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

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branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1776 by gezelter, Thu Aug 9 15:52:59 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1903 by gezelter, Tue Jul 16 18:58:08 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
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
67
68		using namespace std;
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();
#	Line 80 | 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
90	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
91	–	evaluator_.loadScriptString(rnemdObjectSelection_);
92	–	seleMan_.setSelectionSet(evaluator_.evaluate());
93	–
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 101 | 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 111 | 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 198 | 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 227 | Line 272 | namespace OpenMD {
272		}
273		if (!hasCorrectFlux) {
274		sprintf(painCave.errMsg,
275	<	"RNEMD: The current method,\n"
231	<	"\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 238 | 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		}
#	Line 267 | 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();
276	<	int nIntegrable = info->getNGlobalIntegrableObjects();
356	>	// do some sanity checking
357
358	<	if (selectionCount > nIntegrable) {
279	<	sprintf(painCave.errMsg,
280	<	"RNEMD: The current objectSelection,\n"
281	<	"\t\t%s\n"
282	<	"\thas resulted in %d selected objects.  However,\n"
283	<	"\tthe total number of integrable objects in the system\n"
284	<	"\tis only %d.  This is almost certainly not what you want\n"
285	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
286	<	"\tselector in the selection script!\n",
287	<	rnemdObjectSelection_.c_str(),
288	<	selectionCount, nIntegrable);
289	<	painCave.isFatal = 0;
290	<	painCave.severity = OPENMD_WARNING;
291	<	simError();
292	<	}
358	>	int selectionCount = seleMan_.getSelectionCount();
359
360	<	areaAccumulator_ = new Accumulator();
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361
362	<	nBins_ = rnemdParams->getOutputBins();
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	<	data_.resize(RNEMD::ENDINDEX);
299	<	OutputData z;
300	<	z.units =  "Angstroms";
301	<	z.title =  "Z";
302	<	z.dataType = "RealType";
303	<	z.accumulator.reserve(nBins_);
304	<	for (unsigned int i = 0; i < nBins_; i++)
305	<	z.accumulator.push_back( new Accumulator() );
306	<	data_[Z] = z;
307	<	outputMap_["Z"] =  Z;
378	>	areaAccumulator_ = new Accumulator();
379
380	<	OutputData temperature;
381	<	temperature.units =  "K";
311	<	temperature.title =  "Temperature";
312	<	temperature.dataType = "RealType";
313	<	temperature.accumulator.reserve(nBins_);
314	<	for (unsigned int i = 0; i < nBins_; i++)
315	<	temperature.accumulator.push_back( new Accumulator() );
316	<	data_[TEMPERATURE] = temperature;
317	<	outputMap_["TEMPERATURE"] =  TEMPERATURE;
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382
383	<	OutputData velocity;
384	<	velocity.units = "amu/fs";
385	<	velocity.title =  "Velocity";
386	<	velocity.dataType = "Vector3d";
387	<	velocity.accumulator.reserve(nBins_);
388	<	for (unsigned int i = 0; i < nBins_; i++)
389	<	velocity.accumulator.push_back( new VectorAccumulator() );
390	<	data_[VELOCITY] = velocity;
391	<	outputMap_["VELOCITY"] = VELOCITY;
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 density;
395	<	density.units =  "g cm^-3";
396	<	density.title =  "Density";
397	<	density.dataType = "RealType";
398	<	density.accumulator.reserve(nBins_);
399	<	for (unsigned int i = 0; i < nBins_; i++)
400	<	density.accumulator.push_back( new Accumulator() );
401	<	data_[DENSITY] = density;
402	<	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);
348	<	break;
349	<	case rnemdPx:
350	<	case rnemdPy:
351	<	outputMask_.set(VELOCITY);
352	<	break;
353	<	case rnemdPz:
354	<	case rnemdPvector:
355	<	outputMask_.set(VELOCITY);
356	<	outputMask_.set(DENSITY);
357	<	break;
358	<	case rnemdKePx:
359	<	case rnemdKePy:
360	<	outputMask_.set(TEMPERATURE);
361	<	outputMask_.set(VELOCITY);
362	<	break;
363	<	case rnemdKePvector:
364	<	outputMask_.set(TEMPERATURE);
365	<	outputMask_.set(VELOCITY);
366	<	outputMask_.set(DENSITY);
367	<	break;
368	<	default:
369	<	break;
370	<	}
371	<	}
372	<
373	<	if (hasOutputFileName) {
374	<	rnemdFileName_ = rnemdParams->getOutputFileName();
375	<	} else {
376	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
377	<	}
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;
396	<	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	+
551	+	} else {
552	+	if (usePeriodicBoundaryConditions_) {
553	+	Mat3x3d hmat = currentSnap_->getHmat();
554	+
555	+	if (hasSlabWidth)
556	+	slabWidth_ = rnemdParams->getSlabWidth();
557	+	else
558	+	slabWidth_ = hmat(2,2) / 10.0;
559	+
560	+	if (hasSlabBCenter)
561	+	slabBCenter_ = rnemdParams->getSlabBCenter();
562	+	else
563	+	slabBCenter_ = hmat(2,2) / 2.0;
564	+
565	+	selectionBstream << "select wrappedz > "
566	+	<< slabBCenter_ - 0.5*slabWidth_
567	+	<<  " && wrappedz < "
568	+	<< slabBCenter_ + 0.5*slabWidth_;
569	+	selectionB_ = selectionBstream.str();
570	+	} else {
571	+	if (hasSphereBRadius_) {
572	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
573	+	selectionBstream << "select r > " << sphereBRadius_;
574	+	selectionB_ = selectionBstream.str();
575	+	} else {
576	+	selectionB_ = "select hull";
577	+	BisHull_ = true;
578	+	hasSelectionB_ = true;
579	+	}
580	+	}
581	+	}
582	+	}
583	+
584	+	// object evaluator:
585	+	evaluator_.loadScriptString(rnemdObjectSelection_);
586	+	seleMan_.setSelectionSet(evaluator_.evaluate());
587	+	evaluatorA_.loadScriptString(selectionA_);
588	+	evaluatorB_.loadScriptString(selectionB_);
589	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
590	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
591	+	commonA_ = seleManA_ & seleMan_;
592	+	commonB_ = seleManB_ & seleMan_;
593		}
594	<
594	>
595	>
596		RNEMD::~RNEMD() {
597		if (!doRNEMD_) return;
598		#ifdef IS_MPI
#	Line 425 | Line 606 | namespace OpenMD {
606		#ifdef IS_MPI
607		}
608		#endif
609	+
610	+	// delete all of the objects we created:
611	+	delete areaAccumulator_;
612	+	data_.clear();
613		}
614
615	<	bool RNEMD::inSlabA(Vector3d pos) {
431	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
432	<	}
433	<	bool RNEMD::inSlabB(Vector3d pos) {
434	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
435	<	}
436	<
437	<	void RNEMD::doSwap() {
615	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
616		if (!doRNEMD_) return;
617	+	int selei;
618	+	int selej;
619	+
620		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
621		Mat3x3d hmat = currentSnap_->getHmat();
622
442	–	seleMan_.setSelectionSet(evaluator_.evaluate());
443	–
444	–	int selei;
623		StuntDouble* sd;
446	–	int idx;
624
625		RealType min_val;
626		bool min_found = false;
#	Line 453 | Line 630 | namespace OpenMD {
630		bool max_found = false;
631		StuntDouble* max_sd;
632
633	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
634	<	sd = seleMan_.nextSelected(selei)) {
633	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
634	>	sd = seleManA_.nextSelected(selei)) {
635
459	–	idx = sd->getLocalIndex();
460	–
636		Vector3d pos = sd->getPos();
637	<
637	>
638		// wrap the stuntdouble's position back into the box:
639	<
639	>
640		if (usePeriodicBoundaryConditions_)
641		currentSnap_->wrapVector(pos);
642	<	bool inA = inSlabA(pos);
643	<	bool inB = inSlabB(pos);
644	<
645	<	if (inA || inB) {
642	>
643	>	RealType mass = sd->getMass();
644	>	Vector3d vel = sd->getVel();
645	>	RealType value;
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649
650	<	RealType mass = sd->getMass();
651	<	Vector3d vel = sd->getVel();
652	<	RealType value;
653	<
654	<	switch(rnemdFluxType_) {
477	<	case rnemdKE :
650	>	value = mass * vel.lengthSquare();
651	>
652	>	if (sd->isDirectional()) {
653	>	Vector3d angMom = sd->getJ();
654	>	Mat3x3d I = sd->getI();
655
656	<	value = mass * vel.lengthSquare();
657	<
658	<	if (sd->isDirectional()) {
659	<	Vector3d angMom = sd->getJ();
660	<	Mat3x3d I = sd->getI();
661	<
662	<	if (sd->isLinear()) {
663	<	int i = sd->linearAxis();
664	<	int j = (i + 1) % 3;
665	<	int k = (i + 2) % 3;
666	<	value += angMom[j] * angMom[j] / I(j, j) +
667	<	angMom[k] * angMom[k] / I(k, k);
668	<	} else {
669	<	value += angMom[0]*angMom[0]/I(0, 0)
670	<	+ angMom[1]*angMom[1]/I(1, 1)
671	<	+ angMom[2]*angMom[2]/I(2, 2);
672	<	}
673	<	} //angular momenta exchange enabled
674	<	//energyConvert temporarily disabled
675	<	//make kineticExchange_ comparable between swap & scale
676	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
677	<	value *= 0.5;
678	<	break;
679	<	case rnemdPx :
680	<	value = mass * vel[0];
681	<	break;
682	<	case rnemdPy :
683	<	value = mass * vel[1];
684	<	break;
685	<	case rnemdPz :
686	<	value = mass * vel[2];
687	<	break;
688	<	default :
689	<	break;
656	>	if (sd->isLinear()) {
657	>	int i = sd->linearAxis();
658	>	int j = (i + 1) % 3;
659	>	int k = (i + 2) % 3;
660	>	value += angMom[j] * angMom[j] / I(j, j) +
661	>	angMom[k] * angMom[k] / I(k, k);
662	>	} else {
663	>	value += angMom[0]*angMom[0]/I(0, 0)
664	>	+ angMom[1]*angMom[1]/I(1, 1)
665	>	+ angMom[2]*angMom[2]/I(2, 2);
666	>	}
667	>	} //angular momenta exchange enabled
668	>	value *= 0.5;
669	>	break;
670	>	case rnemdPx :
671	>	value = mass * vel[0];
672	>	break;
673	>	case rnemdPy :
674	>	value = mass * vel[1];
675	>	break;
676	>	case rnemdPz :
677	>	value = mass * vel[2];
678	>	break;
679	>	default :
680	>	break;
681	>	}
682	>	if (!max_found) {
683	>	max_val = value;
684	>	max_sd = sd;
685	>	max_found = true;
686	>	} else {
687	>	if (max_val < value) {
688	>	max_val = value;
689	>	max_sd = sd;
690		}
691	+	}
692	+	}
693
694	<	if (inA == 0) {
695	<	if (!min_found) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	min_found = true;
699	<	} else {
700	<	if (min_val > value) {
701	<	min_val = value;
702	<	min_sd = sd;
703	<	}
704	<	}
705	<	} else {
706	<	if (!max_found) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	max_found = true;
710	<	} else {
711	<	if (max_val < value) {
712	<	max_val = value;
713	<	max_sd = sd;
714	<	}
715	<	}
716	<	}
694	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
695	>	sd = seleManB_.nextSelected(selej)) {
696	>
697	>	Vector3d pos = sd->getPos();
698	>
699	>	// wrap the stuntdouble's position back into the box:
700	>
701	>	if (usePeriodicBoundaryConditions_)
702	>	currentSnap_->wrapVector(pos);
703	>
704	>	RealType mass = sd->getMass();
705	>	Vector3d vel = sd->getVel();
706	>	RealType value;
707	>
708	>	switch(rnemdFluxType_) {
709	>	case rnemdKE :
710	>
711	>	value = mass * vel.lengthSquare();
712	>
713	>	if (sd->isDirectional()) {
714	>	Vector3d angMom = sd->getJ();
715	>	Mat3x3d I = sd->getI();
716	>
717	>	if (sd->isLinear()) {
718	>	int i = sd->linearAxis();
719	>	int j = (i + 1) % 3;
720	>	int k = (i + 2) % 3;
721	>	value += angMom[j] * angMom[j] / I(j, j) +
722	>	angMom[k] * angMom[k] / I(k, k);
723	>	} else {
724	>	value += angMom[0]*angMom[0]/I(0, 0)
725	>	+ angMom[1]*angMom[1]/I(1, 1)
726	>	+ angMom[2]*angMom[2]/I(2, 2);
727	>	}
728	>	} //angular momenta exchange enabled
729	>	value *= 0.5;
730	>	break;
731	>	case rnemdPx :
732	>	value = mass * vel[0];
733	>	break;
734	>	case rnemdPy :
735	>	value = mass * vel[1];
736	>	break;
737	>	case rnemdPz :
738	>	value = mass * vel[2];
739	>	break;
740	>	default :
741	>	break;
742		}
743	+
744	+	if (!min_found) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	min_found = true;
748	+	} else {
749	+	if (min_val > value) {
750	+	min_val = value;
751	+	min_sd = sd;
752	+	}
753	+	}
754		}
755
756	<	#ifdef IS_MPI
757	<	int nProc, worldRank;
756	>	#ifdef IS_MPI
757	>	int worldRank = MPI::COMM_WORLD.Get_rank();
758
544	–	nProc = MPI::COMM_WORLD.Get_size();
545	–	worldRank = MPI::COMM_WORLD.Get_rank();
546	–
759		bool my_min_found = min_found;
760		bool my_max_found = max_found;
761
#	Line 734 | Line 946 | namespace OpenMD {
946
947		switch(rnemdFluxType_) {
948		case rnemdKE:
737	–	cerr << "KE\n";
949		kineticExchange_ += max_val - min_val;
950		break;
951		case rnemdPx:
#	Line 747 | Line 958 | namespace OpenMD {
958		momentumExchange_.z() += max_val - min_val;
959		break;
960		default:
750	–	cerr << "default\n";
961		break;
962		}
963		} else {
#	Line 769 | Line 979 | namespace OpenMD {
979		}
980		}
981
982	<	void RNEMD::doNIVS() {
982	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
983		if (!doRNEMD_) return;
984	+	int selei;
985	+	int selej;
986	+
987		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
988	+	RealType time = currentSnap_->getTime();
989		Mat3x3d hmat = currentSnap_->getHmat();
990
777	–	seleMan_.setSelectionSet(evaluator_.evaluate());
778	–
779	–	int selei;
991		StuntDouble* sd;
781	–	int idx;
992
993		vector<StuntDouble*> hotBin, coldBin;
994
#	Line 797 | Line 1007 | namespace OpenMD {
1007		RealType Kcz = 0.0;
1008		RealType Kcw = 0.0;
1009
1010	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1011	<	sd = seleMan_.nextSelected(selei)) {
802	<
803	<	idx = sd->getLocalIndex();
804	<
805	<	Vector3d pos = sd->getPos();
1010	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1011	>	sd = smanA.nextSelected(selei)) {
1012
1013	+	Vector3d pos = sd->getPos();
1014	+
1015		// wrap the stuntdouble's position back into the box:
1016	<
1016	>
1017		if (usePeriodicBoundaryConditions_)
1018		currentSnap_->wrapVector(pos);
1019	+
1020	+
1021	+	RealType mass = sd->getMass();
1022	+	Vector3d vel = sd->getVel();
1023	+
1024	+	hotBin.push_back(sd);
1025	+	Phx += mass * vel.x();
1026	+	Phy += mass * vel.y();
1027	+	Phz += mass * vel.z();
1028	+	Khx += mass * vel.x() * vel.x();
1029	+	Khy += mass * vel.y() * vel.y();
1030	+	Khz += mass * vel.z() * vel.z();
1031	+	if (sd->isDirectional()) {
1032	+	Vector3d angMom = sd->getJ();
1033	+	Mat3x3d I = sd->getI();
1034	+	if (sd->isLinear()) {
1035	+	int i = sd->linearAxis();
1036	+	int j = (i + 1) % 3;
1037	+	int k = (i + 2) % 3;
1038	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1039	+	angMom[k] * angMom[k] / I(k, k);
1040	+	} else {
1041	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1042	+	+ angMom[1]*angMom[1]/I(1, 1)
1043	+	+ angMom[2]*angMom[2]/I(2, 2);
1044	+	}
1045	+	}
1046	+	}
1047	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1048	+	sd = smanB.nextSelected(selej)) {
1049	+	Vector3d pos = sd->getPos();
1050	+
1051	+	// wrap the stuntdouble's position back into the box:
1052	+
1053	+	if (usePeriodicBoundaryConditions_)
1054	+	currentSnap_->wrapVector(pos);
1055	+
1056	+	RealType mass = sd->getMass();
1057	+	Vector3d vel = sd->getVel();
1058
1059	<	// which bin is this stuntdouble in?
1060	<	bool inA = inSlabA(pos);
1061	<	bool inB = inSlabB(pos);
1062	<
1063	<	if (inA || inB) {
1064	<
1065	<	RealType mass = sd->getMass();
1066	<	Vector3d vel = sd->getVel();
1067	<
1068	<	if (inA) {
1069	<	hotBin.push_back(sd);
1070	<	Phx += mass * vel.x();
1071	<	Phy += mass * vel.y();
1072	<	Phz += mass * vel.z();
1073	<	Khx += mass * vel.x() * vel.x();
1074	<	Khy += mass * vel.y() * vel.y();
1075	<	Khz += mass * vel.z() * vel.z();
1076	<	if (sd->isDirectional()) {
1077	<	Vector3d angMom = sd->getJ();
1078	<	Mat3x3d I = sd->getI();
1079	<	if (sd->isLinear()) {
833	<	int i = sd->linearAxis();
834	<	int j = (i + 1) % 3;
835	<	int k = (i + 2) % 3;
836	<	Khw += angMom[j] * angMom[j] / I(j, j) +
837	<	angMom[k] * angMom[k] / I(k, k);
838	<	} else {
839	<	Khw += angMom[0]*angMom[0]/I(0, 0)
840	<	+ angMom[1]*angMom[1]/I(1, 1)
841	<	+ angMom[2]*angMom[2]/I(2, 2);
842	<	}
843	<	}
844	<	} else {
845	<	coldBin.push_back(sd);
846	<	Pcx += mass * vel.x();
847	<	Pcy += mass * vel.y();
848	<	Pcz += mass * vel.z();
849	<	Kcx += mass * vel.x() * vel.x();
850	<	Kcy += mass * vel.y() * vel.y();
851	<	Kcz += mass * vel.z() * vel.z();
852	<	if (sd->isDirectional()) {
853	<	Vector3d angMom = sd->getJ();
854	<	Mat3x3d I = sd->getI();
855	<	if (sd->isLinear()) {
856	<	int i = sd->linearAxis();
857	<	int j = (i + 1) % 3;
858	<	int k = (i + 2) % 3;
859	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
860	<	angMom[k] * angMom[k] / I(k, k);
861	<	} else {
862	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
863	<	+ angMom[1]*angMom[1]/I(1, 1)
864	<	+ angMom[2]*angMom[2]/I(2, 2);
865	<	}
866	<	}
867	<	}
1059	>	coldBin.push_back(sd);
1060	>	Pcx += mass * vel.x();
1061	>	Pcy += mass * vel.y();
1062	>	Pcz += mass * vel.z();
1063	>	Kcx += mass * vel.x() * vel.x();
1064	>	Kcy += mass * vel.y() * vel.y();
1065	>	Kcz += mass * vel.z() * vel.z();
1066	>	if (sd->isDirectional()) {
1067	>	Vector3d angMom = sd->getJ();
1068	>	Mat3x3d I = sd->getI();
1069	>	if (sd->isLinear()) {
1070	>	int i = sd->linearAxis();
1071	>	int j = (i + 1) % 3;
1072	>	int k = (i + 2) % 3;
1073	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1074	>	angMom[k] * angMom[k] / I(k, k);
1075	>	} else {
1076	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1077	>	+ angMom[1]*angMom[1]/I(1, 1)
1078	>	+ angMom[2]*angMom[2]/I(2, 2);
1079	>	}
1080		}
1081		}
1082
#	Line 914 | Line 1126 | namespace OpenMD {
1126
1127		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1128		c = sqrt(c);
1129	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
918	<	//now convert to hotBin coefficient
1129	>
1130		RealType w = 0.0;
1131		if (rnemdFluxType_ ==  rnemdFullKE) {
1132		x = 1.0 + px * (1.0 - c);
#	Line 942 | Line 1153 | namespace OpenMD {
1153		//if w is in the right range, so should be x, y, z.
1154		vector<StuntDouble*>::iterator sdi;
1155		Vector3d vel;
1156	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1156	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1157		if (rnemdFluxType_ == rnemdFullKE) {
1158		vel = (*sdi)->getVel() * c;
1159		(*sdi)->setVel(vel);
#	Line 953 | Line 1164 | namespace OpenMD {
1164		}
1165		}
1166		w = sqrt(w);
1167	<	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
957	<	//           << "\twh= " << w << endl;
958	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1167	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1168		if (rnemdFluxType_ == rnemdFullKE) {
1169		vel = (*sdi)->getVel();
1170		vel.x() *= x;
#	Line 1074 | Line 1283 | namespace OpenMD {
1283		vector<RealType>::iterator ri;
1284		RealType r1, r2, alpha0;
1285		vector<pair<RealType,RealType> > rps;
1286	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1286	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1287		r2 = *ri;
1288		//check if FindRealRoots() give the right answer
1289		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1106 | Line 1315 | namespace OpenMD {
1315		RealType diff;
1316		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1317		vector<pair<RealType,RealType> >::iterator rpi;
1318	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1318	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1319		r1 = (*rpi).first;
1320		r2 = (*rpi).second;
1321		switch(rnemdFluxType_) {
#	Line 1173 | Line 1382 | namespace OpenMD {
1382		}
1383		vector<StuntDouble*>::iterator sdi;
1384		Vector3d vel;
1385	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1385	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1386		vel = (*sdi)->getVel();
1387		vel.x() *= x;
1388		vel.y() *= y;
#	Line 1184 | Line 1393 | namespace OpenMD {
1393		x = 1.0 + px * (1.0 - x);
1394		y = 1.0 + py * (1.0 - y);
1395		z = 1.0 + pz * (1.0 - z);
1396	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1396	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1397		vel = (*sdi)->getVel();
1398		vel.x() *= x;
1399		vel.y() *= y;
#	Line 1217 | Line 1426 | namespace OpenMD {
1426		failTrialCount_++;
1427		}
1428		}
1429	<
1430	<	void RNEMD::doVSS() {
1429	>
1430	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1431		if (!doRNEMD_) return;
1432	+	int selei;
1433	+	int selej;
1434	+
1435		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1436		RealType time = currentSnap_->getTime();
1437		Mat3x3d hmat = currentSnap_->getHmat();
1438
1227	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1228	–
1229	–	int selei;
1439		StuntDouble* sd;
1231	–	int idx;
1440
1441		vector<StuntDouble*> hotBin, coldBin;
1442
1443		Vector3d Ph(V3Zero);
1444	+	Vector3d Lh(V3Zero);
1445		RealType Mh = 0.0;
1446	+	Mat3x3d Ih(0.0);
1447		RealType Kh = 0.0;
1448		Vector3d Pc(V3Zero);
1449	+	Vector3d Lc(V3Zero);
1450		RealType Mc = 0.0;
1451	+	Mat3x3d Ic(0.0);
1452		RealType Kc = 0.0;
1241	–
1453
1454	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1455	<	sd = seleMan_.nextSelected(selei)) {
1454	>	// Constraints can be on only the linear or angular momentum, but
1455	>	// not both.  Usually, the user will specify which they want, but
1456	>	// in case they don't, the use of periodic boundaries should make
1457	>	// the choice for us.
1458	>	bool doLinearPart = false;
1459	>	bool doAngularPart = false;
1460
1461	<	idx = sd->getLocalIndex();
1461	>	switch (rnemdFluxType_) {
1462	>	case rnemdPx:
1463	>	case rnemdPy:
1464	>	case rnemdPz:
1465	>	case rnemdPvector:
1466	>	case rnemdKePx:
1467	>	case rnemdKePy:
1468	>	case rnemdKePvector:
1469	>	doLinearPart = true;
1470	>	break;
1471	>	case rnemdLx:
1472	>	case rnemdLy:
1473	>	case rnemdLz:
1474	>	case rnemdLvector:
1475	>	case rnemdKeLx:
1476	>	case rnemdKeLy:
1477	>	case rnemdKeLz:
1478	>	case rnemdKeLvector:
1479	>	doAngularPart = true;
1480	>	break;
1481	>	case rnemdKE:
1482	>	case rnemdRotKE:
1483	>	case rnemdFullKE:
1484	>	default:
1485	>	if (usePeriodicBoundaryConditions_)
1486	>	doLinearPart = true;
1487	>	else
1488	>	doAngularPart = true;
1489	>	break;
1490	>	}
1491	>
1492	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1493	>	sd = smanA.nextSelected(selei)) {
1494
1495		Vector3d pos = sd->getPos();
1496
1497		// wrap the stuntdouble's position back into the box:
1498	+
1499	+	if (usePeriodicBoundaryConditions_)
1500	+	currentSnap_->wrapVector(pos);
1501	+
1502	+	RealType mass = sd->getMass();
1503	+	Vector3d vel = sd->getVel();
1504	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1505	+	RealType r2;
1506	+
1507	+	hotBin.push_back(sd);
1508	+	Ph += mass * vel;
1509	+	Mh += mass;
1510	+	Kh += mass * vel.lengthSquare();
1511	+	Lh += mass * cross(rPos, vel);
1512	+	Ih -= outProduct(rPos, rPos) * mass;
1513	+	r2 = rPos.lengthSquare();
1514	+	Ih(0, 0) += mass * r2;
1515	+	Ih(1, 1) += mass * r2;
1516	+	Ih(2, 2) += mass * r2;
1517	+
1518	+	if (rnemdFluxType_ == rnemdFullKE) {
1519	+	if (sd->isDirectional()) {
1520	+	Vector3d angMom = sd->getJ();
1521	+	Mat3x3d I = sd->getI();
1522	+	if (sd->isLinear()) {
1523	+	int i = sd->linearAxis();
1524	+	int j = (i + 1) % 3;
1525	+	int k = (i + 2) % 3;
1526	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1527	+	angMom[k] * angMom[k] / I(k, k);
1528	+	} else {
1529	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1530	+	angMom[1] * angMom[1] / I(1, 1) +
1531	+	angMom[2] * angMom[2] / I(2, 2);
1532	+	}
1533	+	}
1534	+	}
1535	+	}
1536	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1537	+	sd = smanB.nextSelected(selej)) {
1538
1539	+	Vector3d pos = sd->getPos();
1540	+
1541	+	// wrap the stuntdouble's position back into the box:
1542	+
1543		if (usePeriodicBoundaryConditions_)
1544		currentSnap_->wrapVector(pos);
1545	+
1546	+	RealType mass = sd->getMass();
1547	+	Vector3d vel = sd->getVel();
1548	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1549	+	RealType r2;
1550
1551	<	// which bin is this stuntdouble in?
1552	<	bool inA = inSlabA(pos);
1553	<	bool inB = inSlabB(pos);
1551	>	coldBin.push_back(sd);
1552	>	Pc += mass * vel;
1553	>	Mc += mass;
1554	>	Kc += mass * vel.lengthSquare();
1555	>	Lc += mass * cross(rPos, vel);
1556	>	Ic -= outProduct(rPos, rPos) * mass;
1557	>	r2 = rPos.lengthSquare();
1558	>	Ic(0, 0) += mass * r2;
1559	>	Ic(1, 1) += mass * r2;
1560	>	Ic(2, 2) += mass * r2;
1561
1562	<	if (inA || inB) {
1563	<
1564	<	RealType mass = sd->getMass();
1565	<	Vector3d vel = sd->getVel();
1566	<
1567	<	if (inA) {
1568	<	hotBin.push_back(sd);
1569	<	//std::cerr << "before, velocity = " << vel << endl;
1570	<	Ph += mass * vel;
1571	<	//std::cerr << "after, velocity = " << vel << endl;
1572	<	Mh += mass;
1573	<	Kh += mass * vel.lengthSquare();
1574	<	if (rnemdFluxType_ == rnemdFullKE) {
1575	<	if (sd->isDirectional()) {
1576	<	Vector3d angMom = sd->getJ();
1577	<	Mat3x3d I = sd->getI();
1275	<	if (sd->isLinear()) {
1276	<	int i = sd->linearAxis();
1277	<	int j = (i + 1) % 3;
1278	<	int k = (i + 2) % 3;
1279	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1280	<	angMom[k] * angMom[k] / I(k, k);
1281	<	} else {
1282	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1283	<	angMom[1] * angMom[1] / I(1, 1) +
1284	<	angMom[2] * angMom[2] / I(2, 2);
1285	<	}
1286	<	}
1287	<	}
1288	<	} else { //midBin_
1289	<	coldBin.push_back(sd);
1290	<	Pc += mass * vel;
1291	<	Mc += mass;
1292	<	Kc += mass * vel.lengthSquare();
1293	<	if (rnemdFluxType_ == rnemdFullKE) {
1294	<	if (sd->isDirectional()) {
1295	<	Vector3d angMom = sd->getJ();
1296	<	Mat3x3d I = sd->getI();
1297	<	if (sd->isLinear()) {
1298	<	int i = sd->linearAxis();
1299	<	int j = (i + 1) % 3;
1300	<	int k = (i + 2) % 3;
1301	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1302	<	angMom[k] * angMom[k] / I(k, k);
1303	<	} else {
1304	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1305	<	angMom[1] * angMom[1] / I(1, 1) +
1306	<	angMom[2] * angMom[2] / I(2, 2);
1307	<	}
1308	<	}
1309	<	}
1310	<	}
1562	>	if (rnemdFluxType_ == rnemdFullKE) {
1563	>	if (sd->isDirectional()) {
1564	>	Vector3d angMom = sd->getJ();
1565	>	Mat3x3d I = sd->getI();
1566	>	if (sd->isLinear()) {
1567	>	int i = sd->linearAxis();
1568	>	int j = (i + 1) % 3;
1569	>	int k = (i + 2) % 3;
1570	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1571	>	angMom[k] * angMom[k] / I(k, k);
1572	>	} else {
1573	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1574	>	angMom[1] * angMom[1] / I(1, 1) +
1575	>	angMom[2] * angMom[2] / I(2, 2);
1576	>	}
1577	>	}
1578		}
1579		}
1580
1581		Kh *= 0.5;
1582		Kc *= 0.5;
1316	–
1317	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1318	–	//        << "\tKc= " << Kc << endl;
1319	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1583
1584		#ifdef IS_MPI
1585		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1586		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1587	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1589		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1590		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1591		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1592		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1596	+	MPI::REALTYPE, MPI::SUM);
1597		#endif
1598	+
1599
1600	+	Vector3d ac, acrec, bc, bcrec;
1601	+	Vector3d ah, ahrec, bh, bhrec;
1602	+
1603		bool successfulExchange = false;
1604		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1605		Vector3d vc = Pc / Mc;
1606	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1607	<	Vector3d acrec = -momentumTarget_ / Mc;
1608	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1606	>	ac = -momentumTarget_ / Mc + vc;
1607	>	acrec = -momentumTarget_ / Mc;
1608	>
1609	>	// We now need the inverse of the inertia tensor to calculate the
1610	>	// angular velocity of the cold slab;
1611	>	Mat3x3d Ici = Ic.inverse();
1612	>	Vector3d omegac = Ici * Lc;
1613	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1614	>	bcrec = bc - omegac;
1615	>
1616	>	RealType cNumerator = Kc - kineticTarget_;
1617	>	if (doLinearPart)
1618	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1619	>
1620	>	if (doAngularPart)
1621	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1622	>
1623		if (cNumerator > 0.0) {
1624	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1624	>
1625	>	RealType cDenominator = Kc;
1626	>
1627	>	if (doLinearPart)
1628	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1629	>
1630	>	if (doAngularPart)
1631	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1632	>
1633		if (cDenominator > 0.0) {
1634		RealType c = sqrt(cNumerator / cDenominator);
1635		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1636	+
1637		Vector3d vh = Ph / Mh;
1638	<	Vector3d ah = momentumTarget_ / Mh + vh;
1639	<	Vector3d ahrec = momentumTarget_ / Mh;
1640	<	RealType hNumerator = Kh + kineticTarget_
1641	<	- 0.5 * Mh * ah.lengthSquare();
1642	<	if (hNumerator > 0.0) {
1643	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1638	>	ah = momentumTarget_ / Mh + vh;
1639	>	ahrec = momentumTarget_ / Mh;
1640	>
1641	>	// We now need the inverse of the inertia tensor to
1642	>	// calculate the angular velocity of the hot slab;
1643	>	Mat3x3d Ihi = Ih.inverse();
1644	>	Vector3d omegah = Ihi * Lh;
1645	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1646	>	bhrec = bh - omegah;
1647	>
1648	>	RealType hNumerator = Kh + kineticTarget_;
1649	>	if (doLinearPart)
1650	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1651	>
1652	>	if (doAngularPart)
1653	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1654	>
1655	>	if (hNumerator > 0.0) {
1656	>
1657	>	RealType hDenominator = Kh;
1658	>	if (doLinearPart)
1659	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1660	>	if (doAngularPart)
1661	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1662	>
1663		if (hDenominator > 0.0) {
1664		RealType h = sqrt(hNumerator / hDenominator);
1665		if ((h > 0.9) && (h < 1.1)) {
1666	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1352	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1666	>
1667		vector<StuntDouble*>::iterator sdi;
1668		Vector3d vel;
1669	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1669	>	Vector3d rPos;
1670	>
1671	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1672		//vel = (*sdi)->getVel();
1673	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1673	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1674	>	if (doLinearPart)
1675	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1676	>	if (doAngularPart)
1677	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1678	>
1679		(*sdi)->setVel(vel);
1680		if (rnemdFluxType_ == rnemdFullKE) {
1681		if ((*sdi)->isDirectional()) {
#	Line 1363 | Line 1684 | namespace OpenMD {
1684		}
1685		}
1686		}
1687	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1687	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1688		//vel = (*sdi)->getVel();
1689	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1689	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1690	>	if (doLinearPart)
1691	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1692	>	if (doAngularPart)
1693	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1694	>
1695		(*sdi)->setVel(vel);
1696		if (rnemdFluxType_ == rnemdFullKE) {
1697		if ((*sdi)->isDirectional()) {
#	Line 1377 | Line 1703 | namespace OpenMD {
1703		successfulExchange = true;
1704		kineticExchange_ += kineticTarget_;
1705		momentumExchange_ += momentumTarget_;
1706	+	angularMomentumExchange_ += angularMomentumTarget_;
1707		}
1708		}
1709		}
#	Line 1396 | Line 1723 | namespace OpenMD {
1723		}
1724		}
1725
1726	+	RealType RNEMD::getDividingArea() {
1727	+
1728	+	if (hasDividingArea_) return dividingArea_;
1729	+
1730	+	RealType areaA, areaB;
1731	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1732	+
1733	+	if (hasSelectionA_) {
1734	+
1735	+	if (evaluatorA_.hasSurfaceArea())
1736	+	areaA = evaluatorA_.getSurfaceArea();
1737	+	else {
1738	+
1739	+	cerr << "selection A did not have surface area, recomputing\n";
1740	+	int isd;
1741	+	StuntDouble* sd;
1742	+	vector<StuntDouble*> aSites;
1743	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1744	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1745	+	sd = seleManA_.nextSelected(isd)) {
1746	+	aSites.push_back(sd);
1747	+	}
1748	+	#if defined(HAVE_QHULL)
1749	+	ConvexHull* surfaceMeshA = new ConvexHull();
1750	+	surfaceMeshA->computeHull(aSites);
1751	+	areaA = surfaceMeshA->getArea();
1752	+	delete surfaceMeshA;
1753	+	#else
1754	+	sprintf( painCave.errMsg,
1755	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1756	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1757	+	painCave.severity = OPENMD_ERROR;
1758	+	painCave.isFatal = 1;
1759	+	simError();
1760	+	#endif
1761	+	}
1762	+
1763	+	} else {
1764	+	if (usePeriodicBoundaryConditions_) {
1765	+	// in periodic boundaries, the surface area is twice the x-y
1766	+	// area of the current box:
1767	+	areaA = 2.0 * snap->getXYarea();
1768	+	} else {
1769	+	// in non-periodic simulations, without explicitly setting
1770	+	// selections, the sphere radius sets the surface area of the
1771	+	// dividing surface:
1772	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1773	+	}
1774	+	}
1775	+
1776	+	if (hasSelectionB_) {
1777	+	if (evaluatorB_.hasSurfaceArea())
1778	+	areaB = evaluatorB_.getSurfaceArea();
1779	+	else {
1780	+	cerr << "selection B did not have surface area, recomputing\n";
1781	+
1782	+	int isd;
1783	+	StuntDouble* sd;
1784	+	vector<StuntDouble*> bSites;
1785	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1786	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1787	+	sd = seleManB_.nextSelected(isd)) {
1788	+	bSites.push_back(sd);
1789	+	}
1790	+
1791	+	#if defined(HAVE_QHULL)
1792	+	ConvexHull* surfaceMeshB = new ConvexHull();
1793	+	surfaceMeshB->computeHull(bSites);
1794	+	areaB = surfaceMeshB->getArea();
1795	+	delete surfaceMeshB;
1796	+	#else
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1799	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1800	+	painCave.severity = OPENMD_ERROR;
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	#endif
1804	+	}
1805	+
1806	+	} else {
1807	+	if (usePeriodicBoundaryConditions_) {
1808	+	// in periodic boundaries, the surface area is twice the x-y
1809	+	// area of the current box:
1810	+	areaB = 2.0 * snap->getXYarea();
1811	+	} else {
1812	+	// in non-periodic simulations, without explicitly setting
1813	+	// selections, but if a sphereBradius has been set, just use that:
1814	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1815	+	}
1816	+	}
1817	+
1818	+	dividingArea_ = min(areaA, areaB);
1819	+	hasDividingArea_ = true;
1820	+	return dividingArea_;
1821	+	}
1822	+
1823		void RNEMD::doRNEMD() {
1824		if (!doRNEMD_) return;
1825		trialCount_++;
1826	+
1827	+	// object evaluator:
1828	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1829	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1830	+
1831	+	evaluatorA_.loadScriptString(selectionA_);
1832	+	evaluatorB_.loadScriptString(selectionB_);
1833	+
1834	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1835	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1836	+
1837	+	commonA_ = seleManA_ & seleMan_;
1838	+	commonB_ = seleManB_ & seleMan_;
1839	+
1840	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1841	+	// dt = exchange time interval
1842	+	// flux = target flux
1843	+	// dividingArea = smallest dividing surface between the two regions
1844	+
1845	+	hasDividingArea_ = false;
1846	+	RealType area = getDividingArea();
1847	+
1848	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1849	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1850	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1851	+
1852		switch(rnemdMethod_) {
1853		case rnemdSwap:
1854	<	doSwap();
1854	>	doSwap(commonA_, commonB_);
1855		break;
1856		case rnemdNIVS:
1857	<	doNIVS();
1857	>	doNIVS(commonA_, commonB_);
1858		break;
1859		case rnemdVSS:
1860	<	doVSS();
1860	>	doVSS(commonA_, commonB_);
1861		break;
1862		case rnemdUnkownMethod:
1863		default :
#	Line 1418 | Line 1868 | namespace OpenMD {
1868		void RNEMD::collectData() {
1869		if (!doRNEMD_) return;
1870		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1871	+
1872	+	// collectData can be called more frequently than the doRNEMD, so use the
1873	+	// computed area from the last exchange time:
1874	+	RealType area = getDividingArea();
1875	+	areaAccumulator_->add(area);
1876		Mat3x3d hmat = currentSnap_->getHmat();
1422	–
1423	–	areaAccumulator_->add(currentSnap_->getXYarea());
1424	–
1877		seleMan_.setSelectionSet(evaluator_.evaluate());
1878
1879	<	int selei;
1879	>	int selei(0);
1880		StuntDouble* sd;
1881	<	int idx;
1881	>	int binNo;
1882
1883		vector<RealType> binMass(nBins_, 0.0);
1884		vector<RealType> binPx(nBins_, 0.0);
1885		vector<RealType> binPy(nBins_, 0.0);
1886		vector<RealType> binPz(nBins_, 0.0);
1887	+	vector<RealType> binOmegax(nBins_, 0.0);
1888	+	vector<RealType> binOmegay(nBins_, 0.0);
1889	+	vector<RealType> binOmegaz(nBins_, 0.0);
1890		vector<RealType> binKE(nBins_, 0.0);
1891		vector<int> binDOF(nBins_, 0);
1892		vector<int> binCount(nBins_, 0);
#	Line 1439 | Line 1894 | namespace OpenMD {
1894		// alternative approach, track all molecules instead of only those
1895		// selected for scaling/swapping:
1896		/*
1897	<	SimInfo::MoleculeIterator miter;
1898	<	vector<StuntDouble*>::iterator iiter;
1899	<	Molecule* mol;
1900	<	StuntDouble* sd;
1901	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1897	>	SimInfo::MoleculeIterator miter;
1898	>	vector<StuntDouble*>::iterator iiter;
1899	>	Molecule* mol;
1900	>	StuntDouble* sd;
1901	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1902		mol = info_->nextMolecule(miter))
1903		sd is essentially sd
1904	<	for (sd = mol->beginIntegrableObject(iiter);
1905	<	sd != NULL;
1906	<	sd = mol->nextIntegrableObject(iiter))
1904	>	for (sd = mol->beginIntegrableObject(iiter);
1905	>	sd != NULL;
1906	>	sd = mol->nextIntegrableObject(iiter))
1907		*/
1908	+
1909		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1910	<	sd = seleMan_.nextSelected(selei)) {
1911	<
1456	<	idx = sd->getLocalIndex();
1457	<
1910	>	sd = seleMan_.nextSelected(selei)) {
1911	>
1912		Vector3d pos = sd->getPos();
1913
1914		// wrap the stuntdouble's position back into the box:
1915
1916	<	if (usePeriodicBoundaryConditions_)
1916	>	if (usePeriodicBoundaryConditions_) {
1917		currentSnap_->wrapVector(pos);
1918	+	// which bin is this stuntdouble in?
1919	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1920	+	// Shift molecules by half a box to have bins start at 0
1921	+	// The modulo operator is used to wrap the case when we are
1922	+	// beyond the end of the bins back to the beginning.
1923	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1924	+	} else {
1925	+	Vector3d rPos = pos - coordinateOrigin_;
1926	+	binNo = int(rPos.length() / binWidth_);
1927	+	}
1928
1465	–
1466	–	// which bin is this stuntdouble in?
1467	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1468	–	// Shift molecules by half a box to have bins start at 0
1469	–	// The modulo operator is used to wrap the case when we are
1470	–	// beyond the end of the bins back to the beginning.
1471	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1472	–
1929		RealType mass = sd->getMass();
1930		Vector3d vel = sd->getVel();
1931	<
1932	<	binCount[binNo]++;
1933	<	binMass[binNo] += mass;
1934	<	binPx[binNo] += mass*vel.x();
1935	<	binPy[binNo] += mass*vel.y();
1936	<	binPz[binNo] += mass*vel.z();
1937	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1938	<	binDOF[binNo] += 3;
1939	<
1940	<	if (sd->isDirectional()) {
1941	<	Vector3d angMom = sd->getJ();
1942	<	Mat3x3d I = sd->getI();
1943	<	if (sd->isLinear()) {
1944	<	int i = sd->linearAxis();
1945	<	int j = (i + 1) % 3;
1946	<	int k = (i + 2) % 3;
1947	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1948	<	angMom[k] * angMom[k] / I(k, k));
1949	<	binDOF[binNo] += 2;
1950	<	} else {
1951	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1952	<	angMom[1] * angMom[1] / I(1, 1) +
1953	<	angMom[2] * angMom[2] / I(2, 2));
1954	<	binDOF[binNo] += 3;
1931	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1932	>	Vector3d aVel = cross(rPos, vel);
1933	>
1934	>	if (binNo >= 0 && binNo < nBins_)  {
1935	>	binCount[binNo]++;
1936	>	binMass[binNo] += mass;
1937	>	binPx[binNo] += mass*vel.x();
1938	>	binPy[binNo] += mass*vel.y();
1939	>	binPz[binNo] += mass*vel.z();
1940	>	binOmegax[binNo] += aVel.x();
1941	>	binOmegay[binNo] += aVel.y();
1942	>	binOmegaz[binNo] += aVel.z();
1943	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1944	>	binDOF[binNo] += 3;
1945	>
1946	>	if (sd->isDirectional()) {
1947	>	Vector3d angMom = sd->getJ();
1948	>	Mat3x3d I = sd->getI();
1949	>	if (sd->isLinear()) {
1950	>	int i = sd->linearAxis();
1951	>	int j = (i + 1) % 3;
1952	>	int k = (i + 2) % 3;
1953	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1954	>	angMom[k] * angMom[k] / I(k, k));
1955	>	binDOF[binNo] += 2;
1956	>	} else {
1957	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1958	>	angMom[1] * angMom[1] / I(1, 1) +
1959	>	angMom[2] * angMom[2] / I(2, 2));
1960	>	binDOF[binNo] += 3;
1961	>	}
1962		}
1963		}
1964		}
1965
1503	–
1966		#ifdef IS_MPI
1967		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1968		nBins_, MPI::INT, MPI::SUM);
#	Line 1512 | Line 1974 | namespace OpenMD {
1974		nBins_, MPI::REALTYPE, MPI::SUM);
1975		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1976		nBins_, MPI::REALTYPE, MPI::SUM);
1977	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1978	+	nBins_, MPI::REALTYPE, MPI::SUM);
1979	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1980	+	nBins_, MPI::REALTYPE, MPI::SUM);
1981	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1982	+	nBins_, MPI::REALTYPE, MPI::SUM);
1983		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1984		nBins_, MPI::REALTYPE, MPI::SUM);
1985		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
#	Line 1519 | Line 1987 | namespace OpenMD {
1987		#endif
1988
1989		Vector3d vel;
1990	+	Vector3d aVel;
1991		RealType den;
1992		RealType temp;
1993		RealType z;
1994	+	RealType r;
1995		for (int i = 0; i < nBins_; i++) {
1996	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1996	>	if (usePeriodicBoundaryConditions_) {
1997	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1998	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1999	>	/ currentSnap_->getVolume() ;
2000	>	} else {
2001	>	r = (((RealType)i + 0.5) * binWidth_);
2002	>	RealType rinner = (RealType)i * binWidth_;
2003	>	RealType router = (RealType)(i+1) * binWidth_;
2004	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2005	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2006	>	}
2007		vel.x() = binPx[i] / binMass[i];
2008		vel.y() = binPy[i] / binMass[i];
2009		vel.z() = binPz[i] / binMass[i];
2010	<	den = binCount[i] * nBins_ / currentSnap_->getVolume();
2011	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2012	<	PhysicalConstants::energyConvert);
2010	>	aVel.x() = binOmegax[i] / binCount[i];
2011	>	aVel.y() = binOmegay[i] / binCount[i];
2012	>	aVel.z() = binOmegaz[i] / binCount[i];
2013
2014	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2015	<	if(outputMask_[j]) {
2016	<	switch(j) {
2017	<	case Z:
2018	<	(data_[j].accumulator[i])->add(z);
2019	<	break;
2020	<	case TEMPERATURE:
2021	<	data_[j].accumulator[i]->add(temp);
2022	<	break;
2023	<	case VELOCITY:
2024	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2025	<	break;
2026	<	case DENSITY:
2027	<	data_[j].accumulator[i]->add(den);
2028	<	break;
2014	>	if (binCount[i] > 0) {
2015	>	// only add values if there are things to add
2016	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2017	>	PhysicalConstants::energyConvert);
2018	>
2019	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2020	>	if(outputMask_[j]) {
2021	>	switch(j) {
2022	>	case Z:
2023	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2024	>	break;
2025	>	case R:
2026	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2027	>	break;
2028	>	case TEMPERATURE:
2029	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2030	>	break;
2031	>	case VELOCITY:
2032	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2033	>	break;
2034	>	case ANGULARVELOCITY:
2035	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2036	>	break;
2037	>	case DENSITY:
2038	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2039	>	break;
2040	>	}
2041		}
2042		}
2043		}
2044		}
2045	+	hasData_ = true;
2046		}
2047
2048		void RNEMD::getStarted() {
2049		if (!doRNEMD_) return;
2050	+	hasDividingArea_ = false;
2051		collectData();
2052		writeOutputFile();
2053		}
#	Line 1581 | Line 2075 | namespace OpenMD {
2075
2076		void RNEMD::writeOutputFile() {
2077		if (!doRNEMD_) return;
2078	+	if (!hasData_) return;
2079
2080		#ifdef IS_MPI
2081		// If we're the root node, should we print out the results
#	Line 1602 | Line 2097 | namespace OpenMD {
2097		RealType time = currentSnap_->getTime();
2098		RealType avgArea;
2099		areaAccumulator_->getAverage(avgArea);
1605	–	RealType Jz = kineticExchange_ / (2.0 * time * avgArea);
1606	–	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
2100
2101	+	RealType Jz(0.0);
2102	+	Vector3d JzP(V3Zero);
2103	+	Vector3d JzL(V3Zero);
2104	+	if (time >= info_->getSimParams()->getDt()) {
2105	+	Jz = kineticExchange_ / (time * avgArea)
2106	+	/ PhysicalConstants::energyConvert;
2107	+	JzP = momentumExchange_ / (time * avgArea);
2108	+	JzL = angularMomentumExchange_ / (time * avgArea);
2109	+	}
2110	+
2111		rnemdFile_ << "#######################################################\n";
2112		rnemdFile_ << "# RNEMD {\n";
2113
#	Line 1623 | Line 2126 | namespace OpenMD {
2126
2127		rnemdFile_ << "#    objectSelection = \""
2128		<< rnemdObjectSelection_ << "\";\n";
2129	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
2130	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1628	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
2129	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2130	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2131		rnemdFile_ << "# }\n";
2132		rnemdFile_ << "#######################################################\n";
2133		rnemdFile_ << "# RNEMD report:\n";
2134	<	rnemdFile_ << "#     running time = " << time << " fs\n";
2135	<	rnemdFile_ << "#     target flux:\n";
2136	<	rnemdFile_ << "#         kinetic = " << kineticFlux_ << "\n";
2137	<	rnemdFile_ << "#         momentum = " << momentumFluxVector_ << "\n";
2138	<	rnemdFile_ << "#     target one-time exchanges:\n";
2139	<	rnemdFile_ << "#         kinetic = " << kineticTarget_ << "\n";
2140	<	rnemdFile_ << "#         momentum = " << momentumTarget_ << "\n";
2141	<	rnemdFile_ << "#     actual exchange totals:\n";
2142	<	rnemdFile_ << "#         kinetic = " << kineticExchange_ << "\n";
2143	<	rnemdFile_ << "#         momentum = " << momentumExchange_  << "\n";
2144	<	rnemdFile_ << "#     actual flux:\n";
2145	<	rnemdFile_ << "#         kinetic = " << Jz << "\n";
2146	<	rnemdFile_ << "#         momentum = " << JzP  << "\n";
2147	<	rnemdFile_ << "#     exchange statistics:\n";
2148	<	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
2149	<	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
2134	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2135	>	rnemdFile_ << "# Target flux:\n";
2136	>	rnemdFile_ << "#           kinetic = "
2137	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2138	>	<< " (kcal/mol/A^2/fs)\n";
2139	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2140	>	<< " (amu/A/fs^2)\n";
2141	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2142	>	<< " (amu/A^2/fs^2)\n";
2143	>	rnemdFile_ << "# Target one-time exchanges:\n";
2144	>	rnemdFile_ << "#          kinetic = "
2145	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2146	>	<< " (kcal/mol)\n";
2147	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2148	>	<< " (amu*A/fs)\n";
2149	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2150	>	<< " (amu*A^2/fs)\n";
2151	>	rnemdFile_ << "# Actual exchange totals:\n";
2152	>	rnemdFile_ << "#          kinetic = "
2153	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2154	>	<< " (kcal/mol)\n";
2155	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2156	>	<< " (amu*A/fs)\n";
2157	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2158	>	<< " (amu*A^2/fs)\n";
2159	>	rnemdFile_ << "# Actual flux:\n";
2160	>	rnemdFile_ << "#          kinetic = " << Jz
2161	>	<< " (kcal/mol/A^2/fs)\n";
2162	>	rnemdFile_ << "#          momentum = " << JzP
2163	>	<< " (amu/A/fs^2)\n";
2164	>	rnemdFile_ << "#  angular momentum = " << JzL
2165	>	<< " (amu/A^2/fs^2)\n";
2166	>	rnemdFile_ << "# Exchange statistics:\n";
2167	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2168	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2169		if (rnemdMethod_ == rnemdNIVS) {
2170	<	rnemdFile_ << "#         NIVS root-check errors = "
2170	>	rnemdFile_ << "#  NIVS root-check errors = "
2171		<< failRootCount_ << "\n";
2172		}
2173		rnemdFile_ << "#######################################################\n";
#	Line 1659 | Line 2180 | namespace OpenMD {
2180		if (outputMask_[i]) {
2181		rnemdFile_ << "\t" << data_[i].title <<
2182		"(" << data_[i].units << ")";
2183	+	// add some extra tabs for column alignment
2184	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2185		}
2186		}
2187		rnemdFile_ << std::endl;
2188
2189		rnemdFile_.precision(8);
2190
2191	<	for (unsigned int j = 0; j < nBins_; j++) {
2191	>	for (int j = 0; j < nBins_; j++) {
2192
2193		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2194		if (outputMask_[i]) {
2195		if (data_[i].dataType == "RealType")
2196		writeReal(i,j);
2197	<	else if (data_[i].dataType == "Vector3d")
2197	>	else if (data_[i].dataType == "Vector3d")
2198		writeVector(i,j);
2199		else {
2200		sprintf( painCave.errMsg,
#	Line 1691 | Line 2214 | namespace OpenMD {
2214		rnemdFile_ << "#######################################################\n";
2215
2216
2217	<	for (unsigned int j = 0; j < nBins_; j++) {
2217	>	for (int j = 0; j < nBins_; j++) {
2218		rnemdFile_ << "#";
2219		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2220		if (outputMask_[i]) {
#	Line 1724 | Line 2247 | namespace OpenMD {
2247		void RNEMD::writeReal(int index, unsigned int bin) {
2248		if (!doRNEMD_) return;
2249		assert(index >=0 && index < ENDINDEX);
2250	<	assert(bin < nBins_);
2250	>	assert(int(bin) < nBins_);
2251		RealType s;
2252	+	int count;
2253
2254	<	data_[index].accumulator[bin]->getAverage(s);
2254	>	count = data_[index].accumulator[bin]->count();
2255	>	if (count == 0) return;
2256
2257	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2258	+
2259		if (! isinf(s) && ! isnan(s)) {
2260		rnemdFile_ << "\t" << s;
2261		} else{
2262		sprintf( painCave.errMsg,
2263	<	"RNEMD detected a numerical error writing: %s for bin %d",
2263	>	"RNEMD detected a numerical error writing: %s for bin %u",
2264		data_[index].title.c_str(), bin);
2265		painCave.isFatal = 1;
2266		simError();
#	Line 1743 | Line 2270 | namespace OpenMD {
2270		void RNEMD::writeVector(int index, unsigned int bin) {
2271		if (!doRNEMD_) return;
2272		assert(index >=0 && index < ENDINDEX);
2273	<	assert(bin < nBins_);
2273	>	assert(int(bin) < nBins_);
2274		Vector3d s;
2275	+	int count;
2276	+
2277	+	count = data_[index].accumulator[bin]->count();
2278	+
2279	+	if (count == 0) return;
2280	+
2281		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2282		if (isinf(s[0]) || isnan(s[0]) ||
2283		isinf(s[1]) || isnan(s[1]) ||
2284		isinf(s[2]) || isnan(s[2]) ) {
2285		sprintf( painCave.errMsg,
2286	<	"RNEMD detected a numerical error writing: %s for bin %d",
2286	>	"RNEMD detected a numerical error writing: %s for bin %u",
2287		data_[index].title.c_str(), bin);
2288		painCave.isFatal = 1;
2289		simError();
#	Line 1762 | Line 2295 | namespace OpenMD {
2295		void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2296		if (!doRNEMD_) return;
2297		assert(index >=0 && index < ENDINDEX);
2298	<	assert(bin < nBins_);
2298	>	assert(int(bin) < nBins_);
2299		RealType s;
2300	+	int count;
2301
2302	<	data_[index].accumulator[bin]->getStdDev(s);
2302	>	count = data_[index].accumulator[bin]->count();
2303	>	if (count == 0) return;
2304
2305	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2306	+
2307		if (! isinf(s) && ! isnan(s)) {
2308		rnemdFile_ << "\t" << s;
2309		} else{
2310		sprintf( painCave.errMsg,
2311	<	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2311	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2312		data_[index].title.c_str(), bin);
2313		painCave.isFatal = 1;
2314		simError();
#	Line 1781 | Line 2318 | namespace OpenMD {
2318		void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2319		if (!doRNEMD_) return;
2320		assert(index >=0 && index < ENDINDEX);
2321	<	assert(bin < nBins_);
2321	>	assert(int(bin) < nBins_);
2322		Vector3d s;
2323	+	int count;
2324	+
2325	+	count = data_[index].accumulator[bin]->count();
2326	+	if (count == 0) return;
2327	+
2328		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2329		if (isinf(s[0]) || isnan(s[0]) ||
2330		isinf(s[1]) || isnan(s[1]) ||
2331		isinf(s[2]) || isnan(s[2]) ) {
2332		sprintf( painCave.errMsg,
2333	<	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2333	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2334		data_[index].title.c_str(), bin);
2335		painCave.isFatal = 1;
2336		simError();

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