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root/OpenMD/trunk/src/rnemd/RNEMD.cpp

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branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

#	Line 40 | Line 40
40		*/
41
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include "rnemd/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	<
52	<	#ifndef IS_MPI
53	<	#include "math/SeqRandNumGen.hpp"
54	<	#else
52	>	#ifdef IS_MPI
53		#include <mpi.h>
56	–	#include "math/ParallelRandNumGen.hpp"
54		#endif
55
56	+	#ifdef _MSC_VER
57	+	#define isnan(x) _isnan((x))
58	+	#define isinf(x) (!_finite(x) && !_isnan(x))
59	+	#endif
60	+
61		#define HONKING_LARGE_VALUE 1.0e10
62
63	+	using namespace std;
64		namespace OpenMD {
65
66	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
66	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
67	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
68
69	+	trialCount_ = 0;
70		failTrialCount_ = 0;
71		failRootCount_ = 0;
72
68	–	int seedValue;
73		Globals * simParams = info->getSimParams();
74	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
75
76	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
77	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
73	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
74	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
75	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
76	<	stringToEnumMap_["Px"] = rnemdPx;
77	<	stringToEnumMap_["Py"] = rnemdPy;
78	<	stringToEnumMap_["Pz"] = rnemdPz;
79	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
76	>	doRNEMD_ = rnemdParams->getUseRNEMD();
77	>	if (!doRNEMD_) return;
78
79	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
79	>	stringToMethod_["Swap"]  = rnemdSwap;
80	>	stringToMethod_["NIVS"]  = rnemdNIVS;
81	>	stringToMethod_["VSS"]   = rnemdVSS;
82	>
83	>	stringToFluxType_["KE"]  = rnemdKE;
84	>	stringToFluxType_["Px"]  = rnemdPx;
85	>	stringToFluxType_["Py"]  = rnemdPy;
86	>	stringToFluxType_["Pz"]  = rnemdPz;
87	>	stringToFluxType_["Pvector"]  = rnemdPvector;
88	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
89	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
90	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
91	>
92	>	runTime_ = simParams->getRunTime();
93	>	statusTime_ = simParams->getStatusTime();
94	>
95	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
96		evaluator_.loadScriptString(rnemdObjectSelection_);
97		seleMan_.setSelectionSet(evaluator_.evaluate());
98
99	+	const string methStr = rnemdParams->getMethod();
100	+	bool hasFluxType = rnemdParams->haveFluxType();
101	+
102	+	string fluxStr;
103	+	if (hasFluxType) {
104	+	fluxStr = rnemdParams->getFluxType();
105	+	} else {
106	+	sprintf(painCave.errMsg,
107	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
108	+	"\twhich must be one of the following values:\n"
109	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
110	+	"\tmust be set to use RNEMD\n");
111	+	painCave.isFatal = 1;
112	+	painCave.severity = OPENMD_ERROR;
113	+	simError();
114	+	}
115	+
116	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
117	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
118	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
119	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
120	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
121	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
122	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
123	+	bool hasOutputFields = rnemdParams->haveOutputFields();
124	+
125	+	map<string, RNEMDMethod>::iterator i;
126	+	i = stringToMethod_.find(methStr);
127	+	if (i != stringToMethod_.end())
128	+	rnemdMethod_ = i->second;
129	+	else {
130	+	sprintf(painCave.errMsg,
131	+	"RNEMD: The current method,\n"
132	+	"\t\t%s is not one of the recognized\n"
133	+	"\texchange methods: Swap, NIVS, or VSS\n",
134	+	methStr.c_str());
135	+	painCave.isFatal = 1;
136	+	painCave.severity = OPENMD_ERROR;
137	+	simError();
138	+	}
139	+
140	+	map<string, RNEMDFluxType>::iterator j;
141	+	j = stringToFluxType_.find(fluxStr);
142	+	if (j != stringToFluxType_.end())
143	+	rnemdFluxType_ = j->second;
144	+	else {
145	+	sprintf(painCave.errMsg,
146	+	"RNEMD: The current fluxType,\n"
147	+	"\t\t%s\n"
148	+	"\tis not one of the recognized flux types.\n",
149	+	fluxStr.c_str());
150	+	painCave.isFatal = 1;
151	+	painCave.severity = OPENMD_ERROR;
152	+	simError();
153	+	}
154	+
155	+	bool methodFluxMismatch = false;
156	+	bool hasCorrectFlux = false;
157	+	switch(rnemdMethod_) {
158	+	case rnemdSwap:
159	+	switch (rnemdFluxType_) {
160	+	case rnemdKE:
161	+	hasCorrectFlux = hasKineticFlux;
162	+	break;
163	+	case rnemdPx:
164	+	case rnemdPy:
165	+	case rnemdPz:
166	+	hasCorrectFlux = hasMomentumFlux;
167	+	break;
168	+	default :
169	+	methodFluxMismatch = true;
170	+	break;
171	+	}
172	+	break;
173	+	case rnemdNIVS:
174	+	switch (rnemdFluxType_) {
175	+	case rnemdKE:
176	+	case rnemdRotKE:
177	+	case rnemdFullKE:
178	+	hasCorrectFlux = hasKineticFlux;
179	+	break;
180	+	case rnemdPx:
181	+	case rnemdPy:
182	+	case rnemdPz:
183	+	hasCorrectFlux = hasMomentumFlux;
184	+	break;
185	+	case rnemdKePx:
186	+	case rnemdKePy:
187	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
188	+	break;
189	+	default:
190	+	methodFluxMismatch = true;
191	+	break;
192	+	}
193	+	break;
194	+	case rnemdVSS:
195	+	switch (rnemdFluxType_) {
196	+	case rnemdKE:
197	+	case rnemdRotKE:
198	+	case rnemdFullKE:
199	+	hasCorrectFlux = hasKineticFlux;
200	+	break;
201	+	case rnemdPx:
202	+	case rnemdPy:
203	+	case rnemdPz:
204	+	hasCorrectFlux = hasMomentumFlux;
205	+	break;
206	+	case rnemdPvector:
207	+	hasCorrectFlux = hasMomentumFluxVector;
208	+	break;
209	+	case rnemdKePx:
210	+	case rnemdKePy:
211	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
212	+	break;
213	+	case rnemdKePvector:
214	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
215	+	break;
216	+	default:
217	+	methodFluxMismatch = true;
218	+	break;
219	+	}
220	+	default:
221	+	break;
222	+	}
223	+
224	+	if (methodFluxMismatch) {
225	+	sprintf(painCave.errMsg,
226	+	"RNEMD: The current method,\n"
227	+	"\t\t%s\n"
228	+	"\tcannot be used with the current flux type, %s\n",
229	+	methStr.c_str(), fluxStr.c_str());
230	+	painCave.isFatal = 1;
231	+	painCave.severity = OPENMD_ERROR;
232	+	simError();
233	+	}
234	+	if (!hasCorrectFlux) {
235	+	sprintf(painCave.errMsg,
236	+	"RNEMD: The current method, %s, and flux type, %s,\n"
237	+	"\tdid not have the correct flux value specified. Options\n"
238	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
239	+	methStr.c_str(), fluxStr.c_str());
240	+	painCave.isFatal = 1;
241	+	painCave.severity = OPENMD_ERROR;
242	+	simError();
243	+	}
244	+
245	+	if (hasKineticFlux) {
246	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
247	+	// into  amu / fs^3:
248	+	kineticFlux_ = rnemdParams->getKineticFlux()
249	+	* PhysicalConstants::energyConvert;
250	+	} else {
251	+	kineticFlux_ = 0.0;
252	+	}
253	+	if (hasMomentumFluxVector) {
254	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
255	+	} else {
256	+	momentumFluxVector_ = V3Zero;
257	+	if (hasMomentumFlux) {
258	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
259	+	switch (rnemdFluxType_) {
260	+	case rnemdPx:
261	+	momentumFluxVector_.x() = momentumFlux;
262	+	break;
263	+	case rnemdPy:
264	+	momentumFluxVector_.y() = momentumFlux;
265	+	break;
266	+	case rnemdPz:
267	+	momentumFluxVector_.z() = momentumFlux;
268	+	break;
269	+	case rnemdKePx:
270	+	momentumFluxVector_.x() = momentumFlux;
271	+	break;
272	+	case rnemdKePy:
273	+	momentumFluxVector_.y() = momentumFlux;
274	+	break;
275	+	default:
276	+	break;
277	+	}
278	+	}
279	+	}
280	+
281		// do some sanity checking
282
283		int selectionCount = seleMan_.getSelectionCount();
#	Line 89 | Line 285 | namespace OpenMD {
285
286		if (selectionCount > nIntegrable) {
287		sprintf(painCave.errMsg,
288	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
288	>	"RNEMD: The current objectSelection,\n"
289		"\t\t%s\n"
290		"\thas resulted in %d selected objects.  However,\n"
291		"\tthe total number of integrable objects in the system\n"
#	Line 99 | Line 295 | namespace OpenMD {
295		rnemdObjectSelection_.c_str(),
296		selectionCount, nIntegrable);
297		painCave.isFatal = 0;
298	+	painCave.severity = OPENMD_WARNING;
299		simError();
103	–
300		}
105	–
106	–	const std::string st = simParams->getRNEMD_exchangeType();
301
302	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
109	<	i = stringToEnumMap_.find(st);
110	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
111	<	if (rnemdType_ == rnemdUnknown) {
112	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
113	<	}
302	>	areaAccumulator_ = new Accumulator();
303
304	<	#ifdef IS_MPI
305	<	if (worldRank == 0) {
306	<	#endif
307	<
308	<	std::string rnemdFileName;
309	<	std::string xTempFileName;
310	<	std::string yTempFileName;
311	<	std::string zTempFileName;
312	<	switch(rnemdType_) {
313	<	case rnemdKineticSwap :
314	<	case rnemdKineticScale :
315	<	rnemdFileName = "temperature.log";
304	>	nBins_ = rnemdParams->getOutputBins();
305	>
306	>	data_.resize(RNEMD::ENDINDEX);
307	>	OutputData z;
308	>	z.units =  "Angstroms";
309	>	z.title =  "Z";
310	>	z.dataType = "RealType";
311	>	z.accumulator.reserve(nBins_);
312	>	for (int i = 0; i < nBins_; i++)
313	>	z.accumulator.push_back( new Accumulator() );
314	>	data_[Z] = z;
315	>	outputMap_["Z"] =  Z;
316	>
317	>	OutputData temperature;
318	>	temperature.units =  "K";
319	>	temperature.title =  "Temperature";
320	>	temperature.dataType = "RealType";
321	>	temperature.accumulator.reserve(nBins_);
322	>	for (int i = 0; i < nBins_; i++)
323	>	temperature.accumulator.push_back( new Accumulator() );
324	>	data_[TEMPERATURE] = temperature;
325	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
326	>
327	>	OutputData velocity;
328	>	velocity.units = "angstroms/fs";
329	>	velocity.title =  "Velocity";
330	>	velocity.dataType = "Vector3d";
331	>	velocity.accumulator.reserve(nBins_);
332	>	for (int i = 0; i < nBins_; i++)
333	>	velocity.accumulator.push_back( new VectorAccumulator() );
334	>	data_[VELOCITY] = velocity;
335	>	outputMap_["VELOCITY"] = VELOCITY;
336	>
337	>	OutputData density;
338	>	density.units =  "g cm^-3";
339	>	density.title =  "Density";
340	>	density.dataType = "RealType";
341	>	density.accumulator.reserve(nBins_);
342	>	for (int i = 0; i < nBins_; i++)
343	>	density.accumulator.push_back( new Accumulator() );
344	>	data_[DENSITY] = density;
345	>	outputMap_["DENSITY"] =  DENSITY;
346	>
347	>	if (hasOutputFields) {
348	>	parseOutputFileFormat(rnemdParams->getOutputFields());
349	>	} else {
350	>	outputMask_.set(Z);
351	>	switch (rnemdFluxType_) {
352	>	case rnemdKE:
353	>	case rnemdRotKE:
354	>	case rnemdFullKE:
355	>	outputMask_.set(TEMPERATURE);
356		break;
357	<	case rnemdPx :
358	<	case rnemdPxScale :
359	<	case rnemdPy :
131	<	case rnemdPyScale :
132	<	rnemdFileName = "momemtum.log";
133	<	xTempFileName = "temperatureX.log";
134	<	yTempFileName = "temperatureY.log";
135	<	zTempFileName = "temperatureZ.log";
136	<	xTempLog_.open(xTempFileName.c_str());
137	<	yTempLog_.open(yTempFileName.c_str());
138	<	zTempLog_.open(zTempFileName.c_str());
357	>	case rnemdPx:
358	>	case rnemdPy:
359	>	outputMask_.set(VELOCITY);
360		break;
361	<	case rnemdPz :
362	<	case rnemdPzScale :
363	<	case rnemdUnknown :
364	<	default :
144	<	rnemdFileName = "rnemd.log";
361	>	case rnemdPz:
362	>	case rnemdPvector:
363	>	outputMask_.set(VELOCITY);
364	>	outputMask_.set(DENSITY);
365		break;
366	+	case rnemdKePx:
367	+	case rnemdKePy:
368	+	outputMask_.set(TEMPERATURE);
369	+	outputMask_.set(VELOCITY);
370	+	break;
371	+	case rnemdKePvector:
372	+	outputMask_.set(TEMPERATURE);
373	+	outputMask_.set(VELOCITY);
374	+	outputMask_.set(DENSITY);
375	+	break;
376	+	default:
377	+	break;
378		}
147	–	rnemdLog_.open(rnemdFileName.c_str());
148	–
149	–	#ifdef IS_MPI
379		}
380	<	#endif
381	<
382	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
154	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
155	<	midBin_ = nBins_ / 2;
156	<	if (simParams->haveRNEMD_logWidth()) {
157	<	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
158	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
159	<	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
160	<	std::cerr << "Automaically set back to default.\n";
161	<	rnemdLogWidth_ = nBins_;
162	<	}
380	>
381	>	if (hasOutputFileName) {
382	>	rnemdFileName_ = rnemdParams->getOutputFileName();
383		} else {
384	<	rnemdLogWidth_ = nBins_;
385	<	}
166	<	valueHist_.resize(rnemdLogWidth_, 0.0);
167	<	valueCount_.resize(rnemdLogWidth_, 0);
168	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
169	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
170	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
384	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
385	>	}
386
387	<	set_RNEMD_exchange_total(0.0);
173	<	if (simParams->haveRNEMD_targetFlux()) {
174	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
175	<	} else {
176	<	set_RNEMD_target_flux(0.0);
177	<	}
387	>	exchangeTime_ = rnemdParams->getExchangeTime();
388
389	<	#ifndef IS_MPI
390	<	if (simParams->haveSeed()) {
181	<	seedValue = simParams->getSeed();
182	<	randNumGen_ = new SeqRandNumGen(seedValue);
183	<	}else {
184	<	randNumGen_ = new SeqRandNumGen();
185	<	}
186	<	#else
187	<	if (simParams->haveSeed()) {
188	<	seedValue = simParams->getSeed();
189	<	randNumGen_ = new ParallelRandNumGen(seedValue);
190	<	}else {
191	<	randNumGen_ = new ParallelRandNumGen();
192	<	}
193	<	#endif
194	<	}
389	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
390	>	Mat3x3d hmat = currentSnap_->getHmat();
391
392	<	RNEMD::~RNEMD() {
393	<	delete randNumGen_;
392	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
393	>	// Lx, Ly = box dimensions in x & y
394	>	// dt = exchange time interval
395	>	// flux = target flux
396	>
397	>	RealType area = currentSnap_->getXYarea();
398	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
399	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
400	>
401	>	// total exchange sums are zeroed out at the beginning:
402	>
403	>	kineticExchange_ = 0.0;
404	>	momentumExchange_ = V3Zero;
405	>
406	>	if (hasSlabWidth)
407	>	slabWidth_ = rnemdParams->getSlabWidth();
408	>	else
409	>	slabWidth_ = hmat(2,2) / 10.0;
410	>
411	>	if (hasSlabACenter)
412	>	slabACenter_ = rnemdParams->getSlabACenter();
413	>	else
414	>	slabACenter_ = 0.0;
415
416	+	if (hasSlabBCenter)
417	+	slabBCenter_ = rnemdParams->getSlabBCenter();
418	+	else
419	+	slabBCenter_ = hmat(2,2) / 2.0;
420	+
421	+	}
422	+
423	+	RNEMD::~RNEMD() {
424	+	if (!doRNEMD_) return;
425		#ifdef IS_MPI
426		if (worldRank == 0) {
427		#endif
428	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
429	<	rnemdLog_.close();
430	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
431	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
432	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	<	xTempLog_.close();
208	<	yTempLog_.close();
209	<	zTempLog_.close();
210	<	}
428	>
429	>	writeOutputFile();
430	>
431	>	rnemdFile_.close();
432	>
433		#ifdef IS_MPI
434		}
435		#endif
436		}
437	+
438	+	bool RNEMD::inSlabA(Vector3d pos) {
439	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
440	+	}
441	+	bool RNEMD::inSlabB(Vector3d pos) {
442	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
443	+	}
444
445		void RNEMD::doSwap() {
446	<
446	>	if (!doRNEMD_) return;
447		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
448		Mat3x3d hmat = currentSnap_->getHmat();
449
#	Line 222 | Line 451 | namespace OpenMD {
451
452		int selei;
453		StuntDouble* sd;
225	–	int idx;
454
455		RealType min_val;
456		bool min_found = false;
#	Line 235 | Line 463 | namespace OpenMD {
463		for (sd = seleMan_.beginSelected(selei); sd != NULL;
464		sd = seleMan_.nextSelected(selei)) {
465
238	–	idx = sd->getLocalIndex();
239	–
466		Vector3d pos = sd->getPos();
467
468		// wrap the stuntdouble's position back into the box:
469
470		if (usePeriodicBoundaryConditions_)
471		currentSnap_->wrapVector(pos);
472	+	bool inA = inSlabA(pos);
473	+	bool inB = inSlabB(pos);
474
475	<	// which bin is this stuntdouble in?
248	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
249	<
250	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
251	<
252	<
253	<	// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin_) {
475	>	if (inA || inB) {
476
477		RealType mass = sd->getMass();
478		Vector3d vel = sd->getVel();
479		RealType value;
480	<
481	<	switch(rnemdType_) {
482	<	case rnemdKineticSwap :
480	>
481	>	switch(rnemdFluxType_) {
482	>	case rnemdKE :
483
484	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
485	<	vel[2]*vel[2]);
486	<	if (sd->isDirectional()) {
484	>	value = mass * vel.lengthSquare();
485	>
486	>	if (sd->isDirectional()) {
487		Vector3d angMom = sd->getJ();
488		Mat3x3d I = sd->getI();
489
490		if (sd->isLinear()) {
491	<	int i = sd->linearAxis();
492	<	int j = (i + 1) % 3;
493	<	int k = (i + 2) % 3;
494	<	value += angMom[j] * angMom[j] / I(j, j) +
495	<	angMom[k] * angMom[k] / I(k, k);
491	>	int i = sd->linearAxis();
492	>	int j = (i + 1) % 3;
493	>	int k = (i + 2) % 3;
494	>	value += angMom[j] * angMom[j] / I(j, j) +
495	>	angMom[k] * angMom[k] / I(k, k);
496		} else {
497	<	value += angMom[0]*angMom[0]/I(0, 0)
498	<	+ angMom[1]*angMom[1]/I(1, 1)
499	<	+ angMom[2]*angMom[2]/I(2, 2);
497	>	value += angMom[0]*angMom[0]/I(0, 0)
498	>	+ angMom[1]*angMom[1]/I(1, 1)
499	>	+ angMom[2]*angMom[2]/I(2, 2);
500		}
501	<	}
281	<	//make exchangeSum_ comparable between swap & scale
282	<	//temporarily without using energyConvert
283	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
501	>	} //angular momenta exchange enabled
502		value *= 0.5;
503		break;
504		case rnemdPx :
#	Line 296 | Line 514 | namespace OpenMD {
514		break;
515		}
516
517	<	if (binNo == 0) {
517	>	if (inA == 0) {
518		if (!min_found) {
519		min_val = value;
520		min_sd = sd;
#	Line 307 | Line 525 | namespace OpenMD {
525		min_sd = sd;
526		}
527		}
528	<	} else { //midBin_
528	>	} else {
529		if (!max_found) {
530		max_val = value;
531		max_sd = sd;
#	Line 321 | Line 539 | namespace OpenMD {
539		}
540		}
541		}
542	<
543	<	#ifdef IS_MPI
544	<	int nProc, worldRank;
545	<
328	<	nProc = MPI::COMM_WORLD.Get_size();
329	<	worldRank = MPI::COMM_WORLD.Get_rank();
330	<
542	>
543	>	#ifdef IS_MPI
544	>	int worldRank = MPI::COMM_WORLD.Get_rank();
545	>
546		bool my_min_found = min_found;
547		bool my_max_found = max_found;
548
549		// Even if we didn't find a minimum, did someone else?
550	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
336	<	1, MPI::BOOL, MPI::LAND);
337	<
550	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
551		// Even if we didn't find a maximum, did someone else?
552	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
553	<	1, MPI::BOOL, MPI::LAND);
554	<
555	<	struct {
556	<	RealType val;
557	<	int rank;
558	<	} max_vals, min_vals;
559	<
560	<	if (min_found) {
561	<	if (my_min_found)
552	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
553	>	#endif
554	>
555	>	if (max_found && min_found) {
556	>
557	>	#ifdef IS_MPI
558	>	struct {
559	>	RealType val;
560	>	int rank;
561	>	} max_vals, min_vals;
562	>
563	>	if (my_min_found) {
564		min_vals.val = min_val;
565	<	else
565	>	} else {
566		min_vals.val = HONKING_LARGE_VALUE;
567	<
567	>	}
568		min_vals.rank = worldRank;
569
570		// Who had the minimum?
571		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
572		1, MPI::REALTYPE_INT, MPI::MINLOC);
573		min_val = min_vals.val;
359	–	}
574
575	<	if (max_found) {
362	<	if (my_max_found)
575	>	if (my_max_found) {
576		max_vals.val = max_val;
577	<	else
577	>	} else {
578		max_vals.val = -HONKING_LARGE_VALUE;
579	<
579	>	}
580		max_vals.rank = worldRank;
581
582		// Who had the maximum?
583		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
584		1, MPI::REALTYPE_INT, MPI::MAXLOC);
585		max_val = max_vals.val;
373	–	}
586		#endif
587	<
588	<	if (max_found && min_found) {
589	<	if (min_val< max_val) {
378	<
587	>
588	>	if (min_val < max_val) {
589	>
590		#ifdef IS_MPI
591		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
592		// I have both maximum and minimum, so proceed like a single
593		// processor version:
594		#endif
595	<	// objects to be swapped: velocity & angular velocity
595	>
596		Vector3d min_vel = min_sd->getVel();
597		Vector3d max_vel = max_sd->getVel();
598		RealType temp_vel;
599
600	<	switch(rnemdType_) {
601	<	case rnemdKineticSwap :
600	>	switch(rnemdFluxType_) {
601	>	case rnemdKE :
602		min_sd->setVel(max_vel);
603		max_sd->setVel(min_vel);
604	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
604	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
605		Vector3d min_angMom = min_sd->getJ();
606		Vector3d max_angMom = max_sd->getJ();
607		min_sd->setJ(max_angMom);
608		max_sd->setJ(min_angMom);
609	<	}
609	>	}//angular momenta exchange enabled
610	>	//assumes same rigid body identity
611		break;
612		case rnemdPx :
613		temp_vel = min_vel.x();
#	Line 421 | Line 633 | namespace OpenMD {
633		default :
634		break;
635		}
636	+
637		#ifdef IS_MPI
638		// the rest of the cases only apply in parallel simulations:
639		} else if (max_vals.rank == worldRank) {
#	Line 436 | Line 649 | namespace OpenMD {
649		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
650		min_vals.rank, 0, status);
651
652	<	switch(rnemdType_) {
653	<	case rnemdKineticSwap :
652	>	switch(rnemdFluxType_) {
653	>	case rnemdKE :
654		max_sd->setVel(min_vel);
655	<
655	>	//angular momenta exchange enabled
656		if (max_sd->isDirectional()) {
657		Vector3d min_angMom;
658		Vector3d max_angMom = max_sd->getJ();
659	<
659	>
660		// point-to-point swap of the angular momentum vector
661		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
662		MPI::REALTYPE, min_vals.rank, 1,
663		min_angMom.getArrayPointer(), 3,
664		MPI::REALTYPE, min_vals.rank, 1,
665		status);
666	<
666	>
667		max_sd->setJ(min_angMom);
668	<	}
668	>	}
669		break;
670		case rnemdPx :
671		max_vel.x() = min_vel.x();
#	Line 482 | Line 695 | namespace OpenMD {
695		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
696		max_vals.rank, 0, status);
697
698	<	switch(rnemdType_) {
699	<	case rnemdKineticSwap :
698	>	switch(rnemdFluxType_) {
699	>	case rnemdKE :
700		min_sd->setVel(max_vel);
701	<
701	>	//angular momenta exchange enabled
702		if (min_sd->isDirectional()) {
703		Vector3d min_angMom = min_sd->getJ();
704		Vector3d max_angMom;
705	<
705	>
706		// point-to-point swap of the angular momentum vector
707		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
708		MPI::REALTYPE, max_vals.rank, 1,
709		max_angMom.getArrayPointer(), 3,
710		MPI::REALTYPE, max_vals.rank, 1,
711		status);
712	<
712	>
713		min_sd->setJ(max_angMom);
714		}
715		break;
#	Line 517 | Line 730 | namespace OpenMD {
730		}
731		}
732		#endif
733	<	exchangeSum_ += max_val - min_val;
734	<	} else {
735	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
733	>
734	>	switch(rnemdFluxType_) {
735	>	case rnemdKE:
736	>	kineticExchange_ += max_val - min_val;
737	>	break;
738	>	case rnemdPx:
739	>	momentumExchange_.x() += max_val - min_val;
740	>	break;
741	>	case rnemdPy:
742	>	momentumExchange_.y() += max_val - min_val;
743	>	break;
744	>	case rnemdPz:
745	>	momentumExchange_.z() += max_val - min_val;
746	>	break;
747	>	default:
748	>	break;
749	>	}
750	>	} else {
751	>	sprintf(painCave.errMsg,
752	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
753	>	painCave.isFatal = 0;
754	>	painCave.severity = OPENMD_INFO;
755	>	simError();
756		failTrialCount_++;
757		}
758		} else {
759	<	std::cerr << "exchange NOT performed!\n";
760	<	std::cerr << "at least one of the two slabs empty.\n";
759	>	sprintf(painCave.errMsg,
760	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
761	>	"\twas not present in at least one of the two slabs.\n");
762	>	painCave.isFatal = 0;
763	>	painCave.severity = OPENMD_INFO;
764	>	simError();
765		failTrialCount_++;
766	<	}
530	<
766	>	}
767		}
768
769	<	void RNEMD::doScale() {
770	<
769	>	void RNEMD::doNIVS() {
770	>	if (!doRNEMD_) return;
771		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
772		Mat3x3d hmat = currentSnap_->getHmat();
773
#	Line 539 | Line 775 | namespace OpenMD {
775
776		int selei;
777		StuntDouble* sd;
542	–	int idx;
778
779	<	std::vector<StuntDouble*> hotBin, coldBin;
779	>	vector<StuntDouble*> hotBin, coldBin;
780
781		RealType Phx = 0.0;
782		RealType Phy = 0.0;
#	Line 549 | Line 784 | namespace OpenMD {
784		RealType Khx = 0.0;
785		RealType Khy = 0.0;
786		RealType Khz = 0.0;
787	+	RealType Khw = 0.0;
788		RealType Pcx = 0.0;
789		RealType Pcy = 0.0;
790		RealType Pcz = 0.0;
791		RealType Kcx = 0.0;
792		RealType Kcy = 0.0;
793		RealType Kcz = 0.0;
794	+	RealType Kcw = 0.0;
795
796		for (sd = seleMan_.beginSelected(selei); sd != NULL;
797		sd = seleMan_.nextSelected(selei)) {
798
562	–	idx = sd->getLocalIndex();
563	–
799		Vector3d pos = sd->getPos();
800
801		// wrap the stuntdouble's position back into the box:
#	Line 569 | Line 804 | namespace OpenMD {
804		currentSnap_->wrapVector(pos);
805
806		// which bin is this stuntdouble in?
807	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
807	>	bool inA = inSlabA(pos);
808	>	bool inB = inSlabB(pos);
809
810	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
811	<
576	<	// if we're in bin 0 or the middleBin
577	<	if (binNo == 0 || binNo == midBin_) {
578	<
810	>	if (inA || inB) {
811	>
812		RealType mass = sd->getMass();
813		Vector3d vel = sd->getVel();
814
815	<	if (binNo == 0) {
815	>	if (inA) {
816		hotBin.push_back(sd);
817		Phx += mass * vel.x();
818		Phy += mass * vel.y();
#	Line 587 | Line 820 | namespace OpenMD {
820		Khx += mass * vel.x() * vel.x();
821		Khy += mass * vel.y() * vel.y();
822		Khz += mass * vel.z() * vel.z();
823	<	} else { //midBin_
823	>	if (sd->isDirectional()) {
824	>	Vector3d angMom = sd->getJ();
825	>	Mat3x3d I = sd->getI();
826	>	if (sd->isLinear()) {
827	>	int i = sd->linearAxis();
828	>	int j = (i + 1) % 3;
829	>	int k = (i + 2) % 3;
830	>	Khw += angMom[j] * angMom[j] / I(j, j) +
831	>	angMom[k] * angMom[k] / I(k, k);
832	>	} else {
833	>	Khw += angMom[0]*angMom[0]/I(0, 0)
834	>	+ angMom[1]*angMom[1]/I(1, 1)
835	>	+ angMom[2]*angMom[2]/I(2, 2);
836	>	}
837	>	}
838	>	} else {
839		coldBin.push_back(sd);
840		Pcx += mass * vel.x();
841		Pcy += mass * vel.y();
#	Line 595 | Line 843 | namespace OpenMD {
843		Kcx += mass * vel.x() * vel.x();
844		Kcy += mass * vel.y() * vel.y();
845		Kcz += mass * vel.z() * vel.z();
846	+	if (sd->isDirectional()) {
847	+	Vector3d angMom = sd->getJ();
848	+	Mat3x3d I = sd->getI();
849	+	if (sd->isLinear()) {
850	+	int i = sd->linearAxis();
851	+	int j = (i + 1) % 3;
852	+	int k = (i + 2) % 3;
853	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
854	+	angMom[k] * angMom[k] / I(k, k);
855	+	} else {
856	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
857	+	+ angMom[1]*angMom[1]/I(1, 1)
858	+	+ angMom[2]*angMom[2]/I(2, 2);
859	+	}
860	+	}
861		}
862		}
863		}
864	<
864	>
865		Khx *= 0.5;
866		Khy *= 0.5;
867		Khz *= 0.5;
868	+	Khw *= 0.5;
869		Kcx *= 0.5;
870		Kcy *= 0.5;
871		Kcz *= 0.5;
872	+	Kcw *= 0.5;
873
874		#ifdef IS_MPI
875		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 617 | Line 882 | namespace OpenMD {
882		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
883		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
884		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
885	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
886	+
887		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
888		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
889		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
890	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
891		#endif
892
893	<	//use coldBin coeff's
893	>	//solve coldBin coeff's first
894		RealType px = Pcx / Phx;
895		RealType py = Pcy / Phy;
896		RealType pz = Pcz / Phz;
897	+	RealType c, x, y, z;
898	+	bool successfulScale = false;
899	+	if ((rnemdFluxType_ == rnemdFullKE) ||
900	+	(rnemdFluxType_ == rnemdRotKE)) {
901	+	//may need sanity check Khw & Kcw > 0
902
903	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
904	<	switch(rnemdType_) {
905	<	case rnemdKineticScale :
906	<	/*used hotBin coeff's & only scale x & y dimensions
907	<	RealType px = Phx / Pcx;
635	<	RealType py = Phy / Pcy;
636	<	a110 = Khy;
637	<	c0 = - Khx - Khy - targetFlux_;
638	<	a000 = Khx;
639	<	a111 = Kcy * py * py
640	<	b11 = -2.0 * Kcy * py * (1.0 + py);
641	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
642	<	b01 = -2.0 * Kcx * px * (1.0 + px);
643	<	a001 = Kcx * px * px;
644	<	*/
903	>	if (rnemdFluxType_ == rnemdFullKE) {
904	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
905	>	} else {
906	>	c = 1.0 - kineticTarget_ / Kcw;
907	>	}
908
909	<	//scale all three dimensions, let c_x = c_y
910	<	a000 = Kcx + Kcy;
911	<	a110 = Kcz;
912	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
913	<	a001 = Khx * px * px + Khy * py * py;
914	<	a111 = Khz * pz * pz;
915	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
916	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
917	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
918	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
919	<	break;
920	<	case rnemdPxScale :
921	<	c = 1 - targetFlux_ / Pcx;
922	<	a000 = Kcy;
923	<	a110 = Kcz;
924	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
925	<	a001 = py * py * Khy;
926	<	a111 = pz * pz * Khz;
927	<	b01 = -2.0 * Khy * py * (1.0 + py);
928	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
929	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
930	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
931	<	break;
932	<	case rnemdPyScale :
933	<	c = 1 - targetFlux_ / Pcy;
934	<	a000 = Kcx;
935	<	a110 = Kcz;
936	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
937	<	a001 = px * px * Khx;
938	<	a111 = pz * pz * Khz;
939	<	b01 = -2.0 * Khx * px * (1.0 + px);
940	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
941	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
942	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
943	<	break;
944	<	case rnemdPzScale ://we don't really do this, do we?
945	<	c = 1 - targetFlux_ / Pcz;
946	<	a000 = Kcx;
947	<	a110 = Kcy;
948	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
949	<	a001 = px * px * Khx;
950	<	a111 = py * py * Khy;
951	<	b01 = -2.0 * Khx * px * (1.0 + px);
952	<	b11 = -2.0 * Khy * py * (1.0 + py);
953	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
954	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
955	<	break;
956	<	default :
957	<	break;
909	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
910	>	c = sqrt(c);
911	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	>	//now convert to hotBin coefficient
913	>	RealType w = 0.0;
914	>	if (rnemdFluxType_ ==  rnemdFullKE) {
915	>	x = 1.0 + px * (1.0 - c);
916	>	y = 1.0 + py * (1.0 - c);
917	>	z = 1.0 + pz * (1.0 - c);
918	>	/* more complicated way
919	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
920	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
921	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
922	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
923	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
924	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
925	>	*/
926	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
927	>	(fabs(z - 1.0) < 0.1)) {
928	>	w = 1.0 + (kineticTarget_
929	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
930	>	+ Khz * (1.0 - z * z)) / Khw;
931	>	}//no need to calculate w if x, y or z is out of range
932	>	} else {
933	>	w = 1.0 + kineticTarget_ / Khw;
934	>	}
935	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
936	>	//if w is in the right range, so should be x, y, z.
937	>	vector<StuntDouble*>::iterator sdi;
938	>	Vector3d vel;
939	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
940	>	if (rnemdFluxType_ == rnemdFullKE) {
941	>	vel = (*sdi)->getVel() * c;
942	>	(*sdi)->setVel(vel);
943	>	}
944	>	if ((*sdi)->isDirectional()) {
945	>	Vector3d angMom = (*sdi)->getJ() * c;
946	>	(*sdi)->setJ(angMom);
947	>	}
948	>	}
949	>	w = sqrt(w);
950	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	>	//           << "\twh= " << w << endl;
952	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
953	>	if (rnemdFluxType_ == rnemdFullKE) {
954	>	vel = (*sdi)->getVel();
955	>	vel.x() *= x;
956	>	vel.y() *= y;
957	>	vel.z() *= z;
958	>	(*sdi)->setVel(vel);
959	>	}
960	>	if ((*sdi)->isDirectional()) {
961	>	Vector3d angMom = (*sdi)->getJ() * w;
962	>	(*sdi)->setJ(angMom);
963	>	}
964	>	}
965	>	successfulScale = true;
966	>	kineticExchange_ += kineticTarget_;
967	>	}
968	>	}
969	>	} else {
970	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
971	>	switch(rnemdFluxType_) {
972	>	case rnemdKE :
973	>	/* used hotBin coeff's & only scale x & y dimensions
974	>	RealType px = Phx / Pcx;
975	>	RealType py = Phy / Pcy;
976	>	a110 = Khy;
977	>	c0 = - Khx - Khy - kineticTarget_;
978	>	a000 = Khx;
979	>	a111 = Kcy * py * py;
980	>	b11 = -2.0 * Kcy * py * (1.0 + py);
981	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
982	>	b01 = -2.0 * Kcx * px * (1.0 + px);
983	>	a001 = Kcx * px * px;
984	>	*/
985	>	//scale all three dimensions, let c_x = c_y
986	>	a000 = Kcx + Kcy;
987	>	a110 = Kcz;
988	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
989	>	a001 = Khx * px * px + Khy * py * py;
990	>	a111 = Khz * pz * pz;
991	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
992	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
993	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
994	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
995	>	break;
996	>	case rnemdPx :
997	>	c = 1 - momentumTarget_.x() / Pcx;
998	>	a000 = Kcy;
999	>	a110 = Kcz;
1000	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1001	>	a001 = py * py * Khy;
1002	>	a111 = pz * pz * Khz;
1003	>	b01 = -2.0 * Khy * py * (1.0 + py);
1004	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1005	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1006	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1007	>	break;
1008	>	case rnemdPy :
1009	>	c = 1 - momentumTarget_.y() / Pcy;
1010	>	a000 = Kcx;
1011	>	a110 = Kcz;
1012	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1013	>	a001 = px * px * Khx;
1014	>	a111 = pz * pz * Khz;
1015	>	b01 = -2.0 * Khx * px * (1.0 + px);
1016	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1017	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1018	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1019	>	break;
1020	>	case rnemdPz ://we don't really do this, do we?
1021	>	c = 1 - momentumTarget_.z() / Pcz;
1022	>	a000 = Kcx;
1023	>	a110 = Kcy;
1024	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1025	>	a001 = px * px * Khx;
1026	>	a111 = py * py * Khy;
1027	>	b01 = -2.0 * Khx * px * (1.0 + px);
1028	>	b11 = -2.0 * Khy * py * (1.0 + py);
1029	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1030	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1031	>	break;
1032	>	default :
1033	>	break;
1034	>	}
1035	>
1036	>	RealType v1 = a000 * a111 - a001 * a110;
1037	>	RealType v2 = a000 * b01;
1038	>	RealType v3 = a000 * b11;
1039	>	RealType v4 = a000 * c1 - a001 * c0;
1040	>	RealType v8 = a110 * b01;
1041	>	RealType v10 = - b01 * c0;
1042	>
1043	>	RealType u0 = v2 * v10 - v4 * v4;
1044	>	RealType u1 = -2.0 * v3 * v4;
1045	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1046	>	RealType u3 = -2.0 * v1 * v3;
1047	>	RealType u4 = - v1 * v1;
1048	>	//rescale coefficients
1049	>	RealType maxAbs = fabs(u0);
1050	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1051	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1052	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1053	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1054	>	u0 /= maxAbs;
1055	>	u1 /= maxAbs;
1056	>	u2 /= maxAbs;
1057	>	u3 /= maxAbs;
1058	>	u4 /= maxAbs;
1059	>	//max_element(start, end) is also available.
1060	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1061	>	poly.setCoefficient(4, u4);
1062	>	poly.setCoefficient(3, u3);
1063	>	poly.setCoefficient(2, u2);
1064	>	poly.setCoefficient(1, u1);
1065	>	poly.setCoefficient(0, u0);
1066	>	vector<RealType> realRoots = poly.FindRealRoots();
1067	>
1068	>	vector<RealType>::iterator ri;
1069	>	RealType r1, r2, alpha0;
1070	>	vector<pair<RealType,RealType> > rps;
1071	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1072	>	r2 = *ri;
1073	>	//check if FindRealRoots() give the right answer
1074	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1075	>	sprintf(painCave.errMsg,
1076	>	"RNEMD Warning: polynomial solve seems to have an error!");
1077	>	painCave.isFatal = 0;
1078	>	simError();
1079	>	failRootCount_++;
1080	>	}
1081	>	//might not be useful w/o rescaling coefficients
1082	>	alpha0 = -c0 - a110 * r2 * r2;
1083	>	if (alpha0 >= 0.0) {
1084	>	r1 = sqrt(alpha0 / a000);
1085	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1086	>	< 1e-6)
1087	>	{ rps.push_back(make_pair(r1, r2)); }
1088	>	if (r1 > 1e-6) { //r1 non-negative
1089	>	r1 = -r1;
1090	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1091	>	< 1e-6)
1092	>	{ rps.push_back(make_pair(r1, r2)); }
1093	>	}
1094	>	}
1095	>	}
1096	>	// Consider combining together the solving pair part w/ the searching
1097	>	// best solution part so that we don't need the pairs vector
1098	>	if (!rps.empty()) {
1099	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1100	>	RealType diff;
1101	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1102	>	vector<pair<RealType,RealType> >::iterator rpi;
1103	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1104	>	r1 = (*rpi).first;
1105	>	r2 = (*rpi).second;
1106	>	switch(rnemdFluxType_) {
1107	>	case rnemdKE :
1108	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1109	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1110	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1111	>	break;
1112	>	case rnemdPx :
1113	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1115	>	break;
1116	>	case rnemdPy :
1117	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1119	>	break;
1120	>	case rnemdPz :
1121	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1122	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1123	>	default :
1124	>	break;
1125	>	}
1126	>	if (diff < smallestDiff) {
1127	>	smallestDiff = diff;
1128	>	bestPair = *rpi;
1129	>	}
1130	>	}
1131	>	#ifdef IS_MPI
1132	>	if (worldRank == 0) {
1133	>	#endif
1134	>	// sprintf(painCave.errMsg,
1135	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1136	>	//         bestPair.first, bestPair.second);
1137	>	// painCave.isFatal = 0;
1138	>	// painCave.severity = OPENMD_INFO;
1139	>	// simError();
1140	>	#ifdef IS_MPI
1141	>	}
1142	>	#endif
1143	>
1144	>	switch(rnemdFluxType_) {
1145	>	case rnemdKE :
1146	>	x = bestPair.first;
1147	>	y = bestPair.first;
1148	>	z = bestPair.second;
1149	>	break;
1150	>	case rnemdPx :
1151	>	x = c;
1152	>	y = bestPair.first;
1153	>	z = bestPair.second;
1154	>	break;
1155	>	case rnemdPy :
1156	>	x = bestPair.first;
1157	>	y = c;
1158	>	z = bestPair.second;
1159	>	break;
1160	>	case rnemdPz :
1161	>	x = bestPair.first;
1162	>	y = bestPair.second;
1163	>	z = c;
1164	>	break;
1165	>	default :
1166	>	break;
1167	>	}
1168	>	vector<StuntDouble*>::iterator sdi;
1169	>	Vector3d vel;
1170	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1171	>	vel = (*sdi)->getVel();
1172	>	vel.x() *= x;
1173	>	vel.y() *= y;
1174	>	vel.z() *= z;
1175	>	(*sdi)->setVel(vel);
1176	>	}
1177	>	//convert to hotBin coefficient
1178	>	x = 1.0 + px * (1.0 - x);
1179	>	y = 1.0 + py * (1.0 - y);
1180	>	z = 1.0 + pz * (1.0 - z);
1181	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1182	>	vel = (*sdi)->getVel();
1183	>	vel.x() *= x;
1184	>	vel.y() *= y;
1185	>	vel.z() *= z;
1186	>	(*sdi)->setVel(vel);
1187	>	}
1188	>	successfulScale = true;
1189	>	switch(rnemdFluxType_) {
1190	>	case rnemdKE :
1191	>	kineticExchange_ += kineticTarget_;
1192	>	break;
1193	>	case rnemdPx :
1194	>	case rnemdPy :
1195	>	case rnemdPz :
1196	>	momentumExchange_ += momentumTarget_;
1197	>	break;
1198	>	default :
1199	>	break;
1200	>	}
1201	>	}
1202		}
1203	+	if (successfulScale != true) {
1204	+	sprintf(painCave.errMsg,
1205	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1206	+	"\tthe constraint equations may not exist or there may be\n"
1207	+	"\tno selected objects in one or both slabs.\n");
1208	+	painCave.isFatal = 0;
1209	+	painCave.severity = OPENMD_INFO;
1210	+	simError();
1211	+	failTrialCount_++;
1212	+	}
1213	+	}
1214
1215	<	RealType v1 = a000 * a111 - a001 * a110;
1216	<	RealType v2 = a000 * b01;
1217	<	RealType v3 = a000 * b11;
1218	<	RealType v4 = a000 * c1 - a001 * c0;
1219	<	RealType v8 = a110 * b01;
702	<	RealType v10 = - b01 * c0;
1215	>	void RNEMD::doVSS() {
1216	>	if (!doRNEMD_) return;
1217	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1218	>	RealType time = currentSnap_->getTime();
1219	>	Mat3x3d hmat = currentSnap_->getHmat();
1220
1221	<	RealType u0 = v2 * v10 - v4 * v4;
705	<	RealType u1 = -2.0 * v3 * v4;
706	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
707	<	RealType u3 = -2.0 * v1 * v3;
708	<	RealType u4 = - v1 * v1;
709	<	//rescale coefficients
710	<	RealType maxAbs = fabs(u0);
711	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
712	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
713	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
714	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
715	<	u0 /= maxAbs;
716	<	u1 /= maxAbs;
717	<	u2 /= maxAbs;
718	<	u3 /= maxAbs;
719	<	u4 /= maxAbs;
720	<	//max_element(start, end) is also available.
721	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
722	<	poly.setCoefficient(4, u4);
723	<	poly.setCoefficient(3, u3);
724	<	poly.setCoefficient(2, u2);
725	<	poly.setCoefficient(1, u1);
726	<	poly.setCoefficient(0, u0);
727	<	std::vector<RealType> realRoots = poly.FindRealRoots();
1221	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1222
1223	<	std::vector<RealType>::iterator ri;
1224	<	RealType r1, r2, alpha0;
1225	<	std::vector<std::pair<RealType,RealType> > rps;
1226	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1227	<	r2 = *ri;
1228	<	//check if FindRealRoots() give the right answer
1229	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1230	<	sprintf(painCave.errMsg,
1231	<	"RNEMD Warning: polynomial solve seems to have an error!");
1232	<	painCave.isFatal = 0;
1233	<	simError();
1234	<	failRootCount_++;
1235	<	}
1236	<	//might not be useful w/o rescaling coefficients
1237	<	alpha0 = -c0 - a110 * r2 * r2;
1238	<	if (alpha0 >= 0.0) {
1239	<	r1 = sqrt(alpha0 / a000);
1240	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
1241	<	{ rps.push_back(std::make_pair(r1, r2)); }
1242	<	if (r1 > 1e-6) { //r1 non-negative
1243	<	r1 = -r1;
1244	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
1245	<	{ rps.push_back(std::make_pair(r1, r2)); }
1246	<	}
1223	>	int selei;
1224	>	StuntDouble* sd;
1225	>
1226	>	vector<StuntDouble*> hotBin, coldBin;
1227	>
1228	>	Vector3d Ph(V3Zero);
1229	>	RealType Mh = 0.0;
1230	>	RealType Kh = 0.0;
1231	>	Vector3d Pc(V3Zero);
1232	>	RealType Mc = 0.0;
1233	>	RealType Kc = 0.0;
1234	>
1235	>
1236	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1237	>	sd = seleMan_.nextSelected(selei)) {
1238	>
1239	>	Vector3d pos = sd->getPos();
1240	>
1241	>	// wrap the stuntdouble's position back into the box:
1242	>
1243	>	if (usePeriodicBoundaryConditions_)
1244	>	currentSnap_->wrapVector(pos);
1245	>
1246	>	// which bin is this stuntdouble in?
1247	>	bool inA = inSlabA(pos);
1248	>	bool inB = inSlabB(pos);
1249	>
1250	>	if (inA || inB) {
1251	>
1252	>	RealType mass = sd->getMass();
1253	>	Vector3d vel = sd->getVel();
1254	>
1255	>	if (inA) {
1256	>	hotBin.push_back(sd);
1257	>	//std::cerr << "before, velocity = " << vel << endl;
1258	>	Ph += mass * vel;
1259	>	//std::cerr << "after, velocity = " << vel << endl;
1260	>	Mh += mass;
1261	>	Kh += mass * vel.lengthSquare();
1262	>	if (rnemdFluxType_ == rnemdFullKE) {
1263	>	if (sd->isDirectional()) {
1264	>	Vector3d angMom = sd->getJ();
1265	>	Mat3x3d I = sd->getI();
1266	>	if (sd->isLinear()) {
1267	>	int i = sd->linearAxis();
1268	>	int j = (i + 1) % 3;
1269	>	int k = (i + 2) % 3;
1270	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1271	>	angMom[k] * angMom[k] / I(k, k);
1272	>	} else {
1273	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1274	>	angMom[1] * angMom[1] / I(1, 1) +
1275	>	angMom[2] * angMom[2] / I(2, 2);
1276	>	}
1277	>	}
1278	>	}
1279	>	} else { //midBin_
1280	>	coldBin.push_back(sd);
1281	>	Pc += mass * vel;
1282	>	Mc += mass;
1283	>	Kc += mass * vel.lengthSquare();
1284	>	if (rnemdFluxType_ == rnemdFullKE) {
1285	>	if (sd->isDirectional()) {
1286	>	Vector3d angMom = sd->getJ();
1287	>	Mat3x3d I = sd->getI();
1288	>	if (sd->isLinear()) {
1289	>	int i = sd->linearAxis();
1290	>	int j = (i + 1) % 3;
1291	>	int k = (i + 2) % 3;
1292	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1293	>	angMom[k] * angMom[k] / I(k, k);
1294	>	} else {
1295	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1296	>	angMom[1] * angMom[1] / I(1, 1) +
1297	>	angMom[2] * angMom[2] / I(2, 2);
1298	>	}
1299	>	}
1300	>	}
1301	>	}
1302		}
1303		}
1304	<	// Consider combininig together the solving pair part w/ the searching
1305	<	// best solution part so that we don't need the pairs vector
1306	<	if (!rps.empty()) {
1307	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1308	<	RealType diff;
1309	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1310	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1311	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
763	<	r1 = (*rpi).first;
764	<	r2 = (*rpi).second;
765	<	switch(rnemdType_) {
766	<	case rnemdKineticScale :
767	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
768	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
769	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
770	<	break;
771	<	case rnemdPxScale :
772	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
773	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
774	<	break;
775	<	case rnemdPyScale :
776	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
777	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
778	<	break;
779	<	case rnemdPzScale :
780	<	default :
781	<	break;
782	<	}
783	<	if (diff < smallestDiff) {
784	<	smallestDiff = diff;
785	<	bestPair = *rpi;
786	<	}
787	<	}
1304	>
1305	>	Kh *= 0.5;
1306	>	Kc *= 0.5;
1307	>
1308	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1309	>	//        << "\tKc= " << Kc << endl;
1310	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1311	>
1312		#ifdef IS_MPI
1313	<	if (worldRank == 0) {
1313	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1314	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1315	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1316	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1317	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1318	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1319		#endif
791	–	std::cerr << "we choose r1 = " << bestPair.first
792	–	<< " and r2 = " << bestPair.second << "\n";
793	–	#ifdef IS_MPI
794	–	}
795	–	#endif
1320
1321	<	RealType x, y, z;
1322	<	switch(rnemdType_) {
1323	<	case rnemdKineticScale :
1324	<	x = bestPair.first;
1325	<	y = bestPair.first;
1326	<	z = bestPair.second;
1327	<	break;
1328	<	case rnemdPxScale :
1329	<	x = c;
1330	<	y = bestPair.first;
1331	<	z = bestPair.second;
1332	<	break;
1333	<	case rnemdPyScale :
1334	<	x = bestPair.first;
1335	<	y = c;
1336	<	z = bestPair.second;
1337	<	break;
1338	<	case rnemdPzScale :
1339	<	x = bestPair.first;
1340	<	y = bestPair.second;
1341	<	z = c;
1342	<	break;
1343	<	default :
1344	<	break;
1345	<	}
1346	<	std::vector<StuntDouble*>::iterator sdi;
1347	<	Vector3d vel;
1348	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1349	<	vel = (*sdi)->getVel();
1350	<	vel.x() *= x;
1351	<	vel.y() *= y;
1352	<	vel.z() *= z;
1353	<	(*sdi)->setVel(vel);
1321	>	bool successfulExchange = false;
1322	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1323	>	Vector3d vc = Pc / Mc;
1324	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1325	>	Vector3d acrec = -momentumTarget_ / Mc;
1326	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1327	>	if (cNumerator > 0.0) {
1328	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1329	>	if (cDenominator > 0.0) {
1330	>	RealType c = sqrt(cNumerator / cDenominator);
1331	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1332	>	Vector3d vh = Ph / Mh;
1333	>	Vector3d ah = momentumTarget_ / Mh + vh;
1334	>	Vector3d ahrec = momentumTarget_ / Mh;
1335	>	RealType hNumerator = Kh + kineticTarget_
1336	>	- 0.5 * Mh * ah.lengthSquare();
1337	>	if (hNumerator > 0.0) {
1338	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1339	>	if (hDenominator > 0.0) {
1340	>	RealType h = sqrt(hNumerator / hDenominator);
1341	>	if ((h > 0.9) && (h < 1.1)) {
1342	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1343	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1344	>	vector<StuntDouble*>::iterator sdi;
1345	>	Vector3d vel;
1346	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1347	>	//vel = (*sdi)->getVel();
1348	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1349	>	(*sdi)->setVel(vel);
1350	>	if (rnemdFluxType_ == rnemdFullKE) {
1351	>	if ((*sdi)->isDirectional()) {
1352	>	Vector3d angMom = (*sdi)->getJ() * c;
1353	>	(*sdi)->setJ(angMom);
1354	>	}
1355	>	}
1356	>	}
1357	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1358	>	//vel = (*sdi)->getVel();
1359	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1360	>	(*sdi)->setVel(vel);
1361	>	if (rnemdFluxType_ == rnemdFullKE) {
1362	>	if ((*sdi)->isDirectional()) {
1363	>	Vector3d angMom = (*sdi)->getJ() * h;
1364	>	(*sdi)->setJ(angMom);
1365	>	}
1366	>	}
1367	>	}
1368	>	successfulExchange = true;
1369	>	kineticExchange_ += kineticTarget_;
1370	>	momentumExchange_ += momentumTarget_;
1371	>	}
1372	>	}
1373	>	}
1374	>	}
1375	>	}
1376		}
1377	<	//convert to hotBin coefficient
1378	<	x = 1.0 + px * (1.0 - x);
1379	<	y = 1.0 + py * (1.0 - y);
1380	<	z = 1.0 + pz * (1.0 - z);
1381	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1382	<	vel = (*sdi)->getVel();
1383	<	vel.x() *= x;
1384	<	vel.y() *= y;
1385	<	vel.z() *= z;
840	<	(*sdi)->setVel(vel);
841	<	}
842	<	exchangeSum_ += targetFlux_;
843	<	//we may want to check whether the exchange has been successful
844	<	} else {
845	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1377	>	}
1378	>	if (successfulExchange != true) {
1379	>	sprintf(painCave.errMsg,
1380	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1381	>	"\tthe constraint equations may not exist or there may be\n"
1382	>	"\tno selected objects in one or both slabs.\n");
1383	>	painCave.isFatal = 0;
1384	>	painCave.severity = OPENMD_INFO;
1385	>	simError();
1386		failTrialCount_++;
1387		}
848	–
1388		}
1389
1390		void RNEMD::doRNEMD() {
1391	<
1392	<	switch(rnemdType_) {
1393	<	case rnemdKineticScale :
1394	<	case rnemdPxScale :
856	<	case rnemdPyScale :
857	<	case rnemdPzScale :
858	<	doScale();
859	<	break;
860	<	case rnemdKineticSwap :
861	<	case rnemdPx :
862	<	case rnemdPy :
863	<	case rnemdPz :
1391	>	if (!doRNEMD_) return;
1392	>	trialCount_++;
1393	>	switch(rnemdMethod_) {
1394	>	case rnemdSwap:
1395		doSwap();
1396		break;
1397	<	case rnemdUnknown :
1397	>	case rnemdNIVS:
1398	>	doNIVS();
1399	>	break;
1400	>	case rnemdVSS:
1401	>	doVSS();
1402	>	break;
1403	>	case rnemdUnkownMethod:
1404		default :
1405		break;
1406		}
1407		}
1408
1409		void RNEMD::collectData() {
1410	<
1410	>	if (!doRNEMD_) return;
1411		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1412		Mat3x3d hmat = currentSnap_->getHmat();
1413
1414	+	areaAccumulator_->add(currentSnap_->getXYarea());
1415	+
1416		seleMan_.setSelectionSet(evaluator_.evaluate());
1417
1418		int selei;
1419		StuntDouble* sd;
881	–	int idx;
1420
1421	+	vector<RealType> binMass(nBins_, 0.0);
1422	+	vector<RealType> binPx(nBins_, 0.0);
1423	+	vector<RealType> binPy(nBins_, 0.0);
1424	+	vector<RealType> binPz(nBins_, 0.0);
1425	+	vector<RealType> binKE(nBins_, 0.0);
1426	+	vector<int> binDOF(nBins_, 0);
1427	+	vector<int> binCount(nBins_, 0);
1428	+
1429	+	// alternative approach, track all molecules instead of only those
1430	+	// selected for scaling/swapping:
1431	+	/*
1432	+	SimInfo::MoleculeIterator miter;
1433	+	vector<StuntDouble*>::iterator iiter;
1434	+	Molecule* mol;
1435	+	StuntDouble* sd;
1436	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1437	+	mol = info_->nextMolecule(miter))
1438	+	sd is essentially sd
1439	+	for (sd = mol->beginIntegrableObject(iiter);
1440	+	sd != NULL;
1441	+	sd = mol->nextIntegrableObject(iiter))
1442	+	*/
1443		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1444	<	sd = seleMan_.nextSelected(selei)) {
1444	>	sd = seleMan_.nextSelected(selei)) {
1445
886	–	idx = sd->getLocalIndex();
887	–
1446		Vector3d pos = sd->getPos();
1447
1448		// wrap the stuntdouble's position back into the box:
1449
1450		if (usePeriodicBoundaryConditions_)
1451		currentSnap_->wrapVector(pos);
1452	<
1452	>
1453	>
1454		// which bin is this stuntdouble in?
1455		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1456	<
1456	>	// Shift molecules by half a box to have bins start at 0
1457	>	// The modulo operator is used to wrap the case when we are
1458	>	// beyond the end of the bins back to the beginning.
1459		int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1460	<
900	<	if (rnemdLogWidth_ == midBin_ + 1)
901	<	if (binNo > midBin_)
902	<	binNo = nBins_ - binNo;
903	<
1460	>
1461		RealType mass = sd->getMass();
1462		Vector3d vel = sd->getVel();
906	–	RealType value;
907	–	RealType xVal, yVal, zVal;
1463
1464	<	switch(rnemdType_) {
1465	<	case rnemdKineticSwap :
1466	<	case rnemdKineticScale :
1467	<
1468	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1469	<	vel[2]*vel[2]);
1470	<
916	<	valueCount_[binNo] += 3;
917	<	if (sd->isDirectional()) {
918	<	Vector3d angMom = sd->getJ();
919	<	Mat3x3d I = sd->getI();
920	<
921	<	if (sd->isLinear()) {
922	<	int i = sd->linearAxis();
923	<	int j = (i + 1) % 3;
924	<	int k = (i + 2) % 3;
925	<	value += angMom[j] * angMom[j] / I(j, j) +
926	<	angMom[k] * angMom[k] / I(k, k);
1464	>	binCount[binNo]++;
1465	>	binMass[binNo] += mass;
1466	>	binPx[binNo] += mass*vel.x();
1467	>	binPy[binNo] += mass*vel.y();
1468	>	binPz[binNo] += mass*vel.z();
1469	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1470	>	binDOF[binNo] += 3;
1471
1472	<	valueCount_[binNo] +=2;
1472	>	if (sd->isDirectional()) {
1473	>	Vector3d angMom = sd->getJ();
1474	>	Mat3x3d I = sd->getI();
1475	>	if (sd->isLinear()) {
1476	>	int i = sd->linearAxis();
1477	>	int j = (i + 1) % 3;
1478	>	int k = (i + 2) % 3;
1479	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1480	>	angMom[k] * angMom[k] / I(k, k));
1481	>	binDOF[binNo] += 2;
1482	>	} else {
1483	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1484	>	angMom[1] * angMom[1] / I(1, 1) +
1485	>	angMom[2] * angMom[2] / I(2, 2));
1486	>	binDOF[binNo] += 3;
1487	>	}
1488	>	}
1489	>	}
1490	>
1491
1492	<	} else {
1493	<	value += angMom[0]*angMom[0]/I(0, 0)
1494	<	+ angMom[1]*angMom[1]/I(1, 1)
1495	<	+ angMom[2]*angMom[2]/I(2, 2);
1496	<	valueCount_[binNo] +=3;
1497	<	}
1498	<	}
1499	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1492	>	#ifdef IS_MPI
1493	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1494	>	nBins_, MPI::INT, MPI::SUM);
1495	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1496	>	nBins_, MPI::REALTYPE, MPI::SUM);
1497	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1498	>	nBins_, MPI::REALTYPE, MPI::SUM);
1499	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1500	>	nBins_, MPI::REALTYPE, MPI::SUM);
1501	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1502	>	nBins_, MPI::REALTYPE, MPI::SUM);
1503	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1504	>	nBins_, MPI::REALTYPE, MPI::SUM);
1505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1506	>	nBins_, MPI::INT, MPI::SUM);
1507	>	#endif
1508
1509	<	break;
1510	<	case rnemdPx :
1511	<	case rnemdPxScale :
1512	<	value = mass * vel[0];
1513	<	valueCount_[binNo]++;
1514	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1515	<	/ PhysicalConstants::kb;
1516	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1517	<	/ PhysicalConstants::kb;
1518	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1519	<	/ PhysicalConstants::kb;
1520	<	xTempHist_[binNo] += xVal;
1521	<	yTempHist_[binNo] += yVal;
1522	<	zTempHist_[binNo] += zVal;
1523	<	break;
1524	<	case rnemdPy :
1525	<	case rnemdPyScale :
1526	<	value = mass * vel[1];
1527	<	valueCount_[binNo]++;
1528	<	break;
1529	<	case rnemdPz :
1530	<	case rnemdPzScale :
1531	<	value = mass * vel[2];
1532	<	valueCount_[binNo]++;
1533	<	break;
1534	<	case rnemdUnknown :
1535	<	default :
1536	<	break;
1509	>	Vector3d vel;
1510	>	RealType den;
1511	>	RealType temp;
1512	>	RealType z;
1513	>	for (int i = 0; i < nBins_; i++) {
1514	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1515	>	vel.x() = binPx[i] / binMass[i];
1516	>	vel.y() = binPy[i] / binMass[i];
1517	>	vel.z() = binPz[i] / binMass[i];
1518	>
1519	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1520	>	/ currentSnap_->getVolume() ;
1521	>
1522	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1523	>	PhysicalConstants::energyConvert);
1524	>
1525	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1526	>	if(outputMask_[j]) {
1527	>	switch(j) {
1528	>	case Z:
1529	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1530	>	break;
1531	>	case TEMPERATURE:
1532	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1533	>	break;
1534	>	case VELOCITY:
1535	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1536	>	break;
1537	>	case DENSITY:
1538	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1539	>	break;
1540	>	}
1541	>	}
1542		}
968	–	valueHist_[binNo] += value;
1543		}
970	–
1544		}
1545
1546		void RNEMD::getStarted() {
1547	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1548	<	Stats& stat = currentSnap_->statData;
1549	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1547	>	if (!doRNEMD_) return;
1548	>	collectData();
1549	>	writeOutputFile();
1550		}
1551
1552	<	void RNEMD::getStatus() {
1553	<
1554	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1555	<	Stats& stat = currentSnap_->statData;
1556	<	RealType time = currentSnap_->getTime();
1557	<
1558	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1559	<	//or to be more meaningful, define another item as exchangeSum_ / time
1560	<	int j;
1561	<
1552	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1553	>	if (!doRNEMD_) return;
1554	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1555	>
1556	>	while(tokenizer.hasMoreTokens()) {
1557	>	std::string token(tokenizer.nextToken());
1558	>	toUpper(token);
1559	>	OutputMapType::iterator i = outputMap_.find(token);
1560	>	if (i != outputMap_.end()) {
1561	>	outputMask_.set(i->second);
1562	>	} else {
1563	>	sprintf( painCave.errMsg,
1564	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1565	>	"\toutputFileFormat keyword.\n", token.c_str() );
1566	>	painCave.isFatal = 0;
1567	>	painCave.severity = OPENMD_ERROR;
1568	>	simError();
1569	>	}
1570	>	}
1571	>	}
1572	>
1573	>	void RNEMD::writeOutputFile() {
1574	>	if (!doRNEMD_) return;
1575	>
1576		#ifdef IS_MPI
990	–
991	–	// all processors have the same number of bins, and STL vectors pack their
992	–	// arrays, so in theory, this should be safe:
993	–
994	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
995	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
996	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
997	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
998	–	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
999	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1000	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1001	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1002	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1003	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1004	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1005	–	}
1577		// If we're the root node, should we print out the results
1578		int worldRank = MPI::COMM_WORLD.Get_rank();
1579		if (worldRank == 0) {
1580		#endif
1581	<	rnemdLog_ << time;
1582	<	for (j = 0; j < rnemdLogWidth_; j++) {
1583	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1581	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1582	>
1583	>	if( !rnemdFile_ ){
1584	>	sprintf( painCave.errMsg,
1585	>	"Could not open \"%s\" for RNEMD output.\n",
1586	>	rnemdFileName_.c_str());
1587	>	painCave.isFatal = 1;
1588	>	simError();
1589		}
1590	<	rnemdLog_ << "\n";
1591	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1592	<	xTempLog_ << time;
1593	<	for (j = 0; j < rnemdLogWidth_; j++) {
1594	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1590	>
1591	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1592	>
1593	>	RealType time = currentSnap_->getTime();
1594	>	RealType avgArea;
1595	>	areaAccumulator_->getAverage(avgArea);
1596	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1597	>	/ PhysicalConstants::energyConvert;
1598	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1599	>
1600	>	rnemdFile_ << "#######################################################\n";
1601	>	rnemdFile_ << "# RNEMD {\n";
1602	>
1603	>	map<string, RNEMDMethod>::iterator mi;
1604	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1605	>	if ( (*mi).second == rnemdMethod_)
1606	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1607	>	}
1608	>	map<string, RNEMDFluxType>::iterator fi;
1609	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1610	>	if ( (*fi).second == rnemdFluxType_)
1611	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1612	>	}
1613	>
1614	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1615	>
1616	>	rnemdFile_ << "#    objectSelection = \""
1617	>	<< rnemdObjectSelection_ << "\";\n";
1618	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1619	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1620	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1621	>	rnemdFile_ << "# }\n";
1622	>	rnemdFile_ << "#######################################################\n";
1623	>	rnemdFile_ << "# RNEMD report:\n";
1624	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1625	>	rnemdFile_ << "#     target flux:\n";
1626	>	rnemdFile_ << "#         kinetic = "
1627	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1628	>	<< " (kcal/mol/A^2/fs)\n";
1629	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1630	>	<< " (amu/A/fs^2)\n";
1631	>	rnemdFile_ << "#     target one-time exchanges:\n";
1632	>	rnemdFile_ << "#         kinetic = "
1633	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1634	>	<< " (kcal/mol)\n";
1635	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1636	>	<< " (amu*A/fs)\n";
1637	>	rnemdFile_ << "#     actual exchange totals:\n";
1638	>	rnemdFile_ << "#         kinetic = "
1639	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1640	>	<< " (kcal/mol)\n";
1641	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1642	>	<< " (amu*A/fs)\n";
1643	>	rnemdFile_ << "#     actual flux:\n";
1644	>	rnemdFile_ << "#         kinetic = " << Jz
1645	>	<< " (kcal/mol/A^2/fs)\n";
1646	>	rnemdFile_ << "#         momentum = " << JzP
1647	>	<< " (amu/A/fs^2)\n";
1648	>	rnemdFile_ << "#     exchange statistics:\n";
1649	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1650	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1651	>	if (rnemdMethod_ == rnemdNIVS) {
1652	>	rnemdFile_ << "#         NIVS root-check errors = "
1653	>	<< failRootCount_ << "\n";
1654	>	}
1655	>	rnemdFile_ << "#######################################################\n";
1656	>
1657	>
1658	>
1659	>	//write title
1660	>	rnemdFile_ << "#";
1661	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1662	>	if (outputMask_[i]) {
1663	>	rnemdFile_ << "\t" << data_[i].title <<
1664	>	"(" << data_[i].units << ")";
1665	>	// add some extra tabs for column alignment
1666	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1667		}
1668	<	xTempLog_ << "\n";
1669	<	yTempLog_ << time;
1670	<	for (j = 0; j < rnemdLogWidth_; j++) {
1671	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1668	>	}
1669	>	rnemdFile_ << std::endl;
1670	>
1671	>	rnemdFile_.precision(8);
1672	>
1673	>	for (int j = 0; j < nBins_; j++) {
1674	>
1675	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1676	>	if (outputMask_[i]) {
1677	>	if (data_[i].dataType == "RealType")
1678	>	writeReal(i,j);
1679	>	else if (data_[i].dataType == "Vector3d")
1680	>	writeVector(i,j);
1681	>	else {
1682	>	sprintf( painCave.errMsg,
1683	>	"RNEMD found an unknown data type for: %s ",
1684	>	data_[i].title.c_str());
1685	>	painCave.isFatal = 1;
1686	>	simError();
1687	>	}
1688	>	}
1689		}
1690	<	yTempLog_ << "\n";
1691	<	zTempLog_ << time;
1692	<	for (j = 0; j < rnemdLogWidth_; j++) {
1693	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1690	>	rnemdFile_ << std::endl;
1691	>
1692	>	}
1693	>
1694	>	rnemdFile_ << "#######################################################\n";
1695	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1696	>	rnemdFile_ << "#######################################################\n";
1697	>
1698	>
1699	>	for (int j = 0; j < nBins_; j++) {
1700	>	rnemdFile_ << "#";
1701	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1702	>	if (outputMask_[i]) {
1703	>	if (data_[i].dataType == "RealType")
1704	>	writeRealStdDev(i,j);
1705	>	else if (data_[i].dataType == "Vector3d")
1706	>	writeVectorStdDev(i,j);
1707	>	else {
1708	>	sprintf( painCave.errMsg,
1709	>	"RNEMD found an unknown data type for: %s ",
1710	>	data_[i].title.c_str());
1711	>	painCave.isFatal = 1;
1712	>	simError();
1713	>	}
1714	>	}
1715		}
1716	<	zTempLog_ << "\n";
1717	<	}
1716	>	rnemdFile_ << std::endl;
1717	>
1718	>	}
1719	>
1720	>	rnemdFile_.flush();
1721	>	rnemdFile_.close();
1722	>
1723		#ifdef IS_MPI
1724		}
1725		#endif
1726	<	for (j = 0; j < rnemdLogWidth_; j++) {
1727	<	valueCount_[j] = 0;
1728	<	valueHist_[j] = 0.0;
1726	>
1727	>	}
1728	>
1729	>	void RNEMD::writeReal(int index, unsigned int bin) {
1730	>	if (!doRNEMD_) return;
1731	>	assert(index >=0 && index < ENDINDEX);
1732	>	assert(bin < nBins_);
1733	>	RealType s;
1734	>
1735	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
1736	>
1737	>	if (! isinf(s) && ! isnan(s)) {
1738	>	rnemdFile_ << "\t" << s;
1739	>	} else{
1740	>	sprintf( painCave.errMsg,
1741	>	"RNEMD detected a numerical error writing: %s for bin %d",
1742	>	data_[index].title.c_str(), bin);
1743	>	painCave.isFatal = 1;
1744	>	simError();
1745	>	}
1746	>	}
1747	>
1748	>	void RNEMD::writeVector(int index, unsigned int bin) {
1749	>	if (!doRNEMD_) return;
1750	>	assert(index >=0 && index < ENDINDEX);
1751	>	assert(bin < nBins_);
1752	>	Vector3d s;
1753	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1754	>	if (isinf(s[0]) || isnan(s[0]) ||
1755	>	isinf(s[1]) || isnan(s[1]) ||
1756	>	isinf(s[2]) || isnan(s[2]) ) {
1757	>	sprintf( painCave.errMsg,
1758	>	"RNEMD detected a numerical error writing: %s for bin %d",
1759	>	data_[index].title.c_str(), bin);
1760	>	painCave.isFatal = 1;
1761	>	simError();
1762	>	} else {
1763	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1764		}
1765	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1766	<	for (j = 0; j < rnemdLogWidth_; j++) {
1767	<	xTempHist_[j] = 0.0;
1768	<	yTempHist_[j] = 0.0;
1769	<	zTempHist_[j] = 0.0;
1770	<	}
1765	>	}
1766	>
1767	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1768	>	if (!doRNEMD_) return;
1769	>	assert(index >=0 && index < ENDINDEX);
1770	>	assert(bin < nBins_);
1771	>	RealType s;
1772	>
1773	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
1774	>
1775	>	if (! isinf(s) && ! isnan(s)) {
1776	>	rnemdFile_ << "\t" << s;
1777	>	} else{
1778	>	sprintf( painCave.errMsg,
1779	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1780	>	data_[index].title.c_str(), bin);
1781	>	painCave.isFatal = 1;
1782	>	simError();
1783	>	}
1784		}
1785	+
1786	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1787	+	if (!doRNEMD_) return;
1788	+	assert(index >=0 && index < ENDINDEX);
1789	+	assert(bin < nBins_);
1790	+	Vector3d s;
1791	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1792	+	if (isinf(s[0]) || isnan(s[0]) ||
1793	+	isinf(s[1]) || isnan(s[1]) ||
1794	+	isinf(s[2]) || isnan(s[2]) ) {
1795	+	sprintf( painCave.errMsg,
1796	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1797	+	data_[index].title.c_str(), bin);
1798	+	painCave.isFatal = 1;
1799	+	simError();
1800	+	} else {
1801	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1802	+	}
1803	+	}
1804		}
1805	+

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