101 |
|
mol->addCutoffGroup(cutoffGroup); |
102 |
|
} |
103 |
|
|
104 |
+ |
//every free atom is a cutoff group |
105 |
+ |
std::set<Atom*> allAtoms; |
106 |
+ |
typename Molecule::AtomIterator ai; |
107 |
+ |
|
108 |
+ |
//add all atoms into allAtoms set |
109 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
110 |
+ |
allAtoms.insert(atom); |
111 |
+ |
} |
112 |
+ |
|
113 |
+ |
typename Molecule::CutoffGroupIterator ci; |
114 |
+ |
CutoffGroup* cg; |
115 |
+ |
std::set<Atom*> cutoffAtoms; |
116 |
+ |
|
117 |
+ |
//add all of the atoms belong to cutoff groups into cutoffAtoms set |
118 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
119 |
+ |
|
120 |
+ |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
121 |
+ |
cutoffAtoms.insert(atom); |
122 |
+ |
} |
123 |
+ |
|
124 |
+ |
} |
125 |
+ |
|
126 |
+ |
//find all free atoms (which do not belong to cutoff groups) |
127 |
+ |
//performs the "difference" operation from set theory, the output range contains a copy of every |
128 |
+ |
//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
129 |
+ |
//[cutoffAtoms.begin(), cutoffAtoms.end()). |
130 |
+ |
std::vector<Atom*> freeAtoms; |
131 |
+ |
std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(), |
132 |
+ |
std::back_inserter(freeAtoms.end())); |
133 |
+ |
|
134 |
+ |
if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) { |
135 |
+ |
//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
136 |
+ |
sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule"); |
137 |
+ |
|
138 |
+ |
painCave.isFatal = 1; |
139 |
+ |
simError(); |
140 |
+ |
} |
141 |
+ |
|
142 |
+ |
//loop over the free atoms and then create one cutoff group for every single free atom |
143 |
+ |
std::vector<Atom*>::iterator fai; |
144 |
+ |
|
145 |
+ |
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
146 |
+ |
createCutoffGroup(mol, *fai); |
147 |
+ |
mol->addCutoffGroup(cutoffGroup); |
148 |
+ |
} |
149 |
|
//create constraints |
150 |
|
|
151 |
|
//the construction of this molecule is finished |
332 |
|
return cg; |
333 |
|
} |
334 |
|
|
335 |
+ |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
336 |
+ |
CutoffGroup* cg; |
337 |
+ |
cg = new CutoffGroup(); |
338 |
+ |
cg->addAtom(); |
339 |
+ |
return cg; |
340 |
+ |
} |
341 |
|
//Constraint* MoleculeCreator::createConstraint() { |
342 |
|
|
343 |
|
//} |