Added usage configs

README.md

@@ -2,9 +2,11 @@
 M++ is a parallel PDE solving software requiring some preinstalled packages. This guide hopefully walks you through the installation process.
 
 ### Prerequisites
-This version of M++ uses CMake as building tool. If you haven't installed CMake Version 3.10 or higher, find out about the installation process on https://cmake.org/download/.
+This version of M++ uses CMake as building tool. If you haven't installed CMake Version 3.15 or higher, find out about
+the installation process on https://cmake.org/download/.
 
-Furthermore, you need the packages BLAS (Basic Linear Algebra Subroutines) and LAPACK (Linear Algebra PACKage). Find out more on https://www.netlib.org/blas/ and https://www.netlib.org/lapack/.
+Furthermore, you need the packages BLAS (Basic Linear Algebra Subroutines) and LAPACK (Linear Algebra PACKage). Find out
+more on https://www.netlib.org/blas/ and https://www.netlib.org/lapack/.
 
 Most importantly, M++ is a is a parallel PDE solving software. In order to distribute your computations on parallel processes you need to have Open MPI (Message Passing Interface) installed.
 If not installed, get a version of Open MPI (e.g. 2.1) on https://www.open-mpi.org/software/ompi/v2.1/ and follow the installation instructions.

USAGE.md

+# Using CardMech-M++
+
+To use the CardMech suite, simply run
+You can run the predefined code by using the command
+
+```./M++``` or ```mpirun -n N M++```
+
+where N is the number of parallel processes you want to start.
+
+When executed, M++ searches for the ```m++.conf``` Config file in the ```conf/``` folder, which specifies all program
+arguments
+
+## .conf Files
+
+The default ```m++.conf``` specifies, which part of the CardMech suite is executed:
+
+```
+#loadconf = electrophysiology/m++.conf;
+loadconf = elasticity/m++.conf;
+#loadconf = coupled/m++.conf;
+```
+
+Only one of these configurations should be loaded at one time, as the different configurations may interfere with each
+other
+
+### Problems
+
+Problems are categorized in elasticity, electrophysiological and coupled problems. They are loaded with the following
+commands:
+
+```
+MechProblem = Default
+ElphyProblem = TetraTestProblem
+CoupledProblem = BiventricleCoarse
+```

conf/coupled/gamm-paper/coarse-biventricle.conf

+Model = Coupled
+CoupledModel = Segregated
+
+#CoupledProblem = BiventricleCoarse
+
+ElphyModelClass = MElphyModel
+ElphyModelName = TenTusscher
+TensionModelName = Rossi
+RossiViscosity = 11.0
+RossiForce = 6.0
+
+ElphyLevel = 3
+MechLevel = 1
+MechPolynomialDegree = 1
+ElphyPolynomialDegree = 1
+
+######################
+#      Time          #
+######################
+StartTime = 0.0
+
+#EndTime=0.00001
+EndTime = 0.8
+#EndTime = 0.02
+
+MechDeltaTime = 0.004
+ElphyDeltaTime = 0.0001
+
+DeltaTime = 0.0001
+DeltaTimeMin = 0.00001
+DeltaTimeMax = 0.001
+
+######################
+#      Plotting      #
+######################
+PlottingSteps = 1
+
+#######################
+#     Coupled Data    #
+#######################
+ClearDistribution = 0
+
+
+MechDiscretization = Conforming
+MechRuntype = Default
+MechDynamics = Newmark
+#MechDynamics = RayleighNewmark
+#MechDynamics = ViscoNewmark
+
+#------------------------
+# Newmark Parameters
+#------------------------
+# Damped Newmark
+NewmarkBeta = 0.4
+NewmarkGamma = 0.7
+# Undamped Newmark
+#NewmarkBeta = 0.25
+#NewmarkGamma = 0.5
+
+
+
+# Amount of pressure steps per iteration
+PressureSteps = 1
+# If Iteration with Pressuresteps fails, recursively restart PressureSolver with Steps*2 until iteration limit is reached
+PressureIterations = 10
+PressureDepth = 0
+
+WithPrestress=true
+PrestressSteps=10
+
+######################
+#       Meshes       #
+######################
+MechMeshPart = with_vessels
+MechMeshPart = vessel_base
+
+StartTime = 0.0
+EndTime = 0.4
+DeltaTime = 0.001
+DeltaTimeMin = 0.0001
+DeltaTimeMax = 0.001
+
+
+TractionK = 0.1
+TractionC = 1e-3
+
+
+#------------------------
+# Stretch Parameters
+#------------------------
+StretchFactorSheet = 4.0
+StretchFactorNormal = 4.0
+
+
+######################
+# Material Parameters#
+######################
+Density = 0.001082
+#------------------------
+# Volumetric Penalty
+# Incompressible should be true or false
+# Penalty Types: None, Ciarlet, Mixed
+#------------------------
+VolumetricSplit = 0
+Incompressible = false
+QuasiCompressiblePenalty = Ciarlet #None, Ciarlet, Mixed
+VolumetricPenalty = 20
+PermeabilityPenalty = 20
+
+DGSign=-1.0
+DGPenalty=20.0
+
+ElphyModel = SemiImplicit
+OrderStaggeredScheme=wcV
+ReassembleRHSonce=1
+
+CrankNicolsonTheta = 0.5
+ElphySplittingMethod =Godunov  #Strang, Stein,Godunov
+
+#Iext splitted in PDE =1, Iext in ODE =0
+IextInPDE=1
+#Glaettung von Anregung  in Zeit: Stepfunction,Arctan,Tanh
+ExternalCurrentSmoothingInTime = Arctan
+#Glättung Anregung im Raum: discrete, linear
+ExternalCurrentSmoothingInSpace = linear
+
+ElphyMeshPart = ventriclesonly
+
+
+# Monodomain Parameters
+SurfaceToVolumeRatio= 140#1/mm
+MembraneCapacitance=0.01#muF/mm^2
+
+IntraLongitudinal = 0.170
+ExtraLongitudinal = 0.620
+IntraTransversal = 0.019
+ExtraTransversal = 0.240
+
+ElphyIntegrator=ExplicitEuler
+CellModelScheme = ExponentialIntegrator
+IonScheme = RungeKutta2 # ExplicitEuler,RungeKutta2,RungeKutta4
+
+ThresholdVForActivation=-40.0
+ScaleExcitationAmplitude=0.04101
+
+EulerReAssemble = 0
+
+SetSolution = 0
+
+# === Linear Solver === #
+LinearSolver = gmres
+LinearEpsilon = 1e-8
+LinearReduction = 1e-8
+LinearReduction = 1e-11
+LinearSteps = 10000
+BasePreconditioner = GaussSeidel
+Preconditioner = GaussSeidel
+Preconditioner = LIB_PS
+
+# =================================================================
+# === Gating Solver ===============================================
+GatingSolver = gmres
+GatingPreconditioner = GaussSeidel
+GatingEpsilon = 1e-8
+GatingReduction = 1e-12
+
+# === Elphy Solver ================================================
+ElphySolver = gmres
+ElphyPreconditioner=Jacobi
+ElphyEpsilon = 1e-8
+ElphyReduction = 1e-12
+
+# === Mechanics Solver ============================================
+MechSolver = gmres
+MechPreconditioner = GaussSeidel
+MechEpsilon = 1e-8
+MechReduction = 1e-12
+MechSteps = 20000
+
+# === Newton Method === #
+NewtonEpsilon = 1e-6
+NewtonReduction = 1e-12
+NewtonSteps = 300
+NewtonLineSearchSteps = 10
+NewtonLinearizationReduction = 1e-12
+
+#Smoother = GaussSeidel
+#Smoother = PointBlockGaussSeidel
+#SmootherDamp = 0.9
+presmoothing = 3
+postsmoothing = 3
+
+ConfigVerbose = 1
+AssembleVerbose = 1
+
+# = Solver Verbose =
+MultigridVerbose = 0
+BaseSolverVerbose = -1
+LinearVerbose = -5
+NewtonVerbose = 0
+EulerVerbose = 0
+LinearImplicitVerbose = -5
+ElphyLinearSolverVerbose =-1
+MonodomainVerbose =-1
+NonLinearVerbose = -5
+ElphySolverVerbose = 0
+CoupledSolverVerbose = 4
+CellModelVerbose = 0
+
+# = Main Verbose =
+ElphyVerbose = 1
+MechVerbose = 1
+
+# = Plot Verbose =
+ElphyVTK = 0 # 0 Disables all plots from Electrophysiology
+MechVTK = 1 # 0 Disables all plots from Elasticity
+
+# = Plot Verbose =
+PressureSolverVTK = 0
+DynamicSolverVTK = 1
+ElphySolverVTK = 0
+CoupledSolverVTK = 1
+
+PlotVTK = 1