Update deal.II scripts (#166)

* Update script and merged parameter files for deal.II

* Apply suggestions from code review

* Update parameter files

* Remove duplicated parameter file

* Update run scripts

* Update last run.sh script

* Fix typos in parameter files

* Update multiple-perpendicular-flaps/solid-right-dealii/parameters.prm

* Add comment on linear residual in parameter file

Co-authored-by: Benjamin Uekermann <[email protected]>

multiple-perpendicular-flaps/solid-left-dealii/nonlinear_elasticity.prm → multiple-perpendicular-flaps/solid-left-dealii/parameters.prm

@@ -9,54 +9,51 @@ 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 2D, this value is best set at 2. In 3D, a value of 1 works fine.
+  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.
+  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
 

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

multiple-perpendicular-flaps/solid-right-dealii/nonlinear_elasticity.prm → multiple-perpendicular-flaps/solid-right-dealii/parameters.prm

@@ -9,54 +9,51 @@ 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 2D, this value is best set at 2. In 3D, a value of 1 works fine.
+  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.
+  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
 

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