Include template for simple case #2

AndreaQuerio · 2022-12-02T09:53:03Z

No description provided.

kysrpex · 2022-12-02T10:00:10Z

Log file

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  8
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
Build  : 8-1c9b5879390b
Exec   : pisoPrecNMC
Date   : Nov 28 2022
Time   : 11:12:52
Host   : "2d441f301e03"
PID    : 192
I/O    : uncollated
Case   : /home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Reading field p

Reading field U

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting turbulence model type RAS
Selecting RAS turbulence model kEpsilon
RAS
{
    turbulence      on;
    model           kEpsilon;
    printCoeffs     on;
    Cmu             0.09;
    C1              1.44;
    C2              1.92;
    C3              0;
    sigmak          1;
    sigmaEps        1.3;
}

Reading field p1

Reading field p2

Reading field p3

Reading field total_Nickel

Reading field total_Manganese

Reading field total_Cobalt

Selecting activity coefficient model: Bromley
Selecting Population Balance Model: constantVelocity
Reading field M0

Reading field M1

Reading field M2

Reading field M3

Selecting growth model for the population balance: powerLaw
Selecting nucleation rate model for the population balance: classicalHeteroHomo
Selecting nucleate size model for the population balance: fixed
Selecting quadrature method for population balance: QMOM
Selecting inversion algorithm for quadrature method: adaptiveWheeler
Creating MRF zone list from MRFProperties
    creating MRF zone: MRF1
No finite volume options present
Courant Number mean: 1.38889e-08 max: 0.00834408
timeActivatedFileUpdate: time vs file list:
    -1	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.cfd"
    59.99	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.0"
    60.01	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.1"
    60.0599	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.2"
    60.1998	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.3"
    60.9991	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.4"
    62.9981	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.5"
    72.991	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.6"
    94.981	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.7"
    144.961	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.8"
    309.921	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.9"
    609.881	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.10"
    1059.84	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.11"


timeActivatedFileUpdate: copying file
"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/controlDict.cfd"
to:
"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/controlDict"

timeActivatedFileUpdate: time vs file list:
    -1	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.0"
    60.01	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.1"
    60.0599	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.2"
    60.1998	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.3"
    60.9991	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.4"
    62.9981	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.5"
    72.991	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.6"
    1059.84	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.11"


timeActivatedFileUpdate: copying file
"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/odeSolver.0"
to:
"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/odeSolver"

timeActivatedFileUpdate: time vs file list:
--> FOAM Warning : 
    From function bool Foam::functionObjectList::read()
    in file db/functionObjects/functionObjectList/functionObjectList.C at line 871
    Caught FatalError 
--> FOAM FATAL ERROR: 
File: "/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/fvSolution.0" not found


    From function virtual bool Foam::functionObjects::timeActivatedFileUpdate::read(const Foam::dictionary&)
    in file timeActivatedFileUpdate/timeActivatedFileUpdate.C at line 120.

timeActivatedFileUpdate: time vs file list:
    -1	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/fvSchemes.0"
    10	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/fvSchemes.1"
    30	"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/fvSchemes.2"


timeActivatedFileUpdate: copying file
"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/updatingFiles/fvSchemes.0"
to:
"/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/fvSchemes"



surfaceFieldValue outflow:
    total faces  = 200
    total area   = 2.81967e-05



Starting time loop

regIOobject::readIfModified() : 
    Re-reading object controlDict from file "/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/controlDict"
timeActivatedFileUpdate: time vs file list:
--> FOAM Warning : 
    From function bool Foam::functionObjectList::read()
    in file db/functionObjects/functionObjectList/functionObjectList.C at line 871
    Caught FatalError 
--> FOAM FATAL ERROR: 
File: "/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/fvSolution.0" not found


    From function virtual bool Foam::functionObjects::timeActivatedFileUpdate::read(const Foam::dictionary&)
    in file timeActivatedFileUpdate/timeActivatedFileUpdate.C at line 120.

regIOobject::readIfModified() : 
    Re-reading object fvSchemes from file "/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/system/fvSchemes"
regIOobject::readIfModified() : 
    Re-reading object odeSolver from file "/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/odeSolver"
timeActivatedFileUpdate: time vs file list:
--> FOAM Warning : 
    From function bool Foam::functionObjectList::read()
    in file db/functionObjects/functionObjectList/functionObjectList.C at line 871
    Caught FatalError 
--> FOAM FATAL ERROR: 
File: "/home/simdomeuser/simdome/wrappers/simdome_wet_synthesis/examples/simulation-wetSynthCfdPbe-4eff9e4a-83c0-4c16-a51f-526ebc9e53a3/constant/updatingFiles/fvSolution.0" not found


    From function virtual bool Foam::functionObjects::timeActivatedFileUpdate::read(const Foam::dictionary&)
    in file timeActivatedFileUpdate/timeActivatedFileUpdate.C at line 120.

surfaceFieldValue outflow write:
    sum(outlet) of phi = 0

Time = 0.0001

Courant Number mean: 1.38889e-08 max: 0.00834408
deltaT = 0.00012
smoothSolver:  Solving for Ux, Initial residual = 1, Final residual = 4.616e-06, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 1, Final residual = 4.47928e-06, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 1, Final residual = 1.3131e-05, No Iterations 2
GAMG:  Solving for p, Initial residual = 1, Final residual = 0.00471466, No Iterations 6
GAMG:  Solving for p, Initial residual = 0.126352, Final residual = 0.000866132, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.00891093, Final residual = 5.89035e-05, No Iterations 6
time step continuity errors : sum local = 3.33976e-09, global = 5.11769e-10, cumulative = 5.11769e-10
GAMG:  Solving for p, Initial residual = 0.00341889, Final residual = 2.37223e-05, No Iterations 6
GAMG:  Solving for p, Initial residual = 0.000795013, Final residual = 7.7229e-06, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.000171536, Final residual = 1.51274e-06, No Iterations 6
time step continuity errors : sum local = 8.62812e-11, global = 1.14548e-11, cumulative = 5.23224e-10
smoothSolver:  Solving for epsilon, Initial residual = 0.00171094, Final residual = 3.98587e-08, No Iterations 2
smoothSolver:  Solving for k, Initial residual = 1, Final residual = 2.56725e-05, No Iterations 2
ExecutionTime = 18.67 s  ClockTime = 19 s

Time = 0.00022

Courant Number mean: 0.000734327 max: 0.229648
deltaT = 0.000144
smoothSolver:  Solving for Ux, Initial residual = 0.367602, Final residual = 0.000131809, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 0.36694, Final residual = 0.000120492, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 0.258011, Final residual = 8.8168e-05, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.536548, Final residual = 0.00208156, No Iterations 6
GAMG:  Solving for p, Initial residual = 0.16342, Final residual = 0.00106159, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.0144001, Final residual = 0.000109589, No Iterations 6
time step continuity errors : sum local = 4.84548e-09, global = -8.87836e-10, cumulative = -3.64612e-10
GAMG:  Solving for p, Initial residual = 0.0460462, Final residual = 0.000257406, No Iterations 5
GAMG:  Solving for p, Initial residual = 0.00648312, Final residual = 3.21697e-05, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.000542388, Final residual = 4.6752e-06, No Iterations 5
time step continuity errors : sum local = 2.03348e-10, global = 6.37879e-11, cumulative = -3.00824e-10
smoothSolver:  Solving for epsilon, Initial residual = 0.00206133, Final residual = 4.96081e-08, No Iterations 2
smoothSolver:  Solving for k, Initial residual = 0.890135, Final residual = 3.56835e-05, No Iterations 2
ExecutionTime = 31.5 s  ClockTime = 32 s

Time = 0.000364

Courant Number mean: 0.000882016 max: 0.275422
deltaT = 0.0001728
smoothSolver:  Solving for Ux, Initial residual = 0.0364693, Final residual = 1.80327e-05, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 0.0349955, Final residual = 1.54565e-05, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 0.0148751, Final residual = 7.92263e-06, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.298215, Final residual = 0.00184483, No Iterations 3
GAMG:  Solving for p, Initial residual = 0.0228199, Final residual = 0.000164962, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.00208657, Final residual = 1.25211e-05, No Iterations 5
time step continuity errors : sum local = 4.94251e-10, global = -3.15694e-11, cumulative = -3.32394e-10
GAMG:  Solving for p, Initial residual = 0.00838979, Final residual = 3.21236e-05, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.000713226, Final residual = 3.24019e-06, No Iterations 5
GAMG:  Solving for p, Initial residual = 8.04161e-05, Final residual = 3.11283e-07, No Iterations 5
time step continuity errors : sum local = 1.23052e-11, global = -9.42948e-13, cumulative = -3.33337e-10
smoothSolver:  Solving for epsilon, Initial residual = 0.00257214, Final residual = 8.65273e-08, No Iterations 2
smoothSolver:  Solving for k, Initial residual = 0.803467, Final residual = 4.60505e-05, No Iterations 2
ExecutionTime = 43.17 s  ClockTime = 43 s

Time = 0.0005368

Courant Number mean: 0.0010583 max: 0.324589
deltaT = 0.00020736
smoothSolver:  Solving for Ux, Initial residual = 0.0178059, Final residual = 1.11019e-05, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 0.0172387, Final residual = 9.73571e-06, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 0.00724488, Final residual = 4.49388e-06, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.196719, Final residual = 0.00145314, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.00878398, Final residual = 6.76585e-05, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.000734855, Final residual = 3.67948e-06, No Iterations 5
time step continuity errors : sum local = 1.50494e-10, global = 1.1606e-11, cumulative = -3.21731e-10
GAMG:  Solving for p, Initial residual = 0.00385221, Final residual = 1.70765e-05, No Iterations 3
GAMG:  Solving for p, Initial residual = 0.000214546, Final residual = 7.13783e-07, No Iterations 5
GAMG:  Solving for p, Initial residual = 2.2453e-05, Final residual = 2.22972e-07, No Iterations 4
time step continuity errors : sum local = 9.1334e-12, global = 1.72861e-12, cumulative = -3.20002e-10
smoothSolver:  Solving for epsilon, Initial residual = 0.00321134, Final residual = 1.49529e-07, No Iterations 2
smoothSolver:  Solving for k, Initial residual = 0.73895, Final residual = 5.88985e-05, No Iterations 2
ExecutionTime = 54.33 s  ClockTime = 55 s

Time = 0.00074416

Courant Number mean: 0.00126972 max: 0.381673
deltaT = 0.000248832
smoothSolver:  Solving for Ux, Initial residual = 0.0125996, Final residual = 1.10446e-05, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 0.0122399, Final residual = 1.02884e-05, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 0.00565142, Final residual = 5.02446e-06, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.15634, Final residual = 0.00091655, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.00473828, Final residual = 3.84661e-05, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.000359396, Final residual = 2.17001e-06, No Iterations 5
time step continuity errors : sum local = 9.67451e-11, global = 4.00904e-12, cumulative = -3.15993e-10
GAMG:  Solving for p, Initial residual = 0.0023618, Final residual = 8.39455e-06, No Iterations 3
GAMG:  Solving for p, Initial residual = 0.000101759, Final residual = 4.89539e-07, No Iterations 5
GAMG:  Solving for p, Initial residual = 9.57791e-06, Final residual = 5.29967e-08, No Iterations 5
time step continuity errors : sum local = 2.36545e-12, global = 1.04665e-13, cumulative = -3.15888e-10
smoothSolver:  Solving for epsilon, Initial residual = 0.00401192, Final residual = 2.57718e-07, No Iterations 2
smoothSolver:  Solving for k, Initial residual = 0.690141, Final residual = 7.55219e-05, No Iterations 2
ExecutionTime = 66.88 s  ClockTime = 67 s

Time = 0.000992992

Courant Number mean: 0.00152343 max: 0.448392
deltaT = 0.000298598
smoothSolver:  Solving for Ux, Initial residual = 0.0102326, Final residual = 1.31695e-05, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 0.0100137, Final residual = 1.25466e-05, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 0.00513865, Final residual = 6.6212e-06, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.128631, Final residual = 0.000731871, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.00301671, Final residual = 2.62991e-05, No Iterations 4
GAMG:  Solving for p, Initial residual = 0.000225736, Final residual = 1.44485e-06, No Iterations 5
time step continuity errors : sum local = 7.25176e-11, global = 2.70163e-12, cumulative = -3.13187e-10
GAMG:  Solving for p, Initial residual = 0.00173893, Final residual = 5.12922e-06, No Iterations 3
GAMG:  Solving for p, Initial residual = 6.33586e-05, Final residual = 3.09059e-07, No Iterations 5
GAMG:  Solving for p, Initial residual = 5.89536e-06, Final residual = 3.05729e-08, No Iterations 5
time step continuity errors : sum local = 1.53527e-12, global = -4.3394e-14, cumulative = -3.1323e-10
smoothSolver:  Solving for epsilon, Initial residual = 0.00501285, Final residual = 4.42827e-07, No Iterations 2
smoothSolver:  Solving for k, Initial residual = 0.652162, Final residual = 9.70504e-05, No Iterations 2
ExecutionTime = 78.64 s  ClockTime = 79 s

Time = 0.00129159

Courant Number mean: 0.00182791 max: 0.526444
deltaT = 0.000358318
smoothSolver:  Solving for Ux, Initial residual = 0.00937531, Final residual = 1.74727e-05, No Iterations 2

Empty commit

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AndreaQuerio requested a review from kysrpex December 2, 2022 09:53

AndreaQuerio self-assigned this Dec 2, 2022

Add Hello

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AndreaQuerio added 3 commits December 2, 2022 15:49

Update simple case

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Update simplified case

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Modify controlDict files

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kysrpex mentioned this pull request Dec 22, 2022

Add Sphinx-based Documentation #4

Merged

AndreaQuerio added 21 commits January 12, 2023 11:28

Remove old version of the session

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Corrections

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AndreaQuerio added 30 commits January 13, 2023 15:35

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Correct reconstruct_log_norm_dist

ce5be0d

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79c403f

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0e0b1b4

Change setup.py

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Change setup.py

b54d842

Remove docker_install.sh

2be74e6

Cahnges packageinfo.py

d498124

Change Dockerfile

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3e08b7d

Correction

cc4a14b

Correction

af1bb91

Corrections

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Correction

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Include template for simple case #2

Include template for simple case #2

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AndreaQuerio commented Dec 2, 2022

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kysrpex commented Dec 2, 2022

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Include template for simple case #2

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Include template for simple case #2

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AndreaQuerio commented Dec 2, 2022

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kysrpex commented Dec 2, 2022

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