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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <cstring> |
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#include "visitors/ReplacementVisitor.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "primitives/RigidBody.hpp" |
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|
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namespace OpenMD { |
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|
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void ReplacementVisitor::addReplacedAtomName(const std::string& repName) { |
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myTypes_.insert(repName); |
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} |
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|
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ReplacementVisitor::~ReplacementVisitor(){ |
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delete sites_; |
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myTypes_.clear(); |
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} |
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|
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bool ReplacementVisitor::isReplacedAtom(const std::string& atomType) { |
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std::set<std::string>::iterator strIter; |
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strIter = myTypes_.find(atomType); |
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return strIter != myTypes_.end() ? true : false; |
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} |
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|
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void ReplacementVisitor::addSite(const std::string& name, |
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const Vector3d refPos) { |
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AtomInfo* atomInfo = new AtomInfo(); |
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atomInfo->atomTypeName = name; |
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atomInfo->pos = refPos; |
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sites_->addAtomInfo(atomInfo); |
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} |
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void ReplacementVisitor::addSite(const std::string& name, |
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const Vector3d refPos, |
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const Vector3d refVec) { |
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AtomInfo* atomInfo = new AtomInfo(); |
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atomInfo->atomTypeName = name; |
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atomInfo->pos = refPos; |
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atomInfo->vec = refVec; |
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atomInfo->hasVector = true; |
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sites_->addAtomInfo(atomInfo); |
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} |
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|
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void ReplacementVisitor::visit(DirectionalAtom *datom) { |
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std::vector<AtomInfo*>atoms; |
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|
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RotMat3x3d A; |
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RotMat3x3d Atrans; |
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Mat3x3d I; |
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Vector3d pos; |
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Vector3d vel; |
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Vector3d frc; |
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Vector3d trq; |
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Vector3d j; |
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Mat3x3d skewMat; |
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|
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Vector3d newVec; |
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AtomInfo * atomInfo; |
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AtomData * atomData; |
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GenericData *data; |
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bool haveAtomData; |
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|
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//if atom is not one of our recognized atom types, just skip it |
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if (!isReplacedAtom(datom->getType())) |
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return; |
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|
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data = datom->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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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else |
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haveAtomData = true; |
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} else { |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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|
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pos = datom->getPos(); |
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vel = datom->getVel(); |
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frc = datom->getFrc(); |
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trq = datom->getTrq(); |
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j = datom->getJ(); |
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I = datom->getI(); |
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A = datom->getA(); |
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skewMat(0, 0) = 0; |
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skewMat(0, 1) = j[2] / I(2, 2); |
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skewMat(0, 2) = -j[1] / I(1, 1); |
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skewMat(1, 0) = -j[2] / I(2, 2); |
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skewMat(1, 1) = 0; |
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skewMat(1, 2) = j[0] / I(0, 0); |
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skewMat(2, 0) = j[1] / I(1, 1); |
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skewMat(2, 1) = -j[0] / I(0, 0); |
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skewMat(2, 2) = 0; |
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|
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Mat3x3d mat = (A * skewMat).transpose(); |
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|
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// We need A^T to convert from body-fixed to space-fixed: |
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Atrans = A.transpose(); |
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|
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AtomInfo* siteInfo; |
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std::vector<AtomInfo*>::iterator iter; |
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|
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for( siteInfo = sites_->beginAtomInfo(iter); siteInfo; |
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siteInfo = sites_->nextAtomInfo(iter) ) { |
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|
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newVec = Atrans * siteInfo->pos; |
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|
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atomInfo = new AtomInfo; |
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atomInfo->atomTypeName = siteInfo->atomTypeName; |
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atomInfo->pos = pos + newVec; |
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|
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if (siteInfo->hasVector) { |
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newVec = Atrans * siteInfo->vec; |
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atomInfo->vec = newVec; |
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} else { |
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atomInfo->vec = V3Zero; |
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} |
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|
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atomInfo->vel = vel + mat * siteInfo->pos; |
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atomInfo->hasVelocity = true; |
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|
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atomData->addAtomInfo(atomInfo); |
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} |
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if (!haveAtomData) { |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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} |
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|
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setVisited(datom); |
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} |
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|
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const std::string ReplacementVisitor::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: replace atom with other sites\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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} |
