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-rw-r--r--src/lib/tng_io.c92
1 files changed, 60 insertions, 32 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 430fc35..2a8979e 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -4864,6 +4864,20 @@ static tng_function_status tng_particle_data_block_write
frame_step = (n_frames % stride_length) ? n_frames / stride_length + 1:
n_frames / stride_length;
+ /* TNG compression will use compression precision to get integers from
+ * floating point data. The compression multiplier stores that information
+ * to be able to return the precision of the compressed data. */
+ if(data->codec_id == TNG_TNG_COMPRESSION)
+ {
+ data->compression_multiplier = 1/tng_data->compression_precision;
+ }
+ /* Uncompressed data blocks do not use compression multipliers at all.
+ * GZip compression does not need it either. */
+ else if(data->codec_id == TNG_UNCOMPRESSED || data->codec_id == TNG_GZIP_COMPRESSION)
+ {
+ data->compression_multiplier = 1.0;
+ }
+
if(mapping && mapping->n_particles != 0)
{
n_particles = mapping->n_particles;
@@ -5107,7 +5121,8 @@ static tng_function_status tng_particle_data_block_write
switch(data->datatype)
{
case TNG_FLOAT_DATA:
- if(data->codec_id == TNG_UNCOMPRESSED)
+ if(data->codec_id == TNG_UNCOMPRESSED || data-> codec_id == TNG_GZIP_COMPRESSION ||
+ data->codec_id == TNG_TNG_COMPRESSION)
{
if(tng_data->input_endianness_swap_func_32)
{
@@ -5160,7 +5175,8 @@ static tng_function_status tng_particle_data_block_write
}
break;
case TNG_DOUBLE_DATA:
- if(data->codec_id == TNG_UNCOMPRESSED)
+ if(data->codec_id == TNG_UNCOMPRESSED || data-> codec_id == TNG_GZIP_COMPRESSION ||
+ data->codec_id == TNG_TNG_COMPRESSION)
{
if(tng_data->input_endianness_swap_func_64)
{
@@ -5762,6 +5778,20 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data,
frame_step = (n_frames % stride_length) ? n_frames / stride_length + 1:
n_frames / stride_length;
+ /* TNG compression will use compression precision to get integers from
+ * floating point data. The compression multiplier stores that information
+ * to be able to return the precision of the compressed data. */
+ if(data->codec_id == TNG_TNG_COMPRESSION)
+ {
+ data->compression_multiplier = 1/tng_data->compression_precision;
+ }
+ /* Uncompressed data blocks do not use compression multipliers at all.
+ * GZip compression does not need it either. */
+ else if(data->codec_id == TNG_UNCOMPRESSED || data->codec_id == TNG_GZIP_COMPRESSION)
+ {
+ data->compression_multiplier = 1.0;
+ }
+
block->block_contents_size = sizeof(char) * 2 +
sizeof(data->n_values_per_frame) +
sizeof(data->codec_id);
@@ -5945,7 +5975,8 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data,
switch(data->datatype)
{
case TNG_FLOAT_DATA:
- if(data->codec_id == TNG_UNCOMPRESSED)
+ if(data->codec_id == TNG_UNCOMPRESSED || data-> codec_id == TNG_GZIP_COMPRESSION ||
+ data->codec_id == TNG_TNG_COMPRESSION)
{
if(tng_data->input_endianness_swap_func_32)
{
@@ -5998,7 +6029,8 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data,
}
break;
case TNG_DOUBLE_DATA:
- if(data->codec_id == TNG_UNCOMPRESSED)
+ if(data->codec_id == TNG_UNCOMPRESSED || data-> codec_id == TNG_GZIP_COMPRESSION ||
+ data->codec_id == TNG_TNG_COMPRESSION)
{
if(tng_data->input_endianness_swap_func_64)
{
@@ -6066,14 +6098,6 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data,
return(TNG_CRITICAL);
}
data->codec_id = TNG_UNCOMPRESSED;
- if(fabs(data->compression_multiplier - 1.0) > 0.00001)
- {
- printf("TNG library: Multiplier applied, but block was not compressed. Data will be wrong.\n");
- printf("TNG library: The block might be completely corrupted.\n");
- /* FIXME: The data should be divided by the multiplier and the data that is only
- * present in blocks containing compressed data (e.g. multiplier) must be
- * removed */
- }
}
/* printf("TNG library: After compression: %"PRId64"\n", block->block_contents_size); */
break;
@@ -7347,7 +7371,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t
&molecule_temp);
if(stat != TNG_SUCCESS)
{
- printf("TNG library: Cannot create new molecule to make a copy.");
+ printf("TNG library: Cannot create new molecule to make a copy. %s: %d\n",
+ __FILE__, __LINE__);
return(stat);
}
molecule_temp->quaternary_str = molecule->quaternary_str;
@@ -7359,7 +7384,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t
&chain_temp);
if(stat != TNG_SUCCESS)
{
- printf("TNG library: Cannot create new chain to make a copy.");
+ printf("TNG library: Cannot create new chain to make a copy. %s: %d\n",
+ __FILE__, __LINE__);
return(stat);
}
for(k = 0; k < chain->n_residues; k++)
@@ -7370,7 +7396,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t
&residue_temp);
if(stat != TNG_SUCCESS)
{
- printf("TNG library: Cannot create new residue to make a copy.");
+ printf("TNG library: Cannot create new residue to make a copy. %s: %d\n",
+ __FILE__, __LINE__);
return(stat);
}
for(l = 0; l < residue->n_atoms; l++)
@@ -7381,7 +7408,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t
atom->id, &atom_temp);
if(stat != TNG_SUCCESS)
{
- printf("TNG library: Cannot create new atom to make a copy.");
+ printf("TNG library: Cannot create new atom to make a copy. %s: %d\n",
+ __FILE__, __LINE__);
return(stat);
}
}
@@ -9283,7 +9311,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_append_file_set
tng_data->output_file_path = temp;
strncpy(tng_data->output_file_path, file_name, len);
-
+
tng_data->output_file = fopen(tng_data->output_file_path, "r+");
if(!tng_data->output_file)
{
@@ -11664,7 +11692,7 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data,
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
frame_set = &tng_data->current_trajectory_frame_set;
-
+
if(frame_set->n_written_frames == frame_set->n_frames)
{
return(TNG_SUCCESS);
@@ -11754,15 +11782,15 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_premature_write
tng_trajectory_frame_set_t frame_set;
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
-
+
frame_set = &tng_data->current_trajectory_frame_set;
-
+
if(frame_set->n_unwritten_frames == 0)
{
return(TNG_SUCCESS);
}
frame_set->n_frames = frame_set->n_unwritten_frames;
-
+
return(tng_frame_set_write(tng_data, hash_mode));
}
@@ -11846,7 +11874,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new
if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
{
- printf("TNG library: Cannot read frame header. %s: %d\n",
+ printf("TNG library: Cannot read frame set header. %s: %d\n",
__FILE__, __LINE__);
tng_data->input_file = temp;
tng_block_destroy(&block);
@@ -11902,7 +11930,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new
if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
{
- printf("TNG library: Cannot read frame header. %s: %d\n",
+ printf("TNG library: Cannot read frame set header. %s: %d\n",
__FILE__, __LINE__);
tng_data->input_file = temp;
tng_block_destroy(&block);
@@ -12162,9 +12190,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add
return(TNG_CRITICAL);
}
- if(n_frames > frame_set->n_written_frames)
+ if(n_frames > frame_set->n_unwritten_frames)
{
- frame_set->n_written_frames = n_frames;
+ frame_set->n_unwritten_frames = n_frames;
}
n_frames_div = (n_frames % stride_length) ?
@@ -12311,9 +12339,9 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
return(TNG_CRITICAL);
}
- if(n_frames > frame_set->n_written_frames)
+ if(n_frames > frame_set->n_unwritten_frames)
{
- frame_set->n_written_frames = n_frames;
+ frame_set->n_unwritten_frames = n_frames;
}
n_frames_div = (n_frames % stride_length) ?
@@ -15185,7 +15213,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open
{
tng_function_status stat;
tng_gen_block_t block;
-
+
TNG_ASSERT(filename, "TNG library: filename must not be a NULL pointer.");
if(mode != 'r' && mode != 'w' && mode != 'a')
@@ -15216,7 +15244,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open
fseek((*tng_data_p)->input_file,
(long)(*tng_data_p)->last_trajectory_frame_set_input_file_pos,
SEEK_SET);
-
+
tng_block_init(&block);
stat = tng_block_header_read(*tng_data_p, block);
@@ -15235,7 +15263,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open
__FILE__, __LINE__);
return(stat);
}
-
+
(*tng_data_p)->first_trajectory_frame_set_output_file_pos =
(*tng_data_p)->first_trajectory_frame_set_input_file_pos;
(*tng_data_p)->last_trajectory_frame_set_output_file_pos =
@@ -15255,7 +15283,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open
free((*tng_data_p)->input_file_path);
(*tng_data_p)->input_file_path = 0;
}
- tng_output_append_file_set(*tng_data_p, filename);
+ tng_output_append_file_set(*tng_data_p, filename);
}
return(TNG_SUCCESS);
@@ -16468,7 +16496,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
}
frame_set->n_unwritten_frames = frame_nr -
frame_set->first_frame + 1;
-
+
n_frames = frame_set->n_frames;
}
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