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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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/** |
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* @file Molecule.hpp |
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* @author tlin |
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* @date 10/25/2004 |
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* @version 1.0 |
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*/ |
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|
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#ifndef PRIMITIVES_MOLECULE_HPP |
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#define PRIMITIVES_MOLECULE_HPP |
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#include <vector> |
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#include <iostream> |
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|
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#include "constraints/ConstraintPair.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Atom.hpp" |
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#include "primitives/RigidBody.hpp" |
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#include "primitives/Bond.hpp" |
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#include "primitives/Bend.hpp" |
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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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#include "primitives/CutoffGroup.hpp" |
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#include "utils/PropertyMap.hpp" |
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|
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namespace OpenMD{ |
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|
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class Constraint; |
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|
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/** |
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* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
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* @brief |
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*/ |
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class Molecule { |
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public: |
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|
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typedef std::vector<Atom*>::iterator AtomIterator; |
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typedef std::vector<Bond*>::iterator BondIterator; |
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typedef std::vector<Bend*>::iterator BendIterator; |
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typedef std::vector<Torsion*>::iterator TorsionIterator; |
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typedef std::vector<Inversion*>::iterator InversionIterator; |
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typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
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typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
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typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
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typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
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typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
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typedef std::vector<Atom*>::iterator FluctuatingChargeIterator; |
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|
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Molecule(int stampId, int globalIndex, const std::string& molName); |
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virtual ~Molecule(); |
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|
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/** |
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* Returns the global index of this molecule. |
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* @return the global index of this molecule |
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*/ |
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int getGlobalIndex() { |
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return globalIndex_; |
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} |
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|
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/** |
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* Returns the stamp id of this molecule |
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* @note Ideally, every molecule should keep a pointer of its |
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* molecule stamp instead of its stamp id. However, the pointer |
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* will become invalid, if the molecule migrate to other |
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* processor. |
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*/ |
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int getStampId() { |
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return stampId_; |
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} |
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|
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/** Returns the name of the molecule */ |
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std::string getType() { |
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return moleculeName_; |
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} |
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|
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/** |
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* Sets the global index of this molecule. |
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* @param new global index to be set |
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*/ |
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void setGlobalIndex(int index) { |
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globalIndex_ = index; |
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} |
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|
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void setConstrainTotalCharge(bool ctc) { |
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constrainTotalCharge_ = ctc; |
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} |
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|
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bool constrainTotalCharge() { |
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return constrainTotalCharge_; |
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} |
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|
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/** add an atom into this molecule */ |
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void addAtom(Atom* atom); |
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|
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/** add a bond into this molecule */ |
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void addBond(Bond* bond); |
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|
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/** add a bend into this molecule */ |
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void addBend(Bend* bend); |
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|
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/** add a torsion into this molecule*/ |
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void addTorsion(Torsion* torsion); |
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|
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/** add an improper torsion into this molecule*/ |
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void addInversion(Inversion* inversion); |
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|
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/** add a rigidbody into this molecule */ |
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void addRigidBody(RigidBody *rb); |
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|
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/** add a cutoff group into this molecule */ |
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void addCutoffGroup(CutoffGroup* cp); |
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|
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void addConstraintPair(ConstraintPair* consPair); |
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|
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void addConstraintElem(ConstraintElem* consElem); |
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|
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/** */ |
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void complete(); |
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|
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/** Returns the total number of atoms in this molecule */ |
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unsigned int getNAtoms() { |
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return atoms_.size(); |
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} |
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|
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/** Returns the total number of bonds in this molecule */ |
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unsigned int getNBonds(){ |
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return bonds_.size(); |
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} |
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|
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/** Returns the total number of bends in this molecule */ |
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unsigned int getNBends() { |
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return bends_.size(); |
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} |
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|
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/** Returns the total number of torsions in this molecule */ |
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unsigned int getNTorsions() { |
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return torsions_.size(); |
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} |
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/** Returns the total number of improper torsions in this molecule */ |
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unsigned int getNInversions() { |
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return inversions_.size(); |
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} |
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|
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/** Returns the total number of rigid bodies in this molecule */ |
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unsigned int getNRigidBodies() { |
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return rigidBodies_.size(); |
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} |
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|
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/** Returns the total number of integrable objects in this molecule */ |
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unsigned int getNIntegrableObjects() { |
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return integrableObjects_.size(); |
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} |
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|
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/** Returns the total number of cutoff groups in this molecule */ |
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unsigned int getNCutoffGroups() { |
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return cutoffGroups_.size(); |
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} |
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|
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/** Returns the total number of constraints in this molecule */ |
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unsigned int getNConstraintPairs() { |
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return constraintPairs_.size(); |
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} |
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|
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/** Returns the total number of fluctuating charges in this molecule */ |
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unsigned int getNFluctuatingCharges() { |
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return fluctuatingCharges_.size(); |
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} |
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|
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Atom* getAtomAt(unsigned int i) { |
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assert(i < atoms_.size()); |
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return atoms_[i]; |
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} |
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|
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RigidBody* getRigidBodyAt(unsigned int i) { |
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assert(i < rigidBodies_.size()); |
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return rigidBodies_[i]; |
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} |
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|
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Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
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i = atoms_.begin(); |
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return (i == atoms_.end()) ? NULL : *i; |
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} |
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|
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Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
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++i; |
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return (i == atoms_.end()) ? NULL : *i; |
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} |
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|
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Bond* beginBond(std::vector<Bond*>::iterator& i) { |
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i = bonds_.begin(); |
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return (i == bonds_.end()) ? NULL : *i; |
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} |
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|
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Bond* nextBond(std::vector<Bond*>::iterator& i) { |
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++i; |
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return (i == bonds_.end()) ? NULL : *i; |
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|
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} |
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|
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Bend* beginBend(std::vector<Bend*>::iterator& i) { |
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i = bends_.begin(); |
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return (i == bends_.end()) ? NULL : *i; |
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} |
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|
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Bend* nextBend(std::vector<Bend*>::iterator& i) { |
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++i; |
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return (i == bends_.end()) ? NULL : *i; |
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} |
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|
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Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) { |
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i = torsions_.begin(); |
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return (i == torsions_.end()) ? NULL : *i; |
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} |
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|
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Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) { |
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++i; |
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return (i == torsions_.end()) ? NULL : *i; |
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} |
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|
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Inversion* beginInversion(std::vector<Inversion*>::iterator& i) { |
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i = inversions_.begin(); |
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return (i == inversions_.end()) ? NULL : *i; |
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} |
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|
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Inversion* nextInversion(std::vector<Inversion*>::iterator& i) { |
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++i; |
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return (i == inversions_.end()) ? NULL : *i; |
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} |
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|
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RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) { |
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i = rigidBodies_.begin(); |
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return (i == rigidBodies_.end()) ? NULL : *i; |
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} |
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|
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RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) { |
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++i; |
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return (i == rigidBodies_.end()) ? NULL : *i; |
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} |
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|
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StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
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i = integrableObjects_.begin(); |
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return (i == integrableObjects_.end()) ? NULL : *i; |
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} |
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|
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StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
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++i; |
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return (i == integrableObjects_.end()) ? NULL : *i; |
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} |
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|
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CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
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i = cutoffGroups_.begin(); |
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return (i == cutoffGroups_.end()) ? NULL : *i; |
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} |
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|
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CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
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++i; |
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return (i == cutoffGroups_.end()) ? NULL : *i; |
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} |
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|
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ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
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i = constraintPairs_.begin(); |
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return (i == constraintPairs_.end()) ? NULL : *i; |
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} |
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|
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ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
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++i; |
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return (i == constraintPairs_.end()) ? NULL : *i; |
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} |
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|
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ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
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i = constraintElems_.begin(); |
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return (i == constraintElems_.end()) ? NULL : *i; |
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} |
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|
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ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
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++i; |
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return (i == constraintElems_.end()) ? NULL : *i; |
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} |
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|
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Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) { |
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i = fluctuatingCharges_.begin(); |
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return (i == fluctuatingCharges_.end()) ? NULL : *i; |
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} |
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|
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Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) { |
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++i; |
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return (i == fluctuatingCharges_.end()) ? NULL : *i; |
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} |
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|
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|
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/** |
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* Returns the total potential energy of short range interaction |
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* of this molecule |
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*/ |
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RealType getPotential(); |
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|
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/** get total mass of this molecule */ |
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RealType getMass(); |
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|
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/** return the center of mass of this molecule */ |
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Vector3d getCom(); |
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|
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/** Moves the center of this molecule */ |
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void moveCom(const Vector3d& delta); |
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|
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/** Returns the velocity of center of mass of this molecule */ |
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Vector3d getComVel(); |
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|
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std::string getMoleculeName() { |
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return moleculeName_; |
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} |
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|
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friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
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|
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//below functions are just forward functions |
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/** |
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* Adds property into property map |
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* @param genData GenericData to be added into PropertyMap |
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*/ |
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void addProperty(GenericData* genData); |
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|
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/** |
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* Removes property from PropertyMap by name |
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* @param propName the name of property to be removed |
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*/ |
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void removeProperty(const std::string& propName); |
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|
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/** |
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* clear all of the properties |
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*/ |
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void clearProperties(); |
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|
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/** |
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* Returns all names of properties |
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* @return all names of properties |
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*/ |
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std::vector<std::string> getPropertyNames(); |
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|
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/** |
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* Returns all of the properties in PropertyMap |
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* @return all of the properties in PropertyMap |
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*/ |
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std::vector<GenericData*> getProperties(); |
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|
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/** |
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* Returns property |
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* @param propName name of property |
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* @return a pointer point to property with propName. If no property named propName |
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* exists, return NULL |
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*/ |
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GenericData* getPropertyByName(const std::string& propName); |
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|
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private: |
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|
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int globalIndex_; |
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|
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std::vector<Atom*> atoms_; |
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std::vector<Bond*> bonds_; |
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std::vector<Bend*> bends_; |
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std::vector<Torsion*> torsions_; |
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std::vector<Inversion*> inversions_; |
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std::vector<RigidBody*> rigidBodies_; |
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std::vector<StuntDouble*> integrableObjects_; |
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std::vector<CutoffGroup*> cutoffGroups_; |
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std::vector<ConstraintPair*> constraintPairs_; |
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std::vector<ConstraintElem*> constraintElems_; |
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std::vector<Atom*> fluctuatingCharges_; |
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int stampId_; |
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std::string moleculeName_; |
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PropertyMap properties_; |
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bool constrainTotalCharge_; |
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|
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}; |
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|
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} //namespace OpenMD |
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#endif // |
