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

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1731 by gezelter, Thu May 31 12:25:30 2012 UTC vs.
Revision 1773 by gezelter, Tue Aug 7 18:26:40 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;
74	<	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	>	stringToMethod_["Swap"]  = rnemdSwap;
73	>	stringToMethod_["NIVS"]  = rnemdNIVS;
74	>	stringToMethod_["VSS"]   = rnemdVSS;
75
76	+	stringToFluxType_["KE"]  = rnemdKE;
77	+	stringToFluxType_["Px"]  = rnemdPx;
78	+	stringToFluxType_["Py"]  = rnemdPy;
79	+	stringToFluxType_["Pz"]  = rnemdPz;
80	+	stringToFluxType_["KE+Px"]  = rnemdKePx;
81	+	stringToFluxType_["KE+Py"]  = rnemdKePy;
82	+	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
83	+
84		runTime_ = simParams->getRunTime();
85		statusTime_ = simParams->getStatusTime();
86
#	Line 93 | Line 88 | namespace OpenMD {
88		evaluator_.loadScriptString(rnemdObjectSelection_);
89		seleMan_.setSelectionSet(evaluator_.evaluate());
90
91	+	const string methStr = rnemdParams->getMethod();
92	+	bool hasFluxType = rnemdParams->haveFluxType();
93	+
94	+	string fluxStr;
95	+	if (hasFluxType) {
96	+	fluxStr = rnemdParams->getFluxType();
97	+	} else {
98	+	sprintf(painCave.errMsg,
99	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
100	+	"\twhich must be one of the following values:\n"
101	+	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
102	+	"\tuse RNEMD\n");
103	+	painCave.isFatal = 1;
104	+	painCave.severity = OPENMD_ERROR;
105	+	simError();
106	+	}
107	+
108	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
109	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
110	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
111	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
112	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
113	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
114	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
115	+	bool hasOutputFields = rnemdParams->haveOutputFields();
116	+
117	+	map<string, RNEMDMethod>::iterator i;
118	+	i = stringToMethod_.find(methStr);
119	+	if (i != stringToMethod_.end())
120	+	rnemdMethod_ = i->second;
121	+	else {
122	+	sprintf(painCave.errMsg,
123	+	"RNEMD: The current method,\n"
124	+	"\t\t%s is not one of the recognized\n"
125	+	"\texchange methods: Swap, NIVS, or VSS\n",
126	+	methStr.c_str());
127	+	painCave.isFatal = 1;
128	+	painCave.severity = OPENMD_ERROR;
129	+	simError();
130	+	}
131	+
132	+	map<string, RNEMDFluxType>::iterator j;
133	+	j = stringToFluxType_.find(fluxStr);
134	+	if (j != stringToFluxType_.end())
135	+	rnemdFluxType_ = j->second;
136	+	else {
137	+	sprintf(painCave.errMsg,
138	+	"RNEMD: The current fluxType,\n"
139	+	"\t\t%s\n"
140	+	"\tis not one of the recognized flux types.\n",
141	+	fluxStr.c_str());
142	+	painCave.isFatal = 1;
143	+	painCave.severity = OPENMD_ERROR;
144	+	simError();
145	+	}
146	+
147	+	bool methodFluxMismatch = false;
148	+	bool hasCorrectFlux = false;
149	+	switch(rnemdMethod_) {
150	+	case rnemdSwap:
151	+	switch (rnemdFluxType_) {
152	+	case rnemdKE:
153	+	hasCorrectFlux = hasKineticFlux;
154	+	break;
155	+	case rnemdPx:
156	+	case rnemdPy:
157	+	case rnemdPz:
158	+	hasCorrectFlux = hasMomentumFlux;
159	+	break;
160	+	default :
161	+	methodFluxMismatch = true;
162	+	break;
163	+	}
164	+	break;
165	+	case rnemdNIVS:
166	+	switch (rnemdFluxType_) {
167	+	case rnemdKE:
168	+	case rnemdRotKE:
169	+	case rnemdFullKE:
170	+	hasCorrectFlux = hasKineticFlux;
171	+	break;
172	+	case rnemdPx:
173	+	case rnemdPy:
174	+	case rnemdPz:
175	+	hasCorrectFlux = hasMomentumFlux;
176	+	break;
177	+	case rnemdKePx:
178	+	case rnemdKePy:
179	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
180	+	break;
181	+	default:
182	+	methodFluxMismatch = true;
183	+	break;
184	+	}
185	+	break;
186	+	case rnemdVSS:
187	+	switch (rnemdFluxType_) {
188	+	case rnemdKE:
189	+	case rnemdRotKE:
190	+	case rnemdFullKE:
191	+	hasCorrectFlux = hasKineticFlux;
192	+	break;
193	+	case rnemdPx:
194	+	case rnemdPy:
195	+	case rnemdPz:
196	+	hasCorrectFlux = hasMomentumFlux;
197	+	break;
198	+	case rnemdPvector:
199	+	hasCorrectFlux = hasMomentumFluxVector;
200	+	case rnemdKePx:
201	+	case rnemdKePy:
202	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
203	+	break;
204	+	case rnemdKePvector:
205	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
206	+	break;
207	+	default:
208	+	methodFluxMismatch = true;
209	+	break;
210	+	}
211	+	default:
212	+	break;
213	+	}
214	+
215	+	if (methodFluxMismatch) {
216	+	sprintf(painCave.errMsg,
217	+	"RNEMD: The current method,\n"
218	+	"\t\t%s\n"
219	+	"\tcannot be used with the current flux type, %s\n",
220	+	methStr.c_str(), fluxStr.c_str());
221	+	painCave.isFatal = 1;
222	+	painCave.severity = OPENMD_ERROR;
223	+	simError();
224	+	}
225	+	if (!hasCorrectFlux) {
226	+	sprintf(painCave.errMsg,
227	+	"RNEMD: The current method,\n"
228	+	"\t%s, and flux type %s\n"
229	+	"\tdid not have the correct flux value specified. Options\n"
230	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
231	+	methStr.c_str(), fluxStr.c_str());
232	+	painCave.isFatal = 1;
233	+	painCave.severity = OPENMD_ERROR;
234	+	simError();
235	+	}
236	+
237	+	if (hasKineticFlux) {
238	+	kineticFlux_ = rnemdParams->getKineticFlux();
239	+	} else {
240	+	kineticFlux_ = 0.0;
241	+	}
242	+	if (hasMomentumFluxVector) {
243	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
244	+	} else {
245	+	momentumFluxVector_ = V3Zero;
246	+	if (hasMomentumFlux) {
247	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
248	+	switch (rnemdFluxType_) {
249	+	case rnemdPx:
250	+	momentumFluxVector_.x() = momentumFlux;
251	+	break;
252	+	case rnemdPy:
253	+	momentumFluxVector_.y() = momentumFlux;
254	+	break;
255	+	case rnemdPz:
256	+	momentumFluxVector_.z() = momentumFlux;
257	+	break;
258	+	case rnemdKePx:
259	+	momentumFluxVector_.x() = momentumFlux;
260	+	break;
261	+	case rnemdKePy:
262	+	momentumFluxVector_.y() = momentumFlux;
263	+	break;
264	+	default:
265	+	break;
266	+	}
267	+	}
268	+	}
269	+
270		// do some sanity checking
271
272		int selectionCount = seleMan_.getSelectionCount();
#	Line 100 | Line 274 | namespace OpenMD {
274
275		if (selectionCount > nIntegrable) {
276		sprintf(painCave.errMsg,
277	<	"RNEMD: The current RNEMD_objectSelection,\n"
277	>	"RNEMD: The current objectSelection,\n"
278		"\t\t%s\n"
279		"\thas resulted in %d selected objects.  However,\n"
280		"\tthe total number of integrable objects in the system\n"
#	Line 113 | Line 287 | namespace OpenMD {
287		painCave.severity = OPENMD_WARNING;
288		simError();
289		}
116	–
117	–	const string st = rnemdParams->getExchangeType();
290
291	<	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	<
291	>	nBins_ = rnemdParams->getOutputBins();
292
293	<	#ifdef IS_MPI
294	<	if (worldRank == 0) {
295	<	#endif
293	>	data_.resize(RNEMD::ENDINDEX);
294	>	OutputData z;
295	>	z.units =  "Angstroms";
296	>	z.title =  "Z";
297	>	z.dataType = "RealType";
298	>	z.accumulator.reserve(nBins_);
299	>	for (unsigned int i = 0; i < nBins_; i++)
300	>	z.accumulator.push_back( new Accumulator() );
301	>	data_[Z] = z;
302	>	outputMap_["Z"] =  Z;
303
304	<	//may have rnemdWriter separately
305	<	string rnemdFileName;
304	>	OutputData temperature;
305	>	temperature.units =  "K";
306	>	temperature.title =  "Temperature";
307	>	temperature.dataType = "RealType";
308	>	temperature.accumulator.reserve(nBins_);
309	>	for (unsigned int i = 0; i < nBins_; i++)
310	>	temperature.accumulator.push_back( new Accumulator() );
311	>	data_[TEMPERATURE] = temperature;
312	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
313
314	<	if (outputTemp_) {
315	<	rnemdFileName = "temperature.log";
316	<	tempLog_.open(rnemdFileName.c_str());
317	<	}
318	<	if (outputVx_) {
319	<	rnemdFileName = "velocityX.log";
320	<	vxzLog_.open(rnemdFileName.c_str());
321	<	}
322	<	if (outputVy_) {
195	<	rnemdFileName = "velocityY.log";
196	<	vyzLog_.open(rnemdFileName.c_str());
197	<	}
314	>	OutputData velocity;
315	>	velocity.units = "amu/fs";
316	>	velocity.title =  "Velocity";
317	>	velocity.dataType = "Vector3d";
318	>	velocity.accumulator.reserve(nBins_);
319	>	for (unsigned int i = 0; i < nBins_; i++)
320	>	velocity.accumulator.push_back( new VectorAccumulator() );
321	>	data_[VELOCITY] = velocity;
322	>	outputMap_["VELOCITY"] = VELOCITY;
323
324	<	if (output3DTemp_) {
325	<	rnemdFileName = "temperatureX.log";
326	<	xTempLog_.open(rnemdFileName.c_str());
327	<	rnemdFileName = "temperatureY.log";
328	<	yTempLog_.open(rnemdFileName.c_str());
329	<	rnemdFileName = "temperatureZ.log";
330	<	zTempLog_.open(rnemdFileName.c_str());
331	<	}
332	<	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
324	>	OutputData density;
325	>	density.units =  "g cm^-3";
326	>	density.title =  "Density";
327	>	density.dataType = "RealType";
328	>	density.accumulator.reserve(nBins_);
329	>	for (unsigned int i = 0; i < nBins_; i++)
330	>	density.accumulator.push_back( new Accumulator() );
331	>	data_[DENSITY] = density;
332	>	outputMap_["DENSITY"] =  DENSITY;
333
334	<	set_RNEMD_exchange_time(rnemdParams->getExchangeTime());
335	<	set_RNEMD_nBins(rnemdParams->getNbins());
232	<	midBin_ = nBins_ / 2;
233	<	if (rnemdParams->haveBinShift()) {
234	<	if (rnemdParams->getBinShift()) {
235	<	zShift_ = 0.5 / (RealType)(nBins_);
236	<	} else {
237	<	zShift_ = 0.0;
238	<	}
334	>	if (hasOutputFields) {
335	>	parseOutputFileFormat(rnemdParams->getOutputFields());
336		} else {
337	<	zShift_ = 0.0;
337	>	outputMask_.set(Z);
338	>	switch (rnemdFluxType_) {
339	>	case rnemdKE:
340	>	case rnemdRotKE:
341	>	case rnemdFullKE:
342	>	outputMask_.set(TEMPERATURE);
343	>	break;
344	>	case rnemdPx:
345	>	case rnemdPy:
346	>	outputMask_.set(VELOCITY);
347	>	break;
348	>	case rnemdPz:
349	>	case rnemdPvector:
350	>	outputMask_.set(VELOCITY);
351	>	outputMask_.set(DENSITY);
352	>	break;
353	>	case rnemdKePx:
354	>	case rnemdKePy:
355	>	outputMask_.set(TEMPERATURE);
356	>	outputMask_.set(VELOCITY);
357	>	break;
358	>	case rnemdKePvector:
359	>	outputMask_.set(TEMPERATURE);
360	>	outputMask_.set(VELOCITY);
361	>	outputMask_.set(DENSITY);
362	>	break;
363	>	default:
364	>	break;
365	>	}
366		}
367	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
368	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
369	<	//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	<	}*/
367	>
368	>	if (hasOutputFileName) {
369	>	rnemdFileName_ = rnemdParams->getOutputFileName();
370		} else {
371	<	set_RNEMD_logWidth(nBins_);
372	<	}
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);
371	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
372	>	}
373
374	<	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);
374	>	exchangeTime_ = rnemdParams->getExchangeTime();
375
376	<	set_RNEMD_exchange_total(0.0);
377	<	if (rnemdParams->haveTargetFlux()) {
378	<	set_RNEMD_target_flux(rnemdParams->getTargetFlux());
379	<	} else {
380	<	set_RNEMD_target_flux(0.0);
381	<	}
382	<	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_;
376	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
377	>	Mat3x3d hmat = currentSnap_->getHmat();
378	>
379	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
380	>	// Lx, Ly = box dimensions in x & y
381	>	// dt = exchange time interval
382	>	// flux = target flux
383
384	<	#ifndef IS_MPI
385	<	if (simParams->haveSeed()) {
386	<	seedValue = simParams->getSeed();
387	<	randNumGen_ = new SeqRandNumGen(seedValue);
388	<	}else {
389	<	randNumGen_ = new SeqRandNumGen();
390	<	}
391	<	#else
392	<	if (simParams->haveSeed()) {
393	<	seedValue = simParams->getSeed();
394	<	randNumGen_ = new ParallelRandNumGen(seedValue);
395	<	}else {
319	<	randNumGen_ = new ParallelRandNumGen();
320	<	}
321	<	#endif
322	<	}
384	>	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
385	>	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
386	>
387	>	// total exchange sums are zeroed out at the beginning:
388	>
389	>	kineticExchange_ = 0.0;
390	>	momentumExchange_ = V3Zero;
391	>
392	>	if (hasSlabWidth)
393	>	slabWidth_ = rnemdParams->getSlabWidth();
394	>	else
395	>	slabWidth_ = hmat(2,2) / 10.0;
396
397	+	if (hasSlabACenter)
398	+	slabACenter_ = rnemdParams->getSlabACenter();
399	+	else
400	+	slabACenter_ = 0.0;
401	+
402	+	if (hasSlabBCenter)
403	+	slabBCenter_ = rnemdParams->getSlabBCenter();
404	+	else
405	+	slabBCenter_ = hmat(2,2) / 2.0;
406	+
407	+	}
408	+
409		RNEMD::~RNEMD() {
325	–	delete randNumGen_;
410
411		#ifdef IS_MPI
412		if (worldRank == 0) {
413		#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();
414
415	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
416	<	rnemdType_ == rnemdPyScale) {
417	<	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();
415	>	writeOutputFile();
416	>
417	>	rnemdFile_.close();
418
419		#ifdef IS_MPI
420		}
421		#endif
422		}
423	+
424	+	bool RNEMD::inSlabA(Vector3d pos) {
425	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
426	+	}
427	+	bool RNEMD::inSlabB(Vector3d pos) {
428	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	+	}
430
431		void RNEMD::doSwap() {
432
#	Line 394 | Line 458 | namespace OpenMD {
458
459		if (usePeriodicBoundaryConditions_)
460		currentSnap_->wrapVector(pos);
461	+	bool inA = inSlabA(pos);
462	+	bool inB = inSlabB(pos);
463
464	<	// 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_) {
464	>	if (inA || inB) {
465
466		RealType mass = sd->getMass();
467		Vector3d vel = sd->getVel();
468		RealType value;
469	<
470	<	switch(rnemdType_) {
471	<	case rnemdKineticSwap :
469	>
470	>	switch(rnemdFluxType_) {
471	>	case rnemdKE :
472
473		value = mass * vel.lengthSquare();
474
#	Line 430 | Line 489 | namespace OpenMD {
489		}
490		} //angular momenta exchange enabled
491		//energyConvert temporarily disabled
492	<	//make exchangeSum_ comparable between swap & scale
492	>	//make kineticExchange_ comparable between swap & scale
493		//value = value * 0.5 / PhysicalConstants::energyConvert;
494		value *= 0.5;
495		break;
#	Line 447 | Line 506 | namespace OpenMD {
506		break;
507		}
508
509	<	if (binNo == 0) {
509	>	if (inA == 0) {
510		if (!min_found) {
511		min_val = value;
512		min_sd = sd;
#	Line 458 | Line 517 | namespace OpenMD {
517		min_sd = sd;
518		}
519		}
520	<	} else { //midBin_
520	>	} else {
521		if (!max_found) {
522		max_val = value;
523		max_sd = sd;
#	Line 472 | Line 531 | namespace OpenMD {
531		}
532		}
533		}
534	<
534	>
535		#ifdef IS_MPI
536		int nProc, worldRank;
537	<
537	>
538		nProc = MPI::COMM_WORLD.Get_size();
539		worldRank = MPI::COMM_WORLD.Get_rank();
540
#	Line 533 | Line 592 | namespace OpenMD {
592		Vector3d max_vel = max_sd->getVel();
593		RealType temp_vel;
594
595	<	switch(rnemdType_) {
596	<	case rnemdKineticSwap :
595	>	switch(rnemdFluxType_) {
596	>	case rnemdKE :
597		min_sd->setVel(max_vel);
598		max_sd->setVel(min_vel);
599		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 585 | Line 644 | namespace OpenMD {
644		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
645		min_vals.rank, 0, status);
646
647	<	switch(rnemdType_) {
648	<	case rnemdKineticSwap :
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649		max_sd->setVel(min_vel);
650		//angular momenta exchange enabled
651		if (max_sd->isDirectional()) {
#	Line 631 | Line 690 | namespace OpenMD {
690		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
691		max_vals.rank, 0, status);
692
693	<	switch(rnemdType_) {
694	<	case rnemdKineticSwap :
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695		min_sd->setVel(max_vel);
696		//angular momenta exchange enabled
697		if (min_sd->isDirectional()) {
#	Line 666 | Line 725 | namespace OpenMD {
725		}
726		}
727		#endif
728	<	exchangeSum_ += max_val - min_val;
728	>
729	>	switch(rnemdFluxType_) {
730	>	case rnemdKE:
731	>	cerr << "KE\n";
732	>	kineticExchange_ += max_val - min_val;
733	>	break;
734	>	case rnemdPx:
735	>	momentumExchange_.x() += max_val - min_val;
736	>	break;
737	>	case rnemdPy:
738	>	momentumExchange_.y() += max_val - min_val;
739	>	break;
740	>	case rnemdPz:
741	>	momentumExchange_.z() += max_val - min_val;
742	>	break;
743	>	default:
744	>	cerr << "default\n";
745	>	break;
746	>	}
747		} else {
748		sprintf(painCave.errMsg,
749	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
749	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
750		painCave.isFatal = 0;
751		painCave.severity = OPENMD_INFO;
752		simError();
#	Line 677 | Line 754 | namespace OpenMD {
754		}
755		} else {
756		sprintf(painCave.errMsg,
757	<	"RNEMD: exchange NOT performed because selected object\n"
758	<	"\tnot present in at least one of the two slabs.\n");
757	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
758	>	"\twas not present in at least one of the two slabs.\n");
759		painCave.isFatal = 0;
760		painCave.severity = OPENMD_INFO;
761		simError();
762		failTrialCount_++;
763	<	}
687	<
763	>	}
764		}
765
766	<	void RNEMD::doScale() {
766	>	void RNEMD::doNIVS() {
767
768		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
769		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 728 | Line 804 | namespace OpenMD {
804		currentSnap_->wrapVector(pos);
805
806		// which bin is this stuntdouble in?
807	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
807	>	bool inA = inSlabA(pos);
808	>	bool inB = inSlabB(pos);
809
810	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
811	<
735	<	// if we're in bin 0 or the middleBin
736	<	if (binNo == 0 || binNo == midBin_) {
737	<
810	>	if (inA || inB) {
811	>
812		RealType mass = sd->getMass();
813		Vector3d vel = sd->getVel();
814
815	<	if (binNo == 0) {
815	>	if (inA) {
816		hotBin.push_back(sd);
817		Phx += mass * vel.x();
818		Phy += mass * vel.y();
#	Line 746 | Line 820 | namespace OpenMD {
820		Khx += mass * vel.x() * vel.x();
821		Khy += mass * vel.y() * vel.y();
822		Khz += mass * vel.z() * vel.z();
749	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
823		if (sd->isDirectional()) {
824		Vector3d angMom = sd->getJ();
825		Mat3x3d I = sd->getI();
#	Line 762 | Line 835 | namespace OpenMD {
835		+ angMom[2]*angMom[2]/I(2, 2);
836		}
837		}
838	<	//}
766	<	} else { //midBin_
838	>	} else {
839		coldBin.push_back(sd);
840		Pcx += mass * vel.x();
841		Pcy += mass * vel.y();
#	Line 771 | Line 843 | namespace OpenMD {
843		Kcx += mass * vel.x() * vel.x();
844		Kcy += mass * vel.y() * vel.y();
845		Kcz += mass * vel.z() * vel.z();
774	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
846		if (sd->isDirectional()) {
847		Vector3d angMom = sd->getJ();
848		Mat3x3d I = sd->getI();
#	Line 787 | Line 858 | namespace OpenMD {
858		+ angMom[2]*angMom[2]/I(2, 2);
859		}
860		}
790	–	//}
861		}
862		}
863		}
#	Line 801 | Line 871 | namespace OpenMD {
871		Kcz *= 0.5;
872		Kcw *= 0.5;
873
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	–
874		#ifdef IS_MPI
875		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
876		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 832 | Line 896 | namespace OpenMD {
896		RealType pz = Pcz / Phz;
897		RealType c, x, y, z;
898		bool successfulScale = false;
899	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
900	<	(rnemdType_ == rnemdKineticScaleAM)) {
899	>	if ((rnemdFluxType_ == rnemdFullKE) ||
900	>	(rnemdFluxType_ == rnemdRotKE)) {
901		//may need sanity check Khw & Kcw > 0
902
903	<	if (rnemdType_ == rnemdKineticScaleVAM) {
904	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
903	>	if (rnemdFluxType_ == rnemdFullKE) {
904	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
905		} else {
906	<	c = 1.0 - targetFlux_ / Kcw;
906	>	c = 1.0 - kineticTarget_ / Kcw;
907		}
908
909		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
910		c = sqrt(c);
911	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
911	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912		//now convert to hotBin coefficient
913		RealType w = 0.0;
914	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
914	>	if (rnemdFluxType_ ==  rnemdFullKE) {
915		x = 1.0 + px * (1.0 - c);
916		y = 1.0 + py * (1.0 - c);
917		z = 1.0 + pz * (1.0 - c);
#	Line 861 | Line 925 | namespace OpenMD {
925		*/
926		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
927		(fabs(z - 1.0) < 0.1)) {
928	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
928	>	w = 1.0 + (kineticTarget_
929	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
930		+ Khz * (1.0 - z * z)) / Khw;
931		}//no need to calculate w if x, y or z is out of range
932		} else {
933	<	w = 1.0 + targetFlux_ / Khw;
933	>	w = 1.0 + kineticTarget_ / Khw;
934		}
935		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
936		//if w is in the right range, so should be x, y, z.
937		vector<StuntDouble*>::iterator sdi;
938		Vector3d vel;
939		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
940	<	if (rnemdType_ == rnemdKineticScaleVAM) {
940	>	if (rnemdFluxType_ == rnemdFullKE) {
941		vel = (*sdi)->getVel() * c;
877	–	//vel.x() *= c;
878	–	//vel.y() *= c;
879	–	//vel.z() *= c;
942		(*sdi)->setVel(vel);
943		}
944		if ((*sdi)->isDirectional()) {
945		Vector3d angMom = (*sdi)->getJ() * c;
884	–	//angMom[0] *= c;
885	–	//angMom[1] *= c;
886	–	//angMom[2] *= c;
946		(*sdi)->setJ(angMom);
947		}
948		}
949		w = sqrt(w);
950	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	<	<< "\twh= " << w << endl;
950	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	>	//           << "\twh= " << w << endl;
952		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
953	<	if (rnemdType_ == rnemdKineticScaleVAM) {
953	>	if (rnemdFluxType_ == rnemdFullKE) {
954		vel = (*sdi)->getVel();
955		vel.x() *= x;
956		vel.y() *= y;
#	Line 900 | Line 959 | namespace OpenMD {
959		}
960		if ((*sdi)->isDirectional()) {
961		Vector3d angMom = (*sdi)->getJ() * w;
903	–	//angMom[0] *= w;
904	–	//angMom[1] *= w;
905	–	//angMom[2] *= w;
962		(*sdi)->setJ(angMom);
963		}
964		}
965		successfulScale = true;
966	<	exchangeSum_ += targetFlux_;
966	>	kineticExchange_ += kineticTarget_;
967		}
968		}
969		} else {
970		RealType a000, a110, c0, a001, a111, b01, b11, c1;
971	<	switch(rnemdType_) {
972	<	case rnemdKineticScale :
971	>	switch(rnemdFluxType_) {
972	>	case rnemdKE :
973		/* used hotBin coeff's & only scale x & y dimensions
974		RealType px = Phx / Pcx;
975		RealType py = Phy / Pcy;
976		a110 = Khy;
977	<	c0 = - Khx - Khy - targetFlux_;
977	>	c0 = - Khx - Khy - kineticTarget_;
978		a000 = Khx;
979		a111 = Kcy * py * py;
980		b11 = -2.0 * Kcy * py * (1.0 + py);
981	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
981	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
982		b01 = -2.0 * Kcx * px * (1.0 + px);
983		a001 = Kcx * px * px;
984		*/
985		//scale all three dimensions, let c_x = c_y
986		a000 = Kcx + Kcy;
987		a110 = Kcz;
988	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
988	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
989		a001 = Khx * px * px + Khy * py * py;
990		a111 = Khz * pz * pz;
991		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
992		b11 = -2.0 * Khz * pz * (1.0 + pz);
993		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
994	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
994	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
995		break;
996	<	case rnemdPxScale :
997	<	c = 1 - targetFlux_ / Pcx;
996	>	case rnemdPx :
997	>	c = 1 - momentumTarget_.x() / Pcx;
998		a000 = Kcy;
999		a110 = Kcz;
1000		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 949 | Line 1005 | namespace OpenMD {
1005		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1006		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1007		break;
1008	<	case rnemdPyScale :
1009	<	c = 1 - targetFlux_ / Pcy;
1008	>	case rnemdPy :
1009	>	c = 1 - momentumTarget_.y() / Pcy;
1010		a000 = Kcx;
1011		a110 = Kcz;
1012		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 961 | Line 1017 | namespace OpenMD {
1017		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1018		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1019		break;
1020	<	case rnemdPzScale ://we don't really do this, do we?
1021	<	c = 1 - targetFlux_ / Pcz;
1020	>	case rnemdPz ://we don't really do this, do we?
1021	>	c = 1 - momentumTarget_.z() / Pcz;
1022		a000 = Kcx;
1023		a110 = Kcy;
1024		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1047 | Line 1103 | namespace OpenMD {
1103		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1104		r1 = (*rpi).first;
1105		r2 = (*rpi).second;
1106	<	switch(rnemdType_) {
1107	<	case rnemdKineticScale :
1106	>	switch(rnemdFluxType_) {
1107	>	case rnemdKE :
1108		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1109		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1110		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1111		break;
1112	<	case rnemdPxScale :
1112	>	case rnemdPx :
1113		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1115		break;
1116	<	case rnemdPyScale :
1116	>	case rnemdPy :
1117		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1119		break;
1120	<	case rnemdPzScale :
1120	>	case rnemdPz :
1121		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1122		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1123		default :
#	Line 1075 | Line 1131 | namespace OpenMD {
1131		#ifdef IS_MPI
1132		if (worldRank == 0) {
1133		#endif
1134	<	sprintf(painCave.errMsg,
1135	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1136	<	bestPair.first, bestPair.second);
1137	<	painCave.isFatal = 0;
1138	<	painCave.severity = OPENMD_INFO;
1139	<	simError();
1134	>	// sprintf(painCave.errMsg,
1135	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1136	>	//         bestPair.first, bestPair.second);
1137	>	// painCave.isFatal = 0;
1138	>	// painCave.severity = OPENMD_INFO;
1139	>	// simError();
1140		#ifdef IS_MPI
1141		}
1142		#endif
1143
1144	<	switch(rnemdType_) {
1145	<	case rnemdKineticScale :
1144	>	switch(rnemdFluxType_) {
1145	>	case rnemdKE :
1146		x = bestPair.first;
1147		y = bestPair.first;
1148		z = bestPair.second;
1149		break;
1150	<	case rnemdPxScale :
1150	>	case rnemdPx :
1151		x = c;
1152		y = bestPair.first;
1153		z = bestPair.second;
1154		break;
1155	<	case rnemdPyScale :
1155	>	case rnemdPy :
1156		x = bestPair.first;
1157		y = c;
1158		z = bestPair.second;
1159		break;
1160	<	case rnemdPzScale :
1160	>	case rnemdPz :
1161		x = bestPair.first;
1162		y = bestPair.second;
1163		z = c;
#	Line 1130 | Line 1186 | namespace OpenMD {
1186		(*sdi)->setVel(vel);
1187		}
1188		successfulScale = true;
1189	<	exchangeSum_ += targetFlux_;
1189	>	switch(rnemdFluxType_) {
1190	>	case rnemdKE :
1191	>	kineticExchange_ += kineticTarget_;
1192	>	break;
1193	>	case rnemdPx :
1194	>	case rnemdPy :
1195	>	case rnemdPz :
1196	>	momentumExchange_ += momentumTarget_;
1197	>	break;
1198	>	default :
1199	>	break;
1200	>	}
1201		}
1202		}
1203		if (successfulScale != true) {
1204		sprintf(painCave.errMsg,
1205	<	"RNEMD: exchange NOT performed!\n");
1205	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1206	>	"\tthe constraint equations may not exist or there may be\n"
1207	>	"\tno selected objects in one or both slabs.\n");
1208		painCave.isFatal = 0;
1209		painCave.severity = OPENMD_INFO;
1210		simError();
#	Line 1143 | Line 1212 | namespace OpenMD {
1212		}
1213		}
1214
1215	<	void RNEMD::doShiftScale() {
1215	>	void RNEMD::doVSS() {
1216
1217		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1218		RealType time = currentSnap_->getTime();
#	Line 1178 | Line 1247 | namespace OpenMD {
1247		currentSnap_->wrapVector(pos);
1248
1249		// which bin is this stuntdouble in?
1250	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1251	<
1252	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1253	<
1185	<	// if we're in bin 0 or the middleBin
1186	<	if (binNo == 0 || binNo == midBin_) {
1250	>	bool inA = inSlabA(pos);
1251	>	bool inB = inSlabB(pos);
1252	>
1253	>	if (inA || inB) {
1254
1255		RealType mass = sd->getMass();
1256		Vector3d vel = sd->getVel();
1257
1258	<	if (binNo == 0) {
1258	>	if (inA) {
1259		hotBin.push_back(sd);
1260		//std::cerr << "before, velocity = " << vel << endl;
1261		Ph += mass * vel;
1262		//std::cerr << "after, velocity = " << vel << endl;
1263		Mh += mass;
1264		Kh += mass * vel.lengthSquare();
1265	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1265	>	if (rnemdFluxType_ == rnemdFullKE) {
1266		if (sd->isDirectional()) {
1267		Vector3d angMom = sd->getJ();
1268		Mat3x3d I = sd->getI();
#	Line 1217 | Line 1284 | namespace OpenMD {
1284		Pc += mass * vel;
1285		Mc += mass;
1286		Kc += mass * vel.lengthSquare();
1287	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1287	>	if (rnemdFluxType_ == rnemdFullKE) {
1288		if (sd->isDirectional()) {
1289		Vector3d angMom = sd->getJ();
1290		Mat3x3d I = sd->getI();
#	Line 1257 | Line 1324 | namespace OpenMD {
1324		bool successfulExchange = false;
1325		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1326		Vector3d vc = Pc / Mc;
1327	<	Vector3d ac = njzp_ / Mc + vc;
1328	<	Vector3d acrec = njzp_ / Mc;
1329	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1327	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1328	>	Vector3d acrec = -momentumTarget_ / Mc;
1329	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1330		if (cNumerator > 0.0) {
1331		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1332		if (cDenominator > 0.0) {
1333		RealType c = sqrt(cNumerator / cDenominator);
1334		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1335		Vector3d vh = Ph / Mh;
1336	<	Vector3d ah = jzp_ / Mh + vh;
1337	<	Vector3d ahrec = jzp_ / Mh;
1338	<	RealType hNumerator = Kh + targetJzKE_
1336	>	Vector3d ah = momentumTarget_ / Mh + vh;
1337	>	Vector3d ahrec = momentumTarget_ / Mh;
1338	>	RealType hNumerator = Kh + kineticTarget_
1339		- 0.5 * Mh * ah.lengthSquare();
1340		if (hNumerator > 0.0) {
1341		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
#	Line 1283 | Line 1350 | namespace OpenMD {
1350		//vel = (*sdi)->getVel();
1351		vel = ((*sdi)->getVel() - vc) * c + ac;
1352		(*sdi)->setVel(vel);
1353	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1353	>	if (rnemdFluxType_ == rnemdFullKE) {
1354		if ((*sdi)->isDirectional()) {
1355		Vector3d angMom = (*sdi)->getJ() * c;
1356		(*sdi)->setJ(angMom);
#	Line 1294 | Line 1361 | namespace OpenMD {
1361		//vel = (*sdi)->getVel();
1362		vel = ((*sdi)->getVel() - vh) * h + ah;
1363		(*sdi)->setVel(vel);
1364	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1364	>	if (rnemdFluxType_ == rnemdFullKE) {
1365		if ((*sdi)->isDirectional()) {
1366		Vector3d angMom = (*sdi)->getJ() * h;
1367		(*sdi)->setJ(angMom);
#	Line 1302 | Line 1369 | namespace OpenMD {
1369		}
1370		}
1371		successfulExchange = true;
1372	<	exchangeSum_ += targetFlux_;
1373	<	// 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	<	}
1372	>	kineticExchange_ += kineticTarget_;
1373	>	momentumExchange_ += momentumTarget_;
1374		}
1375		}
1376		}
#	Line 1325 | Line 1379 | namespace OpenMD {
1379		}
1380		}
1381		if (successfulExchange != true) {
1382	<	//   sprintf(painCave.errMsg,
1383	<	//              "RNEMD: exchange NOT performed!\n");
1384	<	//   painCave.isFatal = 0;
1385	<	//   painCave.severity = OPENMD_INFO;
1386	<	//   simError();
1382	>	sprintf(painCave.errMsg,
1383	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1384	>	"\tthe constraint equations may not exist or there may be\n"
1385	>	"\tno selected objects in one or both slabs.\n");
1386	>	painCave.isFatal = 0;
1387	>	painCave.severity = OPENMD_INFO;
1388	>	simError();
1389		failTrialCount_++;
1390		}
1391		}
1392
1393		void RNEMD::doRNEMD() {
1394
1395	<	switch(rnemdType_) {
1396	<	case rnemdKineticScale :
1397	<	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 :
1395	>	trialCount_++;
1396	>	switch(rnemdMethod_) {
1397	>	case rnemdSwap:
1398		doSwap();
1399		break;
1400	<	case rnemdShiftScaleV :
1401	<	case rnemdShiftScaleVAM :
1356	<	doShiftScale();
1400	>	case rnemdNIVS:
1401	>	doNIVS();
1402		break;
1403	<	case rnemdUnknown :
1403	>	case rnemdVSS:
1404	>	doVSS();
1405	>	break;
1406	>	case rnemdUnkownMethod:
1407		default :
1408		break;
1409		}
#	Line 1372 | Line 1420 | namespace OpenMD {
1420		StuntDouble* sd;
1421		int idx;
1422
1423	<	logFrameCount_++;
1423	>	vector<RealType> binMass(nBins_, 0.0);
1424	>	vector<RealType> binPx(nBins_, 0.0);
1425	>	vector<RealType> binPy(nBins_, 0.0);
1426	>	vector<RealType> binPz(nBins_, 0.0);
1427	>	vector<RealType> binKE(nBins_, 0.0);
1428	>	vector<int> binDOF(nBins_, 0);
1429	>	vector<int> binCount(nBins_, 0);
1430
1431		// alternative approach, track all molecules instead of only those
1432		// selected for scaling/swapping:
#	Line 1380 | Line 1434 | namespace OpenMD {
1434		SimInfo::MoleculeIterator miter;
1435		vector<StuntDouble*>::iterator iiter;
1436		Molecule* mol;
1437	<	StuntDouble* integrableObject;
1437	>	StuntDouble* sd;
1438		for (mol = info_->beginMolecule(miter); mol != NULL;
1439		mol = info_->nextMolecule(miter))
1440	<	integrableObject is essentially sd
1441	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1442	<	integrableObject != NULL;
1443	<	integrableObject = mol->nextIntegrableObject(iiter))
1440	>	sd is essentially sd
1441	>	for (sd = mol->beginIntegrableObject(iiter);
1442	>	sd != NULL;
1443	>	sd = mol->nextIntegrableObject(iiter))
1444		*/
1445		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1446		sd = seleMan_.nextSelected(selei)) {
#	Line 1399 | Line 1453 | namespace OpenMD {
1453
1454		if (usePeriodicBoundaryConditions_)
1455		currentSnap_->wrapVector(pos);
1456	<
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(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1461	<	rnemdLogWidth_;
1462	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1463	<	/*
1464	<	if (rnemdLogWidth_ == midBin_ + 1)
1411	<	if (binNo > midBin_)
1412	<	binNo = nBins_ - binNo;
1413	<	*/
1414	<	RealType mass = sd->getMass();
1415	<	mHist_[binNo] += mass;
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();
1417	–	RealType value;
1418	–	//RealType xVal, yVal, zVal;
1466
1467	<	if (outputTemp_) {
1468	<	value = mass * vel.lengthSquare();
1469	<	tempCount_[binNo] += 3;
1470	<	if (sd->isDirectional()) {
1471	<	Vector3d angMom = sd->getJ();
1472	<	Mat3x3d I = sd->getI();
1473	<	if (sd->isLinear()) {
1474	<	int i = sd->linearAxis();
1475	<	int j = (i + 1) % 3;
1476	<	int k = (i + 2) % 3;
1477	<	value += angMom[j] * angMom[j] / I(j, j) +
1478	<	angMom[k] * angMom[k] / I(k, k);
1479	<	tempCount_[binNo] +=2;
1480	<	} else {
1481	<	value += angMom[0] * angMom[0] / I(0, 0) +
1482	<	angMom[1]*angMom[1]/I(1, 1) +
1483	<	angMom[2]*angMom[2]/I(2, 2);
1484	<	tempCount_[binNo] +=3;
1485	<	}
1486	<	}
1487	<	value = value / PhysicalConstants::energyConvert
1488	<	/ PhysicalConstants::kb;//may move to getStatus()
1489	<	tempHist_[binNo] += value;
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	>	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	<	if (outputVx_) {
1493	<	value = mass * vel[0];
1446	<	//vxzCount_[binNo]++;
1447	<	pxzHist_[binNo] += value;
1448	<	}
1449	<	if (outputVy_) {
1450	<	value = mass * vel[1];
1451	<	//vyzCount_[binNo]++;
1452	<	pyzHist_[binNo] += value;
1453	<	}
1492	>	}
1493	>
1494
1495	<	if (output3DTemp_) {
1496	<	value = mass * vel.x() * vel.x();
1497	<	xTempHist_[binNo] += value;
1498	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1499	<	/ PhysicalConstants::kb;
1500	<	yTempHist_[binNo] += value;
1501	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1502	<	/ PhysicalConstants::kb;
1503	<	zTempHist_[binNo] += value;
1504	<	xyzTempCount_[binNo]++;
1495	>	#ifdef IS_MPI
1496	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1497	>	nBins_, MPI::INT, MPI::SUM);
1498	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1499	>	nBins_, MPI::REALTYPE, MPI::SUM);
1500	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1501	>	nBins_, MPI::REALTYPE, MPI::SUM);
1502	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1503	>	nBins_, MPI::REALTYPE, MPI::SUM);
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1505	>	nBins_, MPI::REALTYPE, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1509	>	nBins_, MPI::INT, MPI::SUM);
1510	>	#endif
1511	>
1512	>	Vector3d vel;
1513	>	RealType den;
1514	>	RealType temp;
1515	>	RealType z;
1516	>	for (int i = 0; i < nBins_; i++) {
1517	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1518	>	vel.x() = binPx[i] / binMass[i];
1519	>	vel.y() = binPy[i] / binMass[i];
1520	>	vel.z() = binPz[i] / binMass[i];
1521	>	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
1522	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1523	>	PhysicalConstants::energyConvert);
1524	>
1525	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1526	>	if(outputMask_[j]) {
1527	>	switch(j) {
1528	>	case Z:
1529	>	(data_[j].accumulator[i])->add(z);
1530	>	break;
1531	>	case TEMPERATURE:
1532	>	data_[j].accumulator[i]->add(temp);
1533	>	break;
1534	>	case VELOCITY:
1535	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1536	>	break;
1537	>	case DENSITY:
1538	>	data_[j].accumulator[i]->add(den);
1539	>	break;
1540	>	}
1541	>	}
1542		}
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	–	}
1543		}
1544		}
1545
1546		void RNEMD::getStarted() {
1547		collectData();
1548	<	/*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();
1548	>	writeOutputFile();
1549		}
1550
1551	<	void RNEMD::getStatus() {
1552	<
1514	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1515	<	Stats& stat = currentSnap_->statData;
1516	<	RealType time = currentSnap_->getTime();
1517	<
1518	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1519	<	//or to be more meaningful, define another item as exchangeSum_ / time
1520	<	int j;
1521	<
1522	<	#ifdef IS_MPI
1523	<
1524	<	// all processors have the same number of bins, and STL vectors pack their
1525	<	// arrays, so in theory, this should be safe:
1526	<
1527	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1528	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1529	<	if (outputTemp_) {
1530	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1531	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1532	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1533	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1534	<	}
1535	<	if (outputVx_) {
1536	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1537	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1538	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1539	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1540	<	}
1541	<	if (outputVy_) {
1542	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1543	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1544	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1545	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1546	<	}
1547	<	if (output3DTemp_) {
1548	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1549	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1550	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1551	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1552	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1553	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1554	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1555	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1556	<	}
1557	<	if (outputRotTemp_) {
1558	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1559	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1560	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1561	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1562	<	}
1563	<	// James put this in
1564	<	if (outputDen_) {
1565	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1566	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1567	<	}
1568	<	if (outputAh_) {
1569	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1570	<	1, MPI::REALTYPE, MPI::SUM);
1571	<	}
1572	<	if (outputVz_) {
1573	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1574	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1575	<	}
1551	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1552	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1553
1554	+	while(tokenizer.hasMoreTokens()) {
1555	+	std::string token(tokenizer.nextToken());
1556	+	toUpper(token);
1557	+	OutputMapType::iterator i = outputMap_.find(token);
1558	+	if (i != outputMap_.end()) {
1559	+	outputMask_.set(i->second);
1560	+	} else {
1561	+	sprintf( painCave.errMsg,
1562	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1563	+	"\toutputFileFormat keyword.\n", token.c_str() );
1564	+	painCave.isFatal = 0;
1565	+	painCave.severity = OPENMD_ERROR;
1566	+	simError();
1567	+	}
1568	+	}
1569	+	}
1570	+
1571	+	void RNEMD::writeOutputFile() {
1572	+
1573	+	#ifdef IS_MPI
1574		// If we're the root node, should we print out the results
1575		int worldRank = MPI::COMM_WORLD.Get_rank();
1576		if (worldRank == 0) {
1577		#endif
1578	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1579	+
1580	+	if( !rnemdFile_ ){
1581	+	sprintf( painCave.errMsg,
1582	+	"Could not open \"%s\" for RNEMD output.\n",
1583	+	rnemdFileName_.c_str());
1584	+	painCave.isFatal = 1;
1585	+	simError();
1586	+	}
1587
1588	<	if (outputTemp_) {
1589	<	tempLog_ << time;
1590	<	for (j = 0; j < rnemdLogWidth_; j++) {
1591	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1592	<	}
1593	<	tempLog_ << endl;
1588	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1589	>
1590	>	RealType time = currentSnap_->getTime();
1591	>
1592	>
1593	>	rnemdFile_ << "#######################################################\n";
1594	>	rnemdFile_ << "# RNEMD {\n";
1595	>
1596	>	map<string, RNEMDMethod>::iterator mi;
1597	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1598	>	if ( (*mi).second == rnemdMethod_)
1599	>	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
1600		}
1601	<	if (outputVx_) {
1602	<	vxzLog_ << time;
1603	<	for (j = 0; j < rnemdLogWidth_; j++) {
1604	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1593	<	}
1594	<	vxzLog_ << endl;
1601	>	map<string, RNEMDFluxType>::iterator fi;
1602	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1603	>	if ( (*fi).second == rnemdFluxType_)
1604	>	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
1605		}
1606	<	if (outputVy_) {
1607	<	vyzLog_ << time;
1608	<	for (j = 0; j < rnemdLogWidth_; j++) {
1609	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1610	<	}
1611	<	vyzLog_ << endl;
1606	>
1607	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
1608	>
1609	>	rnemdFile_ << "#    objectSelection = \""
1610	>	<< rnemdObjectSelection_ << "\"\n";
1611	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
1612	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
1614	>	rnemdFile_ << "# }\n";
1615	>	rnemdFile_ << "#######################################################\n";
1616	>
1617	>	rnemdFile_ << "# running time = " << time << " fs\n";
1618	>	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
1619	>	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
1620	>
1621	>	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
1622	>	<< "\n";
1623	>	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
1624	>	<< "\n";
1625	>
1626	>	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
1627	>	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
1628	>	<< "\n";
1629	>
1630	>	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
1631	>	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
1632	>
1633	>
1634	>	if (rnemdMethod_ == rnemdNIVS) {
1635	>	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
1636		}
1637
1638	<	if (output3DTemp_) {
1639	<	RealType temp;
1640	<	xTempLog_ << time;
1641	<	for (j = 0; j < rnemdLogWidth_; j++) {
1642	<	if (outputVx_)
1643	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1644	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1645	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1646	<	xTempLog_ << "\t" << temp;
1638	>	rnemdFile_ << "#######################################################\n";
1639	>
1640	>
1641	>
1642	>	//write title
1643	>	rnemdFile_ << "#";
1644	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1645	>	if (outputMask_[i]) {
1646	>	rnemdFile_ << "\t" << data_[i].title <<
1647	>	"(" << data_[i].units << ")";
1648		}
1614	–	xTempLog_ << endl;
1615	–	yTempLog_ << time;
1616	–	for (j = 0; j < rnemdLogWidth_; j++) {
1617	–	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1618	–	}
1619	–	yTempLog_ << endl;
1620	–	zTempLog_ << time;
1621	–	for (j = 0; j < rnemdLogWidth_; j++) {
1622	–	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1623	–	}
1624	–	zTempLog_ << endl;
1649		}
1650	<	if (outputRotTemp_) {
1651	<	rotTempLog_ << time;
1652	<	for (j = 0; j < rnemdLogWidth_; j++) {
1653	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1654	<	}
1655	<	rotTempLog_ << endl;
1656	<	}
1657	<	// James put this in.
1658	<	Mat3x3d hmat = currentSnap_->getHmat();
1659	<	if (outputDen_) {
1660	<	denLog_ << time;
1661	<	for (j = 0; j < rnemdLogWidth_; j++) {
1662	<
1663	<	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1664	<	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1665	<	}
1666	<	denLog_ << endl;
1667	<	}
1668	<	if (outputVz_) {
1669	<	vzzLog_ << time;
1670	<	for (j = 0; j < rnemdLogWidth_; j++) {
1671	<	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1672	<	}
1673	<	vzzLog_ << endl;
1674	<	}
1650	>	rnemdFile_ << std::endl;
1651	>
1652	>	rnemdFile_.precision(8);
1653	>
1654	>	for (unsigned int j = 0; j < nBins_; j++) {
1655	>
1656	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1657	>	if (outputMask_[i]) {
1658	>	if (data_[i].dataType == "RealType")
1659	>	writeReal(i,j);
1660	>	else if (data_[i].dataType == "Vector3d")
1661	>	writeVector(i,j);
1662	>	else {
1663	>	sprintf( painCave.errMsg,
1664	>	"RNEMD found an unknown data type for: %s ",
1665	>	data_[i].title.c_str());
1666	>	painCave.isFatal = 1;
1667	>	simError();
1668	>	}
1669	>	}
1670	>	}
1671	>	rnemdFile_ << std::endl;
1672	>
1673	>	}
1674	>
1675	>	rnemdFile_.flush();
1676	>	rnemdFile_.close();
1677	>
1678		#ifdef IS_MPI
1679		}
1680		#endif
1654	–
1655	–	for (j = 0; j < rnemdLogWidth_; j++) {
1656	–	mHist_[j] = 0.0;
1657	–	}
1658	–	if (outputTemp_)
1659	–	for (j = 0; j < rnemdLogWidth_; j++) {
1660	–	tempCount_[j] = 0;
1661	–	tempHist_[j] = 0.0;
1662	–	}
1663	–	if (outputVx_)
1664	–	for (j = 0; j < rnemdLogWidth_; j++) {
1665	–	//pxzCount_[j] = 0;
1666	–	pxzHist_[j] = 0.0;
1667	–	}
1668	–	if (outputVy_)
1669	–	for (j = 0; j < rnemdLogWidth_; j++) {
1670	–	//pyzCount_[j] = 0;
1671	–	pyzHist_[j] = 0.0;
1672	–	}
1673	–
1674	–	if (output3DTemp_)
1675	–	for (j = 0; j < rnemdLogWidth_; j++) {
1676	–	xTempHist_[j] = 0.0;
1677	–	yTempHist_[j] = 0.0;
1678	–	zTempHist_[j] = 0.0;
1679	–	xyzTempCount_[j] = 0;
1680	–	}
1681	–	if (outputRotTemp_)
1682	–	for (j = 0; j < rnemdLogWidth_; j++) {
1683	–	rotTempCount_[j] = 0;
1684	–	rotTempHist_[j] = 0.0;
1685	–	}
1686	–	// James put this in
1687	–	if (outputDen_)
1688	–	for (j = 0; j < rnemdLogWidth_; j++) {
1689	–	//pyzCount_[j] = 0;
1690	–	DenHist_[j] = 0.0;
1691	–	}
1692	–	if (outputVz_)
1693	–	for (j = 0; j < rnemdLogWidth_; j++) {
1694	–	//pyzCount_[j] = 0;
1695	–	pzzHist_[j] = 0.0;
1696	–	}
1697	–	// reset the counter
1698	–
1699	–	Numcount_++;
1700	–	if (Numcount_ > int(runTime_/statusTime_))
1701	–	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1702	–	if (Numcount_ > int(runTime_/statusTime_))
1703	–	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
1681
1705	–	logFrameCount_ = 0;
1682		}
1683	+
1684	+	void RNEMD::writeReal(int index, unsigned int bin) {
1685	+	assert(index >=0 && index < ENDINDEX);
1686	+	assert(bin >=0 && bin < nBins_);
1687	+	RealType s;
1688	+
1689	+	data_[index].accumulator[bin]->getAverage(s);
1690	+
1691	+	if (! isinf(s) && ! isnan(s)) {
1692	+	rnemdFile_ << "\t" << s;
1693	+	} else{
1694	+	sprintf( painCave.errMsg,
1695	+	"RNEMD detected a numerical error writing: %s for bin %d",
1696	+	data_[index].title.c_str(), bin);
1697	+	painCave.isFatal = 1;
1698	+	simError();
1699	+	}
1700	+	}
1701	+
1702	+	void RNEMD::writeVector(int index, unsigned int bin) {
1703	+	assert(index >=0 && index < ENDINDEX);
1704	+	assert(bin >=0 && bin < nBins_);
1705	+	Vector3d s;
1706	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1707	+	if (isinf(s[0]) || isnan(s[0]) ||
1708	+	isinf(s[1]) || isnan(s[1]) ||
1709	+	isinf(s[2]) || isnan(s[2]) ) {
1710	+	sprintf( painCave.errMsg,
1711	+	"RNEMD detected a numerical error writing: %s for bin %d",
1712	+	data_[index].title.c_str(), bin);
1713	+	painCave.isFatal = 1;
1714	+	simError();
1715	+	} else {
1716	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1717	+	}
1718	+	}
1719		}
1720

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