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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 1561 by gezelter, Wed May 11 19:04:40 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	>	using namespace std;
61	>	namespace OpenMD {
62
63	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
64	<
63	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
64	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
65	>
66	>	failTrialCount_ = 0;
67	>	failRootCount_ = 0;
68	>
69		int seedValue;
70		Globals * simParams = info->getSimParams();
71
72	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
72	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
74	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
75	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
76	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
77		stringToEnumMap_["Px"] = rnemdPx;
78		stringToEnumMap_["Py"] = rnemdPy;
79		stringToEnumMap_["Pz"] = rnemdPz;
80		stringToEnumMap_["Unknown"] = rnemdUnknown;
81
82		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
77	–
78	–	std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
83		evaluator_.loadScriptString(rnemdObjectSelection_);
84	<	std::cerr << "done\n";
84	>	seleMan_.setSelectionSet(evaluator_.evaluate());
85	>
86	>	// do some sanity checking
87	>
88	>	int selectionCount = seleMan_.getSelectionCount();
89	>	int nIntegrable = info->getNGlobalIntegrableObjects();
90	>
91	>	if (selectionCount > nIntegrable) {
92	>	sprintf(painCave.errMsg,
93	>	"RNEMD: The current RNEMD_objectSelection,\n"
94	>	"\t\t%s\n"
95	>	"\thas resulted in %d selected objects.  However,\n"
96	>	"\tthe total number of integrable objects in the system\n"
97	>	"\tis only %d.  This is almost certainly not what you want\n"
98	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
99	>	"\tselector in the selection script!\n",
100	>	rnemdObjectSelection_.c_str(),
101	>	selectionCount, nIntegrable);
102	>	painCave.isFatal = 0;
103	>	painCave.severity = OPENMD_WARNING;
104	>	simError();
105	>	}
106
107	<	const std::string st = simParams->getRNEMD_swapType();
107	>	const string st = simParams->getRNEMD_exchangeType();
108
109	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
109	>	map<string, RNEMDTypeEnum>::iterator i;
110		i = stringToEnumMap_.find(st);
111	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
111	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
112	>	if (rnemdType_ == rnemdUnknown) {
113	>	sprintf(painCave.errMsg,
114	>	"RNEMD: The current RNEMD_exchangeType,\n"
115	>	"\t\t%s\n"
116	>	"\tis not one of the recognized exchange types.\n",
117	>	st.c_str());
118	>	painCave.isFatal = 1;
119	>	painCave.severity = OPENMD_ERROR;
120	>	simError();
121	>	}
122	>
123	>	output3DTemp_ = false;
124	>	if (simParams->haveRNEMD_outputDimensionalTemperature()) {
125	>	output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature();
126	>	}
127
128	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
128	>	#ifdef IS_MPI
129	>	if (worldRank == 0) {
130	>	#endif
131	>
132	>	string rnemdFileName;
133	>	switch(rnemdType_) {
134	>	case rnemdKineticSwap :
135	>	case rnemdKineticScale :
136	>	rnemdFileName = "temperature.log";
137	>	break;
138	>	case rnemdPx :
139	>	case rnemdPxScale :
140	>	case rnemdPy :
141	>	case rnemdPyScale :
142	>	rnemdFileName = "momemtum.log";
143	>	break;
144	>	case rnemdPz :
145	>	case rnemdPzScale :
146	>	case rnemdUnknown :
147	>	default :
148	>	rnemdFileName = "rnemd.log";
149	>	break;
150	>	}
151	>	rnemdLog_.open(rnemdFileName.c_str());
152	>
153	>	string xTempFileName;
154	>	string yTempFileName;
155	>	string zTempFileName;
156	>	if (output3DTemp_) {
157	>	xTempFileName = "temperatureX.log";
158	>	yTempFileName = "temperatureY.log";
159	>	zTempFileName = "temperatureZ.log";
160	>	xTempLog_.open(xTempFileName.c_str());
161	>	yTempLog_.open(yTempFileName.c_str());
162	>	zTempLog_.open(zTempFileName.c_str());
163	>	}
164	>
165	>	#ifdef IS_MPI
166	>	}
167	>	#endif
168	>
169	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
170		set_RNEMD_nBins(simParams->getRNEMD_nBins());
171	<	exchangeSum_ = 0.0;
172	<	counter_ = 0; //added by shenyu
173	<	//profile_.open("profile", std::ios::out);
171	>	midBin_ = nBins_ / 2;
172	>	if (simParams->haveRNEMD_binShift()) {
173	>	if (simParams->getRNEMD_binShift()) {
174	>	zShift_ = 0.5 / (RealType)(nBins_);
175	>	} else {
176	>	zShift_ = 0.0;
177	>	}
178	>	} else {
179	>	zShift_ = 0.0;
180	>	}
181	>	//cerr << "we have zShift_ = " << zShift_ << "\n";
182	>	//shift slabs by half slab width, might be useful in heterogeneous systems
183	>	//set to 0.0 if not using it; can NOT be used in status output yet
184	>	if (simParams->haveRNEMD_logWidth()) {
185	>	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
186	>	/*arbitary rnemdLogWidth_ no checking
187	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
188	>	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
189	>	cerr << "Automaically set back to default.\n";
190	>	rnemdLogWidth_ = nBins_;
191	>	}*/
192	>	} else {
193	>	set_RNEMD_logWidth(nBins_);
194	>	}
195	>	valueHist_.resize(rnemdLogWidth_, 0.0);
196	>	valueCount_.resize(rnemdLogWidth_, 0);
197	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
198	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
199	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
200	>	xyzTempCount_.resize(rnemdLogWidth_, 0);
201
202	+	set_RNEMD_exchange_total(0.0);
203	+	if (simParams->haveRNEMD_targetFlux()) {
204	+	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
205	+	} else {
206	+	set_RNEMD_target_flux(0.0);
207	+	}
208	+
209		#ifndef IS_MPI
210		if (simParams->haveSeed()) {
211		seedValue = simParams->getSeed();
#	Line 110 | Line 225 | namespace oopse {
225
226		RNEMD::~RNEMD() {
227		delete randNumGen_;
228	<	//profile_.close();
228	>
229	>	#ifdef IS_MPI
230	>	if (worldRank == 0) {
231	>	#endif
232	>
233	>	sprintf(painCave.errMsg,
234	>	"RNEMD: total failed trials: %d\n",
235	>	failTrialCount_);
236	>	painCave.isFatal = 0;
237	>	painCave.severity = OPENMD_INFO;
238	>	simError();
239	>
240	>	rnemdLog_.close();
241	>	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) {
242	>	sprintf(painCave.errMsg,
243	>	"RNEMD: total root-checking warnings: %d\n",
244	>	failRootCount_);
245	>	painCave.isFatal = 0;
246	>	painCave.severity = OPENMD_INFO;
247	>	simError();
248	>	}
249	>	if (output3DTemp_) {
250	>	xTempLog_.close();
251	>	yTempLog_.close();
252	>	zTempLog_.close();
253	>	}
254	>	#ifdef IS_MPI
255	>	}
256	>	#endif
257		}
258
259		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";
260
261		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
262		Mat3x3d hmat = currentSnap_->getHmat();
263
128	–	//std::cerr << "hmat = " << hmat << "\n";
129	–
264		seleMan_.setSelectionSet(evaluator_.evaluate());
265
132	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
133	–
266		int selei;
267		StuntDouble* sd;
268		int idx;
#	Line 158 | Line 290 | namespace oopse {
290		// which bin is this stuntdouble in?
291		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
292
293	<	int binNo = int((nBins_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2));
293	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
294
163	–	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
295
296		// if we're in bin 0 or the middleBin
297	<	if (binNo == 0 || binNo == midBin) {
297	>	if (binNo == 0 || binNo == midBin_) {
298
299		RealType mass = sd->getMass();
300		Vector3d vel = sd->getVel();
301		RealType value;
302
303		switch(rnemdType_) {
304	<	case rnemdKinetic :
304	>	case rnemdKineticSwap :
305
306		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
307		vel[2]*vel[2]);
308	<
309	<	if (sd->isDirectional()) {
308	>	/*
309	>	if (sd->isDirectional()) {
310		Vector3d angMom = sd->getJ();
311		Mat3x3d I = sd->getI();
312
313		if (sd->isLinear()) {
314	<	int i = sd->linearAxis();
315	<	int j = (i + 1) % 3;
316	<	int k = (i + 2) % 3;
317	<	value += angMom[j] * angMom[j] / I(j, j) +
318	<	angMom[k] * angMom[k] / I(k, k);
314	>	int i = sd->linearAxis();
315	>	int j = (i + 1) % 3;
316	>	int k = (i + 2) % 3;
317	>	value += angMom[j] * angMom[j] / I(j, j) +
318	>	angMom[k] * angMom[k] / I(k, k);
319		} else {
320	<	value += angMom[0]*angMom[0]/I(0, 0)
321	<	+ angMom[1]*angMom[1]/I(1, 1)
322	<	+ angMom[2]*angMom[2]/I(2, 2);
320	>	value += angMom[0]*angMom[0]/I(0, 0)
321	>	+ angMom[1]*angMom[1]/I(1, 1)
322	>	+ angMom[2]*angMom[2]/I(2, 2);
323		}
324	<	}
325	<	value = value * 0.5 / OOPSEConstant::energyConvert;
324	>	} no exchange of angular momenta
325	>	*/
326	>	//make exchangeSum_ comparable between swap & scale
327	>	//temporarily without using energyConvert
328	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
329	>	value *= 0.5;
330		break;
331		case rnemdPx :
332		value = mass * vel[0];
#	Line 202 | Line 337 | namespace oopse {
337		case rnemdPz :
338		value = mass * vel[2];
339		break;
205	–	case rnemdUnknown :
340		default :
341		break;
342		}
#	Line 218 | Line 352 | namespace oopse {
352		min_sd = sd;
353		}
354		}
355	<	} else {
355	>	} else { //midBin_
356		if (!max_found) {
357		max_val = value;
358		max_sd = sd;
#	Line 232 | Line 366 | namespace oopse {
366		}
367		}
368		}
369	<	//std::cerr << "smallest value = " << min_val  << "\n";
370	<	//std::cerr << "largest value = " << max_val << "\n";
371	<
372	<	// missing:  swap information in parallel
369	>
370	>	#ifdef IS_MPI
371	>	int nProc, worldRank;
372	>
373	>	nProc = MPI::COMM_WORLD.Get_size();
374	>	worldRank = MPI::COMM_WORLD.Get_rank();
375	>
376	>	bool my_min_found = min_found;
377	>	bool my_max_found = max_found;
378
379	+	// Even if we didn't find a minimum, did someone else?
380	+	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
381	+	// Even if we didn't find a maximum, did someone else?
382	+	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
383	+	struct {
384	+	RealType val;
385	+	int rank;
386	+	} max_vals, min_vals;
387	+
388	+	if (min_found) {
389	+	if (my_min_found)
390	+	min_vals.val = min_val;
391	+	else
392	+	min_vals.val = HONKING_LARGE_VALUE;
393	+
394	+	min_vals.rank = worldRank;
395	+
396	+	// Who had the minimum?
397	+	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
398	+	1, MPI::REALTYPE_INT, MPI::MINLOC);
399	+	min_val = min_vals.val;
400	+	}
401	+
402	+	if (max_found) {
403	+	if (my_max_found)
404	+	max_vals.val = max_val;
405	+	else
406	+	max_vals.val = -HONKING_LARGE_VALUE;
407	+
408	+	max_vals.rank = worldRank;
409	+
410	+	// Who had the maximum?
411	+	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
412	+	1, MPI::REALTYPE_INT, MPI::MAXLOC);
413	+	max_val = max_vals.val;
414	+	}
415	+	#endif
416	+
417		if (max_found && min_found) {
418	<	if (min_val< max_val) {
419	<	Vector3d min_vel = min_sd->getVel();
420	<	Vector3d max_vel = max_sd->getVel();
421	<	RealType temp_vel;
422	<	switch(rnemdType_) {
423	<	case rnemdKinetic :
424	<	min_sd->setVel(max_vel);
425	<	max_sd->setVel(min_vel);
426	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
427	<	Vector3d min_angMom = min_sd->getJ();
428	<	Vector3d max_angMom = max_sd->getJ();
429	<	min_sd->setJ(max_angMom);
430	<	max_sd->setJ(min_angMom);
431	<	}
432	<	break;
433	<	case rnemdPx :
434	<	temp_vel = min_vel.x();
435	<	min_vel.x() = max_vel.x();
436	<	max_vel.x() = temp_vel;
437	<	min_sd->setVel(min_vel);
438	<	max_sd->setVel(max_vel);
439	<	break;
440	<	case rnemdPy :
441	<	temp_vel = min_vel.y();
442	<	min_vel.y() = max_vel.y();
443	<	max_vel.y() = temp_vel;
444	<	min_sd->setVel(min_vel);
445	<	max_sd->setVel(max_vel);
446	<	break;
447	<	case rnemdPz :
448	<	temp_vel = min_vel.z();
449	<	min_vel.z() = max_vel.z();
450	<	max_vel.z() = temp_vel;
451	<	min_sd->setVel(min_vel);
452	<	max_sd->setVel(max_vel);
453	<	break;
454	<	case rnemdUnknown :
455	<	default :
456	<	break;
418	>	if (min_val < max_val) {
419	>
420	>	#ifdef IS_MPI
421	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
422	>	// I have both maximum and minimum, so proceed like a single
423	>	// processor version:
424	>	#endif
425	>	// objects to be swapped: velocity ONLY
426	>	Vector3d min_vel = min_sd->getVel();
427	>	Vector3d max_vel = max_sd->getVel();
428	>	RealType temp_vel;
429	>
430	>	switch(rnemdType_) {
431	>	case rnemdKineticSwap :
432	>	min_sd->setVel(max_vel);
433	>	max_sd->setVel(min_vel);
434	>	/*
435	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
436	>	Vector3d min_angMom = min_sd->getJ();
437	>	Vector3d max_angMom = max_sd->getJ();
438	>	min_sd->setJ(max_angMom);
439	>	max_sd->setJ(min_angMom);
440	>	} no angular momentum exchange
441	>	*/
442	>	break;
443	>	case rnemdPx :
444	>	temp_vel = min_vel.x();
445	>	min_vel.x() = max_vel.x();
446	>	max_vel.x() = temp_vel;
447	>	min_sd->setVel(min_vel);
448	>	max_sd->setVel(max_vel);
449	>	break;
450	>	case rnemdPy :
451	>	temp_vel = min_vel.y();
452	>	min_vel.y() = max_vel.y();
453	>	max_vel.y() = temp_vel;
454	>	min_sd->setVel(min_vel);
455	>	max_sd->setVel(max_vel);
456	>	break;
457	>	case rnemdPz :
458	>	temp_vel = min_vel.z();
459	>	min_vel.z() = max_vel.z();
460	>	max_vel.z() = temp_vel;
461	>	min_sd->setVel(min_vel);
462	>	max_sd->setVel(max_vel);
463	>	break;
464	>	default :
465	>	break;
466	>	}
467	>	#ifdef IS_MPI
468	>	// the rest of the cases only apply in parallel simulations:
469	>	} else if (max_vals.rank == worldRank) {
470	>	// I had the max, but not the minimum
471	>
472	>	Vector3d min_vel;
473	>	Vector3d max_vel = max_sd->getVel();
474	>	MPI::Status status;
475	>
476	>	// point-to-point swap of the velocity vector
477	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
478	>	min_vals.rank, 0,
479	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
480	>	min_vals.rank, 0, status);
481	>
482	>	switch(rnemdType_) {
483	>	case rnemdKineticSwap :
484	>	max_sd->setVel(min_vel);
485	>	//no angular momentum exchange for now
486	>	/*
487	>	if (max_sd->isDirectional()) {
488	>	Vector3d min_angMom;
489	>	Vector3d max_angMom = max_sd->getJ();
490	>
491	>	// point-to-point swap of the angular momentum vector
492	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
493	>	MPI::REALTYPE, min_vals.rank, 1,
494	>	min_angMom.getArrayPointer(), 3,
495	>	MPI::REALTYPE, min_vals.rank, 1,
496	>	status);
497	>
498	>	max_sd->setJ(min_angMom);
499	>	}
500	>	*/
501	>	break;
502	>	case rnemdPx :
503	>	max_vel.x() = min_vel.x();
504	>	max_sd->setVel(max_vel);
505	>	break;
506	>	case rnemdPy :
507	>	max_vel.y() = min_vel.y();
508	>	max_sd->setVel(max_vel);
509	>	break;
510	>	case rnemdPz :
511	>	max_vel.z() = min_vel.z();
512	>	max_sd->setVel(max_vel);
513	>	break;
514	>	default :
515	>	break;
516	>	}
517	>	} else if (min_vals.rank == worldRank) {
518	>	// I had the minimum but not the maximum:
519	>
520	>	Vector3d max_vel;
521	>	Vector3d min_vel = min_sd->getVel();
522	>	MPI::Status status;
523	>
524	>	// point-to-point swap of the velocity vector
525	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
526	>	max_vals.rank, 0,
527	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
528	>	max_vals.rank, 0, status);
529	>
530	>	switch(rnemdType_) {
531	>	case rnemdKineticSwap :
532	>	min_sd->setVel(max_vel);
533	>	// no angular momentum exchange for now
534	>	/*
535	>	if (min_sd->isDirectional()) {
536	>	Vector3d min_angMom = min_sd->getJ();
537	>	Vector3d max_angMom;
538	>
539	>	// point-to-point swap of the angular momentum vector
540	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
541	>	MPI::REALTYPE, max_vals.rank, 1,
542	>	max_angMom.getArrayPointer(), 3,
543	>	MPI::REALTYPE, max_vals.rank, 1,
544	>	status);
545	>
546	>	min_sd->setJ(max_angMom);
547	>	}
548	>	*/
549	>	break;
550	>	case rnemdPx :
551	>	min_vel.x() = max_vel.x();
552	>	min_sd->setVel(min_vel);
553	>	break;
554	>	case rnemdPy :
555	>	min_vel.y() = max_vel.y();
556	>	min_sd->setVel(min_vel);
557	>	break;
558	>	case rnemdPz :
559	>	min_vel.z() = max_vel.z();
560	>	min_sd->setVel(min_vel);
561	>	break;
562	>	default :
563	>	break;
564	>	}
565	>	}
566	>	#endif
567	>	exchangeSum_ += max_val - min_val;
568	>	} else {
569	>	sprintf(painCave.errMsg,
570	>	"RNEMD: exchange NOT performed because min_val > max_val\n");
571	>	painCave.isFatal = 0;
572	>	painCave.severity = OPENMD_INFO;
573	>	simError();
574	>	failTrialCount_++;
575	>	}
576	>	} else {
577	>	sprintf(painCave.errMsg,
578	>	"RNEMD: exchange NOT performed because at least one\n"
579	>	"\tof the two slabs is empty\n");
580	>	painCave.isFatal = 0;
581	>	painCave.severity = OPENMD_INFO;
582	>	simError();
583	>	failTrialCount_++;
584	>	}
585	>
586	>	}
587	>
588	>	void RNEMD::doScale() {
589	>
590	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
591	>	Mat3x3d hmat = currentSnap_->getHmat();
592	>
593	>	seleMan_.setSelectionSet(evaluator_.evaluate());
594	>
595	>	int selei;
596	>	StuntDouble* sd;
597	>	int idx;
598	>
599	>	vector<StuntDouble*> hotBin, coldBin;
600	>
601	>	RealType Phx = 0.0;
602	>	RealType Phy = 0.0;
603	>	RealType Phz = 0.0;
604	>	RealType Khx = 0.0;
605	>	RealType Khy = 0.0;
606	>	RealType Khz = 0.0;
607	>	RealType Pcx = 0.0;
608	>	RealType Pcy = 0.0;
609	>	RealType Pcz = 0.0;
610	>	RealType Kcx = 0.0;
611	>	RealType Kcy = 0.0;
612	>	RealType Kcz = 0.0;
613	>
614	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
615	>	sd = seleMan_.nextSelected(selei)) {
616	>
617	>	idx = sd->getLocalIndex();
618	>
619	>	Vector3d pos = sd->getPos();
620	>
621	>	// wrap the stuntdouble's position back into the box:
622	>
623	>	if (usePeriodicBoundaryConditions_)
624	>	currentSnap_->wrapVector(pos);
625	>
626	>	// which bin is this stuntdouble in?
627	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
628	>
629	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
630	>
631	>	// if we're in bin 0 or the middleBin
632	>	if (binNo == 0 || binNo == midBin_) {
633	>
634	>	RealType mass = sd->getMass();
635	>	Vector3d vel = sd->getVel();
636	>
637	>	if (binNo == 0) {
638	>	hotBin.push_back(sd);
639	>	Phx += mass * vel.x();
640	>	Phy += mass * vel.y();
641	>	Phz += mass * vel.z();
642	>	Khx += mass * vel.x() * vel.x();
643	>	Khy += mass * vel.y() * vel.y();
644	>	Khz += mass * vel.z() * vel.z();
645	>	} else { //midBin_
646	>	coldBin.push_back(sd);
647	>	Pcx += mass * vel.x();
648	>	Pcy += mass * vel.y();
649	>	Pcz += mass * vel.z();
650	>	Kcx += mass * vel.x() * vel.x();
651	>	Kcy += mass * vel.y() * vel.y();
652	>	Kcz += mass * vel.z() * vel.z();
653		}
281	–	exchangeSum_ += max_val - min_val;
282	–	} else {
283	–	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
654		}
655	+	}
656	+
657	+	Khx *= 0.5;
658	+	Khy *= 0.5;
659	+	Khz *= 0.5;
660	+	Kcx *= 0.5;
661	+	Kcy *= 0.5;
662	+	Kcz *= 0.5;
663	+
664	+	#ifdef IS_MPI
665	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
666	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
667	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
668	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
669	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
670	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
671	+
672	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
673	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
674	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
675	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
676	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
677	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
678	+	#endif
679	+
680	+	//use coldBin coeff's
681	+	RealType px = Pcx / Phx;
682	+	RealType py = Pcy / Phy;
683	+	RealType pz = Pcz / Phz;
684	+
685	+	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
686	+	switch(rnemdType_) {
687	+	case rnemdKineticScale :
688	+	// used hotBin coeff's & only scale x & y dimensions
689	+	/*
690	+	RealType px = Phx / Pcx;
691	+	RealType py = Phy / Pcy;
692	+	a110 = Khy;
693	+	c0 = - Khx - Khy - targetFlux_;
694	+	a000 = Khx;
695	+	a111 = Kcy * py * py;
696	+	b11 = -2.0 * Kcy * py * (1.0 + py);
697	+	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
698	+	b01 = -2.0 * Kcx * px * (1.0 + px);
699	+	a001 = Kcx * px * px;
700	+	*/
701	+	//scale all three dimensions, let c_x = c_y
702	+	a000 = Kcx + Kcy;
703	+	a110 = Kcz;
704	+	c0 = targetFlux_ - Kcx - Kcy - Kcz;
705	+	a001 = Khx * px * px + Khy * py * py;
706	+	a111 = Khz * pz * pz;
707	+	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
708	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
709	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
710	+	+ Khz * pz * (2.0 + pz) - targetFlux_;
711	+	break;
712	+	case rnemdPxScale :
713	+	c = 1 - targetFlux_ / Pcx;
714	+	a000 = Kcy;
715	+	a110 = Kcz;
716	+	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
717	+	a001 = py * py * Khy;
718	+	a111 = pz * pz * Khz;
719	+	b01 = -2.0 * Khy * py * (1.0 + py);
720	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
721	+	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
722	+	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
723	+	break;
724	+	case rnemdPyScale :
725	+	c = 1 - targetFlux_ / Pcy;
726	+	a000 = Kcx;
727	+	a110 = Kcz;
728	+	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
729	+	a001 = px * px * Khx;
730	+	a111 = pz * pz * Khz;
731	+	b01 = -2.0 * Khx * px * (1.0 + px);
732	+	b11 = -2.0 * Khz * pz * (1.0 + pz);
733	+	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
734	+	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
735	+	break;
736	+	case rnemdPzScale ://we don't really do this, do we?
737	+	c = 1 - targetFlux_ / Pcz;
738	+	a000 = Kcx;
739	+	a110 = Kcy;
740	+	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
741	+	a001 = px * px * Khx;
742	+	a111 = py * py * Khy;
743	+	b01 = -2.0 * Khx * px * (1.0 + px);
744	+	b11 = -2.0 * Khy * py * (1.0 + py);
745	+	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
746	+	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
747	+	break;
748	+	default :
749	+	break;
750	+	}
751	+
752	+	RealType v1 = a000 * a111 - a001 * a110;
753	+	RealType v2 = a000 * b01;
754	+	RealType v3 = a000 * b11;
755	+	RealType v4 = a000 * c1 - a001 * c0;
756	+	RealType v8 = a110 * b01;
757	+	RealType v10 = - b01 * c0;
758	+
759	+	RealType u0 = v2 * v10 - v4 * v4;
760	+	RealType u1 = -2.0 * v3 * v4;
761	+	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
762	+	RealType u3 = -2.0 * v1 * v3;
763	+	RealType u4 = - v1 * v1;
764	+	//rescale coefficients
765	+	RealType maxAbs = fabs(u0);
766	+	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
767	+	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
768	+	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
769	+	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
770	+	u0 /= maxAbs;
771	+	u1 /= maxAbs;
772	+	u2 /= maxAbs;
773	+	u3 /= maxAbs;
774	+	u4 /= maxAbs;
775	+	//max_element(start, end) is also available.
776	+	Polynomial<RealType> poly; //same as DoublePolynomial poly;
777	+	poly.setCoefficient(4, u4);
778	+	poly.setCoefficient(3, u3);
779	+	poly.setCoefficient(2, u2);
780	+	poly.setCoefficient(1, u1);
781	+	poly.setCoefficient(0, u0);
782	+	vector<RealType> realRoots = poly.FindRealRoots();
783	+
784	+	vector<RealType>::iterator ri;
785	+	RealType r1, r2, alpha0;
786	+	vector<pair<RealType,RealType> > rps;
787	+	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
788	+	r2 = *ri;
789	+	//check if FindRealRoots() give the right answer
790	+	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
791	+	sprintf(painCave.errMsg,
792	+	"RNEMD Warning: polynomial solve seems to have an error!");
793	+	painCave.isFatal = 0;
794	+	simError();
795	+	failRootCount_++;
796	+	}
797	+	//might not be useful w/o rescaling coefficients
798	+	alpha0 = -c0 - a110 * r2 * r2;
799	+	if (alpha0 >= 0.0) {
800	+	r1 = sqrt(alpha0 / a000);
801	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
802	+	{ rps.push_back(make_pair(r1, r2)); }
803	+	if (r1 > 1e-6) { //r1 non-negative
804	+	r1 = -r1;
805	+	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
806	+	{ rps.push_back(make_pair(r1, r2)); }
807	+	}
808	+	}
809	+	}
810	+	// Consider combining together the solving pair part w/ the searching
811	+	// best solution part so that we don't need the pairs vector
812	+	if (!rps.empty()) {
813	+	RealType smallestDiff = HONKING_LARGE_VALUE;
814	+	RealType diff;
815	+	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
816	+	vector<pair<RealType,RealType> >::iterator rpi;
817	+	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
818	+	r1 = (*rpi).first;
819	+	r2 = (*rpi).second;
820	+	switch(rnemdType_) {
821	+	case rnemdKineticScale :
822	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
823	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
824	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
825	+	break;
826	+	case rnemdPxScale :
827	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
828	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
829	+	break;
830	+	case rnemdPyScale :
831	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
832	+	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
833	+	break;
834	+	case rnemdPzScale :
835	+	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
836	+	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
837	+	default :
838	+	break;
839	+	}
840	+	if (diff < smallestDiff) {
841	+	smallestDiff = diff;
842	+	bestPair = *rpi;
843	+	}
844	+	}
845	+	#ifdef IS_MPI
846	+	if (worldRank == 0) {
847	+	#endif
848	+	sprintf(painCave.errMsg,
849	+	"RNEMD: roots r1= %lf\tr2 = %lf\n",
850	+	bestPair.first, bestPair.second);
851	+	painCave.isFatal = 0;
852	+	painCave.severity = OPENMD_INFO;
853	+	simError();
854	+	#ifdef IS_MPI
855	+	}
856	+	#endif
857	+
858	+	RealType x, y, z;
859	+	switch(rnemdType_) {
860	+	case rnemdKineticScale :
861	+	x = bestPair.first;
862	+	y = bestPair.first;
863	+	z = bestPair.second;
864	+	break;
865	+	case rnemdPxScale :
866	+	x = c;
867	+	y = bestPair.first;
868	+	z = bestPair.second;
869	+	break;
870	+	case rnemdPyScale :
871	+	x = bestPair.first;
872	+	y = c;
873	+	z = bestPair.second;
874	+	break;
875	+	case rnemdPzScale :
876	+	x = bestPair.first;
877	+	y = bestPair.second;
878	+	z = c;
879	+	break;
880	+	default :
881	+	break;
882	+	}
883	+	vector<StuntDouble*>::iterator sdi;
884	+	Vector3d vel;
885	+	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
886	+	vel = (*sdi)->getVel();
887	+	vel.x() *= x;
888	+	vel.y() *= y;
889	+	vel.z() *= z;
890	+	(*sdi)->setVel(vel);
891	+	}
892	+	//convert to hotBin coefficient
893	+	x = 1.0 + px * (1.0 - x);
894	+	y = 1.0 + py * (1.0 - y);
895	+	z = 1.0 + pz * (1.0 - z);
896	+	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
897	+	vel = (*sdi)->getVel();
898	+	vel.x() *= x;
899	+	vel.y() *= y;
900	+	vel.z() *= z;
901	+	(*sdi)->setVel(vel);
902	+	}
903	+	exchangeSum_ += targetFlux_;
904	+	//we may want to check whether the exchange has been successful
905		} else {
906	<	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
906	>	sprintf(painCave.errMsg,
907	>	"RNEMD: exchange NOT performed!\n");
908	>	painCave.isFatal = 0;
909	>	painCave.severity = OPENMD_INFO;
910	>	simError();
911	>	failTrialCount_++;
912		}
913	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
913	>
914		}
915
916	<	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";
916	>	void RNEMD::doRNEMD() {
917
918	+	switch(rnemdType_) {
919	+	case rnemdKineticScale :
920	+	case rnemdPxScale :
921	+	case rnemdPyScale :
922	+	case rnemdPzScale :
923	+	doScale();
924	+	break;
925	+	case rnemdKineticSwap :
926	+	case rnemdPx :
927	+	case rnemdPy :
928	+	case rnemdPz :
929	+	doSwap();
930	+	break;
931	+	case rnemdUnknown :
932	+	default :
933	+	break;
934	+	}
935	+	}
936	+
937	+	void RNEMD::collectData() {
938	+
939		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
940		Mat3x3d hmat = currentSnap_->getHmat();
941
304	–	//std::cerr << "hmat = " << hmat << "\n";
305	–
942		seleMan_.setSelectionSet(evaluator_.evaluate());
943
308	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
309	–
944		int selei;
945		StuntDouble* sd;
946		int idx;
313	–	/*
314	–	RealType min_val;
315	–	bool min_found = false;
316	–	StuntDouble* min_sd;
947
948	<	RealType max_val;
949	<	bool max_found = false;
950	<	StuntDouble* max_sd;
948	>	// alternative approach, track all molecules instead of only those
949	>	// selected for scaling/swapping:
950	>	/*
951	>	SimInfo::MoleculeIterator miter;
952	>	vector<StuntDouble*>::iterator iiter;
953	>	Molecule* mol;
954	>	StuntDouble* integrableObject;
955	>	for (mol = info_->beginMolecule(miter); mol != NULL;
956	>	mol = info_->nextMolecule(miter))
957	>	integrableObject is essentially sd
958	>	for (integrableObject = mol->beginIntegrableObject(iiter);
959	>	integrableObject != NULL;
960	>	integrableObject = mol->nextIntegrableObject(iiter))
961		*/
322	–	std::vector<RealType> valueHist;  // keeps track of what's being averaged
323	–	std::vector<int> valueCount; // keeps track of the number of degrees of
324	–	// freedom being averaged
325	–	valueHist.resize(nBins_);
326	–	valueCount.resize(nBins_);
327	–	//do they initialize themselves to zero automatically?
962		for (sd = seleMan_.beginSelected(selei); sd != NULL;
963		sd = seleMan_.nextSelected(selei)) {
964
#	Line 340 | Line 974 | namespace oopse {
974		// which bin is this stuntdouble in?
975		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
976
977	<	int binNo = int((nBins_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2));
978	<
979	<	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
980	<
977	>	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
978	>	rnemdLogWidth_;
979	>	// no symmetrization allowed due to arbitary rnemdLogWidth_ value
980	>	/*
981	>	if (rnemdLogWidth_ == midBin_ + 1)
982	>	if (binNo > midBin_)
983	>	binNo = nBins_ - binNo;
984	>	*/
985		RealType mass = sd->getMass();
986		Vector3d vel = sd->getVel();
349	–	//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
987		RealType value;
988	+	RealType xVal, yVal, zVal;
989
990		switch(rnemdType_) {
991	<	case rnemdKinetic :
991	>	case rnemdKineticSwap :
992	>	case rnemdKineticScale :
993
994	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
356	<	vel[2]*vel[2]);
994	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
995
996	<	valueCount[binNo] += 3;
359	<
996	>	valueCount_[binNo] += 3;
997		if (sd->isDirectional()) {
998		Vector3d angMom = sd->getJ();
999		Mat3x3d I = sd->getI();
#	Line 367 | Line 1004 | namespace oopse {
1004		int k = (i + 2) % 3;
1005		value += angMom[j] * angMom[j] / I(j, j) +
1006		angMom[k] * angMom[k] / I(k, k);
1007	<
1008	<	valueCount[binNo] +=2;
1009	<
1010	<	} else {
1007	>
1008	>	valueCount_[binNo] +=2;
1009	>
1010	>	} else {
1011		value += angMom[0]*angMom[0]/I(0, 0)
1012		+ angMom[1]*angMom[1]/I(1, 1)
1013		+ angMom[2]*angMom[2]/I(2, 2);
1014	<	valueCount[binNo] +=3;
378	<
1014	>	valueCount_[binNo] +=3;
1015		}
1016		}
1017	<	//std::cerr <<"this value = " << value << "\n";
1018	<	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";
1017	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
1018	>
1019		break;
1020		case rnemdPx :
1021	+	case rnemdPxScale :
1022		value = mass * vel[0];
1023	<	valueCount[binNo]++;
1023	>	valueCount_[binNo]++;
1024		break;
1025		case rnemdPy :
1026	+	case rnemdPyScale :
1027		value = mass * vel[1];
1028	<	valueCount[binNo]++;
1028	>	valueCount_[binNo]++;
1029		break;
1030		case rnemdPz :
1031	<	value = mass * vel[2];
1032	<	valueCount[binNo]++;
1031	>	case rnemdPzScale :
1032	>	value = pos.z(); //temporarily for homogeneous systems ONLY
1033	>	valueCount_[binNo]++;
1034		break;
1035		case rnemdUnknown :
1036		default :
1037	+	value = 1.0;
1038	+	valueCount_[binNo]++;
1039		break;
1040		}
1041	<	//std::cerr << "bin = " << binNo << " value = " << value ;
1042	<	valueHist[binNo] += value;
1043	<	//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
1041	>	valueHist_[binNo] += value;
1042	>
1043	>	if (output3DTemp_) {
1044	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
1045	>	/ PhysicalConstants::kb;
1046	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1047	>	/ PhysicalConstants::kb;
1048	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1049	>	/ PhysicalConstants::kb;
1050	>	xTempHist_[binNo] += xVal;
1051	>	yTempHist_[binNo] += yVal;
1052	>	zTempHist_[binNo] += zVal;
1053	>	xyzTempCount_[binNo]++;
1054	>	}
1055		}
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";
1056		}
1057	+
1058	+	void RNEMD::getStarted() {
1059	+	collectData();
1060	+	/* now should be able to output profile in step 0, but might not be useful
1061	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1062	+	Stats& stat = currentSnap_->statData;
1063	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1064	+	*/
1065	+	getStatus();
1066	+	}
1067	+
1068	+	void RNEMD::getStatus() {
1069	+
1070	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1071	+	Stats& stat = currentSnap_->statData;
1072	+	RealType time = currentSnap_->getTime();
1073	+
1074	+	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1075	+	//or to be more meaningful, define another item as exchangeSum_ / time
1076	+	int j;
1077	+
1078	+	#ifdef IS_MPI
1079	+
1080	+	// all processors have the same number of bins, and STL vectors pack their
1081	+	// arrays, so in theory, this should be safe:
1082	+
1083	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
1084	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1085	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
1086	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1087	+	if (output3DTemp_) {
1088	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1089	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1090	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1091	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1092	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1093	+	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1094	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1095	+	rnemdLogWidth_, MPI::INT, MPI::SUM);
1096	+	}
1097	+	// If we're the root node, should we print out the results
1098	+	int worldRank = MPI::COMM_WORLD.Get_rank();
1099	+	if (worldRank == 0) {
1100	+	#endif
1101	+	rnemdLog_ << time;
1102	+	for (j = 0; j < rnemdLogWidth_; j++) {
1103	+	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1104	+	}
1105	+	rnemdLog_ << "\n";
1106	+	if (output3DTemp_) {
1107	+	xTempLog_ << time;
1108	+	for (j = 0; j < rnemdLogWidth_; j++) {
1109	+	xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j];
1110	+	}
1111	+	xTempLog_ << "\n";
1112	+	yTempLog_ << time;
1113	+	for (j = 0; j < rnemdLogWidth_; j++) {
1114	+	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1115	+	}
1116	+	yTempLog_ << "\n";
1117	+	zTempLog_ << time;
1118	+	for (j = 0; j < rnemdLogWidth_; j++) {
1119	+	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1120	+	}
1121	+	zTempLog_ << "\n";
1122	+	}
1123	+	#ifdef IS_MPI
1124	+	}
1125	+	#endif
1126	+	for (j = 0; j < rnemdLogWidth_; j++) {
1127	+	valueCount_[j] = 0;
1128	+	valueHist_[j] = 0.0;
1129	+	}
1130	+	if (output3DTemp_)
1131	+	for (j = 0; j < rnemdLogWidth_; j++) {
1132	+	xTempHist_[j] = 0.0;
1133	+	yTempHist_[j] = 0.0;
1134	+	zTempHist_[j] = 0.0;
1135	+	xyzTempCount_[j] = 0;
1136	+	}
1137	+	}
1138		}

Comparing trunk/src/integrators/RNEMD.cpp (property svn:keywords):
Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
Revision 1561 by gezelter, Wed May 11 19:04:40 2011 UTC

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