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

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC vs.
Revision 1854 by gezelter, Thu Mar 28 20:54:06 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <cmath>
43	+	#include <sstream>
44	+	#include <string>
45	+
46		#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48		#include "math/Vector.hpp"
#	Line 49 | Line 52
52		#include "primitives/StuntDouble.hpp"
53		#include "utils/PhysicalConstants.hpp"
54		#include "utils/Tuple.hpp"
55	<
56	<	#ifndef IS_MPI
57	<	#include "math/SeqRandNumGen.hpp"
55	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
55	>	#include "brains/Thermo.hpp"
56	>	#include "math/ConvexHull.hpp"
57	>	#ifdef IS_MPI
58		#include <mpi.h>
59		#endif
60
61	+	#ifdef _MSC_VER
62	+	#define isnan(x) _isnan((x))
63	+	#define isinf(x) (!_finite(x) && !_isnan(x))
64	+	#endif
65	+
66		#define HONKING_LARGE_VALUE 1.0e10
67
68		using namespace std;
69		namespace OpenMD {
70
71		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
76
77	+	trialCount_ = 0;
78		failTrialCount_ = 0;
79		failRootCount_ = 0;
80
81	<	int seedValue;
72	<	Globals * simParams = info->getSimParams();
81	>	Globals* simParams = info->getSimParams();
82		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83
84	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
85	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
77	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
78	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
79	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
80	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
81	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
82	<	stringToEnumMap_["Px"] = rnemdPx;
83	<	stringToEnumMap_["Py"] = rnemdPy;
84	<	stringToEnumMap_["Pz"] = rnemdPz;
85	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
86	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
87	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
84	>	doRNEMD_ = rnemdParams->getUseRNEMD();
85	>	if (!doRNEMD_) return;
86
87	+	stringToMethod_["Swap"]  = rnemdSwap;
88	+	stringToMethod_["NIVS"]  = rnemdNIVS;
89	+	stringToMethod_["VSS"]   = rnemdVSS;
90	+
91	+	stringToFluxType_["KE"]  = rnemdKE;
92	+	stringToFluxType_["Px"]  = rnemdPx;
93	+	stringToFluxType_["Py"]  = rnemdPy;
94	+	stringToFluxType_["Pz"]  = rnemdPz;
95	+	stringToFluxType_["Pvector"]  = rnemdPvector;
96	+	stringToFluxType_["Lx"]  = rnemdLx;
97	+	stringToFluxType_["Ly"]  = rnemdLy;
98	+	stringToFluxType_["Lz"]  = rnemdLz;
99	+	stringToFluxType_["Lvector"]  = rnemdLvector;
100	+	stringToFluxType_["KE+Px"]  = rnemdKePx;
101	+	stringToFluxType_["KE+Py"]  = rnemdKePy;
102	+	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
103	+	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
104	+	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
105	+	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
106	+	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
107	+
108		runTime_ = simParams->getRunTime();
109		statusTime_ = simParams->getStatusTime();
110
111	+	const string methStr = rnemdParams->getMethod();
112	+	bool hasFluxType = rnemdParams->haveFluxType();
113	+
114		rnemdObjectSelection_ = rnemdParams->getObjectSelection();
93	–	evaluator_.loadScriptString(rnemdObjectSelection_);
94	–	seleMan_.setSelectionSet(evaluator_.evaluate());
115
116	<	// do some sanity checking
117	<
118	<	int selectionCount = seleMan_.getSelectionCount();
119	<	int nIntegrable = info->getNGlobalIntegrableObjects();
100	<
101	<	if (selectionCount > nIntegrable) {
116	>	string fluxStr;
117	>	if (hasFluxType) {
118	>	fluxStr = rnemdParams->getFluxType();
119	>	} else {
120		sprintf(painCave.errMsg,
121	<	"RNEMD: The current RNEMD_objectSelection,\n"
122	<	"\t\t%s\n"
123	<	"\thas resulted in %d selected objects.  However,\n"
124	<	"\tthe total number of integrable objects in the system\n"
125	<	"\tis only %d.  This is almost certainly not what you want\n"
126	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
127	<	"\tselector in the selection script!\n",
110	<	rnemdObjectSelection_.c_str(),
111	<	selectionCount, nIntegrable);
112	<	painCave.isFatal = 0;
113	<	painCave.severity = OPENMD_WARNING;
121	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
122	>	"\twhich must be one of the following values:\n"
123	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
124	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
125	>	"\tmust be set to use RNEMD\n");
126	>	painCave.isFatal = 1;
127	>	painCave.severity = OPENMD_ERROR;
128		simError();
129		}
130	+
131	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
132	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
133	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
134	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
135	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
136	+	hasSelectionA_ = rnemdParams->haveSelectionA();
137	+	hasSelectionB_ = rnemdParams->haveSelectionB();
138	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
139	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
140	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
141	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
142	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
143	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
144	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
145	+	bool hasOutputFields = rnemdParams->haveOutputFields();
146
147	<	const string st = rnemdParams->getExchangeType();
147	>	map<string, RNEMDMethod>::iterator i;
148	>	i = stringToMethod_.find(methStr);
149	>	if (i != stringToMethod_.end())
150	>	rnemdMethod_ = i->second;
151	>	else {
152	>	sprintf(painCave.errMsg,
153	>	"RNEMD: The current method,\n"
154	>	"\t\t%s is not one of the recognized\n"
155	>	"\texchange methods: Swap, NIVS, or VSS\n",
156	>	methStr.c_str());
157	>	painCave.isFatal = 1;
158	>	painCave.severity = OPENMD_ERROR;
159	>	simError();
160	>	}
161
162	<	map<string, RNEMDTypeEnum>::iterator i;
163	<	i = stringToEnumMap_.find(st);
164	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
165	<	if (rnemdType_ == rnemdUnknown) {
162	>	map<string, RNEMDFluxType>::iterator j;
163	>	j = stringToFluxType_.find(fluxStr);
164	>	if (j != stringToFluxType_.end())
165	>	rnemdFluxType_ = j->second;
166	>	else {
167		sprintf(painCave.errMsg,
168	<	"RNEMD: The current RNEMD_exchangeType,\n"
168	>	"RNEMD: The current fluxType,\n"
169		"\t\t%s\n"
170	<	"\tis not one of the recognized exchange types.\n",
171	<	st.c_str());
170	>	"\tis not one of the recognized flux types.\n",
171	>	fluxStr.c_str());
172		painCave.isFatal = 1;
173		painCave.severity = OPENMD_ERROR;
174		simError();
175		}
132	–
133	–	outputTemp_ = false;
134	–	if (rnemdParams->haveOutputTemperature()) {
135	–	outputTemp_ = rnemdParams->getOutputTemperature();
136	–	} else if ((rnemdType_ == rnemdKineticSwap) ||
137	–	(rnemdType_ == rnemdKineticScale) ||
138	–	(rnemdType_ == rnemdKineticScaleVAM) ||
139	–	(rnemdType_ == rnemdKineticScaleAM)) {
140	–	outputTemp_ = true;
141	–	}
142	–	outputVx_ = false;
143	–	if (rnemdParams->haveOutputVx()) {
144	–	outputVx_ = rnemdParams->getOutputVx();
145	–	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
146	–	outputVx_ = true;
147	–	}
148	–	outputVy_ = false;
149	–	if (rnemdParams->haveOutputVy()) {
150	–	outputVy_ = rnemdParams->getOutputVy();
151	–	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
152	–	outputVy_ = true;
153	–	}
154	–	output3DTemp_ = false;
155	–	if (rnemdParams->haveOutputXyzTemperature()) {
156	–	output3DTemp_ = rnemdParams->getOutputXyzTemperature();
157	–	}
158	–	outputRotTemp_ = false;
159	–	if (rnemdParams->haveOutputRotTemperature()) {
160	–	outputRotTemp_ = rnemdParams->getOutputRotTemperature();
161	–	}
162	–	// James put this in.
163	–	outputDen_ = false;
164	–	if (rnemdParams->haveOutputDen()) {
165	–	outputDen_ = rnemdParams->getOutputDen();
166	–	}
167	–	outputAh_ = false;
168	–	if (rnemdParams->haveOutputAh()) {
169	–	outputAh_ = rnemdParams->getOutputAh();
170	–	}
171	–	outputVz_ = false;
172	–	if (rnemdParams->haveOutputVz()) {
173	–	outputVz_ = rnemdParams->getOutputVz();
174	–	} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
175	–	outputVz_ = true;
176	–	}
177	–
176
177	<	#ifdef IS_MPI
178	<	if (worldRank == 0) {
179	<	#endif
180	<
181	<	//may have rnemdWriter separately
182	<	string rnemdFileName;
183	<
184	<	if (outputTemp_) {
185	<	rnemdFileName = "temperature.log";
186	<	tempLog_.open(rnemdFileName.c_str());
177	>	bool methodFluxMismatch = false;
178	>	bool hasCorrectFlux = false;
179	>	switch(rnemdMethod_) {
180	>	case rnemdSwap:
181	>	switch (rnemdFluxType_) {
182	>	case rnemdKE:
183	>	hasCorrectFlux = hasKineticFlux;
184	>	break;
185	>	case rnemdPx:
186	>	case rnemdPy:
187	>	case rnemdPz:
188	>	hasCorrectFlux = hasMomentumFlux;
189	>	break;
190	>	default :
191	>	methodFluxMismatch = true;
192	>	break;
193		}
194	<	if (outputVx_) {
195	<	rnemdFileName = "velocityX.log";
196	<	vxzLog_.open(rnemdFileName.c_str());
194	>	break;
195	>	case rnemdNIVS:
196	>	switch (rnemdFluxType_) {
197	>	case rnemdKE:
198	>	case rnemdRotKE:
199	>	case rnemdFullKE:
200	>	hasCorrectFlux = hasKineticFlux;
201	>	break;
202	>	case rnemdPx:
203	>	case rnemdPy:
204	>	case rnemdPz:
205	>	hasCorrectFlux = hasMomentumFlux;
206	>	break;
207	>	case rnemdKePx:
208	>	case rnemdKePy:
209	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
210	>	break;
211	>	default:
212	>	methodFluxMismatch = true;
213	>	break;
214		}
215	<	if (outputVy_) {
216	<	rnemdFileName = "velocityY.log";
217	<	vyzLog_.open(rnemdFileName.c_str());
215	>	break;
216	>	case rnemdVSS:
217	>	switch (rnemdFluxType_) {
218	>	case rnemdKE:
219	>	case rnemdRotKE:
220	>	case rnemdFullKE:
221	>	hasCorrectFlux = hasKineticFlux;
222	>	break;
223	>	case rnemdPx:
224	>	case rnemdPy:
225	>	case rnemdPz:
226	>	hasCorrectFlux = hasMomentumFlux;
227	>	break;
228	>	case rnemdLx:
229	>	case rnemdLy:
230	>	case rnemdLz:
231	>	hasCorrectFlux = hasAngularMomentumFlux;
232	>	break;
233	>	case rnemdPvector:
234	>	hasCorrectFlux = hasMomentumFluxVector;
235	>	break;
236	>	case rnemdLvector:
237	>	hasCorrectFlux = hasAngularMomentumFluxVector;
238	>	break;
239	>	case rnemdKePx:
240	>	case rnemdKePy:
241	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
242	>	break;
243	>	case rnemdKeLx:
244	>	case rnemdKeLy:
245	>	case rnemdKeLz:
246	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
247	>	break;
248	>	case rnemdKePvector:
249	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
250	>	break;
251	>	case rnemdKeLvector:
252	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
253	>	break;
254	>	default:
255	>	methodFluxMismatch = true;
256	>	break;
257		}
258	+	default:
259	+	break;
260	+	}
261
262	<	if (output3DTemp_) {
263	<	rnemdFileName = "temperatureX.log";
264	<	xTempLog_.open(rnemdFileName.c_str());
265	<	rnemdFileName = "temperatureY.log";
266	<	yTempLog_.open(rnemdFileName.c_str());
267	<	rnemdFileName = "temperatureZ.log";
268	<	zTempLog_.open(rnemdFileName.c_str());
262	>	if (methodFluxMismatch) {
263	>	sprintf(painCave.errMsg,
264	>	"RNEMD: The current method,\n"
265	>	"\t\t%s\n"
266	>	"\tcannot be used with the current flux type, %s\n",
267	>	methStr.c_str(), fluxStr.c_str());
268	>	painCave.isFatal = 1;
269	>	painCave.severity = OPENMD_ERROR;
270	>	simError();
271	>	}
272	>	if (!hasCorrectFlux) {
273	>	sprintf(painCave.errMsg,
274	>	"RNEMD: The current method, %s, and flux type, %s,\n"
275	>	"\tdid not have the correct flux value specified. Options\n"
276	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
277	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
278	>	methStr.c_str(), fluxStr.c_str());
279	>	painCave.isFatal = 1;
280	>	painCave.severity = OPENMD_ERROR;
281	>	simError();
282	>	}
283	>
284	>	if (hasKineticFlux) {
285	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
286	>	// into  amu / fs^3:
287	>	kineticFlux_ = rnemdParams->getKineticFlux()
288	>	* PhysicalConstants::energyConvert;
289	>	} else {
290	>	kineticFlux_ = 0.0;
291	>	}
292	>	if (hasMomentumFluxVector) {
293	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
294	>	} else {
295	>	momentumFluxVector_ = V3Zero;
296	>	if (hasMomentumFlux) {
297	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
298	>	switch (rnemdFluxType_) {
299	>	case rnemdPx:
300	>	momentumFluxVector_.x() = momentumFlux;
301	>	break;
302	>	case rnemdPy:
303	>	momentumFluxVector_.y() = momentumFlux;
304	>	break;
305	>	case rnemdPz:
306	>	momentumFluxVector_.z() = momentumFlux;
307	>	break;
308	>	case rnemdKePx:
309	>	momentumFluxVector_.x() = momentumFlux;
310	>	break;
311	>	case rnemdKePy:
312	>	momentumFluxVector_.y() = momentumFlux;
313	>	break;
314	>	default:
315	>	break;
316	>	}
317		}
318	<	if (outputRotTemp_) {
319	<	rnemdFileName = "temperatureR.log";
320	<	rotTempLog_.open(rnemdFileName.c_str());
318	>	if (hasAngularMomentumFluxVector) {
319	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
320	>	} else {
321	>	angularMomentumFluxVector_ = V3Zero;
322	>	if (hasAngularMomentumFlux) {
323	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
324	>	switch (rnemdFluxType_) {
325	>	case rnemdLx:
326	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
327	>	break;
328	>	case rnemdLy:
329	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
330	>	break;
331	>	case rnemdLz:
332	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
333	>	break;
334	>	case rnemdKeLx:
335	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
336	>	break;
337	>	case rnemdKeLy:
338	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
339	>	break;
340	>	case rnemdKeLz:
341	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
342	>	break;
343	>	default:
344	>	break;
345	>	}
346	>	}
347		}
211	–
212	–	//James put this in
213	–	if (outputDen_) {
214	–	rnemdFileName = "Density.log";
215	–	denLog_.open(rnemdFileName.c_str());
216	–	}
217	–	if (outputAh_) {
218	–	rnemdFileName = "Ah.log";
219	–	AhLog_.open(rnemdFileName.c_str());
220	–	}
221	–	if (outputVz_) {
222	–	rnemdFileName = "velocityZ.log";
223	–	vzzLog_.open(rnemdFileName.c_str());
224	–	}
225	–	logFrameCount_ = 0;
226	–	#ifdef IS_MPI
227	–	}
228	–	#endif
348
349	<	set_RNEMD_exchange_time(rnemdParams->getExchangeTime());
350	<	set_RNEMD_nBins(rnemdParams->getNbins());
232	<	midBin_ = nBins_ / 2;
233	<	if (rnemdParams->haveBinShift()) {
234	<	if (rnemdParams->getBinShift()) {
235	<	zShift_ = 0.5 / (RealType)(nBins_);
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351		} else {
352	<	zShift_ = 0.0;
352	>	coordinateOrigin_ = V3Zero;
353		}
239	–	} else {
240	–	zShift_ = 0.0;
241	–	}
242	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
243	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
244	–	//set to 0.0 if not using it; N/A in status output yet
245	–	if (rnemdParams->haveLogWidth()) {
246	–	set_RNEMD_logWidth(rnemdParams->getLogWidth());
247	–	/*arbitary rnemdLogWidth_, no checking;
248	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
249	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
250	–	cerr << "Automaically set back to default.\n";
251	–	rnemdLogWidth_ = nBins_;
252	–	}*/
253	–	} else {
254	–	set_RNEMD_logWidth(nBins_);
255	–	}
256	–	tempHist_.resize(rnemdLogWidth_, 0.0);
257	–	tempCount_.resize(rnemdLogWidth_, 0);
258	–	pxzHist_.resize(rnemdLogWidth_, 0.0);
259	–	//vxzCount_.resize(rnemdLogWidth_, 0);
260	–	pyzHist_.resize(rnemdLogWidth_, 0.0);
261	–	//vyzCount_.resize(rnemdLogWidth_, 0);
354
355	<	mHist_.resize(rnemdLogWidth_, 0.0);
264	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
265	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
266	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
267	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
268	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
269	<	rotTempCount_.resize(rnemdLogWidth_, 0);
270	<	// James put this in
271	<	DenHist_.resize(rnemdLogWidth_, 0.0);
272	<	pzzHist_.resize(rnemdLogWidth_, 0.0);
355	>	// do some sanity checking
356
357	<	set_RNEMD_exchange_total(0.0);
275	<	if (rnemdParams->haveTargetFlux()) {
276	<	set_RNEMD_target_flux(rnemdParams->getTargetFlux());
277	<	} else {
278	<	set_RNEMD_target_flux(0.0);
279	<	}
280	<	if (rnemdParams->haveTargetJzKE()) {
281	<	set_RNEMD_target_JzKE(rnemdParams->getTargetJzKE());
282	<	} else {
283	<	set_RNEMD_target_JzKE(0.0);
284	<	}
285	<	if (rnemdParams->haveTargetJzpx()) {
286	<	set_RNEMD_target_jzpx(rnemdParams->getTargetJzpx());
287	<	} else {
288	<	set_RNEMD_target_jzpx(0.0);
289	<	}
290	<	jzp_.x() = targetJzpx_;
291	<	njzp_.x() = -targetJzpx_;
292	<	if (rnemdParams->haveTargetJzpy()) {
293	<	set_RNEMD_target_jzpy(rnemdParams->getTargetJzpy());
294	<	} else {
295	<	set_RNEMD_target_jzpy(0.0);
296	<	}
297	<	jzp_.y() = targetJzpy_;
298	<	njzp_.y() = -targetJzpy_;
299	<	if (rnemdParams->haveTargetJzpz()) {
300	<	set_RNEMD_target_jzpz(rnemdParams->getTargetJzpz());
301	<	} else {
302	<	set_RNEMD_target_jzpz(0.0);
303	<	}
304	<	jzp_.z() = targetJzpz_;
305	<	njzp_.z() = -targetJzpz_;
357	>	int selectionCount = seleMan_.getSelectionCount();
358
359	<	#ifndef IS_MPI
360	<	if (simParams->haveSeed()) {
361	<	seedValue = simParams->getSeed();
362	<	randNumGen_ = new SeqRandNumGen(seedValue);
363	<	}else {
364	<	randNumGen_ = new SeqRandNumGen();
365	<	}
366	<	#else
367	<	if (simParams->haveSeed()) {
368	<	seedValue = simParams->getSeed();
369	<	randNumGen_ = new ParallelRandNumGen(seedValue);
370	<	}else {
371	<	randNumGen_ = new ParallelRandNumGen();
372	<	}
373	<	#endif
359	>	int nIntegrable = info->getNGlobalIntegrableObjects();
360	>
361	>	if (selectionCount > nIntegrable) {
362	>	sprintf(painCave.errMsg,
363	>	"RNEMD: The current objectSelection,\n"
364	>	"\t\t%s\n"
365	>	"\thas resulted in %d selected objects.  However,\n"
366	>	"\tthe total number of integrable objects in the system\n"
367	>	"\tis only %d.  This is almost certainly not what you want\n"
368	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
369	>	"\tselector in the selection script!\n",
370	>	rnemdObjectSelection_.c_str(),
371	>	selectionCount, nIntegrable);
372	>	painCave.isFatal = 0;
373	>	painCave.severity = OPENMD_WARNING;
374	>	simError();
375	>	}
376	>
377	>	areaAccumulator_ = new Accumulator();
378	>
379	>	nBins_ = rnemdParams->getOutputBins();
380	>	binWidth_ = rnemdParams->getOutputBinWidth();
381	>
382	>	data_.resize(RNEMD::ENDINDEX);
383	>	OutputData z;
384	>	z.units =  "Angstroms";
385	>	z.title =  "Z";
386	>	z.dataType = "RealType";
387	>	z.accumulator.reserve(nBins_);
388	>	for (int i = 0; i < nBins_; i++)
389	>	z.accumulator.push_back( new Accumulator() );
390	>	data_[Z] = z;
391	>	outputMap_["Z"] =  Z;
392	>
393	>	OutputData r;
394	>	r.units =  "Angstroms";
395	>	r.title =  "R";
396	>	r.dataType = "RealType";
397	>	r.accumulator.reserve(nBins_);
398	>	for (int i = 0; i < nBins_; i++)
399	>	r.accumulator.push_back( new Accumulator() );
400	>	data_[R] = r;
401	>	outputMap_["R"] =  R;
402	>
403	>	OutputData temperature;
404	>	temperature.units =  "K";
405	>	temperature.title =  "Temperature";
406	>	temperature.dataType = "RealType";
407	>	temperature.accumulator.reserve(nBins_);
408	>	for (int i = 0; i < nBins_; i++)
409	>	temperature.accumulator.push_back( new Accumulator() );
410	>	data_[TEMPERATURE] = temperature;
411	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
412	>
413	>	OutputData velocity;
414	>	velocity.units = "angstroms/fs";
415	>	velocity.title =  "Velocity";
416	>	velocity.dataType = "Vector3d";
417	>	velocity.accumulator.reserve(nBins_);
418	>	for (int i = 0; i < nBins_; i++)
419	>	velocity.accumulator.push_back( new VectorAccumulator() );
420	>	data_[VELOCITY] = velocity;
421	>	outputMap_["VELOCITY"] = VELOCITY;
422	>
423	>	OutputData density;
424	>	density.units =  "g cm^-3";
425	>	density.title =  "Density";
426	>	density.dataType = "RealType";
427	>	density.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	density.accumulator.push_back( new Accumulator() );
430	>	data_[DENSITY] = density;
431	>	outputMap_["DENSITY"] =  DENSITY;
432	>
433	>	if (hasOutputFields) {
434	>	parseOutputFileFormat(rnemdParams->getOutputFields());
435	>	} else {
436	>	if (usePeriodicBoundaryConditions_)
437	>	outputMask_.set(Z);
438	>	else
439	>	outputMask_.set(R);
440	>	switch (rnemdFluxType_) {
441	>	case rnemdKE:
442	>	case rnemdRotKE:
443	>	case rnemdFullKE:
444	>	outputMask_.set(TEMPERATURE);
445	>	break;
446	>	case rnemdPx:
447	>	case rnemdPy:
448	>	outputMask_.set(VELOCITY);
449	>	break;
450	>	case rnemdPz:
451	>	case rnemdPvector:
452	>	outputMask_.set(VELOCITY);
453	>	outputMask_.set(DENSITY);
454	>	break;
455	>	case rnemdLx:
456	>	case rnemdLy:
457	>	case rnemdLz:
458	>	case rnemdLvector:
459	>	outputMask_.set(ANGULARVELOCITY);
460	>	break;
461	>	case rnemdKeLx:
462	>	case rnemdKeLy:
463	>	case rnemdKeLz:
464	>	case rnemdKeLvector:
465	>	outputMask_.set(TEMPERATURE);
466	>	outputMask_.set(ANGULARVELOCITY);
467	>	break;
468	>	case rnemdKePx:
469	>	case rnemdKePy:
470	>	outputMask_.set(TEMPERATURE);
471	>	outputMask_.set(VELOCITY);
472	>	break;
473	>	case rnemdKePvector:
474	>	outputMask_.set(TEMPERATURE);
475	>	outputMask_.set(VELOCITY);
476	>	outputMask_.set(DENSITY);
477	>	break;
478	>	default:
479	>	break;
480	>	}
481	>	}
482	>
483	>	if (hasOutputFileName) {
484	>	rnemdFileName_ = rnemdParams->getOutputFileName();
485	>	} else {
486	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
487	>	}
488	>
489	>	exchangeTime_ = rnemdParams->getExchangeTime();
490	>
491	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
492	>	// total exchange sums are zeroed out at the beginning:
493	>
494	>	kineticExchange_ = 0.0;
495	>	momentumExchange_ = V3Zero;
496	>	angularMomentumExchange_ = V3Zero;
497	>
498	>	std::ostringstream selectionAstream;
499	>	std::ostringstream selectionBstream;
500	>
501	>	if (hasSelectionA_) {
502	>	selectionA_ = rnemdParams->getSelectionA();
503	>	} else {
504	>	if (usePeriodicBoundaryConditions_) {
505	>	Mat3x3d hmat = currentSnap_->getHmat();
506	>
507	>	if (hasSlabWidth)
508	>	slabWidth_ = rnemdParams->getSlabWidth();
509	>	else
510	>	slabWidth_ = hmat(2,2) / 10.0;
511	>
512	>	if (hasSlabACenter)
513	>	slabACenter_ = rnemdParams->getSlabACenter();
514	>	else
515	>	slabACenter_ = 0.0;
516	>
517	>	selectionAstream << "select wrappedz > "
518	>	<< slabACenter_ - 0.5*slabWidth_
519	>	<<  " && wrappedz < "
520	>	<< slabACenter_ + 0.5*slabWidth_;
521	>	selectionA_ = selectionAstream.str();
522	>	} else {
523	>	if (hasSphereARadius)
524	>	sphereARadius_ = rnemdParams->getSphereARadius();
525	>	else {
526	>	// use an initial guess to the size of the inner slab to be 1/10 the
527	>	// radius of an approximately spherical hull:
528	>	Thermo thermo(info);
529	>	RealType hVol = thermo.getHullVolume();
530	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
531	>	}
532	>	selectionAstream << "select r < " << sphereARadius_;
533	>	selectionA_ = selectionAstream.str();
534	>	}
535	>	}
536	>
537	>	if (hasSelectionB_) {
538	>	selectionB_ = rnemdParams->getSelectionB();
539	>	} else {
540	>	if (usePeriodicBoundaryConditions_) {
541	>	Mat3x3d hmat = currentSnap_->getHmat();
542	>
543	>	if (hasSlabWidth)
544	>	slabWidth_ = rnemdParams->getSlabWidth();
545	>	else
546	>	slabWidth_ = hmat(2,2) / 10.0;
547	>
548	>	if (hasSlabBCenter)
549	>	slabBCenter_ = rnemdParams->getSlabACenter();
550	>	else
551	>	slabBCenter_ = hmat(2,2) / 2.0;
552	>
553	>	selectionBstream << "select wrappedz > "
554	>	<< slabBCenter_ - 0.5*slabWidth_
555	>	<<  " && wrappedz < "
556	>	<< slabBCenter_ + 0.5*slabWidth_;
557	>	selectionB_ = selectionBstream.str();
558	>	} else {
559	>	if (hasSphereBRadius_) {
560	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
561	>	selectionBstream << "select r > " << sphereBRadius_;
562	>	selectionB_ = selectionBstream.str();
563	>	} else {
564	>	selectionB_ = "select hull";
565	>	hasSelectionB_ = true;
566	>	}
567	>	}
568	>	}
569	>	}
570	>	// object evaluator:
571	>	evaluator_.loadScriptString(rnemdObjectSelection_);
572	>	seleMan_.setSelectionSet(evaluator_.evaluate());
573	>
574	>	evaluatorA_.loadScriptString(selectionA_);
575	>	evaluatorB_.loadScriptString(selectionB_);
576	>
577	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
578	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
579	>
580	>	commonA_ = seleManA_ & seleMan_;
581	>	commonB_ = seleManB_ & seleMan_;
582		}
583
324	–	RNEMD::~RNEMD() {
325	–	delete randNumGen_;
584
585	+	RNEMD::~RNEMD() {
586	+	if (!doRNEMD_) return;
587		#ifdef IS_MPI
588		if (worldRank == 0) {
589		#endif
330	–
331	–	sprintf(painCave.errMsg,
332	–	"RNEMD: total failed trials: %d\n",
333	–	failTrialCount_);
334	–	painCave.isFatal = 0;
335	–	painCave.severity = OPENMD_INFO;
336	–	simError();
337	–
338	–	if (outputTemp_) tempLog_.close();
339	–	if (outputVx_)   vxzLog_.close();
340	–	if (outputVy_)   vyzLog_.close();
590
591	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
592	<	rnemdType_ == rnemdPyScale) {
593	<	sprintf(painCave.errMsg,
345	<	"RNEMD: total root-checking warnings: %d\n",
346	<	failRootCount_);
347	<	painCave.isFatal = 0;
348	<	painCave.severity = OPENMD_INFO;
349	<	simError();
350	<	}
351	<	if (output3DTemp_) {
352	<	xTempLog_.close();
353	<	yTempLog_.close();
354	<	zTempLog_.close();
355	<	}
356	<	if (outputRotTemp_) rotTempLog_.close();
357	<	// James put this in
358	<	if (outputDen_) denLog_.close();
359	<	if (outputAh_)  AhLog_.close();
360	<	if (outputVz_)  vzzLog_.close();
591	>	writeOutputFile();
592	>
593	>	rnemdFile_.close();
594
595		#ifdef IS_MPI
596		}
597		#endif
598		}
599	+
600	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
601	+	if (!doRNEMD_) return;
602	+	int selei;
603	+	int selej;
604
367	–	void RNEMD::doSwap() {
368	–
605		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
606		Mat3x3d hmat = currentSnap_->getHmat();
607
372	–	seleMan_.setSelectionSet(evaluator_.evaluate());
373	–
374	–	int selei;
608		StuntDouble* sd;
376	–	int idx;
609
610		RealType min_val;
611		bool min_found = false;
#	Line 383 | Line 615 | namespace OpenMD {
615		bool max_found = false;
616		StuntDouble* max_sd;
617
618	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
619	<	sd = seleMan_.nextSelected(selei)) {
618	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
619	>	sd = seleManA_.nextSelected(selei)) {
620
389	–	idx = sd->getLocalIndex();
390	–
621		Vector3d pos = sd->getPos();
622	<
622	>
623		// wrap the stuntdouble's position back into the box:
624	<
624	>
625		if (usePeriodicBoundaryConditions_)
626		currentSnap_->wrapVector(pos);
627	<
628	<	// which bin is this stuntdouble in?
629	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
630	<
631	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
632	<
633	<
404	<	// if we're in bin 0 or the middleBin
405	<	if (binNo == 0 || binNo == midBin_) {
627	>
628	>	RealType mass = sd->getMass();
629	>	Vector3d vel = sd->getVel();
630	>	RealType value;
631	>
632	>	switch(rnemdFluxType_) {
633	>	case rnemdKE :
634
635	<	RealType mass = sd->getMass();
636	<	Vector3d vel = sd->getVel();
637	<	RealType value;
638	<
639	<	switch(rnemdType_) {
412	<	case rnemdKineticSwap :
635	>	value = mass * vel.lengthSquare();
636	>
637	>	if (sd->isDirectional()) {
638	>	Vector3d angMom = sd->getJ();
639	>	Mat3x3d I = sd->getI();
640
641	<	value = mass * vel.lengthSquare();
642	<
643	<	if (sd->isDirectional()) {
644	<	Vector3d angMom = sd->getJ();
645	<	Mat3x3d I = sd->getI();
646	<
647	<	if (sd->isLinear()) {
648	<	int i = sd->linearAxis();
649	<	int j = (i + 1) % 3;
650	<	int k = (i + 2) % 3;
651	<	value += angMom[j] * angMom[j] / I(j, j) +
652	<	angMom[k] * angMom[k] / I(k, k);
653	<	} else {
654	<	value += angMom[0]*angMom[0]/I(0, 0)
655	<	+ angMom[1]*angMom[1]/I(1, 1)
656	<	+ angMom[2]*angMom[2]/I(2, 2);
657	<	}
658	<	} //angular momenta exchange enabled
659	<	//energyConvert temporarily disabled
660	<	//make exchangeSum_ comparable between swap & scale
661	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
662	<	value *= 0.5;
663	<	break;
664	<	case rnemdPx :
665	<	value = mass * vel[0];
666	<	break;
667	<	case rnemdPy :
668	<	value = mass * vel[1];
669	<	break;
670	<	case rnemdPz :
671	<	value = mass * vel[2];
672	<	break;
673	<	default :
674	<	break;
641	>	if (sd->isLinear()) {
642	>	int i = sd->linearAxis();
643	>	int j = (i + 1) % 3;
644	>	int k = (i + 2) % 3;
645	>	value += angMom[j] * angMom[j] / I(j, j) +
646	>	angMom[k] * angMom[k] / I(k, k);
647	>	} else {
648	>	value += angMom[0]*angMom[0]/I(0, 0)
649	>	+ angMom[1]*angMom[1]/I(1, 1)
650	>	+ angMom[2]*angMom[2]/I(2, 2);
651	>	}
652	>	} //angular momenta exchange enabled
653	>	value *= 0.5;
654	>	break;
655	>	case rnemdPx :
656	>	value = mass * vel[0];
657	>	break;
658	>	case rnemdPy :
659	>	value = mass * vel[1];
660	>	break;
661	>	case rnemdPz :
662	>	value = mass * vel[2];
663	>	break;
664	>	default :
665	>	break;
666	>	}
667	>	if (!max_found) {
668	>	max_val = value;
669	>	max_sd = sd;
670	>	max_found = true;
671	>	} else {
672	>	if (max_val < value) {
673	>	max_val = value;
674	>	max_sd = sd;
675		}
676	+	}
677	+	}
678
679	<	if (binNo == 0) {
680	<	if (!min_found) {
681	<	min_val = value;
682	<	min_sd = sd;
683	<	min_found = true;
684	<	} else {
685	<	if (min_val > value) {
686	<	min_val = value;
687	<	min_sd = sd;
688	<	}
689	<	}
690	<	} else { //midBin_
691	<	if (!max_found) {
692	<	max_val = value;
693	<	max_sd = sd;
694	<	max_found = true;
695	<	} else {
696	<	if (max_val < value) {
697	<	max_val = value;
698	<	max_sd = sd;
699	<	}
700	<	}
701	<	}
679	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
680	>	sd = seleManB_.nextSelected(selej)) {
681	>
682	>	Vector3d pos = sd->getPos();
683	>
684	>	// wrap the stuntdouble's position back into the box:
685	>
686	>	if (usePeriodicBoundaryConditions_)
687	>	currentSnap_->wrapVector(pos);
688	>
689	>	RealType mass = sd->getMass();
690	>	Vector3d vel = sd->getVel();
691	>	RealType value;
692	>
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695	>
696	>	value = mass * vel.lengthSquare();
697	>
698	>	if (sd->isDirectional()) {
699	>	Vector3d angMom = sd->getJ();
700	>	Mat3x3d I = sd->getI();
701	>
702	>	if (sd->isLinear()) {
703	>	int i = sd->linearAxis();
704	>	int j = (i + 1) % 3;
705	>	int k = (i + 2) % 3;
706	>	value += angMom[j] * angMom[j] / I(j, j) +
707	>	angMom[k] * angMom[k] / I(k, k);
708	>	} else {
709	>	value += angMom[0]*angMom[0]/I(0, 0)
710	>	+ angMom[1]*angMom[1]/I(1, 1)
711	>	+ angMom[2]*angMom[2]/I(2, 2);
712	>	}
713	>	} //angular momenta exchange enabled
714	>	value *= 0.5;
715	>	break;
716	>	case rnemdPx :
717	>	value = mass * vel[0];
718	>	break;
719	>	case rnemdPy :
720	>	value = mass * vel[1];
721	>	break;
722	>	case rnemdPz :
723	>	value = mass * vel[2];
724	>	break;
725	>	default :
726	>	break;
727		}
728	+
729	+	if (!min_found) {
730	+	min_val = value;
731	+	min_sd = sd;
732	+	min_found = true;
733	+	} else {
734	+	if (min_val > value) {
735	+	min_val = value;
736	+	min_sd = sd;
737	+	}
738	+	}
739		}
740	<
741	<	#ifdef IS_MPI
742	<	int nProc, worldRank;
743	<
479	<	nProc = MPI::COMM_WORLD.Get_size();
480	<	worldRank = MPI::COMM_WORLD.Get_rank();
481	<
740	>
741	>	#ifdef IS_MPI
742	>	int worldRank = MPI::COMM_WORLD.Get_rank();
743	>
744		bool my_min_found = min_found;
745		bool my_max_found = max_found;
746
#	Line 533 | Line 795 | namespace OpenMD {
795		Vector3d max_vel = max_sd->getVel();
796		RealType temp_vel;
797
798	<	switch(rnemdType_) {
799	<	case rnemdKineticSwap :
798	>	switch(rnemdFluxType_) {
799	>	case rnemdKE :
800		min_sd->setVel(max_vel);
801		max_sd->setVel(min_vel);
802		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 585 | Line 847 | namespace OpenMD {
847		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
848		min_vals.rank, 0, status);
849
850	<	switch(rnemdType_) {
851	<	case rnemdKineticSwap :
850	>	switch(rnemdFluxType_) {
851	>	case rnemdKE :
852		max_sd->setVel(min_vel);
853		//angular momenta exchange enabled
854		if (max_sd->isDirectional()) {
#	Line 631 | Line 893 | namespace OpenMD {
893		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
894		max_vals.rank, 0, status);
895
896	<	switch(rnemdType_) {
897	<	case rnemdKineticSwap :
896	>	switch(rnemdFluxType_) {
897	>	case rnemdKE :
898		min_sd->setVel(max_vel);
899		//angular momenta exchange enabled
900		if (min_sd->isDirectional()) {
#	Line 666 | Line 928 | namespace OpenMD {
928		}
929		}
930		#endif
931	<	exchangeSum_ += max_val - min_val;
931	>
932	>	switch(rnemdFluxType_) {
933	>	case rnemdKE:
934	>	kineticExchange_ += max_val - min_val;
935	>	break;
936	>	case rnemdPx:
937	>	momentumExchange_.x() += max_val - min_val;
938	>	break;
939	>	case rnemdPy:
940	>	momentumExchange_.y() += max_val - min_val;
941	>	break;
942	>	case rnemdPz:
943	>	momentumExchange_.z() += max_val - min_val;
944	>	break;
945	>	default:
946	>	break;
947	>	}
948		} else {
949		sprintf(painCave.errMsg,
950	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
950	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
951		painCave.isFatal = 0;
952		painCave.severity = OPENMD_INFO;
953		simError();
#	Line 677 | Line 955 | namespace OpenMD {
955		}
956		} else {
957		sprintf(painCave.errMsg,
958	<	"RNEMD: exchange NOT performed because selected object\n"
959	<	"\tnot present in at least one of the two slabs.\n");
958	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
959	>	"\twas not present in at least one of the two slabs.\n");
960		painCave.isFatal = 0;
961		painCave.severity = OPENMD_INFO;
962		simError();
963		failTrialCount_++;
964	<	}
687	<
964	>	}
965		}
966
967	<	void RNEMD::doScale() {
967	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
968	>	if (!doRNEMD_) return;
969	>	int selei;
970	>	int selej;
971
972		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
973	+	RealType time = currentSnap_->getTime();
974		Mat3x3d hmat = currentSnap_->getHmat();
975
695	–	seleMan_.setSelectionSet(evaluator_.evaluate());
696	–
697	–	int selei;
976		StuntDouble* sd;
699	–	int idx;
977
978		vector<StuntDouble*> hotBin, coldBin;
979
#	Line 715 | Line 992 | namespace OpenMD {
992		RealType Kcz = 0.0;
993		RealType Kcw = 0.0;
994
995	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
996	<	sd = seleMan_.nextSelected(selei)) {
995	>	for (sd = smanA.beginSelected(selei); sd != NULL;
996	>	sd = smanA.nextSelected(selei)) {
997
721	–	idx = sd->getLocalIndex();
722	–
998		Vector3d pos = sd->getPos();
999	<
999	>
1000		// wrap the stuntdouble's position back into the box:
1001	<
1001	>
1002		if (usePeriodicBoundaryConditions_)
1003		currentSnap_->wrapVector(pos);
1004	<
1005	<	// which bin is this stuntdouble in?
1006	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1007	<
1008	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1009	<
1010	<	// if we're in bin 0 or the middleBin
1011	<	if (binNo == 0 || binNo == midBin_) {
1012	<
1013	<	RealType mass = sd->getMass();
1014	<	Vector3d vel = sd->getVel();
1015	<
1016	<	if (binNo == 0) {
1017	<	hotBin.push_back(sd);
1018	<	Phx += mass * vel.x();
1019	<	Phy += mass * vel.y();
1020	<	Phz += mass * vel.z();
1021	<	Khx += mass * vel.x() * vel.x();
1022	<	Khy += mass * vel.y() * vel.y();
1023	<	Khz += mass * vel.z() * vel.z();
1024	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1025	<	if (sd->isDirectional()) {
1026	<	Vector3d angMom = sd->getJ();
1027	<	Mat3x3d I = sd->getI();
1028	<	if (sd->isLinear()) {
1029	<	int i = sd->linearAxis();
755	<	int j = (i + 1) % 3;
756	<	int k = (i + 2) % 3;
757	<	Khw += angMom[j] * angMom[j] / I(j, j) +
758	<	angMom[k] * angMom[k] / I(k, k);
759	<	} else {
760	<	Khw += angMom[0]*angMom[0]/I(0, 0)
761	<	+ angMom[1]*angMom[1]/I(1, 1)
762	<	+ angMom[2]*angMom[2]/I(2, 2);
763	<	}
764	<	}
765	<	//}
766	<	} else { //midBin_
767	<	coldBin.push_back(sd);
768	<	Pcx += mass * vel.x();
769	<	Pcy += mass * vel.y();
770	<	Pcz += mass * vel.z();
771	<	Kcx += mass * vel.x() * vel.x();
772	<	Kcy += mass * vel.y() * vel.y();
773	<	Kcz += mass * vel.z() * vel.z();
774	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
775	<	if (sd->isDirectional()) {
776	<	Vector3d angMom = sd->getJ();
777	<	Mat3x3d I = sd->getI();
778	<	if (sd->isLinear()) {
779	<	int i = sd->linearAxis();
780	<	int j = (i + 1) % 3;
781	<	int k = (i + 2) % 3;
782	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
783	<	angMom[k] * angMom[k] / I(k, k);
784	<	} else {
785	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
786	<	+ angMom[1]*angMom[1]/I(1, 1)
787	<	+ angMom[2]*angMom[2]/I(2, 2);
788	<	}
789	<	}
790	<	//}
791	<	}
1004	>
1005	>
1006	>	RealType mass = sd->getMass();
1007	>	Vector3d vel = sd->getVel();
1008	>
1009	>	hotBin.push_back(sd);
1010	>	Phx += mass * vel.x();
1011	>	Phy += mass * vel.y();
1012	>	Phz += mass * vel.z();
1013	>	Khx += mass * vel.x() * vel.x();
1014	>	Khy += mass * vel.y() * vel.y();
1015	>	Khz += mass * vel.z() * vel.z();
1016	>	if (sd->isDirectional()) {
1017	>	Vector3d angMom = sd->getJ();
1018	>	Mat3x3d I = sd->getI();
1019	>	if (sd->isLinear()) {
1020	>	int i = sd->linearAxis();
1021	>	int j = (i + 1) % 3;
1022	>	int k = (i + 2) % 3;
1023	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1024	>	angMom[k] * angMom[k] / I(k, k);
1025	>	} else {
1026	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1027	>	+ angMom[1]*angMom[1]/I(1, 1)
1028	>	+ angMom[2]*angMom[2]/I(2, 2);
1029	>	}
1030		}
1031		}
1032	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1033	+	sd = smanB.nextSelected(selej)) {
1034	+	Vector3d pos = sd->getPos();
1035	+
1036	+	// wrap the stuntdouble's position back into the box:
1037	+
1038	+	if (usePeriodicBoundaryConditions_)
1039	+	currentSnap_->wrapVector(pos);
1040	+
1041	+	RealType mass = sd->getMass();
1042	+	Vector3d vel = sd->getVel();
1043	+
1044	+	coldBin.push_back(sd);
1045	+	Pcx += mass * vel.x();
1046	+	Pcy += mass * vel.y();
1047	+	Pcz += mass * vel.z();
1048	+	Kcx += mass * vel.x() * vel.x();
1049	+	Kcy += mass * vel.y() * vel.y();
1050	+	Kcz += mass * vel.z() * vel.z();
1051	+	if (sd->isDirectional()) {
1052	+	Vector3d angMom = sd->getJ();
1053	+	Mat3x3d I = sd->getI();
1054	+	if (sd->isLinear()) {
1055	+	int i = sd->linearAxis();
1056	+	int j = (i + 1) % 3;
1057	+	int k = (i + 2) % 3;
1058	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
1059	+	angMom[k] * angMom[k] / I(k, k);
1060	+	} else {
1061	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
1062	+	+ angMom[1]*angMom[1]/I(1, 1)
1063	+	+ angMom[2]*angMom[2]/I(2, 2);
1064	+	}
1065	+	}
1066	+	}
1067
1068		Khx *= 0.5;
1069		Khy *= 0.5;
#	Line 801 | Line 1074 | namespace OpenMD {
1074		Kcz *= 0.5;
1075		Kcw *= 0.5;
1076
804	–	// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
805	–	//        << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
806	–	//        << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
807	–	// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
808	–	//        << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
809	–
1077		#ifdef IS_MPI
1078		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1079		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 832 | Line 1099 | namespace OpenMD {
1099		RealType pz = Pcz / Phz;
1100		RealType c, x, y, z;
1101		bool successfulScale = false;
1102	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1103	<	(rnemdType_ == rnemdKineticScaleAM)) {
1102	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1103	>	(rnemdFluxType_ == rnemdRotKE)) {
1104		//may need sanity check Khw & Kcw > 0
1105
1106	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1107	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1106	>	if (rnemdFluxType_ == rnemdFullKE) {
1107	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1108		} else {
1109	<	c = 1.0 - targetFlux_ / Kcw;
1109	>	c = 1.0 - kineticTarget_ / Kcw;
1110		}
1111
1112		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1113		c = sqrt(c);
1114	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
848	<	//now convert to hotBin coefficient
1114	>
1115		RealType w = 0.0;
1116	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1116	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1117		x = 1.0 + px * (1.0 - c);
1118		y = 1.0 + py * (1.0 - c);
1119		z = 1.0 + pz * (1.0 - c);
#	Line 861 | Line 1127 | namespace OpenMD {
1127		*/
1128		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1129		(fabs(z - 1.0) < 0.1)) {
1130	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1130	>	w = 1.0 + (kineticTarget_
1131	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1132		+ Khz * (1.0 - z * z)) / Khw;
1133		}//no need to calculate w if x, y or z is out of range
1134		} else {
1135	<	w = 1.0 + targetFlux_ / Khw;
1135	>	w = 1.0 + kineticTarget_ / Khw;
1136		}
1137		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1138		//if w is in the right range, so should be x, y, z.
1139		vector<StuntDouble*>::iterator sdi;
1140		Vector3d vel;
1141		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1142	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1142	>	if (rnemdFluxType_ == rnemdFullKE) {
1143		vel = (*sdi)->getVel() * c;
877	–	//vel.x() *= c;
878	–	//vel.y() *= c;
879	–	//vel.z() *= c;
1144		(*sdi)->setVel(vel);
1145		}
1146		if ((*sdi)->isDirectional()) {
1147		Vector3d angMom = (*sdi)->getJ() * c;
884	–	//angMom[0] *= c;
885	–	//angMom[1] *= c;
886	–	//angMom[2] *= c;
1148		(*sdi)->setJ(angMom);
1149		}
1150		}
1151		w = sqrt(w);
891	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
892	–	<< "\twh= " << w << endl;
1152		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1153	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1153	>	if (rnemdFluxType_ == rnemdFullKE) {
1154		vel = (*sdi)->getVel();
1155		vel.x() *= x;
1156		vel.y() *= y;
#	Line 900 | Line 1159 | namespace OpenMD {
1159		}
1160		if ((*sdi)->isDirectional()) {
1161		Vector3d angMom = (*sdi)->getJ() * w;
903	–	//angMom[0] *= w;
904	–	//angMom[1] *= w;
905	–	//angMom[2] *= w;
1162		(*sdi)->setJ(angMom);
1163		}
1164		}
1165		successfulScale = true;
1166	<	exchangeSum_ += targetFlux_;
1166	>	kineticExchange_ += kineticTarget_;
1167		}
1168		}
1169		} else {
1170		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1171	<	switch(rnemdType_) {
1172	<	case rnemdKineticScale :
1171	>	switch(rnemdFluxType_) {
1172	>	case rnemdKE :
1173		/* used hotBin coeff's & only scale x & y dimensions
1174		RealType px = Phx / Pcx;
1175		RealType py = Phy / Pcy;
1176		a110 = Khy;
1177	<	c0 = - Khx - Khy - targetFlux_;
1177	>	c0 = - Khx - Khy - kineticTarget_;
1178		a000 = Khx;
1179		a111 = Kcy * py * py;
1180		b11 = -2.0 * Kcy * py * (1.0 + py);
1181	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1181	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1182		b01 = -2.0 * Kcx * px * (1.0 + px);
1183		a001 = Kcx * px * px;
1184		*/
1185		//scale all three dimensions, let c_x = c_y
1186		a000 = Kcx + Kcy;
1187		a110 = Kcz;
1188	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1188	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1189		a001 = Khx * px * px + Khy * py * py;
1190		a111 = Khz * pz * pz;
1191		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1192		b11 = -2.0 * Khz * pz * (1.0 + pz);
1193		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1194	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1194	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1195		break;
1196	<	case rnemdPxScale :
1197	<	c = 1 - targetFlux_ / Pcx;
1196	>	case rnemdPx :
1197	>	c = 1 - momentumTarget_.x() / Pcx;
1198		a000 = Kcy;
1199		a110 = Kcz;
1200		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 949 | Line 1205 | namespace OpenMD {
1205		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1206		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1207		break;
1208	<	case rnemdPyScale :
1209	<	c = 1 - targetFlux_ / Pcy;
1208	>	case rnemdPy :
1209	>	c = 1 - momentumTarget_.y() / Pcy;
1210		a000 = Kcx;
1211		a110 = Kcz;
1212		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 961 | Line 1217 | namespace OpenMD {
1217		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1218		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1219		break;
1220	<	case rnemdPzScale ://we don't really do this, do we?
1221	<	c = 1 - targetFlux_ / Pcz;
1220	>	case rnemdPz ://we don't really do this, do we?
1221	>	c = 1 - momentumTarget_.z() / Pcz;
1222		a000 = Kcx;
1223		a110 = Kcy;
1224		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1047 | Line 1303 | namespace OpenMD {
1303		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1304		r1 = (*rpi).first;
1305		r2 = (*rpi).second;
1306	<	switch(rnemdType_) {
1307	<	case rnemdKineticScale :
1306	>	switch(rnemdFluxType_) {
1307	>	case rnemdKE :
1308		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1309		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1310		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1311		break;
1312	<	case rnemdPxScale :
1312	>	case rnemdPx :
1313		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1314		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1315		break;
1316	<	case rnemdPyScale :
1316	>	case rnemdPy :
1317		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1318		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1319		break;
1320	<	case rnemdPzScale :
1320	>	case rnemdPz :
1321		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1323		default :
#	Line 1075 | Line 1331 | namespace OpenMD {
1331		#ifdef IS_MPI
1332		if (worldRank == 0) {
1333		#endif
1334	<	sprintf(painCave.errMsg,
1335	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1336	<	bestPair.first, bestPair.second);
1337	<	painCave.isFatal = 0;
1338	<	painCave.severity = OPENMD_INFO;
1339	<	simError();
1334	>	// sprintf(painCave.errMsg,
1335	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1336	>	//         bestPair.first, bestPair.second);
1337	>	// painCave.isFatal = 0;
1338	>	// painCave.severity = OPENMD_INFO;
1339	>	// simError();
1340		#ifdef IS_MPI
1341		}
1342		#endif
1343
1344	<	switch(rnemdType_) {
1345	<	case rnemdKineticScale :
1344	>	switch(rnemdFluxType_) {
1345	>	case rnemdKE :
1346		x = bestPair.first;
1347		y = bestPair.first;
1348		z = bestPair.second;
1349		break;
1350	<	case rnemdPxScale :
1350	>	case rnemdPx :
1351		x = c;
1352		y = bestPair.first;
1353		z = bestPair.second;
1354		break;
1355	<	case rnemdPyScale :
1355	>	case rnemdPy :
1356		x = bestPair.first;
1357		y = c;
1358		z = bestPair.second;
1359		break;
1360	<	case rnemdPzScale :
1360	>	case rnemdPz :
1361		x = bestPair.first;
1362		y = bestPair.second;
1363		z = c;
#	Line 1130 | Line 1386 | namespace OpenMD {
1386		(*sdi)->setVel(vel);
1387		}
1388		successfulScale = true;
1389	<	exchangeSum_ += targetFlux_;
1389	>	switch(rnemdFluxType_) {
1390	>	case rnemdKE :
1391	>	kineticExchange_ += kineticTarget_;
1392	>	break;
1393	>	case rnemdPx :
1394	>	case rnemdPy :
1395	>	case rnemdPz :
1396	>	momentumExchange_ += momentumTarget_;
1397	>	break;
1398	>	default :
1399	>	break;
1400	>	}
1401		}
1402		}
1403		if (successfulScale != true) {
1404		sprintf(painCave.errMsg,
1405	<	"RNEMD: exchange NOT performed!\n");
1405	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1406	>	"\tthe constraint equations may not exist or there may be\n"
1407	>	"\tno selected objects in one or both slabs.\n");
1408		painCave.isFatal = 0;
1409		painCave.severity = OPENMD_INFO;
1410		simError();
1411		failTrialCount_++;
1412		}
1413		}
1414	+
1415	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1416	+	if (!doRNEMD_) return;
1417	+	int selei;
1418	+	int selej;
1419
1146	–	void RNEMD::doShiftScale() {
1147	–
1420		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1421		RealType time = currentSnap_->getTime();
1422		Mat3x3d hmat = currentSnap_->getHmat();
1423
1152	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1153	–
1154	–	int selei;
1424		StuntDouble* sd;
1156	–	int idx;
1425
1426		vector<StuntDouble*> hotBin, coldBin;
1427
1428		Vector3d Ph(V3Zero);
1429	+	Vector3d Lh(V3Zero);
1430		RealType Mh = 0.0;
1431	+	Mat3x3d Ih(0.0);
1432		RealType Kh = 0.0;
1433		Vector3d Pc(V3Zero);
1434	+	Vector3d Lc(V3Zero);
1435		RealType Mc = 0.0;
1436	+	Mat3x3d Ic(0.0);
1437		RealType Kc = 0.0;
1438
1439	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1440	+	sd = smanA.nextSelected(selei)) {
1441
1168	–	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1169	–	sd = seleMan_.nextSelected(selei)) {
1170	–
1171	–	idx = sd->getLocalIndex();
1172	–
1442		Vector3d pos = sd->getPos();
1443
1444		// wrap the stuntdouble's position back into the box:
1445	<
1445	>
1446		if (usePeriodicBoundaryConditions_)
1447		currentSnap_->wrapVector(pos);
1448	<
1449	<	// which bin is this stuntdouble in?
1450	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1448	>
1449	>	RealType mass = sd->getMass();
1450	>	Vector3d vel = sd->getVel();
1451	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1452	>	RealType r2;
1453	>
1454	>	hotBin.push_back(sd);
1455	>	Ph += mass * vel;
1456	>	Mh += mass;
1457	>	Kh += mass * vel.lengthSquare();
1458	>	Lh += mass * cross(rPos, vel);
1459	>	Ih -= outProduct(rPos, rPos) * mass;
1460	>	r2 = rPos.lengthSquare();
1461	>	Ih(0, 0) += mass * r2;
1462	>	Ih(1, 1) += mass * r2;
1463	>	Ih(2, 2) += mass * r2;
1464	>
1465	>	if (rnemdFluxType_ == rnemdFullKE) {
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	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1474	>	angMom[k] * angMom[k] / I(k, k);
1475	>	} else {
1476	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1477	>	angMom[1] * angMom[1] / I(1, 1) +
1478	>	angMom[2] * angMom[2] / I(2, 2);
1479	>	}
1480	>	}
1481	>	}
1482	>	}
1483	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1484	>	sd = smanB.nextSelected(selej)) {
1485
1486	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1486	>	Vector3d pos = sd->getPos();
1487	>
1488	>	// wrap the stuntdouble's position back into the box:
1489	>
1490	>	if (usePeriodicBoundaryConditions_)
1491	>	currentSnap_->wrapVector(pos);
1492	>
1493	>	RealType mass = sd->getMass();
1494	>	Vector3d vel = sd->getVel();
1495	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1496	>	RealType r2;
1497
1498	<	// if we're in bin 0 or the middleBin
1499	<	if (binNo == 0 || binNo == midBin_) {
1500	<
1501	<	RealType mass = sd->getMass();
1502	<	Vector3d vel = sd->getVel();
1503	<
1504	<	if (binNo == 0) {
1505	<	hotBin.push_back(sd);
1506	<	//std::cerr << "before, velocity = " << vel << endl;
1507	<	Ph += mass * vel;
1508	<	//std::cerr << "after, velocity = " << vel << endl;
1509	<	Mh += mass;
1510	<	Kh += mass * vel.lengthSquare();
1511	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1512	<	if (sd->isDirectional()) {
1513	<	Vector3d angMom = sd->getJ();
1514	<	Mat3x3d I = sd->getI();
1515	<	if (sd->isLinear()) {
1516	<	int i = sd->linearAxis();
1517	<	int j = (i + 1) % 3;
1518	<	int k = (i + 2) % 3;
1519	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1520	<	angMom[k] * angMom[k] / I(k, k);
1521	<	} else {
1522	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1523	<	angMom[1] * angMom[1] / I(1, 1) +
1524	<	angMom[2] * angMom[2] / I(2, 2);
1212	<	}
1213	<	}
1214	<	}
1215	<	} else { //midBin_
1216	<	coldBin.push_back(sd);
1217	<	Pc += mass * vel;
1218	<	Mc += mass;
1219	<	Kc += mass * vel.lengthSquare();
1220	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1221	<	if (sd->isDirectional()) {
1222	<	Vector3d angMom = sd->getJ();
1223	<	Mat3x3d I = sd->getI();
1224	<	if (sd->isLinear()) {
1225	<	int i = sd->linearAxis();
1226	<	int j = (i + 1) % 3;
1227	<	int k = (i + 2) % 3;
1228	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1229	<	angMom[k] * angMom[k] / I(k, k);
1230	<	} else {
1231	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1232	<	angMom[1] * angMom[1] / I(1, 1) +
1233	<	angMom[2] * angMom[2] / I(2, 2);
1234	<	}
1235	<	}
1236	<	}
1237	<	}
1498	>	coldBin.push_back(sd);
1499	>	Pc += mass * vel;
1500	>	Mc += mass;
1501	>	Kc += mass * vel.lengthSquare();
1502	>	Lc += mass * cross(rPos, vel);
1503	>	Ic -= outProduct(rPos, rPos) * mass;
1504	>	r2 = rPos.lengthSquare();
1505	>	Ic(0, 0) += mass * r2;
1506	>	Ic(1, 1) += mass * r2;
1507	>	Ic(2, 2) += mass * r2;
1508	>
1509	>	if (rnemdFluxType_ == rnemdFullKE) {
1510	>	if (sd->isDirectional()) {
1511	>	Vector3d angMom = sd->getJ();
1512	>	Mat3x3d I = sd->getI();
1513	>	if (sd->isLinear()) {
1514	>	int i = sd->linearAxis();
1515	>	int j = (i + 1) % 3;
1516	>	int k = (i + 2) % 3;
1517	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1518	>	angMom[k] * angMom[k] / I(k, k);
1519	>	} else {
1520	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1521	>	angMom[1] * angMom[1] / I(1, 1) +
1522	>	angMom[2] * angMom[2] / I(2, 2);
1523	>	}
1524	>	}
1525		}
1526		}
1527
1528		Kh *= 0.5;
1529		Kc *= 0.5;
1243	–
1244	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1245	–	//        << "\tKc= " << Kc << endl;
1246	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1530
1531		#ifdef IS_MPI
1532		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1533		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1534	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1535	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1536		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1537		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1538		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1539		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1540	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1541	+	MPI::REALTYPE, MPI::SUM);
1542	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1543	+	MPI::REALTYPE, MPI::SUM);
1544		#endif
1545	<
1545	>
1546		bool successfulExchange = false;
1547		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1548		Vector3d vc = Pc / Mc;
1549	<	Vector3d ac = njzp_ / Mc + vc;
1550	<	Vector3d acrec = njzp_ / Mc;
1551	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1549	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1550	>	Vector3d acrec = -momentumTarget_ / Mc;
1551	>
1552	>	// We now need the inverse of the inertia tensor to calculate the
1553	>	// angular velocity of the cold slab;
1554	>	Mat3x3d Ici = Ic.inverse();
1555	>	Vector3d omegac = Ici * Lc;
1556	>	Vector3d bc  = -(Ici * angularMomentumTarget_) + omegac;
1557	>	Vector3d bcrec = bc - omegac;
1558	>
1559	>	RealType cNumerator = Kc - kineticTarget_
1560	>	- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc));
1561		if (cNumerator > 0.0) {
1562	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1562	>
1563	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare()
1564	>	- 0.5*(dot(omegac, Ic * omegac));
1565	>
1566		if (cDenominator > 0.0) {
1567		RealType c = sqrt(cNumerator / cDenominator);
1568		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1569	+
1570		Vector3d vh = Ph / Mh;
1571	<	Vector3d ah = jzp_ / Mh + vh;
1572	<	Vector3d ahrec = jzp_ / Mh;
1573	<	RealType hNumerator = Kh + targetJzKE_
1574	<	- 0.5 * Mh * ah.lengthSquare();
1575	<	if (hNumerator > 0.0) {
1576	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1571	>	Vector3d ah = momentumTarget_ / Mh + vh;
1572	>	Vector3d ahrec = momentumTarget_ / Mh;
1573	>
1574	>	// We now need the inverse of the inertia tensor to
1575	>	// calculate the angular velocity of the hot slab;
1576	>	Mat3x3d Ihi = Ih.inverse();
1577	>	Vector3d omegah = Ihi * Lh;
1578	>	Vector3d bh  = (Ihi * angularMomentumTarget_) + omegah;
1579	>	Vector3d bhrec = bh - omegah;
1580	>
1581	>	RealType hNumerator = Kh + kineticTarget_
1582	>	- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));;
1583	>	if (hNumerator > 0.0) {
1584	>
1585	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare()
1586	>	- 0.5*(dot(omegah, Ih * omegah));
1587	>
1588		if (hDenominator > 0.0) {
1589		RealType h = sqrt(hNumerator / hDenominator);
1590		if ((h > 0.9) && (h < 1.1)) {
1591	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1279	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1591	>
1592		vector<StuntDouble*>::iterator sdi;
1593		Vector3d vel;
1594	+	Vector3d rPos;
1595	+
1596		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1597		//vel = (*sdi)->getVel();
1598	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1598	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1599	>	vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c
1600	>	+ ac + cross(bc, rPos);
1601		(*sdi)->setVel(vel);
1602	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1602	>	if (rnemdFluxType_ == rnemdFullKE) {
1603		if ((*sdi)->isDirectional()) {
1604		Vector3d angMom = (*sdi)->getJ() * c;
1605		(*sdi)->setJ(angMom);
#	Line 1292 | Line 1608 | namespace OpenMD {
1608		}
1609		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1610		//vel = (*sdi)->getVel();
1611	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1611	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1612	>	vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1613	>	+ ah + cross(bh, rPos);
1614		(*sdi)->setVel(vel);
1615	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1615	>	if (rnemdFluxType_ == rnemdFullKE) {
1616		if ((*sdi)->isDirectional()) {
1617		Vector3d angMom = (*sdi)->getJ() * h;
1618		(*sdi)->setJ(angMom);
#	Line 1302 | Line 1620 | namespace OpenMD {
1620		}
1621		}
1622		successfulExchange = true;
1623	<	exchangeSum_ += targetFlux_;
1624	<	// this is a redundant variable for doShiftScale() so that
1625	<	// RNEMD can output one exchange quantity needed in a job.
1308	<	// need a better way to do this.
1309	<	//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n';
1310	<	//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n';
1311	<	//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n';
1312	<	Asum_ += (ahrec.z() - acrec.z());
1313	<	Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc)));
1314	<	AhCount_ = ahrec.z();
1315	<	if (outputAh_) {
1316	<	AhLog_ << time << "   ";
1317	<	AhLog_ << AhCount_;
1318	<	AhLog_ << endl;
1319	<	}
1623	>	kineticExchange_ += kineticTarget_;
1624	>	momentumExchange_ += momentumTarget_;
1625	>	angularMomentumExchange_ += angularMomentumTarget_;
1626		}
1627		}
1628		}
#	Line 1325 | Line 1631 | namespace OpenMD {
1631		}
1632		}
1633		if (successfulExchange != true) {
1634	<	//   sprintf(painCave.errMsg,
1635	<	//              "RNEMD: exchange NOT performed!\n");
1636	<	//   painCave.isFatal = 0;
1637	<	//   painCave.severity = OPENMD_INFO;
1638	<	//   simError();
1634	>	sprintf(painCave.errMsg,
1635	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1636	>	"\tthe constraint equations may not exist or there may be\n"
1637	>	"\tno selected objects in one or both slabs.\n");
1638	>	painCave.isFatal = 0;
1639	>	painCave.severity = OPENMD_INFO;
1640	>	simError();
1641		failTrialCount_++;
1642		}
1643		}
1644
1645	+	RealType RNEMD::getDividingArea() {
1646	+
1647	+	if (hasDividingArea_) return dividingArea_;
1648	+
1649	+	RealType areaA, areaB;
1650	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1651	+
1652	+	if (hasSelectionA_) {
1653	+	int isd;
1654	+	StuntDouble* sd;
1655	+	vector<StuntDouble*> aSites;
1656	+	ConvexHull* surfaceMeshA = new ConvexHull();
1657	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1658	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1659	+	sd = seleManA_.nextSelected(isd)) {
1660	+	aSites.push_back(sd);
1661	+	}
1662	+	surfaceMeshA->computeHull(aSites);
1663	+	areaA = surfaceMeshA->getArea();
1664	+	} else {
1665	+	if (usePeriodicBoundaryConditions_) {
1666	+	// in periodic boundaries, the surface area is twice the x-y
1667	+	// area of the current box:
1668	+	areaA = 2.0 * snap->getXYarea();
1669	+	} else {
1670	+	// in non-periodic simulations, without explicitly setting
1671	+	// selections, the sphere radius sets the surface area of the
1672	+	// dividing surface:
1673	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1674	+	}
1675	+	}
1676	+
1677	+	if (hasSelectionB_) {
1678	+	int isd;
1679	+	StuntDouble* sd;
1680	+	vector<StuntDouble*> bSites;
1681	+	ConvexHull* surfaceMeshB = new ConvexHull();
1682	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1683	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1684	+	sd = seleManB_.nextSelected(isd)) {
1685	+	bSites.push_back(sd);
1686	+	}
1687	+	surfaceMeshB->computeHull(bSites);
1688	+	areaB = surfaceMeshB->getArea();
1689	+	} else {
1690	+	if (usePeriodicBoundaryConditions_) {
1691	+	// in periodic boundaries, the surface area is twice the x-y
1692	+	// area of the current box:
1693	+	areaB = 2.0 * snap->getXYarea();
1694	+	} else {
1695	+	// in non-periodic simulations, without explicitly setting
1696	+	// selections, but if a sphereBradius has been set, just use that:
1697	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1698	+	}
1699	+	}
1700	+
1701	+	dividingArea_ = min(areaA, areaB);
1702	+	hasDividingArea_ = true;
1703	+	return dividingArea_;
1704	+	}
1705	+
1706		void RNEMD::doRNEMD() {
1707	+	if (!doRNEMD_) return;
1708	+	trialCount_++;
1709
1710	<	switch(rnemdType_) {
1711	<	case rnemdKineticScale :
1712	<	case rnemdKineticScaleVAM :
1713	<	case rnemdKineticScaleAM :
1714	<	case rnemdPxScale :
1715	<	case rnemdPyScale :
1716	<	case rnemdPzScale :
1717	<	doScale();
1710	>	// object evaluator:
1711	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1712	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1713	>
1714	>	evaluatorA_.loadScriptString(selectionA_);
1715	>	evaluatorB_.loadScriptString(selectionB_);
1716	>
1717	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1718	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1719	>
1720	>	commonA_ = seleManA_ & seleMan_;
1721	>	commonB_ = seleManB_ & seleMan_;
1722	>
1723	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1724	>	// dt = exchange time interval
1725	>	// flux = target flux
1726	>	// dividingArea = smallest dividing surface between the two regions
1727	>
1728	>	hasDividingArea_ = false;
1729	>	RealType area = getDividingArea();
1730	>
1731	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1732	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1733	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1734	>
1735	>	switch(rnemdMethod_) {
1736	>	case rnemdSwap:
1737	>	doSwap(commonA_, commonB_);
1738		break;
1739	<	case rnemdKineticSwap :
1740	<	case rnemdPx :
1350	<	case rnemdPy :
1351	<	case rnemdPz :
1352	<	doSwap();
1739	>	case rnemdNIVS:
1740	>	doNIVS(commonA_, commonB_);
1741		break;
1742	<	case rnemdShiftScaleV :
1743	<	case rnemdShiftScaleVAM :
1356	<	doShiftScale();
1742	>	case rnemdVSS:
1743	>	doVSS(commonA_, commonB_);
1744		break;
1745	<	case rnemdUnknown :
1745	>	case rnemdUnkownMethod:
1746		default :
1747		break;
1748		}
1749		}
1750
1751		void RNEMD::collectData() {
1752	<
1752	>	if (!doRNEMD_) return;
1753		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1367	–	Mat3x3d hmat = currentSnap_->getHmat();
1754
1755	+	// collectData can be called more frequently than the doRNEMD, so use the
1756	+	// computed area from the last exchange time:
1757	+
1758	+	areaAccumulator_->add(getDividingArea());
1759	+	Mat3x3d hmat = currentSnap_->getHmat();
1760		seleMan_.setSelectionSet(evaluator_.evaluate());
1761
1762	<	int selei;
1762	>	int selei(0);
1763		StuntDouble* sd;
1764	<	int idx;
1764	>	int binNo;
1765
1766	<	logFrameCount_++;
1766	>	vector<RealType> binMass(nBins_, 0.0);
1767	>	vector<RealType> binPx(nBins_, 0.0);
1768	>	vector<RealType> binPy(nBins_, 0.0);
1769	>	vector<RealType> binPz(nBins_, 0.0);
1770	>	vector<RealType> binOmegax(nBins_, 0.0);
1771	>	vector<RealType> binOmegay(nBins_, 0.0);
1772	>	vector<RealType> binOmegaz(nBins_, 0.0);
1773	>	vector<RealType> binKE(nBins_, 0.0);
1774	>	vector<int> binDOF(nBins_, 0);
1775	>	vector<int> binCount(nBins_, 0);
1776
1777		// alternative approach, track all molecules instead of only those
1778		// selected for scaling/swapping:
1779		/*
1780	<	SimInfo::MoleculeIterator miter;
1781	<	vector<StuntDouble*>::iterator iiter;
1782	<	Molecule* mol;
1783	<	StuntDouble* sd;
1784	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1780	>	SimInfo::MoleculeIterator miter;
1781	>	vector<StuntDouble*>::iterator iiter;
1782	>	Molecule* mol;
1783	>	StuntDouble* sd;
1784	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1785		mol = info_->nextMolecule(miter))
1786		sd is essentially sd
1787	<	for (sd = mol->beginIntegrableObject(iiter);
1788	<	sd != NULL;
1789	<	sd = mol->nextIntegrableObject(iiter))
1787	>	for (sd = mol->beginIntegrableObject(iiter);
1788	>	sd != NULL;
1789	>	sd = mol->nextIntegrableObject(iiter))
1790		*/
1791	+
1792		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1793	<	sd = seleMan_.nextSelected(selei)) {
1794	<
1394	<	idx = sd->getLocalIndex();
1395	<
1793	>	sd = seleMan_.nextSelected(selei)) {
1794	>
1795		Vector3d pos = sd->getPos();
1796
1797		// wrap the stuntdouble's position back into the box:
1798
1799	<	if (usePeriodicBoundaryConditions_)
1799	>	if (usePeriodicBoundaryConditions_) {
1800		currentSnap_->wrapVector(pos);
1801	<
1802	<	// which bin is this stuntdouble in?
1803	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1804	<
1805	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1806	<	rnemdLogWidth_;
1807	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1808	<	/*
1809	<	if (rnemdLogWidth_ == midBin_ + 1)
1810	<	if (binNo > midBin_)
1811	<	binNo = nBins_ - binNo;
1812	<	*/
1414	<	RealType mass = sd->getMass();
1415	<	mHist_[binNo] += mass;
1801	>	// which bin is this stuntdouble in?
1802	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1803	>	// Shift molecules by half a box to have bins start at 0
1804	>	// The modulo operator is used to wrap the case when we are
1805	>	// beyond the end of the bins back to the beginning.
1806	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1807	>	} else {
1808	>	Vector3d rPos = pos - coordinateOrigin_;
1809	>	binNo = int(rPos.length() / binWidth_);
1810	>	}
1811	>
1812	>	RealType mass = sd->getMass();
1813		Vector3d vel = sd->getVel();
1814	<	RealType value;
1815	<	//RealType xVal, yVal, zVal;
1814	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1815	>	Vector3d aVel = cross(rPos, vel);
1816	>
1817	>	if (binNo < nBins_)  {
1818	>	binCount[binNo]++;
1819	>	binMass[binNo] += mass;
1820	>	binPx[binNo] += mass*vel.x();
1821	>	binPy[binNo] += mass*vel.y();
1822	>	binPz[binNo] += mass*vel.z();
1823	>	binOmegax[binNo] += aVel.x();
1824	>	binOmegay[binNo] += aVel.y();
1825	>	binOmegaz[binNo] += aVel.z();
1826	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1827	>	binDOF[binNo] += 3;
1828	>
1829	>	if (sd->isDirectional()) {
1830	>	Vector3d angMom = sd->getJ();
1831	>	Mat3x3d I = sd->getI();
1832	>	if (sd->isLinear()) {
1833	>	int i = sd->linearAxis();
1834	>	int j = (i + 1) % 3;
1835	>	int k = (i + 2) % 3;
1836	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1837	>	angMom[k] * angMom[k] / I(k, k));
1838	>	binDOF[binNo] += 2;
1839	>	} else {
1840	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1841	>	angMom[1] * angMom[1] / I(1, 1) +
1842	>	angMom[2] * angMom[2] / I(2, 2));
1843	>	binDOF[binNo] += 3;
1844	>	}
1845	>	}
1846	>	}
1847	>	}
1848	>
1849	>	#ifdef IS_MPI
1850	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1851	>	nBins_, MPI::INT, MPI::SUM);
1852	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1853	>	nBins_, MPI::REALTYPE, MPI::SUM);
1854	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1855	>	nBins_, MPI::REALTYPE, MPI::SUM);
1856	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1857	>	nBins_, MPI::REALTYPE, MPI::SUM);
1858	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1859	>	nBins_, MPI::REALTYPE, MPI::SUM);
1860	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1861	>	nBins_, MPI::REALTYPE, MPI::SUM);
1862	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1863	>	nBins_, MPI::REALTYPE, MPI::SUM);
1864	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1865	>	nBins_, MPI::REALTYPE, MPI::SUM);
1866	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1867	>	nBins_, MPI::REALTYPE, MPI::SUM);
1868	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1869	>	nBins_, MPI::INT, MPI::SUM);
1870	>	#endif
1871
1872	<	if (outputTemp_) {
1873	<	value = mass * vel.lengthSquare();
1874	<	tempCount_[binNo] += 3;
1875	<	if (sd->isDirectional()) {
1876	<	Vector3d angMom = sd->getJ();
1877	<	Mat3x3d I = sd->getI();
1878	<	if (sd->isLinear()) {
1879	<	int i = sd->linearAxis();
1880	<	int j = (i + 1) % 3;
1881	<	int k = (i + 2) % 3;
1882	<	value += angMom[j] * angMom[j] / I(j, j) +
1883	<	angMom[k] * angMom[k] / I(k, k);
1884	<	tempCount_[binNo] +=2;
1885	<	} else {
1886	<	value += angMom[0] * angMom[0] / I(0, 0) +
1887	<	angMom[1]*angMom[1]/I(1, 1) +
1888	<	angMom[2]*angMom[2]/I(2, 2);
1437	<	tempCount_[binNo] +=3;
1438	<	}
1439	<	}
1440	<	value = value / PhysicalConstants::energyConvert
1441	<	/ PhysicalConstants::kb;//may move to getStatus()
1442	<	tempHist_[binNo] += value;
1872	>	Vector3d vel;
1873	>	Vector3d aVel;
1874	>	RealType den;
1875	>	RealType temp;
1876	>	RealType z;
1877	>	RealType r;
1878	>	for (int i = 0; i < nBins_; i++) {
1879	>	if (usePeriodicBoundaryConditions_) {
1880	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1881	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1882	>	/ currentSnap_->getVolume() ;
1883	>	} else {
1884	>	r = (((RealType)i + 0.5) * binWidth_);
1885	>	RealType rinner = (RealType)i * binWidth_;
1886	>	RealType router = (RealType)(i+1) * binWidth_;
1887	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1888	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1889		}
1890	<	if (outputVx_) {
1891	<	value = mass * vel[0];
1892	<	//vxzCount_[binNo]++;
1893	<	pxzHist_[binNo] += value;
1894	<	}
1895	<	if (outputVy_) {
1450	<	value = mass * vel[1];
1451	<	//vyzCount_[binNo]++;
1452	<	pyzHist_[binNo] += value;
1453	<	}
1890	>	vel.x() = binPx[i] / binMass[i];
1891	>	vel.y() = binPy[i] / binMass[i];
1892	>	vel.z() = binPz[i] / binMass[i];
1893	>	aVel.x() = binOmegax[i];
1894	>	aVel.y() = binOmegay[i];
1895	>	aVel.z() = binOmegaz[i];
1896
1897	<	if (output3DTemp_) {
1898	<	value = mass * vel.x() * vel.x();
1899	<	xTempHist_[binNo] += value;
1900	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1901	<	/ PhysicalConstants::kb;
1902	<	yTempHist_[binNo] += value;
1903	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1904	<	/ PhysicalConstants::kb;
1905	<	zTempHist_[binNo] += value;
1906	<	xyzTempCount_[binNo]++;
1897	>	if (binCount[i] > 0) {
1898	>	// only add values if there are things to add
1899	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1900	>	PhysicalConstants::energyConvert);
1901	>
1902	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1903	>	if(outputMask_[j]) {
1904	>	switch(j) {
1905	>	case Z:
1906	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1907	>	break;
1908	>	case R:
1909	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1910	>	break;
1911	>	case TEMPERATURE:
1912	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1913	>	break;
1914	>	case VELOCITY:
1915	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1916	>	break;
1917	>	case ANGULARVELOCITY:
1918	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1919	>	break;
1920	>	case DENSITY:
1921	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1922	>	break;
1923	>	}
1924	>	}
1925	>	}
1926		}
1466	–	if (outputRotTemp_) {
1467	–	if (sd->isDirectional()) {
1468	–	Vector3d angMom = sd->getJ();
1469	–	Mat3x3d I = sd->getI();
1470	–	if (sd->isLinear()) {
1471	–	int i = sd->linearAxis();
1472	–	int j = (i + 1) % 3;
1473	–	int k = (i + 2) % 3;
1474	–	value = angMom[j] * angMom[j] / I(j, j) +
1475	–	angMom[k] * angMom[k] / I(k, k);
1476	–	rotTempCount_[binNo] +=2;
1477	–	} else {
1478	–	value = angMom[0] * angMom[0] / I(0, 0) +
1479	–	angMom[1] * angMom[1] / I(1, 1) +
1480	–	angMom[2] * angMom[2] / I(2, 2);
1481	–	rotTempCount_[binNo] +=3;
1482	–	}
1483	–	}
1484	–	value = value / PhysicalConstants::energyConvert
1485	–	/ PhysicalConstants::kb;//may move to getStatus()
1486	–	rotTempHist_[binNo] += value;
1487	–	}
1488	–	// James put this in.
1489	–	if (outputDen_) {
1490	–	//value = 1.0;
1491	–	DenHist_[binNo] += 1;
1492	–	}
1493	–	if (outputVz_) {
1494	–	value = mass * vel[2];
1495	–	//vyzCount_[binNo]++;
1496	–	pzzHist_[binNo] += value;
1497	–	}
1927		}
1928		}
1929
1930		void RNEMD::getStarted() {
1931	+	if (!doRNEMD_) return;
1932	+	hasDividingArea_ = false;
1933		collectData();
1934	<	/*now can output profile in step 0, but might not be useful;
1504	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1505	<	Stats& stat = currentSnap_->statData;
1506	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1507	<	*/
1508	<	//may output a header for the log file here
1509	<	getStatus();
1934	>	writeOutputFile();
1935		}
1936
1937	<	void RNEMD::getStatus() {
1938	<
1939	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1515	<	RealType time = currentSnap_->getTime();
1516	<	//or to be more meaningful, define another item as exchangeSum_ / time
1517	<	int j;
1518	<
1519	<	#ifdef IS_MPI
1520	<
1521	<	// all processors have the same number of bins, and STL vectors pack their
1522	<	// arrays, so in theory, this should be safe:
1523	<
1524	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1525	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1526	<	if (outputTemp_) {
1527	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1528	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1529	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1530	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1531	<	}
1532	<	if (outputVx_) {
1533	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1534	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1535	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1536	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1537	<	}
1538	<	if (outputVy_) {
1539	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1540	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1541	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1542	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1543	<	}
1544	<	if (output3DTemp_) {
1545	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1546	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1547	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1548	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1549	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1550	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1551	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1552	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1553	<	}
1554	<	if (outputRotTemp_) {
1555	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1556	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1557	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1558	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1559	<	}
1560	<	// James put this in
1561	<	if (outputDen_) {
1562	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1563	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1564	<	}
1565	<	if (outputAh_) {
1566	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1567	<	1, MPI::REALTYPE, MPI::SUM);
1568	<	}
1569	<	if (outputVz_) {
1570	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1571	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1572	<	}
1937	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1938	>	if (!doRNEMD_) return;
1939	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1940
1941	+	while(tokenizer.hasMoreTokens()) {
1942	+	std::string token(tokenizer.nextToken());
1943	+	toUpper(token);
1944	+	OutputMapType::iterator i = outputMap_.find(token);
1945	+	if (i != outputMap_.end()) {
1946	+	outputMask_.set(i->second);
1947	+	} else {
1948	+	sprintf( painCave.errMsg,
1949	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1950	+	"\toutputFileFormat keyword.\n", token.c_str() );
1951	+	painCave.isFatal = 0;
1952	+	painCave.severity = OPENMD_ERROR;
1953	+	simError();
1954	+	}
1955	+	}
1956	+	}
1957	+
1958	+	void RNEMD::writeOutputFile() {
1959	+	if (!doRNEMD_) return;
1960	+
1961	+	#ifdef IS_MPI
1962		// If we're the root node, should we print out the results
1963		int worldRank = MPI::COMM_WORLD.Get_rank();
1964		if (worldRank == 0) {
1965		#endif
1966	<
1967	<	if (outputTemp_) {
1968	<	tempLog_ << time;
1969	<	for (j = 0; j < rnemdLogWidth_; j++) {
1970	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1971	<	}
1972	<	tempLog_ << endl;
1966	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1967	>
1968	>	if( !rnemdFile_ ){
1969	>	sprintf( painCave.errMsg,
1970	>	"Could not open \"%s\" for RNEMD output.\n",
1971	>	rnemdFileName_.c_str());
1972	>	painCave.isFatal = 1;
1973	>	simError();
1974		}
1975	<	if (outputVx_) {
1976	<	vxzLog_ << time;
1977	<	for (j = 0; j < rnemdLogWidth_; j++) {
1978	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1979	<	}
1980	<	vxzLog_ << endl;
1975	>
1976	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1977	>
1978	>	RealType time = currentSnap_->getTime();
1979	>	RealType avgArea;
1980	>	areaAccumulator_->getAverage(avgArea);
1981	>	RealType Jz = kineticExchange_ / (time * avgArea)
1982	>	/ PhysicalConstants::energyConvert;
1983	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
1984	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
1985	>
1986	>	rnemdFile_ << "#######################################################\n";
1987	>	rnemdFile_ << "# RNEMD {\n";
1988	>
1989	>	map<string, RNEMDMethod>::iterator mi;
1990	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1991	>	if ( (*mi).second == rnemdMethod_)
1992	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1993		}
1994	<	if (outputVy_) {
1995	<	vyzLog_ << time;
1996	<	for (j = 0; j < rnemdLogWidth_; j++) {
1997	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1597	<	}
1598	<	vyzLog_ << endl;
1994	>	map<string, RNEMDFluxType>::iterator fi;
1995	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1996	>	if ( (*fi).second == rnemdFluxType_)
1997	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1998		}
1999	+
2000	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2001
2002	<	if (output3DTemp_) {
2003	<	RealType temp;
2004	<	xTempLog_ << time;
2005	<	for (j = 0; j < rnemdLogWidth_; j++) {
2006	<	if (outputVx_)
2007	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2008	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2009	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2010	<	xTempLog_ << "\t" << temp;
2002	>	rnemdFile_ << "#    objectSelection = \""
2003	>	<< rnemdObjectSelection_ << "\";\n";
2004	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2005	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2006	>	rnemdFile_ << "# }\n";
2007	>	rnemdFile_ << "#######################################################\n";
2008	>	rnemdFile_ << "# RNEMD report:\n";
2009	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2010	>	rnemdFile_ << "# Target flux:\n";
2011	>	rnemdFile_ << "#           kinetic = "
2012	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2013	>	<< " (kcal/mol/A^2/fs)\n";
2014	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2015	>	<< " (amu/A/fs^2)\n";
2016	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2017	>	<< " (amu/A^2/fs^2)\n";
2018	>	rnemdFile_ << "# Target one-time exchanges:\n";
2019	>	rnemdFile_ << "#          kinetic = "
2020	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2021	>	<< " (kcal/mol)\n";
2022	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2023	>	<< " (amu*A/fs)\n";
2024	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2025	>	<< " (amu*A^2/fs)\n";
2026	>	rnemdFile_ << "# Actual exchange totals:\n";
2027	>	rnemdFile_ << "#          kinetic = "
2028	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2029	>	<< " (kcal/mol)\n";
2030	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2031	>	<< " (amu*A/fs)\n";
2032	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2033	>	<< " (amu*A^2/fs)\n";
2034	>	rnemdFile_ << "# Actual flux:\n";
2035	>	rnemdFile_ << "#          kinetic = " << Jz
2036	>	<< " (kcal/mol/A^2/fs)\n";
2037	>	rnemdFile_ << "#          momentum = " << JzP
2038	>	<< " (amu/A/fs^2)\n";
2039	>	rnemdFile_ << "#  angular momentum = " << JzL
2040	>	<< " (amu/A^2/fs^2)\n";
2041	>	rnemdFile_ << "# Exchange statistics:\n";
2042	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2043	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2044	>	if (rnemdMethod_ == rnemdNIVS) {
2045	>	rnemdFile_ << "#  NIVS root-check errors = "
2046	>	<< failRootCount_ << "\n";
2047	>	}
2048	>	rnemdFile_ << "#######################################################\n";
2049	>
2050	>
2051	>
2052	>	//write title
2053	>	rnemdFile_ << "#";
2054	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2055	>	if (outputMask_[i]) {
2056	>	rnemdFile_ << "\t" << data_[i].title <<
2057	>	"(" << data_[i].units << ")";
2058	>	// add some extra tabs for column alignment
2059	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2060		}
2061	<	xTempLog_ << endl;
2062	<	yTempLog_ << time;
2063	<	for (j = 0; j < rnemdLogWidth_; j++) {
2064	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
2061	>	}
2062	>	rnemdFile_ << std::endl;
2063	>
2064	>	rnemdFile_.precision(8);
2065	>
2066	>	for (int j = 0; j < nBins_; j++) {
2067	>
2068	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2069	>	if (outputMask_[i]) {
2070	>	if (data_[i].dataType == "RealType")
2071	>	writeReal(i,j);
2072	>	else if (data_[i].dataType == "Vector3d")
2073	>	writeVector(i,j);
2074	>	else {
2075	>	sprintf( painCave.errMsg,
2076	>	"RNEMD found an unknown data type for: %s ",
2077	>	data_[i].title.c_str());
2078	>	painCave.isFatal = 1;
2079	>	simError();
2080	>	}
2081	>	}
2082		}
2083	<	yTempLog_ << endl;
2084	<	zTempLog_ << time;
2085	<	for (j = 0; j < rnemdLogWidth_; j++) {
2086	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
2083	>	rnemdFile_ << std::endl;
2084	>
2085	>	}
2086	>
2087	>	rnemdFile_ << "#######################################################\n";
2088	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2089	>	rnemdFile_ << "#######################################################\n";
2090	>
2091	>
2092	>	for (int j = 0; j < nBins_; j++) {
2093	>	rnemdFile_ << "#";
2094	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2095	>	if (outputMask_[i]) {
2096	>	if (data_[i].dataType == "RealType")
2097	>	writeRealStdDev(i,j);
2098	>	else if (data_[i].dataType == "Vector3d")
2099	>	writeVectorStdDev(i,j);
2100	>	else {
2101	>	sprintf( painCave.errMsg,
2102	>	"RNEMD found an unknown data type for: %s ",
2103	>	data_[i].title.c_str());
2104	>	painCave.isFatal = 1;
2105	>	simError();
2106	>	}
2107	>	}
2108		}
2109	<	zTempLog_ << endl;
2110	<	}
2111	<	if (outputRotTemp_) {
2112	<	rotTempLog_ << time;
2113	<	for (j = 0; j < rnemdLogWidth_; j++) {
2114	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2115	<	}
1628	<	rotTempLog_ << endl;
1629	<	}
1630	<	// James put this in.
1631	<	Mat3x3d hmat = currentSnap_->getHmat();
1632	<	if (outputDen_) {
1633	<	denLog_ << time;
1634	<	for (j = 0; j < rnemdLogWidth_; j++) {
1635	<
1636	<	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1637	<	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1638	<	}
1639	<	denLog_ << endl;
1640	<	}
1641	<	if (outputVz_) {
1642	<	vzzLog_ << time;
1643	<	for (j = 0; j < rnemdLogWidth_; j++) {
1644	<	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1645	<	}
1646	<	vzzLog_ << endl;
1647	<	}
2109	>	rnemdFile_ << std::endl;
2110	>
2111	>	}
2112	>
2113	>	rnemdFile_.flush();
2114	>	rnemdFile_.close();
2115	>
2116		#ifdef IS_MPI
2117		}
2118		#endif
2119	+
2120	+	}
2121	+
2122	+	void RNEMD::writeReal(int index, unsigned int bin) {
2123	+	if (!doRNEMD_) return;
2124	+	assert(index >=0 && index < ENDINDEX);
2125	+	assert(int(bin) < nBins_);
2126	+	RealType s;
2127	+	int count;
2128	+
2129	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2130	+	if (count == 0) return;
2131	+
2132	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2133	+
2134	+	if (! isinf(s) && ! isnan(s)) {
2135	+	rnemdFile_ << "\t" << s;
2136	+	} else{
2137	+	sprintf( painCave.errMsg,
2138	+	"RNEMD detected a numerical error writing: %s for bin %d",
2139	+	data_[index].title.c_str(), bin);
2140	+	painCave.isFatal = 1;
2141	+	simError();
2142	+	}
2143	+	}
2144	+
2145	+	void RNEMD::writeVector(int index, unsigned int bin) {
2146	+	if (!doRNEMD_) return;
2147	+	assert(index >=0 && index < ENDINDEX);
2148	+	assert(int(bin) < nBins_);
2149	+	Vector3d s;
2150	+	int count;
2151	+
2152	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2153	+	if (count == 0) return;
2154
2155	<	for (j = 0; j < rnemdLogWidth_; j++) {
2156	<	mHist_[j] = 0.0;
2155	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2156	>	if (isinf(s[0]) || isnan(s[0]) ||
2157	>	isinf(s[1]) || isnan(s[1]) ||
2158	>	isinf(s[2]) || isnan(s[2]) ) {
2159	>	sprintf( painCave.errMsg,
2160	>	"RNEMD detected a numerical error writing: %s for bin %d",
2161	>	data_[index].title.c_str(), bin);
2162	>	painCave.isFatal = 1;
2163	>	simError();
2164	>	} else {
2165	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2166		}
2167	<	if (outputTemp_)
1656	<	for (j = 0; j < rnemdLogWidth_; j++) {
1657	<	tempCount_[j] = 0;
1658	<	tempHist_[j] = 0.0;
1659	<	}
1660	<	if (outputVx_)
1661	<	for (j = 0; j < rnemdLogWidth_; j++) {
1662	<	//pxzCount_[j] = 0;
1663	<	pxzHist_[j] = 0.0;
1664	<	}
1665	<	if (outputVy_)
1666	<	for (j = 0; j < rnemdLogWidth_; j++) {
1667	<	//pyzCount_[j] = 0;
1668	<	pyzHist_[j] = 0.0;
1669	<	}
2167	>	}
2168
2169	<	if (output3DTemp_)
2170	<	for (j = 0; j < rnemdLogWidth_; j++) {
2171	<	xTempHist_[j] = 0.0;
2172	<	yTempHist_[j] = 0.0;
2173	<	zTempHist_[j] = 0.0;
2174	<	xyzTempCount_[j] = 0;
1677	<	}
1678	<	if (outputRotTemp_)
1679	<	for (j = 0; j < rnemdLogWidth_; j++) {
1680	<	rotTempCount_[j] = 0;
1681	<	rotTempHist_[j] = 0.0;
1682	<	}
1683	<	// James put this in
1684	<	if (outputDen_)
1685	<	for (j = 0; j < rnemdLogWidth_; j++) {
1686	<	//pyzCount_[j] = 0;
1687	<	DenHist_[j] = 0.0;
1688	<	}
1689	<	if (outputVz_)
1690	<	for (j = 0; j < rnemdLogWidth_; j++) {
1691	<	//pyzCount_[j] = 0;
1692	<	pzzHist_[j] = 0.0;
1693	<	}
1694	<	// reset the counter
1695	<
1696	<	Numcount_++;
1697	<	if (Numcount_ > int(runTime_/statusTime_))
1698	<	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1699	<	if (Numcount_ > int(runTime_/statusTime_))
1700	<	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
2169	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2170	>	if (!doRNEMD_) return;
2171	>	assert(index >=0 && index < ENDINDEX);
2172	>	assert(int(bin) < nBins_);
2173	>	RealType s;
2174	>	int count;
2175
2176	<	logFrameCount_ = 0;
2176	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2177	>	if (count == 0) return;
2178	>
2179	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2180	>
2181	>	if (! isinf(s) && ! isnan(s)) {
2182	>	rnemdFile_ << "\t" << s;
2183	>	} else{
2184	>	sprintf( painCave.errMsg,
2185	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2186	>	data_[index].title.c_str(), bin);
2187	>	painCave.isFatal = 1;
2188	>	simError();
2189	>	}
2190		}
2191	+
2192	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2193	+	if (!doRNEMD_) return;
2194	+	assert(index >=0 && index < ENDINDEX);
2195	+	assert(int(bin) < nBins_);
2196	+	Vector3d s;
2197	+	int count;
2198	+
2199	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2200	+	if (count == 0) return;
2201	+
2202	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2203	+	if (isinf(s[0]) || isnan(s[0]) ||
2204	+	isinf(s[1]) || isnan(s[1]) ||
2205	+	isinf(s[2]) || isnan(s[2]) ) {
2206	+	sprintf( painCave.errMsg,
2207	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2208	+	data_[index].title.c_str(), bin);
2209	+	painCave.isFatal = 1;
2210	+	simError();
2211	+	} else {
2212	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2213	+	}
2214	+	}
2215		}
2216

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