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Author SHA1 Message Date
Grzegorz Kowal
be7e0ea5f2 PYTHON: Add faster block interpolation using ndimage.zoom. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-05-26 18:18:09 -03:00
Grzegorz Kowal
b350ecdedd PYTHON: Add direction derivatives of velocity and magnetic field. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-30 10:10:49 -03:00
Grzegorz Kowal
3b14ea26d0 PYTHON: Fix AmunXML.dataset_vtk(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-19 18:38:04 -03:00
Grzegorz Kowal
2a30d3d6d1 PYTHON: Add reading vectors of velocity and magnetic field to AmunXML. 
Add these vector to dataset() and to dataset_to_vtk() of AmunXML.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-19 18:30:56 -03:00
Grzegorz Kowal
ec16bdff05 IO: Fix restart from XML format when nghosts becomes smaller. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-18 17:26:52 -03:00
Grzegorz Kowal
e51da1c696 IO: Restart correctly from XML format for different nghosts. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-18 16:59:57 -03:00
Grzegorz Kowal
3c1e8a521a PYTHON: Rewrite octree classes. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 19:15:14 -03:00
Grzegorz Kowal
a22ce343ce PYTHON: Fix VTK file names in amun_dataset_vtk(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 10:37:48 -03:00
Grzegorz Kowal
b274a3636d PYTHON: Add compression level to subroutines to convert to VTK files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:50:18 -03:00
Grzegorz Kowal
5a75d7e08c PYTHON: Use getItemsFromLevel() in amun_dataset_vtk(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:42:40 -03:00
Grzegorz Kowal
500d001d4d PYTHON: Fix spelling in AmunXML.dataset_to_vtk(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:29:57 -03:00
Grzegorz Kowal
4f1042586b PYTHON: Remove unused functions from octree. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:19:34 -03:00
Grzegorz Kowal
1698246f26 PYTHON: Improve formatting of the VTK filename in AmunXML. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:18:15 -03:00
Grzegorz Kowal
315c3207d0 PYTHON: Use getItemsFromLevel() to iterate over level items in AmunXML. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:09:37 -03:00
Grzegorz Kowal
1147923801 PYTHON: Calculate the correct index position of OcNode. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 09:05:24 -03:00
Grzegorz Kowal
59714a7bda PYTHON: Add index position at the current level to octree nodes. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 08:58:01 -03:00
Grzegorz Kowal
e4ae2ce194 PYTHON: Add octree's function to return a list of items from a given level. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 08:53:50 -03:00
Grzegorz Kowal
80c3fc1d34 PYTHON: Use itertools for nested loops in octree submodule. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 08:26:39 -03:00
Grzegorz Kowal
f38122cc71 PYTHON: Slightly improve AmunXML.dataset_to_vtk(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-16 06:47:18 -03:00
Grzegorz Kowal
b94f8584d3 PYTHON: Update package version. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 15:58:31 -03:00
Grzegorz Kowal
bd481a2e91 PYTHON: Update version to 0.6.2. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 15:56:06 -03:00
Grzegorz Kowal
fc5a846af3 PYTHON: Add amun_dataset_vtk() function. 
This function works only with HDF5 files and its purpose is to convert
the dataset and store it as the OverlappedAMR VTK files, which can be
read by ParaView.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 15:54:26 -03:00
Grzegorz Kowal
a2c3666ef2 PYTHON: Add AmunXML's function to store data as AMR VTK files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 12:13:36 -03:00
Grzegorz Kowal
2f83136ed9 PYTHON: Add submodule to write VTK files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 12:12:34 -03:00
Grzegorz Kowal
0e1bc57c9c PYTHON: Add submodule to handle octree of AMR blocks. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 11:49:09 -03:00
Grzegorz Kowal
7fd7575bf4 PYTHON: Initialize meta block indices and bounds. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 11:17:05 -03:00
Grzegorz Kowal
8d8be029c4 PYTHON: Remove unnecessary import from AmunXML.dataset(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 10:29:44 -03:00
Grzegorz Kowal
f120808f45 PYTHON: Reorganize AmunXML.dataset(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 10:27:02 -03:00
Grzegorz Kowal
439eb4ea67 PYTHON: Reduce the number of variables in AmunXML.dataset(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 10:21:53 -03:00
Grzegorz Kowal
4dfd7a657f PYTHON: Put dataset reading in a private subroutine. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 10:13:53 -03:00
Grzegorz Kowal
d66811c41d PYTHON: Initialize levels and coordinates of meta blocks. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 10:02:21 -03:00
Grzegorz Kowal
ec9acf3c12 PYTHON: Make read_binary_data() private. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 09:39:12 -03:00
Grzegorz Kowal
7ee5cde0a8 PYTHON: Make read_binary_meta() private. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 09:37:52 -03:00
Grzegorz Kowal
9d24d7b469 PYTHON: Make check_digest() private. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 09:37:11 -03:00
Grzegorz Kowal
f8a7039a94 PYTHON: Split module into submodules. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-15 09:07:48 -03:00
Grzegorz Kowal
c1c68c3516 PYTHON: Reorganize AmunPy package structure. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-14 21:47:34 -03:00
Grzegorz Kowal
797deb9ae0 PYTHON: Move AmunPy to separate subdirectory. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-03-14 19:27:55 -03:00
Grzegorz Kowal
118d643524 PARAMETERS: Initialize status flag in read_parameters(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-25 20:05:27 -03:00
Grzegorz Kowal
3cbb8da21e EVOLUTION: Add missing update_variables() in SSPRK(m,2). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-05 16:16:26 -03:00
Grzegorz Kowal
18a25d3775 EVOLUTION: Make sure the system is always consistent for SSPRK(m,3). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-05 16:15:43 -03:00
Grzegorz Kowal
ce1a9739cc README: Add requirements for compression libraries. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-05 10:17:07 -03:00
Grzegorz Kowal
5728c1cab5 IO: Use stream access to store/read binary files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-04 22:26:15 -03:00
Grzegorz Kowal
fa8cfa8f8f COMPRESSION: Remove the 2GiB limit in compress(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-04 17:40:17 -03:00
Grzegorz Kowal
3f0bd444c8 HASH: Remove the 2GiB limit for xxh64(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-04 17:37:53 -03:00
Grzegorz Kowal
ad7f1da604 CMake: -ftree-vectorize seems to be problematic in some cases. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-04 17:36:37 -03:00
Grzegorz Kowal
3d16d5c13d Update copyrights. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-02-04 17:35:04 -03:00
Grzegorz Kowal
8c0e6dea29 PYTHON: Add argument 'maxlev' to function dataset(). 
This argument is an alternative way to reduce the resolution of the
data. It specifies that the output cube resolution should be
corresponding to the 'maxlev' refinement level.

If the maximum level of simulation changes during the evolution, the
parameter allows to read all snapshots with the same output resolution.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-01-05 10:48:00 -03:00
Grzegorz Kowal
575bcc1d27 PYTHON: Move shrink and interpolation arguments to dataset(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-01-05 10:17:44 -03:00
Grzegorz Kowal
b3c51569f1 PYTHON: Correct the sign of the electric field components. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-12-30 22:10:07 -03:00
Grzegorz Kowal
ca1cc9fb31 COORDINATES: Add indices for nb-1, nb+1, ne-1, ne+1. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-12-29 17:42:20 -03:00