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Hamo fixes oct 2023 #253

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Hamo fixes oct 2023 #253

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In this branch I implemented roughness model for LES as well as Monin-Obukov Similarity Theory (MOST) for Atmospheric Boundary Layer when LES is used. The implementation is tested on GABLS2 benchmark case.

On branch bojan_more_robust_communicator

modified:   Documentation/fortran.vim
modified:   Sources/Convert/Convert_Mod.f90
modified:   Sources/Generate/Range_Mod.f90
modified:   Sources/Generate/Smooths_Mod.f90
modified:   Sources/Process/Front_Mod.f90
modified:   Sources/Process/Results_Mod/Save_Vtu_Front.f90
modified:   Sources/Process/Results_Mod/Save_Vtu_Surf.f90
modified:   Sources/Process/Surf_Mod.f90
modified:   Sources/Process/Surf_Mod/Check_Side.f90
modified:   Sources/Process/Vof_Mod/Utilities/Mass_Transfer_Estimate.f90
On branch bojan_more_robust_communicator

modified:   Documentation/fortran.vim
On branch bojan_more_robust_communicator

new file:   divide.1.scr
new file:   divide.2.scr
new file:   lower_dom.msh.gz
new file:   upper_dom.msh.gz
On branch bojan_more_robust_communicator

deleted:    Dimensional_Solvers/Bicg.f90
deleted:    Dimensional_Solvers/Cg.f90
deleted:    Dimensional_Solvers/Cgs.f90
deleted:    Normalized_Solvers/Bicg.f90
deleted:    Normalized_Solvers/Cg.f90
deleted:    Normalized_Solvers/Cgs.f90
This should have only a small update in fortran.vim
On branch bojan_more_robust_communicator

modified:   Documentation/fortran.vim
On branch bojan_more_robust_communicator

modified:   Process/Petsc_Mod/True/Create_Petsc.f90
On branch bojan_more_robust_communicator

modified:   Documentation/all_control_keywords
On branch bojan_more_robust_communicator

new file:   Tests/Swarm/Three_Phase_Flow/sphere.stl
new file:   Tests/Vof/Rising_Bubble/sphere.stl
They include: line alignment, removing the features
which do not exist in the code any more, fixing the
syntax of features which do exist.

On branch bojan_more_robust_communicator

modified:   Tests/Laminar/Convective_Outflow/control
modified:   Tests/Laminar/Flat_Plate/control
modified:   Tests/Laminar/Module/control
modified:   Tests/Les/Barc/control
modified:   Tests/Les/Forrest/control
modified:   Tests/Les/Pipe_Re_Tau_180/control
modified:   Tests/Les/Rayleigh_Benard_Convection_Ra_10e09/control
modified:   Tests/Manual/Rising_Bubble/control
modified:   Tests/Rans/Channel_Re_Tau_590/Long_Domain/control
modified:   Tests/Rans/Rayleigh_Benard_Convection_Ra_10e09/control
modified:   Tests/Swarm/Three_Phase_Flow/control
modified:   Tests/Vof/Fuel_Bundle/control
modified:   Tests/Vof/Rising_Bubble/control
modified:   Tests/Vof/Stefan/control
modified:   Tests/Vof/Sucking/control
No idea what I am merging, but I hope it's something good.
On branch bojan_more_robust_communicator

modified:   test_build.sh
On branch bojan_more_robust_communicator

modified:   all_control_keywords
On branch bojan_more_robust_communicator

modified:   Functionality/Eddies/control
modified:   Functionality/Gradients/control
modified:   Functionality/Omp/control
modified:   Hybrid_Les_Rans/Channel_Re_Tau_2000/Stretched_Mesh/control
modified:   Hybrid_Les_Rans/Channel_Re_Tau_2000/Uniform_Mesh/control
modified:   Hybrid_Les_Rans/Cylinder/control-ra-1e09
modified:   Hybrid_Les_Rans/Cylinder/control-ra-1e10
modified:   Hybrid_Les_Rans/Cylinder/control-ra-1e11
modified:   Hybrid_Les_Rans/Cylinder/control-ra-1e12
modified:   Laminar/Accuracy_Test/Channel_Re_2000/control
modified:   Laminar/Backstep/Nonorthogonal/control
modified:   Laminar/Backstep/Orthogonal/Solvers_Scaling/control
modified:   Laminar/Backstep/Orthogonal/control
modified:   Laminar/Backstep/Orthogonal_With_Eddies/control
modified:   Laminar/Backstep/Polyhedral/control
modified:   Laminar/Cavity/Hydrostatic/control
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_0100/control
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_0100/control_piso
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_0100/control_simple
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_0400/control
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_0400/control_piso
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_0400/control_simple
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_1000/control
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_1000/control_piso
modified:   Laminar/Cavity/Lid_Driven/Hexahedral/Re_1000/control_simple
modified:   Laminar/Cavity/Lid_Driven/Skewed/control
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_0.1/Ra_10e3/control.1
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_0.1/Ra_10e3/control.2
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_0.1/Ra_10e3/control.3
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_0.1/Ra_10e5/control.1
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_0.1/Ra_10e5/control.2
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_0.1/Ra_10e5/control.3
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_1.0/Ra_10e3/control.1
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_1.0/Ra_10e3/control.2
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_1.0/Ra_10e3/control.3
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_1.0/Ra_10e5/control.1
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_1.0/Ra_10e5/control.2
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_1.0/Ra_10e5/control.3
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_10.0/Ra_10e3/control.1
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_10.0/Ra_10e3/control.2
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_10.0/Ra_10e3/control.3
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_10.0/Ra_10e5/control.1
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_10.0/Ra_10e5/control.2
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/K_10.0/Ra_10e5/control.3
modified:   Laminar/Cavity/Thermally_Driven/Conjugate/control.0
modified:   Laminar/Cavity/Thermally_Driven/Direct/Ra_10e3/control
modified:   Laminar/Cavity/Thermally_Driven/Direct/Ra_10e4/control
modified:   Laminar/Cavity/Thermally_Driven/Direct/Ra_10e5/control
modified:   Laminar/Cavity/Thermally_Driven/Direct/Ra_10e6/control
modified:   Laminar/Cavity/Thermally_Driven/Direct/Ra_10e7/control
modified:   Laminar/Cavity/Thermally_Driven/Direct/Ra_10e8/control
modified:   Laminar/Cavity/Thermally_Driven/Direct/Variable_Properties_Air/control
modified:   Laminar/Cavity/Thermally_Driven/Skewed/control
modified:   Laminar/Channel/control
modified:   Laminar/Convective_Outflow/control
modified:   Laminar/Copy_Inlet/control.0
modified:   Laminar/Copy_Inlet/control.1
modified:   Laminar/Copy_Inlet/control.2
modified:   Laminar/Cylinder/Horizontal/Re_100_A/control-m1-p2-s1
modified:   Laminar/Cylinder/Horizontal/Re_100_A/control-m2-p3-s2
modified:   Laminar/Cylinder/Horizontal/Re_100_A/control-m3-p4-s3
modified:   Laminar/Cylinder/Horizontal/Re_100_A/control-m4-p5-s4
modified:   Laminar/Cylinder/Horizontal/Re_100_A/control-m5-p6-s5
modified:   Laminar/Cylinder/Horizontal/Re_100_A/control-m6-p7-s6
modified:   Laminar/Cylinder/Horizontal/Re_100_B/control-m1-p2-s1-g2
modified:   Laminar/Cylinder/Horizontal/Re_100_B/control-m2-p3-s2-g3
modified:   Laminar/Cylinder/Horizontal/Re_100_B/control-m3-p4-s3-g4
modified:   Laminar/Cylinder/Horizontal/Re_100_B/control-m4-p5-s4-g5
modified:   Laminar/Cylinder/Horizontal/Re_100_B/control-m5-p6-s5-g6
modified:   Laminar/Cylinder/Horizontal/Re_100_B/control-m6-p7-s6-g7
modified:   Laminar/Cylinder/Horizontal/Re_100_C/control-m1-p2-s1-g2
modified:   Laminar/Cylinder/Horizontal/Re_100_C/control-m2-p3-s2-g3
modified:   Laminar/Cylinder/Horizontal/Re_100_C/control-m3-p4-s3-g4
modified:   Laminar/Cylinder/Horizontal/Re_100_C/control-m4-p5-s4-g5
modified:   Laminar/Cylinder/Horizontal/Re_100_C/control-m5-p6-s5-g6
modified:   Laminar/Cylinder/Horizontal/Re_100_C/control-m6-p7-s6-g7
modified:   Laminar/Cylinder/Horizontal/Re_100_D/control-m1-p2-s1-g2
modified:   Laminar/Cylinder/Horizontal/Re_100_D/control-m2-p3-s2-g3
modified:   Laminar/Cylinder/Horizontal/Re_100_D/control-m3-p4-s3-g4
modified:   Laminar/Cylinder/Horizontal/Re_100_D/control-m4-p5-s4-g5
modified:   Laminar/Cylinder/Horizontal/Re_100_D/control-m5-p6-s5-g6
modified:   Laminar/Cylinder/Horizontal/Re_100_D/control-m6-p7-s6-g7
modified:   Laminar/Cylinder/Vertical/control-ra-1e05
modified:   Laminar/Cylinder/Vertical/control-ra-1e06
modified:   Laminar/Cylinder/Vertical/control-ra-1e07
modified:   Laminar/Cylinder/Vertical/control-ra-1e08
modified:   Laminar/Cylinder/Vertical/control-ra-1e5
modified:   Laminar/Cylinder/Vertical/control-ra-1e6
modified:   Laminar/Cylinder/Vertical/control-ra-1e7
modified:   Laminar/Flat_Plate/control
modified:   Laminar/Heat_Exchanger/2_Domains/control.0
modified:   Laminar/Heat_Exchanger/2_Domains/control.1
modified:   Laminar/Heat_Exchanger/2_Domains/control.2
modified:   Laminar/Heat_Exchanger/3_Domains/control.0
modified:   Laminar/Heat_Exchanger/3_Domains/control.1
modified:   Laminar/Heat_Exchanger/3_Domains/control.2
modified:   Laminar/Heat_Exchanger/3_Domains/control.3
modified:   Laminar/Membrane/2_Domains/control.0
modified:   Laminar/Membrane/2_Domains/control.1
modified:   Laminar/Membrane/2_Domains/control.2
modified:   Laminar/Membrane/Spacers/Concave/control
modified:   Laminar/Membrane/Spacers/Parallelogram/control
modified:   Laminar/Membrane/Spacers/Teardrop/control
modified:   Laminar/Membrane/Spiral/control.0
modified:   Laminar/Membrane/Spiral/control.1
modified:   Laminar/Membrane/Spiral/control.2
modified:   Laminar/Membrane/Spiral_Poly/control.0
modified:   Laminar/Membrane/Spiral_Poly/control.1
modified:   Laminar/Membrane/Spiral_Poly/control.2
modified:   Laminar/Module/control
modified:   Les/Barc/control
modified:   Les/Channel_Re_Tau_180/Long_Domain/control
modified:   Les/Channel_Re_Tau_180/Periodic_Domain/control
modified:   Les/Forrest/control
modified:   Les/Matrix_Of_Cubes/control
modified:   Les/Pipe_Re_Tau_180/control
modified:   Les/Rayleigh_Benard_Convection_Ra_10e09/control
modified:   Manual/Channel_Re_Tau_590/Stretched_Mesh/control
modified:   Manual/Conjugate/control
modified:   Manual/Conjugate/control.1
modified:   Manual/Conjugate/control.2
modified:   Manual/Conjugate/control.3
modified:   Manual/Impinging_Jet_2d_Distant_Re_23000/control
modified:   Manual/Inflows/Option_1/control
modified:   Manual/Inflows/Option_2/control
modified:   Manual/Inflows/Option_3/control
modified:   Manual/Inflows/Option_4/control
modified:   Manual/Inflows/Option_4/control.1
modified:   Manual/Inflows/Option_4/control.2
modified:   Manual/Matrix_Of_Cubes/control
modified:   Manual/Parallel/control
modified:   Manual/Rising_Bubble/control
modified:   Manual/Thermally_Driven/Varible/control
modified:   Rans/Backstep_Re_05100/control
modified:   Rans/Backstep_Re_28000/control
modified:   Rans/Channel_Re_Tau_590/Long_Domain/control
modified:   Rans/Channel_Re_Tau_590/Rsm/control_air
modified:   Rans/Channel_Re_Tau_590/Rsm/control_water
modified:   Rans/Channel_Re_Tau_590/Stretched_Mesh/control
modified:   Rans/Fuel_Bundle/control
modified:   Rans/Impinging_Jet_2d_Distant_Re_23000/control
modified:   Rans/Membrane/control.0
modified:   Rans/Membrane/control.1
modified:   Rans/Membrane/control.2
modified:   Rans/Membrane/control.3
modified:   Rans/Negative_Buoyant_Fountain/control-1
modified:   Rans/Negative_Buoyant_Fountain/control-2
modified:   Rans/Negative_Buoyant_Fountain/control-3
modified:   Rans/Negative_Buoyant_Fountain/control-4
modified:   Rans/Pipe_Re_Tau_550/control
modified:   Rans/Rayleigh_Benard_Convection_Ra_10e09/control
modified:   Rans/Single_Rod/control.0
modified:   Rans/Single_Rod/control.1
modified:   Rans/Single_Rod/control.2
modified:   Rans/Single_Rod/control.3
modified:   Swarm/Bend_90_Degrees/Control_Flow_Development/control
modified:   Swarm/Bend_90_Degrees/Control_Flow_Development/control.1
modified:   Swarm/Bend_90_Degrees/Control_Flow_Development/control.2
modified:   Swarm/Bend_90_Degrees/Control_Particle_Tracking/control
modified:   Swarm/Bend_90_Degrees/Control_Particle_Tracking/control.1
modified:   Swarm/Bend_90_Degrees/Control_Particle_Tracking/control.2
modified:   Swarm/Channel_Re_Tau_150/control_a_flow_development
modified:   Swarm/Channel_Re_Tau_150/control_b_particles
modified:   Swarm/Channel_Re_Tau_590/control_a_flow_development
modified:   Swarm/Channel_Re_Tau_590/control_b_particles
modified:   Swarm/Cylinders_Periodic/control
modified:   Swarm/Rod_Bundle_Hexagonal/control
modified:   Swarm/Rod_Bundle_Polyhedral/control
modified:   Swarm/T_Junction_Circular/control
modified:   Swarm/T_Junction_Square/control-1
modified:   Swarm/T_Junction_Square/control-2
modified:   Swarm/Three_Phase_Flow/control
modified:   Vof/Dam_Break_2d/control
modified:   Vof/Dam_Break_3d/control
modified:   Vof/Fuel_Bundle/control
modified:   Vof/Mencinger_And_Zun/control
modified:   Vof/Rising_Bubble/control
modified:   Vof/Stefan/control
modified:   Vof/Sucking/control
... which was preventing perfornance of backup tests

On branch bojan_more_robust_communicator

modified:   test_build.sh
That's actually pretty useful since T-Flows ignores lines
which it doesn't recognize, thus leaving potentially many
errors un-recognized.

On branch bojan_more_robust_communicator

new file:   Documentation/Syntax/.vim/ftdetect/control.vim
new file:   Documentation/Syntax/.vim/syntax/control.vim
renamed:    Documentation/fortran.vim -> Documentation/Syntax/.vim/syntax/fortran.vim
new file:   Documentation/Syntax/readme
It seems that previously_running should be an array (for
nested calls), not just a single integer number.

On branch bojan_more_robust_communicator

modified:   Shared/Profiler_Mod.f90
modified:   Shared/Profiler_Mod/Start.f90
modified:   Shared/Profiler_Mod/Stop.f90
On branch bojan_more_robust_communicator

modified:   Tests/Laminar/Backstep/Nonorthogonal/control
modified:   Tests/Laminar/Backstep/Orthogonal/control
modified:   Tests/Laminar/Backstep/Orthogonal_With_Eddies/control
modified:   Tests/Laminar/Backstep/Polyhedral/control
On branch bojan_more_robust_communicator

modified:   Documentation/Syntax/.vim/syntax/fortran.vim
modified:   Sources/Shared/Profiler_Mod.f90
modified:   Sources/Shared/Profiler_Mod/Start.f90
modified:   Sources/Shared/Profiler_Mod/Statistics.f90
modified:   Sources/Shared/Profiler_Mod/Stop.f90
modified:   Sources/Shared/Profiler_Mod/Update_By_Rank.f90
On branch bojan_more_robust_communicator

modified:   Sources/Process/Turb_Mod/Src_F22_Rsm_Manceau_Hanjalic.f90
modified:   Sources/Process/Turb_Mod/Src_Rsm_Hanjalic_Jakirlic.f90
modified:   Sources/Process/Turb_Mod/Src_Rsm_Manceau_Hanjalic.f90
modified:   Sources/Process/Turb_Mod/Vis_T_Rsm.f90
renamed:    User_Mod/Save_Vtu_Results.f90 -> User_Mod/Save_Results.f90
renamed:    User_Mod/Save_Vtu_Swarm.f90 -> User_Mod/Save_Swarm.f90

modified:   Results_Mod/Main_Results.f90
modified:   User_Mod.f90
On branch bojan_more_robust_communicator

modified:   User_Mod/Save_Results.f90
modified:   control
On branch bojan_more_robust_communicator

modified:   Process/Vof_Mod/Core/Initialize_From_Stl.f90
On branch bojan_more_robust_communicator

modified:   Process/Front_Mod/Save_Debug_Front_Vtu.f90
On branch bojan_more_robust_communicator

modified:   Process/Front_Mod/Save_Debug_Front_Vtu.f90
modified:   Process/Results_Mod/Save_Vtu_Front.f90
modified:   Process/Results_Mod/Save_Vtu_Surf.f90
modified:   Process/Results_Mod/Save_Vtu_Swarm.f90
On branch bojan_more_robust_communicator

modified:   Process/Field_Mod.f90
new file:   Process/Field_Mod/Utilities/Volume_Average.f90
On branch bojan_more_robust_communicator

modified:   Process/Read_Controls_Mod/Physical_Models.f90
Got rid of one ghost number along the way.

On branch bojan_more_robust_communicator

modified:   Info_Mod.f90
modified:   Info_Mod/Bulk_Fill.f90
modified:   Info_Mod/Bulk_Print.f90
modified:   Info_Mod/Bulk_Start.f90
modified:   Info_Mod/Iter_Fill.f90
modified:   Info_Mod/Iter_Fill_At.f90
new file:   Info_Mod/Iter_Fill_Scalar_At.f90
deleted:    Info_Mod/Iter_Fill_User_At.f90
modified:   Info_Mod/Iter_Print.f90
modified:   Info_Mod/Iter_Start.f90
modified:   Info_Mod/Start.f90
modified:   Info_Mod/Time_Fill.f90
modified:   Info_Mod/Time_Print.f90
modified:   Info_Mod/Time_Start.f90
modified:   Info_Mod/Time_To_Exit.f90
modified:   Main_Pro.f90
modified:   Process_Mod/Compute_Energy.f90
modified:   Process_Mod/Compute_Momentum.f90
modified:   Process_Mod/Compute_Pressure.f90
modified:   Process_Mod/Compute_Scalar.f90
modified:   Process_Mod/Correct_Velocity.f90
modified:   Process_Mod/Piso_Algorithm.f90
modified:   Turb_Mod/Compute_F22.f90
modified:   Turb_Mod/Compute_Stress.f90
modified:   Turb_Mod/Compute_Variable.f90
modified:   Vof_Mod/Core/Solve_System.f90
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