Merge branch 'master.dev' into 'master'

Release 1.5.2

See merge request piclas/piclas!296

.gitlab-ci.yml

@@ -283,14 +283,21 @@ gnu_NIG_tracking_DSMC:
 # ----------------------------------------------------------------------------------------------------------------------------------------------------
 # Stage "reggie_superB_nightly": Build and run superB examples on nightly
 # ----------------------------------------------------------------------------------------------------------------------------------------------------
-gnu_NIG_SuperB:
+gnu_NIG_SuperB_piclas:
   <<: *defaults_gnu
   stage: reggie_superB_nightly
   tags:
     - withmodules-concurrent
   script:
     - if [ -n "${DO_NIGHTLY}" ]; then cd build_gnu ; python ./reggie/reggie.py ../regressioncheck/checks/NIG_SuperB -e ./bin/piclas ; fi
-    - if [ -n "${DO_NIGHTLY}" ]; then python ./reggie/reggie.py ../regressioncheck/checks/NIG_SuperB -e ./bin/superB ; fi
+
+gnu_NIG_SuperB_standalone:
+  <<: *defaults_gnu
+  stage: reggie_superB_nightly
+  tags:
+    - withmodules-concurrent
+  script:
+    - if [ -n "${DO_NIGHTLY}" ]; then cd build_gnu ; python ./reggie/reggie.py ../regressioncheck/checks/NIG_SuperB -e ./bin/superB ; fi
 
 # ----------------------------------------------------------------------------------------------------------------------------------------------------
 # Stage "reggie_nightly": Build and run

CMakeLists.txt

@@ -593,6 +593,17 @@ ELSE()
   ADD_DEFINITIONS(-DUSE_QDS_DG=0)
 ENDIF()
 
+# =========================================================================
+# Coffee Lib
+# =========================================================================
+OPTION(CMAKE_ANS_COFFEE "Enable coffee lib" OFF)
+MARK_AS_ADVANCED(CMAKE_ANS_COFFEE)
+IF(CMAKE_ANS_COFFEE)
+  ADD_DEFINITIONS(-DUSE_COFFEE=1)
+ELSE()
+  ADD_DEFINITIONS(-DUSE_COFFEE=0)
+ENDIF()
+
 # =========================================================================
 # PICLas sources & targets
 # =========================================================================

doc/userguide/030_features_models.md

@@ -151,12 +151,12 @@ where the following pre-defined cases are available as given in table \ref{tab:d
 
 Table: Dielectric Test Cases \label{tab:dielectric_test_cases}
 
-| Option                       | Additional Parameters                           | Notes                                                                                                               |
-| :-------------------------:  | :------------------------:                        | :-------------------------------------------------------:                                                           |
-| `FishEyeLens`                | none                                            | function with radial dependence: $\varepsilon_{r}=n_{0}^{2}/(1 + (r/r_{max})^{2})^{2}$                              |
-| `Circle`                     | `DielectricRadiusValue, DielectricRadiusValueB` | Circular dielectric in x-y-direction (constant in z-direction)  with optional cut-out radius DielectricRadiusValueB |
-| `DielectricResonatorAntenna` | `DielectricRadiusValue`                         | Circular dielectric in x-y-direction (only elements with $z>0$)                                                     |
-| `FH_lens`                    | none                                            | specific geometry (see `SUBROUTINE SetGeometry` for more information)                                               |
+  | Option                       | Additional Parameters                                                   | Notes                                                                                                                                                            |
+  | :-------------------------:  | :------------------------:                                              | :-------------------------------------------------------:                                                                                                        |
+  | `FishEyeLens`                | none                                                                    | function with radial dependence: $\varepsilon_{r}=n_{0}^{2}/(1 + (r/r_{max})^{2})^{2}$                                                                           |
+  | `Circle`                     | `DielectricRadiusValue, DielectricRadiusValueB`, `DielectricCircleAxis` | Circular dielectric in x-y-direction (constant in z-direction)  with optional cut-out radius DielectricRadiusValueB along the axis given by DielectricCircleAxis |
+  | `DielectricResonatorAntenna` | `DielectricRadiusValue`                                                 | Circular dielectric in x-y-direction (only elements with $z>0$)                                                                                                  |
+  | `FH_lens`                    | none                                                                    | specific geometry (see `SUBROUTINE SetGeometry` for more information)                                                                                            |
 
 For the Maxwell solver (DGSEM), the interface fluxes between vacuum and dielectric regions can
 either be conserving or non-conserving, which is selected by
@@ -550,26 +550,25 @@ where the radius ${r=|\boldsymbol{x}-\boldsymbol{x}_{n}|}$ is the distance betwe
 grid point at position $\boldsymbol{x}$ and the $n$-th particle at position $\boldsymbol{x}_{n}$ and
 $R$ is the cut-off radius.
 
-## Background Field \label{sec:superB}
+## Magnetic Background Field (superB) \label{sec:superB}
 
-Certain application cases allow the utilization of a constant magnetic background field. The magnetic field resulting from certain types of coils and permanent magnets can be calculated during the initialization within PICLas or with the standalone tool **superB** (see Section \ref{sec:compileroptions} for compilation).
+Certain application cases allow the utilization of a constant magnetic background field. The magnetic field resulting from certain types of coils and permanent magnets can be calculated during the initialization within PICLas or with the standalone tool **superB** (see Section \ref{sec:compileroptions} for compilation), which can be used to solely create a .h5 file that contains the B-field data via
 
-The background field can be enabled by
+    superB parameter_superB.ini
+
+For usage in PICLas, the background field can be enabled by
 
     PIC-BG-Field = T
 
 The first option is to use a previously calculated background field. It can be read-in with
 
-    PIC-BGFileName = BField.h5
-    PIC-NBG = 1
-    PIC-BGFieldScaling = 1.
-
-Additionally, the polynomial degree for the background field can be set by ``PIC-NBG`` and might differ from the actually read-in polynomial degree. Optionally, the read-in field can be scaled by the last of the three parameters above.
-
-The second option is to calculate the magnetic field during the initialization, which will produce an output of the field. The calculation is enabled by
+    PIC-BGFileName     = BField.h5 ! Path to a .h5 file that contains the B-field data
+    PIC-NBG            = 1         ! Polynomial degree of the B-field
+    PIC-BGFieldScaling = 1.        ! Scaling factor for the B-field
 
-    PIC-CalcBField = T
+Additionally, the polynomial degree for the background field can be set by ``PIC-NBG`` and might differ from the actually read-in polynomial degree that is used to represent the numerical solution for the field solver. Optionally, the read-in field can be scaled by the last of the three parameters above.
 
+The second option is to calculate the magnetic field during the initialization, which will produce an output .h5 file of the field. The field will automatically be calculated from the supplied parameters, if the corresponding .h5 file does not exist.
 For this purpose, different coil and permanent magnet geometries can be defined. For visualization purposes, the geometry of the respective coils and permanent magnets can be directly written out as a VTK with
 
     PIC-CalcBField-OutputVTK = T
@@ -583,7 +582,7 @@ First, the total number of permanent magnets has to be defined and the type sele
     NumOfPermanentMagnets = 1
     PermanentMagnet1-Type = cuboid
                             sphere
-                            cylinder
+                            cylinder ! also used for hollow cylinders
                             conic
 
 All options require the input of a base/origin vector, a number of discretization nodes (results in a different number of total points depending on the chosen geometry) and a magnetisation in [A/m]
@@ -602,7 +601,8 @@ The geometries require different input parameters given below
     PermanentMagnet1-Radius = 1.
     ! Height vector required for a cylindrical and conical magnet
     PermanentMagnet1-HeightVector = (/0.,0.,1./)
-    ! Second radius only required for a conical magnet
+    ! Second radius only required for a conical magnet or a hollow cylinder with inner radius
+    ! 'Radius2' and outer radius "Radius1'
     PermanentMagnet1-Radius2 = 1.
 
 ### Magnetic Field by Coils
@@ -1008,7 +1008,7 @@ where $\mathbf{A}$ is the drift vector and $\mathcal{D}$ the diffusion matrix.
 
 The current implementation supports:
 
-- 2 different methods: Cubic (only atomic species) and Ellipsoidal Statistical (ES)
+- 2 different methods: Cubic and Ellipsoidal Statistical (ES)
 - Single species, monoatomic and polyatomic gases
 - Thermal non-equilibrium with rotational and vibrational excitation (continuous or quantized treatment)
 - 2D/Axisymmetric simulations
@@ -1028,7 +1028,7 @@ A parameter file and species initialization file is required, analogous to the D
 
     Particles-FP-CollModel = 2
 
-The **recommended method is ESFP**. The vibrational excitation can be controlled with the following flags, including the choice between continuous and quantized vibrational energy:
+The vibrational excitation can be controlled with the following flags, including the choice between continuous and quantized vibrational energy:
 
     Particles-FP-DoVibRelaxation = T
     Particles-FP-UseQuantVibEn   = T

doc/userguide/080_cluster_guide.md

@@ -2,7 +2,7 @@
 
 # Cluster guidelines \label{chap:cluster_guide}
 
-## Simulating at the HLRS \label{sec:cloninghlrs}
+## Simulating at HLRS \label{sec:cloninghlrs}
 
 Unfortunately, the GitHub and GitLab servers are not available on machines at the HLRS, such as the Hazelhen, due to restricted internet access. The workaround is to use ssh tunneling and remote forwarding to access the repositories.
 
@@ -23,6 +23,18 @@ and login with `ssh hlrs`. Now you can clone the repository when logged onto the
 
     git clone ssh://git@localhost:7777/piclas/piclas.git
 
+Note that if you experience problems when connecting, e.g., when the warning
+
+    Warning: remote port forwarding failed for listen port 7777
+
+is issued,
+you have to choose a different port, e.g., 1827 (or any other 4-digit number) and re-connect.
+If the code has already been cloned using the original port, the number of the port must be changed
+in `./git/config` to the new number for git fetch/pull operations, which would then look like
+
+    [remote "origin"]
+      url = ssh://git@localhost:1827/piclas/piclas.git
+      fetch = +refs/heads/*:refs/remotes/origin/*
 
 ### Cloning with the HTTPS protocol
 
@@ -72,7 +84,7 @@ Section last updated: 27.03.2019
 * Program has to finish normally! Enough time during execution. Note, that the profiled version is slower, hence, the testqueue is maybe too short. 
 * Visualize the *.app2 files 
 
-## Simulating at the forHLR \label{sec:forhlr}
+## Simulating at forHLR \label{sec:forhlr}
 
 For building with *CMake* on the forhlr1 cluster, the following modules (Intel compiler) should be loaded and included in the .bashrc or .profile:
 
@@ -101,7 +113,7 @@ More information about the cluster and the batch system can be found at the [For
 
 Section last updated: 27.03.2019
 
-## Simulating at the bwUniCluster \label{sec:bwuni}
+## Simulating at bwUniCluster \label{sec:bwuni}
 
 For building with *CMake* on the bwUniCluster cluster, the following modules (Intel compiler) should be loaded and included in the .bashrc or .profile:
 

ini/Particles/Cylinder/cylinder.ini

@@ -61,7 +61,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=300000
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=4
 Part-Boundary1-SourceName=BC_Inflow
 Part-Boundary1-Condition=open

ini/Particles/DSMCTest/DSMCTest.ini

@@ -74,7 +74,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=420000
 Part-nSpecies=2
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=1
 Part-Boundary1-SourceName=BC_outflow
 Part-Boundary1-Condition=open

ini/Particles/HangingParticle/parameter.ini

@@ -76,7 +76,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=4000
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=1
 Part-Boundary1-SourceName=BC_Wall
 Part-Boundary1-Condition=reflective

ini/Particles/MaxwellJuettner/maxwell_juettner.ini

@@ -64,7 +64,7 @@ mu             = 12.566370614e-7
 Part-PartLorentzType=3
 Part-maxParticleNumber=13510
 Part-nSpecies=2
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=6
 Part-Boundary1-SourceName=BC_periodicx+
 Part-Boundary1-Condition=periodic

ini/Particles/QKIonization/DSMCIonization.ini

@@ -73,7 +73,7 @@ mu             = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=1000001
 Part-nSpecies=3
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=1
 Part-Boundary1-SourceName=BC_wall
 Part-Boundary1-Condition=reflective

ini/Particles/QK_Reaction_exchange/parameter_boltzplatz.ini

@@ -75,7 +75,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=4000001
 Part-nSpecies=5
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=1
   !Part-Boundary1-SourceName=BC_outflow
   !Part-Boundary1-Condition=open

ini/Particles/SurfaceFlux/parameter_nonconform.ini

@@ -75,7 +75,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=200000
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=1
 Part-Boundary1-SourceName=BC_Wall
 Part-Boundary1-Condition=open

ini/Particles/Test_for_innerBC/parameter.ini

@@ -66,7 +66,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=500000
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 Part-nBounds              = 2
 

ini/Particles/TwoStreamInstability/twostream.ini

@@ -104,7 +104,7 @@ Part-Species3-IsImplicit=T
 Part-LorentzType=5
 Part-maxParticleNumber=5000
 Part-nSpecies=3
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=6
 Part-Boundary1-SourceName=BC_periodicx+
 Part-Boundary1-Condition=periodic

ini/Particles/Verification_for_LD/Oblique-Shock-Wave/Rampe.ini

@@ -64,7 +64,7 @@ mu         = 12.566370614e-7
 epsMapping=1e-12
 Part-maxParticleNumber=10000000
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=6
 Part-Boundary1-SourceName=OFFEN
 Part-Boundary1-Condition=open

ini/Particles/cube_test/parameter.ini

@@ -74,7 +74,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=420000
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 Part-nBounds=1
 Part-Boundary1-SourceName=BC_outflow
 Part-Boundary1-Condition=reflective

ini/Particles/mortar/Test.ini

@@ -82,7 +82,7 @@ PrecondType=2    !0: off, 1: side-block-Jacobi 2: diagonal Jacobi
 ! =============================================================================== !
 Part-maxParticleNumber=20
 Part-nSpecies=1
-Part-externalField=(/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 ;Part-nBounds=1
 ;Part-Boundary1-SourceName=BC_WALL
 ;Part-Boundary1-Condition=reflective

regressioncheck/checks/CHE_DSMC/BC_InnerReflective_8elems/externals.ini

@@ -0,0 +1,7 @@
+! --- Externals Tool Reggie
+mpirun            = 1                                              ! Single execution
+externalbinary    = ./bin/h5piclas2vtk                             ! Relative binary path in build directory
+externaldirectory = post-vtk-statefile-conversion                  ! Directory name, where the files are located for the external tool reggie
+externalruntime   = post                                           ! Run after piclas is completed (post: after, pre: before)
+cmd_suffix        = ../InnerBC_Test_State_000.00000300000000000.h5 ! Suffix for the binary execution
+cmd_pre_execute   = ln\s-s\s../cube_mesh.h5

regressioncheck/checks/CHE_DSMC/BC_InnerReflective_8elems/post-vtk-statefile-conversion/parameter.ini

@@ -0,0 +1,2 @@
+VisuParticles = T
+NVisu = 1

regressioncheck/checks/CHE_PIC_maxwell_RK4/IMD_coupling/parameter.ini

@@ -55,7 +55,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=10000000
 Part-nSpecies=5
-Part-externalField=(/0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 Part-FIBGMdeltas=(/1.35055e-8,1.35055e-8,1.35055e-8/)
 

regressioncheck/checks/CHE_poisson/poisson/parameter.ini

@@ -84,7 +84,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=5000
 Part-nSpecies=4
-Part-externalField=(/0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
   !Part-nBounds=3
   !Part-Boundary1-SourceName=BC_open
   !Part-Boundary1-Condition=open

regressioncheck/checks/NIG_PIC_poisson_Leapfrog/Dielectric_sphere_surface_charging/parameter.ini

@@ -100,7 +100,7 @@ DielectricRadiusValue = 1.0
 ! =============================================================================== !
 Part-maxParticleNumber           = 1000000
 Part-nSpecies                    = 3
-Part-externalField               = (/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 Part-FIBGMdeltas                 = (/0.05,0.05,0.05/)
 

regressioncheck/checks/NIG_PIC_poisson_Leapfrog/Dielectric_sphere_surface_charging_PStateBound/parameter.ini

@@ -100,7 +100,7 @@ DielectricRadiusValue = 1.0
 ! =============================================================================== !
 Part-maxParticleNumber           = 1000000
 Part-nSpecies                    = 3
-Part-externalField               = (/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 Part-FIBGMdeltas                 = (/0.05,0.05,0.05/)
 

regressioncheck/checks/NIG_PIC_poisson_Leapfrog/Dielectric_sphere_surface_charging_mortar/parameter.ini

@@ -99,7 +99,7 @@ DielectricRadiusValue = 1.0
 ! =============================================================================== !
 Part-maxParticleNumber           = 1000000
 Part-nSpecies                    = 3
-Part-externalField               = (/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 Part-FIBGMdeltas                 = (/0.05,0.05,0.05/)
 

regressioncheck/checks/NIG_PIC_poisson_RK3/turner/parameter.ini

@@ -78,7 +78,7 @@ mu         = 12.566370614e-7
 ! =============================================================================== !
 Part-maxParticleNumber=5000000
 Part-nSpecies=4
-Part-externalField=(/0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
   !Part-nBounds=3
   !Part-Boundary1-SourceName=BC_open
   !Part-Boundary1-Condition=open

regressioncheck/checks/NIG_Reservoir/CHEM_QK_multi-ionization_C_to_C6+/parameter.ini

@@ -128,7 +128,7 @@ Particles-DSMC-PartitionInterval= 20.
 ! PARTICLES
 ! =============================================================================== !
 Part-maxParticleNumber    = 5000000
-Part-externalField        = (/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 !PIC-Deposition-Type       = shape_function_simple
 PIC-shapefunction-alpha   = 8

regressioncheck/checks/NIG_Reservoir/RELAX_N2/parameter.ini

@@ -131,7 +131,7 @@ Particles-DSMC-PartitionInterval= 20.
 ! PARTICLES
 ! =============================================================================== !
 Part-maxParticleNumber    = 5000000
-Part-externalField        = (/0.,0.,0.,0.,0.,0.,0.,0./)
+PIC-externalField=(/0.,0.,0.,0.,0.,0./)
 
 !PIC-Deposition-Type       = shape_function_simple
 PIC-shapefunction-alpha   = 8

regressioncheck/checks/NIG_SuperB/CuboidMagnet/readme.md

@@ -1,2 +1,2 @@
 # SuperB: Cuboid permanent magnet
-* Magnetic field of a hexahedral permanent magnet below the computational domain
+* Magnetic field of a hexahedral permanent magnet that has been placed below the computational domain

regressioncheck/checks/NIG_SuperB/CylindricalMagnet/readme.md

@@ -1,2 +1,2 @@
-# SuperB: Cuboid permanent magnet
-* Magnetic field of a hexahedral permanent magnet below the computational domain
+# SuperB: Cylindrical permanent magnet
+* Magnetic field of a cylindrical permanent magnet that has been placed below the computational domain