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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include "brains/SimInfo.hpp" |
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namespace oopse { |
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|
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//----------------------------------------------------------------------------// |
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void IgnoreVisitor::visit(Atom *atom) { |
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if (isIgnoreType(atom->getType())) |
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internalVisit(atom); |
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} |
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void WrappingVisitor::visit(Atom *atom) { |
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internalVisit(atom); |
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} |
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|
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void IgnoreVisitor::visit(DirectionalAtom *datom) { |
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if (isIgnoreType(datom->getType())) |
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internalVisit(datom); |
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} |
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void WrappingVisitor::visit(DirectionalAtom *datom) { |
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internalVisit(datom); |
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} |
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|
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void IgnoreVisitor::visit(RigidBody *rb) { |
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std::vector<Atom *> myAtoms; |
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std::vector<Atom *>::iterator atomIter; |
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AtomInfo * atomInfo; |
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void WrappingVisitor::visit(RigidBody *rb) { |
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internalVisit(rb); |
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} |
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|
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if (isIgnoreType(rb->getType())) { |
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internalVisit(rb); |
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|
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myAtoms = rb->getAtoms(); |
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|
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for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
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internalVisit(*atomIter); |
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} |
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} |
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|
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bool IgnoreVisitor::isIgnoreType(const std::string&name) { |
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return itList.find(name) != itList.end() ? true : false; |
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} |
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|
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void IgnoreVisitor::internalVisit(StuntDouble *sd) { |
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info->getSelectionManager()->clearSelection(sd); |
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//GenericData *data; |
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//data = sd->getPropertyByName("IGNORE"); |
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// |
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////if this stuntdoulbe is already marked as ignore just skip it |
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//if (data == NULL) { |
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// data = new GenericData; |
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// data->setID("IGNORE"); |
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// sd->addProperty(data); |
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//} |
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} |
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|
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const std::string IgnoreVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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std::set<std::string>::iterator i; |
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|
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sprintf(buffer, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer, "Visitor Description: ignore stuntdoubles\n"); |
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result += buffer; |
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|
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//print the ignore type list |
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sprintf(buffer, "Ignore type list contains below types:\n"); |
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result += buffer; |
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|
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for( i = itList.begin(); i != itList.end(); ++i ) { |
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sprintf(buffer, "%s\t", i->c_str()); |
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result += buffer; |
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} |
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|
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sprintf(buffer, "\n"); |
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result += buffer; |
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|
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sprintf(buffer, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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|
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//----------------------------------------------------------------------------// |
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|
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void WrappingVisitor::visit(Atom *atom) { |
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internalVisit(atom); |
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} |
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|
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void WrappingVisitor::visit(DirectionalAtom *datom) { |
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internalVisit(datom); |
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} |
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|
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void WrappingVisitor::visit(RigidBody *rb) { |
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internalVisit(rb); |
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} |
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|
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void WrappingVisitor::internalVisit(StuntDouble *sd) { |
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void WrappingVisitor::internalVisit(StuntDouble *sd) { |
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GenericData * data; |
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AtomData * atomData; |
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AtomInfo * atomInfo; |
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data = sd->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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atomData = dynamic_cast<AtomData *>(data); |
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|
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if (atomData == NULL) |
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return; |
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if (atomData == NULL) |
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return; |
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} else |
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return; |
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return; |
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|
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Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
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|
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for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) { |
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currSnapshot->wrapVector(atomInfo->pos); |
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currSnapshot->wrapVector(atomInfo->pos); |
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} |
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} |
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} |
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|
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const std::string WrappingVisitor::toString() { |
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const std::string WrappingVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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|
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result += buffer; |
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|
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return result; |
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} |
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} |
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|
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//----------------------------------------------------------------------------// |
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//----------------------------------------------------------------------------// |
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|
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ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
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ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
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BaseVisitor() { |
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this->info = info; |
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visitorName = "ReplicateVisitor"; |
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this->replicateOpt = opt; |
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this->info = info; |
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visitorName = "ReplicateVisitor"; |
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this->replicateOpt = opt; |
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|
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//generate the replicate directions |
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for( int i = 0; i <= replicateOpt[0]; i++ ) { |
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//generate the replicate directions |
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for( int i = 0; i <= replicateOpt[0]; i++ ) { |
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for( int j = 0; j <= replicateOpt[1]; j++ ) { |
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for( int k = 0; k <= replicateOpt[2]; k++ ) { |
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//skip original frame |
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if (i == 0 && j == 0 && k == 0) { |
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continue; |
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} else { |
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dir.push_back(Vector3i(i, j, k)); |
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} |
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} |
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for( int k = 0; k <= replicateOpt[2]; k++ ) { |
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//skip original frame |
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if (i == 0 && j == 0 && k == 0) { |
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continue; |
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} else { |
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dir.push_back(Vector3i(i, j, k)); |
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} |
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} |
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} |
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} |
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} |
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|
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} |
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} |
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|
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void ReplicateVisitor::visit(Atom *atom) { |
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internalVisit(atom); |
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} |
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void ReplicateVisitor::visit(Atom *atom) { |
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internalVisit(atom); |
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} |
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|
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void ReplicateVisitor::visit(DirectionalAtom *datom) { |
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internalVisit(datom); |
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} |
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void ReplicateVisitor::visit(DirectionalAtom *datom) { |
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internalVisit(datom); |
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} |
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|
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void ReplicateVisitor::visit(RigidBody *rb) { |
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internalVisit(rb); |
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} |
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void ReplicateVisitor::visit(RigidBody *rb) { |
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internalVisit(rb); |
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} |
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|
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void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
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void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
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GenericData * data; |
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AtomData * atomData; |
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|
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data = sd->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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atomData = dynamic_cast<AtomData *>(data); |
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|
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if (atomData == NULL) { |
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return; |
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} |
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if (atomData == NULL) { |
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return; |
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} |
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} else { |
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return; |
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return; |
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} |
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|
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Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
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std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
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|
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replicate(atomInfoList, atomData, box); |
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} |
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} |
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|
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void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
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void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
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AtomInfo* newAtomInfo; |
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std::vector<Vector3i>::iterator dirIter; |
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std::vector<AtomInfo *>::iterator i; |
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for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
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for( i = infoList.begin(); i != infoList.end(); i++ ) { |
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newAtomInfo = new AtomInfo(); |
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*newAtomInfo = *(*i); |
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for( i = infoList.begin(); i != infoList.end(); i++ ) { |
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newAtomInfo = new AtomInfo(); |
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*newAtomInfo = *(*i); |
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|
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for( int j = 0; j < 3; j++ ) |
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newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
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for( int j = 0; j < 3; j++ ) |
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newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
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|
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data->addAtomInfo(newAtomInfo); |
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} |
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data->addAtomInfo(newAtomInfo); |
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} |
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} // end for(dirIter) |
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} |
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} |
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|
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const std::string ReplicateVisitor::toString() { |
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const std::string ReplicateVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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std::set<std::string>::iterator i; |
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result += buffer; |
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|
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return result; |
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} |
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} |
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|
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//----------------------------------------------------------------------------// |
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//----------------------------------------------------------------------------// |
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|
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XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) : |
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BaseVisitor() { |
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this->info = info; |
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visitorName = "XYZVisitor"; |
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this->printDipole = printDipole; |
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} |
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XYZVisitor::XYZVisitor(SimInfo *info) : |
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BaseVisitor(), seleMan(info), evaluator(info){ |
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this->info = info; |
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visitorName = "XYZVisitor"; |
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|
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void XYZVisitor::visit(Atom *atom) { |
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if (isSelected(atom)) |
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internalVisit(atom); |
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} |
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evaluator.loadScriptString("select all"); |
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|
227 |
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void XYZVisitor::visit(DirectionalAtom *datom) { |
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if (isSelected(datom)) |
229 |
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internalVisit(datom); |
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} |
227 |
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if (!evaluator.isDynamic()) { |
228 |
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seleMan.setSelectionSet(evaluator.evaluate()); |
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} |
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|
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void XYZVisitor::visit(RigidBody *rb) { |
317 |
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if (isSelected(rb)) |
318 |
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internalVisit(rb); |
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} |
231 |
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} |
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|
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void XYZVisitor::internalVisit(StuntDouble *sd) { |
233 |
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XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
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BaseVisitor(), seleMan(info), evaluator(info) { |
235 |
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this->info = info; |
236 |
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visitorName = "XYZVisitor"; |
237 |
> |
|
238 |
> |
evaluator.loadScriptString(script); |
239 |
> |
|
240 |
> |
if (!evaluator.isDynamic()) { |
241 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
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} |
243 |
> |
|
244 |
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} |
245 |
> |
|
246 |
> |
void XYZVisitor::visit(Atom *atom) { |
247 |
> |
if (isSelected(atom)) |
248 |
> |
internalVisit(atom); |
249 |
> |
} |
250 |
> |
|
251 |
> |
void XYZVisitor::visit(DirectionalAtom *datom) { |
252 |
> |
if (isSelected(datom)) |
253 |
> |
internalVisit(datom); |
254 |
> |
} |
255 |
> |
|
256 |
> |
void XYZVisitor::visit(RigidBody *rb) { |
257 |
> |
if (isSelected(rb)) |
258 |
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internalVisit(rb); |
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} |
260 |
> |
|
261 |
> |
void XYZVisitor::update() { |
262 |
> |
//if dynamic, we need to re-evaluate the selection |
263 |
> |
if (evaluator.isDynamic()) { |
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seleMan.setSelectionSet(evaluator.evaluate()); |
265 |
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} |
266 |
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} |
267 |
> |
|
268 |
> |
void XYZVisitor::internalVisit(StuntDouble *sd) { |
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GenericData * data; |
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AtomData * atomData; |
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AtomInfo * atomInfo; |
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data = sd->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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atomData = dynamic_cast<AtomData *>(data); |
280 |
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|
281 |
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if (atomData == NULL) |
282 |
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return; |
281 |
> |
if (atomData == NULL) |
282 |
> |
return; |
283 |
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} else |
284 |
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return; |
284 |
> |
return; |
285 |
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|
286 |
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for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
287 |
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atomInfo = atomData->nextAtomInfo(i) ) { |
288 |
< |
if (printDipole) |
289 |
< |
sprintf(buffer, |
290 |
< |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
291 |
< |
atomInfo->AtomType.c_str(), |
292 |
< |
atomInfo->pos[0], |
293 |
< |
atomInfo->pos[1], |
294 |
< |
atomInfo->pos[2], |
295 |
< |
atomInfo->dipole[0], |
296 |
< |
atomInfo->dipole[1], |
297 |
< |
atomInfo->dipole[2]); else |
351 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
352 |
< |
atomInfo->AtomType.c_str(), atomInfo->pos[0], |
353 |
< |
atomInfo->pos[1], atomInfo->pos[2]); |
354 |
< |
|
355 |
< |
frame.push_back(buffer); |
287 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
288 |
> |
sprintf(buffer, |
289 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
290 |
> |
atomInfo->atomTypeName.c_str(), |
291 |
> |
atomInfo->pos[0], |
292 |
> |
atomInfo->pos[1], |
293 |
> |
atomInfo->pos[2], |
294 |
> |
atomInfo->dipole[0], |
295 |
> |
atomInfo->dipole[1], |
296 |
> |
atomInfo->dipole[2]); |
297 |
> |
frame.push_back(buffer); |
298 |
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} |
299 |
< |
} |
299 |
> |
} |
300 |
|
|
301 |
< |
bool XYZVisitor::isSelected(StuntDouble *sd) { |
302 |
< |
return info->getSelectionManager()->isSelected(sd); |
303 |
< |
} |
301 |
> |
bool XYZVisitor::isSelected(StuntDouble *sd) { |
302 |
> |
return seleMan.isSelected(sd); |
303 |
> |
} |
304 |
|
|
305 |
< |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
305 |
> |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
306 |
|
std::vector<std::string>::iterator i; |
307 |
|
char buffer[1024]; |
308 |
|
|
309 |
|
if (frame.size() == 0) |
310 |
< |
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
310 |
> |
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
311 |
|
|
312 |
|
//total number of atoms |
313 |
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outStream << frame.size() << std::endl; |
326 |
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outStream << buffer << std::endl; |
327 |
|
|
328 |
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for( i = frame.begin(); i != frame.end(); ++i ) |
329 |
< |
outStream << *i << std::endl; |
330 |
< |
} |
329 |
> |
outStream << *i << std::endl; |
330 |
> |
} |
331 |
|
|
332 |
< |
const std::string XYZVisitor::toString() { |
332 |
> |
const std::string XYZVisitor::toString() { |
333 |
|
char buffer[65535]; |
334 |
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std::string result; |
335 |
|
|
349 |
|
result += buffer; |
350 |
|
|
351 |
|
return result; |
352 |
< |
} |
352 |
> |
} |
353 |
|
|
354 |
< |
//----------------------------------------------------------------------------// |
354 |
> |
//----------------------------------------------------------------------------// |
355 |
|
|
356 |
< |
void PrepareVisitor::internalVisit(Atom *atom) { |
356 |
> |
void PrepareVisitor::internalVisit(Atom *atom) { |
357 |
|
GenericData *data; |
358 |
|
AtomData * atomData; |
359 |
|
|
361 |
|
data = atom->getPropertyByName("VISITED"); |
362 |
|
|
363 |
|
if (data != NULL) { |
364 |
< |
atom->removeProperty("VISITED"); |
364 |
> |
atom->removeProperty("VISITED"); |
365 |
|
} |
366 |
|
|
367 |
|
//remove atomdata |
368 |
|
data = atom->getPropertyByName("ATOMDATA"); |
369 |
|
|
370 |
|
if (data != NULL) { |
371 |
< |
atomData = dynamic_cast<AtomData *>(data); |
371 |
> |
atomData = dynamic_cast<AtomData *>(data); |
372 |
|
|
373 |
< |
if (atomData != NULL) |
374 |
< |
atom->removeProperty("ATOMDATA"); |
373 |
> |
if (atomData != NULL) |
374 |
> |
atom->removeProperty("ATOMDATA"); |
375 |
|
} |
376 |
< |
} |
376 |
> |
} |
377 |
|
|
378 |
< |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
378 |
> |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
379 |
|
GenericData* data; |
380 |
|
AtomData* atomData; |
381 |
|
std::vector<Atom *> myAtoms; |
385 |
|
data = rb->getPropertyByName("VISITED"); |
386 |
|
|
387 |
|
if (data != NULL) { |
388 |
< |
rb->removeProperty("VISITED"); |
388 |
> |
rb->removeProperty("VISITED"); |
389 |
|
} |
390 |
|
|
391 |
|
//remove atomdata |
392 |
|
data = rb->getPropertyByName("ATOMDATA"); |
393 |
|
|
394 |
|
if (data != NULL) { |
395 |
< |
atomData = dynamic_cast<AtomData *>(data); |
395 |
> |
atomData = dynamic_cast<AtomData *>(data); |
396 |
|
|
397 |
< |
if (atomData != NULL) |
398 |
< |
rb->removeProperty("ATOMDATA"); |
397 |
> |
if (atomData != NULL) |
398 |
> |
rb->removeProperty("ATOMDATA"); |
399 |
|
} |
400 |
|
|
401 |
|
myAtoms = rb->getAtoms(); |
402 |
|
|
403 |
|
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
404 |
< |
internalVisit(*atomIter); |
405 |
< |
} |
404 |
> |
internalVisit(*atomIter); |
405 |
> |
} |
406 |
|
|
407 |
< |
const std::string PrepareVisitor::toString() { |
408 |
< |
char buffer[65535]; |
409 |
< |
std::string result; |
407 |
> |
const std::string PrepareVisitor::toString() { |
408 |
> |
char buffer[65535]; |
409 |
> |
std::string result; |
410 |
|
|
411 |
< |
sprintf(buffer, |
412 |
< |
"------------------------------------------------------------------\n"); |
413 |
< |
result += buffer; |
411 |
> |
sprintf(buffer, |
412 |
> |
"------------------------------------------------------------------\n"); |
413 |
> |
result += buffer; |
414 |
|
|
415 |
< |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
416 |
< |
result += buffer; |
415 |
> |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
416 |
> |
result += buffer; |
417 |
|
|
418 |
< |
sprintf(buffer, |
419 |
< |
"Visitor Description: prepare for operation of other vistors\n"); |
420 |
< |
result += buffer; |
418 |
> |
sprintf(buffer, |
419 |
> |
"Visitor Description: prepare for operation of other vistors\n"); |
420 |
> |
result += buffer; |
421 |
|
|
422 |
< |
sprintf(buffer, |
423 |
< |
"------------------------------------------------------------------\n"); |
424 |
< |
result += buffer; |
422 |
> |
sprintf(buffer, |
423 |
> |
"------------------------------------------------------------------\n"); |
424 |
> |
result += buffer; |
425 |
|
|
426 |
< |
return result; |
427 |
< |
} |
426 |
> |
return result; |
427 |
> |
} |
428 |
|
|
429 |
< |
//----------------------------------------------------------------------------// |
429 |
> |
//----------------------------------------------------------------------------// |
430 |
|
|
431 |
< |
WaterTypeVisitor::WaterTypeVisitor() { |
431 |
> |
WaterTypeVisitor::WaterTypeVisitor() { |
432 |
|
visitorName = "WaterTypeVisitor"; |
433 |
|
waterTypeList.insert("TIP3P_RB_0"); |
434 |
|
waterTypeList.insert("TIP4P_RB_0"); |
435 |
|
waterTypeList.insert("TIP5P_RB_0"); |
436 |
|
waterTypeList.insert("SPCE_RB_0"); |
437 |
< |
} |
437 |
> |
} |
438 |
|
|
439 |
< |
void WaterTypeVisitor::visit(RigidBody *rb) { |
439 |
> |
void WaterTypeVisitor::visit(RigidBody *rb) { |
440 |
|
std::string rbName; |
441 |
|
std::vector<Atom *> myAtoms; |
442 |
|
std::vector<Atom *>::iterator atomIter; |
448 |
|
rbName = rb->getType(); |
449 |
|
|
450 |
|
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
451 |
< |
myAtoms = rb->getAtoms(); |
451 |
> |
myAtoms = rb->getAtoms(); |
452 |
|
|
453 |
< |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
454 |
< |
++atomIter ) { |
455 |
< |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
453 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
454 |
> |
++atomIter ) { |
455 |
> |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
456 |
|
|
457 |
< |
if (data != NULL) { |
458 |
< |
atomData = dynamic_cast<AtomData *>(data); |
457 |
> |
if (data != NULL) { |
458 |
> |
atomData = dynamic_cast<AtomData *>(data); |
459 |
|
|
460 |
< |
if (atomData == NULL) |
461 |
< |
continue; |
462 |
< |
} else |
463 |
< |
continue; |
460 |
> |
if (atomData == NULL) |
461 |
> |
continue; |
462 |
> |
} else |
463 |
> |
continue; |
464 |
|
|
465 |
< |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
466 |
< |
atomInfo = atomData->nextAtomInfo(i) ) { |
467 |
< |
replaceType(atomInfo->AtomType); |
468 |
< |
} //end for(atomInfo) |
469 |
< |
} //end for(atomIter) |
465 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
466 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
467 |
> |
atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName); |
468 |
> |
} //end for(atomInfo) |
469 |
> |
} //end for(atomIter) |
470 |
|
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
471 |
< |
} |
471 |
> |
} |
472 |
|
|
473 |
< |
void WaterTypeVisitor::replaceType(std::string&atomType) { |
474 |
< |
atomType = atomType.substr(0, atomType.find('_')); |
475 |
< |
} |
473 |
> |
std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) { |
474 |
> |
return atomTypeName.substr(0, atomTypeName.find('_')); |
475 |
> |
} |
476 |
|
|
477 |
< |
const std::string WaterTypeVisitor::toString() { |
477 |
> |
const std::string WaterTypeVisitor::toString() { |
478 |
|
char buffer[65535]; |
479 |
|
std::string result; |
480 |
|
|
494 |
|
result += buffer; |
495 |
|
|
496 |
|
return result; |
497 |
< |
} |
497 |
> |
} |
498 |
|
|
499 |
|
} //namespace oopse |