diff --git a/examples/main.c b/examples/main.c
index 43b56291c4eb023238c39556d536ab88c3daad0c..6bb16d711cb3d44e8843279e76d4cd24f5ce0cc4 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -362,8 +362,8 @@ 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, &Ngas, &periodic, myrank, nr_nodes,
- MPI_COMM_WORLD, MPI_INFO_NULL);
+ read_ic_parallel(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
+ myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
#else
read_ic_serial(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
diff --git a/src/common_io.c b/src/common_io.c
index 4be334ccd602c7b0c450f5dbe4aedd9155b35ff1..5fb2d9513ec2acc0cd8d389a226b14d427e02539 100644
--- a/src/common_io.c
+++ b/src/common_io.c
@@ -45,6 +45,9 @@
#include "kernel.h"
#include "version.h"
+const char* particle_type_names[NUM_PARTICLE_TYPES] = {
+ "Gas", "DM", "Boundary", "Dummy", "Star", "BH"};
+
/**
* @brief Converts a C data type to the HDF5 equivalent.
*
@@ -402,52 +405,68 @@ void createXMFfile() {
*snapshot
*
* @param xmfFile The file to write in.
- * @param Nparts The number of particles.
* @param hdfFileName The name of the HDF5 file corresponding to this output.
* @param time The current simulation time.
*/
-void writeXMFheader(FILE* xmfFile, long long Nparts, char* hdfFileName,
- float time) {
+void writeXMFoutputheader(FILE* xmfFile, char* hdfFileName, float time) {
/* Write end of file */
+ fprintf(xmfFile, "<!-- XMF description for file: %s -->\n", hdfFileName);
fprintf(xmfFile,
"<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
fprintf(xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", time);
- fprintf(xmfFile, "<Grid Name=\"Gas\" GridType=\"Uniform\">\n");
- fprintf(xmfFile,
- "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%lld\"/>\n",
- Nparts);
- fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
- fprintf(xmfFile,
- "<DataItem Dimensions=\"%lld 3\" NumberType=\"Double\" "
- "Precision=\"8\" "
- "Format=\"HDF\">%s:/PartType0/Coordinates</DataItem>\n",
- Nparts, hdfFileName);
- fprintf(xmfFile, "</Geometry>");
}
/**
* @brief Writes the end of the XMF file (closes all open markups)
*
* @param xmfFile The file to write in.
+ * @param output The number of this output.
+ * @param time The current simulation time.
*/
-void writeXMFfooter(FILE* xmfFile) {
+void writeXMFoutputfooter(FILE* xmfFile, int output, float time) {
/* Write end of the section of this time step */
- fprintf(xmfFile, "\n</Grid>\n");
- fprintf(xmfFile, "</Grid>\n");
- fprintf(xmfFile, "\n</Grid>\n");
+ fprintf(xmfFile,
+ "\n</Grid> <!-- End of meta-data for output=%03i, time=%f -->\n",
+ output, time);
+ fprintf(xmfFile, "\n</Grid> <!-- timeSeries -->\n");
fprintf(xmfFile, "</Domain>\n");
fprintf(xmfFile, "</Xdmf>\n");
fclose(xmfFile);
}
+void writeXMFgroupheader(FILE* xmfFile, char* hdfFileName, size_t N,
+ enum PARTICLE_TYPE ptype) {
+ fprintf(xmfFile, "\n<Grid Name=\"%s\" GridType=\"Uniform\">\n",
+ particle_type_names[ptype]);
+ fprintf(xmfFile,
+ "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%zi\"/>\n", N);
+ fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
+ fprintf(xmfFile,
+ "<DataItem Dimensions=\"%zi 3\" NumberType=\"Double\" "
+ "Precision=\"8\" "
+ "Format=\"HDF\">%s:/PartType%d/Coordinates</DataItem>\n",
+ N, hdfFileName, ptype);
+ fprintf(xmfFile,
+ "</Geometry>\n <!-- Done geometry for %s, start of particle fields "
+ "list -->\n",
+ particle_type_names[ptype]);
+}
+
+void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype) {
+ fprintf(xmfFile, "</Grid> <!-- End of meta-data for parttype=%s -->\n",
+ particle_type_names[ptype]);
+}
+
/**
* @brief Writes the lines corresponding to an array of the HDF5 output
*
* @param xmfFile The file in which to write
* @param fileName The name of the HDF5 file associated to this XMF descriptor.
+ * @param partTypeGroupName The name of the group containing the particles in
+ *the HDF5 file.
* @param name The name of the array in the HDF5 file.
* @param N The number of particles.
* @param dim The dimension of the quantity (1 for scalars, 3 for vectors).
@@ -455,21 +474,21 @@ void writeXMFfooter(FILE* xmfFile) {
*
* @todo Treat the types in a better way.
*/
-void writeXMFline(FILE* xmfFile, char* fileName, char* name, long long N,
- int dim, enum DATA_TYPE type) {
+void writeXMFline(FILE* xmfFile, char* fileName, char* partTypeGroupName,
+ 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");
if (dim == 1)
fprintf(xmfFile,
- "<DataItem Dimensions=\"%lld\" NumberType=\"Double\" "
- "Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n",
- N, type == FLOAT ? 4 : 8, fileName, name);
+ "<DataItem Dimensions=\"%zi\" NumberType=\"Double\" "
+ "Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
+ N, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
else
fprintf(xmfFile,
- "<DataItem Dimensions=\"%lld %d\" NumberType=\"Double\" "
- "Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n",
- N, dim, type == FLOAT ? 4 : 8, fileName, name);
+ "<DataItem Dimensions=\"%zi %d\" NumberType=\"Double\" "
+ "Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
+ N, dim, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
fprintf(xmfFile, "</Attribute>\n");
}
diff --git a/src/common_io.h b/src/common_io.h
index 426fa6a01ec87a4413eceaaeb0d0880cbef8a214..4ad0c6fb754c4288a0c731e2b1e2392998719d52 100644
--- a/src/common_io.h
+++ b/src/common_io.h
@@ -70,6 +70,8 @@ enum PARTICLE_TYPE {
NUM_PARTICLE_TYPES
};
+extern const char* particle_type_names[];
+
#define FILENAME_BUFFER_SIZE 150
#define PARTICLE_GROUP_BUFFER_SIZE 20
@@ -95,10 +97,13 @@ void writeAttribute_s(hid_t grp, char* name, const char* str);
void createXMFfile();
FILE* prepareXMFfile();
-void writeXMFfooter(FILE* xmfFile);
-void writeXMFheader(FILE* xmfFile, long long N, char* hdfFileName, float time);
-void writeXMFline(FILE* xmfFile, char* fileName, char* name, long long N,
- int dim, enum DATA_TYPE type);
+void writeXMFoutputheader(FILE* xmfFile, char* hdfFileName, float time);
+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 writeCodeDescription(hid_t h_file);
void writeSPHflavour(hid_t h_file);
diff --git a/src/gravity/Default/gravity_io.h b/src/gravity/Default/gravity_io.h
index d707d69631e65eed8ad21a7fa9601c07d3c71263..129c4b39828ca73d2d80d79edbdaa8ec4d5a9e01 100644
--- a/src/gravity/Default/gravity_io.h
+++ b/src/gravity/Default/gravity_io.h
@@ -48,6 +48,8 @@ __attribute__((always_inline)) INLINE static void darkmatter_read_particles(
*
* @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)
@@ -59,17 +61,20 @@ __attribute__((always_inline)) INLINE static void darkmatter_read_particles(
*
*/
__attribute__((always_inline)) INLINE static void darkmatter_write_particles(
- hid_t h_grp, char* fileName, FILE* xmfFile, int Ndm, long long Ndm_total,
- int mpi_rank, long long offset, struct gpart* gparts,
- struct UnitSystem* us) {
+ 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) {
/* Write arrays */
- writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, Ndm, 3, gparts,
- Ndm_total, mpi_rank, offset, x, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, Ndm, 1, gparts,
- Ndm_total, mpi_rank, offset, mass, us, UNIT_CONV_MASS);
- writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, Ndm, 3, gparts,
- Ndm_total, mpi_rank, offset, v_full, us, UNIT_CONV_SPEED);
- writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, Ndm, 1, gparts,
- Ndm_total, mpi_rank, offset, id, us, UNIT_CONV_NO_UNITS);
+ 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, us,
+ UNIT_CONV_NO_UNITS);
}
diff --git a/src/hydro/Default/hydro_io.h b/src/hydro/Default/hydro_io.h
index 958bf5a1869718b57678246ff3b1985e54145824..0e9ad46ddc1d4e8c8d3ffdbf3e81262ec49a7092 100644
--- a/src/hydro/Default/hydro_io.h
+++ b/src/hydro/Default/hydro_io.h
@@ -56,6 +56,8 @@ __attribute__((always_inline)) INLINE static void hydro_read_particles(
*
* @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)
@@ -67,26 +69,31 @@ __attribute__((always_inline)) INLINE static void hydro_read_particles(
*
*/
__attribute__((always_inline)) INLINE static void hydro_write_particles(
- hid_t h_grp, char* fileName, FILE* xmfFile, int N, long long N_total,
- int mpi_rank, long long offset, struct part* parts, struct UnitSystem* us) {
+ 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) {
/* Write arrays */
- writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts,
- N_total, mpi_rank, offset, x, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, N, 3, parts,
- N_total, mpi_rank, offset, v, us, UNIT_CONV_SPEED);
- writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, N, 1, parts, N_total,
- mpi_rank, offset, mass, us, UNIT_CONV_MASS);
- writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts,
- N_total, mpi_rank, offset, h, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts,
- N_total, mpi_rank, offset, u, us, UNIT_CONV_ENERGY_PER_UNIT_MASS);
- writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts,
- N_total, mpi_rank, offset, id, us, UNIT_CONV_NO_UNITS);
- writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts,
- N_total, mpi_rank, offset, a_hydro, us, UNIT_CONV_ACCELERATION);
- writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, N_total,
- mpi_rank, offset, rho, us, UNIT_CONV_DENSITY);
+ 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);
}
/**
diff --git a/src/hydro/Gadget2/hydro_io.h b/src/hydro/Gadget2/hydro_io.h
index 17c3d3013644c3572f3c26fc3e270b1c1bc465ed..c1c59dfa4980a2843e7e13bee4c964c9b254cae6 100644
--- a/src/hydro/Gadget2/hydro_io.h
+++ b/src/hydro/Gadget2/hydro_io.h
@@ -56,6 +56,8 @@ __attribute__((always_inline)) INLINE static void hydro_read_particles(
*
* @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)
@@ -67,27 +69,31 @@ __attribute__((always_inline)) INLINE static void hydro_read_particles(
*
*/
__attribute__((always_inline)) INLINE static void hydro_write_particles(
- hid_t h_grp, char* fileName, FILE* xmfFile, int N, long long N_total,
- int mpi_rank, long long offset, struct part* parts, struct UnitSystem* us) {
+ 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) {
/* Write arrays */
- writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts,
- N_total, mpi_rank, offset, x, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, N, 3, parts,
- N_total, mpi_rank, offset, v, us, UNIT_CONV_SPEED);
- writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, N, 1, parts, N_total,
- mpi_rank, offset, mass, us, UNIT_CONV_MASS);
- writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts,
- N_total, mpi_rank, offset, h, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts,
- N_total, mpi_rank, offset, entropy, us,
+ 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, entropy, us,
UNIT_CONV_ENTROPY_PER_UNIT_MASS);
- writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts,
- N_total, mpi_rank, offset, id, us, UNIT_CONV_NO_UNITS);
- writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts,
- N_total, mpi_rank, offset, a_hydro, us, UNIT_CONV_ACCELERATION);
- writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, N_total,
- mpi_rank, offset, rho, us, UNIT_CONV_DENSITY);
+ 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);
}
/**
diff --git a/src/hydro/Minimal/hydro_io.h b/src/hydro/Minimal/hydro_io.h
index 2c56fb489ab84ca7c30426b54cf95e26e3821084..afe5de83f423e43b4d2480cca1ac3e84d6c549de 100644
--- a/src/hydro/Minimal/hydro_io.h
+++ b/src/hydro/Minimal/hydro_io.h
@@ -56,6 +56,8 @@ __attribute__((always_inline)) INLINE static void hydro_read_particles(
*
* @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)
@@ -67,26 +69,31 @@ __attribute__((always_inline)) INLINE static void hydro_read_particles(
*
*/
__attribute__((always_inline)) INLINE static void hydro_write_particles(
- hid_t h_grp, char* fileName, FILE* xmfFile, int N, long long N_total,
- int mpi_rank, long long offset, struct part* parts, struct UnitSystem* us) {
+ 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) {
/* Write arrays */
- writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts,
- N_total, mpi_rank, offset, x, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, N, 3, parts,
- N_total, mpi_rank, offset, v, us, UNIT_CONV_SPEED);
- writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, N, 1, parts, N_total,
- mpi_rank, offset, mass, us, UNIT_CONV_MASS);
- writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts,
- N_total, mpi_rank, offset, h, us, UNIT_CONV_LENGTH);
- writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts,
- N_total, mpi_rank, offset, u, us, UNIT_CONV_ENERGY_PER_UNIT_MASS);
- writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts,
- N_total, mpi_rank, offset, id, us, UNIT_CONV_NO_UNITS);
- writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts,
- N_total, mpi_rank, offset, a_hydro, us, UNIT_CONV_ACCELERATION);
- writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, N_total,
- mpi_rank, offset, rho, us, UNIT_CONV_DENSITY);
+ 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);
}
/**
diff --git a/src/parallel_io.c b/src/parallel_io.c
index cffa99a0fd75566ec3e850076d15e104504eeb40..0076c225e1c5361287280f8a567c8062aefd914e 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -178,9 +178,10 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
*
* Calls #error() if an error occurs.
*/
-void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
- enum DATA_TYPE type, int N, int dim, long long N_total,
- int mpi_rank, long long offset, char* part_c,
+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;
@@ -189,7 +190,6 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
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;
char buffer[150];
@@ -269,7 +269,9 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
}
/* Write XMF description for this data set */
- if (mpi_rank == 0) writeXMFline(xmfFile, fileName, name, N_total, dim, type);
+ if (mpi_rank == 0)
+ writeXMFline(xmfFile, fileName, partTypeGroupName, name, N_total, dim,
+ type);
/* Write unit conversion factors for this data set */
conversionString(buffer, us, convFactor);
@@ -328,14 +330,16 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @param convFactor The UnitConversionFactor for this array
*
*/
-#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, N_total, \
- mpi_rank, offset, field, us, convFactor) \
- writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, N_total, \
- mpi_rank, offset, (char*)(&(part[0]).field), us, \
- convFactor)
+#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
@@ -357,16 +361,17 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
*
*/
void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
- size_t* N, int* periodic, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info) {
+ struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
+ int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
+ MPI_Info info) {
hid_t h_file = 0, h_grp = 0;
- double boxSize[3] = {
- 0.0, -1.0, -1.0}; /* GADGET has only cubic boxes (in cosmological mode) */
- int numParticles[6] = {
- 0}; /* GADGET has 6 particle types. We only keep the type 0*/
- int numParticles_highWord[6] = {0};
- long long offset = 0;
- long long N_total = 0;
+ /* GADGET has only cubic boxes (in cosmological mode) */
+ double boxSize[3] = {0.0, -1.0, -1.0};
+ int numParticles[NUM_PARTICLE_TYPES] = {0};
+ int numParticles_highWord[NUM_PARTICLE_TYPES] = {0};
+ size_t N[NUM_PARTICLE_TYPES] = {0};
+ long long N_total[NUM_PARTICLE_TYPES] = {0};
+ long long offset[NUM_PARTICLE_TYPES] = {0};
/* Open file */
/* message("Opening file '%s' as IC.", fileName); */
@@ -398,58 +403,116 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
readAttribute(h_grp, "NumPart_Total", UINT, numParticles);
readAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticles_highWord);
- N_total = ((long long)numParticles[0]) +
- ((long long)numParticles_highWord[0] << 32);
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ N_total[ptype] = ((long long)numParticles[ptype]) +
+ ((long long)numParticles_highWord[ptype] << 32);
+
dim[0] = boxSize[0];
dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
- /* message("Found %d particles in a %speriodic box of size [%f %f %f].", */
- /* N_total, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
+ /* message("Found %d particles in a %speriodic box of size
+ * [%f %f %f].", */
+ /* N_total, (periodic ? "": "non-"), dim[0],
+ * dim[1], dim[2]); */
/* Divide the particles among the tasks. */
- offset = mpi_rank * N_total / mpi_size;
- *N = (mpi_rank + 1) * N_total / mpi_size - offset;
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ offset[ptype] = mpi_rank * N_total[ptype] / mpi_size;
+ N[ptype] = (mpi_rank + 1) * N_total[ptype] / mpi_size - offset[ptype];
+ }
/* Close header */
H5Gclose(h_grp);
- /* Allocate memory to store particles */
- if (posix_memalign((void*)parts, part_align, *N * sizeof(struct part)) != 0)
+ /* Allocate memory to store SPH particles */
+ *Ngas = N[0];
+ if (posix_memalign((void*)parts, part_align, (*Ngas) * sizeof(struct part)) !=
+ 0)
error("Error while allocating memory for particles");
- bzero(*parts, *N * sizeof(struct part));
+ bzero(*parts, *Ngas * sizeof(struct part));
- /* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) /
+ /* Allocate memory to store all particles */
+ const size_t Ndm = N[1];
+ *Ngparts = N[1] + N[0];
+ if (posix_memalign((void*)gparts, gpart_align,
+ *Ngparts * sizeof(struct gpart)) != 0)
+ error(
+ "Error while allocating memory for gravity "
+ "particles");
+ bzero(*gparts, *Ngparts * sizeof(struct gpart));
+
+ /* message("Allocated %8.2f MB for particles.", *N *
+ * sizeof(struct part) /
* (1024.*1024.)); */
- /* Open SPH particles group */
- /* message("Reading particle arrays..."); */
- h_grp = H5Gopen(h_file, "/PartType0", H5P_DEFAULT);
- if (h_grp < 0) error("Error while opening particle group.\n");
+ /* message("BoxSize = %lf", dim[0]); */
+ /* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm,
+ * *Ngparts); */
- /* Read particle fields into the particle structure */
- hydro_read_particles(h_grp, *N, N_total, offset, *parts);
+ /* Loop over all particle types */
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
- /* Close particle group */
- H5Gclose(h_grp);
+ /* Don't do anything if no particle of this kind */
+ if (N_total[ptype] == 0) continue;
+
+ /* Open the particle group in the file */
+ char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
+ snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
+ ptype);
+ h_grp = H5Gopen(h_file, partTypeGroupName, H5P_DEFAULT);
+ if (h_grp < 0) {
+ error("Error while opening particle group %s.", partTypeGroupName);
+ }
+
+ /* Read particle fields into the particle structure */
+ switch (ptype) {
+
+ case GAS:
+ hydro_read_particles(h_grp, N[ptype], N_total[ptype], offset[ptype],
+ *parts);
+ break;
+
+ case DM:
+ darkmatter_read_particles(h_grp, N[ptype], N_total[ptype],
+ offset[ptype], *gparts);
+ break;
+
+ default:
+ error("Particle Type %d not yet supported. Aborting", ptype);
+ }
+
+ /* Close particle group */
+ H5Gclose(h_grp);
+ }
+
+ /* Prepare the DM particles */
+ prepare_dm_gparts(*gparts, Ndm);
+
+ /* Now duplicate the hydro particle into gparts */
+ duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+
+ /* message("Done Reading particles..."); */
/* Close property handler */
H5Pclose(h_plist_id);
/* Close file */
H5Fclose(h_file);
-
- /* message("Done Reading particles..."); */
}
/**
- * @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
+ * @brief Writes an HDF5 output file (GADGET-3 type) with
+ *its XMF descriptor
*
* @param e The engine containing all the system.
- * @param us The UnitSystem used for the conversion of units in the output
+ * @param us The UnitSystem used for the conversion of units
+ *in the output
*
- * Creates an HDF5 output file and writes the particles contained
- * in the engine. If such a file already exists, it is erased and replaced
+ * 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.
* The companion XMF file is also updated accordingly.
*
@@ -459,23 +522,27 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
void write_output_parallel(struct engine* e, struct UnitSystem* us,
int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info) {
-
hid_t h_file = 0, h_grp = 0, h_grpsph = 0;
- int N = e->s->nr_parts;
+ const size_t Ngas = e->s->nr_parts;
+ const size_t Ntot = e->s->nr_gparts;
int periodic = e->s->periodic;
- unsigned int numParticles[6] = {N, 0};
- unsigned int numParticlesHighWord[6] = {0};
- unsigned int flagEntropy[6] = {0};
- long long N_total = 0, offset = 0;
- double offset_d = 0., N_d = 0., N_total_d = 0.;
int numFiles = 1;
struct part* parts = e->s->parts;
- FILE* xmfFile = 0;
+ struct gpart* gparts = e->s->gparts;
+ struct gpart* dmparts = NULL;
static int outputCount = 0;
+ FILE* xmfFile = 0;
+
+ /* Number of particles of each type */
+ // const size_t Ndm = Ntot - Ngas;
+
+ /* MATTHIEU: Temporary fix to preserve master */
+ const size_t Ndm = Ntot > 0 ? Ntot - Ngas : 0;
+ /* MATTHIEU: End temporary fix */
/* File name */
- char fileName[200];
- sprintf(fileName, "output_%03i.hdf5", outputCount);
+ char fileName[FILENAME_BUFFER_SIZE];
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "output_%03i.hdf5", outputCount);
/* First time, we need to create the XMF file */
if (outputCount == 0 && mpi_rank == 0) createXMFfile();
@@ -491,21 +558,26 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
error("Error while opening file '%s'.", fileName);
}
- /* Compute offset in the file and total number of particles */
- /* Done using double to allow for up to 2^50=10^15 particles */
- N_d = (double)N;
- MPI_Exscan(&N_d, &offset_d, 1, MPI_DOUBLE, MPI_SUM, comm);
- N_total_d = offset_d + N_d;
- MPI_Bcast(&N_total_d, 1, MPI_DOUBLE, mpi_size - 1, comm);
- if (N_total_d > 1.e15)
- error(
- "Error while computing the offset for parallel output: Simulation has "
- "more than 10^15 particles.\n");
- N_total = (long long)N_total_d;
- offset = (long long)offset_d;
+ /* Compute offset in the file and total number of
+ * particles */
+ size_t N[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0};
+ long long N_total[NUM_PARTICLE_TYPES] = {0};
+ long long offset[NUM_PARTICLE_TYPES] = {0};
+ MPI_Exscan(&N, &offset, NUM_PARTICLE_TYPES, MPI_LONG_LONG, MPI_SUM, comm);
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ N_total[ptype] = offset[ptype] + N[ptype];
+
+ /* The last rank now has the correct N_total. Let's
+ * broadcast from there */
+ MPI_Bcast(&N_total, 6, MPI_LONG_LONG, mpi_size - 1, comm);
- /* Write the part of the XMF file corresponding to this specific output */
- if (mpi_rank == 0) writeXMFheader(xmfFile, N_total, fileName, e->time);
+ /* Now everybody konws its offset and the total number of
+ * particles of each
+ * type */
+
+ /* Write the part of the XMF file corresponding to this
+ * specific output */
+ if (mpi_rank == 0) writeXMFoutputheader(xmfFile, fileName, e->time);
/* Open header to write simulation properties */
/* message("Writing runtime parameters..."); */
@@ -526,19 +598,28 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
/* Print the relevant information and print status */
writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
- writeAttribute(h_grp, "NumPart_ThisFile", UINT, numParticles, 6);
double dblTime = e->time;
writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
/* GADGET-2 legacy values */
- numParticles[0] = (unsigned int)N_total;
- writeAttribute(h_grp, "NumPart_Total", UINT, numParticles, 6);
- numParticlesHighWord[0] = (unsigned int)(N_total >> 32);
+ /* Number of particles of each type */
+ unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
+ unsigned int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ numParticles[ptype] = (unsigned int)N_total[ptype];
+ numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
+ }
+ writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
+ NUM_PARTICLE_TYPES);
+ writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
- 6);
+ NUM_PARTICLE_TYPES);
double MassTable[6] = {0., 0., 0., 0., 0., 0.};
- writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, 6);
- writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy, 6);
+ writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, NUM_PARTICLE_TYPES);
+ unsigned int flagEntropy[NUM_PARTICLE_TYPES] = {0};
+ writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
@@ -556,21 +637,71 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
/* Print the system of Units */
writeUnitSystem(h_file, us);
- /* Create SPH particles group */
- /* message("Writing particle arrays..."); */
- h_grp =
- H5Gcreate(h_file, "/PartType0", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating particle group.\n");
+ /* Loop over all particle types */
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+
+ /* Don't do anything if no particle of this kind */
+ if (N_total[ptype] == 0) continue;
+
+ /* Add the global information for that particle type to
+ * the XMF meta-file */
+ if (mpi_rank == 0)
+ writeXMFgroupheader(xmfFile, fileName, N_total[ptype], ptype);
+
+ /* Open the particle group in the file */
+ char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
+ snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
+ ptype);
+ h_grp = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (h_grp < 0) {
+ error("Error while opening particle group %s.", partTypeGroupName);
+ }
- /* Write particle fields from the particle structure */
- hydro_write_particles(h_grp, fileName, xmfFile, N, N_total, mpi_rank, offset,
- parts, us);
+ /* Read particle fields into the particle structure */
+ switch (ptype) {
- /* Close particle group */
- H5Gclose(h_grp);
+ case GAS:
+ hydro_write_particles(h_grp, fileName, partTypeGroupName, xmfFile,
+ N[ptype], N_total[ptype], mpi_rank, offset[ptype],
+ parts, us);
+
+ break;
+
+ case DM:
+ /* Allocate temporary array */
+ if (posix_memalign((void*)&dmparts, gpart_align,
+ Ndm * sizeof(struct gpart)) != 0)
+ error(
+ "Error while allocating temporart memory for "
+ "DM particles");
+ bzero(dmparts, Ndm * sizeof(struct gpart));
+
+ /* Collect the DM particles from gpart */
+ 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);
+
+ /* Free temporary array */
+ free(dmparts);
+ break;
+
+ default:
+ error("Particle Type %d not yet supported. Aborting", ptype);
+ }
+
+ /* Close particle group */
+ H5Gclose(h_grp);
+
+ /* Close this particle group in the XMF file as well */
+ if (mpi_rank == 0) writeXMFgroupfooter(xmfFile, ptype);
+ }
/* Write LXMF file descriptor */
- if (mpi_rank == 0) writeXMFfooter(xmfFile);
+ if (mpi_rank == 0) writeXMFoutputfooter(xmfFile, outputCount, e->time);
/* message("Done writing particles..."); */
diff --git a/src/parallel_io.h b/src/parallel_io.h
index a0589944ec845c712abde1e64e305980748db0e7..663f0aabac44c08682b964512839b925673ea5c5 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -32,8 +32,9 @@
#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
- size_t* N, int* periodic, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info);
+ struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
+ int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
+ MPI_Info info);
void write_output_parallel(struct engine* e, struct UnitSystem* us,
int mpi_rank, int mpi_size, MPI_Comm comm,
diff --git a/src/serial_io.c b/src/serial_io.c
index 3fb1a1d1b743e48be4e8e6d81413c28e8034b870..40bd2b1c8921f4acbfa0950984d6915ebd3d241e 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -57,14 +57,13 @@
* @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param part_c A (char*) pointer on the first occurrence of the field of
*interest in the parts array
+ * @param partSize The size in bytes of the particle structure.
* @param importance If COMPULSORY, the data must be present in the IC file. If
*OPTIONAL, the array will be zeroed when the data is not present.
*
* @todo A better version using HDF5 hyper-slabs to read the file directly into
*the part array
* will be written once the structures have been stabilized.
- *
- * 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,
@@ -172,9 +171,10 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
* Routines writing an output file
*-----------------------------------------------------------------------------*/
-void prepareArray(hid_t grp, char* fileName, FILE* xmfFile, char* name,
- enum DATA_TYPE type, long long N_total, int dim,
- struct UnitSystem* us, enum UnitConversionFactor convFactor) {
+void prepareArray(hid_t grp, char* fileName, FILE* xmfFile,
+ char* partTypeGroupName, char* name, enum DATA_TYPE type,
+ long long N_total, int dim, struct UnitSystem* us,
+ enum UnitConversionFactor convFactor) {
hid_t h_data = 0, h_err = 0, h_space = 0, h_prop = 0;
int rank = 0;
hsize_t shape[2];
@@ -234,7 +234,7 @@ void prepareArray(hid_t grp, char* fileName, FILE* xmfFile, char* name,
}
/* Write XMF description for this data set */
- writeXMFline(xmfFile, fileName, name, N_total, dim, type);
+ writeXMFline(xmfFile, fileName, partTypeGroupName, name, N_total, dim, type);
/* Write unit conversion factors for this data set */
conversionString(buffer, us, convFactor);
@@ -255,22 +255,23 @@ void prepareArray(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @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 partTypeGroupName The name of the group containing the particles in
+ *the HDF5 file.
* @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 part_c A (char*) pointer on the first occurrence of the field of
*interest in the parts array
+ * @param partSize The size in bytes of the particle structure.
* @param us The UnitSystem currently in use
- * @param convFactor The UnitConversionFactor for this array
- *
- *
- * Calls #error() if an error occurs.
+ * @param convFactor The UnitConversionFactor for this arrayo
*/
-void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, 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,
+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;
@@ -285,8 +286,8 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
/* Prepare the arrays in the file */
if (mpi_rank == 0)
- prepareArray(grp, fileName, xmfFile, name, type, N_total, dim, us,
- convFactor);
+ prepareArray(grp, fileName, xmfFile, partTypeGroupName, name, type, N_total,
+ dim, us, convFactor);
/* Allocate temporary buffer */
temp = malloc(N * dim * sizeOfType(type));
@@ -370,21 +371,26 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @param fileName Unused parameter in non-MPI mode
* @param xmfFile Unused parameter in non-MPI mode
* @param name The name of the array to write.
+ * @param partTypeGroupName The name of the group containing the particles in
+ *the HDF5 file.
* @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 part A (char*) pointer on the first occurrence of the field of
- *interest
- *in the parts array
+ *interest in the parts array
+ * @param N_total Unused parameter in non-MPI mode
+ * @param mpi_rank Unused parameter in non-MPI mode
+ * @param offset Unused parameter in non-MPI mode
* @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, name, type, N, dim, part, N_total, \
- mpi_rank, offset, field, us, convFactor) \
- writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, N_total, \
- mpi_rank, offset, (char*)(&(part[0]).field), \
+#define writeArray(grp, fileName, xmfFile, partTypeGroupName, name, type, N, \
+ dim, part, N_total, mpi_rank, offset, field, us, \
+ convFactor) \
+ writeArrayBackEnd(grp, fileName, xmfFile, partTypeGroupName, name, type, N, \
+ dim, N_total, mpi_rank, offset, (char*)(&(part[0]).field), \
sizeof(part[0]), us, convFactor)
/* Import the right hydro definition */
@@ -609,12 +615,12 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
FILE* xmfFile = 0;
/* Number of particles of each type */
- //const size_t Ndm = Ntot - Ngas;
+ // const size_t Ndm = Ntot - Ngas;
/* MATTHIEU: Temporary fix to preserve master */
- const size_t Ndm = Ntot > 0 ? Ntot - Ngas: 0;
+ const size_t Ndm = Ntot > 0 ? Ntot - Ngas : 0;
/* MATTHIEU: End temporary fix */
-
+
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
snprintf(fileName, FILENAME_BUFFER_SIZE, "output_%03i.hdf5", outputCount);
@@ -643,7 +649,7 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
xmfFile = prepareXMFfile();
/* Write the part corresponding to this specific output */
- // writeXMFheader(xmfFile, N_total, fileName, e->time);
+ writeXMFoutputheader(xmfFile, fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
@@ -750,6 +756,11 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
+ /* Add the global information for that particle type to the XMF
+ * meta-file */
+ if (mpi_rank == 0)
+ writeXMFgroupheader(xmfFile, fileName, N_total[ptype], ptype);
+
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
@@ -763,9 +774,9 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
switch (ptype) {
case GAS:
- hydro_write_particles(h_grp, fileName, xmfFile, N[ptype],
- N_total[ptype], mpi_rank, offset[ptype],
- parts, us);
+ hydro_write_particles(h_grp, fileName, partTypeGroupName, xmfFile,
+ N[ptype], N_total[ptype], mpi_rank,
+ offset[ptype], parts, us);
break;
@@ -780,9 +791,9 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
- darkmatter_write_particles(h_grp, fileName, xmfFile, N[ptype],
- N_total[ptype], mpi_rank, offset[ptype],
- dmparts, us);
+ darkmatter_write_particles(h_grp, fileName, partTypeGroupName,
+ xmfFile, N[ptype], N_total[ptype],
+ mpi_rank, offset[ptype], dmparts, us);
/* Free temporary array */
free(dmparts);
@@ -794,6 +805,9 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
/* Close particle group */
H5Gclose(h_grp);
+
+ /* Close this particle group in the XMF file as well */
+ if (mpi_rank == 0) writeXMFgroupfooter(xmfFile, ptype);
}
/* Close file */
@@ -805,7 +819,7 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
}
/* Write footer of LXMF file descriptor */
- if (mpi_rank == 0) writeXMFfooter(xmfFile);
+ if (mpi_rank == 0) writeXMFoutputfooter(xmfFile, outputCount, e->time);
/* message("Done writing particles..."); */
++outputCount;
diff --git a/src/single_io.c b/src/single_io.c
index 54ace5c4e369cd6b9a02d44f8a8f03ef6cbadd5f..801428433ef5170082b68dec425e52f845bb41ae 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -53,14 +53,13 @@
* @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param part_c A (char*) pointer on the first occurrence of the field of
*interest in the parts array
+ * @param partSize The size in bytes of the particle structure.
* @param importance If COMPULSORY, the data must be present in the IC file. If
*OPTIONAL, the array will be zeroed when the data is not present.
*
* @todo A better version using HDF5 hyper-slabs to read the file directly into
*the part array
* will be written once the structures have been stabilized.
- *
- * Calls #error() if an error occurs.
*/
void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
int dim, char* part_c, size_t partSize,
@@ -138,24 +137,26 @@ 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 partTypeGroupName The name of the group containing the particles in
+ *the HDF5 file.
* @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 part_c A (char*) pointer on the first occurrence of the field of
- *interest in the parts array
+ *interest in the parts array.
+ * @param partSize The size in bytes of the particle structure.
* @param us The UnitSystem currently in use
* @param convFactor The UnitConversionFactor for this array
*
* @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.
- *
- * Calls #error() if an error occurs.
*/
-void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
- enum DATA_TYPE type, int N, int dim, char* part_c,
- size_t partSize, struct UnitSystem* us,
+void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
+ char* partTypeGroupName, char* name, enum DATA_TYPE type,
+ int N, int dim, char* part_c, size_t partSize,
+ struct UnitSystem* us,
enum UnitConversionFactor convFactor) {
hid_t h_data = 0, h_err = 0, h_space = 0, h_prop = 0;
void* temp = 0;
@@ -237,7 +238,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
}
/* Write XMF description for this data set */
- writeXMFline(xmfFile, fileName, name, N, dim, type);
+ writeXMFline(xmfFile, fileName, partTypeGroupName, name, N, dim, type);
/* Write unit conversion factors for this data set */
conversionString(buffer, us, convFactor);
@@ -281,6 +282,8 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @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 partTypeGroupName The name of the group containing the particles in
+ *the HDF5 file.
* @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)
@@ -294,10 +297,11 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @param convFactor The UnitConversionFactor for this array
*
*/
-#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, N_total, \
- mpi_rank, offset, field, us, convFactor) \
- writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, \
- (char*)(&(part[0]).field), sizeof(part[0]), us, \
+#define writeArray(grp, fileName, xmfFile, partTypeGroupName, name, type, N, \
+ dim, part, N_total, mpi_rank, offset, field, us, \
+ convFactor) \
+ writeArrayBackEnd(grp, fileName, xmfFile, partTypeGroupName, name, type, N, \
+ dim, (char*)(&(part[0]).field), sizeof(part[0]), us, \
convFactor)
/* Import the right hydro definition */
@@ -476,10 +480,10 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
static int outputCount = 0;
/* Number of particles of each type */
- //const size_t Ndm = Ntot - Ngas;
+ // const size_t Ndm = Ntot - Ngas;
/* MATTHIEU: Temporary fix to preserve master */
- const size_t Ndm = Ntot > 0 ? Ntot - Ngas: 0;
+ const size_t Ndm = Ntot > 0 ? Ntot - Ngas : 0;
/* MATTHIEU: End temporary fix */
long long N_total[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0};
@@ -496,7 +500,7 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
xmfFile = prepareXMFfile();
/* Write the part corresponding to this specific output */
- writeXMFheader(xmfFile, Ngas, fileName, e->time);
+ writeXMFoutputheader(xmfFile, fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
@@ -569,6 +573,9 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
/* Don't do anything if no particle of this kind */
if (numParticles[ptype] == 0) continue;
+ /* Add the global information for that particle type to the XMF meta-file */
+ writeXMFgroupheader(xmfFile, fileName, numParticles[ptype], ptype);
+
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
@@ -585,8 +592,8 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
switch (ptype) {
case GAS:
- hydro_write_particles(h_grp, fileName, xmfFile, Ngas, Ngas, 0, 0, parts,
- us);
+ hydro_write_particles(h_grp, fileName, partTypeGroupName, xmfFile, Ngas,
+ Ngas, 0, 0, parts, us);
break;
case DM:
@@ -600,8 +607,8 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
- darkmatter_write_particles(h_grp, fileName, xmfFile, Ndm, Ndm, 0, 0,
- dmparts, us);
+ darkmatter_write_particles(h_grp, fileName, partTypeGroupName, xmfFile,
+ Ndm, Ndm, 0, 0, dmparts, us);
/* Free temporary array */
free(dmparts);
@@ -613,10 +620,13 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
/* Close particle group */
H5Gclose(h_grp);
+
+ /* Close this particle group in the XMF file as well */
+ writeXMFgroupfooter(xmfFile, ptype);
}
/* Write LXMF file descriptor */
- writeXMFfooter(xmfFile);
+ writeXMFoutputfooter(xmfFile, outputCount, e->time);
/* message("Done writing particles..."); */