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

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1774 by gezelter, Wed Aug 8 16:03:02 2012 UTC vs.
Revision 1861 by gezelter, Tue Apr 9 19:45:54 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		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
76
77		trialCount_ = 0;
78		failTrialCount_ = 0;
79		failRootCount_ = 0;
80
81	<	int seedValue;
69	<	Globals * simParams = info->getSimParams();
81	>	Globals* simParams = info->getSimParams();
82		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83
84	+	doRNEMD_ = rnemdParams->getUseRNEMD();
85	+	if (!doRNEMD_) return;
86	+
87		stringToMethod_["Swap"]  = rnemdSwap;
88		stringToMethod_["NIVS"]  = rnemdNIVS;
89		stringToMethod_["VSS"]   = rnemdVSS;
#	Line 77 | Line 92 | namespace OpenMD {
92		stringToFluxType_["Px"]  = rnemdPx;
93		stringToFluxType_["Py"]  = rnemdPy;
94		stringToFluxType_["Pz"]  = rnemdPz;
95	+	stringToFluxType_["Pvector"]  = rnemdPvector;
96	+	stringToFluxType_["Lx"]  = rnemdLx;
97	+	stringToFluxType_["Ly"]  = rnemdLy;
98	+	stringToFluxType_["Lz"]  = rnemdLz;
99	+	stringToFluxType_["Lvector"]  = rnemdLvector;
100		stringToFluxType_["KE+Px"]  = rnemdKePx;
101		stringToFluxType_["KE+Py"]  = rnemdKePy;
102		stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
103	+	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
104	+	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
105	+	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
106	+	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
107
108		runTime_ = simParams->getRunTime();
109		statusTime_ = simParams->getStatusTime();
110
87	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88	–	evaluator_.loadScriptString(rnemdObjectSelection_);
89	–	seleMan_.setSelectionSet(evaluator_.evaluate());
90	–
111		const string methStr = rnemdParams->getMethod();
112		bool hasFluxType = rnemdParams->haveFluxType();
113
114	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115	+
116		string fluxStr;
117		if (hasFluxType) {
118		fluxStr = rnemdParams->getFluxType();
#	Line 98 | Line 120 | namespace OpenMD {
120		sprintf(painCave.errMsg,
121		"RNEMD: No fluxType was set in the md file.  This parameter,\n"
122		"\twhich must be one of the following values:\n"
123	<	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
124	<	"\tuse RNEMD\n");
123	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
124	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
125	>	"\tmust be set to use RNEMD\n");
126		painCave.isFatal = 1;
127		painCave.severity = OPENMD_ERROR;
128		simError();
#	Line 108 | Line 131 | namespace OpenMD {
131		bool hasKineticFlux = rnemdParams->haveKineticFlux();
132		bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
133		bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
134	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
135	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
136	+	hasSelectionA_ = rnemdParams->haveSelectionA();
137	+	hasSelectionB_ = rnemdParams->haveSelectionB();
138		bool hasSlabWidth = rnemdParams->haveSlabWidth();
139		bool hasSlabACenter = rnemdParams->haveSlabACenter();
140		bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
141	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
142	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
143	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
144		bool hasOutputFileName = rnemdParams->haveOutputFileName();
145		bool hasOutputFields = rnemdParams->haveOutputFields();
146
#	Line 195 | Line 225 | namespace OpenMD {
225		case rnemdPz:
226		hasCorrectFlux = hasMomentumFlux;
227		break;
228	+	case rnemdLx:
229	+	case rnemdLy:
230	+	case rnemdLz:
231	+	hasCorrectFlux = hasAngularMomentumFlux;
232	+	break;
233		case rnemdPvector:
234		hasCorrectFlux = hasMomentumFluxVector;
235	+	break;
236	+	case rnemdLvector:
237	+	hasCorrectFlux = hasAngularMomentumFluxVector;
238	+	break;
239		case rnemdKePx:
240		case rnemdKePy:
241		hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
242		break;
243	+	case rnemdKeLx:
244	+	case rnemdKeLy:
245	+	case rnemdKeLz:
246	+	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
247	+	break;
248		case rnemdKePvector:
249		hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
250		break;
251	+	case rnemdKeLvector:
252	+	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
253	+	break;
254		default:
255		methodFluxMismatch = true;
256		break;
#	Line 224 | Line 271 | namespace OpenMD {
271		}
272		if (!hasCorrectFlux) {
273		sprintf(painCave.errMsg,
274	<	"RNEMD: The current method,\n"
228	<	"\t%s, and flux type %s\n"
274	>	"RNEMD: The current method, %s, and flux type, %s,\n"
275		"\tdid not have the correct flux value specified. Options\n"
276	<	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
276	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
277	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
278		methStr.c_str(), fluxStr.c_str());
279		painCave.isFatal = 1;
280		painCave.severity = OPENMD_ERROR;
#	Line 235 | Line 282 | namespace OpenMD {
282		}
283
284		if (hasKineticFlux) {
285	<	kineticFlux_ = rnemdParams->getKineticFlux();
285	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
286	>	// into  amu / fs^3:
287	>	kineticFlux_ = rnemdParams->getKineticFlux()
288	>	* PhysicalConstants::energyConvert;
289		} else {
290		kineticFlux_ = 0.0;
291		}
#	Line 264 | Line 314 | namespace OpenMD {
314		default:
315		break;
316		}
317	<	}
318	<	}
319	<
320	<	// do some sanity checking
321	<
322	<	int selectionCount = seleMan_.getSelectionCount();
323	<	int nIntegrable = info->getNGlobalIntegrableObjects();
324	<
325	<	if (selectionCount > nIntegrable) {
326	<	sprintf(painCave.errMsg,
327	<	"RNEMD: The current objectSelection,\n"
328	<	"\t\t%s\n"
329	<	"\thas resulted in %d selected objects.  However,\n"
330	<	"\tthe total number of integrable objects in the system\n"
331	<	"\tis only %d.  This is almost certainly not what you want\n"
332	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
333	<	"\tselector in the selection script!\n",
334	<	rnemdObjectSelection_.c_str(),
335	<	selectionCount, nIntegrable);
336	<	painCave.isFatal = 0;
337	<	painCave.severity = OPENMD_WARNING;
338	<	simError();
339	<	}
340	<
341	<	areaAccumulator_ = new Accumulator();
342	<
343	<	nBins_ = rnemdParams->getOutputBins();
317	>	}
318	>	if (hasAngularMomentumFluxVector) {
319	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
320	>	} else {
321	>	angularMomentumFluxVector_ = V3Zero;
322	>	if (hasAngularMomentumFlux) {
323	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
324	>	switch (rnemdFluxType_) {
325	>	case rnemdLx:
326	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
327	>	break;
328	>	case rnemdLy:
329	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
330	>	break;
331	>	case rnemdLz:
332	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
333	>	break;
334	>	case rnemdKeLx:
335	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
336	>	break;
337	>	case rnemdKeLy:
338	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
339	>	break;
340	>	case rnemdKeLz:
341	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
342	>	break;
343	>	default:
344	>	break;
345	>	}
346	>	}
347	>	}
348
349	<	data_.resize(RNEMD::ENDINDEX);
350	<	OutputData z;
351	<	z.units =  "Angstroms";
352	<	z.title =  "Z";
353	<	z.dataType = "RealType";
300	<	z.accumulator.reserve(nBins_);
301	<	for (unsigned int i = 0; i < nBins_; i++)
302	<	z.accumulator.push_back( new Accumulator() );
303	<	data_[Z] = z;
304	<	outputMap_["Z"] =  Z;
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351	>	} else {
352	>	coordinateOrigin_ = V3Zero;
353	>	}
354
355	<	OutputData temperature;
307	<	temperature.units =  "K";
308	<	temperature.title =  "Temperature";
309	<	temperature.dataType = "RealType";
310	<	temperature.accumulator.reserve(nBins_);
311	<	for (unsigned int i = 0; i < nBins_; i++)
312	<	temperature.accumulator.push_back( new Accumulator() );
313	<	data_[TEMPERATURE] = temperature;
314	<	outputMap_["TEMPERATURE"] =  TEMPERATURE;
355	>	// do some sanity checking
356
357	<	OutputData velocity;
317	<	velocity.units = "amu/fs";
318	<	velocity.title =  "Velocity";
319	<	velocity.dataType = "Vector3d";
320	<	velocity.accumulator.reserve(nBins_);
321	<	for (unsigned int i = 0; i < nBins_; i++)
322	<	velocity.accumulator.push_back( new VectorAccumulator() );
323	<	data_[VELOCITY] = velocity;
324	<	outputMap_["VELOCITY"] = VELOCITY;
357	>	int selectionCount = seleMan_.getSelectionCount();
358
359	<	OutputData density;
360	<	density.units =  "g cm^-3";
361	<	density.title =  "Density";
362	<	density.dataType = "RealType";
363	<	density.accumulator.reserve(nBins_);
364	<	for (unsigned int i = 0; i < nBins_; i++)
365	<	density.accumulator.push_back( new Accumulator() );
366	<	data_[DENSITY] = density;
367	<	outputMap_["DENSITY"] =  DENSITY;
359	>	int nIntegrable = info->getNGlobalIntegrableObjects();
360	>
361	>	if (selectionCount > nIntegrable) {
362	>	sprintf(painCave.errMsg,
363	>	"RNEMD: The current objectSelection,\n"
364	>	"\t\t%s\n"
365	>	"\thas resulted in %d selected objects.  However,\n"
366	>	"\tthe total number of integrable objects in the system\n"
367	>	"\tis only %d.  This is almost certainly not what you want\n"
368	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
369	>	"\tselector in the selection script!\n",
370	>	rnemdObjectSelection_.c_str(),
371	>	selectionCount, nIntegrable);
372	>	painCave.isFatal = 0;
373	>	painCave.severity = OPENMD_WARNING;
374	>	simError();
375	>	}
376	>
377	>	areaAccumulator_ = new Accumulator();
378	>
379	>	nBins_ = rnemdParams->getOutputBins();
380	>	binWidth_ = rnemdParams->getOutputBinWidth();
381	>
382	>	data_.resize(RNEMD::ENDINDEX);
383	>	OutputData z;
384	>	z.units =  "Angstroms";
385	>	z.title =  "Z";
386	>	z.dataType = "RealType";
387	>	z.accumulator.reserve(nBins_);
388	>	for (int i = 0; i < nBins_; i++)
389	>	z.accumulator.push_back( new Accumulator() );
390	>	data_[Z] = z;
391	>	outputMap_["Z"] =  Z;
392
393	<	if (hasOutputFields) {
394	<	parseOutputFileFormat(rnemdParams->getOutputFields());
395	<	} else {
396	<	outputMask_.set(Z);
397	<	switch (rnemdFluxType_) {
398	<	case rnemdKE:
399	<	case rnemdRotKE:
400	<	case rnemdFullKE:
401	<	outputMask_.set(TEMPERATURE);
345	<	break;
346	<	case rnemdPx:
347	<	case rnemdPy:
348	<	outputMask_.set(VELOCITY);
349	<	break;
350	<	case rnemdPz:
351	<	case rnemdPvector:
352	<	outputMask_.set(VELOCITY);
353	<	outputMask_.set(DENSITY);
354	<	break;
355	<	case rnemdKePx:
356	<	case rnemdKePy:
357	<	outputMask_.set(TEMPERATURE);
358	<	outputMask_.set(VELOCITY);
359	<	break;
360	<	case rnemdKePvector:
361	<	outputMask_.set(TEMPERATURE);
362	<	outputMask_.set(VELOCITY);
363	<	outputMask_.set(DENSITY);
364	<	break;
365	<	default:
366	<	break;
367	<	}
368	<	}
369	<
370	<	if (hasOutputFileName) {
371	<	rnemdFileName_ = rnemdParams->getOutputFileName();
372	<	} else {
373	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
374	<	}
393	>	OutputData r;
394	>	r.units =  "Angstroms";
395	>	r.title =  "R";
396	>	r.dataType = "RealType";
397	>	r.accumulator.reserve(nBins_);
398	>	for (int i = 0; i < nBins_; i++)
399	>	r.accumulator.push_back( new Accumulator() );
400	>	data_[R] = r;
401	>	outputMap_["R"] =  R;
402
403	<	exchangeTime_ = rnemdParams->getExchangeTime();
403	>	OutputData temperature;
404	>	temperature.units =  "K";
405	>	temperature.title =  "Temperature";
406	>	temperature.dataType = "RealType";
407	>	temperature.accumulator.reserve(nBins_);
408	>	for (int i = 0; i < nBins_; i++)
409	>	temperature.accumulator.push_back( new Accumulator() );
410	>	data_[TEMPERATURE] = temperature;
411	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
412
413	<	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
414	<	Mat3x3d hmat = currentSnap_->getHmat();
415	<
416	<	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
417	<	// Lx, Ly = box dimensions in x & y
418	<	// dt = exchange time interval
419	<	// flux = target flux
413	>	OutputData velocity;
414	>	velocity.units = "angstroms/fs";
415	>	velocity.title =  "Velocity";
416	>	velocity.dataType = "Vector3d";
417	>	velocity.accumulator.reserve(nBins_);
418	>	for (int i = 0; i < nBins_; i++)
419	>	velocity.accumulator.push_back( new VectorAccumulator() );
420	>	data_[VELOCITY] = velocity;
421	>	outputMap_["VELOCITY"] = VELOCITY;
422
423	<	RealType area = currentSnap_->getXYarea();
424	<	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
425	<	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
423	>	OutputData angularVelocity;
424	>	angularVelocity.units = "angstroms^2/fs";
425	>	angularVelocity.title =  "AngularVelocity";
426	>	angularVelocity.dataType = "Vector3d";
427	>	angularVelocity.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
430	>	data_[ANGULARVELOCITY] = angularVelocity;
431	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
432
433	<	// total exchange sums are zeroed out at the beginning:
433	>	OutputData density;
434	>	density.units =  "g cm^-3";
435	>	density.title =  "Density";
436	>	density.dataType = "RealType";
437	>	density.accumulator.reserve(nBins_);
438	>	for (int i = 0; i < nBins_; i++)
439	>	density.accumulator.push_back( new Accumulator() );
440	>	data_[DENSITY] = density;
441	>	outputMap_["DENSITY"] =  DENSITY;
442
443	<	kineticExchange_ = 0.0;
444	<	momentumExchange_ = V3Zero;
443	>	if (hasOutputFields) {
444	>	parseOutputFileFormat(rnemdParams->getOutputFields());
445	>	} else {
446	>	if (usePeriodicBoundaryConditions_)
447	>	outputMask_.set(Z);
448	>	else
449	>	outputMask_.set(R);
450	>	switch (rnemdFluxType_) {
451	>	case rnemdKE:
452	>	case rnemdRotKE:
453	>	case rnemdFullKE:
454	>	outputMask_.set(TEMPERATURE);
455	>	break;
456	>	case rnemdPx:
457	>	case rnemdPy:
458	>	outputMask_.set(VELOCITY);
459	>	break;
460	>	case rnemdPz:
461	>	case rnemdPvector:
462	>	outputMask_.set(VELOCITY);
463	>	outputMask_.set(DENSITY);
464	>	break;
465	>	case rnemdLx:
466	>	case rnemdLy:
467	>	case rnemdLz:
468	>	case rnemdLvector:
469	>	outputMask_.set(ANGULARVELOCITY);
470	>	break;
471	>	case rnemdKeLx:
472	>	case rnemdKeLy:
473	>	case rnemdKeLz:
474	>	case rnemdKeLvector:
475	>	outputMask_.set(TEMPERATURE);
476	>	outputMask_.set(ANGULARVELOCITY);
477	>	break;
478	>	case rnemdKePx:
479	>	case rnemdKePy:
480	>	outputMask_.set(TEMPERATURE);
481	>	outputMask_.set(VELOCITY);
482	>	break;
483	>	case rnemdKePvector:
484	>	outputMask_.set(TEMPERATURE);
485	>	outputMask_.set(VELOCITY);
486	>	outputMask_.set(DENSITY);
487	>	break;
488	>	default:
489	>	break;
490	>	}
491	>	}
492	>
493	>	if (hasOutputFileName) {
494	>	rnemdFileName_ = rnemdParams->getOutputFileName();
495	>	} else {
496	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
497	>	}
498
499	<	if (hasSlabWidth)
500	<	slabWidth_ = rnemdParams->getSlabWidth();
501	<	else
502	<	slabWidth_ = hmat(2,2) / 10.0;
503	<
504	<	if (hasSlabACenter)
505	<	slabACenter_ = rnemdParams->getSlabACenter();
506	<	else
507	<	slabACenter_ = 0.0;
499	>	exchangeTime_ = rnemdParams->getExchangeTime();
500	>
501	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
502	>	// total exchange sums are zeroed out at the beginning:
503	>
504	>	kineticExchange_ = 0.0;
505	>	momentumExchange_ = V3Zero;
506	>	angularMomentumExchange_ = V3Zero;
507	>
508	>	std::ostringstream selectionAstream;
509	>	std::ostringstream selectionBstream;
510
511	<	if (hasSlabBCenter)
512	<	slabBCenter_ = rnemdParams->getSlabBCenter();
513	<	else
514	<	slabBCenter_ = hmat(2,2) / 2.0;
511	>	if (hasSelectionA_) {
512	>	selectionA_ = rnemdParams->getSelectionA();
513	>	} else {
514	>	if (usePeriodicBoundaryConditions_) {
515	>	Mat3x3d hmat = currentSnap_->getHmat();
516	>
517	>	if (hasSlabWidth)
518	>	slabWidth_ = rnemdParams->getSlabWidth();
519	>	else
520	>	slabWidth_ = hmat(2,2) / 10.0;
521	>
522	>	if (hasSlabACenter)
523	>	slabACenter_ = rnemdParams->getSlabACenter();
524	>	else
525	>	slabACenter_ = 0.0;
526	>
527	>	selectionAstream << "select wrappedz > "
528	>	<< slabACenter_ - 0.5*slabWidth_
529	>	<<  " && wrappedz < "
530	>	<< slabACenter_ + 0.5*slabWidth_;
531	>	selectionA_ = selectionAstream.str();
532	>	} else {
533	>	if (hasSphereARadius)
534	>	sphereARadius_ = rnemdParams->getSphereARadius();
535	>	else {
536	>	// use an initial guess to the size of the inner slab to be 1/10 the
537	>	// radius of an approximately spherical hull:
538	>	Thermo thermo(info);
539	>	RealType hVol = thermo.getHullVolume();
540	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
541	>	}
542	>	selectionAstream << "select r < " << sphereARadius_;
543	>	selectionA_ = selectionAstream.str();
544	>	}
545	>	}
546
547	+	if (hasSelectionB_) {
548	+	selectionB_ = rnemdParams->getSelectionB();
549	+	} else {
550	+	if (usePeriodicBoundaryConditions_) {
551	+	Mat3x3d hmat = currentSnap_->getHmat();
552	+
553	+	if (hasSlabWidth)
554	+	slabWidth_ = rnemdParams->getSlabWidth();
555	+	else
556	+	slabWidth_ = hmat(2,2) / 10.0;
557	+
558	+	if (hasSlabBCenter)
559	+	slabBCenter_ = rnemdParams->getSlabACenter();
560	+	else
561	+	slabBCenter_ = hmat(2,2) / 2.0;
562	+
563	+	selectionBstream << "select wrappedz > "
564	+	<< slabBCenter_ - 0.5*slabWidth_
565	+	<<  " && wrappedz < "
566	+	<< slabBCenter_ + 0.5*slabWidth_;
567	+	selectionB_ = selectionBstream.str();
568	+	} else {
569	+	if (hasSphereBRadius_) {
570	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
571	+	selectionBstream << "select r > " << sphereBRadius_;
572	+	selectionB_ = selectionBstream.str();
573	+	} else {
574	+	selectionB_ = "select hull";
575	+	hasSelectionB_ = true;
576	+	}
577	+	}
578	+	}
579	+	}
580	+	// object evaluator:
581	+	evaluator_.loadScriptString(rnemdObjectSelection_);
582	+	seleMan_.setSelectionSet(evaluator_.evaluate());
583	+
584	+	evaluatorA_.loadScriptString(selectionA_);
585	+	evaluatorB_.loadScriptString(selectionB_);
586	+
587	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	+
590	+	commonA_ = seleManA_ & seleMan_;
591	+	commonB_ = seleManB_ & seleMan_;
592		}
593	<
412	<	RNEMD::~RNEMD() {
593	>
594
595	+	RNEMD::~RNEMD() {
596	+	if (!doRNEMD_) return;
597		#ifdef IS_MPI
598		if (worldRank == 0) {
599		#endif
#	Line 424 | Line 607 | namespace OpenMD {
607		#endif
608		}
609
610	<	bool RNEMD::inSlabA(Vector3d pos) {
611	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
612	<	}
613	<	bool RNEMD::inSlabB(Vector3d pos) {
431	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
432	<	}
610	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
611	>	if (!doRNEMD_) return;
612	>	int selei;
613	>	int selej;
614
434	–	void RNEMD::doSwap() {
435	–
615		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
616		Mat3x3d hmat = currentSnap_->getHmat();
617
439	–	seleMan_.setSelectionSet(evaluator_.evaluate());
440	–
441	–	int selei;
618		StuntDouble* sd;
443	–	int idx;
619
620		RealType min_val;
621		bool min_found = false;
#	Line 450 | Line 625 | namespace OpenMD {
625		bool max_found = false;
626		StuntDouble* max_sd;
627
628	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
629	<	sd = seleMan_.nextSelected(selei)) {
628	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
629	>	sd = seleManA_.nextSelected(selei)) {
630
456	–	idx = sd->getLocalIndex();
457	–
631		Vector3d pos = sd->getPos();
632	<
632	>
633		// wrap the stuntdouble's position back into the box:
634	<
634	>
635		if (usePeriodicBoundaryConditions_)
636		currentSnap_->wrapVector(pos);
637	<	bool inA = inSlabA(pos);
638	<	bool inB = inSlabB(pos);
639	<
640	<	if (inA || inB) {
637	>
638	>	RealType mass = sd->getMass();
639	>	Vector3d vel = sd->getVel();
640	>	RealType value;
641	>
642	>	switch(rnemdFluxType_) {
643	>	case rnemdKE :
644
645	<	RealType mass = sd->getMass();
646	<	Vector3d vel = sd->getVel();
647	<	RealType value;
648	<
649	<	switch(rnemdFluxType_) {
474	<	case rnemdKE :
645	>	value = mass * vel.lengthSquare();
646	>
647	>	if (sd->isDirectional()) {
648	>	Vector3d angMom = sd->getJ();
649	>	Mat3x3d I = sd->getI();
650
651	<	value = mass * vel.lengthSquare();
652	<
653	<	if (sd->isDirectional()) {
654	<	Vector3d angMom = sd->getJ();
655	<	Mat3x3d I = sd->getI();
656	<
657	<	if (sd->isLinear()) {
658	<	int i = sd->linearAxis();
659	<	int j = (i + 1) % 3;
660	<	int k = (i + 2) % 3;
661	<	value += angMom[j] * angMom[j] / I(j, j) +
662	<	angMom[k] * angMom[k] / I(k, k);
663	<	} else {
664	<	value += angMom[0]*angMom[0]/I(0, 0)
665	<	+ angMom[1]*angMom[1]/I(1, 1)
666	<	+ angMom[2]*angMom[2]/I(2, 2);
667	<	}
668	<	} //angular momenta exchange enabled
669	<	//energyConvert temporarily disabled
670	<	//make kineticExchange_ comparable between swap & scale
671	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
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;
651	>	if (sd->isLinear()) {
652	>	int i = sd->linearAxis();
653	>	int j = (i + 1) % 3;
654	>	int k = (i + 2) % 3;
655	>	value += angMom[j] * angMom[j] / I(j, j) +
656	>	angMom[k] * angMom[k] / I(k, k);
657	>	} else {
658	>	value += angMom[0]*angMom[0]/I(0, 0)
659	>	+ angMom[1]*angMom[1]/I(1, 1)
660	>	+ angMom[2]*angMom[2]/I(2, 2);
661	>	}
662	>	} //angular momenta exchange enabled
663	>	value *= 0.5;
664	>	break;
665	>	case rnemdPx :
666	>	value = mass * vel[0];
667	>	break;
668	>	case rnemdPy :
669	>	value = mass * vel[1];
670	>	break;
671	>	case rnemdPz :
672	>	value = mass * vel[2];
673	>	break;
674	>	default :
675	>	break;
676	>	}
677	>	if (!max_found) {
678	>	max_val = value;
679	>	max_sd = sd;
680	>	max_found = true;
681	>	} else {
682	>	if (max_val < value) {
683	>	max_val = value;
684	>	max_sd = sd;
685		}
686	+	}
687	+	}
688
689	<	if (inA == 0) {
690	<	if (!min_found) {
691	<	min_val = value;
692	<	min_sd = sd;
693	<	min_found = true;
694	<	} else {
695	<	if (min_val > value) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	}
699	<	}
700	<	} else {
701	<	if (!max_found) {
702	<	max_val = value;
703	<	max_sd = sd;
704	<	max_found = true;
705	<	} else {
706	<	if (max_val < value) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	}
710	<	}
711	<	}
689	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
690	>	sd = seleManB_.nextSelected(selej)) {
691	>
692	>	Vector3d pos = sd->getPos();
693	>
694	>	// wrap the stuntdouble's position back into the box:
695	>
696	>	if (usePeriodicBoundaryConditions_)
697	>	currentSnap_->wrapVector(pos);
698	>
699	>	RealType mass = sd->getMass();
700	>	Vector3d vel = sd->getVel();
701	>	RealType value;
702	>
703	>	switch(rnemdFluxType_) {
704	>	case rnemdKE :
705	>
706	>	value = mass * vel.lengthSquare();
707	>
708	>	if (sd->isDirectional()) {
709	>	Vector3d angMom = sd->getJ();
710	>	Mat3x3d I = sd->getI();
711	>
712	>	if (sd->isLinear()) {
713	>	int i = sd->linearAxis();
714	>	int j = (i + 1) % 3;
715	>	int k = (i + 2) % 3;
716	>	value += angMom[j] * angMom[j] / I(j, j) +
717	>	angMom[k] * angMom[k] / I(k, k);
718	>	} else {
719	>	value += angMom[0]*angMom[0]/I(0, 0)
720	>	+ angMom[1]*angMom[1]/I(1, 1)
721	>	+ angMom[2]*angMom[2]/I(2, 2);
722	>	}
723	>	} //angular momenta exchange enabled
724	>	value *= 0.5;
725	>	break;
726	>	case rnemdPx :
727	>	value = mass * vel[0];
728	>	break;
729	>	case rnemdPy :
730	>	value = mass * vel[1];
731	>	break;
732	>	case rnemdPz :
733	>	value = mass * vel[2];
734	>	break;
735	>	default :
736	>	break;
737		}
738	+
739	+	if (!min_found) {
740	+	min_val = value;
741	+	min_sd = sd;
742	+	min_found = true;
743	+	} else {
744	+	if (min_val > value) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	}
748	+	}
749		}
750
751	<	#ifdef IS_MPI
752	<	int nProc, worldRank;
751	>	#ifdef IS_MPI
752	>	int worldRank = MPI::COMM_WORLD.Get_rank();
753
541	–	nProc = MPI::COMM_WORLD.Get_size();
542	–	worldRank = MPI::COMM_WORLD.Get_rank();
543	–
754		bool my_min_found = min_found;
755		bool my_max_found = max_found;
756
#	Line 731 | Line 941 | namespace OpenMD {
941
942		switch(rnemdFluxType_) {
943		case rnemdKE:
734	–	cerr << "KE\n";
944		kineticExchange_ += max_val - min_val;
945		break;
946		case rnemdPx:
#	Line 744 | Line 953 | namespace OpenMD {
953		momentumExchange_.z() += max_val - min_val;
954		break;
955		default:
747	–	cerr << "default\n";
956		break;
957		}
958		} else {
#	Line 766 | Line 974 | namespace OpenMD {
974		}
975		}
976
977	<	void RNEMD::doNIVS() {
977	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
978	>	if (!doRNEMD_) return;
979	>	int selei;
980	>	int selej;
981
982		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
983	+	RealType time = currentSnap_->getTime();
984		Mat3x3d hmat = currentSnap_->getHmat();
985
774	–	seleMan_.setSelectionSet(evaluator_.evaluate());
775	–
776	–	int selei;
986		StuntDouble* sd;
778	–	int idx;
987
988		vector<StuntDouble*> hotBin, coldBin;
989
#	Line 794 | Line 1002 | namespace OpenMD {
1002		RealType Kcz = 0.0;
1003		RealType Kcw = 0.0;
1004
1005	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1006	<	sd = seleMan_.nextSelected(selei)) {
799	<
800	<	idx = sd->getLocalIndex();
801	<
802	<	Vector3d pos = sd->getPos();
1005	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1006	>	sd = smanA.nextSelected(selei)) {
1007
1008	+	Vector3d pos = sd->getPos();
1009	+
1010		// wrap the stuntdouble's position back into the box:
1011	<
1011	>
1012		if (usePeriodicBoundaryConditions_)
1013		currentSnap_->wrapVector(pos);
1014	<
1015	<	// which bin is this stuntdouble in?
1016	<	bool inA = inSlabA(pos);
1017	<	bool inB = inSlabB(pos);
1014	>
1015	>
1016	>	RealType mass = sd->getMass();
1017	>	Vector3d vel = sd->getVel();
1018	>
1019	>	hotBin.push_back(sd);
1020	>	Phx += mass * vel.x();
1021	>	Phy += mass * vel.y();
1022	>	Phz += mass * vel.z();
1023	>	Khx += mass * vel.x() * vel.x();
1024	>	Khy += mass * vel.y() * vel.y();
1025	>	Khz += mass * vel.z() * vel.z();
1026	>	if (sd->isDirectional()) {
1027	>	Vector3d angMom = sd->getJ();
1028	>	Mat3x3d I = sd->getI();
1029	>	if (sd->isLinear()) {
1030	>	int i = sd->linearAxis();
1031	>	int j = (i + 1) % 3;
1032	>	int k = (i + 2) % 3;
1033	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1034	>	angMom[k] * angMom[k] / I(k, k);
1035	>	} else {
1036	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1037	>	+ angMom[1]*angMom[1]/I(1, 1)
1038	>	+ angMom[2]*angMom[2]/I(2, 2);
1039	>	}
1040	>	}
1041	>	}
1042	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1043	>	sd = smanB.nextSelected(selej)) {
1044	>	Vector3d pos = sd->getPos();
1045	>
1046	>	// wrap the stuntdouble's position back into the box:
1047	>
1048	>	if (usePeriodicBoundaryConditions_)
1049	>	currentSnap_->wrapVector(pos);
1050	>
1051	>	RealType mass = sd->getMass();
1052	>	Vector3d vel = sd->getVel();
1053
1054	<	if (inA || inB) {
1055	<
1056	<	RealType mass = sd->getMass();
1057	<	Vector3d vel = sd->getVel();
1058	<
1059	<	if (inA) {
1060	<	hotBin.push_back(sd);
1061	<	Phx += mass * vel.x();
1062	<	Phy += mass * vel.y();
1063	<	Phz += mass * vel.z();
1064	<	Khx += mass * vel.x() * vel.x();
1065	<	Khy += mass * vel.y() * vel.y();
1066	<	Khz += mass * vel.z() * vel.z();
1067	<	if (sd->isDirectional()) {
1068	<	Vector3d angMom = sd->getJ();
1069	<	Mat3x3d I = sd->getI();
1070	<	if (sd->isLinear()) {
1071	<	int i = sd->linearAxis();
1072	<	int j = (i + 1) % 3;
1073	<	int k = (i + 2) % 3;
1074	<	Khw += angMom[j] * angMom[j] / I(j, j) +
834	<	angMom[k] * angMom[k] / I(k, k);
835	<	} else {
836	<	Khw += angMom[0]*angMom[0]/I(0, 0)
837	<	+ angMom[1]*angMom[1]/I(1, 1)
838	<	+ angMom[2]*angMom[2]/I(2, 2);
839	<	}
840	<	}
841	<	} else {
842	<	coldBin.push_back(sd);
843	<	Pcx += mass * vel.x();
844	<	Pcy += mass * vel.y();
845	<	Pcz += mass * vel.z();
846	<	Kcx += mass * vel.x() * vel.x();
847	<	Kcy += mass * vel.y() * vel.y();
848	<	Kcz += mass * vel.z() * vel.z();
849	<	if (sd->isDirectional()) {
850	<	Vector3d angMom = sd->getJ();
851	<	Mat3x3d I = sd->getI();
852	<	if (sd->isLinear()) {
853	<	int i = sd->linearAxis();
854	<	int j = (i + 1) % 3;
855	<	int k = (i + 2) % 3;
856	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
857	<	angMom[k] * angMom[k] / I(k, k);
858	<	} else {
859	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
860	<	+ angMom[1]*angMom[1]/I(1, 1)
861	<	+ angMom[2]*angMom[2]/I(2, 2);
862	<	}
863	<	}
864	<	}
1054	>	coldBin.push_back(sd);
1055	>	Pcx += mass * vel.x();
1056	>	Pcy += mass * vel.y();
1057	>	Pcz += mass * vel.z();
1058	>	Kcx += mass * vel.x() * vel.x();
1059	>	Kcy += mass * vel.y() * vel.y();
1060	>	Kcz += mass * vel.z() * vel.z();
1061	>	if (sd->isDirectional()) {
1062	>	Vector3d angMom = sd->getJ();
1063	>	Mat3x3d I = sd->getI();
1064	>	if (sd->isLinear()) {
1065	>	int i = sd->linearAxis();
1066	>	int j = (i + 1) % 3;
1067	>	int k = (i + 2) % 3;
1068	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1069	>	angMom[k] * angMom[k] / I(k, k);
1070	>	} else {
1071	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1072	>	+ angMom[1]*angMom[1]/I(1, 1)
1073	>	+ angMom[2]*angMom[2]/I(2, 2);
1074	>	}
1075		}
1076		}
1077
#	Line 911 | Line 1121 | namespace OpenMD {
1121
1122		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1123		c = sqrt(c);
1124	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
915	<	//now convert to hotBin coefficient
1124	>
1125		RealType w = 0.0;
1126		if (rnemdFluxType_ ==  rnemdFullKE) {
1127		x = 1.0 + px * (1.0 - c);
#	Line 950 | Line 1159 | namespace OpenMD {
1159		}
1160		}
1161		w = sqrt(w);
953	–	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
954	–	//           << "\twh= " << w << endl;
1162		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1163		if (rnemdFluxType_ == rnemdFullKE) {
1164		vel = (*sdi)->getVel();
#	Line 1214 | Line 1421 | namespace OpenMD {
1421		failTrialCount_++;
1422		}
1423		}
1424	<
1425	<	void RNEMD::doVSS() {
1424	>
1425	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1426	>	if (!doRNEMD_) return;
1427	>	int selei;
1428	>	int selej;
1429
1430		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1431		RealType time = currentSnap_->getTime();
1432		Mat3x3d hmat = currentSnap_->getHmat();
1433
1224	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1225	–
1226	–	int selei;
1434		StuntDouble* sd;
1228	–	int idx;
1435
1436		vector<StuntDouble*> hotBin, coldBin;
1437
1438		Vector3d Ph(V3Zero);
1439	+	Vector3d Lh(V3Zero);
1440		RealType Mh = 0.0;
1441	+	Mat3x3d Ih(0.0);
1442		RealType Kh = 0.0;
1443		Vector3d Pc(V3Zero);
1444	+	Vector3d Lc(V3Zero);
1445		RealType Mc = 0.0;
1446	+	Mat3x3d Ic(0.0);
1447		RealType Kc = 0.0;
1238	–
1448
1449	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1450	<	sd = seleMan_.nextSelected(selei)) {
1449	>	// Constraints can be on only the linear or angular momentum, but
1450	>	// not both.  Usually, the user will specify which they want, but
1451	>	// in case they don't, the use of periodic boundaries should make
1452	>	// the choice for us.
1453	>	bool doLinearPart = false;
1454	>	bool doAngularPart = false;
1455
1456	<	idx = sd->getLocalIndex();
1456	>	switch (rnemdFluxType_) {
1457	>	case rnemdPx:
1458	>	case rnemdPy:
1459	>	case rnemdPz:
1460	>	case rnemdPvector:
1461	>	case rnemdKePx:
1462	>	case rnemdKePy:
1463	>	case rnemdKePvector:
1464	>	doLinearPart = true;
1465	>	break;
1466	>	case rnemdLx:
1467	>	case rnemdLy:
1468	>	case rnemdLz:
1469	>	case rnemdLvector:
1470	>	case rnemdKeLx:
1471	>	case rnemdKeLy:
1472	>	case rnemdKeLz:
1473	>	case rnemdKeLvector:
1474	>	doAngularPart = true;
1475	>	break;
1476	>	case rnemdKE:
1477	>	case rnemdRotKE:
1478	>	case rnemdFullKE:
1479	>	default:
1480	>	if (usePeriodicBoundaryConditions_)
1481	>	doLinearPart = true;
1482	>	else
1483	>	doAngularPart = true;
1484	>	break;
1485	>	}
1486	>
1487	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1488	>	sd = smanA.nextSelected(selei)) {
1489
1490		Vector3d pos = sd->getPos();
1491
1492		// wrap the stuntdouble's position back into the box:
1493	+
1494	+	if (usePeriodicBoundaryConditions_)
1495	+	currentSnap_->wrapVector(pos);
1496	+
1497	+	RealType mass = sd->getMass();
1498	+	Vector3d vel = sd->getVel();
1499	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1500	+	RealType r2;
1501	+
1502	+	hotBin.push_back(sd);
1503	+	Ph += mass * vel;
1504	+	Mh += mass;
1505	+	Kh += mass * vel.lengthSquare();
1506	+	Lh += mass * cross(rPos, vel);
1507	+	Ih -= outProduct(rPos, rPos) * mass;
1508	+	r2 = rPos.lengthSquare();
1509	+	Ih(0, 0) += mass * r2;
1510	+	Ih(1, 1) += mass * r2;
1511	+	Ih(2, 2) += mass * r2;
1512	+
1513	+	if (rnemdFluxType_ == rnemdFullKE) {
1514	+	if (sd->isDirectional()) {
1515	+	Vector3d angMom = sd->getJ();
1516	+	Mat3x3d I = sd->getI();
1517	+	if (sd->isLinear()) {
1518	+	int i = sd->linearAxis();
1519	+	int j = (i + 1) % 3;
1520	+	int k = (i + 2) % 3;
1521	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1522	+	angMom[k] * angMom[k] / I(k, k);
1523	+	} else {
1524	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1525	+	angMom[1] * angMom[1] / I(1, 1) +
1526	+	angMom[2] * angMom[2] / I(2, 2);
1527	+	}
1528	+	}
1529	+	}
1530	+	}
1531	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1532	+	sd = smanB.nextSelected(selej)) {
1533
1534	+	Vector3d pos = sd->getPos();
1535	+
1536	+	// wrap the stuntdouble's position back into the box:
1537	+
1538		if (usePeriodicBoundaryConditions_)
1539		currentSnap_->wrapVector(pos);
1540	+
1541	+	RealType mass = sd->getMass();
1542	+	Vector3d vel = sd->getVel();
1543	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1544	+	RealType r2;
1545
1546	<	// which bin is this stuntdouble in?
1547	<	bool inA = inSlabA(pos);
1548	<	bool inB = inSlabB(pos);
1546	>	coldBin.push_back(sd);
1547	>	Pc += mass * vel;
1548	>	Mc += mass;
1549	>	Kc += mass * vel.lengthSquare();
1550	>	Lc += mass * cross(rPos, vel);
1551	>	Ic -= outProduct(rPos, rPos) * mass;
1552	>	r2 = rPos.lengthSquare();
1553	>	Ic(0, 0) += mass * r2;
1554	>	Ic(1, 1) += mass * r2;
1555	>	Ic(2, 2) += mass * r2;
1556
1557	<	if (inA || inB) {
1558	<
1559	<	RealType mass = sd->getMass();
1560	<	Vector3d vel = sd->getVel();
1561	<
1562	<	if (inA) {
1563	<	hotBin.push_back(sd);
1564	<	//std::cerr << "before, velocity = " << vel << endl;
1565	<	Ph += mass * vel;
1566	<	//std::cerr << "after, velocity = " << vel << endl;
1567	<	Mh += mass;
1568	<	Kh += mass * vel.lengthSquare();
1569	<	if (rnemdFluxType_ == rnemdFullKE) {
1570	<	if (sd->isDirectional()) {
1571	<	Vector3d angMom = sd->getJ();
1572	<	Mat3x3d I = sd->getI();
1272	<	if (sd->isLinear()) {
1273	<	int i = sd->linearAxis();
1274	<	int j = (i + 1) % 3;
1275	<	int k = (i + 2) % 3;
1276	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1277	<	angMom[k] * angMom[k] / I(k, k);
1278	<	} else {
1279	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1280	<	angMom[1] * angMom[1] / I(1, 1) +
1281	<	angMom[2] * angMom[2] / I(2, 2);
1282	<	}
1283	<	}
1284	<	}
1285	<	} else { //midBin_
1286	<	coldBin.push_back(sd);
1287	<	Pc += mass * vel;
1288	<	Mc += mass;
1289	<	Kc += mass * vel.lengthSquare();
1290	<	if (rnemdFluxType_ == rnemdFullKE) {
1291	<	if (sd->isDirectional()) {
1292	<	Vector3d angMom = sd->getJ();
1293	<	Mat3x3d I = sd->getI();
1294	<	if (sd->isLinear()) {
1295	<	int i = sd->linearAxis();
1296	<	int j = (i + 1) % 3;
1297	<	int k = (i + 2) % 3;
1298	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1299	<	angMom[k] * angMom[k] / I(k, k);
1300	<	} else {
1301	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1302	<	angMom[1] * angMom[1] / I(1, 1) +
1303	<	angMom[2] * angMom[2] / I(2, 2);
1304	<	}
1305	<	}
1306	<	}
1307	<	}
1557	>	if (rnemdFluxType_ == rnemdFullKE) {
1558	>	if (sd->isDirectional()) {
1559	>	Vector3d angMom = sd->getJ();
1560	>	Mat3x3d I = sd->getI();
1561	>	if (sd->isLinear()) {
1562	>	int i = sd->linearAxis();
1563	>	int j = (i + 1) % 3;
1564	>	int k = (i + 2) % 3;
1565	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1566	>	angMom[k] * angMom[k] / I(k, k);
1567	>	} else {
1568	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1569	>	angMom[1] * angMom[1] / I(1, 1) +
1570	>	angMom[2] * angMom[2] / I(2, 2);
1571	>	}
1572	>	}
1573		}
1574		}
1575
1576		Kh *= 0.5;
1577		Kc *= 0.5;
1313	–
1314	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1315	–	//        << "\tKc= " << Kc << endl;
1316	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1578
1579		#ifdef IS_MPI
1580		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1581		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1582	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1583	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1585		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1586		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1587		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1589	+	MPI::REALTYPE, MPI::SUM);
1590	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1591	+	MPI::REALTYPE, MPI::SUM);
1592		#endif
1593	+
1594
1595	+	Vector3d ac, acrec, bc, bcrec;
1596	+	Vector3d ah, ahrec, bh, bhrec;
1597	+	RealType cNumerator, cDenominator;
1598	+	RealType hNumerator, hDenominator;
1599	+
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	>	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	>	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	>	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	>	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	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1349	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1664	>
1665		vector<StuntDouble*>::iterator sdi;
1666		Vector3d vel;
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 1362 | Line 1684 | namespace OpenMD {
1684		}
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 1374 | Line 1701 | namespace OpenMD {
1701		successfulExchange = true;
1702		kineticExchange_ += kineticTarget_;
1703		momentumExchange_ += momentumTarget_;
1704	+	angularMomentumExchange_ += angularMomentumTarget_;
1705		}
1706		}
1707		}
#	Line 1393 | Line 1721 | namespace OpenMD {
1721		}
1722		}
1723
1724	<	void RNEMD::doRNEMD() {
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	+	ConvexHull* surfaceMeshA = new ConvexHull();
1736	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1737	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1738	+	sd = seleManA_.nextSelected(isd)) {
1739	+	aSites.push_back(sd);
1740	+	}
1741	+	surfaceMeshA->computeHull(aSites);
1742	+	areaA = surfaceMeshA->getArea();
1743	+	} else {
1744	+	if (usePeriodicBoundaryConditions_) {
1745	+	// in periodic boundaries, the surface area is twice the x-y
1746	+	// area of the current box:
1747	+	areaA = 2.0 * snap->getXYarea();
1748	+	} else {
1749	+	// in non-periodic simulations, without explicitly setting
1750	+	// selections, the sphere radius sets the surface area of the
1751	+	// dividing surface:
1752	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1753	+	}
1754	+	}
1755	+
1756	+	if (hasSelectionB_) {
1757	+	int isd;
1758	+	StuntDouble* sd;
1759	+	vector<StuntDouble*> bSites;
1760	+	ConvexHull* surfaceMeshB = new ConvexHull();
1761	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1762	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1763	+	sd = seleManB_.nextSelected(isd)) {
1764	+	bSites.push_back(sd);
1765	+	}
1766	+	surfaceMeshB->computeHull(bSites);
1767	+	areaB = surfaceMeshB->getArea();
1768	+	} else {
1769	+	if (usePeriodicBoundaryConditions_) {
1770	+	// in periodic boundaries, the surface area is twice the x-y
1771	+	// area of the current box:
1772	+	areaB = 2.0 * snap->getXYarea();
1773	+	} else {
1774	+	// in non-periodic simulations, without explicitly setting
1775	+	// selections, but if a sphereBradius has been set, just use that:
1776	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1777	+	}
1778	+	}
1779	+
1780	+	dividingArea_ = min(areaA, areaB);
1781	+	hasDividingArea_ = true;
1782	+	return dividingArea_;
1783	+	}
1784	+
1785	+	void RNEMD::doRNEMD() {
1786	+	if (!doRNEMD_) return;
1787		trialCount_++;
1788	+
1789	+	// object evaluator:
1790	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1791	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1792	+
1793	+	evaluatorA_.loadScriptString(selectionA_);
1794	+	evaluatorB_.loadScriptString(selectionB_);
1795	+
1796	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1797	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1798	+
1799	+	commonA_ = seleManA_ & seleMan_;
1800	+	commonB_ = seleManB_ & seleMan_;
1801	+
1802	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1803	+	// dt = exchange time interval
1804	+	// flux = target flux
1805	+	// dividingArea = smallest dividing surface between the two regions
1806	+
1807	+	hasDividingArea_ = false;
1808	+	RealType area = getDividingArea();
1809	+
1810	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1811	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1812	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1813	+
1814		switch(rnemdMethod_) {
1815		case rnemdSwap:
1816	<	doSwap();
1816	>	doSwap(commonA_, commonB_);
1817		break;
1818		case rnemdNIVS:
1819	<	doNIVS();
1819	>	doNIVS(commonA_, commonB_);
1820		break;
1821		case rnemdVSS:
1822	<	doVSS();
1822	>	doVSS(commonA_, commonB_);
1823		break;
1824		case rnemdUnkownMethod:
1825		default :
#	Line 1413 | Line 1828 | namespace OpenMD {
1828		}
1829
1830		void RNEMD::collectData() {
1831	<
1831	>	if (!doRNEMD_) return;
1832		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1833	+
1834	+	// collectData can be called more frequently than the doRNEMD, so use the
1835	+	// computed area from the last exchange time:
1836	+	RealType area = getDividingArea();
1837	+	areaAccumulator_->add(area);
1838		Mat3x3d hmat = currentSnap_->getHmat();
1419	–
1420	–	areaAccumulator_->add(currentSnap_->getXYarea());
1421	–
1839		seleMan_.setSelectionSet(evaluator_.evaluate());
1840
1841	<	int selei;
1841	>	int selei(0);
1842		StuntDouble* sd;
1843	<	int idx;
1843	>	int binNo;
1844
1845		vector<RealType> binMass(nBins_, 0.0);
1846		vector<RealType> binPx(nBins_, 0.0);
1847		vector<RealType> binPy(nBins_, 0.0);
1848		vector<RealType> binPz(nBins_, 0.0);
1849	+	vector<RealType> binOmegax(nBins_, 0.0);
1850	+	vector<RealType> binOmegay(nBins_, 0.0);
1851	+	vector<RealType> binOmegaz(nBins_, 0.0);
1852		vector<RealType> binKE(nBins_, 0.0);
1853		vector<int> binDOF(nBins_, 0);
1854		vector<int> binCount(nBins_, 0);
#	Line 1436 | Line 1856 | namespace OpenMD {
1856		// alternative approach, track all molecules instead of only those
1857		// selected for scaling/swapping:
1858		/*
1859	<	SimInfo::MoleculeIterator miter;
1860	<	vector<StuntDouble*>::iterator iiter;
1861	<	Molecule* mol;
1862	<	StuntDouble* sd;
1863	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1859	>	SimInfo::MoleculeIterator miter;
1860	>	vector<StuntDouble*>::iterator iiter;
1861	>	Molecule* mol;
1862	>	StuntDouble* sd;
1863	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1864		mol = info_->nextMolecule(miter))
1865		sd is essentially sd
1866	<	for (sd = mol->beginIntegrableObject(iiter);
1867	<	sd != NULL;
1868	<	sd = mol->nextIntegrableObject(iiter))
1866	>	for (sd = mol->beginIntegrableObject(iiter);
1867	>	sd != NULL;
1868	>	sd = mol->nextIntegrableObject(iiter))
1869		*/
1870	+
1871		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1872	<	sd = seleMan_.nextSelected(selei)) {
1873	<
1453	<	idx = sd->getLocalIndex();
1454	<
1872	>	sd = seleMan_.nextSelected(selei)) {
1873	>
1874		Vector3d pos = sd->getPos();
1875
1876		// wrap the stuntdouble's position back into the box:
1877
1878	<	if (usePeriodicBoundaryConditions_)
1878	>	if (usePeriodicBoundaryConditions_) {
1879		currentSnap_->wrapVector(pos);
1880	+	// which bin is this stuntdouble in?
1881	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1882	+	// Shift molecules by half a box to have bins start at 0
1883	+	// The modulo operator is used to wrap the case when we are
1884	+	// beyond the end of the bins back to the beginning.
1885	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1886	+	} else {
1887	+	Vector3d rPos = pos - coordinateOrigin_;
1888	+	binNo = int(rPos.length() / binWidth_);
1889	+	}
1890
1462	–
1463	–	// which bin is this stuntdouble in?
1464	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1465	–	// Shift molecules by half a box to have bins start at 0
1466	–	// The modulo operator is used to wrap the case when we are
1467	–	// beyond the end of the bins back to the beginning.
1468	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1469	–
1891		RealType mass = sd->getMass();
1892		Vector3d vel = sd->getVel();
1893	<
1894	<	binCount[binNo]++;
1895	<	binMass[binNo] += mass;
1896	<	binPx[binNo] += mass*vel.x();
1897	<	binPy[binNo] += mass*vel.y();
1898	<	binPz[binNo] += mass*vel.z();
1899	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1900	<	binDOF[binNo] += 3;
1901	<
1902	<	if (sd->isDirectional()) {
1903	<	Vector3d angMom = sd->getJ();
1904	<	Mat3x3d I = sd->getI();
1905	<	if (sd->isLinear()) {
1906	<	int i = sd->linearAxis();
1907	<	int j = (i + 1) % 3;
1908	<	int k = (i + 2) % 3;
1909	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1910	<	angMom[k] * angMom[k] / I(k, k));
1911	<	binDOF[binNo] += 2;
1912	<	} else {
1913	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1914	<	angMom[1] * angMom[1] / I(1, 1) +
1915	<	angMom[2] * angMom[2] / I(2, 2));
1916	<	binDOF[binNo] += 3;
1893	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1894	>	Vector3d aVel = cross(rPos, vel);
1895	>
1896	>	if (binNo >= 0 && binNo < nBins_)  {
1897	>	binCount[binNo]++;
1898	>	binMass[binNo] += mass;
1899	>	binPx[binNo] += mass*vel.x();
1900	>	binPy[binNo] += mass*vel.y();
1901	>	binPz[binNo] += mass*vel.z();
1902	>	binOmegax[binNo] += aVel.x();
1903	>	binOmegay[binNo] += aVel.y();
1904	>	binOmegaz[binNo] += aVel.z();
1905	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1906	>	binDOF[binNo] += 3;
1907	>
1908	>	if (sd->isDirectional()) {
1909	>	Vector3d angMom = sd->getJ();
1910	>	Mat3x3d I = sd->getI();
1911	>	if (sd->isLinear()) {
1912	>	int i = sd->linearAxis();
1913	>	int j = (i + 1) % 3;
1914	>	int k = (i + 2) % 3;
1915	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1916	>	angMom[k] * angMom[k] / I(k, k));
1917	>	binDOF[binNo] += 2;
1918	>	} else {
1919	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1920	>	angMom[1] * angMom[1] / I(1, 1) +
1921	>	angMom[2] * angMom[2] / I(2, 2));
1922	>	binDOF[binNo] += 3;
1923	>	}
1924		}
1925		}
1926		}
1927
1500	–
1928		#ifdef IS_MPI
1929		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1930		nBins_, MPI::INT, MPI::SUM);
#	Line 1508 | Line 1935 | namespace OpenMD {
1935		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1936		nBins_, MPI::REALTYPE, MPI::SUM);
1937		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1938	+	nBins_, MPI::REALTYPE, MPI::SUM);
1939	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1940	+	nBins_, MPI::REALTYPE, MPI::SUM);
1941	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1942	+	nBins_, MPI::REALTYPE, MPI::SUM);
1943	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1944		nBins_, MPI::REALTYPE, MPI::SUM);
1945		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1946		nBins_, MPI::REALTYPE, MPI::SUM);
#	Line 1516 | Line 1949 | namespace OpenMD {
1949		#endif
1950
1951		Vector3d vel;
1952	+	Vector3d aVel;
1953		RealType den;
1954		RealType temp;
1955		RealType z;
1956	+	RealType r;
1957		for (int i = 0; i < nBins_; i++) {
1958	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1958	>	if (usePeriodicBoundaryConditions_) {
1959	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1960	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1961	>	/ currentSnap_->getVolume() ;
1962	>	} else {
1963	>	r = (((RealType)i + 0.5) * binWidth_);
1964	>	RealType rinner = (RealType)i * binWidth_;
1965	>	RealType router = (RealType)(i+1) * binWidth_;
1966	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1967	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1968	>	}
1969		vel.x() = binPx[i] / binMass[i];
1970		vel.y() = binPy[i] / binMass[i];
1971		vel.z() = binPz[i] / binMass[i];
1972	<	den = binCount[i] * nBins_ / currentSnap_->getVolume();
1973	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1974	<	PhysicalConstants::energyConvert);
1972	>	aVel.x() = binOmegax[i] / binCount[i];
1973	>	aVel.y() = binOmegay[i] / binCount[i];
1974	>	aVel.z() = binOmegaz[i] / binCount[i];
1975
1976	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1977	<	if(outputMask_[j]) {
1978	<	switch(j) {
1979	<	case Z:
1980	<	(data_[j].accumulator[i])->add(z);
1981	<	break;
1982	<	case TEMPERATURE:
1983	<	data_[j].accumulator[i]->add(temp);
1984	<	break;
1985	<	case VELOCITY:
1986	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1987	<	break;
1988	<	case DENSITY:
1989	<	data_[j].accumulator[i]->add(den);
1990	<	break;
1976	>	if (binCount[i] > 0) {
1977	>	// only add values if there are things to add
1978	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1979	>	PhysicalConstants::energyConvert);
1980	>
1981	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1982	>	if(outputMask_[j]) {
1983	>	switch(j) {
1984	>	case Z:
1985	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1986	>	break;
1987	>	case R:
1988	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1989	>	break;
1990	>	case TEMPERATURE:
1991	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1992	>	break;
1993	>	case VELOCITY:
1994	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1995	>	break;
1996	>	case ANGULARVELOCITY:
1997	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1998	>	break;
1999	>	case DENSITY:
2000	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2001	>	break;
2002	>	}
2003		}
2004		}
2005		}
#	Line 1550 | Line 2007 | namespace OpenMD {
2007		}
2008
2009		void RNEMD::getStarted() {
2010	+	if (!doRNEMD_) return;
2011	+	hasDividingArea_ = false;
2012		collectData();
2013		writeOutputFile();
2014		}
2015
2016		void RNEMD::parseOutputFileFormat(const std::string& format) {
2017	+	if (!doRNEMD_) return;
2018		StringTokenizer tokenizer(format, " ,;|\t\n\r");
2019
2020		while(tokenizer.hasMoreTokens()) {
#	Line 1575 | Line 2035 | namespace OpenMD {
2035		}
2036
2037		void RNEMD::writeOutputFile() {
2038	+	if (!doRNEMD_) return;
2039
2040		#ifdef IS_MPI
2041		// If we're the root node, should we print out the results
#	Line 1596 | Line 2057 | namespace OpenMD {
2057		RealType time = currentSnap_->getTime();
2058		RealType avgArea;
2059		areaAccumulator_->getAverage(avgArea);
2060	<	RealType Jz = kineticExchange_ / (2.0 * time * avgArea);
2061	<	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
2060	>	RealType Jz = kineticExchange_ / (time * avgArea)
2061	>	/ PhysicalConstants::energyConvert;
2062	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
2063	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
2064
2065		rnemdFile_ << "#######################################################\n";
2066		rnemdFile_ << "# RNEMD {\n";
#	Line 1613 | Line 2076 | namespace OpenMD {
2076		rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2077		}
2078
2079	<	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << "; fs\n";
2079	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2080
2081		rnemdFile_ << "#    objectSelection = \""
2082		<< rnemdObjectSelection_ << "\";\n";
2083	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
2084	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1622	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
2083	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2084	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2085		rnemdFile_ << "# }\n";
2086		rnemdFile_ << "#######################################################\n";
2087		rnemdFile_ << "# RNEMD report:\n";
2088	<	rnemdFile_ << "#     running time = " << time << " fs\n";
2089	<	rnemdFile_ << "#     target flux:\n";
2090	<	rnemdFile_ << "#         kinetic = " << kineticFlux_ << "\n";
2091	<	rnemdFile_ << "#         momentum = " << momentumFluxVector_ << "\n";
2092	<	rnemdFile_ << "#     target one-time exchanges:\n";
2093	<	rnemdFile_ << "#         kinetic = " << kineticTarget_ << "\n";
2094	<	rnemdFile_ << "#         momentum = " << momentumTarget_ << "\n";
2095	<	rnemdFile_ << "#     actual exchange totals:\n";
2096	<	rnemdFile_ << "#         kinetic = " << kineticExchange_ << "\n";
2097	<	rnemdFile_ << "#         momentum = " << momentumExchange_  << "\n";
2098	<	rnemdFile_ << "#     actual flux:\n";
2099	<	rnemdFile_ << "#         kinetic = " << Jz << "\n";
2100	<	rnemdFile_ << "#         momentum = " << JzP  << "\n";
2101	<	rnemdFile_ << "#     exchange statistics:\n";
2102	<	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
2103	<	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
2088	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2089	>	rnemdFile_ << "# Target flux:\n";
2090	>	rnemdFile_ << "#           kinetic = "
2091	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2092	>	<< " (kcal/mol/A^2/fs)\n";
2093	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2094	>	<< " (amu/A/fs^2)\n";
2095	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2096	>	<< " (amu/A^2/fs^2)\n";
2097	>	rnemdFile_ << "# Target one-time exchanges:\n";
2098	>	rnemdFile_ << "#          kinetic = "
2099	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2100	>	<< " (kcal/mol)\n";
2101	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2102	>	<< " (amu*A/fs)\n";
2103	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2104	>	<< " (amu*A^2/fs)\n";
2105	>	rnemdFile_ << "# Actual exchange totals:\n";
2106	>	rnemdFile_ << "#          kinetic = "
2107	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2108	>	<< " (kcal/mol)\n";
2109	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2110	>	<< " (amu*A/fs)\n";
2111	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2112	>	<< " (amu*A^2/fs)\n";
2113	>	rnemdFile_ << "# Actual flux:\n";
2114	>	rnemdFile_ << "#          kinetic = " << Jz
2115	>	<< " (kcal/mol/A^2/fs)\n";
2116	>	rnemdFile_ << "#          momentum = " << JzP
2117	>	<< " (amu/A/fs^2)\n";
2118	>	rnemdFile_ << "#  angular momentum = " << JzL
2119	>	<< " (amu/A^2/fs^2)\n";
2120	>	rnemdFile_ << "# Exchange statistics:\n";
2121	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2122	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2123		if (rnemdMethod_ == rnemdNIVS) {
2124	<	rnemdFile_ << "#         NIVS root-check errors = "
2124	>	rnemdFile_ << "#  NIVS root-check errors = "
2125		<< failRootCount_ << "\n";
2126		}
2127		rnemdFile_ << "#######################################################\n";
#	Line 1653 | Line 2134 | namespace OpenMD {
2134		if (outputMask_[i]) {
2135		rnemdFile_ << "\t" << data_[i].title <<
2136		"(" << data_[i].units << ")";
2137	+	// add some extra tabs for column alignment
2138	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2139		}
2140		}
2141		rnemdFile_ << std::endl;
2142
2143		rnemdFile_.precision(8);
2144
2145	<	for (unsigned int j = 0; j < nBins_; j++) {
2145	>	for (int j = 0; j < nBins_; j++) {
2146
2147		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2148		if (outputMask_[i]) {
2149		if (data_[i].dataType == "RealType")
2150		writeReal(i,j);
2151	<	else if (data_[i].dataType == "Vector3d")
2151	>	else if (data_[i].dataType == "Vector3d")
2152		writeVector(i,j);
2153		else {
2154		sprintf( painCave.errMsg,
#	Line 1685 | Line 2168 | namespace OpenMD {
2168		rnemdFile_ << "#######################################################\n";
2169
2170
2171	<	for (unsigned int j = 0; j < nBins_; j++) {
2171	>	for (int j = 0; j < nBins_; j++) {
2172		rnemdFile_ << "#";
2173		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2174		if (outputMask_[i]) {
#	Line 1716 | Line 2199 | namespace OpenMD {
2199		}
2200
2201		void RNEMD::writeReal(int index, unsigned int bin) {
2202	+	if (!doRNEMD_) return;
2203		assert(index >=0 && index < ENDINDEX);
2204	<	assert(bin < nBins_);
2204	>	assert(int(bin) < nBins_);
2205		RealType s;
2206	+	int count;
2207
2208	<	data_[index].accumulator[bin]->getAverage(s);
2208	>	count = data_[index].accumulator[bin]->count();
2209	>	if (count == 0) return;
2210
2211	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2212	+
2213		if (! isinf(s) && ! isnan(s)) {
2214		rnemdFile_ << "\t" << s;
2215		} else{
#	Line 1734 | Line 2222 | namespace OpenMD {
2222		}
2223
2224		void RNEMD::writeVector(int index, unsigned int bin) {
2225	+	if (!doRNEMD_) return;
2226		assert(index >=0 && index < ENDINDEX);
2227	<	assert(bin < nBins_);
2227	>	assert(int(bin) < nBins_);
2228		Vector3d s;
2229	+	int count;
2230	+
2231	+	count = data_[index].accumulator[bin]->count();
2232	+
2233	+	if (count == 0) return;
2234	+
2235		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2236		if (isinf(s[0]) || isnan(s[0]) ||
2237		isinf(s[1]) || isnan(s[1]) ||
#	Line 1752 | Line 2247 | namespace OpenMD {
2247		}
2248
2249		void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2250	+	if (!doRNEMD_) return;
2251		assert(index >=0 && index < ENDINDEX);
2252	<	assert(bin < nBins_);
2252	>	assert(int(bin) < nBins_);
2253		RealType s;
2254	+	int count;
2255
2256	<	data_[index].accumulator[bin]->getStdDev(s);
2256	>	count = data_[index].accumulator[bin]->count();
2257	>	if (count == 0) return;
2258
2259	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2260	+
2261		if (! isinf(s) && ! isnan(s)) {
2262		rnemdFile_ << "\t" << s;
2263		} else{
#	Line 1770 | Line 2270 | namespace OpenMD {
2270		}
2271
2272		void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2273	+	if (!doRNEMD_) return;
2274		assert(index >=0 && index < ENDINDEX);
2275	<	assert(bin < nBins_);
2275	>	assert(int(bin) < nBins_);
2276		Vector3d s;
2277	+	int count;
2278	+
2279	+	count = data_[index].accumulator[bin]->count();
2280	+	if (count == 0) return;
2281	+
2282		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2283		if (isinf(s[0]) || isnan(s[0]) ||
2284		isinf(s[1]) || isnan(s[1]) ||

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