elastic_problems.cc

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//LIC// ====================================================================
//LIC// This file forms part of oomph-lib, the object-oriented, 
//LIC// multi-physics finite-element library, available 
//LIC// at http://www.oomph-lib.org.
//LIC// 
//LIC//    Version 1.0; svn revision $LastChangedRevision$
//LIC//
//LIC// $LastChangedDate$
//LIC// 
//LIC// Copyright (C) 2006-2016 Matthias Heil and Andrew Hazel
//LIC// 
//LIC// This library is free software; you can redistribute it and/or
//LIC// modify it under the terms of the GNU Lesser General Public
//LIC// License as published by the Free Software Foundation; either
//LIC// version 2.1 of the License, or (at your option) any later version.
//LIC// 
//LIC// This library is distributed in the hope that it will be useful,
//LIC// but WITHOUT ANY WARRANTY; without even the implied warranty of
//LIC// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
//LIC// Lesser General Public License for more details.
//LIC// 
//LIC// You should have received a copy of the GNU Lesser General Public
//LIC// License along with this library; if not, write to the Free Software
//LIC// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
//LIC// 02110-1301  USA.
//LIC// 
//LIC// The authors may be contacted at oomph-lib@maths.man.ac.uk.
//LIC// 
//LIC//====================================================================

#include "problem.h"
#include "fsi.h"
#include "elastic_problems.h"


namespace oomph
{


//////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////


//======================================================================
/// Setup IC problem by:
/// - Pinning all nodal values in the mesh
/// - Pinning the internal data of all elements. 
/// - Freeing/unpinnning all positional data.
/// - Flushing the pointers to the elements' external data.
/// - Setting the pointer to the IC object for all elements to 
///   ensure that the correct residuals/Jacobians are computed.
//======================================================================
void SolidICProblem::setup_problem()
{

 //Find out how many nodes there are
 unsigned long n_node = mesh_pt()->nnode();
 
 //Loop over all the nodes
 for(unsigned n=0;n<n_node;n++)
  {
   // Cast to an elastic node
   SolidNode* node_pt=dynamic_cast<SolidNode*>(mesh_pt()->node_pt(n));
   
#ifdef PARANOID
   if (node_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidNode\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   // Get spatial dimension of node
   unsigned ndim=node_pt->ndim();
   
   //Find out how many positional dofs there are
   SolidFiniteElement* elem_pt=
    dynamic_cast<SolidFiniteElement*>(mesh_pt()->element_pt(0));

#ifdef PARANOID
   if (elem_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidFiniteElement\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   unsigned ntype = elem_pt->nnodal_position_type();
   
   //Loop over coordinate directions
   for(unsigned i=0;i<ndim;i++)
    {
     //Loop over type of dof
     for(unsigned k=0;k<ntype;k++)
      {
       // Unpin them
       node_pt->unpin_position(k,i);
      }
    }
 
   // Loop over nodal values
   unsigned nval=node_pt->nvalue();
   for (unsigned ival=0;ival<nval;ival++)
    {
     // Pin them
     node_pt->pin(ival);
    }
  }

 
// Loop over the elements
 unsigned Nelement=mesh_pt()->nelement();
 for(unsigned i=0;i<Nelement;i++)
  {

   //Cast to proper element type
   SolidFiniteElement* elem_pt = dynamic_cast<SolidFiniteElement*>(
    mesh_pt()->element_pt(i));
   
#ifdef PARANOID
   if (elem_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidFiniteElement\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   
   // Set flag for setting initial condition
   elem_pt->solid_ic_pt() = IC_pt;

   // We've backed up the element's external data: Flush it
   elem_pt->flush_external_data();

   //IF it's an FSI wall element then kill external stuff
   if(FSIWallElement* fsi_elem_pt = dynamic_cast<FSIWallElement*>(elem_pt))
    {
     fsi_elem_pt->exclude_external_load_data();
    }

   // Find out number of internal data
   unsigned nint=elem_pt->ninternal_data();

   // Loop over internal data
   for (unsigned j=0;j<nint;j++)
    {
     Data* data_pt=elem_pt->internal_data_pt(j);
    
     // Loop over internal values
     unsigned nval=data_pt->nvalue();
     for (unsigned ival=0;ival<nval;ival++)
      {
       // Pin internal values
       data_pt->pin(ival);
      }
    }
     
#ifdef PARANOID
   //Is there internal solid data
   if (elem_pt->has_internal_solid_data())
    {
     std::string error_message = 
      "Automatic assignment of initial conditions doesn't work yet\n";
     error_message +=
      "for elasticity elements with internal solid dofs (pressures)\n";
     
     throw OomphLibError(error_message,
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif
//    for(unsigned i=0;i<nint_solid;i++)
//     {
//      Data* data_pt=elem_pt->internal_solid_data_pt(i);
     
//      // Loop over values
//      unsigned nval=data_pt->nvalue();
//      for (unsigned ival=0;ival<nval;ival++)
//       {
//        // Pin internal values
//        data_pt->pin(ival);
//       }
//     }
   
  }
 
 // Setup equation numbers for IC problem
 oomph_info << "# of dofs for wall initial guess" 
            << assign_eqn_numbers() << std::endl; 

}



//======================================================================
/// Backup pinned status of all data associated with the mesh.
/// Also backup the (pointers to the) elements' external data.
//======================================================================
void SolidICProblem::backup_original_state()
{

 //Find out how many nodes there are
 unsigned long n_node = mesh_pt()->nnode();
 
 // Flush vector which holds backup of pinned status
 Backup_pinned.clear();

 // Flush vector which holds vectors with backup of (pointers to) external data
 Backup_ext_data.clear();

 //Loop over all the nodes
 for(unsigned n=0;n<n_node;n++)
  {
   // Cast to an elastic node
   SolidNode* node_pt=dynamic_cast<SolidNode*>(mesh_pt()->node_pt(n));

#ifdef PARANOID
   if (node_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidNode\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   // Get spatial dimension of node
   unsigned ndim=node_pt->ndim();

   //Find out how many positional dofs there are
   SolidFiniteElement* elem_pt=
    dynamic_cast<SolidFiniteElement*>(mesh_pt()->element_pt(0));

#ifdef PARANOID
   if (elem_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidFiniteElement\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   unsigned ntype = elem_pt->nnodal_position_type();
   

   //Loop over coordinate directions
   for(unsigned i=0;i<ndim;i++)
    {
     //Loop over type of dof
     for(unsigned k=0;k<ntype;k++)
      {
       // Backup pinned status
       Backup_pinned.push_back(node_pt->position_is_pinned(k,i));
      }
    }

   // Loop over nodal values
   unsigned nval=node_pt->nvalue();
   for (unsigned ival=0;ival<nval;ival++)
    {
     // Backup pinned status
     Backup_pinned.push_back(node_pt->is_pinned(ival));
    }
  }

 // Loop over the elements
 unsigned Nelement=mesh_pt()->nelement();
 Backup_ext_data.resize(Nelement);
 for(unsigned i=0;i<Nelement;i++)
  {
   //Cast to proper element type
   SolidFiniteElement* elem_pt = dynamic_cast<SolidFiniteElement*>(
    mesh_pt()->element_pt(i));

#ifdef PARANOID
   if (elem_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidFiniteElement\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   // Find out number of external data
   unsigned next=elem_pt->nexternal_data();
   Backup_ext_data[i].resize(next);

   // Loop over external data
   for (unsigned j=0;j<next;j++)
    {
     Data* data_pt=elem_pt->external_data_pt(j);
     
     // Backup the pointer to external data 
     Backup_ext_data[i][j]=data_pt;
    }

   // Find out number of internal data
   unsigned nint=elem_pt->ninternal_data();

   // Loop over internal data
   for (unsigned j=0;j<nint;j++)
    {
     Data* data_pt=elem_pt->internal_data_pt(j);
    
     // Loop over internal values
     unsigned nval=data_pt->nvalue();
     for (unsigned ival=0;ival<nval;ival++)
      {
       // Backup pinned status
       Backup_pinned.push_back(data_pt->is_pinned(ival));
      }
    }


#ifdef PARANOID
   //If there is internal solid data, complain
   if (elem_pt->has_internal_solid_data())
    {
     std::string error_message = 
      "Automatic assignment of initial conditions doesn't work yet\n";
     error_message +=
      "for elasticity elements with internal solid dofs (pressures)\n";
     
     throw OomphLibError(error_message,
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif
//    for(unsigned i=0;i<nint_solid;i++)
//     {
//      Data* data_pt=elem_pt->internal_solid_data_pt(i);
     
//      // Loop over values
//      unsigned nval=data_pt->nvalue();
//      for (unsigned ival=0;ival<nval;ival++)
//       {
//        // Backup pinned status
//        Backup_pinned.push_back(data_pt->is_pinned(ival));
//       }
//     }

  }
 
 // Record number of dofs whose status was pinned
 //oomph_info << "Number of backed up values " << Backup_pinned.size() << std::endl; 

}




//======================================================================
/// Reset pinned status of all data and re-instate the pointers
/// to the elements' external data.
//======================================================================
void SolidICProblem::reset_original_state()
{

 //Find out how many nodes there are
 unsigned long n_node = mesh_pt()->nnode();
 
 // Initialise counter for backed up dofs
 unsigned count=0;

 //Loop over all the nodes
 for(unsigned n=0;n<n_node;n++)
  {
   // Cast to an elastic node
   SolidNode* node_pt=dynamic_cast<SolidNode*>(mesh_pt()->node_pt(n));

#ifdef PARANOID
   if (node_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidNode\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   // Get spatial dimension of node
   unsigned ndim=node_pt->ndim();

   //Find out how many positional dofs there are
   SolidFiniteElement* elem_pt=
    dynamic_cast<SolidFiniteElement*>(mesh_pt()->element_pt(0));

#ifdef PARANOID
   if (elem_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidFiniteElement\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif

   unsigned ntype = elem_pt->nnodal_position_type();

   //Loop over coordinate directions
   for(unsigned i=0;i<ndim;i++)
    {
     //Loop over type of dof
     for(unsigned k=0;k<ntype;k++)
      {
       // Reset pinned status (positional dofs were all unpinned)
       if (Backup_pinned[count])
        {
         node_pt->pin_position(k,i);
        }
       count++;
      }
    }

   // Loop over nodal values
   unsigned nval=node_pt->nvalue();
   for (unsigned ival=0;ival<nval;ival++)
    {
     // Reset pinned status (nodal values were all pinned)
     if (Backup_pinned[count])
      {
       node_pt->unpin(ival);
      }
    }
  }


 // Loop over the elements
 unsigned Nelement=mesh_pt()->nelement();
 for(unsigned i=0;i<Nelement;i++)
  {

   //Cast to proper element type
   SolidFiniteElement *elem_pt = dynamic_cast<SolidFiniteElement*>(
    mesh_pt()->element_pt(i));
   
#ifdef PARANOID
   if (elem_pt==0)
    {
     throw OomphLibError("Wasn't able to cast to SolidFiniteElement\n",
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif
   
   // Switch back to normal Jacobian
   dynamic_cast<SolidFiniteElement*>(elem_pt)->
    disable_solve_for_consistent_newmark_accel();

   // Switch off flag for setting initial condition
   dynamic_cast<SolidFiniteElement*>(elem_pt)->solid_ic_pt() = 0;
   
   //IF it's an FSI wall element then turn on external stuff again
   if(FSIWallElement* fsi_elem_pt = dynamic_cast<FSIWallElement*>(elem_pt))
    {
     fsi_elem_pt->include_external_load_data();
    }

   // Find out number of external data
   unsigned next=Backup_ext_data[i].size();

   // Loop over external data
   for (unsigned j=0;j<next;j++)
    {
     // Backed up external data
     Data* data_pt=Backup_ext_data[i][j];

     // Add external data
     elem_pt->add_external_data(data_pt);
    }

   // Find out number of internal data
   unsigned nint=elem_pt->ninternal_data();

   // Loop over internal data
   for (unsigned j=0;j<nint;j++)
    {
     Data* data_pt=elem_pt->internal_data_pt(j);
    
     // Loop over internal values
     unsigned nval=data_pt->nvalue();
     for (unsigned ival=0;ival<nval;ival++)
      {
       // Restore pinned status (values were all pinned)
       if (!Backup_pinned[count])
        {
         data_pt->unpin(ival);
        }
      }
    }


#ifdef PARANOID
   //If there is internal solid data, complain
   if (elem_pt->has_internal_solid_data())
    {
     std::string error_message = 
      "Automatic assignment of initial conditions doesn't work yet\n";
     error_message +=
      "for elasticity elements with internal solid dofs (pressures)\n";
     
     throw OomphLibError(error_message,
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
    }
#endif
//    for(unsigned i=0;i<nint_solid;i++)
//     {
//      Data* data_pt=elem_pt->internal_solid_data_pt(i);

//      // Loop over values
//      unsigned nval=data_pt->nvalue();
//      for (unsigned ival=0;ival<nval;ival++)
//       {
//        // Restore pinned status (values were all pinned)
//        if (!Backup_pinned[count])
//         {
//          data_pt->unpin(ival);
//         }
//       }
//     }

  }
 
 // Check number of recovered pinned values
 //oomph_info << "Recovered pin values " << count << std::endl; 

 // Flush vector which holds backup of pinned status
 Backup_pinned.clear();

 // Flush vector which holds vectors with backup of (pointers to) external data
 Backup_ext_data.clear();

}


//======================================================================
/// IC problem for wall: Deform wall into the static initial shape
/// described by the IC object at given time.
//======================================================================
void SolidICProblem::set_static_initial_condition(Problem* problem_pt,
                                                  Mesh* wall_mesh_pt, 
                                                  SolidInitialCondition* ic_pt,
                                                  const double& time)
{
 // Tell this sub-problem it is distributed if the main problem is distributed
#ifdef OOMPH_HAS_MPI
 if (problem_pt->problem_has_been_distributed())
  {
   Problem_has_been_distributed=true;
  }
 // This (sub-)problem needs to know about the oomph communicator
 delete Communicator_pt;
 Communicator_pt=new OomphCommunicator(problem_pt->communicator_pt());
#endif


 // Backup value of time
 double backup_time=0.0;

 // Set value of time for IC object (needs to be backed up and 
 // restored since it might be pointed to by other objects)
 TimeStepper* timestepper_pt=ic_pt->geom_object_pt()->time_stepper_pt();
 if (timestepper_pt!=0)
  {
   backup_time=timestepper_pt->time_pt()->time();
   timestepper_pt->time_pt()->time()=time;
  }

 // Delete dummy mesh
 delete mesh_pt();

 // Set pointer to mesh
 mesh_pt()=wall_mesh_pt;

 // Set pointer to initial condition object
 IC_pt=ic_pt;

 // Backup the pinned status of all dofs and remove external data
 // of all elements
 backup_original_state();

 // Now alter the pinned status so that the IC problem for the
 // positional variables can be solved; setup equation numbering
 // scheme
 setup_problem();

 // Assign displacements
 IC_pt->ic_time_deriv()=0;

 // Solve the problem for initial shape
 newton_solve();
 
 // Impulsive start
 assign_initial_values_impulsive();

 // Reset the pinned status and re-attach the external data to the elements
 reset_original_state();

 // Reset time
  if (timestepper_pt!=0)
  {
   timestepper_pt->time_pt()->time()=backup_time;
  }

 // Set pointer to dummy mesh so there's something that can be deleted
 // when static problem finally goes out of scope.
 mesh_pt()=new DummyMesh;
 
 // We have temporarily over-written equation numbers -- need
 // to reset them now
 oomph_info << "Number of equations in big problem: " 
           << problem_pt->assign_eqn_numbers() << std::endl;
}

}