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

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC vs.
Revision 1868 by gezelter, Tue Apr 30 15:56:54 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		forceField_ = info_->getForceField();
72		interactionMan_ = new InteractionManager();
73		fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74	+	thermo = new Thermo(info_);
75		}
76
77	+	ForceManager::~ForceManager() {
78	+	perturbations_.clear();
79	+
80	+	delete switcher_;
81	+	delete interactionMan_;
82	+	delete fDecomp_;
83	+	delete thermo;
84	+	}
85	+
86		/**
87		* setupCutoffs
88		*
#	Line 108 \| Line 119 \| namespace OpenMD {
119
120		Globals* simParams_ = info_->getSimParams();
121		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
122	+	int mdFileVersion;
123	+	rCut_ = 0.0; //Needs a value for a later max() call;
124
125	+	if (simParams_->haveMDfileVersion())
126	+	mdFileVersion = simParams_->getMDfileVersion();
127	+	else
128	+	mdFileVersion = 0;
129	+
130	+	// We need the list of simulated atom types to figure out cutoffs
131	+	// as well as long range corrections.
132	+
133	+	set<AtomType*>::iterator i;
134	+	set<AtomType*> atomTypes_;
135	+	atomTypes_ = info_->getSimulatedAtomTypes();
136	+
137		if (simParams_->haveCutoffRadius()) {
138		rCut_ = simParams_->getCutoffRadius();
139		} else {
#	Line 123 \| Line 148 \| namespace OpenMD {
148		rCut_ = 12.0;
149		} else {
150		RealType thisCut;
151	<	set<AtomType*>::iterator i;
127	<	set<AtomType*> atomTypes;
128	<	atomTypes = info_->getSimulatedAtomTypes();
129	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
151	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
152		thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
153		rCut_ = max(thisCut, rCut_);
154		}
#	Line 166 \| Line 188 \| namespace OpenMD {
188		cutoffMethod_ = i->second;
189		}
190		} else {
191	<	sprintf(painCave.errMsg,
192	<	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
193	<	"\tOpenMD will use SHIFTED_FORCE.\n");
194	<	painCave.isFatal = 0;
195	<	painCave.severity = OPENMD_INFO;
196	<	simError();
197	<	cutoffMethod_ = SHIFTED_FORCE;
191	>	if (mdFileVersion > 1) {
192	>	sprintf(painCave.errMsg,
193	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
194	>	"\tOpenMD will use SHIFTED_FORCE.\n");
195	>	painCave.isFatal = 0;
196	>	painCave.severity = OPENMD_INFO;
197	>	simError();
198	>	cutoffMethod_ = SHIFTED_FORCE;
199	>	} else {
200	>	// handle the case where the old file version was in play
201	>	// (there should be no cutoffMethod, so we have to deduce it
202	>	// from other data).
203	>
204	>	sprintf(painCave.errMsg,
205	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
206	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
207	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
208	>	"\tbehavior of the older (version 1) code. To remove this\n"
209	>	"\twarning, add an explicit cutoffMethod and change the top\n"
210	>	"\tof the file so that it begins with <OpenMD version=2>\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_WARNING;
213	>	simError();
214	>
215	>	// The old file version tethered the shifting behavior to the
216	>	// electrostaticSummationMethod keyword.
217	>
218	>	if (simParams_->haveElectrostaticSummationMethod()) {
219	>	string myMethod = simParams_->getElectrostaticSummationMethod();
220	>	toUpper(myMethod);
221	>
222	>	if (myMethod == "SHIFTED_POTENTIAL") {
223	>	cutoffMethod_ = SHIFTED_POTENTIAL;
224	>	} else if (myMethod == "SHIFTED_FORCE") {
225	>	cutoffMethod_ = SHIFTED_FORCE;
226	>	}
227	>
228	>	if (simParams_->haveSwitchingRadius())
229	>	rSwitch_ = simParams_->getSwitchingRadius();
230	>
231	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
232	>	if (simParams_->haveSwitchingRadius()){
233	>	sprintf(painCave.errMsg,
234	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
235	>	"\tA value was set for the switchingRadius\n"
236	>	"\teven though the electrostaticSummationMethod was\n"
237	>	"\tset to %s\n", myMethod.c_str());
238	>	painCave.severity = OPENMD_WARNING;
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242	>	}
243	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
244	>	if (cutoffMethod_ == SHIFTED_FORCE) {
245	>	sprintf(painCave.errMsg,
246	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
247	>	"\tcutoffRadius and switchingRadius are set to the\n"
248	>	"\tsame value. OpenMD will use shifted force\n"
249	>	"\tpotentials instead of switching functions.\n");
250	>	painCave.isFatal = 0;
251	>	painCave.severity = OPENMD_WARNING;
252	>	simError();
253	>	} else {
254	>	cutoffMethod_ = SHIFTED_POTENTIAL;
255	>	sprintf(painCave.errMsg,
256	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
257	>	"\tcutoffRadius and switchingRadius are set to the\n"
258	>	"\tsame value. OpenMD will use shifted potentials\n"
259	>	"\tinstead of switching functions.\n");
260	>	painCave.isFatal = 0;
261	>	painCave.severity = OPENMD_WARNING;
262	>	simError();
263	>	}
264	>	}
265	>	}
266	>	}
267		}
268
269		map<string, CutoffPolicy> stringToCutoffPolicy;
#	Line 180 \| Line 271 \| namespace OpenMD {
271		stringToCutoffPolicy["MAX"] = MAX;
272		stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
273
274	<	std::string cutPolicy;
274	>	string cutPolicy;
275		if (forceFieldOptions_.haveCutoffPolicy()){
276		cutPolicy = forceFieldOptions_.getCutoffPolicy();
277		}else if (simParams_->haveCutoffPolicy()) {
#	Line 242 \| Line 333 \| namespace OpenMD {
333		simError();
334		}
335		} else {
336	<	if (simParams_->haveSwitchingRadius()) {
337	<	map<string, CutoffMethod>::const_iterator it;
338	<	string theMeth;
339	<	for (it = stringToCutoffMethod.begin();
340	<	it != stringToCutoffMethod.end(); ++it) {
341	<	if (it->second == cutoffMethod_) {
342	<	theMeth = it->first;
343	<	break;
336	>	if (mdFileVersion > 1) {
337	>	// throw an error if we define a switching radius and don't need one.
338	>	// older file versions should not do this.
339	>	if (simParams_->haveSwitchingRadius()) {
340	>	map<string, CutoffMethod>::const_iterator it;
341	>	string theMeth;
342	>	for (it = stringToCutoffMethod.begin();
343	>	it != stringToCutoffMethod.end(); ++it) {
344	>	if (it->second == cutoffMethod_) {
345	>	theMeth = it->first;
346	>	break;
347	>	}
348		}
349	+	sprintf(painCave.errMsg,
350	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
351	+	"\tis not set to SWITCHED, so switchingRadius value\n"
352	+	"\twill be ignored for this simulation\n", theMeth.c_str());
353	+	painCave.isFatal = 0;
354	+	painCave.severity = OPENMD_WARNING;
355	+	simError();
356		}
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();
357		}
263	–
358		rSwitch_ = rCut_;
359		}
360
#	Line 289 \| Line 383 \| namespace OpenMD {
383		}
384		switcher_->setSwitchType(sft_);
385		switcher_->setSwitch(rSwitch_, rCut_);
292	–	interactionMan_->setSwitchingRadius(rSwitch_);
386		}
387	+
388	+
389	+
390
391		void ForceManager::initialize() {
392
#	Line 306 \| Line 402 \| namespace OpenMD {
402		setupCutoffs();
403
404		info_->prepareTopology();
405	+
406	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
407	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
408	+	if (doHeatFlux_) doParticlePot_ = true;
409	+
410	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
411	+
412		}
413
414		ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
#	Line 335 \| Line 438 \| namespace OpenMD {
438		electrostaticScale_[2] = fopts.getelectrostatic13scale();
439		electrostaticScale_[3] = fopts.getelectrostatic14scale();
440
441	+	if (info_->getSimParams()->haveElectricField()) {
442	+	ElectricField* eField = new ElectricField(info_);
443	+	perturbations_.push_back(eField);
444	+	}
445	+
446	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
447	+
448		fDecomp_->distributeInitialData();
449	<
449	>
450		initialized_ = true;
451	<
451	>
452		}
453	<
453	>
454		void ForceManager::calcForces() {
455
456		if (!initialized_) initialize();
457	<
457	>
458		preCalculation();
459		shortRangeInteractions();
460		longRangeInteractions();
#	Line 361 \| Line 471 \| namespace OpenMD {
471		Molecule::CutoffGroupIterator ci;
472		CutoffGroup* cg;
473
474	<	// forces are zeroed here, before any are accumulated.
474	>	// forces and potentials are zeroed here, before any are
475	>	// accumulated.
476
477	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
478	+
479	+	snap->setBondPotential(0.0);
480	+	snap->setBendPotential(0.0);
481	+	snap->setTorsionPotential(0.0);
482	+	snap->setInversionPotential(0.0);
483	+
484	+	potVec zeroPot(0.0);
485	+	snap->setLongRangePotential(zeroPot);
486	+	snap->setExcludedPotentials(zeroPot);
487	+
488	+	snap->setRestraintPotential(0.0);
489	+	snap->setRawPotential(0.0);
490	+
491		for (mol = info_->beginMolecule(mi); mol != NULL;
492		mol = info_->nextMolecule(mi)) {
493		for(atom = mol->beginAtom(ai); atom != NULL;
494		atom = mol->nextAtom(ai)) {
495		atom->zeroForcesAndTorques();
371	–	cerr << "apos = " << atom->getPos() << "\n";
496		}
497
498		//change the positions of atoms which belong to the rigidbodies
#	Line 382 \| Line 506 \| namespace OpenMD {
506		cg = mol->nextCutoffGroup(ci)) {
507		//calculate the center of mass of cutoff group
508		cg->updateCOM();
385	–	cerr << "cgpos = " << cg->getPos() << "\n";
509		}
510		}
511		}
512
513		// Zero out the stress tensor
514	<	tau *= 0.0;
515	<
514	>	stressTensor *= 0.0;
515	>	// Zero out the heatFlux
516	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
517		}
518
519		void ForceManager::shortRangeInteractions() {
#	Line 422 \| Line 546 \| namespace OpenMD {
546
547		for (bond = mol->beginBond(bondIter); bond != NULL;
548		bond = mol->nextBond(bondIter)) {
549	<	bond->calcForce();
549	>	bond->calcForce(doParticlePot_);
550		bondPotential += bond->getPotential();
551		}
552
#	Line 430 \| Line 554 \| namespace OpenMD {
554		bend = mol->nextBend(bendIter)) {
555
556		RealType angle;
557	<	bend->calcForce(angle);
557	>	bend->calcForce(angle, doParticlePot_);
558		RealType currBendPot = bend->getPotential();
559
560		bendPotential += bend->getPotential();
#	Line 455 \| Line 579 \| namespace OpenMD {
579		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
580		torsion = mol->nextTorsion(torsionIter)) {
581		RealType angle;
582	<	torsion->calcForce(angle);
582	>	torsion->calcForce(angle, doParticlePot_);
583		RealType currTorsionPot = torsion->getPotential();
584		torsionPotential += torsion->getPotential();
585		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 479 \| Line 603 \| namespace OpenMD {
603		inversion != NULL;
604		inversion = mol->nextInversion(inversionIter)) {
605		RealType angle;
606	<	inversion->calcForce(angle);
606	>	inversion->calcForce(angle, doParticlePot_);
607		RealType currInversionPot = inversion->getPotential();
608		inversionPotential += inversion->getPotential();
609		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 499 \| Line 623 \| namespace OpenMD {
623		}
624		}
625		}
626	<
627	<	RealType shortRangePotential = bondPotential + bendPotential +
628	<	torsionPotential + inversionPotential;
626	>
627	>	#ifdef IS_MPI
628	>	// Collect from all nodes. This should eventually be moved into a
629	>	// SystemDecomposition, but this is a better place than in
630	>	// Thermo to do the collection.
631	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
632	>	MPI::SUM);
633	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
634	>	MPI::SUM);
635	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
636	>	MPI::REALTYPE, MPI::SUM);
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
638	>	MPI::REALTYPE, MPI::SUM);
639	>	#endif
640	>
641		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
643	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
644	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
645	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
646	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
642	>
643	>	curSnapshot->setBondPotential(bondPotential);
644	>	curSnapshot->setBendPotential(bendPotential);
645	>	curSnapshot->setTorsionPotential(torsionPotential);
646	>	curSnapshot->setInversionPotential(inversionPotential);
647	>
648	>	// RealType shortRangePotential = bondPotential + bendPotential +
649	>	// torsionPotential + inversionPotential;
650	>
651	>	// curSnapshot->setShortRangePotential(shortRangePotential);
652		}
653
654		void ForceManager::longRangeInteractions() {
655
656	+
657		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
658		DataStorage* config = &(curSnapshot->atomData);
659		DataStorage* cgConfig = &(curSnapshot->cgData);
#	Line 528 \| Line 670 \| namespace OpenMD {
670		mol = info_->nextMolecule(mi)) {
671		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
672		cg = mol->nextCutoffGroup(ci)) {
531	–	cerr << "branch1\n";
532	–	cerr << "globind = " << cg->getGlobalIndex() << "\n";
673		cg->updateCOM();
674		}
675		}
676		} else {
677		// center of mass of the group is the same as position of the atom
678		// if cutoff group does not exist
539	–	cerr << "branch2\n";
679		cgConfig->position = config->position;
680	+	cgConfig->velocity = config->velocity;
681		}
682
683		fDecomp_->zeroWorkArrays();
684		fDecomp_->distributeData();
685
686		int cg1, cg2, atom1, atom2, topoDist;
687	<	Vector3d d_grp, dag, d;
687	>	Vector3d d_grp, dag, d, gvel2, vel2;
688		RealType rgrpsq, rgrp, r2, r;
689		RealType electroMult, vdwMult;
690		RealType vij;
#	Line 557 \| Line 697 \| namespace OpenMD {
697		InteractionData idat;
698		SelfData sdat;
699		RealType mf;
560	–	RealType lrPot;
700		RealType vpair;
701	+	RealType dVdFQ1(0.0);
702	+	RealType dVdFQ2(0.0);
703		potVec longRangePotential(0.0);
704		potVec workPot(0.0);
705	+	potVec exPot(0.0);
706	+	Vector3d eField1(0.0);
707	+	Vector3d eField2(0.0);
708	+	vector<int>::iterator ia, jb;
709
710		int loopStart, loopEnd;
711
712		idat.vdwMult = &vdwMult;
713		idat.electroMult = &electroMult;
714		idat.pot = &workPot;
715	+	idat.excludedPot = &exPot;
716		sdat.pot = fDecomp_->getEmbeddingPotential();
717	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
718		idat.vpair = &vpair;
719	+	idat.dVdFQ1 = &dVdFQ1;
720	+	idat.dVdFQ2 = &dVdFQ2;
721	+	idat.eField1 = &eField1;
722	+	idat.eField2 = &eField2;
723		idat.f1 = &f1;
724		idat.sw = &sw;
725		idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
726		idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
727	+	idat.doParticlePot = doParticlePot_;
728	+	idat.doElectricField = doElectricField_;
729	+	sdat.doParticlePot = doParticlePot_;
730
731		loopEnd = PAIR_LOOP;
732		if (info_->requiresPrepair() ) {
#	Line 580 \| Line 734 \| namespace OpenMD {
734		} else {
735		loopStart = PAIR_LOOP;
736		}
583	–
737		for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
738
739		if (iLoop == loopStart) {
740		bool update_nlist = fDecomp_->checkNeighborList();
741	<	if (update_nlist)
741	>	if (update_nlist) {
742	>	if (!usePeriodicBoundaryConditions_)
743	>	Mat3x3d bbox = thermo->getBoundingBox();
744		neighborList = fDecomp_->buildNeighborList();
745	<	}
746	<
745	>	}
746	>	}
747	>
748		for (vector<pair<int, int> >::iterator it = neighborList.begin();
749		it != neighborList.end(); ++it) {
750
#	Line 598 \| Line 754 \| namespace OpenMD {
754		cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
755
756		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
757	+
758		curSnapshot->wrapVector(d_grp);
759		rgrpsq = d_grp.lengthSquare();
603	–
760		rCutSq = cuts.second;
761
762		if (rgrpsq < rCutSq) {
#	Line 608 \| Line 764 \| namespace OpenMD {
764		if (iLoop == PAIR_LOOP) {
765		vij = 0.0;
766		fij = V3Zero;
767	+	eField1 = V3Zero;
768	+	eField2 = V3Zero;
769		}
770
771		in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
772		rgrp);
773	<
773	>
774		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
775		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
776
777	<	for (vector<int>::iterator ia = atomListRow.begin();
777	>	if (doHeatFlux_)
778	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
779	>
780	>	for (ia = atomListRow.begin();
781		ia != atomListRow.end(); ++ia) {
782		atom1 = (*ia);
783	<
784	<	for (vector<int>::iterator jb = atomListColumn.begin();
783	>
784	>	for (jb = atomListColumn.begin();
785		jb != atomListColumn.end(); ++jb) {
786		atom2 = (*jb);
787
788	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
788	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
789	>
790		vpair = 0.0;
791		workPot = 0.0;
792	+	exPot = 0.0;
793		f1 = V3Zero;
794	+	dVdFQ1 = 0.0;
795	+	dVdFQ2 = 0.0;
796
797		fDecomp_->fillInteractionData(idat, atom1, atom2);
798	<
798	>
799		topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
800		vdwMult = vdwScale_[topoDist];
801		electroMult = electrostaticScale_[topoDist];
#	Line 638 \| Line 803 \| namespace OpenMD {
803		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
804		idat.d = &d_grp;
805		idat.r2 = &rgrpsq;
806	<	cerr << "dgrp = " << d_grp << "\n";
806	>	if (doHeatFlux_)
807	>	vel2 = gvel2;
808		} else {
809		d = fDecomp_->getInteratomicVector(atom1, atom2);
810		curSnapshot->wrapVector( d );
811		r2 = d.lengthSquare();
646	–	cerr << "datm = " << d<< "\n";
812		idat.d = &d;
813		idat.r2 = &r2;
814	+	if (doHeatFlux_)
815	+	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
816		}
817	<
651	<	cerr << "idat.d = " << *(idat.d) << "\n";
817	>
818		r = sqrt( *(idat.r2) );
819		idat.rij = &r;
820
#	Line 657 \| Line 823 \| namespace OpenMD {
823		} else {
824		interactionMan_->doPair(idat);
825		fDecomp_->unpackInteractionData(idat, atom1, atom2);
660	–
661	–	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
826		vij += vpair;
827		fij += f1;
828	<	tau -= outProduct( *(idat.d), f1);
828	>	stressTensor -= outProduct( *(idat.d), f1);
829	>	if (doHeatFlux_)
830	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
831		}
832		}
833		}
#	Line 674 \| Line 840 \| namespace OpenMD {
840		fij += fg;
841
842		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
843	<	tau -= outProduct( *(idat.d), fg);
843	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
844	>	atomListColumn[0],
845	>	cg1, cg2)) {
846	>	stressTensor -= outProduct( *(idat.d), fg);
847	>	if (doHeatFlux_)
848	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
849	>	}
850		}
851
852	<	for (vector<int>::iterator ia = atomListRow.begin();
852	>	for (ia = atomListRow.begin();
853		ia != atomListRow.end(); ++ia) {
854		atom1 = (*ia);
855		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 685 \| Line 857 \| namespace OpenMD {
857		// presence in switching region
858		fg = swderiv * d_grp * mf;
859		fDecomp_->addForceToAtomRow(atom1, fg);
688	–
860		if (atomListRow.size() > 1) {
861		if (info_->usesAtomicVirial()) {
862		// find the distance between the atom
863		// and the center of the cutoff group:
864		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
865	<	tau -= outProduct(dag, fg);
865	>	stressTensor -= outProduct(dag, fg);
866	>	if (doHeatFlux_)
867	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
868		}
869		}
870		}
871	<	for (vector<int>::iterator jb = atomListColumn.begin();
871	>	for (jb = atomListColumn.begin();
872		jb != atomListColumn.end(); ++jb) {
873		atom2 = (*jb);
874		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 709 \| Line 882 \| namespace OpenMD {
882		// find the distance between the atom
883		// and the center of the cutoff group:
884		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
885	<	tau -= outProduct(dag, fg);
885	>	stressTensor -= outProduct(dag, fg);
886	>	if (doHeatFlux_)
887	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
888		}
889		}
890		}
891		}
892	<	//if (!SIM_uses_AtomicVirial) {
893	<	// tau -= outProduct(d_grp, fij);
892	>	//if (!info_->usesAtomicVirial()) {
893	>	// stressTensor -= outProduct(d_grp, fij);
894	>	// if (doHeatFlux_)
895	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
896		//}
897		}
898		}
#	Line 726 \| Line 903 \| namespace OpenMD {
903
904		fDecomp_->collectIntermediateData();
905
906	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
906	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907		fDecomp_->fillSelfData(sdat, atom1);
908		interactionMan_->doPreForce(sdat);
909		}
#	Line 735 \| Line 912 \| namespace OpenMD {
912
913		}
914		}
738	–
915		}
916
917	+	// collects pairwise information
918		fDecomp_->collectData();
919
920		if (info_->requiresSelfCorrection()) {
921	<
745	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
921	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
922		fDecomp_->fillSelfData(sdat, atom1);
923		interactionMan_->doSelfCorrection(sdat);
924		}
749	–
925		}
926
927	+	// collects single-atom information
928	+	fDecomp_->collectSelfData();
929	+
930		longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
931		*(fDecomp_->getPairwisePotential());
932
933	<	lrPot = longRangePotential.sum();
933	>	curSnapshot->setLongRangePotential(longRangePotential);
934	>
935	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
936	>	*(fDecomp_->getExcludedPotential()));
937
757	–	//store the tau and long range potential
758	–	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
759	–	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
760	–	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
938		}
939
940
941		void ForceManager::postCalculation() {
942	+
943	+	vector<Perturbation*>::iterator pi;
944	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
945	+	(*pi)->applyPerturbation();
946	+	}
947	+
948		SimInfo::MoleculeIterator mi;
949		Molecule* mol;
950		Molecule::RigidBodyIterator rbIter;
951		RigidBody* rb;
952		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
953	<
953	>
954		// collect the atomic forces onto rigid bodies
955
956		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 775 \| Line 958 \| namespace OpenMD {
958		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
959		rb = mol->nextRigidBody(rbIter)) {
960		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
961	<	tau += rbTau;
961	>	stressTensor += rbTau;
962		}
963		}
964
965		#ifdef IS_MPI
966	<	Mat3x3d tmpTau(tau);
967	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
785	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
966	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
967	>	MPI::REALTYPE, MPI::SUM);
968		#endif
969	<	curSnapshot->statData.setTau(tau);
970	<	}
969	>	curSnapshot->setStressTensor(stressTensor);
970	>
971	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
972	>	/*
973	>	RealType vol = curSnapshot->getVolume();
974	>	RealType Elrc(0.0);
975	>	RealType Wlrc(0.0);
976
977	<	} //end namespace OpenMD
977	>	set<AtomType*>::iterator i;
978	>	set<AtomType*>::iterator j;
979	>
980	>	RealType n_i, n_j;
981	>	RealType rho_i, rho_j;
982	>	pair<RealType, RealType> LRI;
983	>
984	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
985	>	n_i = RealType(info_->getGlobalCountOfType(*i));
986	>	rho_i = n_i / vol;
987	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
988	>	n_j = RealType(info_->getGlobalCountOfType(*j));
989	>	rho_j = n_j / vol;
990	>
991	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
992	>
993	>	Elrc += n_i * rho_j * LRI.first;
994	>	Wlrc -= rho_i * rho_j * LRI.second;
995	>	}
996	>	}
997	>	Elrc = 2.0 NumericConstant::PI;
998	>	Wlrc = 2.0 NumericConstant::PI;
999	>
1000	>	RealType lrp = curSnapshot->getLongRangePotential();
1001	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1002	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1003	>	curSnapshot->setStressTensor(stressTensor);
1004	>	*/
1005	>
1006	>	}
1007	>	}
1008	>	}

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Comparing branches/development/src/brains/ForceManager.cpp (file contents): Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC vs. Revision 1868 by gezelter, Tue Apr 30 15:56:54 2013 UTC

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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC vs.
Revision 1868 by gezelter, Tue Apr 30 15:56:54 2013 UTC