poroelastic.cc

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/*
 * 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 <acl/aclGenerators.h>
#include <num/aslFDPoroElasticity.h>
#include <num/aslFDElasticityBC.h>
#include <num/aslFDPoroElasticityBC.h>
#include <utilities/aslTimer.h>
#include <utilities/aslParametersManager.h>
#include <math/aslTemplates.h>
#include <aslGeomInc.h>
#include <math/aslDistanceFunction.h>
#include <acl/aclMath/aclVectorOfElements.h>
#include <acl/aclUtilities.h>
#include <math/aslIndex2Position.h>
#include <readers/aslVTKFormatReaders.h>
#include <writers/aslVTKFormatWriters.h>
 
 
typedef float FlT;
//typedef double FlT;
typedef asl::UValue<FlT> Param;
 
 
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::SPDataWithGhostNodesACLData map0(asl::read(input.v(), 0));
//  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);
  asl::SPDistanceFunction scf(asl::generateDFPlane(asl::AVec<>(g.v()),center));
  
  auto force((1.-acl::sign(scf->getDistance(i2p.positionWithInit)))/2.*
              acl::generateVEConstant(gNum));
  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;
}