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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1777 by gezelter, Thu Aug 9 18:35:09 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		#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;
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;
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();
#	Line 89 | Line 281 | namespace OpenMD {
281
282		if (selectionCount > nIntegrable) {
283		sprintf(painCave.errMsg,
284	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
284	>	"RNEMD: The current objectSelection,\n"
285		"\t\t%s\n"
286		"\thas resulted in %d selected objects.  However,\n"
287		"\tthe total number of integrable objects in the system\n"
#	Line 99 | Line 291 | namespace OpenMD {
291		rnemdObjectSelection_.c_str(),
292		selectionCount, nIntegrable);
293		painCave.isFatal = 0;
294	+	painCave.severity = OPENMD_WARNING;
295		simError();
103	–
296		}
105	–
106	–	const std::string st = simParams->getRNEMD_exchangeType();
297
298	<	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	<	}
298	>	areaAccumulator_ = new Accumulator();
299
300	<	#ifdef IS_MPI
116	<	if (worldRank == 0) {
117	<	#endif
300	>	nBins_ = rnemdParams->getOutputBins();
301
302	<	std::string rnemdFileName;
303	<	std::string xTempFileName;
304	<	std::string yTempFileName;
305	<	std::string zTempFileName;
306	<	switch(rnemdType_) {
307	<	case rnemdKineticSwap :
308	<	case rnemdKineticScale :
309	<	rnemdFileName = "temperature.log";
302	>	data_.resize(RNEMD::ENDINDEX);
303	>	OutputData z;
304	>	z.units =  "Angstroms";
305	>	z.title =  "Z";
306	>	z.dataType = "RealType";
307	>	z.accumulator.reserve(nBins_);
308	>	for (unsigned int i = 0; i < nBins_; i++)
309	>	z.accumulator.push_back( new Accumulator() );
310	>	data_[Z] = z;
311	>	outputMap_["Z"] =  Z;
312	>
313	>	OutputData temperature;
314	>	temperature.units =  "K";
315	>	temperature.title =  "Temperature";
316	>	temperature.dataType = "RealType";
317	>	temperature.accumulator.reserve(nBins_);
318	>	for (unsigned int i = 0; i < nBins_; i++)
319	>	temperature.accumulator.push_back( new Accumulator() );
320	>	data_[TEMPERATURE] = temperature;
321	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
322	>
323	>	OutputData velocity;
324	>	velocity.units = "angstroms/fs";
325	>	velocity.title =  "Velocity";
326	>	velocity.dataType = "Vector3d";
327	>	velocity.accumulator.reserve(nBins_);
328	>	for (unsigned int i = 0; i < nBins_; i++)
329	>	velocity.accumulator.push_back( new VectorAccumulator() );
330	>	data_[VELOCITY] = velocity;
331	>	outputMap_["VELOCITY"] = VELOCITY;
332	>
333	>	OutputData density;
334	>	density.units =  "g cm^-3";
335	>	density.title =  "Density";
336	>	density.dataType = "RealType";
337	>	density.accumulator.reserve(nBins_);
338	>	for (unsigned int i = 0; i < nBins_; i++)
339	>	density.accumulator.push_back( new Accumulator() );
340	>	data_[DENSITY] = density;
341	>	outputMap_["DENSITY"] =  DENSITY;
342	>
343	>	if (hasOutputFields) {
344	>	parseOutputFileFormat(rnemdParams->getOutputFields());
345	>	} else {
346	>	outputMask_.set(Z);
347	>	switch (rnemdFluxType_) {
348	>	case rnemdKE:
349	>	case rnemdRotKE:
350	>	case rnemdFullKE:
351	>	outputMask_.set(TEMPERATURE);
352		break;
353	<	case rnemdPx :
354	<	case rnemdPxScale :
355	<	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());
353	>	case rnemdPx:
354	>	case rnemdPy:
355	>	outputMask_.set(VELOCITY);
356		break;
357	<	case rnemdPz :
358	<	case rnemdPzScale :
359	<	case rnemdUnknown :
360	<	default :
144	<	rnemdFileName = "rnemd.log";
357	>	case rnemdPz:
358	>	case rnemdPvector:
359	>	outputMask_.set(VELOCITY);
360	>	outputMask_.set(DENSITY);
361		break;
362	+	case rnemdKePx:
363	+	case rnemdKePy:
364	+	outputMask_.set(TEMPERATURE);
365	+	outputMask_.set(VELOCITY);
366	+	break;
367	+	case rnemdKePvector:
368	+	outputMask_.set(TEMPERATURE);
369	+	outputMask_.set(VELOCITY);
370	+	outputMask_.set(DENSITY);
371	+	break;
372	+	default:
373	+	break;
374		}
147	–	rnemdLog_.open(rnemdFileName.c_str());
148	–
149	–	#ifdef IS_MPI
375		}
376	<	#endif
377	<
378	<	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	<	}
376	>
377	>	if (hasOutputFileName) {
378	>	rnemdFileName_ = rnemdParams->getOutputFileName();
379		} else {
380	<	rnemdLogWidth_ = nBins_;
381	<	}
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);
380	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
381	>	}
382
383	<	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	<	}
383	>	exchangeTime_ = rnemdParams->getExchangeTime();
384
385	<	#ifndef IS_MPI
386	<	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	<	}
385	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
386	>	Mat3x3d hmat = currentSnap_->getHmat();
387
388	<	RNEMD::~RNEMD() {
389	<	delete randNumGen_;
388	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
389	>	// Lx, Ly = box dimensions in x & y
390	>	// dt = exchange time interval
391	>	// flux = target flux
392	>
393	>	RealType area = currentSnap_->getXYarea();
394	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
395	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
396	>
397	>	// total exchange sums are zeroed out at the beginning:
398	>
399	>	kineticExchange_ = 0.0;
400	>	momentumExchange_ = V3Zero;
401	>
402	>	if (hasSlabWidth)
403	>	slabWidth_ = rnemdParams->getSlabWidth();
404	>	else
405	>	slabWidth_ = hmat(2,2) / 10.0;
406	>
407	>	if (hasSlabACenter)
408	>	slabACenter_ = rnemdParams->getSlabACenter();
409	>	else
410	>	slabACenter_ = 0.0;
411
412	+	if (hasSlabBCenter)
413	+	slabBCenter_ = rnemdParams->getSlabBCenter();
414	+	else
415	+	slabBCenter_ = hmat(2,2) / 2.0;
416	+
417	+	}
418	+
419	+	RNEMD::~RNEMD() {
420	+	if (!doRNEMD_) return;
421		#ifdef IS_MPI
422		if (worldRank == 0) {
423		#endif
424	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
425	<	rnemdLog_.close();
426	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
427	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
428	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	<	xTempLog_.close();
208	<	yTempLog_.close();
209	<	zTempLog_.close();
210	<	}
424	>
425	>	writeOutputFile();
426	>
427	>	rnemdFile_.close();
428	>
429		#ifdef IS_MPI
430		}
431		#endif
432		}
433	+
434	+	bool RNEMD::inSlabA(Vector3d pos) {
435	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
436	+	}
437	+	bool RNEMD::inSlabB(Vector3d pos) {
438	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
439	+	}
440
441		void RNEMD::doSwap() {
442	<
442	>	if (!doRNEMD_) return;
443		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
444		Mat3x3d hmat = currentSnap_->getHmat();
445
#	Line 243 | Line 468 | namespace OpenMD {
468
469		if (usePeriodicBoundaryConditions_)
470		currentSnap_->wrapVector(pos);
471	+	bool inA = inSlabA(pos);
472	+	bool inB = inSlabB(pos);
473
474	<	// 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_) {
474	>	if (inA || inB) {
475
476		RealType mass = sd->getMass();
477		Vector3d vel = sd->getVel();
478		RealType value;
479	<
480	<	switch(rnemdType_) {
481	<	case rnemdKineticSwap :
479	>
480	>	switch(rnemdFluxType_) {
481	>	case rnemdKE :
482
483	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
484	<	vel[2]*vel[2]);
485	<	if (sd->isDirectional()) {
483	>	value = mass * vel.lengthSquare();
484	>
485	>	if (sd->isDirectional()) {
486		Vector3d angMom = sd->getJ();
487		Mat3x3d I = sd->getI();
488
489		if (sd->isLinear()) {
490	<	int i = sd->linearAxis();
491	<	int j = (i + 1) % 3;
492	<	int k = (i + 2) % 3;
493	<	value += angMom[j] * angMom[j] / I(j, j) +
494	<	angMom[k] * angMom[k] / I(k, k);
490	>	int i = sd->linearAxis();
491	>	int j = (i + 1) % 3;
492	>	int k = (i + 2) % 3;
493	>	value += angMom[j] * angMom[j] / I(j, j) +
494	>	angMom[k] * angMom[k] / I(k, k);
495		} else {
496	<	value += angMom[0]*angMom[0]/I(0, 0)
497	<	+ angMom[1]*angMom[1]/I(1, 1)
498	<	+ angMom[2]*angMom[2]/I(2, 2);
496	>	value += angMom[0]*angMom[0]/I(0, 0)
497	>	+ angMom[1]*angMom[1]/I(1, 1)
498	>	+ angMom[2]*angMom[2]/I(2, 2);
499		}
500	<	}
281	<	//make exchangeSum_ comparable between swap & scale
282	<	//temporarily without using energyConvert
283	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
500	>	} //angular momenta exchange enabled
501		value *= 0.5;
502		break;
503		case rnemdPx :
#	Line 296 | Line 513 | namespace OpenMD {
513		break;
514		}
515
516	<	if (binNo == 0) {
516	>	if (inA == 0) {
517		if (!min_found) {
518		min_val = value;
519		min_sd = sd;
#	Line 307 | Line 524 | namespace OpenMD {
524		min_sd = sd;
525		}
526		}
527	<	} else { //midBin_
527	>	} else {
528		if (!max_found) {
529		max_val = value;
530		max_sd = sd;
#	Line 321 | Line 538 | namespace OpenMD {
538		}
539		}
540		}
541	<
541	>
542		#ifdef IS_MPI
543		int nProc, worldRank;
544	<
544	>
545		nProc = MPI::COMM_WORLD.Get_size();
546		worldRank = MPI::COMM_WORLD.Get_rank();
547
#	Line 332 | Line 549 | namespace OpenMD {
549		bool my_max_found = max_found;
550
551		// Even if we didn't find a minimum, did someone else?
552	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
336	<	1, MPI::BOOL, MPI::LAND);
337	<
552	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
553		// Even if we didn't find a maximum, did someone else?
554	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
555	<	1, MPI::BOOL, MPI::LAND);
556	<
557	<	struct {
558	<	RealType val;
559	<	int rank;
560	<	} max_vals, min_vals;
561	<
562	<	if (min_found) {
563	<	if (my_min_found)
554	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
555	>	#endif
556	>
557	>	if (max_found && min_found) {
558	>
559	>	#ifdef IS_MPI
560	>	struct {
561	>	RealType val;
562	>	int rank;
563	>	} max_vals, min_vals;
564	>
565	>	if (my_min_found) {
566		min_vals.val = min_val;
567	<	else
567	>	} else {
568		min_vals.val = HONKING_LARGE_VALUE;
569	<
569	>	}
570		min_vals.rank = worldRank;
571
572		// Who had the minimum?
573		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
574		1, MPI::REALTYPE_INT, MPI::MINLOC);
575		min_val = min_vals.val;
359	–	}
576
577	<	if (max_found) {
362	<	if (my_max_found)
577	>	if (my_max_found) {
578		max_vals.val = max_val;
579	<	else
579	>	} else {
580		max_vals.val = -HONKING_LARGE_VALUE;
581	<
581	>	}
582		max_vals.rank = worldRank;
583
584		// Who had the maximum?
585		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
586		1, MPI::REALTYPE_INT, MPI::MAXLOC);
587		max_val = max_vals.val;
373	–	}
588		#endif
589	<
590	<	if (max_found && min_found) {
591	<	if (min_val< max_val) {
378	<
589	>
590	>	if (min_val < max_val) {
591	>
592		#ifdef IS_MPI
593		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
594		// I have both maximum and minimum, so proceed like a single
595		// processor version:
596		#endif
597	<	// objects to be swapped: velocity & angular velocity
597	>
598		Vector3d min_vel = min_sd->getVel();
599		Vector3d max_vel = max_sd->getVel();
600		RealType temp_vel;
601
602	<	switch(rnemdType_) {
603	<	case rnemdKineticSwap :
602	>	switch(rnemdFluxType_) {
603	>	case rnemdKE :
604		min_sd->setVel(max_vel);
605		max_sd->setVel(min_vel);
606	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
606	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
607		Vector3d min_angMom = min_sd->getJ();
608		Vector3d max_angMom = max_sd->getJ();
609		min_sd->setJ(max_angMom);
610		max_sd->setJ(min_angMom);
611	<	}
611	>	}//angular momenta exchange enabled
612	>	//assumes same rigid body identity
613		break;
614		case rnemdPx :
615		temp_vel = min_vel.x();
#	Line 421 | Line 635 | namespace OpenMD {
635		default :
636		break;
637		}
638	+
639		#ifdef IS_MPI
640		// the rest of the cases only apply in parallel simulations:
641		} else if (max_vals.rank == worldRank) {
#	Line 436 | Line 651 | namespace OpenMD {
651		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
652		min_vals.rank, 0, status);
653
654	<	switch(rnemdType_) {
655	<	case rnemdKineticSwap :
654	>	switch(rnemdFluxType_) {
655	>	case rnemdKE :
656		max_sd->setVel(min_vel);
657	<
657	>	//angular momenta exchange enabled
658		if (max_sd->isDirectional()) {
659		Vector3d min_angMom;
660		Vector3d max_angMom = max_sd->getJ();
661	<
661	>
662		// point-to-point swap of the angular momentum vector
663		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
664		MPI::REALTYPE, min_vals.rank, 1,
665		min_angMom.getArrayPointer(), 3,
666		MPI::REALTYPE, min_vals.rank, 1,
667		status);
668	<
668	>
669		max_sd->setJ(min_angMom);
670	<	}
670	>	}
671		break;
672		case rnemdPx :
673		max_vel.x() = min_vel.x();
#	Line 482 | Line 697 | namespace OpenMD {
697		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
698		max_vals.rank, 0, status);
699
700	<	switch(rnemdType_) {
701	<	case rnemdKineticSwap :
700	>	switch(rnemdFluxType_) {
701	>	case rnemdKE :
702		min_sd->setVel(max_vel);
703	<
703	>	//angular momenta exchange enabled
704		if (min_sd->isDirectional()) {
705		Vector3d min_angMom = min_sd->getJ();
706		Vector3d max_angMom;
707	<
707	>
708		// point-to-point swap of the angular momentum vector
709		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
710		MPI::REALTYPE, max_vals.rank, 1,
711		max_angMom.getArrayPointer(), 3,
712		MPI::REALTYPE, max_vals.rank, 1,
713		status);
714	<
714	>
715		min_sd->setJ(max_angMom);
716		}
717		break;
#	Line 517 | Line 732 | namespace OpenMD {
732		}
733		}
734		#endif
735	<	exchangeSum_ += max_val - min_val;
736	<	} else {
737	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
735	>
736	>	switch(rnemdFluxType_) {
737	>	case rnemdKE:
738	>	kineticExchange_ += max_val - min_val;
739	>	break;
740	>	case rnemdPx:
741	>	momentumExchange_.x() += max_val - min_val;
742	>	break;
743	>	case rnemdPy:
744	>	momentumExchange_.y() += max_val - min_val;
745	>	break;
746	>	case rnemdPz:
747	>	momentumExchange_.z() += max_val - min_val;
748	>	break;
749	>	default:
750	>	break;
751	>	}
752	>	} else {
753	>	sprintf(painCave.errMsg,
754	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
755	>	painCave.isFatal = 0;
756	>	painCave.severity = OPENMD_INFO;
757	>	simError();
758		failTrialCount_++;
759		}
760		} else {
761	<	std::cerr << "exchange NOT performed!\n";
762	<	std::cerr << "at least one of the two slabs empty.\n";
761	>	sprintf(painCave.errMsg,
762	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
763	>	"\twas not present in at least one of the two slabs.\n");
764	>	painCave.isFatal = 0;
765	>	painCave.severity = OPENMD_INFO;
766	>	simError();
767		failTrialCount_++;
768	<	}
530	<
768	>	}
769		}
770
771	<	void RNEMD::doScale() {
772	<
771	>	void RNEMD::doNIVS() {
772	>	if (!doRNEMD_) return;
773		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
774		Mat3x3d hmat = currentSnap_->getHmat();
775
#	Line 541 | Line 779 | namespace OpenMD {
779		StuntDouble* sd;
780		int idx;
781
782	<	std::vector<StuntDouble*> hotBin, coldBin;
782	>	vector<StuntDouble*> hotBin, coldBin;
783
784		RealType Phx = 0.0;
785		RealType Phy = 0.0;
#	Line 549 | Line 787 | namespace OpenMD {
787		RealType Khx = 0.0;
788		RealType Khy = 0.0;
789		RealType Khz = 0.0;
790	+	RealType Khw = 0.0;
791		RealType Pcx = 0.0;
792		RealType Pcy = 0.0;
793		RealType Pcz = 0.0;
794		RealType Kcx = 0.0;
795		RealType Kcy = 0.0;
796		RealType Kcz = 0.0;
797	+	RealType Kcw = 0.0;
798
799		for (sd = seleMan_.beginSelected(selei); sd != NULL;
800		sd = seleMan_.nextSelected(selei)) {
#	Line 569 | Line 809 | namespace OpenMD {
809		currentSnap_->wrapVector(pos);
810
811		// which bin is this stuntdouble in?
812	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
812	>	bool inA = inSlabA(pos);
813	>	bool inB = inSlabB(pos);
814
815	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
816	<
576	<	// if we're in bin 0 or the middleBin
577	<	if (binNo == 0 || binNo == midBin_) {
578	<
815	>	if (inA || inB) {
816	>
817		RealType mass = sd->getMass();
818		Vector3d vel = sd->getVel();
819
820	<	if (binNo == 0) {
820	>	if (inA) {
821		hotBin.push_back(sd);
822		Phx += mass * vel.x();
823		Phy += mass * vel.y();
#	Line 587 | Line 825 | namespace OpenMD {
825		Khx += mass * vel.x() * vel.x();
826		Khy += mass * vel.y() * vel.y();
827		Khz += mass * vel.z() * vel.z();
828	<	} else { //midBin_
828	>	if (sd->isDirectional()) {
829	>	Vector3d angMom = sd->getJ();
830	>	Mat3x3d I = sd->getI();
831	>	if (sd->isLinear()) {
832	>	int i = sd->linearAxis();
833	>	int j = (i + 1) % 3;
834	>	int k = (i + 2) % 3;
835	>	Khw += angMom[j] * angMom[j] / I(j, j) +
836	>	angMom[k] * angMom[k] / I(k, k);
837	>	} else {
838	>	Khw += angMom[0]*angMom[0]/I(0, 0)
839	>	+ angMom[1]*angMom[1]/I(1, 1)
840	>	+ angMom[2]*angMom[2]/I(2, 2);
841	>	}
842	>	}
843	>	} else {
844		coldBin.push_back(sd);
845		Pcx += mass * vel.x();
846		Pcy += mass * vel.y();
#	Line 595 | Line 848 | namespace OpenMD {
848		Kcx += mass * vel.x() * vel.x();
849		Kcy += mass * vel.y() * vel.y();
850		Kcz += mass * vel.z() * vel.z();
851	+	if (sd->isDirectional()) {
852	+	Vector3d angMom = sd->getJ();
853	+	Mat3x3d I = sd->getI();
854	+	if (sd->isLinear()) {
855	+	int i = sd->linearAxis();
856	+	int j = (i + 1) % 3;
857	+	int k = (i + 2) % 3;
858	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
859	+	angMom[k] * angMom[k] / I(k, k);
860	+	} else {
861	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
862	+	+ angMom[1]*angMom[1]/I(1, 1)
863	+	+ angMom[2]*angMom[2]/I(2, 2);
864	+	}
865	+	}
866		}
867		}
868		}
869	<
869	>
870		Khx *= 0.5;
871		Khy *= 0.5;
872		Khz *= 0.5;
873	+	Khw *= 0.5;
874		Kcx *= 0.5;
875		Kcy *= 0.5;
876		Kcz *= 0.5;
877	+	Kcw *= 0.5;
878
879		#ifdef IS_MPI
880		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 617 | Line 887 | namespace OpenMD {
887		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
888		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
889		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
890	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
891	+
892		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
893		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
894		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
895	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
896		#endif
897
898	<	//use coldBin coeff's
898	>	//solve coldBin coeff's first
899		RealType px = Pcx / Phx;
900		RealType py = Pcy / Phy;
901		RealType pz = Pcz / Phz;
902	+	RealType c, x, y, z;
903	+	bool successfulScale = false;
904	+	if ((rnemdFluxType_ == rnemdFullKE) ||
905	+	(rnemdFluxType_ == rnemdRotKE)) {
906	+	//may need sanity check Khw & Kcw > 0
907
908	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
909	<	switch(rnemdType_) {
910	<	case rnemdKineticScale :
911	<	/*used hotBin coeff's & only scale x & y dimensions
912	<	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	<	*/
908	>	if (rnemdFluxType_ == rnemdFullKE) {
909	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
910	>	} else {
911	>	c = 1.0 - kineticTarget_ / Kcw;
912	>	}
913
914	<	//scale all three dimensions, let c_x = c_y
915	<	a000 = Kcx + Kcy;
916	<	a110 = Kcz;
917	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
918	<	a001 = Khx * px * px + Khy * py * py;
919	<	a111 = Khz * pz * pz;
920	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
921	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
922	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
923	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
924	<	break;
925	<	case rnemdPxScale :
926	<	c = 1 - targetFlux_ / Pcx;
927	<	a000 = Kcy;
928	<	a110 = Kcz;
929	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
930	<	a001 = py * py * Khy;
931	<	a111 = pz * pz * Khz;
932	<	b01 = -2.0 * Khy * py * (1.0 + py);
933	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
934	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
935	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
936	<	break;
937	<	case rnemdPyScale :
938	<	c = 1 - targetFlux_ / Pcy;
939	<	a000 = Kcx;
940	<	a110 = Kcz;
941	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
942	<	a001 = px * px * Khx;
943	<	a111 = pz * pz * Khz;
944	<	b01 = -2.0 * Khx * px * (1.0 + px);
945	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
946	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
947	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
948	<	break;
949	<	case rnemdPzScale ://we don't really do this, do we?
950	<	c = 1 - targetFlux_ / Pcz;
951	<	a000 = Kcx;
952	<	a110 = Kcy;
953	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
954	<	a001 = px * px * Khx;
955	<	a111 = py * py * Khy;
956	<	b01 = -2.0 * Khx * px * (1.0 + px);
957	<	b11 = -2.0 * Khy * py * (1.0 + py);
958	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
959	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
960	<	break;
961	<	default :
962	<	break;
914	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
915	>	c = sqrt(c);
916	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
917	>	//now convert to hotBin coefficient
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	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
956	>	//           << "\twh= " << w << endl;
957	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
958	>	if (rnemdFluxType_ == rnemdFullKE) {
959	>	vel = (*sdi)->getVel();
960	>	vel.x() *= x;
961	>	vel.y() *= y;
962	>	vel.z() *= z;
963	>	(*sdi)->setVel(vel);
964	>	}
965	>	if ((*sdi)->isDirectional()) {
966	>	Vector3d angMom = (*sdi)->getJ() * w;
967	>	(*sdi)->setJ(angMom);
968	>	}
969	>	}
970	>	successfulScale = true;
971	>	kineticExchange_ += kineticTarget_;
972	>	}
973	>	}
974	>	} else {
975	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
976	>	switch(rnemdFluxType_) {
977	>	case rnemdKE :
978	>	/* used hotBin coeff's & only scale x & y dimensions
979	>	RealType px = Phx / Pcx;
980	>	RealType py = Phy / Pcy;
981	>	a110 = Khy;
982	>	c0 = - Khx - Khy - kineticTarget_;
983	>	a000 = Khx;
984	>	a111 = Kcy * py * py;
985	>	b11 = -2.0 * Kcy * py * (1.0 + py);
986	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
987	>	b01 = -2.0 * Kcx * px * (1.0 + px);
988	>	a001 = Kcx * px * px;
989	>	*/
990	>	//scale all three dimensions, let c_x = c_y
991	>	a000 = Kcx + Kcy;
992	>	a110 = Kcz;
993	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
994	>	a001 = Khx * px * px + Khy * py * py;
995	>	a111 = Khz * pz * pz;
996	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
997	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
998	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
999	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1000	>	break;
1001	>	case rnemdPx :
1002	>	c = 1 - momentumTarget_.x() / Pcx;
1003	>	a000 = Kcy;
1004	>	a110 = Kcz;
1005	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1006	>	a001 = py * py * Khy;
1007	>	a111 = pz * pz * Khz;
1008	>	b01 = -2.0 * Khy * py * (1.0 + py);
1009	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1010	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1011	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1012	>	break;
1013	>	case rnemdPy :
1014	>	c = 1 - momentumTarget_.y() / Pcy;
1015	>	a000 = Kcx;
1016	>	a110 = Kcz;
1017	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1018	>	a001 = px * px * Khx;
1019	>	a111 = pz * pz * Khz;
1020	>	b01 = -2.0 * Khx * px * (1.0 + px);
1021	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1022	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1023	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1024	>	break;
1025	>	case rnemdPz ://we don't really do this, do we?
1026	>	c = 1 - momentumTarget_.z() / Pcz;
1027	>	a000 = Kcx;
1028	>	a110 = Kcy;
1029	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1030	>	a001 = px * px * Khx;
1031	>	a111 = py * py * Khy;
1032	>	b01 = -2.0 * Khx * px * (1.0 + px);
1033	>	b11 = -2.0 * Khy * py * (1.0 + py);
1034	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1035	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1036	>	break;
1037	>	default :
1038	>	break;
1039	>	}
1040	>
1041	>	RealType v1 = a000 * a111 - a001 * a110;
1042	>	RealType v2 = a000 * b01;
1043	>	RealType v3 = a000 * b11;
1044	>	RealType v4 = a000 * c1 - a001 * c0;
1045	>	RealType v8 = a110 * b01;
1046	>	RealType v10 = - b01 * c0;
1047	>
1048	>	RealType u0 = v2 * v10 - v4 * v4;
1049	>	RealType u1 = -2.0 * v3 * v4;
1050	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1051	>	RealType u3 = -2.0 * v1 * v3;
1052	>	RealType u4 = - v1 * v1;
1053	>	//rescale coefficients
1054	>	RealType maxAbs = fabs(u0);
1055	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1056	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1057	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1058	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1059	>	u0 /= maxAbs;
1060	>	u1 /= maxAbs;
1061	>	u2 /= maxAbs;
1062	>	u3 /= maxAbs;
1063	>	u4 /= maxAbs;
1064	>	//max_element(start, end) is also available.
1065	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1066	>	poly.setCoefficient(4, u4);
1067	>	poly.setCoefficient(3, u3);
1068	>	poly.setCoefficient(2, u2);
1069	>	poly.setCoefficient(1, u1);
1070	>	poly.setCoefficient(0, u0);
1071	>	vector<RealType> realRoots = poly.FindRealRoots();
1072	>
1073	>	vector<RealType>::iterator ri;
1074	>	RealType r1, r2, alpha0;
1075	>	vector<pair<RealType,RealType> > rps;
1076	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1077	>	r2 = *ri;
1078	>	//check if FindRealRoots() give the right answer
1079	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1080	>	sprintf(painCave.errMsg,
1081	>	"RNEMD Warning: polynomial solve seems to have an error!");
1082	>	painCave.isFatal = 0;
1083	>	simError();
1084	>	failRootCount_++;
1085	>	}
1086	>	//might not be useful w/o rescaling coefficients
1087	>	alpha0 = -c0 - a110 * r2 * r2;
1088	>	if (alpha0 >= 0.0) {
1089	>	r1 = sqrt(alpha0 / a000);
1090	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1091	>	< 1e-6)
1092	>	{ rps.push_back(make_pair(r1, r2)); }
1093	>	if (r1 > 1e-6) { //r1 non-negative
1094	>	r1 = -r1;
1095	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1096	>	< 1e-6)
1097	>	{ rps.push_back(make_pair(r1, r2)); }
1098	>	}
1099	>	}
1100	>	}
1101	>	// Consider combining together the solving pair part w/ the searching
1102	>	// best solution part so that we don't need the pairs vector
1103	>	if (!rps.empty()) {
1104	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1105	>	RealType diff;
1106	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1107	>	vector<pair<RealType,RealType> >::iterator rpi;
1108	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1109	>	r1 = (*rpi).first;
1110	>	r2 = (*rpi).second;
1111	>	switch(rnemdFluxType_) {
1112	>	case rnemdKE :
1113	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1115	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1116	>	break;
1117	>	case rnemdPx :
1118	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1119	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120	>	break;
1121	>	case rnemdPy :
1122	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1124	>	break;
1125	>	case rnemdPz :
1126	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1128	>	default :
1129	>	break;
1130	>	}
1131	>	if (diff < smallestDiff) {
1132	>	smallestDiff = diff;
1133	>	bestPair = *rpi;
1134	>	}
1135	>	}
1136	>	#ifdef IS_MPI
1137	>	if (worldRank == 0) {
1138	>	#endif
1139	>	// sprintf(painCave.errMsg,
1140	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1141	>	//         bestPair.first, bestPair.second);
1142	>	// painCave.isFatal = 0;
1143	>	// painCave.severity = OPENMD_INFO;
1144	>	// simError();
1145	>	#ifdef IS_MPI
1146	>	}
1147	>	#endif
1148	>
1149	>	switch(rnemdFluxType_) {
1150	>	case rnemdKE :
1151	>	x = bestPair.first;
1152	>	y = bestPair.first;
1153	>	z = bestPair.second;
1154	>	break;
1155	>	case rnemdPx :
1156	>	x = c;
1157	>	y = bestPair.first;
1158	>	z = bestPair.second;
1159	>	break;
1160	>	case rnemdPy :
1161	>	x = bestPair.first;
1162	>	y = c;
1163	>	z = bestPair.second;
1164	>	break;
1165	>	case rnemdPz :
1166	>	x = bestPair.first;
1167	>	y = bestPair.second;
1168	>	z = c;
1169	>	break;
1170	>	default :
1171	>	break;
1172	>	}
1173	>	vector<StuntDouble*>::iterator sdi;
1174	>	Vector3d vel;
1175	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1176	>	vel = (*sdi)->getVel();
1177	>	vel.x() *= x;
1178	>	vel.y() *= y;
1179	>	vel.z() *= z;
1180	>	(*sdi)->setVel(vel);
1181	>	}
1182	>	//convert to hotBin coefficient
1183	>	x = 1.0 + px * (1.0 - x);
1184	>	y = 1.0 + py * (1.0 - y);
1185	>	z = 1.0 + pz * (1.0 - z);
1186	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1187	>	vel = (*sdi)->getVel();
1188	>	vel.x() *= x;
1189	>	vel.y() *= y;
1190	>	vel.z() *= z;
1191	>	(*sdi)->setVel(vel);
1192	>	}
1193	>	successfulScale = true;
1194	>	switch(rnemdFluxType_) {
1195	>	case rnemdKE :
1196	>	kineticExchange_ += kineticTarget_;
1197	>	break;
1198	>	case rnemdPx :
1199	>	case rnemdPy :
1200	>	case rnemdPz :
1201	>	momentumExchange_ += momentumTarget_;
1202	>	break;
1203	>	default :
1204	>	break;
1205	>	}
1206	>	}
1207		}
1208	+	if (successfulScale != true) {
1209	+	sprintf(painCave.errMsg,
1210	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1211	+	"\tthe constraint equations may not exist or there may be\n"
1212	+	"\tno selected objects in one or both slabs.\n");
1213	+	painCave.isFatal = 0;
1214	+	painCave.severity = OPENMD_INFO;
1215	+	simError();
1216	+	failTrialCount_++;
1217	+	}
1218	+	}
1219
1220	<	RealType v1 = a000 * a111 - a001 * a110;
1221	<	RealType v2 = a000 * b01;
1222	<	RealType v3 = a000 * b11;
1223	<	RealType v4 = a000 * c1 - a001 * c0;
1224	<	RealType v8 = a110 * b01;
702	<	RealType v10 = - b01 * c0;
1220	>	void RNEMD::doVSS() {
1221	>	if (!doRNEMD_) return;
1222	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1223	>	RealType time = currentSnap_->getTime();
1224	>	Mat3x3d hmat = currentSnap_->getHmat();
1225
1226	<	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();
1226	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1227
1228	<	std::vector<RealType>::iterator ri;
1229	<	RealType r1, r2, alpha0;
1230	<	std::vector<std::pair<RealType,RealType> > rps;
1231	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1232	<	r2 = *ri;
1233	<	//check if FindRealRoots() give the right answer
1234	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1235	<	sprintf(painCave.errMsg,
1236	<	"RNEMD Warning: polynomial solve seems to have an error!");
1237	<	painCave.isFatal = 0;
1238	<	simError();
1239	<	failRootCount_++;
1240	<	}
1241	<	//might not be useful w/o rescaling coefficients
1242	<	alpha0 = -c0 - a110 * r2 * r2;
1243	<	if (alpha0 >= 0.0) {
1244	<	r1 = sqrt(alpha0 / a000);
1245	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
1246	<	{ rps.push_back(std::make_pair(r1, r2)); }
1247	<	if (r1 > 1e-6) { //r1 non-negative
1248	<	r1 = -r1;
1249	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
1250	<	{ rps.push_back(std::make_pair(r1, r2)); }
1251	<	}
1228	>	int selei;
1229	>	StuntDouble* sd;
1230	>	int idx;
1231	>
1232	>	vector<StuntDouble*> hotBin, coldBin;
1233	>
1234	>	Vector3d Ph(V3Zero);
1235	>	RealType Mh = 0.0;
1236	>	RealType Kh = 0.0;
1237	>	Vector3d Pc(V3Zero);
1238	>	RealType Mc = 0.0;
1239	>	RealType Kc = 0.0;
1240	>
1241	>
1242	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1243	>	sd = seleMan_.nextSelected(selei)) {
1244	>
1245	>	idx = sd->getLocalIndex();
1246	>
1247	>	Vector3d pos = sd->getPos();
1248	>
1249	>	// wrap the stuntdouble's position back into the box:
1250	>
1251	>	if (usePeriodicBoundaryConditions_)
1252	>	currentSnap_->wrapVector(pos);
1253	>
1254	>	// which bin is this stuntdouble in?
1255	>	bool inA = inSlabA(pos);
1256	>	bool inB = inSlabB(pos);
1257	>
1258	>	if (inA || inB) {
1259	>
1260	>	RealType mass = sd->getMass();
1261	>	Vector3d vel = sd->getVel();
1262	>
1263	>	if (inA) {
1264	>	hotBin.push_back(sd);
1265	>	//std::cerr << "before, velocity = " << vel << endl;
1266	>	Ph += mass * vel;
1267	>	//std::cerr << "after, velocity = " << vel << endl;
1268	>	Mh += mass;
1269	>	Kh += mass * vel.lengthSquare();
1270	>	if (rnemdFluxType_ == rnemdFullKE) {
1271	>	if (sd->isDirectional()) {
1272	>	Vector3d angMom = sd->getJ();
1273	>	Mat3x3d I = sd->getI();
1274	>	if (sd->isLinear()) {
1275	>	int i = sd->linearAxis();
1276	>	int j = (i + 1) % 3;
1277	>	int k = (i + 2) % 3;
1278	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1279	>	angMom[k] * angMom[k] / I(k, k);
1280	>	} else {
1281	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1282	>	angMom[1] * angMom[1] / I(1, 1) +
1283	>	angMom[2] * angMom[2] / I(2, 2);
1284	>	}
1285	>	}
1286	>	}
1287	>	} else { //midBin_
1288	>	coldBin.push_back(sd);
1289	>	Pc += mass * vel;
1290	>	Mc += mass;
1291	>	Kc += mass * vel.lengthSquare();
1292	>	if (rnemdFluxType_ == rnemdFullKE) {
1293	>	if (sd->isDirectional()) {
1294	>	Vector3d angMom = sd->getJ();
1295	>	Mat3x3d I = sd->getI();
1296	>	if (sd->isLinear()) {
1297	>	int i = sd->linearAxis();
1298	>	int j = (i + 1) % 3;
1299	>	int k = (i + 2) % 3;
1300	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1301	>	angMom[k] * angMom[k] / I(k, k);
1302	>	} else {
1303	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1304	>	angMom[1] * angMom[1] / I(1, 1) +
1305	>	angMom[2] * angMom[2] / I(2, 2);
1306	>	}
1307	>	}
1308	>	}
1309	>	}
1310		}
1311		}
1312	<	// Consider combininig together the solving pair part w/ the searching
1313	<	// best solution part so that we don't need the pairs vector
1314	<	if (!rps.empty()) {
1315	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1316	<	RealType diff;
1317	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1318	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1319	<	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	<	}
1312	>
1313	>	Kh *= 0.5;
1314	>	Kc *= 0.5;
1315	>
1316	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1317	>	//        << "\tKc= " << Kc << endl;
1318	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1319	>
1320		#ifdef IS_MPI
1321	<	if (worldRank == 0) {
1321	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1322	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1323	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1324	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1325	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1326	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1327		#endif
791	–	std::cerr << "we choose r1 = " << bestPair.first
792	–	<< " and r2 = " << bestPair.second << "\n";
793	–	#ifdef IS_MPI
794	–	}
795	–	#endif
1328
1329	<	RealType x, y, z;
1330	<	switch(rnemdType_) {
1331	<	case rnemdKineticScale :
1332	<	x = bestPair.first;
1333	<	y = bestPair.first;
1334	<	z = bestPair.second;
1335	<	break;
1336	<	case rnemdPxScale :
1337	<	x = c;
1338	<	y = bestPair.first;
1339	<	z = bestPair.second;
1340	<	break;
1341	<	case rnemdPyScale :
1342	<	x = bestPair.first;
1343	<	y = c;
1344	<	z = bestPair.second;
1345	<	break;
1346	<	case rnemdPzScale :
1347	<	x = bestPair.first;
1348	<	y = bestPair.second;
1349	<	z = c;
1350	<	break;
1351	<	default :
1352	<	break;
1353	<	}
1354	<	std::vector<StuntDouble*>::iterator sdi;
1355	<	Vector3d vel;
1356	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1357	<	vel = (*sdi)->getVel();
1358	<	vel.x() *= x;
1359	<	vel.y() *= y;
1360	<	vel.z() *= z;
1361	<	(*sdi)->setVel(vel);
1329	>	bool successfulExchange = false;
1330	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1331	>	Vector3d vc = Pc / Mc;
1332	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1333	>	Vector3d acrec = -momentumTarget_ / Mc;
1334	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1335	>	if (cNumerator > 0.0) {
1336	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1337	>	if (cDenominator > 0.0) {
1338	>	RealType c = sqrt(cNumerator / cDenominator);
1339	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1340	>	Vector3d vh = Ph / Mh;
1341	>	Vector3d ah = momentumTarget_ / Mh + vh;
1342	>	Vector3d ahrec = momentumTarget_ / Mh;
1343	>	RealType hNumerator = Kh + kineticTarget_
1344	>	- 0.5 * Mh * ah.lengthSquare();
1345	>	if (hNumerator > 0.0) {
1346	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1347	>	if (hDenominator > 0.0) {
1348	>	RealType h = sqrt(hNumerator / hDenominator);
1349	>	if ((h > 0.9) && (h < 1.1)) {
1350	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1351	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1352	>	vector<StuntDouble*>::iterator sdi;
1353	>	Vector3d vel;
1354	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1355	>	//vel = (*sdi)->getVel();
1356	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1357	>	(*sdi)->setVel(vel);
1358	>	if (rnemdFluxType_ == rnemdFullKE) {
1359	>	if ((*sdi)->isDirectional()) {
1360	>	Vector3d angMom = (*sdi)->getJ() * c;
1361	>	(*sdi)->setJ(angMom);
1362	>	}
1363	>	}
1364	>	}
1365	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1366	>	//vel = (*sdi)->getVel();
1367	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1368	>	(*sdi)->setVel(vel);
1369	>	if (rnemdFluxType_ == rnemdFullKE) {
1370	>	if ((*sdi)->isDirectional()) {
1371	>	Vector3d angMom = (*sdi)->getJ() * h;
1372	>	(*sdi)->setJ(angMom);
1373	>	}
1374	>	}
1375	>	}
1376	>	successfulExchange = true;
1377	>	kineticExchange_ += kineticTarget_;
1378	>	momentumExchange_ += momentumTarget_;
1379	>	}
1380	>	}
1381	>	}
1382	>	}
1383	>	}
1384		}
1385	<	//convert to hotBin coefficient
1386	<	x = 1.0 + px * (1.0 - x);
1387	<	y = 1.0 + py * (1.0 - y);
1388	<	z = 1.0 + pz * (1.0 - z);
1389	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1390	<	vel = (*sdi)->getVel();
1391	<	vel.x() *= x;
1392	<	vel.y() *= y;
1393	<	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
1385	>	}
1386	>	if (successfulExchange != true) {
1387	>	sprintf(painCave.errMsg,
1388	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1389	>	"\tthe constraint equations may not exist or there may be\n"
1390	>	"\tno selected objects in one or both slabs.\n");
1391	>	painCave.isFatal = 0;
1392	>	painCave.severity = OPENMD_INFO;
1393	>	simError();
1394		failTrialCount_++;
1395		}
848	–
1396		}
1397
1398		void RNEMD::doRNEMD() {
1399	<
1400	<	switch(rnemdType_) {
1401	<	case rnemdKineticScale :
1402	<	case rnemdPxScale :
856	<	case rnemdPyScale :
857	<	case rnemdPzScale :
858	<	doScale();
859	<	break;
860	<	case rnemdKineticSwap :
861	<	case rnemdPx :
862	<	case rnemdPy :
863	<	case rnemdPz :
1399	>	if (!doRNEMD_) return;
1400	>	trialCount_++;
1401	>	switch(rnemdMethod_) {
1402	>	case rnemdSwap:
1403		doSwap();
1404		break;
1405	<	case rnemdUnknown :
1405	>	case rnemdNIVS:
1406	>	doNIVS();
1407	>	break;
1408	>	case rnemdVSS:
1409	>	doVSS();
1410	>	break;
1411	>	case rnemdUnkownMethod:
1412		default :
1413		break;
1414		}
1415		}
1416
1417		void RNEMD::collectData() {
1418	<
1418	>	if (!doRNEMD_) return;
1419		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1420		Mat3x3d hmat = currentSnap_->getHmat();
1421
1422	+	areaAccumulator_->add(currentSnap_->getXYarea());
1423	+
1424		seleMan_.setSelectionSet(evaluator_.evaluate());
1425
1426		int selei;
1427		StuntDouble* sd;
1428		int idx;
1429
1430	+	vector<RealType> binMass(nBins_, 0.0);
1431	+	vector<RealType> binPx(nBins_, 0.0);
1432	+	vector<RealType> binPy(nBins_, 0.0);
1433	+	vector<RealType> binPz(nBins_, 0.0);
1434	+	vector<RealType> binKE(nBins_, 0.0);
1435	+	vector<int> binDOF(nBins_, 0);
1436	+	vector<int> binCount(nBins_, 0);
1437	+
1438	+	// alternative approach, track all molecules instead of only those
1439	+	// selected for scaling/swapping:
1440	+	/*
1441	+	SimInfo::MoleculeIterator miter;
1442	+	vector<StuntDouble*>::iterator iiter;
1443	+	Molecule* mol;
1444	+	StuntDouble* sd;
1445	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1446	+	mol = info_->nextMolecule(miter))
1447	+	sd is essentially sd
1448	+	for (sd = mol->beginIntegrableObject(iiter);
1449	+	sd != NULL;
1450	+	sd = mol->nextIntegrableObject(iiter))
1451	+	*/
1452		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453		sd = seleMan_.nextSelected(selei)) {
1454
#	Line 891 | Line 1460 | namespace OpenMD {
1460
1461		if (usePeriodicBoundaryConditions_)
1462		currentSnap_->wrapVector(pos);
1463	<
1463	>
1464	>
1465		// which bin is this stuntdouble in?
1466		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1467	<
1467	>	// Shift molecules by half a box to have bins start at 0
1468	>	// The modulo operator is used to wrap the case when we are
1469	>	// beyond the end of the bins back to the beginning.
1470		int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1471	<
900	<	if (rnemdLogWidth_ == midBin_ + 1)
901	<	if (binNo > midBin_)
902	<	binNo = nBins_ - binNo;
903	<
1471	>
1472		RealType mass = sd->getMass();
1473		Vector3d vel = sd->getVel();
906	–	RealType value;
907	–	RealType xVal, yVal, zVal;
1474
1475	<	switch(rnemdType_) {
1476	<	case rnemdKineticSwap :
1477	<	case rnemdKineticScale :
1478	<
1479	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1480	<	vel[2]*vel[2]);
1481	<
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);
1475	>	binCount[binNo]++;
1476	>	binMass[binNo] += mass;
1477	>	binPx[binNo] += mass*vel.x();
1478	>	binPy[binNo] += mass*vel.y();
1479	>	binPz[binNo] += mass*vel.z();
1480	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1481	>	binDOF[binNo] += 3;
1482
1483	<	valueCount_[binNo] +=2;
1483	>	if (sd->isDirectional()) {
1484	>	Vector3d angMom = sd->getJ();
1485	>	Mat3x3d I = sd->getI();
1486	>	if (sd->isLinear()) {
1487	>	int i = sd->linearAxis();
1488	>	int j = (i + 1) % 3;
1489	>	int k = (i + 2) % 3;
1490	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1491	>	angMom[k] * angMom[k] / I(k, k));
1492	>	binDOF[binNo] += 2;
1493	>	} else {
1494	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1495	>	angMom[1] * angMom[1] / I(1, 1) +
1496	>	angMom[2] * angMom[2] / I(2, 2));
1497	>	binDOF[binNo] += 3;
1498	>	}
1499	>	}
1500	>	}
1501	>
1502
1503	<	} else {
1504	<	value += angMom[0]*angMom[0]/I(0, 0)
1505	<	+ angMom[1]*angMom[1]/I(1, 1)
1506	<	+ angMom[2]*angMom[2]/I(2, 2);
1507	<	valueCount_[binNo] +=3;
1508	<	}
1509	<	}
1510	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1503	>	#ifdef IS_MPI
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1505	>	nBins_, MPI::INT, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1509	>	nBins_, MPI::REALTYPE, MPI::SUM);
1510	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1511	>	nBins_, MPI::REALTYPE, MPI::SUM);
1512	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1513	>	nBins_, MPI::REALTYPE, MPI::SUM);
1514	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1515	>	nBins_, MPI::REALTYPE, MPI::SUM);
1516	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1517	>	nBins_, MPI::INT, MPI::SUM);
1518	>	#endif
1519
1520	<	break;
1521	<	case rnemdPx :
1522	<	case rnemdPxScale :
1523	<	value = mass * vel[0];
1524	<	valueCount_[binNo]++;
1525	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1526	<	/ PhysicalConstants::kb;
1527	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1528	<	/ PhysicalConstants::kb;
1529	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1530	<	/ PhysicalConstants::kb;
1531	<	xTempHist_[binNo] += xVal;
1532	<	yTempHist_[binNo] += yVal;
1533	<	zTempHist_[binNo] += zVal;
1534	<	break;
1535	<	case rnemdPy :
1536	<	case rnemdPyScale :
1537	<	value = mass * vel[1];
1538	<	valueCount_[binNo]++;
1539	<	break;
1540	<	case rnemdPz :
1541	<	case rnemdPzScale :
1542	<	value = mass * vel[2];
1543	<	valueCount_[binNo]++;
1544	<	break;
1545	<	case rnemdUnknown :
1546	<	default :
1547	<	break;
1520	>	Vector3d vel;
1521	>	RealType den;
1522	>	RealType temp;
1523	>	RealType z;
1524	>	for (int i = 0; i < nBins_; i++) {
1525	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1526	>	vel.x() = binPx[i] / binMass[i];
1527	>	vel.y() = binPy[i] / binMass[i];
1528	>	vel.z() = binPz[i] / binMass[i];
1529	>
1530	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1531	>	/ currentSnap_->getVolume() ;
1532	>
1533	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1534	>	PhysicalConstants::energyConvert);
1535	>
1536	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1537	>	if(outputMask_[j]) {
1538	>	switch(j) {
1539	>	case Z:
1540	>	(data_[j].accumulator[i])->add(z);
1541	>	break;
1542	>	case TEMPERATURE:
1543	>	data_[j].accumulator[i]->add(temp);
1544	>	break;
1545	>	case VELOCITY:
1546	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1547	>	break;
1548	>	case DENSITY:
1549	>	data_[j].accumulator[i]->add(den);
1550	>	break;
1551	>	}
1552	>	}
1553		}
968	–	valueHist_[binNo] += value;
1554		}
970	–
1555		}
1556
1557		void RNEMD::getStarted() {
1558	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1559	<	Stats& stat = currentSnap_->statData;
1560	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1558	>	if (!doRNEMD_) return;
1559	>	collectData();
1560	>	writeOutputFile();
1561		}
1562
1563	<	void RNEMD::getStatus() {
1564	<
1565	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1566	<	Stats& stat = currentSnap_->statData;
1567	<	RealType time = currentSnap_->getTime();
1568	<
1569	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1570	<	//or to be more meaningful, define another item as exchangeSum_ / time
1571	<	int j;
1572	<
1563	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1564	>	if (!doRNEMD_) return;
1565	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1566	>
1567	>	while(tokenizer.hasMoreTokens()) {
1568	>	std::string token(tokenizer.nextToken());
1569	>	toUpper(token);
1570	>	OutputMapType::iterator i = outputMap_.find(token);
1571	>	if (i != outputMap_.end()) {
1572	>	outputMask_.set(i->second);
1573	>	} else {
1574	>	sprintf( painCave.errMsg,
1575	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1576	>	"\toutputFileFormat keyword.\n", token.c_str() );
1577	>	painCave.isFatal = 0;
1578	>	painCave.severity = OPENMD_ERROR;
1579	>	simError();
1580	>	}
1581	>	}
1582	>	}
1583	>
1584	>	void RNEMD::writeOutputFile() {
1585	>	if (!doRNEMD_) return;
1586	>
1587		#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	–	}
1588		// If we're the root node, should we print out the results
1589		int worldRank = MPI::COMM_WORLD.Get_rank();
1590		if (worldRank == 0) {
1591		#endif
1592	<	rnemdLog_ << time;
1593	<	for (j = 0; j < rnemdLogWidth_; j++) {
1594	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1592	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1593	>
1594	>	if( !rnemdFile_ ){
1595	>	sprintf( painCave.errMsg,
1596	>	"Could not open \"%s\" for RNEMD output.\n",
1597	>	rnemdFileName_.c_str());
1598	>	painCave.isFatal = 1;
1599	>	simError();
1600		}
1601	<	rnemdLog_ << "\n";
1602	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1603	<	xTempLog_ << time;
1604	<	for (j = 0; j < rnemdLogWidth_; j++) {
1605	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1601	>
1602	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1603	>
1604	>	RealType time = currentSnap_->getTime();
1605	>	RealType avgArea;
1606	>	areaAccumulator_->getAverage(avgArea);
1607	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1608	>	/ PhysicalConstants::energyConvert;
1609	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1610	>
1611	>	rnemdFile_ << "#######################################################\n";
1612	>	rnemdFile_ << "# RNEMD {\n";
1613	>
1614	>	map<string, RNEMDMethod>::iterator mi;
1615	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1616	>	if ( (*mi).second == rnemdMethod_)
1617	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1618	>	}
1619	>	map<string, RNEMDFluxType>::iterator fi;
1620	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1621	>	if ( (*fi).second == rnemdFluxType_)
1622	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1623	>	}
1624	>
1625	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1626	>
1627	>	rnemdFile_ << "#    objectSelection = \""
1628	>	<< rnemdObjectSelection_ << "\";\n";
1629	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1630	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1631	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1632	>	rnemdFile_ << "# }\n";
1633	>	rnemdFile_ << "#######################################################\n";
1634	>	rnemdFile_ << "# RNEMD report:\n";
1635	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1636	>	rnemdFile_ << "#     target flux:\n";
1637	>	rnemdFile_ << "#         kinetic = "
1638	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1639	>	<< " (kcal/mol/A^2/fs)\n";
1640	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1641	>	<< " (amu/A/fs^2)\n";
1642	>	rnemdFile_ << "#     target one-time exchanges:\n";
1643	>	rnemdFile_ << "#         kinetic = "
1644	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1645	>	<< " (kcal/mol)\n";
1646	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1647	>	<< " (amu*A/fs)\n";
1648	>	rnemdFile_ << "#     actual exchange totals:\n";
1649	>	rnemdFile_ << "#         kinetic = "
1650	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1651	>	<< " (kcal/mol)\n";
1652	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1653	>	<< " (amu*A/fs)\n";
1654	>	rnemdFile_ << "#     actual flux:\n";
1655	>	rnemdFile_ << "#         kinetic = " << Jz
1656	>	<< " (kcal/mol/A^2/fs)\n";
1657	>	rnemdFile_ << "#         momentum = " << JzP
1658	>	<< " (amu/A/fs^2)\n";
1659	>	rnemdFile_ << "#     exchange statistics:\n";
1660	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1661	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1662	>	if (rnemdMethod_ == rnemdNIVS) {
1663	>	rnemdFile_ << "#         NIVS root-check errors = "
1664	>	<< failRootCount_ << "\n";
1665	>	}
1666	>	rnemdFile_ << "#######################################################\n";
1667	>
1668	>
1669	>
1670	>	//write title
1671	>	rnemdFile_ << "#";
1672	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1673	>	if (outputMask_[i]) {
1674	>	rnemdFile_ << "\t" << data_[i].title <<
1675	>	"(" << data_[i].units << ")";
1676	>	// add some extra tabs for column alignment
1677	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1678		}
1679	<	xTempLog_ << "\n";
1680	<	yTempLog_ << time;
1681	<	for (j = 0; j < rnemdLogWidth_; j++) {
1682	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1679	>	}
1680	>	rnemdFile_ << std::endl;
1681	>
1682	>	rnemdFile_.precision(8);
1683	>
1684	>	for (unsigned int j = 0; j < nBins_; j++) {
1685	>
1686	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1687	>	if (outputMask_[i]) {
1688	>	if (data_[i].dataType == "RealType")
1689	>	writeReal(i,j);
1690	>	else if (data_[i].dataType == "Vector3d")
1691	>	writeVector(i,j);
1692	>	else {
1693	>	sprintf( painCave.errMsg,
1694	>	"RNEMD found an unknown data type for: %s ",
1695	>	data_[i].title.c_str());
1696	>	painCave.isFatal = 1;
1697	>	simError();
1698	>	}
1699	>	}
1700		}
1701	<	yTempLog_ << "\n";
1702	<	zTempLog_ << time;
1703	<	for (j = 0; j < rnemdLogWidth_; j++) {
1704	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1701	>	rnemdFile_ << std::endl;
1702	>
1703	>	}
1704	>
1705	>	rnemdFile_ << "#######################################################\n";
1706	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1707	>	rnemdFile_ << "#######################################################\n";
1708	>
1709	>
1710	>	for (unsigned int j = 0; j < nBins_; j++) {
1711	>	rnemdFile_ << "#";
1712	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1713	>	if (outputMask_[i]) {
1714	>	if (data_[i].dataType == "RealType")
1715	>	writeRealStdDev(i,j);
1716	>	else if (data_[i].dataType == "Vector3d")
1717	>	writeVectorStdDev(i,j);
1718	>	else {
1719	>	sprintf( painCave.errMsg,
1720	>	"RNEMD found an unknown data type for: %s ",
1721	>	data_[i].title.c_str());
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>	}
1726		}
1727	<	zTempLog_ << "\n";
1728	<	}
1727	>	rnemdFile_ << std::endl;
1728	>
1729	>	}
1730	>
1731	>	rnemdFile_.flush();
1732	>	rnemdFile_.close();
1733	>
1734		#ifdef IS_MPI
1735		}
1736		#endif
1737	<	for (j = 0; j < rnemdLogWidth_; j++) {
1738	<	valueCount_[j] = 0;
1739	<	valueHist_[j] = 0.0;
1737	>
1738	>	}
1739	>
1740	>	void RNEMD::writeReal(int index, unsigned int bin) {
1741	>	if (!doRNEMD_) return;
1742	>	assert(index >=0 && index < ENDINDEX);
1743	>	assert(bin < nBins_);
1744	>	RealType s;
1745	>
1746	>	data_[index].accumulator[bin]->getAverage(s);
1747	>
1748	>	if (! isinf(s) && ! isnan(s)) {
1749	>	rnemdFile_ << "\t" << s;
1750	>	} else{
1751	>	sprintf( painCave.errMsg,
1752	>	"RNEMD detected a numerical error writing: %s for bin %d",
1753	>	data_[index].title.c_str(), bin);
1754	>	painCave.isFatal = 1;
1755	>	simError();
1756	>	}
1757	>	}
1758	>
1759	>	void RNEMD::writeVector(int index, unsigned int bin) {
1760	>	if (!doRNEMD_) return;
1761	>	assert(index >=0 && index < ENDINDEX);
1762	>	assert(bin < nBins_);
1763	>	Vector3d s;
1764	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1765	>	if (isinf(s[0]) || isnan(s[0]) ||
1766	>	isinf(s[1]) || isnan(s[1]) ||
1767	>	isinf(s[2]) || isnan(s[2]) ) {
1768	>	sprintf( painCave.errMsg,
1769	>	"RNEMD detected a numerical error writing: %s for bin %d",
1770	>	data_[index].title.c_str(), bin);
1771	>	painCave.isFatal = 1;
1772	>	simError();
1773	>	} else {
1774	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1775		}
1776	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1777	<	for (j = 0; j < rnemdLogWidth_; j++) {
1778	<	xTempHist_[j] = 0.0;
1779	<	yTempHist_[j] = 0.0;
1780	<	zTempHist_[j] = 0.0;
1781	<	}
1776	>	}
1777	>
1778	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1779	>	if (!doRNEMD_) return;
1780	>	assert(index >=0 && index < ENDINDEX);
1781	>	assert(bin < nBins_);
1782	>	RealType s;
1783	>
1784	>	data_[index].accumulator[bin]->getStdDev(s);
1785	>
1786	>	if (! isinf(s) && ! isnan(s)) {
1787	>	rnemdFile_ << "\t" << s;
1788	>	} else{
1789	>	sprintf( painCave.errMsg,
1790	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1791	>	data_[index].title.c_str(), bin);
1792	>	painCave.isFatal = 1;
1793	>	simError();
1794	>	}
1795		}
1796	+
1797	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1798	+	if (!doRNEMD_) return;
1799	+	assert(index >=0 && index < ENDINDEX);
1800	+	assert(bin < nBins_);
1801	+	Vector3d s;
1802	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1803	+	if (isinf(s[0]) || isnan(s[0]) ||
1804	+	isinf(s[1]) || isnan(s[1]) ||
1805	+	isinf(s[2]) || isnan(s[2]) ) {
1806	+	sprintf( painCave.errMsg,
1807	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1808	+	data_[index].title.c_str(), bin);
1809	+	painCave.isFatal = 1;
1810	+	simError();
1811	+	} else {
1812	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1813	+	}
1814	+	}
1815		}
1816	+

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