diff --git a/examples/main.c b/examples/main.c
index 21357d971f238c4d1979b9769b5247aadd997bbd..01acdeff9893fce88f146e64742857c8c1b778a6 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -336,9 +336,9 @@ 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,
&flag_entropy_ICs, myrank, nr_nodes, MPI_COMM_WORLD,
diff --git a/src/engine.c b/src/engine.c
index d7aa3cd64b2852a039218c190e0903566c10dacc..414724fb81bcde280e9fe1cf875507f0bf6da8f2 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -2672,8 +2672,9 @@ 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);
diff --git a/src/parallel_io.c b/src/parallel_io.c
index 8f08302316c76b5a8d4d872021694200370507e2..d62123a3dd6ed517826de8adcc5aba8a6bde1c1b 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -39,25 +39,13 @@
#include "common_io.h"
#include "engine.h"
#include "error.h"
+#include "gravity_io.h"
+#include "hydro_io.h"
+#include "io_properties.h"
#include "kernel_hydro.h"
#include "part.h"
#include "units.h"
-void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
- struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
- int* periodic, int* flag_entropy, int mpi_rank,
- int mpi_size, MPI_Comm comm, MPI_Info info, int dry_run) {
-}
-
-void write_output_parallel(struct engine* e, const char* baseName,
- struct UnitSystem* us, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info) {}
-
-#endif
-
-#if 0
-
-
/**
* @brief Reads a data array from a given HDF5 group.
*
@@ -77,55 +65,53 @@ void write_output_parallel(struct engine* e, const char* baseName,
*
* Calls #error() if an error occurs.
*/
-void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
- int dim, long long N_total, long long offset,
- char* part_c, enum DATA_IMPORTANCE importance) {
- hid_t h_data = 0, h_err = 0, h_type = 0, h_memspace = 0, h_filespace = 0,
- h_plist_id = 0;
- hsize_t shape[2], offsets[2];
- htri_t exist = 0;
- void* temp;
- int i = 0, rank = 0;
- const size_t typeSize = sizeOfType(type);
- const size_t copySize = typeSize * dim;
- const size_t partSize = sizeof(struct part);
- char* temp_c = 0;
+void readArray(hid_t grp, const struct io_props prop, int N, long long N_total,
+ long long offset, const struct UnitSystem* internal_units,
+ const struct UnitSystem* ic_units) {
+
+ const size_t typeSize = sizeOfType(prop.type);
+ const size_t copySize = typeSize * prop.dimension;
+ const size_t num_elements = N * prop.dimension;
/* Check whether the dataspace exists or not */
- exist = H5Lexists(grp, name, 0);
+ const htri_t exist = H5Lexists(grp, prop.name, 0);
if (exist < 0) {
- error("Error while checking the existence of data set '%s'.", name);
+ error("Error while checking the existence of data set '%s'.", prop.name);
} else if (exist == 0) {
- if (importance == COMPULSORY) {
- error("Compulsory data set '%s' not present in the file.", name);
+ if (prop.importance == COMPULSORY) {
+ error("Compulsory data set '%s' not present in the file.", prop.name);
} else {
- for (i = 0; i < N; ++i) memset(part_c + i * partSize, 0, copySize);
+ for (size_t i = 0; i < N; ++i)
+ memset(prop.field + i * prop.partSize, 0, copySize);
return;
}
}
- /* message( "Reading %s '%s' array...", importance == COMPULSORY ?
- * "compulsory": "optional ", name); */
+ message("Reading %s '%s' array...",
+ prop.importance == COMPULSORY ? "compulsory" : "optional ",
+ prop.name);
/* Open data space in file */
- h_data = H5Dopen2(grp, name, H5P_DEFAULT);
- if (h_data < 0) error("Error while opening data space '%s'.", name);
+ const hid_t h_data = H5Dopen2(grp, prop.name, H5P_DEFAULT);
+ if (h_data < 0) error("Error while opening data space '%s'.", prop.name);
/* Check data type */
- h_type = H5Dget_type(h_data);
+ const hid_t h_type = H5Dget_type(h_data);
if (h_type < 0) error("Unable to retrieve data type from the file");
/* if (!H5Tequal(h_type, hdf5Type(type))) */
/* error("Non-matching types between the code and the file"); */
/* Allocate temporary buffer */
- temp = malloc(N * dim * typeSize);
+ void* temp = malloc(num_elements * typeSize);
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Prepare information for hyper-slab */
- if (dim > 1) {
+ hsize_t shape[2], offsets[2];
+ int rank;
+ if (prop.dimension > 1) {
rank = 2;
shape[0] = N;
- shape[1] = dim;
+ shape[1] = prop.dimension;
offsets[0] = offset;
offsets[1] = 0;
} else {
@@ -137,29 +123,45 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
}
/* Create data space in memory */
- h_memspace = H5Screate_simple(rank, shape, NULL);
+ const hid_t h_memspace = H5Screate_simple(rank, shape, NULL);
/* Select hyper-slab in file */
- h_filespace = H5Dget_space(h_data);
+ const hid_t h_filespace = H5Dget_space(h_data);
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Set collective reading properties */
- h_plist_id = H5Pcreate(H5P_DATASET_XFER);
+ const hid_t h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
- h_err = H5Dread(h_data, hdf5Type(type), h_memspace, h_filespace, h_plist_id,
- temp);
+ const hid_t h_err = H5Dread(h_data, hdf5Type(prop.type), h_memspace,
+ h_filespace, h_plist_id, temp);
if (h_err < 0) {
- error("Error while reading data array '%s'.", name);
+ error("Error while reading data array '%s'.", prop.name);
+ }
+
+ /* Unit conversion if necessary */
+ const double factor =
+ units_conversion_factor(ic_units, internal_units, prop.units);
+ if (factor != 1. && exist != 0) {
+
+ message("aaa");
+
+ if (isDoublePrecision(prop.type)) {
+ double* temp_d = temp;
+ for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
+ } else {
+ float* temp_f = temp;
+ for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
+ }
}
/* Copy temporary buffer to particle data */
- temp_c = temp;
- for (i = 0; i < N; ++i)
- memcpy(part_c + i * partSize, &temp_c[i * copySize], copySize);
+ char* temp_c = temp;
+ for (size_t i = 0; i < N; ++i)
+ memcpy(prop.field + i * prop.partSize, &temp_c[i * copySize], copySize);
/* Free and close everything */
free(temp);
@@ -180,66 +182,75 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
* @param grp The group in which to write.
* @param fileName The name of the file in which the data is written
* @param xmfFile The FILE used to write the XMF description
- * @param name The name of the array to write.
- * @param type The #DATA_TYPE of the array.
* @param N The number of particles to write.
- * @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param N_total Total number of particles across all cores
* @param offset Offset in the array where this mpi task starts writing
- * @param part_c A (char*) pointer on the first occurrence of the field of
- *interest in the parts array
- * @param us The UnitSystem currently in use
- * @param convFactor The UnitConversionFactor for this array
+ * @param internal_units The #UnitSystem used internally
+ * @param snapshot_units The #UnitSystem used in the snapshots
*
* @todo A better version using HDF5 hyper-slabs to write the file directly from
- *the part array
- * will be written once the structures have been stabilized.
+ * the part array will be written once the structures have been stabilized.
*
- * Calls #error() if an error occurs.
*/
-void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
- char* partTypeGroupName, char* name, enum DATA_TYPE type,
- int N, int dim, long long N_total, int mpi_rank,
- long long offset, char* part_c, size_t partSize,
- struct UnitSystem* us,
- enum UnitConversionFactor convFactor) {
- hid_t h_data = 0, h_err = 0, h_memspace = 0, h_filespace = 0, h_plist_id = 0;
- hsize_t shape[2], shape_total[2], offsets[2];
- void* temp = 0;
- int i = 0, rank = 0;
- const size_t typeSize = sizeOfType(type);
- const size_t copySize = typeSize * dim;
- char* temp_c = 0;
- char buffer[150];
-
- /* message("Writing '%s' array...", name); */
+void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
+ char* partTypeGroupName, const struct io_props props, size_t N,
+ long long N_total, int mpi_rank, long long offset,
+ const struct UnitSystem* internal_units,
+ const struct UnitSystem* snapshot_units) {
+
+ const size_t typeSize = sizeOfType(props.type);
+ const size_t copySize = typeSize * props.dimension;
+ const size_t num_elements = N * props.dimension;
+
+ message("Writing '%s' array...", props.name);
/* Allocate temporary buffer */
- temp = malloc(N * dim * sizeOfType(type));
+ void* temp = malloc(num_elements * sizeOfType(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Copy particle data to temporary buffer */
- temp_c = temp;
- for (i = 0; i < N; ++i)
- memcpy(&temp_c[i * copySize], part_c + i * partSize, copySize);
+ char* temp_c = temp;
+ for (size_t i = 0; i < N; ++i)
+ memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
+
+ /* Unit conversion if necessary */
+ const double factor =
+ units_conversion_factor(internal_units, snapshot_units, props.units);
+ if (factor != 1.) {
+
+ message("aaa");
+
+ if (isDoublePrecision(props.type)) {
+ double* temp_d = temp;
+ for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
+ } else {
+ float* temp_f = temp;
+ for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
+ }
+ }
/* Create data space */
- h_memspace = H5Screate(H5S_SIMPLE);
+ const hid_t h_memspace = H5Screate(H5S_SIMPLE);
if (h_memspace < 0) {
- error("Error while creating data space (memory) for field '%s'.", name);
+ error("Error while creating data space (memory) for field '%s'.",
+ props.name);
}
- h_filespace = H5Screate(H5S_SIMPLE);
+ hid_t h_filespace = H5Screate(H5S_SIMPLE);
if (h_filespace < 0) {
- error("Error while creating data space (file) for field '%s'.", name);
+ error("Error while creating data space (file) for field '%s'.", props.name);
}
- if (dim > 1) {
+ int rank;
+ hsize_t shape[2];
+ hsize_t shape_total[2];
+ hsize_t offsets[2];
+ if (props.dimension > 1) {
rank = 2;
shape[0] = N;
- shape[1] = dim;
+ shape[1] = props.dimension;
shape_total[0] = N_total;
- shape_total[1] = dim;
+ shape_total[1] = props.dimension;
offsets[0] = offset;
offsets[1] = 0;
} else {
@@ -253,23 +264,25 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
}
/* Change shape of memory data space */
- h_err = H5Sset_extent_simple(h_memspace, rank, shape, NULL);
+ hid_t h_err = H5Sset_extent_simple(h_memspace, rank, shape, NULL);
if (h_err < 0) {
error("Error while changing data space (memory) shape for field '%s'.",
- name);
+ props.name);
}
/* Change shape of file data space */
h_err = H5Sset_extent_simple(h_filespace, rank, shape_total, NULL);
if (h_err < 0) {
- error("Error while changing data space (file) shape for field '%s'.", name);
+ error("Error while changing data space (file) shape for field '%s'.",
+ props.name);
}
/* Create dataset */
- h_data = H5Dcreate(grp, name, hdf5Type(type), h_filespace, H5P_DEFAULT,
- H5P_DEFAULT, H5P_DEFAULT);
+ const hid_t h_data =
+ H5Dcreate(grp, props.name, hdf5Type(props.type), h_filespace, H5P_DEFAULT,
+ H5P_DEFAULT, H5P_DEFAULT);
if (h_data < 0) {
- error("Error while creating dataset '%s'.", name);
+ error("Error while creating dataset '%s'.", props.name);
}
H5Sclose(h_filespace);
@@ -277,27 +290,30 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Create property list for collective dataset write. */
- h_plist_id = H5Pcreate(H5P_DATASET_XFER);
+ const hid_t h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Write temporary buffer to HDF5 dataspace */
- h_err = H5Dwrite(h_data, hdf5Type(type), h_memspace, h_filespace, h_plist_id,
- temp);
+ h_err = H5Dwrite(h_data, hdf5Type(props.type), h_memspace, h_filespace,
+ h_plist_id, temp);
if (h_err < 0) {
- error("Error while writing data array '%s'.", name);
+ error("Error while writing data array '%s'.", props.name);
}
/* Write XMF description for this data set */
if (mpi_rank == 0)
- writeXMFline(xmfFile, fileName, partTypeGroupName, name, N_total, dim,
- type);
+ writeXMFline(xmfFile, fileName, partTypeGroupName, props.name, N_total,
+ props.dimension, props.type);
/* Write unit conversion factors for this data set */
- units_conversion_string(buffer, us, convFactor);
+ char buffer[FIELD_BUFFER_SIZE];
+ units_cgs_conversion_string(buffer, snapshot_units, props.units);
writeAttribute_d(h_data, "CGS conversion factor",
- units_conversion_factor(us, convFactor));
- writeAttribute_f(h_data, "h-scale exponent", units_h_factor(us, convFactor));
- writeAttribute_f(h_data, "a-scale exponent", units_a_factor(us, convFactor));
+ units_cgs_conversion_factor(snapshot_units, props.units));
+ writeAttribute_f(h_data, "h-scale exponent",
+ units_h_factor(snapshot_units, props.units));
+ writeAttribute_f(h_data, "a-scale exponent",
+ units_a_factor(snapshot_units, props.units));
writeAttribute_s(h_data, "Conversion factor", buffer);
/* Free and close everything */
@@ -308,66 +324,18 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
H5Sclose(h_filespace);
}
-/**
- * @brief A helper macro to call the readArrayBackEnd function more easily.
- *
- * @param grp The group from which to read.
- * @param name The name of the array to read.
- * @param type The #DATA_TYPE of the attribute.
- * @param N The number of particles on this MPI task.
- * @param dim The dimension of the data (1 for scalar, 3 for vector)
- * @param part The array of particles to fill
- * @param N_total Total number of particles
- * @param offset Offset in the array where this task starts reading
- * @param field The name of the field (C code name as defined in part.h) to fill
- * @param importance Is the data compulsory or not
- *
- */
-#define readArray(grp, name, type, N, dim, part, N_total, offset, field, \
- importance) \
- readArrayBackEnd(grp, name, type, N, dim, N_total, offset, \
- (char*)(&(part[0]).field), importance)
-
-/**
- * @brief A helper macro to call the writeArrayBackEnd function more easily.
- *
- * @param grp The group in which to write.
- * @param fileName The name of the file in which the data is written
- * @param xmfFile The FILE used to write the XMF description
- * @param name The name of the array to write.
- * @param type The #DATA_TYPE of the array.
- * @param N The number of particles to write from this core.
- * @param dim The dimension of the data (1 for scalar, 3 for vector)
- * @param N_total Total number of particles across all cores
- * @param mpi_rank The MPI task rank calling the function
- * @param offset Offset in the array where this mpi task starts writing
- * @param part A (char*) pointer on the first occurrence of the field of
- *interest
- *in the parts array
- * @param field The name (code name) of the field to read from.
- * @param us The UnitSystem currently in use
- * @param convFactor The UnitConversionFactor for this array
- *
- */
-#define writeArray(grp, fileName, xmfFile, pTypeGroupName, name, type, N, dim, \
- part, N_total, mpi_rank, offset, field, us, convFactor) \
- writeArrayBackEnd(grp, fileName, xmfFile, pTypeGroupName, name, type, N, \
- dim, N_total, mpi_rank, offset, (char*)(&(part[0]).field), \
- sizeof(part[0]), us, convFactor)
-
-/* Import the right hydro definition */
-#include "hydro_io.h"
-/* Import the right gravity definition */
-#include "gravity_io.h"
-
/**
* @brief Reads an HDF5 initial condition file (GADGET-3 type) in parallel
*
* @param fileName The file to read.
+ * @param internal_units The system units used internally
* @param dim (output) The dimension of the volume read from the file.
* @param parts (output) The array of #part read from the file.
* @param N (output) The number of particles read from the file.
* @param periodic (output) 1 if the volume is periodic, 0 if not.
+ * @param flag_entropy (output) 1 if the ICs contained Entropy in the
+ * InternalEnergy
+ * field
* @param dry_run If 1, don't read the particle. Only allocates the arrays.
*
* Opens the HDF5 file fileName and reads the particles contained
@@ -380,10 +348,11 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
* Calls #error() if an error occurs.
*
*/
-void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
- struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
- int* periodic, int* flag_entropy, int mpi_rank,
- int mpi_size, MPI_Comm comm, MPI_Info info, int dry_run) {
+void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
+ double dim[3], struct part** parts, struct gpart** gparts,
+ size_t* Ngas, size_t* Ngparts, int* periodic,
+ int* flag_entropy, int mpi_rank, int mpi_size,
+ MPI_Comm comm, MPI_Info info, int dry_run) {
hid_t h_file = 0, h_grp = 0;
/* GADGET has only cubic boxes (in cosmological mode) */
double boxSize[3] = {0.0, -1.0, -1.0};
@@ -446,6 +415,42 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
/* Close header */
H5Gclose(h_grp);
+ /* Read the unit system used in the ICs */
+ struct UnitSystem* ic_units = malloc(sizeof(struct UnitSystem));
+ if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
+ readUnitSystem(h_file, ic_units);
+
+ /* Tell the user if a conversion will be needed */
+ if (mpi_rank == 0) {
+ if (units_are_equal(ic_units, internal_units)) {
+
+ message("IC and internal units match. No conversion needed");
+
+ } else {
+
+ message("Conversion needed from:");
+ message("(ICs) Unit system: U_M = %e g.", ic_units->UnitMass_in_cgs);
+ message("(ICs) Unit system: U_L = %e cm.",
+ ic_units->UnitLength_in_cgs);
+ message("(ICs) Unit system: U_t = %e s.", ic_units->UnitTime_in_cgs);
+ message("(ICs) Unit system: U_I = %e A.",
+ ic_units->UnitCurrent_in_cgs);
+ message("(ICs) Unit system: U_T = %e K.",
+ ic_units->UnitTemperature_in_cgs);
+ message("to:");
+ message("(internal) Unit system: U_M = %e g.",
+ internal_units->UnitMass_in_cgs);
+ message("(internal) Unit system: U_L = %e cm.",
+ internal_units->UnitLength_in_cgs);
+ message("(internal) Unit system: U_t = %e s.",
+ internal_units->UnitTime_in_cgs);
+ message("(internal) Unit system: U_I = %e A.",
+ internal_units->UnitCurrent_in_cgs);
+ message("(internal) Unit system: U_T = %e K.",
+ internal_units->UnitTemperature_in_cgs);
+ }
+ }
+
/* Allocate memory to store SPH particles */
*Ngas = N[0];
if (posix_memalign((void*)parts, part_align, (*Ngas) * sizeof(struct part)) !=
@@ -486,25 +491,42 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
error("Error while opening particle group %s.", partTypeGroupName);
}
+ int num_fields = 0;
+ struct io_props list[100];
+ size_t N;
+
/* Read particle fields into the particle structure */
switch (ptype) {
case GAS:
- if (!dry_run)
- hydro_read_particles(h_grp, N[ptype], N_total[ptype], offset[ptype],
- *parts);
+ /* if (!dry_run) */
+ /* hydro_read_particles(h_grp, N[ptype], N_total[ptype],
+ * offset[ptype], */
+ /* *parts); */
+ /* break; */
+ N = *Ngas;
+ hydro_read_particles(*parts, list, &num_fields);
break;
case DM:
- if (!dry_run)
- darkmatter_read_particles(h_grp, N[ptype], N_total[ptype],
- offset[ptype], *gparts);
+ /* if (!dry_run) */
+ /* darkmatter_read_particles(h_grp, N[ptype], N_total[ptype], */
+ /* offset[ptype], *gparts); */
+ /* break; */
+ N = Ndm;
+ darkmatter_read_particles(*gparts, list, &num_fields);
break;
default:
message("Particle Type %d not yet supported. Particles ignored", ptype);
}
+ /* Read everything */
+ if (!dry_run)
+ for (int i = 0; i < num_fields; ++i)
+ readArray(h_grp, list[i], N, N_total[ptype], offset[ptype],
+ internal_units, ic_units);
+
/* Close particle group */
H5Gclose(h_grp);
}
@@ -517,6 +539,9 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
/* message("Done Reading particles..."); */
+ /* Clean up */
+ free(ic_units);
+
/* Close property handler */
H5Pclose(h_plist_id);
@@ -530,25 +555,27 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
*
* @param e The engine containing all the system.
* @param baseName The common part of the snapshot file name.
- * @param us The UnitSystem used for the conversion of units in the output.
+ * @param internal_units The #UnitSystem used internally
+ * @param snapshot_units The #UnitSystem used in the snapshots
* @param mpi_rank The MPI rank of this node.
* @param mpi_size The number of MPI ranks.
* @param comm The MPI communicator.
* @param info The MPI information object
*
* Creates an HDF5 output file and writes the particles
- *contained
- * in the engine. If such a file already exists, it is
- *erased and replaced
- * by the new one.
+ * contained in the engine. If such a file already exists, it is
+ * erased and replaced by the new one.
* The companion XMF file is also updated accordingly.
*
* Calls #error() if an error occurs.
*
*/
void write_output_parallel(struct engine* e, const char* baseName,
- struct UnitSystem* us, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info) {
+ const struct UnitSystem* internal_units,
+ const struct UnitSystem* snapshot_units,
+ int mpi_rank, int mpi_size, MPI_Comm comm,
+ MPI_Info info) {
+
hid_t h_file = 0, h_grp = 0;
const size_t Ngas = e->s->nr_parts;
const size_t Ntot = e->s->nr_gparts;
@@ -666,8 +693,11 @@ void write_output_parallel(struct engine* e, const char* baseName,
parser_write_params_to_hdf5(e->parameter_file, h_grp);
H5Gclose(h_grp);
- /* Print the system of Units */
- writeUnitSystem(h_file, us);
+ /* Print the system of Units used in the spashot */
+ writeUnitSystem(h_file, snapshot_units, "Units");
+
+ /* Print the system of Units used internally */
+ writeUnitSystem(h_file, internal_units, "InternalUnits");
/* Loop over all particle types */
for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
@@ -690,14 +720,16 @@ void write_output_parallel(struct engine* e, const char* baseName,
error("Error while opening particle group %s.", partTypeGroupName);
}
- /* Read particle fields into the particle structure */
+ int num_fields = 0;
+ struct io_props list[100];
+ size_t N;
+
+ /* Write particle fields from the particle structure */
switch (ptype) {
case GAS:
- hydro_write_particles(h_grp, fileName, partTypeGroupName, xmfFile,
- N[ptype], N_total[ptype], mpi_rank, offset[ptype],
- parts, us);
-
+ N = Ngas;
+ hydro_write_particles(parts, list, &num_fields);
break;
case DM:
@@ -713,9 +745,8 @@ void write_output_parallel(struct engine* e, const char* baseName,
collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
- darkmatter_write_particles(h_grp, fileName, partTypeGroupName, xmfFile,
- N[ptype], N_total[ptype], mpi_rank,
- offset[ptype], dmparts, us);
+ N = Ndm;
+ darkmatter_write_particles(dmparts, list, &num_fields);
/* Free temporary array */
free(dmparts);
@@ -725,6 +756,15 @@ void write_output_parallel(struct engine* e, const char* baseName,
error("Particle Type %d not yet supported. Aborting", ptype);
}
+ /* Write everything */
+ for (int i = 0; i < num_fields; ++i)
+ writeArray(h_grp, fileName, xmfFile, partTypeGroupName, list[i], N,
+ N_total[ptype], mpi_rank, offset[ptype], internal_units,
+ snapshot_units);
+
+ /* Free temporary array */
+ free(dmparts);
+
/* Close particle group */
H5Gclose(h_grp);
diff --git a/src/parallel_io.h b/src/parallel_io.h
index 709479fab029e862caddb36c4216b85077e96cec..e5b12aa50c30b4d63ccc81835d2d8454e01b3889 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -34,15 +34,17 @@
#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
-void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
- struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
- int* periodic, int* flag_entropy, int mpi_rank,
- int mpi_size, MPI_Comm comm, MPI_Info info, int dry_run);
+void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
+ double dim[3], struct part** parts, struct gpart** gparts,
+ size_t* Ngas, size_t* Ngparts, int* periodic,
+ int* flag_entropy, int mpi_rank, int mpi_size,
+ MPI_Comm comm, MPI_Info info, int dry_run);
void write_output_parallel(struct engine* e, const char* baseName,
- struct UnitSystem* us, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info);
-
+ const struct UnitSystem* internal_units,
+ const struct UnitSystem* snapshot_units,
+ int mpi_rank, int mpi_size, MPI_Comm comm,
+ MPI_Info info);
#endif
#endif /* SWIFT_PARALLEL_IO_H */
diff --git a/src/single_io.c b/src/single_io.c
index decbaf89267c6fceb7455623d6664f79ee651866..dfd3dac54b839d4c5075fce7e501e2d94161465f 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -81,7 +81,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
/* message("Optional data set '%s' not present. Zeroing this particle
* prop...", name); */
- for (int i = 0; i < N; ++i)
+ for (size_t i = 0; i < N; ++i)
memset(prop.field + i * prop.partSize, 0, copySize);
return;
@@ -126,16 +126,16 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
if (isDoublePrecision(prop.type)) {
double* temp_d = temp;
- for (int i = 0; i < num_elements; ++i) temp_d[i] *= factor;
+ for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = temp;
- for (int i = 0; i < num_elements; ++i) temp_f[i] *= factor;
+ for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
/* Copy temporary buffer to particle data */
char* temp_c = temp;
- for (int i = 0; i < N; ++i)
+ for (size_t i = 0; i < N; ++i)
memcpy(prop.field + i * prop.partSize, &temp_c[i * copySize], copySize);
/* Free and close everything */
@@ -162,8 +162,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
* @param snapshot_units The #UnitSystem used in the snapshots
*
* @todo A better version using HDF5 hyper-slabs to write the file directly from
- * the part array
- * will be written once the structures have been stabilized.
+ * the part array will be written once the structures have been stabilized.
*/
void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, const struct io_props props, size_t N,
@@ -182,7 +181,7 @@ void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
/* Copy particle data to temporary buffer */
char* temp_c = temp;
- for (int i = 0; i < N; ++i)
+ for (size_t i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
/* Unit conversion if necessary */
@@ -194,10 +193,10 @@ void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
if (isDoublePrecision(props.type)) {
double* temp_d = temp;
- for (int i = 0; i < num_elements; ++i) temp_d[i] *= factor;
+ for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = temp;
- for (int i = 0; i < num_elements; ++i) temp_f[i] *= factor;
+ for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
@@ -297,7 +296,8 @@ void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
* @param Ngas (output) number of Gas particles read.
* @param Ngparts (output) The number of #gpart read.
* @param periodic (output) 1 if the volume is periodic, 0 if not.
- * @param flag_entropy 1 if the ICs contained Entropy in the InternalEnergy
+ * @param flag_entropy (output) 1 if the ICs contained Entropy in the
+ * InternalEnergy
* field
* @param dry_run If 1, don't read the particle. Only allocates the arrays.
*
@@ -366,7 +366,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* Close header */
H5Gclose(h_grp);
- /* Read the unit system used in the snapshots */
+ /* Read the unit system used in the ICs */
struct UnitSystem* ic_units = malloc(sizeof(struct UnitSystem));
if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
readUnitSystem(h_file, ic_units);