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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1333 by gezelter, Thu Apr 2 18:11:59 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 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	<	/* Remove me after testing*/
57	<	/*
58	<	#include <cstdio>
59	<	#include <iostream>
60	<	*/
61	<	/*End remove me*/
59	>	#define HONKING_LARGE_VALUE 1.0e10
60
61	<	namespace oopse {
61	>	namespace OpenMD {
62
63	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info) {
64	<
63	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
64	>
65	>	failTrialCount_ = 0;
66	>	failRootCount_ = 0;
67	>
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70
71	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
71	>	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
72	>	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
73	>	stringToEnumMap_["PxScale"] = rnemdPxScale;
74	>	stringToEnumMap_["PyScale"] = rnemdPyScale;
75	>	stringToEnumMap_["PzScale"] = rnemdPzScale;
76		stringToEnumMap_["Px"] = rnemdPx;
77		stringToEnumMap_["Py"] = rnemdPy;
78		stringToEnumMap_["Pz"] = rnemdPz;
79		stringToEnumMap_["Unknown"] = rnemdUnknown;
80
81		rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
77	–
78	–	std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
82		evaluator_.loadScriptString(rnemdObjectSelection_);
83	<	std::cerr << "done";
83	>	seleMan_.setSelectionSet(evaluator_.evaluate());
84	>
85	>	// do some sanity checking
86	>
87	>	int selectionCount = seleMan_.getSelectionCount();
88	>	int nIntegrable = info->getNGlobalIntegrableObjects();
89	>
90	>	if (selectionCount > nIntegrable) {
91	>	sprintf(painCave.errMsg,
92	>	"RNEMD warning: The current RNEMD_objectSelection,\n"
93	>	"\t\t%s\n"
94	>	"\thas resulted in %d selected objects.  However,\n"
95	>	"\tthe total number of integrable objects in the system\n"
96	>	"\tis only %d.  This is almost certainly not what you want\n"
97	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
98	>	"\tselector in the selection script!\n",
99	>	rnemdObjectSelection_.c_str(),
100	>	selectionCount, nIntegrable);
101	>	painCave.isFatal = 0;
102	>	simError();
103	>
104	>	}
105
106	<	const std::string st = simParams->getRNEMD_swapType();
106	>	const std::string st = simParams->getRNEMD_exchangeType();
107
108		std::map<std::string, RNEMDTypeEnum>::iterator i;
109		i = stringToEnumMap_.find(st);
110	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
110	>	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
111	>	if (rnemdType_ == rnemdUnknown) {
112	>	std::cerr << "WARNING! RNEMD Type Unknown!\n";
113	>	}
114
115	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
115	>	#ifdef IS_MPI
116	>	if (worldRank == 0) {
117	>	#endif
118	>
119	>	std::string rnemdFileName;
120	>	std::string xTempFileName;
121	>	std::string yTempFileName;
122	>	std::string zTempFileName;
123	>	switch(rnemdType_) {
124	>	case rnemdKineticSwap :
125	>	case rnemdKineticScale :
126	>	rnemdFileName = "temperature.log";
127	>	break;
128	>	case rnemdPx :
129	>	case rnemdPxScale :
130	>	case rnemdPy :
131	>	case rnemdPyScale :
132	>	rnemdFileName = "momemtum.log";
133	>	xTempFileName = "temperatureX.log";
134	>	yTempFileName = "temperatureY.log";
135	>	zTempFileName = "temperatureZ.log";
136	>	xTempLog_.open(xTempFileName.c_str());
137	>	yTempLog_.open(yTempFileName.c_str());
138	>	zTempLog_.open(zTempFileName.c_str());
139	>	break;
140	>	case rnemdPz :
141	>	case rnemdPzScale :
142	>	case rnemdUnknown :
143	>	default :
144	>	rnemdFileName = "rnemd.log";
145	>	break;
146	>	}
147	>	rnemdLog_.open(rnemdFileName.c_str());
148	>
149	>	#ifdef IS_MPI
150	>	}
151	>	#endif
152	>
153	>	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
154		set_RNEMD_nBins(simParams->getRNEMD_nBins());
155	<	exchangeSum_ = 0.0;
156	<
155	>	midBin_ = nBins_ / 2;
156	>	if (simParams->haveRNEMD_logWidth()) {
157	>	rnemdLogWidth_ = simParams->getRNEMD_logWidth();
158	>	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
159	>	std::cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
160	>	std::cerr << "Automaically set back to default.\n";
161	>	rnemdLogWidth_ = nBins_;
162	>	}
163	>	} else {
164	>	rnemdLogWidth_ = nBins_;
165	>	}
166	>	valueHist_.resize(rnemdLogWidth_, 0.0);
167	>	valueCount_.resize(rnemdLogWidth_, 0);
168	>	xTempHist_.resize(rnemdLogWidth_, 0.0);
169	>	yTempHist_.resize(rnemdLogWidth_, 0.0);
170	>	zTempHist_.resize(rnemdLogWidth_, 0.0);
171	>
172	>	set_RNEMD_exchange_total(0.0);
173	>	if (simParams->haveRNEMD_targetFlux()) {
174	>	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
175	>	} else {
176	>	set_RNEMD_target_flux(0.0);
177	>	}
178	>
179		#ifndef IS_MPI
180		if (simParams->haveSeed()) {
181		seedValue = simParams->getSeed();
#	Line 108 | Line 195 | namespace oopse {
195
196		RNEMD::~RNEMD() {
197		delete randNumGen_;
198	+
199	+	#ifdef IS_MPI
200	+	if (worldRank == 0) {
201	+	#endif
202	+	std::cerr << "total fail trials: " << failTrialCount_ << "\n";
203	+	rnemdLog_.close();
204	+	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale)
205	+	std::cerr<< "total root-checking warnings: " << failRootCount_ << "\n";
206	+	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPy || rnemdType_ == rnemdPyScale) {
207	+	xTempLog_.close();
208	+	yTempLog_.close();
209	+	zTempLog_.close();
210	+	}
211	+	#ifdef IS_MPI
212	+	}
213	+	#endif
214		}
215
216		void RNEMD::doSwap() {
114	–	std::cerr << "in RNEMD!\n";
115	–	std::cerr << "nBins = " << nBins_ << "\n";
116	–	int midBin = nBins_ / 2;
117	–	std::cerr << "midBin = " << midBin << "\n";
118	–	std::cerr << "swapTime = " << swapTime_ << "\n";
119	–	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
120	–	std::cerr << "swapType = " << rnemdType_ << "\n";
121	–	std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
217
218		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
219		Mat3x3d hmat = currentSnap_->getHmat();
220
126	–	std::cerr << "hmat = " << hmat << "\n";
127	–
221		seleMan_.setSelectionSet(evaluator_.evaluate());
222
130	–	std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
131	–
223		int selei;
224		StuntDouble* sd;
225		int idx;
226
227	<	std::vector<tuple3<RealType, int, StuntDouble* > > endSlice;
228	<	std::vector<tuple3<RealType, int, StuntDouble* > > midSlice;
229	<
227	>	RealType min_val;
228	>	bool min_found = false;
229	>	StuntDouble* min_sd;
230	>
231	>	RealType max_val;
232	>	bool max_found = false;
233	>	StuntDouble* max_sd;
234	>
235		for (sd = seleMan_.beginSelected(selei); sd != NULL;
236		sd = seleMan_.nextSelected(selei)) {
237
#	Line 143 | Line 239 | namespace oopse {
239
240		Vector3d pos = sd->getPos();
241
146	–	std::cerr << "idx = " << idx << "pos = " << pos << "\n";
242		// wrap the stuntdouble's position back into the box:
243
244		if (usePeriodicBoundaryConditions_)
245		currentSnap_->wrapVector(pos);
151	–	std::cerr << "new pos.z = " << pos.z() << "\n";
246
247		// which bin is this stuntdouble in?
248	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
249
250	<	int binNo = int(nBins_ * (pos.z()) / hmat(2,2));
250	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
251
157	–	std::cerr << "bin = " << binNo << "\n";
252
253		// if we're in bin 0 or the middleBin
254	<	if (binNo == 0 || binNo == midBin) {
254	>	if (binNo == 0 || binNo == midBin_) {
255
256		RealType mass = sd->getMass();
257		Vector3d vel = sd->getVel();
258		RealType value;
259
260		switch(rnemdType_) {
261	<	case rnemdKinetic :
261	>	case rnemdKineticSwap :
262
263		value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
264		vel[2]*vel[2]);
171	–
265		if (sd->isDirectional()) {
266		Vector3d angMom = sd->getJ();
267		Mat3x3d I = sd->getI();
#	Line 185 | Line 278 | namespace oopse {
278		+ angMom[2]*angMom[2]/I(2, 2);
279		}
280		}
281	<	value = value * 0.5 / OOPSEConstant::energyConvert;
281	>	//make exchangeSum_ comparable between swap & scale
282	>	//temporarily without using energyConvert
283	>	//value = value * 0.5 / PhysicalConstants::energyConvert;
284	>	value *= 0.5;
285		break;
286		case rnemdPx :
287		value = mass * vel[0];
#	Line 196 | Line 292 | namespace oopse {
292		case rnemdPz :
293		value = mass * vel[2];
294		break;
199	–	case rnemdUnknown :
295		default :
296		break;
297		}
298
299	<	if (binNo == 0)
300	<	endSlice.push_back( make_tuple3(value, idx, sd));
301	<
302	<	if (binNo == midBin)
303	<	midSlice.push_back( make_tuple3(value, idx, sd));
299	>	if (binNo == 0) {
300	>	if (!min_found) {
301	>	min_val = value;
302	>	min_sd = sd;
303	>	min_found = true;
304	>	} else {
305	>	if (min_val > value) {
306	>	min_val = value;
307	>	min_sd = sd;
308	>	}
309	>	}
310	>	} else { //midBin_
311	>	if (!max_found) {
312	>	max_val = value;
313	>	max_sd = sd;
314	>	max_found = true;
315	>	} else {
316	>	if (max_val < value) {
317	>	max_val = value;
318	>	max_sd = sd;
319	>	}
320	>	}
321	>	}
322		}
323	+	}
324
325	<	// find smallest value in endSlice:
326	<	std::sort(endSlice.begin(), endSlice.end());
213	<	RealType min_val = endSlice[0].first;
214	<	int min_idx = endSlice[0].second;
215	<	StuntDouble* min_sd = endSlice[0].third;
325	>	#ifdef IS_MPI
326	>	int nProc, worldRank;
327
328	<	std::cerr << "smallest value = " << min_val << " idx = " << min_idx << "\n";
328	>	nProc = MPI::COMM_WORLD.Get_size();
329	>	worldRank = MPI::COMM_WORLD.Get_rank();
330
331	<	// find largest value in midSlice:
332	<	std::sort(midSlice.rbegin(), midSlice.rend());
221	<	RealType max_val = midSlice[0].first;
222	<	int max_idx = midSlice[0].second;
223	<	StuntDouble* max_sd = midSlice[0].third;
331	>	bool my_min_found = min_found;
332	>	bool my_max_found = max_found;
333
334	<	std::cerr << "largest value = " << max_val << " idx = " << max_idx << "\n";
334	>	// Even if we didn't find a minimum, did someone else?
335	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
336	>	1, MPI::BOOL, MPI::LAND);
337	>
338	>	// Even if we didn't find a maximum, did someone else?
339	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
340	>	1, MPI::BOOL, MPI::LAND);
341	>
342	>	struct {
343	>	RealType val;
344	>	int rank;
345	>	} max_vals, min_vals;
346	>
347	>	if (min_found) {
348	>	if (my_min_found)
349	>	min_vals.val = min_val;
350	>	else
351	>	min_vals.val = HONKING_LARGE_VALUE;
352	>
353	>	min_vals.rank = worldRank;
354	>
355	>	// Who had the minimum?
356	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
357	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
358	>	min_val = min_vals.val;
359	>	}
360	>
361	>	if (max_found) {
362	>	if (my_max_found)
363	>	max_vals.val = max_val;
364	>	else
365	>	max_vals.val = -HONKING_LARGE_VALUE;
366	>
367	>	max_vals.rank = worldRank;
368	>
369	>	// Who had the maximum?
370	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
371	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
372	>	max_val = max_vals.val;
373	>	}
374	>	#endif
375
376	+	if (max_found && min_found) {
377	+	if (min_val< max_val) {
378	+
379	+	#ifdef IS_MPI
380	+	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
381	+	// I have both maximum and minimum, so proceed like a single
382	+	// processor version:
383	+	#endif
384	+	// objects to be swapped: velocity & angular velocity
385	+	Vector3d min_vel = min_sd->getVel();
386	+	Vector3d max_vel = max_sd->getVel();
387	+	RealType temp_vel;
388	+
389	+	switch(rnemdType_) {
390	+	case rnemdKineticSwap :
391	+	min_sd->setVel(max_vel);
392	+	max_sd->setVel(min_vel);
393	+	if (min_sd->isDirectional() && max_sd->isDirectional()) {
394	+	Vector3d min_angMom = min_sd->getJ();
395	+	Vector3d max_angMom = max_sd->getJ();
396	+	min_sd->setJ(max_angMom);
397	+	max_sd->setJ(min_angMom);
398	+	}
399	+	break;
400	+	case rnemdPx :
401	+	temp_vel = min_vel.x();
402	+	min_vel.x() = max_vel.x();
403	+	max_vel.x() = temp_vel;
404	+	min_sd->setVel(min_vel);
405	+	max_sd->setVel(max_vel);
406	+	break;
407	+	case rnemdPy :
408	+	temp_vel = min_vel.y();
409	+	min_vel.y() = max_vel.y();
410	+	max_vel.y() = temp_vel;
411	+	min_sd->setVel(min_vel);
412	+	max_sd->setVel(max_vel);
413	+	break;
414	+	case rnemdPz :
415	+	temp_vel = min_vel.z();
416	+	min_vel.z() = max_vel.z();
417	+	max_vel.z() = temp_vel;
418	+	min_sd->setVel(min_vel);
419	+	max_sd->setVel(max_vel);
420	+	break;
421	+	default :
422	+	break;
423	+	}
424	+	#ifdef IS_MPI
425	+	// the rest of the cases only apply in parallel simulations:
426	+	} else if (max_vals.rank == worldRank) {
427	+	// I had the max, but not the minimum
428	+
429	+	Vector3d min_vel;
430	+	Vector3d max_vel = max_sd->getVel();
431	+	MPI::Status status;
432	+
433	+	// point-to-point swap of the velocity vector
434	+	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
435	+	min_vals.rank, 0,
436	+	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
437	+	min_vals.rank, 0, status);
438	+
439	+	switch(rnemdType_) {
440	+	case rnemdKineticSwap :
441	+	max_sd->setVel(min_vel);
442	+
443	+	if (max_sd->isDirectional()) {
444	+	Vector3d min_angMom;
445	+	Vector3d max_angMom = max_sd->getJ();
446	+
447	+	// point-to-point swap of the angular momentum vector
448	+	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
449	+	MPI::REALTYPE, min_vals.rank, 1,
450	+	min_angMom.getArrayPointer(), 3,
451	+	MPI::REALTYPE, min_vals.rank, 1,
452	+	status);
453	+
454	+	max_sd->setJ(min_angMom);
455	+	}
456	+	break;
457	+	case rnemdPx :
458	+	max_vel.x() = min_vel.x();
459	+	max_sd->setVel(max_vel);
460	+	break;
461	+	case rnemdPy :
462	+	max_vel.y() = min_vel.y();
463	+	max_sd->setVel(max_vel);
464	+	break;
465	+	case rnemdPz :
466	+	max_vel.z() = min_vel.z();
467	+	max_sd->setVel(max_vel);
468	+	break;
469	+	default :
470	+	break;
471	+	}
472	+	} else if (min_vals.rank == worldRank) {
473	+	// I had the minimum but not the maximum:
474	+
475	+	Vector3d max_vel;
476	+	Vector3d min_vel = min_sd->getVel();
477	+	MPI::Status status;
478	+
479	+	// point-to-point swap of the velocity vector
480	+	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
481	+	max_vals.rank, 0,
482	+	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
483	+	max_vals.rank, 0, status);
484	+
485	+	switch(rnemdType_) {
486	+	case rnemdKineticSwap :
487	+	min_sd->setVel(max_vel);
488	+
489	+	if (min_sd->isDirectional()) {
490	+	Vector3d min_angMom = min_sd->getJ();
491	+	Vector3d max_angMom;
492	+
493	+	// point-to-point swap of the angular momentum vector
494	+	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
495	+	MPI::REALTYPE, max_vals.rank, 1,
496	+	max_angMom.getArrayPointer(), 3,
497	+	MPI::REALTYPE, max_vals.rank, 1,
498	+	status);
499	+
500	+	min_sd->setJ(max_angMom);
501	+	}
502	+	break;
503	+	case rnemdPx :
504	+	min_vel.x() = max_vel.x();
505	+	min_sd->setVel(min_vel);
506	+	break;
507	+	case rnemdPy :
508	+	min_vel.y() = max_vel.y();
509	+	min_sd->setVel(min_vel);
510	+	break;
511	+	case rnemdPz :
512	+	min_vel.z() = max_vel.z();
513	+	min_sd->setVel(min_vel);
514	+	break;
515	+	default :
516	+	break;
517	+	}
518	+	}
519	+	#endif
520	+	exchangeSum_ += max_val - min_val;
521	+	} else {
522	+	std::cerr << "exchange NOT performed!\nmin_val > max_val.\n";
523	+	failTrialCount_++;
524	+	}
525	+	} else {
526	+	std::cerr << "exchange NOT performed!\n";
527	+	std::cerr << "at least one of the two slabs empty.\n";
528	+	failTrialCount_++;
529		}
530	<	}
530	>
531	>	}
532	>
533	>	void RNEMD::doScale() {
534	>
535	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
536	>	Mat3x3d hmat = currentSnap_->getHmat();
537	>
538	>	seleMan_.setSelectionSet(evaluator_.evaluate());
539	>
540	>	int selei;
541	>	StuntDouble* sd;
542	>	int idx;
543	>
544	>	std::vector<StuntDouble*> hotBin, coldBin;
545	>
546	>	RealType Phx = 0.0;
547	>	RealType Phy = 0.0;
548	>	RealType Phz = 0.0;
549	>	RealType Khx = 0.0;
550	>	RealType Khy = 0.0;
551	>	RealType Khz = 0.0;
552	>	RealType Pcx = 0.0;
553	>	RealType Pcy = 0.0;
554	>	RealType Pcz = 0.0;
555	>	RealType Kcx = 0.0;
556	>	RealType Kcy = 0.0;
557	>	RealType Kcz = 0.0;
558	>
559	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
560	>	sd = seleMan_.nextSelected(selei)) {
561	>
562	>	idx = sd->getLocalIndex();
563	>
564	>	Vector3d pos = sd->getPos();
565	>
566	>	// wrap the stuntdouble's position back into the box:
567	>
568	>	if (usePeriodicBoundaryConditions_)
569	>	currentSnap_->wrapVector(pos);
570	>
571	>	// which bin is this stuntdouble in?
572	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
573	>
574	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
575	>
576	>	// if we're in bin 0 or the middleBin
577	>	if (binNo == 0 || binNo == midBin_) {
578	>
579	>	RealType mass = sd->getMass();
580	>	Vector3d vel = sd->getVel();
581	>
582	>	if (binNo == 0) {
583	>	hotBin.push_back(sd);
584	>	Phx += mass * vel.x();
585	>	Phy += mass * vel.y();
586	>	Phz += mass * vel.z();
587	>	Khx += mass * vel.x() * vel.x();
588	>	Khy += mass * vel.y() * vel.y();
589	>	Khz += mass * vel.z() * vel.z();
590	>	} else { //midBin_
591	>	coldBin.push_back(sd);
592	>	Pcx += mass * vel.x();
593	>	Pcy += mass * vel.y();
594	>	Pcz += mass * vel.z();
595	>	Kcx += mass * vel.x() * vel.x();
596	>	Kcy += mass * vel.y() * vel.y();
597	>	Kcz += mass * vel.z() * vel.z();
598	>	}
599	>	}
600	>	}
601	>
602	>	Khx *= 0.5;
603	>	Khy *= 0.5;
604	>	Khz *= 0.5;
605	>	Kcx *= 0.5;
606	>	Kcy *= 0.5;
607	>	Kcz *= 0.5;
608	>
609	>	#ifdef IS_MPI
610	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
612	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
613	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
614	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
615	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
616	>
617	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
618	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
620	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
622	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
623	>	#endif
624	>
625	>	//use coldBin coeff's
626	>	RealType px = Pcx / Phx;
627	>	RealType py = Pcy / Phy;
628	>	RealType pz = Pcz / Phz;
629	>
630	>	RealType a000, a110, c0, a001, a111, b01, b11, c1, c;
631	>	switch(rnemdType_) {
632	>	case rnemdKineticScale :
633	>	/*used hotBin coeff's & only scale x & y dimensions
634	>	RealType px = Phx / Pcx;
635	>	RealType py = Phy / Pcy;
636	>	a110 = Khy;
637	>	c0 = - Khx - Khy - targetFlux_;
638	>	a000 = Khx;
639	>	a111 = Kcy * py * py
640	>	b11 = -2.0 * Kcy * py * (1.0 + py);
641	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
642	>	b01 = -2.0 * Kcx * px * (1.0 + px);
643	>	a001 = Kcx * px * px;
644	>	*/
645	>
646	>	//scale all three dimensions, let c_x = c_y
647	>	a000 = Kcx + Kcy;
648	>	a110 = Kcz;
649	>	c0 = targetFlux_ - Kcx - Kcy - Kcz;
650	>	a001 = Khx * px * px + Khy * py * py;
651	>	a111 = Khz * pz * pz;
652	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
653	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
654	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
655	>	+ Khz * pz * (2.0 + pz) - targetFlux_;
656	>	break;
657	>	case rnemdPxScale :
658	>	c = 1 - targetFlux_ / Pcx;
659	>	a000 = Kcy;
660	>	a110 = Kcz;
661	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
662	>	a001 = py * py * Khy;
663	>	a111 = pz * pz * Khz;
664	>	b01 = -2.0 * Khy * py * (1.0 + py);
665	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
666	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
667	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
668	>	break;
669	>	case rnemdPyScale :
670	>	c = 1 - targetFlux_ / Pcy;
671	>	a000 = Kcx;
672	>	a110 = Kcz;
673	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
674	>	a001 = px * px * Khx;
675	>	a111 = pz * pz * Khz;
676	>	b01 = -2.0 * Khx * px * (1.0 + px);
677	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
678	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
679	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
680	>	break;
681	>	case rnemdPzScale ://we don't really do this, do we?
682	>	c = 1 - targetFlux_ / Pcz;
683	>	a000 = Kcx;
684	>	a110 = Kcy;
685	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
686	>	a001 = px * px * Khx;
687	>	a111 = py * py * Khy;
688	>	b01 = -2.0 * Khx * px * (1.0 + px);
689	>	b11 = -2.0 * Khy * py * (1.0 + py);
690	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
691	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
692	>	break;
693	>	default :
694	>	break;
695	>	}
696	>
697	>	RealType v1 = a000 * a111 - a001 * a110;
698	>	RealType v2 = a000 * b01;
699	>	RealType v3 = a000 * b11;
700	>	RealType v4 = a000 * c1 - a001 * c0;
701	>	RealType v8 = a110 * b01;
702	>	RealType v10 = - b01 * c0;
703	>
704	>	RealType u0 = v2 * v10 - v4 * v4;
705	>	RealType u1 = -2.0 * v3 * v4;
706	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
707	>	RealType u3 = -2.0 * v1 * v3;
708	>	RealType u4 = - v1 * v1;
709	>	//rescale coefficients
710	>	RealType maxAbs = fabs(u0);
711	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
712	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
713	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
714	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
715	>	u0 /= maxAbs;
716	>	u1 /= maxAbs;
717	>	u2 /= maxAbs;
718	>	u3 /= maxAbs;
719	>	u4 /= maxAbs;
720	>	//max_element(start, end) is also available.
721	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
722	>	poly.setCoefficient(4, u4);
723	>	poly.setCoefficient(3, u3);
724	>	poly.setCoefficient(2, u2);
725	>	poly.setCoefficient(1, u1);
726	>	poly.setCoefficient(0, u0);
727	>	std::vector<RealType> realRoots = poly.FindRealRoots();
728	>
729	>	std::vector<RealType>::iterator ri;
730	>	RealType r1, r2, alpha0;
731	>	std::vector<std::pair<RealType,RealType> > rps;
732	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
733	>	r2 = *ri;
734	>	//check if FindRealRoots() give the right answer
735	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
736	>	sprintf(painCave.errMsg,
737	>	"RNEMD Warning: polynomial solve seems to have an error!");
738	>	painCave.isFatal = 0;
739	>	simError();
740	>	failRootCount_++;
741	>	}
742	>	//might not be useful w/o rescaling coefficients
743	>	alpha0 = -c0 - a110 * r2 * r2;
744	>	if (alpha0 >= 0.0) {
745	>	r1 = sqrt(alpha0 / a000);
746	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6)
747	>	{ rps.push_back(std::make_pair(r1, r2)); }
748	>	if (r1 > 1e-6) { //r1 non-negative
749	>	r1 = -r1;
750	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6)
751	>	{ rps.push_back(std::make_pair(r1, r2)); }
752	>	}
753	>	}
754	>	}
755	>	// Consider combininig together the solving pair part w/ the searching
756	>	// best solution part so that we don't need the pairs vector
757	>	if (!rps.empty()) {
758	>	RealType smallestDiff = HONKING_LARGE_VALUE;
759	>	RealType diff;
760	>	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
761	>	std::vector<std::pair<RealType,RealType> >::iterator rpi;
762	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
763	>	r1 = (*rpi).first;
764	>	r2 = (*rpi).second;
765	>	switch(rnemdType_) {
766	>	case rnemdKineticScale :
767	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
768	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
769	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
770	>	break;
771	>	case rnemdPxScale :
772	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
773	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
774	>	break;
775	>	case rnemdPyScale :
776	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
777	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
778	>	break;
779	>	case rnemdPzScale :
780	>	default :
781	>	break;
782	>	}
783	>	if (diff < smallestDiff) {
784	>	smallestDiff = diff;
785	>	bestPair = *rpi;
786	>	}
787	>	}
788	>	#ifdef IS_MPI
789	>	if (worldRank == 0) {
790	>	#endif
791	>	std::cerr << "we choose r1 = " << bestPair.first
792	>	<< " and r2 = " << bestPair.second << "\n";
793	>	#ifdef IS_MPI
794	>	}
795	>	#endif
796	>
797	>	RealType x, y, z;
798	>	switch(rnemdType_) {
799	>	case rnemdKineticScale :
800	>	x = bestPair.first;
801	>	y = bestPair.first;
802	>	z = bestPair.second;
803	>	break;
804	>	case rnemdPxScale :
805	>	x = c;
806	>	y = bestPair.first;
807	>	z = bestPair.second;
808	>	break;
809	>	case rnemdPyScale :
810	>	x = bestPair.first;
811	>	y = c;
812	>	z = bestPair.second;
813	>	break;
814	>	case rnemdPzScale :
815	>	x = bestPair.first;
816	>	y = bestPair.second;
817	>	z = c;
818	>	break;
819	>	default :
820	>	break;
821	>	}
822	>	std::vector<StuntDouble*>::iterator sdi;
823	>	Vector3d vel;
824	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
825	>	vel = (*sdi)->getVel();
826	>	vel.x() *= x;
827	>	vel.y() *= y;
828	>	vel.z() *= z;
829	>	(*sdi)->setVel(vel);
830	>	}
831	>	//convert to hotBin coefficient
832	>	x = 1.0 + px * (1.0 - x);
833	>	y = 1.0 + py * (1.0 - y);
834	>	z = 1.0 + pz * (1.0 - z);
835	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
836	>	vel = (*sdi)->getVel();
837	>	vel.x() *= x;
838	>	vel.y() *= y;
839	>	vel.z() *= z;
840	>	(*sdi)->setVel(vel);
841	>	}
842	>	exchangeSum_ += targetFlux_;
843	>	//we may want to check whether the exchange has been successful
844	>	} else {
845	>	std::cerr << "exchange NOT performed!\n";//MPI incompatible
846	>	failTrialCount_++;
847	>	}
848	>
849	>	}
850	>
851	>	void RNEMD::doRNEMD() {
852	>
853	>	switch(rnemdType_) {
854	>	case rnemdKineticScale :
855	>	case rnemdPxScale :
856	>	case rnemdPyScale :
857	>	case rnemdPzScale :
858	>	doScale();
859	>	break;
860	>	case rnemdKineticSwap :
861	>	case rnemdPx :
862	>	case rnemdPy :
863	>	case rnemdPz :
864	>	doSwap();
865	>	break;
866	>	case rnemdUnknown :
867	>	default :
868	>	break;
869	>	}
870	>	}
871	>
872	>	void RNEMD::collectData() {
873	>
874	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
875	>	Mat3x3d hmat = currentSnap_->getHmat();
876	>
877	>	seleMan_.setSelectionSet(evaluator_.evaluate());
878	>
879	>	int selei;
880	>	StuntDouble* sd;
881	>	int idx;
882	>
883	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
884	>	sd = seleMan_.nextSelected(selei)) {
885	>
886	>	idx = sd->getLocalIndex();
887	>
888	>	Vector3d pos = sd->getPos();
889	>
890	>	// wrap the stuntdouble's position back into the box:
891	>
892	>	if (usePeriodicBoundaryConditions_)
893	>	currentSnap_->wrapVector(pos);
894	>
895	>	// which bin is this stuntdouble in?
896	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
897	>
898	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
899	>
900	>	if (rnemdLogWidth_ == midBin_ + 1)
901	>	if (binNo > midBin_)
902	>	binNo = nBins_ - binNo;
903	>
904	>	RealType mass = sd->getMass();
905	>	Vector3d vel = sd->getVel();
906	>	RealType value;
907	>	RealType xVal, yVal, zVal;
908	>
909	>	switch(rnemdType_) {
910	>	case rnemdKineticSwap :
911	>	case rnemdKineticScale :
912	>
913	>	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
914	>	vel[2]*vel[2]);
915	>
916	>	valueCount_[binNo] += 3;
917	>	if (sd->isDirectional()) {
918	>	Vector3d angMom = sd->getJ();
919	>	Mat3x3d I = sd->getI();
920	>
921	>	if (sd->isLinear()) {
922	>	int i = sd->linearAxis();
923	>	int j = (i + 1) % 3;
924	>	int k = (i + 2) % 3;
925	>	value += angMom[j] * angMom[j] / I(j, j) +
926	>	angMom[k] * angMom[k] / I(k, k);
927	>
928	>	valueCount_[binNo] +=2;
929	>
930	>	} else {
931	>	value += angMom[0]*angMom[0]/I(0, 0)
932	>	+ angMom[1]*angMom[1]/I(1, 1)
933	>	+ angMom[2]*angMom[2]/I(2, 2);
934	>	valueCount_[binNo] +=3;
935	>	}
936	>	}
937	>	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
938	>
939	>	break;
940	>	case rnemdPx :
941	>	case rnemdPxScale :
942	>	value = mass * vel[0];
943	>	valueCount_[binNo]++;
944	>	xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
945	>	/ PhysicalConstants::kb;
946	>	yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
947	>	/ PhysicalConstants::kb;
948	>	zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
949	>	/ PhysicalConstants::kb;
950	>	xTempHist_[binNo] += xVal;
951	>	yTempHist_[binNo] += yVal;
952	>	zTempHist_[binNo] += zVal;
953	>	break;
954	>	case rnemdPy :
955	>	case rnemdPyScale :
956	>	value = mass * vel[1];
957	>	valueCount_[binNo]++;
958	>	break;
959	>	case rnemdPz :
960	>	case rnemdPzScale :
961	>	value = mass * vel[2];
962	>	valueCount_[binNo]++;
963	>	break;
964	>	case rnemdUnknown :
965	>	default :
966	>	break;
967	>	}
968	>	valueHist_[binNo] += value;
969	>	}
970	>
971	>	}
972	>
973	>	void RNEMD::getStarted() {
974	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
975	>	Stats& stat = currentSnap_->statData;
976	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
977	>	}
978	>
979	>	void RNEMD::getStatus() {
980	>
981	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
982	>	Stats& stat = currentSnap_->statData;
983	>	RealType time = currentSnap_->getTime();
984	>
985	>	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
986	>	//or to be more meaningful, define another item as exchangeSum_ / time
987	>	int j;
988	>
989	>	#ifdef IS_MPI
990	>
991	>	// all processors have the same number of bins, and STL vectors pack their
992	>	// arrays, so in theory, this should be safe:
993	>
994	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0],
995	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
996	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0],
997	>	rnemdLogWidth_, MPI::INT, MPI::SUM);
998	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale) {
999	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1000	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1001	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1002	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1003	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1004	>	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1005	>	}
1006	>	// If we're the root node, should we print out the results
1007	>	int worldRank = MPI::COMM_WORLD.Get_rank();
1008	>	if (worldRank == 0) {
1009	>	#endif
1010	>	rnemdLog_ << time;
1011	>	for (j = 0; j < rnemdLogWidth_; j++) {
1012	>	rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j];
1013	>	}
1014	>	rnemdLog_ << "\n";
1015	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale ) {
1016	>	xTempLog_ << time;
1017	>	for (j = 0; j < rnemdLogWidth_; j++) {
1018	>	xTempLog_ << "\t" << xTempHist_[j] / (RealType)valueCount_[j];
1019	>	}
1020	>	xTempLog_ << "\n";
1021	>	yTempLog_ << time;
1022	>	for (j = 0; j < rnemdLogWidth_; j++) {
1023	>	yTempLog_ << "\t" << yTempHist_[j] / (RealType)valueCount_[j];
1024	>	}
1025	>	yTempLog_ << "\n";
1026	>	zTempLog_ << time;
1027	>	for (j = 0; j < rnemdLogWidth_; j++) {
1028	>	zTempLog_ << "\t" << zTempHist_[j] / (RealType)valueCount_[j];
1029	>	}
1030	>	zTempLog_ << "\n";
1031	>	}
1032	>	#ifdef IS_MPI
1033	>	}
1034	>	#endif
1035	>	for (j = 0; j < rnemdLogWidth_; j++) {
1036	>	valueCount_[j] = 0;
1037	>	valueHist_[j] = 0.0;
1038	>	}
1039	>	if (rnemdType_ == rnemdPx || rnemdType_ == rnemdPxScale)
1040	>	for (j = 0; j < rnemdLogWidth_; j++) {
1041	>	xTempHist_[j] = 0.0;
1042	>	yTempHist_[j] = 0.0;
1043	>	zTempHist_[j] = 0.0;
1044	>	}
1045	>	}
1046		}

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1333 by gezelter, Thu Apr 2 18:11:59 2009 UTC vs.
branches/development/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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