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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 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/PhysicalConstants.hpp"
51	+	#include "utils/Tuple.hpp"
52
53		#ifndef IS_MPI
54		#include "math/SeqRandNumGen.hpp"
55		#else
56		#include "math/ParallelRandNumGen.hpp"
57	+	#include <mpi.h>
58		#endif
59
60	<	/* Remove me after testing*/
54	<	/*
55	<	#include <cstdio>
56	<	#include <iostream>
57	<	*/
58	<	/*End remove me*/
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) {
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_["KineticScaleVAM"] = rnemdKineticScaleVAM;
77	>	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
78	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
79	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
80	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
81		stringToEnumMap_["Px"] = rnemdPx;
82		stringToEnumMap_["Py"] = rnemdPy;
83		stringToEnumMap_["Pz"] = rnemdPz;
84	+	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
85	+	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
86		stringToEnumMap_["Unknown"] = rnemdUnknown;
87
88	<	const std::string st = simParams->getRNEMD_swapType();
88	>	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
89	>	evaluator_.loadScriptString(rnemdObjectSelection_);
90	>	seleMan_.setSelectionSet(evaluator_.evaluate());
91
92	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
92	>	// do some sanity checking
93	>
94	>	int selectionCount = seleMan_.getSelectionCount();
95	>	int nIntegrable = info->getNGlobalIntegrableObjects();
96	>
97	>	if (selectionCount > nIntegrable) {
98	>	sprintf(painCave.errMsg,
99	>	"RNEMD: The current RNEMD_objectSelection,\n"
100	>	"\t\t%s\n"
101	>	"\thas resulted in %d selected objects.  However,\n"
102	>	"\tthe total number of integrable objects in the system\n"
103	>	"\tis only %d.  This is almost certainly not what you want\n"
104	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
105	>	"\tselector in the selection script!\n",
106	>	rnemdObjectSelection_.c_str(),
107	>	selectionCount, nIntegrable);
108	>	painCave.isFatal = 0;
109	>	painCave.severity = OPENMD_WARNING;
110	>	simError();
111	>	}
112	>
113	>	const string st = simParams->getRNEMD_exchangeType();
114	>
115	>	map<string, RNEMDTypeEnum>::iterator i;
116		i = stringToEnumMap_.find(st);
117	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
117	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
118	>	if (rnemdType_ == rnemdUnknown) {
119	>	sprintf(painCave.errMsg,
120	>	"RNEMD: The current RNEMD_exchangeType,\n"
121	>	"\t\t%s\n"
122	>	"\tis not one of the recognized exchange types.\n",
123	>	st.c_str());
124	>	painCave.isFatal = 1;
125	>	painCave.severity = OPENMD_ERROR;
126	>	simError();
127	>	}
128	>
129	>	outputTemp_ = false;
130	>	if (simParams->haveRNEMD_outputTemperature()) {
131	>	outputTemp_ = simParams->getRNEMD_outputTemperature();
132	>	} else if ((rnemdType_ == rnemdKineticSwap) ||
133	>	(rnemdType_ == rnemdKineticScale) ||
134	>	(rnemdType_ == rnemdKineticScaleVAM) ||
135	>	(rnemdType_ == rnemdKineticScaleAM)) {
136	>	outputTemp_ = true;
137	>	}
138	>	outputVx_ = false;
139	>	if (simParams->haveRNEMD_outputVx()) {
140	>	outputVx_ = simParams->getRNEMD_outputVx();
141	>	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
142	>	outputVx_ = true;
143	>	}
144	>	outputVy_ = false;
145	>	if (simParams->haveRNEMD_outputVy()) {
146	>	outputVy_ = simParams->getRNEMD_outputVy();
147	>	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
148	>	outputVy_ = true;
149	>	}
150	>	output3DTemp_ = false;
151	>	if (simParams->haveRNEMD_outputXyzTemperature()) {
152	>	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
153	>	}
154	>	outputRotTemp_ = false;
155	>	if (simParams->haveRNEMD_outputRotTemperature()) {
156	>	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
157	>	}
158
159	+	#ifdef IS_MPI
160	+	if (worldRank == 0) {
161	+	#endif
162
163	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
163	>	//may have rnemdWriter separately
164	>	string rnemdFileName;
165	>
166	>	if (outputTemp_) {
167	>	rnemdFileName = "temperature.log";
168	>	tempLog_.open(rnemdFileName.c_str());
169	>	}
170	>	if (outputVx_) {
171	>	rnemdFileName = "velocityX.log";
172	>	vxzLog_.open(rnemdFileName.c_str());
173	>	}
174	>	if (outputVy_) {
175	>	rnemdFileName = "velocityY.log";
176	>	vyzLog_.open(rnemdFileName.c_str());
177	>	}
178	>
179	>	if (output3DTemp_) {
180	>	rnemdFileName = "temperatureX.log";
181	>	xTempLog_.open(rnemdFileName.c_str());
182	>	rnemdFileName = "temperatureY.log";
183	>	yTempLog_.open(rnemdFileName.c_str());
184	>	rnemdFileName = "temperatureZ.log";
185	>	zTempLog_.open(rnemdFileName.c_str());
186	>	}
187	>	if (outputRotTemp_) {
188	>	rnemdFileName = "temperatureR.log";
189	>	rotTempLog_.open(rnemdFileName.c_str());
190	>	}
191	>
192	>	#ifdef IS_MPI
193	>	}
194	>	#endif
195	>
196	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
197		set_RNEMD_nBins(simParams->getRNEMD_nBins());
198	<	exchangeSum_ = 0.0;
199	<
198	>	midBin_ = nBins_ / 2;
199	>	if (simParams->haveRNEMD_binShift()) {
200	>	if (simParams->getRNEMD_binShift()) {
201	>	zShift_ = 0.5 / (RealType)(nBins_);
202	>	} else {
203	>	zShift_ = 0.0;
204	>	}
205	>	} else {
206	>	zShift_ = 0.0;
207	>	}
208	>	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
209	>	//shift slabs by half slab width, maybe useful in heterogeneous systems
210	>	//set to 0.0 if not using it; N/A in status output yet
211	>	if (simParams->haveRNEMD_logWidth()) {
212	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
213	>	/*arbitary rnemdLogWidth_, no checking;
214	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
215	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
216	>	cerr << "Automaically set back to default.\n";
217	>	rnemdLogWidth_ = nBins_;
218	>	}*/
219	>	} else {
220	>	set_RNEMD_logWidth(nBins_);
221	>	}
222	>	tempHist_.resize(rnemdLogWidth_, 0.0);
223	>	tempCount_.resize(rnemdLogWidth_, 0);
224	>	pxzHist_.resize(rnemdLogWidth_, 0.0);
225	>	//vxzCount_.resize(rnemdLogWidth_, 0);
226	>	pyzHist_.resize(rnemdLogWidth_, 0.0);
227	>	//vyzCount_.resize(rnemdLogWidth_, 0);
228	>
229	>	mHist_.resize(rnemdLogWidth_, 0.0);
230	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
231	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
232	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
233	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
234	>	rotTempHist_.resize(rnemdLogWidth_, 0.0);
235	>	rotTempCount_.resize(rnemdLogWidth_, 0);
236	>
237	>	set_RNEMD_exchange_total(0.0);
238	>	if (simParams->haveRNEMD_targetFlux()) {
239	>	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
240	>	} else {
241	>	set_RNEMD_target_flux(0.0);
242	>	}
243	>	if (simParams->haveRNEMD_targetJzKE()) {
244	>	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
245	>	} else {
246	>	set_RNEMD_target_JzKE(0.0);
247	>	}
248	>	if (simParams->haveRNEMD_targetJzpx()) {
249	>	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
250	>	} else {
251	>	set_RNEMD_target_jzpx(0.0);
252	>	}
253	>	jzp_.x() = targetJzpx_;
254	>	njzp_.x() = -targetJzpx_;
255	>	if (simParams->haveRNEMD_targetJzpy()) {
256	>	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
257	>	} else {
258	>	set_RNEMD_target_jzpy(0.0);
259	>	}
260	>	jzp_.y() = targetJzpy_;
261	>	njzp_.y() = -targetJzpy_;
262	>	if (simParams->haveRNEMD_targetJzpz()) {
263	>	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
264	>	} else {
265	>	set_RNEMD_target_jzpz(0.0);
266	>	}
267	>	jzp_.z() = targetJzpz_;
268	>	njzp_.z() = -targetJzpz_;
269	>
270		#ifndef IS_MPI
271		if (simParams->haveSeed()) {
272		seedValue = simParams->getSeed();
#	Line 100 | Line 286 | namespace oopse {
286
287		RNEMD::~RNEMD() {
288		delete randNumGen_;
289	+
290	+	#ifdef IS_MPI
291	+	if (worldRank == 0) {
292	+	#endif
293	+
294	+	sprintf(painCave.errMsg,
295	+	"RNEMD: total failed trials: %d\n",
296	+	failTrialCount_);
297	+	painCave.isFatal = 0;
298	+	painCave.severity = OPENMD_INFO;
299	+	simError();
300	+
301	+	if (outputTemp_) tempLog_.close();
302	+	if (outputVx_)   vxzLog_.close();
303	+	if (outputVy_)   vyzLog_.close();
304	+
305	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
306	+	rnemdType_ == rnemdPyScale) {
307	+	sprintf(painCave.errMsg,
308	+	"RNEMD: total root-checking warnings: %d\n",
309	+	failRootCount_);
310	+	painCave.isFatal = 0;
311	+	painCave.severity = OPENMD_INFO;
312	+	simError();
313	+	}
314	+	if (output3DTemp_) {
315	+	xTempLog_.close();
316	+	yTempLog_.close();
317	+	zTempLog_.close();
318	+	}
319	+	if (outputRotTemp_) rotTempLog_.close();
320	+
321	+	#ifdef IS_MPI
322	+	}
323	+	#endif
324		}
325
326		void RNEMD::doSwap() {
327	<	std::cerr << "in RNEMD!\n";
328	<	std::cerr << "nBins = " << nBins_ << "\n";
329	<	std::cerr << "swapTime = " << swapTime_ << "\n";
330	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
331	<	std::cerr << "swapType = " << rnemdType_ << "\n";
332	<	}
327	>
328	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
329	>	Mat3x3d hmat = currentSnap_->getHmat();
330	>
331	>	seleMan_.setSelectionSet(evaluator_.evaluate());
332	>
333	>	int selei;
334	>	StuntDouble* sd;
335	>	int idx;
336	>
337	>	RealType min_val;
338	>	bool min_found = false;
339	>	StuntDouble* min_sd;
340	>
341	>	RealType max_val;
342	>	bool max_found = false;
343	>	StuntDouble* max_sd;
344	>
345	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
346	>	sd = seleMan_.nextSelected(selei)) {
347	>
348	>	idx = sd->getLocalIndex();
349	>
350	>	Vector3d pos = sd->getPos();
351	>
352	>	// wrap the stuntdouble's position back into the box:
353	>
354	>	if (usePeriodicBoundaryConditions_)
355	>	currentSnap_->wrapVector(pos);
356	>
357	>	// which bin is this stuntdouble in?
358	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
359	>
360	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
361	>
362	>
363	>	// if we're in bin 0 or the middleBin
364	>	if (binNo == 0 || binNo == midBin_) {
365	>
366	>	RealType mass = sd->getMass();
367	>	Vector3d vel = sd->getVel();
368	>	RealType value;
369	>
370	>	switch(rnemdType_) {
371	>	case rnemdKineticSwap :
372	>
373	>	value = mass * vel.lengthSquare();
374	>
375	>	if (sd->isDirectional()) {
376	>	Vector3d angMom = sd->getJ();
377	>	Mat3x3d I = sd->getI();
378	>
379	>	if (sd->isLinear()) {
380	>	int i = sd->linearAxis();
381	>	int j = (i + 1) % 3;
382	>	int k = (i + 2) % 3;
383	>	value += angMom[j] * angMom[j] / I(j, j) +
384	>	angMom[k] * angMom[k] / I(k, k);
385	>	} else {
386	>	value += angMom[0]*angMom[0]/I(0, 0)
387	>	+ angMom[1]*angMom[1]/I(1, 1)
388	>	+ angMom[2]*angMom[2]/I(2, 2);
389	>	}
390	>	} //angular momenta exchange enabled
391	>	//energyConvert temporarily disabled
392	>	//make exchangeSum_ comparable between swap & scale
393	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
394	>	value *= 0.5;
395	>	break;
396	>	case rnemdPx :
397	>	value = mass * vel[0];
398	>	break;
399	>	case rnemdPy :
400	>	value = mass * vel[1];
401	>	break;
402	>	case rnemdPz :
403	>	value = mass * vel[2];
404	>	break;
405	>	default :
406	>	break;
407	>	}
408	>
409	>	if (binNo == 0) {
410	>	if (!min_found) {
411	>	min_val = value;
412	>	min_sd = sd;
413	>	min_found = true;
414	>	} else {
415	>	if (min_val > value) {
416	>	min_val = value;
417	>	min_sd = sd;
418	>	}
419	>	}
420	>	} else { //midBin_
421	>	if (!max_found) {
422	>	max_val = value;
423	>	max_sd = sd;
424	>	max_found = true;
425	>	} else {
426	>	if (max_val < value) {
427	>	max_val = value;
428	>	max_sd = sd;
429	>	}
430	>	}
431	>	}
432	>	}
433	>	}
434	>
435	>	#ifdef IS_MPI
436	>	int nProc, worldRank;
437	>
438	>	nProc = MPI::COMM_WORLD.Get_size();
439	>	worldRank = MPI::COMM_WORLD.Get_rank();
440	>
441	>	bool my_min_found = min_found;
442	>	bool my_max_found = max_found;
443	>
444	>	// Even if we didn't find a minimum, did someone else?
445	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
446	>	// Even if we didn't find a maximum, did someone else?
447	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
448	>	#endif
449	>
450	>	if (max_found && min_found) {
451	>
452	>	#ifdef IS_MPI
453	>	struct {
454	>	RealType val;
455	>	int rank;
456	>	} max_vals, min_vals;
457	>
458	>	if (my_min_found) {
459	>	min_vals.val = min_val;
460	>	} else {
461	>	min_vals.val = HONKING_LARGE_VALUE;
462	>	}
463	>	min_vals.rank = worldRank;
464	>
465	>	// Who had the minimum?
466	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
467	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
468	>	min_val = min_vals.val;
469	>
470	>	if (my_max_found) {
471	>	max_vals.val = max_val;
472	>	} else {
473	>	max_vals.val = -HONKING_LARGE_VALUE;
474	>	}
475	>	max_vals.rank = worldRank;
476	>
477	>	// Who had the maximum?
478	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
479	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
480	>	max_val = max_vals.val;
481	>	#endif
482	>
483	>	if (min_val < max_val) {
484	>
485	>	#ifdef IS_MPI
486	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
487	>	// I have both maximum and minimum, so proceed like a single
488	>	// processor version:
489	>	#endif
490	>
491	>	Vector3d min_vel = min_sd->getVel();
492	>	Vector3d max_vel = max_sd->getVel();
493	>	RealType temp_vel;
494	>
495	>	switch(rnemdType_) {
496	>	case rnemdKineticSwap :
497	>	min_sd->setVel(max_vel);
498	>	max_sd->setVel(min_vel);
499	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
500	>	Vector3d min_angMom = min_sd->getJ();
501	>	Vector3d max_angMom = max_sd->getJ();
502	>	min_sd->setJ(max_angMom);
503	>	max_sd->setJ(min_angMom);
504	>	}//angular momenta exchange enabled
505	>	//assumes same rigid body identity
506	>	break;
507	>	case rnemdPx :
508	>	temp_vel = min_vel.x();
509	>	min_vel.x() = max_vel.x();
510	>	max_vel.x() = temp_vel;
511	>	min_sd->setVel(min_vel);
512	>	max_sd->setVel(max_vel);
513	>	break;
514	>	case rnemdPy :
515	>	temp_vel = min_vel.y();
516	>	min_vel.y() = max_vel.y();
517	>	max_vel.y() = temp_vel;
518	>	min_sd->setVel(min_vel);
519	>	max_sd->setVel(max_vel);
520	>	break;
521	>	case rnemdPz :
522	>	temp_vel = min_vel.z();
523	>	min_vel.z() = max_vel.z();
524	>	max_vel.z() = temp_vel;
525	>	min_sd->setVel(min_vel);
526	>	max_sd->setVel(max_vel);
527	>	break;
528	>	default :
529	>	break;
530	>	}
531	>
532	>	#ifdef IS_MPI
533	>	// the rest of the cases only apply in parallel simulations:
534	>	} else if (max_vals.rank == worldRank) {
535	>	// I had the max, but not the minimum
536	>
537	>	Vector3d min_vel;
538	>	Vector3d max_vel = max_sd->getVel();
539	>	MPI::Status status;
540	>
541	>	// point-to-point swap of the velocity vector
542	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
543	>	min_vals.rank, 0,
544	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
545	>	min_vals.rank, 0, status);
546	>
547	>	switch(rnemdType_) {
548	>	case rnemdKineticSwap :
549	>	max_sd->setVel(min_vel);
550	>	//angular momenta exchange enabled
551	>	if (max_sd->isDirectional()) {
552	>	Vector3d min_angMom;
553	>	Vector3d max_angMom = max_sd->getJ();
554	>
555	>	// point-to-point swap of the angular momentum vector
556	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
557	>	MPI::REALTYPE, min_vals.rank, 1,
558	>	min_angMom.getArrayPointer(), 3,
559	>	MPI::REALTYPE, min_vals.rank, 1,
560	>	status);
561	>
562	>	max_sd->setJ(min_angMom);
563	>	}
564	>	break;
565	>	case rnemdPx :
566	>	max_vel.x() = min_vel.x();
567	>	max_sd->setVel(max_vel);
568	>	break;
569	>	case rnemdPy :
570	>	max_vel.y() = min_vel.y();
571	>	max_sd->setVel(max_vel);
572	>	break;
573	>	case rnemdPz :
574	>	max_vel.z() = min_vel.z();
575	>	max_sd->setVel(max_vel);
576	>	break;
577	>	default :
578	>	break;
579	>	}
580	>	} else if (min_vals.rank == worldRank) {
581	>	// I had the minimum but not the maximum:
582	>
583	>	Vector3d max_vel;
584	>	Vector3d min_vel = min_sd->getVel();
585	>	MPI::Status status;
586	>
587	>	// point-to-point swap of the velocity vector
588	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
589	>	max_vals.rank, 0,
590	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
591	>	max_vals.rank, 0, status);
592	>
593	>	switch(rnemdType_) {
594	>	case rnemdKineticSwap :
595	>	min_sd->setVel(max_vel);
596	>	//angular momenta exchange enabled
597	>	if (min_sd->isDirectional()) {
598	>	Vector3d min_angMom = min_sd->getJ();
599	>	Vector3d max_angMom;
600	>
601	>	// point-to-point swap of the angular momentum vector
602	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
603	>	MPI::REALTYPE, max_vals.rank, 1,
604	>	max_angMom.getArrayPointer(), 3,
605	>	MPI::REALTYPE, max_vals.rank, 1,
606	>	status);
607	>
608	>	min_sd->setJ(max_angMom);
609	>	}
610	>	break;
611	>	case rnemdPx :
612	>	min_vel.x() = max_vel.x();
613	>	min_sd->setVel(min_vel);
614	>	break;
615	>	case rnemdPy :
616	>	min_vel.y() = max_vel.y();
617	>	min_sd->setVel(min_vel);
618	>	break;
619	>	case rnemdPz :
620	>	min_vel.z() = max_vel.z();
621	>	min_sd->setVel(min_vel);
622	>	break;
623	>	default :
624	>	break;
625	>	}
626	>	}
627	>	#endif
628	>	exchangeSum_ += max_val - min_val;
629	>	} else {
630	>	sprintf(painCave.errMsg,
631	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
632	>	painCave.isFatal = 0;
633	>	painCave.severity = OPENMD_INFO;
634	>	simError();
635	>	failTrialCount_++;
636	>	}
637	>	} else {
638	>	sprintf(painCave.errMsg,
639	>	"RNEMD: exchange NOT performed because selected object\n"
640	>	"\tnot present in at least one of the two slabs.\n");
641	>	painCave.isFatal = 0;
642	>	painCave.severity = OPENMD_INFO;
643	>	simError();
644	>	failTrialCount_++;
645	>	}
646	>
647	>	}
648	>
649	>	void RNEMD::doScale() {
650	>
651	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
652	>	Mat3x3d hmat = currentSnap_->getHmat();
653	>
654	>	seleMan_.setSelectionSet(evaluator_.evaluate());
655	>
656	>	int selei;
657	>	StuntDouble* sd;
658	>	int idx;
659	>
660	>	vector<StuntDouble*> hotBin, coldBin;
661	>
662	>	RealType Phx = 0.0;
663	>	RealType Phy = 0.0;
664	>	RealType Phz = 0.0;
665	>	RealType Khx = 0.0;
666	>	RealType Khy = 0.0;
667	>	RealType Khz = 0.0;
668	>	RealType Khw = 0.0;
669	>	RealType Pcx = 0.0;
670	>	RealType Pcy = 0.0;
671	>	RealType Pcz = 0.0;
672	>	RealType Kcx = 0.0;
673	>	RealType Kcy = 0.0;
674	>	RealType Kcz = 0.0;
675	>	RealType Kcw = 0.0;
676	>
677	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
678	>	sd = seleMan_.nextSelected(selei)) {
679	>
680	>	idx = sd->getLocalIndex();
681	>
682	>	Vector3d pos = sd->getPos();
683	>
684	>	// wrap the stuntdouble's position back into the box:
685	>
686	>	if (usePeriodicBoundaryConditions_)
687	>	currentSnap_->wrapVector(pos);
688	>
689	>	// which bin is this stuntdouble in?
690	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
691	>
692	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
693	>
694	>	// if we're in bin 0 or the middleBin
695	>	if (binNo == 0 || binNo == midBin_) {
696	>
697	>	RealType mass = sd->getMass();
698	>	Vector3d vel = sd->getVel();
699	>
700	>	if (binNo == 0) {
701	>	hotBin.push_back(sd);
702	>	Phx += mass * vel.x();
703	>	Phy += mass * vel.y();
704	>	Phz += mass * vel.z();
705	>	Khx += mass * vel.x() * vel.x();
706	>	Khy += mass * vel.y() * vel.y();
707	>	Khz += mass * vel.z() * vel.z();
708	>	//if (rnemdType_ == rnemdKineticScaleVAM) {
709	>	if (sd->isDirectional()) {
710	>	Vector3d angMom = sd->getJ();
711	>	Mat3x3d I = sd->getI();
712	>	if (sd->isLinear()) {
713	>	int i = sd->linearAxis();
714	>	int j = (i + 1) % 3;
715	>	int k = (i + 2) % 3;
716	>	Khw += angMom[j] * angMom[j] / I(j, j) +
717	>	angMom[k] * angMom[k] / I(k, k);
718	>	} else {
719	>	Khw += angMom[0]*angMom[0]/I(0, 0)
720	>	+ angMom[1]*angMom[1]/I(1, 1)
721	>	+ angMom[2]*angMom[2]/I(2, 2);
722	>	}
723	>	}
724	>	//}
725	>	} else { //midBin_
726	>	coldBin.push_back(sd);
727	>	Pcx += mass * vel.x();
728	>	Pcy += mass * vel.y();
729	>	Pcz += mass * vel.z();
730	>	Kcx += mass * vel.x() * vel.x();
731	>	Kcy += mass * vel.y() * vel.y();
732	>	Kcz += mass * vel.z() * vel.z();
733	>	//if (rnemdType_ == rnemdKineticScaleVAM) {
734	>	if (sd->isDirectional()) {
735	>	Vector3d angMom = sd->getJ();
736	>	Mat3x3d I = sd->getI();
737	>	if (sd->isLinear()) {
738	>	int i = sd->linearAxis();
739	>	int j = (i + 1) % 3;
740	>	int k = (i + 2) % 3;
741	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
742	>	angMom[k] * angMom[k] / I(k, k);
743	>	} else {
744	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
745	>	+ angMom[1]*angMom[1]/I(1, 1)
746	>	+ angMom[2]*angMom[2]/I(2, 2);
747	>	}
748	>	}
749	>	//}
750	>	}
751	>	}
752	>	}
753	>
754	>	Khx *= 0.5;
755	>	Khy *= 0.5;
756	>	Khz *= 0.5;
757	>	Khw *= 0.5;
758	>	Kcx *= 0.5;
759	>	Kcy *= 0.5;
760	>	Kcz *= 0.5;
761	>	Kcw *= 0.5;
762	>
763	>	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
764	>	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
765	>	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
766	>	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
767	>	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
768	>
769	>	#ifdef IS_MPI
770	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
771	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
772	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
773	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
774	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
775	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
776	>
777	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
778	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
779	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
780	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
781	>
782	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
783	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
784	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
785	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
786	>	#endif
787	>
788	>	//solve coldBin coeff's first
789	>	RealType px = Pcx / Phx;
790	>	RealType py = Pcy / Phy;
791	>	RealType pz = Pcz / Phz;
792	>	RealType c, x, y, z;
793	>	bool successfulScale = false;
794	>	if ((rnemdType_ == rnemdKineticScaleVAM) ||
795	>	(rnemdType_ == rnemdKineticScaleAM)) {
796	>	//may need sanity check Khw & Kcw > 0
797	>
798	>	if (rnemdType_ == rnemdKineticScaleVAM) {
799	>	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
800	>	} else {
801	>	c = 1.0 - targetFlux_ / Kcw;
802	>	}
803	>
804	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
805	>	c = sqrt(c);
806	>	std::cerr << "cold slab scaling coefficient: " << c << endl;
807	>	//now convert to hotBin coefficient
808	>	RealType w = 0.0;
809	>	if (rnemdType_ ==  rnemdKineticScaleVAM) {
810	>	x = 1.0 + px * (1.0 - c);
811	>	y = 1.0 + py * (1.0 - c);
812	>	z = 1.0 + pz * (1.0 - c);
813	>	/* more complicated way
814	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
815	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
816	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
817	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
818	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
819	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
820	>	*/
821	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
822	>	(fabs(z - 1.0) < 0.1)) {
823	>	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
824	>	+ Khz * (1.0 - z * z)) / Khw;
825	>	}//no need to calculate w if x, y or z is out of range
826	>	} else {
827	>	w = 1.0 + targetFlux_ / Khw;
828	>	}
829	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
830	>	//if w is in the right range, so should be x, y, z.
831	>	vector<StuntDouble*>::iterator sdi;
832	>	Vector3d vel;
833	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
834	>	if (rnemdType_ == rnemdKineticScaleVAM) {
835	>	vel = (*sdi)->getVel() * c;
836	>	//vel.x() *= c;
837	>	//vel.y() *= c;
838	>	//vel.z() *= c;
839	>	(*sdi)->setVel(vel);
840	>	}
841	>	if ((*sdi)->isDirectional()) {
842	>	Vector3d angMom = (*sdi)->getJ() * c;
843	>	//angMom[0] *= c;
844	>	//angMom[1] *= c;
845	>	//angMom[2] *= c;
846	>	(*sdi)->setJ(angMom);
847	>	}
848	>	}
849	>	w = sqrt(w);
850	>	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
851	>	<< "\twh= " << w << endl;
852	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
853	>	if (rnemdType_ == rnemdKineticScaleVAM) {
854	>	vel = (*sdi)->getVel();
855	>	vel.x() *= x;
856	>	vel.y() *= y;
857	>	vel.z() *= z;
858	>	(*sdi)->setVel(vel);
859	>	}
860	>	if ((*sdi)->isDirectional()) {
861	>	Vector3d angMom = (*sdi)->getJ() * w;
862	>	//angMom[0] *= w;
863	>	//angMom[1] *= w;
864	>	//angMom[2] *= w;
865	>	(*sdi)->setJ(angMom);
866	>	}
867	>	}
868	>	successfulScale = true;
869	>	exchangeSum_ += targetFlux_;
870	>	}
871	>	}
872	>	} else {
873	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
874	>	switch(rnemdType_) {
875	>	case rnemdKineticScale :
876	>	/* used hotBin coeff's & only scale x & y dimensions
877	>	RealType px = Phx / Pcx;
878	>	RealType py = Phy / Pcy;
879	>	a110 = Khy;
880	>	c0 = - Khx - Khy - targetFlux_;
881	>	a000 = Khx;
882	>	a111 = Kcy * py * py;
883	>	b11 = -2.0 * Kcy * py * (1.0 + py);
884	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
885	>	b01 = -2.0 * Kcx * px * (1.0 + px);
886	>	a001 = Kcx * px * px;
887	>	*/
888	>	//scale all three dimensions, let c_x = c_y
889	>	a000 = Kcx + Kcy;
890	>	a110 = Kcz;
891	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
892	>	a001 = Khx * px * px + Khy * py * py;
893	>	a111 = Khz * pz * pz;
894	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
895	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
896	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
897	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
898	>	break;
899	>	case rnemdPxScale :
900	>	c = 1 - targetFlux_ / Pcx;
901	>	a000 = Kcy;
902	>	a110 = Kcz;
903	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
904	>	a001 = py * py * Khy;
905	>	a111 = pz * pz * Khz;
906	>	b01 = -2.0 * Khy * py * (1.0 + py);
907	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
908	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
909	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
910	>	break;
911	>	case rnemdPyScale :
912	>	c = 1 - targetFlux_ / Pcy;
913	>	a000 = Kcx;
914	>	a110 = Kcz;
915	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
916	>	a001 = px * px * Khx;
917	>	a111 = pz * pz * Khz;
918	>	b01 = -2.0 * Khx * px * (1.0 + px);
919	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
920	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
921	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
922	>	break;
923	>	case rnemdPzScale ://we don't really do this, do we?
924	>	c = 1 - targetFlux_ / Pcz;
925	>	a000 = Kcx;
926	>	a110 = Kcy;
927	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
928	>	a001 = px * px * Khx;
929	>	a111 = py * py * Khy;
930	>	b01 = -2.0 * Khx * px * (1.0 + px);
931	>	b11 = -2.0 * Khy * py * (1.0 + py);
932	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
933	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
934	>	break;
935	>	default :
936	>	break;
937	>	}
938	>
939	>	RealType v1 = a000 * a111 - a001 * a110;
940	>	RealType v2 = a000 * b01;
941	>	RealType v3 = a000 * b11;
942	>	RealType v4 = a000 * c1 - a001 * c0;
943	>	RealType v8 = a110 * b01;
944	>	RealType v10 = - b01 * c0;
945	>
946	>	RealType u0 = v2 * v10 - v4 * v4;
947	>	RealType u1 = -2.0 * v3 * v4;
948	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
949	>	RealType u3 = -2.0 * v1 * v3;
950	>	RealType u4 = - v1 * v1;
951	>	//rescale coefficients
952	>	RealType maxAbs = fabs(u0);
953	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
954	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
955	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
956	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
957	>	u0 /= maxAbs;
958	>	u1 /= maxAbs;
959	>	u2 /= maxAbs;
960	>	u3 /= maxAbs;
961	>	u4 /= maxAbs;
962	>	//max_element(start, end) is also available.
963	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
964	>	poly.setCoefficient(4, u4);
965	>	poly.setCoefficient(3, u3);
966	>	poly.setCoefficient(2, u2);
967	>	poly.setCoefficient(1, u1);
968	>	poly.setCoefficient(0, u0);
969	>	vector<RealType> realRoots = poly.FindRealRoots();
970	>
971	>	vector<RealType>::iterator ri;
972	>	RealType r1, r2, alpha0;
973	>	vector<pair<RealType,RealType> > rps;
974	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
975	>	r2 = *ri;
976	>	//check if FindRealRoots() give the right answer
977	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
978	>	sprintf(painCave.errMsg,
979	>	"RNEMD Warning: polynomial solve seems to have an error!");
980	>	painCave.isFatal = 0;
981	>	simError();
982	>	failRootCount_++;
983	>	}
984	>	//might not be useful w/o rescaling coefficients
985	>	alpha0 = -c0 - a110 * r2 * r2;
986	>	if (alpha0 >= 0.0) {
987	>	r1 = sqrt(alpha0 / a000);
988	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
989	>	< 1e-6)
990	>	{ rps.push_back(make_pair(r1, r2)); }
991	>	if (r1 > 1e-6) { //r1 non-negative
992	>	r1 = -r1;
993	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
994	>	< 1e-6)
995	>	{ rps.push_back(make_pair(r1, r2)); }
996	>	}
997	>	}
998	>	}
999	>	// Consider combining together the solving pair part w/ the searching
1000	>	// best solution part so that we don't need the pairs vector
1001	>	if (!rps.empty()) {
1002	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1003	>	RealType diff;
1004	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1005	>	vector<pair<RealType,RealType> >::iterator rpi;
1006	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1007	>	r1 = (*rpi).first;
1008	>	r2 = (*rpi).second;
1009	>	switch(rnemdType_) {
1010	>	case rnemdKineticScale :
1011	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1012	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1013	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1014	>	break;
1015	>	case rnemdPxScale :
1016	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1017	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1018	>	break;
1019	>	case rnemdPyScale :
1020	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1021	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1022	>	break;
1023	>	case rnemdPzScale :
1024	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1025	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1026	>	default :
1027	>	break;
1028	>	}
1029	>	if (diff < smallestDiff) {
1030	>	smallestDiff = diff;
1031	>	bestPair = *rpi;
1032	>	}
1033	>	}
1034	>	#ifdef IS_MPI
1035	>	if (worldRank == 0) {
1036	>	#endif
1037	>	sprintf(painCave.errMsg,
1038	>	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1039	>	bestPair.first, bestPair.second);
1040	>	painCave.isFatal = 0;
1041	>	painCave.severity = OPENMD_INFO;
1042	>	simError();
1043	>	#ifdef IS_MPI
1044	>	}
1045	>	#endif
1046	>
1047	>	switch(rnemdType_) {
1048	>	case rnemdKineticScale :
1049	>	x = bestPair.first;
1050	>	y = bestPair.first;
1051	>	z = bestPair.second;
1052	>	break;
1053	>	case rnemdPxScale :
1054	>	x = c;
1055	>	y = bestPair.first;
1056	>	z = bestPair.second;
1057	>	break;
1058	>	case rnemdPyScale :
1059	>	x = bestPair.first;
1060	>	y = c;
1061	>	z = bestPair.second;
1062	>	break;
1063	>	case rnemdPzScale :
1064	>	x = bestPair.first;
1065	>	y = bestPair.second;
1066	>	z = c;
1067	>	break;
1068	>	default :
1069	>	break;
1070	>	}
1071	>	vector<StuntDouble*>::iterator sdi;
1072	>	Vector3d vel;
1073	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1074	>	vel = (*sdi)->getVel();
1075	>	vel.x() *= x;
1076	>	vel.y() *= y;
1077	>	vel.z() *= z;
1078	>	(*sdi)->setVel(vel);
1079	>	}
1080	>	//convert to hotBin coefficient
1081	>	x = 1.0 + px * (1.0 - x);
1082	>	y = 1.0 + py * (1.0 - y);
1083	>	z = 1.0 + pz * (1.0 - z);
1084	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1085	>	vel = (*sdi)->getVel();
1086	>	vel.x() *= x;
1087	>	vel.y() *= y;
1088	>	vel.z() *= z;
1089	>	(*sdi)->setVel(vel);
1090	>	}
1091	>	successfulScale = true;
1092	>	exchangeSum_ += targetFlux_;
1093	>	}
1094	>	}
1095	>	if (successfulScale != true) {
1096	>	sprintf(painCave.errMsg,
1097	>	"RNEMD: exchange NOT performed!\n");
1098	>	painCave.isFatal = 0;
1099	>	painCave.severity = OPENMD_INFO;
1100	>	simError();
1101	>	failTrialCount_++;
1102	>	}
1103	>	}
1104	>
1105	>	void RNEMD::doShiftScale() {
1106	>
1107	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1108	>	Mat3x3d hmat = currentSnap_->getHmat();
1109	>
1110	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1111	>
1112	>	int selei;
1113	>	StuntDouble* sd;
1114	>	int idx;
1115	>
1116	>	vector<StuntDouble*> hotBin, coldBin;
1117	>
1118	>	Vector3d Ph(V3Zero);
1119	>	RealType Mh = 0.0;
1120	>	RealType Kh = 0.0;
1121	>	Vector3d Pc(V3Zero);
1122	>	RealType Mc = 0.0;
1123	>	RealType Kc = 0.0;
1124	>
1125	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1126	>	sd = seleMan_.nextSelected(selei)) {
1127	>
1128	>	idx = sd->getLocalIndex();
1129	>
1130	>	Vector3d pos = sd->getPos();
1131	>
1132	>	// wrap the stuntdouble's position back into the box:
1133	>
1134	>	if (usePeriodicBoundaryConditions_)
1135	>	currentSnap_->wrapVector(pos);
1136	>
1137	>	// which bin is this stuntdouble in?
1138	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1139	>
1140	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1141	>
1142	>	// if we're in bin 0 or the middleBin
1143	>	if (binNo == 0 || binNo == midBin_) {
1144	>
1145	>	RealType mass = sd->getMass();
1146	>	Vector3d vel = sd->getVel();
1147	>
1148	>	if (binNo == 0) {
1149	>	hotBin.push_back(sd);
1150	>	//std::cerr << "before, velocity = " << vel << endl;
1151	>	Ph += mass * vel;
1152	>	//std::cerr << "after, velocity = " << vel << endl;
1153	>	Mh += mass;
1154	>	Kh += mass * vel.lengthSquare();
1155	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1156	>	if (sd->isDirectional()) {
1157	>	Vector3d angMom = sd->getJ();
1158	>	Mat3x3d I = sd->getI();
1159	>	if (sd->isLinear()) {
1160	>	int i = sd->linearAxis();
1161	>	int j = (i + 1) % 3;
1162	>	int k = (i + 2) % 3;
1163	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1164	>	angMom[k] * angMom[k] / I(k, k);
1165	>	} else {
1166	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1167	>	angMom[1] * angMom[1] / I(1, 1) +
1168	>	angMom[2] * angMom[2] / I(2, 2);
1169	>	}
1170	>	}
1171	>	}
1172	>	} else { //midBin_
1173	>	coldBin.push_back(sd);
1174	>	Pc += mass * vel;
1175	>	Mc += mass;
1176	>	Kc += mass * vel.lengthSquare();
1177	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1178	>	if (sd->isDirectional()) {
1179	>	Vector3d angMom = sd->getJ();
1180	>	Mat3x3d I = sd->getI();
1181	>	if (sd->isLinear()) {
1182	>	int i = sd->linearAxis();
1183	>	int j = (i + 1) % 3;
1184	>	int k = (i + 2) % 3;
1185	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1186	>	angMom[k] * angMom[k] / I(k, k);
1187	>	} else {
1188	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1189	>	angMom[1] * angMom[1] / I(1, 1) +
1190	>	angMom[2] * angMom[2] / I(2, 2);
1191	>	}
1192	>	}
1193	>	}
1194	>	}
1195	>	}
1196	>	}
1197	>
1198	>	Kh *= 0.5;
1199	>	Kc *= 0.5;
1200	>
1201	>	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	>	<< "\tKc= " << Kc << endl;
1203	>	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	>
1205	>	#ifdef IS_MPI
1206	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1207	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1208	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1209	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1210	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1211	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1212	>	#endif
1213	>
1214	>	bool successfulExchange = false;
1215	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1216	>	Vector3d vc = Pc / Mc;
1217	>	Vector3d ac = njzp_ / Mc + vc;
1218	>	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1219	>	if (cNumerator > 0.0) {
1220	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1221	>	if (cDenominator > 0.0) {
1222	>	RealType c = sqrt(cNumerator / cDenominator);
1223	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1224	>	Vector3d vh = Ph / Mh;
1225	>	Vector3d ah = jzp_ / Mh + vh;
1226	>	RealType hNumerator = Kh + targetJzKE_
1227	>	- 0.5 * Mh * ah.lengthSquare();
1228	>	if (hNumerator > 0.0) {
1229	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1230	>	if (hDenominator > 0.0) {
1231	>	RealType h = sqrt(hNumerator / hDenominator);
1232	>	if ((h > 0.9) && (h < 1.1)) {
1233	>	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	>	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1235	>	vector<StuntDouble*>::iterator sdi;
1236	>	Vector3d vel;
1237	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1238	>	//vel = (*sdi)->getVel();
1239	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1240	>	(*sdi)->setVel(vel);
1241	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1242	>	if ((*sdi)->isDirectional()) {
1243	>	Vector3d angMom = (*sdi)->getJ() * c;
1244	>	(*sdi)->setJ(angMom);
1245	>	}
1246	>	}
1247	>	}
1248	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1249	>	//vel = (*sdi)->getVel();
1250	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1251	>	(*sdi)->setVel(vel);
1252	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1253	>	if ((*sdi)->isDirectional()) {
1254	>	Vector3d angMom = (*sdi)->getJ() * h;
1255	>	(*sdi)->setJ(angMom);
1256	>	}
1257	>	}
1258	>	}
1259	>	successfulExchange = true;
1260	>	exchangeSum_ += targetFlux_;
1261	>	// this is a redundant variable for doShiftScale() so that
1262	>	// RNEMD can output one exchange quantity needed in a job.
1263	>	// need a better way to do this.
1264	>	}
1265	>	}
1266	>	}
1267	>	}
1268	>	}
1269	>	}
1270	>	}
1271	>	if (successfulExchange != true) {
1272	>	sprintf(painCave.errMsg,
1273	>	"RNEMD: exchange NOT performed!\n");
1274	>	painCave.isFatal = 0;
1275	>	painCave.severity = OPENMD_INFO;
1276	>	simError();
1277	>	failTrialCount_++;
1278	>	}
1279	>	}
1280	>
1281	>	void RNEMD::doRNEMD() {
1282	>
1283	>	switch(rnemdType_) {
1284	>	case rnemdKineticScale :
1285	>	case rnemdKineticScaleVAM :
1286	>	case rnemdKineticScaleAM :
1287	>	case rnemdPxScale :
1288	>	case rnemdPyScale :
1289	>	case rnemdPzScale :
1290	>	doScale();
1291	>	break;
1292	>	case rnemdKineticSwap :
1293	>	case rnemdPx :
1294	>	case rnemdPy :
1295	>	case rnemdPz :
1296	>	doSwap();
1297	>	break;
1298	>	case rnemdShiftScaleV :
1299	>	case rnemdShiftScaleVAM :
1300	>	doShiftScale();
1301	>	break;
1302	>	case rnemdUnknown :
1303	>	default :
1304	>	break;
1305	>	}
1306	>	}
1307	>
1308	>	void RNEMD::collectData() {
1309	>
1310	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1311	>	Mat3x3d hmat = currentSnap_->getHmat();
1312	>
1313	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1314	>
1315	>	int selei;
1316	>	StuntDouble* sd;
1317	>	int idx;
1318	>
1319	>	// alternative approach, track all molecules instead of only those
1320	>	// selected for scaling/swapping:
1321	>	/*
1322	>	SimInfo::MoleculeIterator miter;
1323	>	vector<StuntDouble*>::iterator iiter;
1324	>	Molecule* mol;
1325	>	StuntDouble* integrableObject;
1326	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1327	>	mol = info_->nextMolecule(miter))
1328	>	integrableObject is essentially sd
1329	>	for (integrableObject = mol->beginIntegrableObject(iiter);
1330	>	integrableObject != NULL;
1331	>	integrableObject = mol->nextIntegrableObject(iiter))
1332	>	*/
1333	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1334	>	sd = seleMan_.nextSelected(selei)) {
1335	>
1336	>	idx = sd->getLocalIndex();
1337	>
1338	>	Vector3d pos = sd->getPos();
1339	>
1340	>	// wrap the stuntdouble's position back into the box:
1341	>
1342	>	if (usePeriodicBoundaryConditions_)
1343	>	currentSnap_->wrapVector(pos);
1344	>
1345	>	// which bin is this stuntdouble in?
1346	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1347	>
1348	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1349	>	rnemdLogWidth_;
1350	>	// no symmetrization allowed due to arbitary rnemdLogWidth_
1351	>	/*
1352	>	if (rnemdLogWidth_ == midBin_ + 1)
1353	>	if (binNo > midBin_)
1354	>	binNo = nBins_ - binNo;
1355	>	*/
1356	>	RealType mass = sd->getMass();
1357	>	mHist_[binNo] += mass;
1358	>	Vector3d vel = sd->getVel();
1359	>	RealType value;
1360	>	//RealType xVal, yVal, zVal;
1361	>
1362	>	if (outputTemp_) {
1363	>	value = mass * vel.lengthSquare();
1364	>	tempCount_[binNo] += 3;
1365	>	if (sd->isDirectional()) {
1366	>	Vector3d angMom = sd->getJ();
1367	>	Mat3x3d I = sd->getI();
1368	>	if (sd->isLinear()) {
1369	>	int i = sd->linearAxis();
1370	>	int j = (i + 1) % 3;
1371	>	int k = (i + 2) % 3;
1372	>	value += angMom[j] * angMom[j] / I(j, j) +
1373	>	angMom[k] * angMom[k] / I(k, k);
1374	>	tempCount_[binNo] +=2;
1375	>	} else {
1376	>	value += angMom[0] * angMom[0] / I(0, 0) +
1377	>	angMom[1]*angMom[1]/I(1, 1) +
1378	>	angMom[2]*angMom[2]/I(2, 2);
1379	>	tempCount_[binNo] +=3;
1380	>	}
1381	>	}
1382	>	value = value / PhysicalConstants::energyConvert
1383	>	/ PhysicalConstants::kb;//may move to getStatus()
1384	>	tempHist_[binNo] += value;
1385	>	}
1386	>	if (outputVx_) {
1387	>	value = mass * vel[0];
1388	>	//vxzCount_[binNo]++;
1389	>	pxzHist_[binNo] += value;
1390	>	}
1391	>	if (outputVy_) {
1392	>	value = mass * vel[1];
1393	>	//vyzCount_[binNo]++;
1394	>	pyzHist_[binNo] += value;
1395	>	}
1396	>
1397	>	if (output3DTemp_) {
1398	>	value = mass * vel.x() * vel.x();
1399	>	xTempHist_[binNo] += value;
1400	>	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1401	>	/ PhysicalConstants::kb;
1402	>	yTempHist_[binNo] += value;
1403	>	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1404	>	/ PhysicalConstants::kb;
1405	>	zTempHist_[binNo] += value;
1406	>	xyzTempCount_[binNo]++;
1407	>	}
1408	>	if (outputRotTemp_) {
1409	>	if (sd->isDirectional()) {
1410	>	Vector3d angMom = sd->getJ();
1411	>	Mat3x3d I = sd->getI();
1412	>	if (sd->isLinear()) {
1413	>	int i = sd->linearAxis();
1414	>	int j = (i + 1) % 3;
1415	>	int k = (i + 2) % 3;
1416	>	value = angMom[j] * angMom[j] / I(j, j) +
1417	>	angMom[k] * angMom[k] / I(k, k);
1418	>	rotTempCount_[binNo] +=2;
1419	>	} else {
1420	>	value = angMom[0] * angMom[0] / I(0, 0) +
1421	>	angMom[1] * angMom[1] / I(1, 1) +
1422	>	angMom[2] * angMom[2] / I(2, 2);
1423	>	rotTempCount_[binNo] +=3;
1424	>	}
1425	>	}
1426	>	value = value / PhysicalConstants::energyConvert
1427	>	/ PhysicalConstants::kb;//may move to getStatus()
1428	>	rotTempHist_[binNo] += value;
1429	>	}
1430	>
1431	>	}
1432	>	}
1433	>
1434	>	void RNEMD::getStarted() {
1435	>	collectData();
1436	>	/*now can output profile in step 0, but might not be useful;
1437	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	>	Stats& stat = currentSnap_->statData;
1439	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1440	>	*/
1441	>	//may output a header for the log file here
1442	>	getStatus();
1443	>	}
1444	>
1445	>	void RNEMD::getStatus() {
1446	>
1447	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1448	>	Stats& stat = currentSnap_->statData;
1449	>	RealType time = currentSnap_->getTime();
1450	>
1451	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1452	>	//or to be more meaningful, define another item as exchangeSum_ / time
1453	>	int j;
1454	>
1455	>	#ifdef IS_MPI
1456	>
1457	>	// all processors have the same number of bins, and STL vectors pack their
1458	>	// arrays, so in theory, this should be safe:
1459	>
1460	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1461	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1462	>	if (outputTemp_) {
1463	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1464	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1465	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1466	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1467	>	}
1468	>	if (outputVx_) {
1469	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1470	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1471	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1472	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1473	>	}
1474	>	if (outputVy_) {
1475	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1476	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1477	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1478	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1479	>	}
1480	>	if (output3DTemp_) {
1481	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1482	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1483	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1484	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1485	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1486	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1487	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1488	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1489	>	}
1490	>	if (outputRotTemp_) {
1491	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1492	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1493	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1494	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1495	>	}
1496	>
1497	>	// If we're the root node, should we print out the results
1498	>	int worldRank = MPI::COMM_WORLD.Get_rank();
1499	>	if (worldRank == 0) {
1500	>	#endif
1501	>
1502	>	if (outputTemp_) {
1503	>	tempLog_ << time;
1504	>	for (j = 0; j < rnemdLogWidth_; j++) {
1505	>	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1506	>	}
1507	>	tempLog_ << endl;
1508	>	}
1509	>	if (outputVx_) {
1510	>	vxzLog_ << time;
1511	>	for (j = 0; j < rnemdLogWidth_; j++) {
1512	>	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1513	>	}
1514	>	vxzLog_ << endl;
1515	>	}
1516	>	if (outputVy_) {
1517	>	vyzLog_ << time;
1518	>	for (j = 0; j < rnemdLogWidth_; j++) {
1519	>	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	>	}
1521	>	vyzLog_ << endl;
1522	>	}
1523	>
1524	>	if (output3DTemp_) {
1525	>	RealType temp;
1526	>	xTempLog_ << time;
1527	>	for (j = 0; j < rnemdLogWidth_; j++) {
1528	>	if (outputVx_)
1529	>	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1530	>	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1531	>	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1532	>	xTempLog_ << "\t" << temp;
1533	>	}
1534	>	xTempLog_ << endl;
1535	>	yTempLog_ << time;
1536	>	for (j = 0; j < rnemdLogWidth_; j++) {
1537	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1538	>	}
1539	>	yTempLog_ << endl;
1540	>	zTempLog_ << time;
1541	>	for (j = 0; j < rnemdLogWidth_; j++) {
1542	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1543	>	}
1544	>	zTempLog_ << endl;
1545	>	}
1546	>	if (outputRotTemp_) {
1547	>	rotTempLog_ << time;
1548	>	for (j = 0; j < rnemdLogWidth_; j++) {
1549	>	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1550	>	}
1551	>	rotTempLog_ << endl;
1552	>	}
1553	>
1554	>	#ifdef IS_MPI
1555	>	}
1556	>	#endif
1557	>
1558	>	for (j = 0; j < rnemdLogWidth_; j++) {
1559	>	mHist_[j] = 0.0;
1560	>	}
1561	>	if (outputTemp_)
1562	>	for (j = 0; j < rnemdLogWidth_; j++) {
1563	>	tempCount_[j] = 0;
1564	>	tempHist_[j] = 0.0;
1565	>	}
1566	>	if (outputVx_)
1567	>	for (j = 0; j < rnemdLogWidth_; j++) {
1568	>	//pxzCount_[j] = 0;
1569	>	pxzHist_[j] = 0.0;
1570	>	}
1571	>	if (outputVy_)
1572	>	for (j = 0; j < rnemdLogWidth_; j++) {
1573	>	//pyzCount_[j] = 0;
1574	>	pyzHist_[j] = 0.0;
1575	>	}
1576	>
1577	>	if (output3DTemp_)
1578	>	for (j = 0; j < rnemdLogWidth_; j++) {
1579	>	xTempHist_[j] = 0.0;
1580	>	yTempHist_[j] = 0.0;
1581	>	zTempHist_[j] = 0.0;
1582	>	xyzTempCount_[j] = 0;
1583	>	}
1584	>	if (outputRotTemp_)
1585	>	for (j = 0; j < rnemdLogWidth_; j++) {
1586	>	rotTempCount_[j] = 0;
1587	>	rotTempHist_[j] = 0.0;
1588	>	}
1589	>	}
1590		}
1591	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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