Merge branch 'improvement.MaxMCSoverMFP' into 'master.dev'

[improvement.MaxMCSoverMFP] Output MaxMCSoverMFP and resolved cells

See merge request piclas/piclas!879

docs/documentation/userguide/features-and-models/DSMC.md

@@ -466,7 +466,11 @@ the mean collision separation distance to the mean free path is written out (`DS
 $$\frac{l_{\mathrm{mcs}}}{\lambda} < 1$$
 
 The mean collision separation distance is determined during every collision and compared to the mean free path, where its ratio
-should be less than unity. Values above unity indicate an insufficient particle discretization. In order to estimate the required
+should be less than unity. Values above unity indicate an insufficient particle discretization.
+
+Additionaly, the above flag writes out the percentage of cells with a resolved timestep (`ResolvedTimestep`), the maximum collision probability of the entire computational domain (`Pmax`), the maximum of the `MCSoverMFP` of the entire domain (`MaxMCSoverMFP`), and the percentage of cells with a resolved time step and resolved weighting factor $w$ (`ResolvedCellPercentage`) to the file `PartAnalyze.csv`. In case of a reservoir simulation, the mean collision probability (`Pmean`) is the output instead of the `ResolvedTimestep`.
+
+In order to estimate the required
 weighting factor $w$, the following equation can be utilized for a 3D simulation
 
 $$w < \frac{1}{\left(\sqrt{2}\pi d_{\mathrm{ref}}^2 n^{2/3}\right)^3},$$

regressioncheck/CHE_DSMC/DSMC_QualityFactors/PartAnalyze_ref.csv

@@ -1,3 +1,3 @@
-001-TIME,002-NumDens-Spec-001,003-TempTra-001,004-TempVib001,005-XiVibMean001,006-TempRot001,007-TempTotal001,008-Pmean,009-Pmax,010-MeanFreePath
-0.0000000000000000E+000,0.1000000000000000E+023,0.5000769421287198E+004,0.4948975354726982E+004,0.1575887951139208E+001,0.4996259759961257E+004,0.4986985584220915E+004,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000
-0.1000000000000000E-007,0.1000000000000000E+023,0.5003185373708683E+004,0.4949437828908193E+004,0.1575924331939683E+001,0.4992329660714551E+004,0.4987003087500717E+004,0.6100164229169058E-001,0.1040428012026279E+000,0.2977138906706071E-003
+001-TIME,002-NumDens-Spec-001,003-TempTra-001,004-TempVib001,005-XiVibMean001,006-TempRot001,007-TempTotal001,008-Pmean,009-Pmax,010-MeanFreePath,011-MaxMCSoverMFP,012-ResolvedCellPercentage
+0,1E+022,5000.7694212872,4948.97535472698,1.57588795113921,4996.25975996126,4986.98558422092,0,0,0,0,0
+0.00000001,1E+022,5003.18537370868,4949.43782890819,1.57592433193968,4992.32966071455,4987.00308750072,0.6100164229169058E-001,0.9655792264656192E-001,0.000297713890670607,0.0001198721096,0.1000000000000000E+003

regressioncheck/CHE_DSMC/DSMC_QualityFactors/analyze.ini

@@ -2,11 +2,3 @@ compare_data_file_name      = PartAnalyze.csv
 compare_data_file_reference = PartAnalyze_ref.csv
 compare_data_file_tolerance = 5E-2
 compare_data_file_tolerance_type = relative
-
-! Compare cell-local values (ignore differences in the velocity vector)
-h5diff_file            = DSMC_QualityFactors_DSMCState_000.00000001000000000.h5
-h5diff_reference_file  = DSMC_QualityFactors_DSMCState_000.00000001000000000_ref.h5
-h5diff_data_set        = ElemData
-h5diff_tolerance_value = 5E-2
-h5diff_tolerance_type  = relative
-h5diff_max_differences = 3

regressioncheck/CHE_DSMC/DSMC_QualityFactors/externals.ini

@@ -0,0 +1,6 @@
+! --- Externals Tool Reggie
+MPI               = 1
+externalbinary    = ./hopr/build/bin/hopr
+externaldirectory = hopr.ini
+externalruntime   = pre
+cmd_suffix        =

regressioncheck/CHE_DSMC/DSMC_QualityFactors/parameter.ini

@@ -18,8 +18,8 @@ TrackingMethod = triatracking
 ! OUTPUT / VISUALIZATION
 ! =============================================================================== !
 ProjectName    = DSMC_QualityFactors
-IterDisplayStep = 100
-Part-AnalyzeStep = 100
+IterDisplayStep = 1
+Part-AnalyzeStep = 1
 CalcNumDens = T
 CalcTemp = T
 ! =============================================================================== !
@@ -71,6 +71,7 @@ Particles-NumberForDSMCOutputs=1
 Part-TimeFracForSampling=1
 Particles-DSMC-CalcSurfaceVal=F
 UseDSMC=true
+Particles-DSMCReservoirSim=true
 Particles-DSMC-CollisMode=2 !(1:elast coll, 2: elast + rela, 3:chem)
 Part-NumberOfRandomSeeds=2
 Particles-RandomSeed1=1

regressioncheck/CHE_DSMC/DSMC_QualityFactors/readme.md

@@ -3,5 +3,5 @@
 * Comparing with the theoretical values from gas kinetic theory
   * Mean collision probability is expected to be 0.06105 (chosen time step divided by the mean collision time, which is mean free path over average thermal velocity)
   * Mean free path is expected to be 2.98E-04 meters (Variable hard sphere model)
-  * Mean collision separation distance over mean free path (only in DSMCState) is 0.0001199, compared to the approximated value of 0.0001558, which assumes that the particles are distributed equidistantly in the cell. The difference is due to a 20% lower mean collision separation distance compared to the equidistant distribution (most likely due to nearest neighbour routine)
+  * Mean collision separation distance over mean free path (MCSoverMFP=MaxMCSoverMFP, because it is only one cell) is 0.0001199, compared to the approximated value of 0.0001558, which assumes that the particles are distributed equidistantly in the cell. The difference is due to a 20% lower mean collision separation distance compared to the equidistant distribution (most likely due to nearest neighbour routine)
 

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/DSMC.ini

@@ -0,0 +1,19 @@
+! =============================================================================== !
+! aus piclas/regressioncheck/NIG_Reservoir/CHEM_EQUI_TCE_AIR_5Spec
+! =======================================================================
+! Data for air taken from
+! Species: Boyd und Schwartzentruber: Nonequilibrium gas dynamics and molecular simulation page 294 und Bird: Molecular Gas Dynamics and the direct simulation of gas flows appendix A
+! Reactions: MONACO-Manual (Dietrich, Boyd) = Parks model (1985)
+! =======================================================================
+
+! =============================================================================== !
+! Species1, O
+! =============================================================================== !
+Part-Species1-SpeciesName       = O		! Species name [$]
+Part-Species1-InteractionID     = 1		! ID for identification of particles (1: Atom, 2: Molecule, ...)
+Part-Species1-Tref              = 273		! Collision parameter: species-specific reference temperature [K] for VHS/VSS model
+Part-Species1-dref              = 3.0E-10	! Collision parameter: species-specific reference diameter [m] for VHS/VSS model
+Part-Species1-omega             = 0.3		! Collision parameter: species-specific temperature exponent for VHS/VSS model !CAUTION: omega = omega_bird1994 - 0.5!
+Part-Species1-HeatOfFormation_K = 29969.88	! Heat of formation of the respective species [K]
+
+

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/PartAnalyze_ref.csv

@@ -0,0 +1,3 @@
+001-TIME,002-nPart-Spec-001,003-ResolvedTimestep,004-Pmax,005-MeanFreePath,006-MaxMCSoverMFP,007-ResolvedCellPercentage
+0.0000000000000000E+000,0.6560000000000000E+003,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000
+0.4000000000000000E-005,0.6560000000000000E+003,0.7500000000000000E+002,0.1459098048714706E+001,0.3977357765940307E-002,0.2823015493546503E+001,0.1250000000000000E+002

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/analyze.ini

@@ -0,0 +1,4 @@
+compare_data_file_name      = PartAnalyze.csv
+compare_data_file_reference = PartAnalyze_ref.csv
+compare_data_file_tolerance = 5E-2
+compare_data_file_tolerance_type = relative

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/command_line.ini

@@ -0,0 +1,2 @@
+MPI=4
+cmd_suffix=DSMC.ini

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/excludeBuild.ini

@@ -0,0 +1,2 @@
+! Skip N=1 hard coded
+PICLAS_POLYNOMIAL_DEGREE=1

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/externals.ini

@@ -0,0 +1,6 @@
+! --- Externals Tool Reggie
+MPI               = 1
+externalbinary    = ./hopr/build/bin/hopr
+externaldirectory = hopr.ini
+externalruntime   = pre
+cmd_suffix        =

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/hopr.ini

@@ -0,0 +1,44 @@
+
+!================================================================================================================================= !
+! OUTPUT
+!================================================================================================================================= !
+ProjectName        = cube_8_cells
+Debugvisu          = T                          ! Visualize mesh and boundary conditions (tecplot ascii)
+Logging		   = F                          ! Write log files
+
+!================================================================================================================================= !
+! MESH
+!================================================================================================================================= !
+Mode   = 1                           ! Mode for Cartesian boxes
+nZones = 1                           ! number of boxes 
+
+! ---------------------------------------------------------------
+! Box 1
+! ---------------------------------------------------------------
+
+Corner       =(/-0.5 , 0.0 , -0.5  ,,   0.5 , 0.0 , -0.5  ,,  0.5 , 1 , -0.5  ,,  -0.5 , 1 , -0.5  ,,  -0.5 , 0.0 , 0.5  ,,  0.5 , 0.0 , 0.5  ,,  0.5 , 1 , 0.5   ,,   -0.5 , 1 , 0.5 /)
+	      ! Corner node positions: (/ x_1,y_1,z_1, x_2,y_2,z_2,..... , x_8,y_8,z_8/)
+nElems       =(/2,2,2/)                      ! number of elements in each direction (/nElemX,nElemY,nElemZ/)
+BCIndex      =(/1  , 1  , 1  , 1  , 1 , 1/)   
+!            =(/z- , y- , x+ , y+ , x- , z+/)  ! Indices of Boundary Conditions for  six Boundary Faces
+elemtype     =108                              ! element type (108: Hexahedral)
+
+
+useCurveds    =F                           ! T if curved boundaries defined
+SpaceQuandt   =1.                          ! characteristic length of the mesh
+ConformConnect=T
+
+!=============================================================================== !
+! BOUNDARY CONDITIONS
+!=============================================================================== !
+nUserDefinedBoundaries=1
+BoundaryName=WALL              ! Outflow: open (absorbing)   [for MAXWELL]
+BoundaryType=(/4,0,0,0/)          ! (/ Type, curveIndex, State, alpha /)
+
+!=============================================================================== !
+! BASIS
+!=============================================================================== !
+NVisu         = 7
+meshscale     = 0.1
+jacobianTolerance=1E-25
+

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/parameter.ini

@@ -0,0 +1,156 @@
+! =============================================================================== !
+! EQUATION (linearscalaradvection)
+! =============================================================================== !
+IniExactFunc = 0
+
+! =============================================================================== !
+! DISCRETIZATION
+! =============================================================================== !
+N        = 1
+NAnalyze = 1
+
+! =============================================================================== !
+! MESH
+! =============================================================================== !
+MeshFile = cube_8_cells_mesh.h5
+TrackingMethod  = triatracking
+
+! =============================================================================== !
+! OUTPUT / VISUALIZATION
+! =============================================================================== !
+ProjectName = DSMC_QualityFactors_MPI
+IterDisplayStep = 1
+CalcNumSpec = T
+
+! =============================================================================== !
+! CALCULATION
+! =============================================================================== !
+TEnd                  = 4.0E-6
+Analyze_dt            = 1E-4 
+CFLscale              = 0.2 
+
+! =============================================================================== !
+! DSMC
+! =============================================================================== !
+ManualTimeStep        = 4.0E-6
+Particles-HaloEpsVelo = 8.0E+4
+Particles-NumberForDSMCOutputs = 1
+Part-TimeFracForSampling = 1
+Particles-DSMC-CalcSurfaceVal = F
+UseDSMC                    = T
+Particles-DSMC-CollisMode  = 2
+Part-NumberOfRandomSeeds = 2
+Particles-RandomSeed1    = 1
+Particles-RandomSeed2    = 2
+Particles-DSMC-UseOctree = F
+Particles-DSMC-UseNearestNeighbour = T
+Particles-DSMC-CalcQualityFactors = T
+
+! =============================================================================== !
+! Boundaries
+! =============================================================================== !
+Part-nBounds               = 1
+Part-Boundary1-SourceName  = WALL
+Part-Boundary1-Condition   = reflective
+Part-Boundary1-WallTemp    = 300
+Part-Boundary1-TransACC    = 1
+Part-Boundary1-MomentumACC = 1
+Part-Boundary1-VibACC      = 1
+Part-Boundary1-RotACC      = 1
+
+! =============================================================================== !
+! PARTICLES
+! =============================================================================== !
+Part-maxParticleNumber = 500000 
+Part-nSpecies          = 1
+Part-FIBGMdeltas       = (/1.0,1.0,1.0/)
+
+! =============================================================================== !
+! Species1 - O
+! =============================================================================== ! 
+Part-Species1-MassIC              = 2.657E-26
+Part-Species1-MacroParticleFactor = 1E15
+Part-Species1-ChargeIC            = 0
+
+! Initialization:
+Part-Species1-nInits = 8
+
+Part-Species1-Init1-SpaceIC               = sphere
+Part-Species1-Init1-RadiusIC              = 0.025
+Part-Species1-Init1-BasePointIC           = (/ 0.025, 0.025, 0.025 /)
+Part-Species1-Init1-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init1-velocityDistribution = maxwell_lpn
+Part-Species1-Init1-MWTemperatureIC = 300
+Part-Species1-Init1-PartDensity = 1E+21
+Part-Species1-Init1-VeloIC = 0
+Part-Species1-Init1-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init2-SpaceIC               = sphere
+Part-Species1-Init2-RadiusIC              = 0.025
+Part-Species1-Init2-BasePointIC           = (/ -0.025, 0.075, 0.025 /)
+Part-Species1-Init2-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init2-velocityDistribution = maxwell_lpn
+Part-Species1-Init2-MWTemperatureIC = 300
+Part-Species1-Init2-PartDensity = 1E+21
+Part-Species1-Init2-VeloIC = 0
+Part-Species1-Init2-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init3-SpaceIC               = sphere
+Part-Species1-Init3-RadiusIC              = 0.025
+Part-Species1-Init3-BasePointIC           = (/ -0.025, 0.025, -0.025 /)
+Part-Species1-Init3-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init3-velocityDistribution = maxwell_lpn
+Part-Species1-Init3-MWTemperatureIC = 300
+Part-Species1-Init3-PartDensity = 1E+21
+Part-Species1-Init3-VeloIC = 0
+Part-Species1-Init3-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init4-SpaceIC               = sphere
+Part-Species1-Init4-RadiusIC              = 0.025
+Part-Species1-Init4-BasePointIC           = (/ 0.025, 0.075, -0.025 /)
+Part-Species1-Init4-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init4-velocityDistribution = maxwell_lpn
+Part-Species1-Init4-MWTemperatureIC = 300
+Part-Species1-Init4-PartDensity = 1E+21
+Part-Species1-Init4-VeloIC = 0
+Part-Species1-Init4-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init5-SpaceIC               = sphere
+Part-Species1-Init5-RadiusIC              = 0.025
+Part-Species1-Init5-BasePointIC           = (/ 0.025, 0.025, -0.025 /)
+Part-Species1-Init5-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init5-velocityDistribution = maxwell_lpn
+Part-Species1-Init5-MWTemperatureIC = 300
+Part-Species1-Init5-PartDensity = 2E+21 
+Part-Species1-Init5-VeloIC = 0
+Part-Species1-Init5-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init6-SpaceIC               = sphere
+Part-Species1-Init6-RadiusIC              = 0.025
+Part-Species1-Init6-BasePointIC           = (/ 0.025, 0.075, 0.025 /)
+Part-Species1-Init6-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init6-velocityDistribution = maxwell_lpn
+Part-Species1-Init6-MWTemperatureIC = 300
+Part-Species1-Init6-PartDensity = 2E+21
+Part-Species1-Init6-VeloIC = 0
+Part-Species1-Init6-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init7-SpaceIC               = sphere
+Part-Species1-Init7-RadiusIC              = 0.025
+Part-Species1-Init7-BasePointIC           = (/ -0.025, 0.025, 0.025 /)
+Part-Species1-Init7-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init7-velocityDistribution = maxwell_lpn
+Part-Species1-Init7-MWTemperatureIC = 300
+Part-Species1-Init7-PartDensity = 1E+20 
+Part-Species1-Init7-VeloIC = 0
+Part-Species1-Init7-VeloVecIC = (/1.,0.,0./)
+
+Part-Species1-Init8-SpaceIC               = sphere
+Part-Species1-Init8-RadiusIC              = 0.025
+Part-Species1-Init8-BasePointIC           = (/ -0.025, 0.075, -0.025 /)
+Part-Species1-Init8-NormalIC              = (/ 0.0, 0.0, 1.0 /)
+Part-Species1-Init8-velocityDistribution = maxwell_lpn
+Part-Species1-Init8-MWTemperatureIC = 300
+Part-Species1-Init8-PartDensity = 2E+21
+Part-Species1-Init8-VeloIC = 0
+Part-Species1-Init8-VeloVecIC = (/1.,0.,0./)

regressioncheck/CHE_DSMC/DSMC_QualityFactors_MPI/readme.md

@@ -0,0 +1,4 @@
+# DSMC: Quality Factors
+* Testing the calculation and MPI communication of the QualityFactors ResolvedTimestep, Pmax, MaxMCSoverMFP and ResolvedCellPercentage
+* The values are not compared to the theoretical values from gas kinetic theory. This is done in the Reggie DSMC_QualityFactors
+

regressioncheck/NIG_Reservoir/CHEM_BGG_MultiSpec_TCE_Air_5Spec/Database_Ttrans_10000_ref.csv

@@ -1,3 +1,3 @@
-001-TIME,002-Pmean,003-Pmax,004-MeanFreePath,005-Reaction001,006-Reaction002,007-Reaction003,008-Reaction004,009-Reaction005
-0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000
-1.00000000000000E-007,3.73688135572668E-001,7.27526232996863E-001,1.32474544582370E-005,2.48777888932569E-019,4.40906095483012E-017,2.28631616080479E-018,2.42390240084106E-019,4.42149510308084E-017
+001-TIME,002-Pmean,003-Pmax,004-MeanFreePath,005-MaxMCSoverMFP,006-ResolvedCellPercentage,007-Reaction001,008-Reaction002,009-Reaction003,010-Reaction004,011-Reaction005
+0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000
+1.00000000000000E-007,3.73688135572668E-001,7.27526232996863E-001,1.32474544582370E-005,0.0000000000000000E+000,0.1000000000000000E+003,2.48777888932569E-019,4.40906095483012E-017,2.28631616080479E-018,2.42390240084106E-019,4.42149510308084E-017

regressioncheck/NIG_Reservoir/CHEM_BGG_MultiSpec_TCE_Air_5Spec/Database_Ttrans_15000_ref.csv

@@ -1,3 +1,3 @@
-001-TIME,002-Pmean,003-Pmax,004-MeanFreePath,005-Reaction001,006-Reaction002,007-Reaction003,008-Reaction004,009-Reaction005
-0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000,0.00000000000000E+000
-1.00000000000000E-007,4.15119539713157E-001,7.81552614396978E-001,1.46013945833773E-005,5.65915325730076E-018,1.71194379397845E-016,5.46193901126186E-018,5.64365826162393E-018,1.71913416028807E-016
+001-TIME,002-Pmean,003-Pmax,004-MeanFreePath,005-MaxMCSoverMFP,006-ResolvedCellPercentage,007-Reaction001,008-Reaction002,009-Reaction003,010-Reaction004,011-Reaction005
+0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000,0.0000000000000000E+000
+1.00000000000000E-007,4.15119539713157E-001,7.81552614396978E-001,1.46013945833773E-005,0.0000000000000000E+000,0.1000000000000000E+003,5.65915325730076E-018,1.71194379397845E-016,5.46193901126186E-018,5.64365826162393E-018,1.71913416028807E-016