Structural concentrated point load and associated example updates.

.gitignore

@@ -6,14 +6,9 @@ build
 # Files generated by CMake.
 src/base/mast_config.h
 
-# Files generated by Python example/documentation preprocessor.
-doc/example_1.dox
-doc/example_2.dox
-doc/example_3.dox
-
 # CLion IDE files.
 .idea/
-cmake-build-debug/
+cmake-build*/
 build2
 
 # Visual Studio Code settings.

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "doc/assets"]
+	path = doc/assets
+	url = https://github.com/MASTmultiphysics/mast-assets.git

.travis.yml

@@ -1,49 +1,50 @@
 language: cpp
-dist: xenial
+
+matrix:
+    include:
+      # macOS/Linux builds - libMesh version 1.5.0
+      - os: osx
+        osx_image: xcode10.2
+        env: LIBMESH_VERSION=1.5.0
+      - os: linux
+        dist: xenial
+        env: LIBMESH_VERSION=1.5.0
+
+      # Doxygen documentation build
+      # - this job also progresses to deployment when on master branch
+      - os: linux
+        dist: xenial
+        env: CI_BUILD_DOCS=true CI_DEPLOY_DOCS=true LIBMESH_VERSION=1.4.1
+
+      # macOS/Linux builds - libMesh version 1.4.1
+      - os: osx
+        osx_image: xcode10.2
+        env: LIBMESH_VERSION=1.4.1
+      - os: linux
+        dist: xenial
+        env: LIBMESH_VERSION=1.4.1
+
+      # macOS/Linux builds - libMesh version 1.3.1
+      - os: osx
+        osx_image: xcode10.2
+        env: LIBMESH_VERSION=1.3.1
+      - os: linux
+        dist: xenial
+        env: LIBMESH_VERSION=1.3.1
 
 before_install:
-- sudo apt-get -qq install -y gfortran wget m4
-- sudo apt-get -qq install -y openmpi-bin libopenmpi-dev
-- sudo apt-get -qq install -y libpetsc3.6 libpetsc3.6.2-dev
-- sudo apt-get -qq install -y libslepc3.6 libslepc3.6.1-dev libparpack2-dev
-- sudo apt-get -qq install -y libboost-all-dev
-- sudo apt-get -qq install -y libeigen3-dev
-- sudo apt-get -qq install -y doxygen graphviz rsync
-- sudo apt-get -qq install -y texlive-latex-base dvi2ps ghostscript
+  - ci/build_dependencies.sh
 
 install:
-- cd ${HOME}
-- wget -nv https://github.com/MASTmultiphysics/mast-ci-packages/releases/download/libmesh-1.3.1-1.deb/libmesh-1.3.1-1.deb
-- sudo apt install ./libmesh-1.3.1-1.deb
-
-before_script:
-- export MAST_INSTALL_DIR=${HOME}/mast
-- cd ${TRAVIS_BUILD_DIR}
-- mkdir build
-- cd build
-- cmake ..
-    -DCMAKE_INSTALL_PREFIX=${MAST_INSTALL_DIR}
-    -DCMAKE_C_COMPILER=mpicc
-    -DCMAKE_CXX_COMPILER=mpic++
-    -DCMAKE_Fortran_COMPILER=mpifort
-    -DlibMesh_DIR=/usr/local
-    -DPETSc_DIR=/usr/lib/petscdir/3.6.2/x86_64-linux-gnu-real
-    -DSLEPc_DIR=/usr/lib/slepcdir/3.6.1/x86_64-linux-gnu-real
-    -DEIGEN3_ROOT=/usr/include/eigen3
-    -DBOOST_ROOT=/usr
-    -DBUILD_DOC=ON
-    -DENABLE_DOT=OFF
-    -DENABLE_GCMMA=OFF
-    -DENABLE_SNOPT=OFF
+  - ci/get_libmesh.sh
 
 script:
-- make -j 2
-- make -j 2 doc_doxygen
-- cd ${TRAVIS_BUILD_DIR}
+  - ci/build_mast.sh
 
 deploy:
-    provider: script
-    script: bash doc/deploy_docs.sh
-    skip_cleanup: true
-    on:
-        branch: master
+  provider: script
+  script: bash ci/deploy_docs.sh
+  skip_cleanup: true
+  on:
+    branch: master
+    condition: ${CI_DEPLOY_DOCS} = true

CMakeLists.txt

@@ -1,8 +1,8 @@
 # PREAMBLE
-cmake_minimum_required(VERSION 3.2)
+cmake_minimum_required(VERSION 3.13)
 project(MAST
-        VERSION 0.3
-        LANGUAGES C CXX)
+    VERSION 2.0.1
+    LANGUAGES C CXX)
 
 # PROJECT WIDE SETUP
 # Get CMake modules and set language standards.
@@ -14,33 +14,34 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 include(GNUInstallDirs)
 
 # Build options with defaults.
-option(ENABLE_GCMMA   "Build with GCMMA interface"  OFF)
-option(ENABLE_DOT     "Build with DOT interface"    OFF)
-option(ENABLE_SNOPT   "Build with SNOPT interface"  OFF)
-option(ENABLE_NLOPT   "Build with NLOPT interface"  OFF)
-option(ENABLE_CYTHON  "Build with CYTHON interface" OFF)
-option(BUILD_DOC      "Build documentation"         OFF)
-
-# Required dependency paths.
+option(ENABLE_GCMMA     "Build with GCMMA interface"  OFF)
+option(ENABLE_DOT       "Build with DOT interface"    OFF)
+option(ENABLE_SNOPT     "Build with SNOPT interface"  OFF)
+option(ENABLE_NLOPT     "Build with NLOPT interface"  OFF)
+option(ENABLE_NASTRANIO "Build with support for reading Nastran meshes" OFF)
+option(ENABLE_CYTHON    "Build with support for Cython development"     OFF)
+option(BUILD_DOC        "Build documentation"         OFF)
+
+# Dependency paths (optional) - these paths help CMake find dependencies.
 set(MAST_ROOT_DIR ${CMAKE_CURRENT_LIST_DIR})
 set(libMesh_DIR "libMesh_DIR" CACHE PATH "Directory containing libMesh include/ and lib/")
 set(PETSc_DIR   "PETSc_DIR"   CACHE PATH "Directory containing PETSc include/ and lib/")
 set(PETSc_ARCH  "PETSc_ARCH"  CACHE STRING "Configuration/build of PETSc that should be used.")
 set(SLEPc_DIR   "SLEPc_DIR"   CACHE PATH "Directory containing SLEPc include/ and lib/")
 set(SLEPc_ARCH  "SLEPc_ARCH"  CACHE STRING "Configuration/build of SLEPc that should be used.")
 set(EIGEN3_ROOT "Eigen_DIR"   CACHE PATH "Directory containing eigen header files")
-set(DOT_DIR "DOT_DIR"   CACHE PATH "Directory containing DOT lib/")
-set(SNOPT_DIR "SNOpt_DIR"   CACHE PATH "Directory containing SNOPT lib/")
-set(NLOPT_DIR "NLOpt_DIR"   CACHE PATH "Directory containing NLOpt include/ and lib/")
+set(DOT_DIR     "DOT_DIR"     CACHE PATH "Directory containing DOT lib/")
+set(SNOPT_DIR   "SNOpt_DIR"   CACHE PATH "Directory containing SNOPT lib/")
+set(NLOPT_DIR   "NLOpt_DIR"   CACHE PATH "Directory containing NLOpt include/ and lib/")
 
 # EXTERNALLY PROVIDED CONTENT
 # None. Use this if we pull something in during the build in the future.
 
 # FIND DEPENDENCIES
 find_package(MPI REQUIRED)
 find_package(LAPACK REQUIRED)
-message("-- Found BLAS libs: ${BLAS_LIBRARIES}")
-message("-- Found LAPACK libs: ${LAPACK_LIBRARIES}")
+message(STATUS "Found BLAS libs: ${BLAS_LIBRARIES}")
+message(STATUS "Found LAPACK libs: ${LAPACK_LIBRARIES}")
 find_package(PETSc REQUIRED)
 find_package(SLEPc REQUIRED)
 find_package(HDF5 REQUIRED)
@@ -52,8 +53,8 @@ find_package(Eigen3 REQUIRED)
 #       Boost CMake configuration in the FindBoost module for now.
 set(Boost_NO_BOOST_CMAKE ON) 
 find_package(Boost COMPONENTS iostreams system filesystem unit_test_framework REQUIRED)
-message("-- Found Boost include: ${Boost_INCLUDE_DIRS}") # To ensure the found Boost is what user expected
-message("-- Found Boost libs:    ${Boost_LIBRARY_DIRS}") # To ensure the found Boost is what user expected
+message(STATUS "Found Boost include: ${Boost_INCLUDE_DIRS}") # To ensure the found Boost is what user expected
+message(STATUS "Found Boost libs:    ${Boost_LIBRARY_DIRS}") # To ensure the found Boost is what user expected
 
 # Find optional packages.
 if (ENABLE_GCMMA)
@@ -83,12 +84,37 @@ else()
     set (MAST_ENABLE_NLOPT 0)
 endif()
 
+if (ENABLE_NASTRANIO)
+    find_package(Python3 REQUIRED)
+
+    # Make sure Python has pyNastran.
+    execute_process(COMMAND ${Python3_EXECUTABLE} -c "import pyNastran"
+        RESULT_VARIABLE PYNASTRAN_ERROR)
+    if(PYNASTRAN_ERROR)
+        message(FATAL_ERROR "Error finding pyNastran package for Python3_EXECUTABLE!")
+    else()
+        message(STATUS "  pyNastran package found")
+    endif()
+
+    # Make sure Python has NumPy.
+    execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy"
+        RESULT_VARIABLE NUMPY_ERROR)
+    if(NUMPY_ERROR)
+        message(FATAL_ERROR "Error finding pyNastran package for Python3_EXECUTABLE!")
+    else()
+        message(STATUS "  Numpy package found")
+    endif()
+
+endif()
+
+# THIRD PARTY/CONTRIB
+# - This directory contains files developed by third parties and are included in the
+#   MAST source for convenience.
+add_subdirectory(contrib)
+
 # MAIN TARGETS
 add_subdirectory(src)
 
-# EXAMPLES
-add_subdirectory(examples)
-
 # DOCUMENTATION
 if(BUILD_DOC)
     add_subdirectory(doc)
@@ -98,3 +124,5 @@ endif()
 enable_testing()
 add_subdirectory(tests)
 
+# EXAMPLES
+add_subdirectory(examples)

README.md

@@ -1,9 +1,20 @@
 MAST: Multidisciplinary-design Adaptation and Sensitivity Toolkit
-Copyright (C) 2013-2019  Manav Bhatia
+Copyright (C) 2013-2020  Manav Bhatia and MAST authors
 
 [![Build Status](https://travis-ci.com/MASTmultiphysics/mast-multiphysics.svg?branch=master)](https://travis-ci.com/MASTmultiphysics/mast-multiphysics)
 
 This code was developed under funding from the Air Force Research Laboratory. 
 MAST was cleared for public release on 08 Nov 2016 with case number 88ABW-2016-5689. 
 
 Documentation for the code is available at [https://mastmultiphysics.github.io](https://mastmultiphysics.github.io).
+
+## Submodules
+To keep the size of this main MAST repository smaller, a git submodule is used 
+to store larger media/assets such as images and animations used for the documentation 
+in a separate repo (doc/assets). To build the documentation locally, you must update
+the submodule. To do this, simply run the following commands from inside the root
+level of this main repository:
+```
+git submodule init
+git submodule update
+```

ci/README.md

@@ -0,0 +1,48 @@
+# Travis CI Testing/Deployment
+
+On the GitHub repository of MAST, Travis CI (https://travis-ci.com) is utilized for build testing on multiple OS's and
+deployment of updated documentation online. In the future we will integrate the execution of both unit tests as well as 
+example problems for integration testing.
+
+This directory contains scripts utilized by the Travis CI process.
+
+## Travis CI Processes
+When a commit is pushed to the MASTmultiphysics/mast-multiphysics GitHub repository, GitHub initiates the continuous
+integration processes on Travis CI. What these processes do is controlled by the `.travis.yml` file in the root of the
+repository. The different phases of a Travis CI are described at https://docs.travis-ci.com/user/job-lifecycle/. This
+repository utilizes a relatively basic subset of the phases and overall capability of Travis CI.
+
+The files in this directory are utilized in the main phases of the Travis CI lifecycle:
+
+1. `before_install` - `build_dependencies.sh` - This script ensures that the Travis CI runner executing the current job
+has the required dependencies for libMesh and building MAST.
+2. `install` - `get_libmesh.sh` - This script fetches pre-built binaries of libMesh on Linux or the entire dependency
+package on macOS. Travis CI jobs have a limited time for execution that is not long enough to build libMesh 
+(which is not available in job runners standard Linux/macOS package managers.)
+3. `script` - `build_mast.sh` - Depending on the job, this script either builds the MAST library/examples or builds the
+doxygen documentation.
+4. `deploy` - `deploy_docs.sh` - For the job satisfying the appropriate conditions, this script pushes the documentation
+website produced by doxygen to the hosting location.
+
+## Multiple OS's/Jobs/Environments
+The `matrix` section of the `.travis.yml` file allows for the definition of multiple jobs to be run that can be done
+in different environments or on different workers. Each item under `matrix/include` causes the execution of different 
+Travis CI worker with the specified environment. In the current setup, we utilize both Linux and macOS to test builds 
+against different compilers as well as different versions of the libMesh dependency, which is periodically updated by 
+that projects maintainers. In this setup, Travis CI allows for the specification of system environment variables that
+are utilized by the scripts in the `ci` folder for distinguishing work that is specific to each environment.
+
+### Linux
+The current Linux build environment utilizes Ubuntu 16.04. Dependencies available in the Ubuntu apt package repositories
+are leveraged; however, in the future these may be updated as versions of PETSc/SLEPc are quite old. The current
+compiler on Linux is GNU GCC-5.4.0. The libMesh dependencies are provided as external binaries that were built in an
+identical environment and archived.
+
+### macOS
+The macOS build on Travis CI current utilizes macOS version 10.14.4 with the default clang C/C++ compiler (Apple LLVM 
+version 10.0.1). Travis CI suggests utilizing Homebrew to install dependencies, which currently does not contain many of
+the packages required for libMesh/MAST. To overcome this, a complete set dependencies (including multiple versions of
+libMesh) is built/archived using Spack on the same environment setup (macOS version/compiler) the Travis CI utilizes. 
+These dependencies are fetched by the Travis CI runner and MAST is built against them. Since macOS does not provide a
+Fortran compiler, GCC-9.1.0 is first built via Spack. The compiler toolchain is then macOS-provided C/C++ and
+gfortran-9.

ci/build_dependencies.sh

@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+
+if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
+
+  if [ "${TRAVIS_DIST}" = xenial ]; then # Ubuntu 16.04 Xenial Xerus
+    cd ${HOME} || exit
+
+    # Python 3.6 apt repository (since its not neatly included in Ubuntu 16.04)
+    sudo add-apt-repository -y ppa:deadsnakes/ppa
+
+    # Regular libMesh/MAST dependencies.
+    sudo apt-get -qq update
+    sudo apt-get -qq install -y gfortran wget m4
+    sudo apt-get -qq install -y openmpi-bin libopenmpi-dev
+    sudo apt-get -qq install -y libpetsc3.6 libpetsc3.6.2-dev
+    sudo apt-get -qq install -y libslepc3.6 libslepc3.6.1-dev libparpack2-dev
+    sudo apt-get -qq install -y libboost-all-dev
+    sudo apt-get -qq install -y libeigen3-dev
+    sudo apt-get -qq install -y doxygen graphviz rsync
+    sudo apt-get -qq install -y texlive-latex-base dvi2ps ghostscript
+    sudo apt-get -qq install -y python3.6 python3.6-dev libpython3.6
+
+    # Get pip working with external Python 3.6.
+    wget https://bootstrap.pypa.io/get-pip.py || exit
+    sudo python3.6 get-pip.py || exit
+
+    sudo python3.6 -m pip install numpy scipy docopt colorama pandas h5py matplotlib cpylog pyNastran
+    sudo python3.6 -m pip install Cython --install-option="--no-cython-compile"
+
+    # Update to later CMake release.
+    wget https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5-Linux-x86_64.sh || exit
+    sudo mkdir /opt/cmake || exit
+    sudo sh cmake-3.15.5-Linux-x86_64.sh --prefix=/opt/cmake --skip-license || exit
+
+  # elif [ "${TRAVIS_DIST}" = bionic ]; then # Ubuntu 18.04 Bionic Beaver
+  #  sudo apt-get -qq update
+  #  sudo apt-get -qq install -y gfortran wget m4
+  #  which gfortran
+  #  gcc --version
+  #  echo "Hello From BIONIC"
+
+  else
+    echo "INVALID LINUX DISTRO: ${TRAVIS_DIST}"
+    exit 1
+  fi
+
+elif [ "${TRAVIS_OS_NAME}" = osx ]; then # macOS 10.14, XCode 10.2
+  # Currently we don't do anything here since we get all dependencies for macOS
+  # from the binary download with "ci/get_libmesh.sh" in the next stage.
+  echo "Hello From OSX"
+
+else
+  echo "INVALID OS: ${TRAVIS_OS_NAME}"
+  exit 1
+fi