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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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|
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#ifndef TYPES_ATOMTYPE_HPP |
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|
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#define TYPES_ATOMTYPE_HPP |
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|
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< |
#include "math/SquareMatrix3.hpp" |
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#include <string> |
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|
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#include "utils/PropertyMap.hpp" |
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– |
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#define __C |
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#include "types/AtomTypeProperties.h" |
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#include "UseTheForce/DarkSide/atype_interface.h" |
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* @class AtomType |
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* AtomType is what OOPSE looks to for unchanging data about an atom. |
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* Things that belong to AtomType are universal properties (i.e. does |
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* this atom have a Charge? What is it's mass?) Dynamic properties of |
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* this atom have a Charge? What is it's mass_?) Dynamic properties of |
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* an atom are not intended to be properties of an atom type |
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*/ |
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class AtomType{ |
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|
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class AtomType { |
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public: |
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|
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|
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AtomType(); |
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~AtomType(); |
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|
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virtual ~AtomType() { } ; |
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|
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virtual void complete(); |
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|
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/** |
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* Finishes off the AtomType by communicating the logical portions of the |
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* structure to the Fortran atype module |
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*/ |
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void complete(); |
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|
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void setMass(double m) { mass = m; } |
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double getMass(void) { return mass; } |
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void makeFortranAtomType(); |
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|
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void setMass(double m) { |
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mass_ = m; |
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} |
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|
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void setIdent(int id) {atp.ident = id;} |
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int getIdent() {return atp.ident;} |
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|
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void setLennardJones() { atp.is_LennardJones = 1; } |
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bool isLennardJones() { return atp.is_LennardJones; } |
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|
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void setElectrostatic() { atp.is_Electrostatic = 1; } |
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bool isElectrostatic() { return atp.is_Electrostatic; } |
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|
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void setSticky() { atp.is_Sticky = 1; } |
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bool isSticky() { return atp.is_Sticky; } |
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|
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void setGayBerne() { atp.is_GayBerne = 1; } |
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bool isGayBerne() { return atp.is_GayBerne; } |
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|
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void setEAM() { atp.is_EAM = 1; } |
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bool isEAM() { return atp.is_EAM; } |
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|
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void setShape() { atp.is_Shape = 1; } |
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bool isShape() { return atp.is_Shape; } |
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|
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void setCharge() { atp.is_Charge = 1; atp.is_Electrostatic = 1;} |
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bool isCharge() { return atp.is_Charge; } |
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|
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void setDipole() { atp.is_Dipole = 1; atp.is_Electrostatic = 1;} |
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bool isDipole() { return atp.is_Dipole; } |
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|
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Mat3x3d getI() { return I; } |
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void setI(Mat3x3d theI) { I = theI; } |
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|
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private: |
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|
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double getMass(void) { |
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return mass_; |
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} |
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|
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void setIdent(int id) { |
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atp.ident = id; |
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} |
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|
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int getIdent() { |
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return atp.ident; |
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} |
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|
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void setName(const std::string&name) { |
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name_ = name; |
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} |
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|
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std::string getName() { |
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return name_; |
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} |
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|
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void setLennardJones() { |
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atp.is_LennardJones = 1; |
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} |
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|
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bool isLennardJones() { |
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return atp.is_LennardJones; |
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} |
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|
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|
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bool isElectrostatic() { |
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return isCharge() || isMultipole(); |
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} |
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|
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void setEAM() { |
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atp.is_EAM = 1; |
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} |
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|
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bool isEAM() { |
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return atp.is_EAM; |
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} |
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|
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void setCharge() { |
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atp.is_Charge = 1; |
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} |
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|
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bool isCharge() { |
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return atp.is_Charge; |
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} |
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|
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bool isDirectional() { |
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return atp.is_Directional; |
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} |
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|
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bool isDipole() { |
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return atp.is_Dipole; |
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} |
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|
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bool isSplitDipole() { |
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return atp.is_SplitDipole; |
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} |
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|
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bool isQuadrupole() { |
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return atp.is_Quadrupole; |
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} |
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|
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bool isMultipole() { |
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return isDipole() || isQuadrupole(); |
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} |
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|
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bool isGayBerne() { |
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return atp.is_GayBerne; |
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} |
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|
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bool isSticky() { |
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return atp.is_Sticky; |
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} |
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|
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bool isShape() { |
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return atp.is_Shape; |
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} |
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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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protected: |
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|
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AtomTypeProperties atp; |
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PropertyMap pm; |
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double mass; |
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Mat3x3d I; |
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|
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double mass_; |
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std::string name_; |
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|
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private: |
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//prevent copy construction and copy assignment, since property map contains |
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//pointers which can not be copied and managered safely, except make the generic data |
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//at PropertyMap as copy on write shared pointer |
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AtomType(const AtomType&); |
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AtomType& operator=(const AtomType& atomType); |
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|
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|
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PropertyMap properties_; |
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|
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}; |
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|
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struct LJParam { |
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double epsilon; |
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double sigma; |
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int soft_pot; |
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}; |
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typedef SimpleTypeData<LJParam> LJParamGenericData; |
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|
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struct EAMParam { |
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double latticeConstant; |
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int nrho; |
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double drho; |
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int nr; |
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double dr; |
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double rcut; |
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std::vector<double> rvals; |
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std::vector<double> rhovals; |
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std::vector<double> Frhovals; |
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}; |
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|
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typedef SimpleTypeData<EAMParam> EAMParamGenericData; |
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} |
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#endif |
