| 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. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#ifndef PRIMITIVES_CUTOFFGROUP_HPP |
| 44 |
|
| 45 |
#define PRIMITIVES_CUTOFFGROUP_HPP |
| 46 |
|
| 47 |
#include "primitives/Atom.hpp" |
| 48 |
#include "math/Vector3.hpp" |
| 49 |
|
| 50 |
namespace OpenMD { |
| 51 |
class CutoffGroup { |
| 52 |
public: |
| 53 |
|
| 54 |
CutoffGroup() : snapshotMan_(NULL) { |
| 55 |
|
| 56 |
storage_ = &Snapshot::cgData; |
| 57 |
haveTotalMass = false; |
| 58 |
totalMass = 0.0; |
| 59 |
} |
| 60 |
|
| 61 |
/** |
| 62 |
* Sets the Snapshot Manager of this cutoffGroup |
| 63 |
*/ |
| 64 |
void setSnapshotManager(SnapshotManager* sman) { |
| 65 |
snapshotMan_ = sman; |
| 66 |
} |
| 67 |
|
| 68 |
|
| 69 |
void addAtom(Atom *atom) { |
| 70 |
cutoffAtomList.push_back(atom); |
| 71 |
} |
| 72 |
|
| 73 |
Atom *beginAtom(std::vector<Atom *>::iterator & i) { |
| 74 |
i = cutoffAtomList.begin(); |
| 75 |
return i != cutoffAtomList.end() ? *i : NULL; |
| 76 |
} |
| 77 |
|
| 78 |
Atom *nextAtom(std::vector<Atom *>::iterator & i) { |
| 79 |
i++; |
| 80 |
return i != cutoffAtomList.end() ? *i : NULL; |
| 81 |
} |
| 82 |
|
| 83 |
std::vector<Atom*> getAtoms() { return cutoffAtomList; } |
| 84 |
RealType getMass() { |
| 85 |
std::vector<Atom *>::iterator i; |
| 86 |
Atom * atom; |
| 87 |
RealType mass; |
| 88 |
|
| 89 |
if (!haveTotalMass) { |
| 90 |
totalMass = 0; |
| 91 |
|
| 92 |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
| 93 |
mass = atom->getMass(); |
| 94 |
totalMass += mass; |
| 95 |
} |
| 96 |
|
| 97 |
haveTotalMass = true; |
| 98 |
} |
| 99 |
|
| 100 |
return totalMass; |
| 101 |
} |
| 102 |
|
| 103 |
void updateCOM() { |
| 104 |
std::vector<Atom *>::iterator i; |
| 105 |
Atom * atom; |
| 106 |
|
| 107 |
DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_; |
| 108 |
|
| 109 |
totalMass = getMass(); |
| 110 |
|
| 111 |
if (cutoffAtomList.size() == 1) { |
| 112 |
data.position[localIndex_] = beginAtom(i)->getPos(); |
| 113 |
} else { |
| 114 |
data.position[localIndex_] = V3Zero; |
| 115 |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
| 116 |
data.position[localIndex_] += atom->getMass() * atom->getPos(); |
| 117 |
} |
| 118 |
data.position[localIndex_] /= totalMass; |
| 119 |
} |
| 120 |
} |
| 121 |
|
| 122 |
|
| 123 |
Vector3d getPos() { |
| 124 |
return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_]; |
| 125 |
} |
| 126 |
|
| 127 |
int getNumAtom() { |
| 128 |
return cutoffAtomList.size(); |
| 129 |
} |
| 130 |
|
| 131 |
int getGlobalIndex() { |
| 132 |
return globalIndex; |
| 133 |
} |
| 134 |
|
| 135 |
void setGlobalIndex(int id) { |
| 136 |
this->globalIndex = id; |
| 137 |
} |
| 138 |
|
| 139 |
/** |
| 140 |
* Returns the local index of this cutoffGroup |
| 141 |
* @return the local index of this cutoffGroup |
| 142 |
*/ |
| 143 |
int getLocalIndex() { |
| 144 |
return localIndex_; |
| 145 |
} |
| 146 |
|
| 147 |
/** |
| 148 |
* Sets the local index of this cutoffGroup |
| 149 |
* @param index new index to be set |
| 150 |
*/ |
| 151 |
void setLocalIndex(int index) { |
| 152 |
localIndex_ = index; |
| 153 |
} |
| 154 |
|
| 155 |
private: |
| 156 |
|
| 157 |
std::vector<Atom *>cutoffAtomList; |
| 158 |
bool haveTotalMass; |
| 159 |
RealType totalMass; |
| 160 |
int globalIndex; |
| 161 |
|
| 162 |
int localIndex_; |
| 163 |
DataStoragePointer storage_; |
| 164 |
SnapshotManager* snapshotMan_; |
| 165 |
|
| 166 |
}; |
| 167 |
} //end namespace OpenMD |
| 168 |
#endif //PRIMITIVES_CUTOFFGROUP_HPP |
