1 |
< |
#ifndef _CUTOFFGROUP_H_ |
2 |
< |
#define _CUTOFFGROUP_H_ |
1 |
> |
#ifndef PRIMITIVES_CUTOFFGROUP_HPP |
2 |
> |
|
3 |
> |
#define PRIMITIVES_CUTOFFGROUP_HPP |
4 |
> |
|
5 |
|
#include "primitives/Atom.hpp" |
6 |
+ |
#include "math/Vector3.hpp" |
7 |
|
|
8 |
< |
class CutoffGroup{ |
9 |
< |
public: |
10 |
< |
|
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) { |
8 |
> |
namespace oopse { |
9 |
> |
class CutoffGroup { |
10 |
> |
public: |
11 |
|
|
12 |
< |
totalMass = 0; |
13 |
< |
|
14 |
< |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){ |
15 |
< |
mass = atom->getMass(); |
36 |
< |
totalMass += mass; |
37 |
< |
} |
12 |
> |
CutoffGroup() { |
13 |
> |
haveTotalMass = false; |
14 |
> |
totalMass = 0.0; |
15 |
> |
} |
16 |
|
|
17 |
< |
haveTotalMass = true; |
18 |
< |
} |
19 |
< |
|
42 |
< |
return totalMass; |
43 |
< |
} |
44 |
< |
|
45 |
< |
void getCOM(double com[3]){ |
17 |
> |
void addAtom(Atom *atom) { |
18 |
> |
cutoffAtomList.push_back(atom); |
19 |
> |
} |
20 |
|
|
21 |
< |
vector<Atom*>::iterator i; |
22 |
< |
Atom* atom; |
23 |
< |
double pos[3]; |
24 |
< |
double mass; |
51 |
< |
|
52 |
< |
com[0] = 0; |
53 |
< |
com[1] = 0; |
54 |
< |
com[2] = 0; |
55 |
< |
totalMass = getMass(); |
56 |
< |
|
57 |
< |
if (cutoffAtomList.size() == 1) { |
58 |
< |
|
59 |
< |
beginAtom(i)->getPos(com); |
60 |
< |
|
61 |
< |
} else { |
62 |
< |
|
63 |
< |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){ |
64 |
< |
mass = atom->getMass(); |
65 |
< |
atom->getPos(pos); |
66 |
< |
com[0] += pos[0] * mass; |
67 |
< |
com[1] += pos[1] * mass; |
68 |
< |
com[2] += pos[2] * mass; |
69 |
< |
} |
70 |
< |
|
71 |
< |
com[0] /= totalMass; |
72 |
< |
com[1] /= totalMass; |
73 |
< |
com[2] /= totalMass; |
74 |
< |
} |
75 |
< |
|
76 |
< |
} |
77 |
< |
|
78 |
< |
int getNumAtom() {return cutoffAtomList.size();} |
21 |
> |
Atom *beginAtom(std::vector<Atom *>::iterator & i) { |
22 |
> |
i = cutoffAtomList.begin(); |
23 |
> |
return i != cutoffAtomList.end() ? *i : NULL; |
24 |
> |
} |
25 |
|
|
26 |
< |
int getGlobalIndex() {return globalIndex;} |
27 |
< |
void setGlobalIndex(int id) {this->globalIndex = id;} |
28 |
< |
private: |
29 |
< |
vector<Atom*> cutoffAtomList; |
84 |
< |
bool haveTotalMass; |
85 |
< |
double totalMass; |
86 |
< |
int globalIndex; |
26 |
> |
Atom *nextAtom(std::vector<Atom *>::iterator & i) { |
27 |
> |
i++; |
28 |
> |
return i != cutoffAtomList.end() ? *i : NULL; |
29 |
> |
} |
30 |
|
|
31 |
+ |
double getMass() { |
32 |
+ |
std::vector<Atom *>::iterator i; |
33 |
+ |
Atom * atom; |
34 |
+ |
double mass; |
35 |
+ |
|
36 |
+ |
if (!haveTotalMass) { |
37 |
+ |
totalMass = 0; |
38 |
+ |
|
39 |
+ |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
40 |
+ |
mass = atom->getMass(); |
41 |
+ |
totalMass += mass; |
42 |
+ |
} |
43 |
+ |
|
44 |
+ |
haveTotalMass = true; |
45 |
+ |
} |
46 |
+ |
|
47 |
+ |
return totalMass; |
48 |
+ |
} |
49 |
+ |
|
50 |
+ |
void getCOM(Vector3d & com) { |
51 |
+ |
std::vector<Atom *>::iterator i; |
52 |
+ |
Atom * atom; |
53 |
+ |
Vector3d pos; |
54 |
+ |
double mass; |
55 |
+ |
|
56 |
+ |
com[0] = 0; |
57 |
+ |
com[1] = 0; |
58 |
+ |
com[2] = 0; |
59 |
+ |
totalMass = getMass(); |
60 |
+ |
|
61 |
+ |
if (cutoffAtomList.size() == 1) { |
62 |
+ |
com = beginAtom(i)->getPos(); |
63 |
+ |
} else { |
64 |
+ |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
65 |
+ |
mass = atom->getMass(); |
66 |
+ |
pos = atom->getPos(); |
67 |
+ |
com += pos * mass; |
68 |
+ |
} |
69 |
+ |
|
70 |
+ |
com /= totalMass; |
71 |
+ |
} |
72 |
+ |
} |
73 |
+ |
|
74 |
+ |
int getNumAtom() { |
75 |
+ |
return cutoffAtomList.size(); |
76 |
+ |
} |
77 |
+ |
|
78 |
+ |
int getGlobalIndex() { |
79 |
+ |
return globalIndex; |
80 |
+ |
} |
81 |
+ |
|
82 |
+ |
void setGlobalIndex(int id) { |
83 |
+ |
this->globalIndex = id; |
84 |
+ |
} |
85 |
+ |
|
86 |
+ |
private: |
87 |
+ |
|
88 |
+ |
std::vector<Atom *>cutoffAtomList; |
89 |
+ |
bool haveTotalMass; |
90 |
+ |
double totalMass; |
91 |
+ |
int globalIndex; |
92 |
|
}; |
93 |
|
|
94 |
< |
#endif |
94 |
> |
} //end namespace oopse |
95 |
> |
|
96 |
> |
#endif //PRIMITIVES_CUTOFFGROUP_HPP |