ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/src/rnemd/RNEMD.cpp

Comparing:
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 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <cmath>
44		#include "integrators/RNEMD.hpp"
45		#include "math/Vector3.hpp"
46		#include "math/SquareMatrix3.hpp"
47	+	#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50	<	#include "utils/OOPSEConstant.hpp"
50	>	#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52
53		#ifndef IS_MPI
54		#include "math/SeqRandNumGen.hpp"
55		#else
56	+	#include <mpi.h>
57		#include "math/ParallelRandNumGen.hpp"
58		#endif
59
60		#define HONKING_LARGE_VALUE 1.0e10
61
62	<	namespace oopse {
62	>	using namespace std;
63	>	namespace OpenMD {
64
65	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
66	<
65	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
66	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
67	>
68	>	failTrialCount_ = 0;
69	>	failRootCount_ = 0;
70	>
71		int seedValue;
72		Globals * simParams = info->getSimParams();
73
74	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
74	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
75	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
77	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
78	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
79		stringToEnumMap_["Px"] = rnemdPx;
80		stringToEnumMap_["Py"] = rnemdPy;
81		stringToEnumMap_["Pz"] = rnemdPz;
#	Line 72 | Line 85 | namespace oopse {
85		evaluator_.loadScriptString(rnemdObjectSelection_);
86		seleMan_.setSelectionSet(evaluator_.evaluate());
87
75	–
88		// do some sanity checking
89
90		int selectionCount = seleMan_.getSelectionCount();
#	Line 80 | Line 92 | namespace oopse {
92
93		if (selectionCount > nIntegrable) {
94		sprintf(painCave.errMsg,
95	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
95	>	"RNEMD: The current RNEMD_objectSelection,\n"
96		"\t\t%s\n"
97		"\thas resulted in %d selected objects.  However,\n"
98		"\tthe total number of integrable objects in the system\n"
#	Line 90 | Line 102 | namespace oopse {
102		rnemdObjectSelection_.c_str(),
103		selectionCount, nIntegrable);
104		painCave.isFatal = 0;
105	+	painCave.severity = OPENMD_WARNING;
106		simError();
94	–
107		}
108
109	<	const std::string st = simParams->getRNEMD_swapType();
109	>	const string st = simParams->getRNEMD_exchangeType();
110
111	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
111	>	map<string, RNEMDTypeEnum>::iterator i;
112		i = stringToEnumMap_.find(st);
113	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
113	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
114	>	if (rnemdType_ == rnemdUnknown) {
115	>	sprintf(painCave.errMsg,
116	>	"RNEMD: The current RNEMD_exchangeType,\n"
117	>	"\t\t%s\n"
118	>	"\tis not one of the recognized exchange types.\n",
119	>	st.c_str());
120	>	painCave.isFatal = 1;
121	>	painCave.severity = OPENMD_ERROR;
122	>	simError();
123	>	}
124	>
125	>	output3DTemp_ = false;
126	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
127	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
128	>	}
129
130	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
130	>	#ifdef IS_MPI
131	>	if (worldRank == 0) {
132	>	#endif
133	>
134	>	string rnemdFileName;
135	>	switch(rnemdType_) {
136	>	case rnemdKineticSwap :
137	>	case rnemdKineticScale :
138	>	rnemdFileName = "temperature.log";
139	>	break;
140	>	case rnemdPx :
141	>	case rnemdPxScale :
142	>	case rnemdPy :
143	>	case rnemdPyScale :
144	>	rnemdFileName = "momemtum.log";
145	>	break;
146	>	case rnemdPz :
147	>	case rnemdPzScale :
148	>	case rnemdUnknown :
149	>	default :
150	>	rnemdFileName = "rnemd.log";
151	>	break;
152	>	}
153	>	rnemdLog_.open(rnemdFileName.c_str());
154	>
155	>	string xTempFileName;
156	>	string yTempFileName;
157	>	string zTempFileName;
158	>	if (output3DTemp_) {
159	>	xTempFileName = "temperatureX.log";
160	>	yTempFileName = "temperatureY.log";
161	>	zTempFileName = "temperatureZ.log";
162	>	xTempLog_.open(xTempFileName.c_str());
163	>	yTempLog_.open(yTempFileName.c_str());
164	>	zTempLog_.open(zTempFileName.c_str());
165	>	}
166	>
167	>	#ifdef IS_MPI
168	>	}
169	>	#endif
170	>
171	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
172		set_RNEMD_nBins(simParams->getRNEMD_nBins());
173	<	exchangeSum_ = 0.0;
173	>	midBin_ = nBins_ / 2;
174	>	if (simParams->haveRNEMD_binShift()) {
175	>	if (simParams->getRNEMD_binShift()) {
176	>	zShift_ = 0.5 / (RealType)(nBins_);
177	>	} else {
178	>	zShift_ = 0.0;
179	>	}
180	>	} else {
181	>	zShift_ = 0.0;
182	>	}
183	>	//cerr << "we have zShift_ = " << zShift_ << "\n";
184	>	//shift slabs by half slab width, might be useful in heterogeneous systems
185	>	//set to 0.0 if not using it; can NOT be used in status output yet
186	>	if (simParams->haveRNEMD_logWidth()) {
187	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
188	>	/*arbitary rnemdLogWidth_ no checking
189	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
190	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
191	>	cerr << "Automaically set back to default.\n";
192	>	rnemdLogWidth_ = nBins_;
193	>	}*/
194	>	} else {
195	>	set_RNEMD_logWidth(nBins_);
196	>	}
197	>	valueHist_.resize(rnemdLogWidth_, 0.0);
198	>	valueCount_.resize(rnemdLogWidth_, 0);
199	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
200	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
201	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
202	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
203
204	+	set_RNEMD_exchange_total(0.0);
205	+	if (simParams->haveRNEMD_targetFlux()) {
206	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
207	+	} else {
208	+	set_RNEMD_target_flux(0.0);
209	+	}
210	+
211		#ifndef IS_MPI
212		if (simParams->haveSeed()) {
213		seedValue = simParams->getSeed();
#	Line 123 | Line 227 | namespace oopse {
227
228		RNEMD::~RNEMD() {
229		delete randNumGen_;
230	+
231	+	#ifdef IS_MPI
232	+	if (worldRank == 0) {
233	+	#endif
234	+
235	+	sprintf(painCave.errMsg,
236	+	"RNEMD: total failed trials: %d\n",
237	+	failTrialCount_);
238	+	painCave.isFatal = 0;
239	+	painCave.severity = OPENMD_INFO;
240	+	simError();
241	+
242	+	rnemdLog_.close();
243	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
244	+	sprintf(painCave.errMsg,
245	+	"RNEMD: total root-checking warnings: %d\n",
246	+	failRootCount_);
247	+	painCave.isFatal = 0;
248	+	painCave.severity = OPENMD_INFO;
249	+	simError();
250	+	}
251	+	if (output3DTemp_) {
252	+	xTempLog_.close();
253	+	yTempLog_.close();
254	+	zTempLog_.close();
255	+	}
256	+	#ifdef IS_MPI
257	+	}
258	+	#endif
259		}
260
261		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
262
263		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
264		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 160 | Line 292 | namespace oopse {
292		// which bin is this stuntdouble in?
293		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
294
295	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
295	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
296
297
298		// if we're in bin 0 or the middleBin
299	<	if (binNo == 0 || binNo == midBin) {
299	>	if (binNo == 0 || binNo == midBin_) {
300
301		RealType mass = sd->getMass();
302		Vector3d vel = sd->getVel();
303		RealType value;
304
305		switch(rnemdType_) {
306	<	case rnemdKinetic :
306	>	case rnemdKineticSwap :
307
308		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
309		vel[2]*vel[2]);
310	<	if (sd->isDirectional()) {
310	>	/*
311	>	if (sd->isDirectional()) {
312		Vector3d angMom = sd->getJ();
313		Mat3x3d I = sd->getI();
314
315		if (sd->isLinear()) {
316	<	int i = sd->linearAxis();
317	<	int j = (i + 1) % 3;
318	<	int k = (i + 2) % 3;
319	<	value += angMom[j] * angMom[j] / I(j, j) +
320	<	angMom[k] * angMom[k] / I(k, k);
321	<	} else {
322	<	value += angMom[0]*angMom[0]/I(0, 0)
323	<	+ angMom[1]*angMom[1]/I(1, 1)
324	<	+ angMom[2]*angMom[2]/I(2, 2);
316	>	int i = sd->linearAxis();
317	>	int j = (i + 1) % 3;
318	>	int k = (i + 2) % 3;
319	>	value += angMom[j] * angMom[j] / I(j, j) +
320	>	angMom[k] * angMom[k] / I(k, k);
321	>	} else {
322	>	value += angMom[0]*angMom[0]/I(0, 0)
323	>	+ angMom[1]*angMom[1]/I(1, 1)
324	>	+ angMom[2]*angMom[2]/I(2, 2);
325		}
326	<	}
327	<	value = value * 0.5 / OOPSEConstant::energyConvert;
326	>	} no exchange of angular momenta
327	>	*/
328	>	//make exchangeSum_ comparable between swap & scale
329	>	//temporarily without using energyConvert
330	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
331	>	value *= 0.5;
332		break;
333		case rnemdPx :
334		value = mass * vel[0];
#	Line 202 | Line 339 | namespace oopse {
339		case rnemdPz :
340		value = mass * vel[2];
341		break;
205	–	case rnemdUnknown :
342		default :
343		break;
344		}
#	Line 218 | Line 354 | namespace oopse {
354		min_sd = sd;
355		}
356		}
357	<	} else {
357	>	} else { //midBin_
358		if (!max_found) {
359		max_val = value;
360		max_sd = sd;
#	Line 243 | Line 379 | namespace oopse {
379		bool my_max_found = max_found;
380
381		// Even if we didn't find a minimum, did someone else?
382	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
382	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
383		// Even if we didn't find a maximum, did someone else?
384	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
251	<	1, MPI::BOOL, MPI::LAND);
252	<
384	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
385		struct {
386		RealType val;
387		int rank;
#	Line 285 | Line 417 | namespace oopse {
417		#endif
418
419		if (max_found && min_found) {
420	<	if (min_val< max_val) {
420	>	if (min_val < max_val) {
421
422		#ifdef IS_MPI
423		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
424		// I have both maximum and minimum, so proceed like a single
425		// processor version:
426		#endif
427	<	// objects to be swapped: velocity & angular velocity
427	>	// objects to be swapped: velocity ONLY
428		Vector3d min_vel = min_sd->getVel();
429		Vector3d max_vel = max_sd->getVel();
430		RealType temp_vel;
431
432		switch(rnemdType_) {
433	<	case rnemdKinetic :
433	>	case rnemdKineticSwap :
434		min_sd->setVel(max_vel);
435		max_sd->setVel(min_vel);
436	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
436	>	/*
437	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
438		Vector3d min_angMom = min_sd->getJ();
439		Vector3d max_angMom = max_sd->getJ();
440		min_sd->setJ(max_angMom);
441		max_sd->setJ(min_angMom);
442	<	}
442	>	} no angular momentum exchange
443	>	*/
444		break;
445		case rnemdPx :
446		temp_vel = min_vel.x();
#	Line 329 | Line 463 | namespace oopse {
463		min_sd->setVel(min_vel);
464		max_sd->setVel(max_vel);
465		break;
332	–	case rnemdUnknown :
466		default :
467		break;
468		}
#	Line 349 | Line 482 | namespace oopse {
482		min_vals.rank, 0, status);
483
484		switch(rnemdType_) {
485	<	case rnemdKinetic :
485	>	case rnemdKineticSwap :
486		max_sd->setVel(min_vel);
487	<
487	>	//no angular momentum exchange for now
488	>	/*
489		if (max_sd->isDirectional()) {
490		Vector3d min_angMom;
491		Vector3d max_angMom = max_sd->getJ();
492	<
492	>
493		// point-to-point swap of the angular momentum vector
494		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
495		MPI::REALTYPE, min_vals.rank, 1,
496		min_angMom.getArrayPointer(), 3,
497		MPI::REALTYPE, min_vals.rank, 1,
498		status);
499	<
499	>
500		max_sd->setJ(min_angMom);
501	<	}
501	>	}
502	>	*/
503		break;
504		case rnemdPx :
505		max_vel.x() = min_vel.x();
#	Line 378 | Line 513 | namespace oopse {
513		max_vel.z() = min_vel.z();
514		max_sd->setVel(max_vel);
515		break;
381	–	case rnemdUnknown :
516		default :
517		break;
518		}
#	Line 396 | Line 530 | namespace oopse {
530		max_vals.rank, 0, status);
531
532		switch(rnemdType_) {
533	<	case rnemdKinetic :
533	>	case rnemdKineticSwap :
534		min_sd->setVel(max_vel);
535	<
535	>	// no angular momentum exchange for now
536	>	/*
537		if (min_sd->isDirectional()) {
538		Vector3d min_angMom = min_sd->getJ();
539		Vector3d max_angMom;
540	<
540	>
541		// point-to-point swap of the angular momentum vector
542		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
543		MPI::REALTYPE, max_vals.rank, 1,
544		max_angMom.getArrayPointer(), 3,
545		MPI::REALTYPE, max_vals.rank, 1,
546		status);
547	<
547	>
548		min_sd->setJ(max_angMom);
549		}
550	+	*/
551		break;
552		case rnemdPx :
553		min_vel.x() = max_vel.x();
#	Line 425 | Line 561 | namespace oopse {
561		min_vel.z() = max_vel.z();
562		min_sd->setVel(min_vel);
563		break;
428	–	case rnemdUnknown :
564		default :
565		break;
566		}
567		}
568		#endif
569		exchangeSum_ += max_val - min_val;
570	<	} else {
571	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
570	>	} else {
571	>	sprintf(painCave.errMsg,
572	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
573	>	painCave.isFatal = 0;
574	>	painCave.severity = OPENMD_INFO;
575	>	simError();
576	>	failTrialCount_++;
577		}
578		} else {
579	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
579	>	sprintf(painCave.errMsg,
580	>	"RNEMD: exchange NOT performed because at least one\n"
581	>	"\tof the two slabs is empty\n");
582	>	painCave.isFatal = 0;
583	>	painCave.severity = OPENMD_INFO;
584	>	simError();
585	>	failTrialCount_++;
586		}
587
588		}
589
590	<	void RNEMD::getStatus() {
590	>	void RNEMD::doScale() {
591
592		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
593		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
594
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
595		seleMan_.setSelectionSet(evaluator_.evaluate());
596
597		int selei;
598		StuntDouble* sd;
599		int idx;
600
601	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
460	<	// being averaged
461	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
462	<	// number of degrees of
463	<	// freedom being averaged
601	>	vector<StuntDouble*> hotBin, coldBin;
602
603	+	RealType Phx = 0.0;
604	+	RealType Phy = 0.0;
605	+	RealType Phz = 0.0;
606	+	RealType Khx = 0.0;
607	+	RealType Khy = 0.0;
608	+	RealType Khz = 0.0;
609	+	RealType Pcx = 0.0;
610	+	RealType Pcy = 0.0;
611	+	RealType Pcz = 0.0;
612	+	RealType Kcx = 0.0;
613	+	RealType Kcy = 0.0;
614	+	RealType Kcz = 0.0;
615	+
616		for (sd = seleMan_.beginSelected(selei); sd != NULL;
617		sd = seleMan_.nextSelected(selei)) {
618	+
619	+	idx = sd->getLocalIndex();
620	+
621	+	Vector3d pos = sd->getPos();
622	+
623	+	// wrap the stuntdouble's position back into the box:
624	+
625	+	if (usePeriodicBoundaryConditions_)
626	+	currentSnap_->wrapVector(pos);
627	+
628	+	// which bin is this stuntdouble in?
629	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
630	+
631	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
632	+
633	+	// if we're in bin 0 or the middleBin
634	+	if (binNo == 0 || binNo == midBin_) {
635	+
636	+	RealType mass = sd->getMass();
637	+	Vector3d vel = sd->getVel();
638	+
639	+	if (binNo == 0) {
640	+	hotBin.push_back(sd);
641	+	Phx += mass * vel.x();
642	+	Phy += mass * vel.y();
643	+	Phz += mass * vel.z();
644	+	Khx += mass * vel.x() * vel.x();
645	+	Khy += mass * vel.y() * vel.y();
646	+	Khz += mass * vel.z() * vel.z();
647	+	} else { //midBin_
648	+	coldBin.push_back(sd);
649	+	Pcx += mass * vel.x();
650	+	Pcy += mass * vel.y();
651	+	Pcz += mass * vel.z();
652	+	Kcx += mass * vel.x() * vel.x();
653	+	Kcy += mass * vel.y() * vel.y();
654	+	Kcz += mass * vel.z() * vel.z();
655	+	}
656	+	}
657	+	}
658	+
659	+	Khx *= 0.5;
660	+	Khy *= 0.5;
661	+	Khz *= 0.5;
662	+	Kcx *= 0.5;
663	+	Kcy *= 0.5;
664	+	Kcz *= 0.5;
665	+
666	+	#ifdef IS_MPI
667	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
668	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
669	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
670	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
671	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
672	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
673	+
674	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
675	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
676	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
677	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
678	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
679	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
680	+	#endif
681	+
682	+	//use coldBin coeff's
683	+	RealType px = Pcx / Phx;
684	+	RealType py = Pcy / Phy;
685	+	RealType pz = Pcz / Phz;
686	+
687	+	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
688	+	switch(rnemdType_) {
689	+	case rnemdKineticScale :
690	+	// used hotBin coeff's & only scale x & y dimensions
691	+	/*
692	+	RealType px = Phx / Pcx;
693	+	RealType py = Phy / Pcy;
694	+	a110 = Khy;
695	+	c0 = - Khx - Khy - targetFlux_;
696	+	a000 = Khx;
697	+	a111 = Kcy * py * py;
698	+	b11 = -2.0 * Kcy * py * (1.0 + py);
699	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
700	+	b01 = -2.0 * Kcx * px * (1.0 + px);
701	+	a001 = Kcx * px * px;
702	+	*/
703	+	//scale all three dimensions, let c_x = c_y
704	+	a000 = Kcx + Kcy;
705	+	a110 = Kcz;
706	+	c0 = targetFlux_ - Kcx - Kcy - Kcz;
707	+	a001 = Khx * px * px + Khy * py * py;
708	+	a111 = Khz * pz * pz;
709	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
710	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
711	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
712	+	+ Khz * pz * (2.0 + pz) - targetFlux_;
713	+	break;
714	+	case rnemdPxScale :
715	+	c = 1 - targetFlux_ / Pcx;
716	+	a000 = Kcy;
717	+	a110 = Kcz;
718	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
719	+	a001 = py * py * Khy;
720	+	a111 = pz * pz * Khz;
721	+	b01 = -2.0 * Khy * py * (1.0 + py);
722	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
723	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
724	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
725	+	break;
726	+	case rnemdPyScale :
727	+	c = 1 - targetFlux_ / Pcy;
728	+	a000 = Kcx;
729	+	a110 = Kcz;
730	+	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
731	+	a001 = px * px * Khx;
732	+	a111 = pz * pz * Khz;
733	+	b01 = -2.0 * Khx * px * (1.0 + px);
734	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
735	+	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
736	+	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
737	+	break;
738	+	case rnemdPzScale ://we don't really do this, do we?
739	+	c = 1 - targetFlux_ / Pcz;
740	+	a000 = Kcx;
741	+	a110 = Kcy;
742	+	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
743	+	a001 = px * px * Khx;
744	+	a111 = py * py * Khy;
745	+	b01 = -2.0 * Khx * px * (1.0 + px);
746	+	b11 = -2.0 * Khy * py * (1.0 + py);
747	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
748	+	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
749	+	break;
750	+	default :
751	+	break;
752	+	}
753	+
754	+	RealType v1 = a000 * a111 - a001 * a110;
755	+	RealType v2 = a000 * b01;
756	+	RealType v3 = a000 * b11;
757	+	RealType v4 = a000 * c1 - a001 * c0;
758	+	RealType v8 = a110 * b01;
759	+	RealType v10 = - b01 * c0;
760	+
761	+	RealType u0 = v2 * v10 - v4 * v4;
762	+	RealType u1 = -2.0 * v3 * v4;
763	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
764	+	RealType u3 = -2.0 * v1 * v3;
765	+	RealType u4 = - v1 * v1;
766	+	//rescale coefficients
767	+	RealType maxAbs = fabs(u0);
768	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
769	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
770	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
771	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
772	+	u0 /= maxAbs;
773	+	u1 /= maxAbs;
774	+	u2 /= maxAbs;
775	+	u3 /= maxAbs;
776	+	u4 /= maxAbs;
777	+	//max_element(start, end) is also available.
778	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
779	+	poly.setCoefficient(4, u4);
780	+	poly.setCoefficient(3, u3);
781	+	poly.setCoefficient(2, u2);
782	+	poly.setCoefficient(1, u1);
783	+	poly.setCoefficient(0, u0);
784	+	vector<RealType> realRoots = poly.FindRealRoots();
785	+
786	+	vector<RealType>::iterator ri;
787	+	RealType r1, r2, alpha0;
788	+	vector<pair<RealType,RealType> > rps;
789	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
790	+	r2 = *ri;
791	+	//check if FindRealRoots() give the right answer
792	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
793	+	sprintf(painCave.errMsg,
794	+	"RNEMD Warning: polynomial solve seems to have an error!");
795	+	painCave.isFatal = 0;
796	+	simError();
797	+	failRootCount_++;
798	+	}
799	+	//might not be useful w/o rescaling coefficients
800	+	alpha0 = -c0 - a110 * r2 * r2;
801	+	if (alpha0 >= 0.0) {
802	+	r1 = sqrt(alpha0 / a000);
803	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
804	+	{ rps.push_back(make_pair(r1, r2)); }
805	+	if (r1 > 1e-6) { //r1 non-negative
806	+	r1 = -r1;
807	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
808	+	{ rps.push_back(make_pair(r1, r2)); }
809	+	}
810	+	}
811	+	}
812	+	// Consider combining together the solving pair part w/ the searching
813	+	// best solution part so that we don't need the pairs vector
814	+	if (!rps.empty()) {
815	+	RealType smallestDiff = HONKING_LARGE_VALUE;
816	+	RealType diff;
817	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
818	+	vector<pair<RealType,RealType> >::iterator rpi;
819	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
820	+	r1 = (*rpi).first;
821	+	r2 = (*rpi).second;
822	+	switch(rnemdType_) {
823	+	case rnemdKineticScale :
824	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
825	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
826	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
827	+	break;
828	+	case rnemdPxScale :
829	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
830	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
831	+	break;
832	+	case rnemdPyScale :
833	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
834	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
835	+	break;
836	+	case rnemdPzScale :
837	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
838	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
839	+	default :
840	+	break;
841	+	}
842	+	if (diff < smallestDiff) {
843	+	smallestDiff = diff;
844	+	bestPair = *rpi;
845	+	}
846	+	}
847	+	#ifdef IS_MPI
848	+	if (worldRank == 0) {
849	+	#endif
850	+	sprintf(painCave.errMsg,
851	+	"RNEMD: roots r1= %lf\tr2 = %lf\n",
852	+	bestPair.first, bestPair.second);
853	+	painCave.isFatal = 0;
854	+	painCave.severity = OPENMD_INFO;
855	+	simError();
856	+	#ifdef IS_MPI
857	+	}
858	+	#endif
859	+
860	+	RealType x, y, z;
861	+	switch(rnemdType_) {
862	+	case rnemdKineticScale :
863	+	x = bestPair.first;
864	+	y = bestPair.first;
865	+	z = bestPair.second;
866	+	break;
867	+	case rnemdPxScale :
868	+	x = c;
869	+	y = bestPair.first;
870	+	z = bestPair.second;
871	+	break;
872	+	case rnemdPyScale :
873	+	x = bestPair.first;
874	+	y = c;
875	+	z = bestPair.second;
876	+	break;
877	+	case rnemdPzScale :
878	+	x = bestPair.first;
879	+	y = bestPair.second;
880	+	z = c;
881	+	break;
882	+	default :
883	+	break;
884	+	}
885	+	vector<StuntDouble*>::iterator sdi;
886	+	Vector3d vel;
887	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
888	+	vel = (*sdi)->getVel();
889	+	vel.x() *= x;
890	+	vel.y() *= y;
891	+	vel.z() *= z;
892	+	(*sdi)->setVel(vel);
893	+	}
894	+	//convert to hotBin coefficient
895	+	x = 1.0 + px * (1.0 - x);
896	+	y = 1.0 + py * (1.0 - y);
897	+	z = 1.0 + pz * (1.0 - z);
898	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
899	+	vel = (*sdi)->getVel();
900	+	vel.x() *= x;
901	+	vel.y() *= y;
902	+	vel.z() *= z;
903	+	(*sdi)->setVel(vel);
904	+	}
905	+	exchangeSum_ += targetFlux_;
906	+	//we may want to check whether the exchange has been successful
907	+	} else {
908	+	sprintf(painCave.errMsg,
909	+	"RNEMD: exchange NOT performed!\n");
910	+	painCave.isFatal = 0;
911	+	painCave.severity = OPENMD_INFO;
912	+	simError();
913	+	failTrialCount_++;
914	+	}
915	+
916	+	}
917	+
918	+	void RNEMD::doRNEMD() {
919	+
920	+	switch(rnemdType_) {
921	+	case rnemdKineticScale :
922	+	case rnemdPxScale :
923	+	case rnemdPyScale :
924	+	case rnemdPzScale :
925	+	doScale();
926	+	break;
927	+	case rnemdKineticSwap :
928	+	case rnemdPx :
929	+	case rnemdPy :
930	+	case rnemdPz :
931	+	doSwap();
932	+	break;
933	+	case rnemdUnknown :
934	+	default :
935	+	break;
936	+	}
937	+	}
938	+
939	+	void RNEMD::collectData() {
940	+
941	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
942	+	Mat3x3d hmat = currentSnap_->getHmat();
943	+
944	+	seleMan_.setSelectionSet(evaluator_.evaluate());
945	+
946	+	int selei;
947	+	StuntDouble* sd;
948	+	int idx;
949	+
950	+	// alternative approach, track all molecules instead of only those
951	+	// selected for scaling/swapping:
952	+	/*
953	+	SimInfo::MoleculeIterator miter;
954	+	vector<StuntDouble*>::iterator iiter;
955	+	Molecule* mol;
956	+	StuntDouble* integrableObject;
957	+	for (mol = info_->beginMolecule(miter); mol != NULL;
958	+	mol = info_->nextMolecule(miter))
959	+	integrableObject is essentially sd
960	+	for (integrableObject = mol->beginIntegrableObject(iiter);
961	+	integrableObject != NULL;
962	+	integrableObject = mol->nextIntegrableObject(iiter))
963	+	*/
964	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
965	+	sd = seleMan_.nextSelected(selei)) {
966
967		idx = sd->getLocalIndex();
968
#	Line 477 | Line 976 | namespace oopse {
976		// which bin is this stuntdouble in?
977		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
978
979	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
980	<
979	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
980	>	rnemdLogWidth_;
981	>	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
982	>	/*
983	>	if (rnemdLogWidth_ == midBin_ + 1)
984	>	if (binNo > midBin_)
985	>	binNo = nBins_ - binNo;
986	>	*/
987		RealType mass = sd->getMass();
988		Vector3d vel = sd->getVel();
989		RealType value;
990	+	RealType xVal, yVal, zVal;
991
992		switch(rnemdType_) {
993	<	case rnemdKinetic :
993	>	case rnemdKineticSwap :
994	>	case rnemdKineticScale :
995
996	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
490	<	vel[2]*vel[2]);
996	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
997
998	<	valueCount[binNo] += 3;
998	>	valueCount_[binNo] += 3;
999		if (sd->isDirectional()) {
1000		Vector3d angMom = sd->getJ();
1001		Mat3x3d I = sd->getI();
#	Line 500 | Line 1006 | namespace oopse {
1006		int k = (i + 2) % 3;
1007		value += angMom[j] * angMom[j] / I(j, j) +
1008		angMom[k] * angMom[k] / I(k, k);
1009	<
1010	<	valueCount[binNo] +=2;
1011	<
1009	>
1010	>	valueCount_[binNo] +=2;
1011	>
1012		} else {
1013		value += angMom[0]*angMom[0]/I(0, 0)
1014		+ angMom[1]*angMom[1]/I(1, 1)
1015		+ angMom[2]*angMom[2]/I(2, 2);
1016	<	valueCount[binNo] +=3;
1016	>	valueCount_[binNo] +=3;
1017		}
1018		}
1019	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
1020	<
1019	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1020	>
1021		break;
1022		case rnemdPx :
1023	+	case rnemdPxScale :
1024		value = mass * vel[0];
1025	<	valueCount[binNo]++;
1025	>	valueCount_[binNo]++;
1026		break;
1027		case rnemdPy :
1028	+	case rnemdPyScale :
1029		value = mass * vel[1];
1030	<	valueCount[binNo]++;
1030	>	valueCount_[binNo]++;
1031		break;
1032		case rnemdPz :
1033	<	value = mass * vel[2];
1034	<	valueCount[binNo]++;
1033	>	case rnemdPzScale :
1034	>	value = pos.z(); //temporarily for homogeneous systems ONLY
1035	>	valueCount_[binNo]++;
1036		break;
1037		case rnemdUnknown :
1038		default :
1039	+	value = 1.0;
1040	+	valueCount_[binNo]++;
1041		break;
1042		}
1043	<	valueHist[binNo] += value;
1043	>	valueHist_[binNo] += value;
1044	>
1045	>	if (output3DTemp_) {
1046	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1047	>	/ PhysicalConstants::kb;
1048	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1049	>	/ PhysicalConstants::kb;
1050	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1051	>	/ PhysicalConstants::kb;
1052	>	xTempHist_[binNo] += xVal;
1053	>	yTempHist_[binNo] += yVal;
1054	>	zTempHist_[binNo] += zVal;
1055	>	xyzTempCount_[binNo]++;
1056	>	}
1057		}
1058	+	}
1059
1060	+	void RNEMD::getStarted() {
1061	+	collectData();
1062	+	/* now should be able to output profile in step 0, but might not be useful
1063	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1064	+	Stats& stat = currentSnap_->statData;
1065	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1066	+	*/
1067	+	getStatus();
1068	+	}
1069	+
1070	+	void RNEMD::getStatus() {
1071	+
1072	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1073	+	Stats& stat = currentSnap_->statData;
1074	+	RealType time = currentSnap_->getTime();
1075	+
1076	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1077	+	//or to be more meaningful, define another item as exchangeSum_ / time
1078	+	int j;
1079	+
1080		#ifdef IS_MPI
1081
1082		// all processors have the same number of bins, and STL vectors pack their
1083		// arrays, so in theory, this should be safe:
1084
1085	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1086	<	nBins_, MPI::REALTYPE, MPI::SUM);
1087	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1088	<	nBins_, MPI::INT, MPI::SUM);
1089	<
1085	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1086	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1087	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1088	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1089	>	if (output3DTemp_) {
1090	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1091	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1092	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1093	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1094	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1095	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1096	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1097	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1098	>	}
1099		// If we're the root node, should we print out the results
1100		int worldRank = MPI::COMM_WORLD.Get_rank();
1101		if (worldRank == 0) {
1102		#endif
1103	<
1104	<	std::cout << time;
1105	<	for (int j = 0; j < nBins_; j++)
1106	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1107	<	std::cout << "\n";
1108	<
1103	>	rnemdLog_ << time;
1104	>	for (j = 0; j < rnemdLogWidth_; j++) {
1105	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1106	>	}
1107	>	rnemdLog_ << "\n";
1108	>	if (output3DTemp_) {
1109	>	xTempLog_ << time;
1110	>	for (j = 0; j < rnemdLogWidth_; j++) {
1111	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1112	>	}
1113	>	xTempLog_ << "\n";
1114	>	yTempLog_ << time;
1115	>	for (j = 0; j < rnemdLogWidth_; j++) {
1116	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1117	>	}
1118	>	yTempLog_ << "\n";
1119	>	zTempLog_ << time;
1120	>	for (j = 0; j < rnemdLogWidth_; j++) {
1121	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1122	>	}
1123	>	zTempLog_ << "\n";
1124	>	}
1125		#ifdef IS_MPI
1126		}
1127		#endif
1128	+	for (j = 0; j < rnemdLogWidth_; j++) {
1129	+	valueCount_[j] = 0;
1130	+	valueHist_[j] = 0.0;
1131	+	}
1132	+	if (output3DTemp_)
1133	+	for (j = 0; j < rnemdLogWidth_; j++) {
1134	+	xTempHist_[j] = 0.0;
1135	+	yTempHist_[j] = 0.0;
1136	+	zTempHist_[j] = 0.0;
1137	+	xyzTempCount_[j] = 0;
1138	+	}
1139		}
1140		}

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines