ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/brains/ForceManager.cpp
(Generate patch)

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1215 by xsun, Wed Jan 23 21:22:37 2008 UTC

# Line 53 | Line 53
53   #define __C
54   #include "UseTheForce/DarkSide/fInteractionMap.h"
55   #include "utils/simError.h"
56 + #include "primitives/Bond.hpp"
57   #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 –  */
60    void ForceManager::calcForces(bool needPotential, bool needStress) {
61 <
61 >    
62      if (!info_->isFortranInitialized()) {
63        info_->update();
64      }
65 <
65 >    
66      preCalculation();
67      
68      calcShortRangeInteraction();
69  
70      calcLongRangeInteraction(needPotential, needStress);
71  
72 <    postCalculation();
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 <    }
72 >    postCalculation(needStress);
73      
109 –    std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110 –    std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111 –    std::cout << "bend" << std::endl;
112 –    for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
113 –        Bend* bend = k->bend;
114 –        std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
115 –        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;
116 –    }
117 –    std::cout << "torsio" << std::endl;
118 –    for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119 –        Torsion* torsion = l->torsion;
120 –        std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121 –        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;
122 –    }
123 –   */
74    }
75 <
75 >  
76    void ForceManager::preCalculation() {
77      SimInfo::MoleculeIterator mi;
78      Molecule* mol;
# Line 133 | Line 83 | namespace oopse {
83      
84      // forces are zeroed here, before any are accumulated.
85      // NOTE: do not rezero the forces in Fortran.
86 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
86 >
87 >    for (mol = info_->beginMolecule(mi); mol != NULL;
88 >         mol = info_->nextMolecule(mi)) {
89        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
90          atom->zeroForcesAndTorques();
91        }
92 <        
92 >      
93        //change the positions of atoms which belong to the rigidbodies
94 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
94 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95 >           rb = mol->nextRigidBody(rbIter)) {
96          rb->zeroForcesAndTorques();
97        }        
98      }
99      
100 +    // Zero out the stress tensor
101 +    tau *= 0.0;
102 +    
103    }
104 <
104 >  
105    void ForceManager::calcShortRangeInteraction() {
106      Molecule* mol;
107      RigidBody* rb;
# Line 157 | Line 113 | namespace oopse {
113      Molecule::BondIterator bondIter;;
114      Molecule::BendIterator  bendIter;
115      Molecule::TorsionIterator  torsionIter;
116 <    double bondPotential = 0.0;
117 <    double bendPotential = 0.0;
118 <    double torsionPotential = 0.0;
116 >    RealType bondPotential = 0.0;
117 >    RealType bendPotential = 0.0;
118 >    RealType torsionPotential = 0.0;
119  
120      //calculate short range interactions    
121 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
121 >    for (mol = info_->beginMolecule(mi); mol != NULL;
122 >         mol = info_->nextMolecule(mi)) {
123  
124        //change the positions of atoms which belong to the rigidbodies
125 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
126 <          rb->updateAtoms();
125 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
126 >           rb = mol->nextRigidBody(rbIter)) {
127 >        rb->updateAtoms();
128        }
129  
130 <      for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
130 >      for (bond = mol->beginBond(bondIter); bond != NULL;
131 >           bond = mol->nextBond(bondIter)) {
132          bond->calcForce();
133          bondPotential += bond->getPotential();
134        }
135  
136 <
137 <      for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
138 <
139 <          double angle;
140 <            bend->calcForce(angle);
141 <          double currBendPot = bend->getPotential();          
142 <            bendPotential += bend->getPotential();
143 <          std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
144 <          if (i == bendDataSets.end()) {
145 <            BendDataSet dataSet;
146 <            dataSet.prev.angle = dataSet.curr.angle = angle;
147 <            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
148 <            dataSet.deltaV = 0.0;
149 <            bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
150 <          }else {
151 <            i->second.prev.angle = i->second.curr.angle;
152 <            i->second.prev.potential = i->second.curr.potential;
153 <            i->second.curr.angle = angle;
154 <            i->second.curr.potential = currBendPot;
155 <            i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
156 <          }
157 <      }
199 <
200 <      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
201 <        double angle;
202 <          torsion->calcForce(angle);
203 <        double currTorsionPot = torsion->getPotential();
204 <          torsionPotential += torsion->getPotential();
205 <          std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
206 <          if (i == torsionDataSets.end()) {
207 <            TorsionDataSet dataSet;
208 <            dataSet.prev.angle = dataSet.curr.angle = angle;
209 <            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
210 <            dataSet.deltaV = 0.0;
211 <            torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
212 <          }else {
213 <            i->second.prev.angle = i->second.curr.angle;
214 <            i->second.prev.potential = i->second.curr.potential;
215 <            i->second.curr.angle = angle;
216 <            i->second.curr.potential = currTorsionPot;
217 <            i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
218 <          }      
136 >      for (bend = mol->beginBend(bendIter); bend != NULL;
137 >           bend = mol->nextBend(bendIter)) {
138 >        
139 >        RealType angle;
140 >        bend->calcForce(angle);
141 >        RealType currBendPot = bend->getPotential();          
142 >        bendPotential += bend->getPotential();
143 >        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
144 >        if (i == bendDataSets.end()) {
145 >          BendDataSet dataSet;
146 >          dataSet.prev.angle = dataSet.curr.angle = angle;
147 >          dataSet.prev.potential = dataSet.curr.potential = currBendPot;
148 >          dataSet.deltaV = 0.0;
149 >          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
150 >        }else {
151 >          i->second.prev.angle = i->second.curr.angle;
152 >          i->second.prev.potential = i->second.curr.potential;
153 >          i->second.curr.angle = angle;
154 >          i->second.curr.potential = currBendPot;
155 >          i->second.deltaV =  fabs(i->second.curr.potential -  
156 >                                   i->second.prev.potential);
157 >        }
158        }
159 <
159 >      
160 >      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
161 >           torsion = mol->nextTorsion(torsionIter)) {
162 >        RealType angle;
163 >        torsion->calcForce(angle);
164 >        RealType currTorsionPot = torsion->getPotential();
165 >        torsionPotential += torsion->getPotential();
166 >        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
167 >        if (i == torsionDataSets.end()) {
168 >          TorsionDataSet dataSet;
169 >          dataSet.prev.angle = dataSet.curr.angle = angle;
170 >          dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
171 >          dataSet.deltaV = 0.0;
172 >          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
173 >        }else {
174 >          i->second.prev.angle = i->second.curr.angle;
175 >          i->second.prev.potential = i->second.curr.potential;
176 >          i->second.curr.angle = angle;
177 >          i->second.curr.potential = currTorsionPot;
178 >          i->second.deltaV =  fabs(i->second.curr.potential -  
179 >                                   i->second.prev.potential);
180 >        }      
181 >      }      
182      }
183      
184 <    double  shortRangePotential = bondPotential + bendPotential + torsionPotential;    
184 >    RealType  shortRangePotential = bondPotential + bendPotential +
185 >      torsionPotential;    
186      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
187      curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
188      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
# Line 228 | Line 190 | namespace oopse {
190      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
191      
192    }
193 <
194 <  void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
193 >  
194 >  void ForceManager::calcLongRangeInteraction(bool needPotential,
195 >                                              bool needStress) {
196      Snapshot* curSnapshot;
197      DataStorage* config;
198 <    double* frc;
199 <    double* pos;
200 <    double* trq;
201 <    double* A;
202 <    double* electroFrame;
203 <    double* rc;
198 >    RealType* frc;
199 >    RealType* pos;
200 >    RealType* trq;
201 >    RealType* A;
202 >    RealType* electroFrame;
203 >    RealType* rc;
204      
205      //get current snapshot from SimInfo
206      curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
207 <
207 >    
208      //get array pointers
209      config = &(curSnapshot->atomData);
210      frc = config->getArrayPointer(DataStorage::dslForce);
# Line 257 | Line 220 | namespace oopse {
220      CutoffGroup* cg;
221      Vector3d com;
222      std::vector<Vector3d> rcGroup;
223 <
223 >    
224      if(info_->getNCutoffGroups() > 0){
225 <
226 <      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
227 <        for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
225 >      
226 >      for (mol = info_->beginMolecule(mi); mol != NULL;
227 >           mol = info_->nextMolecule(mi)) {
228 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
229 >            cg = mol->nextCutoffGroup(ci)) {
230            cg->getCOM(com);
231            rcGroup.push_back(com);
232          }
# Line 269 | Line 234 | namespace oopse {
234        
235        rc = rcGroup[0].getArrayPointer();
236      } else {
237 <      // center of mass of the group is the same as position of the atom  if cutoff group does not exist
237 >      // center of mass of the group is the same as position of the atom  
238 >      // if cutoff group does not exist
239        rc = pos;
240      }
275 –  
276 –    //initialize data before passing to fortran
277 –    double longRangePotential[LR_POT_TYPES];
278 –    double lrPot = 0.0;
241      
242 <    Mat3x3d tau;
242 >    //initialize data before passing to fortran
243 >    RealType longRangePotential[LR_POT_TYPES];
244 >    RealType lrPot = 0.0;
245 >    Vector3d totalDipole;
246      short int passedCalcPot = needPotential;
247      short int passedCalcStress = needStress;
248      int isError = 0;
# Line 285 | Line 250 | namespace oopse {
250      for (int i=0; i<LR_POT_TYPES;i++){
251        longRangePotential[i]=0.0; //Initialize array
252      }
253 <
254 <    doForceLoop( pos,
255 <                 rc,
256 <                 A,
257 <                 electroFrame,
258 <                 frc,
259 <                 trq,
260 <                 tau.getArrayPointer(),
261 <                 longRangePotential,
262 <                 &passedCalcPot,
263 <                 &passedCalcStress,
264 <                 &isError );
265 <
253 >    
254 >    doForceLoop(pos,
255 >                rc,
256 >                A,
257 >                electroFrame,
258 >                frc,
259 >                trq,
260 >                tau.getArrayPointer(),
261 >                longRangePotential,
262 >                &passedCalcPot,
263 >                &passedCalcStress,
264 >                &isError );
265 >    
266      if( isError ){
267        sprintf( painCave.errMsg,
268                 "Error returned from the fortran force calculation.\n" );
# Line 307 | Line 272 | namespace oopse {
272      for (int i=0; i<LR_POT_TYPES;i++){
273        lrPot += longRangePotential[i]; //Quick hack
274      }
275 <
275 >    
276 >    // grab the simulation box dipole moment if specified
277 >    if (info_->getCalcBoxDipole()){
278 >      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
279 >      
280 >      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
281 >      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
282 >      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
283 >    }
284 >    
285      //store the tau and long range potential    
286      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
287      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
288      curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315 –
316 –    curSnapshot->statData.setTau(tau);
289    }
290  
291 <
292 <  void ForceManager::postCalculation() {
291 >  
292 >  void ForceManager::postCalculation(bool needStress) {
293      SimInfo::MoleculeIterator mi;
294      Molecule* mol;
295      Molecule::RigidBodyIterator rbIter;
296      RigidBody* rb;
297 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
298      
299      // collect the atomic forces onto rigid bodies
300 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
301 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
302 <        rb->calcForcesAndTorques();
300 >    
301 >    for (mol = info_->beginMolecule(mi); mol != NULL;
302 >         mol = info_->nextMolecule(mi)) {
303 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
304 >           rb = mol->nextRigidBody(rbIter)) {
305 >        if (needStress) {          
306 >          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
307 >          tau += rbTau;
308 >        } else{
309 >          rb->calcForcesAndTorques();
310 >        }
311        }
312      }
313  
314 +    if (needStress) {
315 + #ifdef IS_MPI
316 +      Mat3x3d tmpTau(tau);
317 +      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
318 +                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
319 + #endif
320 +      curSnapshot->statData.setTau(tau);
321 +    }
322    }
323  
324   } //end namespace oopse

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines