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

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branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1789 by gezelter, Wed Aug 29 20:52:19 2012 UTC

#	Line 40 | Line 40
40		*/
41
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include "rnemd/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45	+	#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
47		#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50		#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52	<
52	<	#ifndef IS_MPI
53	<	#include "math/SeqRandNumGen.hpp"
54	<	#else
52	>	#ifdef IS_MPI
53		#include <mpi.h>
56	–	#include "math/ParallelRandNumGen.hpp"
54		#endif
55
56	+	#ifdef _MSC_VER
57	+	#define isnan(x) _isnan((x))
58	+	#define isinf(x) (!_finite(x) && !_isnan(x))
59	+	#endif
60	+
61		#define HONKING_LARGE_VALUE 1.0e10
62
63	+	using namespace std;
64		namespace OpenMD {
65
66	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
66	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
67	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
68
69	+	trialCount_ = 0;
70		failTrialCount_ = 0;
71		failRootCount_ = 0;
72
68	–	int seedValue;
73		Globals * simParams = info->getSimParams();
74	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
75
76	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
77	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
73	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
74	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
75	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
76	<	stringToEnumMap_["Px"] = rnemdPx;
77	<	stringToEnumMap_["Py"] = rnemdPy;
78	<	stringToEnumMap_["Pz"] = rnemdPz;
79	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
76	>	doRNEMD_ = rnemdParams->getUseRNEMD();
77	>	if (!doRNEMD_) return;
78
79	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
79	>	stringToMethod_["Swap"]  = rnemdSwap;
80	>	stringToMethod_["NIVS"]  = rnemdNIVS;
81	>	stringToMethod_["VSS"]   = rnemdVSS;
82	>
83	>	stringToFluxType_["KE"]  = rnemdKE;
84	>	stringToFluxType_["Px"]  = rnemdPx;
85	>	stringToFluxType_["Py"]  = rnemdPy;
86	>	stringToFluxType_["Pz"]  = rnemdPz;
87	>	stringToFluxType_["Pvector"]  = rnemdPvector;
88	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
89	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
90	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
91	>
92	>	runTime_ = simParams->getRunTime();
93	>	statusTime_ = simParams->getStatusTime();
94	>
95	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
96		evaluator_.loadScriptString(rnemdObjectSelection_);
97		seleMan_.setSelectionSet(evaluator_.evaluate());
98
99	+	const string methStr = rnemdParams->getMethod();
100	+	bool hasFluxType = rnemdParams->haveFluxType();
101	+
102	+	string fluxStr;
103	+	if (hasFluxType) {
104	+	fluxStr = rnemdParams->getFluxType();
105	+	} else {
106	+	sprintf(painCave.errMsg,
107	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
108	+	"\twhich must be one of the following values:\n"
109	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
110	+	"\tmust be set to use RNEMD\n");
111	+	painCave.isFatal = 1;
112	+	painCave.severity = OPENMD_ERROR;
113	+	simError();
114	+	}
115	+
116	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
117	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
118	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
119	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
120	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
121	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
122	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
123	+	bool hasOutputFields = rnemdParams->haveOutputFields();
124	+
125	+	map<string, RNEMDMethod>::iterator i;
126	+	i = stringToMethod_.find(methStr);
127	+	if (i != stringToMethod_.end())
128	+	rnemdMethod_ = i->second;
129	+	else {
130	+	sprintf(painCave.errMsg,
131	+	"RNEMD: The current method,\n"
132	+	"\t\t%s is not one of the recognized\n"
133	+	"\texchange methods: Swap, NIVS, or VSS\n",
134	+	methStr.c_str());
135	+	painCave.isFatal = 1;
136	+	painCave.severity = OPENMD_ERROR;
137	+	simError();
138	+	}
139	+
140	+	map<string, RNEMDFluxType>::iterator j;
141	+	j = stringToFluxType_.find(fluxStr);
142	+	if (j != stringToFluxType_.end())
143	+	rnemdFluxType_ = j->second;
144	+	else {
145	+	sprintf(painCave.errMsg,
146	+	"RNEMD: The current fluxType,\n"
147	+	"\t\t%s\n"
148	+	"\tis not one of the recognized flux types.\n",
149	+	fluxStr.c_str());
150	+	painCave.isFatal = 1;
151	+	painCave.severity = OPENMD_ERROR;
152	+	simError();
153	+	}
154	+
155	+	bool methodFluxMismatch = false;
156	+	bool hasCorrectFlux = false;
157	+	switch(rnemdMethod_) {
158	+	case rnemdSwap:
159	+	switch (rnemdFluxType_) {
160	+	case rnemdKE:
161	+	hasCorrectFlux = hasKineticFlux;
162	+	break;
163	+	case rnemdPx:
164	+	case rnemdPy:
165	+	case rnemdPz:
166	+	hasCorrectFlux = hasMomentumFlux;
167	+	break;
168	+	default :
169	+	methodFluxMismatch = true;
170	+	break;
171	+	}
172	+	break;
173	+	case rnemdNIVS:
174	+	switch (rnemdFluxType_) {
175	+	case rnemdKE:
176	+	case rnemdRotKE:
177	+	case rnemdFullKE:
178	+	hasCorrectFlux = hasKineticFlux;
179	+	break;
180	+	case rnemdPx:
181	+	case rnemdPy:
182	+	case rnemdPz:
183	+	hasCorrectFlux = hasMomentumFlux;
184	+	break;
185	+	case rnemdKePx:
186	+	case rnemdKePy:
187	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
188	+	break;
189	+	default:
190	+	methodFluxMismatch = true;
191	+	break;
192	+	}
193	+	break;
194	+	case rnemdVSS:
195	+	switch (rnemdFluxType_) {
196	+	case rnemdKE:
197	+	case rnemdRotKE:
198	+	case rnemdFullKE:
199	+	hasCorrectFlux = hasKineticFlux;
200	+	break;
201	+	case rnemdPx:
202	+	case rnemdPy:
203	+	case rnemdPz:
204	+	hasCorrectFlux = hasMomentumFlux;
205	+	break;
206	+	case rnemdPvector:
207	+	hasCorrectFlux = hasMomentumFluxVector;
208	+	break;
209	+	case rnemdKePx:
210	+	case rnemdKePy:
211	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
212	+	break;
213	+	case rnemdKePvector:
214	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
215	+	break;
216	+	default:
217	+	methodFluxMismatch = true;
218	+	break;
219	+	}
220	+	default:
221	+	break;
222	+	}
223	+
224	+	if (methodFluxMismatch) {
225	+	sprintf(painCave.errMsg,
226	+	"RNEMD: The current method,\n"
227	+	"\t\t%s\n"
228	+	"\tcannot be used with the current flux type, %s\n",
229	+	methStr.c_str(), fluxStr.c_str());
230	+	painCave.isFatal = 1;
231	+	painCave.severity = OPENMD_ERROR;
232	+	simError();
233	+	}
234	+	if (!hasCorrectFlux) {
235	+	sprintf(painCave.errMsg,
236	+	"RNEMD: The current method, %s, and flux type, %s,\n"
237	+	"\tdid not have the correct flux value specified. Options\n"
238	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
239	+	methStr.c_str(), fluxStr.c_str());
240	+	painCave.isFatal = 1;
241	+	painCave.severity = OPENMD_ERROR;
242	+	simError();
243	+	}
244	+
245	+	if (hasKineticFlux) {
246	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
247	+	// into  amu / fs^3:
248	+	kineticFlux_ = rnemdParams->getKineticFlux()
249	+	* PhysicalConstants::energyConvert;
250	+	} else {
251	+	kineticFlux_ = 0.0;
252	+	}
253	+	if (hasMomentumFluxVector) {
254	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
255	+	} else {
256	+	momentumFluxVector_ = V3Zero;
257	+	if (hasMomentumFlux) {
258	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
259	+	switch (rnemdFluxType_) {
260	+	case rnemdPx:
261	+	momentumFluxVector_.x() = momentumFlux;
262	+	break;
263	+	case rnemdPy:
264	+	momentumFluxVector_.y() = momentumFlux;
265	+	break;
266	+	case rnemdPz:
267	+	momentumFluxVector_.z() = momentumFlux;
268	+	break;
269	+	case rnemdKePx:
270	+	momentumFluxVector_.x() = momentumFlux;
271	+	break;
272	+	case rnemdKePy:
273	+	momentumFluxVector_.y() = momentumFlux;
274	+	break;
275	+	default:
276	+	break;
277	+	}
278	+	}
279	+	}
280	+
281		// do some sanity checking
282
283		int selectionCount = seleMan_.getSelectionCount();
#	Line 89 | Line 285 | namespace OpenMD {
285
286		if (selectionCount > nIntegrable) {
287		sprintf(painCave.errMsg,
288	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
288	>	"RNEMD: The current objectSelection,\n"
289		"\t\t%s\n"
290		"\thas resulted in %d selected objects.  However,\n"
291		"\tthe total number of integrable objects in the system\n"
#	Line 99 | Line 295 | namespace OpenMD {
295		rnemdObjectSelection_.c_str(),
296		selectionCount, nIntegrable);
297		painCave.isFatal = 0;
298	+	painCave.severity = OPENMD_WARNING;
299		simError();
103	–
300		}
105	–
106	–	const std::string st = simParams->getRNEMD_exchangeType();
301
302	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
109	<	i = stringToEnumMap_.find(st);
110	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
111	<	if (rnemdType_ == rnemdUnknown) {
112	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
113	<	}
302	>	areaAccumulator_ = new Accumulator();
303
304	<	#ifdef IS_MPI
116	<	if (worldRank == 0) {
117	<	#endif
304	>	nBins_ = rnemdParams->getOutputBins();
305
306	<	std::string rnemdFileName;
307	<	std::string xTempFileName;
308	<	std::string yTempFileName;
309	<	std::string zTempFileName;
310	<	switch(rnemdType_) {
311	<	case rnemdKineticSwap :
312	<	case rnemdKineticScale :
313	<	rnemdFileName = "temperature.log";
306	>	data_.resize(RNEMD::ENDINDEX);
307	>	OutputData z;
308	>	z.units =  "Angstroms";
309	>	z.title =  "Z";
310	>	z.dataType = "RealType";
311	>	z.accumulator.reserve(nBins_);
312	>	for (int i = 0; i < nBins_; i++)
313	>	z.accumulator.push_back( new Accumulator() );
314	>	data_[Z] = z;
315	>	outputMap_["Z"] =  Z;
316	>
317	>	OutputData temperature;
318	>	temperature.units =  "K";
319	>	temperature.title =  "Temperature";
320	>	temperature.dataType = "RealType";
321	>	temperature.accumulator.reserve(nBins_);
322	>	for (int i = 0; i < nBins_; i++)
323	>	temperature.accumulator.push_back( new Accumulator() );
324	>	data_[TEMPERATURE] = temperature;
325	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
326	>
327	>	OutputData velocity;
328	>	velocity.units = "angstroms/fs";
329	>	velocity.title =  "Velocity";
330	>	velocity.dataType = "Vector3d";
331	>	velocity.accumulator.reserve(nBins_);
332	>	for (int i = 0; i < nBins_; i++)
333	>	velocity.accumulator.push_back( new VectorAccumulator() );
334	>	data_[VELOCITY] = velocity;
335	>	outputMap_["VELOCITY"] = VELOCITY;
336	>
337	>	OutputData density;
338	>	density.units =  "g cm^-3";
339	>	density.title =  "Density";
340	>	density.dataType = "RealType";
341	>	density.accumulator.reserve(nBins_);
342	>	for (int i = 0; i < nBins_; i++)
343	>	density.accumulator.push_back( new Accumulator() );
344	>	data_[DENSITY] = density;
345	>	outputMap_["DENSITY"] =  DENSITY;
346	>
347	>	if (hasOutputFields) {
348	>	parseOutputFileFormat(rnemdParams->getOutputFields());
349	>	} else {
350	>	outputMask_.set(Z);
351	>	switch (rnemdFluxType_) {
352	>	case rnemdKE:
353	>	case rnemdRotKE:
354	>	case rnemdFullKE:
355	>	outputMask_.set(TEMPERATURE);
356		break;
357	<	case rnemdPx :
358	<	case rnemdPxScale :
359	<	case rnemdPy :
131	<	case rnemdPyScale :
132	<	rnemdFileName = "momemtum.log";
133	<	xTempFileName = "temperatureX.log";
134	<	yTempFileName = "temperatureY.log";
135	<	zTempFileName = "temperatureZ.log";
136	<	xTempLog_.open(xTempFileName.c_str());
137	<	yTempLog_.open(yTempFileName.c_str());
138	<	zTempLog_.open(zTempFileName.c_str());
357	>	case rnemdPx:
358	>	case rnemdPy:
359	>	outputMask_.set(VELOCITY);
360		break;
361	<	case rnemdPz :
362	<	case rnemdPzScale :
363	<	case rnemdUnknown :
364	<	default :
144	<	rnemdFileName = "rnemd.log";
361	>	case rnemdPz:
362	>	case rnemdPvector:
363	>	outputMask_.set(VELOCITY);
364	>	outputMask_.set(DENSITY);
365		break;
366	+	case rnemdKePx:
367	+	case rnemdKePy:
368	+	outputMask_.set(TEMPERATURE);
369	+	outputMask_.set(VELOCITY);
370	+	break;
371	+	case rnemdKePvector:
372	+	outputMask_.set(TEMPERATURE);
373	+	outputMask_.set(VELOCITY);
374	+	outputMask_.set(DENSITY);
375	+	break;
376	+	default:
377	+	break;
378		}
147	–	rnemdLog_.open(rnemdFileName.c_str());
148	–
149	–	#ifdef IS_MPI
379		}
380	<	#endif
381	<
382	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
154	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
155	<	midBin_ = nBins_ / 2;
156	<	if (simParams->haveRNEMD_logWidth()) {
157	<	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
158	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
159	<	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
160	<	std::cerr << "Automaically set back to default.\n";
161	<	rnemdLogWidth_ = nBins_;
162	<	}
380	>
381	>	if (hasOutputFileName) {
382	>	rnemdFileName_ = rnemdParams->getOutputFileName();
383		} else {
384	<	rnemdLogWidth_ = nBins_;
385	<	}
166	<	valueHist_.resize(rnemdLogWidth_, 0.0);
167	<	valueCount_.resize(rnemdLogWidth_, 0);
168	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
169	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
170	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
384	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
385	>	}
386
387	<	set_RNEMD_exchange_total(0.0);
173	<	if (simParams->haveRNEMD_targetFlux()) {
174	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
175	<	} else {
176	<	set_RNEMD_target_flux(0.0);
177	<	}
387	>	exchangeTime_ = rnemdParams->getExchangeTime();
388
389	<	#ifndef IS_MPI
390	<	if (simParams->haveSeed()) {
181	<	seedValue = simParams->getSeed();
182	<	randNumGen_ = new SeqRandNumGen(seedValue);
183	<	}else {
184	<	randNumGen_ = new SeqRandNumGen();
185	<	}
186	<	#else
187	<	if (simParams->haveSeed()) {
188	<	seedValue = simParams->getSeed();
189	<	randNumGen_ = new ParallelRandNumGen(seedValue);
190	<	}else {
191	<	randNumGen_ = new ParallelRandNumGen();
192	<	}
193	<	#endif
194	<	}
389	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
390	>	Mat3x3d hmat = currentSnap_->getHmat();
391
392	<	RNEMD::~RNEMD() {
393	<	delete randNumGen_;
392	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
393	>	// Lx, Ly = box dimensions in x & y
394	>	// dt = exchange time interval
395	>	// flux = target flux
396	>
397	>	RealType area = currentSnap_->getXYarea();
398	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
399	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
400	>
401	>	// total exchange sums are zeroed out at the beginning:
402	>
403	>	kineticExchange_ = 0.0;
404	>	momentumExchange_ = V3Zero;
405	>
406	>	if (hasSlabWidth)
407	>	slabWidth_ = rnemdParams->getSlabWidth();
408	>	else
409	>	slabWidth_ = hmat(2,2) / 10.0;
410	>
411	>	if (hasSlabACenter)
412	>	slabACenter_ = rnemdParams->getSlabACenter();
413	>	else
414	>	slabACenter_ = 0.0;
415
416	+	if (hasSlabBCenter)
417	+	slabBCenter_ = rnemdParams->getSlabBCenter();
418	+	else
419	+	slabBCenter_ = hmat(2,2) / 2.0;
420	+
421	+	}
422	+
423	+	RNEMD::~RNEMD() {
424	+	if (!doRNEMD_) return;
425		#ifdef IS_MPI
426		if (worldRank == 0) {
427		#endif
428	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
429	<	rnemdLog_.close();
430	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
431	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
432	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	<	xTempLog_.close();
208	<	yTempLog_.close();
209	<	zTempLog_.close();
210	<	}
428	>
429	>	writeOutputFile();
430	>
431	>	rnemdFile_.close();
432	>
433		#ifdef IS_MPI
434		}
435		#endif
436		}
437	+
438	+	bool RNEMD::inSlabA(Vector3d pos) {
439	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
440	+	}
441	+	bool RNEMD::inSlabB(Vector3d pos) {
442	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
443	+	}
444
445		void RNEMD::doSwap() {
446	<
446	>	if (!doRNEMD_) return;
447		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
448		Mat3x3d hmat = currentSnap_->getHmat();
449
#	Line 243 | Line 472 | namespace OpenMD {
472
473		if (usePeriodicBoundaryConditions_)
474		currentSnap_->wrapVector(pos);
475	+	bool inA = inSlabA(pos);
476	+	bool inB = inSlabB(pos);
477
478	<	// which bin is this stuntdouble in?
248	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
249	<
250	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
251	<
252	<
253	<	// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin_) {
478	>	if (inA || inB) {
479
480		RealType mass = sd->getMass();
481		Vector3d vel = sd->getVel();
482		RealType value;
483	<
484	<	switch(rnemdType_) {
485	<	case rnemdKineticSwap :
483	>
484	>	switch(rnemdFluxType_) {
485	>	case rnemdKE :
486
487	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
488	<	vel[2]*vel[2]);
489	<	if (sd->isDirectional()) {
487	>	value = mass * vel.lengthSquare();
488	>
489	>	if (sd->isDirectional()) {
490		Vector3d angMom = sd->getJ();
491		Mat3x3d I = sd->getI();
492
493		if (sd->isLinear()) {
494	<	int i = sd->linearAxis();
495	<	int j = (i + 1) % 3;
496	<	int k = (i + 2) % 3;
497	<	value += angMom[j] * angMom[j] / I(j, j) +
498	<	angMom[k] * angMom[k] / I(k, k);
494	>	int i = sd->linearAxis();
495	>	int j = (i + 1) % 3;
496	>	int k = (i + 2) % 3;
497	>	value += angMom[j] * angMom[j] / I(j, j) +
498	>	angMom[k] * angMom[k] / I(k, k);
499		} else {
500	<	value += angMom[0]*angMom[0]/I(0, 0)
501	<	+ angMom[1]*angMom[1]/I(1, 1)
502	<	+ angMom[2]*angMom[2]/I(2, 2);
500	>	value += angMom[0]*angMom[0]/I(0, 0)
501	>	+ angMom[1]*angMom[1]/I(1, 1)
502	>	+ angMom[2]*angMom[2]/I(2, 2);
503		}
504	<	}
281	<	//make exchangeSum_ comparable between swap & scale
282	<	//temporarily without using energyConvert
283	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
504	>	} //angular momenta exchange enabled
505		value *= 0.5;
506		break;
507		case rnemdPx :
#	Line 296 | Line 517 | namespace OpenMD {
517		break;
518		}
519
520	<	if (binNo == 0) {
520	>	if (inA == 0) {
521		if (!min_found) {
522		min_val = value;
523		min_sd = sd;
#	Line 307 | Line 528 | namespace OpenMD {
528		min_sd = sd;
529		}
530		}
531	<	} else { //midBin_
531	>	} else {
532		if (!max_found) {
533		max_val = value;
534		max_sd = sd;
#	Line 321 | Line 542 | namespace OpenMD {
542		}
543		}
544		}
545	<
545	>
546		#ifdef IS_MPI
547		int nProc, worldRank;
548	<
548	>
549		nProc = MPI::COMM_WORLD.Get_size();
550		worldRank = MPI::COMM_WORLD.Get_rank();
551
#	Line 332 | Line 553 | namespace OpenMD {
553		bool my_max_found = max_found;
554
555		// Even if we didn't find a minimum, did someone else?
556	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
336	<	1, MPI::BOOL, MPI::LAND);
337	<
556	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
557		// Even if we didn't find a maximum, did someone else?
558	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
559	<	1, MPI::BOOL, MPI::LAND);
560	<
561	<	struct {
562	<	RealType val;
563	<	int rank;
564	<	} max_vals, min_vals;
565	<
566	<	if (min_found) {
567	<	if (my_min_found)
558	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
559	>	#endif
560	>
561	>	if (max_found && min_found) {
562	>
563	>	#ifdef IS_MPI
564	>	struct {
565	>	RealType val;
566	>	int rank;
567	>	} max_vals, min_vals;
568	>
569	>	if (my_min_found) {
570		min_vals.val = min_val;
571	<	else
571	>	} else {
572		min_vals.val = HONKING_LARGE_VALUE;
573	<
573	>	}
574		min_vals.rank = worldRank;
575
576		// Who had the minimum?
577		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
578		1, MPI::REALTYPE_INT, MPI::MINLOC);
579		min_val = min_vals.val;
359	–	}
580
581	<	if (max_found) {
362	<	if (my_max_found)
581	>	if (my_max_found) {
582		max_vals.val = max_val;
583	<	else
583	>	} else {
584		max_vals.val = -HONKING_LARGE_VALUE;
585	<
585	>	}
586		max_vals.rank = worldRank;
587
588		// Who had the maximum?
589		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
590		1, MPI::REALTYPE_INT, MPI::MAXLOC);
591		max_val = max_vals.val;
373	–	}
592		#endif
593	<
594	<	if (max_found && min_found) {
595	<	if (min_val< max_val) {
378	<
593	>
594	>	if (min_val < max_val) {
595	>
596		#ifdef IS_MPI
597		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
598		// I have both maximum and minimum, so proceed like a single
599		// processor version:
600		#endif
601	<	// objects to be swapped: velocity & angular velocity
601	>
602		Vector3d min_vel = min_sd->getVel();
603		Vector3d max_vel = max_sd->getVel();
604		RealType temp_vel;
605
606	<	switch(rnemdType_) {
607	<	case rnemdKineticSwap :
606	>	switch(rnemdFluxType_) {
607	>	case rnemdKE :
608		min_sd->setVel(max_vel);
609		max_sd->setVel(min_vel);
610	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
610	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
611		Vector3d min_angMom = min_sd->getJ();
612		Vector3d max_angMom = max_sd->getJ();
613		min_sd->setJ(max_angMom);
614		max_sd->setJ(min_angMom);
615	<	}
615	>	}//angular momenta exchange enabled
616	>	//assumes same rigid body identity
617		break;
618		case rnemdPx :
619		temp_vel = min_vel.x();
#	Line 421 | Line 639 | namespace OpenMD {
639		default :
640		break;
641		}
642	+
643		#ifdef IS_MPI
644		// the rest of the cases only apply in parallel simulations:
645		} else if (max_vals.rank == worldRank) {
#	Line 436 | Line 655 | namespace OpenMD {
655		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
656		min_vals.rank, 0, status);
657
658	<	switch(rnemdType_) {
659	<	case rnemdKineticSwap :
658	>	switch(rnemdFluxType_) {
659	>	case rnemdKE :
660		max_sd->setVel(min_vel);
661	<
661	>	//angular momenta exchange enabled
662		if (max_sd->isDirectional()) {
663		Vector3d min_angMom;
664		Vector3d max_angMom = max_sd->getJ();
665	<
665	>
666		// point-to-point swap of the angular momentum vector
667		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
668		MPI::REALTYPE, min_vals.rank, 1,
669		min_angMom.getArrayPointer(), 3,
670		MPI::REALTYPE, min_vals.rank, 1,
671		status);
672	<
672	>
673		max_sd->setJ(min_angMom);
674	<	}
674	>	}
675		break;
676		case rnemdPx :
677		max_vel.x() = min_vel.x();
#	Line 482 | Line 701 | namespace OpenMD {
701		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
702		max_vals.rank, 0, status);
703
704	<	switch(rnemdType_) {
705	<	case rnemdKineticSwap :
704	>	switch(rnemdFluxType_) {
705	>	case rnemdKE :
706		min_sd->setVel(max_vel);
707	<
707	>	//angular momenta exchange enabled
708		if (min_sd->isDirectional()) {
709		Vector3d min_angMom = min_sd->getJ();
710		Vector3d max_angMom;
711	<
711	>
712		// point-to-point swap of the angular momentum vector
713		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
714		MPI::REALTYPE, max_vals.rank, 1,
715		max_angMom.getArrayPointer(), 3,
716		MPI::REALTYPE, max_vals.rank, 1,
717		status);
718	<
718	>
719		min_sd->setJ(max_angMom);
720		}
721		break;
#	Line 517 | Line 736 | namespace OpenMD {
736		}
737		}
738		#endif
739	<	exchangeSum_ += max_val - min_val;
740	<	} else {
741	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
739	>
740	>	switch(rnemdFluxType_) {
741	>	case rnemdKE:
742	>	kineticExchange_ += max_val - min_val;
743	>	break;
744	>	case rnemdPx:
745	>	momentumExchange_.x() += max_val - min_val;
746	>	break;
747	>	case rnemdPy:
748	>	momentumExchange_.y() += max_val - min_val;
749	>	break;
750	>	case rnemdPz:
751	>	momentumExchange_.z() += max_val - min_val;
752	>	break;
753	>	default:
754	>	break;
755	>	}
756	>	} else {
757	>	sprintf(painCave.errMsg,
758	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
759	>	painCave.isFatal = 0;
760	>	painCave.severity = OPENMD_INFO;
761	>	simError();
762		failTrialCount_++;
763		}
764		} else {
765	<	std::cerr << "exchange NOT performed!\n";
766	<	std::cerr << "at least one of the two slabs empty.\n";
765	>	sprintf(painCave.errMsg,
766	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
767	>	"\twas not present in at least one of the two slabs.\n");
768	>	painCave.isFatal = 0;
769	>	painCave.severity = OPENMD_INFO;
770	>	simError();
771		failTrialCount_++;
772	<	}
530	<
772	>	}
773		}
774
775	<	void RNEMD::doScale() {
776	<
775	>	void RNEMD::doNIVS() {
776	>	if (!doRNEMD_) return;
777		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
778		Mat3x3d hmat = currentSnap_->getHmat();
779
#	Line 541 | Line 783 | namespace OpenMD {
783		StuntDouble* sd;
784		int idx;
785
786	<	std::vector<StuntDouble*> hotBin, coldBin;
786	>	vector<StuntDouble*> hotBin, coldBin;
787
788		RealType Phx = 0.0;
789		RealType Phy = 0.0;
#	Line 549 | Line 791 | namespace OpenMD {
791		RealType Khx = 0.0;
792		RealType Khy = 0.0;
793		RealType Khz = 0.0;
794	+	RealType Khw = 0.0;
795		RealType Pcx = 0.0;
796		RealType Pcy = 0.0;
797		RealType Pcz = 0.0;
798		RealType Kcx = 0.0;
799		RealType Kcy = 0.0;
800		RealType Kcz = 0.0;
801	+	RealType Kcw = 0.0;
802
803		for (sd = seleMan_.beginSelected(selei); sd != NULL;
804		sd = seleMan_.nextSelected(selei)) {
#	Line 569 | Line 813 | namespace OpenMD {
813		currentSnap_->wrapVector(pos);
814
815		// which bin is this stuntdouble in?
816	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
816	>	bool inA = inSlabA(pos);
817	>	bool inB = inSlabB(pos);
818
819	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
820	<
576	<	// if we're in bin 0 or the middleBin
577	<	if (binNo == 0 || binNo == midBin_) {
578	<
819	>	if (inA || inB) {
820	>
821		RealType mass = sd->getMass();
822		Vector3d vel = sd->getVel();
823
824	<	if (binNo == 0) {
824	>	if (inA) {
825		hotBin.push_back(sd);
826		Phx += mass * vel.x();
827		Phy += mass * vel.y();
#	Line 587 | Line 829 | namespace OpenMD {
829		Khx += mass * vel.x() * vel.x();
830		Khy += mass * vel.y() * vel.y();
831		Khz += mass * vel.z() * vel.z();
832	<	} else { //midBin_
832	>	if (sd->isDirectional()) {
833	>	Vector3d angMom = sd->getJ();
834	>	Mat3x3d I = sd->getI();
835	>	if (sd->isLinear()) {
836	>	int i = sd->linearAxis();
837	>	int j = (i + 1) % 3;
838	>	int k = (i + 2) % 3;
839	>	Khw += angMom[j] * angMom[j] / I(j, j) +
840	>	angMom[k] * angMom[k] / I(k, k);
841	>	} else {
842	>	Khw += angMom[0]*angMom[0]/I(0, 0)
843	>	+ angMom[1]*angMom[1]/I(1, 1)
844	>	+ angMom[2]*angMom[2]/I(2, 2);
845	>	}
846	>	}
847	>	} else {
848		coldBin.push_back(sd);
849		Pcx += mass * vel.x();
850		Pcy += mass * vel.y();
#	Line 595 | Line 852 | namespace OpenMD {
852		Kcx += mass * vel.x() * vel.x();
853		Kcy += mass * vel.y() * vel.y();
854		Kcz += mass * vel.z() * vel.z();
855	+	if (sd->isDirectional()) {
856	+	Vector3d angMom = sd->getJ();
857	+	Mat3x3d I = sd->getI();
858	+	if (sd->isLinear()) {
859	+	int i = sd->linearAxis();
860	+	int j = (i + 1) % 3;
861	+	int k = (i + 2) % 3;
862	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
863	+	angMom[k] * angMom[k] / I(k, k);
864	+	} else {
865	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
866	+	+ angMom[1]*angMom[1]/I(1, 1)
867	+	+ angMom[2]*angMom[2]/I(2, 2);
868	+	}
869	+	}
870		}
871		}
872		}
873	<
873	>
874		Khx *= 0.5;
875		Khy *= 0.5;
876		Khz *= 0.5;
877	+	Khw *= 0.5;
878		Kcx *= 0.5;
879		Kcy *= 0.5;
880		Kcz *= 0.5;
881	+	Kcw *= 0.5;
882
883		#ifdef IS_MPI
884		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 617 | Line 891 | namespace OpenMD {
891		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
892		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
893		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
894	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
895	+
896		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
897		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
898		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
899	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
900		#endif
901
902	<	//use coldBin coeff's
902	>	//solve coldBin coeff's first
903		RealType px = Pcx / Phx;
904		RealType py = Pcy / Phy;
905		RealType pz = Pcz / Phz;
906	+	RealType c, x, y, z;
907	+	bool successfulScale = false;
908	+	if ((rnemdFluxType_ == rnemdFullKE) ||
909	+	(rnemdFluxType_ == rnemdRotKE)) {
910	+	//may need sanity check Khw & Kcw > 0
911
912	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
913	<	switch(rnemdType_) {
914	<	case rnemdKineticScale :
915	<	/*used hotBin coeff's & only scale x & y dimensions
916	<	RealType px = Phx / Pcx;
635	<	RealType py = Phy / Pcy;
636	<	a110 = Khy;
637	<	c0 = - Khx - Khy - targetFlux_;
638	<	a000 = Khx;
639	<	a111 = Kcy * py * py
640	<	b11 = -2.0 * Kcy * py * (1.0 + py);
641	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
642	<	b01 = -2.0 * Kcx * px * (1.0 + px);
643	<	a001 = Kcx * px * px;
644	<	*/
912	>	if (rnemdFluxType_ == rnemdFullKE) {
913	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
914	>	} else {
915	>	c = 1.0 - kineticTarget_ / Kcw;
916	>	}
917
918	<	//scale all three dimensions, let c_x = c_y
919	<	a000 = Kcx + Kcy;
920	<	a110 = Kcz;
921	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
922	<	a001 = Khx * px * px + Khy * py * py;
923	<	a111 = Khz * pz * pz;
924	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
925	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
926	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
927	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
928	<	break;
929	<	case rnemdPxScale :
930	<	c = 1 - targetFlux_ / Pcx;
931	<	a000 = Kcy;
932	<	a110 = Kcz;
933	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
934	<	a001 = py * py * Khy;
935	<	a111 = pz * pz * Khz;
936	<	b01 = -2.0 * Khy * py * (1.0 + py);
937	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
938	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
939	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
940	<	break;
941	<	case rnemdPyScale :
942	<	c = 1 - targetFlux_ / Pcy;
943	<	a000 = Kcx;
944	<	a110 = Kcz;
945	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
946	<	a001 = px * px * Khx;
947	<	a111 = pz * pz * Khz;
948	<	b01 = -2.0 * Khx * px * (1.0 + px);
949	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
950	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
951	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
952	<	break;
953	<	case rnemdPzScale ://we don't really do this, do we?
954	<	c = 1 - targetFlux_ / Pcz;
955	<	a000 = Kcx;
956	<	a110 = Kcy;
957	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
958	<	a001 = px * px * Khx;
959	<	a111 = py * py * Khy;
960	<	b01 = -2.0 * Khx * px * (1.0 + px);
961	<	b11 = -2.0 * Khy * py * (1.0 + py);
962	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
963	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
964	<	break;
965	<	default :
966	<	break;
918	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
919	>	c = sqrt(c);
920	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
921	>	//now convert to hotBin coefficient
922	>	RealType w = 0.0;
923	>	if (rnemdFluxType_ ==  rnemdFullKE) {
924	>	x = 1.0 + px * (1.0 - c);
925	>	y = 1.0 + py * (1.0 - c);
926	>	z = 1.0 + pz * (1.0 - c);
927	>	/* more complicated way
928	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
929	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
930	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
931	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
932	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
933	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
934	>	*/
935	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
936	>	(fabs(z - 1.0) < 0.1)) {
937	>	w = 1.0 + (kineticTarget_
938	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
939	>	+ Khz * (1.0 - z * z)) / Khw;
940	>	}//no need to calculate w if x, y or z is out of range
941	>	} else {
942	>	w = 1.0 + kineticTarget_ / Khw;
943	>	}
944	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
945	>	//if w is in the right range, so should be x, y, z.
946	>	vector<StuntDouble*>::iterator sdi;
947	>	Vector3d vel;
948	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
949	>	if (rnemdFluxType_ == rnemdFullKE) {
950	>	vel = (*sdi)->getVel() * c;
951	>	(*sdi)->setVel(vel);
952	>	}
953	>	if ((*sdi)->isDirectional()) {
954	>	Vector3d angMom = (*sdi)->getJ() * c;
955	>	(*sdi)->setJ(angMom);
956	>	}
957	>	}
958	>	w = sqrt(w);
959	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
960	>	//           << "\twh= " << w << endl;
961	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
962	>	if (rnemdFluxType_ == rnemdFullKE) {
963	>	vel = (*sdi)->getVel();
964	>	vel.x() *= x;
965	>	vel.y() *= y;
966	>	vel.z() *= z;
967	>	(*sdi)->setVel(vel);
968	>	}
969	>	if ((*sdi)->isDirectional()) {
970	>	Vector3d angMom = (*sdi)->getJ() * w;
971	>	(*sdi)->setJ(angMom);
972	>	}
973	>	}
974	>	successfulScale = true;
975	>	kineticExchange_ += kineticTarget_;
976	>	}
977	>	}
978	>	} else {
979	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
980	>	switch(rnemdFluxType_) {
981	>	case rnemdKE :
982	>	/* used hotBin coeff's & only scale x & y dimensions
983	>	RealType px = Phx / Pcx;
984	>	RealType py = Phy / Pcy;
985	>	a110 = Khy;
986	>	c0 = - Khx - Khy - kineticTarget_;
987	>	a000 = Khx;
988	>	a111 = Kcy * py * py;
989	>	b11 = -2.0 * Kcy * py * (1.0 + py);
990	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
991	>	b01 = -2.0 * Kcx * px * (1.0 + px);
992	>	a001 = Kcx * px * px;
993	>	*/
994	>	//scale all three dimensions, let c_x = c_y
995	>	a000 = Kcx + Kcy;
996	>	a110 = Kcz;
997	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
998	>	a001 = Khx * px * px + Khy * py * py;
999	>	a111 = Khz * pz * pz;
1000	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1001	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1002	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1003	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1004	>	break;
1005	>	case rnemdPx :
1006	>	c = 1 - momentumTarget_.x() / Pcx;
1007	>	a000 = Kcy;
1008	>	a110 = Kcz;
1009	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1010	>	a001 = py * py * Khy;
1011	>	a111 = pz * pz * Khz;
1012	>	b01 = -2.0 * Khy * py * (1.0 + py);
1013	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1014	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1015	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1016	>	break;
1017	>	case rnemdPy :
1018	>	c = 1 - momentumTarget_.y() / Pcy;
1019	>	a000 = Kcx;
1020	>	a110 = Kcz;
1021	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1022	>	a001 = px * px * Khx;
1023	>	a111 = pz * pz * Khz;
1024	>	b01 = -2.0 * Khx * px * (1.0 + px);
1025	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1026	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1027	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1028	>	break;
1029	>	case rnemdPz ://we don't really do this, do we?
1030	>	c = 1 - momentumTarget_.z() / Pcz;
1031	>	a000 = Kcx;
1032	>	a110 = Kcy;
1033	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1034	>	a001 = px * px * Khx;
1035	>	a111 = py * py * Khy;
1036	>	b01 = -2.0 * Khx * px * (1.0 + px);
1037	>	b11 = -2.0 * Khy * py * (1.0 + py);
1038	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1039	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1040	>	break;
1041	>	default :
1042	>	break;
1043	>	}
1044	>
1045	>	RealType v1 = a000 * a111 - a001 * a110;
1046	>	RealType v2 = a000 * b01;
1047	>	RealType v3 = a000 * b11;
1048	>	RealType v4 = a000 * c1 - a001 * c0;
1049	>	RealType v8 = a110 * b01;
1050	>	RealType v10 = - b01 * c0;
1051	>
1052	>	RealType u0 = v2 * v10 - v4 * v4;
1053	>	RealType u1 = -2.0 * v3 * v4;
1054	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1055	>	RealType u3 = -2.0 * v1 * v3;
1056	>	RealType u4 = - v1 * v1;
1057	>	//rescale coefficients
1058	>	RealType maxAbs = fabs(u0);
1059	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1060	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1061	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1062	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1063	>	u0 /= maxAbs;
1064	>	u1 /= maxAbs;
1065	>	u2 /= maxAbs;
1066	>	u3 /= maxAbs;
1067	>	u4 /= maxAbs;
1068	>	//max_element(start, end) is also available.
1069	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1070	>	poly.setCoefficient(4, u4);
1071	>	poly.setCoefficient(3, u3);
1072	>	poly.setCoefficient(2, u2);
1073	>	poly.setCoefficient(1, u1);
1074	>	poly.setCoefficient(0, u0);
1075	>	vector<RealType> realRoots = poly.FindRealRoots();
1076	>
1077	>	vector<RealType>::iterator ri;
1078	>	RealType r1, r2, alpha0;
1079	>	vector<pair<RealType,RealType> > rps;
1080	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1081	>	r2 = *ri;
1082	>	//check if FindRealRoots() give the right answer
1083	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1084	>	sprintf(painCave.errMsg,
1085	>	"RNEMD Warning: polynomial solve seems to have an error!");
1086	>	painCave.isFatal = 0;
1087	>	simError();
1088	>	failRootCount_++;
1089	>	}
1090	>	//might not be useful w/o rescaling coefficients
1091	>	alpha0 = -c0 - a110 * r2 * r2;
1092	>	if (alpha0 >= 0.0) {
1093	>	r1 = sqrt(alpha0 / a000);
1094	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1095	>	< 1e-6)
1096	>	{ rps.push_back(make_pair(r1, r2)); }
1097	>	if (r1 > 1e-6) { //r1 non-negative
1098	>	r1 = -r1;
1099	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1100	>	< 1e-6)
1101	>	{ rps.push_back(make_pair(r1, r2)); }
1102	>	}
1103	>	}
1104	>	}
1105	>	// Consider combining together the solving pair part w/ the searching
1106	>	// best solution part so that we don't need the pairs vector
1107	>	if (!rps.empty()) {
1108	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1109	>	RealType diff;
1110	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1111	>	vector<pair<RealType,RealType> >::iterator rpi;
1112	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1113	>	r1 = (*rpi).first;
1114	>	r2 = (*rpi).second;
1115	>	switch(rnemdFluxType_) {
1116	>	case rnemdKE :
1117	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1119	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120	>	break;
1121	>	case rnemdPx :
1122	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1124	>	break;
1125	>	case rnemdPy :
1126	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1128	>	break;
1129	>	case rnemdPz :
1130	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1131	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1132	>	default :
1133	>	break;
1134	>	}
1135	>	if (diff < smallestDiff) {
1136	>	smallestDiff = diff;
1137	>	bestPair = *rpi;
1138	>	}
1139	>	}
1140	>	#ifdef IS_MPI
1141	>	if (worldRank == 0) {
1142	>	#endif
1143	>	// sprintf(painCave.errMsg,
1144	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1145	>	//         bestPair.first, bestPair.second);
1146	>	// painCave.isFatal = 0;
1147	>	// painCave.severity = OPENMD_INFO;
1148	>	// simError();
1149	>	#ifdef IS_MPI
1150	>	}
1151	>	#endif
1152	>
1153	>	switch(rnemdFluxType_) {
1154	>	case rnemdKE :
1155	>	x = bestPair.first;
1156	>	y = bestPair.first;
1157	>	z = bestPair.second;
1158	>	break;
1159	>	case rnemdPx :
1160	>	x = c;
1161	>	y = bestPair.first;
1162	>	z = bestPair.second;
1163	>	break;
1164	>	case rnemdPy :
1165	>	x = bestPair.first;
1166	>	y = c;
1167	>	z = bestPair.second;
1168	>	break;
1169	>	case rnemdPz :
1170	>	x = bestPair.first;
1171	>	y = bestPair.second;
1172	>	z = c;
1173	>	break;
1174	>	default :
1175	>	break;
1176	>	}
1177	>	vector<StuntDouble*>::iterator sdi;
1178	>	Vector3d vel;
1179	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1180	>	vel = (*sdi)->getVel();
1181	>	vel.x() *= x;
1182	>	vel.y() *= y;
1183	>	vel.z() *= z;
1184	>	(*sdi)->setVel(vel);
1185	>	}
1186	>	//convert to hotBin coefficient
1187	>	x = 1.0 + px * (1.0 - x);
1188	>	y = 1.0 + py * (1.0 - y);
1189	>	z = 1.0 + pz * (1.0 - z);
1190	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1191	>	vel = (*sdi)->getVel();
1192	>	vel.x() *= x;
1193	>	vel.y() *= y;
1194	>	vel.z() *= z;
1195	>	(*sdi)->setVel(vel);
1196	>	}
1197	>	successfulScale = true;
1198	>	switch(rnemdFluxType_) {
1199	>	case rnemdKE :
1200	>	kineticExchange_ += kineticTarget_;
1201	>	break;
1202	>	case rnemdPx :
1203	>	case rnemdPy :
1204	>	case rnemdPz :
1205	>	momentumExchange_ += momentumTarget_;
1206	>	break;
1207	>	default :
1208	>	break;
1209	>	}
1210	>	}
1211		}
1212	+	if (successfulScale != true) {
1213	+	sprintf(painCave.errMsg,
1214	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1215	+	"\tthe constraint equations may not exist or there may be\n"
1216	+	"\tno selected objects in one or both slabs.\n");
1217	+	painCave.isFatal = 0;
1218	+	painCave.severity = OPENMD_INFO;
1219	+	simError();
1220	+	failTrialCount_++;
1221	+	}
1222	+	}
1223
1224	<	RealType v1 = a000 * a111 - a001 * a110;
1225	<	RealType v2 = a000 * b01;
1226	<	RealType v3 = a000 * b11;
1227	<	RealType v4 = a000 * c1 - a001 * c0;
1228	<	RealType v8 = a110 * b01;
702	<	RealType v10 = - b01 * c0;
1224	>	void RNEMD::doVSS() {
1225	>	if (!doRNEMD_) return;
1226	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1227	>	RealType time = currentSnap_->getTime();
1228	>	Mat3x3d hmat = currentSnap_->getHmat();
1229
1230	<	RealType u0 = v2 * v10 - v4 * v4;
705	<	RealType u1 = -2.0 * v3 * v4;
706	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
707	<	RealType u3 = -2.0 * v1 * v3;
708	<	RealType u4 = - v1 * v1;
709	<	//rescale coefficients
710	<	RealType maxAbs = fabs(u0);
711	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
712	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
713	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
714	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
715	<	u0 /= maxAbs;
716	<	u1 /= maxAbs;
717	<	u2 /= maxAbs;
718	<	u3 /= maxAbs;
719	<	u4 /= maxAbs;
720	<	//max_element(start, end) is also available.
721	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
722	<	poly.setCoefficient(4, u4);
723	<	poly.setCoefficient(3, u3);
724	<	poly.setCoefficient(2, u2);
725	<	poly.setCoefficient(1, u1);
726	<	poly.setCoefficient(0, u0);
727	<	std::vector<RealType> realRoots = poly.FindRealRoots();
1230	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1231
1232	<	std::vector<RealType>::iterator ri;
1233	<	RealType r1, r2, alpha0;
1234	<	std::vector<std::pair<RealType,RealType> > rps;
1235	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1236	<	r2 = *ri;
1237	<	//check if FindRealRoots() give the right answer
1238	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1239	<	sprintf(painCave.errMsg,
1240	<	"RNEMD Warning: polynomial solve seems to have an error!");
1241	<	painCave.isFatal = 0;
1242	<	simError();
1243	<	failRootCount_++;
1244	<	}
1245	<	//might not be useful w/o rescaling coefficients
1246	<	alpha0 = -c0 - a110 * r2 * r2;
1247	<	if (alpha0 >= 0.0) {
1248	<	r1 = sqrt(alpha0 / a000);
1249	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
1250	<	{ rps.push_back(std::make_pair(r1, r2)); }
1251	<	if (r1 > 1e-6) { //r1 non-negative
1252	<	r1 = -r1;
1253	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
1254	<	{ rps.push_back(std::make_pair(r1, r2)); }
1255	<	}
1232	>	int selei;
1233	>	StuntDouble* sd;
1234	>	int idx;
1235	>
1236	>	vector<StuntDouble*> hotBin, coldBin;
1237	>
1238	>	Vector3d Ph(V3Zero);
1239	>	RealType Mh = 0.0;
1240	>	RealType Kh = 0.0;
1241	>	Vector3d Pc(V3Zero);
1242	>	RealType Mc = 0.0;
1243	>	RealType Kc = 0.0;
1244	>
1245	>
1246	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1247	>	sd = seleMan_.nextSelected(selei)) {
1248	>
1249	>	idx = sd->getLocalIndex();
1250	>
1251	>	Vector3d pos = sd->getPos();
1252	>
1253	>	// wrap the stuntdouble's position back into the box:
1254	>
1255	>	if (usePeriodicBoundaryConditions_)
1256	>	currentSnap_->wrapVector(pos);
1257	>
1258	>	// which bin is this stuntdouble in?
1259	>	bool inA = inSlabA(pos);
1260	>	bool inB = inSlabB(pos);
1261	>
1262	>	if (inA || inB) {
1263	>
1264	>	RealType mass = sd->getMass();
1265	>	Vector3d vel = sd->getVel();
1266	>
1267	>	if (inA) {
1268	>	hotBin.push_back(sd);
1269	>	//std::cerr << "before, velocity = " << vel << endl;
1270	>	Ph += mass * vel;
1271	>	//std::cerr << "after, velocity = " << vel << endl;
1272	>	Mh += mass;
1273	>	Kh += mass * vel.lengthSquare();
1274	>	if (rnemdFluxType_ == rnemdFullKE) {
1275	>	if (sd->isDirectional()) {
1276	>	Vector3d angMom = sd->getJ();
1277	>	Mat3x3d I = sd->getI();
1278	>	if (sd->isLinear()) {
1279	>	int i = sd->linearAxis();
1280	>	int j = (i + 1) % 3;
1281	>	int k = (i + 2) % 3;
1282	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1283	>	angMom[k] * angMom[k] / I(k, k);
1284	>	} else {
1285	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1286	>	angMom[1] * angMom[1] / I(1, 1) +
1287	>	angMom[2] * angMom[2] / I(2, 2);
1288	>	}
1289	>	}
1290	>	}
1291	>	} else { //midBin_
1292	>	coldBin.push_back(sd);
1293	>	Pc += mass * vel;
1294	>	Mc += mass;
1295	>	Kc += mass * vel.lengthSquare();
1296	>	if (rnemdFluxType_ == rnemdFullKE) {
1297	>	if (sd->isDirectional()) {
1298	>	Vector3d angMom = sd->getJ();
1299	>	Mat3x3d I = sd->getI();
1300	>	if (sd->isLinear()) {
1301	>	int i = sd->linearAxis();
1302	>	int j = (i + 1) % 3;
1303	>	int k = (i + 2) % 3;
1304	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1305	>	angMom[k] * angMom[k] / I(k, k);
1306	>	} else {
1307	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1308	>	angMom[1] * angMom[1] / I(1, 1) +
1309	>	angMom[2] * angMom[2] / I(2, 2);
1310	>	}
1311	>	}
1312	>	}
1313	>	}
1314		}
1315		}
1316	<	// Consider combininig together the solving pair part w/ the searching
1317	<	// best solution part so that we don't need the pairs vector
1318	<	if (!rps.empty()) {
1319	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1320	<	RealType diff;
1321	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1322	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1323	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
763	<	r1 = (*rpi).first;
764	<	r2 = (*rpi).second;
765	<	switch(rnemdType_) {
766	<	case rnemdKineticScale :
767	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
768	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
769	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
770	<	break;
771	<	case rnemdPxScale :
772	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
773	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
774	<	break;
775	<	case rnemdPyScale :
776	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
777	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
778	<	break;
779	<	case rnemdPzScale :
780	<	default :
781	<	break;
782	<	}
783	<	if (diff < smallestDiff) {
784	<	smallestDiff = diff;
785	<	bestPair = *rpi;
786	<	}
787	<	}
1316	>
1317	>	Kh *= 0.5;
1318	>	Kc *= 0.5;
1319	>
1320	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1321	>	//        << "\tKc= " << Kc << endl;
1322	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1323	>
1324		#ifdef IS_MPI
1325	<	if (worldRank == 0) {
1325	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1326	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1327	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1328	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1329	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1330	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1331		#endif
791	–	std::cerr << "we choose r1 = " << bestPair.first
792	–	<< " and r2 = " << bestPair.second << "\n";
793	–	#ifdef IS_MPI
794	–	}
795	–	#endif
1332
1333	<	RealType x, y, z;
1334	<	switch(rnemdType_) {
1335	<	case rnemdKineticScale :
1336	<	x = bestPair.first;
1337	<	y = bestPair.first;
1338	<	z = bestPair.second;
1339	<	break;
1340	<	case rnemdPxScale :
1341	<	x = c;
1342	<	y = bestPair.first;
1343	<	z = bestPair.second;
1344	<	break;
1345	<	case rnemdPyScale :
1346	<	x = bestPair.first;
1347	<	y = c;
1348	<	z = bestPair.second;
1349	<	break;
1350	<	case rnemdPzScale :
1351	<	x = bestPair.first;
1352	<	y = bestPair.second;
1353	<	z = c;
1354	<	break;
1355	<	default :
1356	<	break;
1357	<	}
1358	<	std::vector<StuntDouble*>::iterator sdi;
1359	<	Vector3d vel;
1360	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1361	<	vel = (*sdi)->getVel();
1362	<	vel.x() *= x;
1363	<	vel.y() *= y;
1364	<	vel.z() *= z;
1365	<	(*sdi)->setVel(vel);
1333	>	bool successfulExchange = false;
1334	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1335	>	Vector3d vc = Pc / Mc;
1336	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1337	>	Vector3d acrec = -momentumTarget_ / Mc;
1338	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1339	>	if (cNumerator > 0.0) {
1340	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1341	>	if (cDenominator > 0.0) {
1342	>	RealType c = sqrt(cNumerator / cDenominator);
1343	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1344	>	Vector3d vh = Ph / Mh;
1345	>	Vector3d ah = momentumTarget_ / Mh + vh;
1346	>	Vector3d ahrec = momentumTarget_ / Mh;
1347	>	RealType hNumerator = Kh + kineticTarget_
1348	>	- 0.5 * Mh * ah.lengthSquare();
1349	>	if (hNumerator > 0.0) {
1350	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1351	>	if (hDenominator > 0.0) {
1352	>	RealType h = sqrt(hNumerator / hDenominator);
1353	>	if ((h > 0.9) && (h < 1.1)) {
1354	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1355	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1356	>	vector<StuntDouble*>::iterator sdi;
1357	>	Vector3d vel;
1358	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1359	>	//vel = (*sdi)->getVel();
1360	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1361	>	(*sdi)->setVel(vel);
1362	>	if (rnemdFluxType_ == rnemdFullKE) {
1363	>	if ((*sdi)->isDirectional()) {
1364	>	Vector3d angMom = (*sdi)->getJ() * c;
1365	>	(*sdi)->setJ(angMom);
1366	>	}
1367	>	}
1368	>	}
1369	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1370	>	//vel = (*sdi)->getVel();
1371	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1372	>	(*sdi)->setVel(vel);
1373	>	if (rnemdFluxType_ == rnemdFullKE) {
1374	>	if ((*sdi)->isDirectional()) {
1375	>	Vector3d angMom = (*sdi)->getJ() * h;
1376	>	(*sdi)->setJ(angMom);
1377	>	}
1378	>	}
1379	>	}
1380	>	successfulExchange = true;
1381	>	kineticExchange_ += kineticTarget_;
1382	>	momentumExchange_ += momentumTarget_;
1383	>	}
1384	>	}
1385	>	}
1386	>	}
1387	>	}
1388		}
1389	<	//convert to hotBin coefficient
1390	<	x = 1.0 + px * (1.0 - x);
1391	<	y = 1.0 + py * (1.0 - y);
1392	<	z = 1.0 + pz * (1.0 - z);
1393	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1394	<	vel = (*sdi)->getVel();
1395	<	vel.x() *= x;
1396	<	vel.y() *= y;
1397	<	vel.z() *= z;
840	<	(*sdi)->setVel(vel);
841	<	}
842	<	exchangeSum_ += targetFlux_;
843	<	//we may want to check whether the exchange has been successful
844	<	} else {
845	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1389	>	}
1390	>	if (successfulExchange != true) {
1391	>	sprintf(painCave.errMsg,
1392	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1393	>	"\tthe constraint equations may not exist or there may be\n"
1394	>	"\tno selected objects in one or both slabs.\n");
1395	>	painCave.isFatal = 0;
1396	>	painCave.severity = OPENMD_INFO;
1397	>	simError();
1398		failTrialCount_++;
1399		}
848	–
1400		}
1401
1402		void RNEMD::doRNEMD() {
1403	<
1404	<	switch(rnemdType_) {
1405	<	case rnemdKineticScale :
1406	<	case rnemdPxScale :
856	<	case rnemdPyScale :
857	<	case rnemdPzScale :
858	<	doScale();
859	<	break;
860	<	case rnemdKineticSwap :
861	<	case rnemdPx :
862	<	case rnemdPy :
863	<	case rnemdPz :
1403	>	if (!doRNEMD_) return;
1404	>	trialCount_++;
1405	>	switch(rnemdMethod_) {
1406	>	case rnemdSwap:
1407		doSwap();
1408		break;
1409	<	case rnemdUnknown :
1409	>	case rnemdNIVS:
1410	>	doNIVS();
1411	>	break;
1412	>	case rnemdVSS:
1413	>	doVSS();
1414	>	break;
1415	>	case rnemdUnkownMethod:
1416		default :
1417		break;
1418		}
1419		}
1420
1421		void RNEMD::collectData() {
1422	<
1422	>	if (!doRNEMD_) return;
1423		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1424		Mat3x3d hmat = currentSnap_->getHmat();
1425
1426	+	areaAccumulator_->add(currentSnap_->getXYarea());
1427	+
1428		seleMan_.setSelectionSet(evaluator_.evaluate());
1429
1430		int selei;
1431		StuntDouble* sd;
1432		int idx;
1433
1434	+	vector<RealType> binMass(nBins_, 0.0);
1435	+	vector<RealType> binPx(nBins_, 0.0);
1436	+	vector<RealType> binPy(nBins_, 0.0);
1437	+	vector<RealType> binPz(nBins_, 0.0);
1438	+	vector<RealType> binKE(nBins_, 0.0);
1439	+	vector<int> binDOF(nBins_, 0);
1440	+	vector<int> binCount(nBins_, 0);
1441	+
1442	+	// alternative approach, track all molecules instead of only those
1443	+	// selected for scaling/swapping:
1444	+	/*
1445	+	SimInfo::MoleculeIterator miter;
1446	+	vector<StuntDouble*>::iterator iiter;
1447	+	Molecule* mol;
1448	+	StuntDouble* sd;
1449	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1450	+	mol = info_->nextMolecule(miter))
1451	+	sd is essentially sd
1452	+	for (sd = mol->beginIntegrableObject(iiter);
1453	+	sd != NULL;
1454	+	sd = mol->nextIntegrableObject(iiter))
1455	+	*/
1456		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1457		sd = seleMan_.nextSelected(selei)) {
1458
#	Line 891 | Line 1464 | namespace OpenMD {
1464
1465		if (usePeriodicBoundaryConditions_)
1466		currentSnap_->wrapVector(pos);
1467	<
1467	>
1468	>
1469		// which bin is this stuntdouble in?
1470		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1471	<
1471	>	// Shift molecules by half a box to have bins start at 0
1472	>	// The modulo operator is used to wrap the case when we are
1473	>	// beyond the end of the bins back to the beginning.
1474		int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1475	<
900	<	if (rnemdLogWidth_ == midBin_ + 1)
901	<	if (binNo > midBin_)
902	<	binNo = nBins_ - binNo;
903	<
1475	>
1476		RealType mass = sd->getMass();
1477		Vector3d vel = sd->getVel();
906	–	RealType value;
907	–	RealType xVal, yVal, zVal;
1478
1479	<	switch(rnemdType_) {
1480	<	case rnemdKineticSwap :
1481	<	case rnemdKineticScale :
1482	<
1483	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1484	<	vel[2]*vel[2]);
1485	<
916	<	valueCount_[binNo] += 3;
917	<	if (sd->isDirectional()) {
918	<	Vector3d angMom = sd->getJ();
919	<	Mat3x3d I = sd->getI();
920	<
921	<	if (sd->isLinear()) {
922	<	int i = sd->linearAxis();
923	<	int j = (i + 1) % 3;
924	<	int k = (i + 2) % 3;
925	<	value += angMom[j] * angMom[j] / I(j, j) +
926	<	angMom[k] * angMom[k] / I(k, k);
1479	>	binCount[binNo]++;
1480	>	binMass[binNo] += mass;
1481	>	binPx[binNo] += mass*vel.x();
1482	>	binPy[binNo] += mass*vel.y();
1483	>	binPz[binNo] += mass*vel.z();
1484	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1485	>	binDOF[binNo] += 3;
1486
1487	<	valueCount_[binNo] +=2;
1487	>	if (sd->isDirectional()) {
1488	>	Vector3d angMom = sd->getJ();
1489	>	Mat3x3d I = sd->getI();
1490	>	if (sd->isLinear()) {
1491	>	int i = sd->linearAxis();
1492	>	int j = (i + 1) % 3;
1493	>	int k = (i + 2) % 3;
1494	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1495	>	angMom[k] * angMom[k] / I(k, k));
1496	>	binDOF[binNo] += 2;
1497	>	} else {
1498	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1499	>	angMom[1] * angMom[1] / I(1, 1) +
1500	>	angMom[2] * angMom[2] / I(2, 2));
1501	>	binDOF[binNo] += 3;
1502	>	}
1503	>	}
1504	>	}
1505	>
1506
1507	<	} else {
1508	<	value += angMom[0]*angMom[0]/I(0, 0)
1509	<	+ angMom[1]*angMom[1]/I(1, 1)
1510	<	+ angMom[2]*angMom[2]/I(2, 2);
1511	<	valueCount_[binNo] +=3;
1512	<	}
1513	<	}
1514	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1507	>	#ifdef IS_MPI
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1509	>	nBins_, MPI::INT, MPI::SUM);
1510	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1511	>	nBins_, MPI::REALTYPE, MPI::SUM);
1512	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1513	>	nBins_, MPI::REALTYPE, MPI::SUM);
1514	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1515	>	nBins_, MPI::REALTYPE, MPI::SUM);
1516	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1517	>	nBins_, MPI::REALTYPE, MPI::SUM);
1518	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1519	>	nBins_, MPI::REALTYPE, MPI::SUM);
1520	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1521	>	nBins_, MPI::INT, MPI::SUM);
1522	>	#endif
1523
1524	<	break;
1525	<	case rnemdPx :
1526	<	case rnemdPxScale :
1527	<	value = mass * vel[0];
1528	<	valueCount_[binNo]++;
1529	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1530	<	/ PhysicalConstants::kb;
1531	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1532	<	/ PhysicalConstants::kb;
1533	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1534	<	/ PhysicalConstants::kb;
1535	<	xTempHist_[binNo] += xVal;
1536	<	yTempHist_[binNo] += yVal;
1537	<	zTempHist_[binNo] += zVal;
1538	<	break;
1539	<	case rnemdPy :
1540	<	case rnemdPyScale :
1541	<	value = mass * vel[1];
1542	<	valueCount_[binNo]++;
1543	<	break;
1544	<	case rnemdPz :
1545	<	case rnemdPzScale :
1546	<	value = mass * vel[2];
1547	<	valueCount_[binNo]++;
1548	<	break;
1549	<	case rnemdUnknown :
1550	<	default :
1551	<	break;
1524	>	Vector3d vel;
1525	>	RealType den;
1526	>	RealType temp;
1527	>	RealType z;
1528	>	for (int i = 0; i < nBins_; i++) {
1529	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1530	>	vel.x() = binPx[i] / binMass[i];
1531	>	vel.y() = binPy[i] / binMass[i];
1532	>	vel.z() = binPz[i] / binMass[i];
1533	>
1534	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1535	>	/ currentSnap_->getVolume() ;
1536	>
1537	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1538	>	PhysicalConstants::energyConvert);
1539	>
1540	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1541	>	if(outputMask_[j]) {
1542	>	switch(j) {
1543	>	case Z:
1544	>	(data_[j].accumulator[i])->add(z);
1545	>	break;
1546	>	case TEMPERATURE:
1547	>	data_[j].accumulator[i]->add(temp);
1548	>	break;
1549	>	case VELOCITY:
1550	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1551	>	break;
1552	>	case DENSITY:
1553	>	data_[j].accumulator[i]->add(den);
1554	>	break;
1555	>	}
1556	>	}
1557		}
968	–	valueHist_[binNo] += value;
1558		}
970	–
1559		}
1560
1561		void RNEMD::getStarted() {
1562	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1563	<	Stats& stat = currentSnap_->statData;
1564	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1562	>	if (!doRNEMD_) return;
1563	>	collectData();
1564	>	writeOutputFile();
1565		}
1566
1567	<	void RNEMD::getStatus() {
1568	<
1569	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1570	<	Stats& stat = currentSnap_->statData;
1571	<	RealType time = currentSnap_->getTime();
1572	<
1573	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1574	<	//or to be more meaningful, define another item as exchangeSum_ / time
1575	<	int j;
1576	<
1567	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1568	>	if (!doRNEMD_) return;
1569	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1570	>
1571	>	while(tokenizer.hasMoreTokens()) {
1572	>	std::string token(tokenizer.nextToken());
1573	>	toUpper(token);
1574	>	OutputMapType::iterator i = outputMap_.find(token);
1575	>	if (i != outputMap_.end()) {
1576	>	outputMask_.set(i->second);
1577	>	} else {
1578	>	sprintf( painCave.errMsg,
1579	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1580	>	"\toutputFileFormat keyword.\n", token.c_str() );
1581	>	painCave.isFatal = 0;
1582	>	painCave.severity = OPENMD_ERROR;
1583	>	simError();
1584	>	}
1585	>	}
1586	>	}
1587	>
1588	>	void RNEMD::writeOutputFile() {
1589	>	if (!doRNEMD_) return;
1590	>
1591		#ifdef IS_MPI
990	–
991	–	// all processors have the same number of bins, and STL vectors pack their
992	–	// arrays, so in theory, this should be safe:
993	–
994	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
995	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
996	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
997	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
998	–	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
999	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1000	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1001	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1002	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1003	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1004	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1005	–	}
1592		// If we're the root node, should we print out the results
1593		int worldRank = MPI::COMM_WORLD.Get_rank();
1594		if (worldRank == 0) {
1595		#endif
1596	<	rnemdLog_ << time;
1597	<	for (j = 0; j < rnemdLogWidth_; j++) {
1598	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1596	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1597	>
1598	>	if( !rnemdFile_ ){
1599	>	sprintf( painCave.errMsg,
1600	>	"Could not open \"%s\" for RNEMD output.\n",
1601	>	rnemdFileName_.c_str());
1602	>	painCave.isFatal = 1;
1603	>	simError();
1604		}
1605	<	rnemdLog_ << "\n";
1606	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1607	<	xTempLog_ << time;
1608	<	for (j = 0; j < rnemdLogWidth_; j++) {
1609	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1605	>
1606	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1607	>
1608	>	RealType time = currentSnap_->getTime();
1609	>	RealType avgArea;
1610	>	areaAccumulator_->getAverage(avgArea);
1611	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1612	>	/ PhysicalConstants::energyConvert;
1613	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1614	>
1615	>	rnemdFile_ << "#######################################################\n";
1616	>	rnemdFile_ << "# RNEMD {\n";
1617	>
1618	>	map<string, RNEMDMethod>::iterator mi;
1619	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1620	>	if ( (*mi).second == rnemdMethod_)
1621	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1622	>	}
1623	>	map<string, RNEMDFluxType>::iterator fi;
1624	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1625	>	if ( (*fi).second == rnemdFluxType_)
1626	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1627	>	}
1628	>
1629	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1630	>
1631	>	rnemdFile_ << "#    objectSelection = \""
1632	>	<< rnemdObjectSelection_ << "\";\n";
1633	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1634	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1635	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1636	>	rnemdFile_ << "# }\n";
1637	>	rnemdFile_ << "#######################################################\n";
1638	>	rnemdFile_ << "# RNEMD report:\n";
1639	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1640	>	rnemdFile_ << "#     target flux:\n";
1641	>	rnemdFile_ << "#         kinetic = "
1642	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1643	>	<< " (kcal/mol/A^2/fs)\n";
1644	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1645	>	<< " (amu/A/fs^2)\n";
1646	>	rnemdFile_ << "#     target one-time exchanges:\n";
1647	>	rnemdFile_ << "#         kinetic = "
1648	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1649	>	<< " (kcal/mol)\n";
1650	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1651	>	<< " (amu*A/fs)\n";
1652	>	rnemdFile_ << "#     actual exchange totals:\n";
1653	>	rnemdFile_ << "#         kinetic = "
1654	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1655	>	<< " (kcal/mol)\n";
1656	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1657	>	<< " (amu*A/fs)\n";
1658	>	rnemdFile_ << "#     actual flux:\n";
1659	>	rnemdFile_ << "#         kinetic = " << Jz
1660	>	<< " (kcal/mol/A^2/fs)\n";
1661	>	rnemdFile_ << "#         momentum = " << JzP
1662	>	<< " (amu/A/fs^2)\n";
1663	>	rnemdFile_ << "#     exchange statistics:\n";
1664	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1665	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1666	>	if (rnemdMethod_ == rnemdNIVS) {
1667	>	rnemdFile_ << "#         NIVS root-check errors = "
1668	>	<< failRootCount_ << "\n";
1669	>	}
1670	>	rnemdFile_ << "#######################################################\n";
1671	>
1672	>
1673	>
1674	>	//write title
1675	>	rnemdFile_ << "#";
1676	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1677	>	if (outputMask_[i]) {
1678	>	rnemdFile_ << "\t" << data_[i].title <<
1679	>	"(" << data_[i].units << ")";
1680	>	// add some extra tabs for column alignment
1681	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1682		}
1683	<	xTempLog_ << "\n";
1684	<	yTempLog_ << time;
1685	<	for (j = 0; j < rnemdLogWidth_; j++) {
1686	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1683	>	}
1684	>	rnemdFile_ << std::endl;
1685	>
1686	>	rnemdFile_.precision(8);
1687	>
1688	>	for (int j = 0; j < nBins_; j++) {
1689	>
1690	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1691	>	if (outputMask_[i]) {
1692	>	if (data_[i].dataType == "RealType")
1693	>	writeReal(i,j);
1694	>	else if (data_[i].dataType == "Vector3d")
1695	>	writeVector(i,j);
1696	>	else {
1697	>	sprintf( painCave.errMsg,
1698	>	"RNEMD found an unknown data type for: %s ",
1699	>	data_[i].title.c_str());
1700	>	painCave.isFatal = 1;
1701	>	simError();
1702	>	}
1703	>	}
1704		}
1705	<	yTempLog_ << "\n";
1706	<	zTempLog_ << time;
1707	<	for (j = 0; j < rnemdLogWidth_; j++) {
1708	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1705	>	rnemdFile_ << std::endl;
1706	>
1707	>	}
1708	>
1709	>	rnemdFile_ << "#######################################################\n";
1710	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1711	>	rnemdFile_ << "#######################################################\n";
1712	>
1713	>
1714	>	for (int j = 0; j < nBins_; j++) {
1715	>	rnemdFile_ << "#";
1716	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1717	>	if (outputMask_[i]) {
1718	>	if (data_[i].dataType == "RealType")
1719	>	writeRealStdDev(i,j);
1720	>	else if (data_[i].dataType == "Vector3d")
1721	>	writeVectorStdDev(i,j);
1722	>	else {
1723	>	sprintf( painCave.errMsg,
1724	>	"RNEMD found an unknown data type for: %s ",
1725	>	data_[i].title.c_str());
1726	>	painCave.isFatal = 1;
1727	>	simError();
1728	>	}
1729	>	}
1730		}
1731	<	zTempLog_ << "\n";
1732	<	}
1731	>	rnemdFile_ << std::endl;
1732	>
1733	>	}
1734	>
1735	>	rnemdFile_.flush();
1736	>	rnemdFile_.close();
1737	>
1738		#ifdef IS_MPI
1739		}
1740		#endif
1741	<	for (j = 0; j < rnemdLogWidth_; j++) {
1742	<	valueCount_[j] = 0;
1743	<	valueHist_[j] = 0.0;
1741	>
1742	>	}
1743	>
1744	>	void RNEMD::writeReal(int index, unsigned int bin) {
1745	>	if (!doRNEMD_) return;
1746	>	assert(index >=0 && index < ENDINDEX);
1747	>	assert(bin < nBins_);
1748	>	RealType s;
1749	>
1750	>	data_[index].accumulator[bin]->getAverage(s);
1751	>
1752	>	if (! isinf(s) && ! isnan(s)) {
1753	>	rnemdFile_ << "\t" << s;
1754	>	} else{
1755	>	sprintf( painCave.errMsg,
1756	>	"RNEMD detected a numerical error writing: %s for bin %d",
1757	>	data_[index].title.c_str(), bin);
1758	>	painCave.isFatal = 1;
1759	>	simError();
1760	>	}
1761	>	}
1762	>
1763	>	void RNEMD::writeVector(int index, unsigned int bin) {
1764	>	if (!doRNEMD_) return;
1765	>	assert(index >=0 && index < ENDINDEX);
1766	>	assert(bin < nBins_);
1767	>	Vector3d s;
1768	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1769	>	if (isinf(s[0]) || isnan(s[0]) ||
1770	>	isinf(s[1]) || isnan(s[1]) ||
1771	>	isinf(s[2]) || isnan(s[2]) ) {
1772	>	sprintf( painCave.errMsg,
1773	>	"RNEMD detected a numerical error writing: %s for bin %d",
1774	>	data_[index].title.c_str(), bin);
1775	>	painCave.isFatal = 1;
1776	>	simError();
1777	>	} else {
1778	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1779		}
1780	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1781	<	for (j = 0; j < rnemdLogWidth_; j++) {
1782	<	xTempHist_[j] = 0.0;
1783	<	yTempHist_[j] = 0.0;
1784	<	zTempHist_[j] = 0.0;
1785	<	}
1780	>	}
1781	>
1782	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1783	>	if (!doRNEMD_) return;
1784	>	assert(index >=0 && index < ENDINDEX);
1785	>	assert(bin < nBins_);
1786	>	RealType s;
1787	>
1788	>	data_[index].accumulator[bin]->getStdDev(s);
1789	>
1790	>	if (! isinf(s) && ! isnan(s)) {
1791	>	rnemdFile_ << "\t" << s;
1792	>	} else{
1793	>	sprintf( painCave.errMsg,
1794	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1795	>	data_[index].title.c_str(), bin);
1796	>	painCave.isFatal = 1;
1797	>	simError();
1798	>	}
1799		}
1800	+
1801	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1802	+	if (!doRNEMD_) return;
1803	+	assert(index >=0 && index < ENDINDEX);
1804	+	assert(bin < nBins_);
1805	+	Vector3d s;
1806	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1807	+	if (isinf(s[0]) || isnan(s[0]) ||
1808	+	isinf(s[1]) || isnan(s[1]) ||
1809	+	isinf(s[2]) || isnan(s[2]) ) {
1810	+	sprintf( painCave.errMsg,
1811	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1812	+	data_[index].title.c_str(), bin);
1813	+	painCave.isFatal = 1;
1814	+	simError();
1815	+	} else {
1816	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1817	+	}
1818	+	}
1819		}
1820	+

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