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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1812 by gezelter, Fri Nov 16 21:18:42 2012 UTC

#	Line 40 | Line 40
40		*/
41
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include "rnemd/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45		#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
#	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
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
77	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
78	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
79	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
80	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
81	<	stringToEnumMap_["Px"] = rnemdPx;
82	<	stringToEnumMap_["Py"] = rnemdPy;
83	<	stringToEnumMap_["Pz"] = rnemdPz;
84	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
85	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
86	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
75	>	stringToMethod_["Swap"]  = rnemdSwap;
76	>	stringToMethod_["NIVS"]  = rnemdNIVS;
77	>	stringToMethod_["VSS"]   = rnemdVSS;
78	>
79	>	stringToFluxType_["KE"]  = rnemdKE;
80	>	stringToFluxType_["Px"]  = rnemdPx;
81	>	stringToFluxType_["Py"]  = rnemdPy;
82	>	stringToFluxType_["Pz"]  = rnemdPz;
83	>	stringToFluxType_["Pvector"]  = rnemdPvector;
84	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
85	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
86	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
87	>
88	>	runTime_ = simParams->getRunTime();
89	>	statusTime_ = simParams->getStatusTime();
90	>
91	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
92		evaluator_.loadScriptString(rnemdObjectSelection_);
93		seleMan_.setSelectionSet(evaluator_.evaluate());
94	+
95	+	const string methStr = rnemdParams->getMethod();
96	+	bool hasFluxType = rnemdParams->haveFluxType();
97	+
98	+	string fluxStr;
99	+	if (hasFluxType) {
100	+	fluxStr = rnemdParams->getFluxType();
101	+	} else {
102	+	sprintf(painCave.errMsg,
103	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
104	+	"\twhich must be one of the following values:\n"
105	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
106	+	"\tmust be set to use RNEMD\n");
107	+	painCave.isFatal = 1;
108	+	painCave.severity = OPENMD_ERROR;
109	+	simError();
110	+	}
111	+
112	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
113	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
114	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
115	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
116	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
117	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
118	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
119	+	bool hasOutputFields = rnemdParams->haveOutputFields();
120	+
121	+	map<string, RNEMDMethod>::iterator i;
122	+	i = stringToMethod_.find(methStr);
123	+	if (i != stringToMethod_.end())
124	+	rnemdMethod_ = i->second;
125	+	else {
126	+	sprintf(painCave.errMsg,
127	+	"RNEMD: The current method,\n"
128	+	"\t\t%s is not one of the recognized\n"
129	+	"\texchange methods: Swap, NIVS, or VSS\n",
130	+	methStr.c_str());
131	+	painCave.isFatal = 1;
132	+	painCave.severity = OPENMD_ERROR;
133	+	simError();
134	+	}
135	+
136	+	map<string, RNEMDFluxType>::iterator j;
137	+	j = stringToFluxType_.find(fluxStr);
138	+	if (j != stringToFluxType_.end())
139	+	rnemdFluxType_ = j->second;
140	+	else {
141	+	sprintf(painCave.errMsg,
142	+	"RNEMD: The current fluxType,\n"
143	+	"\t\t%s\n"
144	+	"\tis not one of the recognized flux types.\n",
145	+	fluxStr.c_str());
146	+	painCave.isFatal = 1;
147	+	painCave.severity = OPENMD_ERROR;
148	+	simError();
149	+	}
150	+
151	+	bool methodFluxMismatch = false;
152	+	bool hasCorrectFlux = false;
153	+	switch(rnemdMethod_) {
154	+	case rnemdSwap:
155	+	switch (rnemdFluxType_) {
156	+	case rnemdKE:
157	+	hasCorrectFlux = hasKineticFlux;
158	+	break;
159	+	case rnemdPx:
160	+	case rnemdPy:
161	+	case rnemdPz:
162	+	hasCorrectFlux = hasMomentumFlux;
163	+	break;
164	+	default :
165	+	methodFluxMismatch = true;
166	+	break;
167	+	}
168	+	break;
169	+	case rnemdNIVS:
170	+	switch (rnemdFluxType_) {
171	+	case rnemdKE:
172	+	case rnemdRotKE:
173	+	case rnemdFullKE:
174	+	hasCorrectFlux = hasKineticFlux;
175	+	break;
176	+	case rnemdPx:
177	+	case rnemdPy:
178	+	case rnemdPz:
179	+	hasCorrectFlux = hasMomentumFlux;
180	+	break;
181	+	case rnemdKePx:
182	+	case rnemdKePy:
183	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
184	+	break;
185	+	default:
186	+	methodFluxMismatch = true;
187	+	break;
188	+	}
189	+	break;
190	+	case rnemdVSS:
191	+	switch (rnemdFluxType_) {
192	+	case rnemdKE:
193	+	case rnemdRotKE:
194	+	case rnemdFullKE:
195	+	hasCorrectFlux = hasKineticFlux;
196	+	break;
197	+	case rnemdPx:
198	+	case rnemdPy:
199	+	case rnemdPz:
200	+	hasCorrectFlux = hasMomentumFlux;
201	+	break;
202	+	case rnemdPvector:
203	+	hasCorrectFlux = hasMomentumFluxVector;
204	+	break;
205	+	case rnemdKePx:
206	+	case rnemdKePy:
207	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
208	+	break;
209	+	case rnemdKePvector:
210	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
211	+	break;
212	+	default:
213	+	methodFluxMismatch = true;
214	+	break;
215	+	}
216	+	default:
217	+	break;
218	+	}
219	+
220	+	if (methodFluxMismatch) {
221	+	sprintf(painCave.errMsg,
222	+	"RNEMD: The current method,\n"
223	+	"\t\t%s\n"
224	+	"\tcannot be used with the current flux type, %s\n",
225	+	methStr.c_str(), fluxStr.c_str());
226	+	painCave.isFatal = 1;
227	+	painCave.severity = OPENMD_ERROR;
228	+	simError();
229	+	}
230	+	if (!hasCorrectFlux) {
231	+	sprintf(painCave.errMsg,
232	+	"RNEMD: The current method, %s, and flux type, %s,\n"
233	+	"\tdid not have the correct flux value specified. Options\n"
234	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
235	+	methStr.c_str(), fluxStr.c_str());
236	+	painCave.isFatal = 1;
237	+	painCave.severity = OPENMD_ERROR;
238	+	simError();
239	+	}
240	+
241	+	if (hasKineticFlux) {
242	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
243	+	// into  amu / fs^3:
244	+	kineticFlux_ = rnemdParams->getKineticFlux()
245	+	* PhysicalConstants::energyConvert;
246	+	} else {
247	+	kineticFlux_ = 0.0;
248	+	}
249	+	if (hasMomentumFluxVector) {
250	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
251	+	} else {
252	+	momentumFluxVector_ = V3Zero;
253	+	if (hasMomentumFlux) {
254	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
255	+	switch (rnemdFluxType_) {
256	+	case rnemdPx:
257	+	momentumFluxVector_.x() = momentumFlux;
258	+	break;
259	+	case rnemdPy:
260	+	momentumFluxVector_.y() = momentumFlux;
261	+	break;
262	+	case rnemdPz:
263	+	momentumFluxVector_.z() = momentumFlux;
264	+	break;
265	+	case rnemdKePx:
266	+	momentumFluxVector_.x() = momentumFlux;
267	+	break;
268	+	case rnemdKePy:
269	+	momentumFluxVector_.y() = momentumFlux;
270	+	break;
271	+	default:
272	+	break;
273	+	}
274	+	}
275	+	}
276
277		// do some sanity checking
278
279		int selectionCount = seleMan_.getSelectionCount();
280	+
281		int nIntegrable = info->getNGlobalIntegrableObjects();
282
283		if (selectionCount > nIntegrable) {
284		sprintf(painCave.errMsg,
285	<	"RNEMD: The current RNEMD_objectSelection,\n"
285	>	"RNEMD: The current objectSelection,\n"
286		"\t\t%s\n"
287		"\thas resulted in %d selected objects.  However,\n"
288		"\tthe total number of integrable objects in the system\n"
#	Line 109 | Line 295 | namespace OpenMD {
295		painCave.severity = OPENMD_WARNING;
296		simError();
297		}
112	–
113	–	const string st = simParams->getRNEMD_exchangeType();
298
299	<	map<string, RNEMDTypeEnum>::iterator i;
116	<	i = stringToEnumMap_.find(st);
117	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
118	<	if (rnemdType_ == rnemdUnknown) {
119	<	sprintf(painCave.errMsg,
120	<	"RNEMD: The current RNEMD_exchangeType,\n"
121	<	"\t\t%s\n"
122	<	"\tis not one of the recognized exchange types.\n",
123	<	st.c_str());
124	<	painCave.isFatal = 1;
125	<	painCave.severity = OPENMD_ERROR;
126	<	simError();
127	<	}
128	<
129	<	outputTemp_ = false;
130	<	if (simParams->haveRNEMD_outputTemperature()) {
131	<	outputTemp_ = simParams->getRNEMD_outputTemperature();
132	<	} else if ((rnemdType_ == rnemdKineticSwap) ||
133	<	(rnemdType_ == rnemdKineticScale) ||
134	<	(rnemdType_ == rnemdKineticScaleVAM) ||
135	<	(rnemdType_ == rnemdKineticScaleAM)) {
136	<	outputTemp_ = true;
137	<	}
138	<	outputVx_ = false;
139	<	if (simParams->haveRNEMD_outputVx()) {
140	<	outputVx_ = simParams->getRNEMD_outputVx();
141	<	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
142	<	outputVx_ = true;
143	<	}
144	<	outputVy_ = false;
145	<	if (simParams->haveRNEMD_outputVy()) {
146	<	outputVy_ = simParams->getRNEMD_outputVy();
147	<	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
148	<	outputVy_ = true;
149	<	}
150	<	output3DTemp_ = false;
151	<	if (simParams->haveRNEMD_outputXyzTemperature()) {
152	<	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
153	<	}
154	<	outputRotTemp_ = false;
155	<	if (simParams->haveRNEMD_outputRotTemperature()) {
156	<	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
157	<	}
299	>	areaAccumulator_ = new Accumulator();
300
301	<	#ifdef IS_MPI
160	<	if (worldRank == 0) {
161	<	#endif
301	>	nBins_ = rnemdParams->getOutputBins();
302
303	<	//may have rnemdWriter separately
304	<	string rnemdFileName;
303	>	data_.resize(RNEMD::ENDINDEX);
304	>	OutputData z;
305	>	z.units =  "Angstroms";
306	>	z.title =  "Z";
307	>	z.dataType = "RealType";
308	>	z.accumulator.reserve(nBins_);
309	>	for (unsigned int i = 0; i < nBins_; i++)
310	>	z.accumulator.push_back( new Accumulator() );
311	>	data_[Z] = z;
312	>	outputMap_["Z"] =  Z;
313
314	<	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_) {
175	<	rnemdFileName = "velocityY.log";
176	<	vyzLog_.open(rnemdFileName.c_str());
177	<	}
314	>	OutputData temperature;
315	>	temperature.units =  "K";
316	>	temperature.title =  "Temperature";
317	>	temperature.dataType = "RealType";
318	>	temperature.accumulator.reserve(nBins_);
319	>	for (unsigned int i = 0; i < nBins_; i++)
320	>	temperature.accumulator.push_back( new Accumulator() );
321	>	data_[TEMPERATURE] = temperature;
322	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
323
324	<	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_) {
188	<	rnemdFileName = "temperatureR.log";
189	<	rotTempLog_.open(rnemdFileName.c_str());
190	<	}
324	>	OutputData velocity;
325	>	velocity.units = "angstroms/fs";
326	>	velocity.title =  "Velocity";
327	>	velocity.dataType = "Vector3d";
328	>	velocity.accumulator.reserve(nBins_);
329	>	for (unsigned int i = 0; i < nBins_; i++)
330	>	velocity.accumulator.push_back( new VectorAccumulator() );
331	>	data_[VELOCITY] = velocity;
332	>	outputMap_["VELOCITY"] = VELOCITY;
333
334	<	#ifdef IS_MPI
335	<	}
336	<	#endif
334	>	OutputData density;
335	>	density.units =  "g cm^-3";
336	>	density.title =  "Density";
337	>	density.dataType = "RealType";
338	>	density.accumulator.reserve(nBins_);
339	>	for (unsigned int i = 0; i < nBins_; i++)
340	>	density.accumulator.push_back( new Accumulator() );
341	>	data_[DENSITY] = density;
342	>	outputMap_["DENSITY"] =  DENSITY;
343
344	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
345	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
198	<	midBin_ = nBins_ / 2;
199	<	if (simParams->haveRNEMD_binShift()) {
200	<	if (simParams->getRNEMD_binShift()) {
201	<	zShift_ = 0.5 / (RealType)(nBins_);
202	<	} else {
203	<	zShift_ = 0.0;
204	<	}
344	>	if (hasOutputFields) {
345	>	parseOutputFileFormat(rnemdParams->getOutputFields());
346		} else {
347	<	zShift_ = 0.0;
348	<	}
349	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
350	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
351	<	//set to 0.0 if not using it; N/A in status output yet
352	<	if (simParams->haveRNEMD_logWidth()) {
353	<	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
354	<	/*arbitary rnemdLogWidth_, no checking;
355	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
356	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
357	<	cerr << "Automaically set back to default.\n";
358	<	rnemdLogWidth_ = nBins_;
359	<	}*/
360	<	} else {
361	<	set_RNEMD_logWidth(nBins_);
347	>	outputMask_.set(Z);
348	>	switch (rnemdFluxType_) {
349	>	case rnemdKE:
350	>	case rnemdRotKE:
351	>	case rnemdFullKE:
352	>	outputMask_.set(TEMPERATURE);
353	>	break;
354	>	case rnemdPx:
355	>	case rnemdPy:
356	>	outputMask_.set(VELOCITY);
357	>	break;
358	>	case rnemdPz:
359	>	case rnemdPvector:
360	>	outputMask_.set(VELOCITY);
361	>	outputMask_.set(DENSITY);
362	>	break;
363	>	case rnemdKePx:
364	>	case rnemdKePy:
365	>	outputMask_.set(TEMPERATURE);
366	>	outputMask_.set(VELOCITY);
367	>	break;
368	>	case rnemdKePvector:
369	>	outputMask_.set(TEMPERATURE);
370	>	outputMask_.set(VELOCITY);
371	>	outputMask_.set(DENSITY);
372	>	break;
373	>	default:
374	>	break;
375	>	}
376		}
377	<	tempHist_.resize(rnemdLogWidth_, 0.0);
378	<	tempCount_.resize(rnemdLogWidth_, 0);
379	<	pxzHist_.resize(rnemdLogWidth_, 0.0);
380	<	//vxzCount_.resize(rnemdLogWidth_, 0);
381	<	pyzHist_.resize(rnemdLogWidth_, 0.0);
382	<	//vyzCount_.resize(rnemdLogWidth_, 0);
377	>
378	>	if (hasOutputFileName) {
379	>	rnemdFileName_ = rnemdParams->getOutputFileName();
380	>	} else {
381	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
382	>	}
383
384	<	mHist_.resize(rnemdLogWidth_, 0.0);
230	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
231	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
232	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
233	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
234	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
235	<	rotTempCount_.resize(rnemdLogWidth_, 0);
384	>	exchangeTime_ = rnemdParams->getExchangeTime();
385
386	<	set_RNEMD_exchange_total(0.0);
387	<	if (simParams->haveRNEMD_targetFlux()) {
388	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
389	<	} else {
390	<	set_RNEMD_target_flux(0.0);
391	<	}
392	<	if (simParams->haveRNEMD_targetJzKE()) {
244	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
245	<	} else {
246	<	set_RNEMD_target_JzKE(0.0);
247	<	}
248	<	if (simParams->haveRNEMD_targetJzpx()) {
249	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
250	<	} else {
251	<	set_RNEMD_target_jzpx(0.0);
252	<	}
253	<	jzp_.x() = targetJzpx_;
254	<	njzp_.x() = -targetJzpx_;
255	<	if (simParams->haveRNEMD_targetJzpy()) {
256	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
257	<	} else {
258	<	set_RNEMD_target_jzpy(0.0);
259	<	}
260	<	jzp_.y() = targetJzpy_;
261	<	njzp_.y() = -targetJzpy_;
262	<	if (simParams->haveRNEMD_targetJzpz()) {
263	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
264	<	} else {
265	<	set_RNEMD_target_jzpz(0.0);
266	<	}
267	<	jzp_.z() = targetJzpz_;
268	<	njzp_.z() = -targetJzpz_;
386	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
387	>	Mat3x3d hmat = currentSnap_->getHmat();
388	>
389	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
390	>	// Lx, Ly = box dimensions in x & y
391	>	// dt = exchange time interval
392	>	// flux = target flux
393
394	<	#ifndef IS_MPI
395	<	if (simParams->haveSeed()) {
396	<	seedValue = simParams->getSeed();
397	<	randNumGen_ = new SeqRandNumGen(seedValue);
398	<	}else {
399	<	randNumGen_ = new SeqRandNumGen();
400	<	}
401	<	#else
402	<	if (simParams->haveSeed()) {
403	<	seedValue = simParams->getSeed();
404	<	randNumGen_ = new ParallelRandNumGen(seedValue);
405	<	}else {
406	<	randNumGen_ = new ParallelRandNumGen();
283	<	}
284	<	#endif
285	<	}
394	>	RealType area = currentSnap_->getXYarea();
395	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
396	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
397	>
398	>	// total exchange sums are zeroed out at the beginning:
399	>
400	>	kineticExchange_ = 0.0;
401	>	momentumExchange_ = V3Zero;
402	>
403	>	if (hasSlabWidth)
404	>	slabWidth_ = rnemdParams->getSlabWidth();
405	>	else
406	>	slabWidth_ = hmat(2,2) / 10.0;
407
408	<	RNEMD::~RNEMD() {
409	<	delete randNumGen_;
408	>	if (hasSlabACenter)
409	>	slabACenter_ = rnemdParams->getSlabACenter();
410	>	else
411	>	slabACenter_ = 0.0;
412
413	+	if (hasSlabBCenter)
414	+	slabBCenter_ = rnemdParams->getSlabBCenter();
415	+	else
416	+	slabBCenter_ = hmat(2,2) / 2.0;
417	+
418	+	}
419	+
420	+	RNEMD::~RNEMD() {
421	+	if (!doRNEMD_) return;
422		#ifdef IS_MPI
423		if (worldRank == 0) {
424		#endif
293	–
294	–	sprintf(painCave.errMsg,
295	–	"RNEMD: total failed trials: %d\n",
296	–	failTrialCount_);
297	–	painCave.isFatal = 0;
298	–	painCave.severity = OPENMD_INFO;
299	–	simError();
425
426	<	if (outputTemp_) tempLog_.close();
302	<	if (outputVx_)   vxzLog_.close();
303	<	if (outputVy_)   vyzLog_.close();
426	>	writeOutputFile();
427
428	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
429	<	rnemdType_ == rnemdPyScale) {
307	<	sprintf(painCave.errMsg,
308	<	"RNEMD: total root-checking warnings: %d\n",
309	<	failRootCount_);
310	<	painCave.isFatal = 0;
311	<	painCave.severity = OPENMD_INFO;
312	<	simError();
313	<	}
314	<	if (output3DTemp_) {
315	<	xTempLog_.close();
316	<	yTempLog_.close();
317	<	zTempLog_.close();
318	<	}
319	<	if (outputRotTemp_) rotTempLog_.close();
320	<
428	>	rnemdFile_.close();
429	>
430		#ifdef IS_MPI
431		}
432		#endif
433		}
434	+
435	+	bool RNEMD::inSlabA(Vector3d pos) {
436	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
437	+	}
438	+	bool RNEMD::inSlabB(Vector3d pos) {
439	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
440	+	}
441
442		void RNEMD::doSwap() {
443	<
443	>	if (!doRNEMD_) return;
444		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
445		Mat3x3d hmat = currentSnap_->getHmat();
446
#	Line 353 | Line 469 | namespace OpenMD {
469
470		if (usePeriodicBoundaryConditions_)
471		currentSnap_->wrapVector(pos);
472	<
473	<	// which bin is this stuntdouble in?
358	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
359	<
360	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
361	<
472	>	bool inA = inSlabA(pos);
473	>	bool inB = inSlabB(pos);
474
475	<	// if we're in bin 0 or the middleBin
364	<	if (binNo == 0 || binNo == midBin_) {
475	>	if (inA || inB) {
476
477		RealType mass = sd->getMass();
478		Vector3d vel = sd->getVel();
479		RealType value;
480	<
481	<	switch(rnemdType_) {
482	<	case rnemdKineticSwap :
480	>
481	>	switch(rnemdFluxType_) {
482	>	case rnemdKE :
483
484		value = mass * vel.lengthSquare();
485
#	Line 388 | Line 499 | namespace OpenMD {
499		+ angMom[2]*angMom[2]/I(2, 2);
500		}
501		} //angular momenta exchange enabled
391	–	//energyConvert temporarily disabled
392	–	//make exchangeSum_ comparable between swap & scale
393	–	//value = value * 0.5 / PhysicalConstants::energyConvert;
502		value *= 0.5;
503		break;
504		case rnemdPx :
#	Line 406 | Line 514 | namespace OpenMD {
514		break;
515		}
516
517	<	if (binNo == 0) {
517	>	if (inA == 0) {
518		if (!min_found) {
519		min_val = value;
520		min_sd = sd;
#	Line 417 | Line 525 | namespace OpenMD {
525		min_sd = sd;
526		}
527		}
528	<	} else { //midBin_
528	>	} else {
529		if (!max_found) {
530		max_val = value;
531		max_sd = sd;
#	Line 431 | Line 539 | namespace OpenMD {
539		}
540		}
541		}
542	<
542	>
543		#ifdef IS_MPI
544		int nProc, worldRank;
545	<
545	>
546		nProc = MPI::COMM_WORLD.Get_size();
547		worldRank = MPI::COMM_WORLD.Get_rank();
548
#	Line 454 | Line 562 | namespace OpenMD {
562		RealType val;
563		int rank;
564		} max_vals, min_vals;
565	<
565	>
566		if (my_min_found) {
567		min_vals.val = min_val;
568		} else {
#	Line 492 | Line 600 | namespace OpenMD {
600		Vector3d max_vel = max_sd->getVel();
601		RealType temp_vel;
602
603	<	switch(rnemdType_) {
604	<	case rnemdKineticSwap :
603	>	switch(rnemdFluxType_) {
604	>	case rnemdKE :
605		min_sd->setVel(max_vel);
606		max_sd->setVel(min_vel);
607		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 544 | Line 652 | namespace OpenMD {
652		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
653		min_vals.rank, 0, status);
654
655	<	switch(rnemdType_) {
656	<	case rnemdKineticSwap :
655	>	switch(rnemdFluxType_) {
656	>	case rnemdKE :
657		max_sd->setVel(min_vel);
658		//angular momenta exchange enabled
659		if (max_sd->isDirectional()) {
#	Line 590 | Line 698 | namespace OpenMD {
698		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
699		max_vals.rank, 0, status);
700
701	<	switch(rnemdType_) {
702	<	case rnemdKineticSwap :
701	>	switch(rnemdFluxType_) {
702	>	case rnemdKE :
703		min_sd->setVel(max_vel);
704		//angular momenta exchange enabled
705		if (min_sd->isDirectional()) {
#	Line 625 | Line 733 | namespace OpenMD {
733		}
734		}
735		#endif
736	<	exchangeSum_ += max_val - min_val;
736	>
737	>	switch(rnemdFluxType_) {
738	>	case rnemdKE:
739	>	kineticExchange_ += max_val - min_val;
740	>	break;
741	>	case rnemdPx:
742	>	momentumExchange_.x() += max_val - min_val;
743	>	break;
744	>	case rnemdPy:
745	>	momentumExchange_.y() += max_val - min_val;
746	>	break;
747	>	case rnemdPz:
748	>	momentumExchange_.z() += max_val - min_val;
749	>	break;
750	>	default:
751	>	break;
752	>	}
753		} else {
754		sprintf(painCave.errMsg,
755	<	"RNEMD: 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 636 | 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	<	}
646	<
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 687 | 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	<
694	<	// if we're in bin 0 or the middleBin
695	<	if (binNo == 0 || binNo == midBin_) {
696	<
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 705 | 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();
708	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
829		if (sd->isDirectional()) {
830		Vector3d angMom = sd->getJ();
831		Mat3x3d I = sd->getI();
#	Line 721 | Line 841 | namespace OpenMD {
841		+ angMom[2]*angMom[2]/I(2, 2);
842		}
843		}
844	<	//}
725	<	} else { //midBin_
844	>	} else {
845		coldBin.push_back(sd);
846		Pcx += mass * vel.x();
847		Pcy += mass * vel.y();
#	Line 730 | 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();
733	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
852		if (sd->isDirectional()) {
853		Vector3d angMom = sd->getJ();
854		Mat3x3d I = sd->getI();
#	Line 746 | Line 864 | namespace OpenMD {
864		+ angMom[2]*angMom[2]/I(2, 2);
865		}
866		}
749	–	//}
867		}
868		}
869		}
#	Line 760 | Line 877 | namespace OpenMD {
877		Kcz *= 0.5;
878		Kcw *= 0.5;
879
763	–	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
764	–	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
765	–	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
766	–	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
767	–	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
768	–
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 791 | 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;
807	<	//now convert to hotBin coefficient
917	>
918		RealType w = 0.0;
919	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
919	>	if (rnemdFluxType_ ==  rnemdFullKE) {
920		x = 1.0 + px * (1.0 - c);
921		y = 1.0 + py * (1.0 - c);
922		z = 1.0 + pz * (1.0 - c);
#	Line 820 | Line 930 | namespace OpenMD {
930		*/
931		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
932		(fabs(z - 1.0) < 0.1)) {
933	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
933	>	w = 1.0 + (kineticTarget_
934	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
935		+ Khz * (1.0 - z * z)) / Khw;
936		}//no need to calculate w if x, y or z is out of range
937		} else {
938	<	w = 1.0 + targetFlux_ / Khw;
938	>	w = 1.0 + kineticTarget_ / Khw;
939		}
940		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
941		//if w is in the right range, so should be x, y, z.
942		vector<StuntDouble*>::iterator sdi;
943		Vector3d vel;
944		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
945	<	if (rnemdType_ == rnemdKineticScaleVAM) {
945	>	if (rnemdFluxType_ == rnemdFullKE) {
946		vel = (*sdi)->getVel() * c;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
947		(*sdi)->setVel(vel);
948		}
949		if ((*sdi)->isDirectional()) {
950		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//angMom[2] *= c;
951		(*sdi)->setJ(angMom);
952		}
953		}
954		w = sqrt(w);
850	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
851	–	<< "\twh= " << w << endl;
955		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
956	<	if (rnemdType_ == rnemdKineticScaleVAM) {
956	>	if (rnemdFluxType_ == rnemdFullKE) {
957		vel = (*sdi)->getVel();
958		vel.x() *= x;
959		vel.y() *= y;
#	Line 859 | Line 962 | namespace OpenMD {
962		}
963		if ((*sdi)->isDirectional()) {
964		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//angMom[2] *= w;
965		(*sdi)->setJ(angMom);
966		}
967		}
968		successfulScale = true;
969	<	exchangeSum_ += targetFlux_;
969	>	kineticExchange_ += kineticTarget_;
970		}
971		}
972		} else {
973		RealType a000, a110, c0, a001, a111, b01, b11, c1;
974	<	switch(rnemdType_) {
975	<	case rnemdKineticScale :
974	>	switch(rnemdFluxType_) {
975	>	case rnemdKE :
976		/* used hotBin coeff's & only scale x & y dimensions
977		RealType px = Phx / Pcx;
978		RealType py = Phy / Pcy;
979		a110 = Khy;
980	<	c0 = - Khx - Khy - targetFlux_;
980	>	c0 = - Khx - Khy - kineticTarget_;
981		a000 = Khx;
982		a111 = Kcy * py * py;
983		b11 = -2.0 * Kcy * py * (1.0 + py);
984	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
984	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
985		b01 = -2.0 * Kcx * px * (1.0 + px);
986		a001 = Kcx * px * px;
987		*/
988		//scale all three dimensions, let c_x = c_y
989		a000 = Kcx + Kcy;
990		a110 = Kcz;
991	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
991	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
992		a001 = Khx * px * px + Khy * py * py;
993		a111 = Khz * pz * pz;
994		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
995		b11 = -2.0 * Khz * pz * (1.0 + pz);
996		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
997	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
997	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
998		break;
999	<	case rnemdPxScale :
1000	<	c = 1 - targetFlux_ / Pcx;
999	>	case rnemdPx :
1000	>	c = 1 - momentumTarget_.x() / Pcx;
1001		a000 = Kcy;
1002		a110 = Kcz;
1003		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 908 | Line 1008 | namespace OpenMD {
1008		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1009		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1010		break;
1011	<	case rnemdPyScale :
1012	<	c = 1 - targetFlux_ / Pcy;
1011	>	case rnemdPy :
1012	>	c = 1 - momentumTarget_.y() / Pcy;
1013		a000 = Kcx;
1014		a110 = Kcz;
1015		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 920 | Line 1020 | namespace OpenMD {
1020		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1021		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1022		break;
1023	<	case rnemdPzScale ://we don't really do this, do we?
1024	<	c = 1 - targetFlux_ / Pcz;
1023	>	case rnemdPz ://we don't really do this, do we?
1024	>	c = 1 - momentumTarget_.z() / Pcz;
1025		a000 = Kcx;
1026		a110 = Kcy;
1027		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1006 | Line 1106 | namespace OpenMD {
1106		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1107		r1 = (*rpi).first;
1108		r2 = (*rpi).second;
1109	<	switch(rnemdType_) {
1110	<	case rnemdKineticScale :
1109	>	switch(rnemdFluxType_) {
1110	>	case rnemdKE :
1111		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1113		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1114		break;
1115	<	case rnemdPxScale :
1115	>	case rnemdPx :
1116		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1117		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1118		break;
1119	<	case rnemdPyScale :
1119	>	case rnemdPy :
1120		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1121		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1122		break;
1123	<	case rnemdPzScale :
1123	>	case rnemdPz :
1124		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1125		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1126		default :
#	Line 1034 | Line 1134 | namespace OpenMD {
1134		#ifdef IS_MPI
1135		if (worldRank == 0) {
1136		#endif
1137	<	sprintf(painCave.errMsg,
1138	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	<	bestPair.first, bestPair.second);
1140	<	painCave.isFatal = 0;
1141	<	painCave.severity = OPENMD_INFO;
1142	<	simError();
1137	>	// sprintf(painCave.errMsg,
1138	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	>	//         bestPair.first, bestPair.second);
1140	>	// painCave.isFatal = 0;
1141	>	// painCave.severity = OPENMD_INFO;
1142	>	// simError();
1143		#ifdef IS_MPI
1144		}
1145		#endif
1146
1147	<	switch(rnemdType_) {
1148	<	case rnemdKineticScale :
1147	>	switch(rnemdFluxType_) {
1148	>	case rnemdKE :
1149		x = bestPair.first;
1150		y = bestPair.first;
1151		z = bestPair.second;
1152		break;
1153	<	case rnemdPxScale :
1153	>	case rnemdPx :
1154		x = c;
1155		y = bestPair.first;
1156		z = bestPair.second;
1157		break;
1158	<	case rnemdPyScale :
1158	>	case rnemdPy :
1159		x = bestPair.first;
1160		y = c;
1161		z = bestPair.second;
1162		break;
1163	<	case rnemdPzScale :
1163	>	case rnemdPz :
1164		x = bestPair.first;
1165		y = bestPair.second;
1166		z = c;
#	Line 1089 | Line 1189 | namespace OpenMD {
1189		(*sdi)->setVel(vel);
1190		}
1191		successfulScale = true;
1192	<	exchangeSum_ += targetFlux_;
1192	>	switch(rnemdFluxType_) {
1193	>	case rnemdKE :
1194	>	kineticExchange_ += kineticTarget_;
1195	>	break;
1196	>	case rnemdPx :
1197	>	case rnemdPy :
1198	>	case rnemdPz :
1199	>	momentumExchange_ += momentumTarget_;
1200	>	break;
1201	>	default :
1202	>	break;
1203	>	}
1204		}
1205		}
1206		if (successfulScale != true) {
1207		sprintf(painCave.errMsg,
1208	<	"RNEMD: exchange NOT performed!\n");
1208	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1209	>	"\tthe constraint equations may not exist or there may be\n"
1210	>	"\tno selected objects in one or both slabs.\n");
1211		painCave.isFatal = 0;
1212		painCave.severity = OPENMD_INFO;
1213		simError();
#	Line 1102 | Line 1215 | namespace OpenMD {
1215		}
1216		}
1217
1218	<	void RNEMD::doShiftScale() {
1219	<
1218	>	void RNEMD::doVSS() {
1219	>	if (!doRNEMD_) return;
1220		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1221	+	RealType time = currentSnap_->getTime();
1222		Mat3x3d hmat = currentSnap_->getHmat();
1223
1224		seleMan_.setSelectionSet(evaluator_.evaluate());
#	Line 1121 | Line 1235 | namespace OpenMD {
1235		Vector3d Pc(V3Zero);
1236		RealType Mc = 0.0;
1237		RealType Kc = 0.0;
1238	+
1239
1240		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1241		sd = seleMan_.nextSelected(selei)) {
#	Line 1135 | Line 1250 | namespace OpenMD {
1250		currentSnap_->wrapVector(pos);
1251
1252		// which bin is this stuntdouble in?
1253	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1254	<
1255	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1256	<
1142	<	// if we're in bin 0 or the middleBin
1143	<	if (binNo == 0 || binNo == midBin_) {
1253	>	bool inA = inSlabA(pos);
1254	>	bool inB = inSlabB(pos);
1255	>
1256	>	if (inA || inB) {
1257
1258		RealType mass = sd->getMass();
1259		Vector3d vel = sd->getVel();
1260
1261	<	if (binNo == 0) {
1261	>	if (inA) {
1262		hotBin.push_back(sd);
1150	–	//std::cerr << "before, velocity = " << vel << endl;
1263		Ph += mass * vel;
1152	–	//std::cerr << "after, velocity = " << vel << endl;
1264		Mh += mass;
1265		Kh += mass * vel.lengthSquare();
1266	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1266	>	if (rnemdFluxType_ == rnemdFullKE) {
1267		if (sd->isDirectional()) {
1268		Vector3d angMom = sd->getJ();
1269		Mat3x3d I = sd->getI();
#	Line 1174 | Line 1285 | namespace OpenMD {
1285		Pc += mass * vel;
1286		Mc += mass;
1287		Kc += mass * vel.lengthSquare();
1288	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1288	>	if (rnemdFluxType_ == rnemdFullKE) {
1289		if (sd->isDirectional()) {
1290		Vector3d angMom = sd->getJ();
1291		Mat3x3d I = sd->getI();
#	Line 1197 | Line 1308 | namespace OpenMD {
1308
1309		Kh *= 0.5;
1310		Kc *= 0.5;
1311	<
1201	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	<	<< "\tKc= " << Kc << endl;
1203	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	<
1311	>
1312		#ifdef IS_MPI
1313		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1314		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
#	Line 1214 | Line 1321 | namespace OpenMD {
1321		bool successfulExchange = false;
1322		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1323		Vector3d vc = Pc / Mc;
1324	<	Vector3d ac = njzp_ / Mc + vc;
1325	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1324	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1325	>	Vector3d acrec = -momentumTarget_ / Mc;
1326	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1327		if (cNumerator > 0.0) {
1328		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1329		if (cDenominator > 0.0) {
1330		RealType c = sqrt(cNumerator / cDenominator);
1331		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1332		Vector3d vh = Ph / Mh;
1333	<	Vector3d ah = jzp_ / Mh + vh;
1334	<	RealType hNumerator = Kh + targetJzKE_
1333	>	Vector3d ah = momentumTarget_ / Mh + vh;
1334	>	Vector3d ahrec = momentumTarget_ / Mh;
1335	>	RealType hNumerator = Kh + kineticTarget_
1336		- 0.5 * Mh * ah.lengthSquare();
1337		if (hNumerator > 0.0) {
1338		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1339		if (hDenominator > 0.0) {
1340		RealType h = sqrt(hNumerator / hDenominator);
1341		if ((h > 0.9) && (h < 1.1)) {
1342	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1342	>
1343		vector<StuntDouble*>::iterator sdi;
1344		Vector3d vel;
1345		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1346		//vel = (*sdi)->getVel();
1347		vel = ((*sdi)->getVel() - vc) * c + ac;
1348		(*sdi)->setVel(vel);
1349	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1349	>	if (rnemdFluxType_ == rnemdFullKE) {
1350		if ((*sdi)->isDirectional()) {
1351		Vector3d angMom = (*sdi)->getJ() * c;
1352		(*sdi)->setJ(angMom);
#	Line 1249 | Line 1357 | namespace OpenMD {
1357		//vel = (*sdi)->getVel();
1358		vel = ((*sdi)->getVel() - vh) * h + ah;
1359		(*sdi)->setVel(vel);
1360	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1360	>	if (rnemdFluxType_ == rnemdFullKE) {
1361		if ((*sdi)->isDirectional()) {
1362		Vector3d angMom = (*sdi)->getJ() * h;
1363		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1365 | namespace OpenMD {
1365		}
1366		}
1367		successfulExchange = true;
1368	<	exchangeSum_ += targetFlux_;
1369	<	// this is a redundant variable for doShiftScale() so that
1262	<	// RNEMD can output one exchange quantity needed in a job.
1263	<	// need a better way to do this.
1368	>	kineticExchange_ += kineticTarget_;
1369	>	momentumExchange_ += momentumTarget_;
1370		}
1371		}
1372		}
#	Line 1270 | Line 1376 | namespace OpenMD {
1376		}
1377		if (successfulExchange != true) {
1378		sprintf(painCave.errMsg,
1379	<	"RNEMD: exchange NOT performed!\n");
1379	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1380	>	"\tthe constraint equations may not exist or there may be\n"
1381	>	"\tno selected objects in one or both slabs.\n");
1382		painCave.isFatal = 0;
1383		painCave.severity = OPENMD_INFO;
1384		simError();
#	Line 1279 | Line 1387 | namespace OpenMD {
1387		}
1388
1389		void RNEMD::doRNEMD() {
1390	<
1391	<	switch(rnemdType_) {
1392	<	case rnemdKineticScale :
1393	<	case rnemdKineticScaleVAM :
1286	<	case rnemdKineticScaleAM :
1287	<	case rnemdPxScale :
1288	<	case rnemdPyScale :
1289	<	case rnemdPzScale :
1290	<	doScale();
1291	<	break;
1292	<	case rnemdKineticSwap :
1293	<	case rnemdPx :
1294	<	case rnemdPy :
1295	<	case rnemdPz :
1390	>	if (!doRNEMD_) return;
1391	>	trialCount_++;
1392	>	switch(rnemdMethod_) {
1393	>	case rnemdSwap:
1394		doSwap();
1395		break;
1396	<	case rnemdShiftScaleV :
1397	<	case rnemdShiftScaleVAM :
1300	<	doShiftScale();
1396	>	case rnemdNIVS:
1397	>	doNIVS();
1398		break;
1399	<	case rnemdUnknown :
1399	>	case rnemdVSS:
1400	>	doVSS();
1401	>	break;
1402	>	case rnemdUnkownMethod:
1403		default :
1404		break;
1405		}
1406		}
1407
1408		void RNEMD::collectData() {
1409	<
1409	>	if (!doRNEMD_) return;
1410		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1411		Mat3x3d hmat = currentSnap_->getHmat();
1412
1413	+	areaAccumulator_->add(currentSnap_->getXYarea());
1414	+
1415		seleMan_.setSelectionSet(evaluator_.evaluate());
1416
1417	<	int selei;
1417	>	int selei(0);
1418		StuntDouble* sd;
1419		int idx;
1420
1421	+	vector<RealType> binMass(nBins_, 0.0);
1422	+	vector<RealType> binPx(nBins_, 0.0);
1423	+	vector<RealType> binPy(nBins_, 0.0);
1424	+	vector<RealType> binPz(nBins_, 0.0);
1425	+	vector<RealType> binKE(nBins_, 0.0);
1426	+	vector<int> binDOF(nBins_, 0);
1427	+	vector<int> binCount(nBins_, 0);
1428	+
1429		// alternative approach, track all molecules instead of only those
1430		// selected for scaling/swapping:
1431		/*
1432		SimInfo::MoleculeIterator miter;
1433		vector<StuntDouble*>::iterator iiter;
1434		Molecule* mol;
1435	<	StuntDouble* integrableObject;
1435	>	StuntDouble* sd;
1436		for (mol = info_->beginMolecule(miter); mol != NULL;
1437	<	mol = info_->nextMolecule(miter))
1438	<	integrableObject is essentially sd
1439	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1440	<	integrableObject != NULL;
1441	<	integrableObject = mol->nextIntegrableObject(iiter))
1437	>	mol = info_->nextMolecule(miter))
1438	>	sd is essentially sd
1439	>	for (sd = mol->beginIntegrableObject(iiter);
1440	>	sd != NULL;
1441	>	sd = mol->nextIntegrableObject(iiter))
1442		*/
1443	+
1444		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1445		sd = seleMan_.nextSelected(selei)) {
1446	<
1446	>
1447		idx = sd->getLocalIndex();
1448
1449		Vector3d pos = sd->getPos();
#	Line 1341 | Line 1452 | namespace OpenMD {
1452
1453		if (usePeriodicBoundaryConditions_)
1454		currentSnap_->wrapVector(pos);
1455	<
1455	>
1456	>
1457		// which bin is this stuntdouble in?
1458		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	<
1460	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1461	<	rnemdLogWidth_;
1462	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1463	<	/*
1352	<	if (rnemdLogWidth_ == midBin_ + 1)
1353	<	if (binNo > midBin_)
1354	<	binNo = nBins_ - binNo;
1355	<	*/
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();
1357	–	mHist_[binNo] += mass;
1465		Vector3d vel = sd->getVel();
1359	–	RealType value;
1360	–	//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()) {
1369	<	int i = sd->linearAxis();
1370	<	int j = (i + 1) % 3;
1371	<	int k = (i + 2) % 3;
1372	<	value += angMom[j] * angMom[j] / I(j, j) +
1373	<	angMom[k] * angMom[k] / I(k, k);
1374	<	tempCount_[binNo] +=2;
1375	<	} else {
1376	<	value += angMom[0] * angMom[0] / I(0, 0) +
1377	<	angMom[1]*angMom[1]/I(1, 1) +
1378	<	angMom[2]*angMom[2]/I(2, 2);
1379	<	tempCount_[binNo] +=3;
1380	<	}
1381	<	}
1382	<	value = value / PhysicalConstants::energyConvert
1383	<	/ PhysicalConstants::kb;//may move to getStatus()
1384	<	tempHist_[binNo] += value;
1385	<	}
1386	<	if (outputVx_) {
1387	<	value = mass * vel[0];
1388	<	//vxzCount_[binNo]++;
1389	<	pxzHist_[binNo] += value;
1390	<	}
1391	<	if (outputVy_) {
1392	<	value = mass * vel[1];
1393	<	//vyzCount_[binNo]++;
1394	<	pyzHist_[binNo] += value;
1395	<	}
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 (output3DTemp_) {
1476	<	value = mass * vel.x() * vel.x();
1477	<	xTempHist_[binNo] += value;
1478	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1479	<	/ PhysicalConstants::kb;
1480	<	yTempHist_[binNo] += value;
1481	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1482	<	/ PhysicalConstants::kb;
1483	<	zTempHist_[binNo] += value;
1484	<	xyzTempCount_[binNo]++;
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 (outputRotTemp_) {
1493	<	if (sd->isDirectional()) {
1494	<	Vector3d angMom = sd->getJ();
1495	<	Mat3x3d I = sd->getI();
1496	<	if (sd->isLinear()) {
1497	<	int i = sd->linearAxis();
1498	<	int j = (i + 1) % 3;
1499	<	int k = (i + 2) % 3;
1500	<	value = angMom[j] * angMom[j] / I(j, j) +
1501	<	angMom[k] * angMom[k] / I(k, k);
1502	<	rotTempCount_[binNo] +=2;
1503	<	} else {
1504	<	value = angMom[0] * angMom[0] / I(0, 0) +
1505	<	angMom[1] * angMom[1] / I(1, 1) +
1506	<	angMom[2] * angMom[2] / I(2, 2);
1507	<	rotTempCount_[binNo] +=3;
1508	<	}
1509	<	}
1426	<	value = value / PhysicalConstants::energyConvert
1427	<	/ PhysicalConstants::kb;//may move to getStatus()
1428	<	rotTempHist_[binNo] += value;
1429	<	}
1492	>	}
1493	>
1494	>	#ifdef IS_MPI
1495	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1496	>	nBins_, MPI::INT, MPI::SUM);
1497	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1498	>	nBins_, MPI::REALTYPE, MPI::SUM);
1499	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1500	>	nBins_, MPI::REALTYPE, MPI::SUM);
1501	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1502	>	nBins_, MPI::REALTYPE, MPI::SUM);
1503	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1504	>	nBins_, MPI::REALTYPE, MPI::SUM);
1505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1506	>	nBins_, MPI::REALTYPE, MPI::SUM);
1507	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1508	>	nBins_, MPI::INT, MPI::SUM);
1509	>	#endif
1510
1511	+	Vector3d vel;
1512	+	RealType den;
1513	+	RealType temp;
1514	+	RealType z;
1515	+	for (int i = 0; i < nBins_; i++) {
1516	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1517	+	vel.x() = binPx[i] / binMass[i];
1518	+	vel.y() = binPy[i] / binMass[i];
1519	+	vel.z() = binPz[i] / binMass[i];
1520	+
1521	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1522	+	/ currentSnap_->getVolume() ;
1523	+
1524	+	if (binCount[i] > 0) {
1525	+	// only add values if there are things to add
1526	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1527	+	PhysicalConstants::energyConvert);
1528	+
1529	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1530	+	if(outputMask_[j]) {
1531	+	switch(j) {
1532	+	case Z:
1533	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1534	+	break;
1535	+	case TEMPERATURE:
1536	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1537	+	break;
1538	+	case VELOCITY:
1539	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1540	+	break;
1541	+	case DENSITY:
1542	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1543	+	break;
1544	+	}
1545	+	}
1546	+	}
1547	+	}
1548		}
1549		}
1550
1551		void RNEMD::getStarted() {
1552	+	if (!doRNEMD_) return;
1553		collectData();
1554	<	/*now can output profile in step 0, but might not be useful;
1437	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	<	Stats& stat = currentSnap_->statData;
1439	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1440	<	*/
1441	<	//may output a header for the log file here
1442	<	getStatus();
1554	>	writeOutputFile();
1555		}
1556
1557	<	void RNEMD::getStatus() {
1558	<
1559	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1560	<	Stats& stat = currentSnap_->statData;
1561	<	RealType time = currentSnap_->getTime();
1562	<
1563	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1564	<	//or to be more meaningful, define another item as exchangeSum_ / time
1565	<	int j;
1566	<
1557	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1558	>	if (!doRNEMD_) return;
1559	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1560	>
1561	>	while(tokenizer.hasMoreTokens()) {
1562	>	std::string token(tokenizer.nextToken());
1563	>	toUpper(token);
1564	>	OutputMapType::iterator i = outputMap_.find(token);
1565	>	if (i != outputMap_.end()) {
1566	>	outputMask_.set(i->second);
1567	>	} else {
1568	>	sprintf( painCave.errMsg,
1569	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1570	>	"\toutputFileFormat keyword.\n", token.c_str() );
1571	>	painCave.isFatal = 0;
1572	>	painCave.severity = OPENMD_ERROR;
1573	>	simError();
1574	>	}
1575	>	}
1576	>	}
1577	>
1578	>	void RNEMD::writeOutputFile() {
1579	>	if (!doRNEMD_) return;
1580	>
1581		#ifdef IS_MPI
1456	–
1457	–	// all processors have the same number of bins, and STL vectors pack their
1458	–	// arrays, so in theory, this should be safe:
1459	–
1460	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1461	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1462	–	if (outputTemp_) {
1463	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1464	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1465	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1466	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1467	–	}
1468	–	if (outputVx_) {
1469	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1470	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1471	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1472	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1473	–	}
1474	–	if (outputVy_) {
1475	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1476	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1477	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1478	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1479	–	}
1480	–	if (output3DTemp_) {
1481	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1482	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1483	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1484	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1485	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1486	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1487	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1488	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1489	–	}
1490	–	if (outputRotTemp_) {
1491	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1492	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1493	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1494	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1495	–	}
1496	–
1582		// If we're the root node, should we print out the results
1583		int worldRank = MPI::COMM_WORLD.Get_rank();
1584		if (worldRank == 0) {
1585		#endif
1586	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1587	+
1588	+	if( !rnemdFile_ ){
1589	+	sprintf( painCave.errMsg,
1590	+	"Could not open \"%s\" for RNEMD output.\n",
1591	+	rnemdFileName_.c_str());
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595
1596	<	if (outputTemp_) {
1597	<	tempLog_ << time;
1598	<	for (j = 0; j < rnemdLogWidth_; j++) {
1599	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1600	<	}
1601	<	tempLog_ << endl;
1596	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1597	>
1598	>	RealType time = currentSnap_->getTime();
1599	>	RealType avgArea;
1600	>	areaAccumulator_->getAverage(avgArea);
1601	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1602	>	/ PhysicalConstants::energyConvert;
1603	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1604	>
1605	>	rnemdFile_ << "#######################################################\n";
1606	>	rnemdFile_ << "# RNEMD {\n";
1607	>
1608	>	map<string, RNEMDMethod>::iterator mi;
1609	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1610	>	if ( (*mi).second == rnemdMethod_)
1611	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1612		}
1613	<	if (outputVx_) {
1614	<	vxzLog_ << time;
1615	<	for (j = 0; j < rnemdLogWidth_; j++) {
1616	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1513	<	}
1514	<	vxzLog_ << endl;
1613	>	map<string, RNEMDFluxType>::iterator fi;
1614	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1615	>	if ( (*fi).second == rnemdFluxType_)
1616	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1617		}
1618	<	if (outputVy_) {
1619	<	vyzLog_ << time;
1518	<	for (j = 0; j < rnemdLogWidth_; j++) {
1519	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
1522	<	}
1618	>
1619	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1620
1621	<	if (output3DTemp_) {
1622	<	RealType temp;
1623	<	xTempLog_ << time;
1624	<	for (j = 0; j < rnemdLogWidth_; j++) {
1625	<	if (outputVx_)
1626	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1627	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1628	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1629	<	xTempLog_ << "\t" << temp;
1621	>	rnemdFile_ << "#    objectSelection = \""
1622	>	<< rnemdObjectSelection_ << "\";\n";
1623	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1624	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1625	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1626	>	rnemdFile_ << "# }\n";
1627	>	rnemdFile_ << "#######################################################\n";
1628	>	rnemdFile_ << "# RNEMD report:\n";
1629	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1630	>	rnemdFile_ << "#     target flux:\n";
1631	>	rnemdFile_ << "#         kinetic = "
1632	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1633	>	<< " (kcal/mol/A^2/fs)\n";
1634	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1635	>	<< " (amu/A/fs^2)\n";
1636	>	rnemdFile_ << "#     target one-time exchanges:\n";
1637	>	rnemdFile_ << "#         kinetic = "
1638	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1639	>	<< " (kcal/mol)\n";
1640	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1641	>	<< " (amu*A/fs)\n";
1642	>	rnemdFile_ << "#     actual exchange totals:\n";
1643	>	rnemdFile_ << "#         kinetic = "
1644	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1645	>	<< " (kcal/mol)\n";
1646	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1647	>	<< " (amu*A/fs)\n";
1648	>	rnemdFile_ << "#     actual flux:\n";
1649	>	rnemdFile_ << "#         kinetic = " << Jz
1650	>	<< " (kcal/mol/A^2/fs)\n";
1651	>	rnemdFile_ << "#         momentum = " << JzP
1652	>	<< " (amu/A/fs^2)\n";
1653	>	rnemdFile_ << "#     exchange statistics:\n";
1654	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1655	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1656	>	if (rnemdMethod_ == rnemdNIVS) {
1657	>	rnemdFile_ << "#         NIVS root-check errors = "
1658	>	<< failRootCount_ << "\n";
1659	>	}
1660	>	rnemdFile_ << "#######################################################\n";
1661	>
1662	>
1663	>
1664	>	//write title
1665	>	rnemdFile_ << "#";
1666	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1667	>	if (outputMask_[i]) {
1668	>	rnemdFile_ << "\t" << data_[i].title <<
1669	>	"(" << data_[i].units << ")";
1670	>	// add some extra tabs for column alignment
1671	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1672		}
1534	–	xTempLog_ << endl;
1535	–	yTempLog_ << time;
1536	–	for (j = 0; j < rnemdLogWidth_; j++) {
1537	–	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1538	–	}
1539	–	yTempLog_ << endl;
1540	–	zTempLog_ << time;
1541	–	for (j = 0; j < rnemdLogWidth_; j++) {
1542	–	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1543	–	}
1544	–	zTempLog_ << endl;
1673		}
1674	<	if (outputRotTemp_) {
1675	<	rotTempLog_ << time;
1676	<	for (j = 0; j < rnemdLogWidth_; j++) {
1677	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1678	<	}
1679	<	rotTempLog_ << endl;
1680	<	}
1674	>	rnemdFile_ << std::endl;
1675	>
1676	>	rnemdFile_.precision(8);
1677	>
1678	>	for (unsigned int j = 0; j < nBins_; j++) {
1679	>
1680	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1681	>	if (outputMask_[i]) {
1682	>	if (data_[i].dataType == "RealType")
1683	>	writeReal(i,j);
1684	>	else if (data_[i].dataType == "Vector3d")
1685	>	writeVector(i,j);
1686	>	else {
1687	>	sprintf( painCave.errMsg,
1688	>	"RNEMD found an unknown data type for: %s ",
1689	>	data_[i].title.c_str());
1690	>	painCave.isFatal = 1;
1691	>	simError();
1692	>	}
1693	>	}
1694	>	}
1695	>	rnemdFile_ << std::endl;
1696	>
1697	>	}
1698
1699	+	rnemdFile_ << "#######################################################\n";
1700	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1701	+	rnemdFile_ << "#######################################################\n";
1702	+
1703	+
1704	+	for (unsigned int j = 0; j < nBins_; j++) {
1705	+	rnemdFile_ << "#";
1706	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1707	+	if (outputMask_[i]) {
1708	+	if (data_[i].dataType == "RealType")
1709	+	writeRealStdDev(i,j);
1710	+	else if (data_[i].dataType == "Vector3d")
1711	+	writeVectorStdDev(i,j);
1712	+	else {
1713	+	sprintf( painCave.errMsg,
1714	+	"RNEMD found an unknown data type for: %s ",
1715	+	data_[i].title.c_str());
1716	+	painCave.isFatal = 1;
1717	+	simError();
1718	+	}
1719	+	}
1720	+	}
1721	+	rnemdFile_ << std::endl;
1722	+
1723	+	}
1724	+
1725	+	rnemdFile_.flush();
1726	+	rnemdFile_.close();
1727	+
1728		#ifdef IS_MPI
1729		}
1730		#endif
1731	<
1732	<	for (j = 0; j < rnemdLogWidth_; j++) {
1733	<	mHist_[j] = 0.0;
1731	>
1732	>	}
1733	>
1734	>	void RNEMD::writeReal(int index, unsigned int bin) {
1735	>	if (!doRNEMD_) return;
1736	>	assert(index >=0 && index < ENDINDEX);
1737	>	assert(bin < nBins_);
1738	>	RealType s;
1739	>
1740	>	data_[index].accumulator[bin]->getAverage(s);
1741	>
1742	>	if (! isinf(s) && ! isnan(s)) {
1743	>	rnemdFile_ << "\t" << s;
1744	>	} else{
1745	>	sprintf( painCave.errMsg,
1746	>	"RNEMD detected a numerical error writing: %s for bin %d",
1747	>	data_[index].title.c_str(), bin);
1748	>	painCave.isFatal = 1;
1749	>	simError();
1750	>	}
1751	>	}
1752	>
1753	>	void RNEMD::writeVector(int index, unsigned int bin) {
1754	>	if (!doRNEMD_) return;
1755	>	assert(index >=0 && index < ENDINDEX);
1756	>	assert(bin < nBins_);
1757	>	Vector3d s;
1758	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1759	>	if (isinf(s[0]) || isnan(s[0]) ||
1760	>	isinf(s[1]) || isnan(s[1]) ||
1761	>	isinf(s[2]) || isnan(s[2]) ) {
1762	>	sprintf( painCave.errMsg,
1763	>	"RNEMD detected a numerical error writing: %s for bin %d",
1764	>	data_[index].title.c_str(), bin);
1765	>	painCave.isFatal = 1;
1766	>	simError();
1767	>	} else {
1768	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1769		}
1770	<	if (outputTemp_)
1562	<	for (j = 0; j < rnemdLogWidth_; j++) {
1563	<	tempCount_[j] = 0;
1564	<	tempHist_[j] = 0.0;
1565	<	}
1566	<	if (outputVx_)
1567	<	for (j = 0; j < rnemdLogWidth_; j++) {
1568	<	//pxzCount_[j] = 0;
1569	<	pxzHist_[j] = 0.0;
1570	<	}
1571	<	if (outputVy_)
1572	<	for (j = 0; j < rnemdLogWidth_; j++) {
1573	<	//pyzCount_[j] = 0;
1574	<	pyzHist_[j] = 0.0;
1575	<	}
1770	>	}
1771
1772	<	if (output3DTemp_)
1773	<	for (j = 0; j < rnemdLogWidth_; j++) {
1774	<	xTempHist_[j] = 0.0;
1775	<	yTempHist_[j] = 0.0;
1776	<	zTempHist_[j] = 0.0;
1777	<	xyzTempCount_[j] = 0;
1778	<	}
1779	<	if (outputRotTemp_)
1780	<	for (j = 0; j < rnemdLogWidth_; j++) {
1781	<	rotTempCount_[j] = 0;
1782	<	rotTempHist_[j] = 0.0;
1783	<	}
1772	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1773	>	if (!doRNEMD_) return;
1774	>	assert(index >=0 && index < ENDINDEX);
1775	>	assert(bin < nBins_);
1776	>	RealType s;
1777	>
1778	>	data_[index].accumulator[bin]->getStdDev(s);
1779	>
1780	>	if (! isinf(s) && ! isnan(s)) {
1781	>	rnemdFile_ << "\t" << s;
1782	>	} else{
1783	>	sprintf( painCave.errMsg,
1784	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1785	>	data_[index].title.c_str(), bin);
1786	>	painCave.isFatal = 1;
1787	>	simError();
1788	>	}
1789		}
1790	+
1791	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1792	+	if (!doRNEMD_) return;
1793	+	assert(index >=0 && index < ENDINDEX);
1794	+	assert(bin < nBins_);
1795	+	Vector3d s;
1796	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1797	+	if (isinf(s[0]) || isnan(s[0]) ||
1798	+	isinf(s[1]) || isnan(s[1]) ||
1799	+	isinf(s[2]) || isnan(s[2]) ) {
1800	+	sprintf( painCave.errMsg,
1801	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1802	+	data_[index].title.c_str(), bin);
1803	+	painCave.isFatal = 1;
1804	+	simError();
1805	+	} else {
1806	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1807	+	}
1808	+	}
1809		}
1810

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