void
IStepped::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"Stepped"))
M_throw() << "Attempting to load Stepped from non Stepped entry";
range.set_ptr(C2Range::getClass(XML,Sim));
try {
intName = XML.getAttribute("Name");
if (!XML.hasNode("Step"))
M_throw() << "No steppings defined for stepped potential "
<< intName;
for (magnet::xml::Node node = XML.fastGetNode("Step"); node.valid(); ++node)
steps.push_back(steppair(node.getAttribute("R").as<double>(),
node.getAttribute("E").as<double>()));
std::sort(steps.rbegin(), steps.rend());
IMultiCapture::loadCaptureMap(XML);
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in CIStepped";
}
if (steps.empty())
M_throw() << "No steps defined in SteppedPotential Interaction with name "
<< getName();
}
void
LOscillatingPlate::operator<<(const magnet::xml::Node& XML)
{
range = shared_ptr<Range>(Range::getClass(XML,Sim));
try {
e = XML.getAttribute("Elasticity").as<double>();
nhat << XML.getNode("Norm");
nhat /= nhat.nrm();
rw0 << XML.getNode("Origin");
rw0 *= Sim->dynamics.units().unitLength();
if (XML.hasAttribute("StrongPlate"))
strongPlate = XML.getAttribute("StrongPlate").as<double>();
omega0 = XML.getAttribute("Omega0").as<double>() / Sim->dynamics.units().unitTime();
sigma = XML.getAttribute("Sigma").as<double>() * Sim->dynamics.units().unitLength();
delta = XML.getAttribute("Delta").as<double>() * Sim->dynamics.units().unitLength();
mass = XML.getAttribute("Mass").as<double>() * Sim->dynamics.units().unitMass();
timeshift = XML.getAttribute("TimeShift").as<double>() * Sim->dynamics.units().unitTime();
localName = XML.getAttribute("Name");
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in LOscillatingPlate";
}
}
void
Topology::operator<<(const magnet::xml::Node& XML)
{
_name = XML.getAttribute("Name");
if (!XML.hasNode("Molecule"))
M_throw() << "Cannot load a Topology which has no molecules!";
}
C2RPair::C2RPair(const magnet::xml::Node& XML, const dynamo::SimData* Sim)
{
if (strcmp(XML.getAttribute("Range"), "Pair"))
M_throw() << "Attempting to load a pair from a non pair";
range1 = shared_ptr<Range>(Range::getClass(XML.getNode("Range1"), Sim));
range2 = shared_ptr<Range>(Range::getClass(XML.getNode("Range2"), Sim));
}
void
IDSMC::operator<<(const magnet::xml::Node& XML)
{
Interaction::operator<<(XML);
_length = Sim->_properties.getProperty(XML.getAttribute("Length"), Property::Units::Length());
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"), Property::Units::Dimensionless());
ICapture::loadCaptureMap(XML);
}
void
OPRGyration::operator<<(const magnet::xml::Node& XML)
{
if (XML.hasAttribute("BinWidthGyration"))
_binWidthGyration = XML.getAttribute("BinWidthGyration").as<double>();
if (XML.hasAttribute("BinWidthGyration"))
_binWidthNematic = XML.getAttribute("BinWidthGyration").as<double>();
}
shared_ptr<Topology>
Topology::getClass(const magnet::xml::Node& XML, dynamo::Simulation* Sim, size_t ID)
{
if (!strcmp(XML.getAttribute("Type"),"Chain"))
return shared_ptr<Topology>(new TChain(XML, Sim, ID));
else
M_throw() << XML.getAttribute("Type")
<< ", Unknown type of Topology encountered";
}
void
SSleep::operator<<(const magnet::xml::Node& XML)
{
sysName = XML.getAttribute("Name");
_sleepVelocity = XML.getAttribute("SleepV").as<double>() * Sim->units.unitVelocity();
_sleepDistance = Sim->units.unitLength() * 0.01;
_sleepTime = Sim->units.unitTime() * 0.0001;
_range = shared_ptr<IDRange>(IDRange::getClass(XML.getNode("IDRange"), Sim));
}
Particle::Particle(const magnet::xml::Node& XML, unsigned long nID):
_ID(nID),
_peculiarTime(0.0),
_state(DEFAULT)
{
if (XML.hasAttribute("Static")) clearState(DYNAMIC);
_pos << XML.getNode("P");
_vel << XML.getNode("V");
}
inline ParticleProperty(const magnet::xml::Node& node):
Property(Property::Units(node.getAttribute("Units").getValue())),
_name(node.getAttribute("Name").getValue())
{
//Move up to the particles nodes, and start loading the property values
for (magnet::xml::Node pNode = node.getParent().getParent()
.getNode("ParticleData").fastGetNode("Pt");
pNode.valid(); ++pNode)
_values.push_back(pNode.getAttribute(_name).as<double>());
}
void
GFrancesco::operator<<(const magnet::xml::Node& XML)
{
globName = XML.getAttribute("Name");
const double MFT = XML.getAttribute("MFT").as<double>() * Sim->units.unitTime();
const double MFTstddev = XML.getAttribute("MFTstddev").as<double>() * Sim->units.unitTime();
_dist = std::normal_distribution<>(MFT, MFTstddev);
_vel = XML.getAttribute("Velocity").as<double>() * Sim->units.unitVelocity();
range = shared_ptr<IDRange>(IDRange::getClass(XML.getNode("IDRange"), Sim));
}
void
SysRescale::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"Rescale"))
M_throw() << "Attempting to load Rescale from "
<< XML.getAttribute("Type") << " entry";
try {
if (XML.hasAttribute("Freq"))
_frequency = XML.getAttribute("Freq").as<size_t>();
if (XML.hasAttribute("kT"))
_kT = XML.getAttribute("kT").as<double>();
_kT *= Sim->dynamics.units().unitEnergy();
if (XML.hasAttribute("TimeStep"))
_timestep = XML.getAttribute("TimeStep").as<double>();
_timestep *= Sim->dynamics.units().unitTime();
sysName = XML.getAttribute("Name");
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in SysRescale";
}
}
void
CSUmbrella::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"Umbrella"))
M_throw() << "Attempting to load Umbrella from a "
<< XML.getAttribute("Type") << " entry";
try {
sysName = XML.getAttribute("Name");
a = XML.getAttribute("a").as<double>()
* Sim->dynamics.units().unitEnergy()
/ Sim->dynamics.units().unitArea();
b = XML.getAttribute("b").as<double>()
* Sim->dynamics.units().unitLength();
delU = XML.getAttribute("delU").as<double>() * Sim->dynamics.units().unitEnergy();
range1.set_ptr(CRange::getClass(XML.getNode("Range1"), Sim));
range2.set_ptr(CRange::getClass(XML.getNode("Range2"), Sim));
if (XML.hasAttribute("currentulevel"))
{
ulevel = XML.getAttribute("currentulevel").as<size_t>();
ulevelset = true;
}
}
catch (boost::bad_lexical_cast &)
{ M_throw() << "Failed a lexical cast in CSUmbrella"; }
}
void
BCLeesEdwards::operator<<(const magnet::xml::Node& XML)
{
if (XML.hasAttribute("DXD"))
_dxd = XML.getAttribute("DXD").as<double>();
_dxd *= Sim->units.unitLength();
if (XML.hasAttribute("Rate"))
_shearRate = XML.getAttribute("Rate").as<double>();
_shearRate /= Sim->units.unitTime();
}
IDPairRangeChainGroups(const magnet::xml::Node& XML, const dynamo::Simulation*):
range1(0),range2(0), length(0)
{
range1 = XML.getAttribute("Start1").as<size_t>();
range2 = XML.getAttribute("Start2").as<size_t>();
length = XML.getAttribute("Length").as<size_t>();
//Guarrantee that they are ordered
if (range1 > range2)
std::swap(range1, range2);
}
void
OPStructureImaging::operator<<(const magnet::xml::Node& XML)
{
if (!XML.hasAttribute("Structure"))
M_throw() << "You must specify the name of the structure to monitor for StructureImaging";
structureName = XML.getAttribute("Structure");
if (XML.hasAttribute("MaxImages"))
imageCount = XML.getAttribute("MaxImages").as<size_t>();
}
shared_ptr<Potential>
Potential::getClass(const magnet::xml::Node& XML)
{
if (!XML.getAttribute("Type").getValue().compare("Stepped"))
return shared_ptr<Potential>(new PotentialStepped(XML));
else if (!XML.getAttribute("Type").getValue().compare("LennardJones"))
return shared_ptr<Potential>(new PotentialLennardJones(XML));
else
M_throw() << XML.getAttribute("Type").getValue()
<< ", Unknown type of Potential encountered";
}
void
IHardSphere::operator<<(const magnet::xml::Node& XML)
{
Interaction::operator<<(XML);
_diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"), Property::Units::Length());
if (XML.hasAttribute("Elasticity"))
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"), Property::Units::Dimensionless());
if (XML.hasAttribute("TangentialElasticity"))
_et = Sim->_properties.getProperty(XML.getAttribute("TangentialElasticity"), Property::Units::Dimensionless());
}
void
Topology::operator<<(const magnet::xml::Node& XML)
{
try { spName = XML.getAttribute("Name"); }
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in CTopology";
}
for (magnet::xml::Node node = XML.fastGetNode("Molecule"); node.valid(); ++node)
ranges.push_back(shared_ptr<Range>(Range::getClass(node, Sim)));
}
void checkNodeNameAttribute(magnet::xml::Node node)
{
//Check for unique names
std::set<std::string> names;
for (; node.valid(); ++node)
{
std::string currentname = node.getAttribute("Name").as<std::string>();
if (names.find(currentname) != names.end())
M_throw() << node.getName() << " at path :" << node.getPath() << "\n Does not have a unique name (Name=\"" << currentname << "\")";
names.insert(currentname);
}
}
void
OPMSDOrientationalCorrelator::operator<<(const magnet::xml::Node& XML)
{
try {
if (XML.hasAttribute("Length"))
length = XML.getAttribute("Length").as<size_t>();
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in OPMSDCorrelator";
}
}
void
ICapture::loadCaptureMap(const magnet::xml::Node& XML)
{
if (XML.hasNode("CaptureMap"))
{
_mapUninitialised = false;
clear();
for (magnet::xml::Node node = XML.getNode("CaptureMap").findNode("Pair"); node.valid(); ++node)
Map::operator[](Map::key_type(node.getAttribute("ID1").as<size_t>(), node.getAttribute("ID2").as<size_t>()))
= node.getAttribute("val").as<size_t>();
}
}
C2RRings::C2RRings(const magnet::xml::Node& XML, const dynamo::SimData*):
range1(0),range2(0), interval(0)
{
if (strcmp(XML.getAttribute("Range"),"Rings"))
M_throw() << "Attempting to load a rings from a non rings";
range1 = XML.getAttribute("Start").as<unsigned long>();
range2 = XML.getAttribute("End").as<unsigned long>();
interval = XML.getAttribute("Interval").as<unsigned long>();
if ((range2-range1 + 1) % interval)
M_throw() << "Range of C2RChains does not split evenly into interval";
}
shared_ptr<Dynamics>
Dynamics::getClass(const magnet::xml::Node& XML, dynamo::Simulation* tmp)
{
if (!strcmp(XML.getAttribute("Type"),"Newtonian"))
return shared_ptr<Dynamics>(new DynNewtonian(tmp));
if (!strcmp(XML.getAttribute("Type"),"NewtonianGravity"))
return shared_ptr<Dynamics>(new DynGravity(tmp, XML));
else if (!strcmp(XML.getAttribute("Type"),"NewtonianMC"))
return shared_ptr<Dynamics>(new DynNewtonianMC(tmp, XML));
else
M_throw() << XML.getAttribute("Type")
<< ", Unknown type of Dynamics encountered";
}
void
OPMFL::operator<<(const magnet::xml::Node& XML)
{
try
{
if (XML.hasAttribute("binwidth"))
binwidth = XML.getAttribute("binwidth").as<double>();
}
catch (boost::bad_lexical_cast&)
{
M_throw() << "Failed a lexical cast in OPMFL";
}
}
shared_ptr<Scheduler>
Scheduler::getClass(const magnet::xml::Node& XML, dynamo::Simulation* const Sim)
{
if (!XML.getAttribute("Type").getValue().compare("NeighbourList"))
return shared_ptr<Scheduler>(new SNeighbourList(XML, Sim));
else if (!XML.getAttribute("Type").getValue().compare("Dumb"))
return shared_ptr<Scheduler>(new SDumb(XML, Sim));
else if (!XML.getAttribute("Type").getValue().compare("SystemOnly"))
return shared_ptr<Scheduler>(new SSystemOnly(XML, Sim));
else
M_throw() << XML.getAttribute("Type").getValue()
<< ", Unknown type of Scheduler encountered";
}
void
IThinThread::operator<<(const magnet::xml::Node& XML)
{
Interaction::operator<<(XML);
_diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"), Property::Units::Length());
_lambda = Sim->_properties.getProperty(XML.getAttribute("Lambda"), Property::Units::Dimensionless());
_wellDepth = Sim->_properties.getProperty(XML.getAttribute("WellDepth"), Property::Units::Energy());
if (XML.hasAttribute("Elasticity"))
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"), Property::Units::Dimensionless());
else
_e = Sim->_properties.getProperty(1.0, Property::Units::Dimensionless());
ICapture::loadCaptureMap(XML);
}
void
CSysGhost::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"Andersen"))
M_throw() << "Attempting to load Andersen from non Andersen entry";
try {
meanFreeTime = XML.getAttribute("MFT").as<double>() * Sim->dynamics.units().unitTime();
Temp = XML.getAttribute("Temperature").as<double>() * Sim->dynamics.units().unitEnergy();
sysName = XML.getAttribute("Name");
if (XML.hasAttribute("SetFrequency") && XML.hasAttribute("SetPoint"))
{
tune = true;
setFrequency = XML.getAttribute("SetFrequency").as<unsigned long long>();
setPoint = boost::lexical_cast<double>(XML.getAttribute("SetPoint"));
}
range = std::tr1::shared_ptr<CRange>(CRange::getClass(XML,Sim));
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in CGGlobal";
}
}
void
Liouvillean::loadParticleXMLData(const magnet::xml::Node& XML)
{
dout << "Loading Particle Data" << std::endl;
bool outofsequence = false;
for (magnet::xml::Node node = XML.getNode("ParticleData").fastGetNode("Pt");
node.valid(); ++node)
{
if (!node.hasAttribute("ID")
|| node.getAttribute("ID").as<size_t>() != Sim->particleList.size())
outofsequence = true;
Particle part(node, Sim->particleList.size());
part.getVelocity() *= Sim->dynamics.units().unitVelocity();
part.getPosition() *= Sim->dynamics.units().unitLength();
Sim->particleList.push_back(part);
}
if (outofsequence)
dout << "Particle ID's out of sequence!\n"
<< "This can result in incorrect capture map loads etc.\n"
<< "Erase any capture maps in the configuration file so they are regenerated." << std::endl;
Sim->N = Sim->particleList.size();
dout << "Particle count " << Sim->N << std::endl;
if (XML.getNode("ParticleData").hasAttribute("OrientationData"))
{
orientationData.resize(Sim->N);
size_t i(0);
for (magnet::xml::Node node = XML.getNode("ParticleData").fastGetNode("Pt");
node.valid(); ++node, ++i)
{
orientationData[i].orientation << node.getNode("U");
orientationData[i].angularVelocity << node.getNode("O");
double oL = orientationData[i].orientation.nrm();
if (!(oL > 0.0))
M_throw() << "Particle ID " << i
<< " orientation vector is zero!";
//Makes the vector a unit vector
orientationData[i].orientation /= oL;
}
}
}
void
LWall::operator<<(const magnet::xml::Node& XML)
{
range = shared_ptr<IDRange>(IDRange::getClass(XML.getNode("IDRange"),Sim));
_diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"), Property::Units::Length());
if (_diameter->getMaxValue() == 0)
M_throw() << "Cannot have a wall with a diameter of zero";
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"), Property::Units::Dimensionless());
sqrtT = 0;
if (XML.hasAttribute("Temperature"))
sqrtT = sqrt(XML.getAttribute("Temperature").as<double>()
* Sim->units.unitEnergy());
if (sqrtT < 0)
M_throw() << "Cannot use negative temperatures on a Wall";
magnet::xml::Node xBrowseNode = XML.getNode("Norm");
localName = XML.getAttribute("Name");
vNorm << xBrowseNode;
if (vNorm.nrm() == 0)
M_throw() << "The normal for the Local Wall named \"" << getName() << "\" has a length of 0. Cannot load";
vNorm /= vNorm.nrm();
xBrowseNode = XML.getNode("Origin");
vPosition << xBrowseNode;
vPosition *= Sim->units.unitLength();
}