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root/OpenMD/trunk/src/integrators/RNEMD.cpp

Comparing trunk/src/integrators/RNEMD.cpp (file contents):
Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
Revision 1560 by skuang, Wed May 11 17:55:32 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42	+	#include <cmath>
43		#include "integrators/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45		#include "math/SquareMatrix3.hpp"
46	+	#include "math/Polynomial.hpp"
47		#include "primitives/Molecule.hpp"
48		#include "primitives/StuntDouble.hpp"
49	<	#include "utils/OOPSEConstant.hpp"
49	>	#include "utils/PhysicalConstants.hpp"
50		#include "utils/Tuple.hpp"
51
52		#ifndef IS_MPI
#	Line 53 | Line 55
55		#include "math/ParallelRandNumGen.hpp"
56		#endif
57
58	<	/* Remove me after testing*/
57	<	/*
58	<	#include <cstdio>
59	<	#include <iostream>
60	<	*/
61	<	/*End remove me*/
58	>	#define HONKING_LARGE_VALUE 1.0e10
59
60	<	namespace oopse {
60	>	namespace OpenMD {
61
62		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63	<
63	>
64	>	failTrialCount_ = 0;
65	>	failRootCount_ = 0;
66	>
67		int seedValue;
68		Globals * simParams = info->getSimParams();
69
70	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
70	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
71	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
72	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
73	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
74	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
75		stringToEnumMap_["Px"] = rnemdPx;
76		stringToEnumMap_["Py"] = rnemdPy;
77		stringToEnumMap_["Pz"] = rnemdPz;
78		stringToEnumMap_["Unknown"] = rnemdUnknown;
79
80		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
77	–
78	–	std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
81		evaluator_.loadScriptString(rnemdObjectSelection_);
82	<	std::cerr << "done\n";
82	>	seleMan_.setSelectionSet(evaluator_.evaluate());
83	>
84	>	// do some sanity checking
85	>
86	>	int selectionCount = seleMan_.getSelectionCount();
87	>	int nIntegrable = info->getNGlobalIntegrableObjects();
88	>
89	>	if (selectionCount > nIntegrable) {
90	>	sprintf(painCave.errMsg,
91	>	"RNEMD warning: The current RNEMD_objectSelection,\n"
92	>	"\t\t%s\n"
93	>	"\thas resulted in %d selected objects.  However,\n"
94	>	"\tthe total number of integrable objects in the system\n"
95	>	"\tis only %d.  This is almost certainly not what you want\n"
96	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
97	>	"\tselector in the selection script!\n",
98	>	rnemdObjectSelection_.c_str(),
99	>	selectionCount, nIntegrable);
100	>	painCave.isFatal = 0;
101	>	simError();
102	>
103	>	}
104
105	<	const std::string st = simParams->getRNEMD_swapType();
105	>	const std::string st = simParams->getRNEMD_exchangeType();
106
107		std::map<std::string, RNEMDTypeEnum>::iterator i;
108		i = stringToEnumMap_.find(st);
109	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
109	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	>	if (rnemdType_ == rnemdUnknown) {
111	>	std::cerr << "WARNING! RNEMD Type Unknown!\n";
112	>	}
113
114	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
114	>	output3DTemp_ = false;
115	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
116	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
117	>	}
118	>
119	>	#ifdef IS_MPI
120	>	if (worldRank == 0) {
121	>	#endif
122	>
123	>	std::string rnemdFileName;
124	>	switch(rnemdType_) {
125	>	case rnemdKineticSwap :
126	>	case rnemdKineticScale :
127	>	rnemdFileName = "temperature.log";
128	>	break;
129	>	case rnemdPx :
130	>	case rnemdPxScale :
131	>	case rnemdPy :
132	>	case rnemdPyScale :
133	>	rnemdFileName = "momemtum.log";
134	>	break;
135	>	case rnemdPz :
136	>	case rnemdPzScale :
137	>	case rnemdUnknown :
138	>	default :
139	>	rnemdFileName = "rnemd.log";
140	>	break;
141	>	}
142	>	rnemdLog_.open(rnemdFileName.c_str());
143	>
144	>	std::string xTempFileName;
145	>	std::string yTempFileName;
146	>	std::string zTempFileName;
147	>	if (output3DTemp_) {
148	>	xTempFileName = "temperatureX.log";
149	>	yTempFileName = "temperatureY.log";
150	>	zTempFileName = "temperatureZ.log";
151	>	xTempLog_.open(xTempFileName.c_str());
152	>	yTempLog_.open(yTempFileName.c_str());
153	>	zTempLog_.open(zTempFileName.c_str());
154	>	}
155	>
156	>	#ifdef IS_MPI
157	>	}
158	>	#endif
159	>
160	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
161		set_RNEMD_nBins(simParams->getRNEMD_nBins());
162	<	exchangeSum_ = 0.0;
163	<	counter_ = 0; //added by shenyu
164	<	//profile_.open("profile", std::ios::out);
162	>	midBin_ = nBins_ / 2;
163	>	if (simParams->haveRNEMD_binShift()) {
164	>	if (simParams->getRNEMD_binShift()) {
165	>	zShift_ = 0.5 / (RealType)(nBins_);
166	>	} else {
167	>	zShift_ = 0.0;
168	>	}
169	>	} else {
170	>	zShift_ = 0.0;
171	>	}
172	>	//std::cerr << "we have zShift_ = " << zShift_ << "\n";
173	>	//shift slabs by half slab width, might be useful in heterogeneous systems
174	>	//set to 0.0 if not using it; can NOT be used in status output yet
175	>	if (simParams->haveRNEMD_logWidth()) {
176	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
177	>	/*arbitary rnemdLogWidth_ no checking
178	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
179	>	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
180	>	std::cerr << "Automaically set back to default.\n";
181	>	rnemdLogWidth_ = nBins_;
182	>	}*/
183	>	} else {
184	>	set_RNEMD_logWidth(nBins_);
185	>	}
186	>	valueHist_.resize(rnemdLogWidth_, 0.0);
187	>	valueCount_.resize(rnemdLogWidth_, 0);
188	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
189	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
190	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
191	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
192
193	+	set_RNEMD_exchange_total(0.0);
194	+	if (simParams->haveRNEMD_targetFlux()) {
195	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
196	+	} else {
197	+	set_RNEMD_target_flux(0.0);
198	+	}
199	+
200		#ifndef IS_MPI
201		if (simParams->haveSeed()) {
202		seedValue = simParams->getSeed();
#	Line 110 | Line 216 | namespace oopse {
216
217		RNEMD::~RNEMD() {
218		delete randNumGen_;
219	<	//profile_.close();
219	>
220	>	#ifdef IS_MPI
221	>	if (worldRank == 0) {
222	>	#endif
223	>	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
224	>	rnemdLog_.close();
225	>	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
226	>	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
227	>	if (output3DTemp_) {
228	>	xTempLog_.close();
229	>	yTempLog_.close();
230	>	zTempLog_.close();
231	>	}
232	>	#ifdef IS_MPI
233	>	}
234	>	#endif
235		}
236
237		void RNEMD::doSwap() {
117	–	//std::cerr << "in RNEMD!\n";
118	–	//std::cerr << "nBins = " << nBins_ << "\n";
119	–	int midBin = nBins_ / 2;
120	–	//std::cerr << "midBin = " << midBin << "\n";
121	–	//std::cerr << "swapTime = " << swapTime_ << "\n";
122	–	//std::cerr << "swapType = " << rnemdType_ << "\n";
123	–	//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
238
239		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
240		Mat3x3d hmat = currentSnap_->getHmat();
241
128	–	//std::cerr << "hmat = " << hmat << "\n";
129	–
242		seleMan_.setSelectionSet(evaluator_.evaluate());
243
132	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
133	–
244		int selei;
245		StuntDouble* sd;
246		int idx;
#	Line 158 | Line 268 | namespace oopse {
268		// which bin is this stuntdouble in?
269		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
270
271	<	int binNo = int((nBins_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2));
271	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
272
163	–	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
273
274		// if we're in bin 0 or the middleBin
275	<	if (binNo == 0 || binNo == midBin) {
275	>	if (binNo == 0 || binNo == midBin_) {
276
277		RealType mass = sd->getMass();
278		Vector3d vel = sd->getVel();
279		RealType value;
280
281		switch(rnemdType_) {
282	<	case rnemdKinetic :
282	>	case rnemdKineticSwap :
283
284		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
285		vel[2]*vel[2]);
286	<
286	>	/*
287		if (sd->isDirectional()) {
288		Vector3d angMom = sd->getJ();
289		Mat3x3d I = sd->getI();
#	Line 190 | Line 299 | namespace oopse {
299		+ angMom[1]*angMom[1]/I(1, 1)
300		+ angMom[2]*angMom[2]/I(2, 2);
301		}
302	<	}
303	<	value = value * 0.5 / OOPSEConstant::energyConvert;
302	>	} no exchange of angular momenta
303	>	*/
304	>	//make exchangeSum_ comparable between swap & scale
305	>	//temporarily without using energyConvert
306	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
307	>	value *= 0.5;
308		break;
309		case rnemdPx :
310		value = mass * vel[0];
#	Line 202 | Line 315 | namespace oopse {
315		case rnemdPz :
316		value = mass * vel[2];
317		break;
205	–	case rnemdUnknown :
318		default :
319		break;
320		}
#	Line 218 | Line 330 | namespace oopse {
330		min_sd = sd;
331		}
332		}
333	<	} else {
333	>	} else { //midBin_
334		if (!max_found) {
335		max_val = value;
336		max_sd = sd;
#	Line 232 | Line 344 | namespace oopse {
344		}
345		}
346		}
347	<	//std::cerr << "smallest value = " << min_val  << "\n";
348	<	//std::cerr << "largest value = " << max_val << "\n";
347	>
348	>	#ifdef IS_MPI
349	>	int nProc, worldRank;
350	>
351	>	nProc = MPI::COMM_WORLD.Get_size();
352	>	worldRank = MPI::COMM_WORLD.Get_rank();
353	>
354	>	bool my_min_found = min_found;
355	>	bool my_max_found = max_found;
356	>
357	>	// Even if we didn't find a minimum, did someone else? debugging...
358	>	//MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
359	>	//                          1, MPI::BOOL, MPI::LAND);
360	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
361	>	// Even if we didn't find a maximum, did someone else?
362	>	//MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
363	>	//                          1, MPI::BOOL, MPI::LAND);
364	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
365	>	struct {
366	>	RealType val;
367	>	int rank;
368	>	} max_vals, min_vals;
369
370	<	// missing:  swap information in parallel
370	>	if (min_found) {
371	>	if (my_min_found)
372	>	min_vals.val = min_val;
373	>	else
374	>	min_vals.val = HONKING_LARGE_VALUE;
375	>
376	>	min_vals.rank = worldRank;
377	>
378	>	// Who had the minimum?
379	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
380	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
381	>	min_val = min_vals.val;
382	>	}
383	>
384	>	if (max_found) {
385	>	if (my_max_found)
386	>	max_vals.val = max_val;
387	>	else
388	>	max_vals.val = -HONKING_LARGE_VALUE;
389	>
390	>	max_vals.rank = worldRank;
391	>
392	>	// Who had the maximum?
393	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
394	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
395	>	max_val = max_vals.val;
396	>	}
397	>	#endif
398
399		if (max_found && min_found) {
400	<	if (min_val< max_val) {
401	<	Vector3d min_vel = min_sd->getVel();
402	<	Vector3d max_vel = max_sd->getVel();
403	<	RealType temp_vel;
404	<	switch(rnemdType_) {
405	<	case rnemdKinetic :
406	<	min_sd->setVel(max_vel);
407	<	max_sd->setVel(min_vel);
408	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
409	<	Vector3d min_angMom = min_sd->getJ();
410	<	Vector3d max_angMom = max_sd->getJ();
411	<	min_sd->setJ(max_angMom);
412	<	max_sd->setJ(min_angMom);
413	<	}
414	<	break;
415	<	case rnemdPx :
416	<	temp_vel = min_vel.x();
417	<	min_vel.x() = max_vel.x();
418	<	max_vel.x() = temp_vel;
419	<	min_sd->setVel(min_vel);
420	<	max_sd->setVel(max_vel);
421	<	break;
422	<	case rnemdPy :
423	<	temp_vel = min_vel.y();
424	<	min_vel.y() = max_vel.y();
425	<	max_vel.y() = temp_vel;
426	<	min_sd->setVel(min_vel);
427	<	max_sd->setVel(max_vel);
428	<	break;
429	<	case rnemdPz :
430	<	temp_vel = min_vel.z();
431	<	min_vel.z() = max_vel.z();
432	<	max_vel.z() = temp_vel;
433	<	min_sd->setVel(min_vel);
434	<	max_sd->setVel(max_vel);
435	<	break;
436	<	case rnemdUnknown :
437	<	default :
438	<	break;
439	<	}
440	<	exchangeSum_ += max_val - min_val;
400	>	if (min_val < max_val) {
401	>
402	>	#ifdef IS_MPI
403	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
404	>	// I have both maximum and minimum, so proceed like a single
405	>	// processor version:
406	>	#endif
407	>	// objects to be swapped: velocity ONLY
408	>	Vector3d min_vel = min_sd->getVel();
409	>	Vector3d max_vel = max_sd->getVel();
410	>	RealType temp_vel;
411	>
412	>	switch(rnemdType_) {
413	>	case rnemdKineticSwap :
414	>	min_sd->setVel(max_vel);
415	>	max_sd->setVel(min_vel);
416	>	/*
417	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
418	>	Vector3d min_angMom = min_sd->getJ();
419	>	Vector3d max_angMom = max_sd->getJ();
420	>	min_sd->setJ(max_angMom);
421	>	max_sd->setJ(min_angMom);
422	>	} no angular momentum exchange
423	>	*/
424	>	break;
425	>	case rnemdPx :
426	>	temp_vel = min_vel.x();
427	>	min_vel.x() = max_vel.x();
428	>	max_vel.x() = temp_vel;
429	>	min_sd->setVel(min_vel);
430	>	max_sd->setVel(max_vel);
431	>	break;
432	>	case rnemdPy :
433	>	temp_vel = min_vel.y();
434	>	min_vel.y() = max_vel.y();
435	>	max_vel.y() = temp_vel;
436	>	min_sd->setVel(min_vel);
437	>	max_sd->setVel(max_vel);
438	>	break;
439	>	case rnemdPz :
440	>	temp_vel = min_vel.z();
441	>	min_vel.z() = max_vel.z();
442	>	max_vel.z() = temp_vel;
443	>	min_sd->setVel(min_vel);
444	>	max_sd->setVel(max_vel);
445	>	break;
446	>	default :
447	>	break;
448	>	}
449	>	#ifdef IS_MPI
450	>	// the rest of the cases only apply in parallel simulations:
451	>	} else if (max_vals.rank == worldRank) {
452	>	// I had the max, but not the minimum
453	>
454	>	Vector3d min_vel;
455	>	Vector3d max_vel = max_sd->getVel();
456	>	MPI::Status status;
457	>
458	>	// point-to-point swap of the velocity vector
459	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
460	>	min_vals.rank, 0,
461	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
462	>	min_vals.rank, 0, status);
463	>
464	>	switch(rnemdType_) {
465	>	case rnemdKineticSwap :
466	>	max_sd->setVel(min_vel);
467	>	/*
468	>	if (max_sd->isDirectional()) {
469	>	Vector3d min_angMom;
470	>	Vector3d max_angMom = max_sd->getJ();
471	>
472	>	// point-to-point swap of the angular momentum vector
473	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
474	>	MPI::REALTYPE, min_vals.rank, 1,
475	>	min_angMom.getArrayPointer(), 3,
476	>	MPI::REALTYPE, min_vals.rank, 1,
477	>	status);
478	>
479	>	max_sd->setJ(min_angMom);
480	>	} no angular momentum exchange
481	>	*/
482	>	break;
483	>	case rnemdPx :
484	>	max_vel.x() = min_vel.x();
485	>	max_sd->setVel(max_vel);
486	>	break;
487	>	case rnemdPy :
488	>	max_vel.y() = min_vel.y();
489	>	max_sd->setVel(max_vel);
490	>	break;
491	>	case rnemdPz :
492	>	max_vel.z() = min_vel.z();
493	>	max_sd->setVel(max_vel);
494	>	break;
495	>	default :
496	>	break;
497	>	}
498	>	} else if (min_vals.rank == worldRank) {
499	>	// I had the minimum but not the maximum:
500	>
501	>	Vector3d max_vel;
502	>	Vector3d min_vel = min_sd->getVel();
503	>	MPI::Status status;
504	>
505	>	// point-to-point swap of the velocity vector
506	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
507	>	max_vals.rank, 0,
508	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
509	>	max_vals.rank, 0, status);
510	>
511	>	switch(rnemdType_) {
512	>	case rnemdKineticSwap :
513	>	min_sd->setVel(max_vel);
514	>	/*
515	>	if (min_sd->isDirectional()) {
516	>	Vector3d min_angMom = min_sd->getJ();
517	>	Vector3d max_angMom;
518	>
519	>	// point-to-point swap of the angular momentum vector
520	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
521	>	MPI::REALTYPE, max_vals.rank, 1,
522	>	max_angMom.getArrayPointer(), 3,
523	>	MPI::REALTYPE, max_vals.rank, 1,
524	>	status);
525	>
526	>	min_sd->setJ(max_angMom);
527	>	} no angular momentum exchange
528	>	*/
529	>	break;
530	>	case rnemdPx :
531	>	min_vel.x() = max_vel.x();
532	>	min_sd->setVel(min_vel);
533	>	break;
534	>	case rnemdPy :
535	>	min_vel.y() = max_vel.y();
536	>	min_sd->setVel(min_vel);
537	>	break;
538	>	case rnemdPz :
539	>	min_vel.z() = max_vel.z();
540	>	min_sd->setVel(min_vel);
541	>	break;
542	>	default :
543	>	break;
544	>	}
545	>	}
546	>	#endif
547	>	exchangeSum_ += max_val - min_val;
548		} else {
549	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
549	>	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
550	>	failTrialCount_++;
551		}
552		} else {
553	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
553	>	std::cerr << "exchange NOT performed!\n";
554	>	std::cerr << "at least one of the two slabs empty.\n";
555	>	failTrialCount_++;
556		}
557	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
557	>
558		}
559	+
560	+	void RNEMD::doScale() {
561
291	–	void RNEMD::getStatus() {
292	–	//std::cerr << "in RNEMD!\n";
293	–	//std::cerr << "nBins = " << nBins_ << "\n";
294	–	int midBin = nBins_ / 2;
295	–	//std::cerr << "midBin = " << midBin << "\n";
296	–	//std::cerr << "swapTime = " << swapTime_ << "\n";
297	–	//std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
298	–	//std::cerr << "swapType = " << rnemdType_ << "\n";
299	–	//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
300	–
562		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
563		Mat3x3d hmat = currentSnap_->getHmat();
564
304	–	//std::cerr << "hmat = " << hmat << "\n";
305	–
565		seleMan_.setSelectionSet(evaluator_.evaluate());
566
308	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
309	–
567		int selei;
568		StuntDouble* sd;
569		int idx;
313	–	/*
314	–	RealType min_val;
315	–	bool min_found = false;
316	–	StuntDouble* min_sd;
570
571	<	RealType max_val;
572	<	bool max_found = false;
573	<	StuntDouble* max_sd;
571	>	std::vector<StuntDouble*> hotBin, coldBin;
572	>
573	>	RealType Phx = 0.0;
574	>	RealType Phy = 0.0;
575	>	RealType Phz = 0.0;
576	>	RealType Khx = 0.0;
577	>	RealType Khy = 0.0;
578	>	RealType Khz = 0.0;
579	>	RealType Pcx = 0.0;
580	>	RealType Pcy = 0.0;
581	>	RealType Pcz = 0.0;
582	>	RealType Kcx = 0.0;
583	>	RealType Kcy = 0.0;
584	>	RealType Kcz = 0.0;
585	>
586	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
587	>	sd = seleMan_.nextSelected(selei)) {
588	>
589	>	idx = sd->getLocalIndex();
590	>
591	>	Vector3d pos = sd->getPos();
592	>
593	>	// wrap the stuntdouble's position back into the box:
594	>
595	>	if (usePeriodicBoundaryConditions_)
596	>	currentSnap_->wrapVector(pos);
597	>
598	>	// which bin is this stuntdouble in?
599	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
600	>
601	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
602	>
603	>	// if we're in bin 0 or the middleBin
604	>	if (binNo == 0 || binNo == midBin_) {
605	>
606	>	RealType mass = sd->getMass();
607	>	Vector3d vel = sd->getVel();
608	>
609	>	if (binNo == 0) {
610	>	hotBin.push_back(sd);
611	>	Phx += mass * vel.x();
612	>	Phy += mass * vel.y();
613	>	Phz += mass * vel.z();
614	>	Khx += mass * vel.x() * vel.x();
615	>	Khy += mass * vel.y() * vel.y();
616	>	Khz += mass * vel.z() * vel.z();
617	>	} else { //midBin_
618	>	coldBin.push_back(sd);
619	>	Pcx += mass * vel.x();
620	>	Pcy += mass * vel.y();
621	>	Pcz += mass * vel.z();
622	>	Kcx += mass * vel.x() * vel.x();
623	>	Kcy += mass * vel.y() * vel.y();
624	>	Kcz += mass * vel.z() * vel.z();
625	>	}
626	>	}
627	>	}
628	>
629	>	Khx *= 0.5;
630	>	Khy *= 0.5;
631	>	Khz *= 0.5;
632	>	Kcx *= 0.5;
633	>	Kcy *= 0.5;
634	>	Kcz *= 0.5;
635	>
636	>	#ifdef IS_MPI
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
638	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
639	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
640	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
641	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
642	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
643	>
644	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
645	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
646	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
647	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
648	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
649	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
650	>	#endif
651	>
652	>	//use coldBin coeff's
653	>	RealType px = Pcx / Phx;
654	>	RealType py = Pcy / Phy;
655	>	RealType pz = Pcz / Phz;
656	>
657	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
658	>	switch(rnemdType_) {
659	>	case rnemdKineticScale :
660	>	/*used hotBin coeff's & only scale x & y dimensions
661	>	RealType px = Phx / Pcx;
662	>	RealType py = Phy / Pcy;
663	>	a110 = Khy;
664	>	c0 = - Khx - Khy - targetFlux_;
665	>	a000 = Khx;
666	>	a111 = Kcy * py * py
667	>	b11 = -2.0 * Kcy * py * (1.0 + py);
668	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
669	>	b01 = -2.0 * Kcx * px * (1.0 + px);
670	>	a001 = Kcx * px * px;
671		*/
672	<	std::vector<RealType> valueHist;  // keeps track of what's being averaged
673	<	std::vector<int> valueCount; // keeps track of the number of degrees of
674	<	// freedom being averaged
675	<	valueHist.resize(nBins_);
676	<	valueCount.resize(nBins_);
677	<	//do they initialize themselves to zero automatically?
672	>
673	>	//scale all three dimensions, let c_x = c_y
674	>	a000 = Kcx + Kcy;
675	>	a110 = Kcz;
676	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
677	>	a001 = Khx * px * px + Khy * py * py;
678	>	a111 = Khz * pz * pz;
679	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
680	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
681	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
682	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
683	>	break;
684	>	case rnemdPxScale :
685	>	c = 1 - targetFlux_ / Pcx;
686	>	a000 = Kcy;
687	>	a110 = Kcz;
688	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
689	>	a001 = py * py * Khy;
690	>	a111 = pz * pz * Khz;
691	>	b01 = -2.0 * Khy * py * (1.0 + py);
692	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
693	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
694	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
695	>	break;
696	>	case rnemdPyScale :
697	>	c = 1 - targetFlux_ / Pcy;
698	>	a000 = Kcx;
699	>	a110 = Kcz;
700	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
701	>	a001 = px * px * Khx;
702	>	a111 = pz * pz * Khz;
703	>	b01 = -2.0 * Khx * px * (1.0 + px);
704	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
705	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
706	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
707	>	break;
708	>	case rnemdPzScale ://we don't really do this, do we?
709	>	c = 1 - targetFlux_ / Pcz;
710	>	a000 = Kcx;
711	>	a110 = Kcy;
712	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
713	>	a001 = px * px * Khx;
714	>	a111 = py * py * Khy;
715	>	b01 = -2.0 * Khx * px * (1.0 + px);
716	>	b11 = -2.0 * Khy * py * (1.0 + py);
717	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
718	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
719	>	break;
720	>	default :
721	>	break;
722	>	}
723	>
724	>	RealType v1 = a000 * a111 - a001 * a110;
725	>	RealType v2 = a000 * b01;
726	>	RealType v3 = a000 * b11;
727	>	RealType v4 = a000 * c1 - a001 * c0;
728	>	RealType v8 = a110 * b01;
729	>	RealType v10 = - b01 * c0;
730	>
731	>	RealType u0 = v2 * v10 - v4 * v4;
732	>	RealType u1 = -2.0 * v3 * v4;
733	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
734	>	RealType u3 = -2.0 * v1 * v3;
735	>	RealType u4 = - v1 * v1;
736	>	//rescale coefficients
737	>	RealType maxAbs = fabs(u0);
738	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
739	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
740	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
741	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
742	>	u0 /= maxAbs;
743	>	u1 /= maxAbs;
744	>	u2 /= maxAbs;
745	>	u3 /= maxAbs;
746	>	u4 /= maxAbs;
747	>	//max_element(start, end) is also available.
748	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
749	>	poly.setCoefficient(4, u4);
750	>	poly.setCoefficient(3, u3);
751	>	poly.setCoefficient(2, u2);
752	>	poly.setCoefficient(1, u1);
753	>	poly.setCoefficient(0, u0);
754	>	std::vector<RealType> realRoots = poly.FindRealRoots();
755	>
756	>	std::vector<RealType>::iterator ri;
757	>	RealType r1, r2, alpha0;
758	>	std::vector<std::pair<RealType,RealType> > rps;
759	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
760	>	r2 = *ri;
761	>	//check if FindRealRoots() give the right answer
762	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
763	>	sprintf(painCave.errMsg,
764	>	"RNEMD Warning: polynomial solve seems to have an error!");
765	>	painCave.isFatal = 0;
766	>	simError();
767	>	failRootCount_++;
768	>	}
769	>	//might not be useful w/o rescaling coefficients
770	>	alpha0 = -c0 - a110 * r2 * r2;
771	>	if (alpha0 >= 0.0) {
772	>	r1 = sqrt(alpha0 / a000);
773	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
774	>	{ rps.push_back(std::make_pair(r1, r2)); }
775	>	if (r1 > 1e-6) { //r1 non-negative
776	>	r1 = -r1;
777	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
778	>	{ rps.push_back(std::make_pair(r1, r2)); }
779	>	}
780	>	}
781	>	}
782	>	// Consider combininig together the solving pair part w/ the searching
783	>	// best solution part so that we don't need the pairs vector
784	>	if (!rps.empty()) {
785	>	RealType smallestDiff = HONKING_LARGE_VALUE;
786	>	RealType diff;
787	>	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
788	>	std::vector<std::pair<RealType,RealType> >::iterator rpi;
789	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
790	>	r1 = (*rpi).first;
791	>	r2 = (*rpi).second;
792	>	switch(rnemdType_) {
793	>	case rnemdKineticScale :
794	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
795	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
796	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
797	>	break;
798	>	case rnemdPxScale :
799	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
800	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
801	>	break;
802	>	case rnemdPyScale :
803	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
804	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
805	>	break;
806	>	case rnemdPzScale :
807	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
808	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
809	>	default :
810	>	break;
811	>	}
812	>	if (diff < smallestDiff) {
813	>	smallestDiff = diff;
814	>	bestPair = *rpi;
815	>	}
816	>	}
817	>	#ifdef IS_MPI
818	>	if (worldRank == 0) {
819	>	#endif
820	>	std::cerr << "we choose r1 = " << bestPair.first
821	>	<< " and r2 = " << bestPair.second << "\n";
822	>	#ifdef IS_MPI
823	>	}
824	>	#endif
825	>
826	>	RealType x, y, z;
827	>	switch(rnemdType_) {
828	>	case rnemdKineticScale :
829	>	x = bestPair.first;
830	>	y = bestPair.first;
831	>	z = bestPair.second;
832	>	break;
833	>	case rnemdPxScale :
834	>	x = c;
835	>	y = bestPair.first;
836	>	z = bestPair.second;
837	>	break;
838	>	case rnemdPyScale :
839	>	x = bestPair.first;
840	>	y = c;
841	>	z = bestPair.second;
842	>	break;
843	>	case rnemdPzScale :
844	>	x = bestPair.first;
845	>	y = bestPair.second;
846	>	z = c;
847	>	break;
848	>	default :
849	>	break;
850	>	}
851	>	std::vector<StuntDouble*>::iterator sdi;
852	>	Vector3d vel;
853	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
854	>	vel = (*sdi)->getVel();
855	>	vel.x() *= x;
856	>	vel.y() *= y;
857	>	vel.z() *= z;
858	>	(*sdi)->setVel(vel);
859	>	}
860	>	//convert to hotBin coefficient
861	>	x = 1.0 + px * (1.0 - x);
862	>	y = 1.0 + py * (1.0 - y);
863	>	z = 1.0 + pz * (1.0 - z);
864	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
865	>	vel = (*sdi)->getVel();
866	>	vel.x() *= x;
867	>	vel.y() *= y;
868	>	vel.z() *= z;
869	>	(*sdi)->setVel(vel);
870	>	}
871	>	exchangeSum_ += targetFlux_;
872	>	//we may want to check whether the exchange has been successful
873	>	} else {
874	>	std::cerr << "exchange NOT performed!\n";//MPI incompatible
875	>	failTrialCount_++;
876	>	}
877	>
878	>	}
879	>
880	>	void RNEMD::doRNEMD() {
881	>
882	>	switch(rnemdType_) {
883	>	case rnemdKineticScale :
884	>	case rnemdPxScale :
885	>	case rnemdPyScale :
886	>	case rnemdPzScale :
887	>	doScale();
888	>	break;
889	>	case rnemdKineticSwap :
890	>	case rnemdPx :
891	>	case rnemdPy :
892	>	case rnemdPz :
893	>	doSwap();
894	>	break;
895	>	case rnemdUnknown :
896	>	default :
897	>	break;
898	>	}
899	>	}
900	>
901	>	void RNEMD::collectData() {
902	>
903	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
904	>	Mat3x3d hmat = currentSnap_->getHmat();
905	>
906	>	seleMan_.setSelectionSet(evaluator_.evaluate());
907	>
908	>	int selei;
909	>	StuntDouble* sd;
910	>	int idx;
911	>
912	>	// alternative approach, track all molecules instead of only those selected for scaling/swapping
913	>	//SimInfo::MoleculeIterator miter;
914	>	//std::vector<StuntDouble*>::iterator iiter;
915	>	//Molecule* mol;
916	>	//StuntDouble* integrableObject;
917	>	//for (mol = info_->beginMolecule(miter); mol != NULL;
918	>	//     mol = info_->nextMolecule(miter))
919	>	// integrableObject is essentially sd
920	>	//for (integrableObject = mol->beginIntegrableObject(iiter);
921	>	//     integrableObject != NULL;
922	>	//     integrableObject = mol->nextIntegrableObject(iiter))
923		for (sd = seleMan_.beginSelected(selei); sd != NULL;
924		sd = seleMan_.nextSelected(selei)) {
925
#	Line 340 | Line 935 | namespace oopse {
935		// which bin is this stuntdouble in?
936		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
937
938	<	int binNo = int((nBins_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2));
939	<
940	<	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
941	<
938	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
939	>	rnemdLogWidth_;
940	>	/* no symmetrization allowed due to arbitary rnemdLogWidth_ value
941	>	if (rnemdLogWidth_ == midBin_ + 1)
942	>	if (binNo > midBin_)
943	>	binNo = nBins_ - binNo;
944	>	*/
945		RealType mass = sd->getMass();
946		Vector3d vel = sd->getVel();
349	–	//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
947		RealType value;
948	+	RealType xVal, yVal, zVal;
949
950		switch(rnemdType_) {
951	<	case rnemdKinetic :
951	>	case rnemdKineticSwap :
952	>	case rnemdKineticScale :
953
954		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
955		vel[2]*vel[2]);
956
957	<	valueCount[binNo] += 3;
359	<
957	>	valueCount_[binNo] += 3;
958		if (sd->isDirectional()) {
959		Vector3d angMom = sd->getJ();
960		Mat3x3d I = sd->getI();
#	Line 368 | Line 966 | namespace oopse {
966		value += angMom[j] * angMom[j] / I(j, j) +
967		angMom[k] * angMom[k] / I(k, k);
968
969	<	valueCount[binNo] +=2;
969	>	valueCount_[binNo] +=2;
970
971	<	} else {
971	>	} else {
972		value += angMom[0]*angMom[0]/I(0, 0)
973		+ angMom[1]*angMom[1]/I(1, 1)
974		+ angMom[2]*angMom[2]/I(2, 2);
975	<	valueCount[binNo] +=3;
378	<
975	>	valueCount_[binNo] +=3;
976		}
977		}
978	<	//std::cerr <<"this value = " << value << "\n";
979	<	value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
383	<	value *= 2.0 / OOPSEConstant::kb;             // convert to temperature
384	<	//std::cerr <<"this value = " << value << "\n";
978	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
979	>
980		break;
981		case rnemdPx :
982	+	case rnemdPxScale :
983		value = mass * vel[0];
984	<	valueCount[binNo]++;
984	>	valueCount_[binNo]++;
985		break;
986		case rnemdPy :
987	+	case rnemdPyScale :
988		value = mass * vel[1];
989	<	valueCount[binNo]++;
989	>	valueCount_[binNo]++;
990		break;
991		case rnemdPz :
992	<	value = mass * vel[2];
993	<	valueCount[binNo]++;
992	>	case rnemdPzScale :
993	>	value = pos.z(); //temporarily for homogeneous systems ONLY
994	>	valueCount_[binNo]++;
995		break;
996		case rnemdUnknown :
997		default :
998	+	value = 1.0;
999	+	valueCount_[binNo]++;
1000		break;
1001		}
1002	<	//std::cerr << "bin = " << binNo << " value = " << value ;
1003	<	valueHist[binNo] += value;
1004	<	//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
1002	>	valueHist_[binNo] += value;
1003	>
1004	>	if (output3DTemp_) {
1005	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1006	>	/ PhysicalConstants::kb;
1007	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1008	>	/ PhysicalConstants::kb;
1009	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1010	>	/ PhysicalConstants::kb;
1011	>	xTempHist_[binNo] += xVal;
1012	>	yTempHist_[binNo] += yVal;
1013	>	zTempHist_[binNo] += zVal;
1014	>	xyzTempCount_[binNo]++;
1015	>	}
1016		}
406	–
407	–	std::cout << counter_++;
408	–	for (int j = 0; j < nBins_; j++)
409	–	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
410	–	std::cout << "\n";
1017		}
1018	+
1019	+	void RNEMD::getStarted() {
1020	+	collectData();
1021	+	/* now should be able to output profile in step 0, but might not be useful
1022	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1023	+	Stats& stat = currentSnap_->statData;
1024	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1025	+	*/
1026	+	getStatus();
1027	+	}
1028	+
1029	+	void RNEMD::getStatus() {
1030	+
1031	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1032	+	Stats& stat = currentSnap_->statData;
1033	+	RealType time = currentSnap_->getTime();
1034	+
1035	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1036	+	//or to be more meaningful, define another item as exchangeSum_ / time
1037	+	int j;
1038	+
1039	+	#ifdef IS_MPI
1040	+
1041	+	// all processors have the same number of bins, and STL vectors pack their
1042	+	// arrays, so in theory, this should be safe:
1043	+
1044	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1045	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1046	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1047	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1048	+	if (output3DTemp_) {
1049	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1050	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1051	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1052	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1053	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1054	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1055	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1056	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1057	+	}
1058	+	// If we're the root node, should we print out the results
1059	+	int worldRank = MPI::COMM_WORLD.Get_rank();
1060	+	if (worldRank == 0) {
1061	+	#endif
1062	+	rnemdLog_ << time;
1063	+	for (j = 0; j < rnemdLogWidth_; j++) {
1064	+	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1065	+	}
1066	+	rnemdLog_ << "\n";
1067	+	if (output3DTemp_) {
1068	+	xTempLog_ << time;
1069	+	for (j = 0; j < rnemdLogWidth_; j++) {
1070	+	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1071	+	}
1072	+	xTempLog_ << "\n";
1073	+	yTempLog_ << time;
1074	+	for (j = 0; j < rnemdLogWidth_; j++) {
1075	+	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1076	+	}
1077	+	yTempLog_ << "\n";
1078	+	zTempLog_ << time;
1079	+	for (j = 0; j < rnemdLogWidth_; j++) {
1080	+	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1081	+	}
1082	+	zTempLog_ << "\n";
1083	+	}
1084	+	#ifdef IS_MPI
1085	+	}
1086	+	#endif
1087	+	for (j = 0; j < rnemdLogWidth_; j++) {
1088	+	valueCount_[j] = 0;
1089	+	valueHist_[j] = 0.0;
1090	+	}
1091	+	if (output3DTemp_)
1092	+	for (j = 0; j < rnemdLogWidth_; j++) {
1093	+	xTempHist_[j] = 0.0;
1094	+	yTempHist_[j] = 0.0;
1095	+	zTempHist_[j] = 0.0;
1096	+	xyzTempCount_[j] = 0;
1097	+	}
1098	+	}
1099		}

Comparing trunk/src/integrators/RNEMD.cpp (property svn:keywords):
Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
Revision 1560 by skuang, Wed May 11 17:55:32 2011 UTC

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