Merge branch 'develop'

This adds the DP-LUR implicit method as wellas prepares the code for implementation of
block LU-SGS and block DP-LUR methods.

Makefile

@@ -1,4 +1,4 @@
-OBJS = main.o plot3d.o input.o boundaryConditions.o eos.o primVars.o procBlock.o output.o matrix.o parallel.o slices.o turbulence.o gradients.o inviscidFlux.o viscousFlux.o source.o resid.o kdtree.o genArray.o fluxJacobian.o
+OBJS = main.o plot3d.o input.o boundaryConditions.o eos.o primVars.o procBlock.o output.o matrix.o parallel.o slices.o turbulence.o gradients.o inviscidFlux.o viscousFlux.o source.o resid.o kdtree.o genArray.o fluxJacobian.o uncoupledScalar.o
 CC = mpic++
 DEBUG = -ggdb -pg
 OPTIM = -O3 -march=native
@@ -22,7 +22,7 @@ input.o : input.cpp input.hpp boundaryConditions.hpp
 primVars.o : primVars.cpp primVars.hpp vector3d.hpp eos.hpp inviscidFlux.hpp boundaryConditions.hpp input.hpp macros.hpp genArray.hpp
 	$(CC) $(CFLAGS) primVars.cpp
 
-procBlock.o : procBlock.cpp procBlock.hpp vector3d.hpp plot3d.hpp eos.hpp primVars.hpp inviscidFlux.hpp input.hpp genArray.hpp viscousFlux.hpp boundaryConditions.hpp macros.hpp turbulence.hpp kdtree.hpp fluxJacobian.hpp
+procBlock.o : procBlock.cpp procBlock.hpp vector3d.hpp plot3d.hpp eos.hpp primVars.hpp inviscidFlux.hpp input.hpp genArray.hpp viscousFlux.hpp boundaryConditions.hpp macros.hpp turbulence.hpp kdtree.hpp uncoupledScalar.hpp fluxJacobian.hpp
 	$(CC) $(CFLAGS) procBlock.cpp
 
 inviscidFlux.o : inviscidFlux.cpp vector3d.hpp eos.hpp primVars.hpp inviscidFlux.hpp input.hpp macros.hpp genArray.hpp turbulence.hpp matrix.hpp
@@ -46,7 +46,7 @@ output.o : output.cpp output.hpp procBlock.hpp tensor.hpp vector3d.hpp plot3d.hp
 parallel.o : parallel.cpp parallel.hpp primVars.hpp procBlock.hpp vector3d.hpp plot3d.hpp boundaryConditions.hpp resid.hpp
 	$(CC) $(CFLAGS) parallel.cpp
 
-matrix.o : matrix.cpp matrix.hpp macros.hpp
+matrix.o : matrix.cpp matrix.hpp macros.hpp genArray.hpp
 	$(CC) $(CFLAGS) matrix.cpp
 
 genArray.o : genArray.cpp genArray.hpp macros.hpp
@@ -67,8 +67,11 @@ resid.o : resid.cpp resid.hpp
 kdtree.o : kdtree.cpp kdtree.hpp vector3d.hpp
 	$(CC) $(CFLAGS) kdtree.cpp
 
-fluxJacobian.o : fluxJacobian.cpp fluxJacobian.hpp turbulence.hpp vector3d.hpp primVars.hpp eos.hpp input.hpp genArray.hpp
+fluxJacobian.o : fluxJacobian.cpp fluxJacobian.hpp turbulence.hpp vector3d.hpp primVars.hpp eos.hpp input.hpp genArray.hpp matrix.hpp inviscidFlux.hpp uncoupledScalar.hpp
 	$(CC) $(CFLAGS) fluxJacobian.cpp
 
+uncoupledScalar.o : uncoupledScalar.cpp uncoupledScalar.hpp genArray.hpp
+	$(CC) $(CFLAGS) uncoupledScalar.cpp
+
 clean:
 	rm *.o *~ $(CODENAME)

README → README.md

@@ -1,18 +1,20 @@
-Accurate Implicit Three-dimensional Efficient RANS (AITHER)
+# Accurate Implicit Three-dimensional Efficient RANS (AITHER)
 
-ABOUT THE CODE
+### 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.
 
-CURRENT STATUS
+### 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) 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.
 
-TO DO LIST
-- Implement block LUSGS implicit method
-- Implement higher order state reconstruction for DES / Hybrid RANS/LES
-- Implement tubulence model for DES / Hybrid RANS/LES
+### To Do List
+* Implement block LUSGS implicit method
+* Implement higher order state reconstruction for DES / Hybrid RANS/LES
+* Implement tubulence model for DES / Hybrid RANS/LES
 
-HOW TO COMPILE
+### How To compile
 Assuming you have g++ (or equivalent) with c++14 support and some version of MPI (I use MPICH), just type 'make'.
 
-HOW TO RUN
-mpirun -np 1 aither inputFile.inp >outputFile.out 2>errorFile.err &
+### How To Run
+```bash
+mpirun -np 1 aither inputFile.inp >outputFile.out 2>errorFile.err &
+```