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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 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
53		#include "math/SeqRandNumGen.hpp"
54		#else
55	+	#include <mpi.h>
56		#include "math/ParallelRandNumGen.hpp"
57		#endif
58
59	+	#define HONKING_LARGE_VALUE 1.0e10
60
61	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
65	<
64	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
65	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
66	>
67	>	failTrialCount_ = 0;
68	>	failRootCount_ = 0;
69	>
70		int seedValue;
71		Globals * simParams = info->getSimParams();
72
73	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
73	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
74	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
75	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
76	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
77	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
78		stringToEnumMap_["Px"] = rnemdPx;
79		stringToEnumMap_["Py"] = rnemdPy;
80		stringToEnumMap_["Pz"] = rnemdPz;
#	Line 71 | Line 84 | namespace oopse {
84		evaluator_.loadScriptString(rnemdObjectSelection_);
85		seleMan_.setSelectionSet(evaluator_.evaluate());
86
74	–
87		// do some sanity checking
88
89		int selectionCount = seleMan_.getSelectionCount();
#	Line 79 | Line 91 | namespace oopse {
91
92		if (selectionCount > nIntegrable) {
93		sprintf(painCave.errMsg,
94	<	"RNEMD warning: The current RNEMD_objectSelection,\n"
94	>	"RNEMD: The current RNEMD_objectSelection,\n"
95		"\t\t%s\n"
96		"\thas resulted in %d selected objects.  However,\n"
97		"\tthe total number of integrable objects in the system\n"
#	Line 89 | Line 101 | namespace oopse {
101		rnemdObjectSelection_.c_str(),
102		selectionCount, nIntegrable);
103		painCave.isFatal = 0;
104	+	painCave.severity = OPENMD_WARNING;
105		simError();
93	–
106		}
107
108	<	const std::string st = simParams->getRNEMD_swapType();
108	>	const string st = simParams->getRNEMD_exchangeType();
109
110	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
110	>	map<string, RNEMDTypeEnum>::iterator i;
111		i = stringToEnumMap_.find(st);
112	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
112	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
113	>	if (rnemdType_ == rnemdUnknown) {
114	>	sprintf(painCave.errMsg,
115	>	"RNEMD: The current RNEMD_exchangeType,\n"
116	>	"\t\t%s\n"
117	>	"\tis not one of the recognized exchange types.\n",
118	>	st.c_str());
119	>	painCave.isFatal = 1;
120	>	painCave.severity = OPENMD_ERROR;
121	>	simError();
122	>	}
123	>
124	>	output3DTemp_ = false;
125	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
126	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
127	>	}
128
129	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
129	>	#ifdef IS_MPI
130	>	if (worldRank == 0) {
131	>	#endif
132	>
133	>	string rnemdFileName;
134	>	switch(rnemdType_) {
135	>	case rnemdKineticSwap :
136	>	case rnemdKineticScale :
137	>	rnemdFileName = "temperature.log";
138	>	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;
151	>	}
152	>	rnemdLog_.open(rnemdFileName.c_str());
153	>
154	>	string xTempFileName;
155	>	string yTempFileName;
156	>	string zTempFileName;
157	>	if (output3DTemp_) {
158	>	xTempFileName = "temperatureX.log";
159	>	yTempFileName = "temperatureY.log";
160	>	zTempFileName = "temperatureZ.log";
161	>	xTempLog_.open(xTempFileName.c_str());
162	>	yTempLog_.open(yTempFileName.c_str());
163	>	zTempLog_.open(zTempFileName.c_str());
164	>	}
165	>
166	>	#ifdef IS_MPI
167	>	}
168	>	#endif
169	>
170	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
171		set_RNEMD_nBins(simParams->getRNEMD_nBins());
172	<	exchangeSum_ = 0.0;
173	<	counter_ = 0; //added by shenyu
172	>	midBin_ = nBins_ / 2;
173	>	if (simParams->haveRNEMD_binShift()) {
174	>	if (simParams->getRNEMD_binShift()) {
175	>	zShift_ = 0.5 / (RealType)(nBins_);
176	>	} else {
177	>	zShift_ = 0.0;
178	>	}
179	>	} else {
180	>	zShift_ = 0.0;
181	>	}
182	>	//cerr << "we have zShift_ = " << zShift_ << "\n";
183	>	//shift slabs by half slab width, might be useful in heterogeneous systems
184	>	//set to 0.0 if not using it; can NOT be used in status output yet
185	>	if (simParams->haveRNEMD_logWidth()) {
186	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
187	>	/*arbitary rnemdLogWidth_ no checking
188	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
189	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
190	>	cerr << "Automaically set back to default.\n";
191	>	rnemdLogWidth_ = nBins_;
192	>	}*/
193	>	} else {
194	>	set_RNEMD_logWidth(nBins_);
195	>	}
196	>	valueHist_.resize(rnemdLogWidth_, 0.0);
197	>	valueCount_.resize(rnemdLogWidth_, 0);
198	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
199	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
200	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
201	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
202
203	+	set_RNEMD_exchange_total(0.0);
204	+	if (simParams->haveRNEMD_targetFlux()) {
205	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
206	+	} else {
207	+	set_RNEMD_target_flux(0.0);
208	+	}
209	+
210		#ifndef IS_MPI
211		if (simParams->haveSeed()) {
212		seedValue = simParams->getSeed();
#	Line 123 | Line 226 | namespace oopse {
226
227		RNEMD::~RNEMD() {
228		delete randNumGen_;
229	+
230	+	#ifdef IS_MPI
231	+	if (worldRank == 0) {
232	+	#endif
233	+
234	+	sprintf(painCave.errMsg,
235	+	"RNEMD: total failed trials: %d\n",
236	+	failTrialCount_);
237	+	painCave.isFatal = 0;
238	+	painCave.severity = OPENMD_INFO;
239	+	simError();
240	+
241	+	rnemdLog_.close();
242	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
243	+	sprintf(painCave.errMsg,
244	+	"RNEMD: total root-checking warnings: %d\n",
245	+	failRootCount_);
246	+	painCave.isFatal = 0;
247	+	painCave.severity = OPENMD_INFO;
248	+	simError();
249	+	}
250	+	if (output3DTemp_) {
251	+	xTempLog_.close();
252	+	yTempLog_.close();
253	+	zTempLog_.close();
254	+	}
255	+	#ifdef IS_MPI
256	+	}
257	+	#endif
258		}
259
260		void RNEMD::doSwap() {
129	–	int midBin = nBins_ / 2;
261
262		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
263		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 160 | Line 291 | namespace oopse {
291		// which bin is this stuntdouble in?
292		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
293
294	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
294	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
295
296
297		// if we're in bin 0 or the middleBin
298	<	if (binNo == 0 || binNo == midBin) {
298	>	if (binNo == 0 || binNo == midBin_) {
299
300		RealType mass = sd->getMass();
301		Vector3d vel = sd->getVel();
302		RealType value;
303
304		switch(rnemdType_) {
305	<	case rnemdKinetic :
305	>	case rnemdKineticSwap :
306
307		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
308		vel[2]*vel[2]);
309	<	if (sd->isDirectional()) {
309	>	/*
310	>	if (sd->isDirectional()) {
311		Vector3d angMom = sd->getJ();
312		Mat3x3d I = sd->getI();
313
314		if (sd->isLinear()) {
315	<	int i = sd->linearAxis();
316	<	int j = (i + 1) % 3;
317	<	int k = (i + 2) % 3;
318	<	value += angMom[j] * angMom[j] / I(j, j) +
319	<	angMom[k] * angMom[k] / I(k, k);
315	>	int i = sd->linearAxis();
316	>	int j = (i + 1) % 3;
317	>	int k = (i + 2) % 3;
318	>	value += angMom[j] * angMom[j] / I(j, j) +
319	>	angMom[k] * angMom[k] / I(k, k);
320		} else {
321	<	value += angMom[0]*angMom[0]/I(0, 0)
322	<	+ angMom[1]*angMom[1]/I(1, 1)
323	<	+ angMom[2]*angMom[2]/I(2, 2);
321	>	value += angMom[0]*angMom[0]/I(0, 0)
322	>	+ angMom[1]*angMom[1]/I(1, 1)
323	>	+ angMom[2]*angMom[2]/I(2, 2);
324		}
325	<	}
326	<	value = value * 0.5 / OOPSEConstant::energyConvert;
325	>	} no exchange of angular momenta
326	>	*/
327	>	//make exchangeSum_ comparable between swap & scale
328	>	//temporarily without using energyConvert
329	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
330	>	value *= 0.5;
331		break;
332		case rnemdPx :
333		value = mass * vel[0];
#	Line 202 | Line 338 | namespace oopse {
338		case rnemdPz :
339		value = mass * vel[2];
340		break;
205	–	case rnemdUnknown :
341		default :
342		break;
343		}
#	Line 218 | Line 353 | namespace oopse {
353		min_sd = sd;
354		}
355		}
356	<	} else {
356	>	} else { //midBin_
357		if (!max_found) {
358		max_val = value;
359		max_sd = sd;
#	Line 233 | Line 368 | namespace oopse {
368		}
369		}
370
371	<	// missing:  swap information in parallel
371	>	#ifdef IS_MPI
372	>	int nProc, worldRank;
373
374	<	if (max_found && min_found) {
375	<	if (min_val< max_val) {
374	>	nProc = MPI::COMM_WORLD.Get_size();
375	>	worldRank = MPI::COMM_WORLD.Get_rank();
376
377	<	Vector3d min_vel = min_sd->getVel();
378	<	Vector3d max_vel = max_sd->getVel();
243	<	RealType temp_vel;
377	>	bool my_min_found = min_found;
378	>	bool my_max_found = max_found;
379
380	<	switch(rnemdType_) {
381	<	case rnemdKinetic :
382	<	min_sd->setVel(max_vel);
383	<	max_sd->setVel(min_vel);
384	<
385	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
386	<	Vector3d min_angMom = min_sd->getJ();
387	<	Vector3d max_angMom = max_sd->getJ();
388	<	min_sd->setJ(max_angMom);
389	<	max_sd->setJ(min_angMom);
380	>	// Even if we didn't find a minimum, did someone else?
381	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
382	>	// Even if we didn't find a maximum, did someone else?
383	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
384	>	struct {
385	>	RealType val;
386	>	int rank;
387	>	} max_vals, min_vals;
388	>
389	>	if (min_found) {
390	>	if (my_min_found)
391	>	min_vals.val = min_val;
392	>	else
393	>	min_vals.val = HONKING_LARGE_VALUE;
394	>
395	>	min_vals.rank = worldRank;
396	>
397	>	// Who had the minimum?
398	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
399	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
400	>	min_val = min_vals.val;
401	>	}
402	>
403	>	if (max_found) {
404	>	if (my_max_found)
405	>	max_vals.val = max_val;
406	>	else
407	>	max_vals.val = -HONKING_LARGE_VALUE;
408	>
409	>	max_vals.rank = worldRank;
410	>
411	>	// Who had the maximum?
412	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
413	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
414	>	max_val = max_vals.val;
415	>	}
416	>	#endif
417	>
418	>	if (max_found && min_found) {
419	>	if (min_val < max_val) {
420	>
421	>	#ifdef IS_MPI
422	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
423	>	// I have both maximum and minimum, so proceed like a single
424	>	// processor version:
425	>	#endif
426	>	// objects to be swapped: velocity ONLY
427	>	Vector3d min_vel = min_sd->getVel();
428	>	Vector3d max_vel = max_sd->getVel();
429	>	RealType temp_vel;
430	>
431	>	switch(rnemdType_) {
432	>	case rnemdKineticSwap :
433	>	min_sd->setVel(max_vel);
434	>	max_sd->setVel(min_vel);
435	>	/*
436	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
437	>	Vector3d min_angMom = min_sd->getJ();
438	>	Vector3d max_angMom = max_sd->getJ();
439	>	min_sd->setJ(max_angMom);
440	>	max_sd->setJ(min_angMom);
441	>	} no angular momentum exchange
442	>	*/
443	>	break;
444	>	case rnemdPx :
445	>	temp_vel = min_vel.x();
446	>	min_vel.x() = max_vel.x();
447	>	max_vel.x() = temp_vel;
448	>	min_sd->setVel(min_vel);
449	>	max_sd->setVel(max_vel);
450	>	break;
451	>	case rnemdPy :
452	>	temp_vel = min_vel.y();
453	>	min_vel.y() = max_vel.y();
454	>	max_vel.y() = temp_vel;
455	>	min_sd->setVel(min_vel);
456	>	max_sd->setVel(max_vel);
457	>	break;
458	>	case rnemdPz :
459	>	temp_vel = min_vel.z();
460	>	min_vel.z() = max_vel.z();
461	>	max_vel.z() = temp_vel;
462	>	min_sd->setVel(min_vel);
463	>	max_sd->setVel(max_vel);
464	>	break;
465	>	default :
466	>	break;
467		}
468	<	break;
469	<	case rnemdPx :
470	<	temp_vel = min_vel.x();
471	<	min_vel.x() = max_vel.x();
472	<	max_vel.x() = temp_vel;
473	<	min_sd->setVel(min_vel);
474	<	max_sd->setVel(max_vel);
475	<	break;
476	<	case rnemdPy :
477	<	temp_vel = min_vel.y();
478	<	min_vel.y() = max_vel.y();
479	<	max_vel.y() = temp_vel;
480	<	min_sd->setVel(min_vel);
481	<	max_sd->setVel(max_vel);
482	<	break;
483	<	case rnemdPz :
484	<	temp_vel = min_vel.z();
485	<	min_vel.z() = max_vel.z();
486	<	max_vel.z() = temp_vel;
487	<	min_sd->setVel(min_vel);
488	<	max_sd->setVel(max_vel);
489	<	break;
490	<	case rnemdUnknown :
491	<	default :
492	<	break;
468	>	#ifdef IS_MPI
469	>	// the rest of the cases only apply in parallel simulations:
470	>	} else if (max_vals.rank == worldRank) {
471	>	// I had the max, but not the minimum
472	>
473	>	Vector3d min_vel;
474	>	Vector3d max_vel = max_sd->getVel();
475	>	MPI::Status status;
476	>
477	>	// point-to-point swap of the velocity vector
478	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
479	>	min_vals.rank, 0,
480	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
481	>	min_vals.rank, 0, status);
482	>
483	>	switch(rnemdType_) {
484	>	case rnemdKineticSwap :
485	>	max_sd->setVel(min_vel);
486	>	//no angular momentum exchange for now
487	>	/*
488	>	if (max_sd->isDirectional()) {
489	>	Vector3d min_angMom;
490	>	Vector3d max_angMom = max_sd->getJ();
491	>
492	>	// point-to-point swap of the angular momentum vector
493	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
494	>	MPI::REALTYPE, min_vals.rank, 1,
495	>	min_angMom.getArrayPointer(), 3,
496	>	MPI::REALTYPE, min_vals.rank, 1,
497	>	status);
498	>
499	>	max_sd->setJ(min_angMom);
500	>	}
501	>	*/
502	>	break;
503	>	case rnemdPx :
504	>	max_vel.x() = min_vel.x();
505	>	max_sd->setVel(max_vel);
506	>	break;
507	>	case rnemdPy :
508	>	max_vel.y() = min_vel.y();
509	>	max_sd->setVel(max_vel);
510	>	break;
511	>	case rnemdPz :
512	>	max_vel.z() = min_vel.z();
513	>	max_sd->setVel(max_vel);
514	>	break;
515	>	default :
516	>	break;
517	>	}
518	>	} else if (min_vals.rank == worldRank) {
519	>	// I had the minimum but not the maximum:
520	>
521	>	Vector3d max_vel;
522	>	Vector3d min_vel = min_sd->getVel();
523	>	MPI::Status status;
524	>
525	>	// point-to-point swap of the velocity vector
526	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
527	>	max_vals.rank, 0,
528	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
529	>	max_vals.rank, 0, status);
530	>
531	>	switch(rnemdType_) {
532	>	case rnemdKineticSwap :
533	>	min_sd->setVel(max_vel);
534	>	// no angular momentum exchange for now
535	>	/*
536	>	if (min_sd->isDirectional()) {
537	>	Vector3d min_angMom = min_sd->getJ();
538	>	Vector3d max_angMom;
539	>
540	>	// point-to-point swap of the angular momentum vector
541	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
542	>	MPI::REALTYPE, max_vals.rank, 1,
543	>	max_angMom.getArrayPointer(), 3,
544	>	MPI::REALTYPE, max_vals.rank, 1,
545	>	status);
546	>
547	>	min_sd->setJ(max_angMom);
548	>	}
549	>	*/
550	>	break;
551	>	case rnemdPx :
552	>	min_vel.x() = max_vel.x();
553	>	min_sd->setVel(min_vel);
554	>	break;
555	>	case rnemdPy :
556	>	min_vel.y() = max_vel.y();
557	>	min_sd->setVel(min_vel);
558	>	break;
559	>	case rnemdPz :
560	>	min_vel.z() = max_vel.z();
561	>	min_sd->setVel(min_vel);
562	>	break;
563	>	default :
564	>	break;
565	>	}
566	>	}
567	>	#endif
568	>	exchangeSum_ += max_val - min_val;
569	>	} else {
570	>	sprintf(painCave.errMsg,
571	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
572	>	painCave.isFatal = 0;
573	>	painCave.severity = OPENMD_INFO;
574	>	simError();
575	>	failTrialCount_++;
576	>	}
577	>	} else {
578	>	sprintf(painCave.errMsg,
579	>	"RNEMD: exchange NOT performed because at least one\n"
580	>	"\tof the two slabs is empty\n");
581	>	painCave.isFatal = 0;
582	>	painCave.severity = OPENMD_INFO;
583	>	simError();
584	>	failTrialCount_++;
585	>	}
586	>
587	>	}
588	>
589	>	void RNEMD::doScale() {
590	>
591	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
592	>	Mat3x3d hmat = currentSnap_->getHmat();
593	>
594	>	seleMan_.setSelectionSet(evaluator_.evaluate());
595	>
596	>	int selei;
597	>	StuntDouble* sd;
598	>	int idx;
599	>
600	>	vector<StuntDouble*> hotBin, coldBin;
601	>
602	>	RealType Phx = 0.0;
603	>	RealType Phy = 0.0;
604	>	RealType Phz = 0.0;
605	>	RealType Khx = 0.0;
606	>	RealType Khy = 0.0;
607	>	RealType Khz = 0.0;
608	>	RealType Pcx = 0.0;
609	>	RealType Pcy = 0.0;
610	>	RealType Pcz = 0.0;
611	>	RealType Kcx = 0.0;
612	>	RealType Kcy = 0.0;
613	>	RealType Kcz = 0.0;
614	>
615	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
616	>	sd = seleMan_.nextSelected(selei)) {
617	>
618	>	idx = sd->getLocalIndex();
619	>
620	>	Vector3d pos = sd->getPos();
621	>
622	>	// wrap the stuntdouble's position back into the box:
623	>
624	>	if (usePeriodicBoundaryConditions_)
625	>	currentSnap_->wrapVector(pos);
626	>
627	>	// which bin is this stuntdouble in?
628	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
629	>
630	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
631	>
632	>	// if we're in bin 0 or the middleBin
633	>	if (binNo == 0 || binNo == midBin_) {
634	>
635	>	RealType mass = sd->getMass();
636	>	Vector3d vel = sd->getVel();
637	>
638	>	if (binNo == 0) {
639	>	hotBin.push_back(sd);
640	>	Phx += mass * vel.x();
641	>	Phy += mass * vel.y();
642	>	Phz += mass * vel.z();
643	>	Khx += mass * vel.x() * vel.x();
644	>	Khy += mass * vel.y() * vel.y();
645	>	Khz += mass * vel.z() * vel.z();
646	>	} else { //midBin_
647	>	coldBin.push_back(sd);
648	>	Pcx += mass * vel.x();
649	>	Pcy += mass * vel.y();
650	>	Pcz += mass * vel.z();
651	>	Kcx += mass * vel.x() * vel.x();
652	>	Kcy += mass * vel.y() * vel.y();
653	>	Kcz += mass * vel.z() * vel.z();
654		}
655	<	exchangeSum_ += max_val - min_val;
656	<	} else {
657	<	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
655	>	}
656	>	}
657	>
658	>	Khx *= 0.5;
659	>	Khy *= 0.5;
660	>	Khz *= 0.5;
661	>	Kcx *= 0.5;
662	>	Kcy *= 0.5;
663	>	Kcz *= 0.5;
664	>
665	>	#ifdef IS_MPI
666	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
667	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
668	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
669	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
670	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
671	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
672	>
673	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
674	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
675	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
676	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
677	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
678	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
679	>	#endif
680	>
681	>	//use coldBin coeff's
682	>	RealType px = Pcx / Phx;
683	>	RealType py = Pcy / Phy;
684	>	RealType pz = Pcz / Phz;
685	>
686	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
687	>	switch(rnemdType_) {
688	>	case rnemdKineticScale :
689	>	// used hotBin coeff's & only scale x & y dimensions
690	>	/*
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	>	}
752	>
753	>	RealType v1 = a000 * a111 - a001 * a110;
754	>	RealType v2 = a000 * b01;
755	>	RealType v3 = a000 * b11;
756	>	RealType v4 = a000 * c1 - a001 * c0;
757	>	RealType v8 = a110 * b01;
758	>	RealType v10 = - b01 * c0;
759	>
760	>	RealType u0 = v2 * v10 - v4 * v4;
761	>	RealType u1 = -2.0 * v3 * v4;
762	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
763	>	RealType u3 = -2.0 * v1 * v3;
764	>	RealType u4 = - v1 * v1;
765	>	//rescale coefficients
766	>	RealType maxAbs = fabs(u0);
767	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
768	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
769	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
770	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
771	>	u0 /= maxAbs;
772	>	u1 /= maxAbs;
773	>	u2 /= maxAbs;
774	>	u3 /= maxAbs;
775	>	u4 /= maxAbs;
776	>	//max_element(start, end) is also available.
777	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
778	>	poly.setCoefficient(4, u4);
779	>	poly.setCoefficient(3, u3);
780	>	poly.setCoefficient(2, u2);
781	>	poly.setCoefficient(1, u1);
782	>	poly.setCoefficient(0, u0);
783	>	vector<RealType> realRoots = poly.FindRealRoots();
784	>
785	>	vector<RealType>::iterator ri;
786	>	RealType r1, r2, alpha0;
787	>	vector<pair<RealType,RealType> > rps;
788	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
789	>	r2 = *ri;
790	>	//check if FindRealRoots() give the right answer
791	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
792	>	sprintf(painCave.errMsg,
793	>	"RNEMD Warning: polynomial solve seems to have an error!");
794	>	painCave.isFatal = 0;
795	>	simError();
796	>	failRootCount_++;
797	>	}
798	>	//might not be useful w/o rescaling coefficients
799	>	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;
860	>	switch(rnemdType_) {
861	>	case rnemdKineticScale :
862	>	x = bestPair.first;
863	>	y = bestPair.first;
864	>	z = bestPair.second;
865	>	break;
866	>	case rnemdPxScale :
867	>	x = c;
868	>	y = bestPair.first;
869	>	z = bestPair.second;
870	>	break;
871	>	case rnemdPyScale :
872	>	x = bestPair.first;
873	>	y = c;
874	>	z = bestPair.second;
875	>	break;
876	>	case rnemdPzScale :
877	>	x = bestPair.first;
878	>	y = bestPair.second;
879	>	z = c;
880	>	break;
881	>	default :
882	>	break;
883		}
884	+	vector<StuntDouble*>::iterator sdi;
885	+	Vector3d vel;
886	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
887	+	vel = (*sdi)->getVel();
888	+	vel.x() *= x;
889	+	vel.y() *= y;
890	+	vel.z() *= z;
891	+	(*sdi)->setVel(vel);
892	+	}
893	+	//convert to hotBin coefficient
894	+	x = 1.0 + px * (1.0 - x);
895	+	y = 1.0 + py * (1.0 - y);
896	+	z = 1.0 + pz * (1.0 - z);
897	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
898	+	vel = (*sdi)->getVel();
899	+	vel.x() *= x;
900	+	vel.y() *= y;
901	+	vel.z() *= z;
902	+	(*sdi)->setVel(vel);
903	+	}
904	+	exchangeSum_ += targetFlux_;
905	+	//we may want to check whether the exchange has been successful
906		} else {
907	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
907	>	sprintf(painCave.errMsg,
908	>	"RNEMD: exchange NOT performed!\n");
909	>	painCave.isFatal = 0;
910	>	painCave.severity = OPENMD_INFO;
911	>	simError();
912	>	failTrialCount_++;
913		}
914	+
915		}
916
917	<	void RNEMD::getStatus() {
917	>	void RNEMD::doRNEMD() {
918
919	+	switch(rnemdType_) {
920	+	case rnemdKineticScale :
921	+	case rnemdPxScale :
922	+	case rnemdPyScale :
923	+	case rnemdPzScale :
924	+	doScale();
925	+	break;
926	+	case rnemdKineticSwap :
927	+	case rnemdPx :
928	+	case rnemdPy :
929	+	case rnemdPz :
930	+	doSwap();
931	+	break;
932	+	case rnemdUnknown :
933	+	default :
934	+	break;
935	+	}
936	+	}
937	+
938	+	void RNEMD::collectData() {
939	+
940		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
941		Mat3x3d hmat = currentSnap_->getHmat();
295	–	Stats& stat = currentSnap_->statData;
942
297	–	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
298	–
943		seleMan_.setSelectionSet(evaluator_.evaluate());
944
945		int selei;
946		StuntDouble* sd;
947		int idx;
948
949	<	std::vector<RealType> valueHist;  // keeps track of what's being averaged
950	<	std::vector<int> valueCount; // keeps track of the number of degrees of
951	<	// freedom being averaged
952	<	valueHist.resize(nBins_);
953	<	valueCount.resize(nBins_);
954	<	//do they initialize themselves to zero automatically?
949	>	// alternative approach, track all molecules instead of only those
950	>	// selected for scaling/swapping:
951	>	/*
952	>	SimInfo::MoleculeIterator miter;
953	>	vector<StuntDouble*>::iterator iiter;
954	>	Molecule* mol;
955	>	StuntDouble* integrableObject;
956	>	for (mol = info_->beginMolecule(miter); mol != NULL;
957	>	mol = info_->nextMolecule(miter))
958	>	integrableObject is essentially sd
959	>	for (integrableObject = mol->beginIntegrableObject(iiter);
960	>	integrableObject != NULL;
961	>	integrableObject = mol->nextIntegrableObject(iiter))
962	>	*/
963		for (sd = seleMan_.beginSelected(selei); sd != NULL;
964		sd = seleMan_.nextSelected(selei)) {
965
#	Line 323 | Line 975 | namespace oopse {
975		// which bin is this stuntdouble in?
976		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
977
978	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
979	<
980	<	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
981	<
978	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
979	>	rnemdLogWidth_;
980	>	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
981	>	/*
982	>	if (rnemdLogWidth_ == midBin_ + 1)
983	>	if (binNo > midBin_)
984	>	binNo = nBins_ - binNo;
985	>	*/
986		RealType mass = sd->getMass();
987		Vector3d vel = sd->getVel();
332	–	//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
988		RealType value;
989	+	RealType xVal, yVal, zVal;
990
991		switch(rnemdType_) {
992	<	case rnemdKinetic :
992	>	case rnemdKineticSwap :
993	>	case rnemdKineticScale :
994
995	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
339	<	vel[2]*vel[2]);
995	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
996
997	<	valueCount[binNo] += 3;
342	<	//std::cerr <<"starting value = " << value << "\n";
997	>	valueCount_[binNo] += 3;
998		if (sd->isDirectional()) {
344	–	//std::cerr << "angMom calculated.\n";
999		Vector3d angMom = sd->getJ();
346	–	//std::cerr << "current angMom: " << angMom << "\n";
1000		Mat3x3d I = sd->getI();
1001
1002		if (sd->isLinear()) {
#	Line 352 | Line 1005 | namespace oopse {
1005		int k = (i + 2) % 3;
1006		value += angMom[j] * angMom[j] / I(j, j) +
1007		angMom[k] * angMom[k] / I(k, k);
1008	<
1009	<	valueCount[binNo] +=2;
1010	<
1008	>
1009	>	valueCount_[binNo] +=2;
1010	>
1011		} else {
359	–	//std::cerr << "non-linear molecule.\n";
1012		value += angMom[0]*angMom[0]/I(0, 0)
1013		+ angMom[1]*angMom[1]/I(1, 1)
1014		+ angMom[2]*angMom[2]/I(2, 2);
1015	<	valueCount[binNo] +=3;
364	<
1015	>	valueCount_[binNo] +=3;
1016		}
1017		}
1018	<	//std::cerr <<"total value = " << value << "\n";
1019	<	//value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
369	<	//value *= 2.0 / OOPSEConstant::kb;            // convert to temperature
370	<	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
371	<	//std::cerr <<"value = " << value << "\n";
1018	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1019	>
1020		break;
1021		case rnemdPx :
1022	+	case rnemdPxScale :
1023		value = mass * vel[0];
1024	<	valueCount[binNo]++;
1024	>	valueCount_[binNo]++;
1025		break;
1026		case rnemdPy :
1027	+	case rnemdPyScale :
1028		value = mass * vel[1];
1029	<	valueCount[binNo]++;
1029	>	valueCount_[binNo]++;
1030		break;
1031		case rnemdPz :
1032	<	value = mass * vel[2];
1033	<	valueCount[binNo]++;
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;
1041		}
1042	<	//std::cerr << "bin = " << binNo << " value = " << value ;
1043	<	valueHist[binNo] += value;
1044	<	//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
1042	>	valueHist_[binNo] += value;
1043	>
1044	>	if (output3DTemp_) {
1045	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1046	>	/ PhysicalConstants::kb;
1047	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1048	>	/ PhysicalConstants::kb;
1049	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1050	>	/ PhysicalConstants::kb;
1051	>	xTempHist_[binNo] += xVal;
1052	>	yTempHist_[binNo] += yVal;
1053	>	zTempHist_[binNo] += zVal;
1054	>	xyzTempCount_[binNo]++;
1055	>	}
1056		}
393	–
394	–	std::cout << counter_++;
395	–	for (int j = 0; j < nBins_; j++)
396	–	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
397	–	std::cout << "\n";
1057		}
1058	+
1059	+	void RNEMD::getStarted() {
1060	+	collectData();
1061	+	/* now should be able to output profile in step 0, but might not be useful
1062	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1063	+	Stats& stat = currentSnap_->statData;
1064	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1065	+	*/
1066	+	getStatus();
1067	+	}
1068	+
1069	+	void RNEMD::getStatus() {
1070	+
1071	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1072	+	Stats& stat = currentSnap_->statData;
1073	+	RealType time = currentSnap_->getTime();
1074	+
1075	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1076	+	//or to be more meaningful, define another item as exchangeSum_ / time
1077	+	int j;
1078	+
1079	+	#ifdef IS_MPI
1080	+
1081	+	// all processors have the same number of bins, and STL vectors pack their
1082	+	// arrays, so in theory, this should be safe:
1083	+
1084	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1085	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1086	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1087	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1088	+	if (output3DTemp_) {
1089	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1090	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1091	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1092	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1093	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1094	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1095	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1096	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1097	+	}
1098	+	// If we're the root node, should we print out the results
1099	+	int worldRank = MPI::COMM_WORLD.Get_rank();
1100	+	if (worldRank == 0) {
1101	+	#endif
1102	+	rnemdLog_ << time;
1103	+	for (j = 0; j < rnemdLogWidth_; j++) {
1104	+	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1105	+	}
1106	+	rnemdLog_ << "\n";
1107	+	if (output3DTemp_) {
1108	+	xTempLog_ << time;
1109	+	for (j = 0; j < rnemdLogWidth_; j++) {
1110	+	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1111	+	}
1112	+	xTempLog_ << "\n";
1113	+	yTempLog_ << time;
1114	+	for (j = 0; j < rnemdLogWidth_; j++) {
1115	+	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1116	+	}
1117	+	yTempLog_ << "\n";
1118	+	zTempLog_ << time;
1119	+	for (j = 0; j < rnemdLogWidth_; j++) {
1120	+	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1121	+	}
1122	+	zTempLog_ << "\n";
1123	+	}
1124	+	#ifdef IS_MPI
1125	+	}
1126	+	#endif
1127	+	for (j = 0; j < rnemdLogWidth_; j++) {
1128	+	valueCount_[j] = 0;
1129	+	valueHist_[j] = 0.0;
1130	+	}
1131	+	if (output3DTemp_)
1132	+	for (j = 0; j < rnemdLogWidth_; j++) {
1133	+	xTempHist_[j] = 0.0;
1134	+	yTempHist_[j] = 0.0;
1135	+	zTempHist_[j] = 0.0;
1136	+	xyzTempCount_[j] = 0;
1137	+	}
1138	+	}
1139		}

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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