Added ex01_inputfile to top-level examples

examples/ex01_inputfile/Makefile

+###############################################################################
+################### MOOSE Application Standard Makefile #######################
+###############################################################################
+#
+# Optional Environment variables
+# MOOSE_DIR     - Root directory of the MOOSE project
+# FRAMEWORK_DIR - Location of the MOOSE framework
+#
+###############################################################################
+EXAMPLE_DIR        ?= $(shell dirname `pwd`)
+MOOSE_DIR          ?= $(shell dirname $(EXAMPLE_DIR))/src/moose
+FRAMEWORK_DIR      ?= $(MOOSE_DIR)/framework
+###############################################################################
+
+TEST := test_ignore
+
+# framework
+include $(FRAMEWORK_DIR)/build.mk
+include $(FRAMEWORK_DIR)/moose.mk
+
+APPLICATION_NAME := ex01
+
+# dep apps
+APPLICATION_DIR    := $(shell pwd)
+APPLICATION_NAME   := ex01
+BUILD_EXEC         := yes
+DEP_APPS           := $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py $(APPLICATION_NAME))
+include            $(FRAMEWORK_DIR)/app.mk
+include            ../test.mk
+
+# Include dependency files for this example
+ex_srcfiles := $(shell find $(APPLICATION_DIR) -name "*.C")
+ex_deps     := $(patsubst %.C, %.$(obj-suffix).d, $(ex_srcfiles))
+-include $(ex_deps)
+
+###############################################################################
+# Additional special case targets should be added here
+
+test: all
+	$(call TEST_exodiff,ex01.i,ex01_out.e)

examples/ex01_inputfile/diffusion_pathological.i

+[Mesh]
+  file = square.e
+  uniform_refine = 4
+[]
+
+# Note: This output block is out of its normal place (should be at the bottom)
+[Outputs]
+  execute_on = 'timestep_end'
+  exodus = true
+[]
+
+# Note: The executioner is out of its normal place (should be just about the output block)
+[Executioner]
+  type = Steady
+  solve_type = 'PJFNK'
+[]
+
+[Variables]
+  active = 'diffused'   # Note the active list here
+  [./diffused]
+    order = FIRST
+    family = LAGRANGE
+  [../]
+
+# This variable is not active in the list above
+# therefore it is not used in the simulation
+  [./convected]
+    order = FIRST
+    family = LAGRANGE
+  [../]
+[]
+
+[Kernels]
+  [./diff]
+    type = Diffusion
+    variable = diffused
+  [../]
+[]
+
+# This example applies DirichletBCs to all four sides of our square domain
+[BCs]
+  [./left]
+    type = DirichletBC
+    variable = diffused
+    boundary = '1'
+    value = 0
+  [../]
+
+  [./right]
+    type = DirichletBC
+    variable = diffused
+    boundary = '2'
+    value = 1
+  [../]
+[]

examples/ex01_inputfile/ex01.i

+[Mesh]
+  file = mug.e
+[]
+
+[Variables]
+  [./diffused]
+    order = FIRST
+    family = LAGRANGE
+  [../]
+[]
+
+[Kernels]
+  [./diff]
+    type = Diffusion
+    variable = diffused
+  [../]
+[]
+
+[BCs]
+  [./bottom]
+    type = DirichletBC
+    variable = diffused
+    boundary = 'bottom'
+    value = 1
+  [../]
+
+  [./top]
+    type = DirichletBC
+    variable = diffused
+    boundary = 'top'
+    value = 0
+  [../]
+[]
+
+[Executioner]
+  type = Steady
+  solve_type = 'PJFNK'
+[]
+
+[Outputs]
+  execute_on = 'timestep_end'
+  exodus = true
+[]

examples/ex01_inputfile/include/README

+This example has no header files.  This directory
+is just included for consistency with the other
+examples.
\ No newline at end of file

examples/ex01_inputfile/include/base/ExampleApp.h

+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/* MOOSE - Multiphysics Object Oriented Simulation Environment  */
+/*                                                              */
+/*           (c) 2010 Battelle Energy Alliance, LLC             */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*          Prepared by Battelle Energy Alliance, LLC           */
+/*            Under Contract No. DE-AC07-05ID14517              */
+/*            With the U. S. Department of Energy               */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+#ifndef EXAMPLEAPP_H
+#define EXAMPLEAPP_H
+
+#include "MooseApp.h"
+
+class ExampleApp;
+
+template<>
+InputParameters validParams<ExampleApp>();
+
+class ExampleApp : public MooseApp
+{
+public:
+  ExampleApp(InputParameters parameters);
+  virtual ~ExampleApp();
+
+  static void registerApps();
+  static void registerObjects(Factory & factory);
+  static void associateSyntax(Syntax& syntax, ActionFactory & action_factory);
+};
+
+#endif /* EXAMPLEAPP_H */

examples/ex01_inputfile/src/base/ExampleApp.C

+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/* MOOSE - Multiphysics Object Oriented Simulation Environment  */
+/*                                                              */
+/*           (c) 2010 Battelle Energy Alliance, LLC             */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*          Prepared by Battelle Energy Alliance, LLC           */
+/*            Under Contract No. DE-AC07-05ID14517              */
+/*            With the U. S. Department of Energy               */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+#include "ExampleApp.h"
+#include "Moose.h"
+#include "Factory.h"
+#include "AppFactory.h"
+#include "MooseSyntax.h"
+
+template<>
+InputParameters validParams<ExampleApp>()
+{
+  InputParameters params = validParams<MooseApp>();
+
+  params.set<bool>("use_legacy_uo_initialization") = false;
+  params.set<bool>("use_legacy_uo_aux_computation") = false;
+  return params;
+}
+
+ExampleApp::ExampleApp(InputParameters parameters) :
+    MooseApp(parameters)
+{
+  srand(processor_id());
+
+  Moose::registerObjects(_factory);
+  ExampleApp::registerObjects(_factory);
+
+  Moose::associateSyntax(_syntax, _action_factory);
+  ExampleApp::associateSyntax(_syntax, _action_factory);
+}
+
+ExampleApp::~ExampleApp()
+{
+}
+
+void
+ExampleApp::registerObjects(Factory & /*factory*/)
+{
+}
+
+void
+ExampleApp::registerApps()
+{
+  registerApp(ExampleApp);
+}
+
+void
+ExampleApp::associateSyntax(Syntax& /*syntax*/, ActionFactory & /*action_factory*/)
+{
+}

examples/ex01_inputfile/src/main.C

+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/* MOOSE - Multiphysics Object Oriented Simulation Environment  */
+/*                                                              */
+/*           (c) 2010 Battelle Energy Alliance, LLC             */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*          Prepared by Battelle Energy Alliance, LLC           */
+/*            Under Contract No. DE-AC07-05ID14517              */
+/*            With the U. S. Department of Energy               */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+/**
+ * Example 1: Input File - The smallest MOOSE based application possible.  It solves
+ * a simple 2D diffusion problem with Dirichlet boundary conditions using built-in
+ * objects from MOOSE.
+ */
+
+#include "ExampleApp.h"
+//Moose Includes
+#include "MooseInit.h"
+#include "Moose.h"
+#include "MooseApp.h"
+#include "AppFactory.h"
+
+// Create a performance log
+PerfLog Moose::perf_log("Example");
+
+// Begin the main program.
+int main(int argc, char *argv[])
+{
+  // Initialize MPI, solvers and MOOSE
+  MooseInit init(argc, argv);
+
+  // Register this application's MooseApp and any it depends on
+  ExampleApp::registerApps();
+
+  // This creates dynamic memory that we're responsible for deleting
+  MooseApp * app = AppFactory::createApp("ExampleApp", argc, argv);
+
+  // Execute the application
+  app->run();
+
+  // Free up the memory we created earlier
+  delete app;
+
+  return 0;
+}

examples/test.mk

+TEST_exodiff = \
+	@./$(APPLICATION_NAME)-$(METHOD) -i $(1) > /dev/null 2>&1 && \
+	$(FRAMEWORK_DIR)/contrib/exodiff/exodiff -quiet -F 1e-8 -t 5.5E-6 $(2) gold/$(2) | grep -qi "files are the same" && \
+	echo $(APPLICATION_NAME) ... OK || \
+	(echo $(APPLICATION_NAME) ... FAILED && exit 1)