d714974b33
PYTHON: Restore zmin/zmax/zblocks for 2D AmunXML snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-05 09:38:49 -03:00
b6edd6ca97
PYTHON: Version 0.9
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-05 09:13:24 -03:00
764c1596b5
PYTHON: Improve comments in AmunH5 structures.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-05 09:09:24 -03:00
919e0ce6c2
PYTHON: Separate deprecated AmunH5 functions.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-05 09:05:57 -03:00
dbf977de36
PYTHON: Rewrite AmunXML class to use Amun base class.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-05 09:03:23 -03:00
61d5eeb839
PYTHON: Convert returns to exceptions in Amun class.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-04 22:24:08 -03:00
8e125253f7
PYTHON: Make AmunH5 class public.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-04 22:19:43 -03:00
da339f1ac9
PYTHON: Implement AmunH5 class for Amun's HDF5 format.
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Mark the previous subroutines deprecated.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-04 22:17:53 -03:00
d28194dc23
PYTHON: Add amun.py defining the base class for Amun snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-04 22:15:59 -03:00
abd1749945
PYTHON: Use None for no compression of VTK files.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-10-04 22:14:30 -03:00
6ffb3f5910
INTERPOLATIONS: Add a couple of limiters.
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Use limiter_average() which is not a limiter, just returns average of
left and right derivatives, as the default limiter for prolongation.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-09-21 11:29:16 -03:00
d3c0737c8d
BOUNDARIES, MESH: Allow to choose prolongation limiter.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-09-21 11:28:23 -03:00
61ed993821
EVOLUTION: Fix decay rate of ψ field.
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This scalar potential tracks the development of div(B). Its decay
depends on the cell size, so make it calculated per refinement level.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-09-20 08:44:38 -03:00
7b79d88b6d
CMAKE: Turn off HDF5 by default.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-09-12 12:02:04 -03:00
9d48cc9367
OPERATORS: Implement high-order differential operators.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-09-10 18:25:11 -03:00
7713df3ebf
EVOLUTION: Add dth to track hydrodynamic timestep.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-08-17 11:23:36 -03:00
c766bb9059
MESH: Redistribute data blocks after each refinement.
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There are situations when one process can suddenly have many data
blocks refined resulting in a significant memory stress before
the new blocks are redistributed among all processes. Just
redistribute data blocks each time the block refinement is
performed to avoid such a situation.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-20 17:58:44 -03:00
6dbda8bf14
IO: Use the same array to store each variable in write_snapshot_xml().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-20 17:56:51 -03:00
a0b6e60d7e
EVOLUTION: Simplify conditions for the new time step.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-19 15:12:08 -03:00
b2a7bd08b6
EVOLUTION: Consider dte only for methods with error control.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-19 13:16:31 -03:00
8ec801228c
EVOLUTION: Fix formatting once again.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-19 13:03:40 -03:00
d8bd7eb800
EVOLUTION: Fix formatting.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-19 13:02:14 -03:00
30215029d4
EVOLUTION: Be explicit about the method with error control.
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Do not show the parameters controlling the integration errors if the
method do not control this error.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-19 12:58:57 -03:00
74693bd7ed
Merge branch 'memory_usage_reduction'
2021-07-18 19:49:33 -03:00
548b7a456d
Revert "IO: Do not read non-existing data blocks during job restart."
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This reverts commit 2a2ab474800cf3653081eb214bb9102528f18e5e.
2021-07-18 19:49:26 -03:00
3817822f6f
HELPERS: Move flush_and_sync() to HELPERS.
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Use it in mesh statistics.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-18 19:25:49 -03:00
92f5905b6b
MESH: Store statistics when the distribution of blocks changes too.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-18 19:07:00 -03:00
7ba3d7ae37
DRIVER: Print message on received signal to error unit.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-16 11:33:49 -03:00
047e9af130
MESH: Balance data blocks not only among processes but nodes too.
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This change tries to maintain a similar number of data blocks per node,
while balancing them across all processes. This should improve the
memory utilization among nodes.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-15 21:10:17 -03:00
19e89c4dd2
MPITOOLS: Add maximum rank of the node.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-15 17:25:32 -03:00
b933c444df
MPITOOLS: Determine the number of nodes, processes per node, and local rank.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-15 17:22:00 -03:00
6532c998fb
IO: Implement restoring from version 2.0 of AmunXML restart snapshots.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-15 12:57:34 -03:00
3b44444211
IO: Implement storing the version 2.0 of AmunXML restart snapshots.
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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
d78b827f37
BOUNDARIES: Fix compilation with MPI=off.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-13 10:58:42 -03:00
2a2ab47480
IO: Do not read non-existing data blocks during job restart.
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If the number of blocks is smaller than the number of processes, the
last processes have no data block associated. Therefore, do not try to
read data blocks on such processes during the job restart.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-13 08:59:51 -03:00
339d8e3ca4
BOUNDARIES: Simplify 2D and 3D cases in boundary_fluxes().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-12 22:10:06 -03:00
b455ddaa6b
BOUNDARIES: Add support for passive scalars to boundary_fluxes().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-12 16:26:01 -03:00
02a516aa6d
BOUNDARIES: Fix missing indices in boundary_fluxes().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-11 12:30:44 -03:00
1836f733c7
BLOCKS: Remove field %f from data block structure.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-11 01:28:12 -03:00
580e1b832e
BOUNDARIES: Rewrite bondary_fluxes() to update dU.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-11 01:26:15 -03:00
2509cf3d5a
BLOCKS, EVOLUTION: Add block interface fluxes and update them.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 19:25:44 -03:00
0a03dd6f2f
EVOLUTION: Separate dU update from the intermitate state update.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 18:52:55 -03:00
8c46b83626
EVOLUTION: Call update_flux() in update_increment().
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Remove update_fluxes().
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 18:26:52 -03:00
c4a0d1df09
BLOCKS, EVOLUTION: Make dU to be blocks field and use it.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 17:51:28 -03:00
9b5e809ca9
IO: Make sure only available block's %uu fields are re/stored.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 14:31:15 -03:00
8d167e3895
MESH: Distribute whole block field %uu in redistribute_blocks().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 14:22:16 -03:00
3d45fcca34
BLOCKS: Use %uu instead of %u0, %u1, and %u2.
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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
3b954802a5
BLOCKS, DRIVER: Pass the number of registers to BLOCKS.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2021-07-10 12:47:01 -03:00
a5d7bc6aff
DRIVER: Initialize EVOLUTION before BLOCKS.
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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
b5540ed58d
EVOLUTION: Add variable for required number of registers.
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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
