diff --git a/logger/logger_header.c b/logger/logger_header.c
index aaebc0fa4547a26d3c49b5444802dd444020c20e..f16673ffcbdaa665c6873a19ada31eed1f5b3d1f 100644
--- a/logger/logger_header.c
+++ b/logger/logger_header.c
@@ -89,7 +89,7 @@ int header_get_field_index(const struct header *h, const char *field) {
*/
void header_change_offset_direction(struct header *h, enum logger_offset_direction new_value) {
h->offset_direction = new_value;
- /* Skip file format and version numbers */
+ /* Skip file format and version numbers. */
size_t offset = LOGGER_VERSION_SIZE + 2 * sizeof(int);
logger_loader_io_write_data(h->log->log.map + offset, sizeof(unsigned int), &new_value);
@@ -104,19 +104,19 @@ void header_change_offset_direction(struct header *h, enum logger_offset_directi
void header_read(struct header *h, struct logger_logfile *log) {
void *map = log->log.map;
- /* Set pointer to log */
+ /* Set pointer to log. */
h->log = log;
- /* read file format */
+ /* read the file format. */
char file_format[STRING_SIZE];
map = logger_loader_io_read_data(map, LOGGER_VERSION_SIZE, &file_format);
if (strcmp(file_format, "SWIFT_LOGGER"))
error("Wrong file format (%s)", file_format);
- /* Read major version number */
+ /* Read the major version number. */
map = logger_loader_io_read_data(map, sizeof(int), &h->major_version);
- /* Read minor version number */
+ /* Read the minor version number. */
map = logger_loader_io_read_data(map, sizeof(int), &h->minor_version);
struct logger_reader *reader = log->reader;
@@ -126,43 +126,43 @@ void header_read(struct header *h, struct logger_logfile *log) {
if (reader->verbose > 0)
message("File version %i.%i", h->major_version, h->minor_version);
- /* read the offset directions */
+ /* Read the offset directions. */
map = logger_loader_io_read_data(map, sizeof(int), &h->offset_direction);
if (!header_is_forward(h) && !header_is_backward(h) &&
!header_is_corrupted(h))
error("Wrong offset value in the header (%i)", h->offset_direction);
- /* read offset to first record */
+ /* Read offset to first record. */
map = logger_loader_io_read_data(map, LOGGER_OFFSET_SIZE, &h->offset_first_record);
- /* read the size of the strings */
+ /* Read the size of the strings. */
map = logger_loader_io_read_data(map, sizeof(unsigned int), &h->string_length);
- /* check if value defined in this file is large enough. */
+ /* Check if value defined in this file is large enough. */
if (STRING_SIZE < h->string_length) {
error("Name too large in log file %i", h->string_length);
}
- /* read the number of masks. */
+ /* Read the number of masks. */
map = logger_loader_io_read_data(map, sizeof(unsigned int), &h->number_mask);
- /* allocate the masks memory. */
+ /* Allocate the masks memory. */
h->masks = malloc(sizeof(struct mask_data) * h->number_mask);
- /* loop over all masks. */
+ /* Loop over all masks. */
for (size_t i = 0; i < h->number_mask; i++) {
- /* read the mask name. */
+ /* Read the mask name. */
map = logger_loader_io_read_data(map, h->string_length, h->masks[i].name);
- /* set the mask value. */
+ /* Set the mask value. */
h->masks[i].mask = 1 << i;
- /* read the mask data size. */
+ /* Read the mask data size. */
map = logger_loader_io_read_data(map, sizeof(unsigned int), &h->masks[i].size);
}
- /* Check the logfile header's size */
+ /* Check the logfile header's size. */
if (map != log->log.map + h->offset_first_record) {
header_print(h);
size_t offset = map - log->log.map;
@@ -181,7 +181,7 @@ void header_read(struct header *h, struct logger_logfile *log) {
*/
size_t header_get_record_size_from_mask(const struct header *h, const size_t mask) {
size_t count = 0;
- /* Loop over each masks */
+ /* Loop over each masks. */
for (size_t i = 0; i < h->number_mask; i++) {
if (mask & h->masks[i].mask) {
count += h->masks[i].size;
diff --git a/logger/logger_header.h b/logger/logger_header.h
index 606e8d74e21c559ac562be225978a004e49721e5..c8cee8634e2e2071d4b8352305efedf90e774474 100644
--- a/logger/logger_header.h
+++ b/logger/logger_header.h
@@ -32,7 +32,7 @@ enum logger_offset_direction {
logger_offset_backward = 0,
logger_offset_forward,
logger_offset_corrupted,
- /* Number of offset type */
+ /* Number of offset type. */
logger_offset_count,
};
@@ -56,10 +56,10 @@ struct logger_logfile;
* The only function that modify the file is #header_change_offset_direction.
*/
struct header {
- /* Dump's major version */
+ /* Dump's major version. */
int major_version;
- /* Dump's minor version */
+ /* Dump's minor version. */
int minor_version;
/* Offset of the first record. */
@@ -77,7 +77,7 @@ struct header {
/* Direction of the offset in the records. */
enum logger_offset_direction offset_direction;
- /* The corresponding log */
+ /* The corresponding log. */
struct logger_logfile *log;
};
diff --git a/logger/logger_index.c b/logger/logger_index.c
index 25e81403e46e40ced3f060c446f4f5b5f984c3a1..4d8ccfd8b0883c0da650c632ca67d434073eda2f 100644
--- a/logger/logger_index.c
+++ b/logger/logger_index.c
@@ -70,7 +70,7 @@ void logger_index_init(struct logger_index *index, struct logger_reader *reader,
*/
void logger_index_free(struct logger_index *index) {
- /* unmap file */
+ /* unmap file. */
logger_loader_io_munmap_file(index->data, index->file_size);
/* Set variables to default value. */
diff --git a/logger/logger_index.h b/logger/logger_index.h
index f19c852a79f27f794062626ecb5b4cadf6fe70aa..57cf7207858c108225a60dc0a13abf547ca27970 100644
--- a/logger/logger_index.h
+++ b/logger/logger_index.h
@@ -30,10 +30,10 @@ struct logger_reader;
struct logger_index_data {
- /* The particle's id */
+ /* The particle's id. */
uint64_t id;
- /* The particle's offset */
+ /* The particle's offset. */
uint64_t offset;
};
@@ -45,25 +45,25 @@ struct logger_index_data {
* #logger_index_free.
*/
struct logger_index {
- /* The reader */
+ /* The reader. */
struct logger_reader *reader;
- /* memory map of the index file */
+ /* memory map of the index file. */
void *data;
- /* Index file size */
+ /* Index file size. */
size_t file_size;
- /* Number of particles */
+ /* Number of particles. */
size_t total_number_particles;
- /* Number of particles per type */
+ /* Number of particles per type. */
long long number_particles[swift_type_count];
- /* Time of the index file */
+ /* Time of the index file. */
double time;
- /* Integer time of the index file */
+ /* Integer time of the index file. */
integertime_t int_time;
};
diff --git a/logger/logger_loader_io.c b/logger/logger_loader_io.c
index bcbe41c0fb5377b4325bd71b2bf78efe46258eb2..6d6593008719a42013c5083babf5e4666ed5906c 100644
--- a/logger/logger_loader_io.c
+++ b/logger/logger_loader_io.c
@@ -88,7 +88,7 @@ void *logger_loader_io_mmap_file(char *filename, size_t *file_size, int read_onl
*
*/
void logger_loader_io_munmap_file(void *map, size_t file_size) {
- /* unmap */
+ /* unmap the file. */
if (munmap(map, file_size) != 0) {
error("Unable to unmap the file (%s)", strerror(errno));
}
diff --git a/logger/logger_logfile.c b/logger/logger_logfile.c
index 89d66084ed0e7a8f13058bbab04d1ef0131ef396..ea791bc955ca2ab87bc59ba7f61133b09b9abfea 100644
--- a/logger/logger_logfile.c
+++ b/logger/logger_logfile.c
@@ -38,7 +38,7 @@ void logger_logfile_init_from_file(
if (&reader->log != log)
error("Wrong link to the reader.");
- /* Set pointers to zero */
+ /* Set pointers to zero. */
time_array_init(&log->times);
/* Open file, map it and get its size. */
@@ -58,26 +58,26 @@ void logger_logfile_init_from_file(
}
/* No need to continue if only the
- header is required */
+ header is required. */
if (only_header)
return;
- /* Check if the offset are corrupted */
+ /* Check if the offset are corrupted. */
if (header_is_corrupted(&log->header)) {
error("The offsets have been corrupted");
}
- /* Reverse the offsets direction */
+ /* Reverse the offsets direction. */
if (header_is_backward(&log->header)) {
logger_logfile_reverse_offset(log, filename);
}
- /* Initialize the time array */
+ /* Initialize the time array. */
if (reader->verbose > 1)
message("Reading the time stamps.");
time_array_populate(&log->times, log);
- /* Print the time array */
+ /* Print the time array. */
if (reader->verbose > 0) {
time_array_print(&log->times);
}
@@ -104,7 +104,7 @@ void logger_logfile_free(struct logger_logfile *log) {
*/
void logger_logfile_reverse_offset(struct logger_logfile *log, char *filename) {
- /* Close and reopen the file in write mode */
+ /* Close and reopen the file in write mode. */
logger_loader_io_munmap_file(log->log.map, log->log.file_size);
log->log.map = logger_loader_io_mmap_file(
filename, &log->log.file_size, /* read_only */ 0);
@@ -115,7 +115,7 @@ void logger_logfile_reverse_offset(struct logger_logfile *log, char *filename) {
if (&reader->log != log)
error("Wrong link to the reader.");
- /* Check if the offsets need to be reversed */
+ /* Check if the offsets need to be reversed. */
if (!header_is_backward(header)) {
error("The offsets are already reversed.");
}
@@ -175,7 +175,7 @@ void logger_logfile_reverse_offset(struct logger_logfile *log, char *filename) {
}
#endif
- /* Close and reopen the file in read mode */
+ /* Close and reopen the file in read mode. */
logger_loader_io_munmap_file(log->log.map, log->log.file_size);
log->log.map = logger_loader_io_mmap_file(
filename, &log->log.file_size, /* read_only */ 1);
diff --git a/logger/logger_logfile.h b/logger/logger_logfile.h
index 4f7d1124932750636675dbead2cd87aa0f4a4a6d..7dc964431f1a2b274c149bee085bb3c285883ab9 100644
--- a/logger/logger_logfile.h
+++ b/logger/logger_logfile.h
@@ -46,15 +46,15 @@ struct logger_logfile {
/* The reader that is using this log file. */
struct logger_reader *reader;
- /* Information about the time records */
+ /* Information about the time records. */
struct time_array times;
/* The log's variables. */
struct {
- /* Mapped data */
+ /* Mapped data. */
void *map;
- /* File size */
+ /* File size. */
size_t file_size;
} log;
diff --git a/logger/logger_particle.c b/logger/logger_particle.c
index 30777834b16c370a2c06b0c41cf30a8bfffcbd3a..daaa0027572e8d26835f9654c8b288ee74feb538 100644
--- a/logger/logger_particle.c
+++ b/logger/logger_particle.c
@@ -77,7 +77,7 @@ void* logger_particle_read_field(struct logger_particle *part, void *map,
const char *field, const size_t size) {
void *p = NULL;
- /* Get the correct pointer */
+ /* Get the correct pointer. */
if (strcmp("positions", field) == 0) {
p = &part->pos;
} else if (strcmp("velocities", field) == 0) {
@@ -96,10 +96,10 @@ void* logger_particle_read_field(struct logger_particle *part, void *map,
error("Type %s not defined", field);
}
- /* read the data */
+ /* read the data. */
map = logger_loader_io_read_data(map, size, p);
- /* Split the required fields */
+ /* Split the required fields. */
if (strcmp("consts", field) == 0) {
part->mass = 0;
part->id = 0;
@@ -128,7 +128,7 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
size_t offset, const double time,
const enum logger_reader_type reader_type) {
- /* Get a few pointers */
+ /* Get a few pointers. */
const struct header *h = &reader->log.header;
void *map = reader->log.log.map;
@@ -139,13 +139,13 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
logger_particle_init(part);
- /* Read the record mask */
+ /* Read the record's mask. */
map = logger_loader_io_read_mask(h, map + offset, &mask, &h_offset);
- /* Check if it is not a time record */
- if (mask != 127) error("Unexpected mask: %lu", mask);
+ /* Check if it is not a time record. */
+ if (mask == 128) error("Unexpected mask: %lu", mask);
- /* Read all the fields */
+ /* Read all the fields. */
for (size_t i = 0; i < h->number_mask; i++) {
if (mask & h->masks[i].mask) {
map = logger_particle_read_field(part, map, h->masks[i].name,
@@ -160,7 +160,7 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
else
part->time = -1;
- /* update the offset */
+ /* update the offset. */
offset = (size_t) (map - reader->log.log.map);
/* Check if an interpolation is required. */
@@ -183,7 +183,7 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
h_offset += offset - header_get_record_size_from_mask(h, mask) - LOGGER_MASK_SIZE -
LOGGER_OFFSET_SIZE;
- /* Get time of next record */
+ /* Get time of next record. */
part_next.time = time_array_get_time(times, h_offset);
/* Read next record. */
@@ -232,7 +232,7 @@ void logger_particle_interpolate(
double tmp;
float ftmp;
- /* interpolate vectors */
+ /* interpolate vectors. */
for (size_t i = 0; i < DIM; i++) {
tmp = (part_next->pos[i] - part_curr->pos[i]);
part_curr->pos[i] += tmp * scaling;
@@ -244,10 +244,10 @@ void logger_particle_interpolate(
part_curr->acc[i] += ftmp * scaling;
}
- /* interpolate scalars */
+ /* interpolate scalars. */
ftmp = (part_next->entropy - part_curr->entropy);
part_curr->entropy += ftmp * scaling;
- /* set time */
+ /* set time. */
part_curr->time = time;
}
diff --git a/logger/logger_particle.h b/logger/logger_particle.h
index 66683266c4f1513e3a6a8f29a555b2270b583424..7b612948c0fd1c3bca916f1f4db4b8412374763e 100644
--- a/logger/logger_particle.h
+++ b/logger/logger_particle.h
@@ -52,31 +52,31 @@ struct logger_reader;
* interpolation is required.
*/
struct logger_particle {
- /* position */
+ /* position. */
double pos[DIM];
- /* velocity */
+ /* velocity. */
float vel[DIM];
- /* acceleration */
+ /* acceleration. */
float acc[DIM];
- /* entropy */
+ /* entropy. */
float entropy;
- /* smoothing length */
+ /* smoothing length. */
float h;
- /* density */
+ /* density. */
float density;
- /* mass */
+ /* mass. */
float mass;
- /* id */
+ /* unique id. */
size_t id;
- /* time */
+ /* time of the record. */
double time;
};
@@ -84,8 +84,8 @@ struct logger_particle {
* @brief Defines the type of interpolation
*/
enum logger_reader_type {
- logger_reader_const, /* Constant interpolation */
- logger_reader_lin, /* Linear interpolation */
+ logger_reader_const, /* Constant interpolation. */
+ logger_reader_lin, /* Linear interpolation. */
};
void logger_particle_print(const struct logger_particle *p);
diff --git a/logger/logger_python_wrapper.c b/logger/logger_python_wrapper.c
index a447d3813e2b1353056c5ae7f2ab25afcc40831a..e50b59ff7b88f4f6db37bc2786de2496887e509c 100644
--- a/logger/logger_python_wrapper.c
+++ b/logger/logger_python_wrapper.c
@@ -44,11 +44,11 @@
static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
PyObject *args) {
- /* input */
+ /* input variables. */
PyArrayObject *offset = NULL;
char *filename = NULL;
- /* output */
+ /* output variables. */
PyArrayObject *pos = NULL;
PyArrayObject *vel = NULL;
PyArrayObject *acc = NULL;
@@ -61,8 +61,7 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
size_t time_offset;
int verbose = 2;
- /* parse arguments */
-
+ /* parse arguments. */
if (!PyArg_ParseTuple(args, "OsL|i", &offset, &filename, &time_offset,
&verbose))
return NULL;
@@ -77,12 +76,12 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
error("Offset does not contain unsigned int");
}
- /* initialize the reader */
+ /* initialize the reader. */
struct logger_reader reader;
logger_reader_init(&reader, filename, verbose);
struct header *h = &reader.log.header;
- /* init array */
+ /* init array. */
npy_intp dim[2];
dim[0] = PyArray_DIMS(offset)[0];
dim[1] = DIM;
@@ -90,7 +89,7 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
/* Get required time. */
double time = time_array_get_time(&reader.log.times, time_offset);
- /* init output */
+ /* init output. */
if (header_get_field_index(h, "positions") != -1) {
pos = (PyArrayObject *)PyArray_SimpleNew(2, dim, NPY_DOUBLE);
}
@@ -127,19 +126,21 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
if (verbose > 1)
message("Reading particles.");
- /* loop over all particles */
+ /* loop over all particles. */
for (npy_intp i = 0; i < PyArray_DIMS(offset)[0]; i++) {
struct logger_particle part;
+ /* Get the offset. */
size_t offset_particle = *(size_t *)PyArray_GETPTR1(offset, i);
+ /* Read the particle. */
logger_particle_read(&part, &reader, offset_particle, time, logger_reader_lin);
double *dtmp;
float *ftmp;
size_t *stmp;
- /* copy data */
+ /* copy the data. */
for (size_t k = 0; k < DIM; k++) {
if (pos) {
dtmp = PyArray_GETPTR2(pos, i, k);
@@ -183,10 +184,10 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
}
}
- /* Free the memory */
+ /* Free the memory. */
logger_reader_free(&reader);
- /* construct return value */
+ /* construct return value. */
PyObject *dict = PyDict_New();
PyObject *key = PyUnicode_FromString("positions");
PyDict_SetItem(dict, key, PyArray_Return(pos));
@@ -237,26 +238,25 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
*/
static PyObject *pyReverseOffset(__attribute__((unused)) PyObject *self,
PyObject *args) {
- /* input */
+ /* input variables. */
char *filename = NULL;
int verbose = 0;
- /* parse arguments */
-
+ /* parse the arguments. */
if (!PyArg_ParseTuple(args, "s|i", &filename, &verbose)) return NULL;
- /* initialize the reader (and reverse the offset if necessary) */
+ /* initialize the reader which reverse the offset if necessary. */
struct logger_reader reader;
logger_reader_init(&reader, filename, verbose);
- /* Free the reader */
+ /* Free the reader. */
logger_reader_free(&reader);
return Py_BuildValue("");
}
-/* definition of the method table */
+/* definition of the method table. */
static PyMethodDef libloggerMethods[] = {
{"loadFromIndex", loadFromIndex, METH_VARARGS,
diff --git a/logger/logger_reader.c b/logger/logger_reader.c
index 7020b5de196bc5b6fb624d4c52ecc4ae7152469c..d1e5eaab42bb3bbd752e816cf90c163c5a3f3bc7 100644
--- a/logger/logger_reader.c
+++ b/logger/logger_reader.c
@@ -30,10 +30,10 @@ void logger_reader_init(struct logger_reader *reader, char *filename, int verbos
if (verbose > 1)
message("Initializing the reader");
- /* Initialize the reader variables */
+ /* Initialize the reader variables. */
reader->verbose = verbose;
- /* Initialize the log file */
+ /* Initialize the log file. */
logger_logfile_init_from_file(&reader->log, filename, reader,
/* only_header */ 0);
@@ -47,6 +47,44 @@ void logger_reader_init(struct logger_reader *reader, char *filename, int verbos
* @param reader The #logger_reader.
*/
void logger_reader_free(struct logger_reader *reader) {
- /* Free the log */
+ /* Free the log. */
logger_logfile_free(&reader->log);
}
+
+/**
+ * @brief Read a record (timestamp or particle)
+ *
+ * @param reader The #reader.
+ * @param lp (out) The #logger_particle (if the record is a particle).
+ * @param time (out) The time read (if the record is a timestamp).
+ * @param is_particle Is the record a particle (or a timestamp)?
+ * @param offset The offset in the file.
+ *
+ * @return The offset after this record.
+ */
+size_t reader_read_record(struct logger_reader *reader, struct logger_particle *lp,
+ double *time, int *is_particle, size_t offset) {
+
+ struct logger_logfile *log = &reader->log;
+
+ /* Read mask to find out if timestamp or particle. */
+ size_t mask = 0;
+ logger_loader_io_read_mask(&log->header, log->log.map + offset, &mask, NULL);
+
+ /* Check if timestamp or not. */
+ int ind = header_get_field_index(&log->header, "timestamp");
+ if (ind == -1) {
+ error("File header does not contain a mask for time");
+ }
+ if (log->header.masks[ind].mask == mask) {
+ *is_particle = 0;
+ integertime_t int_time = 0;
+ offset = time_read(&int_time, time, reader, offset);
+ }
+ else {
+ *is_particle = 1;
+ offset = logger_particle_read(lp, reader, offset, *time, logger_reader_const);
+ }
+
+ return offset;
+}
diff --git a/logger/logger_reader.h b/logger/logger_reader.h
index ab20f5008af2192c89341efc1a878d67bf301ff0..863327bc6d6b4c5ebe4ba31de31596680825935e 100644
--- a/logger/logger_reader.h
+++ b/logger/logger_reader.h
@@ -41,8 +41,10 @@
#ifndef __LOGGER_LOGGER_READER_H__
#define __LOGGER_LOGGER_READER_H__
+#include "logger_loader_io.h"
#include "logger_logfile.h"
#include "logger_index.h"
+#include "logger_particle.h"
/**
* @brief Main structure of the logger.
@@ -55,20 +57,21 @@
*/
struct logger_reader {
- /* Time of each index file #TODO */
+ /* Time of each index file. #TODO */
double *times;
- /* Information contained in the index file */
+ /* Information contained in the index file. */
struct logger_index index;
- /* Informations contained in the file header */
+ /* Informations contained in the file header. */
struct logger_logfile log;
- /* Level of verbosity */
+ /* Level of verbosity. */
int verbose;
};
void logger_reader_init(struct logger_reader *reader, char *filename, int verbose);
void logger_reader_free(struct logger_reader *reader);
-
+size_t reader_read_record(struct logger_reader *reader, struct logger_particle *lp,
+ double *time, int *is_particle, size_t offset);
#endif // __LOGGER_LOGGER_READER_H__
diff --git a/logger/logger_time.c b/logger/logger_time.c
index 96bdc6267e60d9948a7f76e0074045b956cc8264..0717c2459c8adae992ef7f2c8a259563ff48fa43 100644
--- a/logger/logger_time.c
+++ b/logger/logger_time.c
@@ -42,7 +42,7 @@ size_t time_read(integertime_t *int_time, double *time, const struct logger_read
*int_time = 0;
*time = 0;
- /* read record header */
+ /* read record header. */
map = logger_loader_io_read_mask(h, map + offset, &mask, &prev_offset);
#ifdef SWIFT_DEBUG_CHECKS
@@ -55,7 +55,7 @@ size_t time_read(integertime_t *int_time, double *time, const struct logger_read
if (h->masks[ind].mask != mask) error("Not a time record");
#endif
- /* read the record */
+ /* read the record. */
map = logger_loader_io_read_data(map, sizeof(unsigned long long int), int_time);
map = logger_loader_io_read_data(map, sizeof(double), time);
@@ -72,7 +72,7 @@ size_t time_read(integertime_t *int_time, double *time, const struct logger_read
*/
size_t time_offset_first_record(const struct header *h) {
- /* Initialize a few variables */
+ /* Initialize a few variables. */
size_t offset = h->offset_first_record;
void *map = h->log->log.map;
@@ -114,10 +114,10 @@ void time_array_populate(struct time_array *t, struct logger_logfile *log) {
integertime_t int_time = 0;
double time = 0;
- /* get file size */
+ /* get file size. */
size_t file_size = log->log.file_size;
- /* get first time stamp */
+ /* get first time stamp. */
size_t offset = time_offset_first_record(&log->header);
while (offset < file_size) {
/* read current time record and store it. */
@@ -127,7 +127,7 @@ void time_array_populate(struct time_array *t, struct logger_logfile *log) {
t->int_time = int_time;
t->time = time;
- /* get next record */
+ /* get next record. */
int test = tools_get_next_record(&log->header, log->log.map, &offset,
log->log.file_size);
if (test == -1) break;
@@ -140,7 +140,7 @@ void time_array_populate(struct time_array *t, struct logger_logfile *log) {
t = tmp;
}
- /* free unused time_array */
+ /* free unused time_array. */
struct time_array *tmp = t->prev;
tmp->next = NULL;
free(t);
@@ -188,7 +188,7 @@ struct time_array *time_array_get_time_array(const struct time_array *t,
if (!t) error("NULL pointer");
#endif
const struct time_array *tmp;
- /* Find the time_array with the correct offset */
+ /* Find the time_array with the correct offset. */
for(tmp = t; tmp->next && tmp->offset <= offset; tmp = tmp->next)
{}
diff --git a/logger/logger_time.h b/logger/logger_time.h
index 351d4936856de573d3276a7beb1365ff6efcaa4c..4e35ad025782de3ca617a191e0677e8b3af454ee 100644
--- a/logger/logger_time.h
+++ b/logger/logger_time.h
@@ -45,19 +45,19 @@ struct logger_reader;
* #time_array_count.
*/
struct time_array {
- /* Pointer to next element */
+ /* Pointer to next element. */
void *next;
- /* Pointer to prev element */
+ /* Pointer to prev element. */
void *prev;
- /* Integertime of this time record */
+ /* Integertime of this time record. */
integertime_t int_time;
- /* Double time of this time record */
+ /* Double time of this time record. */
double time;
- /* Offset in the file of this time record */
+ /* Offset in the file of this time record. */
size_t offset;
};
diff --git a/logger/logger_tools.c b/logger/logger_tools.c
index 34c1e9ad724829779609bcaa0909b131b6ec3523..81e2b36a5f5ba60dc2fe3df15a20bed58dd06006 100644
--- a/logger/logger_tools.c
+++ b/logger/logger_tools.c
@@ -58,12 +58,12 @@ int _tools_get_next_record_forward(const struct header *h, void *map,
size_t *offset) {
size_t diff_offset = 0;
- /* read offset */
+ /* Read the offset. */
map = logger_loader_io_read_mask(h, map + *offset, NULL, &diff_offset);
if (diff_offset == 0) return -1;
- /* set absolute offset */
+ /* Set the absolute offset. */
*offset += diff_offset;
return 0;
}
@@ -120,19 +120,19 @@ size_t tools_reverse_offset(const struct header *h, void *file_map, size_t offse
const size_t cur_offset = offset;
void *map = file_map;
- /* read mask + offset */
+ /* read mask + offset. */
map = logger_loader_io_read_mask(h, map + offset, &mask, &prev_offset);
- /* write offset of zero (in case it is the last record) */
+ /* write offset of zero (in case it is the last record). */
const size_t zero = 0;
map -= LOGGER_OFFSET_SIZE;
map = logger_loader_io_write_data(map, LOGGER_OFFSET_SIZE, &zero);
- /* set offset after current record */
+ /* set offset after current record. */
map += header_get_record_size_from_mask(h, mask);
size_t after_current_record = (size_t) (map - file_map);
- /* first records do not have a previous partner */
+ /* first records do not have a previous partner. */
if (prev_offset == cur_offset)
return after_current_record;
@@ -140,7 +140,7 @@ size_t tools_reverse_offset(const struct header *h, void *file_map, size_t offse
error("Unexpected offset, header %lu, current %lu", prev_offset,
cur_offset);
- /* modify previous offset */
+ /* modify previous offset. */
map = file_map + cur_offset - prev_offset + LOGGER_MASK_SIZE;
map = logger_loader_io_write_data(map, LOGGER_OFFSET_SIZE, &prev_offset);
@@ -149,7 +149,9 @@ size_t tools_reverse_offset(const struct header *h, void *file_map, size_t offse
map -= LOGGER_MASK_SIZE + LOGGER_OFFSET_SIZE;
logger_loader_io_read_mask(h, map, &prev_mask, NULL);
- if (prev_mask != mask)
+ /* Check if we are not mixing time stamp and particles */
+ if ((prev_mask != 128 && mask == 128) ||
+ (prev_mask == 128 && mask != 128))
error("Unexpected mask: %lu, got %lu", mask, prev_mask);
#endif // SWIFT_DEBUG_CHECKS
@@ -180,10 +182,10 @@ size_t tools_check_record_consistency(const struct logger_reader *reader, size_t
size_t mask;
size_t pointed_offset;
- /* read mask + offset */
+ /* read mask + offset. */
map = logger_loader_io_read_mask(h, map, &mask, &pointed_offset);
- /* get absolute offset */
+ /* get absolute offset. */
if (header_is_forward(h))
pointed_offset += offset;
else if (header_is_backward(h)) {
@@ -196,18 +198,19 @@ size_t tools_check_record_consistency(const struct logger_reader *reader, size_t
error("Offset are corrupted");
}
- /* set offset after current record */
+ /* set offset after current record. */
map += header_get_record_size_from_mask(h, mask);
if (pointed_offset == offset || pointed_offset == 0)
return (size_t) (map - file_init);
- /* read mask of the pointed record */
+ /* read mask of the pointed record. */
size_t pointed_mask = 0;
logger_loader_io_read_mask(h, file_init + pointed_offset, &pointed_mask, NULL);
- /* check masks */
- if (pointed_mask != mask)
+ /* check if not mixing time stamp and particles. */
+ if ((pointed_mask != 128 && mask == 128) ||
+ (pointed_mask == 128 && mask != 128))
error("Error in the offset (mask %lu at %lu != %lu at %lu)", mask, offset,
pointed_mask, pointed_offset);
diff --git a/logger/tests/testLogfileHeader.c b/logger/tests/testLogfileHeader.c
index 069a83122bd133ffa6c63ff389429c3c4b5e1304..a97eee0ade578b4c60a81626f931c3d6d9662217 100644
--- a/logger/tests/testLogfileHeader.c
+++ b/logger/tests/testLogfileHeader.c
@@ -30,7 +30,7 @@ int main(int argc, char *argv[]) {
message("Generating the dump.");
/* Create required structures. */
- struct logger log;
+ struct logger_writer log;
struct swift_params params;
char filename[200] = "testLogfileHeader.yml";
@@ -40,7 +40,7 @@ int main(int argc, char *argv[]) {
/* Initialize the logger. */
logger_init(&log, ¶ms);
- /* get dump filename */
+ /* get dump filename. */
char dump_filename[PARSER_MAX_LINE_SIZE];
strcpy(dump_filename, log.base_name);
strcat(dump_filename, ".dump");
@@ -48,7 +48,7 @@ int main(int argc, char *argv[]) {
/* Write file header. */
logger_write_file_header(&log);
- /* clean memory */
+ /* clean memory. */
logger_free(&log);
/*
Then read the file.
@@ -60,14 +60,14 @@ int main(int argc, char *argv[]) {
struct logger_logfile *logfile = &reader.log;
logfile->reader = &reader;
- /* Set verbose level */
+ /* Set verbose level. */
reader.verbose = 1;
/* Read the header */
logger_logfile_init_from_file(logfile, dump_filename, &reader,
/* only_header */ 1);
/*
- Finally check everything
+ Finally check everything.
*/
struct header *h = &logfile->header;
diff --git a/logger/tests/testLogfileReader.c b/logger/tests/testLogfileReader.c
index f6ad0e44d37c65113f2ef724b023b68afe8260cb..3f9686e8c45a6a1dea329263b6ea91a3af099e3d 100644
--- a/logger/tests/testLogfileReader.c
+++ b/logger/tests/testLogfileReader.c
@@ -24,6 +24,11 @@
#include "logger_reader.h"
#define number_parts 100
+/* Not all the fields are written at every step.
+ * Here we define how often a few fields are written.
+ */
+#define period_rho 2
+#define period_h 4
/**
* @brief Initialize the particles.
@@ -52,6 +57,9 @@ void init_particles(struct part *p, struct xpart *xp) {
p[i].id = i;
hydro_set_mass(&p[i], 1.5);
xp[i].logger_data.last_offset = 0;
+
+ /* Add time bin in order to skip particles. */
+ p[i].time_bin = (i % 10) + 1;
}
}
@@ -66,33 +74,19 @@ double get_double_time(int step) {
return step * time_base;
}
+
/**
* @brief Write a few particles during multiple time steps.
*
* As only the logger is tested, there is no need to really
* evolve the particles.
*/
-void write_particles(struct logger *log) {
+void write_particles(struct logger_writer *log, struct part *parts, struct xpart *xparts) {
const int number_steps = 100;
- /* Create particles and initialize them. */
- struct part *parts;
- if ((parts = (struct part *)malloc(sizeof(struct part) * number_parts)) == NULL)
- error("Failed to allocate particles array.");
-
- struct xpart *xparts;
- if ((xparts = (struct xpart *)malloc(sizeof(struct xpart) * number_parts)) == NULL)
- error("Failed to allocate xparticles array.");
-
- init_particles(parts, xparts);
-
- /*
- Init logger
- */
-
- /* Do step */
+ /* Loop over all the steps. */
for(int i = 0; i < number_steps; i++) {
integertime_t ti_int = get_integer_time(i);
double ti_double = get_double_time(i);
@@ -104,23 +98,35 @@ void write_particles(struct logger *log) {
* to store the particles in current time step. */
logger_ensure_size(log, number_parts, /* number gpart */0, 0);
- /* Run step */
+ /* Loop over all the particles. */
for(int j = 0; j < number_parts; j++) {
- /* Write particle */
- /* TODO Currently writing everything, should adapt it through time */
- logger_log_part(log, &parts[j],
- logger_mask_data[logger_x].mask |
- logger_mask_data[logger_v].mask |
- logger_mask_data[logger_a].mask |
- logger_mask_data[logger_u].mask |
- logger_mask_data[logger_h].mask |
- logger_mask_data[logger_rho].mask |
- logger_mask_data[logger_consts].mask,
+ /* Skip some particles. */
+ if (i % parts[j].time_bin != 0)
+ continue;
+
+ /* Write a time information to check that the correct particle is read. */
+ parts[j].x[0] = i;
+
+ /* Write this particle. */
+ unsigned int mask = logger_mask_data[logger_x].mask |
+ logger_mask_data[logger_v].mask |
+ logger_mask_data[logger_a].mask |
+ logger_mask_data[logger_u].mask |
+ logger_mask_data[logger_consts].mask;
+
+ int number_particle_step = i / parts[j].time_bin;
+
+ if (number_particle_step % period_h == 0)
+ mask |= logger_mask_data[logger_h].mask;
+ if (number_particle_step % period_rho == 0)
+ mask |= logger_mask_data[logger_rho].mask;
+
+ logger_log_part(log, &parts[j], mask,
&xparts[j].logger_data.last_offset);
}
- // TODO write index files
+ // TODO write index files.
}
/* Mark the current time step in the particle logger file. */
@@ -130,107 +136,112 @@ void write_particles(struct logger *log) {
&log->timestamp_offset);
- /* Cleanup */
- free(parts);
- free(xparts);
}
-/**
- * @brief Read a record (timestamp or particle)
- *
- * @param reader The #reader.
- * @param lp (out) The #logger_particle (if the record is a particle).
- * @param time (out) The time read (if the record is a timestamp).
- * @param is_particle Is the record a particle (or a timestamp)?
- * @param offset The offset in the file.
- *
- * @return The offset after this record.
- */
-size_t read_record(struct logger_reader *reader, struct logger_particle *lp,
- double *time, int *is_particle, size_t offset) {
-
- struct logger_logfile *log = &reader->log;
-
- /* Read mask to find out if timestamp or particle */
- size_t mask = 0;
- logger_loader_io_read_mask(&log->header, log->log.map + offset, &mask, NULL);
-
- /* Check if timestamp or not */
- int ind = header_get_field_index(&log->header, "timestamp");
- if (ind == -1) {
- error("File header does not contain a mask for time");
- }
- if (log->header.masks[ind].mask == mask) {
- *is_particle = 0;
- integertime_t int_time = 0;
- offset = time_read(&int_time, time, reader, offset);
- }
- else {
- *is_particle = 1;
- offset = logger_particle_read(lp, reader, offset, *time, logger_reader_const);
+/** Count the number of active particles. */
+int get_number_active_particles(int step, struct part *p) {
+ int count = 0;
+ for(int i = 0; i < number_parts; i++) {
+ if (step % p[i].time_bin == 0)
+ count += 1;
}
-
- return offset;
+ return count;
}
-
/**
* @brief Check that the reader contains the correct data
*
* @param reader The #logger_reader.
*/
-void check_data(struct logger_reader *reader) {
+void check_data(struct logger_reader *reader, struct part *parts, struct xpart *xparts) {
/* No need to check the header, this is already done in testHeader.c */
- /* Get required structures */
+ /* Get required structures. */
struct logger_logfile *logfile = &reader->log;
struct logger_particle lp;
logger_particle_init(&lp);
- /* Generate the particles again */
- struct part *parts;
- if ((parts = (struct part *)malloc(sizeof(struct part) * number_parts)) == NULL)
- error("Failed to allocate particles array.");
-
- struct xpart *xparts;
- if ((xparts = (struct xpart *)malloc(sizeof(struct xpart) * number_parts)) == NULL)
- error("Failed to allocate xparticles array.");
-
- init_particles(parts, xparts);
-
+ /* Define a few variables */
double time = get_double_time(0);
int is_particle = 0;
- int step = 0;
+ int step = -1;
+
+ /* Number of particle found during this time step. */
+ int count = 0;
+ /* Set it to an impossible value in order to flag it. */
+ const size_t id_flag = 5 * number_parts;
+ size_t previous_id = id_flag;
- /* Loop over each record */
- for(size_t offset = read_record(reader, &lp, &time, &is_particle, logfile->header.offset_first_record);
+ /* Loop over each record. */
+ for(size_t offset = reader_read_record(reader, &lp, &time, &is_particle, logfile->header.offset_first_record);
offset < logfile->log.file_size;
- offset = read_record(reader, &lp, &time, &is_particle, offset)) {
+ offset = reader_read_record(reader, &lp, &time, &is_particle, offset)) {
+ /* Do the particle case */
if (is_particle) {
- /* Check data if it is a particle */
+ count += 1;
+
+ /*
+ Check that we are really increasing the id in the logfile.
+ See the writing part to see that we are always increasing the id.
+ */
+ if (previous_id != id_flag && previous_id >= lp.id) {
+ error("Wrong particle found");
+ previous_id = lp.id;
+ }
+
+ /* Get the corresponding particle */
if (lp.id >= number_parts)
error("Wrong id %zi", lp.id);
struct part *p = &parts[lp.id];
+ /* Check the record's data. */
for(int i = 0; i < 3; i++) {
- assert(p->x[i] == lp.pos[i]);
+ /* in the first index, we are storing the step information. */
+ if (i == 0)
+ assert(step == lp.pos[i]);
+ else
+ assert(p->x[i] == lp.pos[i]);
assert(p->v[i] == lp.vel[i]);
assert(p->a_hydro[i] == lp.acc[i]);
}
assert(p->entropy == lp.entropy);
- assert(p->h == lp.h);
- assert(p->rho == lp.density);
assert(p->mass == lp.mass);
+
+ /* Check optional fields. */
+ int number_steps = step / p->time_bin;
+ if (number_steps % period_h == 0) {
+ assert(p->h == lp.h);
+ }
+ else {
+ assert(-1 == lp.h);
+ }
+ if (number_steps % period_rho == 0) {
+ assert(p->rho == lp.density);
+ }
+ else {
+ assert(-1 == lp.density);
+ }
}
+ /* Time stamp case. */
else {
- /* Check data if it is a timestamp */
- assert(time == get_double_time(step));
+
+ /* Check if we have the current amount of particles in previous step. */
+ if (step != -1 && count != get_number_active_particles(step, parts))
+ error("The reader did not find the correct number of particles during step %i", step);
step += 1;
+
+ /* Reset some variables. */
+ previous_id = id_flag;
+ count = 0;
+
+ /* Check the record's data. */
+ assert(time == get_double_time(step));
+
}
}
@@ -246,17 +257,28 @@ int main(int argc, char *argv[]) {
message("Generating the dump.");
/* Create required structures. */
- struct logger log;
+ struct logger_writer log;
struct swift_params params;
char filename[200] = "testLogfileReader.yml";
/* Read parameters. */
parser_read_file(filename, ¶ms);
+ /* Initialize the particles. */
+ struct part *parts;
+ if ((parts = (struct part *)malloc(sizeof(struct part) * number_parts)) == NULL)
+ error("Failed to allocate particles array.");
+
+ struct xpart *xparts;
+ if ((xparts = (struct xpart *)malloc(sizeof(struct xpart) * number_parts)) == NULL)
+ error("Failed to allocate xparticles array.");
+
+ init_particles(parts, xparts);
+
/* Initialize the logger. */
logger_init(&log, ¶ms);
- /* get dump filename */
+ /* get dump filename. */
char dump_filename[PARSER_MAX_LINE_SIZE];
message("%s", log.base_name);
strcpy(dump_filename, log.base_name);
@@ -266,7 +288,7 @@ int main(int argc, char *argv[]) {
logger_write_file_header(&log);
/* Write particles. */
- write_particles(&log);
+ write_particles(&log, parts, xparts);
/* clean memory */
logger_free(&log);
@@ -279,17 +301,21 @@ int main(int argc, char *argv[]) {
/* Generate required structure for reading. */
struct logger_reader reader;
- /* Set verbose level */
+ /* Set verbose level. */
reader.verbose = 1;
- /* Read the header */
+ /* Read the header. */
logger_reader_init(&reader, dump_filename, /* verbose */ 1);
/*
- Finally check everything
+ Finally check everything.
*/
- check_data(&reader);
+ check_data(&reader, parts, xparts);
+
+ /* Do some cleanup. */
+ free(parts);
+ free(xparts);
return 0;
}
diff --git a/src/engine.c b/src/engine.c
index 00cd294c4ad764341b010e0fa4e2041e7a285d37..2b9cbd3895c21246c3f89fe1b69436e4a84185cb 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -5009,7 +5009,7 @@ void engine_init(struct engine *e, struct space *s, struct swift_params *params,
e->total_nr_tasks = 0;
#if defined(WITH_LOGGER)
- e->logger = (struct logger *)malloc(sizeof(struct logger));
+ e->logger = (struct logger_writer *)malloc(sizeof(struct logger_writer));
logger_init(e->logger, params);
#endif
diff --git a/src/engine.h b/src/engine.h
index 3c74f89dfcade93bb67d21eb6607cdd4cb80155d..3484336039c64baa43469b1152f1856f70ee2823 100644
--- a/src/engine.h
+++ b/src/engine.h
@@ -379,7 +379,7 @@ struct engine {
struct repartition *reparttype;
#ifdef WITH_LOGGER
- struct logger *logger;
+ struct logger_writer *logger;
#endif
/* How many steps have we done with the same set of tasks? */
diff --git a/src/logger.c b/src/logger.c
index 078f0a6e38b830c919ec6f28861f71120cef6e08..f46cdcf9e89b3d80f096f5429fbd9fad4a280193 100644
--- a/src/logger.c
+++ b/src/logger.c
@@ -44,41 +44,41 @@
/*
* Thoses are definitions from the format and therefore should not be changed!
*/
-/* number of bytes for a mask */
+/* Number of bytes for a mask. */
// TODO change this to number of bits
#define logger_mask_size 1
-/* number of bits for chunk header */
+/* Number of bits for chunk header. */
#define logger_header_bytes 8
-/* number bytes for an offset */
+/* Number bytes for an offset. */
#define logger_offset_size logger_header_bytes - logger_mask_size
-/* number of bytes for the file format information */
+/* Number of bytes for the file format information. */
#define logger_format_size 20
-/* number of bytes for the labels in the header */
+/* Number of bytes for the labels in the header. */
#define logger_label_size 20
char logger_file_format[logger_format_size] = "SWIFT_LOGGER";
const struct mask_data logger_mask_data[logger_count_mask] = {
- /* Particle's position */
+ /* Particle's position. */
{3 * sizeof(double), 1 << logger_x, "positions"},
- /* Particle's velocity */
+ /* Particle's velocity. */
{3 * sizeof(float), 1 << logger_v, "velocities"},
- /* Particle's acceleration */
+ /* Particle's acceleration. */
{3 * sizeof(float), 1 << logger_a, "accelerations"},
- /* Particle's entropy */
+ /* Particle's entropy. */
{sizeof(float), 1 << logger_u, "entropy"},
- /* Particle's smoothing length */
+ /* Particle's smoothing length. */
{sizeof(float), 1 << logger_h, "smoothing length"},
- /* Particle's density */
+ /* Particle's density. */
{sizeof(float), 1 << logger_rho, "density"},
- /* Particle's constants: mass (float) and ID (long long) */
+ /* Particle's constants: mass (float) and ID (long long). */
{sizeof(float) + sizeof(long long), 1 << logger_consts, "consts"},
/* Simulation time stamp: integertime and double time (e.g. scale
- factor or time) */
+ factor or time). */
{sizeof(integertime_t) + sizeof(double), 1 << logger_timestamp,
"timestamp"}};
@@ -96,11 +96,11 @@ const struct mask_data logger_mask_data[logger_count_mask] = {
*/
char *logger_write_chunk_header(char *buff, const unsigned int *mask,
const size_t *offset, const size_t offset_new) {
- /* write mask */
+ /* write mask. */
memcpy(buff, mask, logger_mask_size);
buff += logger_mask_size;
- /* write offset */
+ /* write offset. */
size_t diff_offset = offset_new - *offset;
memcpy(buff, &diff_offset, logger_offset_size);
buff += logger_offset_size;
@@ -109,7 +109,7 @@ char *logger_write_chunk_header(char *buff, const unsigned int *mask,
}
/**
- * @brief Write to the dump
+ * @brief Write to the dump.
*
* @param d #dump file
* @param offset (return) offset of the data
@@ -118,13 +118,13 @@ char *logger_write_chunk_header(char *buff, const unsigned int *mask,
*/
void logger_write_data(struct dump *d, size_t *offset, size_t size,
const void *p) {
- /* get buffer */
+ /* get buffer. */
char *buff = dump_get(d, size, offset);
- /* write data to the buffer */
+ /* write data to the buffer. */
memcpy(buff, p, size);
- /* Update offset to end of chunk */
+ /* Update offset to end of chunk. */
*offset += size;
}
@@ -168,15 +168,15 @@ int logger_compute_chunk_size(unsigned int mask) {
* @param log The #logger
* @param e The #engine
*/
-void logger_log_all(struct logger *log, const struct engine *e) {
+void logger_log_all(struct logger_writer *log, const struct engine *e) {
- /* Ensure that enough space is available */
+ /* Ensure that enough space is available. */
logger_ensure_size(log, e->total_nr_parts, e->total_nr_gparts, 0);
#ifdef SWIFT_DEBUG_CHECKS
message("Need to implement stars");
#endif
- /* some constants */
+ /* some constants. */
const struct space *s = e->s;
const unsigned int mask =
logger_mask_data[logger_x].mask | logger_mask_data[logger_v].mask |
@@ -184,17 +184,17 @@ void logger_log_all(struct logger *log, const struct engine *e) {
logger_mask_data[logger_h].mask | logger_mask_data[logger_rho].mask |
logger_mask_data[logger_consts].mask;
- /* loop over all parts */
+ /* 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);
s->xparts[i].logger_data.steps_since_last_output = 0;
}
- /* loop over all gparts */
+ /* loop over all gparts. */
if (e->total_nr_gparts > 0) error("Not implemented");
- /* loop over all sparts */
+ /* loop over all sparts. */
// TODO
}
@@ -207,7 +207,7 @@ void logger_log_all(struct logger *log, const struct engine *e) {
* @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,
+void logger_log_part(struct logger_writer *log, const struct part *p,
unsigned int mask, size_t *offset) {
/* Make sure we're not writing a timestamp. */
@@ -286,7 +286,7 @@ void logger_log_part(struct logger *log, const struct part *p,
* @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,
+void logger_log_gpart(struct logger_writer *log, const struct gpart *p,
unsigned int mask, size_t *offset) {
/* Make sure we're not writing a timestamp. */
@@ -328,7 +328,7 @@ void logger_log_gpart(struct logger *log, const struct gpart *p,
/* Particle constants, which is a bit more complicated. */
if (mask & logger_mask_data[logger_consts].mask) {
- // TODO make it dependent of logger_mask_data
+ // TODO make it dependent of logger_mask_data.
memcpy(buff, &p->mass, sizeof(float));
buff += sizeof(float);
memcpy(buff, &p->id_or_neg_offset, sizeof(long long));
@@ -348,7 +348,7 @@ void logger_log_gpart(struct logger *log, const struct gpart *p,
* @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,
+void logger_log_timestamp(struct logger_writer *log, integertime_t timestamp,
double time, size_t *offset) {
struct dump *dump = &log->dump;
@@ -365,11 +365,11 @@ void logger_log_timestamp(struct logger *log, integertime_t timestamp,
buff = logger_write_chunk_header(buff, &mask, offset, offset_new);
/* Store the timestamp. */
- // TODO make it dependent of logger_mask_data
+ // TODO make it dependent of logger_mask_data.
memcpy(buff, ×tamp, sizeof(integertime_t));
buff += sizeof(integertime_t);
- /* Store the time */
+ /* Store the time. */
memcpy(buff, &time, sizeof(double));
/* Update the log message offset. */
@@ -387,21 +387,21 @@ void logger_log_timestamp(struct logger *log, integertime_t timestamp,
* @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,
+void logger_ensure_size(struct logger_writer *log, size_t total_nr_parts,
size_t total_nr_gparts, size_t total_nr_sparts) {
- /* count part memory */
+ /* count part memory. */
size_t limit = log->max_chunk_size;
limit *= total_nr_parts;
- /* count gpart memory */
+ /* count gpart memory. */
if (total_nr_gparts > 0) error("Not implemented");
- /* count spart memory */
+ /* count spart memory. */
if (total_nr_sparts > 0) error("Not implemented");
- /* ensure enough space in dump */
+ /* ensure enough space in dump. */
dump_ensure(&log->dump, limit, log->buffer_scale * limit);
}
@@ -411,8 +411,8 @@ void logger_ensure_size(struct logger *log, size_t total_nr_parts,
* @param log The #logger
* @param params The #swift_params
*/
-void logger_init(struct logger *log, struct swift_params *params) {
- /* read parameters */
+void logger_init(struct logger_writer *log, struct swift_params *params) {
+ /* read parameters. */
log->delta_step = parser_get_param_int(params, "Logger:delta_step");
size_t buffer_size =
parser_get_opt_param_float(params, "Logger:initial_buffer_size", 0.5) *
@@ -421,24 +421,24 @@ void logger_init(struct logger *log, struct swift_params *params) {
parser_get_opt_param_float(params, "Logger:buffer_scale", 10);
parser_get_param_string(params, "Logger:basename", log->base_name);
- /* set initial value of parameters */
+ /* set initial value of parameters. */
log->timestamp_offset = 0;
- /* generate dump filename */
+ /* generate dump filename. */
char logger_name_file[PARSER_MAX_LINE_SIZE];
strcpy(logger_name_file, log->base_name);
strcat(logger_name_file, ".dump");
- /* Compute max size for a particle chunk */
+ /* Compute max size for a particle chunk. */
int max_size = logger_offset_size + logger_mask_size;
- /* Loop over all fields except timestamp */
+ /* Loop over all fields except timestamp. */
for (int i = 0; i < logger_count_mask - 1; i++) {
max_size += logger_mask_data[i].size;
}
log->max_chunk_size = max_size;
- /* init dump */
+ /* init dump. */
dump_init(&log->dump, logger_name_file, buffer_size);
}
@@ -447,7 +447,7 @@ void logger_init(struct logger *log, struct swift_params *params) {
*
* @param log The #logger
*/
-void logger_free(struct logger *log) { dump_close(&log->dump); }
+void logger_free(struct logger_writer *log) { dump_close(&log->dump); }
/**
* @brief Write a file header to a logger file
@@ -455,9 +455,9 @@ void logger_free(struct logger *log) { dump_close(&log->dump); }
* @param log The #logger
*
*/
-void logger_write_file_header(struct logger *log) {
+void logger_write_file_header(struct logger_writer *log) {
- /* get required variables */
+ /* get required variables. */
struct dump *dump = &log->dump;
size_t file_offset = dump->file_offset;
@@ -467,45 +467,45 @@ void logger_write_file_header(struct logger *log) {
"The logger is not empty."
"This function should be called before writing anything in the logger");
- /* Write format information */
+ /* Write format information. */
logger_write_data(dump, &file_offset, logger_format_size, &logger_file_format);
- /* Write the major version number */
+ /* Write the major version number. */
int major = logger_major_version;
logger_write_data(dump, &file_offset, sizeof(int), &major);
- /* Write the minor version number */
+ /* Write the minor version number. */
int minor = logger_minor_version;
logger_write_data(dump, &file_offset, sizeof(int), &minor);
- /* write offset direction */
+ /* write offset direction. */
const int reversed = 0;
logger_write_data(dump, &file_offset, sizeof(int), &reversed);
- /* placeholder to write the offset of the first log here */
+ /* placeholder to write the offset of the first log here. */
char *skip_header = dump_get(dump, logger_offset_size, &file_offset);
- /* write number of bytes used for names */
+ /* write number of bytes used for names. */
const unsigned int label_size = logger_label_size;
logger_write_data(dump, &file_offset, sizeof(unsigned int), &label_size);
- /* write number of masks */
+ /* write number of masks. */
const unsigned int count_mask = logger_count_mask;
logger_write_data(dump, &file_offset, sizeof(unsigned int), &count_mask);
- /* write masks */
- // loop over all mask type
+ /* write masks. */
+ // loop over all mask type.
for (int i = 0; i < logger_count_mask; i++) {
- // mask name
+ // mask name.
logger_write_data(dump, &file_offset, logger_label_size,
&logger_mask_data[i].name);
- // mask size
+ // mask size.
logger_write_data(dump, &file_offset, sizeof(unsigned int),
&logger_mask_data[i].size);
}
- /* last step: write first offset */
+ /* last step: write first offset. */
memcpy(skip_header, &file_offset, logger_offset_size);
}
@@ -595,7 +595,7 @@ int logger_read_part(struct part *p, size_t *offset, const char *buff) {
/* Particle constants, which is a bit more complicated. */
if (mask & logger_mask_data[logger_rho].mask) {
- // TODO make it dependent of logger_mask_data
+ // TODO make it dependent of logger_mask_data.
memcpy(&p->mass, buff, sizeof(float));
buff += sizeof(float);
memcpy(&p->id, buff, sizeof(long long));
@@ -698,7 +698,7 @@ int logger_read_timestamp(unsigned long long int *t, double *time,
error("Timestamp message contains extra fields.");
/* Copy the timestamp value from the buffer. */
- // TODO make it dependent of logger_mask_data
+ // TODO make it dependent of logger_mask_data.
memcpy(t, buff, sizeof(unsigned long long int));
buff += sizeof(unsigned long long int);
diff --git a/src/logger.h b/src/logger.h
index 1df13296bb339b9648caf3a5877d6cebd6095808..0ba3408e99a31c0cb34cb7553f90f113696a8de2 100644
--- a/src/logger.h
+++ b/src/logger.h
@@ -28,11 +28,10 @@
#include "timeline.h"
#include "units.h"
-/* Forward declaration */
+/* Forward declaration. */
struct dump;
struct gpart;
struct part;
-/* TODO remove dependency */
struct engine;
#define logger_major_version 0
@@ -85,18 +84,18 @@ enum logger_masks_number {
logger_h = 4,
logger_rho = 5,
logger_consts = 6,
- logger_timestamp = 7, /* expect it to be before count */
- logger_count_mask = 8, /* Need to be the last */
+ logger_timestamp = 7, /* expect it to be before count. */
+ logger_count_mask = 8, /* Need to be the last. */
} __attribute__((packed));
struct mask_data {
- /* Number of bytes for a mask */
+ /* Number of bytes for a mask. */
int size;
- /* Mask value */
+ /* Mask value. */
unsigned int mask;
- /* name of the mask */
+ /* Name of the mask. */
char name[100];
};
@@ -105,51 +104,51 @@ extern const struct mask_data logger_mask_data[logger_count_mask];
/* Size of the strings. */
#define logger_string_length 200
-/* structure containing global data */
-struct logger {
- /* Number of particle steps between dumping a chunk of data */
+/* structure containing global data. */
+struct logger_writer {
+ /* Number of particle steps between dumping a chunk of data. */
short int delta_step;
- /* Logger basename */
+ /* Logger basename. */
char base_name[logger_string_length];
- /* Dump file */
+ /* Dump file (In the reader, the dump is cleaned, therefore it is renamed logfile). */
struct dump dump;
- /* timestamp offset for logger*/
+ /* timestamp offset for logger. */
size_t timestamp_offset;
- /* scaling factor when buffer is too small */
+ /* scaling factor when buffer is too small. */
float buffer_scale;
- /* Size of a chunk if every mask are activated */
+ /* Size of a chunk if every mask are activated. */
int max_chunk_size;
} SWIFT_STRUCT_ALIGN;
-/* required structure for each particle type */
+/* required structure for each particle type. */
struct logger_part_data {
- /* Number of particle updates since last output */
+ /* Number of particle updates since last output. */
int steps_since_last_output;
- /* offset of last particle log entry */
+ /* offset of last particle log entry. */
size_t last_offset;
};
/* 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,
+void logger_log_all(struct logger_writer *log, const struct engine *e);
+void logger_log_part(struct logger_writer *log, const struct part *p,
unsigned int mask, size_t *offset);
-void logger_log_gpart(struct logger *log, const struct gpart *p,
+void logger_log_gpart(struct logger_writer *log, const struct gpart *p,
unsigned int mask, size_t *offset);
-void logger_init(struct logger *log, struct swift_params *params);
-void logger_free(struct logger *log);
-void logger_log_timestamp(struct logger *log, integertime_t t, double time,
+void logger_init(struct logger_writer *log, struct swift_params *params);
+void logger_free(struct logger_writer *log);
+void logger_log_timestamp(struct logger_writer *log, integertime_t t, double time,
size_t *offset);
-void logger_ensure_size(struct logger *log, size_t total_nr_parts,
+void logger_ensure_size(struct logger_writer *log, size_t total_nr_parts,
size_t total_nr_gparts, size_t total_nr_sparts);
-void logger_write_file_header(struct logger *log);
+void logger_write_file_header(struct logger_writer *log);
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);
@@ -169,12 +168,13 @@ INLINE static void logger_part_data_init(struct logger_part_data *logger) {
/**
* @brief Should this particle write its data now ?
*
- * @param xp The #xpart.
- * @param e The #engine containing information about the current time.
- * @return 1 if the #part should write, 0 otherwise.
+ * @param logger_data The #logger_part_data of a particle.
+ * @param log The #logger.
+ *
+ * @return 1 if the particule should be writen, 0 otherwise.
*/
__attribute__((always_inline)) INLINE static int logger_should_write(
- const struct logger_part_data *logger_data, const struct logger *log) {
+ const struct logger_part_data *logger_data, const struct logger_writer *log) {
return (logger_data->steps_since_last_output > log->delta_step);
}
diff --git a/src/logger_io.c b/src/logger_io.c
index 3cef3497b2912411cea6763f5418bc76a7f5ece0..9a4f10ea2e256e738f29d92057c824e7d948d735 100644
--- a/src/logger_io.c
+++ b/src/logger_io.c
@@ -87,7 +87,7 @@ void write_index_single(struct engine* e, const char* baseName,
// struct spart* sparts = e->s->sparts;
static int outputCount = 0;
- struct logger* log = e->logger;
+ struct logger_writer* log = e->logger;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;