diff --git a/src/parallel_io.c b/src/parallel_io.c
index aafce0a4fbf39537604e652e70eb324865d61660..0076c225e1c5361287280f8a567c8062aefd914e 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -178,10 +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* 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,
+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;
@@ -269,7 +269,9 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
}
/* Write XMF description for this data set */
- if (mpi_rank == 0) writeXMFline(xmfFile, fileName, partTypeGroupName, 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);
@@ -328,19 +330,17 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
* @param convFactor The UnitConversionFactor for this array
*
*/
-#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)
+#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
*
@@ -361,12 +361,12 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
*
*/
void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
- struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
- 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;
/* GADGET has only cubic boxes (in cosmological mode) */
- double boxSize[3] = {0.0, -1.0, -1.0};
+ 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};
@@ -411,8 +411,10 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
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. */
for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
@@ -423,7 +425,6 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
/* Close header */
H5Gclose(h_grp);
-
/* Allocate memory to store SPH particles */
*Ngas = N[0];
if (posix_memalign((void*)parts, part_align, (*Ngas) * sizeof(struct part)) !=
@@ -436,47 +437,51 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
*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");
+ 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) /
+ /* message("Allocated %8.2f MB for particles.", *N *
+ * sizeof(struct part) /
* (1024.*1024.)); */
/* message("BoxSize = %lf", dim[0]); */
- /* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
+ /* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm,
+ * *Ngparts); */
/* 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;
-
+
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
- ptype);
+ 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);
+
+ 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);
}
@@ -497,13 +502,17 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
}
/**
- * @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.
*
@@ -549,7 +558,8 @@ 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 */
+ /* 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};
@@ -557,13 +567,16 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
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 */
+ /* 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);
- /* Now everybody konws its offset and the total number of particles of each
+ /* 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 */
+ /* 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 */
@@ -582,12 +595,12 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
/* message("Writing file header..."); */
h_grp = H5Gcreate(h_file, "/Header", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating file header\n");
-
+
/* Print the relevant information and print status */
writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
double dblTime = e->time;
writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
-
+
/* GADGET-2 legacy values */
/* Number of particles of each type */
unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
@@ -597,21 +610,21 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
}
writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
- NUM_PARTICLE_TYPES);
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
- NUM_PARTICLE_TYPES);
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
- NUM_PARTICLE_TYPES);
+ NUM_PARTICLE_TYPES);
double MassTable[6] = {0., 0., 0., 0., 0., 0.};
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);
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
-
+
/* Close header */
H5Gclose(h_grp);
-
+
/* Print the code version */
writeCodeDescription(h_file);
@@ -624,78 +637,80 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
/* Print the system of Units */
writeUnitSystem(h_file, us);
-
/* 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 */
+
+ /* 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);
+ 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);
}
-
+
/* Read particle fields into 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);
-
- 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);
+
+ 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);
+ if (mpi_rank == 0) writeXMFgroupfooter(xmfFile, ptype);
}
-
+
/* Write LXMF file descriptor */
if (mpi_rank == 0) writeXMFoutputfooter(xmfFile, outputCount, e->time);
-
+
/* message("Done writing particles..."); */
-
+
/* Close property descriptor */
H5Pclose(plist_id);
-
+
/* Close file */
H5Fclose(h_file);
-
+
++outputCount;
}
diff --git a/src/parallel_io.h b/src/parallel_io.h
index 09d6574309646d33416670e4c726cc7da0321a2e..663f0aabac44c08682b964512839b925673ea5c5 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -32,9 +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,
- struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
+ struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
- MPI_Info info);
+ 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 c3878061464adb8a90aba149ab3397b03ac84772..40bd2b1c8921f4acbfa0950984d6915ebd3d241e 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -756,9 +756,10 @@ 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);
+ /* 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];
@@ -805,9 +806,8 @@ 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 this particle group in the XMF file as well */
+ if (mpi_rank == 0) writeXMFgroupfooter(xmfFile, ptype);
}
/* Close file */