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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 1764 by gezelter, Tue Jul 3 18:32:27 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"
#	Line 53 | Line 54
54		#include "math/SeqRandNumGen.hpp"
55		#else
56		#include "math/ParallelRandNumGen.hpp"
57	+	#include <mpi.h>
58		#endif
59
60		#define HONKING_LARGE_VALUE 1.0e10
61
62	+	using namespace std;
63		namespace OpenMD {
64
65	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
65	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
66	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
67
68		failTrialCount_ = 0;
69		failRootCount_ = 0;
70
71		int seedValue;
72		Globals * simParams = info->getSimParams();
73	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
74
75		stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
76		stringToEnumMap_["KineticScale"] = rnemdKineticScale;
77	+	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
78	+	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
79		stringToEnumMap_["PxScale"] = rnemdPxScale;
80		stringToEnumMap_["PyScale"] = rnemdPyScale;
81		stringToEnumMap_["PzScale"] = rnemdPzScale;
82		stringToEnumMap_["Px"] = rnemdPx;
83		stringToEnumMap_["Py"] = rnemdPy;
84		stringToEnumMap_["Pz"] = rnemdPz;
85	+	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
86	+	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
87		stringToEnumMap_["Unknown"] = rnemdUnknown;
88
89	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
89	>	runTime_ = simParams->getRunTime();
90	>	statusTime_ = simParams->getStatusTime();
91	>
92	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
93		evaluator_.loadScriptString(rnemdObjectSelection_);
94		seleMan_.setSelectionSet(evaluator_.evaluate());
95
#	Line 88 | Line 100 | namespace OpenMD {
100
101		if (selectionCount > nIntegrable) {
102		sprintf(painCave.errMsg,
103	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
103	>	"RNEMD: The current RNEMD_objectSelection,\n"
104		"\t\t%s\n"
105		"\thas resulted in %d selected objects.  However,\n"
106		"\tthe total number of integrable objects in the system\n"
#	Line 98 | Line 110 | namespace OpenMD {
110		rnemdObjectSelection_.c_str(),
111		selectionCount, nIntegrable);
112		painCave.isFatal = 0;
113	+	painCave.severity = OPENMD_WARNING;
114		simError();
102	–
115		}
116
117	<	const std::string st = simParams->getRNEMD_exchangeType();
117	>	const string st = rnemdParams->getExchangeType();
118
119	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
119	>	map<string, RNEMDTypeEnum>::iterator i;
120		i = stringToEnumMap_.find(st);
121		rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
122		if (rnemdType_ == rnemdUnknown) {
123	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
123	>	sprintf(painCave.errMsg,
124	>	"RNEMD: The current RNEMD_exchangeType,\n"
125	>	"\t\t%s\n"
126	>	"\tis not one of the recognized exchange types.\n",
127	>	st.c_str());
128	>	painCave.isFatal = 1;
129	>	painCave.severity = OPENMD_ERROR;
130	>	simError();
131		}
132	+
133	+	outputTemp_ = false;
134	+	if (rnemdParams->haveOutputTemperature()) {
135	+	outputTemp_ = rnemdParams->getOutputTemperature();
136	+	} else if ((rnemdType_ == rnemdKineticSwap) ||
137	+	(rnemdType_ == rnemdKineticScale) ||
138	+	(rnemdType_ == rnemdKineticScaleVAM) ||
139	+	(rnemdType_ == rnemdKineticScaleAM)) {
140	+	outputTemp_ = true;
141	+	}
142	+	outputVx_ = false;
143	+	if (rnemdParams->haveOutputVx()) {
144	+	outputVx_ = rnemdParams->getOutputVx();
145	+	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
146	+	outputVx_ = true;
147	+	}
148	+	outputVy_ = false;
149	+	if (rnemdParams->haveOutputVy()) {
150	+	outputVy_ = rnemdParams->getOutputVy();
151	+	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
152	+	outputVy_ = true;
153	+	}
154	+	output3DTemp_ = false;
155	+	if (rnemdParams->haveOutputXyzTemperature()) {
156	+	output3DTemp_ = rnemdParams->getOutputXyzTemperature();
157	+	}
158	+	outputRotTemp_ = false;
159	+	if (rnemdParams->haveOutputRotTemperature()) {
160	+	outputRotTemp_ = rnemdParams->getOutputRotTemperature();
161	+	}
162	+	// James put this in.
163	+	outputDen_ = false;
164	+	if (rnemdParams->haveOutputDen()) {
165	+	outputDen_ = rnemdParams->getOutputDen();
166	+	}
167	+	outputAh_ = false;
168	+	if (rnemdParams->haveOutputAh()) {
169	+	outputAh_ = rnemdParams->getOutputAh();
170	+	}
171	+	outputVz_ = false;
172	+	if (rnemdParams->haveOutputVz()) {
173	+	outputVz_ = rnemdParams->getOutputVz();
174	+	} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
175	+	outputVz_ = true;
176	+	}
177	+
178
179		#ifdef IS_MPI
180		if (worldRank == 0) {
181		#endif
182
183	<	std::string rnemdFileName;
184	<	std::string xTempFileName;
185	<	std::string yTempFileName;
186	<	std::string zTempFileName;
122	<	switch(rnemdType_) {
123	<	case rnemdKineticSwap :
124	<	case rnemdKineticScale :
183	>	//may have rnemdWriter separately
184	>	string rnemdFileName;
185	>
186	>	if (outputTemp_) {
187		rnemdFileName = "temperature.log";
188	<	break;
127	<	case rnemdPx :
128	<	case rnemdPxScale :
129	<	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());
138	<	break;
139	<	case rnemdPz :
140	<	case rnemdPzScale :
141	<	case rnemdUnknown :
142	<	default :
143	<	rnemdFileName = "rnemd.log";
144	<	break;
188	>	tempLog_.open(rnemdFileName.c_str());
189		}
190	<	rnemdLog_.open(rnemdFileName.c_str());
190	>	if (outputVx_) {
191	>	rnemdFileName = "velocityX.log";
192	>	vxzLog_.open(rnemdFileName.c_str());
193	>	}
194	>	if (outputVy_) {
195	>	rnemdFileName = "velocityY.log";
196	>	vyzLog_.open(rnemdFileName.c_str());
197	>	}
198
199	+	if (output3DTemp_) {
200	+	rnemdFileName = "temperatureX.log";
201	+	xTempLog_.open(rnemdFileName.c_str());
202	+	rnemdFileName = "temperatureY.log";
203	+	yTempLog_.open(rnemdFileName.c_str());
204	+	rnemdFileName = "temperatureZ.log";
205	+	zTempLog_.open(rnemdFileName.c_str());
206	+	}
207	+	if (outputRotTemp_) {
208	+	rnemdFileName = "temperatureR.log";
209	+	rotTempLog_.open(rnemdFileName.c_str());
210	+	}
211	+
212	+	//James put this in
213	+	if (outputDen_) {
214	+	rnemdFileName = "Density.log";
215	+	denLog_.open(rnemdFileName.c_str());
216	+	}
217	+	if (outputAh_) {
218	+	rnemdFileName = "Ah.log";
219	+	AhLog_.open(rnemdFileName.c_str());
220	+	}
221	+	if (outputVz_) {
222	+	rnemdFileName = "velocityZ.log";
223	+	vzzLog_.open(rnemdFileName.c_str());
224	+	}
225	+	logFrameCount_ = 0;
226		#ifdef IS_MPI
227		}
228		#endif
229
230	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
231	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
230	>	set_RNEMD_exchange_time(rnemdParams->getExchangeTime());
231	>	set_RNEMD_nBins(rnemdParams->getNbins());
232		midBin_ = nBins_ / 2;
233	<	if (simParams->haveRNEMD_logWidth()) {
234	<	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
233	>	if (rnemdParams->haveBinShift()) {
234	>	if (rnemdParams->getBinShift()) {
235	>	zShift_ = 0.5 / (RealType)(nBins_);
236	>	} else {
237	>	zShift_ = 0.0;
238	>	}
239	>	} else {
240	>	zShift_ = 0.0;
241	>	}
242	>	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
243	>	//shift slabs by half slab width, maybe useful in heterogeneous systems
244	>	//set to 0.0 if not using it; N/A in status output yet
245	>	if (rnemdParams->haveLogWidth()) {
246	>	set_RNEMD_logWidth(rnemdParams->getLogWidth());
247	>	/*arbitary rnemdLogWidth_, no checking;
248		if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
249	<	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
250	<	std::cerr << "Automaically set back to default.\n";
249	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
250	>	cerr << "Automaically set back to default.\n";
251		rnemdLogWidth_ = nBins_;
252	<	}
252	>	}*/
253		} else {
254	<	rnemdLogWidth_ = nBins_;
254	>	set_RNEMD_logWidth(nBins_);
255		}
256	<	valueHist_.resize(rnemdLogWidth_, 0.0);
257	<	valueCount_.resize(rnemdLogWidth_, 0);
256	>	tempHist_.resize(rnemdLogWidth_, 0.0);
257	>	tempCount_.resize(rnemdLogWidth_, 0);
258	>	pxzHist_.resize(rnemdLogWidth_, 0.0);
259	>	//vxzCount_.resize(rnemdLogWidth_, 0);
260	>	pyzHist_.resize(rnemdLogWidth_, 0.0);
261	>	//vyzCount_.resize(rnemdLogWidth_, 0);
262	>
263	>	mHist_.resize(rnemdLogWidth_, 0.0);
264		xTempHist_.resize(rnemdLogWidth_, 0.0);
265		yTempHist_.resize(rnemdLogWidth_, 0.0);
266		zTempHist_.resize(rnemdLogWidth_, 0.0);
267	+	xyzTempCount_.resize(rnemdLogWidth_, 0);
268	+	rotTempHist_.resize(rnemdLogWidth_, 0.0);
269	+	rotTempCount_.resize(rnemdLogWidth_, 0);
270	+	// James put this in
271	+	DenHist_.resize(rnemdLogWidth_, 0.0);
272	+	pzzHist_.resize(rnemdLogWidth_, 0.0);
273
274		set_RNEMD_exchange_total(0.0);
275	<	if (simParams->haveRNEMD_targetFlux()) {
276	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
275	>	if (rnemdParams->haveTargetFlux()) {
276	>	set_RNEMD_target_flux(rnemdParams->getTargetFlux());
277		} else {
278		set_RNEMD_target_flux(0.0);
279		}
280	+	if (rnemdParams->haveTargetJzKE()) {
281	+	set_RNEMD_target_JzKE(rnemdParams->getTargetJzKE());
282	+	} else {
283	+	set_RNEMD_target_JzKE(0.0);
284	+	}
285	+	if (rnemdParams->haveTargetJzpx()) {
286	+	set_RNEMD_target_jzpx(rnemdParams->getTargetJzpx());
287	+	} else {
288	+	set_RNEMD_target_jzpx(0.0);
289	+	}
290	+	jzp_.x() = targetJzpx_;
291	+	njzp_.x() = -targetJzpx_;
292	+	if (rnemdParams->haveTargetJzpy()) {
293	+	set_RNEMD_target_jzpy(rnemdParams->getTargetJzpy());
294	+	} else {
295	+	set_RNEMD_target_jzpy(0.0);
296	+	}
297	+	jzp_.y() = targetJzpy_;
298	+	njzp_.y() = -targetJzpy_;
299	+	if (rnemdParams->haveTargetJzpz()) {
300	+	set_RNEMD_target_jzpz(rnemdParams->getTargetJzpz());
301	+	} else {
302	+	set_RNEMD_target_jzpz(0.0);
303	+	}
304	+	jzp_.z() = targetJzpz_;
305	+	njzp_.z() = -targetJzpz_;
306
307		#ifndef IS_MPI
308		if (simParams->haveSeed()) {
#	Line 198 | Line 327 | namespace OpenMD {
327		#ifdef IS_MPI
328		if (worldRank == 0) {
329		#endif
330	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
331	<	rnemdLog_.close();
332	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
333	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
334	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
330	>
331	>	sprintf(painCave.errMsg,
332	>	"RNEMD: total failed trials: %d\n",
333	>	failTrialCount_);
334	>	painCave.isFatal = 0;
335	>	painCave.severity = OPENMD_INFO;
336	>	simError();
337	>
338	>	if (outputTemp_) tempLog_.close();
339	>	if (outputVx_)   vxzLog_.close();
340	>	if (outputVy_)   vyzLog_.close();
341	>
342	>	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
343	>	rnemdType_ == rnemdPyScale) {
344	>	sprintf(painCave.errMsg,
345	>	"RNEMD: total root-checking warnings: %d\n",
346	>	failRootCount_);
347	>	painCave.isFatal = 0;
348	>	painCave.severity = OPENMD_INFO;
349	>	simError();
350	>	}
351	>	if (output3DTemp_) {
352		xTempLog_.close();
353		yTempLog_.close();
354		zTempLog_.close();
355		}
356	+	if (outputRotTemp_) rotTempLog_.close();
357	+	// James put this in
358	+	if (outputDen_) denLog_.close();
359	+	if (outputAh_)  AhLog_.close();
360	+	if (outputVz_)  vzzLog_.close();
361	+
362		#ifdef IS_MPI
363		}
364		#endif
#	Line 246 | Line 398 | namespace OpenMD {
398		// which bin is this stuntdouble in?
399		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
400
401	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
401	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
402
403
404		// if we're in bin 0 or the middleBin
#	Line 259 | Line 411 | namespace OpenMD {
411		switch(rnemdType_) {
412		case rnemdKineticSwap :
413
414	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
415	<	vel[2]*vel[2]);
416	<	if (sd->isDirectional()) {
414	>	value = mass * vel.lengthSquare();
415	>
416	>	if (sd->isDirectional()) {
417		Vector3d angMom = sd->getJ();
418		Mat3x3d I = sd->getI();
419
420		if (sd->isLinear()) {
421	<	int i = sd->linearAxis();
422	<	int j = (i + 1) % 3;
423	<	int k = (i + 2) % 3;
424	<	value += angMom[j] * angMom[j] / I(j, j) +
425	<	angMom[k] * angMom[k] / I(k, k);
421	>	int i = sd->linearAxis();
422	>	int j = (i + 1) % 3;
423	>	int k = (i + 2) % 3;
424	>	value += angMom[j] * angMom[j] / I(j, j) +
425	>	angMom[k] * angMom[k] / I(k, k);
426		} else {
427	<	value += angMom[0]*angMom[0]/I(0, 0)
428	<	+ angMom[1]*angMom[1]/I(1, 1)
429	<	+ angMom[2]*angMom[2]/I(2, 2);
427	>	value += angMom[0]*angMom[0]/I(0, 0)
428	>	+ angMom[1]*angMom[1]/I(1, 1)
429	>	+ angMom[2]*angMom[2]/I(2, 2);
430		}
431	<	}
431	>	} //angular momenta exchange enabled
432	>	//energyConvert temporarily disabled
433		//make exchangeSum_ comparable between swap & scale
281	–	//temporarily without using energyConvert
434		//value = value * 0.5 / PhysicalConstants::energyConvert;
435		value *= 0.5;
436		break;
#	Line 331 | Line 483 | namespace OpenMD {
483		bool my_max_found = max_found;
484
485		// Even if we didn't find a minimum, did someone else?
486	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
335	<	1, MPI::BOOL, MPI::LAND);
336	<
486	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
487		// Even if we didn't find a maximum, did someone else?
488	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
489	<	1, MPI::BOOL, MPI::LAND);
490	<
491	<	struct {
492	<	RealType val;
493	<	int rank;
494	<	} max_vals, min_vals;
495	<
496	<	if (min_found) {
497	<	if (my_min_found)
488	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
489	>	#endif
490	>
491	>	if (max_found && min_found) {
492	>
493	>	#ifdef IS_MPI
494	>	struct {
495	>	RealType val;
496	>	int rank;
497	>	} max_vals, min_vals;
498	>
499	>	if (my_min_found) {
500		min_vals.val = min_val;
501	<	else
501	>	} else {
502		min_vals.val = HONKING_LARGE_VALUE;
503	<
503	>	}
504		min_vals.rank = worldRank;
505
506		// Who had the minimum?
507		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
508		1, MPI::REALTYPE_INT, MPI::MINLOC);
509		min_val = min_vals.val;
358	–	}
510
511	<	if (max_found) {
361	<	if (my_max_found)
511	>	if (my_max_found) {
512		max_vals.val = max_val;
513	<	else
513	>	} else {
514		max_vals.val = -HONKING_LARGE_VALUE;
515	<
515	>	}
516		max_vals.rank = worldRank;
517
518		// Who had the maximum?
519		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
520		1, MPI::REALTYPE_INT, MPI::MAXLOC);
521		max_val = max_vals.val;
372	–	}
522		#endif
523	<
524	<	if (max_found && min_found) {
525	<	if (min_val< max_val) {
377	<
523	>
524	>	if (min_val < max_val) {
525	>
526		#ifdef IS_MPI
527		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
528		// I have both maximum and minimum, so proceed like a single
529		// processor version:
530		#endif
531	<	// objects to be swapped: velocity & angular velocity
531	>
532		Vector3d min_vel = min_sd->getVel();
533		Vector3d max_vel = max_sd->getVel();
534		RealType temp_vel;
#	Line 389 | Line 537 | namespace OpenMD {
537		case rnemdKineticSwap :
538		min_sd->setVel(max_vel);
539		max_sd->setVel(min_vel);
540	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
540	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
541		Vector3d min_angMom = min_sd->getJ();
542		Vector3d max_angMom = max_sd->getJ();
543		min_sd->setJ(max_angMom);
544		max_sd->setJ(min_angMom);
545	<	}
545	>	}//angular momenta exchange enabled
546	>	//assumes same rigid body identity
547		break;
548		case rnemdPx :
549		temp_vel = min_vel.x();
#	Line 420 | Line 569 | namespace OpenMD {
569		default :
570		break;
571		}
572	+
573		#ifdef IS_MPI
574		// the rest of the cases only apply in parallel simulations:
575		} else if (max_vals.rank == worldRank) {
#	Line 438 | Line 588 | namespace OpenMD {
588		switch(rnemdType_) {
589		case rnemdKineticSwap :
590		max_sd->setVel(min_vel);
591	<
591	>	//angular momenta exchange enabled
592		if (max_sd->isDirectional()) {
593		Vector3d min_angMom;
594		Vector3d max_angMom = max_sd->getJ();
595	<
595	>
596		// point-to-point swap of the angular momentum vector
597		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
598		MPI::REALTYPE, min_vals.rank, 1,
599		min_angMom.getArrayPointer(), 3,
600		MPI::REALTYPE, min_vals.rank, 1,
601		status);
602	<
602	>
603		max_sd->setJ(min_angMom);
604	<	}
604	>	}
605		break;
606		case rnemdPx :
607		max_vel.x() = min_vel.x();
#	Line 484 | Line 634 | namespace OpenMD {
634		switch(rnemdType_) {
635		case rnemdKineticSwap :
636		min_sd->setVel(max_vel);
637	<
637	>	//angular momenta exchange enabled
638		if (min_sd->isDirectional()) {
639		Vector3d min_angMom = min_sd->getJ();
640		Vector3d max_angMom;
641	<
641	>
642		// point-to-point swap of the angular momentum vector
643		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
644		MPI::REALTYPE, max_vals.rank, 1,
645		max_angMom.getArrayPointer(), 3,
646		MPI::REALTYPE, max_vals.rank, 1,
647		status);
648	<
648	>
649		min_sd->setJ(max_angMom);
650		}
651		break;
#	Line 517 | Line 667 | namespace OpenMD {
667		}
668		#endif
669		exchangeSum_ += max_val - min_val;
670	<	} else {
671	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
670	>	} else {
671	>	sprintf(painCave.errMsg,
672	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
673	>	painCave.isFatal = 0;
674	>	painCave.severity = OPENMD_INFO;
675	>	simError();
676		failTrialCount_++;
677		}
678		} else {
679	<	std::cerr << "exchange NOT performed!\n";
680	<	std::cerr << "at least one of the two slabs empty.\n";
679	>	sprintf(painCave.errMsg,
680	>	"RNEMD: exchange NOT performed because selected object\n"
681	>	"\tnot present in at least one of the two slabs.\n");
682	>	painCave.isFatal = 0;
683	>	painCave.severity = OPENMD_INFO;
684	>	simError();
685		failTrialCount_++;
686		}
687
#	Line 540 | Line 698 | namespace OpenMD {
698		StuntDouble* sd;
699		int idx;
700
701	<	std::vector<StuntDouble*> hotBin, coldBin;
701	>	vector<StuntDouble*> hotBin, coldBin;
702
703		RealType Phx = 0.0;
704		RealType Phy = 0.0;
#	Line 548 | Line 706 | namespace OpenMD {
706		RealType Khx = 0.0;
707		RealType Khy = 0.0;
708		RealType Khz = 0.0;
709	+	RealType Khw = 0.0;
710		RealType Pcx = 0.0;
711		RealType Pcy = 0.0;
712		RealType Pcz = 0.0;
713		RealType Kcx = 0.0;
714		RealType Kcy = 0.0;
715		RealType Kcz = 0.0;
716	+	RealType Kcw = 0.0;
717
718		for (sd = seleMan_.beginSelected(selei); sd != NULL;
719		sd = seleMan_.nextSelected(selei)) {
#	Line 570 | Line 730 | namespace OpenMD {
730		// which bin is this stuntdouble in?
731		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
732
733	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
733	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
734
735		// if we're in bin 0 or the middleBin
736		if (binNo == 0 || binNo == midBin_) {
#	Line 586 | Line 746 | namespace OpenMD {
746		Khx += mass * vel.x() * vel.x();
747		Khy += mass * vel.y() * vel.y();
748		Khz += mass * vel.z() * vel.z();
749	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
750	+	if (sd->isDirectional()) {
751	+	Vector3d angMom = sd->getJ();
752	+	Mat3x3d I = sd->getI();
753	+	if (sd->isLinear()) {
754	+	int i = sd->linearAxis();
755	+	int j = (i + 1) % 3;
756	+	int k = (i + 2) % 3;
757	+	Khw += angMom[j] * angMom[j] / I(j, j) +
758	+	angMom[k] * angMom[k] / I(k, k);
759	+	} else {
760	+	Khw += angMom[0]*angMom[0]/I(0, 0)
761	+	+ angMom[1]*angMom[1]/I(1, 1)
762	+	+ angMom[2]*angMom[2]/I(2, 2);
763	+	}
764	+	}
765	+	//}
766		} else { //midBin_
767		coldBin.push_back(sd);
768		Pcx += mass * vel.x();
#	Line 594 | Line 771 | namespace OpenMD {
771		Kcx += mass * vel.x() * vel.x();
772		Kcy += mass * vel.y() * vel.y();
773		Kcz += mass * vel.z() * vel.z();
774	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
775	+	if (sd->isDirectional()) {
776	+	Vector3d angMom = sd->getJ();
777	+	Mat3x3d I = sd->getI();
778	+	if (sd->isLinear()) {
779	+	int i = sd->linearAxis();
780	+	int j = (i + 1) % 3;
781	+	int k = (i + 2) % 3;
782	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
783	+	angMom[k] * angMom[k] / I(k, k);
784	+	} else {
785	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
786	+	+ angMom[1]*angMom[1]/I(1, 1)
787	+	+ angMom[2]*angMom[2]/I(2, 2);
788	+	}
789	+	}
790	+	//}
791		}
792		}
793		}
794	<
794	>
795		Khx *= 0.5;
796		Khy *= 0.5;
797		Khz *= 0.5;
798	+	Khw *= 0.5;
799		Kcx *= 0.5;
800		Kcy *= 0.5;
801		Kcz *= 0.5;
802	+	Kcw *= 0.5;
803
804	+	// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
805	+	//        << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
806	+	//        << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
807	+	// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
808	+	//        << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
809	+
810		#ifdef IS_MPI
811		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
812		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 616 | Line 818 | namespace OpenMD {
818		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
819		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
820		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
821	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
822	+
823		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
824		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
825		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
826	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
827		#endif
828
829	<	//use coldBin coeff's
829	>	//solve coldBin coeff's first
830		RealType px = Pcx / Phx;
831		RealType py = Pcy / Phy;
832		RealType pz = Pcz / Phz;
833	+	RealType c, x, y, z;
834	+	bool successfulScale = false;
835	+	if ((rnemdType_ == rnemdKineticScaleVAM) ||
836	+	(rnemdType_ == rnemdKineticScaleAM)) {
837	+	//may need sanity check Khw & Kcw > 0
838
839	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
840	<	switch(rnemdType_) {
841	<	case rnemdKineticScale :
842	<	/*used hotBin coeff's & only scale x & y dimensions
843	<	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	<	*/
839	>	if (rnemdType_ == rnemdKineticScaleVAM) {
840	>	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
841	>	} else {
842	>	c = 1.0 - targetFlux_ / Kcw;
843	>	}
844
845	<	//scale all three dimensions, let c_x = c_y
846	<	a000 = Kcx + Kcy;
847	<	a110 = Kcz;
848	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
849	<	a001 = Khx * px * px + Khy * py * py;
850	<	a111 = Khz * pz * pz;
851	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
852	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
853	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
854	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
855	<	break;
856	<	case rnemdPxScale :
857	<	c = 1 - targetFlux_ / Pcx;
858	<	a000 = Kcy;
859	<	a110 = Kcz;
860	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
861	<	a001 = py * py * Khy;
862	<	a111 = pz * pz * Khz;
863	<	b01 = -2.0 * Khy * py * (1.0 + py);
864	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
865	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
866	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
867	<	break;
868	<	case rnemdPyScale :
869	<	c = 1 - targetFlux_ / Pcy;
870	<	a000 = Kcx;
871	<	a110 = Kcz;
872	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
873	<	a001 = px * px * Khx;
874	<	a111 = pz * pz * Khz;
875	<	b01 = -2.0 * Khx * px * (1.0 + px);
876	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
877	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
878	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
879	<	break;
880	<	case rnemdPzScale ://we don't really do this, do we?
881	<	c = 1 - targetFlux_ / Pcz;
882	<	a000 = Kcx;
883	<	a110 = Kcy;
884	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
885	<	a001 = px * px * Khx;
886	<	a111 = py * py * Khy;
887	<	b01 = -2.0 * Khx * px * (1.0 + px);
888	<	b11 = -2.0 * Khy * py * (1.0 + py);
889	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
890	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
891	<	break;
892	<	default :
893	<	break;
894	<	}
895	<
896	<	RealType v1 = a000 * a111 - a001 * a110;
897	<	RealType v2 = a000 * b01;
898	<	RealType v3 = a000 * b11;
899	<	RealType v4 = a000 * c1 - a001 * c0;
900	<	RealType v8 = a110 * b01;
901	<	RealType v10 = - b01 * c0;
902	<
903	<	RealType u0 = v2 * v10 - v4 * v4;
904	<	RealType u1 = -2.0 * v3 * v4;
905	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
906	<	RealType u3 = -2.0 * v1 * v3;
907	<	RealType u4 = - v1 * v1;
908	<	//rescale coefficients
909	<	RealType maxAbs = fabs(u0);
910	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
911	<	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();
727	<
728	<	std::vector<RealType>::iterator ri;
729	<	RealType r1, r2, alpha0;
730	<	std::vector<std::pair<RealType,RealType> > rps;
731	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
732	<	r2 = *ri;
733	<	//check if FindRealRoots() give the right answer
734	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
735	<	sprintf(painCave.errMsg,
736	<	"RNEMD Warning: polynomial solve seems to have an error!");
737	<	painCave.isFatal = 0;
738	<	simError();
739	<	failRootCount_++;
845	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
846	>	c = sqrt(c);
847	>	std::cerr << "cold slab scaling coefficient: " << c << endl;
848	>	//now convert to hotBin coefficient
849	>	RealType w = 0.0;
850	>	if (rnemdType_ ==  rnemdKineticScaleVAM) {
851	>	x = 1.0 + px * (1.0 - c);
852	>	y = 1.0 + py * (1.0 - c);
853	>	z = 1.0 + pz * (1.0 - c);
854	>	/* more complicated way
855	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
856	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
857	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
858	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
859	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
860	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
861	>	*/
862	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
863	>	(fabs(z - 1.0) < 0.1)) {
864	>	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
865	>	+ Khz * (1.0 - z * z)) / Khw;
866	>	}//no need to calculate w if x, y or z is out of range
867	>	} else {
868	>	w = 1.0 + targetFlux_ / Khw;
869	>	}
870	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
871	>	//if w is in the right range, so should be x, y, z.
872	>	vector<StuntDouble*>::iterator sdi;
873	>	Vector3d vel;
874	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
875	>	if (rnemdType_ == rnemdKineticScaleVAM) {
876	>	vel = (*sdi)->getVel() * c;
877	>	//vel.x() *= c;
878	>	//vel.y() *= c;
879	>	//vel.z() *= c;
880	>	(*sdi)->setVel(vel);
881	>	}
882	>	if ((*sdi)->isDirectional()) {
883	>	Vector3d angMom = (*sdi)->getJ() * c;
884	>	//angMom[0] *= c;
885	>	//angMom[1] *= c;
886	>	//angMom[2] *= c;
887	>	(*sdi)->setJ(angMom);
888	>	}
889	>	}
890	>	w = sqrt(w);
891	>	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
892	>	<< "\twh= " << w << endl;
893	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
894	>	if (rnemdType_ == rnemdKineticScaleVAM) {
895	>	vel = (*sdi)->getVel();
896	>	vel.x() *= x;
897	>	vel.y() *= y;
898	>	vel.z() *= z;
899	>	(*sdi)->setVel(vel);
900	>	}
901	>	if ((*sdi)->isDirectional()) {
902	>	Vector3d angMom = (*sdi)->getJ() * w;
903	>	//angMom[0] *= w;
904	>	//angMom[1] *= w;
905	>	//angMom[2] *= w;
906	>	(*sdi)->setJ(angMom);
907	>	}
908	>	}
909	>	successfulScale = true;
910	>	exchangeSum_ += targetFlux_;
911	>	}
912		}
913	<	//might not be useful w/o rescaling coefficients
914	<	alpha0 = -c0 - a110 * r2 * r2;
915	<	if (alpha0 >= 0.0) {
916	<	r1 = sqrt(alpha0 / a000);
917	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
918	<	{ rps.push_back(std::make_pair(r1, r2)); }
919	<	if (r1 > 1e-6) { //r1 non-negative
920	<	r1 = -r1;
921	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
922	<	{ rps.push_back(std::make_pair(r1, r2)); }
923	<	}
913	>	} else {
914	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
915	>	switch(rnemdType_) {
916	>	case rnemdKineticScale :
917	>	/* used hotBin coeff's & only scale x & y dimensions
918	>	RealType px = Phx / Pcx;
919	>	RealType py = Phy / Pcy;
920	>	a110 = Khy;
921	>	c0 = - Khx - Khy - targetFlux_;
922	>	a000 = Khx;
923	>	a111 = Kcy * py * py;
924	>	b11 = -2.0 * Kcy * py * (1.0 + py);
925	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
926	>	b01 = -2.0 * Kcx * px * (1.0 + px);
927	>	a001 = Kcx * px * px;
928	>	*/
929	>	//scale all three dimensions, let c_x = c_y
930	>	a000 = Kcx + Kcy;
931	>	a110 = Kcz;
932	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
933	>	a001 = Khx * px * px + Khy * py * py;
934	>	a111 = Khz * pz * pz;
935	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
936	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
937	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
938	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
939	>	break;
940	>	case rnemdPxScale :
941	>	c = 1 - targetFlux_ / Pcx;
942	>	a000 = Kcy;
943	>	a110 = Kcz;
944	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
945	>	a001 = py * py * Khy;
946	>	a111 = pz * pz * Khz;
947	>	b01 = -2.0 * Khy * py * (1.0 + py);
948	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
949	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
950	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
951	>	break;
952	>	case rnemdPyScale :
953	>	c = 1 - targetFlux_ / Pcy;
954	>	a000 = Kcx;
955	>	a110 = Kcz;
956	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
957	>	a001 = px * px * Khx;
958	>	a111 = pz * pz * Khz;
959	>	b01 = -2.0 * Khx * px * (1.0 + px);
960	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
961	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
962	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
963	>	break;
964	>	case rnemdPzScale ://we don't really do this, do we?
965	>	c = 1 - targetFlux_ / Pcz;
966	>	a000 = Kcx;
967	>	a110 = Kcy;
968	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
969	>	a001 = px * px * Khx;
970	>	a111 = py * py * Khy;
971	>	b01 = -2.0 * Khx * px * (1.0 + px);
972	>	b11 = -2.0 * Khy * py * (1.0 + py);
973	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
974	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
975	>	break;
976	>	default :
977	>	break;
978		}
979	<	}
980	<	// Consider combininig 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	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
986	<	std::vector<std::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	<	default :
1006	<	break;
1007	<	}
1008	<	if (diff < smallestDiff) {
1009	<	smallestDiff = diff;
1010	<	bestPair = *rpi;
1011	<	}
979	>
980	>	RealType v1 = a000 * a111 - a001 * a110;
981	>	RealType v2 = a000 * b01;
982	>	RealType v3 = a000 * b11;
983	>	RealType v4 = a000 * c1 - a001 * c0;
984	>	RealType v8 = a110 * b01;
985	>	RealType v10 = - b01 * c0;
986	>
987	>	RealType u0 = v2 * v10 - v4 * v4;
988	>	RealType u1 = -2.0 * v3 * v4;
989	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
990	>	RealType u3 = -2.0 * v1 * v3;
991	>	RealType u4 = - v1 * v1;
992	>	//rescale coefficients
993	>	RealType maxAbs = fabs(u0);
994	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
995	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
996	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
997	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
998	>	u0 /= maxAbs;
999	>	u1 /= maxAbs;
1000	>	u2 /= maxAbs;
1001	>	u3 /= maxAbs;
1002	>	u4 /= maxAbs;
1003	>	//max_element(start, end) is also available.
1004	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1005	>	poly.setCoefficient(4, u4);
1006	>	poly.setCoefficient(3, u3);
1007	>	poly.setCoefficient(2, u2);
1008	>	poly.setCoefficient(1, u1);
1009	>	poly.setCoefficient(0, u0);
1010	>	vector<RealType> realRoots = poly.FindRealRoots();
1011	>
1012	>	vector<RealType>::iterator ri;
1013	>	RealType r1, r2, alpha0;
1014	>	vector<pair<RealType,RealType> > rps;
1015	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1016	>	r2 = *ri;
1017	>	//check if FindRealRoots() give the right answer
1018	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1019	>	sprintf(painCave.errMsg,
1020	>	"RNEMD Warning: polynomial solve seems to have an error!");
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	failRootCount_++;
1024	>	}
1025	>	//might not be useful w/o rescaling coefficients
1026	>	alpha0 = -c0 - a110 * r2 * r2;
1027	>	if (alpha0 >= 0.0) {
1028	>	r1 = sqrt(alpha0 / a000);
1029	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1030	>	< 1e-6)
1031	>	{ rps.push_back(make_pair(r1, r2)); }
1032	>	if (r1 > 1e-6) { //r1 non-negative
1033	>	r1 = -r1;
1034	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1035	>	< 1e-6)
1036	>	{ rps.push_back(make_pair(r1, r2)); }
1037	>	}
1038	>	}
1039		}
1040	+	// Consider combining together the solving pair part w/ the searching
1041	+	// best solution part so that we don't need the pairs vector
1042	+	if (!rps.empty()) {
1043	+	RealType smallestDiff = HONKING_LARGE_VALUE;
1044	+	RealType diff;
1045	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1046	+	vector<pair<RealType,RealType> >::iterator rpi;
1047	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1048	+	r1 = (*rpi).first;
1049	+	r2 = (*rpi).second;
1050	+	switch(rnemdType_) {
1051	+	case rnemdKineticScale :
1052	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1053	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1054	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1055	+	break;
1056	+	case rnemdPxScale :
1057	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1058	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1059	+	break;
1060	+	case rnemdPyScale :
1061	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1062	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1063	+	break;
1064	+	case rnemdPzScale :
1065	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1066	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1067	+	default :
1068	+	break;
1069	+	}
1070	+	if (diff < smallestDiff) {
1071	+	smallestDiff = diff;
1072	+	bestPair = *rpi;
1073	+	}
1074	+	}
1075		#ifdef IS_MPI
1076	<	if (worldRank == 0) {
1076	>	if (worldRank == 0) {
1077		#endif
1078	<	std::cerr << "we choose r1 = " << bestPair.first
1079	<	<< " and r2 = " << bestPair.second << "\n";
1078	>	sprintf(painCave.errMsg,
1079	>	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1080	>	bestPair.first, bestPair.second);
1081	>	painCave.isFatal = 0;
1082	>	painCave.severity = OPENMD_INFO;
1083	>	simError();
1084		#ifdef IS_MPI
1085	<	}
1085	>	}
1086		#endif
1087	+
1088	+	switch(rnemdType_) {
1089	+	case rnemdKineticScale :
1090	+	x = bestPair.first;
1091	+	y = bestPair.first;
1092	+	z = bestPair.second;
1093	+	break;
1094	+	case rnemdPxScale :
1095	+	x = c;
1096	+	y = bestPair.first;
1097	+	z = bestPair.second;
1098	+	break;
1099	+	case rnemdPyScale :
1100	+	x = bestPair.first;
1101	+	y = c;
1102	+	z = bestPair.second;
1103	+	break;
1104	+	case rnemdPzScale :
1105	+	x = bestPair.first;
1106	+	y = bestPair.second;
1107	+	z = c;
1108	+	break;
1109	+	default :
1110	+	break;
1111	+	}
1112	+	vector<StuntDouble*>::iterator sdi;
1113	+	Vector3d vel;
1114	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1115	+	vel = (*sdi)->getVel();
1116	+	vel.x() *= x;
1117	+	vel.y() *= y;
1118	+	vel.z() *= z;
1119	+	(*sdi)->setVel(vel);
1120	+	}
1121	+	//convert to hotBin coefficient
1122	+	x = 1.0 + px * (1.0 - x);
1123	+	y = 1.0 + py * (1.0 - y);
1124	+	z = 1.0 + pz * (1.0 - z);
1125	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1126	+	vel = (*sdi)->getVel();
1127	+	vel.x() *= x;
1128	+	vel.y() *= y;
1129	+	vel.z() *= z;
1130	+	(*sdi)->setVel(vel);
1131	+	}
1132	+	successfulScale = true;
1133	+	exchangeSum_ += targetFlux_;
1134	+	}
1135	+	}
1136	+	if (successfulScale != true) {
1137	+	sprintf(painCave.errMsg,
1138	+	"RNEMD: exchange NOT performed!\n");
1139	+	painCave.isFatal = 0;
1140	+	painCave.severity = OPENMD_INFO;
1141	+	simError();
1142	+	failTrialCount_++;
1143	+	}
1144	+	}
1145
1146	<	RealType x, y, z;
1147	<	switch(rnemdType_) {
1148	<	case rnemdKineticScale :
1149	<	x = bestPair.first;
1150	<	y = bestPair.first;
1151	<	z = bestPair.second;
1152	<	break;
1153	<	case rnemdPxScale :
1154	<	x = c;
1155	<	y = bestPair.first;
1156	<	z = bestPair.second;
1157	<	break;
1158	<	case rnemdPyScale :
1159	<	x = bestPair.first;
1160	<	y = c;
1161	<	z = bestPair.second;
1162	<	break;
1163	<	case rnemdPzScale :
1164	<	x = bestPair.first;
1165	<	y = bestPair.second;
1166	<	z = c;
1167	<	break;
1168	<	default :
1169	<	break;
1170	<	}
1171	<	std::vector<StuntDouble*>::iterator sdi;
1172	<	Vector3d vel;
1173	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1174	<	vel = (*sdi)->getVel();
1175	<	vel.x() *= x;
1176	<	vel.y() *= y;
1177	<	vel.z() *= z;
1178	<	(*sdi)->setVel(vel);
1146	>	void RNEMD::doShiftScale() {
1147	>
1148	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1149	>	RealType time = currentSnap_->getTime();
1150	>	Mat3x3d hmat = currentSnap_->getHmat();
1151	>
1152	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1153	>
1154	>	int selei;
1155	>	StuntDouble* sd;
1156	>	int idx;
1157	>
1158	>	vector<StuntDouble*> hotBin, coldBin;
1159	>
1160	>	Vector3d Ph(V3Zero);
1161	>	RealType Mh = 0.0;
1162	>	RealType Kh = 0.0;
1163	>	Vector3d Pc(V3Zero);
1164	>	RealType Mc = 0.0;
1165	>	RealType Kc = 0.0;
1166	>
1167	>
1168	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1169	>	sd = seleMan_.nextSelected(selei)) {
1170	>
1171	>	idx = sd->getLocalIndex();
1172	>
1173	>	Vector3d pos = sd->getPos();
1174	>
1175	>	// wrap the stuntdouble's position back into the box:
1176	>
1177	>	if (usePeriodicBoundaryConditions_)
1178	>	currentSnap_->wrapVector(pos);
1179	>
1180	>	// which bin is this stuntdouble in?
1181	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1182	>
1183	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1184	>
1185	>	// if we're in bin 0 or the middleBin
1186	>	if (binNo == 0 || binNo == midBin_) {
1187	>
1188	>	RealType mass = sd->getMass();
1189	>	Vector3d vel = sd->getVel();
1190	>
1191	>	if (binNo == 0) {
1192	>	hotBin.push_back(sd);
1193	>	//std::cerr << "before, velocity = " << vel << endl;
1194	>	Ph += mass * vel;
1195	>	//std::cerr << "after, velocity = " << vel << endl;
1196	>	Mh += mass;
1197	>	Kh += mass * vel.lengthSquare();
1198	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1199	>	if (sd->isDirectional()) {
1200	>	Vector3d angMom = sd->getJ();
1201	>	Mat3x3d I = sd->getI();
1202	>	if (sd->isLinear()) {
1203	>	int i = sd->linearAxis();
1204	>	int j = (i + 1) % 3;
1205	>	int k = (i + 2) % 3;
1206	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1207	>	angMom[k] * angMom[k] / I(k, k);
1208	>	} else {
1209	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1210	>	angMom[1] * angMom[1] / I(1, 1) +
1211	>	angMom[2] * angMom[2] / I(2, 2);
1212	>	}
1213	>	}
1214	>	}
1215	>	} else { //midBin_
1216	>	coldBin.push_back(sd);
1217	>	Pc += mass * vel;
1218	>	Mc += mass;
1219	>	Kc += mass * vel.lengthSquare();
1220	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1221	>	if (sd->isDirectional()) {
1222	>	Vector3d angMom = sd->getJ();
1223	>	Mat3x3d I = sd->getI();
1224	>	if (sd->isLinear()) {
1225	>	int i = sd->linearAxis();
1226	>	int j = (i + 1) % 3;
1227	>	int k = (i + 2) % 3;
1228	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1229	>	angMom[k] * angMom[k] / I(k, k);
1230	>	} else {
1231	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1232	>	angMom[1] * angMom[1] / I(1, 1) +
1233	>	angMom[2] * angMom[2] / I(2, 2);
1234	>	}
1235	>	}
1236	>	}
1237	>	}
1238		}
1239	<	//convert to hotBin coefficient
1240	<	x = 1.0 + px * (1.0 - x);
1241	<	y = 1.0 + py * (1.0 - y);
1242	<	z = 1.0 + pz * (1.0 - z);
1243	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1244	<	vel = (*sdi)->getVel();
1245	<	vel.x() *= x;
1246	<	vel.y() *= y;
1247	<	vel.z() *= z;
1248	<	(*sdi)->setVel(vel);
1239	>	}
1240	>
1241	>	Kh *= 0.5;
1242	>	Kc *= 0.5;
1243	>
1244	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1245	>	//        << "\tKc= " << Kc << endl;
1246	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1247	>
1248	>	#ifdef IS_MPI
1249	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1250	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1251	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1252	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1253	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1254	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1255	>	#endif
1256	>
1257	>	bool successfulExchange = false;
1258	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1259	>	Vector3d vc = Pc / Mc;
1260	>	Vector3d ac = njzp_ / Mc + vc;
1261	>	Vector3d acrec = njzp_ / Mc;
1262	>	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1263	>	if (cNumerator > 0.0) {
1264	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1265	>	if (cDenominator > 0.0) {
1266	>	RealType c = sqrt(cNumerator / cDenominator);
1267	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1268	>	Vector3d vh = Ph / Mh;
1269	>	Vector3d ah = jzp_ / Mh + vh;
1270	>	Vector3d ahrec = jzp_ / Mh;
1271	>	RealType hNumerator = Kh + targetJzKE_
1272	>	- 0.5 * Mh * ah.lengthSquare();
1273	>	if (hNumerator > 0.0) {
1274	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1275	>	if (hDenominator > 0.0) {
1276	>	RealType h = sqrt(hNumerator / hDenominator);
1277	>	if ((h > 0.9) && (h < 1.1)) {
1278	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1279	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1280	>	vector<StuntDouble*>::iterator sdi;
1281	>	Vector3d vel;
1282	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1283	>	//vel = (*sdi)->getVel();
1284	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1285	>	(*sdi)->setVel(vel);
1286	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1287	>	if ((*sdi)->isDirectional()) {
1288	>	Vector3d angMom = (*sdi)->getJ() * c;
1289	>	(*sdi)->setJ(angMom);
1290	>	}
1291	>	}
1292	>	}
1293	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1294	>	//vel = (*sdi)->getVel();
1295	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1296	>	(*sdi)->setVel(vel);
1297	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1298	>	if ((*sdi)->isDirectional()) {
1299	>	Vector3d angMom = (*sdi)->getJ() * h;
1300	>	(*sdi)->setJ(angMom);
1301	>	}
1302	>	}
1303	>	}
1304	>	successfulExchange = true;
1305	>	exchangeSum_ += targetFlux_;
1306	>	// this is a redundant variable for doShiftScale() so that
1307	>	// RNEMD can output one exchange quantity needed in a job.
1308	>	// need a better way to do this.
1309	>	//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n';
1310	>	//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n';
1311	>	//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n';
1312	>	Asum_ += (ahrec.z() - acrec.z());
1313	>	Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc)));
1314	>	AhCount_ = ahrec.z();
1315	>	if (outputAh_) {
1316	>	AhLog_ << time << "   ";
1317	>	AhLog_ << AhCount_;
1318	>	AhLog_ << endl;
1319	>	}
1320	>	}
1321	>	}
1322	>	}
1323	>	}
1324	>	}
1325		}
1326	<	exchangeSum_ += targetFlux_;
1327	<	//we may want to check whether the exchange has been successful
1328	<	} else {
1329	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1326	>	}
1327	>	if (successfulExchange != true) {
1328	>	//   sprintf(painCave.errMsg,
1329	>	//              "RNEMD: exchange NOT performed!\n");
1330	>	//   painCave.isFatal = 0;
1331	>	//   painCave.severity = OPENMD_INFO;
1332	>	//   simError();
1333		failTrialCount_++;
1334		}
847	–
1335		}
1336
1337		void RNEMD::doRNEMD() {
1338
1339		switch(rnemdType_) {
1340		case rnemdKineticScale :
1341	+	case rnemdKineticScaleVAM :
1342	+	case rnemdKineticScaleAM :
1343		case rnemdPxScale :
1344		case rnemdPyScale :
1345		case rnemdPzScale :
#	Line 862 | Line 1351 | namespace OpenMD {
1351		case rnemdPz :
1352		doSwap();
1353		break;
1354	+	case rnemdShiftScaleV :
1355	+	case rnemdShiftScaleVAM :
1356	+	doShiftScale();
1357	+	break;
1358		case rnemdUnknown :
1359		default :
1360		break;
#	Line 879 | Line 1372 | namespace OpenMD {
1372		StuntDouble* sd;
1373		int idx;
1374
1375	+	logFrameCount_++;
1376	+
1377	+	// alternative approach, track all molecules instead of only those
1378	+	// selected for scaling/swapping:
1379	+	/*
1380	+	SimInfo::MoleculeIterator miter;
1381	+	vector<StuntDouble*>::iterator iiter;
1382	+	Molecule* mol;
1383	+	StuntDouble* integrableObject;
1384	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1385	+	mol = info_->nextMolecule(miter))
1386	+	integrableObject is essentially sd
1387	+	for (integrableObject = mol->beginIntegrableObject(iiter);
1388	+	integrableObject != NULL;
1389	+	integrableObject = mol->nextIntegrableObject(iiter))
1390	+	*/
1391		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1392		sd = seleMan_.nextSelected(selei)) {
1393
#	Line 894 | Line 1403 | namespace OpenMD {
1403		// which bin is this stuntdouble in?
1404		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1405
1406	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1407	<
1406	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1407	>	rnemdLogWidth_;
1408	>	// no symmetrization allowed due to arbitary rnemdLogWidth_
1409	>	/*
1410		if (rnemdLogWidth_ == midBin_ + 1)
1411		if (binNo > midBin_)
1412		binNo = nBins_ - binNo;
1413	<
1413	>	*/
1414		RealType mass = sd->getMass();
1415	+	mHist_[binNo] += mass;
1416		Vector3d vel = sd->getVel();
1417		RealType value;
1418	<	RealType xVal, yVal, zVal;
1418	>	//RealType xVal, yVal, zVal;
1419
1420	<	switch(rnemdType_) {
1421	<	case rnemdKineticSwap :
1422	<	case rnemdKineticScale :
911	<
912	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
913	<	vel[2]*vel[2]);
914	<
915	<	valueCount_[binNo] += 3;
1420	>	if (outputTemp_) {
1421	>	value = mass * vel.lengthSquare();
1422	>	tempCount_[binNo] += 3;
1423		if (sd->isDirectional()) {
1424		Vector3d angMom = sd->getJ();
1425		Mat3x3d I = sd->getI();
919	–
1426		if (sd->isLinear()) {
1427		int i = sd->linearAxis();
1428		int j = (i + 1) % 3;
1429		int k = (i + 2) % 3;
1430		value += angMom[j] * angMom[j] / I(j, j) +
1431		angMom[k] * angMom[k] / I(k, k);
1432	<
927	<	valueCount_[binNo] +=2;
928	<
1432	>	tempCount_[binNo] +=2;
1433		} else {
1434	<	value += angMom[0]*angMom[0]/I(0, 0)
1435	<	+ angMom[1]*angMom[1]/I(1, 1)
1436	<	+ angMom[2]*angMom[2]/I(2, 2);
1437	<	valueCount_[binNo] +=3;
1434	>	value += angMom[0] * angMom[0] / I(0, 0) +
1435	>	angMom[1]*angMom[1]/I(1, 1) +
1436	>	angMom[2]*angMom[2]/I(2, 2);
1437	>	tempCount_[binNo] +=3;
1438		}
1439		}
1440	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1441	<
1442	<	break;
1443	<	case rnemdPx :
1444	<	case rnemdPxScale :
1440	>	value = value / PhysicalConstants::energyConvert
1441	>	/ PhysicalConstants::kb;//may move to getStatus()
1442	>	tempHist_[binNo] += value;
1443	>	}
1444	>	if (outputVx_) {
1445		value = mass * vel[0];
1446	<	valueCount_[binNo]++;
1447	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1448	<	/ PhysicalConstants::kb;
1449	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
946	<	/ PhysicalConstants::kb;
947	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
948	<	/ PhysicalConstants::kb;
949	<	xTempHist_[binNo] += xVal;
950	<	yTempHist_[binNo] += yVal;
951	<	zTempHist_[binNo] += zVal;
952	<	break;
953	<	case rnemdPy :
954	<	case rnemdPyScale :
1446	>	//vxzCount_[binNo]++;
1447	>	pxzHist_[binNo] += value;
1448	>	}
1449	>	if (outputVy_) {
1450		value = mass * vel[1];
1451	<	valueCount_[binNo]++;
1452	<	break;
958	<	case rnemdPz :
959	<	case rnemdPzScale :
960	<	value = mass * vel[2];
961	<	valueCount_[binNo]++;
962	<	break;
963	<	case rnemdUnknown :
964	<	default :
965	<	break;
1451	>	//vyzCount_[binNo]++;
1452	>	pyzHist_[binNo] += value;
1453		}
967	–	valueHist_[binNo] += value;
968	–	}
1454
1455	+	if (output3DTemp_) {
1456	+	value = mass * vel.x() * vel.x();
1457	+	xTempHist_[binNo] += value;
1458	+	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1459	+	/ PhysicalConstants::kb;
1460	+	yTempHist_[binNo] += value;
1461	+	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1462	+	/ PhysicalConstants::kb;
1463	+	zTempHist_[binNo] += value;
1464	+	xyzTempCount_[binNo]++;
1465	+	}
1466	+	if (outputRotTemp_) {
1467	+	if (sd->isDirectional()) {
1468	+	Vector3d angMom = sd->getJ();
1469	+	Mat3x3d I = sd->getI();
1470	+	if (sd->isLinear()) {
1471	+	int i = sd->linearAxis();
1472	+	int j = (i + 1) % 3;
1473	+	int k = (i + 2) % 3;
1474	+	value = angMom[j] * angMom[j] / I(j, j) +
1475	+	angMom[k] * angMom[k] / I(k, k);
1476	+	rotTempCount_[binNo] +=2;
1477	+	} else {
1478	+	value = angMom[0] * angMom[0] / I(0, 0) +
1479	+	angMom[1] * angMom[1] / I(1, 1) +
1480	+	angMom[2] * angMom[2] / I(2, 2);
1481	+	rotTempCount_[binNo] +=3;
1482	+	}
1483	+	}
1484	+	value = value / PhysicalConstants::energyConvert
1485	+	/ PhysicalConstants::kb;//may move to getStatus()
1486	+	rotTempHist_[binNo] += value;
1487	+	}
1488	+	// James put this in.
1489	+	if (outputDen_) {
1490	+	//value = 1.0;
1491	+	DenHist_[binNo] += 1;
1492	+	}
1493	+	if (outputVz_) {
1494	+	value = mass * vel[2];
1495	+	//vyzCount_[binNo]++;
1496	+	pzzHist_[binNo] += value;
1497	+	}
1498	+	}
1499		}
1500
1501		void RNEMD::getStarted() {
1502	+	collectData();
1503	+	/*now can output profile in step 0, but might not be useful;
1504		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1505		Stats& stat = currentSnap_->statData;
1506		stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1507	+	*/
1508	+	//may output a header for the log file here
1509	+	getStatus();
1510		}
1511
1512		void RNEMD::getStatus() {
1513
1514		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
981	–	Stats& stat = currentSnap_->statData;
1515		RealType time = currentSnap_->getTime();
983	–
984	–	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1516		//or to be more meaningful, define another item as exchangeSum_ / time
1517		int j;
1518
#	Line 990 | Line 1521 | namespace OpenMD {
1521		// all processors have the same number of bins, and STL vectors pack their
1522		// arrays, so in theory, this should be safe:
1523
1524	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1525	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1526	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1527	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1528	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
1524	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1525	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1526	>	if (outputTemp_) {
1527	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1528	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1529	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1530	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1531	>	}
1532	>	if (outputVx_) {
1533	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1534	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1535	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1536	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1537	>	}
1538	>	if (outputVy_) {
1539	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1540	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1541	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1542	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1543	>	}
1544	>	if (output3DTemp_) {
1545		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1546		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1547		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1548		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1549		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1550		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1551	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1552	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1553		}
1554	+	if (outputRotTemp_) {
1555	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1556	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1557	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1558	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1559	+	}
1560	+	// James put this in
1561	+	if (outputDen_) {
1562	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1563	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1564	+	}
1565	+	if (outputAh_) {
1566	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1567	+	1, MPI::REALTYPE, MPI::SUM);
1568	+	}
1569	+	if (outputVz_) {
1570	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1571	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1572	+	}
1573	+
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	>
1579	>	if (outputTemp_) {
1580	>	tempLog_ << time;
1581	>	for (j = 0; j < rnemdLogWidth_; j++) {
1582	>	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1583	>	}
1584	>	tempLog_ << endl;
1585		}
1586	<	rnemdLog_ << "\n";
1587	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1588	<	xTempLog_ << time;
1586	>	if (outputVx_) {
1587	>	vxzLog_ << time;
1588	>	for (j = 0; j < rnemdLogWidth_; j++) {
1589	>	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1590	>	}
1591	>	vxzLog_ << endl;
1592	>	}
1593	>	if (outputVy_) {
1594	>	vyzLog_ << time;
1595	>	for (j = 0; j < rnemdLogWidth_; j++) {
1596	>	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1597	>	}
1598	>	vyzLog_ << endl;
1599	>	}
1600	>
1601	>	if (output3DTemp_) {
1602	>	RealType temp;
1603	>	xTempLog_ << time;
1604		for (j = 0; j < rnemdLogWidth_; j++) {
1605	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1605	>	if (outputVx_)
1606	>	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1607	>	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1608	>	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1609	>	xTempLog_ << "\t" << temp;
1610		}
1611	<	xTempLog_ << "\n";
1611	>	xTempLog_ << endl;
1612		yTempLog_ << time;
1613		for (j = 0; j < rnemdLogWidth_; j++) {
1614	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1614	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1615		}
1616	<	yTempLog_ << "\n";
1616	>	yTempLog_ << endl;
1617		zTempLog_ << time;
1618		for (j = 0; j < rnemdLogWidth_; j++) {
1619	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1619	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1620		}
1621	<	zTempLog_ << "\n";
1621	>	zTempLog_ << endl;
1622		}
1623	+	if (outputRotTemp_) {
1624	+	rotTempLog_ << time;
1625	+	for (j = 0; j < rnemdLogWidth_; j++) {
1626	+	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1627	+	}
1628	+	rotTempLog_ << endl;
1629	+	}
1630	+	// James put this in.
1631	+	Mat3x3d hmat = currentSnap_->getHmat();
1632	+	if (outputDen_) {
1633	+	denLog_ << time;
1634	+	for (j = 0; j < rnemdLogWidth_; j++) {
1635	+
1636	+	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1637	+	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1638	+	}
1639	+	denLog_ << endl;
1640	+	}
1641	+	if (outputVz_) {
1642	+	vzzLog_ << time;
1643	+	for (j = 0; j < rnemdLogWidth_; j++) {
1644	+	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1645	+	}
1646	+	vzzLog_ << endl;
1647	+	}
1648		#ifdef IS_MPI
1649		}
1650		#endif
1651	+
1652		for (j = 0; j < rnemdLogWidth_; j++) {
1653	<	valueCount_[j] = 0;
1036	<	valueHist_[j] = 0.0;
1653	>	mHist_[j] = 0.0;
1654		}
1655	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1655	>	if (outputTemp_)
1656		for (j = 0; j < rnemdLogWidth_; j++) {
1657	+	tempCount_[j] = 0;
1658	+	tempHist_[j] = 0.0;
1659	+	}
1660	+	if (outputVx_)
1661	+	for (j = 0; j < rnemdLogWidth_; j++) {
1662	+	//pxzCount_[j] = 0;
1663	+	pxzHist_[j] = 0.0;
1664	+	}
1665	+	if (outputVy_)
1666	+	for (j = 0; j < rnemdLogWidth_; j++) {
1667	+	//pyzCount_[j] = 0;
1668	+	pyzHist_[j] = 0.0;
1669	+	}
1670	+
1671	+	if (output3DTemp_)
1672	+	for (j = 0; j < rnemdLogWidth_; j++) {
1673		xTempHist_[j] = 0.0;
1674		yTempHist_[j] = 0.0;
1675		zTempHist_[j] = 0.0;
1676	+	xyzTempCount_[j] = 0;
1677		}
1678	+	if (outputRotTemp_)
1679	+	for (j = 0; j < rnemdLogWidth_; j++) {
1680	+	rotTempCount_[j] = 0;
1681	+	rotTempHist_[j] = 0.0;
1682	+	}
1683	+	// James put this in
1684	+	if (outputDen_)
1685	+	for (j = 0; j < rnemdLogWidth_; j++) {
1686	+	//pyzCount_[j] = 0;
1687	+	DenHist_[j] = 0.0;
1688	+	}
1689	+	if (outputVz_)
1690	+	for (j = 0; j < rnemdLogWidth_; j++) {
1691	+	//pyzCount_[j] = 0;
1692	+	pzzHist_[j] = 0.0;
1693	+	}
1694	+	// reset the counter
1695	+
1696	+	Numcount_++;
1697	+	if (Numcount_ > int(runTime_/statusTime_))
1698	+	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1699	+	if (Numcount_ > int(runTime_/statusTime_))
1700	+	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
1701	+
1702	+	logFrameCount_ = 0;
1703		}
1704		}
1705	+

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