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Fix restart transient with variable time step #1093

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merged 14 commits into from
Apr 16, 2024
Merged

Fix restart transient with variable time step #1093

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5ea629a
Reset the time-step value correctly when restart
blaisb Apr 16, 2024
e98090c
Add a test for variable time step restart
blaisb Apr 16, 2024
4f563b9
Add changelog entry
blaisb Apr 16, 2024
e7c86dc
Fix files for test
blaisb Apr 16, 2024
e8441e4
Update applications_tests/lethe-fluid/taylor-green-vortex-restart-bdf…
blaisb Apr 16, 2024
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blaisb Apr 16, 2024
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blaisb Apr 16, 2024
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blaisb Apr 16, 2024
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,12 @@
All notable changes to the Lethe project will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/).

## [Master] - 2024-04-16

### Fixed

- MINOR Simulations with adaptive time-stepping would checkpoint correctly, but would not restart with the correct time-step due to the way the time-step was read from the checkpointing files. This is now fixed and tested. [#1093](https://github.com/lethe-cfd/lethe/pull/1093)

## [Master] - 2024-04-07

### Added
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9 changes: 9 additions & 0 deletions applications_tests/lethe-fluid/CMakeLists.txt
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Expand Up @@ -33,6 +33,15 @@ file(COPY taylor-green-vortex-restart_gls_bdf1/enstrophy.checkpoint DESTINATION
file(COPY taylor-green-vortex-restart_gls_bdf1/kinetic_energy.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart_gls_bdf1/L2Error_FD.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart_gls_bdf1.${_build_type}/mpirun=1/")

file(COPY taylor-green-vortex-restart-bdf1-adaptive/restart.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/restart.simulationcontrol DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/restart.triangulation DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/restart.triangulation_fixed.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/restart.triangulation.info DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/enstrophy.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/kinetic_energy.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")
file(COPY taylor-green-vortex-restart-bdf1-adaptive/L2Error_FD.checkpoint DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/taylor-green-vortex-restart-bdf1-adaptive.${_build_type}/mpirun=1/")


file(COPY cylinder_unstructured.msh DESTINATION "${CMAKE_CURRENT_BINARY_DIR}")
file(COPY poiseuille_restart_files/poiseuille_restart.averagevelocities DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/poiseuille_restart.${_build_type}/mpirun=1/")
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50 changes: 50 additions & 0 deletions applications_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive.mpirun=1.output
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Running on 1 MPI rank(s)...
Number of active cells: 1
Number of degrees of freedom: 12
Volume of triangulation: 39.4784
************************
---> Simulation Restart
************************
Number of active cells: 1024
Number of degrees of freedom: 3267
Volume of triangulation: 39.4784

*********************************************************************************
Transient iteration: 19 Time: 0.511589 Time step: 0.0555984 CFL: 0.0937518
*********************************************************************************
Enstrophy : 0.0686874
Kinetic energy : 0.0342889

*********************************************************************************
Transient iteration: 20 Time: 0.572748 Time step: 0.0611582 CFL: 0.0927773
*********************************************************************************
Enstrophy : 0.0544932
Kinetic energy : 0.0272031

*********************************************************************************
Transient iteration: 21 Time: 0.6 Time step: 0.0272524 CFL: 0.0909005
*********************************************************************************
Enstrophy : 0.0489892
Kinetic energy : 0.0244555
time error_velocity
0.0100 9.702604e-04
0.0210 1.497541e-03
0.0331 2.266297e-03
0.0464 3.238495e-03
0.0611 4.415871e-03
0.0772 5.813999e-03
0.0949 7.453486e-03
0.1144 9.356386e-03
0.1358 1.154396e-02
0.1594 1.403464e-02
0.1853 1.684182e-02
0.2138 1.997132e-02
0.2452 2.341851e-02
0.2797 2.716517e-02
0.3177 3.117615e-02
0.3595 3.539619e-02
0.4054 3.974710e-02
0.4560 4.412568e-02
0.5116 4.840382e-02
0.5727 5.242945e-02
0.6000 5.140802e-02
144 changes: 144 additions & 0 deletions applications_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive.prm
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# Listing of Parameters
#----------------------

set dimension = 2

#---------------------------------------------------
# Simulation Control
#---------------------------------------------------

subsection simulation control
set method = bdf1
set adapt = true
set max cfl = 1
set time step = 0.01 # Time step
set time end = 0.60 # End time of simulation
set output frequency = 0 # Frequency of simulation output
end

#---------------------------------------------------
# FEM
#---------------------------------------------------

subsection FEM
set velocity order = 1
set pressure order = 1
end

#---------------------------------------------------
# Initial condition
#---------------------------------------------------

subsection initial conditions
set type = L2projection
subsection uvwp
set Function expression = cos(x)*sin(y); -sin(x)*cos(y); -1./4*(cos(2*x)+cos(2*y));
end
end

#---------------------------------------------------
# Physical Properties
#---------------------------------------------------

subsection physical properties
set number of fluids = 1
subsection fluid 0
set kinematic viscosity = 1.000
end
end

#---------------------------------------------------
# Analytical Solution
#---------------------------------------------------

subsection analytical solution
set verbosity = quiet
set enable = true
subsection uvwp
set Function constants = viscosity=1
set Function expression = exp(-2*viscosity*t)* cos(x) * sin(y) ; -sin(x) * cos(y) * exp(-2*viscosity*t); 0
end
end

#--------------------------------------------------
# Restart
#--------------------------------------------------

subsection restart
# Enable checkpointing
set checkpoint = false
# Prefix for the filename of checkpoints
set filename = restart
# Frequency for checkpointing
set frequency = 1
# Enable restart from checkpoint
set restart = true
end

#---------------------------------------------------
# Post-Processing
#---------------------------------------------------

subsection post-processing
set verbosity = verbose
set calculate enstrophy = true
set calculate kinetic energy = true
end

#---------------------------------------------------
# Mesh
#---------------------------------------------------

subsection mesh
set type = dealii
set grid type = hyper_cube
set grid arguments = 0 : 6.28318530718 : true
set initial refinement = 5 # initial mesh refinement
end

#---------------------------------------------------
# Boundary Conditions
#---------------------------------------------------

subsection boundary conditions
set number = 2
subsection bc 0
set type = periodic
set id = 0
set periodic_id = 1
set periodic_direction = 0
end
subsection bc 1
set type = periodic
set id = 2
set periodic_id = 3
set periodic_direction = 1
end
end

#---------------------------------------------------
# Non-Linear Solver Control
#---------------------------------------------------

subsection non-linear solver
subsection fluid dynamics
set verbosity = quiet
set tolerance = 1e-6
set max iterations = 5
end
end

#---------------------------------------------------
# Linear Solver Control
#---------------------------------------------------

subsection linear solver
subsection fluid dynamics
set verbosity = quiet
set method = gmres
set max iters = 5000
set relative residual = 1e-4
set minimum residual = 1e-9
set ilu preconditioner absolute tolerance = 1e-10
end
end
1 change: 1 addition & 0 deletions ...cations_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/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 18 0 0 0 100 9.70260438756596509e-04 100 1.49754055734914893e-03 100 2.26629717992125413e-03 100 3.23849465845258604e-03 100 4.41587088391762368e-03 100 5.81399899031224618e-03 100 7.45348605033036363e-03 100 9.35638645623649082e-03 100 1.15439608889093444e-02 100 1.40346418651400764e-02 100 1.68418208442545417e-02 100 1.99713182759173012e-02 100 2.34185102245543161e-02 100 2.71651688444639501e-02 100 3.11761540150923208e-02 100 3.53961946713119632e-02 100 3.97471025974981060e-02 100 4.41256835874094810e-02 14 error_velocity 1 c 4 0 0 6 4 time 18 0 100 1.00000000000000002e-02 100 2.10000000000000013e-02 100 3.31000000000000044e-02 100 4.64100000000000068e-02 100 6.10510000000000080e-02 100 7.71561000000000052e-02 100 9.48717100000000119e-02 100 1.14358881000000023e-01 100 1.35794769100000046e-01 100 1.59374246010000054e-01 100 1.85311670611000068e-01 100 2.13842837672100078e-01 100 2.45227121439310108e-01 100 2.79749833583241125e-01 100 3.17724816941565291e-01 100 3.59497298635721829e-01 100 4.05447028499294038e-01 100 4.55990999999999980e-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 ...ications_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/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 19 0 0 0 100 5.00800056059643506e-01 100 4.81292453184982649e-01 100 4.60730446886153500e-01 100 4.39148232491193169e-01 100 4.16599769896649319e-01 100 3.93161107437332569e-01 100 3.68932426473623065e-01 100 3.44039621819007491e-01 100 3.18635202496210468e-01 100 2.92898273914864504e-01 100 2.67033353019284048e-01 100 2.41267778667671601e-01 100 2.15847518126948579e-01 100 1.91031244145675655e-01 100 1.67082671187051279e-01 100 1.44261294302352155e-01 100 1.22811866702692465e-01 100 1.02953166017756031e-01 100 8.48670369593871599e-02 9 enstrophy 1 c 12 0 0 14 4 time 19 0 100 0.00000000000000000e+00 100 1.00000000000000002e-02 100 2.10000000000000013e-02 100 3.31000000000000044e-02 100 4.64100000000000068e-02 100 6.10510000000000080e-02 100 7.71561000000000052e-02 100 9.48717100000000119e-02 100 1.14358881000000023e-01 100 1.35794769100000046e-01 100 1.59374246010000054e-01 100 1.85311670611000068e-01 100 2.13842837672100078e-01 100 2.45227121439310108e-01 100 2.79749833583241125e-01 100 3.17724816941565291e-01 100 3.59497298635721829e-01 100 4.05447028499294038e-01 100 4.55990999999999980e-01 4 time 1 c 12 0 0 14 0 0 0 0 0 0 0 0 0 0 0
144 changes: 144 additions & 0 deletions applications_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/generator.prm
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# Listing of Parameters
#----------------------

set dimension = 2

#---------------------------------------------------
# Simulation Control
#---------------------------------------------------

subsection simulation control
set method = bdf1
set adapt = true
set max cfl = 1
set time step = 0.01 # Time step
set time end = 0.455991 # End time of simulation
set output frequency = 0 # Frequency of simulation output
end

#---------------------------------------------------
# FEM
#---------------------------------------------------

subsection FEM
set velocity order = 1
set pressure order = 1
end

#---------------------------------------------------
# Initial condition
#---------------------------------------------------

subsection initial conditions
set type = L2projection
subsection uvwp
set Function expression = cos(x)*sin(y); -sin(x)*cos(y); -1./4*(cos(2*x)+cos(2*y));
end
end

#---------------------------------------------------
# Physical Properties
#---------------------------------------------------

subsection physical properties
set number of fluids = 1
subsection fluid 0
set kinematic viscosity = 1.000
end
end

#---------------------------------------------------
# Analytical Solution
#---------------------------------------------------

subsection analytical solution
set verbosity = quiet
set enable = true
subsection uvwp
set Function constants = viscosity=1
set Function expression = exp(-2*viscosity*t)* cos(x) * sin(y) ; -sin(x) * cos(y) * exp(-2*viscosity*t); 0
end
end

#--------------------------------------------------
# Restart
#--------------------------------------------------

subsection restart
# Enable checkpointing
set checkpoint = true
# Prefix for the filename of checkpoints
set filename = restart
# Frequency for checkpointing
set frequency = 1
# Enable restart from checkpoint
set restart = false
end

#---------------------------------------------------
# Post-Processing
#---------------------------------------------------

subsection post-processing
set verbosity = verbose
set calculate enstrophy = true
set calculate kinetic energy = true
end

#---------------------------------------------------
# Mesh
#---------------------------------------------------

subsection mesh
set type = dealii
set grid type = hyper_cube
set grid arguments = 0 : 6.28318530718 : true
set initial refinement = 5 # initial mesh refinement
end

#---------------------------------------------------
# Boundary Conditions
#---------------------------------------------------

subsection boundary conditions
set number = 2
subsection bc 0
set type = periodic
set id = 0
set periodic_id = 1
set periodic_direction = 0
end
subsection bc 1
set type = periodic
set id = 2
set periodic_id = 3
set periodic_direction = 1
end
end

#---------------------------------------------------
# Non-Linear Solver Control
#---------------------------------------------------

subsection non-linear solver
subsection fluid dynamics
set verbosity = verbose
set tolerance = 1e-6
set max iterations = 5
end
end

#---------------------------------------------------
# Linear Solver Control
#---------------------------------------------------

subsection linear solver
subsection fluid dynamics
set verbosity = verbose
set method = gmres
set max iters = 5000
set relative residual = 1e-4
set minimum residual = 1e-9
set ilu preconditioner absolute tolerance = 1e-10
end
end
1 change: 1 addition & 0 deletions ...ons_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/kinetic_energy.checkpoint
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0 0 0 0 2 0 4 time 14 kinetic-energy 0 0 2 0 0 0 14 kinetic-energy 0 0 0 0 19 0 0 0 100 2.49999992602278481e-01 100 2.40261774191911137e-01 100 2.29997195802589066e-01 100 2.19223328289914227e-01 100 2.07967108505439036e-01 100 1.96266499870904693e-01 100 1.84171513043521584e-01 100 1.71744994867286033e-01 100 1.59063078031495136e-01 100 1.46215172173789792e-01 100 1.33303372400469994e-01 100 1.20441166544648065e-01 100 1.07751341763395181e-01 100 9.53630278053799463e-02 100 8.34078712491547469e-02 100 7.20154123375654071e-02 100 6.13078321689155964e-02 100 5.13943447997732006e-02 100 4.23657273294573145e-02 14 kinetic-energy 1 c 12 0 0 14 4 time 19 0 100 0.00000000000000000e+00 100 1.00000000000000002e-02 100 2.10000000000000013e-02 100 3.31000000000000044e-02 100 4.64100000000000068e-02 100 6.10510000000000080e-02 100 7.71561000000000052e-02 100 9.48717100000000119e-02 100 1.14358881000000023e-01 100 1.35794769100000046e-01 100 1.59374246010000054e-01 100 1.85311670611000068e-01 100 2.13842837672100078e-01 100 2.45227121439310108e-01 100 2.79749833583241125e-01 100 3.17724816941565291e-01 100 3.59497298635721829e-01 100 4.05447028499294038e-01 100 4.55990999999999980e-01 4 time 1 c 12 0 0 14 0 0 0 0 0 0 0 0 0 0 0
2 changes: 2 additions & 0 deletions applications_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/restart.pvdhandler
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0
Time File
8 changes: 8 additions & 0 deletions ...ons_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/restart.simulationcontrol
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Simulation control
dt_0 0.050544
dt_1 0.0459497
dt_2 0.0417725
dt_3 0.037975
CFL 0.0937518
Time 0.455991
Iter 18
Binary file added ...cations_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/restart.triangulation
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2 changes: 2 additions & 0 deletions ...ns_tests/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/restart.triangulation.info
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version nproc n_attached_fixed_size_objs n_attached_variable_size_objs n_coarse_cells
5 1 1 0 1
Binary file added ...ts/lethe-fluid/taylor-green-vortex-restart-bdf1-adaptive/restart.triangulation_fixed.data
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