This merge consists of the 0.3 release. Additional implicit solvers (…

…BLU-SGS, DPLUR, & BDPLUR) have been added. An option to specify the output variables has also been added.

Merge branch 'develop'

Makefile

@@ -1,19 +1,19 @@
-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
+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 inviscidFlux.o viscousFlux.o source.o resid.o kdtree.o genArray.o fluxJacobian.o uncoupledScalar.o utility.o
 CC = mpic++
-DEBUG = -ggdb -pg
+DEBUG = -O0 -ggdb -pg
 OPTIM = -O3 -march=native
 PROF = -O3 -march=native -pg
 CODENAME = aither
-CFLAGS = -std=c++14 -Wall -c $(OPTIM)
-LFLAGS = -std=c++14 -Wall $(OPTIM) -o $(CODENAME)
+CFLAGS = -std=c++14 -Wall -pedantic -c $(OPTIM)
+LFLAGS = -std=c++14 -Wall -pedantic $(OPTIM) -o $(CODENAME)
 
 $(CODENAME) : $(OBJS)
 	$(CC) $(LFLAGS) $(OBJS)
 
 plot3d.o : plot3d.cpp plot3d.hpp vector3d.hpp multiArray3d.hpp
 	$(CC) $(CFLAGS) plot3d.cpp
 
-main.o : main.cpp plot3d.hpp vector3d.hpp input.hpp procBlock.hpp eos.hpp primVars.hpp boundaryConditions.hpp inviscidFlux.hpp tensor.hpp viscousFlux.hpp output.hpp parallel.hpp turbulence.hpp gradients.hpp resid.hpp multiArray3d.hpp genArray.hpp
+main.o : main.cpp plot3d.hpp vector3d.hpp input.hpp procBlock.hpp eos.hpp primVars.hpp boundaryConditions.hpp inviscidFlux.hpp tensor.hpp viscousFlux.hpp output.hpp parallel.hpp turbulence.hpp resid.hpp multiArray3d.hpp genArray.hpp fluxJacobian.hpp utility.hpp
 	$(CC) $(CFLAGS) main.cpp
 
 input.o : input.cpp input.hpp boundaryConditions.hpp
@@ -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 uncoupledScalar.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 matrix.hpp utility.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
@@ -52,26 +52,26 @@ matrix.o : matrix.cpp matrix.hpp macros.hpp genArray.hpp
 genArray.o : genArray.cpp genArray.hpp macros.hpp
 	$(CC) $(CFLAGS) genArray.cpp
 
-turbulence.o : turbulence.cpp turbulence.hpp
+turbulence.o : turbulence.cpp turbulence.hpp matrix.hpp vector3d.hpp tensor.hpp primVars.hpp eos.hpp
 	$(CC) $(CFLAGS) turbulence.cpp
 
-source.o : source.cpp source.hpp macros.hpp turbulence.hpp primVars.hpp gradients.hpp
+source.o : source.cpp source.hpp macros.hpp turbulence.hpp primVars.hpp matrix.hpp
 	$(CC) $(CFLAGS) source.cpp
 
-gradients.o : gradients.cpp gradients.hpp primVars.hpp vector3d.hpp tensor.hpp procBlock.hpp
-	$(CC) $(CFLAGS) gradients.cpp
-
 resid.o : resid.cpp resid.hpp
 	$(CC) $(CFLAGS) resid.cpp
 
 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 matrix.hpp inviscidFlux.hpp uncoupledScalar.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 tensor.hpp utility.hpp
 	$(CC) $(CFLAGS) fluxJacobian.cpp
 
 uncoupledScalar.o : uncoupledScalar.cpp uncoupledScalar.hpp genArray.hpp
 	$(CC) $(CFLAGS) uncoupledScalar.cpp
 
+utility.o : utility.cpp utility.hpp genArray.hpp vector3d.hpp multiArray3d.hpp procBlock.hpp eos.hpp input.hpp turbulence.hpp slices.hpp fluxJacobian.hpp kdtree.hpp resid.hpp
+	$(CC) $(CFLAGS) utility.cpp
+
 clean:
 	rm *.o *~ $(CODENAME)

README.md

@@ -4,15 +4,19 @@
 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
-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.
+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.
 
 ### To Do List
-* Implement block LUSGS implicit method
+* Add build system (autotools or cmake)
+* Add a library for matrix operations (Eigen and PETSc being considered)
 * Implement higher order state reconstruction for DES / Hybrid RANS/LES
 * Implement tubulence model for DES / Hybrid RANS/LES
 
+### Dependencies
+Aither depends on an MPI implementation. OpenMPI and MPICH have both been used in the past. Currently Aither is developed with OpenMPI.
+
 ### How To compile
-Assuming you have g++ (or equivalent) with c++14 support and some version of MPI (I use MPICH), just type 'make'.
+Assuming you have a c++ compiler with c++14 support, just type 'make'.
 
 ### How To Run
 ```bash