gkowal/amun-code
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
2,343 Commits 5 Branches 0 Tags
Commit Graph

2343 Commits

This Branch
This Branch
All Branches
Author SHA1 Message Date
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
Grzegorz Kowal
4833067bea SCHEMES: Improve detection of numerical degeneracies in HLLD solvers. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-12-27 11:37:07 -03:00
Grzegorz Kowal
052ce7e05a PYTHON: Implement reading subvolume of the datasets in AmunXML. 
The subvolume to be read is controlled by additional parameter 'extent'
passed to function dataset(). The syntax of this parameters is

  extent=(xmin, xmax, ymin, ymax, zmin, zmax)

for 3D snapshots or

  extent=(xmin, xmax, ymin, ymax)

for 2D snapshots.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-12-20 22:49:14 -03:00
Grzegorz Kowal
9ae09e2c46 PYTHON: Fix block counter for 'divv' and 'divb' in AmunXML. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-12-02 17:43:37 -03:00
Grzegorz Kowal
37fdafd28d EVOLUTION: Fix unphysical cells after applying shapes. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-26 10:50:49 -03:00
Grzegorz Kowal
f453d86bc4 PYTHON: Add logarithm of density and pressure to AmunXML. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-26 09:52:28 -03:00
Grzegorz Kowal
2dfcecf789 PYTHON: Fix calculation of temperature in class AmunXML. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-26 09:48:46 -03:00
Grzegorz Kowal
7fdac2f584 SCHEMES: Make HD ROE solvers numerically symmetric. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-17 17:52:22 -03:00
Grzegorz Kowal
56fb625e59 SCHEMES: Make adiabatic MHD ROE solver numerically symmetric. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-17 17:49:05 -03:00
Grzegorz Kowal
52747633f8 SCHEMES: Make isothermal MHD ROE solver numerically symmetric. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-17 17:27:37 -03:00
Grzegorz Kowal
c677e18ecf INTEGRALS: Add subroutine to flush and sync specific IO unit. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-12 07:22:49 -03:00
Grzegorz Kowal
b2f2b35d0b INTEGRALS: Flush integral buffers. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-12 06:33:56 -03:00
Grzegorz Kowal
0b1da7d42d INTERPOLATIONS: Enable positivity fix by default. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-11 08:49:27 -03:00
Grzegorz Kowal
0b6797ede7 INTERPOLATIONS: OCMP7 method requires 6 ghost cells. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-10 14:54:17 -03:00
Grzegorz Kowal
16a7842fc0 SCHEMES: Make adiabatic MHD HLLD solver numerically symmetric. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-10 12:04:03 -03:00
Grzegorz Kowal
ff7ba2e015 SCHEMES: Make isothermal MHD HLLD solver numerically symmetric. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2020-11-10 12:03:03 -03:00