diff --git a/src/chemistry/GEAR/csds_chemistry.c b/src/chemistry/GEAR/csds_chemistry.c
index 9e8a7a5bafb10c183994c190a537a05eb114def4..a06ba2e701cc84cb9ea36b14252aaecd9d823580 100644
--- a/src/chemistry/GEAR/csds_chemistry.c
+++ b/src/chemistry/GEAR/csds_chemistry.c
@@ -24,18 +24,16 @@
#include "csds_tools.h"
/* Hydro part */
-const int chemistry_csds_field_size_part[chemistry_csds_field_part_count] =
- {
- member_size(struct part, chemistry_data.smoothed_metal_mass_fraction) +
- member_size(struct part, chemistry_data.metal_mass),
+const int chemistry_csds_field_size_part[chemistry_csds_field_part_count] = {
+ member_size(struct part, chemistry_data.smoothed_metal_mass_fraction) +
+ member_size(struct part, chemistry_data.metal_mass),
};
int chemistry_csds_local_to_global_part[chemistry_csds_field_part_count];
/* Stellar part */
-const int
- chemistry_csds_field_size_spart[chemistry_csds_field_spart_count] = {
- member_size(struct spart, chemistry_data.metal_mass_fraction),
+const int chemistry_csds_field_size_spart[chemistry_csds_field_spart_count] = {
+ member_size(struct spart, chemistry_data.metal_mass_fraction),
};
int chemistry_csds_local_to_global_spart[chemistry_csds_field_spart_count];
diff --git a/src/chemistry/GEAR/csds_chemistry.h b/src/chemistry/GEAR/csds_chemistry.h
index 43c3b24f32fd46b5c4060a9817d0d3ce18e0abf0..bf5997f190584586432f93ce23693686d5a368d9 100644
--- a/src/chemistry/GEAR/csds_chemistry.h
+++ b/src/chemistry/GEAR/csds_chemistry.h
@@ -29,8 +29,7 @@
#include "csds_python_tools.h"
/* Index of the mask in the header mask array */
-extern int
- chemistry_csds_local_to_global_part[chemistry_csds_field_part_count];
+extern int chemistry_csds_local_to_global_part[chemistry_csds_field_part_count];
extern int
chemistry_csds_local_to_global_spart[chemistry_csds_field_spart_count];
@@ -74,11 +73,13 @@ chemistry_csds_reader_link_derivatives_spart(struct header *head) {}
* @param params The simulation's #csds_parameters.
*/
__attribute__((always_inline)) INLINE static void
-chemistry_csds_interpolate_field_part(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t, const int field,
- const struct csds_parameters *params) {
+chemistry_csds_interpolate_field_part(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
if (t_before > t || t_after < t) {
@@ -92,8 +93,8 @@ chemistry_csds_interpolate_field_part(
switch (field) {
case chemistry_csds_field_part_all:
interpolate_linear_double_ND(t_before, before, t_after, after, output, t,
- 2 * GEAR_CHEMISTRY_ELEMENT_COUNT, /* periodic */0,
- params);
+ 2 * GEAR_CHEMISTRY_ELEMENT_COUNT,
+ /* periodic */ 0, params);
break;
default:
@@ -119,11 +120,13 @@ chemistry_csds_interpolate_field_part(
* @param params The simulation's #csds_parameters.
*/
__attribute__((always_inline)) INLINE static void
-chemistry_csds_interpolate_field_spart(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t, const int field,
- const struct csds_parameters *params) {
+chemistry_csds_interpolate_field_spart(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
diff --git a/src/chemistry/none/csds_chemistry.c b/src/chemistry/none/csds_chemistry.c
index 8a3b440ac5a54ad9fd15eacb131ae98f0c071217..98e364fa54e2c76f6b02a1b6d34ca3c10432f4c3 100644
--- a/src/chemistry/none/csds_chemistry.c
+++ b/src/chemistry/none/csds_chemistry.c
@@ -24,13 +24,12 @@
#include "csds_tools.h"
/* Hydro part */
-const int chemistry_csds_field_size_part[chemistry_csds_field_part_count] =
- {};
+const int chemistry_csds_field_size_part[chemistry_csds_field_part_count] = {};
int chemistry_csds_local_to_global_part[chemistry_csds_field_part_count];
/* Stellar part */
-const int
- chemistry_csds_field_size_spart[chemistry_csds_field_spart_count] = {};
+const int chemistry_csds_field_size_spart[chemistry_csds_field_spart_count] =
+ {};
int chemistry_csds_local_to_global_spart[chemistry_csds_field_spart_count];
diff --git a/src/chemistry/none/csds_chemistry.h b/src/chemistry/none/csds_chemistry.h
index 2ff913cc1edea79cec3d13002dcd51d064a1ec90..4e44f2dcd3a06b0bbc9b71b10a4c80fc3478c30f 100644
--- a/src/chemistry/none/csds_chemistry.h
+++ b/src/chemistry/none/csds_chemistry.h
@@ -29,8 +29,7 @@
#include "csds_python_tools.h"
/* Index of the mask in the header mask array */
-extern int
- chemistry_csds_local_to_global_part[chemistry_csds_field_part_count];
+extern int chemistry_csds_local_to_global_part[chemistry_csds_field_part_count];
extern int
chemistry_csds_local_to_global_spart[chemistry_csds_field_spart_count];
@@ -74,11 +73,13 @@ chemistry_csds_reader_link_derivatives_spart(struct header *head) {}
* @param params The simulation's #csds_parameters.
*/
__attribute__((always_inline)) INLINE static void
-chemistry_csds_interpolate_field_part(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t, const int field,
- const struct csds_parameters *params) {}
+chemistry_csds_interpolate_field_part(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {}
/**
* @brief Interpolate a field of the #spart at the given time.
@@ -98,11 +99,13 @@ chemistry_csds_interpolate_field_part(
* @param params The simulation's #csds_parameters.
*/
__attribute__((always_inline)) INLINE static void
-chemistry_csds_interpolate_field_spart(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t, const int field,
- const struct csds_parameters *params) {}
+chemistry_csds_interpolate_field_spart(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {}
#ifdef HAVE_PYTHON
/**
diff --git a/src/csds_header.c b/src/csds_header.c
index 6d15de01586b6d7476b2571445e9e5ee81b9838d..e75c3137f33d7f5dfe6ca9feca9be24684e7e1a5 100644
--- a/src/csds_header.c
+++ b/src/csds_header.c
@@ -94,35 +94,34 @@ void header_change_offset_direction(struct header *h,
size_t offset = CSDS_VERSION_SIZE + 2 * sizeof(int);
csds_loader_io_write_data(h->log->log.map + offset, sizeof(unsigned int),
- &new_value);
+ &new_value);
}
/**
* @brief Set the links between the local (module) and global (header) indexes.
*/
-#define set_links_local_global_internal(MODULE, PART) \
- for (int j = 0; j < MODULE##_csds_field##PART##_count; j++) { \
- MODULE##_csds_local_to_global##PART[j] = -1; \
- for (int i = 0; i < h->masks_count; i++) { \
- if (strcmp(h->masks[i].name, MODULE##_csds_field_names##PART[j]) == \
- 0) { \
- MODULE##_csds_local_to_global##PART[j] = i; \
- break; \
- } \
- } \
- \
- /* Check if everything is fine. */ \
- const int index = MODULE##_csds_local_to_global##PART[j]; \
- if (index == -1) { \
- error("Field %s in " #MODULE " is not set", \
- MODULE##_csds_field_names##PART[j]); \
- } \
- if (h->masks[index].size != MODULE##_csds_field_size##PART[j]) { \
- error("Field %s in " #MODULE " does not have the correct size", \
- MODULE##_csds_field_names##PART[j]); \
- } \
- } \
- \
+#define set_links_local_global_internal(MODULE, PART) \
+ for (int j = 0; j < MODULE##_csds_field##PART##_count; j++) { \
+ MODULE##_csds_local_to_global##PART[j] = -1; \
+ for (int i = 0; i < h->masks_count; i++) { \
+ if (strcmp(h->masks[i].name, MODULE##_csds_field_names##PART[j]) == 0) { \
+ MODULE##_csds_local_to_global##PART[j] = i; \
+ break; \
+ } \
+ } \
+ \
+ /* Check if everything is fine. */ \
+ const int index = MODULE##_csds_local_to_global##PART[j]; \
+ if (index == -1) { \
+ error("Field %s in " #MODULE " is not set", \
+ MODULE##_csds_field_names##PART[j]); \
+ } \
+ if (h->masks[index].size != MODULE##_csds_field_size##PART[j]) { \
+ error("Field %s in " #MODULE " does not have the correct size", \
+ MODULE##_csds_field_names##PART[j]); \
+ } \
+ } \
+ \
MODULE##_csds_reader_link_derivatives##PART(h);
/**
@@ -178,13 +177,12 @@ void header_read(struct header *h, struct csds_logfile *log) {
/* Read offset to first record. */
h->offset_first_record = 0;
- map = csds_loader_io_read_data(map, CSDS_OFFSET_SIZE,
- &h->offset_first_record);
+ map =
+ csds_loader_io_read_data(map, CSDS_OFFSET_SIZE, &h->offset_first_record);
/* Read the size of the strings. */
h->string_length = 0;
- map =
- csds_loader_io_read_data(map, sizeof(unsigned int), &h->string_length);
+ map = csds_loader_io_read_data(map, sizeof(unsigned int), &h->string_length);
/* Check if value defined in this file is large enough. */
if (STRING_SIZE < h->string_length) {
@@ -210,8 +208,8 @@ void header_read(struct header *h, struct csds_logfile *log) {
h->masks[i].mask = 1 << i;
/* Read the mask data size. */
- map = csds_loader_io_read_data(map, sizeof(unsigned int),
- &h->masks[i].size);
+ map =
+ csds_loader_io_read_data(map, sizeof(unsigned int), &h->masks[i].size);
/* Print the information. */
if (reader->verbose > 1) {
diff --git a/src/csds_index.c b/src/csds_index.c
index 13bafda28ea1e25871702dab71e459cd5ceba190..be3c640ef756cce7315850d490233cc02d38949b 100644
--- a/src/csds_index.c
+++ b/src/csds_index.c
@@ -56,8 +56,7 @@
* @param index The #csds_index.
* @param filename The filename of the index file.
*/
-void csds_index_read_header(struct csds_index *index,
- const char *filename) {
+void csds_index_read_header(struct csds_index *index, const char *filename) {
/* Open the file */
if (index->reader->verbose > 1) {
@@ -157,7 +156,7 @@ struct index_data *csds_index_get_data(struct csds_index *index, int type) {
* @param type The particle type.
*/
struct index_data *csds_index_get_created_history(struct csds_index *index,
- int type) {
+ int type) {
/* Get the position after the previous array. */
char *ret = (char *)csds_index_get_data(index, swift_type_count);
@@ -184,7 +183,7 @@ struct index_data *csds_index_get_created_history(struct csds_index *index,
* @param type The particle type.
*/
struct index_data *csds_index_get_removed_history(struct csds_index *index,
- int type) {
+ int type) {
/* Get the position after the previous array. */
char *ret = (char *)csds_index_get_created_history(index, swift_type_count);
@@ -230,7 +229,7 @@ int csds_index_contains_time_array(struct csds_index *index) {
* @param sorted Does the file needs to be sorted?
*/
void csds_index_map_file(struct csds_index *index, const char *filename,
- int sorted) {
+ int sorted) {
/* Un-map previous file */
if (index->index.map != NULL) {
error_python("Trying to remap.");
@@ -243,7 +242,7 @@ void csds_index_map_file(struct csds_index *index, const char *filename,
}
/* Map the index file */
csds_loader_io_mmap_file(&index->index, filename,
- /* read_only */ 0);
+ /* read_only */ 0);
/* Sort the file */
for (int i = 0; i < swift_type_count; i++) {
if (index->nparts[i] != 0) {
@@ -265,7 +264,7 @@ void csds_index_map_file(struct csds_index *index, const char *filename,
/* Map the index file */
csds_loader_io_mmap_file(&index->index, filename,
- /* read_only */ 1);
+ /* read_only */ 1);
}
/**
@@ -289,8 +288,8 @@ void csds_index_free(struct csds_index *index) {
*
* @return The offset of the particle or 0 if not found.
*/
-size_t csds_index_get_particle_offset(struct csds_index *index,
- long long id, int type) {
+size_t csds_index_get_particle_offset(struct csds_index *index, long long id,
+ int type) {
/* Define a few variables */
const struct index_data *data = csds_index_get_data(index, type);
size_t left = 0;
@@ -317,8 +316,7 @@ size_t csds_index_get_particle_offset(struct csds_index *index,
* @param index The #csds_index.
* @param reader The #csds_reader.
*/
-void csds_index_init(struct csds_index *index,
- struct csds_reader *reader) {
+void csds_index_init(struct csds_index *index, struct csds_reader *reader) {
/* Set the mapped file to NULL */
index->index.map = NULL;
@@ -340,7 +338,7 @@ void csds_index_init(struct csds_index *index,
* @return Did we find the particle?
*/
int csds_index_get_offset(struct csds_index *index, int64_t id, int type,
- uint64_t *offset) {
+ uint64_t *offset) {
/* Ensure that the file is sorted according to the ids. */
if (!index->is_sorted) {
diff --git a/src/csds_index.h b/src/csds_index.h
index 80181f35023beaca624ab200839ab08b2e3ed59e..128cc2b650c384631419aedc59dcf21c4fc88d1f 100644
--- a/src/csds_index.h
+++ b/src/csds_index.h
@@ -78,21 +78,20 @@ struct csds_index {
int csds_index_contains_time_array(struct csds_index *index);
void csds_index_write_sorted(struct csds_index *index);
-void csds_index_init(struct csds_index *index,
- struct csds_reader *reader);
+void csds_index_init(struct csds_index *index, struct csds_reader *reader);
void csds_index_read_header(struct csds_index *index, const char *filename);
void csds_index_map_file(struct csds_index *index, const char *filename,
- int sorted);
-size_t csds_index_get_particle_offset(struct csds_index *index,
- long long id, int type);
+ int sorted);
+size_t csds_index_get_particle_offset(struct csds_index *index, long long id,
+ int type);
void csds_index_free(struct csds_index *index);
void csds_index_sort_file(struct csds_index *index);
int csds_index_get_offset(struct csds_index *index, int64_t id, int type,
- uint64_t *offset);
+ uint64_t *offset);
struct index_data *csds_index_get_data(struct csds_index *index, int type);
struct index_data *csds_index_get_created_history(struct csds_index *index,
- int type);
+ int type);
struct index_data *csds_index_get_removed_history(struct csds_index *index,
- int type);
+ int type);
#endif // CSDS_CSDS_INDEX_H
diff --git a/src/csds_loader_io.c b/src/csds_loader_io.c
index 71af9b542336879631082c9d8de89a620f48383e..d6874bb0c684b8d4bcb6c36e05963b47dad62197 100644
--- a/src/csds_loader_io.c
+++ b/src/csds_loader_io.c
@@ -52,7 +52,7 @@ size_t csds_loader_io_get_file_size(int fd) {
*
*/
void csds_loader_io_mmap_file(struct mapped_file *map, const char *filename,
- int read_only) {
+ int read_only) {
/* open the file. */
int fd;
diff --git a/src/csds_loader_io.h b/src/csds_loader_io.h
index 4829fb56c6d0a0fecc020c3b1f9000a29dd77e11..56ba179c3d4626935f8b7c01fd1862b8854385e1 100644
--- a/src/csds_loader_io.h
+++ b/src/csds_loader_io.h
@@ -40,7 +40,7 @@ struct mapped_file {
size_t csds_loader_io_get_file_size(int fd);
void csds_loader_io_mmap_file(struct mapped_file *map, const char *filename,
- int read_only);
+ int read_only);
void csds_loader_io_munmap_file(struct mapped_file *map);
/**
diff --git a/src/csds_logfile.c b/src/csds_logfile.c
index 39efabaa979f9c2d54917ae23358b9077ef4e96a..39541b5a03bcb32f816b2fb171605dbe85b1d3a1 100644
--- a/src/csds_logfile.c
+++ b/src/csds_logfile.c
@@ -31,8 +31,7 @@
* @param only_header Read only the header.
*/
void csds_logfile_init_from_file(struct csds_logfile *log, char *filename,
- struct csds_reader *reader,
- int only_header) {
+ struct csds_reader *reader, int only_header) {
/* Set the pointer to the reader. */
log->reader = reader;
@@ -44,7 +43,7 @@ void csds_logfile_init_from_file(struct csds_logfile *log, char *filename,
/* Open file, map it and get its size. */
if (reader->verbose > 1) message("Mapping the log file.");
csds_loader_io_mmap_file(&log->log, filename,
- /* read_only */ 1);
+ /* read_only */ 1);
/* Read the header. */
if (reader->verbose > 1) message("Reading the header.");
@@ -165,7 +164,7 @@ void csds_logfile_reverse_offset(struct csds_logfile *log, char *filename) {
/* Close and reopen the file in write mode. */
csds_loader_io_munmap_file(&log->log);
csds_loader_io_mmap_file(&log->log, filename,
- /* read_only */ 0);
+ /* read_only */ 0);
/* Get pointers */
struct header *header = &log->header;
@@ -238,5 +237,5 @@ void csds_logfile_reverse_offset(struct csds_logfile *log, char *filename) {
/* Close and reopen the file in read mode. */
csds_loader_io_munmap_file(&log->log);
csds_loader_io_mmap_file(&log->log, filename,
- /* read_only */ 1);
+ /* read_only */ 1);
}
diff --git a/src/csds_logfile.h b/src/csds_logfile.h
index 8d2bc92f6d981851fb528cae9e4365435c6851b9..6e4c6cae3fb70fea889aa71aaf158bf0810d1340 100644
--- a/src/csds_logfile.h
+++ b/src/csds_logfile.h
@@ -55,8 +55,7 @@ struct csds_logfile {
};
void csds_logfile_init_from_file(struct csds_logfile *log, char *filename,
- struct csds_reader *reader,
- int only_header);
+ struct csds_reader *reader, int only_header);
void csds_logfile_reverse_offset(struct csds_logfile *log, char *filename);
void csds_logfile_free(struct csds_logfile *log);
diff --git a/src/csds_parameters.c b/src/csds_parameters.c
index b2bd59e59ffc83c07c522dc1287d6fd8c3ab2e93..bd2f7f65f2c252bad379fc67ba9ce80c7bd7fa74 100644
--- a/src/csds_parameters.c
+++ b/src/csds_parameters.c
@@ -37,8 +37,8 @@
*
*/
void csds_parameters_init(struct csds_parameters *params,
- const struct csds_reader *reader,
- int number_threads) {
+ const struct csds_reader *reader,
+ int number_threads) {
/* Generate filename */
char filename[STRING_SIZE];
@@ -78,17 +78,17 @@ void csds_parameters_init(struct csds_parameters *params,
}
/* Read the initial number of particles. */
- for(int i = 0; i < swift_type_count; i++) {
+ for (int i = 0; i < swift_type_count; i++) {
params->approximate_number_particles[i] = 0;
}
params->approximate_number_particles[swift_type_gas] =
- parser_get_param_longlong(&swift_params, "Header:NumberParts");
+ parser_get_param_longlong(&swift_params, "Header:NumberParts");
params->approximate_number_particles[swift_type_stars] =
- parser_get_param_longlong(&swift_params, "Header:NumberSParts");
+ parser_get_param_longlong(&swift_params, "Header:NumberSParts");
params->approximate_number_particles[swift_type_dark_matter] =
- parser_get_param_longlong(&swift_params, "Header:NumberGParts");
+ parser_get_param_longlong(&swift_params, "Header:NumberGParts");
/* Read the maximal fraction of tagged elements */
params->arrays_maximal_tagged_fraction = parser_get_opt_param_float(
- &swift_params, "ReaderOptions:arrays_maximal_tagged_fraction", 0.15);
+ &swift_params, "ReaderOptions:arrays_maximal_tagged_fraction", 0.15);
}
diff --git a/src/csds_parameters.h b/src/csds_parameters.h
index 7b1361a0e9d36070a1c43edc6993eaafc9a62c1e..e9c40e8830975b62773a92c878e21a96790a4274 100644
--- a/src/csds_parameters.h
+++ b/src/csds_parameters.h
@@ -57,7 +57,6 @@ struct csds_parameters {
};
void csds_parameters_init(struct csds_parameters *params,
- const struct csds_reader *reader,
- int number_threads);
+ const struct csds_reader *reader, int number_threads);
#endif // CSDS_CSDS_PARAMETERS_H
diff --git a/src/csds_particle.c b/src/csds_particle.c
index cac3ec6d39bf4a4cf52e3415fcbbf7e2e82fd4da..d63c9d1a88202aadda5f37370d50548c6e7a8f4e 100644
--- a/src/csds_particle.c
+++ b/src/csds_particle.c
@@ -106,9 +106,9 @@ __attribute__((always_inline)) INLINE size_t csds_particle_read_field(
* @return The special flag.
*/
__attribute__((always_inline)) INLINE enum csds_special_flags
-csds_particle_read_special_flag(const struct csds_reader *reader,
- size_t offset, size_t *mask, size_t *h_offset,
- int *data, int *part_type) {
+csds_particle_read_special_flag(const struct csds_reader *reader, size_t offset,
+ size_t *mask, size_t *h_offset, int *data,
+ int *part_type) {
/* Get a few pointers. */
const struct header *h = &reader->log.header;
@@ -132,8 +132,8 @@ csds_particle_read_special_flag(const struct csds_reader *reader,
/* Read the special flag */
uint32_t packed_data = 0;
- map = csds_loader_io_read_data(
- map, h->masks[csds_index_special_flags].size, &packed_data);
+ map = csds_loader_io_read_data(map, h->masks[csds_index_special_flags].size,
+ &packed_data);
return csds_unpack_flags_and_data(packed_data, data, part_type);
}
@@ -150,12 +150,14 @@ csds_particle_read_special_flag(const struct csds_reader *reader,
* @param field The field to reconstruct.
* @param params The simulation's #csds_parameters.
*/
-void csds_particle_interpolate_field(
- const double time_before, const struct csds_field *restrict before,
- const double time_after, const struct csds_field *restrict after,
- void *restrict output, const double time,
- const struct field_information *field, enum part_type type,
- const struct csds_parameters *params) {
+void csds_particle_interpolate_field(const double time_before,
+ const struct csds_field *restrict before,
+ const double time_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double time,
+ const struct field_information *field,
+ enum part_type type,
+ const struct csds_parameters *params) {
/* Select the correct interpolation */
switch (type) {
@@ -165,14 +167,14 @@ void csds_particle_interpolate_field(
switch (field->module) {
case field_module_default:
hydro_csds_interpolate_field(time_before, before, time_after, after,
- output, time, field->local_index,
- params);
+ output, time, field->local_index,
+ params);
break;
case field_module_chemistry:
- chemistry_csds_interpolate_field_part(
- time_before, before, time_after, after, output, time,
- field->local_index, params);
+ chemistry_csds_interpolate_field_part(time_before, before, time_after,
+ after, output, time,
+ field->local_index, params);
break;
default:
@@ -187,8 +189,7 @@ void csds_particle_interpolate_field(
if (field->module != field_module_default)
error("Module not implemented");
gravity_csds_interpolate_field(time_before, before, time_after, after,
- output, time, field->local_index,
- params);
+ output, time, field->local_index, params);
break;
/* Stars */
@@ -196,8 +197,8 @@ void csds_particle_interpolate_field(
switch (field->module) {
case field_module_default:
stars_csds_interpolate_field(time_before, before, time_after, after,
- output, time, field->local_index,
- params);
+ output, time, field->local_index,
+ params);
break;
case field_module_chemistry:
@@ -207,9 +208,9 @@ void csds_particle_interpolate_field(
break;
case field_module_star_formation:
- star_formation_csds_interpolate_field(
- time_before, before, time_after, after, output, time,
- field->local_index, params);
+ star_formation_csds_interpolate_field(time_before, before, time_after,
+ after, output, time,
+ field->local_index, params);
break;
default:
diff --git a/src/csds_particle.h b/src/csds_particle.h
index 2c8424f17ca75f93e11df4ebf52b0106fbc9f323..189b2dab77f88b054849165eba8dd0c21354c075 100644
--- a/src/csds_particle.h
+++ b/src/csds_particle.h
@@ -43,19 +43,21 @@ 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 struct field_information *all_fields,
- const int all_fields_count,
- const int global_index, size_t *mask,
- size_t *h_offset);
+size_t csds_particle_read_field(const struct csds_reader *reader, size_t offset,
+ void *output,
+ const struct field_information *all_fields,
+ const int all_fields_count,
+ const int global_index, size_t *mask,
+ size_t *h_offset);
-void csds_particle_interpolate_field(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t,
- const struct field_information *field, enum part_type type,
- const struct csds_parameters *params);
+void csds_particle_interpolate_field(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const struct field_information *field,
+ enum part_type type,
+ const struct csds_parameters *params);
enum csds_special_flags csds_particle_read_special_flag(
const struct csds_reader *reader, size_t offset, size_t *mask,
diff --git a/src/csds_python_tools.h b/src/csds_python_tools.h
index 3947c0decd03e91d2a8f5b13b01fd3d3d3766008..a7da56d26117207c2d8004cf73787b58c2c8bb92 100644
--- a/src/csds_python_tools.h
+++ b/src/csds_python_tools.h
@@ -106,8 +106,8 @@ csds_loader_python_field(int dimension, int numpy_type) {
*/
__attribute__((always_inline)) INLINE static void
csds_loader_python_field_add_subfield(struct csds_python_field *field,
- const char *name, size_t offset,
- int dimension, int numpy_type) {
+ const char *name, size_t offset,
+ int dimension, int numpy_type) {
/* Ensure that we still have enough place */
if (field->subfields_registred == field->dimension) {
@@ -134,8 +134,8 @@ csds_loader_python_field_add_subfield(struct csds_python_field *field,
*
* @param field The #csds_python_field to clean.
*/
-__attribute__((always_inline)) INLINE static void
-csds_loader_python_field_free(struct csds_python_field *field) {
+__attribute__((always_inline)) INLINE static void csds_loader_python_field_free(
+ struct csds_python_field *field) {
if (field->typenum == CUSTOM_NPY_TYPE) {
free(field->subfields);
field->subfields = NULL;
diff --git a/src/csds_python_wrapper.c b/src/csds_python_wrapper.c
index 3376266cd2e88184bf74877f08f555b64408d497..c514fda7456922a2d422df6c9e8a35b17575c47e 100644
--- a/src/csds_python_wrapper.c
+++ b/src/csds_python_wrapper.c
@@ -140,7 +140,8 @@ static int Reader_init(PyObjectReader *self, PyObject *args, PyObject *kwds) {
int number_index = 10;
/* List of keyword arguments. */
- static char *kwlist[] = {"basename", "verbose", "number_threads", "number_index", NULL};
+ static char *kwlist[] = {"basename", "verbose", "number_threads",
+ "number_index", NULL};
/* parse the arguments. */
if (!PyArg_ParseTupleAndKeywords(args, kwds, "s|iii", kwlist, &basename,
@@ -216,8 +217,8 @@ static PyObject *get_box_size(PyObject *self, PyObject *Py_UNUSED(ignored)) {
}
#define find_field_in_module_internal(MODULE, PART) \
- for (int local = 0; local < MODULE##_csds_field##PART##_count; local++) { \
- const int global = MODULE##_csds_local_to_global##PART[local]; \
+ for (int local = 0; local < MODULE##_csds_field##PART##_count; local++) { \
+ const int global = MODULE##_csds_local_to_global##PART[local]; \
const int local_shifted = local + total_number_fields; \
if (field_indices[i] == global) { \
/* Check if we have the same fields for the different modules */ \
@@ -228,10 +229,10 @@ static PyObject *get_box_size(PyObject *self, PyObject *Py_UNUSED(ignored)) {
error_python( \
"The python definition of the field %s does not correspond " \
"between the modules.", \
- MODULE##_csds_field_names##PART[local]); \
+ MODULE##_csds_field_names##PART[local]); \
} \
} \
- strcpy(field_name, MODULE##_csds_field_names##PART[local]); \
+ strcpy(field_name, MODULE##_csds_field_names##PART[local]); \
current_field = &python_fields[local_shifted]; \
break; \
} \
@@ -264,8 +265,8 @@ static PyObject *get_box_size(PyObject *self, PyObject *Py_UNUSED(ignored)) {
*/
__attribute__((always_inline)) INLINE static PyObject *
csds_loader_create_output(void **output, const int *field_indices,
- const int n_fields, const uint64_t *n_part,
- uint64_t n_tot) {
+ const int n_fields, const uint64_t *n_part,
+ uint64_t n_tot) {
struct csds_python_field python_fields[100];
@@ -785,8 +786,8 @@ static PyObject *pyGetData(__attribute__((unused)) PyObject *self,
/* Enable multithreading */
Py_BEGIN_ALLOW_THREADS;
- csds_reader_read_all_particles(reader, time, csds_reader_lin,
- field_indices, n_fields, output, n_part);
+ csds_reader_read_all_particles(reader, time, csds_reader_lin, field_indices,
+ n_fields, output, n_part);
/* Disable multithreading */
Py_END_ALLOW_THREADS;
@@ -815,8 +816,8 @@ static PyObject *pyGetData(__attribute__((unused)) PyObject *self,
/* Read the particles. */
csds_reader_read_particles_from_ids(reader, time, csds_reader_lin,
- field_indices, n_fields, output,
- n_part, c_part_ids);
+ field_indices, n_fields, output, n_part,
+ c_part_ids);
/* Disable multithreading */
Py_END_ALLOW_THREADS;
@@ -831,8 +832,8 @@ static PyObject *pyGetData(__attribute__((unused)) PyObject *self,
}
/* Create the python output. */
- PyObject *array = csds_loader_create_output(output, field_indices, n_fields,
- n_part, n_tot);
+ PyObject *array =
+ csds_loader_create_output(output, field_indices, n_fields, n_part, n_tot);
/* Free the reader. */
free(field_indices);
diff --git a/src/csds_reader.c b/src/csds_reader.c
index 2aa6db61365d15e105396c08d8ad2a362e4b62da..395bf11a178db5d8cdcf886bcbd38e9e1277eb34 100644
--- a/src/csds_reader.c
+++ b/src/csds_reader.c
@@ -62,7 +62,7 @@ void csds_reader_init(struct csds_reader *reader, const char *basename,
/* Initialize the log file. */
csds_logfile_init_from_file(&reader->log, logfile_name, reader,
- /* only_header */ 0);
+ /* only_header */ 0);
/* Initialize the index files and creates them if needed */
csds_reader_init_index(reader, number_index);
@@ -102,11 +102,11 @@ void csds_reader_init_index(struct csds_reader *reader, int number_index) {
if (count == 0) {
csds_reader_generate_index_files(reader, number_index);
count = number_index;
- }
- else if (reader->verbose > 0 && count != number_index) {
- message("Found %i index files. If you wish to have the"
- " requested %i files, please delete the old ones.",
- count, number_index);
+ } else if (reader->verbose > 0 && count != number_index) {
+ message(
+ "Found %i index files. If you wish to have the"
+ " requested %i files, please delete the old ones.",
+ count, number_index);
}
reader->index.n_files = count;
@@ -198,11 +198,11 @@ void csds_reader_set_time(struct csds_reader *reader, double time) {
/* Read the file */
csds_index_read_header(&reader->index.index_prev, filename_prev);
csds_index_map_file(&reader->index.index_prev, filename_prev,
- /* sorted */ 1);
+ /* sorted */ 1);
csds_index_read_header(&reader->index.index_next, filename_next);
csds_index_map_file(&reader->index.index_next, filename_next,
- /* sorted */ 1);
+ /* sorted */ 1);
/* Get the offset of the time chunk */
size_t ind = time_array_get_index_from_time(&reader->log.times, time);
@@ -234,7 +234,7 @@ void csds_reader_set_time(struct csds_reader *reader, double time) {
* @param The number of new particles.
*/
size_t csds_reader_count_number_new_particles(struct csds_reader *reader,
- enum part_type part_type) {
+ enum part_type part_type) {
const size_t threshold = reader->time.time_offset;
@@ -284,8 +284,8 @@ size_t csds_reader_count_number_new_particles(struct csds_reader *reader,
*
* @param The number of removed particles.
*/
-size_t csds_reader_count_number_removed_particles(
- struct csds_reader *reader, enum part_type part_type) {
+size_t csds_reader_count_number_removed_particles(struct csds_reader *reader,
+ enum part_type part_type) {
const size_t threshold = reader->time.time_offset;
@@ -333,8 +333,8 @@ size_t csds_reader_count_number_removed_particles(
* @param read_types Should we read this type of particles?
*/
void csds_reader_get_number_particles(struct csds_reader *reader,
- uint64_t *n_parts,
- const int *read_types) {
+ uint64_t *n_parts,
+ const int *read_types) {
for (enum part_type i = (enum part_type)0; i < swift_type_count; i++) {
/* Should we skip this type of particles? */
if (read_types[i] == 0) {
@@ -425,8 +425,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
*/
while (offset < offset_time) {
/* Read the particle. */
- csds_loader_io_read_mask(h, 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 & h->masks[csds_index_special_flags].mask) {
@@ -463,7 +462,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
/* Read the field */
csds_particle_read_field(reader, offset_before, output, all_fields,
- all_fields_count, global, &mask, &h_offset);
+ all_fields_count, global, &mask, &h_offset);
/* Deal with the first derivative. */
const size_t size_first = mask_first == NULL ? 0 : mask_first->size;
@@ -473,8 +472,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
if (first_found) {
/* Read the first derivative */
csds_particle_read_field(reader, offset_before, first_deriv, all_fields,
- all_fields_count, global_first, &mask,
- &h_offset);
+ all_fields_count, global_first, &mask, &h_offset);
}
/* Deal with the second derivative. */
@@ -485,8 +483,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
if (second_found) {
/* Read the first derivative */
csds_particle_read_field(reader, offset_before, second_deriv, all_fields,
- all_fields_count, global_second, &mask,
- &h_offset);
+ all_fields_count, global_second, &mask, &h_offset);
}
/* Get the time. */
@@ -503,7 +500,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
/* Read the particle. */
csds_loader_io_read_mask(h, reader->log.log.map + offset, &mask,
- &h_offset);
+ &h_offset);
/* Do we have the field? */
if (mask & mask_field->mask) {
@@ -524,7 +521,7 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
/* Read the field */
csds_particle_read_field(reader, offset, output_after, all_fields,
- all_fields_count, global, &mask, &h_offset);
+ all_fields_count, global, &mask, &h_offset);
/* Deal with the first derivative. */
char first_deriv_after[size_first];
@@ -534,8 +531,8 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
if (first_found) {
/* Read the first derivative */
csds_particle_read_field(reader, offset, first_deriv_after, all_fields,
- all_fields_count, global_first, &mask,
- &h_offset);
+ all_fields_count, global_first, &mask,
+ &h_offset);
}
/* Deal with the second derivative. */
@@ -547,8 +544,8 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
if (second_found) {
/* Read the second derivative */
csds_particle_read_field(reader, offset, second_deriv_after, all_fields,
- all_fields_count, global_second, &mask,
- &h_offset);
+ all_fields_count, global_second, &mask,
+ &h_offset);
}
/* Get the time. */
@@ -567,8 +564,8 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
/* Interpolate the data. */
csds_particle_interpolate_field(time_before, &before, time_after, &after,
- output, time, field_wanted, type,
- &reader->params);
+ output, time, field_wanted, type,
+ &reader->params);
}
return 0;
}
@@ -586,12 +583,11 @@ int csds_reader_read_field(struct csds_reader *reader, double time,
* @param type The type of the particle.
*/
void csds_reader_get_fields_wanted(const struct csds_reader *reader,
- const int *global_fields_wanted,
- struct field_information *fields_wanted,
- const int n_fields_wanted,
- struct field_information *all_fields,
- int all_fields_count,
- enum part_type type) {
+ const int *global_fields_wanted,
+ struct field_information *fields_wanted,
+ const int n_fields_wanted,
+ struct field_information *all_fields,
+ int all_fields_count, enum part_type type) {
const struct header *h = &reader->log.header;
@@ -676,8 +672,8 @@ struct extra_data_read_all {
* @param extra_data Pointer to a #extra_data_read_all.
*/
void csds_reader_read_all_particles_single_type_mapper(void *map_data,
- int num_elements,
- void *extra_data) {
+ int num_elements,
+ void *extra_data) {
/* Extract the data */
struct extra_data_read_all *data_tp =
@@ -799,10 +795,9 @@ void csds_reader_read_all_particles_single_type_mapper(void *map_data,
* @param type The particle type
*/
void csds_reader_read_all_particles_single_type(
- struct csds_reader *reader, double time,
- enum csds_reader_type interp_type, const int *global_fields_wanted,
- const int n_fields_wanted, void **output, const uint64_t *n_part,
- enum part_type type) {
+ struct csds_reader *reader, double time, enum csds_reader_type interp_type,
+ const int *global_fields_wanted, const int n_fields_wanted, void **output,
+ const uint64_t *n_part, enum part_type type) {
const struct header *h = &reader->log.header;
/* Allocate temporary memory. */
@@ -820,8 +815,8 @@ void csds_reader_read_all_particles_single_type(
/* Convert fields into the local array. */
csds_reader_get_fields_wanted(reader, global_fields_wanted, fields_wanted,
- n_fields_wanted, all_fields, all_fields_count,
- type);
+ n_fields_wanted, all_fields, all_fields_count,
+ type);
/* Compact the data */
struct extra_data_read_all extra = {reader,
@@ -869,10 +864,10 @@ void csds_reader_read_all_particles_single_type(
* @param n_part Number of particles of each type.
*/
void csds_reader_read_all_particles(struct csds_reader *reader, double time,
- enum csds_reader_type interp_type,
- const int *global_fields_wanted,
- const int n_fields_wanted, void **output,
- const uint64_t *n_part) {
+ enum csds_reader_type interp_type,
+ const int *global_fields_wanted,
+ const int n_fields_wanted, void **output,
+ const uint64_t *n_part) {
/* Read the gas */
if (n_part[swift_type_gas] != 0) {
@@ -924,10 +919,9 @@ void csds_reader_read_all_particles(struct csds_reader *reader, double time,
* The ids not found are removed from this array.
*/
void csds_reader_read_particles_from_ids_single_type(
- struct csds_reader *reader, double time,
- enum csds_reader_type interp_type, const int *global_fields_wanted,
- const int n_fields_wanted, void **output, uint64_t *n_part,
- enum part_type type, long long *ids) {
+ struct csds_reader *reader, double time, enum csds_reader_type interp_type,
+ const int *global_fields_wanted, const int n_fields_wanted, void **output,
+ uint64_t *n_part, enum part_type type, long long *ids) {
const struct header *h = &reader->log.header;
@@ -952,16 +946,16 @@ void csds_reader_read_particles_from_ids_single_type(
/* Convert fields into the local array. */
csds_reader_get_fields_wanted(reader, global_fields_wanted, fields_wanted,
- n_fields_wanted, all_fields, all_fields_count,
- type);
+ n_fields_wanted, all_fields, all_fields_count,
+ type);
/* Read the particles */
for (size_t i = 0; i < n_part[type]; i++) {
/* Get the offset */
size_t offset = 0;
- int found = csds_index_get_offset(&reader->index.index_prev, ids[i], type,
- &offset);
+ int found =
+ csds_index_get_offset(&reader->index.index_prev, ids[i], type, &offset);
/* Deal with the particles not found */
if (!found) {
@@ -1013,13 +1007,10 @@ void csds_reader_read_particles_from_ids_single_type(
* @param ids The particles' ids.
* The ids not found are removed from this array.
*/
-void csds_reader_read_particles_from_ids(struct csds_reader *reader,
- double time,
- enum csds_reader_type interp_type,
- const int *global_fields_wanted,
- const int n_fields_wanted,
- void **output, uint64_t *n_part,
- long long **ids) {
+void csds_reader_read_particles_from_ids(
+ struct csds_reader *reader, double time, enum csds_reader_type interp_type,
+ const int *global_fields_wanted, const int n_fields_wanted, void **output,
+ uint64_t *n_part, long long **ids) {
/* Read the gas */
if (n_part[swift_type_gas] != 0) {
@@ -1081,7 +1072,7 @@ double csds_reader_get_time_end(struct csds_reader *reader) {
* @return The offset of the timestamp.
*/
size_t csds_reader_get_next_offset_from_time(struct csds_reader *reader,
- double time) {
+ double time) {
size_t ind = time_array_get_index_from_time(&reader->log.times, time);
/* We do not want to have the sentiel */
if (reader->log.times.size - 2 == ind) {
@@ -1106,8 +1097,7 @@ size_t csds_reader_get_next_offset_from_time(struct csds_reader *reader,
* @return The offset after the record.
*/
size_t csds_reader_read_record(struct csds_reader *reader, void **output,
- double *time, int *is_particle,
- size_t offset) {
+ double *time, int *is_particle, size_t offset) {
/* Get a few pointers. */
const struct header *h = &reader->log.header;
diff --git a/src/csds_reader.h b/src/csds_reader.h
index 6bda900a200bbf32b9229e272fd6ea22514fc74c..6f5fbe410f5523886e24a10c6f5881d94530f666 100644
--- a/src/csds_reader.h
+++ b/src/csds_reader.h
@@ -112,7 +112,7 @@ struct csds_reader {
enum csds_reader_event {
csds_reader_event_null, /* No event */
csds_reader_event_deleted, /* Particle has been deleted */
- csds_reader_event_stars, /* The particle has been transformed into a star */
+ csds_reader_event_stars, /* The particle has been transformed into a star */
};
void csds_reader_init_index(struct csds_reader *reader, int number_index);
@@ -125,28 +125,29 @@ void csds_reader_set_time(struct csds_reader *reader, double time);
double csds_reader_get_time_begin(struct csds_reader *reader);
double csds_reader_get_time_end(struct csds_reader *reader);
size_t csds_reader_get_next_offset_from_time(struct csds_reader *reader,
- double time);
+ double time);
void csds_reader_get_number_particles(struct csds_reader *reader,
- uint64_t *n_parts,
- const int *read_types);
+ uint64_t *n_parts, const int *read_types);
void csds_reader_read_all_particles(struct csds_reader *reader, double time,
- enum csds_reader_type interp_type,
- const int *id_masks_wanted,
- const int n_mask_wanted, void **output,
- const uint64_t *n_part);
-void csds_reader_read_particles_from_ids(
- struct csds_reader *reader, double time,
- enum csds_reader_type interp_type, const int *id_masks_wanted,
- const int n_mask_wanted, void **output, uint64_t *n_part, long long **ids);
+ enum csds_reader_type interp_type,
+ const int *id_masks_wanted,
+ const int n_mask_wanted, void **output,
+ const uint64_t *n_part);
+void csds_reader_read_particles_from_ids(struct csds_reader *reader,
+ double time,
+ enum csds_reader_type interp_type,
+ const int *id_masks_wanted,
+ const int n_mask_wanted, void **output,
+ uint64_t *n_part, long long **ids);
size_t csds_reader_read_record(struct csds_reader *reader, void **output,
- double *time, int *is_particle, size_t offset);
-void csds_reader_generate_index_files(const struct csds_reader *reader, int number_index);
+ double *time, int *is_particle, size_t offset);
+void csds_reader_generate_index_files(const struct csds_reader *reader,
+ int number_index);
void csds_reader_get_fields_wanted(const struct csds_reader *reader,
const int *global_fields_wanted,
struct field_information *fields_wanted,
const int n_fields_wanted,
struct field_information *all_fields,
- int all_fields_count,
- enum part_type type);
+ int all_fields_count, enum part_type type);
#endif // CSDS_CSDS_READER_H
diff --git a/src/csds_reader_generate_index.c b/src/csds_reader_generate_index.c
index d5f0c6edd91d8a6e57833e569a9dcc197af1a98a..b17c9aa2481dfc9583841bd2ff9928dcafeb788a 100644
--- a/src/csds_reader_generate_index.c
+++ b/src/csds_reader_generate_index.c
@@ -75,8 +75,8 @@ void index_writer_init(struct index_writer *writer, size_t init_size,
}
/* Allocate the memory */
- writer->data = (struct index_data *)
- malloc(sizeof(struct index_data) * init_size);
+ writer->data =
+ (struct index_data *)malloc(sizeof(struct index_data) * init_size);
if (writer->data == NULL) {
error("Failed to allocate memory for the index_writer.");
}
@@ -88,8 +88,7 @@ void index_writer_init(struct index_writer *writer, size_t init_size,
* @param writer The #index_writer.
*/
void index_writer_reset(struct index_writer *writer) {
- if (writer->size == 0)
- return;
+ if (writer->size == 0) return;
free(writer->data);
index_writer_init(writer, writer->init_size, writer->max_frac_tag);
@@ -124,9 +123,10 @@ void index_writer_log(struct index_writer *writer, const int64_t id,
/* Ensure that it was correctly allocated */
if (writer->capacity == 0) {
- error("Trying to add a particle to an empty index_writer."
- " If your are sure that your particle type is implemented, "
- "please increase the value of ReaderOptions:Number*.");
+ error(
+ "Trying to add a particle to an empty index_writer."
+ " If your are sure that your particle type is implemented, "
+ "please increase the value of ReaderOptions:Number*.");
}
#ifdef SWIFT_DEBUG_CHECKS
@@ -146,8 +146,7 @@ void index_writer_log(struct index_writer *writer, const int64_t id,
writer->capacity *= 2;
/* Allocate the new array and copy the content of the previous one */
- struct index_data *tmp =
- (struct index_data *) malloc(2 * memsize);
+ struct index_data *tmp = (struct index_data *)malloc(2 * memsize);
memcpy(tmp, writer->data, memsize);
@@ -171,8 +170,8 @@ void index_writer_log(struct index_writer *writer, const int64_t id,
* @param writer The #index_writer.
* @param force Force the removal?
*/
-void index_writer_remove_tagged_particles(
- struct index_writer *writer, const int force) {
+void index_writer_remove_tagged_particles(struct index_writer *writer,
+ const int force) {
/* No need to clean the empty arrays. */
if (writer->size == 0) {
@@ -180,19 +179,17 @@ void index_writer_remove_tagged_particles(
}
/* Do we need to clean? */
- const float frac = (float) writer->number_tag / (float) writer->size;
- if (!force && frac < writer->max_frac_tag)
- return;
+ const float frac = (float)writer->number_tag / (float)writer->size;
+ if (!force && frac < writer->max_frac_tag) return;
/* Clean */
size_t count = 0;
- for(size_t i = 0; i < writer->size; i++) {
- if (writer->data[i].offset != PARTICLE_REMOVED)
- continue;
+ for (size_t i = 0; i < writer->size; i++) {
+ if (writer->data[i].offset != PARTICLE_REMOVED) continue;
count += 1;
/* Now replace it with the last particle. */
- writer->data[i] = writer->data[writer->size-1];
+ writer->data[i] = writer->data[writer->size - 1];
writer->size--;
/* We need to ensure that the last particle was not
@@ -208,7 +205,7 @@ void index_writer_remove_tagged_particles(
// TODO sort the particles
#ifdef SWIFT_DEBUG_CHECKS
- for(size_t i = 0; i < writer->size; i++) {
+ for (size_t i = 0; i < writer->size; i++) {
if (writer->data[i].offset == PARTICLE_REMOVED)
error("Found a tagged particle after cleaning.");
}
@@ -229,7 +226,7 @@ void index_writer_remove_part(struct index_writer *current_state,
// TODO use a binary search + ensure ids are sorted
// Do not forget to write in the index file that the files are sorted
- for(size_t j = 0; j < current_state->size; j++) {
+ for (size_t j = 0; j < current_state->size; j++) {
if (current_state->data[j].offset == PARTICLE_REMOVED ||
part_id != current_state->data[j].id) {
continue;
@@ -263,23 +260,21 @@ void index_writer_check_implemented(const struct index_writer *writers) {
/**
* @brief Write the number of particles and their data into the index file
*/
-void index_writer_write_in_index(const struct index_writer *writers,
- FILE *f) {
+void index_writer_write_in_index(const struct index_writer *writers, FILE *f) {
/* Write the number of particles */
uint64_t N_total[swift_type_count];
- for(int type = 0; type < swift_type_count; type++) {
+ for (int type = 0; type < swift_type_count; type++) {
N_total[type] = writers[type].size;
}
fwrite(N_total, sizeof(uint64_t), swift_type_count, f);
/* Write the index data */
- for(int type = 0; type < swift_type_count; type++) {
- if (N_total[type] == 0)
- continue;
+ for (int type = 0; type < swift_type_count; type++) {
+ if (N_total[type] == 0) continue;
- fwrite(writers[type].data, sizeof(struct index_data),
- writers[type].size, f);
+ fwrite(writers[type].data, sizeof(struct index_data), writers[type].size,
+ f);
}
}
@@ -293,14 +288,16 @@ void index_writer_write_in_index(const struct index_writer *writers,
* (since last index file) of created particles
* (size given by swift_type_count).
* @param parts_removed The arrays containing the last reference
- * (since last index file) of removed particles (size given by swift_type_count).
+ * (since last index file) of removed particles (size given by
+ * swift_type_count).
* @param time The time corresponding to the current index file.
* @param file_number The current file number.
*/
-void csds_reader_write_index(
- const struct csds_reader *reader, struct index_writer *current_state,
- struct index_writer *parts_created, struct index_writer *parts_removed,
- const struct time_record *time, int file_number) {
+void csds_reader_write_index(const struct csds_reader *reader,
+ struct index_writer *current_state,
+ struct index_writer *parts_created,
+ struct index_writer *parts_removed,
+ const struct time_record *time, int file_number) {
/* Get the filename */
char filename[STRING_SIZE + 15];
@@ -308,7 +305,7 @@ void csds_reader_write_index(
/* Trigger a cleaning of the arrays */
// TODO Remove this and skip the particles when writing?
- for(int i = 0; i < swift_type_count; i++) {
+ for (int i = 0; i < swift_type_count; i++) {
index_writer_remove_tagged_particles(¤t_state[i], /* force */ 1);
}
@@ -318,7 +315,7 @@ void csds_reader_write_index(
index_writer_check_implemented(parts_removed);
/* Open file */
- FILE* f = NULL;
+ FILE *f = NULL;
f = fopen(filename, "wb");
if (f == NULL) {
@@ -332,7 +329,7 @@ void csds_reader_write_index(
/* Write number of particles */
uint64_t N_total[swift_type_count];
- for(int type = 0; type < swift_type_count; type++) {
+ for (int type = 0; type < swift_type_count; type++) {
N_total[type] = current_state[type].size;
}
fwrite(N_total, sizeof(uint64_t), swift_type_count, f);
@@ -352,9 +349,8 @@ void csds_reader_write_index(
}
/* Write the arrays */
- for(int type = 0; type < swift_type_count; type++) {
- if (N_total[type] == 0)
- continue;
+ for (int type = 0; type < swift_type_count; type++) {
+ if (N_total[type] == 0) continue;
fwrite(current_state[type].data, sizeof(struct index_data),
current_state[type].size, f);
@@ -368,7 +364,7 @@ void csds_reader_write_index(
fclose(f);
/* Cleanup the arrays */
- for(int type = 0; type < swift_type_count; type++) {
+ for (int type = 0; type < swift_type_count; type++) {
index_writer_reset(&parts_created[type]);
index_writer_reset(&parts_removed[type]);
}
@@ -378,10 +374,14 @@ void csds_reader_write_index(
* @brief Get the initial state of the simulation.
*
* @param reader The #csds_reader.
- * @param current_state The arrays that will be updated with (size swift_type_count).
- * @param all_fields The complete list of fields for the different particles (size swift_type_count).
- * @param all_fields_count The number of fields for each particle type (size swift_type_count).
- * @param time_record (output) The first #time_record in the logfile (for writing the index file).
+ * @param current_state The arrays that will be updated with (size
+ * swift_type_count).
+ * @param all_fields The complete list of fields for the different particles
+ * (size swift_type_count).
+ * @param all_fields_count The number of fields for each particle type (size
+ * swift_type_count).
+ * @param time_record (output) The first #time_record in the logfile (for
+ * writing the index file).
*
* @return The offset of the second #time_record
* (the first record that does not correspond to the IC).
@@ -416,12 +416,13 @@ size_t csds_reader_get_initial_state(const struct csds_reader *reader,
/* Skip the time record */
size_t time_mask = 0;
- csds_loader_io_read_mask(header, log->log.map + offset_first, &time_mask, NULL);
+ csds_loader_io_read_mask(header, log->log.map + offset_first, &time_mask,
+ NULL);
const int time_size = header_get_record_size_from_mask(header, time_mask);
offset_first += time_size + size_record_header;
/* Get the initial state */
- for(size_t offset = offset_first; offset < offset_max; ) {
+ for (size_t offset = offset_first; offset < offset_max;) {
/* Get the particle type */
size_t mask = 0;
size_t prev_offset = 0;
@@ -437,8 +438,7 @@ size_t csds_reader_get_initial_state(const struct csds_reader *reader,
/* TODO Implement missing particle types */
if (part_type == swift_type_neutrino || part_type == swift_type_sink ||
part_type == swift_type_black_hole) {
- error("Particle type not implemented (%s)",
- part_type_names[part_type]);
+ error("Particle type not implemented (%s)", part_type_names[part_type]);
}
/* Get the particle ID */
@@ -449,8 +449,8 @@ size_t csds_reader_get_initial_state(const struct csds_reader *reader,
/* Read the particle ID */
int64_t id = 0;
csds_particle_read_field(reader, offset, &id, all_fields[part_type],
- all_fields_count[part_type], index_mask_id,
- &mask, &prev_offset);
+ all_fields_count[part_type], index_mask_id, &mask,
+ &prev_offset);
/* Log the particle */
index_writer_log(¤t_state[part_type], id, offset);
@@ -463,26 +463,31 @@ size_t csds_reader_get_initial_state(const struct csds_reader *reader,
return offset_max;
}
-
/**
- * @brief Update the state of the simulation until the next index file along with the history.
+ * @brief Update the state of the simulation until the next index file along
+ * with the history.
*
* @param reader The #csds_reader.
* @param init_offset The initial offset to read.
* @param time_record The #time_record of the next index file.
- * @param all_fields The complete list of fields for the different particles (size swift_type_count).
- * @param all_fields_count The number of fields for each particle type (size swift_type_count).
- * @param current_state The arrays containing the state of the simulation (size swift_type_count).
- * @param parts_created The arrays containing the particles created since last index (size swift_type_count).
- * @param parts_removed The arrays containing the particles removed since last index (size swift_type_count).
+ * @param all_fields The complete list of fields for the different particles
+ * (size swift_type_count).
+ * @param all_fields_count The number of fields for each particle type (size
+ * swift_type_count).
+ * @param current_state The arrays containing the state of the simulation (size
+ * swift_type_count).
+ * @param parts_created The arrays containing the particles created since last
+ * index (size swift_type_count).
+ * @param parts_removed The arrays containing the particles removed since last
+ * index (size swift_type_count).
*
* @return The starting offset for the update.
*/
size_t csds_reader_update_state_to_next_index(
- const struct csds_reader *reader, size_t init_offset, struct time_record time_record,
- struct field_information **all_fields, int *all_fields_count,
- struct index_writer *current_state, struct index_writer *parts_created,
- struct index_writer *parts_removed) {
+ const struct csds_reader *reader, size_t init_offset,
+ struct time_record time_record, struct field_information **all_fields,
+ int *all_fields_count, struct index_writer *current_state,
+ struct index_writer *parts_created, struct index_writer *parts_removed) {
const struct csds_logfile *log = &reader->log;
const struct header *header = &log->header;
const int size_record_header = CSDS_MASK_SIZE + CSDS_OFFSET_SIZE;
@@ -495,113 +500,113 @@ size_t csds_reader_update_state_to_next_index(
/* Look for all the created / removed particles */
size_t offset = init_offset;
- while(offset < time_record.offset) {
- size_t mask = 0;
- size_t h_offset = 0;
- int part_type = 0; // only available if the record is flagged.
- int data = 0;
+ while (offset < time_record.offset) {
+ size_t mask = 0;
+ size_t h_offset = 0;
+ int part_type = 0; // only available if the record is flagged.
+ int data = 0;
- /* Get the mask */
- csds_loader_io_read_mask(header, log->log.map + offset, &mask, &h_offset);
+ /* Get the mask */
+ csds_loader_io_read_mask(header, log->log.map + offset, &mask, &h_offset);
- /* Go to the next record */
- const size_t old_offset = offset;
- offset += header_get_record_size_from_mask(header, mask);
- offset += size_record_header;
+ /* Go to the next record */
+ const size_t old_offset = offset;
+ offset += header_get_record_size_from_mask(header, mask);
+ offset += size_record_header;
- /* Check if we have a particle with a flag */
- if (mask & header->masks[csds_index_timestamp].mask ||
- !(mask & header->masks[csds_index_special_flags].mask)) {
- continue;
- }
+ /* Check if we have a particle with a flag */
+ if (mask & header->masks[csds_index_timestamp].mask ||
+ !(mask & header->masks[csds_index_special_flags].mask)) {
+ continue;
+ }
- /* Get the special flag */
- enum csds_special_flags flag = csds_particle_read_special_flag(
- reader, old_offset, &mask, &h_offset, &data, &part_type);
+ /* Get the special flag */
+ enum csds_special_flags flag = csds_particle_read_special_flag(
+ reader, old_offset, &mask, &h_offset, &data, &part_type);
#ifdef SWIFT_DEBUG_CHECKS
- if (flag == csds_flag_none) {
- error("A record should not have a mask "
- "for a flag and the flag set to 0");
- }
+ if (flag == csds_flag_none) {
+ error(
+ "A record should not have a mask "
+ "for a flag and the flag set to 0");
+ }
#endif
- /* Read the ID */
- int64_t id = 0;
- csds_particle_read_field(reader, old_offset, &id, all_fields[part_type],
- all_fields_count[part_type], index_mask_id,
- &mask, &h_offset);
-
- /* Add the particle to the arrays */
- if (flag == csds_flag_change_type || flag == csds_flag_mpi_exit ||
- flag == csds_flag_delete) {
- index_writer_log(&parts_removed[part_type], id, old_offset);
- index_writer_remove_part(¤t_state[part_type], id);
- }
- else if (flag == csds_flag_create || flag == csds_flag_mpi_enter) {
- index_writer_log(&parts_created[part_type], id, old_offset);
- index_writer_log(¤t_state[part_type], id, old_offset);
- }
+ /* Read the ID */
+ int64_t id = 0;
+ csds_particle_read_field(reader, old_offset, &id, all_fields[part_type],
+ all_fields_count[part_type], index_mask_id, &mask,
+ &h_offset);
+
+ /* Add the particle to the arrays */
+ if (flag == csds_flag_change_type || flag == csds_flag_mpi_exit ||
+ flag == csds_flag_delete) {
+ index_writer_log(&parts_removed[part_type], id, old_offset);
+ index_writer_remove_part(¤t_state[part_type], id);
+ } else if (flag == csds_flag_create || flag == csds_flag_mpi_enter) {
+ index_writer_log(&parts_created[part_type], id, old_offset);
+ index_writer_log(¤t_state[part_type], id, old_offset);
}
+ }
- /* Update the offsets of current_state
- * No need to update the others as they contain
- * when particles are removed/created*/
- for(int type = 0; type < swift_type_count; type++) {
- for(size_t i = 0; i < current_state[type].size; i++) {
- size_t current_offset = current_state[type].data[i].offset;
-
- /* Skip the flagged particles. */
- if (current_offset == PARTICLE_REMOVED)
- continue;
-
- /* Get the full mask */
- size_t full_mask = 0;
- size_t h_offset = 0;
- csds_loader_io_read_mask(header, log->log.map + current_offset, &full_mask, &h_offset);
+ /* Update the offsets of current_state
+ * No need to update the others as they contain
+ * data about when particles are removed/created*/
+ for (int type = 0; type < swift_type_count; type++) {
+ for (size_t i = 0; i < current_state[type].size; i++) {
+ size_t current_offset = current_state[type].data[i].offset;
- /* Remove the special mask */
- full_mask = full_mask & !header->masks[csds_index_special_flags].mask;
+ /* Skip the flagged particles. */
+ if (current_offset == PARTICLE_REMOVED) continue;
- /* Find the last offset before the current time */
- size_t last_full_offset = current_offset;
+ /* Get the full mask */
+ size_t full_mask = 0;
+ size_t h_offset = 0;
+ csds_loader_io_read_mask(header, log->log.map + current_offset,
+ &full_mask, &h_offset);
+
+ /* Remove the special mask */
+ full_mask = full_mask & !header->masks[csds_index_special_flags].mask;
+
+ /* Find the last offset before the current time */
+ size_t last_full_offset = current_offset;
+ current_offset += h_offset;
+ while (1) {
+ /* Get the mask */
+ size_t mask = 0;
+ h_offset = 0;
+ csds_loader_io_read_mask(header, log->log.map + current_offset, &mask,
+ &h_offset);
+
+ /* update the offset */
current_offset += h_offset;
- while(1) {
- /* Get the mask */
- size_t mask = 0;
- h_offset = 0;
- csds_loader_io_read_mask(header, log->log.map + current_offset, &mask, &h_offset);
-
- /* update the offset */
- current_offset += h_offset;
- if (current_offset > time_record.offset) {
- break;
- }
-
- /* The particle should not have a special flag
- due to the previous loop */
- if (mask & header->masks[csds_index_special_flags].mask) {
- error("Found a special flag when updating the particles.");
- }
-
- /* Update the last full offset */
- if (full_mask == mask) {
- last_full_offset = current_offset;
- }
-
- /* Are we at the end of the file? */
- if (h_offset == 0) {
- break;
- }
+ if (current_offset > time_record.offset) {
+ break;
+ }
+ /* The particle should not have a special flag
+ due to the previous loop */
+ if (mask & header->masks[csds_index_special_flags].mask) {
+ error("Found a special flag when updating the particles.");
}
- /* Update the offset */
- current_state[type].data[i].offset = last_full_offset;
+ /* Update the last full offset */
+ if (full_mask == mask) {
+ last_full_offset = current_offset;
+ }
+
+ /* Are we at the end of the file? */
+ if (h_offset == 0) {
+ break;
+ }
}
+
+ /* Update the offset */
+ current_state[type].data[i].offset = last_full_offset;
}
+ }
- return offset;
+ return offset;
}
/**
@@ -610,7 +615,8 @@ size_t csds_reader_update_state_to_next_index(
* @param reader The #csds_reader.
* @param number_index The number of index to generate.
*/
-void csds_reader_generate_index_files(const struct csds_reader *reader, int number_index) {
+void csds_reader_generate_index_files(const struct csds_reader *reader,
+ int number_index) {
/* Get a few pointers */
const struct csds_logfile *log = &reader->log;
const struct header *header = &log->header;
@@ -641,7 +647,7 @@ void csds_reader_generate_index_files(const struct csds_reader *reader, int numb
int all_fields_count[swift_type_count];
struct field_information *all_fields[swift_type_count];
struct field_information field_id[swift_type_count];
- for(int type = 0; type < swift_type_count; type++) {
+ for (int type = 0; type < swift_type_count; type++) {
/* TODO Implement missing particle types */
if (type == swift_type_neutrino || type == swift_type_sink ||
type == swift_type_black_hole)
@@ -653,12 +659,12 @@ void csds_reader_generate_index_files(const struct csds_reader *reader, int numb
tools_get_list_fields(all_fields[type], type, header);
/* Convert fields into the local array. */
- csds_reader_get_fields_wanted(reader, &global_fields_wanted, &field_id[type],
+ csds_reader_get_fields_wanted(reader, &global_fields_wanted,
+ &field_id[type],
/* n_fields_wanted */ 1, all_fields[type],
all_fields_count[type], type);
}
-
/* Create the different arrays that will store the information */
struct index_writer current_state[swift_type_count];
struct index_writer parts_created[swift_type_count];
@@ -666,8 +672,9 @@ void csds_reader_generate_index_files(const struct csds_reader *reader, int numb
const size_t default_size = 1024;
/* Allocate the arrays */
- for(int i = 0; i < swift_type_count; i++) {
- index_writer_init(¤t_state[i], reader->params.approximate_number_particles[i],
+ for (int i = 0; i < swift_type_count; i++) {
+ index_writer_init(¤t_state[i],
+ reader->params.approximate_number_particles[i],
reader->params.arrays_maximal_tagged_fraction);
index_writer_init(&parts_created[i], default_size,
reader->params.arrays_maximal_tagged_fraction);
@@ -675,25 +682,24 @@ void csds_reader_generate_index_files(const struct csds_reader *reader, int numb
reader->params.arrays_maximal_tagged_fraction);
}
-
/* Get the initial state */
struct time_record time_record;
size_t offset = csds_reader_get_initial_state(
reader, current_state, all_fields, all_fields_count, &time_record);
/* Write the first index file */
- csds_reader_write_index(reader, current_state, parts_created,
- parts_removed, &time_record, /* file_number */0);
-
+ csds_reader_write_index(reader, current_state, parts_created, parts_removed,
+ &time_record, /* file_number */ 0);
/* Compute the state of all the other files and write them. */
const double t_min = time_record.time;
const double t_max = log->times.records[log->times.size - 1].time;
const double dt = (t_max - t_min) / (number_index - 1);
- for(int file_number = 1; file_number < number_index; file_number++) {
+ for (int file_number = 1; file_number < number_index; file_number++) {
/* Get the corresponding time record */
const double current_approximate_time = t_min + file_number * dt;
- const size_t index_time = time_array_get_index_from_time(&log->times, current_approximate_time);
+ const size_t index_time =
+ time_array_get_index_from_time(&log->times, current_approximate_time);
time_record = log->times.records[index_time];
/* Ensure that we really have the final time (rounding error). */
@@ -712,7 +718,7 @@ void csds_reader_generate_index_files(const struct csds_reader *reader, int numb
}
/* Free the memory */
- for(int type = 0; type < swift_type_count; type++) {
+ for (int type = 0; type < swift_type_count; type++) {
index_writer_free(¤t_state[type]);
index_writer_free(&parts_created[type]);
index_writer_free(&parts_removed[type]);
diff --git a/src/csds_time.c b/src/csds_time.c
index a8cb1dc5ae8be1c5ddb69926d578d39ac5743516..1b1ad7141073d50d70628830bdeef41d5fe1c014 100644
--- a/src/csds_time.c
+++ b/src/csds_time.c
@@ -108,8 +108,8 @@ size_t time_read(struct time_record *time_record,
#endif
/* read the record. */
- map =
- csds_loader_io_read_data(map, sizeof(unsigned long long int), &time_record->int_time);
+ map = csds_loader_io_read_data(map, sizeof(unsigned long long int),
+ &time_record->int_time);
map = csds_loader_io_read_data(map, sizeof(double), &time_record->time);
return map - h->log->log.map;
@@ -231,7 +231,7 @@ void time_array_load(struct time_array *t, struct csds_index *index) {
/* Read the elements */
csds_loader_io_read_data(map, t->size * sizeof(struct time_record),
- t->records);
+ t->records);
}
/**
@@ -247,8 +247,7 @@ int time_array_restore(struct time_array *t, struct csds_logfile *log) {
char filename[STRING_SIZE + 50];
int savefile = time_array_get_filename_savefile(log, filename);
- if (!savefile)
- return 0;
+ if (!savefile) return 0;
/* Initialize the index file that might contain the time array */
struct csds_index index;
diff --git a/src/csds_time.h b/src/csds_time.h
index a52fbc8ac4d73cf9b263eedb69d40e0490c34e31..71ae20d0e60ece22f12dae4694d5a37378eb2936 100644
--- a/src/csds_time.h
+++ b/src/csds_time.h
@@ -71,8 +71,8 @@ struct time_array {
void time_array_append(struct time_array *t, const integertime_t int_time,
const double time, const size_t offset);
-size_t time_read(struct time_record *time,
- const struct csds_reader *reader, size_t offset);
+size_t time_read(struct time_record *time, const struct csds_reader *reader,
+ size_t offset);
void time_array_init(struct time_array *t, size_t initial_size);
void time_array_populate(struct time_array *t, struct csds_logfile *log);
diff --git a/src/csds_tools.c b/src/csds_tools.c
index 0301774b4bff0ef8a4b2f70dc536044d30cbc608..8a12429b2f0d792e46656c0951e638241694e760 100644
--- a/src/csds_tools.c
+++ b/src/csds_tools.c
@@ -58,48 +58,48 @@ int tools_get_number_fields(enum part_type type) {
}
}
-#define copy_field_to_struct_internal(MODULE, PART, TYPE) \
+#define copy_field_to_struct_internal(MODULE, PART, TYPE) \
for (int j = 0; j < MODULE##_csds_field##PART##_count; j++) { \
- \
- /* Save the main properties */ \
- fields[i].module = TYPE; \
+ \
+ /* Save the main properties */ \
+ fields[i].module = TYPE; \
fields[i].name = MODULE##_csds_field_names##PART[j]; \
- \
- /* Get the indexes */ \
+ \
+ /* Get the indexes */ \
const int global = MODULE##_csds_local_to_global##PART[j]; \
- int first = h->masks[global].reader.first_deriv; \
- int second = h->masks[global].reader.second_deriv; \
- \
- /* Save the global indexes */ \
- fields[i].global_index = global; \
- fields[i].global_index_first = first; \
- fields[i].global_index_second = second; \
- \
- /* Convert the first derivatives into local index */ \
- if (first != -1) { \
+ int first = h->masks[global].reader.first_deriv; \
+ int second = h->masks[global].reader.second_deriv; \
+ \
+ /* Save the global indexes */ \
+ fields[i].global_index = global; \
+ fields[i].global_index_first = first; \
+ fields[i].global_index_second = second; \
+ \
+ /* Convert the first derivatives into local index */ \
+ if (first != -1) { \
for (int k = 0; k < MODULE##_csds_field##PART##_count; k++) { \
if (MODULE##_csds_local_to_global##PART[k] == first) { \
- first = k; \
- break; \
- } \
- } \
- } \
- \
- /* Convert the second derivatives into local index */ \
- if (second != -1) { \
+ first = k; \
+ break; \
+ } \
+ } \
+ } \
+ \
+ /* Convert the second derivatives into local index */ \
+ if (second != -1) { \
for (int k = 0; k < MODULE##_csds_field##PART##_count; k++) { \
if (MODULE##_csds_local_to_global##PART[k] == second) { \
- second = k; \
- break; \
- } \
- } \
- } \
- \
- /* Initialize the structure */ \
- fields[i].local_index = j; \
- fields[i].local_index_first = first; \
- fields[i].local_index_second = second; \
- i++; \
+ second = k; \
+ break; \
+ } \
+ } \
+ } \
+ \
+ /* Initialize the structure */ \
+ fields[i].local_index = j; \
+ fields[i].local_index_first = first; \
+ fields[i].local_index_second = second; \
+ i++; \
}
/**
@@ -339,8 +339,7 @@ size_t tools_check_record_consistency(const struct csds_reader *reader,
/* read mask of the pointed record. */
size_t pointed_mask = 0;
- csds_loader_io_read_mask(h, 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 != h->timestamp_mask && mask == h->timestamp_mask) ||
diff --git a/src/csds_tools.h b/src/csds_tools.h
index 2d7f7e4cbcc63a2869be8df2ed220d69c861eee1..74c2974751a86b8a385d31aa54dfdd641ce4bf42 100644
--- a/src/csds_tools.h
+++ b/src/csds_tools.h
@@ -25,11 +25,11 @@
#include "../config.h"
/* Swift include */
+#include "../src/csds.h"
+#include "../src/csds_io.h"
#include "../src/dimension.h"
#include "../src/error.h"
#include "../src/inline.h"
-#include "../src/csds.h"
-#include "../src/csds_io.h"
#include "../src/part_type.h"
#ifdef HAVE_PYTHON
@@ -140,10 +140,10 @@ __attribute__((always_inline)) INLINE static void csds_loader_print_traceback(
PyGILState_Release(gstate);
}
-#define error_python(s, ...) \
- ({ \
+#define error_python(s, ...) \
+ ({ \
csds_loader_print_traceback(); \
- error(s, ##__VA_ARGS__); \
+ error(s, ##__VA_ARGS__); \
})
#endif
diff --git a/src/gravity/MultiSoftening/csds_gravity.h b/src/gravity/MultiSoftening/csds_gravity.h
index 6aebf6ff38c21dda153b4a5dc677d6228a322722..c0f4c79aa44a9cbbfcf877b931b9c28b97afefce 100644
--- a/src/gravity/MultiSoftening/csds_gravity.h
+++ b/src/gravity/MultiSoftening/csds_gravity.h
@@ -22,11 +22,11 @@
#include "../config.h"
/* local includes */
-#include "gravity_csds.h"
#include "csds_interpolation.h"
#include "csds_loader_io.h"
#include "csds_parameters.h"
#include "csds_python_tools.h"
+#include "gravity_csds.h"
/* Index of the mask in the header mask array */
extern int gravity_csds_local_to_global[gravity_csds_field_count];
@@ -77,12 +77,12 @@ gravity_csds_reader_link_derivatives(struct header *head) {
*/
__attribute__((always_inline)) INLINE static void
gravity_csds_interpolate_field(const double t_before,
- const struct csds_field *restrict before,
- const double t_after,
- const struct csds_field *restrict after,
- void *restrict output, const double t,
- const int field,
- const struct csds_parameters *params) {
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
@@ -122,8 +122,8 @@ gravity_csds_interpolate_field(const double t_before,
}
#ifdef HAVE_PYTHON
-__attribute__((always_inline)) INLINE static void
-gravity_csds_generate_python(struct csds_python_field *fields) {
+__attribute__((always_inline)) INLINE static void gravity_csds_generate_python(
+ struct csds_python_field *fields) {
fields[gravity_csds_field_coordinates] =
csds_loader_python_field(/* Dimension */ 3, NPY_DOUBLE);
diff --git a/src/hydro/Gadget2/csds_hydro.h b/src/hydro/Gadget2/csds_hydro.h
index d4a414383adda4f58d844c4544b02368c6806deb..5aad453e6b260d48946b7c13bdc653baea72c3cd 100644
--- a/src/hydro/Gadget2/csds_hydro.h
+++ b/src/hydro/Gadget2/csds_hydro.h
@@ -22,11 +22,11 @@
#include "../config.h"
/* local includes */
-#include "hydro_csds.h"
#include "csds_interpolation.h"
#include "csds_loader_io.h"
#include "csds_parameters.h"
#include "csds_python_tools.h"
+#include "hydro_csds.h"
/* Index of the mask in the header mask array */
extern int hydro_csds_local_to_global[hydro_csds_field_count];
@@ -43,12 +43,9 @@ __attribute__((always_inline)) INLINE static void
hydro_csds_reader_link_derivatives(struct header *head) {
/* Set the first and second derivatives */
- const int pos_id =
- hydro_csds_local_to_global[hydro_csds_field_coordinates];
- const int vel_id =
- hydro_csds_local_to_global[hydro_csds_field_velocities];
- const int acc_id =
- hydro_csds_local_to_global[hydro_csds_field_accelerations];
+ const int pos_id = hydro_csds_local_to_global[hydro_csds_field_coordinates];
+ const int vel_id = hydro_csds_local_to_global[hydro_csds_field_velocities];
+ const int acc_id = hydro_csds_local_to_global[hydro_csds_field_accelerations];
/* Coordinates */
header_set_first_derivative(head, pos_id, vel_id);
@@ -75,14 +72,11 @@ hydro_csds_reader_link_derivatives(struct header *head) {
* #hydro_csds_fields).
* @param params The simulation's #csds_parameters.
*/
-__attribute__((always_inline)) INLINE static void
-hydro_csds_interpolate_field(const double t_before,
- const struct csds_field *restrict before,
- const double t_after,
- const struct csds_field *restrict after,
- void *restrict output, const double t,
- const int field,
- const struct csds_parameters *params) {
+__attribute__((always_inline)) INLINE static void hydro_csds_interpolate_field(
+ const double t_before, const struct csds_field *restrict before,
+ const double t_after, const struct csds_field *restrict after,
+ void *restrict output, const double t, const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
diff --git a/src/hydro/SPHENIX/csds_hydro.h b/src/hydro/SPHENIX/csds_hydro.h
index adea342d4b8641e263506d16de6ad9b612715033..2560deb29f3a400c256f468a999f12c27f8d275f 100644
--- a/src/hydro/SPHENIX/csds_hydro.h
+++ b/src/hydro/SPHENIX/csds_hydro.h
@@ -22,12 +22,12 @@
#include "../config.h"
/* local includes */
-#include "hydro.h"
-#include "hydro_csds.h"
#include "csds_interpolation.h"
#include "csds_loader_io.h"
#include "csds_parameters.h"
#include "csds_python_tools.h"
+#include "hydro.h"
+#include "hydro_csds.h"
/* Index of the mask in the header mask array */
extern int hydro_csds_local_to_global[hydro_csds_field_count];
@@ -44,12 +44,9 @@ __attribute__((always_inline)) INLINE static void
hydro_csds_reader_link_derivatives(struct header *head) {
/* Set the first and second derivatives */
- const int pos_id =
- hydro_csds_local_to_global[hydro_csds_field_coordinates];
- const int vel_id =
- hydro_csds_local_to_global[hydro_csds_field_velocities];
- const int acc_id =
- hydro_csds_local_to_global[hydro_csds_field_accelerations];
+ const int pos_id = hydro_csds_local_to_global[hydro_csds_field_coordinates];
+ const int vel_id = hydro_csds_local_to_global[hydro_csds_field_velocities];
+ const int acc_id = hydro_csds_local_to_global[hydro_csds_field_accelerations];
/* Coordinates */
header_set_first_derivative(head, pos_id, vel_id);
@@ -76,14 +73,11 @@ hydro_csds_reader_link_derivatives(struct header *head) {
* #hydro_csds_fields).
* @param params The simulation's #csds_parameters.
*/
-__attribute__((always_inline)) INLINE static void
-hydro_csds_interpolate_field(const double t_before,
- const struct csds_field *restrict before,
- const double t_after,
- const struct csds_field *restrict after,
- void *restrict output, const double t,
- const int field,
- const struct csds_parameters *params) {
+__attribute__((always_inline)) INLINE static void hydro_csds_interpolate_field(
+ const double t_before, const struct csds_field *restrict before,
+ const double t_after, const struct csds_field *restrict after,
+ void *restrict output, const double t, const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
diff --git a/src/star_formation/GEAR/csds_star_formation.c b/src/star_formation/GEAR/csds_star_formation.c
index 59e634401c83198e4514f4a7eb5638fe76add8ef..e8e41f34b46d6cd62244a69a3a6a72881e083250 100644
--- a/src/star_formation/GEAR/csds_star_formation.c
+++ b/src/star_formation/GEAR/csds_star_formation.c
@@ -23,11 +23,10 @@
/* Local headers */
#include "csds_tools.h"
-const int star_formation_csds_field_size[star_formation_csds_field_count] =
- {
- member_size(struct spart, sf_data.birth_density) +
- member_size(struct spart, sf_data.birth_mass) +
- member_size(struct spart, sf_data.progenitor_id),
+const int star_formation_csds_field_size[star_formation_csds_field_count] = {
+ member_size(struct spart, sf_data.birth_density) +
+ member_size(struct spart, sf_data.birth_mass) +
+ member_size(struct spart, sf_data.progenitor_id),
};
int star_formation_csds_local_to_global[star_formation_csds_field_count];
diff --git a/src/star_formation/GEAR/csds_star_formation.h b/src/star_formation/GEAR/csds_star_formation.h
index c73c6e052acca85287734d888c3349a32f7e15f0..0c79210a387f260079370ee21351bef524b7a897 100644
--- a/src/star_formation/GEAR/csds_star_formation.h
+++ b/src/star_formation/GEAR/csds_star_formation.h
@@ -29,8 +29,7 @@
#include "star_formation_csds.h"
/* Index of the mask in the header mask array */
-extern int
- star_formation_csds_local_to_global[star_formation_csds_field_count];
+extern int star_formation_csds_local_to_global[star_formation_csds_field_count];
/* Size for each mask */
extern const int
@@ -62,11 +61,13 @@ star_formation_csds_reader_link_derivatives(struct header *head) {}
* @param params The simulation's #csds_parameters.
*/
__attribute__((always_inline)) INLINE static void
-star_formation_csds_interpolate_field(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t, const int field,
- const struct csds_parameters *params) {
+star_formation_csds_interpolate_field(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
diff --git a/src/star_formation/none/csds_star_formation.c b/src/star_formation/none/csds_star_formation.c
index 767190eec9f68e440afeaa4d32dade2d5b33d223..53f5b7ce0cd7dedc6e1a0cb0d4c3b02b2d2ff9af 100644
--- a/src/star_formation/none/csds_star_formation.c
+++ b/src/star_formation/none/csds_star_formation.c
@@ -23,7 +23,6 @@
/* Local headers */
#include "csds_tools.h"
-const int star_formation_csds_field_size[star_formation_csds_field_count] =
- {};
+const int star_formation_csds_field_size[star_formation_csds_field_count] = {};
int star_formation_csds_local_to_global[star_formation_csds_field_count];
diff --git a/src/star_formation/none/csds_star_formation.h b/src/star_formation/none/csds_star_formation.h
index 13f806cf75bd7c2104a552383ba5c0e2635fa4a9..2e129a7cab58fc7ffc968d7f1f15f8ad43b4d3f0 100644
--- a/src/star_formation/none/csds_star_formation.h
+++ b/src/star_formation/none/csds_star_formation.h
@@ -29,8 +29,7 @@
#include "star_formation_csds.h"
/* Index of the mask in the header mask array */
-extern int
- star_formation_csds_local_to_global[star_formation_csds_field_count];
+extern int star_formation_csds_local_to_global[star_formation_csds_field_count];
/* Size for each mask */
extern const int
@@ -62,11 +61,13 @@ star_formation_csds_reader_link_derivatives(struct header *head) {}
* @param params The simulation's #csds_parameters.
*/
__attribute__((always_inline)) INLINE static void
-star_formation_csds_interpolate_field(
- const double t_before, const struct csds_field *restrict before,
- const double t_after, const struct csds_field *restrict after,
- void *restrict output, const double t, const int field,
- const struct csds_parameters *params) {}
+star_formation_csds_interpolate_field(const double t_before,
+ const struct csds_field *restrict before,
+ const double t_after,
+ const struct csds_field *restrict after,
+ void *restrict output, const double t,
+ const int field,
+ const struct csds_parameters *params) {}
#ifdef HAVE_PYTHON
__attribute__((always_inline)) INLINE static void
diff --git a/src/stars/Basic/csds_stars.h b/src/stars/Basic/csds_stars.h
index 1f989f672d833e9d470e3452214d0af1e2cf1eea..d3dbc427b61a5bd05556c18f5a0e84679ad48a9f 100644
--- a/src/stars/Basic/csds_stars.h
+++ b/src/stars/Basic/csds_stars.h
@@ -43,12 +43,9 @@ __attribute__((always_inline)) INLINE static void
stars_csds_reader_link_derivatives(struct header *head) {
/* Set the first and second derivatives */
- const int pos_id =
- stars_csds_local_to_global[stars_csds_field_coordinates];
- const int vel_id =
- stars_csds_local_to_global[stars_csds_field_velocities];
- const int acc_id =
- stars_csds_local_to_global[stars_csds_field_accelerations];
+ const int pos_id = stars_csds_local_to_global[stars_csds_field_coordinates];
+ const int vel_id = stars_csds_local_to_global[stars_csds_field_velocities];
+ const int acc_id = stars_csds_local_to_global[stars_csds_field_accelerations];
/* Coordinates */
header_set_first_derivative(head, pos_id, vel_id);
@@ -75,14 +72,11 @@ stars_csds_reader_link_derivatives(struct header *head) {
* #stars_csds_fields).
* @param params The simulation's #csds_parameters.
*/
-__attribute__((always_inline)) INLINE static void
-stars_csds_interpolate_field(const double t_before,
- const struct csds_field *restrict before,
- const double t_after,
- const struct csds_field *restrict after,
- void *restrict output, const double t,
- const int field,
- const struct csds_parameters *params) {
+__attribute__((always_inline)) INLINE static void stars_csds_interpolate_field(
+ const double t_before, const struct csds_field *restrict before,
+ const double t_after, const struct csds_field *restrict after,
+ void *restrict output, const double t, const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
diff --git a/src/stars/GEAR/csds_stars.h b/src/stars/GEAR/csds_stars.h
index 9609f1d03a5a85f6c66c46ef921cc2c498d464f6..65f7831c4c78a7bb201f8400d03370228917c8c9 100644
--- a/src/stars/GEAR/csds_stars.h
+++ b/src/stars/GEAR/csds_stars.h
@@ -43,12 +43,9 @@ __attribute__((always_inline)) INLINE static void
stars_csds_reader_link_derivatives(struct header *head) {
/* Set the first and second derivatives */
- const int pos_id =
- stars_csds_local_to_global[stars_csds_field_coordinates];
- const int vel_id =
- stars_csds_local_to_global[stars_csds_field_velocities];
- const int acc_id =
- stars_csds_local_to_global[stars_csds_field_accelerations];
+ const int pos_id = stars_csds_local_to_global[stars_csds_field_coordinates];
+ const int vel_id = stars_csds_local_to_global[stars_csds_field_velocities];
+ const int acc_id = stars_csds_local_to_global[stars_csds_field_accelerations];
/* Coordinates */
header_set_first_derivative(head, pos_id, vel_id);
@@ -75,14 +72,11 @@ stars_csds_reader_link_derivatives(struct header *head) {
* #stars_csds_fields).
* @param params The simulation's #csds_parameters.
*/
-__attribute__((always_inline)) INLINE static void
-stars_csds_interpolate_field(const double t_before,
- const struct csds_field *restrict before,
- const double t_after,
- const struct csds_field *restrict after,
- void *restrict output, const double t,
- const int field,
- const struct csds_parameters *params) {
+__attribute__((always_inline)) INLINE static void stars_csds_interpolate_field(
+ const double t_before, const struct csds_field *restrict before,
+ const double t_after, const struct csds_field *restrict after,
+ void *restrict output, const double t, const int field,
+ const struct csds_parameters *params) {
#ifdef SWIFT_DEBUG_CHECKS
/* Check the times */
diff --git a/tests/generate_log.h b/tests/generate_log.h
index 62387bb355e869abbde233ae1f8626f4a6b4fef4..270aba9d0b3f0772c8416c68a6eb59c43fcb18c4 100644
--- a/tests/generate_log.h
+++ b/tests/generate_log.h
@@ -21,10 +21,10 @@
#include "../../config.h"
/* Local headers */
-#include "engine.h"
-#include "hydro.h"
#include "csds.h"
#include "csds_io.h"
+#include "engine.h"
+#include "hydro.h"
/* Not all the fields are written at every step.
* Here we define how often a few fields are written.
@@ -118,7 +118,7 @@ void write_particles(struct csds_writer *log, struct engine *e) {
// TODO write only a few masks at the time
csds_log_part(log, &parts[j], &xparts[j], e, /* log_all */ 0,
- /* flag */ 0, /* flag_data */ 0);
+ /* flag */ 0, /* flag_data */ 0);
}
}
}
@@ -184,21 +184,19 @@ void generate_log(struct swift_params *params, struct part *parts,
csds_ensure_size(&log, nparts, /* number gpart */ 0, 0);
/* Log all the particles before starting */
- csds_log_all_particles(&log, &e, /* first_log */1);
+ csds_log_all_particles(&log, &e, /* first_log */ 1);
/* Write particles */
write_particles(&log, &e);
/* Write a sentinel timestamp */
- csds_log_timestamp(e.csds, e.ti_current, e.time,
- &e.csds->timestamp_offset);
+ csds_log_timestamp(e.csds, e.ti_current, e.time, &e.csds->timestamp_offset);
/* Write all the particles at the end */
- csds_log_all_particles(e.csds, &e, /* first_log */0);
+ csds_log_all_particles(e.csds, &e, /* first_log */ 0);
/* Write a sentinel timestamp */
- csds_log_timestamp(e.csds, e.ti_current, e.time,
- &e.csds->timestamp_offset);
+ csds_log_timestamp(e.csds, e.ti_current, e.time, &e.csds->timestamp_offset);
/* Cleanup the memory */
csds_free(&log);
diff --git a/tests/testLogfileHeader.c b/tests/testLogfileHeader.c
index dbe07b7555301e811dd77fefcca434d31a36d009..3890a761b7d3f9795d510245131aee4eac3a8ea1 100644
--- a/tests/testLogfileHeader.c
+++ b/tests/testLogfileHeader.c
@@ -77,7 +77,7 @@ int main(int argc, char *argv[]) {
/* Read the header */
csds_logfile_init_from_file(logfile, dump_filename, &reader,
- /* only_header */ 1);
+ /* only_header */ 1);
/*
Finally check everything.
*/
diff --git a/tests/testLogfileReader.c b/tests/testLogfileReader.c
index e9bd7663babc475459e172cd25b856039a103404..5d33ce98d9e4eff0e1d236b829ac639a2c3d691f 100644
--- a/tests/testLogfileReader.c
+++ b/tests/testLogfileReader.c
@@ -80,7 +80,7 @@ void check_data(struct csds_reader *reader, struct part *parts,
/* Loop over each record. */
for (size_t offset =
csds_reader_read_record(reader, output, &time, &is_particle,
- logfile->header.offset_first_record);
+ logfile->header.offset_first_record);
offset < logfile->log.mmap_size;
offset = csds_reader_read_record(reader, output, &time, &is_particle,
offset)) {
diff --git a/tests/testVirtualReality.c b/tests/testVirtualReality.c
index 132a8d69886daea06038f6d46f066cd460270141..183e62ea9117fef8f5980bdb72782a2cf9126c70 100644
--- a/tests/testVirtualReality.c
+++ b/tests/testVirtualReality.c
@@ -25,10 +25,10 @@
#include <stdlib.h>
/* Local include */
-#include "generate_log.h"
-#include "hydro.h"
#include "csds.h"
#include "csds_reader.h"
+#include "generate_log.h"
+#include "hydro.h"
#define number_steps 10.
#define number_parts 100
@@ -67,7 +67,7 @@ int main(int argc, char *argv[]) {
strcat(basename, "_0000");
csds_reader_init(&reader, basename,
/* Verbose */ 0, /* number_threads */ 1,
- /* number_index */5);
+ /* number_index */ 5);
/* Read the time limits */
double begin = csds_reader_get_time_begin(&reader);
@@ -135,9 +135,8 @@ int main(int argc, char *argv[]) {
csds_reader_set_time(&reader, t);
/* Read the next time */
- csds_reader_read_all_particles(&reader, t, csds_reader_lin,
- required_fields, n_fields, output,
- n_parts);
+ csds_reader_read_all_particles(&reader, t, csds_reader_lin, required_fields,
+ n_fields, output, n_parts);
message("Particle %lli: %f %f %f %f", ids[part_ind], pos[3 * part_ind + 0],
pos[3 * part_ind + 1], pos[3 * part_ind + 2], t);