ASL  0.1.7
Advanced Simulation Library
poroelastic.cc

Required input file: brain.vti

/*
* Advanced Simulation Library <http://asl.org.il>
*
* Copyright 2015 Avtech Scientific <http://avtechscientific.com>
*
*
* This file is part of Advanced Simulation Library (ASL).
*
* ASL is free software: you can redistribute it and/or modify it
* under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, version 3 of the License.
*
* ASL 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with ASL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <aslDataInc.h>
#include <aslGeomInc.h>
typedef float FlT;
//typedef double FlT;
int main(int argc, char* argv[])
{
asl::ApplicationParametersManager appParamsManager("poroelastic", "1.0");
asl::Parameter<asl::AVec<int> > size(asl::makeAVec<int>(50, 50, 50), "size", "3D size");
asl::Parameter<cl_float> dx(4e-3, "dx", "dx");
asl::Parameter<cl_float> dt(0.0001, "dt", "dt");
asl::Parameter<cl_float> bulkModulus(1000.0, "bulk_modulus", "bulk modulus");
asl::Parameter<cl_float> shearModulus(30.0, "shear_modulus", "shear modulus");
asl::Parameter<cl_float> hydraulicConductivity(1e-10, "hydraulic_conductivity", "hydraulic conductivity");
asl::Parameter<cl_float> rho(1e3, "rho", "density");
asl::Parameter<asl::AVec<FlT> > g(asl::makeAVec<FlT>(-9.8, 0.0, 0.0), "g", "gravity vector");
asl::Parameter<string> input("input", "path to the brain geometry input file");
asl::Parameter<unsigned int> tsim(20000, "num_iterations", "number of iterations");
asl::Parameter<unsigned int> tout(500, "num_it_out", "number of iterations between outputs");
appParamsManager.load(argc, argv);
std::cout << "Data initialization... " << flush;
// asl::Block block(size.v(), dx.v());
asl::Block block(map0->getInternalBlock());
dx.v() = block.dx*1e-3;
dt.v() = 0.0001f;
Param bulkModulusNum(bulkModulus.v()/rho.v()/dx.v()/dx.v());
Param shearModulusNum(shearModulus.v()/rho.v()/dx.v()/dx.v());
asl::AVec<FlT> gNum(g.v()/dx.v());
Param hydraulicConductivityNum(hydraulicConductivity.v()/dx.v()/dx.v()/dx.v());
cout << gNum << "; " << bulkModulusNum.v() << "; " << hydraulicConductivityNum.v() << endl;
auto displacement(asl::generateDataContainerACL_SP<FlT>(block, 3, 1u));
auto pressure(asl::generateDataContainerACL_SP<FlT>(block, 1, 1u));
acl::initData(displacement->getEContainer(), acl::generateVEConstantN(3,0));
acl::initData(pressure->getEContainer(), acl::generateVEConstant(0));
// auto mapDF(asl::generateDFInBlock(block, 0));
// auto map(asl::generateDataContainer_SP(block, mapDF, 1u, acl::typeToTypeID<FlT>()));
auto mapX(asl::generateDataContainerACL_SP<FlT>(block, 1, 1u));
// initData(mapX->getEContainer(), map->getEContainer());
initData(mapX->getEContainer(), map0->getEContainer()*2.-1., acl::KERNEL_BASIC);
asl::WriterVTKXML writer(appParamsManager.getDir() + "poroelastic");
writer.addVector("displacement", *displacement);
writer.addScalars("pressure", *pressure);
writer.addScalars("map", *mapX);
// writer.write();
std::cout << "Finished" << endl;
std::cout << "Numerics initialization... " << flush;
auto elasticity(make_shared<asl::FDPoroElasticity>(displacement,
pressure,
acl::generateVEConstant(bulkModulusNum.v()),
acl::generateVEConstant(shearModulusNum.v()),
acl::generateVEConstant(hydraulicConductivityNum.v()),
&asl::d3q15()));
asl::Index2PositionACL i2p(displacement->getBlock(),acl::typeToTypeID<FlT>());
asl::AVec<> center(asl::AVec<>(displacement->getBlock().getSize())*.5 *
displacement->getBlock().dx +
displacement->getBlock().position);
auto force((1.-acl::sign(scf->getDistance(i2p.positionWithInit)))/2.*
auto forceField(asl::generateDataContainer_SP(block, force, 1u));
elasticity->setForce(forceField->getSubContainer());
elasticity->init();
vector<asl::SPNumMethod> bcl;
bcl.push_back(asl::generateBCZeroStress(elasticity, mapX));
asl::addBCRigidWall(bcl, elasticity, {asl::X0});
initAll(bcl);
std::cout << "Finished" << endl;
std::cout << "Computing..." << flush;
asl::Timer timer;
executeAll(bcl);
writer.write();
timer.start();
for (unsigned int i(0); i < tsim.v(); ++i)
{
elasticity->execute();
executeAll(bcl);
if (!(i % tout.v()))
writer.write();
}
timer.stop();
cout << "Finished" << endl;
cout << "Computation statistic:" << endl;
cout << "Real Time = " << timer.realTime() << "; Processor Time = "
<< timer.processorTime() << "; Processor Load = "
<< timer.processorLoad() * 100 << "%" << endl;
return 0;
}