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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1728 by jmarr, Wed May 30 16:07:03 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1830 by gezelter, Wed Jan 9 22:02:30 2013 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	+	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_ = simParams->getRNEMD_objectSelection();
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();
284	+
285		int nIntegrable = info->getNGlobalIntegrableObjects();
286
287		if (selectionCount > nIntegrable) {
288		sprintf(painCave.errMsg,
289	<	"RNEMD: The current RNEMD_objectSelection,\n"
289	>	"RNEMD: The current objectSelection,\n"
290		"\t\t%s\n"
291		"\thas resulted in %d selected objects.  However,\n"
292		"\tthe total number of integrable objects in the system\n"
#	Line 112 | Line 299 | namespace OpenMD {
299		painCave.severity = OPENMD_WARNING;
300		simError();
301		}
115	–
116	–	const string st = simParams->getRNEMD_exchangeType();
302
303	<	map<string, RNEMDTypeEnum>::iterator i;
119	<	i = stringToEnumMap_.find(st);
120	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
121	<	if (rnemdType_ == rnemdUnknown) {
122	<	sprintf(painCave.errMsg,
123	<	"RNEMD: The current RNEMD_exchangeType,\n"
124	<	"\t\t%s\n"
125	<	"\tis not one of the recognized exchange types.\n",
126	<	st.c_str());
127	<	painCave.isFatal = 1;
128	<	painCave.severity = OPENMD_ERROR;
129	<	simError();
130	<	}
131	<
132	<	outputTemp_ = false;
133	<	if (simParams->haveRNEMD_outputTemperature()) {
134	<	outputTemp_ = simParams->getRNEMD_outputTemperature();
135	<	} else if ((rnemdType_ == rnemdKineticSwap) ||
136	<	(rnemdType_ == rnemdKineticScale) ||
137	<	(rnemdType_ == rnemdKineticScaleVAM) ||
138	<	(rnemdType_ == rnemdKineticScaleAM)) {
139	<	outputTemp_ = true;
140	<	}
141	<	outputVx_ = false;
142	<	if (simParams->haveRNEMD_outputVx()) {
143	<	outputVx_ = simParams->getRNEMD_outputVx();
144	<	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
145	<	outputVx_ = true;
146	<	}
147	<	outputVy_ = false;
148	<	if (simParams->haveRNEMD_outputVy()) {
149	<	outputVy_ = simParams->getRNEMD_outputVy();
150	<	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
151	<	outputVy_ = true;
152	<	}
153	<	output3DTemp_ = false;
154	<	if (simParams->haveRNEMD_outputXyzTemperature()) {
155	<	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
156	<	}
157	<	outputRotTemp_ = false;
158	<	if (simParams->haveRNEMD_outputRotTemperature()) {
159	<	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
160	<	}
161	<	// James put this in.
162	<	outputDen_ = false;
163	<	if (simParams->haveRNEMD_outputDen()) {
164	<	outputDen_ = simParams->getRNEMD_outputDen();
165	<	}
166	<	outputAh_ = false;
167	<	if (simParams->haveRNEMD_outputAh()) {
168	<	outputAh_ = simParams->getRNEMD_outputAh();
169	<	}
170	<	outputVz_ = false;
171	<	if (simParams->haveRNEMD_outputVz()) {
172	<	outputVz_ = simParams->getRNEMD_outputVz();
173	<	} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
174	<	outputVz_ = true;
175	<	}
176	<
303	>	areaAccumulator_ = new Accumulator();
304
305	<	#ifdef IS_MPI
179	<	if (worldRank == 0) {
180	<	#endif
305	>	nBins_ = rnemdParams->getOutputBins();
306
307	<	//may have rnemdWriter separately
308	<	string rnemdFileName;
307	>	data_.resize(RNEMD::ENDINDEX);
308	>	OutputData z;
309	>	z.units =  "Angstroms";
310	>	z.title =  "Z";
311	>	z.dataType = "RealType";
312	>	z.accumulator.reserve(nBins_);
313	>	for (int i = 0; i < nBins_; i++)
314	>	z.accumulator.push_back( new Accumulator() );
315	>	data_[Z] = z;
316	>	outputMap_["Z"] =  Z;
317
318	<	if (outputTemp_) {
319	<	rnemdFileName = "temperature.log";
320	<	tempLog_.open(rnemdFileName.c_str());
321	<	}
322	<	if (outputVx_) {
323	<	rnemdFileName = "velocityX.log";
324	<	vxzLog_.open(rnemdFileName.c_str());
325	<	}
326	<	if (outputVy_) {
194	<	rnemdFileName = "velocityY.log";
195	<	vyzLog_.open(rnemdFileName.c_str());
196	<	}
318	>	OutputData temperature;
319	>	temperature.units =  "K";
320	>	temperature.title =  "Temperature";
321	>	temperature.dataType = "RealType";
322	>	temperature.accumulator.reserve(nBins_);
323	>	for (int i = 0; i < nBins_; i++)
324	>	temperature.accumulator.push_back( new Accumulator() );
325	>	data_[TEMPERATURE] = temperature;
326	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
327
328	<	if (output3DTemp_) {
329	<	rnemdFileName = "temperatureX.log";
330	<	xTempLog_.open(rnemdFileName.c_str());
331	<	rnemdFileName = "temperatureY.log";
332	<	yTempLog_.open(rnemdFileName.c_str());
333	<	rnemdFileName = "temperatureZ.log";
334	<	zTempLog_.open(rnemdFileName.c_str());
335	<	}
336	<	if (outputRotTemp_) {
207	<	rnemdFileName = "temperatureR.log";
208	<	rotTempLog_.open(rnemdFileName.c_str());
209	<	}
210	<
211	<	//James put this in
212	<	if (outputDen_) {
213	<	rnemdFileName = "Density.log";
214	<	denLog_.open(rnemdFileName.c_str());
215	<	}
216	<	if (outputAh_) {
217	<	rnemdFileName = "Ah.log";
218	<	AhLog_.open(rnemdFileName.c_str());
219	<	}
220	<	if (outputVz_) {
221	<	rnemdFileName = "velocityZ.log";
222	<	vzzLog_.open(rnemdFileName.c_str());
223	<	}
224	<	logFrameCount_ = 0;
225	<	#ifdef IS_MPI
226	<	}
227	<	#endif
328	>	OutputData velocity;
329	>	velocity.units = "angstroms/fs";
330	>	velocity.title =  "Velocity";
331	>	velocity.dataType = "Vector3d";
332	>	velocity.accumulator.reserve(nBins_);
333	>	for (int i = 0; i < nBins_; i++)
334	>	velocity.accumulator.push_back( new VectorAccumulator() );
335	>	data_[VELOCITY] = velocity;
336	>	outputMap_["VELOCITY"] = VELOCITY;
337
338	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
339	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
340	<	midBin_ = nBins_ / 2;
341	<	if (simParams->haveRNEMD_binShift()) {
342	<	if (simParams->getRNEMD_binShift()) {
343	<	zShift_ = 0.5 / (RealType)(nBins_);
344	<	} else {
345	<	zShift_ = 0.0;
346	<	}
338	>	OutputData density;
339	>	density.units =  "g cm^-3";
340	>	density.title =  "Density";
341	>	density.dataType = "RealType";
342	>	density.accumulator.reserve(nBins_);
343	>	for (int i = 0; i < nBins_; i++)
344	>	density.accumulator.push_back( new Accumulator() );
345	>	data_[DENSITY] = density;
346	>	outputMap_["DENSITY"] =  DENSITY;
347	>
348	>	if (hasOutputFields) {
349	>	parseOutputFileFormat(rnemdParams->getOutputFields());
350		} else {
351	<	zShift_ = 0.0;
352	<	}
353	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
354	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
355	<	//set to 0.0 if not using it; N/A in status output yet
356	<	if (simParams->haveRNEMD_logWidth()) {
357	<	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
358	<	/*arbitary rnemdLogWidth_, no checking;
359	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
360	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
361	<	cerr << "Automaically set back to default.\n";
362	<	rnemdLogWidth_ = nBins_;
363	<	}*/
364	<	} else {
365	<	set_RNEMD_logWidth(nBins_);
351	>	outputMask_.set(Z);
352	>	switch (rnemdFluxType_) {
353	>	case rnemdKE:
354	>	case rnemdRotKE:
355	>	case rnemdFullKE:
356	>	outputMask_.set(TEMPERATURE);
357	>	break;
358	>	case rnemdPx:
359	>	case rnemdPy:
360	>	outputMask_.set(VELOCITY);
361	>	break;
362	>	case rnemdPz:
363	>	case rnemdPvector:
364	>	outputMask_.set(VELOCITY);
365	>	outputMask_.set(DENSITY);
366	>	break;
367	>	case rnemdKePx:
368	>	case rnemdKePy:
369	>	outputMask_.set(TEMPERATURE);
370	>	outputMask_.set(VELOCITY);
371	>	break;
372	>	case rnemdKePvector:
373	>	outputMask_.set(TEMPERATURE);
374	>	outputMask_.set(VELOCITY);
375	>	outputMask_.set(DENSITY);
376	>	break;
377	>	default:
378	>	break;
379	>	}
380		}
381	<	tempHist_.resize(rnemdLogWidth_, 0.0);
382	<	tempCount_.resize(rnemdLogWidth_, 0);
383	<	pxzHist_.resize(rnemdLogWidth_, 0.0);
384	<	//vxzCount_.resize(rnemdLogWidth_, 0);
385	<	pyzHist_.resize(rnemdLogWidth_, 0.0);
386	<	//vyzCount_.resize(rnemdLogWidth_, 0);
381	>
382	>	if (hasOutputFileName) {
383	>	rnemdFileName_ = rnemdParams->getOutputFileName();
384	>	} else {
385	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
386	>	}
387
388	<	mHist_.resize(rnemdLogWidth_, 0.0);
263	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
264	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
265	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
266	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
267	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
268	<	rotTempCount_.resize(rnemdLogWidth_, 0);
269	<	// James put this in
270	<	DenHist_.resize(rnemdLogWidth_, 0.0);
271	<	pzzHist_.resize(rnemdLogWidth_, 0.0);
388	>	exchangeTime_ = rnemdParams->getExchangeTime();
389
390	<	set_RNEMD_exchange_total(0.0);
391	<	if (simParams->haveRNEMD_targetFlux()) {
392	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
393	<	} else {
394	<	set_RNEMD_target_flux(0.0);
395	<	}
396	<	if (simParams->haveRNEMD_targetJzKE()) {
280	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
281	<	} else {
282	<	set_RNEMD_target_JzKE(0.0);
283	<	}
284	<	if (simParams->haveRNEMD_targetJzpx()) {
285	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
286	<	} else {
287	<	set_RNEMD_target_jzpx(0.0);
288	<	}
289	<	jzp_.x() = targetJzpx_;
290	<	njzp_.x() = -targetJzpx_;
291	<	if (simParams->haveRNEMD_targetJzpy()) {
292	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
293	<	} else {
294	<	set_RNEMD_target_jzpy(0.0);
295	<	}
296	<	jzp_.y() = targetJzpy_;
297	<	njzp_.y() = -targetJzpy_;
298	<	if (simParams->haveRNEMD_targetJzpz()) {
299	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
300	<	} else {
301	<	set_RNEMD_target_jzpz(0.0);
302	<	}
303	<	jzp_.z() = targetJzpz_;
304	<	njzp_.z() = -targetJzpz_;
390	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
391	>	Mat3x3d hmat = currentSnap_->getHmat();
392	>
393	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
394	>	// Lx, Ly = box dimensions in x & y
395	>	// dt = exchange time interval
396	>	// flux = target flux
397
398	<	#ifndef IS_MPI
399	<	if (simParams->haveSeed()) {
400	<	seedValue = simParams->getSeed();
401	<	randNumGen_ = new SeqRandNumGen(seedValue);
402	<	}else {
403	<	randNumGen_ = new SeqRandNumGen();
404	<	}
405	<	#else
406	<	if (simParams->haveSeed()) {
407	<	seedValue = simParams->getSeed();
408	<	randNumGen_ = new ParallelRandNumGen(seedValue);
409	<	}else {
410	<	randNumGen_ = new ParallelRandNumGen();
319	<	}
320	<	#endif
321	<	}
398	>	RealType area = currentSnap_->getXYarea();
399	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
400	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
401	>
402	>	// total exchange sums are zeroed out at the beginning:
403	>
404	>	kineticExchange_ = 0.0;
405	>	momentumExchange_ = V3Zero;
406	>
407	>	if (hasSlabWidth)
408	>	slabWidth_ = rnemdParams->getSlabWidth();
409	>	else
410	>	slabWidth_ = hmat(2,2) / 10.0;
411
412	<	RNEMD::~RNEMD() {
413	<	delete randNumGen_;
412	>	if (hasSlabACenter)
413	>	slabACenter_ = rnemdParams->getSlabACenter();
414	>	else
415	>	slabACenter_ = 0.0;
416
417	+	if (hasSlabBCenter)
418	+	slabBCenter_ = rnemdParams->getSlabBCenter();
419	+	else
420	+	slabBCenter_ = hmat(2,2) / 2.0;
421	+
422	+	}
423	+
424	+	RNEMD::~RNEMD() {
425	+	if (!doRNEMD_) return;
426		#ifdef IS_MPI
427		if (worldRank == 0) {
428		#endif
329	–
330	–	sprintf(painCave.errMsg,
331	–	"RNEMD: total failed trials: %d\n",
332	–	failTrialCount_);
333	–	painCave.isFatal = 0;
334	–	painCave.severity = OPENMD_INFO;
335	–	simError();
336	–
337	–	if (outputTemp_) tempLog_.close();
338	–	if (outputVx_)   vxzLog_.close();
339	–	if (outputVy_)   vyzLog_.close();
429
430	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
431	<	rnemdType_ == rnemdPyScale) {
432	<	sprintf(painCave.errMsg,
344	<	"RNEMD: total root-checking warnings: %d\n",
345	<	failRootCount_);
346	<	painCave.isFatal = 0;
347	<	painCave.severity = OPENMD_INFO;
348	<	simError();
349	<	}
350	<	if (output3DTemp_) {
351	<	xTempLog_.close();
352	<	yTempLog_.close();
353	<	zTempLog_.close();
354	<	}
355	<	if (outputRotTemp_) rotTempLog_.close();
356	<	// James put this in
357	<	if (outputDen_) denLog_.close();
358	<	if (outputAh_)  AhLog_.close();
359	<	if (outputVz_)  vzzLog_.close();
430	>	writeOutputFile();
431	>
432	>	rnemdFile_.close();
433
434		#ifdef IS_MPI
435		}
436		#endif
437		}
438	+
439	+	bool RNEMD::inSlabA(Vector3d pos) {
440	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
441	+	}
442	+	bool RNEMD::inSlabB(Vector3d pos) {
443	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
444	+	}
445
446		void RNEMD::doSwap() {
447	<
447	>	if (!doRNEMD_) return;
448		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
449		Mat3x3d hmat = currentSnap_->getHmat();
450
#	Line 372 | Line 452 | namespace OpenMD {
452
453		int selei;
454		StuntDouble* sd;
375	–	int idx;
455
456		RealType min_val;
457		bool min_found = false;
#	Line 385 | Line 464 | namespace OpenMD {
464		for (sd = seleMan_.beginSelected(selei); sd != NULL;
465		sd = seleMan_.nextSelected(selei)) {
466
388	–	idx = sd->getLocalIndex();
389	–
467		Vector3d pos = sd->getPos();
468
469		// wrap the stuntdouble's position back into the box:
470
471		if (usePeriodicBoundaryConditions_)
472		currentSnap_->wrapVector(pos);
473	+	bool inA = inSlabA(pos);
474	+	bool inB = inSlabB(pos);
475
476	<	// which bin is this stuntdouble in?
398	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
399	<
400	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
401	<
402	<
403	<	// if we're in bin 0 or the middleBin
404	<	if (binNo == 0 || binNo == midBin_) {
476	>	if (inA || inB) {
477
478		RealType mass = sd->getMass();
479		Vector3d vel = sd->getVel();
480		RealType value;
481	<
482	<	switch(rnemdType_) {
483	<	case rnemdKineticSwap :
481	>
482	>	switch(rnemdFluxType_) {
483	>	case rnemdKE :
484
485		value = mass * vel.lengthSquare();
486
#	Line 428 | Line 500 | namespace OpenMD {
500		+ angMom[2]*angMom[2]/I(2, 2);
501		}
502		} //angular momenta exchange enabled
431	–	//energyConvert temporarily disabled
432	–	//make exchangeSum_ comparable between swap & scale
433	–	//value = value * 0.5 / PhysicalConstants::energyConvert;
503		value *= 0.5;
504		break;
505		case rnemdPx :
#	Line 446 | Line 515 | namespace OpenMD {
515		break;
516		}
517
518	<	if (binNo == 0) {
518	>	if (inA == 0) {
519		if (!min_found) {
520		min_val = value;
521		min_sd = sd;
#	Line 457 | Line 526 | namespace OpenMD {
526		min_sd = sd;
527		}
528		}
529	<	} else { //midBin_
529	>	} else {
530		if (!max_found) {
531		max_val = value;
532		max_sd = sd;
#	Line 471 | Line 540 | namespace OpenMD {
540		}
541		}
542		}
543	<
544	<	#ifdef IS_MPI
545	<	int nProc, worldRank;
546	<
478	<	nProc = MPI::COMM_WORLD.Get_size();
479	<	worldRank = MPI::COMM_WORLD.Get_rank();
480	<
543	>
544	>	#ifdef IS_MPI
545	>	int worldRank = MPI::COMM_WORLD.Get_rank();
546	>
547		bool my_min_found = min_found;
548		bool my_max_found = max_found;
549
#	Line 532 | Line 598 | namespace OpenMD {
598		Vector3d max_vel = max_sd->getVel();
599		RealType temp_vel;
600
601	<	switch(rnemdType_) {
602	<	case rnemdKineticSwap :
601	>	switch(rnemdFluxType_) {
602	>	case rnemdKE :
603		min_sd->setVel(max_vel);
604		max_sd->setVel(min_vel);
605		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 584 | Line 650 | namespace OpenMD {
650		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
651		min_vals.rank, 0, status);
652
653	<	switch(rnemdType_) {
654	<	case rnemdKineticSwap :
653	>	switch(rnemdFluxType_) {
654	>	case rnemdKE :
655		max_sd->setVel(min_vel);
656		//angular momenta exchange enabled
657		if (max_sd->isDirectional()) {
#	Line 630 | Line 696 | namespace OpenMD {
696		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
697		max_vals.rank, 0, status);
698
699	<	switch(rnemdType_) {
700	<	case rnemdKineticSwap :
699	>	switch(rnemdFluxType_) {
700	>	case rnemdKE :
701		min_sd->setVel(max_vel);
702		//angular momenta exchange enabled
703		if (min_sd->isDirectional()) {
#	Line 665 | Line 731 | namespace OpenMD {
731		}
732		}
733		#endif
734	<	exchangeSum_ += max_val - min_val;
734	>
735	>	switch(rnemdFluxType_) {
736	>	case rnemdKE:
737	>	kineticExchange_ += max_val - min_val;
738	>	break;
739	>	case rnemdPx:
740	>	momentumExchange_.x() += max_val - min_val;
741	>	break;
742	>	case rnemdPy:
743	>	momentumExchange_.y() += max_val - min_val;
744	>	break;
745	>	case rnemdPz:
746	>	momentumExchange_.z() += max_val - min_val;
747	>	break;
748	>	default:
749	>	break;
750	>	}
751		} else {
752		sprintf(painCave.errMsg,
753	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
753	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
754		painCave.isFatal = 0;
755		painCave.severity = OPENMD_INFO;
756		simError();
#	Line 676 | Line 758 | namespace OpenMD {
758		}
759		} else {
760		sprintf(painCave.errMsg,
761	<	"RNEMD: exchange NOT performed because selected object\n"
762	<	"\tnot present in at least one of the two slabs.\n");
761	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
762	>	"\twas not present in at least one of the two slabs.\n");
763		painCave.isFatal = 0;
764		painCave.severity = OPENMD_INFO;
765		simError();
766		failTrialCount_++;
767	<	}
686	<
767	>	}
768		}
769
770	<	void RNEMD::doScale() {
771	<
770	>	void RNEMD::doNIVS() {
771	>	if (!doRNEMD_) return;
772		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
773		Mat3x3d hmat = currentSnap_->getHmat();
774
#	Line 695 | Line 776 | namespace OpenMD {
776
777		int selei;
778		StuntDouble* sd;
698	–	int idx;
779
780		vector<StuntDouble*> hotBin, coldBin;
781
#	Line 717 | Line 797 | namespace OpenMD {
797		for (sd = seleMan_.beginSelected(selei); sd != NULL;
798		sd = seleMan_.nextSelected(selei)) {
799
720	–	idx = sd->getLocalIndex();
721	–
800		Vector3d pos = sd->getPos();
801
802		// wrap the stuntdouble's position back into the box:
#	Line 727 | Line 805 | namespace OpenMD {
805		currentSnap_->wrapVector(pos);
806
807		// which bin is this stuntdouble in?
808	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
808	>	bool inA = inSlabA(pos);
809	>	bool inB = inSlabB(pos);
810
811	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
812	<
734	<	// if we're in bin 0 or the middleBin
735	<	if (binNo == 0 || binNo == midBin_) {
736	<
811	>	if (inA || inB) {
812	>
813		RealType mass = sd->getMass();
814		Vector3d vel = sd->getVel();
815
816	<	if (binNo == 0) {
816	>	if (inA) {
817		hotBin.push_back(sd);
818		Phx += mass * vel.x();
819		Phy += mass * vel.y();
#	Line 745 | Line 821 | namespace OpenMD {
821		Khx += mass * vel.x() * vel.x();
822		Khy += mass * vel.y() * vel.y();
823		Khz += mass * vel.z() * vel.z();
748	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
824		if (sd->isDirectional()) {
825		Vector3d angMom = sd->getJ();
826		Mat3x3d I = sd->getI();
#	Line 761 | Line 836 | namespace OpenMD {
836		+ angMom[2]*angMom[2]/I(2, 2);
837		}
838		}
839	<	//}
765	<	} else { //midBin_
839	>	} else {
840		coldBin.push_back(sd);
841		Pcx += mass * vel.x();
842		Pcy += mass * vel.y();
#	Line 770 | Line 844 | namespace OpenMD {
844		Kcx += mass * vel.x() * vel.x();
845		Kcy += mass * vel.y() * vel.y();
846		Kcz += mass * vel.z() * vel.z();
773	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
847		if (sd->isDirectional()) {
848		Vector3d angMom = sd->getJ();
849		Mat3x3d I = sd->getI();
#	Line 786 | Line 859 | namespace OpenMD {
859		+ angMom[2]*angMom[2]/I(2, 2);
860		}
861		}
789	–	//}
862		}
863		}
864		}
#	Line 800 | Line 872 | namespace OpenMD {
872		Kcz *= 0.5;
873		Kcw *= 0.5;
874
803	–	// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
804	–	//        << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
805	–	//        << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
806	–	// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
807	–	//        << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
808	–
875		#ifdef IS_MPI
876		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
877		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 831 | Line 897 | namespace OpenMD {
897		RealType pz = Pcz / Phz;
898		RealType c, x, y, z;
899		bool successfulScale = false;
900	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
901	<	(rnemdType_ == rnemdKineticScaleAM)) {
900	>	if ((rnemdFluxType_ == rnemdFullKE) ||
901	>	(rnemdFluxType_ == rnemdRotKE)) {
902		//may need sanity check Khw & Kcw > 0
903
904	<	if (rnemdType_ == rnemdKineticScaleVAM) {
905	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
904	>	if (rnemdFluxType_ == rnemdFullKE) {
905	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
906		} else {
907	<	c = 1.0 - targetFlux_ / Kcw;
907	>	c = 1.0 - kineticTarget_ / Kcw;
908		}
909
910		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
911		c = sqrt(c);
912	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
847	<	//now convert to hotBin coefficient
912	>
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 860 | 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;
876	–	//vel.x() *= c;
877	–	//vel.y() *= c;
878	–	//vel.z() *= c;
942		(*sdi)->setVel(vel);
943		}
944		if ((*sdi)->isDirectional()) {
945		Vector3d angMom = (*sdi)->getJ() * c;
883	–	//angMom[0] *= c;
884	–	//angMom[1] *= c;
885	–	//angMom[2] *= c;
946		(*sdi)->setJ(angMom);
947		}
948		}
949		w = sqrt(w);
890	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
891	–	<< "\twh= " << w << endl;
950		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
951	<	if (rnemdType_ == rnemdKineticScaleVAM) {
951	>	if (rnemdFluxType_ == rnemdFullKE) {
952		vel = (*sdi)->getVel();
953		vel.x() *= x;
954		vel.y() *= y;
#	Line 899 | Line 957 | namespace OpenMD {
957		}
958		if ((*sdi)->isDirectional()) {
959		Vector3d angMom = (*sdi)->getJ() * w;
902	–	//angMom[0] *= w;
903	–	//angMom[1] *= w;
904	–	//angMom[2] *= w;
960		(*sdi)->setJ(angMom);
961		}
962		}
963		successfulScale = true;
964	<	exchangeSum_ += targetFlux_;
964	>	kineticExchange_ += kineticTarget_;
965		}
966		}
967		} else {
968		RealType a000, a110, c0, a001, a111, b01, b11, c1;
969	<	switch(rnemdType_) {
970	<	case rnemdKineticScale :
969	>	switch(rnemdFluxType_) {
970	>	case rnemdKE :
971		/* used hotBin coeff's & only scale x & y dimensions
972		RealType px = Phx / Pcx;
973		RealType py = Phy / Pcy;
974		a110 = Khy;
975	<	c0 = - Khx - Khy - targetFlux_;
975	>	c0 = - Khx - Khy - kineticTarget_;
976		a000 = Khx;
977		a111 = Kcy * py * py;
978		b11 = -2.0 * Kcy * py * (1.0 + py);
979	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
979	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
980		b01 = -2.0 * Kcx * px * (1.0 + px);
981		a001 = Kcx * px * px;
982		*/
983		//scale all three dimensions, let c_x = c_y
984		a000 = Kcx + Kcy;
985		a110 = Kcz;
986	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
986	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
987		a001 = Khx * px * px + Khy * py * py;
988		a111 = Khz * pz * pz;
989		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
990		b11 = -2.0 * Khz * pz * (1.0 + pz);
991		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
992	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
992	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
993		break;
994	<	case rnemdPxScale :
995	<	c = 1 - targetFlux_ / Pcx;
994	>	case rnemdPx :
995	>	c = 1 - momentumTarget_.x() / Pcx;
996		a000 = Kcy;
997		a110 = Kcz;
998		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 948 | Line 1003 | namespace OpenMD {
1003		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1004		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1005		break;
1006	<	case rnemdPyScale :
1007	<	c = 1 - targetFlux_ / Pcy;
1006	>	case rnemdPy :
1007	>	c = 1 - momentumTarget_.y() / Pcy;
1008		a000 = Kcx;
1009		a110 = Kcz;
1010		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 960 | Line 1015 | namespace OpenMD {
1015		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1016		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1017		break;
1018	<	case rnemdPzScale ://we don't really do this, do we?
1019	<	c = 1 - targetFlux_ / Pcz;
1018	>	case rnemdPz ://we don't really do this, do we?
1019	>	c = 1 - momentumTarget_.z() / Pcz;
1020		a000 = Kcx;
1021		a110 = Kcy;
1022		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1046 | Line 1101 | namespace OpenMD {
1101		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1102		r1 = (*rpi).first;
1103		r2 = (*rpi).second;
1104	<	switch(rnemdType_) {
1105	<	case rnemdKineticScale :
1104	>	switch(rnemdFluxType_) {
1105	>	case rnemdKE :
1106		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1107		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1108		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1109		break;
1110	<	case rnemdPxScale :
1110	>	case rnemdPx :
1111		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1113		break;
1114	<	case rnemdPyScale :
1114	>	case rnemdPy :
1115		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1116		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1117		break;
1118	<	case rnemdPzScale :
1118	>	case rnemdPz :
1119		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1120		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1121		default :
#	Line 1074 | Line 1129 | namespace OpenMD {
1129		#ifdef IS_MPI
1130		if (worldRank == 0) {
1131		#endif
1132	<	sprintf(painCave.errMsg,
1133	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1134	<	bestPair.first, bestPair.second);
1135	<	painCave.isFatal = 0;
1136	<	painCave.severity = OPENMD_INFO;
1137	<	simError();
1132	>	// sprintf(painCave.errMsg,
1133	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1134	>	//         bestPair.first, bestPair.second);
1135	>	// painCave.isFatal = 0;
1136	>	// painCave.severity = OPENMD_INFO;
1137	>	// simError();
1138		#ifdef IS_MPI
1139		}
1140		#endif
1141
1142	<	switch(rnemdType_) {
1143	<	case rnemdKineticScale :
1142	>	switch(rnemdFluxType_) {
1143	>	case rnemdKE :
1144		x = bestPair.first;
1145		y = bestPair.first;
1146		z = bestPair.second;
1147		break;
1148	<	case rnemdPxScale :
1148	>	case rnemdPx :
1149		x = c;
1150		y = bestPair.first;
1151		z = bestPair.second;
1152		break;
1153	<	case rnemdPyScale :
1153	>	case rnemdPy :
1154		x = bestPair.first;
1155		y = c;
1156		z = bestPair.second;
1157		break;
1158	<	case rnemdPzScale :
1158	>	case rnemdPz :
1159		x = bestPair.first;
1160		y = bestPair.second;
1161		z = c;
#	Line 1129 | Line 1184 | namespace OpenMD {
1184		(*sdi)->setVel(vel);
1185		}
1186		successfulScale = true;
1187	<	exchangeSum_ += targetFlux_;
1187	>	switch(rnemdFluxType_) {
1188	>	case rnemdKE :
1189	>	kineticExchange_ += kineticTarget_;
1190	>	break;
1191	>	case rnemdPx :
1192	>	case rnemdPy :
1193	>	case rnemdPz :
1194	>	momentumExchange_ += momentumTarget_;
1195	>	break;
1196	>	default :
1197	>	break;
1198	>	}
1199		}
1200		}
1201		if (successfulScale != true) {
1202		sprintf(painCave.errMsg,
1203	<	"RNEMD: exchange NOT performed!\n");
1203	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1204	>	"\tthe constraint equations may not exist or there may be\n"
1205	>	"\tno selected objects in one or both slabs.\n");
1206		painCave.isFatal = 0;
1207		painCave.severity = OPENMD_INFO;
1208		simError();
#	Line 1142 | Line 1210 | namespace OpenMD {
1210		}
1211		}
1212
1213	<	void RNEMD::doShiftScale() {
1214	<
1213	>	void RNEMD::doVSS() {
1214	>	if (!doRNEMD_) return;
1215		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1216		RealType time = currentSnap_->getTime();
1217		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 1152 | Line 1220 | namespace OpenMD {
1220
1221		int selei;
1222		StuntDouble* sd;
1155	–	int idx;
1223
1224		vector<StuntDouble*> hotBin, coldBin;
1225
#	Line 1167 | Line 1234 | namespace OpenMD {
1234		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1235		sd = seleMan_.nextSelected(selei)) {
1236
1170	–	idx = sd->getLocalIndex();
1171	–
1237		Vector3d pos = sd->getPos();
1238
1239		// wrap the stuntdouble's position back into the box:
#	Line 1177 | Line 1242 | namespace OpenMD {
1242		currentSnap_->wrapVector(pos);
1243
1244		// which bin is this stuntdouble in?
1245	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1246	<
1247	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1248	<
1184	<	// if we're in bin 0 or the middleBin
1185	<	if (binNo == 0 || binNo == midBin_) {
1245	>	bool inA = inSlabA(pos);
1246	>	bool inB = inSlabB(pos);
1247	>
1248	>	if (inA || inB) {
1249
1250		RealType mass = sd->getMass();
1251		Vector3d vel = sd->getVel();
1252
1253	<	if (binNo == 0) {
1253	>	if (inA) {
1254		hotBin.push_back(sd);
1192	–	//std::cerr << "before, velocity = " << vel << endl;
1255		Ph += mass * vel;
1194	–	//std::cerr << "after, velocity = " << vel << endl;
1256		Mh += mass;
1257		Kh += mass * vel.lengthSquare();
1258	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1258	>	if (rnemdFluxType_ == rnemdFullKE) {
1259		if (sd->isDirectional()) {
1260		Vector3d angMom = sd->getJ();
1261		Mat3x3d I = sd->getI();
#	Line 1216 | Line 1277 | namespace OpenMD {
1277		Pc += mass * vel;
1278		Mc += mass;
1279		Kc += mass * vel.lengthSquare();
1280	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1280	>	if (rnemdFluxType_ == rnemdFullKE) {
1281		if (sd->isDirectional()) {
1282		Vector3d angMom = sd->getJ();
1283		Mat3x3d I = sd->getI();
#	Line 1239 | Line 1300 | namespace OpenMD {
1300
1301		Kh *= 0.5;
1302		Kc *= 0.5;
1242	–
1243	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1244	–	//        << "\tKc= " << Kc << endl;
1245	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1303
1304		#ifdef IS_MPI
1305		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
#	Line 1256 | Line 1313 | namespace OpenMD {
1313		bool successfulExchange = false;
1314		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1315		Vector3d vc = Pc / Mc;
1316	<	Vector3d ac = njzp_ / Mc + vc;
1317	<	Vector3d acrec = njzp_ / Mc;
1318	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1316	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1317	>	Vector3d acrec = -momentumTarget_ / Mc;
1318	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1319		if (cNumerator > 0.0) {
1320		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1321		if (cDenominator > 0.0) {
1322		RealType c = sqrt(cNumerator / cDenominator);
1323		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1324		Vector3d vh = Ph / Mh;
1325	<	Vector3d ah = jzp_ / Mh + vh;
1326	<	Vector3d ahrec = jzp_ / Mh;
1327	<	RealType hNumerator = Kh + targetJzKE_
1325	>	Vector3d ah = momentumTarget_ / Mh + vh;
1326	>	Vector3d ahrec = momentumTarget_ / Mh;
1327	>	RealType hNumerator = Kh + kineticTarget_
1328		- 0.5 * Mh * ah.lengthSquare();
1329		if (hNumerator > 0.0) {
1330		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1331		if (hDenominator > 0.0) {
1332		RealType h = sqrt(hNumerator / hDenominator);
1333		if ((h > 0.9) && (h < 1.1)) {
1334	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1278	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1334	>
1335		vector<StuntDouble*>::iterator sdi;
1336		Vector3d vel;
1337		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1338		//vel = (*sdi)->getVel();
1339		vel = ((*sdi)->getVel() - vc) * c + ac;
1340		(*sdi)->setVel(vel);
1341	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1341	>	if (rnemdFluxType_ == rnemdFullKE) {
1342		if ((*sdi)->isDirectional()) {
1343		Vector3d angMom = (*sdi)->getJ() * c;
1344		(*sdi)->setJ(angMom);
#	Line 1293 | Line 1349 | namespace OpenMD {
1349		//vel = (*sdi)->getVel();
1350		vel = ((*sdi)->getVel() - vh) * h + ah;
1351		(*sdi)->setVel(vel);
1352	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1352	>	if (rnemdFluxType_ == rnemdFullKE) {
1353		if ((*sdi)->isDirectional()) {
1354		Vector3d angMom = (*sdi)->getJ() * h;
1355		(*sdi)->setJ(angMom);
#	Line 1301 | Line 1357 | namespace OpenMD {
1357		}
1358		}
1359		successfulExchange = true;
1360	<	exchangeSum_ += targetFlux_;
1361	<	// this is a redundant variable for doShiftScale() so that
1306	<	// RNEMD can output one exchange quantity needed in a job.
1307	<	// need a better way to do this.
1308	<	//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n';
1309	<	//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n';
1310	<	//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n';
1311	<	Asum_ += (ahrec.z() - acrec.z());
1312	<	Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc)));
1313	<	AhCount_ = ahrec.z();
1314	<	if (outputAh_) {
1315	<	AhLog_ << time << "   ";
1316	<	AhLog_ << AhCount_;
1317	<	AhLog_ << endl;
1318	<	}
1360	>	kineticExchange_ += kineticTarget_;
1361	>	momentumExchange_ += momentumTarget_;
1362		}
1363		}
1364		}
#	Line 1324 | Line 1367 | namespace OpenMD {
1367		}
1368		}
1369		if (successfulExchange != true) {
1370	<	//   sprintf(painCave.errMsg,
1371	<	//              "RNEMD: exchange NOT performed!\n");
1372	<	//   painCave.isFatal = 0;
1373	<	//   painCave.severity = OPENMD_INFO;
1374	<	//   simError();
1370	>	sprintf(painCave.errMsg,
1371	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1372	>	"\tthe constraint equations may not exist or there may be\n"
1373	>	"\tno selected objects in one or both slabs.\n");
1374	>	painCave.isFatal = 0;
1375	>	painCave.severity = OPENMD_INFO;
1376	>	simError();
1377		failTrialCount_++;
1378		}
1379		}
1380
1381		void RNEMD::doRNEMD() {
1382	<
1383	<	switch(rnemdType_) {
1384	<	case rnemdKineticScale :
1385	<	case rnemdKineticScaleVAM :
1341	<	case rnemdKineticScaleAM :
1342	<	case rnemdPxScale :
1343	<	case rnemdPyScale :
1344	<	case rnemdPzScale :
1345	<	doScale();
1346	<	break;
1347	<	case rnemdKineticSwap :
1348	<	case rnemdPx :
1349	<	case rnemdPy :
1350	<	case rnemdPz :
1382	>	if (!doRNEMD_) return;
1383	>	trialCount_++;
1384	>	switch(rnemdMethod_) {
1385	>	case rnemdSwap:
1386		doSwap();
1387		break;
1388	<	case rnemdShiftScaleV :
1389	<	case rnemdShiftScaleVAM :
1355	<	doShiftScale();
1388	>	case rnemdNIVS:
1389	>	doNIVS();
1390		break;
1391	<	case rnemdUnknown :
1391	>	case rnemdVSS:
1392	>	doVSS();
1393	>	break;
1394	>	case rnemdUnkownMethod:
1395		default :
1396		break;
1397		}
1398		}
1399
1400		void RNEMD::collectData() {
1401	<
1401	>	if (!doRNEMD_) return;
1402		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1403		Mat3x3d hmat = currentSnap_->getHmat();
1404
1405	+	areaAccumulator_->add(currentSnap_->getXYarea());
1406	+
1407		seleMan_.setSelectionSet(evaluator_.evaluate());
1408
1409	<	int selei;
1409	>	int selei(0);
1410		StuntDouble* sd;
1372	–	int idx;
1411
1412	<	logFrameCount_++;
1412	>	vector<RealType> binMass(nBins_, 0.0);
1413	>	vector<RealType> binPx(nBins_, 0.0);
1414	>	vector<RealType> binPy(nBins_, 0.0);
1415	>	vector<RealType> binPz(nBins_, 0.0);
1416	>	vector<RealType> binKE(nBins_, 0.0);
1417	>	vector<int> binDOF(nBins_, 0);
1418	>	vector<int> binCount(nBins_, 0);
1419
1420		// alternative approach, track all molecules instead of only those
1421		// selected for scaling/swapping:
#	Line 1379 | Line 1423 | namespace OpenMD {
1423		SimInfo::MoleculeIterator miter;
1424		vector<StuntDouble*>::iterator iiter;
1425		Molecule* mol;
1426	<	StuntDouble* integrableObject;
1426	>	StuntDouble* sd;
1427		for (mol = info_->beginMolecule(miter); mol != NULL;
1428		mol = info_->nextMolecule(miter))
1429	<	integrableObject is essentially sd
1430	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1431	<	integrableObject != NULL;
1432	<	integrableObject = mol->nextIntegrableObject(iiter))
1429	>	sd is essentially sd
1430	>	for (sd = mol->beginIntegrableObject(iiter);
1431	>	sd != NULL;
1432	>	sd = mol->nextIntegrableObject(iiter))
1433		*/
1434	+
1435		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1436	<	sd = seleMan_.nextSelected(selei)) {
1437	<
1393	<	idx = sd->getLocalIndex();
1394	<
1436	>	sd = seleMan_.nextSelected(selei)) {
1437	>
1438		Vector3d pos = sd->getPos();
1439
1440		// wrap the stuntdouble's position back into the box:
1441
1442		if (usePeriodicBoundaryConditions_)
1443		currentSnap_->wrapVector(pos);
1444	<
1444	>
1445	>
1446		// which bin is this stuntdouble in?
1447		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1448	<
1449	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1450	<	rnemdLogWidth_;
1451	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1452	<	/*
1409	<	if (rnemdLogWidth_ == midBin_ + 1)
1410	<	if (binNo > midBin_)
1411	<	binNo = nBins_ - binNo;
1412	<	*/
1448	>	// Shift molecules by half a box to have bins start at 0
1449	>	// The modulo operator is used to wrap the case when we are
1450	>	// beyond the end of the bins back to the beginning.
1451	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1452	>
1453		RealType mass = sd->getMass();
1414	–	mHist_[binNo] += mass;
1454		Vector3d vel = sd->getVel();
1416	–	RealType value;
1417	–	//RealType xVal, yVal, zVal;
1455
1456	<	if (outputTemp_) {
1457	<	value = mass * vel.lengthSquare();
1458	<	tempCount_[binNo] += 3;
1459	<	if (sd->isDirectional()) {
1460	<	Vector3d angMom = sd->getJ();
1461	<	Mat3x3d I = sd->getI();
1462	<	if (sd->isLinear()) {
1463	<	int i = sd->linearAxis();
1464	<	int j = (i + 1) % 3;
1465	<	int k = (i + 2) % 3;
1466	<	value += angMom[j] * angMom[j] / I(j, j) +
1467	<	angMom[k] * angMom[k] / I(k, k);
1468	<	tempCount_[binNo] +=2;
1469	<	} else {
1470	<	value += angMom[0] * angMom[0] / I(0, 0) +
1471	<	angMom[1]*angMom[1]/I(1, 1) +
1472	<	angMom[2]*angMom[2]/I(2, 2);
1473	<	tempCount_[binNo] +=3;
1474	<	}
1475	<	}
1476	<	value = value / PhysicalConstants::energyConvert
1477	<	/ PhysicalConstants::kb;//may move to getStatus()
1478	<	tempHist_[binNo] += value;
1456	>	binCount[binNo]++;
1457	>	binMass[binNo] += mass;
1458	>	binPx[binNo] += mass*vel.x();
1459	>	binPy[binNo] += mass*vel.y();
1460	>	binPz[binNo] += mass*vel.z();
1461	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1462	>	binDOF[binNo] += 3;
1463	>
1464	>	if (sd->isDirectional()) {
1465	>	Vector3d angMom = sd->getJ();
1466	>	Mat3x3d I = sd->getI();
1467	>	if (sd->isLinear()) {
1468	>	int i = sd->linearAxis();
1469	>	int j = (i + 1) % 3;
1470	>	int k = (i + 2) % 3;
1471	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1472	>	angMom[k] * angMom[k] / I(k, k));
1473	>	binDOF[binNo] += 2;
1474	>	} else {
1475	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1476	>	angMom[1] * angMom[1] / I(1, 1) +
1477	>	angMom[2] * angMom[2] / I(2, 2));
1478	>	binDOF[binNo] += 3;
1479	>	}
1480		}
1481	<	if (outputVx_) {
1482	<	value = mass * vel[0];
1483	<	//vxzCount_[binNo]++;
1484	<	pxzHist_[binNo] += value;
1485	<	}
1486	<	if (outputVy_) {
1487	<	value = mass * vel[1];
1488	<	//vyzCount_[binNo]++;
1489	<	pyzHist_[binNo] += value;
1490	<	}
1481	>	}
1482	>
1483	>	#ifdef IS_MPI
1484	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1485	>	nBins_, MPI::INT, MPI::SUM);
1486	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1487	>	nBins_, MPI::REALTYPE, MPI::SUM);
1488	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1489	>	nBins_, MPI::REALTYPE, MPI::SUM);
1490	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1491	>	nBins_, MPI::REALTYPE, MPI::SUM);
1492	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1493	>	nBins_, MPI::REALTYPE, MPI::SUM);
1494	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1495	>	nBins_, MPI::REALTYPE, MPI::SUM);
1496	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1497	>	nBins_, MPI::INT, MPI::SUM);
1498	>	#endif
1499
1500	<	if (output3DTemp_) {
1501	<	value = mass * vel.x() * vel.x();
1502	<	xTempHist_[binNo] += value;
1503	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1504	<	/ PhysicalConstants::kb;
1505	<	yTempHist_[binNo] += value;
1506	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1507	<	/ PhysicalConstants::kb;
1508	<	zTempHist_[binNo] += value;
1509	<	xyzTempCount_[binNo]++;
1500	>	Vector3d vel;
1501	>	RealType den;
1502	>	RealType temp;
1503	>	RealType z;
1504	>	for (int i = 0; i < nBins_; i++) {
1505	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1506	>	vel.x() = binPx[i] / binMass[i];
1507	>	vel.y() = binPy[i] / binMass[i];
1508	>	vel.z() = binPz[i] / binMass[i];
1509	>
1510	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1511	>	/ currentSnap_->getVolume() ;
1512	>
1513	>	if (binCount[i] > 0) {
1514	>	// only add values if there are things to add
1515	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1516	>	PhysicalConstants::energyConvert);
1517	>
1518	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1519	>	if(outputMask_[j]) {
1520	>	switch(j) {
1521	>	case Z:
1522	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1523	>	break;
1524	>	case TEMPERATURE:
1525	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1526	>	break;
1527	>	case VELOCITY:
1528	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1529	>	break;
1530	>	case DENSITY:
1531	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1532	>	break;
1533	>	}
1534	>	}
1535	>	}
1536		}
1465	–	if (outputRotTemp_) {
1466	–	if (sd->isDirectional()) {
1467	–	Vector3d angMom = sd->getJ();
1468	–	Mat3x3d I = sd->getI();
1469	–	if (sd->isLinear()) {
1470	–	int i = sd->linearAxis();
1471	–	int j = (i + 1) % 3;
1472	–	int k = (i + 2) % 3;
1473	–	value = angMom[j] * angMom[j] / I(j, j) +
1474	–	angMom[k] * angMom[k] / I(k, k);
1475	–	rotTempCount_[binNo] +=2;
1476	–	} else {
1477	–	value = angMom[0] * angMom[0] / I(0, 0) +
1478	–	angMom[1] * angMom[1] / I(1, 1) +
1479	–	angMom[2] * angMom[2] / I(2, 2);
1480	–	rotTempCount_[binNo] +=3;
1481	–	}
1482	–	}
1483	–	value = value / PhysicalConstants::energyConvert
1484	–	/ PhysicalConstants::kb;//may move to getStatus()
1485	–	rotTempHist_[binNo] += value;
1486	–	}
1487	–	// James put this in.
1488	–	if (outputDen_) {
1489	–	//value = 1.0;
1490	–	DenHist_[binNo] += 1;
1491	–	}
1492	–	if (outputVz_) {
1493	–	value = mass * vel[2];
1494	–	//vyzCount_[binNo]++;
1495	–	pzzHist_[binNo] += value;
1496	–	}
1537		}
1538		}
1539
1540		void RNEMD::getStarted() {
1541	+	if (!doRNEMD_) return;
1542		collectData();
1543	<	/*now can output profile in step 0, but might not be useful;
1503	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1504	<	Stats& stat = currentSnap_->statData;
1505	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1506	<	*/
1507	<	//may output a header for the log file here
1508	<	getStatus();
1543	>	writeOutputFile();
1544		}
1545
1546	<	void RNEMD::getStatus() {
1547	<
1548	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1549	<	Stats& stat = currentSnap_->statData;
1550	<	RealType time = currentSnap_->getTime();
1551	<
1552	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1553	<	//or to be more meaningful, define another item as exchangeSum_ / time
1554	<	int j;
1555	<
1546	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1547	>	if (!doRNEMD_) return;
1548	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1549	>
1550	>	while(tokenizer.hasMoreTokens()) {
1551	>	std::string token(tokenizer.nextToken());
1552	>	toUpper(token);
1553	>	OutputMapType::iterator i = outputMap_.find(token);
1554	>	if (i != outputMap_.end()) {
1555	>	outputMask_.set(i->second);
1556	>	} else {
1557	>	sprintf( painCave.errMsg,
1558	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1559	>	"\toutputFileFormat keyword.\n", token.c_str() );
1560	>	painCave.isFatal = 0;
1561	>	painCave.severity = OPENMD_ERROR;
1562	>	simError();
1563	>	}
1564	>	}
1565	>	}
1566	>
1567	>	void RNEMD::writeOutputFile() {
1568	>	if (!doRNEMD_) return;
1569	>
1570		#ifdef IS_MPI
1522	–
1523	–	// all processors have the same number of bins, and STL vectors pack their
1524	–	// arrays, so in theory, this should be safe:
1525	–
1526	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1527	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1528	–	if (outputTemp_) {
1529	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1530	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1531	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1532	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1533	–	}
1534	–	if (outputVx_) {
1535	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1536	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1537	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1538	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1539	–	}
1540	–	if (outputVy_) {
1541	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1542	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1543	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1544	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1545	–	}
1546	–	if (output3DTemp_) {
1547	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1548	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1549	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1550	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1551	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1552	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1553	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1554	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1555	–	}
1556	–	if (outputRotTemp_) {
1557	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1558	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1559	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1560	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1561	–	}
1562	–	// James put this in
1563	–	if (outputDen_) {
1564	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1565	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1566	–	}
1567	–	if (outputAh_) {
1568	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1569	–	1, MPI::REALTYPE, MPI::SUM);
1570	–	}
1571	–	if (outputVz_) {
1572	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1573	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1574	–	}
1575	–
1571		// If we're the root node, should we print out the results
1572		int worldRank = MPI::COMM_WORLD.Get_rank();
1573		if (worldRank == 0) {
1574		#endif
1575	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1576	+
1577	+	if( !rnemdFile_ ){
1578	+	sprintf( painCave.errMsg,
1579	+	"Could not open \"%s\" for RNEMD output.\n",
1580	+	rnemdFileName_.c_str());
1581	+	painCave.isFatal = 1;
1582	+	simError();
1583	+	}
1584
1585	<	if (outputTemp_) {
1586	<	tempLog_ << time;
1587	<	for (j = 0; j < rnemdLogWidth_; j++) {
1588	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1589	<	}
1590	<	tempLog_ << endl;
1585	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1586	>
1587	>	RealType time = currentSnap_->getTime();
1588	>	RealType avgArea;
1589	>	areaAccumulator_->getAverage(avgArea);
1590	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1591	>	/ PhysicalConstants::energyConvert;
1592	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1593	>
1594	>	rnemdFile_ << "#######################################################\n";
1595	>	rnemdFile_ << "# RNEMD {\n";
1596	>
1597	>	map<string, RNEMDMethod>::iterator mi;
1598	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1599	>	if ( (*mi).second == rnemdMethod_)
1600	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1601		}
1602	<	if (outputVx_) {
1603	<	vxzLog_ << time;
1604	<	for (j = 0; j < rnemdLogWidth_; j++) {
1605	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1592	<	}
1593	<	vxzLog_ << endl;
1602	>	map<string, RNEMDFluxType>::iterator fi;
1603	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1604	>	if ( (*fi).second == rnemdFluxType_)
1605	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1606		}
1607	<	if (outputVy_) {
1608	<	vyzLog_ << time;
1597	<	for (j = 0; j < rnemdLogWidth_; j++) {
1598	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	<	}
1600	<	vyzLog_ << endl;
1601	<	}
1607	>
1608	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1609
1610	<	if (output3DTemp_) {
1611	<	RealType temp;
1612	<	xTempLog_ << time;
1613	<	for (j = 0; j < rnemdLogWidth_; j++) {
1614	<	if (outputVx_)
1615	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1616	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1617	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1618	<	xTempLog_ << "\t" << temp;
1610	>	rnemdFile_ << "#    objectSelection = \""
1611	>	<< rnemdObjectSelection_ << "\";\n";
1612	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1613	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1614	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1615	>	rnemdFile_ << "# }\n";
1616	>	rnemdFile_ << "#######################################################\n";
1617	>	rnemdFile_ << "# RNEMD report:\n";
1618	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1619	>	rnemdFile_ << "#     target flux:\n";
1620	>	rnemdFile_ << "#         kinetic = "
1621	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1622	>	<< " (kcal/mol/A^2/fs)\n";
1623	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1624	>	<< " (amu/A/fs^2)\n";
1625	>	rnemdFile_ << "#     target one-time exchanges:\n";
1626	>	rnemdFile_ << "#         kinetic = "
1627	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1628	>	<< " (kcal/mol)\n";
1629	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1630	>	<< " (amu*A/fs)\n";
1631	>	rnemdFile_ << "#     actual exchange totals:\n";
1632	>	rnemdFile_ << "#         kinetic = "
1633	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1634	>	<< " (kcal/mol)\n";
1635	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1636	>	<< " (amu*A/fs)\n";
1637	>	rnemdFile_ << "#     actual flux:\n";
1638	>	rnemdFile_ << "#         kinetic = " << Jz
1639	>	<< " (kcal/mol/A^2/fs)\n";
1640	>	rnemdFile_ << "#         momentum = " << JzP
1641	>	<< " (amu/A/fs^2)\n";
1642	>	rnemdFile_ << "#     exchange statistics:\n";
1643	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1644	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1645	>	if (rnemdMethod_ == rnemdNIVS) {
1646	>	rnemdFile_ << "#         NIVS root-check errors = "
1647	>	<< failRootCount_ << "\n";
1648	>	}
1649	>	rnemdFile_ << "#######################################################\n";
1650	>
1651	>
1652	>
1653	>	//write title
1654	>	rnemdFile_ << "#";
1655	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1656	>	if (outputMask_[i]) {
1657	>	rnemdFile_ << "\t" << data_[i].title <<
1658	>	"(" << data_[i].units << ")";
1659	>	// add some extra tabs for column alignment
1660	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1661		}
1662	<	xTempLog_ << endl;
1663	<	yTempLog_ << time;
1664	<	for (j = 0; j < rnemdLogWidth_; j++) {
1665	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1662	>	}
1663	>	rnemdFile_ << std::endl;
1664	>
1665	>	rnemdFile_.precision(8);
1666	>
1667	>	for (int j = 0; j < nBins_; j++) {
1668	>
1669	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1670	>	if (outputMask_[i]) {
1671	>	if (data_[i].dataType == "RealType")
1672	>	writeReal(i,j);
1673	>	else if (data_[i].dataType == "Vector3d")
1674	>	writeVector(i,j);
1675	>	else {
1676	>	sprintf( painCave.errMsg,
1677	>	"RNEMD found an unknown data type for: %s ",
1678	>	data_[i].title.c_str());
1679	>	painCave.isFatal = 1;
1680	>	simError();
1681	>	}
1682	>	}
1683		}
1684	<	yTempLog_ << endl;
1685	<	zTempLog_ << time;
1686	<	for (j = 0; j < rnemdLogWidth_; j++) {
1687	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1684	>	rnemdFile_ << std::endl;
1685	>
1686	>	}
1687	>
1688	>	rnemdFile_ << "#######################################################\n";
1689	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1690	>	rnemdFile_ << "#######################################################\n";
1691	>
1692	>
1693	>	for (int j = 0; j < nBins_; j++) {
1694	>	rnemdFile_ << "#";
1695	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1696	>	if (outputMask_[i]) {
1697	>	if (data_[i].dataType == "RealType")
1698	>	writeRealStdDev(i,j);
1699	>	else if (data_[i].dataType == "Vector3d")
1700	>	writeVectorStdDev(i,j);
1701	>	else {
1702	>	sprintf( painCave.errMsg,
1703	>	"RNEMD found an unknown data type for: %s ",
1704	>	data_[i].title.c_str());
1705	>	painCave.isFatal = 1;
1706	>	simError();
1707	>	}
1708	>	}
1709		}
1710	<	zTempLog_ << endl;
1711	<	}
1712	<	if (outputRotTemp_) {
1713	<	rotTempLog_ << time;
1714	<	for (j = 0; j < rnemdLogWidth_; j++) {
1715	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1716	<	}
1630	<	rotTempLog_ << endl;
1631	<	}
1632	<	// James put this in.
1633	<	Mat3x3d hmat = currentSnap_->getHmat();
1634	<	if (outputDen_) {
1635	<	denLog_ << time;
1636	<	for (j = 0; j < rnemdLogWidth_; j++) {
1637	<
1638	<	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1639	<	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1640	<	}
1641	<	denLog_ << endl;
1642	<	}
1643	<	if (outputVz_) {
1644	<	vzzLog_ << time;
1645	<	for (j = 0; j < rnemdLogWidth_; j++) {
1646	<	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1647	<	}
1648	<	vzzLog_ << endl;
1649	<	}
1710	>	rnemdFile_ << std::endl;
1711	>
1712	>	}
1713	>
1714	>	rnemdFile_.flush();
1715	>	rnemdFile_.close();
1716	>
1717		#ifdef IS_MPI
1718		}
1719		#endif
1720	<
1721	<	for (j = 0; j < rnemdLogWidth_; j++) {
1722	<	mHist_[j] = 0.0;
1720	>
1721	>	}
1722	>
1723	>	void RNEMD::writeReal(int index, unsigned int bin) {
1724	>	if (!doRNEMD_) return;
1725	>	assert(index >=0 && index < ENDINDEX);
1726	>	assert(int(bin) < nBins_);
1727	>	RealType s;
1728	>
1729	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
1730	>
1731	>	if (! isinf(s) && ! isnan(s)) {
1732	>	rnemdFile_ << "\t" << s;
1733	>	} else{
1734	>	sprintf( painCave.errMsg,
1735	>	"RNEMD detected a numerical error writing: %s for bin %d",
1736	>	data_[index].title.c_str(), bin);
1737	>	painCave.isFatal = 1;
1738	>	simError();
1739	>	}
1740	>	}
1741	>
1742	>	void RNEMD::writeVector(int index, unsigned int bin) {
1743	>	if (!doRNEMD_) return;
1744	>	assert(index >=0 && index < ENDINDEX);
1745	>	assert(int(bin) < nBins_);
1746	>	Vector3d s;
1747	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1748	>	if (isinf(s[0]) || isnan(s[0]) ||
1749	>	isinf(s[1]) || isnan(s[1]) ||
1750	>	isinf(s[2]) || isnan(s[2]) ) {
1751	>	sprintf( painCave.errMsg,
1752	>	"RNEMD detected a numerical error writing: %s for bin %d",
1753	>	data_[index].title.c_str(), bin);
1754	>	painCave.isFatal = 1;
1755	>	simError();
1756	>	} else {
1757	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1758		}
1759	<	if (outputTemp_)
1658	<	for (j = 0; j < rnemdLogWidth_; j++) {
1659	<	tempCount_[j] = 0;
1660	<	tempHist_[j] = 0.0;
1661	<	}
1662	<	if (outputVx_)
1663	<	for (j = 0; j < rnemdLogWidth_; j++) {
1664	<	//pxzCount_[j] = 0;
1665	<	pxzHist_[j] = 0.0;
1666	<	}
1667	<	if (outputVy_)
1668	<	for (j = 0; j < rnemdLogWidth_; j++) {
1669	<	//pyzCount_[j] = 0;
1670	<	pyzHist_[j] = 0.0;
1671	<	}
1759	>	}
1760
1761	<	if (output3DTemp_)
1762	<	for (j = 0; j < rnemdLogWidth_; j++) {
1763	<	xTempHist_[j] = 0.0;
1764	<	yTempHist_[j] = 0.0;
1765	<	zTempHist_[j] = 0.0;
1678	<	xyzTempCount_[j] = 0;
1679	<	}
1680	<	if (outputRotTemp_)
1681	<	for (j = 0; j < rnemdLogWidth_; j++) {
1682	<	rotTempCount_[j] = 0;
1683	<	rotTempHist_[j] = 0.0;
1684	<	}
1685	<	// James put this in
1686	<	if (outputDen_)
1687	<	for (j = 0; j < rnemdLogWidth_; j++) {
1688	<	//pyzCount_[j] = 0;
1689	<	DenHist_[j] = 0.0;
1690	<	}
1691	<	if (outputVz_)
1692	<	for (j = 0; j < rnemdLogWidth_; j++) {
1693	<	//pyzCount_[j] = 0;
1694	<	pzzHist_[j] = 0.0;
1695	<	}
1696	<	// reset the counter
1697	<
1698	<	Numcount_++;
1699	<	if (Numcount_ > int(runTime_/statusTime_))
1700	<	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1701	<	if (Numcount_ > int(runTime_/statusTime_))
1702	<	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
1761	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1762	>	if (!doRNEMD_) return;
1763	>	assert(index >=0 && index < ENDINDEX);
1764	>	assert(int(bin) < nBins_);
1765	>	RealType s;
1766
1767	<	logFrameCount_ = 0;
1767	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
1768	>
1769	>	if (! isinf(s) && ! isnan(s)) {
1770	>	rnemdFile_ << "\t" << s;
1771	>	} else{
1772	>	sprintf( painCave.errMsg,
1773	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1774	>	data_[index].title.c_str(), bin);
1775	>	painCave.isFatal = 1;
1776	>	simError();
1777	>	}
1778		}
1779	+
1780	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1781	+	if (!doRNEMD_) return;
1782	+	assert(index >=0 && index < ENDINDEX);
1783	+	assert(int(bin) < nBins_);
1784	+	Vector3d s;
1785	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1786	+	if (isinf(s[0]) || isnan(s[0]) ||
1787	+	isinf(s[1]) || isnan(s[1]) ||
1788	+	isinf(s[2]) || isnan(s[2]) ) {
1789	+	sprintf( painCave.errMsg,
1790	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1791	+	data_[index].title.c_str(), bin);
1792	+	painCave.isFatal = 1;
1793	+	simError();
1794	+	} else {
1795	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1796	+	}
1797	+	}
1798		}
1799

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