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root/OpenMD/trunk/src/rnemd/RNEMD.cpp

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1789 by gezelter, Wed Aug 29 20:52:19 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	<	#include "utils/OOPSEConstant.hpp"
50	>	#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52	+	#ifdef IS_MPI
53	+	#include <mpi.h>
54	+	#endif
55
56	<	#ifndef IS_MPI
57	<	#include "math/SeqRandNumGen.hpp"
58	<	#else
53	<	#include "math/ParallelRandNumGen.hpp"
56	>	#ifdef _MSC_VER
57	>	#define isnan(x) _isnan((x))
58	>	#define isinf(x) (!_finite(x) && !_isnan(x))
59		#endif
60
61		#define HONKING_LARGE_VALUE 1.0e10
62
63	<	namespace oopse {
63	>	using namespace std;
64	>	namespace OpenMD {
65
66	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
67	<
68	<	int seedValue;
66	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
67	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
68	>
69	>	trialCount_ = 0;
70	>	failTrialCount_ = 0;
71	>	failRootCount_ = 0;
72	>
73		Globals * simParams = info->getSimParams();
74	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
75
76	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
77	<	stringToEnumMap_["Px"] = rnemdPx;
67	<	stringToEnumMap_["Py"] = rnemdPy;
68	<	stringToEnumMap_["Pz"] = rnemdPz;
69	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
76	>	doRNEMD_ = rnemdParams->getUseRNEMD();
77	>	if (!doRNEMD_) return;
78
79	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
79	>	stringToMethod_["Swap"]  = rnemdSwap;
80	>	stringToMethod_["NIVS"]  = rnemdNIVS;
81	>	stringToMethod_["VSS"]   = rnemdVSS;
82	>
83	>	stringToFluxType_["KE"]  = rnemdKE;
84	>	stringToFluxType_["Px"]  = rnemdPx;
85	>	stringToFluxType_["Py"]  = rnemdPy;
86	>	stringToFluxType_["Pz"]  = rnemdPz;
87	>	stringToFluxType_["Pvector"]  = rnemdPvector;
88	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
89	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
90	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
91	>
92	>	runTime_ = simParams->getRunTime();
93	>	statusTime_ = simParams->getStatusTime();
94	>
95	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
96		evaluator_.loadScriptString(rnemdObjectSelection_);
97		seleMan_.setSelectionSet(evaluator_.evaluate());
98
99	+	const string methStr = rnemdParams->getMethod();
100	+	bool hasFluxType = rnemdParams->haveFluxType();
101
102	+	string fluxStr;
103	+	if (hasFluxType) {
104	+	fluxStr = rnemdParams->getFluxType();
105	+	} else {
106	+	sprintf(painCave.errMsg,
107	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
108	+	"\twhich must be one of the following values:\n"
109	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
110	+	"\tmust be set to use RNEMD\n");
111	+	painCave.isFatal = 1;
112	+	painCave.severity = OPENMD_ERROR;
113	+	simError();
114	+	}
115	+
116	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
117	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
118	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
119	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
120	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
121	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
122	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
123	+	bool hasOutputFields = rnemdParams->haveOutputFields();
124	+
125	+	map<string, RNEMDMethod>::iterator i;
126	+	i = stringToMethod_.find(methStr);
127	+	if (i != stringToMethod_.end())
128	+	rnemdMethod_ = i->second;
129	+	else {
130	+	sprintf(painCave.errMsg,
131	+	"RNEMD: The current method,\n"
132	+	"\t\t%s is not one of the recognized\n"
133	+	"\texchange methods: Swap, NIVS, or VSS\n",
134	+	methStr.c_str());
135	+	painCave.isFatal = 1;
136	+	painCave.severity = OPENMD_ERROR;
137	+	simError();
138	+	}
139	+
140	+	map<string, RNEMDFluxType>::iterator j;
141	+	j = stringToFluxType_.find(fluxStr);
142	+	if (j != stringToFluxType_.end())
143	+	rnemdFluxType_ = j->second;
144	+	else {
145	+	sprintf(painCave.errMsg,
146	+	"RNEMD: The current fluxType,\n"
147	+	"\t\t%s\n"
148	+	"\tis not one of the recognized flux types.\n",
149	+	fluxStr.c_str());
150	+	painCave.isFatal = 1;
151	+	painCave.severity = OPENMD_ERROR;
152	+	simError();
153	+	}
154	+
155	+	bool methodFluxMismatch = false;
156	+	bool hasCorrectFlux = false;
157	+	switch(rnemdMethod_) {
158	+	case rnemdSwap:
159	+	switch (rnemdFluxType_) {
160	+	case rnemdKE:
161	+	hasCorrectFlux = hasKineticFlux;
162	+	break;
163	+	case rnemdPx:
164	+	case rnemdPy:
165	+	case rnemdPz:
166	+	hasCorrectFlux = hasMomentumFlux;
167	+	break;
168	+	default :
169	+	methodFluxMismatch = true;
170	+	break;
171	+	}
172	+	break;
173	+	case rnemdNIVS:
174	+	switch (rnemdFluxType_) {
175	+	case rnemdKE:
176	+	case rnemdRotKE:
177	+	case rnemdFullKE:
178	+	hasCorrectFlux = hasKineticFlux;
179	+	break;
180	+	case rnemdPx:
181	+	case rnemdPy:
182	+	case rnemdPz:
183	+	hasCorrectFlux = hasMomentumFlux;
184	+	break;
185	+	case rnemdKePx:
186	+	case rnemdKePy:
187	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
188	+	break;
189	+	default:
190	+	methodFluxMismatch = true;
191	+	break;
192	+	}
193	+	break;
194	+	case rnemdVSS:
195	+	switch (rnemdFluxType_) {
196	+	case rnemdKE:
197	+	case rnemdRotKE:
198	+	case rnemdFullKE:
199	+	hasCorrectFlux = hasKineticFlux;
200	+	break;
201	+	case rnemdPx:
202	+	case rnemdPy:
203	+	case rnemdPz:
204	+	hasCorrectFlux = hasMomentumFlux;
205	+	break;
206	+	case rnemdPvector:
207	+	hasCorrectFlux = hasMomentumFluxVector;
208	+	break;
209	+	case rnemdKePx:
210	+	case rnemdKePy:
211	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
212	+	break;
213	+	case rnemdKePvector:
214	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
215	+	break;
216	+	default:
217	+	methodFluxMismatch = true;
218	+	break;
219	+	}
220	+	default:
221	+	break;
222	+	}
223	+
224	+	if (methodFluxMismatch) {
225	+	sprintf(painCave.errMsg,
226	+	"RNEMD: The current method,\n"
227	+	"\t\t%s\n"
228	+	"\tcannot be used with the current flux type, %s\n",
229	+	methStr.c_str(), fluxStr.c_str());
230	+	painCave.isFatal = 1;
231	+	painCave.severity = OPENMD_ERROR;
232	+	simError();
233	+	}
234	+	if (!hasCorrectFlux) {
235	+	sprintf(painCave.errMsg,
236	+	"RNEMD: The current method, %s, and flux type, %s,\n"
237	+	"\tdid not have the correct flux value specified. Options\n"
238	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
239	+	methStr.c_str(), fluxStr.c_str());
240	+	painCave.isFatal = 1;
241	+	painCave.severity = OPENMD_ERROR;
242	+	simError();
243	+	}
244	+
245	+	if (hasKineticFlux) {
246	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
247	+	// into  amu / fs^3:
248	+	kineticFlux_ = rnemdParams->getKineticFlux()
249	+	* PhysicalConstants::energyConvert;
250	+	} else {
251	+	kineticFlux_ = 0.0;
252	+	}
253	+	if (hasMomentumFluxVector) {
254	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
255	+	} else {
256	+	momentumFluxVector_ = V3Zero;
257	+	if (hasMomentumFlux) {
258	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
259	+	switch (rnemdFluxType_) {
260	+	case rnemdPx:
261	+	momentumFluxVector_.x() = momentumFlux;
262	+	break;
263	+	case rnemdPy:
264	+	momentumFluxVector_.y() = momentumFlux;
265	+	break;
266	+	case rnemdPz:
267	+	momentumFluxVector_.z() = momentumFlux;
268	+	break;
269	+	case rnemdKePx:
270	+	momentumFluxVector_.x() = momentumFlux;
271	+	break;
272	+	case rnemdKePy:
273	+	momentumFluxVector_.y() = momentumFlux;
274	+	break;
275	+	default:
276	+	break;
277	+	}
278	+	}
279	+	}
280	+
281		// do some sanity checking
282
283		int selectionCount = seleMan_.getSelectionCount();
#	Line 80 | Line 285 | namespace oopse {
285
286		if (selectionCount > nIntegrable) {
287		sprintf(painCave.errMsg,
288	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
288	>	"RNEMD: The current objectSelection,\n"
289		"\t\t%s\n"
290		"\thas resulted in %d selected objects.  However,\n"
291		"\tthe total number of integrable objects in the system\n"
#	Line 90 | Line 295 | namespace oopse {
295		rnemdObjectSelection_.c_str(),
296		selectionCount, nIntegrable);
297		painCave.isFatal = 0;
298	+	painCave.severity = OPENMD_WARNING;
299		simError();
300	+	}
301
302	+	areaAccumulator_ = new Accumulator();
303	+
304	+	nBins_ = rnemdParams->getOutputBins();
305	+
306	+	data_.resize(RNEMD::ENDINDEX);
307	+	OutputData z;
308	+	z.units =  "Angstroms";
309	+	z.title =  "Z";
310	+	z.dataType = "RealType";
311	+	z.accumulator.reserve(nBins_);
312	+	for (int i = 0; i < nBins_; i++)
313	+	z.accumulator.push_back( new Accumulator() );
314	+	data_[Z] = z;
315	+	outputMap_["Z"] =  Z;
316	+
317	+	OutputData temperature;
318	+	temperature.units =  "K";
319	+	temperature.title =  "Temperature";
320	+	temperature.dataType = "RealType";
321	+	temperature.accumulator.reserve(nBins_);
322	+	for (int i = 0; i < nBins_; i++)
323	+	temperature.accumulator.push_back( new Accumulator() );
324	+	data_[TEMPERATURE] = temperature;
325	+	outputMap_["TEMPERATURE"] =  TEMPERATURE;
326	+
327	+	OutputData velocity;
328	+	velocity.units = "angstroms/fs";
329	+	velocity.title =  "Velocity";
330	+	velocity.dataType = "Vector3d";
331	+	velocity.accumulator.reserve(nBins_);
332	+	for (int i = 0; i < nBins_; i++)
333	+	velocity.accumulator.push_back( new VectorAccumulator() );
334	+	data_[VELOCITY] = velocity;
335	+	outputMap_["VELOCITY"] = VELOCITY;
336	+
337	+	OutputData density;
338	+	density.units =  "g cm^-3";
339	+	density.title =  "Density";
340	+	density.dataType = "RealType";
341	+	density.accumulator.reserve(nBins_);
342	+	for (int i = 0; i < nBins_; i++)
343	+	density.accumulator.push_back( new Accumulator() );
344	+	data_[DENSITY] = density;
345	+	outputMap_["DENSITY"] =  DENSITY;
346	+
347	+	if (hasOutputFields) {
348	+	parseOutputFileFormat(rnemdParams->getOutputFields());
349	+	} else {
350	+	outputMask_.set(Z);
351	+	switch (rnemdFluxType_) {
352	+	case rnemdKE:
353	+	case rnemdRotKE:
354	+	case rnemdFullKE:
355	+	outputMask_.set(TEMPERATURE);
356	+	break;
357	+	case rnemdPx:
358	+	case rnemdPy:
359	+	outputMask_.set(VELOCITY);
360	+	break;
361	+	case rnemdPz:
362	+	case rnemdPvector:
363	+	outputMask_.set(VELOCITY);
364	+	outputMask_.set(DENSITY);
365	+	break;
366	+	case rnemdKePx:
367	+	case rnemdKePy:
368	+	outputMask_.set(TEMPERATURE);
369	+	outputMask_.set(VELOCITY);
370	+	break;
371	+	case rnemdKePvector:
372	+	outputMask_.set(TEMPERATURE);
373	+	outputMask_.set(VELOCITY);
374	+	outputMask_.set(DENSITY);
375	+	break;
376	+	default:
377	+	break;
378	+	}
379		}
380	<
381	<	const std::string st = simParams->getRNEMD_swapType();
380	>
381	>	if (hasOutputFileName) {
382	>	rnemdFileName_ = rnemdParams->getOutputFileName();
383	>	} else {
384	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
385	>	}
386
387	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
100	<	i = stringToEnumMap_.find(st);
101	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
387	>	exchangeTime_ = rnemdParams->getExchangeTime();
388
389	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
390	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
391	<	exchangeSum_ = 0.0;
389	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
390	>	Mat3x3d hmat = currentSnap_->getHmat();
391	>
392	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
393	>	// Lx, Ly = box dimensions in x & y
394	>	// dt = exchange time interval
395	>	// flux = target flux
396
397	<	#ifndef IS_MPI
398	<	if (simParams->haveSeed()) {
399	<	seedValue = simParams->getSeed();
400	<	randNumGen_ = new SeqRandNumGen(seedValue);
401	<	}else {
402	<	randNumGen_ = new SeqRandNumGen();
403	<	}
404	<	#else
405	<	if (simParams->haveSeed()) {
406	<	seedValue = simParams->getSeed();
407	<	randNumGen_ = new ParallelRandNumGen(seedValue);
408	<	}else {
409	<	randNumGen_ = new ParallelRandNumGen();
120	<	}
121	<	#endif
122	<	}
397	>	RealType area = currentSnap_->getXYarea();
398	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
399	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
400	>
401	>	// total exchange sums are zeroed out at the beginning:
402	>
403	>	kineticExchange_ = 0.0;
404	>	momentumExchange_ = V3Zero;
405	>
406	>	if (hasSlabWidth)
407	>	slabWidth_ = rnemdParams->getSlabWidth();
408	>	else
409	>	slabWidth_ = hmat(2,2) / 10.0;
410
411	+	if (hasSlabACenter)
412	+	slabACenter_ = rnemdParams->getSlabACenter();
413	+	else
414	+	slabACenter_ = 0.0;
415	+
416	+	if (hasSlabBCenter)
417	+	slabBCenter_ = rnemdParams->getSlabBCenter();
418	+	else
419	+	slabBCenter_ = hmat(2,2) / 2.0;
420	+
421	+	}
422	+
423		RNEMD::~RNEMD() {
424	<	delete randNumGen_;
424	>	if (!doRNEMD_) return;
425	>	#ifdef IS_MPI
426	>	if (worldRank == 0) {
427	>	#endif
428	>
429	>	writeOutputFile();
430	>
431	>	rnemdFile_.close();
432	>
433	>	#ifdef IS_MPI
434	>	}
435	>	#endif
436		}
437	+
438	+	bool RNEMD::inSlabA(Vector3d pos) {
439	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
440	+	}
441	+	bool RNEMD::inSlabB(Vector3d pos) {
442	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
443	+	}
444
445		void RNEMD::doSwap() {
446	<	int midBin = nBins_ / 2;
130	<
446	>	if (!doRNEMD_) return;
447		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
448		Mat3x3d hmat = currentSnap_->getHmat();
449
#	Line 156 | Line 472 | namespace oopse {
472
473		if (usePeriodicBoundaryConditions_)
474		currentSnap_->wrapVector(pos);
475	+	bool inA = inSlabA(pos);
476	+	bool inB = inSlabB(pos);
477
478	<	// which bin is this stuntdouble in?
161	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
162	<
163	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
164	<
165	<
166	<	// if we're in bin 0 or the middleBin
167	<	if (binNo == 0 || binNo == midBin) {
478	>	if (inA || inB) {
479
480		RealType mass = sd->getMass();
481		Vector3d vel = sd->getVel();
482		RealType value;
483	<
484	<	switch(rnemdType_) {
485	<	case rnemdKinetic :
483	>
484	>	switch(rnemdFluxType_) {
485	>	case rnemdKE :
486
487	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
488	<	vel[2]*vel[2]);
489	<	if (sd->isDirectional()) {
487	>	value = mass * vel.lengthSquare();
488	>
489	>	if (sd->isDirectional()) {
490		Vector3d angMom = sd->getJ();
491		Mat3x3d I = sd->getI();
492
493		if (sd->isLinear()) {
494	<	int i = sd->linearAxis();
495	<	int j = (i + 1) % 3;
496	<	int k = (i + 2) % 3;
497	<	value += angMom[j] * angMom[j] / I(j, j) +
498	<	angMom[k] * angMom[k] / I(k, k);
494	>	int i = sd->linearAxis();
495	>	int j = (i + 1) % 3;
496	>	int k = (i + 2) % 3;
497	>	value += angMom[j] * angMom[j] / I(j, j) +
498	>	angMom[k] * angMom[k] / I(k, k);
499		} else {
500	<	value += angMom[0]*angMom[0]/I(0, 0)
501	<	+ angMom[1]*angMom[1]/I(1, 1)
502	<	+ angMom[2]*angMom[2]/I(2, 2);
500	>	value += angMom[0]*angMom[0]/I(0, 0)
501	>	+ angMom[1]*angMom[1]/I(1, 1)
502	>	+ angMom[2]*angMom[2]/I(2, 2);
503		}
504	<	}
505	<	value = value * 0.5 / OOPSEConstant::energyConvert;
504	>	} //angular momenta exchange enabled
505	>	value *= 0.5;
506		break;
507		case rnemdPx :
508		value = mass * vel[0];
#	Line 202 | Line 513 | namespace oopse {
513		case rnemdPz :
514		value = mass * vel[2];
515		break;
205	–	case rnemdUnknown :
516		default :
517		break;
518		}
519
520	<	if (binNo == 0) {
520	>	if (inA == 0) {
521		if (!min_found) {
522		min_val = value;
523		min_sd = sd;
#	Line 218 | Line 528 | namespace oopse {
528		min_sd = sd;
529		}
530		}
531	<	} else {
531	>	} else {
532		if (!max_found) {
533		max_val = value;
534		max_sd = sd;
#	Line 232 | Line 542 | namespace oopse {
542		}
543		}
544		}
545	<
545	>
546		#ifdef IS_MPI
547		int nProc, worldRank;
548	<
548	>
549		nProc = MPI::COMM_WORLD.Get_size();
550		worldRank = MPI::COMM_WORLD.Get_rank();
551
#	Line 243 | Line 553 | namespace oopse {
553		bool my_max_found = max_found;
554
555		// Even if we didn't find a minimum, did someone else?
556	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
556	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
557		// Even if we didn't find a maximum, did someone else?
558	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
559	<	1, MPI::BOOL, MPI::LAND);
560	<
561	<	struct {
562	<	RealType val;
563	<	int rank;
564	<	} max_vals, min_vals;
565	<
566	<	if (min_found) {
567	<	if (my_min_found)
558	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
559	>	#endif
560	>
561	>	if (max_found && min_found) {
562	>
563	>	#ifdef IS_MPI
564	>	struct {
565	>	RealType val;
566	>	int rank;
567	>	} max_vals, min_vals;
568	>
569	>	if (my_min_found) {
570		min_vals.val = min_val;
571	<	else
571	>	} else {
572		min_vals.val = HONKING_LARGE_VALUE;
573	<
573	>	}
574		min_vals.rank = worldRank;
575
576		// Who had the minimum?
577		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
578		1, MPI::REALTYPE_INT, MPI::MINLOC);
579		min_val = min_vals.val;
270	–	}
580
581	<	if (max_found) {
273	<	if (my_max_found)
581	>	if (my_max_found) {
582		max_vals.val = max_val;
583	<	else
583	>	} else {
584		max_vals.val = -HONKING_LARGE_VALUE;
585	<
585	>	}
586		max_vals.rank = worldRank;
587
588		// Who had the maximum?
589		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
590		1, MPI::REALTYPE_INT, MPI::MAXLOC);
591		max_val = max_vals.val;
284	–	}
592		#endif
593	<
594	<	if (max_found && min_found) {
595	<	if (min_val< max_val) {
289	<
593	>
594	>	if (min_val < max_val) {
595	>
596		#ifdef IS_MPI
597		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
598		// I have both maximum and minimum, so proceed like a single
599		// processor version:
600		#endif
601	<	// objects to be swapped: velocity & angular velocity
601	>
602		Vector3d min_vel = min_sd->getVel();
603		Vector3d max_vel = max_sd->getVel();
604		RealType temp_vel;
605
606	<	switch(rnemdType_) {
607	<	case rnemdKinetic :
606	>	switch(rnemdFluxType_) {
607	>	case rnemdKE :
608		min_sd->setVel(max_vel);
609		max_sd->setVel(min_vel);
610	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
610	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
611		Vector3d min_angMom = min_sd->getJ();
612		Vector3d max_angMom = max_sd->getJ();
613		min_sd->setJ(max_angMom);
614		max_sd->setJ(min_angMom);
615	<	}
615	>	}//angular momenta exchange enabled
616	>	//assumes same rigid body identity
617		break;
618		case rnemdPx :
619		temp_vel = min_vel.x();
#	Line 329 | Line 636 | namespace oopse {
636		min_sd->setVel(min_vel);
637		max_sd->setVel(max_vel);
638		break;
332	–	case rnemdUnknown :
639		default :
640		break;
641		}
642	+
643		#ifdef IS_MPI
644		// the rest of the cases only apply in parallel simulations:
645		} else if (max_vals.rank == worldRank) {
#	Line 348 | Line 655 | namespace oopse {
655		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
656		min_vals.rank, 0, status);
657
658	<	switch(rnemdType_) {
659	<	case rnemdKinetic :
658	>	switch(rnemdFluxType_) {
659	>	case rnemdKE :
660		max_sd->setVel(min_vel);
661	<
661	>	//angular momenta exchange enabled
662		if (max_sd->isDirectional()) {
663		Vector3d min_angMom;
664		Vector3d max_angMom = max_sd->getJ();
665	<
665	>
666		// point-to-point swap of the angular momentum vector
667		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
668		MPI::REALTYPE, min_vals.rank, 1,
669		min_angMom.getArrayPointer(), 3,
670		MPI::REALTYPE, min_vals.rank, 1,
671		status);
672	<
672	>
673		max_sd->setJ(min_angMom);
674	<	}
674	>	}
675		break;
676		case rnemdPx :
677		max_vel.x() = min_vel.x();
#	Line 378 | Line 685 | namespace oopse {
685		max_vel.z() = min_vel.z();
686		max_sd->setVel(max_vel);
687		break;
381	–	case rnemdUnknown :
688		default :
689		break;
690		}
#	Line 395 | Line 701 | namespace oopse {
701		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
702		max_vals.rank, 0, status);
703
704	<	switch(rnemdType_) {
705	<	case rnemdKinetic :
704	>	switch(rnemdFluxType_) {
705	>	case rnemdKE :
706		min_sd->setVel(max_vel);
707	<
707	>	//angular momenta exchange enabled
708		if (min_sd->isDirectional()) {
709		Vector3d min_angMom = min_sd->getJ();
710		Vector3d max_angMom;
711	<
711	>
712		// point-to-point swap of the angular momentum vector
713		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
714		MPI::REALTYPE, max_vals.rank, 1,
715		max_angMom.getArrayPointer(), 3,
716		MPI::REALTYPE, max_vals.rank, 1,
717		status);
718	<
718	>
719		min_sd->setJ(max_angMom);
720		}
721		break;
#	Line 425 | Line 731 | namespace oopse {
731		min_vel.z() = max_vel.z();
732		min_sd->setVel(min_vel);
733		break;
428	–	case rnemdUnknown :
734		default :
735		break;
736		}
737		}
738		#endif
739	<	exchangeSum_ += max_val - min_val;
740	<	} else {
741	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
739	>
740	>	switch(rnemdFluxType_) {
741	>	case rnemdKE:
742	>	kineticExchange_ += max_val - min_val;
743	>	break;
744	>	case rnemdPx:
745	>	momentumExchange_.x() += max_val - min_val;
746	>	break;
747	>	case rnemdPy:
748	>	momentumExchange_.y() += max_val - min_val;
749	>	break;
750	>	case rnemdPz:
751	>	momentumExchange_.z() += max_val - min_val;
752	>	break;
753	>	default:
754	>	break;
755	>	}
756	>	} else {
757	>	sprintf(painCave.errMsg,
758	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
759	>	painCave.isFatal = 0;
760	>	painCave.severity = OPENMD_INFO;
761	>	simError();
762	>	failTrialCount_++;
763		}
764		} else {
765	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
766	<	}
767	<
765	>	sprintf(painCave.errMsg,
766	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
767	>	"\twas not present in at least one of the two slabs.\n");
768	>	painCave.isFatal = 0;
769	>	painCave.severity = OPENMD_INFO;
770	>	simError();
771	>	failTrialCount_++;
772	>	}
773		}
774
775	<	void RNEMD::getStatus() {
776	<
775	>	void RNEMD::doNIVS() {
776	>	if (!doRNEMD_) return;
777		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
778		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
779
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
780		seleMan_.setSelectionSet(evaluator_.evaluate());
781
782		int selei;
783		StuntDouble* sd;
784		int idx;
785
786	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
460	<	// being averaged
461	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
462	<	// number of degrees of
463	<	// freedom being averaged
786	>	vector<StuntDouble*> hotBin, coldBin;
787
788	+	RealType Phx = 0.0;
789	+	RealType Phy = 0.0;
790	+	RealType Phz = 0.0;
791	+	RealType Khx = 0.0;
792	+	RealType Khy = 0.0;
793	+	RealType Khz = 0.0;
794	+	RealType Khw = 0.0;
795	+	RealType Pcx = 0.0;
796	+	RealType Pcy = 0.0;
797	+	RealType Pcz = 0.0;
798	+	RealType Kcx = 0.0;
799	+	RealType Kcy = 0.0;
800	+	RealType Kcz = 0.0;
801	+	RealType Kcw = 0.0;
802	+
803		for (sd = seleMan_.beginSelected(selei); sd != NULL;
804		sd = seleMan_.nextSelected(selei)) {
805	<
805	>
806		idx = sd->getLocalIndex();
807	<
807	>
808		Vector3d pos = sd->getPos();
809
810		// wrap the stuntdouble's position back into the box:
811	<
811	>
812		if (usePeriodicBoundaryConditions_)
813		currentSnap_->wrapVector(pos);
814	<
814	>
815		// which bin is this stuntdouble in?
816	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
817	<
480	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
481	<
482	<	RealType mass = sd->getMass();
483	<	Vector3d vel = sd->getVel();
484	<	RealType value;
816	>	bool inA = inSlabA(pos);
817	>	bool inB = inSlabB(pos);
818
819	<	switch(rnemdType_) {
820	<	case rnemdKinetic :
821	<
822	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
823	<	vel[2]*vel[2]);
824	<
825	<	valueCount[binNo] += 3;
826	<	if (sd->isDirectional()) {
827	<	Vector3d angMom = sd->getJ();
828	<	Mat3x3d I = sd->getI();
829	<
830	<	if (sd->isLinear()) {
831	<	int i = sd->linearAxis();
832	<	int j = (i + 1) % 3;
833	<	int k = (i + 2) % 3;
834	<	value += angMom[j] * angMom[j] / I(j, j) +
835	<	angMom[k] * angMom[k] / I(k, k);
819	>	if (inA || inB) {
820	>
821	>	RealType mass = sd->getMass();
822	>	Vector3d vel = sd->getVel();
823	>
824	>	if (inA) {
825	>	hotBin.push_back(sd);
826	>	Phx += mass * vel.x();
827	>	Phy += mass * vel.y();
828	>	Phz += mass * vel.z();
829	>	Khx += mass * vel.x() * vel.x();
830	>	Khy += mass * vel.y() * vel.y();
831	>	Khz += mass * vel.z() * vel.z();
832	>	if (sd->isDirectional()) {
833	>	Vector3d angMom = sd->getJ();
834	>	Mat3x3d I = sd->getI();
835	>	if (sd->isLinear()) {
836	>	int i = sd->linearAxis();
837	>	int j = (i + 1) % 3;
838	>	int k = (i + 2) % 3;
839	>	Khw += angMom[j] * angMom[j] / I(j, j) +
840	>	angMom[k] * angMom[k] / I(k, k);
841	>	} else {
842	>	Khw += angMom[0]*angMom[0]/I(0, 0)
843	>	+ angMom[1]*angMom[1]/I(1, 1)
844	>	+ angMom[2]*angMom[2]/I(2, 2);
845	>	}
846	>	}
847	>	} else {
848	>	coldBin.push_back(sd);
849	>	Pcx += mass * vel.x();
850	>	Pcy += mass * vel.y();
851	>	Pcz += mass * vel.z();
852	>	Kcx += mass * vel.x() * vel.x();
853	>	Kcy += mass * vel.y() * vel.y();
854	>	Kcz += mass * vel.z() * vel.z();
855	>	if (sd->isDirectional()) {
856	>	Vector3d angMom = sd->getJ();
857	>	Mat3x3d I = sd->getI();
858	>	if (sd->isLinear()) {
859	>	int i = sd->linearAxis();
860	>	int j = (i + 1) % 3;
861	>	int k = (i + 2) % 3;
862	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
863	>	angMom[k] * angMom[k] / I(k, k);
864	>	} else {
865	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
866	>	+ angMom[1]*angMom[1]/I(1, 1)
867	>	+ angMom[2]*angMom[2]/I(2, 2);
868	>	}
869	>	}
870	>	}
871	>	}
872	>	}
873	>
874	>	Khx *= 0.5;
875	>	Khy *= 0.5;
876	>	Khz *= 0.5;
877	>	Khw *= 0.5;
878	>	Kcx *= 0.5;
879	>	Kcy *= 0.5;
880	>	Kcz *= 0.5;
881	>	Kcw *= 0.5;
882
883	<	valueCount[binNo] +=2;
883	>	#ifdef IS_MPI
884	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
885	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
886	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
887	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
888	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
889	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
890
891	<	} else {
892	<	value += angMom[0]*angMom[0]/I(0, 0)
893	<	+ angMom[1]*angMom[1]/I(1, 1)
894	<	+ angMom[2]*angMom[2]/I(2, 2);
895	<	valueCount[binNo] +=3;
891	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
892	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
893	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
894	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
895	>
896	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
897	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
898	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
899	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
900	>	#endif
901	>
902	>	//solve coldBin coeff's first
903	>	RealType px = Pcx / Phx;
904	>	RealType py = Pcy / Phy;
905	>	RealType pz = Pcz / Phz;
906	>	RealType c, x, y, z;
907	>	bool successfulScale = false;
908	>	if ((rnemdFluxType_ == rnemdFullKE) ||
909	>	(rnemdFluxType_ == rnemdRotKE)) {
910	>	//may need sanity check Khw & Kcw > 0
911	>
912	>	if (rnemdFluxType_ == rnemdFullKE) {
913	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
914	>	} else {
915	>	c = 1.0 - kineticTarget_ / Kcw;
916	>	}
917	>
918	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
919	>	c = sqrt(c);
920	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
921	>	//now convert to hotBin coefficient
922	>	RealType w = 0.0;
923	>	if (rnemdFluxType_ ==  rnemdFullKE) {
924	>	x = 1.0 + px * (1.0 - c);
925	>	y = 1.0 + py * (1.0 - c);
926	>	z = 1.0 + pz * (1.0 - c);
927	>	/* more complicated way
928	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
929	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
930	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
931	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
932	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
933	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
934	>	*/
935	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
936	>	(fabs(z - 1.0) < 0.1)) {
937	>	w = 1.0 + (kineticTarget_
938	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
939	>	+ Khz * (1.0 - z * z)) / Khw;
940	>	}//no need to calculate w if x, y or z is out of range
941	>	} else {
942	>	w = 1.0 + kineticTarget_ / Khw;
943	>	}
944	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
945	>	//if w is in the right range, so should be x, y, z.
946	>	vector<StuntDouble*>::iterator sdi;
947	>	Vector3d vel;
948	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
949	>	if (rnemdFluxType_ == rnemdFullKE) {
950	>	vel = (*sdi)->getVel() * c;
951	>	(*sdi)->setVel(vel);
952	>	}
953	>	if ((*sdi)->isDirectional()) {
954	>	Vector3d angMom = (*sdi)->getJ() * c;
955	>	(*sdi)->setJ(angMom);
956	>	}
957		}
958	+	w = sqrt(w);
959	+	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
960	+	//           << "\twh= " << w << endl;
961	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
962	+	if (rnemdFluxType_ == rnemdFullKE) {
963	+	vel = (*sdi)->getVel();
964	+	vel.x() *= x;
965	+	vel.y() *= y;
966	+	vel.z() *= z;
967	+	(*sdi)->setVel(vel);
968	+	}
969	+	if ((*sdi)->isDirectional()) {
970	+	Vector3d angMom = (*sdi)->getJ() * w;
971	+	(*sdi)->setJ(angMom);
972	+	}
973	+	}
974	+	successfulScale = true;
975	+	kineticExchange_ += kineticTarget_;
976		}
977	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
978	<
979	<	break;
980	<	case rnemdPx :
981	<	value = mass * vel[0];
982	<	valueCount[binNo]++;
977	>	}
978	>	} else {
979	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
980	>	switch(rnemdFluxType_) {
981	>	case rnemdKE :
982	>	/* used hotBin coeff's & only scale x & y dimensions
983	>	RealType px = Phx / Pcx;
984	>	RealType py = Phy / Pcy;
985	>	a110 = Khy;
986	>	c0 = - Khx - Khy - kineticTarget_;
987	>	a000 = Khx;
988	>	a111 = Kcy * py * py;
989	>	b11 = -2.0 * Kcy * py * (1.0 + py);
990	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
991	>	b01 = -2.0 * Kcx * px * (1.0 + px);
992	>	a001 = Kcx * px * px;
993	>	*/
994	>	//scale all three dimensions, let c_x = c_y
995	>	a000 = Kcx + Kcy;
996	>	a110 = Kcz;
997	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
998	>	a001 = Khx * px * px + Khy * py * py;
999	>	a111 = Khz * pz * pz;
1000	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1001	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1002	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1003	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1004		break;
1005	+	case rnemdPx :
1006	+	c = 1 - momentumTarget_.x() / Pcx;
1007	+	a000 = Kcy;
1008	+	a110 = Kcz;
1009	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1010	+	a001 = py * py * Khy;
1011	+	a111 = pz * pz * Khz;
1012	+	b01 = -2.0 * Khy * py * (1.0 + py);
1013	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
1014	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1015	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1016	+	break;
1017		case rnemdPy :
1018	<	value = mass * vel[1];
1019	<	valueCount[binNo]++;
1018	>	c = 1 - momentumTarget_.y() / Pcy;
1019	>	a000 = Kcx;
1020	>	a110 = Kcz;
1021	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1022	>	a001 = px * px * Khx;
1023	>	a111 = pz * pz * Khz;
1024	>	b01 = -2.0 * Khx * px * (1.0 + px);
1025	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1026	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1027	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1028		break;
1029	<	case rnemdPz :
1030	<	value = mass * vel[2];
1031	<	valueCount[binNo]++;
1029	>	case rnemdPz ://we don't really do this, do we?
1030	>	c = 1 - momentumTarget_.z() / Pcz;
1031	>	a000 = Kcx;
1032	>	a110 = Kcy;
1033	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1034	>	a001 = px * px * Khx;
1035	>	a111 = py * py * Khy;
1036	>	b01 = -2.0 * Khx * px * (1.0 + px);
1037	>	b11 = -2.0 * Khy * py * (1.0 + py);
1038	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1039	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1040		break;
528	–	case rnemdUnknown :
1041		default :
1042		break;
1043		}
1044	<	valueHist[binNo] += value;
1044	>
1045	>	RealType v1 = a000 * a111 - a001 * a110;
1046	>	RealType v2 = a000 * b01;
1047	>	RealType v3 = a000 * b11;
1048	>	RealType v4 = a000 * c1 - a001 * c0;
1049	>	RealType v8 = a110 * b01;
1050	>	RealType v10 = - b01 * c0;
1051	>
1052	>	RealType u0 = v2 * v10 - v4 * v4;
1053	>	RealType u1 = -2.0 * v3 * v4;
1054	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1055	>	RealType u3 = -2.0 * v1 * v3;
1056	>	RealType u4 = - v1 * v1;
1057	>	//rescale coefficients
1058	>	RealType maxAbs = fabs(u0);
1059	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1060	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1061	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1062	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1063	>	u0 /= maxAbs;
1064	>	u1 /= maxAbs;
1065	>	u2 /= maxAbs;
1066	>	u3 /= maxAbs;
1067	>	u4 /= maxAbs;
1068	>	//max_element(start, end) is also available.
1069	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1070	>	poly.setCoefficient(4, u4);
1071	>	poly.setCoefficient(3, u3);
1072	>	poly.setCoefficient(2, u2);
1073	>	poly.setCoefficient(1, u1);
1074	>	poly.setCoefficient(0, u0);
1075	>	vector<RealType> realRoots = poly.FindRealRoots();
1076	>
1077	>	vector<RealType>::iterator ri;
1078	>	RealType r1, r2, alpha0;
1079	>	vector<pair<RealType,RealType> > rps;
1080	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1081	>	r2 = *ri;
1082	>	//check if FindRealRoots() give the right answer
1083	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1084	>	sprintf(painCave.errMsg,
1085	>	"RNEMD Warning: polynomial solve seems to have an error!");
1086	>	painCave.isFatal = 0;
1087	>	simError();
1088	>	failRootCount_++;
1089	>	}
1090	>	//might not be useful w/o rescaling coefficients
1091	>	alpha0 = -c0 - a110 * r2 * r2;
1092	>	if (alpha0 >= 0.0) {
1093	>	r1 = sqrt(alpha0 / a000);
1094	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1095	>	< 1e-6)
1096	>	{ rps.push_back(make_pair(r1, r2)); }
1097	>	if (r1 > 1e-6) { //r1 non-negative
1098	>	r1 = -r1;
1099	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1100	>	< 1e-6)
1101	>	{ rps.push_back(make_pair(r1, r2)); }
1102	>	}
1103	>	}
1104	>	}
1105	>	// Consider combining together the solving pair part w/ the searching
1106	>	// best solution part so that we don't need the pairs vector
1107	>	if (!rps.empty()) {
1108	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1109	>	RealType diff;
1110	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1111	>	vector<pair<RealType,RealType> >::iterator rpi;
1112	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1113	>	r1 = (*rpi).first;
1114	>	r2 = (*rpi).second;
1115	>	switch(rnemdFluxType_) {
1116	>	case rnemdKE :
1117	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1119	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120	>	break;
1121	>	case rnemdPx :
1122	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1124	>	break;
1125	>	case rnemdPy :
1126	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1128	>	break;
1129	>	case rnemdPz :
1130	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1131	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1132	>	default :
1133	>	break;
1134	>	}
1135	>	if (diff < smallestDiff) {
1136	>	smallestDiff = diff;
1137	>	bestPair = *rpi;
1138	>	}
1139	>	}
1140	>	#ifdef IS_MPI
1141	>	if (worldRank == 0) {
1142	>	#endif
1143	>	// sprintf(painCave.errMsg,
1144	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1145	>	//         bestPair.first, bestPair.second);
1146	>	// painCave.isFatal = 0;
1147	>	// painCave.severity = OPENMD_INFO;
1148	>	// simError();
1149	>	#ifdef IS_MPI
1150	>	}
1151	>	#endif
1152	>
1153	>	switch(rnemdFluxType_) {
1154	>	case rnemdKE :
1155	>	x = bestPair.first;
1156	>	y = bestPair.first;
1157	>	z = bestPair.second;
1158	>	break;
1159	>	case rnemdPx :
1160	>	x = c;
1161	>	y = bestPair.first;
1162	>	z = bestPair.second;
1163	>	break;
1164	>	case rnemdPy :
1165	>	x = bestPair.first;
1166	>	y = c;
1167	>	z = bestPair.second;
1168	>	break;
1169	>	case rnemdPz :
1170	>	x = bestPair.first;
1171	>	y = bestPair.second;
1172	>	z = c;
1173	>	break;
1174	>	default :
1175	>	break;
1176	>	}
1177	>	vector<StuntDouble*>::iterator sdi;
1178	>	Vector3d vel;
1179	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1180	>	vel = (*sdi)->getVel();
1181	>	vel.x() *= x;
1182	>	vel.y() *= y;
1183	>	vel.z() *= z;
1184	>	(*sdi)->setVel(vel);
1185	>	}
1186	>	//convert to hotBin coefficient
1187	>	x = 1.0 + px * (1.0 - x);
1188	>	y = 1.0 + py * (1.0 - y);
1189	>	z = 1.0 + pz * (1.0 - z);
1190	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1191	>	vel = (*sdi)->getVel();
1192	>	vel.x() *= x;
1193	>	vel.y() *= y;
1194	>	vel.z() *= z;
1195	>	(*sdi)->setVel(vel);
1196	>	}
1197	>	successfulScale = true;
1198	>	switch(rnemdFluxType_) {
1199	>	case rnemdKE :
1200	>	kineticExchange_ += kineticTarget_;
1201	>	break;
1202	>	case rnemdPx :
1203	>	case rnemdPy :
1204	>	case rnemdPz :
1205	>	momentumExchange_ += momentumTarget_;
1206	>	break;
1207	>	default :
1208	>	break;
1209	>	}
1210	>	}
1211		}
1212	+	if (successfulScale != true) {
1213	+	sprintf(painCave.errMsg,
1214	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1215	+	"\tthe constraint equations may not exist or there may be\n"
1216	+	"\tno selected objects in one or both slabs.\n");
1217	+	painCave.isFatal = 0;
1218	+	painCave.severity = OPENMD_INFO;
1219	+	simError();
1220	+	failTrialCount_++;
1221	+	}
1222	+	}
1223
1224	<	#ifdef IS_MPI
1224	>	void RNEMD::doVSS() {
1225	>	if (!doRNEMD_) return;
1226	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1227	>	RealType time = currentSnap_->getTime();
1228	>	Mat3x3d hmat = currentSnap_->getHmat();
1229
1230	<	// all processors have the same number of bins, and STL vectors pack their
538	<	// arrays, so in theory, this should be safe:
1230	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1231
1232	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1233	<	nBins_, MPI::REALTYPE, MPI::SUM);
1234	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
543	<	nBins_, MPI::INT, MPI::SUM);
1232	>	int selei;
1233	>	StuntDouble* sd;
1234	>	int idx;
1235
1236	+	vector<StuntDouble*> hotBin, coldBin;
1237	+
1238	+	Vector3d Ph(V3Zero);
1239	+	RealType Mh = 0.0;
1240	+	RealType Kh = 0.0;
1241	+	Vector3d Pc(V3Zero);
1242	+	RealType Mc = 0.0;
1243	+	RealType Kc = 0.0;
1244	+
1245	+
1246	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1247	+	sd = seleMan_.nextSelected(selei)) {
1248	+
1249	+	idx = sd->getLocalIndex();
1250	+
1251	+	Vector3d pos = sd->getPos();
1252	+
1253	+	// wrap the stuntdouble's position back into the box:
1254	+
1255	+	if (usePeriodicBoundaryConditions_)
1256	+	currentSnap_->wrapVector(pos);
1257	+
1258	+	// which bin is this stuntdouble in?
1259	+	bool inA = inSlabA(pos);
1260	+	bool inB = inSlabB(pos);
1261	+
1262	+	if (inA || inB) {
1263	+
1264	+	RealType mass = sd->getMass();
1265	+	Vector3d vel = sd->getVel();
1266	+
1267	+	if (inA) {
1268	+	hotBin.push_back(sd);
1269	+	//std::cerr << "before, velocity = " << vel << endl;
1270	+	Ph += mass * vel;
1271	+	//std::cerr << "after, velocity = " << vel << endl;
1272	+	Mh += mass;
1273	+	Kh += mass * vel.lengthSquare();
1274	+	if (rnemdFluxType_ == rnemdFullKE) {
1275	+	if (sd->isDirectional()) {
1276	+	Vector3d angMom = sd->getJ();
1277	+	Mat3x3d I = sd->getI();
1278	+	if (sd->isLinear()) {
1279	+	int i = sd->linearAxis();
1280	+	int j = (i + 1) % 3;
1281	+	int k = (i + 2) % 3;
1282	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1283	+	angMom[k] * angMom[k] / I(k, k);
1284	+	} else {
1285	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1286	+	angMom[1] * angMom[1] / I(1, 1) +
1287	+	angMom[2] * angMom[2] / I(2, 2);
1288	+	}
1289	+	}
1290	+	}
1291	+	} else { //midBin_
1292	+	coldBin.push_back(sd);
1293	+	Pc += mass * vel;
1294	+	Mc += mass;
1295	+	Kc += mass * vel.lengthSquare();
1296	+	if (rnemdFluxType_ == rnemdFullKE) {
1297	+	if (sd->isDirectional()) {
1298	+	Vector3d angMom = sd->getJ();
1299	+	Mat3x3d I = sd->getI();
1300	+	if (sd->isLinear()) {
1301	+	int i = sd->linearAxis();
1302	+	int j = (i + 1) % 3;
1303	+	int k = (i + 2) % 3;
1304	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1305	+	angMom[k] * angMom[k] / I(k, k);
1306	+	} else {
1307	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1308	+	angMom[1] * angMom[1] / I(1, 1) +
1309	+	angMom[2] * angMom[2] / I(2, 2);
1310	+	}
1311	+	}
1312	+	}
1313	+	}
1314	+	}
1315	+	}
1316	+
1317	+	Kh *= 0.5;
1318	+	Kc *= 0.5;
1319	+
1320	+	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1321	+	//        << "\tKc= " << Kc << endl;
1322	+	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1323	+
1324	+	#ifdef IS_MPI
1325	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1326	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1327	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1328	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1329	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1330	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1331	+	#endif
1332	+
1333	+	bool successfulExchange = false;
1334	+	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1335	+	Vector3d vc = Pc / Mc;
1336	+	Vector3d ac = -momentumTarget_ / Mc + vc;
1337	+	Vector3d acrec = -momentumTarget_ / Mc;
1338	+	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1339	+	if (cNumerator > 0.0) {
1340	+	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1341	+	if (cDenominator > 0.0) {
1342	+	RealType c = sqrt(cNumerator / cDenominator);
1343	+	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1344	+	Vector3d vh = Ph / Mh;
1345	+	Vector3d ah = momentumTarget_ / Mh + vh;
1346	+	Vector3d ahrec = momentumTarget_ / Mh;
1347	+	RealType hNumerator = Kh + kineticTarget_
1348	+	- 0.5 * Mh * ah.lengthSquare();
1349	+	if (hNumerator > 0.0) {
1350	+	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1351	+	if (hDenominator > 0.0) {
1352	+	RealType h = sqrt(hNumerator / hDenominator);
1353	+	if ((h > 0.9) && (h < 1.1)) {
1354	+	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1355	+	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1356	+	vector<StuntDouble*>::iterator sdi;
1357	+	Vector3d vel;
1358	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1359	+	//vel = (*sdi)->getVel();
1360	+	vel = ((*sdi)->getVel() - vc) * c + ac;
1361	+	(*sdi)->setVel(vel);
1362	+	if (rnemdFluxType_ == rnemdFullKE) {
1363	+	if ((*sdi)->isDirectional()) {
1364	+	Vector3d angMom = (*sdi)->getJ() * c;
1365	+	(*sdi)->setJ(angMom);
1366	+	}
1367	+	}
1368	+	}
1369	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1370	+	//vel = (*sdi)->getVel();
1371	+	vel = ((*sdi)->getVel() - vh) * h + ah;
1372	+	(*sdi)->setVel(vel);
1373	+	if (rnemdFluxType_ == rnemdFullKE) {
1374	+	if ((*sdi)->isDirectional()) {
1375	+	Vector3d angMom = (*sdi)->getJ() * h;
1376	+	(*sdi)->setJ(angMom);
1377	+	}
1378	+	}
1379	+	}
1380	+	successfulExchange = true;
1381	+	kineticExchange_ += kineticTarget_;
1382	+	momentumExchange_ += momentumTarget_;
1383	+	}
1384	+	}
1385	+	}
1386	+	}
1387	+	}
1388	+	}
1389	+	}
1390	+	if (successfulExchange != true) {
1391	+	sprintf(painCave.errMsg,
1392	+	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1393	+	"\tthe constraint equations may not exist or there may be\n"
1394	+	"\tno selected objects in one or both slabs.\n");
1395	+	painCave.isFatal = 0;
1396	+	painCave.severity = OPENMD_INFO;
1397	+	simError();
1398	+	failTrialCount_++;
1399	+	}
1400	+	}
1401	+
1402	+	void RNEMD::doRNEMD() {
1403	+	if (!doRNEMD_) return;
1404	+	trialCount_++;
1405	+	switch(rnemdMethod_) {
1406	+	case rnemdSwap:
1407	+	doSwap();
1408	+	break;
1409	+	case rnemdNIVS:
1410	+	doNIVS();
1411	+	break;
1412	+	case rnemdVSS:
1413	+	doVSS();
1414	+	break;
1415	+	case rnemdUnkownMethod:
1416	+	default :
1417	+	break;
1418	+	}
1419	+	}
1420	+
1421	+	void RNEMD::collectData() {
1422	+	if (!doRNEMD_) return;
1423	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1424	+	Mat3x3d hmat = currentSnap_->getHmat();
1425	+
1426	+	areaAccumulator_->add(currentSnap_->getXYarea());
1427	+
1428	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1429	+
1430	+	int selei;
1431	+	StuntDouble* sd;
1432	+	int idx;
1433	+
1434	+	vector<RealType> binMass(nBins_, 0.0);
1435	+	vector<RealType> binPx(nBins_, 0.0);
1436	+	vector<RealType> binPy(nBins_, 0.0);
1437	+	vector<RealType> binPz(nBins_, 0.0);
1438	+	vector<RealType> binKE(nBins_, 0.0);
1439	+	vector<int> binDOF(nBins_, 0);
1440	+	vector<int> binCount(nBins_, 0);
1441	+
1442	+	// alternative approach, track all molecules instead of only those
1443	+	// selected for scaling/swapping:
1444	+	/*
1445	+	SimInfo::MoleculeIterator miter;
1446	+	vector<StuntDouble*>::iterator iiter;
1447	+	Molecule* mol;
1448	+	StuntDouble* sd;
1449	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1450	+	mol = info_->nextMolecule(miter))
1451	+	sd is essentially sd
1452	+	for (sd = mol->beginIntegrableObject(iiter);
1453	+	sd != NULL;
1454	+	sd = mol->nextIntegrableObject(iiter))
1455	+	*/
1456	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1457	+	sd = seleMan_.nextSelected(selei)) {
1458	+
1459	+	idx = sd->getLocalIndex();
1460	+
1461	+	Vector3d pos = sd->getPos();
1462	+
1463	+	// wrap the stuntdouble's position back into the box:
1464	+
1465	+	if (usePeriodicBoundaryConditions_)
1466	+	currentSnap_->wrapVector(pos);
1467	+
1468	+
1469	+	// which bin is this stuntdouble in?
1470	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1471	+	// Shift molecules by half a box to have bins start at 0
1472	+	// The modulo operator is used to wrap the case when we are
1473	+	// beyond the end of the bins back to the beginning.
1474	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1475	+
1476	+	RealType mass = sd->getMass();
1477	+	Vector3d vel = sd->getVel();
1478	+
1479	+	binCount[binNo]++;
1480	+	binMass[binNo] += mass;
1481	+	binPx[binNo] += mass*vel.x();
1482	+	binPy[binNo] += mass*vel.y();
1483	+	binPz[binNo] += mass*vel.z();
1484	+	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1485	+	binDOF[binNo] += 3;
1486	+
1487	+	if (sd->isDirectional()) {
1488	+	Vector3d angMom = sd->getJ();
1489	+	Mat3x3d I = sd->getI();
1490	+	if (sd->isLinear()) {
1491	+	int i = sd->linearAxis();
1492	+	int j = (i + 1) % 3;
1493	+	int k = (i + 2) % 3;
1494	+	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1495	+	angMom[k] * angMom[k] / I(k, k));
1496	+	binDOF[binNo] += 2;
1497	+	} else {
1498	+	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1499	+	angMom[1] * angMom[1] / I(1, 1) +
1500	+	angMom[2] * angMom[2] / I(2, 2));
1501	+	binDOF[binNo] += 3;
1502	+	}
1503	+	}
1504	+	}
1505	+
1506	+
1507	+	#ifdef IS_MPI
1508	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1509	+	nBins_, MPI::INT, MPI::SUM);
1510	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1511	+	nBins_, MPI::REALTYPE, MPI::SUM);
1512	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1513	+	nBins_, MPI::REALTYPE, MPI::SUM);
1514	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1515	+	nBins_, MPI::REALTYPE, MPI::SUM);
1516	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1517	+	nBins_, MPI::REALTYPE, MPI::SUM);
1518	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1519	+	nBins_, MPI::REALTYPE, MPI::SUM);
1520	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1521	+	nBins_, MPI::INT, MPI::SUM);
1522	+	#endif
1523	+
1524	+	Vector3d vel;
1525	+	RealType den;
1526	+	RealType temp;
1527	+	RealType z;
1528	+	for (int i = 0; i < nBins_; i++) {
1529	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1530	+	vel.x() = binPx[i] / binMass[i];
1531	+	vel.y() = binPy[i] / binMass[i];
1532	+	vel.z() = binPz[i] / binMass[i];
1533	+
1534	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1535	+	/ currentSnap_->getVolume() ;
1536	+
1537	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1538	+	PhysicalConstants::energyConvert);
1539	+
1540	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1541	+	if(outputMask_[j]) {
1542	+	switch(j) {
1543	+	case Z:
1544	+	(data_[j].accumulator[i])->add(z);
1545	+	break;
1546	+	case TEMPERATURE:
1547	+	data_[j].accumulator[i]->add(temp);
1548	+	break;
1549	+	case VELOCITY:
1550	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1551	+	break;
1552	+	case DENSITY:
1553	+	data_[j].accumulator[i]->add(den);
1554	+	break;
1555	+	}
1556	+	}
1557	+	}
1558	+	}
1559	+	}
1560	+
1561	+	void RNEMD::getStarted() {
1562	+	if (!doRNEMD_) return;
1563	+	collectData();
1564	+	writeOutputFile();
1565	+	}
1566	+
1567	+	void RNEMD::parseOutputFileFormat(const std::string& format) {
1568	+	if (!doRNEMD_) return;
1569	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1570	+
1571	+	while(tokenizer.hasMoreTokens()) {
1572	+	std::string token(tokenizer.nextToken());
1573	+	toUpper(token);
1574	+	OutputMapType::iterator i = outputMap_.find(token);
1575	+	if (i != outputMap_.end()) {
1576	+	outputMask_.set(i->second);
1577	+	} else {
1578	+	sprintf( painCave.errMsg,
1579	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1580	+	"\toutputFileFormat keyword.\n", token.c_str() );
1581	+	painCave.isFatal = 0;
1582	+	painCave.severity = OPENMD_ERROR;
1583	+	simError();
1584	+	}
1585	+	}
1586	+	}
1587	+
1588	+	void RNEMD::writeOutputFile() {
1589	+	if (!doRNEMD_) return;
1590	+
1591	+	#ifdef IS_MPI
1592		// If we're the root node, should we print out the results
1593		int worldRank = MPI::COMM_WORLD.Get_rank();
1594		if (worldRank == 0) {
1595		#endif
1596	<
550	<	std::cout << time;
551	<	for (int j = 0; j < nBins_; j++)
552	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
553	<	std::cout << "\n";
1596	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1597
1598	+	if( !rnemdFile_ ){
1599	+	sprintf( painCave.errMsg,
1600	+	"Could not open \"%s\" for RNEMD output.\n",
1601	+	rnemdFileName_.c_str());
1602	+	painCave.isFatal = 1;
1603	+	simError();
1604	+	}
1605	+
1606	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1607	+
1608	+	RealType time = currentSnap_->getTime();
1609	+	RealType avgArea;
1610	+	areaAccumulator_->getAverage(avgArea);
1611	+	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1612	+	/ PhysicalConstants::energyConvert;
1613	+	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1614	+
1615	+	rnemdFile_ << "#######################################################\n";
1616	+	rnemdFile_ << "# RNEMD {\n";
1617	+
1618	+	map<string, RNEMDMethod>::iterator mi;
1619	+	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1620	+	if ( (*mi).second == rnemdMethod_)
1621	+	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1622	+	}
1623	+	map<string, RNEMDFluxType>::iterator fi;
1624	+	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1625	+	if ( (*fi).second == rnemdFluxType_)
1626	+	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1627	+	}
1628	+
1629	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1630	+
1631	+	rnemdFile_ << "#    objectSelection = \""
1632	+	<< rnemdObjectSelection_ << "\";\n";
1633	+	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1634	+	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1635	+	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1636	+	rnemdFile_ << "# }\n";
1637	+	rnemdFile_ << "#######################################################\n";
1638	+	rnemdFile_ << "# RNEMD report:\n";
1639	+	rnemdFile_ << "#     running time = " << time << " fs\n";
1640	+	rnemdFile_ << "#     target flux:\n";
1641	+	rnemdFile_ << "#         kinetic = "
1642	+	<< kineticFlux_ / PhysicalConstants::energyConvert
1643	+	<< " (kcal/mol/A^2/fs)\n";
1644	+	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1645	+	<< " (amu/A/fs^2)\n";
1646	+	rnemdFile_ << "#     target one-time exchanges:\n";
1647	+	rnemdFile_ << "#         kinetic = "
1648	+	<< kineticTarget_ / PhysicalConstants::energyConvert
1649	+	<< " (kcal/mol)\n";
1650	+	rnemdFile_ << "#         momentum = " << momentumTarget_
1651	+	<< " (amu*A/fs)\n";
1652	+	rnemdFile_ << "#     actual exchange totals:\n";
1653	+	rnemdFile_ << "#         kinetic = "
1654	+	<< kineticExchange_ / PhysicalConstants::energyConvert
1655	+	<< " (kcal/mol)\n";
1656	+	rnemdFile_ << "#         momentum = " << momentumExchange_
1657	+	<< " (amu*A/fs)\n";
1658	+	rnemdFile_ << "#     actual flux:\n";
1659	+	rnemdFile_ << "#         kinetic = " << Jz
1660	+	<< " (kcal/mol/A^2/fs)\n";
1661	+	rnemdFile_ << "#         momentum = " << JzP
1662	+	<< " (amu/A/fs^2)\n";
1663	+	rnemdFile_ << "#     exchange statistics:\n";
1664	+	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1665	+	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1666	+	if (rnemdMethod_ == rnemdNIVS) {
1667	+	rnemdFile_ << "#         NIVS root-check errors = "
1668	+	<< failRootCount_ << "\n";
1669	+	}
1670	+	rnemdFile_ << "#######################################################\n";
1671	+
1672	+
1673	+
1674	+	//write title
1675	+	rnemdFile_ << "#";
1676	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1677	+	if (outputMask_[i]) {
1678	+	rnemdFile_ << "\t" << data_[i].title <<
1679	+	"(" << data_[i].units << ")";
1680	+	// add some extra tabs for column alignment
1681	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1682	+	}
1683	+	}
1684	+	rnemdFile_ << std::endl;
1685	+
1686	+	rnemdFile_.precision(8);
1687	+
1688	+	for (int j = 0; j < nBins_; j++) {
1689	+
1690	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1691	+	if (outputMask_[i]) {
1692	+	if (data_[i].dataType == "RealType")
1693	+	writeReal(i,j);
1694	+	else if (data_[i].dataType == "Vector3d")
1695	+	writeVector(i,j);
1696	+	else {
1697	+	sprintf( painCave.errMsg,
1698	+	"RNEMD found an unknown data type for: %s ",
1699	+	data_[i].title.c_str());
1700	+	painCave.isFatal = 1;
1701	+	simError();
1702	+	}
1703	+	}
1704	+	}
1705	+	rnemdFile_ << std::endl;
1706	+
1707	+	}
1708	+
1709	+	rnemdFile_ << "#######################################################\n";
1710	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1711	+	rnemdFile_ << "#######################################################\n";
1712	+
1713	+
1714	+	for (int j = 0; j < nBins_; j++) {
1715	+	rnemdFile_ << "#";
1716	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1717	+	if (outputMask_[i]) {
1718	+	if (data_[i].dataType == "RealType")
1719	+	writeRealStdDev(i,j);
1720	+	else if (data_[i].dataType == "Vector3d")
1721	+	writeVectorStdDev(i,j);
1722	+	else {
1723	+	sprintf( painCave.errMsg,
1724	+	"RNEMD found an unknown data type for: %s ",
1725	+	data_[i].title.c_str());
1726	+	painCave.isFatal = 1;
1727	+	simError();
1728	+	}
1729	+	}
1730	+	}
1731	+	rnemdFile_ << std::endl;
1732	+
1733	+	}
1734	+
1735	+	rnemdFile_.flush();
1736	+	rnemdFile_.close();
1737	+
1738		#ifdef IS_MPI
1739		}
1740		#endif
1741	+
1742		}
1743	+
1744	+	void RNEMD::writeReal(int index, unsigned int bin) {
1745	+	if (!doRNEMD_) return;
1746	+	assert(index >=0 && index < ENDINDEX);
1747	+	assert(bin < nBins_);
1748	+	RealType s;
1749	+
1750	+	data_[index].accumulator[bin]->getAverage(s);
1751	+
1752	+	if (! isinf(s) && ! isnan(s)) {
1753	+	rnemdFile_ << "\t" << s;
1754	+	} else{
1755	+	sprintf( painCave.errMsg,
1756	+	"RNEMD detected a numerical error writing: %s for bin %d",
1757	+	data_[index].title.c_str(), bin);
1758	+	painCave.isFatal = 1;
1759	+	simError();
1760	+	}
1761	+	}
1762	+
1763	+	void RNEMD::writeVector(int index, unsigned int bin) {
1764	+	if (!doRNEMD_) return;
1765	+	assert(index >=0 && index < ENDINDEX);
1766	+	assert(bin < nBins_);
1767	+	Vector3d s;
1768	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1769	+	if (isinf(s[0]) || isnan(s[0]) ||
1770	+	isinf(s[1]) || isnan(s[1]) ||
1771	+	isinf(s[2]) || isnan(s[2]) ) {
1772	+	sprintf( painCave.errMsg,
1773	+	"RNEMD detected a numerical error writing: %s for bin %d",
1774	+	data_[index].title.c_str(), bin);
1775	+	painCave.isFatal = 1;
1776	+	simError();
1777	+	} else {
1778	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1779	+	}
1780	+	}
1781	+
1782	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1783	+	if (!doRNEMD_) return;
1784	+	assert(index >=0 && index < ENDINDEX);
1785	+	assert(bin < nBins_);
1786	+	RealType s;
1787	+
1788	+	data_[index].accumulator[bin]->getStdDev(s);
1789	+
1790	+	if (! isinf(s) && ! isnan(s)) {
1791	+	rnemdFile_ << "\t" << s;
1792	+	} else{
1793	+	sprintf( painCave.errMsg,
1794	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1795	+	data_[index].title.c_str(), bin);
1796	+	painCave.isFatal = 1;
1797	+	simError();
1798	+	}
1799	+	}
1800	+
1801	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1802	+	if (!doRNEMD_) return;
1803	+	assert(index >=0 && index < ENDINDEX);
1804	+	assert(bin < nBins_);
1805	+	Vector3d s;
1806	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1807	+	if (isinf(s[0]) || isnan(s[0]) ||
1808	+	isinf(s[1]) || isnan(s[1]) ||
1809	+	isinf(s[2]) || isnan(s[2]) ) {
1810	+	sprintf( painCave.errMsg,
1811	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1812	+	data_[index].title.c_str(), bin);
1813	+	painCave.isFatal = 1;
1814	+	simError();
1815	+	} else {
1816	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1817	+	}
1818	+	}
1819		}
1820	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
trunk/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1789 by gezelter, Wed Aug 29 20:52:19 2012 UTC

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