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-rw-r--r--include/tng_io.h2
-rw-r--r--src/lib/tng_io.c219
-rw-r--r--src/tests/md_openmp_util.c20
3 files changed, 143 insertions, 98 deletions
diff --git a/include/tng_io.h b/include/tng_io.h
index 2e47e58..5609647 100644
--- a/include/tng_io.h
+++ b/include/tng_io.h
@@ -1728,7 +1728,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get
const int64_t start_frame_nr,
const int64_t end_frame_nr,
const tng_hash_mode hash_mode,
- union data_values ***values,
+ void **values,
int64_t *stride_length,
int64_t *n_values_per_frame,
tng_data_type *type);
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 6c41b67..b412582 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -21,6 +21,7 @@
#include <stdlib.h>
#include <string.h>
#include <time.h>
+#include <math.h>
#ifdef USE_ZLIB
#include <zlib.h>
#endif
@@ -3681,6 +3682,20 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
return(TNG_FAILURE);
}
+// #if 1
+// {
+// int iframe,i,j;
+// for (iframe=0; iframe<n_frames; iframe++)
+// for (i=0; i<n_particles; i++)
+// {
+// printf("tng_io: %d %d: ",iframe,i);
+// for (j=0; j<3; j++)
+// printf(" %g",((float*)start_pos)[iframe*n_particles*3+i*3+j]);
+// printf("\n");
+// }
+// }
+// #endif
+
if(block->id == TNG_TRAJ_POSITIONS)
{
if(!tng_data->compress_algo_pos)
@@ -3734,19 +3749,6 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
if(type == TNG_FLOAT_DATA)
{
-#if 1
- {
- int iframe,i,j;
- for (iframe=0; iframe<n_frames; iframe++)
- for (i=0; i<n_particles; i++)
- {
- printf("vel tng_io: %d %d: ",iframe,i);
- for (j=0; j<3; j++)
- printf(" %g",((float*)start_pos)[iframe*n_particles*3+i*3+j]);
- printf("\n");
- }
- }
-#endif
dest = tng_compress_vel_float_find_algo(start_pos, n_particles,
n_frames,
0.01, 0,
@@ -3785,9 +3787,17 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
}
}
- memcpy(start_pos, dest, new_len);
+ if(dest)
+ {
+ memcpy(start_pos, dest, new_len);
- free(dest);
+ free(dest);
+ }
+ else
+ {
+ printf("Error during TNG compression. %s: %d\n", __FILE__, __LINE__);
+ return(TNG_FAILURE);
+ }
block->block_contents_size = new_len + (block->block_contents_size - len);
@@ -4031,7 +4041,7 @@ static tng_function_status tng_allocate_particle_data_mem
const int64_t n_values_per_frame)
{
void ***values;
- int64_t i, j, k, size;
+ int64_t i, j, k, size, frame_alloc;
if(data->strings && data->datatype == TNG_CHAR_DATA)
{
@@ -4057,11 +4067,12 @@ static tng_function_status tng_allocate_particle_data_mem
n_frames = tng_max(1, n_frames);
data->stride_length = tng_max(1, stride_length);
data->n_values_per_frame = n_values_per_frame;
+ frame_alloc = tng_max(1, n_frames/data->stride_length);
if(data->datatype == TNG_CHAR_DATA)
{
- data->strings = malloc(sizeof(char ***) * n_frames);
- for(i = n_frames; i-- ;)
+ data->strings = malloc(sizeof(char ***) * frame_alloc);
+ for(i = frame_alloc; i-- ;)
{
data->strings[i] = malloc(sizeof(char **) *
n_particles);
@@ -4106,12 +4117,12 @@ static tng_function_status tng_allocate_particle_data_mem
}
values = realloc(data->values,
- size * (n_frames/data->stride_length) *
+ size * frame_alloc *
n_particles * n_values_per_frame);
if(!values)
{
printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- size * (n_frames/data->stride_length) *
+ size * frame_alloc *
n_particles * n_values_per_frame,
__FILE__, __LINE__);
free(data->values);
@@ -4826,40 +4837,9 @@ static tng_function_status tng_particle_data_block_write
}
else if(data->values)
{
-
- if(block->id == TNG_TRAJ_VELOCITIES)
- {
- for(i=0; i<n_frames / stride_length; i++)
- {
- printf("%d\n", i);
- for(j=0; j<n_particles; j++)
- {
- printf("%d: %f %f %f %"PRId64"\n", j, *(float *)(data->values + sizeof(float) * (i * n_particles * 3 + j * 3)),
- *(float *)(data->values + sizeof(float) * (i * n_particles * 3 + j * 3 +1)),
- *(float *)(data->values + sizeof(float) * (i * n_particles * 3 + j * 3 +2)),
- sizeof(float) * (i * n_particles * 3 + j * 3));
- }
- }
- }
-
memcpy(block->block_contents + offset, data->values,
block->block_contents_size - offset);
- if(block->id == TNG_TRAJ_VELOCITIES)
- {
- for(i=0; i<n_frames / stride_length; i++)
- {
- printf("%d\n", i);
- for(j=0; j<n_particles; j++)
- {
- printf("%d: %f %f %f %"PRId64"\n", j, *(float *)(block->block_contents + offset + sizeof(float) * (i * n_particles * 3 + j * 3)),
- *(float *)(block->block_contents + offset + sizeof(float) * (i * n_particles * 3 + j * 3 +1)),
- *(float *)(block->block_contents + offset + sizeof(float) * (i * n_particles * 3 + j * 3 +2)),
- sizeof(float) * (i * n_particles * 3 + j * 3));
- }
- }
- }
-
switch(data->datatype)
{
case TNG_FLOAT_DATA:
@@ -4867,7 +4847,7 @@ static tng_function_status tng_particle_data_block_write
{
if(tng_data->input_endianness_swap_func_32)
{
- for(i = 0; i < (block->block_contents_size - offset) / size; i++)
+ for(i = offset; i < block->block_contents_size; i+=size)
{
if(tng_data->input_endianness_swap_func_32(tng_data,
(int32_t *)(block->block_contents + i))
@@ -4882,16 +4862,20 @@ static tng_function_status tng_particle_data_block_write
else
{
multiplier = data->compression_multiplier;
- for(i = 0; i < (block->block_contents_size - offset) / size; i++)
+ if(fabs(multiplier - 1.0) > 0.00001 ||
+ tng_data->input_endianness_swap_func_32)
{
- *(float *)(block->block_contents + i) *= multiplier;
- if(tng_data->input_endianness_swap_func_32 &&
- tng_data->input_endianness_swap_func_32(tng_data,
- (int32_t *)(block->block_contents + i))
- != TNG_SUCCESS)
+ for(i = offset; i < block->block_contents_size; i+=size)
{
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
+ *(float *)(block->block_contents + i) *= multiplier;
+ if(tng_data->input_endianness_swap_func_32 &&
+ tng_data->input_endianness_swap_func_32(tng_data,
+ (int32_t *)(block->block_contents + i))
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
}
}
}
@@ -4931,16 +4915,20 @@ static tng_function_status tng_particle_data_block_write
else
{
multiplier = data->compression_multiplier;
- for(i = offset; i < block->block_contents_size; i+=size)
+ if(fabs(multiplier - 1.0) > 0.00001 ||
+ tng_data->input_endianness_swap_func_64)
{
- *(double *)(block->block_contents + i) *= multiplier;
- if(tng_data->input_endianness_swap_func_64 &&
- tng_data->input_endianness_swap_func_64(tng_data,
- (int64_t *)(block->block_contents + i))
- != TNG_SUCCESS)
+ for(i = offset; i < block->block_contents_size; i+=size)
{
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
+ *(double *)(block->block_contents + i) *= multiplier;
+ if(tng_data->input_endianness_swap_func_64 &&
+ tng_data->input_endianness_swap_func_64(tng_data,
+ (int64_t *)(block->block_contents + i))
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
}
}
}
@@ -5084,7 +5072,7 @@ static tng_function_status tng_allocate_data_mem
const int64_t n_values_per_frame)
{
void **values;
- int64_t i, j, size;
+ int64_t i, j, size, frame_alloc;
if(data->strings && data->datatype == TNG_CHAR_DATA)
{
@@ -5106,11 +5094,12 @@ static tng_function_status tng_allocate_data_mem
data->stride_length = tng_max(1, stride_length);
n_frames = tng_max(1, n_frames);
data->n_values_per_frame = n_values_per_frame;
+ frame_alloc = tng_max(1, n_frames/data->stride_length) + 1;
if(data->datatype == TNG_CHAR_DATA)
{
- data->strings = malloc(sizeof(char **) * n_frames);
- for(i = n_frames; i-- ;)
+ data->strings = malloc(sizeof(char **) * frame_alloc);
+ for(i = frame_alloc; i-- ;)
{
data->strings[i] = malloc(sizeof(char *) * n_values_per_frame);
if(!data->strings[i])
@@ -5142,12 +5131,12 @@ static tng_function_status tng_allocate_data_mem
}
values = realloc(data->values,
- size * (n_frames/data->stride_length) *
+ size * frame_alloc *
n_values_per_frame);
if(!values)
{
printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- size * (n_frames/data->stride_length) *
+ size * frame_alloc *
n_values_per_frame,
__FILE__, __LINE__);
free(data->values);
@@ -12165,7 +12154,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get
const int64_t start_frame_nr,
const int64_t end_frame_nr,
const tng_hash_mode hash_mode,
- union data_values ***values,
+ void **values,
int64_t *stride_length,
int64_t *n_values_per_frame,
tng_data_type *type)
@@ -13216,6 +13205,31 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read
return(stat);
}
+tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read
+ (tng_trajectory_t tng_data,
+ float **box_shape,
+ int64_t *stride_length)
+{
+ int64_t n_frames, n_values_per_frame;
+ tng_data_type type;
+ tng_function_status stat;
+
+ stat = tng_num_frames_get(tng_data, &n_frames);
+ if(stat != TNG_SUCCESS)
+ {
+ return(stat);
+ }
+
+ stat = tng_data_vector_interval_get(tng_data, TNG_TRAJ_BOX_SHAPE,
+ 0, n_frames - 1, TNG_USE_HASH,
+ (void **)box_shape,
+ stride_length,
+ &n_values_per_frame,
+ &type);
+
+ return(stat);
+}
+
tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range
(tng_trajectory_t tng_data,
const int64_t first_frame,
@@ -13285,6 +13299,28 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range
return(stat);
}
+tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range
+ (tng_trajectory_t tng_data,
+ const int64_t first_frame,
+ const int64_t last_frame,
+ float **box_shape,
+ int64_t *stride_length)
+{
+ int64_t n_values_per_frame;
+ tng_data_type type;
+ tng_function_status stat;
+
+ stat = tng_data_vector_interval_get(tng_data, TNG_TRAJ_BOX_SHAPE,
+ first_frame, last_frame,
+ TNG_USE_HASH,
+ (void **)box_shape,
+ stride_length,
+ &n_values_per_frame,
+ &type);
+
+ return(stat);
+}
+
tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set
(tng_trajectory_t tng_data,
const int64_t f,
@@ -13439,6 +13475,22 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
tng_num_particles_get(tng_data, &n_particles);
+// #if 1
+// if(block_id == TNG_TRAJ_VELOCITIES)
+// {
+// int i,j;
+// for (i=0; i<n_particles; i++)
+// {
+// printf("generic write input: %"PRId64" %d: ",frame_nr,i);
+// for (j=0; j<3; j++)
+// {
+// printf(" %g",((float *)values)[i*3+j]);
+// }
+// printf("\n");
+// }
+// }
+// #endif
+
if(tng_particle_data_find(tng_data, block_id, &data)
!= TNG_SUCCESS)
{
@@ -13461,9 +13513,6 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
stride_length, n_particles,
3);
}
- printf("frame nr: %"PRId64" first frame: %"PRId64" stride_length: %"PRId64" frame pos: %"PRId64"\n",
- frame_nr, frame_set->first_frame, stride_length, frame_pos);
- printf("pos: %"PRId64" length: %"PRId64"\n", sizeof(float) * frame_pos * n_particles * 3, sizeof(float) * n_particles * 3);
memcpy(data->values + sizeof(float) * frame_pos * n_particles * 3,
values, sizeof(float) * n_particles * 3);
@@ -13491,15 +13540,25 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write
}
tng_function_status DECLSPECDLLEXPORT tng_util_force_write
- (tng_trajectory_t tng_data,
- const int64_t frame_nr,
- const float *forces)
+ (tng_trajectory_t tng_data,
+ const int64_t frame_nr,
+ const float *forces)
{
return(tng_util_generic_write(tng_data, frame_nr, forces,
TNG_TRAJ_FORCES, "FORCES",
TNG_GZIP_COMPRESSION));
}
+tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write
+ (tng_trajectory_t tng_data,
+ const int64_t frame_nr,
+ const float *box_shape)
+{
+ return(tng_util_generic_write(tng_data, frame_nr, box_shape,
+ TNG_TRAJ_BOX_SHAPE, "BOX SHAPE",
+ TNG_GZIP_COMPRESSION));
+}
+
#ifdef BUILD_FORTRAN
/* The following is for calling the library from fortran */
diff --git a/src/tests/md_openmp_util.c b/src/tests/md_openmp_util.c
index 41ccff5..6955df9 100644
--- a/src/tests/md_openmp_util.c
+++ b/src/tests/md_openmp_util.c
@@ -70,7 +70,7 @@ int main ( int argc, char *argv[] )
float kinetic;
float mass = 1.0;
int nd = 3;
- int np = 50;
+ int np = 10;
float *pos;
float potential;
int proc_num;
@@ -188,7 +188,7 @@ int main ( int argc, char *argv[] )
step_print = 0;
step_print_index = 0;
- step_print_num = 100;
+ step_print_num = 10;
/*
This is the main time stepping loop:
@@ -269,21 +269,6 @@ int main ( int argc, char *argv[] )
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
}
-#if 1
- {
- int j,i;
- for ( j = 0; j < np; j++ )
- {
- printf("vel in md for %d %d:",step,j);
- for ( i = 0; i < nd; i++ )
- {
- printf (" %g",vel[i+j*nd]);
- }
- printf("\n");
- }
- }
-#endif
-
if(tng_util_vel_write(traj, step, vel) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
@@ -305,6 +290,7 @@ int main ( int argc, char *argv[] )
free ( acc );
free ( box );
+ free ( box_shape );
free ( force );
free ( pos );
free ( vel );
contact: Jan Huwald // Impressum