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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 1561 by gezelter, Wed May 11 19:04:40 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	>	using namespace std;
61	>	namespace OpenMD {
62
63	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
64	<
63	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
64	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
65	>
66	>	failTrialCount_ = 0;
67	>	failRootCount_ = 0;
68	>
69		int seedValue;
70		Globals * simParams = info->getSimParams();
71
72	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
72	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
74	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
75	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
76	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
77		stringToEnumMap_["Px"] = rnemdPx;
78		stringToEnumMap_["Py"] = rnemdPy;
79		stringToEnumMap_["Pz"] = rnemdPz;
#	Line 72 | Line 83 | namespace oopse {
83		evaluator_.loadScriptString(rnemdObjectSelection_);
84		seleMan_.setSelectionSet(evaluator_.evaluate());
85
75	–
86		// do some sanity checking
87
88		int selectionCount = seleMan_.getSelectionCount();
#	Line 80 | Line 90 | namespace oopse {
90
91		if (selectionCount > nIntegrable) {
92		sprintf(painCave.errMsg,
93	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
93	>	"RNEMD: The current RNEMD_objectSelection,\n"
94		"\t\t%s\n"
95		"\thas resulted in %d selected objects.  However,\n"
96		"\tthe total number of integrable objects in the system\n"
#	Line 90 | Line 100 | namespace oopse {
100		rnemdObjectSelection_.c_str(),
101		selectionCount, nIntegrable);
102		painCave.isFatal = 0;
103	+	painCave.severity = OPENMD_WARNING;
104		simError();
94	–
105		}
106
107	<	const std::string st = simParams->getRNEMD_swapType();
107	>	const string st = simParams->getRNEMD_exchangeType();
108
109	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
109	>	map<string, RNEMDTypeEnum>::iterator i;
110		i = stringToEnumMap_.find(st);
111	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
111	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
112	>	if (rnemdType_ == rnemdUnknown) {
113	>	sprintf(painCave.errMsg,
114	>	"RNEMD: The current RNEMD_exchangeType,\n"
115	>	"\t\t%s\n"
116	>	"\tis not one of the recognized exchange types.\n",
117	>	st.c_str());
118	>	painCave.isFatal = 1;
119	>	painCave.severity = OPENMD_ERROR;
120	>	simError();
121	>	}
122	>
123	>	output3DTemp_ = false;
124	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
125	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
126	>	}
127
128	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
128	>	#ifdef IS_MPI
129	>	if (worldRank == 0) {
130	>	#endif
131	>
132	>	string rnemdFileName;
133	>	switch(rnemdType_) {
134	>	case rnemdKineticSwap :
135	>	case rnemdKineticScale :
136	>	rnemdFileName = "temperature.log";
137	>	break;
138	>	case rnemdPx :
139	>	case rnemdPxScale :
140	>	case rnemdPy :
141	>	case rnemdPyScale :
142	>	rnemdFileName = "momemtum.log";
143	>	break;
144	>	case rnemdPz :
145	>	case rnemdPzScale :
146	>	case rnemdUnknown :
147	>	default :
148	>	rnemdFileName = "rnemd.log";
149	>	break;
150	>	}
151	>	rnemdLog_.open(rnemdFileName.c_str());
152	>
153	>	string xTempFileName;
154	>	string yTempFileName;
155	>	string zTempFileName;
156	>	if (output3DTemp_) {
157	>	xTempFileName = "temperatureX.log";
158	>	yTempFileName = "temperatureY.log";
159	>	zTempFileName = "temperatureZ.log";
160	>	xTempLog_.open(xTempFileName.c_str());
161	>	yTempLog_.open(yTempFileName.c_str());
162	>	zTempLog_.open(zTempFileName.c_str());
163	>	}
164	>
165	>	#ifdef IS_MPI
166	>	}
167	>	#endif
168	>
169	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
170		set_RNEMD_nBins(simParams->getRNEMD_nBins());
171	<	exchangeSum_ = 0.0;
171	>	midBin_ = nBins_ / 2;
172	>	if (simParams->haveRNEMD_binShift()) {
173	>	if (simParams->getRNEMD_binShift()) {
174	>	zShift_ = 0.5 / (RealType)(nBins_);
175	>	} else {
176	>	zShift_ = 0.0;
177	>	}
178	>	} else {
179	>	zShift_ = 0.0;
180	>	}
181	>	//cerr << "we have zShift_ = " << zShift_ << "\n";
182	>	//shift slabs by half slab width, might be useful in heterogeneous systems
183	>	//set to 0.0 if not using it; can NOT be used in status output yet
184	>	if (simParams->haveRNEMD_logWidth()) {
185	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
186	>	/*arbitary rnemdLogWidth_ no checking
187	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
188	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
189	>	cerr << "Automaically set back to default.\n";
190	>	rnemdLogWidth_ = nBins_;
191	>	}*/
192	>	} else {
193	>	set_RNEMD_logWidth(nBins_);
194	>	}
195	>	valueHist_.resize(rnemdLogWidth_, 0.0);
196	>	valueCount_.resize(rnemdLogWidth_, 0);
197	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
198	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
199	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
200	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
201
202	+	set_RNEMD_exchange_total(0.0);
203	+	if (simParams->haveRNEMD_targetFlux()) {
204	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
205	+	} else {
206	+	set_RNEMD_target_flux(0.0);
207	+	}
208	+
209		#ifndef IS_MPI
210		if (simParams->haveSeed()) {
211		seedValue = simParams->getSeed();
#	Line 123 | Line 225 | namespace oopse {
225
226		RNEMD::~RNEMD() {
227		delete randNumGen_;
228	+
229	+	#ifdef IS_MPI
230	+	if (worldRank == 0) {
231	+	#endif
232	+
233	+	sprintf(painCave.errMsg,
234	+	"RNEMD: total failed trials: %d\n",
235	+	failTrialCount_);
236	+	painCave.isFatal = 0;
237	+	painCave.severity = OPENMD_INFO;
238	+	simError();
239	+
240	+	rnemdLog_.close();
241	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
242	+	sprintf(painCave.errMsg,
243	+	"RNEMD: total root-checking warnings: %d\n",
244	+	failRootCount_);
245	+	painCave.isFatal = 0;
246	+	painCave.severity = OPENMD_INFO;
247	+	simError();
248	+	}
249	+	if (output3DTemp_) {
250	+	xTempLog_.close();
251	+	yTempLog_.close();
252	+	zTempLog_.close();
253	+	}
254	+	#ifdef IS_MPI
255	+	}
256	+	#endif
257		}
258
259		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
260
261		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
262		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 160 | Line 290 | namespace oopse {
290		// which bin is this stuntdouble in?
291		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
292
293	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
293	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
294
295
296		// if we're in bin 0 or the middleBin
297	<	if (binNo == 0 || binNo == midBin) {
297	>	if (binNo == 0 || binNo == midBin_) {
298
299		RealType mass = sd->getMass();
300		Vector3d vel = sd->getVel();
301		RealType value;
302
303		switch(rnemdType_) {
304	<	case rnemdKinetic :
304	>	case rnemdKineticSwap :
305
306		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
307		vel[2]*vel[2]);
308	<	if (sd->isDirectional()) {
308	>	/*
309	>	if (sd->isDirectional()) {
310		Vector3d angMom = sd->getJ();
311		Mat3x3d I = sd->getI();
312
313		if (sd->isLinear()) {
314	<	int i = sd->linearAxis();
315	<	int j = (i + 1) % 3;
316	<	int k = (i + 2) % 3;
317	<	value += angMom[j] * angMom[j] / I(j, j) +
318	<	angMom[k] * angMom[k] / I(k, k);
314	>	int i = sd->linearAxis();
315	>	int j = (i + 1) % 3;
316	>	int k = (i + 2) % 3;
317	>	value += angMom[j] * angMom[j] / I(j, j) +
318	>	angMom[k] * angMom[k] / I(k, k);
319		} else {
320	<	value += angMom[0]*angMom[0]/I(0, 0)
321	<	+ angMom[1]*angMom[1]/I(1, 1)
322	<	+ angMom[2]*angMom[2]/I(2, 2);
320	>	value += angMom[0]*angMom[0]/I(0, 0)
321	>	+ angMom[1]*angMom[1]/I(1, 1)
322	>	+ angMom[2]*angMom[2]/I(2, 2);
323		}
324	<	}
325	<	value = value * 0.5 / OOPSEConstant::energyConvert;
324	>	} no exchange of angular momenta
325	>	*/
326	>	//make exchangeSum_ comparable between swap & scale
327	>	//temporarily without using energyConvert
328	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
329	>	value *= 0.5;
330		break;
331		case rnemdPx :
332		value = mass * vel[0];
#	Line 202 | Line 337 | namespace oopse {
337		case rnemdPz :
338		value = mass * vel[2];
339		break;
205	–	case rnemdUnknown :
340		default :
341		break;
342		}
#	Line 218 | Line 352 | namespace oopse {
352		min_sd = sd;
353		}
354		}
355	<	} else {
355	>	} else { //midBin_
356		if (!max_found) {
357		max_val = value;
358		max_sd = sd;
#	Line 243 | Line 377 | namespace oopse {
377		bool my_max_found = max_found;
378
379		// Even if we didn't find a minimum, did someone else?
380	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
380	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
381		// Even if we didn't find a maximum, did someone else?
382	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
251	<	1, MPI::BOOL, MPI::LAND);
252	<
382	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
383		struct {
384		RealType val;
385		int rank;
#	Line 285 | Line 415 | namespace oopse {
415		#endif
416
417		if (max_found && min_found) {
418	<	if (min_val< max_val) {
418	>	if (min_val < max_val) {
419
420		#ifdef IS_MPI
421		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
422		// I have both maximum and minimum, so proceed like a single
423		// processor version:
424		#endif
425	<	// objects to be swapped: velocity & angular velocity
425	>	// objects to be swapped: velocity ONLY
426		Vector3d min_vel = min_sd->getVel();
427		Vector3d max_vel = max_sd->getVel();
428		RealType temp_vel;
429
430		switch(rnemdType_) {
431	<	case rnemdKinetic :
431	>	case rnemdKineticSwap :
432		min_sd->setVel(max_vel);
433		max_sd->setVel(min_vel);
434	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
434	>	/*
435	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
436		Vector3d min_angMom = min_sd->getJ();
437		Vector3d max_angMom = max_sd->getJ();
438		min_sd->setJ(max_angMom);
439		max_sd->setJ(min_angMom);
440	<	}
440	>	} no angular momentum exchange
441	>	*/
442		break;
443		case rnemdPx :
444		temp_vel = min_vel.x();
#	Line 329 | Line 461 | namespace oopse {
461		min_sd->setVel(min_vel);
462		max_sd->setVel(max_vel);
463		break;
332	–	case rnemdUnknown :
464		default :
465		break;
466		}
#	Line 349 | Line 480 | namespace oopse {
480		min_vals.rank, 0, status);
481
482		switch(rnemdType_) {
483	<	case rnemdKinetic :
483	>	case rnemdKineticSwap :
484		max_sd->setVel(min_vel);
485	<
485	>	//no angular momentum exchange for now
486	>	/*
487		if (max_sd->isDirectional()) {
488		Vector3d min_angMom;
489		Vector3d max_angMom = max_sd->getJ();
490	<
490	>
491		// point-to-point swap of the angular momentum vector
492		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
493		MPI::REALTYPE, min_vals.rank, 1,
494		min_angMom.getArrayPointer(), 3,
495		MPI::REALTYPE, min_vals.rank, 1,
496		status);
497	<
497	>
498		max_sd->setJ(min_angMom);
499	<	}
499	>	}
500	>	*/
501		break;
502		case rnemdPx :
503		max_vel.x() = min_vel.x();
#	Line 378 | Line 511 | namespace oopse {
511		max_vel.z() = min_vel.z();
512		max_sd->setVel(max_vel);
513		break;
381	–	case rnemdUnknown :
514		default :
515		break;
516		}
#	Line 396 | Line 528 | namespace oopse {
528		max_vals.rank, 0, status);
529
530		switch(rnemdType_) {
531	<	case rnemdKinetic :
531	>	case rnemdKineticSwap :
532		min_sd->setVel(max_vel);
533	<
533	>	// no angular momentum exchange for now
534	>	/*
535		if (min_sd->isDirectional()) {
536		Vector3d min_angMom = min_sd->getJ();
537		Vector3d max_angMom;
538	<
538	>
539		// point-to-point swap of the angular momentum vector
540		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
541		MPI::REALTYPE, max_vals.rank, 1,
542		max_angMom.getArrayPointer(), 3,
543		MPI::REALTYPE, max_vals.rank, 1,
544		status);
545	<
545	>
546		min_sd->setJ(max_angMom);
547		}
548	+	*/
549		break;
550		case rnemdPx :
551		min_vel.x() = max_vel.x();
#	Line 425 | Line 559 | namespace oopse {
559		min_vel.z() = max_vel.z();
560		min_sd->setVel(min_vel);
561		break;
428	–	case rnemdUnknown :
562		default :
563		break;
564		}
565		}
566		#endif
567		exchangeSum_ += max_val - min_val;
568	<	} else {
569	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
568	>	} else {
569	>	sprintf(painCave.errMsg,
570	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
571	>	painCave.isFatal = 0;
572	>	painCave.severity = OPENMD_INFO;
573	>	simError();
574	>	failTrialCount_++;
575		}
576		} else {
577	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
577	>	sprintf(painCave.errMsg,
578	>	"RNEMD: exchange NOT performed because at least one\n"
579	>	"\tof the two slabs is empty\n");
580	>	painCave.isFatal = 0;
581	>	painCave.severity = OPENMD_INFO;
582	>	simError();
583	>	failTrialCount_++;
584		}
585
586		}
587
588	<	void RNEMD::getStatus() {
588	>	void RNEMD::doScale() {
589
590		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
591		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
592
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
593		seleMan_.setSelectionSet(evaluator_.evaluate());
594
595		int selei;
596		StuntDouble* sd;
597		int idx;
598
599	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
600	<	// being averaged
601	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
602	<	// number of degrees of
603	<	// freedom being averaged
599	>	vector<StuntDouble*> hotBin, coldBin;
600	>
601	>	RealType Phx = 0.0;
602	>	RealType Phy = 0.0;
603	>	RealType Phz = 0.0;
604	>	RealType Khx = 0.0;
605	>	RealType Khy = 0.0;
606	>	RealType Khz = 0.0;
607	>	RealType Pcx = 0.0;
608	>	RealType Pcy = 0.0;
609	>	RealType Pcz = 0.0;
610	>	RealType Kcx = 0.0;
611	>	RealType Kcy = 0.0;
612	>	RealType Kcz = 0.0;
613
614		for (sd = seleMan_.beginSelected(selei); sd != NULL;
615		sd = seleMan_.nextSelected(selei)) {
616	+
617	+	idx = sd->getLocalIndex();
618	+
619	+	Vector3d pos = sd->getPos();
620	+
621	+	// wrap the stuntdouble's position back into the box:
622	+
623	+	if (usePeriodicBoundaryConditions_)
624	+	currentSnap_->wrapVector(pos);
625	+
626	+	// which bin is this stuntdouble in?
627	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
628	+
629	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
630	+
631	+	// if we're in bin 0 or the middleBin
632	+	if (binNo == 0 || binNo == midBin_) {
633	+
634	+	RealType mass = sd->getMass();
635	+	Vector3d vel = sd->getVel();
636	+
637	+	if (binNo == 0) {
638	+	hotBin.push_back(sd);
639	+	Phx += mass * vel.x();
640	+	Phy += mass * vel.y();
641	+	Phz += mass * vel.z();
642	+	Khx += mass * vel.x() * vel.x();
643	+	Khy += mass * vel.y() * vel.y();
644	+	Khz += mass * vel.z() * vel.z();
645	+	} else { //midBin_
646	+	coldBin.push_back(sd);
647	+	Pcx += mass * vel.x();
648	+	Pcy += mass * vel.y();
649	+	Pcz += mass * vel.z();
650	+	Kcx += mass * vel.x() * vel.x();
651	+	Kcy += mass * vel.y() * vel.y();
652	+	Kcz += mass * vel.z() * vel.z();
653	+	}
654	+	}
655	+	}
656	+
657	+	Khx *= 0.5;
658	+	Khy *= 0.5;
659	+	Khz *= 0.5;
660	+	Kcx *= 0.5;
661	+	Kcy *= 0.5;
662	+	Kcz *= 0.5;
663	+
664	+	#ifdef IS_MPI
665	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
666	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
667	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
668	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
669	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
670	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
671	+
672	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
673	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
674	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
675	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
676	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
677	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
678	+	#endif
679	+
680	+	//use coldBin coeff's
681	+	RealType px = Pcx / Phx;
682	+	RealType py = Pcy / Phy;
683	+	RealType pz = Pcz / Phz;
684	+
685	+	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
686	+	switch(rnemdType_) {
687	+	case rnemdKineticScale :
688	+	// used hotBin coeff's & only scale x & y dimensions
689	+	/*
690	+	RealType px = Phx / Pcx;
691	+	RealType py = Phy / Pcy;
692	+	a110 = Khy;
693	+	c0 = - Khx - Khy - targetFlux_;
694	+	a000 = Khx;
695	+	a111 = Kcy * py * py;
696	+	b11 = -2.0 * Kcy * py * (1.0 + py);
697	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
698	+	b01 = -2.0 * Kcx * px * (1.0 + px);
699	+	a001 = Kcx * px * px;
700	+	*/
701	+	//scale all three dimensions, let c_x = c_y
702	+	a000 = Kcx + Kcy;
703	+	a110 = Kcz;
704	+	c0 = targetFlux_ - Kcx - Kcy - Kcz;
705	+	a001 = Khx * px * px + Khy * py * py;
706	+	a111 = Khz * pz * pz;
707	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
708	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
709	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
710	+	+ Khz * pz * (2.0 + pz) - targetFlux_;
711	+	break;
712	+	case rnemdPxScale :
713	+	c = 1 - targetFlux_ / Pcx;
714	+	a000 = Kcy;
715	+	a110 = Kcz;
716	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
717	+	a001 = py * py * Khy;
718	+	a111 = pz * pz * Khz;
719	+	b01 = -2.0 * Khy * py * (1.0 + py);
720	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
721	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
722	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
723	+	break;
724	+	case rnemdPyScale :
725	+	c = 1 - targetFlux_ / Pcy;
726	+	a000 = Kcx;
727	+	a110 = Kcz;
728	+	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
729	+	a001 = px * px * Khx;
730	+	a111 = pz * pz * Khz;
731	+	b01 = -2.0 * Khx * px * (1.0 + px);
732	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
733	+	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
734	+	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
735	+	break;
736	+	case rnemdPzScale ://we don't really do this, do we?
737	+	c = 1 - targetFlux_ / Pcz;
738	+	a000 = Kcx;
739	+	a110 = Kcy;
740	+	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
741	+	a001 = px * px * Khx;
742	+	a111 = py * py * Khy;
743	+	b01 = -2.0 * Khx * px * (1.0 + px);
744	+	b11 = -2.0 * Khy * py * (1.0 + py);
745	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
746	+	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
747	+	break;
748	+	default :
749	+	break;
750	+	}
751	+
752	+	RealType v1 = a000 * a111 - a001 * a110;
753	+	RealType v2 = a000 * b01;
754	+	RealType v3 = a000 * b11;
755	+	RealType v4 = a000 * c1 - a001 * c0;
756	+	RealType v8 = a110 * b01;
757	+	RealType v10 = - b01 * c0;
758	+
759	+	RealType u0 = v2 * v10 - v4 * v4;
760	+	RealType u1 = -2.0 * v3 * v4;
761	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
762	+	RealType u3 = -2.0 * v1 * v3;
763	+	RealType u4 = - v1 * v1;
764	+	//rescale coefficients
765	+	RealType maxAbs = fabs(u0);
766	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
767	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
768	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
769	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
770	+	u0 /= maxAbs;
771	+	u1 /= maxAbs;
772	+	u2 /= maxAbs;
773	+	u3 /= maxAbs;
774	+	u4 /= maxAbs;
775	+	//max_element(start, end) is also available.
776	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
777	+	poly.setCoefficient(4, u4);
778	+	poly.setCoefficient(3, u3);
779	+	poly.setCoefficient(2, u2);
780	+	poly.setCoefficient(1, u1);
781	+	poly.setCoefficient(0, u0);
782	+	vector<RealType> realRoots = poly.FindRealRoots();
783	+
784	+	vector<RealType>::iterator ri;
785	+	RealType r1, r2, alpha0;
786	+	vector<pair<RealType,RealType> > rps;
787	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
788	+	r2 = *ri;
789	+	//check if FindRealRoots() give the right answer
790	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
791	+	sprintf(painCave.errMsg,
792	+	"RNEMD Warning: polynomial solve seems to have an error!");
793	+	painCave.isFatal = 0;
794	+	simError();
795	+	failRootCount_++;
796	+	}
797	+	//might not be useful w/o rescaling coefficients
798	+	alpha0 = -c0 - a110 * r2 * r2;
799	+	if (alpha0 >= 0.0) {
800	+	r1 = sqrt(alpha0 / a000);
801	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
802	+	{ rps.push_back(make_pair(r1, r2)); }
803	+	if (r1 > 1e-6) { //r1 non-negative
804	+	r1 = -r1;
805	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
806	+	{ rps.push_back(make_pair(r1, r2)); }
807	+	}
808	+	}
809	+	}
810	+	// Consider combining together the solving pair part w/ the searching
811	+	// best solution part so that we don't need the pairs vector
812	+	if (!rps.empty()) {
813	+	RealType smallestDiff = HONKING_LARGE_VALUE;
814	+	RealType diff;
815	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
816	+	vector<pair<RealType,RealType> >::iterator rpi;
817	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
818	+	r1 = (*rpi).first;
819	+	r2 = (*rpi).second;
820	+	switch(rnemdType_) {
821	+	case rnemdKineticScale :
822	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
823	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
824	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
825	+	break;
826	+	case rnemdPxScale :
827	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
828	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
829	+	break;
830	+	case rnemdPyScale :
831	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
832	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
833	+	break;
834	+	case rnemdPzScale :
835	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
836	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
837	+	default :
838	+	break;
839	+	}
840	+	if (diff < smallestDiff) {
841	+	smallestDiff = diff;
842	+	bestPair = *rpi;
843	+	}
844	+	}
845	+	#ifdef IS_MPI
846	+	if (worldRank == 0) {
847	+	#endif
848	+	sprintf(painCave.errMsg,
849	+	"RNEMD: roots r1= %lf\tr2 = %lf\n",
850	+	bestPair.first, bestPair.second);
851	+	painCave.isFatal = 0;
852	+	painCave.severity = OPENMD_INFO;
853	+	simError();
854	+	#ifdef IS_MPI
855	+	}
856	+	#endif
857
858	+	RealType x, y, z;
859	+	switch(rnemdType_) {
860	+	case rnemdKineticScale :
861	+	x = bestPair.first;
862	+	y = bestPair.first;
863	+	z = bestPair.second;
864	+	break;
865	+	case rnemdPxScale :
866	+	x = c;
867	+	y = bestPair.first;
868	+	z = bestPair.second;
869	+	break;
870	+	case rnemdPyScale :
871	+	x = bestPair.first;
872	+	y = c;
873	+	z = bestPair.second;
874	+	break;
875	+	case rnemdPzScale :
876	+	x = bestPair.first;
877	+	y = bestPair.second;
878	+	z = c;
879	+	break;
880	+	default :
881	+	break;
882	+	}
883	+	vector<StuntDouble*>::iterator sdi;
884	+	Vector3d vel;
885	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
886	+	vel = (*sdi)->getVel();
887	+	vel.x() *= x;
888	+	vel.y() *= y;
889	+	vel.z() *= z;
890	+	(*sdi)->setVel(vel);
891	+	}
892	+	//convert to hotBin coefficient
893	+	x = 1.0 + px * (1.0 - x);
894	+	y = 1.0 + py * (1.0 - y);
895	+	z = 1.0 + pz * (1.0 - z);
896	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
897	+	vel = (*sdi)->getVel();
898	+	vel.x() *= x;
899	+	vel.y() *= y;
900	+	vel.z() *= z;
901	+	(*sdi)->setVel(vel);
902	+	}
903	+	exchangeSum_ += targetFlux_;
904	+	//we may want to check whether the exchange has been successful
905	+	} else {
906	+	sprintf(painCave.errMsg,
907	+	"RNEMD: exchange NOT performed!\n");
908	+	painCave.isFatal = 0;
909	+	painCave.severity = OPENMD_INFO;
910	+	simError();
911	+	failTrialCount_++;
912	+	}
913	+
914	+	}
915	+
916	+	void RNEMD::doRNEMD() {
917	+
918	+	switch(rnemdType_) {
919	+	case rnemdKineticScale :
920	+	case rnemdPxScale :
921	+	case rnemdPyScale :
922	+	case rnemdPzScale :
923	+	doScale();
924	+	break;
925	+	case rnemdKineticSwap :
926	+	case rnemdPx :
927	+	case rnemdPy :
928	+	case rnemdPz :
929	+	doSwap();
930	+	break;
931	+	case rnemdUnknown :
932	+	default :
933	+	break;
934	+	}
935	+	}
936	+
937	+	void RNEMD::collectData() {
938	+
939	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
940	+	Mat3x3d hmat = currentSnap_->getHmat();
941	+
942	+	seleMan_.setSelectionSet(evaluator_.evaluate());
943	+
944	+	int selei;
945	+	StuntDouble* sd;
946	+	int idx;
947	+
948	+	// alternative approach, track all molecules instead of only those
949	+	// selected for scaling/swapping:
950	+	/*
951	+	SimInfo::MoleculeIterator miter;
952	+	vector<StuntDouble*>::iterator iiter;
953	+	Molecule* mol;
954	+	StuntDouble* integrableObject;
955	+	for (mol = info_->beginMolecule(miter); mol != NULL;
956	+	mol = info_->nextMolecule(miter))
957	+	integrableObject is essentially sd
958	+	for (integrableObject = mol->beginIntegrableObject(iiter);
959	+	integrableObject != NULL;
960	+	integrableObject = mol->nextIntegrableObject(iiter))
961	+	*/
962	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
963	+	sd = seleMan_.nextSelected(selei)) {
964	+
965		idx = sd->getLocalIndex();
966
967		Vector3d pos = sd->getPos();
#	Line 477 | Line 974 | namespace oopse {
974		// which bin is this stuntdouble in?
975		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
976
977	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
978	<
977	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
978	>	rnemdLogWidth_;
979	>	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
980	>	/*
981	>	if (rnemdLogWidth_ == midBin_ + 1)
982	>	if (binNo > midBin_)
983	>	binNo = nBins_ - binNo;
984	>	*/
985		RealType mass = sd->getMass();
986		Vector3d vel = sd->getVel();
987		RealType value;
988	+	RealType xVal, yVal, zVal;
989
990		switch(rnemdType_) {
991	<	case rnemdKinetic :
991	>	case rnemdKineticSwap :
992	>	case rnemdKineticScale :
993
994	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
490	<	vel[2]*vel[2]);
994	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
995
996	<	valueCount[binNo] += 3;
996	>	valueCount_[binNo] += 3;
997		if (sd->isDirectional()) {
998		Vector3d angMom = sd->getJ();
999		Mat3x3d I = sd->getI();
#	Line 500 | Line 1004 | namespace oopse {
1004		int k = (i + 2) % 3;
1005		value += angMom[j] * angMom[j] / I(j, j) +
1006		angMom[k] * angMom[k] / I(k, k);
1007	<
1008	<	valueCount[binNo] +=2;
1009	<
1007	>
1008	>	valueCount_[binNo] +=2;
1009	>
1010		} else {
1011		value += angMom[0]*angMom[0]/I(0, 0)
1012		+ angMom[1]*angMom[1]/I(1, 1)
1013		+ angMom[2]*angMom[2]/I(2, 2);
1014	<	valueCount[binNo] +=3;
1014	>	valueCount_[binNo] +=3;
1015		}
1016		}
1017	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
1018	<
1017	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1018	>
1019		break;
1020		case rnemdPx :
1021	+	case rnemdPxScale :
1022		value = mass * vel[0];
1023	<	valueCount[binNo]++;
1023	>	valueCount_[binNo]++;
1024		break;
1025		case rnemdPy :
1026	+	case rnemdPyScale :
1027		value = mass * vel[1];
1028	<	valueCount[binNo]++;
1028	>	valueCount_[binNo]++;
1029		break;
1030		case rnemdPz :
1031	<	value = mass * vel[2];
1032	<	valueCount[binNo]++;
1031	>	case rnemdPzScale :
1032	>	value = pos.z(); //temporarily for homogeneous systems ONLY
1033	>	valueCount_[binNo]++;
1034		break;
1035		case rnemdUnknown :
1036		default :
1037	+	value = 1.0;
1038	+	valueCount_[binNo]++;
1039		break;
1040		}
1041	<	valueHist[binNo] += value;
1041	>	valueHist_[binNo] += value;
1042	>
1043	>	if (output3DTemp_) {
1044	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1045	>	/ PhysicalConstants::kb;
1046	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1047	>	/ PhysicalConstants::kb;
1048	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1049	>	/ PhysicalConstants::kb;
1050	>	xTempHist_[binNo] += xVal;
1051	>	yTempHist_[binNo] += yVal;
1052	>	zTempHist_[binNo] += zVal;
1053	>	xyzTempCount_[binNo]++;
1054	>	}
1055		}
1056	+	}
1057
1058	+	void RNEMD::getStarted() {
1059	+	collectData();
1060	+	/* now should be able to output profile in step 0, but might not be useful
1061	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1062	+	Stats& stat = currentSnap_->statData;
1063	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1064	+	*/
1065	+	getStatus();
1066	+	}
1067	+
1068	+	void RNEMD::getStatus() {
1069	+
1070	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1071	+	Stats& stat = currentSnap_->statData;
1072	+	RealType time = currentSnap_->getTime();
1073	+
1074	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1075	+	//or to be more meaningful, define another item as exchangeSum_ / time
1076	+	int j;
1077	+
1078		#ifdef IS_MPI
1079
1080		// all processors have the same number of bins, and STL vectors pack their
1081		// arrays, so in theory, this should be safe:
1082
1083	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1084	<	nBins_, MPI::REALTYPE, MPI::SUM);
1085	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1086	<	nBins_, MPI::INT, MPI::SUM);
1087	<
1083	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1084	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1085	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1086	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1087	>	if (output3DTemp_) {
1088	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1089	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1090	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1091	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1092	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1093	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1094	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1095	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1096	>	}
1097		// If we're the root node, should we print out the results
1098		int worldRank = MPI::COMM_WORLD.Get_rank();
1099		if (worldRank == 0) {
1100		#endif
1101	<
1102	<	std::cout << time;
1103	<	for (int j = 0; j < nBins_; j++)
1104	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1105	<	std::cout << "\n";
1106	<
1101	>	rnemdLog_ << time;
1102	>	for (j = 0; j < rnemdLogWidth_; j++) {
1103	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1104	>	}
1105	>	rnemdLog_ << "\n";
1106	>	if (output3DTemp_) {
1107	>	xTempLog_ << time;
1108	>	for (j = 0; j < rnemdLogWidth_; j++) {
1109	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1110	>	}
1111	>	xTempLog_ << "\n";
1112	>	yTempLog_ << time;
1113	>	for (j = 0; j < rnemdLogWidth_; j++) {
1114	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1115	>	}
1116	>	yTempLog_ << "\n";
1117	>	zTempLog_ << time;
1118	>	for (j = 0; j < rnemdLogWidth_; j++) {
1119	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1120	>	}
1121	>	zTempLog_ << "\n";
1122	>	}
1123		#ifdef IS_MPI
1124		}
1125		#endif
1126	+	for (j = 0; j < rnemdLogWidth_; j++) {
1127	+	valueCount_[j] = 0;
1128	+	valueHist_[j] = 0.0;
1129	+	}
1130	+	if (output3DTemp_)
1131	+	for (j = 0; j < rnemdLogWidth_; j++) {
1132	+	xTempHist_[j] = 0.0;
1133	+	yTempHist_[j] = 0.0;
1134	+	zTempHist_[j] = 0.0;
1135	+	xyzTempCount_[j] = 0;
1136	+	}
1137		}
1138		}

Comparing trunk/src/integrators/RNEMD.cpp (property svn:keywords):
Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
Revision 1561 by gezelter, Wed May 11 19:04:40 2011 UTC

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