void TestArchiving()
{
EXIT_IF_PARALLEL;
#ifdef CHASTE_CVODE
OutputFileHandler handler("archive", false);
std::string archive_filename = handler.GetOutputDirectoryFullPath() + "mirams_ode.arch";
{
double wnt_level = 0.5;
boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
Mirams2010WntOdeSystem ode_system(wnt_level, p_state);
TS_ASSERT_DELTA(ode_system.GetWntLevel(), 0.50, 1e-6);
TS_ASSERT_EQUALS(ode_system.GetMutationState()->IsType<WildTypeCellMutationState>(), true);
std::vector<double> initial_conditions = ode_system.GetInitialConditions();
TS_ASSERT_EQUALS(initial_conditions.size(), 3u);
TS_ASSERT_DELTA(initial_conditions[0], 64.1863, 1e-4);
TS_ASSERT_DELTA(initial_conditions[1], 64.1863, 1e-4);
TS_ASSERT_DELTA(initial_conditions[2], 0.5, 1e-6);
// Create an output archive
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
// Archive ODE system
AbstractOdeSystem* const p_const_ode_system = &ode_system;
output_arch << p_const_ode_system;
}
{
AbstractOdeSystem* p_ode_system;
// Create an input archive
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
// Restore from the archive
input_arch >> p_ode_system;
// Check that archiving worked correctly
TS_ASSERT_DELTA(static_cast<Mirams2010WntOdeSystem*>(p_ode_system)->GetWntLevel(), 0.50, 1e-6);
TS_ASSERT_EQUALS(static_cast<Mirams2010WntOdeSystem*>(p_ode_system)->GetMutationState()->IsType<WildTypeCellMutationState>(), true);
std::vector<double> initial_conditions = p_ode_system->GetInitialConditions();
TS_ASSERT_EQUALS(initial_conditions.size(), 3u);
TS_ASSERT_DELTA(initial_conditions[0], 64.1863, 1e-4);
TS_ASSERT_DELTA(initial_conditions[1], 64.1863, 1e-4);
TS_ASSERT_DELTA(initial_conditions[2], 0.5, 1e-6);
// Tidy up
delete p_ode_system;
}
#else
std::cout << "CVODE is not enabled. " << std::endl;
std::cout << "If required please install and alter your hostconfig settings to switch on chaste support." << std::endl;
#endif //CHASTE_CVODE
}
void TestAbstractOdeSystemForCoupledPdeSystem()
{
// Create ODE system
OdeSystemForCoupledHeatEquation ode_system(1.0);
// Test setting/getting a PDE solution vector with the correct size
std::vector<double> solution(1);
solution[0] = 12.3;
ode_system.SetPdeSolution(solution);
TS_ASSERT_EQUALS(ode_system.GetPdeSolutionSize(), 1u);
std::vector<double> obtained_solution = ode_system.rGetPdeSolution();
TS_ASSERT_DELTA(obtained_solution[0], solution[0], 1e-6);
// Test an exception is thrown if setting a PDE solution vector with incorrect size
std::vector<double> bad_solution(2);
bad_solution[0] = 2.1;
bad_solution[1] = 4.9;
TS_ASSERT_THROWS_THIS(ode_system.SetPdeSolution(bad_solution),
"The supplied vector is not the correct size.");
}
void TestArchiving()
{
OutputFileHandler handler("archive", false);
std::string archive_filename = handler.GetOutputDirectoryFullPath() + "alarcon_ode.arch";
{
double oxygen_concentration = 0.7;
bool is_labelled = true;
Alarcon2004OxygenBasedCellCycleOdeSystem ode_system(oxygen_concentration, is_labelled);
TS_ASSERT_DELTA(ode_system.GetOxygenConcentration(), 0.70, 1e-6);
TS_ASSERT_EQUALS(ode_system.IsLabelled(), true);
ode_system.SetDefaultInitialCondition(2, 3.25);
std::vector<double> initial_conditions = ode_system.GetInitialConditions();
TS_ASSERT_EQUALS(initial_conditions.size(), 6u);
TS_ASSERT_DELTA(initial_conditions[0], 0.90, 1e-6);
TS_ASSERT_DELTA(initial_conditions[1], 0.01, 1e-6);
TS_ASSERT_DELTA(initial_conditions[2], 3.25, 1e-6);
TS_ASSERT_DELTA(initial_conditions[3], 5.00, 1e-6);
TS_ASSERT_DELTA(initial_conditions[4], 1.00, 1e-6);
TS_ASSERT_DELTA(initial_conditions[5], 0.70, 1e-6);
// Create an output archive
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
// Archive ODE system
AbstractOdeSystem* const p_const_ode_system = &ode_system;
output_arch << p_const_ode_system;
}
{
AbstractOdeSystem* p_ode_system;
// Create an input archive
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
// Restore from the archive
input_arch >> p_ode_system;
// Check that archiving worked correctly
TS_ASSERT_DELTA(static_cast<Alarcon2004OxygenBasedCellCycleOdeSystem*>(p_ode_system)->GetOxygenConcentration(), 0.70, 1e-6);
TS_ASSERT_EQUALS(static_cast<Alarcon2004OxygenBasedCellCycleOdeSystem*>(p_ode_system)->IsLabelled(), true);
std::vector<double> initial_conditions = p_ode_system->GetInitialConditions();
TS_ASSERT_EQUALS(initial_conditions.size(), 6u);
TS_ASSERT_DELTA(initial_conditions[0], 0.90, 1e-6);
TS_ASSERT_DELTA(initial_conditions[1], 0.01, 1e-6);
TS_ASSERT_DELTA(initial_conditions[2], 0.0, 1e-6);
TS_ASSERT_DELTA(initial_conditions[3], 5.00, 1e-6);
TS_ASSERT_DELTA(initial_conditions[4], 1.00, 1e-6);
TS_ASSERT_DELTA(initial_conditions[5], 0.70, 1e-6);
// Tidy up
delete p_ode_system;
}
}
