09f032faba
DOMAINS, DRIVER: Initialize and finalize domains module.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 17:46:57 -02:00
ea993ed8d0
BLOCKS, DRIVER: Initialize block dimensions in initialize_blocks().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 17:26:24 -02:00
b5d177bc72
COORDINATES, DRIVER: Separate coordinate info from initialization.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 17:02:50 -02:00
2ecdf030d6
DRIVER, EQUATIONS: Separate equation info from initialization.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 15:54:02 -02:00
7a2d694629
DRIVER, IO: Initialize I/O after reading parameters.
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Use it to handle parameters from restart snapshots. Also separate
printing I/O parameters from I/O module initialization.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 15:07:50 -02:00
0f0e14dfed
DRIVER: Organize IO and mesh initialization and finalization.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 11:02:57 -02:00
220e881b58
DRIVER: Initialize evolution, schemes, interpolations after shapes.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:56:20 -02:00
908b94c482
DRIVER: Initialize shapes after refinement.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:52:08 -02:00
86bf933f05
DRIVER: Initialize refinement after boundaries.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:47:47 -02:00
e045c30e1a
DRIVER: Initialize blocks and boundaries after coordinates.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:45:50 -02:00
2a6062cbd5
DRIVER, COORDINATES, IO: Pass more fixed parameters to initialize_coordinates().
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Parameters such block dimensions, the base level dimensions, or the
domain extrema cannot be modified when the job is restarted, so read
them from the restart snapshots.
Also add new subroutine to IO read integer vector attribute from the
HDF5 snapshots.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:38:16 -02:00
b0953016a5
DRIVER, SOURCES: Initialize sources after equations.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 10:05:36 -02:00
4aa92643ab
DRIVER, PROBLEMS, IO: Initiate problems earlier.
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Also store the problem name in the restart snapshot.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 09:59:09 -02:00
2ae8cd14f1
DRIVER: Move initialize_equations() to be called earlier.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-29 09:25:15 -02:00
bdddceae06
DRIVER: Print timings at the end and remove error info.
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The error info is not complete and probably broken. It should be
rewritten.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 22:25:41 -02:00
b843baa638
PARAMETERS: Make get_parameter_*() private.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:37:18 -02:00
4b0d4409eb
USER_PROBLEM: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:33:24 -02:00
93342fb333
SOURCES: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:32:37 -02:00
9a93239240
SHAPES: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:32:08 -02:00
54f5a6084f
SCHEMES: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:31:30 -02:00
da1a8e3d9f
REFINEMENT: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:30:45 -02:00
49208321b6
RANDOM: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:30:07 -02:00
c877fa6481
PROBLEMS: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:29:32 -02:00
bb5d8da088
INTERPOLATIONS: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:27:22 -02:00
d8c2331bfe
INTEGRALS: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:26:23 -02:00
f392c1644c
GRAVITY: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:25:38 -02:00
a853f0b700
EVOLUTION: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:24:53 -02:00
927642bf3e
EQUATIONS: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:23:55 -02:00
419cf04363
DOMAINS: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:22:01 -02:00
572ef0f503
COORDINATES: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:21:17 -02:00
e634ef1583
BOUNDARIES: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:19:15 -02:00
305ed8ed13
IO: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:17:10 -02:00
e884804f8c
DRIVER: Replace explicit calls to get_parameter_*() with unified one.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:06:32 -02:00
9c5841d9f3
PARAMETERS: Add interface for get_parameter_*() subroutines.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 21:05:12 -02:00
26bf99d4c1
DRIVER, EQUATIONS: Reset eqsys and eos for restarted jobs.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 20:21:38 -02:00
fc5db6dd29
DRIVER, IO, COORDINATES: Reset toplev for restarted jobs.
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If the job was restart with different maxlev, then
initialize_coordinates() has to know about it, so it generate
appropriate coordinates.
Read maxlev from the restart snapshot, if the job was restarted, and set
toplev as the maximum value between the previous and current maxlev.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 18:56:39 -02:00
6fbd567130
IO: Implement subroutine to read parameters from the restart snapshots.
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If we run a job from a restart snapshot and modify some of the
parameters in the parameter file, this could lead to problems. Some
parameters, like the set of equations, equation of state, or block
dimensions, simply cannot be modified. Therefore, any such parameter,
modifies in the parameter file, should be overwritten with the value
from the restart snapshot. The purpose of these subroutines is to read
these parameters from restart snapshots.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 18:19:31 -02:00
01276925ee
DRIVER: Add flag to identify if the run is for restarted job.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 15:53:50 -02:00
4f7248533f
DRIVER, PARAMETERS: Log problems with parameters file in error output.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 15:45:35 -02:00
cf8f0e8003
MPITOOLS: Implement the return flag for initialize_mpitools().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 15:30:52 -02:00
50cf1b57b7
DRIVER: Print parallelization info just after the code intro.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 15:03:19 -02:00
ec79b9eeca
PARAMETERS: Print the name of parameter file in a consistent way.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 14:58:17 -02:00
f8b65842af
Move source files from src/ to sources/.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 09:14:20 -02:00
a489837d63
Update copyright info.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-28 09:06:57 -02:00
21ded794e8
IO: Remove coordinate scaling factors dcor and ucor.
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These factors aren't necessary, since the block coordinate is calculate
with respecto the all blocks at given level. Therefore, even if we
change the maximum refinement level during job restart, these coordinate
do not change.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-27 09:47:40 -02:00
d88a1396dd
COORDINATES: Update toplev only if it was not changed before.
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If we restart a job from a run with different maximum refinement level,
toplev parameter is set from a restart file and coordinate variables are
recreated. Setting toplev to maxlev all the time fails in recreating
correct coordinate variables and results in crashes.
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2019-01-26 11:35:53 -02:00
a9123e466a
PYTHON: Make sure indices are integers in rebin().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2018-11-07 12:10:28 -02:00
5b28e11182
PYTHON: Rewrite subroutine amun_dataset().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2018-11-06 12:45:07 -02:00
43e5b0b5f2
PYTHON: Rename amun_coordinates() to amun_coordinate().
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2018-11-06 12:35:30 -02:00
5fa42b71cc
PYTHON: Reorganize amun.py.
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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
2018-11-06 12:34:39 -02:00
