From 5a6453e27c08616bf173a3de179706101b2ee6ac Mon Sep 17 00:00:00 2001
From: Loic Hausammann <loic.hausammann@protonmail.ch>
Date: Fri, 21 Aug 2020 14:41:19 +0100
Subject: [PATCH] Fix API
---
configure.ac | 2 +-
doc/RTD/source/SubgridModels/GEAR/index.rst | 5 +++-
examples/Cooling/CoolingBox/coolingBox.yml | 30 +++++++++++---------
src/chemistry/none/chemistry.h | 11 +++++++
src/chemistry/none/chemistry_struct.h | 7 +++++
src/cooling/grackle/cooling.c | 2 +-
src/cooling/grackle/cooling.h | 2 +-
src/parallel_io.c | 2 ++
src/serial_io.c | 2 ++
src/single_io.c | 2 ++
src/star_formation/EAGLE/star_formation_io.h | 13 +++++++++
src/star_formation/GEAR/star_formation.h | 1 +
src/star_formation/GEAR/star_formation_io.h | 22 +++++++++++++-
src/star_formation/QLA/star_formation_io.h | 13 +++++++++
src/star_formation/none/star_formation_io.h | 13 +++++++++
src/stars/GEAR/stars.h | 2 --
src/stars/GEAR/stars_io.h | 7 ++---
tools/task_plots/plot_tasks.py | 2 +-
18 files changed, 112 insertions(+), 26 deletions(-)
diff --git a/configure.ac b/configure.ac
index cae9bb28c8..933460fb7e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1222,7 +1222,7 @@ if test "x$with_grackle" != "xno"; then
[AC_DEFINE([HAVE_GRACKLE],1,[The GRACKLE library appears to be present.])
AC_DEFINE([CONFIG_BFLOAT_8],1,[Use doubles in grackle])
],
- [AC_MSG_ERROR(Cannot find grackle library!)],
+ [AC_MSG_ERROR(Cannot find grackle library! You need to have a version >= 3.1.1)],
[$GRACKLE_LIBS])
fi
AC_SUBST([GRACKLE_LIBS])
diff --git a/doc/RTD/source/SubgridModels/GEAR/index.rst b/doc/RTD/source/SubgridModels/GEAR/index.rst
index 89ee949fb3..9faaef245b 100644
--- a/doc/RTD/source/SubgridModels/GEAR/index.rst
+++ b/doc/RTD/source/SubgridModels/GEAR/index.rst
@@ -57,7 +57,7 @@ The code uses an iterative method in order to find the correct initial compositi
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``).
-You will need a Grackle version later than 3.1. To compile it, run
+You will need a Grackle version later than 3.1.1. To compile it, run
the following commands from the root directory of Grackle:
``./configure; cd src/clib``.
Update the variables ``LOCAL_HDF5_INSTALL`` and ``MACH_INSTALL_PREFIX`` in
@@ -103,6 +103,9 @@ A particle is in the star forming regime if:
A star will be able to form if a randomly drawn number is below :math:`\frac{m_g}{m_\star}\left(1 - \exp\left(-c_\star \Delta t / t_\textrm{ff}\right)\right)` where :math:`t_\textrm{ff}` is the free fall time, :math:`\Delta t` is the time step of the particle and :math:`c_\star` is the star formation coefficient (``GEARStarFormation:star_formation_efficiency``), :math:`m_g` the mass of the gas particle and :math:`m_\star` the mass of the possible future star. The mass of the star is computed from the average gas mass in the initial conditions divided by the number of possible stars formed per gas particle (``GEARStarFormation:n_stars_per_particle``). When we cannot have enough mass to form a second star (defined with the fraction of mass ``GEARStarFormation:min_mass_frac``), we fully convert the gas particle into a stellar particle. Once the star is formed, we move it a bit in a random direction and fraction of the smoothing length in order to avoid any division by 0.
+Currently, only the following hydro schemes are compatible: SPHENIX and Gadget2.
+Implementing the other hydro schemes is not complicated but requires some careful thinking about the cosmological terms in the definition of the velocity divergence (comoving vs non comoving coordinates and if the Hubble flow is included or not).
+
.. code:: YAML
GEARStarFormation:
diff --git a/examples/Cooling/CoolingBox/coolingBox.yml b/examples/Cooling/CoolingBox/coolingBox.yml
index f776823d1b..3907f16d6e 100644
--- a/examples/Cooling/CoolingBox/coolingBox.yml
+++ b/examples/Cooling/CoolingBox/coolingBox.yml
@@ -39,20 +39,22 @@ LambdaCooling:
lambda_nH2_cgs: 1e-22 # Cooling rate divided by square Hydrogen number density (in cgs units [erg * s^-1 * cm^3])
cooling_tstep_mult: 1.0 # Dimensionless pre-factor for the time-step condition
-# Cooling with Grackle 2.0
+# Cooling with Grackle 3.0
GrackleCooling:
- CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
- WithUVbackground: 0 # Enable or not the UV background
- Redshift: 0 # Redshift to use (-1 means time based redshift)
- WithMetalCooling: 1 # Enable or not the metal cooling
- ProvideVolumetricHeatingRates: 0 # User provide volumetric heating rates
- ProvideSpecificHeatingRates: 0 # User provide specific heating rates
- SelfShieldingMethod: 0 # Grackle (<= 3) or Gear self shielding method
- MaxSteps: 1000
- ConvergenceLimit: 1e-2
-
-GearChemistry:
- InitialMetallicity: 0.01295
+ cloudy_table: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
+ with_UV_background: 0 # Enable or not the UV background
+ redshift: 0 # Redshift to use (-1 means time based redshift)
+ with_metal_cooling: 1 # Enable or not the metal cooling
+ provide_volumetric_heating_rates: 0 # (optional) User provide volumetric heating rates
+ provide_specific_heating_rates: 0 # (optional) User provide specific heating rates
+ max_steps: 10000 # (optional) Max number of step when computing the initial composition
+ convergence_limit: 1e-2 # (optional) Convergence threshold (relative) for initial composition
+ thermal_time_myr: 5 # (optional) Time (in Myr) for adiabatic cooling after a feedback event.
+ self_shielding_method: 0 # (optional) Grackle (1->3 for Grackle's ones, 0 for none and -1 for GEAR)
+ self_shielding_threshold_atom_per_cm3: 0.007 # Required only with GEAR's self shielding. Density threshold of the self shielding
+
+GEARChemistry:
+ initial_metallicity: 0.01295
EAGLECooling:
dir_name: ./coolingtables/
@@ -74,3 +76,5 @@ EAGLEChemistry: # Solar abundances
init_abundance_Silicon: 6.825874e-4
init_abundance_Iron: 1.1032152e-3
+GEARPressureFloor:
+ jeans_factor: 0. # Number of particles required to suppose a resolved clump and avoid the pressure floor.
diff --git a/src/chemistry/none/chemistry.h b/src/chemistry/none/chemistry.h
index 4070c4fe7e..3bd4e41a86 100644
--- a/src/chemistry/none/chemistry.h
+++ b/src/chemistry/none/chemistry.h
@@ -49,6 +49,17 @@ chemistry_get_element_name(enum chemistry_element elem) {
return chemistry_element_names[elem];
}
+/**
+ * @brief Copies the chemistry properties of the gas particle over to the
+ * star particle.
+ *
+ * @param p the gas particles.
+ * @param xp the additional properties of the gas particles.
+ * @param sp the new created star particle with its properties.
+ */
+INLINE static void chemistry_copy_star_formation_properties(
+ const struct part* p, const struct xpart* xp, struct spart* sp) {}
+
/**
* @brief Initialises the chemistry properties.
*
diff --git a/src/chemistry/none/chemistry_struct.h b/src/chemistry/none/chemistry_struct.h
index 3b065bcdf6..78f9aed11f 100644
--- a/src/chemistry/none/chemistry_struct.h
+++ b/src/chemistry/none/chemistry_struct.h
@@ -43,6 +43,13 @@ struct chemistry_global_data {};
*/
struct chemistry_part_data {};
+/**
+ * @brief Chemistry properties carried by the #spart.
+ *
+ * Nothing here.
+ */
+struct chemistry_spart_data {};
+
/**
* @brief Chemistry properties carried by the #bpart.
*
diff --git a/src/cooling/grackle/cooling.c b/src/cooling/grackle/cooling.c
index 30c0a50cf8..84b9fa4457 100644
--- a/src/cooling/grackle/cooling.c
+++ b/src/cooling/grackle/cooling.c
@@ -18,7 +18,7 @@
******************************************************************************/
/**
* @file src/cooling/grackle/cooling.c
- * @brief Cooling using the GRACKLE 3.0 library.
+ * @brief Cooling using the GRACKLE 3.1.1 library.
*/
#include "../config.h"
diff --git a/src/cooling/grackle/cooling.h b/src/cooling/grackle/cooling.h
index 55dbb609f1..a629f6fb71 100644
--- a/src/cooling/grackle/cooling.h
+++ b/src/cooling/grackle/cooling.h
@@ -21,7 +21,7 @@
/**
* @file src/cooling/grackle/cooling.h
- * @brief Cooling using the GRACKLE 3.0 library.
+ * @brief Cooling using the GRACKLE 3.1.1 library.
*/
/* Some standard headers. */
diff --git a/src/parallel_io.c b/src/parallel_io.c
index a8cbdbeca9..01fef7fc65 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -1010,6 +1010,8 @@ void read_ic_parallel(char* fileName, const struct unit_system* internal_units,
if (with_stars) {
Nparticles = *Nstars;
stars_read_particles(*sparts, list, &num_fields);
+ num_fields +=
+ star_formation_read_particles(*sparts, list + num_fields);
}
break;
diff --git a/src/serial_io.c b/src/serial_io.c
index 1fe5a1a7b6..c170a0ff4f 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -804,6 +804,8 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
if (with_stars) {
Nparticles = *Nstars;
stars_read_particles(*sparts, list, &num_fields);
+ num_fields +=
+ star_formation_read_particles(*sparts, list + num_fields);
}
break;
diff --git a/src/single_io.c b/src/single_io.c
index 5952a7bb4e..865f0c9be6 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -675,6 +675,8 @@ void read_ic_single(const char* fileName,
if (with_stars) {
Nparticles = *Nstars;
stars_read_particles(*sparts, list, &num_fields);
+ num_fields +=
+ star_formation_read_particles(*sparts, list + num_fields);
}
break;
diff --git a/src/star_formation/EAGLE/star_formation_io.h b/src/star_formation/EAGLE/star_formation_io.h
index fd4b870a7d..aac87d8c07 100644
--- a/src/star_formation/EAGLE/star_formation_io.h
+++ b/src/star_formation/EAGLE/star_formation_io.h
@@ -25,6 +25,19 @@
/* Local includes */
#include "io_properties.h"
+/**
+ * @brief Specifies which s-particle fields to read from a dataset
+ *
+ * @param sparts The s-particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return num_fields The number of i/o fields to read.
+ */
+INLINE static int star_formation_read_particles(struct spart* sparts,
+ struct io_props* list) {
+ return 0;
+}
+
/**
* @brief Specifies which particle fields to write to a dataset
*
diff --git a/src/star_formation/GEAR/star_formation.h b/src/star_formation/GEAR/star_formation.h
index 3ef5714756..341ed815b1 100644
--- a/src/star_formation/GEAR/star_formation.h
+++ b/src/star_formation/GEAR/star_formation.h
@@ -21,6 +21,7 @@
#define SWIFT_GEAR_STAR_FORMATION_H
/* Local includes */
+#include "chemistry.h"
#include "cooling.h"
#include "cosmology.h"
#include "engine.h"
diff --git a/src/star_formation/GEAR/star_formation_io.h b/src/star_formation/GEAR/star_formation_io.h
index fc64cb893a..46ac7c6e3d 100644
--- a/src/star_formation/GEAR/star_formation_io.h
+++ b/src/star_formation/GEAR/star_formation_io.h
@@ -26,6 +26,24 @@
/* Local includes */
#include "io_properties.h"
+/**
+ * @brief Specifies which s-particle fields to read from a dataset
+ *
+ * @param sparts The s-particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return num_fields The number of i/o fields to read.
+ */
+INLINE static int star_formation_read_particles(struct spart* sparts,
+ struct io_props* list) {
+
+ /* List what we want to read */
+ list[0] = io_make_input_field("BirthMass", FLOAT, 1, OPTIONAL, UNIT_CONV_MASS,
+ sparts, sf_data.birth_mass);
+
+ return 1;
+}
+
/**
* @brief Specifies which particle fields to write to a dataset
*
@@ -113,7 +131,9 @@ INLINE static void starformation_init_backend(
starform->min_mass_frac_plus_one += 1.;
/* Get the jeans factor */
- starform->n_jeans_2_3 = pow(pressure_floor_props.n_jeans, 2. / 3.);
+ starform->n_jeans_2_3 =
+ parser_get_param_float(parameter_file, "GEARPressureFloor:jeans_factor");
+ starform->n_jeans_2_3 = pow(starform->n_jeans_2_3, 2. / 3.);
/* Apply unit change */
starform->maximal_temperature *=
diff --git a/src/star_formation/QLA/star_formation_io.h b/src/star_formation/QLA/star_formation_io.h
index bbdde40761..d65a40bf70 100644
--- a/src/star_formation/QLA/star_formation_io.h
+++ b/src/star_formation/QLA/star_formation_io.h
@@ -25,6 +25,19 @@
/* Local includes */
#include "io_properties.h"
+/**
+ * @brief Specifies which s-particle fields to read from a dataset
+ *
+ * @param sparts The s-particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return num_fields The number of i/o fields to read.
+ */
+INLINE static int star_formation_read_particles(struct spart* sparts,
+ struct io_props* list) {
+ return 0;
+}
+
/**
* @brief Specifies which particle fields to write to a dataset
*
diff --git a/src/star_formation/none/star_formation_io.h b/src/star_formation/none/star_formation_io.h
index 8240c42e54..5c2329b397 100644
--- a/src/star_formation/none/star_formation_io.h
+++ b/src/star_formation/none/star_formation_io.h
@@ -25,6 +25,19 @@
/* Local includes */
#include "io_properties.h"
+/**
+ * @brief Specifies which s-particle fields to read from a dataset
+ *
+ * @param sparts The s-particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return num_fields The number of i/o fields to read.
+ */
+INLINE static int star_formation_read_particles(struct spart* sparts,
+ struct io_props* list) {
+ return 0;
+}
+
/**
* @brief Specifies which particle fields to write to a dataset
*
diff --git a/src/stars/GEAR/stars.h b/src/stars/GEAR/stars.h
index 3a6d6ba203..a4a9b2ecdc 100644
--- a/src/stars/GEAR/stars.h
+++ b/src/stars/GEAR/stars.h
@@ -68,8 +68,6 @@ __attribute__((always_inline)) INLINE static void stars_first_init_spart(
const int with_cosmology, const double scale_factor, const double time) {
sp->time_bin = 0;
- sp->sf_data.birth_density = 0.f;
- // sp->birth_time = 0.;
stars_init_spart(sp);
}
diff --git a/src/stars/GEAR/stars_io.h b/src/stars/GEAR/stars_io.h
index 97d9f29826..7a1ed1fddd 100644
--- a/src/stars/GEAR/stars_io.h
+++ b/src/stars/GEAR/stars_io.h
@@ -34,7 +34,7 @@ INLINE static void stars_read_particles(struct spart *sparts,
int *num_fields) {
/* Say how much we want to read */
- *num_fields = 7;
+ *num_fields = 6;
/* List what we want to read */
list[0] = io_make_input_field("Coordinates", DOUBLE, 3, COMPULSORY,
@@ -47,10 +47,7 @@ INLINE static void stars_read_particles(struct spart *sparts,
UNIT_CONV_NO_UNITS, sparts, id);
list[4] = io_make_input_field("SmoothingLength", FLOAT, 1, OPTIONAL,
UNIT_CONV_LENGTH, sparts, h);
- list[5] = io_make_input_field("BirthMass", FLOAT, 1, OPTIONAL, UNIT_CONV_MASS,
- sparts, sf_data.birth_mass);
-
- list[6] = io_make_input_field("BirthTime", FLOAT, 1, OPTIONAL, UNIT_CONV_MASS,
+ list[5] = io_make_input_field("BirthTime", FLOAT, 1, OPTIONAL, UNIT_CONV_MASS,
sparts, birth_time);
}
diff --git a/tools/task_plots/plot_tasks.py b/tools/task_plots/plot_tasks.py
index a0eb356cac..45f5feb03d 100755
--- a/tools/task_plots/plot_tasks.py
+++ b/tools/task_plots/plot_tasks.py
@@ -584,7 +584,7 @@ for rank in ranks:
ax.yaxis.set_major_locator(loc)
ax.grid(True, which="major", axis="y", linestyle="-")
- pl.show()
+ # pl.show()
if mpimode:
outpng = outbase + str(rank) + ".png"
else:
--
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