run make beautify

Makefile.in

@@ -4243,13 +4243,13 @@ vtkversion = @vtkversion@
 # 	   test/Makefile.in                         \
 # 	   test/common/Makefile.in 		    \
 # 	   test/comp_ns/Makefile.in		    \
-# 	   test/unit/Makefile.in                    
+# 	   test/unit/Makefile.in
 SUBDIRS = include contrib $(am__append_6) $(am__append_10)
-AUTOMAKE_OPTIONS = subdir-objects 
+AUTOMAKE_OPTIONS = subdir-objects
 ACLOCAL_AMFLAGS = -I m4
 AM_CFLAGS = $(libmesh_CFLAGS)
 
-# AM_CPPFLAGS are method-independent cppflags that 
+# AM_CPPFLAGS are method-independent cppflags that
 # we use when compiling libmesh proper, or its utility
 # codes.  These will be augmented with method-specific
 # cppflags later on
@@ -4724,33 +4724,33 @@ libmesh_SOURCES = \
         src/utils/xdr_cxx.C 
 
 
-# A convenience library to hold proper libMesh 
-# objects.  This will get appended with any contributed 
+# A convenience library to hold proper libMesh
+# objects.  This will get appended with any contributed
 # sources to create the final library.
 lib_LTLIBRARIES = $(am__append_1) $(am__append_2) $(am__append_3) \
 	$(am__append_4) $(am__append_5)
 @LIBMESH_DBG_MODE_TRUE@libmesh_dbg_la_SOURCES = $(libmesh_SOURCES)
-@LIBMESH_DBG_MODE_TRUE@libmesh_dbg_la_CPPFLAGS = $(CPPFLAGS_DBG) $(AM_CPPFLAGS) 
+@LIBMESH_DBG_MODE_TRUE@libmesh_dbg_la_CPPFLAGS = $(CPPFLAGS_DBG) $(AM_CPPFLAGS)
 @LIBMESH_DBG_MODE_TRUE@libmesh_dbg_la_CXXFLAGS = $(CXXFLAGS_DBG)
 @LIBMESH_DBG_MODE_TRUE@libmesh_dbg_la_CFLAGS = $(CFLAGS_DBG)
 @LIBMESH_DBG_MODE_TRUE@libmesh_dbg_la_LIBADD = contrib/libcontrib_dbg.la $(LIBS)
 @LIBMESH_DEVEL_MODE_TRUE@libmesh_devel_la_SOURCES = $(libmesh_SOURCES)
-@LIBMESH_DEVEL_MODE_TRUE@libmesh_devel_la_CPPFLAGS = $(CPPFLAGS_DEVEL) $(AM_CPPFLAGS) 
+@LIBMESH_DEVEL_MODE_TRUE@libmesh_devel_la_CPPFLAGS = $(CPPFLAGS_DEVEL) $(AM_CPPFLAGS)
 @LIBMESH_DEVEL_MODE_TRUE@libmesh_devel_la_CXXFLAGS = $(CXXFLAGS_DEVEL)
 @LIBMESH_DEVEL_MODE_TRUE@libmesh_devel_la_CFLAGS = $(CFLAGS_DEVEL)
 @LIBMESH_DEVEL_MODE_TRUE@libmesh_devel_la_LIBADD = contrib/libcontrib_devel.la $(LIBS)
 @LIBMESH_OPT_MODE_TRUE@libmesh_opt_la_SOURCES = $(libmesh_SOURCES)
-@LIBMESH_OPT_MODE_TRUE@libmesh_opt_la_CPPFLAGS = $(CPPFLAGS_OPT) $(AM_CPPFLAGS) 
+@LIBMESH_OPT_MODE_TRUE@libmesh_opt_la_CPPFLAGS = $(CPPFLAGS_OPT) $(AM_CPPFLAGS)
 @LIBMESH_OPT_MODE_TRUE@libmesh_opt_la_CXXFLAGS = $(CXXFLAGS_OPT)
 @LIBMESH_OPT_MODE_TRUE@libmesh_opt_la_CFLAGS = $(CFLAGS_OPT)
 @LIBMESH_OPT_MODE_TRUE@libmesh_opt_la_LIBADD = contrib/libcontrib_opt.la $(LIBS)
 @LIBMESH_PROF_MODE_TRUE@libmesh_prof_la_SOURCES = $(libmesh_SOURCES)
-@LIBMESH_PROF_MODE_TRUE@libmesh_prof_la_CPPFLAGS = $(CPPFLAGS_PROF) $(AM_CPPFLAGS) 
+@LIBMESH_PROF_MODE_TRUE@libmesh_prof_la_CPPFLAGS = $(CPPFLAGS_PROF) $(AM_CPPFLAGS)
 @LIBMESH_PROF_MODE_TRUE@libmesh_prof_la_CXXFLAGS = $(CXXFLAGS_PROF)
 @LIBMESH_PROF_MODE_TRUE@libmesh_prof_la_CFLAGS = $(CFLAGS_PROF)
 @LIBMESH_PROF_MODE_TRUE@libmesh_prof_la_LIBADD = contrib/libcontrib_prof.la $(LIBS)
 @LIBMESH_OPROF_MODE_TRUE@libmesh_oprof_la_SOURCES = $(libmesh_SOURCES)
-@LIBMESH_OPROF_MODE_TRUE@libmesh_oprof_la_CPPFLAGS = $(CPPFLAGS_OPROF) $(AM_CPPFLAGS) 
+@LIBMESH_OPROF_MODE_TRUE@libmesh_oprof_la_CPPFLAGS = $(CPPFLAGS_OPROF) $(AM_CPPFLAGS)
 @LIBMESH_OPROF_MODE_TRUE@libmesh_oprof_la_CXXFLAGS = $(CXXFLAGS_OPROF)
 @LIBMESH_OPROF_MODE_TRUE@libmesh_oprof_la_CFLAGS = $(CFLAGS_OPROF)
 @LIBMESH_OPROF_MODE_TRUE@libmesh_oprof_la_LIBADD = contrib/libcontrib_oprof.la $(LIBS)
@@ -27331,6 +27331,13 @@ install-data-hook:
 	cat $(DESTDIR)$(libmesh_configdir)/libmesh-config | $(SED) "s/has_been_installed=no/has_been_installed=yes/g" > $(DESTDIR)$(libmesh_configdir)/libmesh-config.installed
 	mv $(DESTDIR)$(libmesh_configdir)/libmesh-config.installed $(DESTDIR)$(libmesh_configdir)/libmesh-config && chmod +x $(DESTDIR)$(libmesh_configdir)/libmesh-config
 
+# this rule invokes emacs on each source file to remove trailing whitespace.
+beautify:
+	for file in `find $(srcdir)/{src,include,examples} -name "*.C" -o -name "*.h" -o -name Makefile.am -type f` ; do \
+	  echo $$file ; \
+	  emacs -batch $$file --eval '(delete-trailing-whitespace)' -f save-buffer 2>/dev/null ; \
+	done
+
 #
 .PHONY: examples_doc doc svnexpand
 
@@ -27384,7 +27391,7 @@ test_headers:
 	@cd $(top_builddir)/include && $(MAKE) test_headers
 
 # General philosophy is to maintain code coverage for the
-# base library as generated by "make check" tests. 
+# base library as generated by "make check" tests.
 
 @CODE_COVERAGE_ENABLED_TRUE@lcov-report:
 @CODE_COVERAGE_ENABLED_TRUE@	@mkdir -p $(lcov_dir)

examples/Makefile.am

@@ -49,7 +49,7 @@ SUBDIRS = \
 	vector_fe/vector_fe_ex2 \
 	vector_fe/vector_fe_ex3
 
-AUTOMAKE_OPTIONS = subdir-objects 
+AUTOMAKE_OPTIONS = subdir-objects
 
 AM_CPPFLAGS  = $(libmesh_CPPFLAGS)
 AM_CFLAGS    = $(libmesh_CFLAGS)
@@ -106,4 +106,3 @@ doc:
 if CODE_COVERAGE_ENABLED
   CLEANFILES = */*/*.gcda */*/*.gcno
 endif
-

examples/adaptivity/adaptivity_ex1/Makefile.am

@@ -4,7 +4,7 @@ install_dir   = $(examples_install_path)/adaptivity/ex1
 data          = adaptivity_ex1.C run.sh
 sources       = $(data) run.sh
 
-CLEANFILES = gnuplot_script_data gnuplot_script 
+CLEANFILES = gnuplot_script_data gnuplot_script
 
 ##############################################
 # include common example environment

examples/adaptivity/adaptivity_ex1/adaptivity_ex1.C

@@ -16,15 +16,15 @@
 /* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA */
 
  // <h1>Adaptivity Example 1 - Solving 1D PDE Using Adaptive Mesh Refinement</h1>
- // 
+ //
  // This example demonstrates how to solve a simple 1D problem
  // using adaptive mesh refinement. The PDE that is solved is:
- // -epsilon*u''(x) + u(x) = 1, on the domain [0,1] with boundary conditions 
+ // -epsilon*u''(x) + u(x) = 1, on the domain [0,1] with boundary conditions
  // u(0) = u(1) = 0 and where epsilon << 1.
  //
  // The approach used to solve 1D problems in libMesh is virtually identical to
  // solving 2D or 3D problems, so in this sense this example represents a good
- // starting point for new users. Note that many concepts are used in this 
+ // starting point for new users. Note that many concepts are used in this
  // example which are explained more fully in subsequent examples.
 
 // Libmesh includes
@@ -52,7 +52,7 @@ using namespace libMesh;
 void assemble_1D(EquationSystems& es, const std::string& system_name);
 
 int main(int argc, char** argv)
-{   
+{
   // Initialize the library.  This is necessary because the library
   // may depend on a number of other libraries (i.e. MPI and PETSc)
   // that require initialization before use.  When the LibMeshInit
@@ -74,7 +74,7 @@ int main(int argc, char** argv)
   if ( command_line.search(1, "-n") )
     n = command_line.next(n);
 
-  // Build a 1D mesh with 4 elements from x=0 to x=1, using 
+  // Build a 1D mesh with 4 elements from x=0 to x=1, using
   // EDGE3 (i.e. quadratic) 1D elements. They are called EDGE3 elements
   // because a quadratic element contains 3 nodes.
   MeshTools::Generation::build_line(mesh,n,0.,1.,EDGE3);
@@ -88,7 +88,7 @@ int main(int argc, char** argv)
   // Add a variable "u" to the system, using second-order approximation
   system.add_variable("u",SECOND);
 
-  // Give the system a pointer to the matrix assembly function. This 
+  // Give the system a pointer to the matrix assembly function. This
   // will be called when needed by the library.
   system.attach_assemble_function(assemble_1D);
 
@@ -97,8 +97,8 @@ int main(int argc, char** argv)
   MeshRefinement mesh_refinement(mesh);
 
   // These parameters determine the proportion of elements that will
-  // be refined and coarsened. Any element within 30% of the maximum 
-  // error on any element will be refined, and any element within 30% 
+  // be refined and coarsened. Any element within 30% of the maximum
+  // error on any element will be refined, and any element within 30%
   // of the minimum error on any element might be coarsened
   mesh_refinement.refine_fraction()  = 0.7;
   mesh_refinement.coarsen_fraction() = 0.3;
@@ -140,7 +140,7 @@ int main(int argc, char** argv)
           mesh_refinement.refine_and_coarsen_elements();
 
           // Reinitialize the equation_systems object for the newly refined
-          // mesh. One of the steps in this is project the solution onto the 
+          // mesh. One of the steps in this is project the solution onto the
           // new mesh
           equation_systems.reinit();
         }
@@ -155,7 +155,7 @@ int main(int argc, char** argv)
   // Load gnuplot, then type "call 'gnuplot_script'" from gnuplot prompt
   plot.write_equation_systems("gnuplot_script",equation_systems);
 #endif // #ifndef LIBMESH_ENABLE_AMR
-  
+
   // All done.  libMesh objects are destroyed here.  Because the
   // LibMeshInit object was created first, its destruction occurs
   // last, and it's destructor finalizes any external libraries and
@@ -189,7 +189,7 @@ void assemble_1D(EquationSystems& es, const std::string& system_name)
   // freedom numbers. DofMap's are discussed in more detail in future examples.
   const DofMap& dof_map = system.get_dof_map();
 
-  // Get a constant reference to the Finite Element type for the first 
+  // Get a constant reference to the Finite Element type for the first
   // (and only) variable in the system.
   FEType fe_type = dof_map.variable_type(0);
 
@@ -203,7 +203,7 @@ void assemble_1D(EquationSystems& es, const std::string& system_name)
   QGauss qrule(dim,FIFTH);
   fe->attach_quadrature_rule(&qrule);
 
-  // Here we define some references to cell-specific data that will be used to 
+  // Here we define some references to cell-specific data that will be used to
   // assemble the linear system.
 
   // The element Jacobian * quadrature weight at each integration point.
@@ -238,21 +238,21 @@ void assemble_1D(EquationSystems& es, const std::string& system_name)
     // It is convenient to store a pointer to the current element
     const Elem* elem = *el;
 
-    // Get the degree of freedom indices for the current element. 
-    // These define where in the global matrix and right-hand-side this 
+    // Get the degree of freedom indices for the current element.
+    // These define where in the global matrix and right-hand-side this
     // element will contribute to.
     dof_map.dof_indices(elem, dof_indices);
 
-    // Compute the element-specific data for the current element. This 
-    // involves computing the location of the quadrature points (q_point) 
+    // Compute the element-specific data for the current element. This
+    // involves computing the location of the quadrature points (q_point)
     // and the shape functions (phi, dphi) for the current element.
     fe->reinit(elem);
 
     // Store the number of local degrees of freedom contained in this element
     const int n_dofs = dof_indices.size();
 
     // We resize and zero out Ke and Fe (resize() also clears the matrix and
-    // vector). In this example, all elements in the mesh are EDGE3's, so 
+    // vector). In this example, all elements in the mesh are EDGE3's, so
     // Ke will always be 3x3, and Fe will always be 3x1. If the mesh contained
     // different element types, then the size of Ke and Fe would change.
     Ke.resize(n_dofs, n_dofs);
@@ -270,7 +270,7 @@ void assemble_1D(EquationSystems& es, const std::string& system_name)
 
         for(unsigned int j=0; j<phi.size(); j++)
         {
-          Ke(i,j) += JxW[qp]*(1.e-3*dphi[i][qp]*dphi[j][qp] + 
+          Ke(i,j) += JxW[qp]*(1.e-3*dphi[i][qp]*dphi[j][qp] +
                                      phi[i][qp]*phi[j][qp]);
         }
       }

examples/adaptivity/adaptivity_ex2/Makefile.am

@@ -1,5 +1,5 @@
 BUILT_SOURCES = exact_solution.C
-exact_solution.C: $(top_srcdir)/examples/transient/transient_ex1/exact_solution.C 
+exact_solution.C: $(top_srcdir)/examples/transient/transient_ex1/exact_solution.C
 	$(AM_V_GEN)$(LN_S) $< $@
 
 DISTCLEANFILES = $(BUILT_SOURCES)