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Author SHA1 Message Date
Grzegorz Kowal
6532c998fb IO: Implement restoring from version 2.0 of AmunXML restart snapshots. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-15 12:57:34 -03:00
Grzegorz Kowal
3b44444211 IO: Implement storing the version 2.0 of AmunXML restart snapshots. 
This version avoids allocation of big arrays to store the array fields
of data blocks. Fields with primitive and conservative variables are
stores separately for each block.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-15 12:06:48 -03:00
Grzegorz Kowal
d78b827f37 BOUNDARIES: Fix compilation with MPI=off. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-13 10:58:42 -03:00
Grzegorz Kowal
339d8e3ca4 BOUNDARIES: Simplify 2D and 3D cases in boundary_fluxes(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-12 22:10:06 -03:00
Grzegorz Kowal
b455ddaa6b BOUNDARIES: Add support for passive scalars to boundary_fluxes(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-12 16:26:01 -03:00
Grzegorz Kowal
02a516aa6d BOUNDARIES: Fix missing indices in boundary_fluxes(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-11 12:30:44 -03:00
Grzegorz Kowal
1836f733c7 BLOCKS: Remove field %f from data block structure. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-11 01:28:12 -03:00
Grzegorz Kowal
580e1b832e BOUNDARIES: Rewrite bondary_fluxes() to update dU. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-11 01:26:15 -03:00
Grzegorz Kowal
2509cf3d5a BLOCKS, EVOLUTION: Add block interface fluxes and update them. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 19:25:44 -03:00
Grzegorz Kowal
0a03dd6f2f EVOLUTION: Separate dU update from the intermitate state update. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 18:52:55 -03:00
Grzegorz Kowal
8c46b83626 EVOLUTION: Call update_flux() in update_increment(). 
Remove update_fluxes().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 18:26:52 -03:00
Grzegorz Kowal
c4a0d1df09 BLOCKS, EVOLUTION: Make dU to be blocks field and use it. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 17:51:28 -03:00
Grzegorz Kowal
9b5e809ca9 IO: Make sure only available block's %uu fields are re/stored. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 14:31:15 -03:00
Grzegorz Kowal
8d167e3895 MESH: Distribute whole block field %uu in redistribute_blocks(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 14:22:16 -03:00
Grzegorz Kowal
3d45fcca34 BLOCKS: Use %uu instead of %u0, %u1, and %u2. 
Block field %uu addopts its size according to the used integration
methods. Use it for all operation insteado of fields %u0, %u1, and %u2.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 14:05:00 -03:00
Grzegorz Kowal
3b954802a5 BLOCKS, DRIVER: Pass the number of registers to BLOCKS. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 12:47:01 -03:00
Grzegorz Kowal
a5d7bc6aff DRIVER: Initialize EVOLUTION before BLOCKS. 
This is required for the number of memory registers to be ready for
using in module BLOCKS.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 12:41:42 -03:00
Grzegorz Kowal
b5540ed58d EVOLUTION: Add variable for required number of registers. 
The number of registers indicates how many memory copies of the
conserved variables are required to perform the integration using a
selected method.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-07-10 12:24:20 -03:00
Grzegorz Kowal
cb7a9fce7b HASH: Remove unused seed, simplify initialization of lane(1). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-06-03 16:26:02 -03:00
Grzegorz Kowal
0315941dd9 PYTHON: Bounds of blocks always assume 3 dimensions. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2021-06-03 16:22:21 -03:00
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