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

Comparing:
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 2071 by gezelter, Sat Mar 7 21:41:51 2015 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 "integrators/RNEMD.hpp"
46	>	#include <sstream>
47	>	#include <string>
48	>
49	>	#include "rnemd/RNEMD.hpp"
50		#include "math/Vector3.hpp"
51	+	#include "math/Vector.hpp"
52		#include "math/SquareMatrix3.hpp"
53		#include "math/Polynomial.hpp"
54		#include "primitives/Molecule.hpp"
55		#include "primitives/StuntDouble.hpp"
56		#include "utils/PhysicalConstants.hpp"
57		#include "utils/Tuple.hpp"
58	+	#include "brains/Thermo.hpp"
59	+	#include "math/ConvexHull.hpp"
60
61	<	#ifndef IS_MPI
62	<	#include "math/SeqRandNumGen.hpp"
63	<	#else
55	<	#include <mpi.h>
56	<	#include "math/ParallelRandNumGen.hpp"
61	>	#ifdef _MSC_VER
62	>	#define isnan(x) _isnan((x))
63	>	#define isinf(x) (!_finite(x) && !_isnan(x))
64		#endif
65
66		#define HONKING_LARGE_VALUE 1.0e10
67
68	+	using namespace std;
69		namespace OpenMD {
70
71	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
71	>	RNEMD::RNEMD(SimInfo* info) : info_(info),
72	>	evaluator_(info_), seleMan_(info_),
73	>	evaluatorA_(info_), seleManA_(info_),
74	>	evaluatorB_(info_), seleManB_(info_),
75	>	commonA_(info_), commonB_(info_),
76	>	usePeriodicBoundaryConditions_(info_->getSimParams()->getUsePeriodicBoundaryConditions()),
77	>	hasDividingArea_(false),
78	>	hasData_(false) {
79
80	+	trialCount_ = 0;
81		failTrialCount_ = 0;
82		failRootCount_ = 0;
83
84	<	int seedValue;
85	<	Globals * simParams = info->getSimParams();
84	>	Globals* simParams = info->getSimParams();
85	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
86
87	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
88	<	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;
87	>	doRNEMD_ = rnemdParams->getUseRNEMD();
88	>	if (!doRNEMD_) return;
89
90	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
91	<	evaluator_.loadScriptString(rnemdObjectSelection_);
92	<	seleMan_.setSelectionSet(evaluator_.evaluate());
90	>	stringToMethod_["Swap"]  = rnemdSwap;
91	>	stringToMethod_["NIVS"]  = rnemdNIVS;
92	>	stringToMethod_["VSS"]   = rnemdVSS;
93
94	<	// do some sanity checking
94	>	stringToFluxType_["KE"]  = rnemdKE;
95	>	stringToFluxType_["Px"]  = rnemdPx;
96	>	stringToFluxType_["Py"]  = rnemdPy;
97	>	stringToFluxType_["Pz"]  = rnemdPz;
98	>	stringToFluxType_["Pvector"]  = rnemdPvector;
99	>	stringToFluxType_["Lx"]  = rnemdLx;
100	>	stringToFluxType_["Ly"]  = rnemdLy;
101	>	stringToFluxType_["Lz"]  = rnemdLz;
102	>	stringToFluxType_["Lvector"]  = rnemdLvector;
103	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
104	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
105	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
106	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
107	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
108	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
109	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
110
111	<	int selectionCount = seleMan_.getSelectionCount();
112	<	int nIntegrable = info->getNGlobalIntegrableObjects();
111	>	runTime_ = simParams->getRunTime();
112	>	statusTime_ = simParams->getStatusTime();
113
114	+	const string methStr = rnemdParams->getMethod();
115	+	bool hasFluxType = rnemdParams->haveFluxType();
116	+
117	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
118	+
119	+	string fluxStr;
120	+	if (hasFluxType) {
121	+	fluxStr = rnemdParams->getFluxType();
122	+	} else {
123	+	sprintf(painCave.errMsg,
124	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
125	+	"\twhich must be one of the following values:\n"
126	+	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
127	+	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
128	+	"\tmust be set to use RNEMD\n");
129	+	painCave.isFatal = 1;
130	+	painCave.severity = OPENMD_ERROR;
131	+	simError();
132	+	}
133	+
134	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
135	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
136	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
137	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
138	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
139	+	hasSelectionA_ = rnemdParams->haveSelectionA();
140	+	hasSelectionB_ = rnemdParams->haveSelectionB();
141	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
142	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
143	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
144	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
145	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
146	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
147	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
148	+	bool hasOutputFields = rnemdParams->haveOutputFields();
149	+
150	+	map<string, RNEMDMethod>::iterator i;
151	+	i = stringToMethod_.find(methStr);
152	+	if (i != stringToMethod_.end())
153	+	rnemdMethod_ = i->second;
154	+	else {
155	+	sprintf(painCave.errMsg,
156	+	"RNEMD: The current method,\n"
157	+	"\t\t%s is not one of the recognized\n"
158	+	"\texchange methods: Swap, NIVS, or VSS\n",
159	+	methStr.c_str());
160	+	painCave.isFatal = 1;
161	+	painCave.severity = OPENMD_ERROR;
162	+	simError();
163	+	}
164	+
165	+	map<string, RNEMDFluxType>::iterator j;
166	+	j = stringToFluxType_.find(fluxStr);
167	+	if (j != stringToFluxType_.end())
168	+	rnemdFluxType_ = j->second;
169	+	else {
170	+	sprintf(painCave.errMsg,
171	+	"RNEMD: The current fluxType,\n"
172	+	"\t\t%s\n"
173	+	"\tis not one of the recognized flux types.\n",
174	+	fluxStr.c_str());
175	+	painCave.isFatal = 1;
176	+	painCave.severity = OPENMD_ERROR;
177	+	simError();
178	+	}
179	+
180	+	bool methodFluxMismatch = false;
181	+	bool hasCorrectFlux = false;
182	+	switch(rnemdMethod_) {
183	+	case rnemdSwap:
184	+	switch (rnemdFluxType_) {
185	+	case rnemdKE:
186	+	hasCorrectFlux = hasKineticFlux;
187	+	break;
188	+	case rnemdPx:
189	+	case rnemdPy:
190	+	case rnemdPz:
191	+	hasCorrectFlux = hasMomentumFlux;
192	+	break;
193	+	default :
194	+	methodFluxMismatch = true;
195	+	break;
196	+	}
197	+	break;
198	+	case rnemdNIVS:
199	+	switch (rnemdFluxType_) {
200	+	case rnemdKE:
201	+	case rnemdRotKE:
202	+	case rnemdFullKE:
203	+	hasCorrectFlux = hasKineticFlux;
204	+	break;
205	+	case rnemdPx:
206	+	case rnemdPy:
207	+	case rnemdPz:
208	+	hasCorrectFlux = hasMomentumFlux;
209	+	break;
210	+	case rnemdKePx:
211	+	case rnemdKePy:
212	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
213	+	break;
214	+	default:
215	+	methodFluxMismatch = true;
216	+	break;
217	+	}
218	+	break;
219	+	case rnemdVSS:
220	+	switch (rnemdFluxType_) {
221	+	case rnemdKE:
222	+	case rnemdRotKE:
223	+	case rnemdFullKE:
224	+	hasCorrectFlux = hasKineticFlux;
225	+	break;
226	+	case rnemdPx:
227	+	case rnemdPy:
228	+	case rnemdPz:
229	+	hasCorrectFlux = hasMomentumFlux;
230	+	break;
231	+	case rnemdLx:
232	+	case rnemdLy:
233	+	case rnemdLz:
234	+	hasCorrectFlux = hasAngularMomentumFlux;
235	+	break;
236	+	case rnemdPvector:
237	+	hasCorrectFlux = hasMomentumFluxVector;
238	+	break;
239	+	case rnemdLvector:
240	+	hasCorrectFlux = hasAngularMomentumFluxVector;
241	+	break;
242	+	case rnemdKePx:
243	+	case rnemdKePy:
244	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
245	+	break;
246	+	case rnemdKeLx:
247	+	case rnemdKeLy:
248	+	case rnemdKeLz:
249	+	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
250	+	break;
251	+	case rnemdKePvector:
252	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
253	+	break;
254	+	case rnemdKeLvector:
255	+	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
256	+	break;
257	+	default:
258	+	methodFluxMismatch = true;
259	+	break;
260	+	}
261	+	default:
262	+	break;
263	+	}
264	+
265	+	if (methodFluxMismatch) {
266	+	sprintf(painCave.errMsg,
267	+	"RNEMD: The current method,\n"
268	+	"\t\t%s\n"
269	+	"\tcannot be used with the current flux type, %s\n",
270	+	methStr.c_str(), fluxStr.c_str());
271	+	painCave.isFatal = 1;
272	+	painCave.severity = OPENMD_ERROR;
273	+	simError();
274	+	}
275	+	if (!hasCorrectFlux) {
276	+	sprintf(painCave.errMsg,
277	+	"RNEMD: The current method, %s, and flux type, %s,\n"
278	+	"\tdid not have the correct flux value specified. Options\n"
279	+	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
280	+	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
281	+	methStr.c_str(), fluxStr.c_str());
282	+	painCave.isFatal = 1;
283	+	painCave.severity = OPENMD_ERROR;
284	+	simError();
285	+	}
286	+
287	+	if (hasKineticFlux) {
288	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
289	+	// into  amu / fs^3:
290	+	kineticFlux_ = rnemdParams->getKineticFlux()
291	+	* PhysicalConstants::energyConvert;
292	+	} else {
293	+	kineticFlux_ = 0.0;
294	+	}
295	+	if (hasMomentumFluxVector) {
296	+	std::vector<RealType> mf = rnemdParams->getMomentumFluxVector();
297	+	if (mf.size() != 3) {
298	+	sprintf(painCave.errMsg,
299	+	"RNEMD: Incorrect number of parameters specified for momentumFluxVector.\n"
300	+	"\tthere should be 3 parameters, but %lu were specified.\n",
301	+	mf.size());
302	+	painCave.isFatal = 1;
303	+	simError();
304	+	}
305	+	momentumFluxVector_.x() = mf[0];
306	+	momentumFluxVector_.y() = mf[1];
307	+	momentumFluxVector_.z() = mf[2];
308	+	} else {
309	+	momentumFluxVector_ = V3Zero;
310	+	if (hasMomentumFlux) {
311	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
312	+	switch (rnemdFluxType_) {
313	+	case rnemdPx:
314	+	momentumFluxVector_.x() = momentumFlux;
315	+	break;
316	+	case rnemdPy:
317	+	momentumFluxVector_.y() = momentumFlux;
318	+	break;
319	+	case rnemdPz:
320	+	momentumFluxVector_.z() = momentumFlux;
321	+	break;
322	+	case rnemdKePx:
323	+	momentumFluxVector_.x() = momentumFlux;
324	+	break;
325	+	case rnemdKePy:
326	+	momentumFluxVector_.y() = momentumFlux;
327	+	break;
328	+	default:
329	+	break;
330	+	}
331	+	}
332	+	}
333	+	if (hasAngularMomentumFluxVector) {
334	+	std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
335	+	if (amf.size() != 3) {
336	+	sprintf(painCave.errMsg,
337	+	"RNEMD: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
338	+	"\tthere should be 3 parameters, but %lu were specified.\n",
339	+	amf.size());
340	+	painCave.isFatal = 1;
341	+	simError();
342	+	}
343	+	angularMomentumFluxVector_.x() = amf[0];
344	+	angularMomentumFluxVector_.y() = amf[1];
345	+	angularMomentumFluxVector_.z() = amf[2];
346	+	} else {
347	+	angularMomentumFluxVector_ = V3Zero;
348	+	if (hasAngularMomentumFlux) {
349	+	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
350	+	switch (rnemdFluxType_) {
351	+	case rnemdLx:
352	+	angularMomentumFluxVector_.x() = angularMomentumFlux;
353	+	break;
354	+	case rnemdLy:
355	+	angularMomentumFluxVector_.y() = angularMomentumFlux;
356	+	break;
357	+	case rnemdLz:
358	+	angularMomentumFluxVector_.z() = angularMomentumFlux;
359	+	break;
360	+	case rnemdKeLx:
361	+	angularMomentumFluxVector_.x() = angularMomentumFlux;
362	+	break;
363	+	case rnemdKeLy:
364	+	angularMomentumFluxVector_.y() = angularMomentumFlux;
365	+	break;
366	+	case rnemdKeLz:
367	+	angularMomentumFluxVector_.z() = angularMomentumFlux;
368	+	break;
369	+	default:
370	+	break;
371	+	}
372	+	}
373	+	}
374	+
375	+	if (hasCoordinateOrigin) {
376	+	std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
377	+	if (co.size() != 3) {
378	+	sprintf(painCave.errMsg,
379	+	"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
380	+	"\tthere should be 3 parameters, but %lu were specified.\n",
381	+	co.size());
382	+	painCave.isFatal = 1;
383	+	simError();
384	+	}
385	+	coordinateOrigin_.x() = co[0];
386	+	coordinateOrigin_.y() = co[1];
387	+	coordinateOrigin_.z() = co[2];
388	+	} else {
389	+	coordinateOrigin_ = V3Zero;
390	+	}
391	+
392	+	// do some sanity checking
393	+
394	+	int selectionCount = seleMan_.getSelectionCount();
395	+	int nIntegrable = info->getNGlobalIntegrableObjects();
396		if (selectionCount > nIntegrable) {
397		sprintf(painCave.errMsg,
398	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
398	>	"RNEMD: The current objectSelection,\n"
399		"\t\t%s\n"
400		"\thas resulted in %d selected objects.  However,\n"
401		"\tthe total number of integrable objects in the system\n"
#	Line 99 | Line 405 | namespace OpenMD {
405		rnemdObjectSelection_.c_str(),
406		selectionCount, nIntegrable);
407		painCave.isFatal = 0;
408	+	painCave.severity = OPENMD_WARNING;
409		simError();
103	–
410		}
411
412	<	const std::string st = simParams->getRNEMD_exchangeType();
413	<
414	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
415	<	i = stringToEnumMap_.find(st);
416	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
417	<	if (rnemdType_ == rnemdUnknown) {
418	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
419	<	}
420	<
421	<	#ifdef IS_MPI
422	<	if (worldRank == 0) {
423	<	#endif
424	<
425	<	std::string rnemdFileName;
426	<	std::string xTempFileName;
427	<	std::string yTempFileName;
428	<	std::string zTempFileName;
429	<	switch(rnemdType_) {
430	<	case rnemdKineticSwap :
431	<	case rnemdKineticScale :
432	<	rnemdFileName = "temperature.log";
412	>	areaAccumulator_ = new Accumulator();
413	>
414	>	nBins_ = rnemdParams->getOutputBins();
415	>	binWidth_ = rnemdParams->getOutputBinWidth();
416	>
417	>	data_.resize(RNEMD::ENDINDEX);
418	>	OutputData z;
419	>	z.units =  "Angstroms";
420	>	z.title =  "Z";
421	>	z.dataType = "RealType";
422	>	z.accumulator.reserve(nBins_);
423	>	for (int i = 0; i < nBins_; i++)
424	>	z.accumulator.push_back( new Accumulator() );
425	>	data_[Z] = z;
426	>	outputMap_["Z"] =  Z;
427	>
428	>	OutputData r;
429	>	r.units =  "Angstroms";
430	>	r.title =  "R";
431	>	r.dataType = "RealType";
432	>	r.accumulator.reserve(nBins_);
433	>	for (int i = 0; i < nBins_; i++)
434	>	r.accumulator.push_back( new Accumulator() );
435	>	data_[R] = r;
436	>	outputMap_["R"] =  R;
437	>
438	>	OutputData temperature;
439	>	temperature.units =  "K";
440	>	temperature.title =  "Temperature";
441	>	temperature.dataType = "RealType";
442	>	temperature.accumulator.reserve(nBins_);
443	>	for (int i = 0; i < nBins_; i++)
444	>	temperature.accumulator.push_back( new Accumulator() );
445	>	data_[TEMPERATURE] = temperature;
446	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
447	>
448	>	OutputData velocity;
449	>	velocity.units = "angstroms/fs";
450	>	velocity.title =  "Velocity";
451	>	velocity.dataType = "Vector3d";
452	>	velocity.accumulator.reserve(nBins_);
453	>	for (int i = 0; i < nBins_; i++)
454	>	velocity.accumulator.push_back( new VectorAccumulator() );
455	>	data_[VELOCITY] = velocity;
456	>	outputMap_["VELOCITY"] = VELOCITY;
457	>
458	>	OutputData angularVelocity;
459	>	angularVelocity.units = "angstroms^2/fs";
460	>	angularVelocity.title =  "AngularVelocity";
461	>	angularVelocity.dataType = "Vector3d";
462	>	angularVelocity.accumulator.reserve(nBins_);
463	>	for (int i = 0; i < nBins_; i++)
464	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
465	>	data_[ANGULARVELOCITY] = angularVelocity;
466	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
467	>
468	>	OutputData density;
469	>	density.units =  "g cm^-3";
470	>	density.title =  "Density";
471	>	density.dataType = "RealType";
472	>	density.accumulator.reserve(nBins_);
473	>	for (int i = 0; i < nBins_; i++)
474	>	density.accumulator.push_back( new Accumulator() );
475	>	data_[DENSITY] = density;
476	>	outputMap_["DENSITY"] =  DENSITY;
477	>
478	>	if (hasOutputFields) {
479	>	parseOutputFileFormat(rnemdParams->getOutputFields());
480	>	} else {
481	>	if (usePeriodicBoundaryConditions_)
482	>	outputMask_.set(Z);
483	>	else
484	>	outputMask_.set(R);
485	>	switch (rnemdFluxType_) {
486	>	case rnemdKE:
487	>	case rnemdRotKE:
488	>	case rnemdFullKE:
489	>	outputMask_.set(TEMPERATURE);
490		break;
491	<	case rnemdPx :
492	<	case rnemdPxScale :
493	<	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());
491	>	case rnemdPx:
492	>	case rnemdPy:
493	>	outputMask_.set(VELOCITY);
494		break;
495	<	case rnemdPz :
496	<	case rnemdPzScale :
497	<	case rnemdUnknown :
498	<	default :
144	<	rnemdFileName = "rnemd.log";
495	>	case rnemdPz:
496	>	case rnemdPvector:
497	>	outputMask_.set(VELOCITY);
498	>	outputMask_.set(DENSITY);
499		break;
500	+	case rnemdLx:
501	+	case rnemdLy:
502	+	case rnemdLz:
503	+	case rnemdLvector:
504	+	outputMask_.set(ANGULARVELOCITY);
505	+	break;
506	+	case rnemdKeLx:
507	+	case rnemdKeLy:
508	+	case rnemdKeLz:
509	+	case rnemdKeLvector:
510	+	outputMask_.set(TEMPERATURE);
511	+	outputMask_.set(ANGULARVELOCITY);
512	+	break;
513	+	case rnemdKePx:
514	+	case rnemdKePy:
515	+	outputMask_.set(TEMPERATURE);
516	+	outputMask_.set(VELOCITY);
517	+	break;
518	+	case rnemdKePvector:
519	+	outputMask_.set(TEMPERATURE);
520	+	outputMask_.set(VELOCITY);
521	+	outputMask_.set(DENSITY);
522	+	break;
523	+	default:
524	+	break;
525		}
147	–	rnemdLog_.open(rnemdFileName.c_str());
148	–
149	–	#ifdef IS_MPI
526		}
527	<	#endif
528	<
529	<	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	<	}
527	>
528	>	if (hasOutputFileName) {
529	>	rnemdFileName_ = rnemdParams->getOutputFileName();
530		} else {
531	<	rnemdLogWidth_ = nBins_;
532	<	}
533	<	valueHist_.resize(rnemdLogWidth_, 0.0);
534	<	valueCount_.resize(rnemdLogWidth_, 0);
535	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
536	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
537	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
538	<
539	<	set_RNEMD_exchange_total(0.0);
540	<	if (simParams->haveRNEMD_targetFlux()) {
541	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
542	<	} else {
543	<	set_RNEMD_target_flux(0.0);
531	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
532	>	}
533	>
534	>	exchangeTime_ = rnemdParams->getExchangeTime();
535	>
536	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
537	>	// total exchange sums are zeroed out at the beginning:
538	>
539	>	kineticExchange_ = 0.0;
540	>	momentumExchange_ = V3Zero;
541	>	angularMomentumExchange_ = V3Zero;
542	>
543	>	std::ostringstream selectionAstream;
544	>	std::ostringstream selectionBstream;
545	>
546	>	if (hasSelectionA_) {
547	>	selectionA_ = rnemdParams->getSelectionA();
548	>	} else {
549	>	if (usePeriodicBoundaryConditions_) {
550	>	Mat3x3d hmat = currentSnap_->getHmat();
551	>
552	>	if (hasSlabWidth)
553	>	slabWidth_ = rnemdParams->getSlabWidth();
554	>	else
555	>	slabWidth_ = hmat(2,2) / 10.0;
556	>
557	>	if (hasSlabACenter)
558	>	slabACenter_ = rnemdParams->getSlabACenter();
559	>	else
560	>	slabACenter_ = 0.0;
561	>
562	>	selectionAstream << "select wrappedz > "
563	>	<< slabACenter_ - 0.5*slabWidth_
564	>	<<  " && wrappedz < "
565	>	<< slabACenter_ + 0.5*slabWidth_;
566	>	selectionA_ = selectionAstream.str();
567	>	} else {
568	>	if (hasSphereARadius)
569	>	sphereARadius_ = rnemdParams->getSphereARadius();
570	>	else {
571	>	// use an initial guess to the size of the inner slab to be 1/10 the
572	>	// radius of an approximately spherical hull:
573	>	Thermo thermo(info);
574	>	RealType hVol = thermo.getHullVolume();
575	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
576	>	}
577	>	selectionAstream << "select r < " << sphereARadius_;
578	>	selectionA_ = selectionAstream.str();
579	>	}
580		}
581	<
582	<	#ifndef IS_MPI
583	<	if (simParams->haveSeed()) {
584	<	seedValue = simParams->getSeed();
585	<	randNumGen_ = new SeqRandNumGen(seedValue);
586	<	}else {
587	<	randNumGen_ = new SeqRandNumGen();
588	<	}
589	<	#else
590	<	if (simParams->haveSeed()) {
591	<	seedValue = simParams->getSeed();
592	<	randNumGen_ = new ParallelRandNumGen(seedValue);
593	<	}else {
594	<	randNumGen_ = new ParallelRandNumGen();
595	<	}
596	<	#endif
581	>
582	>	if (hasSelectionB_) {
583	>	selectionB_ = rnemdParams->getSelectionB();
584	>
585	>	} else {
586	>	if (usePeriodicBoundaryConditions_) {
587	>	Mat3x3d hmat = currentSnap_->getHmat();
588	>
589	>	if (hasSlabWidth)
590	>	slabWidth_ = rnemdParams->getSlabWidth();
591	>	else
592	>	slabWidth_ = hmat(2,2) / 10.0;
593	>
594	>	if (hasSlabBCenter)
595	>	slabBCenter_ = rnemdParams->getSlabBCenter();
596	>	else
597	>	slabBCenter_ = hmat(2,2) / 2.0;
598	>
599	>	selectionBstream << "select wrappedz > "
600	>	<< slabBCenter_ - 0.5*slabWidth_
601	>	<<  " && wrappedz < "
602	>	<< slabBCenter_ + 0.5*slabWidth_;
603	>	selectionB_ = selectionBstream.str();
604	>	} else {
605	>	if (hasSphereBRadius_) {
606	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
607	>	selectionBstream << "select r > " << sphereBRadius_;
608	>	selectionB_ = selectionBstream.str();
609	>	} else {
610	>	selectionB_ = "select hull";
611	>	BisHull_ = true;
612	>	hasSelectionB_ = true;
613	>	}
614	>	}
615	>	}
616	>
617	>
618	>	// object evaluator:
619	>	evaluator_.loadScriptString(rnemdObjectSelection_);
620	>	seleMan_.setSelectionSet(evaluator_.evaluate());
621	>	evaluatorA_.loadScriptString(selectionA_);
622	>	evaluatorB_.loadScriptString(selectionB_);
623	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
624	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
625	>	commonA_ = seleManA_ & seleMan_;
626	>	commonB_ = seleManB_ & seleMan_;
627		}
628
196	–	RNEMD::~RNEMD() {
197	–	delete randNumGen_;
629
630	+	RNEMD::~RNEMD() {
631	+	if (!doRNEMD_) return;
632		#ifdef IS_MPI
633		if (worldRank == 0) {
634		#endif
635	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
636	<	rnemdLog_.close();
637	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
638	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
639	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	<	xTempLog_.close();
208	<	yTempLog_.close();
209	<	zTempLog_.close();
210	<	}
635	>
636	>	writeOutputFile();
637	>
638	>	rnemdFile_.close();
639	>
640		#ifdef IS_MPI
641		}
642		#endif
643	+
644	+	// delete all of the objects we created:
645	+	delete areaAccumulator_;
646	+	data_.clear();
647		}
648	+
649	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
650	+	if (!doRNEMD_) return;
651	+	int selei;
652	+	int selej;
653
216	–	void RNEMD::doSwap() {
217	–
654		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
655		Mat3x3d hmat = currentSnap_->getHmat();
656
221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
222	–
223	–	int selei;
657		StuntDouble* sd;
225	–	int idx;
658
659	<	RealType min_val;
660	<	bool min_found = false;
661	<	StuntDouble* min_sd;
659	>	RealType min_val(0.0);
660	>	int min_found = 0;
661	>	StuntDouble* min_sd = NULL;
662
663	<	RealType max_val;
664	<	bool max_found = false;
665	<	StuntDouble* max_sd;
663	>	RealType max_val(0.0);
664	>	int max_found = 0;
665	>	StuntDouble* max_sd = NULL;
666
667	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
668	<	sd = seleMan_.nextSelected(selei)) {
667	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
668	>	sd = seleManA_.nextSelected(selei)) {
669
238	–	idx = sd->getLocalIndex();
239	–
670		Vector3d pos = sd->getPos();
671	<
671	>
672		// wrap the stuntdouble's position back into the box:
673	<
673	>
674		if (usePeriodicBoundaryConditions_)
675		currentSnap_->wrapVector(pos);
676	<
677	<	// which bin is this stuntdouble in?
678	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
679	<
680	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
681	<
682	<
253	<	// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin_) {
676	>
677	>	RealType mass = sd->getMass();
678	>	Vector3d vel = sd->getVel();
679	>	RealType value(0.0);
680	>
681	>	switch(rnemdFluxType_) {
682	>	case rnemdKE :
683
684	<	RealType mass = sd->getMass();
685	<	Vector3d vel = sd->getVel();
686	<	RealType value;
687	<
688	<	switch(rnemdType_) {
261	<	case rnemdKineticSwap :
684	>	value = mass * vel.lengthSquare();
685	>
686	>	if (sd->isDirectional()) {
687	>	Vector3d angMom = sd->getJ();
688	>	Mat3x3d I = sd->getI();
689
690	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
691	<	vel[2]*vel[2]);
692	<	if (sd->isDirectional()) {
693	<	Vector3d angMom = sd->getJ();
694	<	Mat3x3d I = sd->getI();
695	<
696	<	if (sd->isLinear()) {
697	<	int i = sd->linearAxis();
698	<	int j = (i + 1) % 3;
699	<	int k = (i + 2) % 3;
273	<	value += angMom[j] * angMom[j] / I(j, j) +
274	<	angMom[k] * angMom[k] / I(k, k);
275	<	} else {
276	<	value += angMom[0]*angMom[0]/I(0, 0)
277	<	+ angMom[1]*angMom[1]/I(1, 1)
278	<	+ angMom[2]*angMom[2]/I(2, 2);
279	<	}
690	>	if (sd->isLinear()) {
691	>	int i = sd->linearAxis();
692	>	int j = (i + 1) % 3;
693	>	int k = (i + 2) % 3;
694	>	value += angMom[j] * angMom[j] / I(j, j) +
695	>	angMom[k] * angMom[k] / I(k, k);
696	>	} else {
697	>	value += angMom[0]*angMom[0]/I(0, 0)
698	>	+ angMom[1]*angMom[1]/I(1, 1)
699	>	+ angMom[2]*angMom[2]/I(2, 2);
700		}
701	<	//make exchangeSum_ comparable between swap & scale
702	<	//temporarily without using energyConvert
703	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
704	<	value *= 0.5;
705	<	break;
706	<	case rnemdPx :
707	<	value = mass * vel[0];
708	<	break;
709	<	case rnemdPy :
710	<	value = mass * vel[1];
711	<	break;
712	<	case rnemdPz :
713	<	value = mass * vel[2];
714	<	break;
715	<	default :
716	<	break;
701	>	} //angular momenta exchange enabled
702	>	value *= 0.5;
703	>	break;
704	>	case rnemdPx :
705	>	value = mass * vel[0];
706	>	break;
707	>	case rnemdPy :
708	>	value = mass * vel[1];
709	>	break;
710	>	case rnemdPz :
711	>	value = mass * vel[2];
712	>	break;
713	>	default :
714	>	break;
715	>	}
716	>	if (!max_found) {
717	>	max_val = value;
718	>	max_sd = sd;
719	>	max_found = 1;
720	>	} else {
721	>	if (max_val < value) {
722	>	max_val = value;
723	>	max_sd = sd;
724		}
725	+	}
726	+	}
727
728	<	if (binNo == 0) {
729	<	if (!min_found) {
730	<	min_val = value;
731	<	min_sd = sd;
732	<	min_found = true;
733	<	} else {
734	<	if (min_val > value) {
735	<	min_val = value;
736	<	min_sd = sd;
737	<	}
738	<	}
739	<	} else { //midBin_
740	<	if (!max_found) {
741	<	max_val = value;
742	<	max_sd = sd;
743	<	max_found = true;
744	<	} else {
745	<	if (max_val < value) {
746	<	max_val = value;
747	<	max_sd = sd;
748	<	}
749	<	}
750	<	}
728	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
729	>	sd = seleManB_.nextSelected(selej)) {
730	>
731	>	Vector3d pos = sd->getPos();
732	>
733	>	// wrap the stuntdouble's position back into the box:
734	>
735	>	if (usePeriodicBoundaryConditions_)
736	>	currentSnap_->wrapVector(pos);
737	>
738	>	RealType mass = sd->getMass();
739	>	Vector3d vel = sd->getVel();
740	>	RealType value(0.0);
741	>
742	>	switch(rnemdFluxType_) {
743	>	case rnemdKE :
744	>
745	>	value = mass * vel.lengthSquare();
746	>
747	>	if (sd->isDirectional()) {
748	>	Vector3d angMom = sd->getJ();
749	>	Mat3x3d I = sd->getI();
750	>
751	>	if (sd->isLinear()) {
752	>	int i = sd->linearAxis();
753	>	int j = (i + 1) % 3;
754	>	int k = (i + 2) % 3;
755	>	value += angMom[j] * angMom[j] / I(j, j) +
756	>	angMom[k] * angMom[k] / I(k, k);
757	>	} else {
758	>	value += angMom[0]*angMom[0]/I(0, 0)
759	>	+ angMom[1]*angMom[1]/I(1, 1)
760	>	+ angMom[2]*angMom[2]/I(2, 2);
761	>	}
762	>	} //angular momenta exchange enabled
763	>	value *= 0.5;
764	>	break;
765	>	case rnemdPx :
766	>	value = mass * vel[0];
767	>	break;
768	>	case rnemdPy :
769	>	value = mass * vel[1];
770	>	break;
771	>	case rnemdPz :
772	>	value = mass * vel[2];
773	>	break;
774	>	default :
775	>	break;
776		}
777	+
778	+	if (!min_found) {
779	+	min_val = value;
780	+	min_sd = sd;
781	+	min_found = 1;
782	+	} else {
783	+	if (min_val > value) {
784	+	min_val = value;
785	+	min_sd = sd;
786	+	}
787	+	}
788		}
789	+
790	+	#ifdef IS_MPI
791	+	int worldRank;
792	+	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
793	+
794	+	int my_min_found = min_found;
795	+	int my_max_found = max_found;
796
325	–	#ifdef IS_MPI
326	–	int nProc, worldRank;
327	–
328	–	nProc = MPI::COMM_WORLD.Get_size();
329	–	worldRank = MPI::COMM_WORLD.Get_rank();
330	–
331	–	bool my_min_found = min_found;
332	–	bool my_max_found = max_found;
333	–
797		// Even if we didn't find a minimum, did someone else?
798	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
799	<	1, MPI::BOOL, MPI::LAND);
337	<
798	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
799	>	MPI_COMM_WORLD);
800		// Even if we didn't find a maximum, did someone else?
801	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
802	<	1, MPI::BOOL, MPI::LAND);
803	<
804	<	struct {
805	<	RealType val;
806	<	int rank;
807	<	} max_vals, min_vals;
808	<
809	<	if (min_found) {
810	<	if (my_min_found)
801	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
802	>	MPI_COMM_WORLD);
803	>	#endif
804	>
805	>	if (max_found && min_found) {
806	>
807	>	#ifdef IS_MPI
808	>	struct {
809	>	RealType val;
810	>	int rank;
811	>	} max_vals, min_vals;
812	>
813	>	if (my_min_found) {
814		min_vals.val = min_val;
815	<	else
815	>	} else {
816		min_vals.val = HONKING_LARGE_VALUE;
817	<
817	>	}
818		min_vals.rank = worldRank;
819
820		// Who had the minimum?
821	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
822	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
821	>	MPI_Allreduce(&min_vals, &min_vals,
822	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
823		min_val = min_vals.val;
359	–	}
824
825	<	if (max_found) {
362	<	if (my_max_found)
825	>	if (my_max_found) {
826		max_vals.val = max_val;
827	<	else
827	>	} else {
828		max_vals.val = -HONKING_LARGE_VALUE;
829	<
829	>	}
830		max_vals.rank = worldRank;
831
832		// Who had the maximum?
833	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
834	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
833	>	MPI_Allreduce(&max_vals, &max_vals,
834	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
835		max_val = max_vals.val;
373	–	}
836		#endif
837	<
838	<	if (max_found && min_found) {
839	<	if (min_val< max_val) {
378	<
837	>
838	>	if (min_val < max_val) {
839	>
840		#ifdef IS_MPI
841		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
842		// I have both maximum and minimum, so proceed like a single
843		// processor version:
844		#endif
845	<	// objects to be swapped: velocity & angular velocity
845	>
846		Vector3d min_vel = min_sd->getVel();
847		Vector3d max_vel = max_sd->getVel();
848		RealType temp_vel;
849
850	<	switch(rnemdType_) {
851	<	case rnemdKineticSwap :
850	>	switch(rnemdFluxType_) {
851	>	case rnemdKE :
852		min_sd->setVel(max_vel);
853		max_sd->setVel(min_vel);
854	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
854	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
855		Vector3d min_angMom = min_sd->getJ();
856		Vector3d max_angMom = max_sd->getJ();
857		min_sd->setJ(max_angMom);
858		max_sd->setJ(min_angMom);
859	<	}
859	>	}//angular momenta exchange enabled
860	>	//assumes same rigid body identity
861		break;
862		case rnemdPx :
863		temp_vel = min_vel.x();
#	Line 421 | Line 883 | namespace OpenMD {
883		default :
884		break;
885		}
886	+
887		#ifdef IS_MPI
888		// the rest of the cases only apply in parallel simulations:
889		} else if (max_vals.rank == worldRank) {
#	Line 428 | Line 891 | namespace OpenMD {
891
892		Vector3d min_vel;
893		Vector3d max_vel = max_sd->getVel();
894	<	MPI::Status status;
894	>	MPI_Status status;
895
896		// point-to-point swap of the velocity vector
897	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
898	<	min_vals.rank, 0,
899	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
900	<	min_vals.rank, 0, status);
897	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
898	>	min_vals.rank, 0,
899	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
900	>	min_vals.rank, 0, MPI_COMM_WORLD, &status);
901
902	<	switch(rnemdType_) {
903	<	case rnemdKineticSwap :
902	>	switch(rnemdFluxType_) {
903	>	case rnemdKE :
904		max_sd->setVel(min_vel);
905	<
905	>	//angular momenta exchange enabled
906		if (max_sd->isDirectional()) {
907		Vector3d min_angMom;
908		Vector3d max_angMom = max_sd->getJ();
909	<
909	>
910		// point-to-point swap of the angular momentum vector
911	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
912	<	MPI::REALTYPE, min_vals.rank, 1,
913	<	min_angMom.getArrayPointer(), 3,
914	<	MPI::REALTYPE, min_vals.rank, 1,
915	<	status);
916	<
911	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
912	>	MPI_REALTYPE, min_vals.rank, 1,
913	>	min_angMom.getArrayPointer(), 3,
914	>	MPI_REALTYPE, min_vals.rank, 1,
915	>	MPI_COMM_WORLD, &status);
916	>
917		max_sd->setJ(min_angMom);
918	<	}
918	>	}
919		break;
920		case rnemdPx :
921		max_vel.x() = min_vel.x();
#	Line 474 | Line 937 | namespace OpenMD {
937
938		Vector3d max_vel;
939		Vector3d min_vel = min_sd->getVel();
940	<	MPI::Status status;
940	>	MPI_Status status;
941
942		// point-to-point swap of the velocity vector
943	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
944	<	max_vals.rank, 0,
945	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
946	<	max_vals.rank, 0, status);
943	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
944	>	max_vals.rank, 0,
945	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
946	>	max_vals.rank, 0, MPI_COMM_WORLD, &status);
947
948	<	switch(rnemdType_) {
949	<	case rnemdKineticSwap :
948	>	switch(rnemdFluxType_) {
949	>	case rnemdKE :
950		min_sd->setVel(max_vel);
951	<
951	>	//angular momenta exchange enabled
952		if (min_sd->isDirectional()) {
953		Vector3d min_angMom = min_sd->getJ();
954		Vector3d max_angMom;
955	<
955	>
956		// point-to-point swap of the angular momentum vector
957	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
958	<	MPI::REALTYPE, max_vals.rank, 1,
959	<	max_angMom.getArrayPointer(), 3,
960	<	MPI::REALTYPE, max_vals.rank, 1,
961	<	status);
962	<
957	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
958	>	MPI_REALTYPE, max_vals.rank, 1,
959	>	max_angMom.getArrayPointer(), 3,
960	>	MPI_REALTYPE, max_vals.rank, 1,
961	>	MPI_COMM_WORLD, &status);
962	>
963		min_sd->setJ(max_angMom);
964		}
965		break;
#	Line 517 | Line 980 | namespace OpenMD {
980		}
981		}
982		#endif
983	<	exchangeSum_ += max_val - min_val;
984	<	} else {
985	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
983	>
984	>	switch(rnemdFluxType_) {
985	>	case rnemdKE:
986	>	kineticExchange_ += max_val - min_val;
987	>	break;
988	>	case rnemdPx:
989	>	momentumExchange_.x() += max_val - min_val;
990	>	break;
991	>	case rnemdPy:
992	>	momentumExchange_.y() += max_val - min_val;
993	>	break;
994	>	case rnemdPz:
995	>	momentumExchange_.z() += max_val - min_val;
996	>	break;
997	>	default:
998	>	break;
999	>	}
1000	>	} else {
1001	>	sprintf(painCave.errMsg,
1002	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
1003	>	painCave.isFatal = 0;
1004	>	painCave.severity = OPENMD_INFO;
1005	>	simError();
1006		failTrialCount_++;
1007		}
1008		} else {
1009	<	std::cerr << "exchange NOT performed!\n";
1010	<	std::cerr << "at least one of the two slabs empty.\n";
1009	>	sprintf(painCave.errMsg,
1010	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
1011	>	"\twas not present in at least one of the two slabs.\n");
1012	>	painCave.isFatal = 0;
1013	>	painCave.severity = OPENMD_INFO;
1014	>	simError();
1015		failTrialCount_++;
1016	<	}
530	<
1016	>	}
1017		}
1018
1019	<	void RNEMD::doScale() {
1019	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
1020	>	if (!doRNEMD_) return;
1021	>	int selei;
1022	>	int selej;
1023
1024		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1025		Mat3x3d hmat = currentSnap_->getHmat();
1026
538	–	seleMan_.setSelectionSet(evaluator_.evaluate());
539	–
540	–	int selei;
1027		StuntDouble* sd;
542	–	int idx;
1028
1029	<	std::vector<StuntDouble*> hotBin, coldBin;
1029	>	vector<StuntDouble*> hotBin, coldBin;
1030
1031		RealType Phx = 0.0;
1032		RealType Phy = 0.0;
#	Line 549 | Line 1034 | namespace OpenMD {
1034		RealType Khx = 0.0;
1035		RealType Khy = 0.0;
1036		RealType Khz = 0.0;
1037	+	RealType Khw = 0.0;
1038		RealType Pcx = 0.0;
1039		RealType Pcy = 0.0;
1040		RealType Pcz = 0.0;
1041		RealType Kcx = 0.0;
1042		RealType Kcy = 0.0;
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
562	–	idx = sd->getLocalIndex();
563	–
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	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1058	<
1059	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1060	<
1061	<	// if we're in bin 0 or the middleBin
1062	<	if (binNo == 0 || binNo == midBin_) {
1063	<
1064	<	RealType mass = sd->getMass();
1065	<	Vector3d vel = sd->getVel();
1066	<
1067	<	if (binNo == 0) {
1068	<	hotBin.push_back(sd);
1069	<	Phx += mass * vel.x();
1070	<	Phy += mass * vel.y();
1071	<	Phz += mass * vel.z();
1072	<	Khx += mass * vel.x() * vel.x();
1073	<	Khy += mass * vel.y() * vel.y();
1074	<	Khz += mass * vel.z() * vel.z();
1075	<	} else { //midBin_
1076	<	coldBin.push_back(sd);
1077	<	Pcx += mass * vel.x();
1078	<	Pcy += mass * vel.y();
1079	<	Pcz += mass * vel.z();
1080	<	Kcx += mass * vel.x() * vel.x();
596	<	Kcy += mass * vel.y() * vel.y();
597	<	Kcz += mass * vel.z() * vel.z();
598	<	}
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	+	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	+
1119		Khx *= 0.5;
1120		Khy *= 0.5;
1121		Khz *= 0.5;
1122	+	Khw *= 0.5;
1123		Kcx *= 0.5;
1124		Kcy *= 0.5;
1125		Kcz *= 0.5;
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, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1140	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1141	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 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_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	<	//use coldBin coeff's
1147	>	//solve coldBin coeff's first
1148		RealType px = Pcx / Phx;
1149		RealType py = Pcy / Phy;
1150		RealType pz = Pcz / Phz;
1151	+	RealType c(0.0), x(0.0), y(0.0), z(0.0);
1152	+	bool successfulScale = false;
1153	+	if ((rnemdFluxType_ == rnemdFullKE) ||
1154	+	(rnemdFluxType_ == rnemdRotKE)) {
1155	+	//may need sanity check Khw & Kcw > 0
1156
1157	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
1158	<	switch(rnemdType_) {
1159	<	case rnemdKineticScale :
1160	<	/*used hotBin coeff's & only scale x & y dimensions
1161	<	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	<	*/
1157	>	if (rnemdFluxType_ == rnemdFullKE) {
1158	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1159	>	} else {
1160	>	c = 1.0 - kineticTarget_ / Kcw;
1161	>	}
1162
1163	<	//scale all three dimensions, let c_x = c_y
1164	<	a000 = Kcx + Kcy;
1165	<	a110 = Kcz;
1166	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1167	<	a001 = Khx * px * px + Khy * py * py;
1168	<	a111 = Khz * pz * pz;
1169	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1170	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1171	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1172	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1173	<	break;
1174	<	case rnemdPxScale :
1175	<	c = 1 - targetFlux_ / Pcx;
1176	<	a000 = Kcy;
1177	<	a110 = Kcz;
1178	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1179	<	a001 = py * py * Khy;
1180	<	a111 = pz * pz * Khz;
1181	<	b01 = -2.0 * Khy * py * (1.0 + py);
1182	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1183	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1184	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1185	<	break;
1186	<	case rnemdPyScale :
1187	<	c = 1 - targetFlux_ / Pcy;
1188	<	a000 = Kcx;
1189	<	a110 = Kcz;
1190	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1191	<	a001 = px * px * Khx;
1192	<	a111 = pz * pz * Khz;
1193	<	b01 = -2.0 * Khx * px * (1.0 + px);
1194	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1195	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1196	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1163	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1164	>	c = sqrt(c);
1165	>
1166	>	RealType w = 0.0;
1167	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1168	>	x = 1.0 + px * (1.0 - c);
1169	>	y = 1.0 + py * (1.0 - c);
1170	>	z = 1.0 + pz * (1.0 - c);
1171	>	/* more complicated way
1172	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1173	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1174	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1175	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1176	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1177	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1178	>	*/
1179	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1180	>	(fabs(z - 1.0) < 0.1)) {
1181	>	w = 1.0 + (kineticTarget_
1182	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1183	>	+ Khz * (1.0 - z * z)) / Khw;
1184	>	}//no need to calculate w if x, y or z is out of range
1185	>	} else {
1186	>	w = 1.0 + kineticTarget_ / Khw;
1187	>	}
1188	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
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) {
1193	>	if (rnemdFluxType_ == rnemdFullKE) {
1194	>	vel = (*sdi)->getVel() * c;
1195	>	(*sdi)->setVel(vel);
1196	>	}
1197	>	if ((*sdi)->isDirectional()) {
1198	>	Vector3d angMom = (*sdi)->getJ() * c;
1199	>	(*sdi)->setJ(angMom);
1200	>	}
1201	>	}
1202	>	w = sqrt(w);
1203	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1204	>	if (rnemdFluxType_ == rnemdFullKE) {
1205	>	vel = (*sdi)->getVel();
1206	>	vel.x() *= x;
1207	>	vel.y() *= y;
1208	>	vel.z() *= z;
1209	>	(*sdi)->setVel(vel);
1210	>	}
1211	>	if ((*sdi)->isDirectional()) {
1212	>	Vector3d angMom = (*sdi)->getJ() * w;
1213	>	(*sdi)->setJ(angMom);
1214	>	}
1215	>	}
1216	>	successfulScale = true;
1217	>	kineticExchange_ += kineticTarget_;
1218	>	}
1219	>	}
1220	>	} else {
1221	>	RealType a000(0.0), a110(0.0), c0(0.0);
1222	>	RealType a001(0.0), a111(0.0), b01(0.0), b11(0.0), c1(0.0);
1223	>	switch(rnemdFluxType_) {
1224	>	case rnemdKE :
1225	>	/* used hotBin coeff's & only scale x & y dimensions
1226	>	RealType px = Phx / Pcx;
1227	>	RealType py = Phy / Pcy;
1228	>	a110 = Khy;
1229	>	c0 = - Khx - Khy - kineticTarget_;
1230	>	a000 = Khx;
1231	>	a111 = Kcy * py * py;
1232	>	b11 = -2.0 * Kcy * py * (1.0 + py);
1233	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1234	>	b01 = -2.0 * Kcx * px * (1.0 + px);
1235	>	a001 = Kcx * px * px;
1236	>	*/
1237	>	//scale all three dimensions, let c_x = c_y
1238	>	a000 = Kcx + Kcy;
1239	>	a110 = Kcz;
1240	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1241	>	a001 = Khx * px * px + Khy * py * py;
1242	>	a111 = Khz * pz * pz;
1243	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1244	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1245	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1246	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1247	>	break;
1248	>	case rnemdPx :
1249	>	c = 1 - momentumTarget_.x() / Pcx;
1250	>	a000 = Kcy;
1251	>	a110 = Kcz;
1252	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1253	>	a001 = py * py * Khy;
1254	>	a111 = pz * pz * Khz;
1255	>	b01 = -2.0 * Khy * py * (1.0 + py);
1256	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1257	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1258	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1259	>	break;
1260	>	case rnemdPy :
1261	>	c = 1 - momentumTarget_.y() / Pcy;
1262	>	a000 = Kcx;
1263	>	a110 = Kcz;
1264	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1265	>	a001 = px * px * Khx;
1266	>	a111 = pz * pz * Khz;
1267	>	b01 = -2.0 * Khx * px * (1.0 + px);
1268	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1269	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1270	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1271	>	break;
1272	>	case rnemdPz ://we don't really do this, do we?
1273	>	c = 1 - momentumTarget_.z() / Pcz;
1274	>	a000 = Kcx;
1275	>	a110 = Kcy;
1276	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1277	>	a001 = px * px * Khx;
1278	>	a111 = py * py * Khy;
1279	>	b01 = -2.0 * Khx * px * (1.0 + px);
1280	>	b11 = -2.0 * Khy * py * (1.0 + py);
1281	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1282	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1283	>	break;
1284	>	default :
1285	>	break;
1286	>	}
1287	>
1288	>	RealType v1 = a000 * a111 - a001 * a110;
1289	>	RealType v2 = a000 * b01;
1290	>	RealType v3 = a000 * b11;
1291	>	RealType v4 = a000 * c1 - a001 * c0;
1292	>	RealType v8 = a110 * b01;
1293	>	RealType v10 = - b01 * c0;
1294	>
1295	>	RealType u0 = v2 * v10 - v4 * v4;
1296	>	RealType u1 = -2.0 * v3 * v4;
1297	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1298	>	RealType u3 = -2.0 * v1 * v3;
1299	>	RealType u4 = - v1 * v1;
1300	>	//rescale coefficients
1301	>	RealType maxAbs = fabs(u0);
1302	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1303	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1304	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1305	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1306	>	u0 /= maxAbs;
1307	>	u1 /= maxAbs;
1308	>	u2 /= maxAbs;
1309	>	u3 /= maxAbs;
1310	>	u4 /= maxAbs;
1311	>	//max_element(start, end) is also available.
1312	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1313	>	poly.setCoefficient(4, u4);
1314	>	poly.setCoefficient(3, u3);
1315	>	poly.setCoefficient(2, u2);
1316	>	poly.setCoefficient(1, u1);
1317	>	poly.setCoefficient(0, u0);
1318	>	vector<RealType> realRoots = poly.FindRealRoots();
1319	>
1320	>	vector<RealType>::iterator ri;
1321	>	RealType r1, r2, alpha0;
1322	>	vector<pair<RealType,RealType> > rps;
1323	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1324	>	r2 = *ri;
1325	>	// Check to see if FindRealRoots() gave the right answer:
1326	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1327	>	sprintf(painCave.errMsg,
1328	>	"RNEMD Warning: polynomial solve seems to have an error!");
1329	>	painCave.isFatal = 0;
1330	>	simError();
1331	>	failRootCount_++;
1332	>	}
1333	>	// Might not be useful w/o rescaling coefficients
1334	>	alpha0 = -c0 - a110 * r2 * r2;
1335	>	if (alpha0 >= 0.0) {
1336	>	r1 = sqrt(alpha0 / a000);
1337	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1338	>	< 1e-6)
1339	>	{ rps.push_back(make_pair(r1, r2)); }
1340	>	if (r1 > 1e-6) { //r1 non-negative
1341	>	r1 = -r1;
1342	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1343	>	< 1e-6)
1344	>	{ rps.push_back(make_pair(r1, r2)); }
1345	>	}
1346	>	}
1347	>	}
1348	>	// Consider combining together the part for solving for the pair
1349	>	// w/ the searching for the best solution part so that we don't
1350	>	// need the pairs vector:
1351	>	if (!rps.empty()) {
1352	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1353	>	RealType diff(0.0);
1354	>	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1355	>	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1356	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1357	>	r1 = (*rpi).first;
1358	>	r2 = (*rpi).second;
1359	>	switch(rnemdFluxType_) {
1360	>	case rnemdKE :
1361	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1362	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1363	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1364	>	break;
1365	>	case rnemdPx :
1366	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1367	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1368	>	break;
1369	>	case rnemdPy :
1370	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1371	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1372	>	break;
1373	>	case rnemdPz :
1374	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1375	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1376	>	default :
1377	>	break;
1378	>	}
1379	>	if (diff < smallestDiff) {
1380	>	smallestDiff = diff;
1381	>	bestPair = *rpi;
1382	>	}
1383	>	}
1384	>	#ifdef IS_MPI
1385	>	if (worldRank == 0) {
1386	>	#endif
1387	>	// sprintf(painCave.errMsg,
1388	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1389	>	//         bestPair.first, bestPair.second);
1390	>	// painCave.isFatal = 0;
1391	>	// painCave.severity = OPENMD_INFO;
1392	>	// simError();
1393	>	#ifdef IS_MPI
1394	>	}
1395	>	#endif
1396	>
1397	>	switch(rnemdFluxType_) {
1398	>	case rnemdKE :
1399	>	x = bestPair.first;
1400	>	y = bestPair.first;
1401	>	z = bestPair.second;
1402	>	break;
1403	>	case rnemdPx :
1404	>	x = c;
1405	>	y = bestPair.first;
1406	>	z = bestPair.second;
1407	>	break;
1408	>	case rnemdPy :
1409	>	x = bestPair.first;
1410	>	y = c;
1411	>	z = bestPair.second;
1412	>	break;
1413	>	case rnemdPz :
1414	>	x = bestPair.first;
1415	>	y = bestPair.second;
1416	>	z = c;
1417	>	break;
1418	>	default :
1419	>	break;
1420	>	}
1421	>	vector<StuntDouble*>::iterator sdi;
1422	>	Vector3d vel;
1423	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1424	>	vel = (*sdi)->getVel();
1425	>	vel.x() *= x;
1426	>	vel.y() *= y;
1427	>	vel.z() *= z;
1428	>	(*sdi)->setVel(vel);
1429	>	}
1430	>	//convert to hotBin coefficient
1431	>	x = 1.0 + px * (1.0 - x);
1432	>	y = 1.0 + py * (1.0 - y);
1433	>	z = 1.0 + pz * (1.0 - z);
1434	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1435	>	vel = (*sdi)->getVel();
1436	>	vel.x() *= x;
1437	>	vel.y() *= y;
1438	>	vel.z() *= z;
1439	>	(*sdi)->setVel(vel);
1440	>	}
1441	>	successfulScale = true;
1442	>	switch(rnemdFluxType_) {
1443	>	case rnemdKE :
1444	>	kineticExchange_ += kineticTarget_;
1445	>	break;
1446	>	case rnemdPx :
1447	>	case rnemdPy :
1448	>	case rnemdPz :
1449	>	momentumExchange_ += momentumTarget_;
1450	>	break;
1451	>	default :
1452	>	break;
1453	>	}
1454	>	}
1455	>	}
1456	>	if (successfulScale != true) {
1457	>	sprintf(painCave.errMsg,
1458	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1459	>	"\tthe constraint equations may not exist or there may be\n"
1460	>	"\tno selected objects in one or both slabs.\n");
1461	>	painCave.isFatal = 0;
1462	>	painCave.severity = OPENMD_INFO;
1463	>	simError();
1464	>	failTrialCount_++;
1465	>	}
1466	>	}
1467	>
1468	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1469	>	if (!doRNEMD_) return;
1470	>	int selei;
1471	>	int selej;
1472	>
1473	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1474	>	Mat3x3d hmat = currentSnap_->getHmat();
1475	>
1476	>	StuntDouble* sd;
1477	>
1478	>	vector<StuntDouble*> hotBin, coldBin;
1479	>
1480	>	Vector3d Ph(V3Zero);
1481	>	Vector3d Lh(V3Zero);
1482	>	RealType Mh = 0.0;
1483	>	Mat3x3d Ih(0.0);
1484	>	RealType Kh = 0.0;
1485	>	Vector3d Pc(V3Zero);
1486	>	Vector3d Lc(V3Zero);
1487	>	RealType Mc = 0.0;
1488	>	Mat3x3d Ic(0.0);
1489	>	RealType Kc = 0.0;
1490	>
1491	>	// Constraints can be on only the linear or angular momentum, but
1492	>	// not both.  Usually, the user will specify which they want, but
1493	>	// in case they don't, the use of periodic boundaries should make
1494	>	// the choice for us.
1495	>	bool doLinearPart = false;
1496	>	bool doAngularPart = false;
1497	>
1498	>	switch (rnemdFluxType_) {
1499	>	case rnemdPx:
1500	>	case rnemdPy:
1501	>	case rnemdPz:
1502	>	case rnemdPvector:
1503	>	case rnemdKePx:
1504	>	case rnemdKePy:
1505	>	case rnemdKePvector:
1506	>	doLinearPart = true;
1507		break;
1508	<	case rnemdPzScale ://we don't really do this, do we?
1509	<	c = 1 - targetFlux_ / Pcz;
1510	<	a000 = Kcx;
1511	<	a110 = Kcy;
1512	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1513	<	a001 = px * px * Khx;
1514	<	a111 = py * py * Khy;
1515	<	b01 = -2.0 * Khx * px * (1.0 + px);
1516	<	b11 = -2.0 * Khy * py * (1.0 + py);
690	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
691	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
692	<	break;
693	<	default :
1508	>	case rnemdLx:
1509	>	case rnemdLy:
1510	>	case rnemdLz:
1511	>	case rnemdLvector:
1512	>	case rnemdKeLx:
1513	>	case rnemdKeLy:
1514	>	case rnemdKeLz:
1515	>	case rnemdKeLvector:
1516	>	doAngularPart = true;
1517		break;
1518	+	case rnemdKE:
1519	+	case rnemdRotKE:
1520	+	case rnemdFullKE:
1521	+	default:
1522	+	if (usePeriodicBoundaryConditions_)
1523	+	doLinearPart = true;
1524	+	else
1525	+	doAngularPart = true;
1526	+	break;
1527		}
1528	+
1529	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1530	+	sd = smanA.nextSelected(selei)) {
1531
1532	<	RealType v1 = a000 * a111 - a001 * a110;
698	<	RealType v2 = a000 * b01;
699	<	RealType v3 = a000 * b11;
700	<	RealType v4 = a000 * c1 - a001 * c0;
701	<	RealType v8 = a110 * b01;
702	<	RealType v10 = - b01 * c0;
1532	>	Vector3d pos = sd->getPos();
1533
1534	<	RealType u0 = v2 * v10 - v4 * v4;
1535	<	RealType u1 = -2.0 * v3 * v4;
1536	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1537	<	RealType u3 = -2.0 * v1 * v3;
1538	<	RealType u4 = - v1 * v1;
1539	<	//rescale coefficients
1540	<	RealType maxAbs = fabs(u0);
1541	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1542	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1543	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1544	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1545	<	u0 /= maxAbs;
1546	<	u1 /= maxAbs;
1547	<	u2 /= maxAbs;
1548	<	u3 /= maxAbs;
1549	<	u4 /= maxAbs;
1550	<	//max_element(start, end) is also available.
1551	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1552	<	poly.setCoefficient(4, u4);
1553	<	poly.setCoefficient(3, u3);
1554	<	poly.setCoefficient(2, u2);
1555	<	poly.setCoefficient(1, u1);
1556	<	poly.setCoefficient(0, u0);
1557	<	std::vector<RealType> realRoots = poly.FindRealRoots();
1558	<
1559	<	std::vector<RealType>::iterator ri;
1560	<	RealType r1, r2, alpha0;
1561	<	std::vector<std::pair<RealType,RealType> > rps;
1562	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1563	<	r2 = *ri;
1564	<	//check if FindRealRoots() give the right answer
1565	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1566	<	sprintf(painCave.errMsg,
1567	<	"RNEMD Warning: polynomial solve seems to have an error!");
1568	<	painCave.isFatal = 0;
1569	<	simError();
740	<	failRootCount_++;
741	<	}
742	<	//might not be useful w/o rescaling coefficients
743	<	alpha0 = -c0 - a110 * r2 * r2;
744	<	if (alpha0 >= 0.0) {
745	<	r1 = sqrt(alpha0 / a000);
746	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
747	<	{ rps.push_back(std::make_pair(r1, r2)); }
748	<	if (r1 > 1e-6) { //r1 non-negative
749	<	r1 = -r1;
750	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
751	<	{ rps.push_back(std::make_pair(r1, r2)); }
1534	>	// wrap the stuntdouble's position back into the box:
1535	>
1536	>	if (usePeriodicBoundaryConditions_)
1537	>	currentSnap_->wrapVector(pos);
1538	>
1539	>	RealType mass = sd->getMass();
1540	>	Vector3d vel = sd->getVel();
1541	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1542	>	RealType r2;
1543	>
1544	>	hotBin.push_back(sd);
1545	>	Ph += mass * vel;
1546	>	Mh += mass;
1547	>	Kh += mass * vel.lengthSquare();
1548	>	Lh += mass * cross(rPos, vel);
1549	>	Ih -= outProduct(rPos, rPos) * mass;
1550	>	r2 = rPos.lengthSquare();
1551	>	Ih(0, 0) += mass * r2;
1552	>	Ih(1, 1) += mass * r2;
1553	>	Ih(2, 2) += mass * r2;
1554	>
1555	>	if (rnemdFluxType_ == rnemdFullKE) {
1556	>	if (sd->isDirectional()) {
1557	>	Vector3d angMom = sd->getJ();
1558	>	Mat3x3d I = sd->getI();
1559	>	if (sd->isLinear()) {
1560	>	int i = sd->linearAxis();
1561	>	int j = (i + 1) % 3;
1562	>	int k = (i + 2) % 3;
1563	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1564	>	angMom[k] * angMom[k] / I(k, k);
1565	>	} else {
1566	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1567	>	angMom[1] * angMom[1] / I(1, 1) +
1568	>	angMom[2] * angMom[2] / I(2, 2);
1569	>	}
1570		}
1571		}
1572		}
1573	<	// Consider combininig together the solving pair part w/ the searching
1574	<	// best solution part so that we don't need the pairs vector
1575	<	if (!rps.empty()) {
1576	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1577	<	RealType diff;
1578	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1579	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1580	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1581	<	r1 = (*rpi).first;
1582	<	r2 = (*rpi).second;
1583	<	switch(rnemdType_) {
1584	<	case rnemdKineticScale :
1585	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1586	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1587	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1588	<	break;
1589	<	case rnemdPxScale :
1590	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1591	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1592	<	break;
1593	<	case rnemdPyScale :
1594	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1595	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1596	<	break;
1597	<	case rnemdPzScale :
1598	<	default :
1599	<	break;
1573	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1574	>	sd = smanB.nextSelected(selej)) {
1575	>
1576	>	Vector3d pos = sd->getPos();
1577	>
1578	>	// wrap the stuntdouble's position back into the box:
1579	>
1580	>	if (usePeriodicBoundaryConditions_)
1581	>	currentSnap_->wrapVector(pos);
1582	>
1583	>	RealType mass = sd->getMass();
1584	>	Vector3d vel = sd->getVel();
1585	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1586	>	RealType r2;
1587	>
1588	>	coldBin.push_back(sd);
1589	>	Pc += mass * vel;
1590	>	Mc += mass;
1591	>	Kc += mass * vel.lengthSquare();
1592	>	Lc += mass * cross(rPos, vel);
1593	>	Ic -= outProduct(rPos, rPos) * mass;
1594	>	r2 = rPos.lengthSquare();
1595	>	Ic(0, 0) += mass * r2;
1596	>	Ic(1, 1) += mass * r2;
1597	>	Ic(2, 2) += mass * r2;
1598	>
1599	>	if (rnemdFluxType_ == rnemdFullKE) {
1600	>	if (sd->isDirectional()) {
1601	>	Vector3d angMom = sd->getJ();
1602	>	Mat3x3d I = sd->getI();
1603	>	if (sd->isLinear()) {
1604	>	int i = sd->linearAxis();
1605	>	int j = (i + 1) % 3;
1606	>	int k = (i + 2) % 3;
1607	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1608	>	angMom[k] * angMom[k] / I(k, k);
1609	>	} else {
1610	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1611	>	angMom[1] * angMom[1] / I(1, 1) +
1612	>	angMom[2] * angMom[2] / I(2, 2);
1613	>	}
1614		}
783	–	if (diff < smallestDiff) {
784	–	smallestDiff = diff;
785	–	bestPair = *rpi;
786	–	}
1615		}
1616	+	}
1617	+
1618	+	Kh *= 0.5;
1619	+	Kc *= 0.5;
1620	+
1621		#ifdef IS_MPI
1622	<	if (worldRank == 0) {
1622	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1623	>	MPI_COMM_WORLD);
1624	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1625	>	MPI_COMM_WORLD);
1626	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1627	>	MPI_COMM_WORLD);
1628	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1629	>	MPI_COMM_WORLD);
1630	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1631	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1632	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1633	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1634	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1635	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1636	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1637	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1638		#endif
1639	<	std::cerr << "we choose r1 = " << bestPair.first
792	<	<< " and r2 = " << bestPair.second << "\n";
793	<	#ifdef IS_MPI
794	<	}
795	<	#endif
1639	>
1640
1641	<	RealType x, y, z;
1642	<	switch(rnemdType_) {
1643	<	case rnemdKineticScale :
1644	<	x = bestPair.first;
1645	<	y = bestPair.first;
1646	<	z = bestPair.second;
1647	<	break;
1648	<	case rnemdPxScale :
1649	<	x = c;
1650	<	y = bestPair.first;
1651	<	z = bestPair.second;
1652	<	break;
1653	<	case rnemdPyScale :
1654	<	x = bestPair.first;
1655	<	y = c;
1656	<	z = bestPair.second;
1657	<	break;
1658	<	case rnemdPzScale :
1659	<	x = bestPair.first;
1660	<	y = bestPair.second;
1661	<	z = c;
1662	<	break;
1663	<	default :
1664	<	break;
1665	<	}
1666	<	std::vector<StuntDouble*>::iterator sdi;
1667	<	Vector3d vel;
1668	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1669	<	vel = (*sdi)->getVel();
1670	<	vel.x() *= x;
1671	<	vel.y() *= y;
1672	<	vel.z() *= z;
1673	<	(*sdi)->setVel(vel);
1674	<	}
1675	<	//convert to hotBin coefficient
1676	<	x = 1.0 + px * (1.0 - x);
1677	<	y = 1.0 + py * (1.0 - y);
1678	<	z = 1.0 + pz * (1.0 - z);
1679	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1680	<	vel = (*sdi)->getVel();
1681	<	vel.x() *= x;
1682	<	vel.y() *= y;
1683	<	vel.z() *= z;
1684	<	(*sdi)->setVel(vel);
1641	>	Vector3d ac, acrec, bc, bcrec;
1642	>	Vector3d ah, ahrec, bh, bhrec;
1643	>
1644	>	bool successfulExchange = false;
1645	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1646	>	Vector3d vc = Pc / Mc;
1647	>	ac = -momentumTarget_ / Mc + vc;
1648	>	acrec = -momentumTarget_ / Mc;
1649	>
1650	>	// We now need the inverse of the inertia tensor to calculate the
1651	>	// angular velocity of the cold slab;
1652	>	Mat3x3d Ici = Ic.inverse();
1653	>	Vector3d omegac = Ici * Lc;
1654	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1655	>	bcrec = bc - omegac;
1656	>
1657	>	RealType cNumerator = Kc - kineticTarget_;
1658	>	if (doLinearPart)
1659	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1660	>
1661	>	if (doAngularPart)
1662	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1663	>
1664	>	if (cNumerator > 0.0) {
1665	>
1666	>	RealType cDenominator = Kc;
1667	>
1668	>	if (doLinearPart)
1669	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1670	>
1671	>	if (doAngularPart)
1672	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1673	>
1674	>	if (cDenominator > 0.0) {
1675	>	RealType c = sqrt(cNumerator / cDenominator);
1676	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1677	>
1678	>	Vector3d vh = Ph / Mh;
1679	>	ah = momentumTarget_ / Mh + vh;
1680	>	ahrec = momentumTarget_ / Mh;
1681	>
1682	>	// We now need the inverse of the inertia tensor to
1683	>	// calculate the angular velocity of the hot slab;
1684	>	Mat3x3d Ihi = Ih.inverse();
1685	>	Vector3d omegah = Ihi * Lh;
1686	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1687	>	bhrec = bh - omegah;
1688	>
1689	>	RealType hNumerator = Kh + kineticTarget_;
1690	>	if (doLinearPart)
1691	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1692	>
1693	>	if (doAngularPart)
1694	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1695	>
1696	>	if (hNumerator > 0.0) {
1697	>
1698	>	RealType hDenominator = Kh;
1699	>	if (doLinearPart)
1700	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1701	>	if (doAngularPart)
1702	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1703	>
1704	>	if (hDenominator > 0.0) {
1705	>	RealType h = sqrt(hNumerator / hDenominator);
1706	>	if ((h > 0.9) && (h < 1.1)) {
1707	>
1708	>	vector<StuntDouble*>::iterator sdi;
1709	>	Vector3d vel;
1710	>	Vector3d rPos;
1711	>
1712	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1713	>	//vel = (*sdi)->getVel();
1714	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1715	>	if (doLinearPart)
1716	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1717	>	if (doAngularPart)
1718	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1719	>
1720	>	(*sdi)->setVel(vel);
1721	>	if (rnemdFluxType_ == rnemdFullKE) {
1722	>	if ((*sdi)->isDirectional()) {
1723	>	Vector3d angMom = (*sdi)->getJ() * c;
1724	>	(*sdi)->setJ(angMom);
1725	>	}
1726	>	}
1727	>	}
1728	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1729	>	//vel = (*sdi)->getVel();
1730	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1731	>	if (doLinearPart)
1732	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1733	>	if (doAngularPart)
1734	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1735	>
1736	>	(*sdi)->setVel(vel);
1737	>	if (rnemdFluxType_ == rnemdFullKE) {
1738	>	if ((*sdi)->isDirectional()) {
1739	>	Vector3d angMom = (*sdi)->getJ() * h;
1740	>	(*sdi)->setJ(angMom);
1741	>	}
1742	>	}
1743	>	}
1744	>	successfulExchange = true;
1745	>	kineticExchange_ += kineticTarget_;
1746	>	momentumExchange_ += momentumTarget_;
1747	>	angularMomentumExchange_ += angularMomentumTarget_;
1748	>	}
1749	>	}
1750	>	}
1751	>	}
1752	>	}
1753		}
1754	<	exchangeSum_ += targetFlux_;
1755	<	//we may want to check whether the exchange has been successful
1756	<	} else {
1757	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1754	>	}
1755	>	if (successfulExchange != true) {
1756	>	sprintf(painCave.errMsg,
1757	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1758	>	"\tthe constraint equations may not exist or there may be\n"
1759	>	"\tno selected objects in one or both slabs.\n");
1760	>	painCave.isFatal = 0;
1761	>	painCave.severity = OPENMD_INFO;
1762	>	simError();
1763		failTrialCount_++;
1764		}
848	–
1765		}
1766
1767	+	RealType RNEMD::getDividingArea() {
1768	+
1769	+	if (hasDividingArea_) return dividingArea_;
1770	+
1771	+	RealType areaA, areaB;
1772	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1773	+
1774	+	if (hasSelectionA_) {
1775	+
1776	+	if (evaluatorA_.hasSurfaceArea())
1777	+	areaA = evaluatorA_.getSurfaceArea();
1778	+	else {
1779	+
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	+	areaA = surfaceMeshA->getArea();
1792	+	delete surfaceMeshA;
1793	+	#else
1794	+	sprintf( painCave.errMsg,
1795	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1796	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1797	+	painCave.severity = OPENMD_ERROR;
1798	+	painCave.isFatal = 1;
1799	+	simError();
1800	+	#endif
1801	+	}
1802	+
1803	+	} else {
1804	+	if (usePeriodicBoundaryConditions_) {
1805	+	// in periodic boundaries, the surface area is twice the x-y
1806	+	// area of the current box:
1807	+	areaA = 2.0 * snap->getXYarea();
1808	+	} else {
1809	+	// in non-periodic simulations, without explicitly setting
1810	+	// selections, the sphere radius sets the surface area of the
1811	+	// dividing surface:
1812	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1813	+	}
1814	+	}
1815	+
1816	+	if (hasSelectionB_) {
1817	+	if (evaluatorB_.hasSurfaceArea()) {
1818	+	areaB = evaluatorB_.getSurfaceArea();
1819	+	} else {
1820	+
1821	+	int isd;
1822	+	StuntDouble* sd;
1823	+	vector<StuntDouble*> bSites;
1824	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1825	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1826	+	sd = seleManB_.nextSelected(isd)) {
1827	+	bSites.push_back(sd);
1828	+	}
1829	+
1830	+	#if defined(HAVE_QHULL)
1831	+	ConvexHull* surfaceMeshB = new ConvexHull();
1832	+	surfaceMeshB->computeHull(bSites);
1833	+	areaB = surfaceMeshB->getArea();
1834	+	delete surfaceMeshB;
1835	+	#else
1836	+	sprintf( painCave.errMsg,
1837	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1838	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1839	+	painCave.severity = OPENMD_ERROR;
1840	+	painCave.isFatal = 1;
1841	+	simError();
1842	+	#endif
1843	+	}
1844	+
1845	+	} else {
1846	+	if (usePeriodicBoundaryConditions_) {
1847	+	// in periodic boundaries, the surface area is twice the x-y
1848	+	// area of the current box:
1849	+	areaB = 2.0 * snap->getXYarea();
1850	+	} else {
1851	+	// in non-periodic simulations, without explicitly setting
1852	+	// selections, but if a sphereBradius has been set, just use that:
1853	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1854	+	}
1855	+	}
1856	+
1857	+	dividingArea_ = min(areaA, areaB);
1858	+	hasDividingArea_ = true;
1859	+	return dividingArea_;
1860	+	}
1861	+
1862		void RNEMD::doRNEMD() {
1863	+	if (!doRNEMD_) return;
1864	+	trialCount_++;
1865
1866	<	switch(rnemdType_) {
1867	<	case rnemdKineticScale :
1868	<	case rnemdPxScale :
1869	<	case rnemdPyScale :
1870	<	case rnemdPzScale :
1871	<	doScale();
1866	>	// object evaluator:
1867	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1868	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1869	>
1870	>	evaluatorA_.loadScriptString(selectionA_);
1871	>	evaluatorB_.loadScriptString(selectionB_);
1872	>
1873	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1874	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1875	>
1876	>	commonA_ = seleManA_ & seleMan_;
1877	>	commonB_ = seleManB_ & seleMan_;
1878	>
1879	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1880	>	// dt = exchange time interval
1881	>	// flux = target flux
1882	>	// dividingArea = smallest dividing surface between the two regions
1883	>
1884	>	hasDividingArea_ = false;
1885	>	RealType area = getDividingArea();
1886	>
1887	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1888	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1889	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1890	>
1891	>	switch(rnemdMethod_) {
1892	>	case rnemdSwap:
1893	>	doSwap(commonA_, commonB_);
1894		break;
1895	<	case rnemdKineticSwap :
1896	<	case rnemdPx :
862	<	case rnemdPy :
863	<	case rnemdPz :
864	<	doSwap();
1895	>	case rnemdNIVS:
1896	>	doNIVS(commonA_, commonB_);
1897		break;
1898	<	case rnemdUnknown :
1898	>	case rnemdVSS:
1899	>	doVSS(commonA_, commonB_);
1900	>	break;
1901	>	case rnemdUnkownMethod:
1902		default :
1903		break;
1904		}
1905		}
1906
1907		void RNEMD::collectData() {
1908	<
1908	>	if (!doRNEMD_) return;
1909		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1910	+
1911	+	// collectData can be called more frequently than the doRNEMD, so use the
1912	+	// computed area from the last exchange time:
1913	+	RealType area = getDividingArea();
1914	+	areaAccumulator_->add(area);
1915		Mat3x3d hmat = currentSnap_->getHmat();
1916	+	Vector3d u = angularMomentumFluxVector_;
1917	+	u.normalize();
1918
1919		seleMan_.setSelectionSet(evaluator_.evaluate());
1920
1921	<	int selei;
1921	>	int selei(0);
1922		StuntDouble* sd;
1923	<	int idx;
1923	>	int binNo;
1924	>	RealType mass;
1925	>	Vector3d vel;
1926	>	Vector3d rPos;
1927	>	RealType KE;
1928	>	Vector3d L;
1929	>	Mat3x3d I;
1930	>	RealType r2;
1931
1932	+	vector<RealType> binMass(nBins_, 0.0);
1933	+	vector<Vector3d> binP(nBins_, V3Zero);
1934	+	vector<RealType> binOmega(nBins_, 0.0);
1935	+	vector<Vector3d> binL(nBins_, V3Zero);
1936	+	vector<Mat3x3d>  binI(nBins_);
1937	+	vector<RealType> binKE(nBins_, 0.0);
1938	+	vector<int> binDOF(nBins_, 0);
1939	+	vector<int> binCount(nBins_, 0);
1940	+
1941	+	// alternative approach, track all molecules instead of only those
1942	+	// selected for scaling/swapping:
1943	+	/*
1944	+	SimInfo::MoleculeIterator miter;
1945	+	vector<StuntDouble*>::iterator iiter;
1946	+	Molecule* mol;
1947	+	StuntDouble* sd;
1948	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1949	+	mol = info_->nextMolecule(miter))
1950	+	sd is essentially sd
1951	+	for (sd = mol->beginIntegrableObject(iiter);
1952	+	sd != NULL;
1953	+	sd = mol->nextIntegrableObject(iiter))
1954	+	*/
1955	+
1956		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1957	<	sd = seleMan_.nextSelected(selei)) {
1958	<
886	<	idx = sd->getLocalIndex();
887	<
1957	>	sd = seleMan_.nextSelected(selei)) {
1958	>
1959		Vector3d pos = sd->getPos();
1960
1961		// wrap the stuntdouble's position back into the box:
1962
1963	<	if (usePeriodicBoundaryConditions_)
1963	>	if (usePeriodicBoundaryConditions_) {
1964		currentSnap_->wrapVector(pos);
1965	<
1966	<	// which bin is this stuntdouble in?
1967	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1968	<
1969	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1965	>	// which bin is this stuntdouble in?
1966	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1967	>	// Shift molecules by half a box to have bins start at 0
1968	>	// The modulo operator is used to wrap the case when we are
1969	>	// beyond the end of the bins back to the beginning.
1970	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1971	>	} else {
1972	>	Vector3d rPos = pos - coordinateOrigin_;
1973	>	binNo = int(rPos.length() / binWidth_);
1974	>	}
1975
1976	<	if (rnemdLogWidth_ == midBin_ + 1)
1977	<	if (binNo > midBin_)
1978	<	binNo = nBins_ - binNo;
1976	>	mass = sd->getMass();
1977	>	vel = sd->getVel();
1978	>	rPos = sd->getPos() - coordinateOrigin_;
1979	>	KE = 0.5 * mass * vel.lengthSquare();
1980	>	L = mass * cross(rPos, vel);
1981	>	I = outProduct(rPos, rPos) * mass;
1982	>	r2 = rPos.lengthSquare();
1983	>	I(0, 0) += mass * r2;
1984	>	I(1, 1) += mass * r2;
1985	>	I(2, 2) += mass * r2;
1986
1987	<	RealType mass = sd->getMass();
1988	<	Vector3d vel = sd->getVel();
1989	<	RealType value;
1990	<	RealType xVal, yVal, zVal;
1987	>	// Project the relative position onto a plane perpendicular to
1988	>	// the angularMomentumFluxVector:
1989	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1990	>	// Project the velocity onto a plane perpendicular to the
1991	>	// angularMomentumFluxVector:
1992	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1993	>	// Compute angular velocity vector (should be nearly parallel to
1994	>	// angularMomentumFluxVector
1995	>	// Vector3d aVel = cross(rProj, vProj);
1996
1997	<	switch(rnemdType_) {
1998	<	case rnemdKineticSwap :
1999	<	case rnemdKineticScale :
2000	<
2001	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
2002	<	vel[2]*vel[2]);
2003	<
2004	<	valueCount_[binNo] += 3;
2005	<	if (sd->isDirectional()) {
2006	<	Vector3d angMom = sd->getJ();
2007	<	Mat3x3d I = sd->getI();
2008	<
2009	<	if (sd->isLinear()) {
2010	<	int i = sd->linearAxis();
2011	<	int j = (i + 1) % 3;
2012	<	int k = (i + 2) % 3;
2013	<	value += angMom[j] * angMom[j] / I(j, j) +
2014	<	angMom[k] * angMom[k] / I(k, k);
1997	>	if (binNo >= 0 && binNo < nBins_)  {
1998	>	binCount[binNo]++;
1999	>	binMass[binNo] += mass;
2000	>	binP[binNo] += mass*vel;
2001	>	binKE[binNo] += KE;
2002	>	binI[binNo] += I;
2003	>	binL[binNo] += L;
2004	>	binDOF[binNo] += 3;
2005	>
2006	>	if (sd->isDirectional()) {
2007	>	Vector3d angMom = sd->getJ();
2008	>	Mat3x3d Ia = sd->getI();
2009	>	if (sd->isLinear()) {
2010	>	int i = sd->linearAxis();
2011	>	int j = (i + 1) % 3;
2012	>	int k = (i + 2) % 3;
2013	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
2014	>	angMom[k] * angMom[k] / Ia(k, k));
2015	>	binDOF[binNo] += 2;
2016	>	} else {
2017	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
2018	>	angMom[1] * angMom[1] / Ia(1, 1) +
2019	>	angMom[2] * angMom[2] / Ia(2, 2));
2020	>	binDOF[binNo] += 3;
2021	>	}
2022	>	}
2023	>	}
2024	>	}
2025
2026	<	valueCount_[binNo] +=2;
2026	>	#ifdef IS_MPI
2027
2028	<	} else {
2029	<	value += angMom[0]*angMom[0]/I(0, 0)
2030	<	+ angMom[1]*angMom[1]/I(1, 1)
2031	<	+ angMom[2]*angMom[2]/I(2, 2);
2032	<	valueCount_[binNo] +=3;
2033	<	}
2034	<	}
2035	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
2036	<
2037	<	break;
2038	<	case rnemdPx :
2039	<	case rnemdPxScale :
2040	<	value = mass * vel[0];
2041	<	valueCount_[binNo]++;
2042	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
2043	<	/ PhysicalConstants::kb;
2044	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
2045	<	/ PhysicalConstants::kb;
948	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
949	<	/ PhysicalConstants::kb;
950	<	xTempHist_[binNo] += xVal;
951	<	yTempHist_[binNo] += yVal;
952	<	zTempHist_[binNo] += zVal;
953	<	break;
954	<	case rnemdPy :
955	<	case rnemdPyScale :
956	<	value = mass * vel[1];
957	<	valueCount_[binNo]++;
958	<	break;
959	<	case rnemdPz :
960	<	case rnemdPzScale :
961	<	value = mass * vel[2];
962	<	valueCount_[binNo]++;
963	<	break;
964	<	case rnemdUnknown :
965	<	default :
966	<	break;
967	<	}
968	<	valueHist_[binNo] += value;
2028	>	for (int i = 0; i < nBins_; i++) {
2029	>
2030	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
2031	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2032	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2033	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2034	>	MPI_Allreduce(MPI_IN_PLACE, binP[i].getArrayPointer(),
2035	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2036	>	MPI_Allreduce(MPI_IN_PLACE, binL[i].getArrayPointer(),
2037	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2038	>	MPI_Allreduce(MPI_IN_PLACE, binI[i].getArrayPointer(),
2039	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2040	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2041	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2042	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2043	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2044	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2045	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2046		}
2047	+
2048	+	#endif
2049
2050	+	Vector3d omega;
2051	+	RealType den;
2052	+	RealType temp;
2053	+	RealType z;
2054	+	RealType r;
2055	+	for (int i = 0; i < nBins_; i++) {
2056	+	if (usePeriodicBoundaryConditions_) {
2057	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2058	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2059	+	/ currentSnap_->getVolume() ;
2060	+	} else {
2061	+	r = (((RealType)i + 0.5) * binWidth_);
2062	+	RealType rinner = (RealType)i * binWidth_;
2063	+	RealType router = (RealType)(i+1) * binWidth_;
2064	+	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2065	+	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2066	+	}
2067	+	vel = binP[i] / binMass[i];
2068	+
2069	+	omega = binI[i].inverse() * binL[i];
2070	+
2071	+	// omega = binOmega[i] / binCount[i];
2072	+
2073	+	if (binCount[i] > 0) {
2074	+	// only add values if there are things to add
2075	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2076	+	PhysicalConstants::energyConvert);
2077	+
2078	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2079	+	if(outputMask_[j]) {
2080	+	switch(j) {
2081	+	case Z:
2082	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2083	+	break;
2084	+	case R:
2085	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2086	+	break;
2087	+	case TEMPERATURE:
2088	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2089	+	break;
2090	+	case VELOCITY:
2091	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2092	+	break;
2093	+	case ANGULARVELOCITY:
2094	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2095	+	break;
2096	+	case DENSITY:
2097	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2098	+	break;
2099	+	}
2100	+	}
2101	+	}
2102	+	}
2103	+	}
2104	+	hasData_ = true;
2105		}
2106
2107		void RNEMD::getStarted() {
2108	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2109	<	Stats& stat = currentSnap_->statData;
2110	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2108	>	if (!doRNEMD_) return;
2109	>	hasDividingArea_ = false;
2110	>	collectData();
2111	>	writeOutputFile();
2112		}
2113
2114	<	void RNEMD::getStatus() {
2114	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2115	>	if (!doRNEMD_) return;
2116	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2117	>
2118	>	while(tokenizer.hasMoreTokens()) {
2119	>	std::string token(tokenizer.nextToken());
2120	>	toUpper(token);
2121	>	OutputMapType::iterator i = outputMap_.find(token);
2122	>	if (i != outputMap_.end()) {
2123	>	outputMask_.set(i->second);
2124	>	} else {
2125	>	sprintf( painCave.errMsg,
2126	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2127	>	"\toutputFileFormat keyword.\n", token.c_str() );
2128	>	painCave.isFatal = 0;
2129	>	painCave.severity = OPENMD_ERROR;
2130	>	simError();
2131	>	}
2132	>	}
2133	>	}
2134	>
2135	>	void RNEMD::writeOutputFile() {
2136	>	if (!doRNEMD_) return;
2137	>	if (!hasData_) return;
2138	>
2139	>	#ifdef IS_MPI
2140	>	// If we're the root node, should we print out the results
2141	>	int worldRank;
2142	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2143
2144	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2145	<	Stats& stat = currentSnap_->statData;
2146	<	RealType time = currentSnap_->getTime();
2144	>	if (worldRank == 0) {
2145	>	#endif
2146	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2147	>
2148	>	if( !rnemdFile_ ){
2149	>	sprintf( painCave.errMsg,
2150	>	"Could not open \"%s\" for RNEMD output.\n",
2151	>	rnemdFileName_.c_str());
2152	>	painCave.isFatal = 1;
2153	>	simError();
2154	>	}
2155
2156	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
986	<	//or to be more meaningful, define another item as exchangeSum_ / time
987	<	int j;
2156	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2157
2158	<	#ifdef IS_MPI
2158	>	RealType time = currentSnap_->getTime();
2159	>	RealType avgArea;
2160	>	areaAccumulator_->getAverage(avgArea);
2161
2162	<	// all processors have the same number of bins, and STL vectors pack their
2163	<	// arrays, so in theory, this should be safe:
2162	>	RealType Jz(0.0);
2163	>	Vector3d JzP(V3Zero);
2164	>	Vector3d JzL(V3Zero);
2165	>	if (time >= info_->getSimParams()->getDt()) {
2166	>	Jz = kineticExchange_ / (time * avgArea)
2167	>	/ PhysicalConstants::energyConvert;
2168	>	JzP = momentumExchange_ / (time * avgArea);
2169	>	JzL = angularMomentumExchange_ / (time * avgArea);
2170	>	}
2171
2172	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
2173	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
2174	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
2175	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
2176	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
2177	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
2178	<	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	<	}
1006	<	// If we're the root node, should we print out the results
1007	<	int worldRank = MPI::COMM_WORLD.Get_rank();
1008	<	if (worldRank == 0) {
1009	<	#endif
1010	<	rnemdLog_ << time;
1011	<	for (j = 0; j < rnemdLogWidth_; j++) {
1012	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
2172	>	rnemdFile_ << "#######################################################\n";
2173	>	rnemdFile_ << "# RNEMD {\n";
2174	>
2175	>	map<string, RNEMDMethod>::iterator mi;
2176	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2177	>	if ( (*mi).second == rnemdMethod_)
2178	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2179		}
2180	<	rnemdLog_ << "\n";
2181	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
2182	<	xTempLog_ << time;
2183	<	for (j = 0; j < rnemdLogWidth_; j++) {
2184	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
2180	>	map<string, RNEMDFluxType>::iterator fi;
2181	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2182	>	if ( (*fi).second == rnemdFluxType_)
2183	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2184	>	}
2185	>
2186	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2187	>
2188	>	rnemdFile_ << "#    objectSelection = \""
2189	>	<< rnemdObjectSelection_ << "\";\n";
2190	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2191	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2192	>	rnemdFile_ << "# }\n";
2193	>	rnemdFile_ << "#######################################################\n";
2194	>	rnemdFile_ << "# RNEMD report:\n";
2195	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2196	>	rnemdFile_ << "# Target flux:\n";
2197	>	rnemdFile_ << "#           kinetic = "
2198	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2199	>	<< " (kcal/mol/A^2/fs)\n";
2200	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2201	>	<< " (amu/A/fs^2)\n";
2202	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2203	>	<< " (amu/A^2/fs^2)\n";
2204	>	rnemdFile_ << "# Target one-time exchanges:\n";
2205	>	rnemdFile_ << "#          kinetic = "
2206	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2207	>	<< " (kcal/mol)\n";
2208	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2209	>	<< " (amu*A/fs)\n";
2210	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2211	>	<< " (amu*A^2/fs)\n";
2212	>	rnemdFile_ << "# Actual exchange totals:\n";
2213	>	rnemdFile_ << "#          kinetic = "
2214	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2215	>	<< " (kcal/mol)\n";
2216	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2217	>	<< " (amu*A/fs)\n";
2218	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2219	>	<< " (amu*A^2/fs)\n";
2220	>	rnemdFile_ << "# Actual flux:\n";
2221	>	rnemdFile_ << "#          kinetic = " << Jz
2222	>	<< " (kcal/mol/A^2/fs)\n";
2223	>	rnemdFile_ << "#          momentum = " << JzP
2224	>	<< " (amu/A/fs^2)\n";
2225	>	rnemdFile_ << "#  angular momentum = " << JzL
2226	>	<< " (amu/A^2/fs^2)\n";
2227	>	rnemdFile_ << "# Exchange statistics:\n";
2228	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2229	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2230	>	if (rnemdMethod_ == rnemdNIVS) {
2231	>	rnemdFile_ << "#  NIVS root-check errors = "
2232	>	<< failRootCount_ << "\n";
2233	>	}
2234	>	rnemdFile_ << "#######################################################\n";
2235	>
2236	>
2237	>
2238	>	//write title
2239	>	rnemdFile_ << "#";
2240	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2241	>	if (outputMask_[i]) {
2242	>	rnemdFile_ << "\t" << data_[i].title <<
2243	>	"(" << data_[i].units << ")";
2244	>	// add some extra tabs for column alignment
2245	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2246		}
2247	<	xTempLog_ << "\n";
2248	<	yTempLog_ << time;
2249	<	for (j = 0; j < rnemdLogWidth_; j++) {
2250	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
2247	>	}
2248	>	rnemdFile_ << std::endl;
2249	>
2250	>	rnemdFile_.precision(8);
2251	>
2252	>	for (int j = 0; j < nBins_; j++) {
2253	>
2254	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2255	>	if (outputMask_[i]) {
2256	>	if (data_[i].dataType == "RealType")
2257	>	writeReal(i,j);
2258	>	else if (data_[i].dataType == "Vector3d")
2259	>	writeVector(i,j);
2260	>	else {
2261	>	sprintf( painCave.errMsg,
2262	>	"RNEMD found an unknown data type for: %s ",
2263	>	data_[i].title.c_str());
2264	>	painCave.isFatal = 1;
2265	>	simError();
2266	>	}
2267	>	}
2268		}
2269	<	yTempLog_ << "\n";
2270	<	zTempLog_ << time;
2271	<	for (j = 0; j < rnemdLogWidth_; j++) {
2272	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
2269	>	rnemdFile_ << std::endl;
2270	>
2271	>	}
2272	>
2273	>	rnemdFile_ << "#######################################################\n";
2274	>	rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2275	>	rnemdFile_ << "#######################################################\n";
2276	>
2277	>
2278	>	for (int j = 0; j < nBins_; j++) {
2279	>	rnemdFile_ << "#";
2280	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2281	>	if (outputMask_[i]) {
2282	>	if (data_[i].dataType == "RealType")
2283	>	writeRealErrorBars(i,j);
2284	>	else if (data_[i].dataType == "Vector3d")
2285	>	writeVectorErrorBars(i,j);
2286	>	else {
2287	>	sprintf( painCave.errMsg,
2288	>	"RNEMD found an unknown data type for: %s ",
2289	>	data_[i].title.c_str());
2290	>	painCave.isFatal = 1;
2291	>	simError();
2292	>	}
2293	>	}
2294		}
2295	<	zTempLog_ << "\n";
2296	<	}
2295	>	rnemdFile_ << std::endl;
2296	>
2297	>	}
2298	>
2299	>	rnemdFile_.flush();
2300	>	rnemdFile_.close();
2301	>
2302		#ifdef IS_MPI
2303		}
2304		#endif
2305	<	for (j = 0; j < rnemdLogWidth_; j++) {
2306	<	valueCount_[j] = 0;
2307	<	valueHist_[j] = 0.0;
2305	>
2306	>	}
2307	>
2308	>	void RNEMD::writeReal(int index, unsigned int bin) {
2309	>	if (!doRNEMD_) return;
2310	>	assert(index >=0 && index < ENDINDEX);
2311	>	assert(int(bin) < nBins_);
2312	>	RealType s;
2313	>	int count;
2314	>
2315	>	count = data_[index].accumulator[bin]->count();
2316	>	if (count == 0) return;
2317	>
2318	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2319	>
2320	>	if (! isinf(s) && ! isnan(s)) {
2321	>	rnemdFile_ << "\t" << s;
2322	>	} else{
2323	>	sprintf( painCave.errMsg,
2324	>	"RNEMD detected a numerical error writing: %s for bin %u",
2325	>	data_[index].title.c_str(), bin);
2326	>	painCave.isFatal = 1;
2327	>	simError();
2328	>	}
2329	>	}
2330	>
2331	>	void RNEMD::writeVector(int index, unsigned int bin) {
2332	>	if (!doRNEMD_) return;
2333	>	assert(index >=0 && index < ENDINDEX);
2334	>	assert(int(bin) < nBins_);
2335	>	Vector3d s;
2336	>	int count;
2337	>
2338	>	count = data_[index].accumulator[bin]->count();
2339	>
2340	>	if (count == 0) return;
2341	>
2342	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2343	>	if (isinf(s[0]) || isnan(s[0]) ||
2344	>	isinf(s[1]) || isnan(s[1]) ||
2345	>	isinf(s[2]) || isnan(s[2]) ) {
2346	>	sprintf( painCave.errMsg,
2347	>	"RNEMD detected a numerical error writing: %s for bin %u",
2348	>	data_[index].title.c_str(), bin);
2349	>	painCave.isFatal = 1;
2350	>	simError();
2351	>	} else {
2352	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2353		}
2354	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
2355	<	for (j = 0; j < rnemdLogWidth_; j++) {
2356	<	xTempHist_[j] = 0.0;
2357	<	yTempHist_[j] = 0.0;
2358	<	zTempHist_[j] = 0.0;
2359	<	}
2354	>	}
2355	>
2356	>	void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2357	>	if (!doRNEMD_) return;
2358	>	assert(index >=0 && index < ENDINDEX);
2359	>	assert(int(bin) < nBins_);
2360	>	RealType s;
2361	>	int count;
2362	>
2363	>	count = data_[index].accumulator[bin]->count();
2364	>	if (count == 0) return;
2365	>
2366	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2367	>
2368	>	if (! isinf(s) && ! isnan(s)) {
2369	>	rnemdFile_ << "\t" << s;
2370	>	} else{
2371	>	sprintf( painCave.errMsg,
2372	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2373	>	data_[index].title.c_str(), bin);
2374	>	painCave.isFatal = 1;
2375	>	simError();
2376	>	}
2377		}
2378	+
2379	+	void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2380	+	if (!doRNEMD_) return;
2381	+	assert(index >=0 && index < ENDINDEX);
2382	+	assert(int(bin) < nBins_);
2383	+	Vector3d s;
2384	+	int count;
2385	+
2386	+	count = data_[index].accumulator[bin]->count();
2387	+	if (count == 0) return;
2388	+
2389	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2390	+	if (isinf(s[0]) || isnan(s[0]) ||
2391	+	isinf(s[1]) || isnan(s[1]) ||
2392	+	isinf(s[2]) || isnan(s[2]) ) {
2393	+	sprintf( painCave.errMsg,
2394	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2395	+	data_[index].title.c_str(), bin);
2396	+	painCave.isFatal = 1;
2397	+	simError();
2398	+	} else {
2399	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2400	+	}
2401	+	}
2402		}
2403	+

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