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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 664 by chuckv, Wed Oct 12 21:57:16 2005 UTC vs.
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC

# Line 53 | Line 53
53   #define __C
54   #include "UseTheForce/DarkSide/fInteractionMap.h"
55   #include "utils/simError.h"
56 + #include "primitives/Bend.hpp"
57 + #include "primitives/Bend.hpp"
58   namespace oopse {
59  
60 + /*
61 +  struct BendOrderStruct {
62 +    Bend* bend;
63 +    BendDataSet dataSet;
64 +  };
65 +  struct TorsionOrderStruct {
66 +    Torsion* torsion;
67 +    TorsionDataSet dataSet;
68 +  };
69 +
70 +  bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71 +    return b1.dataSet.deltaV < b2.dataSet.deltaV;
72 +  }
73 +
74 +  bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
75 +    return t1.dataSet.deltaV < t2.dataSet.deltaV;
76 +  }
77 +  */
78    void ForceManager::calcForces(bool needPotential, bool needStress) {
79  
80      if (!info_->isFortranInitialized()) {
# Line 68 | Line 88 | namespace oopse {
88      calcLongRangeInteraction(needPotential, needStress);
89  
90      postCalculation();
91 <        
91 >
92 > /*
93 >    std::vector<BendOrderStruct> bendOrderStruct;
94 >    for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
95 >        BendOrderStruct tmp;
96 >        tmp.bend= const_cast<Bend*>(i->first);
97 >        tmp.dataSet = i->second;
98 >        bendOrderStruct.push_back(tmp);
99 >    }
100 >
101 >    std::vector<TorsionOrderStruct> torsionOrderStruct;
102 >    for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
103 >        TorsionOrderStruct tmp;
104 >        tmp.torsion = const_cast<Torsion*>(j->first);
105 >        tmp.dataSet = j->second;
106 >        torsionOrderStruct.push_back(tmp);
107 >    }
108 >    
109 >    std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110 >    std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111 >    for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
112 >        Bend* bend = k->bend;
113 >        std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
114 >        std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
115 >    }
116 >    for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
117 >        Torsion* torsion = l->torsion;
118 >        std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
119 >        std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
120 >    }
121 >   */
122    }
123  
124    void ForceManager::preCalculation() {
# Line 105 | Line 155 | namespace oopse {
155      Molecule::BondIterator bondIter;;
156      Molecule::BendIterator  bendIter;
157      Molecule::TorsionIterator  torsionIter;
158 +    RealType bondPotential = 0.0;
159 +    RealType bendPotential = 0.0;
160 +    RealType torsionPotential = 0.0;
161  
162      //calculate short range interactions    
163      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
164  
165        //change the positions of atoms which belong to the rigidbodies
166        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
167 <        rb->updateAtoms();
167 >          rb->updateAtoms();
168        }
169  
170        for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
171 <        bond->calcForce();
171 >        bond->calcForce();
172 >        bondPotential += bond->getPotential();
173        }
174  
175 +
176        for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
177 <        bend->calcForce();
177 >
178 >          RealType angle;
179 >            bend->calcForce(angle);
180 >          RealType currBendPot = bend->getPotential();          
181 >            bendPotential += bend->getPotential();
182 >          std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
183 >          if (i == bendDataSets.end()) {
184 >            BendDataSet dataSet;
185 >            dataSet.prev.angle = dataSet.curr.angle = angle;
186 >            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
187 >            dataSet.deltaV = 0.0;
188 >            bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
189 >          }else {
190 >            i->second.prev.angle = i->second.curr.angle;
191 >            i->second.prev.potential = i->second.curr.potential;
192 >            i->second.curr.angle = angle;
193 >            i->second.curr.potential = currBendPot;
194 >            i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
195 >          }
196        }
197  
198        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
199 <        torsion->calcForce();
199 >        RealType angle;
200 >          torsion->calcForce(angle);
201 >        RealType currTorsionPot = torsion->getPotential();
202 >          torsionPotential += torsion->getPotential();
203 >          std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
204 >          if (i == torsionDataSets.end()) {
205 >            TorsionDataSet dataSet;
206 >            dataSet.prev.angle = dataSet.curr.angle = angle;
207 >            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
208 >            dataSet.deltaV = 0.0;
209 >            torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
210 >          }else {
211 >            i->second.prev.angle = i->second.curr.angle;
212 >            i->second.prev.potential = i->second.curr.potential;
213 >            i->second.curr.angle = angle;
214 >            i->second.curr.potential = currTorsionPot;
215 >            i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
216 >          }      
217        }
218  
219      }
220      
221 <    double  shortRangePotential = 0.0;
132 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
133 <      shortRangePotential += mol->getPotential();
134 <    }
135 <
221 >    RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;    
222      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
223      curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
224 +    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
225 +    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
226 +    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
227 +    
228    }
229  
230    void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
231      Snapshot* curSnapshot;
232      DataStorage* config;
233 <    double* frc;
234 <    double* pos;
235 <    double* trq;
236 <    double* A;
237 <    double* electroFrame;
238 <    double* rc;
233 >    RealType* frc;
234 >    RealType* pos;
235 >    RealType* trq;
236 >    RealType* A;
237 >    RealType* electroFrame;
238 >    RealType* rc;
239      
240      //get current snapshot from SimInfo
241      curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 182 | Line 272 | namespace oopse {
272      }
273    
274      //initialize data before passing to fortran
275 <    double longRangePotential[LR_POT_TYPES];
276 <    double lrPot = 0.0;
277 <    
275 >    RealType longRangePotential[LR_POT_TYPES];
276 >    RealType lrPot = 0.0;
277 >    Vector3d totalDipole;
278      Mat3x3d tau;
279      short int passedCalcPot = needPotential;
280      short int passedCalcStress = needStress;
# Line 194 | Line 284 | namespace oopse {
284        longRangePotential[i]=0.0; //Initialize array
285      }
286  
197 –
198 –
287      doForceLoop( pos,
288                   rc,
289                   A,
# Line 218 | Line 306 | namespace oopse {
306        lrPot += longRangePotential[i]; //Quick hack
307      }
308  
309 +    // grab the simulation box dipole moment if specified
310 +    if (info_->getCalcBoxDipole()){
311 +      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
312 +
313 +      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
314 +      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
315 +      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
316 +    }
317 +
318      //store the tau and long range potential    
319      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
320 <    //  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
320 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
321 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
322 >
323      curSnapshot->statData.setTau(tau);
324    }
325  
# Line 236 | Line 335 | namespace oopse {
335        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
336          rb->calcForcesAndTorques();
337        }
338 <    }
338 >    }    
339  
340    }
341  

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