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/*
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gezelter |
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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
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* research, please cite the appropriate papers when you publish your
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* work. Good starting points are:
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*
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
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gezelter |
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* [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
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gezelter |
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*/
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#include <sstream>
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#include <fstream>
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#include "visitors/AtomNameVisitor.hpp"
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#include "utils/Trim.hpp"
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#include "utils/StringTokenizer.hpp"
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#include "brains/SimInfo.hpp"
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namespace OpenMD {
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AtomNameVisitor::AtomNameVisitor(SimInfo* info) : BaseVisitor(),
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info_(info) {
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visitorName = "AtomNameVisitor";
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ff_ = info_->getForceField();
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}
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void AtomNameVisitor::visitAtom(Atom* atom) {
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AtomData* atomData;
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GenericData* data;
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data = atom->getPropertyByName("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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std::cerr << "can not get Atom Data from " << atom->getType()
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<< std::endl;
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atomData = new AtomData;
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} else {
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}
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} else {
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atomData = new AtomData;
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}
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std::vector<AtomInfo*>::iterator i;
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for (AtomInfo* atomInfo = atomData->beginAtomInfo(i);
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atomInfo != NULL;
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atomInfo = atomData->nextAtomInfo(i)) {
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// query the force field for the AtomType associated with this
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// atomTypeName:
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AtomType* at = ff_->getAtomType(atomInfo->atomTypeName);
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// get the chain of base types for this atom type:
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std::vector<AtomType*> ayb = at->allYourBase();
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// use the last type in the chain of base types for the name:
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std::string bn = ayb[ayb.size()-1]->getName();
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atomInfo->atomTypeName = bn;
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}
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}
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void AtomNameVisitor::visit(RigidBody* rb) {
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std::vector<Atom*>::iterator i;
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for (Atom* atom = rb->beginAtom(i); atom != NULL; atom = rb->nextAtom(i)) {
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visit(atom);
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}
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}
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const std::string AtomNameVisitor::toString() {
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char buffer[65535];
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std::string result;
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sprintf(buffer,
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"------------------------------------------------------------------\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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sprintf(buffer,
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"Visitor Description: print base atom types\n");
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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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return result;
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}
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}
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