diff --git a/src/csds_loader_io.h b/src/csds_loader_io.h
index ca7ae26b93a29442dca3a95ccb55db619abbfb1c..91b60bc44584b788bfc41c0fd5e608dc3ad81400 100644
--- a/src/csds_loader_io.h
+++ b/src/csds_loader_io.h
@@ -51,6 +51,7 @@ void csds_loader_io_munmap_file(struct mapped_file *map);
/**
* @brief read a mask with its offset.
*
+ * @param h #header file structure.
* @param data Pointer to the data to read.
* @param mask (output) mask read from the data.
* @param diff_offset (output) offset difference to previous/next corresponding
@@ -59,7 +60,7 @@ void csds_loader_io_munmap_file(struct mapped_file *map);
* @return memory after the record header.
*/
__attribute__((always_inline)) INLINE static char *csds_loader_io_read_mask(
- char *data, mask_type *mask, size_t *diff_offset) {
+ const struct header *h, char *data, mask_type *mask, size_t *diff_offset) {
/* read mask */
if (mask) {
*mask = 0;
diff --git a/src/csds_particle.c b/src/csds_particle.c
index a23b831264649463cd011f6f9c89410ba678fa6e..70e62d4a23045c681a8fde6b30bd66ea3f1c9aec 100644
--- a/src/csds_particle.c
+++ b/src/csds_particle.c
@@ -29,6 +29,83 @@
#include <stdio.h>
#include <stdlib.h>
+/**
+ * @brief Read a particle (of any type) record in the log file.
+ *
+ * @param reader The #csds_reader.
+ * @param offset offset of the record to read.
+ * @param output Buffer for the requested field.
+ * @param part_type The particle type.
+ * @param field_read The field to read.
+ * @param derivative The derivative to read (0 for the field).
+ * @param mask (out) The mask of the record.
+ * @param h_offset (out) Difference of offset with the next record.
+ *
+ * @return position after the record.
+ */
+__attribute__((always_inline)) INLINE size_t csds_particle_read_field(
+ const struct csds_reader *reader, size_t offset, void *output,
+ const enum part_type part_type, const struct field_information *field_read,
+ const int derivative, mask_type *mask, size_t *h_offset) {
+
+ /* Get a few pointers. */
+ const struct header *h = &reader->log.header;
+ const struct field_information *fields = h->fields[part_type];
+ char *map = reader->log.log.map;
+
+ *mask = 0;
+ *h_offset = 0;
+
+ /* Read the record's mask. */
+ map = csds_loader_io_read_mask(h, map + offset, mask, h_offset);
+
+ /* Check if it is not a time record. */
+ if (*mask == TIMESTAMP_MASK) {
+ error_python("Cannot read a particle from timestep record.");
+ }
+
+#ifdef SWIFT_DEBUG_CHECKS
+ if (derivative == 1 && field_read->first.field == field_enum_none) {
+ error("Trying to read the non existing first derivative.");
+ }
+ if (derivative == 2 && field_read->second.field == field_enum_none) {
+ error("Trying to read the non existing second derivative.");
+ }
+#endif
+
+ /* Get the position of the field to read */
+ const int position = derivative == 0
+ ? field_read->field.position
+ : derivative == 1 ? field_read->first.position
+ : field_read->second.position;
+
+#ifdef SWIFT_DEBUG_CHECKS
+ if (position < 0) {
+ error("Position not set (derivative %i of %s)", derivative,
+ field_enum_get_name(field_read->field.field));
+ }
+#endif
+
+ /* Read the record and copy it to a particle. */
+ for (int i = 0; i < h->number_fields[part_type]; i++) {
+
+ /* Is the mask present? */
+ if (!(*mask & fields[i].field.mask)) {
+ continue;
+ }
+
+ if (position == i) {
+ /* Read the data. */
+ map = csds_loader_io_read_data(map, fields[i].field.size, output);
+ } else {
+ /* Update the buffer's position. */
+ map += fields[i].field.size;
+ }
+ }
+
+ return map - reader->log.log.map;
+}
+
/**
* @brief Read the special flag of a particle (of any type) in the log file.
*
@@ -47,13 +124,14 @@ csds_particle_read_special_flag(const struct csds_reader *reader, size_t offset,
int *part_type) {
/* Get a few pointers. */
+ const struct header *h = &reader->log.header;
char *map = reader->log.log.map;
*mask = 0;
*h_offset = 0;
/* Read the record's mask. */
- map = csds_loader_io_read_mask(map + offset, mask, h_offset);
+ map = csds_loader_io_read_mask(h, map + offset, mask, h_offset);
/* Check if it is not a time record. */
if (*mask == TIMESTAMP_MASK) {
diff --git a/src/csds_particle.h b/src/csds_particle.h
index 505e42076c40409553573a3e100b62781856e1f8..67fbad442ee005073bc11024b69aacb02c06959b 100644
--- a/src/csds_particle.h
+++ b/src/csds_particle.h
@@ -24,7 +24,6 @@
/* Include the other local files. */
#include "csds_header.h"
-#include "csds_loader_io.h"
#include "csds_parameters.h"
#include "csds_time.h"
@@ -39,6 +38,12 @@ enum csds_reader_type {
csds_reader_lin, /* Linear interpolation. */
};
+size_t csds_particle_read_field(const struct csds_reader *reader, size_t offset,
+ void *output, const enum part_type part_type,
+ const struct field_information *field,
+ const int derivative, mask_type *mask,
+ size_t *h_offset);
+
void csds_particle_interpolate_field(
const double t_before, const struct csds_reader_field *restrict before,
const double t_after, const struct csds_reader_field *restrict after,
@@ -50,80 +55,6 @@ enum csds_special_flags csds_particle_read_special_flag(
const struct csds_reader *reader, size_t offset, mask_type *mask,
size_t *h_offset, int *data, int *part_type);
-/**
- * @brief Read a particle (of any type) record in the log file.
- *
- * @param reader The #csds_reader.
- * @param offset offset of the record to read.
- * @param output Buffer for the requested field.
- * @param part_type The particle type.
- * @param field_read The field to read.
- * @param derivative The derivative to read (0 for the field).
- * @param mask (out) The mask of the record.
- * @param h_offset (out) Difference of offset with the next record.
- *
- * @return position after the record.
- */
-__attribute__((always_inline)) INLINE static size_t csds_particle_read_field(
- size_t offset, void *output, const struct field_information *field_read,
- const int derivative, mask_type *mask, size_t *h_offset,
- const struct field_information *fields, int number_fields, char *log_map) {
-
- char *map = log_map;
-
- *mask = 0;
- *h_offset = 0;
-
- /* Read the record's mask. */
- map = csds_loader_io_read_mask(map + offset, mask, h_offset);
-
- /* Check if it is not a time record. */
- if (*mask == TIMESTAMP_MASK) {
- error_python("Cannot read a particle from timestep record.");
- }
-
-#ifdef SWIFT_DEBUG_CHECKS
- if (derivative == 1 && field_read->first.field == field_enum_none) {
- error("Trying to read the non existing first derivative.");
- }
- if (derivative == 2 && field_read->second.field == field_enum_none) {
- error("Trying to read the non existing second derivative.");
- }
-#endif
-
- /* Get the position of the field to read */
- const int position = derivative == 0
- ? field_read->field.position
- : derivative == 1 ? field_read->first.position
- : field_read->second.position;
-
-#ifdef SWIFT_DEBUG_CHECKS
- if (position < 0) {
- error("Position not set (derivative %i of %s)", derivative,
- field_enum_get_name(field_read->field.field));
- }
-#endif
-
- /* Read the record and copy it to a particle. */
- for (int i = 0; i < number_fields; i++) {
-
- /* Is the mask present? */
- if (!(*mask & fields[i].field.mask)) {
- continue;
- }
-
- if (position == i) {
- /* Read the data. */
- map = csds_loader_io_read_data(map, fields[i].field.size, output);
- } else {
- /* Update the buffer's position. */
- map += fields[i].field.size;
- }
- }
-
- return map - log_map;
-}
-
/**
* @brief Extract the flag and its related data from the data inside a record.
*
diff --git a/src/csds_reader.c b/src/csds_reader.c
index b09e9d7309603722d6c17ddf277d21fe9463ccbf..03546871d0645fa17ce1c63f6768d265ec3d66cf 100644
--- a/src/csds_reader.c
+++ b/src/csds_reader.c
@@ -424,7 +424,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
*/
while (offset < offset_time) {
/* Read the particle. */
- csds_loader_io_read_mask(reader->log.log.map + offset, &mask, &h_offset);
+ csds_loader_io_read_mask(h, reader->log.log.map + offset, &mask, &h_offset);
/* Is the particle removed from the logfile? */
if (mask & SPECIAL_FLAGS_MASK) {
@@ -460,10 +460,8 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
}
/* Read the field */
- csds_particle_read_field(offset_before, output, field_wanted,
- /* derivative */ 0, &mask, &h_offset,
- h->fields[type], h->number_fields[type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset_before, output, type, field_wanted,
+ /* derivative */ 0, &mask, &h_offset);
/* Deal with the first derivative. */
int first_found = field_wanted->first.field != field_enum_none &&
@@ -472,10 +470,9 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
if (first_found) {
/* Read the first derivative */
- csds_particle_read_field(offset_before, first_deriv, field_wanted,
- /* derivative */ 1, &mask, &h_offset,
- h->fields[type], h->number_fields[type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset_before, first_deriv, type,
+ field_wanted, /* derivative */ 1, &mask,
+ &h_offset);
}
/* Deal with the second derivative. */
@@ -486,10 +483,9 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
if (second_found) {
/* Read the first derivative */
- csds_particle_read_field(offset_before, second_deriv, field_wanted,
- /* derivative */ 2, &mask, &h_offset,
- h->fields[type], h->number_fields[type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset_before, second_deriv, type,
+ field_wanted, /* derivative */ 2, &mask,
+ &h_offset);
}
/* Get the time. */
@@ -505,7 +501,8 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
while (1) {
/* Read the particle. */
- csds_loader_io_read_mask(reader->log.log.map + offset, &mask, &h_offset);
+ csds_loader_io_read_mask(h, reader->log.log.map + offset, &mask,
+ &h_offset);
/* Do we have the field? */
if (mask & field_wanted->field.mask) {
@@ -525,10 +522,8 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
char output_after[field_wanted->field.size];
/* Read the field */
- csds_particle_read_field(offset, output_after, field_wanted,
- /* derivative */ 0, &mask, &h_offset,
- h->fields[type], h->number_fields[type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset, output_after, type, field_wanted,
+ /* derivative */ 0, &mask, &h_offset);
/* Deal with the first derivative. */
char first_deriv_after[field_wanted->first.size];
@@ -538,10 +533,9 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
mask & field_wanted->first.mask;
if (first_found) {
/* Read the first derivative */
- csds_particle_read_field(offset, first_deriv_after, field_wanted,
- /*derivative*/ 1, &mask, &h_offset,
- h->fields[type], h->number_fields[type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset, first_deriv_after, type,
+ field_wanted, /*derivative*/ 1, &mask,
+ &h_offset);
}
/* Deal with the second derivative. */
@@ -552,10 +546,9 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
second_found && mask & field_wanted->second.mask;
if (second_found) {
/* Read the second derivative */
- csds_particle_read_field(offset, second_deriv_after, field_wanted,
- /* derivative */ 2, &mask, &h_offset,
- h->fields[type], h->number_fields[type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset, second_deriv_after, type,
+ field_wanted, /* derivative */ 2, &mask,
+ &h_offset);
}
/* Get the time. */
@@ -1092,7 +1085,7 @@ size_t csds_reader_read_record(struct csds_reader *reader, void **output,
size_t h_offset = 0;
/* Read the record's mask. */
- map = csds_loader_io_read_mask(map + offset, &mask, &h_offset);
+ map = csds_loader_io_read_mask(h, map + offset, &mask, &h_offset);
*is_particle = !(mask & TIMESTAMP_MASK);
/* The record is a particle. */
@@ -1100,9 +1093,8 @@ size_t csds_reader_read_record(struct csds_reader *reader, void **output,
size_t offset_tmp = offset;
for (int i = 0; i < h->number_fields[swift_type_gas]; i++) {
offset = csds_particle_read_field(
- offset_tmp, output[i], &h->fields[swift_type_gas][i],
- /* derivative */ 0, &mask, &h_offset, h->fields[swift_type_gas],
- h->number_fields[swift_type_gas], reader->log.log.map);
+ reader, offset_tmp, output[i], swift_type_gas,
+ &h->fields[swift_type_gas][i], /* derivative */ 0, &mask, &h_offset);
}
}
/* The record is a timestamp. */
diff --git a/src/csds_reader_generate_index.c b/src/csds_reader_generate_index.c
index b820dba3e32c2e96dde56b2a9299c9de31566993..eff5397b91efbb8efee0413a0d9be3d9290e73ce 100644
--- a/src/csds_reader_generate_index.c
+++ b/src/csds_reader_generate_index.c
@@ -317,7 +317,7 @@ size_t csds_reader_get_initial_state(const struct csds_reader *reader,
/* Skip the time record */
mask_type time_mask = 0;
- csds_loader_io_read_mask(log->log.map + offset_first, &time_mask, NULL);
+ csds_loader_io_read_mask(h, log->log.map + offset_first, &time_mask, NULL);
const int time_size = header_get_record_size_from_mask(h, time_mask);
offset_first += time_size + size_record_header;
@@ -352,10 +352,8 @@ size_t csds_reader_get_initial_state(const struct csds_reader *reader,
/* Read the particle ID */
int64_t id = 0;
- csds_particle_read_field(offset, &id, field_id,
- /* derivative */ 0, &mask, &prev_offset,
- h->fields[part_type], h->number_fields[part_type],
- reader->log.log.map);
+ csds_particle_read_field(reader, offset, &id, part_type, field_id,
+ /* derivative */ 0, &mask, &prev_offset);
/* Log the particle */
struct index_data item = {id, offset};
@@ -425,6 +423,7 @@ void csds_reader_update_particles_to_next_index_mapper(void *map_data,
struct update_particle_data *data = (struct update_particle_data *)extra_data;
const struct csds_reader *reader = data->reader;
const struct csds_logfile *log = &reader->log;
+ const struct header *h = &log->header;
struct csds_hashmap *current_state = data->current_state;
/* Loop over the particles */
@@ -443,7 +442,7 @@ void csds_reader_update_particles_to_next_index_mapper(void *map_data,
/* Get the full mask */
mask_type full_mask = 0;
size_t h_offset = 0;
- csds_loader_io_read_mask(log->log.map + current_offset, &full_mask,
+ csds_loader_io_read_mask(h, log->log.map + current_offset, &full_mask,
&h_offset);
/* Ensures that a special flag is present in the mask */
@@ -459,7 +458,8 @@ void csds_reader_update_particles_to_next_index_mapper(void *map_data,
/* Get the mask */
mask_type mask = 0;
h_offset = 0;
- csds_loader_io_read_mask(log->log.map + current_offset, &mask, &h_offset);
+ csds_loader_io_read_mask(h, log->log.map + current_offset, &mask,
+ &h_offset);
/* update the offset */
current_offset += h_offset;
@@ -579,7 +579,7 @@ size_t csds_reader_update_state_to_next_index(
int data = 0;
/* Get the mask */
- csds_loader_io_read_mask(log->log.map + offset, &mask, &h_offset);
+ csds_loader_io_read_mask(h, log->log.map + offset, &mask, &h_offset);
/* Go to the next record */
const size_t old_offset = offset;
@@ -613,10 +613,8 @@ size_t csds_reader_update_state_to_next_index(
/* Read the ID */
int64_t id = 0;
- csds_particle_read_field(old_offset, &id, field_id,
- /* derivative */ 0, &mask, &h_offset,
- h->fields[part_type], h->number_fields[part_type],
- reader->log.log.map);
+ csds_particle_read_field(reader, old_offset, &id, part_type, field_id,
+ /* derivative */ 0, &mask, &h_offset);
/* Add the particle to the arrays */
if (flag == csds_flag_change_type || flag == csds_flag_mpi_exit ||
diff --git a/src/csds_time.c b/src/csds_time.c
index 7875af497c0cc190add18cd7d60745d8575a81f3..8e73367d773edc07d7e47d024c8e5da5c2856a91 100644
--- a/src/csds_time.c
+++ b/src/csds_time.c
@@ -95,7 +95,7 @@ size_t time_read(struct time_record *time_record,
time_record->time = 0;
/* read record header. */
- map = csds_loader_io_read_mask(map + offset, &mask, &prev_offset);
+ map = csds_loader_io_read_mask(h, map + offset, &mask, &prev_offset);
/* check if reading a time record. */
if (TIMESTAMP_MASK != mask) error_python("Not a time record.");
@@ -122,7 +122,7 @@ size_t time_offset_first_record(const struct header *h) {
char *map = h->log->log.map;
mask_type mask = 0;
- csds_loader_io_read_mask(map + offset, &mask, NULL);
+ csds_loader_io_read_mask(h, map + offset, &mask, NULL);
if (mask != TIMESTAMP_MASK)
error_python("Log file should begin by timestep.");
diff --git a/src/csds_tools.c b/src/csds_tools.c
index a1f796d92c9e553abe006613aa46082c6875dd06..efdfd1a2732cc1753f466695df5a015a07a9f537 100644
--- a/src/csds_tools.c
+++ b/src/csds_tools.c
@@ -60,7 +60,7 @@ int _tools_get_next_record_forward(const struct header *h, char *map,
size_t diff_offset = 0;
/* Read the offset. */
- map = csds_loader_io_read_mask(map + *offset, NULL, &diff_offset);
+ map = csds_loader_io_read_mask(h, map + *offset, NULL, &diff_offset);
if (diff_offset == 0) return -1;
@@ -91,7 +91,7 @@ int _tools_get_next_record_backward(const struct header *h, char *map,
while (current_offset < file_size) {
mask_type mask = 0;
size_t prev_offset;
- csds_loader_io_read_mask(map + current_offset, &mask, &prev_offset);
+ csds_loader_io_read_mask(h, map + current_offset, &mask, &prev_offset);
prev_offset = current_offset - prev_offset - record_header;
if (*offset == prev_offset) {
@@ -123,7 +123,7 @@ size_t tools_reverse_offset(const struct header *h, char *file_map,
char *map = file_map;
/* read mask + offset. */
- map = csds_loader_io_read_mask(map + offset, &mask, &prev_offset);
+ map = csds_loader_io_read_mask(h, map + offset, &mask, &prev_offset);
/* write offset of zero (in case it is the last record). */
const size_t zero = 0;
@@ -147,7 +147,7 @@ size_t tools_reverse_offset(const struct header *h, char *file_map,
#ifdef SWIFT_DEBUG_CHECKS
mask_type prev_mask = 0;
map = map - CSDS_MASK_SIZE - CSDS_OFFSET_SIZE;
- csds_loader_io_read_mask(map, &prev_mask, NULL);
+ csds_loader_io_read_mask(h, map, &prev_mask, NULL);
/* Check if we are not mixing timestamp and particles */
if ((prev_mask != TIMESTAMP_MASK && mask == TIMESTAMP_MASK) ||
@@ -184,7 +184,7 @@ size_t tools_check_record_consistency(const struct csds_reader *reader,
size_t pointed_offset;
/* read mask + offset. */
- map = csds_loader_io_read_mask(map, &mask, &pointed_offset);
+ map = csds_loader_io_read_mask(h, map, &mask, &pointed_offset);
/* set offset after current record. */
map = map + header_get_record_size_from_mask(h, mask);
@@ -211,7 +211,7 @@ size_t tools_check_record_consistency(const struct csds_reader *reader,
/* read mask of the pointed record. */
mask_type pointed_mask = 0;
- csds_loader_io_read_mask(file_init + pointed_offset, &pointed_mask, NULL);
+ csds_loader_io_read_mask(h, file_init + pointed_offset, &pointed_mask, NULL);
/* check if not mixing timestamp and particles. */
if ((pointed_mask != TIMESTAMP_MASK && mask == TIMESTAMP_MASK) ||