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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 1777 by gezelter, Thu Aug 9 18:35:09 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;
69	<	stringToEnumMap_["Py"] = rnemdPy;
70	<	stringToEnumMap_["Pz"] = rnemdPz;
71	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	<	const std::string st = simParams->getRNEMD_swapType();
75	>	stringToMethod_["Swap"]  = rnemdSwap;
76	>	stringToMethod_["NIVS"]  = rnemdNIVS;
77	>	stringToMethod_["VSS"]   = rnemdVSS;
78
79	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
80	<	i = stringToEnumMap_.find(st);
81	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
79	>	stringToFluxType_["KE"]  = rnemdKE;
80	>	stringToFluxType_["Px"]  = rnemdPx;
81	>	stringToFluxType_["Py"]  = rnemdPy;
82	>	stringToFluxType_["Pz"]  = rnemdPz;
83	>	stringToFluxType_["Pvector"]  = rnemdPvector;
84	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
85	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
86	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
87
88	+	runTime_ = simParams->getRunTime();
89	+	statusTime_ = simParams->getStatusTime();
90
91	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
92	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
93	<	exchangeSum_ = 0.0;
91	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
92	>	evaluator_.loadScriptString(rnemdObjectSelection_);
93	>	seleMan_.setSelectionSet(evaluator_.evaluate());
94	>
95	>	const string methStr = rnemdParams->getMethod();
96	>	bool hasFluxType = rnemdParams->haveFluxType();
97	>
98	>	string fluxStr;
99	>	if (hasFluxType) {
100	>	fluxStr = rnemdParams->getFluxType();
101	>	} else {
102	>	sprintf(painCave.errMsg,
103	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
104	>	"\twhich must be one of the following values:\n"
105	>	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
106	>	"\tmust be set to use RNEMD\n");
107	>	painCave.isFatal = 1;
108	>	painCave.severity = OPENMD_ERROR;
109	>	simError();
110	>	}
111	>
112	>	bool hasKineticFlux = rnemdParams->haveKineticFlux();
113	>	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
114	>	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
115	>	bool hasSlabWidth = rnemdParams->haveSlabWidth();
116	>	bool hasSlabACenter = rnemdParams->haveSlabACenter();
117	>	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
118	>	bool hasOutputFileName = rnemdParams->haveOutputFileName();
119	>	bool hasOutputFields = rnemdParams->haveOutputFields();
120
121	<	#ifndef IS_MPI
122	<	if (simParams->haveSeed()) {
123	<	seedValue = simParams->getSeed();
124	<	randNumGen_ = new SeqRandNumGen(seedValue);
125	<	}else {
126	<	randNumGen_ = new SeqRandNumGen();
127	<	}
128	<	#else
129	<	if (simParams->haveSeed()) {
130	<	seedValue = simParams->getSeed();
131	<	randNumGen_ = new ParallelRandNumGen(seedValue);
132	<	}else {
133	<	randNumGen_ = new ParallelRandNumGen();
134	<	}
135	<	#endif
136	<	}
121	>	map<string, RNEMDMethod>::iterator i;
122	>	i = stringToMethod_.find(methStr);
123	>	if (i != stringToMethod_.end())
124	>	rnemdMethod_ = i->second;
125	>	else {
126	>	sprintf(painCave.errMsg,
127	>	"RNEMD: The current method,\n"
128	>	"\t\t%s is not one of the recognized\n"
129	>	"\texchange methods: Swap, NIVS, or VSS\n",
130	>	methStr.c_str());
131	>	painCave.isFatal = 1;
132	>	painCave.severity = OPENMD_ERROR;
133	>	simError();
134	>	}
135	>
136	>	map<string, RNEMDFluxType>::iterator j;
137	>	j = stringToFluxType_.find(fluxStr);
138	>	if (j != stringToFluxType_.end())
139	>	rnemdFluxType_ = j->second;
140	>	else {
141	>	sprintf(painCave.errMsg,
142	>	"RNEMD: The current fluxType,\n"
143	>	"\t\t%s\n"
144	>	"\tis not one of the recognized flux types.\n",
145	>	fluxStr.c_str());
146	>	painCave.isFatal = 1;
147	>	painCave.severity = OPENMD_ERROR;
148	>	simError();
149	>	}
150	>
151	>	bool methodFluxMismatch = false;
152	>	bool hasCorrectFlux = false;
153	>	switch(rnemdMethod_) {
154	>	case rnemdSwap:
155	>	switch (rnemdFluxType_) {
156	>	case rnemdKE:
157	>	hasCorrectFlux = hasKineticFlux;
158	>	break;
159	>	case rnemdPx:
160	>	case rnemdPy:
161	>	case rnemdPz:
162	>	hasCorrectFlux = hasMomentumFlux;
163	>	break;
164	>	default :
165	>	methodFluxMismatch = true;
166	>	break;
167	>	}
168	>	break;
169	>	case rnemdNIVS:
170	>	switch (rnemdFluxType_) {
171	>	case rnemdKE:
172	>	case rnemdRotKE:
173	>	case rnemdFullKE:
174	>	hasCorrectFlux = hasKineticFlux;
175	>	break;
176	>	case rnemdPx:
177	>	case rnemdPy:
178	>	case rnemdPz:
179	>	hasCorrectFlux = hasMomentumFlux;
180	>	break;
181	>	case rnemdKePx:
182	>	case rnemdKePy:
183	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
184	>	break;
185	>	default:
186	>	methodFluxMismatch = true;
187	>	break;
188	>	}
189	>	break;
190	>	case rnemdVSS:
191	>	switch (rnemdFluxType_) {
192	>	case rnemdKE:
193	>	case rnemdRotKE:
194	>	case rnemdFullKE:
195	>	hasCorrectFlux = hasKineticFlux;
196	>	break;
197	>	case rnemdPx:
198	>	case rnemdPy:
199	>	case rnemdPz:
200	>	hasCorrectFlux = hasMomentumFlux;
201	>	break;
202	>	case rnemdPvector:
203	>	hasCorrectFlux = hasMomentumFluxVector;
204	>	break;
205	>	case rnemdKePx:
206	>	case rnemdKePy:
207	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
208	>	break;
209	>	case rnemdKePvector:
210	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
211	>	break;
212	>	default:
213	>	methodFluxMismatch = true;
214	>	break;
215	>	}
216	>	default:
217	>	break;
218	>	}
219	>
220	>	if (methodFluxMismatch) {
221	>	sprintf(painCave.errMsg,
222	>	"RNEMD: The current method,\n"
223	>	"\t\t%s\n"
224	>	"\tcannot be used with the current flux type, %s\n",
225	>	methStr.c_str(), fluxStr.c_str());
226	>	painCave.isFatal = 1;
227	>	painCave.severity = OPENMD_ERROR;
228	>	simError();
229	>	}
230	>	if (!hasCorrectFlux) {
231	>	sprintf(painCave.errMsg,
232	>	"RNEMD: The current method, %s, and flux type, %s,\n"
233	>	"\tdid not have the correct flux value specified. Options\n"
234	>	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
235	>	methStr.c_str(), fluxStr.c_str());
236	>	painCave.isFatal = 1;
237	>	painCave.severity = OPENMD_ERROR;
238	>	simError();
239	>	}
240	>
241	>	if (hasKineticFlux) {
242	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
243	>	// into  amu / fs^3:
244	>	kineticFlux_ = rnemdParams->getKineticFlux()
245	>	* PhysicalConstants::energyConvert;
246	>	} else {
247	>	kineticFlux_ = 0.0;
248	>	}
249	>	if (hasMomentumFluxVector) {
250	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
251	>	} else {
252	>	momentumFluxVector_ = V3Zero;
253	>	if (hasMomentumFlux) {
254	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
255	>	switch (rnemdFluxType_) {
256	>	case rnemdPx:
257	>	momentumFluxVector_.x() = momentumFlux;
258	>	break;
259	>	case rnemdPy:
260	>	momentumFluxVector_.y() = momentumFlux;
261	>	break;
262	>	case rnemdPz:
263	>	momentumFluxVector_.z() = momentumFlux;
264	>	break;
265	>	case rnemdKePx:
266	>	momentumFluxVector_.x() = momentumFlux;
267	>	break;
268	>	case rnemdKePy:
269	>	momentumFluxVector_.y() = momentumFlux;
270	>	break;
271	>	default:
272	>	break;
273	>	}
274	>	}
275	>	}
276	>
277	>	// do some sanity checking
278	>
279	>	int selectionCount = seleMan_.getSelectionCount();
280	>	int nIntegrable = info->getNGlobalIntegrableObjects();
281	>
282	>	if (selectionCount > nIntegrable) {
283	>	sprintf(painCave.errMsg,
284	>	"RNEMD: The current objectSelection,\n"
285	>	"\t\t%s\n"
286	>	"\thas resulted in %d selected objects.  However,\n"
287	>	"\tthe total number of integrable objects in the system\n"
288	>	"\tis only %d.  This is almost certainly not what you want\n"
289	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
290	>	"\tselector in the selection script!\n",
291	>	rnemdObjectSelection_.c_str(),
292	>	selectionCount, nIntegrable);
293	>	painCave.isFatal = 0;
294	>	painCave.severity = OPENMD_WARNING;
295	>	simError();
296	>	}
297	>
298	>	areaAccumulator_ = new Accumulator();
299	>
300	>	nBins_ = rnemdParams->getOutputBins();
301	>
302	>	data_.resize(RNEMD::ENDINDEX);
303	>	OutputData z;
304	>	z.units =  "Angstroms";
305	>	z.title =  "Z";
306	>	z.dataType = "RealType";
307	>	z.accumulator.reserve(nBins_);
308	>	for (unsigned int i = 0; i < nBins_; i++)
309	>	z.accumulator.push_back( new Accumulator() );
310	>	data_[Z] = z;
311	>	outputMap_["Z"] =  Z;
312	>
313	>	OutputData temperature;
314	>	temperature.units =  "K";
315	>	temperature.title =  "Temperature";
316	>	temperature.dataType = "RealType";
317	>	temperature.accumulator.reserve(nBins_);
318	>	for (unsigned int i = 0; i < nBins_; i++)
319	>	temperature.accumulator.push_back( new Accumulator() );
320	>	data_[TEMPERATURE] = temperature;
321	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
322	>
323	>	OutputData velocity;
324	>	velocity.units = "angstroms/fs";
325	>	velocity.title =  "Velocity";
326	>	velocity.dataType = "Vector3d";
327	>	velocity.accumulator.reserve(nBins_);
328	>	for (unsigned int i = 0; i < nBins_; i++)
329	>	velocity.accumulator.push_back( new VectorAccumulator() );
330	>	data_[VELOCITY] = velocity;
331	>	outputMap_["VELOCITY"] = VELOCITY;
332	>
333	>	OutputData density;
334	>	density.units =  "g cm^-3";
335	>	density.title =  "Density";
336	>	density.dataType = "RealType";
337	>	density.accumulator.reserve(nBins_);
338	>	for (unsigned int i = 0; i < nBins_; i++)
339	>	density.accumulator.push_back( new Accumulator() );
340	>	data_[DENSITY] = density;
341	>	outputMap_["DENSITY"] =  DENSITY;
342	>
343	>	if (hasOutputFields) {
344	>	parseOutputFileFormat(rnemdParams->getOutputFields());
345	>	} else {
346	>	outputMask_.set(Z);
347	>	switch (rnemdFluxType_) {
348	>	case rnemdKE:
349	>	case rnemdRotKE:
350	>	case rnemdFullKE:
351	>	outputMask_.set(TEMPERATURE);
352	>	break;
353	>	case rnemdPx:
354	>	case rnemdPy:
355	>	outputMask_.set(VELOCITY);
356	>	break;
357	>	case rnemdPz:
358	>	case rnemdPvector:
359	>	outputMask_.set(VELOCITY);
360	>	outputMask_.set(DENSITY);
361	>	break;
362	>	case rnemdKePx:
363	>	case rnemdKePy:
364	>	outputMask_.set(TEMPERATURE);
365	>	outputMask_.set(VELOCITY);
366	>	break;
367	>	case rnemdKePvector:
368	>	outputMask_.set(TEMPERATURE);
369	>	outputMask_.set(VELOCITY);
370	>	outputMask_.set(DENSITY);
371	>	break;
372	>	default:
373	>	break;
374	>	}
375	>	}
376	>
377	>	if (hasOutputFileName) {
378	>	rnemdFileName_ = rnemdParams->getOutputFileName();
379	>	} else {
380	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
381	>	}
382	>
383	>	exchangeTime_ = rnemdParams->getExchangeTime();
384	>
385	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
386	>	Mat3x3d hmat = currentSnap_->getHmat();
387
388	+	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
389	+	// Lx, Ly = box dimensions in x & y
390	+	// dt = exchange time interval
391	+	// flux = target flux
392	+
393	+	RealType area = currentSnap_->getXYarea();
394	+	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
395	+	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
396	+
397	+	// total exchange sums are zeroed out at the beginning:
398	+
399	+	kineticExchange_ = 0.0;
400	+	momentumExchange_ = V3Zero;
401	+
402	+	if (hasSlabWidth)
403	+	slabWidth_ = rnemdParams->getSlabWidth();
404	+	else
405	+	slabWidth_ = hmat(2,2) / 10.0;
406	+
407	+	if (hasSlabACenter)
408	+	slabACenter_ = rnemdParams->getSlabACenter();
409	+	else
410	+	slabACenter_ = 0.0;
411	+
412	+	if (hasSlabBCenter)
413	+	slabBCenter_ = rnemdParams->getSlabBCenter();
414	+	else
415	+	slabBCenter_ = hmat(2,2) / 2.0;
416	+
417	+	}
418	+
419		RNEMD::~RNEMD() {
420	<	delete randNumGen_;
420	>	if (!doRNEMD_) return;
421	>	#ifdef IS_MPI
422	>	if (worldRank == 0) {
423	>	#endif
424	>
425	>	writeOutputFile();
426	>
427	>	rnemdFile_.close();
428	>
429	>	#ifdef IS_MPI
430	>	}
431	>	#endif
432		}
433	+
434	+	bool RNEMD::inSlabA(Vector3d pos) {
435	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
436	+	}
437	+	bool RNEMD::inSlabB(Vector3d pos) {
438	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
439	+	}
440
441		void RNEMD::doSwap() {
442	<	std::cerr << "in RNEMD!\n";
443	<	std::cerr << "nBins = " << nBins_ << "\n";
444	<	std::cerr << "swapTime = " << swapTime_ << "\n";
445	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
446	<	std::cerr << "swapType = " << rnemdType_ << "\n";
447	<	}
442	>	if (!doRNEMD_) return;
443	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
444	>	Mat3x3d hmat = currentSnap_->getHmat();
445	>
446	>	seleMan_.setSelectionSet(evaluator_.evaluate());
447	>
448	>	int selei;
449	>	StuntDouble* sd;
450	>	int idx;
451	>
452	>	RealType min_val;
453	>	bool min_found = false;
454	>	StuntDouble* min_sd;
455	>
456	>	RealType max_val;
457	>	bool max_found = false;
458	>	StuntDouble* max_sd;
459	>
460	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
461	>	sd = seleMan_.nextSelected(selei)) {
462	>
463	>	idx = sd->getLocalIndex();
464	>
465	>	Vector3d pos = sd->getPos();
466	>
467	>	// wrap the stuntdouble's position back into the box:
468	>
469	>	if (usePeriodicBoundaryConditions_)
470	>	currentSnap_->wrapVector(pos);
471	>	bool inA = inSlabA(pos);
472	>	bool inB = inSlabB(pos);
473	>
474	>	if (inA || inB) {
475	>
476	>	RealType mass = sd->getMass();
477	>	Vector3d vel = sd->getVel();
478	>	RealType value;
479	>
480	>	switch(rnemdFluxType_) {
481	>	case rnemdKE :
482	>
483	>	value = mass * vel.lengthSquare();
484	>
485	>	if (sd->isDirectional()) {
486	>	Vector3d angMom = sd->getJ();
487	>	Mat3x3d I = sd->getI();
488	>
489	>	if (sd->isLinear()) {
490	>	int i = sd->linearAxis();
491	>	int j = (i + 1) % 3;
492	>	int k = (i + 2) % 3;
493	>	value += angMom[j] * angMom[j] / I(j, j) +
494	>	angMom[k] * angMom[k] / I(k, k);
495	>	} else {
496	>	value += angMom[0]*angMom[0]/I(0, 0)
497	>	+ angMom[1]*angMom[1]/I(1, 1)
498	>	+ angMom[2]*angMom[2]/I(2, 2);
499	>	}
500	>	} //angular momenta exchange enabled
501	>	value *= 0.5;
502	>	break;
503	>	case rnemdPx :
504	>	value = mass * vel[0];
505	>	break;
506	>	case rnemdPy :
507	>	value = mass * vel[1];
508	>	break;
509	>	case rnemdPz :
510	>	value = mass * vel[2];
511	>	break;
512	>	default :
513	>	break;
514	>	}
515	>
516	>	if (inA == 0) {
517	>	if (!min_found) {
518	>	min_val = value;
519	>	min_sd = sd;
520	>	min_found = true;
521	>	} else {
522	>	if (min_val > value) {
523	>	min_val = value;
524	>	min_sd = sd;
525	>	}
526	>	}
527	>	} else {
528	>	if (!max_found) {
529	>	max_val = value;
530	>	max_sd = sd;
531	>	max_found = true;
532	>	} else {
533	>	if (max_val < value) {
534	>	max_val = value;
535	>	max_sd = sd;
536	>	}
537	>	}
538	>	}
539	>	}
540	>	}
541	>
542	>	#ifdef IS_MPI
543	>	int nProc, worldRank;
544	>
545	>	nProc = MPI::COMM_WORLD.Get_size();
546	>	worldRank = MPI::COMM_WORLD.Get_rank();
547	>
548	>	bool my_min_found = min_found;
549	>	bool my_max_found = max_found;
550	>
551	>	// Even if we didn't find a minimum, did someone else?
552	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
553	>	// Even if we didn't find a maximum, did someone else?
554	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
555	>	#endif
556	>
557	>	if (max_found && min_found) {
558	>
559	>	#ifdef IS_MPI
560	>	struct {
561	>	RealType val;
562	>	int rank;
563	>	} max_vals, min_vals;
564	>
565	>	if (my_min_found) {
566	>	min_vals.val = min_val;
567	>	} else {
568	>	min_vals.val = HONKING_LARGE_VALUE;
569	>	}
570	>	min_vals.rank = worldRank;
571	>
572	>	// Who had the minimum?
573	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
574	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
575	>	min_val = min_vals.val;
576	>
577	>	if (my_max_found) {
578	>	max_vals.val = max_val;
579	>	} else {
580	>	max_vals.val = -HONKING_LARGE_VALUE;
581	>	}
582	>	max_vals.rank = worldRank;
583	>
584	>	// Who had the maximum?
585	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
586	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
587	>	max_val = max_vals.val;
588	>	#endif
589	>
590	>	if (min_val < max_val) {
591	>
592	>	#ifdef IS_MPI
593	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
594	>	// I have both maximum and minimum, so proceed like a single
595	>	// processor version:
596	>	#endif
597	>
598	>	Vector3d min_vel = min_sd->getVel();
599	>	Vector3d max_vel = max_sd->getVel();
600	>	RealType temp_vel;
601	>
602	>	switch(rnemdFluxType_) {
603	>	case rnemdKE :
604	>	min_sd->setVel(max_vel);
605	>	max_sd->setVel(min_vel);
606	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
607	>	Vector3d min_angMom = min_sd->getJ();
608	>	Vector3d max_angMom = max_sd->getJ();
609	>	min_sd->setJ(max_angMom);
610	>	max_sd->setJ(min_angMom);
611	>	}//angular momenta exchange enabled
612	>	//assumes same rigid body identity
613	>	break;
614	>	case rnemdPx :
615	>	temp_vel = min_vel.x();
616	>	min_vel.x() = max_vel.x();
617	>	max_vel.x() = temp_vel;
618	>	min_sd->setVel(min_vel);
619	>	max_sd->setVel(max_vel);
620	>	break;
621	>	case rnemdPy :
622	>	temp_vel = min_vel.y();
623	>	min_vel.y() = max_vel.y();
624	>	max_vel.y() = temp_vel;
625	>	min_sd->setVel(min_vel);
626	>	max_sd->setVel(max_vel);
627	>	break;
628	>	case rnemdPz :
629	>	temp_vel = min_vel.z();
630	>	min_vel.z() = max_vel.z();
631	>	max_vel.z() = temp_vel;
632	>	min_sd->setVel(min_vel);
633	>	max_sd->setVel(max_vel);
634	>	break;
635	>	default :
636	>	break;
637	>	}
638	>
639	>	#ifdef IS_MPI
640	>	// the rest of the cases only apply in parallel simulations:
641	>	} else if (max_vals.rank == worldRank) {
642	>	// I had the max, but not the minimum
643	>
644	>	Vector3d min_vel;
645	>	Vector3d max_vel = max_sd->getVel();
646	>	MPI::Status status;
647	>
648	>	// point-to-point swap of the velocity vector
649	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
650	>	min_vals.rank, 0,
651	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
652	>	min_vals.rank, 0, status);
653	>
654	>	switch(rnemdFluxType_) {
655	>	case rnemdKE :
656	>	max_sd->setVel(min_vel);
657	>	//angular momenta exchange enabled
658	>	if (max_sd->isDirectional()) {
659	>	Vector3d min_angMom;
660	>	Vector3d max_angMom = max_sd->getJ();
661	>
662	>	// point-to-point swap of the angular momentum vector
663	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
664	>	MPI::REALTYPE, min_vals.rank, 1,
665	>	min_angMom.getArrayPointer(), 3,
666	>	MPI::REALTYPE, min_vals.rank, 1,
667	>	status);
668	>
669	>	max_sd->setJ(min_angMom);
670	>	}
671	>	break;
672	>	case rnemdPx :
673	>	max_vel.x() = min_vel.x();
674	>	max_sd->setVel(max_vel);
675	>	break;
676	>	case rnemdPy :
677	>	max_vel.y() = min_vel.y();
678	>	max_sd->setVel(max_vel);
679	>	break;
680	>	case rnemdPz :
681	>	max_vel.z() = min_vel.z();
682	>	max_sd->setVel(max_vel);
683	>	break;
684	>	default :
685	>	break;
686	>	}
687	>	} else if (min_vals.rank == worldRank) {
688	>	// I had the minimum but not the maximum:
689	>
690	>	Vector3d max_vel;
691	>	Vector3d min_vel = min_sd->getVel();
692	>	MPI::Status status;
693	>
694	>	// point-to-point swap of the velocity vector
695	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
696	>	max_vals.rank, 0,
697	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
698	>	max_vals.rank, 0, status);
699	>
700	>	switch(rnemdFluxType_) {
701	>	case rnemdKE :
702	>	min_sd->setVel(max_vel);
703	>	//angular momenta exchange enabled
704	>	if (min_sd->isDirectional()) {
705	>	Vector3d min_angMom = min_sd->getJ();
706	>	Vector3d max_angMom;
707	>
708	>	// point-to-point swap of the angular momentum vector
709	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
710	>	MPI::REALTYPE, max_vals.rank, 1,
711	>	max_angMom.getArrayPointer(), 3,
712	>	MPI::REALTYPE, max_vals.rank, 1,
713	>	status);
714	>
715	>	min_sd->setJ(max_angMom);
716	>	}
717	>	break;
718	>	case rnemdPx :
719	>	min_vel.x() = max_vel.x();
720	>	min_sd->setVel(min_vel);
721	>	break;
722	>	case rnemdPy :
723	>	min_vel.y() = max_vel.y();
724	>	min_sd->setVel(min_vel);
725	>	break;
726	>	case rnemdPz :
727	>	min_vel.z() = max_vel.z();
728	>	min_sd->setVel(min_vel);
729	>	break;
730	>	default :
731	>	break;
732	>	}
733	>	}
734	>	#endif
735	>
736	>	switch(rnemdFluxType_) {
737	>	case rnemdKE:
738	>	kineticExchange_ += max_val - min_val;
739	>	break;
740	>	case rnemdPx:
741	>	momentumExchange_.x() += max_val - min_val;
742	>	break;
743	>	case rnemdPy:
744	>	momentumExchange_.y() += max_val - min_val;
745	>	break;
746	>	case rnemdPz:
747	>	momentumExchange_.z() += max_val - min_val;
748	>	break;
749	>	default:
750	>	break;
751	>	}
752	>	} else {
753	>	sprintf(painCave.errMsg,
754	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
755	>	painCave.isFatal = 0;
756	>	painCave.severity = OPENMD_INFO;
757	>	simError();
758	>	failTrialCount_++;
759	>	}
760	>	} else {
761	>	sprintf(painCave.errMsg,
762	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
763	>	"\twas not present in at least one of the two slabs.\n");
764	>	painCave.isFatal = 0;
765	>	painCave.severity = OPENMD_INFO;
766	>	simError();
767	>	failTrialCount_++;
768	>	}
769	>	}
770	>
771	>	void RNEMD::doNIVS() {
772	>	if (!doRNEMD_) return;
773	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
774	>	Mat3x3d hmat = currentSnap_->getHmat();
775	>
776	>	seleMan_.setSelectionSet(evaluator_.evaluate());
777	>
778	>	int selei;
779	>	StuntDouble* sd;
780	>	int idx;
781	>
782	>	vector<StuntDouble*> hotBin, coldBin;
783	>
784	>	RealType Phx = 0.0;
785	>	RealType Phy = 0.0;
786	>	RealType Phz = 0.0;
787	>	RealType Khx = 0.0;
788	>	RealType Khy = 0.0;
789	>	RealType Khz = 0.0;
790	>	RealType Khw = 0.0;
791	>	RealType Pcx = 0.0;
792	>	RealType Pcy = 0.0;
793	>	RealType Pcz = 0.0;
794	>	RealType Kcx = 0.0;
795	>	RealType Kcy = 0.0;
796	>	RealType Kcz = 0.0;
797	>	RealType Kcw = 0.0;
798	>
799	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
800	>	sd = seleMan_.nextSelected(selei)) {
801	>
802	>	idx = sd->getLocalIndex();
803	>
804	>	Vector3d pos = sd->getPos();
805	>
806	>	// wrap the stuntdouble's position back into the box:
807	>
808	>	if (usePeriodicBoundaryConditions_)
809	>	currentSnap_->wrapVector(pos);
810	>
811	>	// which bin is this stuntdouble in?
812	>	bool inA = inSlabA(pos);
813	>	bool inB = inSlabB(pos);
814	>
815	>	if (inA || inB) {
816	>
817	>	RealType mass = sd->getMass();
818	>	Vector3d vel = sd->getVel();
819	>
820	>	if (inA) {
821	>	hotBin.push_back(sd);
822	>	Phx += mass * vel.x();
823	>	Phy += mass * vel.y();
824	>	Phz += mass * vel.z();
825	>	Khx += mass * vel.x() * vel.x();
826	>	Khy += mass * vel.y() * vel.y();
827	>	Khz += mass * vel.z() * vel.z();
828	>	if (sd->isDirectional()) {
829	>	Vector3d angMom = sd->getJ();
830	>	Mat3x3d I = sd->getI();
831	>	if (sd->isLinear()) {
832	>	int i = sd->linearAxis();
833	>	int j = (i + 1) % 3;
834	>	int k = (i + 2) % 3;
835	>	Khw += angMom[j] * angMom[j] / I(j, j) +
836	>	angMom[k] * angMom[k] / I(k, k);
837	>	} else {
838	>	Khw += angMom[0]*angMom[0]/I(0, 0)
839	>	+ angMom[1]*angMom[1]/I(1, 1)
840	>	+ angMom[2]*angMom[2]/I(2, 2);
841	>	}
842	>	}
843	>	} else {
844	>	coldBin.push_back(sd);
845	>	Pcx += mass * vel.x();
846	>	Pcy += mass * vel.y();
847	>	Pcz += mass * vel.z();
848	>	Kcx += mass * vel.x() * vel.x();
849	>	Kcy += mass * vel.y() * vel.y();
850	>	Kcz += mass * vel.z() * vel.z();
851	>	if (sd->isDirectional()) {
852	>	Vector3d angMom = sd->getJ();
853	>	Mat3x3d I = sd->getI();
854	>	if (sd->isLinear()) {
855	>	int i = sd->linearAxis();
856	>	int j = (i + 1) % 3;
857	>	int k = (i + 2) % 3;
858	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
859	>	angMom[k] * angMom[k] / I(k, k);
860	>	} else {
861	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
862	>	+ angMom[1]*angMom[1]/I(1, 1)
863	>	+ angMom[2]*angMom[2]/I(2, 2);
864	>	}
865	>	}
866	>	}
867	>	}
868	>	}
869	>
870	>	Khx *= 0.5;
871	>	Khy *= 0.5;
872	>	Khz *= 0.5;
873	>	Khw *= 0.5;
874	>	Kcx *= 0.5;
875	>	Kcy *= 0.5;
876	>	Kcz *= 0.5;
877	>	Kcw *= 0.5;
878	>
879	>	#ifdef IS_MPI
880	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
881	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
882	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
883	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
884	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
885	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
886	>
887	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
888	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
889	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
890	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
891	>
892	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
893	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
894	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
895	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
896	>	#endif
897	>
898	>	//solve coldBin coeff's first
899	>	RealType px = Pcx / Phx;
900	>	RealType py = Pcy / Phy;
901	>	RealType pz = Pcz / Phz;
902	>	RealType c, x, y, z;
903	>	bool successfulScale = false;
904	>	if ((rnemdFluxType_ == rnemdFullKE) ||
905	>	(rnemdFluxType_ == rnemdRotKE)) {
906	>	//may need sanity check Khw & Kcw > 0
907	>
908	>	if (rnemdFluxType_ == rnemdFullKE) {
909	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
910	>	} else {
911	>	c = 1.0 - kineticTarget_ / Kcw;
912	>	}
913	>
914	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
915	>	c = sqrt(c);
916	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
917	>	//now convert to hotBin coefficient
918	>	RealType w = 0.0;
919	>	if (rnemdFluxType_ ==  rnemdFullKE) {
920	>	x = 1.0 + px * (1.0 - c);
921	>	y = 1.0 + py * (1.0 - c);
922	>	z = 1.0 + pz * (1.0 - c);
923	>	/* more complicated way
924	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
925	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
926	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
927	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
928	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
929	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
930	>	*/
931	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
932	>	(fabs(z - 1.0) < 0.1)) {
933	>	w = 1.0 + (kineticTarget_
934	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
935	>	+ Khz * (1.0 - z * z)) / Khw;
936	>	}//no need to calculate w if x, y or z is out of range
937	>	} else {
938	>	w = 1.0 + kineticTarget_ / Khw;
939	>	}
940	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
941	>	//if w is in the right range, so should be x, y, z.
942	>	vector<StuntDouble*>::iterator sdi;
943	>	Vector3d vel;
944	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
945	>	if (rnemdFluxType_ == rnemdFullKE) {
946	>	vel = (*sdi)->getVel() * c;
947	>	(*sdi)->setVel(vel);
948	>	}
949	>	if ((*sdi)->isDirectional()) {
950	>	Vector3d angMom = (*sdi)->getJ() * c;
951	>	(*sdi)->setJ(angMom);
952	>	}
953	>	}
954	>	w = sqrt(w);
955	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
956	>	//           << "\twh= " << w << endl;
957	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
958	>	if (rnemdFluxType_ == rnemdFullKE) {
959	>	vel = (*sdi)->getVel();
960	>	vel.x() *= x;
961	>	vel.y() *= y;
962	>	vel.z() *= z;
963	>	(*sdi)->setVel(vel);
964	>	}
965	>	if ((*sdi)->isDirectional()) {
966	>	Vector3d angMom = (*sdi)->getJ() * w;
967	>	(*sdi)->setJ(angMom);
968	>	}
969	>	}
970	>	successfulScale = true;
971	>	kineticExchange_ += kineticTarget_;
972	>	}
973	>	}
974	>	} else {
975	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
976	>	switch(rnemdFluxType_) {
977	>	case rnemdKE :
978	>	/* used hotBin coeff's & only scale x & y dimensions
979	>	RealType px = Phx / Pcx;
980	>	RealType py = Phy / Pcy;
981	>	a110 = Khy;
982	>	c0 = - Khx - Khy - kineticTarget_;
983	>	a000 = Khx;
984	>	a111 = Kcy * py * py;
985	>	b11 = -2.0 * Kcy * py * (1.0 + py);
986	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
987	>	b01 = -2.0 * Kcx * px * (1.0 + px);
988	>	a001 = Kcx * px * px;
989	>	*/
990	>	//scale all three dimensions, let c_x = c_y
991	>	a000 = Kcx + Kcy;
992	>	a110 = Kcz;
993	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
994	>	a001 = Khx * px * px + Khy * py * py;
995	>	a111 = Khz * pz * pz;
996	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
997	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
998	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
999	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1000	>	break;
1001	>	case rnemdPx :
1002	>	c = 1 - momentumTarget_.x() / Pcx;
1003	>	a000 = Kcy;
1004	>	a110 = Kcz;
1005	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1006	>	a001 = py * py * Khy;
1007	>	a111 = pz * pz * Khz;
1008	>	b01 = -2.0 * Khy * py * (1.0 + py);
1009	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1010	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1011	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1012	>	break;
1013	>	case rnemdPy :
1014	>	c = 1 - momentumTarget_.y() / Pcy;
1015	>	a000 = Kcx;
1016	>	a110 = Kcz;
1017	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1018	>	a001 = px * px * Khx;
1019	>	a111 = pz * pz * Khz;
1020	>	b01 = -2.0 * Khx * px * (1.0 + px);
1021	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1022	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1023	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1024	>	break;
1025	>	case rnemdPz ://we don't really do this, do we?
1026	>	c = 1 - momentumTarget_.z() / Pcz;
1027	>	a000 = Kcx;
1028	>	a110 = Kcy;
1029	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1030	>	a001 = px * px * Khx;
1031	>	a111 = py * py * Khy;
1032	>	b01 = -2.0 * Khx * px * (1.0 + px);
1033	>	b11 = -2.0 * Khy * py * (1.0 + py);
1034	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1035	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1036	>	break;
1037	>	default :
1038	>	break;
1039	>	}
1040	>
1041	>	RealType v1 = a000 * a111 - a001 * a110;
1042	>	RealType v2 = a000 * b01;
1043	>	RealType v3 = a000 * b11;
1044	>	RealType v4 = a000 * c1 - a001 * c0;
1045	>	RealType v8 = a110 * b01;
1046	>	RealType v10 = - b01 * c0;
1047	>
1048	>	RealType u0 = v2 * v10 - v4 * v4;
1049	>	RealType u1 = -2.0 * v3 * v4;
1050	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1051	>	RealType u3 = -2.0 * v1 * v3;
1052	>	RealType u4 = - v1 * v1;
1053	>	//rescale coefficients
1054	>	RealType maxAbs = fabs(u0);
1055	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1056	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1057	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1058	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1059	>	u0 /= maxAbs;
1060	>	u1 /= maxAbs;
1061	>	u2 /= maxAbs;
1062	>	u3 /= maxAbs;
1063	>	u4 /= maxAbs;
1064	>	//max_element(start, end) is also available.
1065	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1066	>	poly.setCoefficient(4, u4);
1067	>	poly.setCoefficient(3, u3);
1068	>	poly.setCoefficient(2, u2);
1069	>	poly.setCoefficient(1, u1);
1070	>	poly.setCoefficient(0, u0);
1071	>	vector<RealType> realRoots = poly.FindRealRoots();
1072	>
1073	>	vector<RealType>::iterator ri;
1074	>	RealType r1, r2, alpha0;
1075	>	vector<pair<RealType,RealType> > rps;
1076	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1077	>	r2 = *ri;
1078	>	//check if FindRealRoots() give the right answer
1079	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1080	>	sprintf(painCave.errMsg,
1081	>	"RNEMD Warning: polynomial solve seems to have an error!");
1082	>	painCave.isFatal = 0;
1083	>	simError();
1084	>	failRootCount_++;
1085	>	}
1086	>	//might not be useful w/o rescaling coefficients
1087	>	alpha0 = -c0 - a110 * r2 * r2;
1088	>	if (alpha0 >= 0.0) {
1089	>	r1 = sqrt(alpha0 / a000);
1090	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1091	>	< 1e-6)
1092	>	{ rps.push_back(make_pair(r1, r2)); }
1093	>	if (r1 > 1e-6) { //r1 non-negative
1094	>	r1 = -r1;
1095	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1096	>	< 1e-6)
1097	>	{ rps.push_back(make_pair(r1, r2)); }
1098	>	}
1099	>	}
1100	>	}
1101	>	// Consider combining together the solving pair part w/ the searching
1102	>	// best solution part so that we don't need the pairs vector
1103	>	if (!rps.empty()) {
1104	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1105	>	RealType diff;
1106	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1107	>	vector<pair<RealType,RealType> >::iterator rpi;
1108	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1109	>	r1 = (*rpi).first;
1110	>	r2 = (*rpi).second;
1111	>	switch(rnemdFluxType_) {
1112	>	case rnemdKE :
1113	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1115	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1116	>	break;
1117	>	case rnemdPx :
1118	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1119	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120	>	break;
1121	>	case rnemdPy :
1122	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1124	>	break;
1125	>	case rnemdPz :
1126	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1128	>	default :
1129	>	break;
1130	>	}
1131	>	if (diff < smallestDiff) {
1132	>	smallestDiff = diff;
1133	>	bestPair = *rpi;
1134	>	}
1135	>	}
1136	>	#ifdef IS_MPI
1137	>	if (worldRank == 0) {
1138	>	#endif
1139	>	// sprintf(painCave.errMsg,
1140	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1141	>	//         bestPair.first, bestPair.second);
1142	>	// painCave.isFatal = 0;
1143	>	// painCave.severity = OPENMD_INFO;
1144	>	// simError();
1145	>	#ifdef IS_MPI
1146	>	}
1147	>	#endif
1148	>
1149	>	switch(rnemdFluxType_) {
1150	>	case rnemdKE :
1151	>	x = bestPair.first;
1152	>	y = bestPair.first;
1153	>	z = bestPair.second;
1154	>	break;
1155	>	case rnemdPx :
1156	>	x = c;
1157	>	y = bestPair.first;
1158	>	z = bestPair.second;
1159	>	break;
1160	>	case rnemdPy :
1161	>	x = bestPair.first;
1162	>	y = c;
1163	>	z = bestPair.second;
1164	>	break;
1165	>	case rnemdPz :
1166	>	x = bestPair.first;
1167	>	y = bestPair.second;
1168	>	z = c;
1169	>	break;
1170	>	default :
1171	>	break;
1172	>	}
1173	>	vector<StuntDouble*>::iterator sdi;
1174	>	Vector3d vel;
1175	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1176	>	vel = (*sdi)->getVel();
1177	>	vel.x() *= x;
1178	>	vel.y() *= y;
1179	>	vel.z() *= z;
1180	>	(*sdi)->setVel(vel);
1181	>	}
1182	>	//convert to hotBin coefficient
1183	>	x = 1.0 + px * (1.0 - x);
1184	>	y = 1.0 + py * (1.0 - y);
1185	>	z = 1.0 + pz * (1.0 - z);
1186	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1187	>	vel = (*sdi)->getVel();
1188	>	vel.x() *= x;
1189	>	vel.y() *= y;
1190	>	vel.z() *= z;
1191	>	(*sdi)->setVel(vel);
1192	>	}
1193	>	successfulScale = true;
1194	>	switch(rnemdFluxType_) {
1195	>	case rnemdKE :
1196	>	kineticExchange_ += kineticTarget_;
1197	>	break;
1198	>	case rnemdPx :
1199	>	case rnemdPy :
1200	>	case rnemdPz :
1201	>	momentumExchange_ += momentumTarget_;
1202	>	break;
1203	>	default :
1204	>	break;
1205	>	}
1206	>	}
1207	>	}
1208	>	if (successfulScale != true) {
1209	>	sprintf(painCave.errMsg,
1210	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1211	>	"\tthe constraint equations may not exist or there may be\n"
1212	>	"\tno selected objects in one or both slabs.\n");
1213	>	painCave.isFatal = 0;
1214	>	painCave.severity = OPENMD_INFO;
1215	>	simError();
1216	>	failTrialCount_++;
1217	>	}
1218	>	}
1219	>
1220	>	void RNEMD::doVSS() {
1221	>	if (!doRNEMD_) return;
1222	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1223	>	RealType time = currentSnap_->getTime();
1224	>	Mat3x3d hmat = currentSnap_->getHmat();
1225	>
1226	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1227	>
1228	>	int selei;
1229	>	StuntDouble* sd;
1230	>	int idx;
1231	>
1232	>	vector<StuntDouble*> hotBin, coldBin;
1233	>
1234	>	Vector3d Ph(V3Zero);
1235	>	RealType Mh = 0.0;
1236	>	RealType Kh = 0.0;
1237	>	Vector3d Pc(V3Zero);
1238	>	RealType Mc = 0.0;
1239	>	RealType Kc = 0.0;
1240	>
1241	>
1242	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1243	>	sd = seleMan_.nextSelected(selei)) {
1244	>
1245	>	idx = sd->getLocalIndex();
1246	>
1247	>	Vector3d pos = sd->getPos();
1248	>
1249	>	// wrap the stuntdouble's position back into the box:
1250	>
1251	>	if (usePeriodicBoundaryConditions_)
1252	>	currentSnap_->wrapVector(pos);
1253	>
1254	>	// which bin is this stuntdouble in?
1255	>	bool inA = inSlabA(pos);
1256	>	bool inB = inSlabB(pos);
1257	>
1258	>	if (inA || inB) {
1259	>
1260	>	RealType mass = sd->getMass();
1261	>	Vector3d vel = sd->getVel();
1262	>
1263	>	if (inA) {
1264	>	hotBin.push_back(sd);
1265	>	//std::cerr << "before, velocity = " << vel << endl;
1266	>	Ph += mass * vel;
1267	>	//std::cerr << "after, velocity = " << vel << endl;
1268	>	Mh += mass;
1269	>	Kh += mass * vel.lengthSquare();
1270	>	if (rnemdFluxType_ == rnemdFullKE) {
1271	>	if (sd->isDirectional()) {
1272	>	Vector3d angMom = sd->getJ();
1273	>	Mat3x3d I = sd->getI();
1274	>	if (sd->isLinear()) {
1275	>	int i = sd->linearAxis();
1276	>	int j = (i + 1) % 3;
1277	>	int k = (i + 2) % 3;
1278	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1279	>	angMom[k] * angMom[k] / I(k, k);
1280	>	} else {
1281	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1282	>	angMom[1] * angMom[1] / I(1, 1) +
1283	>	angMom[2] * angMom[2] / I(2, 2);
1284	>	}
1285	>	}
1286	>	}
1287	>	} else { //midBin_
1288	>	coldBin.push_back(sd);
1289	>	Pc += mass * vel;
1290	>	Mc += mass;
1291	>	Kc += mass * vel.lengthSquare();
1292	>	if (rnemdFluxType_ == rnemdFullKE) {
1293	>	if (sd->isDirectional()) {
1294	>	Vector3d angMom = sd->getJ();
1295	>	Mat3x3d I = sd->getI();
1296	>	if (sd->isLinear()) {
1297	>	int i = sd->linearAxis();
1298	>	int j = (i + 1) % 3;
1299	>	int k = (i + 2) % 3;
1300	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1301	>	angMom[k] * angMom[k] / I(k, k);
1302	>	} else {
1303	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1304	>	angMom[1] * angMom[1] / I(1, 1) +
1305	>	angMom[2] * angMom[2] / I(2, 2);
1306	>	}
1307	>	}
1308	>	}
1309	>	}
1310	>	}
1311	>	}
1312	>
1313	>	Kh *= 0.5;
1314	>	Kc *= 0.5;
1315	>
1316	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1317	>	//        << "\tKc= " << Kc << endl;
1318	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1319	>
1320	>	#ifdef IS_MPI
1321	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1322	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1323	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1324	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1325	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1326	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1327	>	#endif
1328	>
1329	>	bool successfulExchange = false;
1330	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1331	>	Vector3d vc = Pc / Mc;
1332	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1333	>	Vector3d acrec = -momentumTarget_ / Mc;
1334	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1335	>	if (cNumerator > 0.0) {
1336	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1337	>	if (cDenominator > 0.0) {
1338	>	RealType c = sqrt(cNumerator / cDenominator);
1339	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1340	>	Vector3d vh = Ph / Mh;
1341	>	Vector3d ah = momentumTarget_ / Mh + vh;
1342	>	Vector3d ahrec = momentumTarget_ / Mh;
1343	>	RealType hNumerator = Kh + kineticTarget_
1344	>	- 0.5 * Mh * ah.lengthSquare();
1345	>	if (hNumerator > 0.0) {
1346	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1347	>	if (hDenominator > 0.0) {
1348	>	RealType h = sqrt(hNumerator / hDenominator);
1349	>	if ((h > 0.9) && (h < 1.1)) {
1350	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1351	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1352	>	vector<StuntDouble*>::iterator sdi;
1353	>	Vector3d vel;
1354	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1355	>	//vel = (*sdi)->getVel();
1356	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1357	>	(*sdi)->setVel(vel);
1358	>	if (rnemdFluxType_ == rnemdFullKE) {
1359	>	if ((*sdi)->isDirectional()) {
1360	>	Vector3d angMom = (*sdi)->getJ() * c;
1361	>	(*sdi)->setJ(angMom);
1362	>	}
1363	>	}
1364	>	}
1365	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1366	>	//vel = (*sdi)->getVel();
1367	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1368	>	(*sdi)->setVel(vel);
1369	>	if (rnemdFluxType_ == rnemdFullKE) {
1370	>	if ((*sdi)->isDirectional()) {
1371	>	Vector3d angMom = (*sdi)->getJ() * h;
1372	>	(*sdi)->setJ(angMom);
1373	>	}
1374	>	}
1375	>	}
1376	>	successfulExchange = true;
1377	>	kineticExchange_ += kineticTarget_;
1378	>	momentumExchange_ += momentumTarget_;
1379	>	}
1380	>	}
1381	>	}
1382	>	}
1383	>	}
1384	>	}
1385	>	}
1386	>	if (successfulExchange != true) {
1387	>	sprintf(painCave.errMsg,
1388	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1389	>	"\tthe constraint equations may not exist or there may be\n"
1390	>	"\tno selected objects in one or both slabs.\n");
1391	>	painCave.isFatal = 0;
1392	>	painCave.severity = OPENMD_INFO;
1393	>	simError();
1394	>	failTrialCount_++;
1395	>	}
1396	>	}
1397	>
1398	>	void RNEMD::doRNEMD() {
1399	>	if (!doRNEMD_) return;
1400	>	trialCount_++;
1401	>	switch(rnemdMethod_) {
1402	>	case rnemdSwap:
1403	>	doSwap();
1404	>	break;
1405	>	case rnemdNIVS:
1406	>	doNIVS();
1407	>	break;
1408	>	case rnemdVSS:
1409	>	doVSS();
1410	>	break;
1411	>	case rnemdUnkownMethod:
1412	>	default :
1413	>	break;
1414	>	}
1415	>	}
1416	>
1417	>	void RNEMD::collectData() {
1418	>	if (!doRNEMD_) return;
1419	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1420	>	Mat3x3d hmat = currentSnap_->getHmat();
1421	>
1422	>	areaAccumulator_->add(currentSnap_->getXYarea());
1423	>
1424	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1425	>
1426	>	int selei;
1427	>	StuntDouble* sd;
1428	>	int idx;
1429	>
1430	>	vector<RealType> binMass(nBins_, 0.0);
1431	>	vector<RealType> binPx(nBins_, 0.0);
1432	>	vector<RealType> binPy(nBins_, 0.0);
1433	>	vector<RealType> binPz(nBins_, 0.0);
1434	>	vector<RealType> binKE(nBins_, 0.0);
1435	>	vector<int> binDOF(nBins_, 0);
1436	>	vector<int> binCount(nBins_, 0);
1437	>
1438	>	// alternative approach, track all molecules instead of only those
1439	>	// selected for scaling/swapping:
1440	>	/*
1441	>	SimInfo::MoleculeIterator miter;
1442	>	vector<StuntDouble*>::iterator iiter;
1443	>	Molecule* mol;
1444	>	StuntDouble* sd;
1445	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1446	>	mol = info_->nextMolecule(miter))
1447	>	sd is essentially sd
1448	>	for (sd = mol->beginIntegrableObject(iiter);
1449	>	sd != NULL;
1450	>	sd = mol->nextIntegrableObject(iiter))
1451	>	*/
1452	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453	>	sd = seleMan_.nextSelected(selei)) {
1454	>
1455	>	idx = sd->getLocalIndex();
1456	>
1457	>	Vector3d pos = sd->getPos();
1458	>
1459	>	// wrap the stuntdouble's position back into the box:
1460	>
1461	>	if (usePeriodicBoundaryConditions_)
1462	>	currentSnap_->wrapVector(pos);
1463	>
1464	>
1465	>	// which bin is this stuntdouble in?
1466	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1467	>	// Shift molecules by half a box to have bins start at 0
1468	>	// The modulo operator is used to wrap the case when we are
1469	>	// beyond the end of the bins back to the beginning.
1470	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1471	>
1472	>	RealType mass = sd->getMass();
1473	>	Vector3d vel = sd->getVel();
1474	>
1475	>	binCount[binNo]++;
1476	>	binMass[binNo] += mass;
1477	>	binPx[binNo] += mass*vel.x();
1478	>	binPy[binNo] += mass*vel.y();
1479	>	binPz[binNo] += mass*vel.z();
1480	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1481	>	binDOF[binNo] += 3;
1482	>
1483	>	if (sd->isDirectional()) {
1484	>	Vector3d angMom = sd->getJ();
1485	>	Mat3x3d I = sd->getI();
1486	>	if (sd->isLinear()) {
1487	>	int i = sd->linearAxis();
1488	>	int j = (i + 1) % 3;
1489	>	int k = (i + 2) % 3;
1490	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1491	>	angMom[k] * angMom[k] / I(k, k));
1492	>	binDOF[binNo] += 2;
1493	>	} else {
1494	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1495	>	angMom[1] * angMom[1] / I(1, 1) +
1496	>	angMom[2] * angMom[2] / I(2, 2));
1497	>	binDOF[binNo] += 3;
1498	>	}
1499	>	}
1500	>	}
1501	>
1502	>
1503	>	#ifdef IS_MPI
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1505	>	nBins_, MPI::INT, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1509	>	nBins_, MPI::REALTYPE, MPI::SUM);
1510	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1511	>	nBins_, MPI::REALTYPE, MPI::SUM);
1512	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1513	>	nBins_, MPI::REALTYPE, MPI::SUM);
1514	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1515	>	nBins_, MPI::REALTYPE, MPI::SUM);
1516	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1517	>	nBins_, MPI::INT, MPI::SUM);
1518	>	#endif
1519	>
1520	>	Vector3d vel;
1521	>	RealType den;
1522	>	RealType temp;
1523	>	RealType z;
1524	>	for (int i = 0; i < nBins_; i++) {
1525	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1526	>	vel.x() = binPx[i] / binMass[i];
1527	>	vel.y() = binPy[i] / binMass[i];
1528	>	vel.z() = binPz[i] / binMass[i];
1529	>
1530	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1531	>	/ currentSnap_->getVolume() ;
1532	>
1533	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1534	>	PhysicalConstants::energyConvert);
1535	>
1536	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1537	>	if(outputMask_[j]) {
1538	>	switch(j) {
1539	>	case Z:
1540	>	(data_[j].accumulator[i])->add(z);
1541	>	break;
1542	>	case TEMPERATURE:
1543	>	data_[j].accumulator[i]->add(temp);
1544	>	break;
1545	>	case VELOCITY:
1546	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1547	>	break;
1548	>	case DENSITY:
1549	>	data_[j].accumulator[i]->add(den);
1550	>	break;
1551	>	}
1552	>	}
1553	>	}
1554	>	}
1555	>	}
1556	>
1557	>	void RNEMD::getStarted() {
1558	>	if (!doRNEMD_) return;
1559	>	collectData();
1560	>	writeOutputFile();
1561	>	}
1562	>
1563	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1564	>	if (!doRNEMD_) return;
1565	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1566	>
1567	>	while(tokenizer.hasMoreTokens()) {
1568	>	std::string token(tokenizer.nextToken());
1569	>	toUpper(token);
1570	>	OutputMapType::iterator i = outputMap_.find(token);
1571	>	if (i != outputMap_.end()) {
1572	>	outputMask_.set(i->second);
1573	>	} else {
1574	>	sprintf( painCave.errMsg,
1575	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1576	>	"\toutputFileFormat keyword.\n", token.c_str() );
1577	>	painCave.isFatal = 0;
1578	>	painCave.severity = OPENMD_ERROR;
1579	>	simError();
1580	>	}
1581	>	}
1582	>	}
1583	>
1584	>	void RNEMD::writeOutputFile() {
1585	>	if (!doRNEMD_) return;
1586	>
1587	>	#ifdef IS_MPI
1588	>	// If we're the root node, should we print out the results
1589	>	int worldRank = MPI::COMM_WORLD.Get_rank();
1590	>	if (worldRank == 0) {
1591	>	#endif
1592	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1593	>
1594	>	if( !rnemdFile_ ){
1595	>	sprintf( painCave.errMsg,
1596	>	"Could not open \"%s\" for RNEMD output.\n",
1597	>	rnemdFileName_.c_str());
1598	>	painCave.isFatal = 1;
1599	>	simError();
1600	>	}
1601	>
1602	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1603	>
1604	>	RealType time = currentSnap_->getTime();
1605	>	RealType avgArea;
1606	>	areaAccumulator_->getAverage(avgArea);
1607	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1608	>	/ PhysicalConstants::energyConvert;
1609	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1610	>
1611	>	rnemdFile_ << "#######################################################\n";
1612	>	rnemdFile_ << "# RNEMD {\n";
1613	>
1614	>	map<string, RNEMDMethod>::iterator mi;
1615	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1616	>	if ( (*mi).second == rnemdMethod_)
1617	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1618	>	}
1619	>	map<string, RNEMDFluxType>::iterator fi;
1620	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1621	>	if ( (*fi).second == rnemdFluxType_)
1622	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1623	>	}
1624	>
1625	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1626	>
1627	>	rnemdFile_ << "#    objectSelection = \""
1628	>	<< rnemdObjectSelection_ << "\";\n";
1629	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1630	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1631	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1632	>	rnemdFile_ << "# }\n";
1633	>	rnemdFile_ << "#######################################################\n";
1634	>	rnemdFile_ << "# RNEMD report:\n";
1635	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1636	>	rnemdFile_ << "#     target flux:\n";
1637	>	rnemdFile_ << "#         kinetic = "
1638	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1639	>	<< " (kcal/mol/A^2/fs)\n";
1640	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1641	>	<< " (amu/A/fs^2)\n";
1642	>	rnemdFile_ << "#     target one-time exchanges:\n";
1643	>	rnemdFile_ << "#         kinetic = "
1644	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1645	>	<< " (kcal/mol)\n";
1646	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1647	>	<< " (amu*A/fs)\n";
1648	>	rnemdFile_ << "#     actual exchange totals:\n";
1649	>	rnemdFile_ << "#         kinetic = "
1650	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1651	>	<< " (kcal/mol)\n";
1652	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1653	>	<< " (amu*A/fs)\n";
1654	>	rnemdFile_ << "#     actual flux:\n";
1655	>	rnemdFile_ << "#         kinetic = " << Jz
1656	>	<< " (kcal/mol/A^2/fs)\n";
1657	>	rnemdFile_ << "#         momentum = " << JzP
1658	>	<< " (amu/A/fs^2)\n";
1659	>	rnemdFile_ << "#     exchange statistics:\n";
1660	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1661	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1662	>	if (rnemdMethod_ == rnemdNIVS) {
1663	>	rnemdFile_ << "#         NIVS root-check errors = "
1664	>	<< failRootCount_ << "\n";
1665	>	}
1666	>	rnemdFile_ << "#######################################################\n";
1667	>
1668	>
1669	>
1670	>	//write title
1671	>	rnemdFile_ << "#";
1672	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1673	>	if (outputMask_[i]) {
1674	>	rnemdFile_ << "\t" << data_[i].title <<
1675	>	"(" << data_[i].units << ")";
1676	>	// add some extra tabs for column alignment
1677	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1678	>	}
1679	>	}
1680	>	rnemdFile_ << std::endl;
1681	>
1682	>	rnemdFile_.precision(8);
1683	>
1684	>	for (unsigned int j = 0; j < nBins_; j++) {
1685	>
1686	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1687	>	if (outputMask_[i]) {
1688	>	if (data_[i].dataType == "RealType")
1689	>	writeReal(i,j);
1690	>	else if (data_[i].dataType == "Vector3d")
1691	>	writeVector(i,j);
1692	>	else {
1693	>	sprintf( painCave.errMsg,
1694	>	"RNEMD found an unknown data type for: %s ",
1695	>	data_[i].title.c_str());
1696	>	painCave.isFatal = 1;
1697	>	simError();
1698	>	}
1699	>	}
1700	>	}
1701	>	rnemdFile_ << std::endl;
1702	>
1703	>	}
1704	>
1705	>	rnemdFile_ << "#######################################################\n";
1706	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1707	>	rnemdFile_ << "#######################################################\n";
1708	>
1709	>
1710	>	for (unsigned int j = 0; j < nBins_; j++) {
1711	>	rnemdFile_ << "#";
1712	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1713	>	if (outputMask_[i]) {
1714	>	if (data_[i].dataType == "RealType")
1715	>	writeRealStdDev(i,j);
1716	>	else if (data_[i].dataType == "Vector3d")
1717	>	writeVectorStdDev(i,j);
1718	>	else {
1719	>	sprintf( painCave.errMsg,
1720	>	"RNEMD found an unknown data type for: %s ",
1721	>	data_[i].title.c_str());
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>	}
1726	>	}
1727	>	rnemdFile_ << std::endl;
1728	>
1729	>	}
1730	>
1731	>	rnemdFile_.flush();
1732	>	rnemdFile_.close();
1733	>
1734	>	#ifdef IS_MPI
1735	>	}
1736	>	#endif
1737	>
1738	>	}
1739	>
1740	>	void RNEMD::writeReal(int index, unsigned int bin) {
1741	>	if (!doRNEMD_) return;
1742	>	assert(index >=0 && index < ENDINDEX);
1743	>	assert(bin < nBins_);
1744	>	RealType s;
1745	>
1746	>	data_[index].accumulator[bin]->getAverage(s);
1747	>
1748	>	if (! isinf(s) && ! isnan(s)) {
1749	>	rnemdFile_ << "\t" << s;
1750	>	} else{
1751	>	sprintf( painCave.errMsg,
1752	>	"RNEMD detected a numerical error writing: %s for bin %d",
1753	>	data_[index].title.c_str(), bin);
1754	>	painCave.isFatal = 1;
1755	>	simError();
1756	>	}
1757	>	}
1758	>
1759	>	void RNEMD::writeVector(int index, unsigned int bin) {
1760	>	if (!doRNEMD_) return;
1761	>	assert(index >=0 && index < ENDINDEX);
1762	>	assert(bin < nBins_);
1763	>	Vector3d s;
1764	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1765	>	if (isinf(s[0]) || isnan(s[0]) ||
1766	>	isinf(s[1]) || isnan(s[1]) ||
1767	>	isinf(s[2]) || isnan(s[2]) ) {
1768	>	sprintf( painCave.errMsg,
1769	>	"RNEMD detected a numerical error writing: %s for bin %d",
1770	>	data_[index].title.c_str(), bin);
1771	>	painCave.isFatal = 1;
1772	>	simError();
1773	>	} else {
1774	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1775	>	}
1776	>	}
1777	>
1778	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1779	>	if (!doRNEMD_) return;
1780	>	assert(index >=0 && index < ENDINDEX);
1781	>	assert(bin < nBins_);
1782	>	RealType s;
1783	>
1784	>	data_[index].accumulator[bin]->getStdDev(s);
1785	>
1786	>	if (! isinf(s) && ! isnan(s)) {
1787	>	rnemdFile_ << "\t" << s;
1788	>	} else{
1789	>	sprintf( painCave.errMsg,
1790	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1791	>	data_[index].title.c_str(), bin);
1792	>	painCave.isFatal = 1;
1793	>	simError();
1794	>	}
1795	>	}
1796	>
1797	>	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1798	>	if (!doRNEMD_) return;
1799	>	assert(index >=0 && index < ENDINDEX);
1800	>	assert(bin < nBins_);
1801	>	Vector3d s;
1802	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1803	>	if (isinf(s[0]) || isnan(s[0]) ||
1804	>	isinf(s[1]) || isnan(s[1]) ||
1805	>	isinf(s[2]) || isnan(s[2]) ) {
1806	>	sprintf( painCave.errMsg,
1807	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1808	>	data_[index].title.c_str(), bin);
1809	>	painCave.isFatal = 1;
1810	>	simError();
1811	>	} else {
1812	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1813	>	}
1814	>	}
1815		}
1816	+

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 1777 by gezelter, Thu Aug 9 18:35:09 2012 UTC

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