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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 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+	#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), evaluator_(info), seleMan_(info),
72	>	evaluatorA_(info), seleManA_(info),
73	>	commonA_(info), evaluatorB_(info),
74	>	seleManB_(info), commonB_(info),
75	>	hasData_(false), hasDividingArea_(false),
76	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
77
78	+	trialCount_ = 0;
79		failTrialCount_ = 0;
80		failRootCount_ = 0;
81
82	<	int seedValue;
83	<	Globals * simParams = info->getSimParams();
82	>	Globals* simParams = info->getSimParams();
83	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84
85	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
86	<	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;
85	>	doRNEMD_ = rnemdParams->getUseRNEMD();
86	>	if (!doRNEMD_) return;
87
88	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
89	<	evaluator_.loadScriptString(rnemdObjectSelection_);
90	<	seleMan_.setSelectionSet(evaluator_.evaluate());
88	>	stringToMethod_["Swap"]  = rnemdSwap;
89	>	stringToMethod_["NIVS"]  = rnemdNIVS;
90	>	stringToMethod_["VSS"]   = rnemdVSS;
91
92	<	// do some sanity checking
92	>	stringToFluxType_["KE"]  = rnemdKE;
93	>	stringToFluxType_["Px"]  = rnemdPx;
94	>	stringToFluxType_["Py"]  = rnemdPy;
95	>	stringToFluxType_["Pz"]  = rnemdPz;
96	>	stringToFluxType_["Pvector"]  = rnemdPvector;
97	>	stringToFluxType_["Lx"]  = rnemdLx;
98	>	stringToFluxType_["Ly"]  = rnemdLy;
99	>	stringToFluxType_["Lz"]  = rnemdLz;
100	>	stringToFluxType_["Lvector"]  = rnemdLvector;
101	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
102	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
103	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
104	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
105	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
106	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
107	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
108
109	<	int selectionCount = seleMan_.getSelectionCount();
110	<	int nIntegrable = info->getNGlobalIntegrableObjects();
109	>	runTime_ = simParams->getRunTime();
110	>	statusTime_ = simParams->getStatusTime();
111
112	<	if (selectionCount > nIntegrable) {
112	>	const string methStr = rnemdParams->getMethod();
113	>	bool hasFluxType = rnemdParams->haveFluxType();
114	>
115	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
116	>
117	>	string fluxStr;
118	>	if (hasFluxType) {
119	>	fluxStr = rnemdParams->getFluxType();
120	>	} else {
121		sprintf(painCave.errMsg,
122	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
123	<	"\t\t%s\n"
124	<	"\thas resulted in %d selected objects.  However,\n"
125	<	"\tthe total number of integrable objects in the system\n"
126	<	"\tis only %d.  This is almost certainly not what you want\n"
127	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
128	<	"\tselector in the selection script!\n",
99	<	rnemdObjectSelection_.c_str(),
100	<	selectionCount, nIntegrable);
101	<	painCave.isFatal = 0;
122	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
123	>	"\twhich must be one of the following values:\n"
124	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
125	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
126	>	"\tmust be set to use RNEMD\n");
127	>	painCave.isFatal = 1;
128	>	painCave.severity = OPENMD_ERROR;
129		simError();
103	–
130		}
131	+
132	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
133	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
134	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
135	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
136	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
137	+	hasSelectionA_ = rnemdParams->haveSelectionA();
138	+	hasSelectionB_ = rnemdParams->haveSelectionB();
139	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
140	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
141	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
142	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
143	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
144	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
145	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
146	+	bool hasOutputFields = rnemdParams->haveOutputFields();
147
148	<	const std::string st = simParams->getRNEMD_exchangeType();
148	>	map<string, RNEMDMethod>::iterator i;
149	>	i = stringToMethod_.find(methStr);
150	>	if (i != stringToMethod_.end())
151	>	rnemdMethod_ = i->second;
152	>	else {
153	>	sprintf(painCave.errMsg,
154	>	"RNEMD: The current method,\n"
155	>	"\t\t%s is not one of the recognized\n"
156	>	"\texchange methods: Swap, NIVS, or VSS\n",
157	>	methStr.c_str());
158	>	painCave.isFatal = 1;
159	>	painCave.severity = OPENMD_ERROR;
160	>	simError();
161	>	}
162
163	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
164	<	i = stringToEnumMap_.find(st);
165	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
166	<	if (rnemdType_ == rnemdUnknown) {
167	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
163	>	map<string, RNEMDFluxType>::iterator j;
164	>	j = stringToFluxType_.find(fluxStr);
165	>	if (j != stringToFluxType_.end())
166	>	rnemdFluxType_ = j->second;
167	>	else {
168	>	sprintf(painCave.errMsg,
169	>	"RNEMD: The current fluxType,\n"
170	>	"\t\t%s\n"
171	>	"\tis not one of the recognized flux types.\n",
172	>	fluxStr.c_str());
173	>	painCave.isFatal = 1;
174	>	painCave.severity = OPENMD_ERROR;
175	>	simError();
176		}
177
178	<	#ifdef IS_MPI
179	<	if (worldRank == 0) {
180	<	#endif
181	<
182	<	std::string rnemdFileName;
183	<	std::string xTempFileName;
184	<	std::string yTempFileName;
122	<	std::string zTempFileName;
123	<	switch(rnemdType_) {
124	<	case rnemdKineticSwap :
125	<	case rnemdKineticScale :
126	<	rnemdFileName = "temperature.log";
178	>	bool methodFluxMismatch = false;
179	>	bool hasCorrectFlux = false;
180	>	switch(rnemdMethod_) {
181	>	case rnemdSwap:
182	>	switch (rnemdFluxType_) {
183	>	case rnemdKE:
184	>	hasCorrectFlux = hasKineticFlux;
185		break;
186	<	case rnemdPx :
187	<	case rnemdPxScale :
188	<	case rnemdPy :
189	<	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());
186	>	case rnemdPx:
187	>	case rnemdPy:
188	>	case rnemdPz:
189	>	hasCorrectFlux = hasMomentumFlux;
190		break;
140	–	case rnemdPz :
141	–	case rnemdPzScale :
142	–	case rnemdUnknown :
191		default :
192	<	rnemdFileName = "rnemd.log";
192	>	methodFluxMismatch = true;
193		break;
194		}
195	<	rnemdLog_.open(rnemdFileName.c_str());
196	<
197	<	#ifdef IS_MPI
195	>	break;
196	>	case rnemdNIVS:
197	>	switch (rnemdFluxType_) {
198	>	case rnemdKE:
199	>	case rnemdRotKE:
200	>	case rnemdFullKE:
201	>	hasCorrectFlux = hasKineticFlux;
202	>	break;
203	>	case rnemdPx:
204	>	case rnemdPy:
205	>	case rnemdPz:
206	>	hasCorrectFlux = hasMomentumFlux;
207	>	break;
208	>	case rnemdKePx:
209	>	case rnemdKePy:
210	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
211	>	break;
212	>	default:
213	>	methodFluxMismatch = true;
214	>	break;
215	>	}
216	>	break;
217	>	case rnemdVSS:
218	>	switch (rnemdFluxType_) {
219	>	case rnemdKE:
220	>	case rnemdRotKE:
221	>	case rnemdFullKE:
222	>	hasCorrectFlux = hasKineticFlux;
223	>	break;
224	>	case rnemdPx:
225	>	case rnemdPy:
226	>	case rnemdPz:
227	>	hasCorrectFlux = hasMomentumFlux;
228	>	break;
229	>	case rnemdLx:
230	>	case rnemdLy:
231	>	case rnemdLz:
232	>	hasCorrectFlux = hasAngularMomentumFlux;
233	>	break;
234	>	case rnemdPvector:
235	>	hasCorrectFlux = hasMomentumFluxVector;
236	>	break;
237	>	case rnemdLvector:
238	>	hasCorrectFlux = hasAngularMomentumFluxVector;
239	>	break;
240	>	case rnemdKePx:
241	>	case rnemdKePy:
242	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
243	>	break;
244	>	case rnemdKeLx:
245	>	case rnemdKeLy:
246	>	case rnemdKeLz:
247	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
248	>	break;
249	>	case rnemdKePvector:
250	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
251	>	break;
252	>	case rnemdKeLvector:
253	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
254	>	break;
255	>	default:
256	>	methodFluxMismatch = true;
257	>	break;
258	>	}
259	>	default:
260	>	break;
261		}
151	–	#endif
262
263	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
264	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
265	<	midBin_ = nBins_ / 2;
266	<	if (simParams->haveRNEMD_logWidth()) {
267	<	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
268	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
269	<	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
270	<	std::cerr << "Automaically set back to default.\n";
271	<	rnemdLogWidth_ = nBins_;
272	<	}
263	>	if (methodFluxMismatch) {
264	>	sprintf(painCave.errMsg,
265	>	"RNEMD: The current method,\n"
266	>	"\t\t%s\n"
267	>	"\tcannot be used with the current flux type, %s\n",
268	>	methStr.c_str(), fluxStr.c_str());
269	>	painCave.isFatal = 1;
270	>	painCave.severity = OPENMD_ERROR;
271	>	simError();
272	>	}
273	>	if (!hasCorrectFlux) {
274	>	sprintf(painCave.errMsg,
275	>	"RNEMD: The current method, %s, and flux type, %s,\n"
276	>	"\tdid not have the correct flux value specified. Options\n"
277	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
278	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
279	>	methStr.c_str(), fluxStr.c_str());
280	>	painCave.isFatal = 1;
281	>	painCave.severity = OPENMD_ERROR;
282	>	simError();
283	>	}
284	>
285	>	if (hasKineticFlux) {
286	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
287	>	// into  amu / fs^3:
288	>	kineticFlux_ = rnemdParams->getKineticFlux()
289	>	* PhysicalConstants::energyConvert;
290		} else {
291	<	rnemdLogWidth_ = nBins_;
291	>	kineticFlux_ = 0.0;
292		}
293	<	valueHist_.resize(rnemdLogWidth_, 0.0);
294	<	valueCount_.resize(rnemdLogWidth_, 0);
168	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
169	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
170	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
171	<
172	<	set_RNEMD_exchange_total(0.0);
173	<	if (simParams->haveRNEMD_targetFlux()) {
174	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
293	>	if (hasMomentumFluxVector) {
294	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
295		} else {
296	<	set_RNEMD_target_flux(0.0);
296	>	momentumFluxVector_ = V3Zero;
297	>	if (hasMomentumFlux) {
298	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
299	>	switch (rnemdFluxType_) {
300	>	case rnemdPx:
301	>	momentumFluxVector_.x() = momentumFlux;
302	>	break;
303	>	case rnemdPy:
304	>	momentumFluxVector_.y() = momentumFlux;
305	>	break;
306	>	case rnemdPz:
307	>	momentumFluxVector_.z() = momentumFlux;
308	>	break;
309	>	case rnemdKePx:
310	>	momentumFluxVector_.x() = momentumFlux;
311	>	break;
312	>	case rnemdKePy:
313	>	momentumFluxVector_.y() = momentumFlux;
314	>	break;
315	>	default:
316	>	break;
317	>	}
318	>	}
319	>	if (hasAngularMomentumFluxVector) {
320	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
321	>	} else {
322	>	angularMomentumFluxVector_ = V3Zero;
323	>	if (hasAngularMomentumFlux) {
324	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
325	>	switch (rnemdFluxType_) {
326	>	case rnemdLx:
327	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
328	>	break;
329	>	case rnemdLy:
330	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
331	>	break;
332	>	case rnemdLz:
333	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
334	>	break;
335	>	case rnemdKeLx:
336	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
337	>	break;
338	>	case rnemdKeLy:
339	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
340	>	break;
341	>	case rnemdKeLz:
342	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
343	>	break;
344	>	default:
345	>	break;
346	>	}
347	>	}
348	>	}
349	>
350	>	if (hasCoordinateOrigin) {
351	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
352	>	} else {
353	>	coordinateOrigin_ = V3Zero;
354	>	}
355	>
356	>	// do some sanity checking
357	>
358	>	int selectionCount = seleMan_.getSelectionCount();
359	>
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361	>
362	>	if (selectionCount > nIntegrable) {
363	>	sprintf(painCave.errMsg,
364	>	"RNEMD: The current objectSelection,\n"
365	>	"\t\t%s\n"
366	>	"\thas resulted in %d selected objects.  However,\n"
367	>	"\tthe total number of integrable objects in the system\n"
368	>	"\tis only %d.  This is almost certainly not what you want\n"
369	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
370	>	"\tselector in the selection script!\n",
371	>	rnemdObjectSelection_.c_str(),
372	>	selectionCount, nIntegrable);
373	>	painCave.isFatal = 0;
374	>	painCave.severity = OPENMD_WARNING;
375	>	simError();
376	>	}
377	>
378	>	areaAccumulator_ = new Accumulator();
379	>
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382	>
383	>	data_.resize(RNEMD::ENDINDEX);
384	>	OutputData z;
385	>	z.units =  "Angstroms";
386	>	z.title =  "Z";
387	>	z.dataType = "RealType";
388	>	z.accumulator.reserve(nBins_);
389	>	for (int i = 0; i < nBins_; i++)
390	>	z.accumulator.push_back( new Accumulator() );
391	>	data_[Z] = z;
392	>	outputMap_["Z"] =  Z;
393	>
394	>	OutputData r;
395	>	r.units =  "Angstroms";
396	>	r.title =  "R";
397	>	r.dataType = "RealType";
398	>	r.accumulator.reserve(nBins_);
399	>	for (int i = 0; i < nBins_; i++)
400	>	r.accumulator.push_back( new Accumulator() );
401	>	data_[R] = r;
402	>	outputMap_["R"] =  R;
403	>
404	>	OutputData temperature;
405	>	temperature.units =  "K";
406	>	temperature.title =  "Temperature";
407	>	temperature.dataType = "RealType";
408	>	temperature.accumulator.reserve(nBins_);
409	>	for (int i = 0; i < nBins_; i++)
410	>	temperature.accumulator.push_back( new Accumulator() );
411	>	data_[TEMPERATURE] = temperature;
412	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
413	>
414	>	OutputData velocity;
415	>	velocity.units = "angstroms/fs";
416	>	velocity.title =  "Velocity";
417	>	velocity.dataType = "Vector3d";
418	>	velocity.accumulator.reserve(nBins_);
419	>	for (int i = 0; i < nBins_; i++)
420	>	velocity.accumulator.push_back( new VectorAccumulator() );
421	>	data_[VELOCITY] = velocity;
422	>	outputMap_["VELOCITY"] = VELOCITY;
423	>
424	>	OutputData angularVelocity;
425	>	angularVelocity.units = "angstroms^2/fs";
426	>	angularVelocity.title =  "AngularVelocity";
427	>	angularVelocity.dataType = "Vector3d";
428	>	angularVelocity.accumulator.reserve(nBins_);
429	>	for (int i = 0; i < nBins_; i++)
430	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
431	>	data_[ANGULARVELOCITY] = angularVelocity;
432	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
433	>
434	>	OutputData density;
435	>	density.units =  "g cm^-3";
436	>	density.title =  "Density";
437	>	density.dataType = "RealType";
438	>	density.accumulator.reserve(nBins_);
439	>	for (int i = 0; i < nBins_; i++)
440	>	density.accumulator.push_back( new Accumulator() );
441	>	data_[DENSITY] = density;
442	>	outputMap_["DENSITY"] =  DENSITY;
443	>
444	>	if (hasOutputFields) {
445	>	parseOutputFileFormat(rnemdParams->getOutputFields());
446	>	} else {
447	>	if (usePeriodicBoundaryConditions_)
448	>	outputMask_.set(Z);
449	>	else
450	>	outputMask_.set(R);
451	>	switch (rnemdFluxType_) {
452	>	case rnemdKE:
453	>	case rnemdRotKE:
454	>	case rnemdFullKE:
455	>	outputMask_.set(TEMPERATURE);
456	>	break;
457	>	case rnemdPx:
458	>	case rnemdPy:
459	>	outputMask_.set(VELOCITY);
460	>	break;
461	>	case rnemdPz:
462	>	case rnemdPvector:
463	>	outputMask_.set(VELOCITY);
464	>	outputMask_.set(DENSITY);
465	>	break;
466	>	case rnemdLx:
467	>	case rnemdLy:
468	>	case rnemdLz:
469	>	case rnemdLvector:
470	>	outputMask_.set(ANGULARVELOCITY);
471	>	break;
472	>	case rnemdKeLx:
473	>	case rnemdKeLy:
474	>	case rnemdKeLz:
475	>	case rnemdKeLvector:
476	>	outputMask_.set(TEMPERATURE);
477	>	outputMask_.set(ANGULARVELOCITY);
478	>	break;
479	>	case rnemdKePx:
480	>	case rnemdKePy:
481	>	outputMask_.set(TEMPERATURE);
482	>	outputMask_.set(VELOCITY);
483	>	break;
484	>	case rnemdKePvector:
485	>	outputMask_.set(TEMPERATURE);
486	>	outputMask_.set(VELOCITY);
487	>	outputMask_.set(DENSITY);
488	>	break;
489	>	default:
490	>	break;
491	>	}
492	>	}
493	>
494	>	if (hasOutputFileName) {
495	>	rnemdFileName_ = rnemdParams->getOutputFileName();
496	>	} else {
497	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	>	}
499	>
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501	>
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504	>
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508	>
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511	>
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547	>
548	>	if (hasSelectionB_) {
549	>	selectionB_ = rnemdParams->getSelectionB();
550	>
551	>	} else {
552	>	if (usePeriodicBoundaryConditions_) {
553	>	Mat3x3d hmat = currentSnap_->getHmat();
554	>
555	>	if (hasSlabWidth)
556	>	slabWidth_ = rnemdParams->getSlabWidth();
557	>	else
558	>	slabWidth_ = hmat(2,2) / 10.0;
559	>
560	>	if (hasSlabBCenter)
561	>	slabBCenter_ = rnemdParams->getSlabBCenter();
562	>	else
563	>	slabBCenter_ = hmat(2,2) / 2.0;
564	>
565	>	selectionBstream << "select wrappedz > "
566	>	<< slabBCenter_ - 0.5*slabWidth_
567	>	<<  " && wrappedz < "
568	>	<< slabBCenter_ + 0.5*slabWidth_;
569	>	selectionB_ = selectionBstream.str();
570	>	} else {
571	>	if (hasSphereBRadius_) {
572	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
573	>	selectionBstream << "select r > " << sphereBRadius_;
574	>	selectionB_ = selectionBstream.str();
575	>	} else {
576	>	selectionB_ = "select hull";
577	>	BisHull_ = true;
578	>	hasSelectionB_ = true;
579	>	}
580	>	}
581	>	}
582		}
583
584	<	#ifndef IS_MPI
585	<	if (simParams->haveSeed()) {
586	<	seedValue = simParams->getSeed();
587	<	randNumGen_ = new SeqRandNumGen(seedValue);
588	<	}else {
589	<	randNumGen_ = new SeqRandNumGen();
590	<	}
591	<	#else
592	<	if (simParams->haveSeed()) {
188	<	seedValue = simParams->getSeed();
189	<	randNumGen_ = new ParallelRandNumGen(seedValue);
190	<	}else {
191	<	randNumGen_ = new ParallelRandNumGen();
192	<	}
193	<	#endif
584	>	// object evaluator:
585	>	evaluator_.loadScriptString(rnemdObjectSelection_);
586	>	seleMan_.setSelectionSet(evaluator_.evaluate());
587	>	evaluatorA_.loadScriptString(selectionA_);
588	>	evaluatorB_.loadScriptString(selectionB_);
589	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
590	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
591	>	commonA_ = seleManA_ & seleMan_;
592	>	commonB_ = seleManB_ & seleMan_;
593		}
594
196	–	RNEMD::~RNEMD() {
197	–	delete randNumGen_;
595
596	+	RNEMD::~RNEMD() {
597	+	if (!doRNEMD_) return;
598		#ifdef IS_MPI
599		if (worldRank == 0) {
600		#endif
601	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
602	<	rnemdLog_.close();
603	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
604	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
605	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	<	xTempLog_.close();
208	<	yTempLog_.close();
209	<	zTempLog_.close();
210	<	}
601	>
602	>	writeOutputFile();
603	>
604	>	rnemdFile_.close();
605	>
606		#ifdef IS_MPI
607		}
608		#endif
609	+
610	+	// delete all of the objects we created:
611	+	delete areaAccumulator_;
612	+	data_.clear();
613		}
614	+
615	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
616	+	if (!doRNEMD_) return;
617	+	int selei;
618	+	int selej;
619
216	–	void RNEMD::doSwap() {
217	–
620		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
621		Mat3x3d hmat = currentSnap_->getHmat();
622
221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
222	–
223	–	int selei;
623		StuntDouble* sd;
225	–	int idx;
624
625		RealType min_val;
626		bool min_found = false;
#	Line 232 | Line 630 | namespace OpenMD {
630		bool max_found = false;
631		StuntDouble* max_sd;
632
633	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
634	<	sd = seleMan_.nextSelected(selei)) {
633	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
634	>	sd = seleManA_.nextSelected(selei)) {
635
238	–	idx = sd->getLocalIndex();
239	–
636		Vector3d pos = sd->getPos();
637	<
637	>
638		// wrap the stuntdouble's position back into the box:
639	<
639	>
640		if (usePeriodicBoundaryConditions_)
641		currentSnap_->wrapVector(pos);
642	<
643	<	// which bin is this stuntdouble in?
644	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
645	<
646	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
647	<
648	<
253	<	// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin_) {
642	>
643	>	RealType mass = sd->getMass();
644	>	Vector3d vel = sd->getVel();
645	>	RealType value;
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649
650	<	RealType mass = sd->getMass();
651	<	Vector3d vel = sd->getVel();
652	<	RealType value;
653	<
654	<	switch(rnemdType_) {
261	<	case rnemdKineticSwap :
650	>	value = mass * vel.lengthSquare();
651	>
652	>	if (sd->isDirectional()) {
653	>	Vector3d angMom = sd->getJ();
654	>	Mat3x3d I = sd->getI();
655
656	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
657	<	vel[2]*vel[2]);
658	<	if (sd->isDirectional()) {
659	<	Vector3d angMom = sd->getJ();
660	<	Mat3x3d I = sd->getI();
661	<
662	<	if (sd->isLinear()) {
663	<	int i = sd->linearAxis();
664	<	int j = (i + 1) % 3;
665	<	int k = (i + 2) % 3;
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	<	}
656	>	if (sd->isLinear()) {
657	>	int i = sd->linearAxis();
658	>	int j = (i + 1) % 3;
659	>	int k = (i + 2) % 3;
660	>	value += angMom[j] * angMom[j] / I(j, j) +
661	>	angMom[k] * angMom[k] / I(k, k);
662	>	} else {
663	>	value += angMom[0]*angMom[0]/I(0, 0)
664	>	+ angMom[1]*angMom[1]/I(1, 1)
665	>	+ angMom[2]*angMom[2]/I(2, 2);
666		}
667	<	//make exchangeSum_ comparable between swap & scale
668	<	//temporarily without using energyConvert
669	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
670	<	value *= 0.5;
671	<	break;
672	<	case rnemdPx :
673	<	value = mass * vel[0];
674	<	break;
675	<	case rnemdPy :
676	<	value = mass * vel[1];
677	<	break;
678	<	case rnemdPz :
679	<	value = mass * vel[2];
680	<	break;
681	<	default :
682	<	break;
667	>	} //angular momenta exchange enabled
668	>	value *= 0.5;
669	>	break;
670	>	case rnemdPx :
671	>	value = mass * vel[0];
672	>	break;
673	>	case rnemdPy :
674	>	value = mass * vel[1];
675	>	break;
676	>	case rnemdPz :
677	>	value = mass * vel[2];
678	>	break;
679	>	default :
680	>	break;
681	>	}
682	>	if (!max_found) {
683	>	max_val = value;
684	>	max_sd = sd;
685	>	max_found = true;
686	>	} else {
687	>	if (max_val < value) {
688	>	max_val = value;
689	>	max_sd = sd;
690		}
691	+	}
692	+	}
693
694	<	if (binNo == 0) {
695	<	if (!min_found) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	min_found = true;
699	<	} else {
700	<	if (min_val > value) {
701	<	min_val = value;
702	<	min_sd = sd;
703	<	}
704	<	}
705	<	} else { //midBin_
706	<	if (!max_found) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	max_found = true;
710	<	} else {
711	<	if (max_val < value) {
712	<	max_val = value;
713	<	max_sd = sd;
714	<	}
715	<	}
716	<	}
694	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
695	>	sd = seleManB_.nextSelected(selej)) {
696	>
697	>	Vector3d pos = sd->getPos();
698	>
699	>	// wrap the stuntdouble's position back into the box:
700	>
701	>	if (usePeriodicBoundaryConditions_)
702	>	currentSnap_->wrapVector(pos);
703	>
704	>	RealType mass = sd->getMass();
705	>	Vector3d vel = sd->getVel();
706	>	RealType value;
707	>
708	>	switch(rnemdFluxType_) {
709	>	case rnemdKE :
710	>
711	>	value = mass * vel.lengthSquare();
712	>
713	>	if (sd->isDirectional()) {
714	>	Vector3d angMom = sd->getJ();
715	>	Mat3x3d I = sd->getI();
716	>
717	>	if (sd->isLinear()) {
718	>	int i = sd->linearAxis();
719	>	int j = (i + 1) % 3;
720	>	int k = (i + 2) % 3;
721	>	value += angMom[j] * angMom[j] / I(j, j) +
722	>	angMom[k] * angMom[k] / I(k, k);
723	>	} else {
724	>	value += angMom[0]*angMom[0]/I(0, 0)
725	>	+ angMom[1]*angMom[1]/I(1, 1)
726	>	+ angMom[2]*angMom[2]/I(2, 2);
727	>	}
728	>	} //angular momenta exchange enabled
729	>	value *= 0.5;
730	>	break;
731	>	case rnemdPx :
732	>	value = mass * vel[0];
733	>	break;
734	>	case rnemdPy :
735	>	value = mass * vel[1];
736	>	break;
737	>	case rnemdPz :
738	>	value = mass * vel[2];
739	>	break;
740	>	default :
741	>	break;
742		}
743	+
744	+	if (!min_found) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	min_found = true;
748	+	} else {
749	+	if (min_val > value) {
750	+	min_val = value;
751	+	min_sd = sd;
752	+	}
753	+	}
754		}
755	<
756	<	#ifdef IS_MPI
757	<	int nProc, worldRank;
758	<
328	<	nProc = MPI::COMM_WORLD.Get_size();
329	<	worldRank = MPI::COMM_WORLD.Get_rank();
330	<
755	>
756	>	#ifdef IS_MPI
757	>	int worldRank = MPI::COMM_WORLD.Get_rank();
758	>
759		bool my_min_found = min_found;
760		bool my_max_found = max_found;
761
762		// Even if we didn't find a minimum, did someone else?
763	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
336	<	1, MPI::BOOL, MPI::LAND);
337	<
763	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
764		// Even if we didn't find a maximum, did someone else?
765	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
766	<	1, MPI::BOOL, MPI::LAND);
767	<
768	<	struct {
769	<	RealType val;
770	<	int rank;
771	<	} max_vals, min_vals;
772	<
773	<	if (min_found) {
774	<	if (my_min_found)
765	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
766	>	#endif
767	>
768	>	if (max_found && min_found) {
769	>
770	>	#ifdef IS_MPI
771	>	struct {
772	>	RealType val;
773	>	int rank;
774	>	} max_vals, min_vals;
775	>
776	>	if (my_min_found) {
777		min_vals.val = min_val;
778	<	else
778	>	} else {
779		min_vals.val = HONKING_LARGE_VALUE;
780	<
780	>	}
781		min_vals.rank = worldRank;
782
783		// Who had the minimum?
784		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
785		1, MPI::REALTYPE_INT, MPI::MINLOC);
786		min_val = min_vals.val;
359	–	}
787
788	<	if (max_found) {
362	<	if (my_max_found)
788	>	if (my_max_found) {
789		max_vals.val = max_val;
790	<	else
790	>	} else {
791		max_vals.val = -HONKING_LARGE_VALUE;
792	<
792	>	}
793		max_vals.rank = worldRank;
794
795		// Who had the maximum?
796		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
797		1, MPI::REALTYPE_INT, MPI::MAXLOC);
798		max_val = max_vals.val;
373	–	}
799		#endif
800	<
801	<	if (max_found && min_found) {
802	<	if (min_val< max_val) {
378	<
800	>
801	>	if (min_val < max_val) {
802	>
803		#ifdef IS_MPI
804		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
805		// I have both maximum and minimum, so proceed like a single
806		// processor version:
807		#endif
808	<	// objects to be swapped: velocity & angular velocity
808	>
809		Vector3d min_vel = min_sd->getVel();
810		Vector3d max_vel = max_sd->getVel();
811		RealType temp_vel;
812
813	<	switch(rnemdType_) {
814	<	case rnemdKineticSwap :
813	>	switch(rnemdFluxType_) {
814	>	case rnemdKE :
815		min_sd->setVel(max_vel);
816		max_sd->setVel(min_vel);
817	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
817	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
818		Vector3d min_angMom = min_sd->getJ();
819		Vector3d max_angMom = max_sd->getJ();
820		min_sd->setJ(max_angMom);
821		max_sd->setJ(min_angMom);
822	<	}
822	>	}//angular momenta exchange enabled
823	>	//assumes same rigid body identity
824		break;
825		case rnemdPx :
826		temp_vel = min_vel.x();
#	Line 421 | Line 846 | namespace OpenMD {
846		default :
847		break;
848		}
849	+
850		#ifdef IS_MPI
851		// the rest of the cases only apply in parallel simulations:
852		} else if (max_vals.rank == worldRank) {
#	Line 436 | Line 862 | namespace OpenMD {
862		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
863		min_vals.rank, 0, status);
864
865	<	switch(rnemdType_) {
866	<	case rnemdKineticSwap :
865	>	switch(rnemdFluxType_) {
866	>	case rnemdKE :
867		max_sd->setVel(min_vel);
868	<
868	>	//angular momenta exchange enabled
869		if (max_sd->isDirectional()) {
870		Vector3d min_angMom;
871		Vector3d max_angMom = max_sd->getJ();
872	<
872	>
873		// point-to-point swap of the angular momentum vector
874		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
875		MPI::REALTYPE, min_vals.rank, 1,
876		min_angMom.getArrayPointer(), 3,
877		MPI::REALTYPE, min_vals.rank, 1,
878		status);
879	<
879	>
880		max_sd->setJ(min_angMom);
881	<	}
881	>	}
882		break;
883		case rnemdPx :
884		max_vel.x() = min_vel.x();
#	Line 482 | Line 908 | namespace OpenMD {
908		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
909		max_vals.rank, 0, status);
910
911	<	switch(rnemdType_) {
912	<	case rnemdKineticSwap :
911	>	switch(rnemdFluxType_) {
912	>	case rnemdKE :
913		min_sd->setVel(max_vel);
914	<
914	>	//angular momenta exchange enabled
915		if (min_sd->isDirectional()) {
916		Vector3d min_angMom = min_sd->getJ();
917		Vector3d max_angMom;
918	<
918	>
919		// point-to-point swap of the angular momentum vector
920		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
921		MPI::REALTYPE, max_vals.rank, 1,
922		max_angMom.getArrayPointer(), 3,
923		MPI::REALTYPE, max_vals.rank, 1,
924		status);
925	<
925	>
926		min_sd->setJ(max_angMom);
927		}
928		break;
#	Line 517 | Line 943 | namespace OpenMD {
943		}
944		}
945		#endif
946	<	exchangeSum_ += max_val - min_val;
947	<	} else {
948	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
946	>
947	>	switch(rnemdFluxType_) {
948	>	case rnemdKE:
949	>	kineticExchange_ += max_val - min_val;
950	>	break;
951	>	case rnemdPx:
952	>	momentumExchange_.x() += max_val - min_val;
953	>	break;
954	>	case rnemdPy:
955	>	momentumExchange_.y() += max_val - min_val;
956	>	break;
957	>	case rnemdPz:
958	>	momentumExchange_.z() += max_val - min_val;
959	>	break;
960	>	default:
961	>	break;
962	>	}
963	>	} else {
964	>	sprintf(painCave.errMsg,
965	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
966	>	painCave.isFatal = 0;
967	>	painCave.severity = OPENMD_INFO;
968	>	simError();
969		failTrialCount_++;
970		}
971		} else {
972	<	std::cerr << "exchange NOT performed!\n";
973	<	std::cerr << "at least one of the two slabs empty.\n";
972	>	sprintf(painCave.errMsg,
973	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
974	>	"\twas not present in at least one of the two slabs.\n");
975	>	painCave.isFatal = 0;
976	>	painCave.severity = OPENMD_INFO;
977	>	simError();
978		failTrialCount_++;
979	<	}
530	<
979	>	}
980		}
981
982	<	void RNEMD::doScale() {
982	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
983	>	if (!doRNEMD_) return;
984	>	int selei;
985	>	int selej;
986
987		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
988	+	RealType time = currentSnap_->getTime();
989		Mat3x3d hmat = currentSnap_->getHmat();
990
538	–	seleMan_.setSelectionSet(evaluator_.evaluate());
539	–
540	–	int selei;
991		StuntDouble* sd;
542	–	int idx;
992
993	<	std::vector<StuntDouble*> hotBin, coldBin;
993	>	vector<StuntDouble*> hotBin, coldBin;
994
995		RealType Phx = 0.0;
996		RealType Phy = 0.0;
#	Line 549 | Line 998 | namespace OpenMD {
998		RealType Khx = 0.0;
999		RealType Khy = 0.0;
1000		RealType Khz = 0.0;
1001	+	RealType Khw = 0.0;
1002		RealType Pcx = 0.0;
1003		RealType Pcy = 0.0;
1004		RealType Pcz = 0.0;
1005		RealType Kcx = 0.0;
1006		RealType Kcy = 0.0;
1007		RealType Kcz = 0.0;
1008	+	RealType Kcw = 0.0;
1009
1010	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1011	<	sd = seleMan_.nextSelected(selei)) {
1010	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1011	>	sd = smanA.nextSelected(selei)) {
1012
562	–	idx = sd->getLocalIndex();
563	–
1013		Vector3d pos = sd->getPos();
1014	<
1014	>
1015		// wrap the stuntdouble's position back into the box:
1016	<
1016	>
1017		if (usePeriodicBoundaryConditions_)
1018		currentSnap_->wrapVector(pos);
1019	<
1020	<	// which bin is this stuntdouble in?
1021	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1022	<
1023	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1024	<
1025	<	// if we're in bin 0 or the middleBin
1026	<	if (binNo == 0 || binNo == midBin_) {
1027	<
1028	<	RealType mass = sd->getMass();
1029	<	Vector3d vel = sd->getVel();
1030	<
1031	<	if (binNo == 0) {
1032	<	hotBin.push_back(sd);
1033	<	Phx += mass * vel.x();
1034	<	Phy += mass * vel.y();
1035	<	Phz += mass * vel.z();
1036	<	Khx += mass * vel.x() * vel.x();
1037	<	Khy += mass * vel.y() * vel.y();
1038	<	Khz += mass * vel.z() * vel.z();
1039	<	} else { //midBin_
1040	<	coldBin.push_back(sd);
1041	<	Pcx += mass * vel.x();
1042	<	Pcy += mass * vel.y();
1043	<	Pcz += mass * vel.z();
1044	<	Kcx += mass * vel.x() * vel.x();
1045	<	Kcy += mass * vel.y() * vel.y();
1046	<	Kcz += mass * vel.z() * vel.z();
1047	<	}
1048	<	}
1049	<	}
1050	<
1051	<	Khx *= 0.5;
1052	<	Khy *= 0.5;
1019	>
1020	>
1021	>	RealType mass = sd->getMass();
1022	>	Vector3d vel = sd->getVel();
1023	>
1024	>	hotBin.push_back(sd);
1025	>	Phx += mass * vel.x();
1026	>	Phy += mass * vel.y();
1027	>	Phz += mass * vel.z();
1028	>	Khx += mass * vel.x() * vel.x();
1029	>	Khy += mass * vel.y() * vel.y();
1030	>	Khz += mass * vel.z() * vel.z();
1031	>	if (sd->isDirectional()) {
1032	>	Vector3d angMom = sd->getJ();
1033	>	Mat3x3d I = sd->getI();
1034	>	if (sd->isLinear()) {
1035	>	int i = sd->linearAxis();
1036	>	int j = (i + 1) % 3;
1037	>	int k = (i + 2) % 3;
1038	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1039	>	angMom[k] * angMom[k] / I(k, k);
1040	>	} else {
1041	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1042	>	+ angMom[1]*angMom[1]/I(1, 1)
1043	>	+ angMom[2]*angMom[2]/I(2, 2);
1044	>	}
1045	>	}
1046	>	}
1047	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1048	>	sd = smanB.nextSelected(selej)) {
1049	>	Vector3d pos = sd->getPos();
1050	>
1051	>	// wrap the stuntdouble's position back into the box:
1052	>
1053	>	if (usePeriodicBoundaryConditions_)
1054	>	currentSnap_->wrapVector(pos);
1055	>
1056	>	RealType mass = sd->getMass();
1057	>	Vector3d vel = sd->getVel();
1058	>
1059	>	coldBin.push_back(sd);
1060	>	Pcx += mass * vel.x();
1061	>	Pcy += mass * vel.y();
1062	>	Pcz += mass * vel.z();
1063	>	Kcx += mass * vel.x() * vel.x();
1064	>	Kcy += mass * vel.y() * vel.y();
1065	>	Kcz += mass * vel.z() * vel.z();
1066	>	if (sd->isDirectional()) {
1067	>	Vector3d angMom = sd->getJ();
1068	>	Mat3x3d I = sd->getI();
1069	>	if (sd->isLinear()) {
1070	>	int i = sd->linearAxis();
1071	>	int j = (i + 1) % 3;
1072	>	int k = (i + 2) % 3;
1073	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1074	>	angMom[k] * angMom[k] / I(k, k);
1075	>	} else {
1076	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1077	>	+ angMom[1]*angMom[1]/I(1, 1)
1078	>	+ angMom[2]*angMom[2]/I(2, 2);
1079	>	}
1080	>	}
1081	>	}
1082	>
1083	>	Khx *= 0.5;
1084	>	Khy *= 0.5;
1085		Khz *= 0.5;
1086	+	Khw *= 0.5;
1087		Kcx *= 0.5;
1088		Kcy *= 0.5;
1089		Kcz *= 0.5;
1090	+	Kcw *= 0.5;
1091
1092		#ifdef IS_MPI
1093		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 617 | Line 1100 | namespace OpenMD {
1100		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1101		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1102		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1103	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1104	+
1105		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1106		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1107		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1108	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1109		#endif
1110
1111	<	//use coldBin coeff's
1111	>	//solve coldBin coeff's first
1112		RealType px = Pcx / Phx;
1113		RealType py = Pcy / Phy;
1114		RealType pz = Pcz / Phz;
1115	+	RealType c, x, y, z;
1116	+	bool successfulScale = false;
1117	+	if ((rnemdFluxType_ == rnemdFullKE) ||
1118	+	(rnemdFluxType_ == rnemdRotKE)) {
1119	+	//may need sanity check Khw & Kcw > 0
1120
1121	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
1122	<	switch(rnemdType_) {
1123	<	case rnemdKineticScale :
1124	<	/*used hotBin coeff's & only scale x & y dimensions
1125	<	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	<	*/
1121	>	if (rnemdFluxType_ == rnemdFullKE) {
1122	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1123	>	} else {
1124	>	c = 1.0 - kineticTarget_ / Kcw;
1125	>	}
1126
1127	<	//scale all three dimensions, let c_x = c_y
1128	<	a000 = Kcx + Kcy;
1129	<	a110 = Kcz;
1130	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1131	<	a001 = Khx * px * px + Khy * py * py;
1132	<	a111 = Khz * pz * pz;
1133	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1134	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1135	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1136	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1137	<	break;
1138	<	case rnemdPxScale :
1139	<	c = 1 - targetFlux_ / Pcx;
1140	<	a000 = Kcy;
1141	<	a110 = Kcz;
1142	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1143	<	a001 = py * py * Khy;
1144	<	a111 = pz * pz * Khz;
1145	<	b01 = -2.0 * Khy * py * (1.0 + py);
1146	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1147	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1148	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1149	<	break;
1150	<	case rnemdPyScale :
1151	<	c = 1 - targetFlux_ / Pcy;
1152	<	a000 = Kcx;
1153	<	a110 = Kcz;
1154	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1155	<	a001 = px * px * Khx;
1156	<	a111 = pz * pz * Khz;
1157	<	b01 = -2.0 * Khx * px * (1.0 + px);
1158	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1159	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1160	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1127	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1128	>	c = sqrt(c);
1129	>
1130	>	RealType w = 0.0;
1131	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1132	>	x = 1.0 + px * (1.0 - c);
1133	>	y = 1.0 + py * (1.0 - c);
1134	>	z = 1.0 + pz * (1.0 - c);
1135	>	/* more complicated way
1136	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1137	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1138	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1139	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1140	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1141	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1142	>	*/
1143	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1144	>	(fabs(z - 1.0) < 0.1)) {
1145	>	w = 1.0 + (kineticTarget_
1146	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1147	>	+ Khz * (1.0 - z * z)) / Khw;
1148	>	}//no need to calculate w if x, y or z is out of range
1149	>	} else {
1150	>	w = 1.0 + kineticTarget_ / Khw;
1151	>	}
1152	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1153	>	//if w is in the right range, so should be x, y, z.
1154	>	vector<StuntDouble*>::iterator sdi;
1155	>	Vector3d vel;
1156	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1157	>	if (rnemdFluxType_ == rnemdFullKE) {
1158	>	vel = (*sdi)->getVel() * c;
1159	>	(*sdi)->setVel(vel);
1160	>	}
1161	>	if ((*sdi)->isDirectional()) {
1162	>	Vector3d angMom = (*sdi)->getJ() * c;
1163	>	(*sdi)->setJ(angMom);
1164	>	}
1165	>	}
1166	>	w = sqrt(w);
1167	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1168	>	if (rnemdFluxType_ == rnemdFullKE) {
1169	>	vel = (*sdi)->getVel();
1170	>	vel.x() *= x;
1171	>	vel.y() *= y;
1172	>	vel.z() *= z;
1173	>	(*sdi)->setVel(vel);
1174	>	}
1175	>	if ((*sdi)->isDirectional()) {
1176	>	Vector3d angMom = (*sdi)->getJ() * w;
1177	>	(*sdi)->setJ(angMom);
1178	>	}
1179	>	}
1180	>	successfulScale = true;
1181	>	kineticExchange_ += kineticTarget_;
1182	>	}
1183	>	}
1184	>	} else {
1185	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1186	>	switch(rnemdFluxType_) {
1187	>	case rnemdKE :
1188	>	/* used hotBin coeff's & only scale x & y dimensions
1189	>	RealType px = Phx / Pcx;
1190	>	RealType py = Phy / Pcy;
1191	>	a110 = Khy;
1192	>	c0 = - Khx - Khy - kineticTarget_;
1193	>	a000 = Khx;
1194	>	a111 = Kcy * py * py;
1195	>	b11 = -2.0 * Kcy * py * (1.0 + py);
1196	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1197	>	b01 = -2.0 * Kcx * px * (1.0 + px);
1198	>	a001 = Kcx * px * px;
1199	>	*/
1200	>	//scale all three dimensions, let c_x = c_y
1201	>	a000 = Kcx + Kcy;
1202	>	a110 = Kcz;
1203	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1204	>	a001 = Khx * px * px + Khy * py * py;
1205	>	a111 = Khz * pz * pz;
1206	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1207	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1208	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1209	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1210	>	break;
1211	>	case rnemdPx :
1212	>	c = 1 - momentumTarget_.x() / Pcx;
1213	>	a000 = Kcy;
1214	>	a110 = Kcz;
1215	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1216	>	a001 = py * py * Khy;
1217	>	a111 = pz * pz * Khz;
1218	>	b01 = -2.0 * Khy * py * (1.0 + py);
1219	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1220	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1221	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1222	>	break;
1223	>	case rnemdPy :
1224	>	c = 1 - momentumTarget_.y() / Pcy;
1225	>	a000 = Kcx;
1226	>	a110 = Kcz;
1227	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1228	>	a001 = px * px * Khx;
1229	>	a111 = pz * pz * Khz;
1230	>	b01 = -2.0 * Khx * px * (1.0 + px);
1231	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1232	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1233	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1234	>	break;
1235	>	case rnemdPz ://we don't really do this, do we?
1236	>	c = 1 - momentumTarget_.z() / Pcz;
1237	>	a000 = Kcx;
1238	>	a110 = Kcy;
1239	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1240	>	a001 = px * px * Khx;
1241	>	a111 = py * py * Khy;
1242	>	b01 = -2.0 * Khx * px * (1.0 + px);
1243	>	b11 = -2.0 * Khy * py * (1.0 + py);
1244	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1245	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1246	>	break;
1247	>	default :
1248	>	break;
1249	>	}
1250	>
1251	>	RealType v1 = a000 * a111 - a001 * a110;
1252	>	RealType v2 = a000 * b01;
1253	>	RealType v3 = a000 * b11;
1254	>	RealType v4 = a000 * c1 - a001 * c0;
1255	>	RealType v8 = a110 * b01;
1256	>	RealType v10 = - b01 * c0;
1257	>
1258	>	RealType u0 = v2 * v10 - v4 * v4;
1259	>	RealType u1 = -2.0 * v3 * v4;
1260	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1261	>	RealType u3 = -2.0 * v1 * v3;
1262	>	RealType u4 = - v1 * v1;
1263	>	//rescale coefficients
1264	>	RealType maxAbs = fabs(u0);
1265	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1266	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1267	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1268	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1269	>	u0 /= maxAbs;
1270	>	u1 /= maxAbs;
1271	>	u2 /= maxAbs;
1272	>	u3 /= maxAbs;
1273	>	u4 /= maxAbs;
1274	>	//max_element(start, end) is also available.
1275	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1276	>	poly.setCoefficient(4, u4);
1277	>	poly.setCoefficient(3, u3);
1278	>	poly.setCoefficient(2, u2);
1279	>	poly.setCoefficient(1, u1);
1280	>	poly.setCoefficient(0, u0);
1281	>	vector<RealType> realRoots = poly.FindRealRoots();
1282	>
1283	>	vector<RealType>::iterator ri;
1284	>	RealType r1, r2, alpha0;
1285	>	vector<pair<RealType,RealType> > rps;
1286	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1287	>	r2 = *ri;
1288	>	//check if FindRealRoots() give the right answer
1289	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1290	>	sprintf(painCave.errMsg,
1291	>	"RNEMD Warning: polynomial solve seems to have an error!");
1292	>	painCave.isFatal = 0;
1293	>	simError();
1294	>	failRootCount_++;
1295	>	}
1296	>	//might not be useful w/o rescaling coefficients
1297	>	alpha0 = -c0 - a110 * r2 * r2;
1298	>	if (alpha0 >= 0.0) {
1299	>	r1 = sqrt(alpha0 / a000);
1300	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1301	>	< 1e-6)
1302	>	{ rps.push_back(make_pair(r1, r2)); }
1303	>	if (r1 > 1e-6) { //r1 non-negative
1304	>	r1 = -r1;
1305	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1306	>	< 1e-6)
1307	>	{ rps.push_back(make_pair(r1, r2)); }
1308	>	}
1309	>	}
1310	>	}
1311	>	// Consider combining together the solving pair part w/ the searching
1312	>	// best solution part so that we don't need the pairs vector
1313	>	if (!rps.empty()) {
1314	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1315	>	RealType diff;
1316	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1317	>	vector<pair<RealType,RealType> >::iterator rpi;
1318	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1319	>	r1 = (*rpi).first;
1320	>	r2 = (*rpi).second;
1321	>	switch(rnemdFluxType_) {
1322	>	case rnemdKE :
1323	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1324	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1325	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1326	>	break;
1327	>	case rnemdPx :
1328	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1329	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1330	>	break;
1331	>	case rnemdPy :
1332	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1333	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1334	>	break;
1335	>	case rnemdPz :
1336	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1337	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1338	>	default :
1339	>	break;
1340	>	}
1341	>	if (diff < smallestDiff) {
1342	>	smallestDiff = diff;
1343	>	bestPair = *rpi;
1344	>	}
1345	>	}
1346	>	#ifdef IS_MPI
1347	>	if (worldRank == 0) {
1348	>	#endif
1349	>	// sprintf(painCave.errMsg,
1350	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1351	>	//         bestPair.first, bestPair.second);
1352	>	// painCave.isFatal = 0;
1353	>	// painCave.severity = OPENMD_INFO;
1354	>	// simError();
1355	>	#ifdef IS_MPI
1356	>	}
1357	>	#endif
1358	>
1359	>	switch(rnemdFluxType_) {
1360	>	case rnemdKE :
1361	>	x = bestPair.first;
1362	>	y = bestPair.first;
1363	>	z = bestPair.second;
1364	>	break;
1365	>	case rnemdPx :
1366	>	x = c;
1367	>	y = bestPair.first;
1368	>	z = bestPair.second;
1369	>	break;
1370	>	case rnemdPy :
1371	>	x = bestPair.first;
1372	>	y = c;
1373	>	z = bestPair.second;
1374	>	break;
1375	>	case rnemdPz :
1376	>	x = bestPair.first;
1377	>	y = bestPair.second;
1378	>	z = c;
1379	>	break;
1380	>	default :
1381	>	break;
1382	>	}
1383	>	vector<StuntDouble*>::iterator sdi;
1384	>	Vector3d vel;
1385	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1386	>	vel = (*sdi)->getVel();
1387	>	vel.x() *= x;
1388	>	vel.y() *= y;
1389	>	vel.z() *= z;
1390	>	(*sdi)->setVel(vel);
1391	>	}
1392	>	//convert to hotBin coefficient
1393	>	x = 1.0 + px * (1.0 - x);
1394	>	y = 1.0 + py * (1.0 - y);
1395	>	z = 1.0 + pz * (1.0 - z);
1396	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1397	>	vel = (*sdi)->getVel();
1398	>	vel.x() *= x;
1399	>	vel.y() *= y;
1400	>	vel.z() *= z;
1401	>	(*sdi)->setVel(vel);
1402	>	}
1403	>	successfulScale = true;
1404	>	switch(rnemdFluxType_) {
1405	>	case rnemdKE :
1406	>	kineticExchange_ += kineticTarget_;
1407	>	break;
1408	>	case rnemdPx :
1409	>	case rnemdPy :
1410	>	case rnemdPz :
1411	>	momentumExchange_ += momentumTarget_;
1412	>	break;
1413	>	default :
1414	>	break;
1415	>	}
1416	>	}
1417	>	}
1418	>	if (successfulScale != true) {
1419	>	sprintf(painCave.errMsg,
1420	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1421	>	"\tthe constraint equations may not exist or there may be\n"
1422	>	"\tno selected objects in one or both slabs.\n");
1423	>	painCave.isFatal = 0;
1424	>	painCave.severity = OPENMD_INFO;
1425	>	simError();
1426	>	failTrialCount_++;
1427	>	}
1428	>	}
1429	>
1430	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1431	>	if (!doRNEMD_) return;
1432	>	int selei;
1433	>	int selej;
1434	>
1435	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1436	>	RealType time = currentSnap_->getTime();
1437	>	Mat3x3d hmat = currentSnap_->getHmat();
1438	>
1439	>	StuntDouble* sd;
1440	>
1441	>	vector<StuntDouble*> hotBin, coldBin;
1442	>
1443	>	Vector3d Ph(V3Zero);
1444	>	Vector3d Lh(V3Zero);
1445	>	RealType Mh = 0.0;
1446	>	Mat3x3d Ih(0.0);
1447	>	RealType Kh = 0.0;
1448	>	Vector3d Pc(V3Zero);
1449	>	Vector3d Lc(V3Zero);
1450	>	RealType Mc = 0.0;
1451	>	Mat3x3d Ic(0.0);
1452	>	RealType Kc = 0.0;
1453	>
1454	>	// Constraints can be on only the linear or angular momentum, but
1455	>	// not both.  Usually, the user will specify which they want, but
1456	>	// in case they don't, the use of periodic boundaries should make
1457	>	// the choice for us.
1458	>	bool doLinearPart = false;
1459	>	bool doAngularPart = false;
1460	>
1461	>	switch (rnemdFluxType_) {
1462	>	case rnemdPx:
1463	>	case rnemdPy:
1464	>	case rnemdPz:
1465	>	case rnemdPvector:
1466	>	case rnemdKePx:
1467	>	case rnemdKePy:
1468	>	case rnemdKePvector:
1469	>	doLinearPart = true;
1470		break;
1471	<	case rnemdPzScale ://we don't really do this, do we?
1472	<	c = 1 - targetFlux_ / Pcz;
1473	<	a000 = Kcx;
1474	<	a110 = Kcy;
1475	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1476	<	a001 = px * px * Khx;
1477	<	a111 = py * py * Khy;
1478	<	b01 = -2.0 * Khx * px * (1.0 + px);
1479	<	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 :
1471	>	case rnemdLx:
1472	>	case rnemdLy:
1473	>	case rnemdLz:
1474	>	case rnemdLvector:
1475	>	case rnemdKeLx:
1476	>	case rnemdKeLy:
1477	>	case rnemdKeLz:
1478	>	case rnemdKeLvector:
1479	>	doAngularPart = true;
1480		break;
1481	+	case rnemdKE:
1482	+	case rnemdRotKE:
1483	+	case rnemdFullKE:
1484	+	default:
1485	+	if (usePeriodicBoundaryConditions_)
1486	+	doLinearPart = true;
1487	+	else
1488	+	doAngularPart = true;
1489	+	break;
1490		}
1491	+
1492	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1493	+	sd = smanA.nextSelected(selei)) {
1494
1495	<	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;
1495	>	Vector3d pos = sd->getPos();
1496
1497	<	RealType u0 = v2 * v10 - v4 * v4;
1498	<	RealType u1 = -2.0 * v3 * v4;
1499	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1500	<	RealType u3 = -2.0 * v1 * v3;
1501	<	RealType u4 = - v1 * v1;
1502	<	//rescale coefficients
1503	<	RealType maxAbs = fabs(u0);
1504	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1505	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1506	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1507	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1508	<	u0 /= maxAbs;
1509	<	u1 /= maxAbs;
1510	<	u2 /= maxAbs;
1511	<	u3 /= maxAbs;
1512	<	u4 /= maxAbs;
1513	<	//max_element(start, end) is also available.
1514	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1515	<	poly.setCoefficient(4, u4);
1516	<	poly.setCoefficient(3, u3);
1517	<	poly.setCoefficient(2, u2);
1518	<	poly.setCoefficient(1, u1);
1519	<	poly.setCoefficient(0, u0);
1520	<	std::vector<RealType> realRoots = poly.FindRealRoots();
1521	<
1522	<	std::vector<RealType>::iterator ri;
1523	<	RealType r1, r2, alpha0;
1524	<	std::vector<std::pair<RealType,RealType> > rps;
1525	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1526	<	r2 = *ri;
1527	<	//check if FindRealRoots() give the right answer
1528	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1529	<	sprintf(painCave.errMsg,
1530	<	"RNEMD Warning: polynomial solve seems to have an error!");
1531	<	painCave.isFatal = 0;
1532	<	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)); }
1497	>	// wrap the stuntdouble's position back into the box:
1498	>
1499	>	if (usePeriodicBoundaryConditions_)
1500	>	currentSnap_->wrapVector(pos);
1501	>
1502	>	RealType mass = sd->getMass();
1503	>	Vector3d vel = sd->getVel();
1504	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1505	>	RealType r2;
1506	>
1507	>	hotBin.push_back(sd);
1508	>	Ph += mass * vel;
1509	>	Mh += mass;
1510	>	Kh += mass * vel.lengthSquare();
1511	>	Lh += mass * cross(rPos, vel);
1512	>	Ih -= outProduct(rPos, rPos) * mass;
1513	>	r2 = rPos.lengthSquare();
1514	>	Ih(0, 0) += mass * r2;
1515	>	Ih(1, 1) += mass * r2;
1516	>	Ih(2, 2) += mass * r2;
1517	>
1518	>	if (rnemdFluxType_ == rnemdFullKE) {
1519	>	if (sd->isDirectional()) {
1520	>	Vector3d angMom = sd->getJ();
1521	>	Mat3x3d I = sd->getI();
1522	>	if (sd->isLinear()) {
1523	>	int i = sd->linearAxis();
1524	>	int j = (i + 1) % 3;
1525	>	int k = (i + 2) % 3;
1526	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1527	>	angMom[k] * angMom[k] / I(k, k);
1528	>	} else {
1529	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1530	>	angMom[1] * angMom[1] / I(1, 1) +
1531	>	angMom[2] * angMom[2] / I(2, 2);
1532	>	}
1533		}
1534		}
1535		}
1536	<	// Consider combininig together the solving pair part w/ the searching
1537	<	// best solution part so that we don't need the pairs vector
1538	<	if (!rps.empty()) {
1539	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1540	<	RealType diff;
1541	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1542	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1543	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1544	<	r1 = (*rpi).first;
1545	<	r2 = (*rpi).second;
1546	<	switch(rnemdType_) {
1547	<	case rnemdKineticScale :
1548	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1549	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1550	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1551	<	break;
1552	<	case rnemdPxScale :
1553	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1554	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1555	<	break;
1556	<	case rnemdPyScale :
1557	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1558	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1559	<	break;
1560	<	case rnemdPzScale :
1561	<	default :
1562	<	break;
1536	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1537	>	sd = smanB.nextSelected(selej)) {
1538	>
1539	>	Vector3d pos = sd->getPos();
1540	>
1541	>	// wrap the stuntdouble's position back into the box:
1542	>
1543	>	if (usePeriodicBoundaryConditions_)
1544	>	currentSnap_->wrapVector(pos);
1545	>
1546	>	RealType mass = sd->getMass();
1547	>	Vector3d vel = sd->getVel();
1548	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1549	>	RealType r2;
1550	>
1551	>	coldBin.push_back(sd);
1552	>	Pc += mass * vel;
1553	>	Mc += mass;
1554	>	Kc += mass * vel.lengthSquare();
1555	>	Lc += mass * cross(rPos, vel);
1556	>	Ic -= outProduct(rPos, rPos) * mass;
1557	>	r2 = rPos.lengthSquare();
1558	>	Ic(0, 0) += mass * r2;
1559	>	Ic(1, 1) += mass * r2;
1560	>	Ic(2, 2) += mass * r2;
1561	>
1562	>	if (rnemdFluxType_ == rnemdFullKE) {
1563	>	if (sd->isDirectional()) {
1564	>	Vector3d angMom = sd->getJ();
1565	>	Mat3x3d I = sd->getI();
1566	>	if (sd->isLinear()) {
1567	>	int i = sd->linearAxis();
1568	>	int j = (i + 1) % 3;
1569	>	int k = (i + 2) % 3;
1570	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1571	>	angMom[k] * angMom[k] / I(k, k);
1572	>	} else {
1573	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1574	>	angMom[1] * angMom[1] / I(1, 1) +
1575	>	angMom[2] * angMom[2] / I(2, 2);
1576	>	}
1577		}
783	–	if (diff < smallestDiff) {
784	–	smallestDiff = diff;
785	–	bestPair = *rpi;
786	–	}
1578		}
1579	+	}
1580	+
1581	+	Kh *= 0.5;
1582	+	Kc *= 0.5;
1583	+
1584		#ifdef IS_MPI
1585	<	if (worldRank == 0) {
1585	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1586	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1587	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1588	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1589	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1590	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1591	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1592	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1593	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1594	>	MPI::REALTYPE, MPI::SUM);
1595	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1596	>	MPI::REALTYPE, MPI::SUM);
1597		#endif
1598	<	std::cerr << "we choose r1 = " << bestPair.first
792	<	<< " and r2 = " << bestPair.second << "\n";
793	<	#ifdef IS_MPI
794	<	}
795	<	#endif
1598	>
1599
1600	<	RealType x, y, z;
1601	<	switch(rnemdType_) {
1602	<	case rnemdKineticScale :
1603	<	x = bestPair.first;
1604	<	y = bestPair.first;
1605	<	z = bestPair.second;
1606	<	break;
1607	<	case rnemdPxScale :
1608	<	x = c;
1609	<	y = bestPair.first;
1610	<	z = bestPair.second;
1611	<	break;
1612	<	case rnemdPyScale :
1613	<	x = bestPair.first;
1614	<	y = c;
1615	<	z = bestPair.second;
1616	<	break;
1617	<	case rnemdPzScale :
1618	<	x = bestPair.first;
1619	<	y = bestPair.second;
1620	<	z = c;
1621	<	break;
1622	<	default :
1623	<	break;
1624	<	}
1625	<	std::vector<StuntDouble*>::iterator sdi;
1626	<	Vector3d vel;
1627	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1628	<	vel = (*sdi)->getVel();
1629	<	vel.x() *= x;
1630	<	vel.y() *= y;
1631	<	vel.z() *= z;
1632	<	(*sdi)->setVel(vel);
1633	<	}
1634	<	//convert to hotBin coefficient
1635	<	x = 1.0 + px * (1.0 - x);
1636	<	y = 1.0 + py * (1.0 - y);
1637	<	z = 1.0 + pz * (1.0 - z);
1638	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1639	<	vel = (*sdi)->getVel();
1640	<	vel.x() *= x;
1641	<	vel.y() *= y;
1642	<	vel.z() *= z;
1643	<	(*sdi)->setVel(vel);
1600	>	Vector3d ac, acrec, bc, bcrec;
1601	>	Vector3d ah, ahrec, bh, bhrec;
1602	>
1603	>	bool successfulExchange = false;
1604	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1605	>	Vector3d vc = Pc / Mc;
1606	>	ac = -momentumTarget_ / Mc + vc;
1607	>	acrec = -momentumTarget_ / Mc;
1608	>
1609	>	// We now need the inverse of the inertia tensor to calculate the
1610	>	// angular velocity of the cold slab;
1611	>	Mat3x3d Ici = Ic.inverse();
1612	>	Vector3d omegac = Ici * Lc;
1613	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1614	>	bcrec = bc - omegac;
1615	>
1616	>	RealType cNumerator = Kc - kineticTarget_;
1617	>	if (doLinearPart)
1618	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1619	>
1620	>	if (doAngularPart)
1621	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1622	>
1623	>	if (cNumerator > 0.0) {
1624	>
1625	>	RealType cDenominator = Kc;
1626	>
1627	>	if (doLinearPart)
1628	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1629	>
1630	>	if (doAngularPart)
1631	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1632	>
1633	>	if (cDenominator > 0.0) {
1634	>	RealType c = sqrt(cNumerator / cDenominator);
1635	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1636	>
1637	>	Vector3d vh = Ph / Mh;
1638	>	ah = momentumTarget_ / Mh + vh;
1639	>	ahrec = momentumTarget_ / Mh;
1640	>
1641	>	// We now need the inverse of the inertia tensor to
1642	>	// calculate the angular velocity of the hot slab;
1643	>	Mat3x3d Ihi = Ih.inverse();
1644	>	Vector3d omegah = Ihi * Lh;
1645	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1646	>	bhrec = bh - omegah;
1647	>
1648	>	RealType hNumerator = Kh + kineticTarget_;
1649	>	if (doLinearPart)
1650	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1651	>
1652	>	if (doAngularPart)
1653	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1654	>
1655	>	if (hNumerator > 0.0) {
1656	>
1657	>	RealType hDenominator = Kh;
1658	>	if (doLinearPart)
1659	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1660	>	if (doAngularPart)
1661	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1662	>
1663	>	if (hDenominator > 0.0) {
1664	>	RealType h = sqrt(hNumerator / hDenominator);
1665	>	if ((h > 0.9) && (h < 1.1)) {
1666	>
1667	>	vector<StuntDouble*>::iterator sdi;
1668	>	Vector3d vel;
1669	>	Vector3d rPos;
1670	>
1671	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1672	>	//vel = (*sdi)->getVel();
1673	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1674	>	if (doLinearPart)
1675	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1676	>	if (doAngularPart)
1677	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1678	>
1679	>	(*sdi)->setVel(vel);
1680	>	if (rnemdFluxType_ == rnemdFullKE) {
1681	>	if ((*sdi)->isDirectional()) {
1682	>	Vector3d angMom = (*sdi)->getJ() * c;
1683	>	(*sdi)->setJ(angMom);
1684	>	}
1685	>	}
1686	>	}
1687	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1688	>	//vel = (*sdi)->getVel();
1689	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1690	>	if (doLinearPart)
1691	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1692	>	if (doAngularPart)
1693	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1694	>
1695	>	(*sdi)->setVel(vel);
1696	>	if (rnemdFluxType_ == rnemdFullKE) {
1697	>	if ((*sdi)->isDirectional()) {
1698	>	Vector3d angMom = (*sdi)->getJ() * h;
1699	>	(*sdi)->setJ(angMom);
1700	>	}
1701	>	}
1702	>	}
1703	>	successfulExchange = true;
1704	>	kineticExchange_ += kineticTarget_;
1705	>	momentumExchange_ += momentumTarget_;
1706	>	angularMomentumExchange_ += angularMomentumTarget_;
1707	>	}
1708	>	}
1709	>	}
1710	>	}
1711	>	}
1712		}
1713	<	exchangeSum_ += targetFlux_;
1714	<	//we may want to check whether the exchange has been successful
1715	<	} else {
1716	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1713	>	}
1714	>	if (successfulExchange != true) {
1715	>	sprintf(painCave.errMsg,
1716	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1717	>	"\tthe constraint equations may not exist or there may be\n"
1718	>	"\tno selected objects in one or both slabs.\n");
1719	>	painCave.isFatal = 0;
1720	>	painCave.severity = OPENMD_INFO;
1721	>	simError();
1722		failTrialCount_++;
1723		}
848	–
1724		}
1725
1726	+	RealType RNEMD::getDividingArea() {
1727	+
1728	+	if (hasDividingArea_) return dividingArea_;
1729	+
1730	+	RealType areaA, areaB;
1731	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1732	+
1733	+	if (hasSelectionA_) {
1734	+
1735	+	if (evaluatorA_.hasSurfaceArea())
1736	+	areaA = evaluatorA_.getSurfaceArea();
1737	+	else {
1738	+
1739	+	cerr << "selection A did not have surface area, recomputing\n";
1740	+	int isd;
1741	+	StuntDouble* sd;
1742	+	vector<StuntDouble*> aSites;
1743	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1744	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1745	+	sd = seleManA_.nextSelected(isd)) {
1746	+	aSites.push_back(sd);
1747	+	}
1748	+	#if defined(HAVE_QHULL)
1749	+	ConvexHull* surfaceMeshA = new ConvexHull();
1750	+	surfaceMeshA->computeHull(aSites);
1751	+	areaA = surfaceMeshA->getArea();
1752	+	delete surfaceMeshA;
1753	+	#else
1754	+	sprintf( painCave.errMsg,
1755	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1756	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1757	+	painCave.severity = OPENMD_ERROR;
1758	+	painCave.isFatal = 1;
1759	+	simError();
1760	+	#endif
1761	+	}
1762	+
1763	+	} else {
1764	+	if (usePeriodicBoundaryConditions_) {
1765	+	// in periodic boundaries, the surface area is twice the x-y
1766	+	// area of the current box:
1767	+	areaA = 2.0 * snap->getXYarea();
1768	+	} else {
1769	+	// in non-periodic simulations, without explicitly setting
1770	+	// selections, the sphere radius sets the surface area of the
1771	+	// dividing surface:
1772	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1773	+	}
1774	+	}
1775	+
1776	+	if (hasSelectionB_) {
1777	+	if (evaluatorB_.hasSurfaceArea())
1778	+	areaB = evaluatorB_.getSurfaceArea();
1779	+	else {
1780	+	cerr << "selection B did not have surface area, recomputing\n";
1781	+
1782	+	int isd;
1783	+	StuntDouble* sd;
1784	+	vector<StuntDouble*> bSites;
1785	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1786	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1787	+	sd = seleManB_.nextSelected(isd)) {
1788	+	bSites.push_back(sd);
1789	+	}
1790	+
1791	+	#if defined(HAVE_QHULL)
1792	+	ConvexHull* surfaceMeshB = new ConvexHull();
1793	+	surfaceMeshB->computeHull(bSites);
1794	+	areaB = surfaceMeshB->getArea();
1795	+	delete surfaceMeshB;
1796	+	#else
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1799	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1800	+	painCave.severity = OPENMD_ERROR;
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	#endif
1804	+	}
1805	+
1806	+	} else {
1807	+	if (usePeriodicBoundaryConditions_) {
1808	+	// in periodic boundaries, the surface area is twice the x-y
1809	+	// area of the current box:
1810	+	areaB = 2.0 * snap->getXYarea();
1811	+	} else {
1812	+	// in non-periodic simulations, without explicitly setting
1813	+	// selections, but if a sphereBradius has been set, just use that:
1814	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1815	+	}
1816	+	}
1817	+
1818	+	dividingArea_ = min(areaA, areaB);
1819	+	hasDividingArea_ = true;
1820	+	return dividingArea_;
1821	+	}
1822	+
1823		void RNEMD::doRNEMD() {
1824	+	if (!doRNEMD_) return;
1825	+	trialCount_++;
1826
1827	<	switch(rnemdType_) {
1828	<	case rnemdKineticScale :
1829	<	case rnemdPxScale :
1830	<	case rnemdPyScale :
1831	<	case rnemdPzScale :
1832	<	doScale();
1827	>	// object evaluator:
1828	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1829	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1830	>
1831	>	evaluatorA_.loadScriptString(selectionA_);
1832	>	evaluatorB_.loadScriptString(selectionB_);
1833	>
1834	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1835	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1836	>
1837	>	commonA_ = seleManA_ & seleMan_;
1838	>	commonB_ = seleManB_ & seleMan_;
1839	>
1840	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1841	>	// dt = exchange time interval
1842	>	// flux = target flux
1843	>	// dividingArea = smallest dividing surface between the two regions
1844	>
1845	>	hasDividingArea_ = false;
1846	>	RealType area = getDividingArea();
1847	>
1848	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1849	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1850	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1851	>
1852	>	switch(rnemdMethod_) {
1853	>	case rnemdSwap:
1854	>	doSwap(commonA_, commonB_);
1855		break;
1856	<	case rnemdKineticSwap :
1857	<	case rnemdPx :
862	<	case rnemdPy :
863	<	case rnemdPz :
864	<	doSwap();
1856	>	case rnemdNIVS:
1857	>	doNIVS(commonA_, commonB_);
1858		break;
1859	<	case rnemdUnknown :
1859	>	case rnemdVSS:
1860	>	doVSS(commonA_, commonB_);
1861	>	break;
1862	>	case rnemdUnkownMethod:
1863		default :
1864		break;
1865		}
1866		}
1867
1868		void RNEMD::collectData() {
1869	<
1869	>	if (!doRNEMD_) return;
1870		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1871	+
1872	+	// collectData can be called more frequently than the doRNEMD, so use the
1873	+	// computed area from the last exchange time:
1874	+	RealType area = getDividingArea();
1875	+	areaAccumulator_->add(area);
1876		Mat3x3d hmat = currentSnap_->getHmat();
876	–
1877		seleMan_.setSelectionSet(evaluator_.evaluate());
1878
1879	<	int selei;
1879	>	int selei(0);
1880		StuntDouble* sd;
1881	<	int idx;
1881	>	int binNo;
1882
1883	+	vector<RealType> binMass(nBins_, 0.0);
1884	+	vector<RealType> binPx(nBins_, 0.0);
1885	+	vector<RealType> binPy(nBins_, 0.0);
1886	+	vector<RealType> binPz(nBins_, 0.0);
1887	+	vector<RealType> binOmegax(nBins_, 0.0);
1888	+	vector<RealType> binOmegay(nBins_, 0.0);
1889	+	vector<RealType> binOmegaz(nBins_, 0.0);
1890	+	vector<RealType> binKE(nBins_, 0.0);
1891	+	vector<int> binDOF(nBins_, 0);
1892	+	vector<int> binCount(nBins_, 0);
1893	+
1894	+	// alternative approach, track all molecules instead of only those
1895	+	// selected for scaling/swapping:
1896	+	/*
1897	+	SimInfo::MoleculeIterator miter;
1898	+	vector<StuntDouble*>::iterator iiter;
1899	+	Molecule* mol;
1900	+	StuntDouble* sd;
1901	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1902	+	mol = info_->nextMolecule(miter))
1903	+	sd is essentially sd
1904	+	for (sd = mol->beginIntegrableObject(iiter);
1905	+	sd != NULL;
1906	+	sd = mol->nextIntegrableObject(iiter))
1907	+	*/
1908	+
1909		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1910	<	sd = seleMan_.nextSelected(selei)) {
1911	<
886	<	idx = sd->getLocalIndex();
887	<
1910	>	sd = seleMan_.nextSelected(selei)) {
1911	>
1912		Vector3d pos = sd->getPos();
1913
1914		// wrap the stuntdouble's position back into the box:
1915
1916	<	if (usePeriodicBoundaryConditions_)
1916	>	if (usePeriodicBoundaryConditions_) {
1917		currentSnap_->wrapVector(pos);
1918	<
1919	<	// which bin is this stuntdouble in?
1920	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1921	<
1922	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1918	>	// which bin is this stuntdouble in?
1919	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1920	>	// Shift molecules by half a box to have bins start at 0
1921	>	// The modulo operator is used to wrap the case when we are
1922	>	// beyond the end of the bins back to the beginning.
1923	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1924	>	} else {
1925	>	Vector3d rPos = pos - coordinateOrigin_;
1926	>	binNo = int(rPos.length() / binWidth_);
1927	>	}
1928
900	–	if (rnemdLogWidth_ == midBin_ + 1)
901	–	if (binNo > midBin_)
902	–	binNo = nBins_ - binNo;
903	–
1929		RealType mass = sd->getMass();
1930		Vector3d vel = sd->getVel();
1931	<	RealType value;
1932	<	RealType xVal, yVal, zVal;
1931	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1932	>	Vector3d aVel = cross(rPos, vel);
1933	>
1934	>	if (binNo >= 0 && binNo < nBins_)  {
1935	>	binCount[binNo]++;
1936	>	binMass[binNo] += mass;
1937	>	binPx[binNo] += mass*vel.x();
1938	>	binPy[binNo] += mass*vel.y();
1939	>	binPz[binNo] += mass*vel.z();
1940	>	binOmegax[binNo] += aVel.x();
1941	>	binOmegay[binNo] += aVel.y();
1942	>	binOmegaz[binNo] += aVel.z();
1943	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1944	>	binDOF[binNo] += 3;
1945	>
1946	>	if (sd->isDirectional()) {
1947	>	Vector3d angMom = sd->getJ();
1948	>	Mat3x3d I = sd->getI();
1949	>	if (sd->isLinear()) {
1950	>	int i = sd->linearAxis();
1951	>	int j = (i + 1) % 3;
1952	>	int k = (i + 2) % 3;
1953	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1954	>	angMom[k] * angMom[k] / I(k, k));
1955	>	binDOF[binNo] += 2;
1956	>	} else {
1957	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1958	>	angMom[1] * angMom[1] / I(1, 1) +
1959	>	angMom[2] * angMom[2] / I(2, 2));
1960	>	binDOF[binNo] += 3;
1961	>	}
1962	>	}
1963	>	}
1964	>	}
1965	>
1966	>	#ifdef IS_MPI
1967	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1968	>	nBins_, MPI::INT, MPI::SUM);
1969	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1970	>	nBins_, MPI::REALTYPE, MPI::SUM);
1971	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1972	>	nBins_, MPI::REALTYPE, MPI::SUM);
1973	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1974	>	nBins_, MPI::REALTYPE, MPI::SUM);
1975	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1976	>	nBins_, MPI::REALTYPE, MPI::SUM);
1977	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1978	>	nBins_, MPI::REALTYPE, MPI::SUM);
1979	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1980	>	nBins_, MPI::REALTYPE, MPI::SUM);
1981	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1982	>	nBins_, MPI::REALTYPE, MPI::SUM);
1983	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1984	>	nBins_, MPI::REALTYPE, MPI::SUM);
1985	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1986	>	nBins_, MPI::INT, MPI::SUM);
1987	>	#endif
1988
1989	<	switch(rnemdType_) {
1990	<	case rnemdKineticSwap :
1991	<	case rnemdKineticScale :
1992	<
1993	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1994	<	vel[2]*vel[2]);
1995	<
1996	<	valueCount_[binNo] += 3;
1997	<	if (sd->isDirectional()) {
1998	<	Vector3d angMom = sd->getJ();
1999	<	Mat3x3d I = sd->getI();
2000	<
2001	<	if (sd->isLinear()) {
2002	<	int i = sd->linearAxis();
2003	<	int j = (i + 1) % 3;
2004	<	int k = (i + 2) % 3;
2005	<	value += angMom[j] * angMom[j] / I(j, j) +
2006	<	angMom[k] * angMom[k] / I(k, k);
1989	>	Vector3d vel;
1990	>	Vector3d aVel;
1991	>	RealType den;
1992	>	RealType temp;
1993	>	RealType z;
1994	>	RealType r;
1995	>	for (int i = 0; i < nBins_; i++) {
1996	>	if (usePeriodicBoundaryConditions_) {
1997	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1998	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1999	>	/ currentSnap_->getVolume() ;
2000	>	} else {
2001	>	r = (((RealType)i + 0.5) * binWidth_);
2002	>	RealType rinner = (RealType)i * binWidth_;
2003	>	RealType router = (RealType)(i+1) * binWidth_;
2004	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2005	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2006	>	}
2007	>	vel.x() = binPx[i] / binMass[i];
2008	>	vel.y() = binPy[i] / binMass[i];
2009	>	vel.z() = binPz[i] / binMass[i];
2010	>	aVel.x() = binOmegax[i] / binCount[i];
2011	>	aVel.y() = binOmegay[i] / binCount[i];
2012	>	aVel.z() = binOmegaz[i] / binCount[i];
2013
2014	<	valueCount_[binNo] +=2;
2015	<
2016	<	} else {
2017	<	value += angMom[0]*angMom[0]/I(0, 0)
2018	<	+ angMom[1]*angMom[1]/I(1, 1)
2019	<	+ angMom[2]*angMom[2]/I(2, 2);
2020	<	valueCount_[binNo] +=3;
2021	<	}
2022	<	}
2023	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
2024	<
2025	<	break;
2026	<	case rnemdPx :
2027	<	case rnemdPxScale :
2028	<	value = mass * vel[0];
2029	<	valueCount_[binNo]++;
2030	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
2031	<	/ PhysicalConstants::kb;
2032	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
2033	<	/ PhysicalConstants::kb;
2034	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
2035	<	/ PhysicalConstants::kb;
2036	<	xTempHist_[binNo] += xVal;
2037	<	yTempHist_[binNo] += yVal;
2038	<	zTempHist_[binNo] += zVal;
2039	<	break;
2040	<	case rnemdPy :
2041	<	case rnemdPyScale :
2042	<	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;
2014	>	if (binCount[i] > 0) {
2015	>	// only add values if there are things to add
2016	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2017	>	PhysicalConstants::energyConvert);
2018	>
2019	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2020	>	if(outputMask_[j]) {
2021	>	switch(j) {
2022	>	case Z:
2023	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2024	>	break;
2025	>	case R:
2026	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2027	>	break;
2028	>	case TEMPERATURE:
2029	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2030	>	break;
2031	>	case VELOCITY:
2032	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2033	>	break;
2034	>	case ANGULARVELOCITY:
2035	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2036	>	break;
2037	>	case DENSITY:
2038	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2039	>	break;
2040	>	}
2041	>	}
2042	>	}
2043		}
968	–	valueHist_[binNo] += value;
2044		}
2045	<
2045	>	hasData_ = true;
2046		}
2047
2048		void RNEMD::getStarted() {
2049	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2050	<	Stats& stat = currentSnap_->statData;
2051	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2049	>	if (!doRNEMD_) return;
2050	>	hasDividingArea_ = false;
2051	>	collectData();
2052	>	writeOutputFile();
2053		}
2054
2055	<	void RNEMD::getStatus() {
2056	<
2057	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2058	<	Stats& stat = currentSnap_->statData;
2059	<	RealType time = currentSnap_->getTime();
2060	<
2061	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2062	<	//or to be more meaningful, define another item as exchangeSum_ / time
2063	<	int j;
2064	<
2055	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2056	>	if (!doRNEMD_) return;
2057	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2058	>
2059	>	while(tokenizer.hasMoreTokens()) {
2060	>	std::string token(tokenizer.nextToken());
2061	>	toUpper(token);
2062	>	OutputMapType::iterator i = outputMap_.find(token);
2063	>	if (i != outputMap_.end()) {
2064	>	outputMask_.set(i->second);
2065	>	} else {
2066	>	sprintf( painCave.errMsg,
2067	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2068	>	"\toutputFileFormat keyword.\n", token.c_str() );
2069	>	painCave.isFatal = 0;
2070	>	painCave.severity = OPENMD_ERROR;
2071	>	simError();
2072	>	}
2073	>	}
2074	>	}
2075	>
2076	>	void RNEMD::writeOutputFile() {
2077	>	if (!doRNEMD_) return;
2078	>	if (!hasData_) return;
2079	>
2080		#ifdef IS_MPI
990	–
991	–	// all processors have the same number of bins, and STL vectors pack their
992	–	// arrays, so in theory, this should be safe:
993	–
994	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
995	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
996	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
997	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
998	–	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
999	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1000	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1001	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1002	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1003	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1004	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1005	–	}
2081		// If we're the root node, should we print out the results
2082		int worldRank = MPI::COMM_WORLD.Get_rank();
2083		if (worldRank == 0) {
2084		#endif
2085	<	rnemdLog_ << time;
2086	<	for (j = 0; j < rnemdLogWidth_; j++) {
2087	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
2085	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2086	>
2087	>	if( !rnemdFile_ ){
2088	>	sprintf( painCave.errMsg,
2089	>	"Could not open \"%s\" for RNEMD output.\n",
2090	>	rnemdFileName_.c_str());
2091	>	painCave.isFatal = 1;
2092	>	simError();
2093		}
2094	<	rnemdLog_ << "\n";
2095	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
2096	<	xTempLog_ << time;
2097	<	for (j = 0; j < rnemdLogWidth_; j++) {
2098	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
2094	>
2095	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2096	>
2097	>	RealType time = currentSnap_->getTime();
2098	>	RealType avgArea;
2099	>	areaAccumulator_->getAverage(avgArea);
2100	>
2101	>	RealType Jz(0.0);
2102	>	Vector3d JzP(V3Zero);
2103	>	Vector3d JzL(V3Zero);
2104	>	if (time >= info_->getSimParams()->getDt()) {
2105	>	Jz = kineticExchange_ / (time * avgArea)
2106	>	/ PhysicalConstants::energyConvert;
2107	>	JzP = momentumExchange_ / (time * avgArea);
2108	>	JzL = angularMomentumExchange_ / (time * avgArea);
2109	>	}
2110	>
2111	>	rnemdFile_ << "#######################################################\n";
2112	>	rnemdFile_ << "# RNEMD {\n";
2113	>
2114	>	map<string, RNEMDMethod>::iterator mi;
2115	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2116	>	if ( (*mi).second == rnemdMethod_)
2117	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2118	>	}
2119	>	map<string, RNEMDFluxType>::iterator fi;
2120	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2121	>	if ( (*fi).second == rnemdFluxType_)
2122	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2123	>	}
2124	>
2125	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2126	>
2127	>	rnemdFile_ << "#    objectSelection = \""
2128	>	<< rnemdObjectSelection_ << "\";\n";
2129	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2130	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2131	>	rnemdFile_ << "# }\n";
2132	>	rnemdFile_ << "#######################################################\n";
2133	>	rnemdFile_ << "# RNEMD report:\n";
2134	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2135	>	rnemdFile_ << "# Target flux:\n";
2136	>	rnemdFile_ << "#           kinetic = "
2137	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2138	>	<< " (kcal/mol/A^2/fs)\n";
2139	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2140	>	<< " (amu/A/fs^2)\n";
2141	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2142	>	<< " (amu/A^2/fs^2)\n";
2143	>	rnemdFile_ << "# Target one-time exchanges:\n";
2144	>	rnemdFile_ << "#          kinetic = "
2145	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2146	>	<< " (kcal/mol)\n";
2147	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2148	>	<< " (amu*A/fs)\n";
2149	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2150	>	<< " (amu*A^2/fs)\n";
2151	>	rnemdFile_ << "# Actual exchange totals:\n";
2152	>	rnemdFile_ << "#          kinetic = "
2153	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2154	>	<< " (kcal/mol)\n";
2155	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2156	>	<< " (amu*A/fs)\n";
2157	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2158	>	<< " (amu*A^2/fs)\n";
2159	>	rnemdFile_ << "# Actual flux:\n";
2160	>	rnemdFile_ << "#          kinetic = " << Jz
2161	>	<< " (kcal/mol/A^2/fs)\n";
2162	>	rnemdFile_ << "#          momentum = " << JzP
2163	>	<< " (amu/A/fs^2)\n";
2164	>	rnemdFile_ << "#  angular momentum = " << JzL
2165	>	<< " (amu/A^2/fs^2)\n";
2166	>	rnemdFile_ << "# Exchange statistics:\n";
2167	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2168	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2169	>	if (rnemdMethod_ == rnemdNIVS) {
2170	>	rnemdFile_ << "#  NIVS root-check errors = "
2171	>	<< failRootCount_ << "\n";
2172	>	}
2173	>	rnemdFile_ << "#######################################################\n";
2174	>
2175	>
2176	>
2177	>	//write title
2178	>	rnemdFile_ << "#";
2179	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2180	>	if (outputMask_[i]) {
2181	>	rnemdFile_ << "\t" << data_[i].title <<
2182	>	"(" << data_[i].units << ")";
2183	>	// add some extra tabs for column alignment
2184	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2185		}
2186	<	xTempLog_ << "\n";
2187	<	yTempLog_ << time;
2188	<	for (j = 0; j < rnemdLogWidth_; j++) {
2189	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
2186	>	}
2187	>	rnemdFile_ << std::endl;
2188	>
2189	>	rnemdFile_.precision(8);
2190	>
2191	>	for (int j = 0; j < nBins_; j++) {
2192	>
2193	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2194	>	if (outputMask_[i]) {
2195	>	if (data_[i].dataType == "RealType")
2196	>	writeReal(i,j);
2197	>	else if (data_[i].dataType == "Vector3d")
2198	>	writeVector(i,j);
2199	>	else {
2200	>	sprintf( painCave.errMsg,
2201	>	"RNEMD found an unknown data type for: %s ",
2202	>	data_[i].title.c_str());
2203	>	painCave.isFatal = 1;
2204	>	simError();
2205	>	}
2206	>	}
2207		}
2208	<	yTempLog_ << "\n";
2209	<	zTempLog_ << time;
2210	<	for (j = 0; j < rnemdLogWidth_; j++) {
2211	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
2208	>	rnemdFile_ << std::endl;
2209	>
2210	>	}
2211	>
2212	>	rnemdFile_ << "#######################################################\n";
2213	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2214	>	rnemdFile_ << "#######################################################\n";
2215	>
2216	>
2217	>	for (int j = 0; j < nBins_; j++) {
2218	>	rnemdFile_ << "#";
2219	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2220	>	if (outputMask_[i]) {
2221	>	if (data_[i].dataType == "RealType")
2222	>	writeRealStdDev(i,j);
2223	>	else if (data_[i].dataType == "Vector3d")
2224	>	writeVectorStdDev(i,j);
2225	>	else {
2226	>	sprintf( painCave.errMsg,
2227	>	"RNEMD found an unknown data type for: %s ",
2228	>	data_[i].title.c_str());
2229	>	painCave.isFatal = 1;
2230	>	simError();
2231	>	}
2232	>	}
2233		}
2234	<	zTempLog_ << "\n";
2235	<	}
2234	>	rnemdFile_ << std::endl;
2235	>
2236	>	}
2237	>
2238	>	rnemdFile_.flush();
2239	>	rnemdFile_.close();
2240	>
2241		#ifdef IS_MPI
2242		}
2243		#endif
2244	<	for (j = 0; j < rnemdLogWidth_; j++) {
2245	<	valueCount_[j] = 0;
2246	<	valueHist_[j] = 0.0;
2244	>
2245	>	}
2246	>
2247	>	void RNEMD::writeReal(int index, unsigned int bin) {
2248	>	if (!doRNEMD_) return;
2249	>	assert(index >=0 && index < ENDINDEX);
2250	>	assert(int(bin) < nBins_);
2251	>	RealType s;
2252	>	int count;
2253	>
2254	>	count = data_[index].accumulator[bin]->count();
2255	>	if (count == 0) return;
2256	>
2257	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2258	>
2259	>	if (! isinf(s) && ! isnan(s)) {
2260	>	rnemdFile_ << "\t" << s;
2261	>	} else{
2262	>	sprintf( painCave.errMsg,
2263	>	"RNEMD detected a numerical error writing: %s for bin %u",
2264	>	data_[index].title.c_str(), bin);
2265	>	painCave.isFatal = 1;
2266	>	simError();
2267	>	}
2268	>	}
2269	>
2270	>	void RNEMD::writeVector(int index, unsigned int bin) {
2271	>	if (!doRNEMD_) return;
2272	>	assert(index >=0 && index < ENDINDEX);
2273	>	assert(int(bin) < nBins_);
2274	>	Vector3d s;
2275	>	int count;
2276	>
2277	>	count = data_[index].accumulator[bin]->count();
2278	>
2279	>	if (count == 0) return;
2280	>
2281	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2282	>	if (isinf(s[0]) || isnan(s[0]) ||
2283	>	isinf(s[1]) || isnan(s[1]) ||
2284	>	isinf(s[2]) || isnan(s[2]) ) {
2285	>	sprintf( painCave.errMsg,
2286	>	"RNEMD detected a numerical error writing: %s for bin %u",
2287	>	data_[index].title.c_str(), bin);
2288	>	painCave.isFatal = 1;
2289	>	simError();
2290	>	} else {
2291	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2292		}
2293	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
2294	<	for (j = 0; j < rnemdLogWidth_; j++) {
2295	<	xTempHist_[j] = 0.0;
2296	<	yTempHist_[j] = 0.0;
2297	<	zTempHist_[j] = 0.0;
2298	<	}
2293	>	}
2294	>
2295	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2296	>	if (!doRNEMD_) return;
2297	>	assert(index >=0 && index < ENDINDEX);
2298	>	assert(int(bin) < nBins_);
2299	>	RealType s;
2300	>	int count;
2301	>
2302	>	count = data_[index].accumulator[bin]->count();
2303	>	if (count == 0) return;
2304	>
2305	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2306	>
2307	>	if (! isinf(s) && ! isnan(s)) {
2308	>	rnemdFile_ << "\t" << s;
2309	>	} else{
2310	>	sprintf( painCave.errMsg,
2311	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2312	>	data_[index].title.c_str(), bin);
2313	>	painCave.isFatal = 1;
2314	>	simError();
2315	>	}
2316		}
2317	+
2318	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2319	+	if (!doRNEMD_) return;
2320	+	assert(index >=0 && index < ENDINDEX);
2321	+	assert(int(bin) < nBins_);
2322	+	Vector3d s;
2323	+	int count;
2324	+
2325	+	count = data_[index].accumulator[bin]->count();
2326	+	if (count == 0) return;
2327	+
2328	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2329	+	if (isinf(s[0]) || isnan(s[0]) ||
2330	+	isinf(s[1]) || isnan(s[1]) ||
2331	+	isinf(s[2]) || isnan(s[2]) ) {
2332	+	sprintf( painCave.errMsg,
2333	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2334	+	data_[index].title.c_str(), bin);
2335	+	painCave.isFatal = 1;
2336	+	simError();
2337	+	} else {
2338	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2339	+	}
2340	+	}
2341		}
2342	+

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