Added basic EAGLE chemistry model. Metal fields exist and get written to snapshots.

configure.ac

@@ -935,7 +935,7 @@ esac
 #  chemistry function
 AC_ARG_WITH([chemistry],
    [AS_HELP_STRING([--with-chemistry=<function>],
-      [chemistry function @<:@none, gear default: none@:>@]
+      [chemistry function @<:@none, gear, EAGLE default: none@:>@]
    )],
    [with_chemistry="$withval"],
    [with_chemistry="none"]
@@ -947,6 +947,9 @@ case "$with_chemistry" in
    gear)
       AC_DEFINE([CHEMISTRY_GEAR], [1], [Chemistry taken from the GEAR model])
    ;; 
+   EAGLE)
+      AC_DEFINE([CHEMISTRY_EAGLE], [1], [Chemistry taken from the EAGLE model])
+   ;; 
    *)
       AC_MSG_ERROR([Unknown chemistry function: $with_chemistry])
    ;;

src/Makefile.am

@@ -125,7 +125,10 @@ nobase_noinst_HEADERS = align.h approx_math.h atomic.h barrier.h cycle.h error.h
 		 chemistry/none/chemistry_struct.h \
                  chemistry/gear/chemistry.h \
 		 chemistry/gear/chemistry_io.h \
-		 chemistry/gear/chemistry_struct.h
+		 chemistry/gear/chemistry_struct.h \
+                 chemistry/EAGLE/chemistry.h \
+		 chemistry/EAGLE/chemistry_io.h \
+		 chemistry/EAGLE/chemistry_struct.h
 
 
 # Sources and flags for regular library

src/chemistry.h

@@ -33,6 +33,8 @@
 #include "./chemistry/none/chemistry.h"
 #elif defined(CHEMISTRY_GEAR)
 #include "./chemistry/gear/chemistry.h"
+#elif defined(CHEMISTRY_EAGLE)
+#include "./chemistry/EAGLE/chemistry.h"
 #else
 #error "Invalid choice of chemistry function."
 #endif

src/chemistry/EAGLE/chemistry.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_CHEMISTRY_EAGLE_H
+#define SWIFT_CHEMISTRY_EAGLE_H
+
+/**
+ * @file src/chemistry/gear/chemistry.h
+ * @brief Empty infrastructure for the cases without chemistry function
+ */
+
+/* Some standard headers. */
+#include <float.h>
+#include <math.h>
+
+/* Local includes. */
+#include "chemistry_struct.h"
+#include "error.h"
+#include "hydro.h"
+#include "parser.h"
+#include "part.h"
+#include "physical_constants.h"
+#include "units.h"
+
+/**
+ * @brief Sets the chemistry properties of the (x-)particles to a valid start
+ * state.
+ *
+ * Nothing to do here.
+ *
+ * @param p Pointer to the particle data.
+ * @param xp Pointer to the extended particle data.
+ */
+__attribute__((always_inline)) INLINE static void chemistry_init_part(
+    const struct part* restrict p, struct xpart* restrict xp) {}
+
+/**
+ * @brief Initialises the chemistry properties.
+ *
+ * Nothing to do here.
+ *
+ * @param parameter_file The parsed parameter file.
+ * @param us The current internal system of units.
+ * @param phys_const The physical constants in internal units.
+ */
+static INLINE void chemistry_init_backend(
+    const struct swift_params* parameter_file, const struct unit_system* us,
+    const struct phys_const* phys_const) {}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ */
+static INLINE void chemistry_print_backend() {
+
+  message("Chemistry model is 'EAGLE'.");
+}
+
+#endif /* SWIFT_CHEMISTRY_EAGLE_H */

src/chemistry/EAGLE/chemistry_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_CHEMISTRY_IO_EAGLE_H
+#define SWIFT_CHEMISTRY_IO_EAGLE_H
+
+#include "io_properties.h"
+
+/**
+ * @brief Specifies which particle fields to read from a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return Returns the number of fields to read.
+ */
+int chemistry_read_particles(struct part* parts, struct io_props* list) {
+
+  /* Nothing to read */
+  return 0;
+}
+
+/**
+ * @brief Specifies which particle fields to write to a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to write.
+ *
+ * @return Returns the number of fields to write.
+ */
+int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+
+  /* List what we want to write */
+  list[0] = io_make_output_field("ElementAbundance", FLOAT, eagle_element_count,
+                                 UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.metal_mass_fraction);
+
+  list[1] = io_make_output_field("SmoothedElementAbundance", FLOAT,
+                                 eagle_element_count, UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.smoothed_metal_mass_fraction);
+
+  list[2] =
+      io_make_output_field("Metallicity", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+                           chemistry_data.metal_mass_fraction_total);
+
+  list[3] = io_make_output_field(
+      "SmoothedMetallicity", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+      chemistry_data.smoothed_metal_mass_fraction_total);
+
+  list[4] = io_make_output_field("TotalMassFromSNIa", FLOAT, 1, UNIT_CONV_MASS,
+                                 parts, chemistry_data.mass_from_SNIa);
+
+  list[5] = io_make_output_field("MetalMassFracFromSNIa", FLOAT, 1,
+                                 UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.metal_mass_fraction_from_SNIa);
+
+  list[6] = io_make_output_field("TotalMassFromAGB", FLOAT, 1, UNIT_CONV_MASS,
+                                 parts, chemistry_data.mass_from_AGB);
+
+  list[7] =
+      io_make_output_field("MetalMassFracFromAGB", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                           parts, chemistry_data.metal_mass_fraction_from_AGB);
+
+  list[8] = io_make_output_field("TotalMassFromSNII", FLOAT, 1, UNIT_CONV_MASS,
+                                 parts, chemistry_data.mass_from_SNII);
+
+  list[9] = io_make_output_field("MetalMassFracFromSNII", FLOAT, 1,
+                                 UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.metal_mass_fraction_from_SNII);
+
+  list[10] =
+      io_make_output_field("IronMassFracFromSNIa", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                           parts, chemistry_data.iron_mass_fraction_from_SNIa);
+
+  list[11] = io_make_output_field(
+      "SmoothedIronMassFracFromSNIa", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+      chemistry_data.smoothed_iron_mass_fraction_from_SNIa);
+
+  return 12;
+}
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+void chemistry_write_flavour(hid_t h_grpsph) {
+
+  io_write_attribute_s(h_grpsph, "Chemistry Model", "EAGLE");
+}
+
+#endif /* SWIFT_CHEMISTRY_IO_EAGLE_H */

src/chemistry/EAGLE/chemistry_struct.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_CHEMISTRY_STRUCT_EAGLE_H
+#define SWIFT_CHEMISTRY_STRUCT_EAGLE_H
+
+/**
+ * @brief The individual elements traced in the EAGLE model.
+ */
+enum eagle_chemisty_element {
+  eagle_element_H = 0,
+  eagle_element_He,
+  eagle_element_C,
+  eagle_element_N,
+  eagle_element_O,
+  eagle_element_Ne,
+  eagle_element_Mg,
+  eagle_element_Si,
+  eagle_element_Fe,
+  eagle_element_count
+};
+
+/**
+ * @brief Chemical abundances traced in the EAGLE model.
+ */
+struct chemistry_part_data {
+
+  /*! Fraction of the particle mass in a given element */
+  float metal_mass_fraction[eagle_element_count];
+
+  /*! Fraction of the particle mass in *all* metals */
+  float metal_mass_fraction_total;
+
+  /*! Smoothed fraction of the particle mass in a given element */
+  float smoothed_metal_mass_fraction[eagle_element_count];
+
+  /*! Smoothed fraction of the particle mass in *all* metals */
+  float smoothed_metal_mass_fraction_total;
+
+  /*! Mass coming from SNIa */
+  float mass_from_SNIa;
+
+  /*! Fraction of total gas mass in metals coming from SNIa */
+  float metal_mass_fraction_from_SNIa;
+
+  /*! Mass coming from AGB */
+  float mass_from_AGB;
+
+  /*! Fraction of total gas mass in metals coming from AGB */
+  float metal_mass_fraction_from_AGB;
+
+  /*! Mass coming from SNII */
+  float mass_from_SNII;
+
+  /*! Fraction of total gas mass in metals coming from SNII */
+  float metal_mass_fraction_from_SNII;
+
+  /*! Fraction of total gas mass in Iron coming from SNIa */
+  float iron_mass_fraction_from_SNIa;
+
+  /*! Smoothed fraction of total gas mass in Iron coming from SNIa */
+  float smoothed_iron_mass_fraction_from_SNIa;
+};
+
+#endif /* SWIFT_CHEMISTRY_STRUCT_EAGLE_H */

src/chemistry_io.h

@@ -27,6 +27,8 @@
 #include "./chemistry/none/chemistry_io.h"
 #elif defined(CHEMISTRY_GEAR)
 #include "./chemistry/gear/chemistry_io.h"
+#elif defined(CHEMISTRY_EAGLE)
+#include "./chemistry/EAGLE/chemistry_io.h"
 #else
 #error "Invalid choice of chemistry function."
 #endif

src/chemistry_struct.h

@@ -32,6 +32,8 @@
 #include "./chemistry/none/chemistry_struct.h"
 #elif defined(CHEMISTRY_GEAR)
 #include "./chemistry/gear/chemistry_struct.h"
+#elif defined(CHEMISTRY_EAGLE)
+#include "./chemistry/EAGLE/chemistry_struct.h"
 #else
 #error "Invalid choice of chemistry function."
 #endif