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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1803 by gezelter, Wed Oct 3 14:20:07 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	<
53	<	#ifndef IS_MPI
51	<	#include "math/SeqRandNumGen.hpp"
52	<	#else
53	<	#include "math/ParallelRandNumGen.hpp"
52	>	#ifdef IS_MPI
53	>	#include <mpi.h>
54		#endif
55
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), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
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;
67	<	stringToEnumMap_["Py"] = rnemdPy;
68	<	stringToEnumMap_["Pz"] = rnemdPz;
69	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
75	>	stringToMethod_["Swap"]  = rnemdSwap;
76	>	stringToMethod_["NIVS"]  = rnemdNIVS;
77	>	stringToMethod_["VSS"]   = rnemdVSS;
78	>
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	>	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	+	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	+
281		int nIntegrable = info->getNGlobalIntegrableObjects();
282
283		if (selectionCount > nIntegrable) {
284		sprintf(painCave.errMsg,
285	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
285	>	"RNEMD: The current objectSelection,\n"
286		"\t\t%s\n"
287		"\thas resulted in %d selected objects.  However,\n"
288		"\tthe total number of integrable objects in the system\n"
#	Line 90 | Line 292 | namespace oopse {
292		rnemdObjectSelection_.c_str(),
293		selectionCount, nIntegrable);
294		painCave.isFatal = 0;
295	+	painCave.severity = OPENMD_WARNING;
296		simError();
297	+	}
298
299	+	areaAccumulator_ = new Accumulator();
300	+
301	+	nBins_ = rnemdParams->getOutputBins();
302	+
303	+	data_.resize(RNEMD::ENDINDEX);
304	+	OutputData z;
305	+	z.units =  "Angstroms";
306	+	z.title =  "Z";
307	+	z.dataType = "RealType";
308	+	z.accumulator.reserve(nBins_);
309	+	for (unsigned int i = 0; i < nBins_; i++)
310	+	z.accumulator.push_back( new Accumulator() );
311	+	data_[Z] = z;
312	+	outputMap_["Z"] =  Z;
313	+
314	+	OutputData temperature;
315	+	temperature.units =  "K";
316	+	temperature.title =  "Temperature";
317	+	temperature.dataType = "RealType";
318	+	temperature.accumulator.reserve(nBins_);
319	+	for (unsigned int i = 0; i < nBins_; i++)
320	+	temperature.accumulator.push_back( new Accumulator() );
321	+	data_[TEMPERATURE] = temperature;
322	+	outputMap_["TEMPERATURE"] =  TEMPERATURE;
323	+
324	+	OutputData velocity;
325	+	velocity.units = "angstroms/fs";
326	+	velocity.title =  "Velocity";
327	+	velocity.dataType = "Vector3d";
328	+	velocity.accumulator.reserve(nBins_);
329	+	for (unsigned int i = 0; i < nBins_; i++)
330	+	velocity.accumulator.push_back( new VectorAccumulator() );
331	+	data_[VELOCITY] = velocity;
332	+	outputMap_["VELOCITY"] = VELOCITY;
333	+
334	+	OutputData density;
335	+	density.units =  "g cm^-3";
336	+	density.title =  "Density";
337	+	density.dataType = "RealType";
338	+	density.accumulator.reserve(nBins_);
339	+	for (unsigned int i = 0; i < nBins_; i++)
340	+	density.accumulator.push_back( new Accumulator() );
341	+	data_[DENSITY] = density;
342	+	outputMap_["DENSITY"] =  DENSITY;
343	+
344	+	if (hasOutputFields) {
345	+	parseOutputFileFormat(rnemdParams->getOutputFields());
346	+	} else {
347	+	outputMask_.set(Z);
348	+	switch (rnemdFluxType_) {
349	+	case rnemdKE:
350	+	case rnemdRotKE:
351	+	case rnemdFullKE:
352	+	outputMask_.set(TEMPERATURE);
353	+	break;
354	+	case rnemdPx:
355	+	case rnemdPy:
356	+	outputMask_.set(VELOCITY);
357	+	break;
358	+	case rnemdPz:
359	+	case rnemdPvector:
360	+	outputMask_.set(VELOCITY);
361	+	outputMask_.set(DENSITY);
362	+	break;
363	+	case rnemdKePx:
364	+	case rnemdKePy:
365	+	outputMask_.set(TEMPERATURE);
366	+	outputMask_.set(VELOCITY);
367	+	break;
368	+	case rnemdKePvector:
369	+	outputMask_.set(TEMPERATURE);
370	+	outputMask_.set(VELOCITY);
371	+	outputMask_.set(DENSITY);
372	+	break;
373	+	default:
374	+	break;
375	+	}
376		}
377	<
378	<	const std::string st = simParams->getRNEMD_swapType();
377	>
378	>	if (hasOutputFileName) {
379	>	rnemdFileName_ = rnemdParams->getOutputFileName();
380	>	} else {
381	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
382	>	}
383
384	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
100	<	i = stringToEnumMap_.find(st);
101	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
384	>	exchangeTime_ = rnemdParams->getExchangeTime();
385
386	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
387	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
388	<	exchangeSum_ = 0.0;
386	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
387	>	Mat3x3d hmat = currentSnap_->getHmat();
388	>
389	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
390	>	// Lx, Ly = box dimensions in x & y
391	>	// dt = exchange time interval
392	>	// flux = target flux
393
394	<	#ifndef IS_MPI
395	<	if (simParams->haveSeed()) {
396	<	seedValue = simParams->getSeed();
397	<	randNumGen_ = new SeqRandNumGen(seedValue);
398	<	}else {
399	<	randNumGen_ = new SeqRandNumGen();
400	<	}
401	<	#else
402	<	if (simParams->haveSeed()) {
403	<	seedValue = simParams->getSeed();
404	<	randNumGen_ = new ParallelRandNumGen(seedValue);
405	<	}else {
406	<	randNumGen_ = new ParallelRandNumGen();
120	<	}
121	<	#endif
122	<	}
394	>	RealType area = currentSnap_->getXYarea();
395	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
396	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
397	>
398	>	// total exchange sums are zeroed out at the beginning:
399	>
400	>	kineticExchange_ = 0.0;
401	>	momentumExchange_ = V3Zero;
402	>
403	>	if (hasSlabWidth)
404	>	slabWidth_ = rnemdParams->getSlabWidth();
405	>	else
406	>	slabWidth_ = hmat(2,2) / 10.0;
407
408	+	if (hasSlabACenter)
409	+	slabACenter_ = rnemdParams->getSlabACenter();
410	+	else
411	+	slabACenter_ = 0.0;
412	+
413	+	if (hasSlabBCenter)
414	+	slabBCenter_ = rnemdParams->getSlabBCenter();
415	+	else
416	+	slabBCenter_ = hmat(2,2) / 2.0;
417	+
418	+	}
419	+
420		RNEMD::~RNEMD() {
421	<	delete randNumGen_;
421	>	if (!doRNEMD_) return;
422	>	#ifdef IS_MPI
423	>	if (worldRank == 0) {
424	>	#endif
425	>
426	>	writeOutputFile();
427	>
428	>	rnemdFile_.close();
429	>
430	>	#ifdef IS_MPI
431	>	}
432	>	#endif
433		}
434	+
435	+	bool RNEMD::inSlabA(Vector3d pos) {
436	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
437	+	}
438	+	bool RNEMD::inSlabB(Vector3d pos) {
439	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
440	+	}
441
442		void RNEMD::doSwap() {
443	<	int midBin = nBins_ / 2;
130	<
443	>	if (!doRNEMD_) return;
444		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
445		Mat3x3d hmat = currentSnap_->getHmat();
446
#	Line 156 | Line 469 | namespace oopse {
469
470		if (usePeriodicBoundaryConditions_)
471		currentSnap_->wrapVector(pos);
472	+	bool inA = inSlabA(pos);
473	+	bool inB = inSlabB(pos);
474
475	<	// 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) {
475	>	if (inA || inB) {
476
477		RealType mass = sd->getMass();
478		Vector3d vel = sd->getVel();
479		RealType value;
480	<
481	<	switch(rnemdType_) {
482	<	case rnemdKinetic :
480	>
481	>	switch(rnemdFluxType_) {
482	>	case rnemdKE :
483
484	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
485	<	vel[2]*vel[2]);
486	<	if (sd->isDirectional()) {
484	>	value = mass * vel.lengthSquare();
485	>
486	>	if (sd->isDirectional()) {
487		Vector3d angMom = sd->getJ();
488		Mat3x3d I = sd->getI();
489
490		if (sd->isLinear()) {
491	<	int i = sd->linearAxis();
492	<	int j = (i + 1) % 3;
493	<	int k = (i + 2) % 3;
494	<	value += angMom[j] * angMom[j] / I(j, j) +
495	<	angMom[k] * angMom[k] / I(k, k);
491	>	int i = sd->linearAxis();
492	>	int j = (i + 1) % 3;
493	>	int k = (i + 2) % 3;
494	>	value += angMom[j] * angMom[j] / I(j, j) +
495	>	angMom[k] * angMom[k] / I(k, k);
496		} else {
497	<	value += angMom[0]*angMom[0]/I(0, 0)
498	<	+ angMom[1]*angMom[1]/I(1, 1)
499	<	+ angMom[2]*angMom[2]/I(2, 2);
497	>	value += angMom[0]*angMom[0]/I(0, 0)
498	>	+ angMom[1]*angMom[1]/I(1, 1)
499	>	+ angMom[2]*angMom[2]/I(2, 2);
500		}
501	<	}
502	<	value = value * 0.5 / OOPSEConstant::energyConvert;
501	>	} //angular momenta exchange enabled
502	>	value *= 0.5;
503		break;
504		case rnemdPx :
505		value = mass * vel[0];
#	Line 202 | Line 510 | namespace oopse {
510		case rnemdPz :
511		value = mass * vel[2];
512		break;
205	–	case rnemdUnknown :
513		default :
514		break;
515		}
516
517	<	if (binNo == 0) {
517	>	if (inA == 0) {
518		if (!min_found) {
519		min_val = value;
520		min_sd = sd;
#	Line 218 | Line 525 | namespace oopse {
525		min_sd = sd;
526		}
527		}
528	<	} else {
528	>	} else {
529		if (!max_found) {
530		max_val = value;
531		max_sd = sd;
#	Line 232 | Line 539 | namespace oopse {
539		}
540		}
541		}
542	<
542	>
543		#ifdef IS_MPI
544		int nProc, worldRank;
545	<
545	>
546		nProc = MPI::COMM_WORLD.Get_size();
547		worldRank = MPI::COMM_WORLD.Get_rank();
548
#	Line 243 | Line 550 | namespace oopse {
550		bool my_max_found = max_found;
551
552		// Even if we didn't find a minimum, did someone else?
553	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
553	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
554		// Even if we didn't find a maximum, did someone else?
555	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
556	<	1, MPI::BOOL, MPI::LAND);
557	<
558	<	struct {
559	<	RealType val;
560	<	int rank;
561	<	} max_vals, min_vals;
562	<
563	<	if (min_found) {
564	<	if (my_min_found)
555	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
556	>	#endif
557	>
558	>	if (max_found && min_found) {
559	>
560	>	#ifdef IS_MPI
561	>	struct {
562	>	RealType val;
563	>	int rank;
564	>	} max_vals, min_vals;
565	>
566	>	if (my_min_found) {
567		min_vals.val = min_val;
568	<	else
568	>	} else {
569		min_vals.val = HONKING_LARGE_VALUE;
570	<
570	>	}
571		min_vals.rank = worldRank;
572
573		// Who had the minimum?
574		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
575		1, MPI::REALTYPE_INT, MPI::MINLOC);
576		min_val = min_vals.val;
270	–	}
577
578	<	if (max_found) {
273	<	if (my_max_found)
578	>	if (my_max_found) {
579		max_vals.val = max_val;
580	<	else
580	>	} else {
581		max_vals.val = -HONKING_LARGE_VALUE;
582	<
582	>	}
583		max_vals.rank = worldRank;
584
585		// Who had the maximum?
586		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
587		1, MPI::REALTYPE_INT, MPI::MAXLOC);
588		max_val = max_vals.val;
284	–	}
589		#endif
590	<
591	<	if (max_found && min_found) {
592	<	if (min_val< max_val) {
289	<
590	>
591	>	if (min_val < max_val) {
592	>
593		#ifdef IS_MPI
594		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
595		// I have both maximum and minimum, so proceed like a single
596		// processor version:
597		#endif
598	<	// objects to be swapped: velocity & angular velocity
598	>
599		Vector3d min_vel = min_sd->getVel();
600		Vector3d max_vel = max_sd->getVel();
601		RealType temp_vel;
602
603	<	switch(rnemdType_) {
604	<	case rnemdKinetic :
603	>	switch(rnemdFluxType_) {
604	>	case rnemdKE :
605		min_sd->setVel(max_vel);
606		max_sd->setVel(min_vel);
607	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
607	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
608		Vector3d min_angMom = min_sd->getJ();
609		Vector3d max_angMom = max_sd->getJ();
610		min_sd->setJ(max_angMom);
611		max_sd->setJ(min_angMom);
612	<	}
612	>	}//angular momenta exchange enabled
613	>	//assumes same rigid body identity
614		break;
615		case rnemdPx :
616		temp_vel = min_vel.x();
#	Line 329 | Line 633 | namespace oopse {
633		min_sd->setVel(min_vel);
634		max_sd->setVel(max_vel);
635		break;
332	–	case rnemdUnknown :
636		default :
637		break;
638		}
639	+
640		#ifdef IS_MPI
641		// the rest of the cases only apply in parallel simulations:
642		} else if (max_vals.rank == worldRank) {
#	Line 348 | Line 652 | namespace oopse {
652		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
653		min_vals.rank, 0, status);
654
655	<	switch(rnemdType_) {
656	<	case rnemdKinetic :
655	>	switch(rnemdFluxType_) {
656	>	case rnemdKE :
657		max_sd->setVel(min_vel);
658	<
658	>	//angular momenta exchange enabled
659		if (max_sd->isDirectional()) {
660		Vector3d min_angMom;
661		Vector3d max_angMom = max_sd->getJ();
662	<
662	>
663		// point-to-point swap of the angular momentum vector
664		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
665		MPI::REALTYPE, min_vals.rank, 1,
666		min_angMom.getArrayPointer(), 3,
667		MPI::REALTYPE, min_vals.rank, 1,
668		status);
669	<
669	>
670		max_sd->setJ(min_angMom);
671	<	}
671	>	}
672		break;
673		case rnemdPx :
674		max_vel.x() = min_vel.x();
#	Line 378 | Line 682 | namespace oopse {
682		max_vel.z() = min_vel.z();
683		max_sd->setVel(max_vel);
684		break;
381	–	case rnemdUnknown :
685		default :
686		break;
687		}
#	Line 395 | Line 698 | namespace oopse {
698		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
699		max_vals.rank, 0, status);
700
701	<	switch(rnemdType_) {
702	<	case rnemdKinetic :
701	>	switch(rnemdFluxType_) {
702	>	case rnemdKE :
703		min_sd->setVel(max_vel);
704	<
704	>	//angular momenta exchange enabled
705		if (min_sd->isDirectional()) {
706		Vector3d min_angMom = min_sd->getJ();
707		Vector3d max_angMom;
708	<
708	>
709		// point-to-point swap of the angular momentum vector
710		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
711		MPI::REALTYPE, max_vals.rank, 1,
712		max_angMom.getArrayPointer(), 3,
713		MPI::REALTYPE, max_vals.rank, 1,
714		status);
715	<
715	>
716		min_sd->setJ(max_angMom);
717		}
718		break;
#	Line 425 | Line 728 | namespace oopse {
728		min_vel.z() = max_vel.z();
729		min_sd->setVel(min_vel);
730		break;
428	–	case rnemdUnknown :
731		default :
732		break;
733		}
734		}
735		#endif
736	<	exchangeSum_ += max_val - min_val;
737	<	} else {
738	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
736	>
737	>	switch(rnemdFluxType_) {
738	>	case rnemdKE:
739	>	kineticExchange_ += max_val - min_val;
740	>	break;
741	>	case rnemdPx:
742	>	momentumExchange_.x() += max_val - min_val;
743	>	break;
744	>	case rnemdPy:
745	>	momentumExchange_.y() += max_val - min_val;
746	>	break;
747	>	case rnemdPz:
748	>	momentumExchange_.z() += max_val - min_val;
749	>	break;
750	>	default:
751	>	break;
752	>	}
753	>	} else {
754	>	sprintf(painCave.errMsg,
755	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
756	>	painCave.isFatal = 0;
757	>	painCave.severity = OPENMD_INFO;
758	>	simError();
759	>	failTrialCount_++;
760		}
761		} else {
762	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
763	<	}
764	<
762	>	sprintf(painCave.errMsg,
763	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
764	>	"\twas not present in at least one of the two slabs.\n");
765	>	painCave.isFatal = 0;
766	>	painCave.severity = OPENMD_INFO;
767	>	simError();
768	>	failTrialCount_++;
769	>	}
770		}
771
772	<	void RNEMD::getStatus() {
773	<
772	>	void RNEMD::doNIVS() {
773	>	if (!doRNEMD_) return;
774		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
775		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
776
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
777		seleMan_.setSelectionSet(evaluator_.evaluate());
778
779		int selei;
780		StuntDouble* sd;
781		int idx;
782
783	<	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
783	>	vector<StuntDouble*> hotBin, coldBin;
784
785	+	RealType Phx = 0.0;
786	+	RealType Phy = 0.0;
787	+	RealType Phz = 0.0;
788	+	RealType Khx = 0.0;
789	+	RealType Khy = 0.0;
790	+	RealType Khz = 0.0;
791	+	RealType Khw = 0.0;
792	+	RealType Pcx = 0.0;
793	+	RealType Pcy = 0.0;
794	+	RealType Pcz = 0.0;
795	+	RealType Kcx = 0.0;
796	+	RealType Kcy = 0.0;
797	+	RealType Kcz = 0.0;
798	+	RealType Kcw = 0.0;
799	+
800		for (sd = seleMan_.beginSelected(selei); sd != NULL;
801		sd = seleMan_.nextSelected(selei)) {
802	<
802	>
803		idx = sd->getLocalIndex();
804	<
804	>
805		Vector3d pos = sd->getPos();
806
807		// wrap the stuntdouble's position back into the box:
808	<
808	>
809		if (usePeriodicBoundaryConditions_)
810		currentSnap_->wrapVector(pos);
811	<
811	>
812		// which bin is this stuntdouble in?
813	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
814	<
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;
813	>	bool inA = inSlabA(pos);
814	>	bool inB = inSlabB(pos);
815
816	<	switch(rnemdType_) {
817	<	case rnemdKinetic :
818	<
819	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
820	<	vel[2]*vel[2]);
821	<
822	<	valueCount[binNo] += 3;
823	<	if (sd->isDirectional()) {
824	<	Vector3d angMom = sd->getJ();
825	<	Mat3x3d I = sd->getI();
826	<
827	<	if (sd->isLinear()) {
828	<	int i = sd->linearAxis();
829	<	int j = (i + 1) % 3;
830	<	int k = (i + 2) % 3;
831	<	value += angMom[j] * angMom[j] / I(j, j) +
832	<	angMom[k] * angMom[k] / I(k, k);
816	>	if (inA || inB) {
817	>
818	>	RealType mass = sd->getMass();
819	>	Vector3d vel = sd->getVel();
820	>
821	>	if (inA) {
822	>	hotBin.push_back(sd);
823	>	Phx += mass * vel.x();
824	>	Phy += mass * vel.y();
825	>	Phz += mass * vel.z();
826	>	Khx += mass * vel.x() * vel.x();
827	>	Khy += mass * vel.y() * vel.y();
828	>	Khz += mass * vel.z() * vel.z();
829	>	if (sd->isDirectional()) {
830	>	Vector3d angMom = sd->getJ();
831	>	Mat3x3d I = sd->getI();
832	>	if (sd->isLinear()) {
833	>	int i = sd->linearAxis();
834	>	int j = (i + 1) % 3;
835	>	int k = (i + 2) % 3;
836	>	Khw += angMom[j] * angMom[j] / I(j, j) +
837	>	angMom[k] * angMom[k] / I(k, k);
838	>	} else {
839	>	Khw += angMom[0]*angMom[0]/I(0, 0)
840	>	+ angMom[1]*angMom[1]/I(1, 1)
841	>	+ angMom[2]*angMom[2]/I(2, 2);
842	>	}
843	>	}
844	>	} else {
845	>	coldBin.push_back(sd);
846	>	Pcx += mass * vel.x();
847	>	Pcy += mass * vel.y();
848	>	Pcz += mass * vel.z();
849	>	Kcx += mass * vel.x() * vel.x();
850	>	Kcy += mass * vel.y() * vel.y();
851	>	Kcz += mass * vel.z() * vel.z();
852	>	if (sd->isDirectional()) {
853	>	Vector3d angMom = sd->getJ();
854	>	Mat3x3d I = sd->getI();
855	>	if (sd->isLinear()) {
856	>	int i = sd->linearAxis();
857	>	int j = (i + 1) % 3;
858	>	int k = (i + 2) % 3;
859	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
860	>	angMom[k] * angMom[k] / I(k, k);
861	>	} else {
862	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
863	>	+ angMom[1]*angMom[1]/I(1, 1)
864	>	+ angMom[2]*angMom[2]/I(2, 2);
865	>	}
866	>	}
867	>	}
868	>	}
869	>	}
870	>
871	>	Khx *= 0.5;
872	>	Khy *= 0.5;
873	>	Khz *= 0.5;
874	>	Khw *= 0.5;
875	>	Kcx *= 0.5;
876	>	Kcy *= 0.5;
877	>	Kcz *= 0.5;
878	>	Kcw *= 0.5;
879
880	<	valueCount[binNo] +=2;
880	>	#ifdef IS_MPI
881	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
882	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
883	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
884	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
885	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
886	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
887
888	<	} else {
889	<	value += angMom[0]*angMom[0]/I(0, 0)
890	<	+ angMom[1]*angMom[1]/I(1, 1)
891	<	+ angMom[2]*angMom[2]/I(2, 2);
892	<	valueCount[binNo] +=3;
888	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
889	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
890	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
891	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
892	>
893	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
894	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
895	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
896	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
897	>	#endif
898	>
899	>	//solve coldBin coeff's first
900	>	RealType px = Pcx / Phx;
901	>	RealType py = Pcy / Phy;
902	>	RealType pz = Pcz / Phz;
903	>	RealType c, x, y, z;
904	>	bool successfulScale = false;
905	>	if ((rnemdFluxType_ == rnemdFullKE) ||
906	>	(rnemdFluxType_ == rnemdRotKE)) {
907	>	//may need sanity check Khw & Kcw > 0
908	>
909	>	if (rnemdFluxType_ == rnemdFullKE) {
910	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
911	>	} else {
912	>	c = 1.0 - kineticTarget_ / Kcw;
913	>	}
914	>
915	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
916	>	c = sqrt(c);
917	>
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	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
956	+	if (rnemdFluxType_ == rnemdFullKE) {
957	+	vel = (*sdi)->getVel();
958	+	vel.x() *= x;
959	+	vel.y() *= y;
960	+	vel.z() *= z;
961	+	(*sdi)->setVel(vel);
962	+	}
963	+	if ((*sdi)->isDirectional()) {
964	+	Vector3d angMom = (*sdi)->getJ() * w;
965	+	(*sdi)->setJ(angMom);
966	+	}
967	+	}
968	+	successfulScale = true;
969	+	kineticExchange_ += kineticTarget_;
970		}
971	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
972	<
973	<	break;
974	<	case rnemdPx :
975	<	value = mass * vel[0];
976	<	valueCount[binNo]++;
971	>	}
972	>	} else {
973	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
974	>	switch(rnemdFluxType_) {
975	>	case rnemdKE :
976	>	/* used hotBin coeff's & only scale x & y dimensions
977	>	RealType px = Phx / Pcx;
978	>	RealType py = Phy / Pcy;
979	>	a110 = Khy;
980	>	c0 = - Khx - Khy - kineticTarget_;
981	>	a000 = Khx;
982	>	a111 = Kcy * py * py;
983	>	b11 = -2.0 * Kcy * py * (1.0 + py);
984	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
985	>	b01 = -2.0 * Kcx * px * (1.0 + px);
986	>	a001 = Kcx * px * px;
987	>	*/
988	>	//scale all three dimensions, let c_x = c_y
989	>	a000 = Kcx + Kcy;
990	>	a110 = Kcz;
991	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
992	>	a001 = Khx * px * px + Khy * py * py;
993	>	a111 = Khz * pz * pz;
994	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
995	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
996	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
997	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
998		break;
999	+	case rnemdPx :
1000	+	c = 1 - momentumTarget_.x() / Pcx;
1001	+	a000 = Kcy;
1002	+	a110 = Kcz;
1003	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1004	+	a001 = py * py * Khy;
1005	+	a111 = pz * pz * Khz;
1006	+	b01 = -2.0 * Khy * py * (1.0 + py);
1007	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
1008	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1009	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1010	+	break;
1011		case rnemdPy :
1012	<	value = mass * vel[1];
1013	<	valueCount[binNo]++;
1012	>	c = 1 - momentumTarget_.y() / Pcy;
1013	>	a000 = Kcx;
1014	>	a110 = Kcz;
1015	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1016	>	a001 = px * px * Khx;
1017	>	a111 = pz * pz * Khz;
1018	>	b01 = -2.0 * Khx * px * (1.0 + px);
1019	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1020	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1021	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1022		break;
1023	<	case rnemdPz :
1024	<	value = mass * vel[2];
1025	<	valueCount[binNo]++;
1023	>	case rnemdPz ://we don't really do this, do we?
1024	>	c = 1 - momentumTarget_.z() / Pcz;
1025	>	a000 = Kcx;
1026	>	a110 = Kcy;
1027	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1028	>	a001 = px * px * Khx;
1029	>	a111 = py * py * Khy;
1030	>	b01 = -2.0 * Khx * px * (1.0 + px);
1031	>	b11 = -2.0 * Khy * py * (1.0 + py);
1032	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1033	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1034		break;
528	–	case rnemdUnknown :
1035		default :
1036		break;
1037		}
1038	<	valueHist[binNo] += value;
1038	>
1039	>	RealType v1 = a000 * a111 - a001 * a110;
1040	>	RealType v2 = a000 * b01;
1041	>	RealType v3 = a000 * b11;
1042	>	RealType v4 = a000 * c1 - a001 * c0;
1043	>	RealType v8 = a110 * b01;
1044	>	RealType v10 = - b01 * c0;
1045	>
1046	>	RealType u0 = v2 * v10 - v4 * v4;
1047	>	RealType u1 = -2.0 * v3 * v4;
1048	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1049	>	RealType u3 = -2.0 * v1 * v3;
1050	>	RealType u4 = - v1 * v1;
1051	>	//rescale coefficients
1052	>	RealType maxAbs = fabs(u0);
1053	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1054	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1055	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1056	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1057	>	u0 /= maxAbs;
1058	>	u1 /= maxAbs;
1059	>	u2 /= maxAbs;
1060	>	u3 /= maxAbs;
1061	>	u4 /= maxAbs;
1062	>	//max_element(start, end) is also available.
1063	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1064	>	poly.setCoefficient(4, u4);
1065	>	poly.setCoefficient(3, u3);
1066	>	poly.setCoefficient(2, u2);
1067	>	poly.setCoefficient(1, u1);
1068	>	poly.setCoefficient(0, u0);
1069	>	vector<RealType> realRoots = poly.FindRealRoots();
1070	>
1071	>	vector<RealType>::iterator ri;
1072	>	RealType r1, r2, alpha0;
1073	>	vector<pair<RealType,RealType> > rps;
1074	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1075	>	r2 = *ri;
1076	>	//check if FindRealRoots() give the right answer
1077	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1078	>	sprintf(painCave.errMsg,
1079	>	"RNEMD Warning: polynomial solve seems to have an error!");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	failRootCount_++;
1083	>	}
1084	>	//might not be useful w/o rescaling coefficients
1085	>	alpha0 = -c0 - a110 * r2 * r2;
1086	>	if (alpha0 >= 0.0) {
1087	>	r1 = sqrt(alpha0 / a000);
1088	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1089	>	< 1e-6)
1090	>	{ rps.push_back(make_pair(r1, r2)); }
1091	>	if (r1 > 1e-6) { //r1 non-negative
1092	>	r1 = -r1;
1093	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1094	>	< 1e-6)
1095	>	{ rps.push_back(make_pair(r1, r2)); }
1096	>	}
1097	>	}
1098	>	}
1099	>	// Consider combining together the solving pair part w/ the searching
1100	>	// best solution part so that we don't need the pairs vector
1101	>	if (!rps.empty()) {
1102	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1103	>	RealType diff;
1104	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1105	>	vector<pair<RealType,RealType> >::iterator rpi;
1106	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1107	>	r1 = (*rpi).first;
1108	>	r2 = (*rpi).second;
1109	>	switch(rnemdFluxType_) {
1110	>	case rnemdKE :
1111	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1113	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1114	>	break;
1115	>	case rnemdPx :
1116	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1117	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1118	>	break;
1119	>	case rnemdPy :
1120	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1121	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1122	>	break;
1123	>	case rnemdPz :
1124	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1125	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1126	>	default :
1127	>	break;
1128	>	}
1129	>	if (diff < smallestDiff) {
1130	>	smallestDiff = diff;
1131	>	bestPair = *rpi;
1132	>	}
1133	>	}
1134	>	#ifdef IS_MPI
1135	>	if (worldRank == 0) {
1136	>	#endif
1137	>	// sprintf(painCave.errMsg,
1138	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	>	//         bestPair.first, bestPair.second);
1140	>	// painCave.isFatal = 0;
1141	>	// painCave.severity = OPENMD_INFO;
1142	>	// simError();
1143	>	#ifdef IS_MPI
1144	>	}
1145	>	#endif
1146	>
1147	>	switch(rnemdFluxType_) {
1148	>	case rnemdKE :
1149	>	x = bestPair.first;
1150	>	y = bestPair.first;
1151	>	z = bestPair.second;
1152	>	break;
1153	>	case rnemdPx :
1154	>	x = c;
1155	>	y = bestPair.first;
1156	>	z = bestPair.second;
1157	>	break;
1158	>	case rnemdPy :
1159	>	x = bestPair.first;
1160	>	y = c;
1161	>	z = bestPair.second;
1162	>	break;
1163	>	case rnemdPz :
1164	>	x = bestPair.first;
1165	>	y = bestPair.second;
1166	>	z = c;
1167	>	break;
1168	>	default :
1169	>	break;
1170	>	}
1171	>	vector<StuntDouble*>::iterator sdi;
1172	>	Vector3d vel;
1173	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1174	>	vel = (*sdi)->getVel();
1175	>	vel.x() *= x;
1176	>	vel.y() *= y;
1177	>	vel.z() *= z;
1178	>	(*sdi)->setVel(vel);
1179	>	}
1180	>	//convert to hotBin coefficient
1181	>	x = 1.0 + px * (1.0 - x);
1182	>	y = 1.0 + py * (1.0 - y);
1183	>	z = 1.0 + pz * (1.0 - z);
1184	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1185	>	vel = (*sdi)->getVel();
1186	>	vel.x() *= x;
1187	>	vel.y() *= y;
1188	>	vel.z() *= z;
1189	>	(*sdi)->setVel(vel);
1190	>	}
1191	>	successfulScale = true;
1192	>	switch(rnemdFluxType_) {
1193	>	case rnemdKE :
1194	>	kineticExchange_ += kineticTarget_;
1195	>	break;
1196	>	case rnemdPx :
1197	>	case rnemdPy :
1198	>	case rnemdPz :
1199	>	momentumExchange_ += momentumTarget_;
1200	>	break;
1201	>	default :
1202	>	break;
1203	>	}
1204	>	}
1205		}
1206	+	if (successfulScale != true) {
1207	+	sprintf(painCave.errMsg,
1208	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1209	+	"\tthe constraint equations may not exist or there may be\n"
1210	+	"\tno selected objects in one or both slabs.\n");
1211	+	painCave.isFatal = 0;
1212	+	painCave.severity = OPENMD_INFO;
1213	+	simError();
1214	+	failTrialCount_++;
1215	+	}
1216	+	}
1217
1218	+	void RNEMD::doVSS() {
1219	+	if (!doRNEMD_) return;
1220	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1221	+	RealType time = currentSnap_->getTime();
1222	+	Mat3x3d hmat = currentSnap_->getHmat();
1223	+
1224	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1225	+
1226	+	int selei;
1227	+	StuntDouble* sd;
1228	+	int idx;
1229	+
1230	+	vector<StuntDouble*> hotBin, coldBin;
1231	+
1232	+	Vector3d Ph(V3Zero);
1233	+	RealType Mh = 0.0;
1234	+	RealType Kh = 0.0;
1235	+	Vector3d Pc(V3Zero);
1236	+	RealType Mc = 0.0;
1237	+	RealType Kc = 0.0;
1238	+
1239	+
1240	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1241	+	sd = seleMan_.nextSelected(selei)) {
1242	+
1243	+	idx = sd->getLocalIndex();
1244	+
1245	+	Vector3d pos = sd->getPos();
1246	+
1247	+	// wrap the stuntdouble's position back into the box:
1248	+
1249	+	if (usePeriodicBoundaryConditions_)
1250	+	currentSnap_->wrapVector(pos);
1251	+
1252	+	// which bin is this stuntdouble in?
1253	+	bool inA = inSlabA(pos);
1254	+	bool inB = inSlabB(pos);
1255	+
1256	+	if (inA || inB) {
1257	+
1258	+	RealType mass = sd->getMass();
1259	+	Vector3d vel = sd->getVel();
1260	+
1261	+	if (inA) {
1262	+	hotBin.push_back(sd);
1263	+	Ph += mass * vel;
1264	+	Mh += mass;
1265	+	Kh += mass * vel.lengthSquare();
1266	+	if (rnemdFluxType_ == rnemdFullKE) {
1267	+	if (sd->isDirectional()) {
1268	+	Vector3d angMom = sd->getJ();
1269	+	Mat3x3d I = sd->getI();
1270	+	if (sd->isLinear()) {
1271	+	int i = sd->linearAxis();
1272	+	int j = (i + 1) % 3;
1273	+	int k = (i + 2) % 3;
1274	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1275	+	angMom[k] * angMom[k] / I(k, k);
1276	+	} else {
1277	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1278	+	angMom[1] * angMom[1] / I(1, 1) +
1279	+	angMom[2] * angMom[2] / I(2, 2);
1280	+	}
1281	+	}
1282	+	}
1283	+	} else { //midBin_
1284	+	coldBin.push_back(sd);
1285	+	Pc += mass * vel;
1286	+	Mc += mass;
1287	+	Kc += mass * vel.lengthSquare();
1288	+	if (rnemdFluxType_ == rnemdFullKE) {
1289	+	if (sd->isDirectional()) {
1290	+	Vector3d angMom = sd->getJ();
1291	+	Mat3x3d I = sd->getI();
1292	+	if (sd->isLinear()) {
1293	+	int i = sd->linearAxis();
1294	+	int j = (i + 1) % 3;
1295	+	int k = (i + 2) % 3;
1296	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1297	+	angMom[k] * angMom[k] / I(k, k);
1298	+	} else {
1299	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1300	+	angMom[1] * angMom[1] / I(1, 1) +
1301	+	angMom[2] * angMom[2] / I(2, 2);
1302	+	}
1303	+	}
1304	+	}
1305	+	}
1306	+	}
1307	+	}
1308	+
1309	+	Kh *= 0.5;
1310	+	Kc *= 0.5;
1311	+
1312		#ifdef IS_MPI
1313	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1314	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1315	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1316	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1317	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1318	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1319	+	#endif
1320
1321	<	// all processors have the same number of bins, and STL vectors pack their
1322	<	// arrays, so in theory, this should be safe:
1321	>	bool successfulExchange = false;
1322	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1323	>	Vector3d vc = Pc / Mc;
1324	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1325	>	Vector3d acrec = -momentumTarget_ / Mc;
1326	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1327	>	if (cNumerator > 0.0) {
1328	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1329	>	if (cDenominator > 0.0) {
1330	>	RealType c = sqrt(cNumerator / cDenominator);
1331	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1332	>	Vector3d vh = Ph / Mh;
1333	>	Vector3d ah = momentumTarget_ / Mh + vh;
1334	>	Vector3d ahrec = momentumTarget_ / Mh;
1335	>	RealType hNumerator = Kh + kineticTarget_
1336	>	- 0.5 * Mh * ah.lengthSquare();
1337	>	if (hNumerator > 0.0) {
1338	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1339	>	if (hDenominator > 0.0) {
1340	>	RealType h = sqrt(hNumerator / hDenominator);
1341	>	if ((h > 0.9) && (h < 1.1)) {
1342
1343	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1344	<	nBins_, MPI::REALTYPE, MPI::SUM);
1345	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1346	<	nBins_, MPI::INT, MPI::SUM);
1343	>	vector<StuntDouble*>::iterator sdi;
1344	>	Vector3d vel;
1345	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1346	>	//vel = (*sdi)->getVel();
1347	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1348	>	(*sdi)->setVel(vel);
1349	>	if (rnemdFluxType_ == rnemdFullKE) {
1350	>	if ((*sdi)->isDirectional()) {
1351	>	Vector3d angMom = (*sdi)->getJ() * c;
1352	>	(*sdi)->setJ(angMom);
1353	>	}
1354	>	}
1355	>	}
1356	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1357	>	//vel = (*sdi)->getVel();
1358	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1359	>	(*sdi)->setVel(vel);
1360	>	if (rnemdFluxType_ == rnemdFullKE) {
1361	>	if ((*sdi)->isDirectional()) {
1362	>	Vector3d angMom = (*sdi)->getJ() * h;
1363	>	(*sdi)->setJ(angMom);
1364	>	}
1365	>	}
1366	>	}
1367	>	successfulExchange = true;
1368	>	kineticExchange_ += kineticTarget_;
1369	>	momentumExchange_ += momentumTarget_;
1370	>	}
1371	>	}
1372	>	}
1373	>	}
1374	>	}
1375	>	}
1376	>	}
1377	>	if (successfulExchange != true) {
1378	>	sprintf(painCave.errMsg,
1379	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1380	>	"\tthe constraint equations may not exist or there may be\n"
1381	>	"\tno selected objects in one or both slabs.\n");
1382	>	painCave.isFatal = 0;
1383	>	painCave.severity = OPENMD_INFO;
1384	>	simError();
1385	>	failTrialCount_++;
1386	>	}
1387	>	}
1388	>
1389	>	void RNEMD::doRNEMD() {
1390	>	if (!doRNEMD_) return;
1391	>	trialCount_++;
1392	>	switch(rnemdMethod_) {
1393	>	case rnemdSwap:
1394	>	doSwap();
1395	>	break;
1396	>	case rnemdNIVS:
1397	>	doNIVS();
1398	>	break;
1399	>	case rnemdVSS:
1400	>	doVSS();
1401	>	break;
1402	>	case rnemdUnkownMethod:
1403	>	default :
1404	>	break;
1405	>	}
1406	>	}
1407
1408	+	void RNEMD::collectData() {
1409	+	if (!doRNEMD_) return;
1410	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1411	+	Mat3x3d hmat = currentSnap_->getHmat();
1412	+
1413	+	areaAccumulator_->add(currentSnap_->getXYarea());
1414	+
1415	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1416	+
1417	+	int selei(0);
1418	+	StuntDouble* sd;
1419	+	int idx;
1420	+
1421	+	vector<RealType> binMass(nBins_, 0.0);
1422	+	vector<RealType> binPx(nBins_, 0.0);
1423	+	vector<RealType> binPy(nBins_, 0.0);
1424	+	vector<RealType> binPz(nBins_, 0.0);
1425	+	vector<RealType> binKE(nBins_, 0.0);
1426	+	vector<int> binDOF(nBins_, 0);
1427	+	vector<int> binCount(nBins_, 0);
1428	+
1429	+	// alternative approach, track all molecules instead of only those
1430	+	// selected for scaling/swapping:
1431	+	/*
1432	+	SimInfo::MoleculeIterator miter;
1433	+	vector<StuntDouble*>::iterator iiter;
1434	+	Molecule* mol;
1435	+	StuntDouble* sd;
1436	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1437	+	mol = info_->nextMolecule(miter))
1438	+	sd is essentially sd
1439	+	for (sd = mol->beginIntegrableObject(iiter);
1440	+	sd != NULL;
1441	+	sd = mol->nextIntegrableObject(iiter))
1442	+	*/
1443	+
1444	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1445	+	sd = seleMan_.nextSelected(selei)) {
1446	+
1447	+	idx = sd->getLocalIndex();
1448	+
1449	+	Vector3d pos = sd->getPos();
1450	+
1451	+	// wrap the stuntdouble's position back into the box:
1452	+
1453	+	if (usePeriodicBoundaryConditions_)
1454	+	currentSnap_->wrapVector(pos);
1455	+
1456	+
1457	+	// which bin is this stuntdouble in?
1458	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	+	// Shift molecules by half a box to have bins start at 0
1460	+	// The modulo operator is used to wrap the case when we are
1461	+	// beyond the end of the bins back to the beginning.
1462	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463	+
1464	+	RealType mass = sd->getMass();
1465	+	Vector3d vel = sd->getVel();
1466	+
1467	+	binCount[binNo]++;
1468	+	binMass[binNo] += mass;
1469	+	binPx[binNo] += mass*vel.x();
1470	+	binPy[binNo] += mass*vel.y();
1471	+	binPz[binNo] += mass*vel.z();
1472	+	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1473	+	binDOF[binNo] += 3;
1474	+
1475	+	if (sd->isDirectional()) {
1476	+	Vector3d angMom = sd->getJ();
1477	+	Mat3x3d I = sd->getI();
1478	+	if (sd->isLinear()) {
1479	+	int i = sd->linearAxis();
1480	+	int j = (i + 1) % 3;
1481	+	int k = (i + 2) % 3;
1482	+	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1483	+	angMom[k] * angMom[k] / I(k, k));
1484	+	binDOF[binNo] += 2;
1485	+	} else {
1486	+	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1487	+	angMom[1] * angMom[1] / I(1, 1) +
1488	+	angMom[2] * angMom[2] / I(2, 2));
1489	+	binDOF[binNo] += 3;
1490	+	}
1491	+	}
1492	+	}
1493	+
1494	+	#ifdef IS_MPI
1495	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1496	+	nBins_, MPI::INT, MPI::SUM);
1497	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1498	+	nBins_, MPI::REALTYPE, MPI::SUM);
1499	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1500	+	nBins_, MPI::REALTYPE, MPI::SUM);
1501	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1502	+	nBins_, MPI::REALTYPE, MPI::SUM);
1503	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1504	+	nBins_, MPI::REALTYPE, MPI::SUM);
1505	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1506	+	nBins_, MPI::REALTYPE, MPI::SUM);
1507	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1508	+	nBins_, MPI::INT, MPI::SUM);
1509	+	#endif
1510	+
1511	+	Vector3d vel;
1512	+	RealType den;
1513	+	RealType temp;
1514	+	RealType z;
1515	+	for (int i = 0; i < nBins_; i++) {
1516	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1517	+	vel.x() = binPx[i] / binMass[i];
1518	+	vel.y() = binPy[i] / binMass[i];
1519	+	vel.z() = binPz[i] / binMass[i];
1520	+
1521	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1522	+	/ currentSnap_->getVolume() ;
1523	+
1524	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1525	+	PhysicalConstants::energyConvert);
1526	+
1527	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1528	+	if(outputMask_[j]) {
1529	+	switch(j) {
1530	+	case Z:
1531	+	(data_[j].accumulator[i])->add(z);
1532	+	break;
1533	+	case TEMPERATURE:
1534	+	data_[j].accumulator[i]->add(temp);
1535	+	break;
1536	+	case VELOCITY:
1537	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1538	+	break;
1539	+	case DENSITY:
1540	+	data_[j].accumulator[i]->add(den);
1541	+	break;
1542	+	}
1543	+	}
1544	+	}
1545	+	}
1546	+	}
1547	+
1548	+	void RNEMD::getStarted() {
1549	+	if (!doRNEMD_) return;
1550	+	collectData();
1551	+	writeOutputFile();
1552	+	}
1553	+
1554	+	void RNEMD::parseOutputFileFormat(const std::string& format) {
1555	+	if (!doRNEMD_) return;
1556	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1557	+
1558	+	while(tokenizer.hasMoreTokens()) {
1559	+	std::string token(tokenizer.nextToken());
1560	+	toUpper(token);
1561	+	OutputMapType::iterator i = outputMap_.find(token);
1562	+	if (i != outputMap_.end()) {
1563	+	outputMask_.set(i->second);
1564	+	} else {
1565	+	sprintf( painCave.errMsg,
1566	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1567	+	"\toutputFileFormat keyword.\n", token.c_str() );
1568	+	painCave.isFatal = 0;
1569	+	painCave.severity = OPENMD_ERROR;
1570	+	simError();
1571	+	}
1572	+	}
1573	+	}
1574	+
1575	+	void RNEMD::writeOutputFile() {
1576	+	if (!doRNEMD_) return;
1577	+
1578	+	#ifdef IS_MPI
1579		// If we're the root node, should we print out the results
1580		int worldRank = MPI::COMM_WORLD.Get_rank();
1581		if (worldRank == 0) {
1582		#endif
1583	<
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";
1583	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1584
1585	+	if( !rnemdFile_ ){
1586	+	sprintf( painCave.errMsg,
1587	+	"Could not open \"%s\" for RNEMD output.\n",
1588	+	rnemdFileName_.c_str());
1589	+	painCave.isFatal = 1;
1590	+	simError();
1591	+	}
1592	+
1593	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1594	+
1595	+	RealType time = currentSnap_->getTime();
1596	+	RealType avgArea;
1597	+	areaAccumulator_->getAverage(avgArea);
1598	+	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1599	+	/ PhysicalConstants::energyConvert;
1600	+	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1601	+
1602	+	rnemdFile_ << "#######################################################\n";
1603	+	rnemdFile_ << "# RNEMD {\n";
1604	+
1605	+	map<string, RNEMDMethod>::iterator mi;
1606	+	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1607	+	if ( (*mi).second == rnemdMethod_)
1608	+	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1609	+	}
1610	+	map<string, RNEMDFluxType>::iterator fi;
1611	+	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1612	+	if ( (*fi).second == rnemdFluxType_)
1613	+	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1614	+	}
1615	+
1616	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1617	+
1618	+	rnemdFile_ << "#    objectSelection = \""
1619	+	<< rnemdObjectSelection_ << "\";\n";
1620	+	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1621	+	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1622	+	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1623	+	rnemdFile_ << "# }\n";
1624	+	rnemdFile_ << "#######################################################\n";
1625	+	rnemdFile_ << "# RNEMD report:\n";
1626	+	rnemdFile_ << "#     running time = " << time << " fs\n";
1627	+	rnemdFile_ << "#     target flux:\n";
1628	+	rnemdFile_ << "#         kinetic = "
1629	+	<< kineticFlux_ / PhysicalConstants::energyConvert
1630	+	<< " (kcal/mol/A^2/fs)\n";
1631	+	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1632	+	<< " (amu/A/fs^2)\n";
1633	+	rnemdFile_ << "#     target one-time exchanges:\n";
1634	+	rnemdFile_ << "#         kinetic = "
1635	+	<< kineticTarget_ / PhysicalConstants::energyConvert
1636	+	<< " (kcal/mol)\n";
1637	+	rnemdFile_ << "#         momentum = " << momentumTarget_
1638	+	<< " (amu*A/fs)\n";
1639	+	rnemdFile_ << "#     actual exchange totals:\n";
1640	+	rnemdFile_ << "#         kinetic = "
1641	+	<< kineticExchange_ / PhysicalConstants::energyConvert
1642	+	<< " (kcal/mol)\n";
1643	+	rnemdFile_ << "#         momentum = " << momentumExchange_
1644	+	<< " (amu*A/fs)\n";
1645	+	rnemdFile_ << "#     actual flux:\n";
1646	+	rnemdFile_ << "#         kinetic = " << Jz
1647	+	<< " (kcal/mol/A^2/fs)\n";
1648	+	rnemdFile_ << "#         momentum = " << JzP
1649	+	<< " (amu/A/fs^2)\n";
1650	+	rnemdFile_ << "#     exchange statistics:\n";
1651	+	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1652	+	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1653	+	if (rnemdMethod_ == rnemdNIVS) {
1654	+	rnemdFile_ << "#         NIVS root-check errors = "
1655	+	<< failRootCount_ << "\n";
1656	+	}
1657	+	rnemdFile_ << "#######################################################\n";
1658	+
1659	+
1660	+
1661	+	//write title
1662	+	rnemdFile_ << "#";
1663	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1664	+	if (outputMask_[i]) {
1665	+	rnemdFile_ << "\t" << data_[i].title <<
1666	+	"(" << data_[i].units << ")";
1667	+	// add some extra tabs for column alignment
1668	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1669	+	}
1670	+	}
1671	+	rnemdFile_ << std::endl;
1672	+
1673	+	rnemdFile_.precision(8);
1674	+
1675	+	for (unsigned int j = 0; j < nBins_; j++) {
1676	+
1677	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1678	+	if (outputMask_[i]) {
1679	+	if (data_[i].dataType == "RealType")
1680	+	writeReal(i,j);
1681	+	else if (data_[i].dataType == "Vector3d")
1682	+	writeVector(i,j);
1683	+	else {
1684	+	sprintf( painCave.errMsg,
1685	+	"RNEMD found an unknown data type for: %s ",
1686	+	data_[i].title.c_str());
1687	+	painCave.isFatal = 1;
1688	+	simError();
1689	+	}
1690	+	}
1691	+	}
1692	+	rnemdFile_ << std::endl;
1693	+
1694	+	}
1695	+
1696	+	rnemdFile_ << "#######################################################\n";
1697	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1698	+	rnemdFile_ << "#######################################################\n";
1699	+
1700	+
1701	+	for (unsigned int j = 0; j < nBins_; j++) {
1702	+	rnemdFile_ << "#";
1703	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1704	+	if (outputMask_[i]) {
1705	+	if (data_[i].dataType == "RealType")
1706	+	writeRealStdDev(i,j);
1707	+	else if (data_[i].dataType == "Vector3d")
1708	+	writeVectorStdDev(i,j);
1709	+	else {
1710	+	sprintf( painCave.errMsg,
1711	+	"RNEMD found an unknown data type for: %s ",
1712	+	data_[i].title.c_str());
1713	+	painCave.isFatal = 1;
1714	+	simError();
1715	+	}
1716	+	}
1717	+	}
1718	+	rnemdFile_ << std::endl;
1719	+
1720	+	}
1721	+
1722	+	rnemdFile_.flush();
1723	+	rnemdFile_.close();
1724	+
1725		#ifdef IS_MPI
1726		}
1727		#endif
1728	+
1729		}
1730	+
1731	+	void RNEMD::writeReal(int index, unsigned int bin) {
1732	+	if (!doRNEMD_) return;
1733	+	assert(index >=0 && index < ENDINDEX);
1734	+	assert(bin < nBins_);
1735	+	RealType s;
1736	+
1737	+	data_[index].accumulator[bin]->getAverage(s);
1738	+
1739	+	if (! isinf(s) && ! isnan(s)) {
1740	+	rnemdFile_ << "\t" << s;
1741	+	} else{
1742	+	sprintf( painCave.errMsg,
1743	+	"RNEMD detected a numerical error writing: %s for bin %d",
1744	+	data_[index].title.c_str(), bin);
1745	+	painCave.isFatal = 1;
1746	+	simError();
1747	+	}
1748	+	}
1749	+
1750	+	void RNEMD::writeVector(int index, unsigned int bin) {
1751	+	if (!doRNEMD_) return;
1752	+	assert(index >=0 && index < ENDINDEX);
1753	+	assert(bin < nBins_);
1754	+	Vector3d s;
1755	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1756	+	if (isinf(s[0]) || isnan(s[0]) ||
1757	+	isinf(s[1]) || isnan(s[1]) ||
1758	+	isinf(s[2]) || isnan(s[2]) ) {
1759	+	sprintf( painCave.errMsg,
1760	+	"RNEMD detected a numerical error writing: %s for bin %d",
1761	+	data_[index].title.c_str(), bin);
1762	+	painCave.isFatal = 1;
1763	+	simError();
1764	+	} else {
1765	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1766	+	}
1767	+	}
1768	+
1769	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1770	+	if (!doRNEMD_) return;
1771	+	assert(index >=0 && index < ENDINDEX);
1772	+	assert(bin < nBins_);
1773	+	RealType s;
1774	+
1775	+	data_[index].accumulator[bin]->getStdDev(s);
1776	+
1777	+	if (! isinf(s) && ! isnan(s)) {
1778	+	rnemdFile_ << "\t" << s;
1779	+	} else{
1780	+	sprintf( painCave.errMsg,
1781	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1782	+	data_[index].title.c_str(), bin);
1783	+	painCave.isFatal = 1;
1784	+	simError();
1785	+	}
1786	+	}
1787	+
1788	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1789	+	if (!doRNEMD_) return;
1790	+	assert(index >=0 && index < ENDINDEX);
1791	+	assert(bin < nBins_);
1792	+	Vector3d s;
1793	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1794	+	if (isinf(s[0]) || isnan(s[0]) ||
1795	+	isinf(s[1]) || isnan(s[1]) ||
1796	+	isinf(s[2]) || isnan(s[2]) ) {
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1799	+	data_[index].title.c_str(), bin);
1800	+	painCave.isFatal = 1;
1801	+	simError();
1802	+	} else {
1803	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1804	+	}
1805	+	}
1806		}
1807	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

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