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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 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	<
53	<	#ifndef IS_MPI
53	<	#include "math/SeqRandNumGen.hpp"
54	<	#else
55	<	#include "math/ParallelRandNumGen.hpp"
52	>	#ifdef IS_MPI
53	>	#include <mpi.h>
54		#endif
55
56		#define HONKING_LARGE_VALUE 1.0e10
57
58	+	using namespace std;
59		namespace OpenMD {
60
61	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
61	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
62	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63
64	+	trialCount_ = 0;
65		failTrialCount_ = 0;
66		failRootCount_ = 0;
67
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
74	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
73	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
74	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
75	<	stringToEnumMap_["Px"] = rnemdPx;
76	<	stringToEnumMap_["Py"] = rnemdPy;
77	<	stringToEnumMap_["Pz"] = rnemdPz;
78	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	stringToMethod_["Swap"]  = rnemdSwap;
73	>	stringToMethod_["NIVS"]  = rnemdNIVS;
74	>	stringToMethod_["VSS"]   = rnemdVSS;
75
76	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
76	>	stringToFluxType_["KE"]  = rnemdKE;
77	>	stringToFluxType_["Px"]  = rnemdPx;
78	>	stringToFluxType_["Py"]  = rnemdPy;
79	>	stringToFluxType_["Pz"]  = rnemdPz;
80	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
81	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
82	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
83	>
84	>	runTime_ = simParams->getRunTime();
85	>	statusTime_ = simParams->getStatusTime();
86	>
87	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88		evaluator_.loadScriptString(rnemdObjectSelection_);
89		seleMan_.setSelectionSet(evaluator_.evaluate());
90
91	+	const string methStr = rnemdParams->getMethod();
92	+	bool hasFluxType = rnemdParams->haveFluxType();
93	+
94	+	string fluxStr;
95	+	if (hasFluxType) {
96	+	fluxStr = rnemdParams->getFluxType();
97	+	} else {
98	+	sprintf(painCave.errMsg,
99	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
100	+	"\twhich must be one of the following values:\n"
101	+	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
102	+	"\tuse RNEMD\n");
103	+	painCave.isFatal = 1;
104	+	painCave.severity = OPENMD_ERROR;
105	+	simError();
106	+	}
107	+
108	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
109	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
110	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
111	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
112	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
113	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
114	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
115	+	bool hasOutputFields = rnemdParams->haveOutputFields();
116	+
117	+	map<string, RNEMDMethod>::iterator i;
118	+	i = stringToMethod_.find(methStr);
119	+	if (i != stringToMethod_.end())
120	+	rnemdMethod_ = i->second;
121	+	else {
122	+	sprintf(painCave.errMsg,
123	+	"RNEMD: The current method,\n"
124	+	"\t\t%s is not one of the recognized\n"
125	+	"\texchange methods: Swap, NIVS, or VSS\n",
126	+	methStr.c_str());
127	+	painCave.isFatal = 1;
128	+	painCave.severity = OPENMD_ERROR;
129	+	simError();
130	+	}
131	+
132	+	map<string, RNEMDFluxType>::iterator j;
133	+	j = stringToFluxType_.find(fluxStr);
134	+	if (j != stringToFluxType_.end())
135	+	rnemdFluxType_ = j->second;
136	+	else {
137	+	sprintf(painCave.errMsg,
138	+	"RNEMD: The current fluxType,\n"
139	+	"\t\t%s\n"
140	+	"\tis not one of the recognized flux types.\n",
141	+	fluxStr.c_str());
142	+	painCave.isFatal = 1;
143	+	painCave.severity = OPENMD_ERROR;
144	+	simError();
145	+	}
146	+
147	+	bool methodFluxMismatch = false;
148	+	bool hasCorrectFlux = false;
149	+	switch(rnemdMethod_) {
150	+	case rnemdSwap:
151	+	switch (rnemdFluxType_) {
152	+	case rnemdKE:
153	+	hasCorrectFlux = hasKineticFlux;
154	+	break;
155	+	case rnemdPx:
156	+	case rnemdPy:
157	+	case rnemdPz:
158	+	hasCorrectFlux = hasMomentumFlux;
159	+	break;
160	+	default :
161	+	methodFluxMismatch = true;
162	+	break;
163	+	}
164	+	break;
165	+	case rnemdNIVS:
166	+	switch (rnemdFluxType_) {
167	+	case rnemdKE:
168	+	case rnemdRotKE:
169	+	case rnemdFullKE:
170	+	hasCorrectFlux = hasKineticFlux;
171	+	break;
172	+	case rnemdPx:
173	+	case rnemdPy:
174	+	case rnemdPz:
175	+	hasCorrectFlux = hasMomentumFlux;
176	+	break;
177	+	case rnemdKePx:
178	+	case rnemdKePy:
179	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
180	+	break;
181	+	default:
182	+	methodFluxMismatch = true;
183	+	break;
184	+	}
185	+	break;
186	+	case rnemdVSS:
187	+	switch (rnemdFluxType_) {
188	+	case rnemdKE:
189	+	case rnemdRotKE:
190	+	case rnemdFullKE:
191	+	hasCorrectFlux = hasKineticFlux;
192	+	break;
193	+	case rnemdPx:
194	+	case rnemdPy:
195	+	case rnemdPz:
196	+	hasCorrectFlux = hasMomentumFlux;
197	+	break;
198	+	case rnemdPvector:
199	+	hasCorrectFlux = hasMomentumFluxVector;
200	+	case rnemdKePx:
201	+	case rnemdKePy:
202	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
203	+	break;
204	+	case rnemdKePvector:
205	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
206	+	break;
207	+	default:
208	+	methodFluxMismatch = true;
209	+	break;
210	+	}
211	+	default:
212	+	break;
213	+	}
214	+
215	+	if (methodFluxMismatch) {
216	+	sprintf(painCave.errMsg,
217	+	"RNEMD: The current method,\n"
218	+	"\t\t%s\n"
219	+	"\tcannot be used with the current flux type, %s\n",
220	+	methStr.c_str(), fluxStr.c_str());
221	+	painCave.isFatal = 1;
222	+	painCave.severity = OPENMD_ERROR;
223	+	simError();
224	+	}
225	+	if (!hasCorrectFlux) {
226	+	sprintf(painCave.errMsg,
227	+	"RNEMD: The current method,\n"
228	+	"\t%s, and flux type %s\n"
229	+	"\tdid not have the correct flux value specified. Options\n"
230	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
231	+	methStr.c_str(), fluxStr.c_str());
232	+	painCave.isFatal = 1;
233	+	painCave.severity = OPENMD_ERROR;
234	+	simError();
235	+	}
236	+
237	+	if (hasKineticFlux) {
238	+	kineticFlux_ = rnemdParams->getKineticFlux();
239	+	} else {
240	+	kineticFlux_ = 0.0;
241	+	}
242	+	if (hasMomentumFluxVector) {
243	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
244	+	} else {
245	+	momentumFluxVector_ = V3Zero;
246	+	if (hasMomentumFlux) {
247	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
248	+	switch (rnemdFluxType_) {
249	+	case rnemdPx:
250	+	momentumFluxVector_.x() = momentumFlux;
251	+	break;
252	+	case rnemdPy:
253	+	momentumFluxVector_.y() = momentumFlux;
254	+	break;
255	+	case rnemdPz:
256	+	momentumFluxVector_.z() = momentumFlux;
257	+	break;
258	+	case rnemdKePx:
259	+	momentumFluxVector_.x() = momentumFlux;
260	+	break;
261	+	case rnemdKePy:
262	+	momentumFluxVector_.y() = momentumFlux;
263	+	break;
264	+	default:
265	+	break;
266	+	}
267	+	}
268	+	}
269	+
270		// do some sanity checking
271
272		int selectionCount = seleMan_.getSelectionCount();
#	Line 88 | Line 274 | namespace OpenMD {
274
275		if (selectionCount > nIntegrable) {
276		sprintf(painCave.errMsg,
277	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
277	>	"RNEMD: The current objectSelection,\n"
278		"\t\t%s\n"
279		"\thas resulted in %d selected objects.  However,\n"
280		"\tthe total number of integrable objects in the system\n"
#	Line 98 | Line 284 | namespace OpenMD {
284		rnemdObjectSelection_.c_str(),
285		selectionCount, nIntegrable);
286		painCave.isFatal = 0;
287	+	painCave.severity = OPENMD_WARNING;
288		simError();
102	–
289		}
104	–
105	–	const std::string st = simParams->getRNEMD_exchangeType();
290
291	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
108	<	i = stringToEnumMap_.find(st);
109	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	<	if (rnemdType_ == rnemdUnknown) {
111	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
112	<	}
291	>	nBins_ = rnemdParams->getOutputBins();
292
293	<	#ifdef IS_MPI
294	<	if (worldRank == 0) {
295	<	#endif
293	>	data_.resize(RNEMD::ENDINDEX);
294	>	OutputData z;
295	>	z.units =  "Angstroms";
296	>	z.title =  "Z";
297	>	z.dataType = "RealType";
298	>	z.accumulator.reserve(nBins_);
299	>	for (unsigned int i = 0; i < nBins_; i++)
300	>	z.accumulator.push_back( new Accumulator() );
301	>	data_[Z] = z;
302	>	outputMap_["Z"] =  Z;
303
304	<	std::string rnemdFileName;
305	<	std::string xTempFileName;
306	<	std::string yTempFileName;
307	<	std::string zTempFileName;
308	<	switch(rnemdType_) {
309	<	case rnemdKineticSwap :
310	<	case rnemdKineticScale :
311	<	rnemdFileName = "temperature.log";
304	>	OutputData temperature;
305	>	temperature.units =  "K";
306	>	temperature.title =  "Temperature";
307	>	temperature.dataType = "RealType";
308	>	temperature.accumulator.reserve(nBins_);
309	>	for (unsigned int i = 0; i < nBins_; i++)
310	>	temperature.accumulator.push_back( new Accumulator() );
311	>	data_[TEMPERATURE] = temperature;
312	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
313	>
314	>	OutputData velocity;
315	>	velocity.units = "amu/fs";
316	>	velocity.title =  "Velocity";
317	>	velocity.dataType = "Vector3d";
318	>	velocity.accumulator.reserve(nBins_);
319	>	for (unsigned int i = 0; i < nBins_; i++)
320	>	velocity.accumulator.push_back( new VectorAccumulator() );
321	>	data_[VELOCITY] = velocity;
322	>	outputMap_["VELOCITY"] = VELOCITY;
323	>
324	>	OutputData density;
325	>	density.units =  "g cm^-3";
326	>	density.title =  "Density";
327	>	density.dataType = "RealType";
328	>	density.accumulator.reserve(nBins_);
329	>	for (unsigned int i = 0; i < nBins_; i++)
330	>	density.accumulator.push_back( new Accumulator() );
331	>	data_[DENSITY] = density;
332	>	outputMap_["DENSITY"] =  DENSITY;
333	>
334	>	if (hasOutputFields) {
335	>	parseOutputFileFormat(rnemdParams->getOutputFields());
336	>	} else {
337	>	outputMask_.set(Z);
338	>	switch (rnemdFluxType_) {
339	>	case rnemdKE:
340	>	case rnemdRotKE:
341	>	case rnemdFullKE:
342	>	outputMask_.set(TEMPERATURE);
343		break;
344	<	case rnemdPx :
345	<	case rnemdPxScale :
346	<	case rnemdPy :
130	<	case rnemdPyScale :
131	<	rnemdFileName = "momemtum.log";
132	<	xTempFileName = "temperatureX.log";
133	<	yTempFileName = "temperatureY.log";
134	<	zTempFileName = "temperatureZ.log";
135	<	xTempLog_.open(xTempFileName.c_str());
136	<	yTempLog_.open(yTempFileName.c_str());
137	<	zTempLog_.open(zTempFileName.c_str());
344	>	case rnemdPx:
345	>	case rnemdPy:
346	>	outputMask_.set(VELOCITY);
347		break;
348	<	case rnemdPz :
349	<	case rnemdPzScale :
350	<	case rnemdUnknown :
351	<	default :
143	<	rnemdFileName = "rnemd.log";
348	>	case rnemdPz:
349	>	case rnemdPvector:
350	>	outputMask_.set(VELOCITY);
351	>	outputMask_.set(DENSITY);
352		break;
353	+	case rnemdKePx:
354	+	case rnemdKePy:
355	+	outputMask_.set(TEMPERATURE);
356	+	outputMask_.set(VELOCITY);
357	+	break;
358	+	case rnemdKePvector:
359	+	outputMask_.set(TEMPERATURE);
360	+	outputMask_.set(VELOCITY);
361	+	outputMask_.set(DENSITY);
362	+	break;
363	+	default:
364	+	break;
365		}
146	–	rnemdLog_.open(rnemdFileName.c_str());
147	–
148	–	#ifdef IS_MPI
366		}
367	<	#endif
368	<
369	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
153	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
154	<	midBin_ = nBins_ / 2;
155	<	if (simParams->haveRNEMD_logWidth()) {
156	<	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
157	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
158	<	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
159	<	std::cerr << "Automaically set back to default.\n";
160	<	rnemdLogWidth_ = nBins_;
161	<	}
367	>
368	>	if (hasOutputFileName) {
369	>	rnemdFileName_ = rnemdParams->getOutputFileName();
370		} else {
371	<	rnemdLogWidth_ = nBins_;
372	<	}
165	<	valueHist_.resize(rnemdLogWidth_, 0.0);
166	<	valueCount_.resize(rnemdLogWidth_, 0);
167	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
168	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
169	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
371	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
372	>	}
373
374	<	set_RNEMD_exchange_total(0.0);
172	<	if (simParams->haveRNEMD_targetFlux()) {
173	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
174	<	} else {
175	<	set_RNEMD_target_flux(0.0);
176	<	}
374	>	exchangeTime_ = rnemdParams->getExchangeTime();
375
376	<	#ifndef IS_MPI
377	<	if (simParams->haveSeed()) {
180	<	seedValue = simParams->getSeed();
181	<	randNumGen_ = new SeqRandNumGen(seedValue);
182	<	}else {
183	<	randNumGen_ = new SeqRandNumGen();
184	<	}
185	<	#else
186	<	if (simParams->haveSeed()) {
187	<	seedValue = simParams->getSeed();
188	<	randNumGen_ = new ParallelRandNumGen(seedValue);
189	<	}else {
190	<	randNumGen_ = new ParallelRandNumGen();
191	<	}
192	<	#endif
193	<	}
376	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
377	>	Mat3x3d hmat = currentSnap_->getHmat();
378
379	+	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
380	+	// Lx, Ly = box dimensions in x & y
381	+	// dt = exchange time interval
382	+	// flux = target flux
383	+
384	+	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
385	+	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
386	+
387	+	// total exchange sums are zeroed out at the beginning:
388	+
389	+	kineticExchange_ = 0.0;
390	+	momentumExchange_ = V3Zero;
391	+
392	+	if (hasSlabWidth)
393	+	slabWidth_ = rnemdParams->getSlabWidth();
394	+	else
395	+	slabWidth_ = hmat(2,2) / 10.0;
396	+
397	+	if (hasSlabACenter)
398	+	slabACenter_ = rnemdParams->getSlabACenter();
399	+	else
400	+	slabACenter_ = 0.0;
401	+
402	+	if (hasSlabBCenter)
403	+	slabBCenter_ = rnemdParams->getSlabBCenter();
404	+	else
405	+	slabBCenter_ = hmat(2,2) / 2.0;
406	+
407	+	}
408	+
409		RNEMD::~RNEMD() {
196	–	delete randNumGen_;
410
411		#ifdef IS_MPI
412		if (worldRank == 0) {
413		#endif
414	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
415	<	rnemdLog_.close();
416	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
417	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
418	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
206	<	xTempLog_.close();
207	<	yTempLog_.close();
208	<	zTempLog_.close();
209	<	}
414	>
415	>	writeOutputFile();
416	>
417	>	rnemdFile_.close();
418	>
419		#ifdef IS_MPI
420		}
421		#endif
422		}
423	+
424	+	bool RNEMD::inSlabA(Vector3d pos) {
425	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
426	+	}
427	+	bool RNEMD::inSlabB(Vector3d pos) {
428	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	+	}
430
431		void RNEMD::doSwap() {
432
#	Line 242 | Line 458 | namespace OpenMD {
458
459		if (usePeriodicBoundaryConditions_)
460		currentSnap_->wrapVector(pos);
461	+	bool inA = inSlabA(pos);
462	+	bool inB = inSlabB(pos);
463
464	<	// which bin is this stuntdouble in?
247	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
248	<
249	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
250	<
251	<
252	<	// if we're in bin 0 or the middleBin
253	<	if (binNo == 0 || binNo == midBin_) {
464	>	if (inA || inB) {
465
466		RealType mass = sd->getMass();
467		Vector3d vel = sd->getVel();
468		RealType value;
469	<
470	<	switch(rnemdType_) {
471	<	case rnemdKineticSwap :
469	>
470	>	switch(rnemdFluxType_) {
471	>	case rnemdKE :
472
473	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
474	<	vel[2]*vel[2]);
475	<	if (sd->isDirectional()) {
473	>	value = mass * vel.lengthSquare();
474	>
475	>	if (sd->isDirectional()) {
476		Vector3d angMom = sd->getJ();
477		Mat3x3d I = sd->getI();
478
479		if (sd->isLinear()) {
480	<	int i = sd->linearAxis();
481	<	int j = (i + 1) % 3;
482	<	int k = (i + 2) % 3;
483	<	value += angMom[j] * angMom[j] / I(j, j) +
484	<	angMom[k] * angMom[k] / I(k, k);
480	>	int i = sd->linearAxis();
481	>	int j = (i + 1) % 3;
482	>	int k = (i + 2) % 3;
483	>	value += angMom[j] * angMom[j] / I(j, j) +
484	>	angMom[k] * angMom[k] / I(k, k);
485		} else {
486	<	value += angMom[0]*angMom[0]/I(0, 0)
487	<	+ angMom[1]*angMom[1]/I(1, 1)
488	<	+ angMom[2]*angMom[2]/I(2, 2);
486	>	value += angMom[0]*angMom[0]/I(0, 0)
487	>	+ angMom[1]*angMom[1]/I(1, 1)
488	>	+ angMom[2]*angMom[2]/I(2, 2);
489		}
490	<	}
491	<	//make exchangeSum_ comparable between swap & scale
492	<	//temporarily without using energyConvert
490	>	} //angular momenta exchange enabled
491	>	//energyConvert temporarily disabled
492	>	//make kineticExchange_ comparable between swap & scale
493		//value = value * 0.5 / PhysicalConstants::energyConvert;
494		value *= 0.5;
495		break;
#	Line 295 | Line 506 | namespace OpenMD {
506		break;
507		}
508
509	<	if (binNo == 0) {
509	>	if (inA == 0) {
510		if (!min_found) {
511		min_val = value;
512		min_sd = sd;
#	Line 306 | Line 517 | namespace OpenMD {
517		min_sd = sd;
518		}
519		}
520	<	} else { //midBin_
520	>	} else {
521		if (!max_found) {
522		max_val = value;
523		max_sd = sd;
#	Line 320 | Line 531 | namespace OpenMD {
531		}
532		}
533		}
534	<
534	>
535		#ifdef IS_MPI
536		int nProc, worldRank;
537	<
537	>
538		nProc = MPI::COMM_WORLD.Get_size();
539		worldRank = MPI::COMM_WORLD.Get_rank();
540
#	Line 331 | Line 542 | namespace OpenMD {
542		bool my_max_found = max_found;
543
544		// Even if we didn't find a minimum, did someone else?
545	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
335	<	1, MPI::BOOL, MPI::LAND);
336	<
545	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
546		// Even if we didn't find a maximum, did someone else?
547	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
548	<	1, MPI::BOOL, MPI::LAND);
549	<
550	<	struct {
551	<	RealType val;
552	<	int rank;
553	<	} max_vals, min_vals;
554	<
555	<	if (min_found) {
556	<	if (my_min_found)
547	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
548	>	#endif
549	>
550	>	if (max_found && min_found) {
551	>
552	>	#ifdef IS_MPI
553	>	struct {
554	>	RealType val;
555	>	int rank;
556	>	} max_vals, min_vals;
557	>
558	>	if (my_min_found) {
559		min_vals.val = min_val;
560	<	else
560	>	} else {
561		min_vals.val = HONKING_LARGE_VALUE;
562	<
562	>	}
563		min_vals.rank = worldRank;
564
565		// Who had the minimum?
566		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
567		1, MPI::REALTYPE_INT, MPI::MINLOC);
568		min_val = min_vals.val;
358	–	}
569
570	<	if (max_found) {
361	<	if (my_max_found)
570	>	if (my_max_found) {
571		max_vals.val = max_val;
572	<	else
572	>	} else {
573		max_vals.val = -HONKING_LARGE_VALUE;
574	<
574	>	}
575		max_vals.rank = worldRank;
576
577		// Who had the maximum?
578		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
579		1, MPI::REALTYPE_INT, MPI::MAXLOC);
580		max_val = max_vals.val;
372	–	}
581		#endif
582	<
583	<	if (max_found && min_found) {
584	<	if (min_val< max_val) {
377	<
582	>
583	>	if (min_val < max_val) {
584	>
585		#ifdef IS_MPI
586		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
587		// I have both maximum and minimum, so proceed like a single
588		// processor version:
589		#endif
590	<	// objects to be swapped: velocity & angular velocity
590	>
591		Vector3d min_vel = min_sd->getVel();
592		Vector3d max_vel = max_sd->getVel();
593		RealType temp_vel;
594
595	<	switch(rnemdType_) {
596	<	case rnemdKineticSwap :
595	>	switch(rnemdFluxType_) {
596	>	case rnemdKE :
597		min_sd->setVel(max_vel);
598		max_sd->setVel(min_vel);
599	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
599	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
600		Vector3d min_angMom = min_sd->getJ();
601		Vector3d max_angMom = max_sd->getJ();
602		min_sd->setJ(max_angMom);
603		max_sd->setJ(min_angMom);
604	<	}
604	>	}//angular momenta exchange enabled
605	>	//assumes same rigid body identity
606		break;
607		case rnemdPx :
608		temp_vel = min_vel.x();
#	Line 420 | Line 628 | namespace OpenMD {
628		default :
629		break;
630		}
631	+
632		#ifdef IS_MPI
633		// the rest of the cases only apply in parallel simulations:
634		} else if (max_vals.rank == worldRank) {
#	Line 435 | Line 644 | namespace OpenMD {
644		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
645		min_vals.rank, 0, status);
646
647	<	switch(rnemdType_) {
648	<	case rnemdKineticSwap :
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649		max_sd->setVel(min_vel);
650	<
650	>	//angular momenta exchange enabled
651		if (max_sd->isDirectional()) {
652		Vector3d min_angMom;
653		Vector3d max_angMom = max_sd->getJ();
654	<
654	>
655		// point-to-point swap of the angular momentum vector
656		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
657		MPI::REALTYPE, min_vals.rank, 1,
658		min_angMom.getArrayPointer(), 3,
659		MPI::REALTYPE, min_vals.rank, 1,
660		status);
661	<
661	>
662		max_sd->setJ(min_angMom);
663	<	}
663	>	}
664		break;
665		case rnemdPx :
666		max_vel.x() = min_vel.x();
#	Line 481 | Line 690 | namespace OpenMD {
690		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
691		max_vals.rank, 0, status);
692
693	<	switch(rnemdType_) {
694	<	case rnemdKineticSwap :
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695		min_sd->setVel(max_vel);
696	<
696	>	//angular momenta exchange enabled
697		if (min_sd->isDirectional()) {
698		Vector3d min_angMom = min_sd->getJ();
699		Vector3d max_angMom;
700	<
700	>
701		// point-to-point swap of the angular momentum vector
702		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
703		MPI::REALTYPE, max_vals.rank, 1,
704		max_angMom.getArrayPointer(), 3,
705		MPI::REALTYPE, max_vals.rank, 1,
706		status);
707	<
707	>
708		min_sd->setJ(max_angMom);
709		}
710		break;
#	Line 516 | Line 725 | namespace OpenMD {
725		}
726		}
727		#endif
728	<	exchangeSum_ += max_val - min_val;
729	<	} else {
730	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
728	>
729	>	switch(rnemdFluxType_) {
730	>	case rnemdKE:
731	>	cerr << "KE\n";
732	>	kineticExchange_ += max_val - min_val;
733	>	break;
734	>	case rnemdPx:
735	>	momentumExchange_.x() += max_val - min_val;
736	>	break;
737	>	case rnemdPy:
738	>	momentumExchange_.y() += max_val - min_val;
739	>	break;
740	>	case rnemdPz:
741	>	momentumExchange_.z() += max_val - min_val;
742	>	break;
743	>	default:
744	>	cerr << "default\n";
745	>	break;
746	>	}
747	>	} else {
748	>	sprintf(painCave.errMsg,
749	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
750	>	painCave.isFatal = 0;
751	>	painCave.severity = OPENMD_INFO;
752	>	simError();
753		failTrialCount_++;
754		}
755		} else {
756	<	std::cerr << "exchange NOT performed!\n";
757	<	std::cerr << "at least one of the two slabs empty.\n";
756	>	sprintf(painCave.errMsg,
757	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
758	>	"\twas not present in at least one of the two slabs.\n");
759	>	painCave.isFatal = 0;
760	>	painCave.severity = OPENMD_INFO;
761	>	simError();
762		failTrialCount_++;
763	<	}
529	<
763	>	}
764		}
765
766	<	void RNEMD::doScale() {
766	>	void RNEMD::doNIVS() {
767
768		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
769		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 540 | Line 774 | namespace OpenMD {
774		StuntDouble* sd;
775		int idx;
776
777	<	std::vector<StuntDouble*> hotBin, coldBin;
777	>	vector<StuntDouble*> hotBin, coldBin;
778
779		RealType Phx = 0.0;
780		RealType Phy = 0.0;
#	Line 548 | Line 782 | namespace OpenMD {
782		RealType Khx = 0.0;
783		RealType Khy = 0.0;
784		RealType Khz = 0.0;
785	+	RealType Khw = 0.0;
786		RealType Pcx = 0.0;
787		RealType Pcy = 0.0;
788		RealType Pcz = 0.0;
789		RealType Kcx = 0.0;
790		RealType Kcy = 0.0;
791		RealType Kcz = 0.0;
792	+	RealType Kcw = 0.0;
793
794		for (sd = seleMan_.beginSelected(selei); sd != NULL;
795		sd = seleMan_.nextSelected(selei)) {
#	Line 568 | Line 804 | namespace OpenMD {
804		currentSnap_->wrapVector(pos);
805
806		// which bin is this stuntdouble in?
807	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
807	>	bool inA = inSlabA(pos);
808	>	bool inB = inSlabB(pos);
809
810	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
811	<
575	<	// if we're in bin 0 or the middleBin
576	<	if (binNo == 0 || binNo == midBin_) {
577	<
810	>	if (inA || inB) {
811	>
812		RealType mass = sd->getMass();
813		Vector3d vel = sd->getVel();
814
815	<	if (binNo == 0) {
815	>	if (inA) {
816		hotBin.push_back(sd);
817		Phx += mass * vel.x();
818		Phy += mass * vel.y();
#	Line 586 | Line 820 | namespace OpenMD {
820		Khx += mass * vel.x() * vel.x();
821		Khy += mass * vel.y() * vel.y();
822		Khz += mass * vel.z() * vel.z();
823	<	} else { //midBin_
823	>	if (sd->isDirectional()) {
824	>	Vector3d angMom = sd->getJ();
825	>	Mat3x3d I = sd->getI();
826	>	if (sd->isLinear()) {
827	>	int i = sd->linearAxis();
828	>	int j = (i + 1) % 3;
829	>	int k = (i + 2) % 3;
830	>	Khw += angMom[j] * angMom[j] / I(j, j) +
831	>	angMom[k] * angMom[k] / I(k, k);
832	>	} else {
833	>	Khw += angMom[0]*angMom[0]/I(0, 0)
834	>	+ angMom[1]*angMom[1]/I(1, 1)
835	>	+ angMom[2]*angMom[2]/I(2, 2);
836	>	}
837	>	}
838	>	} else {
839		coldBin.push_back(sd);
840		Pcx += mass * vel.x();
841		Pcy += mass * vel.y();
#	Line 594 | Line 843 | namespace OpenMD {
843		Kcx += mass * vel.x() * vel.x();
844		Kcy += mass * vel.y() * vel.y();
845		Kcz += mass * vel.z() * vel.z();
846	+	if (sd->isDirectional()) {
847	+	Vector3d angMom = sd->getJ();
848	+	Mat3x3d I = sd->getI();
849	+	if (sd->isLinear()) {
850	+	int i = sd->linearAxis();
851	+	int j = (i + 1) % 3;
852	+	int k = (i + 2) % 3;
853	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
854	+	angMom[k] * angMom[k] / I(k, k);
855	+	} else {
856	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
857	+	+ angMom[1]*angMom[1]/I(1, 1)
858	+	+ angMom[2]*angMom[2]/I(2, 2);
859	+	}
860	+	}
861		}
862		}
863		}
864	<
864	>
865		Khx *= 0.5;
866		Khy *= 0.5;
867		Khz *= 0.5;
868	+	Khw *= 0.5;
869		Kcx *= 0.5;
870		Kcy *= 0.5;
871		Kcz *= 0.5;
872	+	Kcw *= 0.5;
873
874		#ifdef IS_MPI
875		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 616 | Line 882 | namespace OpenMD {
882		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
883		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
884		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
885	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
886	+
887		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
888		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
889		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
890	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
891		#endif
892
893	<	//use coldBin coeff's
893	>	//solve coldBin coeff's first
894		RealType px = Pcx / Phx;
895		RealType py = Pcy / Phy;
896		RealType pz = Pcz / Phz;
897	+	RealType c, x, y, z;
898	+	bool successfulScale = false;
899	+	if ((rnemdFluxType_ == rnemdFullKE) ||
900	+	(rnemdFluxType_ == rnemdRotKE)) {
901	+	//may need sanity check Khw & Kcw > 0
902
903	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
904	<	switch(rnemdType_) {
905	<	case rnemdKineticScale :
906	<	/*used hotBin coeff's & only scale x & y dimensions
907	<	RealType px = Phx / Pcx;
634	<	RealType py = Phy / Pcy;
635	<	a110 = Khy;
636	<	c0 = - Khx - Khy - targetFlux_;
637	<	a000 = Khx;
638	<	a111 = Kcy * py * py
639	<	b11 = -2.0 * Kcy * py * (1.0 + py);
640	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
641	<	b01 = -2.0 * Kcx * px * (1.0 + px);
642	<	a001 = Kcx * px * px;
643	<	*/
903	>	if (rnemdFluxType_ == rnemdFullKE) {
904	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
905	>	} else {
906	>	c = 1.0 - kineticTarget_ / Kcw;
907	>	}
908
909	<	//scale all three dimensions, let c_x = c_y
910	<	a000 = Kcx + Kcy;
911	<	a110 = Kcz;
912	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
913	<	a001 = Khx * px * px + Khy * py * py;
914	<	a111 = Khz * pz * pz;
915	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
916	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
917	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
918	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
919	<	break;
920	<	case rnemdPxScale :
921	<	c = 1 - targetFlux_ / Pcx;
922	<	a000 = Kcy;
923	<	a110 = Kcz;
924	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
925	<	a001 = py * py * Khy;
926	<	a111 = pz * pz * Khz;
927	<	b01 = -2.0 * Khy * py * (1.0 + py);
928	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
929	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
930	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
931	<	break;
932	<	case rnemdPyScale :
933	<	c = 1 - targetFlux_ / Pcy;
934	<	a000 = Kcx;
935	<	a110 = Kcz;
936	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
937	<	a001 = px * px * Khx;
938	<	a111 = pz * pz * Khz;
939	<	b01 = -2.0 * Khx * px * (1.0 + px);
940	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
941	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
942	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
943	<	break;
944	<	case rnemdPzScale ://we don't really do this, do we?
945	<	c = 1 - targetFlux_ / Pcz;
946	<	a000 = Kcx;
947	<	a110 = Kcy;
948	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
949	<	a001 = px * px * Khx;
950	<	a111 = py * py * Khy;
951	<	b01 = -2.0 * Khx * px * (1.0 + px);
952	<	b11 = -2.0 * Khy * py * (1.0 + py);
953	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
954	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
955	<	break;
956	<	default :
957	<	break;
909	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
910	>	c = sqrt(c);
911	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	>	//now convert to hotBin coefficient
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	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	>	//           << "\twh= " << w << endl;
952	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
953	>	if (rnemdFluxType_ == rnemdFullKE) {
954	>	vel = (*sdi)->getVel();
955	>	vel.x() *= x;
956	>	vel.y() *= y;
957	>	vel.z() *= z;
958	>	(*sdi)->setVel(vel);
959	>	}
960	>	if ((*sdi)->isDirectional()) {
961	>	Vector3d angMom = (*sdi)->getJ() * w;
962	>	(*sdi)->setJ(angMom);
963	>	}
964	>	}
965	>	successfulScale = true;
966	>	kineticExchange_ += kineticTarget_;
967	>	}
968	>	}
969	>	} else {
970	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
971	>	switch(rnemdFluxType_) {
972	>	case rnemdKE :
973	>	/* used hotBin coeff's & only scale x & y dimensions
974	>	RealType px = Phx / Pcx;
975	>	RealType py = Phy / Pcy;
976	>	a110 = Khy;
977	>	c0 = - Khx - Khy - kineticTarget_;
978	>	a000 = Khx;
979	>	a111 = Kcy * py * py;
980	>	b11 = -2.0 * Kcy * py * (1.0 + py);
981	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
982	>	b01 = -2.0 * Kcx * px * (1.0 + px);
983	>	a001 = Kcx * px * px;
984	>	*/
985	>	//scale all three dimensions, let c_x = c_y
986	>	a000 = Kcx + Kcy;
987	>	a110 = Kcz;
988	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
989	>	a001 = Khx * px * px + Khy * py * py;
990	>	a111 = Khz * pz * pz;
991	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
992	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
993	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
994	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
995	>	break;
996	>	case rnemdPx :
997	>	c = 1 - momentumTarget_.x() / Pcx;
998	>	a000 = Kcy;
999	>	a110 = Kcz;
1000	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1001	>	a001 = py * py * Khy;
1002	>	a111 = pz * pz * Khz;
1003	>	b01 = -2.0 * Khy * py * (1.0 + py);
1004	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1005	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1006	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1007	>	break;
1008	>	case rnemdPy :
1009	>	c = 1 - momentumTarget_.y() / Pcy;
1010	>	a000 = Kcx;
1011	>	a110 = Kcz;
1012	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1013	>	a001 = px * px * Khx;
1014	>	a111 = pz * pz * Khz;
1015	>	b01 = -2.0 * Khx * px * (1.0 + px);
1016	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1017	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1018	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1019	>	break;
1020	>	case rnemdPz ://we don't really do this, do we?
1021	>	c = 1 - momentumTarget_.z() / Pcz;
1022	>	a000 = Kcx;
1023	>	a110 = Kcy;
1024	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1025	>	a001 = px * px * Khx;
1026	>	a111 = py * py * Khy;
1027	>	b01 = -2.0 * Khx * px * (1.0 + px);
1028	>	b11 = -2.0 * Khy * py * (1.0 + py);
1029	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1030	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1031	>	break;
1032	>	default :
1033	>	break;
1034	>	}
1035	>
1036	>	RealType v1 = a000 * a111 - a001 * a110;
1037	>	RealType v2 = a000 * b01;
1038	>	RealType v3 = a000 * b11;
1039	>	RealType v4 = a000 * c1 - a001 * c0;
1040	>	RealType v8 = a110 * b01;
1041	>	RealType v10 = - b01 * c0;
1042	>
1043	>	RealType u0 = v2 * v10 - v4 * v4;
1044	>	RealType u1 = -2.0 * v3 * v4;
1045	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1046	>	RealType u3 = -2.0 * v1 * v3;
1047	>	RealType u4 = - v1 * v1;
1048	>	//rescale coefficients
1049	>	RealType maxAbs = fabs(u0);
1050	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1051	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1052	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1053	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1054	>	u0 /= maxAbs;
1055	>	u1 /= maxAbs;
1056	>	u2 /= maxAbs;
1057	>	u3 /= maxAbs;
1058	>	u4 /= maxAbs;
1059	>	//max_element(start, end) is also available.
1060	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1061	>	poly.setCoefficient(4, u4);
1062	>	poly.setCoefficient(3, u3);
1063	>	poly.setCoefficient(2, u2);
1064	>	poly.setCoefficient(1, u1);
1065	>	poly.setCoefficient(0, u0);
1066	>	vector<RealType> realRoots = poly.FindRealRoots();
1067	>
1068	>	vector<RealType>::iterator ri;
1069	>	RealType r1, r2, alpha0;
1070	>	vector<pair<RealType,RealType> > rps;
1071	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1072	>	r2 = *ri;
1073	>	//check if FindRealRoots() give the right answer
1074	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1075	>	sprintf(painCave.errMsg,
1076	>	"RNEMD Warning: polynomial solve seems to have an error!");
1077	>	painCave.isFatal = 0;
1078	>	simError();
1079	>	failRootCount_++;
1080	>	}
1081	>	//might not be useful w/o rescaling coefficients
1082	>	alpha0 = -c0 - a110 * r2 * r2;
1083	>	if (alpha0 >= 0.0) {
1084	>	r1 = sqrt(alpha0 / a000);
1085	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1086	>	< 1e-6)
1087	>	{ rps.push_back(make_pair(r1, r2)); }
1088	>	if (r1 > 1e-6) { //r1 non-negative
1089	>	r1 = -r1;
1090	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1091	>	< 1e-6)
1092	>	{ rps.push_back(make_pair(r1, r2)); }
1093	>	}
1094	>	}
1095	>	}
1096	>	// Consider combining together the solving pair part w/ the searching
1097	>	// best solution part so that we don't need the pairs vector
1098	>	if (!rps.empty()) {
1099	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1100	>	RealType diff;
1101	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1102	>	vector<pair<RealType,RealType> >::iterator rpi;
1103	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1104	>	r1 = (*rpi).first;
1105	>	r2 = (*rpi).second;
1106	>	switch(rnemdFluxType_) {
1107	>	case rnemdKE :
1108	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1109	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1110	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1111	>	break;
1112	>	case rnemdPx :
1113	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1115	>	break;
1116	>	case rnemdPy :
1117	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1119	>	break;
1120	>	case rnemdPz :
1121	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1122	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1123	>	default :
1124	>	break;
1125	>	}
1126	>	if (diff < smallestDiff) {
1127	>	smallestDiff = diff;
1128	>	bestPair = *rpi;
1129	>	}
1130	>	}
1131	>	#ifdef IS_MPI
1132	>	if (worldRank == 0) {
1133	>	#endif
1134	>	// sprintf(painCave.errMsg,
1135	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1136	>	//         bestPair.first, bestPair.second);
1137	>	// painCave.isFatal = 0;
1138	>	// painCave.severity = OPENMD_INFO;
1139	>	// simError();
1140	>	#ifdef IS_MPI
1141	>	}
1142	>	#endif
1143	>
1144	>	switch(rnemdFluxType_) {
1145	>	case rnemdKE :
1146	>	x = bestPair.first;
1147	>	y = bestPair.first;
1148	>	z = bestPair.second;
1149	>	break;
1150	>	case rnemdPx :
1151	>	x = c;
1152	>	y = bestPair.first;
1153	>	z = bestPair.second;
1154	>	break;
1155	>	case rnemdPy :
1156	>	x = bestPair.first;
1157	>	y = c;
1158	>	z = bestPair.second;
1159	>	break;
1160	>	case rnemdPz :
1161	>	x = bestPair.first;
1162	>	y = bestPair.second;
1163	>	z = c;
1164	>	break;
1165	>	default :
1166	>	break;
1167	>	}
1168	>	vector<StuntDouble*>::iterator sdi;
1169	>	Vector3d vel;
1170	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1171	>	vel = (*sdi)->getVel();
1172	>	vel.x() *= x;
1173	>	vel.y() *= y;
1174	>	vel.z() *= z;
1175	>	(*sdi)->setVel(vel);
1176	>	}
1177	>	//convert to hotBin coefficient
1178	>	x = 1.0 + px * (1.0 - x);
1179	>	y = 1.0 + py * (1.0 - y);
1180	>	z = 1.0 + pz * (1.0 - z);
1181	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1182	>	vel = (*sdi)->getVel();
1183	>	vel.x() *= x;
1184	>	vel.y() *= y;
1185	>	vel.z() *= z;
1186	>	(*sdi)->setVel(vel);
1187	>	}
1188	>	successfulScale = true;
1189	>	switch(rnemdFluxType_) {
1190	>	case rnemdKE :
1191	>	kineticExchange_ += kineticTarget_;
1192	>	break;
1193	>	case rnemdPx :
1194	>	case rnemdPy :
1195	>	case rnemdPz :
1196	>	momentumExchange_ += momentumTarget_;
1197	>	break;
1198	>	default :
1199	>	break;
1200	>	}
1201	>	}
1202		}
1203	+	if (successfulScale != true) {
1204	+	sprintf(painCave.errMsg,
1205	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1206	+	"\tthe constraint equations may not exist or there may be\n"
1207	+	"\tno selected objects in one or both slabs.\n");
1208	+	painCave.isFatal = 0;
1209	+	painCave.severity = OPENMD_INFO;
1210	+	simError();
1211	+	failTrialCount_++;
1212	+	}
1213	+	}
1214
1215	<	RealType v1 = a000 * a111 - a001 * a110;
697	<	RealType v2 = a000 * b01;
698	<	RealType v3 = a000 * b11;
699	<	RealType v4 = a000 * c1 - a001 * c0;
700	<	RealType v8 = a110 * b01;
701	<	RealType v10 = - b01 * c0;
1215	>	void RNEMD::doVSS() {
1216
1217	<	RealType u0 = v2 * v10 - v4 * v4;
1218	<	RealType u1 = -2.0 * v3 * v4;
1219	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
706	<	RealType u3 = -2.0 * v1 * v3;
707	<	RealType u4 = - v1 * v1;
708	<	//rescale coefficients
709	<	RealType maxAbs = fabs(u0);
710	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
711	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
712	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
713	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
714	<	u0 /= maxAbs;
715	<	u1 /= maxAbs;
716	<	u2 /= maxAbs;
717	<	u3 /= maxAbs;
718	<	u4 /= maxAbs;
719	<	//max_element(start, end) is also available.
720	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
721	<	poly.setCoefficient(4, u4);
722	<	poly.setCoefficient(3, u3);
723	<	poly.setCoefficient(2, u2);
724	<	poly.setCoefficient(1, u1);
725	<	poly.setCoefficient(0, u0);
726	<	std::vector<RealType> realRoots = poly.FindRealRoots();
1217	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1218	>	RealType time = currentSnap_->getTime();
1219	>	Mat3x3d hmat = currentSnap_->getHmat();
1220
1221	<	std::vector<RealType>::iterator ri;
1222	<	RealType r1, r2, alpha0;
1223	<	std::vector<std::pair<RealType,RealType> > rps;
1224	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1225	<	r2 = *ri;
1226	<	//check if FindRealRoots() give the right answer
1227	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1228	<	sprintf(painCave.errMsg,
1229	<	"RNEMD Warning: polynomial solve seems to have an error!");
1230	<	painCave.isFatal = 0;
1231	<	simError();
1232	<	failRootCount_++;
1221	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	>
1223	>	int selei;
1224	>	StuntDouble* sd;
1225	>	int idx;
1226	>
1227	>	vector<StuntDouble*> hotBin, coldBin;
1228	>
1229	>	Vector3d Ph(V3Zero);
1230	>	RealType Mh = 0.0;
1231	>	RealType Kh = 0.0;
1232	>	Vector3d Pc(V3Zero);
1233	>	RealType Mc = 0.0;
1234	>	RealType Kc = 0.0;
1235	>
1236	>
1237	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1238	>	sd = seleMan_.nextSelected(selei)) {
1239	>
1240	>	idx = sd->getLocalIndex();
1241	>
1242	>	Vector3d pos = sd->getPos();
1243	>
1244	>	// wrap the stuntdouble's position back into the box:
1245	>
1246	>	if (usePeriodicBoundaryConditions_)
1247	>	currentSnap_->wrapVector(pos);
1248	>
1249	>	// which bin is this stuntdouble in?
1250	>	bool inA = inSlabA(pos);
1251	>	bool inB = inSlabB(pos);
1252	>
1253	>	if (inA || inB) {
1254	>
1255	>	RealType mass = sd->getMass();
1256	>	Vector3d vel = sd->getVel();
1257	>
1258	>	if (inA) {
1259	>	hotBin.push_back(sd);
1260	>	//std::cerr << "before, velocity = " << vel << endl;
1261	>	Ph += mass * vel;
1262	>	//std::cerr << "after, velocity = " << vel << endl;
1263	>	Mh += mass;
1264	>	Kh += mass * vel.lengthSquare();
1265	>	if (rnemdFluxType_ == rnemdFullKE) {
1266	>	if (sd->isDirectional()) {
1267	>	Vector3d angMom = sd->getJ();
1268	>	Mat3x3d I = sd->getI();
1269	>	if (sd->isLinear()) {
1270	>	int i = sd->linearAxis();
1271	>	int j = (i + 1) % 3;
1272	>	int k = (i + 2) % 3;
1273	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1274	>	angMom[k] * angMom[k] / I(k, k);
1275	>	} else {
1276	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1277	>	angMom[1] * angMom[1] / I(1, 1) +
1278	>	angMom[2] * angMom[2] / I(2, 2);
1279	>	}
1280	>	}
1281	>	}
1282	>	} else { //midBin_
1283	>	coldBin.push_back(sd);
1284	>	Pc += mass * vel;
1285	>	Mc += mass;
1286	>	Kc += mass * vel.lengthSquare();
1287	>	if (rnemdFluxType_ == rnemdFullKE) {
1288	>	if (sd->isDirectional()) {
1289	>	Vector3d angMom = sd->getJ();
1290	>	Mat3x3d I = sd->getI();
1291	>	if (sd->isLinear()) {
1292	>	int i = sd->linearAxis();
1293	>	int j = (i + 1) % 3;
1294	>	int k = (i + 2) % 3;
1295	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1296	>	angMom[k] * angMom[k] / I(k, k);
1297	>	} else {
1298	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1299	>	angMom[1] * angMom[1] / I(1, 1) +
1300	>	angMom[2] * angMom[2] / I(2, 2);
1301	>	}
1302	>	}
1303	>	}
1304	>	}
1305		}
741	–	//might not be useful w/o rescaling coefficients
742	–	alpha0 = -c0 - a110 * r2 * r2;
743	–	if (alpha0 >= 0.0) {
744	–	r1 = sqrt(alpha0 / a000);
745	–	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
746	–	{ rps.push_back(std::make_pair(r1, r2)); }
747	–	if (r1 > 1e-6) { //r1 non-negative
748	–	r1 = -r1;
749	–	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
750	–	{ rps.push_back(std::make_pair(r1, r2)); }
751	–	}
752	–	}
1306		}
1307	<	// Consider combininig together the solving pair part w/ the searching
1308	<	// best solution part so that we don't need the pairs vector
1309	<	if (!rps.empty()) {
1310	<	RealType smallestDiff = HONKING_LARGE_VALUE;
1311	<	RealType diff;
1312	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1313	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1314	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
762	<	r1 = (*rpi).first;
763	<	r2 = (*rpi).second;
764	<	switch(rnemdType_) {
765	<	case rnemdKineticScale :
766	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
767	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
768	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
769	<	break;
770	<	case rnemdPxScale :
771	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
772	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
773	<	break;
774	<	case rnemdPyScale :
775	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
776	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
777	<	break;
778	<	case rnemdPzScale :
779	<	default :
780	<	break;
781	<	}
782	<	if (diff < smallestDiff) {
783	<	smallestDiff = diff;
784	<	bestPair = *rpi;
785	<	}
786	<	}
1307	>
1308	>	Kh *= 0.5;
1309	>	Kc *= 0.5;
1310	>
1311	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1312	>	//        << "\tKc= " << Kc << endl;
1313	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1314	>
1315		#ifdef IS_MPI
1316	<	if (worldRank == 0) {
1316	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1317	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1318	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1319	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1320	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1321	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1322		#endif
790	–	std::cerr << "we choose r1 = " << bestPair.first
791	–	<< " and r2 = " << bestPair.second << "\n";
792	–	#ifdef IS_MPI
793	–	}
794	–	#endif
1323
1324	<	RealType x, y, z;
1325	<	switch(rnemdType_) {
1326	<	case rnemdKineticScale :
1327	<	x = bestPair.first;
1328	<	y = bestPair.first;
1329	<	z = bestPair.second;
1330	<	break;
1331	<	case rnemdPxScale :
1332	<	x = c;
1333	<	y = bestPair.first;
1334	<	z = bestPair.second;
1335	<	break;
1336	<	case rnemdPyScale :
1337	<	x = bestPair.first;
1338	<	y = c;
1339	<	z = bestPair.second;
1340	<	break;
1341	<	case rnemdPzScale :
1342	<	x = bestPair.first;
1343	<	y = bestPair.second;
1344	<	z = c;
1345	<	break;
1346	<	default :
1347	<	break;
1348	<	}
1349	<	std::vector<StuntDouble*>::iterator sdi;
1350	<	Vector3d vel;
1351	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1352	<	vel = (*sdi)->getVel();
1353	<	vel.x() *= x;
1354	<	vel.y() *= y;
1355	<	vel.z() *= z;
1356	<	(*sdi)->setVel(vel);
1324	>	bool successfulExchange = false;
1325	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1326	>	Vector3d vc = Pc / Mc;
1327	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1328	>	Vector3d acrec = -momentumTarget_ / Mc;
1329	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1330	>	if (cNumerator > 0.0) {
1331	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1332	>	if (cDenominator > 0.0) {
1333	>	RealType c = sqrt(cNumerator / cDenominator);
1334	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1335	>	Vector3d vh = Ph / Mh;
1336	>	Vector3d ah = momentumTarget_ / Mh + vh;
1337	>	Vector3d ahrec = momentumTarget_ / Mh;
1338	>	RealType hNumerator = Kh + kineticTarget_
1339	>	- 0.5 * Mh * ah.lengthSquare();
1340	>	if (hNumerator > 0.0) {
1341	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1342	>	if (hDenominator > 0.0) {
1343	>	RealType h = sqrt(hNumerator / hDenominator);
1344	>	if ((h > 0.9) && (h < 1.1)) {
1345	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1347	>	vector<StuntDouble*>::iterator sdi;
1348	>	Vector3d vel;
1349	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1350	>	//vel = (*sdi)->getVel();
1351	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1352	>	(*sdi)->setVel(vel);
1353	>	if (rnemdFluxType_ == rnemdFullKE) {
1354	>	if ((*sdi)->isDirectional()) {
1355	>	Vector3d angMom = (*sdi)->getJ() * c;
1356	>	(*sdi)->setJ(angMom);
1357	>	}
1358	>	}
1359	>	}
1360	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1361	>	//vel = (*sdi)->getVel();
1362	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1363	>	(*sdi)->setVel(vel);
1364	>	if (rnemdFluxType_ == rnemdFullKE) {
1365	>	if ((*sdi)->isDirectional()) {
1366	>	Vector3d angMom = (*sdi)->getJ() * h;
1367	>	(*sdi)->setJ(angMom);
1368	>	}
1369	>	}
1370	>	}
1371	>	successfulExchange = true;
1372	>	kineticExchange_ += kineticTarget_;
1373	>	momentumExchange_ += momentumTarget_;
1374	>	}
1375	>	}
1376	>	}
1377	>	}
1378	>	}
1379		}
1380	<	//convert to hotBin coefficient
1381	<	x = 1.0 + px * (1.0 - x);
1382	<	y = 1.0 + py * (1.0 - y);
1383	<	z = 1.0 + pz * (1.0 - z);
1384	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1385	<	vel = (*sdi)->getVel();
1386	<	vel.x() *= x;
1387	<	vel.y() *= y;
1388	<	vel.z() *= z;
839	<	(*sdi)->setVel(vel);
840	<	}
841	<	exchangeSum_ += targetFlux_;
842	<	//we may want to check whether the exchange has been successful
843	<	} else {
844	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1380	>	}
1381	>	if (successfulExchange != true) {
1382	>	sprintf(painCave.errMsg,
1383	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1384	>	"\tthe constraint equations may not exist or there may be\n"
1385	>	"\tno selected objects in one or both slabs.\n");
1386	>	painCave.isFatal = 0;
1387	>	painCave.severity = OPENMD_INFO;
1388	>	simError();
1389		failTrialCount_++;
1390		}
847	–
1391		}
1392
1393		void RNEMD::doRNEMD() {
1394
1395	<	switch(rnemdType_) {
1396	<	case rnemdKineticScale :
1397	<	case rnemdPxScale :
855	<	case rnemdPyScale :
856	<	case rnemdPzScale :
857	<	doScale();
858	<	break;
859	<	case rnemdKineticSwap :
860	<	case rnemdPx :
861	<	case rnemdPy :
862	<	case rnemdPz :
1395	>	trialCount_++;
1396	>	switch(rnemdMethod_) {
1397	>	case rnemdSwap:
1398		doSwap();
1399		break;
1400	<	case rnemdUnknown :
1400	>	case rnemdNIVS:
1401	>	doNIVS();
1402	>	break;
1403	>	case rnemdVSS:
1404	>	doVSS();
1405	>	break;
1406	>	case rnemdUnkownMethod:
1407		default :
1408		break;
1409		}
#	Line 879 | Line 1420 | namespace OpenMD {
1420		StuntDouble* sd;
1421		int idx;
1422
1423	+	vector<RealType> binMass(nBins_, 0.0);
1424	+	vector<RealType> binPx(nBins_, 0.0);
1425	+	vector<RealType> binPy(nBins_, 0.0);
1426	+	vector<RealType> binPz(nBins_, 0.0);
1427	+	vector<RealType> binKE(nBins_, 0.0);
1428	+	vector<int> binDOF(nBins_, 0);
1429	+	vector<int> binCount(nBins_, 0);
1430	+
1431	+	// alternative approach, track all molecules instead of only those
1432	+	// selected for scaling/swapping:
1433	+	/*
1434	+	SimInfo::MoleculeIterator miter;
1435	+	vector<StuntDouble*>::iterator iiter;
1436	+	Molecule* mol;
1437	+	StuntDouble* sd;
1438	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1439	+	mol = info_->nextMolecule(miter))
1440	+	sd is essentially sd
1441	+	for (sd = mol->beginIntegrableObject(iiter);
1442	+	sd != NULL;
1443	+	sd = mol->nextIntegrableObject(iiter))
1444	+	*/
1445		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1446		sd = seleMan_.nextSelected(selei)) {
1447
#	Line 890 | Line 1453 | namespace OpenMD {
1453
1454		if (usePeriodicBoundaryConditions_)
1455		currentSnap_->wrapVector(pos);
1456	<
1456	>
1457		// which bin is this stuntdouble in?
1458		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	<
1459	>	// Shift molecules by half a box to have bins start at 0
1460	>	// The modulo operator is used to wrap the case when we are
1461	>	// beyond the end of the bins back to the beginning.
1462		int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463	<
899	<	if (rnemdLogWidth_ == midBin_ + 1)
900	<	if (binNo > midBin_)
901	<	binNo = nBins_ - binNo;
902	<
1463	>
1464		RealType mass = sd->getMass();
1465		Vector3d vel = sd->getVel();
905	–	RealType value;
906	–	RealType xVal, yVal, zVal;
1466
1467	<	switch(rnemdType_) {
1468	<	case rnemdKineticSwap :
1469	<	case rnemdKineticScale :
1470	<
1471	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1472	<	vel[2]*vel[2]);
1473	<
915	<	valueCount_[binNo] += 3;
916	<	if (sd->isDirectional()) {
917	<	Vector3d angMom = sd->getJ();
918	<	Mat3x3d I = sd->getI();
919	<
920	<	if (sd->isLinear()) {
921	<	int i = sd->linearAxis();
922	<	int j = (i + 1) % 3;
923	<	int k = (i + 2) % 3;
924	<	value += angMom[j] * angMom[j] / I(j, j) +
925	<	angMom[k] * angMom[k] / I(k, k);
1467	>	binCount[binNo]++;
1468	>	binMass[binNo] += mass;
1469	>	binPx[binNo] += mass*vel.x();
1470	>	binPy[binNo] += mass*vel.y();
1471	>	binPz[binNo] += mass*vel.z();
1472	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1473	>	binDOF[binNo] += 3;
1474
1475	<	valueCount_[binNo] +=2;
1475	>	if (sd->isDirectional()) {
1476	>	Vector3d angMom = sd->getJ();
1477	>	Mat3x3d I = sd->getI();
1478	>	if (sd->isLinear()) {
1479	>	int i = sd->linearAxis();
1480	>	int j = (i + 1) % 3;
1481	>	int k = (i + 2) % 3;
1482	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1483	>	angMom[k] * angMom[k] / I(k, k));
1484	>	binDOF[binNo] += 2;
1485	>	} else {
1486	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1487	>	angMom[1] * angMom[1] / I(1, 1) +
1488	>	angMom[2] * angMom[2] / I(2, 2));
1489	>	binDOF[binNo] += 3;
1490	>	}
1491	>	}
1492	>	}
1493	>
1494
1495	<	} else {
1496	<	value += angMom[0]*angMom[0]/I(0, 0)
1497	<	+ angMom[1]*angMom[1]/I(1, 1)
1498	<	+ angMom[2]*angMom[2]/I(2, 2);
1499	<	valueCount_[binNo] +=3;
1500	<	}
1501	<	}
1502	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1495	>	#ifdef IS_MPI
1496	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1497	>	nBins_, MPI::INT, MPI::SUM);
1498	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1499	>	nBins_, MPI::REALTYPE, MPI::SUM);
1500	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1501	>	nBins_, MPI::REALTYPE, MPI::SUM);
1502	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1503	>	nBins_, MPI::REALTYPE, MPI::SUM);
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1505	>	nBins_, MPI::REALTYPE, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1509	>	nBins_, MPI::INT, MPI::SUM);
1510	>	#endif
1511
1512	<	break;
1513	<	case rnemdPx :
1514	<	case rnemdPxScale :
1515	<	value = mass * vel[0];
1516	<	valueCount_[binNo]++;
1517	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1518	<	/ PhysicalConstants::kb;
1519	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1520	<	/ PhysicalConstants::kb;
1521	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1522	<	/ PhysicalConstants::kb;
1523	<	xTempHist_[binNo] += xVal;
1524	<	yTempHist_[binNo] += yVal;
1525	<	zTempHist_[binNo] += zVal;
1526	<	break;
1527	<	case rnemdPy :
1528	<	case rnemdPyScale :
1529	<	value = mass * vel[1];
1530	<	valueCount_[binNo]++;
1531	<	break;
1532	<	case rnemdPz :
1533	<	case rnemdPzScale :
1534	<	value = mass * vel[2];
1535	<	valueCount_[binNo]++;
1536	<	break;
1537	<	case rnemdUnknown :
1538	<	default :
1539	<	break;
1512	>	Vector3d vel;
1513	>	RealType den;
1514	>	RealType temp;
1515	>	RealType z;
1516	>	for (int i = 0; i < nBins_; i++) {
1517	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1518	>	vel.x() = binPx[i] / binMass[i];
1519	>	vel.y() = binPy[i] / binMass[i];
1520	>	vel.z() = binPz[i] / binMass[i];
1521	>	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
1522	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1523	>	PhysicalConstants::energyConvert);
1524	>
1525	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1526	>	if(outputMask_[j]) {
1527	>	switch(j) {
1528	>	case Z:
1529	>	(data_[j].accumulator[i])->add(z);
1530	>	break;
1531	>	case TEMPERATURE:
1532	>	data_[j].accumulator[i]->add(temp);
1533	>	break;
1534	>	case VELOCITY:
1535	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1536	>	break;
1537	>	case DENSITY:
1538	>	data_[j].accumulator[i]->add(den);
1539	>	break;
1540	>	}
1541	>	}
1542		}
967	–	valueHist_[binNo] += value;
1543		}
969	–
1544		}
1545
1546		void RNEMD::getStarted() {
1547	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1548	<	Stats& stat = currentSnap_->statData;
975	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1547	>	collectData();
1548	>	writeOutputFile();
1549		}
1550
1551	<	void RNEMD::getStatus() {
1552	<
1553	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1554	<	Stats& stat = currentSnap_->statData;
1555	<	RealType time = currentSnap_->getTime();
1556	<
1557	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1558	<	//or to be more meaningful, define another item as exchangeSum_ / time
1559	<	int j;
1560	<
1551	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1552	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1553	>
1554	>	while(tokenizer.hasMoreTokens()) {
1555	>	std::string token(tokenizer.nextToken());
1556	>	toUpper(token);
1557	>	OutputMapType::iterator i = outputMap_.find(token);
1558	>	if (i != outputMap_.end()) {
1559	>	outputMask_.set(i->second);
1560	>	} else {
1561	>	sprintf( painCave.errMsg,
1562	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1563	>	"\toutputFileFormat keyword.\n", token.c_str() );
1564	>	painCave.isFatal = 0;
1565	>	painCave.severity = OPENMD_ERROR;
1566	>	simError();
1567	>	}
1568	>	}
1569	>	}
1570	>
1571	>	void RNEMD::writeOutputFile() {
1572	>
1573		#ifdef IS_MPI
989	–
990	–	// all processors have the same number of bins, and STL vectors pack their
991	–	// arrays, so in theory, this should be safe:
992	–
993	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
994	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
995	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
996	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
997	–	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
998	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
999	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1000	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1001	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1002	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1003	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1004	–	}
1574		// If we're the root node, should we print out the results
1575		int worldRank = MPI::COMM_WORLD.Get_rank();
1576		if (worldRank == 0) {
1577		#endif
1578	<	rnemdLog_ << time;
1579	<	for (j = 0; j < rnemdLogWidth_; j++) {
1580	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1578	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1579	>
1580	>	if( !rnemdFile_ ){
1581	>	sprintf( painCave.errMsg,
1582	>	"Could not open \"%s\" for RNEMD output.\n",
1583	>	rnemdFileName_.c_str());
1584	>	painCave.isFatal = 1;
1585	>	simError();
1586		}
1587	<	rnemdLog_ << "\n";
1588	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1589	<	xTempLog_ << time;
1590	<	for (j = 0; j < rnemdLogWidth_; j++) {
1591	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1587	>
1588	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1589	>
1590	>	RealType time = currentSnap_->getTime();
1591	>
1592	>
1593	>	rnemdFile_ << "#######################################################\n";
1594	>	rnemdFile_ << "# RNEMD {\n";
1595	>
1596	>	map<string, RNEMDMethod>::iterator mi;
1597	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1598	>	if ( (*mi).second == rnemdMethod_)
1599	>	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
1600	>	}
1601	>	map<string, RNEMDFluxType>::iterator fi;
1602	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1603	>	if ( (*fi).second == rnemdFluxType_)
1604	>	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
1605	>	}
1606	>
1607	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
1608	>
1609	>	rnemdFile_ << "#    objectSelection = \""
1610	>	<< rnemdObjectSelection_ << "\"\n";
1611	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
1612	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
1614	>	rnemdFile_ << "# }\n";
1615	>	rnemdFile_ << "#######################################################\n";
1616	>
1617	>	rnemdFile_ << "# running time = " << time << " fs\n";
1618	>	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
1619	>	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
1620	>
1621	>	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
1622	>	<< "\n";
1623	>	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
1624	>	<< "\n";
1625	>
1626	>	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
1627	>	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
1628	>	<< "\n";
1629	>
1630	>	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
1631	>	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
1632	>
1633	>
1634	>	if (rnemdMethod_ == rnemdNIVS) {
1635	>	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
1636	>	}
1637	>
1638	>	rnemdFile_ << "#######################################################\n";
1639	>
1640	>
1641	>
1642	>	//write title
1643	>	rnemdFile_ << "#";
1644	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1645	>	if (outputMask_[i]) {
1646	>	rnemdFile_ << "\t" << data_[i].title <<
1647	>	"(" << data_[i].units << ")";
1648		}
1019	–	xTempLog_ << "\n";
1020	–	yTempLog_ << time;
1021	–	for (j = 0; j < rnemdLogWidth_; j++) {
1022	–	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1023	–	}
1024	–	yTempLog_ << "\n";
1025	–	zTempLog_ << time;
1026	–	for (j = 0; j < rnemdLogWidth_; j++) {
1027	–	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1028	–	}
1029	–	zTempLog_ << "\n";
1649		}
1650	+	rnemdFile_ << std::endl;
1651	+
1652	+	rnemdFile_.precision(8);
1653	+
1654	+	for (unsigned int j = 0; j < nBins_; j++) {
1655	+
1656	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1657	+	if (outputMask_[i]) {
1658	+	if (data_[i].dataType == "RealType")
1659	+	writeReal(i,j);
1660	+	else if (data_[i].dataType == "Vector3d")
1661	+	writeVector(i,j);
1662	+	else {
1663	+	sprintf( painCave.errMsg,
1664	+	"RNEMD found an unknown data type for: %s ",
1665	+	data_[i].title.c_str());
1666	+	painCave.isFatal = 1;
1667	+	simError();
1668	+	}
1669	+	}
1670	+	}
1671	+	rnemdFile_ << std::endl;
1672	+
1673	+	}
1674	+
1675	+	rnemdFile_.flush();
1676	+	rnemdFile_.close();
1677	+
1678		#ifdef IS_MPI
1679		}
1680		#endif
1681	<	for (j = 0; j < rnemdLogWidth_; j++) {
1035	<	valueCount_[j] = 0;
1036	<	valueHist_[j] = 0.0;
1037	<	}
1038	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1039	<	for (j = 0; j < rnemdLogWidth_; j++) {
1040	<	xTempHist_[j] = 0.0;
1041	<	yTempHist_[j] = 0.0;
1042	<	zTempHist_[j] = 0.0;
1043	<	}
1681	>
1682		}
1683	+
1684	+	void RNEMD::writeReal(int index, unsigned int bin) {
1685	+	assert(index >=0 && index < ENDINDEX);
1686	+	assert(bin >=0 && bin < nBins_);
1687	+	RealType s;
1688	+
1689	+	data_[index].accumulator[bin]->getAverage(s);
1690	+
1691	+	if (! isinf(s) && ! isnan(s)) {
1692	+	rnemdFile_ << "\t" << s;
1693	+	} else{
1694	+	sprintf( painCave.errMsg,
1695	+	"RNEMD detected a numerical error writing: %s for bin %d",
1696	+	data_[index].title.c_str(), bin);
1697	+	painCave.isFatal = 1;
1698	+	simError();
1699	+	}
1700	+	}
1701	+
1702	+	void RNEMD::writeVector(int index, unsigned int bin) {
1703	+	assert(index >=0 && index < ENDINDEX);
1704	+	assert(bin >=0 && bin < nBins_);
1705	+	Vector3d s;
1706	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1707	+	if (isinf(s[0]) || isnan(s[0]) ||
1708	+	isinf(s[1]) || isnan(s[1]) ||
1709	+	isinf(s[2]) || isnan(s[2]) ) {
1710	+	sprintf( painCave.errMsg,
1711	+	"RNEMD detected a numerical error writing: %s for bin %d",
1712	+	data_[index].title.c_str(), bin);
1713	+	painCave.isFatal = 1;
1714	+	simError();
1715	+	} else {
1716	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1717	+	}
1718	+	}
1719		}
1720	+

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