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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] 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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|
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#include "applications/hydrodynamics/BeadModel.hpp" |
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|
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namespace OpenMD { |
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bool BeadModel::createBeads(std::vector<BeadParam>& beads) { |
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|
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if (sd_->isAtom()) { |
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if (!createSingleBead(static_cast<Atom*>(sd_), beads)) { |
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sprintf( painCave.errMsg, |
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"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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return false; |
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} |
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} |
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else if (sd_->isRigidBody()) { |
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RigidBody* rb = static_cast<RigidBody*>(sd_); |
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std::vector<Atom*>::iterator ai; |
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Atom* atom; |
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for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
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if (!createSingleBead(atom, beads)) { |
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sprintf( painCave.errMsg, |
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"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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return false; |
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} |
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} |
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} |
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return true; |
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} |
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|
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bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) { |
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AtomType* atomType = atom->getAtomType(); |
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|
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if (atomType->isGayBerne()) { |
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return false; |
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} else if (atomType->isLennardJones()){ |
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GenericData* data = atomType->getPropertyByName("LennardJones"); |
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if (data != NULL) { |
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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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|
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if (ljData != NULL) { |
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LJParam ljParam = ljData->getData(); |
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BeadParam currBead; |
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currBead.atomName = atom->getType(); |
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currBead.pos = atom->getPos(); |
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currBead.radius = ljParam.sigma/2.0; |
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beads.push_back(currBead); |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to LJParam\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} else { |
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int obanum = etab.GetAtomicNum((atom->getType()).c_str()); |
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if (obanum != 0) { |
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BeadParam currBead; |
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currBead.atomName = atom->getType(); |
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currBead.pos = atom->getPos(); |
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currBead.radius = etab.GetVdwRad(obanum); |
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std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n"; |
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beads.push_back(currBead); |
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} else { |
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sprintf( painCave.errMsg, |
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"Could not find atom type in default element.txt\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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return true; |
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} |
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} |
