Merge branch 'develop'

Release 0.4.0
This release changes the input files so that the boundary indices start at 0 instead of 1

.gitignore

@@ -18,6 +18,7 @@ aither
 *.res
 *.out
 *_center.xyz
+*.resid
 
 #Ignore blog files
 _site

README.md

@@ -7,7 +7,6 @@ This code is for a 3D Navier-Stokes computational fluid dynamics solver. It is a
 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
-* 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
 
@@ -25,7 +24,7 @@ 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.
 
 ### How To Run
 ```bash

include/boundaryConditions.hpp

@@ -21,16 +21,19 @@
 
 /* This header contains the class boundaryConditions.
 
-This class stores the information needed to specify the boundary_ conditions for one block_. */
+This class stores the information needed to specify the boundary conditions for
+one block. */
 
 #include <vector> // vector
+#include <array> // array
 #include <string> // string
 #include <iostream> // ostream
 #include "mpi.h" // parallelism
 #include "vector3d.hpp"
 
 using std::ostream;
 using std::vector;
+using std::array;
 using std::string;
 using std::cout;
 using std::endl;
@@ -45,8 +48,10 @@ class boundarySurface {
 
  public:
  // Constructor
- boundarySurface(const string&, const int&, const int&, const int&,
- const int&, const int&, const int&, const int&);
+ boundarySurface(const string &name, const int &imin, const int &imax,
+ const int &jmin, const int &jmax, const int &kmin,
+ const int &kmax, const int &tag) :
+ bcType_(name), data_{imin, imax, jmin, jmax, kmin, kmax, tag} {}
  boundarySurface() : boundarySurface("undefined", 0, 0, 0, 0, 0, 0, 0) {}
 
  // move constructor and assignment operator
@@ -120,9 +125,8 @@ class patch {
  const bool(&)[4]);
  patch(const boundarySurface &surf, const plot3dBlock &blk, const int &bNum,
  const bool (&border)[4], int r = 0, int l = 0) :
- patch(surf.SurfaceType(), bNum, surf.IMin() - 1, surf.IMax() - 1,
- surf.JMin() -1, surf.JMax() - 1, surf.KMin() - 1,
- surf.KMax() - 1, blk, r, l, border) {}
+ patch(surf.SurfaceType(), bNum, surf.IMin(), surf.IMax(), surf.JMin(),
+ surf.JMax(), surf.KMin(), surf.KMax(), blk, r, l, border) {}
 
  // move constructor and assignment operator
  patch(patch&&) noexcept = default;
@@ -393,7 +397,7 @@ ostream & operator<< (ostream &os, const decomposition&);
 ostream & operator<< (ostream &os, const interblock&);
 
 
-vector3d<int> GetSwapLoc(const int &, const int &, const int &,
+array<int, 3> GetSwapLoc(const int &, const int &, const int &,
  const interblock &, const bool &);
 
 #endif

include/multiArray3d.hpp

@@ -222,7 +222,7 @@ T multiArray3d<T>::GetElem(const int &ii, const int &jj, const int &kk) const {
  cerr << "Tried to access " << ii << ", " << jj << ", " << kk << endl;
  cerr << "Maximum locations are " << numI_ - 1 << ", " << numJ_ - 1 << ", "
  << numK_ - 1 << endl;
- exit(1);
+ exit(EXIT_FAILURE);
  }
 }
 
@@ -403,7 +403,7 @@ multiArray3d<T> multiArray3d<T>::Slice(const int &is, const int &ie,
  << "boundaries " << is << ", " << ie << ", " << js << ", " << je
  << ", " << ks << ", " << ke << " from array with dimensions " <<
  numI_ << ", " << numJ_ << ", " << numK_ << endl;
- exit(1);
+ exit(EXIT_FAILURE);
  }
 
  multiArray3d<T> array(ie - is + 1, je - js + 1, ke - ks + 1);
@@ -442,7 +442,7 @@ void multiArray3d<T>::Insert(const int &is, const int &ie, const int &js,
  ", " << array.numK_ << endl;
  cerr << "Size of location is " << ie - is + 1 << ", " << je - js + 1 <<
  ", " << ke - ks + 1 << endl;
- exit(1);
+ exit(EXIT_FAILURE);
  }
 
  // s is for index of sliced array, p is for index of parent array
@@ -504,7 +504,7 @@ void multiArray3d<T>::SameSizeResize(const int &ii, const int&jj,
  cerr << "ERROR: Error in multiArray3d<T>::SameSizeResize. Attempting to "
  << "resize array of " << this->Size() << " cells to " <<
  ii * jj * kk << " cells." << endl;
- exit(1);
+ exit(EXIT_FAILURE);
  }
  numI_ = ii;
  numJ_ = jj;
@@ -565,7 +565,7 @@ void multiArray3d<T>::PutSlice(const multiArray3d<T> &array,
  << inter.Dir2EndFirst() - inter.Dir2StartFirst() << ", " << d3 << endl;
  cerr << "Direction I, J, K of multiArray3d<T> to insert: " << array.NumI()
  << ", " << array.NumJ() << ", " << array.NumK() << endl;
- exit(1);
+ exit(EXIT_FAILURE);
  }
 
  // adjust insertion indices if patch borders another interblock on the same
@@ -687,7 +687,7 @@ void multiArray3d<T>::SwapSliceMPI(const interblock &inter, const int &rank,
  } else {
  cerr << "ERROR: Error in procBlock::SwapSliceMPI(). Processor rank does "
  "not match either of interblock ranks!" << endl;
- exit(1);
+ exit(EXIT_FAILURE);
  }
 
  // get local state slice to swap

src/CMakeLists.txt

@@ -2,8 +2,8 @@ project (aither)
 
 # set version number
 set (aither_VERSION_MAJOR 0)
-set (aither_VERSION_MINOR 3)
-set (aither_VERSION_PATCH 1)
+set (aither_VERSION_MINOR 4)
+set (aither_VERSION_PATCH 0)
 
 message (STATUS "Cmake version ${CMAKE_VERSION}")
 message (STATUS "Configuring aither v${aither_VERSION_MAJOR}.${aither_VERSION_MINOR}.${aither_VERSION_PATCH}")