Merge branch 'io_unit_conversion' into 'master'

Io unit conversion

This implements two changes:

 - Unit conversion from ICs to internal units and from internal units to snapshots when doing i/o.
 - A much simpler interface to add/remove fields to be written/read during i/o.

Could you let me know whether your usual tests still run with this ? 

See merge request !194

examples/ExternalPointMass/makeIC.py

@@ -89,6 +89,14 @@ grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
 grp = file.create_group("/RuntimePars")
 grp.attrs["PeriodicBoundariesOn"] = periodic
 
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 3.0856776e21
+grp.attrs["Unit mass in cgs (U_M)"] = 1.9885e33
+grp.attrs["Unit time in cgs (U_t)"] = 3.0856776e16
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
 #Particle group
 #grp0 = file.create_group("/PartType0")
 grp1 = file.create_group("/PartType1")

examples/UniformBox/uniformBox.yml

@@ -38,3 +38,11 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./uniformBox.hdf5     # The file to read
+
+
+  # External potential parameters
+PointMass:
+  position_x:      50.     # location of external point mass in internal units
+  position_y:      50.
+  position_z:      50.	
+  mass:            1e10     # mass of external point mass in internal units

examples/main.c

@@ -291,7 +291,7 @@ int main(int argc, char *argv[]) {
   struct swift_params *params = malloc(sizeof(struct swift_params));
   if (params == NULL) error("Error allocating memory for the parameter file.");
   if (myrank == 0) {
-    message("Reading parameters from file '%s'", paramFileName);
+    message("Reading runtime parameters from file '%s'", paramFileName);
     parser_read_file(paramFileName, params);
     // parser_print_params(&params);
     parser_write_params_to_file(params, "used_parameters.yml");
@@ -324,11 +324,11 @@ int main(int argc, char *argv[]) {
   units_init(&us, params, "InternalUnitSystem");
   phys_const_init(&us, &prog_const);
   if (myrank == 0 && verbose > 0) {
-    message("Unit system: U_M = %e g.", us.UnitMass_in_cgs);
-    message("Unit system: U_L = %e cm.", us.UnitLength_in_cgs);
-    message("Unit system: U_t = %e s.", us.UnitTime_in_cgs);
-    message("Unit system: U_I = %e A.", us.UnitCurrent_in_cgs);
-    message("Unit system: U_T = %e K.", us.UnitTemperature_in_cgs);
+    message("Internal unit system: U_M = %e g.", us.UnitMass_in_cgs);
+    message("Internal unit system: U_L = %e cm.", us.UnitLength_in_cgs);
+    message("Internal unit system: U_t = %e s.", us.UnitTime_in_cgs);
+    message("Internal unit system: U_I = %e A.", us.UnitCurrent_in_cgs);
+    message("Internal unit system: U_T = %e K.", us.UnitTemperature_in_cgs);
     phys_const_print(&prog_const);
   }
 
@@ -354,17 +354,17 @@ int main(int argc, char *argv[]) {
   if (myrank == 0) clocks_gettime(&tic);
 #if defined(WITH_MPI)
 #if defined(HAVE_PARALLEL_HDF5)
-  read_ic_parallel(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
-                   &flag_entropy_ICs, myrank, nr_nodes, MPI_COMM_WORLD,
-                   MPI_INFO_NULL, dry_run);
+  read_ic_parallel(ICfileName, &us, dim, &parts, &gparts, &Ngas, &Ngpart,
+                   &periodic, &flag_entropy_ICs, myrank, nr_nodes,
+                   MPI_COMM_WORLD, MPI_INFO_NULL, dry_run);
 #else
-  read_ic_serial(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
+  read_ic_serial(ICfileName, &us, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
                  &flag_entropy_ICs, myrank, nr_nodes, MPI_COMM_WORLD,
                  MPI_INFO_NULL, dry_run);
 #endif
 #else
-  read_ic_single(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
-                 &flag_entropy_ICs, dry_run);
+  read_ic_single(ICfileName, &us, dim, &parts, &gparts, &Ngas, &Ngpart,
+                 &periodic, &flag_entropy_ICs, dry_run);
 #endif
   if (myrank == 0) {
     clocks_gettime(&toc);
@@ -452,7 +452,7 @@ int main(int argc, char *argv[]) {
   if (myrank == 0) clocks_gettime(&tic);
   struct engine e;
   engine_init(&e, &s, params, nr_nodes, myrank, nr_threads, with_aff,
-              engine_policies, talking, &prog_const, &hydro_properties,
+              engine_policies, talking, &us, &prog_const, &hydro_properties,
               &potential);
   if (myrank == 0) {
     clocks_gettime(&toc);

src/Makefile.am

@@ -54,7 +54,7 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
 # Include files for distribution, not installation.
 nobase_noinst_HEADERS = approx_math.h atomic.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \
 		 vector.h runner_doiact.h runner_doiact_grav.h units.h intrinsics.h minmax.h kick.h \
-		 timestep.h drift.h adiabatic_index.h \
+		 timestep.h drift.h adiabatic_index.h io_properties.h \
 		 gravity.h gravity_io.h \
 		 gravity/Default/gravity.h gravity/Default/gravity_iact.h gravity/Default/gravity_io.h \
 		 gravity/Default/gravity_debug.h gravity/Default/gravity_part.h  \

src/common_io.c

@@ -58,6 +58,7 @@ const char* particle_type_names[NUM_PARTICLE_TYPES] = {
  *way.
  */
 hid_t hdf5Type(enum DATA_TYPE type) {
+
   switch (type) {
     case INT:
       return H5T_NATIVE_INT;
@@ -87,6 +88,7 @@ hid_t hdf5Type(enum DATA_TYPE type) {
  * @brief Returns the memory size of the data type
  */
 size_t sizeOfType(enum DATA_TYPE type) {
+
   switch (type) {
     case INT:
       return sizeof(int);
@@ -112,6 +114,24 @@ size_t sizeOfType(enum DATA_TYPE type) {
   }
 }
 
+/**
+ * @brief Return 1 if the type has double precision
+ *
+ * Returns an error if the type is not FLOAT or DOUBLE
+ */
+int isDoublePrecision(enum DATA_TYPE type) {
+  
+  switch (type) {
+    case FLOAT:
+      return 0;
+    case DOUBLE:
+      return 1;
+    default:
+      error("Invalid type");
+      return 0;
+  }
+}
+
 /**
  * @brief Reads an attribute from a given HDF5 group.
  *
@@ -273,15 +293,55 @@ void writeAttribute_s(hid_t grp, const char* name, const char* str) {
   writeStringAttribute(grp, name, str, strlen(str));
 }
 
+/**
+ * @brief Reads the Unit System from an IC file.
+ * @param h_file The (opened) HDF5 file from which to read.
+ * @param us The UnitSystem to fill.
+ *
+ * If the 'Units' group does not exist in the ICs, cgs units will be assumed
+ */
+void readUnitSystem(hid_t h_file, struct UnitSystem* us) {
+
+  hid_t h_grp = H5Gopen(h_file, "/Units", H5P_DEFAULT);
+
+  if (h_grp < 0) {
+    message("'Units' group not found in ICs. Assuming CGS unit system.");
+
+    /* Default to CGS */
+    us->UnitMass_in_cgs = 1.;
+    us->UnitLength_in_cgs = 1.;
+    us->UnitTime_in_cgs = 1.;
+    us->UnitCurrent_in_cgs = 1.;
+    us->UnitTemperature_in_cgs = 1.;
+
+    return;
+  }
+
+  /* Ok, Read the damn thing */
+  readAttribute(h_grp, "Unit length in cgs (U_L)", DOUBLE,
+                &us->UnitLength_in_cgs);
+  readAttribute(h_grp, "Unit mass in cgs (U_M)", DOUBLE, &us->UnitMass_in_cgs);
+  readAttribute(h_grp, "Unit time in cgs (U_t)", DOUBLE, &us->UnitTime_in_cgs);
+  readAttribute(h_grp, "Unit current in cgs (U_I)", DOUBLE,
+                &us->UnitCurrent_in_cgs);
+  readAttribute(h_grp, "Unit temperature in cgs (U_T)", DOUBLE,
+                &us->UnitTemperature_in_cgs);
+
+  /* Clean up */
+  H5Gclose(h_grp);
+}
+
 /**
  * @brief Writes the current Unit System
  * @param h_file The (opened) HDF5 file in which to write
- * @param us The UnitSystem used in the run
+ * @param us The UnitSystem to dump
+ * @param groupName The name of the HDF5 group to write to
  */
-void writeUnitSystem(hid_t h_file, struct UnitSystem* us) {
-  hid_t h_grpunit = 0;
+void writeUnitSystem(hid_t h_file, const struct UnitSystem* us,
+                     const char* groupName) {
 
-  h_grpunit = H5Gcreate1(h_file, "/Units", 0);
+  hid_t h_grpunit = 0;
+  h_grpunit = H5Gcreate1(h_file, groupName, 0);
   if (h_grpunit < 0) error("Error while creating Unit System group");
 
   writeAttribute_d(h_grpunit, "Unit mass in cgs (U_M)",
@@ -484,8 +544,9 @@ void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype) {
  *
  * @todo Treat the types in a better way.
  */
-void writeXMFline(FILE* xmfFile, char* fileName, char* partTypeGroupName,
-                  char* name, size_t N, int dim, enum DATA_TYPE type) {
+void writeXMFline(FILE* xmfFile, const char* fileName,
+                  const char* partTypeGroupName, const char* name, size_t N,
+                  int dim, enum DATA_TYPE type) {
   fprintf(xmfFile,
           "<Attribute Name=\"%s\" AttributeType=\"%s\" Center=\"Node\">\n",
           name, dim == 1 ? "Scalar" : "Vector");

src/common_io.h

@@ -45,13 +45,6 @@ enum DATA_TYPE {
   CHAR
 };
 
-/**
- * @brief The two sorts of data present in the GADGET IC files: compulsory to
- *start a run or optional.
- *
- */
-enum DATA_IMPORTANCE { COMPULSORY = 1, OPTIONAL = 0 };
-
 /**
  * @brief The different particle types present in a GADGET IC file
  *
@@ -69,10 +62,12 @@ enum PARTICLE_TYPE {
 extern const char* particle_type_names[];
 
 #define FILENAME_BUFFER_SIZE 150
-#define PARTICLE_GROUP_BUFFER_SIZE 20
+#define FIELD_BUFFER_SIZE 200
+#define PARTICLE_GROUP_BUFFER_SIZE 50
 
 hid_t hdf5Type(enum DATA_TYPE type);
 size_t sizeOfType(enum DATA_TYPE type);
+int isDoublePrecision(enum DATA_TYPE type);
 
 void collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
                        struct gpart* const dmparts, size_t Ndm);
@@ -99,11 +94,15 @@ void writeXMFoutputfooter(FILE* xmfFile, int outputCount, float time);
 void writeXMFgroupheader(FILE* xmfFile, char* hdfFileName, size_t N,
                          enum PARTICLE_TYPE ptype);
 void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype);
-void writeXMFline(FILE* xmfFile, char* fileName, char* partTypeGroupName,
-                  char* name, size_t N, int dim, enum DATA_TYPE type);
+void writeXMFline(FILE* xmfFile, const char* fileName,
+                  const char* partTypeGroupName, const char* name, size_t N,
+                  int dim, enum DATA_TYPE type);
 
 void writeCodeDescription(hid_t h_file);
-void writeUnitSystem(hid_t h_file, struct UnitSystem* us);
+
+void readUnitSystem(hid_t h_file, struct UnitSystem* us);
+void writeUnitSystem(hid_t h_grp, const struct UnitSystem* us,
+                     const char* groupName);
 
 #endif /* defined HDF5 */
 

src/engine.c

@@ -2677,14 +2677,17 @@ void engine_dump_snapshot(struct engine *e) {
 /* Dump... */
 #if defined(WITH_MPI)
 #if defined(HAVE_PARALLEL_HDF5)
-  write_output_parallel(e, e->snapshotBaseName, e->snapshotUnits, e->nodeID,
-                        e->nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+  write_output_parallel(e, e->snapshotBaseName, e->internalUnits,
+                        e->snapshotUnits, e->nodeID, e->nr_nodes,
+                        MPI_COMM_WORLD, MPI_INFO_NULL);
 #else
-  write_output_serial(e, e->snapshotBaseName, e->snapshotUnits, e->nodeID,
-                      e->nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+  write_output_serial(e, e->snapshotBaseName, e->internalUnits,
+                      e->snapshotUnits, e->nodeID, e->nr_nodes, MPI_COMM_WORLD,
+                      MPI_INFO_NULL);
 #endif
 #else
-  write_output_single(e, e->snapshotBaseName, e->snapshotUnits);
+  write_output_single(e, e->snapshotBaseName, e->internalUnits,
+                      e->snapshotUnits);
 #endif
 
   clocks_gettime(&time2);
@@ -2759,6 +2762,7 @@ void engine_unpin() {
  * @param with_aff use processor affinity, if supported.
  * @param policy The queuing policy to use.
  * @param verbose Is this #engine talkative ?
+ * @param internal_units The system of units used internally.
  * @param physical_constants The #phys_const used for this run.
  * @param hydro The #hydro_props used for this run.
  * @param potential The properties of the external potential.
@@ -2766,6 +2770,7 @@ void engine_unpin() {
 void engine_init(struct engine *e, struct space *s,
                  const struct swift_params *params, int nr_nodes, int nodeID,
                  int nr_threads, int with_aff, int policy, int verbose,
+                 const struct UnitSystem *internal_units,
                  const struct phys_const *physical_constants,
                  const struct hydro_props *hydro,
                  const struct external_potential *potential) {
@@ -2795,6 +2800,7 @@ void engine_init(struct engine *e, struct space *s,
   e->timeStep = 0.;
   e->timeBase = 0.;
   e->timeBase_inv = 0.;
+  e->internalUnits = internal_units;
   e->timeFirstSnapshot =
       parser_get_param_double(params, "Snapshots:time_first");
   e->deltaTimeSnapshot =

src/engine.h

@@ -139,6 +139,9 @@ struct engine {
   /* Number of particles updated */
   size_t updates, g_updates;
 
+  /* The internal system of units */
+  const struct UnitSystem *internalUnits;
+
   /* Snapshot information */
   double timeFirstSnapshot;
   double deltaTimeSnapshot;
@@ -212,6 +215,7 @@ void engine_dump_snapshot(struct engine *e);
 void engine_init(struct engine *e, struct space *s,
                  const struct swift_params *params, int nr_nodes, int nodeID,
                  int nr_threads, int with_aff, int policy, int verbose,
+                 const struct UnitSystem *internal_units,
                  const struct phys_const *physical_constants,
                  const struct hydro_props *hydro,
                  const struct external_potential *potential);

src/gravity/Default/gravity_io.h

@@ -17,64 +17,54 @@
  *
  ******************************************************************************/
 
+#include "io_properties.h"
+
 /**
- * @brief Read dark matter particles from HDF5.
- *
- * @param h_grp The HDF5 group in which to read the arrays.
- * @param N The number of particles on that MPI rank.
- * @param N_total The total number of particles (only used in MPI mode)
- * @param offset The offset of the particles for this MPI rank (only used in MPI
- *mode)
- * @param gparts The particle array
+ * @brief Specifies which g-particle fields to read from a dataset
  *
+ * @param gparts The g-particle array.
+ * @param list The list of i/o properties to read.
+ * @param num_fields The number of i/o fields to read.
  */
-__attribute__((always_inline)) INLINE static void darkmatter_read_particles(
-    hid_t h_grp, int N, long long N_total, long long offset,
-    struct gpart* gparts) {
+void darkmatter_read_particles(struct gpart* gparts, struct io_props* list,
+                               int* num_fields) {
+
+  /* Say how much we want to read */
+  *num_fields = 4;
 
-  /* Read arrays */
-  readArray(h_grp, "Coordinates", DOUBLE, N, 3, gparts, N_total, offset, x,
-            COMPULSORY);
-  readArray(h_grp, "Masses", FLOAT, N, 1, gparts, N_total, offset, mass,
-            COMPULSORY);
-  readArray(h_grp, "Velocities", FLOAT, N, 3, gparts, N_total, offset, v_full,
-            COMPULSORY);
-  readArray(h_grp, "ParticleIDs", ULONGLONG, N, 1, gparts, N_total, offset,
-            id_or_neg_offset, COMPULSORY);
+  /* List what we want to read */
+  list[0] = io_make_input_field("Coordinates", DOUBLE, 3, COMPULSORY,
+                                UNIT_CONV_LENGTH, gparts, x);
+  list[1] = io_make_input_field("Velocities", FLOAT, 3, COMPULSORY,
+                                UNIT_CONV_SPEED, gparts, v_full);
+  list[2] = io_make_input_field("Masses", FLOAT, 1, COMPULSORY, UNIT_CONV_MASS,
+                                gparts, mass);
+  list[3] = io_make_input_field("ParticleIDs", ULONGLONG, 1, COMPULSORY,
+                                UNIT_CONV_NO_UNITS, gparts, id_or_neg_offset);
 }
 
 /**
- * @brief Writes the different particles to the HDF5 file
- *
- * @param h_grp The HDF5 group in which to write the arrays.
- * @param fileName The name of the file (unsued in MPI mode).
- * @param partTypeGroupName The name of the group containing the particles in
- *the HDF5 file.
- * @param xmfFile The XMF file to write to (unused in MPI mode).
- * @param Ndm The number of DM particles on that MPI rank.
- * @param Ndm_total The total number of g-particles (only used in MPI mode)
- * @param mpi_rank The MPI rank of this node (only used in MPI mode)
- * @param offset The offset of the particles for this MPI rank (only used in MPI
- *mode)
- * @param gparts The #gpart array
- * @param us The unit system to use
+ * @brief Specifies which g-particle fields to write to a dataset
  *
+ * @param gparts The g-particle array.
+ * @param list The list of i/o properties to write.
+ * @param num_fields The number of i/o fields to write.
  */
-__attribute__((always_inline)) INLINE static void darkmatter_write_particles(
-    hid_t h_grp, char* fileName, char* partTypeGroupName, FILE* xmfFile,
-    int Ndm, long long Ndm_total, int mpi_rank, long long offset,
-    struct gpart* gparts, struct UnitSystem* us) {
+void darkmatter_write_particles(struct gpart* gparts, struct io_props* list,
+                                int* num_fields) {
+
+  /* Say how much we want to read */
+  *num_fields = 5;
 
-  /* Write arrays */
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Coordinates", DOUBLE,
-             Ndm, 3, gparts, Ndm_total, mpi_rank, offset, x, us,
-             UNIT_CONV_LENGTH);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Masses", FLOAT, Ndm,
-             1, gparts, Ndm_total, mpi_rank, offset, mass, us, UNIT_CONV_MASS);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Velocities", FLOAT,
-             Ndm, 3, gparts, Ndm_total, mpi_rank, offset, v_full, us,
-             UNIT_CONV_SPEED);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "ParticleIDs",
-             ULONGLONG, Ndm, 1, gparts, Ndm_total, mpi_rank, offset,
-             id_or_neg_offset, us, UNIT_CONV_NO_UNITS);
+  /* List what we want to read */
+  list[0] = io_make_output_field("Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH,
+                                 gparts, x);
+  list[1] = io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED,
+                                 gparts, v_full);
+  list[2] =
+      io_make_output_field("Masses", FLOAT, 1, UNIT_CONV_MASS, gparts, mass);
+  list[3] = io_make_output_field("ParticleIDs", ULONGLONG, 1,
+                                 UNIT_CONV_NO_UNITS, gparts, id_or_neg_offset);
+  list[4] = io_make_output_field("Acceleration", FLOAT, 3,
+                                 UNIT_CONV_ACCELERATION, gparts, a_grav);
 }

src/hydro/Default/hydro_io.h

@@ -17,83 +17,69 @@
  *
  ******************************************************************************/
 
+#include "io_properties.h"
+#include "kernel_hydro.h"
+
 /**
- * @brief Reads the different particles to the HDF5 file
- *
- * @param h_grp The HDF5 group in which to read the arrays.
- * @param N The number of particles on that MPI rank.
- * @param N_total The total number of particles (only used in MPI mode)
- * @param offset The offset of the particles for this MPI rank (only used in MPI
- *mode)
- * @param parts The particle array
+ * @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.
  */
-__attribute__((always_inline)) INLINE static void hydro_read_particles(
-    hid_t h_grp, int N, long long N_total, long long offset,
-    struct part* parts) {
+void hydro_read_particles(struct part* parts, struct io_props* list,
+                          int* num_fields) {
+
+  *num_fields = 8;
 
-  /* Read arrays */
-  readArray(h_grp, "Coordinates", DOUBLE, N, 3, parts, N_total, offset, x,
-            COMPULSORY);
-  readArray(h_grp, "Velocities", FLOAT, N, 3, parts, N_total, offset, v,
-            COMPULSORY);
-  readArray(h_grp, "Masses", FLOAT, N, 1, parts, N_total, offset, mass,
-            COMPULSORY);
-  readArray(h_grp, "SmoothingLength", FLOAT, N, 1, parts, N_total, offset, h,
-            COMPULSORY);
-  readArray(h_grp, "InternalEnergy", FLOAT, N, 1, parts, N_total, offset, u,
-            COMPULSORY);
-  readArray(h_grp, "ParticleIDs", ULONGLONG, N, 1, parts, N_total, offset, id,
-            COMPULSORY);
-  readArray(h_grp, "Acceleration", FLOAT, N, 3, parts, N_total, offset, a_hydro,
-            OPTIONAL);
-  readArray(h_grp, "Density", FLOAT, N, 1, parts, N_total, offset, rho,
-            OPTIONAL);
+  /* List what we want to read */
+  list[0] = io_make_input_field("Coordinates", DOUBLE, 3, COMPULSORY,
+                                UNIT_CONV_LENGTH, parts, x);
+  list[1] = io_make_input_field("Velocities", FLOAT, 3, COMPULSORY,
+                                UNIT_CONV_SPEED, parts, v);
+  list[2] = io_make_input_field("Masses", FLOAT, 1, COMPULSORY, UNIT_CONV_MASS,
+                                parts, mass);
+  list[3] = io_make_input_field("SmoothingLength", FLOAT, 1, COMPULSORY,
+                                UNIT_CONV_LENGTH, parts, h);
+  list[4] = io_make_input_field("InternalEnergy", FLOAT, 1, COMPULSORY,
+                                UNIT_CONV_ENERGY, parts, u);
+  list[5] = io_make_input_field("ParticleIDs", ULONGLONG, 1, COMPULSORY,
+                                UNIT_CONV_NO_UNITS, parts, id);
+  list[6] = io_make_input_field("Accelerations", FLOAT, 3, OPTIONAL,
+                                UNIT_CONV_ACCELERATION, parts, a_hydro);
+  list[7] = io_make_input_field("Density", FLOAT, 1, OPTIONAL,
+                                UNIT_CONV_DENSITY, parts, rho);
 }
 
 /**
- * @brief Writes the different particles to the HDF5 file
- *
- * @param h_grp The HDF5 group in which to write the arrays.
- * @param fileName The name of the file (unsued in MPI mode).
- * @param partTypeGroupName The name of the group containing the particles in
- *the HDF5 file.
- * @param xmfFile The XMF file to write to (unused in MPI mode).
- * @param N The number of particles on that MPI rank.
- * @param N_total The total number of particles (only used in MPI mode)
- * @param mpi_rank The MPI rank of this node (only used in MPI mode)
- * @param offset The offset of the particles for this MPI rank (only used in MPI
- *mode)
- * @param parts The particle array
- * @param us The unit system to use
+ * @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.
  */
-__attribute__((always_inline)) INLINE static void hydro_write_particles(
-    hid_t h_grp, char* fileName, char* partTypeGroupName, FILE* xmfFile, int N,
-    long long N_total, int mpi_rank, long long offset, struct part* parts,
-    struct UnitSystem* us) {
+void hydro_write_particles(struct part* parts, struct io_props* list,
+                           int* num_fields) {
+
+  *num_fields = 8;
 
-  /* Write arrays */
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Coordinates", DOUBLE,
-             N, 3, parts, N_total, mpi_rank, offset, x, us, UNIT_CONV_LENGTH);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Velocities", FLOAT,
-             N, 3, parts, N_total, mpi_rank, offset, v, us, UNIT_CONV_SPEED);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Masses", FLOAT, N, 1,
-             parts, N_total, mpi_rank, offset, mass, us, UNIT_CONV_MASS);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "SmoothingLength",
-             FLOAT, N, 1, parts, N_total, mpi_rank, offset, h, us,
-             UNIT_CONV_LENGTH);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "InternalEnergy",
-             FLOAT, N, 1, parts, N_total, mpi_rank, offset, u, us,
-             UNIT_CONV_ENERGY_PER_UNIT_MASS);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "ParticleIDs",
-             ULONGLONG, N, 1, parts, N_total, mpi_rank, offset, id, us,
-             UNIT_CONV_NO_UNITS);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Acceleration", FLOAT,
-             N, 3, parts, N_total, mpi_rank, offset, a_hydro, us,
-             UNIT_CONV_ACCELERATION);
-  writeArray(h_grp, fileName, xmfFile, partTypeGroupName, "Density", FLOAT, N,
-             1, parts, N_total, mpi_rank, offset, rho, us, UNIT_CONV_DENSITY);
+  /* List what we want to write */
+  list[0] = io_make_output_field("Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH,
+                                 parts, x);
+  list[1] =
+      io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED, parts, v);
+  list[2] =
+      io_make_output_field("Masses", FLOAT, 1, UNIT_CONV_MASS, parts, mass);
+  list[3] = io_make_output_field("SmoothingLength", FLOAT, 1, UNIT_CONV_LENGTH,
+                                 parts, h);
+  list[4] = io_make_output_field("Entropy", FLOAT, 1,
+                                 UNIT_CONV_ENERGY_PER_UNIT_MASS, parts, u);
+  list[5] = io_make_output_field("ParticleIDs", ULONGLONG, 1,
+                                 UNIT_CONV_NO_UNITS, parts, id);
+  list[6] = io_make_output_field("Acceleration", FLOAT, 3,
+                                 UNIT_CONV_ACCELERATION, parts, a_hydro);
+  list[7] =
+      io_make_output_field("Density", FLOAT, 1, UNIT_CONV_DENSITY, parts, rho);
 }
 
 /**

src/hydro/Gadget2/hydro_io.h

@@ -17,83 +17,69 @@
  *
  ******************************************************************************/
 
+#include "io_properties.h"
+#include "kernel_hydro.h"
+
 /**
- * @brief Reads the different particles to the HDF5 file
- *
- * @param h_grp The HDF5 group in which to read the arrays.
- * @param N The number of particles on that MPI rank.
- * @param N_total The total number of particles (only used in MPI mode)
- * @param offset The offset of the particles for this MPI rank (only used in MPI
- *mode)
- * @param parts The particle array
+ * @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.
  */
-__attribute__((always_inline)) INLINE static void hydro_read_particles(
-    hid_t h_grp, int N, long long N_total, long long offset,