Removing references to SPN.

README.rst

@@ -23,7 +23,6 @@ to be useful as proof-of-concept for actual production work.
 Profugus is also used as a test-bed mini-app for the ASCR projects
 XPRESS and MCREX.
 
-
 Profugus Development Team
 =========================
 
@@ -61,10 +60,6 @@ Profugus Packages
 
 Profugus constains the following code mini-apps:
 
-**SPn**
-   Mini-app of Simplified Spherical Harmonics ("SPn") computational
-   kernel.
-
 **MC**
    Mini-app of Monte Carlo computational kernel.
 
@@ -103,12 +98,8 @@ Building The Code
 The most straightforward method for building Profugus is to use the
 scripts in `Profugus/install`.  Profugus uses the `TriBITS` build
 system.  This system is a set of package-based extensions to standard
-cmake.  So, first you need to obtain *Trilinos* and *TriBITS* and put
-them in your top-level Profugus directory::
-
-   > cd Profugus
-   > git clone https://github.com/TriBITSPub/TriBITS.git
-   > ln -s $PATH_TO_TRILINOS .
+cmake.  The components of TriBITS and Trilinos that are required are
+included in the Profugus distribution.
 
 The preferred mechanism for using the build scripts is to make a
 *target* directory where the build is to be performed::
@@ -131,9 +122,6 @@ configure time) are specified in the `install/base.cmake`::
    ##---------------------------------------------------------------------------##
 
    # Default build all packages
-   SET(Profugus_ENABLE_Utils   ON CACHE BOOL "")
-   SET(Profugus_ENABLE_Matprop ON CACHE BOOL "")
-   SET(Profugus_ENABLE_SPn     ON CACHE BOOL "")
    SET(Profugus_ENABLE_MC      ON CACHE BOOL "")
 
    # Turn on tests
@@ -145,101 +133,31 @@ configure time) are specified in the `install/base.cmake`::
    SET(Profugus_ENABLE_ALL_OPTIONAL_PACKAGES    ON  CACHE BOOL "")
    SET(Profugus_ENABLE_SECONDARY_STABLE_CODE    ON  CACHE BOOL "")
 
-   # Up the max num procs
-   SET(MPI_EXEC_MAX_NUMPROCS 8 CACHE STRING "")
-
-   # Turn off binutils
-   SET(Teuchos_ENABLE_BinUtils OFF CACHE BOOL "")
-
-   # Turn off Zoltan2
-   SET(Profugus_ENABLE_Zoltan2 OFF CACHE BOOL "")
-
    # Compiler options
    SET(BUILD_SHARED_LIBS ON CACHE BOOL "")
    SET(CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated-declarations" CACHE STRING "")
    SET(Profugus_ENABLE_CXX11:BOOL=ON)
 
-   # TriBITS stuff
-   SET(Profugus_ENABLE_INSTALL_CMAKE_CONFIG_FILES OFF CACHE BOOL "")
-   SET(Profugus_DEPS_XML_OUTPUT_FILE "" CACHE FILEPATH "")
-
 By default, all of the packages inside of Profugus are turned on.
 Furthermore, *C++-11* is **required**.  The default options specify
 the appropriate compiler flags for gcc.  The tests are also turned on
 by default; to disable tests in any upstream package simply do not
-explicitly *ENABLE* that package.  For example, to build the *SPn*
+explicitly *ENABLE* that package.  For example, to build the *MC*
 package and all of its tests but only include required *source* from
 upstream packages, the user would specify::
 
-   SET(Profugus_ENABLE_SPn ON CACHE BOOL "")
+   SET(Profugus_ENABLE_MC ON CACHE BOOL "")
 
-In this case, only the pieces of *Utils* needed to build *SPn* are
+In this case, only the pieces of *Utils* needed to build *MC* are
 compiled. All tests can be turned off by setting
 **Profugus_ENABLE_TESTS** to **OFF**.
 
 The `install` directory contains several build scripts that are all
-suffixed by the platform name.  For example, to build on a Linux
-*x86_64* system the "install/cmake_x86_64.sh" script can be used::
-
-   #!/bin/sh
-   ##---------------------------------------------------------------------------##
-   ## CMAKE FOR X86_64
-   ##---------------------------------------------------------------------------##
-
-   # CLEANUP
-   rm -rf CMakeCache.txt
-   rm -rf CMakeFiles
-
-   # SOURCE AND INSTALL
-   SOURCE=<SET_SOURCE_DIR>
-   INSTALL=<SET_INSTALL_DIR>
-
-   # BUILD OPTIONS
-   BUILD="DEBUG"
-   MPI="ON"
-
-   # TPL PATHS
-   HDF5_PATH="/vendors/hdf5_parallel"
-   MPI_PATH="/opt/openmpi/gcc/current"
-
-   ##---------------------------------------------------------------------------##
-
-   cmake \
-   -DCMAKE_BUILD_TYPE:STRING="$BUILD" \
-   -DTPL_ENABLE_MPI:BOOL=$MPI \
-   -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL \
-   \
-   -DMPI_BASE_DIR:PATH=$MPI_PATH \
-   \
-   -DTPL_ENABLE_HDF5:BOOL=ON \
-   -DHDF5_INCLUDE_DIRS:PATH=$HDF5_PATH/include \
-   -DHDF5_LIBRARY_DIRS:PATH=$HDF5_PATH/lib \
-   \
-   -DBLAS_LIBRARY_DIRS:PATH=/vendors/gcc/atlas/lib \
-   -DLAPACK_LIBRARY_DIRS:PATH=/vendors/gcc/atlas/lib \
-   -DBLAS_LIBRARY_NAMES:STRING="f77blas;cblas;atlas" \
-   -DLAPACK_LIBRARY_NAMES:STRING="lapack" \
-   \
-   -DProfugus_CONFIGURE_OPTIONS_FILE:FILEPATH="${SOURCE}/install/base.cmake" \
-   -DProfugus_ASSERT_MISSING_PACKAGES:BOOL=OFF \
-   \
-   ${SOURCE}
-
-   ##---------------------------------------------------------------------------##
-   ## end of cmake_x86_64.sh
-   ##---------------------------------------------------------------------------##
-
-The source and install locations must be set. Also, to enable a
-optimized build set **BUILD** to **RELEASE**.  Adjust the paths and
-libraries for LAPACK to fit your platform.  The example assumes that
-the ATLAS LAPACK is available.  Any standard LAPACK distribution will
-work. HDF5 is **not** required, to build/run/test the applications;
-however, problem output will be severely curtailed if a parallel HDF5
-option is not provided.  If HDF5 is not available, setting::
-
-   -DTPL_ENABLE_HDF5:BOOL=OFF \
-
-will disable HDF5.
+suffixed by the platform name.  The source and install locations
+must be set. Also, to enable a optimized build set **BUILD** to
+**RELEASE**.  Adjust the paths and libraries for LAPACK to fit your
+platform.  The example assumes that the ATLAS LAPACK is available.
+Any standard LAPACK distribution will work.
 
 To complete the configuration, execute this script inside the *target*
 directory and then make/test/install::

TPLsList.cmake

@@ -11,7 +11,6 @@
 #   Trilinos/cmake/TrilinosTPLs.cmake
 #
 SET(Profugus_TPLS_FINDMODS_CLASSIFICATIONS
-  SILO   "cmake/TPLs/"   SS
   HDF5   "cmake/TPLs/"   SS
   )
 

packages/MC/CMakeLists.txt

@@ -24,13 +24,6 @@ TRIBITS_PACKAGE(MC)
 ## B) Set up package-specific options
 ##---------------------------------------------------------------------------##
 
-## ML OPTIONS
-
-## Turn on ML if that package is enabled
-IF (${PROJECT_NAME}_ENABLE_ML)
-  SET(USE_ML 1)
-ENDIF()
-
 # Setup M4 for FORTRAN processing
 APPEND_SET(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
@@ -240,5 +233,5 @@ TRIBITS_EXCLUDE_AUTOTOOLS_FILES()
 TRIBITS_PACKAGE_POSTPROCESS()
 
 ##---------------------------------------------------------------------------##
-##                      end of Utils/CMakeLists.txt
+##                      end of MC/CMakeLists.txt
 ##---------------------------------------------------------------------------##

packages/MC/cmake/Dependencies.cmake

@@ -11,7 +11,7 @@
 SET(LIB_REQUIRED_DEP_PACKAGES
   Teuchos Matprop Utils)
 
-SET(LIB_OPTIONAL_DEP_PACKAGES CudaUtils Epetra SPn)
+SET(LIB_OPTIONAL_DEP_PACKAGES CudaUtils)
 
 SET(TEST_REQUIRED_DEP_PACKAGES)
 SET(TEST_OPTIONAL_DEP_PACKAGES)

packages/MC/mc/test/CMakeLists.txt

@@ -5,7 +5,7 @@
 ##---------------------------------------------------------------------------##
 ## Copyright (C) 2014 Oak Ridge National Laboratory, UT-Battelle, LLC.
 ##---------------------------------------------------------------------------##
-## CMAKE for spn
+## CMAKE for MC
 ##---------------------------------------------------------------------------##
 
 INCLUDE(UtilsTest)

packages/MC/mc/test/mesh4x4.xml

 <?xml version='1.0' encoding='ASCII'?>
-<ParameterList name="profugus SPN input">
+<ParameterList name="profugus MC input">
   <ParameterList name="CORE">
     <Parameter name="axial list" type="Array(string)" value="{core}"/>
     <Parameter name="axial height" type="Array(double)" value="{0.25}"/>
@@ -19,7 +19,6 @@
     <Parameter name="axial mesh" type="Array(int)" value="{1}"/>
     <Parameter name="symmetry" type="string" value="full"/>
     <Parameter name="Pn_order" type="int" value="0"/>
-    <Parameter name="SPn_order" type="int" value="3"/>
     <Parameter name="problem_name" type="string" value="acceleration"/>
   </ParameterList>
 </ParameterList>

packages/MC/mc_driver/mc.cc

@@ -3,7 +3,7 @@
  * \file   mc_driver/mc.cc
  * \author Thomas M. Evans
  * \date   Wed Mar 12 22:24:55 2014
- * \brief  SPn Mini-App executable.
+ * \brief  MC Mini-App executable.
  * \note   Copyright (C) 2014 Oak Ridge National Laboratory, UT-Battelle, LLC.
  */
 //---------------------------------------------------------------------------//

packages/MC/sim_ce/Composition.hh

-//---------------------------------*-C++-*-----------------------------------//
-/*!
- * \file   MC/sim_ce/Composition.hh
- * \author Thomas M Evans
- * \date   Fri Jan 08 15:23:48 2016
- * \brief  Composition class declaration.
- * \note   Copyright (c) 2016 Oak Ridge National Laboratory, UT-Battelle, LLC.
- */
-//---------------------------------------------------------------------------//
-
-#ifndef MC_sim_ce_Composition_hh
-#define MC_sim_ce_Composition_hh
-
-#include <cstdint>
-#include <vector>
-
-#include "harness/DBC.hh"
-
-namespace profugus
-{
-
-//===========================================================================//
-/*!
- * \class Composition
- * \brief Simple composition definition for simulated CE data.
- */
-/*!
- * \example sim_ce/test/tstComposition.cc
- *
- * Test of Composition.
- */
-//===========================================================================//
-
-class Composition
-{
-  public:
-    //@{
-    //! Typedefs.
-    using size_t    = std::uint32_t;
-    using Vec_Zaids = std::vector<size_t>;
-    using Vec_Dbl   = std::vector<double>;
-    //@}
-
-  private:
-    // ZAID.
-    Vec_Zaids d_zaids;
-
-    // Number density (/barn-cm).
-    Vec_Dbl d_N;
-
-  public:
-    Composition() = default;
-
-    //! Add zaids and number densities.
-    void add(Vec_Zaids zaids, Vec_Dbl num_den)
-    {
-        d_zaids = std::move(zaids);
-        d_N     = std::move(num_den);
-    }
-
-    //! Number of nuclides.
-    size_t num_nuclides() const { return d_N.size(); }
-
-    //@{
-    //! ZAID access.
-    const Vec_Zaids& zaids() const { return d_zaids; }
-    size_t zaid(size_t n) const
-    {
-        REQUIRE(n < d_zaids.size());
-        return d_zaids[n];
-    }
-    //@}
-
-    //@{
-    //! Number density access.
-    const Vec_Dbl& number_dens() const { return d_N; }
-    double number_den(size_t n) const
-    {
-        REQUIRE(n < d_N.size());
-        return d_N[n];
-    }
-    //@}
-};
-
-} // end namespace profugus
-
-#endif // MC_sim_ce_Composition_hh
-
-//---------------------------------------------------------------------------//
-// end of MC/sim_ce/Composition.hh
-//---------------------------------------------------------------------------//

packages/MC/sim_ce/test/CMakeLists.txt

-##---------------------------------------------------------------------------##
-## File  : MC/sim_ce/test/CMakeLists.txt
-## Author: 9te
-## Date  : Mon Jan 11 14:58:03 2016
-## Copyright (c) 2016 Oak Ridge National Laboratory, UT-Battelle, LLC.
-##---------------------------------------------------------------------------##
-## TriBITS package file for MC/sim_ce
-##---------------------------------------------------------------------------##
-
-ADD_UTILS_TEST(tstComposition.cc NP 1)
-
-##---------------------------------------------------------------------------##
-## end of MC/sim_ce/test/CMakeLists.txt
-##---------------------------------------------------------------------------##

packages/MC/sim_ce/test/tstComposition.cc

-//---------------------------------*-C++-*-----------------------------------//
-/*!
- * \file   MC/sim_ce/test/tstComposition.cc
- * \author Thomas M Evans
- * \date   Mon Jan 11 15:24:34 2016
- * \brief  Composition class definitions.
- * \note   Copyright (c) 2016 Oak Ridge National Laboratory, UT-Battelle, LLC.
- */
-//---------------------------------------------------------------------------//
-
-#include "../Composition.hh"
-
-#include "gtest/utils_gtest.hh"
-
-//---------------------------------------------------------------------------//
-// Test fixture
-//---------------------------------------------------------------------------//
-
-class CompositionTest : public ::testing::Test
-{
-  protected:
-    // >>> TYPEDEFS
-    using Composition = profugus::Composition;
-    using Vec_Zaids   = Composition::Vec_Zaids;
-    using Vec_Dbl     = Composition::Vec_Dbl;
-
-  protected:
-    void SetUp()
-    {
-        /* * */
-    }
-
-  protected:
-    // >>> DATA
-};
-
-//---------------------------------------------------------------------------//
-// TESTS
-//---------------------------------------------------------------------------//
-
-TEST_F(CompositionTest, construction)
-{
-    Composition a, b;
-
-    // construct a
-    {
-        Vec_Zaids z = {1001, 8016};
-        Vec_Dbl   N = {0.06684, 0.03342};
-
-        a.add(z, N);
-    }
-
-    // construct b (with move)
-    {
-        Vec_Zaids z = {8016, 92234, 92235, 92236, 92238};
-        Vec_Dbl   N = {0.046227, 7.49947e-06, 0.000865724, 3.96543e-06,
-                       0.0222363};
-
-        b.add(std::move(z), std::move(N));
-    }
-
-    EXPECT_EQ(2, a.num_nuclides());
-    EXPECT_EQ(5, b.num_nuclides());
-
-    Vec_Zaids rza = {1001, 8016};
-    Vec_Dbl   rNa = {0.06684, 0.03342};
-    Vec_Zaids rzb = {8016, 92234, 92235, 92236, 92238};
-    Vec_Dbl   rNb = {0.046227, 7.49947e-06, 0.000865724, 3.96543e-06,
-                     0.0222363};
-
-    EXPECT_VEC_EQ(rza, a.zaids());
-    EXPECT_VEC_EQ(rzb, b.zaids());
-
-    EXPECT_VEC_EQ(rNa, a.number_dens());
-    EXPECT_VEC_EQ(rNb, b.number_dens());
-
-    for (int n = 0; n < 2; ++n)
-    {
-        EXPECT_EQ(rza[n], a.zaid(n));
-        EXPECT_EQ(rNa[n], a.number_den(n));
-    }
-}
-
-//---------------------------------------------------------------------------//
-// end of MC/sim_ce/test/tstComposition.cc
-//---------------------------------------------------------------------------//