void
ESingleSimulation::initialisation()
{
preSimInit();
if (!(vm.count("config-file")) ||
(vm["config-file"].as<std::vector<std::string> >().size() != 1))
M_throw() << "You must only provide one input file in single mode";
setupSim(simulation, vm["config-file"].as<std::vector<std::string> >()[0]);
#ifdef DYNAMO_visualizer
simulation.systems.push_back(shared_ptr<System>(new SVisualizer(&simulation, vm["config-file"].as<std::vector<std::string> >()[0], simulation.lastRunMFT)));
#endif
if (vm.count("snapshot"))
simulation.systems.push_back(shared_ptr<System>(new SysSnapshot(&simulation, vm["snapshot"].as<double>(), "SnapshotTimer", "%COUNT", !vm.count("unwrapped"))));
if (vm.count("snapshot-events"))
simulation.systems.push_back(shared_ptr<System>(new SysSnapshot(&simulation, vm["snapshot-events"].as<size_t>(), "SnapshotEventTimer", "%COUNTe", !vm.count("unwrapped"))));
simulation.initialise();
postSimInit(simulation);
if (vm.count("ticker-period"))
simulation.setTickerPeriod(vm["ticker-period"].as<double>());
}
void
ESingleSimulation::initialisation()
{
preSimInit();
if (!(vm.count("config-file")) ||
(vm["config-file"].as<std::vector<std::string> >().size() != 1))
M_throw() << "You must only provide one input file in single mode";
setupSim(simulation, vm["config-file"].as<std::vector<std::string> >()[0]);
simulation.initialise();
postSimInit(simulation);
if (vm.count("ticker-period"))
simulation.setTickerPeriod(vm["ticker-period"].as<double>());
}
void
EReplicaExchangeSimulation::initialisation()
{
preSimInit();
for (unsigned int i = 0; i < nSims; i++)
{
setupSim(Simulations[i],
vm["config-file"].as<std::vector<std::string> >()[i]);
Simulations[i].initialise();
postSimInit(Simulations[i]);
}
//Ensure we are in the right ensemble for all simulations
for (size_t i = nSims; i != 0;)
if (dynamic_cast<const dynamo::EnsembleNVT* >(Simulations[--i].getEnsemble().get()) == NULL)
M_throw() << vm["config-file"].as<std::vector<std::string> >()[i]
<< " does not have an NVT ensemble";
//Ensure the types of the simulation Liouvilleans match
for (size_t i(1); i < nSims; ++i)
if (typeid(Simulations[i].dynamics.getLiouvillean())
!= typeid(Simulations[0].dynamics.getLiouvillean()))
M_throw() << vm["config-file"].as<std::vector<std::string> >()[i]
<< " does not have the same Liouvillean type as "
<< vm["config-file"].as<std::vector<std::string> >()[0];
//Test a thermostat is available
for (unsigned int i = 0; i < nSims; i++)
if (Simulations[i].getSystem("Thermostat") == NULL)
M_throw() << "Could not find the Thermostat for system " << i
<< "\nFilename " << vm["config-file"].as<std::vector<std::string> >()[i];
//Set up the replex organisation
temperatureList.clear();
for (unsigned int i = 1; i < nSims; i++)
if (Simulations[0].N != Simulations[i].N)
M_throw() << "Every replica configuration file must have the same number of particles!";
for (unsigned int i = 0; i < nSims; i++)
{
bool didWork = false;
BOOST_FOREACH(shared_ptr<System>& sysPtr1, Simulations[i].dynamics.getSystemEvents())
if (sysPtr1->getName() == "Thermostat")
{
if (dynamic_cast<SysAndersen*>(sysPtr1.get()) == NULL)
M_throw() << "Could not upcast thermostat to Andersens";
temperatureList.push_back
(replexPair
(Simulations[i].getEnsemble()->getEnsembleVals()[2],
simData(i,Simulations[i].getEnsemble()->getReducedEnsembleVals()[2])));
didWork = true;
break;
}
#ifdef DYNAMO_DEBUG
if (!didWork)
{
std::cout << "Could not find thermostat system event";
exit(1);
}
#endif
}
std::sort(temperatureList.begin(), temperatureList.end());
SimDirection.resize(temperatureList.size(), 0);
roundtrip.resize(temperatureList.size(), false);
SimDirection[temperatureList.front().second.simID] = 1; //Going up
SimDirection[temperatureList.back().second.simID] = -1; //Going down
//If a system ticker is set we scale the ticker time such that the
//number of ticks in all systems is equal.
if (vm.count("ticker-period"))
for (size_t i = 0; i < nSims; ++i)
{
double tFactor
= std::sqrt(temperatureList.begin()->second.realTemperature
/ Simulations[i].getEnsemble()->getReducedEnsembleVals()[2]);
Simulations[i].setTickerPeriod(vm["ticker-period"].as<double>() * tFactor);
}
}
