void
OPMSD::output(magnet::xml::XmlStream &XML)
{
//Required to get the correct results
Sim->dynamics->updateAllParticles();
XML << magnet::xml::tag("MSD");
for (const shared_ptr<Species>& sp : Sim->species)
{
double MSD = calcMSD(*sp->getRange()) / Sim->units.unitArea();
XML << magnet::xml::tag("Species")
<< magnet::xml::attr("Name") << sp->getName()
<< magnet::xml::attr("val") << MSD
<< magnet::xml::attr("diffusionCoeff")
<< MSD * Sim->units.unitTime() / (2 * NDIM * Sim->systemTime)
<< magnet::xml::endtag("Species");
}
if (!Sim->topology.empty())
{
XML << magnet::xml::tag("Structures");
for (const shared_ptr<Topology>& topo : Sim->topology)
{
double MSD = calcStructMSD(*topo) / Sim->units.unitArea();
XML << magnet::xml::tag("Structure")
<< magnet::xml::attr("Name") << topo->getName()
<< magnet::xml::attr("val") << MSD
<< magnet::xml::attr("diffusionCoeff")
<< MSD * Sim->units.unitTime() / (2 * NDIM * Sim->systemTime)
<< magnet::xml::endtag("Structure");
}
XML << magnet::xml::endtag("Structures");
}
XML << magnet::xml::endtag("MSD");
}
void
OPMSD::output(magnet::xml::XmlStream &XML)
{
//Required to get the correct results
Sim->dynamics.getLiouvillean().updateAllParticles();
XML << magnet::xml::tag("MSD");
BOOST_FOREACH(const magnet::ClonePtr<Species>& sp, Sim->dynamics.getSpecies())
{
double MSD(calcMSD(*(sp->getRange())));
XML << magnet::xml::tag("Species")
<< magnet::xml::attr("Name") << sp->getName()
<< magnet::xml::attr("val") << MSD
<< magnet::xml::attr("diffusionCoeff")
<< MSD * Sim->dynamics.units().unitTime() / Sim->dSysTime
<< magnet::xml::endtag("Species");
}
if (!Sim->dynamics.getTopology().empty())
{
XML << magnet::xml::tag("Structures");
BOOST_FOREACH(const magnet::ClonePtr<Topology>& topo, Sim->dynamics.getTopology())
{
double MSD(calcStructMSD(*topo));
XML << magnet::xml::tag("Structure")
<< magnet::xml::attr("Name") << topo->getName()
<< magnet::xml::attr("val") << MSD
<< magnet::xml::attr("diffusionCoeff")
<< MSD * Sim->dynamics.units().unitTime() / Sim->dSysTime
<< magnet::xml::endtag("Structure");
}
XML << magnet::xml::endtag("Structures");
}
double
OPMSD::calcD(const IDRange& range) const
{
return calcMSD(range) / (2 * NDIM * Sim->systemTime);
}
