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root/OpenMD/trunk/src/integrators/RNEMD.cpp

Comparing trunk/src/integrators/RNEMD.cpp (file contents):
Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
Revision 1560 by skuang, Wed May 11 17:55:32 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
#	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	>	output3DTemp_ = false;
115	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
116	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
117	>	}
118	>
119	>	#ifdef IS_MPI
120	>	if (worldRank == 0) {
121	>	#endif
122	>
123	>	std::string rnemdFileName;
124	>	switch(rnemdType_) {
125	>	case rnemdKineticSwap :
126	>	case rnemdKineticScale :
127	>	rnemdFileName = "temperature.log";
128	>	break;
129	>	case rnemdPx :
130	>	case rnemdPxScale :
131	>	case rnemdPy :
132	>	case rnemdPyScale :
133	>	rnemdFileName = "momemtum.log";
134	>	break;
135	>	case rnemdPz :
136	>	case rnemdPzScale :
137	>	case rnemdUnknown :
138	>	default :
139	>	rnemdFileName = "rnemd.log";
140	>	break;
141	>	}
142	>	rnemdLog_.open(rnemdFileName.c_str());
143	>
144	>	std::string xTempFileName;
145	>	std::string yTempFileName;
146	>	std::string zTempFileName;
147	>	if (output3DTemp_) {
148	>	xTempFileName = "temperatureX.log";
149	>	yTempFileName = "temperatureY.log";
150	>	zTempFileName = "temperatureZ.log";
151	>	xTempLog_.open(xTempFileName.c_str());
152	>	yTempLog_.open(yTempFileName.c_str());
153	>	zTempLog_.open(zTempFileName.c_str());
154	>	}
155	>
156	>	#ifdef IS_MPI
157	>	}
158	>	#endif
159	>
160	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
161		set_RNEMD_nBins(simParams->getRNEMD_nBins());
162	<	exchangeSum_ = 0.0;
162	>	midBin_ = nBins_ / 2;
163	>	if (simParams->haveRNEMD_binShift()) {
164	>	if (simParams->getRNEMD_binShift()) {
165	>	zShift_ = 0.5 / (RealType)(nBins_);
166	>	} else {
167	>	zShift_ = 0.0;
168	>	}
169	>	} else {
170	>	zShift_ = 0.0;
171	>	}
172	>	//std::cerr << "we have zShift_ = " << zShift_ << "\n";
173	>	//shift slabs by half slab width, might be useful in heterogeneous systems
174	>	//set to 0.0 if not using it; can NOT be used in status output yet
175	>	if (simParams->haveRNEMD_logWidth()) {
176	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
177	>	/*arbitary rnemdLogWidth_ no checking
178	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
179	>	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
180	>	std::cerr << "Automaically set back to default.\n";
181	>	rnemdLogWidth_ = nBins_;
182	>	}*/
183	>	} else {
184	>	set_RNEMD_logWidth(nBins_);
185	>	}
186	>	valueHist_.resize(rnemdLogWidth_, 0.0);
187	>	valueCount_.resize(rnemdLogWidth_, 0);
188	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
189	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
190	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
191	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
192
193	+	set_RNEMD_exchange_total(0.0);
194	+	if (simParams->haveRNEMD_targetFlux()) {
195	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
196	+	} else {
197	+	set_RNEMD_target_flux(0.0);
198	+	}
199	+
200		#ifndef IS_MPI
201		if (simParams->haveSeed()) {
202		seedValue = simParams->getSeed();
#	Line 123 | Line 216 | namespace oopse {
216
217		RNEMD::~RNEMD() {
218		delete randNumGen_;
219	+
220	+	#ifdef IS_MPI
221	+	if (worldRank == 0) {
222	+	#endif
223	+	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
224	+	rnemdLog_.close();
225	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
226	+	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
227	+	if (output3DTemp_) {
228	+	xTempLog_.close();
229	+	yTempLog_.close();
230	+	zTempLog_.close();
231	+	}
232	+	#ifdef IS_MPI
233	+	}
234	+	#endif
235		}
236
237		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
238
239		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
240		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 160 | Line 268 | namespace oopse {
268		// which bin is this stuntdouble in?
269		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
270
271	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
271	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
272
273
274		// if we're in bin 0 or the middleBin
275	<	if (binNo == 0 || binNo == midBin) {
275	>	if (binNo == 0 || binNo == midBin_) {
276
277		RealType mass = sd->getMass();
278		Vector3d vel = sd->getVel();
279		RealType value;
280
281		switch(rnemdType_) {
282	<	case rnemdKinetic :
282	>	case rnemdKineticSwap :
283
284		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
285		vel[2]*vel[2]);
286	+	/*
287		if (sd->isDirectional()) {
288		Vector3d angMom = sd->getJ();
289		Mat3x3d I = sd->getI();
#	Line 190 | Line 299 | namespace oopse {
299		+ angMom[1]*angMom[1]/I(1, 1)
300		+ angMom[2]*angMom[2]/I(2, 2);
301		}
302	<	}
303	<	value = value * 0.5 / OOPSEConstant::energyConvert;
302	>	} no exchange of angular momenta
303	>	*/
304	>	//make exchangeSum_ comparable between swap & scale
305	>	//temporarily without using energyConvert
306	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
307	>	value *= 0.5;
308		break;
309		case rnemdPx :
310		value = mass * vel[0];
#	Line 202 | Line 315 | namespace oopse {
315		case rnemdPz :
316		value = mass * vel[2];
317		break;
205	–	case rnemdUnknown :
318		default :
319		break;
320		}
#	Line 218 | Line 330 | namespace oopse {
330		min_sd = sd;
331		}
332		}
333	<	} else {
333	>	} else { //midBin_
334		if (!max_found) {
335		max_val = value;
336		max_sd = sd;
#	Line 242 | Line 354 | namespace oopse {
354		bool my_min_found = min_found;
355		bool my_max_found = max_found;
356
357	<	// Even if we didn't find a minimum, did someone else?
358	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
359	<	1, MPI::BOOL, MPI::LAND);
360	<
357	>	// Even if we didn't find a minimum, did someone else? debugging...
358	>	//MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
359	>	//                          1, MPI::BOOL, MPI::LAND);
360	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
361		// Even if we didn't find a maximum, did someone else?
362	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
363	<	1, MPI::BOOL, MPI::LAND);
364	<
362	>	//MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
363	>	//                          1, MPI::BOOL, MPI::LAND);
364	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
365		struct {
366		RealType val;
367		int rank;
#	Line 285 | Line 397 | namespace oopse {
397		#endif
398
399		if (max_found && min_found) {
400	<	if (min_val< max_val) {
400	>	if (min_val < max_val) {
401
402		#ifdef IS_MPI
403		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
404		// I have both maximum and minimum, so proceed like a single
405		// processor version:
406		#endif
407	<	// objects to be swapped: velocity & angular velocity
407	>	// objects to be swapped: velocity ONLY
408		Vector3d min_vel = min_sd->getVel();
409		Vector3d max_vel = max_sd->getVel();
410		RealType temp_vel;
411
412		switch(rnemdType_) {
413	<	case rnemdKinetic :
413	>	case rnemdKineticSwap :
414		min_sd->setVel(max_vel);
415		max_sd->setVel(min_vel);
416	+	/*
417		if (min_sd->isDirectional() && max_sd->isDirectional()) {
418		Vector3d min_angMom = min_sd->getJ();
419		Vector3d max_angMom = max_sd->getJ();
420		min_sd->setJ(max_angMom);
421		max_sd->setJ(min_angMom);
422	<	}
422	>	} no angular momentum exchange
423	>	*/
424		break;
425		case rnemdPx :
426		temp_vel = min_vel.x();
#	Line 329 | Line 443 | namespace oopse {
443		min_sd->setVel(min_vel);
444		max_sd->setVel(max_vel);
445		break;
332	–	case rnemdUnknown :
446		default :
447		break;
448		}
#	Line 349 | Line 462 | namespace oopse {
462		min_vals.rank, 0, status);
463
464		switch(rnemdType_) {
465	<	case rnemdKinetic :
465	>	case rnemdKineticSwap :
466		max_sd->setVel(min_vel);
467	<
467	>	/*
468		if (max_sd->isDirectional()) {
469		Vector3d min_angMom;
470		Vector3d max_angMom = max_sd->getJ();
#	Line 364 | Line 477 | namespace oopse {
477		status);
478
479		max_sd->setJ(min_angMom);
480	<	}
480	>	} no angular momentum exchange
481	>	*/
482		break;
483		case rnemdPx :
484		max_vel.x() = min_vel.x();
#	Line 378 | Line 492 | namespace oopse {
492		max_vel.z() = min_vel.z();
493		max_sd->setVel(max_vel);
494		break;
381	–	case rnemdUnknown :
495		default :
496		break;
497		}
#	Line 396 | Line 509 | namespace oopse {
509		max_vals.rank, 0, status);
510
511		switch(rnemdType_) {
512	<	case rnemdKinetic :
512	>	case rnemdKineticSwap :
513		min_sd->setVel(max_vel);
514	<
514	>	/*
515		if (min_sd->isDirectional()) {
516		Vector3d min_angMom = min_sd->getJ();
517		Vector3d max_angMom;
#	Line 411 | Line 524 | namespace oopse {
524		status);
525
526		min_sd->setJ(max_angMom);
527	<	}
527	>	} no angular momentum exchange
528	>	*/
529		break;
530		case rnemdPx :
531		min_vel.x() = max_vel.x();
#	Line 425 | Line 539 | namespace oopse {
539		min_vel.z() = max_vel.z();
540		min_sd->setVel(min_vel);
541		break;
428	–	case rnemdUnknown :
542		default :
543		break;
544		}
#	Line 433 | Line 546 | namespace oopse {
546		#endif
547		exchangeSum_ += max_val - min_val;
548		} else {
549	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
549	>	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
550	>	failTrialCount_++;
551		}
552		} else {
553	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
553	>	std::cerr << "exchange NOT performed!\n";
554	>	std::cerr << "at least one of the two slabs empty.\n";
555	>	failTrialCount_++;
556		}
557
558		}
559
560	<	void RNEMD::getStatus() {
560	>	void RNEMD::doScale() {
561
562		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
563		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
564
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
565		seleMan_.setSelectionSet(evaluator_.evaluate());
566
567		int selei;
568		StuntDouble* sd;
569		int idx;
570
571	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
572	<	// being averaged
573	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
574	<	// number of degrees of
575	<	// freedom being averaged
571	>	std::vector<StuntDouble*> hotBin, coldBin;
572	>
573	>	RealType Phx = 0.0;
574	>	RealType Phy = 0.0;
575	>	RealType Phz = 0.0;
576	>	RealType Khx = 0.0;
577	>	RealType Khy = 0.0;
578	>	RealType Khz = 0.0;
579	>	RealType Pcx = 0.0;
580	>	RealType Pcy = 0.0;
581	>	RealType Pcz = 0.0;
582	>	RealType Kcx = 0.0;
583	>	RealType Kcy = 0.0;
584	>	RealType Kcz = 0.0;
585	>
586	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
587	>	sd = seleMan_.nextSelected(selei)) {
588	>
589	>	idx = sd->getLocalIndex();
590	>
591	>	Vector3d pos = sd->getPos();
592	>
593	>	// wrap the stuntdouble's position back into the box:
594	>
595	>	if (usePeriodicBoundaryConditions_)
596	>	currentSnap_->wrapVector(pos);
597	>
598	>	// which bin is this stuntdouble in?
599	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
600	>
601	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
602	>
603	>	// if we're in bin 0 or the middleBin
604	>	if (binNo == 0 || binNo == midBin_) {
605	>
606	>	RealType mass = sd->getMass();
607	>	Vector3d vel = sd->getVel();
608	>
609	>	if (binNo == 0) {
610	>	hotBin.push_back(sd);
611	>	Phx += mass * vel.x();
612	>	Phy += mass * vel.y();
613	>	Phz += mass * vel.z();
614	>	Khx += mass * vel.x() * vel.x();
615	>	Khy += mass * vel.y() * vel.y();
616	>	Khz += mass * vel.z() * vel.z();
617	>	} else { //midBin_
618	>	coldBin.push_back(sd);
619	>	Pcx += mass * vel.x();
620	>	Pcy += mass * vel.y();
621	>	Pcz += mass * vel.z();
622	>	Kcx += mass * vel.x() * vel.x();
623	>	Kcy += mass * vel.y() * vel.y();
624	>	Kcz += mass * vel.z() * vel.z();
625	>	}
626	>	}
627	>	}
628	>
629	>	Khx *= 0.5;
630	>	Khy *= 0.5;
631	>	Khz *= 0.5;
632	>	Kcx *= 0.5;
633	>	Kcy *= 0.5;
634	>	Kcz *= 0.5;
635	>
636	>	#ifdef IS_MPI
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
638	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
639	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
640	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
641	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
642	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
643	>
644	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
645	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
646	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
647	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
648	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
649	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
650	>	#endif
651	>
652	>	//use coldBin coeff's
653	>	RealType px = Pcx / Phx;
654	>	RealType py = Pcy / Phy;
655	>	RealType pz = Pcz / Phz;
656	>
657	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
658	>	switch(rnemdType_) {
659	>	case rnemdKineticScale :
660	>	/*used hotBin coeff's & only scale x & y dimensions
661	>	RealType px = Phx / Pcx;
662	>	RealType py = Phy / Pcy;
663	>	a110 = Khy;
664	>	c0 = - Khx - Khy - targetFlux_;
665	>	a000 = Khx;
666	>	a111 = Kcy * py * py
667	>	b11 = -2.0 * Kcy * py * (1.0 + py);
668	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
669	>	b01 = -2.0 * Kcx * px * (1.0 + px);
670	>	a001 = Kcx * px * px;
671	>	*/
672	>
673	>	//scale all three dimensions, let c_x = c_y
674	>	a000 = Kcx + Kcy;
675	>	a110 = Kcz;
676	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
677	>	a001 = Khx * px * px + Khy * py * py;
678	>	a111 = Khz * pz * pz;
679	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
680	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
681	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
682	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
683	>	break;
684	>	case rnemdPxScale :
685	>	c = 1 - targetFlux_ / Pcx;
686	>	a000 = Kcy;
687	>	a110 = Kcz;
688	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
689	>	a001 = py * py * Khy;
690	>	a111 = pz * pz * Khz;
691	>	b01 = -2.0 * Khy * py * (1.0 + py);
692	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
693	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
694	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
695	>	break;
696	>	case rnemdPyScale :
697	>	c = 1 - targetFlux_ / Pcy;
698	>	a000 = Kcx;
699	>	a110 = Kcz;
700	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
701	>	a001 = px * px * Khx;
702	>	a111 = pz * pz * Khz;
703	>	b01 = -2.0 * Khx * px * (1.0 + px);
704	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
705	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
706	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
707	>	break;
708	>	case rnemdPzScale ://we don't really do this, do we?
709	>	c = 1 - targetFlux_ / Pcz;
710	>	a000 = Kcx;
711	>	a110 = Kcy;
712	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
713	>	a001 = px * px * Khx;
714	>	a111 = py * py * Khy;
715	>	b01 = -2.0 * Khx * px * (1.0 + px);
716	>	b11 = -2.0 * Khy * py * (1.0 + py);
717	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
718	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
719	>	break;
720	>	default :
721	>	break;
722	>	}
723
724	+	RealType v1 = a000 * a111 - a001 * a110;
725	+	RealType v2 = a000 * b01;
726	+	RealType v3 = a000 * b11;
727	+	RealType v4 = a000 * c1 - a001 * c0;
728	+	RealType v8 = a110 * b01;
729	+	RealType v10 = - b01 * c0;
730	+
731	+	RealType u0 = v2 * v10 - v4 * v4;
732	+	RealType u1 = -2.0 * v3 * v4;
733	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
734	+	RealType u3 = -2.0 * v1 * v3;
735	+	RealType u4 = - v1 * v1;
736	+	//rescale coefficients
737	+	RealType maxAbs = fabs(u0);
738	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
739	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
740	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
741	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
742	+	u0 /= maxAbs;
743	+	u1 /= maxAbs;
744	+	u2 /= maxAbs;
745	+	u3 /= maxAbs;
746	+	u4 /= maxAbs;
747	+	//max_element(start, end) is also available.
748	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
749	+	poly.setCoefficient(4, u4);
750	+	poly.setCoefficient(3, u3);
751	+	poly.setCoefficient(2, u2);
752	+	poly.setCoefficient(1, u1);
753	+	poly.setCoefficient(0, u0);
754	+	std::vector<RealType> realRoots = poly.FindRealRoots();
755	+
756	+	std::vector<RealType>::iterator ri;
757	+	RealType r1, r2, alpha0;
758	+	std::vector<std::pair<RealType,RealType> > rps;
759	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
760	+	r2 = *ri;
761	+	//check if FindRealRoots() give the right answer
762	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
763	+	sprintf(painCave.errMsg,
764	+	"RNEMD Warning: polynomial solve seems to have an error!");
765	+	painCave.isFatal = 0;
766	+	simError();
767	+	failRootCount_++;
768	+	}
769	+	//might not be useful w/o rescaling coefficients
770	+	alpha0 = -c0 - a110 * r2 * r2;
771	+	if (alpha0 >= 0.0) {
772	+	r1 = sqrt(alpha0 / a000);
773	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
774	+	{ rps.push_back(std::make_pair(r1, r2)); }
775	+	if (r1 > 1e-6) { //r1 non-negative
776	+	r1 = -r1;
777	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
778	+	{ rps.push_back(std::make_pair(r1, r2)); }
779	+	}
780	+	}
781	+	}
782	+	// Consider combininig together the solving pair part w/ the searching
783	+	// best solution part so that we don't need the pairs vector
784	+	if (!rps.empty()) {
785	+	RealType smallestDiff = HONKING_LARGE_VALUE;
786	+	RealType diff;
787	+	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
788	+	std::vector<std::pair<RealType,RealType> >::iterator rpi;
789	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
790	+	r1 = (*rpi).first;
791	+	r2 = (*rpi).second;
792	+	switch(rnemdType_) {
793	+	case rnemdKineticScale :
794	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
795	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
796	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
797	+	break;
798	+	case rnemdPxScale :
799	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
800	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
801	+	break;
802	+	case rnemdPyScale :
803	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
804	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
805	+	break;
806	+	case rnemdPzScale :
807	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
808	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
809	+	default :
810	+	break;
811	+	}
812	+	if (diff < smallestDiff) {
813	+	smallestDiff = diff;
814	+	bestPair = *rpi;
815	+	}
816	+	}
817	+	#ifdef IS_MPI
818	+	if (worldRank == 0) {
819	+	#endif
820	+	std::cerr << "we choose r1 = " << bestPair.first
821	+	<< " and r2 = " << bestPair.second << "\n";
822	+	#ifdef IS_MPI
823	+	}
824	+	#endif
825	+
826	+	RealType x, y, z;
827	+	switch(rnemdType_) {
828	+	case rnemdKineticScale :
829	+	x = bestPair.first;
830	+	y = bestPair.first;
831	+	z = bestPair.second;
832	+	break;
833	+	case rnemdPxScale :
834	+	x = c;
835	+	y = bestPair.first;
836	+	z = bestPair.second;
837	+	break;
838	+	case rnemdPyScale :
839	+	x = bestPair.first;
840	+	y = c;
841	+	z = bestPair.second;
842	+	break;
843	+	case rnemdPzScale :
844	+	x = bestPair.first;
845	+	y = bestPair.second;
846	+	z = c;
847	+	break;
848	+	default :
849	+	break;
850	+	}
851	+	std::vector<StuntDouble*>::iterator sdi;
852	+	Vector3d vel;
853	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
854	+	vel = (*sdi)->getVel();
855	+	vel.x() *= x;
856	+	vel.y() *= y;
857	+	vel.z() *= z;
858	+	(*sdi)->setVel(vel);
859	+	}
860	+	//convert to hotBin coefficient
861	+	x = 1.0 + px * (1.0 - x);
862	+	y = 1.0 + py * (1.0 - y);
863	+	z = 1.0 + pz * (1.0 - z);
864	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
865	+	vel = (*sdi)->getVel();
866	+	vel.x() *= x;
867	+	vel.y() *= y;
868	+	vel.z() *= z;
869	+	(*sdi)->setVel(vel);
870	+	}
871	+	exchangeSum_ += targetFlux_;
872	+	//we may want to check whether the exchange has been successful
873	+	} else {
874	+	std::cerr << "exchange NOT performed!\n";//MPI incompatible
875	+	failTrialCount_++;
876	+	}
877	+
878	+	}
879	+
880	+	void RNEMD::doRNEMD() {
881	+
882	+	switch(rnemdType_) {
883	+	case rnemdKineticScale :
884	+	case rnemdPxScale :
885	+	case rnemdPyScale :
886	+	case rnemdPzScale :
887	+	doScale();
888	+	break;
889	+	case rnemdKineticSwap :
890	+	case rnemdPx :
891	+	case rnemdPy :
892	+	case rnemdPz :
893	+	doSwap();
894	+	break;
895	+	case rnemdUnknown :
896	+	default :
897	+	break;
898	+	}
899	+	}
900	+
901	+	void RNEMD::collectData() {
902	+
903	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
904	+	Mat3x3d hmat = currentSnap_->getHmat();
905	+
906	+	seleMan_.setSelectionSet(evaluator_.evaluate());
907	+
908	+	int selei;
909	+	StuntDouble* sd;
910	+	int idx;
911	+
912	+	// alternative approach, track all molecules instead of only those selected for scaling/swapping
913	+	//SimInfo::MoleculeIterator miter;
914	+	//std::vector<StuntDouble*>::iterator iiter;
915	+	//Molecule* mol;
916	+	//StuntDouble* integrableObject;
917	+	//for (mol = info_->beginMolecule(miter); mol != NULL;
918	+	//     mol = info_->nextMolecule(miter))
919	+	// integrableObject is essentially sd
920	+	//for (integrableObject = mol->beginIntegrableObject(iiter);
921	+	//     integrableObject != NULL;
922	+	//     integrableObject = mol->nextIntegrableObject(iiter))
923		for (sd = seleMan_.beginSelected(selei); sd != NULL;
924		sd = seleMan_.nextSelected(selei)) {
925
#	Line 477 | Line 935 | namespace oopse {
935		// which bin is this stuntdouble in?
936		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
937
938	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
939	<
938	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
939	>	rnemdLogWidth_;
940	>	/* no symmetrization allowed due to arbitary rnemdLogWidth_ value
941	>	if (rnemdLogWidth_ == midBin_ + 1)
942	>	if (binNo > midBin_)
943	>	binNo = nBins_ - binNo;
944	>	*/
945		RealType mass = sd->getMass();
946		Vector3d vel = sd->getVel();
947		RealType value;
948	+	RealType xVal, yVal, zVal;
949
950		switch(rnemdType_) {
951	<	case rnemdKinetic :
951	>	case rnemdKineticSwap :
952	>	case rnemdKineticScale :
953
954		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
955		vel[2]*vel[2]);
956
957	<	valueCount[binNo] += 3;
957	>	valueCount_[binNo] += 3;
958		if (sd->isDirectional()) {
959		Vector3d angMom = sd->getJ();
960		Mat3x3d I = sd->getI();
#	Line 501 | Line 966 | namespace oopse {
966		value += angMom[j] * angMom[j] / I(j, j) +
967		angMom[k] * angMom[k] / I(k, k);
968
969	<	valueCount[binNo] +=2;
969	>	valueCount_[binNo] +=2;
970
971		} else {
972		value += angMom[0]*angMom[0]/I(0, 0)
973		+ angMom[1]*angMom[1]/I(1, 1)
974		+ angMom[2]*angMom[2]/I(2, 2);
975	<	valueCount[binNo] +=3;
975	>	valueCount_[binNo] +=3;
976		}
977		}
978	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
978	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
979
980		break;
981		case rnemdPx :
982	+	case rnemdPxScale :
983		value = mass * vel[0];
984	<	valueCount[binNo]++;
984	>	valueCount_[binNo]++;
985		break;
986		case rnemdPy :
987	+	case rnemdPyScale :
988		value = mass * vel[1];
989	<	valueCount[binNo]++;
989	>	valueCount_[binNo]++;
990		break;
991		case rnemdPz :
992	<	value = mass * vel[2];
993	<	valueCount[binNo]++;
992	>	case rnemdPzScale :
993	>	value = pos.z(); //temporarily for homogeneous systems ONLY
994	>	valueCount_[binNo]++;
995		break;
996		case rnemdUnknown :
997		default :
998	+	value = 1.0;
999	+	valueCount_[binNo]++;
1000		break;
1001		}
1002	<	valueHist[binNo] += value;
1002	>	valueHist_[binNo] += value;
1003	>
1004	>	if (output3DTemp_) {
1005	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1006	>	/ PhysicalConstants::kb;
1007	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1008	>	/ PhysicalConstants::kb;
1009	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1010	>	/ PhysicalConstants::kb;
1011	>	xTempHist_[binNo] += xVal;
1012	>	yTempHist_[binNo] += yVal;
1013	>	zTempHist_[binNo] += zVal;
1014	>	xyzTempCount_[binNo]++;
1015	>	}
1016		}
1017	+	}
1018
1019	+	void RNEMD::getStarted() {
1020	+	collectData();
1021	+	/* now should be able to output profile in step 0, but might not be useful
1022	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1023	+	Stats& stat = currentSnap_->statData;
1024	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1025	+	*/
1026	+	getStatus();
1027	+	}
1028	+
1029	+	void RNEMD::getStatus() {
1030	+
1031	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1032	+	Stats& stat = currentSnap_->statData;
1033	+	RealType time = currentSnap_->getTime();
1034	+
1035	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1036	+	//or to be more meaningful, define another item as exchangeSum_ / time
1037	+	int j;
1038	+
1039		#ifdef IS_MPI
1040
1041		// all processors have the same number of bins, and STL vectors pack their
1042		// arrays, so in theory, this should be safe:
1043
1044	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1045	<	nBins_, MPI::REALTYPE, MPI::SUM);
1046	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1047	<	nBins_, MPI::INT, MPI::SUM);
1048	<
1044	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1045	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1046	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1047	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1048	>	if (output3DTemp_) {
1049	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1050	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1051	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1052	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1053	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1054	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1055	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1056	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1057	>	}
1058		// If we're the root node, should we print out the results
1059		int worldRank = MPI::COMM_WORLD.Get_rank();
1060		if (worldRank == 0) {
1061		#endif
1062	<
1063	<	std::cout << time;
1064	<	for (int j = 0; j < nBins_; j++)
1065	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1066	<	std::cout << "\n";
1067	<
1062	>	rnemdLog_ << time;
1063	>	for (j = 0; j < rnemdLogWidth_; j++) {
1064	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1065	>	}
1066	>	rnemdLog_ << "\n";
1067	>	if (output3DTemp_) {
1068	>	xTempLog_ << time;
1069	>	for (j = 0; j < rnemdLogWidth_; j++) {
1070	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1071	>	}
1072	>	xTempLog_ << "\n";
1073	>	yTempLog_ << time;
1074	>	for (j = 0; j < rnemdLogWidth_; j++) {
1075	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1076	>	}
1077	>	yTempLog_ << "\n";
1078	>	zTempLog_ << time;
1079	>	for (j = 0; j < rnemdLogWidth_; j++) {
1080	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1081	>	}
1082	>	zTempLog_ << "\n";
1083	>	}
1084		#ifdef IS_MPI
1085		}
1086		#endif
1087	+	for (j = 0; j < rnemdLogWidth_; j++) {
1088	+	valueCount_[j] = 0;
1089	+	valueHist_[j] = 0.0;
1090	+	}
1091	+	if (output3DTemp_)
1092	+	for (j = 0; j < rnemdLogWidth_; j++) {
1093	+	xTempHist_[j] = 0.0;
1094	+	yTempHist_[j] = 0.0;
1095	+	zTempHist_[j] = 0.0;
1096	+	xyzTempCount_[j] = 0;
1097	+	}
1098		}
1099		}

Comparing trunk/src/integrators/RNEMD.cpp (property svn:keywords):
Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
Revision 1560 by skuang, Wed May 11 17:55:32 2011 UTC

#	Line 0 | Line 1
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