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

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 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 "integrators/RNEMD.hpp"
42	>	#include <cmath>
43	>	#include "rnemd/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45	+	#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
47	+	#include "math/Polynomial.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "primitives/StuntDouble.hpp"
50	<	#include "utils/OOPSEConstant.hpp"
50	>	#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52	<
53	<	#ifndef IS_MPI
51	<	#include "math/SeqRandNumGen.hpp"
52	<	#else
53	<	#include "math/ParallelRandNumGen.hpp"
52	>	#ifdef IS_MPI
53	>	#include <mpi.h>
54		#endif
55
56	<	/* Remove me after testing*/
57	<	/*
58	<	#include <cstdio>
59	<	#include <iostream>
60	<	*/
61	<	/*End remove me*/
56	>	#define HONKING_LARGE_VALUE 1.0e10
57
58	<	namespace oopse {
58	>	using namespace std;
59	>	namespace OpenMD {
60
61	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
62	<
61	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
62	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63	>
64	>	trialCount_ = 0;
65	>	failTrialCount_ = 0;
66	>	failRootCount_ = 0;
67	>
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
73	<	stringToEnumMap_["Px"] = rnemdPx;
72	<	stringToEnumMap_["Py"] = rnemdPy;
73	<	stringToEnumMap_["Pz"] = rnemdPz;
74	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
75	>	stringToMethod_["Swap"]  = rnemdSwap;
76	>	stringToMethod_["NIVS"]  = rnemdNIVS;
77	>	stringToMethod_["VSS"]   = rnemdVSS;
78
79	<	std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
79	>	stringToFluxType_["KE"]  = rnemdKE;
80	>	stringToFluxType_["Px"]  = rnemdPx;
81	>	stringToFluxType_["Py"]  = rnemdPy;
82	>	stringToFluxType_["Pz"]  = rnemdPz;
83	>	stringToFluxType_["Pvector"]  = rnemdPvector;
84	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
85	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
86	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
87	>
88	>	runTime_ = simParams->getRunTime();
89	>	statusTime_ = simParams->getStatusTime();
90	>
91	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
92		evaluator_.loadScriptString(rnemdObjectSelection_);
93	<	std::cerr << "done\n";
93	>	seleMan_.setSelectionSet(evaluator_.evaluate());
94	>
95	>	const string methStr = rnemdParams->getMethod();
96	>	bool hasFluxType = rnemdParams->haveFluxType();
97	>
98	>	string fluxStr;
99	>	if (hasFluxType) {
100	>	fluxStr = rnemdParams->getFluxType();
101	>	} else {
102	>	sprintf(painCave.errMsg,
103	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
104	>	"\twhich must be one of the following values:\n"
105	>	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
106	>	"\tmust be set to use RNEMD\n");
107	>	painCave.isFatal = 1;
108	>	painCave.severity = OPENMD_ERROR;
109	>	simError();
110	>	}
111	>
112	>	bool hasKineticFlux = rnemdParams->haveKineticFlux();
113	>	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
114	>	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
115	>	bool hasSlabWidth = rnemdParams->haveSlabWidth();
116	>	bool hasSlabACenter = rnemdParams->haveSlabACenter();
117	>	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
118	>	bool hasOutputFileName = rnemdParams->haveOutputFileName();
119	>	bool hasOutputFields = rnemdParams->haveOutputFields();
120
121	<	const std::string st = simParams->getRNEMD_swapType();
121	>	map<string, RNEMDMethod>::iterator i;
122	>	i = stringToMethod_.find(methStr);
123	>	if (i != stringToMethod_.end())
124	>	rnemdMethod_ = i->second;
125	>	else {
126	>	sprintf(painCave.errMsg,
127	>	"RNEMD: The current method,\n"
128	>	"\t\t%s is not one of the recognized\n"
129	>	"\texchange methods: Swap, NIVS, or VSS\n",
130	>	methStr.c_str());
131	>	painCave.isFatal = 1;
132	>	painCave.severity = OPENMD_ERROR;
133	>	simError();
134	>	}
135
136	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
137	<	i = stringToEnumMap_.find(st);
138	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
136	>	map<string, RNEMDFluxType>::iterator j;
137	>	j = stringToFluxType_.find(fluxStr);
138	>	if (j != stringToFluxType_.end())
139	>	rnemdFluxType_ = j->second;
140	>	else {
141	>	sprintf(painCave.errMsg,
142	>	"RNEMD: The current fluxType,\n"
143	>	"\t\t%s\n"
144	>	"\tis not one of the recognized flux types.\n",
145	>	fluxStr.c_str());
146	>	painCave.isFatal = 1;
147	>	painCave.severity = OPENMD_ERROR;
148	>	simError();
149	>	}
150
151	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
152	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
153	<	exchangeSum_ = 0.0;
154	<	counter_ = 0; //added by shenyu
155	<	//profile_.open("profile", std::ios::out);
151	>	bool methodFluxMismatch = false;
152	>	bool hasCorrectFlux = false;
153	>	switch(rnemdMethod_) {
154	>	case rnemdSwap:
155	>	switch (rnemdFluxType_) {
156	>	case rnemdKE:
157	>	hasCorrectFlux = hasKineticFlux;
158	>	break;
159	>	case rnemdPx:
160	>	case rnemdPy:
161	>	case rnemdPz:
162	>	hasCorrectFlux = hasMomentumFlux;
163	>	break;
164	>	default :
165	>	methodFluxMismatch = true;
166	>	break;
167	>	}
168	>	break;
169	>	case rnemdNIVS:
170	>	switch (rnemdFluxType_) {
171	>	case rnemdKE:
172	>	case rnemdRotKE:
173	>	case rnemdFullKE:
174	>	hasCorrectFlux = hasKineticFlux;
175	>	break;
176	>	case rnemdPx:
177	>	case rnemdPy:
178	>	case rnemdPz:
179	>	hasCorrectFlux = hasMomentumFlux;
180	>	break;
181	>	case rnemdKePx:
182	>	case rnemdKePy:
183	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
184	>	break;
185	>	default:
186	>	methodFluxMismatch = true;
187	>	break;
188	>	}
189	>	break;
190	>	case rnemdVSS:
191	>	switch (rnemdFluxType_) {
192	>	case rnemdKE:
193	>	case rnemdRotKE:
194	>	case rnemdFullKE:
195	>	hasCorrectFlux = hasKineticFlux;
196	>	break;
197	>	case rnemdPx:
198	>	case rnemdPy:
199	>	case rnemdPz:
200	>	hasCorrectFlux = hasMomentumFlux;
201	>	break;
202	>	case rnemdPvector:
203	>	hasCorrectFlux = hasMomentumFluxVector;
204	>	break;
205	>	case rnemdKePx:
206	>	case rnemdKePy:
207	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
208	>	break;
209	>	case rnemdKePvector:
210	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
211	>	break;
212	>	default:
213	>	methodFluxMismatch = true;
214	>	break;
215	>	}
216	>	default:
217	>	break;
218	>	}
219
220	<	#ifndef IS_MPI
221	<	if (simParams->haveSeed()) {
222	<	seedValue = simParams->getSeed();
223	<	randNumGen_ = new SeqRandNumGen(seedValue);
224	<	}else {
225	<	randNumGen_ = new SeqRandNumGen();
226	<	}
227	<	#else
228	<	if (simParams->haveSeed()) {
229	<	seedValue = simParams->getSeed();
230	<	randNumGen_ = new ParallelRandNumGen(seedValue);
231	<	}else {
232	<	randNumGen_ = new ParallelRandNumGen();
233	<	}
234	<	#endif
235	<	}
220	>	if (methodFluxMismatch) {
221	>	sprintf(painCave.errMsg,
222	>	"RNEMD: The current method,\n"
223	>	"\t\t%s\n"
224	>	"\tcannot be used with the current flux type, %s\n",
225	>	methStr.c_str(), fluxStr.c_str());
226	>	painCave.isFatal = 1;
227	>	painCave.severity = OPENMD_ERROR;
228	>	simError();
229	>	}
230	>	if (!hasCorrectFlux) {
231	>	sprintf(painCave.errMsg,
232	>	"RNEMD: The current method, %s, and flux type, %s,\n"
233	>	"\tdid not have the correct flux value specified. Options\n"
234	>	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
235	>	methStr.c_str(), fluxStr.c_str());
236	>	painCave.isFatal = 1;
237	>	painCave.severity = OPENMD_ERROR;
238	>	simError();
239	>	}
240	>
241	>	if (hasKineticFlux) {
242	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
243	>	// into  amu / fs^3:
244	>	kineticFlux_ = rnemdParams->getKineticFlux()
245	>	* PhysicalConstants::energyConvert;
246	>	} else {
247	>	kineticFlux_ = 0.0;
248	>	}
249	>	if (hasMomentumFluxVector) {
250	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
251	>	} else {
252	>	momentumFluxVector_ = V3Zero;
253	>	if (hasMomentumFlux) {
254	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
255	>	switch (rnemdFluxType_) {
256	>	case rnemdPx:
257	>	momentumFluxVector_.x() = momentumFlux;
258	>	break;
259	>	case rnemdPy:
260	>	momentumFluxVector_.y() = momentumFlux;
261	>	break;
262	>	case rnemdPz:
263	>	momentumFluxVector_.z() = momentumFlux;
264	>	break;
265	>	case rnemdKePx:
266	>	momentumFluxVector_.x() = momentumFlux;
267	>	break;
268	>	case rnemdKePy:
269	>	momentumFluxVector_.y() = momentumFlux;
270	>	break;
271	>	default:
272	>	break;
273	>	}
274	>	}
275	>	}
276	>
277	>	// do some sanity checking
278	>
279	>	int selectionCount = seleMan_.getSelectionCount();
280	>
281	>	int nIntegrable = info->getNGlobalIntegrableObjects();
282	>
283	>	if (selectionCount > nIntegrable) {
284	>	sprintf(painCave.errMsg,
285	>	"RNEMD: The current objectSelection,\n"
286	>	"\t\t%s\n"
287	>	"\thas resulted in %d selected objects.  However,\n"
288	>	"\tthe total number of integrable objects in the system\n"
289	>	"\tis only %d.  This is almost certainly not what you want\n"
290	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
291	>	"\tselector in the selection script!\n",
292	>	rnemdObjectSelection_.c_str(),
293	>	selectionCount, nIntegrable);
294	>	painCave.isFatal = 0;
295	>	painCave.severity = OPENMD_WARNING;
296	>	simError();
297	>	}
298	>
299	>	areaAccumulator_ = new Accumulator();
300	>
301	>	nBins_ = rnemdParams->getOutputBins();
302	>
303	>	data_.resize(RNEMD::ENDINDEX);
304	>	OutputData z;
305	>	z.units =  "Angstroms";
306	>	z.title =  "Z";
307	>	z.dataType = "RealType";
308	>	z.accumulator.reserve(nBins_);
309	>	for (unsigned int i = 0; i < nBins_; i++)
310	>	z.accumulator.push_back( new Accumulator() );
311	>	data_[Z] = z;
312	>	outputMap_["Z"] =  Z;
313	>
314	>	OutputData temperature;
315	>	temperature.units =  "K";
316	>	temperature.title =  "Temperature";
317	>	temperature.dataType = "RealType";
318	>	temperature.accumulator.reserve(nBins_);
319	>	for (unsigned int i = 0; i < nBins_; i++)
320	>	temperature.accumulator.push_back( new Accumulator() );
321	>	data_[TEMPERATURE] = temperature;
322	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
323	>
324	>	OutputData velocity;
325	>	velocity.units = "angstroms/fs";
326	>	velocity.title =  "Velocity";
327	>	velocity.dataType = "Vector3d";
328	>	velocity.accumulator.reserve(nBins_);
329	>	for (unsigned int i = 0; i < nBins_; i++)
330	>	velocity.accumulator.push_back( new VectorAccumulator() );
331	>	data_[VELOCITY] = velocity;
332	>	outputMap_["VELOCITY"] = VELOCITY;
333	>
334	>	OutputData density;
335	>	density.units =  "g cm^-3";
336	>	density.title =  "Density";
337	>	density.dataType = "RealType";
338	>	density.accumulator.reserve(nBins_);
339	>	for (unsigned int i = 0; i < nBins_; i++)
340	>	density.accumulator.push_back( new Accumulator() );
341	>	data_[DENSITY] = density;
342	>	outputMap_["DENSITY"] =  DENSITY;
343	>
344	>	if (hasOutputFields) {
345	>	parseOutputFileFormat(rnemdParams->getOutputFields());
346	>	} else {
347	>	outputMask_.set(Z);
348	>	switch (rnemdFluxType_) {
349	>	case rnemdKE:
350	>	case rnemdRotKE:
351	>	case rnemdFullKE:
352	>	outputMask_.set(TEMPERATURE);
353	>	break;
354	>	case rnemdPx:
355	>	case rnemdPy:
356	>	outputMask_.set(VELOCITY);
357	>	break;
358	>	case rnemdPz:
359	>	case rnemdPvector:
360	>	outputMask_.set(VELOCITY);
361	>	outputMask_.set(DENSITY);
362	>	break;
363	>	case rnemdKePx:
364	>	case rnemdKePy:
365	>	outputMask_.set(TEMPERATURE);
366	>	outputMask_.set(VELOCITY);
367	>	break;
368	>	case rnemdKePvector:
369	>	outputMask_.set(TEMPERATURE);
370	>	outputMask_.set(VELOCITY);
371	>	outputMask_.set(DENSITY);
372	>	break;
373	>	default:
374	>	break;
375	>	}
376	>	}
377	>
378	>	if (hasOutputFileName) {
379	>	rnemdFileName_ = rnemdParams->getOutputFileName();
380	>	} else {
381	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
382	>	}
383	>
384	>	exchangeTime_ = rnemdParams->getExchangeTime();
385	>
386	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
387	>	Mat3x3d hmat = currentSnap_->getHmat();
388
389	+	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
390	+	// Lx, Ly = box dimensions in x & y
391	+	// dt = exchange time interval
392	+	// flux = target flux
393	+
394	+	RealType area = currentSnap_->getXYarea();
395	+	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
396	+	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
397	+
398	+	// total exchange sums are zeroed out at the beginning:
399	+
400	+	kineticExchange_ = 0.0;
401	+	momentumExchange_ = V3Zero;
402	+
403	+	if (hasSlabWidth)
404	+	slabWidth_ = rnemdParams->getSlabWidth();
405	+	else
406	+	slabWidth_ = hmat(2,2) / 10.0;
407	+
408	+	if (hasSlabACenter)
409	+	slabACenter_ = rnemdParams->getSlabACenter();
410	+	else
411	+	slabACenter_ = 0.0;
412	+
413	+	if (hasSlabBCenter)
414	+	slabBCenter_ = rnemdParams->getSlabBCenter();
415	+	else
416	+	slabBCenter_ = hmat(2,2) / 2.0;
417	+
418	+	}
419	+
420		RNEMD::~RNEMD() {
421	<	delete randNumGen_;
422	<	//profile_.close();
421	>	if (!doRNEMD_) return;
422	>	#ifdef IS_MPI
423	>	if (worldRank == 0) {
424	>	#endif
425	>
426	>	writeOutputFile();
427	>
428	>	rnemdFile_.close();
429	>
430	>	#ifdef IS_MPI
431	>	}
432	>	#endif
433		}
434	+
435	+	bool RNEMD::inSlabA(Vector3d pos) {
436	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
437	+	}
438	+	bool RNEMD::inSlabB(Vector3d pos) {
439	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
440	+	}
441
442		void RNEMD::doSwap() {
443	<	//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";
124	<
443	>	if (!doRNEMD_) return;
444		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
445		Mat3x3d hmat = currentSnap_->getHmat();
446
128	–	//std::cerr << "hmat = " << hmat << "\n";
129	–
447		seleMan_.setSelectionSet(evaluator_.evaluate());
448
132	–	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
133	–
449		int selei;
450		StuntDouble* sd;
451		int idx;
#	Line 154 | Line 469 | namespace oopse {
469
470		if (usePeriodicBoundaryConditions_)
471		currentSnap_->wrapVector(pos);
472	+	bool inA = inSlabA(pos);
473	+	bool inB = inSlabB(pos);
474
475	<	// which bin is this stuntdouble in?
159	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
160	<
161	<	int binNo = int((nBins_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2));
162	<
163	<	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
164	<
165	<	// if we're in bin 0 or the middleBin
166	<	if (binNo == 0 || binNo == midBin) {
475	>	if (inA || inB) {
476
477		RealType mass = sd->getMass();
478		Vector3d vel = sd->getVel();
479		RealType value;
480	<
481	<	switch(rnemdType_) {
482	<	case rnemdKinetic :
480	>
481	>	switch(rnemdFluxType_) {
482	>	case rnemdKE :
483
484	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
485	<	vel[2]*vel[2]);
486	<
178	<	if (sd->isDirectional()) {
484	>	value = mass * vel.lengthSquare();
485	>
486	>	if (sd->isDirectional()) {
487		Vector3d angMom = sd->getJ();
488		Mat3x3d I = sd->getI();
489
490		if (sd->isLinear()) {
491	<	int i = sd->linearAxis();
492	<	int j = (i + 1) % 3;
493	<	int k = (i + 2) % 3;
494	<	value += angMom[j] * angMom[j] / I(j, j) +
495	<	angMom[k] * angMom[k] / I(k, k);
491	>	int i = sd->linearAxis();
492	>	int j = (i + 1) % 3;
493	>	int k = (i + 2) % 3;
494	>	value += angMom[j] * angMom[j] / I(j, j) +
495	>	angMom[k] * angMom[k] / I(k, k);
496		} else {
497	<	value += angMom[0]*angMom[0]/I(0, 0)
498	<	+ angMom[1]*angMom[1]/I(1, 1)
499	<	+ angMom[2]*angMom[2]/I(2, 2);
497	>	value += angMom[0]*angMom[0]/I(0, 0)
498	>	+ angMom[1]*angMom[1]/I(1, 1)
499	>	+ angMom[2]*angMom[2]/I(2, 2);
500		}
501	<	}
502	<	value = value * 0.5 / OOPSEConstant::energyConvert;
501	>	} //angular momenta exchange enabled
502	>	value *= 0.5;
503		break;
504		case rnemdPx :
505		value = mass * vel[0];
#	Line 202 | Line 510 | namespace oopse {
510		case rnemdPz :
511		value = mass * vel[2];
512		break;
205	–	case rnemdUnknown :
513		default :
514		break;
515		}
516
517	<	if (binNo == 0) {
517	>	if (inA == 0) {
518		if (!min_found) {
519		min_val = value;
520		min_sd = sd;
#	Line 218 | Line 525 | namespace oopse {
525		min_sd = sd;
526		}
527		}
528	<	} else {
528	>	} else {
529		if (!max_found) {
530		max_val = value;
531		max_sd = sd;
#	Line 232 | Line 539 | namespace oopse {
539		}
540		}
541		}
235	–	//std::cerr << "smallest value = " << min_val  << "\n";
236	–	//std::cerr << "largest value = " << max_val << "\n";
542
543	<	// missing:  swap information in parallel
543	>	#ifdef IS_MPI
544	>	int nProc, worldRank;
545	>
546	>	nProc = MPI::COMM_WORLD.Get_size();
547	>	worldRank = MPI::COMM_WORLD.Get_rank();
548
549	+	bool my_min_found = min_found;
550	+	bool my_max_found = max_found;
551	+
552	+	// Even if we didn't find a minimum, did someone else?
553	+	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
554	+	// Even if we didn't find a maximum, did someone else?
555	+	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
556	+	#endif
557	+
558		if (max_found && min_found) {
559	<	if (min_val< max_val) {
560	<	Vector3d min_vel = min_sd->getVel();
561	<	Vector3d max_vel = max_sd->getVel();
562	<	RealType temp_vel;
563	<	switch(rnemdType_) {
564	<	case rnemdKinetic :
565	<	min_sd->setVel(max_vel);
566	<	max_sd->setVel(min_vel);
567	<	if (min_sd->isDirectional() && max_sd->isDirectional()) {
568	<	Vector3d min_angMom = min_sd->getJ();
569	<	Vector3d max_angMom = max_sd->getJ();
570	<	min_sd->setJ(max_angMom);
571	<	max_sd->setJ(min_angMom);
559	>
560	>	#ifdef IS_MPI
561	>	struct {
562	>	RealType val;
563	>	int rank;
564	>	} max_vals, min_vals;
565	>
566	>	if (my_min_found) {
567	>	min_vals.val = min_val;
568	>	} else {
569	>	min_vals.val = HONKING_LARGE_VALUE;
570	>	}
571	>	min_vals.rank = worldRank;
572	>
573	>	// Who had the minimum?
574	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
575	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
576	>	min_val = min_vals.val;
577	>
578	>	if (my_max_found) {
579	>	max_vals.val = max_val;
580	>	} else {
581	>	max_vals.val = -HONKING_LARGE_VALUE;
582	>	}
583	>	max_vals.rank = worldRank;
584	>
585	>	// Who had the maximum?
586	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
587	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
588	>	max_val = max_vals.val;
589	>	#endif
590	>
591	>	if (min_val < max_val) {
592	>
593	>	#ifdef IS_MPI
594	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
595	>	// I have both maximum and minimum, so proceed like a single
596	>	// processor version:
597	>	#endif
598	>
599	>	Vector3d min_vel = min_sd->getVel();
600	>	Vector3d max_vel = max_sd->getVel();
601	>	RealType temp_vel;
602	>
603	>	switch(rnemdFluxType_) {
604	>	case rnemdKE :
605	>	min_sd->setVel(max_vel);
606	>	max_sd->setVel(min_vel);
607	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
608	>	Vector3d min_angMom = min_sd->getJ();
609	>	Vector3d max_angMom = max_sd->getJ();
610	>	min_sd->setJ(max_angMom);
611	>	max_sd->setJ(min_angMom);
612	>	}//angular momenta exchange enabled
613	>	//assumes same rigid body identity
614	>	break;
615	>	case rnemdPx :
616	>	temp_vel = min_vel.x();
617	>	min_vel.x() = max_vel.x();
618	>	max_vel.x() = temp_vel;
619	>	min_sd->setVel(min_vel);
620	>	max_sd->setVel(max_vel);
621	>	break;
622	>	case rnemdPy :
623	>	temp_vel = min_vel.y();
624	>	min_vel.y() = max_vel.y();
625	>	max_vel.y() = temp_vel;
626	>	min_sd->setVel(min_vel);
627	>	max_sd->setVel(max_vel);
628	>	break;
629	>	case rnemdPz :
630	>	temp_vel = min_vel.z();
631	>	min_vel.z() = max_vel.z();
632	>	max_vel.z() = temp_vel;
633	>	min_sd->setVel(min_vel);
634	>	max_sd->setVel(max_vel);
635	>	break;
636	>	default :
637	>	break;
638	>	}
639	>
640	>	#ifdef IS_MPI
641	>	// the rest of the cases only apply in parallel simulations:
642	>	} else if (max_vals.rank == worldRank) {
643	>	// I had the max, but not the minimum
644	>
645	>	Vector3d min_vel;
646	>	Vector3d max_vel = max_sd->getVel();
647	>	MPI::Status status;
648	>
649	>	// point-to-point swap of the velocity vector
650	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
651	>	min_vals.rank, 0,
652	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
653	>	min_vals.rank, 0, status);
654	>
655	>	switch(rnemdFluxType_) {
656	>	case rnemdKE :
657	>	max_sd->setVel(min_vel);
658	>	//angular momenta exchange enabled
659	>	if (max_sd->isDirectional()) {
660	>	Vector3d min_angMom;
661	>	Vector3d max_angMom = max_sd->getJ();
662	>
663	>	// point-to-point swap of the angular momentum vector
664	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
665	>	MPI::REALTYPE, min_vals.rank, 1,
666	>	min_angMom.getArrayPointer(), 3,
667	>	MPI::REALTYPE, min_vals.rank, 1,
668	>	status);
669	>
670	>	max_sd->setJ(min_angMom);
671	>	}
672	>	break;
673	>	case rnemdPx :
674	>	max_vel.x() = min_vel.x();
675	>	max_sd->setVel(max_vel);
676	>	break;
677	>	case rnemdPy :
678	>	max_vel.y() = min_vel.y();
679	>	max_sd->setVel(max_vel);
680	>	break;
681	>	case rnemdPz :
682	>	max_vel.z() = min_vel.z();
683	>	max_sd->setVel(max_vel);
684	>	break;
685	>	default :
686	>	break;
687	>	}
688	>	} else if (min_vals.rank == worldRank) {
689	>	// I had the minimum but not the maximum:
690	>
691	>	Vector3d max_vel;
692	>	Vector3d min_vel = min_sd->getVel();
693	>	MPI::Status status;
694	>
695	>	// point-to-point swap of the velocity vector
696	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
697	>	max_vals.rank, 0,
698	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
699	>	max_vals.rank, 0, status);
700	>
701	>	switch(rnemdFluxType_) {
702	>	case rnemdKE :
703	>	min_sd->setVel(max_vel);
704	>	//angular momenta exchange enabled
705	>	if (min_sd->isDirectional()) {
706	>	Vector3d min_angMom = min_sd->getJ();
707	>	Vector3d max_angMom;
708	>
709	>	// point-to-point swap of the angular momentum vector
710	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
711	>	MPI::REALTYPE, max_vals.rank, 1,
712	>	max_angMom.getArrayPointer(), 3,
713	>	MPI::REALTYPE, max_vals.rank, 1,
714	>	status);
715	>
716	>	min_sd->setJ(max_angMom);
717	>	}
718	>	break;
719	>	case rnemdPx :
720	>	min_vel.x() = max_vel.x();
721	>	min_sd->setVel(min_vel);
722	>	break;
723	>	case rnemdPy :
724	>	min_vel.y() = max_vel.y();
725	>	min_sd->setVel(min_vel);
726	>	break;
727	>	case rnemdPz :
728	>	min_vel.z() = max_vel.z();
729	>	min_sd->setVel(min_vel);
730	>	break;
731	>	default :
732	>	break;
733	>	}
734	>	}
735	>	#endif
736	>
737	>	switch(rnemdFluxType_) {
738	>	case rnemdKE:
739	>	kineticExchange_ += max_val - min_val;
740	>	break;
741	>	case rnemdPx:
742	>	momentumExchange_.x() += max_val - min_val;
743	>	break;
744	>	case rnemdPy:
745	>	momentumExchange_.y() += max_val - min_val;
746	>	break;
747	>	case rnemdPz:
748	>	momentumExchange_.z() += max_val - min_val;
749	>	break;
750	>	default:
751	>	break;
752	>	}
753	>	} else {
754	>	sprintf(painCave.errMsg,
755	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
756	>	painCave.isFatal = 0;
757	>	painCave.severity = OPENMD_INFO;
758	>	simError();
759	>	failTrialCount_++;
760	>	}
761	>	} else {
762	>	sprintf(painCave.errMsg,
763	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
764	>	"\twas not present in at least one of the two slabs.\n");
765	>	painCave.isFatal = 0;
766	>	painCave.severity = OPENMD_INFO;
767	>	simError();
768	>	failTrialCount_++;
769	>	}
770	>	}
771	>
772	>	void RNEMD::doNIVS() {
773	>	if (!doRNEMD_) return;
774	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
775	>	Mat3x3d hmat = currentSnap_->getHmat();
776	>
777	>	seleMan_.setSelectionSet(evaluator_.evaluate());
778	>
779	>	int selei;
780	>	StuntDouble* sd;
781	>	int idx;
782	>
783	>	vector<StuntDouble*> hotBin, coldBin;
784	>
785	>	RealType Phx = 0.0;
786	>	RealType Phy = 0.0;
787	>	RealType Phz = 0.0;
788	>	RealType Khx = 0.0;
789	>	RealType Khy = 0.0;
790	>	RealType Khz = 0.0;
791	>	RealType Khw = 0.0;
792	>	RealType Pcx = 0.0;
793	>	RealType Pcy = 0.0;
794	>	RealType Pcz = 0.0;
795	>	RealType Kcx = 0.0;
796	>	RealType Kcy = 0.0;
797	>	RealType Kcz = 0.0;
798	>	RealType Kcw = 0.0;
799	>
800	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
801	>	sd = seleMan_.nextSelected(selei)) {
802	>
803	>	idx = sd->getLocalIndex();
804	>
805	>	Vector3d pos = sd->getPos();
806	>
807	>	// wrap the stuntdouble's position back into the box:
808	>
809	>	if (usePeriodicBoundaryConditions_)
810	>	currentSnap_->wrapVector(pos);
811	>
812	>	// which bin is this stuntdouble in?
813	>	bool inA = inSlabA(pos);
814	>	bool inB = inSlabB(pos);
815	>
816	>	if (inA || inB) {
817	>
818	>	RealType mass = sd->getMass();
819	>	Vector3d vel = sd->getVel();
820	>
821	>	if (inA) {
822	>	hotBin.push_back(sd);
823	>	Phx += mass * vel.x();
824	>	Phy += mass * vel.y();
825	>	Phz += mass * vel.z();
826	>	Khx += mass * vel.x() * vel.x();
827	>	Khy += mass * vel.y() * vel.y();
828	>	Khz += mass * vel.z() * vel.z();
829	>	if (sd->isDirectional()) {
830	>	Vector3d angMom = sd->getJ();
831	>	Mat3x3d I = sd->getI();
832	>	if (sd->isLinear()) {
833	>	int i = sd->linearAxis();
834	>	int j = (i + 1) % 3;
835	>	int k = (i + 2) % 3;
836	>	Khw += angMom[j] * angMom[j] / I(j, j) +
837	>	angMom[k] * angMom[k] / I(k, k);
838	>	} else {
839	>	Khw += angMom[0]*angMom[0]/I(0, 0)
840	>	+ angMom[1]*angMom[1]/I(1, 1)
841	>	+ angMom[2]*angMom[2]/I(2, 2);
842	>	}
843		}
844	<	break;
845	<	case rnemdPx :
846	<	temp_vel = min_vel.x();
847	<	min_vel.x() = max_vel.x();
848	<	max_vel.x() = temp_vel;
849	<	min_sd->setVel(min_vel);
850	<	max_sd->setVel(max_vel);
844	>	} else {
845	>	coldBin.push_back(sd);
846	>	Pcx += mass * vel.x();
847	>	Pcy += mass * vel.y();
848	>	Pcz += mass * vel.z();
849	>	Kcx += mass * vel.x() * vel.x();
850	>	Kcy += mass * vel.y() * vel.y();
851	>	Kcz += mass * vel.z() * vel.z();
852	>	if (sd->isDirectional()) {
853	>	Vector3d angMom = sd->getJ();
854	>	Mat3x3d I = sd->getI();
855	>	if (sd->isLinear()) {
856	>	int i = sd->linearAxis();
857	>	int j = (i + 1) % 3;
858	>	int k = (i + 2) % 3;
859	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
860	>	angMom[k] * angMom[k] / I(k, k);
861	>	} else {
862	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
863	>	+ angMom[1]*angMom[1]/I(1, 1)
864	>	+ angMom[2]*angMom[2]/I(2, 2);
865	>	}
866	>	}
867	>	}
868	>	}
869	>	}
870	>
871	>	Khx *= 0.5;
872	>	Khy *= 0.5;
873	>	Khz *= 0.5;
874	>	Khw *= 0.5;
875	>	Kcx *= 0.5;
876	>	Kcy *= 0.5;
877	>	Kcz *= 0.5;
878	>	Kcw *= 0.5;
879	>
880	>	#ifdef IS_MPI
881	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
882	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
883	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
884	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
885	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
886	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
887	>
888	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
889	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
890	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
891	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
892	>
893	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
894	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
895	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
896	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
897	>	#endif
898	>
899	>	//solve coldBin coeff's first
900	>	RealType px = Pcx / Phx;
901	>	RealType py = Pcy / Phy;
902	>	RealType pz = Pcz / Phz;
903	>	RealType c, x, y, z;
904	>	bool successfulScale = false;
905	>	if ((rnemdFluxType_ == rnemdFullKE) ||
906	>	(rnemdFluxType_ == rnemdRotKE)) {
907	>	//may need sanity check Khw & Kcw > 0
908	>
909	>	if (rnemdFluxType_ == rnemdFullKE) {
910	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
911	>	} else {
912	>	c = 1.0 - kineticTarget_ / Kcw;
913	>	}
914	>
915	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
916	>	c = sqrt(c);
917	>
918	>	RealType w = 0.0;
919	>	if (rnemdFluxType_ ==  rnemdFullKE) {
920	>	x = 1.0 + px * (1.0 - c);
921	>	y = 1.0 + py * (1.0 - c);
922	>	z = 1.0 + pz * (1.0 - c);
923	>	/* more complicated way
924	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
925	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
926	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
927	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
928	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
929	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
930	>	*/
931	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
932	>	(fabs(z - 1.0) < 0.1)) {
933	>	w = 1.0 + (kineticTarget_
934	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
935	>	+ Khz * (1.0 - z * z)) / Khw;
936	>	}//no need to calculate w if x, y or z is out of range
937	>	} else {
938	>	w = 1.0 + kineticTarget_ / Khw;
939	>	}
940	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
941	>	//if w is in the right range, so should be x, y, z.
942	>	vector<StuntDouble*>::iterator sdi;
943	>	Vector3d vel;
944	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
945	>	if (rnemdFluxType_ == rnemdFullKE) {
946	>	vel = (*sdi)->getVel() * c;
947	>	(*sdi)->setVel(vel);
948	>	}
949	>	if ((*sdi)->isDirectional()) {
950	>	Vector3d angMom = (*sdi)->getJ() * c;
951	>	(*sdi)->setJ(angMom);
952	>	}
953	>	}
954	>	w = sqrt(w);
955	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
956	>	if (rnemdFluxType_ == rnemdFullKE) {
957	>	vel = (*sdi)->getVel();
958	>	vel.x() *= x;
959	>	vel.y() *= y;
960	>	vel.z() *= z;
961	>	(*sdi)->setVel(vel);
962	>	}
963	>	if ((*sdi)->isDirectional()) {
964	>	Vector3d angMom = (*sdi)->getJ() * w;
965	>	(*sdi)->setJ(angMom);
966	>	}
967	>	}
968	>	successfulScale = true;
969	>	kineticExchange_ += kineticTarget_;
970	>	}
971	>	}
972	>	} else {
973	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
974	>	switch(rnemdFluxType_) {
975	>	case rnemdKE :
976	>	/* used hotBin coeff's & only scale x & y dimensions
977	>	RealType px = Phx / Pcx;
978	>	RealType py = Phy / Pcy;
979	>	a110 = Khy;
980	>	c0 = - Khx - Khy - kineticTarget_;
981	>	a000 = Khx;
982	>	a111 = Kcy * py * py;
983	>	b11 = -2.0 * Kcy * py * (1.0 + py);
984	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
985	>	b01 = -2.0 * Kcx * px * (1.0 + px);
986	>	a001 = Kcx * px * px;
987	>	*/
988	>	//scale all three dimensions, let c_x = c_y
989	>	a000 = Kcx + Kcy;
990	>	a110 = Kcz;
991	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
992	>	a001 = Khx * px * px + Khy * py * py;
993	>	a111 = Khz * pz * pz;
994	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
995	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
996	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
997	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
998	>	break;
999	>	case rnemdPx :
1000	>	c = 1 - momentumTarget_.x() / Pcx;
1001	>	a000 = Kcy;
1002	>	a110 = Kcz;
1003	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1004	>	a001 = py * py * Khy;
1005	>	a111 = pz * pz * Khz;
1006	>	b01 = -2.0 * Khy * py * (1.0 + py);
1007	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1008	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1009	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1010	>	break;
1011	>	case rnemdPy :
1012	>	c = 1 - momentumTarget_.y() / Pcy;
1013	>	a000 = Kcx;
1014	>	a110 = Kcz;
1015	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1016	>	a001 = px * px * Khx;
1017	>	a111 = pz * pz * Khz;
1018	>	b01 = -2.0 * Khx * px * (1.0 + px);
1019	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1020	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1021	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1022	>	break;
1023	>	case rnemdPz ://we don't really do this, do we?
1024	>	c = 1 - momentumTarget_.z() / Pcz;
1025	>	a000 = Kcx;
1026	>	a110 = Kcy;
1027	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1028	>	a001 = px * px * Khx;
1029	>	a111 = py * py * Khy;
1030	>	b01 = -2.0 * Khx * px * (1.0 + px);
1031	>	b11 = -2.0 * Khy * py * (1.0 + py);
1032	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1033	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1034	>	break;
1035	>	default :
1036	>	break;
1037	>	}
1038	>
1039	>	RealType v1 = a000 * a111 - a001 * a110;
1040	>	RealType v2 = a000 * b01;
1041	>	RealType v3 = a000 * b11;
1042	>	RealType v4 = a000 * c1 - a001 * c0;
1043	>	RealType v8 = a110 * b01;
1044	>	RealType v10 = - b01 * c0;
1045	>
1046	>	RealType u0 = v2 * v10 - v4 * v4;
1047	>	RealType u1 = -2.0 * v3 * v4;
1048	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1049	>	RealType u3 = -2.0 * v1 * v3;
1050	>	RealType u4 = - v1 * v1;
1051	>	//rescale coefficients
1052	>	RealType maxAbs = fabs(u0);
1053	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1054	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1055	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1056	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1057	>	u0 /= maxAbs;
1058	>	u1 /= maxAbs;
1059	>	u2 /= maxAbs;
1060	>	u3 /= maxAbs;
1061	>	u4 /= maxAbs;
1062	>	//max_element(start, end) is also available.
1063	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1064	>	poly.setCoefficient(4, u4);
1065	>	poly.setCoefficient(3, u3);
1066	>	poly.setCoefficient(2, u2);
1067	>	poly.setCoefficient(1, u1);
1068	>	poly.setCoefficient(0, u0);
1069	>	vector<RealType> realRoots = poly.FindRealRoots();
1070	>
1071	>	vector<RealType>::iterator ri;
1072	>	RealType r1, r2, alpha0;
1073	>	vector<pair<RealType,RealType> > rps;
1074	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1075	>	r2 = *ri;
1076	>	//check if FindRealRoots() give the right answer
1077	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1078	>	sprintf(painCave.errMsg,
1079	>	"RNEMD Warning: polynomial solve seems to have an error!");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	failRootCount_++;
1083	>	}
1084	>	//might not be useful w/o rescaling coefficients
1085	>	alpha0 = -c0 - a110 * r2 * r2;
1086	>	if (alpha0 >= 0.0) {
1087	>	r1 = sqrt(alpha0 / a000);
1088	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1089	>	< 1e-6)
1090	>	{ rps.push_back(make_pair(r1, r2)); }
1091	>	if (r1 > 1e-6) { //r1 non-negative
1092	>	r1 = -r1;
1093	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1094	>	< 1e-6)
1095	>	{ rps.push_back(make_pair(r1, r2)); }
1096	>	}
1097	>	}
1098	>	}
1099	>	// Consider combining together the solving pair part w/ the searching
1100	>	// best solution part so that we don't need the pairs vector
1101	>	if (!rps.empty()) {
1102	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1103	>	RealType diff;
1104	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1105	>	vector<pair<RealType,RealType> >::iterator rpi;
1106	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1107	>	r1 = (*rpi).first;
1108	>	r2 = (*rpi).second;
1109	>	switch(rnemdFluxType_) {
1110	>	case rnemdKE :
1111	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1113	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1114	>	break;
1115	>	case rnemdPx :
1116	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1117	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1118	>	break;
1119	>	case rnemdPy :
1120	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1121	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1122	>	break;
1123	>	case rnemdPz :
1124	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1125	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1126	>	default :
1127	>	break;
1128	>	}
1129	>	if (diff < smallestDiff) {
1130	>	smallestDiff = diff;
1131	>	bestPair = *rpi;
1132	>	}
1133	>	}
1134	>	#ifdef IS_MPI
1135	>	if (worldRank == 0) {
1136	>	#endif
1137	>	// sprintf(painCave.errMsg,
1138	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	>	//         bestPair.first, bestPair.second);
1140	>	// painCave.isFatal = 0;
1141	>	// painCave.severity = OPENMD_INFO;
1142	>	// simError();
1143	>	#ifdef IS_MPI
1144	>	}
1145	>	#endif
1146	>
1147	>	switch(rnemdFluxType_) {
1148	>	case rnemdKE :
1149	>	x = bestPair.first;
1150	>	y = bestPair.first;
1151	>	z = bestPair.second;
1152		break;
1153	+	case rnemdPx :
1154	+	x = c;
1155	+	y = bestPair.first;
1156	+	z = bestPair.second;
1157	+	break;
1158		case rnemdPy :
1159	<	temp_vel = min_vel.y();
1160	<	min_vel.y() = max_vel.y();
1161	<	max_vel.y() = temp_vel;
267	<	min_sd->setVel(min_vel);
268	<	max_sd->setVel(max_vel);
1159	>	x = bestPair.first;
1160	>	y = c;
1161	>	z = bestPair.second;
1162		break;
1163		case rnemdPz :
1164	<	temp_vel = min_vel.z();
1165	<	min_vel.z() = max_vel.z();
1166	<	max_vel.z() = temp_vel;
1167	<	min_sd->setVel(min_vel);
1168	<	max_sd->setVel(max_vel);
1164	>	x = bestPair.first;
1165	>	y = bestPair.second;
1166	>	z = c;
1167	>	break;
1168	>	default :
1169		break;
1170	<	case rnemdUnknown :
1170	>	}
1171	>	vector<StuntDouble*>::iterator sdi;
1172	>	Vector3d vel;
1173	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1174	>	vel = (*sdi)->getVel();
1175	>	vel.x() *= x;
1176	>	vel.y() *= y;
1177	>	vel.z() *= z;
1178	>	(*sdi)->setVel(vel);
1179	>	}
1180	>	//convert to hotBin coefficient
1181	>	x = 1.0 + px * (1.0 - x);
1182	>	y = 1.0 + py * (1.0 - y);
1183	>	z = 1.0 + pz * (1.0 - z);
1184	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1185	>	vel = (*sdi)->getVel();
1186	>	vel.x() *= x;
1187	>	vel.y() *= y;
1188	>	vel.z() *= z;
1189	>	(*sdi)->setVel(vel);
1190	>	}
1191	>	successfulScale = true;
1192	>	switch(rnemdFluxType_) {
1193	>	case rnemdKE :
1194	>	kineticExchange_ += kineticTarget_;
1195	>	break;
1196	>	case rnemdPx :
1197	>	case rnemdPy :
1198	>	case rnemdPz :
1199	>	momentumExchange_ += momentumTarget_;
1200	>	break;
1201		default :
1202		break;
1203	+	}
1204	+	}
1205	+	}
1206	+	if (successfulScale != true) {
1207	+	sprintf(painCave.errMsg,
1208	+	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1209	+	"\tthe constraint equations may not exist or there may be\n"
1210	+	"\tno selected objects in one or both slabs.\n");
1211	+	painCave.isFatal = 0;
1212	+	painCave.severity = OPENMD_INFO;
1213	+	simError();
1214	+	failTrialCount_++;
1215	+	}
1216	+	}
1217	+
1218	+	void RNEMD::doVSS() {
1219	+	if (!doRNEMD_) return;
1220	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1221	+	RealType time = currentSnap_->getTime();
1222	+	Mat3x3d hmat = currentSnap_->getHmat();
1223	+
1224	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1225	+
1226	+	int selei;
1227	+	StuntDouble* sd;
1228	+	int idx;
1229	+
1230	+	vector<StuntDouble*> hotBin, coldBin;
1231	+
1232	+	Vector3d Ph(V3Zero);
1233	+	RealType Mh = 0.0;
1234	+	RealType Kh = 0.0;
1235	+	Vector3d Pc(V3Zero);
1236	+	RealType Mc = 0.0;
1237	+	RealType Kc = 0.0;
1238	+
1239	+
1240	+	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1241	+	sd = seleMan_.nextSelected(selei)) {
1242	+
1243	+	idx = sd->getLocalIndex();
1244	+
1245	+	Vector3d pos = sd->getPos();
1246	+
1247	+	// wrap the stuntdouble's position back into the box:
1248	+
1249	+	if (usePeriodicBoundaryConditions_)
1250	+	currentSnap_->wrapVector(pos);
1251	+
1252	+	// which bin is this stuntdouble in?
1253	+	bool inA = inSlabA(pos);
1254	+	bool inB = inSlabB(pos);
1255	+
1256	+	if (inA || inB) {
1257	+
1258	+	RealType mass = sd->getMass();
1259	+	Vector3d vel = sd->getVel();
1260	+
1261	+	if (inA) {
1262	+	hotBin.push_back(sd);
1263	+	Ph += mass * vel;
1264	+	Mh += mass;
1265	+	Kh += mass * vel.lengthSquare();
1266	+	if (rnemdFluxType_ == rnemdFullKE) {
1267	+	if (sd->isDirectional()) {
1268	+	Vector3d angMom = sd->getJ();
1269	+	Mat3x3d I = sd->getI();
1270	+	if (sd->isLinear()) {
1271	+	int i = sd->linearAxis();
1272	+	int j = (i + 1) % 3;
1273	+	int k = (i + 2) % 3;
1274	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1275	+	angMom[k] * angMom[k] / I(k, k);
1276	+	} else {
1277	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1278	+	angMom[1] * angMom[1] / I(1, 1) +
1279	+	angMom[2] * angMom[2] / I(2, 2);
1280	+	}
1281	+	}
1282	+	}
1283	+	} else { //midBin_
1284	+	coldBin.push_back(sd);
1285	+	Pc += mass * vel;
1286	+	Mc += mass;
1287	+	Kc += mass * vel.lengthSquare();
1288	+	if (rnemdFluxType_ == rnemdFullKE) {
1289	+	if (sd->isDirectional()) {
1290	+	Vector3d angMom = sd->getJ();
1291	+	Mat3x3d I = sd->getI();
1292	+	if (sd->isLinear()) {
1293	+	int i = sd->linearAxis();
1294	+	int j = (i + 1) % 3;
1295	+	int k = (i + 2) % 3;
1296	+	Kc += angMom[j] * angMom[j] / I(j, j) +
1297	+	angMom[k] * angMom[k] / I(k, k);
1298	+	} else {
1299	+	Kc += angMom[0] * angMom[0] / I(0, 0) +
1300	+	angMom[1] * angMom[1] / I(1, 1) +
1301	+	angMom[2] * angMom[2] / I(2, 2);
1302	+	}
1303	+	}
1304	+	}
1305		}
281	–	exchangeSum_ += max_val - min_val;
282	–	} else {
283	–	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
1306		}
285	–	} else {
286	–	std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
1307		}
1308	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
1308	>
1309	>	Kh *= 0.5;
1310	>	Kc *= 0.5;
1311	>
1312	>	#ifdef IS_MPI
1313	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1314	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1315	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1316	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1317	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1318	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1319	>	#endif
1320	>
1321	>	bool successfulExchange = false;
1322	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1323	>	Vector3d vc = Pc / Mc;
1324	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1325	>	Vector3d acrec = -momentumTarget_ / Mc;
1326	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1327	>	if (cNumerator > 0.0) {
1328	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1329	>	if (cDenominator > 0.0) {
1330	>	RealType c = sqrt(cNumerator / cDenominator);
1331	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1332	>	Vector3d vh = Ph / Mh;
1333	>	Vector3d ah = momentumTarget_ / Mh + vh;
1334	>	Vector3d ahrec = momentumTarget_ / Mh;
1335	>	RealType hNumerator = Kh + kineticTarget_
1336	>	- 0.5 * Mh * ah.lengthSquare();
1337	>	if (hNumerator > 0.0) {
1338	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1339	>	if (hDenominator > 0.0) {
1340	>	RealType h = sqrt(hNumerator / hDenominator);
1341	>	if ((h > 0.9) && (h < 1.1)) {
1342	>
1343	>	vector<StuntDouble*>::iterator sdi;
1344	>	Vector3d vel;
1345	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1346	>	//vel = (*sdi)->getVel();
1347	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1348	>	(*sdi)->setVel(vel);
1349	>	if (rnemdFluxType_ == rnemdFullKE) {
1350	>	if ((*sdi)->isDirectional()) {
1351	>	Vector3d angMom = (*sdi)->getJ() * c;
1352	>	(*sdi)->setJ(angMom);
1353	>	}
1354	>	}
1355	>	}
1356	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1357	>	//vel = (*sdi)->getVel();
1358	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1359	>	(*sdi)->setVel(vel);
1360	>	if (rnemdFluxType_ == rnemdFullKE) {
1361	>	if ((*sdi)->isDirectional()) {
1362	>	Vector3d angMom = (*sdi)->getJ() * h;
1363	>	(*sdi)->setJ(angMom);
1364	>	}
1365	>	}
1366	>	}
1367	>	successfulExchange = true;
1368	>	kineticExchange_ += kineticTarget_;
1369	>	momentumExchange_ += momentumTarget_;
1370	>	}
1371	>	}
1372	>	}
1373	>	}
1374	>	}
1375	>	}
1376	>	}
1377	>	if (successfulExchange != true) {
1378	>	sprintf(painCave.errMsg,
1379	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1380	>	"\tthe constraint equations may not exist or there may be\n"
1381	>	"\tno selected objects in one or both slabs.\n");
1382	>	painCave.isFatal = 0;
1383	>	painCave.severity = OPENMD_INFO;
1384	>	simError();
1385	>	failTrialCount_++;
1386	>	}
1387		}
1388
1389	<	void RNEMD::getStatus() {
1390	<	//std::cerr << "in RNEMD!\n";
1391	<	//std::cerr << "nBins = " << nBins_ << "\n";
1392	<	int midBin = nBins_ / 2;
1393	<	//std::cerr << "midBin = " << midBin << "\n";
1394	<	//std::cerr << "swapTime = " << swapTime_ << "\n";
1395	<	//std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
1396	<	//std::cerr << "swapType = " << rnemdType_ << "\n";
1397	<	//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
1389	>	void RNEMD::doRNEMD() {
1390	>	if (!doRNEMD_) return;
1391	>	trialCount_++;
1392	>	switch(rnemdMethod_) {
1393	>	case rnemdSwap:
1394	>	doSwap();
1395	>	break;
1396	>	case rnemdNIVS:
1397	>	doNIVS();
1398	>	break;
1399	>	case rnemdVSS:
1400	>	doVSS();
1401	>	break;
1402	>	case rnemdUnkownMethod:
1403	>	default :
1404	>	break;
1405	>	}
1406	>	}
1407
1408	+	void RNEMD::collectData() {
1409	+	if (!doRNEMD_) return;
1410		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1411		Mat3x3d hmat = currentSnap_->getHmat();
1412
1413	<	//std::cerr << "hmat = " << hmat << "\n";
1413	>	areaAccumulator_->add(currentSnap_->getXYarea());
1414
1415		seleMan_.setSelectionSet(evaluator_.evaluate());
1416
1417	<	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
309	<
310	<	int selei;
1417	>	int selei(0);
1418		StuntDouble* sd;
1419		int idx;
313	–	/*
314	–	RealType min_val;
315	–	bool min_found = false;
316	–	StuntDouble* min_sd;
1420
1421	<	RealType max_val;
1422	<	bool max_found = false;
1423	<	StuntDouble* max_sd;
1421	>	vector<RealType> binMass(nBins_, 0.0);
1422	>	vector<RealType> binPx(nBins_, 0.0);
1423	>	vector<RealType> binPy(nBins_, 0.0);
1424	>	vector<RealType> binPz(nBins_, 0.0);
1425	>	vector<RealType> binKE(nBins_, 0.0);
1426	>	vector<int> binDOF(nBins_, 0);
1427	>	vector<int> binCount(nBins_, 0);
1428	>
1429	>	// alternative approach, track all molecules instead of only those
1430	>	// selected for scaling/swapping:
1431	>	/*
1432	>	SimInfo::MoleculeIterator miter;
1433	>	vector<StuntDouble*>::iterator iiter;
1434	>	Molecule* mol;
1435	>	StuntDouble* sd;
1436	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1437	>	mol = info_->nextMolecule(miter))
1438	>	sd is essentially sd
1439	>	for (sd = mol->beginIntegrableObject(iiter);
1440	>	sd != NULL;
1441	>	sd = mol->nextIntegrableObject(iiter))
1442		*/
1443	<	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?
1443	>
1444		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1445		sd = seleMan_.nextSelected(selei)) {
1446	<
1446	>
1447		idx = sd->getLocalIndex();
1448
1449		Vector3d pos = sd->getPos();
#	Line 336 | Line 1452 | namespace oopse {
1452
1453		if (usePeriodicBoundaryConditions_)
1454		currentSnap_->wrapVector(pos);
1455	<
1455	>
1456	>
1457		// which bin is this stuntdouble in?
1458		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	<
1460	<	int binNo = int((nBins_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2));
1461	<
1462	<	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
1463	<
1459	>	// Shift molecules by half a box to have bins start at 0
1460	>	// The modulo operator is used to wrap the case when we are
1461	>	// beyond the end of the bins back to the beginning.
1462	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463	>
1464		RealType mass = sd->getMass();
1465		Vector3d vel = sd->getVel();
349	–	//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
350	–	RealType value;
1466
1467	<	switch(rnemdType_) {
1468	<	case rnemdKinetic :
1469	<
1470	<	value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
1471	<	vel[2]*vel[2]);
1472	<
1473	<	valueCount[binNo] += 3;
1467	>	binCount[binNo]++;
1468	>	binMass[binNo] += mass;
1469	>	binPx[binNo] += mass*vel.x();
1470	>	binPy[binNo] += mass*vel.y();
1471	>	binPz[binNo] += mass*vel.z();
1472	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1473	>	binDOF[binNo] += 3;
1474
1475	<	if (sd->isDirectional()) {
1476	<	Vector3d angMom = sd->getJ();
1477	<	Mat3x3d I = sd->getI();
1478	<
1479	<	if (sd->isLinear()) {
1480	<	int i = sd->linearAxis();
1481	<	int j = (i + 1) % 3;
1482	<	int k = (i + 2) % 3;
1483	<	value += angMom[j] * angMom[j] / I(j, j) +
1484	<	angMom[k] * angMom[k] / I(k, k);
1475	>	if (sd->isDirectional()) {
1476	>	Vector3d angMom = sd->getJ();
1477	>	Mat3x3d I = sd->getI();
1478	>	if (sd->isLinear()) {
1479	>	int i = sd->linearAxis();
1480	>	int j = (i + 1) % 3;
1481	>	int k = (i + 2) % 3;
1482	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1483	>	angMom[k] * angMom[k] / I(k, k));
1484	>	binDOF[binNo] += 2;
1485	>	} else {
1486	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1487	>	angMom[1] * angMom[1] / I(1, 1) +
1488	>	angMom[2] * angMom[2] / I(2, 2));
1489	>	binDOF[binNo] += 3;
1490	>	}
1491	>	}
1492	>	}
1493	>
1494	>	#ifdef IS_MPI
1495	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1496	>	nBins_, MPI::INT, MPI::SUM);
1497	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1498	>	nBins_, MPI::REALTYPE, MPI::SUM);
1499	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1500	>	nBins_, MPI::REALTYPE, MPI::SUM);
1501	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1502	>	nBins_, MPI::REALTYPE, MPI::SUM);
1503	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1504	>	nBins_, MPI::REALTYPE, MPI::SUM);
1505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1506	>	nBins_, MPI::REALTYPE, MPI::SUM);
1507	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1508	>	nBins_, MPI::INT, MPI::SUM);
1509	>	#endif
1510
1511	<	valueCount[binNo] +=2;
1511	>	Vector3d vel;
1512	>	RealType den;
1513	>	RealType temp;
1514	>	RealType z;
1515	>	for (int i = 0; i < nBins_; i++) {
1516	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1517	>	vel.x() = binPx[i] / binMass[i];
1518	>	vel.y() = binPy[i] / binMass[i];
1519	>	vel.z() = binPz[i] / binMass[i];
1520
1521	<	} else {
1522	<	value += angMom[0]*angMom[0]/I(0, 0)
375	<	+ angMom[1]*angMom[1]/I(1, 1)
376	<	+ angMom[2]*angMom[2]/I(2, 2);
377	<	valueCount[binNo] +=3;
1521	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1522	>	/ currentSnap_->getVolume() ;
1523
1524	<	}
1525	<	}
1526	<	//std::cerr <<"this value = " << value << "\n";
1527	<	value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
1528	<	value *= 2.0 / OOPSEConstant::kb;             // convert to temperature
1529	<	//std::cerr <<"this value = " << value << "\n";
1530	<	break;
1531	<	case rnemdPx :
1532	<	value = mass * vel[0];
1533	<	valueCount[binNo]++;
1534	<	break;
1535	<	case rnemdPy :
1536	<	value = mass * vel[1];
1537	<	valueCount[binNo]++;
1538	<	break;
1539	<	case rnemdPz :
1540	<	value = mass * vel[2];
1541	<	valueCount[binNo]++;
1542	<	break;
1543	<	case rnemdUnknown :
399	<	default :
400	<	break;
1524	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1525	>	PhysicalConstants::energyConvert);
1526	>
1527	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1528	>	if(outputMask_[j]) {
1529	>	switch(j) {
1530	>	case Z:
1531	>	(data_[j].accumulator[i])->add(z);
1532	>	break;
1533	>	case TEMPERATURE:
1534	>	data_[j].accumulator[i]->add(temp);
1535	>	break;
1536	>	case VELOCITY:
1537	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1538	>	break;
1539	>	case DENSITY:
1540	>	data_[j].accumulator[i]->add(den);
1541	>	break;
1542	>	}
1543	>	}
1544		}
402	–	//std::cerr << "bin = " << binNo << " value = " << value ;
403	–	valueHist[binNo] += value;
404	–	//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
1545		}
1546	+	}
1547	+
1548	+	void RNEMD::getStarted() {
1549	+	if (!doRNEMD_) return;
1550	+	collectData();
1551	+	writeOutputFile();
1552	+	}
1553	+
1554	+	void RNEMD::parseOutputFileFormat(const std::string& format) {
1555	+	if (!doRNEMD_) return;
1556	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1557
1558	<	std::cout << counter_++;
1559	<	for (int j = 0; j < nBins_; j++)
1560	<	std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
1561	<	std::cout << "\n";
1558	>	while(tokenizer.hasMoreTokens()) {
1559	>	std::string token(tokenizer.nextToken());
1560	>	toUpper(token);
1561	>	OutputMapType::iterator i = outputMap_.find(token);
1562	>	if (i != outputMap_.end()) {
1563	>	outputMask_.set(i->second);
1564	>	} else {
1565	>	sprintf( painCave.errMsg,
1566	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1567	>	"\toutputFileFormat keyword.\n", token.c_str() );
1568	>	painCave.isFatal = 0;
1569	>	painCave.severity = OPENMD_ERROR;
1570	>	simError();
1571	>	}
1572	>	}
1573		}
1574	+
1575	+	void RNEMD::writeOutputFile() {
1576	+	if (!doRNEMD_) return;
1577	+
1578	+	#ifdef IS_MPI
1579	+	// If we're the root node, should we print out the results
1580	+	int worldRank = MPI::COMM_WORLD.Get_rank();
1581	+	if (worldRank == 0) {
1582	+	#endif
1583	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1584	+
1585	+	if( !rnemdFile_ ){
1586	+	sprintf( painCave.errMsg,
1587	+	"Could not open \"%s\" for RNEMD output.\n",
1588	+	rnemdFileName_.c_str());
1589	+	painCave.isFatal = 1;
1590	+	simError();
1591	+	}
1592	+
1593	+	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1594	+
1595	+	RealType time = currentSnap_->getTime();
1596	+	RealType avgArea;
1597	+	areaAccumulator_->getAverage(avgArea);
1598	+	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1599	+	/ PhysicalConstants::energyConvert;
1600	+	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1601	+
1602	+	rnemdFile_ << "#######################################################\n";
1603	+	rnemdFile_ << "# RNEMD {\n";
1604	+
1605	+	map<string, RNEMDMethod>::iterator mi;
1606	+	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1607	+	if ( (*mi).second == rnemdMethod_)
1608	+	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1609	+	}
1610	+	map<string, RNEMDFluxType>::iterator fi;
1611	+	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1612	+	if ( (*fi).second == rnemdFluxType_)
1613	+	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1614	+	}
1615	+
1616	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1617	+
1618	+	rnemdFile_ << "#    objectSelection = \""
1619	+	<< rnemdObjectSelection_ << "\";\n";
1620	+	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1621	+	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1622	+	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1623	+	rnemdFile_ << "# }\n";
1624	+	rnemdFile_ << "#######################################################\n";
1625	+	rnemdFile_ << "# RNEMD report:\n";
1626	+	rnemdFile_ << "#     running time = " << time << " fs\n";
1627	+	rnemdFile_ << "#     target flux:\n";
1628	+	rnemdFile_ << "#         kinetic = "
1629	+	<< kineticFlux_ / PhysicalConstants::energyConvert
1630	+	<< " (kcal/mol/A^2/fs)\n";
1631	+	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1632	+	<< " (amu/A/fs^2)\n";
1633	+	rnemdFile_ << "#     target one-time exchanges:\n";
1634	+	rnemdFile_ << "#         kinetic = "
1635	+	<< kineticTarget_ / PhysicalConstants::energyConvert
1636	+	<< " (kcal/mol)\n";
1637	+	rnemdFile_ << "#         momentum = " << momentumTarget_
1638	+	<< " (amu*A/fs)\n";
1639	+	rnemdFile_ << "#     actual exchange totals:\n";
1640	+	rnemdFile_ << "#         kinetic = "
1641	+	<< kineticExchange_ / PhysicalConstants::energyConvert
1642	+	<< " (kcal/mol)\n";
1643	+	rnemdFile_ << "#         momentum = " << momentumExchange_
1644	+	<< " (amu*A/fs)\n";
1645	+	rnemdFile_ << "#     actual flux:\n";
1646	+	rnemdFile_ << "#         kinetic = " << Jz
1647	+	<< " (kcal/mol/A^2/fs)\n";
1648	+	rnemdFile_ << "#         momentum = " << JzP
1649	+	<< " (amu/A/fs^2)\n";
1650	+	rnemdFile_ << "#     exchange statistics:\n";
1651	+	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1652	+	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1653	+	if (rnemdMethod_ == rnemdNIVS) {
1654	+	rnemdFile_ << "#         NIVS root-check errors = "
1655	+	<< failRootCount_ << "\n";
1656	+	}
1657	+	rnemdFile_ << "#######################################################\n";
1658	+
1659	+
1660	+
1661	+	//write title
1662	+	rnemdFile_ << "#";
1663	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1664	+	if (outputMask_[i]) {
1665	+	rnemdFile_ << "\t" << data_[i].title <<
1666	+	"(" << data_[i].units << ")";
1667	+	// add some extra tabs for column alignment
1668	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1669	+	}
1670	+	}
1671	+	rnemdFile_ << std::endl;
1672	+
1673	+	rnemdFile_.precision(8);
1674	+
1675	+	for (unsigned int j = 0; j < nBins_; j++) {
1676	+
1677	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1678	+	if (outputMask_[i]) {
1679	+	if (data_[i].dataType == "RealType")
1680	+	writeReal(i,j);
1681	+	else if (data_[i].dataType == "Vector3d")
1682	+	writeVector(i,j);
1683	+	else {
1684	+	sprintf( painCave.errMsg,
1685	+	"RNEMD found an unknown data type for: %s ",
1686	+	data_[i].title.c_str());
1687	+	painCave.isFatal = 1;
1688	+	simError();
1689	+	}
1690	+	}
1691	+	}
1692	+	rnemdFile_ << std::endl;
1693	+
1694	+	}
1695	+
1696	+	rnemdFile_ << "#######################################################\n";
1697	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1698	+	rnemdFile_ << "#######################################################\n";
1699	+
1700	+
1701	+	for (unsigned int j = 0; j < nBins_; j++) {
1702	+	rnemdFile_ << "#";
1703	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1704	+	if (outputMask_[i]) {
1705	+	if (data_[i].dataType == "RealType")
1706	+	writeRealStdDev(i,j);
1707	+	else if (data_[i].dataType == "Vector3d")
1708	+	writeVectorStdDev(i,j);
1709	+	else {
1710	+	sprintf( painCave.errMsg,
1711	+	"RNEMD found an unknown data type for: %s ",
1712	+	data_[i].title.c_str());
1713	+	painCave.isFatal = 1;
1714	+	simError();
1715	+	}
1716	+	}
1717	+	}
1718	+	rnemdFile_ << std::endl;
1719	+
1720	+	}
1721	+
1722	+	rnemdFile_.flush();
1723	+	rnemdFile_.close();
1724	+
1725	+	#ifdef IS_MPI
1726	+	}
1727	+	#endif
1728	+
1729	+	}
1730	+
1731	+	void RNEMD::writeReal(int index, unsigned int bin) {
1732	+	if (!doRNEMD_) return;
1733	+	assert(index >=0 && index < ENDINDEX);
1734	+	assert(bin < nBins_);
1735	+	RealType s;
1736	+
1737	+	data_[index].accumulator[bin]->getAverage(s);
1738	+
1739	+	if (! isinf(s) && ! isnan(s)) {
1740	+	rnemdFile_ << "\t" << s;
1741	+	} else{
1742	+	sprintf( painCave.errMsg,
1743	+	"RNEMD detected a numerical error writing: %s for bin %d",
1744	+	data_[index].title.c_str(), bin);
1745	+	painCave.isFatal = 1;
1746	+	simError();
1747	+	}
1748	+	}
1749	+
1750	+	void RNEMD::writeVector(int index, unsigned int bin) {
1751	+	if (!doRNEMD_) return;
1752	+	assert(index >=0 && index < ENDINDEX);
1753	+	assert(bin < nBins_);
1754	+	Vector3d s;
1755	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1756	+	if (isinf(s[0]) || isnan(s[0]) ||
1757	+	isinf(s[1]) || isnan(s[1]) ||
1758	+	isinf(s[2]) || isnan(s[2]) ) {
1759	+	sprintf( painCave.errMsg,
1760	+	"RNEMD detected a numerical error writing: %s for bin %d",
1761	+	data_[index].title.c_str(), bin);
1762	+	painCave.isFatal = 1;
1763	+	simError();
1764	+	} else {
1765	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1766	+	}
1767	+	}
1768	+
1769	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1770	+	if (!doRNEMD_) return;
1771	+	assert(index >=0 && index < ENDINDEX);
1772	+	assert(bin < nBins_);
1773	+	RealType s;
1774	+
1775	+	data_[index].accumulator[bin]->getStdDev(s);
1776	+
1777	+	if (! isinf(s) && ! isnan(s)) {
1778	+	rnemdFile_ << "\t" << s;
1779	+	} else{
1780	+	sprintf( painCave.errMsg,
1781	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1782	+	data_[index].title.c_str(), bin);
1783	+	painCave.isFatal = 1;
1784	+	simError();
1785	+	}
1786	+	}
1787	+
1788	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1789	+	if (!doRNEMD_) return;
1790	+	assert(index >=0 && index < ENDINDEX);
1791	+	assert(bin < nBins_);
1792	+	Vector3d s;
1793	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1794	+	if (isinf(s[0]) || isnan(s[0]) ||
1795	+	isinf(s[1]) || isnan(s[1]) ||
1796	+	isinf(s[2]) || isnan(s[2]) ) {
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1799	+	data_[index].title.c_str(), bin);
1800	+	painCave.isFatal = 1;
1801	+	simError();
1802	+	} else {
1803	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1804	+	}
1805	+	}
1806		}
1807	+

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1339 by gezelter, Thu Apr 23 18:31:05 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

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