| 1 |
#include "visitors/OtherVisitor.hpp" |
| 2 |
#include "primitives/DirectionalAtom.hpp" |
| 3 |
#include "primitives/RigidBody.hpp" |
| 4 |
#include "primitives/Molecule.hpp" |
| 5 |
#include "brains/SimInfo.hpp" |
| 6 |
|
| 7 |
namespace oopse { |
| 8 |
|
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//----------------------------------------------------------------------------// |
| 10 |
void IgnoreVisitor::visit(Atom* atom){ |
| 11 |
if(isIgnoreType(atom->getType())) |
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internalVisit(atom); |
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} |
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|
| 15 |
void IgnoreVisitor::visit(DirectionalAtom* datom){ |
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if(isIgnoreType(datom->getType())) |
| 17 |
internalVisit(datom); |
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} |
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|
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void IgnoreVisitor::visit(RigidBody* rb){ |
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vector<Atom*> myAtoms; |
| 22 |
vector<Atom*>::iterator atomIter; |
| 23 |
AtomInfo* atomInfo; |
| 24 |
|
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if(isIgnoreType(rb->getType())){ |
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|
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internalVisit(rb); |
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|
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myAtoms = rb->getAtoms(); |
| 30 |
|
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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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} |
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|
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bool IgnoreVisitor::isIgnoreType(const 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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GenericData* data; |
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data = sd->getProperty("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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|
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const string IgnoreVisitor::toString(){ |
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char buffer[65535]; |
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string result; |
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set<string>::iterator i; |
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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 ,"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 ,"------------------------------------------------------------------\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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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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GenericData* data; |
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AtomData* atomData; |
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AtomInfo* atomInfo; |
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vector<AtomInfo*>::iterator i; |
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|
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data = sd->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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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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|
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for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)) |
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info->wrapVector(atomInfo->pos); |
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|
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|
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} |
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|
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const string WrappingVisitor::toString(){ |
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char buffer[65535]; |
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string result; |
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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 ,"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: wrapping atoms back to periodic box\n"); |
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result += buffer; |
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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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return result; |
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} |
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|
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//----------------------------------------------------------------------------// |
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|
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ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : 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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//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(IntVec3(i, j, k)); |
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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(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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|
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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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AtomInfo* atomInfo; |
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double box[3][3]; |
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vector<AtomInfo*> atomInfoList; |
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IntVec3 dir; |
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|
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//if there is not atom data, just skip it |
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data = sd->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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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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|
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|
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info->getBoxM(box); |
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|
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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(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){ |
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AtomInfo * newAtomInfo; |
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vector<IntVec3>::iterator dirIter; |
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vector<AtomInfo*>::iterator i; |
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|
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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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|
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for(int j = 0; j < 3; j++) |
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newAtomInfo->pos[j] += (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2]; |
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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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const string ReplicateVisitor::toString(){ |
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char buffer[65535]; |
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string result; |
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set<string>::iterator i; |
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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 ,"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: replicate the atoms in different direction\n"); |
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result += buffer; |
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|
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//print the replicate direction |
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sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]); |
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result += buffer; |
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|
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sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]); |
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result += buffer; |
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|
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sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]); |
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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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return result; |
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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) : 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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|
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void XYZVisitor::visit(Atom* atom){ |
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if(!isIgnore(atom)) |
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internalVisit(atom); |
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} |
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|
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void XYZVisitor::visit(DirectionalAtom* datom){ |
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if(!isIgnore(datom)) |
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internalVisit(datom); |
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} |
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|
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void XYZVisitor::visit(RigidBody* rb){ |
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if(!isIgnore(rb)) |
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internalVisit(rb); |
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|
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} |
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|
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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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vector<AtomInfo*>::iterator i; |
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char buffer[1024]; |
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|
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//if there is not atom data, just skip it |
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data = sd->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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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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|
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for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
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|
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if(printDipole) |
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sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
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atomInfo->AtomType.c_str(), |
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atomInfo->pos[0], |
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atomInfo->pos[1], |
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atomInfo->pos[2], |
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atomInfo->dipole[0], |
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atomInfo->dipole[1], |
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atomInfo->dipole[2]); |
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else |
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sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
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atomInfo->AtomType.c_str(), |
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atomInfo->pos[0], |
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atomInfo->pos[1], |
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atomInfo->pos[2]); |
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|
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frame.push_back(buffer); |
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|
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} |
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|
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} |
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|
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bool XYZVisitor::isIgnore(StuntDouble* sd){ |
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GenericData* data; |
| 311 |
|
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data = sd->getProperty("IGNORE"); |
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return data ==NULL ? false : true; |
| 314 |
} |
| 315 |
|
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void XYZVisitor::writeFrame(ostream& outStream){ |
| 317 |
vector<string>::iterator i; |
| 318 |
double box[3][3]; |
| 319 |
char buffer[1024]; |
| 320 |
|
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if(frame.size() == 0) |
| 322 |
cerr << "Current Frame does not contain any atoms" << endl; |
| 323 |
|
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//total number of atoms |
| 325 |
outStream << frame.size() << endl; |
| 326 |
|
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//write comment line |
| 328 |
info->getBoxM(box); |
| 329 |
sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
| 330 |
info->getTime(), |
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box[0][0], box[0][1], box[0][2], |
| 332 |
box[1][0], box[1][1], box[1][2], |
| 333 |
box[2][0], box[2][1], box[2][2]); |
| 334 |
|
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outStream << buffer << endl; |
| 336 |
|
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for(i = frame.begin(); i != frame.end(); ++i) |
| 338 |
outStream << *i << endl; |
| 339 |
} |
| 340 |
|
| 341 |
const string XYZVisitor::toString(){ |
| 342 |
char buffer[65535]; |
| 343 |
string result; |
| 344 |
|
| 345 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 346 |
result += buffer; |
| 347 |
|
| 348 |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 349 |
result += buffer; |
| 350 |
|
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sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n"); |
| 352 |
result += buffer; |
| 353 |
|
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sprintf(buffer,"------------------------------------------------------------------\n"); |
| 355 |
result += buffer; |
| 356 |
|
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return result; |
| 358 |
} |
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|
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//----------------------------------------------------------------------------// |
| 361 |
|
| 362 |
void PrepareVisitor::internalVisit(Atom * atom){ |
| 363 |
GenericData* data; |
| 364 |
AtomData* atomData; |
| 365 |
|
| 366 |
//if visited property is existed, remove it |
| 367 |
data = atom->getProperty("VISITED"); |
| 368 |
if(data != NULL){ |
| 369 |
atom->removeProperty("VISITED"); |
| 370 |
} |
| 371 |
|
| 372 |
//remove atomdata |
| 373 |
data = atom->getProperty("ATOMDATA"); |
| 374 |
if(data != NULL){ |
| 375 |
atomData = dynamic_cast<AtomData*>(data); |
| 376 |
if(atomData != NULL) |
| 377 |
atom->removeProperty("ATOMDATA"); |
| 378 |
} |
| 379 |
|
| 380 |
} |
| 381 |
|
| 382 |
void PrepareVisitor::internalVisit(RigidBody * rb){ |
| 383 |
GenericData* data; |
| 384 |
AtomData* atomData; |
| 385 |
vector<Atom*> myAtoms; |
| 386 |
vector<Atom*>::iterator atomIter; |
| 387 |
|
| 388 |
//if visited property is existed, remove it |
| 389 |
data = rb->getProperty("VISITED"); |
| 390 |
if(data != NULL){ |
| 391 |
rb->removeProperty("VISITED"); |
| 392 |
} |
| 393 |
|
| 394 |
//remove atomdata |
| 395 |
data = rb->getProperty("ATOMDATA"); |
| 396 |
if(data != NULL){ |
| 397 |
atomData = dynamic_cast<AtomData*>(data); |
| 398 |
if(atomData != NULL) |
| 399 |
rb->removeProperty("ATOMDATA"); |
| 400 |
} |
| 401 |
|
| 402 |
myAtoms = rb->getAtoms(); |
| 403 |
|
| 404 |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
| 405 |
internalVisit (*atomIter); |
| 406 |
} |
| 407 |
|
| 408 |
const string PrepareVisitor::toString(){ |
| 409 |
char buffer[65535]; |
| 410 |
string result; |
| 411 |
|
| 412 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 413 |
result += buffer; |
| 414 |
|
| 415 |
sprintf(buffer ,"Visitor name: %s", visitorName.c_str()); |
| 416 |
result += buffer; |
| 417 |
|
| 418 |
sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n"); |
| 419 |
result += buffer; |
| 420 |
|
| 421 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 422 |
result += buffer; |
| 423 |
|
| 424 |
return result; |
| 425 |
} |
| 426 |
|
| 427 |
//----------------------------------------------------------------------------// |
| 428 |
|
| 429 |
WaterTypeVisitor:: WaterTypeVisitor(){ |
| 430 |
visitorName = "WaterTypeVisitor"; |
| 431 |
waterTypeList.insert("TIP3P_RB_0"); |
| 432 |
waterTypeList.insert("TIP4P_RB_0"); |
| 433 |
waterTypeList.insert("TIP5P_RB_0"); |
| 434 |
waterTypeList.insert("SPCE_RB_0"); |
| 435 |
} |
| 436 |
|
| 437 |
|
| 438 |
void WaterTypeVisitor:: visit(RigidBody* rb){ |
| 439 |
string rbName; |
| 440 |
vector<Atom*> myAtoms; |
| 441 |
vector<Atom*>::iterator atomIter; |
| 442 |
GenericData* data; |
| 443 |
AtomData* atomData; |
| 444 |
AtomInfo* atomInfo; |
| 445 |
vector<AtomInfo*>::iterator i; |
| 446 |
|
| 447 |
rbName = rb->getType(); |
| 448 |
|
| 449 |
if(waterTypeList.find(rbName) != waterTypeList.end()){ |
| 450 |
|
| 451 |
myAtoms = rb->getAtoms(); |
| 452 |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){ |
| 453 |
|
| 454 |
data = (*atomIter)->getProperty("ATOMDATA"); |
| 455 |
if(data != NULL){ |
| 456 |
atomData = dynamic_cast<AtomData*>(data); |
| 457 |
if(atomData == NULL) |
| 458 |
continue; |
| 459 |
} |
| 460 |
else |
| 461 |
continue; |
| 462 |
|
| 463 |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
| 464 |
replaceType(atomInfo->AtomType); |
| 465 |
}//end for(atomInfo) |
| 466 |
|
| 467 |
}//end for(atomIter) |
| 468 |
|
| 469 |
}//end if (waterTypeList.find(rbName) != waterTypeList.end()) |
| 470 |
|
| 471 |
} |
| 472 |
|
| 473 |
void WaterTypeVisitor:: replaceType(string& atomType){ |
| 474 |
atomType = atomType.substr(0, atomType.find('_')); |
| 475 |
} |
| 476 |
|
| 477 |
const string WaterTypeVisitor:: toString(){ |
| 478 |
char buffer[65535]; |
| 479 |
string result; |
| 480 |
|
| 481 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 482 |
result += buffer; |
| 483 |
|
| 484 |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 485 |
result += buffer; |
| 486 |
|
| 487 |
sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n"); |
| 488 |
result += buffer; |
| 489 |
|
| 490 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 491 |
result += buffer; |
| 492 |
|
| 493 |
return result; |
| 494 |
} |
| 495 |
|
| 496 |
|
| 497 |
}//namespace oopse |
