Logger: implement pedro's comments

logger/Makefile.am

 # This file is part of SWIFT.
 # Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
 #                    Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+#                    Loic Hausammann (loic.hausammann@epfl.ch)
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

logger/logger_header.c

@@ -119,7 +119,11 @@ void header_read(struct header *h, struct logger_logfile *log) {
   /* Read minor version number */
   map = logger_loader_io_read_data(map, sizeof(int), &h->minor_version);
 
-  if (h->log->reader->verbose > 0)
+  struct logger_reader *reader = log->reader;
+  if (&reader->log != log)
+    error("Wrong link to the reader.");
+
+  if (reader->verbose > 0)
     message("File version %i.%i", h->major_version, h->minor_version);
 
   /* read the offset directions */

logger/logger_logfile.c

@@ -29,15 +29,17 @@
  * @param reader The #logger_reader.
  * @param only_header Read only the header.
  */
-void logger_logfile_init(
+void logger_logfile_init_from_file(
     struct logger_logfile *log, char *filename,
     struct logger_reader *reader, int only_header) {
 
   /* Set the pointer to the reader. */
   log->reader = reader;
+  if (&reader->log != log)
+    error("Wrong link to the reader.");
 
   /* Set pointers to zero */
-  time_array_init_to_zero(&log->times);
+  time_array_init(&log->times);
 
   /* Open file, map it and get its size. */
   if (reader->verbose > 1)
@@ -73,7 +75,7 @@ void logger_logfile_init(
   /* Initialize the time array */
   if (reader->verbose > 1)
     message("Reading the time stamps.");
-  time_array_init(&log->times, log);
+  time_array_populate(&log->times, log);
 
   /* Print the time array */
   if (reader->verbose > 0) {
@@ -90,6 +92,7 @@ void logger_logfile_init(
 void logger_logfile_free(struct logger_logfile *log) {
   logger_loader_io_munmap_file(log->log.map, log->log.file_size);
 
+  time_array_free(&log->times);
 }
 
 
@@ -109,6 +112,8 @@ void logger_logfile_reverse_offset(struct logger_logfile *log, char *filename) {
   /* Get pointers */
   struct header *header = &log->header;
   const struct logger_reader *reader = log->reader;
+  if (&reader->log != log)
+    error("Wrong link to the reader.");
 
   /* Check if the offsets need to be reversed */
   if (!header_is_backward(header)) {

logger/logger_logfile.h

@@ -35,7 +35,7 @@ struct logger_reader;
  * and deals with the log file.
  * It maps it, reverse the offsets (if required) and unmap it.
  *
- * The structure is initialized with #logger_logfile_init and
+ * The structure is initialized with #logger_logfile_init_from_file and
  * freed with #logger_logfile_free.
  */
 struct logger_logfile {
@@ -62,7 +62,7 @@ struct logger_logfile {
 };
 
 
-void logger_logfile_init(struct logger_logfile *log, char *filename, struct logger_reader *reader,
+void logger_logfile_init_from_file(struct logger_logfile *log, char *filename, struct logger_reader *reader,
 			 int only_header);
 void logger_logfile_reverse_offset(struct logger_logfile *log, char *filename);
 void logger_logfile_free(struct logger_logfile *log);

logger/logger_reader.c

@@ -34,8 +34,8 @@ void logger_reader_init(struct logger_reader *reader, char *filename, int verbos
   reader->verbose = verbose;
 
   /* Initialize the log file */
-  logger_logfile_init(&reader->log, filename, reader,
-		      /* only_header */ 0);
+  logger_logfile_init_from_file(&reader->log, filename, reader,
+				/* only_header */ 0);
 
   if (verbose > 1)
     message("Initialization done.");

logger/logger_time.c

@@ -94,18 +94,18 @@ size_t time_offset_first_record(const struct header *h) {
  *
  * @param t #time_array to initialize.
  */
-void time_array_init_to_zero(struct time_array *t) {
+void time_array_init(struct time_array *t) {
   t->next = NULL;
   t->prev = NULL;
 }
 
 /**
- * @brief Initialize a time array.
+ * @brief Initialize a time array from a file.
  *
  * @param t #time_array to initialize.
  * @param log The #logger_logfile.
  */
-void time_array_init(struct time_array *t, struct logger_logfile *log) {
+void time_array_populate(struct time_array *t, struct logger_logfile *log) {
 
   /* Initialize a few variables. */
   t->next = NULL;

logger/logger_time.h

@@ -34,7 +34,7 @@ struct logger_reader;
  * this structure is required. It contains all the time step
  * with their integer time, double time and position in the file.
  *
- * This structure is initialized with #time_array_init and
+ * This structure is initialized with #time_array_init and #time_array_populate, and
  * freed with #time_array_free.
  *
  * The time step of an offset can be obtained with
@@ -64,8 +64,8 @@ struct time_array {
 size_t time_read(integertime_t *int_time, double *time,
 	       const struct logger_reader *reader, size_t offset);
 
-void time_array_init_to_zero(struct time_array *t);
-void time_array_init(struct time_array *t, struct logger_logfile *log);
+void time_array_init(struct time_array *t);
+void time_array_populate(struct time_array *t, struct logger_logfile *log);
 
 integertime_t time_array_get_integertime(struct time_array *t, const size_t offset);
 

logger/tests/Makefile.am

@@ -20,18 +20,18 @@ AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/logger $(HDF5_CPPFLAGS) $(GSL_IN
 AM_LDFLAGS = ../../src/.libs/libswiftsim.a ../.libs/liblogger.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(FFTW_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS) $(PROFILER_LIBS)
 
 # List of programs and scripts to run in the test suite
-TESTS = testHeader testReader # testIndex
+TESTS = testLogfileHeader testLogfileReader # testIndex
 
 # List of test programs to compile
-check_PROGRAMS = testHeader testReader
+check_PROGRAMS = testLogfileHeader testLogfileReader
 
 # Rebuild tests when SWIFT is updated.
 $(check_PROGRAMS): ../../src/.libs/libswiftsim.a
 
 # Sources for the individual programs
-testHeader_SOURCES = testHeader.c
-testReader_SOURCES = testReader.c
+testLogfileHeader_SOURCES = testLogfileHeader.c
+testReader_SOURCES = testLogfileReader.c
 # testIndex_SOURCES = testIndex.c
 
 # Files necessary for distribution
-EXTRA_DIST = testHeader.yml testReader.yml testIndex.yml
+EXTRA_DIST = testLogfileHeader.yml testLogfileReader.yml testIndex.yml

logger/tests/testHeader.c → logger/tests/testLogfileHeader.c

 /*******************************************************************************
  * This file is part of SWIFT.
- * Copyright (C) 2015 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ * Copyright (C) 2019 Loic Hausammann (loic.hausammann@epfl.ch)
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as published
@@ -32,7 +32,7 @@ int main(int argc, char *argv[]) {
   /* Create required structures. */
   struct logger log;
   struct swift_params params;
-  char filename[200] = "testHeader.yml";
+  char filename[200] = "testLogfileHeader.yml";
 
   /* Read parameters. */
   parser_read_file(filename, &params);
@@ -49,33 +49,34 @@ int main(int argc, char *argv[]) {
   logger_write_file_header(&log);
 
   /* clean memory */
-  logger_clean(&log);
+  logger_free(&log);
   /*
     Then read the file.
   */
 
   message("Reading the header.");
   /* Generate required structure for reading. */
-  struct logger_logfile logfile;
   struct logger_reader reader;
+  struct logger_logfile *logfile = &reader.log;
+  logfile->reader = &reader;
 
   /* Set verbose level */
   reader.verbose = 1;
   
   /* Read the header */
-  logger_logfile_init(&logfile, dump_filename, &reader,
+  logger_logfile_init_from_file(logfile, dump_filename, &reader,
 		      /* only_header */ 1);
   /*
     Finally check everything
   */
 
-  struct header *h = &logfile.header;
+  struct header *h = &logfile->header;
   message("Checking versions.");
   assert(h->major_version == logger_major_version);
   assert(h->minor_version == logger_minor_version);
 
   message("Checking offset of first record");
-  assert(h->offset_first_record == logfile.log.file_size);
+  assert(h->offset_first_record == logfile->log.file_size);
 
   message("Checking number of masks");
   assert(h->number_mask == logger_count_mask);

logger/tests/testReader.c → logger/tests/testLogfileReader.c

 /*******************************************************************************
  * This file is part of SWIFT.
- * Copyright (C) 2015 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ * Copyright (C) 2019 Loic Hausammann (loic.hausammann@epfl.ch).
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as published
@@ -44,8 +44,8 @@ void init_particles(struct part *p, struct xpart *xp) {
 
     for(int j = 0; j < 3; j++) {
       p[i].x[j] = i;
-      p[i].v[j] = j == 0 ? -1 : 0;
-      p[i].a_hydro[j] = j == 1 ? 1e-2 : 0;
+      p[i].v[j] = (j == 0) ? -1 : 0;
+      p[i].a_hydro[j] = (j == 1) ? 1e-2 : 0;
     }
     p[i].h = 15;
     p[i].rho = 50;
@@ -55,20 +55,12 @@ void init_particles(struct part *p, struct xpart *xp) {
   }
 }
 
-/**
- * @brief Provides a time given the step number.
- *
- * @param step The required step.
- */
+/** Provides a integer time given the step number.*/
 integertime_t get_integer_time(int step) {
   return step;
 }
 
-/**
- * @brief Provides a time given the step number.
- *
- * @param step The required step.
- */
+/** Provides a double time given the step number. */
 double get_double_time(int step) {
   const double time_base = 1e-4;
   return step * time_base;
@@ -217,6 +209,7 @@ void check_data(struct logger_reader *reader) {
       offset = read_record(reader, &lp, &time, &is_particle, offset)) {
 
     if (is_particle) {
+      /* Check data if it is a particle */
       if (lp.id >= number_parts)
 	error("Wrong id %zi", lp.id);
 
@@ -234,6 +227,7 @@ void check_data(struct logger_reader *reader) {
       assert(p->mass == lp.mass);
     }
     else {
+      /* Check data if it is a timestamp */
       assert(time == get_double_time(step));
 
       step += 1;
@@ -254,7 +248,7 @@ int main(int argc, char *argv[]) {
   /* Create required structures. */
   struct logger log;
   struct swift_params params;
-  char filename[200] = "testReader.yml";
+  char filename[200] = "testLogfileReader.yml";
 
   /* Read parameters. */
   parser_read_file(filename, &params);
@@ -275,7 +269,7 @@ int main(int argc, char *argv[]) {
   write_particles(&log);
 
   /* clean memory */
-  logger_clean(&log);
+  logger_free(&log);
   /*
     Then read the file.
   */

src/engine.c

@@ -6270,7 +6270,7 @@ void engine_clean(struct engine *e, const int fof) {
 
   swift_free("links", e->links);
 #if defined(WITH_LOGGER)
-  logger_clean(e->logger);
+  logger_free(e->logger);
   free(e->logger);
 #endif
   scheduler_clean(&e->sched);

src/logger.c

@@ -447,7 +447,7 @@ void logger_init(struct logger *log, struct swift_params *params) {
  *
  * @param log The #logger
  */
-void logger_clean(struct logger *log) { dump_close(&log->dump); }
+void logger_free(struct logger *log) { dump_close(&log->dump); }
 
 /**
  * @brief Write a file header to a logger file

src/logger.h

@@ -144,7 +144,7 @@ void logger_log_part(struct logger *log, const struct part *p,
 void logger_log_gpart(struct logger *log, const struct gpart *p,
                       unsigned int mask, size_t *offset);
 void logger_init(struct logger *log, struct swift_params *params);
-void logger_clean(struct logger *log);
+void logger_free(struct logger *log);
 void logger_log_timestamp(struct logger *log, integertime_t t, double time,
                           size_t *offset);
 void logger_ensure_size(struct logger *log, size_t total_nr_parts,