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root/OpenMD/branches/development/src/integrators/NPT.cpp

Comparing:
trunk/src/integrators/NPT.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/integrators/NPT.cpp (file contents), Revision 1759 by gezelter, Thu Jun 21 18:55:33 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 273 | Line 277 | namespace OpenMD {
277		integrableObject = mol->nextIntegrableObject(j)) {
278
279		oldVel[index] = integrableObject->getVel();
280	<	oldJi[index] = integrableObject->getJ();
280	>
281	>	if (integrableObject->isDirectional())
282	>	oldJi[index] = integrableObject->getJ();
283	>
284		++index;
285		}
286		}
#	Line 323 | Line 330 | namespace OpenMD {
330		}
331		}
332
333	<	rattle->constraintB();
333	>	rattle_->constraintB();
334
335		if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
336		break;
#	Line 335 | Line 342 | namespace OpenMD {
342		currentSnapshot_->setChi(chi);
343		currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
344
345	+	flucQ_->moveB();
346		saveEta();
347		}
348

Comparing:
trunk/src/integrators/NPT.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/integrators/NPT.cpp (property svn:keywords), Revision 1759 by gezelter, Thu Jun 21 18:55:33 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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