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-rw-r--r--src/lib/tng_io.c395
1 files changed, 274 insertions, 121 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 12b7a4e..954d1d7 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -7032,6 +7032,7 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data,
tng_data->current_trajectory_frame_set_output_file_pos =
+ tng_data->last_trajectory_frame_set_output_file_pos =
ftell(tng_data->output_file);
tng_block_init(&block);
@@ -7300,6 +7301,7 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data,
int i, j, block_index, size, len;
tng_trajectory_frame_set_t frame_set;
tng_non_particle_data_t data;
+ union data_values *first_dim_values;
void *orig;
frame_set = &tng_data->current_trajectory_frame_set;
@@ -7399,71 +7401,89 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data,
break;
}
- orig = new_data;
-
- switch(datatype)
+ if(new_data)
{
- case TNG_FLOAT_DATA:
- for(i = 0; i < n_frames; i++)
+ orig = new_data;
+
+ switch(datatype)
{
- for(j = 0; j < n_values_per_frame; j++)
+ case TNG_FLOAT_DATA:
+ for(i = 0; i < n_frames; i++)
{
- memcpy(&data->values[i][j].f,
- new_data, size);
- new_data += size;
+ first_dim_values = data->values[i];
+ for(j = 0; j < n_values_per_frame; j++)
+ {
+ memcpy(&first_dim_values[j].f,
+ new_data, size);
+ new_data += size;
+ }
}
- }
- break;
- case TNG_CHAR_DATA:
- for(i = 0; i < n_frames; i++)
- {
- for(j = 0; j < n_values_per_frame; j++)
+ break;
+ case TNG_CHAR_DATA:
+ for(i = 0; i < n_frames; i++)
{
- len = min(strlen(new_data) + 1,
- TNG_MAX_STR_LEN);
- if(data->values[i][j].c)
+ first_dim_values = data->values[i];
+ for(j = 0; j < n_values_per_frame; j++)
{
- free(data->values[i][j].c);
+ len = min(strlen(new_data) + 1,
+ TNG_MAX_STR_LEN);
+ if(first_dim_values[j].c)
+ {
+ free(first_dim_values[j].c);
+ }
+ first_dim_values[j].c = malloc(len);
+ if(!first_dim_values[j].c)
+ {
+ printf("Cannot allocate memory (%d bytes). %s: %d\n",
+ len, __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+ strncpy(first_dim_values[j].c,
+ new_data, len);
+ new_data += len;
}
- data->values[i][j].c = malloc(len);
- if(!data->values[i][j].c)
+ }
+ break;
+ case TNG_INT_DATA:
+ for(i = 0; i < n_frames; i++)
+ {
+ first_dim_values = data->values[i];
+ for(j = 0; j < n_values_per_frame; j++)
{
- printf("Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
- return(TNG_CRITICAL);
+ memcpy(&first_dim_values[j].i,
+ new_data, size);
+ new_data += size;
}
- strncpy(data->values[i][j].c,
- new_data, len);
- new_data += len;
}
- }
- break;
- case TNG_INT_DATA:
- for(i = 0; i < n_frames; i++)
- {
- for(j = 0; j < n_values_per_frame; j++)
+ break;
+ case TNG_DOUBLE_DATA:
+ default:
+ for(i = 0; i < n_frames; i++)
{
- memcpy(&data->values[i][j].i,
- new_data, size);
- new_data += size;
+ first_dim_values = data->values[i];
+ for(j = 0; j < n_values_per_frame; j++)
+ {
+ memcpy(&first_dim_values[j].d,
+ new_data, size);
+ new_data += size;
+ }
}
}
- break;
- case TNG_DOUBLE_DATA:
- default:
+
+ new_data = orig;
+ }
+ else
+ {
for(i = 0; i < n_frames; i++)
{
+ first_dim_values = data->values[i];
for(j = 0; j < n_values_per_frame; j++)
{
- memcpy(&data->values[i][j].d,
- new_data, size);
- new_data += size;
+ first_dim_values[j].d = 0;
}
}
}
-
- new_data = orig;
-
+
return(TNG_SUCCESS);
}
@@ -7581,79 +7601,105 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data,
}
}
- orig = new_data;
-
- switch(datatype)
+ /* If data values are supplied add that data to the data block. */
+ if(new_data)
{
- case TNG_FLOAT_DATA:
- size = sizeof(float);
- for(i = 0; i < n_frames; i++)
+ orig = new_data;
+
+ switch(datatype)
{
- first_dim_values = data->values[i];
- for(j = num_first_particle; j < num_first_particle + n_particles;
- j++)
+ case TNG_FLOAT_DATA:
+ size = sizeof(float);
+ for(i = 0; i < n_frames; i++)
{
- second_dim_values = first_dim_values[j];
- for(k = 0; k < n_values_per_frame; k++)
+ first_dim_values = data->values[i];
+ for(j = num_first_particle; j < num_first_particle + n_particles;
+ j++)
{
- memcpy(&second_dim_values[k].f,
- new_data, size);
- new_data += size;
+ second_dim_values = first_dim_values[j];
+ for(k = 0; k < n_values_per_frame; k++)
+ {
+ memcpy(&second_dim_values[k].f,
+ new_data, size);
+ new_data += size;
+ }
}
}
- }
- break;
- case TNG_INT_DATA:
- size = sizeof(int64_t);
- for(i = 0; i < n_frames; i++)
- {
- first_dim_values = data->values[i];
- for(j = num_first_particle; j < num_first_particle + n_particles;
- j++)
+ break;
+ case TNG_INT_DATA:
+ size = sizeof(int64_t);
+ for(i = 0; i < n_frames; i++)
{
- second_dim_values = first_dim_values[j];
- for(k = 0; k < n_values_per_frame; k++)
+ first_dim_values = data->values[i];
+ for(j = num_first_particle; j < num_first_particle + n_particles;
+ j++)
{
- memcpy(&second_dim_values[k].i,
- new_data, size);
- new_data += size;
+ second_dim_values = first_dim_values[j];
+ for(k = 0; k < n_values_per_frame; k++)
+ {
+ memcpy(&second_dim_values[k].i,
+ new_data, size);
+ new_data += size;
+ }
}
}
- }
- break;
- case TNG_CHAR_DATA:
- for(i = 0; i < n_frames; i++)
- {
- first_dim_values = data->values[i];
- for(j = num_first_particle; j < num_first_particle + n_particles;
- j++)
+ break;
+ case TNG_CHAR_DATA:
+ for(i = 0; i < n_frames; i++)
{
- second_dim_values = first_dim_values[j];
- for(k = 0; k < n_values_per_frame; k++)
+ first_dim_values = data->values[i];
+ for(j = num_first_particle; j < num_first_particle + n_particles;
+ j++)
{
- len = min(strlen(new_data) + 1,
- TNG_MAX_STR_LEN);
- if(second_dim_values[k].c)
+ second_dim_values = first_dim_values[j];
+ for(k = 0; k < n_values_per_frame; k++)
{
- free(second_dim_values[k].c);
+ len = min(strlen(new_data) + 1,
+ TNG_MAX_STR_LEN);
+ if(second_dim_values[k].c)
+ {
+ free(second_dim_values[k].c);
+ }
+ second_dim_values[k].c = malloc(len);
+ if(!second_dim_values[k].c)
+ {
+ printf("Cannot allocate memory (%d bytes). %s: %d\n",
+ len, __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+ strncpy(second_dim_values[k].c,
+ new_data, len);
+ new_data += len;
}
- second_dim_values[k].c = malloc(len);
- if(!second_dim_values[k].c)
+ }
+ }
+ break;
+ case TNG_DOUBLE_DATA:
+ default:
+ size = sizeof(double);
+ for(i = 0; i < n_frames; i++)
+ {
+ first_dim_values = data->values[i];
+ for(j = num_first_particle; j < num_first_particle + n_particles;
+ j++)
+ {
+ second_dim_values = first_dim_values[j];
+ for(k = 0; k < n_values_per_frame; k++)
{
- printf("Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
- return(TNG_CRITICAL);
+ memcpy(&second_dim_values[k].d,
+ new_data, size);
+ new_data += size;
}
- strncpy(second_dim_values[k].c,
- new_data, len);
- new_data += len;
}
}
+ break;
}
- break;
- case TNG_DOUBLE_DATA:
- default:
- size = sizeof(double);
+
+ new_data = orig;
+ }
+ /* Otherwise fill the data block with zeroes */
+ else
+ {
for(i = 0; i < n_frames; i++)
{
first_dim_values = data->values[i];
@@ -7663,16 +7709,12 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data,
second_dim_values = first_dim_values[j];
for(k = 0; k < n_values_per_frame; k++)
{
- memcpy(&second_dim_values[k].d,
- new_data, size);
- new_data += size;
+ second_dim_values[k].d = 0;
}
}
}
- break;
}
-
- new_data = orig;
+
return(TNG_SUCCESS);
}
@@ -7686,12 +7728,14 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data,
int64_t header_pos, file_pos;
int64_t output_file_len, n_values_per_frame, size, contents_size;
int64_t header_size, temp_first, temp_last, temp_current;
+ int64_t i, last_frame;
tng_gen_block_t block;
tng_trajectory_frame_set_t frame_set;
FILE *temp = tng_data->input_file;
struct tng_non_particle_data data;
tng_function_status stat;
char dependency, sparse_data, datatype;
+ void *copy;
if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS)
{
@@ -7716,11 +7760,33 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data,
if(stat != TNG_SUCCESS)
{
- tng_data->input_file = temp;
- tng_data->first_trajectory_frame_set_input_file_pos = temp_first;
- tng_data->last_trajectory_frame_set_input_file_pos = temp_last;
- tng_data->current_trajectory_frame_set_input_file_pos = temp_current;
- return(stat);
+ last_frame = tng_data->current_trajectory_frame_set.first_frame +
+ tng_data->current_trajectory_frame_set.n_frames - 1;
+ /* If the wanted frame would be in the frame set after the last
+ * frame set create a new frame set. */
+ if(stat == TNG_FAILURE &&
+ (last_frame < frame_nr &&
+ tng_data->current_trajectory_frame_set.first_frame +
+ tng_data->frame_set_n_frames > frame_nr))
+ {
+ tng_frame_set_new(tng_data,
+ last_frame+1,
+ tng_data->frame_set_n_frames);
+ /* Write the frame set to disk */
+ if(tng_frame_set_write(tng_data, hash_mode) != TNG_SUCCESS)
+ {
+ printf("Error writing frame set. %s: %d\n", __FILE__, __LINE__);
+ exit(1);
+ }
+ }
+ else
+ {
+ tng_data->input_file = temp;
+ tng_data->first_trajectory_frame_set_input_file_pos = temp_first;
+ tng_data->last_trajectory_frame_set_input_file_pos = temp_last;
+ tng_data->current_trajectory_frame_set_input_file_pos = temp_current;
+ return(stat);
+ }
}
tng_block_init(&block);
@@ -7911,7 +7977,39 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data,
fseek(tng_data->output_file, file_pos, SEEK_CUR);
- fwrite(values, n_values_per_frame, size, tng_data->output_file);
+ /* If the endianness is not big endian the data needs to be swapped */
+ if((data.datatype == TNG_INT_DATA ||
+ data.datatype == TNG_DOUBLE_DATA) &&
+ tng_data->endianness_64 != TNG_BIG_ENDIAN_64)
+ {
+ copy = malloc(n_values_per_frame * size);
+ memcpy(copy, values, n_values_per_frame * size);
+ for(i = 0; i < n_values_per_frame; i++)
+ {
+ tng_swap_byte_order_64(tng_data, (int64_t *)copy+i);
+ }
+ fwrite(copy, n_values_per_frame, size,
+ tng_data->output_file);
+ free(copy);
+ }
+ else if(data.datatype == TNG_FLOAT_DATA &&
+ tng_data->endianness_32 != TNG_BIG_ENDIAN_32)
+ {
+ copy = malloc(n_values_per_frame * size);
+ memcpy(copy, values, n_values_per_frame * size);
+ for(i = 0; i < n_values_per_frame; i++)
+ {
+ tng_swap_byte_order_32(tng_data, (int32_t *)copy+i);
+ }
+ fwrite(copy, n_values_per_frame, size,
+ tng_data->output_file);
+ free(copy);
+ }
+
+ else
+ {
+ fwrite(values, n_values_per_frame, size, tng_data->output_file);
+ }
fflush(tng_data->output_file);
@@ -7941,7 +8039,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data,
int64_t output_file_len, n_values_per_frame, size, contents_size;
int64_t header_size, temp_first, temp_last, temp_current;
int64_t mapping_block_end_pos, num_first_particle, block_n_particles;
- int64_t i;
+ int64_t i, last_frame;
tng_gen_block_t block;
tng_trajectory_frame_set_t frame_set;
FILE *temp = tng_data->input_file;
@@ -7972,20 +8070,75 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data,
stat = tng_frame_set_find(tng_data, frame_nr);
+ frame_set = &tng_data->current_trajectory_frame_set;
+
if(stat != TNG_SUCCESS)
{
- tng_data->input_file = temp;
+ last_frame = tng_data->current_trajectory_frame_set.first_frame +
+ tng_data->current_trajectory_frame_set.n_frames - 1;
+// printf("Frame %"PRId64" not found. Last frame: %"PRId64"\n", frame_nr,
+// last_frame);
+ /* If the wanted frame would be in the frame set after the last
+ * frame set create a new frame set. */
+ if(stat == TNG_FAILURE &&
+ (last_frame < frame_nr &&
+ last_frame + tng_data->frame_set_n_frames >= frame_nr))
+ {
+ tng_frame_set_new(tng_data,
+ last_frame+1,
+ tng_data->frame_set_n_frames);
- tng_data->first_trajectory_frame_set_input_file_pos = temp_first;
- tng_data->last_trajectory_frame_set_input_file_pos = temp_last;
- tng_data->current_trajectory_frame_set_input_file_pos = temp_current;
- return(stat);
+ file_pos = ftell(tng_data->output_file);
+ fseek(tng_data->output_file, 0, SEEK_END);
+ output_file_len = ftell(tng_data->output_file);
+ fseek(tng_data->output_file, file_pos, SEEK_SET);
+
+ /* Read mapping blocks from the last frame set */
+ tng_block_init(&block);
+
+ stat = tng_block_header_read(tng_data, block);
+ while(file_pos < output_file_len &&
+ stat != TNG_CRITICAL &&
+ block->id != TNG_TRAJECTORY_FRAME_SET)
+ {
+ if(block->id == TNG_PARTICLE_MAPPING)
+ {
+ tng_trajectory_mapping_block_read(tng_data, block,
+ hash_mode);
+ }
+ else
+ {
+ fseek(tng_data->output_file, block->block_contents_size,
+ SEEK_CUR);
+ }
+ file_pos = ftell(tng_data->output_file);
+ if(file_pos < output_file_len)
+ {
+ stat = tng_block_header_read(tng_data, block);
+ }
+ }
+
+ tng_block_destroy(&block);
+ /* Write the frame set to disk */
+ if(tng_frame_set_write(tng_data, hash_mode) != TNG_SUCCESS)
+ {
+ printf("Error writing frame set. %s: %d\n", __FILE__, __LINE__);
+ exit(1);
+ }
+ }
+ else
+ {
+ tng_data->input_file = temp;
+ tng_data->first_trajectory_frame_set_input_file_pos = temp_first;
+ tng_data->last_trajectory_frame_set_input_file_pos = temp_last;
+ tng_data->current_trajectory_frame_set_input_file_pos = temp_current;
+ return(stat);
+ }
}
+
tng_block_init(&block);
- frame_set = &tng_data->current_trajectory_frame_set;
-
file_pos = tng_data->current_trajectory_frame_set_output_file_pos;
fseek(tng_data->output_file, 0, SEEK_END);
@@ -8275,7 +8428,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data,
memcpy(copy, values, val_n_particles * n_values_per_frame * size);
for(i = 0; i < val_n_particles * n_values_per_frame; i++)
{
- tng_swap_byte_order_64(tng_data, (int64_t *)copy+i*size);
+ tng_swap_byte_order_64(tng_data, (int64_t *)copy+i);
}
fwrite(copy, val_n_particles * n_values_per_frame, size,
tng_data->output_file);
@@ -8288,7 +8441,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data,
memcpy(copy, values, val_n_particles * n_values_per_frame * size);
for(i = 0; i < val_n_particles * n_values_per_frame; i++)
{
- tng_swap_byte_order_32(tng_data, (int32_t *)copy+i*size);
+ tng_swap_byte_order_32(tng_data, (int32_t *)copy+i);
}
fwrite(copy, val_n_particles * n_values_per_frame, size,
tng_data->output_file);
contact: Jan Huwald // Impressum