Add output for grackle

src/cooling/grackle/cooling.h

@@ -31,6 +31,7 @@
 
 /* Local includes. */
 #include "../config.h"
+#include "cooling_io.h"
 #include "error.h"
 #include "hydro.h"
 #include "io_properties.h"
@@ -43,19 +44,6 @@
 #define GRACKLE_NPART 1
 #define GRACKLE_RANK 3
 
-#ifdef HAVE_HDF5
-
-/**
- * @brief Writes the current model of SPH to the file
- * @param h_grpsph The HDF5 group in which to write
- */
-__attribute__((always_inline)) INLINE static void cooling_write_flavour(
-    hid_t h_grpsph) {
-
-  io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle");
-}
-#endif
-
 /**
  * @brief Sets the cooling properties of the (x-)particles to a valid start
  * state.
@@ -446,36 +434,6 @@ __attribute__((always_inline)) INLINE static float cooling_timestep(
 }
 
 
-/**
- * @brief Parser the parameter file and initialize the #cooling_function_data
- * @param parameter_file The parser parameter file
- * @param cooling The cooling properties to initialize
- */
-__attribute__((always_inline)) INLINE static void cooling_parse_arguments(
-    const struct swift_params* parameter_file,
-    struct cooling_function_data* cooling) {
-
-  parser_get_param_string(parameter_file, "GrackleCooling:CloudyTable",
-                          cooling->cloudy_table);
-  cooling->with_uv_background =
-      parser_get_param_int(parameter_file, "GrackleCooling:WithUVbackground");
-
-  cooling->redshift =
-      parser_get_param_double(parameter_file, "GrackleCooling:Redshift");
-
-  cooling->with_metal_cooling =
-    parser_get_param_int(parameter_file, "GrackleCooling:WithMetalCooling");
-
-  cooling->provide_volumetric_heating_rates =
-    parser_get_param_int(parameter_file, "GrackleCooling:ProvideVolumetricHeatingRates");
-
-  cooling->provide_specific_heating_rates =
-    parser_get_param_int(parameter_file, "GrackleCooling:ProvideSpecificHeatingRates");
-
-  cooling->self_shielding_method =
-    parser_get_param_int(parameter_file, "GrackleCooling:SelfShieldingMethod");
-}
-
 
 /**
  * @brief Initialises the cooling unit system.

src/cooling/grackle/cooling_io.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_COOLING_GRACKLE_IO_H
+#define SWIFT_COOLING_GRACKLE_IO_H
+
+#include "../config.h"
+#include "cooling_struct.h"
+#include "io_properties.h"
+
+#ifdef HAVE_HDF5
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+__attribute__((always_inline)) INLINE static void cooling_write_flavour(
+    hid_t h_grpsph) {
+
+  io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle");
+}
+#endif
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+__attribute__((always_inline)) INLINE static int cooling_write_particles(
+    const struct xpart* xparts, struct io_props* list,
+    const struct cooling_function_data *cooling) {
+
+  int num = 0;
+
+  if (cooling->output_mode == 0)
+    return num;
+
+#if COOLING_GRACKLE_MODE >= 1
+  /* List what we want to write */
+  list[0] = io_make_output_field("HI", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HI_frac);
+
+  list[1] = io_make_output_field("HII", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HII_frac);
+  
+  list[2] = io_make_output_field("HeI", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HeI_frac);
+
+  list[3] = io_make_output_field("HeII", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HeII_frac);
+
+  list[4] = io_make_output_field("HeIII", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HeIII_frac);
+
+  list[5] = io_make_output_field("e", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.e_frac);
+
+  num += 6;
+#endif
+
+  if (cooling->output_mode == 1)
+    return num;
+
+#if COOLING_GRACKLE_MODE >= 2
+  list += num;
+
+  list[0] = io_make_output_field("HM", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HM_frac);
+    
+  list[1] = io_make_output_field("H2I", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.H2I_frac);
+
+  list[2] = io_make_output_field("H2II", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.H2II_frac);
+
+  num += 3;
+#endif
+
+  if (cooling->output_mode == 2)
+    return num;
+
+#if COOLING_GRACKLE_MODE >= 3
+  list += num;
+
+  list[0] = io_make_output_field("DI", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.DI_frac);
+    
+  list[1] = io_make_output_field("DII", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.DII_frac);
+
+  list[2] = io_make_output_field("HDI", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                                 xparts, cooling_data.HDI_frac);
+
+  num += 3;
+#endif
+
+  return num;
+
+}
+
+/**
+ * @brief Parser the parameter file and initialize the #cooling_function_data
+ * @param parameter_file The parser parameter file
+ * @param cooling The cooling properties to initialize
+ */
+__attribute__((always_inline)) INLINE static void cooling_parse_arguments(
+    const struct swift_params* parameter_file,
+    struct cooling_function_data* cooling) {
+
+  parser_get_param_string(parameter_file, "GrackleCooling:CloudyTable",
+                          cooling->cloudy_table);
+  cooling->with_uv_background =
+      parser_get_param_int(parameter_file, "GrackleCooling:WithUVbackground");
+
+  cooling->redshift =
+      parser_get_param_double(parameter_file, "GrackleCooling:Redshift");
+
+  cooling->with_metal_cooling =
+    parser_get_param_int(parameter_file, "GrackleCooling:WithMetalCooling");
+
+  cooling->provide_volumetric_heating_rates =
+    parser_get_param_int(parameter_file, "GrackleCooling:ProvideVolumetricHeatingRates");
+
+  cooling->provide_specific_heating_rates =
+    parser_get_param_int(parameter_file, "GrackleCooling:ProvideSpecificHeatingRates");
+
+  cooling->self_shielding_method =
+    parser_get_param_int(parameter_file, "GrackleCooling:SelfShieldingMethod");
+
+  cooling->output_mode =
+    parser_get_param_int(parameter_file, "GrackleCooling:OutputMode");
+}
+
+
+#endif // SWIFT_COOLING_GRACKLE_IO_H

src/cooling/grackle/cooling_struct.h

@@ -60,6 +60,9 @@ struct cooling_function_data {
 
   /* Self shielding method (<= 3) means grackle modes */
   int self_shielding_method;
+
+  /* Output mode (correspond to primordial chemistry mode */
+  int output_mode;
 };
 
 /**