ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1775 by gezelter, Wed Aug 8 18:45:52 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;
74	<	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	>	stringToMethod_["Swap"]  = rnemdSwap;
73	>	stringToMethod_["NIVS"]  = rnemdNIVS;
74	>	stringToMethod_["VSS"]   = rnemdVSS;
75
76	+	stringToFluxType_["KE"]  = rnemdKE;
77	+	stringToFluxType_["Px"]  = rnemdPx;
78	+	stringToFluxType_["Py"]  = rnemdPy;
79	+	stringToFluxType_["Pz"]  = rnemdPz;
80	+	stringToFluxType_["KE+Px"]  = rnemdKePx;
81	+	stringToFluxType_["KE+Py"]  = rnemdKePy;
82	+	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
83	+
84		runTime_ = simParams->getRunTime();
85		statusTime_ = simParams->getStatusTime();
86
87	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
87	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88		evaluator_.loadScriptString(rnemdObjectSelection_);
89		seleMan_.setSelectionSet(evaluator_.evaluate());
90	+
91	+	const string methStr = rnemdParams->getMethod();
92	+	bool hasFluxType = rnemdParams->haveFluxType();
93	+
94	+	string fluxStr;
95	+	if (hasFluxType) {
96	+	fluxStr = rnemdParams->getFluxType();
97	+	} else {
98	+	sprintf(painCave.errMsg,
99	+	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
100	+	"\twhich must be one of the following values:\n"
101	+	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
102	+	"\tuse RNEMD\n");
103	+	painCave.isFatal = 1;
104	+	painCave.severity = OPENMD_ERROR;
105	+	simError();
106	+	}
107	+
108	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
109	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
110	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
111	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
112	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
113	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
114	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
115	+	bool hasOutputFields = rnemdParams->haveOutputFields();
116	+
117	+	map<string, RNEMDMethod>::iterator i;
118	+	i = stringToMethod_.find(methStr);
119	+	if (i != stringToMethod_.end())
120	+	rnemdMethod_ = i->second;
121	+	else {
122	+	sprintf(painCave.errMsg,
123	+	"RNEMD: The current method,\n"
124	+	"\t\t%s is not one of the recognized\n"
125	+	"\texchange methods: Swap, NIVS, or VSS\n",
126	+	methStr.c_str());
127	+	painCave.isFatal = 1;
128	+	painCave.severity = OPENMD_ERROR;
129	+	simError();
130	+	}
131	+
132	+	map<string, RNEMDFluxType>::iterator j;
133	+	j = stringToFluxType_.find(fluxStr);
134	+	if (j != stringToFluxType_.end())
135	+	rnemdFluxType_ = j->second;
136	+	else {
137	+	sprintf(painCave.errMsg,
138	+	"RNEMD: The current fluxType,\n"
139	+	"\t\t%s\n"
140	+	"\tis not one of the recognized flux types.\n",
141	+	fluxStr.c_str());
142	+	painCave.isFatal = 1;
143	+	painCave.severity = OPENMD_ERROR;
144	+	simError();
145	+	}
146	+
147	+	bool methodFluxMismatch = false;
148	+	bool hasCorrectFlux = false;
149	+	switch(rnemdMethod_) {
150	+	case rnemdSwap:
151	+	switch (rnemdFluxType_) {
152	+	case rnemdKE:
153	+	hasCorrectFlux = hasKineticFlux;
154	+	break;
155	+	case rnemdPx:
156	+	case rnemdPy:
157	+	case rnemdPz:
158	+	hasCorrectFlux = hasMomentumFlux;
159	+	break;
160	+	default :
161	+	methodFluxMismatch = true;
162	+	break;
163	+	}
164	+	break;
165	+	case rnemdNIVS:
166	+	switch (rnemdFluxType_) {
167	+	case rnemdKE:
168	+	case rnemdRotKE:
169	+	case rnemdFullKE:
170	+	hasCorrectFlux = hasKineticFlux;
171	+	break;
172	+	case rnemdPx:
173	+	case rnemdPy:
174	+	case rnemdPz:
175	+	hasCorrectFlux = hasMomentumFlux;
176	+	break;
177	+	case rnemdKePx:
178	+	case rnemdKePy:
179	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
180	+	break;
181	+	default:
182	+	methodFluxMismatch = true;
183	+	break;
184	+	}
185	+	break;
186	+	case rnemdVSS:
187	+	switch (rnemdFluxType_) {
188	+	case rnemdKE:
189	+	case rnemdRotKE:
190	+	case rnemdFullKE:
191	+	hasCorrectFlux = hasKineticFlux;
192	+	break;
193	+	case rnemdPx:
194	+	case rnemdPy:
195	+	case rnemdPz:
196	+	hasCorrectFlux = hasMomentumFlux;
197	+	break;
198	+	case rnemdPvector:
199	+	hasCorrectFlux = hasMomentumFluxVector;
200	+	case rnemdKePx:
201	+	case rnemdKePy:
202	+	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
203	+	break;
204	+	case rnemdKePvector:
205	+	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
206	+	break;
207	+	default:
208	+	methodFluxMismatch = true;
209	+	break;
210	+	}
211	+	default:
212	+	break;
213	+	}
214	+
215	+	if (methodFluxMismatch) {
216	+	sprintf(painCave.errMsg,
217	+	"RNEMD: The current method,\n"
218	+	"\t\t%s\n"
219	+	"\tcannot be used with the current flux type, %s\n",
220	+	methStr.c_str(), fluxStr.c_str());
221	+	painCave.isFatal = 1;
222	+	painCave.severity = OPENMD_ERROR;
223	+	simError();
224	+	}
225	+	if (!hasCorrectFlux) {
226	+	sprintf(painCave.errMsg,
227	+	"RNEMD: The current method,\n"
228	+	"\t%s, and flux type %s\n"
229	+	"\tdid not have the correct flux value specified. Options\n"
230	+	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
231	+	methStr.c_str(), fluxStr.c_str());
232	+	painCave.isFatal = 1;
233	+	painCave.severity = OPENMD_ERROR;
234	+	simError();
235	+	}
236	+
237	+	if (hasKineticFlux) {
238	+	kineticFlux_ = rnemdParams->getKineticFlux();
239	+	} else {
240	+	kineticFlux_ = 0.0;
241	+	}
242	+	if (hasMomentumFluxVector) {
243	+	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
244	+	} else {
245	+	momentumFluxVector_ = V3Zero;
246	+	if (hasMomentumFlux) {
247	+	RealType momentumFlux = rnemdParams->getMomentumFlux();
248	+	switch (rnemdFluxType_) {
249	+	case rnemdPx:
250	+	momentumFluxVector_.x() = momentumFlux;
251	+	break;
252	+	case rnemdPy:
253	+	momentumFluxVector_.y() = momentumFlux;
254	+	break;
255	+	case rnemdPz:
256	+	momentumFluxVector_.z() = momentumFlux;
257	+	break;
258	+	case rnemdKePx:
259	+	momentumFluxVector_.x() = momentumFlux;
260	+	break;
261	+	case rnemdKePy:
262	+	momentumFluxVector_.y() = momentumFlux;
263	+	break;
264	+	default:
265	+	break;
266	+	}
267	+	}
268	+	}
269
270		// do some sanity checking
271
#	Line 99 | Line 274 | namespace OpenMD {
274
275		if (selectionCount > nIntegrable) {
276		sprintf(painCave.errMsg,
277	<	"RNEMD: The current RNEMD_objectSelection,\n"
277	>	"RNEMD: The current objectSelection,\n"
278		"\t\t%s\n"
279		"\thas resulted in %d selected objects.  However,\n"
280		"\tthe total number of integrable objects in the system\n"
#	Line 112 | Line 287 | namespace OpenMD {
287		painCave.severity = OPENMD_WARNING;
288		simError();
289		}
115	–
116	–	const string st = simParams->getRNEMD_exchangeType();
290
291	<	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	<
291	>	areaAccumulator_ = new Accumulator();
292
293	<	#ifdef IS_MPI
179	<	if (worldRank == 0) {
180	<	#endif
293	>	nBins_ = rnemdParams->getOutputBins();
294
295	<	//may have rnemdWriter separately
296	<	string rnemdFileName;
295	>	data_.resize(RNEMD::ENDINDEX);
296	>	OutputData z;
297	>	z.units =  "Angstroms";
298	>	z.title =  "Z";
299	>	z.dataType = "RealType";
300	>	z.accumulator.reserve(nBins_);
301	>	for (unsigned int i = 0; i < nBins_; i++)
302	>	z.accumulator.push_back( new Accumulator() );
303	>	data_[Z] = z;
304	>	outputMap_["Z"] =  Z;
305
306	<	if (outputTemp_) {
307	<	rnemdFileName = "temperature.log";
308	<	tempLog_.open(rnemdFileName.c_str());
309	<	}
310	<	if (outputVx_) {
311	<	rnemdFileName = "velocityX.log";
312	<	vxzLog_.open(rnemdFileName.c_str());
313	<	}
314	<	if (outputVy_) {
194	<	rnemdFileName = "velocityY.log";
195	<	vyzLog_.open(rnemdFileName.c_str());
196	<	}
306	>	OutputData temperature;
307	>	temperature.units =  "K";
308	>	temperature.title =  "Temperature";
309	>	temperature.dataType = "RealType";
310	>	temperature.accumulator.reserve(nBins_);
311	>	for (unsigned int i = 0; i < nBins_; i++)
312	>	temperature.accumulator.push_back( new Accumulator() );
313	>	data_[TEMPERATURE] = temperature;
314	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
315
316	<	if (output3DTemp_) {
317	<	rnemdFileName = "temperatureX.log";
318	<	xTempLog_.open(rnemdFileName.c_str());
319	<	rnemdFileName = "temperatureY.log";
320	<	yTempLog_.open(rnemdFileName.c_str());
321	<	rnemdFileName = "temperatureZ.log";
322	<	zTempLog_.open(rnemdFileName.c_str());
323	<	}
324	<	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
316	>	OutputData velocity;
317	>	velocity.units = "amu/fs";
318	>	velocity.title =  "Velocity";
319	>	velocity.dataType = "Vector3d";
320	>	velocity.accumulator.reserve(nBins_);
321	>	for (unsigned int i = 0; i < nBins_; i++)
322	>	velocity.accumulator.push_back( new VectorAccumulator() );
323	>	data_[VELOCITY] = velocity;
324	>	outputMap_["VELOCITY"] = VELOCITY;
325
326	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
327	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
328	<	midBin_ = nBins_ / 2;
329	<	if (simParams->haveRNEMD_binShift()) {
330	<	if (simParams->getRNEMD_binShift()) {
331	<	zShift_ = 0.5 / (RealType)(nBins_);
332	<	} else {
333	<	zShift_ = 0.0;
334	<	}
326	>	OutputData density;
327	>	density.units =  "g cm^-3";
328	>	density.title =  "Density";
329	>	density.dataType = "RealType";
330	>	density.accumulator.reserve(nBins_);
331	>	for (unsigned int i = 0; i < nBins_; i++)
332	>	density.accumulator.push_back( new Accumulator() );
333	>	data_[DENSITY] = density;
334	>	outputMap_["DENSITY"] =  DENSITY;
335	>
336	>	if (hasOutputFields) {
337	>	parseOutputFileFormat(rnemdParams->getOutputFields());
338		} else {
339	<	zShift_ = 0.0;
339	>	outputMask_.set(Z);
340	>	switch (rnemdFluxType_) {
341	>	case rnemdKE:
342	>	case rnemdRotKE:
343	>	case rnemdFullKE:
344	>	outputMask_.set(TEMPERATURE);
345	>	break;
346	>	case rnemdPx:
347	>	case rnemdPy:
348	>	outputMask_.set(VELOCITY);
349	>	break;
350	>	case rnemdPz:
351	>	case rnemdPvector:
352	>	outputMask_.set(VELOCITY);
353	>	outputMask_.set(DENSITY);
354	>	break;
355	>	case rnemdKePx:
356	>	case rnemdKePy:
357	>	outputMask_.set(TEMPERATURE);
358	>	outputMask_.set(VELOCITY);
359	>	break;
360	>	case rnemdKePvector:
361	>	outputMask_.set(TEMPERATURE);
362	>	outputMask_.set(VELOCITY);
363	>	outputMask_.set(DENSITY);
364	>	break;
365	>	default:
366	>	break;
367	>	}
368		}
369	<	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
370	<	//shift slabs by half slab width, maybe useful in heterogeneous systems
371	<	//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	<	}*/
369	>
370	>	if (hasOutputFileName) {
371	>	rnemdFileName_ = rnemdParams->getOutputFileName();
372		} else {
373	<	set_RNEMD_logWidth(nBins_);
374	<	}
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);
373	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
374	>	}
375
376	<	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);
376	>	exchangeTime_ = rnemdParams->getExchangeTime();
377
378	<	set_RNEMD_exchange_total(0.0);
379	<	if (simParams->haveRNEMD_targetFlux()) {
380	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
381	<	} else {
382	<	set_RNEMD_target_flux(0.0);
383	<	}
384	<	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_;
378	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
379	>	Mat3x3d hmat = currentSnap_->getHmat();
380	>
381	>	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
382	>	// Lx, Ly = box dimensions in x & y
383	>	// dt = exchange time interval
384	>	// flux = target flux
385
386	<	#ifndef IS_MPI
387	<	if (simParams->haveSeed()) {
388	<	seedValue = simParams->getSeed();
389	<	randNumGen_ = new SeqRandNumGen(seedValue);
390	<	}else {
391	<	randNumGen_ = new SeqRandNumGen();
392	<	}
393	<	#else
394	<	if (simParams->haveSeed()) {
395	<	seedValue = simParams->getSeed();
396	<	randNumGen_ = new ParallelRandNumGen(seedValue);
397	<	}else {
398	<	randNumGen_ = new ParallelRandNumGen();
319	<	}
320	<	#endif
321	<	}
386	>	RealType area = currentSnap_->getXYarea();
387	>	kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area;
388	>	momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area;
389	>
390	>	// total exchange sums are zeroed out at the beginning:
391	>
392	>	kineticExchange_ = 0.0;
393	>	momentumExchange_ = V3Zero;
394	>
395	>	if (hasSlabWidth)
396	>	slabWidth_ = rnemdParams->getSlabWidth();
397	>	else
398	>	slabWidth_ = hmat(2,2) / 10.0;
399
400	+	if (hasSlabACenter)
401	+	slabACenter_ = rnemdParams->getSlabACenter();
402	+	else
403	+	slabACenter_ = 0.0;
404	+
405	+	if (hasSlabBCenter)
406	+	slabBCenter_ = rnemdParams->getSlabBCenter();
407	+	else
408	+	slabBCenter_ = hmat(2,2) / 2.0;
409	+
410	+	}
411	+
412		RNEMD::~RNEMD() {
324	–	delete randNumGen_;
413
414		#ifdef IS_MPI
415		if (worldRank == 0) {
416		#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();
417
418	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
419	<	rnemdType_ == rnemdPyScale) {
420	<	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();
418	>	writeOutputFile();
419	>
420	>	rnemdFile_.close();
421
422		#ifdef IS_MPI
423		}
424		#endif
425	+	}
426	+
427	+	bool RNEMD::inSlabA(Vector3d pos) {
428	+	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
429	+	}
430	+	bool RNEMD::inSlabB(Vector3d pos) {
431	+	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
432		}
433
434		void RNEMD::doSwap() {
#	Line 393 | Line 461 | namespace OpenMD {
461
462		if (usePeriodicBoundaryConditions_)
463		currentSnap_->wrapVector(pos);
464	+	bool inA = inSlabA(pos);
465	+	bool inB = inSlabB(pos);
466
467	<	// 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_) {
467	>	if (inA || inB) {
468
469		RealType mass = sd->getMass();
470		Vector3d vel = sd->getVel();
471		RealType value;
472	<
473	<	switch(rnemdType_) {
474	<	case rnemdKineticSwap :
472	>
473	>	switch(rnemdFluxType_) {
474	>	case rnemdKE :
475
476		value = mass * vel.lengthSquare();
477
#	Line 429 | Line 492 | namespace OpenMD {
492		}
493		} //angular momenta exchange enabled
494		//energyConvert temporarily disabled
495	<	//make exchangeSum_ comparable between swap & scale
495	>	//make kineticExchange_ comparable between swap & scale
496		//value = value * 0.5 / PhysicalConstants::energyConvert;
497		value *= 0.5;
498		break;
#	Line 446 | Line 509 | namespace OpenMD {
509		break;
510		}
511
512	<	if (binNo == 0) {
512	>	if (inA == 0) {
513		if (!min_found) {
514		min_val = value;
515		min_sd = sd;
#	Line 457 | Line 520 | namespace OpenMD {
520		min_sd = sd;
521		}
522		}
523	<	} else { //midBin_
523	>	} else {
524		if (!max_found) {
525		max_val = value;
526		max_sd = sd;
#	Line 471 | Line 534 | namespace OpenMD {
534		}
535		}
536		}
537	<
537	>
538		#ifdef IS_MPI
539		int nProc, worldRank;
540	<
540	>
541		nProc = MPI::COMM_WORLD.Get_size();
542		worldRank = MPI::COMM_WORLD.Get_rank();
543
#	Line 532 | Line 595 | namespace OpenMD {
595		Vector3d max_vel = max_sd->getVel();
596		RealType temp_vel;
597
598	<	switch(rnemdType_) {
599	<	case rnemdKineticSwap :
598	>	switch(rnemdFluxType_) {
599	>	case rnemdKE :
600		min_sd->setVel(max_vel);
601		max_sd->setVel(min_vel);
602		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 584 | Line 647 | namespace OpenMD {
647		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
648		min_vals.rank, 0, status);
649
650	<	switch(rnemdType_) {
651	<	case rnemdKineticSwap :
650	>	switch(rnemdFluxType_) {
651	>	case rnemdKE :
652		max_sd->setVel(min_vel);
653		//angular momenta exchange enabled
654		if (max_sd->isDirectional()) {
#	Line 630 | Line 693 | namespace OpenMD {
693		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
694		max_vals.rank, 0, status);
695
696	<	switch(rnemdType_) {
697	<	case rnemdKineticSwap :
696	>	switch(rnemdFluxType_) {
697	>	case rnemdKE :
698		min_sd->setVel(max_vel);
699		//angular momenta exchange enabled
700		if (min_sd->isDirectional()) {
#	Line 665 | Line 728 | namespace OpenMD {
728		}
729		}
730		#endif
731	<	exchangeSum_ += max_val - min_val;
731	>
732	>	switch(rnemdFluxType_) {
733	>	case rnemdKE:
734	>	cerr << "KE\n";
735	>	kineticExchange_ += max_val - min_val;
736	>	break;
737	>	case rnemdPx:
738	>	momentumExchange_.x() += max_val - min_val;
739	>	break;
740	>	case rnemdPy:
741	>	momentumExchange_.y() += max_val - min_val;
742	>	break;
743	>	case rnemdPz:
744	>	momentumExchange_.z() += max_val - min_val;
745	>	break;
746	>	default:
747	>	cerr << "default\n";
748	>	break;
749	>	}
750		} else {
751		sprintf(painCave.errMsg,
752	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
752	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
753		painCave.isFatal = 0;
754		painCave.severity = OPENMD_INFO;
755		simError();
#	Line 676 | Line 757 | namespace OpenMD {
757		}
758		} else {
759		sprintf(painCave.errMsg,
760	<	"RNEMD: exchange NOT performed because selected object\n"
761	<	"\tnot present in at least one of the two slabs.\n");
760	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
761	>	"\twas not present in at least one of the two slabs.\n");
762		painCave.isFatal = 0;
763		painCave.severity = OPENMD_INFO;
764		simError();
765		failTrialCount_++;
766	<	}
686	<
766	>	}
767		}
768
769	<	void RNEMD::doScale() {
769	>	void RNEMD::doNIVS() {
770
771		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
772		Mat3x3d hmat = currentSnap_->getHmat();
#	Line 727 | Line 807 | namespace OpenMD {
807		currentSnap_->wrapVector(pos);
808
809		// which bin is this stuntdouble in?
810	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
810	>	bool inA = inSlabA(pos);
811	>	bool inB = inSlabB(pos);
812
813	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
814	<
734	<	// if we're in bin 0 or the middleBin
735	<	if (binNo == 0 || binNo == midBin_) {
736	<
813	>	if (inA || inB) {
814	>
815		RealType mass = sd->getMass();
816		Vector3d vel = sd->getVel();
817
818	<	if (binNo == 0) {
818	>	if (inA) {
819		hotBin.push_back(sd);
820		Phx += mass * vel.x();
821		Phy += mass * vel.y();
#	Line 745 | Line 823 | namespace OpenMD {
823		Khx += mass * vel.x() * vel.x();
824		Khy += mass * vel.y() * vel.y();
825		Khz += mass * vel.z() * vel.z();
748	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
826		if (sd->isDirectional()) {
827		Vector3d angMom = sd->getJ();
828		Mat3x3d I = sd->getI();
#	Line 761 | Line 838 | namespace OpenMD {
838		+ angMom[2]*angMom[2]/I(2, 2);
839		}
840		}
841	<	//}
765	<	} else { //midBin_
841	>	} else {
842		coldBin.push_back(sd);
843		Pcx += mass * vel.x();
844		Pcy += mass * vel.y();
#	Line 770 | Line 846 | namespace OpenMD {
846		Kcx += mass * vel.x() * vel.x();
847		Kcy += mass * vel.y() * vel.y();
848		Kcz += mass * vel.z() * vel.z();
773	–	//if (rnemdType_ == rnemdKineticScaleVAM) {
849		if (sd->isDirectional()) {
850		Vector3d angMom = sd->getJ();
851		Mat3x3d I = sd->getI();
#	Line 786 | Line 861 | namespace OpenMD {
861		+ angMom[2]*angMom[2]/I(2, 2);
862		}
863		}
789	–	//}
864		}
865		}
866		}
#	Line 800 | Line 874 | namespace OpenMD {
874		Kcz *= 0.5;
875		Kcw *= 0.5;
876
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	–
877		#ifdef IS_MPI
878		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
879		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 831 | Line 899 | namespace OpenMD {
899		RealType pz = Pcz / Phz;
900		RealType c, x, y, z;
901		bool successfulScale = false;
902	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
903	<	(rnemdType_ == rnemdKineticScaleAM)) {
902	>	if ((rnemdFluxType_ == rnemdFullKE) ||
903	>	(rnemdFluxType_ == rnemdRotKE)) {
904		//may need sanity check Khw & Kcw > 0
905
906	<	if (rnemdType_ == rnemdKineticScaleVAM) {
907	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
906	>	if (rnemdFluxType_ == rnemdFullKE) {
907	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
908		} else {
909	<	c = 1.0 - targetFlux_ / Kcw;
909	>	c = 1.0 - kineticTarget_ / Kcw;
910		}
911
912		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
913		c = sqrt(c);
914	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
914	>	//std::cerr << "cold slab scaling coefficient: " << c << endl;
915		//now convert to hotBin coefficient
916		RealType w = 0.0;
917	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
917	>	if (rnemdFluxType_ ==  rnemdFullKE) {
918		x = 1.0 + px * (1.0 - c);
919		y = 1.0 + py * (1.0 - c);
920		z = 1.0 + pz * (1.0 - c);
#	Line 860 | Line 928 | namespace OpenMD {
928		*/
929		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
930		(fabs(z - 1.0) < 0.1)) {
931	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
931	>	w = 1.0 + (kineticTarget_
932	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
933		+ Khz * (1.0 - z * z)) / Khw;
934		}//no need to calculate w if x, y or z is out of range
935		} else {
936	<	w = 1.0 + targetFlux_ / Khw;
936	>	w = 1.0 + kineticTarget_ / Khw;
937		}
938		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
939		//if w is in the right range, so should be x, y, z.
940		vector<StuntDouble*>::iterator sdi;
941		Vector3d vel;
942		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
943	<	if (rnemdType_ == rnemdKineticScaleVAM) {
943	>	if (rnemdFluxType_ == rnemdFullKE) {
944		vel = (*sdi)->getVel() * c;
876	–	//vel.x() *= c;
877	–	//vel.y() *= c;
878	–	//vel.z() *= c;
945		(*sdi)->setVel(vel);
946		}
947		if ((*sdi)->isDirectional()) {
948		Vector3d angMom = (*sdi)->getJ() * c;
883	–	//angMom[0] *= c;
884	–	//angMom[1] *= c;
885	–	//angMom[2] *= c;
949		(*sdi)->setJ(angMom);
950		}
951		}
952		w = sqrt(w);
953	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
954	<	<< "\twh= " << w << endl;
953	>	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
954	>	//           << "\twh= " << w << endl;
955		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
956	<	if (rnemdType_ == rnemdKineticScaleVAM) {
956	>	if (rnemdFluxType_ == rnemdFullKE) {
957		vel = (*sdi)->getVel();
958		vel.x() *= x;
959		vel.y() *= y;
#	Line 899 | Line 962 | namespace OpenMD {
962		}
963		if ((*sdi)->isDirectional()) {
964		Vector3d angMom = (*sdi)->getJ() * w;
902	–	//angMom[0] *= w;
903	–	//angMom[1] *= w;
904	–	//angMom[2] *= w;
965		(*sdi)->setJ(angMom);
966		}
967		}
968		successfulScale = true;
969	<	exchangeSum_ += targetFlux_;
969	>	kineticExchange_ += kineticTarget_;
970		}
971		}
972		} else {
973		RealType a000, a110, c0, a001, a111, b01, b11, c1;
974	<	switch(rnemdType_) {
975	<	case rnemdKineticScale :
974	>	switch(rnemdFluxType_) {
975	>	case rnemdKE :
976		/* used hotBin coeff's & only scale x & y dimensions
977		RealType px = Phx / Pcx;
978		RealType py = Phy / Pcy;
979		a110 = Khy;
980	<	c0 = - Khx - Khy - targetFlux_;
980	>	c0 = - Khx - Khy - kineticTarget_;
981		a000 = Khx;
982		a111 = Kcy * py * py;
983		b11 = -2.0 * Kcy * py * (1.0 + py);
984	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
984	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
985		b01 = -2.0 * Kcx * px * (1.0 + px);
986		a001 = Kcx * px * px;
987		*/
988		//scale all three dimensions, let c_x = c_y
989		a000 = Kcx + Kcy;
990		a110 = Kcz;
991	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
991	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
992		a001 = Khx * px * px + Khy * py * py;
993		a111 = Khz * pz * pz;
994		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
995		b11 = -2.0 * Khz * pz * (1.0 + pz);
996		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
997	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
997	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
998		break;
999	<	case rnemdPxScale :
1000	<	c = 1 - targetFlux_ / Pcx;
999	>	case rnemdPx :
1000	>	c = 1 - momentumTarget_.x() / Pcx;
1001		a000 = Kcy;
1002		a110 = Kcz;
1003		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 948 | Line 1008 | namespace OpenMD {
1008		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1009		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1010		break;
1011	<	case rnemdPyScale :
1012	<	c = 1 - targetFlux_ / Pcy;
1011	>	case rnemdPy :
1012	>	c = 1 - momentumTarget_.y() / Pcy;
1013		a000 = Kcx;
1014		a110 = Kcz;
1015		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 960 | Line 1020 | namespace OpenMD {
1020		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1021		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1022		break;
1023	<	case rnemdPzScale ://we don't really do this, do we?
1024	<	c = 1 - targetFlux_ / Pcz;
1023	>	case rnemdPz ://we don't really do this, do we?
1024	>	c = 1 - momentumTarget_.z() / Pcz;
1025		a000 = Kcx;
1026		a110 = Kcy;
1027		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1046 | Line 1106 | namespace OpenMD {
1106		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1107		r1 = (*rpi).first;
1108		r2 = (*rpi).second;
1109	<	switch(rnemdType_) {
1110	<	case rnemdKineticScale :
1109	>	switch(rnemdFluxType_) {
1110	>	case rnemdKE :
1111		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1112		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1113		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1114		break;
1115	<	case rnemdPxScale :
1115	>	case rnemdPx :
1116		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1117		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1118		break;
1119	<	case rnemdPyScale :
1119	>	case rnemdPy :
1120		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1121		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1122		break;
1123	<	case rnemdPzScale :
1123	>	case rnemdPz :
1124		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1125		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1126		default :
#	Line 1074 | Line 1134 | namespace OpenMD {
1134		#ifdef IS_MPI
1135		if (worldRank == 0) {
1136		#endif
1137	<	sprintf(painCave.errMsg,
1138	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	<	bestPair.first, bestPair.second);
1140	<	painCave.isFatal = 0;
1141	<	painCave.severity = OPENMD_INFO;
1142	<	simError();
1137	>	// sprintf(painCave.errMsg,
1138	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1139	>	//         bestPair.first, bestPair.second);
1140	>	// painCave.isFatal = 0;
1141	>	// painCave.severity = OPENMD_INFO;
1142	>	// simError();
1143		#ifdef IS_MPI
1144		}
1145		#endif
1146
1147	<	switch(rnemdType_) {
1148	<	case rnemdKineticScale :
1147	>	switch(rnemdFluxType_) {
1148	>	case rnemdKE :
1149		x = bestPair.first;
1150		y = bestPair.first;
1151		z = bestPair.second;
1152		break;
1153	<	case rnemdPxScale :
1153	>	case rnemdPx :
1154		x = c;
1155		y = bestPair.first;
1156		z = bestPair.second;
1157		break;
1158	<	case rnemdPyScale :
1158	>	case rnemdPy :
1159		x = bestPair.first;
1160		y = c;
1161		z = bestPair.second;
1162		break;
1163	<	case rnemdPzScale :
1163	>	case rnemdPz :
1164		x = bestPair.first;
1165		y = bestPair.second;
1166		z = c;
#	Line 1129 | Line 1189 | namespace OpenMD {
1189		(*sdi)->setVel(vel);
1190		}
1191		successfulScale = true;
1192	<	exchangeSum_ += targetFlux_;
1192	>	switch(rnemdFluxType_) {
1193	>	case rnemdKE :
1194	>	kineticExchange_ += kineticTarget_;
1195	>	break;
1196	>	case rnemdPx :
1197	>	case rnemdPy :
1198	>	case rnemdPz :
1199	>	momentumExchange_ += momentumTarget_;
1200	>	break;
1201	>	default :
1202	>	break;
1203	>	}
1204		}
1205		}
1206		if (successfulScale != true) {
1207		sprintf(painCave.errMsg,
1208	<	"RNEMD: exchange NOT performed!\n");
1208	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1209	>	"\tthe constraint equations may not exist or there may be\n"
1210	>	"\tno selected objects in one or both slabs.\n");
1211		painCave.isFatal = 0;
1212		painCave.severity = OPENMD_INFO;
1213		simError();
#	Line 1142 | Line 1215 | namespace OpenMD {
1215		}
1216		}
1217
1218	<	void RNEMD::doShiftScale() {
1218	>	void RNEMD::doVSS() {
1219
1220		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1221		RealType time = currentSnap_->getTime();
#	Line 1177 | Line 1250 | namespace OpenMD {
1250		currentSnap_->wrapVector(pos);
1251
1252		// which bin is this stuntdouble in?
1253	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1254	<
1255	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1256	<
1184	<	// if we're in bin 0 or the middleBin
1185	<	if (binNo == 0 || binNo == midBin_) {
1253	>	bool inA = inSlabA(pos);
1254	>	bool inB = inSlabB(pos);
1255	>
1256	>	if (inA || inB) {
1257
1258		RealType mass = sd->getMass();
1259		Vector3d vel = sd->getVel();
1260
1261	<	if (binNo == 0) {
1261	>	if (inA) {
1262		hotBin.push_back(sd);
1263		//std::cerr << "before, velocity = " << vel << endl;
1264		Ph += mass * vel;
1265		//std::cerr << "after, velocity = " << vel << endl;
1266		Mh += mass;
1267		Kh += mass * vel.lengthSquare();
1268	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1268	>	if (rnemdFluxType_ == rnemdFullKE) {
1269		if (sd->isDirectional()) {
1270		Vector3d angMom = sd->getJ();
1271		Mat3x3d I = sd->getI();
#	Line 1216 | Line 1287 | namespace OpenMD {
1287		Pc += mass * vel;
1288		Mc += mass;
1289		Kc += mass * vel.lengthSquare();
1290	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1290	>	if (rnemdFluxType_ == rnemdFullKE) {
1291		if (sd->isDirectional()) {
1292		Vector3d angMom = sd->getJ();
1293		Mat3x3d I = sd->getI();
#	Line 1256 | Line 1327 | namespace OpenMD {
1327		bool successfulExchange = false;
1328		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1329		Vector3d vc = Pc / Mc;
1330	<	Vector3d ac = njzp_ / Mc + vc;
1331	<	Vector3d acrec = njzp_ / Mc;
1332	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1330	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1331	>	Vector3d acrec = -momentumTarget_ / Mc;
1332	>	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1333		if (cNumerator > 0.0) {
1334		RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1335		if (cDenominator > 0.0) {
1336		RealType c = sqrt(cNumerator / cDenominator);
1337		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1338		Vector3d vh = Ph / Mh;
1339	<	Vector3d ah = jzp_ / Mh + vh;
1340	<	Vector3d ahrec = jzp_ / Mh;
1341	<	RealType hNumerator = Kh + targetJzKE_
1339	>	Vector3d ah = momentumTarget_ / Mh + vh;
1340	>	Vector3d ahrec = momentumTarget_ / Mh;
1341	>	RealType hNumerator = Kh + kineticTarget_
1342		- 0.5 * Mh * ah.lengthSquare();
1343		if (hNumerator > 0.0) {
1344		RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
#	Line 1282 | Line 1353 | namespace OpenMD {
1353		//vel = (*sdi)->getVel();
1354		vel = ((*sdi)->getVel() - vc) * c + ac;
1355		(*sdi)->setVel(vel);
1356	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1356	>	if (rnemdFluxType_ == rnemdFullKE) {
1357		if ((*sdi)->isDirectional()) {
1358		Vector3d angMom = (*sdi)->getJ() * c;
1359		(*sdi)->setJ(angMom);
#	Line 1293 | Line 1364 | namespace OpenMD {
1364		//vel = (*sdi)->getVel();
1365		vel = ((*sdi)->getVel() - vh) * h + ah;
1366		(*sdi)->setVel(vel);
1367	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1367	>	if (rnemdFluxType_ == rnemdFullKE) {
1368		if ((*sdi)->isDirectional()) {
1369		Vector3d angMom = (*sdi)->getJ() * h;
1370		(*sdi)->setJ(angMom);
#	Line 1301 | Line 1372 | namespace OpenMD {
1372		}
1373		}
1374		successfulExchange = true;
1375	<	exchangeSum_ += targetFlux_;
1376	<	// 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	<	}
1375	>	kineticExchange_ += kineticTarget_;
1376	>	momentumExchange_ += momentumTarget_;
1377		}
1378		}
1379		}
#	Line 1324 | Line 1382 | namespace OpenMD {
1382		}
1383		}
1384		if (successfulExchange != true) {
1385	<	//   sprintf(painCave.errMsg,
1386	<	//              "RNEMD: exchange NOT performed!\n");
1387	<	//   painCave.isFatal = 0;
1388	<	//   painCave.severity = OPENMD_INFO;
1389	<	//   simError();
1385	>	sprintf(painCave.errMsg,
1386	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1387	>	"\tthe constraint equations may not exist or there may be\n"
1388	>	"\tno selected objects in one or both slabs.\n");
1389	>	painCave.isFatal = 0;
1390	>	painCave.severity = OPENMD_INFO;
1391	>	simError();
1392		failTrialCount_++;
1393		}
1394		}
1395
1396		void RNEMD::doRNEMD() {
1397
1398	<	switch(rnemdType_) {
1399	<	case rnemdKineticScale :
1400	<	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 :
1398	>	trialCount_++;
1399	>	switch(rnemdMethod_) {
1400	>	case rnemdSwap:
1401		doSwap();
1402		break;
1403	<	case rnemdShiftScaleV :
1404	<	case rnemdShiftScaleVAM :
1355	<	doShiftScale();
1403	>	case rnemdNIVS:
1404	>	doNIVS();
1405		break;
1406	<	case rnemdUnknown :
1406	>	case rnemdVSS:
1407	>	doVSS();
1408	>	break;
1409	>	case rnemdUnkownMethod:
1410		default :
1411		break;
1412		}
#	Line 1365 | Line 1417 | namespace OpenMD {
1417		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1418		Mat3x3d hmat = currentSnap_->getHmat();
1419
1420	+	areaAccumulator_->add(currentSnap_->getXYarea());
1421	+
1422		seleMan_.setSelectionSet(evaluator_.evaluate());
1423
1424		int selei;
1425		StuntDouble* sd;
1426		int idx;
1427
1428	<	logFrameCount_++;
1428	>	vector<RealType> binMass(nBins_, 0.0);
1429	>	vector<RealType> binPx(nBins_, 0.0);
1430	>	vector<RealType> binPy(nBins_, 0.0);
1431	>	vector<RealType> binPz(nBins_, 0.0);
1432	>	vector<RealType> binKE(nBins_, 0.0);
1433	>	vector<int> binDOF(nBins_, 0);
1434	>	vector<int> binCount(nBins_, 0);
1435
1436		// alternative approach, track all molecules instead of only those
1437		// selected for scaling/swapping:
#	Line 1379 | Line 1439 | namespace OpenMD {
1439		SimInfo::MoleculeIterator miter;
1440		vector<StuntDouble*>::iterator iiter;
1441		Molecule* mol;
1442	<	StuntDouble* integrableObject;
1442	>	StuntDouble* sd;
1443		for (mol = info_->beginMolecule(miter); mol != NULL;
1444		mol = info_->nextMolecule(miter))
1445	<	integrableObject is essentially sd
1446	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1447	<	integrableObject != NULL;
1448	<	integrableObject = mol->nextIntegrableObject(iiter))
1445	>	sd is essentially sd
1446	>	for (sd = mol->beginIntegrableObject(iiter);
1447	>	sd != NULL;
1448	>	sd = mol->nextIntegrableObject(iiter))
1449		*/
1450		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1451		sd = seleMan_.nextSelected(selei)) {
#	Line 1398 | Line 1458 | namespace OpenMD {
1458
1459		if (usePeriodicBoundaryConditions_)
1460		currentSnap_->wrapVector(pos);
1461	<
1461	>
1462	>
1463		// which bin is this stuntdouble in?
1464		// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1465	<
1466	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1467	<	rnemdLogWidth_;
1468	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1469	<	/*
1409	<	if (rnemdLogWidth_ == midBin_ + 1)
1410	<	if (binNo > midBin_)
1411	<	binNo = nBins_ - binNo;
1412	<	*/
1465	>	// Shift molecules by half a box to have bins start at 0
1466	>	// The modulo operator is used to wrap the case when we are
1467	>	// beyond the end of the bins back to the beginning.
1468	>	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1469	>
1470		RealType mass = sd->getMass();
1414	–	mHist_[binNo] += mass;
1471		Vector3d vel = sd->getVel();
1416	–	RealType value;
1417	–	//RealType xVal, yVal, zVal;
1472
1473	<	if (outputTemp_) {
1474	<	value = mass * vel.lengthSquare();
1475	<	tempCount_[binNo] += 3;
1476	<	if (sd->isDirectional()) {
1477	<	Vector3d angMom = sd->getJ();
1478	<	Mat3x3d I = sd->getI();
1479	<	if (sd->isLinear()) {
1480	<	int i = sd->linearAxis();
1481	<	int j = (i + 1) % 3;
1482	<	int k = (i + 2) % 3;
1483	<	value += angMom[j] * angMom[j] / I(j, j) +
1484	<	angMom[k] * angMom[k] / I(k, k);
1485	<	tempCount_[binNo] +=2;
1486	<	} else {
1487	<	value += angMom[0] * angMom[0] / I(0, 0) +
1488	<	angMom[1]*angMom[1]/I(1, 1) +
1489	<	angMom[2]*angMom[2]/I(2, 2);
1490	<	tempCount_[binNo] +=3;
1491	<	}
1492	<	}
1493	<	value = value / PhysicalConstants::energyConvert
1494	<	/ PhysicalConstants::kb;//may move to getStatus()
1495	<	tempHist_[binNo] += value;
1473	>	binCount[binNo]++;
1474	>	binMass[binNo] += mass;
1475	>	binPx[binNo] += mass*vel.x();
1476	>	binPy[binNo] += mass*vel.y();
1477	>	binPz[binNo] += mass*vel.z();
1478	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1479	>	binDOF[binNo] += 3;
1480	>
1481	>	if (sd->isDirectional()) {
1482	>	Vector3d angMom = sd->getJ();
1483	>	Mat3x3d I = sd->getI();
1484	>	if (sd->isLinear()) {
1485	>	int i = sd->linearAxis();
1486	>	int j = (i + 1) % 3;
1487	>	int k = (i + 2) % 3;
1488	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1489	>	angMom[k] * angMom[k] / I(k, k));
1490	>	binDOF[binNo] += 2;
1491	>	} else {
1492	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1493	>	angMom[1] * angMom[1] / I(1, 1) +
1494	>	angMom[2] * angMom[2] / I(2, 2));
1495	>	binDOF[binNo] += 3;
1496	>	}
1497		}
1498	<	if (outputVx_) {
1499	<	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;
1452	<	}
1498	>	}
1499	>
1500
1501	<	if (output3DTemp_) {
1502	<	value = mass * vel.x() * vel.x();
1503	<	xTempHist_[binNo] += value;
1504	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1505	<	/ PhysicalConstants::kb;
1506	<	yTempHist_[binNo] += value;
1507	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1508	<	/ PhysicalConstants::kb;
1509	<	zTempHist_[binNo] += value;
1510	<	xyzTempCount_[binNo]++;
1501	>	#ifdef IS_MPI
1502	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1503	>	nBins_, MPI::INT, MPI::SUM);
1504	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1505	>	nBins_, MPI::REALTYPE, MPI::SUM);
1506	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1507	>	nBins_, MPI::REALTYPE, MPI::SUM);
1508	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1509	>	nBins_, MPI::REALTYPE, MPI::SUM);
1510	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1511	>	nBins_, MPI::REALTYPE, MPI::SUM);
1512	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1513	>	nBins_, MPI::REALTYPE, MPI::SUM);
1514	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1515	>	nBins_, MPI::INT, MPI::SUM);
1516	>	#endif
1517	>
1518	>	Vector3d vel;
1519	>	RealType den;
1520	>	RealType temp;
1521	>	RealType z;
1522	>	for (int i = 0; i < nBins_; i++) {
1523	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1524	>	vel.x() = binPx[i] / binMass[i];
1525	>	vel.y() = binPy[i] / binMass[i];
1526	>	vel.z() = binPz[i] / binMass[i];
1527	>	den = binCount[i] * nBins_ / currentSnap_->getVolume();
1528	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1529	>	PhysicalConstants::energyConvert);
1530	>
1531	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1532	>	if(outputMask_[j]) {
1533	>	switch(j) {
1534	>	case Z:
1535	>	(data_[j].accumulator[i])->add(z);
1536	>	break;
1537	>	case TEMPERATURE:
1538	>	data_[j].accumulator[i]->add(temp);
1539	>	break;
1540	>	case VELOCITY:
1541	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1542	>	break;
1543	>	case DENSITY:
1544	>	data_[j].accumulator[i]->add(den);
1545	>	break;
1546	>	}
1547	>	}
1548		}
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	–	}
1549		}
1550		}
1551
1552		void RNEMD::getStarted() {
1553		collectData();
1554	<	/*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();
1554	>	writeOutputFile();
1555		}
1556
1557	<	void RNEMD::getStatus() {
1558	<
1559	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1560	<	Stats& stat = currentSnap_->statData;
1561	<	RealType time = currentSnap_->getTime();
1562	<
1563	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1564	<	//or to be more meaningful, define another item as exchangeSum_ / time
1565	<	int j;
1566	<
1557	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1558	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1559	>
1560	>	while(tokenizer.hasMoreTokens()) {
1561	>	std::string token(tokenizer.nextToken());
1562	>	toUpper(token);
1563	>	OutputMapType::iterator i = outputMap_.find(token);
1564	>	if (i != outputMap_.end()) {
1565	>	outputMask_.set(i->second);
1566	>	} else {
1567	>	sprintf( painCave.errMsg,
1568	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1569	>	"\toutputFileFormat keyword.\n", token.c_str() );
1570	>	painCave.isFatal = 0;
1571	>	painCave.severity = OPENMD_ERROR;
1572	>	simError();
1573	>	}
1574	>	}
1575	>	}
1576	>
1577	>	void RNEMD::writeOutputFile() {
1578	>
1579		#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	–
1580		// If we're the root node, should we print out the results
1581		int worldRank = MPI::COMM_WORLD.Get_rank();
1582		if (worldRank == 0) {
1583		#endif
1584	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1585	+
1586	+	if( !rnemdFile_ ){
1587	+	sprintf( painCave.errMsg,
1588	+	"Could not open \"%s\" for RNEMD output.\n",
1589	+	rnemdFileName_.c_str());
1590	+	painCave.isFatal = 1;
1591	+	simError();
1592	+	}
1593
1594	<	if (outputTemp_) {
1595	<	tempLog_ << time;
1596	<	for (j = 0; j < rnemdLogWidth_; j++) {
1597	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1598	<	}
1599	<	tempLog_ << endl;
1594	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1595	>
1596	>	RealType time = currentSnap_->getTime();
1597	>	RealType avgArea;
1598	>	areaAccumulator_->getAverage(avgArea);
1599	>	RealType Jz = kineticExchange_ / (2.0 * time * avgArea);
1600	>	Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea);
1601	>
1602	>	rnemdFile_ << "#######################################################\n";
1603	>	rnemdFile_ << "# RNEMD {\n";
1604	>
1605	>	map<string, RNEMDMethod>::iterator mi;
1606	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1607	>	if ( (*mi).second == rnemdMethod_)
1608	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1609		}
1610	<	if (outputVx_) {
1611	<	vxzLog_ << time;
1612	<	for (j = 0; j < rnemdLogWidth_; j++) {
1613	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1592	<	}
1593	<	vxzLog_ << endl;
1610	>	map<string, RNEMDFluxType>::iterator fi;
1611	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1612	>	if ( (*fi).second == rnemdFluxType_)
1613	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1614		}
1615	<	if (outputVy_) {
1616	<	vyzLog_ << time;
1597	<	for (j = 0; j < rnemdLogWidth_; j++) {
1598	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	<	}
1600	<	vyzLog_ << endl;
1601	<	}
1615	>
1616	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
1617
1618	<	if (output3DTemp_) {
1619	<	RealType temp;
1620	<	xTempLog_ << time;
1621	<	for (j = 0; j < rnemdLogWidth_; j++) {
1622	<	if (outputVx_)
1623	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1624	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1625	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1626	<	xTempLog_ << "\t" << temp;
1618	>	rnemdFile_ << "#    objectSelection = \""
1619	>	<< rnemdObjectSelection_ << "\";\n";
1620	>	rnemdFile_ << "#    slabWidth = " << slabWidth_ << ";\n";
1621	>	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << ";\n";
1622	>	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << ";\n";
1623	>	rnemdFile_ << "# }\n";
1624	>	rnemdFile_ << "#######################################################\n";
1625	>	rnemdFile_ << "# RNEMD report:\n";
1626	>	rnemdFile_ << "#     running time = " << time << " fs\n";
1627	>	rnemdFile_ << "#     target flux:\n";
1628	>	rnemdFile_ << "#         kinetic = " << kineticFlux_ << "\n";
1629	>	rnemdFile_ << "#         momentum = " << momentumFluxVector_ << "\n";
1630	>	rnemdFile_ << "#     target one-time exchanges:\n";
1631	>	rnemdFile_ << "#         kinetic = " << kineticTarget_ << "\n";
1632	>	rnemdFile_ << "#         momentum = " << momentumTarget_ << "\n";
1633	>	rnemdFile_ << "#     actual exchange totals:\n";
1634	>	rnemdFile_ << "#         kinetic = " << kineticExchange_ << "\n";
1635	>	rnemdFile_ << "#         momentum = " << momentumExchange_  << "\n";
1636	>	rnemdFile_ << "#     actual flux:\n";
1637	>	rnemdFile_ << "#         kinetic = " << Jz << "\n";
1638	>	rnemdFile_ << "#         momentum = " << JzP  << "\n";
1639	>	rnemdFile_ << "#     exchange statistics:\n";
1640	>	rnemdFile_ << "#         attempted = " << trialCount_ << "\n";
1641	>	rnemdFile_ << "#         failed = " << failTrialCount_ << "\n";
1642	>	if (rnemdMethod_ == rnemdNIVS) {
1643	>	rnemdFile_ << "#         NIVS root-check errors = "
1644	>	<< failRootCount_ << "\n";
1645	>	}
1646	>	rnemdFile_ << "#######################################################\n";
1647	>
1648	>
1649	>
1650	>	//write title
1651	>	rnemdFile_ << "#";
1652	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1653	>	if (outputMask_[i]) {
1654	>	rnemdFile_ << "\t" << data_[i].title <<
1655	>	"(" << data_[i].units << ")";
1656		}
1657	<	xTempLog_ << endl;
1658	<	yTempLog_ << time;
1659	<	for (j = 0; j < rnemdLogWidth_; j++) {
1660	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1657	>	}
1658	>	rnemdFile_ << std::endl;
1659	>
1660	>	rnemdFile_.precision(8);
1661	>
1662	>	for (unsigned int j = 0; j < nBins_; j++) {
1663	>
1664	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1665	>	if (outputMask_[i]) {
1666	>	if (data_[i].dataType == "RealType")
1667	>	writeReal(i,j);
1668	>	else if (data_[i].dataType == "Vector3d")
1669	>	writeVector(i,j);
1670	>	else {
1671	>	sprintf( painCave.errMsg,
1672	>	"RNEMD found an unknown data type for: %s ",
1673	>	data_[i].title.c_str());
1674	>	painCave.isFatal = 1;
1675	>	simError();
1676	>	}
1677	>	}
1678		}
1679	<	yTempLog_ << endl;
1680	<	zTempLog_ << time;
1681	<	for (j = 0; j < rnemdLogWidth_; j++) {
1682	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1679	>	rnemdFile_ << std::endl;
1680	>
1681	>	}
1682	>
1683	>	rnemdFile_ << "#######################################################\n";
1684	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
1685	>	rnemdFile_ << "#######################################################\n";
1686	>
1687	>
1688	>	for (unsigned int j = 0; j < nBins_; j++) {
1689	>	rnemdFile_ << "#";
1690	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
1691	>	if (outputMask_[i]) {
1692	>	if (data_[i].dataType == "RealType")
1693	>	writeRealStdDev(i,j);
1694	>	else if (data_[i].dataType == "Vector3d")
1695	>	writeVectorStdDev(i,j);
1696	>	else {
1697	>	sprintf( painCave.errMsg,
1698	>	"RNEMD found an unknown data type for: %s ",
1699	>	data_[i].title.c_str());
1700	>	painCave.isFatal = 1;
1701	>	simError();
1702	>	}
1703	>	}
1704		}
1705	<	zTempLog_ << endl;
1706	<	}
1707	<	if (outputRotTemp_) {
1708	<	rotTempLog_ << time;
1709	<	for (j = 0; j < rnemdLogWidth_; j++) {
1710	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1711	<	}
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	<	}
1705	>	rnemdFile_ << std::endl;
1706	>
1707	>	}
1708	>
1709	>	rnemdFile_.flush();
1710	>	rnemdFile_.close();
1711	>
1712		#ifdef IS_MPI
1713		}
1714		#endif
1715	<
1716	<	for (j = 0; j < rnemdLogWidth_; j++) {
1717	<	mHist_[j] = 0.0;
1715	>
1716	>	}
1717	>
1718	>	void RNEMD::writeReal(int index, unsigned int bin) {
1719	>	assert(index >=0 && index < ENDINDEX);
1720	>	assert(bin < nBins_);
1721	>	RealType s;
1722	>
1723	>	data_[index].accumulator[bin]->getAverage(s);
1724	>
1725	>	if (! isinf(s) && ! isnan(s)) {
1726	>	rnemdFile_ << "\t" << s;
1727	>	} else{
1728	>	sprintf( painCave.errMsg,
1729	>	"RNEMD detected a numerical error writing: %s for bin %d",
1730	>	data_[index].title.c_str(), bin);
1731	>	painCave.isFatal = 1;
1732	>	simError();
1733	>	}
1734	>	}
1735	>
1736	>	void RNEMD::writeVector(int index, unsigned int bin) {
1737	>	assert(index >=0 && index < ENDINDEX);
1738	>	assert(bin < nBins_);
1739	>	Vector3d s;
1740	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
1741	>	if (isinf(s[0]) || isnan(s[0]) ||
1742	>	isinf(s[1]) || isnan(s[1]) ||
1743	>	isinf(s[2]) || isnan(s[2]) ) {
1744	>	sprintf( painCave.errMsg,
1745	>	"RNEMD detected a numerical error writing: %s for bin %d",
1746	>	data_[index].title.c_str(), bin);
1747	>	painCave.isFatal = 1;
1748	>	simError();
1749	>	} else {
1750	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1751		}
1752	<	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	<	}
1752	>	}
1753
1754	<	if (output3DTemp_)
1755	<	for (j = 0; j < rnemdLogWidth_; j++) {
1756	<	xTempHist_[j] = 0.0;
1757	<	yTempHist_[j] = 0.0;
1677	<	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';
1754	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
1755	>	assert(index >=0 && index < ENDINDEX);
1756	>	assert(bin < nBins_);
1757	>	RealType s;
1758
1759	<	logFrameCount_ = 0;
1759	>	data_[index].accumulator[bin]->getStdDev(s);
1760	>
1761	>	if (! isinf(s) && ! isnan(s)) {
1762	>	rnemdFile_ << "\t" << s;
1763	>	} else{
1764	>	sprintf( painCave.errMsg,
1765	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1766	>	data_[index].title.c_str(), bin);
1767	>	painCave.isFatal = 1;
1768	>	simError();
1769	>	}
1770		}
1771	+
1772	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
1773	+	assert(index >=0 && index < ENDINDEX);
1774	+	assert(bin < nBins_);
1775	+	Vector3d s;
1776	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
1777	+	if (isinf(s[0]) || isnan(s[0]) ||
1778	+	isinf(s[1]) || isnan(s[1]) ||
1779	+	isinf(s[2]) || isnan(s[2]) ) {
1780	+	sprintf( painCave.errMsg,
1781	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
1782	+	data_[index].title.c_str(), bin);
1783	+	painCave.isFatal = 1;
1784	+	simError();
1785	+	} else {
1786	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
1787	+	}
1788	+	}
1789		}
1790

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines