| 1 |
< |
#ifndef _CUTOFFGROUP_H_ |
| 2 |
< |
#define _CUTOFFGROUP_H_ |
| 3 |
< |
#include "primitives/Atom.hpp" |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#ifndef PRIMITIVES_CUTOFFGROUP_HPP |
| 43 |
|
|
| 44 |
< |
class CutoffGroup{ |
| 6 |
< |
public: |
| 7 |
< |
|
| 8 |
< |
CutoffGroup() { |
| 9 |
< |
haveTotalMass = false; |
| 10 |
< |
totalMass = 0.0; |
| 11 |
< |
} |
| 12 |
< |
|
| 13 |
< |
void addAtom(Atom* atom) {cutoffAtomList.push_back(atom);} |
| 14 |
< |
|
| 15 |
< |
Atom* beginAtom(vector<Atom*>::iterator& i){ |
| 16 |
< |
i = cutoffAtomList.begin(); |
| 17 |
< |
return i != cutoffAtomList.end()? *i : NULL; |
| 18 |
< |
} |
| 19 |
< |
|
| 20 |
< |
Atom* nextAtom(vector<Atom*>::iterator& i){ |
| 21 |
< |
i++; |
| 22 |
< |
return i != cutoffAtomList.end()? *i : NULL; |
| 23 |
< |
} |
| 24 |
< |
|
| 25 |
< |
double getMass(){ |
| 26 |
< |
vector<Atom*>::iterator i; |
| 27 |
< |
Atom* atom; |
| 28 |
< |
double mass; |
| 29 |
< |
|
| 30 |
< |
if (!haveTotalMass) { |
| 44 |
> |
#define PRIMITIVES_CUTOFFGROUP_HPP |
| 45 |
|
|
| 46 |
< |
totalMass = 0; |
| 47 |
< |
|
| 34 |
< |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){ |
| 35 |
< |
mass = atom->getMass(); |
| 36 |
< |
totalMass += mass; |
| 37 |
< |
} |
| 46 |
> |
#include "primitives/Atom.hpp" |
| 47 |
> |
#include "math/Vector3.hpp" |
| 48 |
|
|
| 49 |
< |
haveTotalMass = true; |
| 49 |
> |
namespace oopse { |
| 50 |
> |
class CutoffGroup { |
| 51 |
> |
public: |
| 52 |
> |
|
| 53 |
> |
CutoffGroup() { |
| 54 |
> |
haveTotalMass = false; |
| 55 |
> |
totalMass = 0.0; |
| 56 |
|
} |
| 57 |
|
|
| 58 |
< |
return totalMass; |
| 59 |
< |
} |
| 60 |
< |
|
| 45 |
< |
void getCOM(double com[3]){ |
| 46 |
< |
|
| 47 |
< |
vector<Atom*>::iterator i; |
| 48 |
< |
Atom* atom; |
| 49 |
< |
double pos[3]; |
| 50 |
< |
double mass; |
| 58 |
> |
void addAtom(Atom *atom) { |
| 59 |
> |
cutoffAtomList.push_back(atom); |
| 60 |
> |
} |
| 61 |
|
|
| 62 |
< |
com[0] = 0; |
| 63 |
< |
com[1] = 0; |
| 64 |
< |
com[2] = 0; |
| 65 |
< |
totalMass = getMass(); |
| 62 |
> |
Atom *beginAtom(std::vector<Atom *>::iterator & i) { |
| 63 |
> |
i = cutoffAtomList.begin(); |
| 64 |
> |
return i != cutoffAtomList.end() ? *i : NULL; |
| 65 |
> |
} |
| 66 |
|
|
| 67 |
< |
if (cutoffAtomList.size() == 1) { |
| 67 |
> |
Atom *nextAtom(std::vector<Atom *>::iterator & i) { |
| 68 |
> |
i++; |
| 69 |
> |
return i != cutoffAtomList.end() ? *i : NULL; |
| 70 |
> |
} |
| 71 |
> |
|
| 72 |
> |
std::vector<Atom*> getAtoms() { return cutoffAtomList; } |
| 73 |
> |
RealType getMass() { |
| 74 |
> |
std::vector<Atom *>::iterator i; |
| 75 |
> |
Atom * atom; |
| 76 |
> |
RealType mass; |
| 77 |
|
|
| 78 |
< |
beginAtom(i)->getPos(com); |
| 78 |
> |
if (!haveTotalMass) { |
| 79 |
> |
totalMass = 0; |
| 80 |
> |
|
| 81 |
> |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
| 82 |
> |
mass = atom->getMass(); |
| 83 |
> |
totalMass += mass; |
| 84 |
> |
} |
| 85 |
> |
|
| 86 |
> |
haveTotalMass = true; |
| 87 |
> |
} |
| 88 |
|
|
| 89 |
< |
} else { |
| 89 |
> |
return totalMass; |
| 90 |
> |
} |
| 91 |
> |
|
| 92 |
> |
void getCOM(Vector3d & com) { |
| 93 |
> |
std::vector<Atom *>::iterator i; |
| 94 |
> |
Atom * atom; |
| 95 |
> |
Vector3d pos; |
| 96 |
> |
RealType mass; |
| 97 |
|
|
| 98 |
< |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){ |
| 99 |
< |
mass = atom->getMass(); |
| 100 |
< |
atom->getPos(pos); |
| 101 |
< |
com[0] += pos[0] * mass; |
| 67 |
< |
com[1] += pos[1] * mass; |
| 68 |
< |
com[2] += pos[2] * mass; |
| 69 |
< |
} |
| 98 |
> |
com[0] = 0; |
| 99 |
> |
com[1] = 0; |
| 100 |
> |
com[2] = 0; |
| 101 |
> |
totalMass = getMass(); |
| 102 |
|
|
| 103 |
< |
com[0] /= totalMass; |
| 104 |
< |
com[1] /= totalMass; |
| 105 |
< |
com[2] /= totalMass; |
| 103 |
> |
if (cutoffAtomList.size() == 1) { |
| 104 |
> |
com = beginAtom(i)->getPos(); |
| 105 |
> |
} else { |
| 106 |
> |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
| 107 |
> |
mass = atom->getMass(); |
| 108 |
> |
pos = atom->getPos(); |
| 109 |
> |
com += pos * mass; |
| 110 |
> |
} |
| 111 |
> |
|
| 112 |
> |
com /= totalMass; |
| 113 |
> |
} |
| 114 |
|
} |
| 115 |
|
|
| 116 |
< |
} |
| 117 |
< |
|
| 118 |
< |
int getNumAtom() {return cutoffAtomList.size();} |
| 119 |
< |
|
| 120 |
< |
int getGlobalIndex() {return globalIndex;} |
| 121 |
< |
void setGlobalIndex(int id) {this->globalIndex = id;} |
| 122 |
< |
private: |
| 123 |
< |
vector<Atom*> cutoffAtomList; |
| 124 |
< |
bool haveTotalMass; |
| 125 |
< |
double totalMass; |
| 126 |
< |
int globalIndex; |
| 127 |
< |
|
| 128 |
< |
}; |
| 129 |
< |
|
| 130 |
< |
#endif |
| 116 |
> |
int getNumAtom() { |
| 117 |
> |
return cutoffAtomList.size(); |
| 118 |
> |
} |
| 119 |
> |
|
| 120 |
> |
int getGlobalIndex() { |
| 121 |
> |
return globalIndex; |
| 122 |
> |
} |
| 123 |
> |
|
| 124 |
> |
void setGlobalIndex(int id) { |
| 125 |
> |
this->globalIndex = id; |
| 126 |
> |
} |
| 127 |
> |
|
| 128 |
> |
private: |
| 129 |
> |
|
| 130 |
> |
std::vector<Atom *>cutoffAtomList; |
| 131 |
> |
bool haveTotalMass; |
| 132 |
> |
RealType totalMass; |
| 133 |
> |
int globalIndex; |
| 134 |
> |
}; |
| 135 |
> |
} //end namespace oopse |
| 136 |
> |
#endif //PRIMITIVES_CUTOFFGROUP_HPP |
