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/* |
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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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* 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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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* [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 "visitors/LipidTransVisitor.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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void LipidTransVisitor::update() { |
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namespace OpenMD { |
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LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript) |
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: BaseVisitor(), info_(info), originEvaluator_(info), originSeleMan_(info), refEvaluator_(info), refSeleMan_(info), refSd_(NULL) { |
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Vector3d ref = refSd_->getPos(); |
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origin_ = originDatom_->getPos(); |
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Vector3d v1 = ref - origin_; |
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info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
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Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2); |
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Vector3d xaxis = cross(v1, zaxis); |
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Vector3d yaxis = cross(zaxis, xaxis); |
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|
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visitorName = "LipidTransVisitor"; |
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|
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originEvaluator_.loadScriptString(originSeleScript); |
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if (!originEvaluator_.isDynamic()) { |
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originSeleMan_.setSelectionSet(originEvaluator_.evaluate()); |
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if (originSeleMan_.getSelectionCount() == 1) { |
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int i; |
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originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i)); |
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if (originDatom_ == NULL) { |
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sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom"); |
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painCave.isFatal = 1; |
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simError(); |
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|
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} |
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} |
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xaxis.normalize(); |
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yaxis.normalize(); |
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zaxis.normalize(); |
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refEvaluator_.loadScriptString(refSeleScript); |
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if (!refEvaluator_.isDynamic()) { |
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refSeleMan_.setSelectionSet(refEvaluator_.evaluate()); |
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if (refSeleMan_.getSelectionCount() == 1) { |
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int i; |
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refSd_ = refSeleMan_.beginSelected(i); |
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} else { |
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//error |
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|
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} |
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} |
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} |
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void LipidTransVisitor::update() { |
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Vector3d ref = refSd_->getPos(); |
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origin_ = originDatom_->getPos(); |
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Vector3d v1 = ref - origin_; |
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info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
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Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2); |
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Vector3d xaxis = cross(v1, zaxis); |
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Vector3d yaxis = cross(zaxis, xaxis); |
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xaxis.normalize(); |
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yaxis.normalize(); |
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zaxis.normalize(); |
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rotMat_.setRow(0, xaxis); |
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rotMat_.setRow(1, yaxis); |
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rotMat_.setRow(2, zaxis); |
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rotMat_.setRow(0, xaxis); |
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rotMat_.setRow(1, yaxis); |
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rotMat_.setRow(2, zaxis); |
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} |
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} |
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void LipidTransVisitor::internalVisit(StuntDouble *sd) { |
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void LipidTransVisitor::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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data = sd->getPropertyByName("ATOMDATA"); |
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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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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if (atomData == NULL) |
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return; |
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} else |
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return; |
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return; |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) { |
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Vector3d tmp= atomInfo->pos - origin_; |
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//we don't need to do the wrapping anymore, since LipidTransVisitor will be execute after |
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//WrappingVistor and ReplicateVisitor |
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atomInfo->pos = rotMat_ * tmp; |
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atomInfo->dipole = rotMat_ * atomInfo->dipole; |
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Vector3d tmp= atomInfo->pos - origin_; |
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currSnapshot->wrapVector(tmp); |
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atomInfo->pos = rotMat_ * tmp;; |
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atomInfo->vec = rotMat_ * atomInfo->vec; |
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} |
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} |
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} |
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const std::string LipidTransVisitor::toString() { |
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const std::string LipidTransVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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result += buffer; |
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return result; |
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} |
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} |
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} |
