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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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).
40		*/
41
42	+	#include <cmath>
43		#include "integrators/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45		#include "math/SquareMatrix3.hpp"
46	+	#include "math/Polynomial.hpp"
47		#include "primitives/Molecule.hpp"
48		#include "primitives/StuntDouble.hpp"
49	<	#include "utils/OOPSEConstant.hpp"
49	>	#include "utils/PhysicalConstants.hpp"
50		#include "utils/Tuple.hpp"
51
52		#ifndef IS_MPI
53		#include "math/SeqRandNumGen.hpp"
54		#else
55	+	#include <mpi.h>
56		#include "math/ParallelRandNumGen.hpp"
57		#endif
58
59		#define HONKING_LARGE_VALUE 1.0e10
60
61	<	namespace oopse {
61	>	namespace OpenMD {
62
63		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
64	<
64	>
65	>	failTrialCount_ = 0;
66	>	failRootCount_ = 0;
67	>
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70
71	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
71	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
72	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
73	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
74	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
75	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
76		stringToEnumMap_["Px"] = rnemdPx;
77		stringToEnumMap_["Py"] = rnemdPy;
78		stringToEnumMap_["Pz"] = rnemdPz;
#	Line 72 | Line 82 | namespace oopse {
82		evaluator_.loadScriptString(rnemdObjectSelection_);
83		seleMan_.setSelectionSet(evaluator_.evaluate());
84
75	–
85		// do some sanity checking
86
87		int selectionCount = seleMan_.getSelectionCount();
#	Line 94 | Line 103 | namespace oopse {
103
104		}
105
106	<	const std::string st = simParams->getRNEMD_swapType();
106	>	const std::string st = simParams->getRNEMD_exchangeType();
107
108		std::map<std::string, RNEMDTypeEnum>::iterator i;
109		i = stringToEnumMap_.find(st);
110	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
111	>	if (rnemdType_ == rnemdUnknown) {
112	>	std::cerr << "WARNING! RNEMD Type Unknown!\n";
113	>	}
114
115	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
115	>	#ifdef IS_MPI
116	>	if (worldRank == 0) {
117	>	#endif
118	>
119	>	std::string rnemdFileName;
120	>	std::string xTempFileName;
121	>	std::string yTempFileName;
122	>	std::string zTempFileName;
123	>	switch(rnemdType_) {
124	>	case rnemdKineticSwap :
125	>	case rnemdKineticScale :
126	>	rnemdFileName = "temperature.log";
127	>	break;
128	>	case rnemdPx :
129	>	case rnemdPxScale :
130	>	case rnemdPy :
131	>	case rnemdPyScale :
132	>	rnemdFileName = "momemtum.log";
133	>	xTempFileName = "temperatureX.log";
134	>	yTempFileName = "temperatureY.log";
135	>	zTempFileName = "temperatureZ.log";
136	>	xTempLog_.open(xTempFileName.c_str());
137	>	yTempLog_.open(yTempFileName.c_str());
138	>	zTempLog_.open(zTempFileName.c_str());
139	>	break;
140	>	case rnemdPz :
141	>	case rnemdPzScale :
142	>	case rnemdUnknown :
143	>	default :
144	>	rnemdFileName = "rnemd.log";
145	>	break;
146	>	}
147	>	rnemdLog_.open(rnemdFileName.c_str());
148	>
149	>	#ifdef IS_MPI
150	>	}
151	>	#endif
152	>
153	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
154		set_RNEMD_nBins(simParams->getRNEMD_nBins());
155	<	exchangeSum_ = 0.0;
155	>	midBin_ = nBins_ / 2;
156	>	if (simParams->haveRNEMD_logWidth()) {
157	>	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
158	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
159	>	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
160	>	std::cerr << "Automaically set back to default.\n";
161	>	rnemdLogWidth_ = nBins_;
162	>	}
163	>	} else {
164	>	rnemdLogWidth_ = nBins_;
165	>	}
166	>	valueHist_.resize(rnemdLogWidth_, 0.0);
167	>	valueCount_.resize(rnemdLogWidth_, 0);
168	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
169	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
170	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
171
172	+	set_RNEMD_exchange_total(0.0);
173	+	if (simParams->haveRNEMD_targetFlux()) {
174	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
175	+	} else {
176	+	set_RNEMD_target_flux(0.0);
177	+	}
178	+
179		#ifndef IS_MPI
180		if (simParams->haveSeed()) {
181		seedValue = simParams->getSeed();
#	Line 123 | Line 195 | namespace oopse {
195
196		RNEMD::~RNEMD() {
197		delete randNumGen_;
198	+
199	+	#ifdef IS_MPI
200	+	if (worldRank == 0) {
201	+	#endif
202	+	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
203	+	rnemdLog_.close();
204	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
205	+	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
206	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	+	xTempLog_.close();
208	+	yTempLog_.close();
209	+	zTempLog_.close();
210	+	}
211	+	#ifdef IS_MPI
212	+	}
213	+	#endif
214		}
215
216		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
217
218		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
219		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 164 | Line 251 | namespace oopse {
251
252
253		// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin) {
254	>	if (binNo == 0 || binNo == midBin_) {
255
256		RealType mass = sd->getMass();
257		Vector3d vel = sd->getVel();
258		RealType value;
259
260		switch(rnemdType_) {
261	<	case rnemdKinetic :
261	>	case rnemdKineticSwap :
262
263		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
264		vel[2]*vel[2]);
#	Line 191 | Line 278 | namespace oopse {
278		+ angMom[2]*angMom[2]/I(2, 2);
279		}
280		}
281	<	value = value * 0.5 / OOPSEConstant::energyConvert;
281	>	//make exchangeSum_ comparable between swap & scale
282	>	//temporarily without using energyConvert
283	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
284	>	value *= 0.5;
285		break;
286		case rnemdPx :
287		value = mass * vel[0];
#	Line 202 | Line 292 | namespace oopse {
292		case rnemdPz :
293		value = mass * vel[2];
294		break;
205	–	case rnemdUnknown :
295		default :
296		break;
297		}
#	Line 218 | Line 307 | namespace oopse {
307		min_sd = sd;
308		}
309		}
310	<	} else {
310	>	} else { //midBin_
311		if (!max_found) {
312		max_val = value;
313		max_sd = sd;
#	Line 298 | Line 387 | namespace oopse {
387		RealType temp_vel;
388
389		switch(rnemdType_) {
390	<	case rnemdKinetic :
390	>	case rnemdKineticSwap :
391		min_sd->setVel(max_vel);
392		max_sd->setVel(min_vel);
393		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 329 | Line 418 | namespace oopse {
418		min_sd->setVel(min_vel);
419		max_sd->setVel(max_vel);
420		break;
332	–	case rnemdUnknown :
421		default :
422		break;
423		}
#	Line 349 | Line 437 | namespace oopse {
437		min_vals.rank, 0, status);
438
439		switch(rnemdType_) {
440	<	case rnemdKinetic :
440	>	case rnemdKineticSwap :
441		max_sd->setVel(min_vel);
442
443		if (max_sd->isDirectional()) {
#	Line 378 | Line 466 | namespace oopse {
466		max_vel.z() = min_vel.z();
467		max_sd->setVel(max_vel);
468		break;
381	–	case rnemdUnknown :
469		default :
470		break;
471		}
#	Line 396 | Line 483 | namespace oopse {
483		max_vals.rank, 0, status);
484
485		switch(rnemdType_) {
486	<	case rnemdKinetic :
486	>	case rnemdKineticSwap :
487		min_sd->setVel(max_vel);
488
489		if (min_sd->isDirectional()) {
#	Line 425 | Line 512 | namespace oopse {
512		min_vel.z() = max_vel.z();
513		min_sd->setVel(min_vel);
514		break;
428	–	case rnemdUnknown :
515		default :
516		break;
517		}
#	Line 433 | Line 519 | namespace oopse {
519		#endif
520		exchangeSum_ += max_val - min_val;
521		} else {
522	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
522	>	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
523	>	failTrialCount_++;
524		}
525		} else {
526	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
526	>	std::cerr << "exchange NOT performed!\n";
527	>	std::cerr << "at least one of the two slabs empty.\n";
528	>	failTrialCount_++;
529		}
530
531		}
532
533	<	void RNEMD::getStatus() {
533	>	void RNEMD::doScale() {
534
535		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
536		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
537
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
538		seleMan_.setSelectionSet(evaluator_.evaluate());
539
540		int selei;
541		StuntDouble* sd;
542		int idx;
543
544	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
460	<	// being averaged
461	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
462	<	// number of degrees of
463	<	// freedom being averaged
544	>	std::vector<StuntDouble*> hotBin, coldBin;
545
546	+	RealType Phx = 0.0;
547	+	RealType Phy = 0.0;
548	+	RealType Phz = 0.0;
549	+	RealType Khx = 0.0;
550	+	RealType Khy = 0.0;
551	+	RealType Khz = 0.0;
552	+	RealType Pcx = 0.0;
553	+	RealType Pcy = 0.0;
554	+	RealType Pcz = 0.0;
555	+	RealType Kcx = 0.0;
556	+	RealType Kcy = 0.0;
557	+	RealType Kcz = 0.0;
558	+
559		for (sd = seleMan_.beginSelected(selei); sd != NULL;
560		sd = seleMan_.nextSelected(selei)) {
561	+
562	+	idx = sd->getLocalIndex();
563	+
564	+	Vector3d pos = sd->getPos();
565	+
566	+	// wrap the stuntdouble's position back into the box:
567	+
568	+	if (usePeriodicBoundaryConditions_)
569	+	currentSnap_->wrapVector(pos);
570	+
571	+	// which bin is this stuntdouble in?
572	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
573	+
574	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
575	+
576	+	// if we're in bin 0 or the middleBin
577	+	if (binNo == 0 || binNo == midBin_) {
578	+
579	+	RealType mass = sd->getMass();
580	+	Vector3d vel = sd->getVel();
581	+
582	+	if (binNo == 0) {
583	+	hotBin.push_back(sd);
584	+	Phx += mass * vel.x();
585	+	Phy += mass * vel.y();
586	+	Phz += mass * vel.z();
587	+	Khx += mass * vel.x() * vel.x();
588	+	Khy += mass * vel.y() * vel.y();
589	+	Khz += mass * vel.z() * vel.z();
590	+	} else { //midBin_
591	+	coldBin.push_back(sd);
592	+	Pcx += mass * vel.x();
593	+	Pcy += mass * vel.y();
594	+	Pcz += mass * vel.z();
595	+	Kcx += mass * vel.x() * vel.x();
596	+	Kcy += mass * vel.y() * vel.y();
597	+	Kcz += mass * vel.z() * vel.z();
598	+	}
599	+	}
600	+	}
601	+
602	+	Khx *= 0.5;
603	+	Khy *= 0.5;
604	+	Khz *= 0.5;
605	+	Kcx *= 0.5;
606	+	Kcy *= 0.5;
607	+	Kcz *= 0.5;
608	+
609	+	#ifdef IS_MPI
610	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
611	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
612	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
613	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
614	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
615	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
616	+
617	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
618	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
619	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
620	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
621	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
622	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
623	+	#endif
624	+
625	+	//use coldBin coeff's
626	+	RealType px = Pcx / Phx;
627	+	RealType py = Pcy / Phy;
628	+	RealType pz = Pcz / Phz;
629	+
630	+	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
631	+	switch(rnemdType_) {
632	+	case rnemdKineticScale :
633	+	/*used hotBin coeff's & only scale x & y dimensions
634	+	RealType px = Phx / Pcx;
635	+	RealType py = Phy / Pcy;
636	+	a110 = Khy;
637	+	c0 = - Khx - Khy - targetFlux_;
638	+	a000 = Khx;
639	+	a111 = Kcy * py * py
640	+	b11 = -2.0 * Kcy * py * (1.0 + py);
641	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
642	+	b01 = -2.0 * Kcx * px * (1.0 + px);
643	+	a001 = Kcx * px * px;
644	+	*/
645	+
646	+	//scale all three dimensions, let c_x = c_y
647	+	a000 = Kcx + Kcy;
648	+	a110 = Kcz;
649	+	c0 = targetFlux_ - Kcx - Kcy - Kcz;
650	+	a001 = Khx * px * px + Khy * py * py;
651	+	a111 = Khz * pz * pz;
652	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
653	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
654	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
655	+	+ Khz * pz * (2.0 + pz) - targetFlux_;
656	+	break;
657	+	case rnemdPxScale :
658	+	c = 1 - targetFlux_ / Pcx;
659	+	a000 = Kcy;
660	+	a110 = Kcz;
661	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
662	+	a001 = py * py * Khy;
663	+	a111 = pz * pz * Khz;
664	+	b01 = -2.0 * Khy * py * (1.0 + py);
665	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
666	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
667	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
668	+	break;
669	+	case rnemdPyScale :
670	+	c = 1 - targetFlux_ / Pcy;
671	+	a000 = Kcx;
672	+	a110 = Kcz;
673	+	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
674	+	a001 = px * px * Khx;
675	+	a111 = pz * pz * Khz;
676	+	b01 = -2.0 * Khx * px * (1.0 + px);
677	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
678	+	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
679	+	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
680	+	break;
681	+	case rnemdPzScale ://we don't really do this, do we?
682	+	c = 1 - targetFlux_ / Pcz;
683	+	a000 = Kcx;
684	+	a110 = Kcy;
685	+	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
686	+	a001 = px * px * Khx;
687	+	a111 = py * py * Khy;
688	+	b01 = -2.0 * Khx * px * (1.0 + px);
689	+	b11 = -2.0 * Khy * py * (1.0 + py);
690	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
691	+	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
692	+	break;
693	+	default :
694	+	break;
695	+	}
696	+
697	+	RealType v1 = a000 * a111 - a001 * a110;
698	+	RealType v2 = a000 * b01;
699	+	RealType v3 = a000 * b11;
700	+	RealType v4 = a000 * c1 - a001 * c0;
701	+	RealType v8 = a110 * b01;
702	+	RealType v10 = - b01 * c0;
703	+
704	+	RealType u0 = v2 * v10 - v4 * v4;
705	+	RealType u1 = -2.0 * v3 * v4;
706	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
707	+	RealType u3 = -2.0 * v1 * v3;
708	+	RealType u4 = - v1 * v1;
709	+	//rescale coefficients
710	+	RealType maxAbs = fabs(u0);
711	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
712	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
713	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
714	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
715	+	u0 /= maxAbs;
716	+	u1 /= maxAbs;
717	+	u2 /= maxAbs;
718	+	u3 /= maxAbs;
719	+	u4 /= maxAbs;
720	+	//max_element(start, end) is also available.
721	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
722	+	poly.setCoefficient(4, u4);
723	+	poly.setCoefficient(3, u3);
724	+	poly.setCoefficient(2, u2);
725	+	poly.setCoefficient(1, u1);
726	+	poly.setCoefficient(0, u0);
727	+	std::vector<RealType> realRoots = poly.FindRealRoots();
728	+
729	+	std::vector<RealType>::iterator ri;
730	+	RealType r1, r2, alpha0;
731	+	std::vector<std::pair<RealType,RealType> > rps;
732	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
733	+	r2 = *ri;
734	+	//check if FindRealRoots() give the right answer
735	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
736	+	sprintf(painCave.errMsg,
737	+	"RNEMD Warning: polynomial solve seems to have an error!");
738	+	painCave.isFatal = 0;
739	+	simError();
740	+	failRootCount_++;
741	+	}
742	+	//might not be useful w/o rescaling coefficients
743	+	alpha0 = -c0 - a110 * r2 * r2;
744	+	if (alpha0 >= 0.0) {
745	+	r1 = sqrt(alpha0 / a000);
746	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
747	+	{ rps.push_back(std::make_pair(r1, r2)); }
748	+	if (r1 > 1e-6) { //r1 non-negative
749	+	r1 = -r1;
750	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
751	+	{ rps.push_back(std::make_pair(r1, r2)); }
752	+	}
753	+	}
754	+	}
755	+	// Consider combininig together the solving pair part w/ the searching
756	+	// best solution part so that we don't need the pairs vector
757	+	if (!rps.empty()) {
758	+	RealType smallestDiff = HONKING_LARGE_VALUE;
759	+	RealType diff;
760	+	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
761	+	std::vector<std::pair<RealType,RealType> >::iterator rpi;
762	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
763	+	r1 = (*rpi).first;
764	+	r2 = (*rpi).second;
765	+	switch(rnemdType_) {
766	+	case rnemdKineticScale :
767	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
768	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
769	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
770	+	break;
771	+	case rnemdPxScale :
772	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
773	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
774	+	break;
775	+	case rnemdPyScale :
776	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
777	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
778	+	break;
779	+	case rnemdPzScale :
780	+	default :
781	+	break;
782	+	}
783	+	if (diff < smallestDiff) {
784	+	smallestDiff = diff;
785	+	bestPair = *rpi;
786	+	}
787	+	}
788	+	#ifdef IS_MPI
789	+	if (worldRank == 0) {
790	+	#endif
791	+	std::cerr << "we choose r1 = " << bestPair.first
792	+	<< " and r2 = " << bestPair.second << "\n";
793	+	#ifdef IS_MPI
794	+	}
795	+	#endif
796	+
797	+	RealType x, y, z;
798	+	switch(rnemdType_) {
799	+	case rnemdKineticScale :
800	+	x = bestPair.first;
801	+	y = bestPair.first;
802	+	z = bestPair.second;
803	+	break;
804	+	case rnemdPxScale :
805	+	x = c;
806	+	y = bestPair.first;
807	+	z = bestPair.second;
808	+	break;
809	+	case rnemdPyScale :
810	+	x = bestPair.first;
811	+	y = c;
812	+	z = bestPair.second;
813	+	break;
814	+	case rnemdPzScale :
815	+	x = bestPair.first;
816	+	y = bestPair.second;
817	+	z = c;
818	+	break;
819	+	default :
820	+	break;
821	+	}
822	+	std::vector<StuntDouble*>::iterator sdi;
823	+	Vector3d vel;
824	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
825	+	vel = (*sdi)->getVel();
826	+	vel.x() *= x;
827	+	vel.y() *= y;
828	+	vel.z() *= z;
829	+	(*sdi)->setVel(vel);
830	+	}
831	+	//convert to hotBin coefficient
832	+	x = 1.0 + px * (1.0 - x);
833	+	y = 1.0 + py * (1.0 - y);
834	+	z = 1.0 + pz * (1.0 - z);
835	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
836	+	vel = (*sdi)->getVel();
837	+	vel.x() *= x;
838	+	vel.y() *= y;
839	+	vel.z() *= z;
840	+	(*sdi)->setVel(vel);
841	+	}
842	+	exchangeSum_ += targetFlux_;
843	+	//we may want to check whether the exchange has been successful
844	+	} else {
845	+	std::cerr << "exchange NOT performed!\n";//MPI incompatible
846	+	failTrialCount_++;
847	+	}
848	+
849	+	}
850	+
851	+	void RNEMD::doRNEMD() {
852	+
853	+	switch(rnemdType_) {
854	+	case rnemdKineticScale :
855	+	case rnemdPxScale :
856	+	case rnemdPyScale :
857	+	case rnemdPzScale :
858	+	doScale();
859	+	break;
860	+	case rnemdKineticSwap :
861	+	case rnemdPx :
862	+	case rnemdPy :
863	+	case rnemdPz :
864	+	doSwap();
865	+	break;
866	+	case rnemdUnknown :
867	+	default :
868	+	break;
869	+	}
870	+	}
871	+
872	+	void RNEMD::collectData() {
873	+
874	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
875	+	Mat3x3d hmat = currentSnap_->getHmat();
876	+
877	+	seleMan_.setSelectionSet(evaluator_.evaluate());
878	+
879	+	int selei;
880	+	StuntDouble* sd;
881	+	int idx;
882	+
883	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
884	+	sd = seleMan_.nextSelected(selei)) {
885
886		idx = sd->getLocalIndex();
887
#	Line 477 | Line 895 | namespace oopse {
895		// which bin is this stuntdouble in?
896		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
897
898	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
899	<
898	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
899	>
900	>	if (rnemdLogWidth_ == midBin_ + 1)
901	>	if (binNo > midBin_)
902	>	binNo = nBins_ - binNo;
903	>
904		RealType mass = sd->getMass();
905		Vector3d vel = sd->getVel();
906		RealType value;
907	+	RealType xVal, yVal, zVal;
908
909		switch(rnemdType_) {
910	<	case rnemdKinetic :
910	>	case rnemdKineticSwap :
911	>	case rnemdKineticScale :
912
913		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
914		vel[2]*vel[2]);
915
916	<	valueCount[binNo] += 3;
916	>	valueCount_[binNo] += 3;
917		if (sd->isDirectional()) {
918		Vector3d angMom = sd->getJ();
919		Mat3x3d I = sd->getI();
#	Line 501 | Line 925 | namespace oopse {
925		value += angMom[j] * angMom[j] / I(j, j) +
926		angMom[k] * angMom[k] / I(k, k);
927
928	<	valueCount[binNo] +=2;
928	>	valueCount_[binNo] +=2;
929
930		} else {
931		value += angMom[0]*angMom[0]/I(0, 0)
932		+ angMom[1]*angMom[1]/I(1, 1)
933		+ angMom[2]*angMom[2]/I(2, 2);
934	<	valueCount[binNo] +=3;
934	>	valueCount_[binNo] +=3;
935		}
936		}
937	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
937	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
938
939		break;
940		case rnemdPx :
941	+	case rnemdPxScale :
942		value = mass * vel[0];
943	<	valueCount[binNo]++;
943	>	valueCount_[binNo]++;
944	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
945	>	/ PhysicalConstants::kb;
946	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
947	>	/ PhysicalConstants::kb;
948	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
949	>	/ PhysicalConstants::kb;
950	>	xTempHist_[binNo] += xVal;
951	>	yTempHist_[binNo] += yVal;
952	>	zTempHist_[binNo] += zVal;
953		break;
954		case rnemdPy :
955	+	case rnemdPyScale :
956		value = mass * vel[1];
957	<	valueCount[binNo]++;
957	>	valueCount_[binNo]++;
958		break;
959		case rnemdPz :
960	+	case rnemdPzScale :
961		value = mass * vel[2];
962	<	valueCount[binNo]++;
962	>	valueCount_[binNo]++;
963		break;
964		case rnemdUnknown :
965		default :
966		break;
967		}
968	<	valueHist[binNo] += value;
968	>	valueHist_[binNo] += value;
969		}
970
971	+	}
972	+
973	+	void RNEMD::getStarted() {
974	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
975	+	Stats& stat = currentSnap_->statData;
976	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
977	+	}
978	+
979	+	void RNEMD::getStatus() {
980	+
981	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
982	+	Stats& stat = currentSnap_->statData;
983	+	RealType time = currentSnap_->getTime();
984	+
985	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
986	+	//or to be more meaningful, define another item as exchangeSum_ / time
987	+	int j;
988	+
989		#ifdef IS_MPI
990
991		// all processors have the same number of bins, and STL vectors pack their
992		// arrays, so in theory, this should be safe:
993
994	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
995	<	nBins_, MPI::REALTYPE, MPI::SUM);
996	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
997	<	nBins_, MPI::INT, MPI::SUM);
998	<
994	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
995	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
996	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
997	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
998	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
999	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1000	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1001	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1002	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1003	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1004	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1005	>	}
1006		// If we're the root node, should we print out the results
1007		int worldRank = MPI::COMM_WORLD.Get_rank();
1008		if (worldRank == 0) {
1009		#endif
1010	<
1011	<	std::cout << time;
1012	<	for (int j = 0; j < nBins_; j++)
1013	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1014	<	std::cout << "\n";
1015	<
1010	>	rnemdLog_ << time;
1011	>	for (j = 0; j < rnemdLogWidth_; j++) {
1012	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1013	>	}
1014	>	rnemdLog_ << "\n";
1015	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1016	>	xTempLog_ << time;
1017	>	for (j = 0; j < rnemdLogWidth_; j++) {
1018	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1019	>	}
1020	>	xTempLog_ << "\n";
1021	>	yTempLog_ << time;
1022	>	for (j = 0; j < rnemdLogWidth_; j++) {
1023	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1024	>	}
1025	>	yTempLog_ << "\n";
1026	>	zTempLog_ << time;
1027	>	for (j = 0; j < rnemdLogWidth_; j++) {
1028	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1029	>	}
1030	>	zTempLog_ << "\n";
1031	>	}
1032		#ifdef IS_MPI
1033		}
1034		#endif
1035	+	for (j = 0; j < rnemdLogWidth_; j++) {
1036	+	valueCount_[j] = 0;
1037	+	valueHist_[j] = 0.0;
1038	+	}
1039	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1040	+	for (j = 0; j < rnemdLogWidth_; j++) {
1041	+	xTempHist_[j] = 0.0;
1042	+	yTempHist_[j] = 0.0;
1043	+	zTempHist_[j] = 0.0;
1044	+	}
1045		}
1046		}

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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