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Comparing branches/development/src/integrators/NPT.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <math.h>
# Line 117 | Line 118 | namespace OpenMD {
118        tt2 = tauThermostat * tauThermostat;
119        tb2 = tauBarostat * tauBarostat;
120  
121 <      update();
121 >      updateSizes();
122      }
123  
124    NPT::~NPT() {
125    }
126  
127 <  void NPT::doUpdate() {
127 >  void NPT::doUpdateSizes() {
128  
129      oldPos.resize(info_->getNIntegrableObjects());
130      oldVel.resize(info_->getNIntegrableObjects());
# Line 188 | Line 189 | namespace OpenMD {
189            //ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi);
190            ji += dt2*PhysicalConstants::energyConvert * Tb - dt2*chi* ji;
191                  
192 <          rotAlgo->rotate(integrableObject, ji, dt);
192 >          rotAlgo_->rotate(integrableObject, ji, dt);
193  
194            integrableObject->setJ(ji);
195          }
# Line 204 | Line 205 | namespace OpenMD {
205      //calculate the integral of chidt
206      integralOfChidt += dt2 * chi;
207      
208 +    flucQ_->moveA();
209 +
210 +
211      index = 0;
212      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
213        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 232 | Line 236 | namespace OpenMD {
236          }
237        }
238  
239 <      rattle->constraintA();
239 >      rattle_->constraintA();
240      }
241  
242      // Scale the box after all the positions have been moved:
# Line 323 | Line 327 | namespace OpenMD {
327          }
328        }
329          
330 <      rattle->constraintB();
330 >      rattle_->constraintB();
331  
332        if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
333          break;
# Line 335 | Line 339 | namespace OpenMD {
339      currentSnapshot_->setChi(chi);
340      currentSnapshot_->setIntegralOfChiDt(integralOfChidt);    
341  
342 +    flucQ_->moveB();
343      saveEta();
344    }
345  

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