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

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC vs.
Revision 1776 by gezelter, Thu Aug 9 15:52:59 2012 UTC

#	Line 49 | Line 49
49		#include "primitives/StuntDouble.hpp"
50		#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52	<
53	<	#ifndef IS_MPI
54	<	#include "math/SeqRandNumGen.hpp"
55	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
52	>	#ifdef IS_MPI
53		#include <mpi.h>
54		#endif
55
#	Line 65 | Line 61 | namespace OpenMD {
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
#	Line 72 | Line 69 | namespace OpenMD {
69		Globals * simParams = info->getSimParams();
70		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
77	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
78	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
79	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
80	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
81	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
82	<	stringToEnumMap_["Px"] = rnemdPx;
83	<	stringToEnumMap_["Py"] = rnemdPy;
84	<	stringToEnumMap_["Pz"] = rnemdPz;
85	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
86	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
87	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	+	stringToMethod_["Swap"]  = rnemdSwap;
76	+	stringToMethod_["NIVS"]  = rnemdNIVS;
77	+	stringToMethod_["VSS"]   = rnemdVSS;
78	+
79	+	stringToFluxType_["KE"]  = rnemdKE;
80	+	stringToFluxType_["Px"]  = rnemdPx;
81	+	stringToFluxType_["Py"]  = rnemdPy;
82	+	stringToFluxType_["Pz"]  = rnemdPz;
83	+	stringToFluxType_["KE+Px"]  = rnemdKePx;
84	+	stringToFluxType_["KE+Py"]  = rnemdKePy;
85	+	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
86	+
87		runTime_ = simParams->getRunTime();
88		statusTime_ = simParams->getStatusTime();
89
90		rnemdObjectSelection_ = rnemdParams->getObjectSelection();
91		evaluator_.loadScriptString(rnemdObjectSelection_);
92		seleMan_.setSelectionSet(evaluator_.evaluate());
93	+
94	+	const string methStr = rnemdParams->getMethod();
95	+	bool hasFluxType = rnemdParams->haveFluxType();
96	+
97	+	string fluxStr;
98	+	if (hasFluxType) {
99	+	fluxStr = rnemdParams->getFluxType();
100	+	} else {
101	+	sprintf(painCave.errMsg,
102	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
103	+	"\twhich must be one of the following values:\n"
104	+	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
105	+	"\tuse RNEMD\n");
106	+	painCave.isFatal = 1;
107	+	painCave.severity = OPENMD_ERROR;
108	+	simError();
109	+	}
110	+
111	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
112	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
113	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
114	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
115	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
116	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
117	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
118	+	bool hasOutputFields = rnemdParams->haveOutputFields();
119	+
120	+	map<string, RNEMDMethod>::iterator i;
121	+	i = stringToMethod_.find(methStr);
122	+	if (i != stringToMethod_.end())
123	+	rnemdMethod_ = i->second;
124	+	else {
125	+	sprintf(painCave.errMsg,
126	+	"RNEMD: The current method,\n"
127	+	"\t\t%s is not one of the recognized\n"
128	+	"\texchange methods: Swap, NIVS, or VSS\n",
129	+	methStr.c_str());
130	+	painCave.isFatal = 1;
131	+	painCave.severity = OPENMD_ERROR;
132	+	simError();
133	+	}
134	+
135	+	map<string, RNEMDFluxType>::iterator j;
136	+	j = stringToFluxType_.find(fluxStr);
137	+	if (j != stringToFluxType_.end())
138	+	rnemdFluxType_ = j->second;
139	+	else {
140	+	sprintf(painCave.errMsg,
141	+	"RNEMD: The current fluxType,\n"
142	+	"\t\t%s\n"
143	+	"\tis not one of the recognized flux types.\n",
144	+	fluxStr.c_str());
145	+	painCave.isFatal = 1;
146	+	painCave.severity = OPENMD_ERROR;
147	+	simError();
148	+	}
149	+
150	+	bool methodFluxMismatch = false;
151	+	bool hasCorrectFlux = false;
152	+	switch(rnemdMethod_) {
153	+	case rnemdSwap:
154	+	switch (rnemdFluxType_) {
155	+	case rnemdKE:
156	+	hasCorrectFlux = hasKineticFlux;
157	+	break;
158	+	case rnemdPx:
159	+	case rnemdPy:
160	+	case rnemdPz:
161	+	hasCorrectFlux = hasMomentumFlux;
162	+	break;
163	+	default :
164	+	methodFluxMismatch = true;
165	+	break;
166	+	}
167	+	break;
168	+	case rnemdNIVS:
169	+	switch (rnemdFluxType_) {
170	+	case rnemdKE:
171	+	case rnemdRotKE:
172	+	case rnemdFullKE:
173	+	hasCorrectFlux = hasKineticFlux;
174	+	break;
175	+	case rnemdPx:
176	+	case rnemdPy:
177	+	case rnemdPz:
178	+	hasCorrectFlux = hasMomentumFlux;
179	+	break;
180	+	case rnemdKePx:
181	+	case rnemdKePy:
182	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
183	+	break;
184	+	default:
185	+	methodFluxMismatch = true;
186	+	break;
187	+	}
188	+	break;
189	+	case rnemdVSS:
190	+	switch (rnemdFluxType_) {
191	+	case rnemdKE:
192	+	case rnemdRotKE:
193	+	case rnemdFullKE:
194	+	hasCorrectFlux = hasKineticFlux;
195	+	break;
196	+	case rnemdPx:
197	+	case rnemdPy:
198	+	case rnemdPz:
199	+	hasCorrectFlux = hasMomentumFlux;
200	+	break;
201	+	case rnemdPvector:
202	+	hasCorrectFlux = hasMomentumFluxVector;
203	+	case rnemdKePx:
204	+	case rnemdKePy:
205	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
206	+	break;
207	+	case rnemdKePvector:
208	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
209	+	break;
210	+	default:
211	+	methodFluxMismatch = true;
212	+	break;
213	+	}
214	+	default:
215	+	break;
216	+	}
217	+
218	+	if (methodFluxMismatch) {
219	+	sprintf(painCave.errMsg,
220	+	"RNEMD: The current method,\n"
221	+	"\t\t%s\n"
222	+	"\tcannot be used with the current flux type, %s\n",
223	+	methStr.c_str(), fluxStr.c_str());
224	+	painCave.isFatal = 1;
225	+	painCave.severity = OPENMD_ERROR;
226	+	simError();
227	+	}
228	+	if (!hasCorrectFlux) {
229	+	sprintf(painCave.errMsg,
230	+	"RNEMD: The current method,\n"
231	+	"\t%s, and flux type %s\n"
232	+	"\tdid not have the correct flux value specified. Options\n"
233	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
234	+	methStr.c_str(), fluxStr.c_str());
235	+	painCave.isFatal = 1;
236	+	painCave.severity = OPENMD_ERROR;
237	+	simError();
238	+	}
239	+
240	+	if (hasKineticFlux) {
241	+	kineticFlux_ = rnemdParams->getKineticFlux();
242	+	} else {
243	+	kineticFlux_ = 0.0;
244	+	}
245	+	if (hasMomentumFluxVector) {
246	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
247	+	} else {
248	+	momentumFluxVector_ = V3Zero;
249	+	if (hasMomentumFlux) {
250	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
251	+	switch (rnemdFluxType_) {
252	+	case rnemdPx:
253	+	momentumFluxVector_.x() = momentumFlux;
254	+	break;
255	+	case rnemdPy:
256	+	momentumFluxVector_.y() = momentumFlux;
257	+	break;
258	+	case rnemdPz:
259	+	momentumFluxVector_.z() = momentumFlux;
260	+	break;
261	+	case rnemdKePx:
262	+	momentumFluxVector_.x() = momentumFlux;
263	+	break;
264	+	case rnemdKePy:
265	+	momentumFluxVector_.y() = momentumFlux;
266	+	break;
267	+	default:
268	+	break;
269	+	}
270	+	}
271	+	}
272
273		// do some sanity checking
274
#	Line 100 | Line 277 | namespace OpenMD {
277
278		if (selectionCount > nIntegrable) {
279		sprintf(painCave.errMsg,
280	<	"RNEMD: The current RNEMD_objectSelection,\n"
280	>	"RNEMD: The current objectSelection,\n"
281		"\t\t%s\n"
282		"\thas resulted in %d selected objects.  However,\n"
283		"\tthe total number of integrable objects in the system\n"
#	Line 113 | Line 290 | namespace OpenMD {
290		painCave.severity = OPENMD_WARNING;
291		simError();
292		}
116	–
117	–	const string st = rnemdParams->getExchangeType();
293
294	<	map<string, RNEMDTypeEnum>::iterator i;
120	<	i = stringToEnumMap_.find(st);
121	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
122	<	if (rnemdType_ == rnemdUnknown) {
123	<	sprintf(painCave.errMsg,
124	<	"RNEMD: The current RNEMD_exchangeType,\n"
125	<	"\t\t%s\n"
126	<	"\tis not one of the recognized exchange types.\n",
127	<	st.c_str());
128	<	painCave.isFatal = 1;
129	<	painCave.severity = OPENMD_ERROR;
130	<	simError();
131	<	}
132	<
133	<	outputTemp_ = false;
134	<	if (rnemdParams->haveOutputTemperature()) {
135	<	outputTemp_ = rnemdParams->getOutputTemperature();
136	<	} else if ((rnemdType_ == rnemdKineticSwap) ||
137	<	(rnemdType_ == rnemdKineticScale) ||
138	<	(rnemdType_ == rnemdKineticScaleVAM) ||
139	<	(rnemdType_ == rnemdKineticScaleAM)) {
140	<	outputTemp_ = true;
141	<	}
142	<	outputVx_ = false;
143	<	if (rnemdParams->haveOutputVx()) {
144	<	outputVx_ = rnemdParams->getOutputVx();
145	<	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
146	<	outputVx_ = true;
147	<	}
148	<	outputVy_ = false;
149	<	if (rnemdParams->haveOutputVy()) {
150	<	outputVy_ = rnemdParams->getOutputVy();
151	<	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
152	<	outputVy_ = true;
153	<	}
154	<	output3DTemp_ = false;
155	<	if (rnemdParams->haveOutputXyzTemperature()) {
156	<	output3DTemp_ = rnemdParams->getOutputXyzTemperature();
157	<	}
158	<	outputRotTemp_ = false;
159	<	if (rnemdParams->haveOutputRotTemperature()) {
160	<	outputRotTemp_ = rnemdParams->getOutputRotTemperature();
161	<	}
162	<	// James put this in.
163	<	outputDen_ = false;
164	<	if (rnemdParams->haveOutputDen()) {
165	<	outputDen_ = rnemdParams->getOutputDen();
166	<	}
167	<	outputAh_ = false;
168	<	if (rnemdParams->haveOutputAh()) {
169	<	outputAh_ = rnemdParams->getOutputAh();
170	<	}
171	<	outputVz_ = false;
172	<	if (rnemdParams->haveOutputVz()) {
173	<	outputVz_ = rnemdParams->getOutputVz();
174	<	} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
175	<	outputVz_ = true;
176	<	}
177	<
294	>	areaAccumulator_ = new Accumulator();
295
296	<	#ifdef IS_MPI
180	<	if (worldRank == 0) {
181	<	#endif
296	>	nBins_ = rnemdParams->getOutputBins();
297
298	<	//may have rnemdWriter separately
299	<	string rnemdFileName;
298	>	data_.resize(RNEMD::ENDINDEX);
299	>	OutputData z;
300	>	z.units =  "Angstroms";
301	>	z.title =  "Z";
302	>	z.dataType = "RealType";
303	>	z.accumulator.reserve(nBins_);
304	>	for (unsigned int i = 0; i < nBins_; i++)
305	>	z.accumulator.push_back( new Accumulator() );
306	>	data_[Z] = z;
307	>	outputMap_["Z"] =  Z;
308
309	<	if (outputTemp_) {
310	<	rnemdFileName = "temperature.log";
311	<	tempLog_.open(rnemdFileName.c_str());
312	<	}
313	<	if (outputVx_) {
314	<	rnemdFileName = "velocityX.log";
315	<	vxzLog_.open(rnemdFileName.c_str());
316	<	}
317	<	if (outputVy_) {
195	<	rnemdFileName = "velocityY.log";
196	<	vyzLog_.open(rnemdFileName.c_str());
197	<	}
309	>	OutputData temperature;
310	>	temperature.units =  "K";
311	>	temperature.title =  "Temperature";
312	>	temperature.dataType = "RealType";
313	>	temperature.accumulator.reserve(nBins_);
314	>	for (unsigned int i = 0; i < nBins_; i++)
315	>	temperature.accumulator.push_back( new Accumulator() );
316	>	data_[TEMPERATURE] = temperature;
317	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
318
319	<	if (output3DTemp_) {
320	<	rnemdFileName = "temperatureX.log";
321	<	xTempLog_.open(rnemdFileName.c_str());
322	<	rnemdFileName = "temperatureY.log";
323	<	yTempLog_.open(rnemdFileName.c_str());
324	<	rnemdFileName = "temperatureZ.log";
325	<	zTempLog_.open(rnemdFileName.c_str());
326	<	}
327	<	if (outputRotTemp_) {
208	<	rnemdFileName = "temperatureR.log";
209	<	rotTempLog_.open(rnemdFileName.c_str());
210	<	}
211	<
212	<	//James put this in
213	<	if (outputDen_) {
214	<	rnemdFileName = "Density.log";
215	<	denLog_.open(rnemdFileName.c_str());
216	<	}
217	<	if (outputAh_) {
218	<	rnemdFileName = "Ah.log";
219	<	AhLog_.open(rnemdFileName.c_str());
220	<	}
221	<	if (outputVz_) {
222	<	rnemdFileName = "velocityZ.log";
223	<	vzzLog_.open(rnemdFileName.c_str());
224	<	}
225	<	logFrameCount_ = 0;
226	<	#ifdef IS_MPI
227	<	}
228	<	#endif
319	>	OutputData velocity;
320	>	velocity.units = "amu/fs";
321	>	velocity.title =  "Velocity";
322	>	velocity.dataType = "Vector3d";
323	>	velocity.accumulator.reserve(nBins_);
324	>	for (unsigned int i = 0; i < nBins_; i++)
325	>	velocity.accumulator.push_back( new VectorAccumulator() );
326	>	data_[VELOCITY] = velocity;
327	>	outputMap_["VELOCITY"] = VELOCITY;
328
329	<	set_RNEMD_exchange_time(rnemdParams->getExchangeTime());
330	<	set_RNEMD_nBins(rnemdParams->getNbins());
331	<	midBin_ = nBins_ / 2;
332	<	if (rnemdParams->haveBinShift()) {
333	<	if (rnemdParams->getBinShift()) {
334	<	zShift_ = 0.5 / (RealType)(nBins_);
335	<	} else {
336	<	zShift_ = 0.0;
337	<	}
329	>	OutputData density;
330	>	density.units =  "g cm^-3";
331	>	density.title =  "Density";
332	>	density.dataType = "RealType";
333	>	density.accumulator.reserve(nBins_);
334	>	for (unsigned int i = 0; i < nBins_; i++)
335	>	density.accumulator.push_back( new Accumulator() );
336	>	data_[DENSITY] = density;
337	>	outputMap_["DENSITY"] =  DENSITY;
338	>
339	>	if (hasOutputFields) {
340	>	parseOutputFileFormat(rnemdParams->getOutputFields());
341		} else {
342	<	zShift_ = 0.0;
342	>	outputMask_.set(Z);
343	>	switch (rnemdFluxType_) {
344	>	case rnemdKE:
345	>	case rnemdRotKE:
346	>	case rnemdFullKE:
347	>	outputMask_.set(TEMPERATURE);
348	>	break;
349	>	case rnemdPx:
350	>	case rnemdPy:
351	>	outputMask_.set(VELOCITY);
352	>	break;
353	>	case rnemdPz:
354	>	case rnemdPvector:
355	>	outputMask_.set(VELOCITY);
356	>	outputMask_.set(DENSITY);
357	>	break;
358	>	case rnemdKePx:
359	>	case rnemdKePy:
360	>	outputMask_.set(TEMPERATURE);
361	>	outputMask_.set(VELOCITY);
362	>	break;
363	>	case rnemdKePvector:
364	>	outputMask_.set(TEMPERATURE);
365	>	outputMask_.set(VELOCITY);
366	>	outputMask_.set(DENSITY);
367	>	break;
368	>	default:
369	>	break;
370	>	}
371		}
372	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
373	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
374	<	//set to 0.0 if not using it; N/A in status output yet
245	<	if (rnemdParams->haveLogWidth()) {
246	<	set_RNEMD_logWidth(rnemdParams->getLogWidth());
247	<	/*arbitary rnemdLogWidth_, no checking;
248	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
249	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
250	<	cerr << "Automaically set back to default.\n";
251	<	rnemdLogWidth_ = nBins_;
252	<	}*/
372	>
373	>	if (hasOutputFileName) {
374	>	rnemdFileName_ = rnemdParams->getOutputFileName();
375		} else {
376	<	set_RNEMD_logWidth(nBins_);
377	<	}
256	<	tempHist_.resize(rnemdLogWidth_, 0.0);
257	<	tempCount_.resize(rnemdLogWidth_, 0);
258	<	pxzHist_.resize(rnemdLogWidth_, 0.0);
259	<	//vxzCount_.resize(rnemdLogWidth_, 0);
260	<	pyzHist_.resize(rnemdLogWidth_, 0.0);
261	<	//vyzCount_.resize(rnemdLogWidth_, 0);
376	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
377	>	}
378
379	<	mHist_.resize(rnemdLogWidth_, 0.0);
264	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
265	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
266	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
267	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
268	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
269	<	rotTempCount_.resize(rnemdLogWidth_, 0);
270	<	// James put this in
271	<	DenHist_.resize(rnemdLogWidth_, 0.0);
272	<	pzzHist_.resize(rnemdLogWidth_, 0.0);
379	>	exchangeTime_ = rnemdParams->getExchangeTime();
380
381	<	set_RNEMD_exchange_total(0.0);
382	<	if (rnemdParams->haveTargetFlux()) {
383	<	set_RNEMD_target_flux(rnemdParams->getTargetFlux());
384	<	} else {
385	<	set_RNEMD_target_flux(0.0);
386	<	}
387	<	if (rnemdParams->haveTargetJzKE()) {
281	<	set_RNEMD_target_JzKE(rnemdParams->getTargetJzKE());
282	<	} else {
283	<	set_RNEMD_target_JzKE(0.0);
284	<	}
285	<	if (rnemdParams->haveTargetJzpx()) {
286	<	set_RNEMD_target_jzpx(rnemdParams->getTargetJzpx());
287	<	} else {
288	<	set_RNEMD_target_jzpx(0.0);
289	<	}
290	<	jzp_.x() = targetJzpx_;
291	<	njzp_.x() = -targetJzpx_;
292	<	if (rnemdParams->haveTargetJzpy()) {
293	<	set_RNEMD_target_jzpy(rnemdParams->getTargetJzpy());
294	<	} else {
295	<	set_RNEMD_target_jzpy(0.0);
296	<	}
297	<	jzp_.y() = targetJzpy_;
298	<	njzp_.y() = -targetJzpy_;
299	<	if (rnemdParams->haveTargetJzpz()) {
300	<	set_RNEMD_target_jzpz(rnemdParams->getTargetJzpz());
301	<	} else {
302	<	set_RNEMD_target_jzpz(0.0);
303	<	}
304	<	jzp_.z() = targetJzpz_;
305	<	njzp_.z() = -targetJzpz_;
381	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
382	>	Mat3x3d hmat = currentSnap_->getHmat();
383	>
384	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
385	>	// Lx, Ly = box dimensions in x & y
386	>	// dt = exchange time interval
387	>	// flux = target flux
388
389	<	#ifndef IS_MPI
390	<	if (simParams->haveSeed()) {
391	<	seedValue = simParams->getSeed();
392	<	randNumGen_ = new SeqRandNumGen(seedValue);
393	<	}else {
394	<	randNumGen_ = new SeqRandNumGen();
395	<	}
396	<	#else
397	<	if (simParams->haveSeed()) {
398	<	seedValue = simParams->getSeed();
399	<	randNumGen_ = new ParallelRandNumGen(seedValue);
400	<	}else {
401	<	randNumGen_ = new ParallelRandNumGen();
320	<	}
321	<	#endif
322	<	}
389	>	RealType area = currentSnap_->getXYarea();
390	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
391	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
392	>
393	>	// total exchange sums are zeroed out at the beginning:
394	>
395	>	kineticExchange_ = 0.0;
396	>	momentumExchange_ = V3Zero;
397	>
398	>	if (hasSlabWidth)
399	>	slabWidth_ = rnemdParams->getSlabWidth();
400	>	else
401	>	slabWidth_ = hmat(2,2) / 10.0;
402
403	<	RNEMD::~RNEMD() {
404	<	delete randNumGen_;
403	>	if (hasSlabACenter)
404	>	slabACenter_ = rnemdParams->getSlabACenter();
405	>	else
406	>	slabACenter_ = 0.0;
407
408	+	if (hasSlabBCenter)
409	+	slabBCenter_ = rnemdParams->getSlabBCenter();
410	+	else
411	+	slabBCenter_ = hmat(2,2) / 2.0;
412	+
413	+	}
414	+
415	+	RNEMD::~RNEMD() {
416	+	if (!doRNEMD_) return;
417		#ifdef IS_MPI
418		if (worldRank == 0) {
419		#endif
330	–
331	–	sprintf(painCave.errMsg,
332	–	"RNEMD: total failed trials: %d\n",
333	–	failTrialCount_);
334	–	painCave.isFatal = 0;
335	–	painCave.severity = OPENMD_INFO;
336	–	simError();
337	–
338	–	if (outputTemp_) tempLog_.close();
339	–	if (outputVx_)   vxzLog_.close();
340	–	if (outputVy_)   vyzLog_.close();
420
421	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
422	<	rnemdType_ == rnemdPyScale) {
423	<	sprintf(painCave.errMsg,
345	<	"RNEMD: total root-checking warnings: %d\n",
346	<	failRootCount_);
347	<	painCave.isFatal = 0;
348	<	painCave.severity = OPENMD_INFO;
349	<	simError();
350	<	}
351	<	if (output3DTemp_) {
352	<	xTempLog_.close();
353	<	yTempLog_.close();
354	<	zTempLog_.close();
355	<	}
356	<	if (outputRotTemp_) rotTempLog_.close();
357	<	// James put this in
358	<	if (outputDen_) denLog_.close();
359	<	if (outputAh_)  AhLog_.close();
360	<	if (outputVz_)  vzzLog_.close();
421	>	writeOutputFile();
422	>
423	>	rnemdFile_.close();
424
425		#ifdef IS_MPI
426		}
427		#endif
428		}
429	+
430	+	bool RNEMD::inSlabA(Vector3d pos) {
431	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
432	+	}
433	+	bool RNEMD::inSlabB(Vector3d pos) {
434	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
435	+	}
436
437		void RNEMD::doSwap() {
438	<
438	>	if (!doRNEMD_) return;
439		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
440		Mat3x3d hmat = currentSnap_->getHmat();
441
#	Line 394 | Line 464 | namespace OpenMD {
464
465		if (usePeriodicBoundaryConditions_)
466		currentSnap_->wrapVector(pos);
467	+	bool inA = inSlabA(pos);
468	+	bool inB = inSlabB(pos);
469
470	<	// which bin is this stuntdouble in?
399	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
400	<
401	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
402	<
403	<
404	<	// if we're in bin 0 or the middleBin
405	<	if (binNo == 0 || binNo == midBin_) {
470	>	if (inA || inB) {
471
472		RealType mass = sd->getMass();
473		Vector3d vel = sd->getVel();
474		RealType value;
475	<
476	<	switch(rnemdType_) {
477	<	case rnemdKineticSwap :
475	>
476	>	switch(rnemdFluxType_) {
477	>	case rnemdKE :
478
479		value = mass * vel.lengthSquare();
480
#	Line 430 | Line 495 | namespace OpenMD {
495		}
496		} //angular momenta exchange enabled
497		//energyConvert temporarily disabled
498	<	//make exchangeSum_ comparable between swap & scale
498	>	//make kineticExchange_ comparable between swap & scale
499		//value = value * 0.5 / PhysicalConstants::energyConvert;
500		value *= 0.5;
501		break;
#	Line 447 | Line 512 | namespace OpenMD {
512		break;
513		}
514
515	<	if (binNo == 0) {
515	>	if (inA == 0) {
516		if (!min_found) {
517		min_val = value;
518		min_sd = sd;
#	Line 458 | Line 523 | namespace OpenMD {
523		min_sd = sd;
524		}
525		}
526	<	} else { //midBin_
526	>	} else {
527		if (!max_found) {
528		max_val = value;
529		max_sd = sd;
#	Line 472 | Line 537 | namespace OpenMD {
537		}
538		}
539		}
540	<
540	>
541		#ifdef IS_MPI
542		int nProc, worldRank;
543	<
543	>
544		nProc = MPI::COMM_WORLD.Get_size();
545		worldRank = MPI::COMM_WORLD.Get_rank();
546
#	Line 533 | Line 598 | namespace OpenMD {
598		Vector3d max_vel = max_sd->getVel();
599		RealType temp_vel;
600
601	<	switch(rnemdType_) {
602	<	case rnemdKineticSwap :
601	>	switch(rnemdFluxType_) {
602	>	case rnemdKE :
603		min_sd->setVel(max_vel);
604		max_sd->setVel(min_vel);
605		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 585 | Line 650 | namespace OpenMD {
650		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
651		min_vals.rank, 0, status);
652
653	<	switch(rnemdType_) {
654	<	case rnemdKineticSwap :
653	>	switch(rnemdFluxType_) {
654	>	case rnemdKE :
655		max_sd->setVel(min_vel);
656		//angular momenta exchange enabled
657		if (max_sd->isDirectional()) {
#	Line 631 | Line 696 | namespace OpenMD {
696		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
697		max_vals.rank, 0, status);
698
699	<	switch(rnemdType_) {
700	<	case rnemdKineticSwap :
699	>	switch(rnemdFluxType_) {
700	>	case rnemdKE :
701		min_sd->setVel(max_vel);
702		//angular momenta exchange enabled
703		if (min_sd->isDirectional()) {
#	Line 666 | Line 731 | namespace OpenMD {
731		}
732		}
733		#endif
734	<	exchangeSum_ += max_val - min_val;
734	>
735	>	switch(rnemdFluxType_) {
736	>	case rnemdKE:
737	>	cerr << "KE\n";
738	>	kineticExchange_ += max_val - min_val;
739	>	break;
740	>	case rnemdPx:
741	>	momentumExchange_.x() += max_val - min_val;
742	>	break;
743	>	case rnemdPy:
744	>	momentumExchange_.y() += max_val - min_val;
745	>	break;
746	>	case rnemdPz:
747	>	momentumExchange_.z() += max_val - min_val;
748	>	break;
749	>	default:
750	>	cerr << "default\n";
751	>	break;
752	>	}
753		} else {
754		sprintf(painCave.errMsg,
755	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
755	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
756		painCave.isFatal = 0;
757		painCave.severity = OPENMD_INFO;
758		simError();
#	Line 677 | Line 760 | namespace OpenMD {
760		}
761		} else {
762		sprintf(painCave.errMsg,
763	<	"RNEMD: exchange NOT performed because selected object\n"
764	<	"\tnot present in at least one of the two slabs.\n");
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	<	}
687	<
769	>	}
770		}
771
772	<	void RNEMD::doScale() {
773	<
772	>	void RNEMD::doNIVS() {
773	>	if (!doRNEMD_) return;
774		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
775		Mat3x3d hmat = currentSnap_->getHmat();
776
#	Line 728 | Line 810 | namespace OpenMD {
810		currentSnap_->wrapVector(pos);
811
812		// which bin is this stuntdouble in?
813	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
813	>	bool inA = inSlabA(pos);
814	>	bool inB = inSlabB(pos);
815
816	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
817	<
735	<	// if we're in bin 0 or the middleBin
736	<	if (binNo == 0 || binNo == midBin_) {
737	<
816	>	if (inA || inB) {
817	>
818		RealType mass = sd->getMass();
819		Vector3d vel = sd->getVel();
820
821	<	if (binNo == 0) {
821	>	if (inA) {
822		hotBin.push_back(sd);
823		Phx += mass * vel.x();
824		Phy += mass * vel.y();
#	Line 746 | Line 826 | namespace OpenMD {
826		Khx += mass * vel.x() * vel.x();
827		Khy += mass * vel.y() * vel.y();
828		Khz += mass * vel.z() * vel.z();
749	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
829		if (sd->isDirectional()) {
830		Vector3d angMom = sd->getJ();
831		Mat3x3d I = sd->getI();
#	Line 762 | Line 841 | namespace OpenMD {
841		+ angMom[2]*angMom[2]/I(2, 2);
842		}
843		}
844	<	//}
766	<	} else { //midBin_
844	>	} else {
845		coldBin.push_back(sd);
846		Pcx += mass * vel.x();
847		Pcy += mass * vel.y();
#	Line 771 | Line 849 | namespace OpenMD {
849		Kcx += mass * vel.x() * vel.x();
850		Kcy += mass * vel.y() * vel.y();
851		Kcz += mass * vel.z() * vel.z();
774	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
852		if (sd->isDirectional()) {
853		Vector3d angMom = sd->getJ();
854		Mat3x3d I = sd->getI();
#	Line 787 | Line 864 | namespace OpenMD {
864		+ angMom[2]*angMom[2]/I(2, 2);
865		}
866		}
790	–	//}
867		}
868		}
869		}
#	Line 801 | Line 877 | namespace OpenMD {
877		Kcz *= 0.5;
878		Kcw *= 0.5;
879
804	–	// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
805	–	//        << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
806	–	//        << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
807	–	// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
808	–	//        << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
809	–
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);
#	Line 832 | Line 902 | namespace OpenMD {
902		RealType pz = Pcz / Phz;
903		RealType c, x, y, z;
904		bool successfulScale = false;
905	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
906	<	(rnemdType_ == rnemdKineticScaleAM)) {
905	>	if ((rnemdFluxType_ == rnemdFullKE) ||
906	>	(rnemdFluxType_ == rnemdRotKE)) {
907		//may need sanity check Khw & Kcw > 0
908
909	<	if (rnemdType_ == rnemdKineticScaleVAM) {
910	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
909	>	if (rnemdFluxType_ == rnemdFullKE) {
910	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
911		} else {
912	<	c = 1.0 - targetFlux_ / Kcw;
912	>	c = 1.0 - kineticTarget_ / Kcw;
913		}
914
915		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
916		c = sqrt(c);
917	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
917	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
918		//now convert to hotBin coefficient
919		RealType w = 0.0;
920	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
920	>	if (rnemdFluxType_ ==  rnemdFullKE) {
921		x = 1.0 + px * (1.0 - c);
922		y = 1.0 + py * (1.0 - c);
923		z = 1.0 + pz * (1.0 - c);
#	Line 861 | Line 931 | namespace OpenMD {
931		*/
932		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
933		(fabs(z - 1.0) < 0.1)) {
934	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
934	>	w = 1.0 + (kineticTarget_
935	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
936		+ Khz * (1.0 - z * z)) / Khw;
937		}//no need to calculate w if x, y or z is out of range
938		} else {
939	<	w = 1.0 + targetFlux_ / Khw;
939	>	w = 1.0 + kineticTarget_ / Khw;
940		}
941		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
942		//if w is in the right range, so should be x, y, z.
943		vector<StuntDouble*>::iterator sdi;
944		Vector3d vel;
945		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
946	<	if (rnemdType_ == rnemdKineticScaleVAM) {
946	>	if (rnemdFluxType_ == rnemdFullKE) {
947		vel = (*sdi)->getVel() * c;
877	–	//vel.x() *= c;
878	–	//vel.y() *= c;
879	–	//vel.z() *= c;
948		(*sdi)->setVel(vel);
949		}
950		if ((*sdi)->isDirectional()) {
951		Vector3d angMom = (*sdi)->getJ() * c;
884	–	//angMom[0] *= c;
885	–	//angMom[1] *= c;
886	–	//angMom[2] *= c;
952		(*sdi)->setJ(angMom);
953		}
954		}
955		w = sqrt(w);
956	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
957	<	<< "\twh= " << w << endl;
956	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
957	>	//           << "\twh= " << w << endl;
958		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
959	<	if (rnemdType_ == rnemdKineticScaleVAM) {
959	>	if (rnemdFluxType_ == rnemdFullKE) {
960		vel = (*sdi)->getVel();
961		vel.x() *= x;
962		vel.y() *= y;
#	Line 900 | Line 965 | namespace OpenMD {
965		}
966		if ((*sdi)->isDirectional()) {
967		Vector3d angMom = (*sdi)->getJ() * w;
903	–	//angMom[0] *= w;
904	–	//angMom[1] *= w;
905	–	//angMom[2] *= w;
968		(*sdi)->setJ(angMom);
969		}
970		}
971		successfulScale = true;
972	<	exchangeSum_ += targetFlux_;
972	>	kineticExchange_ += kineticTarget_;
973		}
974		}
975		} else {
976		RealType a000, a110, c0, a001, a111, b01, b11, c1;
977	<	switch(rnemdType_) {
978	<	case rnemdKineticScale :
977	>	switch(rnemdFluxType_) {
978	>	case rnemdKE :
979		/* used hotBin coeff's & only scale x & y dimensions
980		RealType px = Phx / Pcx;
981		RealType py = Phy / Pcy;
982		a110 = Khy;
983	<	c0 = - Khx - Khy - targetFlux_;
983	>	c0 = - Khx - Khy - kineticTarget_;
984		a000 = Khx;
985		a111 = Kcy * py * py;
986		b11 = -2.0 * Kcy * py * (1.0 + py);
987	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
987	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
988		b01 = -2.0 * Kcx * px * (1.0 + px);
989		a001 = Kcx * px * px;
990		*/
991		//scale all three dimensions, let c_x = c_y
992		a000 = Kcx + Kcy;
993		a110 = Kcz;
994	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
994	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
995		a001 = Khx * px * px + Khy * py * py;
996		a111 = Khz * pz * pz;
997		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
998		b11 = -2.0 * Khz * pz * (1.0 + pz);
999		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1000	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1000	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1001		break;
1002	<	case rnemdPxScale :
1003	<	c = 1 - targetFlux_ / Pcx;
1002	>	case rnemdPx :
1003	>	c = 1 - momentumTarget_.x() / Pcx;
1004		a000 = Kcy;
1005		a110 = Kcz;
1006		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 949 | Line 1011 | namespace OpenMD {
1011		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1012		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1013		break;
1014	<	case rnemdPyScale :
1015	<	c = 1 - targetFlux_ / Pcy;
1014	>	case rnemdPy :
1015	>	c = 1 - momentumTarget_.y() / Pcy;
1016		a000 = Kcx;
1017		a110 = Kcz;
1018		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 961 | Line 1023 | namespace OpenMD {
1023		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1024		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1025		break;
1026	<	case rnemdPzScale ://we don't really do this, do we?
1027	<	c = 1 - targetFlux_ / Pcz;
1026	>	case rnemdPz ://we don't really do this, do we?
1027	>	c = 1 - momentumTarget_.z() / Pcz;
1028		a000 = Kcx;
1029		a110 = Kcy;
1030		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1047 | Line 1109 | namespace OpenMD {
1109		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1110		r1 = (*rpi).first;
1111		r2 = (*rpi).second;
1112	<	switch(rnemdType_) {
1113	<	case rnemdKineticScale :
1112	>	switch(rnemdFluxType_) {
1113	>	case rnemdKE :
1114		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1115		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1116		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1117		break;
1118	<	case rnemdPxScale :
1118	>	case rnemdPx :
1119		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1120		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1121		break;
1122	<	case rnemdPyScale :
1122	>	case rnemdPy :
1123		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1124		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1125		break;
1126	<	case rnemdPzScale :
1126	>	case rnemdPz :
1127		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1128		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1129		default :
#	Line 1075 | Line 1137 | namespace OpenMD {
1137		#ifdef IS_MPI
1138		if (worldRank == 0) {
1139		#endif
1140	<	sprintf(painCave.errMsg,
1141	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1142	<	bestPair.first, bestPair.second);
1143	<	painCave.isFatal = 0;
1144	<	painCave.severity = OPENMD_INFO;
1145	<	simError();
1140	>	// sprintf(painCave.errMsg,
1141	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1142	>	//         bestPair.first, bestPair.second);
1143	>	// painCave.isFatal = 0;
1144	>	// painCave.severity = OPENMD_INFO;
1145	>	// simError();
1146		#ifdef IS_MPI
1147		}
1148		#endif
1149
1150	<	switch(rnemdType_) {
1151	<	case rnemdKineticScale :
1150	>	switch(rnemdFluxType_) {
1151	>	case rnemdKE :
1152		x = bestPair.first;
1153		y = bestPair.first;
1154		z = bestPair.second;
1155		break;
1156	<	case rnemdPxScale :
1156	>	case rnemdPx :
1157		x = c;
1158		y = bestPair.first;
1159		z = bestPair.second;
1160		break;
1161	<	case rnemdPyScale :
1161	>	case rnemdPy :
1162		x = bestPair.first;
1163		y = c;
1164		z = bestPair.second;
1165		break;
1166	<	case rnemdPzScale :
1166	>	case rnemdPz :
1167		x = bestPair.first;
1168		y = bestPair.second;
1169		z = c;
#	Line 1130 | Line 1192 | namespace OpenMD {
1192		(*sdi)->setVel(vel);
1193		}
1194		successfulScale = true;
1195	<	exchangeSum_ += targetFlux_;
1195	>	switch(rnemdFluxType_) {
1196	>	case rnemdKE :
1197	>	kineticExchange_ += kineticTarget_;
1198	>	break;
1199	>	case rnemdPx :
1200	>	case rnemdPy :
1201	>	case rnemdPz :
1202	>	momentumExchange_ += momentumTarget_;
1203	>	break;
1204	>	default :
1205	>	break;
1206	>	}
1207		}
1208		}
1209		if (successfulScale != true) {
1210		sprintf(painCave.errMsg,
1211	<	"RNEMD: exchange NOT performed!\n");
1211	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1212	>	"\tthe constraint equations may not exist or there may be\n"
1213	>	"\tno selected objects in one or both slabs.\n");
1214		painCave.isFatal = 0;
1215		painCave.severity = OPENMD_INFO;
1216		simError();
#	Line 1143 | Line 1218 | namespace OpenMD {
1218		}
1219		}
1220
1221	<	void RNEMD::doShiftScale() {
1222	<
1221	>	void RNEMD::doVSS() {
1222	>	if (!doRNEMD_) return;
1223		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1224		RealType time = currentSnap_->getTime();
1225		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 1178 | Line 1253 | namespace OpenMD {
1253		currentSnap_->wrapVector(pos);
1254
1255		// which bin is this stuntdouble in?
1256	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1257	<
1258	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1259	<
1185	<	// if we're in bin 0 or the middleBin
1186	<	if (binNo == 0 || binNo == midBin_) {
1256	>	bool inA = inSlabA(pos);
1257	>	bool inB = inSlabB(pos);
1258	>
1259	>	if (inA || inB) {
1260
1261		RealType mass = sd->getMass();
1262		Vector3d vel = sd->getVel();
1263
1264	<	if (binNo == 0) {
1264	>	if (inA) {
1265		hotBin.push_back(sd);
1266		//std::cerr << "before, velocity = " << vel << endl;
1267		Ph += mass * vel;
1268		//std::cerr << "after, velocity = " << vel << endl;
1269		Mh += mass;
1270		Kh += mass * vel.lengthSquare();
1271	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1271	>	if (rnemdFluxType_ == rnemdFullKE) {
1272		if (sd->isDirectional()) {
1273		Vector3d angMom = sd->getJ();
1274		Mat3x3d I = sd->getI();
#	Line 1217 | Line 1290 | namespace OpenMD {
1290		Pc += mass * vel;
1291		Mc += mass;
1292		Kc += mass * vel.lengthSquare();
1293	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1293	>	if (rnemdFluxType_ == rnemdFullKE) {
1294		if (sd->isDirectional()) {
1295		Vector3d angMom = sd->getJ();
1296		Mat3x3d I = sd->getI();
#	Line 1257 | Line 1330 | namespace OpenMD {
1330		bool successfulExchange = false;
1331		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1332		Vector3d vc = Pc / Mc;
1333	<	Vector3d ac = njzp_ / Mc + vc;
1334	<	Vector3d acrec = njzp_ / Mc;
1335	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1333	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1334	>	Vector3d acrec = -momentumTarget_ / Mc;
1335	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1336		if (cNumerator > 0.0) {
1337		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1338		if (cDenominator > 0.0) {
1339		RealType c = sqrt(cNumerator / cDenominator);
1340		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1341		Vector3d vh = Ph / Mh;
1342	<	Vector3d ah = jzp_ / Mh + vh;
1343	<	Vector3d ahrec = jzp_ / Mh;
1344	<	RealType hNumerator = Kh + targetJzKE_
1342	>	Vector3d ah = momentumTarget_ / Mh + vh;
1343	>	Vector3d ahrec = momentumTarget_ / Mh;
1344	>	RealType hNumerator = Kh + kineticTarget_
1345		- 0.5 * Mh * ah.lengthSquare();
1346		if (hNumerator > 0.0) {
1347		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
#	Line 1283 | Line 1356 | namespace OpenMD {
1356		//vel = (*sdi)->getVel();
1357		vel = ((*sdi)->getVel() - vc) * c + ac;
1358		(*sdi)->setVel(vel);
1359	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1359	>	if (rnemdFluxType_ == rnemdFullKE) {
1360		if ((*sdi)->isDirectional()) {
1361		Vector3d angMom = (*sdi)->getJ() * c;
1362		(*sdi)->setJ(angMom);
#	Line 1294 | Line 1367 | namespace OpenMD {
1367		//vel = (*sdi)->getVel();
1368		vel = ((*sdi)->getVel() - vh) * h + ah;
1369		(*sdi)->setVel(vel);
1370	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1370	>	if (rnemdFluxType_ == rnemdFullKE) {
1371		if ((*sdi)->isDirectional()) {
1372		Vector3d angMom = (*sdi)->getJ() * h;
1373		(*sdi)->setJ(angMom);
#	Line 1302 | Line 1375 | namespace OpenMD {
1375		}
1376		}
1377		successfulExchange = true;
1378	<	exchangeSum_ += targetFlux_;
1379	<	// this is a redundant variable for doShiftScale() so that
1307	<	// RNEMD can output one exchange quantity needed in a job.
1308	<	// need a better way to do this.
1309	<	//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n';
1310	<	//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n';
1311	<	//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n';
1312	<	Asum_ += (ahrec.z() - acrec.z());
1313	<	Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc)));
1314	<	AhCount_ = ahrec.z();
1315	<	if (outputAh_) {
1316	<	AhLog_ << time << "   ";
1317	<	AhLog_ << AhCount_;
1318	<	AhLog_ << endl;
1319	<	}
1378	>	kineticExchange_ += kineticTarget_;
1379	>	momentumExchange_ += momentumTarget_;
1380		}
1381		}
1382		}
#	Line 1325 | Line 1385 | namespace OpenMD {
1385		}
1386		}
1387		if (successfulExchange != true) {
1388	<	//   sprintf(painCave.errMsg,
1389	<	//              "RNEMD: exchange NOT performed!\n");
1390	<	//   painCave.isFatal = 0;
1391	<	//   painCave.severity = OPENMD_INFO;
1392	<	//   simError();
1388	>	sprintf(painCave.errMsg,
1389	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1390	>	"\tthe constraint equations may not exist or there may be\n"
1391	>	"\tno selected objects in one or both slabs.\n");
1392	>	painCave.isFatal = 0;
1393	>	painCave.severity = OPENMD_INFO;
1394	>	simError();
1395		failTrialCount_++;
1396		}
1397		}
1398
1399		void RNEMD::doRNEMD() {
1400	<
1401	<	switch(rnemdType_) {
1402	<	case rnemdKineticScale :
1403	<	case rnemdKineticScaleVAM :
1342	<	case rnemdKineticScaleAM :
1343	<	case rnemdPxScale :
1344	<	case rnemdPyScale :
1345	<	case rnemdPzScale :
1346	<	doScale();
1347	<	break;
1348	<	case rnemdKineticSwap :
1349	<	case rnemdPx :
1350	<	case rnemdPy :
1351	<	case rnemdPz :
1400	>	if (!doRNEMD_) return;
1401	>	trialCount_++;
1402	>	switch(rnemdMethod_) {
1403	>	case rnemdSwap:
1404		doSwap();
1405		break;
1406	<	case rnemdShiftScaleV :
1407	<	case rnemdShiftScaleVAM :
1356	<	doShiftScale();
1406	>	case rnemdNIVS:
1407	>	doNIVS();
1408		break;
1409	<	case rnemdUnknown :
1409	>	case rnemdVSS:
1410	>	doVSS();
1411	>	break;
1412	>	case rnemdUnkownMethod:
1413		default :
1414		break;
1415		}
1416		}
1417
1418		void RNEMD::collectData() {
1419	<
1419	>	if (!doRNEMD_) return;
1420		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1421		Mat3x3d hmat = currentSnap_->getHmat();
1422
1423	+	areaAccumulator_->add(currentSnap_->getXYarea());
1424	+
1425		seleMan_.setSelectionSet(evaluator_.evaluate());
1426
1427		int selei;
1428		StuntDouble* sd;
1429		int idx;
1430
1431	<	logFrameCount_++;
1431	>	vector<RealType> binMass(nBins_, 0.0);
1432	>	vector<RealType> binPx(nBins_, 0.0);
1433	>	vector<RealType> binPy(nBins_, 0.0);
1434	>	vector<RealType> binPz(nBins_, 0.0);
1435	>	vector<RealType> binKE(nBins_, 0.0);
1436	>	vector<int> binDOF(nBins_, 0);
1437	>	vector<int> binCount(nBins_, 0);
1438
1439		// alternative approach, track all molecules instead of only those
1440		// selected for scaling/swapping:
#	Line 1399 | Line 1461 | namespace OpenMD {
1461
1462		if (usePeriodicBoundaryConditions_)
1463		currentSnap_->wrapVector(pos);
1464	<
1464	>
1465	>
1466		// which bin is this stuntdouble in?
1467		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1468	<
1469	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1470	<	rnemdLogWidth_;
1471	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1472	<	/*
1410	<	if (rnemdLogWidth_ == midBin_ + 1)
1411	<	if (binNo > midBin_)
1412	<	binNo = nBins_ - binNo;
1413	<	*/
1468	>	// Shift molecules by half a box to have bins start at 0
1469	>	// The modulo operator is used to wrap the case when we are
1470	>	// beyond the end of the bins back to the beginning.
1471	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1472	>
1473		RealType mass = sd->getMass();
1415	–	mHist_[binNo] += mass;
1474		Vector3d vel = sd->getVel();
1417	–	RealType value;
1418	–	//RealType xVal, yVal, zVal;
1475
1476	<	if (outputTemp_) {
1477	<	value = mass * vel.lengthSquare();
1478	<	tempCount_[binNo] += 3;
1479	<	if (sd->isDirectional()) {
1480	<	Vector3d angMom = sd->getJ();
1481	<	Mat3x3d I = sd->getI();
1482	<	if (sd->isLinear()) {
1483	<	int i = sd->linearAxis();
1484	<	int j = (i + 1) % 3;
1485	<	int k = (i + 2) % 3;
1486	<	value += angMom[j] * angMom[j] / I(j, j) +
1487	<	angMom[k] * angMom[k] / I(k, k);
1488	<	tempCount_[binNo] +=2;
1489	<	} else {
1490	<	value += angMom[0] * angMom[0] / I(0, 0) +
1491	<	angMom[1]*angMom[1]/I(1, 1) +
1492	<	angMom[2]*angMom[2]/I(2, 2);
1493	<	tempCount_[binNo] +=3;
1494	<	}
1495	<	}
1496	<	value = value / PhysicalConstants::energyConvert
1497	<	/ PhysicalConstants::kb;//may move to getStatus()
1498	<	tempHist_[binNo] += value;
1499	<	}
1444	<	if (outputVx_) {
1445	<	value = mass * vel[0];
1446	<	//vxzCount_[binNo]++;
1447	<	pxzHist_[binNo] += value;
1476	>	binCount[binNo]++;
1477	>	binMass[binNo] += mass;
1478	>	binPx[binNo] += mass*vel.x();
1479	>	binPy[binNo] += mass*vel.y();
1480	>	binPz[binNo] += mass*vel.z();
1481	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1482	>	binDOF[binNo] += 3;
1483	>
1484	>	if (sd->isDirectional()) {
1485	>	Vector3d angMom = sd->getJ();
1486	>	Mat3x3d I = sd->getI();
1487	>	if (sd->isLinear()) {
1488	>	int i = sd->linearAxis();
1489	>	int j = (i + 1) % 3;
1490	>	int k = (i + 2) % 3;
1491	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1492	>	angMom[k] * angMom[k] / I(k, k));
1493	>	binDOF[binNo] += 2;
1494	>	} else {
1495	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1496	>	angMom[1] * angMom[1] / I(1, 1) +
1497	>	angMom[2] * angMom[2] / I(2, 2));
1498	>	binDOF[binNo] += 3;
1499	>	}
1500		}
1501	<	if (outputVy_) {
1502	<	value = mass * vel[1];
1451	<	//vyzCount_[binNo]++;
1452	<	pyzHist_[binNo] += value;
1453	<	}
1501	>	}
1502	>
1503
1504	<	if (output3DTemp_) {
1505	<	value = mass * vel.x() * vel.x();
1506	<	xTempHist_[binNo] += value;
1507	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1508	<	/ PhysicalConstants::kb;
1509	<	yTempHist_[binNo] += value;
1510	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1511	<	/ PhysicalConstants::kb;
1512	<	zTempHist_[binNo] += value;
1513	<	xyzTempCount_[binNo]++;
1504	>	#ifdef IS_MPI
1505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1506	>	nBins_, MPI::INT, MPI::SUM);
1507	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1508	>	nBins_, MPI::REALTYPE, MPI::SUM);
1509	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1510	>	nBins_, MPI::REALTYPE, MPI::SUM);
1511	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1512	>	nBins_, MPI::REALTYPE, MPI::SUM);
1513	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1514	>	nBins_, MPI::REALTYPE, MPI::SUM);
1515	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1516	>	nBins_, MPI::REALTYPE, MPI::SUM);
1517	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1518	>	nBins_, MPI::INT, MPI::SUM);
1519	>	#endif
1520	>
1521	>	Vector3d vel;
1522	>	RealType den;
1523	>	RealType temp;
1524	>	RealType z;
1525	>	for (int i = 0; i < nBins_; i++) {
1526	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1527	>	vel.x() = binPx[i] / binMass[i];
1528	>	vel.y() = binPy[i] / binMass[i];
1529	>	vel.z() = binPz[i] / binMass[i];
1530	>	den = binCount[i] * nBins_ / currentSnap_->getVolume();
1531	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1532	>	PhysicalConstants::energyConvert);
1533	>
1534	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1535	>	if(outputMask_[j]) {
1536	>	switch(j) {
1537	>	case Z:
1538	>	(data_[j].accumulator[i])->add(z);
1539	>	break;
1540	>	case TEMPERATURE:
1541	>	data_[j].accumulator[i]->add(temp);
1542	>	break;
1543	>	case VELOCITY:
1544	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1545	>	break;
1546	>	case DENSITY:
1547	>	data_[j].accumulator[i]->add(den);
1548	>	break;
1549	>	}
1550	>	}
1551		}
1466	–	if (outputRotTemp_) {
1467	–	if (sd->isDirectional()) {
1468	–	Vector3d angMom = sd->getJ();
1469	–	Mat3x3d I = sd->getI();
1470	–	if (sd->isLinear()) {
1471	–	int i = sd->linearAxis();
1472	–	int j = (i + 1) % 3;
1473	–	int k = (i + 2) % 3;
1474	–	value = angMom[j] * angMom[j] / I(j, j) +
1475	–	angMom[k] * angMom[k] / I(k, k);
1476	–	rotTempCount_[binNo] +=2;
1477	–	} else {
1478	–	value = angMom[0] * angMom[0] / I(0, 0) +
1479	–	angMom[1] * angMom[1] / I(1, 1) +
1480	–	angMom[2] * angMom[2] / I(2, 2);
1481	–	rotTempCount_[binNo] +=3;
1482	–	}
1483	–	}
1484	–	value = value / PhysicalConstants::energyConvert
1485	–	/ PhysicalConstants::kb;//may move to getStatus()
1486	–	rotTempHist_[binNo] += value;
1487	–	}
1488	–	// James put this in.
1489	–	if (outputDen_) {
1490	–	//value = 1.0;
1491	–	DenHist_[binNo] += 1;
1492	–	}
1493	–	if (outputVz_) {
1494	–	value = mass * vel[2];
1495	–	//vyzCount_[binNo]++;
1496	–	pzzHist_[binNo] += value;
1497	–	}
1552		}
1553		}
1554
1555		void RNEMD::getStarted() {
1556	+	if (!doRNEMD_) return;
1557		collectData();
1558	<	/*now can output profile in step 0, but might not be useful;
1504	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1505	<	Stats& stat = currentSnap_->statData;
1506	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1507	<	*/
1508	<	//may output a header for the log file here
1509	<	getStatus();
1558	>	writeOutputFile();
1559		}
1560
1561	<	void RNEMD::getStatus() {
1562	<
1563	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1564	<	RealType time = currentSnap_->getTime();
1565	<	//or to be more meaningful, define another item as exchangeSum_ / time
1566	<	int j;
1567	<
1561	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1562	>	if (!doRNEMD_) return;
1563	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1564	>
1565	>	while(tokenizer.hasMoreTokens()) {
1566	>	std::string token(tokenizer.nextToken());
1567	>	toUpper(token);
1568	>	OutputMapType::iterator i = outputMap_.find(token);
1569	>	if (i != outputMap_.end()) {
1570	>	outputMask_.set(i->second);
1571	>	} else {
1572	>	sprintf( painCave.errMsg,
1573	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1574	>	"\toutputFileFormat keyword.\n", token.c_str() );
1575	>	painCave.isFatal = 0;
1576	>	painCave.severity = OPENMD_ERROR;
1577	>	simError();
1578	>	}
1579	>	}
1580	>	}
1581	>
1582	>	void RNEMD::writeOutputFile() {
1583	>	if (!doRNEMD_) return;
1584	>
1585		#ifdef IS_MPI
1520	–
1521	–	// all processors have the same number of bins, and STL vectors pack their
1522	–	// arrays, so in theory, this should be safe:
1523	–
1524	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1525	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1526	–	if (outputTemp_) {
1527	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1528	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1529	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1530	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1531	–	}
1532	–	if (outputVx_) {
1533	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1534	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1535	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1536	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1537	–	}
1538	–	if (outputVy_) {
1539	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1540	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1541	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1542	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1543	–	}
1544	–	if (output3DTemp_) {
1545	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1546	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1547	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1548	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1549	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1550	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1551	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1552	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1553	–	}
1554	–	if (outputRotTemp_) {
1555	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1556	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1557	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1558	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1559	–	}
1560	–	// James put this in
1561	–	if (outputDen_) {
1562	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1563	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1564	–	}
1565	–	if (outputAh_) {
1566	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1567	–	1, MPI::REALTYPE, MPI::SUM);
1568	–	}
1569	–	if (outputVz_) {
1570	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1571	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1572	–	}
1573	–
1586		// If we're the root node, should we print out the results
1587		int worldRank = MPI::COMM_WORLD.Get_rank();
1588		if (worldRank == 0) {
1589		#endif
1590	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1591	+
1592	+	if( !rnemdFile_ ){
1593	+	sprintf( painCave.errMsg,
1594	+	"Could not open \"%s\" for RNEMD output.\n",
1595	+	rnemdFileName_.c_str());
1596	+	painCave.isFatal = 1;
1597	+	simError();
1598	+	}
1599
1600	<	if (outputTemp_) {
1601	<	tempLog_ << time;
1602	<	for (j = 0; j < rnemdLogWidth_; j++) {
1603	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1604	<	}
1605	<	tempLog_ << endl;
1600	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1601	>
1602	>	RealType time = currentSnap_->getTime();
1603	>	RealType avgArea;
1604	>	areaAccumulator_->getAverage(avgArea);
1605	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea);
1606	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1607	>
1608	>	rnemdFile_ << "#######################################################\n";
1609	>	rnemdFile_ << "# RNEMD {\n";
1610	>
1611	>	map<string, RNEMDMethod>::iterator mi;
1612	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1613	>	if ( (*mi).second == rnemdMethod_)
1614	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1615		}
1616	<	if (outputVx_) {
1617	<	vxzLog_ << time;
1618	<	for (j = 0; j < rnemdLogWidth_; j++) {
1619	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1590	<	}
1591	<	vxzLog_ << endl;
1616	>	map<string, RNEMDFluxType>::iterator fi;
1617	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1618	>	if ( (*fi).second == rnemdFluxType_)
1619	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1620		}
1621	<	if (outputVy_) {
1622	<	vyzLog_ << time;
1595	<	for (j = 0; j < rnemdLogWidth_; j++) {
1596	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1597	<	}
1598	<	vyzLog_ << endl;
1599	<	}
1621	>
1622	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1623
1624	<	if (output3DTemp_) {
1625	<	RealType temp;
1626	<	xTempLog_ << time;
1627	<	for (j = 0; j < rnemdLogWidth_; j++) {
1628	<	if (outputVx_)
1629	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1630	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1631	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1632	<	xTempLog_ << "\t" << temp;
1624	>	rnemdFile_ << "#    objectSelection = \""
1625	>	<< rnemdObjectSelection_ << "\";\n";
1626	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1627	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1628	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1629	>	rnemdFile_ << "# }\n";
1630	>	rnemdFile_ << "#######################################################\n";
1631	>	rnemdFile_ << "# RNEMD report:\n";
1632	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1633	>	rnemdFile_ << "#     target flux:\n";
1634	>	rnemdFile_ << "#         kinetic = " << kineticFlux_ << "\n";
1635	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_ << "\n";
1636	>	rnemdFile_ << "#     target one-time exchanges:\n";
1637	>	rnemdFile_ << "#         kinetic = " << kineticTarget_ << "\n";
1638	>	rnemdFile_ << "#         momentum = " << momentumTarget_ << "\n";
1639	>	rnemdFile_ << "#     actual exchange totals:\n";
1640	>	rnemdFile_ << "#         kinetic = " << kineticExchange_ << "\n";
1641	>	rnemdFile_ << "#         momentum = " << momentumExchange_  << "\n";
1642	>	rnemdFile_ << "#     actual flux:\n";
1643	>	rnemdFile_ << "#         kinetic = " << Jz << "\n";
1644	>	rnemdFile_ << "#         momentum = " << JzP  << "\n";
1645	>	rnemdFile_ << "#     exchange statistics:\n";
1646	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1647	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1648	>	if (rnemdMethod_ == rnemdNIVS) {
1649	>	rnemdFile_ << "#         NIVS root-check errors = "
1650	>	<< failRootCount_ << "\n";
1651	>	}
1652	>	rnemdFile_ << "#######################################################\n";
1653	>
1654	>
1655	>
1656	>	//write title
1657	>	rnemdFile_ << "#";
1658	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1659	>	if (outputMask_[i]) {
1660	>	rnemdFile_ << "\t" << data_[i].title <<
1661	>	"(" << data_[i].units << ")";
1662		}
1663	<	xTempLog_ << endl;
1664	<	yTempLog_ << time;
1665	<	for (j = 0; j < rnemdLogWidth_; j++) {
1666	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1663	>	}
1664	>	rnemdFile_ << std::endl;
1665	>
1666	>	rnemdFile_.precision(8);
1667	>
1668	>	for (unsigned int j = 0; j < nBins_; j++) {
1669	>
1670	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1671	>	if (outputMask_[i]) {
1672	>	if (data_[i].dataType == "RealType")
1673	>	writeReal(i,j);
1674	>	else if (data_[i].dataType == "Vector3d")
1675	>	writeVector(i,j);
1676	>	else {
1677	>	sprintf( painCave.errMsg,
1678	>	"RNEMD found an unknown data type for: %s ",
1679	>	data_[i].title.c_str());
1680	>	painCave.isFatal = 1;
1681	>	simError();
1682	>	}
1683	>	}
1684		}
1685	<	yTempLog_ << endl;
1686	<	zTempLog_ << time;
1687	<	for (j = 0; j < rnemdLogWidth_; j++) {
1688	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1685	>	rnemdFile_ << std::endl;
1686	>
1687	>	}
1688	>
1689	>	rnemdFile_ << "#######################################################\n";
1690	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1691	>	rnemdFile_ << "#######################################################\n";
1692	>
1693	>
1694	>	for (unsigned int j = 0; j < nBins_; j++) {
1695	>	rnemdFile_ << "#";
1696	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1697	>	if (outputMask_[i]) {
1698	>	if (data_[i].dataType == "RealType")
1699	>	writeRealStdDev(i,j);
1700	>	else if (data_[i].dataType == "Vector3d")
1701	>	writeVectorStdDev(i,j);
1702	>	else {
1703	>	sprintf( painCave.errMsg,
1704	>	"RNEMD found an unknown data type for: %s ",
1705	>	data_[i].title.c_str());
1706	>	painCave.isFatal = 1;
1707	>	simError();
1708	>	}
1709	>	}
1710		}
1711	<	zTempLog_ << endl;
1712	<	}
1713	<	if (outputRotTemp_) {
1714	<	rotTempLog_ << time;
1715	<	for (j = 0; j < rnemdLogWidth_; j++) {
1716	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1717	<	}
1628	<	rotTempLog_ << endl;
1629	<	}
1630	<	// James put this in.
1631	<	Mat3x3d hmat = currentSnap_->getHmat();
1632	<	if (outputDen_) {
1633	<	denLog_ << time;
1634	<	for (j = 0; j < rnemdLogWidth_; j++) {
1635	<
1636	<	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1637	<	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1638	<	}
1639	<	denLog_ << endl;
1640	<	}
1641	<	if (outputVz_) {
1642	<	vzzLog_ << time;
1643	<	for (j = 0; j < rnemdLogWidth_; j++) {
1644	<	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1645	<	}
1646	<	vzzLog_ << endl;
1647	<	}
1711	>	rnemdFile_ << std::endl;
1712	>
1713	>	}
1714	>
1715	>	rnemdFile_.flush();
1716	>	rnemdFile_.close();
1717	>
1718		#ifdef IS_MPI
1719		}
1720		#endif
1721	<
1722	<	for (j = 0; j < rnemdLogWidth_; j++) {
1723	<	mHist_[j] = 0.0;
1721	>
1722	>	}
1723	>
1724	>	void RNEMD::writeReal(int index, unsigned int bin) {
1725	>	if (!doRNEMD_) return;
1726	>	assert(index >=0 && index < ENDINDEX);
1727	>	assert(bin < nBins_);
1728	>	RealType s;
1729	>
1730	>	data_[index].accumulator[bin]->getAverage(s);
1731	>
1732	>	if (! isinf(s) && ! isnan(s)) {
1733	>	rnemdFile_ << "\t" << s;
1734	>	} else{
1735	>	sprintf( painCave.errMsg,
1736	>	"RNEMD detected a numerical error writing: %s for bin %d",
1737	>	data_[index].title.c_str(), bin);
1738	>	painCave.isFatal = 1;
1739	>	simError();
1740	>	}
1741	>	}
1742	>
1743	>	void RNEMD::writeVector(int index, unsigned int bin) {
1744	>	if (!doRNEMD_) return;
1745	>	assert(index >=0 && index < ENDINDEX);
1746	>	assert(bin < nBins_);
1747	>	Vector3d s;
1748	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1749	>	if (isinf(s[0]) || isnan(s[0]) ||
1750	>	isinf(s[1]) || isnan(s[1]) ||
1751	>	isinf(s[2]) || isnan(s[2]) ) {
1752	>	sprintf( painCave.errMsg,
1753	>	"RNEMD detected a numerical error writing: %s for bin %d",
1754	>	data_[index].title.c_str(), bin);
1755	>	painCave.isFatal = 1;
1756	>	simError();
1757	>	} else {
1758	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1759		}
1760	<	if (outputTemp_)
1656	<	for (j = 0; j < rnemdLogWidth_; j++) {
1657	<	tempCount_[j] = 0;
1658	<	tempHist_[j] = 0.0;
1659	<	}
1660	<	if (outputVx_)
1661	<	for (j = 0; j < rnemdLogWidth_; j++) {
1662	<	//pxzCount_[j] = 0;
1663	<	pxzHist_[j] = 0.0;
1664	<	}
1665	<	if (outputVy_)
1666	<	for (j = 0; j < rnemdLogWidth_; j++) {
1667	<	//pyzCount_[j] = 0;
1668	<	pyzHist_[j] = 0.0;
1669	<	}
1760	>	}
1761
1762	<	if (output3DTemp_)
1763	<	for (j = 0; j < rnemdLogWidth_; j++) {
1764	<	xTempHist_[j] = 0.0;
1765	<	yTempHist_[j] = 0.0;
1766	<	zTempHist_[j] = 0.0;
1676	<	xyzTempCount_[j] = 0;
1677	<	}
1678	<	if (outputRotTemp_)
1679	<	for (j = 0; j < rnemdLogWidth_; j++) {
1680	<	rotTempCount_[j] = 0;
1681	<	rotTempHist_[j] = 0.0;
1682	<	}
1683	<	// James put this in
1684	<	if (outputDen_)
1685	<	for (j = 0; j < rnemdLogWidth_; j++) {
1686	<	//pyzCount_[j] = 0;
1687	<	DenHist_[j] = 0.0;
1688	<	}
1689	<	if (outputVz_)
1690	<	for (j = 0; j < rnemdLogWidth_; j++) {
1691	<	//pyzCount_[j] = 0;
1692	<	pzzHist_[j] = 0.0;
1693	<	}
1694	<	// reset the counter
1695	<
1696	<	Numcount_++;
1697	<	if (Numcount_ > int(runTime_/statusTime_))
1698	<	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1699	<	if (Numcount_ > int(runTime_/statusTime_))
1700	<	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
1762	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1763	>	if (!doRNEMD_) return;
1764	>	assert(index >=0 && index < ENDINDEX);
1765	>	assert(bin < nBins_);
1766	>	RealType s;
1767
1768	<	logFrameCount_ = 0;
1768	>	data_[index].accumulator[bin]->getStdDev(s);
1769	>
1770	>	if (! isinf(s) && ! isnan(s)) {
1771	>	rnemdFile_ << "\t" << s;
1772	>	} else{
1773	>	sprintf( painCave.errMsg,
1774	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1775	>	data_[index].title.c_str(), bin);
1776	>	painCave.isFatal = 1;
1777	>	simError();
1778	>	}
1779		}
1780	+
1781	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1782	+	if (!doRNEMD_) return;
1783	+	assert(index >=0 && index < ENDINDEX);
1784	+	assert(bin < nBins_);
1785	+	Vector3d s;
1786	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1787	+	if (isinf(s[0]) || isnan(s[0]) ||
1788	+	isinf(s[1]) || isnan(s[1]) ||
1789	+	isinf(s[2]) || isnan(s[2]) ) {
1790	+	sprintf( painCave.errMsg,
1791	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1792	+	data_[index].title.c_str(), bin);
1793	+	painCave.isFatal = 1;
1794	+	simError();
1795	+	} else {
1796	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1797	+	}
1798	+	}
1799		}
1800

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