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

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1813 by gezelter, Fri Nov 16 21:39:55 2012 UTC vs.
Revision 1876 by gezelter, Fri May 17 17:10:11 2013 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
42		#include <cmath>
43	+	#include <sstream>
44	+	#include <string>
45	+
46		#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48		#include "math/Vector.hpp"
#	Line 49 | Line 52
52		#include "primitives/StuntDouble.hpp"
53		#include "utils/PhysicalConstants.hpp"
54		#include "utils/Tuple.hpp"
55	+	#include "brains/Thermo.hpp"
56	+	#include "math/ConvexHull.hpp"
57		#ifdef IS_MPI
58		#include <mpi.h>
59		#endif
#	Line 64 | 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	<	Globals * simParams = info->getSimParams();
82	>	Globals* simParams = info->getSimParams();
83		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84
85		doRNEMD_ = rnemdParams->getUseRNEMD();
#	Line 85 | Line 94 | namespace OpenMD {
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
95	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
96	–	evaluator_.loadScriptString(rnemdObjectSelection_);
97	–	seleMan_.setSelectionSet(evaluator_.evaluate());
98	–
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 106 | 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, Pvector, KE+Px, KE+Py, KE+Pvector\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;
#	Line 116 | 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 203 | 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 235 | Line 274 | namespace OpenMD {
274		sprintf(painCave.errMsg,
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 275 | Line 315 | namespace OpenMD {
315		default:
316		break;
317		}
318	<	}
319	<	}
318	>	}
319	>	if (hasAngularMomentumFluxVector) {
320	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
321	>	} else {
322	>	angularMomentumFluxVector_ = V3Zero;
323	>	if (hasAngularMomentumFlux) {
324	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
325	>	switch (rnemdFluxType_) {
326	>	case rnemdLx:
327	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
328	>	break;
329	>	case rnemdLy:
330	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
331	>	break;
332	>	case rnemdLz:
333	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
334	>	break;
335	>	case rnemdKeLx:
336	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
337	>	break;
338	>	case rnemdKeLy:
339	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
340	>	break;
341	>	case rnemdKeLz:
342	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
343	>	break;
344	>	default:
345	>	break;
346	>	}
347	>	}
348	>	}
349
350	<	// do some sanity checking
350	>	if (hasCoordinateOrigin) {
351	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
352	>	} else {
353	>	coordinateOrigin_ = V3Zero;
354	>	}
355
356	<	int selectionCount = seleMan_.getSelectionCount();
356	>	// do some sanity checking
357
358	<	int nIntegrable = info->getNGlobalIntegrableObjects();
358	>	int selectionCount = seleMan_.getSelectionCount();
359
360	<	if (selectionCount > nIntegrable) {
288	<	sprintf(painCave.errMsg,
289	<	"RNEMD: The current objectSelection,\n"
290	<	"\t\t%s\n"
291	<	"\thas resulted in %d selected objects.  However,\n"
292	<	"\tthe total number of integrable objects in the system\n"
293	<	"\tis only %d.  This is almost certainly not what you want\n"
294	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
295	<	"\tselector in the selection script!\n",
296	<	rnemdObjectSelection_.c_str(),
297	<	selectionCount, nIntegrable);
298	<	painCave.isFatal = 0;
299	<	painCave.severity = OPENMD_WARNING;
300	<	simError();
301	<	}
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361
362	<	areaAccumulator_ = new Accumulator();
362	>	if (selectionCount > nIntegrable) {
363	>	sprintf(painCave.errMsg,
364	>	"RNEMD: The current objectSelection,\n"
365	>	"\t\t%s\n"
366	>	"\thas resulted in %d selected objects.  However,\n"
367	>	"\tthe total number of integrable objects in the system\n"
368	>	"\tis only %d.  This is almost certainly not what you want\n"
369	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
370	>	"\tselector in the selection script!\n",
371	>	rnemdObjectSelection_.c_str(),
372	>	selectionCount, nIntegrable);
373	>	painCave.isFatal = 0;
374	>	painCave.severity = OPENMD_WARNING;
375	>	simError();
376	>	}
377
378	<	nBins_ = rnemdParams->getOutputBins();
378	>	areaAccumulator_ = new Accumulator();
379
380	<	data_.resize(RNEMD::ENDINDEX);
381	<	OutputData z;
309	<	z.units =  "Angstroms";
310	<	z.title =  "Z";
311	<	z.dataType = "RealType";
312	<	z.accumulator.reserve(nBins_);
313	<	for (int i = 0; i < nBins_; i++)
314	<	z.accumulator.push_back( new Accumulator() );
315	<	data_[Z] = z;
316	<	outputMap_["Z"] =  Z;
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382
383	<	OutputData temperature;
384	<	temperature.units =  "K";
385	<	temperature.title =  "Temperature";
386	<	temperature.dataType = "RealType";
387	<	temperature.accumulator.reserve(nBins_);
388	<	for (int i = 0; i < nBins_; i++)
389	<	temperature.accumulator.push_back( new Accumulator() );
390	<	data_[TEMPERATURE] = temperature;
391	<	outputMap_["TEMPERATURE"] =  TEMPERATURE;
383	>	data_.resize(RNEMD::ENDINDEX);
384	>	OutputData z;
385	>	z.units =  "Angstroms";
386	>	z.title =  "Z";
387	>	z.dataType = "RealType";
388	>	z.accumulator.reserve(nBins_);
389	>	for (int i = 0; i < nBins_; i++)
390	>	z.accumulator.push_back( new Accumulator() );
391	>	data_[Z] = z;
392	>	outputMap_["Z"] =  Z;
393
394	<	OutputData velocity;
395	<	velocity.units = "angstroms/fs";
396	<	velocity.title =  "Velocity";
397	<	velocity.dataType = "Vector3d";
398	<	velocity.accumulator.reserve(nBins_);
399	<	for (int i = 0; i < nBins_; i++)
400	<	velocity.accumulator.push_back( new VectorAccumulator() );
401	<	data_[VELOCITY] = velocity;
402	<	outputMap_["VELOCITY"] = VELOCITY;
337	<
338	<	OutputData density;
339	<	density.units =  "g cm^-3";
340	<	density.title =  "Density";
341	<	density.dataType = "RealType";
342	<	density.accumulator.reserve(nBins_);
343	<	for (int i = 0; i < nBins_; i++)
344	<	density.accumulator.push_back( new Accumulator() );
345	<	data_[DENSITY] = density;
346	<	outputMap_["DENSITY"] =  DENSITY;
394	>	OutputData r;
395	>	r.units =  "Angstroms";
396	>	r.title =  "R";
397	>	r.dataType = "RealType";
398	>	r.accumulator.reserve(nBins_);
399	>	for (int i = 0; i < nBins_; i++)
400	>	r.accumulator.push_back( new Accumulator() );
401	>	data_[R] = r;
402	>	outputMap_["R"] =  R;
403
404	<	if (hasOutputFields) {
405	<	parseOutputFileFormat(rnemdParams->getOutputFields());
406	<	} else {
407	<	outputMask_.set(Z);
408	<	switch (rnemdFluxType_) {
409	<	case rnemdKE:
410	<	case rnemdRotKE:
411	<	case rnemdFullKE:
412	<	outputMask_.set(TEMPERATURE);
357	<	break;
358	<	case rnemdPx:
359	<	case rnemdPy:
360	<	outputMask_.set(VELOCITY);
361	<	break;
362	<	case rnemdPz:
363	<	case rnemdPvector:
364	<	outputMask_.set(VELOCITY);
365	<	outputMask_.set(DENSITY);
366	<	break;
367	<	case rnemdKePx:
368	<	case rnemdKePy:
369	<	outputMask_.set(TEMPERATURE);
370	<	outputMask_.set(VELOCITY);
371	<	break;
372	<	case rnemdKePvector:
373	<	outputMask_.set(TEMPERATURE);
374	<	outputMask_.set(VELOCITY);
375	<	outputMask_.set(DENSITY);
376	<	break;
377	<	default:
378	<	break;
379	<	}
380	<	}
381	<
382	<	if (hasOutputFileName) {
383	<	rnemdFileName_ = rnemdParams->getOutputFileName();
384	<	} else {
385	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
386	<	}
404	>	OutputData temperature;
405	>	temperature.units =  "K";
406	>	temperature.title =  "Temperature";
407	>	temperature.dataType = "RealType";
408	>	temperature.accumulator.reserve(nBins_);
409	>	for (int i = 0; i < nBins_; i++)
410	>	temperature.accumulator.push_back( new Accumulator() );
411	>	data_[TEMPERATURE] = temperature;
412	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
413
414	<	exchangeTime_ = rnemdParams->getExchangeTime();
414	>	OutputData velocity;
415	>	velocity.units = "angstroms/fs";
416	>	velocity.title =  "Velocity";
417	>	velocity.dataType = "Vector3d";
418	>	velocity.accumulator.reserve(nBins_);
419	>	for (int i = 0; i < nBins_; i++)
420	>	velocity.accumulator.push_back( new VectorAccumulator() );
421	>	data_[VELOCITY] = velocity;
422	>	outputMap_["VELOCITY"] = VELOCITY;
423
424	<	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
425	<	Mat3x3d hmat = currentSnap_->getHmat();
426	<
427	<	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
428	<	// Lx, Ly = box dimensions in x & y
429	<	// dt = exchange time interval
430	<	// flux = target flux
424	>	OutputData angularVelocity;
425	>	angularVelocity.units = "angstroms^2/fs";
426	>	angularVelocity.title =  "AngularVelocity";
427	>	angularVelocity.dataType = "Vector3d";
428	>	angularVelocity.accumulator.reserve(nBins_);
429	>	for (int i = 0; i < nBins_; i++)
430	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
431	>	data_[ANGULARVELOCITY] = angularVelocity;
432	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
433
434	<	RealType area = currentSnap_->getXYarea();
435	<	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
436	<	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
434	>	OutputData density;
435	>	density.units =  "g cm^-3";
436	>	density.title =  "Density";
437	>	density.dataType = "RealType";
438	>	density.accumulator.reserve(nBins_);
439	>	for (int i = 0; i < nBins_; i++)
440	>	density.accumulator.push_back( new Accumulator() );
441	>	data_[DENSITY] = density;
442	>	outputMap_["DENSITY"] =  DENSITY;
443
444	<	// total exchange sums are zeroed out at the beginning:
444	>	if (hasOutputFields) {
445	>	parseOutputFileFormat(rnemdParams->getOutputFields());
446	>	} else {
447	>	if (usePeriodicBoundaryConditions_)
448	>	outputMask_.set(Z);
449	>	else
450	>	outputMask_.set(R);
451	>	switch (rnemdFluxType_) {
452	>	case rnemdKE:
453	>	case rnemdRotKE:
454	>	case rnemdFullKE:
455	>	outputMask_.set(TEMPERATURE);
456	>	break;
457	>	case rnemdPx:
458	>	case rnemdPy:
459	>	outputMask_.set(VELOCITY);
460	>	break;
461	>	case rnemdPz:
462	>	case rnemdPvector:
463	>	outputMask_.set(VELOCITY);
464	>	outputMask_.set(DENSITY);
465	>	break;
466	>	case rnemdLx:
467	>	case rnemdLy:
468	>	case rnemdLz:
469	>	case rnemdLvector:
470	>	outputMask_.set(ANGULARVELOCITY);
471	>	break;
472	>	case rnemdKeLx:
473	>	case rnemdKeLy:
474	>	case rnemdKeLz:
475	>	case rnemdKeLvector:
476	>	outputMask_.set(TEMPERATURE);
477	>	outputMask_.set(ANGULARVELOCITY);
478	>	break;
479	>	case rnemdKePx:
480	>	case rnemdKePy:
481	>	outputMask_.set(TEMPERATURE);
482	>	outputMask_.set(VELOCITY);
483	>	break;
484	>	case rnemdKePvector:
485	>	outputMask_.set(TEMPERATURE);
486	>	outputMask_.set(VELOCITY);
487	>	outputMask_.set(DENSITY);
488	>	break;
489	>	default:
490	>	break;
491	>	}
492	>	}
493	>
494	>	if (hasOutputFileName) {
495	>	rnemdFileName_ = rnemdParams->getOutputFileName();
496	>	} else {
497	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	>	}
499
500	<	kineticExchange_ = 0.0;
405	<	momentumExchange_ = V3Zero;
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501
502	<	if (hasSlabWidth)
503	<	slabWidth_ = rnemdParams->getSlabWidth();
504	<	else
505	<	slabWidth_ = hmat(2,2) / 10.0;
506	<
507	<	if (hasSlabACenter)
508	<	slabACenter_ = rnemdParams->getSlabACenter();
509	<	else
510	<	slabACenter_ = 0.0;
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504	>
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508	>
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511
512	<	if (hasSlabBCenter)
513	<	slabBCenter_ = rnemdParams->getSlabBCenter();
514	<	else
515	<	slabBCenter_ = hmat(2,2) / 2.0;
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547
548	+	if (hasSelectionB_) {
549	+	selectionB_ = rnemdParams->getSelectionB();
550	+	} else {
551	+	if (usePeriodicBoundaryConditions_) {
552	+	Mat3x3d hmat = currentSnap_->getHmat();
553	+
554	+	if (hasSlabWidth)
555	+	slabWidth_ = rnemdParams->getSlabWidth();
556	+	else
557	+	slabWidth_ = hmat(2,2) / 10.0;
558	+
559	+	if (hasSlabBCenter)
560	+	slabBCenter_ = rnemdParams->getSlabBCenter();
561	+	else
562	+	slabBCenter_ = hmat(2,2) / 2.0;
563	+
564	+	selectionBstream << "select wrappedz > "
565	+	<< slabBCenter_ - 0.5*slabWidth_
566	+	<<  " && wrappedz < "
567	+	<< slabBCenter_ + 0.5*slabWidth_;
568	+	selectionB_ = selectionBstream.str();
569	+	} else {
570	+	if (hasSphereBRadius_) {
571	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
572	+	selectionBstream << "select r > " << sphereBRadius_;
573	+	selectionB_ = selectionBstream.str();
574	+	} else {
575	+	selectionB_ = "select hull";
576	+	hasSelectionB_ = true;
577	+	}
578	+	}
579	+	}
580	+	}
581	+
582	+	// object evaluator:
583	+	evaluator_.loadScriptString(rnemdObjectSelection_);
584	+	seleMan_.setSelectionSet(evaluator_.evaluate());
585	+	evaluatorA_.loadScriptString(selectionA_);
586	+	evaluatorB_.loadScriptString(selectionB_);
587	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	+	commonA_ = seleManA_ & seleMan_;
590	+	commonB_ = seleManB_ & seleMan_;
591		}
592	<
592	>
593	>
594		RNEMD::~RNEMD() {
595		if (!doRNEMD_) return;
596		#ifdef IS_MPI
#	Line 434 | Line 604 | namespace OpenMD {
604		#ifdef IS_MPI
605		}
606		#endif
607	+
608	+	// delete all of the objects we created:
609	+	delete areaAccumulator_;
610	+	data_.clear();
611		}
612
613	<	bool RNEMD::inSlabA(Vector3d pos) {
440	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
441	<	}
442	<	bool RNEMD::inSlabB(Vector3d pos) {
443	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
444	<	}
445	<
446	<	void RNEMD::doSwap() {
613	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
614		if (!doRNEMD_) return;
615	+	int selei;
616	+	int selej;
617	+
618		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
619		Mat3x3d hmat = currentSnap_->getHmat();
620
451	–	seleMan_.setSelectionSet(evaluator_.evaluate());
452	–
453	–	int selei;
621		StuntDouble* sd;
622
623		RealType min_val;
#	Line 461 | Line 628 | namespace OpenMD {
628		bool max_found = false;
629		StuntDouble* max_sd;
630
631	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
632	<	sd = seleMan_.nextSelected(selei)) {
631	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
632	>	sd = seleManA_.nextSelected(selei)) {
633
634		Vector3d pos = sd->getPos();
635	<
635	>
636		// wrap the stuntdouble's position back into the box:
637	<
637	>
638		if (usePeriodicBoundaryConditions_)
639		currentSnap_->wrapVector(pos);
640	<	bool inA = inSlabA(pos);
641	<	bool inB = inSlabB(pos);
642	<
643	<	if (inA || inB) {
640	>
641	>	RealType mass = sd->getMass();
642	>	Vector3d vel = sd->getVel();
643	>	RealType value;
644	>
645	>	switch(rnemdFluxType_) {
646	>	case rnemdKE :
647
648	<	RealType mass = sd->getMass();
649	<	Vector3d vel = sd->getVel();
650	<	RealType value;
651	<
652	<	switch(rnemdFluxType_) {
483	<	case rnemdKE :
648	>	value = mass * vel.lengthSquare();
649	>
650	>	if (sd->isDirectional()) {
651	>	Vector3d angMom = sd->getJ();
652	>	Mat3x3d I = sd->getI();
653
654	<	value = mass * vel.lengthSquare();
655	<
656	<	if (sd->isDirectional()) {
657	<	Vector3d angMom = sd->getJ();
658	<	Mat3x3d I = sd->getI();
659	<
660	<	if (sd->isLinear()) {
661	<	int i = sd->linearAxis();
662	<	int j = (i + 1) % 3;
663	<	int k = (i + 2) % 3;
664	<	value += angMom[j] * angMom[j] / I(j, j) +
665	<	angMom[k] * angMom[k] / I(k, k);
666	<	} else {
667	<	value += angMom[0]*angMom[0]/I(0, 0)
668	<	+ angMom[1]*angMom[1]/I(1, 1)
669	<	+ angMom[2]*angMom[2]/I(2, 2);
670	<	}
671	<	} //angular momenta exchange enabled
672	<	value *= 0.5;
673	<	break;
674	<	case rnemdPx :
675	<	value = mass * vel[0];
676	<	break;
677	<	case rnemdPy :
678	<	value = mass * vel[1];
679	<	break;
680	<	case rnemdPz :
681	<	value = mass * vel[2];
682	<	break;
683	<	default :
684	<	break;
654	>	if (sd->isLinear()) {
655	>	int i = sd->linearAxis();
656	>	int j = (i + 1) % 3;
657	>	int k = (i + 2) % 3;
658	>	value += angMom[j] * angMom[j] / I(j, j) +
659	>	angMom[k] * angMom[k] / I(k, k);
660	>	} else {
661	>	value += angMom[0]*angMom[0]/I(0, 0)
662	>	+ angMom[1]*angMom[1]/I(1, 1)
663	>	+ angMom[2]*angMom[2]/I(2, 2);
664	>	}
665	>	} //angular momenta exchange enabled
666	>	value *= 0.5;
667	>	break;
668	>	case rnemdPx :
669	>	value = mass * vel[0];
670	>	break;
671	>	case rnemdPy :
672	>	value = mass * vel[1];
673	>	break;
674	>	case rnemdPz :
675	>	value = mass * vel[2];
676	>	break;
677	>	default :
678	>	break;
679	>	}
680	>	if (!max_found) {
681	>	max_val = value;
682	>	max_sd = sd;
683	>	max_found = true;
684	>	} else {
685	>	if (max_val < value) {
686	>	max_val = value;
687	>	max_sd = sd;
688		}
689	+	}
690	+	}
691
692	<	if (inA == 0) {
693	<	if (!min_found) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	min_found = true;
697	<	} else {
698	<	if (min_val > value) {
699	<	min_val = value;
700	<	min_sd = sd;
701	<	}
702	<	}
703	<	} else {
704	<	if (!max_found) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	max_found = true;
708	<	} else {
709	<	if (max_val < value) {
710	<	max_val = value;
711	<	max_sd = sd;
712	<	}
713	<	}
714	<	}
692	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
693	>	sd = seleManB_.nextSelected(selej)) {
694	>
695	>	Vector3d pos = sd->getPos();
696	>
697	>	// wrap the stuntdouble's position back into the box:
698	>
699	>	if (usePeriodicBoundaryConditions_)
700	>	currentSnap_->wrapVector(pos);
701	>
702	>	RealType mass = sd->getMass();
703	>	Vector3d vel = sd->getVel();
704	>	RealType value;
705	>
706	>	switch(rnemdFluxType_) {
707	>	case rnemdKE :
708	>
709	>	value = mass * vel.lengthSquare();
710	>
711	>	if (sd->isDirectional()) {
712	>	Vector3d angMom = sd->getJ();
713	>	Mat3x3d I = sd->getI();
714	>
715	>	if (sd->isLinear()) {
716	>	int i = sd->linearAxis();
717	>	int j = (i + 1) % 3;
718	>	int k = (i + 2) % 3;
719	>	value += angMom[j] * angMom[j] / I(j, j) +
720	>	angMom[k] * angMom[k] / I(k, k);
721	>	} else {
722	>	value += angMom[0]*angMom[0]/I(0, 0)
723	>	+ angMom[1]*angMom[1]/I(1, 1)
724	>	+ angMom[2]*angMom[2]/I(2, 2);
725	>	}
726	>	} //angular momenta exchange enabled
727	>	value *= 0.5;
728	>	break;
729	>	case rnemdPx :
730	>	value = mass * vel[0];
731	>	break;
732	>	case rnemdPy :
733	>	value = mass * vel[1];
734	>	break;
735	>	case rnemdPz :
736	>	value = mass * vel[2];
737	>	break;
738	>	default :
739	>	break;
740		}
741	+
742	+	if (!min_found) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	min_found = true;
746	+	} else {
747	+	if (min_val > value) {
748	+	min_val = value;
749	+	min_sd = sd;
750	+	}
751	+	}
752		}
753
754		#ifdef IS_MPI
#	Line 767 | Line 977 | namespace OpenMD {
977		}
978		}
979
980	<	void RNEMD::doNIVS() {
980	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
981		if (!doRNEMD_) return;
982	+	int selei;
983	+	int selej;
984	+
985		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
986	+	RealType time = currentSnap_->getTime();
987		Mat3x3d hmat = currentSnap_->getHmat();
988
775	–	seleMan_.setSelectionSet(evaluator_.evaluate());
776	–
777	–	int selei;
989		StuntDouble* sd;
990
991		vector<StuntDouble*> hotBin, coldBin;
#	Line 794 | Line 1005 | namespace OpenMD {
1005		RealType Kcz = 0.0;
1006		RealType Kcw = 0.0;
1007
1008	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1009	<	sd = seleMan_.nextSelected(selei)) {
1008	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1009	>	sd = smanA.nextSelected(selei)) {
1010
1011		Vector3d pos = sd->getPos();
1012	<
1012	>
1013		// wrap the stuntdouble's position back into the box:
1014	<
1014	>
1015		if (usePeriodicBoundaryConditions_)
1016		currentSnap_->wrapVector(pos);
1017	<
1018	<	// which bin is this stuntdouble in?
1019	<	bool inA = inSlabA(pos);
1020	<	bool inB = inSlabB(pos);
1017	>
1018	>
1019	>	RealType mass = sd->getMass();
1020	>	Vector3d vel = sd->getVel();
1021	>
1022	>	hotBin.push_back(sd);
1023	>	Phx += mass * vel.x();
1024	>	Phy += mass * vel.y();
1025	>	Phz += mass * vel.z();
1026	>	Khx += mass * vel.x() * vel.x();
1027	>	Khy += mass * vel.y() * vel.y();
1028	>	Khz += mass * vel.z() * vel.z();
1029	>	if (sd->isDirectional()) {
1030	>	Vector3d angMom = sd->getJ();
1031	>	Mat3x3d I = sd->getI();
1032	>	if (sd->isLinear()) {
1033	>	int i = sd->linearAxis();
1034	>	int j = (i + 1) % 3;
1035	>	int k = (i + 2) % 3;
1036	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1037	>	angMom[k] * angMom[k] / I(k, k);
1038	>	} else {
1039	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1040	>	+ angMom[1]*angMom[1]/I(1, 1)
1041	>	+ angMom[2]*angMom[2]/I(2, 2);
1042	>	}
1043	>	}
1044	>	}
1045	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1046	>	sd = smanB.nextSelected(selej)) {
1047	>	Vector3d pos = sd->getPos();
1048	>
1049	>	// wrap the stuntdouble's position back into the box:
1050	>
1051	>	if (usePeriodicBoundaryConditions_)
1052	>	currentSnap_->wrapVector(pos);
1053	>
1054	>	RealType mass = sd->getMass();
1055	>	Vector3d vel = sd->getVel();
1056
1057	<	if (inA || inB) {
1058	<
1059	<	RealType mass = sd->getMass();
1060	<	Vector3d vel = sd->getVel();
1061	<
1062	<	if (inA) {
1063	<	hotBin.push_back(sd);
1064	<	Phx += mass * vel.x();
1065	<	Phy += mass * vel.y();
1066	<	Phz += mass * vel.z();
1067	<	Khx += mass * vel.x() * vel.x();
1068	<	Khy += mass * vel.y() * vel.y();
1069	<	Khz += mass * vel.z() * vel.z();
1070	<	if (sd->isDirectional()) {
1071	<	Vector3d angMom = sd->getJ();
1072	<	Mat3x3d I = sd->getI();
1073	<	if (sd->isLinear()) {
1074	<	int i = sd->linearAxis();
1075	<	int j = (i + 1) % 3;
1076	<	int k = (i + 2) % 3;
1077	<	Khw += angMom[j] * angMom[j] / I(j, j) +
832	<	angMom[k] * angMom[k] / I(k, k);
833	<	} else {
834	<	Khw += angMom[0]*angMom[0]/I(0, 0)
835	<	+ angMom[1]*angMom[1]/I(1, 1)
836	<	+ angMom[2]*angMom[2]/I(2, 2);
837	<	}
838	<	}
839	<	} else {
840	<	coldBin.push_back(sd);
841	<	Pcx += mass * vel.x();
842	<	Pcy += mass * vel.y();
843	<	Pcz += mass * vel.z();
844	<	Kcx += mass * vel.x() * vel.x();
845	<	Kcy += mass * vel.y() * vel.y();
846	<	Kcz += mass * vel.z() * vel.z();
847	<	if (sd->isDirectional()) {
848	<	Vector3d angMom = sd->getJ();
849	<	Mat3x3d I = sd->getI();
850	<	if (sd->isLinear()) {
851	<	int i = sd->linearAxis();
852	<	int j = (i + 1) % 3;
853	<	int k = (i + 2) % 3;
854	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
855	<	angMom[k] * angMom[k] / I(k, k);
856	<	} else {
857	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
858	<	+ angMom[1]*angMom[1]/I(1, 1)
859	<	+ angMom[2]*angMom[2]/I(2, 2);
860	<	}
861	<	}
862	<	}
1057	>	coldBin.push_back(sd);
1058	>	Pcx += mass * vel.x();
1059	>	Pcy += mass * vel.y();
1060	>	Pcz += mass * vel.z();
1061	>	Kcx += mass * vel.x() * vel.x();
1062	>	Kcy += mass * vel.y() * vel.y();
1063	>	Kcz += mass * vel.z() * vel.z();
1064	>	if (sd->isDirectional()) {
1065	>	Vector3d angMom = sd->getJ();
1066	>	Mat3x3d I = sd->getI();
1067	>	if (sd->isLinear()) {
1068	>	int i = sd->linearAxis();
1069	>	int j = (i + 1) % 3;
1070	>	int k = (i + 2) % 3;
1071	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1072	>	angMom[k] * angMom[k] / I(k, k);
1073	>	} else {
1074	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1075	>	+ angMom[1]*angMom[1]/I(1, 1)
1076	>	+ angMom[2]*angMom[2]/I(2, 2);
1077	>	}
1078		}
1079		}
1080
#	Line 936 | Line 1151 | namespace OpenMD {
1151		//if w is in the right range, so should be x, y, z.
1152		vector<StuntDouble*>::iterator sdi;
1153		Vector3d vel;
1154	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1154	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1155		if (rnemdFluxType_ == rnemdFullKE) {
1156		vel = (*sdi)->getVel() * c;
1157		(*sdi)->setVel(vel);
#	Line 947 | Line 1162 | namespace OpenMD {
1162		}
1163		}
1164		w = sqrt(w);
1165	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1165	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1166		if (rnemdFluxType_ == rnemdFullKE) {
1167		vel = (*sdi)->getVel();
1168		vel.x() *= x;
#	Line 1066 | Line 1281 | namespace OpenMD {
1281		vector<RealType>::iterator ri;
1282		RealType r1, r2, alpha0;
1283		vector<pair<RealType,RealType> > rps;
1284	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1284	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1285		r2 = *ri;
1286		//check if FindRealRoots() give the right answer
1287		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1098 | Line 1313 | namespace OpenMD {
1313		RealType diff;
1314		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1315		vector<pair<RealType,RealType> >::iterator rpi;
1316	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1316	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1317		r1 = (*rpi).first;
1318		r2 = (*rpi).second;
1319		switch(rnemdFluxType_) {
#	Line 1165 | Line 1380 | namespace OpenMD {
1380		}
1381		vector<StuntDouble*>::iterator sdi;
1382		Vector3d vel;
1383	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1383	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1384		vel = (*sdi)->getVel();
1385		vel.x() *= x;
1386		vel.y() *= y;
#	Line 1176 | Line 1391 | namespace OpenMD {
1391		x = 1.0 + px * (1.0 - x);
1392		y = 1.0 + py * (1.0 - y);
1393		z = 1.0 + pz * (1.0 - z);
1394	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1394	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1395		vel = (*sdi)->getVel();
1396		vel.x() *= x;
1397		vel.y() *= y;
#	Line 1209 | Line 1424 | namespace OpenMD {
1424		failTrialCount_++;
1425		}
1426		}
1427	<
1428	<	void RNEMD::doVSS() {
1427	>
1428	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1429		if (!doRNEMD_) return;
1430	+	int selei;
1431	+	int selej;
1432	+
1433		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1434		RealType time = currentSnap_->getTime();
1435		Mat3x3d hmat = currentSnap_->getHmat();
1436
1219	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1220	–
1221	–	int selei;
1437		StuntDouble* sd;
1438
1439		vector<StuntDouble*> hotBin, coldBin;
1440
1441		Vector3d Ph(V3Zero);
1442	+	Vector3d Lh(V3Zero);
1443		RealType Mh = 0.0;
1444	+	Mat3x3d Ih(0.0);
1445		RealType Kh = 0.0;
1446		Vector3d Pc(V3Zero);
1447	+	Vector3d Lc(V3Zero);
1448		RealType Mc = 0.0;
1449	+	Mat3x3d Ic(0.0);
1450		RealType Kc = 0.0;
1232	–
1451
1452	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453	<	sd = seleMan_.nextSelected(selei)) {
1452	>	// Constraints can be on only the linear or angular momentum, but
1453	>	// not both.  Usually, the user will specify which they want, but
1454	>	// in case they don't, the use of periodic boundaries should make
1455	>	// the choice for us.
1456	>	bool doLinearPart = false;
1457	>	bool doAngularPart = false;
1458
1459	+	switch (rnemdFluxType_) {
1460	+	case rnemdPx:
1461	+	case rnemdPy:
1462	+	case rnemdPz:
1463	+	case rnemdPvector:
1464	+	case rnemdKePx:
1465	+	case rnemdKePy:
1466	+	case rnemdKePvector:
1467	+	doLinearPart = true;
1468	+	break;
1469	+	case rnemdLx:
1470	+	case rnemdLy:
1471	+	case rnemdLz:
1472	+	case rnemdLvector:
1473	+	case rnemdKeLx:
1474	+	case rnemdKeLy:
1475	+	case rnemdKeLz:
1476	+	case rnemdKeLvector:
1477	+	doAngularPart = true;
1478	+	break;
1479	+	case rnemdKE:
1480	+	case rnemdRotKE:
1481	+	case rnemdFullKE:
1482	+	default:
1483	+	if (usePeriodicBoundaryConditions_)
1484	+	doLinearPart = true;
1485	+	else
1486	+	doAngularPart = true;
1487	+	break;
1488	+	}
1489	+
1490	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1491	+	sd = smanA.nextSelected(selei)) {
1492	+
1493		Vector3d pos = sd->getPos();
1494
1495		// wrap the stuntdouble's position back into the box:
1496	+
1497	+	if (usePeriodicBoundaryConditions_)
1498	+	currentSnap_->wrapVector(pos);
1499	+
1500	+	RealType mass = sd->getMass();
1501	+	Vector3d vel = sd->getVel();
1502	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1503	+	RealType r2;
1504	+
1505	+	hotBin.push_back(sd);
1506	+	Ph += mass * vel;
1507	+	Mh += mass;
1508	+	Kh += mass * vel.lengthSquare();
1509	+	Lh += mass * cross(rPos, vel);
1510	+	Ih -= outProduct(rPos, rPos) * mass;
1511	+	r2 = rPos.lengthSquare();
1512	+	Ih(0, 0) += mass * r2;
1513	+	Ih(1, 1) += mass * r2;
1514	+	Ih(2, 2) += mass * r2;
1515	+
1516	+	if (rnemdFluxType_ == rnemdFullKE) {
1517	+	if (sd->isDirectional()) {
1518	+	Vector3d angMom = sd->getJ();
1519	+	Mat3x3d I = sd->getI();
1520	+	if (sd->isLinear()) {
1521	+	int i = sd->linearAxis();
1522	+	int j = (i + 1) % 3;
1523	+	int k = (i + 2) % 3;
1524	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1525	+	angMom[k] * angMom[k] / I(k, k);
1526	+	} else {
1527	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1528	+	angMom[1] * angMom[1] / I(1, 1) +
1529	+	angMom[2] * angMom[2] / I(2, 2);
1530	+	}
1531	+	}
1532	+	}
1533	+	}
1534	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1535	+	sd = smanB.nextSelected(selej)) {
1536
1537	+	Vector3d pos = sd->getPos();
1538	+
1539	+	// wrap the stuntdouble's position back into the box:
1540	+
1541		if (usePeriodicBoundaryConditions_)
1542		currentSnap_->wrapVector(pos);
1543	+
1544	+	RealType mass = sd->getMass();
1545	+	Vector3d vel = sd->getVel();
1546	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1547	+	RealType r2;
1548
1549	<	// which bin is this stuntdouble in?
1550	<	bool inA = inSlabA(pos);
1551	<	bool inB = inSlabB(pos);
1549	>	coldBin.push_back(sd);
1550	>	Pc += mass * vel;
1551	>	Mc += mass;
1552	>	Kc += mass * vel.lengthSquare();
1553	>	Lc += mass * cross(rPos, vel);
1554	>	Ic -= outProduct(rPos, rPos) * mass;
1555	>	r2 = rPos.lengthSquare();
1556	>	Ic(0, 0) += mass * r2;
1557	>	Ic(1, 1) += mass * r2;
1558	>	Ic(2, 2) += mass * r2;
1559
1560	<	if (inA || inB) {
1561	<
1562	<	RealType mass = sd->getMass();
1563	<	Vector3d vel = sd->getVel();
1564	<
1565	<	if (inA) {
1566	<	hotBin.push_back(sd);
1567	<	Ph += mass * vel;
1568	<	Mh += mass;
1569	<	Kh += mass * vel.lengthSquare();
1570	<	if (rnemdFluxType_ == rnemdFullKE) {
1571	<	if (sd->isDirectional()) {
1572	<	Vector3d angMom = sd->getJ();
1573	<	Mat3x3d I = sd->getI();
1574	<	if (sd->isLinear()) {
1575	<	int i = sd->linearAxis();
1264	<	int j = (i + 1) % 3;
1265	<	int k = (i + 2) % 3;
1266	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1267	<	angMom[k] * angMom[k] / I(k, k);
1268	<	} else {
1269	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1270	<	angMom[1] * angMom[1] / I(1, 1) +
1271	<	angMom[2] * angMom[2] / I(2, 2);
1272	<	}
1273	<	}
1274	<	}
1275	<	} else { //midBin_
1276	<	coldBin.push_back(sd);
1277	<	Pc += mass * vel;
1278	<	Mc += mass;
1279	<	Kc += mass * vel.lengthSquare();
1280	<	if (rnemdFluxType_ == rnemdFullKE) {
1281	<	if (sd->isDirectional()) {
1282	<	Vector3d angMom = sd->getJ();
1283	<	Mat3x3d I = sd->getI();
1284	<	if (sd->isLinear()) {
1285	<	int i = sd->linearAxis();
1286	<	int j = (i + 1) % 3;
1287	<	int k = (i + 2) % 3;
1288	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1289	<	angMom[k] * angMom[k] / I(k, k);
1290	<	} else {
1291	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1292	<	angMom[1] * angMom[1] / I(1, 1) +
1293	<	angMom[2] * angMom[2] / I(2, 2);
1294	<	}
1295	<	}
1296	<	}
1297	<	}
1560	>	if (rnemdFluxType_ == rnemdFullKE) {
1561	>	if (sd->isDirectional()) {
1562	>	Vector3d angMom = sd->getJ();
1563	>	Mat3x3d I = sd->getI();
1564	>	if (sd->isLinear()) {
1565	>	int i = sd->linearAxis();
1566	>	int j = (i + 1) % 3;
1567	>	int k = (i + 2) % 3;
1568	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1569	>	angMom[k] * angMom[k] / I(k, k);
1570	>	} else {
1571	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1572	>	angMom[1] * angMom[1] / I(1, 1) +
1573	>	angMom[2] * angMom[2] / I(2, 2);
1574	>	}
1575	>	}
1576		}
1577		}
1578
#	Line 1304 | Line 1582 | namespace OpenMD {
1582		#ifdef IS_MPI
1583		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1585	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1587		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1588		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1589		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1590		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1591	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1592	+	MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595		#endif
1596	+
1597
1598	+	Vector3d ac, acrec, bc, bcrec;
1599	+	Vector3d ah, ahrec, bh, bhrec;
1600	+
1601		bool successfulExchange = false;
1602		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1603		Vector3d vc = Pc / Mc;
1604	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1605	<	Vector3d acrec = -momentumTarget_ / Mc;
1606	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1604	>	ac = -momentumTarget_ / Mc + vc;
1605	>	acrec = -momentumTarget_ / Mc;
1606	>
1607	>	// We now need the inverse of the inertia tensor to calculate the
1608	>	// angular velocity of the cold slab;
1609	>	Mat3x3d Ici = Ic.inverse();
1610	>	Vector3d omegac = Ici * Lc;
1611	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1612	>	bcrec = bc - omegac;
1613	>
1614	>	RealType cNumerator = Kc - kineticTarget_;
1615	>	if (doLinearPart)
1616	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1617	>
1618	>	if (doAngularPart)
1619	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1620	>
1621		if (cNumerator > 0.0) {
1622	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1622	>
1623	>	RealType cDenominator = Kc;
1624	>
1625	>	if (doLinearPart)
1626	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1627	>
1628	>	if (doAngularPart)
1629	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1630	>
1631		if (cDenominator > 0.0) {
1632		RealType c = sqrt(cNumerator / cDenominator);
1633		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1634	+
1635		Vector3d vh = Ph / Mh;
1636	<	Vector3d ah = momentumTarget_ / Mh + vh;
1637	<	Vector3d ahrec = momentumTarget_ / Mh;
1638	<	RealType hNumerator = Kh + kineticTarget_
1639	<	- 0.5 * Mh * ah.lengthSquare();
1640	<	if (hNumerator > 0.0) {
1641	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1636	>	ah = momentumTarget_ / Mh + vh;
1637	>	ahrec = momentumTarget_ / Mh;
1638	>
1639	>	// We now need the inverse of the inertia tensor to
1640	>	// calculate the angular velocity of the hot slab;
1641	>	Mat3x3d Ihi = Ih.inverse();
1642	>	Vector3d omegah = Ihi * Lh;
1643	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1644	>	bhrec = bh - omegah;
1645	>
1646	>	RealType hNumerator = Kh + kineticTarget_;
1647	>	if (doLinearPart)
1648	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1649	>
1650	>	if (doAngularPart)
1651	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1652	>
1653	>	if (hNumerator > 0.0) {
1654	>
1655	>	RealType hDenominator = Kh;
1656	>	if (doLinearPart)
1657	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1658	>	if (doAngularPart)
1659	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1660	>
1661		if (hDenominator > 0.0) {
1662		RealType h = sqrt(hNumerator / hDenominator);
1663		if ((h > 0.9) && (h < 1.1)) {
1664	<
1664	>
1665		vector<StuntDouble*>::iterator sdi;
1666		Vector3d vel;
1667	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1667	>	Vector3d rPos;
1668	>
1669	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1670		//vel = (*sdi)->getVel();
1671	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1671	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1672	>	if (doLinearPart)
1673	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1674	>	if (doAngularPart)
1675	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1676	>
1677		(*sdi)->setVel(vel);
1678		if (rnemdFluxType_ == rnemdFullKE) {
1679		if ((*sdi)->isDirectional()) {
#	Line 1345 | Line 1682 | namespace OpenMD {
1682		}
1683		}
1684		}
1685	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1685	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1686		//vel = (*sdi)->getVel();
1687	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1687	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1688	>	if (doLinearPart)
1689	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1690	>	if (doAngularPart)
1691	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1692	>
1693		(*sdi)->setVel(vel);
1694		if (rnemdFluxType_ == rnemdFullKE) {
1695		if ((*sdi)->isDirectional()) {
#	Line 1359 | Line 1701 | namespace OpenMD {
1701		successfulExchange = true;
1702		kineticExchange_ += kineticTarget_;
1703		momentumExchange_ += momentumTarget_;
1704	+	angularMomentumExchange_ += angularMomentumTarget_;
1705		}
1706		}
1707		}
#	Line 1378 | Line 1721 | namespace OpenMD {
1721		}
1722		}
1723
1724	+	RealType RNEMD::getDividingArea() {
1725	+
1726	+	if (hasDividingArea_) return dividingArea_;
1727	+
1728	+	RealType areaA, areaB;
1729	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1730	+
1731	+	if (hasSelectionA_) {
1732	+	int isd;
1733	+	StuntDouble* sd;
1734	+	vector<StuntDouble*> aSites;
1735	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1736	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1737	+	sd = seleManA_.nextSelected(isd)) {
1738	+	aSites.push_back(sd);
1739	+	}
1740	+	#if defined(HAVE_QHULL)
1741	+	ConvexHull* surfaceMeshA = new ConvexHull();
1742	+	surfaceMeshA->computeHull(aSites);
1743	+	areaA = surfaceMeshA->getArea();
1744	+	delete surfaceMeshA;
1745	+	#else
1746	+	sprintf( painCave.errMsg,
1747	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1748	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1749	+	painCave.severity = OPENMD_ERROR;
1750	+	painCave.isFatal = 1;
1751	+	simError();
1752	+	#endif
1753	+
1754	+	} else {
1755	+	if (usePeriodicBoundaryConditions_) {
1756	+	// in periodic boundaries, the surface area is twice the x-y
1757	+	// area of the current box:
1758	+	areaA = 2.0 * snap->getXYarea();
1759	+	} else {
1760	+	// in non-periodic simulations, without explicitly setting
1761	+	// selections, the sphere radius sets the surface area of the
1762	+	// dividing surface:
1763	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1764	+	}
1765	+	}
1766	+
1767	+	if (hasSelectionB_) {
1768	+	int isd;
1769	+	StuntDouble* sd;
1770	+	vector<StuntDouble*> bSites;
1771	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1772	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1773	+	sd = seleManB_.nextSelected(isd)) {
1774	+	bSites.push_back(sd);
1775	+	}
1776	+
1777	+	#if defined(HAVE_QHULL)
1778	+	ConvexHull* surfaceMeshB = new ConvexHull();
1779	+	surfaceMeshB->computeHull(bSites);
1780	+	areaB = surfaceMeshB->getArea();
1781	+	delete surfaceMeshB;
1782	+	#else
1783	+	sprintf( painCave.errMsg,
1784	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1785	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1786	+	painCave.severity = OPENMD_ERROR;
1787	+	painCave.isFatal = 1;
1788	+	simError();
1789	+	#endif
1790	+
1791	+
1792	+	} else {
1793	+	if (usePeriodicBoundaryConditions_) {
1794	+	// in periodic boundaries, the surface area is twice the x-y
1795	+	// area of the current box:
1796	+	areaB = 2.0 * snap->getXYarea();
1797	+	} else {
1798	+	// in non-periodic simulations, without explicitly setting
1799	+	// selections, but if a sphereBradius has been set, just use that:
1800	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1801	+	}
1802	+	}
1803	+
1804	+	dividingArea_ = min(areaA, areaB);
1805	+	hasDividingArea_ = true;
1806	+	return dividingArea_;
1807	+	}
1808	+
1809		void RNEMD::doRNEMD() {
1810		if (!doRNEMD_) return;
1811		trialCount_++;
1812	+
1813	+	// object evaluator:
1814	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1815	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1816	+
1817	+	evaluatorA_.loadScriptString(selectionA_);
1818	+	evaluatorB_.loadScriptString(selectionB_);
1819	+
1820	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1821	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1822	+
1823	+	commonA_ = seleManA_ & seleMan_;
1824	+	commonB_ = seleManB_ & seleMan_;
1825	+
1826	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1827	+	// dt = exchange time interval
1828	+	// flux = target flux
1829	+	// dividingArea = smallest dividing surface between the two regions
1830	+
1831	+	hasDividingArea_ = false;
1832	+	RealType area = getDividingArea();
1833	+
1834	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1835	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1836	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1837	+
1838		switch(rnemdMethod_) {
1839		case rnemdSwap:
1840	<	doSwap();
1840	>	doSwap(commonA_, commonB_);
1841		break;
1842		case rnemdNIVS:
1843	<	doNIVS();
1843	>	doNIVS(commonA_, commonB_);
1844		break;
1845		case rnemdVSS:
1846	<	doVSS();
1846	>	doVSS(commonA_, commonB_);
1847		break;
1848		case rnemdUnkownMethod:
1849		default :
#	Line 1400 | Line 1854 | namespace OpenMD {
1854		void RNEMD::collectData() {
1855		if (!doRNEMD_) return;
1856		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1857	+
1858	+	// collectData can be called more frequently than the doRNEMD, so use the
1859	+	// computed area from the last exchange time:
1860	+	RealType area = getDividingArea();
1861	+	areaAccumulator_->add(area);
1862		Mat3x3d hmat = currentSnap_->getHmat();
1404	–
1405	–	areaAccumulator_->add(currentSnap_->getXYarea());
1406	–
1863		seleMan_.setSelectionSet(evaluator_.evaluate());
1864
1865		int selei(0);
1866		StuntDouble* sd;
1867	+	int binNo;
1868
1869		vector<RealType> binMass(nBins_, 0.0);
1870		vector<RealType> binPx(nBins_, 0.0);
1871		vector<RealType> binPy(nBins_, 0.0);
1872		vector<RealType> binPz(nBins_, 0.0);
1873	+	vector<RealType> binOmegax(nBins_, 0.0);
1874	+	vector<RealType> binOmegay(nBins_, 0.0);
1875	+	vector<RealType> binOmegaz(nBins_, 0.0);
1876		vector<RealType> binKE(nBins_, 0.0);
1877		vector<int> binDOF(nBins_, 0);
1878		vector<int> binCount(nBins_, 0);
#	Line 1420 | Line 1880 | namespace OpenMD {
1880		// alternative approach, track all molecules instead of only those
1881		// selected for scaling/swapping:
1882		/*
1883	<	SimInfo::MoleculeIterator miter;
1884	<	vector<StuntDouble*>::iterator iiter;
1885	<	Molecule* mol;
1886	<	StuntDouble* sd;
1887	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1883	>	SimInfo::MoleculeIterator miter;
1884	>	vector<StuntDouble*>::iterator iiter;
1885	>	Molecule* mol;
1886	>	StuntDouble* sd;
1887	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1888		mol = info_->nextMolecule(miter))
1889		sd is essentially sd
1890	<	for (sd = mol->beginIntegrableObject(iiter);
1891	<	sd != NULL;
1892	<	sd = mol->nextIntegrableObject(iiter))
1890	>	for (sd = mol->beginIntegrableObject(iiter);
1891	>	sd != NULL;
1892	>	sd = mol->nextIntegrableObject(iiter))
1893		*/
1894
1895		for (sd = seleMan_.beginSelected(selei); sd != NULL;
#	Line 1439 | Line 1899 | namespace OpenMD {
1899
1900		// wrap the stuntdouble's position back into the box:
1901
1902	<	if (usePeriodicBoundaryConditions_)
1902	>	if (usePeriodicBoundaryConditions_) {
1903		currentSnap_->wrapVector(pos);
1904	+	// which bin is this stuntdouble in?
1905	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1906	+	// Shift molecules by half a box to have bins start at 0
1907	+	// The modulo operator is used to wrap the case when we are
1908	+	// beyond the end of the bins back to the beginning.
1909	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1910	+	} else {
1911	+	Vector3d rPos = pos - coordinateOrigin_;
1912	+	binNo = int(rPos.length() / binWidth_);
1913	+	}
1914
1445	–
1446	–	// which bin is this stuntdouble in?
1447	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1448	–	// Shift molecules by half a box to have bins start at 0
1449	–	// The modulo operator is used to wrap the case when we are
1450	–	// beyond the end of the bins back to the beginning.
1451	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1452	–
1915		RealType mass = sd->getMass();
1916		Vector3d vel = sd->getVel();
1917	<
1918	<	binCount[binNo]++;
1919	<	binMass[binNo] += mass;
1920	<	binPx[binNo] += mass*vel.x();
1921	<	binPy[binNo] += mass*vel.y();
1922	<	binPz[binNo] += mass*vel.z();
1923	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1924	<	binDOF[binNo] += 3;
1925	<
1926	<	if (sd->isDirectional()) {
1927	<	Vector3d angMom = sd->getJ();
1928	<	Mat3x3d I = sd->getI();
1929	<	if (sd->isLinear()) {
1930	<	int i = sd->linearAxis();
1931	<	int j = (i + 1) % 3;
1932	<	int k = (i + 2) % 3;
1933	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1934	<	angMom[k] * angMom[k] / I(k, k));
1935	<	binDOF[binNo] += 2;
1936	<	} else {
1937	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1938	<	angMom[1] * angMom[1] / I(1, 1) +
1939	<	angMom[2] * angMom[2] / I(2, 2));
1940	<	binDOF[binNo] += 3;
1917	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1918	>	Vector3d aVel = cross(rPos, vel);
1919	>
1920	>	if (binNo >= 0 && binNo < nBins_)  {
1921	>	binCount[binNo]++;
1922	>	binMass[binNo] += mass;
1923	>	binPx[binNo] += mass*vel.x();
1924	>	binPy[binNo] += mass*vel.y();
1925	>	binPz[binNo] += mass*vel.z();
1926	>	binOmegax[binNo] += aVel.x();
1927	>	binOmegay[binNo] += aVel.y();
1928	>	binOmegaz[binNo] += aVel.z();
1929	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1930	>	binDOF[binNo] += 3;
1931	>
1932	>	if (sd->isDirectional()) {
1933	>	Vector3d angMom = sd->getJ();
1934	>	Mat3x3d I = sd->getI();
1935	>	if (sd->isLinear()) {
1936	>	int i = sd->linearAxis();
1937	>	int j = (i + 1) % 3;
1938	>	int k = (i + 2) % 3;
1939	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1940	>	angMom[k] * angMom[k] / I(k, k));
1941	>	binDOF[binNo] += 2;
1942	>	} else {
1943	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1944	>	angMom[1] * angMom[1] / I(1, 1) +
1945	>	angMom[2] * angMom[2] / I(2, 2));
1946	>	binDOF[binNo] += 3;
1947	>	}
1948		}
1949		}
1950		}
#	Line 1491 | Line 1960 | namespace OpenMD {
1960		nBins_, MPI::REALTYPE, MPI::SUM);
1961		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1962		nBins_, MPI::REALTYPE, MPI::SUM);
1963	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1964	+	nBins_, MPI::REALTYPE, MPI::SUM);
1965	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1966	+	nBins_, MPI::REALTYPE, MPI::SUM);
1967	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1968	+	nBins_, MPI::REALTYPE, MPI::SUM);
1969		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1970		nBins_, MPI::REALTYPE, MPI::SUM);
1971		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
#	Line 1498 | Line 1973 | namespace OpenMD {
1973		#endif
1974
1975		Vector3d vel;
1976	+	Vector3d aVel;
1977		RealType den;
1978		RealType temp;
1979		RealType z;
1980	+	RealType r;
1981		for (int i = 0; i < nBins_; i++) {
1982	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1982	>	if (usePeriodicBoundaryConditions_) {
1983	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1984	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1985	>	/ currentSnap_->getVolume() ;
1986	>	} else {
1987	>	r = (((RealType)i + 0.5) * binWidth_);
1988	>	RealType rinner = (RealType)i * binWidth_;
1989	>	RealType router = (RealType)(i+1) * binWidth_;
1990	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1991	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1992	>	}
1993		vel.x() = binPx[i] / binMass[i];
1994		vel.y() = binPy[i] / binMass[i];
1995		vel.z() = binPz[i] / binMass[i];
1996	+	aVel.x() = binOmegax[i] / binCount[i];
1997	+	aVel.y() = binOmegay[i] / binCount[i];
1998	+	aVel.z() = binOmegaz[i] / binCount[i];
1999
1510	–	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1511	–	/ currentSnap_->getVolume() ;
1512	–
2000		if (binCount[i] > 0) {
2001		// only add values if there are things to add
2002		temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
#	Line 1521 | Line 2008 | namespace OpenMD {
2008		case Z:
2009		dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2010		break;
2011	+	case R:
2012	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2013	+	break;
2014		case TEMPERATURE:
2015		dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2016		break;
2017		case VELOCITY:
2018		dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2019		break;
2020	+	case ANGULARVELOCITY:
2021	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2022	+	break;
2023		case DENSITY:
2024		dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2025		break;
#	Line 1535 | Line 2028 | namespace OpenMD {
2028		}
2029		}
2030		}
2031	+	hasData_ = true;
2032		}
2033
2034		void RNEMD::getStarted() {
2035		if (!doRNEMD_) return;
2036	+	hasDividingArea_ = false;
2037		collectData();
2038		writeOutputFile();
2039		}
#	Line 1566 | Line 2061 | namespace OpenMD {
2061
2062		void RNEMD::writeOutputFile() {
2063		if (!doRNEMD_) return;
2064	+	if (!hasData_) return;
2065
2066		#ifdef IS_MPI
2067		// If we're the root node, should we print out the results
#	Line 1587 | Line 2083 | namespace OpenMD {
2083		RealType time = currentSnap_->getTime();
2084		RealType avgArea;
2085		areaAccumulator_->getAverage(avgArea);
1590	–	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1591	–	/ PhysicalConstants::energyConvert;
1592	–	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
2086
2087	+	RealType Jz(0.0);
2088	+	Vector3d JzP(V3Zero);
2089	+	Vector3d JzL(V3Zero);
2090	+	if (time >= info_->getSimParams()->getDt()) {
2091	+	Jz = kineticExchange_ / (time * avgArea)
2092	+	/ PhysicalConstants::energyConvert;
2093	+	JzP = momentumExchange_ / (time * avgArea);
2094	+	JzL = angularMomentumExchange_ / (time * avgArea);
2095	+	}
2096	+
2097		rnemdFile_ << "#######################################################\n";
2098		rnemdFile_ << "# RNEMD {\n";
2099
#	Line 1609 | Line 2112 | namespace OpenMD {
2112
2113		rnemdFile_ << "#    objectSelection = \""
2114		<< rnemdObjectSelection_ << "\";\n";
2115	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
2116	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1614	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
2115	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2116	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2117		rnemdFile_ << "# }\n";
2118		rnemdFile_ << "#######################################################\n";
2119		rnemdFile_ << "# RNEMD report:\n";
2120	<	rnemdFile_ << "#     running time = " << time << " fs\n";
2121	<	rnemdFile_ << "#     target flux:\n";
2122	<	rnemdFile_ << "#         kinetic = "
2120	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2121	>	rnemdFile_ << "# Target flux:\n";
2122	>	rnemdFile_ << "#           kinetic = "
2123		<< kineticFlux_ / PhysicalConstants::energyConvert
2124		<< " (kcal/mol/A^2/fs)\n";
2125	<	rnemdFile_ << "#         momentum = " << momentumFluxVector_
2125	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2126		<< " (amu/A/fs^2)\n";
2127	<	rnemdFile_ << "#     target one-time exchanges:\n";
2128	<	rnemdFile_ << "#         kinetic = "
2127	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2128	>	<< " (amu/A^2/fs^2)\n";
2129	>	rnemdFile_ << "# Target one-time exchanges:\n";
2130	>	rnemdFile_ << "#          kinetic = "
2131		<< kineticTarget_ / PhysicalConstants::energyConvert
2132		<< " (kcal/mol)\n";
2133	<	rnemdFile_ << "#         momentum = " << momentumTarget_
2133	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2134		<< " (amu*A/fs)\n";
2135	<	rnemdFile_ << "#     actual exchange totals:\n";
2136	<	rnemdFile_ << "#         kinetic = "
2135	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2136	>	<< " (amu*A^2/fs)\n";
2137	>	rnemdFile_ << "# Actual exchange totals:\n";
2138	>	rnemdFile_ << "#          kinetic = "
2139		<< kineticExchange_ / PhysicalConstants::energyConvert
2140		<< " (kcal/mol)\n";
2141	<	rnemdFile_ << "#         momentum = " << momentumExchange_
2141	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2142		<< " (amu*A/fs)\n";
2143	<	rnemdFile_ << "#     actual flux:\n";
2144	<	rnemdFile_ << "#         kinetic = " << Jz
2143	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2144	>	<< " (amu*A^2/fs)\n";
2145	>	rnemdFile_ << "# Actual flux:\n";
2146	>	rnemdFile_ << "#          kinetic = " << Jz
2147		<< " (kcal/mol/A^2/fs)\n";
2148	<	rnemdFile_ << "#         momentum = " << JzP
2148	>	rnemdFile_ << "#          momentum = " << JzP
2149		<< " (amu/A/fs^2)\n";
2150	<	rnemdFile_ << "#     exchange statistics:\n";
2151	<	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
2152	<	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
2150	>	rnemdFile_ << "#  angular momentum = " << JzL
2151	>	<< " (amu/A^2/fs^2)\n";
2152	>	rnemdFile_ << "# Exchange statistics:\n";
2153	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2154	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2155		if (rnemdMethod_ == rnemdNIVS) {
2156	<	rnemdFile_ << "#         NIVS root-check errors = "
2156	>	rnemdFile_ << "#  NIVS root-check errors = "
2157		<< failRootCount_ << "\n";
2158		}
2159		rnemdFile_ << "#######################################################\n";
#	Line 1670 | Line 2180 | namespace OpenMD {
2180		if (outputMask_[i]) {
2181		if (data_[i].dataType == "RealType")
2182		writeReal(i,j);
2183	<	else if (data_[i].dataType == "Vector3d")
2183	>	else if (data_[i].dataType == "Vector3d")
2184		writeVector(i,j);
2185		else {
2186		sprintf( painCave.errMsg,
#	Line 1723 | Line 2233 | namespace OpenMD {
2233		void RNEMD::writeReal(int index, unsigned int bin) {
2234		if (!doRNEMD_) return;
2235		assert(index >=0 && index < ENDINDEX);
2236	<	assert(bin < nBins_);
2236	>	assert(int(bin) < nBins_);
2237		RealType s;
2238	+	int count;
2239
2240	+	count = data_[index].accumulator[bin]->count();
2241	+	if (count == 0) return;
2242	+
2243		dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2244
2245		if (! isinf(s) && ! isnan(s)) {
2246		rnemdFile_ << "\t" << s;
2247		} else{
2248		sprintf( painCave.errMsg,
2249	<	"RNEMD detected a numerical error writing: %s for bin %d",
2249	>	"RNEMD detected a numerical error writing: %s for bin %u",
2250		data_[index].title.c_str(), bin);
2251		painCave.isFatal = 1;
2252		simError();
#	Line 1742 | Line 2256 | namespace OpenMD {
2256		void RNEMD::writeVector(int index, unsigned int bin) {
2257		if (!doRNEMD_) return;
2258		assert(index >=0 && index < ENDINDEX);
2259	<	assert(bin < nBins_);
2259	>	assert(int(bin) < nBins_);
2260		Vector3d s;
2261	+	int count;
2262	+
2263	+	count = data_[index].accumulator[bin]->count();
2264	+
2265	+	if (count == 0) return;
2266	+
2267		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2268		if (isinf(s[0]) || isnan(s[0]) ||
2269		isinf(s[1]) || isnan(s[1]) ||
2270		isinf(s[2]) || isnan(s[2]) ) {
2271		sprintf( painCave.errMsg,
2272	<	"RNEMD detected a numerical error writing: %s for bin %d",
2272	>	"RNEMD detected a numerical error writing: %s for bin %u",
2273		data_[index].title.c_str(), bin);
2274		painCave.isFatal = 1;
2275		simError();
#	Line 1761 | Line 2281 | namespace OpenMD {
2281		void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2282		if (!doRNEMD_) return;
2283		assert(index >=0 && index < ENDINDEX);
2284	<	assert(bin < nBins_);
2284	>	assert(int(bin) < nBins_);
2285		RealType s;
2286	+	int count;
2287
2288	+	count = data_[index].accumulator[bin]->count();
2289	+	if (count == 0) return;
2290	+
2291		dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2292
2293		if (! isinf(s) && ! isnan(s)) {
2294		rnemdFile_ << "\t" << s;
2295		} else{
2296		sprintf( painCave.errMsg,
2297	<	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2297	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2298		data_[index].title.c_str(), bin);
2299		painCave.isFatal = 1;
2300		simError();
#	Line 1780 | Line 2304 | namespace OpenMD {
2304		void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2305		if (!doRNEMD_) return;
2306		assert(index >=0 && index < ENDINDEX);
2307	<	assert(bin < nBins_);
2307	>	assert(int(bin) < nBins_);
2308		Vector3d s;
2309	+	int count;
2310	+
2311	+	count = data_[index].accumulator[bin]->count();
2312	+	if (count == 0) return;
2313	+
2314		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2315		if (isinf(s[0]) || isnan(s[0]) ||
2316		isinf(s[1]) || isnan(s[1]) ||
2317		isinf(s[2]) || isnan(s[2]) ) {
2318		sprintf( painCave.errMsg,
2319	<	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2319	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2320		data_[index].title.c_str(), bin);
2321		painCave.isFatal = 1;
2322		simError();

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