From e78c4d7a52a7b51aaa485fc4d73661237be8400a Mon Sep 17 00:00:00 2001
From: Matthieu Schaller <matthieu.schaller@durham.ac.uk>
Date: Sun, 24 Apr 2016 23:06:46 +0100
Subject: [PATCH] Read snapshot basename and interval between snapshots from
yaml file.
---
examples/UniformBox/uniformBox.yml | 6 ++++++
examples/main.c | 22 ++++++++++++----------
examples/parameter_example.yml | 6 ++++++
src/common_io.c | 23 +++++++++++++++--------
src/common_io.h | 4 ++--
src/engine.c | 15 +++++++++++++++
src/engine.h | 4 ++++
src/parallel_io.c | 27 ++++++++++++++-------------
src/parallel_io.h | 6 +++---
src/serial_io.c | 19 +++++++++----------
src/serial_io.h | 5 +++--
src/single_io.c | 19 +++++++++----------
src/single_io.h | 3 ++-
13 files changed, 100 insertions(+), 59 deletions(-)
diff --git a/examples/UniformBox/uniformBox.yml b/examples/UniformBox/uniformBox.yml
index 0474b0f820..dcde96be9e 100644
--- a/examples/UniformBox/uniformBox.yml
+++ b/examples/UniformBox/uniformBox.yml
@@ -21,6 +21,12 @@ TimeIntegration:
dt_min: 1e-6 # The minimal time-step size of the simulation (in internal units).
dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+# Parameters governing the snapshots
+Snapshots:
+ basename: uniformBox # Common part of the name of output files
+ time_first: 0. # Time of the frist output (in internal units)
+ delta_time: 0.01 # Time difference between consecutive outputs (in internal units)
+
# Parameters for the hydrodynamics scheme
SPH:
resolution_eta: 1.2349 # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
diff --git a/examples/main.c b/examples/main.c
index 481a6bf43a..e8b4e08a06 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -422,24 +422,22 @@ int main(int argc, char *argv[]) {
fflush(stdout);
}
- /* Now that everything is ready, no need for the parameters any more */
- free(params);
- params = NULL;
-
int with_outputs = 1;
+ char baseName[200];
+ parser_get_param_string(params, "Snapshots:basename", baseName);
if (with_outputs && !dry_run) {
/* Write the state of the system before starting time integration. */
if (myrank == 0) clocks_gettime(&tic);
#if defined(WITH_MPI)
#if defined(HAVE_PARALLEL_HDF5)
- write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD,
+ write_output_parallel(&e, baseName, &us, myrank, nr_nodes, MPI_COMM_WORLD,
MPI_INFO_NULL);
#else
- write_output_serial(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD,
+ write_output_serial(&e, baseName, &us, myrank, nr_nodes, MPI_COMM_WORLD,
MPI_INFO_NULL);
#endif
#else
- write_output_single(&e, &us);
+ write_output_single(&e, baseName, &us);
#endif
if (myrank == 0 && verbose) {
clocks_gettime(&toc);
@@ -449,6 +447,10 @@ int main(int argc, char *argv[]) {
}
}
+ /* Now that everything is ready, no need for the parameters any more */
+ free(params);
+ params = NULL;
+
/* Init the runner history. */
#ifdef HIST
for (k = 0; k < runner_hist_N; k++) runner_hist_bins[k] = 0;
@@ -505,7 +507,7 @@ int main(int argc, char *argv[]) {
/* Take a step. */
engine_step(&e);
- if (with_outputs && j % 100 == 0) {
+ if (with_outputs && j % 10 == 0) {
if (myrank == 0) clocks_gettime(&tic);
#if defined(WITH_MPI)
@@ -517,7 +519,7 @@ int main(int argc, char *argv[]) {
MPI_INFO_NULL);
#endif
#else
- write_output_single(&e, &us);
+ write_output_single(&e, baseName, &us);
#endif
if (myrank == 0 && verbose) {
clocks_gettime(&toc);
@@ -621,7 +623,7 @@ int main(int argc, char *argv[]) {
MPI_INFO_NULL);
#endif
#else
- write_output_single(&e, &us);
+ write_output_single(&e, baseName, &us);
#endif
if (myrank == 0 && verbose) {
clocks_gettime(&toc);
diff --git a/examples/parameter_example.yml b/examples/parameter_example.yml
index 228e748f3b..38b0a7c76f 100644
--- a/examples/parameter_example.yml
+++ b/examples/parameter_example.yml
@@ -21,6 +21,12 @@ TimeIntegration:
dt_min: 1e-6 # The minimal time-step size of the simulation (in internal units).
dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+# Parameters governing the snapshots
+Snapshots:
+ basename: uniformBox # Common part of the name of output files
+ time_first: 0. # Time of the frist output (in internal units)
+ delta_time: 0.01 # Time difference between consecutive outputs (in internal units)
+
# Parameters for the hydrodynamics scheme
SPH:
resolution_eta: 1.2349 # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
diff --git a/src/common_io.c b/src/common_io.c
index 2a635723d5..143c1ca941 100644
--- a/src/common_io.c
+++ b/src/common_io.c
@@ -335,11 +335,15 @@ void writeCodeDescription(hid_t h_file) {
*
* @todo Use a proper XML library to avoid stupid copies.
*/
-FILE* prepareXMFfile() {
+FILE* prepareXMFfile(const char* baseName) {
char buffer[1024];
- FILE* xmfFile = fopen("output.xmf", "r");
- FILE* tempFile = fopen("output_temp.xmf", "w");
+ char fileName[FILENAME_BUFFER_SIZE];
+ char tempFileName[FILENAME_BUFFER_SIZE];
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
+ snprintf(tempFileName, FILENAME_BUFFER_SIZE, "%s_temp.xmf", baseName);
+ FILE* xmfFile = fopen(fileName, "r");
+ FILE* tempFile = fopen(tempFileName, "w");
if (xmfFile == NULL) error("Unable to open current XMF file.");
@@ -355,8 +359,8 @@ FILE* prepareXMFfile() {
fclose(xmfFile);
/* We then copy the XMF file back up to the closing lines */
- xmfFile = fopen("output.xmf", "w");
- tempFile = fopen("output_temp.xmf", "r");
+ xmfFile = fopen(fileName, "w");
+ tempFile = fopen(tempFileName, "r");
if (xmfFile == NULL) error("Unable to open current XMF file.");
@@ -369,7 +373,7 @@ FILE* prepareXMFfile() {
}
fprintf(xmfFile, "\n");
fclose(tempFile);
- remove("output_temp.xmf");
+ remove(tempFileName);
return xmfFile;
}
@@ -380,8 +384,11 @@ FILE* prepareXMFfile() {
* @todo Exploit the XML nature of the XMF format to write a proper XML writer
*and simplify all the XMF-related stuff.
*/
-void createXMFfile() {
- FILE* xmfFile = fopen("output.xmf", "w");
+void createXMFfile(const char* baseName) {
+
+ char fileName[FILENAME_BUFFER_SIZE];
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
+ FILE* xmfFile = fopen(fileName, "w");
fprintf(xmfFile, "<?xml version=\"1.0\" ?> \n");
fprintf(xmfFile, "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []> \n");
diff --git a/src/common_io.h b/src/common_io.h
index b7f3a1a317..70ed25993c 100644
--- a/src/common_io.h
+++ b/src/common_io.h
@@ -97,8 +97,8 @@ void writeAttribute_i(hid_t grp, char* name, int data);
void writeAttribute_l(hid_t grp, char* name, long data);
void writeAttribute_s(hid_t grp, char* name, const char* str);
-void createXMFfile();
-FILE* prepareXMFfile();
+void createXMFfile(const char* baseName);
+FILE* prepareXMFfile(const char* baseName);
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,
diff --git a/src/engine.c b/src/engine.c
index 7af7c05661..ab250aaea4 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -2381,6 +2381,11 @@ void engine_init(struct engine *e, struct space *s,
e->ti_old = 0;
e->ti_current = 0;
e->timeStep = 0.;
+ e->timeBase = 0.;
+ e->timeFirstSnapshot =
+ parser_get_param_double(params, "Snapshots:time_first");
+ e->deltaTimeSnapshot =
+ parser_get_param_double(params, "Snapshots:delta_time");
e->dt_min = parser_get_param_double(params, "TimeIntegration:dt_min");
e->dt_max = parser_get_param_double(params, "TimeIntegration:dt_max");
e->file_stats = NULL;
@@ -2557,6 +2562,16 @@ void engine_init(struct engine *e, struct space *s,
error("Maximal time-step size larger than the simulation run time t=%e",
e->timeEnd - e->timeBegin);
+ /* Deal with outputs */
+ if (e->deltaTimeSnapshot < 0.)
+ error("Time between snapshots (%e) must be positive.",
+ e->deltaTimeSnapshot);
+
+ if (e->timeFirstSnapshot < e->timeBegin)
+ error(
+ "Time of first snapshot (%e) must be after the simulation start t=%e.",
+ e->timeFirstSnapshot, e->timeBegin);
+
/* Construct types for MPI communications */
#ifdef WITH_MPI
part_create_mpi_types();
diff --git a/src/engine.h b/src/engine.h
index 82e76481f8..3acc53e012 100644
--- a/src/engine.h
+++ b/src/engine.h
@@ -131,6 +131,10 @@ struct engine {
/* Time base */
double timeBase;
+ /* Snapshot times */
+ double timeFirstSnapshot;
+ double deltaTimeSnapshot;
+
/* File for statistics */
FILE *file_stats;
diff --git a/src/parallel_io.c b/src/parallel_io.c
index d1c739b590..4579be8f04 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -509,8 +509,12 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
*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 baseName The common part of the snapshot file name.
+ * @param us The UnitSystem used for the conversion of units in the output.
+ * @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
@@ -522,9 +526,9 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
* Calls #error() if an error occurs.
*
*/
-void write_output_parallel(struct engine* e, struct UnitSystem* us,
- int mpi_rank, int mpi_size, MPI_Comm comm,
- MPI_Info info) {
+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) {
hid_t h_file = 0, h_grp = 0, h_grpsph = 0;
const size_t Ngas = e->s->nr_parts;
const size_t Ntot = e->s->nr_gparts;
@@ -536,22 +540,19 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
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 */
+ /* Number of unassociated gparts */
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);
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%03i.hdf5", baseName,
+ outputCount);
/* First time, we need to create the XMF file */
- if (outputCount == 0 && mpi_rank == 0) createXMFfile();
+ if (outputCount == 0 && mpi_rank == 0) createXMFfile(baseName);
/* Prepare the XMF file for the new entry */
- if (mpi_rank == 0) xmfFile = prepareXMFfile();
+ if (mpi_rank == 0) xmfFile = prepareXMFfile(baseName);
/* Open HDF5 file */
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
diff --git a/src/parallel_io.h b/src/parallel_io.h
index f3691cb29b..970ad8c41d 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -36,9 +36,9 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info, int dry_run);
-void write_output_parallel(struct engine* e, struct UnitSystem* us,
- int mpi_rank, int mpi_size, MPI_Comm comm,
- MPI_Info info);
+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
diff --git a/src/serial_io.c b/src/serial_io.c
index 10eab97f1b..f2c0dcce1c 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -590,6 +590,7 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
* @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
*
* @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 mpi_rank The MPI rank of this node.
* @param mpi_size The number of MPI ranks.
@@ -604,8 +605,9 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
* Calls #error() if an error occurs.
*
*/
-void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
- int mpi_size, MPI_Comm comm, MPI_Info info) {
+void write_output_serial(struct engine* e, const char* baseName,
+ 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;
const size_t Ngas = e->s->nr_parts;
const size_t Ntot = e->s->nr_gparts;
@@ -617,16 +619,13 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
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 */
+ /* Number of unassociated gparts */
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);
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%03i.hdf5", baseName,
+ outputCount);
/* Compute offset in the file and total number of particles */
size_t N[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0};
@@ -646,10 +645,10 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
if (mpi_rank == 0) {
/* First time, we need to create the XMF file */
- if (outputCount == 0) createXMFfile();
+ if (outputCount == 0) createXMFfile(baseName);
/* Prepare the XMF file for the new entry */
- xmfFile = prepareXMFfile();
+ xmfFile = prepareXMFfile(baseName);
/* Write the part corresponding to this specific output */
writeXMFoutputheader(xmfFile, fileName, e->time);
diff --git a/src/serial_io.h b/src/serial_io.h
index 74ab8326db..b7ed6eb62d 100644
--- a/src/serial_io.h
+++ b/src/serial_io.h
@@ -36,8 +36,9 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info, int dry_run);
-void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
- int mpi_size, MPI_Comm comm, MPI_Info info);
+void write_output_serial(struct engine* e, const char* baseName,
+ struct UnitSystem* us, int mpi_rank, int mpi_size,
+ MPI_Comm comm, MPI_Info info);
#endif
diff --git a/src/single_io.c b/src/single_io.c
index 1dc71087e1..d545fb086f 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -456,7 +456,8 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
* @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 baseName The common part of the snapshot file name.
+ * @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
@@ -466,7 +467,8 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
* Calls #error() if an error occurs.
*
*/
-void write_output_single(struct engine* e, struct UnitSystem* us) {
+void write_output_single(struct engine* e, const char* baseName,
+ struct UnitSystem* us) {
hid_t h_file = 0, h_grp = 0;
const size_t Ngas = e->s->nr_parts;
@@ -478,25 +480,22 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
struct gpart* dmparts = NULL;
static int outputCount = 0;
- /* Number of particles of each type */
- // const size_t Ndm = Ntot - Ngas;
-
- /* MATTHIEU: Temporary fix to preserve master */
+ /* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - Ngas : 0;
- /* MATTHIEU: End temporary fix */
long long N_total[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0};
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
- snprintf(fileName, FILENAME_BUFFER_SIZE, "output_%03i.hdf5", outputCount);
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%03i.hdf5", baseName,
+ outputCount);
/* First time, we need to create the XMF file */
- if (outputCount == 0) createXMFfile();
+ if (outputCount == 0) createXMFfile(baseName);
/* Prepare the XMF file for the new entry */
FILE* xmfFile = 0;
- xmfFile = prepareXMFfile();
+ xmfFile = prepareXMFfile(baseName);
/* Write the part corresponding to this specific output */
writeXMFoutputheader(xmfFile, fileName, e->time);
diff --git a/src/single_io.h b/src/single_io.h
index 587ebe07b6..adfc5b4394 100644
--- a/src/single_io.h
+++ b/src/single_io.h
@@ -30,7 +30,8 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
struct gpart** gparts, size_t* Ngas, size_t* Ndm,
int* periodic, int dry_run);
-void write_output_single(struct engine* e, struct UnitSystem* us);
+void write_output_single(struct engine* e, const char* baseName,
+ struct UnitSystem* us);
#endif
--
GitLab