Remove BlockDiagonalMatrix: it has never been used in the code

Author: Roberto Di Remigio

CMakeLists.txt

@@ -16,7 +16,7 @@ project(PCMSolver CXX C Fortran)
 option(ENABLE_MPI              "Enable MPI parallelization"                                       OFF)
 option(ENABLE_OPENMP           "Enable OpenMP parallelization"                                    OFF)
 option(ENABLE_VECTORIZATION    "Enable vectorization"                                             OFF)
-option(ENABLE_TESTS            "Enable compilation of unit tests"                                 OFF)
+option(ENABLE_TESTS            "Enable compilation of unit tests"                                 ON)
 option(ENABLE_CODE_COVERAGE    "Enable code coverage"                                             OFF)
 option(DISABLE_EIGEN_OWN       "Do not use Eigen3 headers shipped with the module"                OFF)
 option(ENABLE_EIGEN_MKL        "Enable Eigen3 automatic fallback to some of Intel MKL algorithms" OFF)
@@ -164,6 +164,10 @@ include_directories(${CMAKE_SOURCE_DIR}
 		    ${CMAKE_BINARY_DIR}/include
                     ${CMAKE_Fortran_MODULE_DIRECTORY})
 
+if(ENABLE_TESTS)
+  # Build also standalone executables in src/bin
+  set(BUILD_STANDALONE TRUE)
+endif()
 add_subdirectory(src)
 include_directories(${header_dir_list})
 

setup

@@ -143,7 +143,7 @@ def parse_input():
             help='link statically [default: %(default)s]')
     group.add_argument('--tests',
             action='store_true',
-            default=False,
+            default=True,
             help='build unit test suite [default: %(default)s]')
     group.add_argument('--vectorization',
             action='store_true',
@@ -317,13 +317,13 @@ def gen_cmake_command(args):
         # remove leading and trailing whitespace
         # otherwise CMake complains
         command += ' -DEXPLICIT_LIBS="%s"' % args.explicit_libs.strip()
-    
+
     if args.boost_headers:
         command += ' -DBOOST_INCLUDEDIR={0}'.format(args.boost_headers)
-    
+
     if args.boost_libs:
         command += ' -DBOOST_LIBRARYDIR={0}'.format(args.boost_libs)
-    
+
     if args.python:
         command += ' -DPYTHON_INTERPRETER={0}'.format(args.python)
 

src/CMakeLists.txt

@@ -21,7 +21,9 @@ add_subdirectory(pedra)
 add_subdirectory(solver)
 add_subdirectory(utils)
 # This directory contains source file for executables
-add_subdirectory(bin)
+if(BUILD_STANDALONE)
+   add_subdirectory(bin)
+endif()
 
 # We need to export header_dir_list one level up
 set(header_dir_list ${header_dir_list} PARENT_SCOPE)

src/solver/CPCMSolver.cpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
- *     PCMSolver is free software: you can redistribute it and/or modify       
+ *
+ *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.github.io/pcmsolver-doc>
  */
@@ -107,9 +107,8 @@ void CPCMSolver::buildIsotropicMatrix(const Cavity & cav)
     	matrixOut << "List of Eigenvalues:\n" << solver.eigenvalues() << std::endl;
     	matrixOut.close();
     */
-    // Pack into a BlockDiagonalMatrix
-    // For the moment just packs into a std::vector<Eigen::MatrixXd> without the syntactic
-    // sugar of the BlockDiagonalMatrix class...
+    // Pack into a block diagonal matrix
+    // For the moment just packs into a std::vector<Eigen::MatrixXd>
     symmetryPacking(blockPCMMatrix, fullPCMMatrix, dimBlock, nrBlocks);
 
     builtIsotropicMatrix = true;
@@ -128,7 +127,6 @@ void CPCMSolver::computeCharge(const Eigen::VectorXd &potential,
     if (builtIsotropicMatrix) {
         charge.segment(irrep*irrDim,
                        irrDim)= - blockPCMMatrix[irrep] * potential.segment(irrep*irrDim, irrDim);
-//		charge = - fullPCMMatrix * potential;
     } else {
         throw std::runtime_error("PCM matrix not initialized!");
     }

src/solver/IEFSolver.cpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
- *     PCMSolver is free software: you can redistribute it and/or modify       
+ *
+ *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.github.io/pcmsolver-doc>
  */
@@ -65,7 +65,7 @@ void IEFSolver::buildAnisotropicMatrix(const Cavity & cav)
 
     // This is the very core of PCMSolver
     throw std::runtime_error("Calculation of anisotropic matrix elements not yet implemented.");
-    /*  
+    /*
     greenInside_->compOffDiagonal(cav.elementCenter(), cav.elementNormal(), SI, DI);
     greenInside_->compDiagonal(cav.elementArea(), cav.elementRadius(), SI, DI);
     greenOutside_->compOffDiagonal(cav.elementCenter(), cav.elementNormal(), SE, DE);
@@ -100,9 +100,8 @@ void IEFSolver::buildAnisotropicMatrix(const Cavity & cav)
     if (hermitivitize_) {
         hermitivitize(fullPCMMatrix);
     }
-    // Pack into a BlockDiagonalMatrix
-    // For the moment just packs into a std::vector<Eigen::MatrixXd> without the syntactic
-    // sugar of the BlockDiagonalMatrix class...
+    // Pack into a block diagonal matrix
+    // For the moment just packs into a std::vector<Eigen::MatrixXd>
     symmetryPacking(blockPCMMatrix, fullPCMMatrix, dimBlock, nrBlocks);
     std::ofstream matrixOut("PCM_matrix");
     matrixOut << "fullPCMMatrix" << std::endl;
@@ -193,9 +192,8 @@ void IEFSolver::buildIsotropicMatrix(const Cavity & cav)
     	matrixOut << "List of Eigenvalues:\n" << solver.eigenvalues() << std::endl;
     	matrixOut.close();
     */
-    // Pack into a BlockDiagonalMatrix
-    // For the moment just packs into a std::vector<Eigen::MatrixXd> without the syntactic
-    // sugar of the BlockDiagonalMatrix class...
+    // Pack into a block diagonal matrix
+    // For the moment just packs into a std::vector<Eigen::MatrixXd>
     symmetryPacking(blockPCMMatrix, fullPCMMatrix, dimBlock, nrBlocks);
     std::ofstream matrixOut("PCM_matrix");
     matrixOut << "fullPCMMatrix" << std::endl;
@@ -221,7 +219,6 @@ void IEFSolver::computeCharge(const Eigen::VectorXd &potential,
     if (builtIsotropicMatrix or builtAnisotropicMatrix) {
         charge.segment(irrep*irrDim,
                        irrDim)= - blockPCMMatrix[irrep] * potential.segment(irrep*irrDim, irrDim);
-//		charge = - fullPCMMatrix * potential;
     } else {
         throw std::runtime_error("PCM matrix not initialized!");
     }