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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42	+	#include <cmath>
43		#include "integrators/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45		#include "math/SquareMatrix3.hpp"
46	+	#include "math/Polynomial.hpp"
47		#include "primitives/Molecule.hpp"
48		#include "primitives/StuntDouble.hpp"
49	<	#include "utils/OOPSEConstant.hpp"
49	>	#include "utils/PhysicalConstants.hpp"
50		#include "utils/Tuple.hpp"
51
52		#ifndef IS_MPI
#	Line 53 | Line 55
55		#include "math/ParallelRandNumGen.hpp"
56		#endif
57
58	<	/* Remove me after testing*/
57	<	/*
58	<	#include <cstdio>
59	<	#include <iostream>
60	<	*/
61	<	/*End remove me*/
58	>	#define HONKING_LARGE_VALUE 1.0e10
59
60	<	namespace oopse {
60	>	namespace OpenMD {
61
62		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63	<
63	>
64	>	failTrialCount_ = 0;
65	>	failRootCount_ = 0;
66	>
67		int seedValue;
68		Globals * simParams = info->getSimParams();
69
70	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
70	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
71	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
72	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
73	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
74	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
75		stringToEnumMap_["Px"] = rnemdPx;
76		stringToEnumMap_["Py"] = rnemdPy;
77		stringToEnumMap_["Pz"] = rnemdPz;
78		stringToEnumMap_["Unknown"] = rnemdUnknown;
79
80		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
77	–
78	–	std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
81		evaluator_.loadScriptString(rnemdObjectSelection_);
82	<	std::cerr << "done\n";
82	>	seleMan_.setSelectionSet(evaluator_.evaluate());
83	>
84	>	// do some sanity checking
85	>
86	>	int selectionCount = seleMan_.getSelectionCount();
87	>	int nIntegrable = info->getNGlobalIntegrableObjects();
88	>
89	>	if (selectionCount > nIntegrable) {
90	>	sprintf(painCave.errMsg,
91	>	"RNEMD warning: The current RNEMD_objectSelection,\n"
92	>	"\t\t%s\n"
93	>	"\thas resulted in %d selected objects.  However,\n"
94	>	"\tthe total number of integrable objects in the system\n"
95	>	"\tis only %d.  This is almost certainly not what you want\n"
96	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
97	>	"\tselector in the selection script!\n",
98	>	rnemdObjectSelection_.c_str(),
99	>	selectionCount, nIntegrable);
100	>	painCave.isFatal = 0;
101	>	simError();
102	>
103	>	}
104
105	<	const std::string st = simParams->getRNEMD_swapType();
105	>	const std::string st = simParams->getRNEMD_exchangeType();
106
107		std::map<std::string, RNEMDTypeEnum>::iterator i;
108		i = stringToEnumMap_.find(st);
109	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
109	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	>	if (rnemdType_ == rnemdUnknown) {
111	>	std::cerr << "WARNING! RNEMD Type Unknown!\n";
112	>	}
113
114	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
114	>	#ifdef IS_MPI
115	>	if (worldRank == 0) {
116	>	#endif
117	>
118	>	std::string rnemdFileName;
119	>	std::string xTempFileName;
120	>	std::string yTempFileName;
121	>	std::string zTempFileName;
122	>	switch(rnemdType_) {
123	>	case rnemdKineticSwap :
124	>	case rnemdKineticScale :
125	>	rnemdFileName = "temperature.log";
126	>	break;
127	>	case rnemdPx :
128	>	case rnemdPxScale :
129	>	case rnemdPy :
130	>	case rnemdPyScale :
131	>	rnemdFileName = "momemtum.log";
132	>	xTempFileName = "temperatureX.log";
133	>	yTempFileName = "temperatureY.log";
134	>	zTempFileName = "temperatureZ.log";
135	>	xTempLog_.open(xTempFileName.c_str());
136	>	yTempLog_.open(yTempFileName.c_str());
137	>	zTempLog_.open(zTempFileName.c_str());
138	>	break;
139	>	case rnemdPz :
140	>	case rnemdPzScale :
141	>	case rnemdUnknown :
142	>	default :
143	>	rnemdFileName = "rnemd.log";
144	>	break;
145	>	}
146	>	rnemdLog_.open(rnemdFileName.c_str());
147	>
148	>	#ifdef IS_MPI
149	>	}
150	>	#endif
151	>
152	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
153		set_RNEMD_nBins(simParams->getRNEMD_nBins());
154	<	exchangeSum_ = 0.0;
155	<	counter_ = 0; //added by shenyu
156	<	//profile_.open("profile", std::ios::out);
154	>	midBin_ = nBins_ / 2;
155	>	if (simParams->haveRNEMD_logWidth()) {
156	>	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
157	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
158	>	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
159	>	std::cerr << "Automaically set back to default.\n";
160	>	rnemdLogWidth_ = nBins_;
161	>	}
162	>	} else {
163	>	rnemdLogWidth_ = nBins_;
164	>	}
165	>	valueHist_.resize(rnemdLogWidth_, 0.0);
166	>	valueCount_.resize(rnemdLogWidth_, 0);
167	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
168	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
169	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
170
171	+	set_RNEMD_exchange_total(0.0);
172	+	if (simParams->haveRNEMD_targetFlux()) {
173	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
174	+	} else {
175	+	set_RNEMD_target_flux(0.0);
176	+	}
177	+
178		#ifndef IS_MPI
179		if (simParams->haveSeed()) {
180		seedValue = simParams->getSeed();
#	Line 110 | Line 194 | namespace oopse {
194
195		RNEMD::~RNEMD() {
196		delete randNumGen_;
197	<	//profile_.close();
197	>
198	>	#ifdef IS_MPI
199	>	if (worldRank == 0) {
200	>	#endif
201	>	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
202	>	rnemdLog_.close();
203	>	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
204	>	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
205	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
206	>	xTempLog_.close();
207	>	yTempLog_.close();
208	>	zTempLog_.close();
209	>	}
210	>	#ifdef IS_MPI
211	>	}
212	>	#endif
213		}
214
215		void RNEMD::doSwap() {
117	–	//std::cerr << "in RNEMD!\n";
118	–	//std::cerr << "nBins = " << nBins_ << "\n";
119	–	int midBin = nBins_ / 2;
120	–	//std::cerr << "midBin = " << midBin << "\n";
121	–	//std::cerr << "swapTime = " << swapTime_ << "\n";
122	–	//std::cerr << "swapType = " << rnemdType_ << "\n";
123	–	//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
216
217		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
218		Mat3x3d hmat = currentSnap_->getHmat();
219
128	–	//std::cerr << "hmat = " << hmat << "\n";
129	–
220		seleMan_.setSelectionSet(evaluator_.evaluate());
221
132	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
133	–
222		int selei;
223		StuntDouble* sd;
224		int idx;
#	Line 158 | Line 246 | namespace oopse {
246		// which bin is this stuntdouble in?
247		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
248
249	<	int binNo = int((nBins_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2));
249	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
250
163	–	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
251
252		// if we're in bin 0 or the middleBin
253	<	if (binNo == 0 || binNo == midBin) {
253	>	if (binNo == 0 || binNo == midBin_) {
254
255		RealType mass = sd->getMass();
256		Vector3d vel = sd->getVel();
257		RealType value;
258
259		switch(rnemdType_) {
260	<	case rnemdKinetic :
260	>	case rnemdKineticSwap :
261
262		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
263		vel[2]*vel[2]);
177	–
264		if (sd->isDirectional()) {
265		Vector3d angMom = sd->getJ();
266		Mat3x3d I = sd->getI();
#	Line 191 | Line 277 | namespace oopse {
277		+ angMom[2]*angMom[2]/I(2, 2);
278		}
279		}
280	<	value = value * 0.5 / OOPSEConstant::energyConvert;
280	>	//make exchangeSum_ comparable between swap & scale
281	>	//temporarily without using energyConvert
282	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
283	>	value *= 0.5;
284		break;
285		case rnemdPx :
286		value = mass * vel[0];
#	Line 202 | Line 291 | namespace oopse {
291		case rnemdPz :
292		value = mass * vel[2];
293		break;
205	–	case rnemdUnknown :
294		default :
295		break;
296		}
#	Line 218 | Line 306 | namespace oopse {
306		min_sd = sd;
307		}
308		}
309	<	} else {
309	>	} else { //midBin_
310		if (!max_found) {
311		max_val = value;
312		max_sd = sd;
#	Line 232 | Line 320 | namespace oopse {
320		}
321		}
322		}
323	<	//std::cerr << "smallest value = " << min_val  << "\n";
324	<	//std::cerr << "largest value = " << max_val << "\n";
323	>
324	>	#ifdef IS_MPI
325	>	int nProc, worldRank;
326	>
327	>	nProc = MPI::COMM_WORLD.Get_size();
328	>	worldRank = MPI::COMM_WORLD.Get_rank();
329	>
330	>	bool my_min_found = min_found;
331	>	bool my_max_found = max_found;
332	>
333	>	// Even if we didn't find a minimum, did someone else?
334	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
335	>	1, MPI::BOOL, MPI::LAND);
336
337	<	// missing:  swap information in parallel
337	>	// Even if we didn't find a maximum, did someone else?
338	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
339	>	1, MPI::BOOL, MPI::LAND);
340	>
341	>	struct {
342	>	RealType val;
343	>	int rank;
344	>	} max_vals, min_vals;
345	>
346	>	if (min_found) {
347	>	if (my_min_found)
348	>	min_vals.val = min_val;
349	>	else
350	>	min_vals.val = HONKING_LARGE_VALUE;
351	>
352	>	min_vals.rank = worldRank;
353	>
354	>	// Who had the minimum?
355	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
356	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
357	>	min_val = min_vals.val;
358	>	}
359	>
360	>	if (max_found) {
361	>	if (my_max_found)
362	>	max_vals.val = max_val;
363	>	else
364	>	max_vals.val = -HONKING_LARGE_VALUE;
365	>
366	>	max_vals.rank = worldRank;
367	>
368	>	// Who had the maximum?
369	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
370	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
371	>	max_val = max_vals.val;
372	>	}
373	>	#endif
374
375		if (max_found && min_found) {
376		if (min_val< max_val) {
377	<	Vector3d min_vel = min_sd->getVel();
378	<	Vector3d max_vel = max_sd->getVel();
379	<	RealType temp_vel;
380	<	switch(rnemdType_) {
381	<	case rnemdKinetic :
382	<	min_sd->setVel(max_vel);
383	<	max_sd->setVel(min_vel);
384	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
385	<	Vector3d min_angMom = min_sd->getJ();
386	<	Vector3d max_angMom = max_sd->getJ();
387	<	min_sd->setJ(max_angMom);
388	<	max_sd->setJ(min_angMom);
389	<	}
390	<	break;
391	<	case rnemdPx :
392	<	temp_vel = min_vel.x();
393	<	min_vel.x() = max_vel.x();
394	<	max_vel.x() = temp_vel;
395	<	min_sd->setVel(min_vel);
396	<	max_sd->setVel(max_vel);
397	<	break;
398	<	case rnemdPy :
399	<	temp_vel = min_vel.y();
400	<	min_vel.y() = max_vel.y();
401	<	max_vel.y() = temp_vel;
402	<	min_sd->setVel(min_vel);
403	<	max_sd->setVel(max_vel);
404	<	break;
405	<	case rnemdPz :
406	<	temp_vel = min_vel.z();
407	<	min_vel.z() = max_vel.z();
408	<	max_vel.z() = temp_vel;
409	<	min_sd->setVel(min_vel);
410	<	max_sd->setVel(max_vel);
411	<	break;
412	<	case rnemdUnknown :
413	<	default :
414	<	break;
415	<	}
416	<	exchangeSum_ += max_val - min_val;
377	>
378	>	#ifdef IS_MPI
379	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
380	>	// I have both maximum and minimum, so proceed like a single
381	>	// processor version:
382	>	#endif
383	>	// objects to be swapped: velocity & angular velocity
384	>	Vector3d min_vel = min_sd->getVel();
385	>	Vector3d max_vel = max_sd->getVel();
386	>	RealType temp_vel;
387	>
388	>	switch(rnemdType_) {
389	>	case rnemdKineticSwap :
390	>	min_sd->setVel(max_vel);
391	>	max_sd->setVel(min_vel);
392	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
393	>	Vector3d min_angMom = min_sd->getJ();
394	>	Vector3d max_angMom = max_sd->getJ();
395	>	min_sd->setJ(max_angMom);
396	>	max_sd->setJ(min_angMom);
397	>	}
398	>	break;
399	>	case rnemdPx :
400	>	temp_vel = min_vel.x();
401	>	min_vel.x() = max_vel.x();
402	>	max_vel.x() = temp_vel;
403	>	min_sd->setVel(min_vel);
404	>	max_sd->setVel(max_vel);
405	>	break;
406	>	case rnemdPy :
407	>	temp_vel = min_vel.y();
408	>	min_vel.y() = max_vel.y();
409	>	max_vel.y() = temp_vel;
410	>	min_sd->setVel(min_vel);
411	>	max_sd->setVel(max_vel);
412	>	break;
413	>	case rnemdPz :
414	>	temp_vel = min_vel.z();
415	>	min_vel.z() = max_vel.z();
416	>	max_vel.z() = temp_vel;
417	>	min_sd->setVel(min_vel);
418	>	max_sd->setVel(max_vel);
419	>	break;
420	>	default :
421	>	break;
422	>	}
423	>	#ifdef IS_MPI
424	>	// the rest of the cases only apply in parallel simulations:
425	>	} else if (max_vals.rank == worldRank) {
426	>	// I had the max, but not the minimum
427	>
428	>	Vector3d min_vel;
429	>	Vector3d max_vel = max_sd->getVel();
430	>	MPI::Status status;
431	>
432	>	// point-to-point swap of the velocity vector
433	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
434	>	min_vals.rank, 0,
435	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
436	>	min_vals.rank, 0, status);
437	>
438	>	switch(rnemdType_) {
439	>	case rnemdKineticSwap :
440	>	max_sd->setVel(min_vel);
441	>
442	>	if (max_sd->isDirectional()) {
443	>	Vector3d min_angMom;
444	>	Vector3d max_angMom = max_sd->getJ();
445	>
446	>	// point-to-point swap of the angular momentum vector
447	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
448	>	MPI::REALTYPE, min_vals.rank, 1,
449	>	min_angMom.getArrayPointer(), 3,
450	>	MPI::REALTYPE, min_vals.rank, 1,
451	>	status);
452	>
453	>	max_sd->setJ(min_angMom);
454	>	}
455	>	break;
456	>	case rnemdPx :
457	>	max_vel.x() = min_vel.x();
458	>	max_sd->setVel(max_vel);
459	>	break;
460	>	case rnemdPy :
461	>	max_vel.y() = min_vel.y();
462	>	max_sd->setVel(max_vel);
463	>	break;
464	>	case rnemdPz :
465	>	max_vel.z() = min_vel.z();
466	>	max_sd->setVel(max_vel);
467	>	break;
468	>	default :
469	>	break;
470	>	}
471	>	} else if (min_vals.rank == worldRank) {
472	>	// I had the minimum but not the maximum:
473	>
474	>	Vector3d max_vel;
475	>	Vector3d min_vel = min_sd->getVel();
476	>	MPI::Status status;
477	>
478	>	// point-to-point swap of the velocity vector
479	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
480	>	max_vals.rank, 0,
481	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
482	>	max_vals.rank, 0, status);
483	>
484	>	switch(rnemdType_) {
485	>	case rnemdKineticSwap :
486	>	min_sd->setVel(max_vel);
487	>
488	>	if (min_sd->isDirectional()) {
489	>	Vector3d min_angMom = min_sd->getJ();
490	>	Vector3d max_angMom;
491	>
492	>	// point-to-point swap of the angular momentum vector
493	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
494	>	MPI::REALTYPE, max_vals.rank, 1,
495	>	max_angMom.getArrayPointer(), 3,
496	>	MPI::REALTYPE, max_vals.rank, 1,
497	>	status);
498	>
499	>	min_sd->setJ(max_angMom);
500	>	}
501	>	break;
502	>	case rnemdPx :
503	>	min_vel.x() = max_vel.x();
504	>	min_sd->setVel(min_vel);
505	>	break;
506	>	case rnemdPy :
507	>	min_vel.y() = max_vel.y();
508	>	min_sd->setVel(min_vel);
509	>	break;
510	>	case rnemdPz :
511	>	min_vel.z() = max_vel.z();
512	>	min_sd->setVel(min_vel);
513	>	break;
514	>	default :
515	>	break;
516	>	}
517	>	}
518	>	#endif
519	>	exchangeSum_ += max_val - min_val;
520		} else {
521	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
521	>	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
522	>	failTrialCount_++;
523		}
524		} else {
525	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
525	>	std::cerr << "exchange NOT performed!\n";
526	>	std::cerr << "at least one of the two slabs empty.\n";
527	>	failTrialCount_++;
528		}
529	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
529	>
530		}
531	+
532	+	void RNEMD::doScale() {
533
291	–	void RNEMD::getStatus() {
292	–	//std::cerr << "in RNEMD!\n";
293	–	//std::cerr << "nBins = " << nBins_ << "\n";
294	–	int midBin = nBins_ / 2;
295	–	//std::cerr << "midBin = " << midBin << "\n";
296	–	//std::cerr << "swapTime = " << swapTime_ << "\n";
297	–	//std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
298	–	//std::cerr << "swapType = " << rnemdType_ << "\n";
299	–	//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
300	–
534		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
535		Mat3x3d hmat = currentSnap_->getHmat();
536
304	–	//std::cerr << "hmat = " << hmat << "\n";
305	–
537		seleMan_.setSelectionSet(evaluator_.evaluate());
538
308	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
309	–
539		int selei;
540		StuntDouble* sd;
541		int idx;
313	–	/*
314	–	RealType min_val;
315	–	bool min_found = false;
316	–	StuntDouble* min_sd;
542
543	<	RealType max_val;
544	<	bool max_found = false;
545	<	StuntDouble* max_sd;
543	>	std::vector<StuntDouble*> hotBin, coldBin;
544	>
545	>	RealType Phx = 0.0;
546	>	RealType Phy = 0.0;
547	>	RealType Phz = 0.0;
548	>	RealType Khx = 0.0;
549	>	RealType Khy = 0.0;
550	>	RealType Khz = 0.0;
551	>	RealType Pcx = 0.0;
552	>	RealType Pcy = 0.0;
553	>	RealType Pcz = 0.0;
554	>	RealType Kcx = 0.0;
555	>	RealType Kcy = 0.0;
556	>	RealType Kcz = 0.0;
557	>
558	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
559	>	sd = seleMan_.nextSelected(selei)) {
560	>
561	>	idx = sd->getLocalIndex();
562	>
563	>	Vector3d pos = sd->getPos();
564	>
565	>	// wrap the stuntdouble's position back into the box:
566	>
567	>	if (usePeriodicBoundaryConditions_)
568	>	currentSnap_->wrapVector(pos);
569	>
570	>	// which bin is this stuntdouble in?
571	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
572	>
573	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
574	>
575	>	// if we're in bin 0 or the middleBin
576	>	if (binNo == 0 || binNo == midBin_) {
577	>
578	>	RealType mass = sd->getMass();
579	>	Vector3d vel = sd->getVel();
580	>
581	>	if (binNo == 0) {
582	>	hotBin.push_back(sd);
583	>	Phx += mass * vel.x();
584	>	Phy += mass * vel.y();
585	>	Phz += mass * vel.z();
586	>	Khx += mass * vel.x() * vel.x();
587	>	Khy += mass * vel.y() * vel.y();
588	>	Khz += mass * vel.z() * vel.z();
589	>	} else { //midBin_
590	>	coldBin.push_back(sd);
591	>	Pcx += mass * vel.x();
592	>	Pcy += mass * vel.y();
593	>	Pcz += mass * vel.z();
594	>	Kcx += mass * vel.x() * vel.x();
595	>	Kcy += mass * vel.y() * vel.y();
596	>	Kcz += mass * vel.z() * vel.z();
597	>	}
598	>	}
599	>	}
600	>
601	>	Khx *= 0.5;
602	>	Khy *= 0.5;
603	>	Khz *= 0.5;
604	>	Kcx *= 0.5;
605	>	Kcy *= 0.5;
606	>	Kcz *= 0.5;
607	>
608	>	#ifdef IS_MPI
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
610	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
612	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
613	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
614	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
615	>
616	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
617	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
618	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
620	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
622	>	#endif
623	>
624	>	//use coldBin coeff's
625	>	RealType px = Pcx / Phx;
626	>	RealType py = Pcy / Phy;
627	>	RealType pz = Pcz / Phz;
628	>
629	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
630	>	switch(rnemdType_) {
631	>	case rnemdKineticScale :
632	>	/*used hotBin coeff's & only scale x & y dimensions
633	>	RealType px = Phx / Pcx;
634	>	RealType py = Phy / Pcy;
635	>	a110 = Khy;
636	>	c0 = - Khx - Khy - targetFlux_;
637	>	a000 = Khx;
638	>	a111 = Kcy * py * py
639	>	b11 = -2.0 * Kcy * py * (1.0 + py);
640	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
641	>	b01 = -2.0 * Kcx * px * (1.0 + px);
642	>	a001 = Kcx * px * px;
643		*/
644	<	std::vector<RealType> valueHist;  // keeps track of what's being averaged
645	<	std::vector<int> valueCount; // keeps track of the number of degrees of
646	<	// freedom being averaged
647	<	valueHist.resize(nBins_);
648	<	valueCount.resize(nBins_);
649	<	//do they initialize themselves to zero automatically?
644	>
645	>	//scale all three dimensions, let c_x = c_y
646	>	a000 = Kcx + Kcy;
647	>	a110 = Kcz;
648	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
649	>	a001 = Khx * px * px + Khy * py * py;
650	>	a111 = Khz * pz * pz;
651	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
652	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
653	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
654	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
655	>	break;
656	>	case rnemdPxScale :
657	>	c = 1 - targetFlux_ / Pcx;
658	>	a000 = Kcy;
659	>	a110 = Kcz;
660	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
661	>	a001 = py * py * Khy;
662	>	a111 = pz * pz * Khz;
663	>	b01 = -2.0 * Khy * py * (1.0 + py);
664	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
665	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
666	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
667	>	break;
668	>	case rnemdPyScale :
669	>	c = 1 - targetFlux_ / Pcy;
670	>	a000 = Kcx;
671	>	a110 = Kcz;
672	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
673	>	a001 = px * px * Khx;
674	>	a111 = pz * pz * Khz;
675	>	b01 = -2.0 * Khx * px * (1.0 + px);
676	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
677	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
678	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
679	>	break;
680	>	case rnemdPzScale ://we don't really do this, do we?
681	>	c = 1 - targetFlux_ / Pcz;
682	>	a000 = Kcx;
683	>	a110 = Kcy;
684	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
685	>	a001 = px * px * Khx;
686	>	a111 = py * py * Khy;
687	>	b01 = -2.0 * Khx * px * (1.0 + px);
688	>	b11 = -2.0 * Khy * py * (1.0 + py);
689	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
690	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
691	>	break;
692	>	default :
693	>	break;
694	>	}
695	>
696	>	RealType v1 = a000 * a111 - a001 * a110;
697	>	RealType v2 = a000 * b01;
698	>	RealType v3 = a000 * b11;
699	>	RealType v4 = a000 * c1 - a001 * c0;
700	>	RealType v8 = a110 * b01;
701	>	RealType v10 = - b01 * c0;
702	>
703	>	RealType u0 = v2 * v10 - v4 * v4;
704	>	RealType u1 = -2.0 * v3 * v4;
705	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
706	>	RealType u3 = -2.0 * v1 * v3;
707	>	RealType u4 = - v1 * v1;
708	>	//rescale coefficients
709	>	RealType maxAbs = fabs(u0);
710	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
711	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
712	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
713	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
714	>	u0 /= maxAbs;
715	>	u1 /= maxAbs;
716	>	u2 /= maxAbs;
717	>	u3 /= maxAbs;
718	>	u4 /= maxAbs;
719	>	//max_element(start, end) is also available.
720	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
721	>	poly.setCoefficient(4, u4);
722	>	poly.setCoefficient(3, u3);
723	>	poly.setCoefficient(2, u2);
724	>	poly.setCoefficient(1, u1);
725	>	poly.setCoefficient(0, u0);
726	>	std::vector<RealType> realRoots = poly.FindRealRoots();
727	>
728	>	std::vector<RealType>::iterator ri;
729	>	RealType r1, r2, alpha0;
730	>	std::vector<std::pair<RealType,RealType> > rps;
731	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
732	>	r2 = *ri;
733	>	//check if FindRealRoots() give the right answer
734	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
735	>	sprintf(painCave.errMsg,
736	>	"RNEMD Warning: polynomial solve seems to have an error!");
737	>	painCave.isFatal = 0;
738	>	simError();
739	>	failRootCount_++;
740	>	}
741	>	//might not be useful w/o rescaling coefficients
742	>	alpha0 = -c0 - a110 * r2 * r2;
743	>	if (alpha0 >= 0.0) {
744	>	r1 = sqrt(alpha0 / a000);
745	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
746	>	{ rps.push_back(std::make_pair(r1, r2)); }
747	>	if (r1 > 1e-6) { //r1 non-negative
748	>	r1 = -r1;
749	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
750	>	{ rps.push_back(std::make_pair(r1, r2)); }
751	>	}
752	>	}
753	>	}
754	>	// Consider combininig together the solving pair part w/ the searching
755	>	// best solution part so that we don't need the pairs vector
756	>	if (!rps.empty()) {
757	>	RealType smallestDiff = HONKING_LARGE_VALUE;
758	>	RealType diff;
759	>	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
760	>	std::vector<std::pair<RealType,RealType> >::iterator rpi;
761	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
762	>	r1 = (*rpi).first;
763	>	r2 = (*rpi).second;
764	>	switch(rnemdType_) {
765	>	case rnemdKineticScale :
766	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
767	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
768	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
769	>	break;
770	>	case rnemdPxScale :
771	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
772	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
773	>	break;
774	>	case rnemdPyScale :
775	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
776	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
777	>	break;
778	>	case rnemdPzScale :
779	>	default :
780	>	break;
781	>	}
782	>	if (diff < smallestDiff) {
783	>	smallestDiff = diff;
784	>	bestPair = *rpi;
785	>	}
786	>	}
787	>	#ifdef IS_MPI
788	>	if (worldRank == 0) {
789	>	#endif
790	>	std::cerr << "we choose r1 = " << bestPair.first
791	>	<< " and r2 = " << bestPair.second << "\n";
792	>	#ifdef IS_MPI
793	>	}
794	>	#endif
795	>
796	>	RealType x, y, z;
797	>	switch(rnemdType_) {
798	>	case rnemdKineticScale :
799	>	x = bestPair.first;
800	>	y = bestPair.first;
801	>	z = bestPair.second;
802	>	break;
803	>	case rnemdPxScale :
804	>	x = c;
805	>	y = bestPair.first;
806	>	z = bestPair.second;
807	>	break;
808	>	case rnemdPyScale :
809	>	x = bestPair.first;
810	>	y = c;
811	>	z = bestPair.second;
812	>	break;
813	>	case rnemdPzScale :
814	>	x = bestPair.first;
815	>	y = bestPair.second;
816	>	z = c;
817	>	break;
818	>	default :
819	>	break;
820	>	}
821	>	std::vector<StuntDouble*>::iterator sdi;
822	>	Vector3d vel;
823	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
824	>	vel = (*sdi)->getVel();
825	>	vel.x() *= x;
826	>	vel.y() *= y;
827	>	vel.z() *= z;
828	>	(*sdi)->setVel(vel);
829	>	}
830	>	//convert to hotBin coefficient
831	>	x = 1.0 + px * (1.0 - x);
832	>	y = 1.0 + py * (1.0 - y);
833	>	z = 1.0 + pz * (1.0 - z);
834	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
835	>	vel = (*sdi)->getVel();
836	>	vel.x() *= x;
837	>	vel.y() *= y;
838	>	vel.z() *= z;
839	>	(*sdi)->setVel(vel);
840	>	}
841	>	exchangeSum_ += targetFlux_;
842	>	//we may want to check whether the exchange has been successful
843	>	} else {
844	>	std::cerr << "exchange NOT performed!\n";//MPI incompatible
845	>	failTrialCount_++;
846	>	}
847	>
848	>	}
849	>
850	>	void RNEMD::doRNEMD() {
851	>
852	>	switch(rnemdType_) {
853	>	case rnemdKineticScale :
854	>	case rnemdPxScale :
855	>	case rnemdPyScale :
856	>	case rnemdPzScale :
857	>	doScale();
858	>	break;
859	>	case rnemdKineticSwap :
860	>	case rnemdPx :
861	>	case rnemdPy :
862	>	case rnemdPz :
863	>	doSwap();
864	>	break;
865	>	case rnemdUnknown :
866	>	default :
867	>	break;
868	>	}
869	>	}
870	>
871	>	void RNEMD::collectData() {
872	>
873	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
874	>	Mat3x3d hmat = currentSnap_->getHmat();
875	>
876	>	seleMan_.setSelectionSet(evaluator_.evaluate());
877	>
878	>	int selei;
879	>	StuntDouble* sd;
880	>	int idx;
881	>
882		for (sd = seleMan_.beginSelected(selei); sd != NULL;
883		sd = seleMan_.nextSelected(selei)) {
884
#	Line 340 | Line 894 | namespace oopse {
894		// which bin is this stuntdouble in?
895		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
896
897	<	int binNo = int((nBins_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2));
898	<
899	<	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
900	<
897	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
898	>
899	>	if (rnemdLogWidth_ == midBin_ + 1)
900	>	if (binNo > midBin_)
901	>	binNo = nBins_ - binNo;
902	>
903		RealType mass = sd->getMass();
904		Vector3d vel = sd->getVel();
349	–	//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
905		RealType value;
906	+	RealType xVal, yVal, zVal;
907
908		switch(rnemdType_) {
909	<	case rnemdKinetic :
909	>	case rnemdKineticSwap :
910	>	case rnemdKineticScale :
911
912		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
913		vel[2]*vel[2]);
914
915	<	valueCount[binNo] += 3;
359	<
915	>	valueCount_[binNo] += 3;
916		if (sd->isDirectional()) {
917		Vector3d angMom = sd->getJ();
918		Mat3x3d I = sd->getI();
#	Line 368 | Line 924 | namespace oopse {
924		value += angMom[j] * angMom[j] / I(j, j) +
925		angMom[k] * angMom[k] / I(k, k);
926
927	<	valueCount[binNo] +=2;
927	>	valueCount_[binNo] +=2;
928
929	<	} else {
929	>	} else {
930		value += angMom[0]*angMom[0]/I(0, 0)
931		+ angMom[1]*angMom[1]/I(1, 1)
932		+ angMom[2]*angMom[2]/I(2, 2);
933	<	valueCount[binNo] +=3;
378	<
933	>	valueCount_[binNo] +=3;
934		}
935		}
936	<	//std::cerr <<"this value = " << value << "\n";
937	<	value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
383	<	value *= 2.0 / OOPSEConstant::kb;             // convert to temperature
384	<	//std::cerr <<"this value = " << value << "\n";
936	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
937	>
938		break;
939		case rnemdPx :
940	+	case rnemdPxScale :
941		value = mass * vel[0];
942	<	valueCount[binNo]++;
942	>	valueCount_[binNo]++;
943	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
944	>	/ PhysicalConstants::kb;
945	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
946	>	/ PhysicalConstants::kb;
947	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
948	>	/ PhysicalConstants::kb;
949	>	xTempHist_[binNo] += xVal;
950	>	yTempHist_[binNo] += yVal;
951	>	zTempHist_[binNo] += zVal;
952		break;
953		case rnemdPy :
954	+	case rnemdPyScale :
955		value = mass * vel[1];
956	<	valueCount[binNo]++;
956	>	valueCount_[binNo]++;
957		break;
958		case rnemdPz :
959	+	case rnemdPzScale :
960		value = mass * vel[2];
961	<	valueCount[binNo]++;
961	>	valueCount_[binNo]++;
962		break;
963		case rnemdUnknown :
964		default :
965		break;
966		}
967	<	//std::cerr << "bin = " << binNo << " value = " << value ;
403	<	valueHist[binNo] += value;
404	<	//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
967	>	valueHist_[binNo] += value;
968		}
969	<
407	<	std::cout << counter_++;
408	<	for (int j = 0; j < nBins_; j++)
409	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
410	<	std::cout << "\n";
969	>
970		}
971	+
972	+	void RNEMD::getStarted() {
973	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
974	+	Stats& stat = currentSnap_->statData;
975	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
976	+	}
977	+
978	+	void RNEMD::getStatus() {
979	+
980	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
981	+	Stats& stat = currentSnap_->statData;
982	+	RealType time = currentSnap_->getTime();
983	+
984	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
985	+	//or to be more meaningful, define another item as exchangeSum_ / time
986	+	int j;
987	+
988	+	#ifdef IS_MPI
989	+
990	+	// all processors have the same number of bins, and STL vectors pack their
991	+	// arrays, so in theory, this should be safe:
992	+
993	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
994	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
995	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
996	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
997	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
998	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
999	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1000	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1001	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1002	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1003	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1004	+	}
1005	+	// If we're the root node, should we print out the results
1006	+	int worldRank = MPI::COMM_WORLD.Get_rank();
1007	+	if (worldRank == 0) {
1008	+	#endif
1009	+	rnemdLog_ << time;
1010	+	for (j = 0; j < rnemdLogWidth_; j++) {
1011	+	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1012	+	}
1013	+	rnemdLog_ << "\n";
1014	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1015	+	xTempLog_ << time;
1016	+	for (j = 0; j < rnemdLogWidth_; j++) {
1017	+	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1018	+	}
1019	+	xTempLog_ << "\n";
1020	+	yTempLog_ << time;
1021	+	for (j = 0; j < rnemdLogWidth_; j++) {
1022	+	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1023	+	}
1024	+	yTempLog_ << "\n";
1025	+	zTempLog_ << time;
1026	+	for (j = 0; j < rnemdLogWidth_; j++) {
1027	+	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1028	+	}
1029	+	zTempLog_ << "\n";
1030	+	}
1031	+	#ifdef IS_MPI
1032	+	}
1033	+	#endif
1034	+	for (j = 0; j < rnemdLogWidth_; j++) {
1035	+	valueCount_[j] = 0;
1036	+	valueHist_[j] = 0.0;
1037	+	}
1038	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1039	+	for (j = 0; j < rnemdLogWidth_; j++) {
1040	+	xTempHist_[j] = 0.0;
1041	+	yTempHist_[j] = 0.0;
1042	+	zTempHist_[j] = 0.0;
1043	+	}
1044	+	}
1045		}

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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