Made some changes to make the code compatible with dealii8.5.0

ferroteam · Jul 30, 2017 · dc5357e · dc5357e
1 parent 02805e7
commit dc5357e
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Showing 7 changed files with 28 additions and 21 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,30 +5,30 @@
 ##Note: Set ALGLIB, LIBXC, PETSC and SLEPC paths below. 
 
 ##set ALGLIB paths
-SET(ALGLIB_INCLUDE "/nfs/mcfs_comp/home/rudraa/software/alglib/cpp/src/") #path to interpolation.h
-SET(ALGLIB_LIB "/nfs/mcfs_comp/home/rudraa/software/alglib/cpp/src/libAlglib.so") #path to libAlglib.so
+SET(ALGLIB_INCLUDE "/home/phanim/softwares/alglib/cpp/src/") #path to interpolation.h
+SET(ALGLIB_LIB "/home/phanim/softwares/alglib/cpp/src/libAlglib.so") #path to libAlglib.so
 ##Note: On some platforms, you may have to set DYLD_LIBRARY_PATH(OSX)/LD_LIBRARY_PATH to include path ALGLIB_LIB. For example:
 ##export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/Algib/.so/file
 
 ##set LIBXC paths
-SET(LIBXC_INCLUDE "/nfs/mcfs_comp/home/rudraa/software/libxc/libxc-2.2.0/installDir/include") #path to xc.h
-SET(LIBXC_LIB "/nfs/mcfs_comp/home/rudraa/software/libxc/libxc-2.2.0/installDir/lib/libxc.a") #path to libxc.a
+SET(LIBXC_INCLUDE "/home/phanim/softwares/libxc/install_caen_libxc/include") #path to xc.h
+SET(LIBXC_LIB "/home/phanim/softwares/libxc/install_caen_libxc/lib/libxc.a") #path to libxc.a
 
 ##set PETSc Real paths
-SET(PETSC_REAL_INCLUDE "/home/vikramg/DFT-FE-softwares/softwareCentos/petsc/intel_petsc3.7.5_double_elemental/include")
-SET(PETSC_REAL_LIB "/home/vikramg/DFT-FE-softwares/softwareCentos/petsc/intel_petsc3.7.5_double_elemental/lib/libpetsc.so")
+SET(PETSC_REAL_INCLUDE "/home/phanim/softwares/PETSc/install_caen_double/include")
+SET(PETSC_REAL_LIB "/home/phanim/softwares/PETSc/install_caen_double/lib/libpetsc.so")
 
 ##set SLEPc Real paths
-SET(SLEPC_REAL_INCLUDE "/home/vikramg/DFT-FE-softwares/softwareCentos/slepc/intel_slepc3.7.3_double_elemental/include")
-SET(SLEPC_REAL_LIB "/home/vikramg/DFT-FE-softwares/softwareCentos/slepc/intel_slepc3.7.3_double_elemental/lib/libslepc.so") 
+SET(SLEPC_REAL_INCLUDE "/home/phanim/softwares/SLEPc/install_caen_double/include")
+SET(SLEPC_REAL_LIB "/home/phanim/softwares/SLEPc/install_caen_double/lib/libslepc.so") 
 
 ##set PETSc Complex paths
-SET(PETSC_COMPLEX_INCLUDE "/home/vikramg/DFT-FE-softwares/softwareCentos/petsc/intel_petsc3.7.5_complex/include")
-SET(PETSC_COMPLEX_LIB "/home/vikramg/DFT-FE-softwares/softwareCentos/petsc/intel_petsc3.7.5_complex/lib/libpetsc.so")
+SET(PETSC_COMPLEX_INCLUDE "/home/phanim/softwares/PETSc/install_caen_complex/include")
+SET(PETSC_COMPLEX_LIB "/home/phanim/softwares/PETSc/install_caen_complex/lib/libpetsc.so")
 
 ##set SLEPc Complex paths
-SET(SLEPC_COMPLEX_INCLUDE "/home/vikramg/DFT-FE-softwares/softwareCentos/slepc/intel_slepc3.7.3_complex/include")
-SET(SLEPC_COMPLEX_LIB "/home/vikramg/DFT-FE-softwares/softwareCentos/slepc/intel_slepc3.7.3_complex/lib/libslepc.so") 
+SET(SLEPC_COMPLEX_INCLUDE "/home/phanim/softwares/SLEPc/install_caen_complex/include")
+SET(SLEPC_COMPLEX_LIB "/home/phanim/softwares/SLEPc/install_caen_complex/lib/libslepc.so") 
 
 #
 # Usually, you will not need to modify anything beyond this point...

diff --git a/examples/allElectron/nonPeriodic/carbonSingleAtom/parameterFile.prm b/examples/allElectron/nonPeriodic/carbonSingleAtom/parameterFile.prm
@@ -1,6 +1,6 @@
 #path specifying the location of the "build" directory which is usually the location of "src" folder 
 #
-set DFT PATH = "/home/phanim/KohnShamCodes/DEALIICode/dft-fe"
+set DFT PATH = "/home/phanim/DFT-FE/dft-fe"
 
 #
 #finite-element related parameters

diff --git a/include/headers.h b/include/headers.h
@@ -13,6 +13,7 @@
 #include <deal.II/fe/fe_system.h>
 #include <deal.II/fe/fe_q.h>
 #include <deal.II/fe/fe_values.h>
+#include <deal.II/fe/mapping_q1.h>
 #include <deal.II/grid/tria.h>
 #include <deal.II/grid/tria_accessor.h>
 #include <deal.II/grid/tria_iterator.h>

diff --git a/setup.sh b/setup.sh
@@ -3,7 +3,7 @@ set -e
 set -o pipefail
 #script to setup and build DFT-FE 
 #set CMAKE path
-cmake=/sw/arcts/centos7/cmake/3.5.2/bin/cmake
+cmake=/usr/bin/cmake
 #
 #Usually, no changes are needed below this line
 #

diff --git a/src/dft/initPseudo.cc b/src/dft/initPseudo.cc
@@ -141,7 +141,7 @@ void dftClass<FEOrder>::initLocalPseudoPotential()
  double *pseudoValuesPtr = &((*pseudoValues)[cell->id()][0]);
  for (unsigned int q = 0; q < n_q_points; ++q)
  {
- MappingQ<3> test(1); 
+ MappingQ1<3,3> test; 
  Point<3> quadPoint(test.transform_unit_to_real_cell(cell, fe_values.get_quadrature().point(q)));
  double pseudoValueAtQuadPt=0.0;
  //loop over atoms
@@ -782,7 +782,7 @@ void dftClass<FEOrder>::computeSparseStructureNonLocalProjectors()
  const int globalSplineId = d_deltaVlIdToFunctionIdDetails[pseudoPotentialId][0];
  for(int iQuadPoint = 0; iQuadPoint < numberQuadraturePoints; ++iQuadPoint)
  {
- MappingQ<3> test(1);
+ MappingQ1<3,3> test;
  Point<3> quadPoint(test.transform_unit_to_real_cell(cell, fe_values.get_quadrature().point(iQuadPoint)));
 
  for(int iImageAtomCount = 0; iImageAtomCount < imageIdsList.size(); ++iImageAtomCount)
@@ -1003,7 +1003,7 @@ void dftClass<FEOrder>::computeElementalProjectorKets()
  for(int iQuadPoint = 0; iQuadPoint < numberQuadraturePoints; ++iQuadPoint)
  {
 
- MappingQ<3> test(1);
+ MappingQ1<3,3> test;
  Point<3> quadPoint(test.transform_unit_to_real_cell(cell, fe_values.get_quadrature().point(iQuadPoint)));
 
  for(int iImageAtomCount = 0; iImageAtomCount < imageIdsList.size(); ++iImageAtomCount)

diff --git a/src/dft/initRho.cc b/src/dft/initRho.cc
@@ -69,7 +69,7 @@ void dftClass<FEOrder>::initRho()
  double *rhoInValuesPtr = &((*rhoInValues)[cell->id()][0]);
  for (unsigned int q = 0; q < n_q_points; ++q)
  {
- MappingQ<3> test(1); 
+ MappingQ1<3,3> test; 
  Point<3> quadPoint(test.transform_unit_to_real_cell(cell, fe_values.get_quadrature().point(q)));
  double rhoValueAtQuadPt = 0.0;
 
@@ -130,7 +130,7 @@ void dftClass<FEOrder>::initRho()
 
  for (unsigned int q = 0; q < n_q_points; ++q)
  {
- MappingQ<3> test(1); 
+ MappingQ1<3,3> test; 
  Point<3> quadPoint(test.transform_unit_to_real_cell(cell, fe_values.get_quadrature().point(q)));
  double gradRhoXValueAtQuadPt = 0.0;
  double gradRhoYValueAtQuadPt = 0.0;

diff --git a/src/poisson/poisson.cc b/src/poisson/poisson.cc
@@ -115,13 +115,18 @@ void poissonClass<FEOrder>::computeRHS2()
  }
  rhs2.compress(VectorOperation::add);
  jacobianDiagonal.compress(VectorOperation::add);
+
  //remove zero entries of the jacobianDiagonal which occur at the hanging nodes
  for (unsigned int i=0; i<jacobianDiagonal.local_size(); i++)
  {
  if (std::abs(jacobianDiagonal.local_element(i))<1.0e-15)
  {
  jacobianDiagonal.local_element(i)=1.0;
  }
+ else
+ {
+ jacobianDiagonal.local_element(i) = 1.0/jacobianDiagonal.local_element(i);
+ }
  }
  jacobianDiagonal.update_ghost_values();
  //pcout << "rhs2: " << rhs2.l2_norm() << std::endl;
@@ -233,7 +238,7 @@ void poissonClass<FEOrder>::computeRHS(std::map<dealii::CellId,std::vector<doubl
  if(!constraintMatrix->is_identity_constrained(i))
  {
  if(rhoValues) rhs(i)=0.0;
- else rhs(i)=constraintMatrix->get_inhomogeneity(i)*jacobianDiagonal(i);
+ else rhs(i)=constraintMatrix->get_inhomogeneity(i)/jacobianDiagonal(i);
  }
  }
  }
@@ -346,7 +351,8 @@ void poissonClass<FEOrder>::vmult(vectorType &dst, const vectorType &src) const
 template<unsigned int FEOrder>
 void poissonClass<FEOrder>::precondition_Jacobi(vectorType& dst, const vectorType& src, const double omega) const
 {
- dst.ratio(src, jacobianDiagonal);
+ dst = src;
+ dst.scale(jacobianDiagonal);
 }
 
 //