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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 1854 by gezelter, Thu Mar 28 20:54:06 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 194 | Line 224 | namespace OpenMD {
224		case rnemdPy:
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	<	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";
298	<	z.accumulator.reserve(nBins_);
299	<	for (unsigned int i = 0; i < nBins_; i++)
300	<	z.accumulator.push_back( new Accumulator() );
301	<	data_[Z] = z;
302	<	outputMap_["Z"] =  Z;
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351	>	} else {
352	>	coordinateOrigin_ = V3Zero;
353	>	}
354
355	<	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;
355	>	// do some sanity checking
356
357	<	OutputData velocity;
315	<	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;
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);
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	<	}
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	<	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
424	<	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
423	>	OutputData density;
424	>	density.units =  "g cm^-3";
425	>	density.title =  "Density";
426	>	density.dataType = "RealType";
427	>	density.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	density.accumulator.push_back( new Accumulator() );
430	>	data_[DENSITY] = density;
431	>	outputMap_["DENSITY"] =  DENSITY;
432
433	<	// total exchange sums are zeroed out at the beginning:
433	>	if (hasOutputFields) {
434	>	parseOutputFileFormat(rnemdParams->getOutputFields());
435	>	} else {
436	>	if (usePeriodicBoundaryConditions_)
437	>	outputMask_.set(Z);
438	>	else
439	>	outputMask_.set(R);
440	>	switch (rnemdFluxType_) {
441	>	case rnemdKE:
442	>	case rnemdRotKE:
443	>	case rnemdFullKE:
444	>	outputMask_.set(TEMPERATURE);
445	>	break;
446	>	case rnemdPx:
447	>	case rnemdPy:
448	>	outputMask_.set(VELOCITY);
449	>	break;
450	>	case rnemdPz:
451	>	case rnemdPvector:
452	>	outputMask_.set(VELOCITY);
453	>	outputMask_.set(DENSITY);
454	>	break;
455	>	case rnemdLx:
456	>	case rnemdLy:
457	>	case rnemdLz:
458	>	case rnemdLvector:
459	>	outputMask_.set(ANGULARVELOCITY);
460	>	break;
461	>	case rnemdKeLx:
462	>	case rnemdKeLy:
463	>	case rnemdKeLz:
464	>	case rnemdKeLvector:
465	>	outputMask_.set(TEMPERATURE);
466	>	outputMask_.set(ANGULARVELOCITY);
467	>	break;
468	>	case rnemdKePx:
469	>	case rnemdKePy:
470	>	outputMask_.set(TEMPERATURE);
471	>	outputMask_.set(VELOCITY);
472	>	break;
473	>	case rnemdKePvector:
474	>	outputMask_.set(TEMPERATURE);
475	>	outputMask_.set(VELOCITY);
476	>	outputMask_.set(DENSITY);
477	>	break;
478	>	default:
479	>	break;
480	>	}
481	>	}
482	>
483	>	if (hasOutputFileName) {
484	>	rnemdFileName_ = rnemdParams->getOutputFileName();
485	>	} else {
486	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
487	>	}
488
489	<	kineticExchange_ = 0.0;
390	<	momentumExchange_ = V3Zero;
489	>	exchangeTime_ = rnemdParams->getExchangeTime();
490
491	<	if (hasSlabWidth)
492	<	slabWidth_ = rnemdParams->getSlabWidth();
493	<	else
494	<	slabWidth_ = hmat(2,2) / 10.0;
495	<
496	<	if (hasSlabACenter)
497	<	slabACenter_ = rnemdParams->getSlabACenter();
498	<	else
499	<	slabACenter_ = 0.0;
491	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
492	>	// total exchange sums are zeroed out at the beginning:
493	>
494	>	kineticExchange_ = 0.0;
495	>	momentumExchange_ = V3Zero;
496	>	angularMomentumExchange_ = V3Zero;
497	>
498	>	std::ostringstream selectionAstream;
499	>	std::ostringstream selectionBstream;
500
501	<	if (hasSlabBCenter)
502	<	slabBCenter_ = rnemdParams->getSlabBCenter();
503	<	else
504	<	slabBCenter_ = hmat(2,2) / 2.0;
501	>	if (hasSelectionA_) {
502	>	selectionA_ = rnemdParams->getSelectionA();
503	>	} else {
504	>	if (usePeriodicBoundaryConditions_) {
505	>	Mat3x3d hmat = currentSnap_->getHmat();
506	>
507	>	if (hasSlabWidth)
508	>	slabWidth_ = rnemdParams->getSlabWidth();
509	>	else
510	>	slabWidth_ = hmat(2,2) / 10.0;
511	>
512	>	if (hasSlabACenter)
513	>	slabACenter_ = rnemdParams->getSlabACenter();
514	>	else
515	>	slabACenter_ = 0.0;
516	>
517	>	selectionAstream << "select wrappedz > "
518	>	<< slabACenter_ - 0.5*slabWidth_
519	>	<<  " && wrappedz < "
520	>	<< slabACenter_ + 0.5*slabWidth_;
521	>	selectionA_ = selectionAstream.str();
522	>	} else {
523	>	if (hasSphereARadius)
524	>	sphereARadius_ = rnemdParams->getSphereARadius();
525	>	else {
526	>	// use an initial guess to the size of the inner slab to be 1/10 the
527	>	// radius of an approximately spherical hull:
528	>	Thermo thermo(info);
529	>	RealType hVol = thermo.getHullVolume();
530	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
531	>	}
532	>	selectionAstream << "select r < " << sphereARadius_;
533	>	selectionA_ = selectionAstream.str();
534	>	}
535	>	}
536
537	+	if (hasSelectionB_) {
538	+	selectionB_ = rnemdParams->getSelectionB();
539	+	} else {
540	+	if (usePeriodicBoundaryConditions_) {
541	+	Mat3x3d hmat = currentSnap_->getHmat();
542	+
543	+	if (hasSlabWidth)
544	+	slabWidth_ = rnemdParams->getSlabWidth();
545	+	else
546	+	slabWidth_ = hmat(2,2) / 10.0;
547	+
548	+	if (hasSlabBCenter)
549	+	slabBCenter_ = rnemdParams->getSlabACenter();
550	+	else
551	+	slabBCenter_ = hmat(2,2) / 2.0;
552	+
553	+	selectionBstream << "select wrappedz > "
554	+	<< slabBCenter_ - 0.5*slabWidth_
555	+	<<  " && wrappedz < "
556	+	<< slabBCenter_ + 0.5*slabWidth_;
557	+	selectionB_ = selectionBstream.str();
558	+	} else {
559	+	if (hasSphereBRadius_) {
560	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
561	+	selectionBstream << "select r > " << sphereBRadius_;
562	+	selectionB_ = selectionBstream.str();
563	+	} else {
564	+	selectionB_ = "select hull";
565	+	hasSelectionB_ = true;
566	+	}
567	+	}
568	+	}
569	+	}
570	+	// object evaluator:
571	+	evaluator_.loadScriptString(rnemdObjectSelection_);
572	+	seleMan_.setSelectionSet(evaluator_.evaluate());
573	+
574	+	evaluatorA_.loadScriptString(selectionA_);
575	+	evaluatorB_.loadScriptString(selectionB_);
576	+
577	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
578	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
579	+
580	+	commonA_ = seleManA_ & seleMan_;
581	+	commonB_ = seleManB_ & seleMan_;
582		}
583	<
409	<	RNEMD::~RNEMD() {
583	>
584
585	+	RNEMD::~RNEMD() {
586	+	if (!doRNEMD_) return;
587		#ifdef IS_MPI
588		if (worldRank == 0) {
589		#endif
#	Line 421 | Line 597 | namespace OpenMD {
597		#endif
598		}
599
600	<	bool RNEMD::inSlabA(Vector3d pos) {
601	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
602	<	}
603	<	bool RNEMD::inSlabB(Vector3d pos) {
428	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	<	}
600	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
601	>	if (!doRNEMD_) return;
602	>	int selei;
603	>	int selej;
604
431	–	void RNEMD::doSwap() {
432	–
605		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
606		Mat3x3d hmat = currentSnap_->getHmat();
607
436	–	seleMan_.setSelectionSet(evaluator_.evaluate());
437	–
438	–	int selei;
608		StuntDouble* sd;
440	–	int idx;
609
610		RealType min_val;
611		bool min_found = false;
#	Line 447 | Line 615 | namespace OpenMD {
615		bool max_found = false;
616		StuntDouble* max_sd;
617
618	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
619	<	sd = seleMan_.nextSelected(selei)) {
618	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
619	>	sd = seleManA_.nextSelected(selei)) {
620
453	–	idx = sd->getLocalIndex();
454	–
621		Vector3d pos = sd->getPos();
622	<
622	>
623		// wrap the stuntdouble's position back into the box:
624	<
624	>
625		if (usePeriodicBoundaryConditions_)
626		currentSnap_->wrapVector(pos);
627	<	bool inA = inSlabA(pos);
628	<	bool inB = inSlabB(pos);
629	<
630	<	if (inA || inB) {
627	>
628	>	RealType mass = sd->getMass();
629	>	Vector3d vel = sd->getVel();
630	>	RealType value;
631	>
632	>	switch(rnemdFluxType_) {
633	>	case rnemdKE :
634
635	<	RealType mass = sd->getMass();
636	<	Vector3d vel = sd->getVel();
637	<	RealType value;
638	<
639	<	switch(rnemdFluxType_) {
471	<	case rnemdKE :
635	>	value = mass * vel.lengthSquare();
636	>
637	>	if (sd->isDirectional()) {
638	>	Vector3d angMom = sd->getJ();
639	>	Mat3x3d I = sd->getI();
640
641	<	value = mass * vel.lengthSquare();
642	<
643	<	if (sd->isDirectional()) {
644	<	Vector3d angMom = sd->getJ();
645	<	Mat3x3d I = sd->getI();
646	<
647	<	if (sd->isLinear()) {
648	<	int i = sd->linearAxis();
649	<	int j = (i + 1) % 3;
650	<	int k = (i + 2) % 3;
651	<	value += angMom[j] * angMom[j] / I(j, j) +
652	<	angMom[k] * angMom[k] / I(k, k);
653	<	} else {
654	<	value += angMom[0]*angMom[0]/I(0, 0)
655	<	+ angMom[1]*angMom[1]/I(1, 1)
656	<	+ angMom[2]*angMom[2]/I(2, 2);
657	<	}
658	<	} //angular momenta exchange enabled
659	<	//energyConvert temporarily disabled
660	<	//make kineticExchange_ comparable between swap & scale
661	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
662	<	value *= 0.5;
663	<	break;
664	<	case rnemdPx :
665	<	value = mass * vel[0];
666	<	break;
667	<	case rnemdPy :
668	<	value = mass * vel[1];
669	<	break;
670	<	case rnemdPz :
671	<	value = mass * vel[2];
672	<	break;
673	<	default :
674	<	break;
641	>	if (sd->isLinear()) {
642	>	int i = sd->linearAxis();
643	>	int j = (i + 1) % 3;
644	>	int k = (i + 2) % 3;
645	>	value += angMom[j] * angMom[j] / I(j, j) +
646	>	angMom[k] * angMom[k] / I(k, k);
647	>	} else {
648	>	value += angMom[0]*angMom[0]/I(0, 0)
649	>	+ angMom[1]*angMom[1]/I(1, 1)
650	>	+ angMom[2]*angMom[2]/I(2, 2);
651	>	}
652	>	} //angular momenta exchange enabled
653	>	value *= 0.5;
654	>	break;
655	>	case rnemdPx :
656	>	value = mass * vel[0];
657	>	break;
658	>	case rnemdPy :
659	>	value = mass * vel[1];
660	>	break;
661	>	case rnemdPz :
662	>	value = mass * vel[2];
663	>	break;
664	>	default :
665	>	break;
666	>	}
667	>	if (!max_found) {
668	>	max_val = value;
669	>	max_sd = sd;
670	>	max_found = true;
671	>	} else {
672	>	if (max_val < value) {
673	>	max_val = value;
674	>	max_sd = sd;
675		}
676	+	}
677	+	}
678
679	<	if (inA == 0) {
680	<	if (!min_found) {
681	<	min_val = value;
682	<	min_sd = sd;
683	<	min_found = true;
684	<	} else {
685	<	if (min_val > value) {
686	<	min_val = value;
687	<	min_sd = sd;
688	<	}
689	<	}
690	<	} else {
691	<	if (!max_found) {
692	<	max_val = value;
693	<	max_sd = sd;
694	<	max_found = true;
695	<	} else {
696	<	if (max_val < value) {
697	<	max_val = value;
698	<	max_sd = sd;
699	<	}
700	<	}
701	<	}
679	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
680	>	sd = seleManB_.nextSelected(selej)) {
681	>
682	>	Vector3d pos = sd->getPos();
683	>
684	>	// wrap the stuntdouble's position back into the box:
685	>
686	>	if (usePeriodicBoundaryConditions_)
687	>	currentSnap_->wrapVector(pos);
688	>
689	>	RealType mass = sd->getMass();
690	>	Vector3d vel = sd->getVel();
691	>	RealType value;
692	>
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695	>
696	>	value = mass * vel.lengthSquare();
697	>
698	>	if (sd->isDirectional()) {
699	>	Vector3d angMom = sd->getJ();
700	>	Mat3x3d I = sd->getI();
701	>
702	>	if (sd->isLinear()) {
703	>	int i = sd->linearAxis();
704	>	int j = (i + 1) % 3;
705	>	int k = (i + 2) % 3;
706	>	value += angMom[j] * angMom[j] / I(j, j) +
707	>	angMom[k] * angMom[k] / I(k, k);
708	>	} else {
709	>	value += angMom[0]*angMom[0]/I(0, 0)
710	>	+ angMom[1]*angMom[1]/I(1, 1)
711	>	+ angMom[2]*angMom[2]/I(2, 2);
712	>	}
713	>	} //angular momenta exchange enabled
714	>	value *= 0.5;
715	>	break;
716	>	case rnemdPx :
717	>	value = mass * vel[0];
718	>	break;
719	>	case rnemdPy :
720	>	value = mass * vel[1];
721	>	break;
722	>	case rnemdPz :
723	>	value = mass * vel[2];
724	>	break;
725	>	default :
726	>	break;
727		}
728	+
729	+	if (!min_found) {
730	+	min_val = value;
731	+	min_sd = sd;
732	+	min_found = true;
733	+	} else {
734	+	if (min_val > value) {
735	+	min_val = value;
736	+	min_sd = sd;
737	+	}
738	+	}
739		}
740
741	<	#ifdef IS_MPI
742	<	int nProc, worldRank;
741	>	#ifdef IS_MPI
742	>	int worldRank = MPI::COMM_WORLD.Get_rank();
743
538	–	nProc = MPI::COMM_WORLD.Get_size();
539	–	worldRank = MPI::COMM_WORLD.Get_rank();
540	–
744		bool my_min_found = min_found;
745		bool my_max_found = max_found;
746
#	Line 728 | Line 931 | namespace OpenMD {
931
932		switch(rnemdFluxType_) {
933		case rnemdKE:
731	–	cerr << "KE\n";
934		kineticExchange_ += max_val - min_val;
935		break;
936		case rnemdPx:
#	Line 741 | Line 943 | namespace OpenMD {
943		momentumExchange_.z() += max_val - min_val;
944		break;
945		default:
744	–	cerr << "default\n";
946		break;
947		}
948		} else {
#	Line 763 | Line 964 | namespace OpenMD {
964		}
965		}
966
967	<	void RNEMD::doNIVS() {
967	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
968	>	if (!doRNEMD_) return;
969	>	int selei;
970	>	int selej;
971
972		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
973	+	RealType time = currentSnap_->getTime();
974		Mat3x3d hmat = currentSnap_->getHmat();
975
771	–	seleMan_.setSelectionSet(evaluator_.evaluate());
772	–
773	–	int selei;
976		StuntDouble* sd;
775	–	int idx;
977
978		vector<StuntDouble*> hotBin, coldBin;
979
#	Line 791 | Line 992 | namespace OpenMD {
992		RealType Kcz = 0.0;
993		RealType Kcw = 0.0;
994
995	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
996	<	sd = seleMan_.nextSelected(selei)) {
796	<
797	<	idx = sd->getLocalIndex();
798	<
799	<	Vector3d pos = sd->getPos();
995	>	for (sd = smanA.beginSelected(selei); sd != NULL;
996	>	sd = smanA.nextSelected(selei)) {
997
998	+	Vector3d pos = sd->getPos();
999	+
1000		// wrap the stuntdouble's position back into the box:
1001	<
1001	>
1002		if (usePeriodicBoundaryConditions_)
1003		currentSnap_->wrapVector(pos);
1004	<
1005	<	// which bin is this stuntdouble in?
1006	<	bool inA = inSlabA(pos);
1007	<	bool inB = inSlabB(pos);
1004	>
1005	>
1006	>	RealType mass = sd->getMass();
1007	>	Vector3d vel = sd->getVel();
1008	>
1009	>	hotBin.push_back(sd);
1010	>	Phx += mass * vel.x();
1011	>	Phy += mass * vel.y();
1012	>	Phz += mass * vel.z();
1013	>	Khx += mass * vel.x() * vel.x();
1014	>	Khy += mass * vel.y() * vel.y();
1015	>	Khz += mass * vel.z() * vel.z();
1016	>	if (sd->isDirectional()) {
1017	>	Vector3d angMom = sd->getJ();
1018	>	Mat3x3d I = sd->getI();
1019	>	if (sd->isLinear()) {
1020	>	int i = sd->linearAxis();
1021	>	int j = (i + 1) % 3;
1022	>	int k = (i + 2) % 3;
1023	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1024	>	angMom[k] * angMom[k] / I(k, k);
1025	>	} else {
1026	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1027	>	+ angMom[1]*angMom[1]/I(1, 1)
1028	>	+ angMom[2]*angMom[2]/I(2, 2);
1029	>	}
1030	>	}
1031	>	}
1032	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1033	>	sd = smanB.nextSelected(selej)) {
1034	>	Vector3d pos = sd->getPos();
1035	>
1036	>	// wrap the stuntdouble's position back into the box:
1037	>
1038	>	if (usePeriodicBoundaryConditions_)
1039	>	currentSnap_->wrapVector(pos);
1040	>
1041	>	RealType mass = sd->getMass();
1042	>	Vector3d vel = sd->getVel();
1043
1044	<	if (inA || inB) {
1045	<
1046	<	RealType mass = sd->getMass();
1047	<	Vector3d vel = sd->getVel();
1048	<
1049	<	if (inA) {
1050	<	hotBin.push_back(sd);
1051	<	Phx += mass * vel.x();
1052	<	Phy += mass * vel.y();
1053	<	Phz += mass * vel.z();
1054	<	Khx += mass * vel.x() * vel.x();
1055	<	Khy += mass * vel.y() * vel.y();
1056	<	Khz += mass * vel.z() * vel.z();
1057	<	if (sd->isDirectional()) {
1058	<	Vector3d angMom = sd->getJ();
1059	<	Mat3x3d I = sd->getI();
1060	<	if (sd->isLinear()) {
1061	<	int i = sd->linearAxis();
1062	<	int j = (i + 1) % 3;
1063	<	int k = (i + 2) % 3;
1064	<	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	<	}
1044	>	coldBin.push_back(sd);
1045	>	Pcx += mass * vel.x();
1046	>	Pcy += mass * vel.y();
1047	>	Pcz += mass * vel.z();
1048	>	Kcx += mass * vel.x() * vel.x();
1049	>	Kcy += mass * vel.y() * vel.y();
1050	>	Kcz += mass * vel.z() * vel.z();
1051	>	if (sd->isDirectional()) {
1052	>	Vector3d angMom = sd->getJ();
1053	>	Mat3x3d I = sd->getI();
1054	>	if (sd->isLinear()) {
1055	>	int i = sd->linearAxis();
1056	>	int j = (i + 1) % 3;
1057	>	int k = (i + 2) % 3;
1058	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1059	>	angMom[k] * angMom[k] / I(k, k);
1060	>	} else {
1061	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1062	>	+ angMom[1]*angMom[1]/I(1, 1)
1063	>	+ angMom[2]*angMom[2]/I(2, 2);
1064	>	}
1065		}
1066		}
1067
#	Line 908 | Line 1111 | namespace OpenMD {
1111
1112		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1113		c = sqrt(c);
1114	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	<	//now convert to hotBin coefficient
1114	>
1115		RealType w = 0.0;
1116		if (rnemdFluxType_ ==  rnemdFullKE) {
1117		x = 1.0 + px * (1.0 - c);
#	Line 947 | Line 1149 | namespace OpenMD {
1149		}
1150		}
1151		w = sqrt(w);
950	–	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	–	//           << "\twh= " << w << endl;
1152		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1153		if (rnemdFluxType_ == rnemdFullKE) {
1154		vel = (*sdi)->getVel();
#	Line 1211 | Line 1411 | namespace OpenMD {
1411		failTrialCount_++;
1412		}
1413		}
1414	<
1415	<	void RNEMD::doVSS() {
1414	>
1415	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1416	>	if (!doRNEMD_) return;
1417	>	int selei;
1418	>	int selej;
1419
1420		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1421		RealType time = currentSnap_->getTime();
1422		Mat3x3d hmat = currentSnap_->getHmat();
1423
1221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	–
1223	–	int selei;
1424		StuntDouble* sd;
1225	–	int idx;
1425
1426		vector<StuntDouble*> hotBin, coldBin;
1427
1428		Vector3d Ph(V3Zero);
1429	+	Vector3d Lh(V3Zero);
1430		RealType Mh = 0.0;
1431	+	Mat3x3d Ih(0.0);
1432		RealType Kh = 0.0;
1433		Vector3d Pc(V3Zero);
1434	+	Vector3d Lc(V3Zero);
1435		RealType Mc = 0.0;
1436	+	Mat3x3d Ic(0.0);
1437		RealType Kc = 0.0;
1438
1439	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1440	+	sd = smanA.nextSelected(selei)) {
1441
1237	–	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1238	–	sd = seleMan_.nextSelected(selei)) {
1239	–
1240	–	idx = sd->getLocalIndex();
1241	–
1442		Vector3d pos = sd->getPos();
1443
1444		// wrap the stuntdouble's position back into the box:
1445	+
1446	+	if (usePeriodicBoundaryConditions_)
1447	+	currentSnap_->wrapVector(pos);
1448	+
1449	+	RealType mass = sd->getMass();
1450	+	Vector3d vel = sd->getVel();
1451	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1452	+	RealType r2;
1453	+
1454	+	hotBin.push_back(sd);
1455	+	Ph += mass * vel;
1456	+	Mh += mass;
1457	+	Kh += mass * vel.lengthSquare();
1458	+	Lh += mass * cross(rPos, vel);
1459	+	Ih -= outProduct(rPos, rPos) * mass;
1460	+	r2 = rPos.lengthSquare();
1461	+	Ih(0, 0) += mass * r2;
1462	+	Ih(1, 1) += mass * r2;
1463	+	Ih(2, 2) += mass * r2;
1464	+
1465	+	if (rnemdFluxType_ == rnemdFullKE) {
1466	+	if (sd->isDirectional()) {
1467	+	Vector3d angMom = sd->getJ();
1468	+	Mat3x3d I = sd->getI();
1469	+	if (sd->isLinear()) {
1470	+	int i = sd->linearAxis();
1471	+	int j = (i + 1) % 3;
1472	+	int k = (i + 2) % 3;
1473	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1474	+	angMom[k] * angMom[k] / I(k, k);
1475	+	} else {
1476	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1477	+	angMom[1] * angMom[1] / I(1, 1) +
1478	+	angMom[2] * angMom[2] / I(2, 2);
1479	+	}
1480	+	}
1481	+	}
1482	+	}
1483	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1484	+	sd = smanB.nextSelected(selej)) {
1485
1486	+	Vector3d pos = sd->getPos();
1487	+
1488	+	// wrap the stuntdouble's position back into the box:
1489	+
1490		if (usePeriodicBoundaryConditions_)
1491		currentSnap_->wrapVector(pos);
1492	+
1493	+	RealType mass = sd->getMass();
1494	+	Vector3d vel = sd->getVel();
1495	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1496	+	RealType r2;
1497
1498	<	// which bin is this stuntdouble in?
1499	<	bool inA = inSlabA(pos);
1500	<	bool inB = inSlabB(pos);
1498	>	coldBin.push_back(sd);
1499	>	Pc += mass * vel;
1500	>	Mc += mass;
1501	>	Kc += mass * vel.lengthSquare();
1502	>	Lc += mass * cross(rPos, vel);
1503	>	Ic -= outProduct(rPos, rPos) * mass;
1504	>	r2 = rPos.lengthSquare();
1505	>	Ic(0, 0) += mass * r2;
1506	>	Ic(1, 1) += mass * r2;
1507	>	Ic(2, 2) += mass * r2;
1508
1509	<	if (inA || inB) {
1510	<
1511	<	RealType mass = sd->getMass();
1512	<	Vector3d vel = sd->getVel();
1513	<
1514	<	if (inA) {
1515	<	hotBin.push_back(sd);
1516	<	//std::cerr << "before, velocity = " << vel << endl;
1517	<	Ph += mass * vel;
1518	<	//std::cerr << "after, velocity = " << vel << endl;
1519	<	Mh += mass;
1520	<	Kh += mass * vel.lengthSquare();
1521	<	if (rnemdFluxType_ == rnemdFullKE) {
1522	<	if (sd->isDirectional()) {
1523	<	Vector3d angMom = sd->getJ();
1524	<	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	<	}
1509	>	if (rnemdFluxType_ == rnemdFullKE) {
1510	>	if (sd->isDirectional()) {
1511	>	Vector3d angMom = sd->getJ();
1512	>	Mat3x3d I = sd->getI();
1513	>	if (sd->isLinear()) {
1514	>	int i = sd->linearAxis();
1515	>	int j = (i + 1) % 3;
1516	>	int k = (i + 2) % 3;
1517	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1518	>	angMom[k] * angMom[k] / I(k, k);
1519	>	} else {
1520	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1521	>	angMom[1] * angMom[1] / I(1, 1) +
1522	>	angMom[2] * angMom[2] / I(2, 2);
1523	>	}
1524	>	}
1525		}
1526		}
1527
1528		Kh *= 0.5;
1529		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;
1530
1531		#ifdef IS_MPI
1532		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1533		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1534	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1535	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1536		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1537		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1538		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1539		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1540	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1541	+	MPI::REALTYPE, MPI::SUM);
1542	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1543	+	MPI::REALTYPE, MPI::SUM);
1544		#endif
1545	<
1545	>
1546		bool successfulExchange = false;
1547		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1548		Vector3d vc = Pc / Mc;
1549		Vector3d ac = -momentumTarget_ / Mc + vc;
1550		Vector3d acrec = -momentumTarget_ / Mc;
1551	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1551	>
1552	>	// We now need the inverse of the inertia tensor to calculate the
1553	>	// angular velocity of the cold slab;
1554	>	Mat3x3d Ici = Ic.inverse();
1555	>	Vector3d omegac = Ici * Lc;
1556	>	Vector3d bc  = -(Ici * angularMomentumTarget_) + omegac;
1557	>	Vector3d bcrec = bc - omegac;
1558	>
1559	>	RealType cNumerator = Kc - kineticTarget_
1560	>	- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc));
1561		if (cNumerator > 0.0) {
1562	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1562	>
1563	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare()
1564	>	- 0.5*(dot(omegac, Ic * omegac));
1565	>
1566		if (cDenominator > 0.0) {
1567		RealType c = sqrt(cNumerator / cDenominator);
1568		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1569	+
1570		Vector3d vh = Ph / Mh;
1571		Vector3d ah = momentumTarget_ / Mh + vh;
1572		Vector3d ahrec = momentumTarget_ / Mh;
1573	<	RealType hNumerator = Kh + kineticTarget_
1574	<	- 0.5 * Mh * ah.lengthSquare();
1575	<	if (hNumerator > 0.0) {
1576	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1573	>
1574	>	// We now need the inverse of the inertia tensor to
1575	>	// calculate the angular velocity of the hot slab;
1576	>	Mat3x3d Ihi = Ih.inverse();
1577	>	Vector3d omegah = Ihi * Lh;
1578	>	Vector3d bh  = (Ihi * angularMomentumTarget_) + omegah;
1579	>	Vector3d bhrec = bh - omegah;
1580	>
1581	>	RealType hNumerator = Kh + kineticTarget_
1582	>	- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));;
1583	>	if (hNumerator > 0.0) {
1584	>
1585	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare()
1586	>	- 0.5*(dot(omegah, Ih * omegah));
1587	>
1588		if (hDenominator > 0.0) {
1589		RealType h = sqrt(hNumerator / hDenominator);
1590		if ((h > 0.9) && (h < 1.1)) {
1591	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1591	>
1592		vector<StuntDouble*>::iterator sdi;
1593		Vector3d vel;
1594	+	Vector3d rPos;
1595	+
1596		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1597		//vel = (*sdi)->getVel();
1598	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1598	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1599	>	vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c
1600	>	+ ac + cross(bc, rPos);
1601		(*sdi)->setVel(vel);
1602		if (rnemdFluxType_ == rnemdFullKE) {
1603		if ((*sdi)->isDirectional()) {
#	Line 1359 | Line 1608 | namespace OpenMD {
1608		}
1609		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1610		//vel = (*sdi)->getVel();
1611	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1611	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1612	>	vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1613	>	+ ah + cross(bh, rPos);
1614		(*sdi)->setVel(vel);
1615		if (rnemdFluxType_ == rnemdFullKE) {
1616		if ((*sdi)->isDirectional()) {
#	Line 1371 | Line 1622 | namespace OpenMD {
1622		successfulExchange = true;
1623		kineticExchange_ += kineticTarget_;
1624		momentumExchange_ += momentumTarget_;
1625	+	angularMomentumExchange_ += angularMomentumTarget_;
1626		}
1627		}
1628		}
#	Line 1390 | Line 1642 | namespace OpenMD {
1642		}
1643		}
1644
1645	<	void RNEMD::doRNEMD() {
1645	>	RealType RNEMD::getDividingArea() {
1646
1647	+	if (hasDividingArea_) return dividingArea_;
1648	+
1649	+	RealType areaA, areaB;
1650	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1651	+
1652	+	if (hasSelectionA_) {
1653	+	int isd;
1654	+	StuntDouble* sd;
1655	+	vector<StuntDouble*> aSites;
1656	+	ConvexHull* surfaceMeshA = new ConvexHull();
1657	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1658	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1659	+	sd = seleManA_.nextSelected(isd)) {
1660	+	aSites.push_back(sd);
1661	+	}
1662	+	surfaceMeshA->computeHull(aSites);
1663	+	areaA = surfaceMeshA->getArea();
1664	+	} else {
1665	+	if (usePeriodicBoundaryConditions_) {
1666	+	// in periodic boundaries, the surface area is twice the x-y
1667	+	// area of the current box:
1668	+	areaA = 2.0 * snap->getXYarea();
1669	+	} else {
1670	+	// in non-periodic simulations, without explicitly setting
1671	+	// selections, the sphere radius sets the surface area of the
1672	+	// dividing surface:
1673	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1674	+	}
1675	+	}
1676	+
1677	+	if (hasSelectionB_) {
1678	+	int isd;
1679	+	StuntDouble* sd;
1680	+	vector<StuntDouble*> bSites;
1681	+	ConvexHull* surfaceMeshB = new ConvexHull();
1682	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1683	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1684	+	sd = seleManB_.nextSelected(isd)) {
1685	+	bSites.push_back(sd);
1686	+	}
1687	+	surfaceMeshB->computeHull(bSites);
1688	+	areaB = surfaceMeshB->getArea();
1689	+	} else {
1690	+	if (usePeriodicBoundaryConditions_) {
1691	+	// in periodic boundaries, the surface area is twice the x-y
1692	+	// area of the current box:
1693	+	areaB = 2.0 * snap->getXYarea();
1694	+	} else {
1695	+	// in non-periodic simulations, without explicitly setting
1696	+	// selections, but if a sphereBradius has been set, just use that:
1697	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1698	+	}
1699	+	}
1700	+
1701	+	dividingArea_ = min(areaA, areaB);
1702	+	hasDividingArea_ = true;
1703	+	return dividingArea_;
1704	+	}
1705	+
1706	+	void RNEMD::doRNEMD() {
1707	+	if (!doRNEMD_) return;
1708		trialCount_++;
1709	+
1710	+	// object evaluator:
1711	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1712	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1713	+
1714	+	evaluatorA_.loadScriptString(selectionA_);
1715	+	evaluatorB_.loadScriptString(selectionB_);
1716	+
1717	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1718	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1719	+
1720	+	commonA_ = seleManA_ & seleMan_;
1721	+	commonB_ = seleManB_ & seleMan_;
1722	+
1723	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1724	+	// dt = exchange time interval
1725	+	// flux = target flux
1726	+	// dividingArea = smallest dividing surface between the two regions
1727	+
1728	+	hasDividingArea_ = false;
1729	+	RealType area = getDividingArea();
1730	+
1731	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1732	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1733	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1734	+
1735		switch(rnemdMethod_) {
1736		case rnemdSwap:
1737	<	doSwap();
1737	>	doSwap(commonA_, commonB_);
1738		break;
1739		case rnemdNIVS:
1740	<	doNIVS();
1740	>	doNIVS(commonA_, commonB_);
1741		break;
1742		case rnemdVSS:
1743	<	doVSS();
1743	>	doVSS(commonA_, commonB_);
1744		break;
1745		case rnemdUnkownMethod:
1746		default :
#	Line 1410 | Line 1749 | namespace OpenMD {
1749		}
1750
1751		void RNEMD::collectData() {
1752	<
1752	>	if (!doRNEMD_) return;
1753		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1415	–	Mat3x3d hmat = currentSnap_->getHmat();
1754
1755	+	// collectData can be called more frequently than the doRNEMD, so use the
1756	+	// computed area from the last exchange time:
1757	+
1758	+	areaAccumulator_->add(getDividingArea());
1759	+	Mat3x3d hmat = currentSnap_->getHmat();
1760		seleMan_.setSelectionSet(evaluator_.evaluate());
1761
1762	<	int selei;
1762	>	int selei(0);
1763		StuntDouble* sd;
1764	<	int idx;
1764	>	int binNo;
1765
1766		vector<RealType> binMass(nBins_, 0.0);
1767		vector<RealType> binPx(nBins_, 0.0);
1768		vector<RealType> binPy(nBins_, 0.0);
1769		vector<RealType> binPz(nBins_, 0.0);
1770	+	vector<RealType> binOmegax(nBins_, 0.0);
1771	+	vector<RealType> binOmegay(nBins_, 0.0);
1772	+	vector<RealType> binOmegaz(nBins_, 0.0);
1773		vector<RealType> binKE(nBins_, 0.0);
1774		vector<int> binDOF(nBins_, 0);
1775		vector<int> binCount(nBins_, 0);
#	Line 1431 | Line 1777 | namespace OpenMD {
1777		// alternative approach, track all molecules instead of only those
1778		// selected for scaling/swapping:
1779		/*
1780	<	SimInfo::MoleculeIterator miter;
1781	<	vector<StuntDouble*>::iterator iiter;
1782	<	Molecule* mol;
1783	<	StuntDouble* sd;
1784	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1780	>	SimInfo::MoleculeIterator miter;
1781	>	vector<StuntDouble*>::iterator iiter;
1782	>	Molecule* mol;
1783	>	StuntDouble* sd;
1784	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1785		mol = info_->nextMolecule(miter))
1786		sd is essentially sd
1787	<	for (sd = mol->beginIntegrableObject(iiter);
1788	<	sd != NULL;
1789	<	sd = mol->nextIntegrableObject(iiter))
1787	>	for (sd = mol->beginIntegrableObject(iiter);
1788	>	sd != NULL;
1789	>	sd = mol->nextIntegrableObject(iiter))
1790		*/
1791	+
1792		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1793	<	sd = seleMan_.nextSelected(selei)) {
1794	<
1448	<	idx = sd->getLocalIndex();
1449	<
1793	>	sd = seleMan_.nextSelected(selei)) {
1794	>
1795		Vector3d pos = sd->getPos();
1796
1797		// wrap the stuntdouble's position back into the box:
1798
1799	<	if (usePeriodicBoundaryConditions_)
1799	>	if (usePeriodicBoundaryConditions_) {
1800		currentSnap_->wrapVector(pos);
1801	+	// which bin is this stuntdouble in?
1802	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1803	+	// Shift molecules by half a box to have bins start at 0
1804	+	// The modulo operator is used to wrap the case when we are
1805	+	// beyond the end of the bins back to the beginning.
1806	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1807	+	} else {
1808	+	Vector3d rPos = pos - coordinateOrigin_;
1809	+	binNo = int(rPos.length() / binWidth_);
1810	+	}
1811
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	–
1812		RealType mass = sd->getMass();
1813		Vector3d vel = sd->getVel();
1814	<
1815	<	binCount[binNo]++;
1816	<	binMass[binNo] += mass;
1817	<	binPx[binNo] += mass*vel.x();
1818	<	binPy[binNo] += mass*vel.y();
1819	<	binPz[binNo] += mass*vel.z();
1820	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1821	<	binDOF[binNo] += 3;
1822	<
1823	<	if (sd->isDirectional()) {
1824	<	Vector3d angMom = sd->getJ();
1825	<	Mat3x3d I = sd->getI();
1826	<	if (sd->isLinear()) {
1827	<	int i = sd->linearAxis();
1828	<	int j = (i + 1) % 3;
1829	<	int k = (i + 2) % 3;
1830	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1831	<	angMom[k] * angMom[k] / I(k, k));
1832	<	binDOF[binNo] += 2;
1833	<	} else {
1834	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1835	<	angMom[1] * angMom[1] / I(1, 1) +
1836	<	angMom[2] * angMom[2] / I(2, 2));
1837	<	binDOF[binNo] += 3;
1814	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1815	>	Vector3d aVel = cross(rPos, vel);
1816	>
1817	>	if (binNo < nBins_)  {
1818	>	binCount[binNo]++;
1819	>	binMass[binNo] += mass;
1820	>	binPx[binNo] += mass*vel.x();
1821	>	binPy[binNo] += mass*vel.y();
1822	>	binPz[binNo] += mass*vel.z();
1823	>	binOmegax[binNo] += aVel.x();
1824	>	binOmegay[binNo] += aVel.y();
1825	>	binOmegaz[binNo] += aVel.z();
1826	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1827	>	binDOF[binNo] += 3;
1828	>
1829	>	if (sd->isDirectional()) {
1830	>	Vector3d angMom = sd->getJ();
1831	>	Mat3x3d I = sd->getI();
1832	>	if (sd->isLinear()) {
1833	>	int i = sd->linearAxis();
1834	>	int j = (i + 1) % 3;
1835	>	int k = (i + 2) % 3;
1836	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1837	>	angMom[k] * angMom[k] / I(k, k));
1838	>	binDOF[binNo] += 2;
1839	>	} else {
1840	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1841	>	angMom[1] * angMom[1] / I(1, 1) +
1842	>	angMom[2] * angMom[2] / I(2, 2));
1843	>	binDOF[binNo] += 3;
1844	>	}
1845		}
1846		}
1847		}
1848
1494	–
1849		#ifdef IS_MPI
1850		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1851		nBins_, MPI::INT, MPI::SUM);
#	Line 1503 | Line 1857 | namespace OpenMD {
1857		nBins_, MPI::REALTYPE, MPI::SUM);
1858		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1859		nBins_, MPI::REALTYPE, MPI::SUM);
1860	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1861	+	nBins_, MPI::REALTYPE, MPI::SUM);
1862	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1863	+	nBins_, MPI::REALTYPE, MPI::SUM);
1864	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1865	+	nBins_, MPI::REALTYPE, MPI::SUM);
1866		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1867		nBins_, MPI::REALTYPE, MPI::SUM);
1868		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
#	Line 1510 | Line 1870 | namespace OpenMD {
1870		#endif
1871
1872		Vector3d vel;
1873	+	Vector3d aVel;
1874		RealType den;
1875		RealType temp;
1876		RealType z;
1877	+	RealType r;
1878		for (int i = 0; i < nBins_; i++) {
1879	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1879	>	if (usePeriodicBoundaryConditions_) {
1880	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1881	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1882	>	/ currentSnap_->getVolume() ;
1883	>	} else {
1884	>	r = (((RealType)i + 0.5) * binWidth_);
1885	>	RealType rinner = (RealType)i * binWidth_;
1886	>	RealType router = (RealType)(i+1) * binWidth_;
1887	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1888	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1889	>	}
1890		vel.x() = binPx[i] / binMass[i];
1891		vel.y() = binPy[i] / binMass[i];
1892		vel.z() = binPz[i] / binMass[i];
1893	<	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
1894	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1895	<	PhysicalConstants::energyConvert);
1893	>	aVel.x() = binOmegax[i];
1894	>	aVel.y() = binOmegay[i];
1895	>	aVel.z() = binOmegaz[i];
1896
1897	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1898	<	if(outputMask_[j]) {
1899	<	switch(j) {
1900	<	case Z:
1901	<	(data_[j].accumulator[i])->add(z);
1902	<	break;
1903	<	case TEMPERATURE:
1904	<	data_[j].accumulator[i]->add(temp);
1905	<	break;
1906	<	case VELOCITY:
1907	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1908	<	break;
1909	<	case DENSITY:
1910	<	data_[j].accumulator[i]->add(den);
1911	<	break;
1897	>	if (binCount[i] > 0) {
1898	>	// only add values if there are things to add
1899	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1900	>	PhysicalConstants::energyConvert);
1901	>
1902	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1903	>	if(outputMask_[j]) {
1904	>	switch(j) {
1905	>	case Z:
1906	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1907	>	break;
1908	>	case R:
1909	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1910	>	break;
1911	>	case TEMPERATURE:
1912	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1913	>	break;
1914	>	case VELOCITY:
1915	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1916	>	break;
1917	>	case ANGULARVELOCITY:
1918	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1919	>	break;
1920	>	case DENSITY:
1921	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1922	>	break;
1923	>	}
1924		}
1925		}
1926		}
#	Line 1544 | Line 1928 | namespace OpenMD {
1928		}
1929
1930		void RNEMD::getStarted() {
1931	+	if (!doRNEMD_) return;
1932	+	hasDividingArea_ = false;
1933		collectData();
1934		writeOutputFile();
1935		}
1936
1937		void RNEMD::parseOutputFileFormat(const std::string& format) {
1938	+	if (!doRNEMD_) return;
1939		StringTokenizer tokenizer(format, " ,;|\t\n\r");
1940
1941		while(tokenizer.hasMoreTokens()) {
#	Line 1569 | Line 1956 | namespace OpenMD {
1956		}
1957
1958		void RNEMD::writeOutputFile() {
1959	+	if (!doRNEMD_) return;
1960
1961		#ifdef IS_MPI
1962		// If we're the root node, should we print out the results
#	Line 1588 | Line 1976 | namespace OpenMD {
1976		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1977
1978		RealType time = currentSnap_->getTime();
1979	<
1980	<
1979	>	RealType avgArea;
1980	>	areaAccumulator_->getAverage(avgArea);
1981	>	RealType Jz = kineticExchange_ / (time * avgArea)
1982	>	/ PhysicalConstants::energyConvert;
1983	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
1984	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
1985	>
1986		rnemdFile_ << "#######################################################\n";
1987		rnemdFile_ << "# RNEMD {\n";
1988
1989		map<string, RNEMDMethod>::iterator mi;
1990		for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1991		if ( (*mi).second == rnemdMethod_)
1992	<	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
1992	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1993		}
1994		map<string, RNEMDFluxType>::iterator fi;
1995		for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1996		if ( (*fi).second == rnemdFluxType_)
1997	<	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
1997	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1998		}
1999
2000	<	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
2000	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2001
2002		rnemdFile_ << "#    objectSelection = \""
2003	<	<< rnemdObjectSelection_ << "\"\n";
2004	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
2005	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
2003	>	<< rnemdObjectSelection_ << "\";\n";
2004	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2005	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2006		rnemdFile_ << "# }\n";
2007		rnemdFile_ << "#######################################################\n";
2008	<
2009	<	rnemdFile_ << "# running time = " << time << " fs\n";
2010	<	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
2011	<	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
2012	<
2013	<	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
2014	<	<< "\n";
2015	<	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
2016	<	<< "\n";
2017	<
2018	<	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
2019	<	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
2020	<	<< "\n";
2021	<
2022	<	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
2023	<	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
2024	<
2025	<
2008	>	rnemdFile_ << "# RNEMD report:\n";
2009	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2010	>	rnemdFile_ << "# Target flux:\n";
2011	>	rnemdFile_ << "#           kinetic = "
2012	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2013	>	<< " (kcal/mol/A^2/fs)\n";
2014	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2015	>	<< " (amu/A/fs^2)\n";
2016	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2017	>	<< " (amu/A^2/fs^2)\n";
2018	>	rnemdFile_ << "# Target one-time exchanges:\n";
2019	>	rnemdFile_ << "#          kinetic = "
2020	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2021	>	<< " (kcal/mol)\n";
2022	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2023	>	<< " (amu*A/fs)\n";
2024	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2025	>	<< " (amu*A^2/fs)\n";
2026	>	rnemdFile_ << "# Actual exchange totals:\n";
2027	>	rnemdFile_ << "#          kinetic = "
2028	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2029	>	<< " (kcal/mol)\n";
2030	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2031	>	<< " (amu*A/fs)\n";
2032	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2033	>	<< " (amu*A^2/fs)\n";
2034	>	rnemdFile_ << "# Actual flux:\n";
2035	>	rnemdFile_ << "#          kinetic = " << Jz
2036	>	<< " (kcal/mol/A^2/fs)\n";
2037	>	rnemdFile_ << "#          momentum = " << JzP
2038	>	<< " (amu/A/fs^2)\n";
2039	>	rnemdFile_ << "#  angular momentum = " << JzL
2040	>	<< " (amu/A^2/fs^2)\n";
2041	>	rnemdFile_ << "# Exchange statistics:\n";
2042	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2043	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2044		if (rnemdMethod_ == rnemdNIVS) {
2045	<	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
2045	>	rnemdFile_ << "#  NIVS root-check errors = "
2046	>	<< failRootCount_ << "\n";
2047		}
1637	–
2048		rnemdFile_ << "#######################################################\n";
2049
2050
#	Line 1645 | Line 2055 | namespace OpenMD {
2055		if (outputMask_[i]) {
2056		rnemdFile_ << "\t" << data_[i].title <<
2057		"(" << data_[i].units << ")";
2058	+	// add some extra tabs for column alignment
2059	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2060		}
2061		}
2062		rnemdFile_ << std::endl;
2063
2064		rnemdFile_.precision(8);
2065
2066	<	for (unsigned int j = 0; j < nBins_; j++) {
2066	>	for (int j = 0; j < nBins_; j++) {
2067
2068		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2069		if (outputMask_[i]) {
#	Line 1671 | Line 2083 | namespace OpenMD {
2083		rnemdFile_ << std::endl;
2084
2085		}
2086	+
2087	+	rnemdFile_ << "#######################################################\n";
2088	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2089	+	rnemdFile_ << "#######################################################\n";
2090	+
2091	+
2092	+	for (int j = 0; j < nBins_; j++) {
2093	+	rnemdFile_ << "#";
2094	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2095	+	if (outputMask_[i]) {
2096	+	if (data_[i].dataType == "RealType")
2097	+	writeRealStdDev(i,j);
2098	+	else if (data_[i].dataType == "Vector3d")
2099	+	writeVectorStdDev(i,j);
2100	+	else {
2101	+	sprintf( painCave.errMsg,
2102	+	"RNEMD found an unknown data type for: %s ",
2103	+	data_[i].title.c_str());
2104	+	painCave.isFatal = 1;
2105	+	simError();
2106	+	}
2107	+	}
2108	+	}
2109	+	rnemdFile_ << std::endl;
2110	+
2111	+	}
2112
2113		rnemdFile_.flush();
2114		rnemdFile_.close();
#	Line 1682 | Line 2120 | namespace OpenMD {
2120		}
2121
2122		void RNEMD::writeReal(int index, unsigned int bin) {
2123	+	if (!doRNEMD_) return;
2124		assert(index >=0 && index < ENDINDEX);
2125	<	assert(bin >=0 && bin < nBins_);
2125	>	assert(int(bin) < nBins_);
2126		RealType s;
2127	+	int count;
2128
2129	<	data_[index].accumulator[bin]->getAverage(s);
2129	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2130	>	if (count == 0) return;
2131
2132	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2133	+
2134		if (! isinf(s) && ! isnan(s)) {
2135		rnemdFile_ << "\t" << s;
2136		} else{
#	Line 1700 | Line 2143 | namespace OpenMD {
2143		}
2144
2145		void RNEMD::writeVector(int index, unsigned int bin) {
2146	+	if (!doRNEMD_) return;
2147		assert(index >=0 && index < ENDINDEX);
2148	<	assert(bin >=0 && bin < nBins_);
2148	>	assert(int(bin) < nBins_);
2149		Vector3d s;
2150	+	int count;
2151	+
2152	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2153	+	if (count == 0) return;
2154	+
2155		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2156		if (isinf(s[0]) || isnan(s[0]) ||
2157		isinf(s[1]) || isnan(s[1]) ||
#	Line 1716 | Line 2165 | namespace OpenMD {
2165		rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2166		}
2167		}
2168	+
2169	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2170	+	if (!doRNEMD_) return;
2171	+	assert(index >=0 && index < ENDINDEX);
2172	+	assert(int(bin) < nBins_);
2173	+	RealType s;
2174	+	int count;
2175	+
2176	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2177	+	if (count == 0) return;
2178	+
2179	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2180	+
2181	+	if (! isinf(s) && ! isnan(s)) {
2182	+	rnemdFile_ << "\t" << s;
2183	+	} else{
2184	+	sprintf( painCave.errMsg,
2185	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2186	+	data_[index].title.c_str(), bin);
2187	+	painCave.isFatal = 1;
2188	+	simError();
2189	+	}
2190	+	}
2191	+
2192	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2193	+	if (!doRNEMD_) return;
2194	+	assert(index >=0 && index < ENDINDEX);
2195	+	assert(int(bin) < nBins_);
2196	+	Vector3d s;
2197	+	int count;
2198	+
2199	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2200	+	if (count == 0) return;
2201	+
2202	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2203	+	if (isinf(s[0]) || isnan(s[0]) ||
2204	+	isinf(s[1]) || isnan(s[1]) ||
2205	+	isinf(s[2]) || isnan(s[2]) ) {
2206	+	sprintf( painCave.errMsg,
2207	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2208	+	data_[index].title.c_str(), bin);
2209	+	painCave.isFatal = 1;
2210	+	simError();
2211	+	} else {
2212	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2213	+	}
2214	+	}
2215		}
2216

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