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

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branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 2068 by gezelter, Thu Mar 5 15:40:58 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 59 | Line 69 | namespace OpenMD {
69		namespace OpenMD {
70
71		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75	+	hasData_(false), hasDividingArea_(false),
76		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
77
78		trialCount_ = 0;
79		failTrialCount_ = 0;
80		failRootCount_ = 0;
81
82	<	int seedValue;
69	<	Globals * simParams = info->getSimParams();
82	>	Globals* simParams = info->getSimParams();
83		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84
85	+	doRNEMD_ = rnemdParams->getUseRNEMD();
86	+	if (!doRNEMD_) return;
87	+
88		stringToMethod_["Swap"]  = rnemdSwap;
89		stringToMethod_["NIVS"]  = rnemdNIVS;
90		stringToMethod_["VSS"]   = rnemdVSS;
#	Line 77 | Line 93 | namespace OpenMD {
93		stringToFluxType_["Px"]  = rnemdPx;
94		stringToFluxType_["Py"]  = rnemdPy;
95		stringToFluxType_["Pz"]  = rnemdPz;
96	+	stringToFluxType_["Pvector"]  = rnemdPvector;
97	+	stringToFluxType_["Lx"]  = rnemdLx;
98	+	stringToFluxType_["Ly"]  = rnemdLy;
99	+	stringToFluxType_["Lz"]  = rnemdLz;
100	+	stringToFluxType_["Lvector"]  = rnemdLvector;
101		stringToFluxType_["KE+Px"]  = rnemdKePx;
102		stringToFluxType_["KE+Py"]  = rnemdKePy;
103		stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
104	+	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
105	+	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
106	+	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
107	+	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
108
109		runTime_ = simParams->getRunTime();
110		statusTime_ = simParams->getStatusTime();
111
87	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88	–	evaluator_.loadScriptString(rnemdObjectSelection_);
89	–	seleMan_.setSelectionSet(evaluator_.evaluate());
90	–
112		const string methStr = rnemdParams->getMethod();
113		bool hasFluxType = rnemdParams->haveFluxType();
114
115	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
116	+
117		string fluxStr;
118		if (hasFluxType) {
119		fluxStr = rnemdParams->getFluxType();
#	Line 98 | Line 121 | namespace OpenMD {
121		sprintf(painCave.errMsg,
122		"RNEMD: No fluxType was set in the md file.  This parameter,\n"
123		"\twhich must be one of the following values:\n"
124	<	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
125	<	"\tuse RNEMD\n");
124	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
125	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
126	>	"\tmust be set to use RNEMD\n");
127		painCave.isFatal = 1;
128		painCave.severity = OPENMD_ERROR;
129		simError();
#	Line 108 | Line 132 | namespace OpenMD {
132		bool hasKineticFlux = rnemdParams->haveKineticFlux();
133		bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
134		bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
135	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
136	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
137	+	hasSelectionA_ = rnemdParams->haveSelectionA();
138	+	hasSelectionB_ = rnemdParams->haveSelectionB();
139		bool hasSlabWidth = rnemdParams->haveSlabWidth();
140		bool hasSlabACenter = rnemdParams->haveSlabACenter();
141		bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
142	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
143	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
144	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
145		bool hasOutputFileName = rnemdParams->haveOutputFileName();
146		bool hasOutputFields = rnemdParams->haveOutputFields();
147
#	Line 195 | Line 226 | namespace OpenMD {
226		case rnemdPz:
227		hasCorrectFlux = hasMomentumFlux;
228		break;
229	+	case rnemdLx:
230	+	case rnemdLy:
231	+	case rnemdLz:
232	+	hasCorrectFlux = hasAngularMomentumFlux;
233	+	break;
234		case rnemdPvector:
235		hasCorrectFlux = hasMomentumFluxVector;
236	+	break;
237	+	case rnemdLvector:
238	+	hasCorrectFlux = hasAngularMomentumFluxVector;
239	+	break;
240		case rnemdKePx:
241		case rnemdKePy:
242		hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
243		break;
244	+	case rnemdKeLx:
245	+	case rnemdKeLy:
246	+	case rnemdKeLz:
247	+	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
248	+	break;
249		case rnemdKePvector:
250		hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
251		break;
252	+	case rnemdKeLvector:
253	+	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
254	+	break;
255		default:
256		methodFluxMismatch = true;
257		break;
#	Line 224 | Line 272 | namespace OpenMD {
272		}
273		if (!hasCorrectFlux) {
274		sprintf(painCave.errMsg,
275	<	"RNEMD: The current method,\n"
228	<	"\t%s, and flux type %s\n"
275	>	"RNEMD: The current method, %s, and flux type, %s,\n"
276		"\tdid not have the correct flux value specified. Options\n"
277	<	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
277	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
278	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
279		methStr.c_str(), fluxStr.c_str());
280		painCave.isFatal = 1;
281		painCave.severity = OPENMD_ERROR;
#	Line 235 | Line 283 | namespace OpenMD {
283		}
284
285		if (hasKineticFlux) {
286	<	kineticFlux_ = rnemdParams->getKineticFlux();
286	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
287	>	// into  amu / fs^3:
288	>	kineticFlux_ = rnemdParams->getKineticFlux()
289	>	* PhysicalConstants::energyConvert;
290		} else {
291		kineticFlux_ = 0.0;
292		}
293		if (hasMomentumFluxVector) {
294	<	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
294	>	std::vector<RealType> mf = rnemdParams->getMomentumFluxVector();
295	>	if (mf.size() != 3) {
296	>	sprintf(painCave.errMsg,
297	>	"RNEMD: Incorrect number of parameters specified for momentumFluxVector.\n"
298	>	"\tthere should be 3 parameters, but %lu were specified.\n",
299	>	mf.size());
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	momentumFluxVector_.x() = mf[0];
304	>	momentumFluxVector_.y() = mf[1];
305	>	momentumFluxVector_.z() = mf[2];
306		} else {
307		momentumFluxVector_ = V3Zero;
308		if (hasMomentumFlux) {
#	Line 264 | Line 326 | namespace OpenMD {
326		default:
327		break;
328		}
329	<	}
329	>	}
330	>	}
331	>	if (hasAngularMomentumFluxVector) {
332	>	std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
333	>	if (amf.size() != 3) {
334	>	sprintf(painCave.errMsg,
335	>	"RNEMD: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
336	>	"\tthere should be 3 parameters, but %lu were specified.\n",
337	>	amf.size());
338	>	painCave.isFatal = 1;
339	>	simError();
340	>	}
341	>	angularMomentumFluxVector_.x() = amf[0];
342	>	angularMomentumFluxVector_.y() = amf[1];
343	>	angularMomentumFluxVector_.z() = amf[2];
344	>	} else {
345	>	angularMomentumFluxVector_ = V3Zero;
346	>	if (hasAngularMomentumFlux) {
347	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
348	>	switch (rnemdFluxType_) {
349	>	case rnemdLx:
350	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
351	>	break;
352	>	case rnemdLy:
353	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
354	>	break;
355	>	case rnemdLz:
356	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
357	>	break;
358	>	case rnemdKeLx:
359	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
360	>	break;
361	>	case rnemdKeLy:
362	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
363	>	break;
364	>	case rnemdKeLz:
365	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
366	>	break;
367	>	default:
368	>	break;
369	>	}
370	>	}
371		}
372
373	+	if (hasCoordinateOrigin) {
374	+	std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
375	+	if (co.size() != 3) {
376	+	sprintf(painCave.errMsg,
377	+	"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
378	+	"\tthere should be 3 parameters, but %lu were specified.\n",
379	+	co.size());
380	+	painCave.isFatal = 1;
381	+	simError();
382	+	}
383	+	coordinateOrigin_.x() = co[0];
384	+	coordinateOrigin_.y() = co[1];
385	+	coordinateOrigin_.z() = co[2];
386	+	} else {
387	+	coordinateOrigin_ = V3Zero;
388	+	}
389	+
390		// do some sanity checking
391	<
392	<	int selectionCount = seleMan_.getSelectionCount();
391	>
392	>	int selectionCount = seleMan_.getSelectionCount();
393		int nIntegrable = info->getNGlobalIntegrableObjects();
274	–
394		if (selectionCount > nIntegrable) {
395		sprintf(painCave.errMsg,
396		"RNEMD: The current objectSelection,\n"
#	Line 287 | Line 406 | namespace OpenMD {
406		painCave.severity = OPENMD_WARNING;
407		simError();
408		}
409	<
409	>
410	>	areaAccumulator_ = new Accumulator();
411	>
412		nBins_ = rnemdParams->getOutputBins();
413	<
413	>	binWidth_ = rnemdParams->getOutputBinWidth();
414	>
415		data_.resize(RNEMD::ENDINDEX);
416		OutputData z;
417		z.units =  "Angstroms";
418		z.title =  "Z";
419		z.dataType = "RealType";
420		z.accumulator.reserve(nBins_);
421	<	for (unsigned int i = 0; i < nBins_; i++)
421	>	for (int i = 0; i < nBins_; i++)
422		z.accumulator.push_back( new Accumulator() );
423		data_[Z] = z;
424		outputMap_["Z"] =  Z;
425	<
425	>
426	>	OutputData r;
427	>	r.units =  "Angstroms";
428	>	r.title =  "R";
429	>	r.dataType = "RealType";
430	>	r.accumulator.reserve(nBins_);
431	>	for (int i = 0; i < nBins_; i++)
432	>	r.accumulator.push_back( new Accumulator() );
433	>	data_[R] = r;
434	>	outputMap_["R"] =  R;
435	>
436		OutputData temperature;
437		temperature.units =  "K";
438		temperature.title =  "Temperature";
439		temperature.dataType = "RealType";
440		temperature.accumulator.reserve(nBins_);
441	<	for (unsigned int i = 0; i < nBins_; i++)
441	>	for (int i = 0; i < nBins_; i++)
442		temperature.accumulator.push_back( new Accumulator() );
443		data_[TEMPERATURE] = temperature;
444		outputMap_["TEMPERATURE"] =  TEMPERATURE;
445	<
445	>
446		OutputData velocity;
447	<	velocity.units = "amu/fs";
447	>	velocity.units = "angstroms/fs";
448		velocity.title =  "Velocity";
449		velocity.dataType = "Vector3d";
450		velocity.accumulator.reserve(nBins_);
451	<	for (unsigned int i = 0; i < nBins_; i++)
451	>	for (int i = 0; i < nBins_; i++)
452		velocity.accumulator.push_back( new VectorAccumulator() );
453		data_[VELOCITY] = velocity;
454		outputMap_["VELOCITY"] = VELOCITY;
455	<
455	>
456	>	OutputData angularVelocity;
457	>	angularVelocity.units = "angstroms^2/fs";
458	>	angularVelocity.title =  "AngularVelocity";
459	>	angularVelocity.dataType = "Vector3d";
460	>	angularVelocity.accumulator.reserve(nBins_);
461	>	for (int i = 0; i < nBins_; i++)
462	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
463	>	data_[ANGULARVELOCITY] = angularVelocity;
464	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
465	>
466		OutputData density;
467		density.units =  "g cm^-3";
468		density.title =  "Density";
469		density.dataType = "RealType";
470		density.accumulator.reserve(nBins_);
471	<	for (unsigned int i = 0; i < nBins_; i++)
471	>	for (int i = 0; i < nBins_; i++)
472		density.accumulator.push_back( new Accumulator() );
473		data_[DENSITY] = density;
474		outputMap_["DENSITY"] =  DENSITY;
475	<
475	>
476		if (hasOutputFields) {
477		parseOutputFileFormat(rnemdParams->getOutputFields());
478		} else {
479	<	outputMask_.set(Z);
479	>	if (usePeriodicBoundaryConditions_)
480	>	outputMask_.set(Z);
481	>	else
482	>	outputMask_.set(R);
483		switch (rnemdFluxType_) {
484		case rnemdKE:
485		case rnemdRotKE:
#	Line 350 | Line 495 | namespace OpenMD {
495		outputMask_.set(VELOCITY);
496		outputMask_.set(DENSITY);
497		break;
498	+	case rnemdLx:
499	+	case rnemdLy:
500	+	case rnemdLz:
501	+	case rnemdLvector:
502	+	outputMask_.set(ANGULARVELOCITY);
503	+	break;
504	+	case rnemdKeLx:
505	+	case rnemdKeLy:
506	+	case rnemdKeLz:
507	+	case rnemdKeLvector:
508	+	outputMask_.set(TEMPERATURE);
509	+	outputMask_.set(ANGULARVELOCITY);
510	+	break;
511		case rnemdKePx:
512		case rnemdKePy:
513		outputMask_.set(TEMPERATURE);
#	Line 364 | Line 522 | namespace OpenMD {
522		break;
523		}
524		}
525	<
525	>
526		if (hasOutputFileName) {
527		rnemdFileName_ = rnemdParams->getOutputFileName();
528		} else {
529		rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
530		}
531	<
531	>
532		exchangeTime_ = rnemdParams->getExchangeTime();
533	<
533	>
534		Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
377	–	Mat3x3d hmat = currentSnap_->getHmat();
378	–
379	–	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
380	–	// Lx, Ly = box dimensions in x & y
381	–	// dt = exchange time interval
382	–	// flux = target flux
383	–
384	–	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
385	–	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
386	–
535		// total exchange sums are zeroed out at the beginning:
536	<
536	>
537		kineticExchange_ = 0.0;
538		momentumExchange_ = V3Zero;
539	<
392	<	if (hasSlabWidth)
393	<	slabWidth_ = rnemdParams->getSlabWidth();
394	<	else
395	<	slabWidth_ = hmat(2,2) / 10.0;
396	<
397	<	if (hasSlabACenter)
398	<	slabACenter_ = rnemdParams->getSlabACenter();
399	<	else
400	<	slabACenter_ = 0.0;
539	>	angularMomentumExchange_ = V3Zero;
540
541	<	if (hasSlabBCenter)
542	<	slabBCenter_ = rnemdParams->getSlabBCenter();
404	<	else
405	<	slabBCenter_ = hmat(2,2) / 2.0;
541	>	std::ostringstream selectionAstream;
542	>	std::ostringstream selectionBstream;
543
544	+	if (hasSelectionA_) {
545	+	selectionA_ = rnemdParams->getSelectionA();
546	+	} else {
547	+	if (usePeriodicBoundaryConditions_) {
548	+	Mat3x3d hmat = currentSnap_->getHmat();
549	+
550	+	if (hasSlabWidth)
551	+	slabWidth_ = rnemdParams->getSlabWidth();
552	+	else
553	+	slabWidth_ = hmat(2,2) / 10.0;
554	+
555	+	if (hasSlabACenter)
556	+	slabACenter_ = rnemdParams->getSlabACenter();
557	+	else
558	+	slabACenter_ = 0.0;
559	+
560	+	selectionAstream << "select wrappedz > "
561	+	<< slabACenter_ - 0.5*slabWidth_
562	+	<<  " && wrappedz < "
563	+	<< slabACenter_ + 0.5*slabWidth_;
564	+	selectionA_ = selectionAstream.str();
565	+	} else {
566	+	if (hasSphereARadius)
567	+	sphereARadius_ = rnemdParams->getSphereARadius();
568	+	else {
569	+	// use an initial guess to the size of the inner slab to be 1/10 the
570	+	// radius of an approximately spherical hull:
571	+	Thermo thermo(info);
572	+	RealType hVol = thermo.getHullVolume();
573	+	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
574	+	}
575	+	selectionAstream << "select r < " << sphereARadius_;
576	+	selectionA_ = selectionAstream.str();
577	+	}
578	+	}
579	+
580	+	if (hasSelectionB_) {
581	+	selectionB_ = rnemdParams->getSelectionB();
582	+
583	+	} else {
584	+	if (usePeriodicBoundaryConditions_) {
585	+	Mat3x3d hmat = currentSnap_->getHmat();
586	+
587	+	if (hasSlabWidth)
588	+	slabWidth_ = rnemdParams->getSlabWidth();
589	+	else
590	+	slabWidth_ = hmat(2,2) / 10.0;
591	+
592	+	if (hasSlabBCenter)
593	+	slabBCenter_ = rnemdParams->getSlabBCenter();
594	+	else
595	+	slabBCenter_ = hmat(2,2) / 2.0;
596	+
597	+	selectionBstream << "select wrappedz > "
598	+	<< slabBCenter_ - 0.5*slabWidth_
599	+	<<  " && wrappedz < "
600	+	<< slabBCenter_ + 0.5*slabWidth_;
601	+	selectionB_ = selectionBstream.str();
602	+	} else {
603	+	if (hasSphereBRadius_) {
604	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
605	+	selectionBstream << "select r > " << sphereBRadius_;
606	+	selectionB_ = selectionBstream.str();
607	+	} else {
608	+	selectionB_ = "select hull";
609	+	BisHull_ = true;
610	+	hasSelectionB_ = true;
611	+	}
612	+	}
613	+	}
614	+
615	+
616	+	// object evaluator:
617	+	evaluator_.loadScriptString(rnemdObjectSelection_);
618	+	seleMan_.setSelectionSet(evaluator_.evaluate());
619	+	evaluatorA_.loadScriptString(selectionA_);
620	+	evaluatorB_.loadScriptString(selectionB_);
621	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
622	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
623	+	commonA_ = seleManA_ & seleMan_;
624	+	commonB_ = seleManB_ & seleMan_;
625		}
626	<
409	<	RNEMD::~RNEMD() {
626	>
627
628	+	RNEMD::~RNEMD() {
629	+	if (!doRNEMD_) return;
630		#ifdef IS_MPI
631		if (worldRank == 0) {
632		#endif
#	Line 419 | Line 638 | namespace OpenMD {
638		#ifdef IS_MPI
639		}
640		#endif
641	+
642	+	// delete all of the objects we created:
643	+	delete areaAccumulator_;
644	+	data_.clear();
645		}
646
647	<	bool RNEMD::inSlabA(Vector3d pos) {
648	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
649	<	}
650	<	bool RNEMD::inSlabB(Vector3d pos) {
428	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	<	}
647	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
648	>	if (!doRNEMD_) return;
649	>	int selei;
650	>	int selej;
651
431	–	void RNEMD::doSwap() {
432	–
652		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
653		Mat3x3d hmat = currentSnap_->getHmat();
654
436	–	seleMan_.setSelectionSet(evaluator_.evaluate());
437	–
438	–	int selei;
655		StuntDouble* sd;
440	–	int idx;
656
657	<	RealType min_val;
658	<	bool min_found = false;
659	<	StuntDouble* min_sd;
657	>	RealType min_val(0.0);
658	>	int min_found = 0;
659	>	StuntDouble* min_sd = NULL;
660
661	<	RealType max_val;
662	<	bool max_found = false;
663	<	StuntDouble* max_sd;
661	>	RealType max_val(0.0);
662	>	int max_found = 0;
663	>	StuntDouble* max_sd = NULL;
664
665	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
666	<	sd = seleMan_.nextSelected(selei)) {
665	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
666	>	sd = seleManA_.nextSelected(selei)) {
667
453	–	idx = sd->getLocalIndex();
454	–
668		Vector3d pos = sd->getPos();
669	<
669	>
670		// wrap the stuntdouble's position back into the box:
671	<
671	>
672		if (usePeriodicBoundaryConditions_)
673		currentSnap_->wrapVector(pos);
674	<	bool inA = inSlabA(pos);
675	<	bool inB = inSlabB(pos);
676	<
677	<	if (inA || inB) {
674	>
675	>	RealType mass = sd->getMass();
676	>	Vector3d vel = sd->getVel();
677	>	RealType value;
678	>
679	>	switch(rnemdFluxType_) {
680	>	case rnemdKE :
681
682	<	RealType mass = sd->getMass();
683	<	Vector3d vel = sd->getVel();
684	<	RealType value;
685	<
686	<	switch(rnemdFluxType_) {
471	<	case rnemdKE :
682	>	value = mass * vel.lengthSquare();
683	>
684	>	if (sd->isDirectional()) {
685	>	Vector3d angMom = sd->getJ();
686	>	Mat3x3d I = sd->getI();
687
688	<	value = mass * vel.lengthSquare();
689	<
690	<	if (sd->isDirectional()) {
691	<	Vector3d angMom = sd->getJ();
692	<	Mat3x3d I = sd->getI();
693	<
694	<	if (sd->isLinear()) {
695	<	int i = sd->linearAxis();
696	<	int j = (i + 1) % 3;
697	<	int k = (i + 2) % 3;
698	<	value += angMom[j] * angMom[j] / I(j, j) +
699	<	angMom[k] * angMom[k] / I(k, k);
700	<	} else {
701	<	value += angMom[0]*angMom[0]/I(0, 0)
702	<	+ angMom[1]*angMom[1]/I(1, 1)
703	<	+ angMom[2]*angMom[2]/I(2, 2);
704	<	}
705	<	} //angular momenta exchange enabled
706	<	//energyConvert temporarily disabled
707	<	//make kineticExchange_ comparable between swap & scale
708	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
709	<	value *= 0.5;
710	<	break;
711	<	case rnemdPx :
712	<	value = mass * vel[0];
713	<	break;
714	<	case rnemdPy :
715	<	value = mass * vel[1];
716	<	break;
717	<	case rnemdPz :
718	<	value = mass * vel[2];
719	<	break;
720	<	default :
721	<	break;
688	>	if (sd->isLinear()) {
689	>	int i = sd->linearAxis();
690	>	int j = (i + 1) % 3;
691	>	int k = (i + 2) % 3;
692	>	value += angMom[j] * angMom[j] / I(j, j) +
693	>	angMom[k] * angMom[k] / I(k, k);
694	>	} else {
695	>	value += angMom[0]*angMom[0]/I(0, 0)
696	>	+ angMom[1]*angMom[1]/I(1, 1)
697	>	+ angMom[2]*angMom[2]/I(2, 2);
698	>	}
699	>	} //angular momenta exchange enabled
700	>	value *= 0.5;
701	>	break;
702	>	case rnemdPx :
703	>	value = mass * vel[0];
704	>	break;
705	>	case rnemdPy :
706	>	value = mass * vel[1];
707	>	break;
708	>	case rnemdPz :
709	>	value = mass * vel[2];
710	>	break;
711	>	default :
712	>	break;
713	>	}
714	>	if (!max_found) {
715	>	max_val = value;
716	>	max_sd = sd;
717	>	max_found = 1;
718	>	} else {
719	>	if (max_val < value) {
720	>	max_val = value;
721	>	max_sd = sd;
722		}
723	+	}
724	+	}
725
726	<	if (inA == 0) {
727	<	if (!min_found) {
728	<	min_val = value;
729	<	min_sd = sd;
730	<	min_found = true;
731	<	} else {
732	<	if (min_val > value) {
733	<	min_val = value;
734	<	min_sd = sd;
735	<	}
736	<	}
737	<	} else {
738	<	if (!max_found) {
739	<	max_val = value;
740	<	max_sd = sd;
741	<	max_found = true;
742	<	} else {
743	<	if (max_val < value) {
744	<	max_val = value;
745	<	max_sd = sd;
746	<	}
747	<	}
748	<	}
726	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
727	>	sd = seleManB_.nextSelected(selej)) {
728	>
729	>	Vector3d pos = sd->getPos();
730	>
731	>	// wrap the stuntdouble's position back into the box:
732	>
733	>	if (usePeriodicBoundaryConditions_)
734	>	currentSnap_->wrapVector(pos);
735	>
736	>	RealType mass = sd->getMass();
737	>	Vector3d vel = sd->getVel();
738	>	RealType value;
739	>
740	>	switch(rnemdFluxType_) {
741	>	case rnemdKE :
742	>
743	>	value = mass * vel.lengthSquare();
744	>
745	>	if (sd->isDirectional()) {
746	>	Vector3d angMom = sd->getJ();
747	>	Mat3x3d I = sd->getI();
748	>
749	>	if (sd->isLinear()) {
750	>	int i = sd->linearAxis();
751	>	int j = (i + 1) % 3;
752	>	int k = (i + 2) % 3;
753	>	value += angMom[j] * angMom[j] / I(j, j) +
754	>	angMom[k] * angMom[k] / I(k, k);
755	>	} else {
756	>	value += angMom[0]*angMom[0]/I(0, 0)
757	>	+ angMom[1]*angMom[1]/I(1, 1)
758	>	+ angMom[2]*angMom[2]/I(2, 2);
759	>	}
760	>	} //angular momenta exchange enabled
761	>	value *= 0.5;
762	>	break;
763	>	case rnemdPx :
764	>	value = mass * vel[0];
765	>	break;
766	>	case rnemdPy :
767	>	value = mass * vel[1];
768	>	break;
769	>	case rnemdPz :
770	>	value = mass * vel[2];
771	>	break;
772	>	default :
773	>	break;
774		}
775	+
776	+	if (!min_found) {
777	+	min_val = value;
778	+	min_sd = sd;
779	+	min_found = 1;
780	+	} else {
781	+	if (min_val > value) {
782	+	min_val = value;
783	+	min_sd = sd;
784	+	}
785	+	}
786		}
787
788	<	#ifdef IS_MPI
789	<	int nProc, worldRank;
790	<
791	<	nProc = MPI::COMM_WORLD.Get_size();
792	<	worldRank = MPI::COMM_WORLD.Get_rank();
788	>	#ifdef IS_MPI
789	>	int worldRank;
790	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
791	>
792	>	int my_min_found = min_found;
793	>	int my_max_found = max_found;
794
541	–	bool my_min_found = min_found;
542	–	bool my_max_found = max_found;
543	–
795		// Even if we didn't find a minimum, did someone else?
796	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
796	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
797	>	MPI_COMM_WORLD);
798		// Even if we didn't find a maximum, did someone else?
799	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
799	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
800	>	MPI_COMM_WORLD);
801		#endif
802
803		if (max_found && min_found) {
#	Line 563 | Line 816 | namespace OpenMD {
816		min_vals.rank = worldRank;
817
818		// Who had the minimum?
819	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
820	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
819	>	MPI_Allreduce(&min_vals, &min_vals,
820	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
821		min_val = min_vals.val;
822
823		if (my_max_found) {
#	Line 575 | Line 828 | namespace OpenMD {
828		max_vals.rank = worldRank;
829
830		// Who had the maximum?
831	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
832	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
831	>	MPI_Allreduce(&max_vals, &max_vals,
832	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
833		max_val = max_vals.val;
834		#endif
835
#	Line 636 | Line 889 | namespace OpenMD {
889
890		Vector3d min_vel;
891		Vector3d max_vel = max_sd->getVel();
892	<	MPI::Status status;
892	>	MPI_Status status;
893
894		// point-to-point swap of the velocity vector
895	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
896	<	min_vals.rank, 0,
897	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
898	<	min_vals.rank, 0, status);
895	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
896	>	min_vals.rank, 0,
897	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
898	>	min_vals.rank, 0, MPI_COMM_WORLD, &status);
899
900		switch(rnemdFluxType_) {
901		case rnemdKE :
#	Line 653 | Line 906 | namespace OpenMD {
906		Vector3d max_angMom = max_sd->getJ();
907
908		// point-to-point swap of the angular momentum vector
909	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
910	<	MPI::REALTYPE, min_vals.rank, 1,
911	<	min_angMom.getArrayPointer(), 3,
912	<	MPI::REALTYPE, min_vals.rank, 1,
913	<	status);
909	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
910	>	MPI_REALTYPE, min_vals.rank, 1,
911	>	min_angMom.getArrayPointer(), 3,
912	>	MPI_REALTYPE, min_vals.rank, 1,
913	>	MPI_COMM_WORLD, &status);
914
915		max_sd->setJ(min_angMom);
916		}
#	Line 682 | Line 935 | namespace OpenMD {
935
936		Vector3d max_vel;
937		Vector3d min_vel = min_sd->getVel();
938	<	MPI::Status status;
938	>	MPI_Status status;
939
940		// point-to-point swap of the velocity vector
941	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
942	<	max_vals.rank, 0,
943	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
944	<	max_vals.rank, 0, status);
941	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
942	>	max_vals.rank, 0,
943	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
944	>	max_vals.rank, 0, MPI_COMM_WORLD, &status);
945
946		switch(rnemdFluxType_) {
947		case rnemdKE :
#	Line 699 | Line 952 | namespace OpenMD {
952		Vector3d max_angMom;
953
954		// point-to-point swap of the angular momentum vector
955	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
956	<	MPI::REALTYPE, max_vals.rank, 1,
957	<	max_angMom.getArrayPointer(), 3,
958	<	MPI::REALTYPE, max_vals.rank, 1,
959	<	status);
955	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
956	>	MPI_REALTYPE, max_vals.rank, 1,
957	>	max_angMom.getArrayPointer(), 3,
958	>	MPI_REALTYPE, max_vals.rank, 1,
959	>	MPI_COMM_WORLD, &status);
960
961		min_sd->setJ(max_angMom);
962		}
#	Line 728 | Line 981 | namespace OpenMD {
981
982		switch(rnemdFluxType_) {
983		case rnemdKE:
731	–	cerr << "KE\n";
984		kineticExchange_ += max_val - min_val;
985		break;
986		case rnemdPx:
#	Line 741 | Line 993 | namespace OpenMD {
993		momentumExchange_.z() += max_val - min_val;
994		break;
995		default:
744	–	cerr << "default\n";
996		break;
997		}
998		} else {
#	Line 763 | Line 1014 | namespace OpenMD {
1014		}
1015		}
1016
1017	<	void RNEMD::doNIVS() {
1017	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
1018	>	if (!doRNEMD_) return;
1019	>	int selei;
1020	>	int selej;
1021
1022		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1023		Mat3x3d hmat = currentSnap_->getHmat();
1024
771	–	seleMan_.setSelectionSet(evaluator_.evaluate());
772	–
773	–	int selei;
1025		StuntDouble* sd;
775	–	int idx;
1026
1027		vector<StuntDouble*> hotBin, coldBin;
1028
#	Line 791 | Line 1041 | namespace OpenMD {
1041		RealType Kcz = 0.0;
1042		RealType Kcw = 0.0;
1043
1044	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1045	<	sd = seleMan_.nextSelected(selei)) {
1044	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1045	>	sd = smanA.nextSelected(selei)) {
1046
797	–	idx = sd->getLocalIndex();
798	–
1047		Vector3d pos = sd->getPos();
1048	<
1048	>
1049		// wrap the stuntdouble's position back into the box:
1050	<
1050	>
1051		if (usePeriodicBoundaryConditions_)
1052		currentSnap_->wrapVector(pos);
1053	+
1054	+
1055	+	RealType mass = sd->getMass();
1056	+	Vector3d vel = sd->getVel();
1057	+
1058	+	hotBin.push_back(sd);
1059	+	Phx += mass * vel.x();
1060	+	Phy += mass * vel.y();
1061	+	Phz += mass * vel.z();
1062	+	Khx += mass * vel.x() * vel.x();
1063	+	Khy += mass * vel.y() * vel.y();
1064	+	Khz += mass * vel.z() * vel.z();
1065	+	if (sd->isDirectional()) {
1066	+	Vector3d angMom = sd->getJ();
1067	+	Mat3x3d I = sd->getI();
1068	+	if (sd->isLinear()) {
1069	+	int i = sd->linearAxis();
1070	+	int j = (i + 1) % 3;
1071	+	int k = (i + 2) % 3;
1072	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1073	+	angMom[k] * angMom[k] / I(k, k);
1074	+	} else {
1075	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1076	+	+ angMom[1]*angMom[1]/I(1, 1)
1077	+	+ angMom[2]*angMom[2]/I(2, 2);
1078	+	}
1079	+	}
1080	+	}
1081	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1082	+	sd = smanB.nextSelected(selej)) {
1083	+	Vector3d pos = sd->getPos();
1084	+
1085	+	// wrap the stuntdouble's position back into the box:
1086	+
1087	+	if (usePeriodicBoundaryConditions_)
1088	+	currentSnap_->wrapVector(pos);
1089	+
1090	+	RealType mass = sd->getMass();
1091	+	Vector3d vel = sd->getVel();
1092
1093	<	// which bin is this stuntdouble in?
1094	<	bool inA = inSlabA(pos);
1095	<	bool inB = inSlabB(pos);
1096	<
1097	<	if (inA || inB) {
1098	<
1099	<	RealType mass = sd->getMass();
1100	<	Vector3d vel = sd->getVel();
1101	<
1102	<	if (inA) {
1103	<	hotBin.push_back(sd);
1104	<	Phx += mass * vel.x();
1105	<	Phy += mass * vel.y();
1106	<	Phz += mass * vel.z();
1107	<	Khx += mass * vel.x() * vel.x();
1108	<	Khy += mass * vel.y() * vel.y();
1109	<	Khz += mass * vel.z() * vel.z();
1110	<	if (sd->isDirectional()) {
1111	<	Vector3d angMom = sd->getJ();
1112	<	Mat3x3d I = sd->getI();
1113	<	if (sd->isLinear()) {
827	<	int i = sd->linearAxis();
828	<	int j = (i + 1) % 3;
829	<	int k = (i + 2) % 3;
830	<	Khw += angMom[j] * angMom[j] / I(j, j) +
831	<	angMom[k] * angMom[k] / I(k, k);
832	<	} else {
833	<	Khw += angMom[0]*angMom[0]/I(0, 0)
834	<	+ angMom[1]*angMom[1]/I(1, 1)
835	<	+ angMom[2]*angMom[2]/I(2, 2);
836	<	}
837	<	}
838	<	} else {
839	<	coldBin.push_back(sd);
840	<	Pcx += mass * vel.x();
841	<	Pcy += mass * vel.y();
842	<	Pcz += mass * vel.z();
843	<	Kcx += mass * vel.x() * vel.x();
844	<	Kcy += mass * vel.y() * vel.y();
845	<	Kcz += mass * vel.z() * vel.z();
846	<	if (sd->isDirectional()) {
847	<	Vector3d angMom = sd->getJ();
848	<	Mat3x3d I = sd->getI();
849	<	if (sd->isLinear()) {
850	<	int i = sd->linearAxis();
851	<	int j = (i + 1) % 3;
852	<	int k = (i + 2) % 3;
853	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
854	<	angMom[k] * angMom[k] / I(k, k);
855	<	} else {
856	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
857	<	+ angMom[1]*angMom[1]/I(1, 1)
858	<	+ angMom[2]*angMom[2]/I(2, 2);
859	<	}
860	<	}
861	<	}
1093	>	coldBin.push_back(sd);
1094	>	Pcx += mass * vel.x();
1095	>	Pcy += mass * vel.y();
1096	>	Pcz += mass * vel.z();
1097	>	Kcx += mass * vel.x() * vel.x();
1098	>	Kcy += mass * vel.y() * vel.y();
1099	>	Kcz += mass * vel.z() * vel.z();
1100	>	if (sd->isDirectional()) {
1101	>	Vector3d angMom = sd->getJ();
1102	>	Mat3x3d I = sd->getI();
1103	>	if (sd->isLinear()) {
1104	>	int i = sd->linearAxis();
1105	>	int j = (i + 1) % 3;
1106	>	int k = (i + 2) % 3;
1107	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1108	>	angMom[k] * angMom[k] / I(k, k);
1109	>	} else {
1110	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1111	>	+ angMom[1]*angMom[1]/I(1, 1)
1112	>	+ angMom[2]*angMom[2]/I(2, 2);
1113	>	}
1114		}
1115		}
1116
#	Line 872 | Line 1124 | namespace OpenMD {
1124		Kcw *= 0.5;
1125
1126		#ifdef IS_MPI
1127	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1128	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1129	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1130	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1131	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1132	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1127	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1128	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1129	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1131	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1132	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1133
1134	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1135	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1136	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1137	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1134	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1135	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1136	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1137	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1138
1139	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1140	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1141	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1142	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1139	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1140	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1141	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1142	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1143		#endif
1144
1145		//solve coldBin coeff's first
#	Line 908 | Line 1160 | namespace OpenMD {
1160
1161		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1162		c = sqrt(c);
1163	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	<	//now convert to hotBin coefficient
1163	>
1164		RealType w = 0.0;
1165		if (rnemdFluxType_ ==  rnemdFullKE) {
1166		x = 1.0 + px * (1.0 - c);
#	Line 936 | Line 1187 | namespace OpenMD {
1187		//if w is in the right range, so should be x, y, z.
1188		vector<StuntDouble*>::iterator sdi;
1189		Vector3d vel;
1190	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1190	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1191		if (rnemdFluxType_ == rnemdFullKE) {
1192		vel = (*sdi)->getVel() * c;
1193		(*sdi)->setVel(vel);
#	Line 947 | Line 1198 | namespace OpenMD {
1198		}
1199		}
1200		w = sqrt(w);
1201	<	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	<	//           << "\twh= " << w << endl;
952	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1201	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1202		if (rnemdFluxType_ == rnemdFullKE) {
1203		vel = (*sdi)->getVel();
1204		vel.x() *= x;
#	Line 1068 | Line 1317 | namespace OpenMD {
1317		vector<RealType>::iterator ri;
1318		RealType r1, r2, alpha0;
1319		vector<pair<RealType,RealType> > rps;
1320	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1320	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1321		r2 = *ri;
1322		//check if FindRealRoots() give the right answer
1323		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1100 | Line 1349 | namespace OpenMD {
1349		RealType diff;
1350		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1351		vector<pair<RealType,RealType> >::iterator rpi;
1352	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1352	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1353		r1 = (*rpi).first;
1354		r2 = (*rpi).second;
1355		switch(rnemdFluxType_) {
#	Line 1167 | Line 1416 | namespace OpenMD {
1416		}
1417		vector<StuntDouble*>::iterator sdi;
1418		Vector3d vel;
1419	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1419	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1420		vel = (*sdi)->getVel();
1421		vel.x() *= x;
1422		vel.y() *= y;
#	Line 1178 | Line 1427 | namespace OpenMD {
1427		x = 1.0 + px * (1.0 - x);
1428		y = 1.0 + py * (1.0 - y);
1429		z = 1.0 + pz * (1.0 - z);
1430	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1430	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1431		vel = (*sdi)->getVel();
1432		vel.x() *= x;
1433		vel.y() *= y;
#	Line 1211 | Line 1460 | namespace OpenMD {
1460		failTrialCount_++;
1461		}
1462		}
1463	<
1464	<	void RNEMD::doVSS() {
1463	>
1464	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1465	>	if (!doRNEMD_) return;
1466	>	int selei;
1467	>	int selej;
1468
1469		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1218	–	RealType time = currentSnap_->getTime();
1470		Mat3x3d hmat = currentSnap_->getHmat();
1471
1221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	–
1223	–	int selei;
1472		StuntDouble* sd;
1225	–	int idx;
1473
1474		vector<StuntDouble*> hotBin, coldBin;
1475
1476		Vector3d Ph(V3Zero);
1477	+	Vector3d Lh(V3Zero);
1478		RealType Mh = 0.0;
1479	+	Mat3x3d Ih(0.0);
1480		RealType Kh = 0.0;
1481		Vector3d Pc(V3Zero);
1482	+	Vector3d Lc(V3Zero);
1483		RealType Mc = 0.0;
1484	+	Mat3x3d Ic(0.0);
1485		RealType Kc = 0.0;
1235	–
1486
1487	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1488	<	sd = seleMan_.nextSelected(selei)) {
1487	>	// Constraints can be on only the linear or angular momentum, but
1488	>	// not both.  Usually, the user will specify which they want, but
1489	>	// in case they don't, the use of periodic boundaries should make
1490	>	// the choice for us.
1491	>	bool doLinearPart = false;
1492	>	bool doAngularPart = false;
1493
1494	<	idx = sd->getLocalIndex();
1494	>	switch (rnemdFluxType_) {
1495	>	case rnemdPx:
1496	>	case rnemdPy:
1497	>	case rnemdPz:
1498	>	case rnemdPvector:
1499	>	case rnemdKePx:
1500	>	case rnemdKePy:
1501	>	case rnemdKePvector:
1502	>	doLinearPart = true;
1503	>	break;
1504	>	case rnemdLx:
1505	>	case rnemdLy:
1506	>	case rnemdLz:
1507	>	case rnemdLvector:
1508	>	case rnemdKeLx:
1509	>	case rnemdKeLy:
1510	>	case rnemdKeLz:
1511	>	case rnemdKeLvector:
1512	>	doAngularPart = true;
1513	>	break;
1514	>	case rnemdKE:
1515	>	case rnemdRotKE:
1516	>	case rnemdFullKE:
1517	>	default:
1518	>	if (usePeriodicBoundaryConditions_)
1519	>	doLinearPart = true;
1520	>	else
1521	>	doAngularPart = true;
1522	>	break;
1523	>	}
1524	>
1525	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1526	>	sd = smanA.nextSelected(selei)) {
1527
1528		Vector3d pos = sd->getPos();
1529
1530		// wrap the stuntdouble's position back into the box:
1531	+
1532	+	if (usePeriodicBoundaryConditions_)
1533	+	currentSnap_->wrapVector(pos);
1534	+
1535	+	RealType mass = sd->getMass();
1536	+	Vector3d vel = sd->getVel();
1537	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1538	+	RealType r2;
1539	+
1540	+	hotBin.push_back(sd);
1541	+	Ph += mass * vel;
1542	+	Mh += mass;
1543	+	Kh += mass * vel.lengthSquare();
1544	+	Lh += mass * cross(rPos, vel);
1545	+	Ih -= outProduct(rPos, rPos) * mass;
1546	+	r2 = rPos.lengthSquare();
1547	+	Ih(0, 0) += mass * r2;
1548	+	Ih(1, 1) += mass * r2;
1549	+	Ih(2, 2) += mass * r2;
1550	+
1551	+	if (rnemdFluxType_ == rnemdFullKE) {
1552	+	if (sd->isDirectional()) {
1553	+	Vector3d angMom = sd->getJ();
1554	+	Mat3x3d I = sd->getI();
1555	+	if (sd->isLinear()) {
1556	+	int i = sd->linearAxis();
1557	+	int j = (i + 1) % 3;
1558	+	int k = (i + 2) % 3;
1559	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1560	+	angMom[k] * angMom[k] / I(k, k);
1561	+	} else {
1562	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1563	+	angMom[1] * angMom[1] / I(1, 1) +
1564	+	angMom[2] * angMom[2] / I(2, 2);
1565	+	}
1566	+	}
1567	+	}
1568	+	}
1569	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1570	+	sd = smanB.nextSelected(selej)) {
1571
1572	+	Vector3d pos = sd->getPos();
1573	+
1574	+	// wrap the stuntdouble's position back into the box:
1575	+
1576		if (usePeriodicBoundaryConditions_)
1577		currentSnap_->wrapVector(pos);
1578	+
1579	+	RealType mass = sd->getMass();
1580	+	Vector3d vel = sd->getVel();
1581	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1582	+	RealType r2;
1583
1584	<	// which bin is this stuntdouble in?
1585	<	bool inA = inSlabA(pos);
1586	<	bool inB = inSlabB(pos);
1584	>	coldBin.push_back(sd);
1585	>	Pc += mass * vel;
1586	>	Mc += mass;
1587	>	Kc += mass * vel.lengthSquare();
1588	>	Lc += mass * cross(rPos, vel);
1589	>	Ic -= outProduct(rPos, rPos) * mass;
1590	>	r2 = rPos.lengthSquare();
1591	>	Ic(0, 0) += mass * r2;
1592	>	Ic(1, 1) += mass * r2;
1593	>	Ic(2, 2) += mass * r2;
1594
1595	<	if (inA || inB) {
1596	<
1597	<	RealType mass = sd->getMass();
1598	<	Vector3d vel = sd->getVel();
1599	<
1600	<	if (inA) {
1601	<	hotBin.push_back(sd);
1602	<	//std::cerr << "before, velocity = " << vel << endl;
1603	<	Ph += mass * vel;
1604	<	//std::cerr << "after, velocity = " << vel << endl;
1605	<	Mh += mass;
1606	<	Kh += mass * vel.lengthSquare();
1607	<	if (rnemdFluxType_ == rnemdFullKE) {
1608	<	if (sd->isDirectional()) {
1609	<	Vector3d angMom = sd->getJ();
1610	<	Mat3x3d I = sd->getI();
1269	<	if (sd->isLinear()) {
1270	<	int i = sd->linearAxis();
1271	<	int j = (i + 1) % 3;
1272	<	int k = (i + 2) % 3;
1273	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1274	<	angMom[k] * angMom[k] / I(k, k);
1275	<	} else {
1276	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1277	<	angMom[1] * angMom[1] / I(1, 1) +
1278	<	angMom[2] * angMom[2] / I(2, 2);
1279	<	}
1280	<	}
1281	<	}
1282	<	} else { //midBin_
1283	<	coldBin.push_back(sd);
1284	<	Pc += mass * vel;
1285	<	Mc += mass;
1286	<	Kc += mass * vel.lengthSquare();
1287	<	if (rnemdFluxType_ == rnemdFullKE) {
1288	<	if (sd->isDirectional()) {
1289	<	Vector3d angMom = sd->getJ();
1290	<	Mat3x3d I = sd->getI();
1291	<	if (sd->isLinear()) {
1292	<	int i = sd->linearAxis();
1293	<	int j = (i + 1) % 3;
1294	<	int k = (i + 2) % 3;
1295	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1296	<	angMom[k] * angMom[k] / I(k, k);
1297	<	} else {
1298	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1299	<	angMom[1] * angMom[1] / I(1, 1) +
1300	<	angMom[2] * angMom[2] / I(2, 2);
1301	<	}
1302	<	}
1303	<	}
1304	<	}
1595	>	if (rnemdFluxType_ == rnemdFullKE) {
1596	>	if (sd->isDirectional()) {
1597	>	Vector3d angMom = sd->getJ();
1598	>	Mat3x3d I = sd->getI();
1599	>	if (sd->isLinear()) {
1600	>	int i = sd->linearAxis();
1601	>	int j = (i + 1) % 3;
1602	>	int k = (i + 2) % 3;
1603	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1604	>	angMom[k] * angMom[k] / I(k, k);
1605	>	} else {
1606	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1607	>	angMom[1] * angMom[1] / I(1, 1) +
1608	>	angMom[2] * angMom[2] / I(2, 2);
1609	>	}
1610	>	}
1611		}
1612		}
1613
1614		Kh *= 0.5;
1615		Kc *= 0.5;
1310	–
1311	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1312	–	//        << "\tKc= " << Kc << endl;
1313	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1616
1617		#ifdef IS_MPI
1618	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1619	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1620	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1621	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1622	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1623	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1618	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1619	>	MPI_COMM_WORLD);
1620	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1621	>	MPI_COMM_WORLD);
1622	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1623	>	MPI_COMM_WORLD);
1624	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1625	>	MPI_COMM_WORLD);
1626	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1627	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1628	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1629	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1630	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1631	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1632	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1633	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1634		#endif
1635	+
1636
1637	+	Vector3d ac, acrec, bc, bcrec;
1638	+	Vector3d ah, ahrec, bh, bhrec;
1639	+
1640		bool successfulExchange = false;
1641		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1642		Vector3d vc = Pc / Mc;
1643	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1644	<	Vector3d acrec = -momentumTarget_ / Mc;
1645	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1643	>	ac = -momentumTarget_ / Mc + vc;
1644	>	acrec = -momentumTarget_ / Mc;
1645	>
1646	>	// We now need the inverse of the inertia tensor to calculate the
1647	>	// angular velocity of the cold slab;
1648	>	Mat3x3d Ici = Ic.inverse();
1649	>	Vector3d omegac = Ici * Lc;
1650	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1651	>	bcrec = bc - omegac;
1652	>
1653	>	RealType cNumerator = Kc - kineticTarget_;
1654	>	if (doLinearPart)
1655	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1656	>
1657	>	if (doAngularPart)
1658	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1659	>
1660		if (cNumerator > 0.0) {
1661	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1661	>
1662	>	RealType cDenominator = Kc;
1663	>
1664	>	if (doLinearPart)
1665	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1666	>
1667	>	if (doAngularPart)
1668	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1669	>
1670		if (cDenominator > 0.0) {
1671		RealType c = sqrt(cNumerator / cDenominator);
1672		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1673	+
1674		Vector3d vh = Ph / Mh;
1675	<	Vector3d ah = momentumTarget_ / Mh + vh;
1676	<	Vector3d ahrec = momentumTarget_ / Mh;
1677	<	RealType hNumerator = Kh + kineticTarget_
1678	<	- 0.5 * Mh * ah.lengthSquare();
1679	<	if (hNumerator > 0.0) {
1680	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1675	>	ah = momentumTarget_ / Mh + vh;
1676	>	ahrec = momentumTarget_ / Mh;
1677	>
1678	>	// We now need the inverse of the inertia tensor to
1679	>	// calculate the angular velocity of the hot slab;
1680	>	Mat3x3d Ihi = Ih.inverse();
1681	>	Vector3d omegah = Ihi * Lh;
1682	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1683	>	bhrec = bh - omegah;
1684	>
1685	>	RealType hNumerator = Kh + kineticTarget_;
1686	>	if (doLinearPart)
1687	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1688	>
1689	>	if (doAngularPart)
1690	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1691	>
1692	>	if (hNumerator > 0.0) {
1693	>
1694	>	RealType hDenominator = Kh;
1695	>	if (doLinearPart)
1696	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1697	>	if (doAngularPart)
1698	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1699	>
1700		if (hDenominator > 0.0) {
1701		RealType h = sqrt(hNumerator / hDenominator);
1702		if ((h > 0.9) && (h < 1.1)) {
1703	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1703	>
1704		vector<StuntDouble*>::iterator sdi;
1705		Vector3d vel;
1706	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1706	>	Vector3d rPos;
1707	>
1708	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1709		//vel = (*sdi)->getVel();
1710	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1710	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1711	>	if (doLinearPart)
1712	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1713	>	if (doAngularPart)
1714	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1715	>
1716		(*sdi)->setVel(vel);
1717		if (rnemdFluxType_ == rnemdFullKE) {
1718		if ((*sdi)->isDirectional()) {
#	Line 1357 | Line 1721 | namespace OpenMD {
1721		}
1722		}
1723		}
1724	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1724	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1725		//vel = (*sdi)->getVel();
1726	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1726	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1727	>	if (doLinearPart)
1728	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1729	>	if (doAngularPart)
1730	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1731	>
1732		(*sdi)->setVel(vel);
1733		if (rnemdFluxType_ == rnemdFullKE) {
1734		if ((*sdi)->isDirectional()) {
#	Line 1371 | Line 1740 | namespace OpenMD {
1740		successfulExchange = true;
1741		kineticExchange_ += kineticTarget_;
1742		momentumExchange_ += momentumTarget_;
1743	+	angularMomentumExchange_ += angularMomentumTarget_;
1744		}
1745		}
1746		}
#	Line 1390 | Line 1760 | namespace OpenMD {
1760		}
1761		}
1762
1763	<	void RNEMD::doRNEMD() {
1763	>	RealType RNEMD::getDividingArea() {
1764
1765	+	if (hasDividingArea_) return dividingArea_;
1766	+
1767	+	RealType areaA, areaB;
1768	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1769	+
1770	+	if (hasSelectionA_) {
1771	+
1772	+	if (evaluatorA_.hasSurfaceArea())
1773	+	areaA = evaluatorA_.getSurfaceArea();
1774	+	else {
1775	+
1776	+	int isd;
1777	+	StuntDouble* sd;
1778	+	vector<StuntDouble*> aSites;
1779	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1780	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1781	+	sd = seleManA_.nextSelected(isd)) {
1782	+	aSites.push_back(sd);
1783	+	}
1784	+	#if defined(HAVE_QHULL)
1785	+	ConvexHull* surfaceMeshA = new ConvexHull();
1786	+	surfaceMeshA->computeHull(aSites);
1787	+	areaA = surfaceMeshA->getArea();
1788	+	delete surfaceMeshA;
1789	+	#else
1790	+	sprintf( painCave.errMsg,
1791	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1792	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1793	+	painCave.severity = OPENMD_ERROR;
1794	+	painCave.isFatal = 1;
1795	+	simError();
1796	+	#endif
1797	+	}
1798	+
1799	+	} else {
1800	+	if (usePeriodicBoundaryConditions_) {
1801	+	// in periodic boundaries, the surface area is twice the x-y
1802	+	// area of the current box:
1803	+	areaA = 2.0 * snap->getXYarea();
1804	+	} else {
1805	+	// in non-periodic simulations, without explicitly setting
1806	+	// selections, the sphere radius sets the surface area of the
1807	+	// dividing surface:
1808	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1809	+	}
1810	+	}
1811	+
1812	+	if (hasSelectionB_) {
1813	+	if (evaluatorB_.hasSurfaceArea()) {
1814	+	areaB = evaluatorB_.getSurfaceArea();
1815	+	} else {
1816	+
1817	+	int isd;
1818	+	StuntDouble* sd;
1819	+	vector<StuntDouble*> bSites;
1820	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1821	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1822	+	sd = seleManB_.nextSelected(isd)) {
1823	+	bSites.push_back(sd);
1824	+	}
1825	+
1826	+	#if defined(HAVE_QHULL)
1827	+	ConvexHull* surfaceMeshB = new ConvexHull();
1828	+	surfaceMeshB->computeHull(bSites);
1829	+	areaB = surfaceMeshB->getArea();
1830	+	delete surfaceMeshB;
1831	+	#else
1832	+	sprintf( painCave.errMsg,
1833	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1834	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1835	+	painCave.severity = OPENMD_ERROR;
1836	+	painCave.isFatal = 1;
1837	+	simError();
1838	+	#endif
1839	+	}
1840	+
1841	+	} else {
1842	+	if (usePeriodicBoundaryConditions_) {
1843	+	// in periodic boundaries, the surface area is twice the x-y
1844	+	// area of the current box:
1845	+	areaB = 2.0 * snap->getXYarea();
1846	+	} else {
1847	+	// in non-periodic simulations, without explicitly setting
1848	+	// selections, but if a sphereBradius has been set, just use that:
1849	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1850	+	}
1851	+	}
1852	+
1853	+	dividingArea_ = min(areaA, areaB);
1854	+	hasDividingArea_ = true;
1855	+	return dividingArea_;
1856	+	}
1857	+
1858	+	void RNEMD::doRNEMD() {
1859	+	if (!doRNEMD_) return;
1860		trialCount_++;
1861	+
1862	+	// object evaluator:
1863	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1864	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1865	+
1866	+	evaluatorA_.loadScriptString(selectionA_);
1867	+	evaluatorB_.loadScriptString(selectionB_);
1868	+
1869	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1870	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1871	+
1872	+	commonA_ = seleManA_ & seleMan_;
1873	+	commonB_ = seleManB_ & seleMan_;
1874	+
1875	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1876	+	// dt = exchange time interval
1877	+	// flux = target flux
1878	+	// dividingArea = smallest dividing surface between the two regions
1879	+
1880	+	hasDividingArea_ = false;
1881	+	RealType area = getDividingArea();
1882	+
1883	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1884	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1885	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1886	+
1887		switch(rnemdMethod_) {
1888		case rnemdSwap:
1889	<	doSwap();
1889	>	doSwap(commonA_, commonB_);
1890		break;
1891		case rnemdNIVS:
1892	<	doNIVS();
1892	>	doNIVS(commonA_, commonB_);
1893		break;
1894		case rnemdVSS:
1895	<	doVSS();
1895	>	doVSS(commonA_, commonB_);
1896		break;
1897		case rnemdUnkownMethod:
1898		default :
#	Line 1410 | Line 1901 | namespace OpenMD {
1901		}
1902
1903		void RNEMD::collectData() {
1904	<
1904	>	if (!doRNEMD_) return;
1905		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1906	+
1907	+	// collectData can be called more frequently than the doRNEMD, so use the
1908	+	// computed area from the last exchange time:
1909	+	RealType area = getDividingArea();
1910	+	areaAccumulator_->add(area);
1911		Mat3x3d hmat = currentSnap_->getHmat();
1912	+	Vector3d u = angularMomentumFluxVector_;
1913	+	u.normalize();
1914
1915		seleMan_.setSelectionSet(evaluator_.evaluate());
1916
1917	<	int selei;
1917	>	int selei(0);
1918		StuntDouble* sd;
1919	<	int idx;
1919	>	int binNo;
1920	>	RealType mass;
1921	>	Vector3d vel;
1922	>	Vector3d rPos;
1923	>	RealType KE;
1924	>	Vector3d L;
1925	>	Mat3x3d I;
1926	>	RealType r2;
1927
1928		vector<RealType> binMass(nBins_, 0.0);
1929	<	vector<RealType> binPx(nBins_, 0.0);
1930	<	vector<RealType> binPy(nBins_, 0.0);
1931	<	vector<RealType> binPz(nBins_, 0.0);
1929	>	vector<Vector3d> binP(nBins_, V3Zero);
1930	>	vector<RealType> binOmega(nBins_, 0.0);
1931	>	vector<Vector3d> binL(nBins_, V3Zero);
1932	>	vector<Mat3x3d>  binI(nBins_);
1933		vector<RealType> binKE(nBins_, 0.0);
1934		vector<int> binDOF(nBins_, 0);
1935		vector<int> binCount(nBins_, 0);
#	Line 1431 | Line 1937 | namespace OpenMD {
1937		// alternative approach, track all molecules instead of only those
1938		// selected for scaling/swapping:
1939		/*
1940	<	SimInfo::MoleculeIterator miter;
1941	<	vector<StuntDouble*>::iterator iiter;
1942	<	Molecule* mol;
1943	<	StuntDouble* sd;
1944	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1940	>	SimInfo::MoleculeIterator miter;
1941	>	vector<StuntDouble*>::iterator iiter;
1942	>	Molecule* mol;
1943	>	StuntDouble* sd;
1944	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1945		mol = info_->nextMolecule(miter))
1946		sd is essentially sd
1947	<	for (sd = mol->beginIntegrableObject(iiter);
1948	<	sd != NULL;
1949	<	sd = mol->nextIntegrableObject(iiter))
1947	>	for (sd = mol->beginIntegrableObject(iiter);
1948	>	sd != NULL;
1949	>	sd = mol->nextIntegrableObject(iiter))
1950		*/
1951	+
1952		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1953	<	sd = seleMan_.nextSelected(selei)) {
1954	<
1448	<	idx = sd->getLocalIndex();
1449	<
1953	>	sd = seleMan_.nextSelected(selei)) {
1954	>
1955		Vector3d pos = sd->getPos();
1956
1957		// wrap the stuntdouble's position back into the box:
1958
1959	<	if (usePeriodicBoundaryConditions_)
1959	>	if (usePeriodicBoundaryConditions_) {
1960		currentSnap_->wrapVector(pos);
1961	+	// which bin is this stuntdouble in?
1962	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1963	+	// Shift molecules by half a box to have bins start at 0
1964	+	// The modulo operator is used to wrap the case when we are
1965	+	// beyond the end of the bins back to the beginning.
1966	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1967	+	} else {
1968	+	Vector3d rPos = pos - coordinateOrigin_;
1969	+	binNo = int(rPos.length() / binWidth_);
1970	+	}
1971
1972	<	// which bin is this stuntdouble in?
1973	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1974	<	// Shift molecules by half a box to have bins start at 0
1975	<	// The modulo operator is used to wrap the case when we are
1976	<	// beyond the end of the bins back to the beginning.
1977	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1978	<
1979	<	RealType mass = sd->getMass();
1980	<	Vector3d vel = sd->getVel();
1972	>	mass = sd->getMass();
1973	>	vel = sd->getVel();
1974	>	rPos = sd->getPos() - coordinateOrigin_;
1975	>	KE = 0.5 * mass * vel.lengthSquare();
1976	>	L = mass * cross(rPos, vel);
1977	>	I = outProduct(rPos, rPos) * mass;
1978	>	r2 = rPos.lengthSquare();
1979	>	I(0, 0) += mass * r2;
1980	>	I(1, 1) += mass * r2;
1981	>	I(2, 2) += mass * r2;
1982
1983	<	binCount[binNo]++;
1984	<	binMass[binNo] += mass;
1985	<	binPx[binNo] += mass*vel.x();
1986	<	binPy[binNo] += mass*vel.y();
1987	<	binPz[binNo] += mass*vel.z();
1988	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1989	<	binDOF[binNo] += 3;
1983	>	// Project the relative position onto a plane perpendicular to
1984	>	// the angularMomentumFluxVector:
1985	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1986	>	// Project the velocity onto a plane perpendicular to the
1987	>	// angularMomentumFluxVector:
1988	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1989	>	// Compute angular velocity vector (should be nearly parallel to
1990	>	// angularMomentumFluxVector
1991	>	// Vector3d aVel = cross(rProj, vProj);
1992
1993	<	if (sd->isDirectional()) {
1994	<	Vector3d angMom = sd->getJ();
1995	<	Mat3x3d I = sd->getI();
1996	<	if (sd->isLinear()) {
1997	<	int i = sd->linearAxis();
1998	<	int j = (i + 1) % 3;
1999	<	int k = (i + 2) % 3;
2000	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
2001	<	angMom[k] * angMom[k] / I(k, k));
2002	<	binDOF[binNo] += 2;
2003	<	} else {
2004	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
2005	<	angMom[1] * angMom[1] / I(1, 1) +
2006	<	angMom[2] * angMom[2] / I(2, 2));
2007	<	binDOF[binNo] += 3;
1993	>	if (binNo >= 0 && binNo < nBins_)  {
1994	>	binCount[binNo]++;
1995	>	binMass[binNo] += mass;
1996	>	binP[binNo] += mass*vel;
1997	>	binKE[binNo] += KE;
1998	>	binI[binNo] += I;
1999	>	binL[binNo] += L;
2000	>	binDOF[binNo] += 3;
2001	>
2002	>	if (sd->isDirectional()) {
2003	>	Vector3d angMom = sd->getJ();
2004	>	Mat3x3d Ia = sd->getI();
2005	>	if (sd->isLinear()) {
2006	>	int i = sd->linearAxis();
2007	>	int j = (i + 1) % 3;
2008	>	int k = (i + 2) % 3;
2009	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
2010	>	angMom[k] * angMom[k] / Ia(k, k));
2011	>	binDOF[binNo] += 2;
2012	>	} else {
2013	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
2014	>	angMom[1] * angMom[1] / Ia(1, 1) +
2015	>	angMom[2] * angMom[2] / Ia(2, 2));
2016	>	binDOF[binNo] += 3;
2017	>	}
2018		}
2019		}
2020		}
1493	–
2021
2022		#ifdef IS_MPI
2023	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
2024	<	nBins_, MPI::INT, MPI::SUM);
2025	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
2026	<	nBins_, MPI::REALTYPE, MPI::SUM);
2027	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
2028	<	nBins_, MPI::REALTYPE, MPI::SUM);
2029	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
2030	<	nBins_, MPI::REALTYPE, MPI::SUM);
2031	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
2032	<	nBins_, MPI::REALTYPE, MPI::SUM);
2033	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
2034	<	nBins_, MPI::REALTYPE, MPI::SUM);
2035	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
2036	<	nBins_, MPI::INT, MPI::SUM);
2023	>
2024	>	for (int i = 0; i < nBins_; i++) {
2025	>
2026	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
2027	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2028	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2029	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2030	>	MPI_Allreduce(MPI_IN_PLACE, binP[i].getArrayPointer(),
2031	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2032	>	MPI_Allreduce(MPI_IN_PLACE, binL[i].getArrayPointer(),
2033	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2034	>	MPI_Allreduce(MPI_IN_PLACE, binI[i].getArrayPointer(),
2035	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2036	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2037	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2038	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2039	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2040	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2041	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2042	>	}
2043	>
2044		#endif
2045
2046	<	Vector3d vel;
2046	>	Vector3d omega;
2047		RealType den;
2048		RealType temp;
2049		RealType z;
2050	+	RealType r;
2051		for (int i = 0; i < nBins_; i++) {
2052	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2053	<	vel.x() = binPx[i] / binMass[i];
2054	<	vel.y() = binPy[i] / binMass[i];
2055	<	vel.z() = binPz[i] / binMass[i];
2056	<	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
2057	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2058	<	PhysicalConstants::energyConvert);
2052	>	if (usePeriodicBoundaryConditions_) {
2053	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2054	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2055	>	/ currentSnap_->getVolume() ;
2056	>	} else {
2057	>	r = (((RealType)i + 0.5) * binWidth_);
2058	>	RealType rinner = (RealType)i * binWidth_;
2059	>	RealType router = (RealType)(i+1) * binWidth_;
2060	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2061	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2062	>	}
2063	>	vel = binP[i] / binMass[i];
2064
2065	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2066	<	if(outputMask_[j]) {
2067	<	switch(j) {
2068	<	case Z:
2069	<	(data_[j].accumulator[i])->add(z);
2070	<	break;
2071	<	case TEMPERATURE:
2072	<	data_[j].accumulator[i]->add(temp);
2073	<	break;
2074	<	case VELOCITY:
2075	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2076	<	break;
2077	<	case DENSITY:
2078	<	data_[j].accumulator[i]->add(den);
2079	<	break;
2065	>	omega = binI[i].inverse() * binL[i];
2066	>
2067	>	// omega = binOmega[i] / binCount[i];
2068	>
2069	>	if (binCount[i] > 0) {
2070	>	// only add values if there are things to add
2071	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2072	>	PhysicalConstants::energyConvert);
2073	>
2074	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2075	>	if(outputMask_[j]) {
2076	>	switch(j) {
2077	>	case Z:
2078	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2079	>	break;
2080	>	case R:
2081	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2082	>	break;
2083	>	case TEMPERATURE:
2084	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2085	>	break;
2086	>	case VELOCITY:
2087	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2088	>	break;
2089	>	case ANGULARVELOCITY:
2090	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2091	>	break;
2092	>	case DENSITY:
2093	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2094	>	break;
2095	>	}
2096		}
2097		}
2098		}
2099		}
2100	+	hasData_ = true;
2101		}
2102
2103		void RNEMD::getStarted() {
2104	+	if (!doRNEMD_) return;
2105	+	hasDividingArea_ = false;
2106		collectData();
2107		writeOutputFile();
2108		}
2109
2110		void RNEMD::parseOutputFileFormat(const std::string& format) {
2111	+	if (!doRNEMD_) return;
2112		StringTokenizer tokenizer(format, " ,;|\t\n\r");
2113
2114		while(tokenizer.hasMoreTokens()) {
#	Line 1565 | Line 2125 | namespace OpenMD {
2125		painCave.severity = OPENMD_ERROR;
2126		simError();
2127		}
2128	<	}
2128	>	}
2129		}
2130
2131		void RNEMD::writeOutputFile() {
2132	+	if (!doRNEMD_) return;
2133	+	if (!hasData_) return;
2134
2135		#ifdef IS_MPI
2136		// If we're the root node, should we print out the results
2137	<	int worldRank = MPI::COMM_WORLD.Get_rank();
2137	>	int worldRank;
2138	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2139	>
2140		if (worldRank == 0) {
2141		#endif
2142		rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
#	Line 1588 | Line 2152 | namespace OpenMD {
2152		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2153
2154		RealType time = currentSnap_->getTime();
2155	<
2156	<
2155	>	RealType avgArea;
2156	>	areaAccumulator_->getAverage(avgArea);
2157	>
2158	>	RealType Jz(0.0);
2159	>	Vector3d JzP(V3Zero);
2160	>	Vector3d JzL(V3Zero);
2161	>	if (time >= info_->getSimParams()->getDt()) {
2162	>	Jz = kineticExchange_ / (time * avgArea)
2163	>	/ PhysicalConstants::energyConvert;
2164	>	JzP = momentumExchange_ / (time * avgArea);
2165	>	JzL = angularMomentumExchange_ / (time * avgArea);
2166	>	}
2167	>
2168		rnemdFile_ << "#######################################################\n";
2169		rnemdFile_ << "# RNEMD {\n";
2170
2171		map<string, RNEMDMethod>::iterator mi;
2172		for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2173		if ( (*mi).second == rnemdMethod_)
2174	<	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
2174	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2175		}
2176		map<string, RNEMDFluxType>::iterator fi;
2177		for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2178		if ( (*fi).second == rnemdFluxType_)
2179	<	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
2179	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2180		}
2181
2182	<	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
2182	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2183
2184		rnemdFile_ << "#    objectSelection = \""
2185	<	<< rnemdObjectSelection_ << "\"\n";
2186	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
2187	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
2185	>	<< rnemdObjectSelection_ << "\";\n";
2186	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2187	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2188		rnemdFile_ << "# }\n";
2189		rnemdFile_ << "#######################################################\n";
2190	<
2191	<	rnemdFile_ << "# running time = " << time << " fs\n";
2192	<	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
2193	<	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
2194	<
2195	<	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
2196	<	<< "\n";
2197	<	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
2198	<	<< "\n";
2199	<
2200	<	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
2201	<	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
2202	<	<< "\n";
2203	<
2204	<	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
2205	<	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
2206	<
2207	<
2190	>	rnemdFile_ << "# RNEMD report:\n";
2191	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2192	>	rnemdFile_ << "# Target flux:\n";
2193	>	rnemdFile_ << "#           kinetic = "
2194	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2195	>	<< " (kcal/mol/A^2/fs)\n";
2196	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2197	>	<< " (amu/A/fs^2)\n";
2198	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2199	>	<< " (amu/A^2/fs^2)\n";
2200	>	rnemdFile_ << "# Target one-time exchanges:\n";
2201	>	rnemdFile_ << "#          kinetic = "
2202	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2203	>	<< " (kcal/mol)\n";
2204	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2205	>	<< " (amu*A/fs)\n";
2206	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2207	>	<< " (amu*A^2/fs)\n";
2208	>	rnemdFile_ << "# Actual exchange totals:\n";
2209	>	rnemdFile_ << "#          kinetic = "
2210	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2211	>	<< " (kcal/mol)\n";
2212	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2213	>	<< " (amu*A/fs)\n";
2214	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2215	>	<< " (amu*A^2/fs)\n";
2216	>	rnemdFile_ << "# Actual flux:\n";
2217	>	rnemdFile_ << "#          kinetic = " << Jz
2218	>	<< " (kcal/mol/A^2/fs)\n";
2219	>	rnemdFile_ << "#          momentum = " << JzP
2220	>	<< " (amu/A/fs^2)\n";
2221	>	rnemdFile_ << "#  angular momentum = " << JzL
2222	>	<< " (amu/A^2/fs^2)\n";
2223	>	rnemdFile_ << "# Exchange statistics:\n";
2224	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2225	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2226		if (rnemdMethod_ == rnemdNIVS) {
2227	<	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
2227	>	rnemdFile_ << "#  NIVS root-check errors = "
2228	>	<< failRootCount_ << "\n";
2229		}
1637	–
2230		rnemdFile_ << "#######################################################\n";
2231
2232
#	Line 1645 | Line 2237 | namespace OpenMD {
2237		if (outputMask_[i]) {
2238		rnemdFile_ << "\t" << data_[i].title <<
2239		"(" << data_[i].units << ")";
2240	+	// add some extra tabs for column alignment
2241	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2242		}
2243		}
2244		rnemdFile_ << std::endl;
2245
2246		rnemdFile_.precision(8);
2247
2248	<	for (unsigned int j = 0; j < nBins_; j++) {
2248	>	for (int j = 0; j < nBins_; j++) {
2249
2250		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2251		if (outputMask_[i]) {
2252		if (data_[i].dataType == "RealType")
2253		writeReal(i,j);
2254	<	else if (data_[i].dataType == "Vector3d")
2254	>	else if (data_[i].dataType == "Vector3d")
2255		writeVector(i,j);
2256		else {
2257		sprintf( painCave.errMsg,
#	Line 1671 | Line 2265 | namespace OpenMD {
2265		rnemdFile_ << std::endl;
2266
2267		}
2268	+
2269	+	rnemdFile_ << "#######################################################\n";
2270	+	rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2271	+	rnemdFile_ << "#######################################################\n";
2272	+
2273	+
2274	+	for (int j = 0; j < nBins_; j++) {
2275	+	rnemdFile_ << "#";
2276	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2277	+	if (outputMask_[i]) {
2278	+	if (data_[i].dataType == "RealType")
2279	+	writeRealErrorBars(i,j);
2280	+	else if (data_[i].dataType == "Vector3d")
2281	+	writeVectorErrorBars(i,j);
2282	+	else {
2283	+	sprintf( painCave.errMsg,
2284	+	"RNEMD found an unknown data type for: %s ",
2285	+	data_[i].title.c_str());
2286	+	painCave.isFatal = 1;
2287	+	simError();
2288	+	}
2289	+	}
2290	+	}
2291	+	rnemdFile_ << std::endl;
2292	+
2293	+	}
2294
2295		rnemdFile_.flush();
2296		rnemdFile_.close();
#	Line 1682 | Line 2302 | namespace OpenMD {
2302		}
2303
2304		void RNEMD::writeReal(int index, unsigned int bin) {
2305	+	if (!doRNEMD_) return;
2306		assert(index >=0 && index < ENDINDEX);
2307	<	assert(bin >=0 && bin < nBins_);
2307	>	assert(int(bin) < nBins_);
2308		RealType s;
2309	+	int count;
2310
2311	<	data_[index].accumulator[bin]->getAverage(s);
2311	>	count = data_[index].accumulator[bin]->count();
2312	>	if (count == 0) return;
2313
2314	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2315	+
2316		if (! isinf(s) && ! isnan(s)) {
2317		rnemdFile_ << "\t" << s;
2318		} else{
2319		sprintf( painCave.errMsg,
2320	<	"RNEMD detected a numerical error writing: %s for bin %d",
2320	>	"RNEMD detected a numerical error writing: %s for bin %u",
2321		data_[index].title.c_str(), bin);
2322		painCave.isFatal = 1;
2323		simError();
#	Line 1700 | Line 2325 | namespace OpenMD {
2325		}
2326
2327		void RNEMD::writeVector(int index, unsigned int bin) {
2328	+	if (!doRNEMD_) return;
2329		assert(index >=0 && index < ENDINDEX);
2330	<	assert(bin >=0 && bin < nBins_);
2330	>	assert(int(bin) < nBins_);
2331		Vector3d s;
2332	+	int count;
2333	+
2334	+	count = data_[index].accumulator[bin]->count();
2335	+
2336	+	if (count == 0) return;
2337	+
2338		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2339		if (isinf(s[0]) || isnan(s[0]) ||
2340		isinf(s[1]) || isnan(s[1]) ||
2341		isinf(s[2]) || isnan(s[2]) ) {
2342		sprintf( painCave.errMsg,
2343	<	"RNEMD detected a numerical error writing: %s for bin %d",
2343	>	"RNEMD detected a numerical error writing: %s for bin %u",
2344		data_[index].title.c_str(), bin);
2345		painCave.isFatal = 1;
2346		simError();
#	Line 1716 | Line 2348 | namespace OpenMD {
2348		rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2349		}
2350		}
2351	+
2352	+	void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2353	+	if (!doRNEMD_) return;
2354	+	assert(index >=0 && index < ENDINDEX);
2355	+	assert(int(bin) < nBins_);
2356	+	RealType s;
2357	+	int count;
2358	+
2359	+	count = data_[index].accumulator[bin]->count();
2360	+	if (count == 0) return;
2361	+
2362	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2363	+
2364	+	if (! isinf(s) && ! isnan(s)) {
2365	+	rnemdFile_ << "\t" << s;
2366	+	} else{
2367	+	sprintf( painCave.errMsg,
2368	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2369	+	data_[index].title.c_str(), bin);
2370	+	painCave.isFatal = 1;
2371	+	simError();
2372	+	}
2373	+	}
2374	+
2375	+	void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2376	+	if (!doRNEMD_) return;
2377	+	assert(index >=0 && index < ENDINDEX);
2378	+	assert(int(bin) < nBins_);
2379	+	Vector3d s;
2380	+	int count;
2381	+
2382	+	count = data_[index].accumulator[bin]->count();
2383	+	if (count == 0) return;
2384	+
2385	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2386	+	if (isinf(s[0]) || isnan(s[0]) ||
2387	+	isinf(s[1]) || isnan(s[1]) ||
2388	+	isinf(s[2]) || isnan(s[2]) ) {
2389	+	sprintf( painCave.errMsg,
2390	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2391	+	data_[index].title.c_str(), bin);
2392	+	painCave.isFatal = 1;
2393	+	simError();
2394	+	} else {
2395	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2396	+	}
2397	+	}
2398		}
2399

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