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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 1874 by gezelter, Wed May 15 15:09:35 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
42	<	#include "integrators/RNEMD.hpp"
42	>	#include <cmath>
43	>	#include <sstream>
44	>	#include <string>
45	>
46	>	#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48	+	#include "math/Vector.hpp"
49		#include "math/SquareMatrix3.hpp"
50	+	#include "math/Polynomial.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "primitives/StuntDouble.hpp"
53	<	#include "utils/OOPSEConstant.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54		#include "utils/Tuple.hpp"
55	+	#include "brains/Thermo.hpp"
56	+	#include "math/ConvexHull.hpp"
57	+	#ifdef IS_MPI
58	+	#include <mpi.h>
59	+	#endif
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	>	} else {
551	>	if (usePeriodicBoundaryConditions_) {
552	>	Mat3x3d hmat = currentSnap_->getHmat();
553	>
554	>	if (hasSlabWidth)
555	>	slabWidth_ = rnemdParams->getSlabWidth();
556	>	else
557	>	slabWidth_ = hmat(2,2) / 10.0;
558	>
559	>	if (hasSlabBCenter)
560	>	slabBCenter_ = rnemdParams->getSlabBCenter();
561	>	else
562	>	slabBCenter_ = hmat(2,2) / 2.0;
563	>
564	>	selectionBstream << "select wrappedz > "
565	>	<< slabBCenter_ - 0.5*slabWidth_
566	>	<<  " && wrappedz < "
567	>	<< slabBCenter_ + 0.5*slabWidth_;
568	>	selectionB_ = selectionBstream.str();
569	>	} else {
570	>	if (hasSphereBRadius_) {
571	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
572	>	selectionBstream << "select r > " << sphereBRadius_;
573	>	selectionB_ = selectionBstream.str();
574	>	} else {
575	>	selectionB_ = "select hull";
576	>	hasSelectionB_ = true;
577	>	}
578	>	}
579	>	}
580	>	}
581	>
582	>	// object evaluator:
583	>	evaluator_.loadScriptString(rnemdObjectSelection_);
584	>	seleMan_.setSelectionSet(evaluator_.evaluate());
585	>	evaluatorA_.loadScriptString(selectionA_);
586	>	evaluatorB_.loadScriptString(selectionB_);
587	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	>	commonA_ = seleManA_ & seleMan_;
590	>	commonB_ = seleManB_ & seleMan_;
591		}
592
593	+
594		RNEMD::~RNEMD() {
595	<	delete randNumGen_;
596	<	}
595	>	if (!doRNEMD_) return;
596	>	#ifdef IS_MPI
597	>	if (worldRank == 0) {
598	>	#endif
599
600	<	void RNEMD::doSwap() {
129	<	int midBin = nBins_ / 2;
600	>	writeOutputFile();
601
602	+	rnemdFile_.close();
603	+
604	+	#ifdef IS_MPI
605	+	}
606	+	#endif
607	+
608	+	// delete all of the objects we created:
609	+	delete areaAccumulator_;
610	+	data_.clear();
611	+	}
612	+
613	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
614	+	if (!doRNEMD_) return;
615	+	int selei;
616	+	int selej;
617	+
618		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
619		Mat3x3d hmat = currentSnap_->getHmat();
620
134	–	seleMan_.setSelectionSet(evaluator_.evaluate());
135	–
136	–	int selei;
621		StuntDouble* sd;
138	–	int idx;
622
623		RealType min_val;
624		bool min_found = false;
#	Line 145 | Line 628 | namespace oopse {
628		bool max_found = false;
629		StuntDouble* max_sd;
630
631	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
632	<	sd = seleMan_.nextSelected(selei)) {
631	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
632	>	sd = seleManA_.nextSelected(selei)) {
633
151	–	idx = sd->getLocalIndex();
152	–
634		Vector3d pos = sd->getPos();
635	<
635	>
636		// wrap the stuntdouble's position back into the box:
637	<
637	>
638		if (usePeriodicBoundaryConditions_)
639		currentSnap_->wrapVector(pos);
640	<
641	<	// which bin is this stuntdouble in?
642	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
643	<
644	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
645	<
646	<
166	<	// if we're in bin 0 or the middleBin
167	<	if (binNo == 0 || binNo == midBin) {
640	>
641	>	RealType mass = sd->getMass();
642	>	Vector3d vel = sd->getVel();
643	>	RealType value;
644	>
645	>	switch(rnemdFluxType_) {
646	>	case rnemdKE :
647
648	<	RealType mass = sd->getMass();
649	<	Vector3d vel = sd->getVel();
650	<	RealType value;
651	<
652	<	switch(rnemdType_) {
174	<	case rnemdKinetic :
648	>	value = mass * vel.lengthSquare();
649	>
650	>	if (sd->isDirectional()) {
651	>	Vector3d angMom = sd->getJ();
652	>	Mat3x3d I = sd->getI();
653
654	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
655	<	vel[2]*vel[2]);
656	<	if (sd->isDirectional()) {
657	<	Vector3d angMom = sd->getJ();
658	<	Mat3x3d I = sd->getI();
659	<
660	<	if (sd->isLinear()) {
661	<	int i = sd->linearAxis();
662	<	int j = (i + 1) % 3;
663	<	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	<	}
654	>	if (sd->isLinear()) {
655	>	int i = sd->linearAxis();
656	>	int j = (i + 1) % 3;
657	>	int k = (i + 2) % 3;
658	>	value += angMom[j] * angMom[j] / I(j, j) +
659	>	angMom[k] * angMom[k] / I(k, k);
660	>	} else {
661	>	value += angMom[0]*angMom[0]/I(0, 0)
662	>	+ angMom[1]*angMom[1]/I(1, 1)
663	>	+ angMom[2]*angMom[2]/I(2, 2);
664		}
665	<	value = value * 0.5 / OOPSEConstant::energyConvert;
666	<	break;
667	<	case rnemdPx :
668	<	value = mass * vel[0];
669	<	break;
670	<	case rnemdPy :
671	<	value = mass * vel[1];
672	<	break;
673	<	case rnemdPz :
674	<	value = mass * vel[2];
675	<	break;
676	<	case rnemdUnknown :
677	<	default :
678	<	break;
665	>	} //angular momenta exchange enabled
666	>	value *= 0.5;
667	>	break;
668	>	case rnemdPx :
669	>	value = mass * vel[0];
670	>	break;
671	>	case rnemdPy :
672	>	value = mass * vel[1];
673	>	break;
674	>	case rnemdPz :
675	>	value = mass * vel[2];
676	>	break;
677	>	default :
678	>	break;
679	>	}
680	>	if (!max_found) {
681	>	max_val = value;
682	>	max_sd = sd;
683	>	max_found = true;
684	>	} else {
685	>	if (max_val < value) {
686	>	max_val = value;
687	>	max_sd = sd;
688		}
689	+	}
690	+	}
691
692	<	if (binNo == 0) {
693	<	if (!min_found) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	min_found = true;
697	<	} else {
698	<	if (min_val > value) {
699	<	min_val = value;
700	<	min_sd = sd;
701	<	}
702	<	}
703	<	} else {
704	<	if (!max_found) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	max_found = true;
708	<	} else {
709	<	if (max_val < value) {
710	<	max_val = value;
711	<	max_sd = sd;
712	<	}
713	<	}
714	<	}
692	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
693	>	sd = seleManB_.nextSelected(selej)) {
694	>
695	>	Vector3d pos = sd->getPos();
696	>
697	>	// wrap the stuntdouble's position back into the box:
698	>
699	>	if (usePeriodicBoundaryConditions_)
700	>	currentSnap_->wrapVector(pos);
701	>
702	>	RealType mass = sd->getMass();
703	>	Vector3d vel = sd->getVel();
704	>	RealType value;
705	>
706	>	switch(rnemdFluxType_) {
707	>	case rnemdKE :
708	>
709	>	value = mass * vel.lengthSquare();
710	>
711	>	if (sd->isDirectional()) {
712	>	Vector3d angMom = sd->getJ();
713	>	Mat3x3d I = sd->getI();
714	>
715	>	if (sd->isLinear()) {
716	>	int i = sd->linearAxis();
717	>	int j = (i + 1) % 3;
718	>	int k = (i + 2) % 3;
719	>	value += angMom[j] * angMom[j] / I(j, j) +
720	>	angMom[k] * angMom[k] / I(k, k);
721	>	} else {
722	>	value += angMom[0]*angMom[0]/I(0, 0)
723	>	+ angMom[1]*angMom[1]/I(1, 1)
724	>	+ angMom[2]*angMom[2]/I(2, 2);
725	>	}
726	>	} //angular momenta exchange enabled
727	>	value *= 0.5;
728	>	break;
729	>	case rnemdPx :
730	>	value = mass * vel[0];
731	>	break;
732	>	case rnemdPy :
733	>	value = mass * vel[1];
734	>	break;
735	>	case rnemdPz :
736	>	value = mass * vel[2];
737	>	break;
738	>	default :
739	>	break;
740		}
741	+
742	+	if (!min_found) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	min_found = true;
746	+	} else {
747	+	if (min_val > value) {
748	+	min_val = value;
749	+	min_sd = sd;
750	+	}
751	+	}
752		}
753	<
754	<	#ifdef IS_MPI
755	<	int nProc, worldRank;
756	<
239	<	nProc = MPI::COMM_WORLD.Get_size();
240	<	worldRank = MPI::COMM_WORLD.Get_rank();
241	<
753	>
754	>	#ifdef IS_MPI
755	>	int worldRank = MPI::COMM_WORLD.Get_rank();
756	>
757		bool my_min_found = min_found;
758		bool my_max_found = max_found;
759
760		// Even if we didn't find a minimum, did someone else?
761	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247	<	1, MPI::BOOL, MPI::LAND);
248	<
761	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
762		// Even if we didn't find a maximum, did someone else?
763	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
764	<	1, MPI::BOOL, MPI::LAND);
765	<
766	<	struct {
767	<	RealType val;
768	<	int rank;
769	<	} max_vals, min_vals;
770	<
771	<	if (min_found) {
772	<	if (my_min_found)
763	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
764	>	#endif
765	>
766	>	if (max_found && min_found) {
767	>
768	>	#ifdef IS_MPI
769	>	struct {
770	>	RealType val;
771	>	int rank;
772	>	} max_vals, min_vals;
773	>
774	>	if (my_min_found) {
775		min_vals.val = min_val;
776	<	else
776	>	} else {
777		min_vals.val = HONKING_LARGE_VALUE;
778	<
778	>	}
779		min_vals.rank = worldRank;
780
781		// Who had the minimum?
782		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
783		1, MPI::REALTYPE_INT, MPI::MINLOC);
784		min_val = min_vals.val;
270	–	}
785
786	<	if (max_found) {
273	<	if (my_max_found)
786	>	if (my_max_found) {
787		max_vals.val = max_val;
788	<	else
788	>	} else {
789		max_vals.val = -HONKING_LARGE_VALUE;
790	<
790	>	}
791		max_vals.rank = worldRank;
792
793		// Who had the maximum?
794		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
795		1, MPI::REALTYPE_INT, MPI::MAXLOC);
796		max_val = max_vals.val;
284	–	}
797		#endif
798	<
799	<	if (max_found && min_found) {
800	<	if (min_val< max_val) {
289	<
798	>
799	>	if (min_val < max_val) {
800	>
801		#ifdef IS_MPI
802		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
803		// I have both maximum and minimum, so proceed like a single
804		// processor version:
805		#endif
806	<	// objects to be swapped: velocity & angular velocity
806	>
807		Vector3d min_vel = min_sd->getVel();
808		Vector3d max_vel = max_sd->getVel();
809		RealType temp_vel;
810
811	<	switch(rnemdType_) {
812	<	case rnemdKinetic :
811	>	switch(rnemdFluxType_) {
812	>	case rnemdKE :
813		min_sd->setVel(max_vel);
814		max_sd->setVel(min_vel);
815	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
815	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
816		Vector3d min_angMom = min_sd->getJ();
817		Vector3d max_angMom = max_sd->getJ();
818		min_sd->setJ(max_angMom);
819		max_sd->setJ(min_angMom);
820	<	}
820	>	}//angular momenta exchange enabled
821	>	//assumes same rigid body identity
822		break;
823		case rnemdPx :
824		temp_vel = min_vel.x();
#	Line 329 | Line 841 | namespace oopse {
841		min_sd->setVel(min_vel);
842		max_sd->setVel(max_vel);
843		break;
332	–	case rnemdUnknown :
844		default :
845		break;
846		}
847	+
848		#ifdef IS_MPI
849		// the rest of the cases only apply in parallel simulations:
850		} else if (max_vals.rank == worldRank) {
#	Line 348 | Line 860 | namespace oopse {
860		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
861		min_vals.rank, 0, status);
862
863	<	switch(rnemdType_) {
864	<	case rnemdKinetic :
863	>	switch(rnemdFluxType_) {
864	>	case rnemdKE :
865		max_sd->setVel(min_vel);
866	<
866	>	//angular momenta exchange enabled
867		if (max_sd->isDirectional()) {
868		Vector3d min_angMom;
869		Vector3d max_angMom = max_sd->getJ();
870	<
870	>
871		// point-to-point swap of the angular momentum vector
872		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
873		MPI::REALTYPE, min_vals.rank, 1,
874		min_angMom.getArrayPointer(), 3,
875		MPI::REALTYPE, min_vals.rank, 1,
876		status);
877	<
877	>
878		max_sd->setJ(min_angMom);
879	<	}
879	>	}
880		break;
881		case rnemdPx :
882		max_vel.x() = min_vel.x();
#	Line 378 | Line 890 | namespace oopse {
890		max_vel.z() = min_vel.z();
891		max_sd->setVel(max_vel);
892		break;
381	–	case rnemdUnknown :
893		default :
894		break;
895		}
#	Line 395 | Line 906 | namespace oopse {
906		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
907		max_vals.rank, 0, status);
908
909	<	switch(rnemdType_) {
910	<	case rnemdKinetic :
909	>	switch(rnemdFluxType_) {
910	>	case rnemdKE :
911		min_sd->setVel(max_vel);
912	<
912	>	//angular momenta exchange enabled
913		if (min_sd->isDirectional()) {
914		Vector3d min_angMom = min_sd->getJ();
915		Vector3d max_angMom;
916	<
916	>
917		// point-to-point swap of the angular momentum vector
918		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
919		MPI::REALTYPE, max_vals.rank, 1,
920		max_angMom.getArrayPointer(), 3,
921		MPI::REALTYPE, max_vals.rank, 1,
922		status);
923	<
923	>
924		min_sd->setJ(max_angMom);
925		}
926		break;
#	Line 425 | Line 936 | namespace oopse {
936		min_vel.z() = max_vel.z();
937		min_sd->setVel(min_vel);
938		break;
428	–	case rnemdUnknown :
939		default :
940		break;
941		}
942		}
943		#endif
944	<	exchangeSum_ += max_val - min_val;
945	<	} else {
946	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
944	>
945	>	switch(rnemdFluxType_) {
946	>	case rnemdKE:
947	>	kineticExchange_ += max_val - min_val;
948	>	break;
949	>	case rnemdPx:
950	>	momentumExchange_.x() += max_val - min_val;
951	>	break;
952	>	case rnemdPy:
953	>	momentumExchange_.y() += max_val - min_val;
954	>	break;
955	>	case rnemdPz:
956	>	momentumExchange_.z() += max_val - min_val;
957	>	break;
958	>	default:
959	>	break;
960	>	}
961	>	} else {
962	>	sprintf(painCave.errMsg,
963	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
964	>	painCave.isFatal = 0;
965	>	painCave.severity = OPENMD_INFO;
966	>	simError();
967	>	failTrialCount_++;
968		}
969		} else {
970	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
971	<	}
972	<
970	>	sprintf(painCave.errMsg,
971	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
972	>	"\twas not present in at least one of the two slabs.\n");
973	>	painCave.isFatal = 0;
974	>	painCave.severity = OPENMD_INFO;
975	>	simError();
976	>	failTrialCount_++;
977	>	}
978		}
979
980	<	void RNEMD::getStatus() {
980	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
981	>	if (!doRNEMD_) return;
982	>	int selei;
983	>	int selej;
984
985		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
986	+	RealType time = currentSnap_->getTime();
987		Mat3x3d hmat = currentSnap_->getHmat();
448	–	Stats& stat = currentSnap_->statData;
449	–	RealType time = currentSnap_->getTime();
988
989	<	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
989	>	StuntDouble* sd;
990
991	<	seleMan_.setSelectionSet(evaluator_.evaluate());
991	>	vector<StuntDouble*> hotBin, coldBin;
992
993	<	int selei;
994	<	StuntDouble* sd;
995	<	int idx;
993	>	RealType Phx = 0.0;
994	>	RealType Phy = 0.0;
995	>	RealType Phz = 0.0;
996	>	RealType Khx = 0.0;
997	>	RealType Khy = 0.0;
998	>	RealType Khz = 0.0;
999	>	RealType Khw = 0.0;
1000	>	RealType Pcx = 0.0;
1001	>	RealType Pcy = 0.0;
1002	>	RealType Pcz = 0.0;
1003	>	RealType Kcx = 0.0;
1004	>	RealType Kcy = 0.0;
1005	>	RealType Kcz = 0.0;
1006	>	RealType Kcw = 0.0;
1007
1008	<	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
1009	<	// being averaged
461	<	std::vector<int> valueCount(nBins_, 0);       // keeps track of the
462	<	// number of degrees of
463	<	// freedom being averaged
1008	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1009	>	sd = smanA.nextSelected(selei)) {
1010
465	–	for (sd = seleMan_.beginSelected(selei); sd != NULL;
466	–	sd = seleMan_.nextSelected(selei)) {
467	–
468	–	idx = sd->getLocalIndex();
469	–
1011		Vector3d pos = sd->getPos();
1012	<
1012	>
1013		// wrap the stuntdouble's position back into the box:
1014
1015		if (usePeriodicBoundaryConditions_)
1016		currentSnap_->wrapVector(pos);
1017
477	–	// which bin is this stuntdouble in?
478	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1018
480	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
481	–
1019		RealType mass = sd->getMass();
1020		Vector3d vel = sd->getVel();
1021	<	RealType value;
1022	<
1023	<	switch(rnemdType_) {
1024	<	case rnemdKinetic :
1025	<
1026	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1027	<	vel[2]*vel[2]);
1028	<
1029	<	valueCount[binNo] += 3;
1030	<	if (sd->isDirectional()) {
1031	<	Vector3d angMom = sd->getJ();
1032	<	Mat3x3d I = sd->getI();
1033	<
1034	<	if (sd->isLinear()) {
1035	<	int i = sd->linearAxis();
1036	<	int j = (i + 1) % 3;
1037	<	int k = (i + 2) % 3;
1038	<	value += angMom[j] * angMom[j] / I(j, j) +
1039	<	angMom[k] * angMom[k] / I(k, k);
1040	<
1041	<	valueCount[binNo] +=2;
1042	<
1043	<	} else {
1044	<	value += angMom[0]*angMom[0]/I(0, 0)
1045	<	+ angMom[1]*angMom[1]/I(1, 1)
1046	<	+ angMom[2]*angMom[2]/I(2, 2);
1047	<	valueCount[binNo] +=3;
1048	<	}
1049	<	}
1050	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
1021	>
1022	>	hotBin.push_back(sd);
1023	>	Phx += mass * vel.x();
1024	>	Phy += mass * vel.y();
1025	>	Phz += mass * vel.z();
1026	>	Khx += mass * vel.x() * vel.x();
1027	>	Khy += mass * vel.y() * vel.y();
1028	>	Khz += mass * vel.z() * vel.z();
1029	>	if (sd->isDirectional()) {
1030	>	Vector3d angMom = sd->getJ();
1031	>	Mat3x3d I = sd->getI();
1032	>	if (sd->isLinear()) {
1033	>	int i = sd->linearAxis();
1034	>	int j = (i + 1) % 3;
1035	>	int k = (i + 2) % 3;
1036	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1037	>	angMom[k] * angMom[k] / I(k, k);
1038	>	} else {
1039	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1040	>	+ angMom[1]*angMom[1]/I(1, 1)
1041	>	+ angMom[2]*angMom[2]/I(2, 2);
1042	>	}
1043	>	}
1044	>	}
1045	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1046	>	sd = smanB.nextSelected(selej)) {
1047	>	Vector3d pos = sd->getPos();
1048	>
1049	>	// wrap the stuntdouble's position back into the box:
1050	>
1051	>	if (usePeriodicBoundaryConditions_)
1052	>	currentSnap_->wrapVector(pos);
1053	>
1054	>	RealType mass = sd->getMass();
1055	>	Vector3d vel = sd->getVel();
1056
1057	+	coldBin.push_back(sd);
1058	+	Pcx += mass * vel.x();
1059	+	Pcy += mass * vel.y();
1060	+	Pcz += mass * vel.z();
1061	+	Kcx += mass * vel.x() * vel.x();
1062	+	Kcy += mass * vel.y() * vel.y();
1063	+	Kcz += mass * vel.z() * vel.z();
1064	+	if (sd->isDirectional()) {
1065	+	Vector3d angMom = sd->getJ();
1066	+	Mat3x3d I = sd->getI();
1067	+	if (sd->isLinear()) {
1068	+	int i = sd->linearAxis();
1069	+	int j = (i + 1) % 3;
1070	+	int k = (i + 2) % 3;
1071	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
1072	+	angMom[k] * angMom[k] / I(k, k);
1073	+	} else {
1074	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
1075	+	+ angMom[1]*angMom[1]/I(1, 1)
1076	+	+ angMom[2]*angMom[2]/I(2, 2);
1077	+	}
1078	+	}
1079	+	}
1080	+
1081	+	Khx *= 0.5;
1082	+	Khy *= 0.5;
1083	+	Khz *= 0.5;
1084	+	Khw *= 0.5;
1085	+	Kcx *= 0.5;
1086	+	Kcy *= 0.5;
1087	+	Kcz *= 0.5;
1088	+	Kcw *= 0.5;
1089	+
1090	+	#ifdef IS_MPI
1091	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1092	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1093	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1094	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1095	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1096	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1097	+
1098	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1099	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1100	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1101	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1102	+
1103	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1104	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1105	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1106	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1107	+	#endif
1108	+
1109	+	//solve coldBin coeff's first
1110	+	RealType px = Pcx / Phx;
1111	+	RealType py = Pcy / Phy;
1112	+	RealType pz = Pcz / Phz;
1113	+	RealType c, x, y, z;
1114	+	bool successfulScale = false;
1115	+	if ((rnemdFluxType_ == rnemdFullKE) ||
1116	+	(rnemdFluxType_ == rnemdRotKE)) {
1117	+	//may need sanity check Khw & Kcw > 0
1118	+
1119	+	if (rnemdFluxType_ == rnemdFullKE) {
1120	+	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1121	+	} else {
1122	+	c = 1.0 - kineticTarget_ / Kcw;
1123	+	}
1124	+
1125	+	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1126	+	c = sqrt(c);
1127	+
1128	+	RealType w = 0.0;
1129	+	if (rnemdFluxType_ ==  rnemdFullKE) {
1130	+	x = 1.0 + px * (1.0 - c);
1131	+	y = 1.0 + py * (1.0 - c);
1132	+	z = 1.0 + pz * (1.0 - c);
1133	+	/* more complicated way
1134	+	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1135	+	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1136	+	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1137	+	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1138	+	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1139	+	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1140	+	*/
1141	+	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1142	+	(fabs(z - 1.0) < 0.1)) {
1143	+	w = 1.0 + (kineticTarget_
1144	+	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1145	+	+ Khz * (1.0 - z * z)) / Khw;
1146	+	}//no need to calculate w if x, y or z is out of range
1147	+	} else {
1148	+	w = 1.0 + kineticTarget_ / Khw;
1149	+	}
1150	+	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1151	+	//if w is in the right range, so should be x, y, z.
1152	+	vector<StuntDouble*>::iterator sdi;
1153	+	Vector3d vel;
1154	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1155	+	if (rnemdFluxType_ == rnemdFullKE) {
1156	+	vel = (*sdi)->getVel() * c;
1157	+	(*sdi)->setVel(vel);
1158	+	}
1159	+	if ((*sdi)->isDirectional()) {
1160	+	Vector3d angMom = (*sdi)->getJ() * c;
1161	+	(*sdi)->setJ(angMom);
1162	+	}
1163	+	}
1164	+	w = sqrt(w);
1165	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1166	+	if (rnemdFluxType_ == rnemdFullKE) {
1167	+	vel = (*sdi)->getVel();
1168	+	vel.x() *= x;
1169	+	vel.y() *= y;
1170	+	vel.z() *= z;
1171	+	(*sdi)->setVel(vel);
1172	+	}
1173	+	if ((*sdi)->isDirectional()) {
1174	+	Vector3d angMom = (*sdi)->getJ() * w;
1175	+	(*sdi)->setJ(angMom);
1176	+	}
1177	+	}
1178	+	successfulScale = true;
1179	+	kineticExchange_ += kineticTarget_;
1180	+	}
1181	+	}
1182	+	} else {
1183	+	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1184	+	switch(rnemdFluxType_) {
1185	+	case rnemdKE :
1186	+	/* used hotBin coeff's & only scale x & y dimensions
1187	+	RealType px = Phx / Pcx;
1188	+	RealType py = Phy / Pcy;
1189	+	a110 = Khy;
1190	+	c0 = - Khx - Khy - kineticTarget_;
1191	+	a000 = Khx;
1192	+	a111 = Kcy * py * py;
1193	+	b11 = -2.0 * Kcy * py * (1.0 + py);
1194	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1195	+	b01 = -2.0 * Kcx * px * (1.0 + px);
1196	+	a001 = Kcx * px * px;
1197	+	*/
1198	+	//scale all three dimensions, let c_x = c_y
1199	+	a000 = Kcx + Kcy;
1200	+	a110 = Kcz;
1201	+	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1202	+	a001 = Khx * px * px + Khy * py * py;
1203	+	a111 = Khz * pz * pz;
1204	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1205	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
1206	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1207	+	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1208		break;
1209		case rnemdPx :
1210	<	value = mass * vel[0];
1211	<	valueCount[binNo]++;
1210	>	c = 1 - momentumTarget_.x() / Pcx;
1211	>	a000 = Kcy;
1212	>	a110 = Kcz;
1213	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1214	>	a001 = py * py * Khy;
1215	>	a111 = pz * pz * Khz;
1216	>	b01 = -2.0 * Khy * py * (1.0 + py);
1217	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1218	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1219	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1220		break;
1221		case rnemdPy :
1222	<	value = mass * vel[1];
1223	<	valueCount[binNo]++;
1222	>	c = 1 - momentumTarget_.y() / Pcy;
1223	>	a000 = Kcx;
1224	>	a110 = Kcz;
1225	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1226	>	a001 = px * px * Khx;
1227	>	a111 = pz * pz * Khz;
1228	>	b01 = -2.0 * Khx * px * (1.0 + px);
1229	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1230	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1231	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1232		break;
1233	<	case rnemdPz :
1234	<	value = mass * vel[2];
1235	<	valueCount[binNo]++;
1233	>	case rnemdPz ://we don't really do this, do we?
1234	>	c = 1 - momentumTarget_.z() / Pcz;
1235	>	a000 = Kcx;
1236	>	a110 = Kcy;
1237	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1238	>	a001 = px * px * Khx;
1239	>	a111 = py * py * Khy;
1240	>	b01 = -2.0 * Khx * px * (1.0 + px);
1241	>	b11 = -2.0 * Khy * py * (1.0 + py);
1242	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1243	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1244		break;
528	–	case rnemdUnknown :
1245		default :
1246		break;
1247		}
1248	<	valueHist[binNo] += value;
1248	>
1249	>	RealType v1 = a000 * a111 - a001 * a110;
1250	>	RealType v2 = a000 * b01;
1251	>	RealType v3 = a000 * b11;
1252	>	RealType v4 = a000 * c1 - a001 * c0;
1253	>	RealType v8 = a110 * b01;
1254	>	RealType v10 = - b01 * c0;
1255	>
1256	>	RealType u0 = v2 * v10 - v4 * v4;
1257	>	RealType u1 = -2.0 * v3 * v4;
1258	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1259	>	RealType u3 = -2.0 * v1 * v3;
1260	>	RealType u4 = - v1 * v1;
1261	>	//rescale coefficients
1262	>	RealType maxAbs = fabs(u0);
1263	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1264	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1265	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1266	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1267	>	u0 /= maxAbs;
1268	>	u1 /= maxAbs;
1269	>	u2 /= maxAbs;
1270	>	u3 /= maxAbs;
1271	>	u4 /= maxAbs;
1272	>	//max_element(start, end) is also available.
1273	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1274	>	poly.setCoefficient(4, u4);
1275	>	poly.setCoefficient(3, u3);
1276	>	poly.setCoefficient(2, u2);
1277	>	poly.setCoefficient(1, u1);
1278	>	poly.setCoefficient(0, u0);
1279	>	vector<RealType> realRoots = poly.FindRealRoots();
1280	>
1281	>	vector<RealType>::iterator ri;
1282	>	RealType r1, r2, alpha0;
1283	>	vector<pair<RealType,RealType> > rps;
1284	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1285	>	r2 = *ri;
1286	>	//check if FindRealRoots() give the right answer
1287	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1288	>	sprintf(painCave.errMsg,
1289	>	"RNEMD Warning: polynomial solve seems to have an error!");
1290	>	painCave.isFatal = 0;
1291	>	simError();
1292	>	failRootCount_++;
1293	>	}
1294	>	//might not be useful w/o rescaling coefficients
1295	>	alpha0 = -c0 - a110 * r2 * r2;
1296	>	if (alpha0 >= 0.0) {
1297	>	r1 = sqrt(alpha0 / a000);
1298	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1299	>	< 1e-6)
1300	>	{ rps.push_back(make_pair(r1, r2)); }
1301	>	if (r1 > 1e-6) { //r1 non-negative
1302	>	r1 = -r1;
1303	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1304	>	< 1e-6)
1305	>	{ rps.push_back(make_pair(r1, r2)); }
1306	>	}
1307	>	}
1308	>	}
1309	>	// Consider combining together the solving pair part w/ the searching
1310	>	// best solution part so that we don't need the pairs vector
1311	>	if (!rps.empty()) {
1312	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1313	>	RealType diff;
1314	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1315	>	vector<pair<RealType,RealType> >::iterator rpi;
1316	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1317	>	r1 = (*rpi).first;
1318	>	r2 = (*rpi).second;
1319	>	switch(rnemdFluxType_) {
1320	>	case rnemdKE :
1321	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1323	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1324	>	break;
1325	>	case rnemdPx :
1326	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1327	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1328	>	break;
1329	>	case rnemdPy :
1330	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1331	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1332	>	break;
1333	>	case rnemdPz :
1334	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1335	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1336	>	default :
1337	>	break;
1338	>	}
1339	>	if (diff < smallestDiff) {
1340	>	smallestDiff = diff;
1341	>	bestPair = *rpi;
1342	>	}
1343	>	}
1344	>	#ifdef IS_MPI
1345	>	if (worldRank == 0) {
1346	>	#endif
1347	>	// sprintf(painCave.errMsg,
1348	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1349	>	//         bestPair.first, bestPair.second);
1350	>	// painCave.isFatal = 0;
1351	>	// painCave.severity = OPENMD_INFO;
1352	>	// simError();
1353	>	#ifdef IS_MPI
1354	>	}
1355	>	#endif
1356	>
1357	>	switch(rnemdFluxType_) {
1358	>	case rnemdKE :
1359	>	x = bestPair.first;
1360	>	y = bestPair.first;
1361	>	z = bestPair.second;
1362	>	break;
1363	>	case rnemdPx :
1364	>	x = c;
1365	>	y = bestPair.first;
1366	>	z = bestPair.second;
1367	>	break;
1368	>	case rnemdPy :
1369	>	x = bestPair.first;
1370	>	y = c;
1371	>	z = bestPair.second;
1372	>	break;
1373	>	case rnemdPz :
1374	>	x = bestPair.first;
1375	>	y = bestPair.second;
1376	>	z = c;
1377	>	break;
1378	>	default :
1379	>	break;
1380	>	}
1381	>	vector<StuntDouble*>::iterator sdi;
1382	>	Vector3d vel;
1383	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1384	>	vel = (*sdi)->getVel();
1385	>	vel.x() *= x;
1386	>	vel.y() *= y;
1387	>	vel.z() *= z;
1388	>	(*sdi)->setVel(vel);
1389	>	}
1390	>	//convert to hotBin coefficient
1391	>	x = 1.0 + px * (1.0 - x);
1392	>	y = 1.0 + py * (1.0 - y);
1393	>	z = 1.0 + pz * (1.0 - z);
1394	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1395	>	vel = (*sdi)->getVel();
1396	>	vel.x() *= x;
1397	>	vel.y() *= y;
1398	>	vel.z() *= z;
1399	>	(*sdi)->setVel(vel);
1400	>	}
1401	>	successfulScale = true;
1402	>	switch(rnemdFluxType_) {
1403	>	case rnemdKE :
1404	>	kineticExchange_ += kineticTarget_;
1405	>	break;
1406	>	case rnemdPx :
1407	>	case rnemdPy :
1408	>	case rnemdPz :
1409	>	momentumExchange_ += momentumTarget_;
1410	>	break;
1411	>	default :
1412	>	break;
1413	>	}
1414	>	}
1415		}
1416	+	if (successfulScale != true) {
1417	+	sprintf(painCave.errMsg,
1418	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1419	+	"\tthe constraint equations may not exist or there may be\n"
1420	+	"\tno selected objects in one or both slabs.\n");
1421	+	painCave.isFatal = 0;
1422	+	painCave.severity = OPENMD_INFO;
1423	+	simError();
1424	+	failTrialCount_++;
1425	+	}
1426	+	}
1427	+
1428	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1429	+	if (!doRNEMD_) return;
1430	+	int selei;
1431	+	int selej;
1432
1433	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1434	+	RealType time = currentSnap_->getTime();
1435	+	Mat3x3d hmat = currentSnap_->getHmat();
1436	+
1437	+	StuntDouble* sd;
1438	+
1439	+	vector<StuntDouble*> hotBin, coldBin;
1440	+
1441	+	Vector3d Ph(V3Zero);
1442	+	Vector3d Lh(V3Zero);
1443	+	RealType Mh = 0.0;
1444	+	Mat3x3d Ih(0.0);
1445	+	RealType Kh = 0.0;
1446	+	Vector3d Pc(V3Zero);
1447	+	Vector3d Lc(V3Zero);
1448	+	RealType Mc = 0.0;
1449	+	Mat3x3d Ic(0.0);
1450	+	RealType Kc = 0.0;
1451	+
1452	+	// Constraints can be on only the linear or angular momentum, but
1453	+	// not both.  Usually, the user will specify which they want, but
1454	+	// in case they don't, the use of periodic boundaries should make
1455	+	// the choice for us.
1456	+	bool doLinearPart = false;
1457	+	bool doAngularPart = false;
1458	+
1459	+	switch (rnemdFluxType_) {
1460	+	case rnemdPx:
1461	+	case rnemdPy:
1462	+	case rnemdPz:
1463	+	case rnemdPvector:
1464	+	case rnemdKePx:
1465	+	case rnemdKePy:
1466	+	case rnemdKePvector:
1467	+	doLinearPart = true;
1468	+	break;
1469	+	case rnemdLx:
1470	+	case rnemdLy:
1471	+	case rnemdLz:
1472	+	case rnemdLvector:
1473	+	case rnemdKeLx:
1474	+	case rnemdKeLy:
1475	+	case rnemdKeLz:
1476	+	case rnemdKeLvector:
1477	+	doAngularPart = true;
1478	+	break;
1479	+	case rnemdKE:
1480	+	case rnemdRotKE:
1481	+	case rnemdFullKE:
1482	+	default:
1483	+	if (usePeriodicBoundaryConditions_)
1484	+	doLinearPart = true;
1485	+	else
1486	+	doAngularPart = true;
1487	+	break;
1488	+	}
1489	+
1490	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1491	+	sd = smanA.nextSelected(selei)) {
1492	+
1493	+	Vector3d pos = sd->getPos();
1494	+
1495	+	// wrap the stuntdouble's position back into the box:
1496	+
1497	+	if (usePeriodicBoundaryConditions_)
1498	+	currentSnap_->wrapVector(pos);
1499	+
1500	+	RealType mass = sd->getMass();
1501	+	Vector3d vel = sd->getVel();
1502	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1503	+	RealType r2;
1504	+
1505	+	hotBin.push_back(sd);
1506	+	Ph += mass * vel;
1507	+	Mh += mass;
1508	+	Kh += mass * vel.lengthSquare();
1509	+	Lh += mass * cross(rPos, vel);
1510	+	Ih -= outProduct(rPos, rPos) * mass;
1511	+	r2 = rPos.lengthSquare();
1512	+	Ih(0, 0) += mass * r2;
1513	+	Ih(1, 1) += mass * r2;
1514	+	Ih(2, 2) += mass * r2;
1515	+
1516	+	if (rnemdFluxType_ == rnemdFullKE) {
1517	+	if (sd->isDirectional()) {
1518	+	Vector3d angMom = sd->getJ();
1519	+	Mat3x3d I = sd->getI();
1520	+	if (sd->isLinear()) {
1521	+	int i = sd->linearAxis();
1522	+	int j = (i + 1) % 3;
1523	+	int k = (i + 2) % 3;
1524	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1525	+	angMom[k] * angMom[k] / I(k, k);
1526	+	} else {
1527	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1528	+	angMom[1] * angMom[1] / I(1, 1) +
1529	+	angMom[2] * angMom[2] / I(2, 2);
1530	+	}
1531	+	}
1532	+	}
1533	+	}
1534	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1535	+	sd = smanB.nextSelected(selej)) {
1536	+
1537	+	Vector3d pos = sd->getPos();
1538	+
1539	+	// wrap the stuntdouble's position back into the box:
1540	+
1541	+	if (usePeriodicBoundaryConditions_)
1542	+	currentSnap_->wrapVector(pos);
1543	+
1544	+	RealType mass = sd->getMass();
1545	+	Vector3d vel = sd->getVel();
1546	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1547	+	RealType r2;
1548	+
1549	+	coldBin.push_back(sd);
1550	+	Pc += mass * vel;
1551	+	Mc += mass;
1552	+	Kc += mass * vel.lengthSquare();
1553	+	Lc += mass * cross(rPos, vel);
1554	+	Ic -= outProduct(rPos, rPos) * mass;
1555	+	r2 = rPos.lengthSquare();
1556	+	Ic(0, 0) += mass * r2;
1557	+	Ic(1, 1) += mass * r2;
1558	+	Ic(2, 2) += mass * r2;
1559	+
1560	+	if (rnemdFluxType_ == rnemdFullKE) {
1561	+	if (sd->isDirectional()) {
1562	+	Vector3d angMom = sd->getJ();
1563	+	Mat3x3d I = sd->getI();
1564	+	if (sd->isLinear()) {
1565	+	int i = sd->linearAxis();
1566	+	int j = (i + 1) % 3;
1567	+	int k = (i + 2) % 3;
1568	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1569	+	angMom[k] * angMom[k] / I(k, k);
1570	+	} else {
1571	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1572	+	angMom[1] * angMom[1] / I(1, 1) +
1573	+	angMom[2] * angMom[2] / I(2, 2);
1574	+	}
1575	+	}
1576	+	}
1577	+	}
1578	+
1579	+	Kh *= 0.5;
1580	+	Kc *= 0.5;
1581	+
1582		#ifdef IS_MPI
1583	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1584	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1585	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1587	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1589	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1590	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1591	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1592	+	MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595	+	#endif
1596	+
1597
1598	<	// all processors have the same number of bins, and STL vectors pack their
1599	<	// arrays, so in theory, this should be safe:
1598	>	Vector3d ac, acrec, bc, bcrec;
1599	>	Vector3d ah, ahrec, bh, bhrec;
1600	>	RealType cNumerator, cDenominator;
1601	>	RealType hNumerator, hDenominator;
1602
540	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
541	–	nBins_, MPI::REALTYPE, MPI::SUM);
542	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
543	–	nBins_, MPI::INT, MPI::SUM);
1603
1604	+	bool successfulExchange = false;
1605	+	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1606	+	Vector3d vc = Pc / Mc;
1607	+	ac = -momentumTarget_ / Mc + vc;
1608	+	acrec = -momentumTarget_ / Mc;
1609	+
1610	+	// We now need the inverse of the inertia tensor to calculate the
1611	+	// angular velocity of the cold slab;
1612	+	Mat3x3d Ici = Ic.inverse();
1613	+	Vector3d omegac = Ici * Lc;
1614	+	bc  = -(Ici * angularMomentumTarget_) + omegac;
1615	+	bcrec = bc - omegac;
1616	+
1617	+	cNumerator = Kc - kineticTarget_;
1618	+	if (doLinearPart)
1619	+	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1620	+
1621	+	if (doAngularPart)
1622	+	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1623	+
1624	+	if (cNumerator > 0.0) {
1625	+
1626	+	cDenominator = Kc;
1627	+
1628	+	if (doLinearPart)
1629	+	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1630	+
1631	+	if (doAngularPart)
1632	+	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1633	+
1634	+	if (cDenominator > 0.0) {
1635	+	RealType c = sqrt(cNumerator / cDenominator);
1636	+	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1637	+
1638	+	Vector3d vh = Ph / Mh;
1639	+	ah = momentumTarget_ / Mh + vh;
1640	+	ahrec = momentumTarget_ / Mh;
1641	+
1642	+	// We now need the inverse of the inertia tensor to
1643	+	// calculate the angular velocity of the hot slab;
1644	+	Mat3x3d Ihi = Ih.inverse();
1645	+	Vector3d omegah = Ihi * Lh;
1646	+	bh  = (Ihi * angularMomentumTarget_) + omegah;
1647	+	bhrec = bh - omegah;
1648	+
1649	+	hNumerator = Kh + kineticTarget_;
1650	+	if (doLinearPart)
1651	+	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1652	+
1653	+	if (doAngularPart)
1654	+	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1655	+
1656	+	if (hNumerator > 0.0) {
1657	+
1658	+	hDenominator = Kh;
1659	+	if (doLinearPart)
1660	+	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1661	+	if (doAngularPart)
1662	+	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1663	+
1664	+	if (hDenominator > 0.0) {
1665	+	RealType h = sqrt(hNumerator / hDenominator);
1666	+	if ((h > 0.9) && (h < 1.1)) {
1667	+
1668	+	vector<StuntDouble*>::iterator sdi;
1669	+	Vector3d vel;
1670	+	Vector3d rPos;
1671	+
1672	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1673	+	//vel = (*sdi)->getVel();
1674	+	rPos = (*sdi)->getPos() - coordinateOrigin_;
1675	+	if (doLinearPart)
1676	+	vel = ((*sdi)->getVel() - vc) * c + ac;
1677	+	if (doAngularPart)
1678	+	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1679	+
1680	+	(*sdi)->setVel(vel);
1681	+	if (rnemdFluxType_ == rnemdFullKE) {
1682	+	if ((*sdi)->isDirectional()) {
1683	+	Vector3d angMom = (*sdi)->getJ() * c;
1684	+	(*sdi)->setJ(angMom);
1685	+	}
1686	+	}
1687	+	}
1688	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1689	+	//vel = (*sdi)->getVel();
1690	+	rPos = (*sdi)->getPos() - coordinateOrigin_;
1691	+	if (doLinearPart)
1692	+	vel = ((*sdi)->getVel() - vh) * h + ah;
1693	+	if (doAngularPart)
1694	+	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1695	+
1696	+	(*sdi)->setVel(vel);
1697	+	if (rnemdFluxType_ == rnemdFullKE) {
1698	+	if ((*sdi)->isDirectional()) {
1699	+	Vector3d angMom = (*sdi)->getJ() * h;
1700	+	(*sdi)->setJ(angMom);
1701	+	}
1702	+	}
1703	+	}
1704	+	successfulExchange = true;
1705	+	kineticExchange_ += kineticTarget_;
1706	+	momentumExchange_ += momentumTarget_;
1707	+	angularMomentumExchange_ += angularMomentumTarget_;
1708	+	}
1709	+	}
1710	+	}
1711	+	}
1712	+	}
1713	+	}
1714	+	}
1715	+	if (successfulExchange != true) {
1716	+	sprintf(painCave.errMsg,
1717	+	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1718	+	"\tthe constraint equations may not exist or there may be\n"
1719	+	"\tno selected objects in one or both slabs.\n");
1720	+	painCave.isFatal = 0;
1721	+	painCave.severity = OPENMD_INFO;
1722	+	simError();
1723	+	failTrialCount_++;
1724	+	}
1725	+	}
1726	+
1727	+	RealType RNEMD::getDividingArea() {
1728	+
1729	+	if (hasDividingArea_) return dividingArea_;
1730	+
1731	+	RealType areaA, areaB;
1732	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1733	+
1734	+	if (hasSelectionA_) {
1735	+	int isd;
1736	+	StuntDouble* sd;
1737	+	vector<StuntDouble*> aSites;
1738	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1739	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1740	+	sd = seleManA_.nextSelected(isd)) {
1741	+	aSites.push_back(sd);
1742	+	}
1743	+	ConvexHull* surfaceMeshA = new ConvexHull();
1744	+	surfaceMeshA->computeHull(aSites);
1745	+	areaA = surfaceMeshA->getArea();
1746	+	delete surfaceMeshA;
1747	+
1748	+	} else {
1749	+	if (usePeriodicBoundaryConditions_) {
1750	+	// in periodic boundaries, the surface area is twice the x-y
1751	+	// area of the current box:
1752	+	areaA = 2.0 * snap->getXYarea();
1753	+	} else {
1754	+	// in non-periodic simulations, without explicitly setting
1755	+	// selections, the sphere radius sets the surface area of the
1756	+	// dividing surface:
1757	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1758	+	}
1759	+	}
1760	+
1761	+
1762	+
1763	+	if (hasSelectionB_) {
1764	+	int isd;
1765	+	StuntDouble* sd;
1766	+	vector<StuntDouble*> bSites;
1767	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1768	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1769	+	sd = seleManB_.nextSelected(isd)) {
1770	+	bSites.push_back(sd);
1771	+	}
1772	+	ConvexHull* surfaceMeshB = new ConvexHull();
1773	+	surfaceMeshB->computeHull(bSites);
1774	+	areaB = surfaceMeshB->getArea();
1775	+	delete surfaceMeshB;
1776	+
1777	+	} else {
1778	+	if (usePeriodicBoundaryConditions_) {
1779	+	// in periodic boundaries, the surface area is twice the x-y
1780	+	// area of the current box:
1781	+	areaB = 2.0 * snap->getXYarea();
1782	+	} else {
1783	+	// in non-periodic simulations, without explicitly setting
1784	+	// selections, but if a sphereBradius has been set, just use that:
1785	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1786	+	}
1787	+	}
1788	+
1789	+	dividingArea_ = min(areaA, areaB);
1790	+	hasDividingArea_ = true;
1791	+	return dividingArea_;
1792	+	}
1793	+
1794	+	void RNEMD::doRNEMD() {
1795	+	if (!doRNEMD_) return;
1796	+	trialCount_++;
1797	+
1798	+	// object evaluator:
1799	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1800	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1801	+
1802	+	evaluatorA_.loadScriptString(selectionA_);
1803	+	evaluatorB_.loadScriptString(selectionB_);
1804	+
1805	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1806	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1807	+
1808	+	commonA_ = seleManA_ & seleMan_;
1809	+	commonB_ = seleManB_ & seleMan_;
1810	+
1811	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1812	+	// dt = exchange time interval
1813	+	// flux = target flux
1814	+	// dividingArea = smallest dividing surface between the two regions
1815	+
1816	+	hasDividingArea_ = false;
1817	+	RealType area = getDividingArea();
1818	+
1819	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1820	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1821	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1822	+
1823	+	switch(rnemdMethod_) {
1824	+	case rnemdSwap:
1825	+	doSwap(commonA_, commonB_);
1826	+	break;
1827	+	case rnemdNIVS:
1828	+	doNIVS(commonA_, commonB_);
1829	+	break;
1830	+	case rnemdVSS:
1831	+	doVSS(commonA_, commonB_);
1832	+	break;
1833	+	case rnemdUnkownMethod:
1834	+	default :
1835	+	break;
1836	+	}
1837	+	}
1838	+
1839	+	void RNEMD::collectData() {
1840	+	if (!doRNEMD_) return;
1841	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1842	+
1843	+	// collectData can be called more frequently than the doRNEMD, so use the
1844	+	// computed area from the last exchange time:
1845	+	RealType area = getDividingArea();
1846	+	areaAccumulator_->add(area);
1847	+	Mat3x3d hmat = currentSnap_->getHmat();
1848	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1849	+
1850	+	int selei(0);
1851	+	StuntDouble* sd;
1852	+	int binNo;
1853	+
1854	+	vector<RealType> binMass(nBins_, 0.0);
1855	+	vector<RealType> binPx(nBins_, 0.0);
1856	+	vector<RealType> binPy(nBins_, 0.0);
1857	+	vector<RealType> binPz(nBins_, 0.0);
1858	+	vector<RealType> binOmegax(nBins_, 0.0);
1859	+	vector<RealType> binOmegay(nBins_, 0.0);
1860	+	vector<RealType> binOmegaz(nBins_, 0.0);
1861	+	vector<RealType> binKE(nBins_, 0.0);
1862	+	vector<int> binDOF(nBins_, 0);
1863	+	vector<int> binCount(nBins_, 0);
1864	+
1865	+	// alternative approach, track all molecules instead of only those
1866	+	// selected for scaling/swapping:
1867	+	/*
1868	+	SimInfo::MoleculeIterator miter;
1869	+	vector<StuntDouble*>::iterator iiter;
1870	+	Molecule* mol;
1871	+	StuntDouble* sd;
1872	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1873	+	mol = info_->nextMolecule(miter))
1874	+	sd is essentially sd
1875	+	for (sd = mol->beginIntegrableObject(iiter);
1876	+	sd != NULL;
1877	+	sd = mol->nextIntegrableObject(iiter))
1878	+	*/
1879	+
1880	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1881	+	sd = seleMan_.nextSelected(selei)) {
1882	+
1883	+	Vector3d pos = sd->getPos();
1884	+
1885	+	// wrap the stuntdouble's position back into the box:
1886	+
1887	+	if (usePeriodicBoundaryConditions_) {
1888	+	currentSnap_->wrapVector(pos);
1889	+	// which bin is this stuntdouble in?
1890	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1891	+	// Shift molecules by half a box to have bins start at 0
1892	+	// The modulo operator is used to wrap the case when we are
1893	+	// beyond the end of the bins back to the beginning.
1894	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1895	+	} else {
1896	+	Vector3d rPos = pos - coordinateOrigin_;
1897	+	binNo = int(rPos.length() / binWidth_);
1898	+	}
1899	+
1900	+	RealType mass = sd->getMass();
1901	+	Vector3d vel = sd->getVel();
1902	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1903	+	Vector3d aVel = cross(rPos, vel);
1904	+
1905	+	if (binNo >= 0 && binNo < nBins_)  {
1906	+	binCount[binNo]++;
1907	+	binMass[binNo] += mass;
1908	+	binPx[binNo] += mass*vel.x();
1909	+	binPy[binNo] += mass*vel.y();
1910	+	binPz[binNo] += mass*vel.z();
1911	+	binOmegax[binNo] += aVel.x();
1912	+	binOmegay[binNo] += aVel.y();
1913	+	binOmegaz[binNo] += aVel.z();
1914	+	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1915	+	binDOF[binNo] += 3;
1916	+
1917	+	if (sd->isDirectional()) {
1918	+	Vector3d angMom = sd->getJ();
1919	+	Mat3x3d I = sd->getI();
1920	+	if (sd->isLinear()) {
1921	+	int i = sd->linearAxis();
1922	+	int j = (i + 1) % 3;
1923	+	int k = (i + 2) % 3;
1924	+	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1925	+	angMom[k] * angMom[k] / I(k, k));
1926	+	binDOF[binNo] += 2;
1927	+	} else {
1928	+	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1929	+	angMom[1] * angMom[1] / I(1, 1) +
1930	+	angMom[2] * angMom[2] / I(2, 2));
1931	+	binDOF[binNo] += 3;
1932	+	}
1933	+	}
1934	+	}
1935	+	}
1936	+
1937	+	#ifdef IS_MPI
1938	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1939	+	nBins_, MPI::INT, MPI::SUM);
1940	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1941	+	nBins_, MPI::REALTYPE, MPI::SUM);
1942	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1943	+	nBins_, MPI::REALTYPE, MPI::SUM);
1944	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1945	+	nBins_, MPI::REALTYPE, MPI::SUM);
1946	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1947	+	nBins_, MPI::REALTYPE, MPI::SUM);
1948	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1949	+	nBins_, MPI::REALTYPE, MPI::SUM);
1950	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1951	+	nBins_, MPI::REALTYPE, MPI::SUM);
1952	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1953	+	nBins_, MPI::REALTYPE, MPI::SUM);
1954	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1955	+	nBins_, MPI::REALTYPE, MPI::SUM);
1956	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1957	+	nBins_, MPI::INT, MPI::SUM);
1958	+	#endif
1959	+
1960	+	Vector3d vel;
1961	+	Vector3d aVel;
1962	+	RealType den;
1963	+	RealType temp;
1964	+	RealType z;
1965	+	RealType r;
1966	+	for (int i = 0; i < nBins_; i++) {
1967	+	if (usePeriodicBoundaryConditions_) {
1968	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1969	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1970	+	/ currentSnap_->getVolume() ;
1971	+	} else {
1972	+	r = (((RealType)i + 0.5) * binWidth_);
1973	+	RealType rinner = (RealType)i * binWidth_;
1974	+	RealType router = (RealType)(i+1) * binWidth_;
1975	+	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1976	+	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1977	+	}
1978	+	vel.x() = binPx[i] / binMass[i];
1979	+	vel.y() = binPy[i] / binMass[i];
1980	+	vel.z() = binPz[i] / binMass[i];
1981	+	aVel.x() = binOmegax[i] / binCount[i];
1982	+	aVel.y() = binOmegay[i] / binCount[i];
1983	+	aVel.z() = binOmegaz[i] / binCount[i];
1984	+
1985	+	if (binCount[i] > 0) {
1986	+	// only add values if there are things to add
1987	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1988	+	PhysicalConstants::energyConvert);
1989	+
1990	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1991	+	if(outputMask_[j]) {
1992	+	switch(j) {
1993	+	case Z:
1994	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1995	+	break;
1996	+	case R:
1997	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1998	+	break;
1999	+	case TEMPERATURE:
2000	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2001	+	break;
2002	+	case VELOCITY:
2003	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2004	+	break;
2005	+	case ANGULARVELOCITY:
2006	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2007	+	break;
2008	+	case DENSITY:
2009	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2010	+	break;
2011	+	}
2012	+	}
2013	+	}
2014	+	}
2015	+	}
2016	+	hasData_ = true;
2017	+	}
2018	+
2019	+	void RNEMD::getStarted() {
2020	+	if (!doRNEMD_) return;
2021	+	hasDividingArea_ = false;
2022	+	collectData();
2023	+	writeOutputFile();
2024	+	}
2025	+
2026	+	void RNEMD::parseOutputFileFormat(const std::string& format) {
2027	+	if (!doRNEMD_) return;
2028	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2029	+
2030	+	while(tokenizer.hasMoreTokens()) {
2031	+	std::string token(tokenizer.nextToken());
2032	+	toUpper(token);
2033	+	OutputMapType::iterator i = outputMap_.find(token);
2034	+	if (i != outputMap_.end()) {
2035	+	outputMask_.set(i->second);
2036	+	} else {
2037	+	sprintf( painCave.errMsg,
2038	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2039	+	"\toutputFileFormat keyword.\n", token.c_str() );
2040	+	painCave.isFatal = 0;
2041	+	painCave.severity = OPENMD_ERROR;
2042	+	simError();
2043	+	}
2044	+	}
2045	+	}
2046	+
2047	+	void RNEMD::writeOutputFile() {
2048	+	if (!doRNEMD_) return;
2049	+	if (!hasData_) return;
2050	+
2051	+	#ifdef IS_MPI
2052		// If we're the root node, should we print out the results
2053		int worldRank = MPI::COMM_WORLD.Get_rank();
2054		if (worldRank == 0) {
2055		#endif
2056	<
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";
2056	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2057
2058	+	if( !rnemdFile_ ){
2059	+	sprintf( painCave.errMsg,
2060	+	"Could not open \"%s\" for RNEMD output.\n",
2061	+	rnemdFileName_.c_str());
2062	+	painCave.isFatal = 1;
2063	+	simError();
2064	+	}
2065	+
2066	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2067	+
2068	+	RealType time = currentSnap_->getTime();
2069	+	RealType avgArea;
2070	+	areaAccumulator_->getAverage(avgArea);
2071	+
2072	+	RealType Jz(0.0);
2073	+	Vector3d JzP(V3Zero);
2074	+	Vector3d JzL(V3Zero);
2075	+	if (time >= info_->getSimParams()->getDt()) {
2076	+	Jz = kineticExchange_ / (time * avgArea)
2077	+	/ PhysicalConstants::energyConvert;
2078	+	JzP = momentumExchange_ / (time * avgArea);
2079	+	JzL = angularMomentumExchange_ / (time * avgArea);
2080	+	}
2081	+
2082	+	rnemdFile_ << "#######################################################\n";
2083	+	rnemdFile_ << "# RNEMD {\n";
2084	+
2085	+	map<string, RNEMDMethod>::iterator mi;
2086	+	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2087	+	if ( (*mi).second == rnemdMethod_)
2088	+	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2089	+	}
2090	+	map<string, RNEMDFluxType>::iterator fi;
2091	+	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2092	+	if ( (*fi).second == rnemdFluxType_)
2093	+	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2094	+	}
2095	+
2096	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2097	+
2098	+	rnemdFile_ << "#    objectSelection = \""
2099	+	<< rnemdObjectSelection_ << "\";\n";
2100	+	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2101	+	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2102	+	rnemdFile_ << "# }\n";
2103	+	rnemdFile_ << "#######################################################\n";
2104	+	rnemdFile_ << "# RNEMD report:\n";
2105	+	rnemdFile_ << "#      running time = " << time << " fs\n";
2106	+	rnemdFile_ << "# Target flux:\n";
2107	+	rnemdFile_ << "#           kinetic = "
2108	+	<< kineticFlux_ / PhysicalConstants::energyConvert
2109	+	<< " (kcal/mol/A^2/fs)\n";
2110	+	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2111	+	<< " (amu/A/fs^2)\n";
2112	+	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2113	+	<< " (amu/A^2/fs^2)\n";
2114	+	rnemdFile_ << "# Target one-time exchanges:\n";
2115	+	rnemdFile_ << "#          kinetic = "
2116	+	<< kineticTarget_ / PhysicalConstants::energyConvert
2117	+	<< " (kcal/mol)\n";
2118	+	rnemdFile_ << "#          momentum = " << momentumTarget_
2119	+	<< " (amu*A/fs)\n";
2120	+	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2121	+	<< " (amu*A^2/fs)\n";
2122	+	rnemdFile_ << "# Actual exchange totals:\n";
2123	+	rnemdFile_ << "#          kinetic = "
2124	+	<< kineticExchange_ / PhysicalConstants::energyConvert
2125	+	<< " (kcal/mol)\n";
2126	+	rnemdFile_ << "#          momentum = " << momentumExchange_
2127	+	<< " (amu*A/fs)\n";
2128	+	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2129	+	<< " (amu*A^2/fs)\n";
2130	+	rnemdFile_ << "# Actual flux:\n";
2131	+	rnemdFile_ << "#          kinetic = " << Jz
2132	+	<< " (kcal/mol/A^2/fs)\n";
2133	+	rnemdFile_ << "#          momentum = " << JzP
2134	+	<< " (amu/A/fs^2)\n";
2135	+	rnemdFile_ << "#  angular momentum = " << JzL
2136	+	<< " (amu/A^2/fs^2)\n";
2137	+	rnemdFile_ << "# Exchange statistics:\n";
2138	+	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2139	+	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2140	+	if (rnemdMethod_ == rnemdNIVS) {
2141	+	rnemdFile_ << "#  NIVS root-check errors = "
2142	+	<< failRootCount_ << "\n";
2143	+	}
2144	+	rnemdFile_ << "#######################################################\n";
2145	+
2146	+
2147	+
2148	+	//write title
2149	+	rnemdFile_ << "#";
2150	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2151	+	if (outputMask_[i]) {
2152	+	rnemdFile_ << "\t" << data_[i].title <<
2153	+	"(" << data_[i].units << ")";
2154	+	// add some extra tabs for column alignment
2155	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2156	+	}
2157	+	}
2158	+	rnemdFile_ << std::endl;
2159	+
2160	+	rnemdFile_.precision(8);
2161	+
2162	+	for (int j = 0; j < nBins_; j++) {
2163	+
2164	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2165	+	if (outputMask_[i]) {
2166	+	if (data_[i].dataType == "RealType")
2167	+	writeReal(i,j);
2168	+	else if (data_[i].dataType == "Vector3d")
2169	+	writeVector(i,j);
2170	+	else {
2171	+	sprintf( painCave.errMsg,
2172	+	"RNEMD found an unknown data type for: %s ",
2173	+	data_[i].title.c_str());
2174	+	painCave.isFatal = 1;
2175	+	simError();
2176	+	}
2177	+	}
2178	+	}
2179	+	rnemdFile_ << std::endl;
2180	+
2181	+	}
2182	+
2183	+	rnemdFile_ << "#######################################################\n";
2184	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2185	+	rnemdFile_ << "#######################################################\n";
2186	+
2187	+
2188	+	for (int j = 0; j < nBins_; j++) {
2189	+	rnemdFile_ << "#";
2190	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2191	+	if (outputMask_[i]) {
2192	+	if (data_[i].dataType == "RealType")
2193	+	writeRealStdDev(i,j);
2194	+	else if (data_[i].dataType == "Vector3d")
2195	+	writeVectorStdDev(i,j);
2196	+	else {
2197	+	sprintf( painCave.errMsg,
2198	+	"RNEMD found an unknown data type for: %s ",
2199	+	data_[i].title.c_str());
2200	+	painCave.isFatal = 1;
2201	+	simError();
2202	+	}
2203	+	}
2204	+	}
2205	+	rnemdFile_ << std::endl;
2206	+
2207	+	}
2208	+
2209	+	rnemdFile_.flush();
2210	+	rnemdFile_.close();
2211	+
2212		#ifdef IS_MPI
2213		}
2214		#endif
2215	+
2216		}
2217	+
2218	+	void RNEMD::writeReal(int index, unsigned int bin) {
2219	+	if (!doRNEMD_) return;
2220	+	assert(index >=0 && index < ENDINDEX);
2221	+	assert(int(bin) < nBins_);
2222	+	RealType s;
2223	+	int count;
2224	+
2225	+	count = data_[index].accumulator[bin]->count();
2226	+	if (count == 0) return;
2227	+
2228	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2229	+
2230	+	if (! isinf(s) && ! isnan(s)) {
2231	+	rnemdFile_ << "\t" << s;
2232	+	} else{
2233	+	sprintf( painCave.errMsg,
2234	+	"RNEMD detected a numerical error writing: %s for bin %u",
2235	+	data_[index].title.c_str(), bin);
2236	+	painCave.isFatal = 1;
2237	+	simError();
2238	+	}
2239	+	}
2240	+
2241	+	void RNEMD::writeVector(int index, unsigned int bin) {
2242	+	if (!doRNEMD_) return;
2243	+	assert(index >=0 && index < ENDINDEX);
2244	+	assert(int(bin) < nBins_);
2245	+	Vector3d s;
2246	+	int count;
2247	+
2248	+	count = data_[index].accumulator[bin]->count();
2249	+
2250	+	if (count == 0) return;
2251	+
2252	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2253	+	if (isinf(s[0]) || isnan(s[0]) ||
2254	+	isinf(s[1]) || isnan(s[1]) ||
2255	+	isinf(s[2]) || isnan(s[2]) ) {
2256	+	sprintf( painCave.errMsg,
2257	+	"RNEMD detected a numerical error writing: %s for bin %u",
2258	+	data_[index].title.c_str(), bin);
2259	+	painCave.isFatal = 1;
2260	+	simError();
2261	+	} else {
2262	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2263	+	}
2264	+	}
2265	+
2266	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2267	+	if (!doRNEMD_) return;
2268	+	assert(index >=0 && index < ENDINDEX);
2269	+	assert(int(bin) < nBins_);
2270	+	RealType s;
2271	+	int count;
2272	+
2273	+	count = data_[index].accumulator[bin]->count();
2274	+	if (count == 0) return;
2275	+
2276	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2277	+
2278	+	if (! isinf(s) && ! isnan(s)) {
2279	+	rnemdFile_ << "\t" << s;
2280	+	} else{
2281	+	sprintf( painCave.errMsg,
2282	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2283	+	data_[index].title.c_str(), bin);
2284	+	painCave.isFatal = 1;
2285	+	simError();
2286	+	}
2287	+	}
2288	+
2289	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2290	+	if (!doRNEMD_) return;
2291	+	assert(index >=0 && index < ENDINDEX);
2292	+	assert(int(bin) < nBins_);
2293	+	Vector3d s;
2294	+	int count;
2295	+
2296	+	count = data_[index].accumulator[bin]->count();
2297	+	if (count == 0) return;
2298	+
2299	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2300	+	if (isinf(s[0]) || isnan(s[0]) ||
2301	+	isinf(s[1]) || isnan(s[1]) ||
2302	+	isinf(s[2]) || isnan(s[2]) ) {
2303	+	sprintf( painCave.errMsg,
2304	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2305	+	data_[index].title.c_str(), bin);
2306	+	painCave.isFatal = 1;
2307	+	simError();
2308	+	} else {
2309	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2310	+	}
2311	+	}
2312		}
2313	+

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 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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