);
......@@ -705,8 +718,9 @@ gr_float cooling_time(const struct phys_const* restrict phys_const,
data.y_velocity = NULL;
data.z_velocity = NULL;
gr_float species_densities[12];
/* copy data from particle to grackle data */
cooling_copy_to_grackle(&data, p, xp, density);
cooling_copy_to_grackle(&data, p, xp, density, species_densities);
/* Apply the self shielding if requested */
cooling_apply_self_shielding(cooling, &chemistry_grackle, p, cosmo);
......
src/cooling/grackle/cooling.h
+ 8
− 4
View file @ 50659c85
......@@ -100,11 +100,14 @@ float cooling_get_radiated_energy(const struct xpart* restrict xp);
void cooling_print_backend(const struct cooling_function_data* cooling);
void cooling_copy_to_grackle1(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
struct xpart* xp, gr_float rho,
gr_float species_densities[12]);
void cooling_copy_to_grackle2(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
struct xpart* xp, gr_float rho,
gr_float species_densities[12]);
void cooling_copy_to_grackle3(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
struct xpart* xp, gr_float rho,
gr_float species_densities[12]);
void cooling_copy_from_grackle1(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
void cooling_copy_from_grackle2(grackle_field_data* data, const struct part* p,
......@@ -112,7 +115,8 @@ void cooling_copy_from_grackle2(grackle_field_data* data, const struct part* p,
void cooling_copy_from_grackle3(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
void cooling_copy_to_grackle(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
struct xpart* xp, gr_float rho,
gr_float species_densities[12]);
void cooling_copy_from_grackle(grackle_field_data* data, const struct part* p,
struct xpart* xp, gr_float rho);
void cooling_apply_self_shielding(
......
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