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

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 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();
86	+	if (!doRNEMD_) return;
87	+
88		stringToMethod_["Swap"]  = rnemdSwap;
89		stringToMethod_["NIVS"]  = rnemdNIVS;
90		stringToMethod_["VSS"]   = rnemdVSS;
#	Line 77 | Line 93 | namespace OpenMD {
93		stringToFluxType_["Px"]  = rnemdPx;
94		stringToFluxType_["Py"]  = rnemdPy;
95		stringToFluxType_["Pz"]  = rnemdPz;
96	+	stringToFluxType_["Pvector"]  = rnemdPvector;
97	+	stringToFluxType_["Lx"]  = rnemdLx;
98	+	stringToFluxType_["Ly"]  = rnemdLy;
99	+	stringToFluxType_["Lz"]  = rnemdLz;
100	+	stringToFluxType_["Lvector"]  = rnemdLvector;
101		stringToFluxType_["KE+Px"]  = rnemdKePx;
102		stringToFluxType_["KE+Py"]  = rnemdKePy;
103		stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
104	+	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
105	+	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
106	+	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
107	+	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
108
109		runTime_ = simParams->getRunTime();
110		statusTime_ = simParams->getStatusTime();
111
87	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88	–	evaluator_.loadScriptString(rnemdObjectSelection_);
89	–	seleMan_.setSelectionSet(evaluator_.evaluate());
90	–
112		const string methStr = rnemdParams->getMethod();
113		bool hasFluxType = rnemdParams->haveFluxType();
114
115	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
116	+
117		string fluxStr;
118		if (hasFluxType) {
119		fluxStr = rnemdParams->getFluxType();
#	Line 98 | Line 121 | namespace OpenMD {
121		sprintf(painCave.errMsg,
122		"RNEMD: No fluxType was set in the md file.  This parameter,\n"
123		"\twhich must be one of the following values:\n"
124	<	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
125	<	"\tuse RNEMD\n");
124	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
125	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
126	>	"\tmust be set to use RNEMD\n");
127		painCave.isFatal = 1;
128		painCave.severity = OPENMD_ERROR;
129		simError();
#	Line 108 | Line 132 | namespace OpenMD {
132		bool hasKineticFlux = rnemdParams->haveKineticFlux();
133		bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
134		bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
135	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
136	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
137	+	hasSelectionA_ = rnemdParams->haveSelectionA();
138	+	hasSelectionB_ = rnemdParams->haveSelectionB();
139		bool hasSlabWidth = rnemdParams->haveSlabWidth();
140		bool hasSlabACenter = rnemdParams->haveSlabACenter();
141		bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
142	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
143	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
144	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
145		bool hasOutputFileName = rnemdParams->haveOutputFileName();
146		bool hasOutputFields = rnemdParams->haveOutputFields();
147
#	Line 195 | Line 226 | namespace OpenMD {
226		case rnemdPz:
227		hasCorrectFlux = hasMomentumFlux;
228		break;
229	+	case rnemdLx:
230	+	case rnemdLy:
231	+	case rnemdLz:
232	+	hasCorrectFlux = hasAngularMomentumFlux;
233	+	break;
234		case rnemdPvector:
235		hasCorrectFlux = hasMomentumFluxVector;
236	+	break;
237	+	case rnemdLvector:
238	+	hasCorrectFlux = hasAngularMomentumFluxVector;
239	+	break;
240		case rnemdKePx:
241		case rnemdKePy:
242		hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
243		break;
244	+	case rnemdKeLx:
245	+	case rnemdKeLy:
246	+	case rnemdKeLz:
247	+	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
248	+	break;
249		case rnemdKePvector:
250		hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
251		break;
252	+	case rnemdKeLvector:
253	+	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
254	+	break;
255		default:
256		methodFluxMismatch = true;
257		break;
#	Line 224 | Line 272 | namespace OpenMD {
272		}
273		if (!hasCorrectFlux) {
274		sprintf(painCave.errMsg,
275	<	"RNEMD: The current method,\n"
228	<	"\t%s, and flux type %s\n"
275	>	"RNEMD: The current method, %s, and flux type, %s,\n"
276		"\tdid not have the correct flux value specified. Options\n"
277	<	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
277	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
278	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
279		methStr.c_str(), fluxStr.c_str());
280		painCave.isFatal = 1;
281		painCave.severity = OPENMD_ERROR;
#	Line 235 | Line 283 | namespace OpenMD {
283		}
284
285		if (hasKineticFlux) {
286	<	kineticFlux_ = rnemdParams->getKineticFlux();
286	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
287	>	// into  amu / fs^3:
288	>	kineticFlux_ = rnemdParams->getKineticFlux()
289	>	* PhysicalConstants::energyConvert;
290		} else {
291		kineticFlux_ = 0.0;
292		}
#	Line 264 | 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();
273	<	int nIntegrable = info->getNGlobalIntegrableObjects();
356	>	// do some sanity checking
357
358	<	if (selectionCount > nIntegrable) {
276	<	sprintf(painCave.errMsg,
277	<	"RNEMD: The current objectSelection,\n"
278	<	"\t\t%s\n"
279	<	"\thas resulted in %d selected objects.  However,\n"
280	<	"\tthe total number of integrable objects in the system\n"
281	<	"\tis only %d.  This is almost certainly not what you want\n"
282	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
283	<	"\tselector in the selection script!\n",
284	<	rnemdObjectSelection_.c_str(),
285	<	selectionCount, nIntegrable);
286	<	painCave.isFatal = 0;
287	<	painCave.severity = OPENMD_WARNING;
288	<	simError();
289	<	}
358	>	int selectionCount = seleMan_.getSelectionCount();
359
360	<	nBins_ = rnemdParams->getOutputBins();
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361
362	<	data_.resize(RNEMD::ENDINDEX);
363	<	OutputData z;
364	<	z.units =  "Angstroms";
365	<	z.title =  "Z";
366	<	z.dataType = "RealType";
367	<	z.accumulator.reserve(nBins_);
368	<	for (unsigned int i = 0; i < nBins_; i++)
369	<	z.accumulator.push_back( new Accumulator() );
370	<	data_[Z] = z;
371	<	outputMap_["Z"] =  Z;
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	<	OutputData temperature;
305	<	temperature.units =  "K";
306	<	temperature.title =  "Temperature";
307	<	temperature.dataType = "RealType";
308	<	temperature.accumulator.reserve(nBins_);
309	<	for (unsigned int i = 0; i < nBins_; i++)
310	<	temperature.accumulator.push_back( new Accumulator() );
311	<	data_[TEMPERATURE] = temperature;
312	<	outputMap_["TEMPERATURE"] =  TEMPERATURE;
378	>	areaAccumulator_ = new Accumulator();
379
380	<	OutputData velocity;
381	<	velocity.units = "amu/fs";
316	<	velocity.title =  "Velocity";
317	<	velocity.dataType = "Vector3d";
318	<	velocity.accumulator.reserve(nBins_);
319	<	for (unsigned int i = 0; i < nBins_; i++)
320	<	velocity.accumulator.push_back( new VectorAccumulator() );
321	<	data_[VELOCITY] = velocity;
322	<	outputMap_["VELOCITY"] = VELOCITY;
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382
383	<	OutputData density;
384	<	density.units =  "g cm^-3";
385	<	density.title =  "Density";
386	<	density.dataType = "RealType";
387	<	density.accumulator.reserve(nBins_);
388	<	for (unsigned int i = 0; i < nBins_; i++)
389	<	density.accumulator.push_back( new Accumulator() );
390	<	data_[DENSITY] = density;
391	<	outputMap_["DENSITY"] =  DENSITY;
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	<	if (hasOutputFields) {
395	<	parseOutputFileFormat(rnemdParams->getOutputFields());
396	<	} else {
397	<	outputMask_.set(Z);
398	<	switch (rnemdFluxType_) {
399	<	case rnemdKE:
400	<	case rnemdRotKE:
401	<	case rnemdFullKE:
402	<	outputMask_.set(TEMPERATURE);
343	<	break;
344	<	case rnemdPx:
345	<	case rnemdPy:
346	<	outputMask_.set(VELOCITY);
347	<	break;
348	<	case rnemdPz:
349	<	case rnemdPvector:
350	<	outputMask_.set(VELOCITY);
351	<	outputMask_.set(DENSITY);
352	<	break;
353	<	case rnemdKePx:
354	<	case rnemdKePy:
355	<	outputMask_.set(TEMPERATURE);
356	<	outputMask_.set(VELOCITY);
357	<	break;
358	<	case rnemdKePvector:
359	<	outputMask_.set(TEMPERATURE);
360	<	outputMask_.set(VELOCITY);
361	<	outputMask_.set(DENSITY);
362	<	break;
363	<	default:
364	<	break;
365	<	}
366	<	}
367	<
368	<	if (hasOutputFileName) {
369	<	rnemdFileName_ = rnemdParams->getOutputFileName();
370	<	} else {
371	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
372	<	}
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	<	exchangeTime_ = rnemdParams->getExchangeTime();
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	<	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
415	<	Mat3x3d hmat = currentSnap_->getHmat();
416	<
417	<	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
418	<	// Lx, Ly = box dimensions in x & y
419	<	// dt = exchange time interval
420	<	// flux = target flux
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	<	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
425	<	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
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	<	// total exchange sums are zeroed out at the beginning:
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	<	kineticExchange_ = 0.0;
445	<	momentumExchange_ = V3Zero;
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	<	if (hasSlabWidth)
501	<	slabWidth_ = rnemdParams->getSlabWidth();
502	<	else
503	<	slabWidth_ = hmat(2,2) / 10.0;
504	<
505	<	if (hasSlabACenter)
506	<	slabACenter_ = rnemdParams->getSlabACenter();
507	<	else
508	<	slabACenter_ = 0.0;
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501	>
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504	>
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508	>
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511
512	<	if (hasSlabBCenter)
513	<	slabBCenter_ = rnemdParams->getSlabBCenter();
514	<	else
515	<	slabBCenter_ = hmat(2,2) / 2.0;
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547
548	+	if (hasSelectionB_) {
549	+	selectionB_ = rnemdParams->getSelectionB();
550	+	} else {
551	+	if (usePeriodicBoundaryConditions_) {
552	+	Mat3x3d hmat = currentSnap_->getHmat();
553	+
554	+	if (hasSlabWidth)
555	+	slabWidth_ = rnemdParams->getSlabWidth();
556	+	else
557	+	slabWidth_ = hmat(2,2) / 10.0;
558	+
559	+	if (hasSlabBCenter)
560	+	slabBCenter_ = rnemdParams->getSlabBCenter();
561	+	else
562	+	slabBCenter_ = hmat(2,2) / 2.0;
563	+
564	+	selectionBstream << "select wrappedz > "
565	+	<< slabBCenter_ - 0.5*slabWidth_
566	+	<<  " && wrappedz < "
567	+	<< slabBCenter_ + 0.5*slabWidth_;
568	+	selectionB_ = selectionBstream.str();
569	+	} else {
570	+	if (hasSphereBRadius_) {
571	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
572	+	selectionBstream << "select r > " << sphereBRadius_;
573	+	selectionB_ = selectionBstream.str();
574	+	} else {
575	+	selectionB_ = "select hull";
576	+	hasSelectionB_ = true;
577	+	}
578	+	}
579	+	}
580	+	}
581	+
582	+	// object evaluator:
583	+	evaluator_.loadScriptString(rnemdObjectSelection_);
584	+	seleMan_.setSelectionSet(evaluator_.evaluate());
585	+	evaluatorA_.loadScriptString(selectionA_);
586	+	evaluatorB_.loadScriptString(selectionB_);
587	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	+	commonA_ = seleManA_ & seleMan_;
590	+	commonB_ = seleManB_ & seleMan_;
591		}
592	<
409	<	RNEMD::~RNEMD() {
592	>
593
594	+	RNEMD::~RNEMD() {
595	+	if (!doRNEMD_) return;
596		#ifdef IS_MPI
597		if (worldRank == 0) {
598		#endif
#	Line 419 | Line 604 | namespace OpenMD {
604		#ifdef IS_MPI
605		}
606		#endif
607	+
608	+	// delete all of the objects we created:
609	+	delete areaAccumulator_;
610	+	data_.clear();
611		}
612
613	<	bool RNEMD::inSlabA(Vector3d pos) {
614	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
615	<	}
616	<	bool RNEMD::inSlabB(Vector3d pos) {
428	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	<	}
613	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
614	>	if (!doRNEMD_) return;
615	>	int selei;
616	>	int selej;
617
431	–	void RNEMD::doSwap() {
432	–
618		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
619		Mat3x3d hmat = currentSnap_->getHmat();
620
436	–	seleMan_.setSelectionSet(evaluator_.evaluate());
437	–
438	–	int selei;
621		StuntDouble* sd;
440	–	int idx;
622
623		RealType min_val;
624		bool min_found = false;
#	Line 447 | Line 628 | namespace OpenMD {
628		bool max_found = false;
629		StuntDouble* max_sd;
630
631	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
632	<	sd = seleMan_.nextSelected(selei)) {
631	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
632	>	sd = seleManA_.nextSelected(selei)) {
633
453	–	idx = sd->getLocalIndex();
454	–
634		Vector3d pos = sd->getPos();
635	<
635	>
636		// wrap the stuntdouble's position back into the box:
637	<
637	>
638		if (usePeriodicBoundaryConditions_)
639		currentSnap_->wrapVector(pos);
640	<	bool inA = inSlabA(pos);
641	<	bool inB = inSlabB(pos);
642	<
643	<	if (inA || inB) {
640	>
641	>	RealType mass = sd->getMass();
642	>	Vector3d vel = sd->getVel();
643	>	RealType value;
644	>
645	>	switch(rnemdFluxType_) {
646	>	case rnemdKE :
647
648	<	RealType mass = sd->getMass();
649	<	Vector3d vel = sd->getVel();
650	<	RealType value;
651	<
652	<	switch(rnemdFluxType_) {
471	<	case rnemdKE :
648	>	value = mass * vel.lengthSquare();
649	>
650	>	if (sd->isDirectional()) {
651	>	Vector3d angMom = sd->getJ();
652	>	Mat3x3d I = sd->getI();
653
654	<	value = mass * vel.lengthSquare();
655	<
656	<	if (sd->isDirectional()) {
657	<	Vector3d angMom = sd->getJ();
658	<	Mat3x3d I = sd->getI();
659	<
660	<	if (sd->isLinear()) {
661	<	int i = sd->linearAxis();
662	<	int j = (i + 1) % 3;
663	<	int k = (i + 2) % 3;
664	<	value += angMom[j] * angMom[j] / I(j, j) +
665	<	angMom[k] * angMom[k] / I(k, k);
666	<	} else {
667	<	value += angMom[0]*angMom[0]/I(0, 0)
668	<	+ angMom[1]*angMom[1]/I(1, 1)
669	<	+ angMom[2]*angMom[2]/I(2, 2);
670	<	}
671	<	} //angular momenta exchange enabled
672	<	//energyConvert temporarily disabled
673	<	//make kineticExchange_ comparable between swap & scale
674	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
675	<	value *= 0.5;
676	<	break;
677	<	case rnemdPx :
678	<	value = mass * vel[0];
679	<	break;
680	<	case rnemdPy :
681	<	value = mass * vel[1];
682	<	break;
683	<	case rnemdPz :
684	<	value = mass * vel[2];
685	<	break;
686	<	default :
687	<	break;
654	>	if (sd->isLinear()) {
655	>	int i = sd->linearAxis();
656	>	int j = (i + 1) % 3;
657	>	int k = (i + 2) % 3;
658	>	value += angMom[j] * angMom[j] / I(j, j) +
659	>	angMom[k] * angMom[k] / I(k, k);
660	>	} else {
661	>	value += angMom[0]*angMom[0]/I(0, 0)
662	>	+ angMom[1]*angMom[1]/I(1, 1)
663	>	+ angMom[2]*angMom[2]/I(2, 2);
664	>	}
665	>	} //angular momenta exchange enabled
666	>	value *= 0.5;
667	>	break;
668	>	case rnemdPx :
669	>	value = mass * vel[0];
670	>	break;
671	>	case rnemdPy :
672	>	value = mass * vel[1];
673	>	break;
674	>	case rnemdPz :
675	>	value = mass * vel[2];
676	>	break;
677	>	default :
678	>	break;
679	>	}
680	>	if (!max_found) {
681	>	max_val = value;
682	>	max_sd = sd;
683	>	max_found = true;
684	>	} else {
685	>	if (max_val < value) {
686	>	max_val = value;
687	>	max_sd = sd;
688		}
689	+	}
690	+	}
691
692	<	if (inA == 0) {
693	<	if (!min_found) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	min_found = true;
697	<	} else {
698	<	if (min_val > value) {
699	<	min_val = value;
700	<	min_sd = sd;
701	<	}
702	<	}
703	<	} else {
704	<	if (!max_found) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	max_found = true;
708	<	} else {
709	<	if (max_val < value) {
710	<	max_val = value;
711	<	max_sd = sd;
712	<	}
713	<	}
714	<	}
692	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
693	>	sd = seleManB_.nextSelected(selej)) {
694	>
695	>	Vector3d pos = sd->getPos();
696	>
697	>	// wrap the stuntdouble's position back into the box:
698	>
699	>	if (usePeriodicBoundaryConditions_)
700	>	currentSnap_->wrapVector(pos);
701	>
702	>	RealType mass = sd->getMass();
703	>	Vector3d vel = sd->getVel();
704	>	RealType value;
705	>
706	>	switch(rnemdFluxType_) {
707	>	case rnemdKE :
708	>
709	>	value = mass * vel.lengthSquare();
710	>
711	>	if (sd->isDirectional()) {
712	>	Vector3d angMom = sd->getJ();
713	>	Mat3x3d I = sd->getI();
714	>
715	>	if (sd->isLinear()) {
716	>	int i = sd->linearAxis();
717	>	int j = (i + 1) % 3;
718	>	int k = (i + 2) % 3;
719	>	value += angMom[j] * angMom[j] / I(j, j) +
720	>	angMom[k] * angMom[k] / I(k, k);
721	>	} else {
722	>	value += angMom[0]*angMom[0]/I(0, 0)
723	>	+ angMom[1]*angMom[1]/I(1, 1)
724	>	+ angMom[2]*angMom[2]/I(2, 2);
725	>	}
726	>	} //angular momenta exchange enabled
727	>	value *= 0.5;
728	>	break;
729	>	case rnemdPx :
730	>	value = mass * vel[0];
731	>	break;
732	>	case rnemdPy :
733	>	value = mass * vel[1];
734	>	break;
735	>	case rnemdPz :
736	>	value = mass * vel[2];
737	>	break;
738	>	default :
739	>	break;
740		}
741	+
742	+	if (!min_found) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	min_found = true;
746	+	} else {
747	+	if (min_val > value) {
748	+	min_val = value;
749	+	min_sd = sd;
750	+	}
751	+	}
752		}
753
754	<	#ifdef IS_MPI
755	<	int nProc, worldRank;
754	>	#ifdef IS_MPI
755	>	int worldRank = MPI::COMM_WORLD.Get_rank();
756
538	–	nProc = MPI::COMM_WORLD.Get_size();
539	–	worldRank = MPI::COMM_WORLD.Get_rank();
540	–
757		bool my_min_found = min_found;
758		bool my_max_found = max_found;
759
#	Line 728 | Line 944 | namespace OpenMD {
944
945		switch(rnemdFluxType_) {
946		case rnemdKE:
731	–	cerr << "KE\n";
947		kineticExchange_ += max_val - min_val;
948		break;
949		case rnemdPx:
#	Line 741 | Line 956 | namespace OpenMD {
956		momentumExchange_.z() += max_val - min_val;
957		break;
958		default:
744	–	cerr << "default\n";
959		break;
960		}
961		} else {
#	Line 763 | Line 977 | namespace OpenMD {
977		}
978		}
979
980	<	void RNEMD::doNIVS() {
980	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
981	>	if (!doRNEMD_) return;
982	>	int selei;
983	>	int selej;
984
985		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
986	+	RealType time = currentSnap_->getTime();
987		Mat3x3d hmat = currentSnap_->getHmat();
988
771	–	seleMan_.setSelectionSet(evaluator_.evaluate());
772	–
773	–	int selei;
989		StuntDouble* sd;
775	–	int idx;
990
991		vector<StuntDouble*> hotBin, coldBin;
992
#	Line 791 | Line 1005 | namespace OpenMD {
1005		RealType Kcz = 0.0;
1006		RealType Kcw = 0.0;
1007
1008	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1009	<	sd = seleMan_.nextSelected(selei)) {
1008	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1009	>	sd = smanA.nextSelected(selei)) {
1010
797	–	idx = sd->getLocalIndex();
798	–
1011		Vector3d pos = sd->getPos();
1012	<
1012	>
1013		// wrap the stuntdouble's position back into the box:
1014	<
1014	>
1015		if (usePeriodicBoundaryConditions_)
1016		currentSnap_->wrapVector(pos);
1017	<
1018	<	// which bin is this stuntdouble in?
1019	<	bool inA = inSlabA(pos);
1020	<	bool inB = inSlabB(pos);
1017	>
1018	>
1019	>	RealType mass = sd->getMass();
1020	>	Vector3d vel = sd->getVel();
1021	>
1022	>	hotBin.push_back(sd);
1023	>	Phx += mass * vel.x();
1024	>	Phy += mass * vel.y();
1025	>	Phz += mass * vel.z();
1026	>	Khx += mass * vel.x() * vel.x();
1027	>	Khy += mass * vel.y() * vel.y();
1028	>	Khz += mass * vel.z() * vel.z();
1029	>	if (sd->isDirectional()) {
1030	>	Vector3d angMom = sd->getJ();
1031	>	Mat3x3d I = sd->getI();
1032	>	if (sd->isLinear()) {
1033	>	int i = sd->linearAxis();
1034	>	int j = (i + 1) % 3;
1035	>	int k = (i + 2) % 3;
1036	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1037	>	angMom[k] * angMom[k] / I(k, k);
1038	>	} else {
1039	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1040	>	+ angMom[1]*angMom[1]/I(1, 1)
1041	>	+ angMom[2]*angMom[2]/I(2, 2);
1042	>	}
1043	>	}
1044	>	}
1045	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1046	>	sd = smanB.nextSelected(selej)) {
1047	>	Vector3d pos = sd->getPos();
1048	>
1049	>	// wrap the stuntdouble's position back into the box:
1050	>
1051	>	if (usePeriodicBoundaryConditions_)
1052	>	currentSnap_->wrapVector(pos);
1053	>
1054	>	RealType mass = sd->getMass();
1055	>	Vector3d vel = sd->getVel();
1056
1057	<	if (inA || inB) {
1058	<
1059	<	RealType mass = sd->getMass();
1060	<	Vector3d vel = sd->getVel();
1061	<
1062	<	if (inA) {
1063	<	hotBin.push_back(sd);
1064	<	Phx += mass * vel.x();
1065	<	Phy += mass * vel.y();
1066	<	Phz += mass * vel.z();
1067	<	Khx += mass * vel.x() * vel.x();
1068	<	Khy += mass * vel.y() * vel.y();
1069	<	Khz += mass * vel.z() * vel.z();
1070	<	if (sd->isDirectional()) {
1071	<	Vector3d angMom = sd->getJ();
1072	<	Mat3x3d I = sd->getI();
1073	<	if (sd->isLinear()) {
1074	<	int i = sd->linearAxis();
1075	<	int j = (i + 1) % 3;
1076	<	int k = (i + 2) % 3;
1077	<	Khw += angMom[j] * angMom[j] / I(j, j) +
831	<	angMom[k] * angMom[k] / I(k, k);
832	<	} else {
833	<	Khw += angMom[0]*angMom[0]/I(0, 0)
834	<	+ angMom[1]*angMom[1]/I(1, 1)
835	<	+ angMom[2]*angMom[2]/I(2, 2);
836	<	}
837	<	}
838	<	} else {
839	<	coldBin.push_back(sd);
840	<	Pcx += mass * vel.x();
841	<	Pcy += mass * vel.y();
842	<	Pcz += mass * vel.z();
843	<	Kcx += mass * vel.x() * vel.x();
844	<	Kcy += mass * vel.y() * vel.y();
845	<	Kcz += mass * vel.z() * vel.z();
846	<	if (sd->isDirectional()) {
847	<	Vector3d angMom = sd->getJ();
848	<	Mat3x3d I = sd->getI();
849	<	if (sd->isLinear()) {
850	<	int i = sd->linearAxis();
851	<	int j = (i + 1) % 3;
852	<	int k = (i + 2) % 3;
853	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
854	<	angMom[k] * angMom[k] / I(k, k);
855	<	} else {
856	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
857	<	+ angMom[1]*angMom[1]/I(1, 1)
858	<	+ angMom[2]*angMom[2]/I(2, 2);
859	<	}
860	<	}
861	<	}
1057	>	coldBin.push_back(sd);
1058	>	Pcx += mass * vel.x();
1059	>	Pcy += mass * vel.y();
1060	>	Pcz += mass * vel.z();
1061	>	Kcx += mass * vel.x() * vel.x();
1062	>	Kcy += mass * vel.y() * vel.y();
1063	>	Kcz += mass * vel.z() * vel.z();
1064	>	if (sd->isDirectional()) {
1065	>	Vector3d angMom = sd->getJ();
1066	>	Mat3x3d I = sd->getI();
1067	>	if (sd->isLinear()) {
1068	>	int i = sd->linearAxis();
1069	>	int j = (i + 1) % 3;
1070	>	int k = (i + 2) % 3;
1071	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1072	>	angMom[k] * angMom[k] / I(k, k);
1073	>	} else {
1074	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1075	>	+ angMom[1]*angMom[1]/I(1, 1)
1076	>	+ angMom[2]*angMom[2]/I(2, 2);
1077	>	}
1078		}
1079		}
1080
#	Line 908 | Line 1124 | namespace OpenMD {
1124
1125		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1126		c = sqrt(c);
1127	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	<	//now convert to hotBin coefficient
1127	>
1128		RealType w = 0.0;
1129		if (rnemdFluxType_ ==  rnemdFullKE) {
1130		x = 1.0 + px * (1.0 - c);
#	Line 936 | Line 1151 | namespace OpenMD {
1151		//if w is in the right range, so should be x, y, z.
1152		vector<StuntDouble*>::iterator sdi;
1153		Vector3d vel;
1154	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1154	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1155		if (rnemdFluxType_ == rnemdFullKE) {
1156		vel = (*sdi)->getVel() * c;
1157		(*sdi)->setVel(vel);
#	Line 947 | Line 1162 | namespace OpenMD {
1162		}
1163		}
1164		w = sqrt(w);
1165	<	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	<	//           << "\twh= " << w << endl;
952	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1165	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1166		if (rnemdFluxType_ == rnemdFullKE) {
1167		vel = (*sdi)->getVel();
1168		vel.x() *= x;
#	Line 1068 | Line 1281 | namespace OpenMD {
1281		vector<RealType>::iterator ri;
1282		RealType r1, r2, alpha0;
1283		vector<pair<RealType,RealType> > rps;
1284	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1284	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1285		r2 = *ri;
1286		//check if FindRealRoots() give the right answer
1287		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1100 | Line 1313 | namespace OpenMD {
1313		RealType diff;
1314		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1315		vector<pair<RealType,RealType> >::iterator rpi;
1316	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1316	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1317		r1 = (*rpi).first;
1318		r2 = (*rpi).second;
1319		switch(rnemdFluxType_) {
#	Line 1167 | Line 1380 | namespace OpenMD {
1380		}
1381		vector<StuntDouble*>::iterator sdi;
1382		Vector3d vel;
1383	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1383	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1384		vel = (*sdi)->getVel();
1385		vel.x() *= x;
1386		vel.y() *= y;
#	Line 1178 | Line 1391 | namespace OpenMD {
1391		x = 1.0 + px * (1.0 - x);
1392		y = 1.0 + py * (1.0 - y);
1393		z = 1.0 + pz * (1.0 - z);
1394	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1394	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1395		vel = (*sdi)->getVel();
1396		vel.x() *= x;
1397		vel.y() *= y;
#	Line 1211 | Line 1424 | namespace OpenMD {
1424		failTrialCount_++;
1425		}
1426		}
1427	+
1428	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1429	+	if (!doRNEMD_) return;
1430	+	int selei;
1431	+	int selej;
1432
1215	–	void RNEMD::doVSS() {
1216	–
1433		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1434		RealType time = currentSnap_->getTime();
1435		Mat3x3d hmat = currentSnap_->getHmat();
1436
1221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	–
1223	–	int selei;
1437		StuntDouble* sd;
1225	–	int idx;
1438
1439		vector<StuntDouble*> hotBin, coldBin;
1440
1441		Vector3d Ph(V3Zero);
1442	+	Vector3d Lh(V3Zero);
1443		RealType Mh = 0.0;
1444	+	Mat3x3d Ih(0.0);
1445		RealType Kh = 0.0;
1446		Vector3d Pc(V3Zero);
1447	+	Vector3d Lc(V3Zero);
1448		RealType Mc = 0.0;
1449	+	Mat3x3d Ic(0.0);
1450		RealType Kc = 0.0;
1235	–
1451
1452	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453	<	sd = seleMan_.nextSelected(selei)) {
1452	>	// Constraints can be on only the linear or angular momentum, but
1453	>	// not both.  Usually, the user will specify which they want, but
1454	>	// in case they don't, the use of periodic boundaries should make
1455	>	// the choice for us.
1456	>	bool doLinearPart = false;
1457	>	bool doAngularPart = false;
1458
1459	<	idx = sd->getLocalIndex();
1459	>	switch (rnemdFluxType_) {
1460	>	case rnemdPx:
1461	>	case rnemdPy:
1462	>	case rnemdPz:
1463	>	case rnemdPvector:
1464	>	case rnemdKePx:
1465	>	case rnemdKePy:
1466	>	case rnemdKePvector:
1467	>	doLinearPart = true;
1468	>	break;
1469	>	case rnemdLx:
1470	>	case rnemdLy:
1471	>	case rnemdLz:
1472	>	case rnemdLvector:
1473	>	case rnemdKeLx:
1474	>	case rnemdKeLy:
1475	>	case rnemdKeLz:
1476	>	case rnemdKeLvector:
1477	>	doAngularPart = true;
1478	>	break;
1479	>	case rnemdKE:
1480	>	case rnemdRotKE:
1481	>	case rnemdFullKE:
1482	>	default:
1483	>	if (usePeriodicBoundaryConditions_)
1484	>	doLinearPart = true;
1485	>	else
1486	>	doAngularPart = true;
1487	>	break;
1488	>	}
1489	>
1490	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1491	>	sd = smanA.nextSelected(selei)) {
1492
1493		Vector3d pos = sd->getPos();
1494
1495		// wrap the stuntdouble's position back into the box:
1496	+
1497	+	if (usePeriodicBoundaryConditions_)
1498	+	currentSnap_->wrapVector(pos);
1499	+
1500	+	RealType mass = sd->getMass();
1501	+	Vector3d vel = sd->getVel();
1502	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1503	+	RealType r2;
1504	+
1505	+	hotBin.push_back(sd);
1506	+	Ph += mass * vel;
1507	+	Mh += mass;
1508	+	Kh += mass * vel.lengthSquare();
1509	+	Lh += mass * cross(rPos, vel);
1510	+	Ih -= outProduct(rPos, rPos) * mass;
1511	+	r2 = rPos.lengthSquare();
1512	+	Ih(0, 0) += mass * r2;
1513	+	Ih(1, 1) += mass * r2;
1514	+	Ih(2, 2) += mass * r2;
1515	+
1516	+	if (rnemdFluxType_ == rnemdFullKE) {
1517	+	if (sd->isDirectional()) {
1518	+	Vector3d angMom = sd->getJ();
1519	+	Mat3x3d I = sd->getI();
1520	+	if (sd->isLinear()) {
1521	+	int i = sd->linearAxis();
1522	+	int j = (i + 1) % 3;
1523	+	int k = (i + 2) % 3;
1524	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1525	+	angMom[k] * angMom[k] / I(k, k);
1526	+	} else {
1527	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1528	+	angMom[1] * angMom[1] / I(1, 1) +
1529	+	angMom[2] * angMom[2] / I(2, 2);
1530	+	}
1531	+	}
1532	+	}
1533	+	}
1534	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1535	+	sd = smanB.nextSelected(selej)) {
1536
1537	+	Vector3d pos = sd->getPos();
1538	+
1539	+	// wrap the stuntdouble's position back into the box:
1540	+
1541		if (usePeriodicBoundaryConditions_)
1542		currentSnap_->wrapVector(pos);
1543	+
1544	+	RealType mass = sd->getMass();
1545	+	Vector3d vel = sd->getVel();
1546	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1547	+	RealType r2;
1548
1549	<	// which bin is this stuntdouble in?
1550	<	bool inA = inSlabA(pos);
1551	<	bool inB = inSlabB(pos);
1549	>	coldBin.push_back(sd);
1550	>	Pc += mass * vel;
1551	>	Mc += mass;
1552	>	Kc += mass * vel.lengthSquare();
1553	>	Lc += mass * cross(rPos, vel);
1554	>	Ic -= outProduct(rPos, rPos) * mass;
1555	>	r2 = rPos.lengthSquare();
1556	>	Ic(0, 0) += mass * r2;
1557	>	Ic(1, 1) += mass * r2;
1558	>	Ic(2, 2) += mass * r2;
1559
1560	<	if (inA || inB) {
1561	<
1562	<	RealType mass = sd->getMass();
1563	<	Vector3d vel = sd->getVel();
1564	<
1565	<	if (inA) {
1566	<	hotBin.push_back(sd);
1567	<	//std::cerr << "before, velocity = " << vel << endl;
1568	<	Ph += mass * vel;
1569	<	//std::cerr << "after, velocity = " << vel << endl;
1570	<	Mh += mass;
1571	<	Kh += mass * vel.lengthSquare();
1572	<	if (rnemdFluxType_ == rnemdFullKE) {
1573	<	if (sd->isDirectional()) {
1574	<	Vector3d angMom = sd->getJ();
1575	<	Mat3x3d I = sd->getI();
1269	<	if (sd->isLinear()) {
1270	<	int i = sd->linearAxis();
1271	<	int j = (i + 1) % 3;
1272	<	int k = (i + 2) % 3;
1273	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1274	<	angMom[k] * angMom[k] / I(k, k);
1275	<	} else {
1276	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1277	<	angMom[1] * angMom[1] / I(1, 1) +
1278	<	angMom[2] * angMom[2] / I(2, 2);
1279	<	}
1280	<	}
1281	<	}
1282	<	} else { //midBin_
1283	<	coldBin.push_back(sd);
1284	<	Pc += mass * vel;
1285	<	Mc += mass;
1286	<	Kc += mass * vel.lengthSquare();
1287	<	if (rnemdFluxType_ == rnemdFullKE) {
1288	<	if (sd->isDirectional()) {
1289	<	Vector3d angMom = sd->getJ();
1290	<	Mat3x3d I = sd->getI();
1291	<	if (sd->isLinear()) {
1292	<	int i = sd->linearAxis();
1293	<	int j = (i + 1) % 3;
1294	<	int k = (i + 2) % 3;
1295	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1296	<	angMom[k] * angMom[k] / I(k, k);
1297	<	} else {
1298	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1299	<	angMom[1] * angMom[1] / I(1, 1) +
1300	<	angMom[2] * angMom[2] / I(2, 2);
1301	<	}
1302	<	}
1303	<	}
1304	<	}
1560	>	if (rnemdFluxType_ == rnemdFullKE) {
1561	>	if (sd->isDirectional()) {
1562	>	Vector3d angMom = sd->getJ();
1563	>	Mat3x3d I = sd->getI();
1564	>	if (sd->isLinear()) {
1565	>	int i = sd->linearAxis();
1566	>	int j = (i + 1) % 3;
1567	>	int k = (i + 2) % 3;
1568	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1569	>	angMom[k] * angMom[k] / I(k, k);
1570	>	} else {
1571	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1572	>	angMom[1] * angMom[1] / I(1, 1) +
1573	>	angMom[2] * angMom[2] / I(2, 2);
1574	>	}
1575	>	}
1576		}
1577		}
1578
1579		Kh *= 0.5;
1580		Kc *= 0.5;
1310	–
1311	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1312	–	//        << "\tKc= " << Kc << endl;
1313	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1581
1582		#ifdef IS_MPI
1583		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1585	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1587		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1588		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1589		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1590		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1591	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1592	+	MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595		#endif
1596	+
1597
1598	+	Vector3d ac, acrec, bc, bcrec;
1599	+	Vector3d ah, ahrec, bh, bhrec;
1600	+	RealType cNumerator, cDenominator;
1601	+	RealType hNumerator, hDenominator;
1602	+
1603	+
1604		bool successfulExchange = false;
1605		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1606		Vector3d vc = Pc / Mc;
1607	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1608	<	Vector3d acrec = -momentumTarget_ / Mc;
1609	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1607	>	ac = -momentumTarget_ / Mc + vc;
1608	>	acrec = -momentumTarget_ / Mc;
1609	>
1610	>	// We now need the inverse of the inertia tensor to calculate the
1611	>	// angular velocity of the cold slab;
1612	>	Mat3x3d Ici = Ic.inverse();
1613	>	Vector3d omegac = Ici * Lc;
1614	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1615	>	bcrec = bc - omegac;
1616	>
1617	>	cNumerator = Kc - kineticTarget_;
1618	>	if (doLinearPart)
1619	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1620	>
1621	>	if (doAngularPart)
1622	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1623	>
1624		if (cNumerator > 0.0) {
1625	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1625	>
1626	>	cDenominator = Kc;
1627	>
1628	>	if (doLinearPart)
1629	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1630	>
1631	>	if (doAngularPart)
1632	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1633	>
1634		if (cDenominator > 0.0) {
1635		RealType c = sqrt(cNumerator / cDenominator);
1636		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1637	+
1638		Vector3d vh = Ph / Mh;
1639	<	Vector3d ah = momentumTarget_ / Mh + vh;
1640	<	Vector3d ahrec = momentumTarget_ / Mh;
1641	<	RealType hNumerator = Kh + kineticTarget_
1642	<	- 0.5 * Mh * ah.lengthSquare();
1643	<	if (hNumerator > 0.0) {
1644	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1639	>	ah = momentumTarget_ / Mh + vh;
1640	>	ahrec = momentumTarget_ / Mh;
1641	>
1642	>	// We now need the inverse of the inertia tensor to
1643	>	// calculate the angular velocity of the hot slab;
1644	>	Mat3x3d Ihi = Ih.inverse();
1645	>	Vector3d omegah = Ihi * Lh;
1646	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1647	>	bhrec = bh - omegah;
1648	>
1649	>	hNumerator = Kh + kineticTarget_;
1650	>	if (doLinearPart)
1651	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1652	>
1653	>	if (doAngularPart)
1654	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1655	>
1656	>	if (hNumerator > 0.0) {
1657	>
1658	>	hDenominator = Kh;
1659	>	if (doLinearPart)
1660	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1661	>	if (doAngularPart)
1662	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1663	>
1664		if (hDenominator > 0.0) {
1665		RealType h = sqrt(hNumerator / hDenominator);
1666		if ((h > 0.9) && (h < 1.1)) {
1667	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1667	>
1668		vector<StuntDouble*>::iterator sdi;
1669		Vector3d vel;
1670	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1670	>	Vector3d rPos;
1671	>
1672	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1673		//vel = (*sdi)->getVel();
1674	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1674	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1675	>	if (doLinearPart)
1676	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1677	>	if (doAngularPart)
1678	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1679	>
1680		(*sdi)->setVel(vel);
1681		if (rnemdFluxType_ == rnemdFullKE) {
1682		if ((*sdi)->isDirectional()) {
#	Line 1357 | Line 1685 | namespace OpenMD {
1685		}
1686		}
1687		}
1688	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1688	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1689		//vel = (*sdi)->getVel();
1690	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1690	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1691	>	if (doLinearPart)
1692	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1693	>	if (doAngularPart)
1694	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1695	>
1696		(*sdi)->setVel(vel);
1697		if (rnemdFluxType_ == rnemdFullKE) {
1698		if ((*sdi)->isDirectional()) {
#	Line 1371 | Line 1704 | namespace OpenMD {
1704		successfulExchange = true;
1705		kineticExchange_ += kineticTarget_;
1706		momentumExchange_ += momentumTarget_;
1707	+	angularMomentumExchange_ += angularMomentumTarget_;
1708		}
1709		}
1710		}
#	Line 1390 | Line 1724 | namespace OpenMD {
1724		}
1725		}
1726
1727	<	void RNEMD::doRNEMD() {
1727	>	RealType RNEMD::getDividingArea() {
1728
1729	+	if (hasDividingArea_) return dividingArea_;
1730	+
1731	+	RealType areaA, areaB;
1732	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1733	+
1734	+	if (hasSelectionA_) {
1735	+	int isd;
1736	+	StuntDouble* sd;
1737	+	vector<StuntDouble*> aSites;
1738	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1739	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1740	+	sd = seleManA_.nextSelected(isd)) {
1741	+	aSites.push_back(sd);
1742	+	}
1743	+	ConvexHull* surfaceMeshA = new ConvexHull();
1744	+	surfaceMeshA->computeHull(aSites);
1745	+	areaA = surfaceMeshA->getArea();
1746	+	delete surfaceMeshA;
1747	+
1748	+	} else {
1749	+	if (usePeriodicBoundaryConditions_) {
1750	+	// in periodic boundaries, the surface area is twice the x-y
1751	+	// area of the current box:
1752	+	areaA = 2.0 * snap->getXYarea();
1753	+	} else {
1754	+	// in non-periodic simulations, without explicitly setting
1755	+	// selections, the sphere radius sets the surface area of the
1756	+	// dividing surface:
1757	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1758	+	}
1759	+	}
1760	+
1761	+
1762	+
1763	+	if (hasSelectionB_) {
1764	+	int isd;
1765	+	StuntDouble* sd;
1766	+	vector<StuntDouble*> bSites;
1767	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1768	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1769	+	sd = seleManB_.nextSelected(isd)) {
1770	+	bSites.push_back(sd);
1771	+	}
1772	+	ConvexHull* surfaceMeshB = new ConvexHull();
1773	+	surfaceMeshB->computeHull(bSites);
1774	+	areaB = surfaceMeshB->getArea();
1775	+	delete surfaceMeshB;
1776	+
1777	+	} else {
1778	+	if (usePeriodicBoundaryConditions_) {
1779	+	// in periodic boundaries, the surface area is twice the x-y
1780	+	// area of the current box:
1781	+	areaB = 2.0 * snap->getXYarea();
1782	+	} else {
1783	+	// in non-periodic simulations, without explicitly setting
1784	+	// selections, but if a sphereBradius has been set, just use that:
1785	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1786	+	}
1787	+	}
1788	+
1789	+	dividingArea_ = min(areaA, areaB);
1790	+	hasDividingArea_ = true;
1791	+	return dividingArea_;
1792	+	}
1793	+
1794	+	void RNEMD::doRNEMD() {
1795	+	if (!doRNEMD_) return;
1796		trialCount_++;
1797	+
1798	+	// object evaluator:
1799	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1800	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1801	+
1802	+	evaluatorA_.loadScriptString(selectionA_);
1803	+	evaluatorB_.loadScriptString(selectionB_);
1804	+
1805	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1806	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1807	+
1808	+	commonA_ = seleManA_ & seleMan_;
1809	+	commonB_ = seleManB_ & seleMan_;
1810	+
1811	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1812	+	// dt = exchange time interval
1813	+	// flux = target flux
1814	+	// dividingArea = smallest dividing surface between the two regions
1815	+
1816	+	hasDividingArea_ = false;
1817	+	RealType area = getDividingArea();
1818	+
1819	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1820	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1821	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1822	+
1823		switch(rnemdMethod_) {
1824		case rnemdSwap:
1825	<	doSwap();
1825	>	doSwap(commonA_, commonB_);
1826		break;
1827		case rnemdNIVS:
1828	<	doNIVS();
1828	>	doNIVS(commonA_, commonB_);
1829		break;
1830		case rnemdVSS:
1831	<	doVSS();
1831	>	doVSS(commonA_, commonB_);
1832		break;
1833		case rnemdUnkownMethod:
1834		default :
#	Line 1410 | Line 1837 | namespace OpenMD {
1837		}
1838
1839		void RNEMD::collectData() {
1840	<
1840	>	if (!doRNEMD_) return;
1841		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1842	+
1843	+	// collectData can be called more frequently than the doRNEMD, so use the
1844	+	// computed area from the last exchange time:
1845	+	RealType area = getDividingArea();
1846	+	areaAccumulator_->add(area);
1847		Mat3x3d hmat = currentSnap_->getHmat();
1416	–
1848		seleMan_.setSelectionSet(evaluator_.evaluate());
1849
1850	<	int selei;
1850	>	int selei(0);
1851		StuntDouble* sd;
1852	<	int idx;
1852	>	int binNo;
1853
1854		vector<RealType> binMass(nBins_, 0.0);
1855		vector<RealType> binPx(nBins_, 0.0);
1856		vector<RealType> binPy(nBins_, 0.0);
1857		vector<RealType> binPz(nBins_, 0.0);
1858	+	vector<RealType> binOmegax(nBins_, 0.0);
1859	+	vector<RealType> binOmegay(nBins_, 0.0);
1860	+	vector<RealType> binOmegaz(nBins_, 0.0);
1861		vector<RealType> binKE(nBins_, 0.0);
1862		vector<int> binDOF(nBins_, 0);
1863		vector<int> binCount(nBins_, 0);
#	Line 1431 | Line 1865 | namespace OpenMD {
1865		// alternative approach, track all molecules instead of only those
1866		// selected for scaling/swapping:
1867		/*
1868	<	SimInfo::MoleculeIterator miter;
1869	<	vector<StuntDouble*>::iterator iiter;
1870	<	Molecule* mol;
1871	<	StuntDouble* sd;
1872	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1868	>	SimInfo::MoleculeIterator miter;
1869	>	vector<StuntDouble*>::iterator iiter;
1870	>	Molecule* mol;
1871	>	StuntDouble* sd;
1872	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1873		mol = info_->nextMolecule(miter))
1874		sd is essentially sd
1875	<	for (sd = mol->beginIntegrableObject(iiter);
1876	<	sd != NULL;
1877	<	sd = mol->nextIntegrableObject(iiter))
1875	>	for (sd = mol->beginIntegrableObject(iiter);
1876	>	sd != NULL;
1877	>	sd = mol->nextIntegrableObject(iiter))
1878		*/
1879	+
1880		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1881	<	sd = seleMan_.nextSelected(selei)) {
1882	<
1448	<	idx = sd->getLocalIndex();
1449	<
1881	>	sd = seleMan_.nextSelected(selei)) {
1882	>
1883		Vector3d pos = sd->getPos();
1884
1885		// wrap the stuntdouble's position back into the box:
1886
1887	<	if (usePeriodicBoundaryConditions_)
1887	>	if (usePeriodicBoundaryConditions_) {
1888		currentSnap_->wrapVector(pos);
1889	+	// which bin is this stuntdouble in?
1890	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1891	+	// Shift molecules by half a box to have bins start at 0
1892	+	// The modulo operator is used to wrap the case when we are
1893	+	// beyond the end of the bins back to the beginning.
1894	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1895	+	} else {
1896	+	Vector3d rPos = pos - coordinateOrigin_;
1897	+	binNo = int(rPos.length() / binWidth_);
1898	+	}
1899
1457	–	// which bin is this stuntdouble in?
1458	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	–	// Shift molecules by half a box to have bins start at 0
1460	–	// The modulo operator is used to wrap the case when we are
1461	–	// beyond the end of the bins back to the beginning.
1462	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463	–
1900		RealType mass = sd->getMass();
1901		Vector3d vel = sd->getVel();
1902	<
1903	<	binCount[binNo]++;
1904	<	binMass[binNo] += mass;
1905	<	binPx[binNo] += mass*vel.x();
1906	<	binPy[binNo] += mass*vel.y();
1907	<	binPz[binNo] += mass*vel.z();
1908	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1909	<	binDOF[binNo] += 3;
1910	<
1911	<	if (sd->isDirectional()) {
1912	<	Vector3d angMom = sd->getJ();
1913	<	Mat3x3d I = sd->getI();
1914	<	if (sd->isLinear()) {
1915	<	int i = sd->linearAxis();
1916	<	int j = (i + 1) % 3;
1917	<	int k = (i + 2) % 3;
1918	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1919	<	angMom[k] * angMom[k] / I(k, k));
1920	<	binDOF[binNo] += 2;
1921	<	} else {
1922	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1923	<	angMom[1] * angMom[1] / I(1, 1) +
1924	<	angMom[2] * angMom[2] / I(2, 2));
1925	<	binDOF[binNo] += 3;
1902	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1903	>	Vector3d aVel = cross(rPos, vel);
1904	>
1905	>	if (binNo >= 0 && binNo < nBins_)  {
1906	>	binCount[binNo]++;
1907	>	binMass[binNo] += mass;
1908	>	binPx[binNo] += mass*vel.x();
1909	>	binPy[binNo] += mass*vel.y();
1910	>	binPz[binNo] += mass*vel.z();
1911	>	binOmegax[binNo] += aVel.x();
1912	>	binOmegay[binNo] += aVel.y();
1913	>	binOmegaz[binNo] += aVel.z();
1914	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1915	>	binDOF[binNo] += 3;
1916	>
1917	>	if (sd->isDirectional()) {
1918	>	Vector3d angMom = sd->getJ();
1919	>	Mat3x3d I = sd->getI();
1920	>	if (sd->isLinear()) {
1921	>	int i = sd->linearAxis();
1922	>	int j = (i + 1) % 3;
1923	>	int k = (i + 2) % 3;
1924	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1925	>	angMom[k] * angMom[k] / I(k, k));
1926	>	binDOF[binNo] += 2;
1927	>	} else {
1928	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1929	>	angMom[1] * angMom[1] / I(1, 1) +
1930	>	angMom[2] * angMom[2] / I(2, 2));
1931	>	binDOF[binNo] += 3;
1932	>	}
1933		}
1934		}
1935		}
1936
1494	–
1937		#ifdef IS_MPI
1938		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1939		nBins_, MPI::INT, MPI::SUM);
#	Line 1503 | Line 1945 | namespace OpenMD {
1945		nBins_, MPI::REALTYPE, MPI::SUM);
1946		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1947		nBins_, MPI::REALTYPE, MPI::SUM);
1948	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1949	+	nBins_, MPI::REALTYPE, MPI::SUM);
1950	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1951	+	nBins_, MPI::REALTYPE, MPI::SUM);
1952	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1953	+	nBins_, MPI::REALTYPE, MPI::SUM);
1954		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1955		nBins_, MPI::REALTYPE, MPI::SUM);
1956		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
#	Line 1510 | Line 1958 | namespace OpenMD {
1958		#endif
1959
1960		Vector3d vel;
1961	+	Vector3d aVel;
1962		RealType den;
1963		RealType temp;
1964		RealType z;
1965	+	RealType r;
1966		for (int i = 0; i < nBins_; i++) {
1967	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1967	>	if (usePeriodicBoundaryConditions_) {
1968	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1969	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1970	>	/ currentSnap_->getVolume() ;
1971	>	} else {
1972	>	r = (((RealType)i + 0.5) * binWidth_);
1973	>	RealType rinner = (RealType)i * binWidth_;
1974	>	RealType router = (RealType)(i+1) * binWidth_;
1975	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1976	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1977	>	}
1978		vel.x() = binPx[i] / binMass[i];
1979		vel.y() = binPy[i] / binMass[i];
1980		vel.z() = binPz[i] / binMass[i];
1981	<	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
1982	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1983	<	PhysicalConstants::energyConvert);
1981	>	aVel.x() = binOmegax[i] / binCount[i];
1982	>	aVel.y() = binOmegay[i] / binCount[i];
1983	>	aVel.z() = binOmegaz[i] / binCount[i];
1984
1985	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1986	<	if(outputMask_[j]) {
1987	<	switch(j) {
1988	<	case Z:
1989	<	(data_[j].accumulator[i])->add(z);
1990	<	break;
1991	<	case TEMPERATURE:
1992	<	data_[j].accumulator[i]->add(temp);
1993	<	break;
1994	<	case VELOCITY:
1995	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1996	<	break;
1997	<	case DENSITY:
1998	<	data_[j].accumulator[i]->add(den);
1999	<	break;
1985	>	if (binCount[i] > 0) {
1986	>	// only add values if there are things to add
1987	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1988	>	PhysicalConstants::energyConvert);
1989	>
1990	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1991	>	if(outputMask_[j]) {
1992	>	switch(j) {
1993	>	case Z:
1994	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1995	>	break;
1996	>	case R:
1997	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1998	>	break;
1999	>	case TEMPERATURE:
2000	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2001	>	break;
2002	>	case VELOCITY:
2003	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2004	>	break;
2005	>	case ANGULARVELOCITY:
2006	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2007	>	break;
2008	>	case DENSITY:
2009	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2010	>	break;
2011	>	}
2012		}
2013		}
2014		}
2015		}
2016	+	hasData_ = true;
2017		}
2018
2019		void RNEMD::getStarted() {
2020	+	if (!doRNEMD_) return;
2021	+	hasDividingArea_ = false;
2022		collectData();
2023		writeOutputFile();
2024		}
2025
2026		void RNEMD::parseOutputFileFormat(const std::string& format) {
2027	+	if (!doRNEMD_) return;
2028		StringTokenizer tokenizer(format, " ,;|\t\n\r");
2029
2030		while(tokenizer.hasMoreTokens()) {
#	Line 1569 | Line 2045 | namespace OpenMD {
2045		}
2046
2047		void RNEMD::writeOutputFile() {
2048	+	if (!doRNEMD_) return;
2049	+	if (!hasData_) return;
2050
2051		#ifdef IS_MPI
2052		// If we're the root node, should we print out the results
#	Line 1588 | Line 2066 | namespace OpenMD {
2066		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2067
2068		RealType time = currentSnap_->getTime();
2069	<
2070	<
2069	>	RealType avgArea;
2070	>	areaAccumulator_->getAverage(avgArea);
2071	>
2072	>	RealType Jz(0.0);
2073	>	Vector3d JzP(V3Zero);
2074	>	Vector3d JzL(V3Zero);
2075	>	if (time >= info_->getSimParams()->getDt()) {
2076	>	Jz = kineticExchange_ / (time * avgArea)
2077	>	/ PhysicalConstants::energyConvert;
2078	>	JzP = momentumExchange_ / (time * avgArea);
2079	>	JzL = angularMomentumExchange_ / (time * avgArea);
2080	>	}
2081	>
2082		rnemdFile_ << "#######################################################\n";
2083		rnemdFile_ << "# RNEMD {\n";
2084
2085		map<string, RNEMDMethod>::iterator mi;
2086		for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2087		if ( (*mi).second == rnemdMethod_)
2088	<	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
2088	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2089		}
2090		map<string, RNEMDFluxType>::iterator fi;
2091		for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2092		if ( (*fi).second == rnemdFluxType_)
2093	<	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
2093	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2094		}
2095
2096	<	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
2096	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2097
2098		rnemdFile_ << "#    objectSelection = \""
2099	<	<< rnemdObjectSelection_ << "\"\n";
2100	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
2101	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
2099	>	<< rnemdObjectSelection_ << "\";\n";
2100	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2101	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2102		rnemdFile_ << "# }\n";
2103		rnemdFile_ << "#######################################################\n";
2104	<
2105	<	rnemdFile_ << "# running time = " << time << " fs\n";
2106	<	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
2107	<	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
2108	<
2109	<	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
2110	<	<< "\n";
2111	<	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
2112	<	<< "\n";
2113	<
2114	<	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
2115	<	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
2116	<	<< "\n";
2117	<
2118	<	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
2119	<	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
2120	<
2121	<
2104	>	rnemdFile_ << "# RNEMD report:\n";
2105	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2106	>	rnemdFile_ << "# Target flux:\n";
2107	>	rnemdFile_ << "#           kinetic = "
2108	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2109	>	<< " (kcal/mol/A^2/fs)\n";
2110	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2111	>	<< " (amu/A/fs^2)\n";
2112	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2113	>	<< " (amu/A^2/fs^2)\n";
2114	>	rnemdFile_ << "# Target one-time exchanges:\n";
2115	>	rnemdFile_ << "#          kinetic = "
2116	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2117	>	<< " (kcal/mol)\n";
2118	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2119	>	<< " (amu*A/fs)\n";
2120	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2121	>	<< " (amu*A^2/fs)\n";
2122	>	rnemdFile_ << "# Actual exchange totals:\n";
2123	>	rnemdFile_ << "#          kinetic = "
2124	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2125	>	<< " (kcal/mol)\n";
2126	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2127	>	<< " (amu*A/fs)\n";
2128	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2129	>	<< " (amu*A^2/fs)\n";
2130	>	rnemdFile_ << "# Actual flux:\n";
2131	>	rnemdFile_ << "#          kinetic = " << Jz
2132	>	<< " (kcal/mol/A^2/fs)\n";
2133	>	rnemdFile_ << "#          momentum = " << JzP
2134	>	<< " (amu/A/fs^2)\n";
2135	>	rnemdFile_ << "#  angular momentum = " << JzL
2136	>	<< " (amu/A^2/fs^2)\n";
2137	>	rnemdFile_ << "# Exchange statistics:\n";
2138	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2139	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2140		if (rnemdMethod_ == rnemdNIVS) {
2141	<	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
2141	>	rnemdFile_ << "#  NIVS root-check errors = "
2142	>	<< failRootCount_ << "\n";
2143		}
1637	–
2144		rnemdFile_ << "#######################################################\n";
2145
2146
#	Line 1645 | Line 2151 | namespace OpenMD {
2151		if (outputMask_[i]) {
2152		rnemdFile_ << "\t" << data_[i].title <<
2153		"(" << data_[i].units << ")";
2154	+	// add some extra tabs for column alignment
2155	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2156		}
2157		}
2158		rnemdFile_ << std::endl;
2159
2160		rnemdFile_.precision(8);
2161
2162	<	for (unsigned int j = 0; j < nBins_; j++) {
2162	>	for (int j = 0; j < nBins_; j++) {
2163
2164		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2165		if (outputMask_[i]) {
2166		if (data_[i].dataType == "RealType")
2167		writeReal(i,j);
2168	<	else if (data_[i].dataType == "Vector3d")
2168	>	else if (data_[i].dataType == "Vector3d")
2169		writeVector(i,j);
2170		else {
2171		sprintf( painCave.errMsg,
#	Line 1671 | Line 2179 | namespace OpenMD {
2179		rnemdFile_ << std::endl;
2180
2181		}
2182	+
2183	+	rnemdFile_ << "#######################################################\n";
2184	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2185	+	rnemdFile_ << "#######################################################\n";
2186	+
2187	+
2188	+	for (int j = 0; j < nBins_; j++) {
2189	+	rnemdFile_ << "#";
2190	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2191	+	if (outputMask_[i]) {
2192	+	if (data_[i].dataType == "RealType")
2193	+	writeRealStdDev(i,j);
2194	+	else if (data_[i].dataType == "Vector3d")
2195	+	writeVectorStdDev(i,j);
2196	+	else {
2197	+	sprintf( painCave.errMsg,
2198	+	"RNEMD found an unknown data type for: %s ",
2199	+	data_[i].title.c_str());
2200	+	painCave.isFatal = 1;
2201	+	simError();
2202	+	}
2203	+	}
2204	+	}
2205	+	rnemdFile_ << std::endl;
2206	+
2207	+	}
2208
2209		rnemdFile_.flush();
2210		rnemdFile_.close();
#	Line 1682 | Line 2216 | namespace OpenMD {
2216		}
2217
2218		void RNEMD::writeReal(int index, unsigned int bin) {
2219	+	if (!doRNEMD_) return;
2220		assert(index >=0 && index < ENDINDEX);
2221	<	assert(bin >=0 && bin < nBins_);
2221	>	assert(int(bin) < nBins_);
2222		RealType s;
2223	+	int count;
2224
2225	<	data_[index].accumulator[bin]->getAverage(s);
2225	>	count = data_[index].accumulator[bin]->count();
2226	>	if (count == 0) return;
2227
2228	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2229	+
2230		if (! isinf(s) && ! isnan(s)) {
2231		rnemdFile_ << "\t" << s;
2232		} else{
2233		sprintf( painCave.errMsg,
2234	<	"RNEMD detected a numerical error writing: %s for bin %d",
2234	>	"RNEMD detected a numerical error writing: %s for bin %u",
2235		data_[index].title.c_str(), bin);
2236		painCave.isFatal = 1;
2237		simError();
#	Line 1700 | Line 2239 | namespace OpenMD {
2239		}
2240
2241		void RNEMD::writeVector(int index, unsigned int bin) {
2242	+	if (!doRNEMD_) return;
2243		assert(index >=0 && index < ENDINDEX);
2244	<	assert(bin >=0 && bin < nBins_);
2244	>	assert(int(bin) < nBins_);
2245		Vector3d s;
2246	+	int count;
2247	+
2248	+	count = data_[index].accumulator[bin]->count();
2249	+
2250	+	if (count == 0) return;
2251	+
2252		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2253		if (isinf(s[0]) || isnan(s[0]) ||
2254		isinf(s[1]) || isnan(s[1]) ||
2255		isinf(s[2]) || isnan(s[2]) ) {
2256		sprintf( painCave.errMsg,
2257	<	"RNEMD detected a numerical error writing: %s for bin %d",
2257	>	"RNEMD detected a numerical error writing: %s for bin %u",
2258		data_[index].title.c_str(), bin);
2259		painCave.isFatal = 1;
2260		simError();
#	Line 1716 | Line 2262 | namespace OpenMD {
2262		rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2263		}
2264		}
2265	+
2266	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2267	+	if (!doRNEMD_) return;
2268	+	assert(index >=0 && index < ENDINDEX);
2269	+	assert(int(bin) < nBins_);
2270	+	RealType s;
2271	+	int count;
2272	+
2273	+	count = data_[index].accumulator[bin]->count();
2274	+	if (count == 0) return;
2275	+
2276	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2277	+
2278	+	if (! isinf(s) && ! isnan(s)) {
2279	+	rnemdFile_ << "\t" << s;
2280	+	} else{
2281	+	sprintf( painCave.errMsg,
2282	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2283	+	data_[index].title.c_str(), bin);
2284	+	painCave.isFatal = 1;
2285	+	simError();
2286	+	}
2287	+	}
2288	+
2289	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2290	+	if (!doRNEMD_) return;
2291	+	assert(index >=0 && index < ENDINDEX);
2292	+	assert(int(bin) < nBins_);
2293	+	Vector3d s;
2294	+	int count;
2295	+
2296	+	count = data_[index].accumulator[bin]->count();
2297	+	if (count == 0) return;
2298	+
2299	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2300	+	if (isinf(s[0]) || isnan(s[0]) ||
2301	+	isinf(s[1]) || isnan(s[1]) ||
2302	+	isinf(s[2]) || isnan(s[2]) ) {
2303	+	sprintf( painCave.errMsg,
2304	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2305	+	data_[index].title.c_str(), bin);
2306	+	painCave.isFatal = 1;
2307	+	simError();
2308	+	} else {
2309	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2310	+	}
2311	+	}
2312		}
2313

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