Merge branch 'develop'

Adding reacting flow capability

Author: mnucci32

.appveyor.yml

@@ -9,7 +9,7 @@ platform: x64
 environment:
   PYTHON: C:\Python35-x64
   PATH: C:\Program Files\Project\bin;C:\Program Files\Microsoft MPI\Bin;%PATH%
-  AITHER_FLUID_DATABASE: C:\Program Files\Project\fluidDatabase
+  AITHER_INSTALL_DIRECTORY: C:\Program Files\Project
 build_script:
 - ps: >-
     powershell ci\appveyor\installMPI.ps1

.travis.yml

@@ -27,7 +27,7 @@ matrix:
         - CXX_COMPILER=g++-5
         - C_COMPILER=gcc-5
         - BUILD_TYPE=release
-        - AITHER_FLUID_DATABASE=$TRAVIS_BUILD_DIR/build/install/fluidDatabase
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
     - os: linux
       dist: trusty
       sudo: required
@@ -42,7 +42,7 @@ matrix:
         - CXX_COMPILER=g++-6
         - C_COMPILER=gcc-6
         - BUILD_TYPE=debug
-        - AITHER_FLUID_DATABASE=$TRAVIS_BUILD_DIR/build/install/fluidDatabase
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
     - os: linux
       dist: trusty
       sudo: required
@@ -57,7 +57,22 @@ matrix:
         - CXX_COMPILER=g++-7
         - C_COMPILER=gcc-7
         - BUILD_TYPE=release
-        - AITHER_FLUID_DATABASE=$TRAVIS_BUILD_DIR/build/install/fluidDatabase
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
+    - os: linux
+      dist: trusty
+      sudo: required
+      compiler: gcc
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-8 gcc-8 libstdc++-8-dev
+      env:
+        - CXX_COMPILER=g++-8
+        - C_COMPILER=gcc-8
+        - BUILD_TYPE=release
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
     - os: linux
       dist: trusty
       sudo: required
@@ -73,17 +88,17 @@ matrix:
         - CXX_COMPILER=clang++-3.8
         - C_COMPILER=clang-3.8
         - BUILD_TYPE=release
-        - AITHER_FLUID_DATABASE=$TRAVIS_BUILD_DIR/build/install/fluidDatabase
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
     - os: osx
       osx_image: xcode8
       compiler: gcc
       env:
-        - CXX_COMPILER=g++-7
-        - C_COMPILER=gcc-7
-        - HOMEBREW_CC=gcc-7
-        - HOMEBREW_CXX=g++-7
+        - CXX_COMPILER=g++-8
+        - C_COMPILER=gcc-8
+        - HOMEBREW_CC=gcc-8
+        - HOMEBREW_CXX=g++-8
         - BUILD_TYPE=release
-        - AITHER_FLUID_DATABASE=$TRAVIS_BUILD_DIR/build/install/fluidDatabase
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
     - os: osx
       osx_image: xcode8
       compiler: clang
@@ -93,14 +108,15 @@ matrix:
         - HOMEBREW_CC=clang
         - HOMEBREW_CXX=clang++
         - BUILD_TYPE=release
-        - AITHER_FLUID_DATABASE=$TRAVIS_BUILD_DIR/build/install/fluidDatabase
+        - AITHER_INSTALL_DIRECTORY=$TRAVIS_BUILD_DIR/build/install
 
 # upgrade packages
 before_install:
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update -qq; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y python3; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gcc python3; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew upgrade python; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gcc; fi
   - test -n $CC && unset CC
   - test -n $CXX && unset CXX
   - which $CXX_COMPILER

README.md

@@ -6,35 +6,36 @@
 | 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 multi-block structured grids in Plot3D 
-format. It uses explicit and implicit time integration methods. It uses MUSCL 
-extrapolation to reconstruct the primitive 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.
+Aither is a 3D Navier-Stokes computational fluid dynamics solver capable of 
+modeling finite rate chemsitry. 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 
+primitive 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 either the Roe flux difference splitting 
+or AUSMPW+ flux vector 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 
+time integration 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. A 
-Multi-species flow capability is in progress. Supported diffusion models will be
-Schmidt number based diffusion.
+large eddy simulations, the WALE subgrid scale model is available. 
+Multispecies flow is supported and a Schmidt number based model is used for
+diffusion. Reacting flow is modeled with a finite rate chemistry model.
 
 ### To Do List
 * Add multigrid scheme for improved convergence
-* Add reacting flow capability
 * Performance improvements
 
 ### Dependencies
@@ -50,7 +51,7 @@ cmake -DCMAKE_INSTALL_PREFIX=/path/to/installation -DCMAKE_BUILD_TYPE=release /p
 make
 make install
 
-export AITHER_FLUID_DATABASE=/path/to/installation/fluidDatabase
+export AITHER_INSTALL_DIRECTORY=/path/to/installation
 ```
 
 Cmake will automatically look for an MPI package. To specify a specific 

chemistryMechanisms/CH4_5s2r.mch

@@ -0,0 +1,2 @@
+CH4 + 1.5 O2 => CO + 2 H2O : forwardRate=arrhenius(C=2e9, eta=0, theta=17866.1); modifyReactants=[CH4=0.9, O2=1.1]
+CO + 0.5 O2 <=> CO2 : forwardRate=arrhenius(C=6.3e4, eta=0, theta=6039.3)

chemistryMechanisms/O2_2s2r.mch

@@ -0,0 +1,8 @@
+# Two reaction, two species dissociating oxygen mechanism
+# Rates from Luke, adjusted to be in mol instead of kmol
+#
+# Luke, E. A. "A Rule-Based Specification System For Computational Fluid 
+# Dynamics". Ph. D. Thesis, December 1999.
+
+2 O2 <=> 2 O + O2 : forwardRate=arrhenius(C=1.9e15, eta=-1.5, theta=59500)
+O2 + O <=> 3 O : forwardRate=arrhenius(C=6.4e17, eta=-2, theta=59500)

fluidDatabase/Ar.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 1.5
 molarMass: 39.948
 vibrationalTemperature: []
+heatOfFormation: 0
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 154.85
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/CH4.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 3.0
 molarMass: 16.0425
 vibrationalTemperature: [4196.38, 2207.18, 2207.18, 4343.43, 4343.43, 4343.43, 1879.13, 1879.13, 1879.13]
+heatOfFormation: -74600
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 186.37
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/CO.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 2.5
 molarMass: 28.0101
 vibrationalTemperature: [3121.5]
+heatOfFormation: -110530
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 197.66
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/CO2.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 2.5
 molarMass: 44.0095
 vibrationalTemperature: [960.1, 960.1, 1932.1, 3380.1]
+heatOfFormation: -393510
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 213.79
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/H.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 1.5
 molarMass: 1.00794
 vibrationalTemperature: []
+heatOfFormation: 218000
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 114.72
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/H2.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 2.5
 molarMass: 2.01588
 vibrationalTemperature: [6338.3]
+heatOfFormation: 0
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 130680
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/H2O.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 3.0
 molarMass: 18.0153
 vibrationalTemperature: [2294.3, 5261.7, 5403.8]
+heatOfFormation: -241810
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 188.84
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/He.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 1.5
 molarMass: 4.002602
 vibrationalTemperature: []
+heatOfFormation: 0
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 126.15
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----

fluidDatabase/N.dat

@@ -1,7 +1,23 @@
+# This data is aggregated from the following sources
+#
+# NIST Computational Chemistry Comparison and Benchmark Database 
+# NIST Standard Reference Database Number 101 
+# Release 18, October 2016, Editor: Russell D. Johnson III 
+# http://cccbdb.nist.gov/
+#
+# P.J. Linstrom and W.G. Mallard, Eds., NIST Chemistry WebBook, 
+# NIST Standard Reference Database Number 69, 
+# National Institute of Standards and Technology, Gaithersburg MD, 20899, 
+# doi:10.18434/T4D303, (retrieved March 3, 2018).
+
 # general fluid properties
 n: 1.5
 molarMass: 14.0067
 vibrationalTemperature: []
+heatOfFormation: 472680
+referencePressure: 101325
+referenceTemperature: 298.15
+referenceEntropy: 153.3
 
 # Sutherland's coefficients for transport properties
 # ----- viscosity -----