Eigenproblem Sensitivity Fix

.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 +1,57 @@
 language: cpp
-dist: xenial
+
+matrix:
+    include:
+      # macOS/Linux builds - libMesh version 1.5.1
+      - os: osx
+        osx_image: xcode10.2
+        env: LIBMESH_VERSION=1.5.1
+      - os: linux
+        dist: bionic
+        env: LIBMESH_VERSION=1.5.1
+
+      # Doxygen documentation build
+      # - this job also progresses to deployment when on master branch
+      - os: linux
+        dist: bionic
+        env: CI_BUILD_DOCS=true CI_DEPLOY_DOCS=true LIBMESH_VERSION=1.5.1
+
+      # macOS/Linux builds - libMesh version 1.4.1
+      - os: osx
+        osx_image: xcode10.2
+        env: LIBMESH_VERSION=1.4.1
+      - os: linux
+        dist: bionic
+        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
+
+before_deploy:
+- openssl aes-256-cbc -K $encrypted_db2095f63ba3_key -iv $encrypted_db2095f63ba3_iv -in doc/deploy_rsa.enc -out /tmp/deploy_rsa -d
+- eval "$(ssh-agent -s)"
+- chmod 600 /tmp/deploy_rsa
+- ssh-add /tmp/deploy_rsa
 
 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:
+    all_branches: true
+    repo: MASTmultiphysics/mast-multiphysics
+    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)