43 |
|
} |
44 |
|
|
45 |
|
SimInfo::~SimInfo() { |
46 |
< |
MemoryUtils::deleteVectorOfPointer(molecules_); |
46 |
> |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
47 |
|
delete sman_; |
48 |
|
|
49 |
|
} |
50 |
|
|
51 |
|
|
52 |
|
bool SimInfo::addMolecule(Molecule* mol) { |
53 |
< |
std::vector<Molecule*>::iterator i; |
53 |
> |
MoleculeIterator i; |
54 |
|
i = std::find(molecules_.begin(), molecules_.end(), mol); |
55 |
|
if (i != molecules_.end() ) { |
56 |
– |
molecules_.push_back(mol); |
56 |
|
|
57 |
+ |
molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
58 |
+ |
|
59 |
|
nAtoms_ += mol->getNAtoms(); |
60 |
|
nBonds_ += mol->getNBonds(); |
61 |
|
nBends_ += mol->getNBends(); |
65 |
|
nCutoffGroups_ += mol->getNCutoffGroups(); |
66 |
|
nConstraints_ += mol->getNConstraints(); |
67 |
|
|
67 |
– |
globalIndexToMol_.insert(make_pair(mol->getGlobalIndex(), mol)); |
68 |
|
return true; |
69 |
|
} else { |
70 |
|
return false; |
72 |
|
} |
73 |
|
|
74 |
|
bool SimInfo::removeMolecule(Molecule* mol) { |
75 |
< |
std::vector<Molecule*>::iterator i; |
75 |
> |
MoleculeIterator i; |
76 |
|
i = std::find(molecules_.begin(), molecules_.end(), mol); |
77 |
|
|
78 |
|
if (i != molecules_.end() ) { |
79 |
< |
molecules_.push_back(mol); |
79 |
> |
|
80 |
|
nAtoms_ -= mol->getNAtoms(); |
81 |
|
nBonds_ -= mol->getNBonds(); |
82 |
|
nBends_ -= mol->getNBends(); |
86 |
|
nCutoffGroups_ -= mol->getNCutoffGroups(); |
87 |
|
nConstraints_ -= mol->getNConstraints(); |
88 |
|
|
89 |
< |
globalIndexToMol_.erase(mol->getGlobalIndex()); |
89 |
> |
molecules_.erase(mol->getGlobalIndex()); |
90 |
> |
|
91 |
> |
delete mol; |
92 |
> |
|
93 |
|
return true; |
94 |
|
} else { |
95 |
|
return false; |
99 |
|
} |
100 |
|
|
101 |
|
|
102 |
< |
Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) { |
102 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
103 |
|
i = molecules_.begin(); |
104 |
|
return i == molecules_.end() ? NULL : *i; |
105 |
|
} |
106 |
|
|
107 |
< |
Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) { |
107 |
> |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
108 |
|
++i; |
109 |
|
return i == molecules_.end() ? NULL : *i; |
110 |
|
} |
112 |
|
|
113 |
|
void SimInfo::calcNdf() { |
114 |
|
int ndf_local; |
115 |
< |
std::vector<Molecule*>::iterator i; |
115 |
> |
MoleculeIterator i; |
116 |
|
std::vector<StuntDouble*>::iterator j; |
117 |
|
Molecule* mol; |
118 |
|
StuntDouble* integrableObject; |
154 |
|
void SimInfo::calcNdfRaw() { |
155 |
|
int ndfRaw_local; |
156 |
|
|
157 |
< |
std::vector<Molecule*>::iterator i; |
157 |
> |
MoleculeIterator i; |
158 |
|
std::vector<StuntDouble*>::iterator j; |
159 |
|
Molecule* mol; |
160 |
|
StuntDouble* integrableObject; |