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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. 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, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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#include "brains/Thermo.hpp" |
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|
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namespace OpenMD { |
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|
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void WrappingVisitor::visit(Atom *atom) { |
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internalVisit(atom); |
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} |
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|
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void WrappingVisitor::visit(DirectionalAtom *datom) { |
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internalVisit(datom); |
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} |
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|
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void WrappingVisitor::visit(RigidBody *rb) { |
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internalVisit(rb); |
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} |
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|
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void WrappingVisitor::internalVisit(StuntDouble *sd) { |
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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->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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|
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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; |
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atomInfo = atomData->nextAtomInfo(i) ) { |
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|
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Vector3d newPos = atomInfo->pos - origin_; |
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currSnapshot->wrapVector(newPos); |
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atomInfo->pos = newPos; |
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|
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} |
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} |
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|
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void WrappingVisitor::update() { |
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if (useCom_){ |
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Thermo thermo(info); |
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origin_ = thermo.getCom(); |
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} |
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} |
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|
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const std::string WrappingVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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|
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sprintf(buffer, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer, |
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"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, |
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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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ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
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BaseVisitor() { |
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this->info = info; |
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visitorName = "ReplicateVisitor"; |
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this->replicateOpt = opt; |
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|
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//generate the replicate directions |
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for( int i = 0; i <= replicateOpt[0]; i++ ) { |
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for( int j = 0; j <= replicateOpt[1]; j++ ) { |
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for( int k = 0; k <= replicateOpt[2]; k++ ) { |
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//skip original frame |
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if (i == 0 && j == 0 && k == 0) { |
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continue; |
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} else { |
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dir.push_back(Vector3i(i, j, k)); |
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} |
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} |
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} |
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} |
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|
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} |
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|
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void ReplicateVisitor::visit(Atom *atom) { |
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internalVisit(atom); |
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} |
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|
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void ReplicateVisitor::visit(DirectionalAtom *datom) { |
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internalVisit(datom); |
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} |
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|
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void ReplicateVisitor::visit(RigidBody *rb) { |
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internalVisit(rb); |
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} |
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|
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void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
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GenericData * data; |
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AtomData * atomData; |
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|
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//if there is not atom data, just skip it |
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data = sd->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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|
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if (atomData == NULL) { |
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return; |
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} |
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} else { |
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return; |
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} |
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|
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Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d box = currSnapshot->getHmat(); |
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|
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std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
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|
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replicate(atomInfoList, atomData, box); |
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} |
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|
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void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
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AtomInfo* newAtomInfo; |
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std::vector<Vector3i>::iterator dirIter; |
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std::vector<AtomInfo *>::iterator i; |
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|
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for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
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for( i = infoList.begin(); i != infoList.end(); i++ ) { |
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newAtomInfo = new AtomInfo(); |
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*newAtomInfo = *(*i); |
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|
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for( int j = 0; j < 3; j++ ) |
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newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
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|
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data->addAtomInfo(newAtomInfo); |
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} |
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} // end for(dirIter) |
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} |
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|
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const std::string ReplicateVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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std::set<std::string>::iterator i; |
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|
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sprintf(buffer, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer, |
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"Visitor Description: replicate the atoms in different direction\n"); |
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result += buffer; |
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|
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//print the replicate direction |
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sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]); |
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result += buffer; |
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|
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sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]); |
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result += buffer; |
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|
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sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]); |
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result += buffer; |
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|
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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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XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info), |
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evaluator(info), doPositions_(true), |
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doVelocities_(false), |
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doForces_(false), doVectors_(false), |
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doCharges_(false) { |
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this->info = info; |
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visitorName = "XYZVisitor"; |
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|
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evaluator.loadScriptString("select all"); |
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|
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if (!evaluator.isDynamic()) { |
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seleMan.setSelectionSet(evaluator.evaluate()); |
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} |
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} |
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|
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XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
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BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true), |
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doVelocities_(false), doForces_(false), doVectors_(false), |
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doCharges_(false) { |
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|
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this->info = info; |
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visitorName = "XYZVisitor"; |
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|
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evaluator.loadScriptString(script); |
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|
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if (!evaluator.isDynamic()) { |
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seleMan.setSelectionSet(evaluator.evaluate()); |
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} |
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} |
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|
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void XYZVisitor::visit(Atom *atom) { |
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if (isSelected(atom)) |
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internalVisit(atom); |
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} |
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|
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void XYZVisitor::visit(DirectionalAtom *datom) { |
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if (isSelected(datom)) |
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internalVisit(datom); |
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} |
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|
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void XYZVisitor::visit(RigidBody *rb) { |
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if (isSelected(rb)) |
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internalVisit(rb); |
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} |
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|
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void XYZVisitor::update() { |
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//if dynamic, we need to re-evaluate the selection |
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if (evaluator.isDynamic()) { |
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seleMan.setSelectionSet(evaluator.evaluate()); |
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} |
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} |
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|
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void XYZVisitor::internalVisit(StuntDouble *sd) { |
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GenericData * data; |
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AtomData * atomData; |
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AtomInfo * atomInfo; |
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std::vector<AtomInfo *>::iterator i; |
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char buffer[1024]; |
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|
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//if there is not atom data, just skip it |
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data = sd->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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|
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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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for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
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atomInfo = atomData->nextAtomInfo(i) ) { |
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|
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std::string line; |
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sprintf(buffer, "%s", atomInfo->atomTypeName.c_str()); |
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line += buffer; |
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|
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if (doPositions_){ |
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sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0], |
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atomInfo->pos[1], atomInfo->pos[2]); |
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line += buffer; |
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} |
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if (doCharges_ && atomInfo->hasCharge) { |
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sprintf(buffer, "%15.8f", atomInfo->charge); |
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line += buffer; |
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} |
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if (doVectors_ && atomInfo->hasVector) { |
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sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0], |
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atomInfo->vec[1], atomInfo->vec[2]); |
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line += buffer; |
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} |
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if (doVelocities_ && atomInfo->hasVelocity) { |
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sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0], |
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atomInfo->vel[1], atomInfo->vel[2]); |
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line += buffer; |
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} |
| 331 |
if (doForces_ && atomInfo->hasForce) { |
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sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0], |
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atomInfo->frc[1], atomInfo->frc[2]); |
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line += buffer; |
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} |
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if (doElectricFields_ && atomInfo->hasElectricField) { |
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sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->eField[0], |
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atomInfo->eField[1], atomInfo->eField[2]); |
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line += buffer; |
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} |
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frame.push_back(line); |
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} |
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} |
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|
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bool XYZVisitor::isSelected(StuntDouble *sd) { |
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return seleMan.isSelected(sd); |
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} |
| 348 |
|
| 349 |
void XYZVisitor::writeFrame(std::ostream &outStream) { |
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std::vector<std::string>::iterator i; |
| 351 |
char buffer[1024]; |
| 352 |
|
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if (frame.size() == 0) |
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std::cerr << "Current Frame does not contain any atoms" << std::endl; |
| 355 |
|
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//total number of atoms |
| 357 |
outStream << frame.size() << std::endl; |
| 358 |
|
| 359 |
//write comment line |
| 360 |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 361 |
Mat3x3d box = currSnapshot->getHmat(); |
| 362 |
|
| 363 |
sprintf(buffer, |
| 364 |
"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
| 365 |
currSnapshot->getTime(), |
| 366 |
box(0, 0), box(0, 1), box(0, 2), |
| 367 |
box(1, 0), box(1, 1), box(1, 2), |
| 368 |
box(2, 0), box(2, 1), box(2, 2)); |
| 369 |
|
| 370 |
outStream << buffer << std::endl; |
| 371 |
|
| 372 |
for( i = frame.begin(); i != frame.end(); ++i ) |
| 373 |
outStream << *i << std::endl; |
| 374 |
} |
| 375 |
|
| 376 |
std::string XYZVisitor::trimmedName(const std::string&atomTypeName) { |
| 377 |
return atomTypeName.substr(0, atomTypeName.find('-')); |
| 378 |
} |
| 379 |
|
| 380 |
const std::string XYZVisitor::toString() { |
| 381 |
char buffer[65535]; |
| 382 |
std::string result; |
| 383 |
|
| 384 |
sprintf(buffer, |
| 385 |
"------------------------------------------------------------------\n"); |
| 386 |
result += buffer; |
| 387 |
|
| 388 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 389 |
result += buffer; |
| 390 |
|
| 391 |
sprintf(buffer, |
| 392 |
"Visitor Description: assemble the atom data and output xyz file\n"); |
| 393 |
result += buffer; |
| 394 |
|
| 395 |
sprintf(buffer, |
| 396 |
"------------------------------------------------------------------\n"); |
| 397 |
result += buffer; |
| 398 |
|
| 399 |
return result; |
| 400 |
} |
| 401 |
|
| 402 |
//----------------------------------------------------------------------------// |
| 403 |
|
| 404 |
void PrepareVisitor::internalVisit(Atom *atom) { |
| 405 |
GenericData *data; |
| 406 |
AtomData * atomData; |
| 407 |
|
| 408 |
//if visited property is existed, remove it |
| 409 |
data = atom->getPropertyByName("VISITED"); |
| 410 |
|
| 411 |
if (data != NULL) { |
| 412 |
atom->removeProperty("VISITED"); |
| 413 |
} |
| 414 |
|
| 415 |
//remove atomdata |
| 416 |
data = atom->getPropertyByName("ATOMDATA"); |
| 417 |
|
| 418 |
if (data != NULL) { |
| 419 |
atomData = dynamic_cast<AtomData *>(data); |
| 420 |
|
| 421 |
if (atomData != NULL) |
| 422 |
atom->removeProperty("ATOMDATA"); |
| 423 |
} |
| 424 |
} |
| 425 |
|
| 426 |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
| 427 |
GenericData* data; |
| 428 |
AtomData* atomData; |
| 429 |
std::vector<Atom *> myAtoms; |
| 430 |
std::vector<Atom *>::iterator atomIter; |
| 431 |
|
| 432 |
//if visited property is existed, remove it |
| 433 |
data = rb->getPropertyByName("VISITED"); |
| 434 |
|
| 435 |
if (data != NULL) { |
| 436 |
rb->removeProperty("VISITED"); |
| 437 |
} |
| 438 |
|
| 439 |
//remove atomdata |
| 440 |
data = rb->getPropertyByName("ATOMDATA"); |
| 441 |
|
| 442 |
if (data != NULL) { |
| 443 |
atomData = dynamic_cast<AtomData *>(data); |
| 444 |
|
| 445 |
if (atomData != NULL) |
| 446 |
rb->removeProperty("ATOMDATA"); |
| 447 |
} |
| 448 |
|
| 449 |
myAtoms = rb->getAtoms(); |
| 450 |
|
| 451 |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
| 452 |
internalVisit(*atomIter); |
| 453 |
} |
| 454 |
|
| 455 |
const std::string PrepareVisitor::toString() { |
| 456 |
char buffer[65535]; |
| 457 |
std::string result; |
| 458 |
|
| 459 |
sprintf(buffer, |
| 460 |
"------------------------------------------------------------------\n"); |
| 461 |
result += buffer; |
| 462 |
|
| 463 |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
| 464 |
result += buffer; |
| 465 |
|
| 466 |
sprintf(buffer, |
| 467 |
"Visitor Description: prepare for operation of other vistors\n"); |
| 468 |
result += buffer; |
| 469 |
|
| 470 |
sprintf(buffer, |
| 471 |
"------------------------------------------------------------------\n"); |
| 472 |
result += buffer; |
| 473 |
|
| 474 |
return result; |
| 475 |
} |
| 476 |
|
| 477 |
//----------------------------------------------------------------------------// |
| 478 |
|
| 479 |
WaterTypeVisitor::WaterTypeVisitor() { |
| 480 |
visitorName = "WaterTypeVisitor"; |
| 481 |
waterTypeList.insert("TIP3P_RB_0"); |
| 482 |
waterTypeList.insert("TIP4P_RB_0"); |
| 483 |
waterTypeList.insert("TIP4P-Ew_RB_0"); |
| 484 |
waterTypeList.insert("TIP5P_RB_0"); |
| 485 |
waterTypeList.insert("TIP5P-E_RB_0"); |
| 486 |
waterTypeList.insert("SPCE_RB_0"); |
| 487 |
waterTypeList.insert("SPC_RB_0"); |
| 488 |
} |
| 489 |
|
| 490 |
void WaterTypeVisitor::visit(RigidBody *rb) { |
| 491 |
std::string rbName; |
| 492 |
std::vector<Atom *> myAtoms; |
| 493 |
std::vector<Atom *>::iterator atomIter; |
| 494 |
GenericData* data; |
| 495 |
AtomData* atomData; |
| 496 |
AtomInfo* atomInfo; |
| 497 |
std::vector<AtomInfo *>::iterator i; |
| 498 |
|
| 499 |
rbName = rb->getType(); |
| 500 |
|
| 501 |
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
| 502 |
myAtoms = rb->getAtoms(); |
| 503 |
|
| 504 |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
| 505 |
++atomIter ) { |
| 506 |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
| 507 |
|
| 508 |
if (data != NULL) { |
| 509 |
atomData = dynamic_cast<AtomData *>(data); |
| 510 |
|
| 511 |
if (atomData == NULL) |
| 512 |
continue; |
| 513 |
} else |
| 514 |
continue; |
| 515 |
|
| 516 |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 517 |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 518 |
atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName); |
| 519 |
} //end for(atomInfo) |
| 520 |
} //end for(atomIter) |
| 521 |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
| 522 |
} |
| 523 |
|
| 524 |
std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) { |
| 525 |
return atomTypeName.substr(0, atomTypeName.find('_')); |
| 526 |
} |
| 527 |
|
| 528 |
const std::string WaterTypeVisitor::toString() { |
| 529 |
char buffer[65535]; |
| 530 |
std::string result; |
| 531 |
|
| 532 |
sprintf(buffer, |
| 533 |
"------------------------------------------------------------------\n"); |
| 534 |
result += buffer; |
| 535 |
|
| 536 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 537 |
result += buffer; |
| 538 |
|
| 539 |
sprintf(buffer, |
| 540 |
"Visitor Description: Replace the atom type in water model\n"); |
| 541 |
result += buffer; |
| 542 |
|
| 543 |
sprintf(buffer, |
| 544 |
"------------------------------------------------------------------\n"); |
| 545 |
result += buffer; |
| 546 |
|
| 547 |
return result; |
| 548 |
} |
| 549 |
|
| 550 |
} //namespace OpenMD |
