boost::program_options::variables_map&
Coordinator::parseOptions(int argc, char *argv[])
{
namespace po = boost::program_options;
boost::program_options::options_description allopts(""),
basicOpts, detailedEngineOpts, systemopts("System Options"),
engineopts("Engine Options")
;
systemopts.add_options()
("help", "Produces this message")
("n-threads,N", po::value<unsigned int>(),
"Number of _threads to spawn for concurrent processing. (Only utilised by certain engine/sim configurations)")
("out-config-file,o", po::value<std::string>(),
"Default config output file,(config.%ID.end.xml.bz2)")
("out-data-file", po::value<std::string>(),
"Default result output file (output.%ID.xml.bz2)")
("config-file", po::value<std::vector<std::string> >(),
"Specify a config file to load, or just list them on the command line")
;
engineopts.add_options()
("engine",boost::program_options::value<size_t>()->default_value(1),
"Select the Engine used to run the simulation:\n"
" Values:\n"
" 1: \tStandard Engine\n"
" 2: \tNVT Replica Exchange Engine\n"
" 3: \tCompression Engine")
;
basicOpts.add(systemopts).add(engineopts);
Engine::getCommonOptions(detailedEngineOpts);
EReplicaExchangeSimulation::getOptions(detailedEngineOpts);
ECompressingSimulation::getOptions(detailedEngineOpts);
allopts.add(basicOpts).add(detailedEngineOpts);
boost::program_options::positional_options_description p;
p.add("config-file", -1);
boost::program_options::store(po::command_line_parser(argc, argv).
options(allopts).positional(p).run(), vm);
boost::program_options::notify(vm);
if (vm.count("help") || (argc==1))
{
std::cout << "Usage : dynarun <OPTION>...<config-file(s)>\n"
<< "Loads a configuration file, calculates the trajectory of the system using the specified engine and"
<< "outputs any collected data, including a the final configuration file.\n"
<< basicOpts << "\n"
<< detailedEngineOpts << "\n";
exit(1);
}
if (vm.count("config-file") == 0)
M_throw() << "No configuration files to load specified";
return vm;
}
int
main(int argc, char *argv[])
{
std::cout << "dynamod Copyright (C) 2013 Marcus N Campbell Bannerman\n"
<< "This program comes with ABSOLUTELY NO WARRANTY.\n"
<< "This is free software, and you are welcome to redistribute it\n"
<< "under certain conditions. See the licence you obtained with\n"
<< "the code\n";
dynamo::Simulation sim;
////////////////////////PROGRAM OPTIONS!!!!!!!!!!!!!!!!!!!!!!!
try
{
po::options_description allopts("General Options"), loadopts("Load Config File Options"),
hiddenopts,
helpOpts;
allopts.add_options()
("help,h", "Produces this message OR if --pack-mode/-m is set, it lists the specific options available for that packer mode.")
("out-config-file,o", po::value<string>()->default_value("config.out.xml.bz2"), "Configuration output file.")
("random-seed,s", po::value<unsigned int>(), "Seed value for the random number generator.")
("rescale-T,r", po::value<double>(), "Rescales the kinetic temperature of the input/generated config to this value.")
("thermostat,T", po::value<double>(), "Change or add a thermostatt with the temperature provided. A temperature of zero will remove the thermostatt.")
("zero-momentum,Z", "Zeros the total momentum of the input/generated config.")
("zero-com", "Zeros the centre of mass of the input/generated config.")
("zero-vel", po::value<size_t>(), "Sets the velocity in the [arg=0,1,or 2] dimension of each particle to zero.")
("set-com-vel", po::value<std::string>(), "Sets the velocity of the COM of the system (format x,y,z no spaces).")
("mirror-system,M",po::value<unsigned int>(), "Mirrors the particle co-ordinates and velocities. Argument is dimension to reverse/mirror.")
("round", "Output the XML config file with one less digit of accuracy to remove rounding errors (used in the test harness).")
("unwrapped", "Don't apply the boundary conditions of the system when writing out the particle positions.")
("check", "Runs tests on the configuration to ensure the system is not in an invalid state.")
;
loadopts.add_options()
("config-file", po::value<string>(), "Config file to initialise from (Non packer mode).")
;
helpOpts.add(allopts);
helpOpts.add(dynamo::IPPacker::getOptions());
allopts.add(loadopts);
allopts.add(dynamo::IPPacker::getOptions());
hiddenopts.add_options()
("b1", "boolean option one.")
("b2", "boolean option two.")
("i1", po::value<size_t>(), "integer option one.")
("i2", po::value<size_t>(), "integer option two.")
("i3", po::value<size_t>(), "integer option three.")
("i4", po::value<size_t>(), "integer option four.")
("s1", po::value<std::string>(), "string option one.")
("s2", po::value<std::string>(), "string option two.")
("f1", po::value<double>(), "double option one.")
("f2", po::value<double>(), "double option two.")
("f3", po::value<double>(), "double option three.")
("f4", po::value<double>(), "double option four.")
("f5", po::value<double>(), "double option five.")
("f6", po::value<double>(), "double option six.")
("f7", po::value<double>(), "double option seven.")
("f8", po::value<double>(), "double option eight.")
("f9", po::value<double>(), "double option nine.")
("f10", po::value<double>(), "double option ten.")
("NCells,C", po::value<unsigned long>()->default_value(7),
"Default number of unit cells per dimension, used for crystal packing of particles.")
("xcell,x", po::value<unsigned long>(),
"Number of unit cells in the x dimension.")
("ycell,y", po::value<unsigned long>(),
"Number of unit cells in the y dimension.")
("zcell,z", po::value<unsigned long>(),
"Number of unit cells in the z dimension.")
("rectangular-box", "Force the simulation box to be deformed so "
"that the x,y,z cells also specify the box aspect ratio.")
("density,d", po::value<double>()->default_value(0.5),
"System number density.")
;
allopts.add(hiddenopts);
po::positional_options_description p;
p.add("config-file", 1);
po::variables_map vm;
po::store(po::command_line_parser(argc, argv).options(allopts).positional(p).run(), vm);
po::notify(vm);
if (vm.count("random-seed"))
sim.ranGenerator.seed(vm["random-seed"].as<unsigned int>());
if (!vm.count("pack-mode") && (vm.count("help") || !vm.count("config-file")))
{
cout << "Usage : dynamod <OPTIONS>...[CONFIG FILE]\n"
<< " Either modifies a config file (if a file name is passed as an argument) OR generates a new config file depending on the packing mode (if --pack-mode/-m is used).\n"
<< helpOpts;
return 1;
}
if (vm.count("pack-mode") && vm.count("config-file"))
{
cout << "You cannot specify a packing mode and pass a configuration file as an argument" << std::endl;
return 1;
}
////////////////////////Simulation Initialisation!!!!!!!!!!!!!
//Now load the config
if (vm.count("pack-mode"))
{
dynamo::IPPacker plug(vm, &sim);
plug.initialise();
//We don't zero momentum and rescale for certain packer modes
if ((vm["pack-mode"].as<size_t>() != 23)
&& (vm["pack-mode"].as<size_t>() != 25)
&& (vm["pack-mode"].as<size_t>() != 28))
{
dynamo::InputPlugin(&sim, "Rescaler").zeroMomentum();
dynamo::InputPlugin(&sim, "Rescaler").rescaleVels(1.0);
}
}
else
sim.loadXMLfile(vm["config-file"].as<string>());
sim.endEventCount = 0;
if (vm.count("thermostat"))
{
if (vm["thermostat"].as<double>() == 0.0)
{
auto thermostat_base_ptr = sim.systems.find("Thermostat");
if (thermostat_base_ptr == sim.systems.end())
M_throw() << "Could not locate thermostat to disable";
if (!std::dynamic_pointer_cast<dynamo::SysAndersen>(*thermostat_base_ptr))
M_throw() << "Could not upcast System event named \"Thermostat\" to Thermostat type";
sim.systems.erase(thermostat_base_ptr);
sim.ensemble = dynamo::Ensemble::loadEnsemble(sim);
}
else
{
if (sim.systems.find("Thermostat") == sim.systems.end())
//Should use reduced temperature here, but we set it later anyway
sim.systems.push_back(dynamo::shared_ptr<dynamo::System>(new dynamo::SysAndersen(&sim, 1.0 / sim.N(), 1.0, "Thermostat")));
auto thermostat_base_ptr = sim.systems.find("Thermostat");
auto thermostat_ptr = std::dynamic_pointer_cast<dynamo::SysAndersen>(*thermostat_base_ptr);
if (!thermostat_ptr)
M_throw() << "Could not upcast System event named \"Thermostat\" to SysAndersen";
thermostat_ptr->setReducedTemperature(vm["thermostat"].as<double>());
sim.ensemble = dynamo::Ensemble::loadEnsemble(sim);
}
}
sim.initialise();
//Here we modify the sim accordingly
if (vm.count("zero-momentum"))
dynamo::InputPlugin(&sim, "MomentumZeroer").zeroMomentum();
if (vm.count("check"))
sim.checkSystem();
if (vm.count("zero-com"))
dynamo::InputPlugin(&sim, "CentreOfMassZeroer").zeroCentreOfMass();
if (vm.count("rescale-T"))
dynamo::InputPlugin(&sim, "Rescaler").rescaleVels(vm["rescale-T"].as<double>());
if (vm.count("mirror-system"))
dynamo::InputPlugin(&sim, "Mirrorer").mirrorDirection(vm["mirror-system"].as<unsigned int>());
if (vm.count("set-com-vel"))
{
boost::tokenizer<boost::char_separator<char> >
tokens(vm["set-com-vel"].as<std::string>(), boost::char_separator<char>(","));
boost::tokenizer<boost::char_separator<char> >::iterator details_iter = tokens.begin();
dynamo::Vector vel(0,0,0);
if (details_iter == tokens.end()) M_throw() << "set-com-vel requires 3 components";
vel[0] = boost::lexical_cast<double>(*(details_iter++));
if (details_iter == tokens.end()) M_throw() << "set-com-vel requires 3 components";
vel[1] = boost::lexical_cast<double>(*(details_iter++));
if (details_iter == tokens.end()) M_throw() << "set-com-vel requires 3 components";
vel[2] = boost::lexical_cast<double>(*(details_iter));
dynamo::InputPlugin(&sim, "velSetter").setCOMVelocity(vel);
}
if (vm.count("zero-vel"))
dynamo::InputPlugin(&sim, "Vel-Component-Zeroer").zeroVelComp(vm["zero-vel"].as<size_t>());
sim.writeXMLfile(vm["out-config-file"].as<string>(), !vm.count("unwrapped"), vm.count("round"));
}
catch (std::exception& cep)
{
std::cout.flush();
magnet::stream::FormattedOStream os(std::cerr, magnet::console::bold() + magnet::console::red_fg() + "Main(): " + magnet::console::reset());
os << cep.what() << std::endl;
#ifndef DYNAMO_DEBUG
os << "Try using the debugging executable for more information on the error." << std::endl;
#endif
return 1;
}
return 0;
}
