Removing global includes in SpatialDomains and StdRegions

git-svn-id: https://gforge.sci.utah.edu/svn/nektar/trunk@4077 305cdda6-5ce1-45b3-a98d-dfc68c8b3305

library/Demos/MultiRegions/Helmholtz2D.cpp

@@ -34,6 +34,7 @@ int main(int argc, char *argv[])
     StdRegions::VarCoeffMap varcoeffs;
     FlagList flags;
     NekDouble    cps = (double)CLOCKS_PER_SEC;
+    NekDouble    st;
 
     if( (argc != 2) && (argc != 3) && (argc != 4))
     {

library/LibUtilities/Foundations/Basis.cpp

@@ -1015,156 +1015,3 @@ namespace Nektar
     } // end of namespace stdregion
 } // end of namespace stdregion
 
-/**
-* $Log: Basis.cpp,v $
-* Revision 1.39  2009/10/22 17:49:51  cbiotto
-* Adding CalculateInterpMatrix and updates for variable order expansion
-*
-* Revision 1.38  2009/06/18 11:47:24  claes
-* changes supporting the static use of Kronrod points
-*
-* Revision 1.37  2009/01/13 02:17:15  ehan
-* Added documentation
-*
-* Revision 1.36  2008/11/23 00:31:19  sherwin
-* Added modified_C and normalised ortho_c
-*
-* Revision 1.35  2008/11/16 23:45:57  sherwin
-* Updates to include Modified_C for tets
-*
-* Revision 1.34  2008/10/04 12:24:18  sherwin
-* moved a few brackets to meet coding standard
-*
-* Revision 1.33  2008/10/01 23:23:21  ehan
-* Changed the alpha value in order to be consistant with the Spen's book.
-*
-* Revision 1.32  2008/06/23 17:58:03  pvos
-* Added proper normalising terms to implementation of Ortho_B
-*
-* Revision 1.31  2008/05/13 01:11:22  ehan
-* Added monomial basis
-*
-* Revision 1.30  2008/05/12 23:45:46  ehan
-* Added monomial basis
-*
-* Revision 1.29  2008/05/07 16:04:24  pvos
-* Mapping + Manager updates
-*
-* Revision 1.28  2008/04/06 22:28:25  bnelson
-* Fixed gcc compiler warnings.
-*
-* Revision 1.27  2008/04/06 05:54:08  bnelson
-* Changed ConstArray to Array<const>
-*
-* Revision 1.26  2008/03/18 14:11:46  pvos
-* Update for nodal triangular helmholtz solver
-*
-* Revision 1.25  2007/12/28 23:28:37  ehan
-* Reimplemented Ortho-B
-*
-* Revision 1.24  2007/10/15 20:45:16  ehan
-* Reimplemented and tested Ortho_C
-*
-* Revision 1.23  2007/10/03 03:00:13  bnelson
-* Added precompiled headers.
-*
-* Revision 1.22  2007/09/27 12:52:03  pvos
-* Column major Blas calls corrections
-*
-* Revision 1.21  2007/09/25 14:24:40  pvos
-* Update for helmholtz1D with different expansion orders
-*
-* Revision 1.20  2007/07/22 23:03:26  bnelson
-* Backed out Nektar::ptr.
-*
-* Revision 1.19  2007/07/20 00:28:24  bnelson
-* Replaced boost::shared_ptr with Nektar::ptr
-*
-* Revision 1.18  2007/05/15 03:37:23  bnelson
-* Updated to use the new Array object.
-*
-* Revision 1.17  2007/04/29 00:31:56  jfrazier
-* Updated to use multi_arrays.
-*
-* Revision 1.16  2007/04/08 03:31:18  jfrazier
-* Modified to use SharedArray.
-*
-* Revision 1.15  2007/04/04 02:10:30  bnelson
-* Made comparison operators const correct.
-*
-* Revision 1.14  2007/04/03 03:58:24  bnelson
-* Moved Lapack.hpp, Blas.hpp, Transf77.hpp to LinearAlgebra
-*
-* Revision 1.13  2007/02/26 15:52:30  sherwin
-* Working version for Fourier points calling from StdRegions. Fourier interpolations not working yet
-*
-* Revision 1.12  2007/02/17 04:06:47  jfrazier
-* Added greater-than operator for easy comparison when using keys that use a basis and provided a method to access the basiskey.
-*
-* Revision 1.11  2007/02/06 17:12:27  jfrazier
-* Fixed a problem with global initialization in libraries.
-*
-* Revision 1.10  2007/02/01 23:28:41  jfrazier
-* Basis is not working, but not fully tested.
-*
-* Revision 1.9  2007/02/01 15:30:07  jfrazier
-* Reformatted.
-*
-Revision 1.8  2007/01/31 23:27:56  kirby
-*** empty log message ***
-
-* Revision 1.7  2007/01/31 18:37:32  kirby
-*
-* fully compiling but not fully tested update to Foundations
-* Basis now should work (Compiles but not tested yet)
-*
-* Revision 1.6  2007/01/29 19:47:29  jfrazier
-* Cleanup and restructuring to accommodate private default and copy constructors.
-*
-* Revision 1.5  2007/01/26 04:00:54  jfrazier
-* Cleanup after initial creation.
-*
-* Revision 1.4  2007/01/24 23:43:01  kirby
-* *** empty log message ***
-*
-* Revision 1.3  2007/01/20 22:21:17  kirby
-* *** empty log message ***
-*
-* Revision 1.2  2007/01/17 11:35:52  pvos
-* updating doxygen documentation
-*
-* Revision 1.1  2006/06/06 18:45:14  kirby
-* *** empty log message ***
-*
-* Revision 1.1  2006/05/04 18:58:30  kirby
-* *** empty log message ***
-*
-* Revision 1.30  2006/04/25 20:23:33  jfrazier
-* Various fixes to correct bugs, calls to ASSERT, etc.
-*
-* Revision 1.29  2006/03/05 22:11:02  sherwin
-*
-* Sorted out Project1D, Project2D and Project_Diff2D as well as some test scripts
-*
-* Revision 1.28  2006/03/03 23:04:54  sherwin
-*
-* Corrected Mistake in StdBasis.cpp to do with eModified_B
-*
-* Revision 1.27  2006/03/01 17:07:33  sherwin
-*
-* Added new location of polylib in header definitions
-*
-* Revision 1.26  2006/02/27 23:47:23  sherwin
-*
-* Standard coding update upto compilation of StdHexExp.cpp
-*
-* Revision 1.25  2006/02/26 23:37:29  sherwin
-*
-* Updates and compiling checks upto StdExpansions1D
-*
-* Revision 1.24  2006/02/19 13:26:13  sherwin
-*
-* Coding standard revisions so that libraries compile
-*
-**/
-

library/LibUtilities/Foundations/GaussPoints.cpp

@@ -393,46 +393,3 @@ namespace Nektar
     } // end of namespace LibUtilities
 } // end of namespace Nektar
 
-/**
-* $Log: GaussPoints.cpp,v $
-* Revision 1.27  2009/06/15 01:59:21  claes
-* Gauss-Kronrod updates
-*
-* Revision 1.26  2009/06/12 15:50:11  mirzaee
-* no message
-*
-* Revision 1.25  2008/04/06 05:54:08  bnelson
-* Changed ConstArray to Array<const>
-*
-* Revision 1.24  2007/10/03 03:00:13  bnelson
-* Added precompiled headers.
-*
-* Revision 1.23  2007/08/06 05:42:28  ehan
-* Fixed m_derivativematrix so that compatible with 3-dimension
-*
-* Revision 1.22  2007/07/27 00:22:26  bnelson
-* Memory manager now accepts non-const parameters to the allocate methods.
-*
-* Revision 1.21  2007/07/22 23:03:26  bnelson
-* Backed out Nektar::ptr.
-*
-* Revision 1.20  2007/07/20 00:28:26  bnelson
-* Replaced boost::shared_ptr with Nektar::ptr
-*
-* Revision 1.19  2007/05/15 05:17:19  bnelson
-* Updated to use the new Array object.
-*
-* Revision 1.18  2007/05/15 03:37:24  bnelson
-* Updated to use the new Array object.
-*
-* Revision 1.17  2007/04/30 23:28:59  jfrazier
-* More conversion to multi_array.
-*
-* Revision 1.16  2007/04/29 03:09:47  jfrazier
-* More conversion to multi_arrays.
-*
-* Revision 1.15  2007/04/29 00:31:57  jfrazier
-* Updated to use multi_arrays.
-*
-*/
-

library/LibUtilities/Foundations/ManagerAccess.cpp

@@ -104,78 +104,3 @@ namespace Nektar
 } // end of namespace Nektar
 
 
-/**
-$Log: ManagerAccess.cpp,v $
-Revision 1.23  2009/06/15 01:59:21  claes
-Gauss-Kronrod updates
-
-Revision 1.22  2009/06/12 18:07:02  claes
-minor Gauss-Kronrod alterations
-
-Revision 1.21  2008/11/12 12:11:52  pvos
-Time Integration update
-
-Revision 1.20  2008/07/17 16:12:41  pvos
-Updated time integration manager into general linear method format
-
-Revision 1.19  2008/07/12 11:37:53  pvos
-Added time integration scheme manager
-
-Revision 1.18  2008/05/27 20:05:50  ehan
-Added NodalTetEvenlySpaced points.
-
-Revision 1.17  2008/05/23 20:02:13  ehan
-Added NodalTriEvenlySpaced points.
-
-Revision 1.16  2008/05/12 23:47:24  ehan
-Added monomial basis
-
-Revision 1.15  2007/10/03 03:00:13  bnelson
-Added precompiled headers.
-
-Revision 1.14  2007/07/20 00:28:26  bnelson
-Replaced boost::shared_ptr with Nektar::ptr
-
-Revision 1.13  2007/06/01 17:08:07  pvos
-Modification to make LocalRegions/Project2D run correctly (PART1)
-
-Revision 1.12  2007/04/30 23:29:09  jfrazier
-More conversion to multi_array.
-
-Revision 1.11  2007/04/29 00:31:57  jfrazier
-Updated to use multi_arrays.
-
-Revision 1.10  2007/04/10 14:00:45  sherwin
-Update to include SharedArray in all 2D element (including Nodal tris). Have also remvoed all new and double from 2D shapes in StdRegions
-
-Revision 1.9  2007/04/10 02:40:53  bnelson
-Updated loki capitalization.
-
-Revision 1.8  2007/03/19 12:46:16  kirby
-*** empty log message ***
-
-Revision 1.7  2007/03/13 21:31:32  kirby
- small update to the numbering.
-
-Revision 1.6  2007/03/13 16:59:04  kirby
- added GaussLobattoChebyshev -- we had forgotten it
-
-Revision 1.5  2007/02/26 15:52:31  sherwin
-Working version for Fourier points calling from StdRegions. Fourier interpolations not working yet
-
-Revision 1.4  2007/02/06 17:12:31  jfrazier
-Fixed a problem with global initialization in libraries.
-
-Revision 1.3  2007/02/01 23:28:42  jfrazier
-Basis is not working, but not fully tested.
-
-Revision 1.2  2007/01/20 21:45:59  kirby
-*** empty log message ***
-
-Revision 1.1  2007/01/19 18:02:26  jfrazier
-Initial checkin.
-
-**/
-
-
-

library/LibUtilities/Foundations/NodalTetElec.cpp

@@ -276,36 +276,3 @@ namespace Nektar
 } // end of namespace stdregion
 
 
-/**
-* $Log: NodalTetElec.cpp,v $
-* Revision 1.14  2008/11/01 22:04:34  bnelson
-* Removed references to MatrixStoragePolicy<T>
-*
-* Revision 1.13  2008/04/06 05:54:08  bnelson
-* Changed ConstArray to Array<const>
-*
-* Revision 1.12  2007/10/03 03:00:13  bnelson
-* Added precompiled headers.
-*
-* Revision 1.11  2007/08/15 01:43:48  ehan
-* Added calculating weights, interpolation, and derivation for Tetrahedron.
-*
-* Revision 1.10  2007/07/31 18:12:01  ehan
-* Updated Tetrahedron symmetry and calculate points
-*
-* Revision 1.9  2007/07/22 23:03:26  bnelson
-* Backed out Nektar::ptr.
-*
-* Revision 1.8  2007/07/20 00:28:26  bnelson
-* Replaced boost::shared_ptr with Nektar::ptr
-*
-* Revision 1.7  2007/05/15 03:37:24  bnelson
-* Updated to use the new Array object.
-*
-* Revision 1.6  2007/04/30 23:29:09  jfrazier
-* More conversion to multi_array.
-*
-* Revision 1.5  2007/04/29 00:31:57  jfrazier
-* Updated to use multi_arrays.
-*
-*/

library/LibUtilities/Foundations/NodalTriElec.cpp

@@ -296,45 +296,3 @@ namespace Nektar
 } // end of namespace stdregion
 
 
-/**
-* $Log: NodalTriElec.cpp,v $
-* Revision 1.18  2008/11/01 22:36:06  bnelson
-* Removed uneeded files.
-*
-* Revision 1.17  2008/04/06 05:54:08  bnelson
-* Changed ConstArray to Array<const>
-*
-* Revision 1.16  2008/04/02 21:12:35  pvos
-* Update of the 2D local to global map
-*
-* Revision 1.15  2008/03/18 14:11:50  pvos
-* Update for nodal triangular helmholtz solver
-*
-* Revision 1.14  2007/10/03 03:00:13  bnelson
-* Added precompiled headers.
-*
-* Revision 1.13  2007/08/15 01:48:39  ehan
-* *** empty log message ***
-*
-* Revision 1.12  2007/08/06 05:41:25  ehan
-* Fixed derivative matrix
-*
-* Revision 1.11  2007/07/31 18:17:21  ehan
-* Conform to Coding Style Standard
-*
-* Revision 1.10  2007/07/26 22:54:40  ehan
-* completed testing and implementation of integration, interpolation, and derivation
-*
-* Revision 1.9  2007/07/22 23:03:26  bnelson
-* Backed out Nektar::ptr.
-*
-* Revision 1.8  2007/07/20 00:28:26  bnelson
-* Replaced boost::shared_ptr with Nektar::ptr
-*
-* Revision 1.7  2007/05/15 03:37:24  bnelson
-* Updated to use the new Array object.
-*
-* Revision 1.6  2007/04/30 23:29:10  jfrazier
-* More conversion to multi_array.
-*
-*/

library/LibUtilities/Foundations/NodalTriFekete.cpp

@@ -296,49 +296,3 @@ namespace Nektar
     } // end of namespace stdregion
 } // end of namespace stdregion
 
-/**
-* $Log: NodalTriFekete.cpp,v $
-* Revision 1.27  2008/12/18 14:07:46  pvos
-* NekConstants update
-*
-* Revision 1.26  2008/11/01 22:04:34  bnelson
-* Removed references to MatrixStoragePolicy<T>
-*
-* Revision 1.25  2008/04/06 05:54:08  bnelson
-* Changed ConstArray to Array<const>
-*
-* Revision 1.24  2008/04/02 21:12:35  pvos
-* Update of the 2D local to global map
-*
-* Revision 1.23  2008/03/18 14:11:50  pvos
-* Update for nodal triangular helmholtz solver
-*
-* Revision 1.22  2007/10/03 03:00:13  bnelson
-* Added precompiled headers.
-*
-* Revision 1.21  2007/08/06 05:41:25  ehan
-* Fixed derivative matrix
-*
-* Revision 1.20  2007/07/31 18:19:11  ehan
-* Conform to Coding Style Standard
-*
-* Revision 1.19  2007/07/26 22:24:24  ehan
-* conform to Coding Style Standard
-*
-* Revision 1.18  2007/07/22 23:03:27  bnelson
-* Backed out Nektar::ptr.
-*
-* Revision 1.17  2007/07/21 05:01:50  ehan
-* Completed version of NodalTriFekete with integration, derivation, and interpolation implemented and tested.
-*
-* Revision 1.12  2007/05/15 03:37:24  bnelson
-* Updated to use the new Array object.
-*
-* Revision 1.11  2007/04/30 23:29:10  jfrazier
-* More conversion to multi_array.
-*
-* Revision 1.10  2007/04/29 00:31:57  jfrazier
-* Updated to use multi_arrays.
-*
-*/
-

library/MultiRegions/AssemblyMap/AssemblyMapCG2D.h

@@ -85,8 +85,8 @@ namespace Nektar
 
 
             /** Construct optimal ordering a two-dimensional expansion
-            /*  given a vector of boundary condition information
-            */
+             *  given a vector of boundary condition information
+             */
             MULTI_REGIONS_EXPORT int SetUp2DGraphC0ContMap(
                                        const ExpList  &locExp,
                                        const Array<OneD, const MultiRegions::ExpListSharedPtr>  &bndCondExp,

library/MultiRegions/ExpList2D.cpp

@@ -38,6 +38,8 @@
 #include <LocalRegions/NodalTriExp.h>
 #include <LocalRegions/Expansion3D.h>
 #include <MultiRegions/ExpList2D.h>
+#include <LibUtilities/Foundations/Interp.h>
+
 
 #include <iomanip>
 

library/SolverUtils/UnsteadySystem.cpp

@@ -36,7 +36,6 @@
 #include <iostream>
 #include <iomanip>
 
-#include <LibUtilities/TimeIntegration/TimeIntegrationScheme.h>
 #include <LibUtilities/BasicUtils/Timer.h>
 #include <MultiRegions/AssemblyMap/AssemblyMapDG.h>
 #include <SolverUtils/UnsteadySystem.h>

library/SolverUtils/UnsteadySystem.h

@@ -36,6 +36,7 @@
 #ifndef NEKTAR_SOLVERUTILS_UNSTEADYSYSTEM_H
 #define NEKTAR_SOLVERUTILS_UNSTEADYSYSTEM_H
 
+#include <LibUtilities/TimeIntegration/TimeIntegrationScheme.h>
 #include <SolverUtils/EquationSystem.h>
 #include <SolverUtils/Filters/Filter.h>
 #include <time.h>

library/SpatialDomains/GeomFactors.cpp

@@ -37,6 +37,7 @@
 
 #include <SpatialDomains/GeomFactors.h>
 #include <SpatialDomains/Geometry2D.h>
+#include <LibUtilities/Foundations/Interp.h>
 
 namespace Nektar
 {

library/SpatialDomains/GeomFactors1D.cpp

@@ -33,10 +33,11 @@
 //
 ///////////////////////////////////////////////////////////////////////////////
 
-#include <SpatialDomains/GeomFactors2D.h>
+//#include <SpatialDomains/GeomFactors2D.h>
 #include <SpatialDomains/Geometry2D.h>
 
 #include <SpatialDomains/GeomFactors1D.h>
+#include <LibUtilities/Foundations/Interp.h>
 
 namespace Nektar
 {

library/SpatialDomains/GeomFactors2D.cpp

@@ -35,6 +35,7 @@
 
 #include <SpatialDomains/GeomFactors2D.h>
 #include <SpatialDomains/Geometry.h>
+#include <LibUtilities/Foundations/Interp.h>
 
 namespace Nektar
 {

library/SpatialDomains/GeomFactors3D.cpp

@@ -37,6 +37,7 @@
 
 #include <SpatialDomains/GeomFactors3D.h>
 #include <SpatialDomains/Geometry.h>
+#include <LibUtilities/Foundations/Interp.h>
 
 namespace Nektar
 {

library/SpatialDomains/Geometry.h

@@ -37,7 +37,7 @@
 #ifndef NEKTAR_SPATIALDOMAINS_GEOMETRY_H
 #define NEKTAR_SPATIALDOMAINS_GEOMETRY_H
 
-#include <SpatialDomains/SpatialDomains.hpp>
+//#include <SpatialDomains/SpatialDomains.hpp>
 #include <SpatialDomains/GeomFactors.h>
 
 #include <boost/unordered_set.hpp>

library/SpatialDomains/Geometry1D.h

@@ -36,7 +36,7 @@
 #ifndef NEKTAR_SPATIALDOMAINS_GEOMETRY1D_H
 #define NEKTAR_SPATIALDOMAINS_GEOMETRY1D_H
 
-#include <SpatialDomains/SpatialDomains.hpp>
+//#include <SpatialDomains/SpatialDomains.hpp>
 #include <SpatialDomains/Geometry.h>
 #include <SpatialDomains/MeshComponents.h>
 #include <SpatialDomains/SpatialDomainsDeclspec.h>

library/SpatialDomains/Geometry2D.h

@@ -37,7 +37,7 @@
 #define NEKTAR_SPATIALDOMAINS_GEOMETRY2D_H
 
 #include <StdRegions/StdRegions.hpp>
-#include <SpatialDomains/SpatialDomains.hpp>
+//#include <SpatialDomains/SpatialDomains.hpp>
 
 #include <SpatialDomains/Geometry.h>
 #include <SpatialDomains/SegGeom.h>

library/SpatialDomains/Geometry3D.h

@@ -37,7 +37,7 @@
 #define NEKTAR_SPATIALDOMAINS_GEOMETRY3D_H
 
 #include <StdRegions/StdRegions.hpp>
-#include <SpatialDomains/SpatialDomains.hpp>
+//#include <SpatialDomains/SpatialDomains.hpp>
 
 #include <SpatialDomains/Geometry.h>
 #include <SpatialDomains/Geometry2D.h>

library/SpatialDomains/MeshComponents.h

@@ -42,6 +42,7 @@
 #include <SpatialDomains/SpatialDomainsDeclspec.h>
 #include <set>
 #include <LibUtilities/BasicUtils/ParseUtils.hpp>
+#include <LibUtilities/Foundations/Graph.h>
 
 namespace Nektar
 {