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root/OpenMD/trunk/src/restraints/ThermoIntegrationForceManager.cpp

Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 35 | Line 35
35		*
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
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
#	Line 90 | Line 91 | namespace OpenMD {
91		ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
92		}
93
94	<	void ThermoIntegrationForceManager::calcForces(bool needPotential,
94	<	bool needStress){
94	>	void ThermoIntegrationForceManager::calcForces(){
95		Snapshot* curSnapshot;
96		SimInfo::MoleculeIterator mi;
97		Molecule* mol;
98		Molecule::IntegrableObjectIterator ii;
99	<	StuntDouble* integrableObject;
99	>	StuntDouble* sd;
100		Vector3d frc;
101		Vector3d trq;
102		Mat3x3d tempTau;
103
104		// perform the standard calcForces first
105	<	ForceManager::calcForces(needPotential, needStress);
105	>	ForceManager::calcForces();
106
107		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
108
109	<	// now scale forces and torques of all the integrableObjects
109	>	// now scale forces and torques of all the sds
110
111		for (mol = info_->beginMolecule(mi); mol != NULL;
112		mol = info_->nextMolecule(mi)) {
113	<	for (integrableObject = mol->beginIntegrableObject(ii);
114	<	integrableObject != NULL;
115	<	integrableObject = mol->nextIntegrableObject(ii)) {
116	<	frc = integrableObject->getFrc();
113	>
114	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
115	>	sd = mol->nextIntegrableObject(ii)) {
116	>
117	>	frc = sd->getFrc();
118		frc *= factor_;
119	<	integrableObject->setFrc(frc);
119	>	sd->setFrc(frc);
120
121	<	if (integrableObject->isDirectional()){
122	<	trq = integrableObject->getTrq();
121	>	if (sd->isDirectional()){
122	>	trq = sd->getTrq();
123		trq *= factor_;
124	<	integrableObject->setTrq(trq);
124	>	sd->setTrq(trq);
125		}
126		}
127		}
128
129	<	// set vraw to be the unmodulated potential
130	<	lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
131	<	curSnapshot->statData[Stats::VRAW] = lrPot_;
129	>	// set rawPotential to be the unmodulated potential
130	>	lrPot_ = curSnapshot->getLongRangePotential();
131	>	curSnapshot->setRawPotential(lrPot_);
132
133		// modulate the potential and update the snapshot
134		lrPot_ *= factor_;
135	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
135	>	curSnapshot->setLongRangePotential(lrPot_);
136
137		// scale the pressure tensor
138	<	tempTau = curSnapshot->statData.getTau();
138	>	tempTau = curSnapshot->getStressTensor();
139		tempTau *= factor_;
140	<	curSnapshot->statData.setTau(tempTau);
140	>	curSnapshot->setStressTensor(tempTau);
141
142		// now, on to the applied restraining potentials (if needed):
143		RealType restPot_local = 0.0;
#	Line 144 | Line 145 | namespace OpenMD {
145
146		if (simParam->getUseRestraints()) {
147		// do restraints from RestraintForceManager:
147	–	//restPot_local = doRestraints(1.0 - factor_);
148		restPot_local = doRestraints(1.0 - factor_);
149		vHarm_local = getUnscaledPotential();
150		}
#	Line 162 | Line 162 | namespace OpenMD {
162		#endif
163
164		// give the final values to stats
165	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
166	<	curSnapshot->statData[Stats::VHARM] = vHarm_;
165	>	curSnapshot->setLongRangePotential(lrPot_);
166	>	curSnapshot->setRestraintPotential(vHarm_);
167		}
168		}

Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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