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Author SHA1 Message Date
Grzegorz Kowal
c85831a386 IO: Rewrite HDF5 compression code and add ZFP compression. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 19:00:24 -03:00
Grzegorz Kowal
80b9c6d6a2 IO: Compress only variable datasets in HDF5 regular snapshots. 
Do not compress HDF5 restart snapshots at all.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 18:59:21 -03:00
Grzegorz Kowal
a364281184 IO: Fix restore_metablocks_h5() for 3D. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 18:17:29 -03:00
Grzegorz Kowal
b85dfafef1 IO: Rewrite file division in read_restart_snapshot_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 09:19:06 -03:00
Grzegorz Kowal
e50c65e7dd IO: Rewrite file division in read_restart_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-12-01 08:55:39 -03:00
Grzegorz Kowal
cc48f69803 IO: Fix the restart from the XML files with less processes. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 22:53:53 -03:00
Grzegorz Kowal
657a608ce0 PYTHON: Add support for XXH3 hash. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 19:02:32 -03:00
Grzegorz Kowal
0ac1fec2d7 IO: Rewrite read_restart_snapshot_xml() a bit. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 18:22:21 -03:00
Grzegorz Kowal
863b7c5a85 IO: Rewrite write_binary_xml() so it accepts a pointer instead of array. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 17:45:33 -03:00
Grzegorz Kowal
cb2d7b09cf HASH, IO: Pass pointers to the hash functions instead of arrays. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 14:23:22 -03:00
Grzegorz Kowal
398b3e331d HASH: Rewrite internal xxh64() to accept pointer instead of array. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 12:59:43 -03:00
Grzegorz Kowal
b5183dfa0e IO: Store hashes as integers in read_restart_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 12:20:14 -03:00
Grzegorz Kowal
a53601ff92 HASH, IO: Rewrite module HASH. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-30 12:04:30 -03:00
Grzegorz Kowal
1fd1ee7602 IO: Add compression suffix to files individually. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-29 12:23:26 -03:00
Grzegorz Kowal
b10b49c8c3 COMPRESSION: Add compression_suffix to store the file extension. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-29 12:08:42 -03:00
Grzegorz Kowal
de81332cf8 COMPRESSION: Reset clen in case the compression is unsupported. 
This will indicate that no compression should be used.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-29 08:27:21 -03:00
Grzegorz Kowal
88cdf23078 COMPRESSION, IO: Remove double buffer for compression. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 23:27:03 -03:00
Grzegorz Kowal
9ddf7c7b44 IO: Use compression_bound() to determine the buffer size. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 22:38:30 -03:00
Grzegorz Kowal
e4ffa62714 COMPRESSION: Add function to determine the compression buffer size. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 22:32:51 -03:00
Grzegorz Kowal
e6fc8e5d24 COMPRESSION: Pass the input length to compress(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 22:19:50 -03:00
Grzegorz Kowal
20282539f9 COMPRESSION: Use ENUM to enumerate compression formats. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-28 09:59:20 -03:00
Grzegorz Kowal
82dfcf3c29 USER_PROBLEM: Remove unused stuff. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 17:15:02 -03:00
Grzegorz Kowal
3081ac0d5f BOUNDARIES: Fix wrong conditions in block_boundary_specific(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 17:07:31 -03:00
Grzegorz Kowal
8fb3abacbf PROBLEM, SYSTEM: Move USER_PROBLEM initialization to SYSTEM. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 16:48:54 -03:00
Grzegorz Kowal
fd40fffc64 BOUNDARIES: Add interface to custom boundaries. 
Also return the call status from block_boundary_specific().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 16:42:53 -03:00
Grzegorz Kowal
4ceb008987 SHAPES: Do not pull update_user_shapes() from module USER_PROBLEM. 
The pointer to update_shapes can be associated in
initialize_user_problem().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 13:47:05 -03:00
Grzegorz Kowal
25ad944f44 SOURCES: Add procedure interface for extra source terms. 
A user defined source terms can be pointer to the procedure pointer
'update_extra_sources'.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-26 13:37:25 -03:00
Grzegorz Kowal
2b60ebaa3f MESH: Fix condition for deferinement of sibling blocks. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 18:01:35 -03:00
Grzegorz Kowal
aa552c7a51 SYSTEM: Reset seeds in initialize_system(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 11:56:01 -03:00
Grzegorz Kowal
54263b263c RANDOM: Add subroutine to reset the seeds. 
This subroutine will restore the initial seeds values.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 11:54:06 -03:00
Grzegorz Kowal
99d9f1c9f1 AMUN: Initialize RNG before module SYSTEM. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 11:48:45 -03:00
Grzegorz Kowal
cfac02db87 MESH: Make procedure pointer setup_domain public. 
If a user decides to write a subroutine to generate a problem specific
domain, it is enough to point this pointer in, e.g.,
initialize_user_problem() to the user's custom domain setup subroutine.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 10:37:47 -03:00
Grzegorz Kowal
a03375122b IO: Resume jobs from HDF5 restart snapshots for different nghosts. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 10:33:55 -03:00
Grzegorz Kowal
1f1ae8084f EVOLUTION: Remove warning in initialize_evolution() if NDIMS=2. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 08:39:52 -03:00
Grzegorz Kowal
3d6bf16f91 USER_PROBLEM: Remove user_gravitational_acceleration(). 
It is an empty subroutine. It is better to describe in the documentation
how to write subroutine for custom gravitational acceleration and point
it to gravitationa_acceleration from module GRAVITY.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 08:34:45 -03:00
Grzegorz Kowal
aea03e669e MESH: Return call status from redistribute_blocks(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-25 08:33:32 -03:00
Grzegorz Kowal
8c83be9cb4 REFINEMENT: Implement the interface for user refinement criterion. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 22:44:28 -03:00
Grzegorz Kowal
a395cf8cda SCHEMES: Remove unused variables. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 13:22:27 -03:00
Grzegorz Kowal
2b04148e88 MESH: Remove unused variables. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 13:20:03 -03:00
Grzegorz Kowal
78ae62528a EVOLUTION: Eliminate uninitialized conditions. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 13:16:59 -03:00
Grzegorz Kowal
a9b13d7d8d BOUNDARIES: Initialize ecount. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 13:04:10 -03:00
Grzegorz Kowal
9805090290 HASH: Clean up the code according to XXHASH flag. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 12:49:40 -03:00
Grzegorz Kowal
fd4029a196 PYTHON: Rewrite Amun module to support old and new snapshots. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-24 12:33:33 -03:00
Grzegorz Kowal
a1cf8f9192 IO: Rewrite and rename store_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 18:03:33 -03:00
Grzegorz Kowal
2dedf75be4 IO: Rewrite and rename store_restart_snapshot_xml(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 17:56:17 -03:00
Grzegorz Kowal
aeb71db1d3 IO: Remove useless comments from initialize_io(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 16:46:41 -03:00
Grzegorz Kowal
d564f2dc5f IO: Import HDF5 module for all IO subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 16:40:30 -03:00
Grzegorz Kowal
4fca13a3e4 IO: Enable compression for HDF5 datasets. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 16:37:19 -03:00
Grzegorz Kowal
e83c9bb09d IO: Remove old HDF5 read_attribute subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 13:09:33 -03:00
Grzegorz Kowal
2658d6385e IO: Add missing group closing in restore_attributes_h5(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-11-23 13:07:46 -03:00