From 5b3c9f93d81c2ac3296a9d85b1eb9a6df40fd26b Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Thu, 18 Mar 2021 16:14:21 +0100
Subject: [PATCH 1/9] Update script and merged parameter files for deal.II

---
 .../solid-dealii/nonlinear_elasticity.prm     | 81 -------------------
 .../{linear_elasticity.prm => parameters.prm} | 30 ++++---
 perpendicular-flap/solid-dealii/run.sh        | 18 +----
 3 files changed, 20 insertions(+), 109 deletions(-)
 delete mode 100644 perpendicular-flap/solid-dealii/nonlinear_elasticity.prm
 rename perpendicular-flap/solid-dealii/{linear_elasticity.prm => parameters.prm} (73%)

diff --git a/perpendicular-flap/solid-dealii/nonlinear_elasticity.prm b/perpendicular-flap/solid-dealii/nonlinear_elasticity.prm
deleted file mode 100644
index cb760534e..000000000
--- a/perpendicular-flap/solid-dealii/nonlinear_elasticity.prm
+++ /dev/null
@@ -1,81 +0,0 @@
-# Listing of Parameters
-# Dimensional quantities are in SI units
-# --------------------------------------
-
-subsection Time
-  # End time
-  set End time        = 5 
-
-  # Time step size
-  set Time step size  = 0.01
-
-  # Output interval
-  set Output interval = 10
-end
-
-subsection Discretization
-  # Newmark beta
-  set beta  = 0.25
-
-  # Newmark gamma
-  set gamma   = 0.5
-
-  # Polynomial degree of the FE system
-  set Polynomial degree   = 4
-end
-
-subsection System properties
-  # Poisson's ratio
-  set Poisson's ratio = 0.3
-
-  # Shear modulus
-  set Shear modulus   = 1538462
-
-  # Density
-  set rho	      = 3000
-
-  # Body forces x,y,z
-  set body forces     = 0.0,0.0,0.0
-end
-
-subsection Linear solver
-  # Linear solver iterations (multiples of the system matrix size)
-  set Max iteration multiplier  = 1
-
-  # Linear solver residual (scaled by residual norm)
-  set Residual                  = 1e-6
-
-  # Linear solver: CG or Direct
-  set Solver type               = Direct
-end
-
-subsection Nonlinear solver
-  # Number of Newton-Raphson iterations allowed
-  set Max iterations Newton-Raphson = 10
-
-  # Displacement error tolerance
-  set Tolerance displacement        = 1.0e-6
-
-  # Force residual tolerance
-  set Tolerance force               = 1.0e-9
-end
-
-subsection precice configuration
-    # Cases: FSI3 or PF for perpendicular flap
-    set Scenario            = PF
-
-    # Name of the precice configuration file
-    set precice config-file = ../precice-config.xml
-
-    # Name of the participant in the precice-config.xml file
-    set Participant name    = Solid
-
-    # Name of the coupling mesh in the precice-config.xml file
-    set Mesh name           = Solid-Mesh
-
-    # Name of the read data in the precice-config.xml file
-    set Read data name      = Force
-
-    # Name of the write data in the precice-config.xml file
-    set Write data name     = Displacement
-end
diff --git a/perpendicular-flap/solid-dealii/linear_elasticity.prm b/perpendicular-flap/solid-dealii/parameters.prm
similarity index 73%
rename from perpendicular-flap/solid-dealii/linear_elasticity.prm
rename to perpendicular-flap/solid-dealii/parameters.prm
index 91b5bb05c..1aea26c27 100644
--- a/perpendicular-flap/solid-dealii/linear_elasticity.prm
+++ b/perpendicular-flap/solid-dealii/parameters.prm
@@ -14,29 +14,28 @@ subsection Time
 end
 
 subsection Discretization
-  # Time integration scheme
-  # 0 = forward, 1 = backward
-  set theta               = 0.5
-
   # Polynomial degree of the FE system
   set Polynomial degree   = 4
 end
 
 subsection System properties
-  # mu (shear modulus)
-  set mu              = 1538462
+  # Poisson's ratio
+  set Poisson's ratio = 0.3
 
-  # lambda
-  set lambda          = 2307692
+  # Shear modulus
+  set Shear modulus   = 1538462
 
-  # density
+  # Density
   set rho             = 3000
 
-  # body forces x,y,z
+  # Body forces x,y,z
   set body forces     = 0.0,0.0,0.0
 end
 
-subsection Linear solver
+subsection Solver
+  # Structural model to be used: linear or neo-Hookean
+  set Model                     = linear
+
   # Linear solver iterations (multiples of the system matrix size)
   set Max iteration multiplier  = 1
 
@@ -45,6 +44,15 @@ subsection Linear solver
 
   # Linear solver: CG or Direct
   set Solver type               = Direct
+
+  # Number of Newton-Raphson iterations allowed
+  set Max iterations Newton-Raphson = 10
+
+  # Displacement error tolerance
+  set Tolerance displacement        = 1.0e-6
+
+  # Force residual tolerance
+  set Tolerance force               = 1.0e-9
 end
 
 subsection precice configuration
diff --git a/perpendicular-flap/solid-dealii/run.sh b/perpendicular-flap/solid-dealii/run.sh
index 7eb9e4d94..80cdec87d 100755
--- a/perpendicular-flap/solid-dealii/run.sh
+++ b/perpendicular-flap/solid-dealii/run.sh
@@ -7,21 +7,5 @@ cd ${0%/*} || exit 1    		    # Run from this directory
 # in another terminal.
 # These scripts present how the two participants would be started manually.
 
-# 1 for true, 0 for false
-nonlinear=0
-if [ "$1" = "-nonlinear" ]; then
-            nonlinear=1
-fi
+./elasticity parameters.prm
 
-linear=0
-if [ "$1" = "-linear" ]; then
-            linear=1
-fi
-
-if [ $linear -eq 1 ]; then
-        ./linear_elasticity linear_elasticity.prm
-elif [ $nonlinear -eq 1 ]; then
-        ./nonlinear_elasticity nonlinear_elasticity.prm
-else
-        echo "No solver type specified. Please specify -linear or -nonlinear as solver type"
-fi

From ed5f7f570194486421c1cefb481d819228ae8fcd Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Sun, 21 Mar 2021 14:19:07 +0100
Subject: [PATCH 2/9] Apply suggestions from code review

---
 .../solid-dealii/parameters.prm               | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/perpendicular-flap/solid-dealii/parameters.prm b/perpendicular-flap/solid-dealii/parameters.prm
index 1aea26c27..697bc6f47 100644
--- a/perpendicular-flap/solid-dealii/parameters.prm
+++ b/perpendicular-flap/solid-dealii/parameters.prm
@@ -34,24 +34,25 @@ end
 
 subsection Solver
   # Structural model to be used: linear or neo-Hookean
-  set Model                     = linear
+  set Model                     = neo-Hookean
 
-  # Linear solver iterations (multiples of the system matrix size)
+  # Linear solver: CG or Direct
+  set Solver type               = Direct
+
+  # Max CG solver iterations (multiples of the system matrix size)
+  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
   set Max iteration multiplier  = 1
 
-  # Linear solver residual (scaled by residual norm)
+  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
   set Residual                  = 1e-6
 
-  # Linear solver: CG or Direct
-  set Solver type               = Direct
-
-  # Number of Newton-Raphson iterations allowed
+  # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
   set Max iterations Newton-Raphson = 10
 
-  # Displacement error tolerance
+  # Relative displacement error tolerance for non-linear iteration (ignored if Model == linear)
   set Tolerance displacement        = 1.0e-6
 
-  # Force residual tolerance
+  # Relative force residual tolerance for non-linear iteration (ignored if Model == linear)
   set Tolerance force               = 1.0e-9
 end
 

From 9675bca3dd3c72f92a45ffb8fa86c76cb701a06e Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Sun, 21 Mar 2021 15:07:23 +0100
Subject: [PATCH 3/9] Update parameter files

---
 .../solid-left-dealii/linear_elasticity.prm   | 71 -----------------
 ...onlinear_elasticity.prm => parameters.prm} | 40 +++++-----
 .../solid-right-dealii/linear_elasticity.prm  | 71 -----------------
 ...onlinear_elasticity.prm => parameters.prm} | 40 +++++-----
 .../solid-dealii/parameters.prm               |  2 +-
 turek-hron-fsi3/solid-dealii/parameters.prm   | 77 +++++++++++++++++++
 6 files changed, 114 insertions(+), 187 deletions(-)
 delete mode 100644 multiple-perpendicular-flaps/solid-left-dealii/linear_elasticity.prm
 rename multiple-perpendicular-flaps/solid-left-dealii/{nonlinear_elasticity.prm => parameters.prm} (65%)
 delete mode 100644 multiple-perpendicular-flaps/solid-right-dealii/linear_elasticity.prm
 rename multiple-perpendicular-flaps/solid-right-dealii/{nonlinear_elasticity.prm => parameters.prm} (65%)
 create mode 100644 turek-hron-fsi3/solid-dealii/parameters.prm

diff --git a/multiple-perpendicular-flaps/solid-left-dealii/linear_elasticity.prm b/multiple-perpendicular-flaps/solid-left-dealii/linear_elasticity.prm
deleted file mode 100644
index 019f7f406..000000000
--- a/multiple-perpendicular-flaps/solid-left-dealii/linear_elasticity.prm
+++ /dev/null
@@ -1,71 +0,0 @@
-# Listing of Parameters
-# Dimensional quantities are in SI units
-# --------------------------------------
-
-subsection Time
-  # End time
-  set End time        = 5 
-
-  # Time step size
-  set Time step size  = 0.01
-
-  # Write results every x timesteps
-  set Output interval       = 10
-end
-
-subsection Discretization
-  # Time integration scheme
-  # 0 = forward, 1 = backward
-  set theta               = 0.5
-
-  # Polynomial degree of the FE system
-  set Polynomial degree   = 4
-end
-
-subsection System properties
-  # mu (shear modulus)
-  set mu              = 153846
-
-  # lambda
-  set lambda          = 230769
-
-  # density
-  set rho             = 3000
-
-  # body forces x,y,z
-  set body forces     = 0.0,0.0,0.0
-end
-
-subsection Linear solver
-  # Linear solver iterations (multiples of the system matrix size)
-  set Max iteration multiplier  = 1
-
-  # Linear solver residual (scaled by residual norm)
-  set Residual                  = 1e-6
-
-  # Linear solver: CG or Direct
-  set Solver type               = Direct
-end
-
-subsection precice configuration
-  # Cases: FSI3 or PF for perpendicular flap
-  set Scenario            = PF
-
-  # Name of the precice configuration file
-  set precice config-file = ../precice-config.xml
-
-  # Name of the participant in the precice-config.xml file
-  set Participant name    = Solid1
-
-  # Name of the coupling mesh in the precice-config.xml file
-  set Mesh name           = Solid1-Mesh
-
-  # Name of the read data in the precice-config.xml file
-  set Read data name      = Stress1
-
-  # Name of the write data in the precice-config.xml file
-  set Write data name     = Displacement1
-  
-  # PF x-location 
-  set Flap location     = -1.0
-end
diff --git a/multiple-perpendicular-flaps/solid-left-dealii/nonlinear_elasticity.prm b/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
similarity index 65%
rename from multiple-perpendicular-flaps/solid-left-dealii/nonlinear_elasticity.prm
rename to multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
index cf1d4fdab..d8740f772 100644
--- a/multiple-perpendicular-flaps/solid-left-dealii/nonlinear_elasticity.prm
+++ b/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
@@ -9,54 +9,50 @@ subsection Time
   # Time step size
   set Time step size  = 0.01
 
-  # Output interval
-  set Output interval = 10
+  # Write results every x timesteps
+  set Output interval       = 10
 end
 
 subsection Discretization
-  # Newmark beta
-  set beta  = 0.25
-
-  # Newmark gamma
-  set gamma   = 0.5
-
   # Polynomial degree of the FE system
   set Polynomial degree   = 4
 end
 
 subsection System properties
   # Poisson's ratio
-  set Poisson's ratio = 0.375
+  set Poisson's ratio = 0.3
 
   # Shear modulus
-  set Shear modulus   = 153846
+  set Shear modulus   = 1538462
 
   # Density
-  set rho	      = 3000
+  set rho             = 3000
 
   # Body forces x,y,z
   set body forces     = 0.0,0.0,0.0
 end
 
-subsection Linear solver
-  # Linear solver iterations (multiples of the system matrix size)
-  set Max iteration multiplier  = 1
-
-  # Linear solver residual (scaled by residual norm)
-  set Residual                  = 1e-6
+subsection Solver
+  # Structural model to be used: linear or neo-Hookean
+  set Model                     = linear
 
   # Linear solver: CG or Direct
   set Solver type               = Direct
-end
 
-subsection Nonlinear solver
-  # Number of Newton-Raphson iterations allowed
+  # Max CG solver iterations (multiples of the system matrix size)
+  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  set Max iteration multiplier  = 1
+
+  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  set Residual                  = 1e-6
+
+  # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
   set Max iterations Newton-Raphson = 10
 
-  # Displacement error tolerance
+  # Relative displacement error tolerance for non-linear iteration (ignored if Model == linear)
   set Tolerance displacement        = 1.0e-6
 
-  # Force residual tolerance
+  # Relative force residual tolerance for non-linear iteration (ignored if Model == linear)
   set Tolerance force               = 1.0e-9
 end
 
diff --git a/multiple-perpendicular-flaps/solid-right-dealii/linear_elasticity.prm b/multiple-perpendicular-flaps/solid-right-dealii/linear_elasticity.prm
deleted file mode 100644
index e5cab3f73..000000000
--- a/multiple-perpendicular-flaps/solid-right-dealii/linear_elasticity.prm
+++ /dev/null
@@ -1,71 +0,0 @@
-# Listing of Parameters
-# Dimensional quantities are in SI units
-# --------------------------------------
-
-subsection Time
-  # End time
-  set End time        = 5 
-
-  # Time step size
-  set Time step size  = 0.01
-
-  # Write results every x timesteps
-  set Output interval       = 10
-end
-
-subsection Discretization
-  # Time integration scheme
-  # 0 = forward, 1 = backward
-  set theta               = 0.5
-
-  # Polynomial degree of the FE system
-  set Polynomial degree   = 4
-end
-
-subsection System properties
-  # mu (shear modulus)
-  set mu              = 153846
-
-  # lambda
-  set lambda          = 230769
-
-  # density
-  set rho             = 3000
-
-  # body forces x,y,z
-  set body forces     = 0.0,0.0,0.0
-end
-
-subsection Linear solver
-  # Linear solver iterations (multiples of the system matrix size)
-  set Max iteration multiplier  = 1
-
-  # Linear solver residual (scaled by residual norm)
-  set Residual                  = 1e-6
-
-  # Linear solver: CG or Direct
-  set Solver type               = Direct
-end
-
-subsection precice configuration
-  # Cases: FSI3 or PF for perpendicular flap
-  set Scenario            = PF
-
-  # Name of the precice configuration file
-  set precice config-file = ../precice-config.xml
-
-  # Name of the participant in the precice-config.xml file
-  set Participant name    = Solid2
-
-  # Name of the coupling mesh in the precice-config.xml file
-  set Mesh name           = Solid2-Mesh
-
-  # Name of the read data in the precice-config.xml file
-  set Read data name      = Stress2
-
-  # Name of the write data in the precice-config.xml file
-  set Write data name     = Displacement2
-  
-  # PF x-location 
-  set Flap location     = 1.0
-end
diff --git a/multiple-perpendicular-flaps/solid-right-dealii/nonlinear_elasticity.prm b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
similarity index 65%
rename from multiple-perpendicular-flaps/solid-right-dealii/nonlinear_elasticity.prm
rename to multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
index f0f1289ee..4df8bf180 100644
--- a/multiple-perpendicular-flaps/solid-right-dealii/nonlinear_elasticity.prm
+++ b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
@@ -9,54 +9,50 @@ subsection Time
   # Time step size
   set Time step size  = 0.01
 
-  # Output interval
-  set Output interval = 10
+  # Write results every x timesteps
+  set Output interval       = 10
 end
 
 subsection Discretization
-  # Newmark beta
-  set beta  = 0.25
-
-  # Newmark gamma
-  set gamma   = 0.5
-
   # Polynomial degree of the FE system
   set Polynomial degree   = 4
 end
 
 subsection System properties
   # Poisson's ratio
-  set Poisson's ratio = 0.375
+  set Poisson's ratio = 0.3
 
   # Shear modulus
-  set Shear modulus   = 153846
+  set Shear modulus   = 1538462
 
   # Density
-  set rho	      = 3000
+  set rho             = 3000
 
   # Body forces x,y,z
   set body forces     = 0.0,0.0,0.0
 end
 
-subsection Linear solver
-  # Linear solver iterations (multiples of the system matrix size)
-  set Max iteration multiplier  = 1
-
-  # Linear solver residual (scaled by residual norm)
-  set Residual                  = 1e-6
+subsection Solver
+  # Structural model to be used: linear or neo-Hookean
+  set Model                     = linear
 
   # Linear solver: CG or Direct
   set Solver type               = Direct
-end
 
-subsection Nonlinear solver
-  # Number of Newton-Raphson iterations allowed
+  # Max CG solver iterations (multiples of the system matrix size)
+  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  set Max iteration multiplier  = 1
+
+  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  set Residual                  = 1e-6
+
+  # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
   set Max iterations Newton-Raphson = 10
 
-  # Displacement error tolerance
+  # Relative displacement error tolerance for non-linear iteration (ignored if Model == linear)
   set Tolerance displacement        = 1.0e-6
 
-  # Force residual tolerance
+  # Relative force residual tolerance for non-linear iteration (ignored if Model == linear)
   set Tolerance force               = 1.0e-9
 end
 
diff --git a/perpendicular-flap/solid-dealii/parameters.prm b/perpendicular-flap/solid-dealii/parameters.prm
index 697bc6f47..d26dd7870 100644
--- a/perpendicular-flap/solid-dealii/parameters.prm
+++ b/perpendicular-flap/solid-dealii/parameters.prm
@@ -34,7 +34,7 @@ end
 
 subsection Solver
   # Structural model to be used: linear or neo-Hookean
-  set Model                     = neo-Hookean
+  set Model                     = linear
 
   # Linear solver: CG or Direct
   set Solver type               = Direct
diff --git a/turek-hron-fsi3/solid-dealii/parameters.prm b/turek-hron-fsi3/solid-dealii/parameters.prm
new file mode 100644
index 000000000..3c41041ec
--- /dev/null
+++ b/turek-hron-fsi3/solid-dealii/parameters.prm
@@ -0,0 +1,77 @@
+# Listing of Parameters
+# Dimensional quantities are in SI units
+# --------------------------------------
+
+subsection Time
+  # End time
+  set End time        = 15
+
+  # Time step size
+  set Time step size  = 0.001
+
+  # Write results every x timesteps
+  set Output interval       = 100
+end
+
+subsection Discretization
+  # Polynomial degree of the FE system
+  set Polynomial degree   = 4
+end
+
+subsection System properties
+  # Poisson's ratio
+  set Poisson's ratio = 0.4
+
+  # Shear modulus
+  set Shear modulus   = 2.0e6
+
+  # Density
+  set rho             = 1000
+
+  # Body forces x,y,z
+  set body forces     = 0.0,0.0,0.0
+end
+
+subsection Solver
+  # Structural model to be used: linear or neo-Hookean
+  set Model                     = neo-Hookean
+
+  # Linear solver: CG or Direct
+  set Solver type               = Direct
+
+  # Max CG solver iterations (multiples of the system matrix size)
+  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  set Max iteration multiplier  = 1
+
+  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  set Residual                  = 1e-6
+
+  # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
+  set Max iterations Newton-Raphson = 10
+
+  # Relative displacement error tolerance for non-linear iteration (ignored if Model == linear)
+  set Tolerance displacement        = 1.0e-6
+
+  # Relative force residual tolerance for non-linear iteration (ignored if Model == linear)
+  set Tolerance force               = 1.0e-9
+end
+
+subsection precice configuration
+  # Cases: FSI3 or PF for perpendicular flap
+  set Scenario            = FSI3
+
+  # Name of the precice configuration file
+  set precice config-file = ../precice-config.xml
+
+  # Name of the participant in the precice-config.xml file
+  set Participant name    = Solid
+
+  # Name of the coupling mesh in the precice-config.xml file
+  set Mesh name           = Solid-Mesh
+
+  # Name of the read data in the precice-config.xml file
+  set Read data name      = Stress
+
+  # Name of the write data in the precice-config.xml file
+  set Write data name     = Displacement
+end

From b97c8599e69026f5a858152d1e579e33d227a393 Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Sun, 21 Mar 2021 15:07:57 +0100
Subject: [PATCH 4/9] Remove duplicated parameter file

---
 .../solid-dealii/nonlinear_elasticity.prm     | 81 -------------------
 1 file changed, 81 deletions(-)
 delete mode 100644 turek-hron-fsi3/solid-dealii/nonlinear_elasticity.prm

diff --git a/turek-hron-fsi3/solid-dealii/nonlinear_elasticity.prm b/turek-hron-fsi3/solid-dealii/nonlinear_elasticity.prm
deleted file mode 100644
index 00167df21..000000000
--- a/turek-hron-fsi3/solid-dealii/nonlinear_elasticity.prm
+++ /dev/null
@@ -1,81 +0,0 @@
-# Listing of Parameters
-# Dimensional quantities are in SI units
-# --------------------------------------
-
-subsection Time
-  # End time
-  set End time        = 15
-
-  # Time step size
-  set Time step size  = 0.001
-
-  # Output interval
-  set Output interval = 100
-end
-
-subsection Discretization
-  # Newmark beta
-  set beta    = 0.25
-
-  # Newmark gamma
-  set gamma   = 0.5
-
-  # Polynomial degree of the FE system
-  set Polynomial degree   = 4
-end
-
-subsection System properties
-  # Poisson's ratio
-  set Poisson's ratio = 0.4
-
-  # Shear modulus
-  set Shear modulus   = 2.0e6
-
-  # Density
-  set rho	      = 1000
-
-  # Body forces x,y,z
-  set body forces     = 0.0,0.0,0.0
-end
-
-subsection Linear solver
-  # Linear solver iterations (multiples of the system matrix size)
-  set Max iteration multiplier  = 1
-
-  # Linear solver residual (scaled by residual norm)
-  set Residual                  = 1e-6
-
-  # Linear solver: CG or Direct
-  set Solver type               = Direct
-end
-
-subsection Nonlinear solver
-  # Number of Newton-Raphson iterations allowed
-  set Max iterations Newton-Raphson = 10
-
-  # Displacement error tolerance
-  set Tolerance displacement        = 1.0e-6
-
-  # Force residual tolerance
-  set Tolerance force               = 1.0e-9
-end
-
-subsection precice configuration
-  # Cases: FSI3 or PF for perpendicular flap
-  set Scenario            = FSI3
-
-  # Name of the precice configuration file
-  set precice config-file = ../precice-config.xml
-
-  # Name of the participant in the precice-config.xml file
-  set Participant name    = Solid
-
-  # Name of the coupling mesh in the precice-config.xml file
-  set Mesh name           = Solid-Mesh
-
-  # Name of the read data in the precice-config.xml file
-  set Read data name      = Stress
-
-  # Name of the write data in the precice-config.xml file
-  set Write data name     = Displacement
-end

From 3d1f49eec16e616281c1a819b3ad6c5c52dfb840 Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Sun, 21 Mar 2021 15:40:27 +0100
Subject: [PATCH 5/9] Update run scripts

---
 .../solid-left-dealii/run.sh                  | 39 ++++++++++---------
 .../solid-right-dealii/run.sh                 | 39 ++++++++++---------
 perpendicular-flap/solid-dealii/run.sh        | 21 +++++++++-
 3 files changed, 62 insertions(+), 37 deletions(-)

diff --git a/multiple-perpendicular-flaps/solid-left-dealii/run.sh b/multiple-perpendicular-flaps/solid-left-dealii/run.sh
index 57978366e..03c71ca0f 100755
--- a/multiple-perpendicular-flaps/solid-left-dealii/run.sh
+++ b/multiple-perpendicular-flaps/solid-left-dealii/run.sh
@@ -1,27 +1,30 @@
 #!/bin/bash
 cd ${0%/*} || exit 1    		    # Run from this directory
 
-# Solid1 participant 
+# Solid participant
 
 # Run this script in one terminal and the execute the Fluid participant 
-# and the Solid2 participant in another terminal.
-# These scripts present how the three participants would be started manually.
+# in another terminal.
+# These scripts present how the two participants would be started manually.
 
-# 1 for true, 0 for false
-nonlinear=0
-if [ "$1" = "-nonlinear" ]; then
-            nonlinear=1
-fi
+for i in "$@"
+do
+case $i in
+    -p=*|--prefix=*)
+    SEARCHPATH="${i#*=}"
+    shift # past argument=value
+    ;;
+    *)
+      # unknown option
+    ;;
+esac
+done
 
-linear=0
-if [ "$1" = "-linear" ]; then
-            linear=1
+if test -f "elasticity"; then
+    ./elasticity parameters.prm
+    elif [ ! -z ${SEARCHPATH} ]; then
+    ${SEARCHPATH}/elasticity parameters.prm
+    else
+    echo "Unable to find the executable 'elasticity'. Either specify a prefix (-p=/path/to/elasticity) or make it discoverable at runtime (e.g. export PATH)"
 fi
 
-if [ $linear -eq 1 ]; then
-        ./linear_elasticity linear_elasticity.prm
-elif [ $nonlinear -eq 1 ]; then
-        ./nonlinear_elasticity nonlinear_elasticity.prm
-else
-        echo "No solver type specified. Please specify -linear or -nonlinear as solver type"
-fi
diff --git a/multiple-perpendicular-flaps/solid-right-dealii/run.sh b/multiple-perpendicular-flaps/solid-right-dealii/run.sh
index c85f04d60..03c71ca0f 100755
--- a/multiple-perpendicular-flaps/solid-right-dealii/run.sh
+++ b/multiple-perpendicular-flaps/solid-right-dealii/run.sh
@@ -1,27 +1,30 @@
 #!/bin/bash
 cd ${0%/*} || exit 1    		    # Run from this directory
 
-# Solid2 participant
+# Solid participant
 
 # Run this script in one terminal and the execute the Fluid participant 
-# and the Solid1 participant in another terminal.
-# These scripts present how the three participants would be started manually.
+# in another terminal.
+# These scripts present how the two participants would be started manually.
 
-# 1 for true, 0 for false
-nonlinear=0
-if [ "$1" = "-nonlinear" ]; then
-            nonlinear=1
-fi
+for i in "$@"
+do
+case $i in
+    -p=*|--prefix=*)
+    SEARCHPATH="${i#*=}"
+    shift # past argument=value
+    ;;
+    *)
+      # unknown option
+    ;;
+esac
+done
 
-linear=0
-if [ "$1" = "-linear" ]; then
-            linear=1
+if test -f "elasticity"; then
+    ./elasticity parameters.prm
+    elif [ ! -z ${SEARCHPATH} ]; then
+    ${SEARCHPATH}/elasticity parameters.prm
+    else
+    echo "Unable to find the executable 'elasticity'. Either specify a prefix (-p=/path/to/elasticity) or make it discoverable at runtime (e.g. export PATH)"
 fi
 
-if [ $linear -eq 1 ]; then
-        ./linear_elasticity linear_elasticity.prm
-elif [ $nonlinear -eq 1 ]; then
-        ./nonlinear_elasticity nonlinear_elasticity.prm
-else
-        echo "No solver type specified. Please specify -linear or -nonlinear as solver type"
-fi
diff --git a/perpendicular-flap/solid-dealii/run.sh b/perpendicular-flap/solid-dealii/run.sh
index 80cdec87d..03c71ca0f 100755
--- a/perpendicular-flap/solid-dealii/run.sh
+++ b/perpendicular-flap/solid-dealii/run.sh
@@ -7,5 +7,24 @@ cd ${0%/*} || exit 1    		    # Run from this directory
 # in another terminal.
 # These scripts present how the two participants would be started manually.
 
-./elasticity parameters.prm
+for i in "$@"
+do
+case $i in
+    -p=*|--prefix=*)
+    SEARCHPATH="${i#*=}"
+    shift # past argument=value
+    ;;
+    *)
+      # unknown option
+    ;;
+esac
+done
+
+if test -f "elasticity"; then
+    ./elasticity parameters.prm
+    elif [ ! -z ${SEARCHPATH} ]; then
+    ${SEARCHPATH}/elasticity parameters.prm
+    else
+    echo "Unable to find the executable 'elasticity'. Either specify a prefix (-p=/path/to/elasticity) or make it discoverable at runtime (e.g. export PATH)"
+fi
 

From 4d7b928533b4d8f441548256c0717eb160b6fd95 Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Sun, 21 Mar 2021 15:41:27 +0100
Subject: [PATCH 6/9] Update last run.sh script

---
 turek-hron-fsi3/solid-dealii/run.sh | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/turek-hron-fsi3/solid-dealii/run.sh b/turek-hron-fsi3/solid-dealii/run.sh
index 7626688c9..03c71ca0f 100755
--- a/turek-hron-fsi3/solid-dealii/run.sh
+++ b/turek-hron-fsi3/solid-dealii/run.sh
@@ -7,4 +7,24 @@ cd ${0%/*} || exit 1    		    # Run from this directory
 # in another terminal.
 # These scripts present how the two participants would be started manually.
 
-./nonlinear_elasticity nonlinear_elasticity.prm
+for i in "$@"
+do
+case $i in
+    -p=*|--prefix=*)
+    SEARCHPATH="${i#*=}"
+    shift # past argument=value
+    ;;
+    *)
+      # unknown option
+    ;;
+esac
+done
+
+if test -f "elasticity"; then
+    ./elasticity parameters.prm
+    elif [ ! -z ${SEARCHPATH} ]; then
+    ${SEARCHPATH}/elasticity parameters.prm
+    else
+    echo "Unable to find the executable 'elasticity'. Either specify a prefix (-p=/path/to/elasticity) or make it discoverable at runtime (e.g. export PATH)"
+fi
+

From cb2c7aa3fc79ef5fa9ceba68e5f47a7e78a1e966 Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Mon, 22 Mar 2021 08:29:28 +0100
Subject: [PATCH 7/9] Fix typos in parameter files

---
 multiple-perpendicular-flaps/solid-left-dealii/parameters.prm  | 2 +-
 multiple-perpendicular-flaps/solid-right-dealii/parameters.prm | 2 +-
 perpendicular-flap/solid-dealii/parameters.prm                 | 2 +-
 turek-hron-fsi3/solid-dealii/parameters.prm                    | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm b/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
index d8740f772..9de97c264 100644
--- a/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
+++ b/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
@@ -40,7 +40,7 @@ subsection Solver
   set Solver type               = Direct
 
   # Max CG solver iterations (multiples of the system matrix size)
-  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
   # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
diff --git a/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
index 4df8bf180..85a76b5e5 100644
--- a/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
+++ b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
@@ -40,7 +40,7 @@ subsection Solver
   set Solver type               = Direct
 
   # Max CG solver iterations (multiples of the system matrix size)
-  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
   # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
diff --git a/perpendicular-flap/solid-dealii/parameters.prm b/perpendicular-flap/solid-dealii/parameters.prm
index d26dd7870..e2763a5ba 100644
--- a/perpendicular-flap/solid-dealii/parameters.prm
+++ b/perpendicular-flap/solid-dealii/parameters.prm
@@ -40,7 +40,7 @@ subsection Solver
   set Solver type               = Direct
 
   # Max CG solver iterations (multiples of the system matrix size)
-  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
   # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
diff --git a/turek-hron-fsi3/solid-dealii/parameters.prm b/turek-hron-fsi3/solid-dealii/parameters.prm
index 3c41041ec..e5dc263e3 100644
--- a/turek-hron-fsi3/solid-dealii/parameters.prm
+++ b/turek-hron-fsi3/solid-dealii/parameters.prm
@@ -40,7 +40,7 @@ subsection Solver
   set Solver type               = Direct
 
   # Max CG solver iterations (multiples of the system matrix size)
-  # In 2-d, this value is best set at 2. In 3-d, a value of 1 work fine.
+  # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
   # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)

From e3161c89e7495cd145d81f9624dce186460022a1 Mon Sep 17 00:00:00 2001
From: Benjamin Uekermann <benjamin.uekermann@gmail.com>
Date: Tue, 23 Mar 2021 14:25:56 +0100
Subject: [PATCH 8/9] Update
 multiple-perpendicular-flaps/solid-right-dealii/parameters.prm

---
 multiple-perpendicular-flaps/solid-right-dealii/parameters.prm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
index 85a76b5e5..5820cf08f 100644
--- a/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
+++ b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
@@ -43,7 +43,8 @@ subsection Solver
   # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
-  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  # Relative drop criterion for CG solver residual (multiplied by residual norm, ignored if Model == linear or solver == direct)
+  # Hard-coded to absolute criterion of 1e-10 for the linear model. 
   set Residual                  = 1e-6
 
   # Number of Newton-Raphson iterations allowed (ignored if Model == linear)

From e5805294003f88d8ca85745ad5542364587f379e Mon Sep 17 00:00:00 2001
From: DavidSCN <david.schneider@ipvs.uni-stuttgart.de>
Date: Tue, 23 Mar 2021 15:34:52 +0100
Subject: [PATCH 9/9] Add comment on linear residual in parameter file

---
 multiple-perpendicular-flaps/solid-left-dealii/parameters.prm  | 3 ++-
 multiple-perpendicular-flaps/solid-right-dealii/parameters.prm | 2 +-
 perpendicular-flap/solid-dealii/parameters.prm                 | 3 ++-
 turek-hron-fsi3/solid-dealii/parameters.prm                    | 3 ++-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm b/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
index 9de97c264..8c9bbd96e 100644
--- a/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
+++ b/multiple-perpendicular-flaps/solid-left-dealii/parameters.prm
@@ -43,7 +43,8 @@ subsection Solver
   # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
-  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  # Relative drop criterion for CG solver residual (multiplied by residual norm, ignored if Model == linear or solver == direct)
+  # Hard-coded to absolute criterion of 1e-10 for the linear model.
   set Residual                  = 1e-6
 
   # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
diff --git a/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
index 5820cf08f..5845d12c5 100644
--- a/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
+++ b/multiple-perpendicular-flaps/solid-right-dealii/parameters.prm
@@ -44,7 +44,7 @@ subsection Solver
   set Max iteration multiplier  = 1
 
   # Relative drop criterion for CG solver residual (multiplied by residual norm, ignored if Model == linear or solver == direct)
-  # Hard-coded to absolute criterion of 1e-10 for the linear model. 
+  # Hard-coded to absolute criterion of 1e-10 for the linear model.
   set Residual                  = 1e-6
 
   # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
diff --git a/perpendicular-flap/solid-dealii/parameters.prm b/perpendicular-flap/solid-dealii/parameters.prm
index e2763a5ba..2dda02e2e 100644
--- a/perpendicular-flap/solid-dealii/parameters.prm
+++ b/perpendicular-flap/solid-dealii/parameters.prm
@@ -43,7 +43,8 @@ subsection Solver
   # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
-  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  # Relative drop criterion for CG solver residual (multiplied by residual norm, ignored if Model == linear or solver == direct)
+  # Hard-coded to absolute criterion of 1e-10 for the linear model.
   set Residual                  = 1e-6
 
   # Number of Newton-Raphson iterations allowed (ignored if Model == linear)
diff --git a/turek-hron-fsi3/solid-dealii/parameters.prm b/turek-hron-fsi3/solid-dealii/parameters.prm
index e5dc263e3..62625fd22 100644
--- a/turek-hron-fsi3/solid-dealii/parameters.prm
+++ b/turek-hron-fsi3/solid-dealii/parameters.prm
@@ -43,7 +43,8 @@ subsection Solver
   # In 2D, this value is best set at 2. In 3D, a value of 1 works fine.
   set Max iteration multiplier  = 1
 
-  # Absolute CG solver residual (multiplied by residual norm, ignored if Model == linear)
+  # Relative drop criterion for CG solver residual (multiplied by residual norm, ignored if Model == linear or solver == direct)
+  # Hard-coded to absolute criterion of 1e-10 for the linear model.
   set Residual                  = 1e-6
 
   # Number of Newton-Raphson iterations allowed (ignored if Model == linear)