/******************
* unit test of QSS2 on lotka_volterra model,
* based on powerdevs results
*
* note: results have to be the same as test_QSS2_LotkaVolterra
******************/
void test_QSS2_LotkaVolterraXY()
{
auto ctx = vu::make_context();
std::cout << " test_QSS2_LotkaVolterraXY " << std::endl;
vle::utils::Package pack(ctx, "vle.ode_test");
std::unique_ptr<vz::Vpz> vpz(new vz::Vpz(pack.getExpFile("LotkaVolterraXY.vpz", vle::utils::PKG_BINARY)));
ttconfOutputPlugins(*vpz);
{
std::vector<std::string> conds;
conds.push_back("condLV");
conds.push_back("condQSS2");
conds.push_back("condQSS2_X");
ttattachConditions(*vpz,conds,"LotkaVolterraX");
}
{
std::vector<std::string> conds;
conds.push_back("condLV");
conds.push_back("condQSS2");
conds.push_back("condQSS2_Y");
ttattachConditions(*vpz,conds,"LotkaVolterraY");
}
//simulation
vm::Error error;
vm::Simulation sim(ctx, vm::LOG_NONE, vm::SIMULATION_NONE,
std::chrono::milliseconds(0), &std::cout);
std::unique_ptr<va::Map> out = sim.run(std::move(vpz), &error);
//checks that simulation has succeeded
EnsuresEqual(error.code, 0);
//checks the number of views
EnsuresEqual(out->size(),1);
//checks the selected view
const va::Matrix& view = out->getMatrix("view");
EnsuresEqual(view.columns(),3);
//note: the number of rows depend on the averaging of sum of 0.01
Ensures(view.rows() <= 15003);
Ensures(view.rows() >= 15002);
//gets X,Y
int colX = ttgetColumnFromView(view, "Top model:LotkaVolterraX", "X");
int colY = ttgetColumnFromView(view, "Top model:LotkaVolterraY", "Y");
//check X,Y line 15000
EnsuresApproximatelyEqual(view.getDouble(colX,15001), 0.69363324986147468, 10e-5);
//previous 0.696088281553273
EnsuresApproximatelyEqual(view.getDouble(colY,15001), 0.07761934820509947, 10e-5);
//previous 0.0774536442779648
}
/******************
* Unit test based on powerdevs
******************/
void test_QSS2_Seir()
{
auto ctx = vu::make_context();
std::cout << " test_QSS2_Seir " << std::endl;
vle::utils::Package pack(ctx, "vle.ode_test");
std::unique_ptr<vz::Vpz> vpz(new vz::Vpz(pack.getExpFile("Seir.vpz", vle::utils::PKG_BINARY)));
ttconfOutputPlugins(*vpz);
std::vector<std::string> conds;
conds.push_back("condQSS2");
conds.push_back("condSeir");
ttattachConditions(*vpz,conds,"Seir");
//simulation
vm::Error error;
vm::Simulation sim(ctx, vm::LOG_NONE, vm::SIMULATION_NONE,
std::chrono::milliseconds(0), &std::cout);
std::unique_ptr<va::Map> out = sim.run(std::move(vpz), &error);
//checks that simulation has succeeded
EnsuresEqual(error.code, 0);
//checks the number of views
EnsuresEqual(out->size(),1);
//checks the selected view
const va::Matrix& view = out->getMatrix("view");
EnsuresEqual(view.columns(),5);
//note: the number of rows depend on the averaging of sum of 0.01
Ensures(view.rows() <= 1503);
Ensures(view.rows() >= 1502);
//gets S,E,I,R
int colS = ttgetColumnFromView(view, "Top model:Seir", "S");
int colE = ttgetColumnFromView(view, "Top model:Seir", "E");
int colI = ttgetColumnFromView(view, "Top model:Seir", "I");
int colR = ttgetColumnFromView(view, "Top model:Seir", "R");
//check S,E,I,R line 1500
EnsuresApproximatelyEqual(view.getDouble(colS,1501), 0.636836529382071, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colE,1501), 0.636051925651117, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colI,1501), 2.95405622447345, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colR,1501), 6.77305532047774, 10e-5);
}
/******************
* Unit test based on deSolve R package
* see R/check.R function test_Euler_Seir
*
* Note: we test that the version of Seir based on four
* differential_equation (SeirXY.vpz) gets the same results
* in the case of Euler integration
******************/
void test_Euler_SeirXY()
{
auto ctx = vu::make_context();
std::cout << " test_Euler_SeirXY " << std::endl;
vle::utils::Package pack(ctx, "vle.ode_test");
std::unique_ptr<vz::Vpz> vpz(new vz::Vpz(pack.getExpFile("SeirXY.vpz",
vle::utils::PKG_BINARY)));
//set all output plugin to storage
vz::Outputs::iterator itb =
vpz->project().experiment().views().outputs().begin();
vz::Outputs::iterator ite =
vpz->project().experiment().views().outputs().end();
for(;itb!=ite;itb++) {
std::unique_ptr<va::Map> configOutput(new va::Map());
configOutput->addInt("rows",10000);
configOutput->addInt("inc_rows",10000);
configOutput->addString("header","top");
vz::Output& output = itb->second;
output.setStream("", "storage", "vle.output");
output.setData(std::move(configOutput));
}
//attach condition condEuler and condLV to atomics models
std::vector<std::string> conds;
{
conds.clear();
conds.push_back("condEuler");
conds.push_back("condSeir");
vz::Model& vpz_mod = vpz->project().model();
vz::BaseModel* mdl = vpz_mod.node()->findModelFromPath("Sm");
Ensures(mdl != 0);
vz::AtomicModel* atomg = mdl->toAtomic();
atomg->setConditions(conds);
}
{
conds.clear();
conds.push_back("condEuler");
conds.push_back("condSeir");
vz::Model& vpz_mod = vpz->project().model();
vz::BaseModel* mdl = vpz_mod.node()->findModelFromPath("Em");
Ensures(mdl != 0);
vz::AtomicModel* atomg = mdl->toAtomic();
atomg->setConditions(conds);
}
{
conds.clear();
conds.push_back("condEuler");
conds.push_back("condSeir");
vz::Model& vpz_mod = vpz->project().model();
vz::BaseModel* mdl = vpz_mod.node()->findModelFromPath("Im");
Ensures(mdl != 0);
vz::AtomicModel* atomg = mdl->toAtomic();
atomg->setConditions(conds);
}
{
conds.clear();
conds.push_back("condEuler");
conds.push_back("condSeir");
vz::Model& vpz_mod = vpz->project().model();
vz::BaseModel* mdl = vpz_mod.node()->findModelFromPath("Rm");
Ensures(mdl != 0);
vz::AtomicModel* atomg = mdl->toAtomic();
atomg->setConditions(conds);
}
//simulation
vm::Error error;
vm::Simulation sim(ctx, vm::LOG_NONE, vm::SIMULATION_NONE,
std::chrono::milliseconds(0), &std::cout);
std::unique_ptr<va::Map> out = sim.run(std::move(vpz), &error);
//checks that simulation has succeeded
EnsuresEqual(error.code, 0);
//checks the number of views
EnsuresEqual(out->size(),1);
//checks the selected view
const va::Matrix& view = out->getMatrix("view");
//note: the number of rows depend on the averaging of sum of 0.01
Ensures(view.rows() <= 1503);
Ensures(view.rows() >= 1502);
//gets S,E,I,R
int colS = ttgetColumnFromView(view, "Top model:Sm", "S");
int colE = ttgetColumnFromView(view, "Top model:Em", "E");
int colI = ttgetColumnFromView(view, "Top model:Im", "I");
int colR = ttgetColumnFromView(view, "Top model:Rm", "R");
//check S,E,I,R line 1501
EnsuresApproximatelyEqual(view.getDouble(colS,1501), 0.634334231496758, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colE,1501), 0.65430775343564, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colI,1501), 2.97798653683738, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colR,1501), 6.73337147823022, 10e-5);
}
/******************
* Unit test based on deSolve R package
* see R/check.R function test_Euler_LotkaVolterra
******************/
void test_Euler_LotkaVolterra()
{
auto ctx = vu::make_context();
std::cout << " test_Euler_LotkaVolterra " << std::endl;
vle::utils::Package pack(ctx, "vle.ode_test");
std::unique_ptr<vz::Vpz> vpz(new vz::Vpz(
pack.getExpFile("LotkaVolterra.vpz", vle::utils::PKG_BINARY)));
//set all output plugin to storage
vz::Outputs::iterator itb =
vpz->project().experiment().views().outputs().begin();
vz::Outputs::iterator ite =
vpz->project().experiment().views().outputs().end();
for(;itb!=ite;itb++) {
std::unique_ptr<va::Map> configOutput(new va::Map());
configOutput->addInt("rows",10000);
configOutput->addInt("inc_rows",10000);
configOutput->addString("header","top");
vz::Output& output = itb->second;
output.setStream("", "storage", "vle.output");
output.setData(std::move(configOutput));
}
//attach condition condEuler and condLV
std::vector<std::string> conds;
conds.push_back("condEuler");
conds.push_back("condLV");
vz::Model& vpz_mod = vpz->project().model();
vz::BaseModel* mdl = vpz_mod.node()->findModelFromPath("LotkaVolterra");
Ensures(mdl != 0);
vz::AtomicModel* atomg = mdl->toAtomic();
atomg->setConditions(conds);
//simulation
vm::Error error;
vm::Simulation sim(ctx, vm::LOG_NONE, vm::SIMULATION_NONE,
std::chrono::milliseconds(0), &std::cout);
std::unique_ptr<va::Map> out = sim.run(std::move(vpz), &error);
//checks that simulation has succeeded
EnsuresEqual(error.code, 0);
//checks the number of views
EnsuresEqual(out->size(),1);
//checks the selected view
const va::Matrix& view = out->getMatrix("view");
EnsuresEqual(view.columns(),3);
//note: the number of rows depend on the averaging of sum of 0.01
Ensures(view.rows() <= 15003);
Ensures(view.rows() >= 15002);
//gets X,Y
int colX = ttgetColumnFromView(view, "Top model:LotkaVolterra", "X");
int colY = ttgetColumnFromView(view, "Top model:LotkaVolterra", "Y");
//check X,Y line 10
EnsuresApproximatelyEqual(view.getDouble(colX,10), 9.677077, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colY,10), 5.317209, 10e-5);
//check X,Y line 30
EnsuresApproximatelyEqual(view.getDouble(colX,30), 8.903716, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colY,30), 6.030680, 10e-5);
//check X,Y line 15000
EnsuresApproximatelyEqual(view.getDouble(colX,15000), 0.5528446, 10e-5);
EnsuresApproximatelyEqual(view.getDouble(colY,15000), 0.09330513, 10e-5);
}
