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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 2056 by gezelter, Fri Feb 20 15:12:07 2015 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
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* kind. All express or implied conditions, representations and
28	<	* warranties, including any implied warranty of merchantability,
29	<	* fitness for a particular purpose or non-infringement, are hereby
30	<	* excluded.  The University of Notre Dame and its licensors shall not
31	<	* be liable for any damages suffered by licensee as a result of
32	<	* using, modifying or distributing the software or its
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* direct, indirect, special, consequential, incidental or punitive
36	<	* damages, however caused and regardless of the theory of liability,
37	<	* arising out of the use of or inability to use software, even if the
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
40	<	*/
41	<
42	<	#include "integrators/RNEMD.hpp"
43	<	#include "math/SquareMatrix3.hpp"
44	<	#include "primitives/Molecule.hpp"
45	<	#include "primitives/StuntDouble.hpp"
46	<
47	<	#ifndef IS_MPI
48	<	#include "math/SeqRandNumGen.hpp"
49	<	#else
50	<	#include "math/ParallelRandNumGen.hpp"
51	<	#endif
52	<
53	<	/* Remove me after testing*/
54	<	/*
55	<	#include <cstdio>
56	<	#include <iostream>
57	<	*/
58	<	/*End remove me*/
59	<
60	<	namespace oopse {
61	<
62	<	RNEMD::RNEMD(SimInfo* info) : info_(info) {
63	<
64	<	int seedValue;
65	<	Globals * simParams = info->getSimParams();
66	<
67	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
68	<	stringToEnumMap_["Px"] = rnemdPx;
69	<	stringToEnumMap_["Py"] = rnemdPy;
70	<	stringToEnumMap_["Pz"] = rnemdPz;
71	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	<
73	<	const std::string st = simParams->getRNEMD_swapType();
74	<
75	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
76	<	i = stringToEnumMap_.find(st);
77	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
78	<
79	<
80	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
81	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
82	<	exchangeSum_ = 0.0;
83	<
84	<	#ifndef IS_MPI
85	<	if (simParams->haveSeed()) {
86	<	seedValue = simParams->getSeed();
87	<	randNumGen_ = new SeqRandNumGen(seedValue);
88	<	}else {
89	<	randNumGen_ = new SeqRandNumGen();
90	<	}
91	<	#else
92	<	if (simParams->haveSeed()) {
93	<	seedValue = simParams->getSeed();
94	<	randNumGen_ = new ParallelRandNumGen(seedValue);
95	<	}else {
96	<	randNumGen_ = new ParallelRandNumGen();
97	<	}
98	<	#endif
99	<	}
100	<
101	<	RNEMD::~RNEMD() {
102	<	delete randNumGen_;
103	<	}
104	<
105	<	void RNEMD::doSwap() {
106	<	std::cerr << "in RNEMD!\n";
107	<	std::cerr << "nBins = " << nBins_ << "\n";
108	<	std::cerr << "swapTime = " << swapTime_ << "\n";
109	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
110	<	std::cerr << "swapType = " << rnemdType_ << "\n";
111	<	}
112	<	}
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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 <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/PhysicalConstants.hpp"
57	>	#include "utils/Tuple.hpp"
58	>	#include "brains/Thermo.hpp"
59	>	#include "math/ConvexHull.hpp"
60	>
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	>	using namespace std;
69	>	namespace OpenMD {
70	>
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	>	trialCount_ = 0;
79	>	failTrialCount_ = 0;
80	>	failRootCount_ = 0;
81	>
82	>	Globals* simParams = info->getSimParams();
83	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84	>
85	>	doRNEMD_ = rnemdParams->getUseRNEMD();
86	>	if (!doRNEMD_) return;
87	>
88	>	stringToMethod_["Swap"]  = rnemdSwap;
89	>	stringToMethod_["NIVS"]  = rnemdNIVS;
90	>	stringToMethod_["VSS"]   = rnemdVSS;
91	>
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	>	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: 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();
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	>	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	>	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	>	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	>	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	>	std::vector<RealType> mf = rnemdParams->getMomentumFluxVector();
295	>	if (mf.size() != 3) {
296	>	sprintf(painCave.errMsg,
297	>	"RNEMD: Incorrect number of parameters specified for momentumFluxVector.\n"
298	>	"\tthere should be 3 parameters, but %lu were specified.\n",
299	>	mf.size());
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	momentumFluxVector_.x() = mf[0];
304	>	momentumFluxVector_.y() = mf[1];
305	>	momentumFluxVector_.z() = mf[2];
306	>	} else {
307	>	momentumFluxVector_ = V3Zero;
308	>	if (hasMomentumFlux) {
309	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
310	>	switch (rnemdFluxType_) {
311	>	case rnemdPx:
312	>	momentumFluxVector_.x() = momentumFlux;
313	>	break;
314	>	case rnemdPy:
315	>	momentumFluxVector_.y() = momentumFlux;
316	>	break;
317	>	case rnemdPz:
318	>	momentumFluxVector_.z() = momentumFlux;
319	>	break;
320	>	case rnemdKePx:
321	>	momentumFluxVector_.x() = momentumFlux;
322	>	break;
323	>	case rnemdKePy:
324	>	momentumFluxVector_.y() = momentumFlux;
325	>	break;
326	>	default:
327	>	break;
328	>	}
329	>	}
330	>	}
331	>	if (hasAngularMomentumFluxVector) {
332	>	std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
333	>	if (amf.size() != 3) {
334	>	sprintf(painCave.errMsg,
335	>	"RNEMD: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
336	>	"\tthere should be 3 parameters, but %lu were specified.\n",
337	>	amf.size());
338	>	painCave.isFatal = 1;
339	>	simError();
340	>	}
341	>	angularMomentumFluxVector_.x() = amf[0];
342	>	angularMomentumFluxVector_.y() = amf[1];
343	>	angularMomentumFluxVector_.z() = amf[2];
344	>	} else {
345	>	angularMomentumFluxVector_ = V3Zero;
346	>	if (hasAngularMomentumFlux) {
347	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
348	>	switch (rnemdFluxType_) {
349	>	case rnemdLx:
350	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
351	>	break;
352	>	case rnemdLy:
353	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
354	>	break;
355	>	case rnemdLz:
356	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
357	>	break;
358	>	case rnemdKeLx:
359	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
360	>	break;
361	>	case rnemdKeLy:
362	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
363	>	break;
364	>	case rnemdKeLz:
365	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
366	>	break;
367	>	default:
368	>	break;
369	>	}
370	>	}
371	>	}
372	>
373	>	if (hasCoordinateOrigin) {
374	>	std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
375	>	if (co.size() != 3) {
376	>	sprintf(painCave.errMsg,
377	>	"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
378	>	"\tthere should be 3 parameters, but %lu were specified.\n",
379	>	co.size());
380	>	painCave.isFatal = 1;
381	>	simError();
382	>	}
383	>	coordinateOrigin_.x() = co[0];
384	>	coordinateOrigin_.y() = co[1];
385	>	coordinateOrigin_.z() = co[2];
386	>	} else {
387	>	coordinateOrigin_ = V3Zero;
388	>	}
389	>
390	>	// do some sanity checking
391	>
392	>	int selectionCount = seleMan_.getSelectionCount();
393	>	int nIntegrable = info->getNGlobalIntegrableObjects();
394	>	if (selectionCount > nIntegrable) {
395	>	sprintf(painCave.errMsg,
396	>	"RNEMD: The current objectSelection,\n"
397	>	"\t\t%s\n"
398	>	"\thas resulted in %d selected objects.  However,\n"
399	>	"\tthe total number of integrable objects in the system\n"
400	>	"\tis only %d.  This is almost certainly not what you want\n"
401	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
402	>	"\tselector in the selection script!\n",
403	>	rnemdObjectSelection_.c_str(),
404	>	selectionCount, nIntegrable);
405	>	painCave.isFatal = 0;
406	>	painCave.severity = OPENMD_WARNING;
407	>	simError();
408	>	}
409	>
410	>	areaAccumulator_ = new Accumulator();
411	>
412	>	nBins_ = rnemdParams->getOutputBins();
413	>	binWidth_ = rnemdParams->getOutputBinWidth();
414	>
415	>	data_.resize(RNEMD::ENDINDEX);
416	>	OutputData z;
417	>	z.units =  "Angstroms";
418	>	z.title =  "Z";
419	>	z.dataType = "RealType";
420	>	z.accumulator.reserve(nBins_);
421	>	for (int i = 0; i < nBins_; i++)
422	>	z.accumulator.push_back( new Accumulator() );
423	>	data_[Z] = z;
424	>	outputMap_["Z"] =  Z;
425	>
426	>	OutputData r;
427	>	r.units =  "Angstroms";
428	>	r.title =  "R";
429	>	r.dataType = "RealType";
430	>	r.accumulator.reserve(nBins_);
431	>	for (int i = 0; i < nBins_; i++)
432	>	r.accumulator.push_back( new Accumulator() );
433	>	data_[R] = r;
434	>	outputMap_["R"] =  R;
435	>
436	>	OutputData temperature;
437	>	temperature.units =  "K";
438	>	temperature.title =  "Temperature";
439	>	temperature.dataType = "RealType";
440	>	temperature.accumulator.reserve(nBins_);
441	>	for (int i = 0; i < nBins_; i++)
442	>	temperature.accumulator.push_back( new Accumulator() );
443	>	data_[TEMPERATURE] = temperature;
444	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
445	>
446	>	OutputData velocity;
447	>	velocity.units = "angstroms/fs";
448	>	velocity.title =  "Velocity";
449	>	velocity.dataType = "Vector3d";
450	>	velocity.accumulator.reserve(nBins_);
451	>	for (int i = 0; i < nBins_; i++)
452	>	velocity.accumulator.push_back( new VectorAccumulator() );
453	>	data_[VELOCITY] = velocity;
454	>	outputMap_["VELOCITY"] = VELOCITY;
455	>
456	>	OutputData angularVelocity;
457	>	angularVelocity.units = "angstroms^2/fs";
458	>	angularVelocity.title =  "AngularVelocity";
459	>	angularVelocity.dataType = "Vector3d";
460	>	angularVelocity.accumulator.reserve(nBins_);
461	>	for (int i = 0; i < nBins_; i++)
462	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
463	>	data_[ANGULARVELOCITY] = angularVelocity;
464	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
465	>
466	>	OutputData density;
467	>	density.units =  "g cm^-3";
468	>	density.title =  "Density";
469	>	density.dataType = "RealType";
470	>	density.accumulator.reserve(nBins_);
471	>	for (int i = 0; i < nBins_; i++)
472	>	density.accumulator.push_back( new Accumulator() );
473	>	data_[DENSITY] = density;
474	>	outputMap_["DENSITY"] =  DENSITY;
475	>
476	>	if (hasOutputFields) {
477	>	parseOutputFileFormat(rnemdParams->getOutputFields());
478	>	} else {
479	>	if (usePeriodicBoundaryConditions_)
480	>	outputMask_.set(Z);
481	>	else
482	>	outputMask_.set(R);
483	>	switch (rnemdFluxType_) {
484	>	case rnemdKE:
485	>	case rnemdRotKE:
486	>	case rnemdFullKE:
487	>	outputMask_.set(TEMPERATURE);
488	>	break;
489	>	case rnemdPx:
490	>	case rnemdPy:
491	>	outputMask_.set(VELOCITY);
492	>	break;
493	>	case rnemdPz:
494	>	case rnemdPvector:
495	>	outputMask_.set(VELOCITY);
496	>	outputMask_.set(DENSITY);
497	>	break;
498	>	case rnemdLx:
499	>	case rnemdLy:
500	>	case rnemdLz:
501	>	case rnemdLvector:
502	>	outputMask_.set(ANGULARVELOCITY);
503	>	break;
504	>	case rnemdKeLx:
505	>	case rnemdKeLy:
506	>	case rnemdKeLz:
507	>	case rnemdKeLvector:
508	>	outputMask_.set(TEMPERATURE);
509	>	outputMask_.set(ANGULARVELOCITY);
510	>	break;
511	>	case rnemdKePx:
512	>	case rnemdKePy:
513	>	outputMask_.set(TEMPERATURE);
514	>	outputMask_.set(VELOCITY);
515	>	break;
516	>	case rnemdKePvector:
517	>	outputMask_.set(TEMPERATURE);
518	>	outputMask_.set(VELOCITY);
519	>	outputMask_.set(DENSITY);
520	>	break;
521	>	default:
522	>	break;
523	>	}
524	>	}
525	>
526	>	if (hasOutputFileName) {
527	>	rnemdFileName_ = rnemdParams->getOutputFileName();
528	>	} else {
529	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
530	>	}
531	>
532	>	exchangeTime_ = rnemdParams->getExchangeTime();
533	>
534	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
535	>	// total exchange sums are zeroed out at the beginning:
536	>
537	>	kineticExchange_ = 0.0;
538	>	momentumExchange_ = V3Zero;
539	>	angularMomentumExchange_ = V3Zero;
540	>
541	>	std::ostringstream selectionAstream;
542	>	std::ostringstream selectionBstream;
543	>
544	>	if (hasSelectionA_) {
545	>	selectionA_ = rnemdParams->getSelectionA();
546	>	} else {
547	>	if (usePeriodicBoundaryConditions_) {
548	>	Mat3x3d hmat = currentSnap_->getHmat();
549	>
550	>	if (hasSlabWidth)
551	>	slabWidth_ = rnemdParams->getSlabWidth();
552	>	else
553	>	slabWidth_ = hmat(2,2) / 10.0;
554	>
555	>	if (hasSlabACenter)
556	>	slabACenter_ = rnemdParams->getSlabACenter();
557	>	else
558	>	slabACenter_ = 0.0;
559	>
560	>	selectionAstream << "select wrappedz > "
561	>	<< slabACenter_ - 0.5*slabWidth_
562	>	<<  " && wrappedz < "
563	>	<< slabACenter_ + 0.5*slabWidth_;
564	>	selectionA_ = selectionAstream.str();
565	>	} else {
566	>	if (hasSphereARadius)
567	>	sphereARadius_ = rnemdParams->getSphereARadius();
568	>	else {
569	>	// use an initial guess to the size of the inner slab to be 1/10 the
570	>	// radius of an approximately spherical hull:
571	>	Thermo thermo(info);
572	>	RealType hVol = thermo.getHullVolume();
573	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
574	>	}
575	>	selectionAstream << "select r < " << sphereARadius_;
576	>	selectionA_ = selectionAstream.str();
577	>	}
578	>	}
579	>
580	>	if (hasSelectionB_) {
581	>	selectionB_ = rnemdParams->getSelectionB();
582	>
583	>	} else {
584	>	if (usePeriodicBoundaryConditions_) {
585	>	Mat3x3d hmat = currentSnap_->getHmat();
586	>
587	>	if (hasSlabWidth)
588	>	slabWidth_ = rnemdParams->getSlabWidth();
589	>	else
590	>	slabWidth_ = hmat(2,2) / 10.0;
591	>
592	>	if (hasSlabBCenter)
593	>	slabBCenter_ = rnemdParams->getSlabBCenter();
594	>	else
595	>	slabBCenter_ = hmat(2,2) / 2.0;
596	>
597	>	selectionBstream << "select wrappedz > "
598	>	<< slabBCenter_ - 0.5*slabWidth_
599	>	<<  " && wrappedz < "
600	>	<< slabBCenter_ + 0.5*slabWidth_;
601	>	selectionB_ = selectionBstream.str();
602	>	} else {
603	>	if (hasSphereBRadius_) {
604	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
605	>	selectionBstream << "select r > " << sphereBRadius_;
606	>	selectionB_ = selectionBstream.str();
607	>	} else {
608	>	selectionB_ = "select hull";
609	>	BisHull_ = true;
610	>	hasSelectionB_ = true;
611	>	}
612	>	}
613	>	}
614	>
615	>
616	>	// object evaluator:
617	>	evaluator_.loadScriptString(rnemdObjectSelection_);
618	>	seleMan_.setSelectionSet(evaluator_.evaluate());
619	>	evaluatorA_.loadScriptString(selectionA_);
620	>	evaluatorB_.loadScriptString(selectionB_);
621	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
622	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
623	>	commonA_ = seleManA_ & seleMan_;
624	>	commonB_ = seleManB_ & seleMan_;
625	>	}
626	>
627	>
628	>	RNEMD::~RNEMD() {
629	>	if (!doRNEMD_) return;
630	>	#ifdef IS_MPI
631	>	if (worldRank == 0) {
632	>	#endif
633	>
634	>	writeOutputFile();
635	>
636	>	rnemdFile_.close();
637	>
638	>	#ifdef IS_MPI
639	>	}
640	>	#endif
641	>
642	>	// delete all of the objects we created:
643	>	delete areaAccumulator_;
644	>	data_.clear();
645	>	}
646	>
647	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
648	>	if (!doRNEMD_) return;
649	>	int selei;
650	>	int selej;
651	>
652	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
653	>	Mat3x3d hmat = currentSnap_->getHmat();
654	>
655	>	StuntDouble* sd;
656	>
657	>	RealType min_val;
658	>	int min_found = 0;
659	>	StuntDouble* min_sd;
660	>
661	>	RealType max_val;
662	>	int max_found = 0;
663	>	StuntDouble* max_sd;
664	>
665	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
666	>	sd = seleManA_.nextSelected(selei)) {
667	>
668	>	Vector3d pos = sd->getPos();
669	>
670	>	// wrap the stuntdouble's position back into the box:
671	>
672	>	if (usePeriodicBoundaryConditions_)
673	>	currentSnap_->wrapVector(pos);
674	>
675	>	RealType mass = sd->getMass();
676	>	Vector3d vel = sd->getVel();
677	>	RealType value;
678	>
679	>	switch(rnemdFluxType_) {
680	>	case rnemdKE :
681	>
682	>	value = mass * vel.lengthSquare();
683	>
684	>	if (sd->isDirectional()) {
685	>	Vector3d angMom = sd->getJ();
686	>	Mat3x3d I = sd->getI();
687	>
688	>	if (sd->isLinear()) {
689	>	int i = sd->linearAxis();
690	>	int j = (i + 1) % 3;
691	>	int k = (i + 2) % 3;
692	>	value += angMom[j] * angMom[j] / I(j, j) +
693	>	angMom[k] * angMom[k] / I(k, k);
694	>	} else {
695	>	value += angMom[0]*angMom[0]/I(0, 0)
696	>	+ angMom[1]*angMom[1]/I(1, 1)
697	>	+ angMom[2]*angMom[2]/I(2, 2);
698	>	}
699	>	} //angular momenta exchange enabled
700	>	value *= 0.5;
701	>	break;
702	>	case rnemdPx :
703	>	value = mass * vel[0];
704	>	break;
705	>	case rnemdPy :
706	>	value = mass * vel[1];
707	>	break;
708	>	case rnemdPz :
709	>	value = mass * vel[2];
710	>	break;
711	>	default :
712	>	break;
713	>	}
714	>	if (!max_found) {
715	>	max_val = value;
716	>	max_sd = sd;
717	>	max_found = 1;
718	>	} else {
719	>	if (max_val < value) {
720	>	max_val = value;
721	>	max_sd = sd;
722	>	}
723	>	}
724	>	}
725	>
726	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
727	>	sd = seleManB_.nextSelected(selej)) {
728	>
729	>	Vector3d pos = sd->getPos();
730	>
731	>	// wrap the stuntdouble's position back into the box:
732	>
733	>	if (usePeriodicBoundaryConditions_)
734	>	currentSnap_->wrapVector(pos);
735	>
736	>	RealType mass = sd->getMass();
737	>	Vector3d vel = sd->getVel();
738	>	RealType value;
739	>
740	>	switch(rnemdFluxType_) {
741	>	case rnemdKE :
742	>
743	>	value = mass * vel.lengthSquare();
744	>
745	>	if (sd->isDirectional()) {
746	>	Vector3d angMom = sd->getJ();
747	>	Mat3x3d I = sd->getI();
748	>
749	>	if (sd->isLinear()) {
750	>	int i = sd->linearAxis();
751	>	int j = (i + 1) % 3;
752	>	int k = (i + 2) % 3;
753	>	value += angMom[j] * angMom[j] / I(j, j) +
754	>	angMom[k] * angMom[k] / I(k, k);
755	>	} else {
756	>	value += angMom[0]*angMom[0]/I(0, 0)
757	>	+ angMom[1]*angMom[1]/I(1, 1)
758	>	+ angMom[2]*angMom[2]/I(2, 2);
759	>	}
760	>	} //angular momenta exchange enabled
761	>	value *= 0.5;
762	>	break;
763	>	case rnemdPx :
764	>	value = mass * vel[0];
765	>	break;
766	>	case rnemdPy :
767	>	value = mass * vel[1];
768	>	break;
769	>	case rnemdPz :
770	>	value = mass * vel[2];
771	>	break;
772	>	default :
773	>	break;
774	>	}
775	>
776	>	if (!min_found) {
777	>	min_val = value;
778	>	min_sd = sd;
779	>	min_found = 1;
780	>	} else {
781	>	if (min_val > value) {
782	>	min_val = value;
783	>	min_sd = sd;
784	>	}
785	>	}
786	>	}
787	>
788	>	#ifdef IS_MPI
789	>	int worldRank;
790	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
791	>
792	>	int my_min_found = min_found;
793	>	int my_max_found = max_found;
794	>
795	>	// Even if we didn't find a minimum, did someone else?
796	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
797	>	MPI_COMM_WORLD);
798	>	// Even if we didn't find a maximum, did someone else?
799	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
800	>	MPI_COMM_WORLD);
801	>	#endif
802	>
803	>	if (max_found && min_found) {
804	>
805	>	#ifdef IS_MPI
806	>	struct {
807	>	RealType val;
808	>	int rank;
809	>	} max_vals, min_vals;
810	>
811	>	if (my_min_found) {
812	>	min_vals.val = min_val;
813	>	} else {
814	>	min_vals.val = HONKING_LARGE_VALUE;
815	>	}
816	>	min_vals.rank = worldRank;
817	>
818	>	// Who had the minimum?
819	>	MPI_Allreduce(&min_vals, &min_vals,
820	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
821	>	min_val = min_vals.val;
822	>
823	>	if (my_max_found) {
824	>	max_vals.val = max_val;
825	>	} else {
826	>	max_vals.val = -HONKING_LARGE_VALUE;
827	>	}
828	>	max_vals.rank = worldRank;
829	>
830	>	// Who had the maximum?
831	>	MPI_Allreduce(&max_vals, &max_vals,
832	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
833	>	max_val = max_vals.val;
834	>	#endif
835	>
836	>	if (min_val < max_val) {
837	>
838	>	#ifdef IS_MPI
839	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
840	>	// I have both maximum and minimum, so proceed like a single
841	>	// processor version:
842	>	#endif
843	>
844	>	Vector3d min_vel = min_sd->getVel();
845	>	Vector3d max_vel = max_sd->getVel();
846	>	RealType temp_vel;
847	>
848	>	switch(rnemdFluxType_) {
849	>	case rnemdKE :
850	>	min_sd->setVel(max_vel);
851	>	max_sd->setVel(min_vel);
852	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
853	>	Vector3d min_angMom = min_sd->getJ();
854	>	Vector3d max_angMom = max_sd->getJ();
855	>	min_sd->setJ(max_angMom);
856	>	max_sd->setJ(min_angMom);
857	>	}//angular momenta exchange enabled
858	>	//assumes same rigid body identity
859	>	break;
860	>	case rnemdPx :
861	>	temp_vel = min_vel.x();
862	>	min_vel.x() = max_vel.x();
863	>	max_vel.x() = temp_vel;
864	>	min_sd->setVel(min_vel);
865	>	max_sd->setVel(max_vel);
866	>	break;
867	>	case rnemdPy :
868	>	temp_vel = min_vel.y();
869	>	min_vel.y() = max_vel.y();
870	>	max_vel.y() = temp_vel;
871	>	min_sd->setVel(min_vel);
872	>	max_sd->setVel(max_vel);
873	>	break;
874	>	case rnemdPz :
875	>	temp_vel = min_vel.z();
876	>	min_vel.z() = max_vel.z();
877	>	max_vel.z() = temp_vel;
878	>	min_sd->setVel(min_vel);
879	>	max_sd->setVel(max_vel);
880	>	break;
881	>	default :
882	>	break;
883	>	}
884	>
885	>	#ifdef IS_MPI
886	>	// the rest of the cases only apply in parallel simulations:
887	>	} else if (max_vals.rank == worldRank) {
888	>	// I had the max, but not the minimum
889	>
890	>	Vector3d min_vel;
891	>	Vector3d max_vel = max_sd->getVel();
892	>	MPI_Status status;
893	>
894	>	// point-to-point swap of the velocity vector
895	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
896	>	min_vals.rank, 0,
897	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
898	>	min_vals.rank, 0, MPI_COMM_WORLD, &status);
899	>
900	>	switch(rnemdFluxType_) {
901	>	case rnemdKE :
902	>	max_sd->setVel(min_vel);
903	>	//angular momenta exchange enabled
904	>	if (max_sd->isDirectional()) {
905	>	Vector3d min_angMom;
906	>	Vector3d max_angMom = max_sd->getJ();
907	>
908	>	// point-to-point swap of the angular momentum vector
909	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
910	>	MPI_REALTYPE, min_vals.rank, 1,
911	>	min_angMom.getArrayPointer(), 3,
912	>	MPI_REALTYPE, min_vals.rank, 1,
913	>	MPI_COMM_WORLD, &status);
914	>
915	>	max_sd->setJ(min_angMom);
916	>	}
917	>	break;
918	>	case rnemdPx :
919	>	max_vel.x() = min_vel.x();
920	>	max_sd->setVel(max_vel);
921	>	break;
922	>	case rnemdPy :
923	>	max_vel.y() = min_vel.y();
924	>	max_sd->setVel(max_vel);
925	>	break;
926	>	case rnemdPz :
927	>	max_vel.z() = min_vel.z();
928	>	max_sd->setVel(max_vel);
929	>	break;
930	>	default :
931	>	break;
932	>	}
933	>	} else if (min_vals.rank == worldRank) {
934	>	// I had the minimum but not the maximum:
935	>
936	>	Vector3d max_vel;
937	>	Vector3d min_vel = min_sd->getVel();
938	>	MPI_Status status;
939	>
940	>	// point-to-point swap of the velocity vector
941	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
942	>	max_vals.rank, 0,
943	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
944	>	max_vals.rank, 0, MPI_COMM_WORLD, &status);
945	>
946	>	switch(rnemdFluxType_) {
947	>	case rnemdKE :
948	>	min_sd->setVel(max_vel);
949	>	//angular momenta exchange enabled
950	>	if (min_sd->isDirectional()) {
951	>	Vector3d min_angMom = min_sd->getJ();
952	>	Vector3d max_angMom;
953	>
954	>	// point-to-point swap of the angular momentum vector
955	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
956	>	MPI_REALTYPE, max_vals.rank, 1,
957	>	max_angMom.getArrayPointer(), 3,
958	>	MPI_REALTYPE, max_vals.rank, 1,
959	>	MPI_COMM_WORLD, &status);
960	>
961	>	min_sd->setJ(max_angMom);
962	>	}
963	>	break;
964	>	case rnemdPx :
965	>	min_vel.x() = max_vel.x();
966	>	min_sd->setVel(min_vel);
967	>	break;
968	>	case rnemdPy :
969	>	min_vel.y() = max_vel.y();
970	>	min_sd->setVel(min_vel);
971	>	break;
972	>	case rnemdPz :
973	>	min_vel.z() = max_vel.z();
974	>	min_sd->setVel(min_vel);
975	>	break;
976	>	default :
977	>	break;
978	>	}
979	>	}
980	>	#endif
981	>
982	>	switch(rnemdFluxType_) {
983	>	case rnemdKE:
984	>	kineticExchange_ += max_val - min_val;
985	>	break;
986	>	case rnemdPx:
987	>	momentumExchange_.x() += max_val - min_val;
988	>	break;
989	>	case rnemdPy:
990	>	momentumExchange_.y() += max_val - min_val;
991	>	break;
992	>	case rnemdPz:
993	>	momentumExchange_.z() += max_val - min_val;
994	>	break;
995	>	default:
996	>	break;
997	>	}
998	>	} else {
999	>	sprintf(painCave.errMsg,
1000	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
1001	>	painCave.isFatal = 0;
1002	>	painCave.severity = OPENMD_INFO;
1003	>	simError();
1004	>	failTrialCount_++;
1005	>	}
1006	>	} else {
1007	>	sprintf(painCave.errMsg,
1008	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
1009	>	"\twas not present in at least one of the two slabs.\n");
1010	>	painCave.isFatal = 0;
1011	>	painCave.severity = OPENMD_INFO;
1012	>	simError();
1013	>	failTrialCount_++;
1014	>	}
1015	>	}
1016	>
1017	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
1018	>	if (!doRNEMD_) return;
1019	>	int selei;
1020	>	int selej;
1021	>
1022	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1023	>	RealType time = currentSnap_->getTime();
1024	>	Mat3x3d hmat = currentSnap_->getHmat();
1025	>
1026	>	StuntDouble* sd;
1027	>
1028	>	vector<StuntDouble*> hotBin, coldBin;
1029	>
1030	>	RealType Phx = 0.0;
1031	>	RealType Phy = 0.0;
1032	>	RealType Phz = 0.0;
1033	>	RealType Khx = 0.0;
1034	>	RealType Khy = 0.0;
1035	>	RealType Khz = 0.0;
1036	>	RealType Khw = 0.0;
1037	>	RealType Pcx = 0.0;
1038	>	RealType Pcy = 0.0;
1039	>	RealType Pcz = 0.0;
1040	>	RealType Kcx = 0.0;
1041	>	RealType Kcy = 0.0;
1042	>	RealType Kcz = 0.0;
1043	>	RealType Kcw = 0.0;
1044	>
1045	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1046	>	sd = smanA.nextSelected(selei)) {
1047	>
1048	>	Vector3d pos = sd->getPos();
1049	>
1050	>	// wrap the stuntdouble's position back into the box:
1051	>
1052	>	if (usePeriodicBoundaryConditions_)
1053	>	currentSnap_->wrapVector(pos);
1054	>
1055	>
1056	>	RealType mass = sd->getMass();
1057	>	Vector3d vel = sd->getVel();
1058	>
1059	>	hotBin.push_back(sd);
1060	>	Phx += mass * vel.x();
1061	>	Phy += mass * vel.y();
1062	>	Phz += mass * vel.z();
1063	>	Khx += mass * vel.x() * vel.x();
1064	>	Khy += mass * vel.y() * vel.y();
1065	>	Khz += 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	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1074	>	angMom[k] * angMom[k] / I(k, k);
1075	>	} else {
1076	>	Khw += 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	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1083	>	sd = smanB.nextSelected(selej)) {
1084	>	Vector3d pos = sd->getPos();
1085	>
1086	>	// wrap the stuntdouble's position back into the box:
1087	>
1088	>	if (usePeriodicBoundaryConditions_)
1089	>	currentSnap_->wrapVector(pos);
1090	>
1091	>	RealType mass = sd->getMass();
1092	>	Vector3d vel = sd->getVel();
1093	>
1094	>	coldBin.push_back(sd);
1095	>	Pcx += mass * vel.x();
1096	>	Pcy += mass * vel.y();
1097	>	Pcz += mass * vel.z();
1098	>	Kcx += mass * vel.x() * vel.x();
1099	>	Kcy += mass * vel.y() * vel.y();
1100	>	Kcz += mass * vel.z() * vel.z();
1101	>	if (sd->isDirectional()) {
1102	>	Vector3d angMom = sd->getJ();
1103	>	Mat3x3d I = sd->getI();
1104	>	if (sd->isLinear()) {
1105	>	int i = sd->linearAxis();
1106	>	int j = (i + 1) % 3;
1107	>	int k = (i + 2) % 3;
1108	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1109	>	angMom[k] * angMom[k] / I(k, k);
1110	>	} else {
1111	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1112	>	+ angMom[1]*angMom[1]/I(1, 1)
1113	>	+ angMom[2]*angMom[2]/I(2, 2);
1114	>	}
1115	>	}
1116	>	}
1117	>
1118	>	Khx *= 0.5;
1119	>	Khy *= 0.5;
1120	>	Khz *= 0.5;
1121	>	Khw *= 0.5;
1122	>	Kcx *= 0.5;
1123	>	Kcy *= 0.5;
1124	>	Kcz *= 0.5;
1125	>	Kcw *= 0.5;
1126	>
1127	>	#ifdef IS_MPI
1128	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1129	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1131	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1132	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1133	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1134	>
1135	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1136	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1137	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1138	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1139	>
1140	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1141	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1142	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1143	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1144	>	#endif
1145	>
1146	>	//solve coldBin coeff's first
1147	>	RealType px = Pcx / Phx;
1148	>	RealType py = Pcy / Phy;
1149	>	RealType pz = Pcz / Phz;
1150	>	RealType c, x, y, z;
1151	>	bool successfulScale = false;
1152	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1153	>	(rnemdFluxType_ == rnemdRotKE)) {
1154	>	//may need sanity check Khw & Kcw > 0
1155	>
1156	>	if (rnemdFluxType_ == rnemdFullKE) {
1157	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1158	>	} else {
1159	>	c = 1.0 - kineticTarget_ / Kcw;
1160	>	}
1161	>
1162	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1163	>	c = sqrt(c);
1164	>
1165	>	RealType w = 0.0;
1166	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1167	>	x = 1.0 + px * (1.0 - c);
1168	>	y = 1.0 + py * (1.0 - c);
1169	>	z = 1.0 + pz * (1.0 - c);
1170	>	/* more complicated way
1171	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1172	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1173	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1174	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1175	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1176	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1177	>	*/
1178	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1179	>	(fabs(z - 1.0) < 0.1)) {
1180	>	w = 1.0 + (kineticTarget_
1181	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1182	>	+ Khz * (1.0 - z * z)) / Khw;
1183	>	}//no need to calculate w if x, y or z is out of range
1184	>	} else {
1185	>	w = 1.0 + kineticTarget_ / Khw;
1186	>	}
1187	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1188	>	//if w is in the right range, so should be x, y, z.
1189	>	vector<StuntDouble*>::iterator sdi;
1190	>	Vector3d vel;
1191	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1192	>	if (rnemdFluxType_ == rnemdFullKE) {
1193	>	vel = (*sdi)->getVel() * c;
1194	>	(*sdi)->setVel(vel);
1195	>	}
1196	>	if ((*sdi)->isDirectional()) {
1197	>	Vector3d angMom = (*sdi)->getJ() * c;
1198	>	(*sdi)->setJ(angMom);
1199	>	}
1200	>	}
1201	>	w = sqrt(w);
1202	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1203	>	if (rnemdFluxType_ == rnemdFullKE) {
1204	>	vel = (*sdi)->getVel();
1205	>	vel.x() *= x;
1206	>	vel.y() *= y;
1207	>	vel.z() *= z;
1208	>	(*sdi)->setVel(vel);
1209	>	}
1210	>	if ((*sdi)->isDirectional()) {
1211	>	Vector3d angMom = (*sdi)->getJ() * w;
1212	>	(*sdi)->setJ(angMom);
1213	>	}
1214	>	}
1215	>	successfulScale = true;
1216	>	kineticExchange_ += kineticTarget_;
1217	>	}
1218	>	}
1219	>	} else {
1220	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1221	>	switch(rnemdFluxType_) {
1222	>	case rnemdKE :
1223	>	/* used hotBin coeff's & only scale x & y dimensions
1224	>	RealType px = Phx / Pcx;
1225	>	RealType py = Phy / Pcy;
1226	>	a110 = Khy;
1227	>	c0 = - Khx - Khy - kineticTarget_;
1228	>	a000 = Khx;
1229	>	a111 = Kcy * py * py;
1230	>	b11 = -2.0 * Kcy * py * (1.0 + py);
1231	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1232	>	b01 = -2.0 * Kcx * px * (1.0 + px);
1233	>	a001 = Kcx * px * px;
1234	>	*/
1235	>	//scale all three dimensions, let c_x = c_y
1236	>	a000 = Kcx + Kcy;
1237	>	a110 = Kcz;
1238	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1239	>	a001 = Khx * px * px + Khy * py * py;
1240	>	a111 = Khz * pz * pz;
1241	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1242	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1243	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1244	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1245	>	break;
1246	>	case rnemdPx :
1247	>	c = 1 - momentumTarget_.x() / Pcx;
1248	>	a000 = Kcy;
1249	>	a110 = Kcz;
1250	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1251	>	a001 = py * py * Khy;
1252	>	a111 = pz * pz * Khz;
1253	>	b01 = -2.0 * Khy * py * (1.0 + py);
1254	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1255	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1256	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1257	>	break;
1258	>	case rnemdPy :
1259	>	c = 1 - momentumTarget_.y() / Pcy;
1260	>	a000 = Kcx;
1261	>	a110 = Kcz;
1262	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1263	>	a001 = px * px * Khx;
1264	>	a111 = pz * pz * Khz;
1265	>	b01 = -2.0 * Khx * px * (1.0 + px);
1266	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1267	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1268	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1269	>	break;
1270	>	case rnemdPz ://we don't really do this, do we?
1271	>	c = 1 - momentumTarget_.z() / Pcz;
1272	>	a000 = Kcx;
1273	>	a110 = Kcy;
1274	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1275	>	a001 = px * px * Khx;
1276	>	a111 = py * py * Khy;
1277	>	b01 = -2.0 * Khx * px * (1.0 + px);
1278	>	b11 = -2.0 * Khy * py * (1.0 + py);
1279	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1280	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1281	>	break;
1282	>	default :
1283	>	break;
1284	>	}
1285	>
1286	>	RealType v1 = a000 * a111 - a001 * a110;
1287	>	RealType v2 = a000 * b01;
1288	>	RealType v3 = a000 * b11;
1289	>	RealType v4 = a000 * c1 - a001 * c0;
1290	>	RealType v8 = a110 * b01;
1291	>	RealType v10 = - b01 * c0;
1292	>
1293	>	RealType u0 = v2 * v10 - v4 * v4;
1294	>	RealType u1 = -2.0 * v3 * v4;
1295	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1296	>	RealType u3 = -2.0 * v1 * v3;
1297	>	RealType u4 = - v1 * v1;
1298	>	//rescale coefficients
1299	>	RealType maxAbs = fabs(u0);
1300	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1301	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1302	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1303	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1304	>	u0 /= maxAbs;
1305	>	u1 /= maxAbs;
1306	>	u2 /= maxAbs;
1307	>	u3 /= maxAbs;
1308	>	u4 /= maxAbs;
1309	>	//max_element(start, end) is also available.
1310	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1311	>	poly.setCoefficient(4, u4);
1312	>	poly.setCoefficient(3, u3);
1313	>	poly.setCoefficient(2, u2);
1314	>	poly.setCoefficient(1, u1);
1315	>	poly.setCoefficient(0, u0);
1316	>	vector<RealType> realRoots = poly.FindRealRoots();
1317	>
1318	>	vector<RealType>::iterator ri;
1319	>	RealType r1, r2, alpha0;
1320	>	vector<pair<RealType,RealType> > rps;
1321	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1322	>	r2 = *ri;
1323	>	//check if FindRealRoots() give the right answer
1324	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1325	>	sprintf(painCave.errMsg,
1326	>	"RNEMD Warning: polynomial solve seems to have an error!");
1327	>	painCave.isFatal = 0;
1328	>	simError();
1329	>	failRootCount_++;
1330	>	}
1331	>	//might not be useful w/o rescaling coefficients
1332	>	alpha0 = -c0 - a110 * r2 * r2;
1333	>	if (alpha0 >= 0.0) {
1334	>	r1 = sqrt(alpha0 / a000);
1335	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1336	>	< 1e-6)
1337	>	{ rps.push_back(make_pair(r1, r2)); }
1338	>	if (r1 > 1e-6) { //r1 non-negative
1339	>	r1 = -r1;
1340	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1341	>	< 1e-6)
1342	>	{ rps.push_back(make_pair(r1, r2)); }
1343	>	}
1344	>	}
1345	>	}
1346	>	// Consider combining together the solving pair part w/ the searching
1347	>	// best solution part so that we don't need the pairs vector
1348	>	if (!rps.empty()) {
1349	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1350	>	RealType diff;
1351	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1352	>	vector<pair<RealType,RealType> >::iterator rpi;
1353	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1354	>	r1 = (*rpi).first;
1355	>	r2 = (*rpi).second;
1356	>	switch(rnemdFluxType_) {
1357	>	case rnemdKE :
1358	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1359	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1360	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1361	>	break;
1362	>	case rnemdPx :
1363	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1364	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1365	>	break;
1366	>	case rnemdPy :
1367	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1368	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1369	>	break;
1370	>	case rnemdPz :
1371	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1372	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1373	>	default :
1374	>	break;
1375	>	}
1376	>	if (diff < smallestDiff) {
1377	>	smallestDiff = diff;
1378	>	bestPair = *rpi;
1379	>	}
1380	>	}
1381	>	#ifdef IS_MPI
1382	>	if (worldRank == 0) {
1383	>	#endif
1384	>	// sprintf(painCave.errMsg,
1385	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1386	>	//         bestPair.first, bestPair.second);
1387	>	// painCave.isFatal = 0;
1388	>	// painCave.severity = OPENMD_INFO;
1389	>	// simError();
1390	>	#ifdef IS_MPI
1391	>	}
1392	>	#endif
1393	>
1394	>	switch(rnemdFluxType_) {
1395	>	case rnemdKE :
1396	>	x = bestPair.first;
1397	>	y = bestPair.first;
1398	>	z = bestPair.second;
1399	>	break;
1400	>	case rnemdPx :
1401	>	x = c;
1402	>	y = bestPair.first;
1403	>	z = bestPair.second;
1404	>	break;
1405	>	case rnemdPy :
1406	>	x = bestPair.first;
1407	>	y = c;
1408	>	z = bestPair.second;
1409	>	break;
1410	>	case rnemdPz :
1411	>	x = bestPair.first;
1412	>	y = bestPair.second;
1413	>	z = c;
1414	>	break;
1415	>	default :
1416	>	break;
1417	>	}
1418	>	vector<StuntDouble*>::iterator sdi;
1419	>	Vector3d vel;
1420	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1421	>	vel = (*sdi)->getVel();
1422	>	vel.x() *= x;
1423	>	vel.y() *= y;
1424	>	vel.z() *= z;
1425	>	(*sdi)->setVel(vel);
1426	>	}
1427	>	//convert to hotBin coefficient
1428	>	x = 1.0 + px * (1.0 - x);
1429	>	y = 1.0 + py * (1.0 - y);
1430	>	z = 1.0 + pz * (1.0 - z);
1431	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1432	>	vel = (*sdi)->getVel();
1433	>	vel.x() *= x;
1434	>	vel.y() *= y;
1435	>	vel.z() *= z;
1436	>	(*sdi)->setVel(vel);
1437	>	}
1438	>	successfulScale = true;
1439	>	switch(rnemdFluxType_) {
1440	>	case rnemdKE :
1441	>	kineticExchange_ += kineticTarget_;
1442	>	break;
1443	>	case rnemdPx :
1444	>	case rnemdPy :
1445	>	case rnemdPz :
1446	>	momentumExchange_ += momentumTarget_;
1447	>	break;
1448	>	default :
1449	>	break;
1450	>	}
1451	>	}
1452	>	}
1453	>	if (successfulScale != true) {
1454	>	sprintf(painCave.errMsg,
1455	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1456	>	"\tthe constraint equations may not exist or there may be\n"
1457	>	"\tno selected objects in one or both slabs.\n");
1458	>	painCave.isFatal = 0;
1459	>	painCave.severity = OPENMD_INFO;
1460	>	simError();
1461	>	failTrialCount_++;
1462	>	}
1463	>	}
1464	>
1465	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1466	>	if (!doRNEMD_) return;
1467	>	int selei;
1468	>	int selej;
1469	>
1470	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1471	>	RealType time = currentSnap_->getTime();
1472	>	Mat3x3d hmat = currentSnap_->getHmat();
1473	>
1474	>	StuntDouble* sd;
1475	>
1476	>	vector<StuntDouble*> hotBin, coldBin;
1477	>
1478	>	Vector3d Ph(V3Zero);
1479	>	Vector3d Lh(V3Zero);
1480	>	RealType Mh = 0.0;
1481	>	Mat3x3d Ih(0.0);
1482	>	RealType Kh = 0.0;
1483	>	Vector3d Pc(V3Zero);
1484	>	Vector3d Lc(V3Zero);
1485	>	RealType Mc = 0.0;
1486	>	Mat3x3d Ic(0.0);
1487	>	RealType Kc = 0.0;
1488	>
1489	>	// Constraints can be on only the linear or angular momentum, but
1490	>	// not both.  Usually, the user will specify which they want, but
1491	>	// in case they don't, the use of periodic boundaries should make
1492	>	// the choice for us.
1493	>	bool doLinearPart = false;
1494	>	bool doAngularPart = false;
1495	>
1496	>	switch (rnemdFluxType_) {
1497	>	case rnemdPx:
1498	>	case rnemdPy:
1499	>	case rnemdPz:
1500	>	case rnemdPvector:
1501	>	case rnemdKePx:
1502	>	case rnemdKePy:
1503	>	case rnemdKePvector:
1504	>	doLinearPart = true;
1505	>	break;
1506	>	case rnemdLx:
1507	>	case rnemdLy:
1508	>	case rnemdLz:
1509	>	case rnemdLvector:
1510	>	case rnemdKeLx:
1511	>	case rnemdKeLy:
1512	>	case rnemdKeLz:
1513	>	case rnemdKeLvector:
1514	>	doAngularPart = true;
1515	>	break;
1516	>	case rnemdKE:
1517	>	case rnemdRotKE:
1518	>	case rnemdFullKE:
1519	>	default:
1520	>	if (usePeriodicBoundaryConditions_)
1521	>	doLinearPart = true;
1522	>	else
1523	>	doAngularPart = true;
1524	>	break;
1525	>	}
1526	>
1527	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1528	>	sd = smanA.nextSelected(selei)) {
1529	>
1530	>	Vector3d pos = sd->getPos();
1531	>
1532	>	// wrap the stuntdouble's position back into the box:
1533	>
1534	>	if (usePeriodicBoundaryConditions_)
1535	>	currentSnap_->wrapVector(pos);
1536	>
1537	>	RealType mass = sd->getMass();
1538	>	Vector3d vel = sd->getVel();
1539	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1540	>	RealType r2;
1541	>
1542	>	hotBin.push_back(sd);
1543	>	Ph += mass * vel;
1544	>	Mh += mass;
1545	>	Kh += mass * vel.lengthSquare();
1546	>	Lh += mass * cross(rPos, vel);
1547	>	Ih -= outProduct(rPos, rPos) * mass;
1548	>	r2 = rPos.lengthSquare();
1549	>	Ih(0, 0) += mass * r2;
1550	>	Ih(1, 1) += mass * r2;
1551	>	Ih(2, 2) += mass * r2;
1552	>
1553	>	if (rnemdFluxType_ == rnemdFullKE) {
1554	>	if (sd->isDirectional()) {
1555	>	Vector3d angMom = sd->getJ();
1556	>	Mat3x3d I = sd->getI();
1557	>	if (sd->isLinear()) {
1558	>	int i = sd->linearAxis();
1559	>	int j = (i + 1) % 3;
1560	>	int k = (i + 2) % 3;
1561	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1562	>	angMom[k] * angMom[k] / I(k, k);
1563	>	} else {
1564	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1565	>	angMom[1] * angMom[1] / I(1, 1) +
1566	>	angMom[2] * angMom[2] / I(2, 2);
1567	>	}
1568	>	}
1569	>	}
1570	>	}
1571	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1572	>	sd = smanB.nextSelected(selej)) {
1573	>
1574	>	Vector3d pos = sd->getPos();
1575	>
1576	>	// wrap the stuntdouble's position back into the box:
1577	>
1578	>	if (usePeriodicBoundaryConditions_)
1579	>	currentSnap_->wrapVector(pos);
1580	>
1581	>	RealType mass = sd->getMass();
1582	>	Vector3d vel = sd->getVel();
1583	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1584	>	RealType r2;
1585	>
1586	>	coldBin.push_back(sd);
1587	>	Pc += mass * vel;
1588	>	Mc += mass;
1589	>	Kc += mass * vel.lengthSquare();
1590	>	Lc += mass * cross(rPos, vel);
1591	>	Ic -= outProduct(rPos, rPos) * mass;
1592	>	r2 = rPos.lengthSquare();
1593	>	Ic(0, 0) += mass * r2;
1594	>	Ic(1, 1) += mass * r2;
1595	>	Ic(2, 2) += mass * r2;
1596	>
1597	>	if (rnemdFluxType_ == rnemdFullKE) {
1598	>	if (sd->isDirectional()) {
1599	>	Vector3d angMom = sd->getJ();
1600	>	Mat3x3d I = sd->getI();
1601	>	if (sd->isLinear()) {
1602	>	int i = sd->linearAxis();
1603	>	int j = (i + 1) % 3;
1604	>	int k = (i + 2) % 3;
1605	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1606	>	angMom[k] * angMom[k] / I(k, k);
1607	>	} else {
1608	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1609	>	angMom[1] * angMom[1] / I(1, 1) +
1610	>	angMom[2] * angMom[2] / I(2, 2);
1611	>	}
1612	>	}
1613	>	}
1614	>	}
1615	>
1616	>	Kh *= 0.5;
1617	>	Kc *= 0.5;
1618	>
1619	>	#ifdef IS_MPI
1620	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1621	>	MPI_COMM_WORLD);
1622	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1623	>	MPI_COMM_WORLD);
1624	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1625	>	MPI_COMM_WORLD);
1626	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1627	>	MPI_COMM_WORLD);
1628	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1629	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1630	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1631	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1632	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1633	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1634	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1635	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1636	>	#endif
1637	>
1638	>
1639	>	Vector3d ac, acrec, bc, bcrec;
1640	>	Vector3d ah, ahrec, bh, bhrec;
1641	>
1642	>	bool successfulExchange = false;
1643	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1644	>	Vector3d vc = Pc / Mc;
1645	>	ac = -momentumTarget_ / Mc + vc;
1646	>	acrec = -momentumTarget_ / Mc;
1647	>
1648	>	// We now need the inverse of the inertia tensor to calculate the
1649	>	// angular velocity of the cold slab;
1650	>	Mat3x3d Ici = Ic.inverse();
1651	>	Vector3d omegac = Ici * Lc;
1652	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1653	>	bcrec = bc - omegac;
1654	>
1655	>	RealType cNumerator = Kc - kineticTarget_;
1656	>	if (doLinearPart)
1657	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1658	>
1659	>	if (doAngularPart)
1660	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1661	>
1662	>	if (cNumerator > 0.0) {
1663	>
1664	>	RealType cDenominator = Kc;
1665	>
1666	>	if (doLinearPart)
1667	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1668	>
1669	>	if (doAngularPart)
1670	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1671	>
1672	>	if (cDenominator > 0.0) {
1673	>	RealType c = sqrt(cNumerator / cDenominator);
1674	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1675	>
1676	>	Vector3d vh = Ph / Mh;
1677	>	ah = momentumTarget_ / Mh + vh;
1678	>	ahrec = momentumTarget_ / Mh;
1679	>
1680	>	// We now need the inverse of the inertia tensor to
1681	>	// calculate the angular velocity of the hot slab;
1682	>	Mat3x3d Ihi = Ih.inverse();
1683	>	Vector3d omegah = Ihi * Lh;
1684	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1685	>	bhrec = bh - omegah;
1686	>
1687	>	RealType hNumerator = Kh + kineticTarget_;
1688	>	if (doLinearPart)
1689	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1690	>
1691	>	if (doAngularPart)
1692	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1693	>
1694	>	if (hNumerator > 0.0) {
1695	>
1696	>	RealType hDenominator = Kh;
1697	>	if (doLinearPart)
1698	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1699	>	if (doAngularPart)
1700	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1701	>
1702	>	if (hDenominator > 0.0) {
1703	>	RealType h = sqrt(hNumerator / hDenominator);
1704	>	if ((h > 0.9) && (h < 1.1)) {
1705	>
1706	>	vector<StuntDouble*>::iterator sdi;
1707	>	Vector3d vel;
1708	>	Vector3d rPos;
1709	>
1710	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1711	>	//vel = (*sdi)->getVel();
1712	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1713	>	if (doLinearPart)
1714	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1715	>	if (doAngularPart)
1716	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1717	>
1718	>	(*sdi)->setVel(vel);
1719	>	if (rnemdFluxType_ == rnemdFullKE) {
1720	>	if ((*sdi)->isDirectional()) {
1721	>	Vector3d angMom = (*sdi)->getJ() * c;
1722	>	(*sdi)->setJ(angMom);
1723	>	}
1724	>	}
1725	>	}
1726	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1727	>	//vel = (*sdi)->getVel();
1728	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1729	>	if (doLinearPart)
1730	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1731	>	if (doAngularPart)
1732	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1733	>
1734	>	(*sdi)->setVel(vel);
1735	>	if (rnemdFluxType_ == rnemdFullKE) {
1736	>	if ((*sdi)->isDirectional()) {
1737	>	Vector3d angMom = (*sdi)->getJ() * h;
1738	>	(*sdi)->setJ(angMom);
1739	>	}
1740	>	}
1741	>	}
1742	>	successfulExchange = true;
1743	>	kineticExchange_ += kineticTarget_;
1744	>	momentumExchange_ += momentumTarget_;
1745	>	angularMomentumExchange_ += angularMomentumTarget_;
1746	>	}
1747	>	}
1748	>	}
1749	>	}
1750	>	}
1751	>	}
1752	>	}
1753	>	if (successfulExchange != true) {
1754	>	sprintf(painCave.errMsg,
1755	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1756	>	"\tthe constraint equations may not exist or there may be\n"
1757	>	"\tno selected objects in one or both slabs.\n");
1758	>	painCave.isFatal = 0;
1759	>	painCave.severity = OPENMD_INFO;
1760	>	simError();
1761	>	failTrialCount_++;
1762	>	}
1763	>	}
1764	>
1765	>	RealType RNEMD::getDividingArea() {
1766	>
1767	>	if (hasDividingArea_) return dividingArea_;
1768	>
1769	>	RealType areaA, areaB;
1770	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1771	>
1772	>	if (hasSelectionA_) {
1773	>
1774	>	if (evaluatorA_.hasSurfaceArea())
1775	>	areaA = evaluatorA_.getSurfaceArea();
1776	>	else {
1777	>
1778	>	int isd;
1779	>	StuntDouble* sd;
1780	>	vector<StuntDouble*> aSites;
1781	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1782	>	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1783	>	sd = seleManA_.nextSelected(isd)) {
1784	>	aSites.push_back(sd);
1785	>	}
1786	>	#if defined(HAVE_QHULL)
1787	>	ConvexHull* surfaceMeshA = new ConvexHull();
1788	>	surfaceMeshA->computeHull(aSites);
1789	>	areaA = surfaceMeshA->getArea();
1790	>	delete surfaceMeshA;
1791	>	#else
1792	>	sprintf( painCave.errMsg,
1793	>	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1794	>	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1795	>	painCave.severity = OPENMD_ERROR;
1796	>	painCave.isFatal = 1;
1797	>	simError();
1798	>	#endif
1799	>	}
1800	>
1801	>	} else {
1802	>	if (usePeriodicBoundaryConditions_) {
1803	>	// in periodic boundaries, the surface area is twice the x-y
1804	>	// area of the current box:
1805	>	areaA = 2.0 * snap->getXYarea();
1806	>	} else {
1807	>	// in non-periodic simulations, without explicitly setting
1808	>	// selections, the sphere radius sets the surface area of the
1809	>	// dividing surface:
1810	>	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1811	>	}
1812	>	}
1813	>
1814	>	if (hasSelectionB_) {
1815	>	if (evaluatorB_.hasSurfaceArea()) {
1816	>	areaB = evaluatorB_.getSurfaceArea();
1817	>	} else {
1818	>
1819	>	int isd;
1820	>	StuntDouble* sd;
1821	>	vector<StuntDouble*> bSites;
1822	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1823	>	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1824	>	sd = seleManB_.nextSelected(isd)) {
1825	>	bSites.push_back(sd);
1826	>	}
1827	>
1828	>	#if defined(HAVE_QHULL)
1829	>	ConvexHull* surfaceMeshB = new ConvexHull();
1830	>	surfaceMeshB->computeHull(bSites);
1831	>	areaB = surfaceMeshB->getArea();
1832	>	delete surfaceMeshB;
1833	>	#else
1834	>	sprintf( painCave.errMsg,
1835	>	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1836	>	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1837	>	painCave.severity = OPENMD_ERROR;
1838	>	painCave.isFatal = 1;
1839	>	simError();
1840	>	#endif
1841	>	}
1842	>
1843	>	} else {
1844	>	if (usePeriodicBoundaryConditions_) {
1845	>	// in periodic boundaries, the surface area is twice the x-y
1846	>	// area of the current box:
1847	>	areaB = 2.0 * snap->getXYarea();
1848	>	} else {
1849	>	// in non-periodic simulations, without explicitly setting
1850	>	// selections, but if a sphereBradius has been set, just use that:
1851	>	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1852	>	}
1853	>	}
1854	>
1855	>	dividingArea_ = min(areaA, areaB);
1856	>	hasDividingArea_ = true;
1857	>	return dividingArea_;
1858	>	}
1859	>
1860	>	void RNEMD::doRNEMD() {
1861	>	if (!doRNEMD_) return;
1862	>	trialCount_++;
1863	>
1864	>	// object evaluator:
1865	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1866	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1867	>
1868	>	evaluatorA_.loadScriptString(selectionA_);
1869	>	evaluatorB_.loadScriptString(selectionB_);
1870	>
1871	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1872	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1873	>
1874	>	commonA_ = seleManA_ & seleMan_;
1875	>	commonB_ = seleManB_ & seleMan_;
1876	>
1877	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1878	>	// dt = exchange time interval
1879	>	// flux = target flux
1880	>	// dividingArea = smallest dividing surface between the two regions
1881	>
1882	>	hasDividingArea_ = false;
1883	>	RealType area = getDividingArea();
1884	>
1885	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1886	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1887	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1888	>
1889	>	switch(rnemdMethod_) {
1890	>	case rnemdSwap:
1891	>	doSwap(commonA_, commonB_);
1892	>	break;
1893	>	case rnemdNIVS:
1894	>	doNIVS(commonA_, commonB_);
1895	>	break;
1896	>	case rnemdVSS:
1897	>	doVSS(commonA_, commonB_);
1898	>	break;
1899	>	case rnemdUnkownMethod:
1900	>	default :
1901	>	break;
1902	>	}
1903	>	}
1904	>
1905	>	void RNEMD::collectData() {
1906	>	if (!doRNEMD_) return;
1907	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1908	>
1909	>	// collectData can be called more frequently than the doRNEMD, so use the
1910	>	// computed area from the last exchange time:
1911	>	RealType area = getDividingArea();
1912	>	areaAccumulator_->add(area);
1913	>	Mat3x3d hmat = currentSnap_->getHmat();
1914	>	Vector3d u = angularMomentumFluxVector_;
1915	>	u.normalize();
1916	>
1917	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1918	>
1919	>	int selei(0);
1920	>	StuntDouble* sd;
1921	>	int binNo;
1922	>	RealType mass;
1923	>	Vector3d vel;
1924	>	Vector3d rPos;
1925	>	RealType KE;
1926	>	Vector3d L;
1927	>	Mat3x3d I;
1928	>	RealType r2;
1929	>
1930	>	vector<RealType> binMass(nBins_, 0.0);
1931	>	vector<Vector3d> binP(nBins_, V3Zero);
1932	>	vector<RealType> binOmega(nBins_, 0.0);
1933	>	vector<Vector3d> binL(nBins_, V3Zero);
1934	>	vector<Mat3x3d>  binI(nBins_);
1935	>	vector<RealType> binKE(nBins_, 0.0);
1936	>	vector<int> binDOF(nBins_, 0);
1937	>	vector<int> binCount(nBins_, 0);
1938	>
1939	>	// alternative approach, track all molecules instead of only those
1940	>	// selected for scaling/swapping:
1941	>	/*
1942	>	SimInfo::MoleculeIterator miter;
1943	>	vector<StuntDouble*>::iterator iiter;
1944	>	Molecule* mol;
1945	>	StuntDouble* sd;
1946	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1947	>	mol = info_->nextMolecule(miter))
1948	>	sd is essentially sd
1949	>	for (sd = mol->beginIntegrableObject(iiter);
1950	>	sd != NULL;
1951	>	sd = mol->nextIntegrableObject(iiter))
1952	>	*/
1953	>
1954	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1955	>	sd = seleMan_.nextSelected(selei)) {
1956	>
1957	>	Vector3d pos = sd->getPos();
1958	>
1959	>	// wrap the stuntdouble's position back into the box:
1960	>
1961	>	if (usePeriodicBoundaryConditions_) {
1962	>	currentSnap_->wrapVector(pos);
1963	>	// which bin is this stuntdouble in?
1964	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1965	>	// Shift molecules by half a box to have bins start at 0
1966	>	// The modulo operator is used to wrap the case when we are
1967	>	// beyond the end of the bins back to the beginning.
1968	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1969	>	} else {
1970	>	Vector3d rPos = pos - coordinateOrigin_;
1971	>	binNo = int(rPos.length() / binWidth_);
1972	>	}
1973	>
1974	>	mass = sd->getMass();
1975	>	vel = sd->getVel();
1976	>	rPos = sd->getPos() - coordinateOrigin_;
1977	>	KE = 0.5 * mass * vel.lengthSquare();
1978	>	L = mass * cross(rPos, vel);
1979	>	I = outProduct(rPos, rPos) * mass;
1980	>	r2 = rPos.lengthSquare();
1981	>	I(0, 0) += mass * r2;
1982	>	I(1, 1) += mass * r2;
1983	>	I(2, 2) += mass * r2;
1984	>
1985	>	// Project the relative position onto a plane perpendicular to
1986	>	// the angularMomentumFluxVector:
1987	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1988	>	// Project the velocity onto a plane perpendicular to the
1989	>	// angularMomentumFluxVector:
1990	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1991	>	// Compute angular velocity vector (should be nearly parallel to
1992	>	// angularMomentumFluxVector
1993	>	// Vector3d aVel = cross(rProj, vProj);
1994	>
1995	>	if (binNo >= 0 && binNo < nBins_)  {
1996	>	binCount[binNo]++;
1997	>	binMass[binNo] += mass;
1998	>	binP[binNo] += mass*vel;
1999	>	binKE[binNo] += KE;
2000	>	binI[binNo] += I;
2001	>	binL[binNo] += L;
2002	>	binDOF[binNo] += 3;
2003	>
2004	>	if (sd->isDirectional()) {
2005	>	Vector3d angMom = sd->getJ();
2006	>	Mat3x3d Ia = sd->getI();
2007	>	if (sd->isLinear()) {
2008	>	int i = sd->linearAxis();
2009	>	int j = (i + 1) % 3;
2010	>	int k = (i + 2) % 3;
2011	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
2012	>	angMom[k] * angMom[k] / Ia(k, k));
2013	>	binDOF[binNo] += 2;
2014	>	} else {
2015	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
2016	>	angMom[1] * angMom[1] / Ia(1, 1) +
2017	>	angMom[2] * angMom[2] / Ia(2, 2));
2018	>	binDOF[binNo] += 3;
2019	>	}
2020	>	}
2021	>	}
2022	>	}
2023	>
2024	>	#ifdef IS_MPI
2025	>
2026	>	for (int i = 0; i < nBins_; i++) {
2027	>
2028	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
2029	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2030	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2031	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2032	>	MPI_Allreduce(MPI_IN_PLACE, binP[i].getArrayPointer(),
2033	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2034	>	MPI_Allreduce(MPI_IN_PLACE, binL[i].getArrayPointer(),
2035	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2036	>	MPI_Allreduce(MPI_IN_PLACE, binI[i].getArrayPointer(),
2037	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2038	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2039	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2040	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2041	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2042	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2043	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2044	>	}
2045	>
2046	>	#endif
2047	>
2048	>	Vector3d omega;
2049	>	RealType den;
2050	>	RealType temp;
2051	>	RealType z;
2052	>	RealType r;
2053	>	for (int i = 0; i < nBins_; i++) {
2054	>	if (usePeriodicBoundaryConditions_) {
2055	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2056	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2057	>	/ currentSnap_->getVolume() ;
2058	>	} else {
2059	>	r = (((RealType)i + 0.5) * binWidth_);
2060	>	RealType rinner = (RealType)i * binWidth_;
2061	>	RealType router = (RealType)(i+1) * binWidth_;
2062	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2063	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2064	>	}
2065	>	vel = binP[i] / binMass[i];
2066	>
2067	>	omega = binI[i].inverse() * binL[i];
2068	>
2069	>	// omega = binOmega[i] / binCount[i];
2070	>
2071	>	if (binCount[i] > 0) {
2072	>	// only add values if there are things to add
2073	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2074	>	PhysicalConstants::energyConvert);
2075	>
2076	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2077	>	if(outputMask_[j]) {
2078	>	switch(j) {
2079	>	case Z:
2080	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2081	>	break;
2082	>	case R:
2083	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2084	>	break;
2085	>	case TEMPERATURE:
2086	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2087	>	break;
2088	>	case VELOCITY:
2089	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2090	>	break;
2091	>	case ANGULARVELOCITY:
2092	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2093	>	break;
2094	>	case DENSITY:
2095	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2096	>	break;
2097	>	}
2098	>	}
2099	>	}
2100	>	}
2101	>	}
2102	>	hasData_ = true;
2103	>	}
2104	>
2105	>	void RNEMD::getStarted() {
2106	>	if (!doRNEMD_) return;
2107	>	hasDividingArea_ = false;
2108	>	collectData();
2109	>	writeOutputFile();
2110	>	}
2111	>
2112	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2113	>	if (!doRNEMD_) return;
2114	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2115	>
2116	>	while(tokenizer.hasMoreTokens()) {
2117	>	std::string token(tokenizer.nextToken());
2118	>	toUpper(token);
2119	>	OutputMapType::iterator i = outputMap_.find(token);
2120	>	if (i != outputMap_.end()) {
2121	>	outputMask_.set(i->second);
2122	>	} else {
2123	>	sprintf( painCave.errMsg,
2124	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2125	>	"\toutputFileFormat keyword.\n", token.c_str() );
2126	>	painCave.isFatal = 0;
2127	>	painCave.severity = OPENMD_ERROR;
2128	>	simError();
2129	>	}
2130	>	}
2131	>	}
2132	>
2133	>	void RNEMD::writeOutputFile() {
2134	>	if (!doRNEMD_) return;
2135	>	if (!hasData_) return;
2136	>
2137	>	#ifdef IS_MPI
2138	>	// If we're the root node, should we print out the results
2139	>	int worldRank;
2140	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2141	>
2142	>	if (worldRank == 0) {
2143	>	#endif
2144	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2145	>
2146	>	if( !rnemdFile_ ){
2147	>	sprintf( painCave.errMsg,
2148	>	"Could not open \"%s\" for RNEMD output.\n",
2149	>	rnemdFileName_.c_str());
2150	>	painCave.isFatal = 1;
2151	>	simError();
2152	>	}
2153	>
2154	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2155	>
2156	>	RealType time = currentSnap_->getTime();
2157	>	RealType avgArea;
2158	>	areaAccumulator_->getAverage(avgArea);
2159	>
2160	>	RealType Jz(0.0);
2161	>	Vector3d JzP(V3Zero);
2162	>	Vector3d JzL(V3Zero);
2163	>	if (time >= info_->getSimParams()->getDt()) {
2164	>	Jz = kineticExchange_ / (time * avgArea)
2165	>	/ PhysicalConstants::energyConvert;
2166	>	JzP = momentumExchange_ / (time * avgArea);
2167	>	JzL = angularMomentumExchange_ / (time * avgArea);
2168	>	}
2169	>
2170	>	rnemdFile_ << "#######################################################\n";
2171	>	rnemdFile_ << "# RNEMD {\n";
2172	>
2173	>	map<string, RNEMDMethod>::iterator mi;
2174	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2175	>	if ( (*mi).second == rnemdMethod_)
2176	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2177	>	}
2178	>	map<string, RNEMDFluxType>::iterator fi;
2179	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2180	>	if ( (*fi).second == rnemdFluxType_)
2181	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2182	>	}
2183	>
2184	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2185	>
2186	>	rnemdFile_ << "#    objectSelection = \""
2187	>	<< rnemdObjectSelection_ << "\";\n";
2188	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2189	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2190	>	rnemdFile_ << "# }\n";
2191	>	rnemdFile_ << "#######################################################\n";
2192	>	rnemdFile_ << "# RNEMD report:\n";
2193	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2194	>	rnemdFile_ << "# Target flux:\n";
2195	>	rnemdFile_ << "#           kinetic = "
2196	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2197	>	<< " (kcal/mol/A^2/fs)\n";
2198	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2199	>	<< " (amu/A/fs^2)\n";
2200	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2201	>	<< " (amu/A^2/fs^2)\n";
2202	>	rnemdFile_ << "# Target one-time exchanges:\n";
2203	>	rnemdFile_ << "#          kinetic = "
2204	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2205	>	<< " (kcal/mol)\n";
2206	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2207	>	<< " (amu*A/fs)\n";
2208	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2209	>	<< " (amu*A^2/fs)\n";
2210	>	rnemdFile_ << "# Actual exchange totals:\n";
2211	>	rnemdFile_ << "#          kinetic = "
2212	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2213	>	<< " (kcal/mol)\n";
2214	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2215	>	<< " (amu*A/fs)\n";
2216	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2217	>	<< " (amu*A^2/fs)\n";
2218	>	rnemdFile_ << "# Actual flux:\n";
2219	>	rnemdFile_ << "#          kinetic = " << Jz
2220	>	<< " (kcal/mol/A^2/fs)\n";
2221	>	rnemdFile_ << "#          momentum = " << JzP
2222	>	<< " (amu/A/fs^2)\n";
2223	>	rnemdFile_ << "#  angular momentum = " << JzL
2224	>	<< " (amu/A^2/fs^2)\n";
2225	>	rnemdFile_ << "# Exchange statistics:\n";
2226	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2227	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2228	>	if (rnemdMethod_ == rnemdNIVS) {
2229	>	rnemdFile_ << "#  NIVS root-check errors = "
2230	>	<< failRootCount_ << "\n";
2231	>	}
2232	>	rnemdFile_ << "#######################################################\n";
2233	>
2234	>
2235	>
2236	>	//write title
2237	>	rnemdFile_ << "#";
2238	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2239	>	if (outputMask_[i]) {
2240	>	rnemdFile_ << "\t" << data_[i].title <<
2241	>	"(" << data_[i].units << ")";
2242	>	// add some extra tabs for column alignment
2243	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2244	>	}
2245	>	}
2246	>	rnemdFile_ << std::endl;
2247	>
2248	>	rnemdFile_.precision(8);
2249	>
2250	>	for (int j = 0; j < nBins_; j++) {
2251	>
2252	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2253	>	if (outputMask_[i]) {
2254	>	if (data_[i].dataType == "RealType")
2255	>	writeReal(i,j);
2256	>	else if (data_[i].dataType == "Vector3d")
2257	>	writeVector(i,j);
2258	>	else {
2259	>	sprintf( painCave.errMsg,
2260	>	"RNEMD found an unknown data type for: %s ",
2261	>	data_[i].title.c_str());
2262	>	painCave.isFatal = 1;
2263	>	simError();
2264	>	}
2265	>	}
2266	>	}
2267	>	rnemdFile_ << std::endl;
2268	>
2269	>	}
2270	>
2271	>	rnemdFile_ << "#######################################################\n";
2272	>	rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2273	>	rnemdFile_ << "#######################################################\n";
2274	>
2275	>
2276	>	for (int j = 0; j < nBins_; j++) {
2277	>	rnemdFile_ << "#";
2278	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2279	>	if (outputMask_[i]) {
2280	>	if (data_[i].dataType == "RealType")
2281	>	writeRealErrorBars(i,j);
2282	>	else if (data_[i].dataType == "Vector3d")
2283	>	writeVectorErrorBars(i,j);
2284	>	else {
2285	>	sprintf( painCave.errMsg,
2286	>	"RNEMD found an unknown data type for: %s ",
2287	>	data_[i].title.c_str());
2288	>	painCave.isFatal = 1;
2289	>	simError();
2290	>	}
2291	>	}
2292	>	}
2293	>	rnemdFile_ << std::endl;
2294	>
2295	>	}
2296	>
2297	>	rnemdFile_.flush();
2298	>	rnemdFile_.close();
2299	>
2300	>	#ifdef IS_MPI
2301	>	}
2302	>	#endif
2303	>
2304	>	}
2305	>
2306	>	void RNEMD::writeReal(int index, unsigned int bin) {
2307	>	if (!doRNEMD_) return;
2308	>	assert(index >=0 && index < ENDINDEX);
2309	>	assert(int(bin) < nBins_);
2310	>	RealType s;
2311	>	int count;
2312	>
2313	>	count = data_[index].accumulator[bin]->count();
2314	>	if (count == 0) return;
2315	>
2316	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2317	>
2318	>	if (! isinf(s) && ! isnan(s)) {
2319	>	rnemdFile_ << "\t" << s;
2320	>	} else{
2321	>	sprintf( painCave.errMsg,
2322	>	"RNEMD detected a numerical error writing: %s for bin %u",
2323	>	data_[index].title.c_str(), bin);
2324	>	painCave.isFatal = 1;
2325	>	simError();
2326	>	}
2327	>	}
2328	>
2329	>	void RNEMD::writeVector(int index, unsigned int bin) {
2330	>	if (!doRNEMD_) return;
2331	>	assert(index >=0 && index < ENDINDEX);
2332	>	assert(int(bin) < nBins_);
2333	>	Vector3d s;
2334	>	int count;
2335	>
2336	>	count = data_[index].accumulator[bin]->count();
2337	>
2338	>	if (count == 0) return;
2339	>
2340	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2341	>	if (isinf(s[0]) || isnan(s[0]) ||
2342	>	isinf(s[1]) || isnan(s[1]) ||
2343	>	isinf(s[2]) || isnan(s[2]) ) {
2344	>	sprintf( painCave.errMsg,
2345	>	"RNEMD detected a numerical error writing: %s for bin %u",
2346	>	data_[index].title.c_str(), bin);
2347	>	painCave.isFatal = 1;
2348	>	simError();
2349	>	} else {
2350	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2351	>	}
2352	>	}
2353	>
2354	>	void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2355	>	if (!doRNEMD_) return;
2356	>	assert(index >=0 && index < ENDINDEX);
2357	>	assert(int(bin) < nBins_);
2358	>	RealType s;
2359	>	int count;
2360	>
2361	>	count = data_[index].accumulator[bin]->count();
2362	>	if (count == 0) return;
2363	>
2364	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2365	>
2366	>	if (! isinf(s) && ! isnan(s)) {
2367	>	rnemdFile_ << "\t" << s;
2368	>	} else{
2369	>	sprintf( painCave.errMsg,
2370	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2371	>	data_[index].title.c_str(), bin);
2372	>	painCave.isFatal = 1;
2373	>	simError();
2374	>	}
2375	>	}
2376	>
2377	>	void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2378	>	if (!doRNEMD_) return;
2379	>	assert(index >=0 && index < ENDINDEX);
2380	>	assert(int(bin) < nBins_);
2381	>	Vector3d s;
2382	>	int count;
2383	>
2384	>	count = data_[index].accumulator[bin]->count();
2385	>	if (count == 0) return;
2386	>
2387	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2388	>	if (isinf(s[0]) || isnan(s[0]) ||
2389	>	isinf(s[1]) || isnan(s[1]) ||
2390	>	isinf(s[2]) || isnan(s[2]) ) {
2391	>	sprintf( painCave.errMsg,
2392	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2393	>	data_[index].title.c_str(), bin);
2394	>	painCave.isFatal = 1;
2395	>	simError();
2396	>	} else {
2397	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2398	>	}
2399	>	}
2400	>	}
2401	>

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
trunk/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 2056 by gezelter, Fri Feb 20 15:12:07 2015 UTC

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