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root/OpenMD/trunk/src/brains/MoleculeCreator.cpp
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Comparing trunk/src/brains/MoleculeCreator.cpp (file contents):
Revision 647 by tim, Wed Oct 5 19:34:01 2005 UTC vs.
Revision 809 by gezelter, Mon Dec 12 19:32:50 2005 UTC

# Line 48 | Line 48
48   */
49  
50   #include <cassert>
51 + #include <typeinfo>
52   #include <set>
53  
54   #include "brains/MoleculeCreator.hpp"
# Line 63 | Line 64 | namespace oopse {
64    Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
65                                              int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
66  
67 <    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
67 >    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
68      
69      //create atoms
70      Atom* atom;
71      AtomStamp* currentAtomStamp;
72      int nAtom = molStamp->getNAtoms();
73      for (int i = 0; i < nAtom; ++i) {
74 <      currentAtomStamp = molStamp->getAtom(i);
74 >      currentAtomStamp = molStamp->getAtomStamp(i);
75        atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
76        mol->addAtom(atom);
77      }
# Line 81 | Line 82 | namespace oopse {
82      int nRigidbodies = molStamp->getNRigidBodies();
83  
84      for (int i = 0; i < nRigidbodies; ++i) {
85 <      currentRigidBodyStamp = molStamp->getRigidBody(i);
85 >      currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
86        rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
87        mol->addRigidBody(rb);
88      }
# Line 92 | Line 93 | namespace oopse {
93      int nBonds = molStamp->getNBonds();
94  
95      for (int i = 0; i < nBonds; ++i) {
96 <      currentBondStamp = molStamp->getBond(i);
96 >      currentBondStamp = molStamp->getBondStamp(i);
97        bond = createBond(ff, mol, currentBondStamp);
98        mol->addBond(bond);
99      }
# Line 102 | Line 103 | namespace oopse {
103      BendStamp* currentBendStamp;
104      int nBends = molStamp->getNBends();
105      for (int i = 0; i < nBends; ++i) {
106 <      currentBendStamp = molStamp->getBend(i);
106 >      currentBendStamp = molStamp->getBendStamp(i);
107        bend = createBend(ff, mol, currentBendStamp);
108        mol->addBend(bend);
109      }
# Line 112 | Line 113 | namespace oopse {
113      TorsionStamp* currentTorsionStamp;
114      int nTorsions = molStamp->getNTorsions();
115      for (int i = 0; i < nTorsions; ++i) {
116 <      currentTorsionStamp = molStamp->getTorsion(i);
116 >      currentTorsionStamp = molStamp->getTorsionStamp(i);
117        torsion = createTorsion(ff, mol, currentTorsionStamp);
118        mol->addTorsion(torsion);
119      }
# Line 122 | Line 123 | namespace oopse {
123      CutoffGroupStamp* currentCutoffGroupStamp;
124      int nCutoffGroups = molStamp->getNCutoffGroups();
125      for (int i = 0; i < nCutoffGroups; ++i) {
126 <      currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
126 >      currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
127        cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
128        mol->addCutoffGroup(cutoffGroup);
129      }
# Line 175 | Line 176 | namespace oopse {
176  
177      if (atomType == NULL) {
178        sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
179 <              stamp->getType());
179 >              stamp->getType().c_str());
180  
181        painCave.isFatal = 1;
182        simError();
# Line 219 | Line 220 | namespace oopse {
220      for (int i = 0; i < nAtoms; ++i) {
221        //rbStamp->getMember(i) return the local index of current atom inside the molecule.
222        //It is not the same as local index of atom which is the index of atom at DataStorage class
223 <      atom = mol->getAtomAt(rbStamp->getMember(i));
224 <      atomStamp= molStamp->getAtom(rbStamp->getMember(i));    
223 >      atom = mol->getAtomAt(rbStamp->getMemberAt(i));
224 >      atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));    
225        rb->addAtom(atom, atomStamp);
226      }
227  
# Line 266 | Line 267 | namespace oopse {
267    }    
268  
269    Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
270 <    bool isGhostBend = false;
271 <    int ghostIndex;
270 >    Bend* bend = NULL;
271 >    std::vector<int> bendAtoms = stamp->getMembers();
272 >    if (bendAtoms.size() == 3) {
273 >      Atom* atomA = mol->getAtomAt(bendAtoms[0]);
274 >      Atom* atomB = mol->getAtomAt(bendAtoms[1]);
275 >      Atom* atomC = mol->getAtomAt(bendAtoms[2]);
276  
277 <    
278 <    //
279 <    if (stamp->haveExtras()){
275 <      LinkedAssign* extras = stamp->getExtras();
276 <      LinkedAssign* currentExtra = extras;
277 >      assert( atomA && atomB && atomC);
278 >
279 >      BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str());
280  
281 <      while (currentExtra != NULL){
282 <        if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
283 <          switch (currentExtra->getType()){
284 <          case 0:
285 <            ghostIndex = currentExtra->getInt();
283 <            isGhostBend = true;
284 <            break;
281 >      if (bendType == NULL) {
282 >        sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
283 >                atomA->getType().c_str(),
284 >                atomB->getType().c_str(),
285 >                atomC->getType().c_str());
286  
287 <          default:
288 <            sprintf(painCave.errMsg,
288 <                    "SimSetup Error: ghostVectorSource must be an int.\n");
289 <            painCave.isFatal = 1;
290 <            simError();
291 <          }
292 <        } else{
293 <          sprintf(painCave.errMsg,
294 <                  "SimSetup Error: unhandled bend assignment:\n");
295 <          painCave.isFatal = 1;
296 <          simError();
297 <        }
298 <        currentExtra = currentExtra->getNext();
299 <      }
300 <        
301 <    }
302 <
303 <    if (isGhostBend) {
304 <
305 <      int indexA = stamp->getA();
306 <      int indexB= stamp->getB();
307 <
308 <      assert(indexA != indexB);
309 <
310 <      int normalIndex;
311 <      if (indexA == ghostIndex) {
312 <        normalIndex = indexB;
313 <      } else if (indexB == ghostIndex) {
314 <        normalIndex = indexA;
287 >        painCave.isFatal = 1;
288 >        simError();
289        }
290 <        
290 >
291 >      bend = new Bend(atomA, atomB, atomC, bendType);
292 >    } else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
293 >      int ghostIndex = stamp->getGhostVectorSource();
294 >      int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
295        Atom* normalAtom = mol->getAtomAt(normalIndex) ;        
296        DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
297        if (ghostAtom == NULL) {
# Line 334 | Line 312 | namespace oopse {
312          simError();
313        }
314          
315 <      return new GhostBend(normalAtom, ghostAtom, bendType);      
315 >      bend = new GhostBend(normalAtom, ghostAtom, bendType);      
316  
317 <    } else {
318 <            
319 <      Atom* atomA = mol->getAtomAt(stamp->getA());
342 <      Atom* atomB = mol->getAtomAt(stamp->getB());
343 <      Atom* atomC = mol->getAtomAt(stamp->getC());
344 <
345 <      assert( atomA && atomB && atomC);
346 <        
347 <      BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
348 <
349 <      if (bendType == NULL) {
350 <        sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
351 <                atomA->getType().c_str(),
352 <                atomB->getType().c_str(),
353 <                atomC->getType().c_str());
354 <
355 <        painCave.isFatal = 1;
356 <        simError();
357 <      }
358 <
359 <      return new Bend(atomA, atomB, atomC, bendType);      
360 <    }
317 >    }
318 >    
319 >    return bend;
320    }    
321  
322    Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
323  
324 <    Atom* atomA = mol->getAtomAt(stamp->getA());
325 <    Atom* atomB = mol->getAtomAt(stamp->getB());
326 <    Atom* atomC = mol->getAtomAt(stamp->getC());
327 <    Torsion* torsion;
324 >    Torsion* torsion = NULL;
325 >    std::vector<int> torsionAtoms = stamp->getMembers();
326 >    if (torsionAtoms.size() < 3) {
327 >        return torsion;
328 >    }
329  
330 <    if (stamp->getD() != -1) {
331 <      Atom* atomD = mol->getAtomAt(stamp->getD());
330 >    Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
331 >    Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
332 >    Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
333  
334 +    if (torsionAtoms.size() == 4) {
335 +      Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
336 +
337        assert(atomA && atomB && atomC && atomD);
338          
339        TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
# Line 390 | Line 354 | namespace oopse {
354      }
355      else {
356  
357 <      DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
357 >      DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
358        if (dAtom == NULL) {
359          sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
360          painCave.isFatal = 1;
# Line 425 | Line 389 | namespace oopse {
389      
390      nAtoms = stamp->getNMembers();
391      for (int i =0; i < nAtoms; ++i) {
392 <      atom = mol->getAtomAt(stamp->getMember(i));
392 >      atom = mol->getAtomAt(stamp->getMemberAt(i));
393        assert(atom);
394        cg->addAtom(atom);
395      }

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