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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 1938 by gezelter, Thu Oct 31 15:32:17 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
42	–
43	–	#include "restraints/ThermoIntegrationForceManager.hpp"
44	–
43		#ifdef IS_MPI
44		#include <mpi.h>
45		#endif
46
47	+	#include "restraints/ThermoIntegrationForceManager.hpp"
48	+
49		namespace OpenMD {
50
51		ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
#	Line 90 | Line 90 | namespace OpenMD {
90		ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
91		}
92
93	<	void ThermoIntegrationForceManager::calcForces(bool needPotential,
94	<	bool needStress){
93	>	void ThermoIntegrationForceManager::calcForces(){
94		Snapshot* curSnapshot;
95		SimInfo::MoleculeIterator mi;
96		Molecule* mol;
97		Molecule::IntegrableObjectIterator ii;
98	<	StuntDouble* integrableObject;
98	>	StuntDouble* sd;
99		Vector3d frc;
100		Vector3d trq;
101		Mat3x3d tempTau;
102
103		// perform the standard calcForces first
104	<	ForceManager::calcForces(needPotential, needStress);
104	>	ForceManager::calcForces();
105
106		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
107
108	<	// now scale forces and torques of all the integrableObjects
108	>	// now scale forces and torques of all the sds
109
110		for (mol = info_->beginMolecule(mi); mol != NULL;
111		mol = info_->nextMolecule(mi)) {
112	<	for (integrableObject = mol->beginIntegrableObject(ii);
113	<	integrableObject != NULL;
114	<	integrableObject = mol->nextIntegrableObject(ii)) {
115	<	frc = integrableObject->getFrc();
112	>
113	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
114	>	sd = mol->nextIntegrableObject(ii)) {
115	>
116	>	frc = sd->getFrc();
117		frc *= factor_;
118	<	integrableObject->setFrc(frc);
118	>	sd->setFrc(frc);
119
120	<	if (integrableObject->isDirectional()){
121	<	trq = integrableObject->getTrq();
120	>	if (sd->isDirectional()){
121	>	trq = sd->getTrq();
122		trq *= factor_;
123	<	integrableObject->setTrq(trq);
123	>	sd->setTrq(trq);
124		}
125		}
126		}
127
128	<	// set vraw to be the unmodulated potential
129	<	lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
130	<	curSnapshot->statData[Stats::VRAW] = lrPot_;
128	>	// set rawPotential to be the unmodulated potential
129	>	lrPot_ = curSnapshot->getLongRangePotential();
130	>	curSnapshot->setRawPotential(lrPot_);
131
132		// modulate the potential and update the snapshot
133		lrPot_ *= factor_;
134	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
134	>	curSnapshot->setLongRangePotential(lrPot_);
135
136		// scale the pressure tensor
137	<	tempTau = curSnapshot->statData.getTau();
137	>	tempTau = curSnapshot->getStressTensor();
138		tempTau *= factor_;
139	<	curSnapshot->statData.setTau(tempTau);
139	>	curSnapshot->setStressTensor(tempTau);
140
141		// now, on to the applied restraining potentials (if needed):
142		RealType restPot_local = 0.0;
#	Line 144 | Line 144 | namespace OpenMD {
144
145		if (simParam->getUseRestraints()) {
146		// do restraints from RestraintForceManager:
147	–	//restPot_local = doRestraints(1.0 - factor_);
147		restPot_local = doRestraints(1.0 - factor_);
148		vHarm_local = getUnscaledPotential();
149		}
#	Line 162 | Line 161 | namespace OpenMD {
161		#endif
162
163		// give the final values to stats
164	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
165	<	curSnapshot->statData[Stats::VHARM] = vHarm_;
164	>	curSnapshot->setLongRangePotential(lrPot_);
165	>	curSnapshot->setRestraintPotential(vHarm_);
166		}
167		}

Comparing trunk/src/restraints/ThermoIntegrationForceManager.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

#	Line 0 | Line 1
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