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-rw-r--r--src/lib/tng_io.c359
1 files changed, 166 insertions, 193 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 6e52646..1f68388 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -12407,28 +12407,29 @@ tng_function_status DECLSPECDLLEXPORT tng_first_frame_nr_of_next_frame_set_get
return(TNG_SUCCESS);
}
-tng_function_status DECLSPECDLLEXPORT tng_data_block_add
+static tng_function_status DECLSPECDLLEXPORT tng_gen_data_block_add
(tng_trajectory_t tng_data,
const int64_t id,
+ const tng_bool is_particle_data,
const char *block_name,
const char datatype,
const char block_type_flag,
int64_t n_frames,
const int64_t n_values_per_frame,
int64_t stride_length,
+ const int64_t num_first_particle,
+ const int64_t n_particles,
const int64_t codec_id,
void *new_data)
{
- int i, j, size, len;
+ int i, size, len;
+ int64_t j, k;
+ int64_t tot_n_particles, n_frames_div;
+ char ***first_dim_values, **second_dim_values;
tng_trajectory_frame_set_t frame_set;
tng_data_t data;
- char **first_dim_values;
char *new_data_c=new_data;
- int64_t n_frames_div;
-
- TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
- TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer.");
- TNG_ASSERT(n_values_per_frame > 0, "TNG library: n_values_per_frame must be a positive integer.");
+ tng_function_status stat;
frame_set = &tng_data->current_trajectory_frame_set;
@@ -12437,184 +12438,55 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add
stride_length = 1;
}
- /* If the block does not exist, create it */
- if(tng_data_find(tng_data, id, &data) != TNG_SUCCESS)
- {
- if(tng_data_block_create(tng_data, block_type_flag) !=
- TNG_SUCCESS)
- {
- fprintf(stderr, "TNG library: Cannot create data block. %s: %d\n",
- __FILE__, __LINE__);
- return(TNG_CRITICAL);
- }
- if(block_type_flag == TNG_TRAJECTORY_BLOCK)
- {
- data = &frame_set->tr_data[frame_set->n_data_blocks - 1];
- }
- else
- {
- data = &tng_data->non_tr_data[tng_data->n_data_blocks - 1];
- }
- data->block_id = id;
-
- data->block_name = malloc(strlen(block_name) + 1);
- if(!data->block_name)
- {
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- (unsigned int)strlen(block_name)+1, __FILE__, __LINE__);
- return(TNG_CRITICAL);
- }
- strncpy(data->block_name, block_name, strlen(block_name) + 1);
-
- data->values = 0;
- /* FIXME: Memory leak from strings. */
- data->strings = 0;
- data->last_retrieved_frame = -1;
- }
-
- data->datatype = datatype;
- data->stride_length = tng_max_i64(stride_length, 1);
- data->n_values_per_frame = n_values_per_frame;
- data->n_frames = n_frames;
- data->dependency = 0;
- if(block_type_flag == TNG_TRAJECTORY_BLOCK &&
- (n_frames > 1 ||
- frame_set->n_frames == n_frames ||
- stride_length > 1))
+ if(is_particle_data)
{
- data->dependency += TNG_FRAME_DEPENDENT;
+ stat = tng_particle_data_find(tng_data, id, &data);
}
- data->codec_id = codec_id;
- data->compression_multiplier = 1.0;
- /* FIXME: This can cause problems. */
- data->first_frame_with_data = frame_set->first_frame;
-
- switch(datatype)
+ else
{
- case TNG_FLOAT_DATA:
- size = sizeof(float);
- break;
- case TNG_INT_DATA:
- size = sizeof(int64_t);
- break;
- case TNG_DOUBLE_DATA:
- default:
- size = sizeof(double);
- break;
+ stat = tng_data_find(tng_data, id, &data);
}
-
- if(new_data_c)
+ /* If the block does not exist, create it */
+ if(stat != TNG_SUCCESS)
{
- /* Allocate memory */
- if(tng_allocate_data_mem(tng_data, data, n_frames, stride_length,
- n_values_per_frame) !=
- TNG_SUCCESS)
- {
- fprintf(stderr, "TNG library: Cannot allocate data memory. %s: %d\n",
- __FILE__, __LINE__);
- return(TNG_CRITICAL);
- }
-
- if(n_frames > frame_set->n_unwritten_frames)
- {
- frame_set->n_unwritten_frames = n_frames;
- }
-
- n_frames_div = (n_frames % stride_length) ?
- n_frames / stride_length + 1:
- n_frames / stride_length;
-
- if(datatype == TNG_CHAR_DATA)
+ if(is_particle_data)
{
- for(i = 0; i < n_frames_div; i++)
- {
- first_dim_values = data->strings[0][i];
- for(j = 0; j < n_values_per_frame; j++)
- {
- len = tng_min_size(strlen(new_data_c) + 1,
- TNG_MAX_STR_LEN);
- if(first_dim_values[j])
- {
- free(first_dim_values[j]);
- }
- first_dim_values[j] = malloc(len);
- if(!first_dim_values[j])
- {
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
- return(TNG_CRITICAL);
- }
- strncpy(first_dim_values[j],
- new_data_c, len);
- new_data_c += len;
- }
- }
+ stat = tng_particle_data_block_create(tng_data, block_type_flag);
}
else
{
- memcpy(data->values, new_data, size * n_frames_div *
- n_values_per_frame);
+ stat = tng_data_block_create(tng_data, block_type_flag);
}
- }
-
- return(TNG_SUCCESS);
-}
-
-tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
- (tng_trajectory_t tng_data,
- const int64_t id,
- const char *block_name,
- const char datatype,
- const char block_type_flag,
- int64_t n_frames,
- const int64_t n_values_per_frame,
- int64_t stride_length,
- const int64_t num_first_particle,
- const int64_t n_particles,
- const int64_t codec_id,
- void *new_data)
-{
- int i, size, len;
- int64_t j, k;
- int64_t tot_n_particles, n_frames_div;
- char ***first_dim_values, **second_dim_values;
- tng_trajectory_frame_set_t frame_set;
- tng_data_t data;
- char *new_data_c=new_data;
-
- TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
- TNG_ASSERT(block_name, "TNG library: block_name mustnot be a NULL pointer.");
- TNG_ASSERT(n_values_per_frame > 0, "TNG library: n_values_per_frame must be a positive integer.");
- TNG_ASSERT(num_first_particle >= 0, "TNG library: num_first_particle must be >= 0.");
- TNG_ASSERT(n_particles >= 0, "TNG library: n_particles must be >= 0.");
-
- frame_set = &tng_data->current_trajectory_frame_set;
-
- if(stride_length <= 0)
- {
- stride_length = 1;
- }
-
- /* If the block does not exist, create it */
- if(tng_particle_data_find(tng_data, id, &data) != TNG_SUCCESS)
- {
- if(tng_particle_data_block_create(tng_data, block_type_flag) !=
- TNG_SUCCESS)
+ if(stat != TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot create particle data block. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
- if(block_type_flag == TNG_TRAJECTORY_BLOCK)
+ if(is_particle_data)
{
- data = &frame_set->tr_particle_data[frame_set->
- n_particle_data_blocks - 1];
+ if(block_type_flag == TNG_TRAJECTORY_BLOCK)
+ {
+ data = &frame_set->tr_particle_data[frame_set->
+ n_particle_data_blocks - 1];
+ }
+ else
+ {
+ data = &tng_data->non_tr_particle_data[tng_data->
+ n_particle_data_blocks - 1];
+ }
}
else
{
- data = &tng_data->non_tr_particle_data[tng_data->
- n_particle_data_blocks - 1];
+ if(block_type_flag == TNG_TRAJECTORY_BLOCK)
+ {
+ data = &frame_set->tr_data[frame_set->n_data_blocks - 1];
+ }
+ else
+ {
+ data = &tng_data->non_tr_data[tng_data->n_data_blocks - 1];
+ }
}
data->block_id = id;
@@ -12627,18 +12499,24 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
}
strncpy(data->block_name, block_name, strlen(block_name) + 1);
- data->datatype = datatype;
-
data->values = 0;
/* FIXME: Memory leak from strings. */
data->strings = 0;
data->last_retrieved_frame = -1;
}
+ data->datatype = datatype;
data->stride_length = tng_max_i64(stride_length, 1);
data->n_values_per_frame = n_values_per_frame;
data->n_frames = n_frames;
- data->dependency = TNG_PARTICLE_DEPENDENT;
+ if(is_particle_data)
+ {
+ data->dependency = TNG_PARTICLE_DEPENDENT;
+ }
+ else
+ {
+ data->dependency = 0;
+ }
if(block_type_flag == TNG_TRAJECTORY_BLOCK &&
(n_frames > 1 ||
frame_set->n_frames == n_frames ||
@@ -12651,23 +12529,34 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
/* FIXME: This can cause problems. */
data->first_frame_with_data = frame_set->first_frame;
- if(block_type_flag == TNG_TRAJECTORY_BLOCK && tng_data->var_num_atoms_flag)
- {
- tot_n_particles = frame_set->n_particles;
- }
- else
+ if(is_particle_data)
{
- tot_n_particles = tng_data->n_particles;
+ if(block_type_flag == TNG_TRAJECTORY_BLOCK && tng_data->var_num_atoms_flag)
+ {
+ tot_n_particles = frame_set->n_particles;
+ }
+ else
+ {
+ tot_n_particles = tng_data->n_particles;
+ }
}
/* If data values are supplied add that data to the data block. */
if(new_data_c)
{
/* Allocate memory */
- if(tng_allocate_particle_data_mem(tng_data, data, n_frames,
- stride_length, tot_n_particles,
- n_values_per_frame) !=
- TNG_SUCCESS)
+ if(is_particle_data)
+ {
+ stat = tng_allocate_particle_data_mem(tng_data, data, n_frames,
+ stride_length, tot_n_particles,
+ n_values_per_frame);
+ }
+ else
+ {
+ stat = tng_allocate_data_mem(tng_data, data, n_frames, stride_length,
+ n_values_per_frame);
+ }
+ if(stat != TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot allocate particle data memory. %s: %d\n",
__FILE__, __LINE__);
@@ -12685,29 +12574,58 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
if(datatype == TNG_CHAR_DATA)
{
- for(i = 0; i < n_frames_div; i++)
+ if(is_particle_data)
{
- first_dim_values = data->strings[i];
- for(j = num_first_particle; j < num_first_particle + n_particles;
- j++)
+ for(i = 0; i < n_frames_div; i++)
{
- second_dim_values = first_dim_values[j];
- for(k = 0; k < n_values_per_frame; k++)
+ first_dim_values = data->strings[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++)
+ {
+ len = tng_min_size(strlen(new_data_c) + 1,
+ TNG_MAX_STR_LEN);
+ if(second_dim_values[k])
+ {
+ free(second_dim_values[k]);
+ }
+ second_dim_values[k] = malloc(len);
+ if(!second_dim_values[k])
+ {
+ fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
+ len, __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+ strncpy(second_dim_values[k],
+ new_data_c, len);
+ new_data_c += len;
+ }
+ }
+ }
+ }
+ else
+ {
+ for(i = 0; i < n_frames_div; i++)
+ {
+ second_dim_values = data->strings[0][i];
+ for(j = 0; j < n_values_per_frame; j++)
{
len = tng_min_size(strlen(new_data_c) + 1,
- TNG_MAX_STR_LEN);
- if(second_dim_values[k])
+ TNG_MAX_STR_LEN);
+ if(second_dim_values[j])
{
- free(second_dim_values[k]);
+ free(second_dim_values[j]);
}
- second_dim_values[k] = malloc(len);
- if(!second_dim_values[k])
+ second_dim_values[j] = malloc(len);
+ if(!second_dim_values[j])
{
fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
len, __FILE__, __LINE__);
return(TNG_CRITICAL);
}
- strncpy(second_dim_values[k],
+ strncpy(second_dim_values[j],
new_data_c, len);
new_data_c += len;
}
@@ -12729,14 +12647,69 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
size = sizeof(double);
}
- memcpy(data->values, new_data, size * n_frames_div *
- n_particles * n_values_per_frame);
+ if(is_particle_data)
+ {
+ memcpy(data->values, new_data, size * n_frames_div *
+ n_particles * n_values_per_frame);
+ }
+ else
+ {
+ memcpy(data->values, new_data, size * n_frames_div *
+ n_values_per_frame);
+ }
}
}
return(TNG_SUCCESS);
}
+tng_function_status DECLSPECDLLEXPORT tng_data_block_add
+ (tng_trajectory_t tng_data,
+ const int64_t id,
+ const char *block_name,
+ const char datatype,
+ const char block_type_flag,
+ int64_t n_frames,
+ const int64_t n_values_per_frame,
+ int64_t stride_length,
+ const int64_t codec_id,
+ void *new_data)
+{
+ TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
+ TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer.");
+ TNG_ASSERT(n_values_per_frame > 0, "TNG library: n_values_per_frame must be a positive integer.");
+
+ return(tng_gen_data_block_add(tng_data, id, TNG_FALSE, block_name, datatype,
+ block_type_flag, n_frames, n_values_per_frame,
+ stride_length, 0, 0, codec_id, new_data));
+}
+
+tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
+ (tng_trajectory_t tng_data,
+ const int64_t id,
+ const char *block_name,
+ const char datatype,
+ const char block_type_flag,
+ int64_t n_frames,
+ const int64_t n_values_per_frame,
+ int64_t stride_length,
+ const int64_t num_first_particle,
+ const int64_t n_particles,
+ const int64_t codec_id,
+ void *new_data)
+{
+ TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
+ TNG_ASSERT(block_name, "TNG library: block_name mustnot be a NULL pointer.");
+ TNG_ASSERT(n_values_per_frame > 0, "TNG library: n_values_per_frame must be a positive integer.");
+ TNG_ASSERT(num_first_particle >= 0, "TNG library: num_first_particle must be >= 0.");
+ TNG_ASSERT(n_particles >= 0, "TNG library: n_particles must be >= 0.");
+
+ return(tng_gen_data_block_add(tng_data, id, TNG_TRUE, block_name, datatype,
+ block_type_flag, n_frames, n_values_per_frame,
+ stride_length, num_first_particle, n_particles,
+ codec_id, new_data));
+}
+
tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get
(tng_trajectory_t tng_data,
int64_t block_id,
contact: Jan Huwald // Impressum