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Checkpoint missing tables (chaos-polymtl#938)
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Description of the problem
A few tables were omitted from being "checkpointed" causing a lost of valuable information when simulations were restarted (Issue: Some tables are not checkpointed chaos-polymtl#916).
Description of the solution
The missing tables have been added to the write_checkpoint() and read_checkpoint() of each physic.
How Has This Been Tested?
CI
Restart application-tests were updated:
 applications_tests/lethe-fluid/cavity_ht_average_velocity_restart
 applications_tests/lethe-fluid/mms-transient-conduction-restart_gls
 applications_tests/lethe-fluid/taylor-green-vortex-restart_gls_bdf1
Documentation
A small correction was made to doc/source/parameters/cfd/restart.rst

Co-authored-by: Bruno Blais <[email protected]>
Co-authored-by: Olivier Guévremont <[email protected]>


Co-authored-by: Bruno Blais <[email protected]>
Co-authored-by: Olivier Guévremont <[email protected]>
Former-commit-id: cda8dbc
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@AmishgaAlphonius @blaisb @oguevremont
3 people authored Nov 28, 2023
1 parent 0f8a6fe commit 6508f7f
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Showing 20 changed files with 332 additions and 51 deletions.
4 changes: 4 additions & 0 deletions applications_tests/lethe-fluid/CMakeLists.txt
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Expand Up @@ -14,12 +14,15 @@ file(COPY cavity_ht_average_velocity_restart_files/restart.simulationcontrol DES
file(COPY cavity_ht_average_velocity_restart_files/restart.triangulation DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavity_ht_average_velocity_restart.${_build_type}")
file(COPY cavity_ht_average_velocity_restart_files/restart.triangulation.info DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavity_ht_average_velocity_restart.${_build_type}")
file(COPY cavity_ht_average_velocity_restart_files/restart.triangulation_fixed.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavity_ht_average_velocity_restart.${_build_type}")
file(COPY cavity_ht_average_velocity_restart_files/temperature_statistics.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavity_ht_average_velocity_restart.${_build_type}")

file(COPY mms-transient-conduction-restart_files/restart.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")
file(COPY mms-transient-conduction-restart_files/restart.simulationcontrol DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")
file(COPY mms-transient-conduction-restart_files/restart.triangulation DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")
file(COPY mms-transient-conduction-restart_files/restart.triangulation_fixed.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")
file(COPY mms-transient-conduction-restart_files/restart.triangulation.info DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")
file(COPY mms-transient-conduction-restart_files/L2Error_FD.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")
file(COPY mms-transient-conduction-restart_files/L2Error_HT.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/mms-transient-conduction-restart_gls.${_build_type}")

file(COPY taylor-green-vortex-restart_gls_bdf1/restart.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}")
file(COPY taylor-green-vortex-restart_gls_bdf1/restart.simulationcontrol DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}")
Expand All @@ -28,6 +31,7 @@ file(COPY taylor-green-vortex-restart_gls_bdf1/restart.triangulation_fixed.data
file(COPY taylor-green-vortex-restart_gls_bdf1/restart.triangulation.info DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}")
file(COPY taylor-green-vortex-restart_gls_bdf1/enstrophy.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}")
file(COPY taylor-green-vortex-restart_gls_bdf1/kinetic_energy.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}")
file(COPY taylor-green-vortex-restart_gls_bdf1/L2Error_FD.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}")


file(COPY cylinder_unstructured.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
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1 change: 1 addition & 0 deletions ...ts/lethe-fluid/cavity_ht_average_velocity_restart_files/temperature_statistics.checkpoint
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0 0 0 0 5 0 4 time 3 min 3 max 7 average 7 std-dev 0 0 5 0 0 0 7 average 0 0 0 0 3 0 0 0 100 7.69042968750000000e-03 100 3.10052583267239612e-02 100 4.50808747856982911e-02 7 average 1 c 4 0 0 6 3 max 3 0 100 7.88675134594812866e-01 100 9.17154969986019863e-01 100 9.48885303937015312e-01 3 max 1 c 4 0 0 6 3 min 3 0 100 0.00000000000000000e+00 100 1.06287853203001900e-17 100 6.86375606880767091e-16 3 min 1 c 4 0 0 6 7 std-dev 3 0 100 7.09977723601980942e-02 100 1.21400942237887569e-01 100 1.49010460321027216e-01 7 std-dev 1 c 4 0 0 6 4 time 3 0 100 0.00000000000000000e+00 100 1.00000000000000006e-01 100 2.00000000000000011e-01 4 time 1 c 4 0 0 6 0 0 0 0 0 0 0 0 0 0 0
1 change: 1 addition & 0 deletions applications_tests/lethe-fluid/mms-transient-conduction-restart_files/L2Error_FD.checkpoint
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0 0 0 0 2 0 4 time 14 error_velocity 0 0 2 0 0 0 14 error_velocity 0 0 0 0 6 0 0 0 100 0.00000000000000000e+00 100 0.00000000000000000e+00 100 0.00000000000000000e+00 100 0.00000000000000000e+00 100 0.00000000000000000e+00 100 0.00000000000000000e+00 14 error_velocity 1 c 4 0 0 6 4 time 6 0 100 4.00000000000000078e-02 100 1.00000000000000006e-01 100 2.00000000000000011e-01 100 3.00000000000000044e-01 100 4.00000000000000022e-01 100 5.00000000000000000e-01 4 time 1 c 4 0 0 6 0 0 0 0 0 0 0 0 0 0 0
1 change: 1 addition & 0 deletions applications_tests/lethe-fluid/mms-transient-conduction-restart_files/L2Error_HT.checkpoint
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0 0 0 0 2 0 5 cells 17 error_temperature 0 0 2 0 0 0 5 cells 0 0 0 0 6 0 0 0 117 256 117 256 117 256 117 256 117 256 117 256 5 cells 1 c 4 0 0 3 17 error_temperature 6 0 100 5.86440236679254870e-11 100 3.73606813189937941e-10 100 2.60392615231316192e-09 100 5.73838445577658764e-09 100 7.09993177685924068e-09 100 7.05848631757968466e-09 17 error_temperature 1 c 4 0 0 6 0 0 0 0 0 0 0 0 0 0 0
Binary file modified ...tests/lethe-fluid/mms-transient-conduction-restart_files/restart.triangulation_fixed.data
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12 changes: 12 additions & 0 deletions applications_tests/lethe-fluid/mms-transient-conduction-restart_gls.output
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Expand Up @@ -42,12 +42,24 @@ Transient iteration: 11 Time: 1 Time step: 0.1 CFL: 0
L2 error velocity : 0
L2 error temperature : 3.71907e-09
time error_velocity
0.0400 0.000000e+00
0.1000 0.000000e+00
0.2000 0.000000e+00
0.3000 0.000000e+00
0.4000 0.000000e+00
0.5000 0.000000e+00
0.6000 0.000000e+00
0.7000 0.000000e+00
0.8000 0.000000e+00
0.9000 0.000000e+00
1.0000 0.000000e+00
cells error_temperature
256 5.864402e-11
256 3.736068e-10
256 2.603926e-09
256 5.738384e-09
256 7.099932e-09
256 7.058486e-09
256 6.505499e-09
256 5.834362e-09
256 5.137808e-09
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2 changes: 1 addition & 1 deletion applications_tests/lethe-fluid/mms-transient-conduction-restart_gls.prm
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Expand Up @@ -40,7 +40,7 @@ subsection restart
# Frequency for checkpointing
set frequency = 1

# Frequency for checkpointing
# Enable restart from checkpoint
set restart = true
end

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50 changes: 50 additions & 0 deletions applications_tests/lethe-fluid/taylor-green-vortex-restart_gls_bdf1.output
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Expand Up @@ -359,6 +359,56 @@ Enstrophy : 0.00942208
Kinetic energy : 0.00470351
L2 error velocity : 0.00812688
time error_velocity
0.0100 9.702604e-04
0.0200 1.373517e-03
0.0300 1.840106e-03
0.0400 2.317500e-03
0.0500 2.788763e-03
0.0600 3.247543e-03
0.0700 3.691204e-03
0.0800 4.118644e-03
0.0900 4.529473e-03
0.1000 4.923664e-03
0.1100 5.301385e-03
0.1200 5.662912e-03
0.1300 6.008589e-03
0.1400 6.338792e-03
0.1500 6.653919e-03
0.1600 6.954380e-03
0.1700 7.240586e-03
0.1800 7.512949e-03
0.1900 7.771878e-03
0.2000 8.017774e-03
0.2100 8.251036e-03
0.2200 8.472051e-03
0.2300 8.681201e-03
0.2400 8.878859e-03
0.2500 9.065390e-03
0.2600 9.241148e-03
0.2700 9.406480e-03
0.2800 9.561726e-03
0.2900 9.707214e-03
0.3000 9.843266e-03
0.3100 9.970194e-03
0.3200 1.008830e-02
0.3300 1.019789e-02
0.3400 1.029924e-02
0.3500 1.039264e-02
0.3600 1.047835e-02
0.3700 1.055665e-02
0.3800 1.062779e-02
0.3900 1.069203e-02
0.4000 1.074960e-02
0.4100 1.080075e-02
0.4200 1.084570e-02
0.4300 1.088467e-02
0.4400 1.091790e-02
0.4500 1.094558e-02
0.4600 1.096792e-02
0.4700 1.098512e-02
0.4800 1.099738e-02
0.4900 1.100489e-02
0.5000 1.100781e-02
0.5100 1.100635e-02
0.5200 1.100065e-02
0.5300 1.099090e-02
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2 changes: 1 addition & 1 deletion applications_tests/lethe-fluid/taylor-green-vortex-restart_gls_bdf1.prm
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Expand Up @@ -78,7 +78,7 @@ subsection restart
set filename = restart
# Frequency for checkpointing
set frequency = 1
# Frequency for checkpointing
# Enable restart from checkpoint
set restart = true
end

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1 change: 1 addition & 0 deletions applications_tests/lethe-fluid/taylor-green-vortex-restart_gls_bdf1/L2Error_FD.checkpoint
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@@ -0,0 +1 @@
0 0 0 0 2 0 4 time 14 error_velocity 0 0 2 0 0 0 14 error_velocity 0 0 0 0 50 0 0 0 100 9.70260438756851947e-04 100 1.37351724439845491e-03 100 1.84010607302818440e-03 100 2.31749994121434625e-03 100 2.78876322761135520e-03 100 3.24754270524175775e-03 100 3.69120352527292075e-03 100 4.11864350666947716e-03 100 4.52947302130056548e-03 100 4.92366418756171736e-03 100 5.30138467716634483e-03 100 5.66291238323648246e-03 100 6.00858869287675037e-03 100 6.33879153008128950e-03 100 6.65391912906595270e-03 100 6.95437992264262127e-03 100 7.24058606285793438e-03 100 7.51294917727212980e-03 100 7.77187754425011975e-03 100 8.01777419334964020e-03 100 8.25103562307126157e-03 100 8.47205093909883522e-03 100 8.68120128407522638e-03 100 8.87885947266102427e-03 100 9.06538977306088449e-03 100 9.24114779421839234e-03 100 9.40648044994206629e-03 100 9.56172597941684979e-03 100 9.70721400924101641e-03 100 9.84326564608971506e-03 100 9.97019359194816109e-03 100 1.00883022758919815e-02 100 1.01978879978666098e-02 100 1.02992390810181089e-02 100 1.03926360299361770e-02 100 1.04783516927750304e-02 100 1.05566514256825311e-02 100 1.06277932583167135e-02 100 1.06920280595025063e-02 100 1.07495997022842796e-02 100 1.08007452277957966e-02 100 1.08456950075020674e-02 100 1.08846729034549842e-02 100 1.09178964262987305e-02 100 1.09455768908119956e-02 100 1.09679195688370847e-02 100 1.09851238394703850e-02 100 1.09973833364404670e-02 100 1.10048860926087438e-02 100 1.10078146815611386e-02 14 error_velocity 1 c 4 0 0 6 4 time 50 0 100 1.00000000000000002e-02 100 2.00000000000000004e-02 100 2.99999999999999989e-02 100 4.00000000000000008e-02 100 5.00000000000000028e-02 100 6.00000000000000047e-02 100 7.00000000000000067e-02 100 8.00000000000000017e-02 100 8.99999999999999967e-02 100 9.99999999999999917e-02 100 1.09999999999999987e-01 100 1.19999999999999982e-01 100 1.29999999999999977e-01 100 1.39999999999999986e-01 100 1.49999999999999994e-01 100 1.60000000000000003e-01 100 1.70000000000000012e-01 100 1.80000000000000021e-01 100 1.90000000000000030e-01 100 2.00000000000000039e-01 100 2.10000000000000048e-01 100 2.20000000000000057e-01 100 2.30000000000000066e-01 100 2.40000000000000074e-01 100 2.50000000000000056e-01 100 2.60000000000000064e-01 100 2.70000000000000073e-01 100 2.80000000000000082e-01 100 2.90000000000000091e-01 100 3.00000000000000100e-01 100 3.10000000000000109e-01 100 3.20000000000000118e-01 100 3.30000000000000127e-01 100 3.40000000000000135e-01 100 3.50000000000000144e-01 100 3.60000000000000153e-01 100 3.70000000000000162e-01 100 3.80000000000000171e-01 100 3.90000000000000180e-01 100 4.00000000000000189e-01 100 4.10000000000000198e-01 100 4.20000000000000207e-01 100 4.30000000000000215e-01 100 4.40000000000000224e-01 100 4.50000000000000233e-01 100 4.60000000000000242e-01 100 4.70000000000000251e-01 100 4.80000000000000260e-01 100 4.90000000000000269e-01 100 5.00000000000000000e-01 4 time 1 c 4 0 0 6 0 0 0 0 0 0 0 0 0 0 0
2 changes: 1 addition & 1 deletion applications_tests/lethe-fluid/taylor-green-vortex-restart_gls_bdf1/enstrophy.checkpoint
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0 0 0 0 2 0 4 time 9 enstrophy 0 0 2 0 0 0 9 enstrophy 0 0 0 0 51 0 0 0 100 5.00800056059643395e-01 100 4.81292453184982816e-01 100 4.62544734156999149e-01 100 4.44527299704690182e-01 100 4.27211702324144738e-01 100 4.10570602690655206e-01 100 3.94577726493181846e-01 100 3.79207822943402051e-01 100 3.64436624901343820e-01 100 3.50240810554676485e-01 100 3.36597966591067554e-01 100 3.23486552805436145e-01 100 3.10885868086191453e-01 100 2.98776017726691989e-01 100 2.87137882010295609e-01 100 2.75953086019365967e-01 100 2.65203970620546070e-01 100 2.54873564580437972e-01 100 2.44945557767675848e-01 100 2.35404275399022506e-01 100 2.26234653288830995e-01 100 2.17422214062759800e-01 100 2.08953044298186369e-01 100 2.00813772555184233e-01 100 1.92991548263393486e-01 100 1.85474021431407621e-01 100 1.78249323146645405e-01 100 1.71306046834909770e-01 100 1.64633230250013030e-01 100 1.58220338165055430e-01 100 1.52057245737990704e-01 100 1.46134222525220320e-01 100 1.40441917117969245e-01 100 1.34971342377177866e-01 100 1.29713861243581335e-01 100 1.24661173100587941e-01 100 1.19805300668398632e-01 100 1.15138577408682011e-01 100 1.10653635419910246e-01 100 1.06343393804241890e-01 100 1.02201047487581423e-01 100 9.82200564751545407e-02 100 9.43941355256398273e-02 100 9.07172442275475110e-02 100 8.71835774621713966e-02 100 8.37875562380576699e-02 100 8.05238188825218165e-02 100 7.73872125762883750e-02 100 7.43727852179072446e-02 100 7.14757776050800736e-02 100 6.86916159205671339e-02 9 enstrophy 1 c 12 0 0 14 4 time 51 0 100 0.00000000000000000e+00 100 1.00000000000000002e-02 100 2.00000000000000004e-02 100 2.99999999999999989e-02 100 4.00000000000000008e-02 100 5.00000000000000028e-02 100 6.00000000000000047e-02 100 7.00000000000000067e-02 100 8.00000000000000017e-02 100 8.99999999999999967e-02 100 9.99999999999999917e-02 100 1.09999999999999987e-01 100 1.19999999999999982e-01 100 1.29999999999999977e-01 100 1.39999999999999986e-01 100 1.49999999999999994e-01 100 1.60000000000000003e-01 100 1.70000000000000012e-01 100 1.80000000000000021e-01 100 1.90000000000000030e-01 100 2.00000000000000039e-01 100 2.10000000000000048e-01 100 2.20000000000000057e-01 100 2.30000000000000066e-01 100 2.40000000000000074e-01 100 2.50000000000000056e-01 100 2.60000000000000064e-01 100 2.70000000000000073e-01 100 2.80000000000000082e-01 100 2.90000000000000091e-01 100 3.00000000000000100e-01 100 3.10000000000000109e-01 100 3.20000000000000118e-01 100 3.30000000000000127e-01 100 3.40000000000000135e-01 100 3.50000000000000144e-01 100 3.60000000000000153e-01 100 3.70000000000000162e-01 100 3.80000000000000171e-01 100 3.90000000000000180e-01 100 4.00000000000000189e-01 100 4.10000000000000198e-01 100 4.20000000000000207e-01 100 4.30000000000000215e-01 100 4.40000000000000224e-01 100 4.50000000000000233e-01 100 4.60000000000000242e-01 100 4.70000000000000251e-01 100 4.80000000000000260e-01 100 4.90000000000000269e-01 100 5.00000000000000000e-01 4 time 1 c 12 0 0 14 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 2 0 4 time 9 enstrophy 0 0 2 0 0 0 9 enstrophy 0 0 0 0 51 0 0 0 100 5.00800056059643395e-01 100 4.81292453184982871e-01 100 4.62544734156999260e-01 100 4.44527299704690182e-01 100 4.27211702324144738e-01 100 4.10570602690655428e-01 100 3.94577726493181846e-01 100 3.79207822943402106e-01 100 3.64436624901343820e-01 100 3.50240810554676485e-01 100 3.36597966591067610e-01 100 3.23486552805436200e-01 100 3.10885868086191564e-01 100 2.98776017726692045e-01 100 2.87137882010295609e-01 100 2.75953086019365912e-01 100 2.65203970620546070e-01 100 2.54873564580438028e-01 100 2.44945557767675820e-01 100 2.35404275399022533e-01 100 2.26234653288830939e-01 100 2.17422214062759800e-01 100 2.08953044298186313e-01 100 2.00813772555184233e-01 100 1.92991548263393459e-01 100 1.85474021431407649e-01 100 1.78249323146645405e-01 100 1.71306046834909798e-01 100 1.64633230250013057e-01 100 1.58220338165055374e-01 100 1.52057245737990759e-01 100 1.46134222525220264e-01 100 1.40441917117969300e-01 100 1.34971342377177811e-01 100 1.29713861243581335e-01 100 1.24661173100587941e-01 100 1.19805300668398645e-01 100 1.15138577408682025e-01 100 1.10653635419910273e-01 100 1.06343393804241890e-01 100 1.02201047487581465e-01 100 9.82200564751545685e-02 100 9.43941355256398690e-02 100 9.07172442275475249e-02 100 8.71835774621714382e-02 100 8.37875562380576699e-02 100 8.05238188825218026e-02 100 7.73872125762883750e-02 100 7.43727852179072585e-02 100 7.14757776050800875e-02 100 6.86916159205671339e-02 9 enstrophy 1 c 12 0 0 14 4 time 51 0 100 0.00000000000000000e+00 100 1.00000000000000002e-02 100 2.00000000000000004e-02 100 2.99999999999999989e-02 100 4.00000000000000008e-02 100 5.00000000000000028e-02 100 6.00000000000000047e-02 100 7.00000000000000067e-02 100 8.00000000000000017e-02 100 8.99999999999999967e-02 100 9.99999999999999917e-02 100 1.09999999999999987e-01 100 1.19999999999999982e-01 100 1.29999999999999977e-01 100 1.39999999999999986e-01 100 1.49999999999999994e-01 100 1.60000000000000003e-01 100 1.70000000000000012e-01 100 1.80000000000000021e-01 100 1.90000000000000030e-01 100 2.00000000000000039e-01 100 2.10000000000000048e-01 100 2.20000000000000057e-01 100 2.30000000000000066e-01 100 2.40000000000000074e-01 100 2.50000000000000056e-01 100 2.60000000000000064e-01 100 2.70000000000000073e-01 100 2.80000000000000082e-01 100 2.90000000000000091e-01 100 3.00000000000000100e-01 100 3.10000000000000109e-01 100 3.20000000000000118e-01 100 3.30000000000000127e-01 100 3.40000000000000135e-01 100 3.50000000000000144e-01 100 3.60000000000000153e-01 100 3.70000000000000162e-01 100 3.80000000000000171e-01 100 3.90000000000000180e-01 100 4.00000000000000189e-01 100 4.10000000000000198e-01 100 4.20000000000000207e-01 100 4.30000000000000215e-01 100 4.40000000000000224e-01 100 4.50000000000000233e-01 100 4.60000000000000242e-01 100 4.70000000000000251e-01 100 4.80000000000000260e-01 100 4.90000000000000269e-01 100 5.00000000000000000e-01 4 time 1 c 12 0 0 14 0 0 0 0 0 0 0 0 0 0 0
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