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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1728 by jmarr, Wed May 30 16:07:03 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1855 by gezelter, Tue Apr 2 18:31:51 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 "integrators/RNEMD.hpp"
43	>	#include <sstream>
44	>	#include <string>
45	>
46	>	#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48		#include "math/Vector.hpp"
49		#include "math/SquareMatrix3.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;
82	<	Globals * simParams = info->getSimParams();
81	>	Globals* simParams = info->getSimParams();
82	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83
84	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
85	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
77	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
78	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
79	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
80	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
81	<	stringToEnumMap_["Px"] = rnemdPx;
82	<	stringToEnumMap_["Py"] = rnemdPy;
83	<	stringToEnumMap_["Pz"] = rnemdPz;
84	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
85	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
86	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
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	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
112	<	evaluator_.loadScriptString(rnemdObjectSelection_);
93	<	seleMan_.setSelectionSet(evaluator_.evaluate());
111	>	const string methStr = rnemdParams->getMethod();
112	>	bool hasFluxType = rnemdParams->haveFluxType();
113
114	<	// do some sanity checking
114	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115
116	<	int selectionCount = seleMan_.getSelectionCount();
117	<	int nIntegrable = info->getNGlobalIntegrableObjects();
118	<
119	<	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",
109	<	rnemdObjectSelection_.c_str(),
110	<	selectionCount, nIntegrable);
111	<	painCave.isFatal = 0;
112	<	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 = simParams->getRNEMD_exchangeType();
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		}
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	–
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		}
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
348
349	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
350	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
231	<	midBin_ = nBins_ / 2;
232	<	if (simParams->haveRNEMD_binShift()) {
233	<	if (simParams->getRNEMD_binShift()) {
234	<	zShift_ = 0.5 / (RealType)(nBins_);
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351		} else {
352	<	zShift_ = 0.0;
352	>	coordinateOrigin_ = V3Zero;
353		}
238	–	} else {
239	–	zShift_ = 0.0;
240	–	}
241	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
242	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
243	–	//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	–	}*/
252	–	} else {
253	–	set_RNEMD_logWidth(nBins_);
254	–	}
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);
354
355	<	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);
355	>	// do some sanity checking
356
357	<	set_RNEMD_exchange_total(0.0);
274	<	if (simParams->haveRNEMD_targetFlux()) {
275	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
276	<	} else {
277	<	set_RNEMD_target_flux(0.0);
278	<	}
279	<	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_;
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 angularVelocity;
424	>	angularVelocity.units = "angstroms^2/fs";
425	>	angularVelocity.title =  "AngularVelocity";
426	>	angularVelocity.dataType = "Vector3d";
427	>	angularVelocity.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
430	>	data_[ANGULARVELOCITY] = angularVelocity;
431	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
432	>
433	>	OutputData density;
434	>	density.units =  "g cm^-3";
435	>	density.title =  "Density";
436	>	density.dataType = "RealType";
437	>	density.accumulator.reserve(nBins_);
438	>	for (int i = 0; i < nBins_; i++)
439	>	density.accumulator.push_back( new Accumulator() );
440	>	data_[DENSITY] = density;
441	>	outputMap_["DENSITY"] =  DENSITY;
442	>
443	>	if (hasOutputFields) {
444	>	parseOutputFileFormat(rnemdParams->getOutputFields());
445	>	} else {
446	>	if (usePeriodicBoundaryConditions_)
447	>	outputMask_.set(Z);
448	>	else
449	>	outputMask_.set(R);
450	>	switch (rnemdFluxType_) {
451	>	case rnemdKE:
452	>	case rnemdRotKE:
453	>	case rnemdFullKE:
454	>	outputMask_.set(TEMPERATURE);
455	>	break;
456	>	case rnemdPx:
457	>	case rnemdPy:
458	>	outputMask_.set(VELOCITY);
459	>	break;
460	>	case rnemdPz:
461	>	case rnemdPvector:
462	>	outputMask_.set(VELOCITY);
463	>	outputMask_.set(DENSITY);
464	>	break;
465	>	case rnemdLx:
466	>	case rnemdLy:
467	>	case rnemdLz:
468	>	case rnemdLvector:
469	>	outputMask_.set(ANGULARVELOCITY);
470	>	break;
471	>	case rnemdKeLx:
472	>	case rnemdKeLy:
473	>	case rnemdKeLz:
474	>	case rnemdKeLvector:
475	>	outputMask_.set(TEMPERATURE);
476	>	outputMask_.set(ANGULARVELOCITY);
477	>	break;
478	>	case rnemdKePx:
479	>	case rnemdKePy:
480	>	outputMask_.set(TEMPERATURE);
481	>	outputMask_.set(VELOCITY);
482	>	break;
483	>	case rnemdKePvector:
484	>	outputMask_.set(TEMPERATURE);
485	>	outputMask_.set(VELOCITY);
486	>	outputMask_.set(DENSITY);
487	>	break;
488	>	default:
489	>	break;
490	>	}
491	>	}
492	>
493	>	if (hasOutputFileName) {
494	>	rnemdFileName_ = rnemdParams->getOutputFileName();
495	>	} else {
496	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
497	>	}
498	>
499	>	exchangeTime_ = rnemdParams->getExchangeTime();
500	>
501	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
502	>	// total exchange sums are zeroed out at the beginning:
503	>
504	>	kineticExchange_ = 0.0;
505	>	momentumExchange_ = V3Zero;
506	>	angularMomentumExchange_ = V3Zero;
507	>
508	>	std::ostringstream selectionAstream;
509	>	std::ostringstream selectionBstream;
510	>
511	>	if (hasSelectionA_) {
512	>	selectionA_ = rnemdParams->getSelectionA();
513	>	} else {
514	>	if (usePeriodicBoundaryConditions_) {
515	>	Mat3x3d hmat = currentSnap_->getHmat();
516	>
517	>	if (hasSlabWidth)
518	>	slabWidth_ = rnemdParams->getSlabWidth();
519	>	else
520	>	slabWidth_ = hmat(2,2) / 10.0;
521	>
522	>	if (hasSlabACenter)
523	>	slabACenter_ = rnemdParams->getSlabACenter();
524	>	else
525	>	slabACenter_ = 0.0;
526	>
527	>	selectionAstream << "select wrappedz > "
528	>	<< slabACenter_ - 0.5*slabWidth_
529	>	<<  " && wrappedz < "
530	>	<< slabACenter_ + 0.5*slabWidth_;
531	>	selectionA_ = selectionAstream.str();
532	>	} else {
533	>	if (hasSphereARadius)
534	>	sphereARadius_ = rnemdParams->getSphereARadius();
535	>	else {
536	>	// use an initial guess to the size of the inner slab to be 1/10 the
537	>	// radius of an approximately spherical hull:
538	>	Thermo thermo(info);
539	>	RealType hVol = thermo.getHullVolume();
540	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
541	>	}
542	>	selectionAstream << "select r < " << sphereARadius_;
543	>	selectionA_ = selectionAstream.str();
544	>	}
545	>	}
546	>
547	>	if (hasSelectionB_) {
548	>	selectionB_ = rnemdParams->getSelectionB();
549	>	} else {
550	>	if (usePeriodicBoundaryConditions_) {
551	>	Mat3x3d hmat = currentSnap_->getHmat();
552	>
553	>	if (hasSlabWidth)
554	>	slabWidth_ = rnemdParams->getSlabWidth();
555	>	else
556	>	slabWidth_ = hmat(2,2) / 10.0;
557	>
558	>	if (hasSlabBCenter)
559	>	slabBCenter_ = rnemdParams->getSlabACenter();
560	>	else
561	>	slabBCenter_ = hmat(2,2) / 2.0;
562	>
563	>	selectionBstream << "select wrappedz > "
564	>	<< slabBCenter_ - 0.5*slabWidth_
565	>	<<  " && wrappedz < "
566	>	<< slabBCenter_ + 0.5*slabWidth_;
567	>	selectionB_ = selectionBstream.str();
568	>	} else {
569	>	if (hasSphereBRadius_) {
570	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
571	>	selectionBstream << "select r > " << sphereBRadius_;
572	>	selectionB_ = selectionBstream.str();
573	>	} else {
574	>	selectionB_ = "select hull";
575	>	hasSelectionB_ = true;
576	>	}
577	>	}
578	>	}
579	>	}
580	>	// object evaluator:
581	>	evaluator_.loadScriptString(rnemdObjectSelection_);
582	>	seleMan_.setSelectionSet(evaluator_.evaluate());
583	>
584	>	evaluatorA_.loadScriptString(selectionA_);
585	>	evaluatorB_.loadScriptString(selectionB_);
586	>
587	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	>
590	>	commonA_ = seleManA_ & seleMan_;
591	>	commonB_ = seleManB_ & seleMan_;
592		}
593
323	–	RNEMD::~RNEMD() {
324	–	delete randNumGen_;
594
595	+	RNEMD::~RNEMD() {
596	+	if (!doRNEMD_) return;
597		#ifdef IS_MPI
598		if (worldRank == 0) {
599		#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();
600
601	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
602	<	rnemdType_ == rnemdPyScale) {
603	<	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();
601	>	writeOutputFile();
602	>
603	>	rnemdFile_.close();
604
605		#ifdef IS_MPI
606		}
607		#endif
608		}
609	+
610	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
611	+	if (!doRNEMD_) return;
612	+	int selei;
613	+	int selej;
614
366	–	void RNEMD::doSwap() {
367	–
615		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
616		Mat3x3d hmat = currentSnap_->getHmat();
617
371	–	seleMan_.setSelectionSet(evaluator_.evaluate());
372	–
373	–	int selei;
618		StuntDouble* sd;
375	–	int idx;
619
620		RealType min_val;
621		bool min_found = false;
#	Line 382 | Line 625 | namespace OpenMD {
625		bool max_found = false;
626		StuntDouble* max_sd;
627
628	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
629	<	sd = seleMan_.nextSelected(selei)) {
387	<
388	<	idx = sd->getLocalIndex();
628	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
629	>	sd = seleManA_.nextSelected(selei)) {
630
631		Vector3d pos = sd->getPos();
632	<
632	>
633		// wrap the stuntdouble's position back into the box:
634	<
634	>
635		if (usePeriodicBoundaryConditions_)
636		currentSnap_->wrapVector(pos);
637	<
638	<	// which bin is this stuntdouble in?
639	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
640	<
641	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
642	<
643	<
403	<	// if we're in bin 0 or the middleBin
404	<	if (binNo == 0 || binNo == midBin_) {
637	>
638	>	RealType mass = sd->getMass();
639	>	Vector3d vel = sd->getVel();
640	>	RealType value;
641	>
642	>	switch(rnemdFluxType_) {
643	>	case rnemdKE :
644
645	<	RealType mass = sd->getMass();
646	<	Vector3d vel = sd->getVel();
647	<	RealType value;
648	<
649	<	switch(rnemdType_) {
411	<	case rnemdKineticSwap :
645	>	value = mass * vel.lengthSquare();
646	>
647	>	if (sd->isDirectional()) {
648	>	Vector3d angMom = sd->getJ();
649	>	Mat3x3d I = sd->getI();
650
651	<	value = mass * vel.lengthSquare();
652	<
653	<	if (sd->isDirectional()) {
654	<	Vector3d angMom = sd->getJ();
655	<	Mat3x3d I = sd->getI();
656	<
657	<	if (sd->isLinear()) {
658	<	int i = sd->linearAxis();
659	<	int j = (i + 1) % 3;
660	<	int k = (i + 2) % 3;
661	<	value += angMom[j] * angMom[j] / I(j, j) +
662	<	angMom[k] * angMom[k] / I(k, k);
663	<	} else {
664	<	value += angMom[0]*angMom[0]/I(0, 0)
665	<	+ angMom[1]*angMom[1]/I(1, 1)
666	<	+ angMom[2]*angMom[2]/I(2, 2);
667	<	}
668	<	} //angular momenta exchange enabled
669	<	//energyConvert temporarily disabled
670	<	//make exchangeSum_ comparable between swap & scale
671	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
672	<	value *= 0.5;
673	<	break;
674	<	case rnemdPx :
675	<	value = mass * vel[0];
676	<	break;
677	<	case rnemdPy :
678	<	value = mass * vel[1];
679	<	break;
680	<	case rnemdPz :
681	<	value = mass * vel[2];
682	<	break;
683	<	default :
684	<	break;
651	>	if (sd->isLinear()) {
652	>	int i = sd->linearAxis();
653	>	int j = (i + 1) % 3;
654	>	int k = (i + 2) % 3;
655	>	value += angMom[j] * angMom[j] / I(j, j) +
656	>	angMom[k] * angMom[k] / I(k, k);
657	>	} else {
658	>	value += angMom[0]*angMom[0]/I(0, 0)
659	>	+ angMom[1]*angMom[1]/I(1, 1)
660	>	+ angMom[2]*angMom[2]/I(2, 2);
661	>	}
662	>	} //angular momenta exchange enabled
663	>	value *= 0.5;
664	>	break;
665	>	case rnemdPx :
666	>	value = mass * vel[0];
667	>	break;
668	>	case rnemdPy :
669	>	value = mass * vel[1];
670	>	break;
671	>	case rnemdPz :
672	>	value = mass * vel[2];
673	>	break;
674	>	default :
675	>	break;
676	>	}
677	>	if (!max_found) {
678	>	max_val = value;
679	>	max_sd = sd;
680	>	max_found = true;
681	>	} else {
682	>	if (max_val < value) {
683	>	max_val = value;
684	>	max_sd = sd;
685		}
686	+	}
687	+	}
688
689	<	if (binNo == 0) {
690	<	if (!min_found) {
691	<	min_val = value;
692	<	min_sd = sd;
693	<	min_found = true;
694	<	} else {
695	<	if (min_val > value) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	}
699	<	}
700	<	} else { //midBin_
701	<	if (!max_found) {
702	<	max_val = value;
703	<	max_sd = sd;
704	<	max_found = true;
705	<	} else {
706	<	if (max_val < value) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	}
710	<	}
711	<	}
689	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
690	>	sd = seleManB_.nextSelected(selej)) {
691	>
692	>	Vector3d pos = sd->getPos();
693	>
694	>	// wrap the stuntdouble's position back into the box:
695	>
696	>	if (usePeriodicBoundaryConditions_)
697	>	currentSnap_->wrapVector(pos);
698	>
699	>	RealType mass = sd->getMass();
700	>	Vector3d vel = sd->getVel();
701	>	RealType value;
702	>
703	>	switch(rnemdFluxType_) {
704	>	case rnemdKE :
705	>
706	>	value = mass * vel.lengthSquare();
707	>
708	>	if (sd->isDirectional()) {
709	>	Vector3d angMom = sd->getJ();
710	>	Mat3x3d I = sd->getI();
711	>
712	>	if (sd->isLinear()) {
713	>	int i = sd->linearAxis();
714	>	int j = (i + 1) % 3;
715	>	int k = (i + 2) % 3;
716	>	value += angMom[j] * angMom[j] / I(j, j) +
717	>	angMom[k] * angMom[k] / I(k, k);
718	>	} else {
719	>	value += angMom[0]*angMom[0]/I(0, 0)
720	>	+ angMom[1]*angMom[1]/I(1, 1)
721	>	+ angMom[2]*angMom[2]/I(2, 2);
722	>	}
723	>	} //angular momenta exchange enabled
724	>	value *= 0.5;
725	>	break;
726	>	case rnemdPx :
727	>	value = mass * vel[0];
728	>	break;
729	>	case rnemdPy :
730	>	value = mass * vel[1];
731	>	break;
732	>	case rnemdPz :
733	>	value = mass * vel[2];
734	>	break;
735	>	default :
736	>	break;
737		}
738	+
739	+	if (!min_found) {
740	+	min_val = value;
741	+	min_sd = sd;
742	+	min_found = true;
743	+	} else {
744	+	if (min_val > value) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	}
748	+	}
749		}
750	<
751	<	#ifdef IS_MPI
752	<	int nProc, worldRank;
753	<
478	<	nProc = MPI::COMM_WORLD.Get_size();
479	<	worldRank = MPI::COMM_WORLD.Get_rank();
480	<
750	>
751	>	#ifdef IS_MPI
752	>	int worldRank = MPI::COMM_WORLD.Get_rank();
753	>
754		bool my_min_found = min_found;
755		bool my_max_found = max_found;
756
#	Line 532 | Line 805 | namespace OpenMD {
805		Vector3d max_vel = max_sd->getVel();
806		RealType temp_vel;
807
808	<	switch(rnemdType_) {
809	<	case rnemdKineticSwap :
808	>	switch(rnemdFluxType_) {
809	>	case rnemdKE :
810		min_sd->setVel(max_vel);
811		max_sd->setVel(min_vel);
812		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 584 | Line 857 | namespace OpenMD {
857		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
858		min_vals.rank, 0, status);
859
860	<	switch(rnemdType_) {
861	<	case rnemdKineticSwap :
860	>	switch(rnemdFluxType_) {
861	>	case rnemdKE :
862		max_sd->setVel(min_vel);
863		//angular momenta exchange enabled
864		if (max_sd->isDirectional()) {
#	Line 630 | Line 903 | namespace OpenMD {
903		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
904		max_vals.rank, 0, status);
905
906	<	switch(rnemdType_) {
907	<	case rnemdKineticSwap :
906	>	switch(rnemdFluxType_) {
907	>	case rnemdKE :
908		min_sd->setVel(max_vel);
909		//angular momenta exchange enabled
910		if (min_sd->isDirectional()) {
#	Line 665 | Line 938 | namespace OpenMD {
938		}
939		}
940		#endif
941	<	exchangeSum_ += max_val - min_val;
941	>
942	>	switch(rnemdFluxType_) {
943	>	case rnemdKE:
944	>	kineticExchange_ += max_val - min_val;
945	>	break;
946	>	case rnemdPx:
947	>	momentumExchange_.x() += max_val - min_val;
948	>	break;
949	>	case rnemdPy:
950	>	momentumExchange_.y() += max_val - min_val;
951	>	break;
952	>	case rnemdPz:
953	>	momentumExchange_.z() += max_val - min_val;
954	>	break;
955	>	default:
956	>	break;
957	>	}
958		} else {
959		sprintf(painCave.errMsg,
960	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
960	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
961		painCave.isFatal = 0;
962		painCave.severity = OPENMD_INFO;
963		simError();
#	Line 676 | Line 965 | namespace OpenMD {
965		}
966		} else {
967		sprintf(painCave.errMsg,
968	<	"RNEMD: exchange NOT performed because selected object\n"
969	<	"\tnot present in at least one of the two slabs.\n");
968	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
969	>	"\twas not present in at least one of the two slabs.\n");
970		painCave.isFatal = 0;
971		painCave.severity = OPENMD_INFO;
972		simError();
973		failTrialCount_++;
974	<	}
686	<
974	>	}
975		}
976
977	<	void RNEMD::doScale() {
977	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
978	>	if (!doRNEMD_) return;
979	>	int selei;
980	>	int selej;
981
982		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
983	+	RealType time = currentSnap_->getTime();
984		Mat3x3d hmat = currentSnap_->getHmat();
985
694	–	seleMan_.setSelectionSet(evaluator_.evaluate());
695	–
696	–	int selei;
986		StuntDouble* sd;
698	–	int idx;
987
988		vector<StuntDouble*> hotBin, coldBin;
989
#	Line 714 | Line 1002 | namespace OpenMD {
1002		RealType Kcz = 0.0;
1003		RealType Kcw = 0.0;
1004
1005	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1006	<	sd = seleMan_.nextSelected(selei)) {
1005	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1006	>	sd = smanA.nextSelected(selei)) {
1007
720	–	idx = sd->getLocalIndex();
721	–
1008		Vector3d pos = sd->getPos();
1009	<
1009	>
1010		// wrap the stuntdouble's position back into the box:
1011	<
1011	>
1012		if (usePeriodicBoundaryConditions_)
1013		currentSnap_->wrapVector(pos);
1014	+
1015	+
1016	+	RealType mass = sd->getMass();
1017	+	Vector3d vel = sd->getVel();
1018	+
1019	+	hotBin.push_back(sd);
1020	+	Phx += mass * vel.x();
1021	+	Phy += mass * vel.y();
1022	+	Phz += mass * vel.z();
1023	+	Khx += mass * vel.x() * vel.x();
1024	+	Khy += mass * vel.y() * vel.y();
1025	+	Khz += mass * vel.z() * vel.z();
1026	+	if (sd->isDirectional()) {
1027	+	Vector3d angMom = sd->getJ();
1028	+	Mat3x3d I = sd->getI();
1029	+	if (sd->isLinear()) {
1030	+	int i = sd->linearAxis();
1031	+	int j = (i + 1) % 3;
1032	+	int k = (i + 2) % 3;
1033	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1034	+	angMom[k] * angMom[k] / I(k, k);
1035	+	} else {
1036	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1037	+	+ angMom[1]*angMom[1]/I(1, 1)
1038	+	+ angMom[2]*angMom[2]/I(2, 2);
1039	+	}
1040	+	}
1041	+	}
1042	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1043	+	sd = smanB.nextSelected(selej)) {
1044	+	Vector3d pos = sd->getPos();
1045	+
1046	+	// wrap the stuntdouble's position back into the box:
1047	+
1048	+	if (usePeriodicBoundaryConditions_)
1049	+	currentSnap_->wrapVector(pos);
1050	+
1051	+	RealType mass = sd->getMass();
1052	+	Vector3d vel = sd->getVel();
1053
1054	<	// which bin is this stuntdouble in?
1055	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1056	<
1057	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1058	<
1059	<	// if we're in bin 0 or the middleBin
1060	<	if (binNo == 0 || binNo == midBin_) {
1061	<
1062	<	RealType mass = sd->getMass();
1063	<	Vector3d vel = sd->getVel();
1064	<
1065	<	if (binNo == 0) {
1066	<	hotBin.push_back(sd);
1067	<	Phx += mass * vel.x();
1068	<	Phy += mass * vel.y();
1069	<	Phz += mass * vel.z();
1070	<	Khx += mass * vel.x() * vel.x();
1071	<	Khy += mass * vel.y() * vel.y();
1072	<	Khz += mass * vel.z() * vel.z();
1073	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1074	<	if (sd->isDirectional()) {
750	<	Vector3d angMom = sd->getJ();
751	<	Mat3x3d I = sd->getI();
752	<	if (sd->isLinear()) {
753	<	int i = sd->linearAxis();
754	<	int j = (i + 1) % 3;
755	<	int k = (i + 2) % 3;
756	<	Khw += angMom[j] * angMom[j] / I(j, j) +
757	<	angMom[k] * angMom[k] / I(k, k);
758	<	} else {
759	<	Khw += angMom[0]*angMom[0]/I(0, 0)
760	<	+ angMom[1]*angMom[1]/I(1, 1)
761	<	+ angMom[2]*angMom[2]/I(2, 2);
762	<	}
763	<	}
764	<	//}
765	<	} else { //midBin_
766	<	coldBin.push_back(sd);
767	<	Pcx += mass * vel.x();
768	<	Pcy += mass * vel.y();
769	<	Pcz += mass * vel.z();
770	<	Kcx += mass * vel.x() * vel.x();
771	<	Kcy += mass * vel.y() * vel.y();
772	<	Kcz += mass * vel.z() * vel.z();
773	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
774	<	if (sd->isDirectional()) {
775	<	Vector3d angMom = sd->getJ();
776	<	Mat3x3d I = sd->getI();
777	<	if (sd->isLinear()) {
778	<	int i = sd->linearAxis();
779	<	int j = (i + 1) % 3;
780	<	int k = (i + 2) % 3;
781	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
782	<	angMom[k] * angMom[k] / I(k, k);
783	<	} else {
784	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
785	<	+ angMom[1]*angMom[1]/I(1, 1)
786	<	+ angMom[2]*angMom[2]/I(2, 2);
787	<	}
788	<	}
789	<	//}
790	<	}
1054	>	coldBin.push_back(sd);
1055	>	Pcx += mass * vel.x();
1056	>	Pcy += mass * vel.y();
1057	>	Pcz += mass * vel.z();
1058	>	Kcx += mass * vel.x() * vel.x();
1059	>	Kcy += mass * vel.y() * vel.y();
1060	>	Kcz += mass * vel.z() * vel.z();
1061	>	if (sd->isDirectional()) {
1062	>	Vector3d angMom = sd->getJ();
1063	>	Mat3x3d I = sd->getI();
1064	>	if (sd->isLinear()) {
1065	>	int i = sd->linearAxis();
1066	>	int j = (i + 1) % 3;
1067	>	int k = (i + 2) % 3;
1068	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1069	>	angMom[k] * angMom[k] / I(k, k);
1070	>	} else {
1071	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1072	>	+ angMom[1]*angMom[1]/I(1, 1)
1073	>	+ angMom[2]*angMom[2]/I(2, 2);
1074	>	}
1075		}
1076		}
1077
#	Line 800 | Line 1084 | namespace OpenMD {
1084		Kcz *= 0.5;
1085		Kcw *= 0.5;
1086
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	–
1087		#ifdef IS_MPI
1088		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1089		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 831 | Line 1109 | namespace OpenMD {
1109		RealType pz = Pcz / Phz;
1110		RealType c, x, y, z;
1111		bool successfulScale = false;
1112	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1113	<	(rnemdType_ == rnemdKineticScaleAM)) {
1112	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1113	>	(rnemdFluxType_ == rnemdRotKE)) {
1114		//may need sanity check Khw & Kcw > 0
1115
1116	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1117	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1116	>	if (rnemdFluxType_ == rnemdFullKE) {
1117	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1118		} else {
1119	<	c = 1.0 - targetFlux_ / Kcw;
1119	>	c = 1.0 - kineticTarget_ / Kcw;
1120		}
1121
1122		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1123		c = sqrt(c);
1124	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
847	<	//now convert to hotBin coefficient
1124	>
1125		RealType w = 0.0;
1126	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1126	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1127		x = 1.0 + px * (1.0 - c);
1128		y = 1.0 + py * (1.0 - c);
1129		z = 1.0 + pz * (1.0 - c);
#	Line 860 | Line 1137 | namespace OpenMD {
1137		*/
1138		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1139		(fabs(z - 1.0) < 0.1)) {
1140	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1140	>	w = 1.0 + (kineticTarget_
1141	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1142		+ Khz * (1.0 - z * z)) / Khw;
1143		}//no need to calculate w if x, y or z is out of range
1144		} else {
1145	<	w = 1.0 + targetFlux_ / Khw;
1145	>	w = 1.0 + kineticTarget_ / Khw;
1146		}
1147		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1148		//if w is in the right range, so should be x, y, z.
1149		vector<StuntDouble*>::iterator sdi;
1150		Vector3d vel;
1151		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1152	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1152	>	if (rnemdFluxType_ == rnemdFullKE) {
1153		vel = (*sdi)->getVel() * c;
876	–	//vel.x() *= c;
877	–	//vel.y() *= c;
878	–	//vel.z() *= c;
1154		(*sdi)->setVel(vel);
1155		}
1156		if ((*sdi)->isDirectional()) {
1157		Vector3d angMom = (*sdi)->getJ() * c;
883	–	//angMom[0] *= c;
884	–	//angMom[1] *= c;
885	–	//angMom[2] *= c;
1158		(*sdi)->setJ(angMom);
1159		}
1160		}
1161		w = sqrt(w);
890	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
891	–	<< "\twh= " << w << endl;
1162		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1163	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1163	>	if (rnemdFluxType_ == rnemdFullKE) {
1164		vel = (*sdi)->getVel();
1165		vel.x() *= x;
1166		vel.y() *= y;
#	Line 899 | Line 1169 | namespace OpenMD {
1169		}
1170		if ((*sdi)->isDirectional()) {
1171		Vector3d angMom = (*sdi)->getJ() * w;
902	–	//angMom[0] *= w;
903	–	//angMom[1] *= w;
904	–	//angMom[2] *= w;
1172		(*sdi)->setJ(angMom);
1173		}
1174		}
1175		successfulScale = true;
1176	<	exchangeSum_ += targetFlux_;
1176	>	kineticExchange_ += kineticTarget_;
1177		}
1178		}
1179		} else {
1180		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1181	<	switch(rnemdType_) {
1182	<	case rnemdKineticScale :
1181	>	switch(rnemdFluxType_) {
1182	>	case rnemdKE :
1183		/* used hotBin coeff's & only scale x & y dimensions
1184		RealType px = Phx / Pcx;
1185		RealType py = Phy / Pcy;
1186		a110 = Khy;
1187	<	c0 = - Khx - Khy - targetFlux_;
1187	>	c0 = - Khx - Khy - kineticTarget_;
1188		a000 = Khx;
1189		a111 = Kcy * py * py;
1190		b11 = -2.0 * Kcy * py * (1.0 + py);
1191	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1191	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1192		b01 = -2.0 * Kcx * px * (1.0 + px);
1193		a001 = Kcx * px * px;
1194		*/
1195		//scale all three dimensions, let c_x = c_y
1196		a000 = Kcx + Kcy;
1197		a110 = Kcz;
1198	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1198	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1199		a001 = Khx * px * px + Khy * py * py;
1200		a111 = Khz * pz * pz;
1201		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1202		b11 = -2.0 * Khz * pz * (1.0 + pz);
1203		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1204	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1204	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1205		break;
1206	<	case rnemdPxScale :
1207	<	c = 1 - targetFlux_ / Pcx;
1206	>	case rnemdPx :
1207	>	c = 1 - momentumTarget_.x() / Pcx;
1208		a000 = Kcy;
1209		a110 = Kcz;
1210		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 948 | Line 1215 | namespace OpenMD {
1215		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1216		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1217		break;
1218	<	case rnemdPyScale :
1219	<	c = 1 - targetFlux_ / Pcy;
1218	>	case rnemdPy :
1219	>	c = 1 - momentumTarget_.y() / Pcy;
1220		a000 = Kcx;
1221		a110 = Kcz;
1222		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 960 | Line 1227 | namespace OpenMD {
1227		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1228		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1229		break;
1230	<	case rnemdPzScale ://we don't really do this, do we?
1231	<	c = 1 - targetFlux_ / Pcz;
1230	>	case rnemdPz ://we don't really do this, do we?
1231	>	c = 1 - momentumTarget_.z() / Pcz;
1232		a000 = Kcx;
1233		a110 = Kcy;
1234		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1046 | Line 1313 | namespace OpenMD {
1313		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1314		r1 = (*rpi).first;
1315		r2 = (*rpi).second;
1316	<	switch(rnemdType_) {
1317	<	case rnemdKineticScale :
1316	>	switch(rnemdFluxType_) {
1317	>	case rnemdKE :
1318		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1319		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1320		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1321		break;
1322	<	case rnemdPxScale :
1322	>	case rnemdPx :
1323		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1324		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1325		break;
1326	<	case rnemdPyScale :
1326	>	case rnemdPy :
1327		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1328		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1329		break;
1330	<	case rnemdPzScale :
1330	>	case rnemdPz :
1331		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1332		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1333		default :
#	Line 1074 | Line 1341 | namespace OpenMD {
1341		#ifdef IS_MPI
1342		if (worldRank == 0) {
1343		#endif
1344	<	sprintf(painCave.errMsg,
1345	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1346	<	bestPair.first, bestPair.second);
1347	<	painCave.isFatal = 0;
1348	<	painCave.severity = OPENMD_INFO;
1349	<	simError();
1344	>	// sprintf(painCave.errMsg,
1345	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1346	>	//         bestPair.first, bestPair.second);
1347	>	// painCave.isFatal = 0;
1348	>	// painCave.severity = OPENMD_INFO;
1349	>	// simError();
1350		#ifdef IS_MPI
1351		}
1352		#endif
1353
1354	<	switch(rnemdType_) {
1355	<	case rnemdKineticScale :
1354	>	switch(rnemdFluxType_) {
1355	>	case rnemdKE :
1356		x = bestPair.first;
1357		y = bestPair.first;
1358		z = bestPair.second;
1359		break;
1360	<	case rnemdPxScale :
1360	>	case rnemdPx :
1361		x = c;
1362		y = bestPair.first;
1363		z = bestPair.second;
1364		break;
1365	<	case rnemdPyScale :
1365	>	case rnemdPy :
1366		x = bestPair.first;
1367		y = c;
1368		z = bestPair.second;
1369		break;
1370	<	case rnemdPzScale :
1370	>	case rnemdPz :
1371		x = bestPair.first;
1372		y = bestPair.second;
1373		z = c;
#	Line 1129 | Line 1396 | namespace OpenMD {
1396		(*sdi)->setVel(vel);
1397		}
1398		successfulScale = true;
1399	<	exchangeSum_ += targetFlux_;
1399	>	switch(rnemdFluxType_) {
1400	>	case rnemdKE :
1401	>	kineticExchange_ += kineticTarget_;
1402	>	break;
1403	>	case rnemdPx :
1404	>	case rnemdPy :
1405	>	case rnemdPz :
1406	>	momentumExchange_ += momentumTarget_;
1407	>	break;
1408	>	default :
1409	>	break;
1410	>	}
1411		}
1412		}
1413		if (successfulScale != true) {
1414		sprintf(painCave.errMsg,
1415	<	"RNEMD: exchange NOT performed!\n");
1415	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1416	>	"\tthe constraint equations may not exist or there may be\n"
1417	>	"\tno selected objects in one or both slabs.\n");
1418		painCave.isFatal = 0;
1419		painCave.severity = OPENMD_INFO;
1420		simError();
1421		failTrialCount_++;
1422		}
1423		}
1424	+
1425	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1426	+	if (!doRNEMD_) return;
1427	+	int selei;
1428	+	int selej;
1429
1145	–	void RNEMD::doShiftScale() {
1146	–
1430		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1431		RealType time = currentSnap_->getTime();
1432		Mat3x3d hmat = currentSnap_->getHmat();
1433
1151	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1152	–
1153	–	int selei;
1434		StuntDouble* sd;
1155	–	int idx;
1435
1436		vector<StuntDouble*> hotBin, coldBin;
1437
1438		Vector3d Ph(V3Zero);
1439	+	Vector3d Lh(V3Zero);
1440		RealType Mh = 0.0;
1441	+	Mat3x3d Ih(0.0);
1442		RealType Kh = 0.0;
1443		Vector3d Pc(V3Zero);
1444	+	Vector3d Lc(V3Zero);
1445		RealType Mc = 0.0;
1446	+	Mat3x3d Ic(0.0);
1447		RealType Kc = 0.0;
1448
1449	<
1450	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1168	<	sd = seleMan_.nextSelected(selei)) {
1169	<
1170	<	idx = sd->getLocalIndex();
1449	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1450	>	sd = smanA.nextSelected(selei)) {
1451
1452		Vector3d pos = sd->getPos();
1453
1454		// wrap the stuntdouble's position back into the box:
1455	+
1456	+	if (usePeriodicBoundaryConditions_)
1457	+	currentSnap_->wrapVector(pos);
1458	+
1459	+	RealType mass = sd->getMass();
1460	+	Vector3d vel = sd->getVel();
1461	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1462	+	RealType r2;
1463	+
1464	+	hotBin.push_back(sd);
1465	+	Ph += mass * vel;
1466	+	Mh += mass;
1467	+	Kh += mass * vel.lengthSquare();
1468	+	Lh += mass * cross(rPos, vel);
1469	+	Ih -= outProduct(rPos, rPos) * mass;
1470	+	r2 = rPos.lengthSquare();
1471	+	Ih(0, 0) += mass * r2;
1472	+	Ih(1, 1) += mass * r2;
1473	+	Ih(2, 2) += mass * r2;
1474	+
1475	+	if (rnemdFluxType_ == rnemdFullKE) {
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	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1484	+	angMom[k] * angMom[k] / I(k, k);
1485	+	} else {
1486	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1487	+	angMom[1] * angMom[1] / I(1, 1) +
1488	+	angMom[2] * angMom[2] / I(2, 2);
1489	+	}
1490	+	}
1491	+	}
1492	+	}
1493	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1494	+	sd = smanB.nextSelected(selej)) {
1495
1496	+	Vector3d pos = sd->getPos();
1497	+
1498	+	// wrap the stuntdouble's position back into the box:
1499	+
1500		if (usePeriodicBoundaryConditions_)
1501		currentSnap_->wrapVector(pos);
1502	+
1503	+	RealType mass = sd->getMass();
1504	+	Vector3d vel = sd->getVel();
1505	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1506	+	RealType r2;
1507
1508	<	// which bin is this stuntdouble in?
1509	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1510	<
1511	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1512	<
1513	<	// if we're in bin 0 or the middleBin
1514	<	if (binNo == 0 || binNo == midBin_) {
1515	<
1516	<	RealType mass = sd->getMass();
1517	<	Vector3d vel = sd->getVel();
1518	<
1519	<	if (binNo == 0) {
1520	<	hotBin.push_back(sd);
1521	<	//std::cerr << "before, velocity = " << vel << endl;
1522	<	Ph += mass * vel;
1523	<	//std::cerr << "after, velocity = " << vel << endl;
1524	<	Mh += mass;
1525	<	Kh += mass * vel.lengthSquare();
1526	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1527	<	if (sd->isDirectional()) {
1528	<	Vector3d angMom = sd->getJ();
1529	<	Mat3x3d I = sd->getI();
1530	<	if (sd->isLinear()) {
1531	<	int i = sd->linearAxis();
1532	<	int j = (i + 1) % 3;
1533	<	int k = (i + 2) % 3;
1534	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1206	<	angMom[k] * angMom[k] / I(k, k);
1207	<	} else {
1208	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1209	<	angMom[1] * angMom[1] / I(1, 1) +
1210	<	angMom[2] * angMom[2] / I(2, 2);
1211	<	}
1212	<	}
1213	<	}
1214	<	} else { //midBin_
1215	<	coldBin.push_back(sd);
1216	<	Pc += mass * vel;
1217	<	Mc += mass;
1218	<	Kc += mass * vel.lengthSquare();
1219	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1220	<	if (sd->isDirectional()) {
1221	<	Vector3d angMom = sd->getJ();
1222	<	Mat3x3d I = sd->getI();
1223	<	if (sd->isLinear()) {
1224	<	int i = sd->linearAxis();
1225	<	int j = (i + 1) % 3;
1226	<	int k = (i + 2) % 3;
1227	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1228	<	angMom[k] * angMom[k] / I(k, k);
1229	<	} else {
1230	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1231	<	angMom[1] * angMom[1] / I(1, 1) +
1232	<	angMom[2] * angMom[2] / I(2, 2);
1233	<	}
1234	<	}
1235	<	}
1236	<	}
1508	>	coldBin.push_back(sd);
1509	>	Pc += mass * vel;
1510	>	Mc += mass;
1511	>	Kc += mass * vel.lengthSquare();
1512	>	Lc += mass * cross(rPos, vel);
1513	>	Ic -= outProduct(rPos, rPos) * mass;
1514	>	r2 = rPos.lengthSquare();
1515	>	Ic(0, 0) += mass * r2;
1516	>	Ic(1, 1) += mass * r2;
1517	>	Ic(2, 2) += mass * r2;
1518	>
1519	>	if (rnemdFluxType_ == rnemdFullKE) {
1520	>	if (sd->isDirectional()) {
1521	>	Vector3d angMom = sd->getJ();
1522	>	Mat3x3d I = sd->getI();
1523	>	if (sd->isLinear()) {
1524	>	int i = sd->linearAxis();
1525	>	int j = (i + 1) % 3;
1526	>	int k = (i + 2) % 3;
1527	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1528	>	angMom[k] * angMom[k] / I(k, k);
1529	>	} else {
1530	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1531	>	angMom[1] * angMom[1] / I(1, 1) +
1532	>	angMom[2] * angMom[2] / I(2, 2);
1533	>	}
1534	>	}
1535		}
1536		}
1537
1538		Kh *= 0.5;
1539		Kc *= 0.5;
1242	–
1243	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1244	–	//        << "\tKc= " << Kc << endl;
1245	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1540
1541		#ifdef IS_MPI
1542		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1543		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1544	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1545	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1546		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1547		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1548		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1549		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1550	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1551	+	MPI::REALTYPE, MPI::SUM);
1552	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1553	+	MPI::REALTYPE, MPI::SUM);
1554		#endif
1555	<
1555	>
1556		bool successfulExchange = false;
1557		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1558		Vector3d vc = Pc / Mc;
1559	<	Vector3d ac = njzp_ / Mc + vc;
1560	<	Vector3d acrec = njzp_ / Mc;
1561	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1559	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1560	>	Vector3d acrec = -momentumTarget_ / Mc;
1561	>
1562	>	// We now need the inverse of the inertia tensor to calculate the
1563	>	// angular velocity of the cold slab;
1564	>	Mat3x3d Ici = Ic.inverse();
1565	>	Vector3d omegac = Ici * Lc;
1566	>	Vector3d bc  = -(Ici * angularMomentumTarget_) + omegac;
1567	>	Vector3d bcrec = bc - omegac;
1568	>
1569	>	RealType cNumerator = Kc - kineticTarget_
1570	>	- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc));
1571		if (cNumerator > 0.0) {
1572	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1572	>
1573	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare()
1574	>	- 0.5*(dot(omegac, Ic * omegac));
1575	>
1576		if (cDenominator > 0.0) {
1577		RealType c = sqrt(cNumerator / cDenominator);
1578		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1579	+
1580		Vector3d vh = Ph / Mh;
1581	<	Vector3d ah = jzp_ / Mh + vh;
1582	<	Vector3d ahrec = jzp_ / Mh;
1583	<	RealType hNumerator = Kh + targetJzKE_
1584	<	- 0.5 * Mh * ah.lengthSquare();
1585	<	if (hNumerator > 0.0) {
1586	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1581	>	Vector3d ah = momentumTarget_ / Mh + vh;
1582	>	Vector3d ahrec = momentumTarget_ / Mh;
1583	>
1584	>	// We now need the inverse of the inertia tensor to
1585	>	// calculate the angular velocity of the hot slab;
1586	>	Mat3x3d Ihi = Ih.inverse();
1587	>	Vector3d omegah = Ihi * Lh;
1588	>	Vector3d bh  = (Ihi * angularMomentumTarget_) + omegah;
1589	>	Vector3d bhrec = bh - omegah;
1590	>
1591	>	RealType hNumerator = Kh + kineticTarget_
1592	>	- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));;
1593	>	if (hNumerator > 0.0) {
1594	>
1595	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare()
1596	>	- 0.5*(dot(omegah, Ih * omegah));
1597	>
1598		if (hDenominator > 0.0) {
1599		RealType h = sqrt(hNumerator / hDenominator);
1600		if ((h > 0.9) && (h < 1.1)) {
1601	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1278	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1601	>
1602		vector<StuntDouble*>::iterator sdi;
1603		Vector3d vel;
1604	+	Vector3d rPos;
1605	+
1606		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1607		//vel = (*sdi)->getVel();
1608	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1608	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1609	>	vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c
1610	>	+ ac + cross(bc, rPos);
1611		(*sdi)->setVel(vel);
1612	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1612	>	if (rnemdFluxType_ == rnemdFullKE) {
1613		if ((*sdi)->isDirectional()) {
1614		Vector3d angMom = (*sdi)->getJ() * c;
1615		(*sdi)->setJ(angMom);
#	Line 1291 | Line 1618 | namespace OpenMD {
1618		}
1619		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1620		//vel = (*sdi)->getVel();
1621	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1621	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1622	>	vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1623	>	+ ah + cross(bh, rPos);
1624	>	cerr << "setting vel to " << vel << "\n";
1625		(*sdi)->setVel(vel);
1626	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1626	>	if (rnemdFluxType_ == rnemdFullKE) {
1627		if ((*sdi)->isDirectional()) {
1628		Vector3d angMom = (*sdi)->getJ() * h;
1629		(*sdi)->setJ(angMom);
#	Line 1301 | Line 1631 | namespace OpenMD {
1631		}
1632		}
1633		successfulExchange = true;
1634	<	exchangeSum_ += targetFlux_;
1635	<	// this is a redundant variable for doShiftScale() so that
1636	<	// 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	<	}
1634	>	kineticExchange_ += kineticTarget_;
1635	>	momentumExchange_ += momentumTarget_;
1636	>	angularMomentumExchange_ += angularMomentumTarget_;
1637		}
1638		}
1639		}
#	Line 1324 | Line 1642 | namespace OpenMD {
1642		}
1643		}
1644		if (successfulExchange != true) {
1645	<	//   sprintf(painCave.errMsg,
1646	<	//              "RNEMD: exchange NOT performed!\n");
1647	<	//   painCave.isFatal = 0;
1648	<	//   painCave.severity = OPENMD_INFO;
1649	<	//   simError();
1645	>	sprintf(painCave.errMsg,
1646	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1647	>	"\tthe constraint equations may not exist or there may be\n"
1648	>	"\tno selected objects in one or both slabs.\n");
1649	>	painCave.isFatal = 0;
1650	>	painCave.severity = OPENMD_INFO;
1651	>	simError();
1652		failTrialCount_++;
1653		}
1654		}
1655
1656	+	RealType RNEMD::getDividingArea() {
1657	+
1658	+	if (hasDividingArea_) return dividingArea_;
1659	+
1660	+	RealType areaA, areaB;
1661	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1662	+
1663	+	if (hasSelectionA_) {
1664	+	int isd;
1665	+	StuntDouble* sd;
1666	+	vector<StuntDouble*> aSites;
1667	+	ConvexHull* surfaceMeshA = new ConvexHull();
1668	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1669	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1670	+	sd = seleManA_.nextSelected(isd)) {
1671	+	aSites.push_back(sd);
1672	+	}
1673	+	surfaceMeshA->computeHull(aSites);
1674	+	areaA = surfaceMeshA->getArea();
1675	+	} else {
1676	+	if (usePeriodicBoundaryConditions_) {
1677	+	// in periodic boundaries, the surface area is twice the x-y
1678	+	// area of the current box:
1679	+	areaA = 2.0 * snap->getXYarea();
1680	+	} else {
1681	+	// in non-periodic simulations, without explicitly setting
1682	+	// selections, the sphere radius sets the surface area of the
1683	+	// dividing surface:
1684	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1685	+	}
1686	+	}
1687	+
1688	+	if (hasSelectionB_) {
1689	+	int isd;
1690	+	StuntDouble* sd;
1691	+	vector<StuntDouble*> bSites;
1692	+	ConvexHull* surfaceMeshB = new ConvexHull();
1693	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1694	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1695	+	sd = seleManB_.nextSelected(isd)) {
1696	+	bSites.push_back(sd);
1697	+	}
1698	+	surfaceMeshB->computeHull(bSites);
1699	+	areaB = surfaceMeshB->getArea();
1700	+	} else {
1701	+	if (usePeriodicBoundaryConditions_) {
1702	+	// in periodic boundaries, the surface area is twice the x-y
1703	+	// area of the current box:
1704	+	areaB = 2.0 * snap->getXYarea();
1705	+	} else {
1706	+	// in non-periodic simulations, without explicitly setting
1707	+	// selections, but if a sphereBradius has been set, just use that:
1708	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1709	+	}
1710	+	}
1711	+
1712	+	dividingArea_ = min(areaA, areaB);
1713	+	hasDividingArea_ = true;
1714	+	return dividingArea_;
1715	+	}
1716	+
1717		void RNEMD::doRNEMD() {
1718	+	if (!doRNEMD_) return;
1719	+	trialCount_++;
1720
1721	<	switch(rnemdType_) {
1722	<	case rnemdKineticScale :
1723	<	case rnemdKineticScaleVAM :
1724	<	case rnemdKineticScaleAM :
1725	<	case rnemdPxScale :
1726	<	case rnemdPyScale :
1727	<	case rnemdPzScale :
1728	<	doScale();
1721	>	cerr << "trialCount = " << trialCount_ << "\n";
1722	>	// object evaluator:
1723	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1724	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1725	>
1726	>	evaluatorA_.loadScriptString(selectionA_);
1727	>	evaluatorB_.loadScriptString(selectionB_);
1728	>
1729	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1730	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1731	>
1732	>	commonA_ = seleManA_ & seleMan_;
1733	>	commonB_ = seleManB_ & seleMan_;
1734	>
1735	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1736	>	// dt = exchange time interval
1737	>	// flux = target flux
1738	>	// dividingArea = smallest dividing surface between the two regions
1739	>
1740	>	hasDividingArea_ = false;
1741	>	RealType area = getDividingArea();
1742	>
1743	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1744	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1745	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1746	>
1747	>	switch(rnemdMethod_) {
1748	>	case rnemdSwap:
1749	>	doSwap(commonA_, commonB_);
1750		break;
1751	<	case rnemdKineticSwap :
1752	<	case rnemdPx :
1349	<	case rnemdPy :
1350	<	case rnemdPz :
1351	<	doSwap();
1751	>	case rnemdNIVS:
1752	>	doNIVS(commonA_, commonB_);
1753		break;
1754	<	case rnemdShiftScaleV :
1755	<	case rnemdShiftScaleVAM :
1355	<	doShiftScale();
1754	>	case rnemdVSS:
1755	>	doVSS(commonA_, commonB_);
1756		break;
1757	<	case rnemdUnknown :
1757	>	case rnemdUnkownMethod:
1758		default :
1759		break;
1760		}
1761		}
1762
1763		void RNEMD::collectData() {
1764	<
1764	>	if (!doRNEMD_) return;
1765		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1766	+
1767	+	cerr << "collecting data\n";
1768	+	// collectData can be called more frequently than the doRNEMD, so use the
1769	+	// computed area from the last exchange time:
1770	+	RealType area = getDividingArea();
1771	+	areaAccumulator_->add(area);
1772		Mat3x3d hmat = currentSnap_->getHmat();
1367	–
1773		seleMan_.setSelectionSet(evaluator_.evaluate());
1774
1775	<	int selei;
1775	>	int selei(0);
1776		StuntDouble* sd;
1777	<	int idx;
1777	>	int binNo;
1778
1779	<	logFrameCount_++;
1779	>	vector<RealType> binMass(nBins_, 0.0);
1780	>	vector<RealType> binPx(nBins_, 0.0);
1781	>	vector<RealType> binPy(nBins_, 0.0);
1782	>	vector<RealType> binPz(nBins_, 0.0);
1783	>	vector<RealType> binOmegax(nBins_, 0.0);
1784	>	vector<RealType> binOmegay(nBins_, 0.0);
1785	>	vector<RealType> binOmegaz(nBins_, 0.0);
1786	>	vector<RealType> binKE(nBins_, 0.0);
1787	>	vector<int> binDOF(nBins_, 0);
1788	>	vector<int> binCount(nBins_, 0);
1789
1790		// alternative approach, track all molecules instead of only those
1791		// selected for scaling/swapping:
1792		/*
1793	<	SimInfo::MoleculeIterator miter;
1794	<	vector<StuntDouble*>::iterator iiter;
1795	<	Molecule* mol;
1796	<	StuntDouble* integrableObject;
1797	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1793	>	SimInfo::MoleculeIterator miter;
1794	>	vector<StuntDouble*>::iterator iiter;
1795	>	Molecule* mol;
1796	>	StuntDouble* sd;
1797	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1798		mol = info_->nextMolecule(miter))
1799	<	integrableObject is essentially sd
1800	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1801	<	integrableObject != NULL;
1802	<	integrableObject = mol->nextIntegrableObject(iiter))
1799	>	sd is essentially sd
1800	>	for (sd = mol->beginIntegrableObject(iiter);
1801	>	sd != NULL;
1802	>	sd = mol->nextIntegrableObject(iiter))
1803		*/
1804	+
1805		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1806	<	sd = seleMan_.nextSelected(selei)) {
1807	<
1393	<	idx = sd->getLocalIndex();
1394	<
1806	>	sd = seleMan_.nextSelected(selei)) {
1807	>
1808		Vector3d pos = sd->getPos();
1809
1810		// wrap the stuntdouble's position back into the box:
1811
1812	<	if (usePeriodicBoundaryConditions_)
1812	>	if (usePeriodicBoundaryConditions_) {
1813		currentSnap_->wrapVector(pos);
1814	<
1815	<	// which bin is this stuntdouble in?
1816	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1817	<
1818	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1819	<	rnemdLogWidth_;
1820	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1821	<	/*
1822	<	if (rnemdLogWidth_ == midBin_ + 1)
1823	<	if (binNo > midBin_)
1824	<	binNo = nBins_ - binNo;
1412	<	*/
1814	>	// which bin is this stuntdouble in?
1815	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1816	>	// Shift molecules by half a box to have bins start at 0
1817	>	// The modulo operator is used to wrap the case when we are
1818	>	// beyond the end of the bins back to the beginning.
1819	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1820	>	} else {
1821	>	Vector3d rPos = pos - coordinateOrigin_;
1822	>	binNo = int(rPos.length() / binWidth_);
1823	>	}
1824	>
1825		RealType mass = sd->getMass();
1414	–	mHist_[binNo] += mass;
1826		Vector3d vel = sd->getVel();
1827	<	RealType value;
1828	<	//RealType xVal, yVal, zVal;
1827	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1828	>	Vector3d aVel = cross(rPos, vel);
1829	>
1830	>	if (binNo >= 0 && binNo < nBins_)  {
1831	>	binCount[binNo]++;
1832	>	binMass[binNo] += mass;
1833	>	binPx[binNo] += mass*vel.x();
1834	>	binPy[binNo] += mass*vel.y();
1835	>	binPz[binNo] += mass*vel.z();
1836	>	binOmegax[binNo] += aVel.x();
1837	>	binOmegay[binNo] += aVel.y();
1838	>	binOmegaz[binNo] += aVel.z();
1839	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1840	>	binDOF[binNo] += 3;
1841	>
1842	>	if (sd->isDirectional()) {
1843	>	Vector3d angMom = sd->getJ();
1844	>	Mat3x3d I = sd->getI();
1845	>	if (sd->isLinear()) {
1846	>	int i = sd->linearAxis();
1847	>	int j = (i + 1) % 3;
1848	>	int k = (i + 2) % 3;
1849	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1850	>	angMom[k] * angMom[k] / I(k, k));
1851	>	binDOF[binNo] += 2;
1852	>	} else {
1853	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1854	>	angMom[1] * angMom[1] / I(1, 1) +
1855	>	angMom[2] * angMom[2] / I(2, 2));
1856	>	binDOF[binNo] += 3;
1857	>	}
1858	>	}
1859	>	}
1860	>	}
1861	>
1862	>	#ifdef IS_MPI
1863	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1864	>	nBins_, MPI::INT, MPI::SUM);
1865	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1866	>	nBins_, MPI::REALTYPE, MPI::SUM);
1867	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1868	>	nBins_, MPI::REALTYPE, MPI::SUM);
1869	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1870	>	nBins_, MPI::REALTYPE, MPI::SUM);
1871	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1872	>	nBins_, MPI::REALTYPE, MPI::SUM);
1873	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1874	>	nBins_, MPI::REALTYPE, MPI::SUM);
1875	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1876	>	nBins_, MPI::REALTYPE, MPI::SUM);
1877	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1878	>	nBins_, MPI::REALTYPE, MPI::SUM);
1879	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1880	>	nBins_, MPI::REALTYPE, MPI::SUM);
1881	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1882	>	nBins_, MPI::INT, MPI::SUM);
1883	>	#endif
1884
1885	<	if (outputTemp_) {
1886	<	value = mass * vel.lengthSquare();
1887	<	tempCount_[binNo] += 3;
1888	<	if (sd->isDirectional()) {
1889	<	Vector3d angMom = sd->getJ();
1890	<	Mat3x3d I = sd->getI();
1891	<	if (sd->isLinear()) {
1892	<	int i = sd->linearAxis();
1893	<	int j = (i + 1) % 3;
1894	<	int k = (i + 2) % 3;
1895	<	value += angMom[j] * angMom[j] / I(j, j) +
1896	<	angMom[k] * angMom[k] / I(k, k);
1897	<	tempCount_[binNo] +=2;
1898	<	} else {
1899	<	value += angMom[0] * angMom[0] / I(0, 0) +
1900	<	angMom[1]*angMom[1]/I(1, 1) +
1901	<	angMom[2]*angMom[2]/I(2, 2);
1436	<	tempCount_[binNo] +=3;
1437	<	}
1438	<	}
1439	<	value = value / PhysicalConstants::energyConvert
1440	<	/ PhysicalConstants::kb;//may move to getStatus()
1441	<	tempHist_[binNo] += value;
1885	>	Vector3d vel;
1886	>	Vector3d aVel;
1887	>	RealType den;
1888	>	RealType temp;
1889	>	RealType z;
1890	>	RealType r;
1891	>	for (int i = 0; i < nBins_; i++) {
1892	>	if (usePeriodicBoundaryConditions_) {
1893	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1894	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1895	>	/ currentSnap_->getVolume() ;
1896	>	} else {
1897	>	r = (((RealType)i + 0.5) * binWidth_);
1898	>	RealType rinner = (RealType)i * binWidth_;
1899	>	RealType router = (RealType)(i+1) * binWidth_;
1900	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1901	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1902		}
1903	<	if (outputVx_) {
1904	<	value = mass * vel[0];
1905	<	//vxzCount_[binNo]++;
1906	<	pxzHist_[binNo] += value;
1907	<	}
1908	<	if (outputVy_) {
1449	<	value = mass * vel[1];
1450	<	//vyzCount_[binNo]++;
1451	<	pyzHist_[binNo] += value;
1452	<	}
1903	>	vel.x() = binPx[i] / binMass[i];
1904	>	vel.y() = binPy[i] / binMass[i];
1905	>	vel.z() = binPz[i] / binMass[i];
1906	>	aVel.x() = binOmegax[i];
1907	>	aVel.y() = binOmegay[i];
1908	>	aVel.z() = binOmegaz[i];
1909
1910	<	if (output3DTemp_) {
1911	<	value = mass * vel.x() * vel.x();
1912	<	xTempHist_[binNo] += value;
1913	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1914	<	/ PhysicalConstants::kb;
1915	<	yTempHist_[binNo] += value;
1916	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1917	<	/ PhysicalConstants::kb;
1918	<	zTempHist_[binNo] += value;
1919	<	xyzTempCount_[binNo]++;
1910	>	if (binCount[i] > 0) {
1911	>	// only add values if there are things to add
1912	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1913	>	PhysicalConstants::energyConvert);
1914	>
1915	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1916	>	if(outputMask_[j]) {
1917	>	switch(j) {
1918	>	case Z:
1919	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1920	>	break;
1921	>	case R:
1922	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1923	>	break;
1924	>	case TEMPERATURE:
1925	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1926	>	break;
1927	>	case VELOCITY:
1928	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1929	>	break;
1930	>	case ANGULARVELOCITY:
1931	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1932	>	break;
1933	>	case DENSITY:
1934	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1935	>	break;
1936	>	}
1937	>	}
1938	>	}
1939		}
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	–	}
1940		}
1941		}
1942
1943		void RNEMD::getStarted() {
1944	+	if (!doRNEMD_) return;
1945	+	hasDividingArea_ = false;
1946		collectData();
1947	<	/*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();
1947	>	writeOutputFile();
1948		}
1949
1950	<	void RNEMD::getStatus() {
1951	<
1952	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1514	<	Stats& stat = currentSnap_->statData;
1515	<	RealType time = currentSnap_->getTime();
1516	<
1517	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1518	<	//or to be more meaningful, define another item as exchangeSum_ / time
1519	<	int j;
1520	<
1521	<	#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	<	}
1950	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1951	>	if (!doRNEMD_) return;
1952	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1953
1954	+	while(tokenizer.hasMoreTokens()) {
1955	+	std::string token(tokenizer.nextToken());
1956	+	toUpper(token);
1957	+	OutputMapType::iterator i = outputMap_.find(token);
1958	+	if (i != outputMap_.end()) {
1959	+	outputMask_.set(i->second);
1960	+	} else {
1961	+	sprintf( painCave.errMsg,
1962	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1963	+	"\toutputFileFormat keyword.\n", token.c_str() );
1964	+	painCave.isFatal = 0;
1965	+	painCave.severity = OPENMD_ERROR;
1966	+	simError();
1967	+	}
1968	+	}
1969	+	}
1970	+
1971	+	void RNEMD::writeOutputFile() {
1972	+	if (!doRNEMD_) return;
1973	+
1974	+	#ifdef IS_MPI
1975		// If we're the root node, should we print out the results
1976		int worldRank = MPI::COMM_WORLD.Get_rank();
1977		if (worldRank == 0) {
1978		#endif
1979	<
1980	<	if (outputTemp_) {
1981	<	tempLog_ << time;
1982	<	for (j = 0; j < rnemdLogWidth_; j++) {
1983	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1984	<	}
1985	<	tempLog_ << endl;
1979	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1980	>
1981	>	if( !rnemdFile_ ){
1982	>	sprintf( painCave.errMsg,
1983	>	"Could not open \"%s\" for RNEMD output.\n",
1984	>	rnemdFileName_.c_str());
1985	>	painCave.isFatal = 1;
1986	>	simError();
1987		}
1988	<	if (outputVx_) {
1989	<	vxzLog_ << time;
1990	<	for (j = 0; j < rnemdLogWidth_; j++) {
1991	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1992	<	}
1993	<	vxzLog_ << endl;
1988	>
1989	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1990	>
1991	>	RealType time = currentSnap_->getTime();
1992	>	RealType avgArea;
1993	>	areaAccumulator_->getAverage(avgArea);
1994	>	RealType Jz = kineticExchange_ / (time * avgArea)
1995	>	/ PhysicalConstants::energyConvert;
1996	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
1997	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
1998	>
1999	>	rnemdFile_ << "#######################################################\n";
2000	>	rnemdFile_ << "# RNEMD {\n";
2001	>
2002	>	map<string, RNEMDMethod>::iterator mi;
2003	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2004	>	if ( (*mi).second == rnemdMethod_)
2005	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2006		}
2007	<	if (outputVy_) {
2008	<	vyzLog_ << time;
2009	<	for (j = 0; j < rnemdLogWidth_; j++) {
2010	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	<	}
1600	<	vyzLog_ << endl;
2007	>	map<string, RNEMDFluxType>::iterator fi;
2008	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2009	>	if ( (*fi).second == rnemdFluxType_)
2010	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2011		}
2012	+
2013	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2014
2015	<	if (output3DTemp_) {
2016	<	RealType temp;
2017	<	xTempLog_ << time;
2018	<	for (j = 0; j < rnemdLogWidth_; j++) {
2019	<	if (outputVx_)
2020	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2021	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2022	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2023	<	xTempLog_ << "\t" << temp;
2015	>	rnemdFile_ << "#    objectSelection = \""
2016	>	<< rnemdObjectSelection_ << "\";\n";
2017	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2018	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2019	>	rnemdFile_ << "# }\n";
2020	>	rnemdFile_ << "#######################################################\n";
2021	>	rnemdFile_ << "# RNEMD report:\n";
2022	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2023	>	rnemdFile_ << "# Target flux:\n";
2024	>	rnemdFile_ << "#           kinetic = "
2025	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2026	>	<< " (kcal/mol/A^2/fs)\n";
2027	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2028	>	<< " (amu/A/fs^2)\n";
2029	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2030	>	<< " (amu/A^2/fs^2)\n";
2031	>	rnemdFile_ << "# Target one-time exchanges:\n";
2032	>	rnemdFile_ << "#          kinetic = "
2033	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2034	>	<< " (kcal/mol)\n";
2035	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2036	>	<< " (amu*A/fs)\n";
2037	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2038	>	<< " (amu*A^2/fs)\n";
2039	>	rnemdFile_ << "# Actual exchange totals:\n";
2040	>	rnemdFile_ << "#          kinetic = "
2041	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2042	>	<< " (kcal/mol)\n";
2043	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2044	>	<< " (amu*A/fs)\n";
2045	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2046	>	<< " (amu*A^2/fs)\n";
2047	>	rnemdFile_ << "# Actual flux:\n";
2048	>	rnemdFile_ << "#          kinetic = " << Jz
2049	>	<< " (kcal/mol/A^2/fs)\n";
2050	>	rnemdFile_ << "#          momentum = " << JzP
2051	>	<< " (amu/A/fs^2)\n";
2052	>	rnemdFile_ << "#  angular momentum = " << JzL
2053	>	<< " (amu/A^2/fs^2)\n";
2054	>	rnemdFile_ << "# Exchange statistics:\n";
2055	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2056	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2057	>	if (rnemdMethod_ == rnemdNIVS) {
2058	>	rnemdFile_ << "#  NIVS root-check errors = "
2059	>	<< failRootCount_ << "\n";
2060	>	}
2061	>	rnemdFile_ << "#######################################################\n";
2062	>
2063	>
2064	>
2065	>	//write title
2066	>	rnemdFile_ << "#";
2067	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2068	>	if (outputMask_[i]) {
2069	>	rnemdFile_ << "\t" << data_[i].title <<
2070	>	"(" << data_[i].units << ")";
2071	>	// add some extra tabs for column alignment
2072	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2073		}
2074	<	xTempLog_ << endl;
2075	<	yTempLog_ << time;
2076	<	for (j = 0; j < rnemdLogWidth_; j++) {
2077	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
2074	>	}
2075	>	rnemdFile_ << std::endl;
2076	>
2077	>	rnemdFile_.precision(8);
2078	>
2079	>	for (int j = 0; j < nBins_; j++) {
2080	>
2081	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2082	>	if (outputMask_[i]) {
2083	>	if (data_[i].dataType == "RealType")
2084	>	writeReal(i,j);
2085	>	else if (data_[i].dataType == "Vector3d")
2086	>	writeVector(i,j);
2087	>	else {
2088	>	sprintf( painCave.errMsg,
2089	>	"RNEMD found an unknown data type for: %s ",
2090	>	data_[i].title.c_str());
2091	>	painCave.isFatal = 1;
2092	>	simError();
2093	>	}
2094	>	}
2095		}
2096	<	yTempLog_ << endl;
2097	<	zTempLog_ << time;
2098	<	for (j = 0; j < rnemdLogWidth_; j++) {
2099	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
2096	>	rnemdFile_ << std::endl;
2097	>
2098	>	}
2099	>
2100	>	rnemdFile_ << "#######################################################\n";
2101	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2102	>	rnemdFile_ << "#######################################################\n";
2103	>
2104	>
2105	>	for (int j = 0; j < nBins_; j++) {
2106	>	rnemdFile_ << "#";
2107	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2108	>	if (outputMask_[i]) {
2109	>	if (data_[i].dataType == "RealType")
2110	>	writeRealStdDev(i,j);
2111	>	else if (data_[i].dataType == "Vector3d")
2112	>	writeVectorStdDev(i,j);
2113	>	else {
2114	>	sprintf( painCave.errMsg,
2115	>	"RNEMD found an unknown data type for: %s ",
2116	>	data_[i].title.c_str());
2117	>	painCave.isFatal = 1;
2118	>	simError();
2119	>	}
2120	>	}
2121		}
2122	<	zTempLog_ << endl;
2123	<	}
2124	<	if (outputRotTemp_) {
2125	<	rotTempLog_ << time;
2126	<	for (j = 0; j < rnemdLogWidth_; j++) {
2127	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2128	<	}
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	<	}
2122	>	rnemdFile_ << std::endl;
2123	>
2124	>	}
2125	>
2126	>	rnemdFile_.flush();
2127	>	rnemdFile_.close();
2128	>
2129		#ifdef IS_MPI
2130		}
2131		#endif
2132	+
2133	+	}
2134	+
2135	+	void RNEMD::writeReal(int index, unsigned int bin) {
2136	+	if (!doRNEMD_) return;
2137	+	assert(index >=0 && index < ENDINDEX);
2138	+	assert(int(bin) < nBins_);
2139	+	RealType s;
2140	+	int count;
2141	+
2142	+	count = data_[index].accumulator[bin]->count();
2143	+	if (count == 0) return;
2144	+
2145	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2146	+
2147	+	if (! isinf(s) && ! isnan(s)) {
2148	+	rnemdFile_ << "\t" << s;
2149	+	} else{
2150	+	sprintf( painCave.errMsg,
2151	+	"RNEMD detected a numerical error writing: %s for bin %d",
2152	+	data_[index].title.c_str(), bin);
2153	+	painCave.isFatal = 1;
2154	+	simError();
2155	+	}
2156	+	}
2157	+
2158	+	void RNEMD::writeVector(int index, unsigned int bin) {
2159	+	if (!doRNEMD_) return;
2160	+	assert(index >=0 && index < ENDINDEX);
2161	+	assert(int(bin) < nBins_);
2162	+	Vector3d s;
2163	+	int count;
2164	+
2165	+	count = data_[index].accumulator[bin]->count();
2166
2167	<	for (j = 0; j < rnemdLogWidth_; j++) {
2168	<	mHist_[j] = 0.0;
2167	>	if (count == 0) return;
2168	>
2169	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2170	>	if (isinf(s[0]) || isnan(s[0]) ||
2171	>	isinf(s[1]) || isnan(s[1]) ||
2172	>	isinf(s[2]) || isnan(s[2]) ) {
2173	>	sprintf( painCave.errMsg,
2174	>	"RNEMD detected a numerical error writing: %s for bin %d",
2175	>	data_[index].title.c_str(), bin);
2176	>	painCave.isFatal = 1;
2177	>	simError();
2178	>	} else {
2179	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2180		}
2181	<	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	<	}
2181	>	}
2182
2183	<	if (output3DTemp_)
2184	<	for (j = 0; j < rnemdLogWidth_; j++) {
2185	<	xTempHist_[j] = 0.0;
2186	<	yTempHist_[j] = 0.0;
2187	<	zTempHist_[j] = 0.0;
2188	<	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';
2183	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2184	>	if (!doRNEMD_) return;
2185	>	assert(index >=0 && index < ENDINDEX);
2186	>	assert(int(bin) < nBins_);
2187	>	RealType s;
2188	>	int count;
2189
2190	<	logFrameCount_ = 0;
2190	>	count = data_[index].accumulator[bin]->count();
2191	>	if (count == 0) return;
2192	>
2193	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2194	>
2195	>	if (! isinf(s) && ! isnan(s)) {
2196	>	rnemdFile_ << "\t" << s;
2197	>	} else{
2198	>	sprintf( painCave.errMsg,
2199	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2200	>	data_[index].title.c_str(), bin);
2201	>	painCave.isFatal = 1;
2202	>	simError();
2203	>	}
2204		}
2205	+
2206	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2207	+	if (!doRNEMD_) return;
2208	+	assert(index >=0 && index < ENDINDEX);
2209	+	assert(int(bin) < nBins_);
2210	+	Vector3d s;
2211	+	int count;
2212	+
2213	+	count = data_[index].accumulator[bin]->count();
2214	+	if (count == 0) return;
2215	+
2216	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2217	+	if (isinf(s[0]) || isnan(s[0]) ||
2218	+	isinf(s[1]) || isnan(s[1]) ||
2219	+	isinf(s[2]) || isnan(s[2]) ) {
2220	+	sprintf( painCave.errMsg,
2221	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2222	+	data_[index].title.c_str(), bin);
2223	+	painCave.isFatal = 1;
2224	+	simError();
2225	+	} else {
2226	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2227	+	}
2228	+	}
2229		}
2230

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