Update deal.II parameter files (#175)

* Centralize dealii run scripts

* Add new deal.II directory option to parameter files

* Update clean_dealii according to default directory

* Replace prefix by executable

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

@@ -11,6 +11,9 @@ subsection Time
 
   # Write results every x timesteps
   set Output interval       = 10
+
+  # Output folder
+  set Output folder   = dealii-output
 end
 
 subsection Discretization

multiple-perpendicular-flaps/solid-left-dealii/run.sh

@@ -0,0 +1 @@
+../../tools/run-dealii.sh

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

@@ -11,6 +11,9 @@ subsection Time
 
   # Write results every x timesteps
   set Output interval       = 10
+
+  # Output folder
+  set Output folder   = dealii-output
 end
 
 subsection Discretization

multiple-perpendicular-flaps/solid-right-dealii/run.sh

@@ -0,0 +1 @@
+../../tools/run-dealii.sh

perpendicular-flap/solid-dealii/parameters.prm

@@ -11,6 +11,9 @@ subsection Time
 
   # Write results every x timesteps
   set Output interval       = 10
+
+  # Output folder
+  set Output folder   = dealii-output
 end
 
 subsection Discretization

perpendicular-flap/solid-dealii/run.sh

@@ -0,0 +1 @@
+../../tools/run-dealii.sh

tools/cleaning-tools.sh

@@ -57,7 +57,7 @@ clean_dealii() {
     (
         cd "$1"
         echo "--- Cleaning up deal.II case in $(pwd)"
-        rm -fv ./dealii_output/solution-*.vtk ./solution-*.vtk
+        rm -fv ./dealii-output/solution-*.vtk
         clean_precice_logs .
     )
 }

tools/run-dealii.sh

@@ -0,0 +1,37 @@
+#!/bin/sh
+set -e -u
+
+EXE=""
+
+for i in "$@"
+do
+case $i in
+    -e=*|--exec=*)
+    EXE="${i#*=}"
+    shift # past argument=value
+    ;;
+    *)
+      # unknown option
+    ;;
+esac
+done
+
+# If the executable has been defined
+if [ -n "${EXE}"  ]; then
+    "${EXE}" parameters.prm
+    exit 0;
+fi
+
+EXE="elasticity"
+# If it is in the global path
+if [ -n "$(command -v "${EXE}")" ]; then
+   "${EXE}" parameters.prm
+   exit 0;
+fi
+
+# If it has been copied to the local directory
+if test -f "elasticity"; then
+    ./"${EXE}" parameters.prm
+    else
+    echo "Unable to find the executable ${EXE}. Either specify the executable explicitly (-e=/path/to/elasticity) or make it discoverable at runtime (e.g. export PATH)"
+fi

turek-hron-fsi3/solid-dealii/parameters.prm

@@ -11,11 +11,14 @@ subsection Time
 
   # Write results every x timesteps
   set Output interval       = 100
+
+  # Output folder
+  set Output folder   = dealii-output
 end
 
 subsection Discretization
   # Polynomial degree of the FE system
-  set Polynomial degree   = 4
+  set Polynomial degree   = 1
 end
 
 subsection System properties

turek-hron-fsi3/solid-dealii/run.sh

@@ -0,0 +1 @@
+../../tools/run-dealii.sh