Merge pull request #50 from MASTmultiphysics/nastran_io

NastranIO support for reading Nastran meshes/subdomains/boundaries.

Author: jdeaton

.gitignore

@@ -6,11 +6,6 @@ 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*/

.gitmodules

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

.travis.yml

@@ -40,7 +40,6 @@ install:
 
 script:
   - ci/build_mast.sh
-  -
 
 deploy:
   provider: script

CMakeLists.txt

@@ -1,5 +1,5 @@
 # PREAMBLE
-cmake_minimum_required(VERSION 3.2)
+cmake_minimum_required(VERSION 3.13)
 project(MAST
         VERSION 0.3
         LANGUAGES C CXX)
@@ -14,24 +14,25 @@ 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.
@@ -83,12 +84,36 @@ 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 +123,6 @@ endif()
 enable_testing()
 add_subdirectory(tests)
 
+# EXAMPLES
+add_subdirectory(examples)
+

README.md

@@ -7,3 +7,14 @@ 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/build_dependencies.sh

@@ -3,6 +3,12 @@
 if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
 
   if [ "${TRAVIS_DIST}" = xenial ]; then # Ubuntu 16.04 Xenial Xerus
+    cd ${HOME} || exit
+
+    # Python 3.6 apt repository (since its not neatly included in Ubuntu 16.04)
+    sudo add-apt-repository -y ppa:deadsnakes/ppa
+
+    # Regular libMesh/MAST dependencies.
     sudo apt-get -qq update
     sudo apt-get -qq install -y gfortran wget m4
     sudo apt-get -qq install -y openmpi-bin libopenmpi-dev
@@ -12,6 +18,19 @@ if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
     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

ci/build_mast.sh

@@ -18,7 +18,7 @@ if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
     # First let us build/install a Release (optimized) version of MAST (-DCMAKE_BUILD_TYPE=Release).
     echo "TEST RELEASE/OPTIMIZED BUILD..."
     cd build_rel || exit
-    cmake .. \
+    /opt/cmake/bin/cmake .. \
       -DCMAKE_BUILD_TYPE=Release \
       -DCMAKE_INSTALL_PREFIX="${MAST_INSTALL_DIR}" \
       -DCMAKE_C_COMPILER=mpicc \
@@ -28,14 +28,19 @@ if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
       -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 \
+      -DPython3_DIR=/usr \
       -DBOOST_ROOT=/usr \
       -DBUILD_DOC=ON \
       -DENABLE_DOT=OFF \
       -DENABLE_GCMMA=OFF \
-      -DENABLE_SNOPT=OFF || exit
+      -DENABLE_SNOPT=OFF \
+      -DENABLE_NASTRANIO=ON \
+      -DENABLE_CYTHON=ON || exit
 
     if [ ${CI_BUILD_DOCS} ]; then
       make doc_doxygen || exit
+      cd ${TRAVIS_BUILD_DIR} || exit
+      ci/prepare_docs.sh || exit
     else
       make -j 2 || exit
       make install || exit
@@ -51,7 +56,7 @@ if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
     else
 
       cd ../build_dbg || exit
-      cmake .. \
+      /opt/cmake/bin/cmake .. \
         -DCMAKE_BUILD_TYPE=Debug \
         -DCMAKE_INSTALL_PREFIX="${MAST_INSTALL_DIR}" \
         -DCMAKE_C_COMPILER=mpicc \
@@ -61,11 +66,14 @@ if [ "${TRAVIS_OS_NAME}" = linux ]; then # Ubuntu Linux
         -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 \
+        -DPython3_DIR=/usr \
         -DBOOST_ROOT=/usr \
         -DBUILD_DOC=ON \
         -DENABLE_DOT=OFF \
         -DENABLE_GCMMA=OFF \
-        -DENABLE_SNOPT=OFF || exit
+        -DENABLE_SNOPT=OFF\
+        -DENABLE_NASTRANIO=ON \
+        -DENABLE_CYTHON=ON || exit
 
       if [ ${CI_BUILD_DOCS} ]; then
         echo "No CI documentation for a Debug build."
@@ -115,12 +123,16 @@ elif [ "${TRAVIS_OS_NAME}" = osx ]; then # macOS 10.14, XCode 10.2
     -DEIGEN3_ROOT=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/eigen-3.3.7-bd2r4aqrkox7dpebj2r3gqvgpqzwuh7x \
     -DLAPACK_LIBRARIES=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.7-xqeap7iegoomce3es67cd7exlnq3neue/lib/libopenblas.dylib \
     -DBLAS_LIBRARIES=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.7-xqeap7iegoomce3es67cd7exlnq3neue/lib/libopenblas.dylib \
+    -DPython3_DIR=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-hh7odiqwzpw2nnfdcfzjxvb3ggyzwvfk \
     -DENABLE_GCMMA=OFF \
     -DENABLE_DOT=OFF \
     -DENABLE_SNOPT=OFF \
     -DENABLE_NLOPT=OFF \
     -DENABLE_CYTHON=OFF \
-    -DBUILD_DOC=OFF || exit
+    -DBUILD_DOC=OFF \
+    -DENABLE_NASTRANIO=ON \
+    -DENABLE_CYTHON=ON || exit
+
   make -j 2 || exit
   make install || exit
 
@@ -141,12 +153,16 @@ elif [ "${TRAVIS_OS_NAME}" = osx ]; then # macOS 10.14, XCode 10.2
     -DEIGEN3_ROOT=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/eigen-3.3.7-bd2r4aqrkox7dpebj2r3gqvgpqzwuh7x \
     -DLAPACK_LIBRARIES=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.7-xqeap7iegoomce3es67cd7exlnq3neue/lib/libopenblas.dylib \
     -DBLAS_LIBRARIES=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.7-xqeap7iegoomce3es67cd7exlnq3neue/lib/libopenblas.dylib \
+    -DPython3_DIR=/Users/travis/Code/spack-mstc/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-hh7odiqwzpw2nnfdcfzjxvb3ggyzwvfk \
     -DENABLE_GCMMA=OFF \
     -DENABLE_DOT=OFF \
     -DENABLE_SNOPT=OFF \
     -DENABLE_NLOPT=OFF \
     -DENABLE_CYTHON=OFF \
-    -DBUILD_DOC=OFF || exit
+    -DBUILD_DOC=OFF \
+    -DENABLE_NASTRANIO=ON \
+    -DENABLE_CYTHON=ON || exit
+
   make -j 2 || exit
 
 else

ci/deploy_docs.sh

@@ -1,31 +1,17 @@
 #!/usr/bin/env bash
 
-# Deploy Doxygen generated HTML documentation to Github for hosting.
+# Deploy organized HTML documentation to Github for hosting.
 #
-#    This script deploys Doxygen generated HTML documentation to the MAST Github repository for hosting. It is meant
-#    to be called during the Travis-CI 'deploy' stage and requires the GH_TOKEN environment variable be set in
-#    the Travis-CI job from an account that can push to https://github.com/MASTmultiphysics/MASTmultiphysics.github.io
+#    This script deploys organized HTML documentation produced by `prepare_docs.sh` to a repository in the MAST Team
+#    GitHub repository for hosting. It is meant to be called during the Travis-CI `deploy` stage and requires the
+#    GH_TOKEN environment variable be set in the Travis-CI job from an account that can push
+#    to https://github.com/MASTmultiphysics/MASTmultiphysics.github.io
 #
-#    Contents of this script were inspired in part by https://gist.github.com/willprice/e07efd73fb7f13f917ea.
-
-# Setup git user for website commit information.
-git config --global user.email "[email protected]"
-git config --global user.name "Travis CI"
-
-# Organize website content. First delete all current contents (except .git directory) and then copy generated
-# HTML and other desired files.
-mkdir ${TRAVIS_BUILD_DIR}/website
-cd ${TRAVIS_BUILD_DIR}/website
-rsync -r ${TRAVIS_BUILD_DIR}/build_rel/doc/doxygen/html/ .
-cp ${TRAVIS_BUILD_DIR}/doc/README.md .
-
-# Initialize empty git repository. Add all files. Commit.
-git init
-git add .
-git commit --quiet --message "Travis build ${TRAVIS_BUILD_NUMBER}, mast-multiphysics commit ${TRAVIS_COMMIT}"
+#    Contents of this script (and `prepare_docs.sh`) were inspired in part
+#    by https://gist.github.com/willprice/e07efd73fb7f13f917ea.
 
 # Set git remote URL. Force push to GitHub website repository.
 # Update git remote URL to include ${GH_TOKEN} key. Push files back to GitHub website repository.
-git remote add origin https://${GH_TOKEN}@github.com/MASTmultiphysics/MASTmultiphysics.github.io.git
-git push --force origin master
+git remote add origin https://${GH_TOKEN}@github.com/MASTmultiphysics/MASTmultiphysics.github.io.git || exit
+git push --force origin master || exit
 

ci/prepare_docs.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+# Prepare/organized Doxygen generated HTML documentation to Github for hosting by `deploy_docs.sh`.
+#
+#    This script organizes the Doxygen generated HTML documentation and commits it to local .git repository.
+#    Doxygen generated HTML documentation to the MAST Github repository for hosting. This script should be called
+#    during the Travis-CI 'script' phase after documentation is built so that if an error occurs we can catch it
+#    on a non-master build (the 'deploy' stage only runs for commits on the `master` branch). We currently call it
+#    inside of `ci/build_mast.sh` on the worker that satisfies ${CI_BUILD_DOCS}=true.
+#
+#    Contents of this script (and `deploy_docs.sh`) were inspired in part by
+#    https://gist.github.com/willprice/e07efd73fb7f13f917ea.
+
+# Setup git user for website commit information.
+git config --global user.email "[email protected]" || exit
+git config --global user.name "Travis CI" || exit
+
+# Organize website content. First delete all current contents (except .git directory) and then copy generated
+# HTML and other desired files.
+mkdir ${TRAVIS_BUILD_DIR}/website || exit
+cd ${TRAVIS_BUILD_DIR}/website || exit
+rsync -r ${TRAVIS_BUILD_DIR}/build_rel/doc/doxygen/html/ . || exit
+
+# Initialize empty git repository. Add all files. Commit.
+git init || exit
+git add . || exit
+git commit --quiet --message "Travis build ${TRAVIS_BUILD_NUMBER}, mast-multiphysics commit ${TRAVIS_COMMIT}" || exit

cmake/FindCython.cmake

@@ -0,0 +1,58 @@
+# Find the Cython compiler.
+#
+# This code sets the following variables:
+#
+#  Cython_FOUND - Cython is available on the system.
+#  Cython_EXECUTABLE - Path to the Cython executable.
+#
+# Note this file is a modified version of that provided by Kitware online.
+# --- see original Kitware copyright statement at bottom of file.
+
+# Use the Cython executable that lives next to the Python executable if it
+# exists. If not, we will use whatever we can find on the system paths.
+if(Python3_FOUND)
+    get_filename_component(_PYTHON_PATH ${Python3_EXECUTABLE} PATH)
+    find_program(Cython_EXECUTABLE
+            NAMES
+            cython
+            cython.bat
+            cython3
+            HINTS ${_PYTHON_PATH})
+else()
+    find_program(Cython_EXECUTABLE
+            NAMES
+            cython
+            cython.bat
+            cython3)
+endif()
+
+# Set standard CMake variables and output status.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Cython
+        REQUIRED_VARS
+        Cython_EXECUTABLE)
+
+# Advance cache variables.
+mark_as_advanced(Cython_EXECUTABLE)
+
+
+
+
+
+# Original Kitware copywrite statement. Modifications to code included
+# formatting changes to utilize MAST-Interface version of FindPython.cmake.
+#=============================================================================
+# Copyright 2011 Kitware, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#=============================================================================