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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 1465 by chuckv, Fri Jul 9 23:08:25 2010 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
#	Line 55 | Line 57
57
58		#define HONKING_LARGE_VALUE 1.0e10
59
60	<	namespace oopse {
60	>	namespace OpenMD {
61
62		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63	<
63	>
64	>	failTrialCount_ = 0;
65	>	failRootCount_ = 0;
66	>
67		int seedValue;
68		Globals * simParams = info->getSimParams();
69
70	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
70	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
71	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
72	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
73	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
74	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
75		stringToEnumMap_["Px"] = rnemdPx;
76		stringToEnumMap_["Py"] = rnemdPy;
77		stringToEnumMap_["Pz"] = rnemdPz;
#	Line 72 | Line 81 | namespace oopse {
81		evaluator_.loadScriptString(rnemdObjectSelection_);
82		seleMan_.setSelectionSet(evaluator_.evaluate());
83
75	–
84		// do some sanity checking
85
86		int selectionCount = seleMan_.getSelectionCount();
#	Line 94 | Line 102 | namespace oopse {
102
103		}
104
105	<	const std::string st = simParams->getRNEMD_swapType();
105	>	const std::string st = simParams->getRNEMD_exchangeType();
106
107		std::map<std::string, RNEMDTypeEnum>::iterator i;
108		i = stringToEnumMap_.find(st);
109	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
109	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	>	if (rnemdType_ == rnemdUnknown) {
111	>	std::cerr << "WARNING! RNEMD Type Unknown!\n";
112	>	}
113
114	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
114	>	#ifdef IS_MPI
115	>	if (worldRank == 0) {
116	>	#endif
117	>
118	>	std::string rnemdFileName;
119	>	std::string xTempFileName;
120	>	std::string yTempFileName;
121	>	std::string zTempFileName;
122	>	switch(rnemdType_) {
123	>	case rnemdKineticSwap :
124	>	case rnemdKineticScale :
125	>	rnemdFileName = "temperature.log";
126	>	break;
127	>	case rnemdPx :
128	>	case rnemdPxScale :
129	>	case rnemdPy :
130	>	case rnemdPyScale :
131	>	rnemdFileName = "momemtum.log";
132	>	xTempFileName = "temperatureX.log";
133	>	yTempFileName = "temperatureY.log";
134	>	zTempFileName = "temperatureZ.log";
135	>	xTempLog_.open(xTempFileName.c_str());
136	>	yTempLog_.open(yTempFileName.c_str());
137	>	zTempLog_.open(zTempFileName.c_str());
138	>	break;
139	>	case rnemdPz :
140	>	case rnemdPzScale :
141	>	case rnemdUnknown :
142	>	default :
143	>	rnemdFileName = "rnemd.log";
144	>	break;
145	>	}
146	>	rnemdLog_.open(rnemdFileName.c_str());
147	>
148	>	#ifdef IS_MPI
149	>	}
150	>	#endif
151	>
152	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
153		set_RNEMD_nBins(simParams->getRNEMD_nBins());
154	<	exchangeSum_ = 0.0;
154	>	midBin_ = nBins_ / 2;
155	>	if (simParams->haveRNEMD_logWidth()) {
156	>	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
157	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
158	>	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
159	>	std::cerr << "Automaically set back to default.\n";
160	>	rnemdLogWidth_ = nBins_;
161	>	}
162	>	} else {
163	>	rnemdLogWidth_ = nBins_;
164	>	}
165	>	valueHist_.resize(rnemdLogWidth_, 0.0);
166	>	valueCount_.resize(rnemdLogWidth_, 0);
167	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
168	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
169	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
170
171	+	set_RNEMD_exchange_total(0.0);
172	+	if (simParams->haveRNEMD_targetFlux()) {
173	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
174	+	} else {
175	+	set_RNEMD_target_flux(0.0);
176	+	}
177	+
178		#ifndef IS_MPI
179		if (simParams->haveSeed()) {
180		seedValue = simParams->getSeed();
#	Line 123 | Line 194 | namespace oopse {
194
195		RNEMD::~RNEMD() {
196		delete randNumGen_;
197	+
198	+	#ifdef IS_MPI
199	+	if (worldRank == 0) {
200	+	#endif
201	+	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
202	+	rnemdLog_.close();
203	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
204	+	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
205	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
206	+	xTempLog_.close();
207	+	yTempLog_.close();
208	+	zTempLog_.close();
209	+	}
210	+	#ifdef IS_MPI
211	+	}
212	+	#endif
213		}
214
215		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
216
217		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
218		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 164 | Line 250 | namespace oopse {
250
251
252		// if we're in bin 0 or the middleBin
253	<	if (binNo == 0 || binNo == midBin) {
253	>	if (binNo == 0 || binNo == midBin_) {
254
255		RealType mass = sd->getMass();
256		Vector3d vel = sd->getVel();
257		RealType value;
258
259		switch(rnemdType_) {
260	<	case rnemdKinetic :
260	>	case rnemdKineticSwap :
261
262		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
263		vel[2]*vel[2]);
#	Line 191 | Line 277 | namespace oopse {
277		+ angMom[2]*angMom[2]/I(2, 2);
278		}
279		}
280	<	value = value * 0.5 / OOPSEConstant::energyConvert;
280	>	//make exchangeSum_ comparable between swap & scale
281	>	//temporarily without using energyConvert
282	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
283	>	value *= 0.5;
284		break;
285		case rnemdPx :
286		value = mass * vel[0];
#	Line 202 | Line 291 | namespace oopse {
291		case rnemdPz :
292		value = mass * vel[2];
293		break;
205	–	case rnemdUnknown :
294		default :
295		break;
296		}
#	Line 218 | Line 306 | namespace oopse {
306		min_sd = sd;
307		}
308		}
309	<	} else {
309	>	} else { //midBin_
310		if (!max_found) {
311		max_val = value;
312		max_sd = sd;
#	Line 298 | Line 386 | namespace oopse {
386		RealType temp_vel;
387
388		switch(rnemdType_) {
389	<	case rnemdKinetic :
389	>	case rnemdKineticSwap :
390		min_sd->setVel(max_vel);
391		max_sd->setVel(min_vel);
392		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 329 | Line 417 | namespace oopse {
417		min_sd->setVel(min_vel);
418		max_sd->setVel(max_vel);
419		break;
332	–	case rnemdUnknown :
420		default :
421		break;
422		}
#	Line 349 | Line 436 | namespace oopse {
436		min_vals.rank, 0, status);
437
438		switch(rnemdType_) {
439	<	case rnemdKinetic :
439	>	case rnemdKineticSwap :
440		max_sd->setVel(min_vel);
441
442		if (max_sd->isDirectional()) {
#	Line 378 | Line 465 | namespace oopse {
465		max_vel.z() = min_vel.z();
466		max_sd->setVel(max_vel);
467		break;
381	–	case rnemdUnknown :
468		default :
469		break;
470		}
#	Line 396 | Line 482 | namespace oopse {
482		max_vals.rank, 0, status);
483
484		switch(rnemdType_) {
485	<	case rnemdKinetic :
485	>	case rnemdKineticSwap :
486		min_sd->setVel(max_vel);
487
488		if (min_sd->isDirectional()) {
#	Line 425 | Line 511 | namespace oopse {
511		min_vel.z() = max_vel.z();
512		min_sd->setVel(min_vel);
513		break;
428	–	case rnemdUnknown :
514		default :
515		break;
516		}
#	Line 433 | Line 518 | namespace oopse {
518		#endif
519		exchangeSum_ += max_val - min_val;
520		} else {
521	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
521	>	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
522	>	failTrialCount_++;
523		}
524		} else {
525	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
525	>	std::cerr << "exchange NOT performed!\n";
526	>	std::cerr << "at least one of the two slabs empty.\n";
527	>	failTrialCount_++;
528		}
529
530		}
531
532	<	void RNEMD::getStatus() {
532	>	void RNEMD::doScale() {
533
534		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
535		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
536
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
537		seleMan_.setSelectionSet(evaluator_.evaluate());
538
539		int selei;
540		StuntDouble* sd;
541		int idx;
542
543	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
544	<	// being averaged
545	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
546	<	// number of degrees of
547	<	// freedom being averaged
543	>	std::vector<StuntDouble*> hotBin, coldBin;
544	>
545	>	RealType Phx = 0.0;
546	>	RealType Phy = 0.0;
547	>	RealType Phz = 0.0;
548	>	RealType Khx = 0.0;
549	>	RealType Khy = 0.0;
550	>	RealType Khz = 0.0;
551	>	RealType Pcx = 0.0;
552	>	RealType Pcy = 0.0;
553	>	RealType Pcz = 0.0;
554	>	RealType Kcx = 0.0;
555	>	RealType Kcy = 0.0;
556	>	RealType Kcz = 0.0;
557	>
558	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
559	>	sd = seleMan_.nextSelected(selei)) {
560	>
561	>	idx = sd->getLocalIndex();
562	>
563	>	Vector3d pos = sd->getPos();
564	>
565	>	// wrap the stuntdouble's position back into the box:
566	>
567	>	if (usePeriodicBoundaryConditions_)
568	>	currentSnap_->wrapVector(pos);
569	>
570	>	// which bin is this stuntdouble in?
571	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
572	>
573	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
574	>
575	>	// if we're in bin 0 or the middleBin
576	>	if (binNo == 0 || binNo == midBin_) {
577	>
578	>	RealType mass = sd->getMass();
579	>	Vector3d vel = sd->getVel();
580	>
581	>	if (binNo == 0) {
582	>	hotBin.push_back(sd);
583	>	Phx += mass * vel.x();
584	>	Phy += mass * vel.y();
585	>	Phz += mass * vel.z();
586	>	Khx += mass * vel.x() * vel.x();
587	>	Khy += mass * vel.y() * vel.y();
588	>	Khz += mass * vel.z() * vel.z();
589	>	} else { //midBin_
590	>	coldBin.push_back(sd);
591	>	Pcx += mass * vel.x();
592	>	Pcy += mass * vel.y();
593	>	Pcz += mass * vel.z();
594	>	Kcx += mass * vel.x() * vel.x();
595	>	Kcy += mass * vel.y() * vel.y();
596	>	Kcz += mass * vel.z() * vel.z();
597	>	}
598	>	}
599	>	}
600	>
601	>	Khx *= 0.5;
602	>	Khy *= 0.5;
603	>	Khz *= 0.5;
604	>	Kcx *= 0.5;
605	>	Kcy *= 0.5;
606	>	Kcz *= 0.5;
607	>
608	>	#ifdef IS_MPI
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
610	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
612	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
613	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
614	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
615	>
616	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
617	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
618	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
620	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
622	>	#endif
623	>
624	>	//use coldBin coeff's
625	>	RealType px = Pcx / Phx;
626	>	RealType py = Pcy / Phy;
627	>	RealType pz = Pcz / Phz;
628	>
629	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
630	>	switch(rnemdType_) {
631	>	case rnemdKineticScale :
632	>	/*used hotBin coeff's & only scale x & y dimensions
633	>	RealType px = Phx / Pcx;
634	>	RealType py = Phy / Pcy;
635	>	a110 = Khy;
636	>	c0 = - Khx - Khy - targetFlux_;
637	>	a000 = Khx;
638	>	a111 = Kcy * py * py
639	>	b11 = -2.0 * Kcy * py * (1.0 + py);
640	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
641	>	b01 = -2.0 * Kcx * px * (1.0 + px);
642	>	a001 = Kcx * px * px;
643	>	*/
644	>
645	>	//scale all three dimensions, let c_x = c_y
646	>	a000 = Kcx + Kcy;
647	>	a110 = Kcz;
648	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
649	>	a001 = Khx * px * px + Khy * py * py;
650	>	a111 = Khz * pz * pz;
651	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
652	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
653	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
654	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
655	>	break;
656	>	case rnemdPxScale :
657	>	c = 1 - targetFlux_ / Pcx;
658	>	a000 = Kcy;
659	>	a110 = Kcz;
660	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
661	>	a001 = py * py * Khy;
662	>	a111 = pz * pz * Khz;
663	>	b01 = -2.0 * Khy * py * (1.0 + py);
664	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
665	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
666	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
667	>	break;
668	>	case rnemdPyScale :
669	>	c = 1 - targetFlux_ / Pcy;
670	>	a000 = Kcx;
671	>	a110 = Kcz;
672	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
673	>	a001 = px * px * Khx;
674	>	a111 = pz * pz * Khz;
675	>	b01 = -2.0 * Khx * px * (1.0 + px);
676	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
677	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
678	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
679	>	break;
680	>	case rnemdPzScale ://we don't really do this, do we?
681	>	c = 1 - targetFlux_ / Pcz;
682	>	a000 = Kcx;
683	>	a110 = Kcy;
684	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
685	>	a001 = px * px * Khx;
686	>	a111 = py * py * Khy;
687	>	b01 = -2.0 * Khx * px * (1.0 + px);
688	>	b11 = -2.0 * Khy * py * (1.0 + py);
689	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
690	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
691	>	break;
692	>	default :
693	>	break;
694	>	}
695
696	+	RealType v1 = a000 * a111 - a001 * a110;
697	+	RealType v2 = a000 * b01;
698	+	RealType v3 = a000 * b11;
699	+	RealType v4 = a000 * c1 - a001 * c0;
700	+	RealType v8 = a110 * b01;
701	+	RealType v10 = - b01 * c0;
702	+
703	+	RealType u0 = v2 * v10 - v4 * v4;
704	+	RealType u1 = -2.0 * v3 * v4;
705	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
706	+	RealType u3 = -2.0 * v1 * v3;
707	+	RealType u4 = - v1 * v1;
708	+	//rescale coefficients
709	+	RealType maxAbs = fabs(u0);
710	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
711	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
712	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
713	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
714	+	u0 /= maxAbs;
715	+	u1 /= maxAbs;
716	+	u2 /= maxAbs;
717	+	u3 /= maxAbs;
718	+	u4 /= maxAbs;
719	+	//max_element(start, end) is also available.
720	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
721	+	poly.setCoefficient(4, u4);
722	+	poly.setCoefficient(3, u3);
723	+	poly.setCoefficient(2, u2);
724	+	poly.setCoefficient(1, u1);
725	+	poly.setCoefficient(0, u0);
726	+	std::vector<RealType> realRoots = poly.FindRealRoots();
727	+
728	+	std::vector<RealType>::iterator ri;
729	+	RealType r1, r2, alpha0;
730	+	std::vector<std::pair<RealType,RealType> > rps;
731	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
732	+	r2 = *ri;
733	+	//check if FindRealRoots() give the right answer
734	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
735	+	sprintf(painCave.errMsg,
736	+	"RNEMD Warning: polynomial solve seems to have an error!");
737	+	painCave.isFatal = 0;
738	+	simError();
739	+	failRootCount_++;
740	+	}
741	+	//might not be useful w/o rescaling coefficients
742	+	alpha0 = -c0 - a110 * r2 * r2;
743	+	if (alpha0 >= 0.0) {
744	+	r1 = sqrt(alpha0 / a000);
745	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
746	+	{ rps.push_back(std::make_pair(r1, r2)); }
747	+	if (r1 > 1e-6) { //r1 non-negative
748	+	r1 = -r1;
749	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
750	+	{ rps.push_back(std::make_pair(r1, r2)); }
751	+	}
752	+	}
753	+	}
754	+	// Consider combininig together the solving pair part w/ the searching
755	+	// best solution part so that we don't need the pairs vector
756	+	if (!rps.empty()) {
757	+	RealType smallestDiff = HONKING_LARGE_VALUE;
758	+	RealType diff;
759	+	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
760	+	std::vector<std::pair<RealType,RealType> >::iterator rpi;
761	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
762	+	r1 = (*rpi).first;
763	+	r2 = (*rpi).second;
764	+	switch(rnemdType_) {
765	+	case rnemdKineticScale :
766	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
767	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
768	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
769	+	break;
770	+	case rnemdPxScale :
771	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
772	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
773	+	break;
774	+	case rnemdPyScale :
775	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
776	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
777	+	break;
778	+	case rnemdPzScale :
779	+	default :
780	+	break;
781	+	}
782	+	if (diff < smallestDiff) {
783	+	smallestDiff = diff;
784	+	bestPair = *rpi;
785	+	}
786	+	}
787	+	#ifdef IS_MPI
788	+	if (worldRank == 0) {
789	+	#endif
790	+	std::cerr << "we choose r1 = " << bestPair.first
791	+	<< " and r2 = " << bestPair.second << "\n";
792	+	#ifdef IS_MPI
793	+	}
794	+	#endif
795	+
796	+	RealType x, y, z;
797	+	switch(rnemdType_) {
798	+	case rnemdKineticScale :
799	+	x = bestPair.first;
800	+	y = bestPair.first;
801	+	z = bestPair.second;
802	+	break;
803	+	case rnemdPxScale :
804	+	x = c;
805	+	y = bestPair.first;
806	+	z = bestPair.second;
807	+	break;
808	+	case rnemdPyScale :
809	+	x = bestPair.first;
810	+	y = c;
811	+	z = bestPair.second;
812	+	break;
813	+	case rnemdPzScale :
814	+	x = bestPair.first;
815	+	y = bestPair.second;
816	+	z = c;
817	+	break;
818	+	default :
819	+	break;
820	+	}
821	+	std::vector<StuntDouble*>::iterator sdi;
822	+	Vector3d vel;
823	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
824	+	vel = (*sdi)->getVel();
825	+	vel.x() *= x;
826	+	vel.y() *= y;
827	+	vel.z() *= z;
828	+	(*sdi)->setVel(vel);
829	+	}
830	+	//convert to hotBin coefficient
831	+	x = 1.0 + px * (1.0 - x);
832	+	y = 1.0 + py * (1.0 - y);
833	+	z = 1.0 + pz * (1.0 - z);
834	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
835	+	vel = (*sdi)->getVel();
836	+	vel.x() *= x;
837	+	vel.y() *= y;
838	+	vel.z() *= z;
839	+	(*sdi)->setVel(vel);
840	+	}
841	+	exchangeSum_ += targetFlux_;
842	+	//we may want to check whether the exchange has been successful
843	+	} else {
844	+	std::cerr << "exchange NOT performed!\n";//MPI incompatible
845	+	failTrialCount_++;
846	+	}
847	+
848	+	}
849	+
850	+	void RNEMD::doRNEMD() {
851	+
852	+	switch(rnemdType_) {
853	+	case rnemdKineticScale :
854	+	case rnemdPxScale :
855	+	case rnemdPyScale :
856	+	case rnemdPzScale :
857	+	doScale();
858	+	break;
859	+	case rnemdKineticSwap :
860	+	case rnemdPx :
861	+	case rnemdPy :
862	+	case rnemdPz :
863	+	doSwap();
864	+	break;
865	+	case rnemdUnknown :
866	+	default :
867	+	break;
868	+	}
869	+	}
870	+
871	+	void RNEMD::collectData() {
872	+
873	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
874	+	Mat3x3d hmat = currentSnap_->getHmat();
875	+
876	+	seleMan_.setSelectionSet(evaluator_.evaluate());
877	+
878	+	int selei;
879	+	StuntDouble* sd;
880	+	int idx;
881	+
882		for (sd = seleMan_.beginSelected(selei); sd != NULL;
883		sd = seleMan_.nextSelected(selei)) {
884
#	Line 477 | Line 894 | namespace oopse {
894		// which bin is this stuntdouble in?
895		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
896
897	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
898	<
897	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
898	>
899	>	if (rnemdLogWidth_ == midBin_ + 1)
900	>	if (binNo > midBin_)
901	>	binNo = nBins_ - binNo;
902	>
903		RealType mass = sd->getMass();
904		Vector3d vel = sd->getVel();
905		RealType value;
906	+	RealType xVal, yVal, zVal;
907
908		switch(rnemdType_) {
909	<	case rnemdKinetic :
909	>	case rnemdKineticSwap :
910	>	case rnemdKineticScale :
911
912		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
913		vel[2]*vel[2]);
914
915	<	valueCount[binNo] += 3;
915	>	valueCount_[binNo] += 3;
916		if (sd->isDirectional()) {
917		Vector3d angMom = sd->getJ();
918		Mat3x3d I = sd->getI();
#	Line 501 | Line 924 | namespace oopse {
924		value += angMom[j] * angMom[j] / I(j, j) +
925		angMom[k] * angMom[k] / I(k, k);
926
927	<	valueCount[binNo] +=2;
927	>	valueCount_[binNo] +=2;
928
929		} else {
930		value += angMom[0]*angMom[0]/I(0, 0)
931		+ angMom[1]*angMom[1]/I(1, 1)
932		+ angMom[2]*angMom[2]/I(2, 2);
933	<	valueCount[binNo] +=3;
933	>	valueCount_[binNo] +=3;
934		}
935		}
936	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
936	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
937
938		break;
939		case rnemdPx :
940	+	case rnemdPxScale :
941		value = mass * vel[0];
942	<	valueCount[binNo]++;
942	>	valueCount_[binNo]++;
943	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
944	>	/ PhysicalConstants::kb;
945	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
946	>	/ PhysicalConstants::kb;
947	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
948	>	/ PhysicalConstants::kb;
949	>	xTempHist_[binNo] += xVal;
950	>	yTempHist_[binNo] += yVal;
951	>	zTempHist_[binNo] += zVal;
952		break;
953		case rnemdPy :
954	+	case rnemdPyScale :
955		value = mass * vel[1];
956	<	valueCount[binNo]++;
956	>	valueCount_[binNo]++;
957		break;
958		case rnemdPz :
959	+	case rnemdPzScale :
960		value = mass * vel[2];
961	<	valueCount[binNo]++;
961	>	valueCount_[binNo]++;
962		break;
963		case rnemdUnknown :
964		default :
965		break;
966		}
967	<	valueHist[binNo] += value;
967	>	valueHist_[binNo] += value;
968		}
969
970	+	}
971	+
972	+	void RNEMD::getStarted() {
973	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
974	+	Stats& stat = currentSnap_->statData;
975	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
976	+	}
977	+
978	+	void RNEMD::getStatus() {
979	+
980	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
981	+	Stats& stat = currentSnap_->statData;
982	+	RealType time = currentSnap_->getTime();
983	+
984	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
985	+	//or to be more meaningful, define another item as exchangeSum_ / time
986	+	int j;
987	+
988		#ifdef IS_MPI
989
990		// all processors have the same number of bins, and STL vectors pack their
991		// arrays, so in theory, this should be safe:
992
993	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
994	<	nBins_, MPI::REALTYPE, MPI::SUM);
995	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
996	<	nBins_, MPI::INT, MPI::SUM);
997	<
993	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
994	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
995	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
996	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
997	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
998	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
999	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1000	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1001	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1002	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1003	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1004	>	}
1005		// If we're the root node, should we print out the results
1006		int worldRank = MPI::COMM_WORLD.Get_rank();
1007		if (worldRank == 0) {
1008		#endif
1009	<
1010	<	std::cout << time;
1011	<	for (int j = 0; j < nBins_; j++)
1012	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1013	<	std::cout << "\n";
1014	<
1009	>	rnemdLog_ << time;
1010	>	for (j = 0; j < rnemdLogWidth_; j++) {
1011	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1012	>	}
1013	>	rnemdLog_ << "\n";
1014	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1015	>	xTempLog_ << time;
1016	>	for (j = 0; j < rnemdLogWidth_; j++) {
1017	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1018	>	}
1019	>	xTempLog_ << "\n";
1020	>	yTempLog_ << time;
1021	>	for (j = 0; j < rnemdLogWidth_; j++) {
1022	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1023	>	}
1024	>	yTempLog_ << "\n";
1025	>	zTempLog_ << time;
1026	>	for (j = 0; j < rnemdLogWidth_; j++) {
1027	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1028	>	}
1029	>	zTempLog_ << "\n";
1030	>	}
1031		#ifdef IS_MPI
1032		}
1033		#endif
1034	+	for (j = 0; j < rnemdLogWidth_; j++) {
1035	+	valueCount_[j] = 0;
1036	+	valueHist_[j] = 0.0;
1037	+	}
1038	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1039	+	for (j = 0; j < rnemdLogWidth_; j++) {
1040	+	xTempHist_[j] = 0.0;
1041	+	yTempHist_[j] = 0.0;
1042	+	zTempHist_[j] = 0.0;
1043	+	}
1044		}
1045		}

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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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