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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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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include "selection/SelectionManager.hpp" |
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#include "visitors/OtherVisitor.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "primitives/RigidBody.hpp" |
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#include "primitives/Molecule.hpp" |
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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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> |
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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|
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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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> |
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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|
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< |
void IgnoreVisitor::visit(RigidBody* rb){ |
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vector<Atom*> myAtoms; |
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vector<Atom*>::iterator atomIter; |
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AtomInfo* atomInfo; |
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|
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if(isIgnoreType(rb->getType())){ |
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|
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internalVisit(rb); |
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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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|
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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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if (isIgnoreType(rb->getType())) { |
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internalVisit(rb); |
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|
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} |
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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 string& name){ |
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return itList.find(name) != itList.end() ? true : false; |
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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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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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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 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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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 ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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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 Description: ignore stuntdoubles\n"); |
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result += buffer; |
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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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//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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sprintf(buffer, "Visitor Description: ignore stuntdoubles\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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//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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} |
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sprintf(buffer ,"\n"); |
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result += buffer; |
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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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sprintf(buffer, "\n"); |
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result += buffer; |
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|
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< |
return result; |
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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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|
|
128 |
< |
void WrappingVisitor::visit(Atom* atom){ |
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< |
internalVisit(atom); |
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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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> |
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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> |
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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> |
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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> |
std::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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> |
data = sd->getPropertyByName("ATOMDATA"); |
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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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> |
if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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|
|
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< |
|
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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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> |
|
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> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
157 |
> |
|
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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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> |
} |
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} |
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|
|
163 |
< |
const string WrappingVisitor::toString(){ |
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< |
char buffer[65535]; |
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< |
string result; |
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|
122 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
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< |
result += buffer; |
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> |
const std::string WrappingVisitor::toString() { |
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> |
char buffer[65535]; |
165 |
> |
std::string result; |
166 |
|
|
167 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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< |
result += buffer; |
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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 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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> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
172 |
> |
result += buffer; |
173 |
|
|
174 |
< |
return result; |
174 |
> |
sprintf(buffer, |
175 |
> |
"Visitor Description: wrapping atoms back to periodic box\n"); |
176 |
> |
result += buffer; |
177 |
> |
|
178 |
> |
sprintf(buffer, |
179 |
> |
"------------------------------------------------------------------\n"); |
180 |
> |
result += buffer; |
181 |
> |
|
182 |
> |
return result; |
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|
} |
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|
|
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|
//----------------------------------------------------------------------------// |
186 |
|
|
187 |
< |
ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){ |
188 |
< |
this->info = info; |
189 |
< |
visitorName = "ReplicateVisitor"; |
190 |
< |
this->replicateOpt = opt; |
191 |
< |
//generate the replicate directions |
192 |
< |
for(int i = 0; i <= replicateOpt[0]; i ++) |
193 |
< |
for(int j = 0; j <= replicateOpt[1]; j ++) |
194 |
< |
for(int k = 0; k <= replicateOpt[2]; k ++) |
195 |
< |
//skip original frame |
196 |
< |
if(i == 0 && j ==0 && k ==0) |
197 |
< |
continue; |
198 |
< |
else |
199 |
< |
dir.push_back(IntVec3(i, j, k)); |
200 |
< |
|
187 |
> |
ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
188 |
> |
BaseVisitor() { |
189 |
> |
this->info = info; |
190 |
> |
visitorName = "ReplicateVisitor"; |
191 |
> |
this->replicateOpt = opt; |
192 |
> |
|
193 |
> |
//generate the replicate directions |
194 |
> |
for( int i = 0; i <= replicateOpt[0]; i++ ) { |
195 |
> |
for( int j = 0; j <= replicateOpt[1]; j++ ) { |
196 |
> |
for( int k = 0; k <= replicateOpt[2]; k++ ) { |
197 |
> |
//skip original frame |
198 |
> |
if (i == 0 && j == 0 && k == 0) { |
199 |
> |
continue; |
200 |
> |
} else { |
201 |
> |
dir.push_back(Vector3i(i, j, k)); |
202 |
> |
} |
203 |
> |
} |
204 |
> |
} |
205 |
> |
} |
206 |
> |
|
207 |
|
} |
208 |
< |
void ReplicateVisitor::visit(Atom* atom){ |
209 |
< |
internalVisit(atom); |
208 |
> |
|
209 |
> |
void ReplicateVisitor::visit(Atom *atom) { |
210 |
> |
internalVisit(atom); |
211 |
|
} |
212 |
< |
void ReplicateVisitor::visit(DirectionalAtom* datom){ |
213 |
< |
internalVisit(datom); |
212 |
> |
|
213 |
> |
void ReplicateVisitor::visit(DirectionalAtom *datom) { |
214 |
> |
internalVisit(datom); |
215 |
|
} |
216 |
|
|
217 |
< |
void ReplicateVisitor::visit(RigidBody* rb){ |
218 |
< |
internalVisit(rb); |
217 |
> |
void ReplicateVisitor::visit(RigidBody *rb) { |
218 |
> |
internalVisit(rb); |
219 |
|
} |
220 |
|
|
221 |
< |
void ReplicateVisitor::internalVisit(StuntDouble* sd){ |
222 |
< |
GenericData* data; |
223 |
< |
AtomData* atomData; |
168 |
< |
AtomInfo* atomInfo; |
169 |
< |
double box[3][3]; |
170 |
< |
vector<AtomInfo*> atomInfoList; |
171 |
< |
IntVec3 dir; |
172 |
< |
|
173 |
< |
//if there is not atom data, just skip it |
174 |
< |
data = sd->getProperty("ATOMDATA"); |
175 |
< |
if(data != NULL){ |
176 |
< |
atomData = dynamic_cast<AtomData*>(data); |
177 |
< |
if(atomData == NULL) |
178 |
< |
return; |
179 |
< |
} |
180 |
< |
else |
181 |
< |
return; |
221 |
> |
void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
222 |
> |
GenericData * data; |
223 |
> |
AtomData * atomData; |
224 |
|
|
225 |
< |
|
226 |
< |
info->getBoxM(box); |
225 |
> |
//if there is not atom data, just skip it |
226 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
227 |
|
|
228 |
< |
atomInfoList = atomData->getData(); |
229 |
< |
|
188 |
< |
replicate(atomInfoList, atomData, box); |
228 |
> |
if (data != NULL) { |
229 |
> |
atomData = dynamic_cast<AtomData *>(data); |
230 |
|
|
231 |
+ |
if (atomData == NULL) { |
232 |
+ |
return; |
233 |
+ |
} |
234 |
+ |
} else { |
235 |
+ |
return; |
236 |
+ |
} |
237 |
+ |
|
238 |
+ |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
239 |
+ |
Mat3x3d box = currSnapshot->getHmat(); |
240 |
+ |
|
241 |
+ |
std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
242 |
+ |
|
243 |
+ |
replicate(atomInfoList, atomData, box); |
244 |
|
} |
245 |
|
|
246 |
< |
void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){ |
247 |
< |
AtomInfo * newAtomInfo; |
248 |
< |
vector<IntVec3>::iterator dirIter; |
249 |
< |
vector<AtomInfo*>::iterator i; |
196 |
< |
|
197 |
< |
for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){ |
198 |
< |
for(i = infoList.begin(); i != infoList.end(); i++){ |
199 |
< |
newAtomInfo = new AtomInfo; |
200 |
< |
*newAtomInfo = *(*i); |
246 |
> |
void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
247 |
> |
AtomInfo* newAtomInfo; |
248 |
> |
std::vector<Vector3i>::iterator dirIter; |
249 |
> |
std::vector<AtomInfo *>::iterator i; |
250 |
|
|
251 |
< |
for(int j = 0; j < 3; j++) |
252 |
< |
newAtomInfo->pos[j] += (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2]; |
251 |
> |
for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
252 |
> |
for( i = infoList.begin(); i != infoList.end(); i++ ) { |
253 |
> |
newAtomInfo = new AtomInfo(); |
254 |
> |
*newAtomInfo = *(*i); |
255 |
|
|
256 |
< |
data->addAtomInfo(newAtomInfo); |
257 |
< |
} |
258 |
< |
}// end for(dirIter) |
256 |
> |
for( int j = 0; j < 3; j++ ) |
257 |
> |
newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
258 |
> |
|
259 |
> |
data->addAtomInfo(newAtomInfo); |
260 |
> |
} |
261 |
> |
} // end for(dirIter) |
262 |
|
} |
263 |
|
|
264 |
< |
const string ReplicateVisitor::toString(){ |
265 |
< |
char buffer[65535]; |
266 |
< |
string result; |
267 |
< |
set<string>::iterator i; |
214 |
< |
|
215 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
216 |
< |
result += buffer; |
264 |
> |
const std::string ReplicateVisitor::toString() { |
265 |
> |
char buffer[65535]; |
266 |
> |
std::string result; |
267 |
> |
std::set<std::string>::iterator i; |
268 |
|
|
269 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
270 |
< |
result += buffer; |
269 |
> |
sprintf(buffer, |
270 |
> |
"------------------------------------------------------------------\n"); |
271 |
> |
result += buffer; |
272 |
|
|
273 |
< |
sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n"); |
274 |
< |
result += buffer; |
223 |
< |
|
224 |
< |
//print the replicate direction |
225 |
< |
sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]); |
226 |
< |
result += buffer; |
273 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
274 |
> |
result += buffer; |
275 |
|
|
276 |
< |
sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]); |
277 |
< |
result += buffer; |
276 |
> |
sprintf(buffer, |
277 |
> |
"Visitor Description: replicate the atoms in different direction\n"); |
278 |
> |
result += buffer; |
279 |
|
|
280 |
< |
sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]); |
281 |
< |
result += buffer; |
280 |
> |
//print the replicate direction |
281 |
> |
sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]); |
282 |
> |
result += buffer; |
283 |
|
|
284 |
+ |
sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]); |
285 |
+ |
result += buffer; |
286 |
|
|
287 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
288 |
< |
result += buffer; |
287 |
> |
sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]); |
288 |
> |
result += buffer; |
289 |
|
|
290 |
< |
return result; |
290 |
> |
sprintf(buffer, |
291 |
> |
"------------------------------------------------------------------\n"); |
292 |
> |
result += buffer; |
293 |
> |
|
294 |
> |
return result; |
295 |
|
} |
296 |
|
|
297 |
|
//----------------------------------------------------------------------------// |
298 |
|
|
299 |
< |
XYZVisitor::XYZVisitor(SimInfo* info, bool printDipole) : BaseVisitor(){ |
300 |
< |
this->info = info; |
301 |
< |
visitorName = "XYZVisitor"; |
302 |
< |
this->printDipole = printDipole; |
299 |
> |
XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) : |
300 |
> |
BaseVisitor() { |
301 |
> |
this->info = info; |
302 |
> |
visitorName = "XYZVisitor"; |
303 |
> |
this->printDipole = printDipole; |
304 |
|
} |
305 |
|
|
306 |
< |
void XYZVisitor::visit(Atom* atom){ |
307 |
< |
if(!isIgnore(atom)) |
308 |
< |
internalVisit(atom); |
306 |
> |
void XYZVisitor::visit(Atom *atom) { |
307 |
> |
if (isSelected(atom)) |
308 |
> |
internalVisit(atom); |
309 |
|
} |
310 |
|
|
311 |
< |
void XYZVisitor::visit(DirectionalAtom* datom){ |
312 |
< |
if(!isIgnore(datom)) |
313 |
< |
internalVisit(datom); |
311 |
> |
void XYZVisitor::visit(DirectionalAtom *datom) { |
312 |
> |
if (isSelected(datom)) |
313 |
> |
internalVisit(datom); |
314 |
|
} |
315 |
|
|
316 |
< |
void XYZVisitor::visit(RigidBody* rb){ |
317 |
< |
if(!isIgnore(rb)) |
318 |
< |
internalVisit(rb); |
316 |
> |
void XYZVisitor::visit(RigidBody *rb) { |
317 |
> |
if (isSelected(rb)) |
318 |
> |
internalVisit(rb); |
319 |
> |
} |
320 |
|
|
321 |
< |
} |
321 |
> |
void XYZVisitor::internalVisit(StuntDouble *sd) { |
322 |
> |
GenericData * data; |
323 |
> |
AtomData * atomData; |
324 |
> |
AtomInfo * atomInfo; |
325 |
> |
std::vector<AtomInfo *>::iterator i; |
326 |
> |
char buffer[1024]; |
327 |
|
|
328 |
< |
void XYZVisitor::internalVisit(StuntDouble* sd){ |
329 |
< |
GenericData* data; |
267 |
< |
AtomData* atomData; |
268 |
< |
AtomInfo* atomInfo; |
269 |
< |
vector<AtomInfo*>::iterator i; |
270 |
< |
char buffer[1024]; |
271 |
< |
|
272 |
< |
//if there is not atom data, just skip it |
273 |
< |
data = sd->getProperty("ATOMDATA"); |
274 |
< |
if(data != NULL){ |
275 |
< |
atomData = dynamic_cast<AtomData*>(data); |
276 |
< |
if(atomData == NULL) |
277 |
< |
return; |
278 |
< |
} |
279 |
< |
else |
280 |
< |
return; |
328 |
> |
//if there is not atom data, just skip it |
329 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
330 |
|
|
331 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
331 |
> |
if (data != NULL) { |
332 |
> |
atomData = dynamic_cast<AtomData *>(data); |
333 |
|
|
334 |
< |
if(printDipole) |
335 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
336 |
< |
atomInfo->AtomType.c_str(), |
337 |
< |
atomInfo->pos[0], |
288 |
< |
atomInfo->pos[1], |
289 |
< |
atomInfo->pos[2], |
290 |
< |
atomInfo->dipole[0], |
291 |
< |
atomInfo->dipole[1], |
292 |
< |
atomInfo->dipole[2]); |
293 |
< |
else |
294 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
295 |
< |
atomInfo->AtomType.c_str(), |
296 |
< |
atomInfo->pos[0], |
297 |
< |
atomInfo->pos[1], |
298 |
< |
atomInfo->pos[2]); |
334 |
> |
if (atomData == NULL) |
335 |
> |
return; |
336 |
> |
} else |
337 |
> |
return; |
338 |
|
|
339 |
< |
frame.push_back(buffer); |
340 |
< |
|
341 |
< |
} |
339 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
340 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
341 |
> |
if (printDipole) |
342 |
> |
sprintf(buffer, |
343 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
344 |
> |
atomInfo->AtomType.c_str(), |
345 |
> |
atomInfo->pos[0], |
346 |
> |
atomInfo->pos[1], |
347 |
> |
atomInfo->pos[2], |
348 |
> |
atomInfo->dipole[0], |
349 |
> |
atomInfo->dipole[1], |
350 |
> |
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); |
356 |
+ |
} |
357 |
|
} |
358 |
|
|
359 |
< |
bool XYZVisitor::isIgnore(StuntDouble* sd){ |
360 |
< |
GenericData* data; |
308 |
< |
|
309 |
< |
data = sd->getProperty("IGNORE"); |
310 |
< |
return data ==NULL ? false : true; |
359 |
> |
bool XYZVisitor::isSelected(StuntDouble *sd) { |
360 |
> |
return info->getSelectionManager()->isSelected(sd); |
361 |
|
} |
362 |
|
|
363 |
< |
void XYZVisitor::writeFrame(ostream& outStream){ |
364 |
< |
vector<string>::iterator i; |
365 |
< |
double box[3][3]; |
316 |
< |
char buffer[1024]; |
363 |
> |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
364 |
> |
std::vector<std::string>::iterator i; |
365 |
> |
char buffer[1024]; |
366 |
|
|
367 |
< |
if(frame.size() == 0) |
368 |
< |
cerr << "Current Frame does not contain any atoms" << endl; |
367 |
> |
if (frame.size() == 0) |
368 |
> |
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
369 |
|
|
370 |
< |
//total number of atoms |
371 |
< |
outStream << frame.size() << endl; |
370 |
> |
//total number of atoms |
371 |
> |
outStream << frame.size() << std::endl; |
372 |
|
|
373 |
< |
//write comment line |
374 |
< |
info->getBoxM(box); |
375 |
< |
sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
376 |
< |
info->getTime(), |
377 |
< |
box[0][0], box[0][1], box[0][2], |
378 |
< |
box[1][0], box[1][1], box[1][2], |
379 |
< |
box[2][0], box[2][1], box[2][2]); |
373 |
> |
//write comment line |
374 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
375 |
> |
Mat3x3d box = currSnapshot->getHmat(); |
376 |
> |
|
377 |
> |
sprintf(buffer, |
378 |
> |
"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
379 |
> |
currSnapshot->getTime(), |
380 |
> |
box(0, 0), box(0, 1), box(0, 2), |
381 |
> |
box(1, 0), box(1, 1), box(1, 2), |
382 |
> |
box(2, 0), box(2, 1), box(2, 2)); |
383 |
|
|
384 |
< |
outStream << buffer << endl; |
384 |
> |
outStream << buffer << std::endl; |
385 |
|
|
386 |
< |
for(i = frame.begin(); i != frame.end(); ++i) |
387 |
< |
outStream << *i << endl; |
386 |
> |
for( i = frame.begin(); i != frame.end(); ++i ) |
387 |
> |
outStream << *i << std::endl; |
388 |
|
} |
389 |
|
|
390 |
< |
const string XYZVisitor::toString(){ |
391 |
< |
char buffer[65535]; |
392 |
< |
string result; |
341 |
< |
|
342 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
343 |
< |
result += buffer; |
390 |
> |
const std::string XYZVisitor::toString() { |
391 |
> |
char buffer[65535]; |
392 |
> |
std::string result; |
393 |
|
|
394 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
395 |
< |
result += buffer; |
394 |
> |
sprintf(buffer, |
395 |
> |
"------------------------------------------------------------------\n"); |
396 |
> |
result += buffer; |
397 |
|
|
398 |
< |
sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n"); |
399 |
< |
result += buffer; |
350 |
< |
|
351 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
352 |
< |
result += buffer; |
398 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
399 |
> |
result += buffer; |
400 |
|
|
401 |
< |
return result; |
401 |
> |
sprintf(buffer, |
402 |
> |
"Visitor Description: assemble the atom data and output xyz file\n"); |
403 |
> |
result += buffer; |
404 |
> |
|
405 |
> |
sprintf(buffer, |
406 |
> |
"------------------------------------------------------------------\n"); |
407 |
> |
result += buffer; |
408 |
> |
|
409 |
> |
return result; |
410 |
|
} |
411 |
|
|
412 |
|
//----------------------------------------------------------------------------// |
413 |
|
|
414 |
< |
void PrepareVisitor::internalVisit(Atom * atom){ |
415 |
< |
GenericData* data; |
416 |
< |
AtomData* atomData; |
414 |
> |
void PrepareVisitor::internalVisit(Atom *atom) { |
415 |
> |
GenericData *data; |
416 |
> |
AtomData * atomData; |
417 |
|
|
418 |
< |
//if visited property is existed, remove it |
419 |
< |
data = atom->getProperty("VISITED"); |
365 |
< |
if(data != NULL){ |
366 |
< |
atom->removeProperty("VISITED"); |
367 |
< |
} |
418 |
> |
//if visited property is existed, remove it |
419 |
> |
data = atom->getPropertyByName("VISITED"); |
420 |
|
|
421 |
< |
//remove atomdata |
422 |
< |
data = atom->getProperty("ATOMDATA"); |
423 |
< |
if(data != NULL){ |
372 |
< |
atomData = dynamic_cast<AtomData*>(data); |
373 |
< |
if(atomData != NULL) |
374 |
< |
atom->removeProperty("ATOMDATA"); |
375 |
< |
} |
376 |
< |
|
377 |
< |
} |
421 |
> |
if (data != NULL) { |
422 |
> |
atom->removeProperty("VISITED"); |
423 |
> |
} |
424 |
|
|
425 |
< |
void PrepareVisitor::internalVisit(RigidBody * rb){ |
426 |
< |
GenericData* data; |
381 |
< |
AtomData* atomData; |
382 |
< |
vector<Atom*> myAtoms; |
383 |
< |
vector<Atom*>::iterator atomIter; |
384 |
< |
|
385 |
< |
//if visited property is existed, remove it |
386 |
< |
data = rb->getProperty("VISITED"); |
387 |
< |
if(data != NULL){ |
388 |
< |
rb->removeProperty("VISITED"); |
389 |
< |
} |
425 |
> |
//remove atomdata |
426 |
> |
data = atom->getPropertyByName("ATOMDATA"); |
427 |
|
|
428 |
< |
//remove atomdata |
429 |
< |
data = rb->getProperty("ATOMDATA"); |
393 |
< |
if(data != NULL){ |
394 |
< |
atomData = dynamic_cast<AtomData*>(data); |
395 |
< |
if(atomData != NULL) |
396 |
< |
rb->removeProperty("ATOMDATA"); |
397 |
< |
} |
428 |
> |
if (data != NULL) { |
429 |
> |
atomData = dynamic_cast<AtomData *>(data); |
430 |
|
|
431 |
< |
myAtoms = rb->getAtoms(); |
432 |
< |
|
433 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
402 |
< |
internalVisit (*atomIter); |
431 |
> |
if (atomData != NULL) |
432 |
> |
atom->removeProperty("ATOMDATA"); |
433 |
> |
} |
434 |
|
} |
435 |
|
|
436 |
< |
const string PrepareVisitor::toString(){ |
437 |
< |
char buffer[65535]; |
438 |
< |
string result; |
439 |
< |
|
440 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
410 |
< |
result += buffer; |
436 |
> |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
437 |
> |
GenericData* data; |
438 |
> |
AtomData* atomData; |
439 |
> |
std::vector<Atom *> myAtoms; |
440 |
> |
std::vector<Atom *>::iterator atomIter; |
441 |
|
|
442 |
< |
sprintf(buffer ,"Visitor name: %s", visitorName.c_str()); |
443 |
< |
result += buffer; |
442 |
> |
//if visited property is existed, remove it |
443 |
> |
data = rb->getPropertyByName("VISITED"); |
444 |
|
|
445 |
< |
sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n"); |
446 |
< |
result += buffer; |
445 |
> |
if (data != NULL) { |
446 |
> |
rb->removeProperty("VISITED"); |
447 |
> |
} |
448 |
|
|
449 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
450 |
< |
result += buffer; |
449 |
> |
//remove atomdata |
450 |
> |
data = rb->getPropertyByName("ATOMDATA"); |
451 |
|
|
452 |
< |
return result; |
452 |
> |
if (data != NULL) { |
453 |
> |
atomData = dynamic_cast<AtomData *>(data); |
454 |
> |
|
455 |
> |
if (atomData != NULL) |
456 |
> |
rb->removeProperty("ATOMDATA"); |
457 |
> |
} |
458 |
> |
|
459 |
> |
myAtoms = rb->getAtoms(); |
460 |
> |
|
461 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
462 |
> |
internalVisit(*atomIter); |
463 |
|
} |
464 |
|
|
465 |
+ |
const std::string PrepareVisitor::toString() { |
466 |
+ |
char buffer[65535]; |
467 |
+ |
std::string result; |
468 |
+ |
|
469 |
+ |
sprintf(buffer, |
470 |
+ |
"------------------------------------------------------------------\n"); |
471 |
+ |
result += buffer; |
472 |
+ |
|
473 |
+ |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
474 |
+ |
result += buffer; |
475 |
+ |
|
476 |
+ |
sprintf(buffer, |
477 |
+ |
"Visitor Description: prepare for operation of other vistors\n"); |
478 |
+ |
result += buffer; |
479 |
+ |
|
480 |
+ |
sprintf(buffer, |
481 |
+ |
"------------------------------------------------------------------\n"); |
482 |
+ |
result += buffer; |
483 |
+ |
|
484 |
+ |
return result; |
485 |
+ |
} |
486 |
+ |
|
487 |
|
//----------------------------------------------------------------------------// |
488 |
|
|
489 |
< |
WaterTypeVisitor:: WaterTypeVisitor(){ |
490 |
< |
visitorName = "WaterTypeVisitor"; |
491 |
< |
waterTypeList.insert("TIP3P_RB_0"); |
492 |
< |
waterTypeList.insert("TIP4P_RB_0"); |
493 |
< |
waterTypeList.insert("TIP5P_RB_0"); |
494 |
< |
waterTypeList.insert("SPCE_RB_0"); |
489 |
> |
WaterTypeVisitor::WaterTypeVisitor() { |
490 |
> |
visitorName = "WaterTypeVisitor"; |
491 |
> |
waterTypeList.insert("TIP3P_RB_0"); |
492 |
> |
waterTypeList.insert("TIP4P_RB_0"); |
493 |
> |
waterTypeList.insert("TIP5P_RB_0"); |
494 |
> |
waterTypeList.insert("SPCE_RB_0"); |
495 |
|
} |
496 |
|
|
497 |
+ |
void WaterTypeVisitor::visit(RigidBody *rb) { |
498 |
+ |
std::string rbName; |
499 |
+ |
std::vector<Atom *> myAtoms; |
500 |
+ |
std::vector<Atom *>::iterator atomIter; |
501 |
+ |
GenericData* data; |
502 |
+ |
AtomData* atomData; |
503 |
+ |
AtomInfo* atomInfo; |
504 |
+ |
std::vector<AtomInfo *>::iterator i; |
505 |
|
|
506 |
< |
void WaterTypeVisitor:: visit(RigidBody* rb){ |
436 |
< |
string rbName; |
437 |
< |
vector<Atom*> myAtoms; |
438 |
< |
vector<Atom*>::iterator atomIter; |
439 |
< |
GenericData* data; |
440 |
< |
AtomData* atomData; |
441 |
< |
AtomInfo* atomInfo; |
442 |
< |
vector<AtomInfo*>::iterator i; |
443 |
< |
|
444 |
< |
rbName = rb->getType(); |
506 |
> |
rbName = rb->getType(); |
507 |
|
|
508 |
< |
if(waterTypeList.find(rbName) != waterTypeList.end()){ |
508 |
> |
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
509 |
> |
myAtoms = rb->getAtoms(); |
510 |
|
|
511 |
< |
myAtoms = rb->getAtoms(); |
512 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){ |
511 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
512 |
> |
++atomIter ) { |
513 |
> |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
514 |
|
|
515 |
< |
data = (*atomIter)->getProperty("ATOMDATA"); |
516 |
< |
if(data != NULL){ |
453 |
< |
atomData = dynamic_cast<AtomData*>(data); |
454 |
< |
if(atomData == NULL) |
455 |
< |
continue; |
456 |
< |
} |
457 |
< |
else |
458 |
< |
continue; |
459 |
< |
|
460 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
461 |
< |
replaceType(atomInfo->AtomType); |
462 |
< |
}//end for(atomInfo) |
515 |
> |
if (data != NULL) { |
516 |
> |
atomData = dynamic_cast<AtomData *>(data); |
517 |
|
|
518 |
< |
}//end for(atomIter) |
519 |
< |
|
520 |
< |
}//end if (waterTypeList.find(rbName) != waterTypeList.end()) |
521 |
< |
|
518 |
> |
if (atomData == NULL) |
519 |
> |
continue; |
520 |
> |
} else |
521 |
> |
continue; |
522 |
> |
|
523 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
524 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
525 |
> |
replaceType(atomInfo->AtomType); |
526 |
> |
} //end for(atomInfo) |
527 |
> |
} //end for(atomIter) |
528 |
> |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
529 |
|
} |
530 |
|
|
531 |
< |
void WaterTypeVisitor:: replaceType(string& atomType){ |
532 |
< |
atomType = atomType.substr(0, atomType.find('_')); |
531 |
> |
void WaterTypeVisitor::replaceType(std::string&atomType) { |
532 |
> |
atomType = atomType.substr(0, atomType.find('_')); |
533 |
|
} |
534 |
|
|
535 |
< |
const string WaterTypeVisitor:: toString(){ |
536 |
< |
char buffer[65535]; |
537 |
< |
string result; |
477 |
< |
|
478 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
479 |
< |
result += buffer; |
535 |
> |
const std::string WaterTypeVisitor::toString() { |
536 |
> |
char buffer[65535]; |
537 |
> |
std::string result; |
538 |
|
|
539 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
540 |
< |
result += buffer; |
539 |
> |
sprintf(buffer, |
540 |
> |
"------------------------------------------------------------------\n"); |
541 |
> |
result += buffer; |
542 |
|
|
543 |
< |
sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n"); |
544 |
< |
result += buffer; |
543 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
544 |
> |
result += buffer; |
545 |
|
|
546 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
547 |
< |
result += buffer; |
546 |
> |
sprintf(buffer, |
547 |
> |
"Visitor Description: Replace the atom type in water model\n"); |
548 |
> |
result += buffer; |
549 |
|
|
550 |
< |
return result; |
550 |
> |
sprintf(buffer, |
551 |
> |
"------------------------------------------------------------------\n"); |
552 |
> |
result += buffer; |
553 |
> |
|
554 |
> |
return result; |
555 |
|
} |
556 |
|
|
557 |
+ |
} //namespace oopse |