StimulusCircle.cpp

Go to the documentation of this file.

///////////////////////////////////////////////////////////////////////////////
//
// File: StimulusCircle.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Circular stimulus file.
//
///////////////////////////////////////////////////////////////////////////////
#include <CardiacEPSolver/Stimuli/StimulusCircle.h>
#include <LibUtilities/BasicUtils/VmathArray.hpp>
#include <iostream>
#include <tinyxml.h>
 
namespace Nektar
{
std::string StimulusCirc::className =
    GetStimulusFactory().RegisterCreatorFunction(
        "StimulusCirc", StimulusCirc::create, "Circular stimulus.");
 
/**
 * @class StimulusCirc
 *
 * The Stimulus class and derived classes implement a range of stimuli.
 * The stimulus contains input stimuli that can be applied throughout the
 * domain, on specified regions determined by the derived classes of
 * Stimulus, at specified frequencies determined by the derived classes of
 * Protocol.
 */
 
/**
 * Stimulus base class constructor.
 */
StimulusCirc::StimulusCirc(const LibUtilities::SessionReaderSharedPtr &pSession,
                           const MultiRegions::ExpListSharedPtr &pField,
                           const TiXmlElement *pXml)
    : Stimulus(pSession, pField, pXml)
{
    m_session = pSession;
    m_field   = pField;
    m_nq      = pField->GetTotPoints();
    m_chiCapMembrane =
        m_session->GetParameter("chi") * m_session->GetParameter("Cm");
 
    if (!pXml)
    {
        return;
    }
 
    const TiXmlElement *pXmlparameter;
 
    pXmlparameter = pXml->FirstChildElement("p_x1");
    m_px1         = atof(pXmlparameter->GetText());
 
    pXmlparameter = pXml->FirstChildElement("p_y1");
    m_py1         = atof(pXmlparameter->GetText());
 
    pXmlparameter = pXml->FirstChildElement("p_z1");
    m_pz1         = atof(pXmlparameter->GetText());
 
    pXmlparameter = pXml->FirstChildElement("p_r1");
    m_pr1         = atof(pXmlparameter->GetText());
 
    pXmlparameter = pXml->FirstChildElement("p_is");
    m_pis         = atof(pXmlparameter->GetText());
 
    pXmlparameter = pXml->FirstChildElement("p_strength");
    m_strength    = atof(pXmlparameter->GetText());
}
 
/**
 * Initialise the stimulus. Allocate workspace and variable storage.
 */
void StimulusCirc::Initialise()
{
}
 
/**
 *
 */
void StimulusCirc::v_Update(Array<OneD, Array<OneD, NekDouble>> &outarray,
                            const NekDouble time)
{
    // Get the dimension of the expansion
    int dim = m_field->GetCoordim(0);
 
    // Retrieve coodrinates of quadrature points
    int nq = m_field->GetNpoints();
    Array<OneD, NekDouble> x0(nq);
    Array<OneD, NekDouble> x1(nq);
    Array<OneD, NekDouble> x2(nq);
 
    // Get the protocol amplitude
    NekDouble v_amp = m_Protocol->GetAmplitude(time) * m_strength;
 
    // get the coordinates
    m_field->GetCoords(x0, x1, x2);
 
    switch (dim)
    {
        case 1:
            for (int j = 0; j < nq; j++)
            {
                outarray[0][j] +=
                    v_amp * (-tanh((m_pis * x0[j] - m_px1 + m_pr1) *
                                   (m_pis * x0[j] - m_px1 - m_pr1)) /
                                 2.0 +
                             0.5);
            }
            break;
        case 2:
            for (int j = 0; j < nq; j++)
            {
                outarray[0][j] +=
                    v_amp * (-tanh((m_pis * x0[j] - m_px1 + m_pr1) *
                                       (m_pis * x0[j] - m_px1 - m_pr1) +
                                   (m_pis * x1[j] - m_py1 + m_pr1) *
                                       (m_pis * x1[j] - m_py1 - m_pr1)) /
                                 2.0 +
                             0.5);
            }
            break;
        case 3:
            for (int j = 0; j < nq; j++)
            {
                outarray[0][j] +=
                    v_amp * (-tanh((m_pis * x0[j] - m_px1 + m_pr1) *
                                       (m_pis * x0[j] - m_px1 - m_pr1) +
                                   (m_pis * x1[j] - m_py1 + m_pr1) *
                                       (m_pis * x1[j] - m_py1 - m_pr1) +
                                   (m_pis * x2[j] - m_pz1 + m_pr1) *
                                       (m_pis * x2[j] - m_pz1 - m_pr1)) /
                                 2.0 +
                             0.5);
            }
            break;
    }
}
 
/**
 *
 */
void StimulusCirc::v_GenerateSummary(
    [[maybe_unused]] SolverUtils::SummaryList &s)
{
}
} // namespace Nektar