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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 39 | Line 39
39   * such damages.
40   */
41  
42 < /**
43 <  * @file ForceManager.cpp
44 <  * @author tlin
45 <  * @date 11/09/2004
46 <  * @time 10:39am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file ForceManager.cpp
44 > * @author tlin
45 > * @date 11/09/2004
46 > * @time 10:39am
47 > * @version 1.0
48 > */
49  
50   #include "brains/ForceManager.hpp"
51   #include "primitives/Molecule.hpp"
52   #include "UseTheForce/doForces_interface.h"
53 + #define __C
54 + #include "UseTheForce/DarkSide/fInteractionMap.h"
55   #include "utils/simError.h"
56 + #include "primitives/Bond.hpp"
57 + #include "primitives/Bend.hpp"
58   namespace oopse {
59  
60 < void ForceManager::calcForces(bool needPotential, bool needStress) {
61 <
60 >  void ForceManager::calcForces(bool needPotential, bool needStress) {
61 >    
62      if (!info_->isFortranInitialized()) {
63 <        info_->update();
63 >      info_->update();
64      }
65 <
65 >    
66      preCalculation();
67      
68      calcShortRangeInteraction();
69  
70      calcLongRangeInteraction(needPotential, needStress);
71  
72 <    postCalculation();
73 <        
74 < }
75 <
76 < void ForceManager::preCalculation() {
72 >    postCalculation(needStress);
73 >    
74 >  }
75 >  
76 >  void ForceManager::preCalculation() {
77      SimInfo::MoleculeIterator mi;
78      Molecule* mol;
79      Molecule::AtomIterator ai;
# Line 79 | Line 83 | void ForceManager::preCalculation() {
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)) {
87 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
88 <            atom->zeroForcesAndTorques();
89 <        }
90 <        
91 <        //change the positions of atoms which belong to the rigidbodies
92 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
93 <            rb->zeroForcesAndTorques();
94 <        }        
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 >          
93 >      //change the positions of atoms which belong to the rigidbodies
94 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95 >           rb = mol->nextRigidBody(rbIter)) {
96 >        rb->zeroForcesAndTorques();
97 >      }        
98 >          
99      }
100      
101 < }
102 <
103 < void ForceManager::calcShortRangeInteraction() {
101 >    // Zero out the stress tensor
102 >    tau *= 0.0;
103 >    
104 >  }
105 >  
106 >  void ForceManager::calcShortRangeInteraction() {
107      Molecule* mol;
108      RigidBody* rb;
109      Bond* bond;
# Line 103 | Line 114 | void ForceManager::calcShortRangeInteraction() {
114      Molecule::BondIterator bondIter;;
115      Molecule::BendIterator  bendIter;
116      Molecule::TorsionIterator  torsionIter;
117 +    RealType bondPotential = 0.0;
118 +    RealType bendPotential = 0.0;
119 +    RealType torsionPotential = 0.0;
120  
121      //calculate short range interactions    
122 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
122 >    for (mol = info_->beginMolecule(mi); mol != NULL;
123 >         mol = info_->nextMolecule(mi)) {
124  
125 <        //change the positions of atoms which belong to the rigidbodies
126 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
127 <            rb->updateAtoms();
128 <        }
125 >      //change the positions of atoms which belong to the rigidbodies
126 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
127 >           rb = mol->nextRigidBody(rbIter)) {
128 >        rb->updateAtoms();
129 >      }
130  
131 <        for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
132 <            bond->calcForce();
133 <        }
131 >      for (bond = mol->beginBond(bondIter); bond != NULL;
132 >           bond = mol->nextBond(bondIter)) {
133 >        bond->calcForce();
134 >        bondPotential += bond->getPotential();
135 >      }
136  
137 <        for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
138 <            bend->calcForce();
137 >      for (bend = mol->beginBend(bendIter); bend != NULL;
138 >           bend = mol->nextBend(bendIter)) {
139 >        
140 >        RealType angle;
141 >        bend->calcForce(angle);
142 >        RealType currBendPot = bend->getPotential();          
143 >        bendPotential += bend->getPotential();
144 >        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
145 >        if (i == bendDataSets.end()) {
146 >          BendDataSet dataSet;
147 >          dataSet.prev.angle = dataSet.curr.angle = angle;
148 >          dataSet.prev.potential = dataSet.curr.potential = currBendPot;
149 >          dataSet.deltaV = 0.0;
150 >          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
151 >        }else {
152 >          i->second.prev.angle = i->second.curr.angle;
153 >          i->second.prev.potential = i->second.curr.potential;
154 >          i->second.curr.angle = angle;
155 >          i->second.curr.potential = currBendPot;
156 >          i->second.deltaV =  fabs(i->second.curr.potential -  
157 >                                   i->second.prev.potential);
158          }
159 <
160 <        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
161 <            torsion->calcForce();
162 <        }
163 <
159 >      }
160 >      
161 >      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
162 >           torsion = mol->nextTorsion(torsionIter)) {
163 >        RealType angle;
164 >        torsion->calcForce(angle);
165 >        RealType currTorsionPot = torsion->getPotential();
166 >        torsionPotential += torsion->getPotential();
167 >        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
168 >        if (i == torsionDataSets.end()) {
169 >          TorsionDataSet dataSet;
170 >          dataSet.prev.angle = dataSet.curr.angle = angle;
171 >          dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
172 >          dataSet.deltaV = 0.0;
173 >          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
174 >        }else {
175 >          i->second.prev.angle = i->second.curr.angle;
176 >          i->second.prev.potential = i->second.curr.potential;
177 >          i->second.curr.angle = angle;
178 >          i->second.curr.potential = currTorsionPot;
179 >          i->second.deltaV =  fabs(i->second.curr.potential -  
180 >                                   i->second.prev.potential);
181 >        }      
182 >      }      
183      }
184      
185 <    double  shortRangePotential = 0.0;
186 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131 <        shortRangePotential += mol->getPotential();
132 <    }
133 <
185 >    RealType  shortRangePotential = bondPotential + bendPotential +
186 >      torsionPotential;    
187      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
188      curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
189 < }
190 <
191 < void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
189 >    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
190 >    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
191 >    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
192 >    
193 >  }
194 >  
195 >  void ForceManager::calcLongRangeInteraction(bool needPotential,
196 >                                              bool needStress) {
197      Snapshot* curSnapshot;
198      DataStorage* config;
199 <    double* frc;
200 <    double* pos;
201 <    double* trq;
202 <    double* A;
203 <    double* electroFrame;
204 <    double* rc;
199 >    RealType* frc;
200 >    RealType* pos;
201 >    RealType* trq;
202 >    RealType* A;
203 >    RealType* electroFrame;
204 >    RealType* rc;
205 >    RealType* particlePot;
206      
207      //get current snapshot from SimInfo
208      curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
209 <
209 >    
210      //get array pointers
211      config = &(curSnapshot->atomData);
212      frc = config->getArrayPointer(DataStorage::dslForce);
# Line 155 | Line 214 | void ForceManager::calcLongRangeInteraction(bool needP
214      trq = config->getArrayPointer(DataStorage::dslTorque);
215      A   = config->getArrayPointer(DataStorage::dslAmat);
216      electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
217 +    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
218  
219      //calculate the center of mass of cutoff group
220      SimInfo::MoleculeIterator mi;
# Line 165 | Line 225 | void ForceManager::calcLongRangeInteraction(bool needP
225      std::vector<Vector3d> rcGroup;
226      
227      if(info_->getNCutoffGroups() > 0){
228 <
229 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
230 <        for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
231 <            cg->getCOM(com);
232 <            rcGroup.push_back(com);
228 >      
229 >      for (mol = info_->beginMolecule(mi); mol != NULL;
230 >           mol = info_->nextMolecule(mi)) {
231 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
232 >            cg = mol->nextCutoffGroup(ci)) {
233 >          cg->getCOM(com);
234 >          rcGroup.push_back(com);
235          }
236 <    }// end for (mol)
236 >      }// end for (mol)
237        
238 <        rc = rcGroup[0].getArrayPointer();
238 >      rc = rcGroup[0].getArrayPointer();
239      } else {
240 <        // center of mass of the group is the same as position of the atom  if cutoff group does not exist
241 <        rc = pos;
240 >      // center of mass of the group is the same as position of the atom  
241 >      // if cutoff group does not exist
242 >      rc = pos;
243      }
244 <  
244 >    
245      //initialize data before passing to fortran
246 <    double longRangePotential = 0.0;
247 <    Mat3x3d tau;
246 >    RealType longRangePotential[LR_POT_TYPES];
247 >    RealType lrPot = 0.0;
248 >    Vector3d totalDipole;
249      short int passedCalcPot = needPotential;
250      short int passedCalcStress = needStress;
251      int isError = 0;
252  
253 <    doForceLoop( pos,
254 <            rc,
255 <            A,
256 <            electroFrame,
257 <            frc,
258 <            trq,
259 <            tau.getArrayPointer(),
260 <            &longRangePotential,
261 <            &passedCalcPot,
262 <            &passedCalcStress,
263 <            &isError );
264 <
253 >    for (int i=0; i<LR_POT_TYPES;i++){
254 >      longRangePotential[i]=0.0; //Initialize array
255 >    }
256 >    
257 >    doForceLoop(pos,
258 >                rc,
259 >                A,
260 >                electroFrame,
261 >                frc,
262 >                trq,
263 >                tau.getArrayPointer(),
264 >                longRangePotential,
265 >                particlePot,
266 >                &passedCalcPot,
267 >                &passedCalcStress,
268 >                &isError );
269 >    
270      if( isError ){
271 <        sprintf( painCave.errMsg,
272 <             "Error returned from the fortran force calculation.\n" );
273 <        painCave.isFatal = 1;
274 <        simError();
271 >      sprintf( painCave.errMsg,
272 >               "Error returned from the fortran force calculation.\n" );
273 >      painCave.isFatal = 1;
274 >      simError();
275      }
276 <
276 >    for (int i=0; i<LR_POT_TYPES;i++){
277 >      lrPot += longRangePotential[i]; //Quick hack
278 >    }
279 >    
280 >    // grab the simulation box dipole moment if specified
281 >    if (info_->getCalcBoxDipole()){
282 >      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
283 >      
284 >      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
285 >      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
286 >      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
287 >    }
288 >    
289      //store the tau and long range potential    
290 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
291 <    curSnapshot->statData.setTau(tau);
292 < }
290 >    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
291 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
292 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
293 >  }
294  
295 <
296 < void ForceManager::postCalculation() {
295 >  
296 >  void ForceManager::postCalculation(bool needStress) {
297      SimInfo::MoleculeIterator mi;
298      Molecule* mol;
299      Molecule::RigidBodyIterator rbIter;
300      RigidBody* rb;
301 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
302      
303      // collect the atomic forces onto rigid bodies
304 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
305 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
306 <            rb->calcForcesAndTorques();
304 >    
305 >    for (mol = info_->beginMolecule(mi); mol != NULL;
306 >         mol = info_->nextMolecule(mi)) {
307 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
308 >           rb = mol->nextRigidBody(rbIter)) {
309 >        if (needStress) {          
310 >          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
311 >          tau += rbTau;
312 >        } else{
313 >          rb->calcForcesAndTorques();
314          }
315 +      }
316      }
317  
318 < }
318 >    if (needStress) {
319 > #ifdef IS_MPI
320 >      Mat3x3d tmpTau(tau);
321 >      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
322 >                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
323 > #endif
324 >      curSnapshot->statData.setTau(tau);
325 >    }
326 >  }
327  
328   } //end namespace oopse

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