transformator_impl.h

/*
 * Copyright (c) 2009-2019: G-CSC, Goethe University Frankfurt
 *
 * Author: Stephan Grein
 * Creation date: 2014-03-17
 *
 * This file is part of NeuroBox, which is based on UG4.
 *
 * NeuroBox and UG4 are free software: You can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License version 3
 * (as published by the Free Software Foundation) with the following additional
 * attribution requirements (according to LGPL/GPL v3 §7):
 *
 * (1) The following notice must be displayed in the appropriate legal notices
 * of covered and combined works: "Based on UG4 (www.ug4.org/license)".
 *
 * (2) The following notice must be displayed at a prominent place in the
 * terminal output of covered works: "Based on UG4 (www.ug4.org/license)".
 *
 * (3) The following bibliography is recommended for citation and must be
 * preserved in all covered files:
 * "Reiter, S., Vogel, A., Heppner, I., Rupp, M., and Wittum, G. A massively
 *   parallel geometric multigrid solver on hierarchically distributed grids.
 *   Computing and visualization in science 16, 4 (2013), 151-164"
 * "Vogel, A., Reiter, S., Rupp, M., Nägel, A., and Wittum, G. UG4 -- a novel
 *   flexible software system for simulating PDE based models on high performance
 *   computers. Computing and visualization in science 16, 4 (2013), 165-179"
 * "Stepniewski, M., Breit, M., Hoffer, M. and Queisser, G.
 *   NeuroBox: computational mathematics in multiscale neuroscience.
 *   Computing and visualization in science (2019).
 * "Breit, M. et al. Anatomically detailed and large-scale simulations studying
 *   synapse loss and synchrony using NeuroBox. Front. Neuroanat. 10 (2016), 8"
 *
 * 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 Lesser General Public License for more details.
 */

#include "transformator.h"

#include <lib_grid/common_attachments.h>
#include <lib_grid/grid/grid_util.h>

#include "lib_disc/dof_manager/dof_distribution.h"
#include "lib_disc/function_spaces/grid_function.h"

namespace ug {
namespace membrane_potential_mapping {


/////////////////////////////////////////////////////////
/// set_grid
/////////////////////////////////////////////////////////
template <typename TGridFunction, typename TDomain>
void Transformator::set_grid(TGridFunction& u, const char* uCmp) {
	SmartPtr<Domain<3> > spDom = u.domain();
	SmartPtr<ug::Grid> spGrid = spDom.get()->grid();
	mGrid = spGrid.get();
}

/////////////////////////////////////////////////////////
/// integrate_feedback
/////////////////////////////////////////////////////////
template <typename TGridFunction, typename TDomain>
number Transformator::integrate_feedback(TGridFunction& u, const char*cmp, const char* subsets, int quadOrder)  {
	m_saved_neuron_point_integral = Integral(u, cmp, subsets, quadOrder);
	return m_saved_neuron_point_integral;
}

/////////////////////////////////////////////////////////
/// integrate_feedbacks
/////////////////////////////////////////////////////////
template <typename TGridFunction, typename TDomain>
void Transformator::integrate_feedbacks(TGridFunction& u, const char*cmp, const char* subsets, int quadOrder)  {
	mIntegrals .push_back( Integral(u, cmp, subsets, quadOrder));
}


} // namespace membrane_potential_mapping
} // namespace ug