void pspParticle::setup(pspParticleSystem* ms, int ind){
mySystem = ms;
systemsManager = mySystem->getSystemsManager();
myConcertRoom = systemsManager->getConcertRoom();
speakers = myConcertRoom->getSpeakers();
index = ind;
sendOsc = true;
specificSetup();
}
bool MicroCanonicalMD::setup(ForceField& my_force_field, SnapShotManager * ssm, const Options& my_options)
{
// First check whether the force field is valid. If not, then it is useless
// to do anything here.
if (!my_force_field.isValid())
{
// The setup has failed for some reason. Output an error message.
Log.error() << "MicroCanonicalMD::setup: setup failed because the force field was not valid!" << std::endl;
valid_ = false;
return false;
}
// call the base class setup method
valid_ = MolecularDynamics::setup(my_force_field, ssm, my_options);
if (!valid_)
return false;
// call the specific Setup
valid_ = specificSetup();
return valid_;
}
// setup methods
bool EnergyMinimizer::setup(ForceField& force_field)
{
// Default: no snapshot manager available
snapshot_ = 0;
// store the specified force field
force_field_ = &force_field;
valid_ = force_field_->isValid();
if (!valid_)
{
Log.error() << "EnergyMinimizer: The force field of the energy minimizer is not valid! "
<< "Check the definition and initialization of the force field! " << endl;
return valid_;
}
// Compute cutlo_
float epsilon = 1.;
float eps = 1.;
while (1. + eps > 1.)
{
epsilon = eps;
eps /= 2.;
}
cutlo_ = sqrt(std::numeric_limits<float>::min()/epsilon);
// Check options
maximal_number_of_iterations_ = (Size)options.setDefaultInteger
(EnergyMinimizer::Option::MAXIMAL_NUMBER_OF_ITERATIONS,
(long)EnergyMinimizer::Default::MAXIMAL_NUMBER_OF_ITERATIONS);
energy_output_frequency_ = (Size)options.setDefaultInteger
(EnergyMinimizer::Option::ENERGY_OUTPUT_FREQUENCY,
(long)EnergyMinimizer::Default::ENERGY_OUTPUT_FREQUENCY);
snapshot_frequency_ = (Size)options.setDefaultInteger
(EnergyMinimizer::Option::SNAPSHOT_FREQUENCY,
(long)EnergyMinimizer::Default::SNAPSHOT_FREQUENCY);
number_of_iterations_ = (Size)options.setDefaultInteger
(EnergyMinimizer::Option::NUMBER_OF_ITERATION,
(long)EnergyMinimizer::Default::NUMBER_OF_ITERATION);
max_same_energy_ = (Size)options.setDefaultInteger
(EnergyMinimizer::Option::MAX_SAME_ENERGY,
(long) EnergyMinimizer::Default::MAX_SAME_ENERGY);
energy_difference_bound_ = options.setDefaultReal
(EnergyMinimizer::Option::ENERGY_DIFFERENCE_BOUND,
EnergyMinimizer::Default::ENERGY_DIFFERENCE_BOUND);
max_gradient_ = options.setDefaultReal
(EnergyMinimizer::Option::MAX_GRADIENT,
EnergyMinimizer::Default::MAX_GRADIENT);
maximum_displacement_ = options.setDefaultReal
(EnergyMinimizer::Option::MAXIMUM_DISPLACEMENT,
EnergyMinimizer::Default::MAXIMUM_DISPLACEMENT);
energy_update_counter_ = 0;
force_update_counter_ = 0;
// Minimizer-specific parts of the setup.
valid_ = specificSetup();
if (!valid_)
{
Log.error() << "EnergyMinimizer::specificSetup failed!" << endl;
}
return valid_;
}
// setup methods
bool ForceField::setup(System& system)
{
unassigned_atoms_.clear();
number_of_errors_ = 0;
// store the specified system
system_ = &system;
// Setup periodic boundary
if (!periodic_boundary.setup())
{
Log.error() << "setup of periodic boundary failed" << endl;
return false;
}
// Update the use_selection_ flag.
use_selection_ = (selection_enabled_ && system_->containsSelection());
// collect the atoms of the system in the atoms_vector_
collectAtoms_(system);
Size old_size = (Size)atoms_.size();
// generate the vector of molecules if periodic boundary is enabled
if (periodic_boundary.isEnabled())
{
periodic_boundary.generateMoleculesVector();
}
// force field specific parts
bool success = false;
try
{
success = specificSetup();
}
catch(...)
{
}
if (!success)
{
Log.error() << "Force Field specificSetup failed!" << endl;
return false;
}
// If specificSetup cleared this array, it wants to tell us
// that it had to change the system a bit (e.g. CHARMM replacing
// hydrogens by united atoms). So, we have to recalculated the vector.
if (atoms_.size() != old_size)
{
collectAtoms_(system);
}
// Call the setup method for each force field component.
vector<ForceFieldComponent*>::iterator it;
for (it = components_.begin(); (it != components_.end()) && success; ++it)
{
success = false;
try
{
success = (*(*it)).setup();
}
catch(...)
{
}
if (!success)
{
Log.error() << "Force Field Component setup of " << (*it)->name_ << " failed!" << endl;
}
}
// ?????
update();
// Remember the setup time
setup_time_stamp_.stamp();
// If the setup failed, our force field becomes invalid!
valid_ = success;
return success;
}