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CirculationModel_aorta.cpp
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CirculationModel_aorta.cpp
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// Filename: CirculationModel_aorta.cpp
// Created on 20 Aug 2007 by Boyce Griffith
// Modified 2019, Alexander D. Kaiser
#include "CirculationModel_aorta.h"
#include "pnpoly.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 <Eigen/Dense>
using namespace Eigen;
namespace
{
// Name of output file.
static const string DATA_FILE_NAME = "bc_data.m";
}
/////////////////////////////// NAMESPACE ////////////////////////////////////
/////////////////////////////// STATIC ///////////////////////////////////////
/////////////////////////////// PUBLIC ///////////////////////////////////////
CirculationModel_aorta::CirculationModel_aorta(Pointer<Database> input_db,
const fourier_series_data *fourier_ventricle,
string ventricle_vertices_file_name,
string aorta_vertices_file_name,
const double cycle_duration,
const double t_offset_bcs_unscaled,
const double initial_time,
double P_initial_aorta,
bool rcr_bcs_on,
bool P_initial_aorta_equal_to_ventricle,
double rcr_on_time)
:
d_object_name("circ_model_aorta"), // constant name here
d_registered_for_restart(true), // always true
d_fourier_ventricle(fourier_ventricle),
d_cycle_duration(cycle_duration),
d_t_offset_bcs_unscaled(t_offset_bcs_unscaled),
d_current_idx_series(0),
d_Q_ventricle(0.0),
d_Q_aorta(0.0),
d_time(initial_time),
d_aorta_P_Wk(P_initial_aorta),
d_p_extender_mean(0.0),
d_p_extender_point(0.0),
d_area_ventricle(0.0),
d_area_aorta(0.0),
d_area_initialized(false),
d_rcr_bcs_on(rcr_bcs_on),
d_P_initial_aorta_equal_to_ventricle(P_initial_aorta_equal_to_ventricle),
d_rcr_on_time(rcr_on_time)
{
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();
}
if (d_rcr_bcs_on){
if (input_db){
// left and right equal for now
d_aorta_R_proximal = input_db->getDouble("R_proximal");
d_aorta_R_distal = input_db->getDouble("R_distal");
d_aorta_C = input_db->getDouble("C");
std::cout << "input db got values:\n";
std::cout << "input db got values R_proximal = " << d_aorta_R_proximal << "\tR_distal = " << d_aorta_R_distal << "\tC = " << d_aorta_C << "\n";
}
else {
TBOX_ERROR("Must provide valid input_db");
}
}
double x,x_prev,y,y_prev,z,z_prev;
double tol = 1.0e-2;
// read vertices from file
ifstream ventricle_file(ventricle_vertices_file_name.c_str(), ios::in);
if(!ventricle_file){
TBOX_ERROR("Aorta file not found\n");
}
ventricle_file >> d_n_pts_ventricle;
d_ventricle_points_idx1 = new double[d_n_pts_ventricle];
d_ventricle_points_idx2 = new double[d_n_pts_ventricle];
for (int i=0; i<d_n_pts_ventricle; i++){
ventricle_file >> x;
ventricle_file >> d_ventricle_points_idx1[i];
ventricle_file >> d_ventricle_points_idx2[i];
if (i>0){
if (fabs(x_prev - x) > tol){
TBOX_ERROR("x coordinates must be consistent\n");
}
}
x_prev = x;
}
pout << "to ventricle file close\n";
ventricle_file.close();
// hardcode to top
d_ventricle_axis = 0;
d_ventricle_side = 1;
// read vertices from file
ifstream aorta_file(aorta_vertices_file_name.c_str(), ios::in);
if(!aorta_file){
TBOX_ERROR("Aorta file not found\n");
}
aorta_file >> d_n_pts_aorta;
d_aorta_points_idx1 = new double[d_n_pts_aorta];
d_aorta_points_idx2 = new double[d_n_pts_aorta];
for (int i=0; i<d_n_pts_aorta; i++){
aorta_file >> d_aorta_points_idx1[i];
aorta_file >> d_aorta_points_idx2[i];
aorta_file >> z;
if (i>0){
if (fabs(z_prev - z) > tol){
TBOX_ERROR("z coordinates must be consistent\n");
}
}
z_prev = z;
}
pout << "to aorta file close\n";
aorta_file.close();
d_aorta_axis = 2;
d_aorta_side = 1;
if (!from_restart){
if (d_P_initial_aorta_equal_to_ventricle){
d_aorta_P = MMHG_TO_CGS * this->d_fourier_ventricle->values[0];
}
else{
d_aorta_P = P_initial_aorta;
}
}
pout << "passed contstructor\n";
pout << "initial aorta pressure = " << P_initial_aorta << ", P_wk = " << d_aorta_P << "\n";
return;
} // CirculationModel
CirculationModel_aorta::~CirculationModel_aorta()
{
return;
} // ~CirculationModel_aorta
void CirculationModel_aorta::advanceTimeDependentData(const double dt,
const Pointer<PatchHierarchy<NDIM> > hierarchy,
const int U_idx,
const int /*P_idx*/,
const int /*wgt_cc_idx*/,
const int wgt_sc_idx)
{
// Compute the mean flow rates in the vicinity of the inflow and outflow
// boundaries.
double Q_ventricle_local = 0.0;
double Q_aorta_local = 0.0;
double area_ventricle_local = 0.0;
double area_aorta_local = 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];
}
for(int axis=0; axis<3; axis++)
{
for(int side=0; side<2; side++)
{
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();
double X[NDIM];
for (int d = 0; d < NDIM; ++d)
{
X[d] = x_lower[d] + dx[d] * (double(i(d) - patch_box.lower(d)) + (d == axis ? 0.0 : 0.5));
}
double X_in_plane_1 = 0.0;
double X_in_plane_2 = 0.0;
if (axis == 0)
{
X_in_plane_1 = X[1];
X_in_plane_2 = X[2];
}
else if (axis == 1)
{
X_in_plane_1 = X[0];
X_in_plane_2 = X[2];
}
else if (axis == 2)
{
X_in_plane_1 = X[0];
X_in_plane_2 = X[1];
}
else{
TBOX_ERROR("Invalid value of axis\n");
}
const int in_ventricle = this->point_in_ventricle(X_in_plane_1, X_in_plane_2, axis, side);
const int in_aorta = this->point_in_aorta (X_in_plane_1, X_in_plane_2, axis, side);
if (in_ventricle && in_aorta){
TBOX_ERROR("Position is within two inlets and outlets, should be impossible\n");
}
if (in_ventricle)
{
const SideIndex<NDIM> i_s(i, axis, SideIndex<NDIM>::Lower);
if ((*wgt_sc_data)(i_s) > std::numeric_limits<double>::epsilon())
{
double dA = dV / dx[axis];
Q_ventricle_local += (*U_data)(i_s)* n[axis] * dA;
if (!d_area_initialized){
area_ventricle_local += dA;
}
}
}
if (in_aorta)
{
const SideIndex<NDIM> i_s(i, axis, SideIndex<NDIM>::Lower);
if ((*wgt_sc_data)(i_s) > std::numeric_limits<double>::epsilon())
{
double dA = dV / dx[axis];
Q_aorta_local += (*U_data)(i_s) * n[axis] * dA;
if (!d_area_initialized){
area_aorta_local += dA;
}
}
}
}
}
}
}
}
}
}
d_Q_ventricle = SAMRAI_MPI::sumReduction(Q_ventricle_local);
d_Q_aorta = SAMRAI_MPI::sumReduction(Q_aorta_local);
if (!d_area_initialized){
d_area_ventricle = SAMRAI_MPI::sumReduction(area_ventricle_local);
d_area_aorta = SAMRAI_MPI::sumReduction(area_aorta_local);
d_area_initialized = true;
}
if (d_rcr_bcs_on){
// The downstream pressure is determined by a three-element Windkessel model.
if ((d_P_initial_aorta_equal_to_ventricle) && (d_time < d_rcr_on_time)){
// linear interpolation
d_aorta_P = (1 - d_time/d_rcr_on_time) * MMHG_TO_CGS * this->d_fourier_ventricle->values[0] +
( d_time/d_rcr_on_time) * d_aorta_P_Wk; // wk pressure is the end pressure for the interpolation
}
else{
d_aorta_P_Wk = ((d_aorta_C / dt) * d_aorta_P_Wk + d_Q_aorta) / (d_aorta_C / dt + 1.0 / d_aorta_R_distal);
d_aorta_P = d_aorta_P_Wk + d_aorta_R_proximal * d_Q_aorta;
}
}
// print_summary();
// bool debug_out_areas = false;
// if (debug_out_areas){
// pout << "d_area_ventricle = " << d_area_ventricle << "\n";
// pout << "d_area_aorta = " << d_area_aorta << "\n";
// }
d_time += dt;
// compute which index in the Fourier series we need here
// always use a time in current cycle
double t_reduced = d_time - d_cycle_duration * floor(d_time/d_cycle_duration);
// fourier series has its own period, scale to that
double t_scaled = t_reduced * (d_fourier_ventricle->L / d_cycle_duration);
// start offset some arbitrary time in the cardiac cycle, but this is relative to the series length
double t_scaled_offset = t_scaled + d_t_offset_bcs_unscaled;
// Fourier data here
// index without periodicity
unsigned int k = (unsigned int) floor(t_scaled_offset / (d_fourier_ventricle->dt));
// // take periodic reduction
d_current_idx_series = k % (d_fourier_ventricle->N_times);
// bool debug_out = false;
// if (debug_out){
// pout << "circ mode: d_time = " << d_time << ", d_current_idx_series = " << d_current_idx_series << "\n";
// pout << "t_reduced = " << t_reduced << " t_scaled = " << t_scaled << " t_scaled_offset = " << t_scaled_offset << "\n";
// pout << "k (unreduced idx) = " << k << " d_current_idx_series = " << d_current_idx_series << "\n\n";
// }
writeDataFile();
} // advanceTimeDependentData
void CirculationModel_aorta::set_Q_valve(double Q_valve){
d_Q_valve = Q_valve;
}
void CirculationModel_aorta::set_extender_pressures(double p_extender_mean, double p_extender_point){
d_p_extender_mean = p_extender_mean;
d_p_extender_point = p_extender_point;
}
void
CirculationModel_aorta::putToDatabase(Pointer<Database> db)
{
db->putInteger("d_current_idx_series", d_current_idx_series);
db->putDouble("d_Q_ventricle", d_Q_ventricle);
db->putDouble("d_Q_aorta", d_Q_aorta);
db->putDouble("d_Q_valve", d_Q_valve);
db->putDouble("d_aorta_P", d_aorta_P);
db->putDouble("d_aorta_P_Wk", d_aorta_P_Wk);
db->putDouble("d_p_extender_mean", d_p_extender_mean);
db->putDouble("d_p_extender_point", d_p_extender_point);
db->putDouble("d_time", d_time);
db->putBool("d_rcr_bcs_on", d_rcr_bcs_on);
return;
} // putToDatabase
void CirculationModel_aorta::print_summary(){
double P_ventricle = d_fourier_ventricle->values[d_current_idx_series];
double P_aorta = d_aorta_P / MMHG_TO_CGS;
if (!d_rcr_bcs_on){
TBOX_ERROR("Not implemented\n");
// P_aorta = d_fourier_aorta->values[d_current_idx_series];
}
pout << "rcr_bcs_on = " << d_rcr_bcs_on << "\n";
pout << "% time \t P_ventricle (mmHg)\t P_aorta (mmHg)\t Q_ventricle (ml/s)\t d_Q_aorta (ml/s)\t d_Q_valve (ml/s)\t Q_current_idx_series \t idx" ;
pout << "\t aorta_P_Wk \t p_extender_mean \t p_extender_point ";
pout << "\n";
pout << d_time << " " << P_ventricle << " " << P_aorta << " " << d_Q_ventricle << " " << d_Q_aorta << " " << d_Q_valve << " " << d_current_idx_series;
pout << " " << d_aorta_P_Wk << " " << d_p_extender_mean/MMHG_TO_CGS << " " << d_p_extender_point/MMHG_TO_CGS;
pout << "\n";
}
int CirculationModel_aorta::point_in_ventricle(double testx, double testy, int axis, int side){
// checks whether given point is in right ventricle
// quick exit for correct side and axis
if ((axis != d_ventricle_axis) || (side != d_ventricle_side))
return 0;
return pnpoly(d_n_pts_ventricle, d_ventricle_points_idx1, d_ventricle_points_idx2, testx, testy);
}
int CirculationModel_aorta::point_in_aorta(double testx, double testy, int axis, int side){
// checks whether given point is in right ventricle
// quick exit for correct side and axis
if ((axis != d_aorta_axis) || (side != d_aorta_side))
return 0;
return pnpoly(d_n_pts_aorta, d_aorta_points_idx1, d_aorta_points_idx2, testx, testy);
}
void CirculationModel_aorta::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 << "times = bc_vals(:,1);\n";
fout << "p_lv = bc_vals(:,2);\n";
fout << "p_aorta = bc_vals(:,3); \n";
fout << "q_ventricle = -bc_vals(:,4);\n";
fout << "q_aorta = bc_vals(:,5);\n";
fout << "q_valve = bc_vals(:,6);\n";
fout << "p_wk = bc_vals(:,7);\n";
fout << "p_extender_mean = bc_vals(:,8);\n";
fout << "p_extender_point = bc_vals(:,9);\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 << "%plot(times, p_extender_mean)\n";
fout << "plot(times, p_extender_point)\n";
fout << "%legend('P_{Ao}', 'P_{Wk}', 'P_{LV}', 'P extender mean', 'P extender point', 'Location','NorthEastOutside');\n";
fout << "%legend('P_{Ao}', 'P_{Wk}', 'P_{LV}', 'P extender point', '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(times, net_flux, '--k')\n";
fout << "plot(times, q_ventricle)\n";
fout << "% plot(times, q_valve)\n";
fout << "plot(bc_vals(:,1), 0*net_flux, ':k')\n";
fout << "%legend('Q', 'net Q', 'Q ventricle', 'Q valve', 'Location','NorthEastOutside')\n";
fout << "legend('Q', 'net Q', 'Q ventricle', '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 << "diary notes.txt\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 << "max_p_exender_mean = max(p_extender_mean)\n";
fout << "max_p_exender_point = max(p_extender_point)\n";
fout << "mean_p_lv = mean(p_lv)\n";
fout << "end_flux = net_flux(end)\n";
fout << "max_flux = max(net_flux)\n";
fout << "diary off\n";
}
return;
}
/////////////////////////////// PROTECTED ////////////////////////////////////
/////////////////////////////// PRIVATE //////////////////////////////////////
void
CirculationModel_aorta::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_ventricle (mmHg)\t P_aorta (mmHg)\t d_Q_ventricle (ml/s)\t d_Q_aorta (ml/s)\t d_Q_valve (ml/s)\t"
<< "d_aorta_P_Wk (mmHg) \t d_p_extender_mean (mmHg) \t d_p_extender_point (mmHg)"
<< "\n"
<< "bc_vals = [";
file_initialized = true;
}
ofstream fout(DATA_FILE_NAME.c_str(), ios::app);
fout << d_time;
fout.setf(ios_base::scientific);
fout.setf(ios_base::showpos);
fout.precision(10);
double P_ventricle = d_fourier_ventricle->values[d_current_idx_series];
double P_aorta = 0.0;
if (d_rcr_bcs_on){
P_aorta = d_aorta_P/MMHG_TO_CGS;
}
else{
TBOX_ERROR("not implemented\n");
// P_aorta = d_fourier_aorta->values[d_current_idx_series];
}
fout << " " << P_ventricle << " " << P_aorta;
fout << " " << d_Q_ventricle << " " << d_Q_aorta << " " << d_Q_valve;
fout << " " << d_aorta_P_Wk/MMHG_TO_CGS;
fout << " " << d_p_extender_mean/MMHG_TO_CGS;
fout << " " << d_p_extender_point/MMHG_TO_CGS;
fout << "; \n";
}
return;
} // writeDataFile
void
CirculationModel_aorta::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_current_idx_series = db->getInteger("d_current_idx_series");
d_Q_ventricle = db->getDouble("d_Q_ventricle");
d_Q_aorta = db->getDouble("d_Q_aorta");
d_Q_valve = db->getDouble("d_Q_valve");
d_aorta_P = db->getDouble("d_aorta_P");
d_aorta_P_Wk = db->getDouble("d_aorta_P_Wk");
d_p_extender_mean = db->getDouble("d_p_extender_mean");
d_p_extender_point = db->getDouble("d_p_extender_point");
d_time = db->getDouble("d_time");
d_rcr_bcs_on = db->getBool("d_rcr_bcs_on");
return;
} // getFromRestart
/////////////////////////////// NAMESPACE ////////////////////////////////////
/////////////////////////////// TEMPLATE INSTANTIATION ///////////////////////
//////////////////////////////////////////////////////////////////////////////