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

Comparing branches/development/src/integrators/RNEMD.cpp (file contents):
Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC vs.
Revision 1723 by gezelter, Thu May 24 20:59:54 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 52 | Line 53
53		#ifndef IS_MPI
54		#include "math/SeqRandNumGen.hpp"
55		#else
55	–	#include <mpi.h>
56		#include "math/ParallelRandNumGen.hpp"
57	+	#include <mpi.h>
58		#endif
59
60		#define HONKING_LARGE_VALUE 1.0e10
#	Line 72 | 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		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
#	Line 121 | Line 126 | namespace OpenMD {
126		simError();
127		}
128
129	+	outputTemp_ = false;
130	+	if (simParams->haveRNEMD_outputTemperature()) {
131	+	outputTemp_ = simParams->getRNEMD_outputTemperature();
132	+	} else if ((rnemdType_ == rnemdKineticSwap) ||
133	+	(rnemdType_ == rnemdKineticScale) ||
134	+	(rnemdType_ == rnemdKineticScaleVAM) ||
135	+	(rnemdType_ == rnemdKineticScaleAM)) {
136	+	outputTemp_ = true;
137	+	}
138	+	outputVx_ = false;
139	+	if (simParams->haveRNEMD_outputVx()) {
140	+	outputVx_ = simParams->getRNEMD_outputVx();
141	+	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
142	+	outputVx_ = true;
143	+	}
144	+	outputVy_ = false;
145	+	if (simParams->haveRNEMD_outputVy()) {
146	+	outputVy_ = simParams->getRNEMD_outputVy();
147	+	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
148	+	outputVy_ = true;
149	+	}
150		output3DTemp_ = false;
151	<	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
152	<	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
151	>	if (simParams->haveRNEMD_outputXyzTemperature()) {
152	>	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
153		}
154	+	outputRotTemp_ = false;
155	+	if (simParams->haveRNEMD_outputRotTemperature()) {
156	+	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
157	+	}
158
159		#ifdef IS_MPI
160		if (worldRank == 0) {
161		#endif
162
163	+	//may have rnemdWriter separately
164		string rnemdFileName;
165	<	switch(rnemdType_) {
166	<	case rnemdKineticSwap :
136	<	case rnemdKineticScale :
165	>
166	>	if (outputTemp_) {
167		rnemdFileName = "temperature.log";
168	<	break;
139	<	case rnemdPx :
140	<	case rnemdPxScale :
141	<	case rnemdPy :
142	<	case rnemdPyScale :
143	<	rnemdFileName = "momemtum.log";
144	<	break;
145	<	case rnemdPz :
146	<	case rnemdPzScale :
147	<	case rnemdUnknown :
148	<	default :
149	<	rnemdFileName = "rnemd.log";
150	<	break;
168	>	tempLog_.open(rnemdFileName.c_str());
169		}
170	<	rnemdLog_.open(rnemdFileName.c_str());
170	>	if (outputVx_) {
171	>	rnemdFileName = "velocityX.log";
172	>	vxzLog_.open(rnemdFileName.c_str());
173	>	}
174	>	if (outputVy_) {
175	>	rnemdFileName = "velocityY.log";
176	>	vyzLog_.open(rnemdFileName.c_str());
177	>	}
178
154	–	string xTempFileName;
155	–	string yTempFileName;
156	–	string zTempFileName;
179		if (output3DTemp_) {
180	<	xTempFileName = "temperatureX.log";
181	<	yTempFileName = "temperatureY.log";
182	<	zTempFileName = "temperatureZ.log";
183	<	xTempLog_.open(xTempFileName.c_str());
184	<	yTempLog_.open(yTempFileName.c_str());
185	<	zTempLog_.open(zTempFileName.c_str());
180	>	rnemdFileName = "temperatureX.log";
181	>	xTempLog_.open(rnemdFileName.c_str());
182	>	rnemdFileName = "temperatureY.log";
183	>	yTempLog_.open(rnemdFileName.c_str());
184	>	rnemdFileName = "temperatureZ.log";
185	>	zTempLog_.open(rnemdFileName.c_str());
186	>	}
187	>	if (outputRotTemp_) {
188	>	rnemdFileName = "temperatureR.log";
189	>	rotTempLog_.open(rnemdFileName.c_str());
190		}
191
192		#ifdef IS_MPI
#	Line 179 | Line 205 | namespace OpenMD {
205		} else {
206		zShift_ = 0.0;
207		}
208	<	//cerr << "we have zShift_ = " << zShift_ << "\n";
209	<	//shift slabs by half slab width, might be useful in heterogeneous systems
210	<	//set to 0.0 if not using it; can NOT be used in status output yet
208	>	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
209	>	//shift slabs by half slab width, maybe useful in heterogeneous systems
210	>	//set to 0.0 if not using it; N/A in status output yet
211		if (simParams->haveRNEMD_logWidth()) {
212		set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
213	<	/*arbitary rnemdLogWidth_ no checking
214	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
213	>	/*arbitary rnemdLogWidth_, no checking;
214	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
215		cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
216		cerr << "Automaically set back to default.\n";
217		rnemdLogWidth_ = nBins_;
218	<	}*/
218	>	}*/
219		} else {
220		set_RNEMD_logWidth(nBins_);
221		}
222	<	valueHist_.resize(rnemdLogWidth_, 0.0);
223	<	valueCount_.resize(rnemdLogWidth_, 0);
222	>	tempHist_.resize(rnemdLogWidth_, 0.0);
223	>	tempCount_.resize(rnemdLogWidth_, 0);
224	>	pxzHist_.resize(rnemdLogWidth_, 0.0);
225	>	//vxzCount_.resize(rnemdLogWidth_, 0);
226	>	pyzHist_.resize(rnemdLogWidth_, 0.0);
227	>	//vyzCount_.resize(rnemdLogWidth_, 0);
228	>
229	>	mHist_.resize(rnemdLogWidth_, 0.0);
230		xTempHist_.resize(rnemdLogWidth_, 0.0);
231		yTempHist_.resize(rnemdLogWidth_, 0.0);
232		zTempHist_.resize(rnemdLogWidth_, 0.0);
233		xyzTempCount_.resize(rnemdLogWidth_, 0);
234	+	rotTempHist_.resize(rnemdLogWidth_, 0.0);
235	+	rotTempCount_.resize(rnemdLogWidth_, 0);
236
237		set_RNEMD_exchange_total(0.0);
238		if (simParams->haveRNEMD_targetFlux()) {
#	Line 206 | Line 240 | namespace OpenMD {
240		} else {
241		set_RNEMD_target_flux(0.0);
242		}
243	+	if (simParams->haveRNEMD_targetJzKE()) {
244	+	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
245	+	} else {
246	+	set_RNEMD_target_JzKE(0.0);
247	+	}
248	+	if (simParams->haveRNEMD_targetJzpx()) {
249	+	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
250	+	} else {
251	+	set_RNEMD_target_jzpx(0.0);
252	+	}
253	+	jzp_.x() = targetJzpx_;
254	+	njzp_.x() = -targetJzpx_;
255	+	if (simParams->haveRNEMD_targetJzpy()) {
256	+	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
257	+	} else {
258	+	set_RNEMD_target_jzpy(0.0);
259	+	}
260	+	jzp_.y() = targetJzpy_;
261	+	njzp_.y() = -targetJzpy_;
262	+	if (simParams->haveRNEMD_targetJzpz()) {
263	+	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
264	+	} else {
265	+	set_RNEMD_target_jzpz(0.0);
266	+	}
267	+	jzp_.z() = targetJzpz_;
268	+	njzp_.z() = -targetJzpz_;
269
270		#ifndef IS_MPI
271		if (simParams->haveSeed()) {
#	Line 238 | Line 298 | namespace OpenMD {
298		painCave.severity = OPENMD_INFO;
299		simError();
300
301	<	rnemdLog_.close();
302	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
301	>	if (outputTemp_) tempLog_.close();
302	>	if (outputVx_)   vxzLog_.close();
303	>	if (outputVy_)   vyzLog_.close();
304	>
305	>	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
306	>	rnemdType_ == rnemdPyScale) {
307		sprintf(painCave.errMsg,
308		"RNEMD: total root-checking warnings: %d\n",
309		failRootCount_);
#	Line 252 | Line 316 | namespace OpenMD {
316		yTempLog_.close();
317		zTempLog_.close();
318		}
319	+	if (outputRotTemp_) rotTempLog_.close();
320	+
321		#ifdef IS_MPI
322		}
323		#endif
#	Line 304 | Line 370 | namespace OpenMD {
370		switch(rnemdType_) {
371		case rnemdKineticSwap :
372
373	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
374	<	vel[2]*vel[2]);
375	<	/*
310	<	if (sd->isDirectional()) {
373	>	value = mass * vel.lengthSquare();
374	>
375	>	if (sd->isDirectional()) {
376		Vector3d angMom = sd->getJ();
377		Mat3x3d I = sd->getI();
378
379		if (sd->isLinear()) {
380	<	int i = sd->linearAxis();
381	<	int j = (i + 1) % 3;
382	<	int k = (i + 2) % 3;
383	<	value += angMom[j] * angMom[j] / I(j, j) +
384	<	angMom[k] * angMom[k] / I(k, k);
385	<	} else {
386	<	value += angMom[0]*angMom[0]/I(0, 0)
387	<	+ angMom[1]*angMom[1]/I(1, 1)
388	<	+ angMom[2]*angMom[2]/I(2, 2);
380	>	int i = sd->linearAxis();
381	>	int j = (i + 1) % 3;
382	>	int k = (i + 2) % 3;
383	>	value += angMom[j] * angMom[j] / I(j, j) +
384	>	angMom[k] * angMom[k] / I(k, k);
385	>	} else {
386	>	value += angMom[0]*angMom[0]/I(0, 0)
387	>	+ angMom[1]*angMom[1]/I(1, 1)
388	>	+ angMom[2]*angMom[2]/I(2, 2);
389		}
390	<	} no exchange of angular momenta
391	<	*/
390	>	} //angular momenta exchange enabled
391	>	//energyConvert temporarily disabled
392		//make exchangeSum_ comparable between swap & scale
328	–	//temporarily without using energyConvert
393		//value = value * 0.5 / PhysicalConstants::energyConvert;
394		value *= 0.5;
395		break;
#	Line 381 | Line 445 | namespace OpenMD {
445		MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
446		// Even if we didn't find a maximum, did someone else?
447		MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
448	<	struct {
449	<	RealType val;
450	<	int rank;
451	<	} max_vals, min_vals;
448	>	#endif
449	>
450	>	if (max_found && min_found) {
451	>
452	>	#ifdef IS_MPI
453	>	struct {
454	>	RealType val;
455	>	int rank;
456	>	} max_vals, min_vals;
457
458	<	if (min_found) {
390	<	if (my_min_found)
458	>	if (my_min_found) {
459		min_vals.val = min_val;
460	<	else
460	>	} else {
461		min_vals.val = HONKING_LARGE_VALUE;
462	<
462	>	}
463		min_vals.rank = worldRank;
464
465		// Who had the minimum?
466		MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
467		1, MPI::REALTYPE_INT, MPI::MINLOC);
468		min_val = min_vals.val;
401	–	}
469
470	<	if (max_found) {
404	<	if (my_max_found)
470	>	if (my_max_found) {
471		max_vals.val = max_val;
472	<	else
472	>	} else {
473		max_vals.val = -HONKING_LARGE_VALUE;
474	<
474	>	}
475		max_vals.rank = worldRank;
476
477		// Who had the maximum?
478		MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
479		1, MPI::REALTYPE_INT, MPI::MAXLOC);
480		max_val = max_vals.val;
415	–	}
481		#endif
482	<
418	<	if (max_found && min_found) {
482	>
483		if (min_val < max_val) {
484	<
484	>
485		#ifdef IS_MPI
486		if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
487		// I have both maximum and minimum, so proceed like a single
488		// processor version:
489		#endif
490	<	// objects to be swapped: velocity ONLY
490	>
491		Vector3d min_vel = min_sd->getVel();
492		Vector3d max_vel = max_sd->getVel();
493		RealType temp_vel;
#	Line 432 | Line 496 | namespace OpenMD {
496		case rnemdKineticSwap :
497		min_sd->setVel(max_vel);
498		max_sd->setVel(min_vel);
499	<	/*
436	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
499	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
500		Vector3d min_angMom = min_sd->getJ();
501		Vector3d max_angMom = max_sd->getJ();
502		min_sd->setJ(max_angMom);
503		max_sd->setJ(min_angMom);
504	<	} no angular momentum exchange
505	<	*/
504	>	}//angular momenta exchange enabled
505	>	//assumes same rigid body identity
506		break;
507		case rnemdPx :
508		temp_vel = min_vel.x();
#	Line 465 | Line 528 | namespace OpenMD {
528		default :
529		break;
530		}
531	+
532		#ifdef IS_MPI
533		// the rest of the cases only apply in parallel simulations:
534		} else if (max_vals.rank == worldRank) {
#	Line 483 | Line 547 | namespace OpenMD {
547		switch(rnemdType_) {
548		case rnemdKineticSwap :
549		max_sd->setVel(min_vel);
550	<	//no angular momentum exchange for now
487	<	/*
550	>	//angular momenta exchange enabled
551		if (max_sd->isDirectional()) {
552		Vector3d min_angMom;
553		Vector3d max_angMom = max_sd->getJ();
#	Line 497 | Line 560 | namespace OpenMD {
560		status);
561
562		max_sd->setJ(min_angMom);
563	<	}
501	<	*/
563	>	}
564		break;
565		case rnemdPx :
566		max_vel.x() = min_vel.x();
#	Line 531 | Line 593 | namespace OpenMD {
593		switch(rnemdType_) {
594		case rnemdKineticSwap :
595		min_sd->setVel(max_vel);
596	<	// no angular momentum exchange for now
535	<	/*
596	>	//angular momenta exchange enabled
597		if (min_sd->isDirectional()) {
598		Vector3d min_angMom = min_sd->getJ();
599		Vector3d max_angMom;
#	Line 546 | Line 607 | namespace OpenMD {
607
608		min_sd->setJ(max_angMom);
609		}
549	–	*/
610		break;
611		case rnemdPx :
612		min_vel.x() = max_vel.x();
#	Line 576 | Line 636 | namespace OpenMD {
636		}
637		} else {
638		sprintf(painCave.errMsg,
639	<	"RNEMD: exchange NOT performed because at least one\n"
640	<	"\tof the two slabs is empty\n");
639	>	"RNEMD: exchange NOT performed because selected object\n"
640	>	"\tnot present in at least one of the two slabs.\n");
641		painCave.isFatal = 0;
642		painCave.severity = OPENMD_INFO;
643		simError();
#	Line 605 | Line 665 | namespace OpenMD {
665		RealType Khx = 0.0;
666		RealType Khy = 0.0;
667		RealType Khz = 0.0;
668	+	RealType Khw = 0.0;
669		RealType Pcx = 0.0;
670		RealType Pcy = 0.0;
671		RealType Pcz = 0.0;
672		RealType Kcx = 0.0;
673		RealType Kcy = 0.0;
674		RealType Kcz = 0.0;
675	+	RealType Kcw = 0.0;
676
677		for (sd = seleMan_.beginSelected(selei); sd != NULL;
678		sd = seleMan_.nextSelected(selei)) {
#	Line 643 | Line 705 | namespace OpenMD {
705		Khx += mass * vel.x() * vel.x();
706		Khy += mass * vel.y() * vel.y();
707		Khz += mass * vel.z() * vel.z();
708	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
709	+	if (sd->isDirectional()) {
710	+	Vector3d angMom = sd->getJ();
711	+	Mat3x3d I = sd->getI();
712	+	if (sd->isLinear()) {
713	+	int i = sd->linearAxis();
714	+	int j = (i + 1) % 3;
715	+	int k = (i + 2) % 3;
716	+	Khw += angMom[j] * angMom[j] / I(j, j) +
717	+	angMom[k] * angMom[k] / I(k, k);
718	+	} else {
719	+	Khw += angMom[0]*angMom[0]/I(0, 0)
720	+	+ angMom[1]*angMom[1]/I(1, 1)
721	+	+ angMom[2]*angMom[2]/I(2, 2);
722	+	}
723	+	}
724	+	//}
725		} else { //midBin_
726		coldBin.push_back(sd);
727		Pcx += mass * vel.x();
#	Line 651 | Line 730 | namespace OpenMD {
730		Kcx += mass * vel.x() * vel.x();
731		Kcy += mass * vel.y() * vel.y();
732		Kcz += mass * vel.z() * vel.z();
733	+	//if (rnemdType_ == rnemdKineticScaleVAM) {
734	+	if (sd->isDirectional()) {
735	+	Vector3d angMom = sd->getJ();
736	+	Mat3x3d I = sd->getI();
737	+	if (sd->isLinear()) {
738	+	int i = sd->linearAxis();
739	+	int j = (i + 1) % 3;
740	+	int k = (i + 2) % 3;
741	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
742	+	angMom[k] * angMom[k] / I(k, k);
743	+	} else {
744	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
745	+	+ angMom[1]*angMom[1]/I(1, 1)
746	+	+ angMom[2]*angMom[2]/I(2, 2);
747	+	}
748	+	}
749	+	//}
750		}
751		}
752		}
753	<
753	>
754		Khx *= 0.5;
755		Khy *= 0.5;
756		Khz *= 0.5;
757	+	Khw *= 0.5;
758		Kcx *= 0.5;
759		Kcy *= 0.5;
760		Kcz *= 0.5;
761	+	Kcw *= 0.5;
762
763	+	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
764	+	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
765	+	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
766	+	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
767	+	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
768	+
769		#ifdef IS_MPI
770		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
771		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 673 | Line 777 | namespace OpenMD {
777		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
778		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
779		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
780	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
781	+
782		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
783		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
784		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
785	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
786		#endif
787
788	<	//use coldBin coeff's
788	>	//solve coldBin coeff's first
789		RealType px = Pcx / Phx;
790		RealType py = Pcy / Phy;
791		RealType pz = Pcz / Phz;
792	+	RealType c, x, y, z;
793	+	bool successfulScale = false;
794	+	if ((rnemdType_ == rnemdKineticScaleVAM) ||
795	+	(rnemdType_ == rnemdKineticScaleAM)) {
796	+	//may need sanity check Khw & Kcw > 0
797
798	<	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
799	<	switch(rnemdType_) {
800	<	case rnemdKineticScale :
801	<	// used hotBin coeff's & only scale x & y dimensions
802	<	/*
691	<	RealType px = Phx / Pcx;
692	<	RealType py = Phy / Pcy;
693	<	a110 = Khy;
694	<	c0 = - Khx - Khy - targetFlux_;
695	<	a000 = Khx;
696	<	a111 = Kcy * py * py;
697	<	b11 = -2.0 * Kcy * py * (1.0 + py);
698	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
699	<	b01 = -2.0 * Kcx * px * (1.0 + px);
700	<	a001 = Kcx * px * px;
701	<	*/
702	<	//scale all three dimensions, let c_x = c_y
703	<	a000 = Kcx + Kcy;
704	<	a110 = Kcz;
705	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
706	<	a001 = Khx * px * px + Khy * py * py;
707	<	a111 = Khz * pz * pz;
708	<	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
709	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
710	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
711	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
712	<	break;
713	<	case rnemdPxScale :
714	<	c = 1 - targetFlux_ / Pcx;
715	<	a000 = Kcy;
716	<	a110 = Kcz;
717	<	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
718	<	a001 = py * py * Khy;
719	<	a111 = pz * pz * Khz;
720	<	b01 = -2.0 * Khy * py * (1.0 + py);
721	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
722	<	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
723	<	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
724	<	break;
725	<	case rnemdPyScale :
726	<	c = 1 - targetFlux_ / Pcy;
727	<	a000 = Kcx;
728	<	a110 = Kcz;
729	<	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
730	<	a001 = px * px * Khx;
731	<	a111 = pz * pz * Khz;
732	<	b01 = -2.0 * Khx * px * (1.0 + px);
733	<	b11 = -2.0 * Khz * pz * (1.0 + pz);
734	<	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
735	<	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
736	<	break;
737	<	case rnemdPzScale ://we don't really do this, do we?
738	<	c = 1 - targetFlux_ / Pcz;
739	<	a000 = Kcx;
740	<	a110 = Kcy;
741	<	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
742	<	a001 = px * px * Khx;
743	<	a111 = py * py * Khy;
744	<	b01 = -2.0 * Khx * px * (1.0 + px);
745	<	b11 = -2.0 * Khy * py * (1.0 + py);
746	<	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
747	<	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
748	<	break;
749	<	default :
750	<	break;
751	<	}
798	>	if (rnemdType_ == rnemdKineticScaleVAM) {
799	>	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
800	>	} else {
801	>	c = 1.0 - targetFlux_ / Kcw;
802	>	}
803
804	<	RealType v1 = a000 * a111 - a001 * a110;
805	<	RealType v2 = a000 * b01;
806	<	RealType v3 = a000 * b11;
807	<	RealType v4 = a000 * c1 - a001 * c0;
808	<	RealType v8 = a110 * b01;
809	<	RealType v10 = - b01 * c0;
810	<
811	<	RealType u0 = v2 * v10 - v4 * v4;
812	<	RealType u1 = -2.0 * v3 * v4;
813	<	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
814	<	RealType u3 = -2.0 * v1 * v3;
815	<	RealType u4 = - v1 * v1;
816	<	//rescale coefficients
817	<	RealType maxAbs = fabs(u0);
818	<	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
819	<	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
820	<	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
821	<	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
822	<	u0 /= maxAbs;
823	<	u1 /= maxAbs;
824	<	u2 /= maxAbs;
825	<	u3 /= maxAbs;
826	<	u4 /= maxAbs;
827	<	//max_element(start, end) is also available.
828	<	Polynomial<RealType> poly; //same as DoublePolynomial poly;
829	<	poly.setCoefficient(4, u4);
830	<	poly.setCoefficient(3, u3);
831	<	poly.setCoefficient(2, u2);
832	<	poly.setCoefficient(1, u1);
833	<	poly.setCoefficient(0, u0);
834	<	vector<RealType> realRoots = poly.FindRealRoots();
835	<
836	<	vector<RealType>::iterator ri;
837	<	RealType r1, r2, alpha0;
838	<	vector<pair<RealType,RealType> > rps;
839	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
840	<	r2 = *ri;
841	<	//check if FindRealRoots() give the right answer
842	<	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
843	<	sprintf(painCave.errMsg,
844	<	"RNEMD Warning: polynomial solve seems to have an error!");
845	<	painCave.isFatal = 0;
846	<	simError();
847	<	failRootCount_++;
804	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
805	>	c = sqrt(c);
806	>	std::cerr << "cold slab scaling coefficient: " << c << endl;
807	>	//now convert to hotBin coefficient
808	>	RealType w = 0.0;
809	>	if (rnemdType_ ==  rnemdKineticScaleVAM) {
810	>	x = 1.0 + px * (1.0 - c);
811	>	y = 1.0 + py * (1.0 - c);
812	>	z = 1.0 + pz * (1.0 - c);
813	>	/* more complicated way
814	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
815	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
816	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
817	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
818	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
819	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
820	>	*/
821	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
822	>	(fabs(z - 1.0) < 0.1)) {
823	>	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
824	>	+ Khz * (1.0 - z * z)) / Khw;
825	>	}//no need to calculate w if x, y or z is out of range
826	>	} else {
827	>	w = 1.0 + targetFlux_ / Khw;
828	>	}
829	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
830	>	//if w is in the right range, so should be x, y, z.
831	>	vector<StuntDouble*>::iterator sdi;
832	>	Vector3d vel;
833	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
834	>	if (rnemdType_ == rnemdKineticScaleVAM) {
835	>	vel = (*sdi)->getVel() * c;
836	>	//vel.x() *= c;
837	>	//vel.y() *= c;
838	>	//vel.z() *= c;
839	>	(*sdi)->setVel(vel);
840	>	}
841	>	if ((*sdi)->isDirectional()) {
842	>	Vector3d angMom = (*sdi)->getJ() * c;
843	>	//angMom[0] *= c;
844	>	//angMom[1] *= c;
845	>	//angMom[2] *= c;
846	>	(*sdi)->setJ(angMom);
847	>	}
848	>	}
849	>	w = sqrt(w);
850	>	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
851	>	<< "\twh= " << w << endl;
852	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
853	>	if (rnemdType_ == rnemdKineticScaleVAM) {
854	>	vel = (*sdi)->getVel();
855	>	vel.x() *= x;
856	>	vel.y() *= y;
857	>	vel.z() *= z;
858	>	(*sdi)->setVel(vel);
859	>	}
860	>	if ((*sdi)->isDirectional()) {
861	>	Vector3d angMom = (*sdi)->getJ() * w;
862	>	//angMom[0] *= w;
863	>	//angMom[1] *= w;
864	>	//angMom[2] *= w;
865	>	(*sdi)->setJ(angMom);
866	>	}
867	>	}
868	>	successfulScale = true;
869	>	exchangeSum_ += targetFlux_;
870	>	}
871		}
872	<	//might not be useful w/o rescaling coefficients
873	<	alpha0 = -c0 - a110 * r2 * r2;
800	<	if (alpha0 >= 0.0) {
801	<	r1 = sqrt(alpha0 / a000);
802	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
803	<	{ rps.push_back(make_pair(r1, r2)); }
804	<	if (r1 > 1e-6) { //r1 non-negative
805	<	r1 = -r1;
806	<	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
807	<	{ rps.push_back(make_pair(r1, r2)); }
808	<	}
809	<	}
810	<	}
811	<	// Consider combining together the solving pair part w/ the searching
812	<	// best solution part so that we don't need the pairs vector
813	<	if (!rps.empty()) {
814	<	RealType smallestDiff = HONKING_LARGE_VALUE;
815	<	RealType diff;
816	<	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
817	<	vector<pair<RealType,RealType> >::iterator rpi;
818	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
819	<	r1 = (*rpi).first;
820	<	r2 = (*rpi).second;
821	<	switch(rnemdType_) {
822	<	case rnemdKineticScale :
823	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
824	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
825	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
826	<	break;
827	<	case rnemdPxScale :
828	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
829	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
830	<	break;
831	<	case rnemdPyScale :
832	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
833	<	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
834	<	break;
835	<	case rnemdPzScale :
836	<	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
837	<	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
838	<	default :
839	<	break;
840	<	}
841	<	if (diff < smallestDiff) {
842	<	smallestDiff = diff;
843	<	bestPair = *rpi;
844	<	}
845	<	}
846	<	#ifdef IS_MPI
847	<	if (worldRank == 0) {
848	<	#endif
849	<	sprintf(painCave.errMsg,
850	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
851	<	bestPair.first, bestPair.second);
852	<	painCave.isFatal = 0;
853	<	painCave.severity = OPENMD_INFO;
854	<	simError();
855	<	#ifdef IS_MPI
856	<	}
857	<	#endif
858	<
859	<	RealType x, y, z;
872	>	} else {
873	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
874		switch(rnemdType_) {
875		case rnemdKineticScale :
876	<	x = bestPair.first;
877	<	y = bestPair.first;
878	<	z = bestPair.second;
879	<	break;
876	>	/* used hotBin coeff's & only scale x & y dimensions
877	>	RealType px = Phx / Pcx;
878	>	RealType py = Phy / Pcy;
879	>	a110 = Khy;
880	>	c0 = - Khx - Khy - targetFlux_;
881	>	a000 = Khx;
882	>	a111 = Kcy * py * py;
883	>	b11 = -2.0 * Kcy * py * (1.0 + py);
884	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
885	>	b01 = -2.0 * Kcx * px * (1.0 + px);
886	>	a001 = Kcx * px * px;
887	>	*/
888	>	//scale all three dimensions, let c_x = c_y
889	>	a000 = Kcx + Kcy;
890	>	a110 = Kcz;
891	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
892	>	a001 = Khx * px * px + Khy * py * py;
893	>	a111 = Khz * pz * pz;
894	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
895	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
896	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
897	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
898	>	break;
899		case rnemdPxScale :
900	<	x = c;
901	<	y = bestPair.first;
902	<	z = bestPair.second;
903	<	break;
900	>	c = 1 - targetFlux_ / Pcx;
901	>	a000 = Kcy;
902	>	a110 = Kcz;
903	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
904	>	a001 = py * py * Khy;
905	>	a111 = pz * pz * Khz;
906	>	b01 = -2.0 * Khy * py * (1.0 + py);
907	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
908	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
909	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
910	>	break;
911		case rnemdPyScale :
912	<	x = bestPair.first;
913	<	y = c;
914	<	z = bestPair.second;
915	<	break;
916	<	case rnemdPzScale :
917	<	x = bestPair.first;
918	<	y = bestPair.second;
919	<	z = c;
920	<	break;
912	>	c = 1 - targetFlux_ / Pcy;
913	>	a000 = Kcx;
914	>	a110 = Kcz;
915	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
916	>	a001 = px * px * Khx;
917	>	a111 = pz * pz * Khz;
918	>	b01 = -2.0 * Khx * px * (1.0 + px);
919	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
920	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
921	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
922	>	break;
923	>	case rnemdPzScale ://we don't really do this, do we?
924	>	c = 1 - targetFlux_ / Pcz;
925	>	a000 = Kcx;
926	>	a110 = Kcy;
927	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
928	>	a001 = px * px * Khx;
929	>	a111 = py * py * Khy;
930	>	b01 = -2.0 * Khx * px * (1.0 + px);
931	>	b11 = -2.0 * Khy * py * (1.0 + py);
932	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
933	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
934	>	break;
935		default :
936	<	break;
936	>	break;
937		}
938	<	vector<StuntDouble*>::iterator sdi;
939	<	Vector3d vel;
940	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
941	<	vel = (*sdi)->getVel();
942	<	vel.x() *= x;
943	<	vel.y() *= y;
944	<	vel.z() *= z;
945	<	(*sdi)->setVel(vel);
938	>
939	>	RealType v1 = a000 * a111 - a001 * a110;
940	>	RealType v2 = a000 * b01;
941	>	RealType v3 = a000 * b11;
942	>	RealType v4 = a000 * c1 - a001 * c0;
943	>	RealType v8 = a110 * b01;
944	>	RealType v10 = - b01 * c0;
945	>
946	>	RealType u0 = v2 * v10 - v4 * v4;
947	>	RealType u1 = -2.0 * v3 * v4;
948	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
949	>	RealType u3 = -2.0 * v1 * v3;
950	>	RealType u4 = - v1 * v1;
951	>	//rescale coefficients
952	>	RealType maxAbs = fabs(u0);
953	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
954	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
955	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
956	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
957	>	u0 /= maxAbs;
958	>	u1 /= maxAbs;
959	>	u2 /= maxAbs;
960	>	u3 /= maxAbs;
961	>	u4 /= maxAbs;
962	>	//max_element(start, end) is also available.
963	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
964	>	poly.setCoefficient(4, u4);
965	>	poly.setCoefficient(3, u3);
966	>	poly.setCoefficient(2, u2);
967	>	poly.setCoefficient(1, u1);
968	>	poly.setCoefficient(0, u0);
969	>	vector<RealType> realRoots = poly.FindRealRoots();
970	>
971	>	vector<RealType>::iterator ri;
972	>	RealType r1, r2, alpha0;
973	>	vector<pair<RealType,RealType> > rps;
974	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
975	>	r2 = *ri;
976	>	//check if FindRealRoots() give the right answer
977	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
978	>	sprintf(painCave.errMsg,
979	>	"RNEMD Warning: polynomial solve seems to have an error!");
980	>	painCave.isFatal = 0;
981	>	simError();
982	>	failRootCount_++;
983	>	}
984	>	//might not be useful w/o rescaling coefficients
985	>	alpha0 = -c0 - a110 * r2 * r2;
986	>	if (alpha0 >= 0.0) {
987	>	r1 = sqrt(alpha0 / a000);
988	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
989	>	< 1e-6)
990	>	{ rps.push_back(make_pair(r1, r2)); }
991	>	if (r1 > 1e-6) { //r1 non-negative
992	>	r1 = -r1;
993	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
994	>	< 1e-6)
995	>	{ rps.push_back(make_pair(r1, r2)); }
996	>	}
997	>	}
998		}
999	<	//convert to hotBin coefficient
1000	<	x = 1.0 + px * (1.0 - x);
1001	<	y = 1.0 + py * (1.0 - y);
1002	<	z = 1.0 + pz * (1.0 - z);
1003	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1004	<	vel = (*sdi)->getVel();
1005	<	vel.x() *= x;
1006	<	vel.y() *= y;
1007	<	vel.z() *= z;
1008	<	(*sdi)->setVel(vel);
999	>	// Consider combining together the solving pair part w/ the searching
1000	>	// best solution part so that we don't need the pairs vector
1001	>	if (!rps.empty()) {
1002	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1003	>	RealType diff;
1004	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1005	>	vector<pair<RealType,RealType> >::iterator rpi;
1006	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1007	>	r1 = (*rpi).first;
1008	>	r2 = (*rpi).second;
1009	>	switch(rnemdType_) {
1010	>	case rnemdKineticScale :
1011	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1012	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1013	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1014	>	break;
1015	>	case rnemdPxScale :
1016	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1017	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1018	>	break;
1019	>	case rnemdPyScale :
1020	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1021	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1022	>	break;
1023	>	case rnemdPzScale :
1024	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1025	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1026	>	default :
1027	>	break;
1028	>	}
1029	>	if (diff < smallestDiff) {
1030	>	smallestDiff = diff;
1031	>	bestPair = *rpi;
1032	>	}
1033	>	}
1034	>	#ifdef IS_MPI
1035	>	if (worldRank == 0) {
1036	>	#endif
1037	>	sprintf(painCave.errMsg,
1038	>	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1039	>	bestPair.first, bestPair.second);
1040	>	painCave.isFatal = 0;
1041	>	painCave.severity = OPENMD_INFO;
1042	>	simError();
1043	>	#ifdef IS_MPI
1044	>	}
1045	>	#endif
1046	>
1047	>	switch(rnemdType_) {
1048	>	case rnemdKineticScale :
1049	>	x = bestPair.first;
1050	>	y = bestPair.first;
1051	>	z = bestPair.second;
1052	>	break;
1053	>	case rnemdPxScale :
1054	>	x = c;
1055	>	y = bestPair.first;
1056	>	z = bestPair.second;
1057	>	break;
1058	>	case rnemdPyScale :
1059	>	x = bestPair.first;
1060	>	y = c;
1061	>	z = bestPair.second;
1062	>	break;
1063	>	case rnemdPzScale :
1064	>	x = bestPair.first;
1065	>	y = bestPair.second;
1066	>	z = c;
1067	>	break;
1068	>	default :
1069	>	break;
1070	>	}
1071	>	vector<StuntDouble*>::iterator sdi;
1072	>	Vector3d vel;
1073	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1074	>	vel = (*sdi)->getVel();
1075	>	vel.x() *= x;
1076	>	vel.y() *= y;
1077	>	vel.z() *= z;
1078	>	(*sdi)->setVel(vel);
1079	>	}
1080	>	//convert to hotBin coefficient
1081	>	x = 1.0 + px * (1.0 - x);
1082	>	y = 1.0 + py * (1.0 - y);
1083	>	z = 1.0 + pz * (1.0 - z);
1084	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1085	>	vel = (*sdi)->getVel();
1086	>	vel.x() *= x;
1087	>	vel.y() *= y;
1088	>	vel.z() *= z;
1089	>	(*sdi)->setVel(vel);
1090	>	}
1091	>	successfulScale = true;
1092	>	exchangeSum_ += targetFlux_;
1093		}
1094	<	exchangeSum_ += targetFlux_;
1095	<	//we may want to check whether the exchange has been successful
906	<	} else {
1094	>	}
1095	>	if (successfulScale != true) {
1096		sprintf(painCave.errMsg,
1097	<	"RNEMD: exchange NOT performed!\n");
1097	>	"RNEMD: exchange NOT performed!\n");
1098		painCave.isFatal = 0;
1099		painCave.severity = OPENMD_INFO;
1100		simError();
1101		failTrialCount_++;
1102		}
1103	+	}
1104
1105	+	void RNEMD::doShiftScale() {
1106	+
1107	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1108	+	Mat3x3d hmat = currentSnap_->getHmat();
1109	+
1110	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1111	+
1112	+	int selei;
1113	+	StuntDouble* sd;
1114	+	int idx;
1115	+
1116	+	vector<StuntDouble*> hotBin, coldBin;
1117	+
1118	+	Vector3d Ph(V3Zero);
1119	+	RealType Mh = 0.0;
1120	+	RealType Kh = 0.0;
1121	+	Vector3d Pc(V3Zero);
1122	+	RealType Mc = 0.0;
1123	+	RealType Kc = 0.0;
1124	+
1125	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1126	+	sd = seleMan_.nextSelected(selei)) {
1127	+
1128	+	idx = sd->getLocalIndex();
1129	+
1130	+	Vector3d pos = sd->getPos();
1131	+
1132	+	// wrap the stuntdouble's position back into the box:
1133	+
1134	+	if (usePeriodicBoundaryConditions_)
1135	+	currentSnap_->wrapVector(pos);
1136	+
1137	+	// which bin is this stuntdouble in?
1138	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1139	+
1140	+	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1141	+
1142	+	// if we're in bin 0 or the middleBin
1143	+	if (binNo == 0 || binNo == midBin_) {
1144	+
1145	+	RealType mass = sd->getMass();
1146	+	Vector3d vel = sd->getVel();
1147	+
1148	+	if (binNo == 0) {
1149	+	hotBin.push_back(sd);
1150	+	//std::cerr << "before, velocity = " << vel << endl;
1151	+	Ph += mass * vel;
1152	+	//std::cerr << "after, velocity = " << vel << endl;
1153	+	Mh += mass;
1154	+	Kh += mass * vel.lengthSquare();
1155	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1156	+	if (sd->isDirectional()) {
1157	+	Vector3d angMom = sd->getJ();
1158	+	Mat3x3d I = sd->getI();
1159	+	if (sd->isLinear()) {
1160	+	int i = sd->linearAxis();
1161	+	int j = (i + 1) % 3;
1162	+	int k = (i + 2) % 3;
1163	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1164	+	angMom[k] * angMom[k] / I(k, k);
1165	+	} else {
1166	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1167	+	angMom[1] * angMom[1] / I(1, 1) +
1168	+	angMom[2] * angMom[2] / I(2, 2);
1169	+	}
1170	+	}
1171	+	}
1172	+	} else { //midBin_
1173	+	coldBin.push_back(sd);
1174	+	Pc += mass * vel;
1175	+	Mc += mass;
1176	+	Kc += mass * vel.lengthSquare();
1177	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1178	+	if (sd->isDirectional()) {
1179	+	Vector3d angMom = sd->getJ();
1180	+	Mat3x3d I = sd->getI();
1181	+	if (sd->isLinear()) {
1182	+	int i = sd->linearAxis();
1183	+	int j = (i + 1) % 3;
1184	+	int k = (i + 2) % 3;
1185	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1186	+	angMom[k] * angMom[k] / I(k, k);
1187	+	} else {
1188	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1189	+	angMom[1] * angMom[1] / I(1, 1) +
1190	+	angMom[2] * angMom[2] / I(2, 2);
1191	+	}
1192	+	}
1193	+	}
1194	+	}
1195	+	}
1196	+	}
1197	+
1198	+	Kh *= 0.5;
1199	+	Kc *= 0.5;
1200	+
1201	+	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	+	<< "\tKc= " << Kc << endl;
1203	+	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	+
1205	+	#ifdef IS_MPI
1206	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1207	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1208	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1209	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1210	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1211	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1212	+	#endif
1213	+
1214	+	bool successfulExchange = false;
1215	+	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1216	+	Vector3d vc = Pc / Mc;
1217	+	Vector3d ac = njzp_ / Mc + vc;
1218	+	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1219	+	if (cNumerator > 0.0) {
1220	+	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1221	+	if (cDenominator > 0.0) {
1222	+	RealType c = sqrt(cNumerator / cDenominator);
1223	+	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1224	+	Vector3d vh = Ph / Mh;
1225	+	Vector3d ah = jzp_ / Mh + vh;
1226	+	RealType hNumerator = Kh + targetJzKE_
1227	+	- 0.5 * Mh * ah.lengthSquare();
1228	+	if (hNumerator > 0.0) {
1229	+	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1230	+	if (hDenominator > 0.0) {
1231	+	RealType h = sqrt(hNumerator / hDenominator);
1232	+	if ((h > 0.9) && (h < 1.1)) {
1233	+	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	+	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1235	+	vector<StuntDouble*>::iterator sdi;
1236	+	Vector3d vel;
1237	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1238	+	//vel = (*sdi)->getVel();
1239	+	vel = ((*sdi)->getVel() - vc) * c + ac;
1240	+	(*sdi)->setVel(vel);
1241	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1242	+	if ((*sdi)->isDirectional()) {
1243	+	Vector3d angMom = (*sdi)->getJ() * c;
1244	+	(*sdi)->setJ(angMom);
1245	+	}
1246	+	}
1247	+	}
1248	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1249	+	//vel = (*sdi)->getVel();
1250	+	vel = ((*sdi)->getVel() - vh) * h + ah;
1251	+	(*sdi)->setVel(vel);
1252	+	if (rnemdType_ == rnemdShiftScaleVAM) {
1253	+	if ((*sdi)->isDirectional()) {
1254	+	Vector3d angMom = (*sdi)->getJ() * h;
1255	+	(*sdi)->setJ(angMom);
1256	+	}
1257	+	}
1258	+	}
1259	+	successfulExchange = true;
1260	+	exchangeSum_ += targetFlux_;
1261	+	// this is a redundant variable for doShiftScale() so that
1262	+	// RNEMD can output one exchange quantity needed in a job.
1263	+	// need a better way to do this.
1264	+	}
1265	+	}
1266	+	}
1267	+	}
1268	+	}
1269	+	}
1270	+	}
1271	+	if (successfulExchange != true) {
1272	+	sprintf(painCave.errMsg,
1273	+	"RNEMD: exchange NOT performed!\n");
1274	+	painCave.isFatal = 0;
1275	+	painCave.severity = OPENMD_INFO;
1276	+	simError();
1277	+	failTrialCount_++;
1278	+	}
1279		}
1280
1281		void RNEMD::doRNEMD() {
1282
1283		switch(rnemdType_) {
1284		case rnemdKineticScale :
1285	+	case rnemdKineticScaleVAM :
1286	+	case rnemdKineticScaleAM :
1287		case rnemdPxScale :
1288		case rnemdPyScale :
1289		case rnemdPzScale :
#	Line 929 | Line 1295 | namespace OpenMD {
1295		case rnemdPz :
1296		doSwap();
1297		break;
1298	+	case rnemdShiftScaleV :
1299	+	case rnemdShiftScaleVAM :
1300	+	doShiftScale();
1301	+	break;
1302		case rnemdUnknown :
1303		default :
1304		break;
#	Line 977 | Line 1347 | namespace OpenMD {
1347
1348		int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1349		rnemdLogWidth_;
1350	<	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
1350	>	// no symmetrization allowed due to arbitary rnemdLogWidth_
1351		/*
1352		if (rnemdLogWidth_ == midBin_ + 1)
1353		if (binNo > midBin_)
1354		binNo = nBins_ - binNo;
1355		*/
1356		RealType mass = sd->getMass();
1357	+	mHist_[binNo] += mass;
1358		Vector3d vel = sd->getVel();
1359		RealType value;
1360	<	RealType xVal, yVal, zVal;
1360	>	//RealType xVal, yVal, zVal;
1361
1362	<	switch(rnemdType_) {
1363	<	case rnemdKineticSwap :
1364	<	case rnemdKineticScale :
994	<
995	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
996	<
997	<	valueCount_[binNo] += 3;
1362	>	if (outputTemp_) {
1363	>	value = mass * vel.lengthSquare();
1364	>	tempCount_[binNo] += 3;
1365		if (sd->isDirectional()) {
1366		Vector3d angMom = sd->getJ();
1367		Mat3x3d I = sd->getI();
1001	–
1368		if (sd->isLinear()) {
1369		int i = sd->linearAxis();
1370		int j = (i + 1) % 3;
1371		int k = (i + 2) % 3;
1372		value += angMom[j] * angMom[j] / I(j, j) +
1373		angMom[k] * angMom[k] / I(k, k);
1374	<
1009	<	valueCount_[binNo] +=2;
1010	<
1374	>	tempCount_[binNo] +=2;
1375		} else {
1376	<	value += angMom[0]*angMom[0]/I(0, 0)
1377	<	+ angMom[1]*angMom[1]/I(1, 1)
1378	<	+ angMom[2]*angMom[2]/I(2, 2);
1379	<	valueCount_[binNo] +=3;
1376	>	value += angMom[0] * angMom[0] / I(0, 0) +
1377	>	angMom[1]*angMom[1]/I(1, 1) +
1378	>	angMom[2]*angMom[2]/I(2, 2);
1379	>	tempCount_[binNo] +=3;
1380		}
1381		}
1382	<	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1383	<
1384	<	break;
1385	<	case rnemdPx :
1386	<	case rnemdPxScale :
1382	>	value = value / PhysicalConstants::energyConvert
1383	>	/ PhysicalConstants::kb;//may move to getStatus()
1384	>	tempHist_[binNo] += value;
1385	>	}
1386	>	if (outputVx_) {
1387		value = mass * vel[0];
1388	<	valueCount_[binNo]++;
1389	<	break;
1390	<	case rnemdPy :
1391	<	case rnemdPyScale :
1388	>	//vxzCount_[binNo]++;
1389	>	pxzHist_[binNo] += value;
1390	>	}
1391	>	if (outputVy_) {
1392		value = mass * vel[1];
1393	<	valueCount_[binNo]++;
1394	<	break;
1031	<	case rnemdPz :
1032	<	case rnemdPzScale :
1033	<	value = pos.z(); //temporarily for homogeneous systems ONLY
1034	<	valueCount_[binNo]++;
1035	<	break;
1036	<	case rnemdUnknown :
1037	<	default :
1038	<	value = 1.0;
1039	<	valueCount_[binNo]++;
1040	<	break;
1393	>	//vyzCount_[binNo]++;
1394	>	pyzHist_[binNo] += value;
1395		}
1042	–	valueHist_[binNo] += value;
1396
1397		if (output3DTemp_) {
1398	<	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1398	>	value = mass * vel.x() * vel.x();
1399	>	xTempHist_[binNo] += value;
1400	>	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1401		/ PhysicalConstants::kb;
1402	<	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1402	>	yTempHist_[binNo] += value;
1403	>	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1404		/ PhysicalConstants::kb;
1405	<	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1050	<	/ PhysicalConstants::kb;
1051	<	xTempHist_[binNo] += xVal;
1052	<	yTempHist_[binNo] += yVal;
1053	<	zTempHist_[binNo] += zVal;
1405	>	zTempHist_[binNo] += value;
1406		xyzTempCount_[binNo]++;
1407	+	}
1408	+	if (outputRotTemp_) {
1409	+	if (sd->isDirectional()) {
1410	+	Vector3d angMom = sd->getJ();
1411	+	Mat3x3d I = sd->getI();
1412	+	if (sd->isLinear()) {
1413	+	int i = sd->linearAxis();
1414	+	int j = (i + 1) % 3;
1415	+	int k = (i + 2) % 3;
1416	+	value = angMom[j] * angMom[j] / I(j, j) +
1417	+	angMom[k] * angMom[k] / I(k, k);
1418	+	rotTempCount_[binNo] +=2;
1419	+	} else {
1420	+	value = angMom[0] * angMom[0] / I(0, 0) +
1421	+	angMom[1] * angMom[1] / I(1, 1) +
1422	+	angMom[2] * angMom[2] / I(2, 2);
1423	+	rotTempCount_[binNo] +=3;
1424	+	}
1425	+	}
1426	+	value = value / PhysicalConstants::energyConvert
1427	+	/ PhysicalConstants::kb;//may move to getStatus()
1428	+	rotTempHist_[binNo] += value;
1429		}
1430	+
1431		}
1432		}
1433
1434		void RNEMD::getStarted() {
1435		collectData();
1436	<	/* now should be able to output profile in step 0, but might not be useful
1437	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	<	Stats& stat = currentSnap_->statData;
1439	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1436	>	/*now can output profile in step 0, but might not be useful;
1437	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	>	Stats& stat = currentSnap_->statData;
1439	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1440		*/
1441	+	//may output a header for the log file here
1442		getStatus();
1443		}
1444
#	Line 1081 | Line 1457 | namespace OpenMD {
1457		// all processors have the same number of bins, and STL vectors pack their
1458		// arrays, so in theory, this should be safe:
1459
1460	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1461	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1462	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1463	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1460	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1461	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1462	>	if (outputTemp_) {
1463	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1464	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1465	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1466	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
1467	>	}
1468	>	if (outputVx_) {
1469	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1470	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1471	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1472	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1473	>	}
1474	>	if (outputVy_) {
1475	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1476	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1477	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1478	>	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1479	>	}
1480		if (output3DTemp_) {
1481		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1482		rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
#	Line 1095 | Line 1487 | namespace OpenMD {
1487		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1488		rnemdLogWidth_, MPI::INT, MPI::SUM);
1489		}
1490	+	if (outputRotTemp_) {
1491	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1492	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1493	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1494	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1495	+	}
1496	+
1497		// If we're the root node, should we print out the results
1498		int worldRank = MPI::COMM_WORLD.Get_rank();
1499		if (worldRank == 0) {
1500		#endif
1501	<	rnemdLog_ << time;
1502	<	for (j = 0; j < rnemdLogWidth_; j++) {
1503	<	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1501	>
1502	>	if (outputTemp_) {
1503	>	tempLog_ << time;
1504	>	for (j = 0; j < rnemdLogWidth_; j++) {
1505	>	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1506	>	}
1507	>	tempLog_ << endl;
1508		}
1509	<	rnemdLog_ << "\n";
1509	>	if (outputVx_) {
1510	>	vxzLog_ << time;
1511	>	for (j = 0; j < rnemdLogWidth_; j++) {
1512	>	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1513	>	}
1514	>	vxzLog_ << endl;
1515	>	}
1516	>	if (outputVy_) {
1517	>	vyzLog_ << time;
1518	>	for (j = 0; j < rnemdLogWidth_; j++) {
1519	>	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	>	}
1521	>	vyzLog_ << endl;
1522	>	}
1523	>
1524		if (output3DTemp_) {
1525	<	xTempLog_ << time;
1525	>	RealType temp;
1526	>	xTempLog_ << time;
1527		for (j = 0; j < rnemdLogWidth_; j++) {
1528	<	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1528	>	if (outputVx_)
1529	>	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1530	>	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1531	>	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1532	>	xTempLog_ << "\t" << temp;
1533		}
1534	<	xTempLog_ << "\n";
1534	>	xTempLog_ << endl;
1535		yTempLog_ << time;
1536		for (j = 0; j < rnemdLogWidth_; j++) {
1537		yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1538		}
1539	<	yTempLog_ << "\n";
1539	>	yTempLog_ << endl;
1540		zTempLog_ << time;
1541		for (j = 0; j < rnemdLogWidth_; j++) {
1542		zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1543		}
1544	<	zTempLog_ << "\n";
1544	>	zTempLog_ << endl;
1545		}
1546	+	if (outputRotTemp_) {
1547	+	rotTempLog_ << time;
1548	+	for (j = 0; j < rnemdLogWidth_; j++) {
1549	+	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1550	+	}
1551	+	rotTempLog_ << endl;
1552	+	}
1553	+
1554		#ifdef IS_MPI
1555		}
1556		#endif
1557	+
1558		for (j = 0; j < rnemdLogWidth_; j++) {
1559	<	valueCount_[j] = 0;
1129	<	valueHist_[j] = 0.0;
1559	>	mHist_[j] = 0.0;
1560		}
1561	+	if (outputTemp_)
1562	+	for (j = 0; j < rnemdLogWidth_; j++) {
1563	+	tempCount_[j] = 0;
1564	+	tempHist_[j] = 0.0;
1565	+	}
1566	+	if (outputVx_)
1567	+	for (j = 0; j < rnemdLogWidth_; j++) {
1568	+	//pxzCount_[j] = 0;
1569	+	pxzHist_[j] = 0.0;
1570	+	}
1571	+	if (outputVy_)
1572	+	for (j = 0; j < rnemdLogWidth_; j++) {
1573	+	//pyzCount_[j] = 0;
1574	+	pyzHist_[j] = 0.0;
1575	+	}
1576	+
1577		if (output3DTemp_)
1578		for (j = 0; j < rnemdLogWidth_; j++) {
1579		xTempHist_[j] = 0.0;
#	Line 1135 | Line 1581 | namespace OpenMD {
1581		zTempHist_[j] = 0.0;
1582		xyzTempCount_[j] = 0;
1583		}
1584	+	if (outputRotTemp_)
1585	+	for (j = 0; j < rnemdLogWidth_; j++) {
1586	+	rotTempCount_[j] = 0;
1587	+	rotTempHist_[j] = 0.0;
1588	+	}
1589		}
1590		}
1591	+

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