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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1855 by gezelter, Tue Apr 2 18:31:51 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).
39	<	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	<	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
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"
55	<	#else
55	>	#include "brains/Thermo.hpp"
56	>	#include "math/ConvexHull.hpp"
57	>	#ifdef IS_MPI
58		#include <mpi.h>
57	–	#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),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
76
77	+	trialCount_ = 0;
78		failTrialCount_ = 0;
79		failRootCount_ = 0;
80
81	<	int seedValue;
82	<	Globals * simParams = info->getSimParams();
81	>	Globals* simParams = info->getSimParams();
82	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83
84	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
85	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
77	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
78	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
79	<	stringToEnumMap_["Px"] = rnemdPx;
80	<	stringToEnumMap_["Py"] = rnemdPy;
81	<	stringToEnumMap_["Pz"] = rnemdPz;
82	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
84	>	doRNEMD_ = rnemdParams->getUseRNEMD();
85	>	if (!doRNEMD_) return;
86
87	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
88	<	evaluator_.loadScriptString(rnemdObjectSelection_);
89	<	seleMan_.setSelectionSet(evaluator_.evaluate());
87	>	stringToMethod_["Swap"]  = rnemdSwap;
88	>	stringToMethod_["NIVS"]  = rnemdNIVS;
89	>	stringToMethod_["VSS"]   = rnemdVSS;
90
91	<	// do some sanity checking
91	>	stringToFluxType_["KE"]  = rnemdKE;
92	>	stringToFluxType_["Px"]  = rnemdPx;
93	>	stringToFluxType_["Py"]  = rnemdPy;
94	>	stringToFluxType_["Pz"]  = rnemdPz;
95	>	stringToFluxType_["Pvector"]  = rnemdPvector;
96	>	stringToFluxType_["Lx"]  = rnemdLx;
97	>	stringToFluxType_["Ly"]  = rnemdLy;
98	>	stringToFluxType_["Lz"]  = rnemdLz;
99	>	stringToFluxType_["Lvector"]  = rnemdLvector;
100	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
101	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
102	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
103	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
104	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
105	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
106	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
107
108	<	int selectionCount = seleMan_.getSelectionCount();
109	<	int nIntegrable = info->getNGlobalIntegrableObjects();
108	>	runTime_ = simParams->getRunTime();
109	>	statusTime_ = simParams->getStatusTime();
110
111	<	if (selectionCount > nIntegrable) {
111	>	const string methStr = rnemdParams->getMethod();
112	>	bool hasFluxType = rnemdParams->haveFluxType();
113	>
114	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115	>
116	>	string fluxStr;
117	>	if (hasFluxType) {
118	>	fluxStr = rnemdParams->getFluxType();
119	>	} else {
120		sprintf(painCave.errMsg,
121	<	"RNEMD: The current RNEMD_objectSelection,\n"
122	<	"\t\t%s\n"
123	<	"\thas resulted in %d selected objects.  However,\n"
124	<	"\tthe total number of integrable objects in the system\n"
125	<	"\tis only %d.  This is almost certainly not what you want\n"
126	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
127	<	"\tselector in the selection script!\n",
102	<	rnemdObjectSelection_.c_str(),
103	<	selectionCount, nIntegrable);
104	<	painCave.isFatal = 0;
105	<	painCave.severity = OPENMD_WARNING;
121	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
122	>	"\twhich must be one of the following values:\n"
123	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
124	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
125	>	"\tmust be set to use RNEMD\n");
126	>	painCave.isFatal = 1;
127	>	painCave.severity = OPENMD_ERROR;
128		simError();
129		}
130	+
131	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
132	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
133	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
134	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
135	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
136	+	hasSelectionA_ = rnemdParams->haveSelectionA();
137	+	hasSelectionB_ = rnemdParams->haveSelectionB();
138	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
139	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
140	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
141	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
142	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
143	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
144	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
145	+	bool hasOutputFields = rnemdParams->haveOutputFields();
146
147	<	const string st = simParams->getRNEMD_exchangeType();
147	>	map<string, RNEMDMethod>::iterator i;
148	>	i = stringToMethod_.find(methStr);
149	>	if (i != stringToMethod_.end())
150	>	rnemdMethod_ = i->second;
151	>	else {
152	>	sprintf(painCave.errMsg,
153	>	"RNEMD: The current method,\n"
154	>	"\t\t%s is not one of the recognized\n"
155	>	"\texchange methods: Swap, NIVS, or VSS\n",
156	>	methStr.c_str());
157	>	painCave.isFatal = 1;
158	>	painCave.severity = OPENMD_ERROR;
159	>	simError();
160	>	}
161
162	<	map<string, RNEMDTypeEnum>::iterator i;
163	<	i = stringToEnumMap_.find(st);
164	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
165	<	if (rnemdType_ == rnemdUnknown) {
162	>	map<string, RNEMDFluxType>::iterator j;
163	>	j = stringToFluxType_.find(fluxStr);
164	>	if (j != stringToFluxType_.end())
165	>	rnemdFluxType_ = j->second;
166	>	else {
167		sprintf(painCave.errMsg,
168	<	"RNEMD: The current RNEMD_exchangeType,\n"
168	>	"RNEMD: The current fluxType,\n"
169		"\t\t%s\n"
170	<	"\tis not one of the recognized exchange types.\n",
171	<	st.c_str());
170	>	"\tis not one of the recognized flux types.\n",
171	>	fluxStr.c_str());
172		painCave.isFatal = 1;
173		painCave.severity = OPENMD_ERROR;
174		simError();
175		}
124	–
125	–	output3DTemp_ = false;
126	–	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
127	–	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
128	–	}
176
177	<	#ifdef IS_MPI
178	<	if (worldRank == 0) {
179	<	#endif
180	<
181	<	string rnemdFileName;
182	<	switch(rnemdType_) {
183	<	case rnemdKineticSwap :
137	<	case rnemdKineticScale :
138	<	rnemdFileName = "temperature.log";
177	>	bool methodFluxMismatch = false;
178	>	bool hasCorrectFlux = false;
179	>	switch(rnemdMethod_) {
180	>	case rnemdSwap:
181	>	switch (rnemdFluxType_) {
182	>	case rnemdKE:
183	>	hasCorrectFlux = hasKineticFlux;
184		break;
185	<	case rnemdPx :
186	<	case rnemdPxScale :
187	<	case rnemdPy :
188	<	case rnemdPyScale :
144	<	rnemdFileName = "momemtum.log";
185	>	case rnemdPx:
186	>	case rnemdPy:
187	>	case rnemdPz:
188	>	hasCorrectFlux = hasMomentumFlux;
189		break;
146	–	case rnemdPz :
147	–	case rnemdPzScale :
148	–	case rnemdUnknown :
190		default :
191	<	rnemdFileName = "rnemd.log";
191	>	methodFluxMismatch = true;
192		break;
193		}
194	<	rnemdLog_.open(rnemdFileName.c_str());
195	<
196	<	string xTempFileName;
197	<	string yTempFileName;
198	<	string zTempFileName;
199	<	if (output3DTemp_) {
200	<	xTempFileName = "temperatureX.log";
201	<	yTempFileName = "temperatureY.log";
202	<	zTempFileName = "temperatureZ.log";
203	<	xTempLog_.open(xTempFileName.c_str());
204	<	yTempLog_.open(yTempFileName.c_str());
205	<	zTempLog_.open(zTempFileName.c_str());
194	>	break;
195	>	case rnemdNIVS:
196	>	switch (rnemdFluxType_) {
197	>	case rnemdKE:
198	>	case rnemdRotKE:
199	>	case rnemdFullKE:
200	>	hasCorrectFlux = hasKineticFlux;
201	>	break;
202	>	case rnemdPx:
203	>	case rnemdPy:
204	>	case rnemdPz:
205	>	hasCorrectFlux = hasMomentumFlux;
206	>	break;
207	>	case rnemdKePx:
208	>	case rnemdKePy:
209	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
210	>	break;
211	>	default:
212	>	methodFluxMismatch = true;
213	>	break;
214		}
215	<
216	<	#ifdef IS_MPI
217	<	}
218	<	#endif
219	<
220	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
221	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
222	<	midBin_ = nBins_ / 2;
223	<	if (simParams->haveRNEMD_binShift()) {
224	<	if (simParams->getRNEMD_binShift()) {
225	<	zShift_ = 0.5 / (RealType)(nBins_);
226	<	} else {
227	<	zShift_ = 0.0;
228	<	}
229	<	} else {
230	<	zShift_ = 0.0;
231	<	}
232	<	//cerr << "we have zShift_ = " << zShift_ << "\n";
233	<	//shift slabs by half slab width, might be useful in heterogeneous systems
234	<	//set to 0.0 if not using it; can NOT be used in status output yet
235	<	if (simParams->haveRNEMD_logWidth()) {
236	<	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
237	<	/*arbitary rnemdLogWidth_ no checking
238	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
239	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
240	<	cerr << "Automaically set back to default.\n";
241	<	rnemdLogWidth_ = nBins_;
242	<	}*/
243	<	} else {
244	<	set_RNEMD_logWidth(nBins_);
245	<	}
246	<	valueHist_.resize(rnemdLogWidth_, 0.0);
247	<	valueCount_.resize(rnemdLogWidth_, 0);
248	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
249	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
250	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
251	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
252	<
253	<	set_RNEMD_exchange_total(0.0);
254	<	if (simParams->haveRNEMD_targetFlux()) {
255	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
215	>	break;
216	>	case rnemdVSS:
217	>	switch (rnemdFluxType_) {
218	>	case rnemdKE:
219	>	case rnemdRotKE:
220	>	case rnemdFullKE:
221	>	hasCorrectFlux = hasKineticFlux;
222	>	break;
223	>	case rnemdPx:
224	>	case rnemdPy:
225	>	case rnemdPz:
226	>	hasCorrectFlux = hasMomentumFlux;
227	>	break;
228	>	case rnemdLx:
229	>	case rnemdLy:
230	>	case rnemdLz:
231	>	hasCorrectFlux = hasAngularMomentumFlux;
232	>	break;
233	>	case rnemdPvector:
234	>	hasCorrectFlux = hasMomentumFluxVector;
235	>	break;
236	>	case rnemdLvector:
237	>	hasCorrectFlux = hasAngularMomentumFluxVector;
238	>	break;
239	>	case rnemdKePx:
240	>	case rnemdKePy:
241	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
242	>	break;
243	>	case rnemdKeLx:
244	>	case rnemdKeLy:
245	>	case rnemdKeLz:
246	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
247	>	break;
248	>	case rnemdKePvector:
249	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
250	>	break;
251	>	case rnemdKeLvector:
252	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
253	>	break;
254	>	default:
255	>	methodFluxMismatch = true;
256	>	break;
257	>	}
258	>	default:
259	>	break;
260	>	}
261	>
262	>	if (methodFluxMismatch) {
263	>	sprintf(painCave.errMsg,
264	>	"RNEMD: The current method,\n"
265	>	"\t\t%s\n"
266	>	"\tcannot be used with the current flux type, %s\n",
267	>	methStr.c_str(), fluxStr.c_str());
268	>	painCave.isFatal = 1;
269	>	painCave.severity = OPENMD_ERROR;
270	>	simError();
271	>	}
272	>	if (!hasCorrectFlux) {
273	>	sprintf(painCave.errMsg,
274	>	"RNEMD: The current method, %s, and flux type, %s,\n"
275	>	"\tdid not have the correct flux value specified. Options\n"
276	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
277	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
278	>	methStr.c_str(), fluxStr.c_str());
279	>	painCave.isFatal = 1;
280	>	painCave.severity = OPENMD_ERROR;
281	>	simError();
282	>	}
283	>
284	>	if (hasKineticFlux) {
285	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
286	>	// into  amu / fs^3:
287	>	kineticFlux_ = rnemdParams->getKineticFlux()
288	>	* PhysicalConstants::energyConvert;
289		} else {
290	<	set_RNEMD_target_flux(0.0);
290	>	kineticFlux_ = 0.0;
291		}
292	+	if (hasMomentumFluxVector) {
293	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
294	+	} else {
295	+	momentumFluxVector_ = V3Zero;
296	+	if (hasMomentumFlux) {
297	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
298	+	switch (rnemdFluxType_) {
299	+	case rnemdPx:
300	+	momentumFluxVector_.x() = momentumFlux;
301	+	break;
302	+	case rnemdPy:
303	+	momentumFluxVector_.y() = momentumFlux;
304	+	break;
305	+	case rnemdPz:
306	+	momentumFluxVector_.z() = momentumFlux;
307	+	break;
308	+	case rnemdKePx:
309	+	momentumFluxVector_.x() = momentumFlux;
310	+	break;
311	+	case rnemdKePy:
312	+	momentumFluxVector_.y() = momentumFlux;
313	+	break;
314	+	default:
315	+	break;
316	+	}
317	+	}
318	+	if (hasAngularMomentumFluxVector) {
319	+	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
320	+	} else {
321	+	angularMomentumFluxVector_ = V3Zero;
322	+	if (hasAngularMomentumFlux) {
323	+	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
324	+	switch (rnemdFluxType_) {
325	+	case rnemdLx:
326	+	angularMomentumFluxVector_.x() = angularMomentumFlux;
327	+	break;
328	+	case rnemdLy:
329	+	angularMomentumFluxVector_.y() = angularMomentumFlux;
330	+	break;
331	+	case rnemdLz:
332	+	angularMomentumFluxVector_.z() = angularMomentumFlux;
333	+	break;
334	+	case rnemdKeLx:
335	+	angularMomentumFluxVector_.x() = angularMomentumFlux;
336	+	break;
337	+	case rnemdKeLy:
338	+	angularMomentumFluxVector_.y() = angularMomentumFlux;
339	+	break;
340	+	case rnemdKeLz:
341	+	angularMomentumFluxVector_.z() = angularMomentumFlux;
342	+	break;
343	+	default:
344	+	break;
345	+	}
346	+	}
347	+	}
348
349	<	#ifndef IS_MPI
350	<	if (simParams->haveSeed()) {
351	<	seedValue = simParams->getSeed();
352	<	randNumGen_ = new SeqRandNumGen(seedValue);
353	<	}else {
354	<	randNumGen_ = new SeqRandNumGen();
355	<	}
356	<	#else
357	<	if (simParams->haveSeed()) {
358	<	seedValue = simParams->getSeed();
359	<	randNumGen_ = new ParallelRandNumGen(seedValue);
360	<	}else {
361	<	randNumGen_ = new ParallelRandNumGen();
362	<	}
363	<	#endif
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351	>	} else {
352	>	coordinateOrigin_ = V3Zero;
353	>	}
354	>
355	>	// do some sanity checking
356	>
357	>	int selectionCount = seleMan_.getSelectionCount();
358	>
359	>	int nIntegrable = info->getNGlobalIntegrableObjects();
360	>
361	>	if (selectionCount > nIntegrable) {
362	>	sprintf(painCave.errMsg,
363	>	"RNEMD: The current objectSelection,\n"
364	>	"\t\t%s\n"
365	>	"\thas resulted in %d selected objects.  However,\n"
366	>	"\tthe total number of integrable objects in the system\n"
367	>	"\tis only %d.  This is almost certainly not what you want\n"
368	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
369	>	"\tselector in the selection script!\n",
370	>	rnemdObjectSelection_.c_str(),
371	>	selectionCount, nIntegrable);
372	>	painCave.isFatal = 0;
373	>	painCave.severity = OPENMD_WARNING;
374	>	simError();
375	>	}
376	>
377	>	areaAccumulator_ = new Accumulator();
378	>
379	>	nBins_ = rnemdParams->getOutputBins();
380	>	binWidth_ = rnemdParams->getOutputBinWidth();
381	>
382	>	data_.resize(RNEMD::ENDINDEX);
383	>	OutputData z;
384	>	z.units =  "Angstroms";
385	>	z.title =  "Z";
386	>	z.dataType = "RealType";
387	>	z.accumulator.reserve(nBins_);
388	>	for (int i = 0; i < nBins_; i++)
389	>	z.accumulator.push_back( new Accumulator() );
390	>	data_[Z] = z;
391	>	outputMap_["Z"] =  Z;
392	>
393	>	OutputData r;
394	>	r.units =  "Angstroms";
395	>	r.title =  "R";
396	>	r.dataType = "RealType";
397	>	r.accumulator.reserve(nBins_);
398	>	for (int i = 0; i < nBins_; i++)
399	>	r.accumulator.push_back( new Accumulator() );
400	>	data_[R] = r;
401	>	outputMap_["R"] =  R;
402	>
403	>	OutputData temperature;
404	>	temperature.units =  "K";
405	>	temperature.title =  "Temperature";
406	>	temperature.dataType = "RealType";
407	>	temperature.accumulator.reserve(nBins_);
408	>	for (int i = 0; i < nBins_; i++)
409	>	temperature.accumulator.push_back( new Accumulator() );
410	>	data_[TEMPERATURE] = temperature;
411	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
412	>
413	>	OutputData velocity;
414	>	velocity.units = "angstroms/fs";
415	>	velocity.title =  "Velocity";
416	>	velocity.dataType = "Vector3d";
417	>	velocity.accumulator.reserve(nBins_);
418	>	for (int i = 0; i < nBins_; i++)
419	>	velocity.accumulator.push_back( new VectorAccumulator() );
420	>	data_[VELOCITY] = velocity;
421	>	outputMap_["VELOCITY"] = VELOCITY;
422	>
423	>	OutputData angularVelocity;
424	>	angularVelocity.units = "angstroms^2/fs";
425	>	angularVelocity.title =  "AngularVelocity";
426	>	angularVelocity.dataType = "Vector3d";
427	>	angularVelocity.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
430	>	data_[ANGULARVELOCITY] = angularVelocity;
431	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
432	>
433	>	OutputData density;
434	>	density.units =  "g cm^-3";
435	>	density.title =  "Density";
436	>	density.dataType = "RealType";
437	>	density.accumulator.reserve(nBins_);
438	>	for (int i = 0; i < nBins_; i++)
439	>	density.accumulator.push_back( new Accumulator() );
440	>	data_[DENSITY] = density;
441	>	outputMap_["DENSITY"] =  DENSITY;
442	>
443	>	if (hasOutputFields) {
444	>	parseOutputFileFormat(rnemdParams->getOutputFields());
445	>	} else {
446	>	if (usePeriodicBoundaryConditions_)
447	>	outputMask_.set(Z);
448	>	else
449	>	outputMask_.set(R);
450	>	switch (rnemdFluxType_) {
451	>	case rnemdKE:
452	>	case rnemdRotKE:
453	>	case rnemdFullKE:
454	>	outputMask_.set(TEMPERATURE);
455	>	break;
456	>	case rnemdPx:
457	>	case rnemdPy:
458	>	outputMask_.set(VELOCITY);
459	>	break;
460	>	case rnemdPz:
461	>	case rnemdPvector:
462	>	outputMask_.set(VELOCITY);
463	>	outputMask_.set(DENSITY);
464	>	break;
465	>	case rnemdLx:
466	>	case rnemdLy:
467	>	case rnemdLz:
468	>	case rnemdLvector:
469	>	outputMask_.set(ANGULARVELOCITY);
470	>	break;
471	>	case rnemdKeLx:
472	>	case rnemdKeLy:
473	>	case rnemdKeLz:
474	>	case rnemdKeLvector:
475	>	outputMask_.set(TEMPERATURE);
476	>	outputMask_.set(ANGULARVELOCITY);
477	>	break;
478	>	case rnemdKePx:
479	>	case rnemdKePy:
480	>	outputMask_.set(TEMPERATURE);
481	>	outputMask_.set(VELOCITY);
482	>	break;
483	>	case rnemdKePvector:
484	>	outputMask_.set(TEMPERATURE);
485	>	outputMask_.set(VELOCITY);
486	>	outputMask_.set(DENSITY);
487	>	break;
488	>	default:
489	>	break;
490	>	}
491	>	}
492	>
493	>	if (hasOutputFileName) {
494	>	rnemdFileName_ = rnemdParams->getOutputFileName();
495	>	} else {
496	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
497	>	}
498	>
499	>	exchangeTime_ = rnemdParams->getExchangeTime();
500	>
501	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
502	>	// total exchange sums are zeroed out at the beginning:
503	>
504	>	kineticExchange_ = 0.0;
505	>	momentumExchange_ = V3Zero;
506	>	angularMomentumExchange_ = V3Zero;
507	>
508	>	std::ostringstream selectionAstream;
509	>	std::ostringstream selectionBstream;
510	>
511	>	if (hasSelectionA_) {
512	>	selectionA_ = rnemdParams->getSelectionA();
513	>	} else {
514	>	if (usePeriodicBoundaryConditions_) {
515	>	Mat3x3d hmat = currentSnap_->getHmat();
516	>
517	>	if (hasSlabWidth)
518	>	slabWidth_ = rnemdParams->getSlabWidth();
519	>	else
520	>	slabWidth_ = hmat(2,2) / 10.0;
521	>
522	>	if (hasSlabACenter)
523	>	slabACenter_ = rnemdParams->getSlabACenter();
524	>	else
525	>	slabACenter_ = 0.0;
526	>
527	>	selectionAstream << "select wrappedz > "
528	>	<< slabACenter_ - 0.5*slabWidth_
529	>	<<  " && wrappedz < "
530	>	<< slabACenter_ + 0.5*slabWidth_;
531	>	selectionA_ = selectionAstream.str();
532	>	} else {
533	>	if (hasSphereARadius)
534	>	sphereARadius_ = rnemdParams->getSphereARadius();
535	>	else {
536	>	// use an initial guess to the size of the inner slab to be 1/10 the
537	>	// radius of an approximately spherical hull:
538	>	Thermo thermo(info);
539	>	RealType hVol = thermo.getHullVolume();
540	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
541	>	}
542	>	selectionAstream << "select r < " << sphereARadius_;
543	>	selectionA_ = selectionAstream.str();
544	>	}
545	>	}
546	>
547	>	if (hasSelectionB_) {
548	>	selectionB_ = rnemdParams->getSelectionB();
549	>	} else {
550	>	if (usePeriodicBoundaryConditions_) {
551	>	Mat3x3d hmat = currentSnap_->getHmat();
552	>
553	>	if (hasSlabWidth)
554	>	slabWidth_ = rnemdParams->getSlabWidth();
555	>	else
556	>	slabWidth_ = hmat(2,2) / 10.0;
557	>
558	>	if (hasSlabBCenter)
559	>	slabBCenter_ = rnemdParams->getSlabACenter();
560	>	else
561	>	slabBCenter_ = hmat(2,2) / 2.0;
562	>
563	>	selectionBstream << "select wrappedz > "
564	>	<< slabBCenter_ - 0.5*slabWidth_
565	>	<<  " && wrappedz < "
566	>	<< slabBCenter_ + 0.5*slabWidth_;
567	>	selectionB_ = selectionBstream.str();
568	>	} else {
569	>	if (hasSphereBRadius_) {
570	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
571	>	selectionBstream << "select r > " << sphereBRadius_;
572	>	selectionB_ = selectionBstream.str();
573	>	} else {
574	>	selectionB_ = "select hull";
575	>	hasSelectionB_ = true;
576	>	}
577	>	}
578	>	}
579	>	}
580	>	// object evaluator:
581	>	evaluator_.loadScriptString(rnemdObjectSelection_);
582	>	seleMan_.setSelectionSet(evaluator_.evaluate());
583	>
584	>	evaluatorA_.loadScriptString(selectionA_);
585	>	evaluatorB_.loadScriptString(selectionB_);
586	>
587	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	>
590	>	commonA_ = seleManA_ & seleMan_;
591	>	commonB_ = seleManB_ & seleMan_;
592		}
593
228	–	RNEMD::~RNEMD() {
229	–	delete randNumGen_;
594
595	+	RNEMD::~RNEMD() {
596	+	if (!doRNEMD_) return;
597		#ifdef IS_MPI
598		if (worldRank == 0) {
599		#endif
234	–
235	–	sprintf(painCave.errMsg,
236	–	"RNEMD: total failed trials: %d\n",
237	–	failTrialCount_);
238	–	painCave.isFatal = 0;
239	–	painCave.severity = OPENMD_INFO;
240	–	simError();
600
601	<	rnemdLog_.close();
602	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
603	<	sprintf(painCave.errMsg,
604	<	"RNEMD: total root-checking warnings: %d\n",
246	<	failRootCount_);
247	<	painCave.isFatal = 0;
248	<	painCave.severity = OPENMD_INFO;
249	<	simError();
250	<	}
251	<	if (output3DTemp_) {
252	<	xTempLog_.close();
253	<	yTempLog_.close();
254	<	zTempLog_.close();
255	<	}
601	>	writeOutputFile();
602	>
603	>	rnemdFile_.close();
604	>
605		#ifdef IS_MPI
606		}
607		#endif
608		}
609	+
610	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
611	+	if (!doRNEMD_) return;
612	+	int selei;
613	+	int selej;
614
261	–	void RNEMD::doSwap() {
262	–
615		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
616		Mat3x3d hmat = currentSnap_->getHmat();
617
266	–	seleMan_.setSelectionSet(evaluator_.evaluate());
267	–
268	–	int selei;
618		StuntDouble* sd;
270	–	int idx;
619
620		RealType min_val;
621		bool min_found = false;
#	Line 277 | Line 625 | namespace OpenMD {
625		bool max_found = false;
626		StuntDouble* max_sd;
627
628	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
629	<	sd = seleMan_.nextSelected(selei)) {
628	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
629	>	sd = seleManA_.nextSelected(selei)) {
630
283	–	idx = sd->getLocalIndex();
284	–
631		Vector3d pos = sd->getPos();
632	<
632	>
633		// wrap the stuntdouble's position back into the box:
634	<
634	>
635		if (usePeriodicBoundaryConditions_)
636		currentSnap_->wrapVector(pos);
637	<
638	<	// which bin is this stuntdouble in?
639	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
640	<
641	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
642	<
643	<
298	<	// if we're in bin 0 or the middleBin
299	<	if (binNo == 0 || binNo == midBin_) {
637	>
638	>	RealType mass = sd->getMass();
639	>	Vector3d vel = sd->getVel();
640	>	RealType value;
641	>
642	>	switch(rnemdFluxType_) {
643	>	case rnemdKE :
644
645	<	RealType mass = sd->getMass();
646	<	Vector3d vel = sd->getVel();
647	<	RealType value;
648	<
649	<	switch(rnemdType_) {
306	<	case rnemdKineticSwap :
645	>	value = mass * vel.lengthSquare();
646	>
647	>	if (sd->isDirectional()) {
648	>	Vector3d angMom = sd->getJ();
649	>	Mat3x3d I = sd->getI();
650
651	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
309	<	vel[2]*vel[2]);
310	<	/*
311	<	if (sd->isDirectional()) {
312	<	Vector3d angMom = sd->getJ();
313	<	Mat3x3d I = sd->getI();
314	<
315	<	if (sd->isLinear()) {
651	>	if (sd->isLinear()) {
652		int i = sd->linearAxis();
653		int j = (i + 1) % 3;
654		int k = (i + 2) % 3;
655		value += angMom[j] * angMom[j] / I(j, j) +
656	<	angMom[k] * angMom[k] / I(k, k);
657	<	} else {
656	>	angMom[k] * angMom[k] / I(k, k);
657	>	} else {
658		value += angMom[0]*angMom[0]/I(0, 0)
659	<	+ angMom[1]*angMom[1]/I(1, 1)
660	<	+ angMom[2]*angMom[2]/I(2, 2);
661	<	}
662	<	} no exchange of angular momenta
663	<	*/
664	<	//make exchangeSum_ comparable between swap & scale
665	<	//temporarily without using energyConvert
666	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
667	<	value *= 0.5;
668	<	break;
669	<	case rnemdPx :
670	<	value = mass * vel[0];
671	<	break;
672	<	case rnemdPy :
673	<	value = mass * vel[1];
674	<	break;
675	<	case rnemdPz :
676	<	value = mass * vel[2];
677	<	break;
678	<	default :
679	<	break;
659	>	+ angMom[1]*angMom[1]/I(1, 1)
660	>	+ angMom[2]*angMom[2]/I(2, 2);
661	>	}
662	>	} //angular momenta exchange enabled
663	>	value *= 0.5;
664	>	break;
665	>	case rnemdPx :
666	>	value = mass * vel[0];
667	>	break;
668	>	case rnemdPy :
669	>	value = mass * vel[1];
670	>	break;
671	>	case rnemdPz :
672	>	value = mass * vel[2];
673	>	break;
674	>	default :
675	>	break;
676	>	}
677	>	if (!max_found) {
678	>	max_val = value;
679	>	max_sd = sd;
680	>	max_found = true;
681	>	} else {
682	>	if (max_val < value) {
683	>	max_val = value;
684	>	max_sd = sd;
685		}
686	+	}
687	+	}
688
689	<	if (binNo == 0) {
690	<	if (!min_found) {
691	<	min_val = value;
692	<	min_sd = sd;
693	<	min_found = true;
694	<	} else {
695	<	if (min_val > value) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	}
699	<	}
700	<	} else { //midBin_
701	<	if (!max_found) {
702	<	max_val = value;
703	<	max_sd = sd;
704	<	max_found = true;
705	<	} else {
706	<	if (max_val < value) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	}
710	<	}
711	<	}
689	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
690	>	sd = seleManB_.nextSelected(selej)) {
691	>
692	>	Vector3d pos = sd->getPos();
693	>
694	>	// wrap the stuntdouble's position back into the box:
695	>
696	>	if (usePeriodicBoundaryConditions_)
697	>	currentSnap_->wrapVector(pos);
698	>
699	>	RealType mass = sd->getMass();
700	>	Vector3d vel = sd->getVel();
701	>	RealType value;
702	>
703	>	switch(rnemdFluxType_) {
704	>	case rnemdKE :
705	>
706	>	value = mass * vel.lengthSquare();
707	>
708	>	if (sd->isDirectional()) {
709	>	Vector3d angMom = sd->getJ();
710	>	Mat3x3d I = sd->getI();
711	>
712	>	if (sd->isLinear()) {
713	>	int i = sd->linearAxis();
714	>	int j = (i + 1) % 3;
715	>	int k = (i + 2) % 3;
716	>	value += angMom[j] * angMom[j] / I(j, j) +
717	>	angMom[k] * angMom[k] / I(k, k);
718	>	} else {
719	>	value += angMom[0]*angMom[0]/I(0, 0)
720	>	+ angMom[1]*angMom[1]/I(1, 1)
721	>	+ angMom[2]*angMom[2]/I(2, 2);
722	>	}
723	>	} //angular momenta exchange enabled
724	>	value *= 0.5;
725	>	break;
726	>	case rnemdPx :
727	>	value = mass * vel[0];
728	>	break;
729	>	case rnemdPy :
730	>	value = mass * vel[1];
731	>	break;
732	>	case rnemdPz :
733	>	value = mass * vel[2];
734	>	break;
735	>	default :
736	>	break;
737		}
738	+
739	+	if (!min_found) {
740	+	min_val = value;
741	+	min_sd = sd;
742	+	min_found = true;
743	+	} else {
744	+	if (min_val > value) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	}
748	+	}
749		}
750	<
751	<	#ifdef IS_MPI
752	<	int nProc, worldRank;
753	<
375	<	nProc = MPI::COMM_WORLD.Get_size();
376	<	worldRank = MPI::COMM_WORLD.Get_rank();
377	<
750	>
751	>	#ifdef IS_MPI
752	>	int worldRank = MPI::COMM_WORLD.Get_rank();
753	>
754		bool my_min_found = min_found;
755		bool my_max_found = max_found;
756
#	Line 382 | Line 758 | namespace OpenMD {
758		MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
759		// Even if we didn't find a maximum, did someone else?
760		MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
761	<	struct {
762	<	RealType val;
763	<	int rank;
764	<	} max_vals, min_vals;
765	<
766	<	if (min_found) {
767	<	if (my_min_found)
761	>	#endif
762	>
763	>	if (max_found && min_found) {
764	>
765	>	#ifdef IS_MPI
766	>	struct {
767	>	RealType val;
768	>	int rank;
769	>	} max_vals, min_vals;
770	>
771	>	if (my_min_found) {
772		min_vals.val = min_val;
773	<	else
773	>	} else {
774		min_vals.val = HONKING_LARGE_VALUE;
775	<
775	>	}
776		min_vals.rank = worldRank;
777
778		// Who had the minimum?
779		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
780		1, MPI::REALTYPE_INT, MPI::MINLOC);
781		min_val = min_vals.val;
402	–	}
782
783	<	if (max_found) {
405	<	if (my_max_found)
783	>	if (my_max_found) {
784		max_vals.val = max_val;
785	<	else
785	>	} else {
786		max_vals.val = -HONKING_LARGE_VALUE;
787	<
787	>	}
788		max_vals.rank = worldRank;
789
790		// Who had the maximum?
791		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
792		1, MPI::REALTYPE_INT, MPI::MAXLOC);
793		max_val = max_vals.val;
416	–	}
794		#endif
795	<
419	<	if (max_found && min_found) {
795	>
796		if (min_val < max_val) {
797	<
797	>
798		#ifdef IS_MPI
799		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
800		// I have both maximum and minimum, so proceed like a single
801		// processor version:
802		#endif
803	<	// objects to be swapped: velocity ONLY
803	>
804		Vector3d min_vel = min_sd->getVel();
805		Vector3d max_vel = max_sd->getVel();
806		RealType temp_vel;
807
808	<	switch(rnemdType_) {
809	<	case rnemdKineticSwap :
808	>	switch(rnemdFluxType_) {
809	>	case rnemdKE :
810		min_sd->setVel(max_vel);
811		max_sd->setVel(min_vel);
812	<	/*
437	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
812	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
813		Vector3d min_angMom = min_sd->getJ();
814		Vector3d max_angMom = max_sd->getJ();
815		min_sd->setJ(max_angMom);
816		max_sd->setJ(min_angMom);
817	<	} no angular momentum exchange
818	<	*/
817	>	}//angular momenta exchange enabled
818	>	//assumes same rigid body identity
819		break;
820		case rnemdPx :
821		temp_vel = min_vel.x();
#	Line 466 | Line 841 | namespace OpenMD {
841		default :
842		break;
843		}
844	+
845		#ifdef IS_MPI
846		// the rest of the cases only apply in parallel simulations:
847		} else if (max_vals.rank == worldRank) {
#	Line 481 | Line 857 | namespace OpenMD {
857		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
858		min_vals.rank, 0, status);
859
860	<	switch(rnemdType_) {
861	<	case rnemdKineticSwap :
860	>	switch(rnemdFluxType_) {
861	>	case rnemdKE :
862		max_sd->setVel(min_vel);
863	<	//no angular momentum exchange for now
488	<	/*
863	>	//angular momenta exchange enabled
864		if (max_sd->isDirectional()) {
865		Vector3d min_angMom;
866		Vector3d max_angMom = max_sd->getJ();
#	Line 498 | Line 873 | namespace OpenMD {
873		status);
874
875		max_sd->setJ(min_angMom);
876	<	}
502	<	*/
876	>	}
877		break;
878		case rnemdPx :
879		max_vel.x() = min_vel.x();
#	Line 529 | Line 903 | namespace OpenMD {
903		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
904		max_vals.rank, 0, status);
905
906	<	switch(rnemdType_) {
907	<	case rnemdKineticSwap :
906	>	switch(rnemdFluxType_) {
907	>	case rnemdKE :
908		min_sd->setVel(max_vel);
909	<	// no angular momentum exchange for now
536	<	/*
909	>	//angular momenta exchange enabled
910		if (min_sd->isDirectional()) {
911		Vector3d min_angMom = min_sd->getJ();
912		Vector3d max_angMom;
#	Line 547 | Line 920 | namespace OpenMD {
920
921		min_sd->setJ(max_angMom);
922		}
550	–	*/
923		break;
924		case rnemdPx :
925		min_vel.x() = max_vel.x();
#	Line 566 | Line 938 | namespace OpenMD {
938		}
939		}
940		#endif
941	<	exchangeSum_ += max_val - min_val;
941	>
942	>	switch(rnemdFluxType_) {
943	>	case rnemdKE:
944	>	kineticExchange_ += max_val - min_val;
945	>	break;
946	>	case rnemdPx:
947	>	momentumExchange_.x() += max_val - min_val;
948	>	break;
949	>	case rnemdPy:
950	>	momentumExchange_.y() += max_val - min_val;
951	>	break;
952	>	case rnemdPz:
953	>	momentumExchange_.z() += max_val - min_val;
954	>	break;
955	>	default:
956	>	break;
957	>	}
958		} else {
959		sprintf(painCave.errMsg,
960	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
960	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
961		painCave.isFatal = 0;
962		painCave.severity = OPENMD_INFO;
963		simError();
#	Line 577 | Line 965 | namespace OpenMD {
965		}
966		} else {
967		sprintf(painCave.errMsg,
968	<	"RNEMD: exchange NOT performed because at least one\n"
969	<	"\tof the two slabs is empty\n");
968	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
969	>	"\twas not present in at least one of the two slabs.\n");
970		painCave.isFatal = 0;
971		painCave.severity = OPENMD_INFO;
972		simError();
973		failTrialCount_++;
974	<	}
587	<
974	>	}
975		}
976
977	<	void RNEMD::doScale() {
977	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
978	>	if (!doRNEMD_) return;
979	>	int selei;
980	>	int selej;
981
982		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
983	+	RealType time = currentSnap_->getTime();
984		Mat3x3d hmat = currentSnap_->getHmat();
985
595	–	seleMan_.setSelectionSet(evaluator_.evaluate());
596	–
597	–	int selei;
986		StuntDouble* sd;
599	–	int idx;
987
988		vector<StuntDouble*> hotBin, coldBin;
989
#	Line 606 | Line 993 | namespace OpenMD {
993		RealType Khx = 0.0;
994		RealType Khy = 0.0;
995		RealType Khz = 0.0;
996	+	RealType Khw = 0.0;
997		RealType Pcx = 0.0;
998		RealType Pcy = 0.0;
999		RealType Pcz = 0.0;
1000		RealType Kcx = 0.0;
1001		RealType Kcy = 0.0;
1002		RealType Kcz = 0.0;
1003	+	RealType Kcw = 0.0;
1004
1005	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1006	<	sd = seleMan_.nextSelected(selei)) {
1005	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1006	>	sd = smanA.nextSelected(selei)) {
1007
619	–	idx = sd->getLocalIndex();
620	–
1008		Vector3d pos = sd->getPos();
1009	<
1009	>
1010		// wrap the stuntdouble's position back into the box:
1011	<
1011	>
1012		if (usePeriodicBoundaryConditions_)
1013		currentSnap_->wrapVector(pos);
1014	+
1015	+
1016	+	RealType mass = sd->getMass();
1017	+	Vector3d vel = sd->getVel();
1018	+
1019	+	hotBin.push_back(sd);
1020	+	Phx += mass * vel.x();
1021	+	Phy += mass * vel.y();
1022	+	Phz += mass * vel.z();
1023	+	Khx += mass * vel.x() * vel.x();
1024	+	Khy += mass * vel.y() * vel.y();
1025	+	Khz += mass * vel.z() * vel.z();
1026	+	if (sd->isDirectional()) {
1027	+	Vector3d angMom = sd->getJ();
1028	+	Mat3x3d I = sd->getI();
1029	+	if (sd->isLinear()) {
1030	+	int i = sd->linearAxis();
1031	+	int j = (i + 1) % 3;
1032	+	int k = (i + 2) % 3;
1033	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1034	+	angMom[k] * angMom[k] / I(k, k);
1035	+	} else {
1036	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1037	+	+ angMom[1]*angMom[1]/I(1, 1)
1038	+	+ angMom[2]*angMom[2]/I(2, 2);
1039	+	}
1040	+	}
1041	+	}
1042	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1043	+	sd = smanB.nextSelected(selej)) {
1044	+	Vector3d pos = sd->getPos();
1045	+
1046	+	// wrap the stuntdouble's position back into the box:
1047	+
1048	+	if (usePeriodicBoundaryConditions_)
1049	+	currentSnap_->wrapVector(pos);
1050	+
1051	+	RealType mass = sd->getMass();
1052	+	Vector3d vel = sd->getVel();
1053
1054	<	// which bin is this stuntdouble in?
1055	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1056	<
1057	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1058	<
1059	<	// if we're in bin 0 or the middleBin
1060	<	if (binNo == 0 || binNo == midBin_) {
1061	<
1062	<	RealType mass = sd->getMass();
1063	<	Vector3d vel = sd->getVel();
1064	<
1065	<	if (binNo == 0) {
1066	<	hotBin.push_back(sd);
1067	<	Phx += mass * vel.x();
1068	<	Phy += mass * vel.y();
1069	<	Phz += mass * vel.z();
1070	<	Khx += mass * vel.x() * vel.x();
1071	<	Khy += mass * vel.y() * vel.y();
1072	<	Khz += mass * vel.z() * vel.z();
1073	<	} else { //midBin_
1074	<	coldBin.push_back(sd);
649	<	Pcx += mass * vel.x();
650	<	Pcy += mass * vel.y();
651	<	Pcz += mass * vel.z();
652	<	Kcx += mass * vel.x() * vel.x();
653	<	Kcy += mass * vel.y() * vel.y();
654	<	Kcz += mass * vel.z() * vel.z();
655	<	}
1054	>	coldBin.push_back(sd);
1055	>	Pcx += mass * vel.x();
1056	>	Pcy += mass * vel.y();
1057	>	Pcz += mass * vel.z();
1058	>	Kcx += mass * vel.x() * vel.x();
1059	>	Kcy += mass * vel.y() * vel.y();
1060	>	Kcz += mass * vel.z() * vel.z();
1061	>	if (sd->isDirectional()) {
1062	>	Vector3d angMom = sd->getJ();
1063	>	Mat3x3d I = sd->getI();
1064	>	if (sd->isLinear()) {
1065	>	int i = sd->linearAxis();
1066	>	int j = (i + 1) % 3;
1067	>	int k = (i + 2) % 3;
1068	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1069	>	angMom[k] * angMom[k] / I(k, k);
1070	>	} else {
1071	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1072	>	+ angMom[1]*angMom[1]/I(1, 1)
1073	>	+ angMom[2]*angMom[2]/I(2, 2);
1074	>	}
1075		}
1076		}
1077	<
1077	>
1078		Khx *= 0.5;
1079		Khy *= 0.5;
1080		Khz *= 0.5;
1081	+	Khw *= 0.5;
1082		Kcx *= 0.5;
1083		Kcy *= 0.5;
1084		Kcz *= 0.5;
1085	+	Kcw *= 0.5;
1086
1087		#ifdef IS_MPI
1088		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 674 | Line 1095 | namespace OpenMD {
1095		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1096		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1097		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1098	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1099	+
1100		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1101		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1102		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1103	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1104		#endif
1105
1106	<	//use coldBin coeff's
1106	>	//solve coldBin coeff's first
1107		RealType px = Pcx / Phx;
1108		RealType py = Pcy / Phy;
1109		RealType pz = Pcz / Phz;
1110	+	RealType c, x, y, z;
1111	+	bool successfulScale = false;
1112	+	if ((rnemdFluxType_ == rnemdFullKE) ||
1113	+	(rnemdFluxType_ == rnemdRotKE)) {
1114	+	//may need sanity check Khw & Kcw > 0
1115
1116	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
1117	<	switch(rnemdType_) {
1118	<	case rnemdKineticScale :
1119	<	// used hotBin coeff's & only scale x & y dimensions
1120	<	/*
692	<	RealType px = Phx / Pcx;
693	<	RealType py = Phy / Pcy;
694	<	a110 = Khy;
695	<	c0 = - Khx - Khy - targetFlux_;
696	<	a000 = Khx;
697	<	a111 = Kcy * py * py;
698	<	b11 = -2.0 * Kcy * py * (1.0 + py);
699	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
700	<	b01 = -2.0 * Kcx * px * (1.0 + px);
701	<	a001 = Kcx * px * px;
702	<	*/
703	<	//scale all three dimensions, let c_x = c_y
704	<	a000 = Kcx + Kcy;
705	<	a110 = Kcz;
706	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
707	<	a001 = Khx * px * px + Khy * py * py;
708	<	a111 = Khz * pz * pz;
709	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
710	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
711	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
712	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
713	<	break;
714	<	case rnemdPxScale :
715	<	c = 1 - targetFlux_ / Pcx;
716	<	a000 = Kcy;
717	<	a110 = Kcz;
718	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
719	<	a001 = py * py * Khy;
720	<	a111 = pz * pz * Khz;
721	<	b01 = -2.0 * Khy * py * (1.0 + py);
722	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
723	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
724	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
725	<	break;
726	<	case rnemdPyScale :
727	<	c = 1 - targetFlux_ / Pcy;
728	<	a000 = Kcx;
729	<	a110 = Kcz;
730	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
731	<	a001 = px * px * Khx;
732	<	a111 = pz * pz * Khz;
733	<	b01 = -2.0 * Khx * px * (1.0 + px);
734	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
735	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
736	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
737	<	break;
738	<	case rnemdPzScale ://we don't really do this, do we?
739	<	c = 1 - targetFlux_ / Pcz;
740	<	a000 = Kcx;
741	<	a110 = Kcy;
742	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
743	<	a001 = px * px * Khx;
744	<	a111 = py * py * Khy;
745	<	b01 = -2.0 * Khx * px * (1.0 + px);
746	<	b11 = -2.0 * Khy * py * (1.0 + py);
747	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
748	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
749	<	break;
750	<	default :
751	<	break;
752	<	}
1116	>	if (rnemdFluxType_ == rnemdFullKE) {
1117	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1118	>	} else {
1119	>	c = 1.0 - kineticTarget_ / Kcw;
1120	>	}
1121
1122	<	RealType v1 = a000 * a111 - a001 * a110;
1123	<	RealType v2 = a000 * b01;
756	<	RealType v3 = a000 * b11;
757	<	RealType v4 = a000 * c1 - a001 * c0;
758	<	RealType v8 = a110 * b01;
759	<	RealType v10 = - b01 * c0;
1122	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1123	>	c = sqrt(c);
1124
1125	<	RealType u0 = v2 * v10 - v4 * v4;
1126	<	RealType u1 = -2.0 * v3 * v4;
1127	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1128	<	RealType u3 = -2.0 * v1 * v3;
1129	<	RealType u4 = - v1 * v1;
1130	<	//rescale coefficients
1131	<	RealType maxAbs = fabs(u0);
1132	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1133	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1134	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1135	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1136	<	u0 /= maxAbs;
1137	<	u1 /= maxAbs;
1138	<	u2 /= maxAbs;
1139	<	u3 /= maxAbs;
1140	<	u4 /= maxAbs;
1141	<	//max_element(start, end) is also available.
1142	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1143	<	poly.setCoefficient(4, u4);
1144	<	poly.setCoefficient(3, u3);
1145	<	poly.setCoefficient(2, u2);
1146	<	poly.setCoefficient(1, u1);
1147	<	poly.setCoefficient(0, u0);
1148	<	vector<RealType> realRoots = poly.FindRealRoots();
1149	<
1150	<	vector<RealType>::iterator ri;
1151	<	RealType r1, r2, alpha0;
1152	<	vector<pair<RealType,RealType> > rps;
1153	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1154	<	r2 = *ri;
1155	<	//check if FindRealRoots() give the right answer
1156	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1157	<	sprintf(painCave.errMsg,
1158	<	"RNEMD Warning: polynomial solve seems to have an error!");
1159	<	painCave.isFatal = 0;
1160	<	simError();
1161	<	failRootCount_++;
1125	>	RealType w = 0.0;
1126	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1127	>	x = 1.0 + px * (1.0 - c);
1128	>	y = 1.0 + py * (1.0 - c);
1129	>	z = 1.0 + pz * (1.0 - c);
1130	>	/* more complicated way
1131	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1132	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1133	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1134	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1135	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1136	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1137	>	*/
1138	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1139	>	(fabs(z - 1.0) < 0.1)) {
1140	>	w = 1.0 + (kineticTarget_
1141	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1142	>	+ Khz * (1.0 - z * z)) / Khw;
1143	>	}//no need to calculate w if x, y or z is out of range
1144	>	} else {
1145	>	w = 1.0 + kineticTarget_ / Khw;
1146	>	}
1147	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1148	>	//if w is in the right range, so should be x, y, z.
1149	>	vector<StuntDouble*>::iterator sdi;
1150	>	Vector3d vel;
1151	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1152	>	if (rnemdFluxType_ == rnemdFullKE) {
1153	>	vel = (*sdi)->getVel() * c;
1154	>	(*sdi)->setVel(vel);
1155	>	}
1156	>	if ((*sdi)->isDirectional()) {
1157	>	Vector3d angMom = (*sdi)->getJ() * c;
1158	>	(*sdi)->setJ(angMom);
1159	>	}
1160	>	}
1161	>	w = sqrt(w);
1162	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1163	>	if (rnemdFluxType_ == rnemdFullKE) {
1164	>	vel = (*sdi)->getVel();
1165	>	vel.x() *= x;
1166	>	vel.y() *= y;
1167	>	vel.z() *= z;
1168	>	(*sdi)->setVel(vel);
1169	>	}
1170	>	if ((*sdi)->isDirectional()) {
1171	>	Vector3d angMom = (*sdi)->getJ() * w;
1172	>	(*sdi)->setJ(angMom);
1173	>	}
1174	>	}
1175	>	successfulScale = true;
1176	>	kineticExchange_ += kineticTarget_;
1177	>	}
1178		}
1179	<	//might not be useful w/o rescaling coefficients
1180	<	alpha0 = -c0 - a110 * r2 * r2;
1181	<	if (alpha0 >= 0.0) {
1182	<	r1 = sqrt(alpha0 / a000);
1183	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
1184	<	{ rps.push_back(make_pair(r1, r2)); }
1185	<	if (r1 > 1e-6) { //r1 non-negative
1186	<	r1 = -r1;
1187	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
1188	<	{ rps.push_back(make_pair(r1, r2)); }
1179	>	} else {
1180	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1181	>	switch(rnemdFluxType_) {
1182	>	case rnemdKE :
1183	>	/* used hotBin coeff's & only scale x & y dimensions
1184	>	RealType px = Phx / Pcx;
1185	>	RealType py = Phy / Pcy;
1186	>	a110 = Khy;
1187	>	c0 = - Khx - Khy - kineticTarget_;
1188	>	a000 = Khx;
1189	>	a111 = Kcy * py * py;
1190	>	b11 = -2.0 * Kcy * py * (1.0 + py);
1191	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1192	>	b01 = -2.0 * Kcx * px * (1.0 + px);
1193	>	a001 = Kcx * px * px;
1194	>	*/
1195	>	//scale all three dimensions, let c_x = c_y
1196	>	a000 = Kcx + Kcy;
1197	>	a110 = Kcz;
1198	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1199	>	a001 = Khx * px * px + Khy * py * py;
1200	>	a111 = Khz * pz * pz;
1201	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1202	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1203	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1204	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1205	>	break;
1206	>	case rnemdPx :
1207	>	c = 1 - momentumTarget_.x() / Pcx;
1208	>	a000 = Kcy;
1209	>	a110 = Kcz;
1210	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1211	>	a001 = py * py * Khy;
1212	>	a111 = pz * pz * Khz;
1213	>	b01 = -2.0 * Khy * py * (1.0 + py);
1214	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1215	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1216	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1217	>	break;
1218	>	case rnemdPy :
1219	>	c = 1 - momentumTarget_.y() / Pcy;
1220	>	a000 = Kcx;
1221	>	a110 = Kcz;
1222	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1223	>	a001 = px * px * Khx;
1224	>	a111 = pz * pz * Khz;
1225	>	b01 = -2.0 * Khx * px * (1.0 + px);
1226	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1227	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1228	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1229	>	break;
1230	>	case rnemdPz ://we don't really do this, do we?
1231	>	c = 1 - momentumTarget_.z() / Pcz;
1232	>	a000 = Kcx;
1233	>	a110 = Kcy;
1234	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1235	>	a001 = px * px * Khx;
1236	>	a111 = py * py * Khy;
1237	>	b01 = -2.0 * Khx * px * (1.0 + px);
1238	>	b11 = -2.0 * Khy * py * (1.0 + py);
1239	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1240	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1241	>	break;
1242	>	default :
1243	>	break;
1244	>	}
1245	>
1246	>	RealType v1 = a000 * a111 - a001 * a110;
1247	>	RealType v2 = a000 * b01;
1248	>	RealType v3 = a000 * b11;
1249	>	RealType v4 = a000 * c1 - a001 * c0;
1250	>	RealType v8 = a110 * b01;
1251	>	RealType v10 = - b01 * c0;
1252	>
1253	>	RealType u0 = v2 * v10 - v4 * v4;
1254	>	RealType u1 = -2.0 * v3 * v4;
1255	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1256	>	RealType u3 = -2.0 * v1 * v3;
1257	>	RealType u4 = - v1 * v1;
1258	>	//rescale coefficients
1259	>	RealType maxAbs = fabs(u0);
1260	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1261	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1262	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1263	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1264	>	u0 /= maxAbs;
1265	>	u1 /= maxAbs;
1266	>	u2 /= maxAbs;
1267	>	u3 /= maxAbs;
1268	>	u4 /= maxAbs;
1269	>	//max_element(start, end) is also available.
1270	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1271	>	poly.setCoefficient(4, u4);
1272	>	poly.setCoefficient(3, u3);
1273	>	poly.setCoefficient(2, u2);
1274	>	poly.setCoefficient(1, u1);
1275	>	poly.setCoefficient(0, u0);
1276	>	vector<RealType> realRoots = poly.FindRealRoots();
1277	>
1278	>	vector<RealType>::iterator ri;
1279	>	RealType r1, r2, alpha0;
1280	>	vector<pair<RealType,RealType> > rps;
1281	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1282	>	r2 = *ri;
1283	>	//check if FindRealRoots() give the right answer
1284	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1285	>	sprintf(painCave.errMsg,
1286	>	"RNEMD Warning: polynomial solve seems to have an error!");
1287	>	painCave.isFatal = 0;
1288	>	simError();
1289	>	failRootCount_++;
1290	>	}
1291	>	//might not be useful w/o rescaling coefficients
1292	>	alpha0 = -c0 - a110 * r2 * r2;
1293	>	if (alpha0 >= 0.0) {
1294	>	r1 = sqrt(alpha0 / a000);
1295	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1296	>	< 1e-6)
1297	>	{ rps.push_back(make_pair(r1, r2)); }
1298	>	if (r1 > 1e-6) { //r1 non-negative
1299	>	r1 = -r1;
1300	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1301	>	< 1e-6)
1302	>	{ rps.push_back(make_pair(r1, r2)); }
1303	>	}
1304	>	}
1305	>	}
1306	>	// Consider combining together the solving pair part w/ the searching
1307	>	// best solution part so that we don't need the pairs vector
1308	>	if (!rps.empty()) {
1309	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1310	>	RealType diff;
1311	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1312	>	vector<pair<RealType,RealType> >::iterator rpi;
1313	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1314	>	r1 = (*rpi).first;
1315	>	r2 = (*rpi).second;
1316	>	switch(rnemdFluxType_) {
1317	>	case rnemdKE :
1318	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1319	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1320	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1321	>	break;
1322	>	case rnemdPx :
1323	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1324	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1325	>	break;
1326	>	case rnemdPy :
1327	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1328	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1329	>	break;
1330	>	case rnemdPz :
1331	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1332	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1333	>	default :
1334	>	break;
1335	>	}
1336	>	if (diff < smallestDiff) {
1337	>	smallestDiff = diff;
1338	>	bestPair = *rpi;
1339	>	}
1340	>	}
1341	>	#ifdef IS_MPI
1342	>	if (worldRank == 0) {
1343	>	#endif
1344	>	// sprintf(painCave.errMsg,
1345	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1346	>	//         bestPair.first, bestPair.second);
1347	>	// painCave.isFatal = 0;
1348	>	// painCave.severity = OPENMD_INFO;
1349	>	// simError();
1350	>	#ifdef IS_MPI
1351	>	}
1352	>	#endif
1353	>
1354	>	switch(rnemdFluxType_) {
1355	>	case rnemdKE :
1356	>	x = bestPair.first;
1357	>	y = bestPair.first;
1358	>	z = bestPair.second;
1359	>	break;
1360	>	case rnemdPx :
1361	>	x = c;
1362	>	y = bestPair.first;
1363	>	z = bestPair.second;
1364	>	break;
1365	>	case rnemdPy :
1366	>	x = bestPair.first;
1367	>	y = c;
1368	>	z = bestPair.second;
1369	>	break;
1370	>	case rnemdPz :
1371	>	x = bestPair.first;
1372	>	y = bestPair.second;
1373	>	z = c;
1374	>	break;
1375	>	default :
1376	>	break;
1377	>	}
1378	>	vector<StuntDouble*>::iterator sdi;
1379	>	Vector3d vel;
1380	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1381	>	vel = (*sdi)->getVel();
1382	>	vel.x() *= x;
1383	>	vel.y() *= y;
1384	>	vel.z() *= z;
1385	>	(*sdi)->setVel(vel);
1386	>	}
1387	>	//convert to hotBin coefficient
1388	>	x = 1.0 + px * (1.0 - x);
1389	>	y = 1.0 + py * (1.0 - y);
1390	>	z = 1.0 + pz * (1.0 - z);
1391	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1392	>	vel = (*sdi)->getVel();
1393	>	vel.x() *= x;
1394	>	vel.y() *= y;
1395	>	vel.z() *= z;
1396	>	(*sdi)->setVel(vel);
1397	>	}
1398	>	successfulScale = true;
1399	>	switch(rnemdFluxType_) {
1400	>	case rnemdKE :
1401	>	kineticExchange_ += kineticTarget_;
1402	>	break;
1403	>	case rnemdPx :
1404	>	case rnemdPy :
1405	>	case rnemdPz :
1406	>	momentumExchange_ += momentumTarget_;
1407	>	break;
1408	>	default :
1409	>	break;
1410	>	}
1411	>	}
1412	>	}
1413	>	if (successfulScale != true) {
1414	>	sprintf(painCave.errMsg,
1415	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1416	>	"\tthe constraint equations may not exist or there may be\n"
1417	>	"\tno selected objects in one or both slabs.\n");
1418	>	painCave.isFatal = 0;
1419	>	painCave.severity = OPENMD_INFO;
1420	>	simError();
1421	>	failTrialCount_++;
1422	>	}
1423	>	}
1424	>
1425	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1426	>	if (!doRNEMD_) return;
1427	>	int selei;
1428	>	int selej;
1429	>
1430	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1431	>	RealType time = currentSnap_->getTime();
1432	>	Mat3x3d hmat = currentSnap_->getHmat();
1433	>
1434	>	StuntDouble* sd;
1435	>
1436	>	vector<StuntDouble*> hotBin, coldBin;
1437	>
1438	>	Vector3d Ph(V3Zero);
1439	>	Vector3d Lh(V3Zero);
1440	>	RealType Mh = 0.0;
1441	>	Mat3x3d Ih(0.0);
1442	>	RealType Kh = 0.0;
1443	>	Vector3d Pc(V3Zero);
1444	>	Vector3d Lc(V3Zero);
1445	>	RealType Mc = 0.0;
1446	>	Mat3x3d Ic(0.0);
1447	>	RealType Kc = 0.0;
1448	>
1449	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1450	>	sd = smanA.nextSelected(selei)) {
1451	>
1452	>	Vector3d pos = sd->getPos();
1453	>
1454	>	// wrap the stuntdouble's position back into the box:
1455	>
1456	>	if (usePeriodicBoundaryConditions_)
1457	>	currentSnap_->wrapVector(pos);
1458	>
1459	>	RealType mass = sd->getMass();
1460	>	Vector3d vel = sd->getVel();
1461	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1462	>	RealType r2;
1463	>
1464	>	hotBin.push_back(sd);
1465	>	Ph += mass * vel;
1466	>	Mh += mass;
1467	>	Kh += mass * vel.lengthSquare();
1468	>	Lh += mass * cross(rPos, vel);
1469	>	Ih -= outProduct(rPos, rPos) * mass;
1470	>	r2 = rPos.lengthSquare();
1471	>	Ih(0, 0) += mass * r2;
1472	>	Ih(1, 1) += mass * r2;
1473	>	Ih(2, 2) += mass * r2;
1474	>
1475	>	if (rnemdFluxType_ == rnemdFullKE) {
1476	>	if (sd->isDirectional()) {
1477	>	Vector3d angMom = sd->getJ();
1478	>	Mat3x3d I = sd->getI();
1479	>	if (sd->isLinear()) {
1480	>	int i = sd->linearAxis();
1481	>	int j = (i + 1) % 3;
1482	>	int k = (i + 2) % 3;
1483	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1484	>	angMom[k] * angMom[k] / I(k, k);
1485	>	} else {
1486	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1487	>	angMom[1] * angMom[1] / I(1, 1) +
1488	>	angMom[2] * angMom[2] / I(2, 2);
1489	>	}
1490		}
1491		}
1492		}
1493	<	// Consider combining together the solving pair part w/ the searching
1494	<	// best solution part so that we don't need the pairs vector
1495	<	if (!rps.empty()) {
1496	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1497	<	RealType diff;
1498	<	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1499	<	vector<pair<RealType,RealType> >::iterator rpi;
1500	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1501	<	r1 = (*rpi).first;
1502	<	r2 = (*rpi).second;
1503	<	switch(rnemdType_) {
1504	<	case rnemdKineticScale :
1505	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1506	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1507	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1508	<	break;
1509	<	case rnemdPxScale :
1510	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1511	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1512	<	break;
1513	<	case rnemdPyScale :
1514	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1515	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1516	<	break;
1517	<	case rnemdPzScale :
1518	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1519	<	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1520	<	default :
1521	<	break;
1493	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1494	>	sd = smanB.nextSelected(selej)) {
1495	>
1496	>	Vector3d pos = sd->getPos();
1497	>
1498	>	// wrap the stuntdouble's position back into the box:
1499	>
1500	>	if (usePeriodicBoundaryConditions_)
1501	>	currentSnap_->wrapVector(pos);
1502	>
1503	>	RealType mass = sd->getMass();
1504	>	Vector3d vel = sd->getVel();
1505	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1506	>	RealType r2;
1507	>
1508	>	coldBin.push_back(sd);
1509	>	Pc += mass * vel;
1510	>	Mc += mass;
1511	>	Kc += mass * vel.lengthSquare();
1512	>	Lc += mass * cross(rPos, vel);
1513	>	Ic -= outProduct(rPos, rPos) * mass;
1514	>	r2 = rPos.lengthSquare();
1515	>	Ic(0, 0) += mass * r2;
1516	>	Ic(1, 1) += mass * r2;
1517	>	Ic(2, 2) += mass * r2;
1518	>
1519	>	if (rnemdFluxType_ == rnemdFullKE) {
1520	>	if (sd->isDirectional()) {
1521	>	Vector3d angMom = sd->getJ();
1522	>	Mat3x3d I = sd->getI();
1523	>	if (sd->isLinear()) {
1524	>	int i = sd->linearAxis();
1525	>	int j = (i + 1) % 3;
1526	>	int k = (i + 2) % 3;
1527	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1528	>	angMom[k] * angMom[k] / I(k, k);
1529	>	} else {
1530	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1531	>	angMom[1] * angMom[1] / I(1, 1) +
1532	>	angMom[2] * angMom[2] / I(2, 2);
1533	>	}
1534		}
842	–	if (diff < smallestDiff) {
843	–	smallestDiff = diff;
844	–	bestPair = *rpi;
845	–	}
1535		}
1536	+	}
1537	+
1538	+	Kh *= 0.5;
1539	+	Kc *= 0.5;
1540	+
1541		#ifdef IS_MPI
1542	<	if (worldRank == 0) {
1542	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1543	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1544	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1545	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1546	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1547	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1548	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1549	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1550	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1551	>	MPI::REALTYPE, MPI::SUM);
1552	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1553	>	MPI::REALTYPE, MPI::SUM);
1554		#endif
1555	<	sprintf(painCave.errMsg,
1556	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1557	<	bestPair.first, bestPair.second);
1558	<	painCave.isFatal = 0;
1559	<	painCave.severity = OPENMD_INFO;
1560	<	simError();
856	<	#ifdef IS_MPI
857	<	}
858	<	#endif
1555	>
1556	>	bool successfulExchange = false;
1557	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1558	>	Vector3d vc = Pc / Mc;
1559	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1560	>	Vector3d acrec = -momentumTarget_ / Mc;
1561
1562	<	RealType x, y, z;
1563	<	switch(rnemdType_) {
1564	<	case rnemdKineticScale :
1565	<	x = bestPair.first;
1566	<	y = bestPair.first;
1567	<	z = bestPair.second;
1568	<	break;
1569	<	case rnemdPxScale :
1570	<	x = c;
1571	<	y = bestPair.first;
1572	<	z = bestPair.second;
1573	<	break;
1574	<	case rnemdPyScale :
1575	<	x = bestPair.first;
1576	<	y = c;
1577	<	z = bestPair.second;
1578	<	break;
1579	<	case rnemdPzScale :
1580	<	x = bestPair.first;
1581	<	y = bestPair.second;
1582	<	z = c;
1583	<	break;
1584	<	default :
1585	<	break;
1586	<	}
1587	<	vector<StuntDouble*>::iterator sdi;
1588	<	Vector3d vel;
1589	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1590	<	vel = (*sdi)->getVel();
1591	<	vel.x() *= x;
1592	<	vel.y() *= y;
1593	<	vel.z() *= z;
1594	<	(*sdi)->setVel(vel);
1595	<	}
1596	<	//convert to hotBin coefficient
1597	<	x = 1.0 + px * (1.0 - x);
1598	<	y = 1.0 + py * (1.0 - y);
1599	<	z = 1.0 + pz * (1.0 - z);
1600	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1601	<	vel = (*sdi)->getVel();
1602	<	vel.x() *= x;
1603	<	vel.y() *= y;
1604	<	vel.z() *= z;
1605	<	(*sdi)->setVel(vel);
1606	<	}
1607	<	exchangeSum_ += targetFlux_;
1608	<	//we may want to check whether the exchange has been successful
1609	<	} else {
1562	>	// We now need the inverse of the inertia tensor to calculate the
1563	>	// angular velocity of the cold slab;
1564	>	Mat3x3d Ici = Ic.inverse();
1565	>	Vector3d omegac = Ici * Lc;
1566	>	Vector3d bc  = -(Ici * angularMomentumTarget_) + omegac;
1567	>	Vector3d bcrec = bc - omegac;
1568	>
1569	>	RealType cNumerator = Kc - kineticTarget_
1570	>	- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc));
1571	>	if (cNumerator > 0.0) {
1572	>
1573	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare()
1574	>	- 0.5*(dot(omegac, Ic * omegac));
1575	>
1576	>	if (cDenominator > 0.0) {
1577	>	RealType c = sqrt(cNumerator / cDenominator);
1578	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1579	>
1580	>	Vector3d vh = Ph / Mh;
1581	>	Vector3d ah = momentumTarget_ / Mh + vh;
1582	>	Vector3d ahrec = momentumTarget_ / Mh;
1583	>
1584	>	// We now need the inverse of the inertia tensor to
1585	>	// calculate the angular velocity of the hot slab;
1586	>	Mat3x3d Ihi = Ih.inverse();
1587	>	Vector3d omegah = Ihi * Lh;
1588	>	Vector3d bh  = (Ihi * angularMomentumTarget_) + omegah;
1589	>	Vector3d bhrec = bh - omegah;
1590	>
1591	>	RealType hNumerator = Kh + kineticTarget_
1592	>	- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));;
1593	>	if (hNumerator > 0.0) {
1594	>
1595	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare()
1596	>	- 0.5*(dot(omegah, Ih * omegah));
1597	>
1598	>	if (hDenominator > 0.0) {
1599	>	RealType h = sqrt(hNumerator / hDenominator);
1600	>	if ((h > 0.9) && (h < 1.1)) {
1601	>
1602	>	vector<StuntDouble*>::iterator sdi;
1603	>	Vector3d vel;
1604	>	Vector3d rPos;
1605	>
1606	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1607	>	//vel = (*sdi)->getVel();
1608	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1609	>	vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c
1610	>	+ ac + cross(bc, rPos);
1611	>	(*sdi)->setVel(vel);
1612	>	if (rnemdFluxType_ == rnemdFullKE) {
1613	>	if ((*sdi)->isDirectional()) {
1614	>	Vector3d angMom = (*sdi)->getJ() * c;
1615	>	(*sdi)->setJ(angMom);
1616	>	}
1617	>	}
1618	>	}
1619	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1620	>	//vel = (*sdi)->getVel();
1621	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1622	>	vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1623	>	+ ah + cross(bh, rPos);
1624	>	cerr << "setting vel to " << vel << "\n";
1625	>	(*sdi)->setVel(vel);
1626	>	if (rnemdFluxType_ == rnemdFullKE) {
1627	>	if ((*sdi)->isDirectional()) {
1628	>	Vector3d angMom = (*sdi)->getJ() * h;
1629	>	(*sdi)->setJ(angMom);
1630	>	}
1631	>	}
1632	>	}
1633	>	successfulExchange = true;
1634	>	kineticExchange_ += kineticTarget_;
1635	>	momentumExchange_ += momentumTarget_;
1636	>	angularMomentumExchange_ += angularMomentumTarget_;
1637	>	}
1638	>	}
1639	>	}
1640	>	}
1641	>	}
1642	>	}
1643	>	}
1644	>	if (successfulExchange != true) {
1645		sprintf(painCave.errMsg,
1646	<	"RNEMD: exchange NOT performed!\n");
1646	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1647	>	"\tthe constraint equations may not exist or there may be\n"
1648	>	"\tno selected objects in one or both slabs.\n");
1649		painCave.isFatal = 0;
1650		painCave.severity = OPENMD_INFO;
1651		simError();
1652		failTrialCount_++;
1653		}
915	–
1654		}
1655
1656	+	RealType RNEMD::getDividingArea() {
1657	+
1658	+	if (hasDividingArea_) return dividingArea_;
1659	+
1660	+	RealType areaA, areaB;
1661	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1662	+
1663	+	if (hasSelectionA_) {
1664	+	int isd;
1665	+	StuntDouble* sd;
1666	+	vector<StuntDouble*> aSites;
1667	+	ConvexHull* surfaceMeshA = new ConvexHull();
1668	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1669	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1670	+	sd = seleManA_.nextSelected(isd)) {
1671	+	aSites.push_back(sd);
1672	+	}
1673	+	surfaceMeshA->computeHull(aSites);
1674	+	areaA = surfaceMeshA->getArea();
1675	+	} else {
1676	+	if (usePeriodicBoundaryConditions_) {
1677	+	// in periodic boundaries, the surface area is twice the x-y
1678	+	// area of the current box:
1679	+	areaA = 2.0 * snap->getXYarea();
1680	+	} else {
1681	+	// in non-periodic simulations, without explicitly setting
1682	+	// selections, the sphere radius sets the surface area of the
1683	+	// dividing surface:
1684	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1685	+	}
1686	+	}
1687	+
1688	+	if (hasSelectionB_) {
1689	+	int isd;
1690	+	StuntDouble* sd;
1691	+	vector<StuntDouble*> bSites;
1692	+	ConvexHull* surfaceMeshB = new ConvexHull();
1693	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1694	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1695	+	sd = seleManB_.nextSelected(isd)) {
1696	+	bSites.push_back(sd);
1697	+	}
1698	+	surfaceMeshB->computeHull(bSites);
1699	+	areaB = surfaceMeshB->getArea();
1700	+	} else {
1701	+	if (usePeriodicBoundaryConditions_) {
1702	+	// in periodic boundaries, the surface area is twice the x-y
1703	+	// area of the current box:
1704	+	areaB = 2.0 * snap->getXYarea();
1705	+	} else {
1706	+	// in non-periodic simulations, without explicitly setting
1707	+	// selections, but if a sphereBradius has been set, just use that:
1708	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1709	+	}
1710	+	}
1711	+
1712	+	dividingArea_ = min(areaA, areaB);
1713	+	hasDividingArea_ = true;
1714	+	return dividingArea_;
1715	+	}
1716	+
1717		void RNEMD::doRNEMD() {
1718	+	if (!doRNEMD_) return;
1719	+	trialCount_++;
1720
1721	<	switch(rnemdType_) {
1722	<	case rnemdKineticScale :
1723	<	case rnemdPxScale :
1724	<	case rnemdPyScale :
1725	<	case rnemdPzScale :
1726	<	doScale();
1721	>	cerr << "trialCount = " << trialCount_ << "\n";
1722	>	// object evaluator:
1723	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1724	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1725	>
1726	>	evaluatorA_.loadScriptString(selectionA_);
1727	>	evaluatorB_.loadScriptString(selectionB_);
1728	>
1729	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1730	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1731	>
1732	>	commonA_ = seleManA_ & seleMan_;
1733	>	commonB_ = seleManB_ & seleMan_;
1734	>
1735	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1736	>	// dt = exchange time interval
1737	>	// flux = target flux
1738	>	// dividingArea = smallest dividing surface between the two regions
1739	>
1740	>	hasDividingArea_ = false;
1741	>	RealType area = getDividingArea();
1742	>
1743	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1744	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1745	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1746	>
1747	>	switch(rnemdMethod_) {
1748	>	case rnemdSwap:
1749	>	doSwap(commonA_, commonB_);
1750		break;
1751	<	case rnemdKineticSwap :
1752	<	case rnemdPx :
929	<	case rnemdPy :
930	<	case rnemdPz :
931	<	doSwap();
1751	>	case rnemdNIVS:
1752	>	doNIVS(commonA_, commonB_);
1753		break;
1754	<	case rnemdUnknown :
1754	>	case rnemdVSS:
1755	>	doVSS(commonA_, commonB_);
1756	>	break;
1757	>	case rnemdUnkownMethod:
1758		default :
1759		break;
1760		}
1761		}
1762
1763		void RNEMD::collectData() {
1764	<
1764	>	if (!doRNEMD_) return;
1765		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1766	+
1767	+	cerr << "collecting data\n";
1768	+	// collectData can be called more frequently than the doRNEMD, so use the
1769	+	// computed area from the last exchange time:
1770	+	RealType area = getDividingArea();
1771	+	areaAccumulator_->add(area);
1772		Mat3x3d hmat = currentSnap_->getHmat();
943	–
1773		seleMan_.setSelectionSet(evaluator_.evaluate());
1774
1775	<	int selei;
1775	>	int selei(0);
1776		StuntDouble* sd;
1777	<	int idx;
1777	>	int binNo;
1778
1779	+	vector<RealType> binMass(nBins_, 0.0);
1780	+	vector<RealType> binPx(nBins_, 0.0);
1781	+	vector<RealType> binPy(nBins_, 0.0);
1782	+	vector<RealType> binPz(nBins_, 0.0);
1783	+	vector<RealType> binOmegax(nBins_, 0.0);
1784	+	vector<RealType> binOmegay(nBins_, 0.0);
1785	+	vector<RealType> binOmegaz(nBins_, 0.0);
1786	+	vector<RealType> binKE(nBins_, 0.0);
1787	+	vector<int> binDOF(nBins_, 0);
1788	+	vector<int> binCount(nBins_, 0);
1789	+
1790		// alternative approach, track all molecules instead of only those
1791		// selected for scaling/swapping:
1792		/*
1793	<	SimInfo::MoleculeIterator miter;
1794	<	vector<StuntDouble*>::iterator iiter;
1795	<	Molecule* mol;
1796	<	StuntDouble* integrableObject;
1797	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1798	<	mol = info_->nextMolecule(miter))
1799	<	integrableObject is essentially sd
1800	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1801	<	integrableObject != NULL;
1802	<	integrableObject = mol->nextIntegrableObject(iiter))
1793	>	SimInfo::MoleculeIterator miter;
1794	>	vector<StuntDouble*>::iterator iiter;
1795	>	Molecule* mol;
1796	>	StuntDouble* sd;
1797	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1798	>	mol = info_->nextMolecule(miter))
1799	>	sd is essentially sd
1800	>	for (sd = mol->beginIntegrableObject(iiter);
1801	>	sd != NULL;
1802	>	sd = mol->nextIntegrableObject(iiter))
1803		*/
1804	+
1805		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1806	<	sd = seleMan_.nextSelected(selei)) {
1807	<
967	<	idx = sd->getLocalIndex();
968	<
1806	>	sd = seleMan_.nextSelected(selei)) {
1807	>
1808		Vector3d pos = sd->getPos();
1809
1810		// wrap the stuntdouble's position back into the box:
1811
1812	<	if (usePeriodicBoundaryConditions_)
1812	>	if (usePeriodicBoundaryConditions_) {
1813		currentSnap_->wrapVector(pos);
1814	<
1815	<	// which bin is this stuntdouble in?
1816	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1817	<
1818	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1819	<	rnemdLogWidth_;
1820	<	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
1821	<	/*
1822	<	if (rnemdLogWidth_ == midBin_ + 1)
1823	<	if (binNo > midBin_)
1824	<	binNo = nBins_ - binNo;
986	<	*/
1814	>	// which bin is this stuntdouble in?
1815	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1816	>	// Shift molecules by half a box to have bins start at 0
1817	>	// The modulo operator is used to wrap the case when we are
1818	>	// beyond the end of the bins back to the beginning.
1819	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1820	>	} else {
1821	>	Vector3d rPos = pos - coordinateOrigin_;
1822	>	binNo = int(rPos.length() / binWidth_);
1823	>	}
1824	>
1825		RealType mass = sd->getMass();
1826		Vector3d vel = sd->getVel();
1827	<	RealType value;
1828	<	RealType xVal, yVal, zVal;
1829	<
1830	<	switch(rnemdType_) {
1831	<	case rnemdKineticSwap :
1832	<	case rnemdKineticScale :
1833	<
1834	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
1835	<
1836	<	valueCount_[binNo] += 3;
1837	<	if (sd->isDirectional()) {
1838	<	Vector3d angMom = sd->getJ();
1839	<	Mat3x3d I = sd->getI();
1840	<
1003	<	if (sd->isLinear()) {
1004	<	int i = sd->linearAxis();
1005	<	int j = (i + 1) % 3;
1006	<	int k = (i + 2) % 3;
1007	<	value += angMom[j] * angMom[j] / I(j, j) +
1008	<	angMom[k] * angMom[k] / I(k, k);
1009	<
1010	<	valueCount_[binNo] +=2;
1011	<
1012	<	} else {
1013	<	value += angMom[0]*angMom[0]/I(0, 0)
1014	<	+ angMom[1]*angMom[1]/I(1, 1)
1015	<	+ angMom[2]*angMom[2]/I(2, 2);
1016	<	valueCount_[binNo] +=3;
1017	<	}
1018	<	}
1019	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1827	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1828	>	Vector3d aVel = cross(rPos, vel);
1829	>
1830	>	if (binNo >= 0 && binNo < nBins_)  {
1831	>	binCount[binNo]++;
1832	>	binMass[binNo] += mass;
1833	>	binPx[binNo] += mass*vel.x();
1834	>	binPy[binNo] += mass*vel.y();
1835	>	binPz[binNo] += mass*vel.z();
1836	>	binOmegax[binNo] += aVel.x();
1837	>	binOmegay[binNo] += aVel.y();
1838	>	binOmegaz[binNo] += aVel.z();
1839	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1840	>	binDOF[binNo] += 3;
1841
1842	<	break;
1843	<	case rnemdPx :
1844	<	case rnemdPxScale :
1845	<	value = mass * vel[0];
1846	<	valueCount_[binNo]++;
1847	<	break;
1848	<	case rnemdPy :
1849	<	case rnemdPyScale :
1850	<	value = mass * vel[1];
1851	<	valueCount_[binNo]++;
1852	<	break;
1853	<	case rnemdPz :
1854	<	case rnemdPzScale :
1855	<	value = pos.z(); //temporarily for homogeneous systems ONLY
1856	<	valueCount_[binNo]++;
1857	<	break;
1858	<	case rnemdUnknown :
1038	<	default :
1039	<	value = 1.0;
1040	<	valueCount_[binNo]++;
1041	<	break;
1842	>	if (sd->isDirectional()) {
1843	>	Vector3d angMom = sd->getJ();
1844	>	Mat3x3d I = sd->getI();
1845	>	if (sd->isLinear()) {
1846	>	int i = sd->linearAxis();
1847	>	int j = (i + 1) % 3;
1848	>	int k = (i + 2) % 3;
1849	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1850	>	angMom[k] * angMom[k] / I(k, k));
1851	>	binDOF[binNo] += 2;
1852	>	} else {
1853	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1854	>	angMom[1] * angMom[1] / I(1, 1) +
1855	>	angMom[2] * angMom[2] / I(2, 2));
1856	>	binDOF[binNo] += 3;
1857	>	}
1858	>	}
1859		}
1860	<	valueHist_[binNo] += value;
1860	>	}
1861	>
1862	>	#ifdef IS_MPI
1863	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1864	>	nBins_, MPI::INT, MPI::SUM);
1865	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1866	>	nBins_, MPI::REALTYPE, MPI::SUM);
1867	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1868	>	nBins_, MPI::REALTYPE, MPI::SUM);
1869	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1870	>	nBins_, MPI::REALTYPE, MPI::SUM);
1871	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1872	>	nBins_, MPI::REALTYPE, MPI::SUM);
1873	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1874	>	nBins_, MPI::REALTYPE, MPI::SUM);
1875	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1876	>	nBins_, MPI::REALTYPE, MPI::SUM);
1877	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1878	>	nBins_, MPI::REALTYPE, MPI::SUM);
1879	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1880	>	nBins_, MPI::REALTYPE, MPI::SUM);
1881	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1882	>	nBins_, MPI::INT, MPI::SUM);
1883	>	#endif
1884
1885	<	if (output3DTemp_) {
1886	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1887	<	/ PhysicalConstants::kb;
1888	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1889	<	/ PhysicalConstants::kb;
1890	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1891	<	/ PhysicalConstants::kb;
1892	<	xTempHist_[binNo] += xVal;
1893	<	yTempHist_[binNo] += yVal;
1894	<	zTempHist_[binNo] += zVal;
1895	<	xyzTempCount_[binNo]++;
1885	>	Vector3d vel;
1886	>	Vector3d aVel;
1887	>	RealType den;
1888	>	RealType temp;
1889	>	RealType z;
1890	>	RealType r;
1891	>	for (int i = 0; i < nBins_; i++) {
1892	>	if (usePeriodicBoundaryConditions_) {
1893	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1894	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1895	>	/ currentSnap_->getVolume() ;
1896	>	} else {
1897	>	r = (((RealType)i + 0.5) * binWidth_);
1898	>	RealType rinner = (RealType)i * binWidth_;
1899	>	RealType router = (RealType)(i+1) * binWidth_;
1900	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1901	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1902		}
1903	+	vel.x() = binPx[i] / binMass[i];
1904	+	vel.y() = binPy[i] / binMass[i];
1905	+	vel.z() = binPz[i] / binMass[i];
1906	+	aVel.x() = binOmegax[i];
1907	+	aVel.y() = binOmegay[i];
1908	+	aVel.z() = binOmegaz[i];
1909	+
1910	+	if (binCount[i] > 0) {
1911	+	// only add values if there are things to add
1912	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1913	+	PhysicalConstants::energyConvert);
1914	+
1915	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1916	+	if(outputMask_[j]) {
1917	+	switch(j) {
1918	+	case Z:
1919	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1920	+	break;
1921	+	case R:
1922	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1923	+	break;
1924	+	case TEMPERATURE:
1925	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1926	+	break;
1927	+	case VELOCITY:
1928	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1929	+	break;
1930	+	case ANGULARVELOCITY:
1931	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1932	+	break;
1933	+	case DENSITY:
1934	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1935	+	break;
1936	+	}
1937	+	}
1938	+	}
1939	+	}
1940		}
1941		}
1942
1943		void RNEMD::getStarted() {
1944	+	if (!doRNEMD_) return;
1945	+	hasDividingArea_ = false;
1946		collectData();
1947	<	/* now should be able to output profile in step 0, but might not be useful
1063	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1064	<	Stats& stat = currentSnap_->statData;
1065	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1066	<	*/
1067	<	getStatus();
1947	>	writeOutputFile();
1948		}
1949
1950	<	void RNEMD::getStatus() {
1951	<
1952	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1953	<	Stats& stat = currentSnap_->statData;
1954	<	RealType time = currentSnap_->getTime();
1955	<
1956	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1957	<	//or to be more meaningful, define another item as exchangeSum_ / time
1958	<	int j;
1959	<
1950	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1951	>	if (!doRNEMD_) return;
1952	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1953	>
1954	>	while(tokenizer.hasMoreTokens()) {
1955	>	std::string token(tokenizer.nextToken());
1956	>	toUpper(token);
1957	>	OutputMapType::iterator i = outputMap_.find(token);
1958	>	if (i != outputMap_.end()) {
1959	>	outputMask_.set(i->second);
1960	>	} else {
1961	>	sprintf( painCave.errMsg,
1962	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1963	>	"\toutputFileFormat keyword.\n", token.c_str() );
1964	>	painCave.isFatal = 0;
1965	>	painCave.severity = OPENMD_ERROR;
1966	>	simError();
1967	>	}
1968	>	}
1969	>	}
1970	>
1971	>	void RNEMD::writeOutputFile() {
1972	>	if (!doRNEMD_) return;
1973	>
1974		#ifdef IS_MPI
1081	–
1082	–	// all processors have the same number of bins, and STL vectors pack their
1083	–	// arrays, so in theory, this should be safe:
1084	–
1085	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1086	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1087	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1088	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1089	–	if (output3DTemp_) {
1090	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1091	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1092	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1093	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1094	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1095	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1096	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1097	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1098	–	}
1975		// If we're the root node, should we print out the results
1976		int worldRank = MPI::COMM_WORLD.Get_rank();
1977		if (worldRank == 0) {
1978		#endif
1979	<	rnemdLog_ << time;
1980	<	for (j = 0; j < rnemdLogWidth_; j++) {
1981	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1979	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1980	>
1981	>	if( !rnemdFile_ ){
1982	>	sprintf( painCave.errMsg,
1983	>	"Could not open \"%s\" for RNEMD output.\n",
1984	>	rnemdFileName_.c_str());
1985	>	painCave.isFatal = 1;
1986	>	simError();
1987		}
1988	<	rnemdLog_ << "\n";
1989	<	if (output3DTemp_) {
1990	<	xTempLog_ << time;
1991	<	for (j = 0; j < rnemdLogWidth_; j++) {
1992	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1988	>
1989	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1990	>
1991	>	RealType time = currentSnap_->getTime();
1992	>	RealType avgArea;
1993	>	areaAccumulator_->getAverage(avgArea);
1994	>	RealType Jz = kineticExchange_ / (time * avgArea)
1995	>	/ PhysicalConstants::energyConvert;
1996	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
1997	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
1998	>
1999	>	rnemdFile_ << "#######################################################\n";
2000	>	rnemdFile_ << "# RNEMD {\n";
2001	>
2002	>	map<string, RNEMDMethod>::iterator mi;
2003	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2004	>	if ( (*mi).second == rnemdMethod_)
2005	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2006	>	}
2007	>	map<string, RNEMDFluxType>::iterator fi;
2008	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2009	>	if ( (*fi).second == rnemdFluxType_)
2010	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2011	>	}
2012	>
2013	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2014	>
2015	>	rnemdFile_ << "#    objectSelection = \""
2016	>	<< rnemdObjectSelection_ << "\";\n";
2017	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2018	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2019	>	rnemdFile_ << "# }\n";
2020	>	rnemdFile_ << "#######################################################\n";
2021	>	rnemdFile_ << "# RNEMD report:\n";
2022	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2023	>	rnemdFile_ << "# Target flux:\n";
2024	>	rnemdFile_ << "#           kinetic = "
2025	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2026	>	<< " (kcal/mol/A^2/fs)\n";
2027	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2028	>	<< " (amu/A/fs^2)\n";
2029	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2030	>	<< " (amu/A^2/fs^2)\n";
2031	>	rnemdFile_ << "# Target one-time exchanges:\n";
2032	>	rnemdFile_ << "#          kinetic = "
2033	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2034	>	<< " (kcal/mol)\n";
2035	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2036	>	<< " (amu*A/fs)\n";
2037	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2038	>	<< " (amu*A^2/fs)\n";
2039	>	rnemdFile_ << "# Actual exchange totals:\n";
2040	>	rnemdFile_ << "#          kinetic = "
2041	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2042	>	<< " (kcal/mol)\n";
2043	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2044	>	<< " (amu*A/fs)\n";
2045	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2046	>	<< " (amu*A^2/fs)\n";
2047	>	rnemdFile_ << "# Actual flux:\n";
2048	>	rnemdFile_ << "#          kinetic = " << Jz
2049	>	<< " (kcal/mol/A^2/fs)\n";
2050	>	rnemdFile_ << "#          momentum = " << JzP
2051	>	<< " (amu/A/fs^2)\n";
2052	>	rnemdFile_ << "#  angular momentum = " << JzL
2053	>	<< " (amu/A^2/fs^2)\n";
2054	>	rnemdFile_ << "# Exchange statistics:\n";
2055	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2056	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2057	>	if (rnemdMethod_ == rnemdNIVS) {
2058	>	rnemdFile_ << "#  NIVS root-check errors = "
2059	>	<< failRootCount_ << "\n";
2060	>	}
2061	>	rnemdFile_ << "#######################################################\n";
2062	>
2063	>
2064	>
2065	>	//write title
2066	>	rnemdFile_ << "#";
2067	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2068	>	if (outputMask_[i]) {
2069	>	rnemdFile_ << "\t" << data_[i].title <<
2070	>	"(" << data_[i].units << ")";
2071	>	// add some extra tabs for column alignment
2072	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2073		}
2074	<	xTempLog_ << "\n";
2075	<	yTempLog_ << time;
2076	<	for (j = 0; j < rnemdLogWidth_; j++) {
2077	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
2074	>	}
2075	>	rnemdFile_ << std::endl;
2076	>
2077	>	rnemdFile_.precision(8);
2078	>
2079	>	for (int j = 0; j < nBins_; j++) {
2080	>
2081	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2082	>	if (outputMask_[i]) {
2083	>	if (data_[i].dataType == "RealType")
2084	>	writeReal(i,j);
2085	>	else if (data_[i].dataType == "Vector3d")
2086	>	writeVector(i,j);
2087	>	else {
2088	>	sprintf( painCave.errMsg,
2089	>	"RNEMD found an unknown data type for: %s ",
2090	>	data_[i].title.c_str());
2091	>	painCave.isFatal = 1;
2092	>	simError();
2093	>	}
2094	>	}
2095		}
2096	<	yTempLog_ << "\n";
2097	<	zTempLog_ << time;
2098	<	for (j = 0; j < rnemdLogWidth_; j++) {
2099	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
2096	>	rnemdFile_ << std::endl;
2097	>
2098	>	}
2099	>
2100	>	rnemdFile_ << "#######################################################\n";
2101	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2102	>	rnemdFile_ << "#######################################################\n";
2103	>
2104	>
2105	>	for (int j = 0; j < nBins_; j++) {
2106	>	rnemdFile_ << "#";
2107	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2108	>	if (outputMask_[i]) {
2109	>	if (data_[i].dataType == "RealType")
2110	>	writeRealStdDev(i,j);
2111	>	else if (data_[i].dataType == "Vector3d")
2112	>	writeVectorStdDev(i,j);
2113	>	else {
2114	>	sprintf( painCave.errMsg,
2115	>	"RNEMD found an unknown data type for: %s ",
2116	>	data_[i].title.c_str());
2117	>	painCave.isFatal = 1;
2118	>	simError();
2119	>	}
2120	>	}
2121		}
2122	<	zTempLog_ << "\n";
2123	<	}
2122	>	rnemdFile_ << std::endl;
2123	>
2124	>	}
2125	>
2126	>	rnemdFile_.flush();
2127	>	rnemdFile_.close();
2128	>
2129		#ifdef IS_MPI
2130		}
2131		#endif
2132	<	for (j = 0; j < rnemdLogWidth_; j++) {
2133	<	valueCount_[j] = 0;
2134	<	valueHist_[j] = 0.0;
2132	>
2133	>	}
2134	>
2135	>	void RNEMD::writeReal(int index, unsigned int bin) {
2136	>	if (!doRNEMD_) return;
2137	>	assert(index >=0 && index < ENDINDEX);
2138	>	assert(int(bin) < nBins_);
2139	>	RealType s;
2140	>	int count;
2141	>
2142	>	count = data_[index].accumulator[bin]->count();
2143	>	if (count == 0) return;
2144	>
2145	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2146	>
2147	>	if (! isinf(s) && ! isnan(s)) {
2148	>	rnemdFile_ << "\t" << s;
2149	>	} else{
2150	>	sprintf( painCave.errMsg,
2151	>	"RNEMD detected a numerical error writing: %s for bin %d",
2152	>	data_[index].title.c_str(), bin);
2153	>	painCave.isFatal = 1;
2154	>	simError();
2155	>	}
2156	>	}
2157	>
2158	>	void RNEMD::writeVector(int index, unsigned int bin) {
2159	>	if (!doRNEMD_) return;
2160	>	assert(index >=0 && index < ENDINDEX);
2161	>	assert(int(bin) < nBins_);
2162	>	Vector3d s;
2163	>	int count;
2164	>
2165	>	count = data_[index].accumulator[bin]->count();
2166	>
2167	>	if (count == 0) return;
2168	>
2169	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2170	>	if (isinf(s[0]) || isnan(s[0]) ||
2171	>	isinf(s[1]) || isnan(s[1]) ||
2172	>	isinf(s[2]) || isnan(s[2]) ) {
2173	>	sprintf( painCave.errMsg,
2174	>	"RNEMD detected a numerical error writing: %s for bin %d",
2175	>	data_[index].title.c_str(), bin);
2176	>	painCave.isFatal = 1;
2177	>	simError();
2178	>	} else {
2179	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2180		}
2181	<	if (output3DTemp_)
2182	<	for (j = 0; j < rnemdLogWidth_; j++) {
2183	<	xTempHist_[j] = 0.0;
2184	<	yTempHist_[j] = 0.0;
2185	<	zTempHist_[j] = 0.0;
2186	<	xyzTempCount_[j] = 0;
2187	<	}
2181	>	}
2182	>
2183	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2184	>	if (!doRNEMD_) return;
2185	>	assert(index >=0 && index < ENDINDEX);
2186	>	assert(int(bin) < nBins_);
2187	>	RealType s;
2188	>	int count;
2189	>
2190	>	count = data_[index].accumulator[bin]->count();
2191	>	if (count == 0) return;
2192	>
2193	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2194	>
2195	>	if (! isinf(s) && ! isnan(s)) {
2196	>	rnemdFile_ << "\t" << s;
2197	>	} else{
2198	>	sprintf( painCave.errMsg,
2199	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2200	>	data_[index].title.c_str(), bin);
2201	>	painCave.isFatal = 1;
2202	>	simError();
2203	>	}
2204		}
2205	+
2206	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2207	+	if (!doRNEMD_) return;
2208	+	assert(index >=0 && index < ENDINDEX);
2209	+	assert(int(bin) < nBins_);
2210	+	Vector3d s;
2211	+	int count;
2212	+
2213	+	count = data_[index].accumulator[bin]->count();
2214	+	if (count == 0) return;
2215	+
2216	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2217	+	if (isinf(s[0]) || isnan(s[0]) ||
2218	+	isinf(s[1]) || isnan(s[1]) ||
2219	+	isinf(s[2]) || isnan(s[2]) ) {
2220	+	sprintf( painCave.errMsg,
2221	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2222	+	data_[index].title.c_str(), bin);
2223	+	painCave.isFatal = 1;
2224	+	simError();
2225	+	} else {
2226	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2227	+	}
2228	+	}
2229		}
2230	+

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