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

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branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1776 by gezelter, Thu Aug 9 15:52:59 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+	#ifdef IS_MPI
42	+	#include <mpi.h>
43	+	#endif
44
45		#include <cmath>
46	+	#include <sstream>
47	+	#include <string>
48	+
49		#include "rnemd/RNEMD.hpp"
50		#include "math/Vector3.hpp"
51		#include "math/Vector.hpp"
#	Line 49 | Line 55
55		#include "primitives/StuntDouble.hpp"
56		#include "utils/PhysicalConstants.hpp"
57		#include "utils/Tuple.hpp"
58	<	#ifdef IS_MPI
59	<	#include <mpi.h>
58	>	#include "brains/Thermo.hpp"
59	>	#include "math/ConvexHull.hpp"
60	>
61	>	#ifdef _MSC_VER
62	>	#define isnan(x) _isnan((x))
63	>	#define isinf(x) (!_finite(x) && !_isnan(x))
64		#endif
65
66		#define HONKING_LARGE_VALUE 1.0e10
#	Line 58 | Line 68 | namespace OpenMD {
68		using namespace std;
69		namespace OpenMD {
70
71	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	<	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
71	>	RNEMD::RNEMD(SimInfo* info) : info_(info),
72	>	evaluator_(info_), seleMan_(info_),
73	>	evaluatorA_(info_), seleManA_(info_),
74	>	evaluatorB_(info_), seleManB_(info_),
75	>	commonA_(info_), commonB_(info_),
76	>	usePeriodicBoundaryConditions_(info_->getSimParams()->getUsePeriodicBoundaryConditions()),
77	>	hasDividingArea_(false),
78	>	hasData_(false) {
79
80		trialCount_ = 0;
81		failTrialCount_ = 0;
82		failRootCount_ = 0;
83
84	<	int seedValue;
69	<	Globals * simParams = info->getSimParams();
84	>	Globals* simParams = info->getSimParams();
85		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
86
87		doRNEMD_ = rnemdParams->getUseRNEMD();
#	Line 80 | Line 95 | namespace OpenMD {
95		stringToFluxType_["Px"]  = rnemdPx;
96		stringToFluxType_["Py"]  = rnemdPy;
97		stringToFluxType_["Pz"]  = rnemdPz;
98	+	stringToFluxType_["Pvector"]  = rnemdPvector;
99	+	stringToFluxType_["Lx"]  = rnemdLx;
100	+	stringToFluxType_["Ly"]  = rnemdLy;
101	+	stringToFluxType_["Lz"]  = rnemdLz;
102	+	stringToFluxType_["Lvector"]  = rnemdLvector;
103		stringToFluxType_["KE+Px"]  = rnemdKePx;
104		stringToFluxType_["KE+Py"]  = rnemdKePy;
105		stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
106	+	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
107	+	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
108	+	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
109	+	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
110
111		runTime_ = simParams->getRunTime();
112		statusTime_ = simParams->getStatusTime();
113
90	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
91	–	evaluator_.loadScriptString(rnemdObjectSelection_);
92	–	seleMan_.setSelectionSet(evaluator_.evaluate());
93	–
114		const string methStr = rnemdParams->getMethod();
115		bool hasFluxType = rnemdParams->haveFluxType();
116
117	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
118	+
119		string fluxStr;
120		if (hasFluxType) {
121		fluxStr = rnemdParams->getFluxType();
#	Line 101 | Line 123 | namespace OpenMD {
123		sprintf(painCave.errMsg,
124		"RNEMD: No fluxType was set in the md file.  This parameter,\n"
125		"\twhich must be one of the following values:\n"
126	<	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
127	<	"\tuse RNEMD\n");
126	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
127	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
128	>	"\tmust be set to use RNEMD\n");
129		painCave.isFatal = 1;
130		painCave.severity = OPENMD_ERROR;
131		simError();
#	Line 111 | Line 134 | namespace OpenMD {
134		bool hasKineticFlux = rnemdParams->haveKineticFlux();
135		bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
136		bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
137	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
138	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
139	+	hasSelectionA_ = rnemdParams->haveSelectionA();
140	+	hasSelectionB_ = rnemdParams->haveSelectionB();
141		bool hasSlabWidth = rnemdParams->haveSlabWidth();
142		bool hasSlabACenter = rnemdParams->haveSlabACenter();
143		bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
144	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
145	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
146	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
147		bool hasOutputFileName = rnemdParams->haveOutputFileName();
148		bool hasOutputFields = rnemdParams->haveOutputFields();
149
#	Line 198 | Line 228 | namespace OpenMD {
228		case rnemdPz:
229		hasCorrectFlux = hasMomentumFlux;
230		break;
231	+	case rnemdLx:
232	+	case rnemdLy:
233	+	case rnemdLz:
234	+	hasCorrectFlux = hasAngularMomentumFlux;
235	+	break;
236		case rnemdPvector:
237		hasCorrectFlux = hasMomentumFluxVector;
238	+	break;
239	+	case rnemdLvector:
240	+	hasCorrectFlux = hasAngularMomentumFluxVector;
241	+	break;
242		case rnemdKePx:
243		case rnemdKePy:
244		hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
245		break;
246	+	case rnemdKeLx:
247	+	case rnemdKeLy:
248	+	case rnemdKeLz:
249	+	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
250	+	break;
251		case rnemdKePvector:
252		hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
253		break;
254	+	case rnemdKeLvector:
255	+	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
256	+	break;
257		default:
258		methodFluxMismatch = true;
259		break;
#	Line 227 | Line 274 | namespace OpenMD {
274		}
275		if (!hasCorrectFlux) {
276		sprintf(painCave.errMsg,
277	<	"RNEMD: The current method,\n"
231	<	"\t%s, and flux type %s\n"
277	>	"RNEMD: The current method, %s, and flux type, %s,\n"
278		"\tdid not have the correct flux value specified. Options\n"
279	<	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
279	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
280	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
281		methStr.c_str(), fluxStr.c_str());
282		painCave.isFatal = 1;
283		painCave.severity = OPENMD_ERROR;
#	Line 238 | Line 285 | namespace OpenMD {
285		}
286
287		if (hasKineticFlux) {
288	<	kineticFlux_ = rnemdParams->getKineticFlux();
288	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
289	>	// into  amu / fs^3:
290	>	kineticFlux_ = rnemdParams->getKineticFlux()
291	>	* PhysicalConstants::energyConvert;
292		} else {
293		kineticFlux_ = 0.0;
294		}
295		if (hasMomentumFluxVector) {
296	<	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
296	>	std::vector<RealType> mf = rnemdParams->getMomentumFluxVector();
297	>	if (mf.size() != 3) {
298	>	sprintf(painCave.errMsg,
299	>	"RNEMD: Incorrect number of parameters specified for momentumFluxVector.\n"
300	>	"\tthere should be 3 parameters, but %lu were specified.\n",
301	>	mf.size());
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>	momentumFluxVector_.x() = mf[0];
306	>	momentumFluxVector_.y() = mf[1];
307	>	momentumFluxVector_.z() = mf[2];
308		} else {
309		momentumFluxVector_ = V3Zero;
310		if (hasMomentumFlux) {
#	Line 267 | Line 328 | namespace OpenMD {
328		default:
329		break;
330		}
331	<	}
331	>	}
332		}
333	+	if (hasAngularMomentumFluxVector) {
334	+	std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
335	+	if (amf.size() != 3) {
336	+	sprintf(painCave.errMsg,
337	+	"RNEMD: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
338	+	"\tthere should be 3 parameters, but %lu were specified.\n",
339	+	amf.size());
340	+	painCave.isFatal = 1;
341	+	simError();
342	+	}
343	+	angularMomentumFluxVector_.x() = amf[0];
344	+	angularMomentumFluxVector_.y() = amf[1];
345	+	angularMomentumFluxVector_.z() = amf[2];
346	+	} else {
347	+	angularMomentumFluxVector_ = V3Zero;
348	+	if (hasAngularMomentumFlux) {
349	+	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
350	+	switch (rnemdFluxType_) {
351	+	case rnemdLx:
352	+	angularMomentumFluxVector_.x() = angularMomentumFlux;
353	+	break;
354	+	case rnemdLy:
355	+	angularMomentumFluxVector_.y() = angularMomentumFlux;
356	+	break;
357	+	case rnemdLz:
358	+	angularMomentumFluxVector_.z() = angularMomentumFlux;
359	+	break;
360	+	case rnemdKeLx:
361	+	angularMomentumFluxVector_.x() = angularMomentumFlux;
362	+	break;
363	+	case rnemdKeLy:
364	+	angularMomentumFluxVector_.y() = angularMomentumFlux;
365	+	break;
366	+	case rnemdKeLz:
367	+	angularMomentumFluxVector_.z() = angularMomentumFlux;
368	+	break;
369	+	default:
370	+	break;
371	+	}
372	+	}
373	+	}
374
375	+	if (hasCoordinateOrigin) {
376	+	std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
377	+	if (co.size() != 3) {
378	+	sprintf(painCave.errMsg,
379	+	"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
380	+	"\tthere should be 3 parameters, but %lu were specified.\n",
381	+	co.size());
382	+	painCave.isFatal = 1;
383	+	simError();
384	+	}
385	+	coordinateOrigin_.x() = co[0];
386	+	coordinateOrigin_.y() = co[1];
387	+	coordinateOrigin_.z() = co[2];
388	+	} else {
389	+	coordinateOrigin_ = V3Zero;
390	+	}
391	+
392		// do some sanity checking
393	<
394	<	int selectionCount = seleMan_.getSelectionCount();
393	>
394	>	int selectionCount = seleMan_.getSelectionCount();
395		int nIntegrable = info->getNGlobalIntegrableObjects();
277	–
396		if (selectionCount > nIntegrable) {
397		sprintf(painCave.errMsg,
398		"RNEMD: The current objectSelection,\n"
#	Line 290 | Line 408 | namespace OpenMD {
408		painCave.severity = OPENMD_WARNING;
409		simError();
410		}
411	<
411	>
412		areaAccumulator_ = new Accumulator();
413	<
413	>
414		nBins_ = rnemdParams->getOutputBins();
415	<
415	>	binWidth_ = rnemdParams->getOutputBinWidth();
416	>
417		data_.resize(RNEMD::ENDINDEX);
418		OutputData z;
419		z.units =  "Angstroms";
420		z.title =  "Z";
421		z.dataType = "RealType";
422		z.accumulator.reserve(nBins_);
423	<	for (unsigned int i = 0; i < nBins_; i++)
423	>	for (int i = 0; i < nBins_; i++)
424		z.accumulator.push_back( new Accumulator() );
425		data_[Z] = z;
426		outputMap_["Z"] =  Z;
427	<
427	>
428	>	OutputData r;
429	>	r.units =  "Angstroms";
430	>	r.title =  "R";
431	>	r.dataType = "RealType";
432	>	r.accumulator.reserve(nBins_);
433	>	for (int i = 0; i < nBins_; i++)
434	>	r.accumulator.push_back( new Accumulator() );
435	>	data_[R] = r;
436	>	outputMap_["R"] =  R;
437	>
438		OutputData temperature;
439		temperature.units =  "K";
440		temperature.title =  "Temperature";
441		temperature.dataType = "RealType";
442		temperature.accumulator.reserve(nBins_);
443	<	for (unsigned int i = 0; i < nBins_; i++)
443	>	for (int i = 0; i < nBins_; i++)
444		temperature.accumulator.push_back( new Accumulator() );
445		data_[TEMPERATURE] = temperature;
446		outputMap_["TEMPERATURE"] =  TEMPERATURE;
447	<
447	>
448		OutputData velocity;
449	<	velocity.units = "amu/fs";
449	>	velocity.units = "angstroms/fs";
450		velocity.title =  "Velocity";
451		velocity.dataType = "Vector3d";
452		velocity.accumulator.reserve(nBins_);
453	<	for (unsigned int i = 0; i < nBins_; i++)
453	>	for (int i = 0; i < nBins_; i++)
454		velocity.accumulator.push_back( new VectorAccumulator() );
455		data_[VELOCITY] = velocity;
456		outputMap_["VELOCITY"] = VELOCITY;
457	<
457	>
458	>	OutputData angularVelocity;
459	>	angularVelocity.units = "angstroms^2/fs";
460	>	angularVelocity.title =  "AngularVelocity";
461	>	angularVelocity.dataType = "Vector3d";
462	>	angularVelocity.accumulator.reserve(nBins_);
463	>	for (int i = 0; i < nBins_; i++)
464	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
465	>	data_[ANGULARVELOCITY] = angularVelocity;
466	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
467	>
468		OutputData density;
469		density.units =  "g cm^-3";
470		density.title =  "Density";
471		density.dataType = "RealType";
472		density.accumulator.reserve(nBins_);
473	<	for (unsigned int i = 0; i < nBins_; i++)
473	>	for (int i = 0; i < nBins_; i++)
474		density.accumulator.push_back( new Accumulator() );
475		data_[DENSITY] = density;
476		outputMap_["DENSITY"] =  DENSITY;
477	<
477	>
478		if (hasOutputFields) {
479		parseOutputFileFormat(rnemdParams->getOutputFields());
480		} else {
481	<	outputMask_.set(Z);
481	>	if (usePeriodicBoundaryConditions_)
482	>	outputMask_.set(Z);
483	>	else
484	>	outputMask_.set(R);
485		switch (rnemdFluxType_) {
486		case rnemdKE:
487		case rnemdRotKE:
#	Line 354 | Line 496 | namespace OpenMD {
496		case rnemdPvector:
497		outputMask_.set(VELOCITY);
498		outputMask_.set(DENSITY);
499	+	break;
500	+	case rnemdLx:
501	+	case rnemdLy:
502	+	case rnemdLz:
503	+	case rnemdLvector:
504	+	outputMask_.set(ANGULARVELOCITY);
505	+	break;
506	+	case rnemdKeLx:
507	+	case rnemdKeLy:
508	+	case rnemdKeLz:
509	+	case rnemdKeLvector:
510	+	outputMask_.set(TEMPERATURE);
511	+	outputMask_.set(ANGULARVELOCITY);
512		break;
513		case rnemdKePx:
514		case rnemdKePy:
#	Line 369 | Line 524 | namespace OpenMD {
524		break;
525		}
526		}
527	<
527	>
528		if (hasOutputFileName) {
529		rnemdFileName_ = rnemdParams->getOutputFileName();
530		} else {
531		rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
532		}
533	<
533	>
534		exchangeTime_ = rnemdParams->getExchangeTime();
535	<
535	>
536		Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
382	–	Mat3x3d hmat = currentSnap_->getHmat();
383	–
384	–	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
385	–	// Lx, Ly = box dimensions in x & y
386	–	// dt = exchange time interval
387	–	// flux = target flux
388	–
389	–	RealType area = currentSnap_->getXYarea();
390	–	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
391	–	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
392	–
537		// total exchange sums are zeroed out at the beginning:
538	<
538	>
539		kineticExchange_ = 0.0;
540		momentumExchange_ = V3Zero;
541	<
398	<	if (hasSlabWidth)
399	<	slabWidth_ = rnemdParams->getSlabWidth();
400	<	else
401	<	slabWidth_ = hmat(2,2) / 10.0;
402	<
403	<	if (hasSlabACenter)
404	<	slabACenter_ = rnemdParams->getSlabACenter();
405	<	else
406	<	slabACenter_ = 0.0;
541	>	angularMomentumExchange_ = V3Zero;
542
543	<	if (hasSlabBCenter)
544	<	slabBCenter_ = rnemdParams->getSlabBCenter();
410	<	else
411	<	slabBCenter_ = hmat(2,2) / 2.0;
543	>	std::ostringstream selectionAstream;
544	>	std::ostringstream selectionBstream;
545
546	+	if (hasSelectionA_) {
547	+	selectionA_ = rnemdParams->getSelectionA();
548	+	} else {
549	+	if (usePeriodicBoundaryConditions_) {
550	+	Mat3x3d hmat = currentSnap_->getHmat();
551	+
552	+	if (hasSlabWidth)
553	+	slabWidth_ = rnemdParams->getSlabWidth();
554	+	else
555	+	slabWidth_ = hmat(2,2) / 10.0;
556	+
557	+	if (hasSlabACenter)
558	+	slabACenter_ = rnemdParams->getSlabACenter();
559	+	else
560	+	slabACenter_ = 0.0;
561	+
562	+	selectionAstream << "select wrappedz > "
563	+	<< slabACenter_ - 0.5*slabWidth_
564	+	<<  " && wrappedz < "
565	+	<< slabACenter_ + 0.5*slabWidth_;
566	+	selectionA_ = selectionAstream.str();
567	+	} else {
568	+	if (hasSphereARadius)
569	+	sphereARadius_ = rnemdParams->getSphereARadius();
570	+	else {
571	+	// use an initial guess to the size of the inner slab to be 1/10 the
572	+	// radius of an approximately spherical hull:
573	+	Thermo thermo(info);
574	+	RealType hVol = thermo.getHullVolume();
575	+	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
576	+	}
577	+	selectionAstream << "select r < " << sphereARadius_;
578	+	selectionA_ = selectionAstream.str();
579	+	}
580	+	}
581	+
582	+	if (hasSelectionB_) {
583	+	selectionB_ = rnemdParams->getSelectionB();
584	+
585	+	} else {
586	+	if (usePeriodicBoundaryConditions_) {
587	+	Mat3x3d hmat = currentSnap_->getHmat();
588	+
589	+	if (hasSlabWidth)
590	+	slabWidth_ = rnemdParams->getSlabWidth();
591	+	else
592	+	slabWidth_ = hmat(2,2) / 10.0;
593	+
594	+	if (hasSlabBCenter)
595	+	slabBCenter_ = rnemdParams->getSlabBCenter();
596	+	else
597	+	slabBCenter_ = hmat(2,2) / 2.0;
598	+
599	+	selectionBstream << "select wrappedz > "
600	+	<< slabBCenter_ - 0.5*slabWidth_
601	+	<<  " && wrappedz < "
602	+	<< slabBCenter_ + 0.5*slabWidth_;
603	+	selectionB_ = selectionBstream.str();
604	+	} else {
605	+	if (hasSphereBRadius_) {
606	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
607	+	selectionBstream << "select r > " << sphereBRadius_;
608	+	selectionB_ = selectionBstream.str();
609	+	} else {
610	+	selectionB_ = "select hull";
611	+	BisHull_ = true;
612	+	hasSelectionB_ = true;
613	+	}
614	+	}
615	+	}
616	+
617	+
618	+	// object evaluator:
619	+	evaluator_.loadScriptString(rnemdObjectSelection_);
620	+	seleMan_.setSelectionSet(evaluator_.evaluate());
621	+	evaluatorA_.loadScriptString(selectionA_);
622	+	evaluatorB_.loadScriptString(selectionB_);
623	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
624	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
625	+	commonA_ = seleManA_ & seleMan_;
626	+	commonB_ = seleManB_ & seleMan_;
627		}
628	<
628	>
629	>
630		RNEMD::~RNEMD() {
631		if (!doRNEMD_) return;
632		#ifdef IS_MPI
#	Line 425 | Line 640 | namespace OpenMD {
640		#ifdef IS_MPI
641		}
642		#endif
643	+
644	+	// delete all of the objects we created:
645	+	delete areaAccumulator_;
646	+	data_.clear();
647		}
648
649	<	bool RNEMD::inSlabA(Vector3d pos) {
431	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
432	<	}
433	<	bool RNEMD::inSlabB(Vector3d pos) {
434	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
435	<	}
436	<
437	<	void RNEMD::doSwap() {
649	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
650		if (!doRNEMD_) return;
651	+	int selei;
652	+	int selej;
653	+
654		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
655		Mat3x3d hmat = currentSnap_->getHmat();
656
442	–	seleMan_.setSelectionSet(evaluator_.evaluate());
443	–
444	–	int selei;
657		StuntDouble* sd;
446	–	int idx;
658
659	<	RealType min_val;
660	<	bool min_found = false;
661	<	StuntDouble* min_sd;
659	>	RealType min_val(0.0);
660	>	int min_found = 0;
661	>	StuntDouble* min_sd = NULL;
662
663	<	RealType max_val;
664	<	bool max_found = false;
665	<	StuntDouble* max_sd;
663	>	RealType max_val(0.0);
664	>	int max_found = 0;
665	>	StuntDouble* max_sd = NULL;
666
667	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
668	<	sd = seleMan_.nextSelected(selei)) {
667	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
668	>	sd = seleManA_.nextSelected(selei)) {
669
459	–	idx = sd->getLocalIndex();
460	–
670		Vector3d pos = sd->getPos();
671	<
671	>
672		// wrap the stuntdouble's position back into the box:
673	<
673	>
674		if (usePeriodicBoundaryConditions_)
675		currentSnap_->wrapVector(pos);
676	<	bool inA = inSlabA(pos);
677	<	bool inB = inSlabB(pos);
678	<
679	<	if (inA || inB) {
676	>
677	>	RealType mass = sd->getMass();
678	>	Vector3d vel = sd->getVel();
679	>	RealType value(0.0);
680	>
681	>	switch(rnemdFluxType_) {
682	>	case rnemdKE :
683
684	<	RealType mass = sd->getMass();
685	<	Vector3d vel = sd->getVel();
686	<	RealType value;
687	<
688	<	switch(rnemdFluxType_) {
477	<	case rnemdKE :
684	>	value = mass * vel.lengthSquare();
685	>
686	>	if (sd->isDirectional()) {
687	>	Vector3d angMom = sd->getJ();
688	>	Mat3x3d I = sd->getI();
689
690	<	value = mass * vel.lengthSquare();
691	<
692	<	if (sd->isDirectional()) {
693	<	Vector3d angMom = sd->getJ();
694	<	Mat3x3d I = sd->getI();
695	<
696	<	if (sd->isLinear()) {
697	<	int i = sd->linearAxis();
698	<	int j = (i + 1) % 3;
699	<	int k = (i + 2) % 3;
700	<	value += angMom[j] * angMom[j] / I(j, j) +
701	<	angMom[k] * angMom[k] / I(k, k);
702	<	} else {
703	<	value += angMom[0]*angMom[0]/I(0, 0)
704	<	+ angMom[1]*angMom[1]/I(1, 1)
705	<	+ angMom[2]*angMom[2]/I(2, 2);
706	<	}
707	<	} //angular momenta exchange enabled
708	<	//energyConvert temporarily disabled
709	<	//make kineticExchange_ comparable between swap & scale
710	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
711	<	value *= 0.5;
712	<	break;
713	<	case rnemdPx :
714	<	value = mass * vel[0];
715	<	break;
716	<	case rnemdPy :
717	<	value = mass * vel[1];
718	<	break;
719	<	case rnemdPz :
720	<	value = mass * vel[2];
721	<	break;
722	<	default :
723	<	break;
690	>	if (sd->isLinear()) {
691	>	int i = sd->linearAxis();
692	>	int j = (i + 1) % 3;
693	>	int k = (i + 2) % 3;
694	>	value += angMom[j] * angMom[j] / I(j, j) +
695	>	angMom[k] * angMom[k] / I(k, k);
696	>	} else {
697	>	value += angMom[0]*angMom[0]/I(0, 0)
698	>	+ angMom[1]*angMom[1]/I(1, 1)
699	>	+ angMom[2]*angMom[2]/I(2, 2);
700	>	}
701	>	} //angular momenta exchange enabled
702	>	value *= 0.5;
703	>	break;
704	>	case rnemdPx :
705	>	value = mass * vel[0];
706	>	break;
707	>	case rnemdPy :
708	>	value = mass * vel[1];
709	>	break;
710	>	case rnemdPz :
711	>	value = mass * vel[2];
712	>	break;
713	>	default :
714	>	break;
715	>	}
716	>	if (!max_found) {
717	>	max_val = value;
718	>	max_sd = sd;
719	>	max_found = 1;
720	>	} else {
721	>	if (max_val < value) {
722	>	max_val = value;
723	>	max_sd = sd;
724		}
725	+	}
726	+	}
727
728	<	if (inA == 0) {
729	<	if (!min_found) {
730	<	min_val = value;
731	<	min_sd = sd;
732	<	min_found = true;
733	<	} else {
734	<	if (min_val > value) {
735	<	min_val = value;
736	<	min_sd = sd;
737	<	}
738	<	}
739	<	} else {
740	<	if (!max_found) {
741	<	max_val = value;
742	<	max_sd = sd;
743	<	max_found = true;
744	<	} else {
745	<	if (max_val < value) {
746	<	max_val = value;
747	<	max_sd = sd;
748	<	}
749	<	}
750	<	}
728	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
729	>	sd = seleManB_.nextSelected(selej)) {
730	>
731	>	Vector3d pos = sd->getPos();
732	>
733	>	// wrap the stuntdouble's position back into the box:
734	>
735	>	if (usePeriodicBoundaryConditions_)
736	>	currentSnap_->wrapVector(pos);
737	>
738	>	RealType mass = sd->getMass();
739	>	Vector3d vel = sd->getVel();
740	>	RealType value(0.0);
741	>
742	>	switch(rnemdFluxType_) {
743	>	case rnemdKE :
744	>
745	>	value = mass * vel.lengthSquare();
746	>
747	>	if (sd->isDirectional()) {
748	>	Vector3d angMom = sd->getJ();
749	>	Mat3x3d I = sd->getI();
750	>
751	>	if (sd->isLinear()) {
752	>	int i = sd->linearAxis();
753	>	int j = (i + 1) % 3;
754	>	int k = (i + 2) % 3;
755	>	value += angMom[j] * angMom[j] / I(j, j) +
756	>	angMom[k] * angMom[k] / I(k, k);
757	>	} else {
758	>	value += angMom[0]*angMom[0]/I(0, 0)
759	>	+ angMom[1]*angMom[1]/I(1, 1)
760	>	+ angMom[2]*angMom[2]/I(2, 2);
761	>	}
762	>	} //angular momenta exchange enabled
763	>	value *= 0.5;
764	>	break;
765	>	case rnemdPx :
766	>	value = mass * vel[0];
767	>	break;
768	>	case rnemdPy :
769	>	value = mass * vel[1];
770	>	break;
771	>	case rnemdPz :
772	>	value = mass * vel[2];
773	>	break;
774	>	default :
775	>	break;
776		}
777	+
778	+	if (!min_found) {
779	+	min_val = value;
780	+	min_sd = sd;
781	+	min_found = 1;
782	+	} else {
783	+	if (min_val > value) {
784	+	min_val = value;
785	+	min_sd = sd;
786	+	}
787	+	}
788		}
789
790	<	#ifdef IS_MPI
791	<	int nProc, worldRank;
792	<
793	<	nProc = MPI::COMM_WORLD.Get_size();
794	<	worldRank = MPI::COMM_WORLD.Get_rank();
790	>	#ifdef IS_MPI
791	>	int worldRank;
792	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
793	>
794	>	int my_min_found = min_found;
795	>	int my_max_found = max_found;
796
547	–	bool my_min_found = min_found;
548	–	bool my_max_found = max_found;
549	–
797		// Even if we didn't find a minimum, did someone else?
798	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
798	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
799	>	MPI_COMM_WORLD);
800		// Even if we didn't find a maximum, did someone else?
801	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
801	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
802	>	MPI_COMM_WORLD);
803		#endif
804
805		if (max_found && min_found) {
#	Line 569 | Line 818 | namespace OpenMD {
818		min_vals.rank = worldRank;
819
820		// Who had the minimum?
821	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
822	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
821	>	MPI_Allreduce(&min_vals, &min_vals,
822	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
823		min_val = min_vals.val;
824
825		if (my_max_found) {
#	Line 581 | Line 830 | namespace OpenMD {
830		max_vals.rank = worldRank;
831
832		// Who had the maximum?
833	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
834	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
833	>	MPI_Allreduce(&max_vals, &max_vals,
834	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
835		max_val = max_vals.val;
836		#endif
837
#	Line 642 | Line 891 | namespace OpenMD {
891
892		Vector3d min_vel;
893		Vector3d max_vel = max_sd->getVel();
894	<	MPI::Status status;
894	>	MPI_Status status;
895
896		// point-to-point swap of the velocity vector
897	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
898	<	min_vals.rank, 0,
899	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
900	<	min_vals.rank, 0, status);
897	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
898	>	min_vals.rank, 0,
899	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
900	>	min_vals.rank, 0, MPI_COMM_WORLD, &status);
901
902		switch(rnemdFluxType_) {
903		case rnemdKE :
#	Line 659 | Line 908 | namespace OpenMD {
908		Vector3d max_angMom = max_sd->getJ();
909
910		// point-to-point swap of the angular momentum vector
911	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
912	<	MPI::REALTYPE, min_vals.rank, 1,
913	<	min_angMom.getArrayPointer(), 3,
914	<	MPI::REALTYPE, min_vals.rank, 1,
915	<	status);
911	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
912	>	MPI_REALTYPE, min_vals.rank, 1,
913	>	min_angMom.getArrayPointer(), 3,
914	>	MPI_REALTYPE, min_vals.rank, 1,
915	>	MPI_COMM_WORLD, &status);
916
917		max_sd->setJ(min_angMom);
918		}
#	Line 688 | Line 937 | namespace OpenMD {
937
938		Vector3d max_vel;
939		Vector3d min_vel = min_sd->getVel();
940	<	MPI::Status status;
940	>	MPI_Status status;
941
942		// point-to-point swap of the velocity vector
943	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
944	<	max_vals.rank, 0,
945	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
946	<	max_vals.rank, 0, status);
943	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
944	>	max_vals.rank, 0,
945	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
946	>	max_vals.rank, 0, MPI_COMM_WORLD, &status);
947
948		switch(rnemdFluxType_) {
949		case rnemdKE :
#	Line 705 | Line 954 | namespace OpenMD {
954		Vector3d max_angMom;
955
956		// point-to-point swap of the angular momentum vector
957	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
958	<	MPI::REALTYPE, max_vals.rank, 1,
959	<	max_angMom.getArrayPointer(), 3,
960	<	MPI::REALTYPE, max_vals.rank, 1,
961	<	status);
957	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
958	>	MPI_REALTYPE, max_vals.rank, 1,
959	>	max_angMom.getArrayPointer(), 3,
960	>	MPI_REALTYPE, max_vals.rank, 1,
961	>	MPI_COMM_WORLD, &status);
962
963		min_sd->setJ(max_angMom);
964		}
#	Line 734 | Line 983 | namespace OpenMD {
983
984		switch(rnemdFluxType_) {
985		case rnemdKE:
737	–	cerr << "KE\n";
986		kineticExchange_ += max_val - min_val;
987		break;
988		case rnemdPx:
#	Line 747 | Line 995 | namespace OpenMD {
995		momentumExchange_.z() += max_val - min_val;
996		break;
997		default:
750	–	cerr << "default\n";
998		break;
999		}
1000		} else {
#	Line 769 | Line 1016 | namespace OpenMD {
1016		}
1017		}
1018
1019	<	void RNEMD::doNIVS() {
1019	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
1020		if (!doRNEMD_) return;
1021	+	int selei;
1022	+	int selej;
1023	+
1024		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1025		Mat3x3d hmat = currentSnap_->getHmat();
776	–
777	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1026
779	–	int selei;
1027		StuntDouble* sd;
781	–	int idx;
1028
1029		vector<StuntDouble*> hotBin, coldBin;
1030
#	Line 797 | Line 1043 | namespace OpenMD {
1043		RealType Kcz = 0.0;
1044		RealType Kcw = 0.0;
1045
1046	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1047	<	sd = seleMan_.nextSelected(selei)) {
1046	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1047	>	sd = smanA.nextSelected(selei)) {
1048
803	–	idx = sd->getLocalIndex();
804	–
1049		Vector3d pos = sd->getPos();
1050	<
1050	>
1051		// wrap the stuntdouble's position back into the box:
1052	<
1052	>
1053		if (usePeriodicBoundaryConditions_)
1054		currentSnap_->wrapVector(pos);
1055	+
1056	+
1057	+	RealType mass = sd->getMass();
1058	+	Vector3d vel = sd->getVel();
1059	+
1060	+	hotBin.push_back(sd);
1061	+	Phx += mass * vel.x();
1062	+	Phy += mass * vel.y();
1063	+	Phz += mass * vel.z();
1064	+	Khx += mass * vel.x() * vel.x();
1065	+	Khy += mass * vel.y() * vel.y();
1066	+	Khz += mass * vel.z() * vel.z();
1067	+	if (sd->isDirectional()) {
1068	+	Vector3d angMom = sd->getJ();
1069	+	Mat3x3d I = sd->getI();
1070	+	if (sd->isLinear()) {
1071	+	int i = sd->linearAxis();
1072	+	int j = (i + 1) % 3;
1073	+	int k = (i + 2) % 3;
1074	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1075	+	angMom[k] * angMom[k] / I(k, k);
1076	+	} else {
1077	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1078	+	+ angMom[1]*angMom[1]/I(1, 1)
1079	+	+ angMom[2]*angMom[2]/I(2, 2);
1080	+	}
1081	+	}
1082	+	}
1083	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1084	+	sd = smanB.nextSelected(selej)) {
1085	+	Vector3d pos = sd->getPos();
1086	+
1087	+	// wrap the stuntdouble's position back into the box:
1088	+
1089	+	if (usePeriodicBoundaryConditions_)
1090	+	currentSnap_->wrapVector(pos);
1091	+
1092	+	RealType mass = sd->getMass();
1093	+	Vector3d vel = sd->getVel();
1094
1095	<	// which bin is this stuntdouble in?
1096	<	bool inA = inSlabA(pos);
1097	<	bool inB = inSlabB(pos);
1098	<
1099	<	if (inA || inB) {
1100	<
1101	<	RealType mass = sd->getMass();
1102	<	Vector3d vel = sd->getVel();
1103	<
1104	<	if (inA) {
1105	<	hotBin.push_back(sd);
1106	<	Phx += mass * vel.x();
1107	<	Phy += mass * vel.y();
1108	<	Phz += mass * vel.z();
1109	<	Khx += mass * vel.x() * vel.x();
1110	<	Khy += mass * vel.y() * vel.y();
1111	<	Khz += mass * vel.z() * vel.z();
1112	<	if (sd->isDirectional()) {
1113	<	Vector3d angMom = sd->getJ();
1114	<	Mat3x3d I = sd->getI();
1115	<	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();
848	<	Pcz += mass * vel.z();
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	<	}
1095	>	coldBin.push_back(sd);
1096	>	Pcx += mass * vel.x();
1097	>	Pcy += mass * vel.y();
1098	>	Pcz += mass * vel.z();
1099	>	Kcx += mass * vel.x() * vel.x();
1100	>	Kcy += mass * vel.y() * vel.y();
1101	>	Kcz += mass * vel.z() * vel.z();
1102	>	if (sd->isDirectional()) {
1103	>	Vector3d angMom = sd->getJ();
1104	>	Mat3x3d I = sd->getI();
1105	>	if (sd->isLinear()) {
1106	>	int i = sd->linearAxis();
1107	>	int j = (i + 1) % 3;
1108	>	int k = (i + 2) % 3;
1109	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1110	>	angMom[k] * angMom[k] / I(k, k);
1111	>	} else {
1112	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1113	>	+ angMom[1]*angMom[1]/I(1, 1)
1114	>	+ angMom[2]*angMom[2]/I(2, 2);
1115	>	}
1116		}
1117		}
1118
#	Line 878 | Line 1126 | namespace OpenMD {
1126		Kcw *= 0.5;
1127
1128		#ifdef IS_MPI
1129	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1130	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1131	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1132	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1133	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1134	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1129	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1131	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1132	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1133	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1134	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1135
1136	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1137	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1138	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1139	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1136	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1137	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1138	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1139	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1140
1141	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1142	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1143	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1144	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1141	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1142	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1143	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1144	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1145		#endif
1146
1147		//solve coldBin coeff's first
1148		RealType px = Pcx / Phx;
1149		RealType py = Pcy / Phy;
1150		RealType pz = Pcz / Phz;
1151	<	RealType c, x, y, z;
1151	>	RealType c(0.0), x(0.0), y(0.0), z(0.0);
1152		bool successfulScale = false;
1153		if ((rnemdFluxType_ == rnemdFullKE) ||
1154		(rnemdFluxType_ == rnemdRotKE)) {
#	Line 914 | Line 1162 | namespace OpenMD {
1162
1163		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1164		c = sqrt(c);
1165	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
918	<	//now convert to hotBin coefficient
1165	>
1166		RealType w = 0.0;
1167		if (rnemdFluxType_ ==  rnemdFullKE) {
1168		x = 1.0 + px * (1.0 - c);
#	Line 942 | Line 1189 | namespace OpenMD {
1189		//if w is in the right range, so should be x, y, z.
1190		vector<StuntDouble*>::iterator sdi;
1191		Vector3d vel;
1192	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1192	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1193		if (rnemdFluxType_ == rnemdFullKE) {
1194		vel = (*sdi)->getVel() * c;
1195		(*sdi)->setVel(vel);
#	Line 953 | Line 1200 | namespace OpenMD {
1200		}
1201		}
1202		w = sqrt(w);
1203	<	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
957	<	//           << "\twh= " << w << endl;
958	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1203	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1204		if (rnemdFluxType_ == rnemdFullKE) {
1205		vel = (*sdi)->getVel();
1206		vel.x() *= x;
#	Line 973 | Line 1218 | namespace OpenMD {
1218		}
1219		}
1220		} else {
1221	<	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1221	>	RealType a000(0.0), a110(0.0), c0(0.0);
1222	>	RealType a001(0.0), a111(0.0), b01(0.0), b11(0.0), c1(0.0);
1223		switch(rnemdFluxType_) {
1224		case rnemdKE :
1225		/* used hotBin coeff's & only scale x & y dimensions
#	Line 1074 | Line 1320 | namespace OpenMD {
1320		vector<RealType>::iterator ri;
1321		RealType r1, r2, alpha0;
1322		vector<pair<RealType,RealType> > rps;
1323	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1323	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1324		r2 = *ri;
1325	<	//check if FindRealRoots() give the right answer
1325	>	// Check to see if FindRealRoots() gave the right answer:
1326		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1327		sprintf(painCave.errMsg,
1328		"RNEMD Warning: polynomial solve seems to have an error!");
#	Line 1084 | Line 1330 | namespace OpenMD {
1330		simError();
1331		failRootCount_++;
1332		}
1333	<	//might not be useful w/o rescaling coefficients
1333	>	// Might not be useful w/o rescaling coefficients
1334		alpha0 = -c0 - a110 * r2 * r2;
1335		if (alpha0 >= 0.0) {
1336		r1 = sqrt(alpha0 / a000);
#	Line 1099 | Line 1345 | namespace OpenMD {
1345		}
1346		}
1347		}
1348	<	// Consider combining together the solving pair part w/ the searching
1349	<	// best solution part so that we don't need the pairs vector
1348	>	// Consider combining together the part for solving for the pair
1349	>	// w/ the searching for the best solution part so that we don't
1350	>	// need the pairs vector:
1351		if (!rps.empty()) {
1352		RealType smallestDiff = HONKING_LARGE_VALUE;
1353	<	RealType diff;
1354	<	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1355	<	vector<pair<RealType,RealType> >::iterator rpi;
1356	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1353	>	RealType diff(0.0);
1354	>	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1355	>	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1356	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1357		r1 = (*rpi).first;
1358		r2 = (*rpi).second;
1359		switch(rnemdFluxType_) {
#	Line 1173 | Line 1420 | namespace OpenMD {
1420		}
1421		vector<StuntDouble*>::iterator sdi;
1422		Vector3d vel;
1423	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1423	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1424		vel = (*sdi)->getVel();
1425		vel.x() *= x;
1426		vel.y() *= y;
#	Line 1184 | Line 1431 | namespace OpenMD {
1431		x = 1.0 + px * (1.0 - x);
1432		y = 1.0 + py * (1.0 - y);
1433		z = 1.0 + pz * (1.0 - z);
1434	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1434	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1435		vel = (*sdi)->getVel();
1436		vel.x() *= x;
1437		vel.y() *= y;
#	Line 1217 | Line 1464 | namespace OpenMD {
1464		failTrialCount_++;
1465		}
1466		}
1467	<
1468	<	void RNEMD::doVSS() {
1467	>
1468	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1469		if (!doRNEMD_) return;
1470	+	int selei;
1471	+	int selej;
1472	+
1473		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1224	–	RealType time = currentSnap_->getTime();
1474		Mat3x3d hmat = currentSnap_->getHmat();
1475
1227	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1228	–
1229	–	int selei;
1476		StuntDouble* sd;
1231	–	int idx;
1477
1478		vector<StuntDouble*> hotBin, coldBin;
1479
1480		Vector3d Ph(V3Zero);
1481	+	Vector3d Lh(V3Zero);
1482		RealType Mh = 0.0;
1483	+	Mat3x3d Ih(0.0);
1484		RealType Kh = 0.0;
1485		Vector3d Pc(V3Zero);
1486	+	Vector3d Lc(V3Zero);
1487		RealType Mc = 0.0;
1488	+	Mat3x3d Ic(0.0);
1489		RealType Kc = 0.0;
1241	–
1490
1491	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1492	<	sd = seleMan_.nextSelected(selei)) {
1491	>	// Constraints can be on only the linear or angular momentum, but
1492	>	// not both.  Usually, the user will specify which they want, but
1493	>	// in case they don't, the use of periodic boundaries should make
1494	>	// the choice for us.
1495	>	bool doLinearPart = false;
1496	>	bool doAngularPart = false;
1497
1498	<	idx = sd->getLocalIndex();
1498	>	switch (rnemdFluxType_) {
1499	>	case rnemdPx:
1500	>	case rnemdPy:
1501	>	case rnemdPz:
1502	>	case rnemdPvector:
1503	>	case rnemdKePx:
1504	>	case rnemdKePy:
1505	>	case rnemdKePvector:
1506	>	doLinearPart = true;
1507	>	break;
1508	>	case rnemdLx:
1509	>	case rnemdLy:
1510	>	case rnemdLz:
1511	>	case rnemdLvector:
1512	>	case rnemdKeLx:
1513	>	case rnemdKeLy:
1514	>	case rnemdKeLz:
1515	>	case rnemdKeLvector:
1516	>	doAngularPart = true;
1517	>	break;
1518	>	case rnemdKE:
1519	>	case rnemdRotKE:
1520	>	case rnemdFullKE:
1521	>	default:
1522	>	if (usePeriodicBoundaryConditions_)
1523	>	doLinearPart = true;
1524	>	else
1525	>	doAngularPart = true;
1526	>	break;
1527	>	}
1528	>
1529	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1530	>	sd = smanA.nextSelected(selei)) {
1531
1532		Vector3d pos = sd->getPos();
1533
1534		// wrap the stuntdouble's position back into the box:
1535	+
1536	+	if (usePeriodicBoundaryConditions_)
1537	+	currentSnap_->wrapVector(pos);
1538	+
1539	+	RealType mass = sd->getMass();
1540	+	Vector3d vel = sd->getVel();
1541	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1542	+	RealType r2;
1543	+
1544	+	hotBin.push_back(sd);
1545	+	Ph += mass * vel;
1546	+	Mh += mass;
1547	+	Kh += mass * vel.lengthSquare();
1548	+	Lh += mass * cross(rPos, vel);
1549	+	Ih -= outProduct(rPos, rPos) * mass;
1550	+	r2 = rPos.lengthSquare();
1551	+	Ih(0, 0) += mass * r2;
1552	+	Ih(1, 1) += mass * r2;
1553	+	Ih(2, 2) += mass * r2;
1554	+
1555	+	if (rnemdFluxType_ == rnemdFullKE) {
1556	+	if (sd->isDirectional()) {
1557	+	Vector3d angMom = sd->getJ();
1558	+	Mat3x3d I = sd->getI();
1559	+	if (sd->isLinear()) {
1560	+	int i = sd->linearAxis();
1561	+	int j = (i + 1) % 3;
1562	+	int k = (i + 2) % 3;
1563	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1564	+	angMom[k] * angMom[k] / I(k, k);
1565	+	} else {
1566	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1567	+	angMom[1] * angMom[1] / I(1, 1) +
1568	+	angMom[2] * angMom[2] / I(2, 2);
1569	+	}
1570	+	}
1571	+	}
1572	+	}
1573	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1574	+	sd = smanB.nextSelected(selej)) {
1575
1576	+	Vector3d pos = sd->getPos();
1577	+
1578	+	// wrap the stuntdouble's position back into the box:
1579	+
1580		if (usePeriodicBoundaryConditions_)
1581		currentSnap_->wrapVector(pos);
1582	+
1583	+	RealType mass = sd->getMass();
1584	+	Vector3d vel = sd->getVel();
1585	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1586	+	RealType r2;
1587
1588	<	// which bin is this stuntdouble in?
1589	<	bool inA = inSlabA(pos);
1590	<	bool inB = inSlabB(pos);
1588	>	coldBin.push_back(sd);
1589	>	Pc += mass * vel;
1590	>	Mc += mass;
1591	>	Kc += mass * vel.lengthSquare();
1592	>	Lc += mass * cross(rPos, vel);
1593	>	Ic -= outProduct(rPos, rPos) * mass;
1594	>	r2 = rPos.lengthSquare();
1595	>	Ic(0, 0) += mass * r2;
1596	>	Ic(1, 1) += mass * r2;
1597	>	Ic(2, 2) += mass * r2;
1598
1599	<	if (inA || inB) {
1600	<
1601	<	RealType mass = sd->getMass();
1602	<	Vector3d vel = sd->getVel();
1603	<
1604	<	if (inA) {
1605	<	hotBin.push_back(sd);
1606	<	//std::cerr << "before, velocity = " << vel << endl;
1607	<	Ph += mass * vel;
1608	<	//std::cerr << "after, velocity = " << vel << endl;
1609	<	Mh += mass;
1610	<	Kh += mass * vel.lengthSquare();
1611	<	if (rnemdFluxType_ == rnemdFullKE) {
1612	<	if (sd->isDirectional()) {
1613	<	Vector3d angMom = sd->getJ();
1614	<	Mat3x3d I = sd->getI();
1275	<	if (sd->isLinear()) {
1276	<	int i = sd->linearAxis();
1277	<	int j = (i + 1) % 3;
1278	<	int k = (i + 2) % 3;
1279	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1280	<	angMom[k] * angMom[k] / I(k, k);
1281	<	} else {
1282	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1283	<	angMom[1] * angMom[1] / I(1, 1) +
1284	<	angMom[2] * angMom[2] / I(2, 2);
1285	<	}
1286	<	}
1287	<	}
1288	<	} else { //midBin_
1289	<	coldBin.push_back(sd);
1290	<	Pc += mass * vel;
1291	<	Mc += mass;
1292	<	Kc += mass * vel.lengthSquare();
1293	<	if (rnemdFluxType_ == rnemdFullKE) {
1294	<	if (sd->isDirectional()) {
1295	<	Vector3d angMom = sd->getJ();
1296	<	Mat3x3d I = sd->getI();
1297	<	if (sd->isLinear()) {
1298	<	int i = sd->linearAxis();
1299	<	int j = (i + 1) % 3;
1300	<	int k = (i + 2) % 3;
1301	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1302	<	angMom[k] * angMom[k] / I(k, k);
1303	<	} else {
1304	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1305	<	angMom[1] * angMom[1] / I(1, 1) +
1306	<	angMom[2] * angMom[2] / I(2, 2);
1307	<	}
1308	<	}
1309	<	}
1310	<	}
1599	>	if (rnemdFluxType_ == rnemdFullKE) {
1600	>	if (sd->isDirectional()) {
1601	>	Vector3d angMom = sd->getJ();
1602	>	Mat3x3d I = sd->getI();
1603	>	if (sd->isLinear()) {
1604	>	int i = sd->linearAxis();
1605	>	int j = (i + 1) % 3;
1606	>	int k = (i + 2) % 3;
1607	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1608	>	angMom[k] * angMom[k] / I(k, k);
1609	>	} else {
1610	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1611	>	angMom[1] * angMom[1] / I(1, 1) +
1612	>	angMom[2] * angMom[2] / I(2, 2);
1613	>	}
1614	>	}
1615		}
1616		}
1617
1618		Kh *= 0.5;
1619		Kc *= 0.5;
1316	–
1317	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1318	–	//        << "\tKc= " << Kc << endl;
1319	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1620
1621		#ifdef IS_MPI
1622	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1623	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1624	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1625	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1626	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1627	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1622	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1623	>	MPI_COMM_WORLD);
1624	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1625	>	MPI_COMM_WORLD);
1626	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1627	>	MPI_COMM_WORLD);
1628	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1629	>	MPI_COMM_WORLD);
1630	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1631	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1632	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1633	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1634	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1635	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1636	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1637	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1638		#endif
1639	+
1640	+
1641	+	Vector3d ac, acrec, bc, bcrec;
1642	+	Vector3d ah, ahrec, bh, bhrec;
1643
1644		bool successfulExchange = false;
1645		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1646		Vector3d vc = Pc / Mc;
1647	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1648	<	Vector3d acrec = -momentumTarget_ / Mc;
1649	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1647	>	ac = -momentumTarget_ / Mc + vc;
1648	>	acrec = -momentumTarget_ / Mc;
1649	>
1650	>	// We now need the inverse of the inertia tensor to calculate the
1651	>	// angular velocity of the cold slab;
1652	>	Mat3x3d Ici = Ic.inverse();
1653	>	Vector3d omegac = Ici * Lc;
1654	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1655	>	bcrec = bc - omegac;
1656	>
1657	>	RealType cNumerator = Kc - kineticTarget_;
1658	>	if (doLinearPart)
1659	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1660	>
1661	>	if (doAngularPart)
1662	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1663	>
1664		if (cNumerator > 0.0) {
1665	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1665	>
1666	>	RealType cDenominator = Kc;
1667	>
1668	>	if (doLinearPart)
1669	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1670	>
1671	>	if (doAngularPart)
1672	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1673	>
1674		if (cDenominator > 0.0) {
1675		RealType c = sqrt(cNumerator / cDenominator);
1676		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1677	+
1678		Vector3d vh = Ph / Mh;
1679	<	Vector3d ah = momentumTarget_ / Mh + vh;
1680	<	Vector3d ahrec = momentumTarget_ / Mh;
1681	<	RealType hNumerator = Kh + kineticTarget_
1682	<	- 0.5 * Mh * ah.lengthSquare();
1683	<	if (hNumerator > 0.0) {
1684	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1679	>	ah = momentumTarget_ / Mh + vh;
1680	>	ahrec = momentumTarget_ / Mh;
1681	>
1682	>	// We now need the inverse of the inertia tensor to
1683	>	// calculate the angular velocity of the hot slab;
1684	>	Mat3x3d Ihi = Ih.inverse();
1685	>	Vector3d omegah = Ihi * Lh;
1686	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1687	>	bhrec = bh - omegah;
1688	>
1689	>	RealType hNumerator = Kh + kineticTarget_;
1690	>	if (doLinearPart)
1691	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1692	>
1693	>	if (doAngularPart)
1694	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1695	>
1696	>	if (hNumerator > 0.0) {
1697	>
1698	>	RealType hDenominator = Kh;
1699	>	if (doLinearPart)
1700	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1701	>	if (doAngularPart)
1702	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1703	>
1704		if (hDenominator > 0.0) {
1705		RealType h = sqrt(hNumerator / hDenominator);
1706		if ((h > 0.9) && (h < 1.1)) {
1707	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1352	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1707	>
1708		vector<StuntDouble*>::iterator sdi;
1709		Vector3d vel;
1710	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1710	>	Vector3d rPos;
1711	>
1712	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1713		//vel = (*sdi)->getVel();
1714	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1714	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1715	>	if (doLinearPart)
1716	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1717	>	if (doAngularPart)
1718	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1719	>
1720		(*sdi)->setVel(vel);
1721		if (rnemdFluxType_ == rnemdFullKE) {
1722		if ((*sdi)->isDirectional()) {
#	Line 1363 | Line 1725 | namespace OpenMD {
1725		}
1726		}
1727		}
1728	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1728	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1729		//vel = (*sdi)->getVel();
1730	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1730	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1731	>	if (doLinearPart)
1732	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1733	>	if (doAngularPart)
1734	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1735	>
1736		(*sdi)->setVel(vel);
1737		if (rnemdFluxType_ == rnemdFullKE) {
1738		if ((*sdi)->isDirectional()) {
#	Line 1377 | Line 1744 | namespace OpenMD {
1744		successfulExchange = true;
1745		kineticExchange_ += kineticTarget_;
1746		momentumExchange_ += momentumTarget_;
1747	+	angularMomentumExchange_ += angularMomentumTarget_;
1748		}
1749		}
1750		}
#	Line 1396 | Line 1764 | namespace OpenMD {
1764		}
1765		}
1766
1767	+	RealType RNEMD::getDividingArea() {
1768	+
1769	+	if (hasDividingArea_) return dividingArea_;
1770	+
1771	+	RealType areaA, areaB;
1772	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1773	+
1774	+	if (hasSelectionA_) {
1775	+
1776	+	if (evaluatorA_.hasSurfaceArea())
1777	+	areaA = evaluatorA_.getSurfaceArea();
1778	+	else {
1779	+
1780	+	int isd;
1781	+	StuntDouble* sd;
1782	+	vector<StuntDouble*> aSites;
1783	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1784	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1785	+	sd = seleManA_.nextSelected(isd)) {
1786	+	aSites.push_back(sd);
1787	+	}
1788	+	#if defined(HAVE_QHULL)
1789	+	ConvexHull* surfaceMeshA = new ConvexHull();
1790	+	surfaceMeshA->computeHull(aSites);
1791	+	areaA = surfaceMeshA->getArea();
1792	+	delete surfaceMeshA;
1793	+	#else
1794	+	sprintf( painCave.errMsg,
1795	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1796	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1797	+	painCave.severity = OPENMD_ERROR;
1798	+	painCave.isFatal = 1;
1799	+	simError();
1800	+	#endif
1801	+	}
1802	+
1803	+	} else {
1804	+	if (usePeriodicBoundaryConditions_) {
1805	+	// in periodic boundaries, the surface area is twice the x-y
1806	+	// area of the current box:
1807	+	areaA = 2.0 * snap->getXYarea();
1808	+	} else {
1809	+	// in non-periodic simulations, without explicitly setting
1810	+	// selections, the sphere radius sets the surface area of the
1811	+	// dividing surface:
1812	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1813	+	}
1814	+	}
1815	+
1816	+	if (hasSelectionB_) {
1817	+	if (evaluatorB_.hasSurfaceArea()) {
1818	+	areaB = evaluatorB_.getSurfaceArea();
1819	+	} else {
1820	+
1821	+	int isd;
1822	+	StuntDouble* sd;
1823	+	vector<StuntDouble*> bSites;
1824	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1825	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1826	+	sd = seleManB_.nextSelected(isd)) {
1827	+	bSites.push_back(sd);
1828	+	}
1829	+
1830	+	#if defined(HAVE_QHULL)
1831	+	ConvexHull* surfaceMeshB = new ConvexHull();
1832	+	surfaceMeshB->computeHull(bSites);
1833	+	areaB = surfaceMeshB->getArea();
1834	+	delete surfaceMeshB;
1835	+	#else
1836	+	sprintf( painCave.errMsg,
1837	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1838	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1839	+	painCave.severity = OPENMD_ERROR;
1840	+	painCave.isFatal = 1;
1841	+	simError();
1842	+	#endif
1843	+	}
1844	+
1845	+	} else {
1846	+	if (usePeriodicBoundaryConditions_) {
1847	+	// in periodic boundaries, the surface area is twice the x-y
1848	+	// area of the current box:
1849	+	areaB = 2.0 * snap->getXYarea();
1850	+	} else {
1851	+	// in non-periodic simulations, without explicitly setting
1852	+	// selections, but if a sphereBradius has been set, just use that:
1853	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1854	+	}
1855	+	}
1856	+
1857	+	dividingArea_ = min(areaA, areaB);
1858	+	hasDividingArea_ = true;
1859	+	return dividingArea_;
1860	+	}
1861	+
1862		void RNEMD::doRNEMD() {
1863		if (!doRNEMD_) return;
1864		trialCount_++;
1865	+
1866	+	// object evaluator:
1867	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1868	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1869	+
1870	+	evaluatorA_.loadScriptString(selectionA_);
1871	+	evaluatorB_.loadScriptString(selectionB_);
1872	+
1873	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1874	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1875	+
1876	+	commonA_ = seleManA_ & seleMan_;
1877	+	commonB_ = seleManB_ & seleMan_;
1878	+
1879	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1880	+	// dt = exchange time interval
1881	+	// flux = target flux
1882	+	// dividingArea = smallest dividing surface between the two regions
1883	+
1884	+	hasDividingArea_ = false;
1885	+	RealType area = getDividingArea();
1886	+
1887	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1888	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1889	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1890	+
1891		switch(rnemdMethod_) {
1892		case rnemdSwap:
1893	<	doSwap();
1893	>	doSwap(commonA_, commonB_);
1894		break;
1895		case rnemdNIVS:
1896	<	doNIVS();
1896	>	doNIVS(commonA_, commonB_);
1897		break;
1898		case rnemdVSS:
1899	<	doVSS();
1899	>	doVSS(commonA_, commonB_);
1900		break;
1901		case rnemdUnkownMethod:
1902		default :
#	Line 1418 | Line 1907 | namespace OpenMD {
1907		void RNEMD::collectData() {
1908		if (!doRNEMD_) return;
1909		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1910	+
1911	+	// collectData can be called more frequently than the doRNEMD, so use the
1912	+	// computed area from the last exchange time:
1913	+	RealType area = getDividingArea();
1914	+	areaAccumulator_->add(area);
1915		Mat3x3d hmat = currentSnap_->getHmat();
1916	+	Vector3d u = angularMomentumFluxVector_;
1917	+	u.normalize();
1918
1423	–	areaAccumulator_->add(currentSnap_->getXYarea());
1424	–
1919		seleMan_.setSelectionSet(evaluator_.evaluate());
1920
1921	<	int selei;
1921	>	int selei(0);
1922		StuntDouble* sd;
1923	<	int idx;
1923	>	int binNo;
1924	>	RealType mass;
1925	>	Vector3d vel;
1926	>	Vector3d rPos;
1927	>	RealType KE;
1928	>	Vector3d L;
1929	>	Mat3x3d I;
1930	>	RealType r2;
1931
1932		vector<RealType> binMass(nBins_, 0.0);
1933	<	vector<RealType> binPx(nBins_, 0.0);
1934	<	vector<RealType> binPy(nBins_, 0.0);
1935	<	vector<RealType> binPz(nBins_, 0.0);
1933	>	vector<Vector3d> binP(nBins_, V3Zero);
1934	>	vector<RealType> binOmega(nBins_, 0.0);
1935	>	vector<Vector3d> binL(nBins_, V3Zero);
1936	>	vector<Mat3x3d>  binI(nBins_);
1937		vector<RealType> binKE(nBins_, 0.0);
1938		vector<int> binDOF(nBins_, 0);
1939		vector<int> binCount(nBins_, 0);
#	Line 1439 | Line 1941 | namespace OpenMD {
1941		// alternative approach, track all molecules instead of only those
1942		// selected for scaling/swapping:
1943		/*
1944	<	SimInfo::MoleculeIterator miter;
1945	<	vector<StuntDouble*>::iterator iiter;
1946	<	Molecule* mol;
1947	<	StuntDouble* sd;
1948	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1944	>	SimInfo::MoleculeIterator miter;
1945	>	vector<StuntDouble*>::iterator iiter;
1946	>	Molecule* mol;
1947	>	StuntDouble* sd;
1948	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1949		mol = info_->nextMolecule(miter))
1950		sd is essentially sd
1951	<	for (sd = mol->beginIntegrableObject(iiter);
1952	<	sd != NULL;
1953	<	sd = mol->nextIntegrableObject(iiter))
1951	>	for (sd = mol->beginIntegrableObject(iiter);
1952	>	sd != NULL;
1953	>	sd = mol->nextIntegrableObject(iiter))
1954		*/
1955	+
1956		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1957	<	sd = seleMan_.nextSelected(selei)) {
1958	<
1456	<	idx = sd->getLocalIndex();
1457	<
1957	>	sd = seleMan_.nextSelected(selei)) {
1958	>
1959		Vector3d pos = sd->getPos();
1960
1961		// wrap the stuntdouble's position back into the box:
1962
1963	<	if (usePeriodicBoundaryConditions_)
1963	>	if (usePeriodicBoundaryConditions_) {
1964		currentSnap_->wrapVector(pos);
1965	+	// which bin is this stuntdouble in?
1966	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1967	+	// Shift molecules by half a box to have bins start at 0
1968	+	// The modulo operator is used to wrap the case when we are
1969	+	// beyond the end of the bins back to the beginning.
1970	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1971	+	} else {
1972	+	Vector3d rPos = pos - coordinateOrigin_;
1973	+	binNo = int(rPos.length() / binWidth_);
1974	+	}
1975
1976	+	mass = sd->getMass();
1977	+	vel = sd->getVel();
1978	+	rPos = sd->getPos() - coordinateOrigin_;
1979	+	KE = 0.5 * mass * vel.lengthSquare();
1980	+	L = mass * cross(rPos, vel);
1981	+	I = outProduct(rPos, rPos) * mass;
1982	+	r2 = rPos.lengthSquare();
1983	+	I(0, 0) += mass * r2;
1984	+	I(1, 1) += mass * r2;
1985	+	I(2, 2) += mass * r2;
1986
1987	<	// which bin is this stuntdouble in?
1988	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1989	<	// Shift molecules by half a box to have bins start at 0
1990	<	// The modulo operator is used to wrap the case when we are
1991	<	// beyond the end of the bins back to the beginning.
1992	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1993	<
1994	<	RealType mass = sd->getMass();
1995	<	Vector3d vel = sd->getVel();
1987	>	// Project the relative position onto a plane perpendicular to
1988	>	// the angularMomentumFluxVector:
1989	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1990	>	// Project the velocity onto a plane perpendicular to the
1991	>	// angularMomentumFluxVector:
1992	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1993	>	// Compute angular velocity vector (should be nearly parallel to
1994	>	// angularMomentumFluxVector
1995	>	// Vector3d aVel = cross(rProj, vProj);
1996
1997	<	binCount[binNo]++;
1998	<	binMass[binNo] += mass;
1999	<	binPx[binNo] += mass*vel.x();
2000	<	binPy[binNo] += mass*vel.y();
2001	<	binPz[binNo] += mass*vel.z();
2002	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
2003	<	binDOF[binNo] += 3;
2004	<
2005	<	if (sd->isDirectional()) {
2006	<	Vector3d angMom = sd->getJ();
2007	<	Mat3x3d I = sd->getI();
2008	<	if (sd->isLinear()) {
2009	<	int i = sd->linearAxis();
2010	<	int j = (i + 1) % 3;
2011	<	int k = (i + 2) % 3;
2012	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
2013	<	angMom[k] * angMom[k] / I(k, k));
2014	<	binDOF[binNo] += 2;
2015	<	} else {
2016	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
2017	<	angMom[1] * angMom[1] / I(1, 1) +
2018	<	angMom[2] * angMom[2] / I(2, 2));
2019	<	binDOF[binNo] += 3;
1997	>	if (binNo >= 0 && binNo < nBins_)  {
1998	>	binCount[binNo]++;
1999	>	binMass[binNo] += mass;
2000	>	binP[binNo] += mass*vel;
2001	>	binKE[binNo] += KE;
2002	>	binI[binNo] += I;
2003	>	binL[binNo] += L;
2004	>	binDOF[binNo] += 3;
2005	>
2006	>	if (sd->isDirectional()) {
2007	>	Vector3d angMom = sd->getJ();
2008	>	Mat3x3d Ia = sd->getI();
2009	>	if (sd->isLinear()) {
2010	>	int i = sd->linearAxis();
2011	>	int j = (i + 1) % 3;
2012	>	int k = (i + 2) % 3;
2013	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
2014	>	angMom[k] * angMom[k] / Ia(k, k));
2015	>	binDOF[binNo] += 2;
2016	>	} else {
2017	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
2018	>	angMom[1] * angMom[1] / Ia(1, 1) +
2019	>	angMom[2] * angMom[2] / Ia(2, 2));
2020	>	binDOF[binNo] += 3;
2021	>	}
2022		}
2023		}
2024		}
1502	–
2025
2026		#ifdef IS_MPI
2027	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
2028	<	nBins_, MPI::INT, MPI::SUM);
2029	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
2030	<	nBins_, MPI::REALTYPE, MPI::SUM);
2031	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
2032	<	nBins_, MPI::REALTYPE, MPI::SUM);
2033	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
2034	<	nBins_, MPI::REALTYPE, MPI::SUM);
2035	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
2036	<	nBins_, MPI::REALTYPE, MPI::SUM);
2037	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
2038	<	nBins_, MPI::REALTYPE, MPI::SUM);
2039	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
2040	<	nBins_, MPI::INT, MPI::SUM);
2027	>
2028	>	for (int i = 0; i < nBins_; i++) {
2029	>
2030	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
2031	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2032	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2033	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2034	>	MPI_Allreduce(MPI_IN_PLACE, binP[i].getArrayPointer(),
2035	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2036	>	MPI_Allreduce(MPI_IN_PLACE, binL[i].getArrayPointer(),
2037	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2038	>	MPI_Allreduce(MPI_IN_PLACE, binI[i].getArrayPointer(),
2039	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2040	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2041	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2042	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2043	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2044	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2045	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2046	>	}
2047	>
2048		#endif
2049
2050	<	Vector3d vel;
2050	>	Vector3d omega;
2051		RealType den;
2052		RealType temp;
2053		RealType z;
2054	+	RealType r;
2055		for (int i = 0; i < nBins_; i++) {
2056	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2057	<	vel.x() = binPx[i] / binMass[i];
2058	<	vel.y() = binPy[i] / binMass[i];
2059	<	vel.z() = binPz[i] / binMass[i];
2060	<	den = binCount[i] * nBins_ / currentSnap_->getVolume();
2061	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2062	<	PhysicalConstants::energyConvert);
2056	>	if (usePeriodicBoundaryConditions_) {
2057	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2058	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2059	>	/ currentSnap_->getVolume() ;
2060	>	} else {
2061	>	r = (((RealType)i + 0.5) * binWidth_);
2062	>	RealType rinner = (RealType)i * binWidth_;
2063	>	RealType router = (RealType)(i+1) * binWidth_;
2064	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2065	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2066	>	}
2067	>	vel = binP[i] / binMass[i];
2068
2069	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2070	<	if(outputMask_[j]) {
2071	<	switch(j) {
2072	<	case Z:
2073	<	(data_[j].accumulator[i])->add(z);
2074	<	break;
2075	<	case TEMPERATURE:
2076	<	data_[j].accumulator[i]->add(temp);
2077	<	break;
2078	<	case VELOCITY:
2079	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2080	<	break;
2081	<	case DENSITY:
2082	<	data_[j].accumulator[i]->add(den);
2083	<	break;
2069	>	omega = binI[i].inverse() * binL[i];
2070	>
2071	>	// omega = binOmega[i] / binCount[i];
2072	>
2073	>	if (binCount[i] > 0) {
2074	>	// only add values if there are things to add
2075	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2076	>	PhysicalConstants::energyConvert);
2077	>
2078	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2079	>	if(outputMask_[j]) {
2080	>	switch(j) {
2081	>	case Z:
2082	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2083	>	break;
2084	>	case R:
2085	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2086	>	break;
2087	>	case TEMPERATURE:
2088	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2089	>	break;
2090	>	case VELOCITY:
2091	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2092	>	break;
2093	>	case ANGULARVELOCITY:
2094	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2095	>	break;
2096	>	case DENSITY:
2097	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2098	>	break;
2099	>	}
2100		}
2101		}
2102		}
2103		}
2104	+	hasData_ = true;
2105		}
2106
2107		void RNEMD::getStarted() {
2108		if (!doRNEMD_) return;
2109	+	hasDividingArea_ = false;
2110		collectData();
2111		writeOutputFile();
2112		}
#	Line 1576 | Line 2129 | namespace OpenMD {
2129		painCave.severity = OPENMD_ERROR;
2130		simError();
2131		}
2132	<	}
2132	>	}
2133		}
2134
2135		void RNEMD::writeOutputFile() {
2136		if (!doRNEMD_) return;
2137	+	if (!hasData_) return;
2138
2139		#ifdef IS_MPI
2140		// If we're the root node, should we print out the results
2141	<	int worldRank = MPI::COMM_WORLD.Get_rank();
2141	>	int worldRank;
2142	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2143	>
2144		if (worldRank == 0) {
2145		#endif
2146		rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
#	Line 1602 | Line 2158 | namespace OpenMD {
2158		RealType time = currentSnap_->getTime();
2159		RealType avgArea;
2160		areaAccumulator_->getAverage(avgArea);
1605	–	RealType Jz = kineticExchange_ / (2.0 * time * avgArea);
1606	–	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
2161
2162	+	RealType Jz(0.0);
2163	+	Vector3d JzP(V3Zero);
2164	+	Vector3d JzL(V3Zero);
2165	+	if (time >= info_->getSimParams()->getDt()) {
2166	+	Jz = kineticExchange_ / (time * avgArea)
2167	+	/ PhysicalConstants::energyConvert;
2168	+	JzP = momentumExchange_ / (time * avgArea);
2169	+	JzL = angularMomentumExchange_ / (time * avgArea);
2170	+	}
2171	+
2172		rnemdFile_ << "#######################################################\n";
2173		rnemdFile_ << "# RNEMD {\n";
2174
#	Line 1623 | Line 2187 | namespace OpenMD {
2187
2188		rnemdFile_ << "#    objectSelection = \""
2189		<< rnemdObjectSelection_ << "\";\n";
2190	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
2191	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1628	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
2190	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2191	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2192		rnemdFile_ << "# }\n";
2193		rnemdFile_ << "#######################################################\n";
2194		rnemdFile_ << "# RNEMD report:\n";
2195	<	rnemdFile_ << "#     running time = " << time << " fs\n";
2196	<	rnemdFile_ << "#     target flux:\n";
2197	<	rnemdFile_ << "#         kinetic = " << kineticFlux_ << "\n";
2198	<	rnemdFile_ << "#         momentum = " << momentumFluxVector_ << "\n";
2199	<	rnemdFile_ << "#     target one-time exchanges:\n";
2200	<	rnemdFile_ << "#         kinetic = " << kineticTarget_ << "\n";
2201	<	rnemdFile_ << "#         momentum = " << momentumTarget_ << "\n";
2202	<	rnemdFile_ << "#     actual exchange totals:\n";
2203	<	rnemdFile_ << "#         kinetic = " << kineticExchange_ << "\n";
2204	<	rnemdFile_ << "#         momentum = " << momentumExchange_  << "\n";
2205	<	rnemdFile_ << "#     actual flux:\n";
2206	<	rnemdFile_ << "#         kinetic = " << Jz << "\n";
2207	<	rnemdFile_ << "#         momentum = " << JzP  << "\n";
2208	<	rnemdFile_ << "#     exchange statistics:\n";
2209	<	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
2210	<	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
2195	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2196	>	rnemdFile_ << "# Target flux:\n";
2197	>	rnemdFile_ << "#           kinetic = "
2198	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2199	>	<< " (kcal/mol/A^2/fs)\n";
2200	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2201	>	<< " (amu/A/fs^2)\n";
2202	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2203	>	<< " (amu/A^2/fs^2)\n";
2204	>	rnemdFile_ << "# Target one-time exchanges:\n";
2205	>	rnemdFile_ << "#          kinetic = "
2206	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2207	>	<< " (kcal/mol)\n";
2208	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2209	>	<< " (amu*A/fs)\n";
2210	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2211	>	<< " (amu*A^2/fs)\n";
2212	>	rnemdFile_ << "# Actual exchange totals:\n";
2213	>	rnemdFile_ << "#          kinetic = "
2214	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2215	>	<< " (kcal/mol)\n";
2216	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2217	>	<< " (amu*A/fs)\n";
2218	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2219	>	<< " (amu*A^2/fs)\n";
2220	>	rnemdFile_ << "# Actual flux:\n";
2221	>	rnemdFile_ << "#          kinetic = " << Jz
2222	>	<< " (kcal/mol/A^2/fs)\n";
2223	>	rnemdFile_ << "#          momentum = " << JzP
2224	>	<< " (amu/A/fs^2)\n";
2225	>	rnemdFile_ << "#  angular momentum = " << JzL
2226	>	<< " (amu/A^2/fs^2)\n";
2227	>	rnemdFile_ << "# Exchange statistics:\n";
2228	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2229	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2230		if (rnemdMethod_ == rnemdNIVS) {
2231	<	rnemdFile_ << "#         NIVS root-check errors = "
2231	>	rnemdFile_ << "#  NIVS root-check errors = "
2232		<< failRootCount_ << "\n";
2233		}
2234		rnemdFile_ << "#######################################################\n";
#	Line 1659 | Line 2241 | namespace OpenMD {
2241		if (outputMask_[i]) {
2242		rnemdFile_ << "\t" << data_[i].title <<
2243		"(" << data_[i].units << ")";
2244	+	// add some extra tabs for column alignment
2245	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2246		}
2247		}
2248		rnemdFile_ << std::endl;
2249
2250		rnemdFile_.precision(8);
2251
2252	<	for (unsigned int j = 0; j < nBins_; j++) {
2252	>	for (int j = 0; j < nBins_; j++) {
2253
2254		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2255		if (outputMask_[i]) {
2256		if (data_[i].dataType == "RealType")
2257		writeReal(i,j);
2258	<	else if (data_[i].dataType == "Vector3d")
2258	>	else if (data_[i].dataType == "Vector3d")
2259		writeVector(i,j);
2260		else {
2261		sprintf( painCave.errMsg,
#	Line 1687 | Line 2271 | namespace OpenMD {
2271		}
2272
2273		rnemdFile_ << "#######################################################\n";
2274	<	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2274	>	rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2275		rnemdFile_ << "#######################################################\n";
2276
2277
2278	<	for (unsigned int j = 0; j < nBins_; j++) {
2278	>	for (int j = 0; j < nBins_; j++) {
2279		rnemdFile_ << "#";
2280		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2281		if (outputMask_[i]) {
2282		if (data_[i].dataType == "RealType")
2283	<	writeRealStdDev(i,j);
2283	>	writeRealErrorBars(i,j);
2284		else if (data_[i].dataType == "Vector3d")
2285	<	writeVectorStdDev(i,j);
2285	>	writeVectorErrorBars(i,j);
2286		else {
2287		sprintf( painCave.errMsg,
2288		"RNEMD found an unknown data type for: %s ",
#	Line 1724 | Line 2308 | namespace OpenMD {
2308		void RNEMD::writeReal(int index, unsigned int bin) {
2309		if (!doRNEMD_) return;
2310		assert(index >=0 && index < ENDINDEX);
2311	<	assert(bin < nBins_);
2311	>	assert(int(bin) < nBins_);
2312		RealType s;
2313	+	int count;
2314
2315	<	data_[index].accumulator[bin]->getAverage(s);
2315	>	count = data_[index].accumulator[bin]->count();
2316	>	if (count == 0) return;
2317
2318	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2319	+
2320		if (! isinf(s) && ! isnan(s)) {
2321		rnemdFile_ << "\t" << s;
2322		} else{
2323		sprintf( painCave.errMsg,
2324	<	"RNEMD detected a numerical error writing: %s for bin %d",
2324	>	"RNEMD detected a numerical error writing: %s for bin %u",
2325		data_[index].title.c_str(), bin);
2326		painCave.isFatal = 1;
2327		simError();
#	Line 1743 | Line 2331 | namespace OpenMD {
2331		void RNEMD::writeVector(int index, unsigned int bin) {
2332		if (!doRNEMD_) return;
2333		assert(index >=0 && index < ENDINDEX);
2334	<	assert(bin < nBins_);
2334	>	assert(int(bin) < nBins_);
2335		Vector3d s;
2336	+	int count;
2337	+
2338	+	count = data_[index].accumulator[bin]->count();
2339	+
2340	+	if (count == 0) return;
2341	+
2342		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2343		if (isinf(s[0]) || isnan(s[0]) ||
2344		isinf(s[1]) || isnan(s[1]) ||
2345		isinf(s[2]) || isnan(s[2]) ) {
2346		sprintf( painCave.errMsg,
2347	<	"RNEMD detected a numerical error writing: %s for bin %d",
2347	>	"RNEMD detected a numerical error writing: %s for bin %u",
2348		data_[index].title.c_str(), bin);
2349		painCave.isFatal = 1;
2350		simError();
#	Line 1759 | Line 2353 | namespace OpenMD {
2353		}
2354		}
2355
2356	<	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2356	>	void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2357		if (!doRNEMD_) return;
2358		assert(index >=0 && index < ENDINDEX);
2359	<	assert(bin < nBins_);
2359	>	assert(int(bin) < nBins_);
2360		RealType s;
2361	+	int count;
2362
2363	<	data_[index].accumulator[bin]->getStdDev(s);
2363	>	count = data_[index].accumulator[bin]->count();
2364	>	if (count == 0) return;
2365
2366	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2367	+
2368		if (! isinf(s) && ! isnan(s)) {
2369		rnemdFile_ << "\t" << s;
2370		} else{
2371		sprintf( painCave.errMsg,
2372	<	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2372	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2373		data_[index].title.c_str(), bin);
2374		painCave.isFatal = 1;
2375		simError();
2376		}
2377		}
2378
2379	<	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2379	>	void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2380		if (!doRNEMD_) return;
2381		assert(index >=0 && index < ENDINDEX);
2382	<	assert(bin < nBins_);
2382	>	assert(int(bin) < nBins_);
2383		Vector3d s;
2384	<	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2384	>	int count;
2385	>
2386	>	count = data_[index].accumulator[bin]->count();
2387	>	if (count == 0) return;
2388	>
2389	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2390		if (isinf(s[0]) || isnan(s[0]) ||
2391		isinf(s[1]) || isnan(s[1]) ||
2392		isinf(s[2]) || isnan(s[2]) ) {
2393		sprintf( painCave.errMsg,
2394	<	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2394	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2395		data_[index].title.c_str(), bin);
2396		painCave.isFatal = 1;
2397		simError();

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