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root/OpenMD/trunk/src/integrators/LDForceManager.cpp
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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 983 by gezelter, Tue Jun 6 17:43:28 2006 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC

# Line 39 | Line 39
39   * such damages.
40   */
41   #include <fstream>
42 + #include <iostream>
43   #include "integrators/LDForceManager.hpp"
44   #include "math/CholeskyDecomposition.hpp"
45   #include "utils/OOPSEConstant.hpp"
# Line 246 | Line 247 | namespace oopse {
247      return props;
248    }
249    
250 <  void LDForceManager::postCalculation() {
250 >  void LDForceManager::postCalculation(bool needStress){
251      SimInfo::MoleculeIterator i;
252      Molecule::IntegrableObjectIterator  j;
253      Molecule* mol;
# Line 258 | Line 259 | namespace oopse {
259      Mat3x3d Atrans;
260      Vector3d Tb;
261      Vector3d ji;
261 –    RealType mass;
262      unsigned int index = 0;
263      bool doLangevinForces;
264      bool freezeMolecule;
265      int fdf;
266  
267 –
267      fdf = 0;
268 +
269      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
270  
271        doLangevinForces = true;          
# Line 275 | Line 275 | namespace oopse {
275          
276          Vector3d molPos = mol->getCom();
277          RealType molRad = molPos.length();
278 <        
278 >
279          doLangevinForces = false;
280          
281          if (molRad > langevinBufferRadius_) {
# Line 294 | Line 294 | namespace oopse {
294          if (freezeMolecule)
295            fdf += integrableObject->freeze();
296          
297 <        if (doLangevinForces) {          
297 >        if (doLangevinForces) {  
298            vel =integrableObject->getVel();
299            if (integrableObject->isDirectional()){
300              //calculate angular velocity in lab frame
# Line 352 | Line 352 | namespace oopse {
352      
353        }
354      }    
355 –    info_->setFdf(fdf);
355  
356 +    info_->setFdf(fdf);
357      veloMunge->removeComDrift();
358      // Remove angular drift if we are not using periodic boundary conditions.
359      if(!simParams->getUsePeriodicBoundaryConditions())
360        veloMunge->removeAngularDrift();
361  
362 <    ForceManager::postCalculation();  
362 >    ForceManager::postCalculation(needStress);  
363    }
364  
365   void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
# Line 367 | Line 367 | void LDForceManager::genRandomForceAndTorque(Vector3d&
367  
368      Vector<RealType, 6> Z;
369      Vector<RealType, 6> generalForce;
370 –
370          
371      Z[0] = randNumGen_.randNorm(0, variance);
372      Z[1] = randNumGen_.randNorm(0, variance);

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