Apply update script to header, source and prm files.

contrib/utilities/update_all_files.sh

@@ -10,14 +10,14 @@ BASE_DIR=`cd ${UTIL_DIR}/../..;pwd`
 echo "Scanning ${BASE_DIR} for changes..."
 
 # Update source files
-SOURCE_FILES=`find $BASE_DIR -type f \( -name *.cc -or -name *.h \) -and -not -name *.bak | grep -v doc`
+SOURCE_FILES=`find $BASE_DIR -type f \( -name \*.cc -or -name \*.h \) -and -not -name \*.bak | grep -v doc`
 bash ${UTIL_DIR}/update_source_files.sh $SOURCE_FILES
 
 # Update prm files
-PRM_FILES=`find $BASE_DIR -type f -name *.prm* -not -name *update_script* -not -name *prmbackslash_2.prm -not -name *.bak`
+PRM_FILES=`find $BASE_DIR -type f -name \*.prm\* -and -not \( -name \*update_script\*.prm -or -name \*prmbackslash_2.prm -or -name \*.bak \)`
 bash ${UTIL_DIR}/update_prm_files.sh $PRM_FILES
 
 # To remove the backup files that are created you will likely want to use the
 # following command. It is commented out by default, because you should think
 # carefully before automatically removing files.
-#find ${BASE_DIR} -name *.bak -delete
+#find ${BASE_DIR} -name \*.bak -delete

contrib/utilities/update_prm_files.sh

@@ -25,20 +25,19 @@ done
 # remove the backup file. We can not use this file
 # instead of the .bak file, because it is overwritten by every script,
 # and so it is only a backup of the last execution.
-for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name *.sed`; do
+for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name \*.sed`; do
   sed -i.tmp -f $script "$@"
 done
 
-for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name *.pl`; do
-  for file in $@ ; do
+for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name \*.pl`; do
+  for file in "$@" ; do
     cat "$file" | perl $script > "$file.tmp"
     mv "$file.tmp" "$file"
   done
 done
 
-for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name *.py`; do
-  for file in $@ ; do
-    echo $file
+for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name \*.py`; do
+  for file in "$@" ; do
     python3 $script $file "$file.tmp"
     mv "$file.tmp" "$file"
   done

contrib/utilities/update_source_files.sh

@@ -25,11 +25,11 @@ done
 # remove the backup file. We can not use this file
 # instead of the .bak file, because it is overwritten by every script,
 # and so it is only a backup of the last execution.
-for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name *.sed`; do
+for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name \*.sed`; do
   sed -i.tmp -f $script "$@"
 done
 
-for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name *.pl`; do
+for script in `find ${SCRIPT_FOLDER} -maxdepth 1 -name \*.pl`; do
   for file in $@ ; do
     cat "$file" | perl $script > "$file.tmp"
     mv "$file.tmp" "$file"

source/postprocess/particles.cc

@@ -365,7 +365,7 @@ namespace aspect
         }
 
       if (write_output == false)
-        return std::make_pair("Number of advected particles", number_of_advected_particles);
+        return std::make_pair("Number of advected particles:", number_of_advected_particles);
 
       if (output_file_number == numbers::invalid_unsigned_int)
         output_file_number = 0;

tests/darcy_convection_step.prm

@@ -158,6 +158,7 @@ end
 # Output the darcy velocity
 subsection Postprocess
   set List of postprocessors = visualization
+
   subsection Visualization
     set List of output variables = darcy velocity
     set Output format            = gnuplot

tests/nonlinear_failure_strategy_abort.prm

@@ -8,6 +8,5 @@ include $ASPECT_SOURCE_DIR/tests/iterated_advection_and_stokes_residual.prm
 
 set Nonlinear solver failure strategy = abort program
 set Max nonlinear iterations = 4
-
 set Dimension = 2
 set End time = 20000

tests/nonlinear_failure_strategy_cut.prm

@@ -6,6 +6,5 @@ include $ASPECT_SOURCE_DIR/tests/iterated_advection_and_stokes_residual.prm
 
 set Nonlinear solver failure strategy = cut timestep size
 set Max nonlinear iterations = 4
-
 set Dimension = 2
 set End time = 20000

tests/particle_interpolator_distance_weighted_average_adaptive.prm

@@ -7,6 +7,7 @@ set Dimension                              = 2
 
 include $ASPECT_SOURCE_DIR/tests/particle_interpolator_distance_weighted_average.prm
 
+
 subsection Mesh refinement
   set Initial adaptive refinement        = 2
   set Strategy                           = composition

tests/particle_multiple_worlds_interpolation_fail_1.prm

@@ -64,7 +64,6 @@ subsection Compositional fields
   set Names of fields  = anomaly, function
   set Compositional field methods =  particles,  particles
   set Mapped particle properties = anomaly: function, function: initial anomaly
-
 end
 
 subsection Initial composition model

tests/particle_multiple_worlds_interpolation_fail_2.prm

@@ -64,7 +64,6 @@ subsection Compositional fields
   set Names of fields  = anomaly, function
   set Compositional field methods =  particles,  particles
   set Mapped particle properties = anomaly: function, function: initial anomaly
-
 end
 
 subsection Initial composition model

tests/update_script/screen-output

@@ -2,8 +2,6 @@
 Loading shared library <./libupdate_script.debug.so>
 Executing the update script:
 cp update_script.x.prm output-update_script/updated.prm &&sed -i.bak 's:set Additional shared libraries = ./libupdate_script.so::' output-update_script/updated.prm &&bash ASPECT_DIR/contrib/utilities/update_prm_files.sh output-update_script/updated.prm &&rm output-update_script/updated.prm.bak
-output-update_script/updated.prm
-output-update_script/updated.prm
 Running ASPECT with updated parameter file:
 ../aspect output-update_script/updated.prm
 

tests/update_script_2/screen-output

@@ -2,10 +2,6 @@
 Loading shared library <./libupdate_script_2.debug.so>
 Executing the update script:
 cp update_script_2.x.prm output-update_script_2/updated2.prm;sed -i.bak 's:set Additional shared libraries = ./libupdate_script_2.so::' output-update_script_2/updated2.prm;bash ASPECT_DIR/contrib/utilities/update_prm_files.sh output-update_script_2/updated2.prm;bash ASPECT_DIR/contrib/utilities/update_prm_files.sh output-update_script_2/updated2.prm;rm output-update_script_2/updated2.prm.bak
-output-update_script_2/updated2.prm
-output-update_script_2/updated2.prm
-output-update_script_2/updated2.prm
-output-update_script_2/updated2.prm
 Running ASPECT with updated parameter file:
 ../aspect output-update_script_2/updated2.prm
 

tests/visco_plastic_adiabatic_pressure_in_plasticity.prm

@@ -82,7 +82,6 @@ subsection Material model
   subsection Visco Plastic
     set Reference strain rate = 1.e-16
     set Viscous flow law = composite
-
     set Use adiabatic pressure in plasticity = true
     set Angles of internal friction = 10
     set Cohesions = 1e6