Add grackle chemistry

src/chemistry.h

@@ -31,6 +31,8 @@
 /* Import the right chemistry definition */
 #if defined(CHEMISTRY_NONE)
 #include "./chemistry/none/chemistry.h"
+#elif defined(CHEMISTRY_GRACKLE)
+#include "./chemistry/grackle/chemistry.h"
 #else
 #error "Invalid choice of chemistry function."
 #endif

src/chemistry/grackle/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_NONE_H
+#define SWIFT_CHEMISTRY_NONE_H
+
+/**
+ * @file src/chemistry/none/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.
+ * @param chemistry The chemistry properties to initialize
+ */
+static INLINE void chemistry_init_backend(
+    const struct swift_params* parameter_file, const struct unit_system* us,
+    const struct phys_const* phys_const,
+    struct chemistry_part_data* chemistry) {}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ *
+ * @param chemistry The properties of the chemistry function.
+ */
+static INLINE void chemistry_print_backend(
+    const struct chemistry_part_data* chemistry) {
+
+  message("Chemistry function is 'grackle'.");
+}
+
+#endif /* SWIFT_CHEMISTRY_NONE_H */

src/chemistry/grackle/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/>.
+ *
+ ******************************************************************************/
+
+#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.
+ * @param num_fields The number of i/o fields to read.
+ */
+void chemistry_read_particles(struct part* parts, struct io_props* list,
+                          int* num_fields) {
+
+  list += *num_fields;
+  *num_fields += 1;
+
+  /* List what we want to read */
+  list[0] = io_make_input_field("HeDensity", FLOAT, 1, COMPULSORY,
+                                UNIT_CONV_DENSITY, parts, chemistry_data.he_density);
+}
+
+
+/**
+ * @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.
+ * @param num_fields The number of i/o fields to write.
+ */
+void chemistry_write_particles(const struct part* parts, struct io_props* list,
+                           int* num_fields) {
+
+  list += *num_fields;
+  *num_fields += 1;
+  
+  list[0] = io_make_output_field("HeDensity", FLOAT, 1, UNIT_CONV_LENGTH,
+                                 parts, chemistry_data.he_density);
+}
+
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+void writeChemistryFlavor(hid_t h_grpsph) {
+
+  /* Viscosity and thermal conduction */
+  io_write_attribute_s(
+      h_grpsph, "Chemistry Model",
+      "Grackle");
+}

src/chemistry/grackle/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_NONE_H
+#define SWIFT_CHEMISTRY_STRUCT_NONE_H
+
+/**
+ * @file src/chemistry/none/chemistry_struct.h
+ * @brief Empty infrastructure for the cases without chemistry function
+ */
+
+/**
+ * @brief Properties of the chemistry function.
+ */
+struct chemistry_part_data {
+  float he_density;
+};
+
+#endif /* SWIFT_CHEMISTRY_STRUCT_NONE_H */

src/chemistry_io.h

@@ -25,6 +25,8 @@
 /* Import the right functions */
 #if defined(CHEMISTRY_NONE)
 #include "./chemistry/none/chemistry_io.h"
+#elif defined(CHEMISTRY_GRACKLE)
+#include "./chemistry/grackle/chemistry_io.h"
 #else
 #error "Invalid choice of chemistry function."
 #endif

src/chemistry_struct.h

@@ -30,6 +30,8 @@
 /* Import the right chemistry definition */
 #if defined(CHEMISTRY_NONE)
 #include "./chemistry/none/chemistry_struct.h"
+#elif defined(CHEMISTRY_GRACKLE)
+#include "./chemistry/grackle/chemistry_struct.h"
 #else
 #error "Invalid choice of chemistry function."
 #endif