2339 Commits

Author SHA1 Message Date
b94f8584d3 PYTHON: Update package version.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 15:58:31 -03:00
bd481a2e91 PYTHON: Update version to 0.6.2.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 15:56:06 -03:00
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
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
2f83136ed9 PYTHON: Add submodule to write VTK files.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 12:12:34 -03:00
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
7fd7575bf4 PYTHON: Initialize meta block indices and bounds.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 11:17:05 -03:00
8d8be029c4 PYTHON: Remove unnecessary import from AmunXML.dataset().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 10:29:44 -03:00
f120808f45 PYTHON: Reorganize AmunXML.dataset().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 10:27:02 -03:00
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
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
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
ec9acf3c12 PYTHON: Make read_binary_data() private.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 09:39:12 -03:00
7ee5cde0a8 PYTHON: Make read_binary_meta() private.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 09:37:52 -03:00
9d24d7b469 PYTHON: Make check_digest() private.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 09:37:11 -03:00
f8a7039a94 PYTHON: Split module into submodules.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-15 09:07:48 -03:00
c1c68c3516 PYTHON: Reorganize AmunPy package structure.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-14 21:47:34 -03:00
797deb9ae0 PYTHON: Move AmunPy to separate subdirectory.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-03-14 19:27:55 -03:00
118d643524 PARAMETERS: Initialize status flag in read_parameters().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-02-25 20:05:27 -03:00
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
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
ce1a9739cc README: Add requirements for compression libraries.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-02-05 10:17:07 -03:00
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
fa8cfa8f8f COMPRESSION: Remove the 2GiB limit in compress().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-02-04 17:40:17 -03:00
3f0bd444c8 HASH: Remove the 2GiB limit for xxh64().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-02-04 17:37:53 -03:00
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
3d16d5c13d Update copyrights.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-02-04 17:35:04 -03:00
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
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
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
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
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
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
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
37fdafd28d EVOLUTION: Fix unphysical cells after applying shapes.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-26 10:50:49 -03:00
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
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
7fdac2f584 SCHEMES: Make HD ROE solvers numerically symmetric.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-17 17:52:22 -03:00
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
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
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
b2f2b35d0b INTEGRALS: Flush integral buffers.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-12 06:33:56 -03:00
0b1da7d42d INTERPOLATIONS: Enable positivity fix by default.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-11 08:49:27 -03:00
0b6797ede7 INTERPOLATIONS: OCMP7 method requires 6 ghost cells.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-10 14:54:17 -03:00
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
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
44b990644d SCHEMES: Make MHD HLLC solver numerically symmetric.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-10 12:02:16 -03:00
87e748feb7 SCHEMES: Make HD HLLC solver numerically symmetric.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-10 12:01:28 -03:00
4a4c363660 SCHEMES: Make HLL solver numerically symmetric.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-10 11:58:17 -03:00
f85c119043 PROBLEMS: Slightly rewrite pressures in tearing problem.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2020-11-10 10:13:31 -03:00