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root/OpenMD/branches/development/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.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1777 by gezelter, Thu Aug 9 18:35:09 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42	<	#include "integrators/RNEMD.hpp"
42	>	#include <cmath>
43	>	#include "rnemd/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45	+	#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
47	+	#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50	<	#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();
#	Line 80 | Line 281 | namespace oopse {
281
282		if (selectionCount > nIntegrable) {
283		sprintf(painCave.errMsg,
284	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
284	>	"RNEMD: The current objectSelection,\n"
285		"\t\t%s\n"
286		"\thas resulted in %d selected objects.  However,\n"
287		"\tthe total number of integrable objects in the system\n"
#	Line 90 | Line 291 | namespace oopse {
291		rnemdObjectSelection_.c_str(),
292		selectionCount, nIntegrable);
293		painCave.isFatal = 0;
294	+	painCave.severity = OPENMD_WARNING;
295		simError();
296	+	}
297
298	+	areaAccumulator_ = new Accumulator();
299	+
300	+	nBins_ = rnemdParams->getOutputBins();
301	+
302	+	data_.resize(RNEMD::ENDINDEX);
303	+	OutputData z;
304	+	z.units =  "Angstroms";
305	+	z.title =  "Z";
306	+	z.dataType = "RealType";
307	+	z.accumulator.reserve(nBins_);
308	+	for (unsigned int i = 0; i < nBins_; i++)
309	+	z.accumulator.push_back( new Accumulator() );
310	+	data_[Z] = z;
311	+	outputMap_["Z"] =  Z;
312	+
313	+	OutputData temperature;
314	+	temperature.units =  "K";
315	+	temperature.title =  "Temperature";
316	+	temperature.dataType = "RealType";
317	+	temperature.accumulator.reserve(nBins_);
318	+	for (unsigned int i = 0; i < nBins_; i++)
319	+	temperature.accumulator.push_back( new Accumulator() );
320	+	data_[TEMPERATURE] = temperature;
321	+	outputMap_["TEMPERATURE"] =  TEMPERATURE;
322	+
323	+	OutputData velocity;
324	+	velocity.units = "angstroms/fs";
325	+	velocity.title =  "Velocity";
326	+	velocity.dataType = "Vector3d";
327	+	velocity.accumulator.reserve(nBins_);
328	+	for (unsigned int i = 0; i < nBins_; i++)
329	+	velocity.accumulator.push_back( new VectorAccumulator() );
330	+	data_[VELOCITY] = velocity;
331	+	outputMap_["VELOCITY"] = VELOCITY;
332	+
333	+	OutputData density;
334	+	density.units =  "g cm^-3";
335	+	density.title =  "Density";
336	+	density.dataType = "RealType";
337	+	density.accumulator.reserve(nBins_);
338	+	for (unsigned int i = 0; i < nBins_; i++)
339	+	density.accumulator.push_back( new Accumulator() );
340	+	data_[DENSITY] = density;
341	+	outputMap_["DENSITY"] =  DENSITY;
342	+
343	+	if (hasOutputFields) {
344	+	parseOutputFileFormat(rnemdParams->getOutputFields());
345	+	} else {
346	+	outputMask_.set(Z);
347	+	switch (rnemdFluxType_) {
348	+	case rnemdKE:
349	+	case rnemdRotKE:
350	+	case rnemdFullKE:
351	+	outputMask_.set(TEMPERATURE);
352	+	break;
353	+	case rnemdPx:
354	+	case rnemdPy:
355	+	outputMask_.set(VELOCITY);
356	+	break;
357	+	case rnemdPz:
358	+	case rnemdPvector:
359	+	outputMask_.set(VELOCITY);
360	+	outputMask_.set(DENSITY);
361	+	break;
362	+	case rnemdKePx:
363	+	case rnemdKePy:
364	+	outputMask_.set(TEMPERATURE);
365	+	outputMask_.set(VELOCITY);
366	+	break;
367	+	case rnemdKePvector:
368	+	outputMask_.set(TEMPERATURE);
369	+	outputMask_.set(VELOCITY);
370	+	outputMask_.set(DENSITY);
371	+	break;
372	+	default:
373	+	break;
374	+	}
375		}
376	<
377	<	const std::string st = simParams->getRNEMD_swapType();
376	>
377	>	if (hasOutputFileName) {
378	>	rnemdFileName_ = rnemdParams->getOutputFileName();
379	>	} else {
380	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
381	>	}
382
383	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
100	<	i = stringToEnumMap_.find(st);
101	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
383	>	exchangeTime_ = rnemdParams->getExchangeTime();
384
385	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
386	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
387	<	exchangeSum_ = 0.0;
385	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
386	>	Mat3x3d hmat = currentSnap_->getHmat();
387	>
388	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
389	>	// Lx, Ly = box dimensions in x & y
390	>	// dt = exchange time interval
391	>	// flux = target flux
392
393	<	#ifndef IS_MPI
394	<	if (simParams->haveSeed()) {
395	<	seedValue = simParams->getSeed();
396	<	randNumGen_ = new SeqRandNumGen(seedValue);
397	<	}else {
398	<	randNumGen_ = new SeqRandNumGen();
399	<	}
400	<	#else
401	<	if (simParams->haveSeed()) {
402	<	seedValue = simParams->getSeed();
403	<	randNumGen_ = new ParallelRandNumGen(seedValue);
404	<	}else {
405	<	randNumGen_ = new ParallelRandNumGen();
120	<	}
121	<	#endif
122	<	}
393	>	RealType area = currentSnap_->getXYarea();
394	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
395	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
396	>
397	>	// total exchange sums are zeroed out at the beginning:
398	>
399	>	kineticExchange_ = 0.0;
400	>	momentumExchange_ = V3Zero;
401	>
402	>	if (hasSlabWidth)
403	>	slabWidth_ = rnemdParams->getSlabWidth();
404	>	else
405	>	slabWidth_ = hmat(2,2) / 10.0;
406
407	+	if (hasSlabACenter)
408	+	slabACenter_ = rnemdParams->getSlabACenter();
409	+	else
410	+	slabACenter_ = 0.0;
411	+
412	+	if (hasSlabBCenter)
413	+	slabBCenter_ = rnemdParams->getSlabBCenter();
414	+	else
415	+	slabBCenter_ = hmat(2,2) / 2.0;
416	+
417	+	}
418	+
419		RNEMD::~RNEMD() {
420	<	delete randNumGen_;
420	>	if (!doRNEMD_) return;
421	>	#ifdef IS_MPI
422	>	if (worldRank == 0) {
423	>	#endif
424	>
425	>	writeOutputFile();
426	>
427	>	rnemdFile_.close();
428	>
429	>	#ifdef IS_MPI
430	>	}
431	>	#endif
432		}
433	+
434	+	bool RNEMD::inSlabA(Vector3d pos) {
435	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
436	+	}
437	+	bool RNEMD::inSlabB(Vector3d pos) {
438	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
439	+	}
440
441		void RNEMD::doSwap() {
442	<	int midBin = nBins_ / 2;
130	<
442	>	if (!doRNEMD_) return;
443		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
444		Mat3x3d hmat = currentSnap_->getHmat();
445
#	Line 156 | Line 468 | namespace oopse {
468
469		if (usePeriodicBoundaryConditions_)
470		currentSnap_->wrapVector(pos);
471	+	bool inA = inSlabA(pos);
472	+	bool inB = inSlabB(pos);
473
474	<	// 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) {
474	>	if (inA || inB) {
475
476		RealType mass = sd->getMass();
477		Vector3d vel = sd->getVel();
478		RealType value;
479	<
480	<	switch(rnemdType_) {
481	<	case rnemdKinetic :
479	>
480	>	switch(rnemdFluxType_) {
481	>	case rnemdKE :
482
483	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
484	<	vel[2]*vel[2]);
485	<	if (sd->isDirectional()) {
483	>	value = mass * vel.lengthSquare();
484	>
485	>	if (sd->isDirectional()) {
486		Vector3d angMom = sd->getJ();
487		Mat3x3d I = sd->getI();
488
489		if (sd->isLinear()) {
490	<	int i = sd->linearAxis();
491	<	int j = (i + 1) % 3;
492	<	int k = (i + 2) % 3;
493	<	value += angMom[j] * angMom[j] / I(j, j) +
494	<	angMom[k] * angMom[k] / I(k, k);
490	>	int i = sd->linearAxis();
491	>	int j = (i + 1) % 3;
492	>	int k = (i + 2) % 3;
493	>	value += angMom[j] * angMom[j] / I(j, j) +
494	>	angMom[k] * angMom[k] / I(k, k);
495		} else {
496	<	value += angMom[0]*angMom[0]/I(0, 0)
497	<	+ angMom[1]*angMom[1]/I(1, 1)
498	<	+ angMom[2]*angMom[2]/I(2, 2);
496	>	value += angMom[0]*angMom[0]/I(0, 0)
497	>	+ angMom[1]*angMom[1]/I(1, 1)
498	>	+ angMom[2]*angMom[2]/I(2, 2);
499		}
500	<	}
501	<	value = value * 0.5 / OOPSEConstant::energyConvert;
500	>	} //angular momenta exchange enabled
501	>	value *= 0.5;
502		break;
503		case rnemdPx :
504		value = mass * vel[0];
#	Line 202 | Line 509 | namespace oopse {
509		case rnemdPz :
510		value = mass * vel[2];
511		break;
205	–	case rnemdUnknown :
512		default :
513		break;
514		}
515
516	<	if (binNo == 0) {
516	>	if (inA == 0) {
517		if (!min_found) {
518		min_val = value;
519		min_sd = sd;
#	Line 218 | Line 524 | namespace oopse {
524		min_sd = sd;
525		}
526		}
527	<	} else {
527	>	} else {
528		if (!max_found) {
529		max_val = value;
530		max_sd = sd;
#	Line 232 | Line 538 | namespace oopse {
538		}
539		}
540		}
541	<
541	>
542		#ifdef IS_MPI
543		int nProc, worldRank;
544	<
544	>
545		nProc = MPI::COMM_WORLD.Get_size();
546		worldRank = MPI::COMM_WORLD.Get_rank();
547
#	Line 243 | Line 549 | namespace oopse {
549		bool my_max_found = max_found;
550
551		// Even if we didn't find a minimum, did someone else?
552	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
552	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
553		// Even if we didn't find a maximum, did someone else?
554	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
555	<	1, MPI::BOOL, MPI::LAND);
556	<
557	<	struct {
558	<	RealType val;
559	<	int rank;
560	<	} max_vals, min_vals;
561	<
562	<	if (min_found) {
563	<	if (my_min_found)
554	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
555	>	#endif
556	>
557	>	if (max_found && min_found) {
558	>
559	>	#ifdef IS_MPI
560	>	struct {
561	>	RealType val;
562	>	int rank;
563	>	} max_vals, min_vals;
564	>
565	>	if (my_min_found) {
566		min_vals.val = min_val;
567	<	else
567	>	} else {
568		min_vals.val = HONKING_LARGE_VALUE;
569	<
569	>	}
570		min_vals.rank = worldRank;
571
572		// Who had the minimum?
573		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
574		1, MPI::REALTYPE_INT, MPI::MINLOC);
575		min_val = min_vals.val;
270	–	}
576
577	<	if (max_found) {
273	<	if (my_max_found)
577	>	if (my_max_found) {
578		max_vals.val = max_val;
579	<	else
579	>	} else {
580		max_vals.val = -HONKING_LARGE_VALUE;
581	<
581	>	}
582		max_vals.rank = worldRank;
583
584		// Who had the maximum?
585		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
586		1, MPI::REALTYPE_INT, MPI::MAXLOC);
587		max_val = max_vals.val;
284	–	}
588		#endif
589	<
590	<	if (max_found && min_found) {
591	<	if (min_val< max_val) {
289	<
589	>
590	>	if (min_val < max_val) {
591	>
592		#ifdef IS_MPI
593		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
594		// I have both maximum and minimum, so proceed like a single
595		// processor version:
596		#endif
597	<	// objects to be swapped: velocity & angular velocity
597	>
598		Vector3d min_vel = min_sd->getVel();
599		Vector3d max_vel = max_sd->getVel();
600		RealType temp_vel;
601
602	<	switch(rnemdType_) {
603	<	case rnemdKinetic :
602	>	switch(rnemdFluxType_) {
603	>	case rnemdKE :
604		min_sd->setVel(max_vel);
605		max_sd->setVel(min_vel);
606	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
606	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
607		Vector3d min_angMom = min_sd->getJ();
608		Vector3d max_angMom = max_sd->getJ();
609		min_sd->setJ(max_angMom);
610		max_sd->setJ(min_angMom);
611	<	}
611	>	}//angular momenta exchange enabled
612	>	//assumes same rigid body identity
613		break;
614		case rnemdPx :
615		temp_vel = min_vel.x();
#	Line 329 | Line 632 | namespace oopse {
632		min_sd->setVel(min_vel);
633		max_sd->setVel(max_vel);
634		break;
332	–	case rnemdUnknown :
635		default :
636		break;
637		}
638	+
639		#ifdef IS_MPI
640		// the rest of the cases only apply in parallel simulations:
641		} else if (max_vals.rank == worldRank) {
#	Line 348 | Line 651 | namespace oopse {
651		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
652		min_vals.rank, 0, status);
653
654	<	switch(rnemdType_) {
655	<	case rnemdKinetic :
654	>	switch(rnemdFluxType_) {
655	>	case rnemdKE :
656		max_sd->setVel(min_vel);
657	<
657	>	//angular momenta exchange enabled
658		if (max_sd->isDirectional()) {
659		Vector3d min_angMom;
660		Vector3d max_angMom = max_sd->getJ();
661	<
661	>
662		// point-to-point swap of the angular momentum vector
663		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
664		MPI::REALTYPE, min_vals.rank, 1,
665		min_angMom.getArrayPointer(), 3,
666		MPI::REALTYPE, min_vals.rank, 1,
667		status);
668	<
668	>
669		max_sd->setJ(min_angMom);
670	<	}
670	>	}
671		break;
672		case rnemdPx :
673		max_vel.x() = min_vel.x();
#	Line 378 | Line 681 | namespace oopse {
681		max_vel.z() = min_vel.z();
682		max_sd->setVel(max_vel);
683		break;
381	–	case rnemdUnknown :
684		default :
685		break;
686		}
#	Line 395 | Line 697 | namespace oopse {
697		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
698		max_vals.rank, 0, status);
699
700	<	switch(rnemdType_) {
701	<	case rnemdKinetic :
700	>	switch(rnemdFluxType_) {
701	>	case rnemdKE :
702		min_sd->setVel(max_vel);
703	<
703	>	//angular momenta exchange enabled
704		if (min_sd->isDirectional()) {
705		Vector3d min_angMom = min_sd->getJ();
706		Vector3d max_angMom;
707	<
707	>
708		// point-to-point swap of the angular momentum vector
709		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
710		MPI::REALTYPE, max_vals.rank, 1,
711		max_angMom.getArrayPointer(), 3,
712		MPI::REALTYPE, max_vals.rank, 1,
713		status);
714	<
714	>
715		min_sd->setJ(max_angMom);
716		}
717		break;
#	Line 425 | Line 727 | namespace oopse {
727		min_vel.z() = max_vel.z();
728		min_sd->setVel(min_vel);
729		break;
428	–	case rnemdUnknown :
730		default :
731		break;
732		}
733		}
734		#endif
735	<	exchangeSum_ += max_val - min_val;
736	<	} else {
737	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
735	>
736	>	switch(rnemdFluxType_) {
737	>	case rnemdKE:
738	>	kineticExchange_ += max_val - min_val;
739	>	break;
740	>	case rnemdPx:
741	>	momentumExchange_.x() += max_val - min_val;
742	>	break;
743	>	case rnemdPy:
744	>	momentumExchange_.y() += max_val - min_val;
745	>	break;
746	>	case rnemdPz:
747	>	momentumExchange_.z() += max_val - min_val;
748	>	break;
749	>	default:
750	>	break;
751	>	}
752	>	} else {
753	>	sprintf(painCave.errMsg,
754	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
755	>	painCave.isFatal = 0;
756	>	painCave.severity = OPENMD_INFO;
757	>	simError();
758	>	failTrialCount_++;
759		}
760		} else {
761	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
762	<	}
763	<
761	>	sprintf(painCave.errMsg,
762	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
763	>	"\twas not present in at least one of the two slabs.\n");
764	>	painCave.isFatal = 0;
765	>	painCave.severity = OPENMD_INFO;
766	>	simError();
767	>	failTrialCount_++;
768	>	}
769		}
770
771	<	void RNEMD::getStatus() {
772	<
771	>	void RNEMD::doNIVS() {
772	>	if (!doRNEMD_) return;
773		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
774		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
775
451	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	–
776		seleMan_.setSelectionSet(evaluator_.evaluate());
777
778		int selei;
779		StuntDouble* sd;
780		int idx;
781
782	<	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
782	>	vector<StuntDouble*> hotBin, coldBin;
783
784	+	RealType Phx = 0.0;
785	+	RealType Phy = 0.0;
786	+	RealType Phz = 0.0;
787	+	RealType Khx = 0.0;
788	+	RealType Khy = 0.0;
789	+	RealType Khz = 0.0;
790	+	RealType Khw = 0.0;
791	+	RealType Pcx = 0.0;
792	+	RealType Pcy = 0.0;
793	+	RealType Pcz = 0.0;
794	+	RealType Kcx = 0.0;
795	+	RealType Kcy = 0.0;
796	+	RealType Kcz = 0.0;
797	+	RealType Kcw = 0.0;
798	+
799		for (sd = seleMan_.beginSelected(selei); sd != NULL;
800		sd = seleMan_.nextSelected(selei)) {
801	<
801	>
802		idx = sd->getLocalIndex();
803	<
803	>
804		Vector3d pos = sd->getPos();
805
806		// wrap the stuntdouble's position back into the box:
807	<
807	>
808		if (usePeriodicBoundaryConditions_)
809		currentSnap_->wrapVector(pos);
476	–
477	–	// which bin is this stuntdouble in?
478	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
479	–
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;
810
811	<	switch(rnemdType_) {
812	<	case rnemdKinetic :
813	<
489	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
490	<	vel[2]*vel[2]);
491	<
492	<	valueCount[binNo] += 3;
493	<	if (sd->isDirectional()) {
494	<	Vector3d angMom = sd->getJ();
495	<	Mat3x3d I = sd->getI();
496	<
497	<	if (sd->isLinear()) {
498	<	int i = sd->linearAxis();
499	<	int j = (i + 1) % 3;
500	<	int k = (i + 2) % 3;
501	<	value += angMom[j] * angMom[j] / I(j, j) +
502	<	angMom[k] * angMom[k] / I(k, k);
811	>	// which bin is this stuntdouble in?
812	>	bool inA = inSlabA(pos);
813	>	bool inB = inSlabB(pos);
814
815	<	valueCount[binNo] +=2;
816	<
817	<	} else {
818	<	value += angMom[0]*angMom[0]/I(0, 0)
819	<	+ angMom[1]*angMom[1]/I(1, 1)
820	<	+ angMom[2]*angMom[2]/I(2, 2);
821	<	valueCount[binNo] +=3;
815	>	if (inA || inB) {
816	>
817	>	RealType mass = sd->getMass();
818	>	Vector3d vel = sd->getVel();
819	>
820	>	if (inA) {
821	>	hotBin.push_back(sd);
822	>	Phx += mass * vel.x();
823	>	Phy += mass * vel.y();
824	>	Phz += mass * vel.z();
825	>	Khx += mass * vel.x() * vel.x();
826	>	Khy += mass * vel.y() * vel.y();
827	>	Khz += mass * vel.z() * vel.z();
828	>	if (sd->isDirectional()) {
829	>	Vector3d angMom = sd->getJ();
830	>	Mat3x3d I = sd->getI();
831	>	if (sd->isLinear()) {
832	>	int i = sd->linearAxis();
833	>	int j = (i + 1) % 3;
834	>	int k = (i + 2) % 3;
835	>	Khw += angMom[j] * angMom[j] / I(j, j) +
836	>	angMom[k] * angMom[k] / I(k, k);
837	>	} else {
838	>	Khw += angMom[0]*angMom[0]/I(0, 0)
839	>	+ angMom[1]*angMom[1]/I(1, 1)
840	>	+ angMom[2]*angMom[2]/I(2, 2);
841	>	}
842		}
843	+	} else {
844	+	coldBin.push_back(sd);
845	+	Pcx += mass * vel.x();
846	+	Pcy += mass * vel.y();
847	+	Pcz += mass * vel.z();
848	+	Kcx += mass * vel.x() * vel.x();
849	+	Kcy += mass * vel.y() * vel.y();
850	+	Kcz += mass * vel.z() * vel.z();
851	+	if (sd->isDirectional()) {
852	+	Vector3d angMom = sd->getJ();
853	+	Mat3x3d I = sd->getI();
854	+	if (sd->isLinear()) {
855	+	int i = sd->linearAxis();
856	+	int j = (i + 1) % 3;
857	+	int k = (i + 2) % 3;
858	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
859	+	angMom[k] * angMom[k] / I(k, k);
860	+	} else {
861	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
862	+	+ angMom[1]*angMom[1]/I(1, 1)
863	+	+ angMom[2]*angMom[2]/I(2, 2);
864	+	}
865	+	}
866		}
867	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
867	>	}
868	>	}
869	>
870	>	Khx *= 0.5;
871	>	Khy *= 0.5;
872	>	Khz *= 0.5;
873	>	Khw *= 0.5;
874	>	Kcx *= 0.5;
875	>	Kcy *= 0.5;
876	>	Kcz *= 0.5;
877	>	Kcw *= 0.5;
878
879	<	break;
880	<	case rnemdPx :
881	<	value = mass * vel[0];
882	<	valueCount[binNo]++;
879	>	#ifdef IS_MPI
880	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
881	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
882	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
883	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
884	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
885	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
886	>
887	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
888	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
889	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
890	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
891	>
892	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
893	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
894	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
895	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
896	>	#endif
897	>
898	>	//solve coldBin coeff's first
899	>	RealType px = Pcx / Phx;
900	>	RealType py = Pcy / Phy;
901	>	RealType pz = Pcz / Phz;
902	>	RealType c, x, y, z;
903	>	bool successfulScale = false;
904	>	if ((rnemdFluxType_ == rnemdFullKE) ||
905	>	(rnemdFluxType_ == rnemdRotKE)) {
906	>	//may need sanity check Khw & Kcw > 0
907	>
908	>	if (rnemdFluxType_ == rnemdFullKE) {
909	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
910	>	} else {
911	>	c = 1.0 - kineticTarget_ / Kcw;
912	>	}
913	>
914	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
915	>	c = sqrt(c);
916	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
917	>	//now convert to hotBin coefficient
918	>	RealType w = 0.0;
919	>	if (rnemdFluxType_ ==  rnemdFullKE) {
920	>	x = 1.0 + px * (1.0 - c);
921	>	y = 1.0 + py * (1.0 - c);
922	>	z = 1.0 + pz * (1.0 - c);
923	>	/* more complicated way
924	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
925	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
926	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
927	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
928	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
929	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
930	>	*/
931	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
932	>	(fabs(z - 1.0) < 0.1)) {
933	>	w = 1.0 + (kineticTarget_
934	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
935	>	+ Khz * (1.0 - z * z)) / Khw;
936	>	}//no need to calculate w if x, y or z is out of range
937	>	} else {
938	>	w = 1.0 + kineticTarget_ / Khw;
939	>	}
940	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
941	>	//if w is in the right range, so should be x, y, z.
942	>	vector<StuntDouble*>::iterator sdi;
943	>	Vector3d vel;
944	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
945	>	if (rnemdFluxType_ == rnemdFullKE) {
946	>	vel = (*sdi)->getVel() * c;
947	>	(*sdi)->setVel(vel);
948	>	}
949	>	if ((*sdi)->isDirectional()) {
950	>	Vector3d angMom = (*sdi)->getJ() * c;
951	>	(*sdi)->setJ(angMom);
952	>	}
953	>	}
954	>	w = sqrt(w);
955	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
956	>	//           << "\twh= " << w << endl;
957	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
958	>	if (rnemdFluxType_ == rnemdFullKE) {
959	>	vel = (*sdi)->getVel();
960	>	vel.x() *= x;
961	>	vel.y() *= y;
962	>	vel.z() *= z;
963	>	(*sdi)->setVel(vel);
964	>	}
965	>	if ((*sdi)->isDirectional()) {
966	>	Vector3d angMom = (*sdi)->getJ() * w;
967	>	(*sdi)->setJ(angMom);
968	>	}
969	>	}
970	>	successfulScale = true;
971	>	kineticExchange_ += kineticTarget_;
972	>	}
973	>	}
974	>	} else {
975	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
976	>	switch(rnemdFluxType_) {
977	>	case rnemdKE :
978	>	/* used hotBin coeff's & only scale x & y dimensions
979	>	RealType px = Phx / Pcx;
980	>	RealType py = Phy / Pcy;
981	>	a110 = Khy;
982	>	c0 = - Khx - Khy - kineticTarget_;
983	>	a000 = Khx;
984	>	a111 = Kcy * py * py;
985	>	b11 = -2.0 * Kcy * py * (1.0 + py);
986	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
987	>	b01 = -2.0 * Kcx * px * (1.0 + px);
988	>	a001 = Kcx * px * px;
989	>	*/
990	>	//scale all three dimensions, let c_x = c_y
991	>	a000 = Kcx + Kcy;
992	>	a110 = Kcz;
993	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
994	>	a001 = Khx * px * px + Khy * py * py;
995	>	a111 = Khz * pz * pz;
996	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
997	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
998	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
999	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1000		break;
1001	+	case rnemdPx :
1002	+	c = 1 - momentumTarget_.x() / Pcx;
1003	+	a000 = Kcy;
1004	+	a110 = Kcz;
1005	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1006	+	a001 = py * py * Khy;
1007	+	a111 = pz * pz * Khz;
1008	+	b01 = -2.0 * Khy * py * (1.0 + py);
1009	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
1010	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1011	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1012	+	break;
1013		case rnemdPy :
1014	<	value = mass * vel[1];
1015	<	valueCount[binNo]++;
1014	>	c = 1 - momentumTarget_.y() / Pcy;
1015	>	a000 = Kcx;
1016	>	a110 = Kcz;
1017	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1018	>	a001 = px * px * Khx;
1019	>	a111 = pz * pz * Khz;
1020	>	b01 = -2.0 * Khx * px * (1.0 + px);
1021	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1022	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1023	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1024		break;
1025	<	case rnemdPz :
1026	<	value = mass * vel[2];
1027	<	valueCount[binNo]++;
1025	>	case rnemdPz ://we don't really do this, do we?
1026	>	c = 1 - momentumTarget_.z() / Pcz;
1027	>	a000 = Kcx;
1028	>	a110 = Kcy;
1029	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1030	>	a001 = px * px * Khx;
1031	>	a111 = py * py * Khy;
1032	>	b01 = -2.0 * Khx * px * (1.0 + px);
1033	>	b11 = -2.0 * Khy * py * (1.0 + py);
1034	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1035	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1036		break;
528	–	case rnemdUnknown :
1037		default :
1038		break;
1039		}
1040	<	valueHist[binNo] += value;
1040	>
1041	>	RealType v1 = a000 * a111 - a001 * a110;
1042	>	RealType v2 = a000 * b01;
1043	>	RealType v3 = a000 * b11;
1044	>	RealType v4 = a000 * c1 - a001 * c0;
1045	>	RealType v8 = a110 * b01;
1046	>	RealType v10 = - b01 * c0;
1047	>
1048	>	RealType u0 = v2 * v10 - v4 * v4;
1049	>	RealType u1 = -2.0 * v3 * v4;
1050	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1051	>	RealType u3 = -2.0 * v1 * v3;
1052	>	RealType u4 = - v1 * v1;
1053	>	//rescale coefficients
1054	>	RealType maxAbs = fabs(u0);
1055	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1056	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1057	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1058	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1059	>	u0 /= maxAbs;
1060	>	u1 /= maxAbs;
1061	>	u2 /= maxAbs;
1062	>	u3 /= maxAbs;
1063	>	u4 /= maxAbs;
1064	>	//max_element(start, end) is also available.
1065	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1066	>	poly.setCoefficient(4, u4);
1067	>	poly.setCoefficient(3, u3);
1068	>	poly.setCoefficient(2, u2);
1069	>	poly.setCoefficient(1, u1);
1070	>	poly.setCoefficient(0, u0);
1071	>	vector<RealType> realRoots = poly.FindRealRoots();
1072	>
1073	>	vector<RealType>::iterator ri;
1074	>	RealType r1, r2, alpha0;
1075	>	vector<pair<RealType,RealType> > rps;
1076	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1077	>	r2 = *ri;
1078	>	//check if FindRealRoots() give the right answer
1079	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1080	>	sprintf(painCave.errMsg,
1081	>	"RNEMD Warning: polynomial solve seems to have an error!");
1082	>	painCave.isFatal = 0;
1083	>	simError();
1084	>	failRootCount_++;
1085	>	}
1086	>	//might not be useful w/o rescaling coefficients
1087	>	alpha0 = -c0 - a110 * r2 * r2;
1088	>	if (alpha0 >= 0.0) {
1089	>	r1 = sqrt(alpha0 / a000);
1090	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1091	>	< 1e-6)
1092	>	{ rps.push_back(make_pair(r1, r2)); }
1093	>	if (r1 > 1e-6) { //r1 non-negative
1094	>	r1 = -r1;
1095	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1096	>	< 1e-6)
1097	>	{ rps.push_back(make_pair(r1, r2)); }
1098	>	}
1099	>	}
1100	>	}
1101	>	// Consider combining together the solving pair part w/ the searching
1102	>	// best solution part so that we don't need the pairs vector
1103	>	if (!rps.empty()) {
1104	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1105	>	RealType diff;
1106	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1107	>	vector<pair<RealType,RealType> >::iterator rpi;
1108	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1109	>	r1 = (*rpi).first;
1110	>	r2 = (*rpi).second;
1111	>	switch(rnemdFluxType_) {
1112	>	case rnemdKE :
1113	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1115	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1116	>	break;
1117	>	case rnemdPx :
1118	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1119	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120	>	break;
1121	>	case rnemdPy :
1122	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1124	>	break;
1125	>	case rnemdPz :
1126	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1128	>	default :
1129	>	break;
1130	>	}
1131	>	if (diff < smallestDiff) {
1132	>	smallestDiff = diff;
1133	>	bestPair = *rpi;
1134	>	}
1135	>	}
1136	>	#ifdef IS_MPI
1137	>	if (worldRank == 0) {
1138	>	#endif
1139	>	// sprintf(painCave.errMsg,
1140	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1141	>	//         bestPair.first, bestPair.second);
1142	>	// painCave.isFatal = 0;
1143	>	// painCave.severity = OPENMD_INFO;
1144	>	// simError();
1145	>	#ifdef IS_MPI
1146	>	}
1147	>	#endif
1148	>
1149	>	switch(rnemdFluxType_) {
1150	>	case rnemdKE :
1151	>	x = bestPair.first;
1152	>	y = bestPair.first;
1153	>	z = bestPair.second;
1154	>	break;
1155	>	case rnemdPx :
1156	>	x = c;
1157	>	y = bestPair.first;
1158	>	z = bestPair.second;
1159	>	break;
1160	>	case rnemdPy :
1161	>	x = bestPair.first;
1162	>	y = c;
1163	>	z = bestPair.second;
1164	>	break;
1165	>	case rnemdPz :
1166	>	x = bestPair.first;
1167	>	y = bestPair.second;
1168	>	z = c;
1169	>	break;
1170	>	default :
1171	>	break;
1172	>	}
1173	>	vector<StuntDouble*>::iterator sdi;
1174	>	Vector3d vel;
1175	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1176	>	vel = (*sdi)->getVel();
1177	>	vel.x() *= x;
1178	>	vel.y() *= y;
1179	>	vel.z() *= z;
1180	>	(*sdi)->setVel(vel);
1181	>	}
1182	>	//convert to hotBin coefficient
1183	>	x = 1.0 + px * (1.0 - x);
1184	>	y = 1.0 + py * (1.0 - y);
1185	>	z = 1.0 + pz * (1.0 - z);
1186	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1187	>	vel = (*sdi)->getVel();
1188	>	vel.x() *= x;
1189	>	vel.y() *= y;
1190	>	vel.z() *= z;
1191	>	(*sdi)->setVel(vel);
1192	>	}
1193	>	successfulScale = true;
1194	>	switch(rnemdFluxType_) {
1195	>	case rnemdKE :
1196	>	kineticExchange_ += kineticTarget_;
1197	>	break;
1198	>	case rnemdPx :
1199	>	case rnemdPy :
1200	>	case rnemdPz :
1201	>	momentumExchange_ += momentumTarget_;
1202	>	break;
1203	>	default :
1204	>	break;
1205	>	}
1206	>	}
1207		}
1208	+	if (successfulScale != true) {
1209	+	sprintf(painCave.errMsg,
1210	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1211	+	"\tthe constraint equations may not exist or there may be\n"
1212	+	"\tno selected objects in one or both slabs.\n");
1213	+	painCave.isFatal = 0;
1214	+	painCave.severity = OPENMD_INFO;
1215	+	simError();
1216	+	failTrialCount_++;
1217	+	}
1218	+	}
1219
1220	+	void RNEMD::doVSS() {
1221	+	if (!doRNEMD_) return;
1222	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1223	+	RealType time = currentSnap_->getTime();
1224	+	Mat3x3d hmat = currentSnap_->getHmat();
1225	+
1226	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1227	+
1228	+	int selei;
1229	+	StuntDouble* sd;
1230	+	int idx;
1231	+
1232	+	vector<StuntDouble*> hotBin, coldBin;
1233	+
1234	+	Vector3d Ph(V3Zero);
1235	+	RealType Mh = 0.0;
1236	+	RealType Kh = 0.0;
1237	+	Vector3d Pc(V3Zero);
1238	+	RealType Mc = 0.0;
1239	+	RealType Kc = 0.0;
1240	+
1241	+
1242	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1243	+	sd = seleMan_.nextSelected(selei)) {
1244	+
1245	+	idx = sd->getLocalIndex();
1246	+
1247	+	Vector3d pos = sd->getPos();
1248	+
1249	+	// wrap the stuntdouble's position back into the box:
1250	+
1251	+	if (usePeriodicBoundaryConditions_)
1252	+	currentSnap_->wrapVector(pos);
1253	+
1254	+	// which bin is this stuntdouble in?
1255	+	bool inA = inSlabA(pos);
1256	+	bool inB = inSlabB(pos);
1257	+
1258	+	if (inA || inB) {
1259	+
1260	+	RealType mass = sd->getMass();
1261	+	Vector3d vel = sd->getVel();
1262	+
1263	+	if (inA) {
1264	+	hotBin.push_back(sd);
1265	+	//std::cerr << "before, velocity = " << vel << endl;
1266	+	Ph += mass * vel;
1267	+	//std::cerr << "after, velocity = " << vel << endl;
1268	+	Mh += mass;
1269	+	Kh += mass * vel.lengthSquare();
1270	+	if (rnemdFluxType_ == rnemdFullKE) {
1271	+	if (sd->isDirectional()) {
1272	+	Vector3d angMom = sd->getJ();
1273	+	Mat3x3d I = sd->getI();
1274	+	if (sd->isLinear()) {
1275	+	int i = sd->linearAxis();
1276	+	int j = (i + 1) % 3;
1277	+	int k = (i + 2) % 3;
1278	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1279	+	angMom[k] * angMom[k] / I(k, k);
1280	+	} else {
1281	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1282	+	angMom[1] * angMom[1] / I(1, 1) +
1283	+	angMom[2] * angMom[2] / I(2, 2);
1284	+	}
1285	+	}
1286	+	}
1287	+	} else { //midBin_
1288	+	coldBin.push_back(sd);
1289	+	Pc += mass * vel;
1290	+	Mc += mass;
1291	+	Kc += mass * vel.lengthSquare();
1292	+	if (rnemdFluxType_ == rnemdFullKE) {
1293	+	if (sd->isDirectional()) {
1294	+	Vector3d angMom = sd->getJ();
1295	+	Mat3x3d I = sd->getI();
1296	+	if (sd->isLinear()) {
1297	+	int i = sd->linearAxis();
1298	+	int j = (i + 1) % 3;
1299	+	int k = (i + 2) % 3;
1300	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1301	+	angMom[k] * angMom[k] / I(k, k);
1302	+	} else {
1303	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1304	+	angMom[1] * angMom[1] / I(1, 1) +
1305	+	angMom[2] * angMom[2] / I(2, 2);
1306	+	}
1307	+	}
1308	+	}
1309	+	}
1310	+	}
1311	+	}
1312	+
1313	+	Kh *= 0.5;
1314	+	Kc *= 0.5;
1315	+
1316	+	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1317	+	//        << "\tKc= " << Kc << endl;
1318	+	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1319	+
1320		#ifdef IS_MPI
1321	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1322	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1323	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1324	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1325	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1326	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1327	+	#endif
1328
1329	<	// all processors have the same number of bins, and STL vectors pack their
1330	<	// arrays, so in theory, this should be safe:
1329	>	bool successfulExchange = false;
1330	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1331	>	Vector3d vc = Pc / Mc;
1332	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1333	>	Vector3d acrec = -momentumTarget_ / Mc;
1334	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1335	>	if (cNumerator > 0.0) {
1336	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1337	>	if (cDenominator > 0.0) {
1338	>	RealType c = sqrt(cNumerator / cDenominator);
1339	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1340	>	Vector3d vh = Ph / Mh;
1341	>	Vector3d ah = momentumTarget_ / Mh + vh;
1342	>	Vector3d ahrec = momentumTarget_ / Mh;
1343	>	RealType hNumerator = Kh + kineticTarget_
1344	>	- 0.5 * Mh * ah.lengthSquare();
1345	>	if (hNumerator > 0.0) {
1346	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1347	>	if (hDenominator > 0.0) {
1348	>	RealType h = sqrt(hNumerator / hDenominator);
1349	>	if ((h > 0.9) && (h < 1.1)) {
1350	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1351	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1352	>	vector<StuntDouble*>::iterator sdi;
1353	>	Vector3d vel;
1354	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1355	>	//vel = (*sdi)->getVel();
1356	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1357	>	(*sdi)->setVel(vel);
1358	>	if (rnemdFluxType_ == rnemdFullKE) {
1359	>	if ((*sdi)->isDirectional()) {
1360	>	Vector3d angMom = (*sdi)->getJ() * c;
1361	>	(*sdi)->setJ(angMom);
1362	>	}
1363	>	}
1364	>	}
1365	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1366	>	//vel = (*sdi)->getVel();
1367	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1368	>	(*sdi)->setVel(vel);
1369	>	if (rnemdFluxType_ == rnemdFullKE) {
1370	>	if ((*sdi)->isDirectional()) {
1371	>	Vector3d angMom = (*sdi)->getJ() * h;
1372	>	(*sdi)->setJ(angMom);
1373	>	}
1374	>	}
1375	>	}
1376	>	successfulExchange = true;
1377	>	kineticExchange_ += kineticTarget_;
1378	>	momentumExchange_ += momentumTarget_;
1379	>	}
1380	>	}
1381	>	}
1382	>	}
1383	>	}
1384	>	}
1385	>	}
1386	>	if (successfulExchange != true) {
1387	>	sprintf(painCave.errMsg,
1388	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1389	>	"\tthe constraint equations may not exist or there may be\n"
1390	>	"\tno selected objects in one or both slabs.\n");
1391	>	painCave.isFatal = 0;
1392	>	painCave.severity = OPENMD_INFO;
1393	>	simError();
1394	>	failTrialCount_++;
1395	>	}
1396	>	}
1397
1398	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1399	<	nBins_, MPI::REALTYPE, MPI::SUM);
1400	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1401	<	nBins_, MPI::INT, MPI::SUM);
1398	>	void RNEMD::doRNEMD() {
1399	>	if (!doRNEMD_) return;
1400	>	trialCount_++;
1401	>	switch(rnemdMethod_) {
1402	>	case rnemdSwap:
1403	>	doSwap();
1404	>	break;
1405	>	case rnemdNIVS:
1406	>	doNIVS();
1407	>	break;
1408	>	case rnemdVSS:
1409	>	doVSS();
1410	>	break;
1411	>	case rnemdUnkownMethod:
1412	>	default :
1413	>	break;
1414	>	}
1415	>	}
1416
1417	+	void RNEMD::collectData() {
1418	+	if (!doRNEMD_) return;
1419	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1420	+	Mat3x3d hmat = currentSnap_->getHmat();
1421	+
1422	+	areaAccumulator_->add(currentSnap_->getXYarea());
1423	+
1424	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1425	+
1426	+	int selei;
1427	+	StuntDouble* sd;
1428	+	int idx;
1429	+
1430	+	vector<RealType> binMass(nBins_, 0.0);
1431	+	vector<RealType> binPx(nBins_, 0.0);
1432	+	vector<RealType> binPy(nBins_, 0.0);
1433	+	vector<RealType> binPz(nBins_, 0.0);
1434	+	vector<RealType> binKE(nBins_, 0.0);
1435	+	vector<int> binDOF(nBins_, 0);
1436	+	vector<int> binCount(nBins_, 0);
1437	+
1438	+	// alternative approach, track all molecules instead of only those
1439	+	// selected for scaling/swapping:
1440	+	/*
1441	+	SimInfo::MoleculeIterator miter;
1442	+	vector<StuntDouble*>::iterator iiter;
1443	+	Molecule* mol;
1444	+	StuntDouble* sd;
1445	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1446	+	mol = info_->nextMolecule(miter))
1447	+	sd is essentially sd
1448	+	for (sd = mol->beginIntegrableObject(iiter);
1449	+	sd != NULL;
1450	+	sd = mol->nextIntegrableObject(iiter))
1451	+	*/
1452	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453	+	sd = seleMan_.nextSelected(selei)) {
1454	+
1455	+	idx = sd->getLocalIndex();
1456	+
1457	+	Vector3d pos = sd->getPos();
1458	+
1459	+	// wrap the stuntdouble's position back into the box:
1460	+
1461	+	if (usePeriodicBoundaryConditions_)
1462	+	currentSnap_->wrapVector(pos);
1463	+
1464	+
1465	+	// which bin is this stuntdouble in?
1466	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1467	+	// Shift molecules by half a box to have bins start at 0
1468	+	// The modulo operator is used to wrap the case when we are
1469	+	// beyond the end of the bins back to the beginning.
1470	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1471	+
1472	+	RealType mass = sd->getMass();
1473	+	Vector3d vel = sd->getVel();
1474	+
1475	+	binCount[binNo]++;
1476	+	binMass[binNo] += mass;
1477	+	binPx[binNo] += mass*vel.x();
1478	+	binPy[binNo] += mass*vel.y();
1479	+	binPz[binNo] += mass*vel.z();
1480	+	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1481	+	binDOF[binNo] += 3;
1482	+
1483	+	if (sd->isDirectional()) {
1484	+	Vector3d angMom = sd->getJ();
1485	+	Mat3x3d I = sd->getI();
1486	+	if (sd->isLinear()) {
1487	+	int i = sd->linearAxis();
1488	+	int j = (i + 1) % 3;
1489	+	int k = (i + 2) % 3;
1490	+	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1491	+	angMom[k] * angMom[k] / I(k, k));
1492	+	binDOF[binNo] += 2;
1493	+	} else {
1494	+	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1495	+	angMom[1] * angMom[1] / I(1, 1) +
1496	+	angMom[2] * angMom[2] / I(2, 2));
1497	+	binDOF[binNo] += 3;
1498	+	}
1499	+	}
1500	+	}
1501	+
1502	+
1503	+	#ifdef IS_MPI
1504	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1505	+	nBins_, MPI::INT, MPI::SUM);
1506	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1507	+	nBins_, MPI::REALTYPE, MPI::SUM);
1508	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1509	+	nBins_, MPI::REALTYPE, MPI::SUM);
1510	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1511	+	nBins_, MPI::REALTYPE, MPI::SUM);
1512	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1513	+	nBins_, MPI::REALTYPE, MPI::SUM);
1514	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1515	+	nBins_, MPI::REALTYPE, MPI::SUM);
1516	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1517	+	nBins_, MPI::INT, MPI::SUM);
1518	+	#endif
1519	+
1520	+	Vector3d vel;
1521	+	RealType den;
1522	+	RealType temp;
1523	+	RealType z;
1524	+	for (int i = 0; i < nBins_; i++) {
1525	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1526	+	vel.x() = binPx[i] / binMass[i];
1527	+	vel.y() = binPy[i] / binMass[i];
1528	+	vel.z() = binPz[i] / binMass[i];
1529	+
1530	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1531	+	/ currentSnap_->getVolume() ;
1532	+
1533	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1534	+	PhysicalConstants::energyConvert);
1535	+
1536	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1537	+	if(outputMask_[j]) {
1538	+	switch(j) {
1539	+	case Z:
1540	+	(data_[j].accumulator[i])->add(z);
1541	+	break;
1542	+	case TEMPERATURE:
1543	+	data_[j].accumulator[i]->add(temp);
1544	+	break;
1545	+	case VELOCITY:
1546	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1547	+	break;
1548	+	case DENSITY:
1549	+	data_[j].accumulator[i]->add(den);
1550	+	break;
1551	+	}
1552	+	}
1553	+	}
1554	+	}
1555	+	}
1556	+
1557	+	void RNEMD::getStarted() {
1558	+	if (!doRNEMD_) return;
1559	+	collectData();
1560	+	writeOutputFile();
1561	+	}
1562	+
1563	+	void RNEMD::parseOutputFileFormat(const std::string& format) {
1564	+	if (!doRNEMD_) return;
1565	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1566	+
1567	+	while(tokenizer.hasMoreTokens()) {
1568	+	std::string token(tokenizer.nextToken());
1569	+	toUpper(token);
1570	+	OutputMapType::iterator i = outputMap_.find(token);
1571	+	if (i != outputMap_.end()) {
1572	+	outputMask_.set(i->second);
1573	+	} else {
1574	+	sprintf( painCave.errMsg,
1575	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1576	+	"\toutputFileFormat keyword.\n", token.c_str() );
1577	+	painCave.isFatal = 0;
1578	+	painCave.severity = OPENMD_ERROR;
1579	+	simError();
1580	+	}
1581	+	}
1582	+	}
1583	+
1584	+	void RNEMD::writeOutputFile() {
1585	+	if (!doRNEMD_) return;
1586	+
1587	+	#ifdef IS_MPI
1588		// If we're the root node, should we print out the results
1589		int worldRank = MPI::COMM_WORLD.Get_rank();
1590		if (worldRank == 0) {
1591		#endif
1592	<
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";
1592	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1593
1594	+	if( !rnemdFile_ ){
1595	+	sprintf( painCave.errMsg,
1596	+	"Could not open \"%s\" for RNEMD output.\n",
1597	+	rnemdFileName_.c_str());
1598	+	painCave.isFatal = 1;
1599	+	simError();
1600	+	}
1601	+
1602	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1603	+
1604	+	RealType time = currentSnap_->getTime();
1605	+	RealType avgArea;
1606	+	areaAccumulator_->getAverage(avgArea);
1607	+	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1608	+	/ PhysicalConstants::energyConvert;
1609	+	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1610	+
1611	+	rnemdFile_ << "#######################################################\n";
1612	+	rnemdFile_ << "# RNEMD {\n";
1613	+
1614	+	map<string, RNEMDMethod>::iterator mi;
1615	+	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1616	+	if ( (*mi).second == rnemdMethod_)
1617	+	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1618	+	}
1619	+	map<string, RNEMDFluxType>::iterator fi;
1620	+	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1621	+	if ( (*fi).second == rnemdFluxType_)
1622	+	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1623	+	}
1624	+
1625	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1626	+
1627	+	rnemdFile_ << "#    objectSelection = \""
1628	+	<< rnemdObjectSelection_ << "\";\n";
1629	+	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1630	+	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1631	+	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1632	+	rnemdFile_ << "# }\n";
1633	+	rnemdFile_ << "#######################################################\n";
1634	+	rnemdFile_ << "# RNEMD report:\n";
1635	+	rnemdFile_ << "#     running time = " << time << " fs\n";
1636	+	rnemdFile_ << "#     target flux:\n";
1637	+	rnemdFile_ << "#         kinetic = "
1638	+	<< kineticFlux_ / PhysicalConstants::energyConvert
1639	+	<< " (kcal/mol/A^2/fs)\n";
1640	+	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1641	+	<< " (amu/A/fs^2)\n";
1642	+	rnemdFile_ << "#     target one-time exchanges:\n";
1643	+	rnemdFile_ << "#         kinetic = "
1644	+	<< kineticTarget_ / PhysicalConstants::energyConvert
1645	+	<< " (kcal/mol)\n";
1646	+	rnemdFile_ << "#         momentum = " << momentumTarget_
1647	+	<< " (amu*A/fs)\n";
1648	+	rnemdFile_ << "#     actual exchange totals:\n";
1649	+	rnemdFile_ << "#         kinetic = "
1650	+	<< kineticExchange_ / PhysicalConstants::energyConvert
1651	+	<< " (kcal/mol)\n";
1652	+	rnemdFile_ << "#         momentum = " << momentumExchange_
1653	+	<< " (amu*A/fs)\n";
1654	+	rnemdFile_ << "#     actual flux:\n";
1655	+	rnemdFile_ << "#         kinetic = " << Jz
1656	+	<< " (kcal/mol/A^2/fs)\n";
1657	+	rnemdFile_ << "#         momentum = " << JzP
1658	+	<< " (amu/A/fs^2)\n";
1659	+	rnemdFile_ << "#     exchange statistics:\n";
1660	+	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1661	+	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1662	+	if (rnemdMethod_ == rnemdNIVS) {
1663	+	rnemdFile_ << "#         NIVS root-check errors = "
1664	+	<< failRootCount_ << "\n";
1665	+	}
1666	+	rnemdFile_ << "#######################################################\n";
1667	+
1668	+
1669	+
1670	+	//write title
1671	+	rnemdFile_ << "#";
1672	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1673	+	if (outputMask_[i]) {
1674	+	rnemdFile_ << "\t" << data_[i].title <<
1675	+	"(" << data_[i].units << ")";
1676	+	// add some extra tabs for column alignment
1677	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1678	+	}
1679	+	}
1680	+	rnemdFile_ << std::endl;
1681	+
1682	+	rnemdFile_.precision(8);
1683	+
1684	+	for (unsigned int j = 0; j < nBins_; j++) {
1685	+
1686	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1687	+	if (outputMask_[i]) {
1688	+	if (data_[i].dataType == "RealType")
1689	+	writeReal(i,j);
1690	+	else if (data_[i].dataType == "Vector3d")
1691	+	writeVector(i,j);
1692	+	else {
1693	+	sprintf( painCave.errMsg,
1694	+	"RNEMD found an unknown data type for: %s ",
1695	+	data_[i].title.c_str());
1696	+	painCave.isFatal = 1;
1697	+	simError();
1698	+	}
1699	+	}
1700	+	}
1701	+	rnemdFile_ << std::endl;
1702	+
1703	+	}
1704	+
1705	+	rnemdFile_ << "#######################################################\n";
1706	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1707	+	rnemdFile_ << "#######################################################\n";
1708	+
1709	+
1710	+	for (unsigned int j = 0; j < nBins_; j++) {
1711	+	rnemdFile_ << "#";
1712	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1713	+	if (outputMask_[i]) {
1714	+	if (data_[i].dataType == "RealType")
1715	+	writeRealStdDev(i,j);
1716	+	else if (data_[i].dataType == "Vector3d")
1717	+	writeVectorStdDev(i,j);
1718	+	else {
1719	+	sprintf( painCave.errMsg,
1720	+	"RNEMD found an unknown data type for: %s ",
1721	+	data_[i].title.c_str());
1722	+	painCave.isFatal = 1;
1723	+	simError();
1724	+	}
1725	+	}
1726	+	}
1727	+	rnemdFile_ << std::endl;
1728	+
1729	+	}
1730	+
1731	+	rnemdFile_.flush();
1732	+	rnemdFile_.close();
1733	+
1734		#ifdef IS_MPI
1735		}
1736		#endif
1737	+
1738		}
1739	+
1740	+	void RNEMD::writeReal(int index, unsigned int bin) {
1741	+	if (!doRNEMD_) return;
1742	+	assert(index >=0 && index < ENDINDEX);
1743	+	assert(bin < nBins_);
1744	+	RealType s;
1745	+
1746	+	data_[index].accumulator[bin]->getAverage(s);
1747	+
1748	+	if (! isinf(s) && ! isnan(s)) {
1749	+	rnemdFile_ << "\t" << s;
1750	+	} else{
1751	+	sprintf( painCave.errMsg,
1752	+	"RNEMD detected a numerical error writing: %s for bin %d",
1753	+	data_[index].title.c_str(), bin);
1754	+	painCave.isFatal = 1;
1755	+	simError();
1756	+	}
1757	+	}
1758	+
1759	+	void RNEMD::writeVector(int index, unsigned int bin) {
1760	+	if (!doRNEMD_) return;
1761	+	assert(index >=0 && index < ENDINDEX);
1762	+	assert(bin < nBins_);
1763	+	Vector3d s;
1764	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1765	+	if (isinf(s[0]) || isnan(s[0]) ||
1766	+	isinf(s[1]) || isnan(s[1]) ||
1767	+	isinf(s[2]) || isnan(s[2]) ) {
1768	+	sprintf( painCave.errMsg,
1769	+	"RNEMD detected a numerical error writing: %s for bin %d",
1770	+	data_[index].title.c_str(), bin);
1771	+	painCave.isFatal = 1;
1772	+	simError();
1773	+	} else {
1774	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1775	+	}
1776	+	}
1777	+
1778	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1779	+	if (!doRNEMD_) return;
1780	+	assert(index >=0 && index < ENDINDEX);
1781	+	assert(bin < nBins_);
1782	+	RealType s;
1783	+
1784	+	data_[index].accumulator[bin]->getStdDev(s);
1785	+
1786	+	if (! isinf(s) && ! isnan(s)) {
1787	+	rnemdFile_ << "\t" << s;
1788	+	} else{
1789	+	sprintf( painCave.errMsg,
1790	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1791	+	data_[index].title.c_str(), bin);
1792	+	painCave.isFatal = 1;
1793	+	simError();
1794	+	}
1795	+	}
1796	+
1797	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1798	+	if (!doRNEMD_) return;
1799	+	assert(index >=0 && index < ENDINDEX);
1800	+	assert(bin < nBins_);
1801	+	Vector3d s;
1802	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1803	+	if (isinf(s[0]) || isnan(s[0]) ||
1804	+	isinf(s[1]) || isnan(s[1]) ||
1805	+	isinf(s[2]) || isnan(s[2]) ) {
1806	+	sprintf( painCave.errMsg,
1807	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1808	+	data_[index].title.c_str(), bin);
1809	+	painCave.isFatal = 1;
1810	+	simError();
1811	+	} else {
1812	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1813	+	}
1814	+	}
1815		}
1816	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1777 by gezelter, Thu Aug 9 18:35:09 2012 UTC

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