void
DynNewtonianMC::swapSystem(Dynamics& oDynamics)
{
#ifdef DYNAMO_DEBUG
if (dynamic_cast<const DynNewtonianMC*>(&oDynamics) == NULL)
M_throw() << "Trying to swap Dynamicss with different derived types!";
#endif
DynNewtonianMC& ol(static_cast<DynNewtonianMC&>(oDynamics));
std::swap(EnergyPotentialStep, ol.EnergyPotentialStep);
std::swap(_W, ol._W);
}
void
GCellsShearing::initialise(size_t nID)
{
ID=nID;
if (!(Sim->dynamics.BCTypeTest<BCLeesEdwards>()))
derr << "You should not use the shearing neighbour list"
<< " in a system without Lees Edwards BC's" << std::endl;
if (overlink != 1) M_throw() << "Cannot shear with overlinking yet";
reinitialise();
}
Event
IHardSphere::getEvent(const Particle &p1, const Particle &p2) const
{
#ifdef DYNAMO_DEBUG
if (!Sim->dynamics->isUpToDate(p1))
M_throw() << "Particle 1 is not up to date: ID1=" << p1.getID() << ", ID2=" << p2.getID() << ", delay1=" << Sim->dynamics->getParticleDelay(p1);
if (!Sim->dynamics->isUpToDate(p2))
M_throw() << "Particle 2 is not up to date: ID1=" << p1.getID() << ", ID2=" << p2.getID() << ", delay2=" << Sim->dynamics->getParticleDelay(p2);
if (p1 == p2)
M_throw() << "You shouldn't pass p1==p2 events to the interactions!";
#endif
const double d = _diameter->getProperty(p1, p2);
const double dt = Sim->dynamics->SphereSphereInRoot(p1, p2, d);
if (dt != HUGE_VAL)
return Event(p1, dt, INTERACTION, CORE, ID, p2);
return Event(p1, HUGE_VAL, INTERACTION, NONE, ID, p2);
}
/*! \brief Destroys any OpenGL resources associated with this
* object.
*/
inline void deinit()
{
#ifdef MAGNET_DEBUG
if (_cl_buffer_acquired)
M_throw() << "Deinitialising a buffer which is acquired by the OpenCL system!";
#endif
_cl_handle = ::cl::BufferGL();
_cl_handle_init = false;
if (_size)
glDeleteBuffersARB(1, &_buffer);
_context = NULL;
_size = 0;
}
void
IThinThread::runEvent(Particle& p1, Particle& p2, const IntEvent& iEvent)
{
++Sim->eventCount;
double d = (_diameter->getProperty(p1.getID())
+ _diameter->getProperty(p2.getID())) * 0.5;
double d2 = d * d;
double e = (_e->getProperty(p1.getID())
+ _e->getProperty(p2.getID())) * 0.5;
double l = (_lambda->getProperty(p1.getID())
+ _lambda->getProperty(p2.getID())) * 0.5;
double ld2 = d * l * d * l;
double wd = (_wellDepth->getProperty(p1.getID())
+ _wellDepth->getProperty(p2.getID())) * 0.5;
switch (iEvent.getType())
{
case CORE:
{
PairEventData retVal(Sim->dynamics->SmoothSpheresColl(iEvent, e, d2, CORE));
IntEvent event(iEvent);
if (!isCaptured(p1, p2))
{
event.setType(STEP_IN);
retVal.setType(STEP_IN);
ICapture::add(p1, p2);
}
(*Sim->_sigParticleUpdate)(retVal);
Sim->ptrScheduler->fullUpdate(p1, p2);
for (shared_ptr<OutputPlugin> & Ptr : Sim->outputPlugins)
Ptr->eventUpdate(event, retVal);
break;
}
case STEP_OUT:
{
PairEventData retVal(Sim->dynamics->SphereWellEvent(iEvent, -wd, ld2, 0));
if (retVal.getType() != BOUNCE) ICapture::remove(p1, p2);
(*Sim->_sigParticleUpdate)(retVal);
Sim->ptrScheduler->fullUpdate(p1, p2);
for (shared_ptr<OutputPlugin> & Ptr : Sim->outputPlugins)
Ptr->eventUpdate(iEvent, retVal);
break;
}
default:
M_throw() << "Unknown collision type";
}
}
int
DynNewtonian::getSquareCellCollision3(const Particle& part, const Vector & origin, const Vector & width) const
{
Vector rpos(part.getPosition() - origin);
Vector vel(part.getVelocity());
Sim->BCs->applyBC(rpos, vel);
int retVal(0);
double time(HUGE_VAL);
#ifdef DYNAMO_DEBUG
for (size_t iDim = 0; iDim < NDIM; ++iDim)
if ((vel[iDim] == 0) && (std::signbit(vel[iDim])))
M_throw() << "You have negative zero velocities, dont use them."
<< "\nPlease think of the neighbour lists.";
#endif
for (size_t iDim = 0; iDim < NDIM; ++iDim)
{
double tmpdt = ((vel[iDim] < 0)
? -rpos[iDim]/vel[iDim]
: (width[iDim]-rpos[iDim]) / vel[iDim]);
if (tmpdt < time)
{
time = tmpdt;
retVal = (vel[iDim] < 0) ? -(iDim+1) : (iDim+1);
}
}
if (((retVal < 0) && (vel[abs(retVal)-1] > 0))
|| ((retVal > 0) && (vel[abs(retVal)-1] < 0)))
M_throw() << "Found an error! retVal " << retVal
<< " vel is " << vel[abs(retVal)-1];
return retVal;
}
IntEvent
IRoughHardSphere::getEvent(const Particle& p1, const Particle& p2) const
{
#ifdef DYNAMO_DEBUG
if (!Sim->dynamics.getLiouvillean().isUpToDate(p1))
M_throw() << "Particle 1 is not up to date";
if (!Sim->dynamics.getLiouvillean().isUpToDate(p2))
M_throw() << "Particle 2 is not up to date";
#endif
#ifdef DYNAMO_DEBUG
if (p1 == p2)
M_throw() << "You shouldn't pass p1==p2 events to the interactions!";
#endif
CPDData colldat(*Sim, p1, p2);
double d2 = (_diameter->getProperty(p1.getID())
+ _diameter->getProperty(p2.getID())) * 0.5;
d2 *= d2;
if (Sim->dynamics.getLiouvillean()
.SphereSphereInRoot(colldat, d2,
p1.testState(Particle::DYNAMIC), p2.testState(Particle::DYNAMIC)))
{
#ifdef DYNAMO_OverlapTesting
if (Sim->dynamics.getLiouvillean().sphereOverlap(colldat, d2))
M_throw() << "Overlapping particles found"
<< ", particle1 " << p1.getID() << ", particle2 "
<< p2.getID() << "\nOverlap = " << (sqrt(colldat.r2) - sqrt(d2))/Sim->dynamics.units().unitLength();
#endif
return IntEvent(p1, p2, colldat.dt, CORE, *this);
}
return IntEvent(p1,p2,HUGE_VAL, NONE, *this);
}
void
SpSphericalTop::operator<<(const magnet::xml::Node& XML)
{
SpPoint::operator<<(XML);
try {
inertiaConstant
= XML.getAttribute("InertiaConstant").as<double>() * Sim->dynamics.units().unitArea();
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in CSSphericalTop";
}
}
void
SpFixedCollider::operator<<(const magnet::xml::Node& XML)
{
range = std::tr1::shared_ptr<CRange>(CRange::getClass(XML, Sim));
try {
spName = XML.getAttribute("Name");
intName = XML.getAttribute("IntName");
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in SpFixedCollider";
}
}
void
IRotatedParallelCubes::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"RotatedParallelCubes"))
M_throw() << "Attempting to load RotatedParallelCubes from "
<< XML.getAttribute("Type") << " entry";
Interaction::operator<<(XML);
try
{
_diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"),
Property::Units::Length());
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"),
Property::Units::Dimensionless());
intName = XML.getAttribute("Name");
magnet::math::operator<<(Rotation, XML.getNode("Rotation"));
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in CIRotatedParallelCubes";
}
}
double eval() const
{
switch (deriv)
{
case 0:
return (rp | nhat) - ( Sigma + wallnHatPosition());
case 1:
return (vp | nhat) - velnHatWall();
case 2:
return Delta * Omega * Omega * std::cos(Omega * t);
default:
M_throw() << "Invalid access";
}
}
size_t padding()
{
switch(_mode)
{
case CPU:
return 1;
case NVIDIA:
return 1024;
case AMD:
return 64 * 256;
default:
M_throw() << "Functor has not yet been built";
}
}
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 << "\"";
}
IDPairRangeChainEnds(const magnet::xml::Node& XML, const dynamo::Simulation*):
rangeStart(0),rangeEnd(0), interval(0)
{
rangeStart = XML.getAttribute("Start").as<size_t>();
rangeEnd = XML.getAttribute("End").as<size_t>();
interval = XML.getAttribute("Interval").as<size_t>();
//Guarrantee that they are ordered
if (rangeStart > rangeEnd) std::swap(rangeStart, rangeEnd);
if ((rangeEnd - rangeStart + 1) % interval)
M_throw() << "Length of range does not split into an integer"
<< " number of intervals";
}
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;
}
}
}
std::unique_ptr<IDRange>
SNeighbourList::getParticleNeighbours(const Particle& part) const
{
#ifdef DYNAMO_DEBUG
if (!std::dynamic_pointer_cast<GNeighbourList>(Sim->globals[NBListID]))
M_throw() << "Not a GNeighbourList!";
#endif
//Grab a reference to the neighbour list
const GNeighbourList& nblist(*static_cast<const GNeighbourList*>(Sim->globals[NBListID].get()));
IDRangeList* range_ptr = new IDRangeList();
nblist.getParticleNeighbours(part, range_ptr->getContainer());
return std::unique_ptr<IDRange>(range_ptr);
}
double max() const
{
switch (deriv)
{
case 1:
return _f1max;
case 2:
return _f2max;
case 3:
return _f3max;
default:
M_throw() << "Invalid access";
}
}
void
ISWSequence::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());
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);
//Load the sequence
sequence.clear();
std::set<size_t> letters;
for (magnet::xml::Node node = XML.getNode("Sequence").findNode("Element");
node.valid(); ++node)
{
if (node.getAttribute("seqID").as<size_t>() != sequence.size())
M_throw() << "Sequence of letters not in order, missing element " << sequence.size();
size_t letter = node.getAttribute("Letter").as<size_t>();
letters.insert(letter);
sequence.push_back(letter);
}
//Initialise all the well depths to 1.0
alphabet.resize(letters.size());
for (std::vector<double>& vec : alphabet)
vec.resize(letters.size(), 0.0);
for (magnet::xml::Node node = XML.getNode("Alphabet").findNode("Word");
node.valid(); ++node)
{
alphabet
.at(node.getAttribute("Letter1").as<size_t>())
.at(node.getAttribute("Letter2").as<size_t>())
= node.getAttribute("Depth").as<double>();
alphabet
.at(node.getAttribute("Letter2").as<size_t>())
.at(node.getAttribute("Letter1").as<size_t>())
= node.getAttribute("Depth").as<double>();
}
}
/*! \brief Method which loads the properties from the XML configuration file.
\param node A xml Node at the root dynamoconfig Node of the config file.
*/
inline PropertyStore& operator<<(const magnet::xml::Node& node)
{
if (node.hasNode("Properties"))
for (magnet::xml::Node propNode = node.getNode("Properties").fastGetNode("Property");
propNode.valid(); ++propNode)
{
if (!std::string("PerParticle").compare(propNode.getAttribute("Type")))
_namedProperties.push_back(Value(new ParticleProperty(propNode)));
else
M_throw() << "Unsupported Property type, " << propNode.getAttribute("Type").getValue();
}
return *this;
}
void
SCENBList::getParticleNeighbourhood(const Particle& part,
const GNeighbourList::nbHoodFunc& func) const
{
#ifdef DYNAMO_DEBUG
if (!isApplicable(part))
M_throw() << "This complexNBlist entry ("
<< name << ") is not valid for this particle ("
<< part.getID() << ") yet it is being used anyway!";
#endif
// static_cast<const GNeighbourList&>(*Sim->globals[nblistID])
// .getParticleNeighbourhood(part, func);
}
void
ILines::runEvent(Particle& p1, Particle& p2, const IntEvent& iEvent)
{
PairEventData retval;
switch (iEvent.getType())
{
case CORE:
{
++Sim->eventCount;
//We have a line interaction! Run it
double e = (_e->getProperty(p1.getID())
+ _e->getProperty(p2.getID())) * 0.5;
double l = (_length->getProperty(p1.getID())
+ _length->getProperty(p2.getID())) * 0.5;
retval = Sim->dynamics->runLineLineCollision(iEvent, e, l);
break;
}
case NBHOOD_IN:
{
ICapture::add(p1, p2);
retval = PairEventData(p1, p2, *Sim->species[p1], *Sim->species[p2], VIRTUAL);
iEvent.setType(VIRTUAL);
break;
}
case NBHOOD_OUT:
{
ICapture::remove(p1, p2);
retval = PairEventData(p1, p2, *Sim->species[p1], *Sim->species[p2], VIRTUAL);
iEvent.setType(VIRTUAL);
break;
}
case VIRTUAL:
{
retval = PairEventData(p1, p2, *Sim->species[p1], *Sim->species[p2], VIRTUAL);
iEvent.setType(VIRTUAL);
break;
}
default:
M_throw() << "Unknown collision type";
}
Sim->_sigParticleUpdate(retval);
Sim->ptrScheduler->fullUpdate(p1, p2);
for (shared_ptr<OutputPlugin> & Ptr : Sim->outputPlugins)
Ptr->eventUpdate(iEvent, retval);
}
void
IRoughHardSphere::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"RoughHardSphere"))
M_throw() << "Attempting to load Hardsphere from non RoughHardSphere entry";
range.set_ptr(C2Range::getClass(XML,Sim));
try
{
_diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"),
Property::Units::Length());
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"),
Property::Units::Dimensionless());
_et = Sim->_properties.getProperty(XML.getAttribute("TangentialElasticity"),
Property::Units::Dimensionless());
intName = XML.getAttribute("Name");
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in IRoughHardSphere";
}
}
shared_ptr<OutputPlugin>
OutputPlugin::getPlugin(std::string Details, const dynamo::Simulation* Sim)
{
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
rapidxml::xml_document<> doc;
rapidxml::xml_node<> *node = doc.allocate_node(rapidxml::node_element,
doc.allocate_string("OP"));
boost::char_separator<char> DetailsSep(":");
boost::char_separator<char> OptionsSep(",");
boost::char_separator<char> ValueSep("=", "", boost::keep_empty_tokens);
tokenizer tokens(Details, DetailsSep);
tokenizer::iterator details_iter = tokens.begin();
node->append_attribute(doc.allocate_attribute
("Type", doc.allocate_string(details_iter->c_str())));
++details_iter;
if (details_iter != tokens.end())
{
tokenizer option_tokens(*details_iter, OptionsSep);
if (++details_iter != tokens.end())
M_throw() << "Two colons in outputplugin options " << *details_iter;
for (tokenizer::iterator options_iter = option_tokens.begin();
options_iter != option_tokens.end(); ++options_iter)
{
tokenizer value_tokens(*options_iter, ValueSep);
tokenizer::iterator value_iter = value_tokens.begin();
std::string opName(*value_iter);
std::string val;
if (++value_iter == value_tokens.end())
//There is no value to save, must be a flag
val = "";
else
val = *value_iter;
node->append_attribute(doc.allocate_attribute
(doc.allocate_string(opName.c_str()),
doc.allocate_string(val.c_str())));
}
}
return getPlugin(magnet::xml::Node(node, NULL), Sim);
}
void
SSystemOnly::initialise()
{
dout << "Reinitialising on collision " << Sim->eventCount << std::endl;
if (Sim->systems.empty())
M_throw() << "A SystemOnlyScheduler used when there are no system events?";
sorter->clear();
sorter->resize(Sim->N+1);
eventCount.clear();
eventCount.resize(Sim->N+1, 0);
sorter->init();
rebuildSystemEvents();
}
void
OPRGyration::replicaExchange(OutputPlugin& plug)
{
std::swap(Sim, static_cast<OPRGyration&>(plug).Sim);
std::list<CTCdata>::iterator iPtr1 = chains.begin(), iPtr2 = static_cast<OPRGyration&>(plug).chains.begin();
#ifdef DYNAMO_DEBUG
if (chains.size() != static_cast<OPRGyration&>(plug).chains.size())
M_throw() << "Size mismatch when exchanging!";
#endif
while (iPtr1 != chains.end())
{
#ifdef DYNAMO_DEBUG
if (iPtr1->chainPtr->getName() != iPtr2->chainPtr->getName())
M_throw() << "Name mismatch while replexing!";
#endif
std::swap(iPtr1->chainPtr, iPtr2->chainPtr);
++iPtr1;
++iPtr2;
}
}
void
IDumbbells::operator<<(const magnet::xml::Node& XML)
{
if (strcmp(XML.getAttribute("Type"),"Dumbbells"))
M_throw() << "Attempting to load Dumbbells from non Dumbbells entry";
Interaction::operator<<(XML);
try
{
_length = Sim->_properties.getProperty(XML.getAttribute("Length"),
Property::Units::Length());
_e = Sim->_properties.getProperty(XML.getAttribute("Elasticity"),
Property::Units::Dimensionless());
_diameter = Sim->_properties.getProperty(XML.getAttribute("Diameter"),
Property::Units::Length());
intName = XML.getAttribute("Name");
ISingleCapture::loadCaptureMap(XML);
}
catch (boost::bad_lexical_cast &)
{
M_throw() << "Failed a lexical cast in CIDumbbells";
}
}
shared_ptr<Scheduler>
Scheduler::getClass(const magnet::xml::Node& XML, dynamo::SimData* const Sim)
{
if (!strcmp(XML.getAttribute("Type"),"NeighbourList"))
return shared_ptr<Scheduler>(new SNeighbourList(XML, Sim));
else if (!strcmp(XML.getAttribute("Type"),"Dumb"))
return shared_ptr<Scheduler>(new SDumb(XML, Sim));
else if (!strcmp(XML.getAttribute("Type"),"SystemOnly"))
return shared_ptr<Scheduler>(new SSystemOnly(XML, Sim));
else if (!strcmp(XML.getAttribute("Type"),"Complex"))
return shared_ptr<Scheduler>(new SComplex(XML, Sim));
else
M_throw() << XML.getAttribute("Type")
<< ", Unknown type of Scheduler encountered";
}
Liouvillean*
Liouvillean::loadClass(const magnet::xml::Node& XML, dynamo::SimData* tmp)
{
if (!strcmp(XML.getAttribute("Type"),"Newtonian"))
return new LNewtonian(tmp);
if (!strcmp(XML.getAttribute("Type"),"NewtonianGravity"))
return new LNewtonianGravity(tmp, XML);
else if (!strcmp(XML.getAttribute("Type"),"SLLOD"))
return new LSLLOD(tmp);
else if (!strcmp(XML.getAttribute("Type"),"NewtonianMC"))
return new LNewtonianMC(tmp, XML);
else
M_throw() << XML.getAttribute("Type")
<< ", Unknown type of Liouvillean encountered";
}
shared_ptr<Dynamics>
Dynamics::getClass(const magnet::xml::Node& XML, dynamo::Simulation* tmp)
{
if (!XML.getAttribute("Type").getValue().compare("Newtonian"))
return shared_ptr<Dynamics>(new DynNewtonian(tmp));
if (!XML.getAttribute("Type").getValue().compare("NewtonianGravity"))
return shared_ptr<Dynamics>(new DynGravity(tmp, XML));
else if (!XML.getAttribute("Type").getValue().compare("NewtonianMC"))
return shared_ptr<Dynamics>(new DynNewtonianMC(tmp, XML));
else if (!XML.getAttribute("Type").getValue().compare("NewtonianMCCMap"))
return shared_ptr<Dynamics>(new DynNewtonianMCCMap(tmp, XML));
else
M_throw() << XML.getAttribute("Type").getValue()
<< ", Unknown type of Dynamics encountered";
}
inline void testAndSetState(const bool newstate, bool& oldstate, const GLenum cap)
{
#ifdef MAGNET_DEBUG
if (glIsEnabled(cap) != oldstate)
M_throw() << "Something is altering the GL state outside of Magnet!";
#endif
if (newstate==oldstate) return;
if (newstate)
glEnable(cap);
else
glDisable(cap);
oldstate = newstate;
}