[ViewVC] Diff of: OpenMD/trunk/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.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 2026 by gezelter, Wed Oct 22 12:23:59 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		}
293		if (hasMomentumFluxVector) {
294	<	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
294	>	std::vector<RealType> mf = rnemdParams->getMomentumFluxVector();
295	>	if (mf.size() != 3) {
296	>	sprintf(painCave.errMsg,
297	>	"RNEMD: Incorrect number of parameters specified for momentumFluxVector.\n"
298	>	"\tthere should be 3 parameters, but %lu were specified.\n",
299	>	mf.size());
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	momentumFluxVector_.x() = mf[0];
304	>	momentumFluxVector_.y() = mf[1];
305	>	momentumFluxVector_.z() = mf[2];
306		} else {
307		momentumFluxVector_ = V3Zero;
308		if (hasMomentumFlux) {
#	Line 264 \| Line 326 \| namespace OpenMD {
326		default:
327		break;
328		}
329	<	}
330	<	}
331	<
332	<	// do some sanity checking
333	<
334	<	int selectionCount = seleMan_.getSelectionCount();
335	<	int nIntegrable = info->getNGlobalIntegrableObjects();
336	<
337	<	if (selectionCount > nIntegrable) {
338	<	sprintf(painCave.errMsg,
339	<	"RNEMD: The current objectSelection,\n"
340	<	"\t\t%s\n"
341	<	"\thas resulted in %d selected objects. However,\n"
342	<	"\tthe total number of integrable objects in the system\n"
343	<	"\tis only %d. This is almost certainly not what you want\n"
344	<	"\tto do. A likely cause of this is forgetting the _RB_0\n"
345	<	"\tselector in the selection script!\n",
346	<	rnemdObjectSelection_.c_str(),
347	<	selectionCount, nIntegrable);
348	<	painCave.isFatal = 0;
349	<	painCave.severity = OPENMD_WARNING;
350	<	simError();
351	<	}
352	<
353	<	nBins_ = rnemdParams->getOutputBins();
329	>	}
330	>	if (hasAngularMomentumFluxVector) {
331	>	std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
332	>	if (amf.size() != 3) {
333	>	sprintf(painCave.errMsg,
334	>	"RNEMD: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
335	>	"\tthere should be 3 parameters, but %lu were specified.\n",
336	>	amf.size());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>	angularMomentumFluxVector_.x() = amf[0];
341	>	angularMomentumFluxVector_.y() = amf[1];
342	>	angularMomentumFluxVector_.z() = amf[2];
343	>	} else {
344	>	angularMomentumFluxVector_ = V3Zero;
345	>	if (hasAngularMomentumFlux) {
346	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
347	>	switch (rnemdFluxType_) {
348	>	case rnemdLx:
349	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
350	>	break;
351	>	case rnemdLy:
352	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
353	>	break;
354	>	case rnemdLz:
355	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
356	>	break;
357	>	case rnemdKeLx:
358	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
359	>	break;
360	>	case rnemdKeLy:
361	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
362	>	break;
363	>	case rnemdKeLz:
364	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
365	>	break;
366	>	default:
367	>	break;
368	>	}
369	>	}
370	>	}
371
372	<	data_.resize(RNEMD::ENDINDEX);
373	<	OutputData z;
374	<	z.units = "Angstroms";
375	<	z.title = "Z";
376	<	z.dataType = "RealType";
377	<	z.accumulator.reserve(nBins_);
378	<	for (unsigned int i = 0; i < nBins_; i++)
379	<	z.accumulator.push_back( new Accumulator() );
380	<	data_[Z] = z;
381	<	outputMap_["Z"] = Z;
372	>	if (hasCoordinateOrigin) {
373	>	std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
374	>	if (co.size() != 3) {
375	>	sprintf(painCave.errMsg,
376	>	"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
377	>	"\tthere should be 3 parameters, but %lu were specified.\n",
378	>	co.size());
379	>	painCave.isFatal = 1;
380	>	simError();
381	>	}
382	>	coordinateOrigin_.x() = co[0];
383	>	coordinateOrigin_.y() = co[1];
384	>	coordinateOrigin_.z() = co[2];
385	>	} else {
386	>	coordinateOrigin_ = V3Zero;
387	>	}
388
389	<	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;
389	>	// do some sanity checking
390
391	<	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;
391	>	int selectionCount = seleMan_.getSelectionCount();
392
393	<	OutputData density;
325	<	density.units = "g cm^-3";
326	<	density.title = "Density";
327	<	density.dataType = "RealType";
328	<	density.accumulator.reserve(nBins_);
329	<	for (unsigned int i = 0; i < nBins_; i++)
330	<	density.accumulator.push_back( new Accumulator() );
331	<	data_[DENSITY] = density;
332	<	outputMap_["DENSITY"] = DENSITY;
393	>	int nIntegrable = info->getNGlobalIntegrableObjects();
394
395	<	if (hasOutputFields) {
396	<	parseOutputFileFormat(rnemdParams->getOutputFields());
397	<	} else {
398	<	outputMask_.set(Z);
399	<	switch (rnemdFluxType_) {
400	<	case rnemdKE:
401	<	case rnemdRotKE:
402	<	case rnemdFullKE:
403	<	outputMask_.set(TEMPERATURE);
404	<	break;
405	<	case rnemdPx:
406	<	case rnemdPy:
407	<	outputMask_.set(VELOCITY);
408	<	break;
409	<	case rnemdPz:
410	<	case rnemdPvector:
411	<	outputMask_.set(VELOCITY);
412	<	outputMask_.set(DENSITY);
413	<	break;
414	<	case rnemdKePx:
415	<	case rnemdKePy:
416	<	outputMask_.set(TEMPERATURE);
417	<	outputMask_.set(VELOCITY);
418	<	break;
419	<	case rnemdKePvector:
420	<	outputMask_.set(TEMPERATURE);
421	<	outputMask_.set(VELOCITY);
422	<	outputMask_.set(DENSITY);
423	<	break;
424	<	default:
425	<	break;
426	<	}
427	<	}
428	<
429	<	if (hasOutputFileName) {
430	<	rnemdFileName_ = rnemdParams->getOutputFileName();
431	<	} else {
432	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
433	<	}
395	>	if (selectionCount > nIntegrable) {
396	>	sprintf(painCave.errMsg,
397	>	"RNEMD: The current objectSelection,\n"
398	>	"\t\t%s\n"
399	>	"\thas resulted in %d selected objects. However,\n"
400	>	"\tthe total number of integrable objects in the system\n"
401	>	"\tis only %d. This is almost certainly not what you want\n"
402	>	"\tto do. A likely cause of this is forgetting the _RB_0\n"
403	>	"\tselector in the selection script!\n",
404	>	rnemdObjectSelection_.c_str(),
405	>	selectionCount, nIntegrable);
406	>	painCave.isFatal = 0;
407	>	painCave.severity = OPENMD_WARNING;
408	>	simError();
409	>	}
410	>
411	>	areaAccumulator_ = new Accumulator();
412	>
413	>	nBins_ = rnemdParams->getOutputBins();
414	>	binWidth_ = rnemdParams->getOutputBinWidth();
415	>
416	>	data_.resize(RNEMD::ENDINDEX);
417	>	OutputData z;
418	>	z.units = "Angstroms";
419	>	z.title = "Z";
420	>	z.dataType = "RealType";
421	>	z.accumulator.reserve(nBins_);
422	>	for (int i = 0; i < nBins_; i++)
423	>	z.accumulator.push_back( new Accumulator() );
424	>	data_[Z] = z;
425	>	outputMap_["Z"] = Z;
426	>
427	>	OutputData r;
428	>	r.units = "Angstroms";
429	>	r.title = "R";
430	>	r.dataType = "RealType";
431	>	r.accumulator.reserve(nBins_);
432	>	for (int i = 0; i < nBins_; i++)
433	>	r.accumulator.push_back( new Accumulator() );
434	>	data_[R] = r;
435	>	outputMap_["R"] = R;
436
437	<	exchangeTime_ = rnemdParams->getExchangeTime();
437	>	OutputData temperature;
438	>	temperature.units = "K";
439	>	temperature.title = "Temperature";
440	>	temperature.dataType = "RealType";
441	>	temperature.accumulator.reserve(nBins_);
442	>	for (int i = 0; i < nBins_; i++)
443	>	temperature.accumulator.push_back( new Accumulator() );
444	>	data_[TEMPERATURE] = temperature;
445	>	outputMap_["TEMPERATURE"] = TEMPERATURE;
446
447	<	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
448	<	Mat3x3d hmat = currentSnap_->getHmat();
449	<
450	<	// Target exchange quantities (in each exchange) = 2 Lx Ly dt flux
451	<	// Lx, Ly = box dimensions in x & y
452	<	// dt = exchange time interval
453	<	// flux = target flux
447	>	OutputData velocity;
448	>	velocity.units = "angstroms/fs";
449	>	velocity.title = "Velocity";
450	>	velocity.dataType = "Vector3d";
451	>	velocity.accumulator.reserve(nBins_);
452	>	for (int i = 0; i < nBins_; i++)
453	>	velocity.accumulator.push_back( new VectorAccumulator() );
454	>	data_[VELOCITY] = velocity;
455	>	outputMap_["VELOCITY"] = VELOCITY;
456
457	<	kineticTarget_ = 2.0kineticFlux_exchangeTime_hmat(0,0)hmat(1,1);
458	<	momentumTarget_ = 2.0momentumFluxVector_exchangeTime_hmat(0,0)hmat(1,1);
457	>	OutputData angularVelocity;
458	>	angularVelocity.units = "angstroms^2/fs";
459	>	angularVelocity.title = "AngularVelocity";
460	>	angularVelocity.dataType = "Vector3d";
461	>	angularVelocity.accumulator.reserve(nBins_);
462	>	for (int i = 0; i < nBins_; i++)
463	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
464	>	data_[ANGULARVELOCITY] = angularVelocity;
465	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
466
467	<	// total exchange sums are zeroed out at the beginning:
467	>	OutputData density;
468	>	density.units = "g cm^-3";
469	>	density.title = "Density";
470	>	density.dataType = "RealType";
471	>	density.accumulator.reserve(nBins_);
472	>	for (int i = 0; i < nBins_; i++)
473	>	density.accumulator.push_back( new Accumulator() );
474	>	data_[DENSITY] = density;
475	>	outputMap_["DENSITY"] = DENSITY;
476
477	<	kineticExchange_ = 0.0;
478	<	momentumExchange_ = V3Zero;
477	>	if (hasOutputFields) {
478	>	parseOutputFileFormat(rnemdParams->getOutputFields());
479	>	} else {
480	>	if (usePeriodicBoundaryConditions_)
481	>	outputMask_.set(Z);
482	>	else
483	>	outputMask_.set(R);
484	>	switch (rnemdFluxType_) {
485	>	case rnemdKE:
486	>	case rnemdRotKE:
487	>	case rnemdFullKE:
488	>	outputMask_.set(TEMPERATURE);
489	>	break;
490	>	case rnemdPx:
491	>	case rnemdPy:
492	>	outputMask_.set(VELOCITY);
493	>	break;
494	>	case rnemdPz:
495	>	case rnemdPvector:
496	>	outputMask_.set(VELOCITY);
497	>	outputMask_.set(DENSITY);
498	>	break;
499	>	case rnemdLx:
500	>	case rnemdLy:
501	>	case rnemdLz:
502	>	case rnemdLvector:
503	>	outputMask_.set(ANGULARVELOCITY);
504	>	break;
505	>	case rnemdKeLx:
506	>	case rnemdKeLy:
507	>	case rnemdKeLz:
508	>	case rnemdKeLvector:
509	>	outputMask_.set(TEMPERATURE);
510	>	outputMask_.set(ANGULARVELOCITY);
511	>	break;
512	>	case rnemdKePx:
513	>	case rnemdKePy:
514	>	outputMask_.set(TEMPERATURE);
515	>	outputMask_.set(VELOCITY);
516	>	break;
517	>	case rnemdKePvector:
518	>	outputMask_.set(TEMPERATURE);
519	>	outputMask_.set(VELOCITY);
520	>	outputMask_.set(DENSITY);
521	>	break;
522	>	default:
523	>	break;
524	>	}
525	>	}
526	>
527	>	if (hasOutputFileName) {
528	>	rnemdFileName_ = rnemdParams->getOutputFileName();
529	>	} else {
530	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
531	>	}
532
533	<	if (hasSlabWidth)
534	<	slabWidth_ = rnemdParams->getSlabWidth();
535	<	else
536	<	slabWidth_ = hmat(2,2) / 10.0;
537	<
538	<	if (hasSlabACenter)
539	<	slabACenter_ = rnemdParams->getSlabACenter();
540	<	else
541	<	slabACenter_ = 0.0;
533	>	exchangeTime_ = rnemdParams->getExchangeTime();
534	>
535	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
536	>	// total exchange sums are zeroed out at the beginning:
537	>
538	>	kineticExchange_ = 0.0;
539	>	momentumExchange_ = V3Zero;
540	>	angularMomentumExchange_ = V3Zero;
541	>
542	>	std::ostringstream selectionAstream;
543	>	std::ostringstream selectionBstream;
544
545	<	if (hasSlabBCenter)
546	<	slabBCenter_ = rnemdParams->getSlabBCenter();
547	<	else
548	<	slabBCenter_ = hmat(2,2) / 2.0;
545	>	if (hasSelectionA_) {
546	>	selectionA_ = rnemdParams->getSelectionA();
547	>	} else {
548	>	if (usePeriodicBoundaryConditions_) {
549	>	Mat3x3d hmat = currentSnap_->getHmat();
550	>
551	>	if (hasSlabWidth)
552	>	slabWidth_ = rnemdParams->getSlabWidth();
553	>	else
554	>	slabWidth_ = hmat(2,2) / 10.0;
555	>
556	>	if (hasSlabACenter)
557	>	slabACenter_ = rnemdParams->getSlabACenter();
558	>	else
559	>	slabACenter_ = 0.0;
560	>
561	>	selectionAstream << "select wrappedz > "
562	>	<< slabACenter_ - 0.5*slabWidth_
563	>	<< " && wrappedz < "
564	>	<< slabACenter_ + 0.5*slabWidth_;
565	>	selectionA_ = selectionAstream.str();
566	>	} else {
567	>	if (hasSphereARadius)
568	>	sphereARadius_ = rnemdParams->getSphereARadius();
569	>	else {
570	>	// use an initial guess to the size of the inner slab to be 1/10 the
571	>	// radius of an approximately spherical hull:
572	>	Thermo thermo(info);
573	>	RealType hVol = thermo.getHullVolume();
574	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
575	>	}
576	>	selectionAstream << "select r < " << sphereARadius_;
577	>	selectionA_ = selectionAstream.str();
578	>	}
579	>	}
580
581	<	}
582	<
583	<	RNEMD::~RNEMD() {
581	>	if (hasSelectionB_) {
582	>	selectionB_ = rnemdParams->getSelectionB();
583	>
584	>	} else {
585	>	if (usePeriodicBoundaryConditions_) {
586	>	Mat3x3d hmat = currentSnap_->getHmat();
587	>
588	>	if (hasSlabWidth)
589	>	slabWidth_ = rnemdParams->getSlabWidth();
590	>	else
591	>	slabWidth_ = hmat(2,2) / 10.0;
592	>
593	>	if (hasSlabBCenter)
594	>	slabBCenter_ = rnemdParams->getSlabBCenter();
595	>	else
596	>	slabBCenter_ = hmat(2,2) / 2.0;
597	>
598	>	selectionBstream << "select wrappedz > "
599	>	<< slabBCenter_ - 0.5*slabWidth_
600	>	<< " && wrappedz < "
601	>	<< slabBCenter_ + 0.5*slabWidth_;
602	>	selectionB_ = selectionBstream.str();
603	>	} else {
604	>	if (hasSphereBRadius_) {
605	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
606	>	selectionBstream << "select r > " << sphereBRadius_;
607	>	selectionB_ = selectionBstream.str();
608	>	} else {
609	>	selectionB_ = "select hull";
610	>	BisHull_ = true;
611	>	hasSelectionB_ = true;
612	>	}
613	>	}
614	>	}
615	>	}
616	>
617	>	// object evaluator:
618	>	evaluator_.loadScriptString(rnemdObjectSelection_);
619	>	seleMan_.setSelectionSet(evaluator_.evaluate());
620	>	evaluatorA_.loadScriptString(selectionA_);
621	>	evaluatorB_.loadScriptString(selectionB_);
622	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
623	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
624	>	commonA_ = seleManA_ & seleMan_;
625	>	commonB_ = seleManB_ & seleMan_;
626	>	}
627	>
628
629	+	RNEMD::~RNEMD() {
630	+	if (!doRNEMD_) return;
631		#ifdef IS_MPI
632		if (worldRank == 0) {
633		#endif
#	Line 419 \| Line 639 \| namespace OpenMD {
639		#ifdef IS_MPI
640		}
641		#endif
642	+
643	+	// delete all of the objects we created:
644	+	delete areaAccumulator_;
645	+	data_.clear();
646		}
647
648	<	bool RNEMD::inSlabA(Vector3d pos) {
649	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
650	<	}
651	<	bool RNEMD::inSlabB(Vector3d pos) {
428	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	<	}
648	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
649	>	if (!doRNEMD_) return;
650	>	int selei;
651	>	int selej;
652
431	–	void RNEMD::doSwap() {
432	–
653		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
654		Mat3x3d hmat = currentSnap_->getHmat();
655
436	–	seleMan_.setSelectionSet(evaluator_.evaluate());
437	–
438	–	int selei;
656		StuntDouble* sd;
440	–	int idx;
657
658		RealType min_val;
659	<	bool min_found = false;
659	>	int min_found = 0;
660		StuntDouble* min_sd;
661
662		RealType max_val;
663	<	bool max_found = false;
663	>	int max_found = 0;
664		StuntDouble* max_sd;
665
666	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
667	<	sd = seleMan_.nextSelected(selei)) {
666	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
667	>	sd = seleManA_.nextSelected(selei)) {
668
453	–	idx = sd->getLocalIndex();
454	–
669		Vector3d pos = sd->getPos();
670	<
670	>
671		// wrap the stuntdouble's position back into the box:
672	<
672	>
673		if (usePeriodicBoundaryConditions_)
674		currentSnap_->wrapVector(pos);
675	<	bool inA = inSlabA(pos);
676	<	bool inB = inSlabB(pos);
677	<
678	<	if (inA \|\| inB) {
675	>
676	>	RealType mass = sd->getMass();
677	>	Vector3d vel = sd->getVel();
678	>	RealType value;
679	>
680	>	switch(rnemdFluxType_) {
681	>	case rnemdKE :
682
683	<	RealType mass = sd->getMass();
684	<	Vector3d vel = sd->getVel();
685	<	RealType value;
686	<
687	<	switch(rnemdFluxType_) {
471	<	case rnemdKE :
683	>	value = mass * vel.lengthSquare();
684	>
685	>	if (sd->isDirectional()) {
686	>	Vector3d angMom = sd->getJ();
687	>	Mat3x3d I = sd->getI();
688
689	<	value = mass * vel.lengthSquare();
690	<
691	<	if (sd->isDirectional()) {
692	<	Vector3d angMom = sd->getJ();
693	<	Mat3x3d I = sd->getI();
694	<
695	<	if (sd->isLinear()) {
696	<	int i = sd->linearAxis();
697	<	int j = (i + 1) % 3;
698	<	int k = (i + 2) % 3;
699	<	value += angMom[j] * angMom[j] / I(j, j) +
700	<	angMom[k] * angMom[k] / I(k, k);
701	<	} else {
702	<	value += angMom[0]*angMom[0]/I(0, 0)
703	<	+ angMom[1]*angMom[1]/I(1, 1)
704	<	+ angMom[2]*angMom[2]/I(2, 2);
705	<	}
706	<	} //angular momenta exchange enabled
707	<	//energyConvert temporarily disabled
708	<	//make kineticExchange_ comparable between swap & scale
709	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
710	<	value *= 0.5;
711	<	break;
712	<	case rnemdPx :
713	<	value = mass * vel[0];
714	<	break;
715	<	case rnemdPy :
716	<	value = mass * vel[1];
717	<	break;
718	<	case rnemdPz :
719	<	value = mass * vel[2];
720	<	break;
721	<	default :
722	<	break;
689	>	if (sd->isLinear()) {
690	>	int i = sd->linearAxis();
691	>	int j = (i + 1) % 3;
692	>	int k = (i + 2) % 3;
693	>	value += angMom[j] * angMom[j] / I(j, j) +
694	>	angMom[k] * angMom[k] / I(k, k);
695	>	} else {
696	>	value += angMom[0]*angMom[0]/I(0, 0)
697	>	+ angMom[1]*angMom[1]/I(1, 1)
698	>	+ angMom[2]*angMom[2]/I(2, 2);
699	>	}
700	>	} //angular momenta exchange enabled
701	>	value *= 0.5;
702	>	break;
703	>	case rnemdPx :
704	>	value = mass * vel[0];
705	>	break;
706	>	case rnemdPy :
707	>	value = mass * vel[1];
708	>	break;
709	>	case rnemdPz :
710	>	value = mass * vel[2];
711	>	break;
712	>	default :
713	>	break;
714	>	}
715	>	if (!max_found) {
716	>	max_val = value;
717	>	max_sd = sd;
718	>	max_found = 1;
719	>	} else {
720	>	if (max_val < value) {
721	>	max_val = value;
722	>	max_sd = sd;
723		}
724	+	}
725	+	}
726
727	<	if (inA == 0) {
728	<	if (!min_found) {
729	<	min_val = value;
730	<	min_sd = sd;
731	<	min_found = true;
732	<	} else {
733	<	if (min_val > value) {
734	<	min_val = value;
735	<	min_sd = sd;
736	<	}
737	<	}
738	<	} else {
739	<	if (!max_found) {
740	<	max_val = value;
741	<	max_sd = sd;
742	<	max_found = true;
743	<	} else {
744	<	if (max_val < value) {
745	<	max_val = value;
746	<	max_sd = sd;
747	<	}
748	<	}
749	<	}
727	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
728	>	sd = seleManB_.nextSelected(selej)) {
729	>
730	>	Vector3d pos = sd->getPos();
731	>
732	>	// wrap the stuntdouble's position back into the box:
733	>
734	>	if (usePeriodicBoundaryConditions_)
735	>	currentSnap_->wrapVector(pos);
736	>
737	>	RealType mass = sd->getMass();
738	>	Vector3d vel = sd->getVel();
739	>	RealType value;
740	>
741	>	switch(rnemdFluxType_) {
742	>	case rnemdKE :
743	>
744	>	value = mass * vel.lengthSquare();
745	>
746	>	if (sd->isDirectional()) {
747	>	Vector3d angMom = sd->getJ();
748	>	Mat3x3d I = sd->getI();
749	>
750	>	if (sd->isLinear()) {
751	>	int i = sd->linearAxis();
752	>	int j = (i + 1) % 3;
753	>	int k = (i + 2) % 3;
754	>	value += angMom[j] * angMom[j] / I(j, j) +
755	>	angMom[k] * angMom[k] / I(k, k);
756	>	} else {
757	>	value += angMom[0]*angMom[0]/I(0, 0)
758	>	+ angMom[1]*angMom[1]/I(1, 1)
759	>	+ angMom[2]*angMom[2]/I(2, 2);
760	>	}
761	>	} //angular momenta exchange enabled
762	>	value *= 0.5;
763	>	break;
764	>	case rnemdPx :
765	>	value = mass * vel[0];
766	>	break;
767	>	case rnemdPy :
768	>	value = mass * vel[1];
769	>	break;
770	>	case rnemdPz :
771	>	value = mass * vel[2];
772	>	break;
773	>	default :
774	>	break;
775	>	}
776	>
777	>	if (!min_found) {
778	>	min_val = value;
779	>	min_sd = sd;
780	>	min_found = 1;
781	>	} else {
782	>	if (min_val > value) {
783	>	min_val = value;
784	>	min_sd = sd;
785	>	}
786		}
787		}
788
789	<	#ifdef IS_MPI
790	<	int nProc, worldRank;
791	<
792	<	nProc = MPI::COMM_WORLD.Get_size();
793	<	worldRank = MPI::COMM_WORLD.Get_rank();
789	>	#ifdef IS_MPI
790	>	int worldRank;
791	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
792	>
793	>	int my_min_found = min_found;
794	>	int my_max_found = max_found;
795
541	–	bool my_min_found = min_found;
542	–	bool my_max_found = max_found;
543	–
796		// Even if we didn't find a minimum, did someone else?
797	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
797	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
798	>	MPI_COMM_WORLD);
799		// Even if we didn't find a maximum, did someone else?
800	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
800	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
801	>	MPI_COMM_WORLD);
802		#endif
803
804		if (max_found && min_found) {
#	Line 563 \| Line 817 \| namespace OpenMD {
817		min_vals.rank = worldRank;
818
819		// Who had the minimum?
820	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
821	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
820	>	MPI_Allreduce(&min_vals, &min_vals,
821	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
822		min_val = min_vals.val;
823
824		if (my_max_found) {
#	Line 575 \| Line 829 \| namespace OpenMD {
829		max_vals.rank = worldRank;
830
831		// Who had the maximum?
832	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
833	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
832	>	MPI_Allreduce(&max_vals, &max_vals,
833	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
834		max_val = max_vals.val;
835		#endif
836
#	Line 636 \| Line 890 \| namespace OpenMD {
890
891		Vector3d min_vel;
892		Vector3d max_vel = max_sd->getVel();
893	<	MPI::Status status;
893	>	MPI_Status status;
894
895		// point-to-point swap of the velocity vector
896	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
897	<	min_vals.rank, 0,
898	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
899	<	min_vals.rank, 0, status);
896	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
897	>	min_vals.rank, 0,
898	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
899	>	min_vals.rank, 0, MPI_COMM_WORLD, &status);
900
901		switch(rnemdFluxType_) {
902		case rnemdKE :
#	Line 653 \| Line 907 \| namespace OpenMD {
907		Vector3d max_angMom = max_sd->getJ();
908
909		// point-to-point swap of the angular momentum vector
910	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
911	<	MPI::REALTYPE, min_vals.rank, 1,
912	<	min_angMom.getArrayPointer(), 3,
913	<	MPI::REALTYPE, min_vals.rank, 1,
914	<	status);
910	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
911	>	MPI_REALTYPE, min_vals.rank, 1,
912	>	min_angMom.getArrayPointer(), 3,
913	>	MPI_REALTYPE, min_vals.rank, 1,
914	>	MPI_COMM_WORLD, &status);
915
916		max_sd->setJ(min_angMom);
917		}
#	Line 682 \| Line 936 \| namespace OpenMD {
936
937		Vector3d max_vel;
938		Vector3d min_vel = min_sd->getVel();
939	<	MPI::Status status;
939	>	MPI_Status status;
940
941		// point-to-point swap of the velocity vector
942	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
943	<	max_vals.rank, 0,
944	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
945	<	max_vals.rank, 0, status);
942	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
943	>	max_vals.rank, 0,
944	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
945	>	max_vals.rank, 0, MPI_COMM_WORLD, &status);
946
947		switch(rnemdFluxType_) {
948		case rnemdKE :
#	Line 699 \| Line 953 \| namespace OpenMD {
953		Vector3d max_angMom;
954
955		// point-to-point swap of the angular momentum vector
956	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
957	<	MPI::REALTYPE, max_vals.rank, 1,
958	<	max_angMom.getArrayPointer(), 3,
959	<	MPI::REALTYPE, max_vals.rank, 1,
960	<	status);
956	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
957	>	MPI_REALTYPE, max_vals.rank, 1,
958	>	max_angMom.getArrayPointer(), 3,
959	>	MPI_REALTYPE, max_vals.rank, 1,
960	>	MPI_COMM_WORLD, &status);
961
962		min_sd->setJ(max_angMom);
963		}
#	Line 728 \| Line 982 \| namespace OpenMD {
982
983		switch(rnemdFluxType_) {
984		case rnemdKE:
731	–	cerr << "KE\n";
985		kineticExchange_ += max_val - min_val;
986		break;
987		case rnemdPx:
#	Line 741 \| Line 994 \| namespace OpenMD {
994		momentumExchange_.z() += max_val - min_val;
995		break;
996		default:
744	–	cerr << "default\n";
997		break;
998		}
999		} else {
#	Line 763 \| Line 1015 \| namespace OpenMD {
1015		}
1016		}
1017
1018	<	void RNEMD::doNIVS() {
1018	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
1019	>	if (!doRNEMD_) return;
1020	>	int selei;
1021	>	int selej;
1022
1023		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1024	+	RealType time = currentSnap_->getTime();
1025		Mat3x3d hmat = currentSnap_->getHmat();
1026
771	–	seleMan_.setSelectionSet(evaluator_.evaluate());
772	–
773	–	int selei;
1027		StuntDouble* sd;
775	–	int idx;
1028
1029		vector<StuntDouble*> hotBin, coldBin;
1030
#	Line 791 \| Line 1043 \| namespace OpenMD {
1043		RealType Kcz = 0.0;
1044		RealType Kcw = 0.0;
1045
1046	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1047	<	sd = seleMan_.nextSelected(selei)) {
1046	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1047	>	sd = smanA.nextSelected(selei)) {
1048
797	–	idx = sd->getLocalIndex();
798	–
1049		Vector3d pos = sd->getPos();
1050	<
1050	>
1051		// wrap the stuntdouble's position back into the box:
1052	<
1052	>
1053		if (usePeriodicBoundaryConditions_)
1054		currentSnap_->wrapVector(pos);
1055	<
1056	<	// which bin is this stuntdouble in?
1057	<	bool inA = inSlabA(pos);
1058	<	bool inB = inSlabB(pos);
1055	>
1056	>
1057	>	RealType mass = sd->getMass();
1058	>	Vector3d vel = sd->getVel();
1059	>
1060	>	hotBin.push_back(sd);
1061	>	Phx += mass * vel.x();
1062	>	Phy += mass * vel.y();
1063	>	Phz += mass * vel.z();
1064	>	Khx += mass * vel.x() * vel.x();
1065	>	Khy += mass * vel.y() * vel.y();
1066	>	Khz += mass * vel.z() * vel.z();
1067	>	if (sd->isDirectional()) {
1068	>	Vector3d angMom = sd->getJ();
1069	>	Mat3x3d I = sd->getI();
1070	>	if (sd->isLinear()) {
1071	>	int i = sd->linearAxis();
1072	>	int j = (i + 1) % 3;
1073	>	int k = (i + 2) % 3;
1074	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1075	>	angMom[k] * angMom[k] / I(k, k);
1076	>	} else {
1077	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1078	>	+ angMom[1]*angMom[1]/I(1, 1)
1079	>	+ angMom[2]*angMom[2]/I(2, 2);
1080	>	}
1081	>	}
1082	>	}
1083	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1084	>	sd = smanB.nextSelected(selej)) {
1085	>	Vector3d pos = sd->getPos();
1086	>
1087	>	// wrap the stuntdouble's position back into the box:
1088	>
1089	>	if (usePeriodicBoundaryConditions_)
1090	>	currentSnap_->wrapVector(pos);
1091	>
1092	>	RealType mass = sd->getMass();
1093	>	Vector3d vel = sd->getVel();
1094
1095	<	if (inA \|\| inB) {
1096	<
1097	<	RealType mass = sd->getMass();
1098	<	Vector3d vel = sd->getVel();
1099	<
1100	<	if (inA) {
1101	<	hotBin.push_back(sd);
1102	<	Phx += mass * vel.x();
1103	<	Phy += mass * vel.y();
1104	<	Phz += mass * vel.z();
1105	<	Khx += mass * vel.x() * vel.x();
1106	<	Khy += mass * vel.y() * vel.y();
1107	<	Khz += mass * vel.z() * vel.z();
1108	<	if (sd->isDirectional()) {
1109	<	Vector3d angMom = sd->getJ();
1110	<	Mat3x3d I = sd->getI();
1111	<	if (sd->isLinear()) {
1112	<	int i = sd->linearAxis();
1113	<	int j = (i + 1) % 3;
1114	<	int k = (i + 2) % 3;
1115	<	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	<	}
1095	>	coldBin.push_back(sd);
1096	>	Pcx += mass * vel.x();
1097	>	Pcy += mass * vel.y();
1098	>	Pcz += mass * vel.z();
1099	>	Kcx += mass * vel.x() * vel.x();
1100	>	Kcy += mass * vel.y() * vel.y();
1101	>	Kcz += mass * vel.z() * vel.z();
1102	>	if (sd->isDirectional()) {
1103	>	Vector3d angMom = sd->getJ();
1104	>	Mat3x3d I = sd->getI();
1105	>	if (sd->isLinear()) {
1106	>	int i = sd->linearAxis();
1107	>	int j = (i + 1) % 3;
1108	>	int k = (i + 2) % 3;
1109	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1110	>	angMom[k] * angMom[k] / I(k, k);
1111	>	} else {
1112	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1113	>	+ angMom[1]*angMom[1]/I(1, 1)
1114	>	+ angMom[2]*angMom[2]/I(2, 2);
1115	>	}
1116		}
1117		}
1118
#	Line 872 \| Line 1126 \| namespace OpenMD {
1126		Kcw *= 0.5;
1127
1128		#ifdef IS_MPI
1129	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1130	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1131	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1132	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1133	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1134	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1129	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1131	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1132	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1133	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1134	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1135
1136	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1137	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1138	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1139	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1136	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1137	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1138	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1139	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1140
1141	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1142	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1143	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1144	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1141	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1142	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1143	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1144	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1145		#endif
1146
1147		//solve coldBin coeff's first
#	Line 908 \| Line 1162 \| namespace OpenMD {
1162
1163		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1164		c = sqrt(c);
1165	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	<	//now convert to hotBin coefficient
1165	>
1166		RealType w = 0.0;
1167		if (rnemdFluxType_ == rnemdFullKE) {
1168		x = 1.0 + px * (1.0 - c);
#	Line 936 \| Line 1189 \| namespace OpenMD {
1189		//if w is in the right range, so should be x, y, z.
1190		vector<StuntDouble*>::iterator sdi;
1191		Vector3d vel;
1192	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1192	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1193		if (rnemdFluxType_ == rnemdFullKE) {
1194		vel = (sdi)->getVel() c;
1195		(*sdi)->setVel(vel);
#	Line 947 \| Line 1200 \| namespace OpenMD {
1200		}
1201		}
1202		w = sqrt(w);
1203	<	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	<	// << "\twh= " << w << endl;
952	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1203	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1204		if (rnemdFluxType_ == rnemdFullKE) {
1205		vel = (*sdi)->getVel();
1206		vel.x() *= x;
#	Line 1068 \| Line 1319 \| namespace OpenMD {
1319		vector<RealType>::iterator ri;
1320		RealType r1, r2, alpha0;
1321		vector<pair<RealType,RealType> > rps;
1322	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1322	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1323		r2 = *ri;
1324		//check if FindRealRoots() give the right answer
1325		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1100 \| Line 1351 \| namespace OpenMD {
1351		RealType diff;
1352		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1353		vector<pair<RealType,RealType> >::iterator rpi;
1354	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1354	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1355		r1 = (*rpi).first;
1356		r2 = (*rpi).second;
1357		switch(rnemdFluxType_) {
#	Line 1167 \| Line 1418 \| namespace OpenMD {
1418		}
1419		vector<StuntDouble*>::iterator sdi;
1420		Vector3d vel;
1421	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1421	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1422		vel = (*sdi)->getVel();
1423		vel.x() *= x;
1424		vel.y() *= y;
#	Line 1178 \| Line 1429 \| namespace OpenMD {
1429		x = 1.0 + px * (1.0 - x);
1430		y = 1.0 + py * (1.0 - y);
1431		z = 1.0 + pz * (1.0 - z);
1432	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1432	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1433		vel = (*sdi)->getVel();
1434		vel.x() *= x;
1435		vel.y() *= y;
#	Line 1211 \| Line 1462 \| namespace OpenMD {
1462		failTrialCount_++;
1463		}
1464		}
1465	<
1466	<	void RNEMD::doVSS() {
1465	>
1466	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1467	>	if (!doRNEMD_) return;
1468	>	int selei;
1469	>	int selej;
1470
1471		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1472		RealType time = currentSnap_->getTime();
1473		Mat3x3d hmat = currentSnap_->getHmat();
1474
1221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	–
1223	–	int selei;
1475		StuntDouble* sd;
1225	–	int idx;
1476
1477		vector<StuntDouble*> hotBin, coldBin;
1478
1479		Vector3d Ph(V3Zero);
1480	+	Vector3d Lh(V3Zero);
1481		RealType Mh = 0.0;
1482	+	Mat3x3d Ih(0.0);
1483		RealType Kh = 0.0;
1484		Vector3d Pc(V3Zero);
1485	+	Vector3d Lc(V3Zero);
1486		RealType Mc = 0.0;
1487	+	Mat3x3d Ic(0.0);
1488		RealType Kc = 0.0;
1235	–
1489
1490	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1491	<	sd = seleMan_.nextSelected(selei)) {
1490	>	// Constraints can be on only the linear or angular momentum, but
1491	>	// not both. Usually, the user will specify which they want, but
1492	>	// in case they don't, the use of periodic boundaries should make
1493	>	// the choice for us.
1494	>	bool doLinearPart = false;
1495	>	bool doAngularPart = false;
1496
1497	<	idx = sd->getLocalIndex();
1497	>	switch (rnemdFluxType_) {
1498	>	case rnemdPx:
1499	>	case rnemdPy:
1500	>	case rnemdPz:
1501	>	case rnemdPvector:
1502	>	case rnemdKePx:
1503	>	case rnemdKePy:
1504	>	case rnemdKePvector:
1505	>	doLinearPart = true;
1506	>	break;
1507	>	case rnemdLx:
1508	>	case rnemdLy:
1509	>	case rnemdLz:
1510	>	case rnemdLvector:
1511	>	case rnemdKeLx:
1512	>	case rnemdKeLy:
1513	>	case rnemdKeLz:
1514	>	case rnemdKeLvector:
1515	>	doAngularPart = true;
1516	>	break;
1517	>	case rnemdKE:
1518	>	case rnemdRotKE:
1519	>	case rnemdFullKE:
1520	>	default:
1521	>	if (usePeriodicBoundaryConditions_)
1522	>	doLinearPart = true;
1523	>	else
1524	>	doAngularPart = true;
1525	>	break;
1526	>	}
1527	>
1528	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1529	>	sd = smanA.nextSelected(selei)) {
1530
1531		Vector3d pos = sd->getPos();
1532
1533		// wrap the stuntdouble's position back into the box:
1534	+
1535	+	if (usePeriodicBoundaryConditions_)
1536	+	currentSnap_->wrapVector(pos);
1537	+
1538	+	RealType mass = sd->getMass();
1539	+	Vector3d vel = sd->getVel();
1540	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1541	+	RealType r2;
1542	+
1543	+	hotBin.push_back(sd);
1544	+	Ph += mass * vel;
1545	+	Mh += mass;
1546	+	Kh += mass * vel.lengthSquare();
1547	+	Lh += mass * cross(rPos, vel);
1548	+	Ih -= outProduct(rPos, rPos) * mass;
1549	+	r2 = rPos.lengthSquare();
1550	+	Ih(0, 0) += mass * r2;
1551	+	Ih(1, 1) += mass * r2;
1552	+	Ih(2, 2) += mass * r2;
1553	+
1554	+	if (rnemdFluxType_ == rnemdFullKE) {
1555	+	if (sd->isDirectional()) {
1556	+	Vector3d angMom = sd->getJ();
1557	+	Mat3x3d I = sd->getI();
1558	+	if (sd->isLinear()) {
1559	+	int i = sd->linearAxis();
1560	+	int j = (i + 1) % 3;
1561	+	int k = (i + 2) % 3;
1562	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1563	+	angMom[k] * angMom[k] / I(k, k);
1564	+	} else {
1565	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1566	+	angMom[1] * angMom[1] / I(1, 1) +
1567	+	angMom[2] * angMom[2] / I(2, 2);
1568	+	}
1569	+	}
1570	+	}
1571	+	}
1572	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1573	+	sd = smanB.nextSelected(selej)) {
1574
1575	+	Vector3d pos = sd->getPos();
1576	+
1577	+	// wrap the stuntdouble's position back into the box:
1578	+
1579		if (usePeriodicBoundaryConditions_)
1580		currentSnap_->wrapVector(pos);
1581	+
1582	+	RealType mass = sd->getMass();
1583	+	Vector3d vel = sd->getVel();
1584	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1585	+	RealType r2;
1586
1587	<	// which bin is this stuntdouble in?
1588	<	bool inA = inSlabA(pos);
1589	<	bool inB = inSlabB(pos);
1587	>	coldBin.push_back(sd);
1588	>	Pc += mass * vel;
1589	>	Mc += mass;
1590	>	Kc += mass * vel.lengthSquare();
1591	>	Lc += mass * cross(rPos, vel);
1592	>	Ic -= outProduct(rPos, rPos) * mass;
1593	>	r2 = rPos.lengthSquare();
1594	>	Ic(0, 0) += mass * r2;
1595	>	Ic(1, 1) += mass * r2;
1596	>	Ic(2, 2) += mass * r2;
1597
1598	<	if (inA \|\| inB) {
1599	<
1600	<	RealType mass = sd->getMass();
1601	<	Vector3d vel = sd->getVel();
1602	<
1603	<	if (inA) {
1604	<	hotBin.push_back(sd);
1605	<	//std::cerr << "before, velocity = " << vel << endl;
1606	<	Ph += mass * vel;
1607	<	//std::cerr << "after, velocity = " << vel << endl;
1608	<	Mh += mass;
1609	<	Kh += mass * vel.lengthSquare();
1610	<	if (rnemdFluxType_ == rnemdFullKE) {
1611	<	if (sd->isDirectional()) {
1612	<	Vector3d angMom = sd->getJ();
1613	<	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	<	}
1598	>	if (rnemdFluxType_ == rnemdFullKE) {
1599	>	if (sd->isDirectional()) {
1600	>	Vector3d angMom = sd->getJ();
1601	>	Mat3x3d I = sd->getI();
1602	>	if (sd->isLinear()) {
1603	>	int i = sd->linearAxis();
1604	>	int j = (i + 1) % 3;
1605	>	int k = (i + 2) % 3;
1606	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1607	>	angMom[k] * angMom[k] / I(k, k);
1608	>	} else {
1609	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1610	>	angMom[1] * angMom[1] / I(1, 1) +
1611	>	angMom[2] * angMom[2] / I(2, 2);
1612	>	}
1613	>	}
1614		}
1615		}
1616
1617		Kh *= 0.5;
1618		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;
1619
1620		#ifdef IS_MPI
1621	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1622	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1623	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1624	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1625	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1626	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1621	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1622	>	MPI_COMM_WORLD);
1623	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1624	>	MPI_COMM_WORLD);
1625	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1626	>	MPI_COMM_WORLD);
1627	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1628	>	MPI_COMM_WORLD);
1629	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1630	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1631	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1632	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1633	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1634	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1635	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1636	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1637		#endif
1638	+
1639
1640	+	Vector3d ac, acrec, bc, bcrec;
1641	+	Vector3d ah, ahrec, bh, bhrec;
1642	+
1643		bool successfulExchange = false;
1644		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1645		Vector3d vc = Pc / Mc;
1646	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1647	<	Vector3d acrec = -momentumTarget_ / Mc;
1648	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1646	>	ac = -momentumTarget_ / Mc + vc;
1647	>	acrec = -momentumTarget_ / Mc;
1648	>
1649	>	// We now need the inverse of the inertia tensor to calculate the
1650	>	// angular velocity of the cold slab;
1651	>	Mat3x3d Ici = Ic.inverse();
1652	>	Vector3d omegac = Ici * Lc;
1653	>	bc = -(Ici * angularMomentumTarget_) + omegac;
1654	>	bcrec = bc - omegac;
1655	>
1656	>	RealType cNumerator = Kc - kineticTarget_;
1657	>	if (doLinearPart)
1658	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1659	>
1660	>	if (doAngularPart)
1661	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1662	>
1663		if (cNumerator > 0.0) {
1664	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1664	>
1665	>	RealType cDenominator = Kc;
1666	>
1667	>	if (doLinearPart)
1668	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1669	>
1670	>	if (doAngularPart)
1671	>	cDenominator -= 0.5(dot(omegac, Ic omegac));
1672	>
1673		if (cDenominator > 0.0) {
1674		RealType c = sqrt(cNumerator / cDenominator);
1675		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1676	+
1677		Vector3d vh = Ph / Mh;
1678	<	Vector3d ah = momentumTarget_ / Mh + vh;
1679	<	Vector3d ahrec = momentumTarget_ / Mh;
1680	<	RealType hNumerator = Kh + kineticTarget_
1681	<	- 0.5 * Mh * ah.lengthSquare();
1682	<	if (hNumerator > 0.0) {
1683	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1678	>	ah = momentumTarget_ / Mh + vh;
1679	>	ahrec = momentumTarget_ / Mh;
1680	>
1681	>	// We now need the inverse of the inertia tensor to
1682	>	// calculate the angular velocity of the hot slab;
1683	>	Mat3x3d Ihi = Ih.inverse();
1684	>	Vector3d omegah = Ihi * Lh;
1685	>	bh = (Ihi * angularMomentumTarget_) + omegah;
1686	>	bhrec = bh - omegah;
1687	>
1688	>	RealType hNumerator = Kh + kineticTarget_;
1689	>	if (doLinearPart)
1690	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1691	>
1692	>	if (doAngularPart)
1693	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1694	>
1695	>	if (hNumerator > 0.0) {
1696	>
1697	>	RealType hDenominator = Kh;
1698	>	if (doLinearPart)
1699	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1700	>	if (doAngularPart)
1701	>	hDenominator -= 0.5(dot(omegah, Ih omegah));
1702	>
1703		if (hDenominator > 0.0) {
1704		RealType h = sqrt(hNumerator / hDenominator);
1705		if ((h > 0.9) && (h < 1.1)) {
1706	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	<	// std::cerr << "hot slab scaling coefficient: " << h << "\n";
1706	>
1707		vector<StuntDouble*>::iterator sdi;
1708		Vector3d vel;
1709	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1709	>	Vector3d rPos;
1710	>
1711	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1712		//vel = (*sdi)->getVel();
1713	<	vel = ((sdi)->getVel() - vc) c + ac;
1713	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1714	>	if (doLinearPart)
1715	>	vel = ((sdi)->getVel() - vc) c + ac;
1716	>	if (doAngularPart)
1717	>	vel = ((sdi)->getVel() - cross(omegac, rPos)) c + cross(bc, rPos);
1718	>
1719		(*sdi)->setVel(vel);
1720		if (rnemdFluxType_ == rnemdFullKE) {
1721		if ((*sdi)->isDirectional()) {
#	Line 1357 \| Line 1724 \| namespace OpenMD {
1724		}
1725		}
1726		}
1727	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1727	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1728		//vel = (*sdi)->getVel();
1729	<	vel = ((sdi)->getVel() - vh) h + ah;
1729	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1730	>	if (doLinearPart)
1731	>	vel = ((sdi)->getVel() - vh) h + ah;
1732	>	if (doAngularPart)
1733	>	vel = ((sdi)->getVel() - cross(omegah, rPos)) h + cross(bh, rPos);
1734	>
1735		(*sdi)->setVel(vel);
1736		if (rnemdFluxType_ == rnemdFullKE) {
1737		if ((*sdi)->isDirectional()) {
#	Line 1371 \| Line 1743 \| namespace OpenMD {
1743		successfulExchange = true;
1744		kineticExchange_ += kineticTarget_;
1745		momentumExchange_ += momentumTarget_;
1746	+	angularMomentumExchange_ += angularMomentumTarget_;
1747		}
1748		}
1749		}
#	Line 1390 \| Line 1763 \| namespace OpenMD {
1763		}
1764		}
1765
1766	<	void RNEMD::doRNEMD() {
1766	>	RealType RNEMD::getDividingArea() {
1767
1768	+	if (hasDividingArea_) return dividingArea_;
1769	+
1770	+	RealType areaA, areaB;
1771	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1772	+
1773	+	if (hasSelectionA_) {
1774	+
1775	+	if (evaluatorA_.hasSurfaceArea())
1776	+	areaA = evaluatorA_.getSurfaceArea();
1777	+	else {
1778	+
1779	+	cerr << "selection A did not have surface area, recomputing\n";
1780	+	int isd;
1781	+	StuntDouble* sd;
1782	+	vector<StuntDouble*> aSites;
1783	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1784	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1785	+	sd = seleManA_.nextSelected(isd)) {
1786	+	aSites.push_back(sd);
1787	+	}
1788	+	#if defined(HAVE_QHULL)
1789	+	ConvexHull* surfaceMeshA = new ConvexHull();
1790	+	surfaceMeshA->computeHull(aSites);
1791	+	cerr << "flag1\n";
1792	+	areaA = surfaceMeshA->getArea();
1793	+	cerr << "Flag2 " << areaA << "\n";
1794	+	delete surfaceMeshA;
1795	+	#else
1796	+	sprintf( painCave.errMsg,
1797	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1798	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1799	+	painCave.severity = OPENMD_ERROR;
1800	+	painCave.isFatal = 1;
1801	+	simError();
1802	+	#endif
1803	+	}
1804	+
1805	+	} else {
1806	+	if (usePeriodicBoundaryConditions_) {
1807	+	// in periodic boundaries, the surface area is twice the x-y
1808	+	// area of the current box:
1809	+	areaA = 2.0 * snap->getXYarea();
1810	+	} else {
1811	+	// in non-periodic simulations, without explicitly setting
1812	+	// selections, the sphere radius sets the surface area of the
1813	+	// dividing surface:
1814	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1815	+	}
1816	+	}
1817	+
1818	+	if (hasSelectionB_) {
1819	+	if (evaluatorB_.hasSurfaceArea())
1820	+	areaB = evaluatorB_.getSurfaceArea();
1821	+	else {
1822	+	cerr << "selection B did not have surface area, recomputing\n";
1823	+
1824	+	int isd;
1825	+	StuntDouble* sd;
1826	+	vector<StuntDouble*> bSites;
1827	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1828	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1829	+	sd = seleManB_.nextSelected(isd)) {
1830	+	bSites.push_back(sd);
1831	+	}
1832	+
1833	+	#if defined(HAVE_QHULL)
1834	+	ConvexHull* surfaceMeshB = new ConvexHull();
1835	+	surfaceMeshB->computeHull(bSites);
1836	+	areaB = surfaceMeshB->getArea();
1837	+	delete surfaceMeshB;
1838	+	#else
1839	+	sprintf( painCave.errMsg,
1840	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1841	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1842	+	painCave.severity = OPENMD_ERROR;
1843	+	painCave.isFatal = 1;
1844	+	simError();
1845	+	#endif
1846	+	}
1847	+
1848	+	} else {
1849	+	if (usePeriodicBoundaryConditions_) {
1850	+	// in periodic boundaries, the surface area is twice the x-y
1851	+	// area of the current box:
1852	+	areaB = 2.0 * snap->getXYarea();
1853	+	} else {
1854	+	// in non-periodic simulations, without explicitly setting
1855	+	// selections, but if a sphereBradius has been set, just use that:
1856	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1857	+	}
1858	+	}
1859	+
1860	+	dividingArea_ = min(areaA, areaB);
1861	+	hasDividingArea_ = true;
1862	+	return dividingArea_;
1863	+	}
1864	+
1865	+	void RNEMD::doRNEMD() {
1866	+	if (!doRNEMD_) return;
1867		trialCount_++;
1868	+
1869	+	// object evaluator:
1870	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1871	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1872	+
1873	+	evaluatorA_.loadScriptString(selectionA_);
1874	+	evaluatorB_.loadScriptString(selectionB_);
1875	+
1876	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1877	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1878	+
1879	+	commonA_ = seleManA_ & seleMan_;
1880	+	commonB_ = seleManB_ & seleMan_;
1881	+
1882	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1883	+	// dt = exchange time interval
1884	+	// flux = target flux
1885	+	// dividingArea = smallest dividing surface between the two regions
1886	+
1887	+	hasDividingArea_ = false;
1888	+	RealType area = getDividingArea();
1889	+
1890	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1891	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1892	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1893	+
1894		switch(rnemdMethod_) {
1895		case rnemdSwap:
1896	<	doSwap();
1896	>	doSwap(commonA_, commonB_);
1897		break;
1898		case rnemdNIVS:
1899	<	doNIVS();
1899	>	doNIVS(commonA_, commonB_);
1900		break;
1901		case rnemdVSS:
1902	<	doVSS();
1902	>	doVSS(commonA_, commonB_);
1903		break;
1904		case rnemdUnkownMethod:
1905		default :
#	Line 1410 \| Line 1908 \| namespace OpenMD {
1908		}
1909
1910		void RNEMD::collectData() {
1911	<
1911	>	if (!doRNEMD_) return;
1912		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1913	+
1914	+	// collectData can be called more frequently than the doRNEMD, so use the
1915	+	// computed area from the last exchange time:
1916	+	RealType area = getDividingArea();
1917	+	areaAccumulator_->add(area);
1918		Mat3x3d hmat = currentSnap_->getHmat();
1919	+	Vector3d u = angularMomentumFluxVector_;
1920	+	u.normalize();
1921
1922		seleMan_.setSelectionSet(evaluator_.evaluate());
1923
1924	<	int selei;
1924	>	int selei(0);
1925		StuntDouble* sd;
1926	<	int idx;
1926	>	int binNo;
1927	>	RealType mass;
1928	>	Vector3d vel;
1929	>	Vector3d rPos;
1930	>	RealType KE;
1931	>	Vector3d L;
1932	>	Mat3x3d I;
1933	>	RealType r2;
1934
1935		vector<RealType> binMass(nBins_, 0.0);
1936	<	vector<RealType> binPx(nBins_, 0.0);
1937	<	vector<RealType> binPy(nBins_, 0.0);
1938	<	vector<RealType> binPz(nBins_, 0.0);
1936	>	vector<Vector3d> binP(nBins_, V3Zero);
1937	>	vector<RealType> binOmega(nBins_, 0.0);
1938	>	vector<Vector3d> binL(nBins_, V3Zero);
1939	>	vector<Mat3x3d> binI(nBins_);
1940		vector<RealType> binKE(nBins_, 0.0);
1941		vector<int> binDOF(nBins_, 0);
1942		vector<int> binCount(nBins_, 0);
#	Line 1431 \| Line 1944 \| namespace OpenMD {
1944		// alternative approach, track all molecules instead of only those
1945		// selected for scaling/swapping:
1946		/*
1947	<	SimInfo::MoleculeIterator miter;
1948	<	vector<StuntDouble*>::iterator iiter;
1949	<	Molecule* mol;
1950	<	StuntDouble* sd;
1951	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1947	>	SimInfo::MoleculeIterator miter;
1948	>	vector<StuntDouble*>::iterator iiter;
1949	>	Molecule* mol;
1950	>	StuntDouble* sd;
1951	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1952		mol = info_->nextMolecule(miter))
1953		sd is essentially sd
1954	<	for (sd = mol->beginIntegrableObject(iiter);
1955	<	sd != NULL;
1956	<	sd = mol->nextIntegrableObject(iiter))
1954	>	for (sd = mol->beginIntegrableObject(iiter);
1955	>	sd != NULL;
1956	>	sd = mol->nextIntegrableObject(iiter))
1957		*/
1958	+
1959		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1960	<	sd = seleMan_.nextSelected(selei)) {
1961	<
1448	<	idx = sd->getLocalIndex();
1449	<
1960	>	sd = seleMan_.nextSelected(selei)) {
1961	>
1962		Vector3d pos = sd->getPos();
1963
1964		// wrap the stuntdouble's position back into the box:
1965
1966	<	if (usePeriodicBoundaryConditions_)
1966	>	if (usePeriodicBoundaryConditions_) {
1967		currentSnap_->wrapVector(pos);
1968	+	// which bin is this stuntdouble in?
1969	+	// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
1970	+	// Shift molecules by half a box to have bins start at 0
1971	+	// The modulo operator is used to wrap the case when we are
1972	+	// beyond the end of the bins back to the beginning.
1973	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1974	+	} else {
1975	+	Vector3d rPos = pos - coordinateOrigin_;
1976	+	binNo = int(rPos.length() / binWidth_);
1977	+	}
1978
1979	<	// which bin is this stuntdouble in?
1980	<	// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
1981	<	// Shift molecules by half a box to have bins start at 0
1982	<	// The modulo operator is used to wrap the case when we are
1983	<	// beyond the end of the bins back to the beginning.
1984	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1985	<
1986	<	RealType mass = sd->getMass();
1987	<	Vector3d vel = sd->getVel();
1979	>	mass = sd->getMass();
1980	>	vel = sd->getVel();
1981	>	rPos = sd->getPos() - coordinateOrigin_;
1982	>	KE = 0.5 * mass * vel.lengthSquare();
1983	>	L = mass * cross(rPos, vel);
1984	>	I = outProduct(rPos, rPos) * mass;
1985	>	r2 = rPos.lengthSquare();
1986	>	I(0, 0) += mass * r2;
1987	>	I(1, 1) += mass * r2;
1988	>	I(2, 2) += mass * r2;
1989
1990	<	binCount[binNo]++;
1991	<	binMass[binNo] += mass;
1992	<	binPx[binNo] += mass*vel.x();
1993	<	binPy[binNo] += mass*vel.y();
1994	<	binPz[binNo] += mass*vel.z();
1995	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1996	<	binDOF[binNo] += 3;
1990	>	// Project the relative position onto a plane perpendicular to
1991	>	// the angularMomentumFluxVector:
1992	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1993	>	// Project the velocity onto a plane perpendicular to the
1994	>	// angularMomentumFluxVector:
1995	>	// Vector3d vProj = vel - dot(vel, u) * u;
1996	>	// Compute angular velocity vector (should be nearly parallel to
1997	>	// angularMomentumFluxVector
1998	>	// Vector3d aVel = cross(rProj, vProj);
1999
2000	<	if (sd->isDirectional()) {
2001	<	Vector3d angMom = sd->getJ();
2002	<	Mat3x3d I = sd->getI();
2003	<	if (sd->isLinear()) {
2004	<	int i = sd->linearAxis();
2005	<	int j = (i + 1) % 3;
2006	<	int k = (i + 2) % 3;
2007	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
2008	<	angMom[k] * angMom[k] / I(k, k));
2009	<	binDOF[binNo] += 2;
2010	<	} else {
2011	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
2012	<	angMom[1] * angMom[1] / I(1, 1) +
2013	<	angMom[2] * angMom[2] / I(2, 2));
2014	<	binDOF[binNo] += 3;
2000	>	if (binNo >= 0 && binNo < nBins_) {
2001	>	binCount[binNo]++;
2002	>	binMass[binNo] += mass;
2003	>	binP[binNo] += mass*vel;
2004	>	binKE[binNo] += KE;
2005	>	binI[binNo] += I;
2006	>	binL[binNo] += L;
2007	>	binDOF[binNo] += 3;
2008	>
2009	>	if (sd->isDirectional()) {
2010	>	Vector3d angMom = sd->getJ();
2011	>	Mat3x3d Ia = sd->getI();
2012	>	if (sd->isLinear()) {
2013	>	int i = sd->linearAxis();
2014	>	int j = (i + 1) % 3;
2015	>	int k = (i + 2) % 3;
2016	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
2017	>	angMom[k] * angMom[k] / Ia(k, k));
2018	>	binDOF[binNo] += 2;
2019	>	} else {
2020	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
2021	>	angMom[1] * angMom[1] / Ia(1, 1) +
2022	>	angMom[2] * angMom[2] / Ia(2, 2));
2023	>	binDOF[binNo] += 3;
2024	>	}
2025		}
2026		}
2027		}
2028
1494	–
2029		#ifdef IS_MPI
2030	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
2031	<	nBins_, MPI::INT, MPI::SUM);
2032	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
2033	<	nBins_, MPI::REALTYPE, MPI::SUM);
2034	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
2035	<	nBins_, MPI::REALTYPE, MPI::SUM);
2036	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
2037	<	nBins_, MPI::REALTYPE, MPI::SUM);
2038	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
2039	<	nBins_, MPI::REALTYPE, MPI::SUM);
2040	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
2041	<	nBins_, MPI::REALTYPE, MPI::SUM);
2042	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
2043	<	nBins_, MPI::INT, MPI::SUM);
2030	>
2031	>	for (int i = 0; i < nBins_; i++) {
2032	>
2033	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
2034	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2035	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2036	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2037	>	MPI_Allreduce(MPI_IN_PLACE, binP[i].getArrayPointer(),
2038	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2039	>	MPI_Allreduce(MPI_IN_PLACE, binL[i].getArrayPointer(),
2040	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2041	>	MPI_Allreduce(MPI_IN_PLACE, binI[i].getArrayPointer(),
2042	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2043	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2044	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2045	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2046	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2047	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2048	>	// 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2049	>	}
2050	>
2051		#endif
2052
2053	<	Vector3d vel;
2053	>	Vector3d omega;
2054		RealType den;
2055		RealType temp;
2056		RealType z;
2057	+	RealType r;
2058		for (int i = 0; i < nBins_; i++) {
2059	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2060	<	vel.x() = binPx[i] / binMass[i];
2061	<	vel.y() = binPy[i] / binMass[i];
2062	<	vel.z() = binPz[i] / binMass[i];
2063	<	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
2064	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2065	<	PhysicalConstants::energyConvert);
2059	>	if (usePeriodicBoundaryConditions_) {
2060	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2061	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2062	>	/ currentSnap_->getVolume() ;
2063	>	} else {
2064	>	r = (((RealType)i + 0.5) * binWidth_);
2065	>	RealType rinner = (RealType)i * binWidth_;
2066	>	RealType router = (RealType)(i+1) * binWidth_;
2067	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2068	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2069	>	}
2070	>	vel = binP[i] / binMass[i];
2071
2072	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2073	<	if(outputMask_[j]) {
2074	<	switch(j) {
2075	<	case Z:
2076	<	(data_[j].accumulator[i])->add(z);
2077	<	break;
2078	<	case TEMPERATURE:
2079	<	data_[j].accumulator[i]->add(temp);
2080	<	break;
2081	<	case VELOCITY:
2082	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2083	<	break;
2084	<	case DENSITY:
2085	<	data_[j].accumulator[i]->add(den);
2086	<	break;
2072	>	omega = binI[i].inverse() * binL[i];
2073	>
2074	>	// omega = binOmega[i] / binCount[i];
2075	>
2076	>	if (binCount[i] > 0) {
2077	>	// only add values if there are things to add
2078	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2079	>	PhysicalConstants::energyConvert);
2080	>
2081	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2082	>	if(outputMask_[j]) {
2083	>	switch(j) {
2084	>	case Z:
2085	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2086	>	break;
2087	>	case R:
2088	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2089	>	break;
2090	>	case TEMPERATURE:
2091	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2092	>	break;
2093	>	case VELOCITY:
2094	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2095	>	break;
2096	>	case ANGULARVELOCITY:
2097	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2098	>	break;
2099	>	case DENSITY:
2100	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2101	>	break;
2102	>	}
2103		}
2104		}
2105		}
2106		}
2107	+	hasData_ = true;
2108		}
2109
2110		void RNEMD::getStarted() {
2111	+	if (!doRNEMD_) return;
2112	+	hasDividingArea_ = false;
2113		collectData();
2114		writeOutputFile();
2115		}
2116
2117		void RNEMD::parseOutputFileFormat(const std::string& format) {
2118	+	if (!doRNEMD_) return;
2119		StringTokenizer tokenizer(format, " ,;\|\t\n\r");
2120
2121		while(tokenizer.hasMoreTokens()) {
#	Line 1569 \| Line 2136 \| namespace OpenMD {
2136		}
2137
2138		void RNEMD::writeOutputFile() {
2139	+	if (!doRNEMD_) return;
2140	+	if (!hasData_) return;
2141
2142		#ifdef IS_MPI
2143		// If we're the root node, should we print out the results
2144	<	int worldRank = MPI::COMM_WORLD.Get_rank();
2144	>	int worldRank;
2145	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2146	>
2147		if (worldRank == 0) {
2148		#endif
2149		rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out \| std::ios::trunc );
#	Line 1588 \| Line 2159 \| namespace OpenMD {
2159		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2160
2161		RealType time = currentSnap_->getTime();
2162	<
2163	<
2162	>	RealType avgArea;
2163	>	areaAccumulator_->getAverage(avgArea);
2164	>
2165	>	RealType Jz(0.0);
2166	>	Vector3d JzP(V3Zero);
2167	>	Vector3d JzL(V3Zero);
2168	>	if (time >= info_->getSimParams()->getDt()) {
2169	>	Jz = kineticExchange_ / (time * avgArea)
2170	>	/ PhysicalConstants::energyConvert;
2171	>	JzP = momentumExchange_ / (time * avgArea);
2172	>	JzL = angularMomentumExchange_ / (time * avgArea);
2173	>	}
2174	>
2175		rnemdFile_ << "#######################################################\n";
2176		rnemdFile_ << "# RNEMD {\n";
2177
2178		map<string, RNEMDMethod>::iterator mi;
2179		for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2180		if ( (*mi).second == rnemdMethod_)
2181	<	rnemdFile_ << "# exchangeMethod = " << (*mi).first << "\n";
2181	>	rnemdFile_ << "# exchangeMethod = \"" << (*mi).first << "\";\n";
2182		}
2183		map<string, RNEMDFluxType>::iterator fi;
2184		for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2185		if ( (*fi).second == rnemdFluxType_)
2186	<	rnemdFile_ << "# fluxType = " << (*fi).first << "\n";
2186	>	rnemdFile_ << "# fluxType = \"" << (*fi).first << "\";\n";
2187		}
2188
2189	<	rnemdFile_ << "# exchangeTime = " << exchangeTime_ << " fs\n";
2189	>	rnemdFile_ << "# exchangeTime = " << exchangeTime_ << ";\n";
2190
2191		rnemdFile_ << "# objectSelection = \""
2192	<	<< rnemdObjectSelection_ << "\"\n";
2193	<	rnemdFile_ << "# slabWidth = " << slabWidth_ << " angstroms\n";
2194	<	rnemdFile_ << "# slabAcenter = " << slabACenter_ << " angstroms\n";
1613	<	rnemdFile_ << "# slabBcenter = " << slabBCenter_ << " angstroms\n";
2192	>	<< rnemdObjectSelection_ << "\";\n";
2193	>	rnemdFile_ << "# selectionA = \"" << selectionA_ << "\";\n";
2194	>	rnemdFile_ << "# selectionB = \"" << selectionB_ << "\";\n";
2195		rnemdFile_ << "# }\n";
2196		rnemdFile_ << "#######################################################\n";
2197	<
2198	<	rnemdFile_ << "# running time = " << time << " fs\n";
2199	<	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
2200	<	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
2201	<
2202	<	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
2203	<	<< "\n";
2204	<	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
2205	<	<< "\n";
2206	<
2207	<	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
2208	<	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
2209	<	<< "\n";
2210	<
2211	<	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
2212	<	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
2213	<
2214	<
2197	>	rnemdFile_ << "# RNEMD report:\n";
2198	>	rnemdFile_ << "# running time = " << time << " fs\n";
2199	>	rnemdFile_ << "# Target flux:\n";
2200	>	rnemdFile_ << "# kinetic = "
2201	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2202	>	<< " (kcal/mol/A^2/fs)\n";
2203	>	rnemdFile_ << "# momentum = " << momentumFluxVector_
2204	>	<< " (amu/A/fs^2)\n";
2205	>	rnemdFile_ << "# angular momentum = " << angularMomentumFluxVector_
2206	>	<< " (amu/A^2/fs^2)\n";
2207	>	rnemdFile_ << "# Target one-time exchanges:\n";
2208	>	rnemdFile_ << "# kinetic = "
2209	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2210	>	<< " (kcal/mol)\n";
2211	>	rnemdFile_ << "# momentum = " << momentumTarget_
2212	>	<< " (amu*A/fs)\n";
2213	>	rnemdFile_ << "# angular momentum = " << angularMomentumTarget_
2214	>	<< " (amu*A^2/fs)\n";
2215	>	rnemdFile_ << "# Actual exchange totals:\n";
2216	>	rnemdFile_ << "# kinetic = "
2217	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2218	>	<< " (kcal/mol)\n";
2219	>	rnemdFile_ << "# momentum = " << momentumExchange_
2220	>	<< " (amu*A/fs)\n";
2221	>	rnemdFile_ << "# angular momentum = " << angularMomentumExchange_
2222	>	<< " (amu*A^2/fs)\n";
2223	>	rnemdFile_ << "# Actual flux:\n";
2224	>	rnemdFile_ << "# kinetic = " << Jz
2225	>	<< " (kcal/mol/A^2/fs)\n";
2226	>	rnemdFile_ << "# momentum = " << JzP
2227	>	<< " (amu/A/fs^2)\n";
2228	>	rnemdFile_ << "# angular momentum = " << JzL
2229	>	<< " (amu/A^2/fs^2)\n";
2230	>	rnemdFile_ << "# Exchange statistics:\n";
2231	>	rnemdFile_ << "# attempted = " << trialCount_ << "\n";
2232	>	rnemdFile_ << "# failed = " << failTrialCount_ << "\n";
2233		if (rnemdMethod_ == rnemdNIVS) {
2234	<	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
2234	>	rnemdFile_ << "# NIVS root-check errors = "
2235	>	<< failRootCount_ << "\n";
2236		}
1637	–
2237		rnemdFile_ << "#######################################################\n";
2238
2239
#	Line 1645 \| Line 2244 \| namespace OpenMD {
2244		if (outputMask_[i]) {
2245		rnemdFile_ << "\t" << data_[i].title <<
2246		"(" << data_[i].units << ")";
2247	+	// add some extra tabs for column alignment
2248	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2249		}
2250		}
2251		rnemdFile_ << std::endl;
2252
2253		rnemdFile_.precision(8);
2254
2255	<	for (unsigned int j = 0; j < nBins_; j++) {
2255	>	for (int j = 0; j < nBins_; j++) {
2256
2257		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2258		if (outputMask_[i]) {
2259		if (data_[i].dataType == "RealType")
2260		writeReal(i,j);
2261	<	else if (data_[i].dataType == "Vector3d")
2261	>	else if (data_[i].dataType == "Vector3d")
2262		writeVector(i,j);
2263		else {
2264		sprintf( painCave.errMsg,
#	Line 1671 \| Line 2272 \| namespace OpenMD {
2272		rnemdFile_ << std::endl;
2273
2274		}
2275	+
2276	+	rnemdFile_ << "#######################################################\n";
2277	+	rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2278	+	rnemdFile_ << "#######################################################\n";
2279	+
2280	+
2281	+	for (int j = 0; j < nBins_; j++) {
2282	+	rnemdFile_ << "#";
2283	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2284	+	if (outputMask_[i]) {
2285	+	if (data_[i].dataType == "RealType")
2286	+	writeRealErrorBars(i,j);
2287	+	else if (data_[i].dataType == "Vector3d")
2288	+	writeVectorErrorBars(i,j);
2289	+	else {
2290	+	sprintf( painCave.errMsg,
2291	+	"RNEMD found an unknown data type for: %s ",
2292	+	data_[i].title.c_str());
2293	+	painCave.isFatal = 1;
2294	+	simError();
2295	+	}
2296	+	}
2297	+	}
2298	+	rnemdFile_ << std::endl;
2299	+
2300	+	}
2301
2302		rnemdFile_.flush();
2303		rnemdFile_.close();
#	Line 1682 \| Line 2309 \| namespace OpenMD {
2309		}
2310
2311		void RNEMD::writeReal(int index, unsigned int bin) {
2312	+	if (!doRNEMD_) return;
2313		assert(index >=0 && index < ENDINDEX);
2314	<	assert(bin >=0 && bin < nBins_);
2314	>	assert(int(bin) < nBins_);
2315		RealType s;
2316	+	int count;
2317
2318	<	data_[index].accumulator[bin]->getAverage(s);
2318	>	count = data_[index].accumulator[bin]->count();
2319	>	if (count == 0) return;
2320
2321	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2322	+
2323		if (! isinf(s) && ! isnan(s)) {
2324		rnemdFile_ << "\t" << s;
2325		} else{
2326		sprintf( painCave.errMsg,
2327	<	"RNEMD detected a numerical error writing: %s for bin %d",
2327	>	"RNEMD detected a numerical error writing: %s for bin %u",
2328		data_[index].title.c_str(), bin);
2329		painCave.isFatal = 1;
2330		simError();
#	Line 1700 \| Line 2332 \| namespace OpenMD {
2332		}
2333
2334		void RNEMD::writeVector(int index, unsigned int bin) {
2335	+	if (!doRNEMD_) return;
2336		assert(index >=0 && index < ENDINDEX);
2337	<	assert(bin >=0 && bin < nBins_);
2337	>	assert(int(bin) < nBins_);
2338		Vector3d s;
2339	+	int count;
2340	+
2341	+	count = data_[index].accumulator[bin]->count();
2342	+
2343	+	if (count == 0) return;
2344	+
2345		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2346		if (isinf(s[0]) \|\| isnan(s[0]) \|\|
2347		isinf(s[1]) \|\| isnan(s[1]) \|\|
2348		isinf(s[2]) \|\| isnan(s[2]) ) {
2349		sprintf( painCave.errMsg,
2350	<	"RNEMD detected a numerical error writing: %s for bin %d",
2350	>	"RNEMD detected a numerical error writing: %s for bin %u",
2351		data_[index].title.c_str(), bin);
2352		painCave.isFatal = 1;
2353		simError();
#	Line 1716 \| Line 2355 \| namespace OpenMD {
2355		rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2356		}
2357		}
2358	+
2359	+	void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2360	+	if (!doRNEMD_) return;
2361	+	assert(index >=0 && index < ENDINDEX);
2362	+	assert(int(bin) < nBins_);
2363	+	RealType s;
2364	+	int count;
2365	+
2366	+	count = data_[index].accumulator[bin]->count();
2367	+	if (count == 0) return;
2368	+
2369	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2370	+
2371	+	if (! isinf(s) && ! isnan(s)) {
2372	+	rnemdFile_ << "\t" << s;
2373	+	} else{
2374	+	sprintf( painCave.errMsg,
2375	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2376	+	data_[index].title.c_str(), bin);
2377	+	painCave.isFatal = 1;
2378	+	simError();
2379	+	}
2380	+	}
2381	+
2382	+	void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2383	+	if (!doRNEMD_) return;
2384	+	assert(index >=0 && index < ENDINDEX);
2385	+	assert(int(bin) < nBins_);
2386	+	Vector3d s;
2387	+	int count;
2388	+
2389	+	count = data_[index].accumulator[bin]->count();
2390	+	if (count == 0) return;
2391	+
2392	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2393	+	if (isinf(s[0]) \|\| isnan(s[0]) \|\|
2394	+	isinf(s[1]) \|\| isnan(s[1]) \|\|
2395	+	isinf(s[2]) \|\| isnan(s[2]) ) {
2396	+	sprintf( painCave.errMsg,
2397	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2398	+	data_[index].title.c_str(), bin);
2399	+	painCave.isFatal = 1;
2400	+	simError();
2401	+	} else {
2402	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2403	+	}
2404	+	}
2405		}
2406

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Comparing: 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 2026 by gezelter, Wed Oct 22 12:23:59 2014 UTC

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Comparing:
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 2026 by gezelter, Wed Oct 22 12:23:59 2014 UTC