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Diffstat (limited to 'src/lib/tng_io.c')
-rw-r--r--src/lib/tng_io.c172
1 files changed, 152 insertions, 20 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 11fa8d6..61280d3 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -1182,7 +1182,7 @@ static tng_function_status tng_frame_set_pointers_update
tng_gen_block_t block;
tng_trajectory_frame_set_t frame_set;
FILE *temp = tng_data->input_file;
- int64_t pos, output_file_pos, header_start_pos, contents_start_pos;
+ int64_t pos, output_file_pos, contents_start_pos;
if(tng_output_file_init(tng_data) != TNG_SUCCESS)
{
@@ -1198,15 +1198,59 @@ static tng_function_status tng_frame_set_pointers_update
frame_set = &tng_data->current_trajectory_frame_set;
+ pos = tng_data->current_trajectory_frame_set_output_file_pos;
+
+ /* Update next frame set */
+ if(frame_set->next_frame_set_file_pos > 0)
+ {
+ fseek(tng_data->output_file, (long)frame_set->next_frame_set_file_pos,
+ SEEK_SET);
+
+ if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot read frame header. %s: %d\n",
+ __FILE__, __LINE__);
+ tng_data->input_file = temp;
+ tng_block_destroy(&block);
+ return(TNG_CRITICAL);
+ }
+
+ contents_start_pos = ftell(tng_data->output_file);
+
+ fseek(tng_data->output_file, (long)block->block_contents_size - (5 *
+ sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
+
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &pos)
+ != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+
+ if(fwrite(&pos, sizeof(int64_t), 1, tng_data->output_file) != 1)
+ {
+ tng_data->input_file = temp;
+ tng_block_destroy(&block);
+ return(TNG_CRITICAL);
+ }
+
+ if(hash_mode == TNG_USE_HASH)
+ {
+ tng_md5_hash_update(tng_data, block, frame_set->next_frame_set_file_pos,
+ contents_start_pos);
+ }
+ fseek(tng_data->output_file, (long)output_file_pos, SEEK_SET);
+ }
/* Update previous frame set */
- if(frame_set->prev_frame_set_file_pos != -1 &&
- frame_set->prev_frame_set_file_pos != 0)
+ if(frame_set->prev_frame_set_file_pos > 0)
{
fseek(tng_data->output_file, (long)frame_set->prev_frame_set_file_pos,
SEEK_SET);
- header_start_pos = frame_set->prev_frame_set_file_pos;
-
if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot read frame header. %s: %d\n",
@@ -1221,8 +1265,6 @@ static tng_function_status tng_frame_set_pointers_update
fseek(tng_data->output_file, (long)block->block_contents_size - (6 *
sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
- pos = tng_data->current_trajectory_frame_set_output_file_pos;
-
if(tng_data->input_endianness_swap_func_64)
{
if(tng_data->input_endianness_swap_func_64(tng_data,
@@ -1243,15 +1285,60 @@ static tng_function_status tng_frame_set_pointers_update
if(hash_mode == TNG_USE_HASH)
{
- tng_md5_hash_update(tng_data, block, header_start_pos,
+ tng_md5_hash_update(tng_data, block, frame_set->prev_frame_set_file_pos,
contents_start_pos);
}
fseek(tng_data->output_file, (long)output_file_pos, SEEK_SET);
}
+ /* Update the frame set one medium stride step after */
+ if(frame_set->medium_stride_next_frame_set_file_pos > 0)
+ {
+ fseek(tng_data->output_file,
+ (long)frame_set->medium_stride_next_frame_set_file_pos,
+ SEEK_SET);
+
+ if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot read frame set header. %s: %d\n",
+ __FILE__, __LINE__);
+ tng_data->input_file = temp;
+ tng_block_destroy(&block);
+ return(TNG_CRITICAL);
+ }
+
+ contents_start_pos = ftell(tng_data->output_file);
+
+ fseek(tng_data->output_file, (long)block->block_contents_size - (3 *
+ sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
+
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &pos)
+ != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+
+ if(fwrite(&pos, sizeof(int64_t), 1, tng_data->output_file) != 1)
+ {
+ tng_data->input_file = temp;
+ tng_block_destroy(&block);
+ return(TNG_CRITICAL);
+ }
+
+ if(hash_mode == TNG_USE_HASH)
+ {
+ tng_md5_hash_update(tng_data, block,
+ frame_set->medium_stride_next_frame_set_file_pos,
+ contents_start_pos);
+ }
+ }
/* Update the frame set one medium stride step before */
- if(frame_set->medium_stride_prev_frame_set_file_pos != -1 &&
- frame_set->medium_stride_prev_frame_set_file_pos != 0)
+ if(frame_set->medium_stride_prev_frame_set_file_pos > 0)
{
fseek(tng_data->output_file,
(long)frame_set->medium_stride_prev_frame_set_file_pos,
@@ -1271,8 +1358,6 @@ static tng_function_status tng_frame_set_pointers_update
fseek(tng_data->output_file, (long)block->block_contents_size - (4 *
sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
- pos = tng_data->current_trajectory_frame_set_output_file_pos;
-
if(tng_data->input_endianness_swap_func_64)
{
if(tng_data->input_endianness_swap_func_64(tng_data,
@@ -1299,9 +1384,54 @@ static tng_function_status tng_frame_set_pointers_update
}
}
+ /* Update the frame set one long stride step after */
+ if(frame_set->long_stride_next_frame_set_file_pos > 0)
+ {
+ fseek(tng_data->output_file,
+ (long)frame_set->long_stride_next_frame_set_file_pos,
+ SEEK_SET);
+
+ if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot read frame set header. %s: %d\n",
+ __FILE__, __LINE__);
+ tng_data->input_file = temp;
+ tng_block_destroy(&block);
+ return(TNG_CRITICAL);
+ }
+
+ contents_start_pos = ftell(tng_data->output_file);
+
+ fseek(tng_data->output_file, (long)block->block_contents_size - (1 *
+ sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
+
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &pos)
+ != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+
+ if(fwrite(&pos, sizeof(int64_t), 1, tng_data->output_file) != 1)
+ {
+ tng_data->input_file = temp;
+ tng_block_destroy(&block);
+ return(TNG_CRITICAL);
+ }
+
+ if(hash_mode == TNG_USE_HASH)
+ {
+ tng_md5_hash_update(tng_data, block,
+ frame_set->long_stride_next_frame_set_file_pos,
+ contents_start_pos);
+ }
+ }
/* Update the frame set one long stride step before */
- if(frame_set->long_stride_prev_frame_set_file_pos != -1 &&
- frame_set->long_stride_prev_frame_set_file_pos != 0)
+ if(frame_set->long_stride_prev_frame_set_file_pos > 0)
{
fseek(tng_data->output_file,
(long)frame_set->long_stride_prev_frame_set_file_pos,
@@ -1321,8 +1451,6 @@ static tng_function_status tng_frame_set_pointers_update
fseek(tng_data->output_file, (long)block->block_contents_size - (2 *
sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
- pos = tng_data->current_trajectory_frame_set_output_file_pos;
-
if(tng_data->input_endianness_swap_func_64)
{
if(tng_data->input_endianness_swap_func_64(tng_data,
@@ -1489,6 +1617,8 @@ static tng_function_status tng_frame_set_complete_migrate
return(TNG_CRITICAL);
}
+ fseek(tng_data->input_file, block_start_pos, SEEK_SET);
+
contents = malloc(block_len);
if(!contents)
{
@@ -1514,6 +1644,8 @@ static tng_function_status tng_frame_set_complete_migrate
return(TNG_CRITICAL);
}
+ tng_data->current_trajectory_frame_set_output_file_pos = new_pos;
+
tng_frame_set_pointers_update(tng_data, TNG_USE_HASH);
/* Update the general info block if needed */
@@ -13083,8 +13215,8 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new
/* Read the next frame set from the previous frame set and one
* medium stride step back */
- fseek(tng_data->output_file, (long)block->block_contents_size - 6 *
- sizeof(int64_t), SEEK_CUR);
+ fseek(tng_data->output_file, (long)block->block_contents_size - (6 *
+ sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
if(fread(&frame_set->medium_stride_prev_frame_set_file_pos,
sizeof(frame_set->medium_stride_prev_frame_set_file_pos),
1, tng_data->output_file) == 0)
@@ -13139,8 +13271,8 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new
/* Read the next frame set from the previous frame set and one
* long stride step back */
- fseek(tng_data->output_file, (long)block->block_contents_size - 6 *
- sizeof(int64_t), SEEK_CUR);
+ fseek(tng_data->output_file, (long)block->block_contents_size - (6 *
+ sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR);
tng_block_destroy(&block);
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