Should finally correct all errors due to simultaneous opening of PEDRA.OUT and cavity.off

We generate a unique suffix for these files so that the file opened is always one and only one per run.
The .off file is now generated C++-side

Author: Roberto Di Remigio

cmake/custom/compilers/GNU.Fortran.cmake

@@ -1,7 +1,7 @@
 # Overrides contents of all variables previously set by CMake
 if(NOT DEFINED ENV{FCFLAGS})
     if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
-        set(CMAKE_Fortran_FLAGS "-DVAR_GFORTRAN -DGFORTRAN=445 -fimplicit-none -fPIC -fautomatic")
+        set(CMAKE_Fortran_FLAGS "-DVAR_GFORTRAN -DGFORTRAN=445 -fimplicit-none -fPIC -fautomatic -fmax-errors=1")
         set(CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g -fbacktrace -Wall -Wextra ${Fcheck_all}")
         set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -funroll-all-loops -ftree-vectorize")
     endif()

cmake/lib/config.py

@@ -9,6 +9,15 @@
 import shutil
 
 
+def module_exists(module_name):
+    try:
+        __import__(module_name)
+    except ImportError:
+        return False
+    else:
+        return True
+
+
 def check_cmake_exists(cmake_command):
     """
     Check whether CMake is installed. If not, print

cmake/update.py

@@ -138,9 +138,11 @@ def gen_setup(config, relative_path, setup_script_name):
     s.append('\nimport os')
     s.append('import sys')
 
-    s.append("\nsys.path.append('%s')" % os.path.join(relative_path, 'lib', 'docopt'))
-    s.append("\nsys.path.append('%s')" % os.path.join(relative_path, 'lib'))
-    s.append('from config import configure')
+    s.append("\nsys.path.insert(0, '{0}')".format(relative_path))
+    s.append("sys.path.insert(0, '{0}')".format(os.path.join(relative_path, 'lib')))
+    s.append("sys.path.insert(0, '{0}')".format(os.path.join(relative_path, 'lib', 'docopt')))
+
+    s.append('import config')
     s.append('import docopt')
 
     s.append('\n\noptions = """')
@@ -171,16 +173,29 @@ def gen_setup(config, relative_path, setup_script_name):
 
     s.append(gen_cmake_command(config))
 
-    s.append("\n\ntry:")
+    s.append("\n")
+    s.append("# parse command line args")
+    s.append("try:")
     s.append("    arguments = docopt.docopt(options, argv=None)")
     s.append("except docopt.DocoptExit:")
     s.append(r"    sys.stderr.write('ERROR: bad input to %s\n' % sys.argv[0])")
     s.append("    sys.stderr.write(options)")
     s.append("    sys.exit(-1)")
-    s.append("\nroot_directory = os.path.dirname(os.path.realpath(__file__))")
+    s.append("\n")
+    s.append("# use extensions to validate/post-process args")
+    s.append("if config.module_exists('extensions'):")
+    s.append("    import extensions")
+    s.append("    arguments = extensions.postprocess_args(sys.argv, arguments)")
+    s.append("\n")
+    s.append("root_directory = os.path.dirname(os.path.realpath(__file__))")
+    s.append("\n")
     s.append("build_path = arguments['<builddir>']")
+    s.append("\n")
+    s.append("# create cmake command")
     s.append("cmake_command = '%s %s' % (gen_cmake_command(options, arguments), root_directory)")
-    s.append("configure(root_directory, build_path, cmake_command, arguments['--show'])")
+    s.append("\n")
+    s.append("# run cmake")
+    s.append("config.configure(root_directory, build_path, cmake_command, arguments['--show'])")
 
     return s
 

doc/gfx/cavity.png

@@ -152,7 +152,7 @@ void Cavity::loadCavity(const std::string & fname)
 	    vertices.resize(Eigen::NoChange, nv); // BOGUS!!!
 	    arcs.resize(Eigen::NoChange, nv); // BOGUS!!
 	    // Populate vertices and arcs
-	    elements_.push_back(Element(nv,
+	    elements_.push_back(Element(nv, 0,
 				        elementArea_(i),
 					elementCenter_.col(i),
 					elementNormal_.col(i),

doc/gfx/dielectric_profile.png

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2015 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     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>
  */
@@ -46,13 +46,14 @@
 class Element
 {
 public:
-    Element(int nv, double w, const Eigen::Vector3d & c, const Eigen::Vector3d & n,
+    Element(int nv, int isphe, double w, const Eigen::Vector3d & c, const Eigen::Vector3d & n,
             bool i, const Sphere & s, const Eigen::Matrix3Xd & v, const Eigen::Matrix3Xd & a) :
-	    nVertices_(nv), area_(w), center_(c), normal_(n), irreducible_(i),
+	    nVertices_(nv), iSphere_(isphe), area_(w), center_(c), normal_(n), irreducible_(i),
 	    sphere_(s), vertices_(v), arcs_(a) {}
     virtual ~Element() {}
 
     int nVertices() const { return nVertices_; }
+    int iSphere() const { return iSphere_; }
     double area() const { return area_; }
     Eigen::Vector3d center() const { return center_; }
     Eigen::Vector3d normal() const { return normal_; }
@@ -79,6 +80,8 @@ class Element
 private:
     /// Number of vertices of the finite element
     int nVertices_;
+    /// Index of the sphere the finite element belongs to
+    int iSphere_;
     /// Area of the finite element
     double area_;
     /// Center of the finite element