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-rw-r--r--src/lib/tng_io.c418
-rw-r--r--src/lib/tng_io.h63
2 files changed, 331 insertions, 150 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 14bdfed..3be1863 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -5435,8 +5435,8 @@ tng_function_status tng_trajectory_init(tng_trajectory_t tng_data)
tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data)
{
- int64_t n_frames, n_particles;
- int i, j, k, l;
+ int64_t n_particles;
+ int i;
struct tng_trajectory_frame_set *frame_set =
&tng_data->current_trajectory_frame_set;
@@ -5547,45 +5547,16 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data)
{
for(i = tng_data->n_particle_data_blocks; i--; )
{
- if(tng_data->non_tr_particle_data[i].values)
- {
- /* Only one frame for non-trajectory data */
- j = 0;
- if(tng_data->non_tr_particle_data[i].values[j])
- {
- for(k = n_particles; k--;)
- {
- if(tng_data->non_tr_particle_data[i].values[j][k])
- {
- if(tng_data->non_tr_particle_data[i].datatype ==
- TNG_CHAR_DATA)
- {
- for(l = tng_data->non_tr_particle_data[i].
- n_values_per_frame;
- l--;)
- {
- if(tng_data->non_tr_particle_data[i].
- values[j][k][l].c)
- {
- free(tng_data->non_tr_particle_data[i].
- values[j][k][l].c);
- tng_data->non_tr_particle_data[i].
- values[j][k][l].c = 0;
- }
- }
- }
- free(tng_data->non_tr_particle_data[i].
- values[j][k]);
- tng_data->non_tr_particle_data[i].
- values[j][k] = 0;
- }
- }
- free(tng_data->non_tr_particle_data[i].values[j]);
- tng_data->non_tr_particle_data[i].values[j] = 0;
- }
- free(tng_data->non_tr_particle_data[i].values);
- tng_data->non_tr_particle_data[i].values = 0;
- }
+ tng_particle_data_values_free(tng_data->non_tr_particle_data[i].
+ values,
+ tng_data->non_tr_particle_data[i].
+ n_frames,
+ n_particles,
+ tng_data->non_tr_particle_data[i].
+ n_values_per_frame,
+ tng_data->non_tr_particle_data[i].
+ datatype);
+
if(tng_data->non_tr_particle_data[i].block_name)
{
free(tng_data->non_tr_particle_data[i].block_name);
@@ -5600,30 +5571,10 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data)
{
for(i = tng_data->n_data_blocks; i--;)
{
- if(tng_data->non_tr_data[i].values)
- {
- /* Only one frame for non-trajectory data */
- if(tng_data->non_tr_data[i].values[0])
- {
- if(tng_data->non_tr_data[i].datatype ==
- TNG_CHAR_DATA)
- {
- for(k = tng_data->non_tr_data[i].n_values_per_frame;
- k--;)
- {
- if(tng_data->non_tr_data[i].values[0][k].c)
- {
- free(tng_data->non_tr_data[i].values[0][k].c);
- tng_data->non_tr_data[i].values[0][k].c = 0;
- }
- }
- }
- free(tng_data->non_tr_data[i].values[0]);
- tng_data->non_tr_data[i].values[0] = 0;
- }
- free(tng_data->non_tr_data[i].values);
- tng_data->non_tr_data[i].values = 0;
- }
+ tng_data_values_free(tng_data->non_tr_data[i].values, 1,
+ tng_data->non_tr_data[i].n_values_per_frame,
+ tng_data->non_tr_data[i].datatype);
+
if(tng_data->non_tr_data[i].block_name)
{
free(tng_data->non_tr_data[i].block_name);
@@ -5641,47 +5592,16 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data)
{
for(i = frame_set->n_particle_data_blocks; i--; )
{
- if(frame_set->tr_particle_data[i].values)
- {
- n_frames = max(1, frame_set->tr_particle_data[i].n_frames);
- for(j = n_frames; j--;)
- {
- if(frame_set->tr_particle_data[i].values[j])
- {
- for(k = n_particles; k--;)
- {
- if(frame_set->tr_particle_data[i].values[j][k])
- {
- if(frame_set->tr_particle_data[i].datatype ==
- TNG_CHAR_DATA)
- {
- for(l = frame_set->tr_particle_data[i].
- n_values_per_frame;
- l--;)
- {
- if(frame_set->tr_particle_data[i].
- values[j][k][l].c)
- {
- free(frame_set->tr_particle_data[i].
- values[j][k][l].c);
-
- frame_set->tr_particle_data[i].
- values[j][k][l].c = 0;
- }
- }
- }
- free(frame_set->tr_particle_data[i].
- values[j][k]);
- frame_set->tr_particle_data[i].values[j][k] = 0;
- }
- }
- free(frame_set->tr_particle_data[i].values[j]);
- frame_set->tr_particle_data[i].values[j] = 0;
- }
- }
- free(frame_set->tr_particle_data[i].values);
- frame_set->tr_particle_data[i].values = 0;
- }
+ tng_particle_data_values_free(frame_set->tr_particle_data[i].
+ values,
+ frame_set->tr_particle_data[i].
+ n_frames,
+ n_particles,
+ frame_set->tr_particle_data[i].
+ n_values_per_frame,
+ frame_set->tr_particle_data[i].
+ datatype);
+
if(frame_set->tr_particle_data[i].block_name)
{
free(frame_set->tr_particle_data[i].block_name);
@@ -5696,36 +5616,10 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data)
{
for(i = frame_set->n_data_blocks; i--;)
{
- if(frame_set->tr_data[i].values)
- {
- n_frames = max(1, frame_set->tr_data[i].n_frames);
- for(j = n_frames; j--;)
- {
- if(frame_set->tr_data[i].values[j])
- {
- if(frame_set->tr_data[i].datatype ==
- TNG_CHAR_DATA)
- {
- for(k = frame_set->tr_data[i].n_values_per_frame;
- k--;)
- {
- if(frame_set->tr_data[i].values[j][k].c)
- {
- free(frame_set->tr_data[i].
- values[j][k].c);
-
- frame_set->tr_data[i].
- values[j][k].c = 0;
- }
- }
- }
- free(frame_set->tr_data[i].values[j]);
- frame_set->tr_data[i].values[j] = 0;
- }
- }
- free(frame_set->tr_data[i].values);
- frame_set->tr_data[i].values = 0;
- }
+ tng_data_values_free(frame_set->tr_data[i].values, 1,
+ frame_set->tr_data[i].
+ n_values_per_frame,
+ frame_set->tr_data[i].datatype);
if(frame_set->tr_data[i].block_name)
{
free(frame_set->tr_data[i].block_name);
@@ -6887,13 +6781,90 @@ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
+tng_function_status tng_data_values_free(union data_values **values,
+ int64_t n_frames,
+ int64_t n_values_per_frame,
+ tng_data_type type)
+{
+ int i, j;
+
+ if(values)
+ {
+ for(i = 0; i < n_frames; i++)
+ {
+ if(values[i])
+ {
+ if(type == TNG_CHAR_DATA)
+ {
+ for(j = n_values_per_frame; j--;)
+ {
+ if(values[i][j].c)
+ {
+ free(values[i][j].c);
+ values[i][j].c = 0;
+ }
+ }
+ }
+ free(values[i]);
+ values[i] = 0;
+ }
+ }
+ free(values);
+ values = 0;
+ }
+
+ return(TNG_SUCCESS);
+}
+
+tng_function_status tng_particle_data_values_free(union data_values ***values,
+ int64_t n_frames,
+ int64_t n_particles,
+ int64_t n_values_per_frame,
+ tng_data_type type)
+{
+ int i, j, k;
+ if(values)
+ {
+ for(i = 0; i < n_frames; i++)
+ {
+ if(values[i])
+ {
+ for(j = 0; j < n_particles; j++)
+ {
+ if(type == TNG_CHAR_DATA)
+ {
+ for(k = n_values_per_frame; k--;)
+ {
+ if(values[i][j][k].c)
+ {
+ free(values[i][j][k].c);
+ values[i][j][k].c = 0;
+ }
+ }
+ }
+ free(values[i][j]);
+ values[i][j] = 0;
+ }
+ free(values[i]);
+ values[i] = 0;
+ }
+ }
+ free(values);
+ values = 0;
+ }
+
+ return(TNG_SUCCESS);
+}
tng_function_status tng_data_get(tng_trajectory_t tng_data,
int64_t block_id,
- union data_values ***values)
+ union data_values ***values,
+ int64_t *n_frames,
+ int64_t *n_values_per_frame,
+ tng_data_type *type)
{
- int i, block_index;
- struct tng_data *data;
+ int i, j, block_index, len;
+ struct tng_data *data, *new_data;
struct tng_trajectory_frame_set *frame_set =
&tng_data->current_trajectory_frame_set;
@@ -6929,7 +6900,67 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data,
}
}
- *values = data->values;
+ /* A bit hackish to create a new data struct before returning the data */
+ new_data = malloc(sizeof(struct tng_data));
+
+ new_data->n_values_per_frame = 0;
+ new_data->n_frames = 0;
+ new_data->values = 0;
+ new_data->datatype = data->datatype;
+ *n_values_per_frame = data->n_values_per_frame;
+ if(tng_allocate_data_mem(tng_data, new_data, data->n_frames,
+ *n_values_per_frame) != TNG_SUCCESS)
+ {
+ return(TNG_CRITICAL);
+ }
+
+ *n_frames = max(1, data->n_frames);
+
+ *values = new_data->values;
+ *type = data->datatype;
+ switch(*type)
+ {
+ case TNG_CHAR_DATA:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_values_per_frame; j--;)
+ {
+ len = strlen(data->values[i][j].c) + 1;
+ (*values)[i][j].c = malloc(len);
+ strncpy((*values)[i][j].c, data->values[i][j].c, len);
+ }
+ }
+ break;
+ case TNG_INT_DATA:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_values_per_frame; j--;)
+ {
+ (*values)[i][j].i = data->values[i][j].i;
+ }
+ }
+ break;
+ case TNG_FLOAT_DATA:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_values_per_frame; j--;)
+ {
+ (*values)[i][j].f = data->values[i][j].f;
+ }
+ }
+ break;
+ case TNG_DOUBLE_DATA:
+ default:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_values_per_frame; j--;)
+ {
+ (*values)[i][j].d = data->values[i][j].d;
+ }
+ }
+ }
+
+ free(new_data);
return(TNG_SUCCESS);
}
@@ -6938,7 +6969,9 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data,
int64_t block_id,
int64_t start_frame_nr,
int64_t end_frame_nr,
- union data_values ***values)
+ union data_values ***values,
+ int64_t *n_values_per_frame,
+ tng_data_type *type)
{
/* STUB */
return(TNG_SUCCESS);
@@ -6946,13 +6979,19 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data,
tng_function_status tng_particle_data_get(tng_trajectory_t tng_data,
int64_t block_id,
- union data_values ****values)
+ union data_values ****values,
+ int64_t *n_frames,
+ int64_t *n_particles,
+ int64_t *n_values_per_frame,
+ tng_data_type *type)
{
- int i, block_index;
- struct tng_particle_data *data;
+ int i, j, k, block_index, len;
+ struct tng_particle_data *data, *new_data;
struct tng_trajectory_frame_set *frame_set =
&tng_data->current_trajectory_frame_set;
+ tng_block_type block_type_flag;
+
block_index = -1;
/* See if there is already a data block of this ID.
* Start checking the last read frame set */
@@ -6962,6 +7001,7 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data,
if(data->block_id == block_id)
{
block_index = i;
+ block_type_flag = TNG_TRAJECTORY_BLOCK;
break;
}
}
@@ -6976,6 +7016,7 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data,
if(data->block_id == block_id)
{
block_index = i;
+ block_type_flag = TNG_NON_TRAJECTORY_BLOCK;
break;
}
}
@@ -6987,7 +7028,90 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data,
}
}
- *values = data->values;
+ if(block_type_flag == TNG_TRAJECTORY_BLOCK &&
+ tng_data->var_num_atoms_flag)
+ {
+ *n_particles = frame_set->n_particles;
+ }
+ else
+ {
+ *n_particles = tng_data->n_particles;
+ }
+
+ /* A bit hackish to create a new data struct before returning the data */
+ new_data = malloc(sizeof(struct tng_particle_data));
+
+ new_data->n_values_per_frame = 0;
+ new_data->n_frames = 0;
+ new_data->values = 0;
+ new_data->datatype = data->datatype;
+ *n_values_per_frame = data->n_values_per_frame;
+ if(tng_allocate_particle_data_mem(tng_data, new_data, data->n_frames,
+ *n_particles, data->n_values_per_frame) !=
+ TNG_SUCCESS)
+ {
+ return(TNG_CRITICAL);
+ }
+
+ *n_frames = max(1, data->n_frames);
+
+ *values = new_data->values;
+ *type = data->datatype;
+ switch(*type)
+ {
+ case TNG_CHAR_DATA:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_particles; j--;)
+ {
+ for(k=*n_values_per_frame; k--;)
+ {
+ len = strlen(data->values[i][j][k].c) + 1;
+ (*values)[i][j][k].c = malloc(len);
+ strncpy((*values)[i][j][k].c, data->values[i][j][k].c, len);
+ }
+ }
+ }
+ break;
+ case TNG_INT_DATA:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_particles; j--;)
+ {
+ for(k=*n_values_per_frame; k--;)
+ {
+ (*values)[i][j][k].i = data->values[i][j][k].i;
+ }
+ }
+ }
+ break;
+ case TNG_FLOAT_DATA:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_particles; j--;)
+ {
+ for(k=*n_values_per_frame; k--;)
+ {
+ (*values)[i][j][k].f = data->values[i][j][k].f;
+ }
+ }
+ }
+ break;
+ case TNG_DOUBLE_DATA:
+ default:
+ for(i=*n_frames; i--;)
+ {
+ for(j=*n_particles; j--;)
+ {
+ for(k=*n_values_per_frame; k--;)
+ {
+ (*values)[i][j][k].d = data->values[i][j][k].d;
+ }
+ }
+ }
+ }
+
+ free(new_data);
return(TNG_SUCCESS);
}
@@ -6998,7 +7122,9 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data,
int64_t end_frame_nr,
int64_t first_particle_number,
int64_t last_particle_number,
- union data_values ****values)
+ union data_values ****values,
+ int64_t *n_values_per_frame,
+ tng_data_type *type)
{
/* STUB */
return(TNG_SUCCESS);
diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h
index 4357285..6d049ca 100644
--- a/src/lib/tng_io.h
+++ b/src/lib/tng_io.h
@@ -693,6 +693,32 @@ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data,
int64_t start_frame_nr,
int64_t end_frame_nr);
+/* Free data is an array of values (2D).
+ **values is the array to free and will be set to 0 afterwards.
+ n_frames is the number of frames in the data array.
+ n_values_per_frame is the number of values per frame in the data array.
+ type is the data type of the data in the array.
+ Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
+ has occurred or TNG_CRITICAL (2) if a major error has occured. */
+tng_function_status tng_data_values_free(union data_values **values,
+ int64_t n_frames,
+ int64_t n_values_per_frame,
+ tng_data_type type);
+
+/* Free data is an array of values (3D).
+ ***values is the array to free and will be set to 0 afterwards.
+ n_frames is the number of frames in the data array.
+ n_particles is the number of particles in the data array.
+ n_values_per_frame is the number of values per frame in the data array.
+ type is the data type of the data in the array.
+ Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
+ has occurred or TNG_CRITICAL (2) if a major error has occured. */
+tng_function_status tng_particle_data_values_free(union data_values ***values,
+ int64_t n_frames,
+ int64_t n_particles,
+ int64_t n_values_per_frame,
+ tng_data_type type);
+
/* Retrieve non-particle data from the last read frame set.
tng_data is a trajectory data container. tng_data->input_file_path specifies which
file to read from. If the file (input_file) is not open it will be opened.
@@ -700,11 +726,20 @@ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data,
***values is a pointer to a 2-dimensional array (memory unallocated), which will
point to the data of the requested data block. The array will be sized
(n_frames * n_values_per_frame).
+ Since ***values is allocated in this function it is the callers responsibility
+ to free the memory.
+ *n_frames is set to the number of frames in the data. This is needed to
+ properly reach and/or free the data.
+ *n_values_per_frame is set to the number of values per frame in the data.
+ This is needed to properly reach and/or free the data.
Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
has occurred or TNG_CRITICAL (2) if a major error has occured. */
tng_function_status tng_data_get(tng_trajectory_t tng_data,
int64_t block_id,
- union data_values ***values);
+ union data_values ***values,
+ int64_t *n_frames,
+ int64_t *n_values_per_frame,
+ tng_data_type *type);
/* Read and retrieve non-particle data, in a specific interval, from the trajectory.
tng_data is a trajectory data container. tng_data->input_file_path specifies which
@@ -716,13 +751,17 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data,
be filled with data. The array will be sized (n_frames * n_values_per_frame).
Since ***values is allocated in this function it is the callers responsibility
to free the memory.
+ *n_values_per_frame is set to the number of values per frame in the data.
+ This is needed to properly reach and/or free the data.
Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
has occurred or TNG_CRITICAL (2) if a major error has occured. */
tng_function_status tng_data_interval_get(tng_trajectory_t tng_data,
int64_t block_id,
int64_t start_frame_nr,
int64_t end_frame_nr,
- union data_values ***values);
+ union data_values ***values,
+ int64_t *n_values_per_frame,
+ tng_data_type *type);
/* Retrieve particle data, from the last read frame set.
tng_data is a trajectory data container. tng_data->input_file_path specifies which
@@ -731,11 +770,23 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data,
****values is a pointer to a 3-dimensional array (memory unallocated), which will
point to the data of the requested data block. The array will be sized
(n_frames * n_particles * n_values_per_frame).
+ Since ****values is allocated in this function it is the callers responsibility
+ to free the memory.
+ *n_frames is set to the number of frames in the data. This is needed to
+ properly reach and/or free the data.
+ *n_particles is set to the number of particles in the returned data. This is
+ needed to properly reach and/or free the data.
+ *n_values_per_frame is set to the number of values per frame in the data.
+ This is needed to properly reach and/or free the data.
Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
has occurred or TNG_CRITICAL (2) if a major error has occured. */
tng_function_status tng_particle_data_get(tng_trajectory_t tng_data,
int64_t block_id,
- union data_values ****values);
+ union data_values ****values,
+ int64_t *n_frames,
+ int64_t *n_particles,
+ int64_t *n_values_per_frame,
+ tng_data_type *type);
/* Read and retrieve particle data, in a specific interval, from the trajectory.
tng_data is a trajectory data container. tng_data->input_file_path specifies which
@@ -749,6 +800,8 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data,
be filled with data. The array will be sized (n_frames * n_particles * n_values_per_frame).
Since ****values is allocated in this function it is the callers responsibility
to free the memory.
+ *n_values_per_frame is set to the number of values per frame in the data.
+ This is needed to properly reach and/or free the data.
Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
has occurred or TNG_CRITICAL (2) if a major error has occured. */
tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data,
@@ -757,7 +810,9 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data,
int64_t end_frame_nr,
int64_t first_particle_number,
int64_t last_particle_number,
- union data_values ****values);
+ union data_values ****values,
+ int64_t *n_values_per_frame,
+ tng_data_type *type);
/* Get the date and time of initial file creation in ISO format (string).
tng_data is a trajectory data container.
contact: Jan Huwald // Impressum