void
destroy(const IdType classId,
const IdType objectId) {
#ifndef PMI_OPTIMIZE
// check whether the class has an associated constructorCaller
if (classId >= destructorCallers.size())
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "does not have a destructorCaller for class id " \
<< classId << ".");
// check if the object is defined
if (objectId >= objects.size() || objects[objectId] == NULL)
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "does not have an initialized object at object id " \
<< objectId << " (destroy).");
// TODO: check if object is of the right class
PMI_REPORT_OK;
#endif
// delete object
LOG4ESPP_INFO(logger, printWorkerId() \
<< "destroys object id " << objectId \
<< " of class id " << classId << ".");
void* voidPtr = objects[objectId];
DestructorCallerType dc = destructorCallers[classId];
(*dc)(voidPtr);
objects[objectId] = NULL;
}
//////////////////////////////////////////////////
// INLINE IMPLEMENTATION
//////////////////////////////////////////////////
template < typename _DihedralPotential > inline void
FixedQuadrupleListInteractionTemplate < _DihedralPotential >::
addForces() {
LOG4ESPP_INFO(theLogger, "add forces computed by FixedQuadrupleList");
const bc::BC& bc = *getSystemRef().bc; // boundary conditions
for (FixedQuadrupleList::QuadrupleList::Iterator it(*fixedquadrupleList); it.isValid(); ++it) {
Particle &p1 = *it->first;
Particle &p2 = *it->second;
Particle &p3 = *it->third;
Particle &p4 = *it->fourth;
Real3D dist21, dist32, dist43; //
bc.getMinimumImageVectorBox(dist21, p2.position(), p1.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
bc.getMinimumImageVectorBox(dist43, p4.position(), p3.position());
Real3D force1, force2, force3, force4; // result forces
potential->_computeForce(force1, force2, force3, force4,
dist21, dist32, dist43);
p1.force() += force1;
p2.force() += force2; //p2.force() -= force2;
p3.force() += force3;
p4.force() += force4;
}
}
void create(const IdType classId,
const IdType objectId) {
#ifndef PMI_OPTIMIZE
// check whether the class has an associated constructorCaller
if (classId >= constructorCallers.size())
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "does not have a constructorCaller for class id " \
<< classId << ".");
// check whether the object is already defined
if (objectId < objects.size() && objects[objectId] != NULL) {
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "has object id " \
<< objectId << " already defined.");
} else if (objectId >= objects.size()+1) {
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< ": object id " << objectId \
<< " overshoots (size " << objects.size() \
<< ").");
}
PMI_REPORT_OK;
#endif
LOG4ESPP_INFO(logger, printWorkerId() \
<< "creates an instance of class id " \
<< classId << ", object id is " << objectId << ".");
// create object
ConstructorCallerType cc = constructorCallers[classId];
if (objectId == objects.size())
objects.push_back((*cc)());
else
objects[objectId] = (*cc)();
}
void invoke(const IdType classId,
const IdType methodId,
const IdType objectId) {
#ifndef PMI_OPTIMIZE
// check whether the method has an associated methodCaller
if (methodId >= methodCallers.size())
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "does not have a methodCaller for method id " \
<< methodId << ".");
if (objectId >= objects.size() || objects[objectId] == NULL)
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "does not have an initialized object at object id " \
<< objectId << " (invoke).");
// TODO: check if object is of the right class
PMI_REPORT_OK;
#endif
// call method
LOG4ESPP_INFO(logger, printWorkerId() \
<< "invokes method id " << methodId \
<< " of object id " << objectId \
<< " of class id " << classId << ".");
void* voidPtr = objects[objectId];
MethodCallerType mc = methodCallers[methodId];
(*mc)(voidPtr);
}
inline real
FixedTripleListTypesInteractionTemplate<_Potential>::
computeVirial() {
LOG4ESPP_INFO(theLogger, "compute the virial for the FixedTriple List with types");
real w = 0.0;
const bc::BC &bc = *getSystemRef().bc; // boundary conditions
for (FixedTripleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
int type1 = p1.type();
int type2 = p2.type();
int type3 = p3.type();
const Potential &potential = getPotential(type1, type2, type3);
Real3D dist12, dist32;
bc.getMinimumImageVectorBox(dist12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
Real3D force12, force32;
potential._computeForce(force12, force32, dist12, dist32);
w += dist12 * force12 + dist32 * force32;
}
// reduce over all CPUs
real wsum;
boost::mpi::all_reduce(*mpiWorld, w, wsum, std::plus<real>());
return wsum;
}
inline void
FixedQuadrupleListInteractionTemplate < _DihedralPotential >::
computeVirialTensor(Tensor& w) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor of the quadruples");
Tensor wlocal(0.0);
const bc::BC& bc = *getSystemRef().bc;
for (FixedQuadrupleList::QuadrupleList::Iterator it(*fixedquadrupleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
const Particle &p4 = *it->fourth;
Real3D dist21, dist32, dist43;
bc.getMinimumImageVectorBox(dist21, p2.position(), p1.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
bc.getMinimumImageVectorBox(dist43, p4.position(), p3.position());
Real3D force1, force2, force3, force4;
potential->_computeForce(force1, force2, force3, force4,
dist21, dist32, dist43);
// TODO: formulas are not correct yet
wlocal += Tensor(dist21, force1) - Tensor(dist32, force2);
}
// reduce over all CPUs
Tensor wsum(0.0);
boost::mpi::all_reduce(*mpiWorld, (double*)&wlocal, 6, (double*)&wsum, std::plus<double>());
w += wsum;
}
//////////////////////////////////////////////////
// INLINE IMPLEMENTATION
//////////////////////////////////////////////////
template < typename _Potential > inline void
FixedPairListTypesInteractionTemplate < _Potential >::addForces() {
LOG4ESPP_INFO(theLogger, "add forces computed by the FixedPair List");
const bc::BC& bc = *getSystemRef().bc;
for (FixedPairList::PairList::Iterator it(*fixedpairList); it.isValid(); ++it) {
Particle &p1 = *it->first;
Particle &p2 = *it->second;
int type1 = p1.type();
int type2 = p2.type();
const Potential &potential = getPotential(type1, type2);
// shared_ptr<Potential> potential = getPotential(type1, type2);
Real3D force(0.0);
//if(potential._computeForce(force, p1, p2)) {
////if(potential->_computeForce(force, p1, p2)) {
// p1.force() += force;
// p2.force() -= force;
// LOG4ESPP_TRACE(theLogger, "id1=" << p1.id() << " id2=" << p2.id() << " force=" << force);
//}
Real3D dist;
bc.getMinimumImageVectorBox(dist, p1.position(), p2.position());
if(potential._computeForce(force, p1, p2, dist)) {
p1.force() += force;
p2.force() -= force;
}
}
}
inline real
FixedQuadrupleListInteractionTemplate < _DihedralPotential >::
computeVirial() {
LOG4ESPP_INFO(theLogger, "compute scalar virial of the quadruples");
real w = 0.0;
const bc::BC& bc = *getSystemRef().bc; // boundary conditions
for (FixedQuadrupleList::QuadrupleList::Iterator it(*fixedquadrupleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
const Particle &p4 = *it->fourth;
Real3D dist21, dist32, dist43;
bc.getMinimumImageVectorBox(dist21, p2.position(), p1.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
bc.getMinimumImageVectorBox(dist43, p4.position(), p3.position());
Real3D force1, force2, force3, force4;
potential->_computeForce(force1, force2, force3, force4,
dist21, dist32, dist43);
// TODO: formulas are not correct yet?
w += dist21 * force1 + dist32 * force2;
}
real wsum;
boost::mpi::all_reduce(*mpiWorld, w, wsum, std::plus<real>());
return w;
}
template < typename _AngularPotential > inline void
FixedTripleAngleListInteractionTemplate < _AngularPotential >::
computeVirialTensor(Tensor *w, int n) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor of the triples");
std::cout << "Warning! At the moment IK computeVirialTensor for fixed triples does'n work"<<std::endl;
}
inline void
FixedTripleListTypesInteractionTemplate<_Potential>::computeVirialTensor(Tensor &w) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor for the FixedTriple List");
Tensor wlocal(0.0);
const bc::BC& bc = *getSystemRef().bc;
for (FixedTripleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
int type1 = p1.type();
int type2 = p2.type();
int type3 = p3.type();
const Potential &potential = getPotential(type1, type2, type3);
Real3D r12, r32;
bc.getMinimumImageVectorBox(r12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(r32, p3.position(), p2.position());
Real3D force12, force32;
potential._computeForce(force12, force32, r12, r32);
wlocal += Tensor(r12, force12) + Tensor(r32, force32);
}
// reduce over all CPUs
Tensor wsum(0.0);
boost::mpi::all_reduce(*mpiWorld, wlocal, wsum, std::plus<Tensor>());
w += wsum;
}
template < typename _AngularPotential > inline void
FixedTripleAngleListInteractionTemplate < _AngularPotential >::
computeVirialTensor(Tensor& w) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor of the triples");
Tensor wlocal(0.0);
const bc::BC& bc = *getSystemRef().bc;
for (FixedTripleAngleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it){
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
//const Potential &potential = getPotential(0, 0);
Real3D r12, r32;
bc.getMinimumImageVectorBox(r12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(r32, p3.position(), p2.position());
Real3D force12, force32;
real currentAngle = fixedtripleList->getAngle(p1.getId(), p2.getId(), p3.getId());
potential->_computeForce(force12, force32, r12, r32, currentAngle);
wlocal += Tensor(r12, force12) + Tensor(r32, force32);
}
// reduce over all CPUs
Tensor wsum(0.0);
boost::mpi::all_reduce(*mpiWorld, (double*)&wlocal,6, (double*)&wsum, std::plus<double>());
w += wsum;
}
inline real
FixedTripleListTypesInteractionTemplate<_Potential>::
computeEnergy() {
LOG4ESPP_INFO(theLogger, "compute energy of the FixedTriple list pairs");
real e = 0.0;
const bc::BC &bc = *getSystemRef().bc; // boundary conditions
for (FixedTripleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
int type1 = p1.type();
int type2 = p2.type();
int type3 = p3.type();
const Potential &potential = getPotential(type1, type2, type3);
Real3D dist12 = bc.getMinimumImageVector(p1.position(), p2.position());
Real3D dist32 = bc.getMinimumImageVector(p3.position(), p2.position());
e += potential._computeEnergy(dist12, dist32);
LOG4ESPP_TRACE(theLogger, "id1=" << p1.id() << " id2="
<< p2.id() << " id3=" << p3.id() << " potential energy=" << e);
}
// reduce over all CPUs
real esum;
boost::mpi::all_reduce(*mpiWorld, e, esum, std::plus<real>());
return esum;
}
template < typename _AngularPotential > inline real
FixedTripleAngleListInteractionTemplate < _AngularPotential >::
computeVirial() {
LOG4ESPP_INFO(theLogger, "compute scalar virial of the triples");
const bc::BC& bc = *getSystemRef().bc;
real w = 0.0;
for (FixedTripleAngleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
//const Potential &potential = getPotential(p1.type(), p2.type());
const espresso::bc::BC& bc = *getSystemRef().bc;
Real3D dist12, dist32;
bc.getMinimumImageVectorBox(dist12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
Real3D force12, force32;
real currentAngle = fixedtripleList->getAngle(p1.getId(), p2.getId(), p3.getId());
potential->_computeForce(force12, force32, dist12, dist32, currentAngle);
w += dist12 * force12 + dist32 * force32;
}
real wsum;
boost::mpi::all_reduce(*mpiWorld, w, wsum, std::plus<real>());
return wsum;
}
template < typename _Potential > inline real
FixedPairListTypesInteractionTemplate < _Potential >::
computeVirial() {
LOG4ESPP_INFO(theLogger, "compute the virial for the Fixed Pair List with types");
std::cout << "Warning! computeVirial in FixedPairListTypesInteractionTemplate has not been tested." << std::endl;
real w = 0.0;
const bc::BC& bc = *getSystemRef().bc; // boundary conditions
for (FixedPairList::PairList::Iterator it(*fixedpairList);
it.isValid(); ++it) {
Particle &p1 = *it->first;
Particle &p2 = *it->second;
int type1 = p1.type();
int type2 = p2.type();
const Potential &potential = getPotential(type1, type2);
// shared_ptr<Potential> potential = getPotential(type1, type2);
Real3D force(0.0, 0.0, 0.0);
Real3D r21;
bc.getMinimumImageVectorBox(r21, p1.position(), p2.position());
if(potential._computeForce(force, p1, p2, r21)) {
// if(potential->_computeForce(force, p1, p2)) {
//Real3D r21 = p1.position() - p2.position();
w = w + r21 * force;
}
}
// reduce over all CPUs
real wsum;
boost::mpi::all_reduce(*mpiWorld, w, wsum, std::plus<real>());
return wsum;
}
inline real
FixedPairListTypesInteractionTemplate < _Potential >::
computeEnergy() {
LOG4ESPP_INFO(theLogger, "compute energy of the FixedPair list pairs");
real e = 0.0;
real es = 0.0;
const bc::BC& bc = *getSystemRef().bc; // boundary conditions
for (FixedPairList::PairList::Iterator it(*fixedpairList);
it.isValid(); ++it) {
Particle &p1 = *it->first;
Particle &p2 = *it->second;
int type1 = p1.type();
int type2 = p2.type();
const Potential &potential = getPotential(type1, type2);
// shared_ptr<Potential> potential = getPotential(type1, type2);
Real3D r21;
bc.getMinimumImageVectorBox(r21, p1.position(), p2.position());
//e = potential._computeEnergy(p1, p2);
// e = potential->_computeEnergy(p1, p2);
e = potential._computeEnergy(p1,p2,r21);
es += e;
LOG4ESPP_TRACE(theLogger, "id1=" << p1.id() << " id2=" << p2.id() << " potential energy=" << e);
//std::cout << "id1=" << p1.id() << " id2=" << p2.id() << " potential energy=" << e << std::endl;
}
// reduce over all CPUs
real esum;
boost::mpi::all_reduce(*mpiWorld, es, esum, std::plus<real>());
return esum;
}
inline real
FixedQuadrupleListInteractionTemplate < _DihedralPotential >::
computeEnergy() {
LOG4ESPP_INFO(theLogger, "compute energy of the quadruples");
const bc::BC& bc = *getSystemRef().bc; // boundary conditions
real e = 0.0;
for (FixedQuadrupleList::QuadrupleList::Iterator it(*fixedquadrupleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
const Particle &p4 = *it->fourth;
Real3D dist21, dist32, dist43; //
bc.getMinimumImageVectorBox(dist21, p2.position(), p1.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
bc.getMinimumImageVectorBox(dist43, p4.position(), p3.position());
e += potential->_computeEnergy(dist21, dist32, dist43);
}
real esum;
boost::mpi::all_reduce(*mpiWorld, e, esum, std::plus<real>());
return esum;
}
FixedListComm::~FixedListComm() {
//std::cout << "~fixedlist" << std::endl;
LOG4ESPP_INFO(theLogger, "~FixedListComm");
con1.disconnect();
con2.disconnect();
con3.disconnect();
}
void FixedListComm::onParticlesChanged() {
LOG4ESPP_INFO(theLogger, "rebuild local bond list from global\n");
//this->clear();
longint lastpid1 = -1;
Particle* p, * pK;
std::vector<Particle*> tmp;
GlobalList::const_iterator it = globalLists.begin();
int size = it->second.size()+1;
if (size == 2) this->PairList::clear();
else if (size == 3) this->TripleList::clear();
else if (size == 4) this->QuadrupleList::clear();
// iterate through keys of map
for (;it != globalLists.end(); ++it) {
if (it->first != lastpid1) { // don't check same pid twice
pK = storage->lookupRealParticle(it->first);
if (pK == NULL) {
printf("SERIOUS ERROR: particle %d not available\n", it->first);
}
lastpid1 = it->first;
}
// iterate through vector in map
for (pvec::const_iterator it2 = it->second.begin(); it2!=it->second.end(); ++it2) {
p = storage->lookupLocalParticle(*it2);
if (p == NULL) {
printf("SERIOUS ERROR: particle %d not available\n", *it2);
}
tmp.push_back(p);
}
// add the particles
if (size == 2) this->PairList::add(pK, tmp.at(0));
else if (size == 3) this->TripleList::add(pK, tmp.at(0), tmp.at(1));
else if (size == 4) this->QuadrupleList::add(pK, tmp.at(0), tmp.at(1), tmp.at(2));
tmp.clear();
}
LOG4ESPP_INFO(theLogger, "regenerated local fixed list from global list");
}
FixedListComm::FixedListComm(shared_ptr <storage::Storage> _storage)
: storage(_storage), globalLists(){
//std::cout << "fixedlist" << std::endl;
LOG4ESPP_INFO(theLogger, "construct FixedPairList");
con1 = storage->beforeSendParticles.connect
(boost::bind(&FixedListComm::beforeSendParticles, this, _1, _2));
con2 = storage->afterRecvParticles.connect
(boost::bind(&FixedListComm::afterRecvParticles, this, _1, _2));
con3 = storage->onParticlesChanged.connect
(boost::bind(&FixedListComm::onParticlesChanged, this));
}
bool FixedListComm::add(pvec pids) {
// ADD THE LOCAL PARTICLES
Particle* p;
std::vector<Particle*> tmp;
pvec::iterator it = pids.begin();
p = storage->lookupRealParticle(*it); //wrong, last particle is key
if (!p) return false;
tmp.push_back(p);
for (++it; it!=pids.end(); ++it) {
p = storage->lookupLocalParticle(*it);
if (!p)
// Particle does not exist here, return false
return false;
tmp.push_back(p);
}
//add(tmp);
if (pids.size() == 2) this->PairList::add(tmp.at(1), tmp.at(0));
else if (pids.size() == 3) this->TripleList::add(tmp.at(0), tmp.at(2), tmp.at(1));
else if (pids.size() == 4) this->QuadrupleList::add(tmp.at(3), tmp.at(0), tmp.at(1), tmp.at(2));
tmp.clear();
// ADD THE GLOBAL PARTICLES
longint pidK = pids.back(); // last pid is key
pids.pop_back(); // remove last pid
std::pair<GlobalList::const_iterator, GlobalList::const_iterator>
equalRange = globalLists.equal_range(pidK);
// see whether the particle already has pairs
if (equalRange.first == globalLists.end()) {
// it hasn't, insert the new pair
//globalLists.insert(make_pair(pid1, pid2));
globalLists.insert(make_pair(pidK, pids));
}
else {// otherwise test whether the pair already exists
for (GlobalList::const_iterator it = equalRange.first;
it != equalRange.second; ++it) {
if (it->second == pids) {
// TODO: Pair already exists, generate error!
}
// if not, insert the new pair
globalLists.insert(equalRange.first, make_pair(pidK, pids));
}
}
LOG4ESPP_INFO(theLogger, "added fixed pair to global pair list");
return true;
}
void FixedListComm::beforeSendParticles
(ParticleList& pl, OutBuffer& buf) {
std::vector<longint> toSend;
// loop over the particle list
for (ParticleList::Iterator pit(pl); pit.isValid(); ++pit) {
longint pid = pit->id();
LOG4ESPP_DEBUG(theLogger, "send particle with pid " << pid << ", find pairs");
// find all particles that involve this particle id
int n = globalLists.count(pid);
if (n > 0) {
std::pair<GlobalList::const_iterator,
GlobalList::const_iterator>
equalRange = globalLists.equal_range(pid);
// get the length of the vector in the map
int l = equalRange.first->second.size();
toSend.reserve(toSend.size()+3+n*l);
// first write the pid of the first particle
toSend.push_back(pid);
// then the number of partners
toSend.push_back(n);
// then the size of the vector
toSend.push_back(l);
// and then the pids of the partners
for (GlobalList::const_iterator it = equalRange.first;
it != equalRange.second; ++it) {
// iterate through vector to add pids
for (pvec::const_iterator it2=it->second.begin();
it2!=it->second.end(); ++it2) {
toSend.push_back(*it2);
LOG4ESPP_DEBUG(theLogger, "send global bond: pid "
<< pid << " and its vector");
}
}
// delete all of these pairs from the global list
globalLists.erase(equalRange.first, equalRange.second);
}
}
// send the list
buf.write(toSend);
LOG4ESPP_INFO(theLogger, "prepared fixed pair list before send particles");
}
inline void
FixedQuadrupleListTypesInteractionTemplate<_DihedralPotential>::
computeVirialTensor(Tensor &w, real z) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor of the quadruples");
Tensor wlocal(0.0);
const bc::BC &bc = *getSystemRef().bc;
std::cout << "Warning!!! computeVirialTensor in specified volume doesn't work for "
"FixedQuadrupleListTypesInteractionTemplate at the moment" << std::endl;
for (FixedQuadrupleList::QuadrupleList::Iterator it(*fixedquadrupleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
const Particle &p4 = *it->fourth;
longint type1 = p1.type();
longint type2 = p2.type();
longint type3 = p3.type();
longint type4 = p4.type();
const Potential &potential = getPotential(type1, type2, type3, type4);
Real3D dist21, dist32, dist43;
bc.getMinimumImageVectorBox(dist21, p2.position(), p1.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
bc.getMinimumImageVectorBox(dist43, p4.position(), p3.position());
Real3D force1, force2, force3, force4;
potential.computeForce(force1, force2, force3, force4,
dist21, dist32, dist43);
// TODO: formulas are not correct yet
wlocal += Tensor(dist21, force1) - Tensor(dist32, force2);
}
// reduce over all CPUs
Tensor wsum(0.0);
boost::mpi::all_reduce(*mpiWorld, (double *) &wlocal, 6, (double *) &wsum, std::plus<double>());
w += wsum;
}
void associateMethod(const string &name, const IdType id) {
if (methodCallersByName().find(name) == methodCallersByName().end())
PMI_REPORT_USER_ERROR(printWorkerId() \
<< "has not registered method \"" << name \
<< "\" (methodCaller undefined).");
#ifndef PMI_OPTIMIZE
// check whether the vector has the right size
if (methodCallers.size() != id)
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "has " << methodCallers.size() \
<< " associated methods, but received id " \
<< id << " as the next id.");
PMI_REPORT_OK;
#endif
LOG4ESPP_INFO(logger, printWorkerId() \
<< "associates method \"" \
<< name << "\" to method id " << id << ".");
MethodCallerType mc = methodCallersByName()[name];
methodCallers.push_back(mc);
methodCallersByName().erase(name);
}
//////////////////////////////////////////////////
// INLINE IMPLEMENTATION
//////////////////////////////////////////////////
template < typename _AngularPotential > inline void
FixedTripleAngleListInteractionTemplate <_AngularPotential>::
addForces() {
LOG4ESPP_INFO(theLogger, "add forces computed by FixedTripleAngleList");
const bc::BC& bc = *getSystemRef().bc; // boundary conditions
for (FixedTripleAngleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
Particle &p1 = *it->first;
Particle &p2 = *it->second;
Particle &p3 = *it->third;
//const Potential &potential = getPotential(p1.type(), p2.type());
Real3D dist12, dist32;
bc.getMinimumImageVectorBox(dist12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
Real3D force12, force32;
real currentAngle = fixedtripleList->getAngle(p1.getId(), p2.getId(), p3.getId());
potential->_computeForce(force12, force32, dist12, dist32, currentAngle);
p1.force() += force12;
p2.force() -= force12 + force32;
p3.force() += force32;
}
}
template < typename _AngularPotential > inline real
FixedTripleAngleListInteractionTemplate < _AngularPotential >::
computeEnergy() {
LOG4ESPP_INFO(theLogger, "compute energy of the triples");
const bc::BC& bc = *getSystemRef().bc;
real e = 0.0;
for (FixedTripleAngleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
//const Potential &potential = getPotential(p1.type(), p2.type());
Real3D dist12 = bc.getMinimumImageVector(p1.position(), p2.position());
Real3D dist32 = bc.getMinimumImageVector(p3.position(), p2.position());
real currentAngle = fixedtripleList->getAngle(p1.getId(), p2.getId(), p3.getId());
e += potential->_computeEnergy(dist12, dist32, currentAngle);
}
real esum;
boost::mpi::all_reduce(*mpiWorld, e, esum, std::plus<real>());
return esum;
}
template < typename _AngularPotential > inline void
FixedTripleAngleListInteractionTemplate < _AngularPotential >::
computeVirialTensor(Tensor& w, real z) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor of the triples");
std::cout << "Warning! At the moment IK computeVirialTensor for fixed triples does'n work"<<std::endl;
/*
Tensor wlocal(0.0);
const bc::BC& bc = *getSystemRef().bc;
for (FixedTripleAngleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it){
const Particle &p1 = *it->first;
const Particle &p2 = *it->second;
const Particle &p3 = *it->third;
Real3D p2pos = p2.position();
if( (p2pos[0]>xmin && p2pos[0]<xmax &&
p2pos[1]>ymin && p2pos[1]<ymax &&
p2pos[2]>zmin && p2pos[2]<zmax) ){
Real3D r12, r32;
bc.getMinimumImageVectorBox(r12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(r32, p3.position(), p2.position());
Real3D force12, force32;
real currentAngle = fixedtripleList->getAngle(p1.getId(), p2.getId(), p3.getId());
potential->_computeForce(force12, force32, r12, r32, currentAngle);
wlocal += Tensor(r12, force12) + Tensor(r32, force32);
}
}
// reduce over all CPUs
Tensor wsum(0.0);
boost::mpi::all_reduce(*mpiWorld, (double*)&wlocal, 6, (double*)&wsum, std::plus<double>());
w += wsum;
*/
}
void FixedListComm::afterRecvParticles
(ParticleList &pl,InBuffer& buf) {
std::vector<longint> received, pids;
int n, l, tl;
longint pid1;
GlobalList::iterator it = globalLists.begin();
// receive the bond list
buf.read(received);
int size = received.size();
int i = 0;
while (i < size) {
// unpack the list
pid1 = received[i++];
n = received[i++];
l = received[i++];
LOG4ESPP_DEBUG(theLogger,
"recv particle " << pid1 << ", has " << n << " global pairs");
for (; n > 0; --n) {
for (tl = l; tl > 0; --tl) {
pids.push_back(received[i++]);
}
// add the bond to the global list
LOG4ESPP_DEBUG(theLogger, "received vector for pid " << pid1);
it = globalLists.insert(it, std::make_pair(pid1, pids));
pids.clear();
}
}
if (i != size) {
LOG4ESPP_ERROR(theLogger,
"recv particles might have read garbage\n");
}
LOG4ESPP_INFO(theLogger,
"received fixed particle list after receive particles");
}
inline void
FixedTripleListTypesInteractionTemplate<_Potential>::addForces() {
LOG4ESPP_INFO(theLogger, "add forces computed by the FixedTriple List");
const bc::BC &bc = *getSystemRef().bc;
for (FixedTripleList::TripleList::Iterator it(*fixedtripleList); it.isValid(); ++it) {
Particle &p1 = *it->first;
Particle &p2 = *it->second;
Particle &p3 = *it->third;
int type1 = p1.type();
int type2 = p2.type();
int type3 = p3.type();
const Potential &potential = getPotential(type1, type2, type3);
Real3D dist12, dist32;
bc.getMinimumImageVectorBox(dist12, p1.position(), p2.position());
bc.getMinimumImageVectorBox(dist32, p3.position(), p2.position());
Real3D force12, force32;
potential._computeForce(force12, force32, dist12, dist32);
p1.force() += force12;
p2.force() -= force12 + force32;
p3.force() += force32;
}
}
void associateClass(const string &name, const IdType id) {
if (constructorCallersByName().find(name) ==
constructorCallersByName().end())
PMI_REPORT_USER_ERROR(printWorkerId() \
<< "has not registered class \"" << name \
<< "\" (constructor undefined).");
#ifndef PMI_OPTIMIZE
if (destructorCallersByName().find(name) == destructorCallersByName().end())
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "has not registered class \"" << name \
<< "\" (constructur defined, but destructor undefined).");
// check whether the vector has the right size
if (constructorCallers.size() != id)
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "has " << constructorCallers.size() \
<< " associated constructors, but received id " \
<< id << " as the next id.");
// check whether the vector has the right size
if (destructorCallers.size() != id)
PMI_REPORT_INTL_ERROR(printWorkerId() \
<< "has " << destructorCallers.size() \
<< " associated destructors, but received id " \
<< id << " as the next id.");
PMI_REPORT_OK;
#endif
LOG4ESPP_INFO(logger, printWorkerId() \
<< "associates class \"" \
<< name << "\" to class id " << id << ".");
ConstructorCallerType cc = constructorCallersByName()[name];
constructorCallers.push_back(cc);
constructorCallersByName().erase(name);
DestructorCallerType dc = destructorCallersByName()[name];
destructorCallers.push_back(dc);
destructorCallersByName().erase(name);
}
inline void
FixedTripleListTypesInteractionTemplate<_Potential>::
computeVirialTensor(Tensor *w, int n) {
LOG4ESPP_INFO(theLogger, "compute the virial tensor for the FixedTriple List");
}