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CirculationModel.cpp
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CirculationModel.cpp
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// Filename: CirculationModel.cpp
// Created on 20 Aug 2007 by Boyce Griffith
// Modified by Alex Kaiser, 7/2016
#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>
/////////////////////////////// NAMESPACE ////////////////////////////////////
/////////////////////////////// STATIC ///////////////////////////////////////
#define MMHG_TO_CGS 1333.22368
namespace
{
// Name of output file.
static const string DATA_FILE_NAME = "bc_data.m";
}
/////////////////////////////// PUBLIC ///////////////////////////////////////
CirculationModel::CirculationModel(const string& object_name, Pointer<Database> input_db, bool register_for_restart, double P_initial)
: d_object_name(object_name),
d_registered_for_restart(register_for_restart),
d_time(0.0),
d_nsrc(1), // number of sets of variables
d_qsrc(d_nsrc, 0.0), // flux
d_psrc(d_nsrc, P_initial), // pressure
d_p_opposite(0.0), // pressure opposite face
d_srcname(d_nsrc),
d_P_Wk(P_initial),
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);
}
if (input_db)
{
d_R_proximal = input_db->getDouble("R_proximal");
d_R_distal = input_db->getDouble("R_distal");
d_C = input_db->getDouble("C");
std::cout << "input db got values R_proximal = " << d_R_proximal << "\tR_distal = " << d_R_distal << "\tC = " << d_C << "\n";
}
else
{
TBOX_ERROR("Must provide valid input_db");
}
// 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) windkessel
d_srcname[0] = "windkessel ";
}
return;
} // CirculationModel
CirculationModel::~CirculationModel()
{
return;
} // ~CirculationModel
void CirculationModel::windkessel_be_update(double& P_Wk, double& P_boundary, const double& Q_l_atrium, const double& dt)
{
// Backward Euler update for windkessel model.
P_Wk = ((d_C / dt) * P_Wk + Q_l_atrium) / (d_C / dt + 1.0 / d_R_distal);
P_boundary = P_Wk + d_R_proximal * Q_l_atrium;
return;
} // windkessel_be_update
void
CirculationModel::advanceTimeDependentData(const double dt, const double Q_input)
{
d_qsrc[0] = Q_input;
// The downstream pressure is determined by a three-element Windkessel model.
double P_boundary;
const double Q_source = d_qsrc[0];
double& P_Wk = d_P_Wk;
windkessel_be_update(P_Wk, P_boundary, Q_source, dt);
d_psrc[0] = P_boundary;
// 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 << "============================================================================\n"
<< "Circulation model variables at time " << d_time << ":\n";
plog.setf(ios_base::showpos);
plog.setf(ios_base::scientific);
plog.precision(5);
plog << "Q = " << d_qsrc[0] << " ml/s\n";
plog << "P_boundary = " << d_psrc[0]/MMHG_TO_CGS << " mmHg\t" << d_psrc[0] << " dynes/cm^2\n";
plog << "P_Wk = " << d_psrc[0]/MMHG_TO_CGS << " mmHg\t" << P_Wk << " dynes/cm^2\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_Wk", d_P_Wk);
db->putDouble("d_p_opposite", d_p_opposite);
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 << "MMHG_TO_CGS = 1333.22368;\n";
fout << "fig = figure;\n";
fout << "times = bc_vals(:,1);\n";
fout << "p_aorta = bc_vals(:,2)/MMHG_TO_CGS;\n";
fout << "q_aorta = bc_vals(:,3);\n";
fout << "p_wk = bc_vals(:,4)/MMHG_TO_CGS;\n";
fout << "p_lv = bc_vals(:,5)/MMHG_TO_CGS;\n";
fout << "subplot(2,1,1)\n";
fout << "plot(times, p_aorta, 'k')\n";
fout << "hold on\n";
fout << "plot(times, p_wk, ':k')\n";
fout << "plot(times, p_lv, '--k')\n";
fout << "legend('P_{Ao}', 'P_{Wk}', 'P_{LV}', 'Location','NorthEastOutside');\n";
fout << "xlabel('t (s)');\n";
fout << "ylabel('P (mmHg)');\n";
fout << "subplot(2,1,2)\n";
fout << "plot(times, q_aorta, 'k')\n";
fout << "hold on\n";
fout << "dt = times(2,1) - times(1);\n";
fout << "net_flux = dt*cumsum(q_aorta);\n";
fout << "plot(bc_vals(:,1), net_flux, '--k')\n";
fout << "plot(bc_vals(:,1), 0*net_flux, ':k')\n";
fout << "legend('Q', 'net Q', 'Location','NorthEastOutside')\n";
fout << "xlabel('t (s)')\n";
fout << "ylabel('Flow (ml/s), Net Flow (ml)')\n";
fout << "set(fig, 'Position', [100, 100, 1000, 750])\n";
fout << "set(fig,'PaperPositionMode','auto')\n";
fout << "printfig(fig, 'bc_model_variables')\n";
fout << "min_p_aorta_after_first_beat = min(p_aorta(floor(end/3):end))\n";
fout << "max_p_aorta_after_first_beat = max(p_aorta(floor(end/3):end))\n";
fout << "mean_p_aorta = mean(p_aorta)\n";
fout << "mean_p_wk = mean(p_wk)\n";
fout << "mean_p_lv = mean(p_lv)\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 "
<< " P_outlet (dynes/cm^2)"
<< " Q (ml/s)"
<< " P_Wk (dynes/cm^2)"
<< " P_opposite (dynes/cm^2)"
<< "\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_psrc[n];
fout.setf(ios_base::scientific);
fout.setf(ios_base::showpos);
fout.precision(10);
fout << " " << d_qsrc[n];
fout.setf(ios_base::scientific);
fout.setf(ios_base::showpos);
fout.precision(10);
fout << " " << d_P_Wk;
fout.setf(ios_base::scientific);
fout.setf(ios_base::showpos);
fout.precision(10);
fout << " " << d_p_opposite;
fout << "; \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_Wk = db->getDouble("d_P_Wk");
d_p_opposite = db->getDouble("d_p_opposite");
d_bdry_interface_level_number = db->getInteger("d_bdry_interface_level_number");
return;
} // getFromRestart
/////////////////////////////// NAMESPACE ////////////////////////////////////
/////////////////////////////// TEMPLATE INSTANTIATION ///////////////////////
//////////////////////////////////////////////////////////////////////////////