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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.
Revision 1728 by jmarr, Wed May 30 16:07:03 2012 UTC

#	Line 42 | Line 42
42		#include <cmath>
43		#include "integrators/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;
#	Line 69 | Line 73 | namespace OpenMD {
73
74		stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
75		stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	+	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
77	+	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
78		stringToEnumMap_["PxScale"] = rnemdPxScale;
79		stringToEnumMap_["PyScale"] = rnemdPyScale;
80		stringToEnumMap_["PzScale"] = rnemdPzScale;
81		stringToEnumMap_["Px"] = rnemdPx;
82		stringToEnumMap_["Py"] = rnemdPy;
83		stringToEnumMap_["Pz"] = rnemdPz;
84	+	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
85	+	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
86		stringToEnumMap_["Unknown"] = rnemdUnknown;
87
88	+	runTime_ = simParams->getRunTime();
89	+	statusTime_ = simParams->getStatusTime();
90	+
91		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
92		evaluator_.loadScriptString(rnemdObjectSelection_);
93		seleMan_.setSelectionSet(evaluator_.evaluate());
#	Line 88 | Line 99 | namespace OpenMD {
99
100		if (selectionCount > nIntegrable) {
101		sprintf(painCave.errMsg,
102	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
102	>	"RNEMD: The current RNEMD_objectSelection,\n"
103		"\t\t%s\n"
104		"\thas resulted in %d selected objects.  However,\n"
105		"\tthe total number of integrable objects in the system\n"
#	Line 98 | Line 109 | namespace OpenMD {
109		rnemdObjectSelection_.c_str(),
110		selectionCount, nIntegrable);
111		painCave.isFatal = 0;
112	+	painCave.severity = OPENMD_WARNING;
113		simError();
102	–
114		}
115
116	<	const std::string st = simParams->getRNEMD_exchangeType();
116	>	const string st = simParams->getRNEMD_exchangeType();
117
118	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
118	>	map<string, RNEMDTypeEnum>::iterator i;
119		i = stringToEnumMap_.find(st);
120		rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
121		if (rnemdType_ == rnemdUnknown) {
122	<	std::cerr << "WARNING! RNEMD Type Unknown!\n";
122	>	sprintf(painCave.errMsg,
123	>	"RNEMD: The current RNEMD_exchangeType,\n"
124	>	"\t\t%s\n"
125	>	"\tis not one of the recognized exchange types.\n",
126	>	st.c_str());
127	>	painCave.isFatal = 1;
128	>	painCave.severity = OPENMD_ERROR;
129	>	simError();
130		}
131	+
132	+	outputTemp_ = false;
133	+	if (simParams->haveRNEMD_outputTemperature()) {
134	+	outputTemp_ = simParams->getRNEMD_outputTemperature();
135	+	} else if ((rnemdType_ == rnemdKineticSwap) ||
136	+	(rnemdType_ == rnemdKineticScale) ||
137	+	(rnemdType_ == rnemdKineticScaleVAM) ||
138	+	(rnemdType_ == rnemdKineticScaleAM)) {
139	+	outputTemp_ = true;
140	+	}
141	+	outputVx_ = false;
142	+	if (simParams->haveRNEMD_outputVx()) {
143	+	outputVx_ = simParams->getRNEMD_outputVx();
144	+	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
145	+	outputVx_ = true;
146	+	}
147	+	outputVy_ = false;
148	+	if (simParams->haveRNEMD_outputVy()) {
149	+	outputVy_ = simParams->getRNEMD_outputVy();
150	+	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
151	+	outputVy_ = true;
152	+	}
153	+	output3DTemp_ = false;
154	+	if (simParams->haveRNEMD_outputXyzTemperature()) {
155	+	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
156	+	}
157	+	outputRotTemp_ = false;
158	+	if (simParams->haveRNEMD_outputRotTemperature()) {
159	+	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
160	+	}
161	+	// James put this in.
162	+	outputDen_ = false;
163	+	if (simParams->haveRNEMD_outputDen()) {
164	+	outputDen_ = simParams->getRNEMD_outputDen();
165	+	}
166	+	outputAh_ = false;
167	+	if (simParams->haveRNEMD_outputAh()) {
168	+	outputAh_ = simParams->getRNEMD_outputAh();
169	+	}
170	+	outputVz_ = false;
171	+	if (simParams->haveRNEMD_outputVz()) {
172	+	outputVz_ = simParams->getRNEMD_outputVz();
173	+	} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
174	+	outputVz_ = true;
175	+	}
176	+
177
178		#ifdef IS_MPI
179		if (worldRank == 0) {
180		#endif
181
182	<	std::string rnemdFileName;
183	<	std::string xTempFileName;
184	<	std::string yTempFileName;
185	<	std::string zTempFileName;
122	<	switch(rnemdType_) {
123	<	case rnemdKineticSwap :
124	<	case rnemdKineticScale :
182	>	//may have rnemdWriter separately
183	>	string rnemdFileName;
184	>
185	>	if (outputTemp_) {
186		rnemdFileName = "temperature.log";
187	<	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;
187	>	tempLog_.open(rnemdFileName.c_str());
188		}
189	<	rnemdLog_.open(rnemdFileName.c_str());
189	>	if (outputVx_) {
190	>	rnemdFileName = "velocityX.log";
191	>	vxzLog_.open(rnemdFileName.c_str());
192	>	}
193	>	if (outputVy_) {
194	>	rnemdFileName = "velocityY.log";
195	>	vyzLog_.open(rnemdFileName.c_str());
196	>	}
197
198	+	if (output3DTemp_) {
199	+	rnemdFileName = "temperatureX.log";
200	+	xTempLog_.open(rnemdFileName.c_str());
201	+	rnemdFileName = "temperatureY.log";
202	+	yTempLog_.open(rnemdFileName.c_str());
203	+	rnemdFileName = "temperatureZ.log";
204	+	zTempLog_.open(rnemdFileName.c_str());
205	+	}
206	+	if (outputRotTemp_) {
207	+	rnemdFileName = "temperatureR.log";
208	+	rotTempLog_.open(rnemdFileName.c_str());
209	+	}
210	+
211	+	//James put this in
212	+	if (outputDen_) {
213	+	rnemdFileName = "Density.log";
214	+	denLog_.open(rnemdFileName.c_str());
215	+	}
216	+	if (outputAh_) {
217	+	rnemdFileName = "Ah.log";
218	+	AhLog_.open(rnemdFileName.c_str());
219	+	}
220	+	if (outputVz_) {
221	+	rnemdFileName = "velocityZ.log";
222	+	vzzLog_.open(rnemdFileName.c_str());
223	+	}
224	+	logFrameCount_ = 0;
225		#ifdef IS_MPI
226		}
227		#endif
#	Line 152 | Line 229 | namespace OpenMD {
229		set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
230		set_RNEMD_nBins(simParams->getRNEMD_nBins());
231		midBin_ = nBins_ / 2;
232	+	if (simParams->haveRNEMD_binShift()) {
233	+	if (simParams->getRNEMD_binShift()) {
234	+	zShift_ = 0.5 / (RealType)(nBins_);
235	+	} else {
236	+	zShift_ = 0.0;
237	+	}
238	+	} else {
239	+	zShift_ = 0.0;
240	+	}
241	+	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
242	+	//shift slabs by half slab width, maybe useful in heterogeneous systems
243	+	//set to 0.0 if not using it; N/A in status output yet
244		if (simParams->haveRNEMD_logWidth()) {
245	<	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
245	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
246	>	/*arbitary rnemdLogWidth_, no checking;
247		if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
248	<	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
249	<	std::cerr << "Automaically set back to default.\n";
248	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
249	>	cerr << "Automaically set back to default.\n";
250		rnemdLogWidth_ = nBins_;
251	<	}
251	>	}*/
252		} else {
253	<	rnemdLogWidth_ = nBins_;
253	>	set_RNEMD_logWidth(nBins_);
254		}
255	<	valueHist_.resize(rnemdLogWidth_, 0.0);
256	<	valueCount_.resize(rnemdLogWidth_, 0);
255	>	tempHist_.resize(rnemdLogWidth_, 0.0);
256	>	tempCount_.resize(rnemdLogWidth_, 0);
257	>	pxzHist_.resize(rnemdLogWidth_, 0.0);
258	>	//vxzCount_.resize(rnemdLogWidth_, 0);
259	>	pyzHist_.resize(rnemdLogWidth_, 0.0);
260	>	//vyzCount_.resize(rnemdLogWidth_, 0);
261	>
262	>	mHist_.resize(rnemdLogWidth_, 0.0);
263		xTempHist_.resize(rnemdLogWidth_, 0.0);
264		yTempHist_.resize(rnemdLogWidth_, 0.0);
265		zTempHist_.resize(rnemdLogWidth_, 0.0);
266	+	xyzTempCount_.resize(rnemdLogWidth_, 0);
267	+	rotTempHist_.resize(rnemdLogWidth_, 0.0);
268	+	rotTempCount_.resize(rnemdLogWidth_, 0);
269	+	// James put this in
270	+	DenHist_.resize(rnemdLogWidth_, 0.0);
271	+	pzzHist_.resize(rnemdLogWidth_, 0.0);
272
273		set_RNEMD_exchange_total(0.0);
274		if (simParams->haveRNEMD_targetFlux()) {
275		set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
276		} else {
277		set_RNEMD_target_flux(0.0);
278	+	}
279	+	if (simParams->haveRNEMD_targetJzKE()) {
280	+	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
281	+	} else {
282	+	set_RNEMD_target_JzKE(0.0);
283	+	}
284	+	if (simParams->haveRNEMD_targetJzpx()) {
285	+	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
286	+	} else {
287	+	set_RNEMD_target_jzpx(0.0);
288	+	}
289	+	jzp_.x() = targetJzpx_;
290	+	njzp_.x() = -targetJzpx_;
291	+	if (simParams->haveRNEMD_targetJzpy()) {
292	+	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
293	+	} else {
294	+	set_RNEMD_target_jzpy(0.0);
295		}
296	+	jzp_.y() = targetJzpy_;
297	+	njzp_.y() = -targetJzpy_;
298	+	if (simParams->haveRNEMD_targetJzpz()) {
299	+	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
300	+	} else {
301	+	set_RNEMD_target_jzpz(0.0);
302	+	}
303	+	jzp_.z() = targetJzpz_;
304	+	njzp_.z() = -targetJzpz_;
305
306		#ifndef IS_MPI
307		if (simParams->haveSeed()) {
#	Line 198 | Line 326 | namespace OpenMD {
326		#ifdef IS_MPI
327		if (worldRank == 0) {
328		#endif
329	<	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
330	<	rnemdLog_.close();
331	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
332	<	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
333	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
329	>
330	>	sprintf(painCave.errMsg,
331	>	"RNEMD: total failed trials: %d\n",
332	>	failTrialCount_);
333	>	painCave.isFatal = 0;
334	>	painCave.severity = OPENMD_INFO;
335	>	simError();
336	>
337	>	if (outputTemp_) tempLog_.close();
338	>	if (outputVx_)   vxzLog_.close();
339	>	if (outputVy_)   vyzLog_.close();
340	>
341	>	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
342	>	rnemdType_ == rnemdPyScale) {
343	>	sprintf(painCave.errMsg,
344	>	"RNEMD: total root-checking warnings: %d\n",
345	>	failRootCount_);
346	>	painCave.isFatal = 0;
347	>	painCave.severity = OPENMD_INFO;
348	>	simError();
349	>	}
350	>	if (output3DTemp_) {
351		xTempLog_.close();
352		yTempLog_.close();
353		zTempLog_.close();
354		}
355	+	if (outputRotTemp_) rotTempLog_.close();
356	+	// James put this in
357	+	if (outputDen_) denLog_.close();
358	+	if (outputAh_)  AhLog_.close();
359	+	if (outputVz_)  vzzLog_.close();
360	+
361		#ifdef IS_MPI
362		}
363		#endif
#	Line 246 | Line 397 | namespace OpenMD {
397		// which bin is this stuntdouble in?
398		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
399
400	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
400	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
401
402
403		// if we're in bin 0 or the middleBin
#	Line 259 | Line 410 | namespace OpenMD {
410		switch(rnemdType_) {
411		case rnemdKineticSwap :
412
413	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
414	<	vel[2]*vel[2]);
415	<	if (sd->isDirectional()) {
413	>	value = mass * vel.lengthSquare();
414	>
415	>	if (sd->isDirectional()) {
416		Vector3d angMom = sd->getJ();
417		Mat3x3d I = sd->getI();
418
419		if (sd->isLinear()) {
420	<	int i = sd->linearAxis();
421	<	int j = (i + 1) % 3;
422	<	int k = (i + 2) % 3;
423	<	value += angMom[j] * angMom[j] / I(j, j) +
424	<	angMom[k] * angMom[k] / I(k, k);
420	>	int i = sd->linearAxis();
421	>	int j = (i + 1) % 3;
422	>	int k = (i + 2) % 3;
423	>	value += angMom[j] * angMom[j] / I(j, j) +
424	>	angMom[k] * angMom[k] / I(k, k);
425		} else {
426	<	value += angMom[0]*angMom[0]/I(0, 0)
427	<	+ angMom[1]*angMom[1]/I(1, 1)
428	<	+ angMom[2]*angMom[2]/I(2, 2);
426	>	value += angMom[0]*angMom[0]/I(0, 0)
427	>	+ angMom[1]*angMom[1]/I(1, 1)
428	>	+ angMom[2]*angMom[2]/I(2, 2);
429		}
430	<	}
430	>	} //angular momenta exchange enabled
431	>	//energyConvert temporarily disabled
432		//make exchangeSum_ comparable between swap & scale
281	–	//temporarily without using energyConvert
433		//value = value * 0.5 / PhysicalConstants::energyConvert;
434		value *= 0.5;
435		break;
#	Line 331 | Line 482 | namespace OpenMD {
482		bool my_max_found = max_found;
483
484		// Even if we didn't find a minimum, did someone else?
485	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
335	<	1, MPI::BOOL, MPI::LAND);
336	<
485	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
486		// Even if we didn't find a maximum, did someone else?
487	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
488	<	1, MPI::BOOL, MPI::LAND);
489	<
490	<	struct {
491	<	RealType val;
492	<	int rank;
493	<	} max_vals, min_vals;
494	<
495	<	if (min_found) {
496	<	if (my_min_found)
348	<	min_vals.val = min_val;
349	<	else
350	<	min_vals.val = HONKING_LARGE_VALUE;
487	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
488	>	#endif
489	>
490	>	if (max_found && min_found) {
491	>
492	>	#ifdef IS_MPI
493	>	struct {
494	>	RealType val;
495	>	int rank;
496	>	} max_vals, min_vals;
497
498	+	if (my_min_found) {
499	+	min_vals.val = min_val;
500	+	} else {
501	+	min_vals.val = HONKING_LARGE_VALUE;
502	+	}
503		min_vals.rank = worldRank;
504
505		// Who had the minimum?
506		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
507		1, MPI::REALTYPE_INT, MPI::MINLOC);
508		min_val = min_vals.val;
358	–	}
509
510	<	if (max_found) {
361	<	if (my_max_found)
510	>	if (my_max_found) {
511		max_vals.val = max_val;
512	<	else
512	>	} else {
513		max_vals.val = -HONKING_LARGE_VALUE;
514	<
514	>	}
515		max_vals.rank = worldRank;
516
517		// Who had the maximum?
518		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
519		1, MPI::REALTYPE_INT, MPI::MAXLOC);
520		max_val = max_vals.val;
372	–	}
521		#endif
522	<
523	<	if (max_found && min_found) {
524	<	if (min_val< max_val) {
377	<
522	>
523	>	if (min_val < max_val) {
524	>
525		#ifdef IS_MPI
526		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
527		// I have both maximum and minimum, so proceed like a single
528		// processor version:
529		#endif
530	<	// objects to be swapped: velocity & angular velocity
530	>
531		Vector3d min_vel = min_sd->getVel();
532		Vector3d max_vel = max_sd->getVel();
533		RealType temp_vel;
#	Line 389 | Line 536 | namespace OpenMD {
536		case rnemdKineticSwap :
537		min_sd->setVel(max_vel);
538		max_sd->setVel(min_vel);
539	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
539	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
540		Vector3d min_angMom = min_sd->getJ();
541		Vector3d max_angMom = max_sd->getJ();
542		min_sd->setJ(max_angMom);
543		max_sd->setJ(min_angMom);
544	<	}
544	>	}//angular momenta exchange enabled
545	>	//assumes same rigid body identity
546		break;
547		case rnemdPx :
548		temp_vel = min_vel.x();
#	Line 420 | Line 568 | namespace OpenMD {
568		default :
569		break;
570		}
571	+
572		#ifdef IS_MPI
573		// the rest of the cases only apply in parallel simulations:
574		} else if (max_vals.rank == worldRank) {
#	Line 438 | Line 587 | namespace OpenMD {
587		switch(rnemdType_) {
588		case rnemdKineticSwap :
589		max_sd->setVel(min_vel);
590	<
590	>	//angular momenta exchange enabled
591		if (max_sd->isDirectional()) {
592		Vector3d min_angMom;
593		Vector3d max_angMom = max_sd->getJ();
594	<
594	>
595		// point-to-point swap of the angular momentum vector
596		MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
597		MPI::REALTYPE, min_vals.rank, 1,
598		min_angMom.getArrayPointer(), 3,
599		MPI::REALTYPE, min_vals.rank, 1,
600		status);
601	<
601	>
602		max_sd->setJ(min_angMom);
603	<	}
603	>	}
604		break;
605		case rnemdPx :
606		max_vel.x() = min_vel.x();
#	Line 484 | Line 633 | namespace OpenMD {
633		switch(rnemdType_) {
634		case rnemdKineticSwap :
635		min_sd->setVel(max_vel);
636	<
636	>	//angular momenta exchange enabled
637		if (min_sd->isDirectional()) {
638		Vector3d min_angMom = min_sd->getJ();
639		Vector3d max_angMom;
640	<
640	>
641		// point-to-point swap of the angular momentum vector
642		MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
643		MPI::REALTYPE, max_vals.rank, 1,
644		max_angMom.getArrayPointer(), 3,
645		MPI::REALTYPE, max_vals.rank, 1,
646		status);
647	<
647	>
648		min_sd->setJ(max_angMom);
649		}
650		break;
#	Line 517 | Line 666 | namespace OpenMD {
666		}
667		#endif
668		exchangeSum_ += max_val - min_val;
669	<	} else {
670	<	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
669	>	} else {
670	>	sprintf(painCave.errMsg,
671	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
672	>	painCave.isFatal = 0;
673	>	painCave.severity = OPENMD_INFO;
674	>	simError();
675		failTrialCount_++;
676		}
677		} else {
678	<	std::cerr << "exchange NOT performed!\n";
679	<	std::cerr << "at least one of the two slabs empty.\n";
678	>	sprintf(painCave.errMsg,
679	>	"RNEMD: exchange NOT performed because selected object\n"
680	>	"\tnot present in at least one of the two slabs.\n");
681	>	painCave.isFatal = 0;
682	>	painCave.severity = OPENMD_INFO;
683	>	simError();
684		failTrialCount_++;
685		}
686
#	Line 540 | Line 697 | namespace OpenMD {
697		StuntDouble* sd;
698		int idx;
699
700	<	std::vector<StuntDouble*> hotBin, coldBin;
700	>	vector<StuntDouble*> hotBin, coldBin;
701
702		RealType Phx = 0.0;
703		RealType Phy = 0.0;
#	Line 548 | Line 705 | namespace OpenMD {
705		RealType Khx = 0.0;
706		RealType Khy = 0.0;
707		RealType Khz = 0.0;
708	+	RealType Khw = 0.0;
709		RealType Pcx = 0.0;
710		RealType Pcy = 0.0;
711		RealType Pcz = 0.0;
712		RealType Kcx = 0.0;
713		RealType Kcy = 0.0;
714		RealType Kcz = 0.0;
715	+	RealType Kcw = 0.0;
716
717		for (sd = seleMan_.beginSelected(selei); sd != NULL;
718		sd = seleMan_.nextSelected(selei)) {
#	Line 570 | Line 729 | namespace OpenMD {
729		// which bin is this stuntdouble in?
730		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
731
732	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
732	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
733
734		// if we're in bin 0 or the middleBin
735		if (binNo == 0 || binNo == midBin_) {
#	Line 586 | Line 745 | namespace OpenMD {
745		Khx += mass * vel.x() * vel.x();
746		Khy += mass * vel.y() * vel.y();
747		Khz += mass * vel.z() * vel.z();
748	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
749	+	if (sd->isDirectional()) {
750	+	Vector3d angMom = sd->getJ();
751	+	Mat3x3d I = sd->getI();
752	+	if (sd->isLinear()) {
753	+	int i = sd->linearAxis();
754	+	int j = (i + 1) % 3;
755	+	int k = (i + 2) % 3;
756	+	Khw += angMom[j] * angMom[j] / I(j, j) +
757	+	angMom[k] * angMom[k] / I(k, k);
758	+	} else {
759	+	Khw += angMom[0]*angMom[0]/I(0, 0)
760	+	+ angMom[1]*angMom[1]/I(1, 1)
761	+	+ angMom[2]*angMom[2]/I(2, 2);
762	+	}
763	+	}
764	+	//}
765		} else { //midBin_
766		coldBin.push_back(sd);
767		Pcx += mass * vel.x();
#	Line 594 | Line 770 | namespace OpenMD {
770		Kcx += mass * vel.x() * vel.x();
771		Kcy += mass * vel.y() * vel.y();
772		Kcz += mass * vel.z() * vel.z();
773	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
774	+	if (sd->isDirectional()) {
775	+	Vector3d angMom = sd->getJ();
776	+	Mat3x3d I = sd->getI();
777	+	if (sd->isLinear()) {
778	+	int i = sd->linearAxis();
779	+	int j = (i + 1) % 3;
780	+	int k = (i + 2) % 3;
781	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
782	+	angMom[k] * angMom[k] / I(k, k);
783	+	} else {
784	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
785	+	+ angMom[1]*angMom[1]/I(1, 1)
786	+	+ angMom[2]*angMom[2]/I(2, 2);
787	+	}
788	+	}
789	+	//}
790		}
791		}
792		}
793	<
793	>
794		Khx *= 0.5;
795		Khy *= 0.5;
796		Khz *= 0.5;
797	+	Khw *= 0.5;
798		Kcx *= 0.5;
799		Kcy *= 0.5;
800		Kcz *= 0.5;
801	+	Kcw *= 0.5;
802
803	+	// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
804	+	//        << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
805	+	//        << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
806	+	// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
807	+	//        << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
808	+
809		#ifdef IS_MPI
810		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
811		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 616 | Line 817 | namespace OpenMD {
817		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
818		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
819		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
820	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
821	+
822		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
823		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
824		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
825	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
826		#endif
827
828	<	//use coldBin coeff's
828	>	//solve coldBin coeff's first
829		RealType px = Pcx / Phx;
830		RealType py = Pcy / Phy;
831		RealType pz = Pcz / Phz;
832	+	RealType c, x, y, z;
833	+	bool successfulScale = false;
834	+	if ((rnemdType_ == rnemdKineticScaleVAM) ||
835	+	(rnemdType_ == rnemdKineticScaleAM)) {
836	+	//may need sanity check Khw & Kcw > 0
837
838	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
839	<	switch(rnemdType_) {
840	<	case rnemdKineticScale :
841	<	/*used hotBin coeff's & only scale x & y dimensions
842	<	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	<	*/
838	>	if (rnemdType_ == rnemdKineticScaleVAM) {
839	>	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
840	>	} else {
841	>	c = 1.0 - targetFlux_ / Kcw;
842	>	}
843
844	<	//scale all three dimensions, let c_x = c_y
845	<	a000 = Kcx + Kcy;
846	<	a110 = Kcz;
847	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
848	<	a001 = Khx * px * px + Khy * py * py;
849	<	a111 = Khz * pz * pz;
850	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
851	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
852	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
853	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
854	<	break;
855	<	case rnemdPxScale :
856	<	c = 1 - targetFlux_ / Pcx;
857	<	a000 = Kcy;
858	<	a110 = Kcz;
859	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
860	<	a001 = py * py * Khy;
861	<	a111 = pz * pz * Khz;
862	<	b01 = -2.0 * Khy * py * (1.0 + py);
863	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
864	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
865	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
866	<	break;
867	<	case rnemdPyScale :
868	<	c = 1 - targetFlux_ / Pcy;
869	<	a000 = Kcx;
870	<	a110 = Kcz;
871	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
872	<	a001 = px * px * Khx;
873	<	a111 = pz * pz * Khz;
874	<	b01 = -2.0 * Khx * px * (1.0 + px);
875	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
876	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
877	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
878	<	break;
879	<	case rnemdPzScale ://we don't really do this, do we?
880	<	c = 1 - targetFlux_ / Pcz;
881	<	a000 = Kcx;
882	<	a110 = Kcy;
883	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
884	<	a001 = px * px * Khx;
885	<	a111 = py * py * Khy;
886	<	b01 = -2.0 * Khx * px * (1.0 + px);
887	<	b11 = -2.0 * Khy * py * (1.0 + py);
888	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
889	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
890	<	break;
891	<	default :
892	<	break;
893	<	}
894	<
895	<	RealType v1 = a000 * a111 - a001 * a110;
896	<	RealType v2 = a000 * b01;
897	<	RealType v3 = a000 * b11;
898	<	RealType v4 = a000 * c1 - a001 * c0;
899	<	RealType v8 = a110 * b01;
900	<	RealType v10 = - b01 * c0;
901	<
902	<	RealType u0 = v2 * v10 - v4 * v4;
903	<	RealType u1 = -2.0 * v3 * v4;
904	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
905	<	RealType u3 = -2.0 * v1 * v3;
906	<	RealType u4 = - v1 * v1;
907	<	//rescale coefficients
908	<	RealType maxAbs = fabs(u0);
909	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
910	<	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_++;
844	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
845	>	c = sqrt(c);
846	>	std::cerr << "cold slab scaling coefficient: " << c << endl;
847	>	//now convert to hotBin coefficient
848	>	RealType w = 0.0;
849	>	if (rnemdType_ ==  rnemdKineticScaleVAM) {
850	>	x = 1.0 + px * (1.0 - c);
851	>	y = 1.0 + py * (1.0 - c);
852	>	z = 1.0 + pz * (1.0 - c);
853	>	/* more complicated way
854	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
855	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
856	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
857	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
858	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
859	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
860	>	*/
861	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
862	>	(fabs(z - 1.0) < 0.1)) {
863	>	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
864	>	+ Khz * (1.0 - z * z)) / Khw;
865	>	}//no need to calculate w if x, y or z is out of range
866	>	} else {
867	>	w = 1.0 + targetFlux_ / Khw;
868	>	}
869	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
870	>	//if w is in the right range, so should be x, y, z.
871	>	vector<StuntDouble*>::iterator sdi;
872	>	Vector3d vel;
873	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
874	>	if (rnemdType_ == rnemdKineticScaleVAM) {
875	>	vel = (*sdi)->getVel() * c;
876	>	//vel.x() *= c;
877	>	//vel.y() *= c;
878	>	//vel.z() *= c;
879	>	(*sdi)->setVel(vel);
880	>	}
881	>	if ((*sdi)->isDirectional()) {
882	>	Vector3d angMom = (*sdi)->getJ() * c;
883	>	//angMom[0] *= c;
884	>	//angMom[1] *= c;
885	>	//angMom[2] *= c;
886	>	(*sdi)->setJ(angMom);
887	>	}
888	>	}
889	>	w = sqrt(w);
890	>	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
891	>	<< "\twh= " << w << endl;
892	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
893	>	if (rnemdType_ == rnemdKineticScaleVAM) {
894	>	vel = (*sdi)->getVel();
895	>	vel.x() *= x;
896	>	vel.y() *= y;
897	>	vel.z() *= z;
898	>	(*sdi)->setVel(vel);
899	>	}
900	>	if ((*sdi)->isDirectional()) {
901	>	Vector3d angMom = (*sdi)->getJ() * w;
902	>	//angMom[0] *= w;
903	>	//angMom[1] *= w;
904	>	//angMom[2] *= w;
905	>	(*sdi)->setJ(angMom);
906	>	}
907	>	}
908	>	successfulScale = true;
909	>	exchangeSum_ += targetFlux_;
910	>	}
911		}
912	<	//might not be useful w/o rescaling coefficients
913	<	alpha0 = -c0 - a110 * r2 * r2;
914	<	if (alpha0 >= 0.0) {
915	<	r1 = sqrt(alpha0 / a000);
916	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
917	<	{ rps.push_back(std::make_pair(r1, r2)); }
918	<	if (r1 > 1e-6) { //r1 non-negative
919	<	r1 = -r1;
920	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
921	<	{ rps.push_back(std::make_pair(r1, r2)); }
922	<	}
912	>	} else {
913	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
914	>	switch(rnemdType_) {
915	>	case rnemdKineticScale :
916	>	/* used hotBin coeff's & only scale x & y dimensions
917	>	RealType px = Phx / Pcx;
918	>	RealType py = Phy / Pcy;
919	>	a110 = Khy;
920	>	c0 = - Khx - Khy - targetFlux_;
921	>	a000 = Khx;
922	>	a111 = Kcy * py * py;
923	>	b11 = -2.0 * Kcy * py * (1.0 + py);
924	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
925	>	b01 = -2.0 * Kcx * px * (1.0 + px);
926	>	a001 = Kcx * px * px;
927	>	*/
928	>	//scale all three dimensions, let c_x = c_y
929	>	a000 = Kcx + Kcy;
930	>	a110 = Kcz;
931	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
932	>	a001 = Khx * px * px + Khy * py * py;
933	>	a111 = Khz * pz * pz;
934	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
935	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
936	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
937	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
938	>	break;
939	>	case rnemdPxScale :
940	>	c = 1 - targetFlux_ / Pcx;
941	>	a000 = Kcy;
942	>	a110 = Kcz;
943	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
944	>	a001 = py * py * Khy;
945	>	a111 = pz * pz * Khz;
946	>	b01 = -2.0 * Khy * py * (1.0 + py);
947	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
948	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
949	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
950	>	break;
951	>	case rnemdPyScale :
952	>	c = 1 - targetFlux_ / Pcy;
953	>	a000 = Kcx;
954	>	a110 = Kcz;
955	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
956	>	a001 = px * px * Khx;
957	>	a111 = pz * pz * Khz;
958	>	b01 = -2.0 * Khx * px * (1.0 + px);
959	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
960	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
961	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
962	>	break;
963	>	case rnemdPzScale ://we don't really do this, do we?
964	>	c = 1 - targetFlux_ / Pcz;
965	>	a000 = Kcx;
966	>	a110 = Kcy;
967	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
968	>	a001 = px * px * Khx;
969	>	a111 = py * py * Khy;
970	>	b01 = -2.0 * Khx * px * (1.0 + px);
971	>	b11 = -2.0 * Khy * py * (1.0 + py);
972	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
973	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
974	>	break;
975	>	default :
976	>	break;
977		}
978	<	}
979	<	// Consider combininig together the solving pair part w/ the searching
980	<	// best solution part so that we don't need the pairs vector
981	<	if (!rps.empty()) {
982	<	RealType smallestDiff = HONKING_LARGE_VALUE;
983	<	RealType diff;
984	<	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
985	<	std::vector<std::pair<RealType,RealType> >::iterator rpi;
986	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
987	<	r1 = (*rpi).first;
988	<	r2 = (*rpi).second;
989	<	switch(rnemdType_) {
990	<	case rnemdKineticScale :
991	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
992	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
993	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
994	<	break;
995	<	case rnemdPxScale :
996	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
997	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
998	<	break;
999	<	case rnemdPyScale :
1000	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1001	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1002	<	break;
1003	<	case rnemdPzScale :
1004	<	default :
1005	<	break;
1006	<	}
1007	<	if (diff < smallestDiff) {
1008	<	smallestDiff = diff;
1009	<	bestPair = *rpi;
1010	<	}
978	>
979	>	RealType v1 = a000 * a111 - a001 * a110;
980	>	RealType v2 = a000 * b01;
981	>	RealType v3 = a000 * b11;
982	>	RealType v4 = a000 * c1 - a001 * c0;
983	>	RealType v8 = a110 * b01;
984	>	RealType v10 = - b01 * c0;
985	>
986	>	RealType u0 = v2 * v10 - v4 * v4;
987	>	RealType u1 = -2.0 * v3 * v4;
988	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
989	>	RealType u3 = -2.0 * v1 * v3;
990	>	RealType u4 = - v1 * v1;
991	>	//rescale coefficients
992	>	RealType maxAbs = fabs(u0);
993	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
994	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
995	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
996	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
997	>	u0 /= maxAbs;
998	>	u1 /= maxAbs;
999	>	u2 /= maxAbs;
1000	>	u3 /= maxAbs;
1001	>	u4 /= maxAbs;
1002	>	//max_element(start, end) is also available.
1003	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1004	>	poly.setCoefficient(4, u4);
1005	>	poly.setCoefficient(3, u3);
1006	>	poly.setCoefficient(2, u2);
1007	>	poly.setCoefficient(1, u1);
1008	>	poly.setCoefficient(0, u0);
1009	>	vector<RealType> realRoots = poly.FindRealRoots();
1010	>
1011	>	vector<RealType>::iterator ri;
1012	>	RealType r1, r2, alpha0;
1013	>	vector<pair<RealType,RealType> > rps;
1014	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1015	>	r2 = *ri;
1016	>	//check if FindRealRoots() give the right answer
1017	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1018	>	sprintf(painCave.errMsg,
1019	>	"RNEMD Warning: polynomial solve seems to have an error!");
1020	>	painCave.isFatal = 0;
1021	>	simError();
1022	>	failRootCount_++;
1023	>	}
1024	>	//might not be useful w/o rescaling coefficients
1025	>	alpha0 = -c0 - a110 * r2 * r2;
1026	>	if (alpha0 >= 0.0) {
1027	>	r1 = sqrt(alpha0 / a000);
1028	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1029	>	< 1e-6)
1030	>	{ rps.push_back(make_pair(r1, r2)); }
1031	>	if (r1 > 1e-6) { //r1 non-negative
1032	>	r1 = -r1;
1033	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1034	>	< 1e-6)
1035	>	{ rps.push_back(make_pair(r1, r2)); }
1036	>	}
1037	>	}
1038		}
1039	+	// Consider combining together the solving pair part w/ the searching
1040	+	// best solution part so that we don't need the pairs vector
1041	+	if (!rps.empty()) {
1042	+	RealType smallestDiff = HONKING_LARGE_VALUE;
1043	+	RealType diff;
1044	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1045	+	vector<pair<RealType,RealType> >::iterator rpi;
1046	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1047	+	r1 = (*rpi).first;
1048	+	r2 = (*rpi).second;
1049	+	switch(rnemdType_) {
1050	+	case rnemdKineticScale :
1051	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1052	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1053	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1054	+	break;
1055	+	case rnemdPxScale :
1056	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1057	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1058	+	break;
1059	+	case rnemdPyScale :
1060	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1061	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1062	+	break;
1063	+	case rnemdPzScale :
1064	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1065	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1066	+	default :
1067	+	break;
1068	+	}
1069	+	if (diff < smallestDiff) {
1070	+	smallestDiff = diff;
1071	+	bestPair = *rpi;
1072	+	}
1073	+	}
1074		#ifdef IS_MPI
1075	<	if (worldRank == 0) {
1075	>	if (worldRank == 0) {
1076		#endif
1077	<	std::cerr << "we choose r1 = " << bestPair.first
1078	<	<< " and r2 = " << bestPair.second << "\n";
1077	>	sprintf(painCave.errMsg,
1078	>	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1079	>	bestPair.first, bestPair.second);
1080	>	painCave.isFatal = 0;
1081	>	painCave.severity = OPENMD_INFO;
1082	>	simError();
1083		#ifdef IS_MPI
1084	<	}
1084	>	}
1085		#endif
1086	+
1087	+	switch(rnemdType_) {
1088	+	case rnemdKineticScale :
1089	+	x = bestPair.first;
1090	+	y = bestPair.first;
1091	+	z = bestPair.second;
1092	+	break;
1093	+	case rnemdPxScale :
1094	+	x = c;
1095	+	y = bestPair.first;
1096	+	z = bestPair.second;
1097	+	break;
1098	+	case rnemdPyScale :
1099	+	x = bestPair.first;
1100	+	y = c;
1101	+	z = bestPair.second;
1102	+	break;
1103	+	case rnemdPzScale :
1104	+	x = bestPair.first;
1105	+	y = bestPair.second;
1106	+	z = c;
1107	+	break;
1108	+	default :
1109	+	break;
1110	+	}
1111	+	vector<StuntDouble*>::iterator sdi;
1112	+	Vector3d vel;
1113	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1114	+	vel = (*sdi)->getVel();
1115	+	vel.x() *= x;
1116	+	vel.y() *= y;
1117	+	vel.z() *= z;
1118	+	(*sdi)->setVel(vel);
1119	+	}
1120	+	//convert to hotBin coefficient
1121	+	x = 1.0 + px * (1.0 - x);
1122	+	y = 1.0 + py * (1.0 - y);
1123	+	z = 1.0 + pz * (1.0 - z);
1124	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1125	+	vel = (*sdi)->getVel();
1126	+	vel.x() *= x;
1127	+	vel.y() *= y;
1128	+	vel.z() *= z;
1129	+	(*sdi)->setVel(vel);
1130	+	}
1131	+	successfulScale = true;
1132	+	exchangeSum_ += targetFlux_;
1133	+	}
1134	+	}
1135	+	if (successfulScale != true) {
1136	+	sprintf(painCave.errMsg,
1137	+	"RNEMD: exchange NOT performed!\n");
1138	+	painCave.isFatal = 0;
1139	+	painCave.severity = OPENMD_INFO;
1140	+	simError();
1141	+	failTrialCount_++;
1142	+	}
1143	+	}
1144
1145	<	RealType x, y, z;
1146	<	switch(rnemdType_) {
1147	<	case rnemdKineticScale :
1148	<	x = bestPair.first;
1149	<	y = bestPair.first;
1150	<	z = bestPair.second;
1151	<	break;
1152	<	case rnemdPxScale :
1153	<	x = c;
1154	<	y = bestPair.first;
1155	<	z = bestPair.second;
1156	<	break;
1157	<	case rnemdPyScale :
1158	<	x = bestPair.first;
1159	<	y = c;
1160	<	z = bestPair.second;
1161	<	break;
1162	<	case rnemdPzScale :
1163	<	x = bestPair.first;
1164	<	y = bestPair.second;
1165	<	z = c;
1166	<	break;
1167	<	default :
1168	<	break;
1169	<	}
1170	<	std::vector<StuntDouble*>::iterator sdi;
1171	<	Vector3d vel;
1172	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1173	<	vel = (*sdi)->getVel();
1174	<	vel.x() *= x;
1175	<	vel.y() *= y;
1176	<	vel.z() *= z;
1177	<	(*sdi)->setVel(vel);
1145	>	void RNEMD::doShiftScale() {
1146	>
1147	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1148	>	RealType time = currentSnap_->getTime();
1149	>	Mat3x3d hmat = currentSnap_->getHmat();
1150	>
1151	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1152	>
1153	>	int selei;
1154	>	StuntDouble* sd;
1155	>	int idx;
1156	>
1157	>	vector<StuntDouble*> hotBin, coldBin;
1158	>
1159	>	Vector3d Ph(V3Zero);
1160	>	RealType Mh = 0.0;
1161	>	RealType Kh = 0.0;
1162	>	Vector3d Pc(V3Zero);
1163	>	RealType Mc = 0.0;
1164	>	RealType Kc = 0.0;
1165	>
1166	>
1167	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1168	>	sd = seleMan_.nextSelected(selei)) {
1169	>
1170	>	idx = sd->getLocalIndex();
1171	>
1172	>	Vector3d pos = sd->getPos();
1173	>
1174	>	// wrap the stuntdouble's position back into the box:
1175	>
1176	>	if (usePeriodicBoundaryConditions_)
1177	>	currentSnap_->wrapVector(pos);
1178	>
1179	>	// which bin is this stuntdouble in?
1180	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1181	>
1182	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1183	>
1184	>	// if we're in bin 0 or the middleBin
1185	>	if (binNo == 0 || binNo == midBin_) {
1186	>
1187	>	RealType mass = sd->getMass();
1188	>	Vector3d vel = sd->getVel();
1189	>
1190	>	if (binNo == 0) {
1191	>	hotBin.push_back(sd);
1192	>	//std::cerr << "before, velocity = " << vel << endl;
1193	>	Ph += mass * vel;
1194	>	//std::cerr << "after, velocity = " << vel << endl;
1195	>	Mh += mass;
1196	>	Kh += mass * vel.lengthSquare();
1197	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1198	>	if (sd->isDirectional()) {
1199	>	Vector3d angMom = sd->getJ();
1200	>	Mat3x3d I = sd->getI();
1201	>	if (sd->isLinear()) {
1202	>	int i = sd->linearAxis();
1203	>	int j = (i + 1) % 3;
1204	>	int k = (i + 2) % 3;
1205	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1206	>	angMom[k] * angMom[k] / I(k, k);
1207	>	} else {
1208	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1209	>	angMom[1] * angMom[1] / I(1, 1) +
1210	>	angMom[2] * angMom[2] / I(2, 2);
1211	>	}
1212	>	}
1213	>	}
1214	>	} else { //midBin_
1215	>	coldBin.push_back(sd);
1216	>	Pc += mass * vel;
1217	>	Mc += mass;
1218	>	Kc += mass * vel.lengthSquare();
1219	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1220	>	if (sd->isDirectional()) {
1221	>	Vector3d angMom = sd->getJ();
1222	>	Mat3x3d I = sd->getI();
1223	>	if (sd->isLinear()) {
1224	>	int i = sd->linearAxis();
1225	>	int j = (i + 1) % 3;
1226	>	int k = (i + 2) % 3;
1227	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1228	>	angMom[k] * angMom[k] / I(k, k);
1229	>	} else {
1230	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1231	>	angMom[1] * angMom[1] / I(1, 1) +
1232	>	angMom[2] * angMom[2] / I(2, 2);
1233	>	}
1234	>	}
1235	>	}
1236	>	}
1237		}
1238	<	//convert to hotBin coefficient
1239	<	x = 1.0 + px * (1.0 - x);
1240	<	y = 1.0 + py * (1.0 - y);
1241	<	z = 1.0 + pz * (1.0 - z);
1242	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1243	<	vel = (*sdi)->getVel();
1244	<	vel.x() *= x;
1245	<	vel.y() *= y;
1246	<	vel.z() *= z;
1247	<	(*sdi)->setVel(vel);
1238	>	}
1239	>
1240	>	Kh *= 0.5;
1241	>	Kc *= 0.5;
1242	>
1243	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1244	>	//        << "\tKc= " << Kc << endl;
1245	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1246	>
1247	>	#ifdef IS_MPI
1248	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1249	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1250	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1251	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1252	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1253	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1254	>	#endif
1255	>
1256	>	bool successfulExchange = false;
1257	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1258	>	Vector3d vc = Pc / Mc;
1259	>	Vector3d ac = njzp_ / Mc + vc;
1260	>	Vector3d acrec = njzp_ / Mc;
1261	>	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1262	>	if (cNumerator > 0.0) {
1263	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1264	>	if (cDenominator > 0.0) {
1265	>	RealType c = sqrt(cNumerator / cDenominator);
1266	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1267	>	Vector3d vh = Ph / Mh;
1268	>	Vector3d ah = jzp_ / Mh + vh;
1269	>	Vector3d ahrec = jzp_ / Mh;
1270	>	RealType hNumerator = Kh + targetJzKE_
1271	>	- 0.5 * Mh * ah.lengthSquare();
1272	>	if (hNumerator > 0.0) {
1273	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1274	>	if (hDenominator > 0.0) {
1275	>	RealType h = sqrt(hNumerator / hDenominator);
1276	>	if ((h > 0.9) && (h < 1.1)) {
1277	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1278	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1279	>	vector<StuntDouble*>::iterator sdi;
1280	>	Vector3d vel;
1281	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1282	>	//vel = (*sdi)->getVel();
1283	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1284	>	(*sdi)->setVel(vel);
1285	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1286	>	if ((*sdi)->isDirectional()) {
1287	>	Vector3d angMom = (*sdi)->getJ() * c;
1288	>	(*sdi)->setJ(angMom);
1289	>	}
1290	>	}
1291	>	}
1292	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1293	>	//vel = (*sdi)->getVel();
1294	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1295	>	(*sdi)->setVel(vel);
1296	>	if (rnemdType_ == rnemdShiftScaleVAM) {
1297	>	if ((*sdi)->isDirectional()) {
1298	>	Vector3d angMom = (*sdi)->getJ() * h;
1299	>	(*sdi)->setJ(angMom);
1300	>	}
1301	>	}
1302	>	}
1303	>	successfulExchange = true;
1304	>	exchangeSum_ += targetFlux_;
1305	>	// this is a redundant variable for doShiftScale() so that
1306	>	// RNEMD can output one exchange quantity needed in a job.
1307	>	// need a better way to do this.
1308	>	//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n';
1309	>	//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n';
1310	>	//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n';
1311	>	Asum_ += (ahrec.z() - acrec.z());
1312	>	Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc)));
1313	>	AhCount_ = ahrec.z();
1314	>	if (outputAh_) {
1315	>	AhLog_ << time << "   ";
1316	>	AhLog_ << AhCount_;
1317	>	AhLog_ << endl;
1318	>	}
1319	>	}
1320	>	}
1321	>	}
1322	>	}
1323	>	}
1324		}
1325	<	exchangeSum_ += targetFlux_;
1326	<	//we may want to check whether the exchange has been successful
1327	<	} else {
1328	<	std::cerr << "exchange NOT performed!\n";//MPI incompatible
1325	>	}
1326	>	if (successfulExchange != true) {
1327	>	//   sprintf(painCave.errMsg,
1328	>	//              "RNEMD: exchange NOT performed!\n");
1329	>	//   painCave.isFatal = 0;
1330	>	//   painCave.severity = OPENMD_INFO;
1331	>	//   simError();
1332		failTrialCount_++;
1333		}
847	–
1334		}
1335
1336		void RNEMD::doRNEMD() {
1337
1338		switch(rnemdType_) {
1339		case rnemdKineticScale :
1340	+	case rnemdKineticScaleVAM :
1341	+	case rnemdKineticScaleAM :
1342		case rnemdPxScale :
1343		case rnemdPyScale :
1344		case rnemdPzScale :
#	Line 862 | Line 1350 | namespace OpenMD {
1350		case rnemdPz :
1351		doSwap();
1352		break;
1353	+	case rnemdShiftScaleV :
1354	+	case rnemdShiftScaleVAM :
1355	+	doShiftScale();
1356	+	break;
1357		case rnemdUnknown :
1358		default :
1359		break;
#	Line 879 | Line 1371 | namespace OpenMD {
1371		StuntDouble* sd;
1372		int idx;
1373
1374	+	logFrameCount_++;
1375	+
1376	+	// alternative approach, track all molecules instead of only those
1377	+	// selected for scaling/swapping:
1378	+	/*
1379	+	SimInfo::MoleculeIterator miter;
1380	+	vector<StuntDouble*>::iterator iiter;
1381	+	Molecule* mol;
1382	+	StuntDouble* integrableObject;
1383	+	for (mol = info_->beginMolecule(miter); mol != NULL;
1384	+	mol = info_->nextMolecule(miter))
1385	+	integrableObject is essentially sd
1386	+	for (integrableObject = mol->beginIntegrableObject(iiter);
1387	+	integrableObject != NULL;
1388	+	integrableObject = mol->nextIntegrableObject(iiter))
1389	+	*/
1390		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1391		sd = seleMan_.nextSelected(selei)) {
1392
#	Line 894 | Line 1402 | namespace OpenMD {
1402		// which bin is this stuntdouble in?
1403		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1404
1405	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1406	<
1405	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1406	>	rnemdLogWidth_;
1407	>	// no symmetrization allowed due to arbitary rnemdLogWidth_
1408	>	/*
1409		if (rnemdLogWidth_ == midBin_ + 1)
1410		if (binNo > midBin_)
1411		binNo = nBins_ - binNo;
1412	<
1412	>	*/
1413		RealType mass = sd->getMass();
1414	+	mHist_[binNo] += mass;
1415		Vector3d vel = sd->getVel();
1416		RealType value;
1417	<	RealType xVal, yVal, zVal;
1417	>	//RealType xVal, yVal, zVal;
1418
1419	<	switch(rnemdType_) {
1420	<	case rnemdKineticSwap :
1421	<	case rnemdKineticScale :
911	<
912	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
913	<	vel[2]*vel[2]);
914	<
915	<	valueCount_[binNo] += 3;
1419	>	if (outputTemp_) {
1420	>	value = mass * vel.lengthSquare();
1421	>	tempCount_[binNo] += 3;
1422		if (sd->isDirectional()) {
1423		Vector3d angMom = sd->getJ();
1424		Mat3x3d I = sd->getI();
919	–
1425		if (sd->isLinear()) {
1426		int i = sd->linearAxis();
1427		int j = (i + 1) % 3;
1428		int k = (i + 2) % 3;
1429		value += angMom[j] * angMom[j] / I(j, j) +
1430		angMom[k] * angMom[k] / I(k, k);
1431	<
927	<	valueCount_[binNo] +=2;
928	<
1431	>	tempCount_[binNo] +=2;
1432		} else {
1433	<	value += angMom[0]*angMom[0]/I(0, 0)
1434	<	+ angMom[1]*angMom[1]/I(1, 1)
1435	<	+ angMom[2]*angMom[2]/I(2, 2);
1436	<	valueCount_[binNo] +=3;
1433	>	value += angMom[0] * angMom[0] / I(0, 0) +
1434	>	angMom[1]*angMom[1]/I(1, 1) +
1435	>	angMom[2]*angMom[2]/I(2, 2);
1436	>	tempCount_[binNo] +=3;
1437		}
1438		}
1439	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1440	<
1441	<	break;
1442	<	case rnemdPx :
1443	<	case rnemdPxScale :
1439	>	value = value / PhysicalConstants::energyConvert
1440	>	/ PhysicalConstants::kb;//may move to getStatus()
1441	>	tempHist_[binNo] += value;
1442	>	}
1443	>	if (outputVx_) {
1444		value = mass * vel[0];
1445	<	valueCount_[binNo]++;
1446	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1447	<	/ PhysicalConstants::kb;
1448	<	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 :
1445	>	//vxzCount_[binNo]++;
1446	>	pxzHist_[binNo] += value;
1447	>	}
1448	>	if (outputVy_) {
1449		value = mass * vel[1];
1450	<	valueCount_[binNo]++;
1451	<	break;
958	<	case rnemdPz :
959	<	case rnemdPzScale :
960	<	value = mass * vel[2];
961	<	valueCount_[binNo]++;
962	<	break;
963	<	case rnemdUnknown :
964	<	default :
965	<	break;
1450	>	//vyzCount_[binNo]++;
1451	>	pyzHist_[binNo] += value;
1452		}
967	–	valueHist_[binNo] += value;
968	–	}
1453
1454	+	if (output3DTemp_) {
1455	+	value = mass * vel.x() * vel.x();
1456	+	xTempHist_[binNo] += value;
1457	+	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1458	+	/ PhysicalConstants::kb;
1459	+	yTempHist_[binNo] += value;
1460	+	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1461	+	/ PhysicalConstants::kb;
1462	+	zTempHist_[binNo] += value;
1463	+	xyzTempCount_[binNo]++;
1464	+	}
1465	+	if (outputRotTemp_) {
1466	+	if (sd->isDirectional()) {
1467	+	Vector3d angMom = sd->getJ();
1468	+	Mat3x3d I = sd->getI();
1469	+	if (sd->isLinear()) {
1470	+	int i = sd->linearAxis();
1471	+	int j = (i + 1) % 3;
1472	+	int k = (i + 2) % 3;
1473	+	value = angMom[j] * angMom[j] / I(j, j) +
1474	+	angMom[k] * angMom[k] / I(k, k);
1475	+	rotTempCount_[binNo] +=2;
1476	+	} else {
1477	+	value = angMom[0] * angMom[0] / I(0, 0) +
1478	+	angMom[1] * angMom[1] / I(1, 1) +
1479	+	angMom[2] * angMom[2] / I(2, 2);
1480	+	rotTempCount_[binNo] +=3;
1481	+	}
1482	+	}
1483	+	value = value / PhysicalConstants::energyConvert
1484	+	/ PhysicalConstants::kb;//may move to getStatus()
1485	+	rotTempHist_[binNo] += value;
1486	+	}
1487	+	// James put this in.
1488	+	if (outputDen_) {
1489	+	//value = 1.0;
1490	+	DenHist_[binNo] += 1;
1491	+	}
1492	+	if (outputVz_) {
1493	+	value = mass * vel[2];
1494	+	//vyzCount_[binNo]++;
1495	+	pzzHist_[binNo] += value;
1496	+	}
1497	+	}
1498		}
1499
1500		void RNEMD::getStarted() {
1501	+	collectData();
1502	+	/*now can output profile in step 0, but might not be useful;
1503		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1504		Stats& stat = currentSnap_->statData;
1505		stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1506	+	*/
1507	+	//may output a header for the log file here
1508	+	getStatus();
1509		}
1510
1511		void RNEMD::getStatus() {
#	Line 990 | Line 1523 | namespace OpenMD {
1523		// all processors have the same number of bins, and STL vectors pack their
1524		// arrays, so in theory, this should be safe:
1525
1526	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1527	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1528	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1529	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1530	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
1526	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1527	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1528	>	if (outputTemp_) {
1529	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1530	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1531	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1532	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1533	>	}
1534	>	if (outputVx_) {
1535	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1536	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1537	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1538	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1539	>	}
1540	>	if (outputVy_) {
1541	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1542	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1543	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1544	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1545	>	}
1546	>	if (output3DTemp_) {
1547		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1548		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1549		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1550		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1551		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1552		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1553	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1554	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1555		}
1556	+	if (outputRotTemp_) {
1557	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1558	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1559	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1560	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1561	+	}
1562	+	// James put this in
1563	+	if (outputDen_) {
1564	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1565	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1566	+	}
1567	+	if (outputAh_) {
1568	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1569	+	1, MPI::REALTYPE, MPI::SUM);
1570	+	}
1571	+	if (outputVz_) {
1572	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1573	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1574	+	}
1575	+
1576		// If we're the root node, should we print out the results
1577		int worldRank = MPI::COMM_WORLD.Get_rank();
1578		if (worldRank == 0) {
1579		#endif
1580	<	rnemdLog_ << time;
1581	<	for (j = 0; j < rnemdLogWidth_; j++) {
1582	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1580	>
1581	>	if (outputTemp_) {
1582	>	tempLog_ << time;
1583	>	for (j = 0; j < rnemdLogWidth_; j++) {
1584	>	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1585	>	}
1586	>	tempLog_ << endl;
1587		}
1588	<	rnemdLog_ << "\n";
1589	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1590	<	xTempLog_ << time;
1588	>	if (outputVx_) {
1589	>	vxzLog_ << time;
1590	>	for (j = 0; j < rnemdLogWidth_; j++) {
1591	>	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1592	>	}
1593	>	vxzLog_ << endl;
1594	>	}
1595	>	if (outputVy_) {
1596	>	vyzLog_ << time;
1597	>	for (j = 0; j < rnemdLogWidth_; j++) {
1598	>	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	>	}
1600	>	vyzLog_ << endl;
1601	>	}
1602	>
1603	>	if (output3DTemp_) {
1604	>	RealType temp;
1605	>	xTempLog_ << time;
1606		for (j = 0; j < rnemdLogWidth_; j++) {
1607	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1607	>	if (outputVx_)
1608	>	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1609	>	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1610	>	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1611	>	xTempLog_ << "\t" << temp;
1612		}
1613	<	xTempLog_ << "\n";
1613	>	xTempLog_ << endl;
1614		yTempLog_ << time;
1615		for (j = 0; j < rnemdLogWidth_; j++) {
1616	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1616	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1617		}
1618	<	yTempLog_ << "\n";
1618	>	yTempLog_ << endl;
1619		zTempLog_ << time;
1620		for (j = 0; j < rnemdLogWidth_; j++) {
1621	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1621	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1622		}
1623	<	zTempLog_ << "\n";
1623	>	zTempLog_ << endl;
1624		}
1625	+	if (outputRotTemp_) {
1626	+	rotTempLog_ << time;
1627	+	for (j = 0; j < rnemdLogWidth_; j++) {
1628	+	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1629	+	}
1630	+	rotTempLog_ << endl;
1631	+	}
1632	+	// James put this in.
1633	+	Mat3x3d hmat = currentSnap_->getHmat();
1634	+	if (outputDen_) {
1635	+	denLog_ << time;
1636	+	for (j = 0; j < rnemdLogWidth_; j++) {
1637	+
1638	+	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1639	+	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1640	+	}
1641	+	denLog_ << endl;
1642	+	}
1643	+	if (outputVz_) {
1644	+	vzzLog_ << time;
1645	+	for (j = 0; j < rnemdLogWidth_; j++) {
1646	+	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1647	+	}
1648	+	vzzLog_ << endl;
1649	+	}
1650		#ifdef IS_MPI
1651		}
1652		#endif
1653	+
1654		for (j = 0; j < rnemdLogWidth_; j++) {
1655	<	valueCount_[j] = 0;
1036	<	valueHist_[j] = 0.0;
1655	>	mHist_[j] = 0.0;
1656		}
1657	<	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1657	>	if (outputTemp_)
1658		for (j = 0; j < rnemdLogWidth_; j++) {
1659	+	tempCount_[j] = 0;
1660	+	tempHist_[j] = 0.0;
1661	+	}
1662	+	if (outputVx_)
1663	+	for (j = 0; j < rnemdLogWidth_; j++) {
1664	+	//pxzCount_[j] = 0;
1665	+	pxzHist_[j] = 0.0;
1666	+	}
1667	+	if (outputVy_)
1668	+	for (j = 0; j < rnemdLogWidth_; j++) {
1669	+	//pyzCount_[j] = 0;
1670	+	pyzHist_[j] = 0.0;
1671	+	}
1672	+
1673	+	if (output3DTemp_)
1674	+	for (j = 0; j < rnemdLogWidth_; j++) {
1675		xTempHist_[j] = 0.0;
1676		yTempHist_[j] = 0.0;
1677		zTempHist_[j] = 0.0;
1678	+	xyzTempCount_[j] = 0;
1679		}
1680	+	if (outputRotTemp_)
1681	+	for (j = 0; j < rnemdLogWidth_; j++) {
1682	+	rotTempCount_[j] = 0;
1683	+	rotTempHist_[j] = 0.0;
1684	+	}
1685	+	// James put this in
1686	+	if (outputDen_)
1687	+	for (j = 0; j < rnemdLogWidth_; j++) {
1688	+	//pyzCount_[j] = 0;
1689	+	DenHist_[j] = 0.0;
1690	+	}
1691	+	if (outputVz_)
1692	+	for (j = 0; j < rnemdLogWidth_; j++) {
1693	+	//pyzCount_[j] = 0;
1694	+	pzzHist_[j] = 0.0;
1695	+	}
1696	+	// reset the counter
1697	+
1698	+	Numcount_++;
1699	+	if (Numcount_ > int(runTime_/statusTime_))
1700	+	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1701	+	if (Numcount_ > int(runTime_/statusTime_))
1702	+	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
1703	+
1704	+	logFrameCount_ = 0;
1705		}
1706		}
1707	+

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