gkowal/amun-code
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
2,369 Commits 5 Branches 0 Tags
Commit Graph

2369 Commits

This Branch
This Branch
All Branches
Author SHA1 Message Date
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
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