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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1803 by gezelter, Wed Oct 3 14:20:07 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	<
53	<	#ifndef IS_MPI
53	<	#include "math/SeqRandNumGen.hpp"
54	<	#else
55	<	#include "math/ParallelRandNumGen.hpp"
52	>	#ifdef IS_MPI
53	>	#include <mpi.h>
54		#endif
55
56		#define HONKING_LARGE_VALUE 1.0e10
57
58	+	using namespace std;
59		namespace OpenMD {
60
61	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
61	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
62	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63
64	+	trialCount_ = 0;
65		failTrialCount_ = 0;
66		failRootCount_ = 0;
67
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	<	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;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
75	>	stringToMethod_["Swap"]  = rnemdSwap;
76	>	stringToMethod_["NIVS"]  = rnemdNIVS;
77	>	stringToMethod_["VSS"]   = rnemdVSS;
78	>
79	>	stringToFluxType_["KE"]  = rnemdKE;
80	>	stringToFluxType_["Px"]  = rnemdPx;
81	>	stringToFluxType_["Py"]  = rnemdPy;
82	>	stringToFluxType_["Pz"]  = rnemdPz;
83	>	stringToFluxType_["Pvector"]  = rnemdPvector;
84	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
85	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
86	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
87	>
88	>	runTime_ = simParams->getRunTime();
89	>	statusTime_ = simParams->getStatusTime();
90	>
91	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
92		evaluator_.loadScriptString(rnemdObjectSelection_);
93		seleMan_.setSelectionSet(evaluator_.evaluate());
94
95	+	const string methStr = rnemdParams->getMethod();
96	+	bool hasFluxType = rnemdParams->haveFluxType();
97	+
98	+	string fluxStr;
99	+	if (hasFluxType) {
100	+	fluxStr = rnemdParams->getFluxType();
101	+	} else {
102	+	sprintf(painCave.errMsg,
103	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
104	+	"\twhich must be one of the following values:\n"
105	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
106	+	"\tmust be set to use RNEMD\n");
107	+	painCave.isFatal = 1;
108	+	painCave.severity = OPENMD_ERROR;
109	+	simError();
110	+	}
111	+
112	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
113	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
114	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
115	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
116	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
117	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
118	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
119	+	bool hasOutputFields = rnemdParams->haveOutputFields();
120	+
121	+	map<string, RNEMDMethod>::iterator i;
122	+	i = stringToMethod_.find(methStr);
123	+	if (i != stringToMethod_.end())
124	+	rnemdMethod_ = i->second;
125	+	else {
126	+	sprintf(painCave.errMsg,
127	+	"RNEMD: The current method,\n"
128	+	"\t\t%s is not one of the recognized\n"
129	+	"\texchange methods: Swap, NIVS, or VSS\n",
130	+	methStr.c_str());
131	+	painCave.isFatal = 1;
132	+	painCave.severity = OPENMD_ERROR;
133	+	simError();
134	+	}
135	+
136	+	map<string, RNEMDFluxType>::iterator j;
137	+	j = stringToFluxType_.find(fluxStr);
138	+	if (j != stringToFluxType_.end())
139	+	rnemdFluxType_ = j->second;
140	+	else {
141	+	sprintf(painCave.errMsg,
142	+	"RNEMD: The current fluxType,\n"
143	+	"\t\t%s\n"
144	+	"\tis not one of the recognized flux types.\n",
145	+	fluxStr.c_str());
146	+	painCave.isFatal = 1;
147	+	painCave.severity = OPENMD_ERROR;
148	+	simError();
149	+	}
150	+
151	+	bool methodFluxMismatch = false;
152	+	bool hasCorrectFlux = false;
153	+	switch(rnemdMethod_) {
154	+	case rnemdSwap:
155	+	switch (rnemdFluxType_) {
156	+	case rnemdKE:
157	+	hasCorrectFlux = hasKineticFlux;
158	+	break;
159	+	case rnemdPx:
160	+	case rnemdPy:
161	+	case rnemdPz:
162	+	hasCorrectFlux = hasMomentumFlux;
163	+	break;
164	+	default :
165	+	methodFluxMismatch = true;
166	+	break;
167	+	}
168	+	break;
169	+	case rnemdNIVS:
170	+	switch (rnemdFluxType_) {
171	+	case rnemdKE:
172	+	case rnemdRotKE:
173	+	case rnemdFullKE:
174	+	hasCorrectFlux = hasKineticFlux;
175	+	break;
176	+	case rnemdPx:
177	+	case rnemdPy:
178	+	case rnemdPz:
179	+	hasCorrectFlux = hasMomentumFlux;
180	+	break;
181	+	case rnemdKePx:
182	+	case rnemdKePy:
183	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
184	+	break;
185	+	default:
186	+	methodFluxMismatch = true;
187	+	break;
188	+	}
189	+	break;
190	+	case rnemdVSS:
191	+	switch (rnemdFluxType_) {
192	+	case rnemdKE:
193	+	case rnemdRotKE:
194	+	case rnemdFullKE:
195	+	hasCorrectFlux = hasKineticFlux;
196	+	break;
197	+	case rnemdPx:
198	+	case rnemdPy:
199	+	case rnemdPz:
200	+	hasCorrectFlux = hasMomentumFlux;
201	+	break;
202	+	case rnemdPvector:
203	+	hasCorrectFlux = hasMomentumFluxVector;
204	+	break;
205	+	case rnemdKePx:
206	+	case rnemdKePy:
207	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
208	+	break;
209	+	case rnemdKePvector:
210	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
211	+	break;
212	+	default:
213	+	methodFluxMismatch = true;
214	+	break;
215	+	}
216	+	default:
217	+	break;
218	+	}
219	+
220	+	if (methodFluxMismatch) {
221	+	sprintf(painCave.errMsg,
222	+	"RNEMD: The current method,\n"
223	+	"\t\t%s\n"
224	+	"\tcannot be used with the current flux type, %s\n",
225	+	methStr.c_str(), fluxStr.c_str());
226	+	painCave.isFatal = 1;
227	+	painCave.severity = OPENMD_ERROR;
228	+	simError();
229	+	}
230	+	if (!hasCorrectFlux) {
231	+	sprintf(painCave.errMsg,
232	+	"RNEMD: The current method, %s, and flux type, %s,\n"
233	+	"\tdid not have the correct flux value specified. Options\n"
234	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
235	+	methStr.c_str(), fluxStr.c_str());
236	+	painCave.isFatal = 1;
237	+	painCave.severity = OPENMD_ERROR;
238	+	simError();
239	+	}
240	+
241	+	if (hasKineticFlux) {
242	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
243	+	// into  amu / fs^3:
244	+	kineticFlux_ = rnemdParams->getKineticFlux()
245	+	* PhysicalConstants::energyConvert;
246	+	} else {
247	+	kineticFlux_ = 0.0;
248	+	}
249	+	if (hasMomentumFluxVector) {
250	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
251	+	} else {
252	+	momentumFluxVector_ = V3Zero;
253	+	if (hasMomentumFlux) {
254	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
255	+	switch (rnemdFluxType_) {
256	+	case rnemdPx:
257	+	momentumFluxVector_.x() = momentumFlux;
258	+	break;
259	+	case rnemdPy:
260	+	momentumFluxVector_.y() = momentumFlux;
261	+	break;
262	+	case rnemdPz:
263	+	momentumFluxVector_.z() = momentumFlux;
264	+	break;
265	+	case rnemdKePx:
266	+	momentumFluxVector_.x() = momentumFlux;
267	+	break;
268	+	case rnemdKePy:
269	+	momentumFluxVector_.y() = momentumFlux;
270	+	break;
271	+	default:
272	+	break;
273	+	}
274	+	}
275	+	}
276	+
277		// do some sanity checking
278
279		int selectionCount = seleMan_.getSelectionCount();
280	+
281		int nIntegrable = info->getNGlobalIntegrableObjects();
282
283		if (selectionCount > nIntegrable) {
284		sprintf(painCave.errMsg,
285	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
285	>	"RNEMD: The current objectSelection,\n"
286		"\t\t%s\n"
287		"\thas resulted in %d selected objects.  However,\n"
288		"\tthe total number of integrable objects in the system\n"
#	Line 98 | Line 292 | namespace OpenMD {
292		rnemdObjectSelection_.c_str(),
293		selectionCount, nIntegrable);
294		painCave.isFatal = 0;
295	+	painCave.severity = OPENMD_WARNING;
296		simError();
102	–
297		}
104	–
105	–	const std::string st = simParams->getRNEMD_exchangeType();
298
299	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
108	<	i = stringToEnumMap_.find(st);
109	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	<	if (rnemdType_ == rnemdUnknown) {
111	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
112	<	}
299	>	areaAccumulator_ = new Accumulator();
300
301	<	#ifdef IS_MPI
115	<	if (worldRank == 0) {
116	<	#endif
301	>	nBins_ = rnemdParams->getOutputBins();
302
303	<	std::string rnemdFileName;
304	<	std::string xTempFileName;
305	<	std::string yTempFileName;
306	<	std::string zTempFileName;
307	<	switch(rnemdType_) {
308	<	case rnemdKineticSwap :
309	<	case rnemdKineticScale :
310	<	rnemdFileName = "temperature.log";
303	>	data_.resize(RNEMD::ENDINDEX);
304	>	OutputData z;
305	>	z.units =  "Angstroms";
306	>	z.title =  "Z";
307	>	z.dataType = "RealType";
308	>	z.accumulator.reserve(nBins_);
309	>	for (unsigned int i = 0; i < nBins_; i++)
310	>	z.accumulator.push_back( new Accumulator() );
311	>	data_[Z] = z;
312	>	outputMap_["Z"] =  Z;
313	>
314	>	OutputData temperature;
315	>	temperature.units =  "K";
316	>	temperature.title =  "Temperature";
317	>	temperature.dataType = "RealType";
318	>	temperature.accumulator.reserve(nBins_);
319	>	for (unsigned int i = 0; i < nBins_; i++)
320	>	temperature.accumulator.push_back( new Accumulator() );
321	>	data_[TEMPERATURE] = temperature;
322	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
323	>
324	>	OutputData velocity;
325	>	velocity.units = "angstroms/fs";
326	>	velocity.title =  "Velocity";
327	>	velocity.dataType = "Vector3d";
328	>	velocity.accumulator.reserve(nBins_);
329	>	for (unsigned int i = 0; i < nBins_; i++)
330	>	velocity.accumulator.push_back( new VectorAccumulator() );
331	>	data_[VELOCITY] = velocity;
332	>	outputMap_["VELOCITY"] = VELOCITY;
333	>
334	>	OutputData density;
335	>	density.units =  "g cm^-3";
336	>	density.title =  "Density";
337	>	density.dataType = "RealType";
338	>	density.accumulator.reserve(nBins_);
339	>	for (unsigned int i = 0; i < nBins_; i++)
340	>	density.accumulator.push_back( new Accumulator() );
341	>	data_[DENSITY] = density;
342	>	outputMap_["DENSITY"] =  DENSITY;
343	>
344	>	if (hasOutputFields) {
345	>	parseOutputFileFormat(rnemdParams->getOutputFields());
346	>	} else {
347	>	outputMask_.set(Z);
348	>	switch (rnemdFluxType_) {
349	>	case rnemdKE:
350	>	case rnemdRotKE:
351	>	case rnemdFullKE:
352	>	outputMask_.set(TEMPERATURE);
353		break;
354	<	case rnemdPx :
355	<	case rnemdPxScale :
356	<	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());
354	>	case rnemdPx:
355	>	case rnemdPy:
356	>	outputMask_.set(VELOCITY);
357		break;
358	<	case rnemdPz :
359	<	case rnemdPzScale :
360	<	case rnemdUnknown :
361	<	default :
143	<	rnemdFileName = "rnemd.log";
358	>	case rnemdPz:
359	>	case rnemdPvector:
360	>	outputMask_.set(VELOCITY);
361	>	outputMask_.set(DENSITY);
362		break;
363	+	case rnemdKePx:
364	+	case rnemdKePy:
365	+	outputMask_.set(TEMPERATURE);
366	+	outputMask_.set(VELOCITY);
367	+	break;
368	+	case rnemdKePvector:
369	+	outputMask_.set(TEMPERATURE);
370	+	outputMask_.set(VELOCITY);
371	+	outputMask_.set(DENSITY);
372	+	break;
373	+	default:
374	+	break;
375		}
146	–	rnemdLog_.open(rnemdFileName.c_str());
147	–
148	–	#ifdef IS_MPI
376		}
377	<	#endif
378	<
379	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
153	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
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	<	}
377	>
378	>	if (hasOutputFileName) {
379	>	rnemdFileName_ = rnemdParams->getOutputFileName();
380		} else {
381	<	rnemdLogWidth_ = nBins_;
382	<	}
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);
381	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
382	>	}
383
384	<	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	<	}
384	>	exchangeTime_ = rnemdParams->getExchangeTime();
385
386	<	#ifndef IS_MPI
387	<	if (simParams->haveSeed()) {
180	<	seedValue = simParams->getSeed();
181	<	randNumGen_ = new SeqRandNumGen(seedValue);
182	<	}else {
183	<	randNumGen_ = new SeqRandNumGen();
184	<	}
185	<	#else
186	<	if (simParams->haveSeed()) {
187	<	seedValue = simParams->getSeed();
188	<	randNumGen_ = new ParallelRandNumGen(seedValue);
189	<	}else {
190	<	randNumGen_ = new ParallelRandNumGen();
191	<	}
192	<	#endif
193	<	}
386	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
387	>	Mat3x3d hmat = currentSnap_->getHmat();
388
389	<	RNEMD::~RNEMD() {
390	<	delete randNumGen_;
389	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
390	>	// Lx, Ly = box dimensions in x & y
391	>	// dt = exchange time interval
392	>	// flux = target flux
393	>
394	>	RealType area = currentSnap_->getXYarea();
395	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
396	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
397	>
398	>	// total exchange sums are zeroed out at the beginning:
399	>
400	>	kineticExchange_ = 0.0;
401	>	momentumExchange_ = V3Zero;
402	>
403	>	if (hasSlabWidth)
404	>	slabWidth_ = rnemdParams->getSlabWidth();
405	>	else
406	>	slabWidth_ = hmat(2,2) / 10.0;
407	>
408	>	if (hasSlabACenter)
409	>	slabACenter_ = rnemdParams->getSlabACenter();
410	>	else
411	>	slabACenter_ = 0.0;
412
413	+	if (hasSlabBCenter)
414	+	slabBCenter_ = rnemdParams->getSlabBCenter();
415	+	else
416	+	slabBCenter_ = hmat(2,2) / 2.0;
417	+
418	+	}
419	+
420	+	RNEMD::~RNEMD() {
421	+	if (!doRNEMD_) return;
422		#ifdef IS_MPI
423		if (worldRank == 0) {
424		#endif
425	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
426	<	rnemdLog_.close();
427	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
428	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
429	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
206	<	xTempLog_.close();
207	<	yTempLog_.close();
208	<	zTempLog_.close();
209	<	}
425	>
426	>	writeOutputFile();
427	>
428	>	rnemdFile_.close();
429	>
430		#ifdef IS_MPI
431		}
432		#endif
433		}
434	+
435	+	bool RNEMD::inSlabA(Vector3d pos) {
436	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
437	+	}
438	+	bool RNEMD::inSlabB(Vector3d pos) {
439	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
440	+	}
441
442		void RNEMD::doSwap() {
443	<
443	>	if (!doRNEMD_) return;
444		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
445		Mat3x3d hmat = currentSnap_->getHmat();
446
#	Line 242 | Line 469 | namespace OpenMD {
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?
247	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
248	<
249	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
250	<
251	<
252	<	// if we're in bin 0 or the middleBin
253	<	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	<	}
280	<	//make exchangeSum_ comparable between swap & scale
281	<	//temporarily without using energyConvert
282	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
501	>	} //angular momenta exchange enabled
502		value *= 0.5;
503		break;
504		case rnemdPx :
#	Line 295 | 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 306 | 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 320 | Line 539 | namespace OpenMD {
539		}
540		}
541		}
542	<
542	>
543		#ifdef IS_MPI
544		int nProc, worldRank;
545	<
545	>
546		nProc = MPI::COMM_WORLD.Get_size();
547		worldRank = MPI::COMM_WORLD.Get_rank();
548
#	Line 331 | Line 550 | namespace OpenMD {
550		bool my_max_found = max_found;
551
552		// Even if we didn't find a minimum, did someone else?
553	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
335	<	1, MPI::BOOL, MPI::LAND);
336	<
553	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
554		// Even if we didn't find a maximum, did someone else?
555	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
556	<	1, MPI::BOOL, MPI::LAND);
557	<
558	<	struct {
559	<	RealType val;
560	<	int rank;
561	<	} max_vals, min_vals;
562	<
563	<	if (min_found) {
564	<	if (my_min_found)
555	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
556	>	#endif
557	>
558	>	if (max_found && min_found) {
559	>
560	>	#ifdef IS_MPI
561	>	struct {
562	>	RealType val;
563	>	int rank;
564	>	} max_vals, min_vals;
565	>
566	>	if (my_min_found) {
567		min_vals.val = min_val;
568	<	else
568	>	} else {
569		min_vals.val = HONKING_LARGE_VALUE;
570	<
570	>	}
571		min_vals.rank = worldRank;
572
573		// Who had the minimum?
574		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
575		1, MPI::REALTYPE_INT, MPI::MINLOC);
576		min_val = min_vals.val;
358	–	}
577
578	<	if (max_found) {
361	<	if (my_max_found)
578	>	if (my_max_found) {
579		max_vals.val = max_val;
580	<	else
580	>	} else {
581		max_vals.val = -HONKING_LARGE_VALUE;
582	<
582	>	}
583		max_vals.rank = worldRank;
584
585		// Who had the maximum?
586		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
587		1, MPI::REALTYPE_INT, MPI::MAXLOC);
588		max_val = max_vals.val;
372	–	}
589		#endif
590	<
591	<	if (max_found && min_found) {
592	<	if (min_val< max_val) {
377	<
590	>
591	>	if (min_val < max_val) {
592	>
593		#ifdef IS_MPI
594		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
595		// I have both maximum and minimum, so proceed like a single
596		// processor version:
597		#endif
598	<	// objects to be swapped: velocity & angular velocity
598	>
599		Vector3d min_vel = min_sd->getVel();
600		Vector3d max_vel = max_sd->getVel();
601		RealType temp_vel;
602
603	<	switch(rnemdType_) {
604	<	case rnemdKineticSwap :
603	>	switch(rnemdFluxType_) {
604	>	case rnemdKE :
605		min_sd->setVel(max_vel);
606		max_sd->setVel(min_vel);
607	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
607	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
608		Vector3d min_angMom = min_sd->getJ();
609		Vector3d max_angMom = max_sd->getJ();
610		min_sd->setJ(max_angMom);
611		max_sd->setJ(min_angMom);
612	<	}
612	>	}//angular momenta exchange enabled
613	>	//assumes same rigid body identity
614		break;
615		case rnemdPx :
616		temp_vel = min_vel.x();
#	Line 420 | Line 636 | namespace OpenMD {
636		default :
637		break;
638		}
639	+
640		#ifdef IS_MPI
641		// the rest of the cases only apply in parallel simulations:
642		} else if (max_vals.rank == worldRank) {
#	Line 435 | Line 652 | namespace OpenMD {
652		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
653		min_vals.rank, 0, status);
654
655	<	switch(rnemdType_) {
656	<	case rnemdKineticSwap :
655	>	switch(rnemdFluxType_) {
656	>	case rnemdKE :
657		max_sd->setVel(min_vel);
658	<
658	>	//angular momenta exchange enabled
659		if (max_sd->isDirectional()) {
660		Vector3d min_angMom;
661		Vector3d max_angMom = max_sd->getJ();
662	<
662	>
663		// point-to-point swap of the angular momentum vector
664		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
665		MPI::REALTYPE, min_vals.rank, 1,
666		min_angMom.getArrayPointer(), 3,
667		MPI::REALTYPE, min_vals.rank, 1,
668		status);
669	<
669	>
670		max_sd->setJ(min_angMom);
671	<	}
671	>	}
672		break;
673		case rnemdPx :
674		max_vel.x() = min_vel.x();
#	Line 481 | Line 698 | namespace OpenMD {
698		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
699		max_vals.rank, 0, status);
700
701	<	switch(rnemdType_) {
702	<	case rnemdKineticSwap :
701	>	switch(rnemdFluxType_) {
702	>	case rnemdKE :
703		min_sd->setVel(max_vel);
704	<
704	>	//angular momenta exchange enabled
705		if (min_sd->isDirectional()) {
706		Vector3d min_angMom = min_sd->getJ();
707		Vector3d max_angMom;
708	<
708	>
709		// point-to-point swap of the angular momentum vector
710		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
711		MPI::REALTYPE, max_vals.rank, 1,
712		max_angMom.getArrayPointer(), 3,
713		MPI::REALTYPE, max_vals.rank, 1,
714		status);
715	<
715	>
716		min_sd->setJ(max_angMom);
717		}
718		break;
#	Line 516 | Line 733 | namespace OpenMD {
733		}
734		}
735		#endif
736	<	exchangeSum_ += max_val - min_val;
737	<	} else {
738	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
736	>
737	>	switch(rnemdFluxType_) {
738	>	case rnemdKE:
739	>	kineticExchange_ += max_val - min_val;
740	>	break;
741	>	case rnemdPx:
742	>	momentumExchange_.x() += max_val - min_val;
743	>	break;
744	>	case rnemdPy:
745	>	momentumExchange_.y() += max_val - min_val;
746	>	break;
747	>	case rnemdPz:
748	>	momentumExchange_.z() += max_val - min_val;
749	>	break;
750	>	default:
751	>	break;
752	>	}
753	>	} else {
754	>	sprintf(painCave.errMsg,
755	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
756	>	painCave.isFatal = 0;
757	>	painCave.severity = OPENMD_INFO;
758	>	simError();
759		failTrialCount_++;
760		}
761		} else {
762	<	std::cerr << "exchange NOT performed!\n";
763	<	std::cerr << "at least one of the two slabs empty.\n";
762	>	sprintf(painCave.errMsg,
763	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
764	>	"\twas not present in at least one of the two slabs.\n");
765	>	painCave.isFatal = 0;
766	>	painCave.severity = OPENMD_INFO;
767	>	simError();
768		failTrialCount_++;
769	<	}
529	<
769	>	}
770		}
771
772	<	void RNEMD::doScale() {
773	<
772	>	void RNEMD::doNIVS() {
773	>	if (!doRNEMD_) return;
774		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
775		Mat3x3d hmat = currentSnap_->getHmat();
776
#	Line 540 | Line 780 | namespace OpenMD {
780		StuntDouble* sd;
781		int idx;
782
783	<	std::vector<StuntDouble*> hotBin, coldBin;
783	>	vector<StuntDouble*> hotBin, coldBin;
784
785		RealType Phx = 0.0;
786		RealType Phy = 0.0;
#	Line 548 | Line 788 | namespace OpenMD {
788		RealType Khx = 0.0;
789		RealType Khy = 0.0;
790		RealType Khz = 0.0;
791	+	RealType Khw = 0.0;
792		RealType Pcx = 0.0;
793		RealType Pcy = 0.0;
794		RealType Pcz = 0.0;
795		RealType Kcx = 0.0;
796		RealType Kcy = 0.0;
797		RealType Kcz = 0.0;
798	+	RealType Kcw = 0.0;
799
800		for (sd = seleMan_.beginSelected(selei); sd != NULL;
801		sd = seleMan_.nextSelected(selei)) {
#	Line 568 | Line 810 | namespace OpenMD {
810		currentSnap_->wrapVector(pos);
811
812		// which bin is this stuntdouble in?
813	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
813	>	bool inA = inSlabA(pos);
814	>	bool inB = inSlabB(pos);
815
816	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
817	<
575	<	// if we're in bin 0 or the middleBin
576	<	if (binNo == 0 || binNo == midBin_) {
577	<
816	>	if (inA || inB) {
817	>
818		RealType mass = sd->getMass();
819		Vector3d vel = sd->getVel();
820
821	<	if (binNo == 0) {
821	>	if (inA) {
822		hotBin.push_back(sd);
823		Phx += mass * vel.x();
824		Phy += mass * vel.y();
#	Line 586 | Line 826 | namespace OpenMD {
826		Khx += mass * vel.x() * vel.x();
827		Khy += mass * vel.y() * vel.y();
828		Khz += mass * vel.z() * vel.z();
829	<	} else { //midBin_
829	>	if (sd->isDirectional()) {
830	>	Vector3d angMom = sd->getJ();
831	>	Mat3x3d I = sd->getI();
832	>	if (sd->isLinear()) {
833	>	int i = sd->linearAxis();
834	>	int j = (i + 1) % 3;
835	>	int k = (i + 2) % 3;
836	>	Khw += angMom[j] * angMom[j] / I(j, j) +
837	>	angMom[k] * angMom[k] / I(k, k);
838	>	} else {
839	>	Khw += angMom[0]*angMom[0]/I(0, 0)
840	>	+ angMom[1]*angMom[1]/I(1, 1)
841	>	+ angMom[2]*angMom[2]/I(2, 2);
842	>	}
843	>	}
844	>	} else {
845		coldBin.push_back(sd);
846		Pcx += mass * vel.x();
847		Pcy += mass * vel.y();
#	Line 594 | Line 849 | namespace OpenMD {
849		Kcx += mass * vel.x() * vel.x();
850		Kcy += mass * vel.y() * vel.y();
851		Kcz += mass * vel.z() * vel.z();
852	+	if (sd->isDirectional()) {
853	+	Vector3d angMom = sd->getJ();
854	+	Mat3x3d I = sd->getI();
855	+	if (sd->isLinear()) {
856	+	int i = sd->linearAxis();
857	+	int j = (i + 1) % 3;
858	+	int k = (i + 2) % 3;
859	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
860	+	angMom[k] * angMom[k] / I(k, k);
861	+	} else {
862	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
863	+	+ angMom[1]*angMom[1]/I(1, 1)
864	+	+ angMom[2]*angMom[2]/I(2, 2);
865	+	}
866	+	}
867		}
868		}
869		}
870	<
870	>
871		Khx *= 0.5;
872		Khy *= 0.5;
873		Khz *= 0.5;
874	+	Khw *= 0.5;
875		Kcx *= 0.5;
876		Kcy *= 0.5;
877		Kcz *= 0.5;
878	+	Kcw *= 0.5;
879
880		#ifdef IS_MPI
881		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 616 | Line 888 | namespace OpenMD {
888		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
889		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
890		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
891	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
892	+
893		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
894		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
895		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
896	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
897		#endif
898
899	<	//use coldBin coeff's
899	>	//solve coldBin coeff's first
900		RealType px = Pcx / Phx;
901		RealType py = Pcy / Phy;
902		RealType pz = Pcz / Phz;
903	+	RealType c, x, y, z;
904	+	bool successfulScale = false;
905	+	if ((rnemdFluxType_ == rnemdFullKE) ||
906	+	(rnemdFluxType_ == rnemdRotKE)) {
907	+	//may need sanity check Khw & Kcw > 0
908
909	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
910	<	switch(rnemdType_) {
911	<	case rnemdKineticScale :
912	<	/*used hotBin coeff's & only scale x & y dimensions
913	<	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	<	*/
909	>	if (rnemdFluxType_ == rnemdFullKE) {
910	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
911	>	} else {
912	>	c = 1.0 - kineticTarget_ / Kcw;
913	>	}
914
915	<	//scale all three dimensions, let c_x = c_y
916	<	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	<	}
915	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
916	>	c = sqrt(c);
917
918	<	RealType v1 = a000 * a111 - a001 * a110;
919	<	RealType v2 = a000 * b01;
920	<	RealType v3 = a000 * b11;
921	<	RealType v4 = a000 * c1 - a001 * c0;
922	<	RealType v8 = a110 * b01;
923	<	RealType v10 = - b01 * c0;
924	<
925	<	RealType u0 = v2 * v10 - v4 * v4;
926	<	RealType u1 = -2.0 * v3 * v4;
927	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
928	<	RealType u3 = -2.0 * v1 * v3;
929	<	RealType u4 = - v1 * v1;
930	<	//rescale coefficients
931	<	RealType maxAbs = fabs(u0);
932	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
933	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
934	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
935	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
936	<	u0 /= maxAbs;
937	<	u1 /= maxAbs;
938	<	u2 /= maxAbs;
939	<	u3 /= maxAbs;
940	<	u4 /= maxAbs;
941	<	//max_element(start, end) is also available.
942	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
943	<	poly.setCoefficient(4, u4);
944	<	poly.setCoefficient(3, u3);
945	<	poly.setCoefficient(2, u2);
946	<	poly.setCoefficient(1, u1);
947	<	poly.setCoefficient(0, u0);
948	<	std::vector<RealType> realRoots = poly.FindRealRoots();
949	<
950	<	std::vector<RealType>::iterator ri;
951	<	RealType r1, r2, alpha0;
952	<	std::vector<std::pair<RealType,RealType> > rps;
953	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
954	<	r2 = *ri;
955	<	//check if FindRealRoots() give the right answer
956	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
957	<	sprintf(painCave.errMsg,
958	<	"RNEMD Warning: polynomial solve seems to have an error!");
959	<	painCave.isFatal = 0;
960	<	simError();
961	<	failRootCount_++;
918	>	RealType w = 0.0;
919	>	if (rnemdFluxType_ ==  rnemdFullKE) {
920	>	x = 1.0 + px * (1.0 - c);
921	>	y = 1.0 + py * (1.0 - c);
922	>	z = 1.0 + pz * (1.0 - c);
923	>	/* more complicated way
924	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
925	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
926	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
927	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
928	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
929	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
930	>	*/
931	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
932	>	(fabs(z - 1.0) < 0.1)) {
933	>	w = 1.0 + (kineticTarget_
934	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
935	>	+ Khz * (1.0 - z * z)) / Khw;
936	>	}//no need to calculate w if x, y or z is out of range
937	>	} else {
938	>	w = 1.0 + kineticTarget_ / Khw;
939	>	}
940	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
941	>	//if w is in the right range, so should be x, y, z.
942	>	vector<StuntDouble*>::iterator sdi;
943	>	Vector3d vel;
944	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
945	>	if (rnemdFluxType_ == rnemdFullKE) {
946	>	vel = (*sdi)->getVel() * c;
947	>	(*sdi)->setVel(vel);
948	>	}
949	>	if ((*sdi)->isDirectional()) {
950	>	Vector3d angMom = (*sdi)->getJ() * c;
951	>	(*sdi)->setJ(angMom);
952	>	}
953	>	}
954	>	w = sqrt(w);
955	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
956	>	if (rnemdFluxType_ == rnemdFullKE) {
957	>	vel = (*sdi)->getVel();
958	>	vel.x() *= x;
959	>	vel.y() *= y;
960	>	vel.z() *= z;
961	>	(*sdi)->setVel(vel);
962	>	}
963	>	if ((*sdi)->isDirectional()) {
964	>	Vector3d angMom = (*sdi)->getJ() * w;
965	>	(*sdi)->setJ(angMom);
966	>	}
967	>	}
968	>	successfulScale = true;
969	>	kineticExchange_ += kineticTarget_;
970	>	}
971		}
972	<	//might not be useful w/o rescaling coefficients
973	<	alpha0 = -c0 - a110 * r2 * r2;
974	<	if (alpha0 >= 0.0) {
975	<	r1 = sqrt(alpha0 / a000);
976	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
977	<	{ rps.push_back(std::make_pair(r1, r2)); }
978	<	if (r1 > 1e-6) { //r1 non-negative
979	<	r1 = -r1;
980	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
981	<	{ rps.push_back(std::make_pair(r1, r2)); }
982	<	}
983	<	}
984	<	}
985	<	// Consider combininig together the solving pair part w/ the searching
986	<	// best solution part so that we don't need the pairs vector
987	<	if (!rps.empty()) {
988	<	RealType smallestDiff = HONKING_LARGE_VALUE;
989	<	RealType diff;
990	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
991	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
992	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
993	<	r1 = (*rpi).first;
994	<	r2 = (*rpi).second;
995	<	switch(rnemdType_) {
996	<	case rnemdKineticScale :
997	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
998	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
999	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1000	<	break;
1001	<	case rnemdPxScale :
1002	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1003	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1004	<	break;
1005	<	case rnemdPyScale :
1006	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1007	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1008	<	break;
1009	<	case rnemdPzScale :
1010	<	default :
1011	<	break;
1012	<	}
1013	<	if (diff < smallestDiff) {
1014	<	smallestDiff = diff;
1015	<	bestPair = *rpi;
1016	<	}
972	>	} else {
973	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
974	>	switch(rnemdFluxType_) {
975	>	case rnemdKE :
976	>	/* used hotBin coeff's & only scale x & y dimensions
977	>	RealType px = Phx / Pcx;
978	>	RealType py = Phy / Pcy;
979	>	a110 = Khy;
980	>	c0 = - Khx - Khy - kineticTarget_;
981	>	a000 = Khx;
982	>	a111 = Kcy * py * py;
983	>	b11 = -2.0 * Kcy * py * (1.0 + py);
984	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
985	>	b01 = -2.0 * Kcx * px * (1.0 + px);
986	>	a001 = Kcx * px * px;
987	>	*/
988	>	//scale all three dimensions, let c_x = c_y
989	>	a000 = Kcx + Kcy;
990	>	a110 = Kcz;
991	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
992	>	a001 = Khx * px * px + Khy * py * py;
993	>	a111 = Khz * pz * pz;
994	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
995	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
996	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
997	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
998	>	break;
999	>	case rnemdPx :
1000	>	c = 1 - momentumTarget_.x() / Pcx;
1001	>	a000 = Kcy;
1002	>	a110 = Kcz;
1003	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1004	>	a001 = py * py * Khy;
1005	>	a111 = pz * pz * Khz;
1006	>	b01 = -2.0 * Khy * py * (1.0 + py);
1007	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1008	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1009	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1010	>	break;
1011	>	case rnemdPy :
1012	>	c = 1 - momentumTarget_.y() / Pcy;
1013	>	a000 = Kcx;
1014	>	a110 = Kcz;
1015	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1016	>	a001 = px * px * Khx;
1017	>	a111 = pz * pz * Khz;
1018	>	b01 = -2.0 * Khx * px * (1.0 + px);
1019	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1020	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1021	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1022	>	break;
1023	>	case rnemdPz ://we don't really do this, do we?
1024	>	c = 1 - momentumTarget_.z() / Pcz;
1025	>	a000 = Kcx;
1026	>	a110 = Kcy;
1027	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1028	>	a001 = px * px * Khx;
1029	>	a111 = py * py * Khy;
1030	>	b01 = -2.0 * Khx * px * (1.0 + px);
1031	>	b11 = -2.0 * Khy * py * (1.0 + py);
1032	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1033	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1034	>	break;
1035	>	default :
1036	>	break;
1037		}
1038	+
1039	+	RealType v1 = a000 * a111 - a001 * a110;
1040	+	RealType v2 = a000 * b01;
1041	+	RealType v3 = a000 * b11;
1042	+	RealType v4 = a000 * c1 - a001 * c0;
1043	+	RealType v8 = a110 * b01;
1044	+	RealType v10 = - b01 * c0;
1045	+
1046	+	RealType u0 = v2 * v10 - v4 * v4;
1047	+	RealType u1 = -2.0 * v3 * v4;
1048	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1049	+	RealType u3 = -2.0 * v1 * v3;
1050	+	RealType u4 = - v1 * v1;
1051	+	//rescale coefficients
1052	+	RealType maxAbs = fabs(u0);
1053	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1054	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1055	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1056	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1057	+	u0 /= maxAbs;
1058	+	u1 /= maxAbs;
1059	+	u2 /= maxAbs;
1060	+	u3 /= maxAbs;
1061	+	u4 /= maxAbs;
1062	+	//max_element(start, end) is also available.
1063	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1064	+	poly.setCoefficient(4, u4);
1065	+	poly.setCoefficient(3, u3);
1066	+	poly.setCoefficient(2, u2);
1067	+	poly.setCoefficient(1, u1);
1068	+	poly.setCoefficient(0, u0);
1069	+	vector<RealType> realRoots = poly.FindRealRoots();
1070	+
1071	+	vector<RealType>::iterator ri;
1072	+	RealType r1, r2, alpha0;
1073	+	vector<pair<RealType,RealType> > rps;
1074	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1075	+	r2 = *ri;
1076	+	//check if FindRealRoots() give the right answer
1077	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1078	+	sprintf(painCave.errMsg,
1079	+	"RNEMD Warning: polynomial solve seems to have an error!");
1080	+	painCave.isFatal = 0;
1081	+	simError();
1082	+	failRootCount_++;
1083	+	}
1084	+	//might not be useful w/o rescaling coefficients
1085	+	alpha0 = -c0 - a110 * r2 * r2;
1086	+	if (alpha0 >= 0.0) {
1087	+	r1 = sqrt(alpha0 / a000);
1088	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1089	+	< 1e-6)
1090	+	{ rps.push_back(make_pair(r1, r2)); }
1091	+	if (r1 > 1e-6) { //r1 non-negative
1092	+	r1 = -r1;
1093	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1094	+	< 1e-6)
1095	+	{ rps.push_back(make_pair(r1, r2)); }
1096	+	}
1097	+	}
1098	+	}
1099	+	// Consider combining together the solving pair part w/ the searching
1100	+	// best solution part so that we don't need the pairs vector
1101	+	if (!rps.empty()) {
1102	+	RealType smallestDiff = HONKING_LARGE_VALUE;
1103	+	RealType diff;
1104	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1105	+	vector<pair<RealType,RealType> >::iterator rpi;
1106	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1107	+	r1 = (*rpi).first;
1108	+	r2 = (*rpi).second;
1109	+	switch(rnemdFluxType_) {
1110	+	case rnemdKE :
1111	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1113	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1114	+	break;
1115	+	case rnemdPx :
1116	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1117	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1118	+	break;
1119	+	case rnemdPy :
1120	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1121	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1122	+	break;
1123	+	case rnemdPz :
1124	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1125	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1126	+	default :
1127	+	break;
1128	+	}
1129	+	if (diff < smallestDiff) {
1130	+	smallestDiff = diff;
1131	+	bestPair = *rpi;
1132	+	}
1133	+	}
1134		#ifdef IS_MPI
1135	<	if (worldRank == 0) {
1135	>	if (worldRank == 0) {
1136		#endif
1137	<	std::cerr << "we choose r1 = " << bestPair.first
1138	<	<< " and r2 = " << bestPair.second << "\n";
1137	>	// sprintf(painCave.errMsg,
1138	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	>	//         bestPair.first, bestPair.second);
1140	>	// painCave.isFatal = 0;
1141	>	// painCave.severity = OPENMD_INFO;
1142	>	// simError();
1143		#ifdef IS_MPI
1144	<	}
1144	>	}
1145		#endif
1146	<
1147	<	RealType x, y, z;
1148	<	switch(rnemdType_) {
1149	<	case rnemdKineticScale :
1150	<	x = bestPair.first;
1151	<	y = bestPair.first;
1152	<	z = bestPair.second;
1153	<	break;
1154	<	case rnemdPxScale :
1155	<	x = c;
1156	<	y = bestPair.first;
1157	<	z = bestPair.second;
1158	<	break;
1159	<	case rnemdPyScale :
1160	<	x = bestPair.first;
1161	<	y = c;
1162	<	z = bestPair.second;
1163	<	break;
1164	<	case rnemdPzScale :
1165	<	x = bestPair.first;
1166	<	y = bestPair.second;
1167	<	z = c;
1168	<	break;
1169	<	default :
1170	<	break;
1171	<	}
1172	<	std::vector<StuntDouble*>::iterator sdi;
1173	<	Vector3d vel;
1174	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1175	<	vel = (*sdi)->getVel();
1176	<	vel.x() *= x;
1177	<	vel.y() *= y;
1178	<	vel.z() *= z;
1179	<	(*sdi)->setVel(vel);
1146	>
1147	>	switch(rnemdFluxType_) {
1148	>	case rnemdKE :
1149	>	x = bestPair.first;
1150	>	y = bestPair.first;
1151	>	z = bestPair.second;
1152	>	break;
1153	>	case rnemdPx :
1154	>	x = c;
1155	>	y = bestPair.first;
1156	>	z = bestPair.second;
1157	>	break;
1158	>	case rnemdPy :
1159	>	x = bestPair.first;
1160	>	y = c;
1161	>	z = bestPair.second;
1162	>	break;
1163	>	case rnemdPz :
1164	>	x = bestPair.first;
1165	>	y = bestPair.second;
1166	>	z = c;
1167	>	break;
1168	>	default :
1169	>	break;
1170	>	}
1171	>	vector<StuntDouble*>::iterator sdi;
1172	>	Vector3d vel;
1173	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1174	>	vel = (*sdi)->getVel();
1175	>	vel.x() *= x;
1176	>	vel.y() *= y;
1177	>	vel.z() *= z;
1178	>	(*sdi)->setVel(vel);
1179	>	}
1180	>	//convert to hotBin coefficient
1181	>	x = 1.0 + px * (1.0 - x);
1182	>	y = 1.0 + py * (1.0 - y);
1183	>	z = 1.0 + pz * (1.0 - z);
1184	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1185	>	vel = (*sdi)->getVel();
1186	>	vel.x() *= x;
1187	>	vel.y() *= y;
1188	>	vel.z() *= z;
1189	>	(*sdi)->setVel(vel);
1190	>	}
1191	>	successfulScale = true;
1192	>	switch(rnemdFluxType_) {
1193	>	case rnemdKE :
1194	>	kineticExchange_ += kineticTarget_;
1195	>	break;
1196	>	case rnemdPx :
1197	>	case rnemdPy :
1198	>	case rnemdPz :
1199	>	momentumExchange_ += momentumTarget_;
1200	>	break;
1201	>	default :
1202	>	break;
1203	>	}
1204		}
1205	<	//convert to hotBin coefficient
1206	<	x = 1.0 + px * (1.0 - x);
1207	<	y = 1.0 + py * (1.0 - y);
1208	<	z = 1.0 + pz * (1.0 - z);
1209	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1210	<	vel = (*sdi)->getVel();
1211	<	vel.x() *= x;
1212	<	vel.y() *= y;
1213	<	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
1205	>	}
1206	>	if (successfulScale != true) {
1207	>	sprintf(painCave.errMsg,
1208	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1209	>	"\tthe constraint equations may not exist or there may be\n"
1210	>	"\tno selected objects in one or both slabs.\n");
1211	>	painCave.isFatal = 0;
1212	>	painCave.severity = OPENMD_INFO;
1213	>	simError();
1214		failTrialCount_++;
1215		}
1216	+	}
1217
1218	+	void RNEMD::doVSS() {
1219	+	if (!doRNEMD_) return;
1220	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1221	+	RealType time = currentSnap_->getTime();
1222	+	Mat3x3d hmat = currentSnap_->getHmat();
1223	+
1224	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1225	+
1226	+	int selei;
1227	+	StuntDouble* sd;
1228	+	int idx;
1229	+
1230	+	vector<StuntDouble*> hotBin, coldBin;
1231	+
1232	+	Vector3d Ph(V3Zero);
1233	+	RealType Mh = 0.0;
1234	+	RealType Kh = 0.0;
1235	+	Vector3d Pc(V3Zero);
1236	+	RealType Mc = 0.0;
1237	+	RealType Kc = 0.0;
1238	+
1239	+
1240	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1241	+	sd = seleMan_.nextSelected(selei)) {
1242	+
1243	+	idx = sd->getLocalIndex();
1244	+
1245	+	Vector3d pos = sd->getPos();
1246	+
1247	+	// wrap the stuntdouble's position back into the box:
1248	+
1249	+	if (usePeriodicBoundaryConditions_)
1250	+	currentSnap_->wrapVector(pos);
1251	+
1252	+	// which bin is this stuntdouble in?
1253	+	bool inA = inSlabA(pos);
1254	+	bool inB = inSlabB(pos);
1255	+
1256	+	if (inA || inB) {
1257	+
1258	+	RealType mass = sd->getMass();
1259	+	Vector3d vel = sd->getVel();
1260	+
1261	+	if (inA) {
1262	+	hotBin.push_back(sd);
1263	+	Ph += mass * vel;
1264	+	Mh += mass;
1265	+	Kh += mass * vel.lengthSquare();
1266	+	if (rnemdFluxType_ == rnemdFullKE) {
1267	+	if (sd->isDirectional()) {
1268	+	Vector3d angMom = sd->getJ();
1269	+	Mat3x3d I = sd->getI();
1270	+	if (sd->isLinear()) {
1271	+	int i = sd->linearAxis();
1272	+	int j = (i + 1) % 3;
1273	+	int k = (i + 2) % 3;
1274	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1275	+	angMom[k] * angMom[k] / I(k, k);
1276	+	} else {
1277	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1278	+	angMom[1] * angMom[1] / I(1, 1) +
1279	+	angMom[2] * angMom[2] / I(2, 2);
1280	+	}
1281	+	}
1282	+	}
1283	+	} else { //midBin_
1284	+	coldBin.push_back(sd);
1285	+	Pc += mass * vel;
1286	+	Mc += mass;
1287	+	Kc += mass * vel.lengthSquare();
1288	+	if (rnemdFluxType_ == rnemdFullKE) {
1289	+	if (sd->isDirectional()) {
1290	+	Vector3d angMom = sd->getJ();
1291	+	Mat3x3d I = sd->getI();
1292	+	if (sd->isLinear()) {
1293	+	int i = sd->linearAxis();
1294	+	int j = (i + 1) % 3;
1295	+	int k = (i + 2) % 3;
1296	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1297	+	angMom[k] * angMom[k] / I(k, k);
1298	+	} else {
1299	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1300	+	angMom[1] * angMom[1] / I(1, 1) +
1301	+	angMom[2] * angMom[2] / I(2, 2);
1302	+	}
1303	+	}
1304	+	}
1305	+	}
1306	+	}
1307	+	}
1308	+
1309	+	Kh *= 0.5;
1310	+	Kc *= 0.5;
1311	+
1312	+	#ifdef IS_MPI
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
1320	+
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	+
1343	+	vector<StuntDouble*>::iterator sdi;
1344	+	Vector3d vel;
1345	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1346	+	//vel = (*sdi)->getVel();
1347	+	vel = ((*sdi)->getVel() - vc) * c + ac;
1348	+	(*sdi)->setVel(vel);
1349	+	if (rnemdFluxType_ == rnemdFullKE) {
1350	+	if ((*sdi)->isDirectional()) {
1351	+	Vector3d angMom = (*sdi)->getJ() * c;
1352	+	(*sdi)->setJ(angMom);
1353	+	}
1354	+	}
1355	+	}
1356	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1357	+	//vel = (*sdi)->getVel();
1358	+	vel = ((*sdi)->getVel() - vh) * h + ah;
1359	+	(*sdi)->setVel(vel);
1360	+	if (rnemdFluxType_ == rnemdFullKE) {
1361	+	if ((*sdi)->isDirectional()) {
1362	+	Vector3d angMom = (*sdi)->getJ() * h;
1363	+	(*sdi)->setJ(angMom);
1364	+	}
1365	+	}
1366	+	}
1367	+	successfulExchange = true;
1368	+	kineticExchange_ += kineticTarget_;
1369	+	momentumExchange_ += momentumTarget_;
1370	+	}
1371	+	}
1372	+	}
1373	+	}
1374	+	}
1375	+	}
1376	+	}
1377	+	if (successfulExchange != true) {
1378	+	sprintf(painCave.errMsg,
1379	+	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1380	+	"\tthe constraint equations may not exist or there may be\n"
1381	+	"\tno selected objects in one or both slabs.\n");
1382	+	painCave.isFatal = 0;
1383	+	painCave.severity = OPENMD_INFO;
1384	+	simError();
1385	+	failTrialCount_++;
1386	+	}
1387		}
1388
1389		void RNEMD::doRNEMD() {
1390	<
1391	<	switch(rnemdType_) {
1392	<	case rnemdKineticScale :
1393	<	case rnemdPxScale :
855	<	case rnemdPyScale :
856	<	case rnemdPzScale :
857	<	doScale();
858	<	break;
859	<	case rnemdKineticSwap :
860	<	case rnemdPx :
861	<	case rnemdPy :
862	<	case rnemdPz :
1390	>	if (!doRNEMD_) return;
1391	>	trialCount_++;
1392	>	switch(rnemdMethod_) {
1393	>	case rnemdSwap:
1394		doSwap();
1395		break;
1396	<	case rnemdUnknown :
1396	>	case rnemdNIVS:
1397	>	doNIVS();
1398	>	break;
1399	>	case rnemdVSS:
1400	>	doVSS();
1401	>	break;
1402	>	case rnemdUnkownMethod:
1403		default :
1404		break;
1405		}
1406		}
1407
1408		void RNEMD::collectData() {
1409	<
1409	>	if (!doRNEMD_) return;
1410		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1411		Mat3x3d hmat = currentSnap_->getHmat();
1412
1413	+	areaAccumulator_->add(currentSnap_->getXYarea());
1414	+
1415		seleMan_.setSelectionSet(evaluator_.evaluate());
1416
1417	<	int selei;
1417	>	int selei(0);
1418		StuntDouble* sd;
1419		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	+
1444		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1445		sd = seleMan_.nextSelected(selei)) {
1446	<
1446	>
1447		idx = sd->getLocalIndex();
1448
1449		Vector3d pos = sd->getPos();
#	Line 890 | Line 1452 | namespace OpenMD {
1452
1453		if (usePeriodicBoundaryConditions_)
1454		currentSnap_->wrapVector(pos);
1455	<
1455	>
1456	>
1457		// which bin is this stuntdouble in?
1458		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	<
1459	>	// Shift molecules by half a box to have bins start at 0
1460	>	// The modulo operator is used to wrap the case when we are
1461	>	// beyond the end of the bins back to the beginning.
1462		int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463
899	–	if (rnemdLogWidth_ == midBin_ + 1)
900	–	if (binNo > midBin_)
901	–	binNo = nBins_ - binNo;
902	–
1464		RealType mass = sd->getMass();
1465		Vector3d vel = sd->getVel();
905	–	RealType value;
906	–	RealType xVal, yVal, zVal;
1466
1467	<	switch(rnemdType_) {
1468	<	case rnemdKineticSwap :
1469	<	case rnemdKineticScale :
1470	<
1471	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1472	<	vel[2]*vel[2]);
1473	<
915	<	valueCount_[binNo] += 3;
916	<	if (sd->isDirectional()) {
917	<	Vector3d angMom = sd->getJ();
918	<	Mat3x3d I = sd->getI();
919	<
920	<	if (sd->isLinear()) {
921	<	int i = sd->linearAxis();
922	<	int j = (i + 1) % 3;
923	<	int k = (i + 2) % 3;
924	<	value += angMom[j] * angMom[j] / I(j, j) +
925	<	angMom[k] * angMom[k] / I(k, k);
1467	>	binCount[binNo]++;
1468	>	binMass[binNo] += mass;
1469	>	binPx[binNo] += mass*vel.x();
1470	>	binPy[binNo] += mass*vel.y();
1471	>	binPz[binNo] += mass*vel.z();
1472	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1473	>	binDOF[binNo] += 3;
1474
1475	<	valueCount_[binNo] +=2;
1475	>	if (sd->isDirectional()) {
1476	>	Vector3d angMom = sd->getJ();
1477	>	Mat3x3d I = sd->getI();
1478	>	if (sd->isLinear()) {
1479	>	int i = sd->linearAxis();
1480	>	int j = (i + 1) % 3;
1481	>	int k = (i + 2) % 3;
1482	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1483	>	angMom[k] * angMom[k] / I(k, k));
1484	>	binDOF[binNo] += 2;
1485	>	} else {
1486	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1487	>	angMom[1] * angMom[1] / I(1, 1) +
1488	>	angMom[2] * angMom[2] / I(2, 2));
1489	>	binDOF[binNo] += 3;
1490	>	}
1491	>	}
1492	>	}
1493	>
1494	>	#ifdef IS_MPI
1495	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1496	>	nBins_, MPI::INT, MPI::SUM);
1497	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1498	>	nBins_, MPI::REALTYPE, MPI::SUM);
1499	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1500	>	nBins_, MPI::REALTYPE, MPI::SUM);
1501	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1502	>	nBins_, MPI::REALTYPE, MPI::SUM);
1503	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1504	>	nBins_, MPI::REALTYPE, MPI::SUM);
1505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1506	>	nBins_, MPI::REALTYPE, MPI::SUM);
1507	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1508	>	nBins_, MPI::INT, MPI::SUM);
1509	>	#endif
1510
1511	<	} else {
1512	<	value += angMom[0]*angMom[0]/I(0, 0)
1513	<	+ angMom[1]*angMom[1]/I(1, 1)
1514	<	+ angMom[2]*angMom[2]/I(2, 2);
1515	<	valueCount_[binNo] +=3;
1516	<	}
1517	<	}
1518	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1511	>	Vector3d vel;
1512	>	RealType den;
1513	>	RealType temp;
1514	>	RealType z;
1515	>	for (int i = 0; i < nBins_; i++) {
1516	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1517	>	vel.x() = binPx[i] / binMass[i];
1518	>	vel.y() = binPy[i] / binMass[i];
1519	>	vel.z() = binPz[i] / binMass[i];
1520
1521	<	break;
1522	<	case rnemdPx :
1523	<	case rnemdPxScale :
1524	<	value = mass * vel[0];
1525	<	valueCount_[binNo]++;
1526	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1527	<	/ PhysicalConstants::kb;
1528	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1529	<	/ PhysicalConstants::kb;
1530	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1531	<	/ PhysicalConstants::kb;
1532	<	xTempHist_[binNo] += xVal;
1533	<	yTempHist_[binNo] += yVal;
1534	<	zTempHist_[binNo] += zVal;
1535	<	break;
1536	<	case rnemdPy :
1537	<	case rnemdPyScale :
1538	<	value = mass * vel[1];
1539	<	valueCount_[binNo]++;
1540	<	break;
1541	<	case rnemdPz :
1542	<	case rnemdPzScale :
1543	<	value = mass * vel[2];
961	<	valueCount_[binNo]++;
962	<	break;
963	<	case rnemdUnknown :
964	<	default :
965	<	break;
1521	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1522	>	/ currentSnap_->getVolume() ;
1523	>
1524	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1525	>	PhysicalConstants::energyConvert);
1526	>
1527	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1528	>	if(outputMask_[j]) {
1529	>	switch(j) {
1530	>	case Z:
1531	>	(data_[j].accumulator[i])->add(z);
1532	>	break;
1533	>	case TEMPERATURE:
1534	>	data_[j].accumulator[i]->add(temp);
1535	>	break;
1536	>	case VELOCITY:
1537	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1538	>	break;
1539	>	case DENSITY:
1540	>	data_[j].accumulator[i]->add(den);
1541	>	break;
1542	>	}
1543	>	}
1544		}
967	–	valueHist_[binNo] += value;
1545		}
969	–
1546		}
1547
1548		void RNEMD::getStarted() {
1549	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1550	<	Stats& stat = currentSnap_->statData;
1551	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1549	>	if (!doRNEMD_) return;
1550	>	collectData();
1551	>	writeOutputFile();
1552		}
1553
1554	<	void RNEMD::getStatus() {
1555	<
1556	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1557	<	Stats& stat = currentSnap_->statData;
1558	<	RealType time = currentSnap_->getTime();
1559	<
1560	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1561	<	//or to be more meaningful, define another item as exchangeSum_ / time
1562	<	int j;
1563	<
1554	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1555	>	if (!doRNEMD_) return;
1556	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1557	>
1558	>	while(tokenizer.hasMoreTokens()) {
1559	>	std::string token(tokenizer.nextToken());
1560	>	toUpper(token);
1561	>	OutputMapType::iterator i = outputMap_.find(token);
1562	>	if (i != outputMap_.end()) {
1563	>	outputMask_.set(i->second);
1564	>	} else {
1565	>	sprintf( painCave.errMsg,
1566	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1567	>	"\toutputFileFormat keyword.\n", token.c_str() );
1568	>	painCave.isFatal = 0;
1569	>	painCave.severity = OPENMD_ERROR;
1570	>	simError();
1571	>	}
1572	>	}
1573	>	}
1574	>
1575	>	void RNEMD::writeOutputFile() {
1576	>	if (!doRNEMD_) return;
1577	>
1578		#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	–	}
1579		// If we're the root node, should we print out the results
1580		int worldRank = MPI::COMM_WORLD.Get_rank();
1581		if (worldRank == 0) {
1582		#endif
1583	<	rnemdLog_ << time;
1584	<	for (j = 0; j < rnemdLogWidth_; j++) {
1585	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1583	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1584	>
1585	>	if( !rnemdFile_ ){
1586	>	sprintf( painCave.errMsg,
1587	>	"Could not open \"%s\" for RNEMD output.\n",
1588	>	rnemdFileName_.c_str());
1589	>	painCave.isFatal = 1;
1590	>	simError();
1591		}
1592	<	rnemdLog_ << "\n";
1593	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1594	<	xTempLog_ << time;
1595	<	for (j = 0; j < rnemdLogWidth_; j++) {
1596	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1592	>
1593	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1594	>
1595	>	RealType time = currentSnap_->getTime();
1596	>	RealType avgArea;
1597	>	areaAccumulator_->getAverage(avgArea);
1598	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1599	>	/ PhysicalConstants::energyConvert;
1600	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1601	>
1602	>	rnemdFile_ << "#######################################################\n";
1603	>	rnemdFile_ << "# RNEMD {\n";
1604	>
1605	>	map<string, RNEMDMethod>::iterator mi;
1606	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1607	>	if ( (*mi).second == rnemdMethod_)
1608	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1609	>	}
1610	>	map<string, RNEMDFluxType>::iterator fi;
1611	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1612	>	if ( (*fi).second == rnemdFluxType_)
1613	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1614	>	}
1615	>
1616	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1617	>
1618	>	rnemdFile_ << "#    objectSelection = \""
1619	>	<< rnemdObjectSelection_ << "\";\n";
1620	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1621	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1622	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1623	>	rnemdFile_ << "# }\n";
1624	>	rnemdFile_ << "#######################################################\n";
1625	>	rnemdFile_ << "# RNEMD report:\n";
1626	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1627	>	rnemdFile_ << "#     target flux:\n";
1628	>	rnemdFile_ << "#         kinetic = "
1629	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1630	>	<< " (kcal/mol/A^2/fs)\n";
1631	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1632	>	<< " (amu/A/fs^2)\n";
1633	>	rnemdFile_ << "#     target one-time exchanges:\n";
1634	>	rnemdFile_ << "#         kinetic = "
1635	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1636	>	<< " (kcal/mol)\n";
1637	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1638	>	<< " (amu*A/fs)\n";
1639	>	rnemdFile_ << "#     actual exchange totals:\n";
1640	>	rnemdFile_ << "#         kinetic = "
1641	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1642	>	<< " (kcal/mol)\n";
1643	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1644	>	<< " (amu*A/fs)\n";
1645	>	rnemdFile_ << "#     actual flux:\n";
1646	>	rnemdFile_ << "#         kinetic = " << Jz
1647	>	<< " (kcal/mol/A^2/fs)\n";
1648	>	rnemdFile_ << "#         momentum = " << JzP
1649	>	<< " (amu/A/fs^2)\n";
1650	>	rnemdFile_ << "#     exchange statistics:\n";
1651	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1652	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1653	>	if (rnemdMethod_ == rnemdNIVS) {
1654	>	rnemdFile_ << "#         NIVS root-check errors = "
1655	>	<< failRootCount_ << "\n";
1656	>	}
1657	>	rnemdFile_ << "#######################################################\n";
1658	>
1659	>
1660	>
1661	>	//write title
1662	>	rnemdFile_ << "#";
1663	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1664	>	if (outputMask_[i]) {
1665	>	rnemdFile_ << "\t" << data_[i].title <<
1666	>	"(" << data_[i].units << ")";
1667	>	// add some extra tabs for column alignment
1668	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1669		}
1670	<	xTempLog_ << "\n";
1671	<	yTempLog_ << time;
1672	<	for (j = 0; j < rnemdLogWidth_; j++) {
1673	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1670	>	}
1671	>	rnemdFile_ << std::endl;
1672	>
1673	>	rnemdFile_.precision(8);
1674	>
1675	>	for (unsigned int j = 0; j < nBins_; j++) {
1676	>
1677	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1678	>	if (outputMask_[i]) {
1679	>	if (data_[i].dataType == "RealType")
1680	>	writeReal(i,j);
1681	>	else if (data_[i].dataType == "Vector3d")
1682	>	writeVector(i,j);
1683	>	else {
1684	>	sprintf( painCave.errMsg,
1685	>	"RNEMD found an unknown data type for: %s ",
1686	>	data_[i].title.c_str());
1687	>	painCave.isFatal = 1;
1688	>	simError();
1689	>	}
1690	>	}
1691		}
1692	<	yTempLog_ << "\n";
1693	<	zTempLog_ << time;
1694	<	for (j = 0; j < rnemdLogWidth_; j++) {
1695	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1692	>	rnemdFile_ << std::endl;
1693	>
1694	>	}
1695	>
1696	>	rnemdFile_ << "#######################################################\n";
1697	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1698	>	rnemdFile_ << "#######################################################\n";
1699	>
1700	>
1701	>	for (unsigned int j = 0; j < nBins_; j++) {
1702	>	rnemdFile_ << "#";
1703	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1704	>	if (outputMask_[i]) {
1705	>	if (data_[i].dataType == "RealType")
1706	>	writeRealStdDev(i,j);
1707	>	else if (data_[i].dataType == "Vector3d")
1708	>	writeVectorStdDev(i,j);
1709	>	else {
1710	>	sprintf( painCave.errMsg,
1711	>	"RNEMD found an unknown data type for: %s ",
1712	>	data_[i].title.c_str());
1713	>	painCave.isFatal = 1;
1714	>	simError();
1715	>	}
1716	>	}
1717		}
1718	<	zTempLog_ << "\n";
1719	<	}
1718	>	rnemdFile_ << std::endl;
1719	>
1720	>	}
1721	>
1722	>	rnemdFile_.flush();
1723	>	rnemdFile_.close();
1724	>
1725		#ifdef IS_MPI
1726		}
1727		#endif
1728	<	for (j = 0; j < rnemdLogWidth_; j++) {
1729	<	valueCount_[j] = 0;
1730	<	valueHist_[j] = 0.0;
1728	>
1729	>	}
1730	>
1731	>	void RNEMD::writeReal(int index, unsigned int bin) {
1732	>	if (!doRNEMD_) return;
1733	>	assert(index >=0 && index < ENDINDEX);
1734	>	assert(bin < nBins_);
1735	>	RealType s;
1736	>
1737	>	data_[index].accumulator[bin]->getAverage(s);
1738	>
1739	>	if (! isinf(s) && ! isnan(s)) {
1740	>	rnemdFile_ << "\t" << s;
1741	>	} else{
1742	>	sprintf( painCave.errMsg,
1743	>	"RNEMD detected a numerical error writing: %s for bin %d",
1744	>	data_[index].title.c_str(), bin);
1745	>	painCave.isFatal = 1;
1746	>	simError();
1747	>	}
1748	>	}
1749	>
1750	>	void RNEMD::writeVector(int index, unsigned int bin) {
1751	>	if (!doRNEMD_) return;
1752	>	assert(index >=0 && index < ENDINDEX);
1753	>	assert(bin < nBins_);
1754	>	Vector3d s;
1755	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1756	>	if (isinf(s[0]) || isnan(s[0]) ||
1757	>	isinf(s[1]) || isnan(s[1]) ||
1758	>	isinf(s[2]) || isnan(s[2]) ) {
1759	>	sprintf( painCave.errMsg,
1760	>	"RNEMD detected a numerical error writing: %s for bin %d",
1761	>	data_[index].title.c_str(), bin);
1762	>	painCave.isFatal = 1;
1763	>	simError();
1764	>	} else {
1765	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1766		}
1767	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1768	<	for (j = 0; j < rnemdLogWidth_; j++) {
1769	<	xTempHist_[j] = 0.0;
1770	<	yTempHist_[j] = 0.0;
1771	<	zTempHist_[j] = 0.0;
1772	<	}
1767	>	}
1768	>
1769	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1770	>	if (!doRNEMD_) return;
1771	>	assert(index >=0 && index < ENDINDEX);
1772	>	assert(bin < nBins_);
1773	>	RealType s;
1774	>
1775	>	data_[index].accumulator[bin]->getStdDev(s);
1776	>
1777	>	if (! isinf(s) && ! isnan(s)) {
1778	>	rnemdFile_ << "\t" << s;
1779	>	} else{
1780	>	sprintf( painCave.errMsg,
1781	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1782	>	data_[index].title.c_str(), bin);
1783	>	painCave.isFatal = 1;
1784	>	simError();
1785	>	}
1786		}
1787	+
1788	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1789	+	if (!doRNEMD_) return;
1790	+	assert(index >=0 && index < ENDINDEX);
1791	+	assert(bin < nBins_);
1792	+	Vector3d s;
1793	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1794	+	if (isinf(s[0]) || isnan(s[0]) ||
1795	+	isinf(s[1]) || isnan(s[1]) ||
1796	+	isinf(s[2]) || isnan(s[2]) ) {
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1799	+	data_[index].title.c_str(), bin);
1800	+	painCave.isFatal = 1;
1801	+	simError();
1802	+	} else {
1803	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1804	+	}
1805	+	}
1806		}
1807	+

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