diff --git a/examples/main.c b/examples/main.c
index d99dec04b59f9d096d154620036a6da4a73f5931..fe93bc4d7d6f69ec7d505f109292661ddcbfd4dc 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -1006,7 +1006,7 @@ int main(int argc, char *argv[]) {
/* Initialise the particles */
engine_init_particles(&e, flag_entropy_ICs, clean_smoothing_length_values);
- /* Write the state of the system before starting time integration. */
+ /* Write the state of the system before starting time integration. */
#ifdef WITH_LOGGER
logger_ensure_size(e.log, e.total_nr_parts, e.total_nr_gparts, 0);
logger_log_all(e.log, &e);
diff --git a/src/cell.h b/src/cell.h
index a95e0f2226f8fd54ae5fab536208990cccd73189..6aae833250958707cd7933478929ad54d17246db 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -279,9 +279,6 @@ struct cell {
/*! Values of h_max before the drifts, used for sub-cell tasks. */
float h_max_old;
- /*! The logger task */
- struct task *logger;
-
/*! The task to compute time-steps */
struct task *timestep;
@@ -556,6 +553,9 @@ struct cell {
/*! Task for source terms */
struct task *sourceterms;
+ /*! The logger task */
+ struct task *logger;
+
/*! Minimum dimension, i.e. smallest edge of this cell (min(width)). */
float dmin;
diff --git a/src/dump.c b/src/dump.c
index bc57e7783287d792e32ade6d667df0568bae5d6c..5824b7081f6f7958e68bd526996eb6adffdad8b7 100644
--- a/src/dump.c
+++ b/src/dump.c
@@ -49,14 +49,12 @@
void *dump_get(struct dump *d, size_t count, size_t *offset) {
size_t local_offset = atomic_add(&d->count, count);
#ifdef SWIFT_DEBUG_CHECKS
- if (d->count > d->size)
- error("A new dump file should have been created.");
+ if (d->count > d->size) error("A new dump file should have been created.");
#endif
*offset = local_offset + d->file_offset;
return (char *)d->data + local_offset;
}
-
/**
* @brief Ensure that at least size bytes are available in the #dump.
*/
@@ -86,7 +84,7 @@ void dump_ensure(struct dump *d, size_t size) {
if ((d->data = mmap(NULL, d->size, PROT_WRITE, MAP_SHARED, d->fd,
d->file_offset)) == MAP_FAILED) {
error("Failed to allocate map of size %zi bytes (%s).", d->size,
- strerror(errno));
+ strerror(errno));
}
}
diff --git a/src/engine.c b/src/engine.c
index 03c0af95dd2726be559710bab8f1f9a1e836c966..45d4836345fec07fc91986e1ce5669424f3ad842 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -115,8 +115,7 @@ const char *engine_policy_names[] = {"none",
"structure finding",
"star formation",
"feedback",
- "logger"
-};
+ "logger"};
/** The rank of the engine as a global variable (for messages). */
int engine_rank;
@@ -233,10 +232,9 @@ void engine_make_hierarchical_tasks_common(struct engine *e, struct cell *c) {
c, NULL);
#if defined(WITH_LOGGER)
- c->logger = scheduler_addtask(s, task_type_logger, task_subtype_none, 0, 0,
- c, NULL);
+ c->logger = scheduler_addtask(s, task_type_logger, task_subtype_none, 0,
+ 0, c, NULL);
#endif
-
c->kick2 = scheduler_addtask(s, task_type_kick2, task_subtype_none, 0, 0,
c, NULL);
@@ -277,7 +275,7 @@ void engine_make_hierarchical_tasks_common(struct engine *e, struct cell *c) {
#if defined(WITH_LOGGER)
scheduler_addunlock(s, c->kick1, c->logger);
#endif
-}
+ }
} else { /* We are above the super-cell so need to go deeper */
@@ -4260,7 +4258,7 @@ void engine_marktasks_mapper(void *map_data, int num_elements,
/* logger tasks ? */
else if (t->type == task_type_logger) {
if (cell_is_active_hydro(t->ci, e) || cell_is_active_gravity(t->ci, e))
- scheduler_activate(s, t);
+ scheduler_activate(s, t);
}
/* Gravity stuff ? */
@@ -5215,10 +5213,9 @@ void engine_init_particles(struct engine *e, int flag_entropy_ICs,
#ifdef WITH_LOGGER
logger_log_timestamp(e->log, e->ti_current, &e->log->timestamp_offset);
- logger_ensure_size(e->log, e->total_nr_parts, e->total_nr_gparts,
- 0);
+ logger_ensure_size(e->log, e->total_nr_parts, e->total_nr_gparts, 0);
#endif
-
+
/* Now, launch the calculation */
TIMER_TIC;
engine_launch(e);
@@ -5470,8 +5467,7 @@ void engine_step(struct engine *e) {
#ifdef WITH_LOGGER
logger_log_timestamp(e->log, e->ti_current, &e->log->timestamp_offset);
- logger_ensure_size(e->log, e->total_nr_parts, e->total_nr_gparts,
- 0);
+ logger_ensure_size(e->log, e->total_nr_parts, e->total_nr_gparts, 0);
#endif
/* Are we drifting everything (a la Gadget/GIZMO) ? */
@@ -5625,9 +5621,9 @@ void engine_check_for_dumps(struct engine *e) {
/* Dump everything */
engine_print_stats(e);
#ifdef WITH_LOGGER
- engine_dump_index(e);
+ engine_dump_index(e);
#else
- engine_dump_snapshot(e);
+ engine_dump_snapshot(e);
#endif
} else if (e->ti_next_stats < e->ti_next_snapshot) {
@@ -5659,9 +5655,9 @@ void engine_check_for_dumps(struct engine *e) {
/* Dump snapshot */
#ifdef WITH_LOGGER
- engine_dump_index(e);
+ engine_dump_index(e);
#else
- engine_dump_snapshot(e);
+ engine_dump_snapshot(e);
#endif
} else if (e->ti_next_stats > e->ti_next_snapshot) {
@@ -5681,9 +5677,9 @@ void engine_check_for_dumps(struct engine *e) {
/* Dump snapshot */
#ifdef WITH_LOGGER
- engine_dump_index(e);
+ engine_dump_index(e);
#else
- engine_dump_snapshot(e);
+ engine_dump_snapshot(e);
#endif
/* Let's fake that we are at the stats dump time */
@@ -6484,8 +6480,8 @@ void engine_dump_snapshot(struct engine *e) {
MPI_INFO_NULL);
#endif
#else
- write_output_single(e, e->snapshot_base_name, e->internal_units,
- e->snapshot_units);
+ write_output_single(e, e->snapshot_base_name, e->internal_units,
+ e->snapshot_units);
#endif
#endif
@@ -6524,7 +6520,7 @@ void engine_dump_index(struct engine *e) {
/* Dump... */
write_index_single(e, e->log->base_name, e->internal_units,
- e->snapshot_units);
+ e->snapshot_units);
e->dump_snapshot = 0;
@@ -6702,9 +6698,8 @@ void engine_init(struct engine *e, struct space *s, struct swift_params *params,
e->last_repartition = 0;
#endif
-
#if defined(WITH_LOGGER)
- e->log = (struct logger *) malloc(sizeof(struct logger));
+ e->log = (struct logger *)malloc(sizeof(struct logger));
logger_init(e->log, params);
#endif
@@ -7166,8 +7161,9 @@ void engine_config(int restart, struct engine *e, struct swift_params *params,
#if defined(WITH_LOGGER)
if (e->nodeID == 0)
- message("WARNING: There is currently no way of predicting the output "
- "size, please use it carefully");
+ message(
+ "WARNING: There is currently no way of predicting the output "
+ "size, please use it carefully");
#endif
/* Find the time of the first snapshot output */
diff --git a/src/gravity/Default/gravity.h b/src/gravity/Default/gravity.h
index 167d2be8618dd7250018915f18a36db656482c00..d446844e8ffc862fd3be0688302ebb3a2efab8fa 100644
--- a/src/gravity/Default/gravity.h
+++ b/src/gravity/Default/gravity.h
@@ -28,7 +28,6 @@
#include "kernel_gravity.h"
#include "minmax.h"
-
/**
* @brief Returns the mass of a particle
*
@@ -147,7 +146,6 @@ __attribute__((always_inline)) INLINE static void gravity_init_gpart(
gp->a_grav[0] = 0.f;
gp->a_grav[1] = 0.f;
gp->a_grav[2] = 0.f;
- gp->last_output = SHRT_MAX;
#ifdef SWIFT_GRAVITY_FORCE_CHECKS
gp->potential_PM = 0.f;
diff --git a/src/hydro/Gadget2/hydro.h b/src/hydro/Gadget2/hydro.h
index 892fb4dd9bff6549925ce6172a94053eea62a963..98dcad4f39a5621bde8e085bc3bc06f060832958 100644
--- a/src/hydro/Gadget2/hydro.h
+++ b/src/hydro/Gadget2/hydro.h
@@ -788,7 +788,7 @@ hydro_set_init_internal_energy(struct part *p, float u_init) {
__attribute__((always_inline)) INLINE static int xpart_should_write(
const struct xpart *xp, const struct engine *e) {
- return (xp->logger_data.last_output > e->log->delta_step);
+ return (xp->logger_data.last_output > e->log->delta_step);
}
#endif
diff --git a/src/hydro/Gadget2/hydro_io.h b/src/hydro/Gadget2/hydro_io.h
index a3828b0b4185e2c7745813ecad5071901fa204aa..dfce1c2c2209f36bacb5263d4fbcb179dadc6303 100644
--- a/src/hydro/Gadget2/hydro_io.h
+++ b/src/hydro/Gadget2/hydro_io.h
@@ -188,19 +188,17 @@ INLINE static void hydro_write_particles(const struct part* parts,
#endif
}
-
/**
* @brief Specifies which particle fields to write to a dataset
*
* @param parts The particle array.
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
- *
+ *
* In this version, we only want the ids and the offset.
*/
__attribute__((always_inline)) INLINE static void hydro_write_index(
- const struct part* parts, const struct xpart* xparts,
- struct io_props* list,
+ const struct part* parts, const struct xpart* xparts, struct io_props* list,
int* num_fields) {
#ifdef WITH_LOGGER
@@ -210,15 +208,13 @@ __attribute__((always_inline)) INLINE static void hydro_write_index(
list[0] = io_make_output_field("ParticleIDs", ULONGLONG, 1,
UNIT_CONV_NO_UNITS, parts, id);
- list[1] = io_make_output_field("Offset", ULONGLONG, 1,
- UNIT_CONV_NO_UNITS, xparts, logger_data.last_offset);
+ list[1] = io_make_output_field("Offset", ULONGLONG, 1, UNIT_CONV_NO_UNITS,
+ xparts, logger_data.last_offset);
#else
error("Cannot write index without logger");
#endif
-
}
-
/**
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
diff --git a/src/logger.c b/src/logger.c
index 828a5a0849e2ff7c91b30cee177fac2355f0fc2e..a104f86061d5282df2449a07fc13cde2379d708d 100644
--- a/src/logger.c
+++ b/src/logger.c
@@ -24,10 +24,10 @@
#ifdef WITH_LOGGER
/* Some standard headers. */
+#include <hdf5.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
-#include <hdf5.h>
/* This object's header. */
#include "logger.h"
@@ -35,21 +35,16 @@
/* Local headers. */
#include "atomic.h"
#include "dump.h"
+#include "engine.h"
#include "error.h"
#include "part.h"
#include "units.h"
-#include "engine.h"
char logger_version[logger_version_size] = "0.1";
-
const unsigned int logger_datatype_size[logger_data_count] = {
- sizeof(int),
- sizeof(float),
- sizeof(double),
- sizeof(char),
- sizeof(long long),
- 1,
+ sizeof(int), sizeof(float), sizeof(double),
+ sizeof(char), sizeof(long long), 1,
};
/**
@@ -62,7 +57,8 @@ const unsigned int logger_datatype_size[logger_data_count] = {
*
* @return updated buff
*/
-char *logger_write_chunk_header(char *buff, const unsigned int *mask, const size_t *offset, const size_t offset_new) {
+char *logger_write_chunk_header(char *buff, const unsigned int *mask,
+ const size_t *offset, const size_t offset_new) {
/* write mask */
memcpy(buff, mask, logger_mask_size);
buff += logger_mask_size;
@@ -83,8 +79,8 @@ char *logger_write_chunk_header(char *buff, const unsigned int *mask, const size
* @param size number of bytes to write
* @param p pointer to the data
*/
-void logger_write_data(struct dump *d, size_t *offset, size_t size, const void * p)
-{
+void logger_write_data(struct dump *d, size_t *offset, size_t size,
+ const void *p) {
/* get buffer */
char *buff = dump_get(d, size, offset);
@@ -105,9 +101,10 @@ void logger_write_data(struct dump *d, size_t *offset, size_t size, const void *
* @param name Label of the parameter (should be smaller than log->name)
* @param data_type #logger_datatype to write
*/
-void logger_write_general_data(struct dump *d, const struct logger_parameters *params, size_t *offset,
- const void *p, char* name, size_t data_type)
-{
+void logger_write_general_data(struct dump *d,
+ const struct logger_parameters *params,
+ size_t *offset, const void *p, char *name,
+ size_t data_type) {
/* write name */
logger_write_data(d, offset, params->label_size, name);
@@ -115,8 +112,7 @@ void logger_write_general_data(struct dump *d, const struct logger_parameters *p
logger_write_data(d, offset, params->data_type_size, &data_type);
/* write value */
- if (data_type >= logger_data_count)
- error("Not implemented");
+ if (data_type >= logger_data_count) error("Not implemented");
size_t size = logger_datatype_size[data_type];
logger_write_data(d, offset, size, p);
@@ -186,22 +182,21 @@ void logger_log_all(struct logger *log, const struct engine *e) {
/* some constants */
const struct space *s = e->s;
const unsigned int mask = logger_mask_x | logger_mask_v | logger_mask_a |
- logger_mask_u | logger_mask_h | logger_mask_rho |
- logger_mask_consts;
+ logger_mask_u | logger_mask_h | logger_mask_rho |
+ logger_mask_consts;
/* loop over all parts */
- for(long long i=0; i < e->total_nr_parts; i++) {
- logger_log_part(log, &s->parts[i], mask, &s->xparts[i].logger_data.last_offset);
+ for (long long i = 0; i < e->total_nr_parts; i++) {
+ logger_log_part(log, &s->parts[i], mask,
+ &s->xparts[i].logger_data.last_offset);
s->xparts[i].logger_data.last_output = 0;
}
/* loop over all gparts */
- if (e->total_nr_gparts > 0)
- error("Not implemented");
+ if (e->total_nr_gparts > 0) error("Not implemented");
/* loop over all sparts */
// TODO
-
}
/**
@@ -210,9 +205,11 @@ void logger_log_all(struct logger *log, const struct engine *e) {
* @param log The #logger
* @param p The #part to dump.
* @param mask The mask of the data to dump.
- * @param offset Pointer to the offset of the previous log of this particle; (return) offset of this log.
+ * @param offset Pointer to the offset of the previous log of this particle;
+ * (return) offset of this log.
*/
-void logger_log_part(struct logger *log, const struct part *p, unsigned int mask, size_t *offset) {
+void logger_log_part(struct logger *log, const struct part *p,
+ unsigned int mask, size_t *offset) {
/* Make sure we're not writing a timestamp. */
if (mask & logger_mask_timestamp)
@@ -286,9 +283,11 @@ void logger_log_part(struct logger *log, const struct part *p, unsigned int mask
* @param log The #logger
* @param p The #gpart to dump.
* @param mask The mask of the data to dump.
- * @param offset Pointer to the offset of the previous log of this particle; (return) offset of this log.
+ * @param offset Pointer to the offset of the previous log of this particle;
+ * (return) offset of this log.
*/
-void logger_log_gpart(struct logger *log, const struct gpart *p, unsigned int mask, size_t *offset) {
+void logger_log_gpart(struct logger *log, const struct gpart *p,
+ unsigned int mask, size_t *offset) {
/* Make sure we're not writing a timestamp. */
if (mask & logger_mask_timestamp)
@@ -343,11 +342,13 @@ void logger_log_gpart(struct logger *log, const struct gpart *p, unsigned int ma
*
* @param log The #logger
* @param timestamp time to write
- * @param offset Pointer to the offset of the previous log of this particle; (return) offset of this log.
+ * @param offset Pointer to the offset of the previous log of this particle;
+ * (return) offset of this log.
*/
-void logger_log_timestamp(struct logger *log, integertime_t timestamp, size_t *offset) {
+void logger_log_timestamp(struct logger *log, integertime_t timestamp,
+ size_t *offset) {
struct dump *dump = log->dump;
-
+
/* Start by computing the size of the message. */
const int size = logger_compute_chunk_size(logger_mask_timestamp);
@@ -366,7 +367,6 @@ void logger_log_timestamp(struct logger *log, integertime_t timestamp, size_t *o
*offset = offset_new;
}
-
/**
* @brief Ensure that the buffer is large enough for a step.
*
@@ -378,16 +378,15 @@ void logger_log_timestamp(struct logger *log, integertime_t timestamp, size_t *o
* @param total_nr_gparts total number of gpart
* @param total_nr_sparts total number of spart
*/
-void logger_ensure_size(
- struct logger *log, size_t total_nr_parts,
- size_t total_nr_gparts, size_t total_nr_sparts) {
+void logger_ensure_size(struct logger *log, size_t total_nr_parts,
+ size_t total_nr_gparts, size_t total_nr_sparts) {
struct logger_parameters *log_params = log->params;
/* count part memory */
size_t limit = log_params->offset_size + log_params->mask_size;
- for(size_t i=0; i < log_params->nber_mask; i++) {
+ for (size_t i = 0; i < log_params->nber_mask; i++) {
if (log_params->masks[i] != logger_mask_timestamp)
limit += log_params->masks_data_size[i];
}
@@ -401,12 +400,10 @@ void logger_ensure_size(
}
/* count gpart memory */
- if (total_nr_gparts > 0)
- error("Not implemented");
+ if (total_nr_gparts > 0) error("Not implemented");
/* count spart memory */
- if (total_nr_sparts > 0)
- error("Not implemented");
+ if (total_nr_sparts > 0) error("Not implemented");
/* ensure enough space in dump */
dump_ensure(log->dump, log->buffer_size);
@@ -418,11 +415,13 @@ void logger_ensure_size(
* @param log The #logger
* @param params The #swift_params
*/
-void logger_init(struct logger *log, const struct swift_params *params) {
+void logger_init(struct logger *log, struct swift_params *params) {
/* read parameters */
log->delta_step = parser_get_param_int(params, "Logger:delta_step");
- log->buffer_size = parser_get_param_float(params, "Logger:mmaped_buffer_size") * 1e9;
- log->buffer_scale = parser_get_opt_param_float(params, "Logger:buffer_scale", 1.2);
+ log->buffer_size =
+ parser_get_param_float(params, "Logger:mmaped_buffer_size") * 1e9;
+ log->buffer_scale =
+ parser_get_opt_param_float(params, "Logger:buffer_scale", 1.2);
parser_get_param_string(params, "Logger:basename", log->base_name);
/* set initial value of parameters */
@@ -434,7 +433,8 @@ void logger_init(struct logger *log, const struct swift_params *params) {
strcat(logger_name_file, ".dump");
/* init parameters */
- log->params = (struct logger_parameters*) malloc(sizeof(struct logger_parameters));
+ log->params =
+ (struct logger_parameters *)malloc(sizeof(struct logger_parameters));
logger_parameters_init(log->params);
/* init dump */
@@ -445,7 +445,6 @@ void logger_init(struct logger *log, const struct swift_params *params) {
/* ensure enough place in dump */
dump_ensure(dump_file, log->buffer_size);
-
}
/**
@@ -471,50 +470,60 @@ void logger_write_file_header(struct logger *log, const struct engine *e) {
/* get required variables */
const struct logger_parameters log_params = *log->params;
struct dump *dump = log->dump;
-
+
size_t file_offset = dump->file_offset;
-
+
if (file_offset != 0)
- error("The logger is not empty."
- "This function should be called before writing anything in the logger");
+ error(
+ "The logger is not empty."
+ "This function should be called before writing anything in the logger");
/* Write version information */
logger_write_data(dump, &file_offset, logger_version_size, &logger_version);
-
+
/* write number of bytes used for the offsets */
- logger_write_data(dump, &file_offset, logger_header_number_size, &log_params.offset_size);
+ logger_write_data(dump, &file_offset, logger_header_number_size,
+ &log_params.offset_size);
/* write offset direction */
int reversed = 0;
- logger_write_data(dump, &file_offset, logger_datatype_size[logger_data_bool], &reversed);
+ logger_write_data(dump, &file_offset, logger_datatype_size[logger_data_bool],
+ &reversed);
/* will write the offset of the first particle here */
char *skip_header = dump_get(dump, log_params.offset_size, &file_offset);
/* write number of bytes used for names */
- logger_write_data(dump, &file_offset, logger_header_number_size, &log_params.label_size);
+ logger_write_data(dump, &file_offset, logger_header_number_size,
+ &log_params.label_size);
/* write number of bytes used for numbers */
- logger_write_data(dump, &file_offset, logger_header_number_size, &log_params.number_size);
+ logger_write_data(dump, &file_offset, logger_header_number_size,
+ &log_params.number_size);
/* write number of bytes used for masks */
- logger_write_data(dump, &file_offset, logger_header_number_size, &log_params.mask_size);
+ logger_write_data(dump, &file_offset, logger_header_number_size,
+ &log_params.mask_size);
/* write number of masks */
- logger_write_data(dump, &file_offset, log_params.number_size, &log_params.nber_mask);
-
+ logger_write_data(dump, &file_offset, log_params.number_size,
+ &log_params.nber_mask);
+
/* write masks */
// loop over all mask type
- for(size_t i=0; i<log_params.nber_mask; i++) {
+ for (size_t i = 0; i < log_params.nber_mask; i++) {
// mask name
size_t j = i * log_params.label_size;
- logger_write_data(dump, &file_offset, log_params.label_size, &log_params.masks_name[j]);
-
+ logger_write_data(dump, &file_offset, log_params.label_size,
+ &log_params.masks_name[j]);
+
// mask
- logger_write_data(dump, &file_offset, log_params.mask_size, &log_params.masks[i]);
+ logger_write_data(dump, &file_offset, log_params.mask_size,
+ &log_params.masks[i]);
// mask size
- logger_write_data(dump, &file_offset, log_params.number_size, &log_params.masks_data_size[i]);
+ logger_write_data(dump, &file_offset, log_params.number_size,
+ &log_params.masks_data_size[i]);
}
/* write mask data */
@@ -523,12 +532,12 @@ void logger_write_file_header(struct logger *log, const struct engine *e) {
/* write number of bytes for each field */
/* write data type (float, double, ...) */
/* write data name (mass, id, ...) */
-
+
/* Write data */
char *name = malloc(sizeof(char) * log_params.label_size);
strcpy(name, "time_base");
logger_write_general_data(dump, &log_params, &file_offset, &e->time_base,
- name, logger_data_double);
+ name, logger_data_double);
/* last step: write first offset */
memcpy(skip_header, &file_offset, log_params.offset_size);
@@ -544,7 +553,7 @@ void logger_write_file_header(struct logger *log, const struct engine *e) {
*
* @param log_params #logger_parameters to initialize
*/
-void logger_parameters_init(struct logger_parameters* log_params) {
+void logger_parameters_init(struct logger_parameters *log_params) {
/* set parameters */
log_params->label_size = 20;
log_params->offset_size = 7;
@@ -553,9 +562,9 @@ void logger_parameters_init(struct logger_parameters* log_params) {
log_params->data_type_size = 1;
log_params->nber_mask = 8;
-
+
/* set masks array */
- log_params->masks = malloc(sizeof(size_t)*log_params->nber_mask);
+ log_params->masks = malloc(sizeof(size_t) * log_params->nber_mask);
log_params->masks[0] = logger_mask_x;
log_params->masks[1] = logger_mask_v;
log_params->masks[2] = logger_mask_a;
@@ -615,7 +624,6 @@ void logger_parameters_init(struct logger_parameters* log_params) {
log_params->masks_data_size[7] = sizeof(integertime_t);
// todo masks_type
-
}
/**
@@ -623,13 +631,12 @@ void logger_parameters_init(struct logger_parameters* log_params) {
*
* @param log_params The #logger_parameters
*/
-void logger_parameters_clean(struct logger_parameters* log_params) {
+void logger_parameters_clean(struct logger_parameters *log_params) {
free(log_params->masks);
free(log_params->masks_name);
free(log_params->masks_data_size);
}
-
/**
* @brief read chunk header
*
@@ -640,14 +647,15 @@ void logger_parameters_clean(struct logger_parameters* log_params) {
*
* @return Number of bytes read
*/
-__attribute__((always_inline)) INLINE static int logger_read_chunk_header(const char *buff, unsigned int *mask, size_t *offset, size_t cur_offset) {
+__attribute__((always_inline)) INLINE static int logger_read_chunk_header(
+ const char *buff, unsigned int *mask, size_t *offset, size_t cur_offset) {
memcpy(mask, buff, logger_mask_size);
buff += logger_mask_size;
*offset = 0;
memcpy(offset, buff, logger_offset_size);
*offset = cur_offset - *offset;
-
+
return logger_mask_size + logger_offset_size;
}
@@ -824,4 +832,3 @@ int logger_read_timestamp(unsigned long long int *t, size_t *offset,
#endif /* WITH_LOGGER */
#endif /* HAVE_POSIX_FALLOCATE */
-
diff --git a/src/logger.h b/src/logger.h
index 82482cfa9c8a472f932a2e37bbacdd58c7621e07..12bbadf31c63783044597bf9c17ea3a0a4ce9db6 100644
--- a/src/logger.h
+++ b/src/logger.h
@@ -118,7 +118,7 @@ struct logger_parameters {
/* size of a data type in bytes */
size_t data_type_size;
-
+
/* number of different mask */
size_t nber_mask;
@@ -127,20 +127,18 @@ struct logger_parameters {
/* data size of each mask */
size_t *masks_data_size;
-
+
/* label of each mask */
char *masks_name;
-
};
-
/* structure containing global data */
struct logger {
/* Number of particle steps between dumping a chunk of data */
short int delta_step;
/* Logger basename */
- char base_name[LOGGER_STRING_LENGTH];
+ char base_name[LOGGER_STRING_LENGTH];
/* File name of the dump file */
struct dump *dump;
@@ -168,8 +166,7 @@ struct logger_part_data {
size_t last_offset;
};
-INLINE static void logger_part_data_init(
- struct logger_part_data *logger ) {
+INLINE static void logger_part_data_init(struct logger_part_data *logger) {
logger->last_offset = 0;
logger->last_output = SHRT_MAX;
}
@@ -189,22 +186,24 @@ extern const unsigned int logger_datatype_size[];
/* Function prototypes. */
int logger_compute_chunk_size(unsigned int mask);
void logger_log_all(struct logger *log, const struct engine *e);
-void logger_log_part(struct logger *log, const struct part *p, unsigned int mask, size_t *offset);
-void logger_log_gpart(struct logger *log, const struct gpart *p, unsigned int mask, size_t *offset);
-void logger_init(struct logger *log, const struct swift_params *params);
+void logger_log_part(struct logger *log, const struct part *p,
+ unsigned int mask, size_t *offset);
+void logger_log_gpart(struct logger *log, const struct gpart *p,
+ unsigned int mask, size_t *offset);
+void logger_init(struct logger *log, struct swift_params *params);
void logger_clean(struct logger *log);
void logger_log_timestamp(struct logger *log, integertime_t t, size_t *offset);
void logger_ensure_size(struct logger *log, size_t total_nr_parts,
- size_t total_nr_gparts, size_t total_nr_sparts);
-void logger_write_file_header(struct logger *log, const struct engine* e);
+ size_t total_nr_gparts, size_t total_nr_sparts);
+void logger_write_file_header(struct logger *log, const struct engine *e);
int logger_read_part(struct part *p, size_t *offset, const char *buff);
int logger_read_gpart(struct gpart *p, size_t *offset, const char *buff);
int logger_read_timestamp(unsigned long long int *t, size_t *offset,
const char *buff);
-void logger_parameters_init(struct logger_parameters* log_params);
-void logger_parameters_clean(struct logger_parameters* log_params);
+void logger_parameters_init(struct logger_parameters *log_params);
+void logger_parameters_clean(struct logger_parameters *log_params);
#endif /* WITH_LOGGER */
diff --git a/src/logger_io.c b/src/logger_io.c
index dc3ca9b4909c844c6067738931b88c044e604313..f80baaee4d9a4d66492d3c303d22ab425674f829 100644
--- a/src/logger_io.c
+++ b/src/logger_io.c
@@ -63,16 +63,16 @@
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
*
- * Creates an HDF5 output file and writes the offset and id of particles contained
- * in the engine. If such a file already exists, it is erased and replaced
- * by the new one.
+ * Creates an HDF5 output file and writes the offset and id of particles
+ * contained in the engine. If such a file already exists, it is erased and
+ * replaced by the new one.
*
* Calls #error() if an error occurs.
*
*/
void write_index_single(struct engine* e, const char* baseName,
- const struct unit_system* internal_units,
- const struct unit_system* snapshot_units) {
+ const struct unit_system* internal_units,
+ const struct unit_system* snapshot_units) {
hid_t h_file = 0, h_grp = 0;
const size_t Ngas = e->s->nr_parts;
@@ -81,13 +81,13 @@ void write_index_single(struct engine* e, const char* baseName,
int periodic = e->s->periodic;
int numFiles = 1;
struct part* parts = e->s->parts;
- struct xpart *xparts = e->s->xparts;
- //struct gpart* gparts = e->s->gparts;
+ struct xpart* xparts = e->s->xparts;
+ // struct gpart* gparts = e->s->gparts;
struct gpart* dmparts = NULL;
- //struct spart* sparts = e->s->sparts;
+ // struct spart* sparts = e->s->sparts;
static int outputCount = 0;
- struct logger *log = e->log;
+ struct logger* log = e->log;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
@@ -182,7 +182,14 @@ void write_index_single(struct engine* e, const char* baseName,
h_grp =
H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
- parser_write_params_to_hdf5(e->parameter_file, h_grp);
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 1);
+ H5Gclose(h_grp);
+
+ /* Print the runtime unused parameters */
+ h_grp = H5Gcreate(h_file, "/UnusedParameters", H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (h_grp < 0) error("Error while creating parameters group");
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 0);
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
@@ -249,17 +256,17 @@ void write_index_single(struct engine* e, const char* baseName,
case swift_type_gas:
N = Ngas;
- hydro_write_index(parts, xparts, list, &num_fields);
+ hydro_write_index(parts, xparts, list, &num_fields);
break;
case swift_type_dark_matter:
- error("TODO");
- break;
-
- case swift_type_star:
+ error("TODO");
+ break;
+
+ case swift_type_stars:
N = Nstars;
- error("TODO");
- //star_write_index(sparts, list, &num_fields);
+ error("TODO");
+ // star_write_index(sparts, list, &num_fields);
break;
default:
@@ -279,7 +286,6 @@ void write_index_single(struct engine* e, const char* baseName,
/* Close particle group */
H5Gclose(h_grp);
-
}
/* message("Done writing particles..."); */
diff --git a/src/logger_io.h b/src/logger_io.h
index 5732cf5b66c3964b9c8c1c3a6c002313afdc4e0d..76b7150043dc25f222ef927c3508b84e423aff4a 100644
--- a/src/logger_io.h
+++ b/src/logger_io.h
@@ -30,8 +30,8 @@
#include "units.h"
void write_index_single(struct engine* e, const char* baseName,
- const struct unit_system* internal_units,
- const struct unit_system* snapshot_units);
+ const struct unit_system* internal_units,
+ const struct unit_system* snapshot_units);
#endif
#endif /* SWIFT_LOGGER_IO_H */
diff --git a/src/parallel_io.h b/src/parallel_io.h
index 35d0a1e18b54d85b8f8532bab5117a511568ea7f..9cd775347f0d5fbb3bc1b17664e0d5dba734d795 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -29,6 +29,7 @@
/* Includes. */
#include "engine.h"
+#include "io_properties.h"
#include "part.h"
#include "units.h"
diff --git a/src/runner.c b/src/runner.c
index a4cee98014b3f1b507762d5052fe1dbb9f40dc92..be628cbfd6888cb7cb6c987b02aa6b5e7186969c 100644
--- a/src/runner.c
+++ b/src/runner.c
@@ -899,7 +899,7 @@ void runner_do_init_grav(struct runner *r, struct cell *c, int timer) {
* @param timer Are we timing this ?
*/
void runner_do_extra_ghost(struct runner *r, struct cell *c, int timer) {
-
+
#ifdef EXTRA_HYDRO_LOOP
struct part *restrict parts = c->hydro.parts;
@@ -2506,7 +2506,6 @@ void *runner_main(void *data) {
t->ti_run = e->ti_current;
#endif
-
/* Different types of tasks... */
switch (t->type) {
case task_type_self:
@@ -2613,8 +2612,8 @@ void *runner_main(void *data) {
runner_do_end_force(r, ci, 1);
break;
case task_type_logger:
- runner_do_logger(r, ci, 1);
- break;
+ runner_do_logger(r, ci, 1);
+ break;
case task_type_timestep:
runner_do_timestep(r, ci, 1);
break;
@@ -2694,7 +2693,6 @@ void *runner_main(void *data) {
return NULL;
}
-
/**
* @brief Write the required particles through the logger.
*
@@ -2708,13 +2706,12 @@ void runner_do_logger(struct runner *r, struct cell *c, int timer) {
TIMER_TIC;
const struct engine *e = r->e;
- struct part *restrict parts = c->parts;
- struct xpart *restrict xparts = c->xparts;
- const int count = c->count;
+ struct part *restrict parts = c->hydro.parts;
+ struct xpart *restrict xparts = c->hydro.xparts;
+ const int count = c->hydro.count;
/* Anything to do here? */
- if (!cell_is_starting_hydro(c, e) && !cell_is_starting_gravity(c, e))
- return;
+ if (!cell_is_starting_hydro(c, e) && !cell_is_starting_gravity(c, e)) return;
/* Recurse? */
if (c->split) {
@@ -2732,35 +2729,30 @@ void runner_do_logger(struct runner *r, struct cell *c, int timer) {
/* If particle needs to be kicked */
if (part_is_starting(p, e)) {
- if (xpart_should_write(xp, e))
- {
- /* Write particle */
- logger_log_part(e->log, p, logger_mask_x | logger_mask_v | logger_mask_a |
- logger_mask_u | logger_mask_h | logger_mask_rho |
- logger_mask_consts,
- &xp->logger_data.last_offset);
- //message("Offset: %lu", p->last_offset);
- /* Set counter back to zero */
- xp->logger_data.last_output = 0;
- }
- else
- /* Update counter */
- xp->logger_data.last_output += 1;
+ if (xpart_should_write(xp, e)) {
+ /* Write particle */
+ logger_log_part(e->log, p,
+ logger_mask_x | logger_mask_v | logger_mask_a |
+ logger_mask_u | logger_mask_h | logger_mask_rho |
+ logger_mask_consts,
+ &xp->logger_data.last_offset);
+ // message("Offset: %lu", p->last_offset);
+ /* Set counter back to zero */
+ xp->logger_data.last_output = 0;
+ } else
+ /* Update counter */
+ xp->logger_data.last_output += 1;
}
}
-
}
- if (c->gcount > 0)
- error("gparts not implemented");
+ if (c->grav.count > 0) error("gparts not implemented");
+
+ if (c->stars.count > 0) error("sparts not implemented");
- if (c->scount > 0)
- error("sparts not implemented");
-
if (timer) TIMER_TOC(timer_logger);
#else
error("Logger disabled, please enable it during configuration");
#endif
-
}
diff --git a/src/single_io.c b/src/single_io.c
index e8cd02ff8114f7b9de086ed44bdd124b6a01a338..99f016809d11abc4f9f31695306850d82fd56c84 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -314,7 +314,7 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
/* Write XMF description for this data set */
if (xmfFile != NULL)
xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N,
- props.dimension, props.type);
+ props.dimension, props.type);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
@@ -995,5 +995,4 @@ void write_output_single(struct engine* e, const char* baseName,
e->snapshot_output_count++;
}
-
#endif /* HAVE_HDF5 */
diff --git a/src/task.c b/src/task.c
index 9aeca8cd7eec7680bcb0148a9bf172a5efd4aa4f..834ae319399fbefcf7379a4ccd1a59f104a9fa28 100644
--- a/src/task.c
+++ b/src/task.c
@@ -47,19 +47,38 @@
#include "lock.h"
/* Task type names. */
-const char *taskID_names[task_type_count] = {
- "none", "sort", "self",
- "pair", "sub_self", "sub_pair",
- "init_grav", "init_grav_out", "ghost_in",
- "ghost", "ghost_out", "extra_ghost",
- "drift_part", "drift_gpart", "end_force",
- "kick1", "kick2", "timestep",
- "send", "recv", "grav_long_range",
- "grav_mm", "grav_down_in", "grav_down",
- "grav_mesh", "cooling", "star_formation",
- "sourceterms", "stars_ghost_in", "stars_ghost",
- "stars_ghost_out","logger"
-};
+const char *taskID_names[task_type_count] = {"none",
+ "sort",
+ "self",
+ "pair",
+ "sub_self",
+ "sub_pair",
+ "init_grav",
+ "init_grav_out",
+ "ghost_in",
+ "ghost",
+ "ghost_out",
+ "extra_ghost",
+ "drift_part",
+ "drift_gpart",
+ "end_force",
+ "kick1",
+ "kick2",
+ "timestep",
+ "send",
+ "recv",
+ "grav_long_range",
+ "grav_mm",
+ "grav_down_in",
+ "grav_down",
+ "grav_mesh",
+ "cooling",
+ "star_formation",
+ "sourceterms",
+ "stars_ghost_in",
+ "stars_ghost",
+ "stars_ghost_out",
+ "logger"};
/* Sub-task type names. */
const char *subtaskID_names[task_subtype_count] = {
diff --git a/src/timers.c b/src/timers.c
index dae35f30295e067263610ba74ea192f1012c0fbf..5cd75cced7433427904e013629dd37c9bf28d009 100644
--- a/src/timers.c
+++ b/src/timers.c
@@ -35,67 +35,65 @@
ticks timers[timer_count];
/* Timer names. */
-const char* timers_names[timer_count] = {
- "none",
- "prepare",
- "init",
- "init_grav",
- "drift_part",
- "drift_gpart",
- "kick1",
- "kick2",
- "timestep",
- "endforce",
- "dosort",
- "doself_density",
- "doself_gradient",
- "doself_force",
- "doself_grav_pp",
- "dopair_density",
- "dopair_gradient",
- "dopair_force",
- "dopair_grav_mm",
- "dopair_grav_pp",
- "dograv_external",
- "dograv_down",
- "dograv_mesh",
- "dograv_top_level",
- "dograv_long_range",
- "dosource",
- "dosub_self_density",
- "dosub_self_gradient",
- "dosub_self_force",
- "dosub_self_grav",
- "dosub_pair_density",
- "dosub_pair_gradient",
- "dosub_pair_force",
- "dosub_pair_grav",
- "doself_subset",
- "dopair_subset",
- "dopair_subset_naive",
- "dosub_subset",
- "do_ghost",
- "do_extra_ghost",
- "dorecv_part",
- "dorecv_gpart",
- "dorecv_spart",
- "do_cooling",
- "do_star_formation",
- "gettask",
- "qget",
- "qsteal",
- "locktree",
- "runners",
- "step",
- "doself_stars_density",
- "dopair_stars_density",
- "do_stars_ghost",
- "doself_subset_stars_density",
- "dopair_subset_stars_density",
- "dosubpair_stars_density",
- "dosub_self_stars_density",
- "logger"
-};
+const char* timers_names[timer_count] = {"none",
+ "prepare",
+ "init",
+ "init_grav",
+ "drift_part",
+ "drift_gpart",
+ "kick1",
+ "kick2",
+ "timestep",
+ "endforce",
+ "dosort",
+ "doself_density",
+ "doself_gradient",
+ "doself_force",
+ "doself_grav_pp",
+ "dopair_density",
+ "dopair_gradient",
+ "dopair_force",
+ "dopair_grav_mm",
+ "dopair_grav_pp",
+ "dograv_external",
+ "dograv_down",
+ "dograv_mesh",
+ "dograv_top_level",
+ "dograv_long_range",
+ "dosource",
+ "dosub_self_density",
+ "dosub_self_gradient",
+ "dosub_self_force",
+ "dosub_self_grav",
+ "dosub_pair_density",
+ "dosub_pair_gradient",
+ "dosub_pair_force",
+ "dosub_pair_grav",
+ "doself_subset",
+ "dopair_subset",
+ "dopair_subset_naive",
+ "dosub_subset",
+ "do_ghost",
+ "do_extra_ghost",
+ "dorecv_part",
+ "dorecv_gpart",
+ "dorecv_spart",
+ "do_cooling",
+ "do_star_formation",
+ "gettask",
+ "qget",
+ "qsteal",
+ "locktree",
+ "runners",
+ "step",
+ "doself_stars_density",
+ "dopair_stars_density",
+ "do_stars_ghost",
+ "doself_subset_stars_density",
+ "dopair_subset_stars_density",
+ "dosubpair_stars_density",
+ "dosub_self_stars_density",
+ "logger"};
/* File to store the timers */
static FILE* timers_file;
diff --git a/tests/testLogger.c b/tests/testLogger.c
index 14e49cdfd3b112949243f7cd6b3c4126c68d696d..2c7339c63560860700d967ac5f9f367803a9746f 100644
--- a/tests/testLogger.c
+++ b/tests/testLogger.c
@@ -20,7 +20,8 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_POSIX_FALLOCATE) && defined(WITH_LOGGER) /* Are we on a sensible platform? */
+#if defined(HAVE_POSIX_FALLOCATE) && \
+ defined(WITH_LOGGER) /* Are we on a sensible platform? */
/* Some standard headers. */
#include <stdio.h>
@@ -44,9 +45,11 @@ void test_log_parts(struct logger *log) {
size_t offset = d->count;
/* Write the full part. */
- logger_log_part(log, &p, logger_mask_x | logger_mask_v | logger_mask_a |
- logger_mask_u | logger_mask_h | logger_mask_rho |
- logger_mask_consts, &offset);
+ logger_log_part(log, &p,
+ logger_mask_x | logger_mask_v | logger_mask_a |
+ logger_mask_u | logger_mask_h | logger_mask_rho |
+ logger_mask_consts,
+ &offset);
printf("Wrote part at offset %#016zx.\n", offset);
/* Write only the position. */
@@ -113,8 +116,10 @@ void test_log_gparts(struct logger *log) {
size_t offset = d->count;
/* Write the full part. */
- logger_log_gpart(log, &p, logger_mask_x | logger_mask_v | logger_mask_a |
- logger_mask_h | logger_mask_consts, &offset);
+ logger_log_gpart(log, &p,
+ logger_mask_x | logger_mask_v | logger_mask_a |
+ logger_mask_h | logger_mask_consts,
+ &offset);
printf("Wrote gpart at offset %#016zx.\n", offset);
/* Write only the position. */