Merge branch 'master.dev' of piclas.boltzplatz.eu:piclas/piclas into …

…feature.HDG_petsc

.gitlab-ci.yml

@@ -373,25 +373,25 @@ poisson_release:
   <<: *defaults_poisson
   stage: reggie_checkin
   script:
-    - cd build_poisson_release ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson/poisson -e ./bin/piclas
+    - cd build_poisson_release ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson -e ./bin/piclas
 
 poisson_debug:
   <<: *defaults_poisson
   stage: reggie_checkin
   script:
-    - cd build_poisson_debug ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson/poisson -e ./bin/piclas
+    - cd build_poisson_debug ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson -e ./bin/piclas
 
 poisson_petsc_release:
   <<: *defaults_poisson_petsc
   stage: reggie_checkin
   script:
-    - cd build_poisson_petsc_release ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson/poisson -e ./bin/piclas
+    - cd build_poisson_petsc_release ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson -e ./bin/piclas
 
 poisson_petsc_debug:
   <<: *defaults_poisson_petsc
   stage: reggie_checkin
   script:
-    - cd build_poisson_petsc_debug ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson/poisson -e ./bin/piclas
+    - cd build_poisson_petsc_debug ; python ./reggie/reggie.py ../regressioncheck/CHE_poisson -e ./bin/piclas
 
 
 # ----------------------------------------------------------------------------------------------------------------------------------------------------

CMakeListsLib.txt

@@ -302,9 +302,16 @@ IF(NOT LIBS_BUILD_MATH_LIB)
   ENDIF()
 
   # VDM inverse, replace lapack with analytical solution
-  IF (CMAKE_BUILD_TYPE MATCHES "Debug" AND "${CMAKE_HOSTNAME}" MATCHES "login" AND "${LSB_RELEASE_ID_SHORT}" MATCHES "CentOS")
-    MESSAGE(STATUS "Compiling PICLas in debug mode on Hawk with system math lib. Setting VDM inverse to analytical solution")
-    ADD_DEFINITIONS(-DVDM_ANALYTICAL)
+  # HLRS HAWK / SuperMUC + DEBUG
+  IF (CMAKE_BUILD_TYPE MATCHES "Debug" AND "${CMAKE_HOSTNAME}" MATCHES "login")
+    # HAWK and SuperMUC name their login nodes identically, so use the Fully Qualified Domain Name (FQDN) to identify
+    CMAKE_HOST_SYSTEM_INFORMATION(RESULT FQDN QUERY FQDN)
+    MARK_AS_ADVANCED(FORCE FQDN)
+    # HLRS HAWK
+    IF ("${FQDN}" MATCHES "hawk.hww.hlrs.de")
+      MESSAGE(STATUS "Compiling PICLas in debug mode on Hawk with system math lib. Setting VDM inverse to analytical solution")
+      ADD_DEFINITIONS(-DVDM_ANALYTICAL)
+    ENDIF()
   ENDIF()
 
 # Build LAPACK/OpenBLAS in FLEXI

REGGIE.md

@@ -314,11 +314,11 @@ Testing PIC compiled with Leapfrog integration (poisson,Leapfrog), solving Poiss
 
 Testing PIC compiled with Boris-Leapfrog integration (poisson,Boris-Leapfrog), solving Poisson's equation: [Link to build](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/builds.ini).
 
-| **No.** |    **Case**    |         **CMAKE-CONFIG**         |                                                                                                                         **Feature**                                                                                                                          | **Execution** |                             **Comparing**                              |                                   **Readme**                                    |
-| :-----: | :------------: | :------------------------------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :-----------: | :--------------------------------------------------------------------: | :-----------------------------------------------------------------------------: |
-|    1    | 2D_HET_Liu2010 | CMAKE_BUILD_TYPE = Release,Debug |                                             2D Poisson-PIC, BGGas distribution, null collision on/off, pre-defined external magnetic field, neutralization BC, SEE model with variable electron bulk temperature                                             | nProcs=3,6,12 | integrate number of electrons impinging the anode (SurfaceAnalyze.csv) | [Link](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/readme.md) |
-|    2    |  2D_Landmark   | CMAKE_BUILD_TYPE = Release,Debug |                                                                                     2D Poisson-PIC, emission models for Landmark (volumetric ionization and neutralizer)                                                                                     |   nProcs=4    | integrate number of electrons impinging the anode (SurfaceAnalyze.csv) |  [Link](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_Landmark/readme.md)   |
-|    3    | 3D_HET_Liu2010 | CMAKE_BUILD_TYPE = Release,Debug | 3D Poisson-PIC, BGGas distribution, null collision on/off, pre-defined external magnetic field, neutralization BC, SEE model with variable electron bulk temperature, dielectric surface charging (hollow cylinder), vMPF=T restart from vMPF=F restart file |   nProcs=6    | integrate number of electrons impinging the anode (SurfaceAnalyze.csv) | [Link](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/3D_HET_Liu2010/readme.md) |
+| **No.** |    **Case**    |  **CMAKE-CONFIG** |                                                                                                                           **Feature**                                                                                                                           | **Execution** |                              **Comparing**                             |                                    **Readme**                                   |
+| :-----: | :------------: | :---------------: | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :-----------: | :--------------------------------------------------------------------: | :-----------------------------------------------------------------------------: |
+|    1    | 2D_HET_Liu2010 |                   |  2D Poisson-PIC, BGGas distribution, null collision on/off, pre-defined external magnetic field, neutralization BC, SEE model with variable electron bulk temperature,  particle flux, total electric current and emitted SEE over time into SurfaceAnalyze.csv | nProcs=3,6,12 | integrate number of electrons impinging the anode (SurfaceAnalyze.csv) | [Link](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/readme.md) |
+|    2    |   2D_Landmark  |                   |                                                                                       2D Poisson-PIC, emission models for Landmark (volumetric ionization and neutralizer)                                                                                      |    nProcs=4   | integrate number of electrons impinging the anode (SurfaceAnalyze.csv) |   [Link](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_Landmark/readme.md)  |
+|    3    | 3D_HET_Liu2010 |                   |   3D Poisson-PIC, BGGas distribution, null collision on/off, pre-defined external magnetic field, neutralization BC, SEE model with variable electron bulk temperature, dielectric surface charging (hollow cylinder), vMPF=T restart from vMPF=F restart file  |    nProcs=6   | integrate number of electrons impinging the anode (SurfaceAnalyze.csv) | [Link](regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/3D_HET_Liu2010/readme.md) |
 
 ### NIG_PIC_poisson_RK3
 

docs/documentation/userguide/installation.md

@@ -212,11 +212,18 @@ For convenience, you can add these lines to your `.bashrc`.
 (sec:petsc-installation)=
 ### Installing PETSc
 
+The following list contains the **recommended/working library versions** for PETSc and PICLas
+
+| PICLas Version |    3.18   |    3.17   |
+| :------------: | :-------: | :-------: |
+|      3.0.0     |    yes    |    yes    |
+|      2.9.0     |    no     |    yes    |
+
 #### Local machine
 Download PETSc from the git repository
 
 ````
-git clone -b main https://gitlab.com/petsc/petsc.git petsc
+git clone -b release-3.17 https://gitlab.com/petsc/petsc.git petsc
 ````
 
 Configure and install PETSc (MPI and BLAS/LAPACK have to be installed)

docs/documentation/userguide/visu_output.md

@@ -338,8 +338,54 @@ impact angle of $0^{\circ}$), number of real particle impacts over the sampling
 per area per second.
 
 ## Integral Variables
-
-WIP, PartAnalyze/FieldAnalyze
+This analysis measures integral values from the field- and/or particle-solver data over time and writes different .csv files.
+
+### Field Variables
+**WIP**
+
+### Particle Variables
+**WIP**
+
+### Surface Variables
+
+The output for different measurements involving particles and surfaces is written to *SurfaceAnalyze.csv*.
+If this analysis is not required in each time step, the parameter `Surface-AnalyzeStep` (default is 1) can be set to an integer
+greater or equal 1. Some values are sampled only during one time step and others are accumulated over the number of time steps
+defined by `Surface-AnalyzeStep`.
+The number of time steps over which the values are calculated is controlled with `Surface-AnalyzeStep` (default is 1).
+
+|           Parameter          |                                   Parameter                                  |
+| ---------------------------- | ---------------------------------------------------------------------------- |
+|       `CalcElectronSEE`      |  Secondary electron emission current for each `Part-Boundary` with SEE model |
+| `CalcBoundaryParticleOutput` |    Particle flux for each user-defined `Part-Boundary` and `Part-Species`    |
+
+**Secondary Electron Emission**
+When `CalcElectronSEE=T` is activated, the secondary electron emission current (on all surfaces where such a model is used) is
+calculated and written to *SurfaceAnalyze.csv*. Note that all secondary electrons between two outputs are accumulated and divided by
+the time difference between these outputs. Hence, the averaging time can be adjusted using `Surface-AnalyzeStep`.
+The output in the .csv file will be similar to this example: `012-ElectricCurrentSEE-BC_WALL`
+
+**BoundaryParticleOutput (BPO)** The flux of particles crossing boundaries where they are removed can be calculated by setting
+`CalcBoundaryParticleOutput = T`. Additionally, the boundaries and species IDs must be supplied for which the output is to be
+created. This is done by setting
+
+    CalcBoundaryParticleOutput = T        ! Activate the analysis
+    BPO-NPartBoundaries        = 2        ! Nbr of particle boundaries where the flux and current are measured
+    BPO-PartBoundaries         = (/4,8/)  ! Only measure the flux and current on Part-Boundary4 and Part-Boundary8
+    BPO-NSpecies               = 2        ! Nbr of species that are considered for Part-Boundary4 and Part-Boundary8
+    BPO-Species                = (/2,3/)  ! Species IDs which should be included
+
+where the number of boundaries and species as well as the corresponding IDs are defined. The other boundaries and species IDs will
+be ignored. Note that this feature is currently only implemented for boundaries of type `Part-BoundaryX-Condition = open` and
+`Part-BoundaryX-Condition = reflective`. The reflective BC must also use either species swap via `Part-BoundaryX-NbrOfSpeciesSwaps`
+or a secondary electron emission surface model via `Part-BoundaryX-SurfaceModel`.
+The output in the .csv file will be similar to this example: `004-Flux-Spec-002-BC_CATHODE`
+Additionally, the total electric current will be calculated if any species that is selected via `BPO-Species` carries a charge
+unequal to zero.
+Note that only species defined via `BPO-Species` will be considered in the calculation of the total electric current.
+Furthermore, the secondary electron emission current is automatically added to the total electric current if
+`CalcBoundaryParticleOutput = T`.
+The output of the total electric current in the .csv file will be similar to this example: `008-TotalElectricCurrent-BC_ANODE`
 
 ## Dynamic Mode Decomposition
 The dynamic mode decomposition is an algorithm that divides a temporal series into a set of modes which are associated with a

regressioncheck/CHE_poisson/SurfFlux_ThermionicEmission_Schottky/parameter.ini

@@ -60,8 +60,12 @@ Part-nSpecies=1
 Part-nBounds=6
 Part-Boundary1-SourceName = BC_Xplus
 Part-Boundary1-Condition  = reflective
+Part-Boundary1-NbrOfSpeciesSwaps = 1
+Part-Boundary1-SpeciesSwaps1     = (/1,0/)
+
 Part-Boundary2-SourceName = BC_Xminus
 Part-Boundary2-Condition  = reflective
+
 Part-Boundary2-WallTemp   = 2700, 2635.24
 Part-Boundary3-SourceName = BC_Yplus
 Part-Boundary3-Condition  = symmetric
@@ -72,6 +76,12 @@ Part-Boundary5-Condition  = symmetric
 Part-Boundary6-SourceName = BC_Zminus
 Part-Boundary6-Condition  = symmetric
 Part-FIBGMdeltas=(/1e-2,1e-2,1e-2/)
+
+CalcBoundaryParticleOutput = T
+BPO-NPartBoundaries        = 1       ! Nbr of bounaries
+BPO-PartBoundaries         = (/1/)   ! Part-Boundary1 and Part-Boundary2
+BPO-NSpecies               = 1       ! Nbr of species
+BPO-Species                = (/1/)   ! electrons
 ! =============================================================================== !
 ! Species1 - electron
 ! =============================================================================== !
@@ -98,4 +108,4 @@ nocrosscombination:Part-Boundary2-WallTemp, Part-Species1-Surfaceflux1-Thermioni
 Particles-HaloEpsVelo=2.0E+07
 Part-NumberOfRandomSeeds=2
 Particles-RandomSeed1=1
-Particles-RandomSeed2=2
+Particles-RandomSeed2=2

regressioncheck/CHE_poisson/SurfFlux_ThermionicEmission_Schottky/readme.md

@@ -3,4 +3,4 @@
 * Schottky effect reduces the work function (and thus the required wall temperature)
 * Comparing the calculated current to the expected value of the Richardson Dushman equation for Tungsten
   * Input: W = 4.54 eV, A = 60 A/(cm^2 K^2), T_w = 2700 K (without Schottky), T_w = 2635.24 K
-  * Output: j = 1.47 A / cm^2 -> I = 1.4675 eV (A = 1 cm^2)
+  * Output: j = 1.47 A / cm^2 -> I = 1.4675 A (A = 1 cm^2)

regressioncheck/CHE_poisson/poisson/SurfaceAnalyze_reference.csv

@@ -1,2 +1,2 @@
-001-TIME,002-nRealPartOut-Spec-002-BC_left
-0.6000000000000000E-008,0.3000000000000000E+003
+001-TIME,002-Flux-Spec-002-BC_left,003-TotalElectricCurrent-BC_left,004-ElectricCurrentSEE-BC_right
+0.6000000000000000E-008,0.4200000000000136E+013,-.6729141426000218E-006,0.0000000000000000E+000

regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/SurfaceAnalyze_refA.csv

@@ -0,0 +1,2 @@
+001-TIME,002-Flux-Spec-002-BC_ANODE,003-Flux-Spec-003-BC_ANODE,004-Flux-Spec-002-BC_CATHODE,005-Flux-Spec-003-BC_CATHODE,006-Flux-Spec-002-BC_WALL,007-Flux-Spec-003-BC_WALL,008-TotalElectricCurrent-BC_ANODE,009-TotalElectricCurrent-BC_CATHODE,010-TotalElectricCurrent-BC_WALL,011-NeutralizationParticles,012-ElectricCurrentSEE-BC_WALL
+0.5000000000000000E-008,0.1007999999999993E+016,0.0000000000000000E+000,0.1329999999999990E+016,0.9999999999999927E+012,0.4979999999999964E+015,0.1999999999999985E+013,-.1614993942239988E-003,-.2129292608369985E-003,0.1228869398509989E-003,0.7700000000000000E+002,0.2023548957389984E-003

regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/SurfaceAnalyze_refB.csv

@@ -0,0 +1,2 @@
+001-TIME,002-Flux-Spec-002-BC_ANODE,003-Flux-Spec-003-BC_ANODE,004-Flux-Spec-002-BC_CATHODE,005-Flux-Spec-003-BC_CATHODE,006-Flux-Spec-002-BC_WALL,007-Flux-Spec-003-BC_WALL,008-TotalElectricCurrent-BC_ANODE,009-TotalElectricCurrent-BC_CATHODE,010-TotalElectricCurrent-BC_WALL,011-NeutralizationParticles,012-ElectricCurrentSEE-BC_WALL
+0.5000000000000000E-008,0.9049999999999934E+015,0.0000000000000000E+000,0.2809999999999979E+015,0.0000000000000000E+000,0.5399999999999961E+015,0.1999999999999985E+013,-.1449969759649989E-003,-.4502116049299967E-004,0.1091082216929991E-003,0.1900000000000000E+002,0.1953053190069984E-003

regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/analyze.ini

@@ -1,6 +1,16 @@
-! integrate the number of electrons impinging on the anode
+! Integrate the number of electrons impinging on the anode
 integrate_line_file            = SurfaceAnalyze.csv    ! Data file name
-integrate_line_columns         = 0:1                   ! Columns x:y for integration y over x
-integrate_line_integral_value  = 0.000118725           ! Number of removed electrons through the anode BC: integrated value from the first single-core simulation
+integrate_line_columns         = 0:1                   ! Columns x:y for integration y over x, .i.e., 002-Flux-Spec-002-BC_ANODE over 001-TIME
+integrate_line_integral_value  = 1.984805e6            ! Number of removed electrons through the anode BC per sec
+!                                                      ! integrated value from the first single-core simulation
 integrate_line_tolerance_value = 15e-2                 ! Tolerance (largest difference was observed to be 12.36% on reggie server)
 integrate_line_tolerance_type  = relative              ! Relative or absolute tolerance
+
+
+! Check last line in .csv file and compare to reference file
+! Note that the tolerance is quite high due to the low number of particles which reduces the computational demand for this test
+compare_data_file_name            = SurfaceAnalyze.csv      , SurfaceAnalyze.csv
+compare_data_file_reference       = SurfaceAnalyze_refA.csv , SurfaceAnalyze_refB.csv
+compare_data_file_tolerance       = 30e-2                   , 50e-2
+compare_data_file_tolerance_type  = relative                , relative
+compare_data_file_max_differences = 4                       , 4

regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/parameter.ini

@@ -58,11 +58,15 @@ CalcPointsPerDebyeLength = T
 Particles-DSMC-CalcQualityFactors = T
 
 CalcBoundaryParticleOutput = T
-BPO-NPartBoundaries        = 2        ! Nbr of boundaries
-BPO-PartBoundaries         = (/1,2/)  ! Part-Boundary1 and Part-Boundary2
+BPO-NPartBoundaries        = 3        ! Nbr of boundaries
+BPO-PartBoundaries         = (/1,2,3/)  ! Part-Boundary1 and Part-Boundary2
 BPO-NSpecies               = 2        ! Nbr of species
 BPO-Species                = (/2,3/)  ! electrons, Xe+
 
+Surface-AnalyzeStep = 10
+
+CalcElectronSEE = T
+
 TimeStampLength            = 16
 ! =============================================================================== !
 ! CALCULATION
@@ -140,6 +144,7 @@ Part-SurfaceModel-SEE-Te            = 5.80226250308285e5 ! Electron temperature
 Part-SurfaceModel-SEE-Te-automatic  = T
 Part-SurfaceModel-SEE-Te-Spec       = 2
 
+
 Part-Boundary4-SourceName = BC_periodicz+
 Part-Boundary4-Condition  = periodic
 

regressioncheck/NIG_PIC_poisson_Boris-Leapfrog/2D_HET_Liu2010/readme.md

@@ -22,11 +22,19 @@
       Part-SurfaceModel-SEE-Te-automatic  = T ! Instead of using a fixed bulk electron temperature, determine the global temperature of the defined species (default is False). Note that Part-SurfaceModel-SEE-Te is used as initial value.
       Part-SurfaceModel-SEE-Te-Spec       = 2 ! For automatic bulk Te determination, state the species ID of the electrons
 
-- Neutralization emission BC via keeping the exiting charge at the right BC zero over time (averged)
+- Neutralization emission BC via keeping the exiting charge at the right BC zero over time (averaged)
 
     Part-Species2-Init2-SpaceIC = 2D_Liu2010_neutralization
 
   or by enforcing a neutral boundary layer at the right exit by emitting electrons if there is an ion surplus in the first row of
   elements
 
     Part-Species2-Init2-SpaceIC = 2D_Liu2010_neutralization_Szabo
+
+- Output of particle flux, total electric current and emitted SEE over time into SurfaceAnalyze.csv for particle boundaries 1,2 and 3via
+
+    CalcBoundaryParticleOutput = T
+    BPO-NPartBoundaries        = 3         ! Nbr of boundaries
+    BPO-PartBoundaries         = (/1,2,3/) ! Part-Boundary1 to Part-Boundary3
+    BPO-NSpecies               = 2         ! Nbr of species
+    BPO-Species                = (/2,3/)   ! electrons, Xe+