Merge branch 'feature.waveguide' into 'master.dev'

[feature.waveguide] Maxwell Coaxial Waveguide See merge request piclas/piclas!692
piclas-framework · Dec 5, 2022 · 10cc6a1 · 10cc6a1
2 parents 4b6eee7 + 2a3a9ef
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diff --git a/REGGIE.md b/REGGIE.md
diff --git a/docs/documentation/references.bib b/docs/documentation/references.bib
@@ -804,4 +804,12 @@ @article{Wu2022
    volume = {132},
    url = {https://aip.scitation.org/doi/10.1063/5.0087909},
    year = {2022},
-}
+}
+
+@inproceedings{Schmid2009,
+  title={Dynamic mode decomposition and proper orthogonal decomposition of flow in a lid-driven cylindrical cavity},
+  author={Schmid, Peter J and Meyer, Knud Erik and Pust, Oliver},
+  booktitle={8th International Symposium on Particle Image Velocimetry},
+  pages={25--28},
+  year={2009}
+}
diff --git a/docs/documentation/userguide/features-and-models/BC-field-solver.md b/docs/documentation/userguide/features-and-models/BC-field-solver.md
@@ -25,6 +25,7 @@ include, periodic, Dirichlet, Silver-Mueller, perfectly conducting, symmetry and
 |   (/1,-1/)   | periodic  | -1: negative (opposite) direction of the 1st periodicity vector                                                           |
 |              |           |                                                                                                                           |
 |   (/2,2/)    | Dirichlet | 2: Coaxial waveguide                                                                                                      |
+|   (/2,22/)   | Dirichlet | 22: Coaxial waveguide BC (boundary condition or exact flux)                                                               |
 |   (/2,3/)    | Dirichlet | 3: Resonator                                                                                                              |
 |   (/2,4/)    | Dirichlet | 4: Electromagnetic dipole (implemented via RHS source terms and shape function deposition)                                |
 |   (/2,40/)   | Dirichlet | 40: Electromagnetic dipole without initial condition (implemented via RHS source terms and shape function deposition)     |
@@ -46,7 +47,7 @@ include, periodic, Dirichlet, Silver-Mueller, perfectly conducting, symmetry and
 |   (/6,0/)    |    SM     | 1st order absorbing BC (Silver-Mueller) - Munz et al. 2000 / Computer Physics Communication 130, 83-117 with fix          |
 |              |           | of div. correction field for low B-fields that only set the correction fields when B is significantly large compared to E |
 |              |           |                                                                                                                           |
-|   (/4,0/)    |    PEC    | Perfectly conducting surface (Munz, Omnes, Schneider 2000, pp. 97-98)                                                     |
+|   (/4,0/)    |    PEC    | Perfectly electric conducting surface (Munz, Omnes, Schneider 2000, pp. 97-98)                                            |
 |              |           |                                                                                                                           |
 |   (/10,0/)   | Symmetry  | Symmetry BC (perfect MAGNETIC conductor, PMC)                                                                             |
 |              |           |                                                                                                                           |
@@ -201,7 +202,7 @@ The dielectric module is activated by setting
 
     DoDielectric = T
 
-and specifying values for the permittivity and permeability constants
+and specifying values for the permittivity $\varepsilon_{R}$ and permeability $\mu_{R}$ constants
 
     DielectricEpsR = X
     DielectricMuR = X
@@ -255,4 +256,16 @@ setting
 
 which is set true by default, hence, removing the particles.
 
+### Dielectric Zones
+Regions or zones (corresponding to zones as defined by hopr) can also be used to define dielectrics.
+In this case, the number of zones must be supplied
 
+    DielectricNbrOfZones = 8
+
+and a vector of the same size for the corresponding zone IDs, $\varepsilon_{R}$ and $\mu_{R}$ for each zone, respectively
+
+    DielectricZoneID     = (/9   , 10  , 11  , 12  , 13  , 14  , 15  , 16/)
+    DielectricZoneEpsR   = (/2.0 , 2.0 , 2.0 , 2.0 , 2.0 , 2.0 , 2.0 , 2.0/)
+    DielectricZoneMuR    = (/1.0 , 1.0 , 1.0 , 1.0 , 1.0 , 1.0 , 1.0 , 1.0/)
+
+Note that this method cannot be used in combination with any other way of defining dielectrics.
diff --git a/docs/documentation/userguide/visu_output.md b/docs/documentation/userguide/visu_output.md
@@ -341,3 +341,83 @@ per area per second.
 
 WIP, PartAnalyze/FieldAnalyze
 
+## 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
+frequency and grow/decay rate.
+The dynamic mode decomposition (DMD) is implemented according to Schmid et al. {cite}`Schmid2009`.
+To use the DMD tool, it needs to be compiled first. In cmake, set the flag
+
+    POSTI_BUILD_DMD = ON (default is OFF)
+
+which creates the executable `./bin/dmd`.
+The input for the DMD tool is provided by a series of state files with a high temporal resolution between each output file in order
+to capture the relevant frequencies that are to be visualized.
+To analyze a specific frequency, multiple state files should be created within one period of the oscillation.
+
+Run the DMD executable with the help command to see the available options
+
+    ./dmd --help
+
+To execute the DMD after a simulation, with e.g. the Maxwell solver, run the command
+
+    dmd dmd.ini coaxial_State_000.00*
+
+with an exemplary `dmd.ini` file
+
+    N            = 4
+    SvdThreshold = 1e-8 ! Define relative lower bound of singular values
+
+where `N=4` is the polynomial degree of the solution and `SvdThreshold = 1e-8` is used to filter singular values of the DMD.
+
+Depending on the available memory one might have to decrease the number of input state files.
+After the execution two additional files **coaxial_DMD.h5** and **coaxial_DMD_Spec.dat** will be created.
+The first file contains the field representation of the different modes and the second file contains the Ritz spectrum of the modes.
+
+### Ritz spectrum (coaxial_DMD_Spec.dat)
+
+With the python script *plot_RitzSpectrum.py* the Ritz spectrum of the DMD can be plotted.
+The script is placed in the tools folder of **piclas**.
+To plot the spectrum execute:
+
+    python [PICLAS_DIRECTORY]/tools/plot_RitzSpectrum.py -d coaxial_DMD_Spec.dat
+
+The result is a Ritz spectrum depicting all the calculated modes and their growth rate.
+On the *x-axis* the frequency of the modes and on the *y-axis* the growth/decay factor is plotted, whereat modes with $\omega_r<0$
+are damped.
+The modes placed directly on the x-axis are the global, the first, the second harmonic mode and so on.
+The color and size of the plotted modes represent the Euclidian norm of the mode which can be interpreted as an energy norm of the mode.
+
+### Mode visualization (coaxial_DMD.h5)
+To visualize the field run the following command:
+
+    piclas2vtk [posti.ini] coaxial_DMD.h5
+
+The new file **coaxial_DMD_000.00000000000000000.vtu** now contains multiple modes to visualize.
+Two additional input parameters are used to control the output of `piclas2vtk` by placing them in the `posti.ini` file
+
+    dmdSingleModeOutput  = 2  ! only extract mode 002
+    dmdMaximumModeOutput = 10 ! only extract modes 001-010
+
+The parameter `dmdSingleModeOutput` is used to convert only a single specific mode to `.vtu` ignoring all other modes and
+`dmdMaximumModeOutput` can be used to dump all output modes up to this number.
+Note that each mode is written to a separate output file because a single might can become quite large very quickly and is then too
+large to visualize.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/regressioncheck/NIG_PIC_maxwell_RK4/TWT_recordpoints/parameter.ini b/regressioncheck/NIG_PIC_maxwell_RK4/TWT_recordpoints/parameter.ini
@@ -48,8 +48,7 @@ BoundaryName =BC_Outflow
 BoundaryType =(/3,0/)   ! (/Type, BCState/)
 
 TEScale        = 4e-9   !.66e-7 !3.8e-9
-TERotation     = -1
-TEPolarization = T
+TEPolarization = r ! former TERotation=T and TERotation = -1
 TEPulse        = T
 TEMode         = (/1,1/)
 
@@ -109,4 +108,4 @@ PMLzetaShape      = 1    ! shape function for damping constant (0=const, 1=linea
 PMLRampLength     = 1    ! ramping length in percent of PML width
 PMLalpha0         = 0    ! CFS-PML aplha factor for complex frequency shift
 PMLspread         = 0        ! spread=1 dont spread=0
-xyzPhysicalMinMax = (/-2.0E+00,2.0E+00,-2.0E+00,2.0E+00,0.0046,0.1932/) ! lower/upper boarder M/PHM-System
+xyzPhysicalMinMax = (/-2.0E+00,2.0E+00,-2.0E+00,2.0E+00,0.0046,0.1932/) ! lower/upper boarder M/PHM-System
diff --git a/regressioncheck/NIG_PIC_maxwell_RK4/builds.ini b/regressioncheck/NIG_PIC_maxwell_RK4/builds.ini
@@ -2,15 +2,13 @@
 binary=./bin/piclas
 
 ! fixed compiler flags
-CMAKE_BUILD_TYPE=Release
-LIBS_BUILD_HDF5  =OFF
-PICLAS_POLYNOMIAL_DEGREE=N
-
-! include combinations
-PICLAS_EQNSYSNAME=maxwell
-PICLAS_TIMEDISCMETHOD=RK4
-LIBS_USE_MPI  =ON
-PICLAS_NODETYPE=GAUSS
+CMAKE_BUILD_TYPE         = Release
+LIBS_BUILD_HDF5          = OFF
+PICLAS_POLYNOMIAL_DEGREE = N
+PICLAS_EQNSYSNAME        = maxwell
+PICLAS_TIMEDISCMETHOD    = RK4
+LIBS_USE_MPI             = ON
+PICLAS_NODETYPE          = GAUSS
 
 ! exclude combinations
 EXCLUDE:PICLAS_EQNSYSNAME=poisson,PICLAS_TIMEDISCMETHOD=DSMC

diff --git a/regressioncheck/NIG_code_analyze/Semicircle/parameter.ini b/regressioncheck/NIG_code_analyze/Semicircle/parameter.ini
@@ -1,7 +1,7 @@
 ! =============================================================================== !
 ! EQUATION (linearscalaradvection)
 ! =============================================================================== !
-IniExactFunc  = 2
+IniExactFunc  = 0
 ! =============================================================================== !
 ! DISCRETIZATION
 ! =============================================================================== !

diff --git a/regressioncheck/NIG_convtest_maxwell/builds.ini b/regressioncheck/NIG_convtest_maxwell/builds.ini
@@ -2,14 +2,14 @@
 binary=./bin/piclas
 
 ! fixed compiler flags
-CMAKE_BUILD_TYPE=Release
-LIBS_BUILD_HDF5  =OFF
-PICLAS_POLYNOMIAL_DEGREE=N
-PICLAS_EQNSYSNAME=maxwell
-PICLAS_TIMEDISCMETHOD=RK4
-LIBS_USE_MPI  =ON
-PICLAS_NODETYPE=GAUSS
-PICLAS_PARTICLES=OFF
+CMAKE_BUILD_TYPE         = Release
+LIBS_BUILD_HDF5          = OFF
+PICLAS_POLYNOMIAL_DEGREE = N
+PICLAS_EQNSYSNAME        = maxwell
+PICLAS_TIMEDISCMETHOD    = RK4
+LIBS_USE_MPI             = ON
+PICLAS_NODETYPE          = GAUSS
+PICLAS_PARTICLES         = OFF
 
 ! include combinations
 !PICLAS_TIMEDISCMETHOD=RK3,RK4, ... .. .. .. 

diff --git a/regressioncheck/NIG_convtest_maxwell/p_cylinder_TE_wave_circular/parameter.ini b/regressioncheck/NIG_convtest_maxwell/p_cylinder_TE_wave_circular/parameter.ini
@@ -36,9 +36,8 @@ BoundaryType =(/2,5/)   ! (/Type, BCState/)
 BoundaryName =BC_Outflow
 BoundaryType =(/3,0/)   ! (/Type, BCState/)
 TEScale      =2e-9 !3.8e-9
-TERotation   =-1
 TEPulse      =F
-TEPolarization=T
+TEPolarization=r ! TEPolarization=T and TERotation=-1
 ! =============================================================================== !
 ! Analysis
 ! =============================================================================== !
@@ -63,4 +62,4 @@ PMLzetaShape      = 1    ! shape function for damping constant (0=const, 1=linea
 PMLRampLength     = 1    ! ramping length in percent of PML width
 PMLalpha0         = 0.    ! CFS-PML aplha factor for complex frequency shift
 PMLspread         = 0        ! spread=1 dont spread=0
-xyzPhysicalMinMax = (/-2.0E+00,2.0E+00,-2.0E+00,2.0E+00,0.011,0.1932/) ! lower/upper boarder M/PHM-System
+xyzPhysicalMinMax = (/-2.0E+00,2.0E+00,-2.0E+00,2.0E+00,0.011,0.1932/) ! lower/upper boarder M/PHM-System
diff --git a/regressioncheck/NIG_convtest_maxwell/p_cylinder_TE_wave_linear/parameter.ini b/regressioncheck/NIG_convtest_maxwell/p_cylinder_TE_wave_linear/parameter.ini
@@ -36,9 +36,9 @@ BoundaryType =(/2,5/)   ! (/Type, BCState/)
 BoundaryName =BC_Outflow    
 BoundaryType =(/3,0/)   ! (/Type, BCState/)
 TEScale      =2e-9 !3.8e-9
-TERotation   =-1
 TEPulse      =F
-TEPolarization=F
+TEPolarization=y ! TEPolarization=F
+TEDirection=1
 ! =============================================================================== !
 ! Analysis
 ! =============================================================================== !
@@ -64,4 +64,4 @@ PMLzetaShape      = 1    ! shape function for damping constant (0=const, 1=linea
 PMLRampLength     = 1    ! ramping length in percent of PML width
 PMLalpha0         = 0.    ! CFS-PML aplha factor for complex frequency shift
 PMLspread         = 0        ! spread=1 dont spread=0
-xyzPhysicalMinMax = (/-2.0E+00,2.0E+00,-2.0E+00,2.0E+00,0.011,0.1932/) ! lower/upper boarder M/PHM-System
+xyzPhysicalMinMax = (/-2.0E+00,2.0E+00,-2.0E+00,2.0E+00,0.011,0.1932/) ! lower/upper boarder M/PHM-System
diff --git a/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/analyze.ini b/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/analyze.ini
@@ -0,0 +1,9 @@
+!L2 error norm
+analyze_L2=1e12
+
+! compare the last row in coaxial_DMD_Spec.dat with a reference file
+compare_data_file_name            = post-dmd/coaxial_DMD_Spec.dat
+compare_data_file_reference       = post-dmd/coaxial_DMD_Spec_ref.dat
+compare_data_file_tolerance       = 1e-3
+compare_data_file_tolerance_type  = relative
+compare_data_file_max_differences = 3 ! the sign in the DMD data can either be positive or negative for some values
diff --git a/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/command_line.ini b/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/command_line.ini
@@ -0,0 +1 @@
+MPI=1,8,13
diff --git a/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/cylinderNgeo2_mesh.h5 b/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/cylinderNgeo2_mesh.h5
diff --git a/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/excludeBuild.ini b/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/excludeBuild.ini
@@ -0,0 +1,2 @@
+! maxwell RK
+PICLAS_EQNSYSNAME=poisson
diff --git a/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/externals.ini b/regressioncheck/NIG_maxwell_RK4/CoaxialCable_DMD/externals.ini
@@ -0,0 +1,9 @@
+! --- Externals Tool Reggie
+MPI               =  1                                ! Single execution
+externalbinary    =  ./bin/dmd                        ! Relative binary path in build directory
+externaldirectory =  post-dmd                         ! 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        =  ../coaxial_State_000.00000*.h5   ! Suffix for the binary execution
+!cmd_pre_execute   =  pwd\s>\stest.txt                ! "\s" resembles a white space character in the command (simply using " " is not allowed)
+
+!nocrosscombination:MPI,externalbinary,externaldirectory,externalruntime,cmd_suffix,cmd_pre_execute