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root/OpenMD/trunk/src/rnemd/RNEMD.cpp

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branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1793 by gezelter, Fri Aug 31 21:16:10 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
56	+	#ifdef _MSC_VER
57	+	#define isnan(x) _isnan((x))
58	+	#define isinf(x) (!_finite(x) && !_isnan(x))
59	+	#endif
60	+
61		#define HONKING_LARGE_VALUE 1.0e10
62
63		using namespace std;
#	Line 65 | Line 66 | namespace OpenMD {
66		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
67		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
68
69	+	trialCount_ = 0;
70		failTrialCount_ = 0;
71		failRootCount_ = 0;
72
71	–	int seedValue;
73		Globals * simParams = info->getSimParams();
74	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
75
76	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
77	<	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;
76	>	doRNEMD_ = rnemdParams->getUseRNEMD();
77	>	if (!doRNEMD_) return;
78
79	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
79	>	stringToMethod_["Swap"]  = rnemdSwap;
80	>	stringToMethod_["NIVS"]  = rnemdNIVS;
81	>	stringToMethod_["VSS"]   = rnemdVSS;
82	>
83	>	stringToFluxType_["KE"]  = rnemdKE;
84	>	stringToFluxType_["Px"]  = rnemdPx;
85	>	stringToFluxType_["Py"]  = rnemdPy;
86	>	stringToFluxType_["Pz"]  = rnemdPz;
87	>	stringToFluxType_["Pvector"]  = rnemdPvector;
88	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
89	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
90	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
91	>
92	>	runTime_ = simParams->getRunTime();
93	>	statusTime_ = simParams->getStatusTime();
94	>
95	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
96		evaluator_.loadScriptString(rnemdObjectSelection_);
97		seleMan_.setSelectionSet(evaluator_.evaluate());
98	+
99	+	const string methStr = rnemdParams->getMethod();
100	+	bool hasFluxType = rnemdParams->haveFluxType();
101	+
102	+	string fluxStr;
103	+	if (hasFluxType) {
104	+	fluxStr = rnemdParams->getFluxType();
105	+	} else {
106	+	sprintf(painCave.errMsg,
107	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
108	+	"\twhich must be one of the following values:\n"
109	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
110	+	"\tmust be set to use RNEMD\n");
111	+	painCave.isFatal = 1;
112	+	painCave.severity = OPENMD_ERROR;
113	+	simError();
114	+	}
115	+
116	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
117	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
118	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
119	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
120	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
121	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
122	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
123	+	bool hasOutputFields = rnemdParams->haveOutputFields();
124	+
125	+	map<string, RNEMDMethod>::iterator i;
126	+	i = stringToMethod_.find(methStr);
127	+	if (i != stringToMethod_.end())
128	+	rnemdMethod_ = i->second;
129	+	else {
130	+	sprintf(painCave.errMsg,
131	+	"RNEMD: The current method,\n"
132	+	"\t\t%s is not one of the recognized\n"
133	+	"\texchange methods: Swap, NIVS, or VSS\n",
134	+	methStr.c_str());
135	+	painCave.isFatal = 1;
136	+	painCave.severity = OPENMD_ERROR;
137	+	simError();
138	+	}
139	+
140	+	map<string, RNEMDFluxType>::iterator j;
141	+	j = stringToFluxType_.find(fluxStr);
142	+	if (j != stringToFluxType_.end())
143	+	rnemdFluxType_ = j->second;
144	+	else {
145	+	sprintf(painCave.errMsg,
146	+	"RNEMD: The current fluxType,\n"
147	+	"\t\t%s\n"
148	+	"\tis not one of the recognized flux types.\n",
149	+	fluxStr.c_str());
150	+	painCave.isFatal = 1;
151	+	painCave.severity = OPENMD_ERROR;
152	+	simError();
153	+	}
154	+
155	+	bool methodFluxMismatch = false;
156	+	bool hasCorrectFlux = false;
157	+	switch(rnemdMethod_) {
158	+	case rnemdSwap:
159	+	switch (rnemdFluxType_) {
160	+	case rnemdKE:
161	+	hasCorrectFlux = hasKineticFlux;
162	+	break;
163	+	case rnemdPx:
164	+	case rnemdPy:
165	+	case rnemdPz:
166	+	hasCorrectFlux = hasMomentumFlux;
167	+	break;
168	+	default :
169	+	methodFluxMismatch = true;
170	+	break;
171	+	}
172	+	break;
173	+	case rnemdNIVS:
174	+	switch (rnemdFluxType_) {
175	+	case rnemdKE:
176	+	case rnemdRotKE:
177	+	case rnemdFullKE:
178	+	hasCorrectFlux = hasKineticFlux;
179	+	break;
180	+	case rnemdPx:
181	+	case rnemdPy:
182	+	case rnemdPz:
183	+	hasCorrectFlux = hasMomentumFlux;
184	+	break;
185	+	case rnemdKePx:
186	+	case rnemdKePy:
187	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
188	+	break;
189	+	default:
190	+	methodFluxMismatch = true;
191	+	break;
192	+	}
193	+	break;
194	+	case rnemdVSS:
195	+	switch (rnemdFluxType_) {
196	+	case rnemdKE:
197	+	case rnemdRotKE:
198	+	case rnemdFullKE:
199	+	hasCorrectFlux = hasKineticFlux;
200	+	break;
201	+	case rnemdPx:
202	+	case rnemdPy:
203	+	case rnemdPz:
204	+	hasCorrectFlux = hasMomentumFlux;
205	+	break;
206	+	case rnemdPvector:
207	+	hasCorrectFlux = hasMomentumFluxVector;
208	+	break;
209	+	case rnemdKePx:
210	+	case rnemdKePy:
211	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
212	+	break;
213	+	case rnemdKePvector:
214	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
215	+	break;
216	+	default:
217	+	methodFluxMismatch = true;
218	+	break;
219	+	}
220	+	default:
221	+	break;
222	+	}
223	+
224	+	if (methodFluxMismatch) {
225	+	sprintf(painCave.errMsg,
226	+	"RNEMD: The current method,\n"
227	+	"\t\t%s\n"
228	+	"\tcannot be used with the current flux type, %s\n",
229	+	methStr.c_str(), fluxStr.c_str());
230	+	painCave.isFatal = 1;
231	+	painCave.severity = OPENMD_ERROR;
232	+	simError();
233	+	}
234	+	if (!hasCorrectFlux) {
235	+	sprintf(painCave.errMsg,
236	+	"RNEMD: The current method, %s, and flux type, %s,\n"
237	+	"\tdid not have the correct flux value specified. Options\n"
238	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
239	+	methStr.c_str(), fluxStr.c_str());
240	+	painCave.isFatal = 1;
241	+	painCave.severity = OPENMD_ERROR;
242	+	simError();
243	+	}
244
245	+	if (hasKineticFlux) {
246	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
247	+	// into  amu / fs^3:
248	+	kineticFlux_ = rnemdParams->getKineticFlux()
249	+	* PhysicalConstants::energyConvert;
250	+	} else {
251	+	kineticFlux_ = 0.0;
252	+	}
253	+	if (hasMomentumFluxVector) {
254	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
255	+	} else {
256	+	momentumFluxVector_ = V3Zero;
257	+	if (hasMomentumFlux) {
258	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
259	+	switch (rnemdFluxType_) {
260	+	case rnemdPx:
261	+	momentumFluxVector_.x() = momentumFlux;
262	+	break;
263	+	case rnemdPy:
264	+	momentumFluxVector_.y() = momentumFlux;
265	+	break;
266	+	case rnemdPz:
267	+	momentumFluxVector_.z() = momentumFlux;
268	+	break;
269	+	case rnemdKePx:
270	+	momentumFluxVector_.x() = momentumFlux;
271	+	break;
272	+	case rnemdKePy:
273	+	momentumFluxVector_.y() = momentumFlux;
274	+	break;
275	+	default:
276	+	break;
277	+	}
278	+	}
279	+	}
280	+
281		// do some sanity checking
282
283		int selectionCount = seleMan_.getSelectionCount();
#	Line 96 | Line 285 | namespace OpenMD {
285
286		if (selectionCount > nIntegrable) {
287		sprintf(painCave.errMsg,
288	<	"RNEMD: The current RNEMD_objectSelection,\n"
288	>	"RNEMD: The current objectSelection,\n"
289		"\t\t%s\n"
290		"\thas resulted in %d selected objects.  However,\n"
291		"\tthe total number of integrable objects in the system\n"
#	Line 109 | Line 298 | namespace OpenMD {
298		painCave.severity = OPENMD_WARNING;
299		simError();
300		}
112	–
113	–	const string st = simParams->getRNEMD_exchangeType();
301
302	<	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	<	}
302	>	areaAccumulator_ = new Accumulator();
303
304	<	#ifdef IS_MPI
160	<	if (worldRank == 0) {
161	<	#endif
304	>	nBins_ = rnemdParams->getOutputBins();
305
306	<	//may have rnemdWriter separately
307	<	string rnemdFileName;
306	>	data_.resize(RNEMD::ENDINDEX);
307	>	OutputData z;
308	>	z.units =  "Angstroms";
309	>	z.title =  "Z";
310	>	z.dataType = "RealType";
311	>	z.accumulator.reserve(nBins_);
312	>	for (int i = 0; i < nBins_; i++)
313	>	z.accumulator.push_back( new Accumulator() );
314	>	data_[Z] = z;
315	>	outputMap_["Z"] =  Z;
316
317	<	if (outputTemp_) {
318	<	rnemdFileName = "temperature.log";
319	<	tempLog_.open(rnemdFileName.c_str());
320	<	}
321	<	if (outputVx_) {
322	<	rnemdFileName = "velocityX.log";
323	<	vxzLog_.open(rnemdFileName.c_str());
324	<	}
325	<	if (outputVy_) {
175	<	rnemdFileName = "velocityY.log";
176	<	vyzLog_.open(rnemdFileName.c_str());
177	<	}
317	>	OutputData temperature;
318	>	temperature.units =  "K";
319	>	temperature.title =  "Temperature";
320	>	temperature.dataType = "RealType";
321	>	temperature.accumulator.reserve(nBins_);
322	>	for (int i = 0; i < nBins_; i++)
323	>	temperature.accumulator.push_back( new Accumulator() );
324	>	data_[TEMPERATURE] = temperature;
325	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
326
327	<	if (output3DTemp_) {
328	<	rnemdFileName = "temperatureX.log";
329	<	xTempLog_.open(rnemdFileName.c_str());
330	<	rnemdFileName = "temperatureY.log";
331	<	yTempLog_.open(rnemdFileName.c_str());
332	<	rnemdFileName = "temperatureZ.log";
333	<	zTempLog_.open(rnemdFileName.c_str());
334	<	}
335	<	if (outputRotTemp_) {
188	<	rnemdFileName = "temperatureR.log";
189	<	rotTempLog_.open(rnemdFileName.c_str());
190	<	}
327	>	OutputData velocity;
328	>	velocity.units = "angstroms/fs";
329	>	velocity.title =  "Velocity";
330	>	velocity.dataType = "Vector3d";
331	>	velocity.accumulator.reserve(nBins_);
332	>	for (int i = 0; i < nBins_; i++)
333	>	velocity.accumulator.push_back( new VectorAccumulator() );
334	>	data_[VELOCITY] = velocity;
335	>	outputMap_["VELOCITY"] = VELOCITY;
336
337	<	#ifdef IS_MPI
338	<	}
339	<	#endif
337	>	OutputData density;
338	>	density.units =  "g cm^-3";
339	>	density.title =  "Density";
340	>	density.dataType = "RealType";
341	>	density.accumulator.reserve(nBins_);
342	>	for (int i = 0; i < nBins_; i++)
343	>	density.accumulator.push_back( new Accumulator() );
344	>	data_[DENSITY] = density;
345	>	outputMap_["DENSITY"] =  DENSITY;
346
347	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
348	<	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	<	}
347	>	if (hasOutputFields) {
348	>	parseOutputFileFormat(rnemdParams->getOutputFields());
349		} else {
350	<	zShift_ = 0.0;
351	<	}
352	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
353	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
354	<	//set to 0.0 if not using it; N/A in status output yet
355	<	if (simParams->haveRNEMD_logWidth()) {
356	<	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
357	<	/*arbitary rnemdLogWidth_, no checking;
358	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
359	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
360	<	cerr << "Automaically set back to default.\n";
361	<	rnemdLogWidth_ = nBins_;
362	<	}*/
363	<	} else {
364	<	set_RNEMD_logWidth(nBins_);
350	>	outputMask_.set(Z);
351	>	switch (rnemdFluxType_) {
352	>	case rnemdKE:
353	>	case rnemdRotKE:
354	>	case rnemdFullKE:
355	>	outputMask_.set(TEMPERATURE);
356	>	break;
357	>	case rnemdPx:
358	>	case rnemdPy:
359	>	outputMask_.set(VELOCITY);
360	>	break;
361	>	case rnemdPz:
362	>	case rnemdPvector:
363	>	outputMask_.set(VELOCITY);
364	>	outputMask_.set(DENSITY);
365	>	break;
366	>	case rnemdKePx:
367	>	case rnemdKePy:
368	>	outputMask_.set(TEMPERATURE);
369	>	outputMask_.set(VELOCITY);
370	>	break;
371	>	case rnemdKePvector:
372	>	outputMask_.set(TEMPERATURE);
373	>	outputMask_.set(VELOCITY);
374	>	outputMask_.set(DENSITY);
375	>	break;
376	>	default:
377	>	break;
378	>	}
379		}
380	<	tempHist_.resize(rnemdLogWidth_, 0.0);
381	<	tempCount_.resize(rnemdLogWidth_, 0);
382	<	pxzHist_.resize(rnemdLogWidth_, 0.0);
383	<	//vxzCount_.resize(rnemdLogWidth_, 0);
384	<	pyzHist_.resize(rnemdLogWidth_, 0.0);
385	<	//vyzCount_.resize(rnemdLogWidth_, 0);
380	>
381	>	if (hasOutputFileName) {
382	>	rnemdFileName_ = rnemdParams->getOutputFileName();
383	>	} else {
384	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
385	>	}
386
387	<	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);
387	>	exchangeTime_ = rnemdParams->getExchangeTime();
388
389	<	set_RNEMD_exchange_total(0.0);
390	<	if (simParams->haveRNEMD_targetFlux()) {
391	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
392	<	} else {
393	<	set_RNEMD_target_flux(0.0);
394	<	}
395	<	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_;
389	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
390	>	Mat3x3d hmat = currentSnap_->getHmat();
391	>
392	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
393	>	// Lx, Ly = box dimensions in x & y
394	>	// dt = exchange time interval
395	>	// flux = target flux
396
397	<	#ifndef IS_MPI
398	<	if (simParams->haveSeed()) {
399	<	seedValue = simParams->getSeed();
400	<	randNumGen_ = new SeqRandNumGen(seedValue);
401	<	}else {
402	<	randNumGen_ = new SeqRandNumGen();
403	<	}
404	<	#else
405	<	if (simParams->haveSeed()) {
406	<	seedValue = simParams->getSeed();
407	<	randNumGen_ = new ParallelRandNumGen(seedValue);
408	<	}else {
409	<	randNumGen_ = new ParallelRandNumGen();
283	<	}
284	<	#endif
285	<	}
397	>	RealType area = currentSnap_->getXYarea();
398	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
399	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
400	>
401	>	// total exchange sums are zeroed out at the beginning:
402	>
403	>	kineticExchange_ = 0.0;
404	>	momentumExchange_ = V3Zero;
405	>
406	>	if (hasSlabWidth)
407	>	slabWidth_ = rnemdParams->getSlabWidth();
408	>	else
409	>	slabWidth_ = hmat(2,2) / 10.0;
410
411	<	RNEMD::~RNEMD() {
412	<	delete randNumGen_;
411	>	if (hasSlabACenter)
412	>	slabACenter_ = rnemdParams->getSlabACenter();
413	>	else
414	>	slabACenter_ = 0.0;
415
416	+	if (hasSlabBCenter)
417	+	slabBCenter_ = rnemdParams->getSlabBCenter();
418	+	else
419	+	slabBCenter_ = hmat(2,2) / 2.0;
420	+
421	+	}
422	+
423	+	RNEMD::~RNEMD() {
424	+	if (!doRNEMD_) return;
425		#ifdef IS_MPI
426		if (worldRank == 0) {
427		#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();
428
429	<	if (outputTemp_) tempLog_.close();
302	<	if (outputVx_)   vxzLog_.close();
303	<	if (outputVy_)   vyzLog_.close();
429	>	writeOutputFile();
430
431	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
432	<	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	<
431	>	rnemdFile_.close();
432	>
433		#ifdef IS_MPI
434		}
435		#endif
436		}
437	+
438	+	bool RNEMD::inSlabA(Vector3d pos) {
439	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
440	+	}
441	+	bool RNEMD::inSlabB(Vector3d pos) {
442	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
443	+	}
444
445		void RNEMD::doSwap() {
446	<
446	>	if (!doRNEMD_) return;
447		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
448		Mat3x3d hmat = currentSnap_->getHmat();
449
#	Line 332 | Line 451 | namespace OpenMD {
451
452		int selei;
453		StuntDouble* sd;
335	–	int idx;
454
455		RealType min_val;
456		bool min_found = false;
#	Line 345 | Line 463 | namespace OpenMD {
463		for (sd = seleMan_.beginSelected(selei); sd != NULL;
464		sd = seleMan_.nextSelected(selei)) {
465
348	–	idx = sd->getLocalIndex();
349	–
466		Vector3d pos = sd->getPos();
467
468		// wrap the stuntdouble's position back into the box:
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_;
472	>	bool inA = inSlabA(pos);
473	>	bool inB = inSlabB(pos);
474
475	<
363	<	// 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	<
543	<	#ifdef IS_MPI
544	<	int nProc, worldRank;
545	<
438	<	nProc = MPI::COMM_WORLD.Get_size();
439	<	worldRank = MPI::COMM_WORLD.Get_rank();
440	<
542	>
543	>	#ifdef IS_MPI
544	>	int worldRank = MPI::COMM_WORLD.Get_rank();
545	>
546		bool my_min_found = min_found;
547		bool my_max_found = max_found;
548
#	Line 454 | Line 559 | namespace OpenMD {
559		RealType val;
560		int rank;
561		} max_vals, min_vals;
562	<
562	>
563		if (my_min_found) {
564		min_vals.val = min_val;
565		} else {
#	Line 492 | Line 597 | namespace OpenMD {
597		Vector3d max_vel = max_sd->getVel();
598		RealType temp_vel;
599
600	<	switch(rnemdType_) {
601	<	case rnemdKineticSwap :
600	>	switch(rnemdFluxType_) {
601	>	case rnemdKE :
602		min_sd->setVel(max_vel);
603		max_sd->setVel(min_vel);
604		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 544 | Line 649 | namespace OpenMD {
649		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
650		min_vals.rank, 0, status);
651
652	<	switch(rnemdType_) {
653	<	case rnemdKineticSwap :
652	>	switch(rnemdFluxType_) {
653	>	case rnemdKE :
654		max_sd->setVel(min_vel);
655		//angular momenta exchange enabled
656		if (max_sd->isDirectional()) {
#	Line 590 | Line 695 | namespace OpenMD {
695		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
696		max_vals.rank, 0, status);
697
698	<	switch(rnemdType_) {
699	<	case rnemdKineticSwap :
698	>	switch(rnemdFluxType_) {
699	>	case rnemdKE :
700		min_sd->setVel(max_vel);
701		//angular momenta exchange enabled
702		if (min_sd->isDirectional()) {
#	Line 625 | Line 730 | namespace OpenMD {
730		}
731		}
732		#endif
733	<	exchangeSum_ += max_val - min_val;
733	>
734	>	switch(rnemdFluxType_) {
735	>	case rnemdKE:
736	>	kineticExchange_ += max_val - min_val;
737	>	break;
738	>	case rnemdPx:
739	>	momentumExchange_.x() += max_val - min_val;
740	>	break;
741	>	case rnemdPy:
742	>	momentumExchange_.y() += max_val - min_val;
743	>	break;
744	>	case rnemdPz:
745	>	momentumExchange_.z() += max_val - min_val;
746	>	break;
747	>	default:
748	>	break;
749	>	}
750		} else {
751		sprintf(painCave.errMsg,
752	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
752	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
753		painCave.isFatal = 0;
754		painCave.severity = OPENMD_INFO;
755		simError();
#	Line 636 | Line 757 | namespace OpenMD {
757		}
758		} else {
759		sprintf(painCave.errMsg,
760	<	"RNEMD: exchange NOT performed because selected object\n"
761	<	"\tnot present in at least one of the two slabs.\n");
760	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
761	>	"\twas not present in at least one of the two slabs.\n");
762		painCave.isFatal = 0;
763		painCave.severity = OPENMD_INFO;
764		simError();
765		failTrialCount_++;
766	<	}
646	<
766	>	}
767		}
768
769	<	void RNEMD::doScale() {
770	<
769	>	void RNEMD::doNIVS() {
770	>	if (!doRNEMD_) return;
771		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
772		Mat3x3d hmat = currentSnap_->getHmat();
773
#	Line 655 | Line 775 | namespace OpenMD {
775
776		int selei;
777		StuntDouble* sd;
658	–	int idx;
778
779		vector<StuntDouble*> hotBin, coldBin;
780
#	Line 677 | Line 796 | namespace OpenMD {
796		for (sd = seleMan_.beginSelected(selei); sd != NULL;
797		sd = seleMan_.nextSelected(selei)) {
798
680	–	idx = sd->getLocalIndex();
681	–
799		Vector3d pos = sd->getPos();
800
801		// wrap the stuntdouble's position back into the box:
#	Line 687 | 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	<
694	<	// if we're in bin 0 or the middleBin
695	<	if (binNo == 0 || binNo == midBin_) {
696	<
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 705 | 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();
708	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
823		if (sd->isDirectional()) {
824		Vector3d angMom = sd->getJ();
825		Mat3x3d I = sd->getI();
#	Line 721 | Line 835 | namespace OpenMD {
835		+ angMom[2]*angMom[2]/I(2, 2);
836		}
837		}
838	<	//}
725	<	} else { //midBin_
838	>	} else {
839		coldBin.push_back(sd);
840		Pcx += mass * vel.x();
841		Pcy += mass * vel.y();
#	Line 730 | 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();
733	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
846		if (sd->isDirectional()) {
847		Vector3d angMom = sd->getJ();
848		Mat3x3d I = sd->getI();
#	Line 746 | Line 858 | namespace OpenMD {
858		+ angMom[2]*angMom[2]/I(2, 2);
859		}
860		}
749	–	//}
861		}
862		}
863		}
#	Line 760 | Line 871 | namespace OpenMD {
871		Kcz *= 0.5;
872		Kcw *= 0.5;
873
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	–
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 791 | 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 820 | 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;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
942		(*sdi)->setVel(vel);
943		}
944		if ((*sdi)->isDirectional()) {
945		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//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 859 | Line 959 | namespace OpenMD {
959		}
960		if ((*sdi)->isDirectional()) {
961		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//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 908 | 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 920 | 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 1006 | 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 1034 | 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 1089 | 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 1102 | Line 1212 | namespace OpenMD {
1212		}
1213		}
1214
1215	<	void RNEMD::doShiftScale() {
1216	<
1215	>	void RNEMD::doVSS() {
1216	>	if (!doRNEMD_) return;
1217		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1218	+	RealType time = currentSnap_->getTime();
1219		Mat3x3d hmat = currentSnap_->getHmat();
1220
1221		seleMan_.setSelectionSet(evaluator_.evaluate());
1222
1223		int selei;
1224		StuntDouble* sd;
1114	–	int idx;
1225
1226		vector<StuntDouble*> hotBin, coldBin;
1227
#	Line 1121 | Line 1231 | namespace OpenMD {
1231		Vector3d Pc(V3Zero);
1232		RealType Mc = 0.0;
1233		RealType Kc = 0.0;
1234	+
1235
1236		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1237		sd = seleMan_.nextSelected(selei)) {
1238
1128	–	idx = sd->getLocalIndex();
1129	–
1239		Vector3d pos = sd->getPos();
1240
1241		// wrap the stuntdouble's position back into the box:
#	Line 1135 | Line 1244 | namespace OpenMD {
1244		currentSnap_->wrapVector(pos);
1245
1246		// which bin is this stuntdouble in?
1247	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1248	<
1249	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1250	<
1142	<	// if we're in bin 0 or the middleBin
1143	<	if (binNo == 0 || binNo == midBin_) {
1247	>	bool inA = inSlabA(pos);
1248	>	bool inB = inSlabB(pos);
1249	>
1250	>	if (inA || inB) {
1251
1252		RealType mass = sd->getMass();
1253		Vector3d vel = sd->getVel();
1254
1255	<	if (binNo == 0) {
1255	>	if (inA) {
1256		hotBin.push_back(sd);
1257		//std::cerr << "before, velocity = " << vel << endl;
1258		Ph += mass * vel;
1259		//std::cerr << "after, velocity = " << vel << endl;
1260		Mh += mass;
1261		Kh += mass * vel.lengthSquare();
1262	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1262	>	if (rnemdFluxType_ == rnemdFullKE) {
1263		if (sd->isDirectional()) {
1264		Vector3d angMom = sd->getJ();
1265		Mat3x3d I = sd->getI();
#	Line 1174 | Line 1281 | namespace OpenMD {
1281		Pc += mass * vel;
1282		Mc += mass;
1283		Kc += mass * vel.lengthSquare();
1284	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1284	>	if (rnemdFluxType_ == rnemdFullKE) {
1285		if (sd->isDirectional()) {
1286		Vector3d angMom = sd->getJ();
1287		Mat3x3d I = sd->getI();
#	Line 1198 | Line 1305 | namespace OpenMD {
1305		Kh *= 0.5;
1306		Kc *= 0.5;
1307
1308	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1309	<	<< "\tKc= " << Kc << endl;
1310	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1311	<
1308	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1309	>	//        << "\tKc= " << Kc << endl;
1310	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
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";
1343	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1342	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1343	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1344		vector<StuntDouble*>::iterator sdi;
1345		Vector3d vel;
1346		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1347		//vel = (*sdi)->getVel();
1348		vel = ((*sdi)->getVel() - vc) * c + ac;
1349		(*sdi)->setVel(vel);
1350	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1350	>	if (rnemdFluxType_ == rnemdFullKE) {
1351		if ((*sdi)->isDirectional()) {
1352		Vector3d angMom = (*sdi)->getJ() * c;
1353		(*sdi)->setJ(angMom);
#	Line 1249 | Line 1358 | namespace OpenMD {
1358		//vel = (*sdi)->getVel();
1359		vel = ((*sdi)->getVel() - vh) * h + ah;
1360		(*sdi)->setVel(vel);
1361	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1361	>	if (rnemdFluxType_ == rnemdFullKE) {
1362		if ((*sdi)->isDirectional()) {
1363		Vector3d angMom = (*sdi)->getJ() * h;
1364		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1366 | namespace OpenMD {
1366		}
1367		}
1368		successfulExchange = true;
1369	<	exchangeSum_ += targetFlux_;
1370	<	// 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.
1369	>	kineticExchange_ += kineticTarget_;
1370	>	momentumExchange_ += momentumTarget_;
1371		}
1372		}
1373		}
#	Line 1270 | Line 1377 | namespace OpenMD {
1377		}
1378		if (successfulExchange != true) {
1379		sprintf(painCave.errMsg,
1380	<	"RNEMD: exchange NOT performed!\n");
1380	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1381	>	"\tthe constraint equations may not exist or there may be\n"
1382	>	"\tno selected objects in one or both slabs.\n");
1383		painCave.isFatal = 0;
1384		painCave.severity = OPENMD_INFO;
1385		simError();
#	Line 1279 | Line 1388 | namespace OpenMD {
1388		}
1389
1390		void RNEMD::doRNEMD() {
1391	<
1392	<	switch(rnemdType_) {
1393	<	case rnemdKineticScale :
1394	<	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 :
1391	>	if (!doRNEMD_) return;
1392	>	trialCount_++;
1393	>	switch(rnemdMethod_) {
1394	>	case rnemdSwap:
1395		doSwap();
1396		break;
1397	<	case rnemdShiftScaleV :
1398	<	case rnemdShiftScaleVAM :
1300	<	doShiftScale();
1397	>	case rnemdNIVS:
1398	>	doNIVS();
1399		break;
1400	<	case rnemdUnknown :
1400	>	case rnemdVSS:
1401	>	doVSS();
1402	>	break;
1403	>	case rnemdUnkownMethod:
1404		default :
1405		break;
1406		}
1407		}
1408
1409		void RNEMD::collectData() {
1410	<
1410	>	if (!doRNEMD_) return;
1411		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1412		Mat3x3d hmat = currentSnap_->getHmat();
1413
1414	+	areaAccumulator_->add(currentSnap_->getXYarea());
1415	+
1416		seleMan_.setSelectionSet(evaluator_.evaluate());
1417
1418		int selei;
1419		StuntDouble* sd;
1317	–	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		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1444	<	sd = seleMan_.nextSelected(selei)) {
1444	>	sd = seleMan_.nextSelected(selei)) {
1445
1336	–	idx = sd->getLocalIndex();
1337	–
1446		Vector3d pos = sd->getPos();
1447
1448		// wrap the stuntdouble's position back into the box:
1449
1450		if (usePeriodicBoundaryConditions_)
1451		currentSnap_->wrapVector(pos);
1452	<
1452	>
1453	>
1454		// which bin is this stuntdouble in?
1455		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1456	<
1457	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1458	<	rnemdLogWidth_;
1459	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1460	<	/*
1461	<	if (rnemdLogWidth_ == midBin_ + 1)
1462	<	if (binNo > midBin_)
1354	<	binNo = nBins_ - binNo;
1355	<	*/
1356	<	RealType mass = sd->getMass();
1357	<	mHist_[binNo] += mass;
1358	<	Vector3d vel = sd->getVel();
1359	<	RealType value;
1360	<	//RealType xVal, yVal, zVal;
1456	>	// Shift molecules by half a box to have bins start at 0
1457	>	// The modulo operator is used to wrap the case when we are
1458	>	// beyond the end of the bins back to the beginning.
1459	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1460	>
1461	>	RealType mass = sd->getMass();
1462	>	Vector3d vel = sd->getVel();
1463
1464	<	if (outputTemp_) {
1465	<	value = mass * vel.lengthSquare();
1466	<	tempCount_[binNo] += 3;
1467	<	if (sd->isDirectional()) {
1468	<	Vector3d angMom = sd->getJ();
1469	<	Mat3x3d I = sd->getI();
1470	<	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	<	}
1464	>	binCount[binNo]++;
1465	>	binMass[binNo] += mass;
1466	>	binPx[binNo] += mass*vel.x();
1467	>	binPy[binNo] += mass*vel.y();
1468	>	binPz[binNo] += mass*vel.z();
1469	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1470	>	binDOF[binNo] += 3;
1471
1472	<	if (output3DTemp_) {
1473	<	value = mass * vel.x() * vel.x();
1474	<	xTempHist_[binNo] += value;
1475	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1476	<	/ PhysicalConstants::kb;
1477	<	yTempHist_[binNo] += value;
1478	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1479	<	/ PhysicalConstants::kb;
1480	<	zTempHist_[binNo] += value;
1481	<	xyzTempCount_[binNo]++;
1472	>	if (sd->isDirectional()) {
1473	>	Vector3d angMom = sd->getJ();
1474	>	Mat3x3d I = sd->getI();
1475	>	if (sd->isLinear()) {
1476	>	int i = sd->linearAxis();
1477	>	int j = (i + 1) % 3;
1478	>	int k = (i + 2) % 3;
1479	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1480	>	angMom[k] * angMom[k] / I(k, k));
1481	>	binDOF[binNo] += 2;
1482	>	} else {
1483	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1484	>	angMom[1] * angMom[1] / I(1, 1) +
1485	>	angMom[2] * angMom[2] / I(2, 2));
1486	>	binDOF[binNo] += 3;
1487	>	}
1488		}
1489	<	if (outputRotTemp_) {
1490	<	if (sd->isDirectional()) {
1410	<	Vector3d angMom = sd->getJ();
1411	<	Mat3x3d I = sd->getI();
1412	<	if (sd->isLinear()) {
1413	<	int i = sd->linearAxis();
1414	<	int j = (i + 1) % 3;
1415	<	int k = (i + 2) % 3;
1416	<	value = angMom[j] * angMom[j] / I(j, j) +
1417	<	angMom[k] * angMom[k] / I(k, k);
1418	<	rotTempCount_[binNo] +=2;
1419	<	} else {
1420	<	value = angMom[0] * angMom[0] / I(0, 0) +
1421	<	angMom[1] * angMom[1] / I(1, 1) +
1422	<	angMom[2] * angMom[2] / I(2, 2);
1423	<	rotTempCount_[binNo] +=3;
1424	<	}
1425	<	}
1426	<	value = value / PhysicalConstants::energyConvert
1427	<	/ PhysicalConstants::kb;//may move to getStatus()
1428	<	rotTempHist_[binNo] += value;
1429	<	}
1489	>	}
1490	>
1491
1492	+	#ifdef IS_MPI
1493	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1494	+	nBins_, MPI::INT, MPI::SUM);
1495	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1496	+	nBins_, MPI::REALTYPE, MPI::SUM);
1497	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1498	+	nBins_, MPI::REALTYPE, MPI::SUM);
1499	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1500	+	nBins_, MPI::REALTYPE, MPI::SUM);
1501	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1502	+	nBins_, MPI::REALTYPE, MPI::SUM);
1503	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1504	+	nBins_, MPI::REALTYPE, MPI::SUM);
1505	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1506	+	nBins_, MPI::INT, MPI::SUM);
1507	+	#endif
1508	+
1509	+	Vector3d vel;
1510	+	RealType den;
1511	+	RealType temp;
1512	+	RealType z;
1513	+	for (int i = 0; i < nBins_; i++) {
1514	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1515	+	vel.x() = binPx[i] / binMass[i];
1516	+	vel.y() = binPy[i] / binMass[i];
1517	+	vel.z() = binPz[i] / binMass[i];
1518	+
1519	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1520	+	/ currentSnap_->getVolume() ;
1521	+
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	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1530	+	break;
1531	+	case TEMPERATURE:
1532	+	dynamic_cast<Accumulator *>(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	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1539	+	break;
1540	+	}
1541	+	}
1542	+	}
1543		}
1544		}
1545
1546		void RNEMD::getStarted() {
1547	+	if (!doRNEMD_) return;
1548		collectData();
1549	<	/*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();
1549	>	writeOutputFile();
1550		}
1551
1552	<	void RNEMD::getStatus() {
1553	<
1554	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1555	<	Stats& stat = currentSnap_->statData;
1556	<	RealType time = currentSnap_->getTime();
1557	<
1558	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1559	<	//or to be more meaningful, define another item as exchangeSum_ / time
1560	<	int j;
1561	<
1552	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1553	>	if (!doRNEMD_) return;
1554	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1555	>
1556	>	while(tokenizer.hasMoreTokens()) {
1557	>	std::string token(tokenizer.nextToken());
1558	>	toUpper(token);
1559	>	OutputMapType::iterator i = outputMap_.find(token);
1560	>	if (i != outputMap_.end()) {
1561	>	outputMask_.set(i->second);
1562	>	} else {
1563	>	sprintf( painCave.errMsg,
1564	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1565	>	"\toutputFileFormat keyword.\n", token.c_str() );
1566	>	painCave.isFatal = 0;
1567	>	painCave.severity = OPENMD_ERROR;
1568	>	simError();
1569	>	}
1570	>	}
1571	>	}
1572	>
1573	>	void RNEMD::writeOutputFile() {
1574	>	if (!doRNEMD_) return;
1575	>
1576		#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	–
1577		// If we're the root node, should we print out the results
1578		int worldRank = MPI::COMM_WORLD.Get_rank();
1579		if (worldRank == 0) {
1580		#endif
1581	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1582	+
1583	+	if( !rnemdFile_ ){
1584	+	sprintf( painCave.errMsg,
1585	+	"Could not open \"%s\" for RNEMD output.\n",
1586	+	rnemdFileName_.c_str());
1587	+	painCave.isFatal = 1;
1588	+	simError();
1589	+	}
1590
1591	<	if (outputTemp_) {
1592	<	tempLog_ << time;
1593	<	for (j = 0; j < rnemdLogWidth_; j++) {
1594	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1595	<	}
1596	<	tempLog_ << endl;
1591	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1592	>
1593	>	RealType time = currentSnap_->getTime();
1594	>	RealType avgArea;
1595	>	areaAccumulator_->getAverage(avgArea);
1596	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1597	>	/ PhysicalConstants::energyConvert;
1598	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1599	>
1600	>	rnemdFile_ << "#######################################################\n";
1601	>	rnemdFile_ << "# RNEMD {\n";
1602	>
1603	>	map<string, RNEMDMethod>::iterator mi;
1604	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1605	>	if ( (*mi).second == rnemdMethod_)
1606	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1607		}
1608	<	if (outputVx_) {
1609	<	vxzLog_ << time;
1610	<	for (j = 0; j < rnemdLogWidth_; j++) {
1611	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1513	<	}
1514	<	vxzLog_ << endl;
1608	>	map<string, RNEMDFluxType>::iterator fi;
1609	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1610	>	if ( (*fi).second == rnemdFluxType_)
1611	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1612		}
1613	<	if (outputVy_) {
1614	<	vyzLog_ << time;
1518	<	for (j = 0; j < rnemdLogWidth_; j++) {
1519	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
1522	<	}
1613	>
1614	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1615
1616	<	if (output3DTemp_) {
1617	<	RealType temp;
1618	<	xTempLog_ << time;
1619	<	for (j = 0; j < rnemdLogWidth_; j++) {
1620	<	if (outputVx_)
1621	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1622	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1623	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1624	<	xTempLog_ << "\t" << temp;
1616	>	rnemdFile_ << "#    objectSelection = \""
1617	>	<< rnemdObjectSelection_ << "\";\n";
1618	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1619	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1620	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1621	>	rnemdFile_ << "# }\n";
1622	>	rnemdFile_ << "#######################################################\n";
1623	>	rnemdFile_ << "# RNEMD report:\n";
1624	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1625	>	rnemdFile_ << "#     target flux:\n";
1626	>	rnemdFile_ << "#         kinetic = "
1627	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1628	>	<< " (kcal/mol/A^2/fs)\n";
1629	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1630	>	<< " (amu/A/fs^2)\n";
1631	>	rnemdFile_ << "#     target one-time exchanges:\n";
1632	>	rnemdFile_ << "#         kinetic = "
1633	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1634	>	<< " (kcal/mol)\n";
1635	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1636	>	<< " (amu*A/fs)\n";
1637	>	rnemdFile_ << "#     actual exchange totals:\n";
1638	>	rnemdFile_ << "#         kinetic = "
1639	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1640	>	<< " (kcal/mol)\n";
1641	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1642	>	<< " (amu*A/fs)\n";
1643	>	rnemdFile_ << "#     actual flux:\n";
1644	>	rnemdFile_ << "#         kinetic = " << Jz
1645	>	<< " (kcal/mol/A^2/fs)\n";
1646	>	rnemdFile_ << "#         momentum = " << JzP
1647	>	<< " (amu/A/fs^2)\n";
1648	>	rnemdFile_ << "#     exchange statistics:\n";
1649	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1650	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1651	>	if (rnemdMethod_ == rnemdNIVS) {
1652	>	rnemdFile_ << "#         NIVS root-check errors = "
1653	>	<< failRootCount_ << "\n";
1654	>	}
1655	>	rnemdFile_ << "#######################################################\n";
1656	>
1657	>
1658	>
1659	>	//write title
1660	>	rnemdFile_ << "#";
1661	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1662	>	if (outputMask_[i]) {
1663	>	rnemdFile_ << "\t" << data_[i].title <<
1664	>	"(" << data_[i].units << ")";
1665	>	// add some extra tabs for column alignment
1666	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1667		}
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;
1668		}
1669	<	if (outputRotTemp_) {
1670	<	rotTempLog_ << time;
1671	<	for (j = 0; j < rnemdLogWidth_; j++) {
1672	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1673	<	}
1674	<	rotTempLog_ << endl;
1675	<	}
1669	>	rnemdFile_ << std::endl;
1670	>
1671	>	rnemdFile_.precision(8);
1672	>
1673	>	for (int j = 0; j < nBins_; j++) {
1674	>
1675	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1676	>	if (outputMask_[i]) {
1677	>	if (data_[i].dataType == "RealType")
1678	>	writeReal(i,j);
1679	>	else if (data_[i].dataType == "Vector3d")
1680	>	writeVector(i,j);
1681	>	else {
1682	>	sprintf( painCave.errMsg,
1683	>	"RNEMD found an unknown data type for: %s ",
1684	>	data_[i].title.c_str());
1685	>	painCave.isFatal = 1;
1686	>	simError();
1687	>	}
1688	>	}
1689	>	}
1690	>	rnemdFile_ << std::endl;
1691	>
1692	>	}
1693
1694	+	rnemdFile_ << "#######################################################\n";
1695	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1696	+	rnemdFile_ << "#######################################################\n";
1697	+
1698	+
1699	+	for (int j = 0; j < nBins_; j++) {
1700	+	rnemdFile_ << "#";
1701	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1702	+	if (outputMask_[i]) {
1703	+	if (data_[i].dataType == "RealType")
1704	+	writeRealStdDev(i,j);
1705	+	else if (data_[i].dataType == "Vector3d")
1706	+	writeVectorStdDev(i,j);
1707	+	else {
1708	+	sprintf( painCave.errMsg,
1709	+	"RNEMD found an unknown data type for: %s ",
1710	+	data_[i].title.c_str());
1711	+	painCave.isFatal = 1;
1712	+	simError();
1713	+	}
1714	+	}
1715	+	}
1716	+	rnemdFile_ << std::endl;
1717	+
1718	+	}
1719	+
1720	+	rnemdFile_.flush();
1721	+	rnemdFile_.close();
1722	+
1723		#ifdef IS_MPI
1724		}
1725		#endif
1726	<
1727	<	for (j = 0; j < rnemdLogWidth_; j++) {
1728	<	mHist_[j] = 0.0;
1726	>
1727	>	}
1728	>
1729	>	void RNEMD::writeReal(int index, unsigned int bin) {
1730	>	if (!doRNEMD_) return;
1731	>	assert(index >=0 && index < ENDINDEX);
1732	>	assert(bin < nBins_);
1733	>	RealType s;
1734	>
1735	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
1736	>
1737	>	if (! isinf(s) && ! isnan(s)) {
1738	>	rnemdFile_ << "\t" << s;
1739	>	} else{
1740	>	sprintf( painCave.errMsg,
1741	>	"RNEMD detected a numerical error writing: %s for bin %d",
1742	>	data_[index].title.c_str(), bin);
1743	>	painCave.isFatal = 1;
1744	>	simError();
1745	>	}
1746	>	}
1747	>
1748	>	void RNEMD::writeVector(int index, unsigned int bin) {
1749	>	if (!doRNEMD_) return;
1750	>	assert(index >=0 && index < ENDINDEX);
1751	>	assert(bin < nBins_);
1752	>	Vector3d s;
1753	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1754	>	if (isinf(s[0]) || isnan(s[0]) ||
1755	>	isinf(s[1]) || isnan(s[1]) ||
1756	>	isinf(s[2]) || isnan(s[2]) ) {
1757	>	sprintf( painCave.errMsg,
1758	>	"RNEMD detected a numerical error writing: %s for bin %d",
1759	>	data_[index].title.c_str(), bin);
1760	>	painCave.isFatal = 1;
1761	>	simError();
1762	>	} else {
1763	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1764		}
1765	<	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	<	}
1765	>	}
1766
1767	<	if (output3DTemp_)
1768	<	for (j = 0; j < rnemdLogWidth_; j++) {
1769	<	xTempHist_[j] = 0.0;
1770	<	yTempHist_[j] = 0.0;
1771	<	zTempHist_[j] = 0.0;
1772	<	xyzTempCount_[j] = 0;
1773	<	}
1774	<	if (outputRotTemp_)
1775	<	for (j = 0; j < rnemdLogWidth_; j++) {
1776	<	rotTempCount_[j] = 0;
1777	<	rotTempHist_[j] = 0.0;
1778	<	}
1767	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1768	>	if (!doRNEMD_) return;
1769	>	assert(index >=0 && index < ENDINDEX);
1770	>	assert(bin < nBins_);
1771	>	RealType s;
1772	>
1773	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
1774	>
1775	>	if (! isinf(s) && ! isnan(s)) {
1776	>	rnemdFile_ << "\t" << s;
1777	>	} else{
1778	>	sprintf( painCave.errMsg,
1779	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1780	>	data_[index].title.c_str(), bin);
1781	>	painCave.isFatal = 1;
1782	>	simError();
1783	>	}
1784		}
1785	+
1786	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1787	+	if (!doRNEMD_) return;
1788	+	assert(index >=0 && index < ENDINDEX);
1789	+	assert(bin < nBins_);
1790	+	Vector3d s;
1791	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1792	+	if (isinf(s[0]) || isnan(s[0]) ||
1793	+	isinf(s[1]) || isnan(s[1]) ||
1794	+	isinf(s[2]) || isnan(s[2]) ) {
1795	+	sprintf( painCave.errMsg,
1796	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1797	+	data_[index].title.c_str(), bin);
1798	+	painCave.isFatal = 1;
1799	+	simError();
1800	+	} else {
1801	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1802	+	}
1803	+	}
1804		}
1805

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