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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1946 by gezelter, Tue Nov 12 02:18:35 2013 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, 234107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+	#ifdef IS_MPI
42	+	#include <mpi.h>
43	+	#endif
44
45	<	#include "integrators/RNEMD.hpp"
45	>	#include <cmath>
46	>	#include <sstream>
47	>	#include <string>
48	>
49	>	#include "rnemd/RNEMD.hpp"
50		#include "math/Vector3.hpp"
51	+	#include "math/Vector.hpp"
52		#include "math/SquareMatrix3.hpp"
53	+	#include "math/Polynomial.hpp"
54		#include "primitives/Molecule.hpp"
55		#include "primitives/StuntDouble.hpp"
56	<	#include "utils/OOPSEConstant.hpp"
56	>	#include "utils/PhysicalConstants.hpp"
57		#include "utils/Tuple.hpp"
58	+	#include "brains/Thermo.hpp"
59	+	#include "math/ConvexHull.hpp"
60
61	<	#ifndef IS_MPI
62	<	#include "math/SeqRandNumGen.hpp"
63	<	#else
53	<	#include "math/ParallelRandNumGen.hpp"
61	>	#ifdef _MSC_VER
62	>	#define isnan(x) _isnan((x))
63	>	#define isinf(x) (!_finite(x) && !_isnan(x))
64		#endif
65
66		#define HONKING_LARGE_VALUE 1.0e10
67
68	<	namespace oopse {
68	>	using namespace std;
69	>	namespace OpenMD {
70
71	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
72	<
73	<	int seedValue;
74	<	Globals * simParams = info->getSimParams();
71	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	>	evaluatorA_(info), seleManA_(info),
73	>	commonA_(info), evaluatorB_(info),
74	>	seleManB_(info), commonB_(info),
75	>	hasData_(false), hasDividingArea_(false),
76	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
77
78	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
79	<	stringToEnumMap_["Px"] = rnemdPx;
80	<	stringToEnumMap_["Py"] = rnemdPy;
68	<	stringToEnumMap_["Pz"] = rnemdPz;
69	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
78	>	trialCount_ = 0;
79	>	failTrialCount_ = 0;
80	>	failRootCount_ = 0;
81
82	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
83	<	evaluator_.loadScriptString(rnemdObjectSelection_);
73	<	seleMan_.setSelectionSet(evaluator_.evaluate());
82	>	Globals* simParams = info->getSimParams();
83	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84
85	+	doRNEMD_ = rnemdParams->getUseRNEMD();
86	+	if (!doRNEMD_) return;
87
88	<	// do some sanity checking
88	>	stringToMethod_["Swap"]  = rnemdSwap;
89	>	stringToMethod_["NIVS"]  = rnemdNIVS;
90	>	stringToMethod_["VSS"]   = rnemdVSS;
91
92	<	int selectionCount = seleMan_.getSelectionCount();
93	<	int nIntegrable = info->getNGlobalIntegrableObjects();
92	>	stringToFluxType_["KE"]  = rnemdKE;
93	>	stringToFluxType_["Px"]  = rnemdPx;
94	>	stringToFluxType_["Py"]  = rnemdPy;
95	>	stringToFluxType_["Pz"]  = rnemdPz;
96	>	stringToFluxType_["Pvector"]  = rnemdPvector;
97	>	stringToFluxType_["Lx"]  = rnemdLx;
98	>	stringToFluxType_["Ly"]  = rnemdLy;
99	>	stringToFluxType_["Lz"]  = rnemdLz;
100	>	stringToFluxType_["Lvector"]  = rnemdLvector;
101	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
102	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
103	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
104	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
105	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
106	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
107	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
108
109	<	if (selectionCount > nIntegrable) {
109	>	runTime_ = simParams->getRunTime();
110	>	statusTime_ = simParams->getStatusTime();
111	>
112	>	const string methStr = rnemdParams->getMethod();
113	>	bool hasFluxType = rnemdParams->haveFluxType();
114	>
115	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
116	>
117	>	string fluxStr;
118	>	if (hasFluxType) {
119	>	fluxStr = rnemdParams->getFluxType();
120	>	} else {
121		sprintf(painCave.errMsg,
122	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
123	<	"\t\t%s\n"
124	<	"\thas resulted in %d selected objects.  However,\n"
125	<	"\tthe total number of integrable objects in the system\n"
126	<	"\tis only %d.  This is almost certainly not what you want\n"
127	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
128	<	"\tselector in the selection script!\n",
90	<	rnemdObjectSelection_.c_str(),
91	<	selectionCount, nIntegrable);
92	<	painCave.isFatal = 0;
122	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
123	>	"\twhich must be one of the following values:\n"
124	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
125	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
126	>	"\tmust be set to use RNEMD\n");
127	>	painCave.isFatal = 1;
128	>	painCave.severity = OPENMD_ERROR;
129		simError();
94	–
130		}
131	+
132	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
133	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
134	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
135	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
136	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
137	+	hasSelectionA_ = rnemdParams->haveSelectionA();
138	+	hasSelectionB_ = rnemdParams->haveSelectionB();
139	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
140	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
141	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
142	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
143	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
144	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
145	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
146	+	bool hasOutputFields = rnemdParams->haveOutputFields();
147
148	<	const std::string st = simParams->getRNEMD_swapType();
148	>	map<string, RNEMDMethod>::iterator i;
149	>	i = stringToMethod_.find(methStr);
150	>	if (i != stringToMethod_.end())
151	>	rnemdMethod_ = i->second;
152	>	else {
153	>	sprintf(painCave.errMsg,
154	>	"RNEMD: The current method,\n"
155	>	"\t\t%s is not one of the recognized\n"
156	>	"\texchange methods: Swap, NIVS, or VSS\n",
157	>	methStr.c_str());
158	>	painCave.isFatal = 1;
159	>	painCave.severity = OPENMD_ERROR;
160	>	simError();
161	>	}
162
163	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
164	<	i = stringToEnumMap_.find(st);
165	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
163	>	map<string, RNEMDFluxType>::iterator j;
164	>	j = stringToFluxType_.find(fluxStr);
165	>	if (j != stringToFluxType_.end())
166	>	rnemdFluxType_ = j->second;
167	>	else {
168	>	sprintf(painCave.errMsg,
169	>	"RNEMD: The current fluxType,\n"
170	>	"\t\t%s\n"
171	>	"\tis not one of the recognized flux types.\n",
172	>	fluxStr.c_str());
173	>	painCave.isFatal = 1;
174	>	painCave.severity = OPENMD_ERROR;
175	>	simError();
176	>	}
177
178	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
179	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
180	<	exchangeSum_ = 0.0;
178	>	bool methodFluxMismatch = false;
179	>	bool hasCorrectFlux = false;
180	>	switch(rnemdMethod_) {
181	>	case rnemdSwap:
182	>	switch (rnemdFluxType_) {
183	>	case rnemdKE:
184	>	hasCorrectFlux = hasKineticFlux;
185	>	break;
186	>	case rnemdPx:
187	>	case rnemdPy:
188	>	case rnemdPz:
189	>	hasCorrectFlux = hasMomentumFlux;
190	>	break;
191	>	default :
192	>	methodFluxMismatch = true;
193	>	break;
194	>	}
195	>	break;
196	>	case rnemdNIVS:
197	>	switch (rnemdFluxType_) {
198	>	case rnemdKE:
199	>	case rnemdRotKE:
200	>	case rnemdFullKE:
201	>	hasCorrectFlux = hasKineticFlux;
202	>	break;
203	>	case rnemdPx:
204	>	case rnemdPy:
205	>	case rnemdPz:
206	>	hasCorrectFlux = hasMomentumFlux;
207	>	break;
208	>	case rnemdKePx:
209	>	case rnemdKePy:
210	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
211	>	break;
212	>	default:
213	>	methodFluxMismatch = true;
214	>	break;
215	>	}
216	>	break;
217	>	case rnemdVSS:
218	>	switch (rnemdFluxType_) {
219	>	case rnemdKE:
220	>	case rnemdRotKE:
221	>	case rnemdFullKE:
222	>	hasCorrectFlux = hasKineticFlux;
223	>	break;
224	>	case rnemdPx:
225	>	case rnemdPy:
226	>	case rnemdPz:
227	>	hasCorrectFlux = hasMomentumFlux;
228	>	break;
229	>	case rnemdLx:
230	>	case rnemdLy:
231	>	case rnemdLz:
232	>	hasCorrectFlux = hasAngularMomentumFlux;
233	>	break;
234	>	case rnemdPvector:
235	>	hasCorrectFlux = hasMomentumFluxVector;
236	>	break;
237	>	case rnemdLvector:
238	>	hasCorrectFlux = hasAngularMomentumFluxVector;
239	>	break;
240	>	case rnemdKePx:
241	>	case rnemdKePy:
242	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
243	>	break;
244	>	case rnemdKeLx:
245	>	case rnemdKeLy:
246	>	case rnemdKeLz:
247	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
248	>	break;
249	>	case rnemdKePvector:
250	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
251	>	break;
252	>	case rnemdKeLvector:
253	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
254	>	break;
255	>	default:
256	>	methodFluxMismatch = true;
257	>	break;
258	>	}
259	>	default:
260	>	break;
261	>	}
262
263	<	#ifndef IS_MPI
264	<	if (simParams->haveSeed()) {
265	<	seedValue = simParams->getSeed();
266	<	randNumGen_ = new SeqRandNumGen(seedValue);
267	<	}else {
268	<	randNumGen_ = new SeqRandNumGen();
269	<	}
270	<	#else
271	<	if (simParams->haveSeed()) {
272	<	seedValue = simParams->getSeed();
273	<	randNumGen_ = new ParallelRandNumGen(seedValue);
274	<	}else {
275	<	randNumGen_ = new ParallelRandNumGen();
276	<	}
277	<	#endif
263	>	if (methodFluxMismatch) {
264	>	sprintf(painCave.errMsg,
265	>	"RNEMD: The current method,\n"
266	>	"\t\t%s\n"
267	>	"\tcannot be used with the current flux type, %s\n",
268	>	methStr.c_str(), fluxStr.c_str());
269	>	painCave.isFatal = 1;
270	>	painCave.severity = OPENMD_ERROR;
271	>	simError();
272	>	}
273	>	if (!hasCorrectFlux) {
274	>	sprintf(painCave.errMsg,
275	>	"RNEMD: The current method, %s, and flux type, %s,\n"
276	>	"\tdid not have the correct flux value specified. Options\n"
277	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
278	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
279	>	methStr.c_str(), fluxStr.c_str());
280	>	painCave.isFatal = 1;
281	>	painCave.severity = OPENMD_ERROR;
282	>	simError();
283	>	}
284	>
285	>	if (hasKineticFlux) {
286	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
287	>	// into  amu / fs^3:
288	>	kineticFlux_ = rnemdParams->getKineticFlux()
289	>	* PhysicalConstants::energyConvert;
290	>	} else {
291	>	kineticFlux_ = 0.0;
292	>	}
293	>	if (hasMomentumFluxVector) {
294	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
295	>	} else {
296	>	momentumFluxVector_ = V3Zero;
297	>	if (hasMomentumFlux) {
298	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
299	>	switch (rnemdFluxType_) {
300	>	case rnemdPx:
301	>	momentumFluxVector_.x() = momentumFlux;
302	>	break;
303	>	case rnemdPy:
304	>	momentumFluxVector_.y() = momentumFlux;
305	>	break;
306	>	case rnemdPz:
307	>	momentumFluxVector_.z() = momentumFlux;
308	>	break;
309	>	case rnemdKePx:
310	>	momentumFluxVector_.x() = momentumFlux;
311	>	break;
312	>	case rnemdKePy:
313	>	momentumFluxVector_.y() = momentumFlux;
314	>	break;
315	>	default:
316	>	break;
317	>	}
318	>	}
319	>	if (hasAngularMomentumFluxVector) {
320	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
321	>	} else {
322	>	angularMomentumFluxVector_ = V3Zero;
323	>	if (hasAngularMomentumFlux) {
324	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
325	>	switch (rnemdFluxType_) {
326	>	case rnemdLx:
327	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
328	>	break;
329	>	case rnemdLy:
330	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
331	>	break;
332	>	case rnemdLz:
333	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
334	>	break;
335	>	case rnemdKeLx:
336	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
337	>	break;
338	>	case rnemdKeLy:
339	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
340	>	break;
341	>	case rnemdKeLz:
342	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
343	>	break;
344	>	default:
345	>	break;
346	>	}
347	>	}
348	>	}
349	>
350	>	if (hasCoordinateOrigin) {
351	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
352	>	} else {
353	>	coordinateOrigin_ = V3Zero;
354	>	}
355	>
356	>	// do some sanity checking
357	>
358	>	int selectionCount = seleMan_.getSelectionCount();
359	>
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361	>
362	>	if (selectionCount > nIntegrable) {
363	>	sprintf(painCave.errMsg,
364	>	"RNEMD: The current objectSelection,\n"
365	>	"\t\t%s\n"
366	>	"\thas resulted in %d selected objects.  However,\n"
367	>	"\tthe total number of integrable objects in the system\n"
368	>	"\tis only %d.  This is almost certainly not what you want\n"
369	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
370	>	"\tselector in the selection script!\n",
371	>	rnemdObjectSelection_.c_str(),
372	>	selectionCount, nIntegrable);
373	>	painCave.isFatal = 0;
374	>	painCave.severity = OPENMD_WARNING;
375	>	simError();
376	>	}
377	>
378	>	areaAccumulator_ = new Accumulator();
379	>
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382	>
383	>	data_.resize(RNEMD::ENDINDEX);
384	>	OutputData z;
385	>	z.units =  "Angstroms";
386	>	z.title =  "Z";
387	>	z.dataType = "RealType";
388	>	z.accumulator.reserve(nBins_);
389	>	for (int i = 0; i < nBins_; i++)
390	>	z.accumulator.push_back( new Accumulator() );
391	>	data_[Z] = z;
392	>	outputMap_["Z"] =  Z;
393	>
394	>	OutputData r;
395	>	r.units =  "Angstroms";
396	>	r.title =  "R";
397	>	r.dataType = "RealType";
398	>	r.accumulator.reserve(nBins_);
399	>	for (int i = 0; i < nBins_; i++)
400	>	r.accumulator.push_back( new Accumulator() );
401	>	data_[R] = r;
402	>	outputMap_["R"] =  R;
403	>
404	>	OutputData temperature;
405	>	temperature.units =  "K";
406	>	temperature.title =  "Temperature";
407	>	temperature.dataType = "RealType";
408	>	temperature.accumulator.reserve(nBins_);
409	>	for (int i = 0; i < nBins_; i++)
410	>	temperature.accumulator.push_back( new Accumulator() );
411	>	data_[TEMPERATURE] = temperature;
412	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
413	>
414	>	OutputData velocity;
415	>	velocity.units = "angstroms/fs";
416	>	velocity.title =  "Velocity";
417	>	velocity.dataType = "Vector3d";
418	>	velocity.accumulator.reserve(nBins_);
419	>	for (int i = 0; i < nBins_; i++)
420	>	velocity.accumulator.push_back( new VectorAccumulator() );
421	>	data_[VELOCITY] = velocity;
422	>	outputMap_["VELOCITY"] = VELOCITY;
423	>
424	>	OutputData angularVelocity;
425	>	angularVelocity.units = "angstroms^2/fs";
426	>	angularVelocity.title =  "AngularVelocity";
427	>	angularVelocity.dataType = "Vector3d";
428	>	angularVelocity.accumulator.reserve(nBins_);
429	>	for (int i = 0; i < nBins_; i++)
430	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
431	>	data_[ANGULARVELOCITY] = angularVelocity;
432	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
433	>
434	>	OutputData density;
435	>	density.units =  "g cm^-3";
436	>	density.title =  "Density";
437	>	density.dataType = "RealType";
438	>	density.accumulator.reserve(nBins_);
439	>	for (int i = 0; i < nBins_; i++)
440	>	density.accumulator.push_back( new Accumulator() );
441	>	data_[DENSITY] = density;
442	>	outputMap_["DENSITY"] =  DENSITY;
443	>
444	>	if (hasOutputFields) {
445	>	parseOutputFileFormat(rnemdParams->getOutputFields());
446	>	} else {
447	>	if (usePeriodicBoundaryConditions_)
448	>	outputMask_.set(Z);
449	>	else
450	>	outputMask_.set(R);
451	>	switch (rnemdFluxType_) {
452	>	case rnemdKE:
453	>	case rnemdRotKE:
454	>	case rnemdFullKE:
455	>	outputMask_.set(TEMPERATURE);
456	>	break;
457	>	case rnemdPx:
458	>	case rnemdPy:
459	>	outputMask_.set(VELOCITY);
460	>	break;
461	>	case rnemdPz:
462	>	case rnemdPvector:
463	>	outputMask_.set(VELOCITY);
464	>	outputMask_.set(DENSITY);
465	>	break;
466	>	case rnemdLx:
467	>	case rnemdLy:
468	>	case rnemdLz:
469	>	case rnemdLvector:
470	>	outputMask_.set(ANGULARVELOCITY);
471	>	break;
472	>	case rnemdKeLx:
473	>	case rnemdKeLy:
474	>	case rnemdKeLz:
475	>	case rnemdKeLvector:
476	>	outputMask_.set(TEMPERATURE);
477	>	outputMask_.set(ANGULARVELOCITY);
478	>	break;
479	>	case rnemdKePx:
480	>	case rnemdKePy:
481	>	outputMask_.set(TEMPERATURE);
482	>	outputMask_.set(VELOCITY);
483	>	break;
484	>	case rnemdKePvector:
485	>	outputMask_.set(TEMPERATURE);
486	>	outputMask_.set(VELOCITY);
487	>	outputMask_.set(DENSITY);
488	>	break;
489	>	default:
490	>	break;
491	>	}
492	>	}
493	>
494	>	if (hasOutputFileName) {
495	>	rnemdFileName_ = rnemdParams->getOutputFileName();
496	>	} else {
497	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	>	}
499	>
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501	>
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504	>
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508	>
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511	>
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547	>
548	>	if (hasSelectionB_) {
549	>	selectionB_ = rnemdParams->getSelectionB();
550	>
551	>	} else {
552	>	if (usePeriodicBoundaryConditions_) {
553	>	Mat3x3d hmat = currentSnap_->getHmat();
554	>
555	>	if (hasSlabWidth)
556	>	slabWidth_ = rnemdParams->getSlabWidth();
557	>	else
558	>	slabWidth_ = hmat(2,2) / 10.0;
559	>
560	>	if (hasSlabBCenter)
561	>	slabBCenter_ = rnemdParams->getSlabBCenter();
562	>	else
563	>	slabBCenter_ = hmat(2,2) / 2.0;
564	>
565	>	selectionBstream << "select wrappedz > "
566	>	<< slabBCenter_ - 0.5*slabWidth_
567	>	<<  " && wrappedz < "
568	>	<< slabBCenter_ + 0.5*slabWidth_;
569	>	selectionB_ = selectionBstream.str();
570	>	} else {
571	>	if (hasSphereBRadius_) {
572	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
573	>	selectionBstream << "select r > " << sphereBRadius_;
574	>	selectionB_ = selectionBstream.str();
575	>	} else {
576	>	selectionB_ = "select hull";
577	>	BisHull_ = true;
578	>	hasSelectionB_ = true;
579	>	}
580	>	}
581	>	}
582	>	}
583	>
584	>	// object evaluator:
585	>	evaluator_.loadScriptString(rnemdObjectSelection_);
586	>	seleMan_.setSelectionSet(evaluator_.evaluate());
587	>	evaluatorA_.loadScriptString(selectionA_);
588	>	evaluatorB_.loadScriptString(selectionB_);
589	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
590	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
591	>	commonA_ = seleManA_ & seleMan_;
592	>	commonB_ = seleManB_ & seleMan_;
593		}
594
595	+
596		RNEMD::~RNEMD() {
597	<	delete randNumGen_;
598	<	}
597	>	if (!doRNEMD_) return;
598	>	#ifdef IS_MPI
599	>	if (worldRank == 0) {
600	>	#endif
601
602	<	void RNEMD::doSwap() {
129	<	int midBin = nBins_ / 2;
602	>	writeOutputFile();
603
604	+	rnemdFile_.close();
605	+
606	+	#ifdef IS_MPI
607	+	}
608	+	#endif
609	+
610	+	// delete all of the objects we created:
611	+	delete areaAccumulator_;
612	+	data_.clear();
613	+	}
614	+
615	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
616	+	if (!doRNEMD_) return;
617	+	int selei;
618	+	int selej;
619	+
620		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
621		Mat3x3d hmat = currentSnap_->getHmat();
622
134	–	seleMan_.setSelectionSet(evaluator_.evaluate());
135	–
136	–	int selei;
623		StuntDouble* sd;
138	–	int idx;
624
625		RealType min_val;
626		bool min_found = false;
#	Line 145 | Line 630 | namespace oopse {
630		bool max_found = false;
631		StuntDouble* max_sd;
632
633	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
634	<	sd = seleMan_.nextSelected(selei)) {
633	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
634	>	sd = seleManA_.nextSelected(selei)) {
635
151	–	idx = sd->getLocalIndex();
152	–
636		Vector3d pos = sd->getPos();
637	<
637	>
638		// wrap the stuntdouble's position back into the box:
639	<
639	>
640		if (usePeriodicBoundaryConditions_)
641		currentSnap_->wrapVector(pos);
642	<
643	<	// which bin is this stuntdouble in?
644	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
645	<
646	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
647	<
648	<
166	<	// if we're in bin 0 or the middleBin
167	<	if (binNo == 0 || binNo == midBin) {
642	>
643	>	RealType mass = sd->getMass();
644	>	Vector3d vel = sd->getVel();
645	>	RealType value;
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649
650	<	RealType mass = sd->getMass();
651	<	Vector3d vel = sd->getVel();
652	<	RealType value;
653	<
654	<	switch(rnemdType_) {
174	<	case rnemdKinetic :
650	>	value = mass * vel.lengthSquare();
651	>
652	>	if (sd->isDirectional()) {
653	>	Vector3d angMom = sd->getJ();
654	>	Mat3x3d I = sd->getI();
655
656	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
657	<	vel[2]*vel[2]);
658	<	if (sd->isDirectional()) {
659	<	Vector3d angMom = sd->getJ();
660	<	Mat3x3d I = sd->getI();
661	<
662	<	if (sd->isLinear()) {
663	<	int i = sd->linearAxis();
664	<	int j = (i + 1) % 3;
665	<	int k = (i + 2) % 3;
186	<	value += angMom[j] * angMom[j] / I(j, j) +
187	<	angMom[k] * angMom[k] / I(k, k);
188	<	} else {
189	<	value += angMom[0]*angMom[0]/I(0, 0)
190	<	+ angMom[1]*angMom[1]/I(1, 1)
191	<	+ angMom[2]*angMom[2]/I(2, 2);
192	<	}
656	>	if (sd->isLinear()) {
657	>	int i = sd->linearAxis();
658	>	int j = (i + 1) % 3;
659	>	int k = (i + 2) % 3;
660	>	value += angMom[j] * angMom[j] / I(j, j) +
661	>	angMom[k] * angMom[k] / I(k, k);
662	>	} else {
663	>	value += angMom[0]*angMom[0]/I(0, 0)
664	>	+ angMom[1]*angMom[1]/I(1, 1)
665	>	+ angMom[2]*angMom[2]/I(2, 2);
666		}
667	<	value = value * 0.5 / OOPSEConstant::energyConvert;
668	<	break;
669	<	case rnemdPx :
670	<	value = mass * vel[0];
671	<	break;
672	<	case rnemdPy :
673	<	value = mass * vel[1];
674	<	break;
675	<	case rnemdPz :
676	<	value = mass * vel[2];
677	<	break;
678	<	case rnemdUnknown :
679	<	default :
680	<	break;
667	>	} //angular momenta exchange enabled
668	>	value *= 0.5;
669	>	break;
670	>	case rnemdPx :
671	>	value = mass * vel[0];
672	>	break;
673	>	case rnemdPy :
674	>	value = mass * vel[1];
675	>	break;
676	>	case rnemdPz :
677	>	value = mass * vel[2];
678	>	break;
679	>	default :
680	>	break;
681	>	}
682	>	if (!max_found) {
683	>	max_val = value;
684	>	max_sd = sd;
685	>	max_found = true;
686	>	} else {
687	>	if (max_val < value) {
688	>	max_val = value;
689	>	max_sd = sd;
690		}
691	+	}
692	+	}
693
694	<	if (binNo == 0) {
695	<	if (!min_found) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	min_found = true;
699	<	} else {
700	<	if (min_val > value) {
701	<	min_val = value;
702	<	min_sd = sd;
703	<	}
704	<	}
705	<	} else {
706	<	if (!max_found) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	max_found = true;
710	<	} else {
711	<	if (max_val < value) {
712	<	max_val = value;
713	<	max_sd = sd;
714	<	}
715	<	}
716	<	}
694	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
695	>	sd = seleManB_.nextSelected(selej)) {
696	>
697	>	Vector3d pos = sd->getPos();
698	>
699	>	// wrap the stuntdouble's position back into the box:
700	>
701	>	if (usePeriodicBoundaryConditions_)
702	>	currentSnap_->wrapVector(pos);
703	>
704	>	RealType mass = sd->getMass();
705	>	Vector3d vel = sd->getVel();
706	>	RealType value;
707	>
708	>	switch(rnemdFluxType_) {
709	>	case rnemdKE :
710	>
711	>	value = mass * vel.lengthSquare();
712	>
713	>	if (sd->isDirectional()) {
714	>	Vector3d angMom = sd->getJ();
715	>	Mat3x3d I = sd->getI();
716	>
717	>	if (sd->isLinear()) {
718	>	int i = sd->linearAxis();
719	>	int j = (i + 1) % 3;
720	>	int k = (i + 2) % 3;
721	>	value += angMom[j] * angMom[j] / I(j, j) +
722	>	angMom[k] * angMom[k] / I(k, k);
723	>	} else {
724	>	value += angMom[0]*angMom[0]/I(0, 0)
725	>	+ angMom[1]*angMom[1]/I(1, 1)
726	>	+ angMom[2]*angMom[2]/I(2, 2);
727	>	}
728	>	} //angular momenta exchange enabled
729	>	value *= 0.5;
730	>	break;
731	>	case rnemdPx :
732	>	value = mass * vel[0];
733	>	break;
734	>	case rnemdPy :
735	>	value = mass * vel[1];
736	>	break;
737	>	case rnemdPz :
738	>	value = mass * vel[2];
739	>	break;
740	>	default :
741	>	break;
742		}
743	+
744	+	if (!min_found) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	min_found = true;
748	+	} else {
749	+	if (min_val > value) {
750	+	min_val = value;
751	+	min_sd = sd;
752	+	}
753	+	}
754		}
755	<
756	<	#ifdef IS_MPI
757	<	int nProc, worldRank;
758	<
239	<	nProc = MPI::COMM_WORLD.Get_size();
240	<	worldRank = MPI::COMM_WORLD.Get_rank();
241	<
755	>
756	>	#ifdef IS_MPI
757	>	int worldRank = MPI::COMM_WORLD.Get_rank();
758	>
759		bool my_min_found = min_found;
760		bool my_max_found = max_found;
761
762		// Even if we didn't find a minimum, did someone else?
763	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
763	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
764		// Even if we didn't find a maximum, did someone else?
765	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
766	<	1, MPI::BOOL, MPI::LAND);
767	<
768	<	struct {
769	<	RealType val;
770	<	int rank;
771	<	} max_vals, min_vals;
772	<
773	<	if (min_found) {
774	<	if (my_min_found)
765	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
766	>	#endif
767	>
768	>	if (max_found && min_found) {
769	>
770	>	#ifdef IS_MPI
771	>	struct {
772	>	RealType val;
773	>	int rank;
774	>	} max_vals, min_vals;
775	>
776	>	if (my_min_found) {
777		min_vals.val = min_val;
778	<	else
778	>	} else {
779		min_vals.val = HONKING_LARGE_VALUE;
780	<
780	>	}
781		min_vals.rank = worldRank;
782
783		// Who had the minimum?
784		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
785		1, MPI::REALTYPE_INT, MPI::MINLOC);
786		min_val = min_vals.val;
270	–	}
787
788	<	if (max_found) {
273	<	if (my_max_found)
788	>	if (my_max_found) {
789		max_vals.val = max_val;
790	<	else
790	>	} else {
791		max_vals.val = -HONKING_LARGE_VALUE;
792	<
792	>	}
793		max_vals.rank = worldRank;
794
795		// Who had the maximum?
796		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
797		1, MPI::REALTYPE_INT, MPI::MAXLOC);
798		max_val = max_vals.val;
284	–	}
799		#endif
800	<
801	<	if (max_found && min_found) {
802	<	if (min_val< max_val) {
289	<
800	>
801	>	if (min_val < max_val) {
802	>
803		#ifdef IS_MPI
804		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
805		// I have both maximum and minimum, so proceed like a single
806		// processor version:
807		#endif
808	<	// objects to be swapped: velocity & angular velocity
808	>
809		Vector3d min_vel = min_sd->getVel();
810		Vector3d max_vel = max_sd->getVel();
811		RealType temp_vel;
812
813	<	switch(rnemdType_) {
814	<	case rnemdKinetic :
813	>	switch(rnemdFluxType_) {
814	>	case rnemdKE :
815		min_sd->setVel(max_vel);
816		max_sd->setVel(min_vel);
817	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
817	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
818		Vector3d min_angMom = min_sd->getJ();
819		Vector3d max_angMom = max_sd->getJ();
820		min_sd->setJ(max_angMom);
821		max_sd->setJ(min_angMom);
822	<	}
822	>	}//angular momenta exchange enabled
823	>	//assumes same rigid body identity
824		break;
825		case rnemdPx :
826		temp_vel = min_vel.x();
#	Line 329 | Line 843 | namespace oopse {
843		min_sd->setVel(min_vel);
844		max_sd->setVel(max_vel);
845		break;
332	–	case rnemdUnknown :
846		default :
847		break;
848		}
849	+
850		#ifdef IS_MPI
851		// the rest of the cases only apply in parallel simulations:
852		} else if (max_vals.rank == worldRank) {
#	Line 348 | Line 862 | namespace oopse {
862		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
863		min_vals.rank, 0, status);
864
865	<	switch(rnemdType_) {
866	<	case rnemdKinetic :
865	>	switch(rnemdFluxType_) {
866	>	case rnemdKE :
867		max_sd->setVel(min_vel);
868	<
868	>	//angular momenta exchange enabled
869		if (max_sd->isDirectional()) {
870		Vector3d min_angMom;
871		Vector3d max_angMom = max_sd->getJ();
872	<
872	>
873		// point-to-point swap of the angular momentum vector
874		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
875		MPI::REALTYPE, min_vals.rank, 1,
876		min_angMom.getArrayPointer(), 3,
877		MPI::REALTYPE, min_vals.rank, 1,
878		status);
879	<
879	>
880		max_sd->setJ(min_angMom);
881	<	}
881	>	}
882		break;
883		case rnemdPx :
884		max_vel.x() = min_vel.x();
#	Line 378 | Line 892 | namespace oopse {
892		max_vel.z() = min_vel.z();
893		max_sd->setVel(max_vel);
894		break;
381	–	case rnemdUnknown :
895		default :
896		break;
897		}
#	Line 395 | Line 908 | namespace oopse {
908		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
909		max_vals.rank, 0, status);
910
911	<	switch(rnemdType_) {
912	<	case rnemdKinetic :
911	>	switch(rnemdFluxType_) {
912	>	case rnemdKE :
913		min_sd->setVel(max_vel);
914	<
914	>	//angular momenta exchange enabled
915		if (min_sd->isDirectional()) {
916		Vector3d min_angMom = min_sd->getJ();
917		Vector3d max_angMom;
918	<
918	>
919		// point-to-point swap of the angular momentum vector
920		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
921		MPI::REALTYPE, max_vals.rank, 1,
922		max_angMom.getArrayPointer(), 3,
923		MPI::REALTYPE, max_vals.rank, 1,
924		status);
925	<
925	>
926		min_sd->setJ(max_angMom);
927		}
928		break;
#	Line 425 | Line 938 | namespace oopse {
938		min_vel.z() = max_vel.z();
939		min_sd->setVel(min_vel);
940		break;
428	–	case rnemdUnknown :
941		default :
942		break;
943		}
944		}
945		#endif
946	<	exchangeSum_ += max_val - min_val;
947	<	} else {
948	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
946	>
947	>	switch(rnemdFluxType_) {
948	>	case rnemdKE:
949	>	kineticExchange_ += max_val - min_val;
950	>	break;
951	>	case rnemdPx:
952	>	momentumExchange_.x() += max_val - min_val;
953	>	break;
954	>	case rnemdPy:
955	>	momentumExchange_.y() += max_val - min_val;
956	>	break;
957	>	case rnemdPz:
958	>	momentumExchange_.z() += max_val - min_val;
959	>	break;
960	>	default:
961	>	break;
962	>	}
963	>	} else {
964	>	sprintf(painCave.errMsg,
965	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
966	>	painCave.isFatal = 0;
967	>	painCave.severity = OPENMD_INFO;
968	>	simError();
969	>	failTrialCount_++;
970		}
971		} else {
972	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
973	<	}
974	<
972	>	sprintf(painCave.errMsg,
973	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
974	>	"\twas not present in at least one of the two slabs.\n");
975	>	painCave.isFatal = 0;
976	>	painCave.severity = OPENMD_INFO;
977	>	simError();
978	>	failTrialCount_++;
979	>	}
980		}
981
982	<	void RNEMD::getStatus() {
982	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
983	>	if (!doRNEMD_) return;
984	>	int selei;
985	>	int selej;
986
987		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
988	+	RealType time = currentSnap_->getTime();
989		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
990
991	<	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
991	>	StuntDouble* sd;
992
993	<	seleMan_.setSelectionSet(evaluator_.evaluate());
993	>	vector<StuntDouble*> hotBin, coldBin;
994
995	<	int selei;
996	<	StuntDouble* sd;
997	<	int idx;
995	>	RealType Phx = 0.0;
996	>	RealType Phy = 0.0;
997	>	RealType Phz = 0.0;
998	>	RealType Khx = 0.0;
999	>	RealType Khy = 0.0;
1000	>	RealType Khz = 0.0;
1001	>	RealType Khw = 0.0;
1002	>	RealType Pcx = 0.0;
1003	>	RealType Pcy = 0.0;
1004	>	RealType Pcz = 0.0;
1005	>	RealType Kcx = 0.0;
1006	>	RealType Kcy = 0.0;
1007	>	RealType Kcz = 0.0;
1008	>	RealType Kcw = 0.0;
1009
1010	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
1011	<	// being averaged
461	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
462	<	// number of degrees of
463	<	// freedom being averaged
1010	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1011	>	sd = smanA.nextSelected(selei)) {
1012
465	–	for (sd = seleMan_.beginSelected(selei); sd != NULL;
466	–	sd = seleMan_.nextSelected(selei)) {
467	–
468	–	idx = sd->getLocalIndex();
469	–
1013		Vector3d pos = sd->getPos();
1014	<
1014	>
1015		// wrap the stuntdouble's position back into the box:
1016
1017		if (usePeriodicBoundaryConditions_)
1018		currentSnap_->wrapVector(pos);
1019
477	–	// which bin is this stuntdouble in?
478	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1020
480	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
481	–
1021		RealType mass = sd->getMass();
1022		Vector3d vel = sd->getVel();
1023	<	RealType value;
1024	<
1025	<	switch(rnemdType_) {
1026	<	case rnemdKinetic :
1027	<
1028	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1029	<	vel[2]*vel[2]);
1030	<
1031	<	valueCount[binNo] += 3;
1032	<	if (sd->isDirectional()) {
1033	<	Vector3d angMom = sd->getJ();
1034	<	Mat3x3d I = sd->getI();
1035	<
1036	<	if (sd->isLinear()) {
1037	<	int i = sd->linearAxis();
1038	<	int j = (i + 1) % 3;
1039	<	int k = (i + 2) % 3;
1040	<	value += angMom[j] * angMom[j] / I(j, j) +
1041	<	angMom[k] * angMom[k] / I(k, k);
1042	<
1043	<	valueCount[binNo] +=2;
1044	<
1045	<	} else {
1046	<	value += angMom[0]*angMom[0]/I(0, 0)
1047	<	+ angMom[1]*angMom[1]/I(1, 1)
1048	<	+ angMom[2]*angMom[2]/I(2, 2);
1049	<	valueCount[binNo] +=3;
1050	<	}
1051	<	}
1052	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
1023	>
1024	>	hotBin.push_back(sd);
1025	>	Phx += mass * vel.x();
1026	>	Phy += mass * vel.y();
1027	>	Phz += mass * vel.z();
1028	>	Khx += mass * vel.x() * vel.x();
1029	>	Khy += mass * vel.y() * vel.y();
1030	>	Khz += mass * vel.z() * vel.z();
1031	>	if (sd->isDirectional()) {
1032	>	Vector3d angMom = sd->getJ();
1033	>	Mat3x3d I = sd->getI();
1034	>	if (sd->isLinear()) {
1035	>	int i = sd->linearAxis();
1036	>	int j = (i + 1) % 3;
1037	>	int k = (i + 2) % 3;
1038	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1039	>	angMom[k] * angMom[k] / I(k, k);
1040	>	} else {
1041	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1042	>	+ angMom[1]*angMom[1]/I(1, 1)
1043	>	+ angMom[2]*angMom[2]/I(2, 2);
1044	>	}
1045	>	}
1046	>	}
1047	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1048	>	sd = smanB.nextSelected(selej)) {
1049	>	Vector3d pos = sd->getPos();
1050	>
1051	>	// wrap the stuntdouble's position back into the box:
1052	>
1053	>	if (usePeriodicBoundaryConditions_)
1054	>	currentSnap_->wrapVector(pos);
1055	>
1056	>	RealType mass = sd->getMass();
1057	>	Vector3d vel = sd->getVel();
1058
1059	+	coldBin.push_back(sd);
1060	+	Pcx += mass * vel.x();
1061	+	Pcy += mass * vel.y();
1062	+	Pcz += mass * vel.z();
1063	+	Kcx += mass * vel.x() * vel.x();
1064	+	Kcy += mass * vel.y() * vel.y();
1065	+	Kcz += mass * vel.z() * vel.z();
1066	+	if (sd->isDirectional()) {
1067	+	Vector3d angMom = sd->getJ();
1068	+	Mat3x3d I = sd->getI();
1069	+	if (sd->isLinear()) {
1070	+	int i = sd->linearAxis();
1071	+	int j = (i + 1) % 3;
1072	+	int k = (i + 2) % 3;
1073	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
1074	+	angMom[k] * angMom[k] / I(k, k);
1075	+	} else {
1076	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
1077	+	+ angMom[1]*angMom[1]/I(1, 1)
1078	+	+ angMom[2]*angMom[2]/I(2, 2);
1079	+	}
1080	+	}
1081	+	}
1082	+
1083	+	Khx *= 0.5;
1084	+	Khy *= 0.5;
1085	+	Khz *= 0.5;
1086	+	Khw *= 0.5;
1087	+	Kcx *= 0.5;
1088	+	Kcy *= 0.5;
1089	+	Kcz *= 0.5;
1090	+	Kcw *= 0.5;
1091	+
1092	+	#ifdef IS_MPI
1093	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1094	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1095	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1096	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1097	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1098	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1099	+
1100	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1101	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1102	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1103	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1104	+
1105	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1106	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1107	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1108	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1109	+	#endif
1110	+
1111	+	//solve coldBin coeff's first
1112	+	RealType px = Pcx / Phx;
1113	+	RealType py = Pcy / Phy;
1114	+	RealType pz = Pcz / Phz;
1115	+	RealType c, x, y, z;
1116	+	bool successfulScale = false;
1117	+	if ((rnemdFluxType_ == rnemdFullKE) ||
1118	+	(rnemdFluxType_ == rnemdRotKE)) {
1119	+	//may need sanity check Khw & Kcw > 0
1120	+
1121	+	if (rnemdFluxType_ == rnemdFullKE) {
1122	+	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1123	+	} else {
1124	+	c = 1.0 - kineticTarget_ / Kcw;
1125	+	}
1126	+
1127	+	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1128	+	c = sqrt(c);
1129	+
1130	+	RealType w = 0.0;
1131	+	if (rnemdFluxType_ ==  rnemdFullKE) {
1132	+	x = 1.0 + px * (1.0 - c);
1133	+	y = 1.0 + py * (1.0 - c);
1134	+	z = 1.0 + pz * (1.0 - c);
1135	+	/* more complicated way
1136	+	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1137	+	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1138	+	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1139	+	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1140	+	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1141	+	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1142	+	*/
1143	+	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1144	+	(fabs(z - 1.0) < 0.1)) {
1145	+	w = 1.0 + (kineticTarget_
1146	+	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1147	+	+ Khz * (1.0 - z * z)) / Khw;
1148	+	}//no need to calculate w if x, y or z is out of range
1149	+	} else {
1150	+	w = 1.0 + kineticTarget_ / Khw;
1151	+	}
1152	+	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1153	+	//if w is in the right range, so should be x, y, z.
1154	+	vector<StuntDouble*>::iterator sdi;
1155	+	Vector3d vel;
1156	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1157	+	if (rnemdFluxType_ == rnemdFullKE) {
1158	+	vel = (*sdi)->getVel() * c;
1159	+	(*sdi)->setVel(vel);
1160	+	}
1161	+	if ((*sdi)->isDirectional()) {
1162	+	Vector3d angMom = (*sdi)->getJ() * c;
1163	+	(*sdi)->setJ(angMom);
1164	+	}
1165	+	}
1166	+	w = sqrt(w);
1167	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1168	+	if (rnemdFluxType_ == rnemdFullKE) {
1169	+	vel = (*sdi)->getVel();
1170	+	vel.x() *= x;
1171	+	vel.y() *= y;
1172	+	vel.z() *= z;
1173	+	(*sdi)->setVel(vel);
1174	+	}
1175	+	if ((*sdi)->isDirectional()) {
1176	+	Vector3d angMom = (*sdi)->getJ() * w;
1177	+	(*sdi)->setJ(angMom);
1178	+	}
1179	+	}
1180	+	successfulScale = true;
1181	+	kineticExchange_ += kineticTarget_;
1182	+	}
1183	+	}
1184	+	} else {
1185	+	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1186	+	switch(rnemdFluxType_) {
1187	+	case rnemdKE :
1188	+	/* used hotBin coeff's & only scale x & y dimensions
1189	+	RealType px = Phx / Pcx;
1190	+	RealType py = Phy / Pcy;
1191	+	a110 = Khy;
1192	+	c0 = - Khx - Khy - kineticTarget_;
1193	+	a000 = Khx;
1194	+	a111 = Kcy * py * py;
1195	+	b11 = -2.0 * Kcy * py * (1.0 + py);
1196	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1197	+	b01 = -2.0 * Kcx * px * (1.0 + px);
1198	+	a001 = Kcx * px * px;
1199	+	*/
1200	+	//scale all three dimensions, let c_x = c_y
1201	+	a000 = Kcx + Kcy;
1202	+	a110 = Kcz;
1203	+	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1204	+	a001 = Khx * px * px + Khy * py * py;
1205	+	a111 = Khz * pz * pz;
1206	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1207	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
1208	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1209	+	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1210		break;
1211		case rnemdPx :
1212	<	value = mass * vel[0];
1213	<	valueCount[binNo]++;
1212	>	c = 1 - momentumTarget_.x() / Pcx;
1213	>	a000 = Kcy;
1214	>	a110 = Kcz;
1215	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1216	>	a001 = py * py * Khy;
1217	>	a111 = pz * pz * Khz;
1218	>	b01 = -2.0 * Khy * py * (1.0 + py);
1219	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1220	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1221	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1222		break;
1223		case rnemdPy :
1224	<	value = mass * vel[1];
1225	<	valueCount[binNo]++;
1224	>	c = 1 - momentumTarget_.y() / Pcy;
1225	>	a000 = Kcx;
1226	>	a110 = Kcz;
1227	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1228	>	a001 = px * px * Khx;
1229	>	a111 = pz * pz * Khz;
1230	>	b01 = -2.0 * Khx * px * (1.0 + px);
1231	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1232	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1233	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1234		break;
1235	<	case rnemdPz :
1236	<	value = mass * vel[2];
1237	<	valueCount[binNo]++;
1235	>	case rnemdPz ://we don't really do this, do we?
1236	>	c = 1 - momentumTarget_.z() / Pcz;
1237	>	a000 = Kcx;
1238	>	a110 = Kcy;
1239	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1240	>	a001 = px * px * Khx;
1241	>	a111 = py * py * Khy;
1242	>	b01 = -2.0 * Khx * px * (1.0 + px);
1243	>	b11 = -2.0 * Khy * py * (1.0 + py);
1244	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1245	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1246		break;
528	–	case rnemdUnknown :
1247		default :
1248		break;
1249		}
1250	<	valueHist[binNo] += value;
1250	>
1251	>	RealType v1 = a000 * a111 - a001 * a110;
1252	>	RealType v2 = a000 * b01;
1253	>	RealType v3 = a000 * b11;
1254	>	RealType v4 = a000 * c1 - a001 * c0;
1255	>	RealType v8 = a110 * b01;
1256	>	RealType v10 = - b01 * c0;
1257	>
1258	>	RealType u0 = v2 * v10 - v4 * v4;
1259	>	RealType u1 = -2.0 * v3 * v4;
1260	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1261	>	RealType u3 = -2.0 * v1 * v3;
1262	>	RealType u4 = - v1 * v1;
1263	>	//rescale coefficients
1264	>	RealType maxAbs = fabs(u0);
1265	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1266	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1267	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1268	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1269	>	u0 /= maxAbs;
1270	>	u1 /= maxAbs;
1271	>	u2 /= maxAbs;
1272	>	u3 /= maxAbs;
1273	>	u4 /= maxAbs;
1274	>	//max_element(start, end) is also available.
1275	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1276	>	poly.setCoefficient(4, u4);
1277	>	poly.setCoefficient(3, u3);
1278	>	poly.setCoefficient(2, u2);
1279	>	poly.setCoefficient(1, u1);
1280	>	poly.setCoefficient(0, u0);
1281	>	vector<RealType> realRoots = poly.FindRealRoots();
1282	>
1283	>	vector<RealType>::iterator ri;
1284	>	RealType r1, r2, alpha0;
1285	>	vector<pair<RealType,RealType> > rps;
1286	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1287	>	r2 = *ri;
1288	>	//check if FindRealRoots() give the right answer
1289	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1290	>	sprintf(painCave.errMsg,
1291	>	"RNEMD Warning: polynomial solve seems to have an error!");
1292	>	painCave.isFatal = 0;
1293	>	simError();
1294	>	failRootCount_++;
1295	>	}
1296	>	//might not be useful w/o rescaling coefficients
1297	>	alpha0 = -c0 - a110 * r2 * r2;
1298	>	if (alpha0 >= 0.0) {
1299	>	r1 = sqrt(alpha0 / a000);
1300	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1301	>	< 1e-6)
1302	>	{ rps.push_back(make_pair(r1, r2)); }
1303	>	if (r1 > 1e-6) { //r1 non-negative
1304	>	r1 = -r1;
1305	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1306	>	< 1e-6)
1307	>	{ rps.push_back(make_pair(r1, r2)); }
1308	>	}
1309	>	}
1310	>	}
1311	>	// Consider combining together the solving pair part w/ the searching
1312	>	// best solution part so that we don't need the pairs vector
1313	>	if (!rps.empty()) {
1314	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1315	>	RealType diff;
1316	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1317	>	vector<pair<RealType,RealType> >::iterator rpi;
1318	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1319	>	r1 = (*rpi).first;
1320	>	r2 = (*rpi).second;
1321	>	switch(rnemdFluxType_) {
1322	>	case rnemdKE :
1323	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1324	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1325	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1326	>	break;
1327	>	case rnemdPx :
1328	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1329	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1330	>	break;
1331	>	case rnemdPy :
1332	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1333	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1334	>	break;
1335	>	case rnemdPz :
1336	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1337	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1338	>	default :
1339	>	break;
1340	>	}
1341	>	if (diff < smallestDiff) {
1342	>	smallestDiff = diff;
1343	>	bestPair = *rpi;
1344	>	}
1345	>	}
1346	>	#ifdef IS_MPI
1347	>	if (worldRank == 0) {
1348	>	#endif
1349	>	// sprintf(painCave.errMsg,
1350	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1351	>	//         bestPair.first, bestPair.second);
1352	>	// painCave.isFatal = 0;
1353	>	// painCave.severity = OPENMD_INFO;
1354	>	// simError();
1355	>	#ifdef IS_MPI
1356	>	}
1357	>	#endif
1358	>
1359	>	switch(rnemdFluxType_) {
1360	>	case rnemdKE :
1361	>	x = bestPair.first;
1362	>	y = bestPair.first;
1363	>	z = bestPair.second;
1364	>	break;
1365	>	case rnemdPx :
1366	>	x = c;
1367	>	y = bestPair.first;
1368	>	z = bestPair.second;
1369	>	break;
1370	>	case rnemdPy :
1371	>	x = bestPair.first;
1372	>	y = c;
1373	>	z = bestPair.second;
1374	>	break;
1375	>	case rnemdPz :
1376	>	x = bestPair.first;
1377	>	y = bestPair.second;
1378	>	z = c;
1379	>	break;
1380	>	default :
1381	>	break;
1382	>	}
1383	>	vector<StuntDouble*>::iterator sdi;
1384	>	Vector3d vel;
1385	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1386	>	vel = (*sdi)->getVel();
1387	>	vel.x() *= x;
1388	>	vel.y() *= y;
1389	>	vel.z() *= z;
1390	>	(*sdi)->setVel(vel);
1391	>	}
1392	>	//convert to hotBin coefficient
1393	>	x = 1.0 + px * (1.0 - x);
1394	>	y = 1.0 + py * (1.0 - y);
1395	>	z = 1.0 + pz * (1.0 - z);
1396	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1397	>	vel = (*sdi)->getVel();
1398	>	vel.x() *= x;
1399	>	vel.y() *= y;
1400	>	vel.z() *= z;
1401	>	(*sdi)->setVel(vel);
1402	>	}
1403	>	successfulScale = true;
1404	>	switch(rnemdFluxType_) {
1405	>	case rnemdKE :
1406	>	kineticExchange_ += kineticTarget_;
1407	>	break;
1408	>	case rnemdPx :
1409	>	case rnemdPy :
1410	>	case rnemdPz :
1411	>	momentumExchange_ += momentumTarget_;
1412	>	break;
1413	>	default :
1414	>	break;
1415	>	}
1416	>	}
1417		}
1418	+	if (successfulScale != true) {
1419	+	sprintf(painCave.errMsg,
1420	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1421	+	"\tthe constraint equations may not exist or there may be\n"
1422	+	"\tno selected objects in one or both slabs.\n");
1423	+	painCave.isFatal = 0;
1424	+	painCave.severity = OPENMD_INFO;
1425	+	simError();
1426	+	failTrialCount_++;
1427	+	}
1428	+	}
1429	+
1430	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1431	+	if (!doRNEMD_) return;
1432	+	int selei;
1433	+	int selej;
1434
1435	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1436	+	RealType time = currentSnap_->getTime();
1437	+	Mat3x3d hmat = currentSnap_->getHmat();
1438	+
1439	+	StuntDouble* sd;
1440	+
1441	+	vector<StuntDouble*> hotBin, coldBin;
1442	+
1443	+	Vector3d Ph(V3Zero);
1444	+	Vector3d Lh(V3Zero);
1445	+	RealType Mh = 0.0;
1446	+	Mat3x3d Ih(0.0);
1447	+	RealType Kh = 0.0;
1448	+	Vector3d Pc(V3Zero);
1449	+	Vector3d Lc(V3Zero);
1450	+	RealType Mc = 0.0;
1451	+	Mat3x3d Ic(0.0);
1452	+	RealType Kc = 0.0;
1453	+
1454	+	// Constraints can be on only the linear or angular momentum, but
1455	+	// not both.  Usually, the user will specify which they want, but
1456	+	// in case they don't, the use of periodic boundaries should make
1457	+	// the choice for us.
1458	+	bool doLinearPart = false;
1459	+	bool doAngularPart = false;
1460	+
1461	+	switch (rnemdFluxType_) {
1462	+	case rnemdPx:
1463	+	case rnemdPy:
1464	+	case rnemdPz:
1465	+	case rnemdPvector:
1466	+	case rnemdKePx:
1467	+	case rnemdKePy:
1468	+	case rnemdKePvector:
1469	+	doLinearPart = true;
1470	+	break;
1471	+	case rnemdLx:
1472	+	case rnemdLy:
1473	+	case rnemdLz:
1474	+	case rnemdLvector:
1475	+	case rnemdKeLx:
1476	+	case rnemdKeLy:
1477	+	case rnemdKeLz:
1478	+	case rnemdKeLvector:
1479	+	doAngularPart = true;
1480	+	break;
1481	+	case rnemdKE:
1482	+	case rnemdRotKE:
1483	+	case rnemdFullKE:
1484	+	default:
1485	+	if (usePeriodicBoundaryConditions_)
1486	+	doLinearPart = true;
1487	+	else
1488	+	doAngularPart = true;
1489	+	break;
1490	+	}
1491	+
1492	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1493	+	sd = smanA.nextSelected(selei)) {
1494	+
1495	+	Vector3d pos = sd->getPos();
1496	+
1497	+	// wrap the stuntdouble's position back into the box:
1498	+
1499	+	if (usePeriodicBoundaryConditions_)
1500	+	currentSnap_->wrapVector(pos);
1501	+
1502	+	RealType mass = sd->getMass();
1503	+	Vector3d vel = sd->getVel();
1504	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1505	+	RealType r2;
1506	+
1507	+	hotBin.push_back(sd);
1508	+	Ph += mass * vel;
1509	+	Mh += mass;
1510	+	Kh += mass * vel.lengthSquare();
1511	+	Lh += mass * cross(rPos, vel);
1512	+	Ih -= outProduct(rPos, rPos) * mass;
1513	+	r2 = rPos.lengthSquare();
1514	+	Ih(0, 0) += mass * r2;
1515	+	Ih(1, 1) += mass * r2;
1516	+	Ih(2, 2) += mass * r2;
1517	+
1518	+	if (rnemdFluxType_ == rnemdFullKE) {
1519	+	if (sd->isDirectional()) {
1520	+	Vector3d angMom = sd->getJ();
1521	+	Mat3x3d I = sd->getI();
1522	+	if (sd->isLinear()) {
1523	+	int i = sd->linearAxis();
1524	+	int j = (i + 1) % 3;
1525	+	int k = (i + 2) % 3;
1526	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1527	+	angMom[k] * angMom[k] / I(k, k);
1528	+	} else {
1529	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1530	+	angMom[1] * angMom[1] / I(1, 1) +
1531	+	angMom[2] * angMom[2] / I(2, 2);
1532	+	}
1533	+	}
1534	+	}
1535	+	}
1536	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1537	+	sd = smanB.nextSelected(selej)) {
1538	+
1539	+	Vector3d pos = sd->getPos();
1540	+
1541	+	// wrap the stuntdouble's position back into the box:
1542	+
1543	+	if (usePeriodicBoundaryConditions_)
1544	+	currentSnap_->wrapVector(pos);
1545	+
1546	+	RealType mass = sd->getMass();
1547	+	Vector3d vel = sd->getVel();
1548	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1549	+	RealType r2;
1550	+
1551	+	coldBin.push_back(sd);
1552	+	Pc += mass * vel;
1553	+	Mc += mass;
1554	+	Kc += mass * vel.lengthSquare();
1555	+	Lc += mass * cross(rPos, vel);
1556	+	Ic -= outProduct(rPos, rPos) * mass;
1557	+	r2 = rPos.lengthSquare();
1558	+	Ic(0, 0) += mass * r2;
1559	+	Ic(1, 1) += mass * r2;
1560	+	Ic(2, 2) += mass * r2;
1561	+
1562	+	if (rnemdFluxType_ == rnemdFullKE) {
1563	+	if (sd->isDirectional()) {
1564	+	Vector3d angMom = sd->getJ();
1565	+	Mat3x3d I = sd->getI();
1566	+	if (sd->isLinear()) {
1567	+	int i = sd->linearAxis();
1568	+	int j = (i + 1) % 3;
1569	+	int k = (i + 2) % 3;
1570	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1571	+	angMom[k] * angMom[k] / I(k, k);
1572	+	} else {
1573	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1574	+	angMom[1] * angMom[1] / I(1, 1) +
1575	+	angMom[2] * angMom[2] / I(2, 2);
1576	+	}
1577	+	}
1578	+	}
1579	+	}
1580	+
1581	+	Kh *= 0.5;
1582	+	Kc *= 0.5;
1583	+
1584		#ifdef IS_MPI
1585	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1587	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1589	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1590	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1591	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1592	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1596	+	MPI::REALTYPE, MPI::SUM);
1597	+	#endif
1598	+
1599
1600	<	// all processors have the same number of bins, and STL vectors pack their
1601	<	// arrays, so in theory, this should be safe:
1600	>	Vector3d ac, acrec, bc, bcrec;
1601	>	Vector3d ah, ahrec, bh, bhrec;
1602
1603	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
1604	<	nBins_, MPI::REALTYPE, MPI::SUM);
1605	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
1606	<	nBins_, MPI::INT, MPI::SUM);
1603	>	bool successfulExchange = false;
1604	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1605	>	Vector3d vc = Pc / Mc;
1606	>	ac = -momentumTarget_ / Mc + vc;
1607	>	acrec = -momentumTarget_ / Mc;
1608	>
1609	>	// We now need the inverse of the inertia tensor to calculate the
1610	>	// angular velocity of the cold slab;
1611	>	Mat3x3d Ici = Ic.inverse();
1612	>	Vector3d omegac = Ici * Lc;
1613	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1614	>	bcrec = bc - omegac;
1615	>
1616	>	RealType cNumerator = Kc - kineticTarget_;
1617	>	if (doLinearPart)
1618	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1619	>
1620	>	if (doAngularPart)
1621	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1622	>
1623	>	if (cNumerator > 0.0) {
1624	>
1625	>	RealType cDenominator = Kc;
1626	>
1627	>	if (doLinearPart)
1628	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1629	>
1630	>	if (doAngularPart)
1631	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1632	>
1633	>	if (cDenominator > 0.0) {
1634	>	RealType c = sqrt(cNumerator / cDenominator);
1635	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1636	>
1637	>	Vector3d vh = Ph / Mh;
1638	>	ah = momentumTarget_ / Mh + vh;
1639	>	ahrec = momentumTarget_ / Mh;
1640	>
1641	>	// We now need the inverse of the inertia tensor to
1642	>	// calculate the angular velocity of the hot slab;
1643	>	Mat3x3d Ihi = Ih.inverse();
1644	>	Vector3d omegah = Ihi * Lh;
1645	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1646	>	bhrec = bh - omegah;
1647	>
1648	>	RealType hNumerator = Kh + kineticTarget_;
1649	>	if (doLinearPart)
1650	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1651	>
1652	>	if (doAngularPart)
1653	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1654	>
1655	>	if (hNumerator > 0.0) {
1656	>
1657	>	RealType hDenominator = Kh;
1658	>	if (doLinearPart)
1659	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1660	>	if (doAngularPart)
1661	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1662	>
1663	>	if (hDenominator > 0.0) {
1664	>	RealType h = sqrt(hNumerator / hDenominator);
1665	>	if ((h > 0.9) && (h < 1.1)) {
1666	>
1667	>	vector<StuntDouble*>::iterator sdi;
1668	>	Vector3d vel;
1669	>	Vector3d rPos;
1670	>
1671	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1672	>	//vel = (*sdi)->getVel();
1673	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1674	>	if (doLinearPart)
1675	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1676	>	if (doAngularPart)
1677	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1678	>
1679	>	(*sdi)->setVel(vel);
1680	>	if (rnemdFluxType_ == rnemdFullKE) {
1681	>	if ((*sdi)->isDirectional()) {
1682	>	Vector3d angMom = (*sdi)->getJ() * c;
1683	>	(*sdi)->setJ(angMom);
1684	>	}
1685	>	}
1686	>	}
1687	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1688	>	//vel = (*sdi)->getVel();
1689	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1690	>	if (doLinearPart)
1691	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1692	>	if (doAngularPart)
1693	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1694
1695	+	(*sdi)->setVel(vel);
1696	+	if (rnemdFluxType_ == rnemdFullKE) {
1697	+	if ((*sdi)->isDirectional()) {
1698	+	Vector3d angMom = (*sdi)->getJ() * h;
1699	+	(*sdi)->setJ(angMom);
1700	+	}
1701	+	}
1702	+	}
1703	+	successfulExchange = true;
1704	+	kineticExchange_ += kineticTarget_;
1705	+	momentumExchange_ += momentumTarget_;
1706	+	angularMomentumExchange_ += angularMomentumTarget_;
1707	+	}
1708	+	}
1709	+	}
1710	+	}
1711	+	}
1712	+	}
1713	+	}
1714	+	if (successfulExchange != true) {
1715	+	sprintf(painCave.errMsg,
1716	+	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1717	+	"\tthe constraint equations may not exist or there may be\n"
1718	+	"\tno selected objects in one or both slabs.\n");
1719	+	painCave.isFatal = 0;
1720	+	painCave.severity = OPENMD_INFO;
1721	+	simError();
1722	+	failTrialCount_++;
1723	+	}
1724	+	}
1725	+
1726	+	RealType RNEMD::getDividingArea() {
1727	+
1728	+	if (hasDividingArea_) return dividingArea_;
1729	+
1730	+	RealType areaA, areaB;
1731	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1732	+
1733	+	if (hasSelectionA_) {
1734	+
1735	+	if (evaluatorA_.hasSurfaceArea())
1736	+	areaA = evaluatorA_.getSurfaceArea();
1737	+	else {
1738	+
1739	+	cerr << "selection A did not have surface area, recomputing\n";
1740	+	int isd;
1741	+	StuntDouble* sd;
1742	+	vector<StuntDouble*> aSites;
1743	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1744	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1745	+	sd = seleManA_.nextSelected(isd)) {
1746	+	aSites.push_back(sd);
1747	+	}
1748	+	#if defined(HAVE_QHULL)
1749	+	ConvexHull* surfaceMeshA = new ConvexHull();
1750	+	surfaceMeshA->computeHull(aSites);
1751	+	areaA = surfaceMeshA->getArea();
1752	+	delete surfaceMeshA;
1753	+	#else
1754	+	sprintf( painCave.errMsg,
1755	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1756	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1757	+	painCave.severity = OPENMD_ERROR;
1758	+	painCave.isFatal = 1;
1759	+	simError();
1760	+	#endif
1761	+	}
1762	+
1763	+	} else {
1764	+	if (usePeriodicBoundaryConditions_) {
1765	+	// in periodic boundaries, the surface area is twice the x-y
1766	+	// area of the current box:
1767	+	areaA = 2.0 * snap->getXYarea();
1768	+	} else {
1769	+	// in non-periodic simulations, without explicitly setting
1770	+	// selections, the sphere radius sets the surface area of the
1771	+	// dividing surface:
1772	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1773	+	}
1774	+	}
1775	+
1776	+	if (hasSelectionB_) {
1777	+	if (evaluatorB_.hasSurfaceArea())
1778	+	areaB = evaluatorB_.getSurfaceArea();
1779	+	else {
1780	+	cerr << "selection B did not have surface area, recomputing\n";
1781	+
1782	+	int isd;
1783	+	StuntDouble* sd;
1784	+	vector<StuntDouble*> bSites;
1785	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1786	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1787	+	sd = seleManB_.nextSelected(isd)) {
1788	+	bSites.push_back(sd);
1789	+	}
1790	+
1791	+	#if defined(HAVE_QHULL)
1792	+	ConvexHull* surfaceMeshB = new ConvexHull();
1793	+	surfaceMeshB->computeHull(bSites);
1794	+	areaB = surfaceMeshB->getArea();
1795	+	delete surfaceMeshB;
1796	+	#else
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1799	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1800	+	painCave.severity = OPENMD_ERROR;
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	#endif
1804	+	}
1805	+
1806	+	} else {
1807	+	if (usePeriodicBoundaryConditions_) {
1808	+	// in periodic boundaries, the surface area is twice the x-y
1809	+	// area of the current box:
1810	+	areaB = 2.0 * snap->getXYarea();
1811	+	} else {
1812	+	// in non-periodic simulations, without explicitly setting
1813	+	// selections, but if a sphereBradius has been set, just use that:
1814	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1815	+	}
1816	+	}
1817	+
1818	+	dividingArea_ = min(areaA, areaB);
1819	+	hasDividingArea_ = true;
1820	+	return dividingArea_;
1821	+	}
1822	+
1823	+	void RNEMD::doRNEMD() {
1824	+	if (!doRNEMD_) return;
1825	+	trialCount_++;
1826	+
1827	+	// object evaluator:
1828	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1829	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1830	+
1831	+	evaluatorA_.loadScriptString(selectionA_);
1832	+	evaluatorB_.loadScriptString(selectionB_);
1833	+
1834	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1835	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1836	+
1837	+	commonA_ = seleManA_ & seleMan_;
1838	+	commonB_ = seleManB_ & seleMan_;
1839	+
1840	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1841	+	// dt = exchange time interval
1842	+	// flux = target flux
1843	+	// dividingArea = smallest dividing surface between the two regions
1844	+
1845	+	hasDividingArea_ = false;
1846	+	RealType area = getDividingArea();
1847	+
1848	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1849	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1850	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1851	+
1852	+	switch(rnemdMethod_) {
1853	+	case rnemdSwap:
1854	+	doSwap(commonA_, commonB_);
1855	+	break;
1856	+	case rnemdNIVS:
1857	+	doNIVS(commonA_, commonB_);
1858	+	break;
1859	+	case rnemdVSS:
1860	+	doVSS(commonA_, commonB_);
1861	+	break;
1862	+	case rnemdUnkownMethod:
1863	+	default :
1864	+	break;
1865	+	}
1866	+	}
1867	+
1868	+	void RNEMD::collectData() {
1869	+	if (!doRNEMD_) return;
1870	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1871	+
1872	+	// collectData can be called more frequently than the doRNEMD, so use the
1873	+	// computed area from the last exchange time:
1874	+	RealType area = getDividingArea();
1875	+	areaAccumulator_->add(area);
1876	+	Mat3x3d hmat = currentSnap_->getHmat();
1877	+	Vector3d u = angularMomentumFluxVector_;
1878	+	u.normalize();
1879	+
1880	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1881	+
1882	+	int selei(0);
1883	+	StuntDouble* sd;
1884	+	int binNo;
1885	+	RealType mass;
1886	+	Vector3d vel;
1887	+	Vector3d rPos;
1888	+	RealType KE;
1889	+	Vector3d L;
1890	+	Mat3x3d I;
1891	+	RealType r2;
1892	+
1893	+	vector<RealType> binMass(nBins_, 0.0);
1894	+	vector<Vector3d> binP(nBins_, V3Zero);
1895	+	vector<RealType> binOmega(nBins_, 0.0);
1896	+	vector<Vector3d> binL(nBins_, V3Zero);
1897	+	vector<Mat3x3d>  binI(nBins_);
1898	+	vector<RealType> binKE(nBins_, 0.0);
1899	+	vector<int> binDOF(nBins_, 0);
1900	+	vector<int> binCount(nBins_, 0);
1901	+
1902	+	// alternative approach, track all molecules instead of only those
1903	+	// selected for scaling/swapping:
1904	+	/*
1905	+	SimInfo::MoleculeIterator miter;
1906	+	vector<StuntDouble*>::iterator iiter;
1907	+	Molecule* mol;
1908	+	StuntDouble* sd;
1909	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1910	+	mol = info_->nextMolecule(miter))
1911	+	sd is essentially sd
1912	+	for (sd = mol->beginIntegrableObject(iiter);
1913	+	sd != NULL;
1914	+	sd = mol->nextIntegrableObject(iiter))
1915	+	*/
1916	+
1917	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1918	+	sd = seleMan_.nextSelected(selei)) {
1919	+
1920	+	Vector3d pos = sd->getPos();
1921	+
1922	+	// wrap the stuntdouble's position back into the box:
1923	+
1924	+	if (usePeriodicBoundaryConditions_) {
1925	+	currentSnap_->wrapVector(pos);
1926	+	// which bin is this stuntdouble in?
1927	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1928	+	// Shift molecules by half a box to have bins start at 0
1929	+	// The modulo operator is used to wrap the case when we are
1930	+	// beyond the end of the bins back to the beginning.
1931	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1932	+	} else {
1933	+	Vector3d rPos = pos - coordinateOrigin_;
1934	+	binNo = int(rPos.length() / binWidth_);
1935	+	}
1936	+
1937	+	mass = sd->getMass();
1938	+	vel = sd->getVel();
1939	+	rPos = sd->getPos() - coordinateOrigin_;
1940	+	KE = 0.5 * mass * vel.lengthSquare();
1941	+	L = mass * cross(rPos, vel);
1942	+	I = outProduct(rPos, rPos) * mass;
1943	+	r2 = rPos.lengthSquare();
1944	+	I(0, 0) += mass * r2;
1945	+	I(1, 1) += mass * r2;
1946	+	I(2, 2) += mass * r2;
1947	+
1948	+	// Project the relative position onto a plane perpendicular to
1949	+	// the angularMomentumFluxVector:
1950	+	// Vector3d rProj = rPos - dot(rPos, u) * u;
1951	+	// Project the velocity onto a plane perpendicular to the
1952	+	// angularMomentumFluxVector:
1953	+	// Vector3d vProj = vel  - dot(vel, u) * u;
1954	+	// Compute angular velocity vector (should be nearly parallel to
1955	+	// angularMomentumFluxVector
1956	+	// Vector3d aVel = cross(rProj, vProj);
1957	+
1958	+	if (binNo >= 0 && binNo < nBins_)  {
1959	+	binCount[binNo]++;
1960	+	binMass[binNo] += mass;
1961	+	binP[binNo] += mass*vel;
1962	+	binKE[binNo] += KE;
1963	+	binI[binNo] += I;
1964	+	binL[binNo] += L;
1965	+	binDOF[binNo] += 3;
1966	+
1967	+	if (sd->isDirectional()) {
1968	+	Vector3d angMom = sd->getJ();
1969	+	Mat3x3d Ia = sd->getI();
1970	+	if (sd->isLinear()) {
1971	+	int i = sd->linearAxis();
1972	+	int j = (i + 1) % 3;
1973	+	int k = (i + 2) % 3;
1974	+	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
1975	+	angMom[k] * angMom[k] / Ia(k, k));
1976	+	binDOF[binNo] += 2;
1977	+	} else {
1978	+	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
1979	+	angMom[1] * angMom[1] / Ia(1, 1) +
1980	+	angMom[2] * angMom[2] / Ia(2, 2));
1981	+	binDOF[binNo] += 3;
1982	+	}
1983	+	}
1984	+	}
1985	+	}
1986	+
1987	+	#ifdef IS_MPI
1988	+
1989	+	for (int i = 0; i < nBins_; i++) {
1990	+
1991	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[i],
1992	+	1, MPI::INT, MPI::SUM);
1993	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[i],
1994	+	1, MPI::REALTYPE, MPI::SUM);
1995	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binP[i],
1996	+	3, MPI::REALTYPE, MPI::SUM);
1997	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binL[i],
1998	+	3, MPI::REALTYPE, MPI::SUM);
1999	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binI[i],
2000	+	9, MPI::REALTYPE, MPI::SUM);
2001	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[i],
2002	+	1, MPI::REALTYPE, MPI::SUM);
2003	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[i],
2004	+	1, MPI::INT, MPI::SUM);
2005	+	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmega[i],
2006	+	//                          1, MPI::REALTYPE, MPI::SUM);
2007	+	}
2008	+
2009	+	#endif
2010	+
2011	+	Vector3d omega;
2012	+	RealType den;
2013	+	RealType temp;
2014	+	RealType z;
2015	+	RealType r;
2016	+	for (int i = 0; i < nBins_; i++) {
2017	+	if (usePeriodicBoundaryConditions_) {
2018	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2019	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2020	+	/ currentSnap_->getVolume() ;
2021	+	} else {
2022	+	r = (((RealType)i + 0.5) * binWidth_);
2023	+	RealType rinner = (RealType)i * binWidth_;
2024	+	RealType router = (RealType)(i+1) * binWidth_;
2025	+	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2026	+	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2027	+	}
2028	+	vel = binP[i] / binMass[i];
2029	+
2030	+	omega = binI[i].inverse() * binL[i];
2031	+
2032	+	// omega = binOmega[i] / binCount[i];
2033	+
2034	+	if (binCount[i] > 0) {
2035	+	// only add values if there are things to add
2036	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2037	+	PhysicalConstants::energyConvert);
2038	+
2039	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2040	+	if(outputMask_[j]) {
2041	+	switch(j) {
2042	+	case Z:
2043	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2044	+	break;
2045	+	case R:
2046	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2047	+	break;
2048	+	case TEMPERATURE:
2049	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2050	+	break;
2051	+	case VELOCITY:
2052	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2053	+	break;
2054	+	case ANGULARVELOCITY:
2055	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2056	+	break;
2057	+	case DENSITY:
2058	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2059	+	break;
2060	+	}
2061	+	}
2062	+	}
2063	+	}
2064	+	}
2065	+	hasData_ = true;
2066	+	}
2067	+
2068	+	void RNEMD::getStarted() {
2069	+	if (!doRNEMD_) return;
2070	+	hasDividingArea_ = false;
2071	+	collectData();
2072	+	writeOutputFile();
2073	+	}
2074	+
2075	+	void RNEMD::parseOutputFileFormat(const std::string& format) {
2076	+	if (!doRNEMD_) return;
2077	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2078	+
2079	+	while(tokenizer.hasMoreTokens()) {
2080	+	std::string token(tokenizer.nextToken());
2081	+	toUpper(token);
2082	+	OutputMapType::iterator i = outputMap_.find(token);
2083	+	if (i != outputMap_.end()) {
2084	+	outputMask_.set(i->second);
2085	+	} else {
2086	+	sprintf( painCave.errMsg,
2087	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2088	+	"\toutputFileFormat keyword.\n", token.c_str() );
2089	+	painCave.isFatal = 0;
2090	+	painCave.severity = OPENMD_ERROR;
2091	+	simError();
2092	+	}
2093	+	}
2094	+	}
2095	+
2096	+	void RNEMD::writeOutputFile() {
2097	+	if (!doRNEMD_) return;
2098	+	if (!hasData_) return;
2099	+
2100	+	#ifdef IS_MPI
2101		// If we're the root node, should we print out the results
2102		int worldRank = MPI::COMM_WORLD.Get_rank();
2103		if (worldRank == 0) {
2104		#endif
2105	<
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";
2105	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2106
2107	+	if( !rnemdFile_ ){
2108	+	sprintf( painCave.errMsg,
2109	+	"Could not open \"%s\" for RNEMD output.\n",
2110	+	rnemdFileName_.c_str());
2111	+	painCave.isFatal = 1;
2112	+	simError();
2113	+	}
2114	+
2115	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2116	+
2117	+	RealType time = currentSnap_->getTime();
2118	+	RealType avgArea;
2119	+	areaAccumulator_->getAverage(avgArea);
2120	+
2121	+	RealType Jz(0.0);
2122	+	Vector3d JzP(V3Zero);
2123	+	Vector3d JzL(V3Zero);
2124	+	if (time >= info_->getSimParams()->getDt()) {
2125	+	Jz = kineticExchange_ / (time * avgArea)
2126	+	/ PhysicalConstants::energyConvert;
2127	+	JzP = momentumExchange_ / (time * avgArea);
2128	+	JzL = angularMomentumExchange_ / (time * avgArea);
2129	+	}
2130	+
2131	+	rnemdFile_ << "#######################################################\n";
2132	+	rnemdFile_ << "# RNEMD {\n";
2133	+
2134	+	map<string, RNEMDMethod>::iterator mi;
2135	+	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2136	+	if ( (*mi).second == rnemdMethod_)
2137	+	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2138	+	}
2139	+	map<string, RNEMDFluxType>::iterator fi;
2140	+	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2141	+	if ( (*fi).second == rnemdFluxType_)
2142	+	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2143	+	}
2144	+
2145	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2146	+
2147	+	rnemdFile_ << "#    objectSelection = \""
2148	+	<< rnemdObjectSelection_ << "\";\n";
2149	+	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2150	+	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2151	+	rnemdFile_ << "# }\n";
2152	+	rnemdFile_ << "#######################################################\n";
2153	+	rnemdFile_ << "# RNEMD report:\n";
2154	+	rnemdFile_ << "#      running time = " << time << " fs\n";
2155	+	rnemdFile_ << "# Target flux:\n";
2156	+	rnemdFile_ << "#           kinetic = "
2157	+	<< kineticFlux_ / PhysicalConstants::energyConvert
2158	+	<< " (kcal/mol/A^2/fs)\n";
2159	+	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2160	+	<< " (amu/A/fs^2)\n";
2161	+	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2162	+	<< " (amu/A^2/fs^2)\n";
2163	+	rnemdFile_ << "# Target one-time exchanges:\n";
2164	+	rnemdFile_ << "#          kinetic = "
2165	+	<< kineticTarget_ / PhysicalConstants::energyConvert
2166	+	<< " (kcal/mol)\n";
2167	+	rnemdFile_ << "#          momentum = " << momentumTarget_
2168	+	<< " (amu*A/fs)\n";
2169	+	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2170	+	<< " (amu*A^2/fs)\n";
2171	+	rnemdFile_ << "# Actual exchange totals:\n";
2172	+	rnemdFile_ << "#          kinetic = "
2173	+	<< kineticExchange_ / PhysicalConstants::energyConvert
2174	+	<< " (kcal/mol)\n";
2175	+	rnemdFile_ << "#          momentum = " << momentumExchange_
2176	+	<< " (amu*A/fs)\n";
2177	+	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2178	+	<< " (amu*A^2/fs)\n";
2179	+	rnemdFile_ << "# Actual flux:\n";
2180	+	rnemdFile_ << "#          kinetic = " << Jz
2181	+	<< " (kcal/mol/A^2/fs)\n";
2182	+	rnemdFile_ << "#          momentum = " << JzP
2183	+	<< " (amu/A/fs^2)\n";
2184	+	rnemdFile_ << "#  angular momentum = " << JzL
2185	+	<< " (amu/A^2/fs^2)\n";
2186	+	rnemdFile_ << "# Exchange statistics:\n";
2187	+	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2188	+	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2189	+	if (rnemdMethod_ == rnemdNIVS) {
2190	+	rnemdFile_ << "#  NIVS root-check errors = "
2191	+	<< failRootCount_ << "\n";
2192	+	}
2193	+	rnemdFile_ << "#######################################################\n";
2194	+
2195	+
2196	+
2197	+	//write title
2198	+	rnemdFile_ << "#";
2199	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2200	+	if (outputMask_[i]) {
2201	+	rnemdFile_ << "\t" << data_[i].title <<
2202	+	"(" << data_[i].units << ")";
2203	+	// add some extra tabs for column alignment
2204	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2205	+	}
2206	+	}
2207	+	rnemdFile_ << std::endl;
2208	+
2209	+	rnemdFile_.precision(8);
2210	+
2211	+	for (int j = 0; j < nBins_; j++) {
2212	+
2213	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2214	+	if (outputMask_[i]) {
2215	+	if (data_[i].dataType == "RealType")
2216	+	writeReal(i,j);
2217	+	else if (data_[i].dataType == "Vector3d")
2218	+	writeVector(i,j);
2219	+	else {
2220	+	sprintf( painCave.errMsg,
2221	+	"RNEMD found an unknown data type for: %s ",
2222	+	data_[i].title.c_str());
2223	+	painCave.isFatal = 1;
2224	+	simError();
2225	+	}
2226	+	}
2227	+	}
2228	+	rnemdFile_ << std::endl;
2229	+
2230	+	}
2231	+
2232	+	rnemdFile_ << "#######################################################\n";
2233	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2234	+	rnemdFile_ << "#######################################################\n";
2235	+
2236	+
2237	+	for (int j = 0; j < nBins_; j++) {
2238	+	rnemdFile_ << "#";
2239	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2240	+	if (outputMask_[i]) {
2241	+	if (data_[i].dataType == "RealType")
2242	+	writeRealStdDev(i,j);
2243	+	else if (data_[i].dataType == "Vector3d")
2244	+	writeVectorStdDev(i,j);
2245	+	else {
2246	+	sprintf( painCave.errMsg,
2247	+	"RNEMD found an unknown data type for: %s ",
2248	+	data_[i].title.c_str());
2249	+	painCave.isFatal = 1;
2250	+	simError();
2251	+	}
2252	+	}
2253	+	}
2254	+	rnemdFile_ << std::endl;
2255	+
2256	+	}
2257	+
2258	+	rnemdFile_.flush();
2259	+	rnemdFile_.close();
2260	+
2261		#ifdef IS_MPI
2262		}
2263		#endif
2264	+
2265		}
2266	+
2267	+	void RNEMD::writeReal(int index, unsigned int bin) {
2268	+	if (!doRNEMD_) return;
2269	+	assert(index >=0 && index < ENDINDEX);
2270	+	assert(int(bin) < nBins_);
2271	+	RealType s;
2272	+	int count;
2273	+
2274	+	count = data_[index].accumulator[bin]->count();
2275	+	if (count == 0) return;
2276	+
2277	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2278	+
2279	+	if (! isinf(s) && ! isnan(s)) {
2280	+	rnemdFile_ << "\t" << s;
2281	+	} else{
2282	+	sprintf( painCave.errMsg,
2283	+	"RNEMD detected a numerical error writing: %s for bin %u",
2284	+	data_[index].title.c_str(), bin);
2285	+	painCave.isFatal = 1;
2286	+	simError();
2287	+	}
2288	+	}
2289	+
2290	+	void RNEMD::writeVector(int index, unsigned int bin) {
2291	+	if (!doRNEMD_) return;
2292	+	assert(index >=0 && index < ENDINDEX);
2293	+	assert(int(bin) < nBins_);
2294	+	Vector3d s;
2295	+	int count;
2296	+
2297	+	count = data_[index].accumulator[bin]->count();
2298	+
2299	+	if (count == 0) return;
2300	+
2301	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2302	+	if (isinf(s[0]) || isnan(s[0]) ||
2303	+	isinf(s[1]) || isnan(s[1]) ||
2304	+	isinf(s[2]) || isnan(s[2]) ) {
2305	+	sprintf( painCave.errMsg,
2306	+	"RNEMD detected a numerical error writing: %s for bin %u",
2307	+	data_[index].title.c_str(), bin);
2308	+	painCave.isFatal = 1;
2309	+	simError();
2310	+	} else {
2311	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2312	+	}
2313	+	}
2314	+
2315	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2316	+	if (!doRNEMD_) return;
2317	+	assert(index >=0 && index < ENDINDEX);
2318	+	assert(int(bin) < nBins_);
2319	+	RealType s;
2320	+	int count;
2321	+
2322	+	count = data_[index].accumulator[bin]->count();
2323	+	if (count == 0) return;
2324	+
2325	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2326	+
2327	+	if (! isinf(s) && ! isnan(s)) {
2328	+	rnemdFile_ << "\t" << s;
2329	+	} else{
2330	+	sprintf( painCave.errMsg,
2331	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2332	+	data_[index].title.c_str(), bin);
2333	+	painCave.isFatal = 1;
2334	+	simError();
2335	+	}
2336	+	}
2337	+
2338	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2339	+	if (!doRNEMD_) return;
2340	+	assert(index >=0 && index < ENDINDEX);
2341	+	assert(int(bin) < nBins_);
2342	+	Vector3d s;
2343	+	int count;
2344	+
2345	+	count = data_[index].accumulator[bin]->count();
2346	+	if (count == 0) return;
2347	+
2348	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2349	+	if (isinf(s[0]) || isnan(s[0]) ||
2350	+	isinf(s[1]) || isnan(s[1]) ||
2351	+	isinf(s[2]) || isnan(s[2]) ) {
2352	+	sprintf( painCave.errMsg,
2353	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2354	+	data_[index].title.c_str(), bin);
2355	+	painCave.isFatal = 1;
2356	+	simError();
2357	+	} else {
2358	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2359	+	}
2360	+	}
2361		}
2362	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1350 by gezelter, Thu May 21 18:56:45 2009 UTC vs.
trunk/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1946 by gezelter, Tue Nov 12 02:18:35 2013 UTC

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