Mercurial > fem-fenics-eugenio

changeset 177:dae73b9eab87

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Remove obsolete files.
author gedeone-octave <marcovass89@hotmail.it>
date Wed, 06 Nov 2013 23:34:54 +0000
parents 32a023fc678a
children 097026c0acb5
files obsolete/Laplace.ufl obsolete/Plot_2d.cc obsolete/Plot_3d.cc obsolete/bin/codeCreator.py obsolete/bin/codeMantainer.py obsolete/bin/create_fs.py obsolete/bin/create_lhs.py obsolete/bin/create_rhs.py obsolete/fem_fs.cc obsolete/fem_func_space.m obsolete/fem_get_mesh.cc obsolete/fem_init_env.cc obsolete/fem_lhs.cc obsolete/fem_rhs.cc obsolete/plot.cc obsolete/test/Laplace.ufl obsolete/test/Makefile obsolete/test/laplace.m obsolete/test/mesh_test.m obsolete/test/test_all.m obsolete/test/test_bc.cpp obsolete/test/test_bc.m obsolete/test/test_coeff.cpp obsolete/test/test_coeff.m obsolete/test/test_expr.cpp obsolete/test/test_expr.m obsolete/test/test_rlhs.cc obsolete/test/test_rlhs.m
diffstat 28 files changed, 0 insertions(+), 2076 deletions(-) [+]
line wrap: on
line diff
--- a/obsolete/Laplace.ufl	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-# Copyright (C) 2005-2009 Anders Logg
-#
-# This file is part of DOLFIN.
-#
-# DOLFIN 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.
-#
-# DOLFIN 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 DOLFIN. If not, see <http://www.gnu.org/licenses/>.
-#
-# First added:  2005
-# Last changed: 2011-03-08
-#
-# The bilinear form a(u, v) and linear form L(v) for
-# Poisson's equation.
-#
-# Compile this form with FFC: ffc -l dolfin Poisson.ufl.
-
-
-element = FiniteElement("Lagrange", triangle, 1)
-# element = FiniteElement("Lagrange", tetrahedron, 2)
-
-u = TrialFunction(element)
-v = TestFunction(element)
-f = Coefficient(element)
-g = Coefficient(element)
-
-a = inner(grad(u), grad(v))*dx
-L = f*v*dx + g*v*ds
--- a/obsolete/Plot_2d.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-#include "mesh.h"
-#include "Plot_2d.h"
-
-DEFUN_DLD (Plot_2d, args, , "-*- texinfo -*-\n\
-@deftypefn {Function File} \
-Plot_2d (@var{msh}, @var{nodal_value})\n\
-The input parameters are a Mesh and a vector which specify the values of the \
-function that you want to plot at each node\n\
-@seealso{fem_func, fem_save}\n\
-@end deftypefn")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-  
-  if (nargin < 2 || nargin > 2)
-    print_usage ();
-  else
-    {
-      if (! mesh_type_loaded)
-        {
-          mesh::register_type ();
-          mesh_type_loaded = true;
-          mlock ();
-        }
-      if (args(0).type_id () == mesh::static_type_id ())
-        {
-          const mesh & msh =
-            static_cast<const mesh&> (args(0).get_rep ());
-          Array <double> myu = args(1).array_value ();
-
-          if (!error_state)
-            {
-              const dolfin::Mesh & mshd = msh.get_msh ();
-              boost::shared_ptr <const dolfin::FunctionSpace> V (new Plot_2d::FunctionSpace (mshd));
-
-              if (V->dim () != myu.length ())
-                error ("Plot_2D: The size of the functional space and of the vector must agree");
-              else
-                {
-                  dolfin::Vector du(myu.length ());
-                  for (std::size_t i = 0; i < myu.length (); ++i)
-                    du.setitem (i, myu(i));
-
-                  boost::shared_ptr<dolfin::Vector> uu (new dolfin::Vector(du));
-                  boost::shared_ptr <const dolfin::Function> u (new dolfin::Function(V, uu));
-                  dolfin::plot (*u);
-                  dolfin::interactive ();
-                  retval = 0;
-                }
-            }
-        }
-    }
-  return retval;
-}
--- a/obsolete/Plot_3d.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-#include "mesh.h"
-#include "Plot_3d.h"
-
-DEFUN_DLD (Plot_3d, args, , "-*- texinfo -*-\n\
-@deftypefn {Function File} \
-Plot_3d (@var{msh}, @var{nodal_value})\n\
-The input parameters are a Mesh and a vector which specify the values of the \
-function that you want to plot at each node\n\
-@seealso{fem_func, fem_save}\n\
-@end deftypefn")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-  
-  if (nargin < 2 || nargin > 2)
-    print_usage ();
-  else
-    {
-      if (! mesh_type_loaded)
-        {
-          mesh::register_type ();
-          mesh_type_loaded = true;
-          mlock ();
-        }
-      if (args(0).type_id () == mesh::static_type_id ())
-        {
-          const mesh & msh =
-            static_cast<const mesh&> (args(0).get_rep ());
-          Array <double> myu = args(1).array_value ();
-
-          if (!error_state)
-            {
-              const dolfin::Mesh & mshd = msh.get_msh ();
-              boost::shared_ptr <const dolfin::FunctionSpace> V (new Plot_3d::FunctionSpace (mshd));
-
-              if (V->dim () != myu.length ())
-                error ("The size of the functional space and of the vector must agree");
-              else
-                {
-                  dolfin::Vector du(myu.length ());
-                  for (std::size_t i = 0; i < myu.length (); ++i)
-                    du.setitem (i, myu(i));
-
-                  boost::shared_ptr<dolfin::Vector> uu (new dolfin::Vector(du));
-                  boost::shared_ptr <const dolfin::Function> u (new dolfin::Function(V, uu));
-                  dolfin::plot (*u);
-                  dolfin::interactive ();
-                  retval = 0;
-                }
-            }
-        }
-    }
-  return retval;
-}
--- a/obsolete/bin/codeCreator.py	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,431 +0,0 @@
-'''
- Copyright (C) 2013 - Juan Pablo Carbajal
- Copyright (C) 2013 - Marco Vassallo
-
- This progrm is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- This program 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 General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-'''
-
-# Author: Juan Pablo Carbajal <ajuanpi+dev@gmail.com>
-# Modified by: Marco Vassallo
-
-from io import open
-from string import Template
-
-class Makefile ():
-
-  def __init__(self,**kwargs):
-    """ Creates a makefile with the names of the files to be compiled.
-
-    Inuts must be all strings.
-    """
-    if map(type,kwargs.values()) != [str]*len(kwargs):
-      raise ValueError("Makefile accepts only str arguments.")
-
-    self.name = "Makefile_"+kwargs["name"]
-    self.body = Template ("""
-DIR = $path
-CPPFLAGS=
-LIBS= -ldolfin
-MKOCTFILE = mkoctfile
-FFC = ffc
-
-OCTFILES = fem_fs_$name.oct
-
-all : $(OCTFILES) 
-fs : fem_fs_$name.oct
-rhs : fem_rhs_$name.oct
-lhs : fem_lhs_$name.oct
-
-fem_fs_$name.o: fem_fs_$name.cc
-	$(MKOCTFILE) -I$(DIR) -I. $(CPPFLAGS) $(LDFLAGS) $< -c $@
-
-fem_fs_$name.oct: $name.h fem_fs_$name.o
-	$(MKOCTFILE) -s fem_fs_$name.o $(DIR)fem_init_env.o $(LDFLAGS) $(LIBS) -o $@
-
-fem_rhs_$name.o: fem_rhs_$name.cc
-	$(MKOCTFILE) -I$(DIR) -I. $(LDFLAGS) $(CPPFLAGS) $< -c $@
-
-fem_rhs_$name.oct: $name.h fem_rhs_$name.o
-	$(MKOCTFILE) -s fem_rhs_$name.o $(DIR)fem_init_env.o $(LDFLAGS) $(LIBS) -o $@
-
-fem_lhs_$name.o: fem_lhs_$name.cc
-	$(MKOCTFILE) -I$(DIR) -I. $(LDFLAGS) $(CPPFLAGS) $< -c $@
-
-fem_lhs_$name.oct: $name.h fem_lhs_$name.o
-	$(MKOCTFILE) -s fem_lhs_$name.o $(DIR)fem_init_env.o $(LDFLAGS) $(LIBS) -o $@
-
-$name.h: $name.ufl
-	$(FFC) -l dolfin $name.ufl
-
-.PHONY: clean
-
-clean:
-	 rm -f fem_fs_$name.o fem_fs_$name.cc $name.h
-	 rm -f fem_rhs_$name.o fem_rhs_$name.cc
-	 rm -f fem_lhs_$name.o fem_lhs_$name.cc
-	 rm -f $makefile
-
-""").safe_substitute(name=kwargs["name"],
-                     makefile=self.name,
-                     path=kwargs["path"])
-
-  def writeout (self):
-    mfile = open (self.name, 'w')
-    mfile.write(unicode(self.body))
-    mfile.close()
-
-class Functionspace ():
-
-  def __init__(self,**kwargs):
-    """ Creates a file fem_fs_$name with the name of the Variational problem to.
-
-    Inuts must be all strings.
-    """
-    if map(type,kwargs.values()) != [str]*len(kwargs):
-      raise ValueError("Functionspace accepts only str arguments.")
-
-    self.name = "fem_fs_"+kwargs["name"]+".cc"
-    self.body = Template ("""
-#include "functionspace.h"
-#include "mesh.h"
-#include "$name.h"
-
-DEFUN_DLD (fem_fs_$name, args, , "initialize a fs from a mesh declared with fem_init_mesh")
-{
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1 || nargin > 1)
-    print_usage ();
-  else
-    {
-
-      if (! mesh_type_loaded)
-        {
-          mesh::register_type ();
-          mesh_type_loaded = true;
-          mlock ();
-        }
-
-      if (args(0).type_id () == mesh::static_type_id ())
-        {
-          const mesh & msho = static_cast<const mesh&> (args(0).get_rep ());
-          const dolfin::Mesh & mshd = msho.get_msh ();
-          boost::shared_ptr <const dolfin::FunctionSpace> g (new $name::FunctionSpace (mshd));
-
-          if (! functionspace_type_loaded)
-            {
-              functionspace::register_type ();
-              functionspace_type_loaded = true;
-              mlock ();
-            }
-
-          retval = new functionspace(g);
-        }
-    }
-  return retval;
-}
-""").safe_substitute(name=kwargs["name"])
-
-  def writeout (self):
-    mfile = open (self.name, 'w')
-    mfile.write(unicode(self.body))
-    mfile.close()
-
-class RHS ():
-
-  def __init__(self,**kwargs):
-    """ Creates a file fem_rhs_$name with the name of the Variational problem to.
-
-    Inuts must be all strings.
-    """
-    if map(type,kwargs.values()) != [str]*len(kwargs):
-      raise ValueError("RHS accepts only str arguments.")
-
-    self.name = "fem_rhs_"+kwargs["name"]+".cc"
-    self.body = Template ("""
-#include "$name.h"
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-#include "function.h"
-
-DEFUN_DLD (fem_rhs_$name, args, , "A = fem_rhs_$name (FUNCTIONAL SPACE, COEFF, BC)")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1)
-    print_usage ();
-  else
-    {
-      if (! functionspace_type_loaded)
-        {
-          functionspace::register_type ();
-          functionspace_type_loaded = true;
-          mlock ();
-        }
-      if (args(0).type_id () == functionspace::static_type_id ())
-        {
-          const functionspace & fspo
-            = static_cast<const functionspace&> (args(0).get_rep ());
-
-          if (! error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              $name::BilinearForm a (V, V);
-              std::size_t ncoef = a.num_coefficients (), nc = 0;
-
-              if (! coefficient_type_loaded)
-                {
-                  coefficient::register_type ();
-                  coefficient_type_loaded = true;
-                  mlock ();
-                }
-
-              if (! function_type_loaded)
-                {
-                  function::register_type ();
-                  function_type_loaded = true;
-                  mlock ();
-                }
-
-              for (std::size_t i = 1; i < nargin; ++i)
-                {
-                  if (args(i).type_id () == coefficient::static_type_id ())
-                    {
-                      const coefficient & cf
-                        = static_cast <const coefficient&> (args(i).get_rep ());
-
-                      std::size_t n = a.coefficient_number (cf.get_str ());
-                      const boost::shared_ptr<const expression> & pexp = cf.get_expr ();
-                      a.set_coefficient (n, pexp);
-                      ++nc;
-                    }
-
-                  if (args(i).type_id () == function::static_type_id ())
-                    {
-                      const function & fun
-                        = static_cast <const function&> (args(i).get_rep ());
-
-                      std::size_t n = a.coefficient_number (fun.get_str ());
-                      const boost::shared_ptr<const dolfin::Function> & pfun = fun.get_pfun ();
-                      a.set_coefficient (n, pfun);
-                      ++nc;
-                    }
-                 }
-
-              if (nc != ncoef)
-                error ("Wrong number of coefficient");
-              else
-                {
-
-                  dolfin::Matrix A;
-                  dolfin::assemble (A, a);
-
-                  if (! boundarycondition_type_loaded)
-                    {
-                      boundarycondition::register_type ();
-                      boundarycondition_type_loaded = true;
-                      mlock ();
-                    }
-
-                  for (std::size_t i = 1; i < nargin; ++i)
-                    {
-                      if (args(i).type_id () == boundarycondition::static_type_id ())
-                        {
-                          const boundarycondition & bc 
-                            = static_cast<const boundarycondition&> (args(i).get_rep ());
-
-                          const std::vector<boost::shared_ptr <const dolfin::DirichletBC> > & pbc
-                                = bc.get_bc ();
-                              for (std::size_t j = 0; j < pbc.size (); ++j)
-                                pbc[j]->apply(A);
-                        }
-                    }
-
-                  int nr = A.size (0), nc = A.size (1);
-                  // nz shoud be estimated in a better way
-                  int nz = nr * nc;
-                  SparseMatrix sm (nr, nc, nz);
-
-                  int ii = 0;
-                  sm.cidx (0) = 0;
-                  for (int j = 0; j < nc; ++j)
-                   {
-                     for (int i = 0; i < nr; i++)
-                       {
-                         double tmp = A(i, j);
-                         if (tmp != 0.)
-                           {
-                             sm.data(ii) = tmp;
-                             sm.ridx(ii) = i;
-                             ii++;
-                           }
-                       }
-                     sm.cidx(j+1) = ii;
-                  }
-                  sm.maybe_compress ();
-
-                  retval = sm;
-
-                }
-            }
-        }
-    }
-  return retval;
-}
-""").safe_substitute(name=kwargs["name"])
-
-  def writeout (self):
-    mfile = open (self.name, 'w')
-    mfile.write(unicode(self.body))
-    mfile.close()
-
-class LHS ():
-
-  def __init__(self,**kwargs):
-    """ Creates a file fem_lhs_$name with the name of the Variational problem to.
-
-    Inuts must be all strings.
-    """
-    if map(type,kwargs.values()) != [str]*len(kwargs):
-      raise ValueError("lhs accepts only str arguments.")
-
-    self.name = "fem_lhs_"+kwargs["name"]+".cc"
-    self.body = Template ("""
-#include "$name.h"
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-#include "function.h"
-
-DEFUN_DLD (fem_lhs_$name, args, , " b = fem_lhs_$name (FUNCTIONAL SPACE, COEFF, BC)")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1)
-    print_usage ();
-  else
-    {
-
-      if (! functionspace_type_loaded)
-        {
-          functionspace::register_type ();
-          functionspace_type_loaded = true;
-          mlock ();
-        }
-      if (args(0).type_id () == functionspace::static_type_id ())
-        {
-          const functionspace & fspo
-            = static_cast<const functionspace&> (args(0).get_rep ());
-
-          if (! error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              $name::LinearForm L (V);
-              std::size_t ncoef = L.num_coefficients (), nc = 0;
-
-              if (! coefficient_type_loaded)
-                {
-                  coefficient::register_type ();
-                  coefficient_type_loaded = true;
-                  mlock ();
-                }
-
-              if (! function_type_loaded)
-                {
-                  function::register_type ();
-                  function_type_loaded = true;
-                  mlock ();
-                }
-
-              for (std::size_t i = 1; i < nargin; ++i)
-                {
-                  if (args(i).type_id () == coefficient::static_type_id ())
-                    {
-                      const coefficient & cf
-                        = static_cast <const coefficient&> (args(i).get_rep ());
-
-                      std::size_t n = L.coefficient_number (cf.get_str ());
-                      const boost::shared_ptr<const expression> & pexp = cf.get_expr ();
-                      L.set_coefficient (n, pexp);
-                      ++nc;
-                    }
-
-                  if (args(i).type_id () == function::static_type_id ())
-                    {
-                      const function & fun
-                        = static_cast <const function&> (args(i).get_rep ());
-
-                      std::size_t n = L.coefficient_number (fun.get_str ());
-                      const boost::shared_ptr<const dolfin::Function> & pfun = fun.get_pfun ();
-                      L.set_coefficient (n, pfun);
-                      ++nc;
-                    }
-                 }
-
-              if (nc != ncoef)
-                error ("Wrong number of coefficient");
-              else
-                {
-
-                  dolfin::Vector b;
-                  dolfin::assemble (b, L);
-
-                  if (! boundarycondition_type_loaded)
-                    {
-                      boundarycondition::register_type ();
-                      boundarycondition_type_loaded = true;
-                      mlock ();
-                    }
-                  for (std::size_t i = 1; i < nargin; ++i)
-                    {
-                      if (args(i).type_id () == boundarycondition::static_type_id ())
-                        {
-                          const boundarycondition & bc 
-                            = static_cast<const boundarycondition&> (args(i).get_rep ());
-
-                          const std::vector<boost::shared_ptr <const dolfin::DirichletBC> > & pbc
-                                = bc.get_bc ();
-                              for (std::size_t j = 0; j < pbc.size (); ++j)
-                                pbc[j]->apply(b);
-                        }
-                    }
-
-                  dim_vector dims;
-                  dims.resize (2);
-                  dims(0) = b.size ();
-                  dims(1) = 1;
-                  Array<double> myb (dims);
-
-                  for (std::size_t i = 0; i < b.size (); ++i)
-                    myb(i) = b[i];
-
-                  retval = myb;
-                }
-            }
-        }
-    }
-  return retval;
-}
-""").safe_substitute(name=kwargs["name"])
-
-  def writeout (self):
-    mfile = open (self.name, 'w')
-    mfile.write(unicode(self.body))
-    mfile.close()
--- a/obsolete/bin/codeMantainer.py	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-'''
- Copyright (C) 2013 - Juan Pablo Carbajal
- Copyright (C) 2013 - Marco Vassallo
-
- This progrm is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- This program 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 General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-'''
-
-# Author: Juan Pablo Carbajal <ajuanpi+dev@gmail.com>
-# Modified by: Marco Vassallo
-
-from subprocess import check_call
-from subprocess import CalledProcessError
-from os import devnull
-
-import codeCreator as cc
-
-class codeMantainer ():
-
-  def __init__ (self,name, path = "./include/"):
-    self.path= path
-    p = dict (path=self.path)
-
-    self.name = dict (name = name)
-
-    self.mk = [] # placeholder for makefile
-
-    self.make = "make"
-    self.mk_options = [r'--file=Makefile_{name}'.format (**self.name)]
-
-  def runFs (self):
-    with open (devnull, "w") as f:
-      check_call ([self.make] + self.mk_options + ["fs"], stdout=f)
-    return 0
-
-  def runRHS (self):
-    with open (devnull, "w") as f:
-      check_call ([self.make] + self.mk_options + ["rhs"], stdout=f)
-    return 0
-
-  def runLHS (self):
-    with open (devnull, "w") as f:
-      check_call ([self.make] + self.mk_options + ["lhs"], stdout=f)
-    return 0
-
-  def clean (self):
-    with open (devnull, "w") as f:
-      check_call ([self.make] + self.mk_options + ["clean"], stdout=f)
-    return 0
-
-  def updateMakefile(self):
-    self.mk = cc.Makefile(path = self.path, **self.name)
-    self.mk.writeout ()
-
-  def updateFs(self):
-    self.fs = cc.Functionspace (path = self.path, **self.name)
-    self.fs.writeout ()
-
-  def updateRHS(self):
-    self.rhs = cc. RHS (path = self.path, **self.name)
-    self.rhs.writeout ()
-
-  def updateLHS(self):
-    self.lhs = cc. LHS (path = self.path, **self.name)
-    self.lhs.writeout ()
--- a/obsolete/bin/create_fs.py	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-#! usr/bin/python
-
-import argparse
-from codeMantainer import *
-
-parser = argparse.ArgumentParser()
-parser.add_argument('name')
-parser.add_argument('path')
-args= parser.parse_args()
-
-myobj = codeMantainer (args.name, args.path)
-myobj.updateMakefile ()
-myobj.updateFs ()
-myobj.runFs ()
-myobj.clean ()
-
-quit()
--- a/obsolete/bin/create_lhs.py	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-#! usr/bin/python
-
-import argparse
-from codeMantainer import *
-
-parser = argparse.ArgumentParser()
-parser.add_argument('name')
-parser.add_argument('path')
-args= parser.parse_args()
-
-myobj = codeMantainer (args.name, args.path)
-myobj.updateMakefile ()
-myobj.updateLHS ()
-myobj.runLHS ()
-myobj.clean ()
-
-quit()
--- a/obsolete/bin/create_rhs.py	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-#! usr/bin/python
-
-import argparse
-from codeMantainer import *
-
-parser = argparse.ArgumentParser()
-parser.add_argument('name')
-parser.add_argument('path')
-args= parser.parse_args()
-
-myobj = codeMantainer (args.name, args.path)
-myobj.updateMakefile ()
-myobj.updateRHS ()
-myobj.runRHS ()
-myobj.clean ()
-
-quit()
--- a/obsolete/fem_fs.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#include "functionspace.h"
-#include "mesh.h"
-#include "Laplace.h"
-
-DEFUN_DLD (fem_fs, args, , "initialize a fs from a mesh declared with fem_init_mesh")
-{
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1 || nargin > 1)
-    print_usage ();
-  else
-    {
-
-      if (! mesh_type_loaded)
-        {
-          mesh::register_type ();
-          mesh_type_loaded = true;
-          mlock ();
-        }
-
-      if (args(0).type_id () == mesh::static_type_id ())
-        {
-          const mesh & msho = static_cast<const mesh&> (args(0).get_rep ());
-          const dolfin::Mesh & mshd = msho.get_msh ();
-          boost::shared_ptr <const dolfin::FunctionSpace> g (new Laplace::FunctionSpace (mshd));
-
-          if (! functionspace_type_loaded)
-            {
-              functionspace::register_type ();
-              functionspace_type_loaded = true;
-              mlock ();
-            }
-
-          retval = new functionspace(g);
-        }
-    }
-  return retval;
-}
--- a/obsolete/fem_func_space.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-## Copyright (C) 2013 Marco Vassallo
-
-## This program is free software; you can redistribute it and/or modify it under
-## the terms of the GNU General Public License as published by the Free Software
-## Foundation; either version 2 of the License, or (at your option) any later
-## version.
-
-## This program 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 General Public License for more
-## details.
-
-## You should have received a copy of the GNU General Public License along with
-## this program; if not, see <http://www.gnu.org/licenses/>.
-
-
-## -*- texinfo -*-
-## @deftypefn {Function File} {} = fem_ffc (myproblem.ufl)
-## This function take as input a .ufl file with a Variationa Problem
-## @example
-## 
-## @end example
-## @seealso{} 
-## @end deftypefn
-
-function res = fem_func_space (mesh, name)
-
-  if nargin != 2
-    error ("fem_ffc: wrong number of input parameters.");
-  elseif ! isstr (name)
-    error ("fem_ffc: first argument is not a valid string");
-  endif
-
-  # fem_fs.cc is the file where I should include name.h
-  # I use name.h at line 35, where I call
-  # "new FunctionSpace (mshd);" 
-  # because FunctionSpace is defined inside of name.h
-  # (correct call would be "name::FunctionSpace (mshd)" but 
-  # I'm using the namespace "name")
-  command = "cp ../src/fem_fs.cc fem_fs.cc";
-  [output, text] = system (command);
-  if output != 0
-    display (text);
-    error ("Compilation failed");
-  endif
-
-  # add line to fem_fs.cc
-  filename = "fem_fs.cc";
-  fid = fopen (filename, "r+");
-  fseek (fid, 671, SEEK_SET ());
-  fprintf (fid, "%c%s.h%c", 34, name, 34);
-  fseek (fid, 721, SEEK_SET ());
-  fprintf (fid, "%s%c", name, 59);
-  fclose (fid);
-
-  #now compile the program
-  command = "mkoctfile -c fem_fs.cc $(LDFLAGS) -o fem_fs.o -I../src/";
-  [output, text] = system (command);
-  if output != 0
-    display (text);
-    error ("Compilation failed");
-  endif
-
-  command = "mkoctfile -s ../src/mesh.o ../src/fem_init_env.o fem_fs.o -o fem_fs.oct $(LDFLAGS) -ldolfin";
-  [output, text] = system (command);
-  if output != 0
-    display (text);
-    error ("Compilation failed");
-  endif
-
-  #run the program and get the result
-  res = fem_fs (mesh);
-
-endfunction
-
--- a/obsolete/fem_get_mesh.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-
-#include "mesh.h"
-
-DEFUN_DLD (fem_get_mesh, args, ,"-*- texinfo -*-\n\
-@deftypefn {Function File} {[@var{mesh}]} = \
-fem_get_mesh (@var{fem_mesh}) \n\
-Return a (p, e, t) representation of @var{fem_mesh}\n\
-The @var{mesh_to_read} should be an object created with \
-fem_init_mesh().\n\
-The output @var{mesh} is a PDE-tool like structure\n\
-with matrix fields (p,e,t).\n\
-@seealso{fem_init_mesh}\n\
-@end deftypefn")
-{
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1 || nargin > 1)
-    print_usage ();
-  else
-    {
-
-      if (! mesh_type_loaded)
-        {
-          mesh::register_type ();
-          mesh_type_loaded = true;
-          mlock ();
-        }
-
-      if (args(0).type_id () == mesh::static_type_id ())
-        {
-          const mesh & msh = static_cast<const mesh&> (args(0).get_rep ());
-          retval = octave_value (msh.get_pet ());
-        }
-      else
-        error ("fem_get_mesh: the argument is not a mesh type");
-    }
-  return retval;
-}
-
-octave_scalar_map
-mesh::get_pet () const
-{
-  const dolfin::Mesh & msh (*pmsh);
-  //p matrix
-  uint D = msh.topology ().dim ();
-  std::size_t num_v = msh.num_vertices ();
-  Matrix p (D, num_v);
-  std::copy (msh.coordinates ().begin (),
-             msh.coordinates ().end (),
-             p.fortran_vec ());
-
-  // e has 7 rows in 2d, 10 rows in 3d
-  msh.init (D - 1, D);
-  std::size_t num_f = msh.num_facets ();
-  dim_vector dims;
-  dims.resize (2);
-  dims(0) = D == 2 ? 7 : 10;
-  dims(1) = num_f;
-  Array<octave_idx_type> e (dims, 0);
-  octave_idx_type *evec = e.fortran_vec ();
-  uint D2 = D * D;
-  octave_idx_type l = 0, m = 0;
-
-  dolfin::MeshFunction <std::size_t> facet_domains;
-  if (! msh.domains ().is_empty ())
-      if (msh.domains ().num_marked (D-1) != 0)
-        facet_domains = * (msh.domains ().facet_domains ());
-
-  for (dolfin::FacetIterator f (msh); ! f.end (); ++f)
-    {
-      if ((*f).exterior () == true)
-        {
-          l = 0;
-          for (dolfin::VertexIterator v (*f); ! v.end (); ++v, ++l)
-            e.xelem (l, m) = (*v).index () + 1;
-
-          if (! facet_domains.empty ())
-            e.xelem (D2, m) = facet_domains[*f];
-
-          ++m;
-        }
-    }
-
-  dims(1) = m;
-  e.resize (dims);
-
-  for (octave_idx_type j = e.rows () - 2;
-       j < e.numel () - 2; j += e.rows ())
-    evec[j] = 1;
-
-  // t matrix
-  dims(0) = D + 2;
-  dims(1) = msh.num_cells ();
-  Array<octave_idx_type> t (dims, 1);
-  std::vector<unsigned int> my_cells = msh.cells ();
-  std::size_t n = 0;
-
-  dolfin::MeshFunction<std::size_t> cell_domains;
-  if (! msh.domains ().is_empty ())
-      if (msh.domains ().num_marked (D) != 0)
-        cell_domains = * (msh.domains ().cell_domains ());
-
-  for (octave_idx_type j = 0; j < t.cols (); ++j)
-    {
-      for (octave_idx_type i = 0; i < D + 1; ++i, ++n)
-        t.xelem (i, j) += my_cells[n];
-
-       if (! cell_domains.empty ())
-         t.xelem (D + 1, j) = cell_domains[j];
-    }
-
-  octave_scalar_map a;
-  a.setfield ("p", p);
-  a.setfield ("e", e);
-  a.setfield ("t", t);
-  return a;
-
-}
--- a/obsolete/fem_init_env.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#include "mesh.h"
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-#include "function.h"
-
-DEFUN_DLD (fem_init_env, args, , "-*- texinfo -*-\n\
-@deftypefn {Function File} {[]} = \
-fem_init_env ( ) \n\
-Initialize the environment for fem-fenics\n\
-@end deftypefn")
-{
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 0 || nargin > 0)
-    print_usage ();
-  else
-    {
-      mesh::register_type ();
-      mesh_type_loaded = true;
-      std::cout << "mesh_type_loaded" << std::endl;
-      functionspace::register_type ();
-      functionspace_type_loaded = true;
-      std::cout << "functionspace_type_loaded" << std::endl;
-      boundarycondition::register_type ();
-      boundarycondition_type_loaded = true;
-      std::cout << "boundarycondition_type_loaded" << std::endl;
-      coefficient::register_type ();
-      coefficient_type_loaded = true;
-      std::cout << "coefficient_type_loaded" << std::endl;
-      function::register_type ();
-      function_type_loaded = true;
-      std::cout << "function_type_loaded" << std::endl;
-      mlock ();
-    }
-  return retval;
-}
--- a/obsolete/fem_lhs.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-
-#include "Laplace.h"
-#include <dolfin.h>
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-
-DEFUN_DLD (fem_lhs, args, , "-*- texinfo -*-\n\
-@deftypefn {Function File} {[@var{bc}]} = \
-fem_rhs (@var{Functional Space}, @var{Coefficient}, \
-@var{Boundary Condition}) \n\
-The input parameters are\n\
-@itemize @bullet \n\
-@item @var{Functional Space} is the fem-fenics functional space where\
-the bilinear form is defined\n\
-@item @var{Boundary Condition} contains the value of the essential bc that\
-we want to apply to the Bilinear Form\n\
-@item @var{Coefficient} is a variable of type coefficient which contains\
-the value of the coefficient for the bilinear form\n\
-@end itemize\n\
-The output @var{A} is a sparse matrix which represents the bilinear form\n\
-@seealso{fem_init_mesh, fem_fs}\n\
-@end deftypefn")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1)
-    print_usage ();
-  else
-    {
-
-      if (! functionspace_type_loaded)
-        {
-          functionspace::register_type ();
-          functionspace_type_loaded = true;
-          mlock ();
-        }
-      if (args(0).type_id () == functionspace::static_type_id ())
-        {
-          const functionspace & fspo
-            = static_cast<const functionspace&> (args(0).get_rep ());
-
-          if (! error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              Laplace::LinearForm L (V);
-              std::size_t ncoef = L.num_coefficients (), nc = 0;
-
-              if (! coefficient_type_loaded)
-                {
-                  coefficient::register_type ();
-                  coefficient_type_loaded = true;
-                  mlock ();
-                }
-              for (std::size_t i = 1; i < nargin; ++i)
-                {
-                  if (args(i).type_id () == coefficient::static_type_id ())
-                    {
-                      const coefficient & cf
-                        = static_cast <const coefficient&> (args(i).get_rep ());
-
-                      std::size_t n = L.coefficient_number (cf.get_str ());
-                      const boost::shared_ptr<const expression> & pexp = cf.get_expr ();
-                      L.set_coefficient (n, pexp);
-                      ++nc;
-                    }
-                 }
-
-              if (nc != ncoef)
-                error ("Wrong number of coefficient");
-              else
-                {
-
-                  dolfin::Vector b;
-                  dolfin::assemble (b, L);
-
-                  if (! boundarycondition_type_loaded)
-                    {
-                      boundarycondition::register_type ();
-                      boundarycondition_type_loaded = true;
-                      mlock ();
-                    }
-                  for (std::size_t i = 1; i < nargin; ++i)
-                    {
-                      if (args(i).type_id () == boundarycondition::static_type_id ())
-                        {
-                          const boundarycondition & bc 
-                            = static_cast<const boundarycondition&> (args(i).get_rep ());
-
-                          const std::vector<boost::shared_ptr <const dolfin::DirichletBC> > & pbc
-                                = bc.get_bc ();
-                              for (std::size_t j = 0; j < pbc.size (); ++j)
-                                pbc[j]->apply(b);
-                        }
-                    }
-
-                  dim_vector dims;
-                  dims.resize (2);
-                  dims(0) = b.size ();
-                  dims(1) = 1;
-                  Array<double> myb (dims);
-
-                  for (std::size_t i = 0; i < b.size (); ++i)
-                    myb(i) = b[i];
-
-                  retval = myb;
-                }
-            }
-        }
-    }
-  return retval;
-}
--- a/obsolete/fem_rhs.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-
-#include "Laplace.h"
-#include <dolfin.h>
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-
-DEFUN_DLD (fem_rhs, args, , "-*- texinfo -*-\n\
-@deftypefn {Function File} {[@var{bc}]} = \
-fem_rhs (@var{Functional Space}, @var{Coefficient}, \
-@var{Boundary Condition}) \n\
-The input parameters are\n\
-@itemize @bullet \n\
-@item @var{Functional Space} is the fem-fenics functional space where\
-the bilinear form is defined\n\
-@item @var{Boundary Condition} contains the value of the essential bc that\
-we want to apply to the Bilinear Form\n\
-@item @var{Coefficient} is a variable of type coefficient which contains\
-the value of the coefficient for the bilinear form\n\
-@end itemize\n\
-The output @var{A} is a sparse matrix which represents the bilinear form\n\
-@seealso{fem_init_mesh, fem_fs}\n\
-@end deftypefn")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-
-  if (nargin < 1)
-    print_usage ();
-  else
-    {
-      if (! functionspace_type_loaded)
-        {
-          functionspace::register_type ();
-          functionspace_type_loaded = true;
-          mlock ();
-        }
-      if (args(0).type_id () == functionspace::static_type_id ())
-        {
-          const functionspace & fspo
-            = static_cast<const functionspace&> (args(0).get_rep ());
-
-          if (! error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              Laplace::BilinearForm a (V, V);
-              std::size_t ncoef = a.num_coefficients (), nc = 0;
-
-              if (! coefficient_type_loaded)
-                {
-                  coefficient::register_type ();
-                  coefficient_type_loaded = true;
-                  mlock ();
-                }
-
-              for (std::size_t i = 1; i < nargin; ++i)
-                {
-                  if (args(i).type_id () == coefficient::static_type_id ())
-                    {
-                      const coefficient & cf
-                        = static_cast <const coefficient&> (args(i).get_rep ());
-
-                      std::size_t n = a.coefficient_number (cf.get_str ());
-                      const boost::shared_ptr<const expression> & pexp = cf.get_expr ();
-                      a.set_coefficient (n, pexp);
-                      ++nc;
-                    }
-                 }
-
-              if (nc != ncoef)
-                error ("Wrong number of coefficient");
-              else
-                {
-
-                  dolfin::Matrix A;
-                  dolfin::assemble (A, a);
-
-                  if (! boundarycondition_type_loaded)
-                    {
-                      boundarycondition::register_type ();
-                      boundarycondition_type_loaded = true;
-                      mlock ();
-                    }
-
-                  for (std::size_t i = 1; i < nargin; ++i)
-                    {
-                      if (args(i).type_id () == boundarycondition::static_type_id ())
-                        {
-                          const boundarycondition & bc 
-                            = static_cast<const boundarycondition&> (args(i).get_rep ());
-
-                          const std::vector<boost::shared_ptr <const dolfin::DirichletBC> > & pbc
-                                = bc.get_bc ();
-                              for (std::size_t j = 0; j < pbc.size (); ++j)
-                                pbc[j]->apply(A);
-                        }
-                    }
-
-                  int nr = A.size (0), nc = A.size (1);
-                  // nz shoud be estimated in a better way
-                  int nz = nr * nc;
-                  SparseMatrix sm (nr, nc, nz);
-
-                  int ii = 0;
-                  sm.cidx (0) = 0;
-                  for (int j = 0; j < nc; ++j)
-                   {
-                     for (int i = 0; i < nr; i++)
-                       {
-                         double tmp = A(i, j);
-                         if (tmp != 0.)
-                           {
-                             sm.data(ii) = tmp;
-                             sm.ridx(ii) = i;
-                             ii++;
-                           }
-                       }
-                     sm.cidx(j+1) = ii;
-                  }
-                  sm.maybe_compress ();
-
-                  retval = sm;
-
-                }
-            }
-        }
-    }
-  return retval;
-}
--- a/obsolete/plot.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
-/*
- Copyright (C) 2013 Marco Vassallo
-
- This program is free software; you can redistribute it and/or modify it under
- the terms of the GNU General Public License as published by the Free Software
- Foundation; either version 2 of the License, or (at your option) any later
- version.
-
- This program 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 General Public License for more
- details.
-
- You should have received a copy of the GNU General Public License along with
- this program; if not, see <http://www.gnu.org/licenses/>.
-*/
-
-#include "function.h"
-#include "mesh.h"
-#include "Plot_2d.h"
-#include "Plot_3d.h"
-
-DEFUN_DLD (plot, args, , "-*- texinfo -*-\n\
-@deftypefn {Function File} \
-fem_func (@var{Function})\n\
-The input parameter is the object that you want to plot\n\
-It can be either a Function or a Mesh \n\
-@seealso{fem_func, fem_save}\n\
-@end deftypefn")
-{
-
-  int nargin = args.length ();
-  octave_value retval;
-  
-  if (nargin < 1 || nargin > 2)
-    print_usage ();
-  else
-    {
-      if (! function_type_loaded)
-        {
-          function::register_type ();
-          function_type_loaded = true;
-          mlock ();
-        }
-
-      if (! mesh_type_loaded)
-        {
-          mesh::register_type ();
-          mesh_type_loaded = true;
-          mlock ();
-        }
-
-      if (args(0).type_id () == function::static_type_id ())
-        {
-          const function & uo =
-            static_cast<const function&> (args(0).get_rep ());
-
-          if (!error_state)
-            {
-              const boost::shared_ptr<const dolfin::Function> & u = uo.get_pfun ();
-              dolfin::plot (*u);
-              dolfin::interactive ();
-              retval = 0;
-            }
-        }
-
-      else if (args(0).type_id () == mesh::static_type_id ())
-        {
-          const mesh & msho = static_cast<const mesh&> (args(0).get_rep ());
-          if (nargin == 1)
-            {
-              if (!error_state)
-                {
-                  const boost::shared_ptr<const dolfin::Mesh> & mshd = msho.get_pmsh ();
-                  dolfin::plot (*mshd);
-                  dolfin::interactive ();
-                  retval = 0;
-                }
-             }
-          else if (nargin == 2)
-
-        }
-
-    }
-  return retval;
-}
--- a/obsolete/test/Laplace.ufl	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-# Copyright (C) 2005-2009 Anders Logg
-#
-# This file is part of DOLFIN.
-#
-# DOLFIN 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.
-#
-# DOLFIN 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 DOLFIN. If not, see <http://www.gnu.org/licenses/>.
-#
-# First added:  2005
-# Last changed: 2011-03-08
-#
-# The bilinear form a(u, v) and linear form L(v) for
-# Poisson's equation.
-#
-# Compile this form with FFC: ffc -l dolfin Poisson.ufl.
-
-
-element = FiniteElement("Lagrange", triangle, 1)
-# element = FiniteElement("Lagrange", tetrahedron, 2)
-
-u = TrialFunction(element)
-v = TestFunction(element)
-f = Coefficient(element)
-g = Coefficient(element)
-
-a = inner(grad(u), grad(v))*dx
-L = f*v*dx + g*v*ds
--- a/obsolete/test/Makefile	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-MKOCTFILE ?= mkoctfile
-
-OCTFILES=test_expr.oct test_bc.oct test_coeff.oct test_rlhs.oct
-
-LIBS += -ldolfin
-
-all: $(OCTFILES)
-
-test_expr.oct: test_expr.o
-	$(MKOCTFILE) -s ../src/fem_init_env.o test_expr.o -o $@ $(LDFLAGS) $(LIBS)
-
-test_expr.o:  test_expr.cpp Laplace.h
-	$(MKOCTFILE) -c test_expr.cpp $(LDFLAGS) -o $@ -I../src/
-
-test_bc.oct: test_bc.o
-	$(MKOCTFILE) -s ../src/fem_init_env.o test_bc.o -o $@ $(LDFLAGS) $(LIBS)
-
-test_bc.o:  test_bc.cpp Laplace.h
-	$(MKOCTFILE) -c test_bc.cpp $(LDFLAGS) -o $@ -I../src/
-
-test_coeff.oct: test_coeff.o
-	$(MKOCTFILE) -s ../src/fem_init_env.o test_coeff.o -o $@ $(LDFLAGS) $(LIBS)
-
-test_coeff.o:  test_coeff.cpp Laplace.h
-	$(MKOCTFILE) -c test_coeff.cpp $(LDFLAGS) -o $@ -I../src/
-
-test_rlhs.oct: test_rlhs.o
-	$(MKOCTFILE) -s ../src/fem_init_env.o test_rlhs.o -o $@ $(LDFLAGS) $(LIBS)
-
-test_rlhs.o:  test_rlhs.cc Laplace.h
-	$(MKOCTFILE) -c test_rlhs.cc $(LDFLAGS) -o $@ -I../src/
-
-
-Laplace.h: Laplace.ufl
-	ffc -l dolfin Laplace.ufl
-
-clean:
-	-rm -f *.o core octave-core *.oct *~ *.xml *.pvd *.vtu Laplace.h
--- a/obsolete/test/laplace.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#Example of how we expect the Octave interface to look like
-#This file is our test for the TDD
-
-# Create mesh 
-fem_init_env ();
-pkg load msh;
-
-msho = msh2m_structured_mesh (0:0.05:1, 0:0.05:1, 1, 1:4);
-mshd = fem_init_mesh (msho);
-
-#Compile the problem defined in the .ufl file
-#fem_ffc ("Laplace.ufl");
-
-# #Import the problem inside Octave
-V  = fem_fs (mshd);
-#Set BC equal to zero on sides with label 2 and 4
-bc = fem_bc (V, @(x, y) 0.0, [2,4]);
-
-##Set the coefficient for the rhs
-fv = @(x,y) 10*exp(-((x - 0.5).^2 + (y - 0.5).^2) / 0.02);
-f = fem_coeff ('f', fv);
-
-gv = @(x,y) sin (5.0 * x);
-g = fem_coeff ('g', gv);
-
-# #Get the matrices
-# A  = BilinearForm (V, V, bc);
-# L  = LinearForm (V, bc, f, g);
-
-# #Solve it
-# u = A\L;
-
-# #Plot
-# uf = Function (V, u);
-# dolfin_plot (uf, "Solution")
--- a/obsolete/test/mesh_test.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-#Example of how we expect the Octave interface to look like
-#This file is our test for the TDD about mesh
-
-# Create mesh 
-fem_init_env ();
-
-msh1 = msh2m_structured_mesh(1:6,1:4,0,3:6);
-msh2 = fem_init_mesh (msh1);
-msh3 = fem_get_mesh (msh2);
-
-# assert (msh1, msh3) doesn't work because the order of column inside "e" and "t"
-# depends on the algorithm used for visiting the mesh
-
-assert (msh1.p, msh3.p);
-
-e= [1    5    9   13   21   17   22   23    1    2    4    3    8   12   16   20
-    5    9   13   17   22   21   23   24    2    3    8    4   12   16   20   24
-    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
-    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
-    3    3    3    3    4    3    4    4    6    6    5    6    5    5    5    5
-    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
-    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0];
-
-assert (msh3.e, e);
-
-t= [1  2  3  5  6  7  9 10 11 13 14 15 17 18 19  1  2  3  5  6  7  9 10 11 13 14 15 17 18 19
-    5  6  7  9 10 11 13 14 15 17 18 19 21 22 23  2  3  4  6  7  8 10 11 12 14 15 16 18 19 20
-    6  7  8 10 11 12 14 15 16 18 19 20 22 23 24  6  7  8 10 11 12 14 15 16 18 19 20 22 23 24
-    0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0];
-
-assert (msh3.t, t);
-
--- a/obsolete/test/test_all.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-# We follow the dolfin example for the Poisson problem
-#    -div ( grad (u) ) = f      on omega
-#                    u = h      on gamma_d;
-#                du/dn = g      on gamma_n;
-# See (http://fenicsproject.org/documentation/dolfin/1.2.0/cpp/demo/pde/poisson/cpp/documentation.html#index-0)
-# we check if: 
-#   1) the classes created within fem-fenics
-#      like "mesh" and "functionspace" hold correctly the dolfin data
-#   2) the class "expression", which we derived from dolfin::Expression
-#      correctly sets up the value for the bc using a function_handle
-#   3) the class "boundarycondition", which handle a vecotr of pointer
-#      to dolfin::DirichletBC correctly stores the value for the bc
-
-
-pkg load msh
-addpath ("../src/")
-fem_init_env ();
-
-# create a unit square mesh using msh: labels for the boundary sides are 1,2,3,4
-# we can use only 2D mesh for the moment
-# if you want to try with a 3D mesh, you need to use tetrahedron instead of
-# triangle inside Laplace.ufl and recompile fem_fs.cpp
-msho = msh2m_structured_mesh (0:0.05:1, 0:0.05:1, 1, 1:4);
-mshd = fem_init_mesh (msho);
-
-V  = fem_fs (mshd);
-
-# fem_bc takes as input the functionspace V, a function handler f,
-# and the sides where we want to apply the condition
-# The value on each point of the boundary is computed using
-# the eval method available inside expression.h
-# if a side is not specified, Neumann conditions are applied
-# with g specified below
-f = @(x,y) 0;
-bc = fem_bc (V, f, [2, 4]);
-
-# fem_coeff takes as input a string and a function handler
-# and is used below to set the value of the coefficient of the rhs
-
-ff = @(x,y) 10*exp(-((x - 0.5).^2 + (y - 0.5).^2) / 0.02);
-f = fem_coeff ('f', ff);
-
-gg = @(x,y) sin (5.0 * x);
-g = fem_coeff ('g', gg);
-
-# fem_rhs and fem_lhs takes as input the functionspace V, and the
-# boundarycondition bc and solve the Poisson problem with
-# the velues specified inside f and g;
-A = fem_rhs (V, bc);
-
-b = fem_lhs (V, f, g, bc);
-
-u = A \ b;
-
-func = fem_func (V, u)
-
-fem_plot (func);
-
-fem_save (func, 'solution');
--- a/obsolete/test/test_bc.cpp	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-#include <dolfin.h>
-#include "Laplace.h"
-#include "functionspace.h"
-#include "boundarycondition.h"
-
-
-class Source : public dolfin::Expression
-{
- public:
-  Source() : dolfin::Expression() {}
-
-  void eval(dolfin::Array<double>& values, const dolfin::Array<double>& x) const
-  {
-    double dx = x[0] - 0.5;
-    double dy = x[1] - 0.5;
-    values[0] = 10*exp(-(dx*dx + dy*dy) / 0.02);
-  }
-};
-
-class dUdN : public dolfin::Expression
-{
- public:
-  dUdN() : dolfin::Expression() {}
-
-  void eval(dolfin::Array<double>& values, const dolfin::Array<double>& x) const
-  {
-    values[0] = sin(5*x[0]);
-  }
-};
-
-
-DEFUN_DLD (test_bc, args, , "test_bc: functionspace V, boundarycondition bc")
-{
-
-  int nargin = args.length ();
-  octave_value retval=0;
-
-  if (nargin < 2 || nargin > 2)
-    print_usage ();
-  else
-    {
-      if (args(0).type_id () == functionspace::static_type_id () &&
-          args(1).type_id () == boundarycondition::static_type_id ())
-        {
-          const functionspace & fspo =
-            static_cast<const functionspace&> (args(0).get_rep ());
-          const boundarycondition & bc =
-            static_cast<const boundarycondition&> (args(1).get_rep ());
-
-          if (!error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              dolfin::Mesh mesh = *(V.mesh());
-
-              const std::vector<boost::shared_ptr <const dolfin::DirichletBC> > &
-              pbc = bc.get_bc ();
-              std::vector<const dolfin::BoundaryCondition*> bcu;
-
-              for (octave_idx_type i = 0; i < pbc.size (); ++i)
-                bcu.push_back (& (* (pbc[i])));
-
-              //We use dolfin now, fem-fenics not yet available
-              Source f;
-              dUdN g;
-              Laplace::BilinearForm a (V, V);
-              Laplace::LinearForm L (V);
-              L.f = f;
-              L.g = g;
-
-              dolfin::Function u (V);
-              dolfin::solve (a == L, u, bcu);
-
-              dolfin::File file ("fem-fenics-bc.pvd");
-              file << u;
-
-              dolfin::plot (u);
-              dolfin::interactive ();
-            }
-        }
-    }
-  return retval;
-
-}
--- a/obsolete/test/test_bc.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-# We follow the dolfin example for the Poisson problem
-#    -div ( grad (u) ) = f      on omega
-#                    u = h      on gamma_d;
-#                du/dn = g      on gamma_n;
-# See (http://fenicsproject.org/documentation/dolfin/1.2.0/cpp/demo/pde/poisson/cpp/documentation.html#index-0)
-# we check if: 
-#   1) the classes created within fem-fenics
-#      like "mesh" and "functionspace" hold correctly the dolfin data
-#   2) the class "expression", which we derived from dolfin::Expression
-#      correctly sets up the value for the bc using a function_handle
-#   3) the class "boundarycondition", which handle a vecotr of pointer
-#      to dolfin::DirichletBC correctly stores the value for the bc
-
-
-pkg load msh
-addpath ("../src/")
-
-# create a unit square mesh using msh: labels for the boundary sides are 1,2,3,4
-# we can use only 2D mesh for the moment
-# if you want to try with a 3D mesh, you need to use tetrahedron instead of
-# triangle inside Laplace.ufl and recompile fem_fs.cpp
-msho = msh2m_structured_mesh (0:0.05:1, 0:0.05:1, 1, 1:4);
-
-mshd = fem_init_mesh (msho);
-V  = fem_fs (mshd);
-
-f = @(x,y) 0;
-
-# fem_bc take as input the functionspace V, a function handler f,
-# and the sides where we want to apply the condition
-# The value on each point of the boundary is computed using
-# the eval method available inside expression.h
-# if a side is not specified, Neumann conditions are applied
-# with g = sin(5*x)
-bc = fem_bc (V, f, [2, 4]);
-
-# test_bc take as input the functionspace V, and the
-# boundarycondition bc and solve the Poisson problem with
-#     f = 10*exp(-(dx*dx + dy*dy) / 0.02);
-test_bc (V, bc);
--- a/obsolete/test/test_coeff.cpp	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-#include "Laplace.h"
-using namespace Laplace;
-
-#include <dolfin.h>
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-
-DEFUN_DLD (test_coeff, args, , "test_bc: functionspace V, boundarycondition bc")
-{
-
-  int nargin = args.length ();
-  octave_value retval=0;
-  
-  if (nargin < 2)
-    print_usage ();
-  else
-    {
-      if (args(0).type_id () == functionspace::static_type_id () &&
-          args(1).type_id () == boundarycondition::static_type_id ())
-        {
-          const functionspace & fspo =
-            static_cast<const functionspace&> (args(0).get_rep ());
-          const boundarycondition & bc =
-            static_cast<const boundarycondition&> (args(1).get_rep ());
-
-          if (!error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              LinearForm L (V);
-              std::size_t ncoef = L.num_coefficients ();
-              if (nargin < 2 + ncoef || nargin > 2 + ncoef)
-                error ("Wrong number of coefficient");
-              else
-                {
-                  for (octave_idx_type i = 0; i < ncoef; ++i)
-                    {
-                      const coefficient & cf =static_cast<const coefficient&> (args(i+2).get_rep ());
-                      std::size_t n = L.coefficient_number (cf.get_str ());
-                      const boost::shared_ptr<const expression> & pexp = cf.get_expr ();
-                      L.set_coefficient (n, pexp);
-                    }
-
-                  const std::vector<boost::shared_ptr <const dolfin::DirichletBC> > &
-                  pbc = bc.get_bc ();
-                  std::vector<const dolfin::BoundaryCondition*> bcu;
-
-                  for (octave_idx_type i = 0; i < pbc.size (); ++i)
-                    bcu.push_back (& (* (pbc[i])));
-
-                  //Now use dolfin, fem-fenics not yet available
-                  dolfin::Vector b;
-                  dolfin::assemble (b, L);
-
-                  for (std::size_t i = 0; i < bcu.size(); i++)
-                    bcu[i]->apply(b);
-
-                  BilinearForm a (V, V);
-                  dolfin::Matrix A;
-                  dolfin::assemble (A, a);
-
-                  for (std::size_t i = 0; i < bcu.size(); i++)
-                    bcu[i]->apply(A);
-
-                  dolfin::Function u(V);
-                  dolfin::solve(A, *u.vector(), b, "gmres", "default");
-
-                  dolfin::File file ("fem-fenics-bc.pvd");
-                  file << u;
-
-                  dolfin::plot (u);
-                  dolfin::interactive ();
-
-                }
-            }
-        }
-    }
-  return retval;
-
-}
--- a/obsolete/test/test_coeff.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-# We follow the dolfin example for the Poisson problem
-#    -div ( grad (u) ) = f      on omega
-#                    u = h      on gamma_d;
-#                du/dn = g      on gamma_n;
-# See (http://fenicsproject.org/documentation/dolfin/1.2.0/cpp/demo/pde/poisson/cpp/documentation.html#index-0)
-# we check if: 
-#   1) the classes created within fem-fenics
-#      like "mesh" and "functionspace" hold correctly the dolfin data
-#   2) the class "expression", which we derived from dolfin::Expression
-#      correctly sets up the value for the bc using a function_handle
-#   3) the class "boundarycondition", which handle a vecotr of pointer
-#      to dolfin::DirichletBC correctly stores the value for the bc
-
-
-pkg load msh
-addpath ("../src/")
-
-# create a unit square mesh using msh: labels for the boundary sides are 1,2,3,4
-# we can use only 2D mesh for the moment
-# if you want to try with a 3D mesh, you need to use tetrahedron instead of
-# triangle inside Laplace.ufl and recompile fem_fs.cpp
-msho = msh2m_structured_mesh (0:0.05:1, 0:0.05:1, 1, 1:4);
-
-mshd = fem_init_mesh (msho);
-V  = fem_fs (mshd);
-
-f = @(x,y) 0;
-
-# fem_bc takes as input the functionspace V, a function handler f,
-# and the sides where we want to apply the condition
-# The value on each point of the boundary is computed using
-# the eval method available inside expression.h
-# if a side is not specified, Neumann conditions are applied
-# with g specified below
-bc = fem_bc (V, f, [2, 4]);
-
-# fem_coeff takes as input a string and a function handler
-# and is used below to set the value of the coefficient of the rhs
-
-ff = @(x,y) 10*exp(-((x - 0.5).^2 + (y - 0.5).^2) / 0.02);
-f = fem_coeff ('f', ff);
-
-gg = @(x,y) sin (5.0 * x);
-g = fem_coeff ('g', gg);
-
-# test_coeff takes as input the functionspace V, and the
-# boundarycondition bc and solve the Poisson problem with
-# the velues specified inside f and g;
-test_coeff (V, bc, f, g);
--- a/obsolete/test/test_expr.cpp	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-#include <dolfin.h>
-#include "Laplace.h"
-#include "expression.h"
-#include "functionspace.h"
-
-
-class Source : public dolfin::Expression
-{
-  void eval(dolfin::Array<double>& values, const dolfin::Array<double>& x) const
-  {
-    double dx = x[0] - 0.5;
-    double dy = x[1] - 0.5;
-    values[0] = 10*exp(-(dx*dx + dy*dy) / 0.02);
-  }
-};
-
-class dUdN : public dolfin::Expression
-{
-  void eval(dolfin::Array<double>& values, const dolfin::Array<double>& x) const
-  {
-    values[0] = sin(5*x[0]);
-  }
-};
-
-
-DEFUN_DLD (test_expr, args, , "test_expr: functionspace V, fcn_handle f, mesh_label label")
-{
-
-  int nargin = args.length ();
-  octave_value retval=0;
-
-  if (nargin < 3 || nargin > 3)
-    print_usage ();
-  else
-    {
-      if (args(0).type_id () == functionspace::static_type_id ())
-        {
-          const functionspace & fspo = static_cast<const functionspace&> (args(0).get_rep ());
-          octave_fcn_handle * fh = args(1).fcn_handle_value ();
-          Array<int> side = args(2).array_value ();
-
-          if (!error_state)
-            {
-              const dolfin::FunctionSpace V = fspo.get_fsp ();
-              dolfin::Mesh mesh = *(V.mesh());
-              expression ff (*fh);
-
-              //We use dolfin now, fem-fenics not yet available
-
-              std::vector<const dolfin::BoundaryCondition*> bcu;
-              Source f;
-              dUdN g;
-
-              for (octave_idx_type i = 0; i < side.length (); ++i)
-                bcu.push_back (new dolfin::DirichletBC (V, ff, side(i)));
-
-
-              Laplace::BilinearForm a (V, V);
-              Laplace::LinearForm L (V);
-              L.f = f;
-              L.g = g;
-
-              dolfin::Function u(V);
-              dolfin::solve(a == L, u, bcu);
-
-              dolfin::File file("fem-fenics.pvd");
-              file << u;
-
-              dolfin::plot(u);
-              dolfin::interactive();
-            }
-        }
-    }
-  return retval;
-
-}
--- a/obsolete/test/test_expr.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-
-# We follow the dolfin example for the Poisson problem 
-# (http://fenicsproject.org/documentation/dolfin/1.2.0/cpp/demo/pde/poisson/cpp/documentation.html#index-0)
-# to check if: 
-#   1) the classes created within fem-fenics
-#      like "mesh" and "functionspace" hold correctly the dolfin data
-#   2) the class "expression", which we derived from dolfin::Expression
-#      correctly sets up the value for the bc using a function_handle
-
-
-pkg load msh
-addpath("../src/")
-
-# create a unit square mesh using msh: labels for the boundary sides are 1,2,3,4
-msho = msh2m_structured_mesh (0:0.05:1, 0:0.05:1, 1, 1:4);
-
-mshd = fem_init_mesh (msho);
-V  = fem_fs (mshd);
-
-f = @(x,y) 0;
-
-# test_expr take as input the functionspace V, a function handler f,
-# and the sides where we want to apply the condition
-# The value on each point of the boundary is computed using
-# the eval method available inside expression.h
-
-test_expr (V, f, [2,4])
--- a/obsolete/test/test_rlhs.cc	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-#include "Laplace.h"
-using namespace Laplace;
-
-#include <dolfin.h>
-#include "functionspace.h"
-#include "boundarycondition.h"
-#include "coefficient.h"
-
-DEFUN_DLD (test_rlhs, args, , "test_bc: functionspace V, boundarycondition bc")
-{
-
-  int nargin = args.length ();
-  octave_value retval=0;
-  
-  if (nargin < 2)
-    print_usage ();
-  else
-    {
-      if (args(0).type_id () == functionspace::static_type_id ())
-        {
-          const functionspace & fspo =
-            static_cast<const functionspace&> (args(0).get_rep ());
-          Array <double> myu = args(1).array_value ();
-
-          if (!error_state)
-            {
-              const boost::shared_ptr<const dolfin::FunctionSpace> & V = fspo.get_pfsp ();
-
-              dolfin::Vector du(myu.length ());
-              for (std::size_t i = 0; i < myu.length (); ++i)
-                du.setitem (i, myu(i));
-
-              boost::shared_ptr<dolfin::Vector> uu (new dolfin::Vector(du));
-              dolfin::Function u(V, uu);
-
-              dolfin::File file ("fem-fenics-rlhs.pvd");
-              file << u;
-
-              dolfin::plot (u);
-              dolfin::interactive ();
-
-            }
-        }
-    }
-  return retval;
-}
--- a/obsolete/test/test_rlhs.m	Wed Nov 06 05:37:11 2013 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-# We follow the dolfin example for the Poisson problem
-#    -div ( grad (u) ) = f      on omega
-#                    u = h      on gamma_d;
-#                du/dn = g      on gamma_n;
-# See (http://fenicsproject.org/documentation/dolfin/1.2.0/cpp/demo/pde/poisson/cpp/documentation.html#index-0)
-# we check if: 
-#   1) the classes created within fem-fenics
-#      like "mesh" and "functionspace" hold correctly the dolfin data
-#   2) the class "expression", which we derived from dolfin::Expression
-#      correctly sets up the value for the bc using a function_handle
-#   3) the class "boundarycondition", which handle a vecotr of pointer
-#      to dolfin::DirichletBC correctly stores the value for the bc
-
-
-pkg load msh
-addpath ("../src/")
-fem_init_env ();
-
-# create a unit square mesh using msh: labels for the boundary sides are 1,2,3,4
-# we can use only 2D mesh for the moment
-# if you want to try with a 3D mesh, you need to use tetrahedron instead of
-# triangle inside Laplace.ufl and recompile fem_fs.cpp
-msho = msh2m_structured_mesh (0:0.05:1, 0:0.05:1, 1, 1:4);
-mshd = fem_init_mesh (msho);
-
-V  = fem_fs (mshd);
-
-# fem_bc takes as input the functionspace V, a function handler f,
-# and the sides where we want to apply the condition
-# The value on each point of the boundary is computed using
-# the eval method available inside expression.h
-# if a side is not specified, Neumann conditions are applied
-# with g specified below
-f = @(x,y) 0;
-bc = fem_bc (V, f, [2, 4]);
-
-# fem_coeff takes as input a string and a function handler
-# and is used below to set the value of the coefficient of the rhs
-
-ff = @(x,y) 10*exp(-((x - 0.5).^2 + (y - 0.5).^2) / 0.02);
-f = fem_coeff ('f', ff);
-
-gg = @(x,y) sin (5.0 * x);
-g = fem_coeff ('g', gg);
-
-# fem_rhs and fem_lhs takes as input the functionspace V, and the
-# boundarycondition bc and solve the Poisson problem with
-# the velues specified inside f and g;
-A = fem_rhs (V, bc);
-
-b = fem_lhs (V, f, g, bc);
-
-u = A \ b;
-
-test_rlhs (V, u);