Adding in new App files

.clang-format

+BasedOnStyle: LLVM
+
+TabWidth: 2
+ColumnLimit: 100
+UseTab: Never
+
+CommentPragmas: '^/'
+ReflowComments: true
+AlignTrailingComments: true
+SpacesBeforeTrailingComments: 1
+
+SpaceBeforeParens: ControlStatements
+SpacesInSquareBrackets: false
+BreakBeforeBraces: Allman
+PointerAlignment: Middle
+
+BinPackParameters: false
+BinPackArguments: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortFunctionsOnASingleLine: true
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+
+SortIncludes: false
+IndentCaseLabels: true
+ConstructorInitializerIndentWidth: 2
+AlwaysBreakAfterDefinitionReturnType: TopLevel
+AlwaysBreakTemplateDeclarations: true

.gitignore

@@ -7,6 +7,8 @@
 *-opt
 *-dbg
 *-oprof
+*-prof
+*-devel
 *.e
 *.nav
 *.log
@@ -16,7 +18,7 @@
 *.csv
 *.dylib
 *.so
-*.gitignore*
+*.so.*
 *.vrb
 *.jou
 *.pyc
@@ -35,6 +37,7 @@
 *.spl
 *.idx
 traceout*.txt
+temp_print_trace.*
 *.xda
 *.xda.*
 *.xdr
@@ -64,8 +67,25 @@ traceout*.txt
 *.out
 *.vtk
 *.vtu
+*.pvtu
 .depend
+*.png
+*.gif
+*.tif
+*.jpg
+*.tiff
+*.ps
+*.bmp
+*.html
+*.xyz
+*Revision.h
+*.json
+*.bak
+*.processor.*
 .clang_complete
+.failed_tests
+compile_commands.json
+build
 
 # Allow certain files in gold directories
 !**/gold/*.e
@@ -73,9 +93,17 @@ traceout*.txt
 !**/gold/*.csv
 !**/gold/*.vtk
 !**/gold/*.vtu
+!**/gold/*.pvtu
 
 peacock_run_tmp.i
 yaml_dump*
+test/tests/outputs/format/dump.i
+
+# Generated header file
+MooseRevision.h
+
+# Precompiled headers
+moose/include/base/Precompiled.h.gch
 
 # test garbagge
 *.FAILED.txt
@@ -92,12 +120,14 @@ yaml_dump*
 .*.swp
 .*.swo
 
+framework/contrib/exodiff/exodiff
+
 # Mac garbage
 .DS_Store
 *.dSYM
 
-# Unit testing stuff
-moose_unit/test_results.xml
+# Unit testing stuffbmoose_unit/test_results.xml
+!unit/data/csv/*.csv
 
 # gcov code coverage files
 *.gcno
@@ -136,20 +166,44 @@ framework/contrib/asio/
 *.cpa-*
 *.cpr-*
 
-# Revision files
-include/base/*Revision.h
-
 # phase_field/tests/solution_rasterizer
 out.xyz
 
-# Nek5000 run files
-*.sch
-SESSION.NAME
-nek5000
-
-# Autconf artifacts
-aclocal.m4
-autom4te.cache/**
-config.log
-config.status
-install-sh
+# JIT and automatic differentiation cache files
+.jitcache/
+.jitdir/
+tmp_jit_*
+
+# Do not store ipython notebook checkpoints
+*-checkpoint.ipynb*
+
+# MooseDocs
+site
+!**/doc/content/**/*.md
+!**/doc/content/**/*.jpg
+!**/doc/content/**/*.jpeg
+!**/doc/content/**/*.gif
+!**/doc/content/**/*.png
+!**/doc/content/**/*.svg
+!**/doc/content/**/*.ogg
+!**/doc/content/**/*.webm
+!**/doc/content/**/*.mp4
+!**/doc/content/**/*.css
+!**/doc/content/**/*.js
+!**/doc/content/**/*.bib
+!**/doc/content/**/*.woff
+!**/doc/content/**/*.woff2
+
+# Chigger
+!python/chigger/tests/**/gold/*.png
+!python/chigger/tests/input/*.e*
+!python/chigger/logos/*.png
+!python/chigger/contrib/*.xml
+
+# Peacock
+python/peacock/tests/exodus_tab/TestOutputPlugin_repr.py
+python/peacock/tests/input_tab/InputFileEditor/fsp_test.i
+python/peacock/tests/postprocessor_tab/TestPostprocessorPluginManager_test_script.py
+!python/peacock/tests/**/gold/*.png
+!python/peacock/icons/**/*.*
+!python/peacock/tests/**/input/*.*

Makefile

+###############################################################################
+################### MOOSE Application Standard Makefile #######################
+###############################################################################
+#
+# Optional Environment variables
+# MOOSE_DIR        - Root directory of the MOOSE project
+#
+###############################################################################
+# Use the MOOSE submodule if it exists and MOOSE_DIR is not set
+MOOSE_SUBMODULE    := $(CURDIR)/moose
+ifneq ($(wildcard $(MOOSE_SUBMODULE)/framework/Makefile),)
+  MOOSE_DIR        ?= $(MOOSE_SUBMODULE)
+else
+  MOOSE_DIR        ?= $(shell dirname `pwd`)/moose
+endif
+
+# framework
+FRAMEWORK_DIR      := $(MOOSE_DIR)/framework
+include $(FRAMEWORK_DIR)/build.mk
+include $(FRAMEWORK_DIR)/moose.mk
+
+################################## MODULES ####################################
+# To use certain physics included with MOOSE, set variables below to
+# yes as needed.  Or set ALL_MODULES to yes to turn on everything (overrides
+# other set variables).
+
+ALL_MODULES         := no
+
+CHEMICAL_REACTIONS  := no
+CONTACT             := no
+FLUID_PROPERTIES    := no
+HEAT_CONDUCTION     := no
+MISC                := no
+NAVIER_STOKES       := no
+PHASE_FIELD         := no
+RDG                 := no
+RICHARDS            := no
+SOLID_MECHANICS     := no
+STOCHASTIC_TOOLS    := no
+TENSOR_MECHANICS    := no
+WATER_STEAM_EOS     := no
+XFEM                := no
+POROUS_FLOW         := no
+
+include $(MOOSE_DIR)/modules/modules.mk
+###############################################################################
+
+# dep apps
+APPLICATION_DIR    := $(CURDIR)
+APPLICATION_NAME   := giraffe
+BUILD_EXEC         := yes
+GEN_REVISION       := no
+include            $(FRAMEWORK_DIR)/app.mk
+
+###############################################################################
+# Additional special case targets should be added here

README.md

+Giraffe
+=====
+
+"Fork Giraffe" to create a new MOOSE-based application.
+
+For more information see: [http://mooseframework.org/create-an-app/](http://mooseframework.org/create-an-app/)

include/base/GiraffeApp.h

+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+#ifndef GIRAFFEAPP_H
+#define GIRAFFEAPP_H
+
+#include "MooseApp.h"
+
+class GiraffeApp;
+
+template <>
+InputParameters validParams<GiraffeApp>();
+
+class GiraffeApp : public MooseApp
+{
+public:
+  GiraffeApp(InputParameters parameters);
+  virtual ~GiraffeApp();
+
+  static void registerApps();
+  static void registerObjects(Factory & factory);
+  static void registerObjectDepends(Factory & factory);
+  static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
+  static void associateSyntaxDepends(Syntax & syntax, ActionFactory & action_factory);
+  static void registerExecFlags(Factory & factory);
+};
+
+#endif /* GIRAFFEAPP_H */

run_tests

+#!/usr/bin/env python
+import sys, os
+
+MOOSE_DIR = os.path.abspath(os.environ.get('MOOSE_DIR', os.path.join(os.path.dirname(__file__), '..', 'moose')))
+if os.path.exists(os.path.abspath(os.path.join('moose', 'framework', 'Makefile'))):
+  MOOSE_DIR = os.path.abspath('moose')
+MOOSE_DIR = os.environ.get('MOOSE_DIR', MOOSE_DIR)
+
+sys.path.append(os.path.join(MOOSE_DIR, 'python'))
+
+from TestHarness import TestHarness
+TestHarness.buildAndRun(sys.argv, None, MOOSE_DIR)

scripts/install-format-hook.sh

+#!/bin/bash
+
+REPO_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/../"
+hookfile="$REPO_DIR/.git/hooks/pre-commit"
+
+if [[ -f $hookfile ]]; then
+    echo "'$hookfile' already exists - aborting" 1>&2
+    exit 1
+fi
+
+echo '#!/bin/bash
+patch=$(git clang-format --diff -- $(git diff --staged --name-only -- src include tests unit))
+if [[ "$patch" =~ "no modified files to format" || "$patch" =~ "clang-format did not modify any files" ]]; then
+    echo "" > /dev/null
+else
+    echo ""
+    echo "Your code is not properly formatted." >&2
+    echo "Run 'git clang-format' to resolve the following issues:" >&2
+    echo ""
+    echo "$patch"
+    exit 1
+fi
+' > $hookfile
+
+chmod a+x $hookfile
+

src/base/GiraffeApp.C

+#include "GiraffeApp.h"
+#include "Moose.h"
+#include "AppFactory.h"
+#include "ModulesApp.h"
+#include "MooseSyntax.h"
+
+template <>
+InputParameters
+validParams<GiraffeApp>()
+{
+  InputParameters params = validParams<MooseApp>();
+  return params;
+}
+
+GiraffeApp::GiraffeApp(InputParameters parameters) : MooseApp(parameters)
+{
+  Moose::registerObjects(_factory);
+  ModulesApp::registerObjects(_factory);
+  GiraffeApp::registerObjects(_factory);
+
+  Moose::associateSyntax(_syntax, _action_factory);
+  ModulesApp::associateSyntax(_syntax, _action_factory);
+  GiraffeApp::associateSyntax(_syntax, _action_factory);
+
+  Moose::registerExecFlags(_factory);
+  ModulesApp::registerExecFlags(_factory);
+  GiraffeApp::registerExecFlags(_factory);
+}
+
+GiraffeApp::~GiraffeApp() {}
+
+void
+GiraffeApp::registerApps()
+{
+  registerApp(GiraffeApp);
+}
+
+void
+GiraffeApp::registerObjects(Factory & factory)
+{
+    Registry::registerObjectsTo(factory, {"GiraffeApp"});
+}
+
+void
+GiraffeApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & action_factory)
+{
+  Registry::registerActionsTo(action_factory, {"GiraffeApp"});
+
+  /* Uncomment Syntax parameter and register your new production objects here! */
+}
+
+void
+GiraffeApp::registerObjectDepends(Factory & /*factory*/)
+{
+}
+
+void
+GiraffeApp::associateSyntaxDepends(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
+{
+}
+
+void
+GiraffeApp::registerExecFlags(Factory & /*factory*/)
+{
+  /* Uncomment Factory parameter and register your new execution flags here! */
+}
+
+/***************************************************************************************************
+ *********************** Dynamic Library Entry Points - DO NOT MODIFY ******************************
+ **************************************************************************************************/
+extern "C" void
+GiraffeApp__registerApps()
+{
+  GiraffeApp::registerApps();
+}
+
+extern "C" void
+GiraffeApp__registerObjects(Factory & factory)
+{
+  GiraffeApp::registerObjects(factory);
+}
+
+extern "C" void
+GiraffeApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory)
+{
+  GiraffeApp::associateSyntax(syntax, action_factory);
+}
+
+extern "C" void
+GiraffeApp__registerExecFlags(Factory & factory)
+{
+  GiraffeApp::registerExecFlags(factory);
+}

src/main.C

+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+#include "GiraffeTestApp.h"
+#include "MooseInit.h"
+#include "Moose.h"
+#include "MooseApp.h"
+#include "AppFactory.h"
+
+// Create a performance log
+PerfLog Moose::perf_log("Giraffe");
+
+// 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
+  GiraffeTestApp::registerApps();
+
+  // Create an instance of the application and store it in a smart pointer for easy cleanup
+  std::shared_ptr<MooseApp> app = AppFactory::createAppShared("GiraffeTestApp", argc, argv);
+
+  // Execute the application
+  app->run();
+
+  return 0;
+}

test/include/base/GiraffeTestApp.h

+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+#ifndef GIRAFFETESTAPP_H
+#define GIRAFFETESTAPP_H
+
+#include "MooseApp.h"
+
+class GiraffeTestApp;
+
+template <>
+InputParameters validParams<GiraffeTestApp>();
+
+class GiraffeTestApp : public MooseApp
+{
+public:
+  GiraffeTestApp(InputParameters parameters);
+  virtual ~GiraffeTestApp();
+
+  static void registerApps();
+  static void registerObjects(Factory & factory);
+  static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
+  static void registerExecFlags(Factory & factory);
+};
+
+#endif /* GIRAFFETESTAPP_H */

test/src/base/GiraffeTestApp.C

+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+#include "GiraffeTestApp.h"
+#include "GiraffeApp.h"
+#include "Moose.h"
+#include "AppFactory.h"
+#include "MooseSyntax.h"
+#include "ModulesApp.h"
+
+template <>
+InputParameters
+validParams<GiraffeTestApp>()
+{
+  InputParameters params = validParams<GiraffeApp>();
+  return params;
+}
+
+GiraffeTestApp::GiraffeTestApp(InputParameters parameters) : MooseApp(parameters)
+{
+  Moose::registerObjects(_factory);
+  ModulesApp::registerObjects(_factory);
+  GiraffeApp::registerObjectDepends(_factory);
+  GiraffeApp::registerObjects(_factory);
+
+  Moose::associateSyntax(_syntax, _action_factory);
+  ModulesApp::associateSyntax(_syntax, _action_factory);
+  GiraffeApp::associateSyntaxDepends(_syntax, _action_factory);
+  GiraffeApp::associateSyntax(_syntax, _action_factory);
+
+  Moose::registerExecFlags(_factory);
+  ModulesApp::registerExecFlags(_factory);
+  GiraffeApp::registerExecFlags(_factory);
+
+  bool use_test_objs = getParam<bool>("allow_test_objects");
+  if (use_test_objs)
+  {
+    GiraffeTestApp::registerObjects(_factory);
+    GiraffeTestApp::associateSyntax(_syntax, _action_factory);
+    GiraffeTestApp::registerExecFlags(_factory);
+  }
+}
+
+GiraffeTestApp::~GiraffeTestApp() {}
+
+void
+GiraffeTestApp::registerApps()
+{
+  registerApp(GiraffeApp);
+  registerApp(GiraffeTestApp);
+}
+
+void
+GiraffeTestApp::registerObjects(Factory & /*factory*/)
+{
+  /* Uncomment Factory parameter and register your new test objects here! */
+}
+
+void
+GiraffeTestApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
+{
+  /* Uncomment Syntax and ActionFactory parameters and register your new test objects here! */
+}
+
+void
+GiraffeTestApp::registerExecFlags(Factory & /*factory*/)
+{
+  /* Uncomment Factory parameter and register your new execute flags here! */
+}
+
+/***************************************************************************************************
+ *********************** Dynamic Library Entry Points - DO NOT MODIFY ******************************
+ **************************************************************************************************/
+// External entry point for dynamic application loading
+extern "C" void
+GiraffeTestApp__registerApps()
+{
+  GiraffeTestApp::registerApps();
+}
+
+// External entry point for dynamic object registration
+extern "C" void
+GiraffeTestApp__registerObjects(Factory & factory)
+{
+  GiraffeTestApp::registerObjects(factory);
+}
+
+// External entry point for dynamic syntax association
+extern "C" void
+GiraffeTestApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory)
+{
+  GiraffeTestApp::associateSyntax(syntax, action_factory);
+}
+
+// External entry point for dynamic execute flag loading
+extern "C" void
+GiraffeTestApp__registerExecFlags(Factory & factory)
+{
+  GiraffeTestApp::registerExecFlags(factory);
+}

test/tests/kernels/simple_diffusion/simple_diffusion.i

+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+  nx = 10
+  ny = 10
+[]
+
+[Variables]
+  [./u]
+  [../]
+[]
+
+[Kernels]
+  [./diff]
+    type = Diffusion
+    variable = u
+  [../]
+[]
+
+[BCs]
+  [./left]
+    type = DirichletBC
+    variable = u
+    boundary = left
+    value = 0
+  [../]
+  [./right]
+    type = DirichletBC
+    variable = u
+    boundary = right
+    value = 1
+  [../]
+[]
+
+[Executioner]
+  type = Steady
+  solve_type = 'PJFNK'
+  petsc_options_iname = '-pc_type -pc_hypre_type'
+  petsc_options_value = 'hypre boomeramg'
+[]
+
+[Outputs]
+  exodus = true
+[]

test/tests/kernels/simple_diffusion/tests

+[Tests]
+  [./test]
+    type = 'Exodiff'
+    input = 'simple_diffusion.i'
+    exodiff = 'simple_diffusion_out.e'
+  [../]
+[]

testroot

+app_name = giraffe
+allow_warnings = false
+allow_unused = false
+allow_override = false

unit/Makefile

+###############################################################################
+################### MOOSE Application Standard Makefile #######################
+###############################################################################
+#
+# Required Environment variables (one of the following)
+# PACKAGES_DIR  - Location of the MOOSE redistributable package
+#
+# Optional Environment variables
+# MOOSE_DIR     - Root directory of the MOOSE project
+# FRAMEWORK_DIR - Location of the MOOSE framework
+#
+###############################################################################
+# Use the MOOSE submodule if it exists and MOOSE_DIR is not set
+MOOSE_SUBMODULE    := $(CURDIR)/../moose
+ifneq ($(wildcard $(MOOSE_SUBMODULE)/framework/Makefile),)
+  MOOSE_DIR        ?= $(MOOSE_SUBMODULE)
+else
+  MOOSE_DIR        ?= $(shell dirname `pwd`)/../moose
+endif
+FRAMEWORK_DIR      ?= $(MOOSE_DIR)/framework
+###############################################################################
+
+# framework
+include $(FRAMEWORK_DIR)/build.mk
+include $(FRAMEWORK_DIR)/moose.mk
+
+################################## MODULES ####################################
+# set desired physics modules equal to 'yes' to enable them
+CHEMICAL_REACTIONS        := no
+CONTACT                   := no
+FLUID_PROPERTIES          := no
+HEAT_CONDUCTION           := no
+MISC                      := no
+NAVIER_STOKES             := no
+PHASE_FIELD               := no
+RDG                       := no
+RICHARDS                  := no
+SOLID_MECHANICS           := no
+STOCHASTIC_TOOLS          := no
+TENSOR_MECHANICS          := no
+WATER_STEAM_EOS           := no
+XFEM                      := no
+POROUS_FLOW               := no
+LEVEL_SET                 := no
+include           $(MOOSE_DIR)/modules/modules.mk
+###############################################################################
+
+# Extra stuff for GTEST
+ADDITIONAL_INCLUDES := -I$(FRAMEWORK_DIR)/contrib/gtest
+ADDITIONAL_LIBS     := $(FRAMEWORK_DIR)/contrib/gtest/libgtest.la
+
+# dep apps
+CURRENT_DIR        := $(shell pwd)
+APPLICATION_DIR    := $(CURRENT_DIR)/..
+APPLICATION_NAME   := giraffe
+include            $(FRAMEWORK_DIR)/app.mk
+
+APPLICATION_DIR    := $(CURRENT_DIR)
+APPLICATION_NAME   := giraffe-unit
+BUILD_EXEC         := yes
+
+DEP_APPS    ?= $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py $(APPLICATION_NAME))
+include $(FRAMEWORK_DIR)/app.mk
+
+# Find all the Giraffe unit test source files and include their dependencies.
+giraffe_unit_srcfiles := $(shell find $(CURRENT_DIR)/src -name "*.C")
+giraffe_unit_deps := $(patsubst %.C, %.$(obj-suffix).d, $(giraffe_unit_srcfiles))
+-include $(giraffe_unit_deps)
+
+###############################################################################
+# Additional special case targets should be added here

unit/run_tests

+#!/bin/bash
+
+APPLICATION_NAME=giraffe
+# If $METHOD is not set, use opt
+if [ -z $METHOD ]; then
+  export METHOD=opt
+fi
+
+if [ -e ./unit/$APPLICATION_NAME-unit-$METHOD ]
+then
+  ./unit/$APPLICATION_NAME-unit-$METHOD
+elif [ -e ./$APPLICATION_NAME-unit-$METHOD ]
+then
+  ./$APPLICATION_NAME-unit-$METHOD
+else
+  echo "Executable missing!"
+  exit 1
+fi

unit/src/SampleTest.C

+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
+#include "gtest/gtest.h"
+
+TEST(MySampleTests, descriptiveTestName)