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Comparing branches/new_design/OOPSE-3.0/src/brains/MoleculeCreator.cpp (file contents):
Revision 1719 by tim, Fri Nov 5 23:38:27 2004 UTC vs.
Revision 1734 by tim, Fri Nov 12 07:05:43 2004 UTC

# Line 37 | Line 37 | Molecule* MoleculeCreator::createMolecule(ForceField*
37   namespace oopse {
38  
39   Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, int stampId, int globalIndex) {
40 <    Molecule* mol = new Molecule(stampId, globalIndex);
40 >    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
41      
42      //create atoms
43      Atom* atom;
# Line 101 | Line 101 | Molecule* MoleculeCreator::createMolecule(ForceField*
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
# Line 117 | Line 162 | Atom* MoleculeCreator::createAtom(ForceField* ff, Mole
162  
163      atomType =  ff->getAtomType(stamp->getType());
164  
165 +    if (bondType == NULL) {
166 +        sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
167 +                   stamp->getType());
168 +
169 +        painCave.isFatal = 1;
170 +        simError();
171 +    }
172 +    
173      //below code still have some kind of hard-coding smell
174      if (stamp->haveOrientation()){
175          DirectionalAtom* dAtom;
# Line 152 | Line 205 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
205      Vector3d refCoor;
206      AtomStamp* atomStamp;
207      
208 <    nAtoms = stamp->getNMembers();
208 >    nAtoms = molStamp->getNMembers();
209  
210      RigidBody* rb = new RigidBody();
211      
# Line 163 | Line 216 | RigidBody* MoleculeCreator::createRigidBody(MoleculeSt
216          atomStamp= molStamp->molStamp->getAtom(rbStamp->getMember(i));    
217          rb->addAtom(atom, atomStamp);
218      }
219 <    
219 >
220 >    //after all of the atoms are added, we need to calculate the reference coordinates
221      rb->calcRefCoords();
222 +
223 +    //set the local index of this rigid body, global index will be set later
224      rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
225 <    rb->setType(mol->getType() + "_" + itoa(mol.getNRigidBodies()));
225 >
226 >    //the rule for naming rigidbody MoleculeName_RB_Integer
227 >    //The first part is the name of the molecule
228 >    //The second part is alway fixed as "RB"
229 >    //The third part is the index of the rigidbody defined in meta-data file
230 >    //For example, Butane_RB_0 is a valid rigid body name of butane molecule
231 >    rb->setType(mol->getType() + "_RB_" + itoa(mol.getNRigidBodies()));
232      
233      return rb;
234   }    
# Line 183 | Line 245 | Bond* MoleculeCreator::createBond(ForceField* ff, Mole
245      
246      bondType = ff->getBondType(atomA, atomB);
247  
248 +    if (bondType == NULL) {
249 +        sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
250 +                   atomA->getType().c_str(),
251 +                   atomB->getType().c_str());
252 +
253 +        painCave.isFatal = 1;
254 +        simError();
255 +    }
256      return new Bond(atomA, atomB, bondType);    
257   }    
258  
259   Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
260 <    BendType* benType;
260 >    BendType* bendType;
261      Atom* atomA;
262      Atom* atomB;
263      Atom* atomC;
# Line 199 | Line 269 | Bend* MoleculeCreator::createBend(ForceField* ff, Mole
269  
270      assert( atomA && atomB && atomC);
271      
272 <    benType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
272 >    bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
273  
274 <    return new Bond(atomA, atomB, benType);      
274 >    if (bendType == NULL) {
275 >        sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
276 >                   atomA->getType().c_str(),
277 >                   atomB->getType().c_str(),
278 >                   atomC->getType().c_str());
279  
280 +        painCave.isFatal = 1;
281 +        simError();
282 +    }
283 +
284 +    return new Bond(atomA, atomB, bendType);      
285 +
286   }    
287  
288   Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
# Line 222 | Line 302 | Torsion* MoleculeCreator::createTorsion(ForceField* ff
302      torsionType = ff->getTosionType(atomA->getType(), atomB->getType(),
303                                                         atomC->getType(), atomD->getType());
304  
305 +    if (torsionType == NULL) {
306 +        sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
307 +                   atomA->getType().c_str(),
308 +                   atomB->getType().c_str(),
309 +                   atomC->getType().c_str(),
310 +                   atomD->getType().c_str());
311 +
312 +        painCave.isFatal = 1;
313 +        simError();
314 +    }
315 +    
316      return new Torsion(atomA, atomB, torsionType);      
317   }    
318  
# Line 241 | Line 332 | CutoffGroup* MoleculeCreator::createCutoffGroup(Molecu
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   //}

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