Commit a0097527 authored by Ron Rahaman's avatar Ron Rahaman

Renamed symbols, moon->giraffe, preserving upper/lower cases.

TODO: Haven't renamed files yet.
parent 6d252060
stages:
- build_libmesh_stage
- configure_moon_stage
- build_moon_stage
- test_moon_stage
- configure_giraffe_stage
- build_giraffe_stage
- test_giraffe_stage
before_script:
- . /opt/moose/environments/moose_profile
......@@ -15,8 +15,8 @@ build_libmesh:
- cd moose
- scripts/update_and_rebuild_libmesh.sh
configure_moon:
stage: configure_moon_stage
configure_giraffe:
stage: configure_giraffe_stage
dependencies:
- build_libmesh
variables:
......@@ -28,10 +28,10 @@ configure_moon:
- cd examples/integration_example/
- ../../configure
build_moon:
stage: build_moon_stage
build_giraffe:
stage: build_giraffe_stage
dependencies:
- configure_moon
- configure_giraffe
variables:
GIT_STRATEGY: none
MOOSE_DIR: "$CI_PROJECT_DIR/moose"
......@@ -40,14 +40,14 @@ build_moon:
- cd examples/integration_example/
- make -j8
test_moon:
stage: test_moon_stage
test_giraffe:
stage: test_giraffe_stage
dependencies:
- build_moon
- build_giraffe
variables:
GIT_STRATEGY: none
MOOSE_DIR: "$CI_PROJECT_DIR/moose"
LIBMESH_DIR: "$CI_PROJECT_DIR/moose/libmesh/installed"
script:
- cd examples/integration_example
- ../../moon-opt -i coefficient_integration.i
- ../../giraffe-opt -i coefficient_integration.i
MOON
Giraffe
=====
[![build status](https://xgitlab.cels.anl.gov/nek5000/moon/badges/develop/build.svg)](https://xgitlab.cels.anl.gov/nek5000/moon/commits/develop)
[![build status](https://xgitlab.cels.anl.gov/nek5000/giraffe/badges/develop/build.svg)](https://xgitlab.cels.anl.gov/nek5000/giraffe/commits/develop)
MOON (Multiphysics Object-Oriented Nek5000) uses the [MOOSE](http://www.mooseframework.org/) framework to implement multiphysics coupling with [Nek5000](https://nek5000.mcs.anl.gov/) CFD simulations. The project is a collaboration between [Idaho National Laboratory](https://www.inl.gov/) and [Argonne National Laboratory](https://www.inl.gov/).
Giraffe uses the [MOOSE](http://www.mooseframework.org/) framework to implement multiphysics coupling with [Nek5000](https://nek5000.mcs.anl.gov/) CFD simulations. The project is a collaboration between [Idaho National Laboratory](https://www.inl.gov/) and [Argonne National Laboratory](https://www.inl.gov/).
Downloading the Repo
--------------------
Cloning the MOON repository requires the `--recursive` flag, since MOOSE and libmesh are included as [Git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules). For example:
Cloning the Giraffe repository requires the `--recursive` flag, since MOOSE and libmesh are included as [Git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules). For example:
```
git clone --recursive https://xgitlab.cels.anl.gov/nek5000/moon.git
git clone --recursive https://xgitlab.cels.anl.gov/nek5000/giraffe.git
```
This will download and populate the src/moose and src/moose/libmesh.
Building PETSc
--------------
MOON requires PETSc, as described in the [MOOSE installation instructions](http://mooseframework.com/getting-started/). PETSc is not distributed with MOON. PETSc must either be compiled from source or installed as part of the MOOSE Environment package. After installing PETSc, you must define the `$PETSC_DIR` variable in your environment.
Giraffe requires PETSc, as described in the [MOOSE installation instructions](http://mooseframework.com/getting-started/). PETSc is not distributed with Giraffe. PETSc must either be compiled from source or installed as part of the MOOSE Environment package. After installing PETSc, you must define the `$PETSC_DIR` variable in your environment.
Building libmesh
----------------
MOON also requires libmesh, as described in the [MOOSE installation instructions](http://mooseframework.com/getting-started/). The libmesh source code is distributed with MOOSE. It should be compiled using the following scripts:
Giraffe also requires libmesh, as described in the [MOOSE installation instructions](http://mooseframework.com/getting-started/). The libmesh source code is distributed with MOOSE. It should be compiled using the following scripts:
```
$ cd moose/
$ scripts/update\_and\_rebuild\_libmesh.sh.
......@@ -34,18 +34,18 @@ After installing libmesh, you must define the `$LIBMESH_DIR` in your environment
The Example Problems
--------------------
Currently, the only working example problem is "integration_example" in `moon/examples/integration_example`.
Currently, the only working example problem is "integration_example" in `giraffe/examples/integration_example`.
### Building Example Problems
To configure and build each example problem, first generate the `configure` script in the top-level MOON directory:
To configure and build each example problem, first generate the `configure` script in the top-level Giraffe directory:
```
$ cd moon
$ cd giraffe
$ ./bootstrap
```
Then cd into the example subdirectory and simply run `configure` && `make`. This will build the MOOSE and Nek5000 libraries, then link them to the executable driver.
```
$ cd moon/examples/integration_example`
$ cd giraffe/examples/integration_example`
$ ../../configure
$ make
```
......@@ -53,24 +53,24 @@ The `configure` script may be run with additional options (for example, to point
### Running Example Problems
To run an example problem, it is recommended to use the convenience script `moon/examples/build_coupled_nek`. This script will automatically setup some input files needed by Nek5000 (such as SESSION.NAME). The script takes one command-line argument for the MOOSE configuration file, `-i <config_file>.i`.
To run an example problem, it is recommended to use the convenience script `giraffe/examples/build_coupled_nek`. This script will automatically setup some input files needed by Nek5000 (such as SESSION.NAME). The script takes one command-line argument for the MOOSE configuration file, `-i <config_file>.i`.
```
$ cd moon/examples/integration_example
$ ../../moon-opt -i coefficient_integration.i
$ cd giraffe/examples/integration_example
$ ../../giraffe-opt -i coefficient_integration.i
```
Linking to libmoon
Linking to libgiraffe
------------------
The MOON libraries are output to the top-level lib/ directory.
The Giraffe libraries are output to the top-level lib/ directory.
Developing Nek5000 in MOON
Developing Nek5000 in Giraffe
--------------------------
Developers may freely modify src/Nek5000 as if it were a normal part of the MOON repo. This is because Nek5000 is included as a Git subtree (rather than a submodule). For routine commits, pushes, and pulls to the MOON repository, no extra Git commands are necessary.
Developers may freely modify src/Nek5000 as if it were a normal part of the Giraffe repo. This is because Nek5000 is included as a Git subtree (rather than a submodule). For routine commits, pushes, and pulls to the Giraffe repository, no extra Git commands are necessary.
With some additional Git commands, developers may easily merge upstream changes from [https://github.com/Nek5000/Nek5000](https://github.com/Nek5000/Nek5000) into src/Nek5000. Finally, developers may also request to merge changes from src/Nek5000 to [https://github.com/Nek5000/Nek5000](https://github.com/Nek5000/Nek5000). This [blog post](http://blogs.atlassian.com/2013/05/alternatives-to-git-submodule-git-subtree/) from Atlassian gives a brief rundown of the procedures.
Developing MOOSE and libmesh in MOON
Developing MOOSE and libmesh in Giraffe
------------------------------------
Modifying src/moose and src/moose/libmesh require additional Git commands, since they are included as Git submodules (rather than subtrees). Modifying either of these libraries for MOON is intended to be unnecessary. Should the situation arise, this [chapter](https://git-scm.com/book/en/v2/Git-Tools-Submodules) from _Pro Git_ describes the procedure for making modifications to submodules.
Modifying src/moose and src/moose/libmesh require additional Git commands, since they are included as Git submodules (rather than subtrees). Modifying either of these libraries for Giraffe is intended to be unnecessary. Should the situation arise, this [chapter](https://git-scm.com/book/en/v2/Git-Tools-Submodules) from _Pro Git_ describes the procedure for making modifications to submodules.
###############################################################################
# MOON MAKEFILE
# GIRAFFE MAKEFILE
###############################################################################
#
# Optional Environment variables
......@@ -7,7 +7,7 @@
# FRAMEWORK_DIR - Location of the MOOSE framework
#
###############################################################################
MOON_DIR := @abs_srcdir@
GIRAFFE_DIR := @abs_srcdir@
MOOSE_DIR := @MOOSE_DIR@
FRAMEWORK_DIR := @MOOSE_DIR@/framework
###############################################################################
......@@ -26,12 +26,12 @@ PHASE_FIELD := no
XFEM := no
include $(MOOSE_DIR)/modules/modules.mk
################################## MOON ########################################
################################## GIRAFFE ####################################
# nek
include moon.mk
APPLICATION_DIR := $(MOON_DIR)
APPLICATION_NAME := moon
include giraffe.mk
APPLICATION_DIR := $(GIRAFFE_DIR)
APPLICATION_NAME := giraffe
MAIN_DIR := $(APPLICATION_DIR)/src
BUILD_EXEC := yes
DEP_APPS := $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py integration_example)
......
......@@ -86,7 +86,7 @@ AC_ARG_ENABLE([libmesh],
[AS_HELP_STRING([--enable-libmesh], [configure with compilers and flags from an existing libmesh installation @<:@default: enabled@:>@])],
[libmesh=${enableval}], [libmesh=yes])
AC_ARG_VAR([MOOSE_DIR], [directory of moose installation @<:@default: moon/moose/@:>@])
AC_ARG_VAR([MOOSE_DIR], [directory of moose installation @<:@default: giraffe/moose/@:>@])
AC_ARG_VAR([LIBMESH_DIR], [directory of libmesh installation @<:@default: \$MOOSE_DIR/libmesh/installed/@:>@])
###############################################################################
......@@ -524,7 +524,7 @@ fi
# ALL DONE!
###############################################################################
AC_CONFIG_FILES([moon.mk:config/moon.mk.in Makefile:config/Makefile.in
AC_CONFIG_FILES([giraffe.mk:config/giraffe.mk.in Makefile:config/Makefile.in
SESSION.NAME:config/SESSION.NAME.in])
......
......@@ -4,7 +4,7 @@
# Project related configuration options
#---------------------------------------------------------------------------
DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = "MOON"
PROJECT_NAME = "Giraffe"
PROJECT_NUMBER =
PROJECT_BRIEF =
PROJECT_LOGO =
......
......@@ -835,7 +835,7 @@
[MultiApps]
[./sub]
type = TransientMultiApp
app_type = MoonApp
app_type = GiraffeApp
sub_cycling = true
positions = '0 0 0'
input_files = picard_sub_subcycling.i
......
......@@ -61,7 +61,7 @@
[MultiApps]
[./sub]
type = TransientMultiApp
app_type = MoonApp
app_type = GiraffeApp
positions = '0 0 0'
input_files = picard_sub.i
[../]
......
......@@ -61,7 +61,7 @@
[MultiApps]
[./sub]
type = TransientMultiApp
app_type = MoonApp
app_type = GiraffeApp
sub_cycling = true
positions = '0 0 0'
input_files = picard_sub_subcycling.i
......
#ifndef MOONAPP_H
#define MOONAPP_H
#ifndef GIRAFFEAPP_H
#define GIRAFFEAPP_H
#include "MooseApp.h"
class MoonApp;
class GiraffeApp;
template<>
InputParameters validParams<MoonApp>();
InputParameters validParams<GiraffeApp>();
class MoonApp : public MooseApp
class GiraffeApp : public MooseApp
{
public:
MoonApp(InputParameters parameters);
virtual ~MoonApp();
GiraffeApp(InputParameters parameters);
virtual ~GiraffeApp();
static void registerApps();
static void registerObjects(Factory & factory);
static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
};
#endif /* MOONAPP_H */
#endif /* GIRAFFEAPP_H */
......@@ -2,8 +2,8 @@
// Created by Ron Rahaman on 10/18/16.
//
#ifndef MOON_NEKEXECUTIONER_H
#define MOON_NEKEXECUTIONER_H
#ifndef GIRAFFE_NEKEXECUTIONER_H
#define GIRAFFE_NEKEXECUTIONER_H
#include "Transient.h"
class NekExecutioner;
......@@ -41,4 +41,4 @@ public:
// virtual bool lastSolveConverged();
};
#endif //MOON_NEKEXECUTIONER_H
#endif //GIRAFFE_NEKEXECUTIONER_H
......@@ -2,8 +2,8 @@
// Created by Ron Rahaman on 10/18/16.
//
#ifndef MOON_NEKTIMESTEPPER_H
#define MOON_NEKTIMESTEPPER_H
#ifndef GIRAFFE_NEKTIMESTEPPER_H
#define GIRAFFE_NEKTIMESTEPPER_H
#include "TimeStepper.h"
......@@ -27,4 +27,4 @@ private:
Real _dt;
};
#endif //MOON_NEKTIMESTEPPER_H
#endif //GIRAFFE_NEKTIMESTEPPER_H
......@@ -5,7 +5,7 @@ import sys, os, inspect
os.chdir(os.path.abspath(os.path.dirname(sys.argv[0])))
#### Set the name of the application here and moose directory relative to the application
app_name = 'MOON'
app_name = 'giraffe'
MOOSE_DIR = os.path.abspath(os.path.join('..', 'moose'))
#### See if a submodule is available
......
#include "MoonApp.h"
#include "GiraffeApp.h"
#include "Moose.h"
#include "AppFactory.h"
#include "ModulesApp.h"
......@@ -13,14 +13,14 @@
// Modules
#include "HeatConductionApp.h"
// Moon
#include "MoonRevision.h"
// Giraffe
#include "GiraffeRevision.h"
#include "NekExecutioner.h"
#include "NekTimeStepper.h"
#include "MultiAppPolynomialToNek.h"
template<>
InputParameters validParams<MoonApp>()
InputParameters validParams<GiraffeApp>()
{
InputParameters params = validParams<MooseApp>();
......@@ -31,45 +31,45 @@ InputParameters validParams<MoonApp>()
return params;
}
MoonApp::MoonApp(InputParameters parameters) :
GiraffeApp::GiraffeApp(InputParameters parameters) :
MooseApp(parameters)
{
Moose::registerObjects(_factory);
ModulesApp::registerObjects(_factory);
HeatConductionApp::registerObjects(_factory);
MoonApp::registerObjects(_factory);
GiraffeApp::registerObjects(_factory);
Moose::associateSyntax(_syntax, _action_factory);
ModulesApp::associateSyntax(_syntax, _action_factory);
HeatConductionApp::associateSyntax(_syntax, _action_factory);
MoonApp::associateSyntax(_syntax, _action_factory);
GiraffeApp::associateSyntax(_syntax, _action_factory);
}
MoonApp::~MoonApp()
GiraffeApp::~GiraffeApp()
{
}
// External entry point for dynamic application loading
extern "C" void
MoonApp__registerApps()
GiraffeApp__registerApps()
{
MoonApp::registerApps();
GiraffeApp::registerApps();
}
void
MoonApp::registerApps()
GiraffeApp::registerApps()
{
registerApp(MoonApp);
registerApp(GiraffeApp);
}
// External entry point for dynamic object registration
extern "C" void
MoonApp__registerObjects(Factory & factory)
GiraffeApp__registerObjects(Factory & factory)
{
MoonApp::registerObjects(factory);
GiraffeApp::registerObjects(factory);
}
void
MoonApp::registerObjects(Factory & factory)
GiraffeApp::registerObjects(Factory & factory)
{
registerAuxKernel(CoupledGradAux);
......@@ -88,11 +88,11 @@ MoonApp::registerObjects(Factory & factory)
// External entry point for dynamic syntax association
extern "C" void
MoonApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory)
GiraffeApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory)
{
MoonApp::associateSyntax(syntax, action_factory);
GiraffeApp::associateSyntax(syntax, action_factory);
}
void
MoonApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
GiraffeApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
{
}
#include "MoonApp.h"
#include "GiraffeApp.h"
#include "Moose.h"
#include "AppFactory.h"
#include "MooseSyntax.h"
template<>
InputParameters validParams<MoonApp>()
InputParameters validParams<GiraffeApp>()
{
InputParameters params = validParams<MooseApp>();
......@@ -15,38 +15,38 @@ InputParameters validParams<MoonApp>()
return params;
}
MoonApp::MoonApp(InputParameters parameters) :
GiraffeApp::GiraffeApp(InputParameters parameters) :
MooseApp(parameters)
{
Moose::registerObjects(_factory);
MoonApp::registerObjects(_factory);
GiraffeApp::registerObjects(_factory);
Moose::associateSyntax(_syntax, _action_factory);
MoonApp::associateSyntax(_syntax, _action_factory);
GiraffeApp::associateSyntax(_syntax, _action_factory);
}
MoonApp::~MoonApp()
GiraffeApp::~GiraffeApp()
{
}
// External entry point for dynamic application loading
extern "C" void MoonApp__registerApps() { MoonApp::registerApps(); }
extern "C" void GiraffeApp__registerApps() { GiraffeApp::registerApps(); }
void
MoonApp::registerApps()
GiraffeApp::registerApps()
{
registerApp(MoonApp);
registerApp(GiraffeApp);
}
// External entry point for dynamic object registration
extern "C" void MoonApp__registerObjects(Factory & factory) { MoonApp::registerObjects(factory); }
extern "C" void GiraffeApp__registerObjects(Factory & factory) { GiraffeApp::registerObjects(factory); }
void
MoonApp::registerObjects(Factory & factory)
GiraffeApp::registerObjects(Factory & factory)
{
}
// External entry point for dynamic syntax association
extern "C" void MoonApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory) { MoonApp::associateSyntax(syntax, action_factory); }
extern "C" void GiraffeApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory) { GiraffeApp::associateSyntax(syntax, action_factory); }
void
MoonApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
GiraffeApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
{
}
#include "MoonApp.h"
#include "GiraffeApp.h"
#include "MooseInit.h"
#include "Moose.h"
#include "MooseApp.h"
#include "AppFactory.h"
// Create a performance log
PerfLog Moose::perf_log("Moon");
PerfLog Moose::perf_log("Giraffe");
// Begin the main program.
int main(int argc, char *argv[])
......@@ -14,10 +14,10 @@ int main(int argc, char *argv[])
MooseInit init(argc, argv);
// Register this application's MooseApp and any it depends on
MoonApp::registerApps();
GiraffeApp::registerApps();
// This creates dynamic memory that we're responsible for deleting
MooseApp * app = AppFactory::createApp("MoonApp", argc, argv);
MooseApp * app = AppFactory::createApp("GiraffeApp", argc, argv);
// Execute the application
app->run();
......
......@@ -31,19 +31,19 @@ ADDITIONAL_LIBS := -L$(CPPUNIT_DIR)/lib -lcppunit
# dep apps
APPLICATION_DIR := $(CURRENT_DIR)/..
APPLICATION_NAME := MOON
APPLICATION_NAME := giraffe
include $(FRAMEWORK_DIR)/app.mk
APPLICATION_DIR := $(CURRENT_DIR)
APPLICATION_NAME := MOON-unit
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 MOON unit test source files and include their dependencies.
MOON-unit_srcfiles := $(shell find $(CURRENT_DIR) -name "*.C")
MOON-unit_deps := $(patsubst %.C, %.$(obj-suffix).d, $(MOON-unit_srcfiles))
-include $(MOON-unit_deps)
# Find all the giraffe unit test source files and include their dependencies.
giraffe-unit_srcfiles := $(shell find $(CURRENT_DIR) -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
#!/bin/bash
APPLICATION_NAME=MOON
APPLICATION_NAME=giraffe
# If $METHOD is not set, use opt
if [ -z $METHOD ]; then
export METHOD=opt
......
......@@ -24,7 +24,7 @@
#include "Factory.h"
#include "AppFactory.h"
#include "MoonApp.h"
#include "GiraffeApp.h"
#include <fstream>
#include <string>
......@@ -35,7 +35,7 @@ int main(int argc, char **argv)
{
MooseInit init(argc, argv);
registerApp(MoonApp);
registerApp(GiraffeApp);
CppUnit::Test *suite = CppUnit::TestFactoryRegistry::getRegistry().makeTest();
......
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