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CirculationModel_la.cpp
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CirculationModel_la.cpp
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// Filename: CirculationModel.cpp
// Created on 20 Aug 2007 by Boyce Griffith
// Modified 2019, Alexander D. Kaiser
#include "CirculationModel.h"
/////////////////////////////// INCLUDES /////////////////////////////////////
#ifndef included_IBAMR_config
#include <IBAMR_config.h>
#define included_IBAMR_config
#endif
#ifndef included_SAMRAI_config
#include <SAMRAI_config.h>
#define included_SAMRAI_config
#endif
// SAMRAI INCLUDES
#include <CartesianGridGeometry.h>
#include <CartesianPatchGeometry.h>
#include <PatchLevel.h>
#include <SideData.h>
#include <tbox/RestartManager.h>
#include <tbox/SAMRAI_MPI.h>
#include <tbox/Utilities.h>
// C++ STDLIB INCLUDES
#include <cassert>
#include <cmath>
#include <Eigen/Dense>
using namespace Eigen;
/////////////////////////////// NAMESPACE ////////////////////////////////////
/////////////////////////////// STATIC ///////////////////////////////////////
#define MIN_PER_L_T0_SEC_PER_ML 60.0e-3 // 60/1000
#define MMHG_TO_CGS 1333.22368
#define USE_WINDKESSEL
// If not defined then this only computes fluxes
// Pressure is set to zero
// Currently hard coded for upper boundary
namespace
{
// Name of output file.
static const string DATA_FILE_NAME = "bc_data.m";
// constants
static const double C_PA = 4.12; // Pulmonary artery compliance, ml / mmHg
static const double C_LA_relaxed = 3*1.6; // Left atrial compliance ml / mmHg
static const double C_PV = 10.0 - C_LA_relaxed; // Pulmonary vein compliance, ml / mmHg
static const double R_P = (9.0/5.6) * MIN_PER_L_T0_SEC_PER_ML; // Pulmonary resistance, mmHg / (ml/s)
static const double beat_time = 0.8;
static const double T_on = .53; // Pulmonary valve open
static const double T_off = .75; // Pulmonary valve closes
static const double T_peak = T_on + 0.4 * (T_off - T_on); // Peak pulmonary valve flow
static const double stroke_volume = 75.0; // ml
static const double h = 2.0 * stroke_volume / (T_off - T_on); // Peak flow to get given stroke volume
static const bool atrial_kick_on = true;
static const double atrial_kick_center = .44;
static const double atrial_kick_time_radius = .09;
static const double atrial_kick_time_width = 2.0 * atrial_kick_time_radius;
inline double compute_Q_R(double t){
// Triangle wave flux
double t_reduced = t - beat_time * floor(t/beat_time);
if (t_reduced <= T_on)
return 0.0;
else if (t_reduced <= T_peak)
return ( h/(T_peak - T_on) )*t_reduced - (h/(T_peak - T_on) )*T_on;
else if (t_reduced <= T_off)
return (-h/(T_off - T_peak))*t_reduced + (h/(T_off - T_peak))*T_off;
else if (t_reduced <= beat_time)
return 0.0;
TBOX_ERROR("Valid time for flux not found.");
return 0.0;
}
inline double compute_C_LA(double t){
if(atrial_kick_on){
double t_reduced = t - beat_time * floor(t/beat_time);
if (abs(t_reduced - atrial_kick_center) < atrial_kick_time_radius)
return C_LA_relaxed * (1.0 - pow(cos(M_PI * (t_reduced - atrial_kick_center) / atrial_kick_time_width),2));
else
return C_LA_relaxed;
}
return C_LA_relaxed;
}
// Backward Euler update for windkessel model.
inline void
windkessel_be_update(double& Q_R, double& P_PA, double& Q_P, double& P_LA, const double Q_mi, const double t, const double dt)
{
Q_R = compute_Q_R(t);
double C_LA_current = compute_C_LA(t);
double C_LA_next = compute_C_LA(t + dt);
double a = C_PA/dt + 1/R_P;
double b = -1/R_P;
double c = -1/R_P;
double d = (C_PV + C_LA_next)/dt + 1/R_P;
double rhs[2];
rhs[0] = (C_PA/dt)*P_PA + Q_R;
rhs[1] = ((C_PV + C_LA_current)/dt)*P_LA - Q_mi;
double det = a*d - b*c;
// Closed form linear system solution
P_PA = (1/det) * ( d*rhs[0] + -b*rhs[1]);
P_LA = (1/det) * (-c*rhs[0] + a*rhs[1]);
Q_P = (1/R_P) * (P_PA - P_LA);
return;
} // windkessel_be_update
}
/////////////////////////////// PUBLIC ///////////////////////////////////////
CirculationModel::CirculationModel(const string& object_name, double P_PA_0, double P_LA_0, double t, bool register_for_restart)
: d_object_name(object_name),
d_registered_for_restart(register_for_restart),
d_time(t),
d_nsrc(1), // number of sets of variables
d_psrc(d_nsrc, 0.0), // pressure
d_qsrc(d_nsrc, 0.0), // flux
d_srcname(d_nsrc),
d_P_PA(P_PA_0),
d_P_LA(P_LA_0),
d_Q_R(0.0),
d_Q_P(0.0),
d_Q_mi(0.0),
d_bdry_interface_level_number(numeric_limits<int>::max())
{
#if !defined(NDEBUG)
assert(!object_name.empty());
#endif
if (d_registered_for_restart)
{
RestartManager::getManager()->registerRestartItem(d_object_name, this);
}
// Initialize object with data read from the input and restart databases.
const bool from_restart = RestartManager::getManager()->isFromRestart();
if (from_restart)
{
getFromRestart();
}
else
{
// nsrcs = the number of sources in the valve tester:
// (1) left atrium
d_srcname[0] = "left atrium ";
}
return;
} // CirculationModel
CirculationModel::~CirculationModel()
{
return;
} // ~CirculationModel
void
CirculationModel::advanceTimeDependentData(const double dt,
const double Q_mi)
{
/*
// Compute the mean flow rates in the vicinity of the inflow and outflow
// boundaries.
std::fill(d_qsrc.begin(), d_qsrc.end(), 0.0);
for (int ln = 0; ln <= hierarchy->getFinestLevelNumber(); ++ln)
{
Pointer<PatchLevel<NDIM> > level = hierarchy->getPatchLevel(ln);
for (PatchLevel<NDIM>::Iterator p(level); p; p++)
{
Pointer<Patch<NDIM> > patch = level->getPatch(p());
Pointer<CartesianPatchGeometry<NDIM> > pgeom = patch->getPatchGeometry();
if (pgeom->getTouchesRegularBoundary())
{
Pointer<SideData<NDIM, double> > U_data = patch->getPatchData(U_idx);
Pointer<SideData<NDIM, double> > wgt_sc_data = patch->getPatchData(wgt_sc_idx);
const Box<NDIM>& patch_box = patch->getBox();
// const double* const x_lower = pgeom->getXLower();
const double* const dx = pgeom->getDx();
double dV = 1.0;
for (int d = 0; d < NDIM; ++d)
{
dV *= dx[d];
}
static const int axis = 2; // Always z axis here
const int side = 1; // Compute flux at the top only
const bool is_lower = side == 0;
if (pgeom->getTouchesRegularBoundary(axis, side))
{
Vector n;
for (int d = 0; d < NDIM; ++d)
{
n[d] = axis == d ? (is_lower ? -1.0 : +1.0) : 0.0;
}
Box<NDIM> side_box = patch_box;
if (is_lower)
{
side_box.lower(axis) = patch_box.lower(axis);
side_box.upper(axis) = patch_box.lower(axis);
}
else
{
side_box.lower(axis) = patch_box.upper(axis) + 1;
side_box.upper(axis) = patch_box.upper(axis) + 1;
}
for (Box<NDIM>::Iterator b(side_box); b; b++)
{
const Index<NDIM>& i = b();
// no conditional here, just add the flux in
const SideIndex<NDIM> i_s(i, axis, SideIndex<NDIM>::Lower);
if ((*wgt_sc_data)(i_s) > std::numeric_limits<double>::epsilon())
{
double dA = n[axis] * dV / dx[axis];
d_qsrc[0] += (*U_data)(i_s)*dA;
// pout << "adding " << (*U_data)(i_s)*dA << "to the flux\n";
}
}
}
}
}
}
SAMRAI_MPI::sumReduction(&d_qsrc[0], d_nsrc);
// pout << "computed flux = " << d_qsrc[0] << "\n";
*/
// The downstream (Atrial) pressure is determined by a zero-d model
const double t = d_time;
double& Q_R = d_Q_R;
double& P_PA = d_P_PA;
double& Q_P = d_Q_P;
double& P_LA = d_P_LA;
// Mitral flux passed in
d_Q_mi = Q_mi;
windkessel_be_update(Q_R, P_PA, Q_P, P_LA, d_Q_mi, t, dt);
// model in mmHg, body force converts
d_psrc[0] = d_P_LA;
// Update the current time.
d_time += dt;
// Output the updated values.
const long precision = plog.precision();
plog.unsetf(ios_base::showpos);
plog.unsetf(ios_base::scientific);
plog.precision(12);
plog << "============================================================================\n"
<< "Circulation model variables at time " << d_time << ":\n";
plog << "P_PA (mmHg)\t P_LA (mmHg)\t Q_R (ml/s)\t Q_P (ml/s)\t Q_mi (ml/s)\n";
plog.setf(ios_base::showpos);
plog.setf(ios_base::scientific);
plog << d_P_PA << ",\t " << d_P_LA << ",\t " << d_Q_R << ",\t " << d_Q_P << ",\t " << d_Q_mi << "\n";
plog << "============================================================================\n";
plog.unsetf(ios_base::showpos);
plog.unsetf(ios_base::scientific);
plog.precision(precision);
// Write the current state to disk.
writeDataFile();
return;
} // advanceTimeDependentData
void
CirculationModel::putToDatabase(Pointer<Database> db)
{
db->putDouble("d_time", d_time);
db->putInteger("d_nsrc", d_nsrc);
db->putDoubleArray("d_qsrc", &d_qsrc[0], d_nsrc);
db->putDoubleArray("d_psrc", &d_psrc[0], d_nsrc);
db->putStringArray("d_srcname", &d_srcname[0], d_nsrc);
db->putDouble("d_P_PA", d_P_PA);
db->putDouble("d_P_LA", d_P_LA);
db->putDouble("d_Q_R", d_Q_R);
db->putDouble("d_Q_P", d_Q_P);
db->putDouble("d_Q_mi", d_Q_mi);
db->putInteger("d_bdry_interface_level_number", d_bdry_interface_level_number);
return;
} // putToDatabase
void CirculationModel::write_plot_code()
{
static const int mpi_root = 0;
if (SAMRAI_MPI::getRank() == mpi_root)
{
ofstream fout(DATA_FILE_NAME.c_str(), ios::app);
fout.setf(ios_base::scientific);
fout.setf(ios_base::showpos);
fout.precision(10);
fout << "];\n";
fout << "fig = figure;\n";
fout << "subplot(3,2,1)\n";
fout << "plot(bc_vals(:,1), bc_vals(:,2))\n";
fout << "title('P_{PA}')\n";
fout << "subplot(3,2,2)\n";
fout << "plot(bc_vals(:,1), bc_vals(:,3))\n";
fout << "title('P_{LA}')\n";
fout << "subplot(3,2,3)\n";
fout << "plot(bc_vals(:,1), bc_vals(:,4))\n";
fout << "title('Q_{R}')\n";
fout << "subplot(3,2,4)\n";
fout << "plot(bc_vals(:,1), bc_vals(:,5))\n";
fout << "title('Q_{P}')\n";
fout << "subplot(3,2,5)\n";
fout << "plot(bc_vals(:,1), bc_vals(:,6))\n";
fout << "title('Q_{mi}')\n";
fout << "dt = bc_vals(2,1) - bc_vals(1,1);\n";
fout << "net_flux = dt*cumsum(bc_vals(:,6));\n";
fout << "subplot(3,2,6)\n";
fout << "plot(bc_vals(:,1), net_flux)\n";
fout << "title('net Q')\n";
fout << "printfig(fig, 'bc_model_variables')\n";
}
return;
}
/////////////////////////////// PROTECTED ////////////////////////////////////
/////////////////////////////// PRIVATE //////////////////////////////////////
void
CirculationModel::writeDataFile() const
{
static const int mpi_root = 0;
if (SAMRAI_MPI::getRank() == mpi_root)
{
static bool file_initialized = false;
const bool from_restart = RestartManager::getManager()->isFromRestart();
if (!from_restart && !file_initialized)
{
ofstream fout(DATA_FILE_NAME.c_str(), ios::out);
fout << "% time \t P_PA (mmHg)\t d_P_LA (mmHg)\t Q_R (ml/s)\t Q_P (ml/s)\t Q_mi (ml/s)"
<< "\n"
<< "bc_vals = [";
file_initialized = true;
}
ofstream fout(DATA_FILE_NAME.c_str(), ios::app);
for (int n = 0; n < d_nsrc; ++n)
{
fout << d_time;
fout.setf(ios_base::scientific);
fout.setf(ios_base::showpos);
fout.precision(10);
fout << " " << d_P_PA << " " << d_P_LA << " " << d_Q_R << " " << d_Q_P << " " << d_Q_mi << "; \n";
}
}
return;
} // writeDataFile
void
CirculationModel::getFromRestart()
{
Pointer<Database> restart_db = RestartManager::getManager()->getRootDatabase();
Pointer<Database> db;
if (restart_db->isDatabase(d_object_name))
{
db = restart_db->getDatabase(d_object_name);
}
else
{
TBOX_ERROR("Restart database corresponding to " << d_object_name << " not found in restart file.");
}
d_time = db->getDouble("d_time");
d_nsrc = db->getInteger("d_nsrc");
d_qsrc.resize(d_nsrc);
d_psrc.resize(d_nsrc);
d_srcname.resize(d_nsrc);
db->getDoubleArray("d_qsrc", &d_qsrc[0], d_nsrc);
db->getDoubleArray("d_psrc", &d_psrc[0], d_nsrc);
db->getStringArray("d_srcname", &d_srcname[0], d_nsrc);
d_P_PA = db->getDouble("d_P_PA");
d_P_LA = db->getDouble("d_P_LA");
d_Q_R = db->getDouble("d_Q_R");
d_Q_P = db->getDouble("d_Q_P");
d_Q_mi = db->getDouble("d_Q_mi");
d_bdry_interface_level_number = db->getInteger("d_bdry_interface_level_number");
return;
} // getFromRestart
/////////////////////////////// NAMESPACE ////////////////////////////////////
/////////////////////////////// TEMPLATE INSTANTIATION ///////////////////////
//////////////////////////////////////////////////////////////////////////////