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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 1789 by gezelter, Wed Aug 29 20:52:19 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;
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	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
381	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
382	<	//set to 0.0 if not using it; N/A in status output yet
211	<	if (simParams->haveRNEMD_logWidth()) {
212	<	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
213	<	/*arbitary rnemdLogWidth_, no checking;
214	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
215	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
216	<	cerr << "Automaically set back to default.\n";
217	<	rnemdLogWidth_ = nBins_;
218	<	}*/
380	>
381	>	if (hasOutputFileName) {
382	>	rnemdFileName_ = rnemdParams->getOutputFileName();
383		} else {
384	<	set_RNEMD_logWidth(nBins_);
385	<	}
222	<	tempHist_.resize(rnemdLogWidth_, 0.0);
223	<	tempCount_.resize(rnemdLogWidth_, 0);
224	<	pxzHist_.resize(rnemdLogWidth_, 0.0);
225	<	//vxzCount_.resize(rnemdLogWidth_, 0);
226	<	pyzHist_.resize(rnemdLogWidth_, 0.0);
227	<	//vyzCount_.resize(rnemdLogWidth_, 0);
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 353 | Line 472 | namespace OpenMD {
472
473		if (usePeriodicBoundaryConditions_)
474		currentSnap_->wrapVector(pos);
475	+	bool inA = inSlabA(pos);
476	+	bool inB = inSlabB(pos);
477
478	<	// 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	<
362	<
363	<	// if we're in bin 0 or the middleBin
364	<	if (binNo == 0 || binNo == midBin_) {
478	>	if (inA || inB) {
479
480		RealType mass = sd->getMass();
481		Vector3d vel = sd->getVel();
482		RealType value;
483	<
484	<	switch(rnemdType_) {
485	<	case rnemdKineticSwap :
483	>
484	>	switch(rnemdFluxType_) {
485	>	case rnemdKE :
486
487		value = mass * vel.lengthSquare();
488
#	Line 388 | Line 502 | namespace OpenMD {
502		+ angMom[2]*angMom[2]/I(2, 2);
503		}
504		} //angular momenta exchange enabled
391	–	//energyConvert temporarily disabled
392	–	//make exchangeSum_ comparable between swap & scale
393	–	//value = value * 0.5 / PhysicalConstants::energyConvert;
505		value *= 0.5;
506		break;
507		case rnemdPx :
#	Line 406 | Line 517 | namespace OpenMD {
517		break;
518		}
519
520	<	if (binNo == 0) {
520	>	if (inA == 0) {
521		if (!min_found) {
522		min_val = value;
523		min_sd = sd;
#	Line 417 | Line 528 | namespace OpenMD {
528		min_sd = sd;
529		}
530		}
531	<	} else { //midBin_
531	>	} else {
532		if (!max_found) {
533		max_val = value;
534		max_sd = sd;
#	Line 431 | Line 542 | namespace OpenMD {
542		}
543		}
544		}
545	<
545	>
546		#ifdef IS_MPI
547		int nProc, worldRank;
548	<
548	>
549		nProc = MPI::COMM_WORLD.Get_size();
550		worldRank = MPI::COMM_WORLD.Get_rank();
551
#	Line 454 | Line 565 | namespace OpenMD {
565		RealType val;
566		int rank;
567		} max_vals, min_vals;
568	<
568	>
569		if (my_min_found) {
570		min_vals.val = min_val;
571		} else {
#	Line 492 | Line 603 | namespace OpenMD {
603		Vector3d max_vel = max_sd->getVel();
604		RealType temp_vel;
605
606	<	switch(rnemdType_) {
607	<	case rnemdKineticSwap :
606	>	switch(rnemdFluxType_) {
607	>	case rnemdKE :
608		min_sd->setVel(max_vel);
609		max_sd->setVel(min_vel);
610		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 544 | Line 655 | namespace OpenMD {
655		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
656		min_vals.rank, 0, status);
657
658	<	switch(rnemdType_) {
659	<	case rnemdKineticSwap :
658	>	switch(rnemdFluxType_) {
659	>	case rnemdKE :
660		max_sd->setVel(min_vel);
661		//angular momenta exchange enabled
662		if (max_sd->isDirectional()) {
#	Line 590 | Line 701 | namespace OpenMD {
701		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
702		max_vals.rank, 0, status);
703
704	<	switch(rnemdType_) {
705	<	case rnemdKineticSwap :
704	>	switch(rnemdFluxType_) {
705	>	case rnemdKE :
706		min_sd->setVel(max_vel);
707		//angular momenta exchange enabled
708		if (min_sd->isDirectional()) {
#	Line 625 | Line 736 | namespace OpenMD {
736		}
737		}
738		#endif
739	<	exchangeSum_ += max_val - min_val;
739	>
740	>	switch(rnemdFluxType_) {
741	>	case rnemdKE:
742	>	kineticExchange_ += max_val - min_val;
743	>	break;
744	>	case rnemdPx:
745	>	momentumExchange_.x() += max_val - min_val;
746	>	break;
747	>	case rnemdPy:
748	>	momentumExchange_.y() += max_val - min_val;
749	>	break;
750	>	case rnemdPz:
751	>	momentumExchange_.z() += max_val - min_val;
752	>	break;
753	>	default:
754	>	break;
755	>	}
756		} else {
757		sprintf(painCave.errMsg,
758	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
758	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
759		painCave.isFatal = 0;
760		painCave.severity = OPENMD_INFO;
761		simError();
#	Line 636 | Line 763 | namespace OpenMD {
763		}
764		} else {
765		sprintf(painCave.errMsg,
766	<	"RNEMD: exchange NOT performed because selected object\n"
767	<	"\tnot present in at least one of the two slabs.\n");
766	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
767	>	"\twas not present in at least one of the two slabs.\n");
768		painCave.isFatal = 0;
769		painCave.severity = OPENMD_INFO;
770		simError();
771		failTrialCount_++;
772	<	}
646	<
772	>	}
773		}
774
775	<	void RNEMD::doScale() {
776	<
775	>	void RNEMD::doNIVS() {
776	>	if (!doRNEMD_) return;
777		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
778		Mat3x3d hmat = currentSnap_->getHmat();
779
#	Line 687 | Line 813 | namespace OpenMD {
813		currentSnap_->wrapVector(pos);
814
815		// which bin is this stuntdouble in?
816	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
816	>	bool inA = inSlabA(pos);
817	>	bool inB = inSlabB(pos);
818
819	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
820	<
694	<	// if we're in bin 0 or the middleBin
695	<	if (binNo == 0 || binNo == midBin_) {
696	<
819	>	if (inA || inB) {
820	>
821		RealType mass = sd->getMass();
822		Vector3d vel = sd->getVel();
823
824	<	if (binNo == 0) {
824	>	if (inA) {
825		hotBin.push_back(sd);
826		Phx += mass * vel.x();
827		Phy += mass * vel.y();
#	Line 705 | Line 829 | namespace OpenMD {
829		Khx += mass * vel.x() * vel.x();
830		Khy += mass * vel.y() * vel.y();
831		Khz += mass * vel.z() * vel.z();
708	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
832		if (sd->isDirectional()) {
833		Vector3d angMom = sd->getJ();
834		Mat3x3d I = sd->getI();
#	Line 721 | Line 844 | namespace OpenMD {
844		+ angMom[2]*angMom[2]/I(2, 2);
845		}
846		}
847	<	//}
725	<	} else { //midBin_
847	>	} else {
848		coldBin.push_back(sd);
849		Pcx += mass * vel.x();
850		Pcy += mass * vel.y();
#	Line 730 | Line 852 | namespace OpenMD {
852		Kcx += mass * vel.x() * vel.x();
853		Kcy += mass * vel.y() * vel.y();
854		Kcz += mass * vel.z() * vel.z();
733	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
855		if (sd->isDirectional()) {
856		Vector3d angMom = sd->getJ();
857		Mat3x3d I = sd->getI();
#	Line 746 | Line 867 | namespace OpenMD {
867		+ angMom[2]*angMom[2]/I(2, 2);
868		}
869		}
749	–	//}
870		}
871		}
872		}
#	Line 760 | Line 880 | namespace OpenMD {
880		Kcz *= 0.5;
881		Kcw *= 0.5;
882
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	–
883		#ifdef IS_MPI
884		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
885		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 791 | Line 905 | namespace OpenMD {
905		RealType pz = Pcz / Phz;
906		RealType c, x, y, z;
907		bool successfulScale = false;
908	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
909	<	(rnemdType_ == rnemdKineticScaleAM)) {
908	>	if ((rnemdFluxType_ == rnemdFullKE) ||
909	>	(rnemdFluxType_ == rnemdRotKE)) {
910		//may need sanity check Khw & Kcw > 0
911
912	<	if (rnemdType_ == rnemdKineticScaleVAM) {
913	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
912	>	if (rnemdFluxType_ == rnemdFullKE) {
913	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
914		} else {
915	<	c = 1.0 - targetFlux_ / Kcw;
915	>	c = 1.0 - kineticTarget_ / Kcw;
916		}
917
918		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
919		c = sqrt(c);
920	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
920	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
921		//now convert to hotBin coefficient
922		RealType w = 0.0;
923	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
923	>	if (rnemdFluxType_ ==  rnemdFullKE) {
924		x = 1.0 + px * (1.0 - c);
925		y = 1.0 + py * (1.0 - c);
926		z = 1.0 + pz * (1.0 - c);
#	Line 820 | Line 934 | namespace OpenMD {
934		*/
935		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
936		(fabs(z - 1.0) < 0.1)) {
937	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
937	>	w = 1.0 + (kineticTarget_
938	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
939		+ Khz * (1.0 - z * z)) / Khw;
940		}//no need to calculate w if x, y or z is out of range
941		} else {
942	<	w = 1.0 + targetFlux_ / Khw;
942	>	w = 1.0 + kineticTarget_ / Khw;
943		}
944		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
945		//if w is in the right range, so should be x, y, z.
946		vector<StuntDouble*>::iterator sdi;
947		Vector3d vel;
948		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
949	<	if (rnemdType_ == rnemdKineticScaleVAM) {
949	>	if (rnemdFluxType_ == rnemdFullKE) {
950		vel = (*sdi)->getVel() * c;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
951		(*sdi)->setVel(vel);
952		}
953		if ((*sdi)->isDirectional()) {
954		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//angMom[2] *= c;
955		(*sdi)->setJ(angMom);
956		}
957		}
958		w = sqrt(w);
959	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
960	<	<< "\twh= " << w << endl;
959	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
960	>	//           << "\twh= " << w << endl;
961		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
962	<	if (rnemdType_ == rnemdKineticScaleVAM) {
962	>	if (rnemdFluxType_ == rnemdFullKE) {
963		vel = (*sdi)->getVel();
964		vel.x() *= x;
965		vel.y() *= y;
#	Line 859 | Line 968 | namespace OpenMD {
968		}
969		if ((*sdi)->isDirectional()) {
970		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//angMom[2] *= w;
971		(*sdi)->setJ(angMom);
972		}
973		}
974		successfulScale = true;
975	<	exchangeSum_ += targetFlux_;
975	>	kineticExchange_ += kineticTarget_;
976		}
977		}
978		} else {
979		RealType a000, a110, c0, a001, a111, b01, b11, c1;
980	<	switch(rnemdType_) {
981	<	case rnemdKineticScale :
980	>	switch(rnemdFluxType_) {
981	>	case rnemdKE :
982		/* used hotBin coeff's & only scale x & y dimensions
983		RealType px = Phx / Pcx;
984		RealType py = Phy / Pcy;
985		a110 = Khy;
986	<	c0 = - Khx - Khy - targetFlux_;
986	>	c0 = - Khx - Khy - kineticTarget_;
987		a000 = Khx;
988		a111 = Kcy * py * py;
989		b11 = -2.0 * Kcy * py * (1.0 + py);
990	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
990	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
991		b01 = -2.0 * Kcx * px * (1.0 + px);
992		a001 = Kcx * px * px;
993		*/
994		//scale all three dimensions, let c_x = c_y
995		a000 = Kcx + Kcy;
996		a110 = Kcz;
997	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
997	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
998		a001 = Khx * px * px + Khy * py * py;
999		a111 = Khz * pz * pz;
1000		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1001		b11 = -2.0 * Khz * pz * (1.0 + pz);
1002		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1003	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1003	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1004		break;
1005	<	case rnemdPxScale :
1006	<	c = 1 - targetFlux_ / Pcx;
1005	>	case rnemdPx :
1006	>	c = 1 - momentumTarget_.x() / Pcx;
1007		a000 = Kcy;
1008		a110 = Kcz;
1009		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 908 | Line 1014 | namespace OpenMD {
1014		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1015		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1016		break;
1017	<	case rnemdPyScale :
1018	<	c = 1 - targetFlux_ / Pcy;
1017	>	case rnemdPy :
1018	>	c = 1 - momentumTarget_.y() / Pcy;
1019		a000 = Kcx;
1020		a110 = Kcz;
1021		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 920 | Line 1026 | namespace OpenMD {
1026		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1027		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1028		break;
1029	<	case rnemdPzScale ://we don't really do this, do we?
1030	<	c = 1 - targetFlux_ / Pcz;
1029	>	case rnemdPz ://we don't really do this, do we?
1030	>	c = 1 - momentumTarget_.z() / Pcz;
1031		a000 = Kcx;
1032		a110 = Kcy;
1033		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1006 | Line 1112 | namespace OpenMD {
1112		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1113		r1 = (*rpi).first;
1114		r2 = (*rpi).second;
1115	<	switch(rnemdType_) {
1116	<	case rnemdKineticScale :
1115	>	switch(rnemdFluxType_) {
1116	>	case rnemdKE :
1117		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1118		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1119		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120		break;
1121	<	case rnemdPxScale :
1121	>	case rnemdPx :
1122		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1124		break;
1125	<	case rnemdPyScale :
1125	>	case rnemdPy :
1126		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1128		break;
1129	<	case rnemdPzScale :
1129	>	case rnemdPz :
1130		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1131		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1132		default :
#	Line 1034 | Line 1140 | namespace OpenMD {
1140		#ifdef IS_MPI
1141		if (worldRank == 0) {
1142		#endif
1143	<	sprintf(painCave.errMsg,
1144	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1145	<	bestPair.first, bestPair.second);
1146	<	painCave.isFatal = 0;
1147	<	painCave.severity = OPENMD_INFO;
1148	<	simError();
1143	>	// sprintf(painCave.errMsg,
1144	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1145	>	//         bestPair.first, bestPair.second);
1146	>	// painCave.isFatal = 0;
1147	>	// painCave.severity = OPENMD_INFO;
1148	>	// simError();
1149		#ifdef IS_MPI
1150		}
1151		#endif
1152
1153	<	switch(rnemdType_) {
1154	<	case rnemdKineticScale :
1153	>	switch(rnemdFluxType_) {
1154	>	case rnemdKE :
1155		x = bestPair.first;
1156		y = bestPair.first;
1157		z = bestPair.second;
1158		break;
1159	<	case rnemdPxScale :
1159	>	case rnemdPx :
1160		x = c;
1161		y = bestPair.first;
1162		z = bestPair.second;
1163		break;
1164	<	case rnemdPyScale :
1164	>	case rnemdPy :
1165		x = bestPair.first;
1166		y = c;
1167		z = bestPair.second;
1168		break;
1169	<	case rnemdPzScale :
1169	>	case rnemdPz :
1170		x = bestPair.first;
1171		y = bestPair.second;
1172		z = c;
#	Line 1089 | Line 1195 | namespace OpenMD {
1195		(*sdi)->setVel(vel);
1196		}
1197		successfulScale = true;
1198	<	exchangeSum_ += targetFlux_;
1198	>	switch(rnemdFluxType_) {
1199	>	case rnemdKE :
1200	>	kineticExchange_ += kineticTarget_;
1201	>	break;
1202	>	case rnemdPx :
1203	>	case rnemdPy :
1204	>	case rnemdPz :
1205	>	momentumExchange_ += momentumTarget_;
1206	>	break;
1207	>	default :
1208	>	break;
1209	>	}
1210		}
1211		}
1212		if (successfulScale != true) {
1213		sprintf(painCave.errMsg,
1214	<	"RNEMD: exchange NOT performed!\n");
1214	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1215	>	"\tthe constraint equations may not exist or there may be\n"
1216	>	"\tno selected objects in one or both slabs.\n");
1217		painCave.isFatal = 0;
1218		painCave.severity = OPENMD_INFO;
1219		simError();
#	Line 1102 | Line 1221 | namespace OpenMD {
1221		}
1222		}
1223
1224	<	void RNEMD::doShiftScale() {
1225	<
1224	>	void RNEMD::doVSS() {
1225	>	if (!doRNEMD_) return;
1226		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1227	+	RealType time = currentSnap_->getTime();
1228		Mat3x3d hmat = currentSnap_->getHmat();
1229
1230		seleMan_.setSelectionSet(evaluator_.evaluate());
#	Line 1121 | Line 1241 | namespace OpenMD {
1241		Vector3d Pc(V3Zero);
1242		RealType Mc = 0.0;
1243		RealType Kc = 0.0;
1244	+
1245
1246		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1247		sd = seleMan_.nextSelected(selei)) {
#	Line 1135 | Line 1256 | namespace OpenMD {
1256		currentSnap_->wrapVector(pos);
1257
1258		// which bin is this stuntdouble in?
1259	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1260	<
1261	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1262	<
1142	<	// if we're in bin 0 or the middleBin
1143	<	if (binNo == 0 || binNo == midBin_) {
1259	>	bool inA = inSlabA(pos);
1260	>	bool inB = inSlabB(pos);
1261	>
1262	>	if (inA || inB) {
1263
1264		RealType mass = sd->getMass();
1265		Vector3d vel = sd->getVel();
1266
1267	<	if (binNo == 0) {
1267	>	if (inA) {
1268		hotBin.push_back(sd);
1269		//std::cerr << "before, velocity = " << vel << endl;
1270		Ph += mass * vel;
1271		//std::cerr << "after, velocity = " << vel << endl;
1272		Mh += mass;
1273		Kh += mass * vel.lengthSquare();
1274	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1274	>	if (rnemdFluxType_ == rnemdFullKE) {
1275		if (sd->isDirectional()) {
1276		Vector3d angMom = sd->getJ();
1277		Mat3x3d I = sd->getI();
#	Line 1174 | Line 1293 | namespace OpenMD {
1293		Pc += mass * vel;
1294		Mc += mass;
1295		Kc += mass * vel.lengthSquare();
1296	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1296	>	if (rnemdFluxType_ == rnemdFullKE) {
1297		if (sd->isDirectional()) {
1298		Vector3d angMom = sd->getJ();
1299		Mat3x3d I = sd->getI();
#	Line 1198 | Line 1317 | namespace OpenMD {
1317		Kh *= 0.5;
1318		Kc *= 0.5;
1319
1320	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1321	<	<< "\tKc= " << Kc << endl;
1322	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1323	<
1320	>	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1321	>	//        << "\tKc= " << Kc << endl;
1322	>	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1323	>
1324		#ifdef IS_MPI
1325		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1326		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
#	Line 1214 | Line 1333 | namespace OpenMD {
1333		bool successfulExchange = false;
1334		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1335		Vector3d vc = Pc / Mc;
1336	<	Vector3d ac = njzp_ / Mc + vc;
1337	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1336	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1337	>	Vector3d acrec = -momentumTarget_ / Mc;
1338	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1339		if (cNumerator > 0.0) {
1340		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1341		if (cDenominator > 0.0) {
1342		RealType c = sqrt(cNumerator / cDenominator);
1343		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1344		Vector3d vh = Ph / Mh;
1345	<	Vector3d ah = jzp_ / Mh + vh;
1346	<	RealType hNumerator = Kh + targetJzKE_
1345	>	Vector3d ah = momentumTarget_ / Mh + vh;
1346	>	Vector3d ahrec = momentumTarget_ / Mh;
1347	>	RealType hNumerator = Kh + kineticTarget_
1348		- 0.5 * Mh * ah.lengthSquare();
1349		if (hNumerator > 0.0) {
1350		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1351		if (hDenominator > 0.0) {
1352		RealType h = sqrt(hNumerator / hDenominator);
1353		if ((h > 0.9) && (h < 1.1)) {
1354	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1355	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1354	>	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1355	>	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1356		vector<StuntDouble*>::iterator sdi;
1357		Vector3d vel;
1358		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1359		//vel = (*sdi)->getVel();
1360		vel = ((*sdi)->getVel() - vc) * c + ac;
1361		(*sdi)->setVel(vel);
1362	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1362	>	if (rnemdFluxType_ == rnemdFullKE) {
1363		if ((*sdi)->isDirectional()) {
1364		Vector3d angMom = (*sdi)->getJ() * c;
1365		(*sdi)->setJ(angMom);
#	Line 1249 | Line 1370 | namespace OpenMD {
1370		//vel = (*sdi)->getVel();
1371		vel = ((*sdi)->getVel() - vh) * h + ah;
1372		(*sdi)->setVel(vel);
1373	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1373	>	if (rnemdFluxType_ == rnemdFullKE) {
1374		if ((*sdi)->isDirectional()) {
1375		Vector3d angMom = (*sdi)->getJ() * h;
1376		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1378 | namespace OpenMD {
1378		}
1379		}
1380		successfulExchange = true;
1381	<	exchangeSum_ += targetFlux_;
1382	<	// 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.
1381	>	kineticExchange_ += kineticTarget_;
1382	>	momentumExchange_ += momentumTarget_;
1383		}
1384		}
1385		}
#	Line 1270 | Line 1389 | namespace OpenMD {
1389		}
1390		if (successfulExchange != true) {
1391		sprintf(painCave.errMsg,
1392	<	"RNEMD: exchange NOT performed!\n");
1392	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1393	>	"\tthe constraint equations may not exist or there may be\n"
1394	>	"\tno selected objects in one or both slabs.\n");
1395		painCave.isFatal = 0;
1396		painCave.severity = OPENMD_INFO;
1397		simError();
#	Line 1279 | Line 1400 | namespace OpenMD {
1400		}
1401
1402		void RNEMD::doRNEMD() {
1403	<
1404	<	switch(rnemdType_) {
1405	<	case rnemdKineticScale :
1406	<	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 :
1403	>	if (!doRNEMD_) return;
1404	>	trialCount_++;
1405	>	switch(rnemdMethod_) {
1406	>	case rnemdSwap:
1407		doSwap();
1408		break;
1409	<	case rnemdShiftScaleV :
1410	<	case rnemdShiftScaleVAM :
1300	<	doShiftScale();
1409	>	case rnemdNIVS:
1410	>	doNIVS();
1411		break;
1412	<	case rnemdUnknown :
1412	>	case rnemdVSS:
1413	>	doVSS();
1414	>	break;
1415	>	case rnemdUnkownMethod:
1416		default :
1417		break;
1418		}
1419		}
1420
1421		void RNEMD::collectData() {
1422	<
1422	>	if (!doRNEMD_) return;
1423		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1424		Mat3x3d hmat = currentSnap_->getHmat();
1425
1426	+	areaAccumulator_->add(currentSnap_->getXYarea());
1427	+
1428		seleMan_.setSelectionSet(evaluator_.evaluate());
1429
1430		int selei;
1431		StuntDouble* sd;
1432		int idx;
1433
1434	+	vector<RealType> binMass(nBins_, 0.0);
1435	+	vector<RealType> binPx(nBins_, 0.0);
1436	+	vector<RealType> binPy(nBins_, 0.0);
1437	+	vector<RealType> binPz(nBins_, 0.0);
1438	+	vector<RealType> binKE(nBins_, 0.0);
1439	+	vector<int> binDOF(nBins_, 0);
1440	+	vector<int> binCount(nBins_, 0);
1441	+
1442		// alternative approach, track all molecules instead of only those
1443		// selected for scaling/swapping:
1444		/*
1445		SimInfo::MoleculeIterator miter;
1446		vector<StuntDouble*>::iterator iiter;
1447		Molecule* mol;
1448	<	StuntDouble* integrableObject;
1448	>	StuntDouble* sd;
1449		for (mol = info_->beginMolecule(miter); mol != NULL;
1450	<	mol = info_->nextMolecule(miter))
1451	<	integrableObject is essentially sd
1452	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1453	<	integrableObject != NULL;
1454	<	integrableObject = mol->nextIntegrableObject(iiter))
1450	>	mol = info_->nextMolecule(miter))
1451	>	sd is essentially sd
1452	>	for (sd = mol->beginIntegrableObject(iiter);
1453	>	sd != NULL;
1454	>	sd = mol->nextIntegrableObject(iiter))
1455		*/
1456		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1457		sd = seleMan_.nextSelected(selei)) {
#	Line 1341 | Line 1464 | namespace OpenMD {
1464
1465		if (usePeriodicBoundaryConditions_)
1466		currentSnap_->wrapVector(pos);
1467	<
1467	>
1468	>
1469		// which bin is this stuntdouble in?
1470		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1471	<
1472	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1473	<	rnemdLogWidth_;
1474	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1475	<	/*
1352	<	if (rnemdLogWidth_ == midBin_ + 1)
1353	<	if (binNo > midBin_)
1354	<	binNo = nBins_ - binNo;
1355	<	*/
1471	>	// Shift molecules by half a box to have bins start at 0
1472	>	// The modulo operator is used to wrap the case when we are
1473	>	// beyond the end of the bins back to the beginning.
1474	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1475	>
1476		RealType mass = sd->getMass();
1357	–	mHist_[binNo] += mass;
1477		Vector3d vel = sd->getVel();
1359	–	RealType value;
1360	–	//RealType xVal, yVal, zVal;
1478
1479	<	if (outputTemp_) {
1480	<	value = mass * vel.lengthSquare();
1481	<	tempCount_[binNo] += 3;
1482	<	if (sd->isDirectional()) {
1483	<	Vector3d angMom = sd->getJ();
1484	<	Mat3x3d I = sd->getI();
1485	<	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	<	}
1479	>	binCount[binNo]++;
1480	>	binMass[binNo] += mass;
1481	>	binPx[binNo] += mass*vel.x();
1482	>	binPy[binNo] += mass*vel.y();
1483	>	binPz[binNo] += mass*vel.z();
1484	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1485	>	binDOF[binNo] += 3;
1486
1487	<	if (output3DTemp_) {
1488	<	value = mass * vel.x() * vel.x();
1489	<	xTempHist_[binNo] += value;
1490	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1491	<	/ PhysicalConstants::kb;
1492	<	yTempHist_[binNo] += value;
1493	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1494	<	/ PhysicalConstants::kb;
1495	<	zTempHist_[binNo] += value;
1496	<	xyzTempCount_[binNo]++;
1487	>	if (sd->isDirectional()) {
1488	>	Vector3d angMom = sd->getJ();
1489	>	Mat3x3d I = sd->getI();
1490	>	if (sd->isLinear()) {
1491	>	int i = sd->linearAxis();
1492	>	int j = (i + 1) % 3;
1493	>	int k = (i + 2) % 3;
1494	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1495	>	angMom[k] * angMom[k] / I(k, k));
1496	>	binDOF[binNo] += 2;
1497	>	} else {
1498	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1499	>	angMom[1] * angMom[1] / I(1, 1) +
1500	>	angMom[2] * angMom[2] / I(2, 2));
1501	>	binDOF[binNo] += 3;
1502	>	}
1503		}
1504	<	if (outputRotTemp_) {
1505	<	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	<	}
1504	>	}
1505	>
1506
1507	+	#ifdef IS_MPI
1508	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1509	+	nBins_, MPI::INT, MPI::SUM);
1510	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1511	+	nBins_, MPI::REALTYPE, MPI::SUM);
1512	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1513	+	nBins_, MPI::REALTYPE, MPI::SUM);
1514	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1515	+	nBins_, MPI::REALTYPE, MPI::SUM);
1516	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1517	+	nBins_, MPI::REALTYPE, MPI::SUM);
1518	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1519	+	nBins_, MPI::REALTYPE, MPI::SUM);
1520	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1521	+	nBins_, MPI::INT, MPI::SUM);
1522	+	#endif
1523	+
1524	+	Vector3d vel;
1525	+	RealType den;
1526	+	RealType temp;
1527	+	RealType z;
1528	+	for (int i = 0; i < nBins_; i++) {
1529	+	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1530	+	vel.x() = binPx[i] / binMass[i];
1531	+	vel.y() = binPy[i] / binMass[i];
1532	+	vel.z() = binPz[i] / binMass[i];
1533	+
1534	+	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1535	+	/ currentSnap_->getVolume() ;
1536	+
1537	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1538	+	PhysicalConstants::energyConvert);
1539	+
1540	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1541	+	if(outputMask_[j]) {
1542	+	switch(j) {
1543	+	case Z:
1544	+	(data_[j].accumulator[i])->add(z);
1545	+	break;
1546	+	case TEMPERATURE:
1547	+	data_[j].accumulator[i]->add(temp);
1548	+	break;
1549	+	case VELOCITY:
1550	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1551	+	break;
1552	+	case DENSITY:
1553	+	data_[j].accumulator[i]->add(den);
1554	+	break;
1555	+	}
1556	+	}
1557	+	}
1558		}
1559		}
1560
1561		void RNEMD::getStarted() {
1562	+	if (!doRNEMD_) return;
1563		collectData();
1564	<	/*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();
1564	>	writeOutputFile();
1565		}
1566
1567	<	void RNEMD::getStatus() {
1568	<
1569	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1570	<	Stats& stat = currentSnap_->statData;
1571	<	RealType time = currentSnap_->getTime();
1572	<
1573	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1574	<	//or to be more meaningful, define another item as exchangeSum_ / time
1575	<	int j;
1576	<
1567	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1568	>	if (!doRNEMD_) return;
1569	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1570	>
1571	>	while(tokenizer.hasMoreTokens()) {
1572	>	std::string token(tokenizer.nextToken());
1573	>	toUpper(token);
1574	>	OutputMapType::iterator i = outputMap_.find(token);
1575	>	if (i != outputMap_.end()) {
1576	>	outputMask_.set(i->second);
1577	>	} else {
1578	>	sprintf( painCave.errMsg,
1579	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1580	>	"\toutputFileFormat keyword.\n", token.c_str() );
1581	>	painCave.isFatal = 0;
1582	>	painCave.severity = OPENMD_ERROR;
1583	>	simError();
1584	>	}
1585	>	}
1586	>	}
1587	>
1588	>	void RNEMD::writeOutputFile() {
1589	>	if (!doRNEMD_) return;
1590	>
1591		#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	–
1592		// If we're the root node, should we print out the results
1593		int worldRank = MPI::COMM_WORLD.Get_rank();
1594		if (worldRank == 0) {
1595		#endif
1596	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1597	+
1598	+	if( !rnemdFile_ ){
1599	+	sprintf( painCave.errMsg,
1600	+	"Could not open \"%s\" for RNEMD output.\n",
1601	+	rnemdFileName_.c_str());
1602	+	painCave.isFatal = 1;
1603	+	simError();
1604	+	}
1605
1606	<	if (outputTemp_) {
1607	<	tempLog_ << time;
1608	<	for (j = 0; j < rnemdLogWidth_; j++) {
1609	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1610	<	}
1611	<	tempLog_ << endl;
1606	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1607	>
1608	>	RealType time = currentSnap_->getTime();
1609	>	RealType avgArea;
1610	>	areaAccumulator_->getAverage(avgArea);
1611	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1612	>	/ PhysicalConstants::energyConvert;
1613	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1614	>
1615	>	rnemdFile_ << "#######################################################\n";
1616	>	rnemdFile_ << "# RNEMD {\n";
1617	>
1618	>	map<string, RNEMDMethod>::iterator mi;
1619	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1620	>	if ( (*mi).second == rnemdMethod_)
1621	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1622		}
1623	<	if (outputVx_) {
1624	<	vxzLog_ << time;
1625	<	for (j = 0; j < rnemdLogWidth_; j++) {
1626	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1513	<	}
1514	<	vxzLog_ << endl;
1623	>	map<string, RNEMDFluxType>::iterator fi;
1624	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1625	>	if ( (*fi).second == rnemdFluxType_)
1626	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1627		}
1628	<	if (outputVy_) {
1629	<	vyzLog_ << time;
1518	<	for (j = 0; j < rnemdLogWidth_; j++) {
1519	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
1522	<	}
1628	>
1629	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1630
1631	<	if (output3DTemp_) {
1632	<	RealType temp;
1633	<	xTempLog_ << time;
1634	<	for (j = 0; j < rnemdLogWidth_; j++) {
1635	<	if (outputVx_)
1636	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1637	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1638	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1639	<	xTempLog_ << "\t" << temp;
1631	>	rnemdFile_ << "#    objectSelection = \""
1632	>	<< rnemdObjectSelection_ << "\";\n";
1633	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1634	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1635	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1636	>	rnemdFile_ << "# }\n";
1637	>	rnemdFile_ << "#######################################################\n";
1638	>	rnemdFile_ << "# RNEMD report:\n";
1639	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1640	>	rnemdFile_ << "#     target flux:\n";
1641	>	rnemdFile_ << "#         kinetic = "
1642	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1643	>	<< " (kcal/mol/A^2/fs)\n";
1644	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1645	>	<< " (amu/A/fs^2)\n";
1646	>	rnemdFile_ << "#     target one-time exchanges:\n";
1647	>	rnemdFile_ << "#         kinetic = "
1648	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1649	>	<< " (kcal/mol)\n";
1650	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1651	>	<< " (amu*A/fs)\n";
1652	>	rnemdFile_ << "#     actual exchange totals:\n";
1653	>	rnemdFile_ << "#         kinetic = "
1654	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1655	>	<< " (kcal/mol)\n";
1656	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1657	>	<< " (amu*A/fs)\n";
1658	>	rnemdFile_ << "#     actual flux:\n";
1659	>	rnemdFile_ << "#         kinetic = " << Jz
1660	>	<< " (kcal/mol/A^2/fs)\n";
1661	>	rnemdFile_ << "#         momentum = " << JzP
1662	>	<< " (amu/A/fs^2)\n";
1663	>	rnemdFile_ << "#     exchange statistics:\n";
1664	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1665	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1666	>	if (rnemdMethod_ == rnemdNIVS) {
1667	>	rnemdFile_ << "#         NIVS root-check errors = "
1668	>	<< failRootCount_ << "\n";
1669	>	}
1670	>	rnemdFile_ << "#######################################################\n";
1671	>
1672	>
1673	>
1674	>	//write title
1675	>	rnemdFile_ << "#";
1676	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1677	>	if (outputMask_[i]) {
1678	>	rnemdFile_ << "\t" << data_[i].title <<
1679	>	"(" << data_[i].units << ")";
1680	>	// add some extra tabs for column alignment
1681	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1682		}
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;
1683		}
1684	<	if (outputRotTemp_) {
1685	<	rotTempLog_ << time;
1686	<	for (j = 0; j < rnemdLogWidth_; j++) {
1687	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1688	<	}
1689	<	rotTempLog_ << endl;
1690	<	}
1684	>	rnemdFile_ << std::endl;
1685	>
1686	>	rnemdFile_.precision(8);
1687	>
1688	>	for (int j = 0; j < nBins_; j++) {
1689	>
1690	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1691	>	if (outputMask_[i]) {
1692	>	if (data_[i].dataType == "RealType")
1693	>	writeReal(i,j);
1694	>	else if (data_[i].dataType == "Vector3d")
1695	>	writeVector(i,j);
1696	>	else {
1697	>	sprintf( painCave.errMsg,
1698	>	"RNEMD found an unknown data type for: %s ",
1699	>	data_[i].title.c_str());
1700	>	painCave.isFatal = 1;
1701	>	simError();
1702	>	}
1703	>	}
1704	>	}
1705	>	rnemdFile_ << std::endl;
1706	>
1707	>	}
1708
1709	+	rnemdFile_ << "#######################################################\n";
1710	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1711	+	rnemdFile_ << "#######################################################\n";
1712	+
1713	+
1714	+	for (int j = 0; j < nBins_; j++) {
1715	+	rnemdFile_ << "#";
1716	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1717	+	if (outputMask_[i]) {
1718	+	if (data_[i].dataType == "RealType")
1719	+	writeRealStdDev(i,j);
1720	+	else if (data_[i].dataType == "Vector3d")
1721	+	writeVectorStdDev(i,j);
1722	+	else {
1723	+	sprintf( painCave.errMsg,
1724	+	"RNEMD found an unknown data type for: %s ",
1725	+	data_[i].title.c_str());
1726	+	painCave.isFatal = 1;
1727	+	simError();
1728	+	}
1729	+	}
1730	+	}
1731	+	rnemdFile_ << std::endl;
1732	+
1733	+	}
1734	+
1735	+	rnemdFile_.flush();
1736	+	rnemdFile_.close();
1737	+
1738		#ifdef IS_MPI
1739		}
1740		#endif
1741	<
1742	<	for (j = 0; j < rnemdLogWidth_; j++) {
1743	<	mHist_[j] = 0.0;
1741	>
1742	>	}
1743	>
1744	>	void RNEMD::writeReal(int index, unsigned int bin) {
1745	>	if (!doRNEMD_) return;
1746	>	assert(index >=0 && index < ENDINDEX);
1747	>	assert(bin < nBins_);
1748	>	RealType s;
1749	>
1750	>	data_[index].accumulator[bin]->getAverage(s);
1751	>
1752	>	if (! isinf(s) && ! isnan(s)) {
1753	>	rnemdFile_ << "\t" << s;
1754	>	} else{
1755	>	sprintf( painCave.errMsg,
1756	>	"RNEMD detected a numerical error writing: %s for bin %d",
1757	>	data_[index].title.c_str(), bin);
1758	>	painCave.isFatal = 1;
1759	>	simError();
1760	>	}
1761	>	}
1762	>
1763	>	void RNEMD::writeVector(int index, unsigned int bin) {
1764	>	if (!doRNEMD_) return;
1765	>	assert(index >=0 && index < ENDINDEX);
1766	>	assert(bin < nBins_);
1767	>	Vector3d s;
1768	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1769	>	if (isinf(s[0]) || isnan(s[0]) ||
1770	>	isinf(s[1]) || isnan(s[1]) ||
1771	>	isinf(s[2]) || isnan(s[2]) ) {
1772	>	sprintf( painCave.errMsg,
1773	>	"RNEMD detected a numerical error writing: %s for bin %d",
1774	>	data_[index].title.c_str(), bin);
1775	>	painCave.isFatal = 1;
1776	>	simError();
1777	>	} else {
1778	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1779		}
1780	<	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	<	}
1780	>	}
1781
1782	<	if (output3DTemp_)
1783	<	for (j = 0; j < rnemdLogWidth_; j++) {
1784	<	xTempHist_[j] = 0.0;
1785	<	yTempHist_[j] = 0.0;
1786	<	zTempHist_[j] = 0.0;
1787	<	xyzTempCount_[j] = 0;
1788	<	}
1789	<	if (outputRotTemp_)
1790	<	for (j = 0; j < rnemdLogWidth_; j++) {
1791	<	rotTempCount_[j] = 0;
1792	<	rotTempHist_[j] = 0.0;
1793	<	}
1782	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1783	>	if (!doRNEMD_) return;
1784	>	assert(index >=0 && index < ENDINDEX);
1785	>	assert(bin < nBins_);
1786	>	RealType s;
1787	>
1788	>	data_[index].accumulator[bin]->getStdDev(s);
1789	>
1790	>	if (! isinf(s) && ! isnan(s)) {
1791	>	rnemdFile_ << "\t" << s;
1792	>	} else{
1793	>	sprintf( painCave.errMsg,
1794	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1795	>	data_[index].title.c_str(), bin);
1796	>	painCave.isFatal = 1;
1797	>	simError();
1798	>	}
1799		}
1800	+
1801	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1802	+	if (!doRNEMD_) return;
1803	+	assert(index >=0 && index < ENDINDEX);
1804	+	assert(bin < nBins_);
1805	+	Vector3d s;
1806	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1807	+	if (isinf(s[0]) || isnan(s[0]) ||
1808	+	isinf(s[1]) || isnan(s[1]) ||
1809	+	isinf(s[2]) || isnan(s[2]) ) {
1810	+	sprintf( painCave.errMsg,
1811	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1812	+	data_[index].title.c_str(), bin);
1813	+	painCave.isFatal = 1;
1814	+	simError();
1815	+	} else {
1816	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1817	+	}
1818	+	}
1819		}
1820

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