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root/OpenMD/branches/development/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.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1876 by gezelter, Fri May 17 17:10:11 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
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include <sstream>
44	>	#include <string>
45	>
46	>	#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48	+	#include "math/Vector.hpp"
49		#include "math/SquareMatrix3.hpp"
50		#include "math/Polynomial.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "primitives/StuntDouble.hpp"
53		#include "utils/PhysicalConstants.hpp"
54		#include "utils/Tuple.hpp"
55	<
56	<	#ifndef IS_MPI
57	<	#include "math/SeqRandNumGen.hpp"
54	<	#else
55	>	#include "brains/Thermo.hpp"
56	>	#include "math/ConvexHull.hpp"
57	>	#ifdef IS_MPI
58		#include <mpi.h>
56	–	#include "math/ParallelRandNumGen.hpp"
59		#endif
60
61	+	#ifdef _MSC_VER
62	+	#define isnan(x) _isnan((x))
63	+	#define isinf(x) (!_finite(x) && !_isnan(x))
64	+	#endif
65	+
66		#define HONKING_LARGE_VALUE 1.0e10
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	>	} else {
551	>	if (usePeriodicBoundaryConditions_) {
552	>	Mat3x3d hmat = currentSnap_->getHmat();
553	>
554	>	if (hasSlabWidth)
555	>	slabWidth_ = rnemdParams->getSlabWidth();
556	>	else
557	>	slabWidth_ = hmat(2,2) / 10.0;
558	>
559	>	if (hasSlabBCenter)
560	>	slabBCenter_ = rnemdParams->getSlabBCenter();
561	>	else
562	>	slabBCenter_ = hmat(2,2) / 2.0;
563	>
564	>	selectionBstream << "select wrappedz > "
565	>	<< slabBCenter_ - 0.5*slabWidth_
566	>	<<  " && wrappedz < "
567	>	<< slabBCenter_ + 0.5*slabWidth_;
568	>	selectionB_ = selectionBstream.str();
569	>	} else {
570	>	if (hasSphereBRadius_) {
571	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
572	>	selectionBstream << "select r > " << sphereBRadius_;
573	>	selectionB_ = selectionBstream.str();
574	>	} else {
575	>	selectionB_ = "select hull";
576	>	hasSelectionB_ = true;
577	>	}
578	>	}
579	>	}
580		}
581
582	<	#ifndef IS_MPI
583	<	if (simParams->haveSeed()) {
584	<	seedValue = simParams->getSeed();
585	<	randNumGen_ = new SeqRandNumGen(seedValue);
586	<	}else {
587	<	randNumGen_ = new SeqRandNumGen();
588	<	}
589	<	#else
590	<	if (simParams->haveSeed()) {
188	<	seedValue = simParams->getSeed();
189	<	randNumGen_ = new ParallelRandNumGen(seedValue);
190	<	}else {
191	<	randNumGen_ = new ParallelRandNumGen();
192	<	}
193	<	#endif
582	>	// object evaluator:
583	>	evaluator_.loadScriptString(rnemdObjectSelection_);
584	>	seleMan_.setSelectionSet(evaluator_.evaluate());
585	>	evaluatorA_.loadScriptString(selectionA_);
586	>	evaluatorB_.loadScriptString(selectionB_);
587	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	>	commonA_ = seleManA_ & seleMan_;
590	>	commonB_ = seleManB_ & seleMan_;
591		}
592
196	–	RNEMD::~RNEMD() {
197	–	delete randNumGen_;
593
594	+	RNEMD::~RNEMD() {
595	+	if (!doRNEMD_) return;
596		#ifdef IS_MPI
597		if (worldRank == 0) {
598		#endif
599	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
600	<	rnemdLog_.close();
601	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
602	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
603	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	<	xTempLog_.close();
208	<	yTempLog_.close();
209	<	zTempLog_.close();
210	<	}
599	>
600	>	writeOutputFile();
601	>
602	>	rnemdFile_.close();
603	>
604		#ifdef IS_MPI
605		}
606		#endif
607	+
608	+	// delete all of the objects we created:
609	+	delete areaAccumulator_;
610	+	data_.clear();
611		}
612	+
613	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
614	+	if (!doRNEMD_) return;
615	+	int selei;
616	+	int selej;
617
216	–	void RNEMD::doSwap() {
217	–
618		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
619		Mat3x3d hmat = currentSnap_->getHmat();
620
221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
222	–
223	–	int selei;
621		StuntDouble* sd;
225	–	int idx;
622
623		RealType min_val;
624		bool min_found = false;
#	Line 232 | Line 628 | namespace OpenMD {
628		bool max_found = false;
629		StuntDouble* max_sd;
630
631	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
632	<	sd = seleMan_.nextSelected(selei)) {
631	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
632	>	sd = seleManA_.nextSelected(selei)) {
633
238	–	idx = sd->getLocalIndex();
239	–
634		Vector3d pos = sd->getPos();
635	<
635	>
636		// wrap the stuntdouble's position back into the box:
637	<
637	>
638		if (usePeriodicBoundaryConditions_)
639		currentSnap_->wrapVector(pos);
640	<
641	<	// which bin is this stuntdouble in?
642	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
643	<
644	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
645	<
646	<
253	<	// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin_) {
640	>
641	>	RealType mass = sd->getMass();
642	>	Vector3d vel = sd->getVel();
643	>	RealType value;
644	>
645	>	switch(rnemdFluxType_) {
646	>	case rnemdKE :
647
648	<	RealType mass = sd->getMass();
649	<	Vector3d vel = sd->getVel();
650	<	RealType value;
651	<
652	<	switch(rnemdType_) {
261	<	case rnemdKineticSwap :
648	>	value = mass * vel.lengthSquare();
649	>
650	>	if (sd->isDirectional()) {
651	>	Vector3d angMom = sd->getJ();
652	>	Mat3x3d I = sd->getI();
653
654	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
655	<	vel[2]*vel[2]);
656	<	if (sd->isDirectional()) {
657	<	Vector3d angMom = sd->getJ();
658	<	Mat3x3d I = sd->getI();
659	<
660	<	if (sd->isLinear()) {
661	<	int i = sd->linearAxis();
662	<	int j = (i + 1) % 3;
663	<	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	<	}
654	>	if (sd->isLinear()) {
655	>	int i = sd->linearAxis();
656	>	int j = (i + 1) % 3;
657	>	int k = (i + 2) % 3;
658	>	value += angMom[j] * angMom[j] / I(j, j) +
659	>	angMom[k] * angMom[k] / I(k, k);
660	>	} else {
661	>	value += angMom[0]*angMom[0]/I(0, 0)
662	>	+ angMom[1]*angMom[1]/I(1, 1)
663	>	+ angMom[2]*angMom[2]/I(2, 2);
664		}
665	<	//make exchangeSum_ comparable between swap & scale
666	<	//temporarily without using energyConvert
667	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
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;
665	>	} //angular momenta exchange enabled
666	>	value *= 0.5;
667	>	break;
668	>	case rnemdPx :
669	>	value = mass * vel[0];
670	>	break;
671	>	case rnemdPy :
672	>	value = mass * vel[1];
673	>	break;
674	>	case rnemdPz :
675	>	value = mass * vel[2];
676	>	break;
677	>	default :
678	>	break;
679	>	}
680	>	if (!max_found) {
681	>	max_val = value;
682	>	max_sd = sd;
683	>	max_found = true;
684	>	} else {
685	>	if (max_val < value) {
686	>	max_val = value;
687	>	max_sd = sd;
688		}
689	+	}
690	+	}
691
692	<	if (binNo == 0) {
693	<	if (!min_found) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	min_found = true;
697	<	} else {
698	<	if (min_val > value) {
699	<	min_val = value;
700	<	min_sd = sd;
701	<	}
702	<	}
703	<	} else { //midBin_
704	<	if (!max_found) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	max_found = true;
708	<	} else {
709	<	if (max_val < value) {
710	<	max_val = value;
711	<	max_sd = sd;
712	<	}
713	<	}
714	<	}
692	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
693	>	sd = seleManB_.nextSelected(selej)) {
694	>
695	>	Vector3d pos = sd->getPos();
696	>
697	>	// wrap the stuntdouble's position back into the box:
698	>
699	>	if (usePeriodicBoundaryConditions_)
700	>	currentSnap_->wrapVector(pos);
701	>
702	>	RealType mass = sd->getMass();
703	>	Vector3d vel = sd->getVel();
704	>	RealType value;
705	>
706	>	switch(rnemdFluxType_) {
707	>	case rnemdKE :
708	>
709	>	value = mass * vel.lengthSquare();
710	>
711	>	if (sd->isDirectional()) {
712	>	Vector3d angMom = sd->getJ();
713	>	Mat3x3d I = sd->getI();
714	>
715	>	if (sd->isLinear()) {
716	>	int i = sd->linearAxis();
717	>	int j = (i + 1) % 3;
718	>	int k = (i + 2) % 3;
719	>	value += angMom[j] * angMom[j] / I(j, j) +
720	>	angMom[k] * angMom[k] / I(k, k);
721	>	} else {
722	>	value += angMom[0]*angMom[0]/I(0, 0)
723	>	+ angMom[1]*angMom[1]/I(1, 1)
724	>	+ angMom[2]*angMom[2]/I(2, 2);
725	>	}
726	>	} //angular momenta exchange enabled
727	>	value *= 0.5;
728	>	break;
729	>	case rnemdPx :
730	>	value = mass * vel[0];
731	>	break;
732	>	case rnemdPy :
733	>	value = mass * vel[1];
734	>	break;
735	>	case rnemdPz :
736	>	value = mass * vel[2];
737	>	break;
738	>	default :
739	>	break;
740		}
741	+
742	+	if (!min_found) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	min_found = true;
746	+	} else {
747	+	if (min_val > value) {
748	+	min_val = value;
749	+	min_sd = sd;
750	+	}
751	+	}
752		}
753	<
754	<	#ifdef IS_MPI
755	<	int nProc, worldRank;
756	<
328	<	nProc = MPI::COMM_WORLD.Get_size();
329	<	worldRank = MPI::COMM_WORLD.Get_rank();
330	<
753	>
754	>	#ifdef IS_MPI
755	>	int worldRank = MPI::COMM_WORLD.Get_rank();
756	>
757		bool my_min_found = min_found;
758		bool my_max_found = max_found;
759
760		// Even if we didn't find a minimum, did someone else?
761	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
336	<	1, MPI::BOOL, MPI::LAND);
337	<
761	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
762		// Even if we didn't find a maximum, did someone else?
763	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
764	<	1, MPI::BOOL, MPI::LAND);
765	<
766	<	struct {
767	<	RealType val;
768	<	int rank;
769	<	} max_vals, min_vals;
770	<
771	<	if (min_found) {
772	<	if (my_min_found)
763	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
764	>	#endif
765	>
766	>	if (max_found && min_found) {
767	>
768	>	#ifdef IS_MPI
769	>	struct {
770	>	RealType val;
771	>	int rank;
772	>	} max_vals, min_vals;
773	>
774	>	if (my_min_found) {
775		min_vals.val = min_val;
776	<	else
776	>	} else {
777		min_vals.val = HONKING_LARGE_VALUE;
778	<
778	>	}
779		min_vals.rank = worldRank;
780
781		// Who had the minimum?
782		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
783		1, MPI::REALTYPE_INT, MPI::MINLOC);
784		min_val = min_vals.val;
359	–	}
785
786	<	if (max_found) {
362	<	if (my_max_found)
786	>	if (my_max_found) {
787		max_vals.val = max_val;
788	<	else
788	>	} else {
789		max_vals.val = -HONKING_LARGE_VALUE;
790	<
790	>	}
791		max_vals.rank = worldRank;
792
793		// Who had the maximum?
794		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
795		1, MPI::REALTYPE_INT, MPI::MAXLOC);
796		max_val = max_vals.val;
373	–	}
797		#endif
798	<
799	<	if (max_found && min_found) {
800	<	if (min_val< max_val) {
378	<
798	>
799	>	if (min_val < max_val) {
800	>
801		#ifdef IS_MPI
802		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
803		// I have both maximum and minimum, so proceed like a single
804		// processor version:
805		#endif
806	<	// objects to be swapped: velocity & angular velocity
806	>
807		Vector3d min_vel = min_sd->getVel();
808		Vector3d max_vel = max_sd->getVel();
809		RealType temp_vel;
810
811	<	switch(rnemdType_) {
812	<	case rnemdKineticSwap :
811	>	switch(rnemdFluxType_) {
812	>	case rnemdKE :
813		min_sd->setVel(max_vel);
814		max_sd->setVel(min_vel);
815	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
815	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
816		Vector3d min_angMom = min_sd->getJ();
817		Vector3d max_angMom = max_sd->getJ();
818		min_sd->setJ(max_angMom);
819		max_sd->setJ(min_angMom);
820	<	}
820	>	}//angular momenta exchange enabled
821	>	//assumes same rigid body identity
822		break;
823		case rnemdPx :
824		temp_vel = min_vel.x();
#	Line 421 | Line 844 | namespace OpenMD {
844		default :
845		break;
846		}
847	+
848		#ifdef IS_MPI
849		// the rest of the cases only apply in parallel simulations:
850		} else if (max_vals.rank == worldRank) {
#	Line 436 | Line 860 | namespace OpenMD {
860		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
861		min_vals.rank, 0, status);
862
863	<	switch(rnemdType_) {
864	<	case rnemdKineticSwap :
863	>	switch(rnemdFluxType_) {
864	>	case rnemdKE :
865		max_sd->setVel(min_vel);
866	<
866	>	//angular momenta exchange enabled
867		if (max_sd->isDirectional()) {
868		Vector3d min_angMom;
869		Vector3d max_angMom = max_sd->getJ();
870	<
870	>
871		// point-to-point swap of the angular momentum vector
872		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
873		MPI::REALTYPE, min_vals.rank, 1,
874		min_angMom.getArrayPointer(), 3,
875		MPI::REALTYPE, min_vals.rank, 1,
876		status);
877	<
877	>
878		max_sd->setJ(min_angMom);
879	<	}
879	>	}
880		break;
881		case rnemdPx :
882		max_vel.x() = min_vel.x();
#	Line 482 | Line 906 | namespace OpenMD {
906		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
907		max_vals.rank, 0, status);
908
909	<	switch(rnemdType_) {
910	<	case rnemdKineticSwap :
909	>	switch(rnemdFluxType_) {
910	>	case rnemdKE :
911		min_sd->setVel(max_vel);
912	<
912	>	//angular momenta exchange enabled
913		if (min_sd->isDirectional()) {
914		Vector3d min_angMom = min_sd->getJ();
915		Vector3d max_angMom;
916	<
916	>
917		// point-to-point swap of the angular momentum vector
918		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
919		MPI::REALTYPE, max_vals.rank, 1,
920		max_angMom.getArrayPointer(), 3,
921		MPI::REALTYPE, max_vals.rank, 1,
922		status);
923	<
923	>
924		min_sd->setJ(max_angMom);
925		}
926		break;
#	Line 517 | Line 941 | namespace OpenMD {
941		}
942		}
943		#endif
944	<	exchangeSum_ += max_val - min_val;
945	<	} else {
946	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
944	>
945	>	switch(rnemdFluxType_) {
946	>	case rnemdKE:
947	>	kineticExchange_ += max_val - min_val;
948	>	break;
949	>	case rnemdPx:
950	>	momentumExchange_.x() += max_val - min_val;
951	>	break;
952	>	case rnemdPy:
953	>	momentumExchange_.y() += max_val - min_val;
954	>	break;
955	>	case rnemdPz:
956	>	momentumExchange_.z() += max_val - min_val;
957	>	break;
958	>	default:
959	>	break;
960	>	}
961	>	} else {
962	>	sprintf(painCave.errMsg,
963	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
964	>	painCave.isFatal = 0;
965	>	painCave.severity = OPENMD_INFO;
966	>	simError();
967		failTrialCount_++;
968		}
969		} else {
970	<	std::cerr << "exchange NOT performed!\n";
971	<	std::cerr << "at least one of the two slabs empty.\n";
970	>	sprintf(painCave.errMsg,
971	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
972	>	"\twas not present in at least one of the two slabs.\n");
973	>	painCave.isFatal = 0;
974	>	painCave.severity = OPENMD_INFO;
975	>	simError();
976		failTrialCount_++;
977	<	}
530	<
977	>	}
978		}
979
980	<	void RNEMD::doScale() {
980	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
981	>	if (!doRNEMD_) return;
982	>	int selei;
983	>	int selej;
984
985		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
986	+	RealType time = currentSnap_->getTime();
987		Mat3x3d hmat = currentSnap_->getHmat();
988
538	–	seleMan_.setSelectionSet(evaluator_.evaluate());
539	–
540	–	int selei;
989		StuntDouble* sd;
542	–	int idx;
990
991	<	std::vector<StuntDouble*> hotBin, coldBin;
991	>	vector<StuntDouble*> hotBin, coldBin;
992
993		RealType Phx = 0.0;
994		RealType Phy = 0.0;
#	Line 549 | Line 996 | namespace OpenMD {
996		RealType Khx = 0.0;
997		RealType Khy = 0.0;
998		RealType Khz = 0.0;
999	+	RealType Khw = 0.0;
1000		RealType Pcx = 0.0;
1001		RealType Pcy = 0.0;
1002		RealType Pcz = 0.0;
1003		RealType Kcx = 0.0;
1004		RealType Kcy = 0.0;
1005		RealType Kcz = 0.0;
1006	+	RealType Kcw = 0.0;
1007
1008	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1009	<	sd = seleMan_.nextSelected(selei)) {
1008	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1009	>	sd = smanA.nextSelected(selei)) {
1010
562	–	idx = sd->getLocalIndex();
563	–
1011		Vector3d pos = sd->getPos();
1012	<
1012	>
1013		// wrap the stuntdouble's position back into the box:
1014	<
1014	>
1015		if (usePeriodicBoundaryConditions_)
1016		currentSnap_->wrapVector(pos);
1017	<
1018	<	// which bin is this stuntdouble in?
1019	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1020	<
1021	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1022	<
1023	<	// if we're in bin 0 or the middleBin
1024	<	if (binNo == 0 || binNo == midBin_) {
1025	<
1026	<	RealType mass = sd->getMass();
1027	<	Vector3d vel = sd->getVel();
1028	<
1029	<	if (binNo == 0) {
1030	<	hotBin.push_back(sd);
1031	<	Phx += mass * vel.x();
1032	<	Phy += mass * vel.y();
1033	<	Phz += mass * vel.z();
1034	<	Khx += mass * vel.x() * vel.x();
1035	<	Khy += mass * vel.y() * vel.y();
1036	<	Khz += mass * vel.z() * vel.z();
1037	<	} else { //midBin_
1038	<	coldBin.push_back(sd);
1039	<	Pcx += mass * vel.x();
1040	<	Pcy += mass * vel.y();
1041	<	Pcz += mass * vel.z();
1042	<	Kcx += mass * vel.x() * vel.x();
1043	<	Kcy += mass * vel.y() * vel.y();
1044	<	Kcz += mass * vel.z() * vel.z();
1045	<	}
1046	<	}
1047	<	}
1048	<
1049	<	Khx *= 0.5;
1050	<	Khy *= 0.5;
1051	<	Khz *= 0.5;
1052	<	Kcx *= 0.5;
1017	>
1018	>
1019	>	RealType mass = sd->getMass();
1020	>	Vector3d vel = sd->getVel();
1021	>
1022	>	hotBin.push_back(sd);
1023	>	Phx += mass * vel.x();
1024	>	Phy += mass * vel.y();
1025	>	Phz += mass * vel.z();
1026	>	Khx += mass * vel.x() * vel.x();
1027	>	Khy += mass * vel.y() * vel.y();
1028	>	Khz += mass * vel.z() * vel.z();
1029	>	if (sd->isDirectional()) {
1030	>	Vector3d angMom = sd->getJ();
1031	>	Mat3x3d I = sd->getI();
1032	>	if (sd->isLinear()) {
1033	>	int i = sd->linearAxis();
1034	>	int j = (i + 1) % 3;
1035	>	int k = (i + 2) % 3;
1036	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1037	>	angMom[k] * angMom[k] / I(k, k);
1038	>	} else {
1039	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1040	>	+ angMom[1]*angMom[1]/I(1, 1)
1041	>	+ angMom[2]*angMom[2]/I(2, 2);
1042	>	}
1043	>	}
1044	>	}
1045	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1046	>	sd = smanB.nextSelected(selej)) {
1047	>	Vector3d pos = sd->getPos();
1048	>
1049	>	// wrap the stuntdouble's position back into the box:
1050	>
1051	>	if (usePeriodicBoundaryConditions_)
1052	>	currentSnap_->wrapVector(pos);
1053	>
1054	>	RealType mass = sd->getMass();
1055	>	Vector3d vel = sd->getVel();
1056	>
1057	>	coldBin.push_back(sd);
1058	>	Pcx += mass * vel.x();
1059	>	Pcy += mass * vel.y();
1060	>	Pcz += mass * vel.z();
1061	>	Kcx += mass * vel.x() * vel.x();
1062	>	Kcy += mass * vel.y() * vel.y();
1063	>	Kcz += mass * vel.z() * vel.z();
1064	>	if (sd->isDirectional()) {
1065	>	Vector3d angMom = sd->getJ();
1066	>	Mat3x3d I = sd->getI();
1067	>	if (sd->isLinear()) {
1068	>	int i = sd->linearAxis();
1069	>	int j = (i + 1) % 3;
1070	>	int k = (i + 2) % 3;
1071	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1072	>	angMom[k] * angMom[k] / I(k, k);
1073	>	} else {
1074	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1075	>	+ angMom[1]*angMom[1]/I(1, 1)
1076	>	+ angMom[2]*angMom[2]/I(2, 2);
1077	>	}
1078	>	}
1079	>	}
1080	>
1081	>	Khx *= 0.5;
1082	>	Khy *= 0.5;
1083	>	Khz *= 0.5;
1084	>	Khw *= 0.5;
1085	>	Kcx *= 0.5;
1086		Kcy *= 0.5;
1087		Kcz *= 0.5;
1088	+	Kcw *= 0.5;
1089
1090		#ifdef IS_MPI
1091		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 617 | Line 1098 | namespace OpenMD {
1098		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1099		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1100		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1101	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1102	+
1103		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1104		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1105		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1106	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1107		#endif
1108
1109	<	//use coldBin coeff's
1109	>	//solve coldBin coeff's first
1110		RealType px = Pcx / Phx;
1111		RealType py = Pcy / Phy;
1112		RealType pz = Pcz / Phz;
1113	+	RealType c, x, y, z;
1114	+	bool successfulScale = false;
1115	+	if ((rnemdFluxType_ == rnemdFullKE) ||
1116	+	(rnemdFluxType_ == rnemdRotKE)) {
1117	+	//may need sanity check Khw & Kcw > 0
1118
1119	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
1120	<	switch(rnemdType_) {
1121	<	case rnemdKineticScale :
1122	<	/*used hotBin coeff's & only scale x & y dimensions
1123	<	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	<	*/
1119	>	if (rnemdFluxType_ == rnemdFullKE) {
1120	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1121	>	} else {
1122	>	c = 1.0 - kineticTarget_ / Kcw;
1123	>	}
1124
1125	<	//scale all three dimensions, let c_x = c_y
1126	<	a000 = Kcx + Kcy;
1127	<	a110 = Kcz;
1128	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1129	<	a001 = Khx * px * px + Khy * py * py;
1130	<	a111 = Khz * pz * pz;
1131	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1132	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1133	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1134	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1135	<	break;
1136	<	case rnemdPxScale :
1137	<	c = 1 - targetFlux_ / Pcx;
1138	<	a000 = Kcy;
1139	<	a110 = Kcz;
1140	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1141	<	a001 = py * py * Khy;
1142	<	a111 = pz * pz * Khz;
1143	<	b01 = -2.0 * Khy * py * (1.0 + py);
1144	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1145	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1146	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1147	<	break;
1148	<	case rnemdPyScale :
1149	<	c = 1 - targetFlux_ / Pcy;
1150	<	a000 = Kcx;
1151	<	a110 = Kcz;
1152	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1153	<	a001 = px * px * Khx;
1154	<	a111 = pz * pz * Khz;
1155	<	b01 = -2.0 * Khx * px * (1.0 + px);
1156	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
1157	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1158	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1125	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1126	>	c = sqrt(c);
1127	>
1128	>	RealType w = 0.0;
1129	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1130	>	x = 1.0 + px * (1.0 - c);
1131	>	y = 1.0 + py * (1.0 - c);
1132	>	z = 1.0 + pz * (1.0 - c);
1133	>	/* more complicated way
1134	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1135	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1136	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1137	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1138	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1139	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1140	>	*/
1141	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1142	>	(fabs(z - 1.0) < 0.1)) {
1143	>	w = 1.0 + (kineticTarget_
1144	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1145	>	+ Khz * (1.0 - z * z)) / Khw;
1146	>	}//no need to calculate w if x, y or z is out of range
1147	>	} else {
1148	>	w = 1.0 + kineticTarget_ / Khw;
1149	>	}
1150	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1151	>	//if w is in the right range, so should be x, y, z.
1152	>	vector<StuntDouble*>::iterator sdi;
1153	>	Vector3d vel;
1154	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1155	>	if (rnemdFluxType_ == rnemdFullKE) {
1156	>	vel = (*sdi)->getVel() * c;
1157	>	(*sdi)->setVel(vel);
1158	>	}
1159	>	if ((*sdi)->isDirectional()) {
1160	>	Vector3d angMom = (*sdi)->getJ() * c;
1161	>	(*sdi)->setJ(angMom);
1162	>	}
1163	>	}
1164	>	w = sqrt(w);
1165	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1166	>	if (rnemdFluxType_ == rnemdFullKE) {
1167	>	vel = (*sdi)->getVel();
1168	>	vel.x() *= x;
1169	>	vel.y() *= y;
1170	>	vel.z() *= z;
1171	>	(*sdi)->setVel(vel);
1172	>	}
1173	>	if ((*sdi)->isDirectional()) {
1174	>	Vector3d angMom = (*sdi)->getJ() * w;
1175	>	(*sdi)->setJ(angMom);
1176	>	}
1177	>	}
1178	>	successfulScale = true;
1179	>	kineticExchange_ += kineticTarget_;
1180	>	}
1181	>	}
1182	>	} else {
1183	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1184	>	switch(rnemdFluxType_) {
1185	>	case rnemdKE :
1186	>	/* used hotBin coeff's & only scale x & y dimensions
1187	>	RealType px = Phx / Pcx;
1188	>	RealType py = Phy / Pcy;
1189	>	a110 = Khy;
1190	>	c0 = - Khx - Khy - kineticTarget_;
1191	>	a000 = Khx;
1192	>	a111 = Kcy * py * py;
1193	>	b11 = -2.0 * Kcy * py * (1.0 + py);
1194	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1195	>	b01 = -2.0 * Kcx * px * (1.0 + px);
1196	>	a001 = Kcx * px * px;
1197	>	*/
1198	>	//scale all three dimensions, let c_x = c_y
1199	>	a000 = Kcx + Kcy;
1200	>	a110 = Kcz;
1201	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1202	>	a001 = Khx * px * px + Khy * py * py;
1203	>	a111 = Khz * pz * pz;
1204	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1205	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1206	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1207	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1208	>	break;
1209	>	case rnemdPx :
1210	>	c = 1 - momentumTarget_.x() / Pcx;
1211	>	a000 = Kcy;
1212	>	a110 = Kcz;
1213	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1214	>	a001 = py * py * Khy;
1215	>	a111 = pz * pz * Khz;
1216	>	b01 = -2.0 * Khy * py * (1.0 + py);
1217	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1218	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1219	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1220	>	break;
1221	>	case rnemdPy :
1222	>	c = 1 - momentumTarget_.y() / Pcy;
1223	>	a000 = Kcx;
1224	>	a110 = Kcz;
1225	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1226	>	a001 = px * px * Khx;
1227	>	a111 = pz * pz * Khz;
1228	>	b01 = -2.0 * Khx * px * (1.0 + px);
1229	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1230	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1231	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1232	>	break;
1233	>	case rnemdPz ://we don't really do this, do we?
1234	>	c = 1 - momentumTarget_.z() / Pcz;
1235	>	a000 = Kcx;
1236	>	a110 = Kcy;
1237	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1238	>	a001 = px * px * Khx;
1239	>	a111 = py * py * Khy;
1240	>	b01 = -2.0 * Khx * px * (1.0 + px);
1241	>	b11 = -2.0 * Khy * py * (1.0 + py);
1242	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1243	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1244	>	break;
1245	>	default :
1246	>	break;
1247	>	}
1248	>
1249	>	RealType v1 = a000 * a111 - a001 * a110;
1250	>	RealType v2 = a000 * b01;
1251	>	RealType v3 = a000 * b11;
1252	>	RealType v4 = a000 * c1 - a001 * c0;
1253	>	RealType v8 = a110 * b01;
1254	>	RealType v10 = - b01 * c0;
1255	>
1256	>	RealType u0 = v2 * v10 - v4 * v4;
1257	>	RealType u1 = -2.0 * v3 * v4;
1258	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1259	>	RealType u3 = -2.0 * v1 * v3;
1260	>	RealType u4 = - v1 * v1;
1261	>	//rescale coefficients
1262	>	RealType maxAbs = fabs(u0);
1263	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1264	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1265	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1266	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1267	>	u0 /= maxAbs;
1268	>	u1 /= maxAbs;
1269	>	u2 /= maxAbs;
1270	>	u3 /= maxAbs;
1271	>	u4 /= maxAbs;
1272	>	//max_element(start, end) is also available.
1273	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1274	>	poly.setCoefficient(4, u4);
1275	>	poly.setCoefficient(3, u3);
1276	>	poly.setCoefficient(2, u2);
1277	>	poly.setCoefficient(1, u1);
1278	>	poly.setCoefficient(0, u0);
1279	>	vector<RealType> realRoots = poly.FindRealRoots();
1280	>
1281	>	vector<RealType>::iterator ri;
1282	>	RealType r1, r2, alpha0;
1283	>	vector<pair<RealType,RealType> > rps;
1284	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1285	>	r2 = *ri;
1286	>	//check if FindRealRoots() give the right answer
1287	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1288	>	sprintf(painCave.errMsg,
1289	>	"RNEMD Warning: polynomial solve seems to have an error!");
1290	>	painCave.isFatal = 0;
1291	>	simError();
1292	>	failRootCount_++;
1293	>	}
1294	>	//might not be useful w/o rescaling coefficients
1295	>	alpha0 = -c0 - a110 * r2 * r2;
1296	>	if (alpha0 >= 0.0) {
1297	>	r1 = sqrt(alpha0 / a000);
1298	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1299	>	< 1e-6)
1300	>	{ rps.push_back(make_pair(r1, r2)); }
1301	>	if (r1 > 1e-6) { //r1 non-negative
1302	>	r1 = -r1;
1303	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1304	>	< 1e-6)
1305	>	{ rps.push_back(make_pair(r1, r2)); }
1306	>	}
1307	>	}
1308	>	}
1309	>	// Consider combining together the solving pair part w/ the searching
1310	>	// best solution part so that we don't need the pairs vector
1311	>	if (!rps.empty()) {
1312	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1313	>	RealType diff;
1314	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1315	>	vector<pair<RealType,RealType> >::iterator rpi;
1316	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1317	>	r1 = (*rpi).first;
1318	>	r2 = (*rpi).second;
1319	>	switch(rnemdFluxType_) {
1320	>	case rnemdKE :
1321	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1323	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1324	>	break;
1325	>	case rnemdPx :
1326	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1327	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1328	>	break;
1329	>	case rnemdPy :
1330	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1331	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1332	>	break;
1333	>	case rnemdPz :
1334	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1335	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1336	>	default :
1337	>	break;
1338	>	}
1339	>	if (diff < smallestDiff) {
1340	>	smallestDiff = diff;
1341	>	bestPair = *rpi;
1342	>	}
1343	>	}
1344	>	#ifdef IS_MPI
1345	>	if (worldRank == 0) {
1346	>	#endif
1347	>	// sprintf(painCave.errMsg,
1348	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1349	>	//         bestPair.first, bestPair.second);
1350	>	// painCave.isFatal = 0;
1351	>	// painCave.severity = OPENMD_INFO;
1352	>	// simError();
1353	>	#ifdef IS_MPI
1354	>	}
1355	>	#endif
1356	>
1357	>	switch(rnemdFluxType_) {
1358	>	case rnemdKE :
1359	>	x = bestPair.first;
1360	>	y = bestPair.first;
1361	>	z = bestPair.second;
1362	>	break;
1363	>	case rnemdPx :
1364	>	x = c;
1365	>	y = bestPair.first;
1366	>	z = bestPair.second;
1367	>	break;
1368	>	case rnemdPy :
1369	>	x = bestPair.first;
1370	>	y = c;
1371	>	z = bestPair.second;
1372	>	break;
1373	>	case rnemdPz :
1374	>	x = bestPair.first;
1375	>	y = bestPair.second;
1376	>	z = c;
1377	>	break;
1378	>	default :
1379	>	break;
1380	>	}
1381	>	vector<StuntDouble*>::iterator sdi;
1382	>	Vector3d vel;
1383	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1384	>	vel = (*sdi)->getVel();
1385	>	vel.x() *= x;
1386	>	vel.y() *= y;
1387	>	vel.z() *= z;
1388	>	(*sdi)->setVel(vel);
1389	>	}
1390	>	//convert to hotBin coefficient
1391	>	x = 1.0 + px * (1.0 - x);
1392	>	y = 1.0 + py * (1.0 - y);
1393	>	z = 1.0 + pz * (1.0 - z);
1394	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1395	>	vel = (*sdi)->getVel();
1396	>	vel.x() *= x;
1397	>	vel.y() *= y;
1398	>	vel.z() *= z;
1399	>	(*sdi)->setVel(vel);
1400	>	}
1401	>	successfulScale = true;
1402	>	switch(rnemdFluxType_) {
1403	>	case rnemdKE :
1404	>	kineticExchange_ += kineticTarget_;
1405	>	break;
1406	>	case rnemdPx :
1407	>	case rnemdPy :
1408	>	case rnemdPz :
1409	>	momentumExchange_ += momentumTarget_;
1410	>	break;
1411	>	default :
1412	>	break;
1413	>	}
1414	>	}
1415	>	}
1416	>	if (successfulScale != true) {
1417	>	sprintf(painCave.errMsg,
1418	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1419	>	"\tthe constraint equations may not exist or there may be\n"
1420	>	"\tno selected objects in one or both slabs.\n");
1421	>	painCave.isFatal = 0;
1422	>	painCave.severity = OPENMD_INFO;
1423	>	simError();
1424	>	failTrialCount_++;
1425	>	}
1426	>	}
1427	>
1428	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1429	>	if (!doRNEMD_) return;
1430	>	int selei;
1431	>	int selej;
1432	>
1433	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1434	>	RealType time = currentSnap_->getTime();
1435	>	Mat3x3d hmat = currentSnap_->getHmat();
1436	>
1437	>	StuntDouble* sd;
1438	>
1439	>	vector<StuntDouble*> hotBin, coldBin;
1440	>
1441	>	Vector3d Ph(V3Zero);
1442	>	Vector3d Lh(V3Zero);
1443	>	RealType Mh = 0.0;
1444	>	Mat3x3d Ih(0.0);
1445	>	RealType Kh = 0.0;
1446	>	Vector3d Pc(V3Zero);
1447	>	Vector3d Lc(V3Zero);
1448	>	RealType Mc = 0.0;
1449	>	Mat3x3d Ic(0.0);
1450	>	RealType Kc = 0.0;
1451	>
1452	>	// Constraints can be on only the linear or angular momentum, but
1453	>	// not both.  Usually, the user will specify which they want, but
1454	>	// in case they don't, the use of periodic boundaries should make
1455	>	// the choice for us.
1456	>	bool doLinearPart = false;
1457	>	bool doAngularPart = false;
1458	>
1459	>	switch (rnemdFluxType_) {
1460	>	case rnemdPx:
1461	>	case rnemdPy:
1462	>	case rnemdPz:
1463	>	case rnemdPvector:
1464	>	case rnemdKePx:
1465	>	case rnemdKePy:
1466	>	case rnemdKePvector:
1467	>	doLinearPart = true;
1468		break;
1469	<	case rnemdPzScale ://we don't really do this, do we?
1470	<	c = 1 - targetFlux_ / Pcz;
1471	<	a000 = Kcx;
1472	<	a110 = Kcy;
1473	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1474	<	a001 = px * px * Khx;
1475	<	a111 = py * py * Khy;
1476	<	b01 = -2.0 * Khx * px * (1.0 + px);
1477	<	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 :
1469	>	case rnemdLx:
1470	>	case rnemdLy:
1471	>	case rnemdLz:
1472	>	case rnemdLvector:
1473	>	case rnemdKeLx:
1474	>	case rnemdKeLy:
1475	>	case rnemdKeLz:
1476	>	case rnemdKeLvector:
1477	>	doAngularPart = true;
1478		break;
1479	+	case rnemdKE:
1480	+	case rnemdRotKE:
1481	+	case rnemdFullKE:
1482	+	default:
1483	+	if (usePeriodicBoundaryConditions_)
1484	+	doLinearPart = true;
1485	+	else
1486	+	doAngularPart = true;
1487	+	break;
1488		}
1489	+
1490	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1491	+	sd = smanA.nextSelected(selei)) {
1492
1493	<	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;
1493	>	Vector3d pos = sd->getPos();
1494
1495	<	RealType u0 = v2 * v10 - v4 * v4;
1496	<	RealType u1 = -2.0 * v3 * v4;
1497	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1498	<	RealType u3 = -2.0 * v1 * v3;
1499	<	RealType u4 = - v1 * v1;
1500	<	//rescale coefficients
1501	<	RealType maxAbs = fabs(u0);
1502	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1503	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1504	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1505	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1506	<	u0 /= maxAbs;
1507	<	u1 /= maxAbs;
1508	<	u2 /= maxAbs;
1509	<	u3 /= maxAbs;
1510	<	u4 /= maxAbs;
1511	<	//max_element(start, end) is also available.
1512	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1513	<	poly.setCoefficient(4, u4);
1514	<	poly.setCoefficient(3, u3);
1515	<	poly.setCoefficient(2, u2);
1516	<	poly.setCoefficient(1, u1);
1517	<	poly.setCoefficient(0, u0);
1518	<	std::vector<RealType> realRoots = poly.FindRealRoots();
1519	<
1520	<	std::vector<RealType>::iterator ri;
1521	<	RealType r1, r2, alpha0;
1522	<	std::vector<std::pair<RealType,RealType> > rps;
1523	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1524	<	r2 = *ri;
1525	<	//check if FindRealRoots() give the right answer
1526	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1527	<	sprintf(painCave.errMsg,
1528	<	"RNEMD Warning: polynomial solve seems to have an error!");
1529	<	painCave.isFatal = 0;
1530	<	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)); }
1495	>	// wrap the stuntdouble's position back into the box:
1496	>
1497	>	if (usePeriodicBoundaryConditions_)
1498	>	currentSnap_->wrapVector(pos);
1499	>
1500	>	RealType mass = sd->getMass();
1501	>	Vector3d vel = sd->getVel();
1502	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1503	>	RealType r2;
1504	>
1505	>	hotBin.push_back(sd);
1506	>	Ph += mass * vel;
1507	>	Mh += mass;
1508	>	Kh += mass * vel.lengthSquare();
1509	>	Lh += mass * cross(rPos, vel);
1510	>	Ih -= outProduct(rPos, rPos) * mass;
1511	>	r2 = rPos.lengthSquare();
1512	>	Ih(0, 0) += mass * r2;
1513	>	Ih(1, 1) += mass * r2;
1514	>	Ih(2, 2) += mass * r2;
1515	>
1516	>	if (rnemdFluxType_ == rnemdFullKE) {
1517	>	if (sd->isDirectional()) {
1518	>	Vector3d angMom = sd->getJ();
1519	>	Mat3x3d I = sd->getI();
1520	>	if (sd->isLinear()) {
1521	>	int i = sd->linearAxis();
1522	>	int j = (i + 1) % 3;
1523	>	int k = (i + 2) % 3;
1524	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1525	>	angMom[k] * angMom[k] / I(k, k);
1526	>	} else {
1527	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1528	>	angMom[1] * angMom[1] / I(1, 1) +
1529	>	angMom[2] * angMom[2] / I(2, 2);
1530	>	}
1531		}
1532		}
1533		}
1534	<	// Consider combininig together the solving pair part w/ the searching
1535	<	// best solution part so that we don't need the pairs vector
1536	<	if (!rps.empty()) {
1537	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1538	<	RealType diff;
1539	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1540	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1541	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1542	<	r1 = (*rpi).first;
1543	<	r2 = (*rpi).second;
1544	<	switch(rnemdType_) {
1545	<	case rnemdKineticScale :
1546	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1547	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1548	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1549	<	break;
1550	<	case rnemdPxScale :
1551	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1552	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1553	<	break;
1554	<	case rnemdPyScale :
1555	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1556	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1557	<	break;
1558	<	case rnemdPzScale :
1559	<	default :
1560	<	break;
1534	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1535	>	sd = smanB.nextSelected(selej)) {
1536	>
1537	>	Vector3d pos = sd->getPos();
1538	>
1539	>	// wrap the stuntdouble's position back into the box:
1540	>
1541	>	if (usePeriodicBoundaryConditions_)
1542	>	currentSnap_->wrapVector(pos);
1543	>
1544	>	RealType mass = sd->getMass();
1545	>	Vector3d vel = sd->getVel();
1546	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1547	>	RealType r2;
1548	>
1549	>	coldBin.push_back(sd);
1550	>	Pc += mass * vel;
1551	>	Mc += mass;
1552	>	Kc += mass * vel.lengthSquare();
1553	>	Lc += mass * cross(rPos, vel);
1554	>	Ic -= outProduct(rPos, rPos) * mass;
1555	>	r2 = rPos.lengthSquare();
1556	>	Ic(0, 0) += mass * r2;
1557	>	Ic(1, 1) += mass * r2;
1558	>	Ic(2, 2) += mass * r2;
1559	>
1560	>	if (rnemdFluxType_ == rnemdFullKE) {
1561	>	if (sd->isDirectional()) {
1562	>	Vector3d angMom = sd->getJ();
1563	>	Mat3x3d I = sd->getI();
1564	>	if (sd->isLinear()) {
1565	>	int i = sd->linearAxis();
1566	>	int j = (i + 1) % 3;
1567	>	int k = (i + 2) % 3;
1568	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1569	>	angMom[k] * angMom[k] / I(k, k);
1570	>	} else {
1571	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1572	>	angMom[1] * angMom[1] / I(1, 1) +
1573	>	angMom[2] * angMom[2] / I(2, 2);
1574	>	}
1575		}
783	–	if (diff < smallestDiff) {
784	–	smallestDiff = diff;
785	–	bestPair = *rpi;
786	–	}
1576		}
1577	+	}
1578	+
1579	+	Kh *= 0.5;
1580	+	Kc *= 0.5;
1581	+
1582		#ifdef IS_MPI
1583	<	if (worldRank == 0) {
1583	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1584	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1585	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1586	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1587	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1588	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1589	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1590	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1591	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1592	>	MPI::REALTYPE, MPI::SUM);
1593	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1594	>	MPI::REALTYPE, MPI::SUM);
1595		#endif
1596	<	std::cerr << "we choose r1 = " << bestPair.first
792	<	<< " and r2 = " << bestPair.second << "\n";
793	<	#ifdef IS_MPI
794	<	}
795	<	#endif
1596	>
1597
1598	<	RealType x, y, z;
1599	<	switch(rnemdType_) {
1600	<	case rnemdKineticScale :
1601	<	x = bestPair.first;
1602	<	y = bestPair.first;
1603	<	z = bestPair.second;
1604	<	break;
1605	<	case rnemdPxScale :
1606	<	x = c;
1607	<	y = bestPair.first;
1608	<	z = bestPair.second;
1609	<	break;
1610	<	case rnemdPyScale :
1611	<	x = bestPair.first;
1612	<	y = c;
1613	<	z = bestPair.second;
1614	<	break;
1615	<	case rnemdPzScale :
1616	<	x = bestPair.first;
1617	<	y = bestPair.second;
1618	<	z = c;
1619	<	break;
1620	<	default :
1621	<	break;
1622	<	}
1623	<	std::vector<StuntDouble*>::iterator sdi;
1624	<	Vector3d vel;
1625	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1626	<	vel = (*sdi)->getVel();
1627	<	vel.x() *= x;
1628	<	vel.y() *= y;
1629	<	vel.z() *= z;
1630	<	(*sdi)->setVel(vel);
1631	<	}
1632	<	//convert to hotBin coefficient
1633	<	x = 1.0 + px * (1.0 - x);
1634	<	y = 1.0 + py * (1.0 - y);
1635	<	z = 1.0 + pz * (1.0 - z);
1636	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1637	<	vel = (*sdi)->getVel();
1638	<	vel.x() *= x;
1639	<	vel.y() *= y;
1640	<	vel.z() *= z;
1641	<	(*sdi)->setVel(vel);
1598	>	Vector3d ac, acrec, bc, bcrec;
1599	>	Vector3d ah, ahrec, bh, bhrec;
1600	>
1601	>	bool successfulExchange = false;
1602	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1603	>	Vector3d vc = Pc / Mc;
1604	>	ac = -momentumTarget_ / Mc + vc;
1605	>	acrec = -momentumTarget_ / Mc;
1606	>
1607	>	// We now need the inverse of the inertia tensor to calculate the
1608	>	// angular velocity of the cold slab;
1609	>	Mat3x3d Ici = Ic.inverse();
1610	>	Vector3d omegac = Ici * Lc;
1611	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1612	>	bcrec = bc - omegac;
1613	>
1614	>	RealType cNumerator = Kc - kineticTarget_;
1615	>	if (doLinearPart)
1616	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1617	>
1618	>	if (doAngularPart)
1619	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1620	>
1621	>	if (cNumerator > 0.0) {
1622	>
1623	>	RealType cDenominator = Kc;
1624	>
1625	>	if (doLinearPart)
1626	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1627	>
1628	>	if (doAngularPart)
1629	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1630	>
1631	>	if (cDenominator > 0.0) {
1632	>	RealType c = sqrt(cNumerator / cDenominator);
1633	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1634	>
1635	>	Vector3d vh = Ph / Mh;
1636	>	ah = momentumTarget_ / Mh + vh;
1637	>	ahrec = momentumTarget_ / Mh;
1638	>
1639	>	// We now need the inverse of the inertia tensor to
1640	>	// calculate the angular velocity of the hot slab;
1641	>	Mat3x3d Ihi = Ih.inverse();
1642	>	Vector3d omegah = Ihi * Lh;
1643	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1644	>	bhrec = bh - omegah;
1645	>
1646	>	RealType hNumerator = Kh + kineticTarget_;
1647	>	if (doLinearPart)
1648	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1649	>
1650	>	if (doAngularPart)
1651	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1652	>
1653	>	if (hNumerator > 0.0) {
1654	>
1655	>	RealType hDenominator = Kh;
1656	>	if (doLinearPart)
1657	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1658	>	if (doAngularPart)
1659	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1660	>
1661	>	if (hDenominator > 0.0) {
1662	>	RealType h = sqrt(hNumerator / hDenominator);
1663	>	if ((h > 0.9) && (h < 1.1)) {
1664	>
1665	>	vector<StuntDouble*>::iterator sdi;
1666	>	Vector3d vel;
1667	>	Vector3d rPos;
1668	>
1669	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1670	>	//vel = (*sdi)->getVel();
1671	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1672	>	if (doLinearPart)
1673	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1674	>	if (doAngularPart)
1675	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1676	>
1677	>	(*sdi)->setVel(vel);
1678	>	if (rnemdFluxType_ == rnemdFullKE) {
1679	>	if ((*sdi)->isDirectional()) {
1680	>	Vector3d angMom = (*sdi)->getJ() * c;
1681	>	(*sdi)->setJ(angMom);
1682	>	}
1683	>	}
1684	>	}
1685	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1686	>	//vel = (*sdi)->getVel();
1687	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1688	>	if (doLinearPart)
1689	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1690	>	if (doAngularPart)
1691	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1692	>
1693	>	(*sdi)->setVel(vel);
1694	>	if (rnemdFluxType_ == rnemdFullKE) {
1695	>	if ((*sdi)->isDirectional()) {
1696	>	Vector3d angMom = (*sdi)->getJ() * h;
1697	>	(*sdi)->setJ(angMom);
1698	>	}
1699	>	}
1700	>	}
1701	>	successfulExchange = true;
1702	>	kineticExchange_ += kineticTarget_;
1703	>	momentumExchange_ += momentumTarget_;
1704	>	angularMomentumExchange_ += angularMomentumTarget_;
1705	>	}
1706	>	}
1707	>	}
1708	>	}
1709	>	}
1710		}
1711	<	exchangeSum_ += targetFlux_;
1712	<	//we may want to check whether the exchange has been successful
1713	<	} else {
1714	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1711	>	}
1712	>	if (successfulExchange != true) {
1713	>	sprintf(painCave.errMsg,
1714	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1715	>	"\tthe constraint equations may not exist or there may be\n"
1716	>	"\tno selected objects in one or both slabs.\n");
1717	>	painCave.isFatal = 0;
1718	>	painCave.severity = OPENMD_INFO;
1719	>	simError();
1720		failTrialCount_++;
1721		}
848	–
1722		}
1723
1724	+	RealType RNEMD::getDividingArea() {
1725	+
1726	+	if (hasDividingArea_) return dividingArea_;
1727	+
1728	+	RealType areaA, areaB;
1729	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1730	+
1731	+	if (hasSelectionA_) {
1732	+	int isd;
1733	+	StuntDouble* sd;
1734	+	vector<StuntDouble*> aSites;
1735	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1736	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1737	+	sd = seleManA_.nextSelected(isd)) {
1738	+	aSites.push_back(sd);
1739	+	}
1740	+	#if defined(HAVE_QHULL)
1741	+	ConvexHull* surfaceMeshA = new ConvexHull();
1742	+	surfaceMeshA->computeHull(aSites);
1743	+	areaA = surfaceMeshA->getArea();
1744	+	delete surfaceMeshA;
1745	+	#else
1746	+	sprintf( painCave.errMsg,
1747	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1748	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1749	+	painCave.severity = OPENMD_ERROR;
1750	+	painCave.isFatal = 1;
1751	+	simError();
1752	+	#endif
1753	+
1754	+	} else {
1755	+	if (usePeriodicBoundaryConditions_) {
1756	+	// in periodic boundaries, the surface area is twice the x-y
1757	+	// area of the current box:
1758	+	areaA = 2.0 * snap->getXYarea();
1759	+	} else {
1760	+	// in non-periodic simulations, without explicitly setting
1761	+	// selections, the sphere radius sets the surface area of the
1762	+	// dividing surface:
1763	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1764	+	}
1765	+	}
1766	+
1767	+	if (hasSelectionB_) {
1768	+	int isd;
1769	+	StuntDouble* sd;
1770	+	vector<StuntDouble*> bSites;
1771	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1772	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1773	+	sd = seleManB_.nextSelected(isd)) {
1774	+	bSites.push_back(sd);
1775	+	}
1776	+
1777	+	#if defined(HAVE_QHULL)
1778	+	ConvexHull* surfaceMeshB = new ConvexHull();
1779	+	surfaceMeshB->computeHull(bSites);
1780	+	areaB = surfaceMeshB->getArea();
1781	+	delete surfaceMeshB;
1782	+	#else
1783	+	sprintf( painCave.errMsg,
1784	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1785	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1786	+	painCave.severity = OPENMD_ERROR;
1787	+	painCave.isFatal = 1;
1788	+	simError();
1789	+	#endif
1790	+
1791	+
1792	+	} else {
1793	+	if (usePeriodicBoundaryConditions_) {
1794	+	// in periodic boundaries, the surface area is twice the x-y
1795	+	// area of the current box:
1796	+	areaB = 2.0 * snap->getXYarea();
1797	+	} else {
1798	+	// in non-periodic simulations, without explicitly setting
1799	+	// selections, but if a sphereBradius has been set, just use that:
1800	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1801	+	}
1802	+	}
1803	+
1804	+	dividingArea_ = min(areaA, areaB);
1805	+	hasDividingArea_ = true;
1806	+	return dividingArea_;
1807	+	}
1808	+
1809		void RNEMD::doRNEMD() {
1810	+	if (!doRNEMD_) return;
1811	+	trialCount_++;
1812
1813	<	switch(rnemdType_) {
1814	<	case rnemdKineticScale :
1815	<	case rnemdPxScale :
1816	<	case rnemdPyScale :
1817	<	case rnemdPzScale :
1818	<	doScale();
1813	>	// object evaluator:
1814	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1815	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1816	>
1817	>	evaluatorA_.loadScriptString(selectionA_);
1818	>	evaluatorB_.loadScriptString(selectionB_);
1819	>
1820	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1821	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1822	>
1823	>	commonA_ = seleManA_ & seleMan_;
1824	>	commonB_ = seleManB_ & seleMan_;
1825	>
1826	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1827	>	// dt = exchange time interval
1828	>	// flux = target flux
1829	>	// dividingArea = smallest dividing surface between the two regions
1830	>
1831	>	hasDividingArea_ = false;
1832	>	RealType area = getDividingArea();
1833	>
1834	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1835	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1836	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1837	>
1838	>	switch(rnemdMethod_) {
1839	>	case rnemdSwap:
1840	>	doSwap(commonA_, commonB_);
1841		break;
1842	<	case rnemdKineticSwap :
1843	<	case rnemdPx :
862	<	case rnemdPy :
863	<	case rnemdPz :
864	<	doSwap();
1842	>	case rnemdNIVS:
1843	>	doNIVS(commonA_, commonB_);
1844		break;
1845	<	case rnemdUnknown :
1845	>	case rnemdVSS:
1846	>	doVSS(commonA_, commonB_);
1847	>	break;
1848	>	case rnemdUnkownMethod:
1849		default :
1850		break;
1851		}
1852		}
1853
1854		void RNEMD::collectData() {
1855	<
1855	>	if (!doRNEMD_) return;
1856		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1857	+
1858	+	// collectData can be called more frequently than the doRNEMD, so use the
1859	+	// computed area from the last exchange time:
1860	+	RealType area = getDividingArea();
1861	+	areaAccumulator_->add(area);
1862		Mat3x3d hmat = currentSnap_->getHmat();
876	–
1863		seleMan_.setSelectionSet(evaluator_.evaluate());
1864
1865	<	int selei;
1865	>	int selei(0);
1866		StuntDouble* sd;
1867	<	int idx;
1867	>	int binNo;
1868
1869	+	vector<RealType> binMass(nBins_, 0.0);
1870	+	vector<RealType> binPx(nBins_, 0.0);
1871	+	vector<RealType> binPy(nBins_, 0.0);
1872	+	vector<RealType> binPz(nBins_, 0.0);
1873	+	vector<RealType> binOmegax(nBins_, 0.0);
1874	+	vector<RealType> binOmegay(nBins_, 0.0);
1875	+	vector<RealType> binOmegaz(nBins_, 0.0);
1876	+	vector<RealType> binKE(nBins_, 0.0);
1877	+	vector<int> binDOF(nBins_, 0);
1878	+	vector<int> binCount(nBins_, 0);
1879	+
1880	+	// alternative approach, track all molecules instead of only those
1881	+	// selected for scaling/swapping:
1882	+	/*
1883	+	SimInfo::MoleculeIterator miter;
1884	+	vector<StuntDouble*>::iterator iiter;
1885	+	Molecule* mol;
1886	+	StuntDouble* sd;
1887	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1888	+	mol = info_->nextMolecule(miter))
1889	+	sd is essentially sd
1890	+	for (sd = mol->beginIntegrableObject(iiter);
1891	+	sd != NULL;
1892	+	sd = mol->nextIntegrableObject(iiter))
1893	+	*/
1894	+
1895		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1896	<	sd = seleMan_.nextSelected(selei)) {
1897	<
886	<	idx = sd->getLocalIndex();
887	<
1896	>	sd = seleMan_.nextSelected(selei)) {
1897	>
1898		Vector3d pos = sd->getPos();
1899
1900		// wrap the stuntdouble's position back into the box:
1901
1902	<	if (usePeriodicBoundaryConditions_)
1902	>	if (usePeriodicBoundaryConditions_) {
1903		currentSnap_->wrapVector(pos);
1904	<
1905	<	// which bin is this stuntdouble in?
1906	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1907	<
1908	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1904	>	// which bin is this stuntdouble in?
1905	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1906	>	// Shift molecules by half a box to have bins start at 0
1907	>	// The modulo operator is used to wrap the case when we are
1908	>	// beyond the end of the bins back to the beginning.
1909	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1910	>	} else {
1911	>	Vector3d rPos = pos - coordinateOrigin_;
1912	>	binNo = int(rPos.length() / binWidth_);
1913	>	}
1914
900	–	if (rnemdLogWidth_ == midBin_ + 1)
901	–	if (binNo > midBin_)
902	–	binNo = nBins_ - binNo;
903	–
1915		RealType mass = sd->getMass();
1916		Vector3d vel = sd->getVel();
1917	<	RealType value;
1918	<	RealType xVal, yVal, zVal;
1917	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1918	>	Vector3d aVel = cross(rPos, vel);
1919	>
1920	>	if (binNo >= 0 && binNo < nBins_)  {
1921	>	binCount[binNo]++;
1922	>	binMass[binNo] += mass;
1923	>	binPx[binNo] += mass*vel.x();
1924	>	binPy[binNo] += mass*vel.y();
1925	>	binPz[binNo] += mass*vel.z();
1926	>	binOmegax[binNo] += aVel.x();
1927	>	binOmegay[binNo] += aVel.y();
1928	>	binOmegaz[binNo] += aVel.z();
1929	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1930	>	binDOF[binNo] += 3;
1931	>
1932	>	if (sd->isDirectional()) {
1933	>	Vector3d angMom = sd->getJ();
1934	>	Mat3x3d I = sd->getI();
1935	>	if (sd->isLinear()) {
1936	>	int i = sd->linearAxis();
1937	>	int j = (i + 1) % 3;
1938	>	int k = (i + 2) % 3;
1939	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1940	>	angMom[k] * angMom[k] / I(k, k));
1941	>	binDOF[binNo] += 2;
1942	>	} else {
1943	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1944	>	angMom[1] * angMom[1] / I(1, 1) +
1945	>	angMom[2] * angMom[2] / I(2, 2));
1946	>	binDOF[binNo] += 3;
1947	>	}
1948	>	}
1949	>	}
1950	>	}
1951	>
1952	>	#ifdef IS_MPI
1953	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1954	>	nBins_, MPI::INT, MPI::SUM);
1955	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1956	>	nBins_, MPI::REALTYPE, MPI::SUM);
1957	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1958	>	nBins_, MPI::REALTYPE, MPI::SUM);
1959	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1960	>	nBins_, MPI::REALTYPE, MPI::SUM);
1961	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1962	>	nBins_, MPI::REALTYPE, MPI::SUM);
1963	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1964	>	nBins_, MPI::REALTYPE, MPI::SUM);
1965	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1966	>	nBins_, MPI::REALTYPE, MPI::SUM);
1967	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1968	>	nBins_, MPI::REALTYPE, MPI::SUM);
1969	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1970	>	nBins_, MPI::REALTYPE, MPI::SUM);
1971	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1972	>	nBins_, MPI::INT, MPI::SUM);
1973	>	#endif
1974
1975	<	switch(rnemdType_) {
1976	<	case rnemdKineticSwap :
1977	<	case rnemdKineticScale :
1978	<
1979	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1980	<	vel[2]*vel[2]);
1981	<
1982	<	valueCount_[binNo] += 3;
1983	<	if (sd->isDirectional()) {
1984	<	Vector3d angMom = sd->getJ();
1985	<	Mat3x3d I = sd->getI();
1986	<
1987	<	if (sd->isLinear()) {
1988	<	int i = sd->linearAxis();
1989	<	int j = (i + 1) % 3;
1990	<	int k = (i + 2) % 3;
1991	<	value += angMom[j] * angMom[j] / I(j, j) +
1992	<	angMom[k] * angMom[k] / I(k, k);
1975	>	Vector3d vel;
1976	>	Vector3d aVel;
1977	>	RealType den;
1978	>	RealType temp;
1979	>	RealType z;
1980	>	RealType r;
1981	>	for (int i = 0; i < nBins_; i++) {
1982	>	if (usePeriodicBoundaryConditions_) {
1983	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1984	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1985	>	/ currentSnap_->getVolume() ;
1986	>	} else {
1987	>	r = (((RealType)i + 0.5) * binWidth_);
1988	>	RealType rinner = (RealType)i * binWidth_;
1989	>	RealType router = (RealType)(i+1) * binWidth_;
1990	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1991	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1992	>	}
1993	>	vel.x() = binPx[i] / binMass[i];
1994	>	vel.y() = binPy[i] / binMass[i];
1995	>	vel.z() = binPz[i] / binMass[i];
1996	>	aVel.x() = binOmegax[i] / binCount[i];
1997	>	aVel.y() = binOmegay[i] / binCount[i];
1998	>	aVel.z() = binOmegaz[i] / binCount[i];
1999
2000	<	valueCount_[binNo] +=2;
2001	<
2002	<	} else {
2003	<	value += angMom[0]*angMom[0]/I(0, 0)
2004	<	+ angMom[1]*angMom[1]/I(1, 1)
2005	<	+ angMom[2]*angMom[2]/I(2, 2);
2006	<	valueCount_[binNo] +=3;
2007	<	}
2008	<	}
2009	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
2010	<
2011	<	break;
2012	<	case rnemdPx :
2013	<	case rnemdPxScale :
2014	<	value = mass * vel[0];
2015	<	valueCount_[binNo]++;
2016	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
2017	<	/ PhysicalConstants::kb;
2018	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
2019	<	/ PhysicalConstants::kb;
2020	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
2021	<	/ PhysicalConstants::kb;
2022	<	xTempHist_[binNo] += xVal;
2023	<	yTempHist_[binNo] += yVal;
2024	<	zTempHist_[binNo] += zVal;
2025	<	break;
2026	<	case rnemdPy :
2027	<	case rnemdPyScale :
2028	<	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;
2000	>	if (binCount[i] > 0) {
2001	>	// only add values if there are things to add
2002	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2003	>	PhysicalConstants::energyConvert);
2004	>
2005	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2006	>	if(outputMask_[j]) {
2007	>	switch(j) {
2008	>	case Z:
2009	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2010	>	break;
2011	>	case R:
2012	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2013	>	break;
2014	>	case TEMPERATURE:
2015	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2016	>	break;
2017	>	case VELOCITY:
2018	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2019	>	break;
2020	>	case ANGULARVELOCITY:
2021	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2022	>	break;
2023	>	case DENSITY:
2024	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2025	>	break;
2026	>	}
2027	>	}
2028	>	}
2029		}
968	–	valueHist_[binNo] += value;
2030		}
2031	<
2031	>	hasData_ = true;
2032		}
2033
2034		void RNEMD::getStarted() {
2035	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2036	<	Stats& stat = currentSnap_->statData;
2037	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2035	>	if (!doRNEMD_) return;
2036	>	hasDividingArea_ = false;
2037	>	collectData();
2038	>	writeOutputFile();
2039		}
2040
2041	<	void RNEMD::getStatus() {
2042	<
2043	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2044	<	Stats& stat = currentSnap_->statData;
2045	<	RealType time = currentSnap_->getTime();
2046	<
2047	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2048	<	//or to be more meaningful, define another item as exchangeSum_ / time
2049	<	int j;
2050	<
2041	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2042	>	if (!doRNEMD_) return;
2043	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2044	>
2045	>	while(tokenizer.hasMoreTokens()) {
2046	>	std::string token(tokenizer.nextToken());
2047	>	toUpper(token);
2048	>	OutputMapType::iterator i = outputMap_.find(token);
2049	>	if (i != outputMap_.end()) {
2050	>	outputMask_.set(i->second);
2051	>	} else {
2052	>	sprintf( painCave.errMsg,
2053	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2054	>	"\toutputFileFormat keyword.\n", token.c_str() );
2055	>	painCave.isFatal = 0;
2056	>	painCave.severity = OPENMD_ERROR;
2057	>	simError();
2058	>	}
2059	>	}
2060	>	}
2061	>
2062	>	void RNEMD::writeOutputFile() {
2063	>	if (!doRNEMD_) return;
2064	>	if (!hasData_) return;
2065	>
2066		#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	–	}
2067		// If we're the root node, should we print out the results
2068		int worldRank = MPI::COMM_WORLD.Get_rank();
2069		if (worldRank == 0) {
2070		#endif
2071	<	rnemdLog_ << time;
2072	<	for (j = 0; j < rnemdLogWidth_; j++) {
2073	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
2071	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2072	>
2073	>	if( !rnemdFile_ ){
2074	>	sprintf( painCave.errMsg,
2075	>	"Could not open \"%s\" for RNEMD output.\n",
2076	>	rnemdFileName_.c_str());
2077	>	painCave.isFatal = 1;
2078	>	simError();
2079		}
2080	<	rnemdLog_ << "\n";
2081	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
2082	<	xTempLog_ << time;
2083	<	for (j = 0; j < rnemdLogWidth_; j++) {
2084	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
2080	>
2081	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2082	>
2083	>	RealType time = currentSnap_->getTime();
2084	>	RealType avgArea;
2085	>	areaAccumulator_->getAverage(avgArea);
2086	>
2087	>	RealType Jz(0.0);
2088	>	Vector3d JzP(V3Zero);
2089	>	Vector3d JzL(V3Zero);
2090	>	if (time >= info_->getSimParams()->getDt()) {
2091	>	Jz = kineticExchange_ / (time * avgArea)
2092	>	/ PhysicalConstants::energyConvert;
2093	>	JzP = momentumExchange_ / (time * avgArea);
2094	>	JzL = angularMomentumExchange_ / (time * avgArea);
2095	>	}
2096	>
2097	>	rnemdFile_ << "#######################################################\n";
2098	>	rnemdFile_ << "# RNEMD {\n";
2099	>
2100	>	map<string, RNEMDMethod>::iterator mi;
2101	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2102	>	if ( (*mi).second == rnemdMethod_)
2103	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2104	>	}
2105	>	map<string, RNEMDFluxType>::iterator fi;
2106	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2107	>	if ( (*fi).second == rnemdFluxType_)
2108	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2109	>	}
2110	>
2111	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2112	>
2113	>	rnemdFile_ << "#    objectSelection = \""
2114	>	<< rnemdObjectSelection_ << "\";\n";
2115	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2116	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2117	>	rnemdFile_ << "# }\n";
2118	>	rnemdFile_ << "#######################################################\n";
2119	>	rnemdFile_ << "# RNEMD report:\n";
2120	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2121	>	rnemdFile_ << "# Target flux:\n";
2122	>	rnemdFile_ << "#           kinetic = "
2123	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2124	>	<< " (kcal/mol/A^2/fs)\n";
2125	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2126	>	<< " (amu/A/fs^2)\n";
2127	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2128	>	<< " (amu/A^2/fs^2)\n";
2129	>	rnemdFile_ << "# Target one-time exchanges:\n";
2130	>	rnemdFile_ << "#          kinetic = "
2131	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2132	>	<< " (kcal/mol)\n";
2133	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2134	>	<< " (amu*A/fs)\n";
2135	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2136	>	<< " (amu*A^2/fs)\n";
2137	>	rnemdFile_ << "# Actual exchange totals:\n";
2138	>	rnemdFile_ << "#          kinetic = "
2139	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2140	>	<< " (kcal/mol)\n";
2141	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2142	>	<< " (amu*A/fs)\n";
2143	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2144	>	<< " (amu*A^2/fs)\n";
2145	>	rnemdFile_ << "# Actual flux:\n";
2146	>	rnemdFile_ << "#          kinetic = " << Jz
2147	>	<< " (kcal/mol/A^2/fs)\n";
2148	>	rnemdFile_ << "#          momentum = " << JzP
2149	>	<< " (amu/A/fs^2)\n";
2150	>	rnemdFile_ << "#  angular momentum = " << JzL
2151	>	<< " (amu/A^2/fs^2)\n";
2152	>	rnemdFile_ << "# Exchange statistics:\n";
2153	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2154	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2155	>	if (rnemdMethod_ == rnemdNIVS) {
2156	>	rnemdFile_ << "#  NIVS root-check errors = "
2157	>	<< failRootCount_ << "\n";
2158	>	}
2159	>	rnemdFile_ << "#######################################################\n";
2160	>
2161	>
2162	>
2163	>	//write title
2164	>	rnemdFile_ << "#";
2165	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2166	>	if (outputMask_[i]) {
2167	>	rnemdFile_ << "\t" << data_[i].title <<
2168	>	"(" << data_[i].units << ")";
2169	>	// add some extra tabs for column alignment
2170	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2171		}
2172	<	xTempLog_ << "\n";
2173	<	yTempLog_ << time;
2174	<	for (j = 0; j < rnemdLogWidth_; j++) {
2175	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
2172	>	}
2173	>	rnemdFile_ << std::endl;
2174	>
2175	>	rnemdFile_.precision(8);
2176	>
2177	>	for (int j = 0; j < nBins_; j++) {
2178	>
2179	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2180	>	if (outputMask_[i]) {
2181	>	if (data_[i].dataType == "RealType")
2182	>	writeReal(i,j);
2183	>	else if (data_[i].dataType == "Vector3d")
2184	>	writeVector(i,j);
2185	>	else {
2186	>	sprintf( painCave.errMsg,
2187	>	"RNEMD found an unknown data type for: %s ",
2188	>	data_[i].title.c_str());
2189	>	painCave.isFatal = 1;
2190	>	simError();
2191	>	}
2192	>	}
2193		}
2194	<	yTempLog_ << "\n";
2195	<	zTempLog_ << time;
2196	<	for (j = 0; j < rnemdLogWidth_; j++) {
2197	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
2194	>	rnemdFile_ << std::endl;
2195	>
2196	>	}
2197	>
2198	>	rnemdFile_ << "#######################################################\n";
2199	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2200	>	rnemdFile_ << "#######################################################\n";
2201	>
2202	>
2203	>	for (int j = 0; j < nBins_; j++) {
2204	>	rnemdFile_ << "#";
2205	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2206	>	if (outputMask_[i]) {
2207	>	if (data_[i].dataType == "RealType")
2208	>	writeRealStdDev(i,j);
2209	>	else if (data_[i].dataType == "Vector3d")
2210	>	writeVectorStdDev(i,j);
2211	>	else {
2212	>	sprintf( painCave.errMsg,
2213	>	"RNEMD found an unknown data type for: %s ",
2214	>	data_[i].title.c_str());
2215	>	painCave.isFatal = 1;
2216	>	simError();
2217	>	}
2218	>	}
2219		}
2220	<	zTempLog_ << "\n";
2221	<	}
2220	>	rnemdFile_ << std::endl;
2221	>
2222	>	}
2223	>
2224	>	rnemdFile_.flush();
2225	>	rnemdFile_.close();
2226	>
2227		#ifdef IS_MPI
2228		}
2229		#endif
2230	<	for (j = 0; j < rnemdLogWidth_; j++) {
2231	<	valueCount_[j] = 0;
2232	<	valueHist_[j] = 0.0;
2230	>
2231	>	}
2232	>
2233	>	void RNEMD::writeReal(int index, unsigned int bin) {
2234	>	if (!doRNEMD_) return;
2235	>	assert(index >=0 && index < ENDINDEX);
2236	>	assert(int(bin) < nBins_);
2237	>	RealType s;
2238	>	int count;
2239	>
2240	>	count = data_[index].accumulator[bin]->count();
2241	>	if (count == 0) return;
2242	>
2243	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2244	>
2245	>	if (! isinf(s) && ! isnan(s)) {
2246	>	rnemdFile_ << "\t" << s;
2247	>	} else{
2248	>	sprintf( painCave.errMsg,
2249	>	"RNEMD detected a numerical error writing: %s for bin %u",
2250	>	data_[index].title.c_str(), bin);
2251	>	painCave.isFatal = 1;
2252	>	simError();
2253	>	}
2254	>	}
2255	>
2256	>	void RNEMD::writeVector(int index, unsigned int bin) {
2257	>	if (!doRNEMD_) return;
2258	>	assert(index >=0 && index < ENDINDEX);
2259	>	assert(int(bin) < nBins_);
2260	>	Vector3d s;
2261	>	int count;
2262	>
2263	>	count = data_[index].accumulator[bin]->count();
2264	>
2265	>	if (count == 0) return;
2266	>
2267	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2268	>	if (isinf(s[0]) || isnan(s[0]) ||
2269	>	isinf(s[1]) || isnan(s[1]) ||
2270	>	isinf(s[2]) || isnan(s[2]) ) {
2271	>	sprintf( painCave.errMsg,
2272	>	"RNEMD detected a numerical error writing: %s for bin %u",
2273	>	data_[index].title.c_str(), bin);
2274	>	painCave.isFatal = 1;
2275	>	simError();
2276	>	} else {
2277	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2278		}
2279	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
2280	<	for (j = 0; j < rnemdLogWidth_; j++) {
2281	<	xTempHist_[j] = 0.0;
2282	<	yTempHist_[j] = 0.0;
2283	<	zTempHist_[j] = 0.0;
2284	<	}
2279	>	}
2280	>
2281	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2282	>	if (!doRNEMD_) return;
2283	>	assert(index >=0 && index < ENDINDEX);
2284	>	assert(int(bin) < nBins_);
2285	>	RealType s;
2286	>	int count;
2287	>
2288	>	count = data_[index].accumulator[bin]->count();
2289	>	if (count == 0) return;
2290	>
2291	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2292	>
2293	>	if (! isinf(s) && ! isnan(s)) {
2294	>	rnemdFile_ << "\t" << s;
2295	>	} else{
2296	>	sprintf( painCave.errMsg,
2297	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2298	>	data_[index].title.c_str(), bin);
2299	>	painCave.isFatal = 1;
2300	>	simError();
2301	>	}
2302		}
2303	+
2304	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2305	+	if (!doRNEMD_) return;
2306	+	assert(index >=0 && index < ENDINDEX);
2307	+	assert(int(bin) < nBins_);
2308	+	Vector3d s;
2309	+	int count;
2310	+
2311	+	count = data_[index].accumulator[bin]->count();
2312	+	if (count == 0) return;
2313	+
2314	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2315	+	if (isinf(s[0]) || isnan(s[0]) ||
2316	+	isinf(s[1]) || isnan(s[1]) ||
2317	+	isinf(s[2]) || isnan(s[2]) ) {
2318	+	sprintf( painCave.errMsg,
2319	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2320	+	data_[index].title.c_str(), bin);
2321	+	painCave.isFatal = 1;
2322	+	simError();
2323	+	} else {
2324	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2325	+	}
2326	+	}
2327		}
2328	+

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