[ViewVC] Diff of: OpenMD/branches/development/src/brains/ForceManager.cpp

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC vs.
Revision 1877 by gezelter, Thu Jun 6 15:43:35 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		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
47		* @version 1.0
48		*/
49
#	Line 57 \| Line 57
57		#include "primitives/Torsion.hpp"
58		#include "primitives/Inversion.hpp"
59		#include "nonbonded/NonBondedInteraction.hpp"
60	+	#include "perturbations/ElectricField.hpp"
61		#include "parallel/ForceMatrixDecomposition.hpp"
62
63		#include <cstdio>
#	Line 66 \| Line 67 \| namespace OpenMD {
67		using namespace std;
68		namespace OpenMD {
69
70	<	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
71	>	initialized_(false) {
72		forceField_ = info_->getForceField();
73		interactionMan_ = new InteractionManager();
74		fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	+	thermo = new Thermo(info_);
76		}
77
78	+	ForceManager::~ForceManager() {
79	+	perturbations_.clear();
80	+
81	+	delete switcher_;
82	+	delete interactionMan_;
83	+	delete fDecomp_;
84	+	delete thermo;
85	+	}
86	+
87		/**
88		* setupCutoffs
89		*
#	Line 86 \| Line 98 \| namespace OpenMD {
98		* simulation for suggested cutoff values (e.g. 2.5 * sigma).
99		* Use the maximum suggested value that was found.
100		*
101	<	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
101	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102		* or SHIFTED_POTENTIAL)
103		* If cutoffMethod was explicitly set, use that choice.
104		* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
#	Line 108 \| Line 120 \| namespace OpenMD {
120
121		Globals* simParams_ = info_->getSimParams();
122		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
123	+	int mdFileVersion;
124	+	rCut_ = 0.0; //Needs a value for a later max() call;
125
126	+	if (simParams_->haveMDfileVersion())
127	+	mdFileVersion = simParams_->getMDfileVersion();
128	+	else
129	+	mdFileVersion = 0;
130	+
131	+	// We need the list of simulated atom types to figure out cutoffs
132	+	// as well as long range corrections.
133	+
134	+	set<AtomType*>::iterator i;
135	+	set<AtomType*> atomTypes_;
136	+	atomTypes_ = info_->getSimulatedAtomTypes();
137	+
138		if (simParams_->haveCutoffRadius()) {
139		rCut_ = simParams_->getCutoffRadius();
140		} else {
#	Line 123 \| Line 149 \| namespace OpenMD {
149		rCut_ = 12.0;
150		} else {
151		RealType thisCut;
152	<	set<AtomType*>::iterator i;
127	<	set<AtomType*> atomTypes;
128	<	atomTypes = info_->getSimulatedAtomTypes();
129	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
152	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153		thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154		rCut_ = max(thisCut, rCut_);
155		}
#	Line 148 \| Line 171 \| namespace OpenMD {
171		stringToCutoffMethod["SWITCHED"] = SWITCHED;
172		stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
173		stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174	+	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175
176		if (simParams_->haveCutoffMethod()) {
177		string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
#	Line 157 \| Line 181 \| namespace OpenMD {
181		sprintf(painCave.errMsg,
182		"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
183		"\tShould be one of: "
184	<	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
184	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
185	>	"\tor SHIFTED_FORCE\n",
186		cutMeth.c_str());
187		painCave.isFatal = 1;
188		painCave.severity = OPENMD_ERROR;
#	Line 166 \| Line 191 \| namespace OpenMD {
191		cutoffMethod_ = i->second;
192		}
193		} else {
194	<	sprintf(painCave.errMsg,
195	<	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
196	<	"\tOpenMD will use SHIFTED_FORCE.\n");
197	<	painCave.isFatal = 0;
198	<	painCave.severity = OPENMD_INFO;
199	<	simError();
200	<	cutoffMethod_ = SHIFTED_FORCE;
194	>	if (mdFileVersion > 1) {
195	>	sprintf(painCave.errMsg,
196	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
197	>	"\tOpenMD will use SHIFTED_FORCE.\n");
198	>	painCave.isFatal = 0;
199	>	painCave.severity = OPENMD_INFO;
200	>	simError();
201	>	cutoffMethod_ = SHIFTED_FORCE;
202	>	} else {
203	>	// handle the case where the old file version was in play
204	>	// (there should be no cutoffMethod, so we have to deduce it
205	>	// from other data).
206	>
207	>	sprintf(painCave.errMsg,
208	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
209	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
210	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
211	>	"\tbehavior of the older (version 1) code. To remove this\n"
212	>	"\twarning, add an explicit cutoffMethod and change the top\n"
213	>	"\tof the file so that it begins with <OpenMD version=2>\n");
214	>	painCave.isFatal = 0;
215	>	painCave.severity = OPENMD_WARNING;
216	>	simError();
217	>
218	>	// The old file version tethered the shifting behavior to the
219	>	// electrostaticSummationMethod keyword.
220	>
221	>	if (simParams_->haveElectrostaticSummationMethod()) {
222	>	string myMethod = simParams_->getElectrostaticSummationMethod();
223	>	toUpper(myMethod);
224	>
225	>	if (myMethod == "SHIFTED_POTENTIAL") {
226	>	cutoffMethod_ = SHIFTED_POTENTIAL;
227	>	} else if (myMethod == "SHIFTED_FORCE") {
228	>	cutoffMethod_ = SHIFTED_FORCE;
229	>	} else if (myMethod == "TAYLOR_SHIFTED") {
230	>	cutoffMethod_ = TAYLOR_SHIFTED;
231	>	}
232	>
233	>	if (simParams_->haveSwitchingRadius())
234	>	rSwitch_ = simParams_->getSwitchingRadius();
235	>
236	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE" \|\|
237	>	myMethod == "TAYLOR_SHIFTED") {
238	>	if (simParams_->haveSwitchingRadius()){
239	>	sprintf(painCave.errMsg,
240	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
241	>	"\tA value was set for the switchingRadius\n"
242	>	"\teven though the electrostaticSummationMethod was\n"
243	>	"\tset to %s\n", myMethod.c_str());
244	>	painCave.severity = OPENMD_WARNING;
245	>	painCave.isFatal = 1;
246	>	simError();
247	>	}
248	>	}
249	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
250	>	if (cutoffMethod_ == SHIFTED_FORCE) {
251	>	sprintf(painCave.errMsg,
252	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
253	>	"\tcutoffRadius and switchingRadius are set to the\n"
254	>	"\tsame value. OpenMD will use shifted force\n"
255	>	"\tpotentials instead of switching functions.\n");
256	>	painCave.isFatal = 0;
257	>	painCave.severity = OPENMD_WARNING;
258	>	simError();
259	>	} else {
260	>	cutoffMethod_ = SHIFTED_POTENTIAL;
261	>	sprintf(painCave.errMsg,
262	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
263	>	"\tcutoffRadius and switchingRadius are set to the\n"
264	>	"\tsame value. OpenMD will use shifted potentials\n"
265	>	"\tinstead of switching functions.\n");
266	>	painCave.isFatal = 0;
267	>	painCave.severity = OPENMD_WARNING;
268	>	simError();
269	>	}
270	>	}
271	>	}
272	>	}
273		}
274
275		map<string, CutoffPolicy> stringToCutoffPolicy;
#	Line 180 \| Line 277 \| namespace OpenMD {
277		stringToCutoffPolicy["MAX"] = MAX;
278		stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
279
280	<	std::string cutPolicy;
280	>	string cutPolicy;
281		if (forceFieldOptions_.haveCutoffPolicy()){
282		cutPolicy = forceFieldOptions_.getCutoffPolicy();
283		}else if (simParams_->haveCutoffPolicy()) {
#	Line 242 \| Line 339 \| namespace OpenMD {
339		simError();
340		}
341		} else {
342	<	if (simParams_->haveSwitchingRadius()) {
343	<	map<string, CutoffMethod>::const_iterator it;
344	<	string theMeth;
345	<	for (it = stringToCutoffMethod.begin();
346	<	it != stringToCutoffMethod.end(); ++it) {
347	<	if (it->second == cutoffMethod_) {
348	<	theMeth = it->first;
349	<	break;
342	>	if (mdFileVersion > 1) {
343	>	// throw an error if we define a switching radius and don't need one.
344	>	// older file versions should not do this.
345	>	if (simParams_->haveSwitchingRadius()) {
346	>	map<string, CutoffMethod>::const_iterator it;
347	>	string theMeth;
348	>	for (it = stringToCutoffMethod.begin();
349	>	it != stringToCutoffMethod.end(); ++it) {
350	>	if (it->second == cutoffMethod_) {
351	>	theMeth = it->first;
352	>	break;
353	>	}
354		}
355	+	sprintf(painCave.errMsg,
356	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
357	+	"\tis not set to SWITCHED, so switchingRadius value\n"
358	+	"\twill be ignored for this simulation\n", theMeth.c_str());
359	+	painCave.isFatal = 0;
360	+	painCave.severity = OPENMD_WARNING;
361	+	simError();
362		}
255	–	sprintf(painCave.errMsg,
256	–	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257	–	"\tis not set to SWITCHED, so switchingRadius value\n"
258	–	"\twill be ignored for this simulation\n", theMeth.c_str());
259	–	painCave.isFatal = 0;
260	–	painCave.severity = OPENMD_WARNING;
261	–	simError();
363		}
263	–
364		rSwitch_ = rCut_;
365		}
366
#	Line 289 \| Line 389 \| namespace OpenMD {
389		}
390		switcher_->setSwitchType(sft_);
391		switcher_->setSwitch(rSwitch_, rCut_);
292	–	interactionMan_->setSwitchingRadius(rSwitch_);
392		}
393	+
394	+
395	+
396
397		void ForceManager::initialize() {
398
#	Line 306 \| Line 408 \| namespace OpenMD {
408		setupCutoffs();
409
410		info_->prepareTopology();
411	+
412	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
413	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
414	+	if (doHeatFlux_) doParticlePot_ = true;
415	+
416	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
417	+
418		}
419
420		ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
#	Line 335 \| Line 444 \| namespace OpenMD {
444		electrostaticScale_[2] = fopts.getelectrostatic13scale();
445		electrostaticScale_[3] = fopts.getelectrostatic14scale();
446
447	+	if (info_->getSimParams()->haveElectricField()) {
448	+	ElectricField* eField = new ElectricField(info_);
449	+	perturbations_.push_back(eField);
450	+	}
451	+
452	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
453	+
454		fDecomp_->distributeInitialData();
455	<
455	>
456		initialized_ = true;
457	<
457	>
458		}
459	<
459	>
460		void ForceManager::calcForces() {
461
462		if (!initialized_) initialize();
463	<
463	>
464		preCalculation();
465		shortRangeInteractions();
466		longRangeInteractions();
#	Line 361 \| Line 477 \| namespace OpenMD {
477		Molecule::CutoffGroupIterator ci;
478		CutoffGroup* cg;
479
480	<	// forces are zeroed here, before any are accumulated.
480	>	// forces and potentials are zeroed here, before any are
481	>	// accumulated.
482
483	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
484	+
485	+	snap->setBondPotential(0.0);
486	+	snap->setBendPotential(0.0);
487	+	snap->setTorsionPotential(0.0);
488	+	snap->setInversionPotential(0.0);
489	+
490	+	potVec zeroPot(0.0);
491	+	snap->setLongRangePotential(zeroPot);
492	+	snap->setExcludedPotentials(zeroPot);
493	+
494	+	snap->setRestraintPotential(0.0);
495	+	snap->setRawPotential(0.0);
496	+
497		for (mol = info_->beginMolecule(mi); mol != NULL;
498		mol = info_->nextMolecule(mi)) {
499		for(atom = mol->beginAtom(ai); atom != NULL;
#	Line 386 \| Line 517 \| namespace OpenMD {
517		}
518
519		// Zero out the stress tensor
520	<	tau *= 0.0;
521	<
520	>	stressTensor *= 0.0;
521	>	// Zero out the heatFlux
522	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
523		}
524
525		void ForceManager::shortRangeInteractions() {
#	Line 420 \| Line 552 \| namespace OpenMD {
552
553		for (bond = mol->beginBond(bondIter); bond != NULL;
554		bond = mol->nextBond(bondIter)) {
555	<	bond->calcForce();
555	>	bond->calcForce(doParticlePot_);
556		bondPotential += bond->getPotential();
557		}
558
#	Line 428 \| Line 560 \| namespace OpenMD {
560		bend = mol->nextBend(bendIter)) {
561
562		RealType angle;
563	<	bend->calcForce(angle);
563	>	bend->calcForce(angle, doParticlePot_);
564		RealType currBendPot = bend->getPotential();
565
566		bendPotential += bend->getPotential();
#	Line 453 \| Line 585 \| namespace OpenMD {
585		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
586		torsion = mol->nextTorsion(torsionIter)) {
587		RealType angle;
588	<	torsion->calcForce(angle);
588	>	torsion->calcForce(angle, doParticlePot_);
589		RealType currTorsionPot = torsion->getPotential();
590		torsionPotential += torsion->getPotential();
591		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 477 \| Line 609 \| namespace OpenMD {
609		inversion != NULL;
610		inversion = mol->nextInversion(inversionIter)) {
611		RealType angle;
612	<	inversion->calcForce(angle);
612	>	inversion->calcForce(angle, doParticlePot_);
613		RealType currInversionPot = inversion->getPotential();
614		inversionPotential += inversion->getPotential();
615		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 497 \| Line 629 \| namespace OpenMD {
629		}
630		}
631		}
632	<
633	<	RealType shortRangePotential = bondPotential + bendPotential +
634	<	torsionPotential + inversionPotential;
632	>
633	>	#ifdef IS_MPI
634	>	// Collect from all nodes. This should eventually be moved into a
635	>	// SystemDecomposition, but this is a better place than in
636	>	// Thermo to do the collection.
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
638	>	MPI::SUM);
639	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
640	>	MPI::SUM);
641	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
642	>	MPI::REALTYPE, MPI::SUM);
643	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
644	>	MPI::REALTYPE, MPI::SUM);
645	>	#endif
646	>
647		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
648	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
649	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
650	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
651	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
652	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
648	>
649	>	curSnapshot->setBondPotential(bondPotential);
650	>	curSnapshot->setBendPotential(bendPotential);
651	>	curSnapshot->setTorsionPotential(torsionPotential);
652	>	curSnapshot->setInversionPotential(inversionPotential);
653	>
654	>	// RealType shortRangePotential = bondPotential + bendPotential +
655	>	// torsionPotential + inversionPotential;
656	>
657	>	// curSnapshot->setShortRangePotential(shortRangePotential);
658		}
659
660		void ForceManager::longRangeInteractions() {
#	Line 533 \| Line 682 \| namespace OpenMD {
682		// center of mass of the group is the same as position of the atom
683		// if cutoff group does not exist
684		cgConfig->position = config->position;
685	+	cgConfig->velocity = config->velocity;
686		}
687
688		fDecomp_->zeroWorkArrays();
689		fDecomp_->distributeData();
690
691		int cg1, cg2, atom1, atom2, topoDist;
692	<	Vector3d d_grp, dag, d;
692	>	Vector3d d_grp, dag, d, gvel2, vel2;
693		RealType rgrpsq, rgrp, r2, r;
694		RealType electroMult, vdwMult;
695		RealType vij;
#	Line 548 \| Line 698 \| namespace OpenMD {
698		RealType rCutSq;
699		bool in_switching_region;
700		RealType sw, dswdr, swderiv;
701	<	vector<int> atomListColumn, atomListRow, atomListLocal;
701	>	vector<int> atomListColumn, atomListRow;
702		InteractionData idat;
703		SelfData sdat;
704		RealType mf;
555	–	RealType lrPot;
705		RealType vpair;
706	+	RealType dVdFQ1(0.0);
707	+	RealType dVdFQ2(0.0);
708		potVec longRangePotential(0.0);
709		potVec workPot(0.0);
710	+	potVec exPot(0.0);
711	+	Vector3d eField1(0.0);
712	+	Vector3d eField2(0.0);
713	+	vector<int>::iterator ia, jb;
714
715		int loopStart, loopEnd;
716
717		idat.vdwMult = &vdwMult;
718		idat.electroMult = &electroMult;
719		idat.pot = &workPot;
720	+	idat.excludedPot = &exPot;
721		sdat.pot = fDecomp_->getEmbeddingPotential();
722	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
723		idat.vpair = &vpair;
724	+	idat.dVdFQ1 = &dVdFQ1;
725	+	idat.dVdFQ2 = &dVdFQ2;
726	+	idat.eField1 = &eField1;
727	+	idat.eField2 = &eField2;
728		idat.f1 = &f1;
729		idat.sw = &sw;
730		idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
731	<	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
731	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE \|\| cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
732	>	idat.doParticlePot = doParticlePot_;
733	>	idat.doElectricField = doElectricField_;
734	>	sdat.doParticlePot = doParticlePot_;
735
736		loopEnd = PAIR_LOOP;
737		if (info_->requiresPrepair() ) {
#	Line 575 \| Line 739 \| namespace OpenMD {
739		} else {
740		loopStart = PAIR_LOOP;
741		}
578	–
742		for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
743
744		if (iLoop == loopStart) {
745		bool update_nlist = fDecomp_->checkNeighborList();
746	<	if (update_nlist)
746	>	if (update_nlist) {
747	>	if (!usePeriodicBoundaryConditions_)
748	>	Mat3x3d bbox = thermo->getBoundingBox();
749		neighborList = fDecomp_->buildNeighborList();
750	<	}
751	<
750	>	}
751	>	}
752	>
753		for (vector<pair<int, int> >::iterator it = neighborList.begin();
754		it != neighborList.end(); ++it) {
755
#	Line 593 \| Line 759 \| namespace OpenMD {
759		cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
760
761		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
762	+
763		curSnapshot->wrapVector(d_grp);
764		rgrpsq = d_grp.lengthSquare();
598	–
765		rCutSq = cuts.second;
766
767		if (rgrpsq < rCutSq) {
768		idat.rcut = &cuts.first;
769		if (iLoop == PAIR_LOOP) {
770		vij = 0.0;
771	<	fij = V3Zero;
771	>	fij.zero();
772	>	eField1.zero();
773	>	eField2.zero();
774		}
775
776		in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
777		rgrp);
778	<
778	>
779		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
780		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
781
782	<	for (vector<int>::iterator ia = atomListRow.begin();
782	>	if (doHeatFlux_)
783	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
784	>
785	>	for (ia = atomListRow.begin();
786		ia != atomListRow.end(); ++ia) {
787		atom1 = (*ia);
788	<
789	<	for (vector<int>::iterator jb = atomListColumn.begin();
788	>
789	>	for (jb = atomListColumn.begin();
790		jb != atomListColumn.end(); ++jb) {
791		atom2 = (*jb);
792	<
793	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
792	>
793	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
794	>
795		vpair = 0.0;
796		workPot = 0.0;
797	<	f1 = V3Zero;
797	>	exPot = 0.0;
798	>	f1.zero();
799	>	dVdFQ1 = 0.0;
800	>	dVdFQ2 = 0.0;
801
802		fDecomp_->fillInteractionData(idat, atom1, atom2);
803	<
803	>
804		topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
805		vdwMult = vdwScale_[topoDist];
806		electroMult = electrostaticScale_[topoDist];
#	Line 633 \| Line 808 \| namespace OpenMD {
808		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
809		idat.d = &d_grp;
810		idat.r2 = &rgrpsq;
811	+	if (doHeatFlux_)
812	+	vel2 = gvel2;
813		} else {
814		d = fDecomp_->getInteratomicVector(atom1, atom2);
815		curSnapshot->wrapVector( d );
816		r2 = d.lengthSquare();
817		idat.d = &d;
818		idat.r2 = &r2;
819	+	if (doHeatFlux_)
820	+	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
821		}
822	<
822	>
823		r = sqrt( *(idat.r2) );
824		idat.rij = &r;
825
#	Line 651 \| Line 830 \| namespace OpenMD {
830		fDecomp_->unpackInteractionData(idat, atom1, atom2);
831		vij += vpair;
832		fij += f1;
833	<	tau -= outProduct( *(idat.d), f1);
833	>	stressTensor -= outProduct( *(idat.d), f1);
834	>	if (doHeatFlux_)
835	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
836		}
837		}
838		}
#	Line 664 \| Line 845 \| namespace OpenMD {
845		fij += fg;
846
847		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
848	<	tau -= outProduct( *(idat.d), fg);
848	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
849	>	atomListColumn[0],
850	>	cg1, cg2)) {
851	>	stressTensor -= outProduct( *(idat.d), fg);
852	>	if (doHeatFlux_)
853	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
854	>	}
855		}
856
857	<	for (vector<int>::iterator ia = atomListRow.begin();
857	>	for (ia = atomListRow.begin();
858		ia != atomListRow.end(); ++ia) {
859		atom1 = (*ia);
860		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 675 \| Line 862 \| namespace OpenMD {
862		// presence in switching region
863		fg = swderiv * d_grp * mf;
864		fDecomp_->addForceToAtomRow(atom1, fg);
678	–
865		if (atomListRow.size() > 1) {
866		if (info_->usesAtomicVirial()) {
867		// find the distance between the atom
868		// and the center of the cutoff group:
869		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
870	<	tau -= outProduct(dag, fg);
870	>	stressTensor -= outProduct(dag, fg);
871	>	if (doHeatFlux_)
872	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873		}
874		}
875		}
876	<	for (vector<int>::iterator jb = atomListColumn.begin();
876	>	for (jb = atomListColumn.begin();
877		jb != atomListColumn.end(); ++jb) {
878		atom2 = (*jb);
879		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 699 \| Line 887 \| namespace OpenMD {
887		// find the distance between the atom
888		// and the center of the cutoff group:
889		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
890	<	tau -= outProduct(dag, fg);
890	>	stressTensor -= outProduct(dag, fg);
891	>	if (doHeatFlux_)
892	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
893		}
894		}
895		}
896		}
897	<	//if (!SIM_uses_AtomicVirial) {
898	<	// tau -= outProduct(d_grp, fij);
897	>	//if (!info_->usesAtomicVirial()) {
898	>	// stressTensor -= outProduct(d_grp, fij);
899	>	// if (doHeatFlux_)
900	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
901		//}
902		}
903		}
#	Line 716 \| Line 908 \| namespace OpenMD {
908
909		fDecomp_->collectIntermediateData();
910
911	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
911	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
912		fDecomp_->fillSelfData(sdat, atom1);
913		interactionMan_->doPreForce(sdat);
914		}
#	Line 725 \| Line 917 \| namespace OpenMD {
917
918		}
919		}
728	–
920		}
921
922	+	// collects pairwise information
923		fDecomp_->collectData();
924
925		if (info_->requiresSelfCorrection()) {
926	<
735	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
926	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
927		fDecomp_->fillSelfData(sdat, atom1);
928		interactionMan_->doSelfCorrection(sdat);
929		}
739	–
930		}
931
932	+	// collects single-atom information
933	+	fDecomp_->collectSelfData();
934	+
935		longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
936		*(fDecomp_->getPairwisePotential());
937
938	<	lrPot = longRangePotential.sum();
938	>	curSnapshot->setLongRangePotential(longRangePotential);
939	>
940	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
941	>	*(fDecomp_->getExcludedPotential()));
942
747	–	//store the tau and long range potential
748	–	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
749	–	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
750	–	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
943		}
944
945
946		void ForceManager::postCalculation() {
947	+
948	+	vector<Perturbation*>::iterator pi;
949	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
950	+	(*pi)->applyPerturbation();
951	+	}
952	+
953		SimInfo::MoleculeIterator mi;
954		Molecule* mol;
955		Molecule::RigidBodyIterator rbIter;
956		RigidBody* rb;
957		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
958	<
958	>
959		// collect the atomic forces onto rigid bodies
960
961		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 765 \| Line 963 \| namespace OpenMD {
963		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
964		rb = mol->nextRigidBody(rbIter)) {
965		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
966	<	tau += rbTau;
966	>	stressTensor += rbTau;
967		}
968		}
969
970		#ifdef IS_MPI
971	<	Mat3x3d tmpTau(tau);
972	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
775	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
971	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
972	>	MPI::REALTYPE, MPI::SUM);
973		#endif
974	<	curSnapshot->statData.setTau(tau);
975	<	}
974	>	curSnapshot->setStressTensor(stressTensor);
975	>
976	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
977	>	/*
978	>	RealType vol = curSnapshot->getVolume();
979	>	RealType Elrc(0.0);
980	>	RealType Wlrc(0.0);
981
982	<	} //end namespace OpenMD
982	>	set<AtomType*>::iterator i;
983	>	set<AtomType*>::iterator j;
984	>
985	>	RealType n_i, n_j;
986	>	RealType rho_i, rho_j;
987	>	pair<RealType, RealType> LRI;
988	>
989	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
990	>	n_i = RealType(info_->getGlobalCountOfType(*i));
991	>	rho_i = n_i / vol;
992	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
993	>	n_j = RealType(info_->getGlobalCountOfType(*j));
994	>	rho_j = n_j / vol;
995	>
996	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
997	>
998	>	Elrc += n_i * rho_j * LRI.first;
999	>	Wlrc -= rho_i * rho_j * LRI.second;
1000	>	}
1001	>	}
1002	>	Elrc = 2.0 NumericConstant::PI;
1003	>	Wlrc = 2.0 NumericConstant::PI;
1004	>
1005	>	RealType lrp = curSnapshot->getLongRangePotential();
1006	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1007	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1008	>	curSnapshot->setStressTensor(stressTensor);
1009	>	*/
1010	>
1011	>	}
1012	>	}
1013	>	}

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Comparing branches/development/src/brains/ForceManager.cpp (file contents): Revision 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC vs. Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 UTC

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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC vs.
Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 UTC