Added exponential of distance unit.

New data added to the general information block to specify
the unit of distances in the trajectory, e.g. -9 for nm or
-10 for Å.

3 files changed, 85 insertions, 5 deletions

diff --git a/Doxyfile.in b/Doxyfile.in
index 32fbaba..84b5770 100644
--- a/Doxyfile.in
+++ b/Doxyfile.in
@@ -32,7 +32,7 @@ PROJECT_NAME           = "TNG API"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = "1.1"
+PROJECT_NUMBER         = "1.3"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
diff --git a/include/tng_io.h b/include/tng_io.h
index eb67dd8..2716ccf 100644
--- a/include/tng_io.h
+++ b/include/tng_io.h
@@ -1,6 +1,6 @@
 /* This code is part of the tng binary trajectory format.
  *
- *                      VERSION 1.1
+ *                      VERSION 1.3
  *
  * Written by Magnus Lundborg
  * Copyright (c) 2012, The GROMACS development team.
@@ -25,7 +25,7 @@
  * Each block can contain MD5 hashes to verify data integrity and the file
  * can be signed by the user to ensure that the origin is correct.
  *
- * This is version 1.1 of the TNG API. The intention is that this version of
+ * This is version 1.3 of the TNG API. The intention is that this version of
  * the API and ABI should be stable, but it is still possible that future
  * changes might make that impossible, in which case that will be clarified.
  *
@@ -343,7 +343,7 @@ typedef unsigned long long int  uint64_t;
 
 
 /** The version of this TNG build */
-#define TNG_VERSION 3
+#define TNG_VERSION 3 /* TNG_VERSION 3 => Api version 1.3 */
 
 /** Flag to indicate frame dependent data. */
 #define TNG_FRAME_DEPENDENT 1
@@ -922,6 +922,30 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get
                  int64_t *n);
 
 /**
+ * @brief Get the exponential used for distances in the trajectory.
+ * @param tng_data is the trajectory from which to get the information.
+ * @param exp is pointing to a value set to the distance unit exponential.
+ * @details Example: If the distances are specified in nm (default) exp is -9.
+ * If the distances are specified in Å exp is -10.
+ * @return TNG_SUCCESS (0) if successful.
+ */
+tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_get
+                (const tng_trajectory_t tng_data,
+                 int64_t *exp);
+
+/**
+ * @brief Set the exponential used for distances in the trajectory.
+ * @param tng_data is the trajectory of which to set the unit exponential.
+ * @param exp is the distance unit exponential to use.
+ * @details Example: If the distances are specified in nm (default) exp is -9.
+ * If the distances are specified in Å exp is -10.
+ * @return TNG_SUCCESS (0) if successful.
+ */
+tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_set
+                (const tng_trajectory_t tng_data,
+                 const int64_t exp);
+
+/**
  * @brief Get the number of frames per frame set.
  * @param tng_data is the trajectory from which to get the number of frames
  * per frame set.
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 0d5f1a8..997a488 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -296,6 +296,10 @@ struct tng_trajectory {
     char *last_pgp_signature;
     /** The time (n seconds since 1970) when the file was created */
     int64_t time;
+    /** The exponential of the value of the distance unit used. The default 
+     * distance unit is nm (1e-9), i.e. distance_unit_exponential = -9. If
+     * the measurements are in Å the distance_unit_exponential = -10. */
+    int64_t distance_unit_exponential;
 
     /** A flag indicating if the number of atoms can vary throughout the
      *  simulation, e.g. using a grand canonical ensemble */
@@ -1417,6 +1421,23 @@ static tng_function_status tng_general_info_block_read
                     __FILE__, __LINE__);
         }
     }
+    offset += sizeof(tng_data->long_stride_length);
+    
+    if(block->block_version >= 3)
+    {
+        memcpy(&tng_data->distance_unit_exponential, block->block_contents+offset,
+            sizeof(tng_data->distance_unit_exponential));
+        if(tng_data->input_endianness_swap_func_64)
+        {
+            if(tng_data->input_endianness_swap_func_64(tng_data,
+                                          &tng_data->distance_unit_exponential)
+                != TNG_SUCCESS)
+            {
+                printf("Cannot swap byte order. %s: %d\n",
+                        __FILE__, __LINE__);
+            }
+        }        
+    }
 
     return(TNG_SUCCESS);
 }
@@ -1589,6 +1610,7 @@ static tng_function_status tng_general_info_block_write
                 sizeof(tng_data->last_trajectory_frame_set_input_file_pos) +
                 sizeof(tng_data->medium_stride_length) +
                 sizeof(tng_data->long_stride_length) +
+                sizeof(tng_data->distance_unit_exponential) +
                 first_program_name_len +
                 last_program_name_len +
                 first_user_name_len +
@@ -1732,6 +1754,20 @@ static tng_function_status tng_general_info_block_write
                     __FILE__, __LINE__);
         }
     }
+    offset += sizeof(tng_data->long_stride_length);
+
+    memcpy(block->block_contents+offset, &tng_data->distance_unit_exponential,
+           sizeof(tng_data->distance_unit_exponential));
+    if(tng_data->output_endianness_swap_func_64)
+    {
+        if(tng_data->output_endianness_swap_func_64(tng_data,
+                                      (int64_t *)block->header_contents+offset)
+            != TNG_SUCCESS)
+        {
+            printf("Cannot swap byte order. %s: %d\n",
+                    __FILE__, __LINE__);
+        }
+    }
 
     if(tng_block_header_write(tng_data, block, hash_mode) != TNG_SUCCESS)
     {
@@ -6146,7 +6182,7 @@ static tng_function_status tng_header_pointers_update
 
     contents_start_pos = ftell(tng_data->output_file);
 
-    fseek(tng_data->output_file, block->block_contents_size - 4 *
+    fseek(tng_data->output_file, block->block_contents_size - 5 *
           sizeof(int64_t), SEEK_CUR);
 
     tng_data->input_file = temp;
@@ -7708,6 +7744,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_
 
     tng_data->compress_algo_pos = 0;
     tng_data->compress_algo_vel = 0;
+    tng_data->distance_unit_exponential = -9;
 
     frame_set->first_frame = -1;
     frame_set->n_mapping_blocks = 0;
@@ -8246,6 +8283,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector
 
     dest->compress_algo_pos = 0;
     dest->compress_algo_vel = 0;
+    dest->distance_unit_exponential = -9;
 
     frame_set->n_mapping_blocks = 0;
     frame_set->mappings = 0;
@@ -9053,6 +9091,24 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get
     return(TNG_SUCCESS);
 }
 
+tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_get
+                (const tng_trajectory_t tng_data,
+                 int64_t *exp)
+{
+    *exp = tng_data->distance_unit_exponential;
+    
+    return(TNG_SUCCESS);
+}
+
+tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_set
+                (const tng_trajectory_t tng_data,
+                 const int64_t exp)
+{
+    tng_data->distance_unit_exponential = exp;
+    
+    return(TNG_SUCCESS);
+}
+                
 tng_function_status DECLSPECDLLEXPORT tng_num_frames_per_frame_set_get
                 (const tng_trajectory_t tng_data,
                  int64_t *n)