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

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branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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	+	#ifdef IS_MPI
42	+	#include <mpi.h>
43	+	#endif
44
45		#include <cmath>
46	+	#include <sstream>
47	+	#include <string>
48	+
49		#include "rnemd/RNEMD.hpp"
50		#include "math/Vector3.hpp"
51		#include "math/Vector.hpp"
#	Line 49 | Line 55
55		#include "primitives/StuntDouble.hpp"
56		#include "utils/PhysicalConstants.hpp"
57		#include "utils/Tuple.hpp"
58	<	#ifdef IS_MPI
59	<	#include <mpi.h>
58	>	#include "brains/Thermo.hpp"
59	>	#include "math/ConvexHull.hpp"
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
#	Line 59 | Line 69 | namespace OpenMD {
69		namespace OpenMD {
70
71		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75	+	hasData_(false), hasDividingArea_(false),
76		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
77
78		trialCount_ = 0;
79		failTrialCount_ = 0;
80		failRootCount_ = 0;
81
82	<	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);
403	<	break;
404	<	case rnemdPx:
405	<	case rnemdPy:
406	<	outputMask_.set(VELOCITY);
407	<	break;
408	<	case rnemdPz:
409	<	case rnemdPvector:
410	<	outputMask_.set(VELOCITY);
411	<	outputMask_.set(DENSITY);
412	<	break;
413	<	case rnemdKePx:
414	<	case rnemdKePy:
415	<	outputMask_.set(TEMPERATURE);
416	<	outputMask_.set(VELOCITY);
417	<	break;
418	<	case rnemdKePvector:
419	<	outputMask_.set(TEMPERATURE);
420	<	outputMask_.set(VELOCITY);
421	<	outputMask_.set(DENSITY);
422	<	break;
423	<	default:
424	<	break;
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	>	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	>	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	>	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	>	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	>	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		}
366	–	}
493
494	<	if (hasOutputFileName) {
495	<	rnemdFileName_ = rnemdParams->getOutputFileName();
496	<	} else {
497	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	<	}
494	>	if (hasOutputFileName) {
495	>	rnemdFileName_ = rnemdParams->getOutputFileName();
496	>	} else {
497	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	>	}
499
500	<	exchangeTime_ = rnemdParams->getExchangeTime();
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501
502	<	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	<	Mat3x3d hmat = currentSnap_->getHmat();
378	<
379	<	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
380	<	// Lx, Ly = box dimensions in x & y
381	<	// dt = exchange time interval
382	<	// flux = target flux
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504
505	<	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
506	<	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508
509	<	// total exchange sums are zeroed out at the beginning:
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511	>
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547	>
548	>	if (hasSelectionB_) {
549	>	selectionB_ = rnemdParams->getSelectionB();
550
551	<	kineticExchange_ = 0.0;
552	<	momentumExchange_ = V3Zero;
551	>	} else {
552	>	if (usePeriodicBoundaryConditions_) {
553	>	Mat3x3d hmat = currentSnap_->getHmat();
554	>
555	>	if (hasSlabWidth)
556	>	slabWidth_ = rnemdParams->getSlabWidth();
557	>	else
558	>	slabWidth_ = hmat(2,2) / 10.0;
559	>
560	>	if (hasSlabBCenter)
561	>	slabBCenter_ = rnemdParams->getSlabBCenter();
562	>	else
563	>	slabBCenter_ = hmat(2,2) / 2.0;
564	>
565	>	selectionBstream << "select wrappedz > "
566	>	<< slabBCenter_ - 0.5*slabWidth_
567	>	<<  " && wrappedz < "
568	>	<< slabBCenter_ + 0.5*slabWidth_;
569	>	selectionB_ = selectionBstream.str();
570	>	} else {
571	>	if (hasSphereBRadius_) {
572	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
573	>	selectionBstream << "select r > " << sphereBRadius_;
574	>	selectionB_ = selectionBstream.str();
575	>	} else {
576	>	selectionB_ = "select hull";
577	>	BisHull_ = true;
578	>	hasSelectionB_ = true;
579	>	}
580	>	}
581	>	}
582	>	}
583
584	<	if (hasSlabWidth)
585	<	slabWidth_ = rnemdParams->getSlabWidth();
586	<	else
587	<	slabWidth_ = hmat(2,2) / 10.0;
584	>	// object evaluator:
585	>	evaluator_.loadScriptString(rnemdObjectSelection_);
586	>	seleMan_.setSelectionSet(evaluator_.evaluate());
587	>	evaluatorA_.loadScriptString(selectionA_);
588	>	evaluatorB_.loadScriptString(selectionB_);
589	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
590	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
591	>	commonA_ = seleManA_ & seleMan_;
592	>	commonB_ = seleManB_ & seleMan_;
593	>	}
594
397	–	if (hasSlabACenter)
398	–	slabACenter_ = rnemdParams->getSlabACenter();
399	–	else
400	–	slabACenter_ = 0.0;
595
596	<	if (hasSlabBCenter)
597	<	slabBCenter_ = rnemdParams->getSlabBCenter();
404	<	else
405	<	slabBCenter_ = hmat(2,2) / 2.0;
406	<
407	<	}
408	<
409	<	RNEMD::~RNEMD() {
410	<
596	>	RNEMD::~RNEMD() {
597	>	if (!doRNEMD_) return;
598		#ifdef IS_MPI
599		if (worldRank == 0) {
600		#endif
#	Line 419 | Line 606 | namespace OpenMD {
606		#ifdef IS_MPI
607		}
608		#endif
609	+
610	+	// delete all of the objects we created:
611	+	delete areaAccumulator_;
612	+	data_.clear();
613		}
614
615	<	bool RNEMD::inSlabA(Vector3d pos) {
616	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
617	<	}
618	<	bool RNEMD::inSlabB(Vector3d pos) {
428	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	<	}
615	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
616	>	if (!doRNEMD_) return;
617	>	int selei;
618	>	int selej;
619
431	–	void RNEMD::doSwap() {
432	–
620		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
621		Mat3x3d hmat = currentSnap_->getHmat();
622
436	–	seleMan_.setSelectionSet(evaluator_.evaluate());
437	–
438	–	int selei;
623		StuntDouble* sd;
440	–	int idx;
624
625		RealType min_val;
626		bool min_found = false;
#	Line 447 | Line 630 | namespace OpenMD {
630		bool max_found = false;
631		StuntDouble* max_sd;
632
633	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
634	<	sd = seleMan_.nextSelected(selei)) {
633	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
634	>	sd = seleManA_.nextSelected(selei)) {
635
453	–	idx = sd->getLocalIndex();
454	–
636		Vector3d pos = sd->getPos();
637	<
637	>
638		// wrap the stuntdouble's position back into the box:
639	<
639	>
640		if (usePeriodicBoundaryConditions_)
641		currentSnap_->wrapVector(pos);
642	<	bool inA = inSlabA(pos);
643	<	bool inB = inSlabB(pos);
644	<
645	<	if (inA || inB) {
642	>
643	>	RealType mass = sd->getMass();
644	>	Vector3d vel = sd->getVel();
645	>	RealType value;
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649
650	<	RealType mass = sd->getMass();
651	<	Vector3d vel = sd->getVel();
652	<	RealType value;
653	<
654	<	switch(rnemdFluxType_) {
471	<	case rnemdKE :
650	>	value = mass * vel.lengthSquare();
651	>
652	>	if (sd->isDirectional()) {
653	>	Vector3d angMom = sd->getJ();
654	>	Mat3x3d I = sd->getI();
655
656	<	value = mass * vel.lengthSquare();
657	<
658	<	if (sd->isDirectional()) {
659	<	Vector3d angMom = sd->getJ();
660	<	Mat3x3d I = sd->getI();
661	<
662	<	if (sd->isLinear()) {
663	<	int i = sd->linearAxis();
664	<	int j = (i + 1) % 3;
665	<	int k = (i + 2) % 3;
666	<	value += angMom[j] * angMom[j] / I(j, j) +
667	<	angMom[k] * angMom[k] / I(k, k);
668	<	} else {
669	<	value += angMom[0]*angMom[0]/I(0, 0)
670	<	+ angMom[1]*angMom[1]/I(1, 1)
671	<	+ angMom[2]*angMom[2]/I(2, 2);
672	<	}
673	<	} //angular momenta exchange enabled
674	<	//energyConvert temporarily disabled
675	<	//make kineticExchange_ comparable between swap & scale
676	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
677	<	value *= 0.5;
678	<	break;
679	<	case rnemdPx :
680	<	value = mass * vel[0];
681	<	break;
682	<	case rnemdPy :
683	<	value = mass * vel[1];
684	<	break;
685	<	case rnemdPz :
686	<	value = mass * vel[2];
687	<	break;
688	<	default :
689	<	break;
656	>	if (sd->isLinear()) {
657	>	int i = sd->linearAxis();
658	>	int j = (i + 1) % 3;
659	>	int k = (i + 2) % 3;
660	>	value += angMom[j] * angMom[j] / I(j, j) +
661	>	angMom[k] * angMom[k] / I(k, k);
662	>	} else {
663	>	value += angMom[0]*angMom[0]/I(0, 0)
664	>	+ angMom[1]*angMom[1]/I(1, 1)
665	>	+ angMom[2]*angMom[2]/I(2, 2);
666	>	}
667	>	} //angular momenta exchange enabled
668	>	value *= 0.5;
669	>	break;
670	>	case rnemdPx :
671	>	value = mass * vel[0];
672	>	break;
673	>	case rnemdPy :
674	>	value = mass * vel[1];
675	>	break;
676	>	case rnemdPz :
677	>	value = mass * vel[2];
678	>	break;
679	>	default :
680	>	break;
681	>	}
682	>	if (!max_found) {
683	>	max_val = value;
684	>	max_sd = sd;
685	>	max_found = true;
686	>	} else {
687	>	if (max_val < value) {
688	>	max_val = value;
689	>	max_sd = sd;
690		}
691	+	}
692	+	}
693
694	<	if (inA == 0) {
695	<	if (!min_found) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	min_found = true;
699	<	} else {
700	<	if (min_val > value) {
701	<	min_val = value;
702	<	min_sd = sd;
703	<	}
704	<	}
705	<	} else {
706	<	if (!max_found) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	max_found = true;
710	<	} else {
711	<	if (max_val < value) {
712	<	max_val = value;
713	<	max_sd = sd;
714	<	}
715	<	}
716	<	}
694	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
695	>	sd = seleManB_.nextSelected(selej)) {
696	>
697	>	Vector3d pos = sd->getPos();
698	>
699	>	// wrap the stuntdouble's position back into the box:
700	>
701	>	if (usePeriodicBoundaryConditions_)
702	>	currentSnap_->wrapVector(pos);
703	>
704	>	RealType mass = sd->getMass();
705	>	Vector3d vel = sd->getVel();
706	>	RealType value;
707	>
708	>	switch(rnemdFluxType_) {
709	>	case rnemdKE :
710	>
711	>	value = mass * vel.lengthSquare();
712	>
713	>	if (sd->isDirectional()) {
714	>	Vector3d angMom = sd->getJ();
715	>	Mat3x3d I = sd->getI();
716	>
717	>	if (sd->isLinear()) {
718	>	int i = sd->linearAxis();
719	>	int j = (i + 1) % 3;
720	>	int k = (i + 2) % 3;
721	>	value += angMom[j] * angMom[j] / I(j, j) +
722	>	angMom[k] * angMom[k] / I(k, k);
723	>	} else {
724	>	value += angMom[0]*angMom[0]/I(0, 0)
725	>	+ angMom[1]*angMom[1]/I(1, 1)
726	>	+ angMom[2]*angMom[2]/I(2, 2);
727	>	}
728	>	} //angular momenta exchange enabled
729	>	value *= 0.5;
730	>	break;
731	>	case rnemdPx :
732	>	value = mass * vel[0];
733	>	break;
734	>	case rnemdPy :
735	>	value = mass * vel[1];
736	>	break;
737	>	case rnemdPz :
738	>	value = mass * vel[2];
739	>	break;
740	>	default :
741	>	break;
742		}
743	+
744	+	if (!min_found) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	min_found = true;
748	+	} else {
749	+	if (min_val > value) {
750	+	min_val = value;
751	+	min_sd = sd;
752	+	}
753	+	}
754		}
755
756	<	#ifdef IS_MPI
757	<	int nProc, worldRank;
758	<
759	<	nProc = MPI::COMM_WORLD.Get_size();
760	<	worldRank = MPI::COMM_WORLD.Get_rank();
756	>	#ifdef IS_MPI
757	>	int worldRank;
758	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
759	>
760	>	int my_min_found = min_found;
761	>	int my_max_found = max_found;
762
541	–	bool my_min_found = min_found;
542	–	bool my_max_found = max_found;
543	–
763		// Even if we didn't find a minimum, did someone else?
764	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
764	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
765	>	MPI_COMM_WORLD);
766		// Even if we didn't find a maximum, did someone else?
767	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
767	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
768	>	MPI_COMM_WORLD);
769		#endif
770
771		if (max_found && min_found) {
#	Line 563 | Line 784 | namespace OpenMD {
784		min_vals.rank = worldRank;
785
786		// Who had the minimum?
787	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
788	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
787	>	MPI_Allreduce(&min_vals, &min_vals,
788	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
789		min_val = min_vals.val;
790
791		if (my_max_found) {
#	Line 575 | Line 796 | namespace OpenMD {
796		max_vals.rank = worldRank;
797
798		// Who had the maximum?
799	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
800	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
799	>	MPI_Allreduce(&max_vals, &max_vals,
800	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
801		max_val = max_vals.val;
802		#endif
803
#	Line 636 | Line 857 | namespace OpenMD {
857
858		Vector3d min_vel;
859		Vector3d max_vel = max_sd->getVel();
860	<	MPI::Status status;
860	>	MPI_Status* status;
861
862		// point-to-point swap of the velocity vector
863	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
864	<	min_vals.rank, 0,
865	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
866	<	min_vals.rank, 0, status);
863	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
864	>	min_vals.rank, 0,
865	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
866	>	min_vals.rank, 0, MPI_COMM_WORLD, status);
867
868		switch(rnemdFluxType_) {
869		case rnemdKE :
#	Line 653 | Line 874 | namespace OpenMD {
874		Vector3d max_angMom = max_sd->getJ();
875
876		// point-to-point swap of the angular momentum vector
877	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
878	<	MPI::REALTYPE, min_vals.rank, 1,
879	<	min_angMom.getArrayPointer(), 3,
880	<	MPI::REALTYPE, min_vals.rank, 1,
881	<	status);
877	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
878	>	MPI_REALTYPE, min_vals.rank, 1,
879	>	min_angMom.getArrayPointer(), 3,
880	>	MPI_REALTYPE, min_vals.rank, 1,
881	>	MPI_COMM_WORLD, status);
882
883		max_sd->setJ(min_angMom);
884		}
#	Line 682 | Line 903 | namespace OpenMD {
903
904		Vector3d max_vel;
905		Vector3d min_vel = min_sd->getVel();
906	<	MPI::Status status;
906	>	MPI_Status* status;
907
908		// point-to-point swap of the velocity vector
909	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
910	<	max_vals.rank, 0,
911	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
912	<	max_vals.rank, 0, status);
909	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
910	>	max_vals.rank, 0,
911	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
912	>	max_vals.rank, 0, MPI_COMM_WORLD, status);
913
914		switch(rnemdFluxType_) {
915		case rnemdKE :
#	Line 699 | Line 920 | namespace OpenMD {
920		Vector3d max_angMom;
921
922		// point-to-point swap of the angular momentum vector
923	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
924	<	MPI::REALTYPE, max_vals.rank, 1,
925	<	max_angMom.getArrayPointer(), 3,
926	<	MPI::REALTYPE, max_vals.rank, 1,
927	<	status);
923	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
924	>	MPI_REALTYPE, max_vals.rank, 1,
925	>	max_angMom.getArrayPointer(), 3,
926	>	MPI_REALTYPE, max_vals.rank, 1,
927	>	MPI_COMM_WORLD, status);
928
929		min_sd->setJ(max_angMom);
930		}
#	Line 728 | Line 949 | namespace OpenMD {
949
950		switch(rnemdFluxType_) {
951		case rnemdKE:
731	–	cerr << "KE\n";
952		kineticExchange_ += max_val - min_val;
953		break;
954		case rnemdPx:
#	Line 741 | Line 961 | namespace OpenMD {
961		momentumExchange_.z() += max_val - min_val;
962		break;
963		default:
744	–	cerr << "default\n";
964		break;
965		}
966		} else {
#	Line 763 | Line 982 | namespace OpenMD {
982		}
983		}
984
985	<	void RNEMD::doNIVS() {
985	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
986	>	if (!doRNEMD_) return;
987	>	int selei;
988	>	int selej;
989
990		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
991	+	RealType time = currentSnap_->getTime();
992		Mat3x3d hmat = currentSnap_->getHmat();
770	–
771	–	seleMan_.setSelectionSet(evaluator_.evaluate());
993
773	–	int selei;
994		StuntDouble* sd;
775	–	int idx;
995
996		vector<StuntDouble*> hotBin, coldBin;
997
#	Line 791 | Line 1010 | namespace OpenMD {
1010		RealType Kcz = 0.0;
1011		RealType Kcw = 0.0;
1012
1013	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1014	<	sd = seleMan_.nextSelected(selei)) {
1013	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1014	>	sd = smanA.nextSelected(selei)) {
1015
797	–	idx = sd->getLocalIndex();
798	–
1016		Vector3d pos = sd->getPos();
1017	<
1017	>
1018		// wrap the stuntdouble's position back into the box:
1019	<
1019	>
1020		if (usePeriodicBoundaryConditions_)
1021		currentSnap_->wrapVector(pos);
1022	+
1023	+
1024	+	RealType mass = sd->getMass();
1025	+	Vector3d vel = sd->getVel();
1026	+
1027	+	hotBin.push_back(sd);
1028	+	Phx += mass * vel.x();
1029	+	Phy += mass * vel.y();
1030	+	Phz += mass * vel.z();
1031	+	Khx += mass * vel.x() * vel.x();
1032	+	Khy += mass * vel.y() * vel.y();
1033	+	Khz += mass * vel.z() * vel.z();
1034	+	if (sd->isDirectional()) {
1035	+	Vector3d angMom = sd->getJ();
1036	+	Mat3x3d I = sd->getI();
1037	+	if (sd->isLinear()) {
1038	+	int i = sd->linearAxis();
1039	+	int j = (i + 1) % 3;
1040	+	int k = (i + 2) % 3;
1041	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1042	+	angMom[k] * angMom[k] / I(k, k);
1043	+	} else {
1044	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1045	+	+ angMom[1]*angMom[1]/I(1, 1)
1046	+	+ angMom[2]*angMom[2]/I(2, 2);
1047	+	}
1048	+	}
1049	+	}
1050	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1051	+	sd = smanB.nextSelected(selej)) {
1052	+	Vector3d pos = sd->getPos();
1053	+
1054	+	// wrap the stuntdouble's position back into the box:
1055	+
1056	+	if (usePeriodicBoundaryConditions_)
1057	+	currentSnap_->wrapVector(pos);
1058	+
1059	+	RealType mass = sd->getMass();
1060	+	Vector3d vel = sd->getVel();
1061
1062	<	// which bin is this stuntdouble in?
1063	<	bool inA = inSlabA(pos);
1064	<	bool inB = inSlabB(pos);
1065	<
1066	<	if (inA || inB) {
1067	<
1068	<	RealType mass = sd->getMass();
1069	<	Vector3d vel = sd->getVel();
1070	<
1071	<	if (inA) {
1072	<	hotBin.push_back(sd);
1073	<	Phx += mass * vel.x();
1074	<	Phy += mass * vel.y();
1075	<	Phz += mass * vel.z();
1076	<	Khx += mass * vel.x() * vel.x();
1077	<	Khy += mass * vel.y() * vel.y();
1078	<	Khz += mass * vel.z() * vel.z();
1079	<	if (sd->isDirectional()) {
1080	<	Vector3d angMom = sd->getJ();
1081	<	Mat3x3d I = sd->getI();
1082	<	if (sd->isLinear()) {
827	<	int i = sd->linearAxis();
828	<	int j = (i + 1) % 3;
829	<	int k = (i + 2) % 3;
830	<	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	<	}
1062	>	coldBin.push_back(sd);
1063	>	Pcx += mass * vel.x();
1064	>	Pcy += mass * vel.y();
1065	>	Pcz += mass * vel.z();
1066	>	Kcx += mass * vel.x() * vel.x();
1067	>	Kcy += mass * vel.y() * vel.y();
1068	>	Kcz += mass * vel.z() * vel.z();
1069	>	if (sd->isDirectional()) {
1070	>	Vector3d angMom = sd->getJ();
1071	>	Mat3x3d I = sd->getI();
1072	>	if (sd->isLinear()) {
1073	>	int i = sd->linearAxis();
1074	>	int j = (i + 1) % 3;
1075	>	int k = (i + 2) % 3;
1076	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1077	>	angMom[k] * angMom[k] / I(k, k);
1078	>	} else {
1079	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1080	>	+ angMom[1]*angMom[1]/I(1, 1)
1081	>	+ angMom[2]*angMom[2]/I(2, 2);
1082	>	}
1083		}
1084		}
1085
#	Line 872 | Line 1093 | namespace OpenMD {
1093		Kcw *= 0.5;
1094
1095		#ifdef IS_MPI
1096	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1097	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1098	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1099	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1100	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1101	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1096	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1097	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1098	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1099	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1100	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1101	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1102
1103	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1104	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1105	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1106	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1103	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1104	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1105	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1106	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1107
1108	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1109	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1110	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1111	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1108	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1109	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1110	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1111	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1112		#endif
1113
1114		//solve coldBin coeff's first
#	Line 908 | Line 1129 | namespace OpenMD {
1129
1130		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1131		c = sqrt(c);
1132	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	<	//now convert to hotBin coefficient
1132	>
1133		RealType w = 0.0;
1134		if (rnemdFluxType_ ==  rnemdFullKE) {
1135		x = 1.0 + px * (1.0 - c);
#	Line 936 | Line 1156 | namespace OpenMD {
1156		//if w is in the right range, so should be x, y, z.
1157		vector<StuntDouble*>::iterator sdi;
1158		Vector3d vel;
1159	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1159	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1160		if (rnemdFluxType_ == rnemdFullKE) {
1161		vel = (*sdi)->getVel() * c;
1162		(*sdi)->setVel(vel);
#	Line 947 | Line 1167 | namespace OpenMD {
1167		}
1168		}
1169		w = sqrt(w);
1170	<	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	<	//           << "\twh= " << w << endl;
952	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1170	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1171		if (rnemdFluxType_ == rnemdFullKE) {
1172		vel = (*sdi)->getVel();
1173		vel.x() *= x;
#	Line 1068 | Line 1286 | namespace OpenMD {
1286		vector<RealType>::iterator ri;
1287		RealType r1, r2, alpha0;
1288		vector<pair<RealType,RealType> > rps;
1289	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1289	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1290		r2 = *ri;
1291		//check if FindRealRoots() give the right answer
1292		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1100 | Line 1318 | namespace OpenMD {
1318		RealType diff;
1319		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1320		vector<pair<RealType,RealType> >::iterator rpi;
1321	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1321	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1322		r1 = (*rpi).first;
1323		r2 = (*rpi).second;
1324		switch(rnemdFluxType_) {
#	Line 1167 | Line 1385 | namespace OpenMD {
1385		}
1386		vector<StuntDouble*>::iterator sdi;
1387		Vector3d vel;
1388	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1388	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1389		vel = (*sdi)->getVel();
1390		vel.x() *= x;
1391		vel.y() *= y;
#	Line 1178 | Line 1396 | namespace OpenMD {
1396		x = 1.0 + px * (1.0 - x);
1397		y = 1.0 + py * (1.0 - y);
1398		z = 1.0 + pz * (1.0 - z);
1399	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1399	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1400		vel = (*sdi)->getVel();
1401		vel.x() *= x;
1402		vel.y() *= y;
#	Line 1211 | Line 1429 | namespace OpenMD {
1429		failTrialCount_++;
1430		}
1431		}
1432	+
1433	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1434	+	if (!doRNEMD_) return;
1435	+	int selei;
1436	+	int selej;
1437
1215	–	void RNEMD::doVSS() {
1216	–
1438		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1439		RealType time = currentSnap_->getTime();
1440		Mat3x3d hmat = currentSnap_->getHmat();
1441
1221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	–
1223	–	int selei;
1442		StuntDouble* sd;
1225	–	int idx;
1443
1444		vector<StuntDouble*> hotBin, coldBin;
1445
1446		Vector3d Ph(V3Zero);
1447	+	Vector3d Lh(V3Zero);
1448		RealType Mh = 0.0;
1449	+	Mat3x3d Ih(0.0);
1450		RealType Kh = 0.0;
1451		Vector3d Pc(V3Zero);
1452	+	Vector3d Lc(V3Zero);
1453		RealType Mc = 0.0;
1454	+	Mat3x3d Ic(0.0);
1455		RealType Kc = 0.0;
1235	–
1456
1457	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1458	<	sd = seleMan_.nextSelected(selei)) {
1457	>	// Constraints can be on only the linear or angular momentum, but
1458	>	// not both.  Usually, the user will specify which they want, but
1459	>	// in case they don't, the use of periodic boundaries should make
1460	>	// the choice for us.
1461	>	bool doLinearPart = false;
1462	>	bool doAngularPart = false;
1463
1464	<	idx = sd->getLocalIndex();
1464	>	switch (rnemdFluxType_) {
1465	>	case rnemdPx:
1466	>	case rnemdPy:
1467	>	case rnemdPz:
1468	>	case rnemdPvector:
1469	>	case rnemdKePx:
1470	>	case rnemdKePy:
1471	>	case rnemdKePvector:
1472	>	doLinearPart = true;
1473	>	break;
1474	>	case rnemdLx:
1475	>	case rnemdLy:
1476	>	case rnemdLz:
1477	>	case rnemdLvector:
1478	>	case rnemdKeLx:
1479	>	case rnemdKeLy:
1480	>	case rnemdKeLz:
1481	>	case rnemdKeLvector:
1482	>	doAngularPart = true;
1483	>	break;
1484	>	case rnemdKE:
1485	>	case rnemdRotKE:
1486	>	case rnemdFullKE:
1487	>	default:
1488	>	if (usePeriodicBoundaryConditions_)
1489	>	doLinearPart = true;
1490	>	else
1491	>	doAngularPart = true;
1492	>	break;
1493	>	}
1494	>
1495	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1496	>	sd = smanA.nextSelected(selei)) {
1497
1498		Vector3d pos = sd->getPos();
1499
1500		// wrap the stuntdouble's position back into the box:
1501	<
1501	>
1502		if (usePeriodicBoundaryConditions_)
1503		currentSnap_->wrapVector(pos);
1504	+
1505	+	RealType mass = sd->getMass();
1506	+	Vector3d vel = sd->getVel();
1507	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1508	+	RealType r2;
1509	+
1510	+	hotBin.push_back(sd);
1511	+	Ph += mass * vel;
1512	+	Mh += mass;
1513	+	Kh += mass * vel.lengthSquare();
1514	+	Lh += mass * cross(rPos, vel);
1515	+	Ih -= outProduct(rPos, rPos) * mass;
1516	+	r2 = rPos.lengthSquare();
1517	+	Ih(0, 0) += mass * r2;
1518	+	Ih(1, 1) += mass * r2;
1519	+	Ih(2, 2) += mass * r2;
1520	+
1521	+	if (rnemdFluxType_ == rnemdFullKE) {
1522	+	if (sd->isDirectional()) {
1523	+	Vector3d angMom = sd->getJ();
1524	+	Mat3x3d I = sd->getI();
1525	+	if (sd->isLinear()) {
1526	+	int i = sd->linearAxis();
1527	+	int j = (i + 1) % 3;
1528	+	int k = (i + 2) % 3;
1529	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1530	+	angMom[k] * angMom[k] / I(k, k);
1531	+	} else {
1532	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1533	+	angMom[1] * angMom[1] / I(1, 1) +
1534	+	angMom[2] * angMom[2] / I(2, 2);
1535	+	}
1536	+	}
1537	+	}
1538	+	}
1539	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1540	+	sd = smanB.nextSelected(selej)) {
1541
1542	<	// which bin is this stuntdouble in?
1250	<	bool inA = inSlabA(pos);
1251	<	bool inB = inSlabB(pos);
1542	>	Vector3d pos = sd->getPos();
1543
1544	<	if (inA || inB) {
1545	<
1546	<	RealType mass = sd->getMass();
1547	<	Vector3d vel = sd->getVel();
1548	<
1549	<	if (inA) {
1550	<	hotBin.push_back(sd);
1551	<	//std::cerr << "before, velocity = " << vel << endl;
1552	<	Ph += mass * vel;
1553	<	//std::cerr << "after, velocity = " << vel << endl;
1554	<	Mh += mass;
1555	<	Kh += mass * vel.lengthSquare();
1556	<	if (rnemdFluxType_ == rnemdFullKE) {
1557	<	if (sd->isDirectional()) {
1558	<	Vector3d angMom = sd->getJ();
1559	<	Mat3x3d I = sd->getI();
1560	<	if (sd->isLinear()) {
1561	<	int i = sd->linearAxis();
1562	<	int j = (i + 1) % 3;
1563	<	int k = (i + 2) % 3;
1564	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1565	<	angMom[k] * angMom[k] / I(k, k);
1566	<	} else {
1567	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1568	<	angMom[1] * angMom[1] / I(1, 1) +
1569	<	angMom[2] * angMom[2] / I(2, 2);
1570	<	}
1571	<	}
1572	<	}
1573	<	} else { //midBin_
1574	<	coldBin.push_back(sd);
1575	<	Pc += mass * vel;
1576	<	Mc += mass;
1577	<	Kc += mass * vel.lengthSquare();
1578	<	if (rnemdFluxType_ == rnemdFullKE) {
1579	<	if (sd->isDirectional()) {
1580	<	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	<	}
1544	>	// wrap the stuntdouble's position back into the box:
1545	>
1546	>	if (usePeriodicBoundaryConditions_)
1547	>	currentSnap_->wrapVector(pos);
1548	>
1549	>	RealType mass = sd->getMass();
1550	>	Vector3d vel = sd->getVel();
1551	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1552	>	RealType r2;
1553	>
1554	>	coldBin.push_back(sd);
1555	>	Pc += mass * vel;
1556	>	Mc += mass;
1557	>	Kc += mass * vel.lengthSquare();
1558	>	Lc += mass * cross(rPos, vel);
1559	>	Ic -= outProduct(rPos, rPos) * mass;
1560	>	r2 = rPos.lengthSquare();
1561	>	Ic(0, 0) += mass * r2;
1562	>	Ic(1, 1) += mass * r2;
1563	>	Ic(2, 2) += mass * r2;
1564	>
1565	>	if (rnemdFluxType_ == rnemdFullKE) {
1566	>	if (sd->isDirectional()) {
1567	>	Vector3d angMom = sd->getJ();
1568	>	Mat3x3d I = sd->getI();
1569	>	if (sd->isLinear()) {
1570	>	int i = sd->linearAxis();
1571	>	int j = (i + 1) % 3;
1572	>	int k = (i + 2) % 3;
1573	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1574	>	angMom[k] * angMom[k] / I(k, k);
1575	>	} else {
1576	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1577	>	angMom[1] * angMom[1] / I(1, 1) +
1578	>	angMom[2] * angMom[2] / I(2, 2);
1579	>	}
1580	>	}
1581		}
1582		}
1583
1584		Kh *= 0.5;
1585		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;
1586
1587		#ifdef IS_MPI
1588	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1589	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1590	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1591	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1592	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1593	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1588	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1589	>	MPI_COMM_WORLD);
1590	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1591	>	MPI_COMM_WORLD);
1592	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1593	>	MPI_COMM_WORLD);
1594	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1595	>	MPI_COMM_WORLD);
1596	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1597	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1598	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1599	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1600	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1601	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1602	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1603	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1604		#endif
1605	+
1606
1607	+	Vector3d ac, acrec, bc, bcrec;
1608	+	Vector3d ah, ahrec, bh, bhrec;
1609	+
1610		bool successfulExchange = false;
1611		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1612		Vector3d vc = Pc / Mc;
1613	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1614	<	Vector3d acrec = -momentumTarget_ / Mc;
1615	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1613	>	ac = -momentumTarget_ / Mc + vc;
1614	>	acrec = -momentumTarget_ / Mc;
1615	>
1616	>	// We now need the inverse of the inertia tensor to calculate the
1617	>	// angular velocity of the cold slab;
1618	>	Mat3x3d Ici = Ic.inverse();
1619	>	Vector3d omegac = Ici * Lc;
1620	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1621	>	bcrec = bc - omegac;
1622	>
1623	>	RealType cNumerator = Kc - kineticTarget_;
1624	>	if (doLinearPart)
1625	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1626	>
1627	>	if (doAngularPart)
1628	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1629	>
1630		if (cNumerator > 0.0) {
1631	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1631	>
1632	>	RealType cDenominator = Kc;
1633	>
1634	>	if (doLinearPart)
1635	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1636	>
1637	>	if (doAngularPart)
1638	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1639	>
1640		if (cDenominator > 0.0) {
1641		RealType c = sqrt(cNumerator / cDenominator);
1642		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1643	+
1644		Vector3d vh = Ph / Mh;
1645	<	Vector3d ah = momentumTarget_ / Mh + vh;
1646	<	Vector3d ahrec = momentumTarget_ / Mh;
1647	<	RealType hNumerator = Kh + kineticTarget_
1648	<	- 0.5 * Mh * ah.lengthSquare();
1649	<	if (hNumerator > 0.0) {
1650	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1645	>	ah = momentumTarget_ / Mh + vh;
1646	>	ahrec = momentumTarget_ / Mh;
1647	>
1648	>	// We now need the inverse of the inertia tensor to
1649	>	// calculate the angular velocity of the hot slab;
1650	>	Mat3x3d Ihi = Ih.inverse();
1651	>	Vector3d omegah = Ihi * Lh;
1652	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1653	>	bhrec = bh - omegah;
1654	>
1655	>	RealType hNumerator = Kh + kineticTarget_;
1656	>	if (doLinearPart)
1657	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1658	>
1659	>	if (doAngularPart)
1660	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1661	>
1662	>	if (hNumerator > 0.0) {
1663	>
1664	>	RealType hDenominator = Kh;
1665	>	if (doLinearPart)
1666	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1667	>	if (doAngularPart)
1668	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1669	>
1670		if (hDenominator > 0.0) {
1671		RealType h = sqrt(hNumerator / hDenominator);
1672		if ((h > 0.9) && (h < 1.1)) {
1673	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1673	>
1674		vector<StuntDouble*>::iterator sdi;
1675		Vector3d vel;
1676	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1676	>	Vector3d rPos;
1677	>
1678	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1679		//vel = (*sdi)->getVel();
1680	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1680	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1681	>	if (doLinearPart)
1682	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1683	>	if (doAngularPart)
1684	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1685	>
1686		(*sdi)->setVel(vel);
1687		if (rnemdFluxType_ == rnemdFullKE) {
1688		if ((*sdi)->isDirectional()) {
#	Line 1357 | Line 1691 | namespace OpenMD {
1691		}
1692		}
1693		}
1694	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1694	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1695		//vel = (*sdi)->getVel();
1696	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1696	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1697	>	if (doLinearPart)
1698	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1699	>	if (doAngularPart)
1700	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1701	>
1702		(*sdi)->setVel(vel);
1703		if (rnemdFluxType_ == rnemdFullKE) {
1704		if ((*sdi)->isDirectional()) {
#	Line 1371 | Line 1710 | namespace OpenMD {
1710		successfulExchange = true;
1711		kineticExchange_ += kineticTarget_;
1712		momentumExchange_ += momentumTarget_;
1713	+	angularMomentumExchange_ += angularMomentumTarget_;
1714		}
1715		}
1716		}
#	Line 1390 | Line 1730 | namespace OpenMD {
1730		}
1731		}
1732
1733	<	void RNEMD::doRNEMD() {
1733	>	RealType RNEMD::getDividingArea() {
1734
1735	+	if (hasDividingArea_) return dividingArea_;
1736	+
1737	+	RealType areaA, areaB;
1738	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1739	+
1740	+	if (hasSelectionA_) {
1741	+
1742	+	if (evaluatorA_.hasSurfaceArea())
1743	+	areaA = evaluatorA_.getSurfaceArea();
1744	+	else {
1745	+
1746	+	cerr << "selection A did not have surface area, recomputing\n";
1747	+	int isd;
1748	+	StuntDouble* sd;
1749	+	vector<StuntDouble*> aSites;
1750	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1751	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1752	+	sd = seleManA_.nextSelected(isd)) {
1753	+	aSites.push_back(sd);
1754	+	}
1755	+	#if defined(HAVE_QHULL)
1756	+	ConvexHull* surfaceMeshA = new ConvexHull();
1757	+	surfaceMeshA->computeHull(aSites);
1758	+	areaA = surfaceMeshA->getArea();
1759	+	delete surfaceMeshA;
1760	+	#else
1761	+	sprintf( painCave.errMsg,
1762	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1763	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1764	+	painCave.severity = OPENMD_ERROR;
1765	+	painCave.isFatal = 1;
1766	+	simError();
1767	+	#endif
1768	+	}
1769	+
1770	+	} else {
1771	+	if (usePeriodicBoundaryConditions_) {
1772	+	// in periodic boundaries, the surface area is twice the x-y
1773	+	// area of the current box:
1774	+	areaA = 2.0 * snap->getXYarea();
1775	+	} else {
1776	+	// in non-periodic simulations, without explicitly setting
1777	+	// selections, the sphere radius sets the surface area of the
1778	+	// dividing surface:
1779	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1780	+	}
1781	+	}
1782	+
1783	+	if (hasSelectionB_) {
1784	+	if (evaluatorB_.hasSurfaceArea())
1785	+	areaB = evaluatorB_.getSurfaceArea();
1786	+	else {
1787	+	cerr << "selection B did not have surface area, recomputing\n";
1788	+
1789	+	int isd;
1790	+	StuntDouble* sd;
1791	+	vector<StuntDouble*> bSites;
1792	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1793	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1794	+	sd = seleManB_.nextSelected(isd)) {
1795	+	bSites.push_back(sd);
1796	+	}
1797	+
1798	+	#if defined(HAVE_QHULL)
1799	+	ConvexHull* surfaceMeshB = new ConvexHull();
1800	+	surfaceMeshB->computeHull(bSites);
1801	+	areaB = surfaceMeshB->getArea();
1802	+	delete surfaceMeshB;
1803	+	#else
1804	+	sprintf( painCave.errMsg,
1805	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1806	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1807	+	painCave.severity = OPENMD_ERROR;
1808	+	painCave.isFatal = 1;
1809	+	simError();
1810	+	#endif
1811	+	}
1812	+
1813	+	} else {
1814	+	if (usePeriodicBoundaryConditions_) {
1815	+	// in periodic boundaries, the surface area is twice the x-y
1816	+	// area of the current box:
1817	+	areaB = 2.0 * snap->getXYarea();
1818	+	} else {
1819	+	// in non-periodic simulations, without explicitly setting
1820	+	// selections, but if a sphereBradius has been set, just use that:
1821	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1822	+	}
1823	+	}
1824	+
1825	+	dividingArea_ = min(areaA, areaB);
1826	+	hasDividingArea_ = true;
1827	+	return dividingArea_;
1828	+	}
1829	+
1830	+	void RNEMD::doRNEMD() {
1831	+	if (!doRNEMD_) return;
1832		trialCount_++;
1833	+
1834	+	// object evaluator:
1835	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1836	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1837	+
1838	+	evaluatorA_.loadScriptString(selectionA_);
1839	+	evaluatorB_.loadScriptString(selectionB_);
1840	+
1841	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1842	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1843	+
1844	+	commonA_ = seleManA_ & seleMan_;
1845	+	commonB_ = seleManB_ & seleMan_;
1846	+
1847	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1848	+	// dt = exchange time interval
1849	+	// flux = target flux
1850	+	// dividingArea = smallest dividing surface between the two regions
1851	+
1852	+	hasDividingArea_ = false;
1853	+	RealType area = getDividingArea();
1854	+
1855	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1856	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1857	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1858	+
1859		switch(rnemdMethod_) {
1860		case rnemdSwap:
1861	<	doSwap();
1861	>	doSwap(commonA_, commonB_);
1862		break;
1863		case rnemdNIVS:
1864	<	doNIVS();
1864	>	doNIVS(commonA_, commonB_);
1865		break;
1866		case rnemdVSS:
1867	<	doVSS();
1867	>	doVSS(commonA_, commonB_);
1868		break;
1869		case rnemdUnkownMethod:
1870		default :
#	Line 1410 | Line 1873 | namespace OpenMD {
1873		}
1874
1875		void RNEMD::collectData() {
1876	<
1876	>	if (!doRNEMD_) return;
1877		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1878	+
1879	+	// collectData can be called more frequently than the doRNEMD, so use the
1880	+	// computed area from the last exchange time:
1881	+	RealType area = getDividingArea();
1882	+	areaAccumulator_->add(area);
1883		Mat3x3d hmat = currentSnap_->getHmat();
1884	+	Vector3d u = angularMomentumFluxVector_;
1885	+	u.normalize();
1886
1887		seleMan_.setSelectionSet(evaluator_.evaluate());
1888
1889	<	int selei;
1889	>	int selei(0);
1890		StuntDouble* sd;
1891	<	int idx;
1891	>	int binNo;
1892	>	RealType mass;
1893	>	Vector3d vel;
1894	>	Vector3d rPos;
1895	>	RealType KE;
1896	>	Vector3d L;
1897	>	Mat3x3d I;
1898	>	RealType r2;
1899
1900		vector<RealType> binMass(nBins_, 0.0);
1901	<	vector<RealType> binPx(nBins_, 0.0);
1902	<	vector<RealType> binPy(nBins_, 0.0);
1903	<	vector<RealType> binPz(nBins_, 0.0);
1901	>	vector<Vector3d> binP(nBins_, V3Zero);
1902	>	vector<RealType> binOmega(nBins_, 0.0);
1903	>	vector<Vector3d> binL(nBins_, V3Zero);
1904	>	vector<Mat3x3d>  binI(nBins_);
1905		vector<RealType> binKE(nBins_, 0.0);
1906		vector<int> binDOF(nBins_, 0);
1907		vector<int> binCount(nBins_, 0);
#	Line 1431 | Line 1909 | namespace OpenMD {
1909		// alternative approach, track all molecules instead of only those
1910		// selected for scaling/swapping:
1911		/*
1912	<	SimInfo::MoleculeIterator miter;
1913	<	vector<StuntDouble*>::iterator iiter;
1914	<	Molecule* mol;
1915	<	StuntDouble* sd;
1916	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1912	>	SimInfo::MoleculeIterator miter;
1913	>	vector<StuntDouble*>::iterator iiter;
1914	>	Molecule* mol;
1915	>	StuntDouble* sd;
1916	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1917		mol = info_->nextMolecule(miter))
1918		sd is essentially sd
1919	<	for (sd = mol->beginIntegrableObject(iiter);
1920	<	sd != NULL;
1921	<	sd = mol->nextIntegrableObject(iiter))
1919	>	for (sd = mol->beginIntegrableObject(iiter);
1920	>	sd != NULL;
1921	>	sd = mol->nextIntegrableObject(iiter))
1922		*/
1923	+
1924		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1925	<	sd = seleMan_.nextSelected(selei)) {
1926	<
1448	<	idx = sd->getLocalIndex();
1449	<
1925	>	sd = seleMan_.nextSelected(selei)) {
1926	>
1927		Vector3d pos = sd->getPos();
1928
1929		// wrap the stuntdouble's position back into the box:
1930
1931	<	if (usePeriodicBoundaryConditions_)
1931	>	if (usePeriodicBoundaryConditions_) {
1932		currentSnap_->wrapVector(pos);
1933	+	// which bin is this stuntdouble in?
1934	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1935	+	// Shift molecules by half a box to have bins start at 0
1936	+	// The modulo operator is used to wrap the case when we are
1937	+	// beyond the end of the bins back to the beginning.
1938	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1939	+	} else {
1940	+	Vector3d rPos = pos - coordinateOrigin_;
1941	+	binNo = int(rPos.length() / binWidth_);
1942	+	}
1943
1944	<	// which bin is this stuntdouble in?
1945	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1946	<	// Shift molecules by half a box to have bins start at 0
1947	<	// The modulo operator is used to wrap the case when we are
1948	<	// beyond the end of the bins back to the beginning.
1949	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1950	<
1951	<	RealType mass = sd->getMass();
1952	<	Vector3d vel = sd->getVel();
1944	>	mass = sd->getMass();
1945	>	vel = sd->getVel();
1946	>	rPos = sd->getPos() - coordinateOrigin_;
1947	>	KE = 0.5 * mass * vel.lengthSquare();
1948	>	L = mass * cross(rPos, vel);
1949	>	I = outProduct(rPos, rPos) * mass;
1950	>	r2 = rPos.lengthSquare();
1951	>	I(0, 0) += mass * r2;
1952	>	I(1, 1) += mass * r2;
1953	>	I(2, 2) += mass * r2;
1954
1955	<	binCount[binNo]++;
1956	<	binMass[binNo] += mass;
1957	<	binPx[binNo] += mass*vel.x();
1958	<	binPy[binNo] += mass*vel.y();
1959	<	binPz[binNo] += mass*vel.z();
1960	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1961	<	binDOF[binNo] += 3;
1955	>	// Project the relative position onto a plane perpendicular to
1956	>	// the angularMomentumFluxVector:
1957	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1958	>	// Project the velocity onto a plane perpendicular to the
1959	>	// angularMomentumFluxVector:
1960	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1961	>	// Compute angular velocity vector (should be nearly parallel to
1962	>	// angularMomentumFluxVector
1963	>	// Vector3d aVel = cross(rProj, vProj);
1964
1965	<	if (sd->isDirectional()) {
1966	<	Vector3d angMom = sd->getJ();
1967	<	Mat3x3d I = sd->getI();
1968	<	if (sd->isLinear()) {
1969	<	int i = sd->linearAxis();
1970	<	int j = (i + 1) % 3;
1971	<	int k = (i + 2) % 3;
1972	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1973	<	angMom[k] * angMom[k] / I(k, k));
1974	<	binDOF[binNo] += 2;
1975	<	} else {
1976	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1977	<	angMom[1] * angMom[1] / I(1, 1) +
1978	<	angMom[2] * angMom[2] / I(2, 2));
1979	<	binDOF[binNo] += 3;
1965	>	if (binNo >= 0 && binNo < nBins_)  {
1966	>	binCount[binNo]++;
1967	>	binMass[binNo] += mass;
1968	>	binP[binNo] += mass*vel;
1969	>	binKE[binNo] += KE;
1970	>	binI[binNo] += I;
1971	>	binL[binNo] += L;
1972	>	binDOF[binNo] += 3;
1973	>
1974	>	if (sd->isDirectional()) {
1975	>	Vector3d angMom = sd->getJ();
1976	>	Mat3x3d Ia = sd->getI();
1977	>	if (sd->isLinear()) {
1978	>	int i = sd->linearAxis();
1979	>	int j = (i + 1) % 3;
1980	>	int k = (i + 2) % 3;
1981	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
1982	>	angMom[k] * angMom[k] / Ia(k, k));
1983	>	binDOF[binNo] += 2;
1984	>	} else {
1985	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
1986	>	angMom[1] * angMom[1] / Ia(1, 1) +
1987	>	angMom[2] * angMom[2] / Ia(2, 2));
1988	>	binDOF[binNo] += 3;
1989	>	}
1990		}
1991		}
1992		}
1993
1494	–
1994		#ifdef IS_MPI
1995	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1996	<	nBins_, MPI::INT, MPI::SUM);
1997	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1998	<	nBins_, MPI::REALTYPE, MPI::SUM);
1999	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
2000	<	nBins_, MPI::REALTYPE, MPI::SUM);
2001	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
2002	<	nBins_, MPI::REALTYPE, MPI::SUM);
2003	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
2004	<	nBins_, MPI::REALTYPE, MPI::SUM);
2005	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
2006	<	nBins_, MPI::REALTYPE, MPI::SUM);
2007	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
2008	<	nBins_, MPI::INT, MPI::SUM);
1995	>
1996	>	for (int i = 0; i < nBins_; i++) {
1997	>
1998	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
1999	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2000	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2001	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2002	>	MPI_Allreduce(MPI_IN_PLACE, &binP[i],
2003	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2004	>	MPI_Allreduce(MPI_IN_PLACE, &binL[i],
2005	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2006	>	MPI_Allreduce(MPI_IN_PLACE, &binI[i],
2007	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2008	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2009	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2010	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2011	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2012	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2013	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2014	>	}
2015	>
2016		#endif
2017
2018	<	Vector3d vel;
2018	>	Vector3d omega;
2019		RealType den;
2020		RealType temp;
2021		RealType z;
2022	+	RealType r;
2023		for (int i = 0; i < nBins_; i++) {
2024	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2025	<	vel.x() = binPx[i] / binMass[i];
2026	<	vel.y() = binPy[i] / binMass[i];
2027	<	vel.z() = binPz[i] / binMass[i];
2028	<	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
2029	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2030	<	PhysicalConstants::energyConvert);
2024	>	if (usePeriodicBoundaryConditions_) {
2025	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2026	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2027	>	/ currentSnap_->getVolume() ;
2028	>	} else {
2029	>	r = (((RealType)i + 0.5) * binWidth_);
2030	>	RealType rinner = (RealType)i * binWidth_;
2031	>	RealType router = (RealType)(i+1) * binWidth_;
2032	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2033	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2034	>	}
2035	>	vel = binP[i] / binMass[i];
2036
2037	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2038	<	if(outputMask_[j]) {
2039	<	switch(j) {
2040	<	case Z:
2041	<	(data_[j].accumulator[i])->add(z);
2042	<	break;
2043	<	case TEMPERATURE:
2044	<	data_[j].accumulator[i]->add(temp);
2045	<	break;
2046	<	case VELOCITY:
2047	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2048	<	break;
2049	<	case DENSITY:
2050	<	data_[j].accumulator[i]->add(den);
2051	<	break;
2037	>	omega = binI[i].inverse() * binL[i];
2038	>
2039	>	// omega = binOmega[i] / binCount[i];
2040	>
2041	>	if (binCount[i] > 0) {
2042	>	// only add values if there are things to add
2043	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2044	>	PhysicalConstants::energyConvert);
2045	>
2046	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2047	>	if(outputMask_[j]) {
2048	>	switch(j) {
2049	>	case Z:
2050	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2051	>	break;
2052	>	case R:
2053	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2054	>	break;
2055	>	case TEMPERATURE:
2056	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2057	>	break;
2058	>	case VELOCITY:
2059	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2060	>	break;
2061	>	case ANGULARVELOCITY:
2062	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2063	>	break;
2064	>	case DENSITY:
2065	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2066	>	break;
2067	>	}
2068		}
2069		}
2070		}
2071		}
2072	+	hasData_ = true;
2073		}
2074
2075		void RNEMD::getStarted() {
2076	+	if (!doRNEMD_) return;
2077	+	hasDividingArea_ = false;
2078		collectData();
2079		writeOutputFile();
2080		}
2081
2082		void RNEMD::parseOutputFileFormat(const std::string& format) {
2083	+	if (!doRNEMD_) return;
2084		StringTokenizer tokenizer(format, " ,;|\t\n\r");
2085
2086		while(tokenizer.hasMoreTokens()) {
#	Line 1569 | Line 2101 | namespace OpenMD {
2101		}
2102
2103		void RNEMD::writeOutputFile() {
2104	+	if (!doRNEMD_) return;
2105	+	if (!hasData_) return;
2106
2107		#ifdef IS_MPI
2108		// If we're the root node, should we print out the results
2109	<	int worldRank = MPI::COMM_WORLD.Get_rank();
2109	>	int worldRank;
2110	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2111	>
2112		if (worldRank == 0) {
2113		#endif
2114		rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
#	Line 1588 | Line 2124 | namespace OpenMD {
2124		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2125
2126		RealType time = currentSnap_->getTime();
2127	<
2128	<
2127	>	RealType avgArea;
2128	>	areaAccumulator_->getAverage(avgArea);
2129	>
2130	>	RealType Jz(0.0);
2131	>	Vector3d JzP(V3Zero);
2132	>	Vector3d JzL(V3Zero);
2133	>	if (time >= info_->getSimParams()->getDt()) {
2134	>	Jz = kineticExchange_ / (time * avgArea)
2135	>	/ PhysicalConstants::energyConvert;
2136	>	JzP = momentumExchange_ / (time * avgArea);
2137	>	JzL = angularMomentumExchange_ / (time * avgArea);
2138	>	}
2139	>
2140		rnemdFile_ << "#######################################################\n";
2141		rnemdFile_ << "# RNEMD {\n";
2142
2143		map<string, RNEMDMethod>::iterator mi;
2144		for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2145		if ( (*mi).second == rnemdMethod_)
2146	<	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
2146	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2147		}
2148		map<string, RNEMDFluxType>::iterator fi;
2149		for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2150		if ( (*fi).second == rnemdFluxType_)
2151	<	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
2151	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2152		}
2153
2154	<	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
2154	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2155
2156		rnemdFile_ << "#    objectSelection = \""
2157	<	<< rnemdObjectSelection_ << "\"\n";
2158	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
2159	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
2157	>	<< rnemdObjectSelection_ << "\";\n";
2158	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2159	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2160		rnemdFile_ << "# }\n";
2161		rnemdFile_ << "#######################################################\n";
2162	<
2163	<	rnemdFile_ << "# running time = " << time << " fs\n";
2164	<	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
2165	<	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
2166	<
2167	<	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
2168	<	<< "\n";
2169	<	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
2170	<	<< "\n";
2171	<
2172	<	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
2173	<	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
2174	<	<< "\n";
2175	<
2176	<	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
2177	<	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
2178	<
2179	<
2162	>	rnemdFile_ << "# RNEMD report:\n";
2163	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2164	>	rnemdFile_ << "# Target flux:\n";
2165	>	rnemdFile_ << "#           kinetic = "
2166	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2167	>	<< " (kcal/mol/A^2/fs)\n";
2168	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2169	>	<< " (amu/A/fs^2)\n";
2170	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2171	>	<< " (amu/A^2/fs^2)\n";
2172	>	rnemdFile_ << "# Target one-time exchanges:\n";
2173	>	rnemdFile_ << "#          kinetic = "
2174	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2175	>	<< " (kcal/mol)\n";
2176	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2177	>	<< " (amu*A/fs)\n";
2178	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2179	>	<< " (amu*A^2/fs)\n";
2180	>	rnemdFile_ << "# Actual exchange totals:\n";
2181	>	rnemdFile_ << "#          kinetic = "
2182	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2183	>	<< " (kcal/mol)\n";
2184	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2185	>	<< " (amu*A/fs)\n";
2186	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2187	>	<< " (amu*A^2/fs)\n";
2188	>	rnemdFile_ << "# Actual flux:\n";
2189	>	rnemdFile_ << "#          kinetic = " << Jz
2190	>	<< " (kcal/mol/A^2/fs)\n";
2191	>	rnemdFile_ << "#          momentum = " << JzP
2192	>	<< " (amu/A/fs^2)\n";
2193	>	rnemdFile_ << "#  angular momentum = " << JzL
2194	>	<< " (amu/A^2/fs^2)\n";
2195	>	rnemdFile_ << "# Exchange statistics:\n";
2196	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2197	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2198		if (rnemdMethod_ == rnemdNIVS) {
2199	<	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
2199	>	rnemdFile_ << "#  NIVS root-check errors = "
2200	>	<< failRootCount_ << "\n";
2201		}
1637	–
2202		rnemdFile_ << "#######################################################\n";
2203
2204
#	Line 1645 | Line 2209 | namespace OpenMD {
2209		if (outputMask_[i]) {
2210		rnemdFile_ << "\t" << data_[i].title <<
2211		"(" << data_[i].units << ")";
2212	+	// add some extra tabs for column alignment
2213	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2214		}
2215		}
2216		rnemdFile_ << std::endl;
2217
2218		rnemdFile_.precision(8);
2219
2220	<	for (unsigned int j = 0; j < nBins_; j++) {
2220	>	for (int j = 0; j < nBins_; j++) {
2221
2222		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2223		if (outputMask_[i]) {
2224		if (data_[i].dataType == "RealType")
2225		writeReal(i,j);
2226	<	else if (data_[i].dataType == "Vector3d")
2226	>	else if (data_[i].dataType == "Vector3d")
2227		writeVector(i,j);
2228		else {
2229		sprintf( painCave.errMsg,
#	Line 1671 | Line 2237 | namespace OpenMD {
2237		rnemdFile_ << std::endl;
2238
2239		}
2240	+
2241	+	rnemdFile_ << "#######################################################\n";
2242	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2243	+	rnemdFile_ << "#######################################################\n";
2244	+
2245	+
2246	+	for (int j = 0; j < nBins_; j++) {
2247	+	rnemdFile_ << "#";
2248	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2249	+	if (outputMask_[i]) {
2250	+	if (data_[i].dataType == "RealType")
2251	+	writeRealStdDev(i,j);
2252	+	else if (data_[i].dataType == "Vector3d")
2253	+	writeVectorStdDev(i,j);
2254	+	else {
2255	+	sprintf( painCave.errMsg,
2256	+	"RNEMD found an unknown data type for: %s ",
2257	+	data_[i].title.c_str());
2258	+	painCave.isFatal = 1;
2259	+	simError();
2260	+	}
2261	+	}
2262	+	}
2263	+	rnemdFile_ << std::endl;
2264	+
2265	+	}
2266
2267		rnemdFile_.flush();
2268		rnemdFile_.close();
#	Line 1682 | Line 2274 | namespace OpenMD {
2274		}
2275
2276		void RNEMD::writeReal(int index, unsigned int bin) {
2277	+	if (!doRNEMD_) return;
2278		assert(index >=0 && index < ENDINDEX);
2279	<	assert(bin >=0 && bin < nBins_);
2279	>	assert(int(bin) < nBins_);
2280		RealType s;
2281	+	int count;
2282
2283	<	data_[index].accumulator[bin]->getAverage(s);
2283	>	count = data_[index].accumulator[bin]->count();
2284	>	if (count == 0) return;
2285
2286	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2287	+
2288		if (! isinf(s) && ! isnan(s)) {
2289		rnemdFile_ << "\t" << s;
2290		} else{
2291		sprintf( painCave.errMsg,
2292	<	"RNEMD detected a numerical error writing: %s for bin %d",
2292	>	"RNEMD detected a numerical error writing: %s for bin %u",
2293		data_[index].title.c_str(), bin);
2294		painCave.isFatal = 1;
2295		simError();
#	Line 1700 | Line 2297 | namespace OpenMD {
2297		}
2298
2299		void RNEMD::writeVector(int index, unsigned int bin) {
2300	+	if (!doRNEMD_) return;
2301		assert(index >=0 && index < ENDINDEX);
2302	<	assert(bin >=0 && bin < nBins_);
2302	>	assert(int(bin) < nBins_);
2303		Vector3d s;
2304	+	int count;
2305	+
2306	+	count = data_[index].accumulator[bin]->count();
2307	+
2308	+	if (count == 0) return;
2309	+
2310		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2311		if (isinf(s[0]) || isnan(s[0]) ||
2312		isinf(s[1]) || isnan(s[1]) ||
2313		isinf(s[2]) || isnan(s[2]) ) {
2314		sprintf( painCave.errMsg,
2315	<	"RNEMD detected a numerical error writing: %s for bin %d",
2315	>	"RNEMD detected a numerical error writing: %s for bin %u",
2316		data_[index].title.c_str(), bin);
2317		painCave.isFatal = 1;
2318		simError();
#	Line 1716 | Line 2320 | namespace OpenMD {
2320		rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2321		}
2322		}
2323	+
2324	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2325	+	if (!doRNEMD_) return;
2326	+	assert(index >=0 && index < ENDINDEX);
2327	+	assert(int(bin) < nBins_);
2328	+	RealType s;
2329	+	int count;
2330	+
2331	+	count = data_[index].accumulator[bin]->count();
2332	+	if (count == 0) return;
2333	+
2334	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2335	+
2336	+	if (! isinf(s) && ! isnan(s)) {
2337	+	rnemdFile_ << "\t" << s;
2338	+	} else{
2339	+	sprintf( painCave.errMsg,
2340	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2341	+	data_[index].title.c_str(), bin);
2342	+	painCave.isFatal = 1;
2343	+	simError();
2344	+	}
2345	+	}
2346	+
2347	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2348	+	if (!doRNEMD_) return;
2349	+	assert(index >=0 && index < ENDINDEX);
2350	+	assert(int(bin) < nBins_);
2351	+	Vector3d s;
2352	+	int count;
2353	+
2354	+	count = data_[index].accumulator[bin]->count();
2355	+	if (count == 0) return;
2356	+
2357	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2358	+	if (isinf(s[0]) || isnan(s[0]) ||
2359	+	isinf(s[1]) || isnan(s[1]) ||
2360	+	isinf(s[2]) || isnan(s[2]) ) {
2361	+	sprintf( painCave.errMsg,
2362	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2363	+	data_[index].title.c_str(), bin);
2364	+	painCave.isFatal = 1;
2365	+	simError();
2366	+	} else {
2367	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2368	+	}
2369	+	}
2370		}
2371

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