Merge branch 'develop'

This adds in wall functions

.appveyor.yml

@@ -0,0 +1,21 @@
+version: 1.0.{build}
+branches:
+  only:
+  - master
+  - develop
+image: Visual Studio 2015
+configuration: release
+platform: x64
+environment:
+  PYTHON: C:\Python35-x64
+  PATH: C:\Program Files\Project\bin;C:\Program Files\Microsoft MPI\Bin;%PATH%
+build_script:
+- ps: >-
+    powershell ci\appveyor\installMPI.ps1
+
+    powershell ci\appveyor\buildAither.ps1
+test_script:
+- cmd: >-
+    cd testCases
+
+    %PYTHON%\python.exe regressionTests.py --mpirunPath=mpiexec.exe --aitherPath=aither.exe

.codecov.yml

@@ -0,0 +1,2 @@
+fixes:
+  - "/home/travis/build/mnucci32/aither::"

.gitignore

@@ -1,16 +1,18 @@
-#Ignore temporary copy files
+# Ignore temporary copy files
 *~
 \#*
 
-#Ignore results files
+# Ignore results files
 *.fun
 *.res
 *.out
 *_center.xyz
 *.resid
 *.p3d
 
-#Ignore blog files
+# Ignore blog files
 .sass-cache/
 _site/
 
+# Ignore VS Code files
+.vscode/

.travis.yml

@@ -26,6 +26,7 @@ matrix:
       env:
         - CXX_COMPILER=g++-5
         - C_COMPILER=gcc-5
+        - BUILD_TYPE=release
     - os: linux
       dist: trusty
       sudo: required
@@ -35,10 +36,11 @@ matrix:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-6 gcc-6 libstdc++-6-dev
+            - g++-6 gcc-6 libstdc++-6-dev lcov
       env:
         - CXX_COMPILER=g++-6
         - C_COMPILER=gcc-6
+        - BUILD_TYPE=debug
     - os: linux
       dist: trusty
       sudo: required
@@ -53,6 +55,7 @@ matrix:
       env:
         - CXX_COMPILER=clang++-3.8
         - C_COMPILER=clang-3.8
+        - BUILD_TYPE=release
     - os: osx
       osx_image: xcode8
       compiler: gcc
@@ -61,6 +64,7 @@ matrix:
         - C_COMPILER=gcc-6
         - HOMEBREW_CC=gcc-6
         - HOMEBREW_CXX=g++-6
+        - BUILD_TYPE=release
     - os: osx
       osx_image: xcode8
       compiler: clang
@@ -69,6 +73,7 @@ matrix:
         - C_COMPILER=clang
         - HOMEBREW_CC=clang
         - HOMEBREW_CXX=clang++
+        - BUILD_TYPE=release
 
 # upgrade packages
 before_install:
@@ -82,14 +87,27 @@ before_install:
 
 # install mpi
 install:
-  - bash travis/installMPI
+  - bash ci/travis/installMPI
 
-# build instructions
-script:
+before_script:
   - mkdir build
   - cd build
-  - cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=$CXX_COMPILER -DCMAKE_C_COMPILER=$C_COMPILER -DMPI_DIR=$TRAVIS_BUILD_DIR/openmpi -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=install ..
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then lcov --directory . --zerocounters; fi
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then ln -s /usr/bin/gcov-6 gcov; fi
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then export PATH=$PWD:$PATH; fi
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then gcov --version; fi
+
+# build instructions
+script:
+  - cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=$CXX_COMPILER -DCMAKE_C_COMPILER=$C_COMPILER -DMPI_DIR=$TRAVIS_BUILD_DIR/openmpi -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_INSTALL_PREFIX=install ..
   - make -j4
   - make install
   - cd ../testCases
-  - python3 regressionTests.py --aitherPath=$TRAVIS_BUILD_DIR/build/install/bin/aither --operatingSystem=$TRAVIS_OS_NAME --mpirunPath=$TRAVIS_BUILD_DIR/openmpi/bin/mpirun
+  - python3 regressionTests.py --aitherPath=$TRAVIS_BUILD_DIR/build/install/bin/aither --operatingSystem=$TRAVIS_OS_NAME --mpirunPath=$TRAVIS_BUILD_DIR/openmpi/bin/mpirun
+  - cd $TRAVIS_BUILD_DIR/build
+
+after_success:
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then lcov --directory . --capture --rc lcov_branch_coverage=1 --output-file coverage.info; fi
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then lcov --remove coverage.info '/usr/*' '/Applications/*' '/Library/*' --rc lcov_branch_coverage=1 --output-file coverage.info; fi
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then lcov --rc lcov_branch_coverage=1 --list coverage.info; fi
+  - if [[ "$BUILD_TYPE" == "debug" ]]; then bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"; fi

README.md

@@ -1,38 +1,67 @@
 # Accurate Implicit Three-dimensional Efficient RANS (AITHER)
 
-[![Build Status](https://travis-ci.org/mnucci32/aither.svg?branch=master)](https://travis-ci.org/mnucci32/aither)
+| Branch  | Linux/macOS Build | Windows Build | Coverage |
+|---      |---    |---    |---    |
+| Master  | [![Build Status](https://travis-ci.org/mnucci32/aither.svg?branch=master)](https://travis-ci.org/mnucci32/aither) | [![Build status](https://ci.appveyor.com/api/projects/status/o7fc231lp9jxlsib/branch/master?svg=true)](https://ci.appveyor.com/project/mnucci32/aither/branch/master) | [![Coverage Status](https://codecov.io/github/mnucci32/aither/coverage.svg?branch=master)](https://codecov.io/github/mnucci32/aither?branch=master) |
+| Develop | [![Build Status](https://travis-ci.org/mnucci32/aither.svg?branch=develop)](https://travis-ci.org/mnucci32/aither) | [![Build status](https://ci.appveyor.com/api/projects/status/o7fc231lp9jxlsib/branch/develop?svg=true)](https://ci.appveyor.com/project/mnucci32/aither/branch/develop) | [![Coverage Status](https://codecov.io/github/mnucci32/aither/coverage.svg?branch=develop)](https://codecov.io/github/mnucci32/aither?branch=develop) |
 
 ### About The code
-This code is for a 3D Navier-Stokes computational fluid dynamics solver. It is a cell centered, structured solver, using mulit-block structured grids in Plot3D format. It uses explicit and implicit time integration methods. It uses MUSCL extrapolation to reconstruct the primative variables from the cell centers to the cell faces. The code uses the Roe flux difference splitting scheme for the inviscid fluxes, and a central scheme for the viscous fluxes. It is second order accurate in both space and time.
+This code is for a 3D Navier-Stokes computational fluid dynamics solver. It is 
+a cell centered, structured solver, using multi-block structured grids in Plot3D 
+format. It uses explicit and implicit time integration methods. It uses MUSCL 
+extrapolation to reconstruct the primative variables from the cell centers to 
+the cell faces for 2nd order accuracy. Higher order reconstruction is acheived 
+with a 5th order WENO reconstruction for the inviscid fluxes, and a 4th order 
+central reconstruction for the viscous fluxes. The code uses the Roe 
+flux difference splitting scheme for the inviscid fluxes, and a central scheme 
+for the viscous fluxes. It is second order accurate in both space and time.
 
 ### Current Status
-The code is 2nd order accurate in space and time. Available explicit time integration methods are forward euler (1st order) and a minimum storage four stage Runge-Kutta method (2nd order). The implicit solver (LU-SGS, BLU-SGS, DPLUR, BDPLUR) is implemented for implicit time integration. Dual time stepping is implemented for time accuracy in the implicit solver. Available implicit time integrations methods come from the Beam and Warming family of methods and are the implicit euler (1st order), Crank-Nicholson (2nd order), and BDF2 (2nd order) methods. The code has been thoroughly commented. It has been made parallel using MPI. Currently the Wilcox K-Omega 2006 and SST 2003 turbulence models are available.
+The code is 2nd order accurate in space and time. Available explicit time 
+integration methods are forward euler (1st order) and a minimum storage four 
+stage Runge-Kutta method (2nd order). The implicit solver (LU-SGS, BLU-SGS, 
+DPLUR, BDPLUR) is implemented for implicit time integration. Dual time stepping 
+is implemented for time accuracy in the implicit solver. Available implicit 
+time integrations methods come from the Beam and Warming family of methods and 
+are the implicit euler (1st order), Crank-Nicholson (2nd order), and BDF2
+(2nd order) methods. The code has been thoroughly commented. It has been made 
+parallel using MPI. For RANS simulations the Wilcox K-Omega 2006 and SST 2003 
+turbulence models are available. Wall functions are supported for both models. 
+For detatched eddy simulations, the SST-DES turbulence model is available. For 
+large eddy simulations, the WALE subgrid scale model is available.
 
 ### To Do List
-* Add SST-DES turbulence model
-* Add WALE and Smagorinsky subgrid scale models for LES
-* Add Couette flow regression test for isothermal wall, moving wall, periodic boundary conditions
-* Add wall functions for turbulence models
+* Add non-reflecting boundary conditions
+* Add thermally perfect gases
+* Add additional inviscid flux option (AUSM)
 * Add multigrid scheme for improved convergence
 
 ### Dependencies
-* MPI - OpenMPI and MPICH have both been used in the past. Aither is currently developed with OpenMPI
+* MPI - OpenMPI, MPICH, & MS-MPI have been used
 * C++ compiler with C++14 support
 * Cmake - Cmake only depends on a C++ compiler
 
 ### How To compile
 Aither is compiled and installed with the standard cmake process.
 
 ```bash
-cmake -DCMAKE_INSTALL_PREFIX=/path/to/installation /path/to/source
+cmake -DCMAKE_INSTALL_PREFIX=/path/to/installation -DCMAKE_BUILD_TYPE=release /path/to/source
 make
 make install
 ```
 
-Cmake will automatically look for an MPI package. To specify a specific installation, set *-DMPI_DIR* to the MPI installation directory.
+Cmake will automatically look for an MPI package. To specify a specific 
+installation, set *-DMPI_DIR* to the MPI installation directory. In addition 
+to *release*, other supported build types are *debug*, *profile*,
+*relwithdebinfo*, and *minsizerel*.
 
 ### How To Run
 ```bash
-mpirun -np 1 aither inputFile.inp <restartFile.rst> >outputFile.out 2>errorFile.err &
+mpirun -np 1 aither inputFile.inp [restartFile.rst] > outputFile.out 2> errorFile.err &
 ```
 The restart file argument is optional.
+
+### Visualizing Results
+Aither writes out Plot3D function files (\*.fun), as well as a Plot3D meta 
+files (\*.p3d) that can be visualized in [ParaView](www.paraview.org). Versions 
+5.3 and newer support reading the meta files.

ci/appveyor/buildAither.ps1

@@ -0,0 +1,15 @@
+function BuildAither() {
+    # Go to build directory and build
+    # Build Aither with cmake
+    md build
+    cd build
+    cmake -G "Visual Studio 14 2015 Win64" -DMPI_DIR="C:\Program Files (x86)\Microsoft SDKs\MPI" ..
+    cmake --build . --target INSTALL --config Release
+    cd ..
+}
+
+function main() {
+    BuildAither
+}
+
+main

ci/appveyor/installMPI.ps1

@@ -0,0 +1,19 @@
+function InstallMPI() {
+    md mpi
+    cd mpi
+    # install MPI SDK and Runtime
+    Write-Host "Installing Microsoft MPI SDK..."
+    appveyor DownloadFile http://download.microsoft.com/download/B/2/E/B2EB83FE-98C2-4156-834A-E1711E6884FB/msmpisdk.msi
+    Start-Process -FilePath msiexec.exe -ArgumentList "/quiet /qn /i msmpisdk.msi" -Wait
+    Write-Host "Microsoft MPI SDK installation complete"
+    Write-Host "Installing Microsoft MPI Runtime..."
+    appveyor DownloadFile http://download.microsoft.com/download/B/2/E/B2EB83FE-98C2-4156-834A-E1711E6884FB/MSMpiSetup.exe
+    Start-Process -FilePath MSMpiSetup.exe -ArgumentList -unattend -Wait
+    cd ..
+}
+
+function main() {
+    InstallMPI
+}
+
+main