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

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <cmath>
44		#include "integrators/RNEMD.hpp"
45	+	#include "math/Vector3.hpp"
46		#include "math/SquareMatrix3.hpp"
47	+	#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50	+	#include "utils/PhysicalConstants.hpp"
51	+	#include "utils/Tuple.hpp"
52
53		#ifndef IS_MPI
54		#include "math/SeqRandNumGen.hpp"
55		#else
56	+	#include <mpi.h>
57		#include "math/ParallelRandNumGen.hpp"
58		#endif
59
60	<	/* 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_["PxScale"] = rnemdPxScale;
77	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
78	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
79		stringToEnumMap_["Px"] = rnemdPx;
80		stringToEnumMap_["Py"] = rnemdPy;
81		stringToEnumMap_["Pz"] = rnemdPz;
82		stringToEnumMap_["Unknown"] = rnemdUnknown;
83
84	<	const std::string st = simParams->getRNEMD_swapType();
84	>	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
85	>	evaluator_.loadScriptString(rnemdObjectSelection_);
86	>	seleMan_.setSelectionSet(evaluator_.evaluate());
87
88	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
88	>	// do some sanity checking
89	>
90	>	int selectionCount = seleMan_.getSelectionCount();
91	>	int nIntegrable = info->getNGlobalIntegrableObjects();
92	>
93	>	if (selectionCount > nIntegrable) {
94	>	sprintf(painCave.errMsg,
95	>	"RNEMD: The current RNEMD_objectSelection,\n"
96	>	"\t\t%s\n"
97	>	"\thas resulted in %d selected objects.  However,\n"
98	>	"\tthe total number of integrable objects in the system\n"
99	>	"\tis only %d.  This is almost certainly not what you want\n"
100	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
101	>	"\tselector in the selection script!\n",
102	>	rnemdObjectSelection_.c_str(),
103	>	selectionCount, nIntegrable);
104	>	painCave.isFatal = 0;
105	>	painCave.severity = OPENMD_WARNING;
106	>	simError();
107	>	}
108	>
109	>	const string st = simParams->getRNEMD_exchangeType();
110	>
111	>	map<string, RNEMDTypeEnum>::iterator i;
112		i = stringToEnumMap_.find(st);
113	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
113	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
114	>	if (rnemdType_ == rnemdUnknown) {
115	>	sprintf(painCave.errMsg,
116	>	"RNEMD: The current RNEMD_exchangeType,\n"
117	>	"\t\t%s\n"
118	>	"\tis not one of the recognized exchange types.\n",
119	>	st.c_str());
120	>	painCave.isFatal = 1;
121	>	painCave.severity = OPENMD_ERROR;
122	>	simError();
123	>	}
124	>
125	>	output3DTemp_ = false;
126	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
127	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
128	>	}
129
130	+	#ifdef IS_MPI
131	+	if (worldRank == 0) {
132	+	#endif
133
134	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
134	>	string rnemdFileName;
135	>	switch(rnemdType_) {
136	>	case rnemdKineticSwap :
137	>	case rnemdKineticScale :
138	>	rnemdFileName = "temperature.log";
139	>	break;
140	>	case rnemdPx :
141	>	case rnemdPxScale :
142	>	case rnemdPy :
143	>	case rnemdPyScale :
144	>	rnemdFileName = "momemtum.log";
145	>	break;
146	>	case rnemdPz :
147	>	case rnemdPzScale :
148	>	case rnemdUnknown :
149	>	default :
150	>	rnemdFileName = "rnemd.log";
151	>	break;
152	>	}
153	>	rnemdLog_.open(rnemdFileName.c_str());
154	>
155	>	string xTempFileName;
156	>	string yTempFileName;
157	>	string zTempFileName;
158	>	if (output3DTemp_) {
159	>	xTempFileName = "temperatureX.log";
160	>	yTempFileName = "temperatureY.log";
161	>	zTempFileName = "temperatureZ.log";
162	>	xTempLog_.open(xTempFileName.c_str());
163	>	yTempLog_.open(yTempFileName.c_str());
164	>	zTempLog_.open(zTempFileName.c_str());
165	>	}
166	>
167	>	#ifdef IS_MPI
168	>	}
169	>	#endif
170	>
171	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
172		set_RNEMD_nBins(simParams->getRNEMD_nBins());
173	<	exchangeSum_ = 0.0;
174	<
173	>	midBin_ = nBins_ / 2;
174	>	if (simParams->haveRNEMD_binShift()) {
175	>	if (simParams->getRNEMD_binShift()) {
176	>	zShift_ = 0.5 / (RealType)(nBins_);
177	>	} else {
178	>	zShift_ = 0.0;
179	>	}
180	>	} else {
181	>	zShift_ = 0.0;
182	>	}
183	>	//cerr << "we have zShift_ = " << zShift_ << "\n";
184	>	//shift slabs by half slab width, might be useful in heterogeneous systems
185	>	//set to 0.0 if not using it; can NOT be used in status output yet
186	>	if (simParams->haveRNEMD_logWidth()) {
187	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
188	>	/*arbitary rnemdLogWidth_ no checking
189	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
190	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
191	>	cerr << "Automaically set back to default.\n";
192	>	rnemdLogWidth_ = nBins_;
193	>	}*/
194	>	} else {
195	>	set_RNEMD_logWidth(nBins_);
196	>	}
197	>	valueHist_.resize(rnemdLogWidth_, 0.0);
198	>	valueCount_.resize(rnemdLogWidth_, 0);
199	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
200	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
201	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
202	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
203	>
204	>	set_RNEMD_exchange_total(0.0);
205	>	if (simParams->haveRNEMD_targetFlux()) {
206	>	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
207	>	} else {
208	>	set_RNEMD_target_flux(0.0);
209	>	}
210	>
211		#ifndef IS_MPI
212		if (simParams->haveSeed()) {
213		seedValue = simParams->getSeed();
#	Line 100 | Line 227 | namespace oopse {
227
228		RNEMD::~RNEMD() {
229		delete randNumGen_;
230	+
231	+	#ifdef IS_MPI
232	+	if (worldRank == 0) {
233	+	#endif
234	+
235	+	sprintf(painCave.errMsg,
236	+	"RNEMD: total failed trials: %d\n",
237	+	failTrialCount_);
238	+	painCave.isFatal = 0;
239	+	painCave.severity = OPENMD_INFO;
240	+	simError();
241	+
242	+	rnemdLog_.close();
243	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
244	+	sprintf(painCave.errMsg,
245	+	"RNEMD: total root-checking warnings: %d\n",
246	+	failRootCount_);
247	+	painCave.isFatal = 0;
248	+	painCave.severity = OPENMD_INFO;
249	+	simError();
250	+	}
251	+	if (output3DTemp_) {
252	+	xTempLog_.close();
253	+	yTempLog_.close();
254	+	zTempLog_.close();
255	+	}
256	+	#ifdef IS_MPI
257	+	}
258	+	#endif
259		}
260
261		void RNEMD::doSwap() {
262	<	std::cerr << "in RNEMD!\n";
263	<	std::cerr << "nBins = " << nBins_ << "\n";
264	<	std::cerr << "swapTime = " << swapTime_ << "\n";
265	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
266	<	std::cerr << "swapType = " << rnemdType_ << "\n";
267	<	}
262	>
263	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
264	>	Mat3x3d hmat = currentSnap_->getHmat();
265	>
266	>	seleMan_.setSelectionSet(evaluator_.evaluate());
267	>
268	>	int selei;
269	>	StuntDouble* sd;
270	>	int idx;
271	>
272	>	RealType min_val;
273	>	bool min_found = false;
274	>	StuntDouble* min_sd;
275	>
276	>	RealType max_val;
277	>	bool max_found = false;
278	>	StuntDouble* max_sd;
279	>
280	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
281	>	sd = seleMan_.nextSelected(selei)) {
282	>
283	>	idx = sd->getLocalIndex();
284	>
285	>	Vector3d pos = sd->getPos();
286	>
287	>	// wrap the stuntdouble's position back into the box:
288	>
289	>	if (usePeriodicBoundaryConditions_)
290	>	currentSnap_->wrapVector(pos);
291	>
292	>	// which bin is this stuntdouble in?
293	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
294	>
295	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
296	>
297	>
298	>	// if we're in bin 0 or the middleBin
299	>	if (binNo == 0 || binNo == midBin_) {
300	>
301	>	RealType mass = sd->getMass();
302	>	Vector3d vel = sd->getVel();
303	>	RealType value;
304	>
305	>	switch(rnemdType_) {
306	>	case rnemdKineticSwap :
307	>
308	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
309	>	vel[2]*vel[2]);
310	>	/*
311	>	if (sd->isDirectional()) {
312	>	Vector3d angMom = sd->getJ();
313	>	Mat3x3d I = sd->getI();
314	>
315	>	if (sd->isLinear()) {
316	>	int i = sd->linearAxis();
317	>	int j = (i + 1) % 3;
318	>	int k = (i + 2) % 3;
319	>	value += angMom[j] * angMom[j] / I(j, j) +
320	>	angMom[k] * angMom[k] / I(k, k);
321	>	} else {
322	>	value += angMom[0]*angMom[0]/I(0, 0)
323	>	+ angMom[1]*angMom[1]/I(1, 1)
324	>	+ angMom[2]*angMom[2]/I(2, 2);
325	>	}
326	>	} no exchange of angular momenta
327	>	*/
328	>	//make exchangeSum_ comparable between swap & scale
329	>	//temporarily without using energyConvert
330	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
331	>	value *= 0.5;
332	>	break;
333	>	case rnemdPx :
334	>	value = mass * vel[0];
335	>	break;
336	>	case rnemdPy :
337	>	value = mass * vel[1];
338	>	break;
339	>	case rnemdPz :
340	>	value = mass * vel[2];
341	>	break;
342	>	default :
343	>	break;
344	>	}
345	>
346	>	if (binNo == 0) {
347	>	if (!min_found) {
348	>	min_val = value;
349	>	min_sd = sd;
350	>	min_found = true;
351	>	} else {
352	>	if (min_val > value) {
353	>	min_val = value;
354	>	min_sd = sd;
355	>	}
356	>	}
357	>	} else { //midBin_
358	>	if (!max_found) {
359	>	max_val = value;
360	>	max_sd = sd;
361	>	max_found = true;
362	>	} else {
363	>	if (max_val < value) {
364	>	max_val = value;
365	>	max_sd = sd;
366	>	}
367	>	}
368	>	}
369	>	}
370	>	}
371	>
372	>	#ifdef IS_MPI
373	>	int nProc, worldRank;
374	>
375	>	nProc = MPI::COMM_WORLD.Get_size();
376	>	worldRank = MPI::COMM_WORLD.Get_rank();
377	>
378	>	bool my_min_found = min_found;
379	>	bool my_max_found = max_found;
380	>
381	>	// Even if we didn't find a minimum, did someone else?
382	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
383	>	// Even if we didn't find a maximum, did someone else?
384	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
385	>	struct {
386	>	RealType val;
387	>	int rank;
388	>	} max_vals, min_vals;
389	>
390	>	if (min_found) {
391	>	if (my_min_found)
392	>	min_vals.val = min_val;
393	>	else
394	>	min_vals.val = HONKING_LARGE_VALUE;
395	>
396	>	min_vals.rank = worldRank;
397	>
398	>	// Who had the minimum?
399	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
400	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
401	>	min_val = min_vals.val;
402	>	}
403	>
404	>	if (max_found) {
405	>	if (my_max_found)
406	>	max_vals.val = max_val;
407	>	else
408	>	max_vals.val = -HONKING_LARGE_VALUE;
409	>
410	>	max_vals.rank = worldRank;
411	>
412	>	// Who had the maximum?
413	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
414	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
415	>	max_val = max_vals.val;
416	>	}
417	>	#endif
418	>
419	>	if (max_found && min_found) {
420	>	if (min_val < max_val) {
421	>
422	>	#ifdef IS_MPI
423	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
424	>	// I have both maximum and minimum, so proceed like a single
425	>	// processor version:
426	>	#endif
427	>	// objects to be swapped: velocity ONLY
428	>	Vector3d min_vel = min_sd->getVel();
429	>	Vector3d max_vel = max_sd->getVel();
430	>	RealType temp_vel;
431	>
432	>	switch(rnemdType_) {
433	>	case rnemdKineticSwap :
434	>	min_sd->setVel(max_vel);
435	>	max_sd->setVel(min_vel);
436	>	/*
437	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
438	>	Vector3d min_angMom = min_sd->getJ();
439	>	Vector3d max_angMom = max_sd->getJ();
440	>	min_sd->setJ(max_angMom);
441	>	max_sd->setJ(min_angMom);
442	>	} no angular momentum exchange
443	>	*/
444	>	break;
445	>	case rnemdPx :
446	>	temp_vel = min_vel.x();
447	>	min_vel.x() = max_vel.x();
448	>	max_vel.x() = temp_vel;
449	>	min_sd->setVel(min_vel);
450	>	max_sd->setVel(max_vel);
451	>	break;
452	>	case rnemdPy :
453	>	temp_vel = min_vel.y();
454	>	min_vel.y() = max_vel.y();
455	>	max_vel.y() = temp_vel;
456	>	min_sd->setVel(min_vel);
457	>	max_sd->setVel(max_vel);
458	>	break;
459	>	case rnemdPz :
460	>	temp_vel = min_vel.z();
461	>	min_vel.z() = max_vel.z();
462	>	max_vel.z() = temp_vel;
463	>	min_sd->setVel(min_vel);
464	>	max_sd->setVel(max_vel);
465	>	break;
466	>	default :
467	>	break;
468	>	}
469	>	#ifdef IS_MPI
470	>	// the rest of the cases only apply in parallel simulations:
471	>	} else if (max_vals.rank == worldRank) {
472	>	// I had the max, but not the minimum
473	>
474	>	Vector3d min_vel;
475	>	Vector3d max_vel = max_sd->getVel();
476	>	MPI::Status status;
477	>
478	>	// point-to-point swap of the velocity vector
479	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
480	>	min_vals.rank, 0,
481	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
482	>	min_vals.rank, 0, status);
483	>
484	>	switch(rnemdType_) {
485	>	case rnemdKineticSwap :
486	>	max_sd->setVel(min_vel);
487	>	//no angular momentum exchange for now
488	>	/*
489	>	if (max_sd->isDirectional()) {
490	>	Vector3d min_angMom;
491	>	Vector3d max_angMom = max_sd->getJ();
492	>
493	>	// point-to-point swap of the angular momentum vector
494	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
495	>	MPI::REALTYPE, min_vals.rank, 1,
496	>	min_angMom.getArrayPointer(), 3,
497	>	MPI::REALTYPE, min_vals.rank, 1,
498	>	status);
499	>
500	>	max_sd->setJ(min_angMom);
501	>	}
502	>	*/
503	>	break;
504	>	case rnemdPx :
505	>	max_vel.x() = min_vel.x();
506	>	max_sd->setVel(max_vel);
507	>	break;
508	>	case rnemdPy :
509	>	max_vel.y() = min_vel.y();
510	>	max_sd->setVel(max_vel);
511	>	break;
512	>	case rnemdPz :
513	>	max_vel.z() = min_vel.z();
514	>	max_sd->setVel(max_vel);
515	>	break;
516	>	default :
517	>	break;
518	>	}
519	>	} else if (min_vals.rank == worldRank) {
520	>	// I had the minimum but not the maximum:
521	>
522	>	Vector3d max_vel;
523	>	Vector3d min_vel = min_sd->getVel();
524	>	MPI::Status status;
525	>
526	>	// point-to-point swap of the velocity vector
527	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
528	>	max_vals.rank, 0,
529	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
530	>	max_vals.rank, 0, status);
531	>
532	>	switch(rnemdType_) {
533	>	case rnemdKineticSwap :
534	>	min_sd->setVel(max_vel);
535	>	// no angular momentum exchange for now
536	>	/*
537	>	if (min_sd->isDirectional()) {
538	>	Vector3d min_angMom = min_sd->getJ();
539	>	Vector3d max_angMom;
540	>
541	>	// point-to-point swap of the angular momentum vector
542	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
543	>	MPI::REALTYPE, max_vals.rank, 1,
544	>	max_angMom.getArrayPointer(), 3,
545	>	MPI::REALTYPE, max_vals.rank, 1,
546	>	status);
547	>
548	>	min_sd->setJ(max_angMom);
549	>	}
550	>	*/
551	>	break;
552	>	case rnemdPx :
553	>	min_vel.x() = max_vel.x();
554	>	min_sd->setVel(min_vel);
555	>	break;
556	>	case rnemdPy :
557	>	min_vel.y() = max_vel.y();
558	>	min_sd->setVel(min_vel);
559	>	break;
560	>	case rnemdPz :
561	>	min_vel.z() = max_vel.z();
562	>	min_sd->setVel(min_vel);
563	>	break;
564	>	default :
565	>	break;
566	>	}
567	>	}
568	>	#endif
569	>	exchangeSum_ += max_val - min_val;
570	>	} else {
571	>	sprintf(painCave.errMsg,
572	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
573	>	painCave.isFatal = 0;
574	>	painCave.severity = OPENMD_INFO;
575	>	simError();
576	>	failTrialCount_++;
577	>	}
578	>	} else {
579	>	sprintf(painCave.errMsg,
580	>	"RNEMD: exchange NOT performed because at least one\n"
581	>	"\tof the two slabs is empty\n");
582	>	painCave.isFatal = 0;
583	>	painCave.severity = OPENMD_INFO;
584	>	simError();
585	>	failTrialCount_++;
586	>	}
587	>
588	>	}
589	>
590	>	void RNEMD::doScale() {
591	>
592	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
593	>	Mat3x3d hmat = currentSnap_->getHmat();
594	>
595	>	seleMan_.setSelectionSet(evaluator_.evaluate());
596	>
597	>	int selei;
598	>	StuntDouble* sd;
599	>	int idx;
600	>
601	>	vector<StuntDouble*> hotBin, coldBin;
602	>
603	>	RealType Phx = 0.0;
604	>	RealType Phy = 0.0;
605	>	RealType Phz = 0.0;
606	>	RealType Khx = 0.0;
607	>	RealType Khy = 0.0;
608	>	RealType Khz = 0.0;
609	>	RealType Pcx = 0.0;
610	>	RealType Pcy = 0.0;
611	>	RealType Pcz = 0.0;
612	>	RealType Kcx = 0.0;
613	>	RealType Kcy = 0.0;
614	>	RealType Kcz = 0.0;
615	>
616	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
617	>	sd = seleMan_.nextSelected(selei)) {
618	>
619	>	idx = sd->getLocalIndex();
620	>
621	>	Vector3d pos = sd->getPos();
622	>
623	>	// wrap the stuntdouble's position back into the box:
624	>
625	>	if (usePeriodicBoundaryConditions_)
626	>	currentSnap_->wrapVector(pos);
627	>
628	>	// which bin is this stuntdouble in?
629	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
630	>
631	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
632	>
633	>	// if we're in bin 0 or the middleBin
634	>	if (binNo == 0 || binNo == midBin_) {
635	>
636	>	RealType mass = sd->getMass();
637	>	Vector3d vel = sd->getVel();
638	>
639	>	if (binNo == 0) {
640	>	hotBin.push_back(sd);
641	>	Phx += mass * vel.x();
642	>	Phy += mass * vel.y();
643	>	Phz += mass * vel.z();
644	>	Khx += mass * vel.x() * vel.x();
645	>	Khy += mass * vel.y() * vel.y();
646	>	Khz += mass * vel.z() * vel.z();
647	>	} else { //midBin_
648	>	coldBin.push_back(sd);
649	>	Pcx += mass * vel.x();
650	>	Pcy += mass * vel.y();
651	>	Pcz += mass * vel.z();
652	>	Kcx += mass * vel.x() * vel.x();
653	>	Kcy += mass * vel.y() * vel.y();
654	>	Kcz += mass * vel.z() * vel.z();
655	>	}
656	>	}
657	>	}
658	>
659	>	Khx *= 0.5;
660	>	Khy *= 0.5;
661	>	Khz *= 0.5;
662	>	Kcx *= 0.5;
663	>	Kcy *= 0.5;
664	>	Kcz *= 0.5;
665	>
666	>	#ifdef IS_MPI
667	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
668	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
669	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
670	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
671	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
672	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
673	>
674	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
675	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
676	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
677	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
678	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
679	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
680	>	#endif
681	>
682	>	//use coldBin coeff's
683	>	RealType px = Pcx / Phx;
684	>	RealType py = Pcy / Phy;
685	>	RealType pz = Pcz / Phz;
686	>
687	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
688	>	switch(rnemdType_) {
689	>	case rnemdKineticScale :
690	>	// used hotBin coeff's & only scale x & y dimensions
691	>	/*
692	>	RealType px = Phx / Pcx;
693	>	RealType py = Phy / Pcy;
694	>	a110 = Khy;
695	>	c0 = - Khx - Khy - targetFlux_;
696	>	a000 = Khx;
697	>	a111 = Kcy * py * py;
698	>	b11 = -2.0 * Kcy * py * (1.0 + py);
699	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
700	>	b01 = -2.0 * Kcx * px * (1.0 + px);
701	>	a001 = Kcx * px * px;
702	>	*/
703	>	//scale all three dimensions, let c_x = c_y
704	>	a000 = Kcx + Kcy;
705	>	a110 = Kcz;
706	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
707	>	a001 = Khx * px * px + Khy * py * py;
708	>	a111 = Khz * pz * pz;
709	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
710	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
711	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
712	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
713	>	break;
714	>	case rnemdPxScale :
715	>	c = 1 - targetFlux_ / Pcx;
716	>	a000 = Kcy;
717	>	a110 = Kcz;
718	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
719	>	a001 = py * py * Khy;
720	>	a111 = pz * pz * Khz;
721	>	b01 = -2.0 * Khy * py * (1.0 + py);
722	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
723	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
724	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
725	>	break;
726	>	case rnemdPyScale :
727	>	c = 1 - targetFlux_ / Pcy;
728	>	a000 = Kcx;
729	>	a110 = Kcz;
730	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
731	>	a001 = px * px * Khx;
732	>	a111 = pz * pz * Khz;
733	>	b01 = -2.0 * Khx * px * (1.0 + px);
734	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
735	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
736	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
737	>	break;
738	>	case rnemdPzScale ://we don't really do this, do we?
739	>	c = 1 - targetFlux_ / Pcz;
740	>	a000 = Kcx;
741	>	a110 = Kcy;
742	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
743	>	a001 = px * px * Khx;
744	>	a111 = py * py * Khy;
745	>	b01 = -2.0 * Khx * px * (1.0 + px);
746	>	b11 = -2.0 * Khy * py * (1.0 + py);
747	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
748	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
749	>	break;
750	>	default :
751	>	break;
752	>	}
753	>
754	>	RealType v1 = a000 * a111 - a001 * a110;
755	>	RealType v2 = a000 * b01;
756	>	RealType v3 = a000 * b11;
757	>	RealType v4 = a000 * c1 - a001 * c0;
758	>	RealType v8 = a110 * b01;
759	>	RealType v10 = - b01 * c0;
760	>
761	>	RealType u0 = v2 * v10 - v4 * v4;
762	>	RealType u1 = -2.0 * v3 * v4;
763	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
764	>	RealType u3 = -2.0 * v1 * v3;
765	>	RealType u4 = - v1 * v1;
766	>	//rescale coefficients
767	>	RealType maxAbs = fabs(u0);
768	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
769	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
770	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
771	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
772	>	u0 /= maxAbs;
773	>	u1 /= maxAbs;
774	>	u2 /= maxAbs;
775	>	u3 /= maxAbs;
776	>	u4 /= maxAbs;
777	>	//max_element(start, end) is also available.
778	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
779	>	poly.setCoefficient(4, u4);
780	>	poly.setCoefficient(3, u3);
781	>	poly.setCoefficient(2, u2);
782	>	poly.setCoefficient(1, u1);
783	>	poly.setCoefficient(0, u0);
784	>	vector<RealType> realRoots = poly.FindRealRoots();
785	>
786	>	vector<RealType>::iterator ri;
787	>	RealType r1, r2, alpha0;
788	>	vector<pair<RealType,RealType> > rps;
789	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
790	>	r2 = *ri;
791	>	//check if FindRealRoots() give the right answer
792	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
793	>	sprintf(painCave.errMsg,
794	>	"RNEMD Warning: polynomial solve seems to have an error!");
795	>	painCave.isFatal = 0;
796	>	simError();
797	>	failRootCount_++;
798	>	}
799	>	//might not be useful w/o rescaling coefficients
800	>	alpha0 = -c0 - a110 * r2 * r2;
801	>	if (alpha0 >= 0.0) {
802	>	r1 = sqrt(alpha0 / a000);
803	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
804	>	{ rps.push_back(make_pair(r1, r2)); }
805	>	if (r1 > 1e-6) { //r1 non-negative
806	>	r1 = -r1;
807	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
808	>	{ rps.push_back(make_pair(r1, r2)); }
809	>	}
810	>	}
811	>	}
812	>	// Consider combining together the solving pair part w/ the searching
813	>	// best solution part so that we don't need the pairs vector
814	>	if (!rps.empty()) {
815	>	RealType smallestDiff = HONKING_LARGE_VALUE;
816	>	RealType diff;
817	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
818	>	vector<pair<RealType,RealType> >::iterator rpi;
819	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
820	>	r1 = (*rpi).first;
821	>	r2 = (*rpi).second;
822	>	switch(rnemdType_) {
823	>	case rnemdKineticScale :
824	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
825	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
826	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
827	>	break;
828	>	case rnemdPxScale :
829	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
830	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
831	>	break;
832	>	case rnemdPyScale :
833	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
834	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
835	>	break;
836	>	case rnemdPzScale :
837	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
838	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
839	>	default :
840	>	break;
841	>	}
842	>	if (diff < smallestDiff) {
843	>	smallestDiff = diff;
844	>	bestPair = *rpi;
845	>	}
846	>	}
847	>	#ifdef IS_MPI
848	>	if (worldRank == 0) {
849	>	#endif
850	>	sprintf(painCave.errMsg,
851	>	"RNEMD: roots r1= %lf\tr2 = %lf\n",
852	>	bestPair.first, bestPair.second);
853	>	painCave.isFatal = 0;
854	>	painCave.severity = OPENMD_INFO;
855	>	simError();
856	>	#ifdef IS_MPI
857	>	}
858	>	#endif
859	>
860	>	RealType x, y, z;
861	>	switch(rnemdType_) {
862	>	case rnemdKineticScale :
863	>	x = bestPair.first;
864	>	y = bestPair.first;
865	>	z = bestPair.second;
866	>	break;
867	>	case rnemdPxScale :
868	>	x = c;
869	>	y = bestPair.first;
870	>	z = bestPair.second;
871	>	break;
872	>	case rnemdPyScale :
873	>	x = bestPair.first;
874	>	y = c;
875	>	z = bestPair.second;
876	>	break;
877	>	case rnemdPzScale :
878	>	x = bestPair.first;
879	>	y = bestPair.second;
880	>	z = c;
881	>	break;
882	>	default :
883	>	break;
884	>	}
885	>	vector<StuntDouble*>::iterator sdi;
886	>	Vector3d vel;
887	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
888	>	vel = (*sdi)->getVel();
889	>	vel.x() *= x;
890	>	vel.y() *= y;
891	>	vel.z() *= z;
892	>	(*sdi)->setVel(vel);
893	>	}
894	>	//convert to hotBin coefficient
895	>	x = 1.0 + px * (1.0 - x);
896	>	y = 1.0 + py * (1.0 - y);
897	>	z = 1.0 + pz * (1.0 - z);
898	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
899	>	vel = (*sdi)->getVel();
900	>	vel.x() *= x;
901	>	vel.y() *= y;
902	>	vel.z() *= z;
903	>	(*sdi)->setVel(vel);
904	>	}
905	>	exchangeSum_ += targetFlux_;
906	>	//we may want to check whether the exchange has been successful
907	>	} else {
908	>	sprintf(painCave.errMsg,
909	>	"RNEMD: exchange NOT performed!\n");
910	>	painCave.isFatal = 0;
911	>	painCave.severity = OPENMD_INFO;
912	>	simError();
913	>	failTrialCount_++;
914	>	}
915	>
916	>	}
917	>
918	>	void RNEMD::doRNEMD() {
919	>
920	>	switch(rnemdType_) {
921	>	case rnemdKineticScale :
922	>	case rnemdPxScale :
923	>	case rnemdPyScale :
924	>	case rnemdPzScale :
925	>	doScale();
926	>	break;
927	>	case rnemdKineticSwap :
928	>	case rnemdPx :
929	>	case rnemdPy :
930	>	case rnemdPz :
931	>	doSwap();
932	>	break;
933	>	case rnemdUnknown :
934	>	default :
935	>	break;
936	>	}
937	>	}
938	>
939	>	void RNEMD::collectData() {
940	>
941	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
942	>	Mat3x3d hmat = currentSnap_->getHmat();
943	>
944	>	seleMan_.setSelectionSet(evaluator_.evaluate());
945	>
946	>	int selei;
947	>	StuntDouble* sd;
948	>	int idx;
949	>
950	>	// alternative approach, track all molecules instead of only those
951	>	// selected for scaling/swapping:
952	>	/*
953	>	SimInfo::MoleculeIterator miter;
954	>	vector<StuntDouble*>::iterator iiter;
955	>	Molecule* mol;
956	>	StuntDouble* integrableObject;
957	>	for (mol = info_->beginMolecule(miter); mol != NULL;
958	>	mol = info_->nextMolecule(miter))
959	>	integrableObject is essentially sd
960	>	for (integrableObject = mol->beginIntegrableObject(iiter);
961	>	integrableObject != NULL;
962	>	integrableObject = mol->nextIntegrableObject(iiter))
963	>	*/
964	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
965	>	sd = seleMan_.nextSelected(selei)) {
966	>
967	>	idx = sd->getLocalIndex();
968	>
969	>	Vector3d pos = sd->getPos();
970	>
971	>	// wrap the stuntdouble's position back into the box:
972	>
973	>	if (usePeriodicBoundaryConditions_)
974	>	currentSnap_->wrapVector(pos);
975	>
976	>	// which bin is this stuntdouble in?
977	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
978	>
979	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
980	>	rnemdLogWidth_;
981	>	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
982	>	/*
983	>	if (rnemdLogWidth_ == midBin_ + 1)
984	>	if (binNo > midBin_)
985	>	binNo = nBins_ - binNo;
986	>	*/
987	>	RealType mass = sd->getMass();
988	>	Vector3d vel = sd->getVel();
989	>	RealType value;
990	>	RealType xVal, yVal, zVal;
991	>
992	>	switch(rnemdType_) {
993	>	case rnemdKineticSwap :
994	>	case rnemdKineticScale :
995	>
996	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
997	>
998	>	valueCount_[binNo] += 3;
999	>	if (sd->isDirectional()) {
1000	>	Vector3d angMom = sd->getJ();
1001	>	Mat3x3d I = sd->getI();
1002	>
1003	>	if (sd->isLinear()) {
1004	>	int i = sd->linearAxis();
1005	>	int j = (i + 1) % 3;
1006	>	int k = (i + 2) % 3;
1007	>	value += angMom[j] * angMom[j] / I(j, j) +
1008	>	angMom[k] * angMom[k] / I(k, k);
1009	>
1010	>	valueCount_[binNo] +=2;
1011	>
1012	>	} else {
1013	>	value += angMom[0]*angMom[0]/I(0, 0)
1014	>	+ angMom[1]*angMom[1]/I(1, 1)
1015	>	+ angMom[2]*angMom[2]/I(2, 2);
1016	>	valueCount_[binNo] +=3;
1017	>	}
1018	>	}
1019	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1020	>
1021	>	break;
1022	>	case rnemdPx :
1023	>	case rnemdPxScale :
1024	>	value = mass * vel[0];
1025	>	valueCount_[binNo]++;
1026	>	break;
1027	>	case rnemdPy :
1028	>	case rnemdPyScale :
1029	>	value = mass * vel[1];
1030	>	valueCount_[binNo]++;
1031	>	break;
1032	>	case rnemdPz :
1033	>	case rnemdPzScale :
1034	>	value = pos.z(); //temporarily for homogeneous systems ONLY
1035	>	valueCount_[binNo]++;
1036	>	break;
1037	>	case rnemdUnknown :
1038	>	default :
1039	>	value = 1.0;
1040	>	valueCount_[binNo]++;
1041	>	break;
1042	>	}
1043	>	valueHist_[binNo] += value;
1044	>
1045	>	if (output3DTemp_) {
1046	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1047	>	/ PhysicalConstants::kb;
1048	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1049	>	/ PhysicalConstants::kb;
1050	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1051	>	/ PhysicalConstants::kb;
1052	>	xTempHist_[binNo] += xVal;
1053	>	yTempHist_[binNo] += yVal;
1054	>	zTempHist_[binNo] += zVal;
1055	>	xyzTempCount_[binNo]++;
1056	>	}
1057	>	}
1058	>	}
1059	>
1060	>	void RNEMD::getStarted() {
1061	>	collectData();
1062	>	/* now should be able to output profile in step 0, but might not be useful
1063	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1064	>	Stats& stat = currentSnap_->statData;
1065	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1066	>	*/
1067	>	getStatus();
1068	>	}
1069	>
1070	>	void RNEMD::getStatus() {
1071	>
1072	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1073	>	Stats& stat = currentSnap_->statData;
1074	>	RealType time = currentSnap_->getTime();
1075	>
1076	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1077	>	//or to be more meaningful, define another item as exchangeSum_ / time
1078	>	int j;
1079	>
1080	>	#ifdef IS_MPI
1081	>
1082	>	// all processors have the same number of bins, and STL vectors pack their
1083	>	// arrays, so in theory, this should be safe:
1084	>
1085	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1086	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1087	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1088	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1089	>	if (output3DTemp_) {
1090	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1091	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1092	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1093	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1094	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1095	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1096	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1097	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1098	>	}
1099	>	// If we're the root node, should we print out the results
1100	>	int worldRank = MPI::COMM_WORLD.Get_rank();
1101	>	if (worldRank == 0) {
1102	>	#endif
1103	>	rnemdLog_ << time;
1104	>	for (j = 0; j < rnemdLogWidth_; j++) {
1105	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1106	>	}
1107	>	rnemdLog_ << "\n";
1108	>	if (output3DTemp_) {
1109	>	xTempLog_ << time;
1110	>	for (j = 0; j < rnemdLogWidth_; j++) {
1111	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1112	>	}
1113	>	xTempLog_ << "\n";
1114	>	yTempLog_ << time;
1115	>	for (j = 0; j < rnemdLogWidth_; j++) {
1116	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1117	>	}
1118	>	yTempLog_ << "\n";
1119	>	zTempLog_ << time;
1120	>	for (j = 0; j < rnemdLogWidth_; j++) {
1121	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1122	>	}
1123	>	zTempLog_ << "\n";
1124	>	}
1125	>	#ifdef IS_MPI
1126	>	}
1127	>	#endif
1128	>	for (j = 0; j < rnemdLogWidth_; j++) {
1129	>	valueCount_[j] = 0;
1130	>	valueHist_[j] = 0.0;
1131	>	}
1132	>	if (output3DTemp_)
1133	>	for (j = 0; j < rnemdLogWidth_; j++) {
1134	>	xTempHist_[j] = 0.0;
1135	>	yTempHist_[j] = 0.0;
1136	>	zTempHist_[j] = 0.0;
1137	>	xyzTempCount_[j] = 0;
1138	>	}
1139	>	}
1140		}

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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