Rewrite of file i/o.

Do not read and write data blocks in whole chunks. Read and
write value by value and do the md5 summing in steps.
This hopefully avoids memory alignment problems reported
on ARM architectures.

Fixed a bug freeing trajectory mapping memory.

Change-Id: I3438b3d3faf5349dcd477a31cfb4bacf236ed582

1 files changed, 22 insertions, 21 deletions

diff --git a/include/tng/tng_io.h b/include/tng/tng_io.h
index 42119a5..aaf66cd 100644
--- a/include/tng/tng_io.h
+++ b/include/tng/tng_io.h
@@ -290,6 +290,8 @@
 #ifndef TNG_IO_H
 #define TNG_IO_H     1
 
+#define _FILE_OFFSET_BITS 64
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -336,7 +338,6 @@ typedef unsigned __int64 uint64_t;
 
 #endif /* USE_STD_INTTYPES_H */
 
-
 #ifndef USE_WINDOWS
 #if defined(WIN32) || defined(_WIN32) || defined(WIN64) || defined(_WIN64)
 #define USE_WINDOWS
@@ -4071,7 +4072,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set
 /**
  * @brief High-level function for writing data of one frame to a data block.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param values is a 1D array of data to add. The array should be of length
  * n_particles * n_values_per_frame if writing particle related data, otherwise
  * it should be n_values_per_frame.
@@ -4090,7 +4092,6 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set
  * Only required if the block did not exist, i.e. a new block is created.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code values != 0 \endcode The pointer to the values array must not
  * be a NULL pointer.
  * @details n_values_per_frame, block_name, particle_dependency and
@@ -4117,7 +4118,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
  * @brief High-level function for writing data of one frame to a double precision
  * data block.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param values is a 1D array of data to add. The array should be of length
  * n_particles * n_values_per_frame if writing particle related data, otherwise
  * it should be n_values_per_frame.
@@ -4136,7 +4138,6 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
  * Only required if the block did not exist, i.e. a new block is created.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code values != 0 \endcode The pointer to the values array must not
  * be a NULL pointer.
  * @details n_values_per_frame, block_name, particle_dependency and
@@ -4162,12 +4163,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write
 /**
  * @brief High-level function for adding data to positions data blocks.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param positions is a 1D array of data to add. The array should be of length
  * n_particles * 3.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code positions != 0 \endcode The pointer to the positions array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4189,12 +4190,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write
  * @brief High-level function for adding data to positions data blocks at double
  * precision.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param positions is a 1D array of data to add. The array should be of length
  * n_particles * 3.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code positions != 0 \endcode The pointer to the positions array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4215,12 +4216,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write
 /**
  * @brief High-level function for adding data to velocities data blocks.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param velocities is a 1D array of data to add. The array should be of length
  * n_particles * 3.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code velocities != 0 \endcode The pointer to the velocities array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4242,12 +4243,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write
  * @brief High-level function for adding data to velocities data blocks at double
  * precision.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param velocities is a 1D array of data to add. The array should be of length
  * n_particles * 3.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code velocities != 0 \endcode The pointer to the velocities array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4268,12 +4269,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write
 /**
  * @brief High-level function for adding data to forces data blocks.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param forces is a 1D array of data to add. The array should be of length
  * n_particles * 3.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code forces != 0 \endcode The pointer to the forces array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4295,12 +4296,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write
  * @brief High-level function for adding data to forces data blocks at double
  * precision.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param forces is a 1D array of data to add. The array should be of length
  * n_particles * 3.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code forces != 0 \endcode The pointer to the forces array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4321,11 +4322,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write
 /**
  * @brief High-level function for adding data to box shape data blocks.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param box_shape is a 1D array of data to add. The array should be of length 9.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code box_shape != 0 \endcode The pointer to the box_shape array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will
@@ -4347,11 +4348,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write
  * @brief High-level function for adding data to box shape data blocks at double
  * precision.
  * @param tng_data is the trajectory to use.
- * @param frame_nr is the frame number of the data.
+ * @param frame_nr is the frame number of the data. If frame_nr < 0 the
+ * data is written as non-trajectory data.
  * @param box_shape is a 1D array of data to add. The array should be of length 9.
  * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
  * must be initialised before using it.
- * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0.
  * @pre \code box_shape != 0 \endcode The pointer to the box_shape array must not
  * be a NULL pointer.
  * @details This function uses tng_util_generic_write() and will