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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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|
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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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|
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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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void IgnoreVisitor::internalVisit(StuntDouble *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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//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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|
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< |
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(); |
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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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} |
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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"); |
126 |
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result += buffer; |
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> |
const std::string WrappingVisitor::toString() { |
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> |
char buffer[65535]; |
164 |
> |
std::string result; |
165 |
|
|
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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: 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()); |
171 |
> |
result += buffer; |
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|
|
173 |
< |
return result; |
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> |
sprintf(buffer, |
174 |
> |
"Visitor Description: wrapping atoms back to periodic box\n"); |
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> |
result += buffer; |
176 |
> |
|
177 |
> |
sprintf(buffer, |
178 |
> |
"------------------------------------------------------------------\n"); |
179 |
> |
result += buffer; |
180 |
> |
|
181 |
> |
return result; |
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|
} |
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|
|
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|
//----------------------------------------------------------------------------// |
185 |
|
|
186 |
< |
ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){ |
187 |
< |
this->info = info; |
188 |
< |
visitorName = "ReplicateVisitor"; |
189 |
< |
this->replicateOpt = opt; |
190 |
< |
//generate the replicate directions |
191 |
< |
for(int i = 0; i <= replicateOpt[0]; i ++) |
192 |
< |
for(int j = 0; j <= replicateOpt[1]; j ++) |
193 |
< |
for(int k = 0; k <= replicateOpt[2]; k ++) |
194 |
< |
//skip original frame |
195 |
< |
if(i == 0 && j ==0 && k ==0) |
196 |
< |
continue; |
197 |
< |
else |
198 |
< |
dir.push_back(IntVec3(i, j, k)); |
199 |
< |
|
186 |
> |
ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
187 |
> |
BaseVisitor() { |
188 |
> |
this->info = info; |
189 |
> |
visitorName = "ReplicateVisitor"; |
190 |
> |
this->replicateOpt = opt; |
191 |
> |
|
192 |
> |
//generate the replicate directions |
193 |
> |
for( int i = 0; i <= replicateOpt[0]; i++ ) { |
194 |
> |
for( int j = 0; j <= replicateOpt[1]; j++ ) { |
195 |
> |
for( int k = 0; k <= replicateOpt[2]; k++ ) { |
196 |
> |
//skip original frame |
197 |
> |
if (i == 0 && j == 0 && k == 0) { |
198 |
> |
continue; |
199 |
> |
} else { |
200 |
> |
dir.push_back(Vector3i(i, j, k)); |
201 |
> |
} |
202 |
> |
} |
203 |
> |
} |
204 |
> |
} |
205 |
> |
|
206 |
|
} |
207 |
< |
void ReplicateVisitor::visit(Atom* atom){ |
208 |
< |
internalVisit(atom); |
207 |
> |
|
208 |
> |
void ReplicateVisitor::visit(Atom *atom) { |
209 |
> |
internalVisit(atom); |
210 |
|
} |
211 |
< |
void ReplicateVisitor::visit(DirectionalAtom* datom){ |
212 |
< |
internalVisit(datom); |
211 |
> |
|
212 |
> |
void ReplicateVisitor::visit(DirectionalAtom *datom) { |
213 |
> |
internalVisit(datom); |
214 |
|
} |
215 |
|
|
216 |
< |
void ReplicateVisitor::visit(RigidBody* rb){ |
217 |
< |
internalVisit(rb); |
216 |
> |
void ReplicateVisitor::visit(RigidBody *rb) { |
217 |
> |
internalVisit(rb); |
218 |
|
} |
219 |
|
|
220 |
< |
void ReplicateVisitor::internalVisit(StuntDouble* sd){ |
221 |
< |
GenericData* data; |
222 |
< |
AtomData* atomData; |
171 |
< |
AtomInfo* atomInfo; |
172 |
< |
double box[3][3]; |
173 |
< |
vector<AtomInfo*> atomInfoList; |
174 |
< |
IntVec3 dir; |
175 |
< |
|
176 |
< |
//if there is not atom data, just skip it |
177 |
< |
data = sd->getProperty("ATOMDATA"); |
178 |
< |
if(data != NULL){ |
179 |
< |
atomData = dynamic_cast<AtomData*>(data); |
180 |
< |
if(atomData == NULL) |
181 |
< |
return; |
182 |
< |
} |
183 |
< |
else |
184 |
< |
return; |
220 |
> |
void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
221 |
> |
GenericData * data; |
222 |
> |
AtomData * atomData; |
223 |
|
|
224 |
< |
|
225 |
< |
info->getBoxM(box); |
224 |
> |
//if there is not atom data, just skip it |
225 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
226 |
|
|
227 |
< |
atomInfoList = atomData->getData(); |
228 |
< |
|
191 |
< |
replicate(atomInfoList, atomData, box); |
227 |
> |
if (data != NULL) { |
228 |
> |
atomData = dynamic_cast<AtomData *>(data); |
229 |
|
|
230 |
+ |
if (atomData == NULL) { |
231 |
+ |
return; |
232 |
+ |
} |
233 |
+ |
} else { |
234 |
+ |
return; |
235 |
+ |
} |
236 |
+ |
|
237 |
+ |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
238 |
+ |
Mat3x3d box = currSnapshot->getHmat(); |
239 |
+ |
|
240 |
+ |
std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
241 |
+ |
|
242 |
+ |
replicate(atomInfoList, atomData, box); |
243 |
|
} |
244 |
|
|
245 |
< |
void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){ |
246 |
< |
AtomInfo * newAtomInfo; |
247 |
< |
vector<IntVec3>::iterator dirIter; |
248 |
< |
vector<AtomInfo*>::iterator i; |
199 |
< |
|
200 |
< |
for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){ |
201 |
< |
for(i = infoList.begin(); i != infoList.end(); i++){ |
202 |
< |
newAtomInfo = new AtomInfo; |
203 |
< |
*newAtomInfo = *(*i); |
245 |
> |
void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
246 |
> |
AtomInfo* newAtomInfo; |
247 |
> |
std::vector<Vector3i>::iterator dirIter; |
248 |
> |
std::vector<AtomInfo *>::iterator i; |
249 |
|
|
250 |
< |
for(int j = 0; j < 3; j++) |
251 |
< |
newAtomInfo->pos[j] += (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2]; |
250 |
> |
for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
251 |
> |
for( i = infoList.begin(); i != infoList.end(); i++ ) { |
252 |
> |
newAtomInfo = new AtomInfo(); |
253 |
> |
*newAtomInfo = *(*i); |
254 |
|
|
255 |
< |
data->addAtomInfo(newAtomInfo); |
256 |
< |
} |
257 |
< |
}// end for(dirIter) |
255 |
> |
for( int j = 0; j < 3; j++ ) |
256 |
> |
newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
257 |
> |
|
258 |
> |
data->addAtomInfo(newAtomInfo); |
259 |
> |
} |
260 |
> |
} // end for(dirIter) |
261 |
|
} |
262 |
|
|
263 |
< |
const string ReplicateVisitor::toString(){ |
264 |
< |
char buffer[65535]; |
265 |
< |
string result; |
266 |
< |
set<string>::iterator i; |
217 |
< |
|
218 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
219 |
< |
result += buffer; |
263 |
> |
const std::string ReplicateVisitor::toString() { |
264 |
> |
char buffer[65535]; |
265 |
> |
std::string result; |
266 |
> |
std::set<std::string>::iterator i; |
267 |
|
|
268 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
269 |
< |
result += buffer; |
268 |
> |
sprintf(buffer, |
269 |
> |
"------------------------------------------------------------------\n"); |
270 |
> |
result += buffer; |
271 |
|
|
272 |
< |
sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n"); |
273 |
< |
result += buffer; |
226 |
< |
|
227 |
< |
//print the replicate direction |
228 |
< |
sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]); |
229 |
< |
result += buffer; |
272 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
273 |
> |
result += buffer; |
274 |
|
|
275 |
< |
sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]); |
276 |
< |
result += buffer; |
275 |
> |
sprintf(buffer, |
276 |
> |
"Visitor Description: replicate the atoms in different direction\n"); |
277 |
> |
result += buffer; |
278 |
|
|
279 |
< |
sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]); |
280 |
< |
result += buffer; |
279 |
> |
//print the replicate direction |
280 |
> |
sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]); |
281 |
> |
result += buffer; |
282 |
|
|
283 |
+ |
sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]); |
284 |
+ |
result += buffer; |
285 |
|
|
286 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
287 |
< |
result += buffer; |
286 |
> |
sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]); |
287 |
> |
result += buffer; |
288 |
|
|
289 |
< |
return result; |
289 |
> |
sprintf(buffer, |
290 |
> |
"------------------------------------------------------------------\n"); |
291 |
> |
result += buffer; |
292 |
> |
|
293 |
> |
return result; |
294 |
|
} |
295 |
|
|
296 |
|
//----------------------------------------------------------------------------// |
297 |
|
|
298 |
< |
XYZVisitor::XYZVisitor(SimInfo* info, bool printDipole) : BaseVisitor(){ |
299 |
< |
this->info = info; |
300 |
< |
visitorName = "XYZVisitor"; |
301 |
< |
this->printDipole = printDipole; |
298 |
> |
XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) : |
299 |
> |
BaseVisitor() { |
300 |
> |
this->info = info; |
301 |
> |
visitorName = "XYZVisitor"; |
302 |
> |
this->printDipole = printDipole; |
303 |
|
} |
304 |
|
|
305 |
< |
void XYZVisitor::visit(Atom* atom){ |
306 |
< |
if(!isIgnore(atom)) |
307 |
< |
internalVisit(atom); |
305 |
> |
void XYZVisitor::visit(Atom *atom) { |
306 |
> |
if (!isIgnore(atom)) |
307 |
> |
internalVisit(atom); |
308 |
|
} |
309 |
|
|
310 |
< |
void XYZVisitor::visit(DirectionalAtom* datom){ |
311 |
< |
if(!isIgnore(datom)) |
312 |
< |
internalVisit(datom); |
310 |
> |
void XYZVisitor::visit(DirectionalAtom *datom) { |
311 |
> |
if (!isIgnore(datom)) |
312 |
> |
internalVisit(datom); |
313 |
|
} |
314 |
|
|
315 |
< |
void XYZVisitor::visit(RigidBody* rb){ |
316 |
< |
if(!isIgnore(rb)) |
317 |
< |
internalVisit(rb); |
315 |
> |
void XYZVisitor::visit(RigidBody *rb) { |
316 |
> |
if (!isIgnore(rb)) |
317 |
> |
internalVisit(rb); |
318 |
> |
} |
319 |
> |
|
320 |
> |
void XYZVisitor::internalVisit(StuntDouble *sd) { |
321 |
> |
GenericData * data; |
322 |
> |
AtomData * atomData; |
323 |
> |
AtomInfo * atomInfo; |
324 |
> |
std::vector<AtomInfo *>::iterator i; |
325 |
> |
char buffer[1024]; |
326 |
> |
|
327 |
> |
//if there is not atom data, just skip it |
328 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
329 |
> |
|
330 |
> |
if (data != NULL) { |
331 |
> |
atomData = dynamic_cast<AtomData *>(data); |
332 |
|
|
333 |
+ |
if (atomData == NULL) |
334 |
+ |
return; |
335 |
+ |
} else |
336 |
+ |
return; |
337 |
+ |
|
338 |
+ |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
339 |
+ |
atomInfo = atomData->nextAtomInfo(i) ) { |
340 |
+ |
if (printDipole) |
341 |
+ |
sprintf(buffer, |
342 |
+ |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
343 |
+ |
atomInfo->AtomType.c_str(), |
344 |
+ |
atomInfo->pos[0], |
345 |
+ |
atomInfo->pos[1], |
346 |
+ |
atomInfo->pos[2], |
347 |
+ |
atomInfo->dipole[0], |
348 |
+ |
atomInfo->dipole[1], |
349 |
+ |
atomInfo->dipole[2]); else |
350 |
+ |
sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
351 |
+ |
atomInfo->AtomType.c_str(), atomInfo->pos[0], |
352 |
+ |
atomInfo->pos[1], atomInfo->pos[2]); |
353 |
+ |
|
354 |
+ |
frame.push_back(buffer); |
355 |
+ |
} |
356 |
|
} |
357 |
|
|
358 |
< |
void XYZVisitor::internalVisit(StuntDouble* sd){ |
359 |
< |
GenericData* data; |
270 |
< |
AtomData* atomData; |
271 |
< |
AtomInfo* atomInfo; |
272 |
< |
vector<AtomInfo*>::iterator i; |
273 |
< |
char buffer[1024]; |
274 |
< |
|
275 |
< |
//if there is not atom data, just skip it |
276 |
< |
data = sd->getProperty("ATOMDATA"); |
277 |
< |
if(data != NULL){ |
278 |
< |
atomData = dynamic_cast<AtomData*>(data); |
279 |
< |
if(atomData == NULL) |
280 |
< |
return; |
281 |
< |
} |
282 |
< |
else |
283 |
< |
return; |
358 |
> |
bool XYZVisitor::isIgnore(StuntDouble *sd) { |
359 |
> |
GenericData *data; |
360 |
|
|
361 |
< |
for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){ |
361 |
> |
data = sd->getPropertyByName("IGNORE"); |
362 |
> |
return data == NULL ? false : true; |
363 |
> |
} |
364 |
|
|
365 |
< |
if(printDipole) |
366 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
367 |
< |
atomInfo->AtomType.c_str(), |
290 |
< |
atomInfo->pos[0], |
291 |
< |
atomInfo->pos[1], |
292 |
< |
atomInfo->pos[2], |
293 |
< |
atomInfo->dipole[0], |
294 |
< |
atomInfo->dipole[1], |
295 |
< |
atomInfo->dipole[2]); |
296 |
< |
else |
297 |
< |
sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
298 |
< |
atomInfo->AtomType.c_str(), |
299 |
< |
atomInfo->pos[0], |
300 |
< |
atomInfo->pos[1], |
301 |
< |
atomInfo->pos[2]); |
365 |
> |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
366 |
> |
std::vector<std::string>::iterator i; |
367 |
> |
char buffer[1024]; |
368 |
|
|
369 |
< |
frame.push_back(buffer); |
370 |
< |
|
305 |
< |
} |
369 |
> |
if (frame.size() == 0) |
370 |
> |
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
371 |
|
|
372 |
< |
} |
372 |
> |
//total number of atoms |
373 |
> |
outStream << frame.size() << std::endl; |
374 |
|
|
375 |
< |
bool XYZVisitor::isIgnore(StuntDouble* sd){ |
376 |
< |
GenericData* data; |
377 |
< |
|
378 |
< |
data = sd->getProperty("IGNORE"); |
379 |
< |
return data ==NULL ? false : true; |
375 |
> |
//write comment line |
376 |
> |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
377 |
> |
Mat3x3d box = currSnapshot->getHmat(); |
378 |
> |
|
379 |
> |
sprintf(buffer, |
380 |
> |
"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
381 |
> |
currSnapshot->getTime(), |
382 |
> |
box(0, 0), box(0, 1), box(0, 2), |
383 |
> |
box(1, 0), box(1, 1), box(1, 2), |
384 |
> |
box(2, 0), box(2, 1), box(2, 2)); |
385 |
> |
|
386 |
> |
outStream << buffer << std::endl; |
387 |
> |
|
388 |
> |
for( i = frame.begin(); i != frame.end(); ++i ) |
389 |
> |
outStream << *i << std::endl; |
390 |
|
} |
391 |
|
|
392 |
< |
void XYZVisitor::writeFrame(ostream& outStream){ |
393 |
< |
vector<string>::iterator i; |
394 |
< |
double box[3][3]; |
319 |
< |
char buffer[1024]; |
392 |
> |
const std::string XYZVisitor::toString() { |
393 |
> |
char buffer[65535]; |
394 |
> |
std::string result; |
395 |
|
|
396 |
< |
if(frame.size() == 0) |
397 |
< |
cerr << "Current Frame does not contain any atoms" << endl; |
396 |
> |
sprintf(buffer, |
397 |
> |
"------------------------------------------------------------------\n"); |
398 |
> |
result += buffer; |
399 |
|
|
400 |
< |
//total number of atoms |
401 |
< |
outStream << frame.size() << endl; |
400 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
401 |
> |
result += buffer; |
402 |
|
|
403 |
< |
//write comment line |
404 |
< |
info->getBoxM(box); |
405 |
< |
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(), |
331 |
< |
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]); |
403 |
> |
sprintf(buffer, |
404 |
> |
"Visitor Description: assemble the atom data and output xyz file\n"); |
405 |
> |
result += buffer; |
406 |
|
|
407 |
< |
outStream << buffer << endl; |
407 |
> |
sprintf(buffer, |
408 |
> |
"------------------------------------------------------------------\n"); |
409 |
> |
result += buffer; |
410 |
|
|
411 |
< |
for(i = frame.begin(); i != frame.end(); ++i) |
338 |
< |
outStream << *i << endl; |
411 |
> |
return result; |
412 |
|
} |
413 |
|
|
414 |
< |
const string XYZVisitor::toString(){ |
342 |
< |
char buffer[65535]; |
343 |
< |
string result; |
344 |
< |
|
345 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
346 |
< |
result += buffer; |
414 |
> |
//----------------------------------------------------------------------------// |
415 |
|
|
416 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
417 |
< |
result += buffer; |
416 |
> |
void PrepareVisitor::internalVisit(Atom *atom) { |
417 |
> |
GenericData *data; |
418 |
> |
AtomData * atomData; |
419 |
|
|
420 |
< |
sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n"); |
421 |
< |
result += buffer; |
353 |
< |
|
354 |
< |
sprintf(buffer,"------------------------------------------------------------------\n"); |
355 |
< |
result += buffer; |
420 |
> |
//if visited property is existed, remove it |
421 |
> |
data = atom->getPropertyByName("VISITED"); |
422 |
|
|
423 |
< |
return result; |
423 |
> |
if (data != NULL) { |
424 |
> |
atom->removeProperty("VISITED"); |
425 |
> |
} |
426 |
> |
|
427 |
> |
//remove atomdata |
428 |
> |
data = atom->getPropertyByName("ATOMDATA"); |
429 |
> |
|
430 |
> |
if (data != NULL) { |
431 |
> |
atomData = dynamic_cast<AtomData *>(data); |
432 |
> |
|
433 |
> |
if (atomData != NULL) |
434 |
> |
atom->removeProperty("ATOMDATA"); |
435 |
> |
} |
436 |
|
} |
437 |
|
|
438 |
< |
//----------------------------------------------------------------------------// |
438 |
> |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
439 |
> |
GenericData* data; |
440 |
> |
AtomData* atomData; |
441 |
> |
std::vector<Atom *> myAtoms; |
442 |
> |
std::vector<Atom *>::iterator atomIter; |
443 |
|
|
444 |
< |
void PrepareVisitor::internalVisit(Atom * atom){ |
445 |
< |
GenericData* data; |
364 |
< |
AtomData* atomData; |
444 |
> |
//if visited property is existed, remove it |
445 |
> |
data = rb->getPropertyByName("VISITED"); |
446 |
|
|
447 |
< |
//if visited property is existed, remove it |
448 |
< |
data = atom->getProperty("VISITED"); |
449 |
< |
if(data != NULL){ |
369 |
< |
atom->removeProperty("VISITED"); |
370 |
< |
} |
447 |
> |
if (data != NULL) { |
448 |
> |
rb->removeProperty("VISITED"); |
449 |
> |
} |
450 |
|
|
451 |
< |
//remove atomdata |
452 |
< |
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 |
< |
} |
451 |
> |
//remove atomdata |
452 |
> |
data = rb->getPropertyByName("ATOMDATA"); |
453 |
|
|
454 |
< |
void PrepareVisitor::internalVisit(RigidBody * rb){ |
455 |
< |
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 |
< |
} |
454 |
> |
if (data != NULL) { |
455 |
> |
atomData = dynamic_cast<AtomData *>(data); |
456 |
|
|
457 |
< |
//remove atomdata |
458 |
< |
data = rb->getProperty("ATOMDATA"); |
459 |
< |
if(data != NULL){ |
397 |
< |
atomData = dynamic_cast<AtomData*>(data); |
398 |
< |
if(atomData != NULL) |
399 |
< |
rb->removeProperty("ATOMDATA"); |
400 |
< |
} |
457 |
> |
if (atomData != NULL) |
458 |
> |
rb->removeProperty("ATOMDATA"); |
459 |
> |
} |
460 |
|
|
461 |
< |
myAtoms = rb->getAtoms(); |
462 |
< |
|
463 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
464 |
< |
internalVisit (*atomIter); |
461 |
> |
myAtoms = rb->getAtoms(); |
462 |
> |
|
463 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
464 |
> |
internalVisit(*atomIter); |
465 |
|
} |
466 |
|
|
467 |
< |
const string PrepareVisitor::toString(){ |
468 |
< |
char buffer[65535]; |
469 |
< |
string result; |
411 |
< |
|
412 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
413 |
< |
result += buffer; |
467 |
> |
const std::string PrepareVisitor::toString() { |
468 |
> |
char buffer[65535]; |
469 |
> |
std::string result; |
470 |
|
|
471 |
< |
sprintf(buffer ,"Visitor name: %s", visitorName.c_str()); |
472 |
< |
result += buffer; |
471 |
> |
sprintf(buffer, |
472 |
> |
"------------------------------------------------------------------\n"); |
473 |
> |
result += buffer; |
474 |
|
|
475 |
< |
sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n"); |
476 |
< |
result += buffer; |
475 |
> |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
476 |
> |
result += buffer; |
477 |
|
|
478 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
479 |
< |
result += buffer; |
478 |
> |
sprintf(buffer, |
479 |
> |
"Visitor Description: prepare for operation of other vistors\n"); |
480 |
> |
result += buffer; |
481 |
|
|
482 |
< |
return result; |
482 |
> |
sprintf(buffer, |
483 |
> |
"------------------------------------------------------------------\n"); |
484 |
> |
result += buffer; |
485 |
> |
|
486 |
> |
return result; |
487 |
|
} |
488 |
|
|
489 |
|
//----------------------------------------------------------------------------// |
490 |
|
|
491 |
< |
WaterTypeVisitor:: WaterTypeVisitor(){ |
492 |
< |
visitorName = "WaterTypeVisitor"; |
493 |
< |
waterTypeList.insert("TIP3P_RB_0"); |
494 |
< |
waterTypeList.insert("TIP4P_RB_0"); |
495 |
< |
waterTypeList.insert("TIP5P_RB_0"); |
496 |
< |
waterTypeList.insert("SPCE_RB_0"); |
491 |
> |
WaterTypeVisitor::WaterTypeVisitor() { |
492 |
> |
visitorName = "WaterTypeVisitor"; |
493 |
> |
waterTypeList.insert("TIP3P_RB_0"); |
494 |
> |
waterTypeList.insert("TIP4P_RB_0"); |
495 |
> |
waterTypeList.insert("TIP5P_RB_0"); |
496 |
> |
waterTypeList.insert("SPCE_RB_0"); |
497 |
|
} |
498 |
|
|
499 |
+ |
void WaterTypeVisitor::visit(RigidBody *rb) { |
500 |
+ |
std::string rbName; |
501 |
+ |
std::vector<Atom *> myAtoms; |
502 |
+ |
std::vector<Atom *>::iterator atomIter; |
503 |
+ |
GenericData* data; |
504 |
+ |
AtomData* atomData; |
505 |
+ |
AtomInfo* atomInfo; |
506 |
+ |
std::vector<AtomInfo *>::iterator i; |
507 |
|
|
508 |
< |
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(); |
508 |
> |
rbName = rb->getType(); |
509 |
|
|
510 |
< |
if(waterTypeList.find(rbName) != waterTypeList.end()){ |
510 |
> |
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
511 |
> |
myAtoms = rb->getAtoms(); |
512 |
|
|
513 |
< |
myAtoms = rb->getAtoms(); |
514 |
< |
for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){ |
513 |
> |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
514 |
> |
++atomIter ) { |
515 |
> |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
516 |
|
|
517 |
< |
data = (*atomIter)->getProperty("ATOMDATA"); |
518 |
< |
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) |
517 |
> |
if (data != NULL) { |
518 |
> |
atomData = dynamic_cast<AtomData *>(data); |
519 |
|
|
520 |
< |
}//end for(atomIter) |
521 |
< |
|
522 |
< |
}//end if (waterTypeList.find(rbName) != waterTypeList.end()) |
523 |
< |
|
520 |
> |
if (atomData == NULL) |
521 |
> |
continue; |
522 |
> |
} else |
523 |
> |
continue; |
524 |
> |
|
525 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
526 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
527 |
> |
replaceType(atomInfo->AtomType); |
528 |
> |
} //end for(atomInfo) |
529 |
> |
} //end for(atomIter) |
530 |
> |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
531 |
|
} |
532 |
|
|
533 |
< |
void WaterTypeVisitor:: replaceType(string& atomType){ |
534 |
< |
atomType = atomType.substr(0, atomType.find('_')); |
533 |
> |
void WaterTypeVisitor::replaceType(std::string&atomType) { |
534 |
> |
atomType = atomType.substr(0, atomType.find('_')); |
535 |
|
} |
536 |
|
|
537 |
< |
const string WaterTypeVisitor:: toString(){ |
538 |
< |
char buffer[65535]; |
539 |
< |
string result; |
480 |
< |
|
481 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
482 |
< |
result += buffer; |
537 |
> |
const std::string WaterTypeVisitor::toString() { |
538 |
> |
char buffer[65535]; |
539 |
> |
std::string result; |
540 |
|
|
541 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
542 |
< |
result += buffer; |
541 |
> |
sprintf(buffer, |
542 |
> |
"------------------------------------------------------------------\n"); |
543 |
> |
result += buffer; |
544 |
|
|
545 |
< |
sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n"); |
546 |
< |
result += buffer; |
545 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
546 |
> |
result += buffer; |
547 |
|
|
548 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
549 |
< |
result += buffer; |
548 |
> |
sprintf(buffer, |
549 |
> |
"Visitor Description: Replace the atom type in water model\n"); |
550 |
> |
result += buffer; |
551 |
|
|
552 |
< |
return result; |
552 |
> |
sprintf(buffer, |
553 |
> |
"------------------------------------------------------------------\n"); |
554 |
> |
result += buffer; |
555 |
> |
|
556 |
> |
return result; |
557 |
|
} |
558 |
|
|
559 |
< |
|
497 |
< |
}//namespace oopse |
559 |
> |
} //namespace oopse |