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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 1777 by gezelter, Thu Aug 9 18:35:09 2012 UTC

#	Line 40 | Line 40
40		*/
41
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include "rnemd/RNEMD.hpp"
44		#include "math/Vector3.hpp"
45		#include "math/Vector.hpp"
46		#include "math/SquareMatrix3.hpp"
#	Line 49 | Line 49
49		#include "primitives/StuntDouble.hpp"
50		#include "utils/PhysicalConstants.hpp"
51		#include "utils/Tuple.hpp"
52	<
53	<	#ifndef IS_MPI
54	<	#include "math/SeqRandNumGen.hpp"
55	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
52	>	#ifdef IS_MPI
53		#include <mpi.h>
54		#endif
55
#	Line 65 | Line 61 | namespace OpenMD {
61		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
62		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
63
64	+	trialCount_ = 0;
65		failTrialCount_ = 0;
66		failRootCount_ = 0;
67
68		int seedValue;
69		Globals * simParams = info->getSimParams();
70	+	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
71
72	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
73	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
77	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
78	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
79	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
80	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
81	<	stringToEnumMap_["Px"] = rnemdPx;
82	<	stringToEnumMap_["Py"] = rnemdPy;
83	<	stringToEnumMap_["Pz"] = rnemdPz;
84	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
85	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
86	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	>	doRNEMD_ = rnemdParams->getUseRNEMD();
73	>	if (!doRNEMD_) return;
74
75	+	stringToMethod_["Swap"]  = rnemdSwap;
76	+	stringToMethod_["NIVS"]  = rnemdNIVS;
77	+	stringToMethod_["VSS"]   = rnemdVSS;
78	+
79	+	stringToFluxType_["KE"]  = rnemdKE;
80	+	stringToFluxType_["Px"]  = rnemdPx;
81	+	stringToFluxType_["Py"]  = rnemdPy;
82	+	stringToFluxType_["Pz"]  = rnemdPz;
83	+	stringToFluxType_["Pvector"]  = rnemdPvector;
84	+	stringToFluxType_["KE+Px"]  = rnemdKePx;
85	+	stringToFluxType_["KE+Py"]  = rnemdKePy;
86	+	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
87	+
88		runTime_ = simParams->getRunTime();
89		statusTime_ = simParams->getStatusTime();
90
91	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
91	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
92		evaluator_.loadScriptString(rnemdObjectSelection_);
93		seleMan_.setSelectionSet(evaluator_.evaluate());
94	+
95	+	const string methStr = rnemdParams->getMethod();
96	+	bool hasFluxType = rnemdParams->haveFluxType();
97	+
98	+	string fluxStr;
99	+	if (hasFluxType) {
100	+	fluxStr = rnemdParams->getFluxType();
101	+	} else {
102	+	sprintf(painCave.errMsg,
103	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
104	+	"\twhich must be one of the following values:\n"
105	+	"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n"
106	+	"\tmust be set to use RNEMD\n");
107	+	painCave.isFatal = 1;
108	+	painCave.severity = OPENMD_ERROR;
109	+	simError();
110	+	}
111	+
112	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
113	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
114	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
115	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
116	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
117	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
118	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
119	+	bool hasOutputFields = rnemdParams->haveOutputFields();
120	+
121	+	map<string, RNEMDMethod>::iterator i;
122	+	i = stringToMethod_.find(methStr);
123	+	if (i != stringToMethod_.end())
124	+	rnemdMethod_ = i->second;
125	+	else {
126	+	sprintf(painCave.errMsg,
127	+	"RNEMD: The current method,\n"
128	+	"\t\t%s is not one of the recognized\n"
129	+	"\texchange methods: Swap, NIVS, or VSS\n",
130	+	methStr.c_str());
131	+	painCave.isFatal = 1;
132	+	painCave.severity = OPENMD_ERROR;
133	+	simError();
134	+	}
135	+
136	+	map<string, RNEMDFluxType>::iterator j;
137	+	j = stringToFluxType_.find(fluxStr);
138	+	if (j != stringToFluxType_.end())
139	+	rnemdFluxType_ = j->second;
140	+	else {
141	+	sprintf(painCave.errMsg,
142	+	"RNEMD: The current fluxType,\n"
143	+	"\t\t%s\n"
144	+	"\tis not one of the recognized flux types.\n",
145	+	fluxStr.c_str());
146	+	painCave.isFatal = 1;
147	+	painCave.severity = OPENMD_ERROR;
148	+	simError();
149	+	}
150	+
151	+	bool methodFluxMismatch = false;
152	+	bool hasCorrectFlux = false;
153	+	switch(rnemdMethod_) {
154	+	case rnemdSwap:
155	+	switch (rnemdFluxType_) {
156	+	case rnemdKE:
157	+	hasCorrectFlux = hasKineticFlux;
158	+	break;
159	+	case rnemdPx:
160	+	case rnemdPy:
161	+	case rnemdPz:
162	+	hasCorrectFlux = hasMomentumFlux;
163	+	break;
164	+	default :
165	+	methodFluxMismatch = true;
166	+	break;
167	+	}
168	+	break;
169	+	case rnemdNIVS:
170	+	switch (rnemdFluxType_) {
171	+	case rnemdKE:
172	+	case rnemdRotKE:
173	+	case rnemdFullKE:
174	+	hasCorrectFlux = hasKineticFlux;
175	+	break;
176	+	case rnemdPx:
177	+	case rnemdPy:
178	+	case rnemdPz:
179	+	hasCorrectFlux = hasMomentumFlux;
180	+	break;
181	+	case rnemdKePx:
182	+	case rnemdKePy:
183	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
184	+	break;
185	+	default:
186	+	methodFluxMismatch = true;
187	+	break;
188	+	}
189	+	break;
190	+	case rnemdVSS:
191	+	switch (rnemdFluxType_) {
192	+	case rnemdKE:
193	+	case rnemdRotKE:
194	+	case rnemdFullKE:
195	+	hasCorrectFlux = hasKineticFlux;
196	+	break;
197	+	case rnemdPx:
198	+	case rnemdPy:
199	+	case rnemdPz:
200	+	hasCorrectFlux = hasMomentumFlux;
201	+	break;
202	+	case rnemdPvector:
203	+	hasCorrectFlux = hasMomentumFluxVector;
204	+	break;
205	+	case rnemdKePx:
206	+	case rnemdKePy:
207	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
208	+	break;
209	+	case rnemdKePvector:
210	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
211	+	break;
212	+	default:
213	+	methodFluxMismatch = true;
214	+	break;
215	+	}
216	+	default:
217	+	break;
218	+	}
219	+
220	+	if (methodFluxMismatch) {
221	+	sprintf(painCave.errMsg,
222	+	"RNEMD: The current method,\n"
223	+	"\t\t%s\n"
224	+	"\tcannot be used with the current flux type, %s\n",
225	+	methStr.c_str(), fluxStr.c_str());
226	+	painCave.isFatal = 1;
227	+	painCave.severity = OPENMD_ERROR;
228	+	simError();
229	+	}
230	+	if (!hasCorrectFlux) {
231	+	sprintf(painCave.errMsg,
232	+	"RNEMD: The current method, %s, and flux type, %s,\n"
233	+	"\tdid not have the correct flux value specified. Options\n"
234	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
235	+	methStr.c_str(), fluxStr.c_str());
236	+	painCave.isFatal = 1;
237	+	painCave.severity = OPENMD_ERROR;
238	+	simError();
239	+	}
240	+
241	+	if (hasKineticFlux) {
242	+	// convert the kcal / mol / Angstroms^2 / fs values in the md file
243	+	// into  amu / fs^3:
244	+	kineticFlux_ = rnemdParams->getKineticFlux()
245	+	* PhysicalConstants::energyConvert;
246	+	} else {
247	+	kineticFlux_ = 0.0;
248	+	}
249	+	if (hasMomentumFluxVector) {
250	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
251	+	} else {
252	+	momentumFluxVector_ = V3Zero;
253	+	if (hasMomentumFlux) {
254	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
255	+	switch (rnemdFluxType_) {
256	+	case rnemdPx:
257	+	momentumFluxVector_.x() = momentumFlux;
258	+	break;
259	+	case rnemdPy:
260	+	momentumFluxVector_.y() = momentumFlux;
261	+	break;
262	+	case rnemdPz:
263	+	momentumFluxVector_.z() = momentumFlux;
264	+	break;
265	+	case rnemdKePx:
266	+	momentumFluxVector_.x() = momentumFlux;
267	+	break;
268	+	case rnemdKePy:
269	+	momentumFluxVector_.y() = momentumFlux;
270	+	break;
271	+	default:
272	+	break;
273	+	}
274	+	}
275	+	}
276
277		// do some sanity checking
278
#	Line 99 | Line 281 | namespace OpenMD {
281
282		if (selectionCount > nIntegrable) {
283		sprintf(painCave.errMsg,
284	<	"RNEMD: The current RNEMD_objectSelection,\n"
284	>	"RNEMD: The current objectSelection,\n"
285		"\t\t%s\n"
286		"\thas resulted in %d selected objects.  However,\n"
287		"\tthe total number of integrable objects in the system\n"
#	Line 112 | Line 294 | namespace OpenMD {
294		painCave.severity = OPENMD_WARNING;
295		simError();
296		}
115	–
116	–	const string st = simParams->getRNEMD_exchangeType();
297
298	<	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	<
298	>	areaAccumulator_ = new Accumulator();
299
300	<	#ifdef IS_MPI
179	<	if (worldRank == 0) {
180	<	#endif
300	>	nBins_ = rnemdParams->getOutputBins();
301
302	<	//may have rnemdWriter separately
303	<	string rnemdFileName;
302	>	data_.resize(RNEMD::ENDINDEX);
303	>	OutputData z;
304	>	z.units =  "Angstroms";
305	>	z.title =  "Z";
306	>	z.dataType = "RealType";
307	>	z.accumulator.reserve(nBins_);
308	>	for (unsigned int i = 0; i < nBins_; i++)
309	>	z.accumulator.push_back( new Accumulator() );
310	>	data_[Z] = z;
311	>	outputMap_["Z"] =  Z;
312
313	<	if (outputTemp_) {
314	<	rnemdFileName = "temperature.log";
315	<	tempLog_.open(rnemdFileName.c_str());
316	<	}
317	<	if (outputVx_) {
318	<	rnemdFileName = "velocityX.log";
319	<	vxzLog_.open(rnemdFileName.c_str());
320	<	}
321	<	if (outputVy_) {
194	<	rnemdFileName = "velocityY.log";
195	<	vyzLog_.open(rnemdFileName.c_str());
196	<	}
313	>	OutputData temperature;
314	>	temperature.units =  "K";
315	>	temperature.title =  "Temperature";
316	>	temperature.dataType = "RealType";
317	>	temperature.accumulator.reserve(nBins_);
318	>	for (unsigned int i = 0; i < nBins_; i++)
319	>	temperature.accumulator.push_back( new Accumulator() );
320	>	data_[TEMPERATURE] = temperature;
321	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
322
323	<	if (output3DTemp_) {
324	<	rnemdFileName = "temperatureX.log";
325	<	xTempLog_.open(rnemdFileName.c_str());
326	<	rnemdFileName = "temperatureY.log";
327	<	yTempLog_.open(rnemdFileName.c_str());
328	<	rnemdFileName = "temperatureZ.log";
329	<	zTempLog_.open(rnemdFileName.c_str());
330	<	}
331	<	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
323	>	OutputData velocity;
324	>	velocity.units = "angstroms/fs";
325	>	velocity.title =  "Velocity";
326	>	velocity.dataType = "Vector3d";
327	>	velocity.accumulator.reserve(nBins_);
328	>	for (unsigned int i = 0; i < nBins_; i++)
329	>	velocity.accumulator.push_back( new VectorAccumulator() );
330	>	data_[VELOCITY] = velocity;
331	>	outputMap_["VELOCITY"] = VELOCITY;
332
333	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
334	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
335	<	midBin_ = nBins_ / 2;
336	<	if (simParams->haveRNEMD_binShift()) {
337	<	if (simParams->getRNEMD_binShift()) {
338	<	zShift_ = 0.5 / (RealType)(nBins_);
339	<	} else {
340	<	zShift_ = 0.0;
341	<	}
333	>	OutputData density;
334	>	density.units =  "g cm^-3";
335	>	density.title =  "Density";
336	>	density.dataType = "RealType";
337	>	density.accumulator.reserve(nBins_);
338	>	for (unsigned int i = 0; i < nBins_; i++)
339	>	density.accumulator.push_back( new Accumulator() );
340	>	data_[DENSITY] = density;
341	>	outputMap_["DENSITY"] =  DENSITY;
342	>
343	>	if (hasOutputFields) {
344	>	parseOutputFileFormat(rnemdParams->getOutputFields());
345		} else {
346	<	zShift_ = 0.0;
346	>	outputMask_.set(Z);
347	>	switch (rnemdFluxType_) {
348	>	case rnemdKE:
349	>	case rnemdRotKE:
350	>	case rnemdFullKE:
351	>	outputMask_.set(TEMPERATURE);
352	>	break;
353	>	case rnemdPx:
354	>	case rnemdPy:
355	>	outputMask_.set(VELOCITY);
356	>	break;
357	>	case rnemdPz:
358	>	case rnemdPvector:
359	>	outputMask_.set(VELOCITY);
360	>	outputMask_.set(DENSITY);
361	>	break;
362	>	case rnemdKePx:
363	>	case rnemdKePy:
364	>	outputMask_.set(TEMPERATURE);
365	>	outputMask_.set(VELOCITY);
366	>	break;
367	>	case rnemdKePvector:
368	>	outputMask_.set(TEMPERATURE);
369	>	outputMask_.set(VELOCITY);
370	>	outputMask_.set(DENSITY);
371	>	break;
372	>	default:
373	>	break;
374	>	}
375		}
376	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
377	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
378	<	//set to 0.0 if not using it; N/A in status output yet
244	<	if (simParams->haveRNEMD_logWidth()) {
245	<	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
246	<	/*arbitary rnemdLogWidth_, no checking;
247	<	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
248	<	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
249	<	cerr << "Automaically set back to default.\n";
250	<	rnemdLogWidth_ = nBins_;
251	<	}*/
376	>
377	>	if (hasOutputFileName) {
378	>	rnemdFileName_ = rnemdParams->getOutputFileName();
379		} else {
380	<	set_RNEMD_logWidth(nBins_);
381	<	}
255	<	tempHist_.resize(rnemdLogWidth_, 0.0);
256	<	tempCount_.resize(rnemdLogWidth_, 0);
257	<	pxzHist_.resize(rnemdLogWidth_, 0.0);
258	<	//vxzCount_.resize(rnemdLogWidth_, 0);
259	<	pyzHist_.resize(rnemdLogWidth_, 0.0);
260	<	//vyzCount_.resize(rnemdLogWidth_, 0);
380	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
381	>	}
382
383	<	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);
383	>	exchangeTime_ = rnemdParams->getExchangeTime();
384
385	<	set_RNEMD_exchange_total(0.0);
386	<	if (simParams->haveRNEMD_targetFlux()) {
387	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
388	<	} else {
389	<	set_RNEMD_target_flux(0.0);
390	<	}
391	<	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_;
385	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
386	>	Mat3x3d hmat = currentSnap_->getHmat();
387	>
388	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
389	>	// Lx, Ly = box dimensions in x & y
390	>	// dt = exchange time interval
391	>	// flux = target flux
392
393	<	#ifndef IS_MPI
394	<	if (simParams->haveSeed()) {
395	<	seedValue = simParams->getSeed();
396	<	randNumGen_ = new SeqRandNumGen(seedValue);
397	<	}else {
398	<	randNumGen_ = new SeqRandNumGen();
399	<	}
400	<	#else
401	<	if (simParams->haveSeed()) {
402	<	seedValue = simParams->getSeed();
403	<	randNumGen_ = new ParallelRandNumGen(seedValue);
404	<	}else {
405	<	randNumGen_ = new ParallelRandNumGen();
319	<	}
320	<	#endif
321	<	}
393	>	RealType area = currentSnap_->getXYarea();
394	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
395	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
396	>
397	>	// total exchange sums are zeroed out at the beginning:
398	>
399	>	kineticExchange_ = 0.0;
400	>	momentumExchange_ = V3Zero;
401	>
402	>	if (hasSlabWidth)
403	>	slabWidth_ = rnemdParams->getSlabWidth();
404	>	else
405	>	slabWidth_ = hmat(2,2) / 10.0;
406
407	<	RNEMD::~RNEMD() {
408	<	delete randNumGen_;
407	>	if (hasSlabACenter)
408	>	slabACenter_ = rnemdParams->getSlabACenter();
409	>	else
410	>	slabACenter_ = 0.0;
411
412	+	if (hasSlabBCenter)
413	+	slabBCenter_ = rnemdParams->getSlabBCenter();
414	+	else
415	+	slabBCenter_ = hmat(2,2) / 2.0;
416	+
417	+	}
418	+
419	+	RNEMD::~RNEMD() {
420	+	if (!doRNEMD_) return;
421		#ifdef IS_MPI
422		if (worldRank == 0) {
423		#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();
424
425	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
426	<	rnemdType_ == rnemdPyScale) {
427	<	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();
425	>	writeOutputFile();
426	>
427	>	rnemdFile_.close();
428
429		#ifdef IS_MPI
430		}
431		#endif
432		}
433	+
434	+	bool RNEMD::inSlabA(Vector3d pos) {
435	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
436	+	}
437	+	bool RNEMD::inSlabB(Vector3d pos) {
438	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
439	+	}
440
441		void RNEMD::doSwap() {
442	<
442	>	if (!doRNEMD_) return;
443		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
444		Mat3x3d hmat = currentSnap_->getHmat();
445
#	Line 393 | Line 468 | namespace OpenMD {
468
469		if (usePeriodicBoundaryConditions_)
470		currentSnap_->wrapVector(pos);
471	<
472	<	// 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	<
471	>	bool inA = inSlabA(pos);
472	>	bool inB = inSlabB(pos);
473
474	<	// if we're in bin 0 or the middleBin
404	<	if (binNo == 0 || binNo == midBin_) {
474	>	if (inA || inB) {
475
476		RealType mass = sd->getMass();
477		Vector3d vel = sd->getVel();
478		RealType value;
479	<
480	<	switch(rnemdType_) {
481	<	case rnemdKineticSwap :
479	>
480	>	switch(rnemdFluxType_) {
481	>	case rnemdKE :
482
483		value = mass * vel.lengthSquare();
484
#	Line 428 | Line 498 | namespace OpenMD {
498		+ angMom[2]*angMom[2]/I(2, 2);
499		}
500		} //angular momenta exchange enabled
431	–	//energyConvert temporarily disabled
432	–	//make exchangeSum_ comparable between swap & scale
433	–	//value = value * 0.5 / PhysicalConstants::energyConvert;
501		value *= 0.5;
502		break;
503		case rnemdPx :
#	Line 446 | Line 513 | namespace OpenMD {
513		break;
514		}
515
516	<	if (binNo == 0) {
516	>	if (inA == 0) {
517		if (!min_found) {
518		min_val = value;
519		min_sd = sd;
#	Line 457 | Line 524 | namespace OpenMD {
524		min_sd = sd;
525		}
526		}
527	<	} else { //midBin_
527	>	} else {
528		if (!max_found) {
529		max_val = value;
530		max_sd = sd;
#	Line 471 | Line 538 | namespace OpenMD {
538		}
539		}
540		}
541	<
541	>
542		#ifdef IS_MPI
543		int nProc, worldRank;
544	<
544	>
545		nProc = MPI::COMM_WORLD.Get_size();
546		worldRank = MPI::COMM_WORLD.Get_rank();
547
#	Line 532 | Line 599 | namespace OpenMD {
599		Vector3d max_vel = max_sd->getVel();
600		RealType temp_vel;
601
602	<	switch(rnemdType_) {
603	<	case rnemdKineticSwap :
602	>	switch(rnemdFluxType_) {
603	>	case rnemdKE :
604		min_sd->setVel(max_vel);
605		max_sd->setVel(min_vel);
606		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 584 | Line 651 | namespace OpenMD {
651		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
652		min_vals.rank, 0, status);
653
654	<	switch(rnemdType_) {
655	<	case rnemdKineticSwap :
654	>	switch(rnemdFluxType_) {
655	>	case rnemdKE :
656		max_sd->setVel(min_vel);
657		//angular momenta exchange enabled
658		if (max_sd->isDirectional()) {
#	Line 630 | Line 697 | namespace OpenMD {
697		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
698		max_vals.rank, 0, status);
699
700	<	switch(rnemdType_) {
701	<	case rnemdKineticSwap :
700	>	switch(rnemdFluxType_) {
701	>	case rnemdKE :
702		min_sd->setVel(max_vel);
703		//angular momenta exchange enabled
704		if (min_sd->isDirectional()) {
#	Line 665 | Line 732 | namespace OpenMD {
732		}
733		}
734		#endif
735	<	exchangeSum_ += max_val - min_val;
735	>
736	>	switch(rnemdFluxType_) {
737	>	case rnemdKE:
738	>	kineticExchange_ += max_val - min_val;
739	>	break;
740	>	case rnemdPx:
741	>	momentumExchange_.x() += max_val - min_val;
742	>	break;
743	>	case rnemdPy:
744	>	momentumExchange_.y() += max_val - min_val;
745	>	break;
746	>	case rnemdPz:
747	>	momentumExchange_.z() += max_val - min_val;
748	>	break;
749	>	default:
750	>	break;
751	>	}
752		} else {
753		sprintf(painCave.errMsg,
754	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
754	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
755		painCave.isFatal = 0;
756		painCave.severity = OPENMD_INFO;
757		simError();
#	Line 676 | Line 759 | namespace OpenMD {
759		}
760		} else {
761		sprintf(painCave.errMsg,
762	<	"RNEMD: exchange NOT performed because selected object\n"
763	<	"\tnot present in at least one of the two slabs.\n");
762	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
763	>	"\twas not present in at least one of the two slabs.\n");
764		painCave.isFatal = 0;
765		painCave.severity = OPENMD_INFO;
766		simError();
767		failTrialCount_++;
768	<	}
686	<
768	>	}
769		}
770
771	<	void RNEMD::doScale() {
772	<
771	>	void RNEMD::doNIVS() {
772	>	if (!doRNEMD_) return;
773		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
774		Mat3x3d hmat = currentSnap_->getHmat();
775
#	Line 727 | Line 809 | namespace OpenMD {
809		currentSnap_->wrapVector(pos);
810
811		// which bin is this stuntdouble in?
812	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
812	>	bool inA = inSlabA(pos);
813	>	bool inB = inSlabB(pos);
814
815	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
816	<
734	<	// if we're in bin 0 or the middleBin
735	<	if (binNo == 0 || binNo == midBin_) {
736	<
815	>	if (inA || inB) {
816	>
817		RealType mass = sd->getMass();
818		Vector3d vel = sd->getVel();
819
820	<	if (binNo == 0) {
820	>	if (inA) {
821		hotBin.push_back(sd);
822		Phx += mass * vel.x();
823		Phy += mass * vel.y();
#	Line 745 | Line 825 | namespace OpenMD {
825		Khx += mass * vel.x() * vel.x();
826		Khy += mass * vel.y() * vel.y();
827		Khz += mass * vel.z() * vel.z();
748	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
828		if (sd->isDirectional()) {
829		Vector3d angMom = sd->getJ();
830		Mat3x3d I = sd->getI();
#	Line 761 | Line 840 | namespace OpenMD {
840		+ angMom[2]*angMom[2]/I(2, 2);
841		}
842		}
843	<	//}
765	<	} else { //midBin_
843	>	} else {
844		coldBin.push_back(sd);
845		Pcx += mass * vel.x();
846		Pcy += mass * vel.y();
#	Line 770 | Line 848 | namespace OpenMD {
848		Kcx += mass * vel.x() * vel.x();
849		Kcy += mass * vel.y() * vel.y();
850		Kcz += mass * vel.z() * vel.z();
773	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
851		if (sd->isDirectional()) {
852		Vector3d angMom = sd->getJ();
853		Mat3x3d I = sd->getI();
#	Line 786 | Line 863 | namespace OpenMD {
863		+ angMom[2]*angMom[2]/I(2, 2);
864		}
865		}
789	–	//}
866		}
867		}
868		}
#	Line 800 | Line 876 | namespace OpenMD {
876		Kcz *= 0.5;
877		Kcw *= 0.5;
878
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	–
879		#ifdef IS_MPI
880		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
881		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 831 | Line 901 | namespace OpenMD {
901		RealType pz = Pcz / Phz;
902		RealType c, x, y, z;
903		bool successfulScale = false;
904	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
905	<	(rnemdType_ == rnemdKineticScaleAM)) {
904	>	if ((rnemdFluxType_ == rnemdFullKE) ||
905	>	(rnemdFluxType_ == rnemdRotKE)) {
906		//may need sanity check Khw & Kcw > 0
907
908	<	if (rnemdType_ == rnemdKineticScaleVAM) {
909	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
908	>	if (rnemdFluxType_ == rnemdFullKE) {
909	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
910		} else {
911	<	c = 1.0 - targetFlux_ / Kcw;
911	>	c = 1.0 - kineticTarget_ / Kcw;
912		}
913
914		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
915		c = sqrt(c);
916	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
916	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
917		//now convert to hotBin coefficient
918		RealType w = 0.0;
919	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
919	>	if (rnemdFluxType_ ==  rnemdFullKE) {
920		x = 1.0 + px * (1.0 - c);
921		y = 1.0 + py * (1.0 - c);
922		z = 1.0 + pz * (1.0 - c);
#	Line 860 | Line 930 | namespace OpenMD {
930		*/
931		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
932		(fabs(z - 1.0) < 0.1)) {
933	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
933	>	w = 1.0 + (kineticTarget_
934	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
935		+ Khz * (1.0 - z * z)) / Khw;
936		}//no need to calculate w if x, y or z is out of range
937		} else {
938	<	w = 1.0 + targetFlux_ / Khw;
938	>	w = 1.0 + kineticTarget_ / Khw;
939		}
940		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
941		//if w is in the right range, so should be x, y, z.
942		vector<StuntDouble*>::iterator sdi;
943		Vector3d vel;
944		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
945	<	if (rnemdType_ == rnemdKineticScaleVAM) {
945	>	if (rnemdFluxType_ == rnemdFullKE) {
946		vel = (*sdi)->getVel() * c;
876	–	//vel.x() *= c;
877	–	//vel.y() *= c;
878	–	//vel.z() *= c;
947		(*sdi)->setVel(vel);
948		}
949		if ((*sdi)->isDirectional()) {
950		Vector3d angMom = (*sdi)->getJ() * c;
883	–	//angMom[0] *= c;
884	–	//angMom[1] *= c;
885	–	//angMom[2] *= c;
951		(*sdi)->setJ(angMom);
952		}
953		}
954		w = sqrt(w);
955	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
956	<	<< "\twh= " << w << endl;
955	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
956	>	//           << "\twh= " << w << endl;
957		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
958	<	if (rnemdType_ == rnemdKineticScaleVAM) {
958	>	if (rnemdFluxType_ == rnemdFullKE) {
959		vel = (*sdi)->getVel();
960		vel.x() *= x;
961		vel.y() *= y;
#	Line 899 | Line 964 | namespace OpenMD {
964		}
965		if ((*sdi)->isDirectional()) {
966		Vector3d angMom = (*sdi)->getJ() * w;
902	–	//angMom[0] *= w;
903	–	//angMom[1] *= w;
904	–	//angMom[2] *= w;
967		(*sdi)->setJ(angMom);
968		}
969		}
970		successfulScale = true;
971	<	exchangeSum_ += targetFlux_;
971	>	kineticExchange_ += kineticTarget_;
972		}
973		}
974		} else {
975		RealType a000, a110, c0, a001, a111, b01, b11, c1;
976	<	switch(rnemdType_) {
977	<	case rnemdKineticScale :
976	>	switch(rnemdFluxType_) {
977	>	case rnemdKE :
978		/* used hotBin coeff's & only scale x & y dimensions
979		RealType px = Phx / Pcx;
980		RealType py = Phy / Pcy;
981		a110 = Khy;
982	<	c0 = - Khx - Khy - targetFlux_;
982	>	c0 = - Khx - Khy - kineticTarget_;
983		a000 = Khx;
984		a111 = Kcy * py * py;
985		b11 = -2.0 * Kcy * py * (1.0 + py);
986	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
986	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
987		b01 = -2.0 * Kcx * px * (1.0 + px);
988		a001 = Kcx * px * px;
989		*/
990		//scale all three dimensions, let c_x = c_y
991		a000 = Kcx + Kcy;
992		a110 = Kcz;
993	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
993	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
994		a001 = Khx * px * px + Khy * py * py;
995		a111 = Khz * pz * pz;
996		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
997		b11 = -2.0 * Khz * pz * (1.0 + pz);
998		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
999	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
999	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1000		break;
1001	<	case rnemdPxScale :
1002	<	c = 1 - targetFlux_ / Pcx;
1001	>	case rnemdPx :
1002	>	c = 1 - momentumTarget_.x() / Pcx;
1003		a000 = Kcy;
1004		a110 = Kcz;
1005		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 948 | Line 1010 | namespace OpenMD {
1010		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1011		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1012		break;
1013	<	case rnemdPyScale :
1014	<	c = 1 - targetFlux_ / Pcy;
1013	>	case rnemdPy :
1014	>	c = 1 - momentumTarget_.y() / Pcy;
1015		a000 = Kcx;
1016		a110 = Kcz;
1017		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 960 | Line 1022 | namespace OpenMD {
1022		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1023		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1024		break;
1025	<	case rnemdPzScale ://we don't really do this, do we?
1026	<	c = 1 - targetFlux_ / Pcz;
1025	>	case rnemdPz ://we don't really do this, do we?
1026	>	c = 1 - momentumTarget_.z() / Pcz;
1027		a000 = Kcx;
1028		a110 = Kcy;
1029		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1046 | Line 1108 | namespace OpenMD {
1108		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1109		r1 = (*rpi).first;
1110		r2 = (*rpi).second;
1111	<	switch(rnemdType_) {
1112	<	case rnemdKineticScale :
1111	>	switch(rnemdFluxType_) {
1112	>	case rnemdKE :
1113		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1114		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1115		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1116		break;
1117	<	case rnemdPxScale :
1117	>	case rnemdPx :
1118		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1119		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1120		break;
1121	<	case rnemdPyScale :
1121	>	case rnemdPy :
1122		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1123		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1124		break;
1125	<	case rnemdPzScale :
1125	>	case rnemdPz :
1126		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1127		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1128		default :
#	Line 1074 | Line 1136 | namespace OpenMD {
1136		#ifdef IS_MPI
1137		if (worldRank == 0) {
1138		#endif
1139	<	sprintf(painCave.errMsg,
1140	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1141	<	bestPair.first, bestPair.second);
1142	<	painCave.isFatal = 0;
1143	<	painCave.severity = OPENMD_INFO;
1144	<	simError();
1139	>	// sprintf(painCave.errMsg,
1140	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1141	>	//         bestPair.first, bestPair.second);
1142	>	// painCave.isFatal = 0;
1143	>	// painCave.severity = OPENMD_INFO;
1144	>	// simError();
1145		#ifdef IS_MPI
1146		}
1147		#endif
1148
1149	<	switch(rnemdType_) {
1150	<	case rnemdKineticScale :
1149	>	switch(rnemdFluxType_) {
1150	>	case rnemdKE :
1151		x = bestPair.first;
1152		y = bestPair.first;
1153		z = bestPair.second;
1154		break;
1155	<	case rnemdPxScale :
1155	>	case rnemdPx :
1156		x = c;
1157		y = bestPair.first;
1158		z = bestPair.second;
1159		break;
1160	<	case rnemdPyScale :
1160	>	case rnemdPy :
1161		x = bestPair.first;
1162		y = c;
1163		z = bestPair.second;
1164		break;
1165	<	case rnemdPzScale :
1165	>	case rnemdPz :
1166		x = bestPair.first;
1167		y = bestPair.second;
1168		z = c;
#	Line 1129 | Line 1191 | namespace OpenMD {
1191		(*sdi)->setVel(vel);
1192		}
1193		successfulScale = true;
1194	<	exchangeSum_ += targetFlux_;
1194	>	switch(rnemdFluxType_) {
1195	>	case rnemdKE :
1196	>	kineticExchange_ += kineticTarget_;
1197	>	break;
1198	>	case rnemdPx :
1199	>	case rnemdPy :
1200	>	case rnemdPz :
1201	>	momentumExchange_ += momentumTarget_;
1202	>	break;
1203	>	default :
1204	>	break;
1205	>	}
1206		}
1207		}
1208		if (successfulScale != true) {
1209		sprintf(painCave.errMsg,
1210	<	"RNEMD: exchange NOT performed!\n");
1210	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1211	>	"\tthe constraint equations may not exist or there may be\n"
1212	>	"\tno selected objects in one or both slabs.\n");
1213		painCave.isFatal = 0;
1214		painCave.severity = OPENMD_INFO;
1215		simError();
#	Line 1142 | Line 1217 | namespace OpenMD {
1217		}
1218		}
1219
1220	<	void RNEMD::doShiftScale() {
1221	<
1220	>	void RNEMD::doVSS() {
1221	>	if (!doRNEMD_) return;
1222		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1223		RealType time = currentSnap_->getTime();
1224		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 1177 | Line 1252 | namespace OpenMD {
1252		currentSnap_->wrapVector(pos);
1253
1254		// which bin is this stuntdouble in?
1255	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1256	<
1257	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1258	<
1184	<	// if we're in bin 0 or the middleBin
1185	<	if (binNo == 0 || binNo == midBin_) {
1255	>	bool inA = inSlabA(pos);
1256	>	bool inB = inSlabB(pos);
1257	>
1258	>	if (inA || inB) {
1259
1260		RealType mass = sd->getMass();
1261		Vector3d vel = sd->getVel();
1262
1263	<	if (binNo == 0) {
1263	>	if (inA) {
1264		hotBin.push_back(sd);
1265		//std::cerr << "before, velocity = " << vel << endl;
1266		Ph += mass * vel;
1267		//std::cerr << "after, velocity = " << vel << endl;
1268		Mh += mass;
1269		Kh += mass * vel.lengthSquare();
1270	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1270	>	if (rnemdFluxType_ == rnemdFullKE) {
1271		if (sd->isDirectional()) {
1272		Vector3d angMom = sd->getJ();
1273		Mat3x3d I = sd->getI();
#	Line 1216 | Line 1289 | namespace OpenMD {
1289		Pc += mass * vel;
1290		Mc += mass;
1291		Kc += mass * vel.lengthSquare();
1292	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1292	>	if (rnemdFluxType_ == rnemdFullKE) {
1293		if (sd->isDirectional()) {
1294		Vector3d angMom = sd->getJ();
1295		Mat3x3d I = sd->getI();
#	Line 1256 | Line 1329 | namespace OpenMD {
1329		bool successfulExchange = false;
1330		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1331		Vector3d vc = Pc / Mc;
1332	<	Vector3d ac = njzp_ / Mc + vc;
1333	<	Vector3d acrec = njzp_ / Mc;
1334	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1332	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1333	>	Vector3d acrec = -momentumTarget_ / Mc;
1334	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1335		if (cNumerator > 0.0) {
1336		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1337		if (cDenominator > 0.0) {
1338		RealType c = sqrt(cNumerator / cDenominator);
1339		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1340		Vector3d vh = Ph / Mh;
1341	<	Vector3d ah = jzp_ / Mh + vh;
1342	<	Vector3d ahrec = jzp_ / Mh;
1343	<	RealType hNumerator = Kh + targetJzKE_
1341	>	Vector3d ah = momentumTarget_ / Mh + vh;
1342	>	Vector3d ahrec = momentumTarget_ / Mh;
1343	>	RealType hNumerator = Kh + kineticTarget_
1344		- 0.5 * Mh * ah.lengthSquare();
1345		if (hNumerator > 0.0) {
1346		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
#	Line 1282 | Line 1355 | namespace OpenMD {
1355		//vel = (*sdi)->getVel();
1356		vel = ((*sdi)->getVel() - vc) * c + ac;
1357		(*sdi)->setVel(vel);
1358	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1358	>	if (rnemdFluxType_ == rnemdFullKE) {
1359		if ((*sdi)->isDirectional()) {
1360		Vector3d angMom = (*sdi)->getJ() * c;
1361		(*sdi)->setJ(angMom);
#	Line 1293 | Line 1366 | namespace OpenMD {
1366		//vel = (*sdi)->getVel();
1367		vel = ((*sdi)->getVel() - vh) * h + ah;
1368		(*sdi)->setVel(vel);
1369	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1369	>	if (rnemdFluxType_ == rnemdFullKE) {
1370		if ((*sdi)->isDirectional()) {
1371		Vector3d angMom = (*sdi)->getJ() * h;
1372		(*sdi)->setJ(angMom);
#	Line 1301 | Line 1374 | namespace OpenMD {
1374		}
1375		}
1376		successfulExchange = true;
1377	<	exchangeSum_ += targetFlux_;
1378	<	// 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	<	}
1377	>	kineticExchange_ += kineticTarget_;
1378	>	momentumExchange_ += momentumTarget_;
1379		}
1380		}
1381		}
#	Line 1324 | Line 1384 | namespace OpenMD {
1384		}
1385		}
1386		if (successfulExchange != true) {
1387	<	//   sprintf(painCave.errMsg,
1388	<	//              "RNEMD: exchange NOT performed!\n");
1389	<	//   painCave.isFatal = 0;
1390	<	//   painCave.severity = OPENMD_INFO;
1391	<	//   simError();
1387	>	sprintf(painCave.errMsg,
1388	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1389	>	"\tthe constraint equations may not exist or there may be\n"
1390	>	"\tno selected objects in one or both slabs.\n");
1391	>	painCave.isFatal = 0;
1392	>	painCave.severity = OPENMD_INFO;
1393	>	simError();
1394		failTrialCount_++;
1395		}
1396		}
1397
1398		void RNEMD::doRNEMD() {
1399	<
1400	<	switch(rnemdType_) {
1401	<	case rnemdKineticScale :
1402	<	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 :
1399	>	if (!doRNEMD_) return;
1400	>	trialCount_++;
1401	>	switch(rnemdMethod_) {
1402	>	case rnemdSwap:
1403		doSwap();
1404		break;
1405	<	case rnemdShiftScaleV :
1406	<	case rnemdShiftScaleVAM :
1355	<	doShiftScale();
1405	>	case rnemdNIVS:
1406	>	doNIVS();
1407		break;
1408	<	case rnemdUnknown :
1408	>	case rnemdVSS:
1409	>	doVSS();
1410	>	break;
1411	>	case rnemdUnkownMethod:
1412		default :
1413		break;
1414		}
1415		}
1416
1417		void RNEMD::collectData() {
1418	<
1418	>	if (!doRNEMD_) return;
1419		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1420		Mat3x3d hmat = currentSnap_->getHmat();
1421
1422	+	areaAccumulator_->add(currentSnap_->getXYarea());
1423	+
1424		seleMan_.setSelectionSet(evaluator_.evaluate());
1425
1426		int selei;
1427		StuntDouble* sd;
1428		int idx;
1429
1430	<	logFrameCount_++;
1430	>	vector<RealType> binMass(nBins_, 0.0);
1431	>	vector<RealType> binPx(nBins_, 0.0);
1432	>	vector<RealType> binPy(nBins_, 0.0);
1433	>	vector<RealType> binPz(nBins_, 0.0);
1434	>	vector<RealType> binKE(nBins_, 0.0);
1435	>	vector<int> binDOF(nBins_, 0);
1436	>	vector<int> binCount(nBins_, 0);
1437
1438		// alternative approach, track all molecules instead of only those
1439		// selected for scaling/swapping:
#	Line 1379 | Line 1441 | namespace OpenMD {
1441		SimInfo::MoleculeIterator miter;
1442		vector<StuntDouble*>::iterator iiter;
1443		Molecule* mol;
1444	<	StuntDouble* integrableObject;
1444	>	StuntDouble* sd;
1445		for (mol = info_->beginMolecule(miter); mol != NULL;
1446		mol = info_->nextMolecule(miter))
1447	<	integrableObject is essentially sd
1448	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1449	<	integrableObject != NULL;
1450	<	integrableObject = mol->nextIntegrableObject(iiter))
1447	>	sd is essentially sd
1448	>	for (sd = mol->beginIntegrableObject(iiter);
1449	>	sd != NULL;
1450	>	sd = mol->nextIntegrableObject(iiter))
1451		*/
1452		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453		sd = seleMan_.nextSelected(selei)) {
#	Line 1398 | Line 1460 | namespace OpenMD {
1460
1461		if (usePeriodicBoundaryConditions_)
1462		currentSnap_->wrapVector(pos);
1463	<
1463	>
1464	>
1465		// which bin is this stuntdouble in?
1466		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1467	<
1468	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1469	<	rnemdLogWidth_;
1470	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1471	<	/*
1409	<	if (rnemdLogWidth_ == midBin_ + 1)
1410	<	if (binNo > midBin_)
1411	<	binNo = nBins_ - binNo;
1412	<	*/
1467	>	// Shift molecules by half a box to have bins start at 0
1468	>	// The modulo operator is used to wrap the case when we are
1469	>	// beyond the end of the bins back to the beginning.
1470	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1471	>
1472		RealType mass = sd->getMass();
1414	–	mHist_[binNo] += mass;
1473		Vector3d vel = sd->getVel();
1416	–	RealType value;
1417	–	//RealType xVal, yVal, zVal;
1474
1475	<	if (outputTemp_) {
1476	<	value = mass * vel.lengthSquare();
1477	<	tempCount_[binNo] += 3;
1478	<	if (sd->isDirectional()) {
1479	<	Vector3d angMom = sd->getJ();
1480	<	Mat3x3d I = sd->getI();
1481	<	if (sd->isLinear()) {
1482	<	int i = sd->linearAxis();
1483	<	int j = (i + 1) % 3;
1484	<	int k = (i + 2) % 3;
1485	<	value += angMom[j] * angMom[j] / I(j, j) +
1486	<	angMom[k] * angMom[k] / I(k, k);
1487	<	tempCount_[binNo] +=2;
1488	<	} else {
1489	<	value += angMom[0] * angMom[0] / I(0, 0) +
1490	<	angMom[1]*angMom[1]/I(1, 1) +
1491	<	angMom[2]*angMom[2]/I(2, 2);
1492	<	tempCount_[binNo] +=3;
1493	<	}
1494	<	}
1495	<	value = value / PhysicalConstants::energyConvert
1496	<	/ PhysicalConstants::kb;//may move to getStatus()
1497	<	tempHist_[binNo] += value;
1498	<	}
1443	<	if (outputVx_) {
1444	<	value = mass * vel[0];
1445	<	//vxzCount_[binNo]++;
1446	<	pxzHist_[binNo] += value;
1447	<	}
1448	<	if (outputVy_) {
1449	<	value = mass * vel[1];
1450	<	//vyzCount_[binNo]++;
1451	<	pyzHist_[binNo] += value;
1475	>	binCount[binNo]++;
1476	>	binMass[binNo] += mass;
1477	>	binPx[binNo] += mass*vel.x();
1478	>	binPy[binNo] += mass*vel.y();
1479	>	binPz[binNo] += mass*vel.z();
1480	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1481	>	binDOF[binNo] += 3;
1482	>
1483	>	if (sd->isDirectional()) {
1484	>	Vector3d angMom = sd->getJ();
1485	>	Mat3x3d I = sd->getI();
1486	>	if (sd->isLinear()) {
1487	>	int i = sd->linearAxis();
1488	>	int j = (i + 1) % 3;
1489	>	int k = (i + 2) % 3;
1490	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1491	>	angMom[k] * angMom[k] / I(k, k));
1492	>	binDOF[binNo] += 2;
1493	>	} else {
1494	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1495	>	angMom[1] * angMom[1] / I(1, 1) +
1496	>	angMom[2] * angMom[2] / I(2, 2));
1497	>	binDOF[binNo] += 3;
1498	>	}
1499		}
1500	+	}
1501	+
1502
1503	<	if (output3DTemp_) {
1504	<	value = mass * vel.x() * vel.x();
1505	<	xTempHist_[binNo] += value;
1506	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1507	<	/ PhysicalConstants::kb;
1508	<	yTempHist_[binNo] += value;
1509	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1510	<	/ PhysicalConstants::kb;
1511	<	zTempHist_[binNo] += value;
1512	<	xyzTempCount_[binNo]++;
1503	>	#ifdef IS_MPI
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1505	>	nBins_, MPI::INT, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1509	>	nBins_, MPI::REALTYPE, MPI::SUM);
1510	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1511	>	nBins_, MPI::REALTYPE, MPI::SUM);
1512	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1513	>	nBins_, MPI::REALTYPE, MPI::SUM);
1514	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1515	>	nBins_, MPI::REALTYPE, MPI::SUM);
1516	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1517	>	nBins_, MPI::INT, MPI::SUM);
1518	>	#endif
1519	>
1520	>	Vector3d vel;
1521	>	RealType den;
1522	>	RealType temp;
1523	>	RealType z;
1524	>	for (int i = 0; i < nBins_; i++) {
1525	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1526	>	vel.x() = binPx[i] / binMass[i];
1527	>	vel.y() = binPy[i] / binMass[i];
1528	>	vel.z() = binPz[i] / binMass[i];
1529	>
1530	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1531	>	/ currentSnap_->getVolume() ;
1532	>
1533	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1534	>	PhysicalConstants::energyConvert);
1535	>
1536	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1537	>	if(outputMask_[j]) {
1538	>	switch(j) {
1539	>	case Z:
1540	>	(data_[j].accumulator[i])->add(z);
1541	>	break;
1542	>	case TEMPERATURE:
1543	>	data_[j].accumulator[i]->add(temp);
1544	>	break;
1545	>	case VELOCITY:
1546	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1547	>	break;
1548	>	case DENSITY:
1549	>	data_[j].accumulator[i]->add(den);
1550	>	break;
1551	>	}
1552	>	}
1553		}
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	–	}
1554		}
1555		}
1556
1557		void RNEMD::getStarted() {
1558	+	if (!doRNEMD_) return;
1559		collectData();
1560	<	/*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();
1560	>	writeOutputFile();
1561		}
1562
1563	<	void RNEMD::getStatus() {
1564	<
1565	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1566	<	Stats& stat = currentSnap_->statData;
1567	<	RealType time = currentSnap_->getTime();
1568	<
1569	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1570	<	//or to be more meaningful, define another item as exchangeSum_ / time
1571	<	int j;
1572	<
1563	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1564	>	if (!doRNEMD_) return;
1565	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1566	>
1567	>	while(tokenizer.hasMoreTokens()) {
1568	>	std::string token(tokenizer.nextToken());
1569	>	toUpper(token);
1570	>	OutputMapType::iterator i = outputMap_.find(token);
1571	>	if (i != outputMap_.end()) {
1572	>	outputMask_.set(i->second);
1573	>	} else {
1574	>	sprintf( painCave.errMsg,
1575	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1576	>	"\toutputFileFormat keyword.\n", token.c_str() );
1577	>	painCave.isFatal = 0;
1578	>	painCave.severity = OPENMD_ERROR;
1579	>	simError();
1580	>	}
1581	>	}
1582	>	}
1583	>
1584	>	void RNEMD::writeOutputFile() {
1585	>	if (!doRNEMD_) return;
1586	>
1587		#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	–
1588		// If we're the root node, should we print out the results
1589		int worldRank = MPI::COMM_WORLD.Get_rank();
1590		if (worldRank == 0) {
1591		#endif
1592	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1593	+
1594	+	if( !rnemdFile_ ){
1595	+	sprintf( painCave.errMsg,
1596	+	"Could not open \"%s\" for RNEMD output.\n",
1597	+	rnemdFileName_.c_str());
1598	+	painCave.isFatal = 1;
1599	+	simError();
1600	+	}
1601
1602	<	if (outputTemp_) {
1603	<	tempLog_ << time;
1604	<	for (j = 0; j < rnemdLogWidth_; j++) {
1605	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1606	<	}
1607	<	tempLog_ << endl;
1602	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1603	>
1604	>	RealType time = currentSnap_->getTime();
1605	>	RealType avgArea;
1606	>	areaAccumulator_->getAverage(avgArea);
1607	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea)
1608	>	/ PhysicalConstants::energyConvert;
1609	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1610	>
1611	>	rnemdFile_ << "#######################################################\n";
1612	>	rnemdFile_ << "# RNEMD {\n";
1613	>
1614	>	map<string, RNEMDMethod>::iterator mi;
1615	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1616	>	if ( (*mi).second == rnemdMethod_)
1617	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1618		}
1619	<	if (outputVx_) {
1620	<	vxzLog_ << time;
1621	<	for (j = 0; j < rnemdLogWidth_; j++) {
1622	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1592	<	}
1593	<	vxzLog_ << endl;
1619	>	map<string, RNEMDFluxType>::iterator fi;
1620	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1621	>	if ( (*fi).second == rnemdFluxType_)
1622	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1623		}
1624	<	if (outputVy_) {
1625	<	vyzLog_ << time;
1597	<	for (j = 0; j < rnemdLogWidth_; j++) {
1598	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	<	}
1600	<	vyzLog_ << endl;
1601	<	}
1624	>
1625	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1626
1627	<	if (output3DTemp_) {
1628	<	RealType temp;
1629	<	xTempLog_ << time;
1630	<	for (j = 0; j < rnemdLogWidth_; j++) {
1631	<	if (outputVx_)
1632	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1633	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1634	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1635	<	xTempLog_ << "\t" << temp;
1627	>	rnemdFile_ << "#    objectSelection = \""
1628	>	<< rnemdObjectSelection_ << "\";\n";
1629	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1630	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1631	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1632	>	rnemdFile_ << "# }\n";
1633	>	rnemdFile_ << "#######################################################\n";
1634	>	rnemdFile_ << "# RNEMD report:\n";
1635	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1636	>	rnemdFile_ << "#     target flux:\n";
1637	>	rnemdFile_ << "#         kinetic = "
1638	>	<< kineticFlux_ / PhysicalConstants::energyConvert
1639	>	<< " (kcal/mol/A^2/fs)\n";
1640	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_
1641	>	<< " (amu/A/fs^2)\n";
1642	>	rnemdFile_ << "#     target one-time exchanges:\n";
1643	>	rnemdFile_ << "#         kinetic = "
1644	>	<< kineticTarget_ / PhysicalConstants::energyConvert
1645	>	<< " (kcal/mol)\n";
1646	>	rnemdFile_ << "#         momentum = " << momentumTarget_
1647	>	<< " (amu*A/fs)\n";
1648	>	rnemdFile_ << "#     actual exchange totals:\n";
1649	>	rnemdFile_ << "#         kinetic = "
1650	>	<< kineticExchange_ / PhysicalConstants::energyConvert
1651	>	<< " (kcal/mol)\n";
1652	>	rnemdFile_ << "#         momentum = " << momentumExchange_
1653	>	<< " (amu*A/fs)\n";
1654	>	rnemdFile_ << "#     actual flux:\n";
1655	>	rnemdFile_ << "#         kinetic = " << Jz
1656	>	<< " (kcal/mol/A^2/fs)\n";
1657	>	rnemdFile_ << "#         momentum = " << JzP
1658	>	<< " (amu/A/fs^2)\n";
1659	>	rnemdFile_ << "#     exchange statistics:\n";
1660	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1661	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1662	>	if (rnemdMethod_ == rnemdNIVS) {
1663	>	rnemdFile_ << "#         NIVS root-check errors = "
1664	>	<< failRootCount_ << "\n";
1665	>	}
1666	>	rnemdFile_ << "#######################################################\n";
1667	>
1668	>
1669	>
1670	>	//write title
1671	>	rnemdFile_ << "#";
1672	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1673	>	if (outputMask_[i]) {
1674	>	rnemdFile_ << "\t" << data_[i].title <<
1675	>	"(" << data_[i].units << ")";
1676	>	// add some extra tabs for column alignment
1677	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
1678		}
1679	<	xTempLog_ << endl;
1680	<	yTempLog_ << time;
1681	<	for (j = 0; j < rnemdLogWidth_; j++) {
1682	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1679	>	}
1680	>	rnemdFile_ << std::endl;
1681	>
1682	>	rnemdFile_.precision(8);
1683	>
1684	>	for (unsigned int j = 0; j < nBins_; j++) {
1685	>
1686	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1687	>	if (outputMask_[i]) {
1688	>	if (data_[i].dataType == "RealType")
1689	>	writeReal(i,j);
1690	>	else if (data_[i].dataType == "Vector3d")
1691	>	writeVector(i,j);
1692	>	else {
1693	>	sprintf( painCave.errMsg,
1694	>	"RNEMD found an unknown data type for: %s ",
1695	>	data_[i].title.c_str());
1696	>	painCave.isFatal = 1;
1697	>	simError();
1698	>	}
1699	>	}
1700		}
1701	<	yTempLog_ << endl;
1702	<	zTempLog_ << time;
1703	<	for (j = 0; j < rnemdLogWidth_; j++) {
1704	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1701	>	rnemdFile_ << std::endl;
1702	>
1703	>	}
1704	>
1705	>	rnemdFile_ << "#######################################################\n";
1706	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1707	>	rnemdFile_ << "#######################################################\n";
1708	>
1709	>
1710	>	for (unsigned int j = 0; j < nBins_; j++) {
1711	>	rnemdFile_ << "#";
1712	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1713	>	if (outputMask_[i]) {
1714	>	if (data_[i].dataType == "RealType")
1715	>	writeRealStdDev(i,j);
1716	>	else if (data_[i].dataType == "Vector3d")
1717	>	writeVectorStdDev(i,j);
1718	>	else {
1719	>	sprintf( painCave.errMsg,
1720	>	"RNEMD found an unknown data type for: %s ",
1721	>	data_[i].title.c_str());
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>	}
1726		}
1727	<	zTempLog_ << endl;
1728	<	}
1729	<	if (outputRotTemp_) {
1730	<	rotTempLog_ << time;
1731	<	for (j = 0; j < rnemdLogWidth_; j++) {
1732	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1733	<	}
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	<	}
1727	>	rnemdFile_ << std::endl;
1728	>
1729	>	}
1730	>
1731	>	rnemdFile_.flush();
1732	>	rnemdFile_.close();
1733	>
1734		#ifdef IS_MPI
1735		}
1736		#endif
1737	<
1738	<	for (j = 0; j < rnemdLogWidth_; j++) {
1739	<	mHist_[j] = 0.0;
1737	>
1738	>	}
1739	>
1740	>	void RNEMD::writeReal(int index, unsigned int bin) {
1741	>	if (!doRNEMD_) return;
1742	>	assert(index >=0 && index < ENDINDEX);
1743	>	assert(bin < nBins_);
1744	>	RealType s;
1745	>
1746	>	data_[index].accumulator[bin]->getAverage(s);
1747	>
1748	>	if (! isinf(s) && ! isnan(s)) {
1749	>	rnemdFile_ << "\t" << s;
1750	>	} else{
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	>	}
1757	>	}
1758	>
1759	>	void RNEMD::writeVector(int index, unsigned int bin) {
1760	>	if (!doRNEMD_) return;
1761	>	assert(index >=0 && index < ENDINDEX);
1762	>	assert(bin < nBins_);
1763	>	Vector3d s;
1764	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1765	>	if (isinf(s[0]) || isnan(s[0]) ||
1766	>	isinf(s[1]) || isnan(s[1]) ||
1767	>	isinf(s[2]) || isnan(s[2]) ) {
1768	>	sprintf( painCave.errMsg,
1769	>	"RNEMD detected a numerical error writing: %s for bin %d",
1770	>	data_[index].title.c_str(), bin);
1771	>	painCave.isFatal = 1;
1772	>	simError();
1773	>	} else {
1774	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1775		}
1776	<	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	<	}
1776	>	}
1777
1778	<	if (output3DTemp_)
1779	<	for (j = 0; j < rnemdLogWidth_; j++) {
1780	<	xTempHist_[j] = 0.0;
1781	<	yTempHist_[j] = 0.0;
1782	<	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';
1778	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1779	>	if (!doRNEMD_) return;
1780	>	assert(index >=0 && index < ENDINDEX);
1781	>	assert(bin < nBins_);
1782	>	RealType s;
1783
1784	<	logFrameCount_ = 0;
1784	>	data_[index].accumulator[bin]->getStdDev(s);
1785	>
1786	>	if (! isinf(s) && ! isnan(s)) {
1787	>	rnemdFile_ << "\t" << s;
1788	>	} else{
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	>	}
1795		}
1796	+
1797	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1798	+	if (!doRNEMD_) return;
1799	+	assert(index >=0 && index < ENDINDEX);
1800	+	assert(bin < nBins_);
1801	+	Vector3d s;
1802	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1803	+	if (isinf(s[0]) || isnan(s[0]) ||
1804	+	isinf(s[1]) || isnan(s[1]) ||
1805	+	isinf(s[2]) || isnan(s[2]) ) {
1806	+	sprintf( painCave.errMsg,
1807	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1808	+	data_[index].title.c_str(), bin);
1809	+	painCave.isFatal = 1;
1810	+	simError();
1811	+	} else {
1812	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1813	+	}
1814	+	}
1815		}
1816

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