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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1722 by gezelter, Thu May 24 14:23:40 2012 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/Vector.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
#	Line 55 | Line 58
58
59		#define HONKING_LARGE_VALUE 1.0e10
60
61	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
65	<
64	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
65	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
66	>
67	>	failTrialCount_ = 0;
68	>	failRootCount_ = 0;
69	>
70		int seedValue;
71		Globals * simParams = info->getSimParams();
72
73	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
73	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
74	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
75	>	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
76	>	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
77	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
78	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
79	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
80		stringToEnumMap_["Px"] = rnemdPx;
81		stringToEnumMap_["Py"] = rnemdPy;
82		stringToEnumMap_["Pz"] = rnemdPz;
83	+	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
84	+	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
85		stringToEnumMap_["Unknown"] = rnemdUnknown;
86
87		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
88		evaluator_.loadScriptString(rnemdObjectSelection_);
89		seleMan_.setSelectionSet(evaluator_.evaluate());
90
75	–
91		// do some sanity checking
92
93		int selectionCount = seleMan_.getSelectionCount();
#	Line 80 | Line 95 | namespace oopse {
95
96		if (selectionCount > nIntegrable) {
97		sprintf(painCave.errMsg,
98	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
98	>	"RNEMD: The current RNEMD_objectSelection,\n"
99		"\t\t%s\n"
100		"\thas resulted in %d selected objects.  However,\n"
101		"\tthe total number of integrable objects in the system\n"
#	Line 90 | Line 105 | namespace oopse {
105		rnemdObjectSelection_.c_str(),
106		selectionCount, nIntegrable);
107		painCave.isFatal = 0;
108	+	painCave.severity = OPENMD_WARNING;
109		simError();
94	–
110		}
111
112	<	const std::string st = simParams->getRNEMD_swapType();
112	>	const string st = simParams->getRNEMD_exchangeType();
113
114	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
114	>	map<string, RNEMDTypeEnum>::iterator i;
115		i = stringToEnumMap_.find(st);
116	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
116	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
117	>	if (rnemdType_ == rnemdUnknown) {
118	>	sprintf(painCave.errMsg,
119	>	"RNEMD: The current RNEMD_exchangeType,\n"
120	>	"\t\t%s\n"
121	>	"\tis not one of the recognized exchange types.\n",
122	>	st.c_str());
123	>	painCave.isFatal = 1;
124	>	painCave.severity = OPENMD_ERROR;
125	>	simError();
126	>	}
127	>
128	>	outputTemp_ = false;
129	>	if (simParams->haveRNEMD_outputTemperature()) {
130	>	outputTemp_ = simParams->getRNEMD_outputTemperature();
131	>	} else if ((rnemdType_ == rnemdKineticSwap) ||
132	>	(rnemdType_ == rnemdKineticScale) ||
133	>	(rnemdType_ == rnemdKineticScaleVAM) ||
134	>	(rnemdType_ == rnemdKineticScaleAM)) {
135	>	outputTemp_ = true;
136	>	}
137	>	outputVx_ = false;
138	>	if (simParams->haveRNEMD_outputVx()) {
139	>	outputVx_ = simParams->getRNEMD_outputVx();
140	>	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
141	>	outputVx_ = true;
142	>	}
143	>	outputVy_ = false;
144	>	if (simParams->haveRNEMD_outputVy()) {
145	>	outputVy_ = simParams->getRNEMD_outputVy();
146	>	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
147	>	outputVy_ = true;
148	>	}
149	>	output3DTemp_ = false;
150	>	if (simParams->haveRNEMD_outputXyzTemperature()) {
151	>	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
152	>	}
153	>	outputRotTemp_ = false;
154	>	if (simParams->haveRNEMD_outputRotTemperature()) {
155	>	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
156	>	}
157
158	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
158	>	#ifdef IS_MPI
159	>	if (worldRank == 0) {
160	>	#endif
161	>
162	>	//may have rnemdWriter separately
163	>	string rnemdFileName;
164	>
165	>	if (outputTemp_) {
166	>	rnemdFileName = "temperature.log";
167	>	tempLog_.open(rnemdFileName.c_str());
168	>	}
169	>	if (outputVx_) {
170	>	rnemdFileName = "velocityX.log";
171	>	vxzLog_.open(rnemdFileName.c_str());
172	>	}
173	>	if (outputVy_) {
174	>	rnemdFileName = "velocityY.log";
175	>	vyzLog_.open(rnemdFileName.c_str());
176	>	}
177	>
178	>	if (output3DTemp_) {
179	>	rnemdFileName = "temperatureX.log";
180	>	xTempLog_.open(rnemdFileName.c_str());
181	>	rnemdFileName = "temperatureY.log";
182	>	yTempLog_.open(rnemdFileName.c_str());
183	>	rnemdFileName = "temperatureZ.log";
184	>	zTempLog_.open(rnemdFileName.c_str());
185	>	}
186	>	if (outputRotTemp_) {
187	>	rnemdFileName = "temperatureR.log";
188	>	rotTempLog_.open(rnemdFileName.c_str());
189	>	}
190	>
191	>	#ifdef IS_MPI
192	>	}
193	>	#endif
194	>
195	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
196		set_RNEMD_nBins(simParams->getRNEMD_nBins());
197	<	exchangeSum_ = 0.0;
197	>	midBin_ = nBins_ / 2;
198	>	if (simParams->haveRNEMD_binShift()) {
199	>	if (simParams->getRNEMD_binShift()) {
200	>	zShift_ = 0.5 / (RealType)(nBins_);
201	>	} else {
202	>	zShift_ = 0.0;
203	>	}
204	>	} else {
205	>	zShift_ = 0.0;
206	>	}
207	>	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
208	>	//shift slabs by half slab width, maybe useful in heterogeneous systems
209	>	//set to 0.0 if not using it; N/A in status output yet
210	>	if (simParams->haveRNEMD_logWidth()) {
211	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
212	>	/*arbitary rnemdLogWidth_, no checking;
213	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
214	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
215	>	cerr << "Automaically set back to default.\n";
216	>	rnemdLogWidth_ = nBins_;
217	>	}*/
218	>	} else {
219	>	set_RNEMD_logWidth(nBins_);
220	>	}
221	>	tempHist_.resize(rnemdLogWidth_, 0.0);
222	>	tempCount_.resize(rnemdLogWidth_, 0);
223	>	pxzHist_.resize(rnemdLogWidth_, 0.0);
224	>	//vxzCount_.resize(rnemdLogWidth_, 0);
225	>	pyzHist_.resize(rnemdLogWidth_, 0.0);
226	>	//vyzCount_.resize(rnemdLogWidth_, 0);
227	>
228	>	mHist_.resize(rnemdLogWidth_, 0.0);
229	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
230	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
231	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
232	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
233	>	rotTempHist_.resize(rnemdLogWidth_, 0.0);
234	>	rotTempCount_.resize(rnemdLogWidth_, 0);
235	>
236	>	set_RNEMD_exchange_total(0.0);
237	>	if (simParams->haveRNEMD_targetFlux()) {
238	>	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
239	>	} else {
240	>	set_RNEMD_target_flux(0.0);
241	>	}
242	>	if (simParams->haveRNEMD_targetJzKE()) {
243	>	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
244	>	} else {
245	>	set_RNEMD_target_JzKE(0.0);
246	>	}
247	>	if (simParams->haveRNEMD_targetJzpx()) {
248	>	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
249	>	} else {
250	>	set_RNEMD_target_jzpx(0.0);
251	>	}
252	>	jzp_.x() = targetJzpx_;
253	>	njzp_.x() = -targetJzpx_;
254	>	if (simParams->haveRNEMD_targetJzpy()) {
255	>	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
256	>	} else {
257	>	set_RNEMD_target_jzpy(0.0);
258	>	}
259	>	jzp_.y() = targetJzpy_;
260	>	njzp_.y() = -targetJzpy_;
261	>	if (simParams->haveRNEMD_targetJzpz()) {
262	>	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
263	>	} else {
264	>	set_RNEMD_target_jzpz(0.0);
265	>	}
266	>	jzp_.z() = targetJzpz_;
267	>	njzp_.z() = -targetJzpz_;
268
269		#ifndef IS_MPI
270		if (simParams->haveSeed()) {
#	Line 123 | Line 285 | namespace oopse {
285
286		RNEMD::~RNEMD() {
287		delete randNumGen_;
288	+
289	+	#ifdef IS_MPI
290	+	if (worldRank == 0) {
291	+	#endif
292	+
293	+	sprintf(painCave.errMsg,
294	+	"RNEMD: total failed trials: %d\n",
295	+	failTrialCount_);
296	+	painCave.isFatal = 0;
297	+	painCave.severity = OPENMD_INFO;
298	+	simError();
299	+
300	+	if (outputTemp_) tempLog_.close();
301	+	if (outputVx_)   vxzLog_.close();
302	+	if (outputVy_)   vyzLog_.close();
303	+
304	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
305	+	rnemdType_ == rnemdPyScale) {
306	+	sprintf(painCave.errMsg,
307	+	"RNEMD: total root-checking warnings: %d\n",
308	+	failRootCount_);
309	+	painCave.isFatal = 0;
310	+	painCave.severity = OPENMD_INFO;
311	+	simError();
312	+	}
313	+	if (output3DTemp_) {
314	+	xTempLog_.close();
315	+	yTempLog_.close();
316	+	zTempLog_.close();
317	+	}
318	+	if (outputRotTemp_) rotTempLog_.close();
319	+
320	+	#ifdef IS_MPI
321	+	}
322	+	#endif
323		}
324
325		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
326
327		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
328		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 160 | Line 356 | namespace oopse {
356		// which bin is this stuntdouble in?
357		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
358
359	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
359	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
360
361
362		// if we're in bin 0 or the middleBin
363	<	if (binNo == 0 || binNo == midBin) {
363	>	if (binNo == 0 || binNo == midBin_) {
364
365		RealType mass = sd->getMass();
366		Vector3d vel = sd->getVel();
367		RealType value;
368
369		switch(rnemdType_) {
370	<	case rnemdKinetic :
370	>	case rnemdKineticSwap :
371
372	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
373	<	vel[2]*vel[2]);
374	<	if (sd->isDirectional()) {
372	>	value = mass * vel.lengthSquare();
373	>
374	>	if (sd->isDirectional()) {
375		Vector3d angMom = sd->getJ();
376		Mat3x3d I = sd->getI();
377
378		if (sd->isLinear()) {
379	<	int i = sd->linearAxis();
380	<	int j = (i + 1) % 3;
381	<	int k = (i + 2) % 3;
382	<	value += angMom[j] * angMom[j] / I(j, j) +
383	<	angMom[k] * angMom[k] / I(k, k);
379	>	int i = sd->linearAxis();
380	>	int j = (i + 1) % 3;
381	>	int k = (i + 2) % 3;
382	>	value += angMom[j] * angMom[j] / I(j, j) +
383	>	angMom[k] * angMom[k] / I(k, k);
384		} else {
385	<	value += angMom[0]*angMom[0]/I(0, 0)
386	<	+ angMom[1]*angMom[1]/I(1, 1)
387	<	+ angMom[2]*angMom[2]/I(2, 2);
385	>	value += angMom[0]*angMom[0]/I(0, 0)
386	>	+ angMom[1]*angMom[1]/I(1, 1)
387	>	+ angMom[2]*angMom[2]/I(2, 2);
388		}
389	<	}
390	<	value = value * 0.5 / OOPSEConstant::energyConvert;
389	>	} //angular momenta exchange enabled
390	>	//energyConvert temporarily disabled
391	>	//make exchangeSum_ comparable between swap & scale
392	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
393	>	value *= 0.5;
394		break;
395		case rnemdPx :
396		value = mass * vel[0];
#	Line 202 | Line 401 | namespace oopse {
401		case rnemdPz :
402		value = mass * vel[2];
403		break;
205	–	case rnemdUnknown :
404		default :
405		break;
406		}
#	Line 218 | Line 416 | namespace oopse {
416		min_sd = sd;
417		}
418		}
419	<	} else {
419	>	} else { //midBin_
420		if (!max_found) {
421		max_val = value;
422		max_sd = sd;
#	Line 243 | Line 441 | namespace oopse {
441		bool my_max_found = max_found;
442
443		// Even if we didn't find a minimum, did someone else?
444	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
444	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
445		// Even if we didn't find a maximum, did someone else?
446	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
447	<	1, MPI::BOOL, MPI::LAND);
446	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
447	>	#endif
448	>
449	>	if (max_found && min_found) {
450	>
451	>	#ifdef IS_MPI
452	>	struct {
453	>	RealType val;
454	>	int rank;
455	>	} max_vals, min_vals;
456
457	<	struct {
254	<	RealType val;
255	<	int rank;
256	<	} max_vals, min_vals;
257	<
258	<	if (min_found) {
259	<	if (my_min_found)
457	>	if (my_min_found) {
458		min_vals.val = min_val;
459	<	else
459	>	} else {
460		min_vals.val = HONKING_LARGE_VALUE;
461	<
461	>	}
462		min_vals.rank = worldRank;
463
464		// Who had the minimum?
465		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
466		1, MPI::REALTYPE_INT, MPI::MINLOC);
467		min_val = min_vals.val;
270	–	}
468
469	<	if (max_found) {
273	<	if (my_max_found)
469	>	if (my_max_found) {
470		max_vals.val = max_val;
471	<	else
471	>	} else {
472		max_vals.val = -HONKING_LARGE_VALUE;
473	<
473	>	}
474		max_vals.rank = worldRank;
475
476		// Who had the maximum?
477		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
478		1, MPI::REALTYPE_INT, MPI::MAXLOC);
479		max_val = max_vals.val;
284	–	}
480		#endif
481	<
482	<	if (max_found && min_found) {
483	<	if (min_val< max_val) {
289	<
481	>
482	>	if (min_val < max_val) {
483	>
484		#ifdef IS_MPI
485		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
486		// I have both maximum and minimum, so proceed like a single
487		// processor version:
488		#endif
489	<	// objects to be swapped: velocity & angular velocity
489	>
490		Vector3d min_vel = min_sd->getVel();
491		Vector3d max_vel = max_sd->getVel();
492		RealType temp_vel;
493
494		switch(rnemdType_) {
495	<	case rnemdKinetic :
495	>	case rnemdKineticSwap :
496		min_sd->setVel(max_vel);
497		max_sd->setVel(min_vel);
498	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
498	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
499		Vector3d min_angMom = min_sd->getJ();
500		Vector3d max_angMom = max_sd->getJ();
501		min_sd->setJ(max_angMom);
502		max_sd->setJ(min_angMom);
503	<	}
503	>	}//angular momenta exchange enabled
504	>	//assumes same rigid body identity
505		break;
506		case rnemdPx :
507		temp_vel = min_vel.x();
#	Line 329 | Line 524 | namespace oopse {
524		min_sd->setVel(min_vel);
525		max_sd->setVel(max_vel);
526		break;
332	–	case rnemdUnknown :
527		default :
528		break;
529		}
530	+
531		#ifdef IS_MPI
532		// the rest of the cases only apply in parallel simulations:
533		} else if (max_vals.rank == worldRank) {
#	Line 349 | Line 544 | namespace oopse {
544		min_vals.rank, 0, status);
545
546		switch(rnemdType_) {
547	<	case rnemdKinetic :
547	>	case rnemdKineticSwap :
548		max_sd->setVel(min_vel);
549	<
549	>	//angular momenta exchange enabled
550		if (max_sd->isDirectional()) {
551		Vector3d min_angMom;
552		Vector3d max_angMom = max_sd->getJ();
553	<
553	>
554		// point-to-point swap of the angular momentum vector
555		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
556		MPI::REALTYPE, min_vals.rank, 1,
557		min_angMom.getArrayPointer(), 3,
558		MPI::REALTYPE, min_vals.rank, 1,
559		status);
560	<
560	>
561		max_sd->setJ(min_angMom);
562	<	}
562	>	}
563		break;
564		case rnemdPx :
565		max_vel.x() = min_vel.x();
#	Line 378 | Line 573 | namespace oopse {
573		max_vel.z() = min_vel.z();
574		max_sd->setVel(max_vel);
575		break;
381	–	case rnemdUnknown :
576		default :
577		break;
578		}
#	Line 396 | Line 590 | namespace oopse {
590		max_vals.rank, 0, status);
591
592		switch(rnemdType_) {
593	<	case rnemdKinetic :
593	>	case rnemdKineticSwap :
594		min_sd->setVel(max_vel);
595	<
595	>	//angular momenta exchange enabled
596		if (min_sd->isDirectional()) {
597		Vector3d min_angMom = min_sd->getJ();
598		Vector3d max_angMom;
599	<
599	>
600		// point-to-point swap of the angular momentum vector
601		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
602		MPI::REALTYPE, max_vals.rank, 1,
603		max_angMom.getArrayPointer(), 3,
604		MPI::REALTYPE, max_vals.rank, 1,
605		status);
606	<
606	>
607		min_sd->setJ(max_angMom);
608		}
609		break;
#	Line 425 | Line 619 | namespace oopse {
619		min_vel.z() = max_vel.z();
620		min_sd->setVel(min_vel);
621		break;
428	–	case rnemdUnknown :
622		default :
623		break;
624		}
625		}
626		#endif
627		exchangeSum_ += max_val - min_val;
628	<	} else {
629	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
628	>	} else {
629	>	sprintf(painCave.errMsg,
630	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
631	>	painCave.isFatal = 0;
632	>	painCave.severity = OPENMD_INFO;
633	>	simError();
634	>	failTrialCount_++;
635		}
636		} else {
637	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
637	>	sprintf(painCave.errMsg,
638	>	"RNEMD: exchange NOT performed because selected object\n"
639	>	"\tnot present in at least one of the two slabs.\n");
640	>	painCave.isFatal = 0;
641	>	painCave.severity = OPENMD_INFO;
642	>	simError();
643	>	failTrialCount_++;
644		}
645
646		}
647
648	<	void RNEMD::getStatus() {
648	>	void RNEMD::doScale() {
649
650		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
651		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
652
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
653		seleMan_.setSelectionSet(evaluator_.evaluate());
654
655		int selei;
656		StuntDouble* sd;
657		int idx;
658
659	<	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
659	>	vector<StuntDouble*> hotBin, coldBin;
660
661	+	RealType Phx = 0.0;
662	+	RealType Phy = 0.0;
663	+	RealType Phz = 0.0;
664	+	RealType Khx = 0.0;
665	+	RealType Khy = 0.0;
666	+	RealType Khz = 0.0;
667	+	RealType Khw = 0.0;
668	+	RealType Pcx = 0.0;
669	+	RealType Pcy = 0.0;
670	+	RealType Pcz = 0.0;
671	+	RealType Kcx = 0.0;
672	+	RealType Kcy = 0.0;
673	+	RealType Kcz = 0.0;
674	+	RealType Kcw = 0.0;
675	+
676		for (sd = seleMan_.beginSelected(selei); sd != NULL;
677		sd = seleMan_.nextSelected(selei)) {
678	+
679	+	idx = sd->getLocalIndex();
680	+
681	+	Vector3d pos = sd->getPos();
682	+
683	+	// wrap the stuntdouble's position back into the box:
684	+
685	+	if (usePeriodicBoundaryConditions_)
686	+	currentSnap_->wrapVector(pos);
687	+
688	+	// which bin is this stuntdouble in?
689	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
690	+
691	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
692	+
693	+	// if we're in bin 0 or the middleBin
694	+	if (binNo == 0 || binNo == midBin_) {
695	+
696	+	RealType mass = sd->getMass();
697	+	Vector3d vel = sd->getVel();
698	+
699	+	if (binNo == 0) {
700	+	hotBin.push_back(sd);
701	+	Phx += mass * vel.x();
702	+	Phy += mass * vel.y();
703	+	Phz += mass * vel.z();
704	+	Khx += mass * vel.x() * vel.x();
705	+	Khy += mass * vel.y() * vel.y();
706	+	Khz += mass * vel.z() * vel.z();
707	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
708	+	if (sd->isDirectional()) {
709	+	Vector3d angMom = sd->getJ();
710	+	Mat3x3d I = sd->getI();
711	+	if (sd->isLinear()) {
712	+	int i = sd->linearAxis();
713	+	int j = (i + 1) % 3;
714	+	int k = (i + 2) % 3;
715	+	Khw += angMom[j] * angMom[j] / I(j, j) +
716	+	angMom[k] * angMom[k] / I(k, k);
717	+	} else {
718	+	Khw += angMom[0]*angMom[0]/I(0, 0)
719	+	+ angMom[1]*angMom[1]/I(1, 1)
720	+	+ angMom[2]*angMom[2]/I(2, 2);
721	+	}
722	+	}
723	+	//}
724	+	} else { //midBin_
725	+	coldBin.push_back(sd);
726	+	Pcx += mass * vel.x();
727	+	Pcy += mass * vel.y();
728	+	Pcz += mass * vel.z();
729	+	Kcx += mass * vel.x() * vel.x();
730	+	Kcy += mass * vel.y() * vel.y();
731	+	Kcz += mass * vel.z() * vel.z();
732	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
733	+	if (sd->isDirectional()) {
734	+	Vector3d angMom = sd->getJ();
735	+	Mat3x3d I = sd->getI();
736	+	if (sd->isLinear()) {
737	+	int i = sd->linearAxis();
738	+	int j = (i + 1) % 3;
739	+	int k = (i + 2) % 3;
740	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
741	+	angMom[k] * angMom[k] / I(k, k);
742	+	} else {
743	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
744	+	+ angMom[1]*angMom[1]/I(1, 1)
745	+	+ angMom[2]*angMom[2]/I(2, 2);
746	+	}
747	+	}
748	+	//}
749	+	}
750	+	}
751	+	}
752	+
753	+	Khx *= 0.5;
754	+	Khy *= 0.5;
755	+	Khz *= 0.5;
756	+	Khw *= 0.5;
757	+	Kcx *= 0.5;
758	+	Kcy *= 0.5;
759	+	Kcz *= 0.5;
760	+	Kcw *= 0.5;
761	+
762	+	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
763	+	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
764	+	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
765	+	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
766	+	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
767	+
768	+	#ifdef IS_MPI
769	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
770	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
771	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
772	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
773	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
774	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
775	+
776	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
777	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
778	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
779	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
780	+
781	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
782	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
783	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
784	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
785	+	#endif
786	+
787	+	//solve coldBin coeff's first
788	+	RealType px = Pcx / Phx;
789	+	RealType py = Pcy / Phy;
790	+	RealType pz = Pcz / Phz;
791	+	RealType c, x, y, z;
792	+	bool successfulScale = false;
793	+	if ((rnemdType_ == rnemdKineticScaleVAM) ||
794	+	(rnemdType_ == rnemdKineticScaleAM)) {
795	+	//may need sanity check Khw & Kcw > 0
796	+
797	+	if (rnemdType_ == rnemdKineticScaleVAM) {
798	+	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
799	+	} else {
800	+	c = 1.0 - targetFlux_ / Kcw;
801	+	}
802	+
803	+	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
804	+	c = sqrt(c);
805	+	std::cerr << "cold slab scaling coefficient: " << c << endl;
806	+	//now convert to hotBin coefficient
807	+	RealType w = 0.0;
808	+	if (rnemdType_ ==  rnemdKineticScaleVAM) {
809	+	x = 1.0 + px * (1.0 - c);
810	+	y = 1.0 + py * (1.0 - c);
811	+	z = 1.0 + pz * (1.0 - c);
812	+	/* more complicated way
813	+	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
814	+	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
815	+	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
816	+	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
817	+	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
818	+	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
819	+	*/
820	+	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
821	+	(fabs(z - 1.0) < 0.1)) {
822	+	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
823	+	+ Khz * (1.0 - z * z)) / Khw;
824	+	}//no need to calculate w if x, y or z is out of range
825	+	} else {
826	+	w = 1.0 + targetFlux_ / Khw;
827	+	}
828	+	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
829	+	//if w is in the right range, so should be x, y, z.
830	+	vector<StuntDouble*>::iterator sdi;
831	+	Vector3d vel;
832	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
833	+	if (rnemdType_ == rnemdKineticScaleVAM) {
834	+	vel = (*sdi)->getVel() * c;
835	+	//vel.x() *= c;
836	+	//vel.y() *= c;
837	+	//vel.z() *= c;
838	+	(*sdi)->setVel(vel);
839	+	}
840	+	if ((*sdi)->isDirectional()) {
841	+	Vector3d angMom = (*sdi)->getJ() * c;
842	+	//angMom[0] *= c;
843	+	//angMom[1] *= c;
844	+	//angMom[2] *= c;
845	+	(*sdi)->setJ(angMom);
846	+	}
847	+	}
848	+	w = sqrt(w);
849	+	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
850	+	<< "\twh= " << w << endl;
851	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
852	+	if (rnemdType_ == rnemdKineticScaleVAM) {
853	+	vel = (*sdi)->getVel();
854	+	vel.x() *= x;
855	+	vel.y() *= y;
856	+	vel.z() *= z;
857	+	(*sdi)->setVel(vel);
858	+	}
859	+	if ((*sdi)->isDirectional()) {
860	+	Vector3d angMom = (*sdi)->getJ() * w;
861	+	//angMom[0] *= w;
862	+	//angMom[1] *= w;
863	+	//angMom[2] *= w;
864	+	(*sdi)->setJ(angMom);
865	+	}
866	+	}
867	+	successfulScale = true;
868	+	exchangeSum_ += targetFlux_;
869	+	}
870	+	}
871	+	} else {
872	+	RealType a000, a110, c0, a001, a111, b01, b11, c1;
873	+	switch(rnemdType_) {
874	+	case rnemdKineticScale :
875	+	/* used hotBin coeff's & only scale x & y dimensions
876	+	RealType px = Phx / Pcx;
877	+	RealType py = Phy / Pcy;
878	+	a110 = Khy;
879	+	c0 = - Khx - Khy - targetFlux_;
880	+	a000 = Khx;
881	+	a111 = Kcy * py * py;
882	+	b11 = -2.0 * Kcy * py * (1.0 + py);
883	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
884	+	b01 = -2.0 * Kcx * px * (1.0 + px);
885	+	a001 = Kcx * px * px;
886	+	*/
887	+	//scale all three dimensions, let c_x = c_y
888	+	a000 = Kcx + Kcy;
889	+	a110 = Kcz;
890	+	c0 = targetFlux_ - Kcx - Kcy - Kcz;
891	+	a001 = Khx * px * px + Khy * py * py;
892	+	a111 = Khz * pz * pz;
893	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
894	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
895	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
896	+	+ Khz * pz * (2.0 + pz) - targetFlux_;
897	+	break;
898	+	case rnemdPxScale :
899	+	c = 1 - targetFlux_ / Pcx;
900	+	a000 = Kcy;
901	+	a110 = Kcz;
902	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
903	+	a001 = py * py * Khy;
904	+	a111 = pz * pz * Khz;
905	+	b01 = -2.0 * Khy * py * (1.0 + py);
906	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
907	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
908	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
909	+	break;
910	+	case rnemdPyScale :
911	+	c = 1 - targetFlux_ / Pcy;
912	+	a000 = Kcx;
913	+	a110 = Kcz;
914	+	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
915	+	a001 = px * px * Khx;
916	+	a111 = pz * pz * Khz;
917	+	b01 = -2.0 * Khx * px * (1.0 + px);
918	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
919	+	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
920	+	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
921	+	break;
922	+	case rnemdPzScale ://we don't really do this, do we?
923	+	c = 1 - targetFlux_ / Pcz;
924	+	a000 = Kcx;
925	+	a110 = Kcy;
926	+	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
927	+	a001 = px * px * Khx;
928	+	a111 = py * py * Khy;
929	+	b01 = -2.0 * Khx * px * (1.0 + px);
930	+	b11 = -2.0 * Khy * py * (1.0 + py);
931	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
932	+	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
933	+	break;
934	+	default :
935	+	break;
936	+	}
937	+
938	+	RealType v1 = a000 * a111 - a001 * a110;
939	+	RealType v2 = a000 * b01;
940	+	RealType v3 = a000 * b11;
941	+	RealType v4 = a000 * c1 - a001 * c0;
942	+	RealType v8 = a110 * b01;
943	+	RealType v10 = - b01 * c0;
944	+
945	+	RealType u0 = v2 * v10 - v4 * v4;
946	+	RealType u1 = -2.0 * v3 * v4;
947	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
948	+	RealType u3 = -2.0 * v1 * v3;
949	+	RealType u4 = - v1 * v1;
950	+	//rescale coefficients
951	+	RealType maxAbs = fabs(u0);
952	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
953	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
954	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
955	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
956	+	u0 /= maxAbs;
957	+	u1 /= maxAbs;
958	+	u2 /= maxAbs;
959	+	u3 /= maxAbs;
960	+	u4 /= maxAbs;
961	+	//max_element(start, end) is also available.
962	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
963	+	poly.setCoefficient(4, u4);
964	+	poly.setCoefficient(3, u3);
965	+	poly.setCoefficient(2, u2);
966	+	poly.setCoefficient(1, u1);
967	+	poly.setCoefficient(0, u0);
968	+	vector<RealType> realRoots = poly.FindRealRoots();
969	+
970	+	vector<RealType>::iterator ri;
971	+	RealType r1, r2, alpha0;
972	+	vector<pair<RealType,RealType> > rps;
973	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
974	+	r2 = *ri;
975	+	//check if FindRealRoots() give the right answer
976	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
977	+	sprintf(painCave.errMsg,
978	+	"RNEMD Warning: polynomial solve seems to have an error!");
979	+	painCave.isFatal = 0;
980	+	simError();
981	+	failRootCount_++;
982	+	}
983	+	//might not be useful w/o rescaling coefficients
984	+	alpha0 = -c0 - a110 * r2 * r2;
985	+	if (alpha0 >= 0.0) {
986	+	r1 = sqrt(alpha0 / a000);
987	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
988	+	< 1e-6)
989	+	{ rps.push_back(make_pair(r1, r2)); }
990	+	if (r1 > 1e-6) { //r1 non-negative
991	+	r1 = -r1;
992	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
993	+	< 1e-6)
994	+	{ rps.push_back(make_pair(r1, r2)); }
995	+	}
996	+	}
997	+	}
998	+	// Consider combining together the solving pair part w/ the searching
999	+	// best solution part so that we don't need the pairs vector
1000	+	if (!rps.empty()) {
1001	+	RealType smallestDiff = HONKING_LARGE_VALUE;
1002	+	RealType diff;
1003	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1004	+	vector<pair<RealType,RealType> >::iterator rpi;
1005	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1006	+	r1 = (*rpi).first;
1007	+	r2 = (*rpi).second;
1008	+	switch(rnemdType_) {
1009	+	case rnemdKineticScale :
1010	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1011	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1012	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1013	+	break;
1014	+	case rnemdPxScale :
1015	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1016	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1017	+	break;
1018	+	case rnemdPyScale :
1019	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1020	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1021	+	break;
1022	+	case rnemdPzScale :
1023	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1024	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1025	+	default :
1026	+	break;
1027	+	}
1028	+	if (diff < smallestDiff) {
1029	+	smallestDiff = diff;
1030	+	bestPair = *rpi;
1031	+	}
1032	+	}
1033	+	#ifdef IS_MPI
1034	+	if (worldRank == 0) {
1035	+	#endif
1036	+	sprintf(painCave.errMsg,
1037	+	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1038	+	bestPair.first, bestPair.second);
1039	+	painCave.isFatal = 0;
1040	+	painCave.severity = OPENMD_INFO;
1041	+	simError();
1042	+	#ifdef IS_MPI
1043	+	}
1044	+	#endif
1045	+
1046	+	switch(rnemdType_) {
1047	+	case rnemdKineticScale :
1048	+	x = bestPair.first;
1049	+	y = bestPair.first;
1050	+	z = bestPair.second;
1051	+	break;
1052	+	case rnemdPxScale :
1053	+	x = c;
1054	+	y = bestPair.first;
1055	+	z = bestPair.second;
1056	+	break;
1057	+	case rnemdPyScale :
1058	+	x = bestPair.first;
1059	+	y = c;
1060	+	z = bestPair.second;
1061	+	break;
1062	+	case rnemdPzScale :
1063	+	x = bestPair.first;
1064	+	y = bestPair.second;
1065	+	z = c;
1066	+	break;
1067	+	default :
1068	+	break;
1069	+	}
1070	+	vector<StuntDouble*>::iterator sdi;
1071	+	Vector3d vel;
1072	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1073	+	vel = (*sdi)->getVel();
1074	+	vel.x() *= x;
1075	+	vel.y() *= y;
1076	+	vel.z() *= z;
1077	+	(*sdi)->setVel(vel);
1078	+	}
1079	+	//convert to hotBin coefficient
1080	+	x = 1.0 + px * (1.0 - x);
1081	+	y = 1.0 + py * (1.0 - y);
1082	+	z = 1.0 + pz * (1.0 - z);
1083	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1084	+	vel = (*sdi)->getVel();
1085	+	vel.x() *= x;
1086	+	vel.y() *= y;
1087	+	vel.z() *= z;
1088	+	(*sdi)->setVel(vel);
1089	+	}
1090	+	successfulScale = true;
1091	+	exchangeSum_ += targetFlux_;
1092	+	}
1093	+	}
1094	+	if (successfulScale != true) {
1095	+	sprintf(painCave.errMsg,
1096	+	"RNEMD: exchange NOT performed!\n");
1097	+	painCave.isFatal = 0;
1098	+	painCave.severity = OPENMD_INFO;
1099	+	simError();
1100	+	failTrialCount_++;
1101	+	}
1102	+	}
1103	+
1104	+	void RNEMD::doShiftScale() {
1105	+
1106	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1107	+	Mat3x3d hmat = currentSnap_->getHmat();
1108	+
1109	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1110	+
1111	+	int selei;
1112	+	StuntDouble* sd;
1113	+	int idx;
1114	+
1115	+	vector<StuntDouble*> hotBin, coldBin;
1116	+
1117	+	Vector3d Ph(V3Zero);
1118	+	RealType Mh = 0.0;
1119	+	RealType Kh = 0.0;
1120	+	Vector3d Pc(V3Zero);
1121	+	RealType Mc = 0.0;
1122	+	RealType Kc = 0.0;
1123	+
1124	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1125	+	sd = seleMan_.nextSelected(selei)) {
1126	+
1127	+	idx = sd->getLocalIndex();
1128	+
1129	+	Vector3d pos = sd->getPos();
1130	+
1131	+	// wrap the stuntdouble's position back into the box:
1132	+
1133	+	if (usePeriodicBoundaryConditions_)
1134	+	currentSnap_->wrapVector(pos);
1135	+
1136	+	// which bin is this stuntdouble in?
1137	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1138	+
1139	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1140	+
1141	+	// if we're in bin 0 or the middleBin
1142	+	if (binNo == 0 || binNo == midBin_) {
1143	+
1144	+	RealType mass = sd->getMass();
1145	+	Vector3d vel = sd->getVel();
1146	+
1147	+	if (binNo == 0) {
1148	+	hotBin.push_back(sd);
1149	+	//std::cerr << "before, velocity = " << vel << endl;
1150	+	Ph += mass * vel;
1151	+	//std::cerr << "after, velocity = " << vel << endl;
1152	+	Mh += mass;
1153	+	Kh += mass * vel.lengthSquare();
1154	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1155	+	if (sd->isDirectional()) {
1156	+	Vector3d angMom = sd->getJ();
1157	+	Mat3x3d I = sd->getI();
1158	+	if (sd->isLinear()) {
1159	+	int i = sd->linearAxis();
1160	+	int j = (i + 1) % 3;
1161	+	int k = (i + 2) % 3;
1162	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1163	+	angMom[k] * angMom[k] / I(k, k);
1164	+	} else {
1165	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1166	+	angMom[1] * angMom[1] / I(1, 1) +
1167	+	angMom[2] * angMom[2] / I(2, 2);
1168	+	}
1169	+	}
1170	+	}
1171	+	} else { //midBin_
1172	+	coldBin.push_back(sd);
1173	+	Pc += mass * vel;
1174	+	Mc += mass;
1175	+	Kc += mass * vel.lengthSquare();
1176	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1177	+	if (sd->isDirectional()) {
1178	+	Vector3d angMom = sd->getJ();
1179	+	Mat3x3d I = sd->getI();
1180	+	if (sd->isLinear()) {
1181	+	int i = sd->linearAxis();
1182	+	int j = (i + 1) % 3;
1183	+	int k = (i + 2) % 3;
1184	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1185	+	angMom[k] * angMom[k] / I(k, k);
1186	+	} else {
1187	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1188	+	angMom[1] * angMom[1] / I(1, 1) +
1189	+	angMom[2] * angMom[2] / I(2, 2);
1190	+	}
1191	+	}
1192	+	}
1193	+	}
1194	+	}
1195	+	}
1196	+
1197	+	Kh *= 0.5;
1198	+	Kc *= 0.5;
1199	+
1200	+	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1201	+	<< "\tKc= " << Kc << endl;
1202	+	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1203	+
1204	+	#ifdef IS_MPI
1205	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1206	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1207	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1208	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1209	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1210	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1211	+	#endif
1212	+
1213	+	bool successfulExchange = false;
1214	+	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1215	+	Vector3d vc = Pc / Mc;
1216	+	Vector3d ac = njzp_ / Mc + vc;
1217	+	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1218	+	if (cNumerator > 0.0) {
1219	+	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1220	+	if (cDenominator > 0.0) {
1221	+	RealType c = sqrt(cNumerator / cDenominator);
1222	+	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1223	+	Vector3d vh = Ph / Mh;
1224	+	Vector3d ah = jzp_ / Mh + vh;
1225	+	RealType hNumerator = Kh + targetJzKE_
1226	+	- 0.5 * Mh * ah.lengthSquare();
1227	+	if (hNumerator > 0.0) {
1228	+	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1229	+	if (hDenominator > 0.0) {
1230	+	RealType h = sqrt(hNumerator / hDenominator);
1231	+	if ((h > 0.9) && (h < 1.1)) {
1232	+	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1233	+	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1234	+	vector<StuntDouble*>::iterator sdi;
1235	+	Vector3d vel;
1236	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1237	+	//vel = (*sdi)->getVel();
1238	+	vel = ((*sdi)->getVel() - vc) * c + ac;
1239	+	(*sdi)->setVel(vel);
1240	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1241	+	if ((*sdi)->isDirectional()) {
1242	+	Vector3d angMom = (*sdi)->getJ() * c;
1243	+	(*sdi)->setJ(angMom);
1244	+	}
1245	+	}
1246	+	}
1247	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1248	+	//vel = (*sdi)->getVel();
1249	+	vel = ((*sdi)->getVel() - vh) * h + ah;
1250	+	(*sdi)->setVel(vel);
1251	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1252	+	if ((*sdi)->isDirectional()) {
1253	+	Vector3d angMom = (*sdi)->getJ() * h;
1254	+	(*sdi)->setJ(angMom);
1255	+	}
1256	+	}
1257	+	}
1258	+	successfulExchange = true;
1259	+	exchangeSum_ += targetFlux_;
1260	+	// this is a redundant variable for doShiftScale() so that
1261	+	// RNEMD can output one exchange quantity needed in a job.
1262	+	// need a better way to do this.
1263	+	}
1264	+	}
1265	+	}
1266	+	}
1267	+	}
1268	+	}
1269	+	}
1270	+	if (successfulExchange != true) {
1271	+	sprintf(painCave.errMsg,
1272	+	"RNEMD: exchange NOT performed!\n");
1273	+	painCave.isFatal = 0;
1274	+	painCave.severity = OPENMD_INFO;
1275	+	simError();
1276	+	failTrialCount_++;
1277	+	}
1278	+	}
1279	+
1280	+	void RNEMD::doRNEMD() {
1281	+
1282	+	switch(rnemdType_) {
1283	+	case rnemdKineticScale :
1284	+	case rnemdKineticScaleVAM :
1285	+	case rnemdKineticScaleAM :
1286	+	case rnemdPxScale :
1287	+	case rnemdPyScale :
1288	+	case rnemdPzScale :
1289	+	doScale();
1290	+	break;
1291	+	case rnemdKineticSwap :
1292	+	case rnemdPx :
1293	+	case rnemdPy :
1294	+	case rnemdPz :
1295	+	doSwap();
1296	+	break;
1297	+	case rnemdShiftScaleV :
1298	+	case rnemdShiftScaleVAM :
1299	+	doShiftScale();
1300	+	break;
1301	+	case rnemdUnknown :
1302	+	default :
1303	+	break;
1304	+	}
1305	+	}
1306	+
1307	+	void RNEMD::collectData() {
1308	+
1309	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1310	+	Mat3x3d hmat = currentSnap_->getHmat();
1311	+
1312	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1313	+
1314	+	int selei;
1315	+	StuntDouble* sd;
1316	+	int idx;
1317	+
1318	+	// alternative approach, track all molecules instead of only those
1319	+	// selected for scaling/swapping:
1320	+	/*
1321	+	SimInfo::MoleculeIterator miter;
1322	+	vector<StuntDouble*>::iterator iiter;
1323	+	Molecule* mol;
1324	+	StuntDouble* integrableObject;
1325	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1326	+	mol = info_->nextMolecule(miter))
1327	+	integrableObject is essentially sd
1328	+	for (integrableObject = mol->beginIntegrableObject(iiter);
1329	+	integrableObject != NULL;
1330	+	integrableObject = mol->nextIntegrableObject(iiter))
1331	+	*/
1332	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1333	+	sd = seleMan_.nextSelected(selei)) {
1334
1335		idx = sd->getLocalIndex();
1336
#	Line 477 | Line 1344 | namespace oopse {
1344		// which bin is this stuntdouble in?
1345		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1346
1347	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1348	<
1347	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1348	>	rnemdLogWidth_;
1349	>	// no symmetrization allowed due to arbitary rnemdLogWidth_
1350	>	/*
1351	>	if (rnemdLogWidth_ == midBin_ + 1)
1352	>	if (binNo > midBin_)
1353	>	binNo = nBins_ - binNo;
1354	>	*/
1355		RealType mass = sd->getMass();
1356	+	mHist_[binNo] += mass;
1357		Vector3d vel = sd->getVel();
1358		RealType value;
1359	+	//RealType xVal, yVal, zVal;
1360
1361	<	switch(rnemdType_) {
1362	<	case rnemdKinetic :
1363	<
489	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
490	<	vel[2]*vel[2]);
491	<
492	<	valueCount[binNo] += 3;
1361	>	if (outputTemp_) {
1362	>	value = mass * vel.lengthSquare();
1363	>	tempCount_[binNo] += 3;
1364		if (sd->isDirectional()) {
1365		Vector3d angMom = sd->getJ();
1366		Mat3x3d I = sd->getI();
496	–
1367		if (sd->isLinear()) {
1368		int i = sd->linearAxis();
1369		int j = (i + 1) % 3;
1370		int k = (i + 2) % 3;
1371		value += angMom[j] * angMom[j] / I(j, j) +
1372		angMom[k] * angMom[k] / I(k, k);
1373	<
504	<	valueCount[binNo] +=2;
505	<
1373	>	tempCount_[binNo] +=2;
1374		} else {
1375	<	value += angMom[0]*angMom[0]/I(0, 0)
1376	<	+ angMom[1]*angMom[1]/I(1, 1)
1377	<	+ angMom[2]*angMom[2]/I(2, 2);
1378	<	valueCount[binNo] +=3;
1375	>	value += angMom[0] * angMom[0] / I(0, 0) +
1376	>	angMom[1]*angMom[1]/I(1, 1) +
1377	>	angMom[2]*angMom[2]/I(2, 2);
1378	>	tempCount_[binNo] +=3;
1379		}
1380		}
1381	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
1382	<
1383	<	break;
1384	<	case rnemdPx :
1381	>	value = value / PhysicalConstants::energyConvert
1382	>	/ PhysicalConstants::kb;//may move to getStatus()
1383	>	tempHist_[binNo] += value;
1384	>	}
1385	>	if (outputVx_) {
1386		value = mass * vel[0];
1387	<	valueCount[binNo]++;
1388	<	break;
1389	<	case rnemdPy :
1387	>	//vxzCount_[binNo]++;
1388	>	pxzHist_[binNo] += value;
1389	>	}
1390	>	if (outputVy_) {
1391		value = mass * vel[1];
1392	<	valueCount[binNo]++;
1393	<	break;
524	<	case rnemdPz :
525	<	value = mass * vel[2];
526	<	valueCount[binNo]++;
527	<	break;
528	<	case rnemdUnknown :
529	<	default :
530	<	break;
1392	>	//vyzCount_[binNo]++;
1393	>	pyzHist_[binNo] += value;
1394		}
1395	<	valueHist[binNo] += value;
1395	>
1396	>	if (output3DTemp_) {
1397	>	value = mass * vel.x() * vel.x();
1398	>	xTempHist_[binNo] += value;
1399	>	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1400	>	/ PhysicalConstants::kb;
1401	>	yTempHist_[binNo] += value;
1402	>	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1403	>	/ PhysicalConstants::kb;
1404	>	zTempHist_[binNo] += value;
1405	>	xyzTempCount_[binNo]++;
1406	>	}
1407	>	if (outputRotTemp_) {
1408	>	if (sd->isDirectional()) {
1409	>	Vector3d angMom = sd->getJ();
1410	>	Mat3x3d I = sd->getI();
1411	>	if (sd->isLinear()) {
1412	>	int i = sd->linearAxis();
1413	>	int j = (i + 1) % 3;
1414	>	int k = (i + 2) % 3;
1415	>	value = angMom[j] * angMom[j] / I(j, j) +
1416	>	angMom[k] * angMom[k] / I(k, k);
1417	>	rotTempCount_[binNo] +=2;
1418	>	} else {
1419	>	value = angMom[0] * angMom[0] / I(0, 0) +
1420	>	angMom[1] * angMom[1] / I(1, 1) +
1421	>	angMom[2] * angMom[2] / I(2, 2);
1422	>	rotTempCount_[binNo] +=3;
1423	>	}
1424	>	}
1425	>	value = value / PhysicalConstants::energyConvert
1426	>	/ PhysicalConstants::kb;//may move to getStatus()
1427	>	rotTempHist_[binNo] += value;
1428	>	}
1429	>
1430		}
1431	+	}
1432
1433	+	void RNEMD::getStarted() {
1434	+	collectData();
1435	+	/*now can output profile in step 0, but might not be useful;
1436	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1437	+	Stats& stat = currentSnap_->statData;
1438	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1439	+	*/
1440	+	//may output a header for the log file here
1441	+	getStatus();
1442	+	}
1443	+
1444	+	void RNEMD::getStatus() {
1445	+
1446	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1447	+	Stats& stat = currentSnap_->statData;
1448	+	RealType time = currentSnap_->getTime();
1449	+
1450	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1451	+	//or to be more meaningful, define another item as exchangeSum_ / time
1452	+	int j;
1453	+
1454		#ifdef IS_MPI
1455
1456		// all processors have the same number of bins, and STL vectors pack their
1457		// arrays, so in theory, this should be safe:
1458
1459	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1460	<	nBins_, MPI::REALTYPE, MPI::SUM);
1461	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1462	<	nBins_, MPI::INT, MPI::SUM);
1459	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1460	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1461	>	if (outputTemp_) {
1462	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1463	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1464	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1465	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1466	>	}
1467	>	if (outputVx_) {
1468	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1469	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1470	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1471	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1472	>	}
1473	>	if (outputVy_) {
1474	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1475	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1476	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1477	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1478	>	}
1479	>	if (output3DTemp_) {
1480	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1481	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1482	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1483	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1484	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1485	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1486	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1487	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1488	>	}
1489	>	if (outputRotTemp_) {
1490	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1491	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1492	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1493	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1494	>	}
1495
1496		// If we're the root node, should we print out the results
1497		int worldRank = MPI::COMM_WORLD.Get_rank();
1498		if (worldRank == 0) {
1499		#endif
1500	<
1501	<	std::cout << time;
1502	<	for (int j = 0; j < nBins_; j++)
1503	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1504	<	std::cout << "\n";
1505	<
1500	>
1501	>	if (outputTemp_) {
1502	>	tempLog_ << time;
1503	>	for (j = 0; j < rnemdLogWidth_; j++) {
1504	>	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1505	>	}
1506	>	tempLog_ << endl;
1507	>	}
1508	>	if (outputVx_) {
1509	>	vxzLog_ << time;
1510	>	for (j = 0; j < rnemdLogWidth_; j++) {
1511	>	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1512	>	}
1513	>	vxzLog_ << endl;
1514	>	}
1515	>	if (outputVy_) {
1516	>	vyzLog_ << time;
1517	>	for (j = 0; j < rnemdLogWidth_; j++) {
1518	>	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1519	>	}
1520	>	vyzLog_ << endl;
1521	>	}
1522	>
1523	>	if (output3DTemp_) {
1524	>	RealType temp;
1525	>	xTempLog_ << time;
1526	>	for (j = 0; j < rnemdLogWidth_; j++) {
1527	>	if (outputVx_)
1528	>	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1529	>	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1530	>	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1531	>	xTempLog_ << "\t" << temp;
1532	>	}
1533	>	xTempLog_ << endl;
1534	>	yTempLog_ << time;
1535	>	for (j = 0; j < rnemdLogWidth_; j++) {
1536	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1537	>	}
1538	>	yTempLog_ << endl;
1539	>	zTempLog_ << time;
1540	>	for (j = 0; j < rnemdLogWidth_; j++) {
1541	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1542	>	}
1543	>	zTempLog_ << endl;
1544	>	}
1545	>	if (outputRotTemp_) {
1546	>	rotTempLog_ << time;
1547	>	for (j = 0; j < rnemdLogWidth_; j++) {
1548	>	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1549	>	}
1550	>	rotTempLog_ << endl;
1551	>	}
1552	>
1553		#ifdef IS_MPI
1554		}
1555		#endif
1556	+
1557	+	for (j = 0; j < rnemdLogWidth_; j++) {
1558	+	mHist_[j] = 0.0;
1559	+	}
1560	+	if (outputTemp_)
1561	+	for (j = 0; j < rnemdLogWidth_; j++) {
1562	+	tempCount_[j] = 0;
1563	+	tempHist_[j] = 0.0;
1564	+	}
1565	+	if (outputVx_)
1566	+	for (j = 0; j < rnemdLogWidth_; j++) {
1567	+	//pxzCount_[j] = 0;
1568	+	pxzHist_[j] = 0.0;
1569	+	}
1570	+	if (outputVy_)
1571	+	for (j = 0; j < rnemdLogWidth_; j++) {
1572	+	//pyzCount_[j] = 0;
1573	+	pyzHist_[j] = 0.0;
1574	+	}
1575	+
1576	+	if (output3DTemp_)
1577	+	for (j = 0; j < rnemdLogWidth_; j++) {
1578	+	xTempHist_[j] = 0.0;
1579	+	yTempHist_[j] = 0.0;
1580	+	zTempHist_[j] = 0.0;
1581	+	xyzTempCount_[j] = 0;
1582	+	}
1583	+	if (outputRotTemp_)
1584	+	for (j = 0; j < rnemdLogWidth_; j++) {
1585	+	rotTempCount_[j] = 0;
1586	+	rotTempHist_[j] = 0.0;
1587	+	}
1588		}
1589		}
1590	+

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 1722 by gezelter, Thu May 24 14:23:40 2012 UTC

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