Example #1
0
  void 
  TChain::operator<<(const magnet::xml::Node& XML) 
  {
    Topology::operator<<(XML);

    for (magnet::xml::Node node = XML.findNode("Molecule"); node.valid(); ++node)
      ranges.push_back(shared_ptr<IDRange>(IDRange::getClass(node.getNode("IDRange"), Sim)));
  
    size_t Clength = (*ranges.begin())->size();
    for (const shared_ptr<IDRange>& nRange : ranges)
      if (nRange->size() != Clength)
	M_throw() << "Size mismatch in loading one of the ranges in Chain topology \"" 
		  << _name << "\"";
  }
Example #2
0
  void 
  LBoundary::operator<<(const magnet::xml::Node& XML)
  {
    range = shared_ptr<IDRange>(IDRange::getClass(XML.getNode("IDRange"),Sim));
    localName = XML.getAttribute("Name");

    _oscillationData._origin << XML.getNode("Origin");
    _oscillationData._origin *= Sim->units.unitLength();
    _diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"), Property::Units::Length());
    if (_diameter->getMaxValue() == 0)
      M_throw() << "Cannot have a boundary with a diameter of zero";

    _oscillationData._amplitude = Vector();
    _oscillationData._freq = 0;
    _oscillationData._t_shift = 0;
    
    const size_t data_count = XML.hasNode("Amplitude") + XML.hasAttribute("Frequency") + XML.hasAttribute("Phase");
    if ((data_count != 3) && (data_count != 0))
      M_throw() << "For oscillating walls you must have an Amplitude, Frequency, and Phase specified."
		<< XML.getPath();

    if (data_count == 3) {
      _oscillationData._freq = XML.getAttribute("Frequency").as<double>() / Sim->units.unitTime();
      _oscillationData._t_shift = XML.getAttribute("Phase").as<double>() * Sim->units.unitTime();
      _oscillationData._amplitude << XML.getNode("Amplitude");
      _oscillationData._amplitude *= Sim->units.unitLength();
    }

    _kT = 0;
    if (XML.hasAttribute("kT")) {
      if (data_count == 3)
	M_throw() << "Cannot have both a thermalised wall and a oscillating wall" 
		  << XML.getPath();
      
      _kT = XML.getAttribute("kT").as<double>() * Sim->units.unitEnergy();
    }

    if (_kT < 0)
      M_throw() << "Temperature is less than zero" << XML.getPath();

    for (magnet::xml::Node node = XML.findNode("Object"); node.valid(); ++node)
      _objects.push_back(boundary::Object::getClass(node, Sim, _oscillationData));

    if (_objects.empty())
      M_throw() << "Boundary Locals must have at least one Object.\n" << XML.getPath();
  }