int main(int argc, char** argv)
{
std::string in_dir;
std::string out_dir;
std::string test_name;
unsigned int level = 0;
unsigned int version = 0;
double start_time = 0.0;
double duration = 0.0;
std::list<std::string> variables;
std::set<std::string> amounts;
std::set<std::string> concentrations;
double absolute_error = 0.0;
double relative_error = 0.0;
if (argc < 6)
{
std::cerr << "Usage: rr-sbml-benchmrk INPUT_DIRECTORY TESTNAME OUTPUTDIRECTORY SBMLLEVEL SBMLVERSION [steps override] [durration] [compiler] [-stiff]" << std::endl;
exit(1);
}
in_dir = argv[1];
test_name = argv[2];
out_dir = argv[3];
level = strtol(argv[4], NULL, 10);
version = strtol(argv[5], NULL, 10);
if (level < 1 || level > 3)
{
std::cerr << "SBML Level " << level << " Version " << version << " not supported." << std::endl;
exit(1);
}
if (level == 1 && (version < 1 || version > 2))
{
std::cerr << "SBML Level " << level << " Version " << version << " not supported." << std::endl;
exit(1);
}
std::ostringstream os;
os << in_dir << "/" << test_name << "/" << test_name << "-settings.txt";
// open the settings file and parse it
std::cout << "parsing file: " << os.str() << std::endl;
std::ifstream f;
std::string settingsFile = in_dir + "/" + test_name + "/" + test_name + "-settings.txt";
std::string sbmlFile;
{
stringstream os;
os << in_dir << "/" << test_name << "/" << test_name << "-sbml-l" << level << "v" << version << ".xml";
sbmlFile = os.str();
}
std::string output_filename;
if (!out_dir.empty() || out_dir.compare("/dev/null") != 0)
{
stringstream os;
os.str("");
os << out_dir << "/" << test_name << ".csv";
output_filename = os.str();
}
RoadRunner roadRunner;
LoadSBMLOptions opt;
// don't generate cache for models
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::RECOMPILE;
// no mutable initial conditions
opt.modelGeneratorOpt = opt.modelGeneratorOpt & ~LoadSBMLOptions::MUTABLE_INITIAL_CONDITIONS;
// read only model
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::READ_ONLY;
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::OPTIMIZE_CFG_SIMPLIFICATION;
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::OPTIMIZE_GVN;
std::cout << "loading file: " << sbmlFile << std::endl;
roadRunner.load(sbmlFile, &opt);
SimulateOptions settings;
settings.loadSBMLSettings(settingsFile);
// override steps
if (argc > 6)
{
int steps = strtol(argv[6], NULL, 0);
if (steps > 0) {
settings.steps = steps;
}
}
if (argc > 7)
{
double dur = atof(argv[7]);
if (dur > 0) {
settings.duration = dur;
}
}
for (int i = 0; i < argc; ++i) {
if (string(argv[i]).find("stiff") != string::npos) {
roadRunner.getIntegrator()->setValue("stiff", true);
}
}
std::cout << "running for " << settings.steps << ", duration " << settings.duration << std::endl;
std::cout << "absolute: " << roadRunner.getIntegrator()->getValue("absolute_tolerance").convert<bool>() << std::endl;
std::cout << "relative: " << roadRunner.getIntegrator()->getValue("relative_tolerance").convert<bool>() << std::endl;
std::cout << "stiff: " << (roadRunner.getIntegrator()->getValue("stiff").convert<bool>() ? "True" : "False") << std::endl;
roadRunner.setSimulateOptions(settings);
const DoubleMatrix& result = *roadRunner.simulate(0);
if (!output_filename.empty())
{
ofstream output;
output.open(output_filename.c_str());
int rows = result.numRows();
int cols = result.numCols();
for (int i = 0; i < rows; ++i)
{
for (int j = 0; j < cols; ++j)
{
output << result(i, j);
if (j + 1 < cols)
{
output << ", ";
}
else
{
output << "\n";
}
}
}
}
return 0;
}
