diff --git a/src/common_io.c b/src/common_io.c
index 4be334ccd602c7b0c450f5dbe4aedd9155b35ff1..3133c64f45df7d2ef3711f375fdd318b154d7919 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", "Stars", "BH" };
+
/**
* @brief Converts a C data type to the HDF5 equivalent.
*
@@ -406,24 +409,13 @@ void createXMFfile() {
* @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>");
}
/**
@@ -431,18 +423,40 @@ void writeXMFheader(FILE* xmfFile, long long Nparts, char* hdfFileName,
*
* @param xmfFile The file to write in.
*/
-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> <!-- 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>");
+}
+
+void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype) {
+ fprintf(xmfFile, "</Grid> <!-- parttype=%s -->\n", particle_type_names[ptype]);
+}
+
+
+
/**
* @brief Writes the lines corresponding to an array of the HDF5 output
*
@@ -455,21 +469,21 @@ 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..6cc79ad51809d461b188003247e8cf021e3cf0fe 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..2a7b0c1fc71b9d6b60f353ddab2e9b097cfed7ec 100644
--- a/src/gravity/Default/gravity_io.h
+++ b/src/gravity/Default/gravity_io.h
@@ -59,17 +59,20 @@ __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/Gadget2/hydro_io.h b/src/hydro/Gadget2/hydro_io.h
index 17c3d3013644c3572f3c26fc3e270b1c1bc465ed..d7e52497e873a00e204c7c7b4c32126897c792fa 100644
--- a/src/hydro/Gadget2/hydro_io.h
+++ b/src/hydro/Gadget2/hydro_io.h
@@ -67,27 +67,31 @@ __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/serial_io.c b/src/serial_io.c
index 3fb1a1d1b743e48be4e8e6d81413c28e8034b870..fe0b0def9e6181ba68c078b6bec14b6b9622ef4e 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -643,7 +643,7 @@ 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);
+ writeXMFheader(xmfFile, N_total[0], fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
diff --git a/src/single_io.c b/src/single_io.c
index 54ace5c4e369cd6b9a02d44f8a8f03ef6cbadd5f..6f6d1d4913c0ff89e8e4aad215baa951d8a43913 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -138,6 +138,7 @@ 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.
@@ -153,7 +154,8 @@ 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,
+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) {
@@ -237,7 +239,7 @@ 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 +283,7 @@ 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)
@@ -294,11 +297,10 @@ 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, \
- convFactor)
+#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 */
#include "hydro_io.h"
@@ -496,7 +498,7 @@ 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 +571,9 @@ 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 */
+ 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 +590,8 @@ 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 +605,8 @@ 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 +618,13 @@ 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..."); */