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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42	<	#include "integrators/RNEMD.hpp"
42	>	#include <cmath>
43	>	#include "rnemd/RNEMD.hpp"
44	>	#include "math/Vector3.hpp"
45	>	#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
47	+	#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50	<
51	<	#ifndef IS_MPI
52	<	#include "math/SeqRandNumGen.hpp"
53	<	#else
50	<	#include "math/ParallelRandNumGen.hpp"
50	>	#include "utils/PhysicalConstants.hpp"
51	>	#include "utils/Tuple.hpp"
52	>	#ifdef IS_MPI
53	>	#include <mpi.h>
54		#endif
55
56	<	/* Remove me after testing*/
54	<	/*
55	<	#include <cstdio>
56	<	#include <iostream>
57	<	*/
58	<	/*End remove me*/
56	>	#define HONKING_LARGE_VALUE 1.0e10
57
58	<	namespace oopse {
58	>	using namespace std;
59	>	namespace OpenMD {
60
61	<	RNEMD::RNEMD(SimInfo* info) : info_(info) {
62	<
61	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
62	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63	>
64	>	trialCount_ = 0;
65	>	failTrialCount_ = 0;
66	>	failRootCount_ = 0;
67	>
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
73	<	stringToEnumMap_["Px"] = rnemdPx;
74	<	stringToEnumMap_["Py"] = rnemdPy;
70	<	stringToEnumMap_["Pz"] = rnemdPz;
71	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	stringToMethod_["Swap"]  = rnemdSwap;
73	>	stringToMethod_["NIVS"]  = rnemdNIVS;
74	>	stringToMethod_["VSS"]   = rnemdVSS;
75
76	<	const std::string st = simParams->getRNEMD_swapType();
76	>	stringToFluxType_["KE"]  = rnemdKE;
77	>	stringToFluxType_["Px"]  = rnemdPx;
78	>	stringToFluxType_["Py"]  = rnemdPy;
79	>	stringToFluxType_["Pz"]  = rnemdPz;
80	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
81	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
82	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
83
84	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
85	<	i = stringToEnumMap_.find(st);
77	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
84	>	runTime_ = simParams->getRunTime();
85	>	statusTime_ = simParams->getStatusTime();
86
87	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88	+	evaluator_.loadScriptString(rnemdObjectSelection_);
89	+	seleMan_.setSelectionSet(evaluator_.evaluate());
90
91	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
92	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
93	<	exchangeSum_ = 0.0;
91	>	const string methStr = rnemdParams->getMethod();
92	>	bool hasFluxType = rnemdParams->haveFluxType();
93	>
94	>	string fluxStr;
95	>	if (hasFluxType) {
96	>	fluxStr = rnemdParams->getFluxType();
97	>	} else {
98	>	sprintf(painCave.errMsg,
99	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
100	>	"\twhich must be one of the following values:\n"
101	>	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
102	>	"\tuse RNEMD\n");
103	>	painCave.isFatal = 1;
104	>	painCave.severity = OPENMD_ERROR;
105	>	simError();
106	>	}
107	>
108	>	bool hasKineticFlux = rnemdParams->haveKineticFlux();
109	>	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
110	>	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
111	>	bool hasSlabWidth = rnemdParams->haveSlabWidth();
112	>	bool hasSlabACenter = rnemdParams->haveSlabACenter();
113	>	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
114	>	bool hasOutputFileName = rnemdParams->haveOutputFileName();
115	>	bool hasOutputFields = rnemdParams->haveOutputFields();
116
117	<	#ifndef IS_MPI
118	<	if (simParams->haveSeed()) {
119	<	seedValue = simParams->getSeed();
120	<	randNumGen_ = new SeqRandNumGen(seedValue);
121	<	}else {
122	<	randNumGen_ = new SeqRandNumGen();
123	<	}
124	<	#else
125	<	if (simParams->haveSeed()) {
126	<	seedValue = simParams->getSeed();
127	<	randNumGen_ = new ParallelRandNumGen(seedValue);
128	<	}else {
129	<	randNumGen_ = new ParallelRandNumGen();
130	<	}
131	<	#endif
132	<	}
117	>	map<string, RNEMDMethod>::iterator i;
118	>	i = stringToMethod_.find(methStr);
119	>	if (i != stringToMethod_.end())
120	>	rnemdMethod_ = i->second;
121	>	else {
122	>	sprintf(painCave.errMsg,
123	>	"RNEMD: The current method,\n"
124	>	"\t\t%s is not one of the recognized\n"
125	>	"\texchange methods: Swap, NIVS, or VSS\n",
126	>	methStr.c_str());
127	>	painCave.isFatal = 1;
128	>	painCave.severity = OPENMD_ERROR;
129	>	simError();
130	>	}
131	>
132	>	map<string, RNEMDFluxType>::iterator j;
133	>	j = stringToFluxType_.find(fluxStr);
134	>	if (j != stringToFluxType_.end())
135	>	rnemdFluxType_ = j->second;
136	>	else {
137	>	sprintf(painCave.errMsg,
138	>	"RNEMD: The current fluxType,\n"
139	>	"\t\t%s\n"
140	>	"\tis not one of the recognized flux types.\n",
141	>	fluxStr.c_str());
142	>	painCave.isFatal = 1;
143	>	painCave.severity = OPENMD_ERROR;
144	>	simError();
145	>	}
146	>
147	>	bool methodFluxMismatch = false;
148	>	bool hasCorrectFlux = false;
149	>	switch(rnemdMethod_) {
150	>	case rnemdSwap:
151	>	switch (rnemdFluxType_) {
152	>	case rnemdKE:
153	>	hasCorrectFlux = hasKineticFlux;
154	>	break;
155	>	case rnemdPx:
156	>	case rnemdPy:
157	>	case rnemdPz:
158	>	hasCorrectFlux = hasMomentumFlux;
159	>	break;
160	>	default :
161	>	methodFluxMismatch = true;
162	>	break;
163	>	}
164	>	break;
165	>	case rnemdNIVS:
166	>	switch (rnemdFluxType_) {
167	>	case rnemdKE:
168	>	case rnemdRotKE:
169	>	case rnemdFullKE:
170	>	hasCorrectFlux = hasKineticFlux;
171	>	break;
172	>	case rnemdPx:
173	>	case rnemdPy:
174	>	case rnemdPz:
175	>	hasCorrectFlux = hasMomentumFlux;
176	>	break;
177	>	case rnemdKePx:
178	>	case rnemdKePy:
179	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
180	>	break;
181	>	default:
182	>	methodFluxMismatch = true;
183	>	break;
184	>	}
185	>	break;
186	>	case rnemdVSS:
187	>	switch (rnemdFluxType_) {
188	>	case rnemdKE:
189	>	case rnemdRotKE:
190	>	case rnemdFullKE:
191	>	hasCorrectFlux = hasKineticFlux;
192	>	break;
193	>	case rnemdPx:
194	>	case rnemdPy:
195	>	case rnemdPz:
196	>	hasCorrectFlux = hasMomentumFlux;
197	>	break;
198	>	case rnemdPvector:
199	>	hasCorrectFlux = hasMomentumFluxVector;
200	>	case rnemdKePx:
201	>	case rnemdKePy:
202	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
203	>	break;
204	>	case rnemdKePvector:
205	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
206	>	break;
207	>	default:
208	>	methodFluxMismatch = true;
209	>	break;
210	>	}
211	>	default:
212	>	break;
213	>	}
214	>
215	>	if (methodFluxMismatch) {
216	>	sprintf(painCave.errMsg,
217	>	"RNEMD: The current method,\n"
218	>	"\t\t%s\n"
219	>	"\tcannot be used with the current flux type, %s\n",
220	>	methStr.c_str(), fluxStr.c_str());
221	>	painCave.isFatal = 1;
222	>	painCave.severity = OPENMD_ERROR;
223	>	simError();
224	>	}
225	>	if (!hasCorrectFlux) {
226	>	sprintf(painCave.errMsg,
227	>	"RNEMD: The current method,\n"
228	>	"\t%s, and flux type %s\n"
229	>	"\tdid not have the correct flux value specified. Options\n"
230	>	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
231	>	methStr.c_str(), fluxStr.c_str());
232	>	painCave.isFatal = 1;
233	>	painCave.severity = OPENMD_ERROR;
234	>	simError();
235	>	}
236	>
237	>	if (hasKineticFlux) {
238	>	kineticFlux_ = rnemdParams->getKineticFlux();
239	>	} else {
240	>	kineticFlux_ = 0.0;
241	>	}
242	>	if (hasMomentumFluxVector) {
243	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
244	>	} else {
245	>	momentumFluxVector_ = V3Zero;
246	>	if (hasMomentumFlux) {
247	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
248	>	switch (rnemdFluxType_) {
249	>	case rnemdPx:
250	>	momentumFluxVector_.x() = momentumFlux;
251	>	break;
252	>	case rnemdPy:
253	>	momentumFluxVector_.y() = momentumFlux;
254	>	break;
255	>	case rnemdPz:
256	>	momentumFluxVector_.z() = momentumFlux;
257	>	break;
258	>	case rnemdKePx:
259	>	momentumFluxVector_.x() = momentumFlux;
260	>	break;
261	>	case rnemdKePy:
262	>	momentumFluxVector_.y() = momentumFlux;
263	>	break;
264	>	default:
265	>	break;
266	>	}
267	>	}
268	>	}
269	>
270	>	// do some sanity checking
271	>
272	>	int selectionCount = seleMan_.getSelectionCount();
273	>	int nIntegrable = info->getNGlobalIntegrableObjects();
274	>
275	>	if (selectionCount > nIntegrable) {
276	>	sprintf(painCave.errMsg,
277	>	"RNEMD: The current objectSelection,\n"
278	>	"\t\t%s\n"
279	>	"\thas resulted in %d selected objects.  However,\n"
280	>	"\tthe total number of integrable objects in the system\n"
281	>	"\tis only %d.  This is almost certainly not what you want\n"
282	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
283	>	"\tselector in the selection script!\n",
284	>	rnemdObjectSelection_.c_str(),
285	>	selectionCount, nIntegrable);
286	>	painCave.isFatal = 0;
287	>	painCave.severity = OPENMD_WARNING;
288	>	simError();
289	>	}
290	>
291	>	nBins_ = rnemdParams->getOutputBins();
292	>
293	>	data_.resize(RNEMD::ENDINDEX);
294	>	OutputData z;
295	>	z.units =  "Angstroms";
296	>	z.title =  "Z";
297	>	z.dataType = "RealType";
298	>	z.accumulator.reserve(nBins_);
299	>	for (unsigned int i = 0; i < nBins_; i++)
300	>	z.accumulator.push_back( new Accumulator() );
301	>	data_[Z] = z;
302	>	outputMap_["Z"] =  Z;
303	>
304	>	OutputData temperature;
305	>	temperature.units =  "K";
306	>	temperature.title =  "Temperature";
307	>	temperature.dataType = "RealType";
308	>	temperature.accumulator.reserve(nBins_);
309	>	for (unsigned int i = 0; i < nBins_; i++)
310	>	temperature.accumulator.push_back( new Accumulator() );
311	>	data_[TEMPERATURE] = temperature;
312	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
313	>
314	>	OutputData velocity;
315	>	velocity.units = "amu/fs";
316	>	velocity.title =  "Velocity";
317	>	velocity.dataType = "Vector3d";
318	>	velocity.accumulator.reserve(nBins_);
319	>	for (unsigned int i = 0; i < nBins_; i++)
320	>	velocity.accumulator.push_back( new VectorAccumulator() );
321	>	data_[VELOCITY] = velocity;
322	>	outputMap_["VELOCITY"] = VELOCITY;
323	>
324	>	OutputData density;
325	>	density.units =  "g cm^-3";
326	>	density.title =  "Density";
327	>	density.dataType = "RealType";
328	>	density.accumulator.reserve(nBins_);
329	>	for (unsigned int i = 0; i < nBins_; i++)
330	>	density.accumulator.push_back( new Accumulator() );
331	>	data_[DENSITY] = density;
332	>	outputMap_["DENSITY"] =  DENSITY;
333	>
334	>	if (hasOutputFields) {
335	>	parseOutputFileFormat(rnemdParams->getOutputFields());
336	>	} else {
337	>	outputMask_.set(Z);
338	>	switch (rnemdFluxType_) {
339	>	case rnemdKE:
340	>	case rnemdRotKE:
341	>	case rnemdFullKE:
342	>	outputMask_.set(TEMPERATURE);
343	>	break;
344	>	case rnemdPx:
345	>	case rnemdPy:
346	>	outputMask_.set(VELOCITY);
347	>	break;
348	>	case rnemdPz:
349	>	case rnemdPvector:
350	>	outputMask_.set(VELOCITY);
351	>	outputMask_.set(DENSITY);
352	>	break;
353	>	case rnemdKePx:
354	>	case rnemdKePy:
355	>	outputMask_.set(TEMPERATURE);
356	>	outputMask_.set(VELOCITY);
357	>	break;
358	>	case rnemdKePvector:
359	>	outputMask_.set(TEMPERATURE);
360	>	outputMask_.set(VELOCITY);
361	>	outputMask_.set(DENSITY);
362	>	break;
363	>	default:
364	>	break;
365	>	}
366	>	}
367	>
368	>	if (hasOutputFileName) {
369	>	rnemdFileName_ = rnemdParams->getOutputFileName();
370	>	} else {
371	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
372	>	}
373	>
374	>	exchangeTime_ = rnemdParams->getExchangeTime();
375	>
376	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
377	>	Mat3x3d hmat = currentSnap_->getHmat();
378
379	+	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
380	+	// Lx, Ly = box dimensions in x & y
381	+	// dt = exchange time interval
382	+	// flux = target flux
383	+
384	+	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
385	+	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
386	+
387	+	// total exchange sums are zeroed out at the beginning:
388	+
389	+	kineticExchange_ = 0.0;
390	+	momentumExchange_ = V3Zero;
391	+
392	+	if (hasSlabWidth)
393	+	slabWidth_ = rnemdParams->getSlabWidth();
394	+	else
395	+	slabWidth_ = hmat(2,2) / 10.0;
396	+
397	+	if (hasSlabACenter)
398	+	slabACenter_ = rnemdParams->getSlabACenter();
399	+	else
400	+	slabACenter_ = 0.0;
401	+
402	+	if (hasSlabBCenter)
403	+	slabBCenter_ = rnemdParams->getSlabBCenter();
404	+	else
405	+	slabBCenter_ = hmat(2,2) / 2.0;
406	+
407	+	}
408	+
409		RNEMD::~RNEMD() {
410	<	delete randNumGen_;
410	>
411	>	#ifdef IS_MPI
412	>	if (worldRank == 0) {
413	>	#endif
414	>
415	>	writeOutputFile();
416	>
417	>	rnemdFile_.close();
418	>
419	>	#ifdef IS_MPI
420	>	}
421	>	#endif
422		}
423	+
424	+	bool RNEMD::inSlabA(Vector3d pos) {
425	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
426	+	}
427	+	bool RNEMD::inSlabB(Vector3d pos) {
428	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	+	}
430
431		void RNEMD::doSwap() {
432	<	std::cerr << "in RNEMD!\n";
433	<	std::cerr << "nBins = " << nBins_ << "\n";
434	<	std::cerr << "swapTime = " << swapTime_ << "\n";
435	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
436	<	std::cerr << "swapType = " << rnemdType_ << "\n";
437	<	}
432	>
433	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
434	>	Mat3x3d hmat = currentSnap_->getHmat();
435	>
436	>	seleMan_.setSelectionSet(evaluator_.evaluate());
437	>
438	>	int selei;
439	>	StuntDouble* sd;
440	>	int idx;
441	>
442	>	RealType min_val;
443	>	bool min_found = false;
444	>	StuntDouble* min_sd;
445	>
446	>	RealType max_val;
447	>	bool max_found = false;
448	>	StuntDouble* max_sd;
449	>
450	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
451	>	sd = seleMan_.nextSelected(selei)) {
452	>
453	>	idx = sd->getLocalIndex();
454	>
455	>	Vector3d pos = sd->getPos();
456	>
457	>	// wrap the stuntdouble's position back into the box:
458	>
459	>	if (usePeriodicBoundaryConditions_)
460	>	currentSnap_->wrapVector(pos);
461	>	bool inA = inSlabA(pos);
462	>	bool inB = inSlabB(pos);
463	>
464	>	if (inA || inB) {
465	>
466	>	RealType mass = sd->getMass();
467	>	Vector3d vel = sd->getVel();
468	>	RealType value;
469	>
470	>	switch(rnemdFluxType_) {
471	>	case rnemdKE :
472	>
473	>	value = mass * vel.lengthSquare();
474	>
475	>	if (sd->isDirectional()) {
476	>	Vector3d angMom = sd->getJ();
477	>	Mat3x3d I = sd->getI();
478	>
479	>	if (sd->isLinear()) {
480	>	int i = sd->linearAxis();
481	>	int j = (i + 1) % 3;
482	>	int k = (i + 2) % 3;
483	>	value += angMom[j] * angMom[j] / I(j, j) +
484	>	angMom[k] * angMom[k] / I(k, k);
485	>	} else {
486	>	value += angMom[0]*angMom[0]/I(0, 0)
487	>	+ angMom[1]*angMom[1]/I(1, 1)
488	>	+ angMom[2]*angMom[2]/I(2, 2);
489	>	}
490	>	} //angular momenta exchange enabled
491	>	//energyConvert temporarily disabled
492	>	//make kineticExchange_ comparable between swap & scale
493	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
494	>	value *= 0.5;
495	>	break;
496	>	case rnemdPx :
497	>	value = mass * vel[0];
498	>	break;
499	>	case rnemdPy :
500	>	value = mass * vel[1];
501	>	break;
502	>	case rnemdPz :
503	>	value = mass * vel[2];
504	>	break;
505	>	default :
506	>	break;
507	>	}
508	>
509	>	if (inA == 0) {
510	>	if (!min_found) {
511	>	min_val = value;
512	>	min_sd = sd;
513	>	min_found = true;
514	>	} else {
515	>	if (min_val > value) {
516	>	min_val = value;
517	>	min_sd = sd;
518	>	}
519	>	}
520	>	} else {
521	>	if (!max_found) {
522	>	max_val = value;
523	>	max_sd = sd;
524	>	max_found = true;
525	>	} else {
526	>	if (max_val < value) {
527	>	max_val = value;
528	>	max_sd = sd;
529	>	}
530	>	}
531	>	}
532	>	}
533	>	}
534	>
535	>	#ifdef IS_MPI
536	>	int nProc, worldRank;
537	>
538	>	nProc = MPI::COMM_WORLD.Get_size();
539	>	worldRank = MPI::COMM_WORLD.Get_rank();
540	>
541	>	bool my_min_found = min_found;
542	>	bool my_max_found = max_found;
543	>
544	>	// Even if we didn't find a minimum, did someone else?
545	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
546	>	// Even if we didn't find a maximum, did someone else?
547	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
548	>	#endif
549	>
550	>	if (max_found && min_found) {
551	>
552	>	#ifdef IS_MPI
553	>	struct {
554	>	RealType val;
555	>	int rank;
556	>	} max_vals, min_vals;
557	>
558	>	if (my_min_found) {
559	>	min_vals.val = min_val;
560	>	} else {
561	>	min_vals.val = HONKING_LARGE_VALUE;
562	>	}
563	>	min_vals.rank = worldRank;
564	>
565	>	// Who had the minimum?
566	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
567	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
568	>	min_val = min_vals.val;
569	>
570	>	if (my_max_found) {
571	>	max_vals.val = max_val;
572	>	} else {
573	>	max_vals.val = -HONKING_LARGE_VALUE;
574	>	}
575	>	max_vals.rank = worldRank;
576	>
577	>	// Who had the maximum?
578	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
579	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
580	>	max_val = max_vals.val;
581	>	#endif
582	>
583	>	if (min_val < max_val) {
584	>
585	>	#ifdef IS_MPI
586	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
587	>	// I have both maximum and minimum, so proceed like a single
588	>	// processor version:
589	>	#endif
590	>
591	>	Vector3d min_vel = min_sd->getVel();
592	>	Vector3d max_vel = max_sd->getVel();
593	>	RealType temp_vel;
594	>
595	>	switch(rnemdFluxType_) {
596	>	case rnemdKE :
597	>	min_sd->setVel(max_vel);
598	>	max_sd->setVel(min_vel);
599	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
600	>	Vector3d min_angMom = min_sd->getJ();
601	>	Vector3d max_angMom = max_sd->getJ();
602	>	min_sd->setJ(max_angMom);
603	>	max_sd->setJ(min_angMom);
604	>	}//angular momenta exchange enabled
605	>	//assumes same rigid body identity
606	>	break;
607	>	case rnemdPx :
608	>	temp_vel = min_vel.x();
609	>	min_vel.x() = max_vel.x();
610	>	max_vel.x() = temp_vel;
611	>	min_sd->setVel(min_vel);
612	>	max_sd->setVel(max_vel);
613	>	break;
614	>	case rnemdPy :
615	>	temp_vel = min_vel.y();
616	>	min_vel.y() = max_vel.y();
617	>	max_vel.y() = temp_vel;
618	>	min_sd->setVel(min_vel);
619	>	max_sd->setVel(max_vel);
620	>	break;
621	>	case rnemdPz :
622	>	temp_vel = min_vel.z();
623	>	min_vel.z() = max_vel.z();
624	>	max_vel.z() = temp_vel;
625	>	min_sd->setVel(min_vel);
626	>	max_sd->setVel(max_vel);
627	>	break;
628	>	default :
629	>	break;
630	>	}
631	>
632	>	#ifdef IS_MPI
633	>	// the rest of the cases only apply in parallel simulations:
634	>	} else if (max_vals.rank == worldRank) {
635	>	// I had the max, but not the minimum
636	>
637	>	Vector3d min_vel;
638	>	Vector3d max_vel = max_sd->getVel();
639	>	MPI::Status status;
640	>
641	>	// point-to-point swap of the velocity vector
642	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
643	>	min_vals.rank, 0,
644	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
645	>	min_vals.rank, 0, status);
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649	>	max_sd->setVel(min_vel);
650	>	//angular momenta exchange enabled
651	>	if (max_sd->isDirectional()) {
652	>	Vector3d min_angMom;
653	>	Vector3d max_angMom = max_sd->getJ();
654	>
655	>	// point-to-point swap of the angular momentum vector
656	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
657	>	MPI::REALTYPE, min_vals.rank, 1,
658	>	min_angMom.getArrayPointer(), 3,
659	>	MPI::REALTYPE, min_vals.rank, 1,
660	>	status);
661	>
662	>	max_sd->setJ(min_angMom);
663	>	}
664	>	break;
665	>	case rnemdPx :
666	>	max_vel.x() = min_vel.x();
667	>	max_sd->setVel(max_vel);
668	>	break;
669	>	case rnemdPy :
670	>	max_vel.y() = min_vel.y();
671	>	max_sd->setVel(max_vel);
672	>	break;
673	>	case rnemdPz :
674	>	max_vel.z() = min_vel.z();
675	>	max_sd->setVel(max_vel);
676	>	break;
677	>	default :
678	>	break;
679	>	}
680	>	} else if (min_vals.rank == worldRank) {
681	>	// I had the minimum but not the maximum:
682	>
683	>	Vector3d max_vel;
684	>	Vector3d min_vel = min_sd->getVel();
685	>	MPI::Status status;
686	>
687	>	// point-to-point swap of the velocity vector
688	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
689	>	max_vals.rank, 0,
690	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
691	>	max_vals.rank, 0, status);
692	>
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695	>	min_sd->setVel(max_vel);
696	>	//angular momenta exchange enabled
697	>	if (min_sd->isDirectional()) {
698	>	Vector3d min_angMom = min_sd->getJ();
699	>	Vector3d max_angMom;
700	>
701	>	// point-to-point swap of the angular momentum vector
702	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
703	>	MPI::REALTYPE, max_vals.rank, 1,
704	>	max_angMom.getArrayPointer(), 3,
705	>	MPI::REALTYPE, max_vals.rank, 1,
706	>	status);
707	>
708	>	min_sd->setJ(max_angMom);
709	>	}
710	>	break;
711	>	case rnemdPx :
712	>	min_vel.x() = max_vel.x();
713	>	min_sd->setVel(min_vel);
714	>	break;
715	>	case rnemdPy :
716	>	min_vel.y() = max_vel.y();
717	>	min_sd->setVel(min_vel);
718	>	break;
719	>	case rnemdPz :
720	>	min_vel.z() = max_vel.z();
721	>	min_sd->setVel(min_vel);
722	>	break;
723	>	default :
724	>	break;
725	>	}
726	>	}
727	>	#endif
728	>
729	>	switch(rnemdFluxType_) {
730	>	case rnemdKE:
731	>	cerr << "KE\n";
732	>	kineticExchange_ += max_val - min_val;
733	>	break;
734	>	case rnemdPx:
735	>	momentumExchange_.x() += max_val - min_val;
736	>	break;
737	>	case rnemdPy:
738	>	momentumExchange_.y() += max_val - min_val;
739	>	break;
740	>	case rnemdPz:
741	>	momentumExchange_.z() += max_val - min_val;
742	>	break;
743	>	default:
744	>	cerr << "default\n";
745	>	break;
746	>	}
747	>	} else {
748	>	sprintf(painCave.errMsg,
749	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
750	>	painCave.isFatal = 0;
751	>	painCave.severity = OPENMD_INFO;
752	>	simError();
753	>	failTrialCount_++;
754	>	}
755	>	} else {
756	>	sprintf(painCave.errMsg,
757	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
758	>	"\twas not present in at least one of the two slabs.\n");
759	>	painCave.isFatal = 0;
760	>	painCave.severity = OPENMD_INFO;
761	>	simError();
762	>	failTrialCount_++;
763	>	}
764	>	}
765	>
766	>	void RNEMD::doNIVS() {
767	>
768	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
769	>	Mat3x3d hmat = currentSnap_->getHmat();
770	>
771	>	seleMan_.setSelectionSet(evaluator_.evaluate());
772	>
773	>	int selei;
774	>	StuntDouble* sd;
775	>	int idx;
776	>
777	>	vector<StuntDouble*> hotBin, coldBin;
778	>
779	>	RealType Phx = 0.0;
780	>	RealType Phy = 0.0;
781	>	RealType Phz = 0.0;
782	>	RealType Khx = 0.0;
783	>	RealType Khy = 0.0;
784	>	RealType Khz = 0.0;
785	>	RealType Khw = 0.0;
786	>	RealType Pcx = 0.0;
787	>	RealType Pcy = 0.0;
788	>	RealType Pcz = 0.0;
789	>	RealType Kcx = 0.0;
790	>	RealType Kcy = 0.0;
791	>	RealType Kcz = 0.0;
792	>	RealType Kcw = 0.0;
793	>
794	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
795	>	sd = seleMan_.nextSelected(selei)) {
796	>
797	>	idx = sd->getLocalIndex();
798	>
799	>	Vector3d pos = sd->getPos();
800	>
801	>	// wrap the stuntdouble's position back into the box:
802	>
803	>	if (usePeriodicBoundaryConditions_)
804	>	currentSnap_->wrapVector(pos);
805	>
806	>	// which bin is this stuntdouble in?
807	>	bool inA = inSlabA(pos);
808	>	bool inB = inSlabB(pos);
809	>
810	>	if (inA || inB) {
811	>
812	>	RealType mass = sd->getMass();
813	>	Vector3d vel = sd->getVel();
814	>
815	>	if (inA) {
816	>	hotBin.push_back(sd);
817	>	Phx += mass * vel.x();
818	>	Phy += mass * vel.y();
819	>	Phz += mass * vel.z();
820	>	Khx += mass * vel.x() * vel.x();
821	>	Khy += mass * vel.y() * vel.y();
822	>	Khz += mass * vel.z() * vel.z();
823	>	if (sd->isDirectional()) {
824	>	Vector3d angMom = sd->getJ();
825	>	Mat3x3d I = sd->getI();
826	>	if (sd->isLinear()) {
827	>	int i = sd->linearAxis();
828	>	int j = (i + 1) % 3;
829	>	int k = (i + 2) % 3;
830	>	Khw += angMom[j] * angMom[j] / I(j, j) +
831	>	angMom[k] * angMom[k] / I(k, k);
832	>	} else {
833	>	Khw += angMom[0]*angMom[0]/I(0, 0)
834	>	+ angMom[1]*angMom[1]/I(1, 1)
835	>	+ angMom[2]*angMom[2]/I(2, 2);
836	>	}
837	>	}
838	>	} else {
839	>	coldBin.push_back(sd);
840	>	Pcx += mass * vel.x();
841	>	Pcy += mass * vel.y();
842	>	Pcz += mass * vel.z();
843	>	Kcx += mass * vel.x() * vel.x();
844	>	Kcy += mass * vel.y() * vel.y();
845	>	Kcz += mass * vel.z() * vel.z();
846	>	if (sd->isDirectional()) {
847	>	Vector3d angMom = sd->getJ();
848	>	Mat3x3d I = sd->getI();
849	>	if (sd->isLinear()) {
850	>	int i = sd->linearAxis();
851	>	int j = (i + 1) % 3;
852	>	int k = (i + 2) % 3;
853	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
854	>	angMom[k] * angMom[k] / I(k, k);
855	>	} else {
856	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
857	>	+ angMom[1]*angMom[1]/I(1, 1)
858	>	+ angMom[2]*angMom[2]/I(2, 2);
859	>	}
860	>	}
861	>	}
862	>	}
863	>	}
864	>
865	>	Khx *= 0.5;
866	>	Khy *= 0.5;
867	>	Khz *= 0.5;
868	>	Khw *= 0.5;
869	>	Kcx *= 0.5;
870	>	Kcy *= 0.5;
871	>	Kcz *= 0.5;
872	>	Kcw *= 0.5;
873	>
874	>	#ifdef IS_MPI
875	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
876	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
877	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
878	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
879	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
880	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
881	>
882	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
883	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
884	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
885	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
886	>
887	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
888	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
889	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
890	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
891	>	#endif
892	>
893	>	//solve coldBin coeff's first
894	>	RealType px = Pcx / Phx;
895	>	RealType py = Pcy / Phy;
896	>	RealType pz = Pcz / Phz;
897	>	RealType c, x, y, z;
898	>	bool successfulScale = false;
899	>	if ((rnemdFluxType_ == rnemdFullKE) ||
900	>	(rnemdFluxType_ == rnemdRotKE)) {
901	>	//may need sanity check Khw & Kcw > 0
902	>
903	>	if (rnemdFluxType_ == rnemdFullKE) {
904	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
905	>	} else {
906	>	c = 1.0 - kineticTarget_ / Kcw;
907	>	}
908	>
909	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
910	>	c = sqrt(c);
911	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	>	//now convert to hotBin coefficient
913	>	RealType w = 0.0;
914	>	if (rnemdFluxType_ ==  rnemdFullKE) {
915	>	x = 1.0 + px * (1.0 - c);
916	>	y = 1.0 + py * (1.0 - c);
917	>	z = 1.0 + pz * (1.0 - c);
918	>	/* more complicated way
919	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
920	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
921	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
922	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
923	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
924	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
925	>	*/
926	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
927	>	(fabs(z - 1.0) < 0.1)) {
928	>	w = 1.0 + (kineticTarget_
929	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
930	>	+ Khz * (1.0 - z * z)) / Khw;
931	>	}//no need to calculate w if x, y or z is out of range
932	>	} else {
933	>	w = 1.0 + kineticTarget_ / Khw;
934	>	}
935	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
936	>	//if w is in the right range, so should be x, y, z.
937	>	vector<StuntDouble*>::iterator sdi;
938	>	Vector3d vel;
939	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
940	>	if (rnemdFluxType_ == rnemdFullKE) {
941	>	vel = (*sdi)->getVel() * c;
942	>	(*sdi)->setVel(vel);
943	>	}
944	>	if ((*sdi)->isDirectional()) {
945	>	Vector3d angMom = (*sdi)->getJ() * c;
946	>	(*sdi)->setJ(angMom);
947	>	}
948	>	}
949	>	w = sqrt(w);
950	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	>	//           << "\twh= " << w << endl;
952	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
953	>	if (rnemdFluxType_ == rnemdFullKE) {
954	>	vel = (*sdi)->getVel();
955	>	vel.x() *= x;
956	>	vel.y() *= y;
957	>	vel.z() *= z;
958	>	(*sdi)->setVel(vel);
959	>	}
960	>	if ((*sdi)->isDirectional()) {
961	>	Vector3d angMom = (*sdi)->getJ() * w;
962	>	(*sdi)->setJ(angMom);
963	>	}
964	>	}
965	>	successfulScale = true;
966	>	kineticExchange_ += kineticTarget_;
967	>	}
968	>	}
969	>	} else {
970	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
971	>	switch(rnemdFluxType_) {
972	>	case rnemdKE :
973	>	/* used hotBin coeff's & only scale x & y dimensions
974	>	RealType px = Phx / Pcx;
975	>	RealType py = Phy / Pcy;
976	>	a110 = Khy;
977	>	c0 = - Khx - Khy - kineticTarget_;
978	>	a000 = Khx;
979	>	a111 = Kcy * py * py;
980	>	b11 = -2.0 * Kcy * py * (1.0 + py);
981	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
982	>	b01 = -2.0 * Kcx * px * (1.0 + px);
983	>	a001 = Kcx * px * px;
984	>	*/
985	>	//scale all three dimensions, let c_x = c_y
986	>	a000 = Kcx + Kcy;
987	>	a110 = Kcz;
988	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
989	>	a001 = Khx * px * px + Khy * py * py;
990	>	a111 = Khz * pz * pz;
991	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
992	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
993	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
994	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
995	>	break;
996	>	case rnemdPx :
997	>	c = 1 - momentumTarget_.x() / Pcx;
998	>	a000 = Kcy;
999	>	a110 = Kcz;
1000	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1001	>	a001 = py * py * Khy;
1002	>	a111 = pz * pz * Khz;
1003	>	b01 = -2.0 * Khy * py * (1.0 + py);
1004	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1005	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1006	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1007	>	break;
1008	>	case rnemdPy :
1009	>	c = 1 - momentumTarget_.y() / Pcy;
1010	>	a000 = Kcx;
1011	>	a110 = Kcz;
1012	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1013	>	a001 = px * px * Khx;
1014	>	a111 = pz * pz * Khz;
1015	>	b01 = -2.0 * Khx * px * (1.0 + px);
1016	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1017	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1018	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1019	>	break;
1020	>	case rnemdPz ://we don't really do this, do we?
1021	>	c = 1 - momentumTarget_.z() / Pcz;
1022	>	a000 = Kcx;
1023	>	a110 = Kcy;
1024	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1025	>	a001 = px * px * Khx;
1026	>	a111 = py * py * Khy;
1027	>	b01 = -2.0 * Khx * px * (1.0 + px);
1028	>	b11 = -2.0 * Khy * py * (1.0 + py);
1029	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1030	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1031	>	break;
1032	>	default :
1033	>	break;
1034	>	}
1035	>
1036	>	RealType v1 = a000 * a111 - a001 * a110;
1037	>	RealType v2 = a000 * b01;
1038	>	RealType v3 = a000 * b11;
1039	>	RealType v4 = a000 * c1 - a001 * c0;
1040	>	RealType v8 = a110 * b01;
1041	>	RealType v10 = - b01 * c0;
1042	>
1043	>	RealType u0 = v2 * v10 - v4 * v4;
1044	>	RealType u1 = -2.0 * v3 * v4;
1045	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1046	>	RealType u3 = -2.0 * v1 * v3;
1047	>	RealType u4 = - v1 * v1;
1048	>	//rescale coefficients
1049	>	RealType maxAbs = fabs(u0);
1050	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1051	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1052	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1053	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1054	>	u0 /= maxAbs;
1055	>	u1 /= maxAbs;
1056	>	u2 /= maxAbs;
1057	>	u3 /= maxAbs;
1058	>	u4 /= maxAbs;
1059	>	//max_element(start, end) is also available.
1060	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1061	>	poly.setCoefficient(4, u4);
1062	>	poly.setCoefficient(3, u3);
1063	>	poly.setCoefficient(2, u2);
1064	>	poly.setCoefficient(1, u1);
1065	>	poly.setCoefficient(0, u0);
1066	>	vector<RealType> realRoots = poly.FindRealRoots();
1067	>
1068	>	vector<RealType>::iterator ri;
1069	>	RealType r1, r2, alpha0;
1070	>	vector<pair<RealType,RealType> > rps;
1071	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1072	>	r2 = *ri;
1073	>	//check if FindRealRoots() give the right answer
1074	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1075	>	sprintf(painCave.errMsg,
1076	>	"RNEMD Warning: polynomial solve seems to have an error!");
1077	>	painCave.isFatal = 0;
1078	>	simError();
1079	>	failRootCount_++;
1080	>	}
1081	>	//might not be useful w/o rescaling coefficients
1082	>	alpha0 = -c0 - a110 * r2 * r2;
1083	>	if (alpha0 >= 0.0) {
1084	>	r1 = sqrt(alpha0 / a000);
1085	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1086	>	< 1e-6)
1087	>	{ rps.push_back(make_pair(r1, r2)); }
1088	>	if (r1 > 1e-6) { //r1 non-negative
1089	>	r1 = -r1;
1090	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1091	>	< 1e-6)
1092	>	{ rps.push_back(make_pair(r1, r2)); }
1093	>	}
1094	>	}
1095	>	}
1096	>	// Consider combining together the solving pair part w/ the searching
1097	>	// best solution part so that we don't need the pairs vector
1098	>	if (!rps.empty()) {
1099	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1100	>	RealType diff;
1101	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1102	>	vector<pair<RealType,RealType> >::iterator rpi;
1103	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1104	>	r1 = (*rpi).first;
1105	>	r2 = (*rpi).second;
1106	>	switch(rnemdFluxType_) {
1107	>	case rnemdKE :
1108	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1109	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1110	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1111	>	break;
1112	>	case rnemdPx :
1113	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1115	>	break;
1116	>	case rnemdPy :
1117	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1119	>	break;
1120	>	case rnemdPz :
1121	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1122	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1123	>	default :
1124	>	break;
1125	>	}
1126	>	if (diff < smallestDiff) {
1127	>	smallestDiff = diff;
1128	>	bestPair = *rpi;
1129	>	}
1130	>	}
1131	>	#ifdef IS_MPI
1132	>	if (worldRank == 0) {
1133	>	#endif
1134	>	// sprintf(painCave.errMsg,
1135	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1136	>	//         bestPair.first, bestPair.second);
1137	>	// painCave.isFatal = 0;
1138	>	// painCave.severity = OPENMD_INFO;
1139	>	// simError();
1140	>	#ifdef IS_MPI
1141	>	}
1142	>	#endif
1143	>
1144	>	switch(rnemdFluxType_) {
1145	>	case rnemdKE :
1146	>	x = bestPair.first;
1147	>	y = bestPair.first;
1148	>	z = bestPair.second;
1149	>	break;
1150	>	case rnemdPx :
1151	>	x = c;
1152	>	y = bestPair.first;
1153	>	z = bestPair.second;
1154	>	break;
1155	>	case rnemdPy :
1156	>	x = bestPair.first;
1157	>	y = c;
1158	>	z = bestPair.second;
1159	>	break;
1160	>	case rnemdPz :
1161	>	x = bestPair.first;
1162	>	y = bestPair.second;
1163	>	z = c;
1164	>	break;
1165	>	default :
1166	>	break;
1167	>	}
1168	>	vector<StuntDouble*>::iterator sdi;
1169	>	Vector3d vel;
1170	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1171	>	vel = (*sdi)->getVel();
1172	>	vel.x() *= x;
1173	>	vel.y() *= y;
1174	>	vel.z() *= z;
1175	>	(*sdi)->setVel(vel);
1176	>	}
1177	>	//convert to hotBin coefficient
1178	>	x = 1.0 + px * (1.0 - x);
1179	>	y = 1.0 + py * (1.0 - y);
1180	>	z = 1.0 + pz * (1.0 - z);
1181	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1182	>	vel = (*sdi)->getVel();
1183	>	vel.x() *= x;
1184	>	vel.y() *= y;
1185	>	vel.z() *= z;
1186	>	(*sdi)->setVel(vel);
1187	>	}
1188	>	successfulScale = true;
1189	>	switch(rnemdFluxType_) {
1190	>	case rnemdKE :
1191	>	kineticExchange_ += kineticTarget_;
1192	>	break;
1193	>	case rnemdPx :
1194	>	case rnemdPy :
1195	>	case rnemdPz :
1196	>	momentumExchange_ += momentumTarget_;
1197	>	break;
1198	>	default :
1199	>	break;
1200	>	}
1201	>	}
1202	>	}
1203	>	if (successfulScale != true) {
1204	>	sprintf(painCave.errMsg,
1205	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1206	>	"\tthe constraint equations may not exist or there may be\n"
1207	>	"\tno selected objects in one or both slabs.\n");
1208	>	painCave.isFatal = 0;
1209	>	painCave.severity = OPENMD_INFO;
1210	>	simError();
1211	>	failTrialCount_++;
1212	>	}
1213	>	}
1214	>
1215	>	void RNEMD::doVSS() {
1216	>
1217	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1218	>	RealType time = currentSnap_->getTime();
1219	>	Mat3x3d hmat = currentSnap_->getHmat();
1220	>
1221	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	>
1223	>	int selei;
1224	>	StuntDouble* sd;
1225	>	int idx;
1226	>
1227	>	vector<StuntDouble*> hotBin, coldBin;
1228	>
1229	>	Vector3d Ph(V3Zero);
1230	>	RealType Mh = 0.0;
1231	>	RealType Kh = 0.0;
1232	>	Vector3d Pc(V3Zero);
1233	>	RealType Mc = 0.0;
1234	>	RealType Kc = 0.0;
1235	>
1236	>
1237	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1238	>	sd = seleMan_.nextSelected(selei)) {
1239	>
1240	>	idx = sd->getLocalIndex();
1241	>
1242	>	Vector3d pos = sd->getPos();
1243	>
1244	>	// wrap the stuntdouble's position back into the box:
1245	>
1246	>	if (usePeriodicBoundaryConditions_)
1247	>	currentSnap_->wrapVector(pos);
1248	>
1249	>	// which bin is this stuntdouble in?
1250	>	bool inA = inSlabA(pos);
1251	>	bool inB = inSlabB(pos);
1252	>
1253	>	if (inA || inB) {
1254	>
1255	>	RealType mass = sd->getMass();
1256	>	Vector3d vel = sd->getVel();
1257	>
1258	>	if (inA) {
1259	>	hotBin.push_back(sd);
1260	>	//std::cerr << "before, velocity = " << vel << endl;
1261	>	Ph += mass * vel;
1262	>	//std::cerr << "after, velocity = " << vel << endl;
1263	>	Mh += mass;
1264	>	Kh += mass * vel.lengthSquare();
1265	>	if (rnemdFluxType_ == rnemdFullKE) {
1266	>	if (sd->isDirectional()) {
1267	>	Vector3d angMom = sd->getJ();
1268	>	Mat3x3d I = sd->getI();
1269	>	if (sd->isLinear()) {
1270	>	int i = sd->linearAxis();
1271	>	int j = (i + 1) % 3;
1272	>	int k = (i + 2) % 3;
1273	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1274	>	angMom[k] * angMom[k] / I(k, k);
1275	>	} else {
1276	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1277	>	angMom[1] * angMom[1] / I(1, 1) +
1278	>	angMom[2] * angMom[2] / I(2, 2);
1279	>	}
1280	>	}
1281	>	}
1282	>	} else { //midBin_
1283	>	coldBin.push_back(sd);
1284	>	Pc += mass * vel;
1285	>	Mc += mass;
1286	>	Kc += mass * vel.lengthSquare();
1287	>	if (rnemdFluxType_ == rnemdFullKE) {
1288	>	if (sd->isDirectional()) {
1289	>	Vector3d angMom = sd->getJ();
1290	>	Mat3x3d I = sd->getI();
1291	>	if (sd->isLinear()) {
1292	>	int i = sd->linearAxis();
1293	>	int j = (i + 1) % 3;
1294	>	int k = (i + 2) % 3;
1295	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1296	>	angMom[k] * angMom[k] / I(k, k);
1297	>	} else {
1298	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1299	>	angMom[1] * angMom[1] / I(1, 1) +
1300	>	angMom[2] * angMom[2] / I(2, 2);
1301	>	}
1302	>	}
1303	>	}
1304	>	}
1305	>	}
1306	>	}
1307	>
1308	>	Kh *= 0.5;
1309	>	Kc *= 0.5;
1310	>
1311	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1312	>	//        << "\tKc= " << Kc << endl;
1313	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1314	>
1315	>	#ifdef IS_MPI
1316	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1317	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1318	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1319	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1320	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1321	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1322	>	#endif
1323	>
1324	>	bool successfulExchange = false;
1325	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1326	>	Vector3d vc = Pc / Mc;
1327	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1328	>	Vector3d acrec = -momentumTarget_ / Mc;
1329	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1330	>	if (cNumerator > 0.0) {
1331	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1332	>	if (cDenominator > 0.0) {
1333	>	RealType c = sqrt(cNumerator / cDenominator);
1334	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1335	>	Vector3d vh = Ph / Mh;
1336	>	Vector3d ah = momentumTarget_ / Mh + vh;
1337	>	Vector3d ahrec = momentumTarget_ / Mh;
1338	>	RealType hNumerator = Kh + kineticTarget_
1339	>	- 0.5 * Mh * ah.lengthSquare();
1340	>	if (hNumerator > 0.0) {
1341	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1342	>	if (hDenominator > 0.0) {
1343	>	RealType h = sqrt(hNumerator / hDenominator);
1344	>	if ((h > 0.9) && (h < 1.1)) {
1345	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1347	>	vector<StuntDouble*>::iterator sdi;
1348	>	Vector3d vel;
1349	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1350	>	//vel = (*sdi)->getVel();
1351	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1352	>	(*sdi)->setVel(vel);
1353	>	if (rnemdFluxType_ == rnemdFullKE) {
1354	>	if ((*sdi)->isDirectional()) {
1355	>	Vector3d angMom = (*sdi)->getJ() * c;
1356	>	(*sdi)->setJ(angMom);
1357	>	}
1358	>	}
1359	>	}
1360	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1361	>	//vel = (*sdi)->getVel();
1362	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1363	>	(*sdi)->setVel(vel);
1364	>	if (rnemdFluxType_ == rnemdFullKE) {
1365	>	if ((*sdi)->isDirectional()) {
1366	>	Vector3d angMom = (*sdi)->getJ() * h;
1367	>	(*sdi)->setJ(angMom);
1368	>	}
1369	>	}
1370	>	}
1371	>	successfulExchange = true;
1372	>	kineticExchange_ += kineticTarget_;
1373	>	momentumExchange_ += momentumTarget_;
1374	>	}
1375	>	}
1376	>	}
1377	>	}
1378	>	}
1379	>	}
1380	>	}
1381	>	if (successfulExchange != true) {
1382	>	sprintf(painCave.errMsg,
1383	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1384	>	"\tthe constraint equations may not exist or there may be\n"
1385	>	"\tno selected objects in one or both slabs.\n");
1386	>	painCave.isFatal = 0;
1387	>	painCave.severity = OPENMD_INFO;
1388	>	simError();
1389	>	failTrialCount_++;
1390	>	}
1391	>	}
1392	>
1393	>	void RNEMD::doRNEMD() {
1394	>
1395	>	trialCount_++;
1396	>	switch(rnemdMethod_) {
1397	>	case rnemdSwap:
1398	>	doSwap();
1399	>	break;
1400	>	case rnemdNIVS:
1401	>	doNIVS();
1402	>	break;
1403	>	case rnemdVSS:
1404	>	doVSS();
1405	>	break;
1406	>	case rnemdUnkownMethod:
1407	>	default :
1408	>	break;
1409	>	}
1410	>	}
1411	>
1412	>	void RNEMD::collectData() {
1413	>
1414	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1415	>	Mat3x3d hmat = currentSnap_->getHmat();
1416	>
1417	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1418	>
1419	>	int selei;
1420	>	StuntDouble* sd;
1421	>	int idx;
1422	>
1423	>	vector<RealType> binMass(nBins_, 0.0);
1424	>	vector<RealType> binPx(nBins_, 0.0);
1425	>	vector<RealType> binPy(nBins_, 0.0);
1426	>	vector<RealType> binPz(nBins_, 0.0);
1427	>	vector<RealType> binKE(nBins_, 0.0);
1428	>	vector<int> binDOF(nBins_, 0);
1429	>	vector<int> binCount(nBins_, 0);
1430	>
1431	>	// alternative approach, track all molecules instead of only those
1432	>	// selected for scaling/swapping:
1433	>	/*
1434	>	SimInfo::MoleculeIterator miter;
1435	>	vector<StuntDouble*>::iterator iiter;
1436	>	Molecule* mol;
1437	>	StuntDouble* sd;
1438	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1439	>	mol = info_->nextMolecule(miter))
1440	>	sd is essentially sd
1441	>	for (sd = mol->beginIntegrableObject(iiter);
1442	>	sd != NULL;
1443	>	sd = mol->nextIntegrableObject(iiter))
1444	>	*/
1445	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1446	>	sd = seleMan_.nextSelected(selei)) {
1447	>
1448	>	idx = sd->getLocalIndex();
1449	>
1450	>	Vector3d pos = sd->getPos();
1451	>
1452	>	// wrap the stuntdouble's position back into the box:
1453	>
1454	>	if (usePeriodicBoundaryConditions_)
1455	>	currentSnap_->wrapVector(pos);
1456	>
1457	>	// which bin is this stuntdouble in?
1458	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	>	// Shift molecules by half a box to have bins start at 0
1460	>	// The modulo operator is used to wrap the case when we are
1461	>	// beyond the end of the bins back to the beginning.
1462	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463	>
1464	>	RealType mass = sd->getMass();
1465	>	Vector3d vel = sd->getVel();
1466	>
1467	>	binCount[binNo]++;
1468	>	binMass[binNo] += mass;
1469	>	binPx[binNo] += mass*vel.x();
1470	>	binPy[binNo] += mass*vel.y();
1471	>	binPz[binNo] += mass*vel.z();
1472	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1473	>	binDOF[binNo] += 3;
1474	>
1475	>	if (sd->isDirectional()) {
1476	>	Vector3d angMom = sd->getJ();
1477	>	Mat3x3d I = sd->getI();
1478	>	if (sd->isLinear()) {
1479	>	int i = sd->linearAxis();
1480	>	int j = (i + 1) % 3;
1481	>	int k = (i + 2) % 3;
1482	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1483	>	angMom[k] * angMom[k] / I(k, k));
1484	>	binDOF[binNo] += 2;
1485	>	} else {
1486	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1487	>	angMom[1] * angMom[1] / I(1, 1) +
1488	>	angMom[2] * angMom[2] / I(2, 2));
1489	>	binDOF[binNo] += 3;
1490	>	}
1491	>	}
1492	>	}
1493	>
1494	>
1495	>	#ifdef IS_MPI
1496	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1497	>	nBins_, MPI::INT, MPI::SUM);
1498	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1499	>	nBins_, MPI::REALTYPE, MPI::SUM);
1500	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1501	>	nBins_, MPI::REALTYPE, MPI::SUM);
1502	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1503	>	nBins_, MPI::REALTYPE, MPI::SUM);
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1505	>	nBins_, MPI::REALTYPE, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1509	>	nBins_, MPI::INT, MPI::SUM);
1510	>	#endif
1511	>
1512	>	Vector3d vel;
1513	>	RealType den;
1514	>	RealType temp;
1515	>	RealType z;
1516	>	for (int i = 0; i < nBins_; i++) {
1517	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1518	>	vel.x() = binPx[i] / binMass[i];
1519	>	vel.y() = binPy[i] / binMass[i];
1520	>	vel.z() = binPz[i] / binMass[i];
1521	>	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
1522	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1523	>	PhysicalConstants::energyConvert);
1524	>
1525	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1526	>	if(outputMask_[j]) {
1527	>	switch(j) {
1528	>	case Z:
1529	>	(data_[j].accumulator[i])->add(z);
1530	>	break;
1531	>	case TEMPERATURE:
1532	>	data_[j].accumulator[i]->add(temp);
1533	>	break;
1534	>	case VELOCITY:
1535	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1536	>	break;
1537	>	case DENSITY:
1538	>	data_[j].accumulator[i]->add(den);
1539	>	break;
1540	>	}
1541	>	}
1542	>	}
1543	>	}
1544	>	}
1545	>
1546	>	void RNEMD::getStarted() {
1547	>	collectData();
1548	>	writeOutputFile();
1549	>	}
1550	>
1551	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1552	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1553	>
1554	>	while(tokenizer.hasMoreTokens()) {
1555	>	std::string token(tokenizer.nextToken());
1556	>	toUpper(token);
1557	>	OutputMapType::iterator i = outputMap_.find(token);
1558	>	if (i != outputMap_.end()) {
1559	>	outputMask_.set(i->second);
1560	>	} else {
1561	>	sprintf( painCave.errMsg,
1562	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1563	>	"\toutputFileFormat keyword.\n", token.c_str() );
1564	>	painCave.isFatal = 0;
1565	>	painCave.severity = OPENMD_ERROR;
1566	>	simError();
1567	>	}
1568	>	}
1569	>	}
1570	>
1571	>	void RNEMD::writeOutputFile() {
1572	>
1573	>	#ifdef IS_MPI
1574	>	// If we're the root node, should we print out the results
1575	>	int worldRank = MPI::COMM_WORLD.Get_rank();
1576	>	if (worldRank == 0) {
1577	>	#endif
1578	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1579	>
1580	>	if( !rnemdFile_ ){
1581	>	sprintf( painCave.errMsg,
1582	>	"Could not open \"%s\" for RNEMD output.\n",
1583	>	rnemdFileName_.c_str());
1584	>	painCave.isFatal = 1;
1585	>	simError();
1586	>	}
1587	>
1588	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1589	>
1590	>	RealType time = currentSnap_->getTime();
1591	>
1592	>
1593	>	rnemdFile_ << "#######################################################\n";
1594	>	rnemdFile_ << "# RNEMD {\n";
1595	>
1596	>	map<string, RNEMDMethod>::iterator mi;
1597	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1598	>	if ( (*mi).second == rnemdMethod_)
1599	>	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
1600	>	}
1601	>	map<string, RNEMDFluxType>::iterator fi;
1602	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1603	>	if ( (*fi).second == rnemdFluxType_)
1604	>	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
1605	>	}
1606	>
1607	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
1608	>
1609	>	rnemdFile_ << "#    objectSelection = \""
1610	>	<< rnemdObjectSelection_ << "\"\n";
1611	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
1612	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
1614	>	rnemdFile_ << "# }\n";
1615	>	rnemdFile_ << "#######################################################\n";
1616	>
1617	>	rnemdFile_ << "# running time = " << time << " fs\n";
1618	>	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
1619	>	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
1620	>
1621	>	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
1622	>	<< "\n";
1623	>	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
1624	>	<< "\n";
1625	>
1626	>	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
1627	>	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
1628	>	<< "\n";
1629	>
1630	>	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
1631	>	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
1632	>
1633	>
1634	>	if (rnemdMethod_ == rnemdNIVS) {
1635	>	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
1636	>	}
1637	>
1638	>	rnemdFile_ << "#######################################################\n";
1639	>
1640	>
1641	>
1642	>	//write title
1643	>	rnemdFile_ << "#";
1644	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1645	>	if (outputMask_[i]) {
1646	>	rnemdFile_ << "\t" << data_[i].title <<
1647	>	"(" << data_[i].units << ")";
1648	>	}
1649	>	}
1650	>	rnemdFile_ << std::endl;
1651	>
1652	>	rnemdFile_.precision(8);
1653	>
1654	>	for (unsigned int j = 0; j < nBins_; j++) {
1655	>
1656	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1657	>	if (outputMask_[i]) {
1658	>	if (data_[i].dataType == "RealType")
1659	>	writeReal(i,j);
1660	>	else if (data_[i].dataType == "Vector3d")
1661	>	writeVector(i,j);
1662	>	else {
1663	>	sprintf( painCave.errMsg,
1664	>	"RNEMD found an unknown data type for: %s ",
1665	>	data_[i].title.c_str());
1666	>	painCave.isFatal = 1;
1667	>	simError();
1668	>	}
1669	>	}
1670	>	}
1671	>	rnemdFile_ << std::endl;
1672	>
1673	>	}
1674	>
1675	>	rnemdFile_.flush();
1676	>	rnemdFile_.close();
1677	>
1678	>	#ifdef IS_MPI
1679	>	}
1680	>	#endif
1681	>
1682	>	}
1683	>
1684	>	void RNEMD::writeReal(int index, unsigned int bin) {
1685	>	assert(index >=0 && index < ENDINDEX);
1686	>	assert(bin >=0 && bin < nBins_);
1687	>	RealType s;
1688	>
1689	>	data_[index].accumulator[bin]->getAverage(s);
1690	>
1691	>	if (! isinf(s) && ! isnan(s)) {
1692	>	rnemdFile_ << "\t" << s;
1693	>	} else{
1694	>	sprintf( painCave.errMsg,
1695	>	"RNEMD detected a numerical error writing: %s for bin %d",
1696	>	data_[index].title.c_str(), bin);
1697	>	painCave.isFatal = 1;
1698	>	simError();
1699	>	}
1700	>	}
1701	>
1702	>	void RNEMD::writeVector(int index, unsigned int bin) {
1703	>	assert(index >=0 && index < ENDINDEX);
1704	>	assert(bin >=0 && bin < nBins_);
1705	>	Vector3d s;
1706	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1707	>	if (isinf(s[0]) || isnan(s[0]) ||
1708	>	isinf(s[1]) || isnan(s[1]) ||
1709	>	isinf(s[2]) || isnan(s[2]) ) {
1710	>	sprintf( painCave.errMsg,
1711	>	"RNEMD detected a numerical error writing: %s for bin %d",
1712	>	data_[index].title.c_str(), bin);
1713	>	painCave.isFatal = 1;
1714	>	simError();
1715	>	} else {
1716	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1717	>	}
1718	>	}
1719		}
1720	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

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