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Comparing branches/new_design/OOPSE-4/src/brains/ForceManager.cpp (file contents):
Revision 1738 by tim, Sat Nov 13 05:08:12 2004 UTC vs.
Revision 1804 by tim, Tue Nov 30 19:58:25 2004 UTC

# Line 32 | Line 32
32    */
33  
34   #include "brains/ForceManager.hpp"
35 <
35 > #include "primitives/Molecule.hpp"
36 > #include "UseTheForce/doForces_interface.h"
37 > #include "utils/simError.h"
38   namespace oopse {
39  
40   void ForceManager::calcForces(bool needPotential, bool needStress) {
# Line 45 | Line 47 | void ForceManager::calcForces(bool needPotential, bool
47      
48      calcShortRangeInteraction();
49  
50 <    calcLongRangeInteraction();
50 >    calcLongRangeInteraction(needPotential, needStress);
51  
52 <    postCalculation()
52 >    postCalculation();
53          
54   }
55  
56   void ForceManager::preCalculation() {
57 <    typename SimInfo::MoleculeIterator mi;
57 >    SimInfo::MoleculeIterator mi;
58      Molecule* mol;
59 <    typename Molecule::AtomIterator ai;
59 >    Molecule::AtomIterator ai;
60      Atom* atom;
61  
62      // forces are zeroed here, before any are accumulated.
# Line 73 | Line 75 | void ForceManager::calcShortRangeInteraction() {
75      Bond* bond;
76      Bend* bend;
77      Torsion* torsion;
78 <    typename SimInfo::MoleculeIterator mi;
79 <    typename Molecule::RigidBodyIterator rbIter;
80 <    typename Molecule::BondIterator bondIter;;
81 <    typename Molecule::BendIterator  bendIter;
82 <    typename Molecule::TorsionIterator  torsionIter;
78 >    SimInfo::MoleculeIterator mi;
79 >    Molecule::RigidBodyIterator rbIter;
80 >    Molecule::BondIterator bondIter;;
81 >    Molecule::BendIterator  bendIter;
82 >    Molecule::TorsionIterator  torsionIter;
83  
84      //calculate short range interactions    
85      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
# Line 88 | Line 90 | void ForceManager::calcShortRangeInteraction() {
90          }
91  
92          for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
93 <            bond->calc_forces();
93 >            bond->calcForce();
94          }
95  
96          for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
97 <            bend->calc_forces();
97 >            bend->calcForce();
98          }
99  
100          for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
101 <            torsion->calc_forces();
101 >            torsion->calcForce();
102          }
103  
104      }
# Line 110 | Line 112 | void ForceManager::calcLongRangeInteraction(bool needP
112      double* pos;
113      double* trq;
114      double* A;
115 <    double* u_l;
115 >    double* unitFrame;
116      double* rc;
117      
118      //get current snapshot from SimInfo
119 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot()
119 >    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
120  
121      //get array pointers
122      config = &(curSnapshot->atomData);
# Line 122 | Line 124 | void ForceManager::calcLongRangeInteraction(bool needP
124      pos = config->getArrayPointer(DataStorage::dslPosition);
125      trq = config->getArrayPointer(DataStorage::dslTorque);
126      A   = config->getArrayPointer(DataStorage::dslAmat);
127 <    u_l = config->getArrayPointer(DataStorage::dslUnitVector);
127 >    unitFrame = config->getArrayPointer(DataStorage::dslUnitFrame);
128  
129      //calculate the center of mass of cutoff group
130 <    typename SimInfo::MoleculeIterator mi;
130 >    SimInfo::MoleculeIterator mi;
131      Molecule* mol;
132 <    typename Molecule::CutoffGroupIterator ci;
132 >    Molecule::CutoffGroupIterator ci;
133      CutoffGroup* cg;
134      Vector3d com;
135      std::vector<Vector3d> rcGroup;
# Line 136 | Line 138 | void ForceManager::calcLongRangeInteraction(bool needP
138  
139      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
140          for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
141 <            cg->getCOM(com)
141 >            cg->getCOM(com);
142              rcGroup.push_back(com);
143          }
144      }// end for (mol)
145        
146 <        rc = rcGroup[0]->getArrayPointer();
146 >        rc = rcGroup[0].getArrayPointer();
147      } else {
148          // center of mass of the group is the same as position of the atom  if cutoff group does not exist
149          rc = pos;
# Line 157 | Line 159 | void ForceManager::calcLongRangeInteraction(bool needP
159      doForceLoop( pos,
160              rc,
161              A,
162 <            u_l,
162 >            unitFrame,
163              frc,
164              trq,
165 <            tau,
165 >            tau.getArrayPointer(),
166              &longRangePotential,
167              &passedCalcPot,
168              &passedCalcStress,
# Line 174 | Line 176 | void ForceManager::calcLongRangeInteraction(bool needP
176      }
177  
178      //store the tau and long range potential    
179 <    curSnapshot->statData[Stats::LONGRANGEPOTENTIAL] = longRangePotential;
179 >    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
180      curSnapshot->statData[Stats::TAUXX] = tau[0];
181      curSnapshot->statData[Stats::TAUXY] = tau[1];
182      curSnapshot->statData[Stats::TAUXZ] = tau[2];
# Line 188 | Line 190 | void ForceManager::postCalculation() {
190  
191  
192   void ForceManager::postCalculation() {
193 <    typename SimInfo::MoleculeIterator mi;
193 >    SimInfo::MoleculeIterator mi;
194      Molecule* mol;
195 <    typename Molecule::RigidBodyIterator rbIter;
195 >    Molecule::RigidBodyIterator rbIter;
196      RigidBody* rb;
197      
198      // collect the atomic forces onto rigid bodies

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