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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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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; atomInfo = atomData->nextAtomInfo(i) ) { |
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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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void WrappingVisitor::update() { |
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if (useCom_){ |
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origin_ = info->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) : |
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BaseVisitor(), seleMan(info), evaluator(info){ |
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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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|
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XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
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BaseVisitor(), seleMan(info), evaluator(info) { |
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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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|
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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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sprintf(buffer, |
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"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
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atomInfo->atomTypeName.c_str(), |
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atomInfo->pos[0], |
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atomInfo->pos[1], |
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atomInfo->pos[2], |
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atomInfo->dipole[0], |
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atomInfo->dipole[1], |
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atomInfo->dipole[2]); |
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frame.push_back(buffer); |
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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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} |
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|
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void XYZVisitor::writeFrame(std::ostream &outStream) { |
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std::vector<std::string>::iterator i; |
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char buffer[1024]; |
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|
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if (frame.size() == 0) |
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std::cerr << "Current Frame does not contain any atoms" << std::endl; |
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|
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//total number of atoms |
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outStream << frame.size() << std::endl; |
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|
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//write comment line |
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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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sprintf(buffer, |
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"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
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currSnapshot->getTime(), |
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box(0, 0), box(0, 1), box(0, 2), |
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box(1, 0), box(1, 1), box(1, 2), |
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box(2, 0), box(2, 1), box(2, 2)); |
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|
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outStream << buffer << std::endl; |
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|
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for( i = frame.begin(); i != frame.end(); ++i ) |
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outStream << *i << std::endl; |
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} |
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|
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const std::string XYZVisitor::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: assemble the atom data and output xyz file\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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void PrepareVisitor::internalVisit(Atom *atom) { |
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GenericData *data; |
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AtomData * atomData; |
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|
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//if visited property is existed, remove it |
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data = atom->getPropertyByName("VISITED"); |
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|
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if (data != NULL) { |
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atom->removeProperty("VISITED"); |
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} |
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|
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//remove atomdata |
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data = atom->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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atom->removeProperty("ATOMDATA"); |
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} |
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} |
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|
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void PrepareVisitor::internalVisit(RigidBody *rb) { |
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GenericData* data; |
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AtomData* atomData; |
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std::vector<Atom *> myAtoms; |
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std::vector<Atom *>::iterator atomIter; |
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|
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//if visited property is existed, remove it |
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data = rb->getPropertyByName("VISITED"); |
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|
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if (data != NULL) { |
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rb->removeProperty("VISITED"); |
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} |
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|
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//remove atomdata |
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data = rb->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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rb->removeProperty("ATOMDATA"); |
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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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const std::string PrepareVisitor::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", 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: prepare for operation of other vistors\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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//----------------------------------------------------------------------------// |
| 438 |
|
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WaterTypeVisitor::WaterTypeVisitor() { |
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visitorName = "WaterTypeVisitor"; |
| 441 |
waterTypeList.insert("TIP3P_RB_0"); |
| 442 |
waterTypeList.insert("TIP4P_RB_0"); |
| 443 |
waterTypeList.insert("TIP5P_RB_0"); |
| 444 |
waterTypeList.insert("SPCE_RB_0"); |
| 445 |
} |
| 446 |
|
| 447 |
void WaterTypeVisitor::visit(RigidBody *rb) { |
| 448 |
std::string rbName; |
| 449 |
std::vector<Atom *> myAtoms; |
| 450 |
std::vector<Atom *>::iterator atomIter; |
| 451 |
GenericData* data; |
| 452 |
AtomData* atomData; |
| 453 |
AtomInfo* atomInfo; |
| 454 |
std::vector<AtomInfo *>::iterator i; |
| 455 |
|
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rbName = rb->getType(); |
| 457 |
|
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if (waterTypeList.find(rbName) != waterTypeList.end()) { |
| 459 |
myAtoms = rb->getAtoms(); |
| 460 |
|
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for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
| 462 |
++atomIter ) { |
| 463 |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
| 464 |
|
| 465 |
if (data != NULL) { |
| 466 |
atomData = dynamic_cast<AtomData *>(data); |
| 467 |
|
| 468 |
if (atomData == NULL) |
| 469 |
continue; |
| 470 |
} else |
| 471 |
continue; |
| 472 |
|
| 473 |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 474 |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 475 |
atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName); |
| 476 |
} //end for(atomInfo) |
| 477 |
} //end for(atomIter) |
| 478 |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
| 479 |
} |
| 480 |
|
| 481 |
std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) { |
| 482 |
return atomTypeName.substr(0, atomTypeName.find('_')); |
| 483 |
} |
| 484 |
|
| 485 |
const std::string WaterTypeVisitor::toString() { |
| 486 |
char buffer[65535]; |
| 487 |
std::string result; |
| 488 |
|
| 489 |
sprintf(buffer, |
| 490 |
"------------------------------------------------------------------\n"); |
| 491 |
result += buffer; |
| 492 |
|
| 493 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 494 |
result += buffer; |
| 495 |
|
| 496 |
sprintf(buffer, |
| 497 |
"Visitor Description: Replace the atom type in water model\n"); |
| 498 |
result += buffer; |
| 499 |
|
| 500 |
sprintf(buffer, |
| 501 |
"------------------------------------------------------------------\n"); |
| 502 |
result += buffer; |
| 503 |
|
| 504 |
return result; |
| 505 |
} |
| 506 |
|
| 507 |
} //namespace oopse |
