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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1813 by gezelter, Fri Nov 16 21:39:55 2012 UTC

#	Line 40 | Line 40
40		*/
41
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include "rnemd/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45	+	#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
47		#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50		#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52	<
52	<	#ifndef IS_MPI
53	<	#include "math/SeqRandNumGen.hpp"
54	<	#else
52	>	#ifdef IS_MPI
53		#include <mpi.h>
56	–	#include "math/ParallelRandNumGen.hpp"
54		#endif
55
56	+	#ifdef _MSC_VER
57	+	#define isnan(x) _isnan((x))
58	+	#define isinf(x) (!_finite(x) && !_isnan(x))
59	+	#endif
60	+
61		#define HONKING_LARGE_VALUE 1.0e10
62
63		using namespace std;
#	Line 64 | Line 66 | namespace OpenMD {
66		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
67		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
68
69	+	trialCount_ = 0;
70		failTrialCount_ = 0;
71		failRootCount_ = 0;
72
70	–	int seedValue;
73		Globals * simParams = info->getSimParams();
74	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
75
76	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
77	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
75	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
76	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
77	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
78	<	stringToEnumMap_["Px"] = rnemdPx;
79	<	stringToEnumMap_["Py"] = rnemdPy;
80	<	stringToEnumMap_["Pz"] = rnemdPz;
81	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
76	>	doRNEMD_ = rnemdParams->getUseRNEMD();
77	>	if (!doRNEMD_) return;
78
79	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
79	>	stringToMethod_["Swap"]  = rnemdSwap;
80	>	stringToMethod_["NIVS"]  = rnemdNIVS;
81	>	stringToMethod_["VSS"]   = rnemdVSS;
82	>
83	>	stringToFluxType_["KE"]  = rnemdKE;
84	>	stringToFluxType_["Px"]  = rnemdPx;
85	>	stringToFluxType_["Py"]  = rnemdPy;
86	>	stringToFluxType_["Pz"]  = rnemdPz;
87	>	stringToFluxType_["Pvector"]  = rnemdPvector;
88	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
89	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
90	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
91	>
92	>	runTime_ = simParams->getRunTime();
93	>	statusTime_ = simParams->getStatusTime();
94	>
95	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
96		evaluator_.loadScriptString(rnemdObjectSelection_);
97		seleMan_.setSelectionSet(evaluator_.evaluate());
98
99	<	// do some sanity checking
99	>	const string methStr = rnemdParams->getMethod();
100	>	bool hasFluxType = rnemdParams->haveFluxType();
101
102	<	int selectionCount = seleMan_.getSelectionCount();
103	<	int nIntegrable = info->getNGlobalIntegrableObjects();
104	<
105	<	if (selectionCount > nIntegrable) {
102	>	string fluxStr;
103	>	if (hasFluxType) {
104	>	fluxStr = rnemdParams->getFluxType();
105	>	} else {
106		sprintf(painCave.errMsg,
107	<	"RNEMD: The current RNEMD_objectSelection,\n"
108	<	"\t\t%s\n"
109	<	"\thas resulted in %d selected objects.  However,\n"
110	<	"\tthe total number of integrable objects in the system\n"
111	<	"\tis only %d.  This is almost certainly not what you want\n"
112	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
100	<	"\tselector in the selection script!\n",
101	<	rnemdObjectSelection_.c_str(),
102	<	selectionCount, nIntegrable);
103	<	painCave.isFatal = 0;
104	<	painCave.severity = OPENMD_WARNING;
107	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
108	>	"\twhich must be one of the following values:\n"
109	>	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
110	>	"\tmust be set to use RNEMD\n");
111	>	painCave.isFatal = 1;
112	>	painCave.severity = OPENMD_ERROR;
113		simError();
114		}
115	+
116	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
117	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
118	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
119	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
120	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
121	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
122	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
123	+	bool hasOutputFields = rnemdParams->haveOutputFields();
124
125	<	const string st = simParams->getRNEMD_exchangeType();
125	>	map<string, RNEMDMethod>::iterator i;
126	>	i = stringToMethod_.find(methStr);
127	>	if (i != stringToMethod_.end())
128	>	rnemdMethod_ = i->second;
129	>	else {
130	>	sprintf(painCave.errMsg,
131	>	"RNEMD: The current method,\n"
132	>	"\t\t%s is not one of the recognized\n"
133	>	"\texchange methods: Swap, NIVS, or VSS\n",
134	>	methStr.c_str());
135	>	painCave.isFatal = 1;
136	>	painCave.severity = OPENMD_ERROR;
137	>	simError();
138	>	}
139
140	<	map<string, RNEMDTypeEnum>::iterator i;
141	<	i = stringToEnumMap_.find(st);
142	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
143	<	if (rnemdType_ == rnemdUnknown) {
140	>	map<string, RNEMDFluxType>::iterator j;
141	>	j = stringToFluxType_.find(fluxStr);
142	>	if (j != stringToFluxType_.end())
143	>	rnemdFluxType_ = j->second;
144	>	else {
145		sprintf(painCave.errMsg,
146	<	"RNEMD: The current RNEMD_exchangeType,\n"
146	>	"RNEMD: The current fluxType,\n"
147		"\t\t%s\n"
148	<	"\tis not one of the recognized exchange types.\n",
149	<	st.c_str());
148	>	"\tis not one of the recognized flux types.\n",
149	>	fluxStr.c_str());
150		painCave.isFatal = 1;
151		painCave.severity = OPENMD_ERROR;
152		simError();
153		}
123	–
124	–	output3DTemp_ = false;
125	–	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
126	–	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
127	–	}
154
155	<	#ifdef IS_MPI
156	<	if (worldRank == 0) {
157	<	#endif
158	<
159	<	string rnemdFileName;
160	<	switch(rnemdType_) {
161	<	case rnemdKineticSwap :
136	<	case rnemdKineticScale :
137	<	rnemdFileName = "temperature.log";
155	>	bool methodFluxMismatch = false;
156	>	bool hasCorrectFlux = false;
157	>	switch(rnemdMethod_) {
158	>	case rnemdSwap:
159	>	switch (rnemdFluxType_) {
160	>	case rnemdKE:
161	>	hasCorrectFlux = hasKineticFlux;
162		break;
163	<	case rnemdPx :
164	<	case rnemdPxScale :
165	<	case rnemdPy :
166	<	case rnemdPyScale :
143	<	rnemdFileName = "momemtum.log";
163	>	case rnemdPx:
164	>	case rnemdPy:
165	>	case rnemdPz:
166	>	hasCorrectFlux = hasMomentumFlux;
167		break;
145	–	case rnemdPz :
146	–	case rnemdPzScale :
147	–	case rnemdUnknown :
168		default :
169	<	rnemdFileName = "rnemd.log";
169	>	methodFluxMismatch = true;
170		break;
171		}
172	<	rnemdLog_.open(rnemdFileName.c_str());
173	<
174	<	string xTempFileName;
175	<	string yTempFileName;
176	<	string zTempFileName;
177	<	if (output3DTemp_) {
178	<	xTempFileName = "temperatureX.log";
179	<	yTempFileName = "temperatureY.log";
180	<	zTempFileName = "temperatureZ.log";
181	<	xTempLog_.open(xTempFileName.c_str());
182	<	yTempLog_.open(yTempFileName.c_str());
183	<	zTempLog_.open(zTempFileName.c_str());
172	>	break;
173	>	case rnemdNIVS:
174	>	switch (rnemdFluxType_) {
175	>	case rnemdKE:
176	>	case rnemdRotKE:
177	>	case rnemdFullKE:
178	>	hasCorrectFlux = hasKineticFlux;
179	>	break;
180	>	case rnemdPx:
181	>	case rnemdPy:
182	>	case rnemdPz:
183	>	hasCorrectFlux = hasMomentumFlux;
184	>	break;
185	>	case rnemdKePx:
186	>	case rnemdKePy:
187	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
188	>	break;
189	>	default:
190	>	methodFluxMismatch = true;
191	>	break;
192		}
193	<
194	<	#ifdef IS_MPI
195	<	}
196	<	#endif
197	<
198	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
199	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
200	<	midBin_ = nBins_ / 2;
201	<	if (simParams->haveRNEMD_binShift()) {
202	<	if (simParams->getRNEMD_binShift()) {
203	<	zShift_ = 0.5 / (RealType)(nBins_);
204	<	} else {
205	<	zShift_ = 0.0;
193	>	break;
194	>	case rnemdVSS:
195	>	switch (rnemdFluxType_) {
196	>	case rnemdKE:
197	>	case rnemdRotKE:
198	>	case rnemdFullKE:
199	>	hasCorrectFlux = hasKineticFlux;
200	>	break;
201	>	case rnemdPx:
202	>	case rnemdPy:
203	>	case rnemdPz:
204	>	hasCorrectFlux = hasMomentumFlux;
205	>	break;
206	>	case rnemdPvector:
207	>	hasCorrectFlux = hasMomentumFluxVector;
208	>	break;
209	>	case rnemdKePx:
210	>	case rnemdKePy:
211	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
212	>	break;
213	>	case rnemdKePvector:
214	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
215	>	break;
216	>	default:
217	>	methodFluxMismatch = true;
218	>	break;
219		}
220	<	} else {
221	<	zShift_ = 0.0;
220	>	default:
221	>	break;
222		}
182	–	//cerr << "we have zShift_ = " << zShift_ << "\n";
183	–	//shift slabs by half slab width, might be useful in heterogeneous systems
184	–	//set to 0.0 if not using it; can NOT be used in status output yet
185	–	if (simParams->haveRNEMD_logWidth()) {
186	–	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
187	–	/*arbitary rnemdLogWidth_ no checking
188	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
189	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
190	–	cerr << "Automaically set back to default.\n";
191	–	rnemdLogWidth_ = nBins_;
192	–	}*/
193	–	} else {
194	–	set_RNEMD_logWidth(nBins_);
195	–	}
196	–	valueHist_.resize(rnemdLogWidth_, 0.0);
197	–	valueCount_.resize(rnemdLogWidth_, 0);
198	–	xTempHist_.resize(rnemdLogWidth_, 0.0);
199	–	yTempHist_.resize(rnemdLogWidth_, 0.0);
200	–	zTempHist_.resize(rnemdLogWidth_, 0.0);
201	–	xyzTempCount_.resize(rnemdLogWidth_, 0);
223
224	<	set_RNEMD_exchange_total(0.0);
225	<	if (simParams->haveRNEMD_targetFlux()) {
226	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
224	>	if (methodFluxMismatch) {
225	>	sprintf(painCave.errMsg,
226	>	"RNEMD: The current method,\n"
227	>	"\t\t%s\n"
228	>	"\tcannot be used with the current flux type, %s\n",
229	>	methStr.c_str(), fluxStr.c_str());
230	>	painCave.isFatal = 1;
231	>	painCave.severity = OPENMD_ERROR;
232	>	simError();
233	>	}
234	>	if (!hasCorrectFlux) {
235	>	sprintf(painCave.errMsg,
236	>	"RNEMD: The current method, %s, and flux type, %s,\n"
237	>	"\tdid not have the correct flux value specified. Options\n"
238	>	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
239	>	methStr.c_str(), fluxStr.c_str());
240	>	painCave.isFatal = 1;
241	>	painCave.severity = OPENMD_ERROR;
242	>	simError();
243	>	}
244	>
245	>	if (hasKineticFlux) {
246	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
247	>	// into  amu / fs^3:
248	>	kineticFlux_ = rnemdParams->getKineticFlux()
249	>	* PhysicalConstants::energyConvert;
250		} else {
251	<	set_RNEMD_target_flux(0.0);
251	>	kineticFlux_ = 0.0;
252		}
253	+	if (hasMomentumFluxVector) {
254	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
255	+	} else {
256	+	momentumFluxVector_ = V3Zero;
257	+	if (hasMomentumFlux) {
258	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
259	+	switch (rnemdFluxType_) {
260	+	case rnemdPx:
261	+	momentumFluxVector_.x() = momentumFlux;
262	+	break;
263	+	case rnemdPy:
264	+	momentumFluxVector_.y() = momentumFlux;
265	+	break;
266	+	case rnemdPz:
267	+	momentumFluxVector_.z() = momentumFlux;
268	+	break;
269	+	case rnemdKePx:
270	+	momentumFluxVector_.x() = momentumFlux;
271	+	break;
272	+	case rnemdKePy:
273	+	momentumFluxVector_.y() = momentumFlux;
274	+	break;
275	+	default:
276	+	break;
277	+	}
278	+	}
279	+	}
280
281	<	#ifndef IS_MPI
282	<	if (simParams->haveSeed()) {
283	<	seedValue = simParams->getSeed();
284	<	randNumGen_ = new SeqRandNumGen(seedValue);
285	<	}else {
286	<	randNumGen_ = new SeqRandNumGen();
287	<	}
288	<	#else
289	<	if (simParams->haveSeed()) {
290	<	seedValue = simParams->getSeed();
291	<	randNumGen_ = new ParallelRandNumGen(seedValue);
292	<	}else {
293	<	randNumGen_ = new ParallelRandNumGen();
294	<	}
295	<	#endif
296	<	}
281	>	// do some sanity checking
282	>
283	>	int selectionCount = seleMan_.getSelectionCount();
284	>
285	>	int nIntegrable = info->getNGlobalIntegrableObjects();
286	>
287	>	if (selectionCount > nIntegrable) {
288	>	sprintf(painCave.errMsg,
289	>	"RNEMD: The current objectSelection,\n"
290	>	"\t\t%s\n"
291	>	"\thas resulted in %d selected objects.  However,\n"
292	>	"\tthe total number of integrable objects in the system\n"
293	>	"\tis only %d.  This is almost certainly not what you want\n"
294	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
295	>	"\tselector in the selection script!\n",
296	>	rnemdObjectSelection_.c_str(),
297	>	selectionCount, nIntegrable);
298	>	painCave.isFatal = 0;
299	>	painCave.severity = OPENMD_WARNING;
300	>	simError();
301	>	}
302	>
303	>	areaAccumulator_ = new Accumulator();
304	>
305	>	nBins_ = rnemdParams->getOutputBins();
306	>
307	>	data_.resize(RNEMD::ENDINDEX);
308	>	OutputData z;
309	>	z.units =  "Angstroms";
310	>	z.title =  "Z";
311	>	z.dataType = "RealType";
312	>	z.accumulator.reserve(nBins_);
313	>	for (int i = 0; i < nBins_; i++)
314	>	z.accumulator.push_back( new Accumulator() );
315	>	data_[Z] = z;
316	>	outputMap_["Z"] =  Z;
317	>
318	>	OutputData temperature;
319	>	temperature.units =  "K";
320	>	temperature.title =  "Temperature";
321	>	temperature.dataType = "RealType";
322	>	temperature.accumulator.reserve(nBins_);
323	>	for (int i = 0; i < nBins_; i++)
324	>	temperature.accumulator.push_back( new Accumulator() );
325	>	data_[TEMPERATURE] = temperature;
326	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
327	>
328	>	OutputData velocity;
329	>	velocity.units = "angstroms/fs";
330	>	velocity.title =  "Velocity";
331	>	velocity.dataType = "Vector3d";
332	>	velocity.accumulator.reserve(nBins_);
333	>	for (int i = 0; i < nBins_; i++)
334	>	velocity.accumulator.push_back( new VectorAccumulator() );
335	>	data_[VELOCITY] = velocity;
336	>	outputMap_["VELOCITY"] = VELOCITY;
337	>
338	>	OutputData density;
339	>	density.units =  "g cm^-3";
340	>	density.title =  "Density";
341	>	density.dataType = "RealType";
342	>	density.accumulator.reserve(nBins_);
343	>	for (int i = 0; i < nBins_; i++)
344	>	density.accumulator.push_back( new Accumulator() );
345	>	data_[DENSITY] = density;
346	>	outputMap_["DENSITY"] =  DENSITY;
347	>
348	>	if (hasOutputFields) {
349	>	parseOutputFileFormat(rnemdParams->getOutputFields());
350	>	} else {
351	>	outputMask_.set(Z);
352	>	switch (rnemdFluxType_) {
353	>	case rnemdKE:
354	>	case rnemdRotKE:
355	>	case rnemdFullKE:
356	>	outputMask_.set(TEMPERATURE);
357	>	break;
358	>	case rnemdPx:
359	>	case rnemdPy:
360	>	outputMask_.set(VELOCITY);
361	>	break;
362	>	case rnemdPz:
363	>	case rnemdPvector:
364	>	outputMask_.set(VELOCITY);
365	>	outputMask_.set(DENSITY);
366	>	break;
367	>	case rnemdKePx:
368	>	case rnemdKePy:
369	>	outputMask_.set(TEMPERATURE);
370	>	outputMask_.set(VELOCITY);
371	>	break;
372	>	case rnemdKePvector:
373	>	outputMask_.set(TEMPERATURE);
374	>	outputMask_.set(VELOCITY);
375	>	outputMask_.set(DENSITY);
376	>	break;
377	>	default:
378	>	break;
379	>	}
380	>	}
381	>
382	>	if (hasOutputFileName) {
383	>	rnemdFileName_ = rnemdParams->getOutputFileName();
384	>	} else {
385	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
386	>	}
387	>
388	>	exchangeTime_ = rnemdParams->getExchangeTime();
389	>
390	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
391	>	Mat3x3d hmat = currentSnap_->getHmat();
392
393	<	RNEMD::~RNEMD() {
394	<	delete randNumGen_;
393	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
394	>	// Lx, Ly = box dimensions in x & y
395	>	// dt = exchange time interval
396	>	// flux = target flux
397	>
398	>	RealType area = currentSnap_->getXYarea();
399	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
400	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
401	>
402	>	// total exchange sums are zeroed out at the beginning:
403	>
404	>	kineticExchange_ = 0.0;
405	>	momentumExchange_ = V3Zero;
406	>
407	>	if (hasSlabWidth)
408	>	slabWidth_ = rnemdParams->getSlabWidth();
409	>	else
410	>	slabWidth_ = hmat(2,2) / 10.0;
411	>
412	>	if (hasSlabACenter)
413	>	slabACenter_ = rnemdParams->getSlabACenter();
414	>	else
415	>	slabACenter_ = 0.0;
416
417	+	if (hasSlabBCenter)
418	+	slabBCenter_ = rnemdParams->getSlabBCenter();
419	+	else
420	+	slabBCenter_ = hmat(2,2) / 2.0;
421	+
422	+	}
423	+
424	+	RNEMD::~RNEMD() {
425	+	if (!doRNEMD_) return;
426		#ifdef IS_MPI
427		if (worldRank == 0) {
428		#endif
233	–
234	–	sprintf(painCave.errMsg,
235	–	"RNEMD: total failed trials: %d\n",
236	–	failTrialCount_);
237	–	painCave.isFatal = 0;
238	–	painCave.severity = OPENMD_INFO;
239	–	simError();
429
430	<	rnemdLog_.close();
431	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
432	<	sprintf(painCave.errMsg,
433	<	"RNEMD: total root-checking warnings: %d\n",
245	<	failRootCount_);
246	<	painCave.isFatal = 0;
247	<	painCave.severity = OPENMD_INFO;
248	<	simError();
249	<	}
250	<	if (output3DTemp_) {
251	<	xTempLog_.close();
252	<	yTempLog_.close();
253	<	zTempLog_.close();
254	<	}
430	>	writeOutputFile();
431	>
432	>	rnemdFile_.close();
433	>
434		#ifdef IS_MPI
435		}
436		#endif
437		}
438	+
439	+	bool RNEMD::inSlabA(Vector3d pos) {
440	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
441	+	}
442	+	bool RNEMD::inSlabB(Vector3d pos) {
443	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
444	+	}
445
446		void RNEMD::doSwap() {
447	<
447	>	if (!doRNEMD_) return;
448		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
449		Mat3x3d hmat = currentSnap_->getHmat();
450
#	Line 266 | Line 452 | namespace OpenMD {
452
453		int selei;
454		StuntDouble* sd;
269	–	int idx;
455
456		RealType min_val;
457		bool min_found = false;
#	Line 279 | Line 464 | namespace OpenMD {
464		for (sd = seleMan_.beginSelected(selei); sd != NULL;
465		sd = seleMan_.nextSelected(selei)) {
466
282	–	idx = sd->getLocalIndex();
283	–
467		Vector3d pos = sd->getPos();
468
469		// wrap the stuntdouble's position back into the box:
470
471		if (usePeriodicBoundaryConditions_)
472		currentSnap_->wrapVector(pos);
473	+	bool inA = inSlabA(pos);
474	+	bool inB = inSlabB(pos);
475
476	<	// which bin is this stuntdouble in?
292	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
293	<
294	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
295	<
296	<
297	<	// if we're in bin 0 or the middleBin
298	<	if (binNo == 0 || binNo == midBin_) {
476	>	if (inA || inB) {
477
478		RealType mass = sd->getMass();
479		Vector3d vel = sd->getVel();
480		RealType value;
481	<
482	<	switch(rnemdType_) {
483	<	case rnemdKineticSwap :
481	>
482	>	switch(rnemdFluxType_) {
483	>	case rnemdKE :
484
485	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
486	<	vel[2]*vel[2]);
487	<	/*
310	<	if (sd->isDirectional()) {
485	>	value = mass * vel.lengthSquare();
486	>
487	>	if (sd->isDirectional()) {
488		Vector3d angMom = sd->getJ();
489		Mat3x3d I = sd->getI();
490
491		if (sd->isLinear()) {
492	<	int i = sd->linearAxis();
493	<	int j = (i + 1) % 3;
494	<	int k = (i + 2) % 3;
495	<	value += angMom[j] * angMom[j] / I(j, j) +
496	<	angMom[k] * angMom[k] / I(k, k);
492	>	int i = sd->linearAxis();
493	>	int j = (i + 1) % 3;
494	>	int k = (i + 2) % 3;
495	>	value += angMom[j] * angMom[j] / I(j, j) +
496	>	angMom[k] * angMom[k] / I(k, k);
497		} else {
498	<	value += angMom[0]*angMom[0]/I(0, 0)
499	<	+ angMom[1]*angMom[1]/I(1, 1)
500	<	+ angMom[2]*angMom[2]/I(2, 2);
498	>	value += angMom[0]*angMom[0]/I(0, 0)
499	>	+ angMom[1]*angMom[1]/I(1, 1)
500	>	+ angMom[2]*angMom[2]/I(2, 2);
501		}
502	<	} no exchange of angular momenta
326	<	*/
327	<	//make exchangeSum_ comparable between swap & scale
328	<	//temporarily without using energyConvert
329	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
502	>	} //angular momenta exchange enabled
503		value *= 0.5;
504		break;
505		case rnemdPx :
#	Line 342 | Line 515 | namespace OpenMD {
515		break;
516		}
517
518	<	if (binNo == 0) {
518	>	if (inA == 0) {
519		if (!min_found) {
520		min_val = value;
521		min_sd = sd;
#	Line 353 | Line 526 | namespace OpenMD {
526		min_sd = sd;
527		}
528		}
529	<	} else { //midBin_
529	>	} else {
530		if (!max_found) {
531		max_val = value;
532		max_sd = sd;
#	Line 367 | Line 540 | namespace OpenMD {
540		}
541		}
542		}
543	<
544	<	#ifdef IS_MPI
545	<	int nProc, worldRank;
546	<
374	<	nProc = MPI::COMM_WORLD.Get_size();
375	<	worldRank = MPI::COMM_WORLD.Get_rank();
376	<
543	>
544	>	#ifdef IS_MPI
545	>	int worldRank = MPI::COMM_WORLD.Get_rank();
546	>
547		bool my_min_found = min_found;
548		bool my_max_found = max_found;
549
#	Line 381 | Line 551 | namespace OpenMD {
551		MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
552		// Even if we didn't find a maximum, did someone else?
553		MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
554	<	struct {
555	<	RealType val;
556	<	int rank;
557	<	} max_vals, min_vals;
558	<
559	<	if (min_found) {
560	<	if (my_min_found)
554	>	#endif
555	>
556	>	if (max_found && min_found) {
557	>
558	>	#ifdef IS_MPI
559	>	struct {
560	>	RealType val;
561	>	int rank;
562	>	} max_vals, min_vals;
563	>
564	>	if (my_min_found) {
565		min_vals.val = min_val;
566	<	else
566	>	} else {
567		min_vals.val = HONKING_LARGE_VALUE;
568	<
568	>	}
569		min_vals.rank = worldRank;
570
571		// Who had the minimum?
572		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
573		1, MPI::REALTYPE_INT, MPI::MINLOC);
574		min_val = min_vals.val;
401	–	}
575
576	<	if (max_found) {
404	<	if (my_max_found)
576	>	if (my_max_found) {
577		max_vals.val = max_val;
578	<	else
578	>	} else {
579		max_vals.val = -HONKING_LARGE_VALUE;
580	<
580	>	}
581		max_vals.rank = worldRank;
582
583		// Who had the maximum?
584		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
585		1, MPI::REALTYPE_INT, MPI::MAXLOC);
586		max_val = max_vals.val;
415	–	}
587		#endif
588	<
418	<	if (max_found && min_found) {
588	>
589		if (min_val < max_val) {
590	<
590	>
591		#ifdef IS_MPI
592		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
593		// I have both maximum and minimum, so proceed like a single
594		// processor version:
595		#endif
596	<	// objects to be swapped: velocity ONLY
596	>
597		Vector3d min_vel = min_sd->getVel();
598		Vector3d max_vel = max_sd->getVel();
599		RealType temp_vel;
600
601	<	switch(rnemdType_) {
602	<	case rnemdKineticSwap :
601	>	switch(rnemdFluxType_) {
602	>	case rnemdKE :
603		min_sd->setVel(max_vel);
604		max_sd->setVel(min_vel);
605	<	/*
436	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
605	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
606		Vector3d min_angMom = min_sd->getJ();
607		Vector3d max_angMom = max_sd->getJ();
608		min_sd->setJ(max_angMom);
609		max_sd->setJ(min_angMom);
610	<	} no angular momentum exchange
611	<	*/
610	>	}//angular momenta exchange enabled
611	>	//assumes same rigid body identity
612		break;
613		case rnemdPx :
614		temp_vel = min_vel.x();
#	Line 465 | Line 634 | namespace OpenMD {
634		default :
635		break;
636		}
637	+
638		#ifdef IS_MPI
639		// the rest of the cases only apply in parallel simulations:
640		} else if (max_vals.rank == worldRank) {
#	Line 480 | Line 650 | namespace OpenMD {
650		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
651		min_vals.rank, 0, status);
652
653	<	switch(rnemdType_) {
654	<	case rnemdKineticSwap :
653	>	switch(rnemdFluxType_) {
654	>	case rnemdKE :
655		max_sd->setVel(min_vel);
656	<	//no angular momentum exchange for now
487	<	/*
656	>	//angular momenta exchange enabled
657		if (max_sd->isDirectional()) {
658		Vector3d min_angMom;
659		Vector3d max_angMom = max_sd->getJ();
#	Line 497 | Line 666 | namespace OpenMD {
666		status);
667
668		max_sd->setJ(min_angMom);
669	<	}
501	<	*/
669	>	}
670		break;
671		case rnemdPx :
672		max_vel.x() = min_vel.x();
#	Line 528 | Line 696 | namespace OpenMD {
696		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
697		max_vals.rank, 0, status);
698
699	<	switch(rnemdType_) {
700	<	case rnemdKineticSwap :
699	>	switch(rnemdFluxType_) {
700	>	case rnemdKE :
701		min_sd->setVel(max_vel);
702	<	// no angular momentum exchange for now
535	<	/*
702	>	//angular momenta exchange enabled
703		if (min_sd->isDirectional()) {
704		Vector3d min_angMom = min_sd->getJ();
705		Vector3d max_angMom;
#	Line 546 | Line 713 | namespace OpenMD {
713
714		min_sd->setJ(max_angMom);
715		}
549	–	*/
716		break;
717		case rnemdPx :
718		min_vel.x() = max_vel.x();
#	Line 565 | Line 731 | namespace OpenMD {
731		}
732		}
733		#endif
734	<	exchangeSum_ += max_val - min_val;
734	>
735	>	switch(rnemdFluxType_) {
736	>	case rnemdKE:
737	>	kineticExchange_ += max_val - min_val;
738	>	break;
739	>	case rnemdPx:
740	>	momentumExchange_.x() += max_val - min_val;
741	>	break;
742	>	case rnemdPy:
743	>	momentumExchange_.y() += max_val - min_val;
744	>	break;
745	>	case rnemdPz:
746	>	momentumExchange_.z() += max_val - min_val;
747	>	break;
748	>	default:
749	>	break;
750	>	}
751		} else {
752		sprintf(painCave.errMsg,
753	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
753	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
754		painCave.isFatal = 0;
755		painCave.severity = OPENMD_INFO;
756		simError();
#	Line 576 | Line 758 | namespace OpenMD {
758		}
759		} else {
760		sprintf(painCave.errMsg,
761	<	"RNEMD: exchange NOT performed because at least one\n"
762	<	"\tof the two slabs is empty\n");
761	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
762	>	"\twas not present in at least one of the two slabs.\n");
763		painCave.isFatal = 0;
764		painCave.severity = OPENMD_INFO;
765		simError();
766		failTrialCount_++;
767	<	}
586	<
767	>	}
768		}
769
770	<	void RNEMD::doScale() {
771	<
770	>	void RNEMD::doNIVS() {
771	>	if (!doRNEMD_) return;
772		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
773		Mat3x3d hmat = currentSnap_->getHmat();
774
#	Line 595 | Line 776 | namespace OpenMD {
776
777		int selei;
778		StuntDouble* sd;
598	–	int idx;
779
780		vector<StuntDouble*> hotBin, coldBin;
781
#	Line 605 | Line 785 | namespace OpenMD {
785		RealType Khx = 0.0;
786		RealType Khy = 0.0;
787		RealType Khz = 0.0;
788	+	RealType Khw = 0.0;
789		RealType Pcx = 0.0;
790		RealType Pcy = 0.0;
791		RealType Pcz = 0.0;
792		RealType Kcx = 0.0;
793		RealType Kcy = 0.0;
794		RealType Kcz = 0.0;
795	+	RealType Kcw = 0.0;
796
797		for (sd = seleMan_.beginSelected(selei); sd != NULL;
798		sd = seleMan_.nextSelected(selei)) {
799
618	–	idx = sd->getLocalIndex();
619	–
800		Vector3d pos = sd->getPos();
801
802		// wrap the stuntdouble's position back into the box:
#	Line 625 | Line 805 | namespace OpenMD {
805		currentSnap_->wrapVector(pos);
806
807		// which bin is this stuntdouble in?
808	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
808	>	bool inA = inSlabA(pos);
809	>	bool inB = inSlabB(pos);
810
811	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
812	<
632	<	// if we're in bin 0 or the middleBin
633	<	if (binNo == 0 || binNo == midBin_) {
634	<
811	>	if (inA || inB) {
812	>
813		RealType mass = sd->getMass();
814		Vector3d vel = sd->getVel();
815
816	<	if (binNo == 0) {
816	>	if (inA) {
817		hotBin.push_back(sd);
818		Phx += mass * vel.x();
819		Phy += mass * vel.y();
#	Line 643 | Line 821 | namespace OpenMD {
821		Khx += mass * vel.x() * vel.x();
822		Khy += mass * vel.y() * vel.y();
823		Khz += mass * vel.z() * vel.z();
824	<	} else { //midBin_
824	>	if (sd->isDirectional()) {
825	>	Vector3d angMom = sd->getJ();
826	>	Mat3x3d I = sd->getI();
827	>	if (sd->isLinear()) {
828	>	int i = sd->linearAxis();
829	>	int j = (i + 1) % 3;
830	>	int k = (i + 2) % 3;
831	>	Khw += angMom[j] * angMom[j] / I(j, j) +
832	>	angMom[k] * angMom[k] / I(k, k);
833	>	} else {
834	>	Khw += angMom[0]*angMom[0]/I(0, 0)
835	>	+ angMom[1]*angMom[1]/I(1, 1)
836	>	+ angMom[2]*angMom[2]/I(2, 2);
837	>	}
838	>	}
839	>	} else {
840		coldBin.push_back(sd);
841		Pcx += mass * vel.x();
842		Pcy += mass * vel.y();
#	Line 651 | Line 844 | namespace OpenMD {
844		Kcx += mass * vel.x() * vel.x();
845		Kcy += mass * vel.y() * vel.y();
846		Kcz += mass * vel.z() * vel.z();
847	+	if (sd->isDirectional()) {
848	+	Vector3d angMom = sd->getJ();
849	+	Mat3x3d I = sd->getI();
850	+	if (sd->isLinear()) {
851	+	int i = sd->linearAxis();
852	+	int j = (i + 1) % 3;
853	+	int k = (i + 2) % 3;
854	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
855	+	angMom[k] * angMom[k] / I(k, k);
856	+	} else {
857	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
858	+	+ angMom[1]*angMom[1]/I(1, 1)
859	+	+ angMom[2]*angMom[2]/I(2, 2);
860	+	}
861	+	}
862		}
863		}
864		}
865	<
865	>
866		Khx *= 0.5;
867		Khy *= 0.5;
868		Khz *= 0.5;
869	+	Khw *= 0.5;
870		Kcx *= 0.5;
871		Kcy *= 0.5;
872		Kcz *= 0.5;
873	+	Kcw *= 0.5;
874
875		#ifdef IS_MPI
876		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 673 | Line 883 | namespace OpenMD {
883		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
884		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
885		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
886	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
887	+
888		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
889		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
890		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
891	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
892		#endif
893
894	<	//use coldBin coeff's
894	>	//solve coldBin coeff's first
895		RealType px = Pcx / Phx;
896		RealType py = Pcy / Phy;
897		RealType pz = Pcz / Phz;
898	+	RealType c, x, y, z;
899	+	bool successfulScale = false;
900	+	if ((rnemdFluxType_ == rnemdFullKE) ||
901	+	(rnemdFluxType_ == rnemdRotKE)) {
902	+	//may need sanity check Khw & Kcw > 0
903
904	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
905	<	switch(rnemdType_) {
906	<	case rnemdKineticScale :
907	<	// used hotBin coeff's & only scale x & y dimensions
908	<	/*
691	<	RealType px = Phx / Pcx;
692	<	RealType py = Phy / Pcy;
693	<	a110 = Khy;
694	<	c0 = - Khx - Khy - targetFlux_;
695	<	a000 = Khx;
696	<	a111 = Kcy * py * py;
697	<	b11 = -2.0 * Kcy * py * (1.0 + py);
698	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
699	<	b01 = -2.0 * Kcx * px * (1.0 + px);
700	<	a001 = Kcx * px * px;
701	<	*/
702	<	//scale all three dimensions, let c_x = c_y
703	<	a000 = Kcx + Kcy;
704	<	a110 = Kcz;
705	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
706	<	a001 = Khx * px * px + Khy * py * py;
707	<	a111 = Khz * pz * pz;
708	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
709	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
710	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
711	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
712	<	break;
713	<	case rnemdPxScale :
714	<	c = 1 - targetFlux_ / Pcx;
715	<	a000 = Kcy;
716	<	a110 = Kcz;
717	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
718	<	a001 = py * py * Khy;
719	<	a111 = pz * pz * Khz;
720	<	b01 = -2.0 * Khy * py * (1.0 + py);
721	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
722	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
723	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
724	<	break;
725	<	case rnemdPyScale :
726	<	c = 1 - targetFlux_ / Pcy;
727	<	a000 = Kcx;
728	<	a110 = Kcz;
729	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
730	<	a001 = px * px * Khx;
731	<	a111 = pz * pz * Khz;
732	<	b01 = -2.0 * Khx * px * (1.0 + px);
733	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
734	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
735	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
736	<	break;
737	<	case rnemdPzScale ://we don't really do this, do we?
738	<	c = 1 - targetFlux_ / Pcz;
739	<	a000 = Kcx;
740	<	a110 = Kcy;
741	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
742	<	a001 = px * px * Khx;
743	<	a111 = py * py * Khy;
744	<	b01 = -2.0 * Khx * px * (1.0 + px);
745	<	b11 = -2.0 * Khy * py * (1.0 + py);
746	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
747	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
748	<	break;
749	<	default :
750	<	break;
751	<	}
904	>	if (rnemdFluxType_ == rnemdFullKE) {
905	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
906	>	} else {
907	>	c = 1.0 - kineticTarget_ / Kcw;
908	>	}
909
910	<	RealType v1 = a000 * a111 - a001 * a110;
911	<	RealType v2 = a000 * b01;
755	<	RealType v3 = a000 * b11;
756	<	RealType v4 = a000 * c1 - a001 * c0;
757	<	RealType v8 = a110 * b01;
758	<	RealType v10 = - b01 * c0;
910	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
911	>	c = sqrt(c);
912
913	<	RealType u0 = v2 * v10 - v4 * v4;
914	<	RealType u1 = -2.0 * v3 * v4;
915	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
916	<	RealType u3 = -2.0 * v1 * v3;
917	<	RealType u4 = - v1 * v1;
918	<	//rescale coefficients
919	<	RealType maxAbs = fabs(u0);
920	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
921	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
922	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
923	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
924	<	u0 /= maxAbs;
925	<	u1 /= maxAbs;
926	<	u2 /= maxAbs;
927	<	u3 /= maxAbs;
928	<	u4 /= maxAbs;
929	<	//max_element(start, end) is also available.
930	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
931	<	poly.setCoefficient(4, u4);
932	<	poly.setCoefficient(3, u3);
933	<	poly.setCoefficient(2, u2);
934	<	poly.setCoefficient(1, u1);
935	<	poly.setCoefficient(0, u0);
936	<	vector<RealType> realRoots = poly.FindRealRoots();
937	<
938	<	vector<RealType>::iterator ri;
939	<	RealType r1, r2, alpha0;
940	<	vector<pair<RealType,RealType> > rps;
941	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
942	<	r2 = *ri;
943	<	//check if FindRealRoots() give the right answer
944	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
945	<	sprintf(painCave.errMsg,
946	<	"RNEMD Warning: polynomial solve seems to have an error!");
947	<	painCave.isFatal = 0;
948	<	simError();
949	<	failRootCount_++;
913	>	RealType w = 0.0;
914	>	if (rnemdFluxType_ ==  rnemdFullKE) {
915	>	x = 1.0 + px * (1.0 - c);
916	>	y = 1.0 + py * (1.0 - c);
917	>	z = 1.0 + pz * (1.0 - c);
918	>	/* more complicated way
919	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
920	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
921	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
922	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
923	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
924	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
925	>	*/
926	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
927	>	(fabs(z - 1.0) < 0.1)) {
928	>	w = 1.0 + (kineticTarget_
929	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
930	>	+ Khz * (1.0 - z * z)) / Khw;
931	>	}//no need to calculate w if x, y or z is out of range
932	>	} else {
933	>	w = 1.0 + kineticTarget_ / Khw;
934	>	}
935	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
936	>	//if w is in the right range, so should be x, y, z.
937	>	vector<StuntDouble*>::iterator sdi;
938	>	Vector3d vel;
939	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
940	>	if (rnemdFluxType_ == rnemdFullKE) {
941	>	vel = (*sdi)->getVel() * c;
942	>	(*sdi)->setVel(vel);
943	>	}
944	>	if ((*sdi)->isDirectional()) {
945	>	Vector3d angMom = (*sdi)->getJ() * c;
946	>	(*sdi)->setJ(angMom);
947	>	}
948	>	}
949	>	w = sqrt(w);
950	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
951	>	if (rnemdFluxType_ == rnemdFullKE) {
952	>	vel = (*sdi)->getVel();
953	>	vel.x() *= x;
954	>	vel.y() *= y;
955	>	vel.z() *= z;
956	>	(*sdi)->setVel(vel);
957	>	}
958	>	if ((*sdi)->isDirectional()) {
959	>	Vector3d angMom = (*sdi)->getJ() * w;
960	>	(*sdi)->setJ(angMom);
961	>	}
962	>	}
963	>	successfulScale = true;
964	>	kineticExchange_ += kineticTarget_;
965	>	}
966		}
967	<	//might not be useful w/o rescaling coefficients
968	<	alpha0 = -c0 - a110 * r2 * r2;
969	<	if (alpha0 >= 0.0) {
970	<	r1 = sqrt(alpha0 / a000);
971	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
972	<	{ rps.push_back(make_pair(r1, r2)); }
973	<	if (r1 > 1e-6) { //r1 non-negative
974	<	r1 = -r1;
975	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
976	<	{ rps.push_back(make_pair(r1, r2)); }
977	<	}
978	<	}
979	<	}
980	<	// Consider combining together the solving pair part w/ the searching
981	<	// best solution part so that we don't need the pairs vector
982	<	if (!rps.empty()) {
983	<	RealType smallestDiff = HONKING_LARGE_VALUE;
984	<	RealType diff;
985	<	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
986	<	vector<pair<RealType,RealType> >::iterator rpi;
987	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
988	<	r1 = (*rpi).first;
989	<	r2 = (*rpi).second;
990	<	switch(rnemdType_) {
991	<	case rnemdKineticScale :
992	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
993	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
994	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
995	<	break;
996	<	case rnemdPxScale :
997	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
998	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
999	<	break;
1000	<	case rnemdPyScale :
1001	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1002	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1003	<	break;
1004	<	case rnemdPzScale :
1005	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1006	<	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1007	<	default :
1008	<	break;
1009	<	}
1010	<	if (diff < smallestDiff) {
1011	<	smallestDiff = diff;
1012	<	bestPair = *rpi;
1013	<	}
1014	<	}
1015	<	#ifdef IS_MPI
1016	<	if (worldRank == 0) {
1017	<	#endif
1018	<	sprintf(painCave.errMsg,
1019	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1020	<	bestPair.first, bestPair.second);
1021	<	painCave.isFatal = 0;
1022	<	painCave.severity = OPENMD_INFO;
1023	<	simError();
1024	<	#ifdef IS_MPI
967	>	} else {
968	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
969	>	switch(rnemdFluxType_) {
970	>	case rnemdKE :
971	>	/* used hotBin coeff's & only scale x & y dimensions
972	>	RealType px = Phx / Pcx;
973	>	RealType py = Phy / Pcy;
974	>	a110 = Khy;
975	>	c0 = - Khx - Khy - kineticTarget_;
976	>	a000 = Khx;
977	>	a111 = Kcy * py * py;
978	>	b11 = -2.0 * Kcy * py * (1.0 + py);
979	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
980	>	b01 = -2.0 * Kcx * px * (1.0 + px);
981	>	a001 = Kcx * px * px;
982	>	*/
983	>	//scale all three dimensions, let c_x = c_y
984	>	a000 = Kcx + Kcy;
985	>	a110 = Kcz;
986	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
987	>	a001 = Khx * px * px + Khy * py * py;
988	>	a111 = Khz * pz * pz;
989	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
990	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
991	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
992	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
993	>	break;
994	>	case rnemdPx :
995	>	c = 1 - momentumTarget_.x() / Pcx;
996	>	a000 = Kcy;
997	>	a110 = Kcz;
998	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
999	>	a001 = py * py * Khy;
1000	>	a111 = pz * pz * Khz;
1001	>	b01 = -2.0 * Khy * py * (1.0 + py);
1002	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1003	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1004	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1005	>	break;
1006	>	case rnemdPy :
1007	>	c = 1 - momentumTarget_.y() / Pcy;
1008	>	a000 = Kcx;
1009	>	a110 = Kcz;
1010	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1011	>	a001 = px * px * Khx;
1012	>	a111 = pz * pz * Khz;
1013	>	b01 = -2.0 * Khx * px * (1.0 + px);
1014	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1015	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1016	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1017	>	break;
1018	>	case rnemdPz ://we don't really do this, do we?
1019	>	c = 1 - momentumTarget_.z() / Pcz;
1020	>	a000 = Kcx;
1021	>	a110 = Kcy;
1022	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1023	>	a001 = px * px * Khx;
1024	>	a111 = py * py * Khy;
1025	>	b01 = -2.0 * Khx * px * (1.0 + px);
1026	>	b11 = -2.0 * Khy * py * (1.0 + py);
1027	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1028	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1029	>	break;
1030	>	default :
1031	>	break;
1032		}
857	–	#endif
1033
1034	<	RealType x, y, z;
1035	<	switch(rnemdType_) {
1036	<	case rnemdKineticScale :
1037	<	x = bestPair.first;
1038	<	y = bestPair.first;
1039	<	z = bestPair.second;
1040	<	break;
1041	<	case rnemdPxScale :
1042	<	x = c;
1043	<	y = bestPair.first;
1044	<	z = bestPair.second;
1045	<	break;
1046	<	case rnemdPyScale :
1047	<	x = bestPair.first;
1048	<	y = c;
1049	<	z = bestPair.second;
1050	<	break;
1051	<	case rnemdPzScale :
1052	<	x = bestPair.first;
1053	<	y = bestPair.second;
1054	<	z = c;
1055	<	break;
1056	<	default :
1057	<	break;
1034	>	RealType v1 = a000 * a111 - a001 * a110;
1035	>	RealType v2 = a000 * b01;
1036	>	RealType v3 = a000 * b11;
1037	>	RealType v4 = a000 * c1 - a001 * c0;
1038	>	RealType v8 = a110 * b01;
1039	>	RealType v10 = - b01 * c0;
1040	>
1041	>	RealType u0 = v2 * v10 - v4 * v4;
1042	>	RealType u1 = -2.0 * v3 * v4;
1043	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1044	>	RealType u3 = -2.0 * v1 * v3;
1045	>	RealType u4 = - v1 * v1;
1046	>	//rescale coefficients
1047	>	RealType maxAbs = fabs(u0);
1048	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1049	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1050	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1051	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1052	>	u0 /= maxAbs;
1053	>	u1 /= maxAbs;
1054	>	u2 /= maxAbs;
1055	>	u3 /= maxAbs;
1056	>	u4 /= maxAbs;
1057	>	//max_element(start, end) is also available.
1058	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1059	>	poly.setCoefficient(4, u4);
1060	>	poly.setCoefficient(3, u3);
1061	>	poly.setCoefficient(2, u2);
1062	>	poly.setCoefficient(1, u1);
1063	>	poly.setCoefficient(0, u0);
1064	>	vector<RealType> realRoots = poly.FindRealRoots();
1065	>
1066	>	vector<RealType>::iterator ri;
1067	>	RealType r1, r2, alpha0;
1068	>	vector<pair<RealType,RealType> > rps;
1069	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1070	>	r2 = *ri;
1071	>	//check if FindRealRoots() give the right answer
1072	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1073	>	sprintf(painCave.errMsg,
1074	>	"RNEMD Warning: polynomial solve seems to have an error!");
1075	>	painCave.isFatal = 0;
1076	>	simError();
1077	>	failRootCount_++;
1078	>	}
1079	>	//might not be useful w/o rescaling coefficients
1080	>	alpha0 = -c0 - a110 * r2 * r2;
1081	>	if (alpha0 >= 0.0) {
1082	>	r1 = sqrt(alpha0 / a000);
1083	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1084	>	< 1e-6)
1085	>	{ rps.push_back(make_pair(r1, r2)); }
1086	>	if (r1 > 1e-6) { //r1 non-negative
1087	>	r1 = -r1;
1088	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1089	>	< 1e-6)
1090	>	{ rps.push_back(make_pair(r1, r2)); }
1091	>	}
1092	>	}
1093		}
1094	<	vector<StuntDouble*>::iterator sdi;
1095	<	Vector3d vel;
1096	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1097	<	vel = (*sdi)->getVel();
1098	<	vel.x() *= x;
1099	<	vel.y() *= y;
1100	<	vel.z() *= z;
1101	<	(*sdi)->setVel(vel);
1094	>	// Consider combining together the solving pair part w/ the searching
1095	>	// best solution part so that we don't need the pairs vector
1096	>	if (!rps.empty()) {
1097	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1098	>	RealType diff;
1099	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1100	>	vector<pair<RealType,RealType> >::iterator rpi;
1101	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1102	>	r1 = (*rpi).first;
1103	>	r2 = (*rpi).second;
1104	>	switch(rnemdFluxType_) {
1105	>	case rnemdKE :
1106	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1107	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1108	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1109	>	break;
1110	>	case rnemdPx :
1111	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1113	>	break;
1114	>	case rnemdPy :
1115	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1116	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1117	>	break;
1118	>	case rnemdPz :
1119	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1120	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1121	>	default :
1122	>	break;
1123	>	}
1124	>	if (diff < smallestDiff) {
1125	>	smallestDiff = diff;
1126	>	bestPair = *rpi;
1127	>	}
1128	>	}
1129	>	#ifdef IS_MPI
1130	>	if (worldRank == 0) {
1131	>	#endif
1132	>	// sprintf(painCave.errMsg,
1133	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1134	>	//         bestPair.first, bestPair.second);
1135	>	// painCave.isFatal = 0;
1136	>	// painCave.severity = OPENMD_INFO;
1137	>	// simError();
1138	>	#ifdef IS_MPI
1139	>	}
1140	>	#endif
1141	>
1142	>	switch(rnemdFluxType_) {
1143	>	case rnemdKE :
1144	>	x = bestPair.first;
1145	>	y = bestPair.first;
1146	>	z = bestPair.second;
1147	>	break;
1148	>	case rnemdPx :
1149	>	x = c;
1150	>	y = bestPair.first;
1151	>	z = bestPair.second;
1152	>	break;
1153	>	case rnemdPy :
1154	>	x = bestPair.first;
1155	>	y = c;
1156	>	z = bestPair.second;
1157	>	break;
1158	>	case rnemdPz :
1159	>	x = bestPair.first;
1160	>	y = bestPair.second;
1161	>	z = c;
1162	>	break;
1163	>	default :
1164	>	break;
1165	>	}
1166	>	vector<StuntDouble*>::iterator sdi;
1167	>	Vector3d vel;
1168	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1169	>	vel = (*sdi)->getVel();
1170	>	vel.x() *= x;
1171	>	vel.y() *= y;
1172	>	vel.z() *= z;
1173	>	(*sdi)->setVel(vel);
1174	>	}
1175	>	//convert to hotBin coefficient
1176	>	x = 1.0 + px * (1.0 - x);
1177	>	y = 1.0 + py * (1.0 - y);
1178	>	z = 1.0 + pz * (1.0 - z);
1179	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1180	>	vel = (*sdi)->getVel();
1181	>	vel.x() *= x;
1182	>	vel.y() *= y;
1183	>	vel.z() *= z;
1184	>	(*sdi)->setVel(vel);
1185	>	}
1186	>	successfulScale = true;
1187	>	switch(rnemdFluxType_) {
1188	>	case rnemdKE :
1189	>	kineticExchange_ += kineticTarget_;
1190	>	break;
1191	>	case rnemdPx :
1192	>	case rnemdPy :
1193	>	case rnemdPz :
1194	>	momentumExchange_ += momentumTarget_;
1195	>	break;
1196	>	default :
1197	>	break;
1198	>	}
1199		}
1200	<	//convert to hotBin coefficient
1201	<	x = 1.0 + px * (1.0 - x);
895	<	y = 1.0 + py * (1.0 - y);
896	<	z = 1.0 + pz * (1.0 - z);
897	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
898	<	vel = (*sdi)->getVel();
899	<	vel.x() *= x;
900	<	vel.y() *= y;
901	<	vel.z() *= z;
902	<	(*sdi)->setVel(vel);
903	<	}
904	<	exchangeSum_ += targetFlux_;
905	<	//we may want to check whether the exchange has been successful
906	<	} else {
1200	>	}
1201	>	if (successfulScale != true) {
1202		sprintf(painCave.errMsg,
1203	<	"RNEMD: exchange NOT performed!\n");
1203	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1204	>	"\tthe constraint equations may not exist or there may be\n"
1205	>	"\tno selected objects in one or both slabs.\n");
1206		painCave.isFatal = 0;
1207		painCave.severity = OPENMD_INFO;
1208		simError();
1209		failTrialCount_++;
1210		}
1211	+	}
1212
1213	+	void RNEMD::doVSS() {
1214	+	if (!doRNEMD_) return;
1215	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1216	+	RealType time = currentSnap_->getTime();
1217	+	Mat3x3d hmat = currentSnap_->getHmat();
1218	+
1219	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1220	+
1221	+	int selei;
1222	+	StuntDouble* sd;
1223	+
1224	+	vector<StuntDouble*> hotBin, coldBin;
1225	+
1226	+	Vector3d Ph(V3Zero);
1227	+	RealType Mh = 0.0;
1228	+	RealType Kh = 0.0;
1229	+	Vector3d Pc(V3Zero);
1230	+	RealType Mc = 0.0;
1231	+	RealType Kc = 0.0;
1232	+
1233	+
1234	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1235	+	sd = seleMan_.nextSelected(selei)) {
1236	+
1237	+	Vector3d pos = sd->getPos();
1238	+
1239	+	// wrap the stuntdouble's position back into the box:
1240	+
1241	+	if (usePeriodicBoundaryConditions_)
1242	+	currentSnap_->wrapVector(pos);
1243	+
1244	+	// which bin is this stuntdouble in?
1245	+	bool inA = inSlabA(pos);
1246	+	bool inB = inSlabB(pos);
1247	+
1248	+	if (inA || inB) {
1249	+
1250	+	RealType mass = sd->getMass();
1251	+	Vector3d vel = sd->getVel();
1252	+
1253	+	if (inA) {
1254	+	hotBin.push_back(sd);
1255	+	Ph += mass * vel;
1256	+	Mh += mass;
1257	+	Kh += mass * vel.lengthSquare();
1258	+	if (rnemdFluxType_ == rnemdFullKE) {
1259	+	if (sd->isDirectional()) {
1260	+	Vector3d angMom = sd->getJ();
1261	+	Mat3x3d I = sd->getI();
1262	+	if (sd->isLinear()) {
1263	+	int i = sd->linearAxis();
1264	+	int j = (i + 1) % 3;
1265	+	int k = (i + 2) % 3;
1266	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1267	+	angMom[k] * angMom[k] / I(k, k);
1268	+	} else {
1269	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1270	+	angMom[1] * angMom[1] / I(1, 1) +
1271	+	angMom[2] * angMom[2] / I(2, 2);
1272	+	}
1273	+	}
1274	+	}
1275	+	} else { //midBin_
1276	+	coldBin.push_back(sd);
1277	+	Pc += mass * vel;
1278	+	Mc += mass;
1279	+	Kc += mass * vel.lengthSquare();
1280	+	if (rnemdFluxType_ == rnemdFullKE) {
1281	+	if (sd->isDirectional()) {
1282	+	Vector3d angMom = sd->getJ();
1283	+	Mat3x3d I = sd->getI();
1284	+	if (sd->isLinear()) {
1285	+	int i = sd->linearAxis();
1286	+	int j = (i + 1) % 3;
1287	+	int k = (i + 2) % 3;
1288	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1289	+	angMom[k] * angMom[k] / I(k, k);
1290	+	} else {
1291	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1292	+	angMom[1] * angMom[1] / I(1, 1) +
1293	+	angMom[2] * angMom[2] / I(2, 2);
1294	+	}
1295	+	}
1296	+	}
1297	+	}
1298	+	}
1299	+	}
1300	+
1301	+	Kh *= 0.5;
1302	+	Kc *= 0.5;
1303	+
1304	+	#ifdef IS_MPI
1305	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1306	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1307	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1308	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1309	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1310	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1311	+	#endif
1312	+
1313	+	bool successfulExchange = false;
1314	+	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1315	+	Vector3d vc = Pc / Mc;
1316	+	Vector3d ac = -momentumTarget_ / Mc + vc;
1317	+	Vector3d acrec = -momentumTarget_ / Mc;
1318	+	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1319	+	if (cNumerator > 0.0) {
1320	+	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1321	+	if (cDenominator > 0.0) {
1322	+	RealType c = sqrt(cNumerator / cDenominator);
1323	+	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1324	+	Vector3d vh = Ph / Mh;
1325	+	Vector3d ah = momentumTarget_ / Mh + vh;
1326	+	Vector3d ahrec = momentumTarget_ / Mh;
1327	+	RealType hNumerator = Kh + kineticTarget_
1328	+	- 0.5 * Mh * ah.lengthSquare();
1329	+	if (hNumerator > 0.0) {
1330	+	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1331	+	if (hDenominator > 0.0) {
1332	+	RealType h = sqrt(hNumerator / hDenominator);
1333	+	if ((h > 0.9) && (h < 1.1)) {
1334	+
1335	+	vector<StuntDouble*>::iterator sdi;
1336	+	Vector3d vel;
1337	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1338	+	//vel = (*sdi)->getVel();
1339	+	vel = ((*sdi)->getVel() - vc) * c + ac;
1340	+	(*sdi)->setVel(vel);
1341	+	if (rnemdFluxType_ == rnemdFullKE) {
1342	+	if ((*sdi)->isDirectional()) {
1343	+	Vector3d angMom = (*sdi)->getJ() * c;
1344	+	(*sdi)->setJ(angMom);
1345	+	}
1346	+	}
1347	+	}
1348	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1349	+	//vel = (*sdi)->getVel();
1350	+	vel = ((*sdi)->getVel() - vh) * h + ah;
1351	+	(*sdi)->setVel(vel);
1352	+	if (rnemdFluxType_ == rnemdFullKE) {
1353	+	if ((*sdi)->isDirectional()) {
1354	+	Vector3d angMom = (*sdi)->getJ() * h;
1355	+	(*sdi)->setJ(angMom);
1356	+	}
1357	+	}
1358	+	}
1359	+	successfulExchange = true;
1360	+	kineticExchange_ += kineticTarget_;
1361	+	momentumExchange_ += momentumTarget_;
1362	+	}
1363	+	}
1364	+	}
1365	+	}
1366	+	}
1367	+	}
1368	+	}
1369	+	if (successfulExchange != true) {
1370	+	sprintf(painCave.errMsg,
1371	+	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1372	+	"\tthe constraint equations may not exist or there may be\n"
1373	+	"\tno selected objects in one or both slabs.\n");
1374	+	painCave.isFatal = 0;
1375	+	painCave.severity = OPENMD_INFO;
1376	+	simError();
1377	+	failTrialCount_++;
1378	+	}
1379		}
1380
1381		void RNEMD::doRNEMD() {
1382	<
1383	<	switch(rnemdType_) {
1384	<	case rnemdKineticScale :
1385	<	case rnemdPxScale :
922	<	case rnemdPyScale :
923	<	case rnemdPzScale :
924	<	doScale();
925	<	break;
926	<	case rnemdKineticSwap :
927	<	case rnemdPx :
928	<	case rnemdPy :
929	<	case rnemdPz :
1382	>	if (!doRNEMD_) return;
1383	>	trialCount_++;
1384	>	switch(rnemdMethod_) {
1385	>	case rnemdSwap:
1386		doSwap();
1387		break;
1388	<	case rnemdUnknown :
1388	>	case rnemdNIVS:
1389	>	doNIVS();
1390	>	break;
1391	>	case rnemdVSS:
1392	>	doVSS();
1393	>	break;
1394	>	case rnemdUnkownMethod:
1395		default :
1396		break;
1397		}
1398		}
1399
1400		void RNEMD::collectData() {
1401	<
1401	>	if (!doRNEMD_) return;
1402		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1403		Mat3x3d hmat = currentSnap_->getHmat();
1404
1405	+	areaAccumulator_->add(currentSnap_->getXYarea());
1406	+
1407		seleMan_.setSelectionSet(evaluator_.evaluate());
1408
1409	<	int selei;
1409	>	int selei(0);
1410		StuntDouble* sd;
947	–	int idx;
1411
1412	+	vector<RealType> binMass(nBins_, 0.0);
1413	+	vector<RealType> binPx(nBins_, 0.0);
1414	+	vector<RealType> binPy(nBins_, 0.0);
1415	+	vector<RealType> binPz(nBins_, 0.0);
1416	+	vector<RealType> binKE(nBins_, 0.0);
1417	+	vector<int> binDOF(nBins_, 0);
1418	+	vector<int> binCount(nBins_, 0);
1419	+
1420		// alternative approach, track all molecules instead of only those
1421		// selected for scaling/swapping:
1422		/*
1423		SimInfo::MoleculeIterator miter;
1424		vector<StuntDouble*>::iterator iiter;
1425		Molecule* mol;
1426	<	StuntDouble* integrableObject;
1426	>	StuntDouble* sd;
1427		for (mol = info_->beginMolecule(miter); mol != NULL;
1428	<	mol = info_->nextMolecule(miter))
1429	<	integrableObject is essentially sd
1430	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1431	<	integrableObject != NULL;
1432	<	integrableObject = mol->nextIntegrableObject(iiter))
1428	>	mol = info_->nextMolecule(miter))
1429	>	sd is essentially sd
1430	>	for (sd = mol->beginIntegrableObject(iiter);
1431	>	sd != NULL;
1432	>	sd = mol->nextIntegrableObject(iiter))
1433		*/
1434	+
1435		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1436	<	sd = seleMan_.nextSelected(selei)) {
1437	<
966	<	idx = sd->getLocalIndex();
967	<
1436	>	sd = seleMan_.nextSelected(selei)) {
1437	>
1438		Vector3d pos = sd->getPos();
1439
1440		// wrap the stuntdouble's position back into the box:
1441
1442		if (usePeriodicBoundaryConditions_)
1443		currentSnap_->wrapVector(pos);
1444	<
1444	>
1445	>
1446		// which bin is this stuntdouble in?
1447		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1448	<
1449	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1450	<	rnemdLogWidth_;
1451	<	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
1452	<	/*
982	<	if (rnemdLogWidth_ == midBin_ + 1)
983	<	if (binNo > midBin_)
984	<	binNo = nBins_ - binNo;
985	<	*/
1448	>	// Shift molecules by half a box to have bins start at 0
1449	>	// The modulo operator is used to wrap the case when we are
1450	>	// beyond the end of the bins back to the beginning.
1451	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1452	>
1453		RealType mass = sd->getMass();
1454		Vector3d vel = sd->getVel();
988	–	RealType value;
989	–	RealType xVal, yVal, zVal;
1455
1456	<	switch(rnemdType_) {
1457	<	case rnemdKineticSwap :
1458	<	case rnemdKineticScale :
1459	<
1460	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
1461	<
1462	<	valueCount_[binNo] += 3;
1463	<	if (sd->isDirectional()) {
1464	<	Vector3d angMom = sd->getJ();
1465	<	Mat3x3d I = sd->getI();
1466	<
1467	<	if (sd->isLinear()) {
1468	<	int i = sd->linearAxis();
1469	<	int j = (i + 1) % 3;
1470	<	int k = (i + 2) % 3;
1471	<	value += angMom[j] * angMom[j] / I(j, j) +
1472	<	angMom[k] * angMom[k] / I(k, k);
1473	<
1474	<	valueCount_[binNo] +=2;
1475	<
1476	<	} else {
1477	<	value += angMom[0]*angMom[0]/I(0, 0)
1478	<	+ angMom[1]*angMom[1]/I(1, 1)
1479	<	+ angMom[2]*angMom[2]/I(2, 2);
1015	<	valueCount_[binNo] +=3;
1016	<	}
1017	<	}
1018	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1019	<
1020	<	break;
1021	<	case rnemdPx :
1022	<	case rnemdPxScale :
1023	<	value = mass * vel[0];
1024	<	valueCount_[binNo]++;
1025	<	break;
1026	<	case rnemdPy :
1027	<	case rnemdPyScale :
1028	<	value = mass * vel[1];
1029	<	valueCount_[binNo]++;
1030	<	break;
1031	<	case rnemdPz :
1032	<	case rnemdPzScale :
1033	<	value = pos.z(); //temporarily for homogeneous systems ONLY
1034	<	valueCount_[binNo]++;
1035	<	break;
1036	<	case rnemdUnknown :
1037	<	default :
1038	<	value = 1.0;
1039	<	valueCount_[binNo]++;
1040	<	break;
1456	>	binCount[binNo]++;
1457	>	binMass[binNo] += mass;
1458	>	binPx[binNo] += mass*vel.x();
1459	>	binPy[binNo] += mass*vel.y();
1460	>	binPz[binNo] += mass*vel.z();
1461	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1462	>	binDOF[binNo] += 3;
1463	>
1464	>	if (sd->isDirectional()) {
1465	>	Vector3d angMom = sd->getJ();
1466	>	Mat3x3d I = sd->getI();
1467	>	if (sd->isLinear()) {
1468	>	int i = sd->linearAxis();
1469	>	int j = (i + 1) % 3;
1470	>	int k = (i + 2) % 3;
1471	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1472	>	angMom[k] * angMom[k] / I(k, k));
1473	>	binDOF[binNo] += 2;
1474	>	} else {
1475	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1476	>	angMom[1] * angMom[1] / I(1, 1) +
1477	>	angMom[2] * angMom[2] / I(2, 2));
1478	>	binDOF[binNo] += 3;
1479	>	}
1480		}
1481	<	valueHist_[binNo] += value;
1481	>	}
1482	>
1483	>	#ifdef IS_MPI
1484	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1485	>	nBins_, MPI::INT, MPI::SUM);
1486	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1487	>	nBins_, MPI::REALTYPE, MPI::SUM);
1488	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1489	>	nBins_, MPI::REALTYPE, MPI::SUM);
1490	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1491	>	nBins_, MPI::REALTYPE, MPI::SUM);
1492	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1493	>	nBins_, MPI::REALTYPE, MPI::SUM);
1494	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1495	>	nBins_, MPI::REALTYPE, MPI::SUM);
1496	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1497	>	nBins_, MPI::INT, MPI::SUM);
1498	>	#endif
1499
1500	<	if (output3DTemp_) {
1501	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1502	<	/ PhysicalConstants::kb;
1503	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1504	<	/ PhysicalConstants::kb;
1505	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1506	<	/ PhysicalConstants::kb;
1507	<	xTempHist_[binNo] += xVal;
1508	<	yTempHist_[binNo] += yVal;
1509	<	zTempHist_[binNo] += zVal;
1510	<	xyzTempCount_[binNo]++;
1500	>	Vector3d vel;
1501	>	RealType den;
1502	>	RealType temp;
1503	>	RealType z;
1504	>	for (int i = 0; i < nBins_; i++) {
1505	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1506	>	vel.x() = binPx[i] / binMass[i];
1507	>	vel.y() = binPy[i] / binMass[i];
1508	>	vel.z() = binPz[i] / binMass[i];
1509	>
1510	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1511	>	/ currentSnap_->getVolume() ;
1512	>
1513	>	if (binCount[i] > 0) {
1514	>	// only add values if there are things to add
1515	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1516	>	PhysicalConstants::energyConvert);
1517	>
1518	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1519	>	if(outputMask_[j]) {
1520	>	switch(j) {
1521	>	case Z:
1522	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1523	>	break;
1524	>	case TEMPERATURE:
1525	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1526	>	break;
1527	>	case VELOCITY:
1528	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1529	>	break;
1530	>	case DENSITY:
1531	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1532	>	break;
1533	>	}
1534	>	}
1535	>	}
1536		}
1537		}
1538		}
1539
1540		void RNEMD::getStarted() {
1541	+	if (!doRNEMD_) return;
1542		collectData();
1543	<	/* now should be able to output profile in step 0, but might not be useful
1062	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1063	<	Stats& stat = currentSnap_->statData;
1064	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1065	<	*/
1066	<	getStatus();
1543	>	writeOutputFile();
1544		}
1545
1546	<	void RNEMD::getStatus() {
1547	<
1548	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1549	<	Stats& stat = currentSnap_->statData;
1550	<	RealType time = currentSnap_->getTime();
1551	<
1552	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1553	<	//or to be more meaningful, define another item as exchangeSum_ / time
1554	<	int j;
1555	<
1546	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1547	>	if (!doRNEMD_) return;
1548	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1549	>
1550	>	while(tokenizer.hasMoreTokens()) {
1551	>	std::string token(tokenizer.nextToken());
1552	>	toUpper(token);
1553	>	OutputMapType::iterator i = outputMap_.find(token);
1554	>	if (i != outputMap_.end()) {
1555	>	outputMask_.set(i->second);
1556	>	} else {
1557	>	sprintf( painCave.errMsg,
1558	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1559	>	"\toutputFileFormat keyword.\n", token.c_str() );
1560	>	painCave.isFatal = 0;
1561	>	painCave.severity = OPENMD_ERROR;
1562	>	simError();
1563	>	}
1564	>	}
1565	>	}
1566	>
1567	>	void RNEMD::writeOutputFile() {
1568	>	if (!doRNEMD_) return;
1569	>
1570		#ifdef IS_MPI
1080	–
1081	–	// all processors have the same number of bins, and STL vectors pack their
1082	–	// arrays, so in theory, this should be safe:
1083	–
1084	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1085	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1086	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1087	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1088	–	if (output3DTemp_) {
1089	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1090	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1091	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1092	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1093	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1094	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1095	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1096	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1097	–	}
1571		// If we're the root node, should we print out the results
1572		int worldRank = MPI::COMM_WORLD.Get_rank();
1573		if (worldRank == 0) {
1574		#endif
1575	<	rnemdLog_ << time;
1576	<	for (j = 0; j < rnemdLogWidth_; j++) {
1577	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1575	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1576	>
1577	>	if( !rnemdFile_ ){
1578	>	sprintf( painCave.errMsg,
1579	>	"Could not open \"%s\" for RNEMD output.\n",
1580	>	rnemdFileName_.c_str());
1581	>	painCave.isFatal = 1;
1582	>	simError();
1583		}
1584	<	rnemdLog_ << "\n";
1585	<	if (output3DTemp_) {
1586	<	xTempLog_ << time;
1587	<	for (j = 0; j < rnemdLogWidth_; j++) {
1588	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1584	>
1585	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1586	>
1587	>	RealType time = currentSnap_->getTime();
1588	>	RealType avgArea;
1589	>	areaAccumulator_->getAverage(avgArea);
1590	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1591	>	/ PhysicalConstants::energyConvert;
1592	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1593	>
1594	>	rnemdFile_ << "#######################################################\n";
1595	>	rnemdFile_ << "# RNEMD {\n";
1596	>
1597	>	map<string, RNEMDMethod>::iterator mi;
1598	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1599	>	if ( (*mi).second == rnemdMethod_)
1600	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1601	>	}
1602	>	map<string, RNEMDFluxType>::iterator fi;
1603	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1604	>	if ( (*fi).second == rnemdFluxType_)
1605	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1606	>	}
1607	>
1608	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1609	>
1610	>	rnemdFile_ << "#    objectSelection = \""
1611	>	<< rnemdObjectSelection_ << "\";\n";
1612	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1613	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1614	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1615	>	rnemdFile_ << "# }\n";
1616	>	rnemdFile_ << "#######################################################\n";
1617	>	rnemdFile_ << "# RNEMD report:\n";
1618	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1619	>	rnemdFile_ << "#     target flux:\n";
1620	>	rnemdFile_ << "#         kinetic = "
1621	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1622	>	<< " (kcal/mol/A^2/fs)\n";
1623	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1624	>	<< " (amu/A/fs^2)\n";
1625	>	rnemdFile_ << "#     target one-time exchanges:\n";
1626	>	rnemdFile_ << "#         kinetic = "
1627	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1628	>	<< " (kcal/mol)\n";
1629	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1630	>	<< " (amu*A/fs)\n";
1631	>	rnemdFile_ << "#     actual exchange totals:\n";
1632	>	rnemdFile_ << "#         kinetic = "
1633	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1634	>	<< " (kcal/mol)\n";
1635	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1636	>	<< " (amu*A/fs)\n";
1637	>	rnemdFile_ << "#     actual flux:\n";
1638	>	rnemdFile_ << "#         kinetic = " << Jz
1639	>	<< " (kcal/mol/A^2/fs)\n";
1640	>	rnemdFile_ << "#         momentum = " << JzP
1641	>	<< " (amu/A/fs^2)\n";
1642	>	rnemdFile_ << "#     exchange statistics:\n";
1643	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1644	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1645	>	if (rnemdMethod_ == rnemdNIVS) {
1646	>	rnemdFile_ << "#         NIVS root-check errors = "
1647	>	<< failRootCount_ << "\n";
1648	>	}
1649	>	rnemdFile_ << "#######################################################\n";
1650	>
1651	>
1652	>
1653	>	//write title
1654	>	rnemdFile_ << "#";
1655	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1656	>	if (outputMask_[i]) {
1657	>	rnemdFile_ << "\t" << data_[i].title <<
1658	>	"(" << data_[i].units << ")";
1659	>	// add some extra tabs for column alignment
1660	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1661		}
1662	<	xTempLog_ << "\n";
1663	<	yTempLog_ << time;
1664	<	for (j = 0; j < rnemdLogWidth_; j++) {
1665	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1662	>	}
1663	>	rnemdFile_ << std::endl;
1664	>
1665	>	rnemdFile_.precision(8);
1666	>
1667	>	for (int j = 0; j < nBins_; j++) {
1668	>
1669	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1670	>	if (outputMask_[i]) {
1671	>	if (data_[i].dataType == "RealType")
1672	>	writeReal(i,j);
1673	>	else if (data_[i].dataType == "Vector3d")
1674	>	writeVector(i,j);
1675	>	else {
1676	>	sprintf( painCave.errMsg,
1677	>	"RNEMD found an unknown data type for: %s ",
1678	>	data_[i].title.c_str());
1679	>	painCave.isFatal = 1;
1680	>	simError();
1681	>	}
1682	>	}
1683		}
1684	<	yTempLog_ << "\n";
1685	<	zTempLog_ << time;
1686	<	for (j = 0; j < rnemdLogWidth_; j++) {
1687	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1684	>	rnemdFile_ << std::endl;
1685	>
1686	>	}
1687	>
1688	>	rnemdFile_ << "#######################################################\n";
1689	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1690	>	rnemdFile_ << "#######################################################\n";
1691	>
1692	>
1693	>	for (int j = 0; j < nBins_; j++) {
1694	>	rnemdFile_ << "#";
1695	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1696	>	if (outputMask_[i]) {
1697	>	if (data_[i].dataType == "RealType")
1698	>	writeRealStdDev(i,j);
1699	>	else if (data_[i].dataType == "Vector3d")
1700	>	writeVectorStdDev(i,j);
1701	>	else {
1702	>	sprintf( painCave.errMsg,
1703	>	"RNEMD found an unknown data type for: %s ",
1704	>	data_[i].title.c_str());
1705	>	painCave.isFatal = 1;
1706	>	simError();
1707	>	}
1708	>	}
1709		}
1710	<	zTempLog_ << "\n";
1711	<	}
1710	>	rnemdFile_ << std::endl;
1711	>
1712	>	}
1713	>
1714	>	rnemdFile_.flush();
1715	>	rnemdFile_.close();
1716	>
1717		#ifdef IS_MPI
1718		}
1719		#endif
1720	<	for (j = 0; j < rnemdLogWidth_; j++) {
1721	<	valueCount_[j] = 0;
1722	<	valueHist_[j] = 0.0;
1720	>
1721	>	}
1722	>
1723	>	void RNEMD::writeReal(int index, unsigned int bin) {
1724	>	if (!doRNEMD_) return;
1725	>	assert(index >=0 && index < ENDINDEX);
1726	>	assert(bin < nBins_);
1727	>	RealType s;
1728	>
1729	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
1730	>
1731	>	if (! isinf(s) && ! isnan(s)) {
1732	>	rnemdFile_ << "\t" << s;
1733	>	} else{
1734	>	sprintf( painCave.errMsg,
1735	>	"RNEMD detected a numerical error writing: %s for bin %d",
1736	>	data_[index].title.c_str(), bin);
1737	>	painCave.isFatal = 1;
1738	>	simError();
1739	>	}
1740	>	}
1741	>
1742	>	void RNEMD::writeVector(int index, unsigned int bin) {
1743	>	if (!doRNEMD_) return;
1744	>	assert(index >=0 && index < ENDINDEX);
1745	>	assert(bin < nBins_);
1746	>	Vector3d s;
1747	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1748	>	if (isinf(s[0]) || isnan(s[0]) ||
1749	>	isinf(s[1]) || isnan(s[1]) ||
1750	>	isinf(s[2]) || isnan(s[2]) ) {
1751	>	sprintf( painCave.errMsg,
1752	>	"RNEMD detected a numerical error writing: %s for bin %d",
1753	>	data_[index].title.c_str(), bin);
1754	>	painCave.isFatal = 1;
1755	>	simError();
1756	>	} else {
1757	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1758		}
1759	<	if (output3DTemp_)
1760	<	for (j = 0; j < rnemdLogWidth_; j++) {
1761	<	xTempHist_[j] = 0.0;
1762	<	yTempHist_[j] = 0.0;
1763	<	zTempHist_[j] = 0.0;
1764	<	xyzTempCount_[j] = 0;
1765	<	}
1759	>	}
1760	>
1761	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1762	>	if (!doRNEMD_) return;
1763	>	assert(index >=0 && index < ENDINDEX);
1764	>	assert(bin < nBins_);
1765	>	RealType s;
1766	>
1767	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
1768	>
1769	>	if (! isinf(s) && ! isnan(s)) {
1770	>	rnemdFile_ << "\t" << s;
1771	>	} else{
1772	>	sprintf( painCave.errMsg,
1773	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1774	>	data_[index].title.c_str(), bin);
1775	>	painCave.isFatal = 1;
1776	>	simError();
1777	>	}
1778		}
1779	+
1780	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1781	+	if (!doRNEMD_) return;
1782	+	assert(index >=0 && index < ENDINDEX);
1783	+	assert(bin < nBins_);
1784	+	Vector3d s;
1785	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1786	+	if (isinf(s[0]) || isnan(s[0]) ||
1787	+	isinf(s[1]) || isnan(s[1]) ||
1788	+	isinf(s[2]) || isnan(s[2]) ) {
1789	+	sprintf( painCave.errMsg,
1790	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1791	+	data_[index].title.c_str(), bin);
1792	+	painCave.isFatal = 1;
1793	+	simError();
1794	+	} else {
1795	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1796	+	}
1797	+	}
1798		}
1799	+

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