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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1861 by gezelter, Tue Apr 9 19:45:54 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	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
88	<	evaluator_.loadScriptString(rnemdObjectSelection_);
89	<	seleMan_.setSelectionSet(evaluator_.evaluate());
87	>	stringToMethod_["Swap"]  = rnemdSwap;
88	>	stringToMethod_["NIVS"]  = rnemdNIVS;
89	>	stringToMethod_["VSS"]   = rnemdVSS;
90
91	<	// do some sanity checking
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	<	int selectionCount = seleMan_.getSelectionCount();
109	<	int nIntegrable = info->getNGlobalIntegrableObjects();
108	>	runTime_ = simParams->getRunTime();
109	>	statusTime_ = simParams->getStatusTime();
110
111	<	if (selectionCount > nIntegrable) {
111	>	const string methStr = rnemdParams->getMethod();
112	>	bool hasFluxType = rnemdParams->haveFluxType();
113	>
114	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115	>
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",
106	<	rnemdObjectSelection_.c_str(),
107	<	selectionCount, nIntegrable);
108	<	painCave.isFatal = 0;
109	<	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		}
128	–
129	–	outputTemp_ = false;
130	–	if (simParams->haveRNEMD_outputTemperature()) {
131	–	outputTemp_ = simParams->getRNEMD_outputTemperature();
132	–	} else if ((rnemdType_ == rnemdKineticSwap) ||
133	–	(rnemdType_ == rnemdKineticScale) ||
134	–	(rnemdType_ == rnemdKineticScaleVAM) ||
135	–	(rnemdType_ == rnemdKineticScaleAM)) {
136	–	outputTemp_ = true;
137	–	}
138	–	outputVx_ = false;
139	–	if (simParams->haveRNEMD_outputVx()) {
140	–	outputVx_ = simParams->getRNEMD_outputVx();
141	–	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
142	–	outputVx_ = true;
143	–	}
144	–	outputVy_ = false;
145	–	if (simParams->haveRNEMD_outputVy()) {
146	–	outputVy_ = simParams->getRNEMD_outputVy();
147	–	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
148	–	outputVy_ = true;
149	–	}
150	–	output3DTemp_ = false;
151	–	if (simParams->haveRNEMD_outputXyzTemperature()) {
152	–	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
153	–	}
154	–	outputRotTemp_ = false;
155	–	if (simParams->haveRNEMD_outputRotTemperature()) {
156	–	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
157	–	}
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		}
348
349	<	#ifdef IS_MPI
350	<	}
194	<	#endif
195	<
196	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
197	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
198	<	midBin_ = nBins_ / 2;
199	<	if (simParams->haveRNEMD_binShift()) {
200	<	if (simParams->getRNEMD_binShift()) {
201	<	zShift_ = 0.5 / (RealType)(nBins_);
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351		} else {
352	<	zShift_ = 0.0;
352	>	coordinateOrigin_ = V3Zero;
353		}
205	–	} else {
206	–	zShift_ = 0.0;
207	–	}
208	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
209	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
210	–	//set to 0.0 if not using it; N/A in status output yet
211	–	if (simParams->haveRNEMD_logWidth()) {
212	–	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
213	–	/*arbitary rnemdLogWidth_, no checking;
214	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
215	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
216	–	cerr << "Automaically set back to default.\n";
217	–	rnemdLogWidth_ = nBins_;
218	–	}*/
219	–	} else {
220	–	set_RNEMD_logWidth(nBins_);
221	–	}
222	–	tempHist_.resize(rnemdLogWidth_, 0.0);
223	–	tempCount_.resize(rnemdLogWidth_, 0);
224	–	pxzHist_.resize(rnemdLogWidth_, 0.0);
225	–	//vxzCount_.resize(rnemdLogWidth_, 0);
226	–	pyzHist_.resize(rnemdLogWidth_, 0.0);
227	–	//vyzCount_.resize(rnemdLogWidth_, 0);
354
355	<	mHist_.resize(rnemdLogWidth_, 0.0);
230	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
231	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
232	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
233	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
234	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
235	<	rotTempCount_.resize(rnemdLogWidth_, 0);
355	>	// do some sanity checking
356
357	<	set_RNEMD_exchange_total(0.0);
238	<	if (simParams->haveRNEMD_targetFlux()) {
239	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
240	<	} else {
241	<	set_RNEMD_target_flux(0.0);
242	<	}
243	<	if (simParams->haveRNEMD_targetJzKE()) {
244	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
245	<	} else {
246	<	set_RNEMD_target_JzKE(0.0);
247	<	}
248	<	if (simParams->haveRNEMD_targetJzpx()) {
249	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
250	<	} else {
251	<	set_RNEMD_target_jzpx(0.0);
252	<	}
253	<	jzp_.x() = targetJzpx_;
254	<	njzp_.x() = -targetJzpx_;
255	<	if (simParams->haveRNEMD_targetJzpy()) {
256	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
257	<	} else {
258	<	set_RNEMD_target_jzpy(0.0);
259	<	}
260	<	jzp_.y() = targetJzpy_;
261	<	njzp_.y() = -targetJzpy_;
262	<	if (simParams->haveRNEMD_targetJzpz()) {
263	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
264	<	} else {
265	<	set_RNEMD_target_jzpz(0.0);
266	<	}
267	<	jzp_.z() = targetJzpz_;
268	<	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
287	–	RNEMD::~RNEMD() {
288	–	delete randNumGen_;
594
595	+	RNEMD::~RNEMD() {
596	+	if (!doRNEMD_) return;
597		#ifdef IS_MPI
598		if (worldRank == 0) {
599		#endif
293	–
294	–	sprintf(painCave.errMsg,
295	–	"RNEMD: total failed trials: %d\n",
296	–	failTrialCount_);
297	–	painCave.isFatal = 0;
298	–	painCave.severity = OPENMD_INFO;
299	–	simError();
600
601	<	if (outputTemp_) tempLog_.close();
302	<	if (outputVx_)   vxzLog_.close();
303	<	if (outputVy_)   vyzLog_.close();
601	>	writeOutputFile();
602
603	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
604	<	rnemdType_ == rnemdPyScale) {
307	<	sprintf(painCave.errMsg,
308	<	"RNEMD: total root-checking warnings: %d\n",
309	<	failRootCount_);
310	<	painCave.isFatal = 0;
311	<	painCave.severity = OPENMD_INFO;
312	<	simError();
313	<	}
314	<	if (output3DTemp_) {
315	<	xTempLog_.close();
316	<	yTempLog_.close();
317	<	zTempLog_.close();
318	<	}
319	<	if (outputRotTemp_) rotTempLog_.close();
320	<
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
326	–	void RNEMD::doSwap() {
327	–
615		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
616		Mat3x3d hmat = currentSnap_->getHmat();
617
331	–	seleMan_.setSelectionSet(evaluator_.evaluate());
332	–
333	–	int selei;
618		StuntDouble* sd;
335	–	int idx;
619
620		RealType min_val;
621		bool min_found = false;
#	Line 342 | 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)) {
628	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
629	>	sd = seleManA_.nextSelected(selei)) {
630
348	–	idx = sd->getLocalIndex();
349	–
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	<
363	<	// if we're in bin 0 or the middleBin
364	<	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_) {
371	<	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	<
438	<	nProc = MPI::COMM_WORLD.Get_size();
439	<	worldRank = MPI::COMM_WORLD.Get_rank();
440	<
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 454 | Line 767 | namespace OpenMD {
767		RealType val;
768		int rank;
769		} max_vals, min_vals;
770	<
770	>
771		if (my_min_found) {
772		min_vals.val = min_val;
773		} else {
#	Line 492 | 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 544 | 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 590 | 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 625 | 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 636 | 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	<	}
646	<
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
654	–	seleMan_.setSelectionSet(evaluator_.evaluate());
655	–
656	–	int selei;
986		StuntDouble* sd;
658	–	int idx;
987
988		vector<StuntDouble*> hotBin, coldBin;
989
#	Line 674 | 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
680	–	idx = sd->getLocalIndex();
681	–
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	<	// which bin is this stuntdouble in?
1016	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1017	<
1018	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1019	<
1020	<	// if we're in bin 0 or the middleBin
1021	<	if (binNo == 0 || binNo == midBin_) {
1022	<
1023	<	RealType mass = sd->getMass();
1024	<	Vector3d vel = sd->getVel();
1025	<
1026	<	if (binNo == 0) {
1027	<	hotBin.push_back(sd);
1028	<	Phx += mass * vel.x();
1029	<	Phy += mass * vel.y();
1030	<	Phz += mass * vel.z();
1031	<	Khx += mass * vel.x() * vel.x();
1032	<	Khy += mass * vel.y() * vel.y();
1033	<	Khz += mass * vel.z() * vel.z();
1034	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1035	<	if (sd->isDirectional()) {
1036	<	Vector3d angMom = sd->getJ();
1037	<	Mat3x3d I = sd->getI();
1038	<	if (sd->isLinear()) {
1039	<	int i = sd->linearAxis();
714	<	int j = (i + 1) % 3;
715	<	int k = (i + 2) % 3;
716	<	Khw += angMom[j] * angMom[j] / I(j, j) +
717	<	angMom[k] * angMom[k] / I(k, k);
718	<	} else {
719	<	Khw += 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	<	}
724	<	//}
725	<	} else { //midBin_
726	<	coldBin.push_back(sd);
727	<	Pcx += mass * vel.x();
728	<	Pcy += mass * vel.y();
729	<	Pcz += mass * vel.z();
730	<	Kcx += mass * vel.x() * vel.x();
731	<	Kcy += mass * vel.y() * vel.y();
732	<	Kcz += mass * vel.z() * vel.z();
733	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
734	<	if (sd->isDirectional()) {
735	<	Vector3d angMom = sd->getJ();
736	<	Mat3x3d I = sd->getI();
737	<	if (sd->isLinear()) {
738	<	int i = sd->linearAxis();
739	<	int j = (i + 1) % 3;
740	<	int k = (i + 2) % 3;
741	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
742	<	angMom[k] * angMom[k] / I(k, k);
743	<	} else {
744	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
745	<	+ angMom[1]*angMom[1]/I(1, 1)
746	<	+ angMom[2]*angMom[2]/I(2, 2);
747	<	}
748	<	}
749	<	//}
750	<	}
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	+	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
1078		Khx *= 0.5;
1079		Khy *= 0.5;
#	Line 760 | Line 1084 | namespace OpenMD {
1084		Kcz *= 0.5;
1085		Kcw *= 0.5;
1086
763	–	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
764	–	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
765	–	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
766	–	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
767	–	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
768	–
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 791 | 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;
807	<	//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 820 | 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;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
1154		(*sdi)->setVel(vel);
1155		}
1156		if ((*sdi)->isDirectional()) {
1157		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//angMom[2] *= c;
1158		(*sdi)->setJ(angMom);
1159		}
1160		}
1161		w = sqrt(w);
850	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
851	–	<< "\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 859 | Line 1169 | namespace OpenMD {
1169		}
1170		if ((*sdi)->isDirectional()) {
1171		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//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 908 | 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 920 | 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 1006 | 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 1034 | 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 1089 | 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
1105	–	void RNEMD::doShiftScale() {
1106	–
1430		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1431	+	RealType time = currentSnap_->getTime();
1432		Mat3x3d hmat = currentSnap_->getHmat();
1433
1110	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1111	–
1112	–	int selei;
1434		StuntDouble* sd;
1114	–	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	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1450	<	sd = seleMan_.nextSelected(selei)) {
1449	>	// Constraints can be on only the linear or angular momentum, but
1450	>	// not both.  Usually, the user will specify which they want, but
1451	>	// in case they don't, the use of periodic boundaries should make
1452	>	// the choice for us.
1453	>	bool doLinearPart = false;
1454	>	bool doAngularPart = false;
1455
1456	<	idx = sd->getLocalIndex();
1456	>	switch (rnemdFluxType_) {
1457	>	case rnemdPx:
1458	>	case rnemdPy:
1459	>	case rnemdPz:
1460	>	case rnemdPvector:
1461	>	case rnemdKePx:
1462	>	case rnemdKePy:
1463	>	case rnemdKePvector:
1464	>	doLinearPart = true;
1465	>	break;
1466	>	case rnemdLx:
1467	>	case rnemdLy:
1468	>	case rnemdLz:
1469	>	case rnemdLvector:
1470	>	case rnemdKeLx:
1471	>	case rnemdKeLy:
1472	>	case rnemdKeLz:
1473	>	case rnemdKeLvector:
1474	>	doAngularPart = true;
1475	>	break;
1476	>	case rnemdKE:
1477	>	case rnemdRotKE:
1478	>	case rnemdFullKE:
1479	>	default:
1480	>	if (usePeriodicBoundaryConditions_)
1481	>	doLinearPart = true;
1482	>	else
1483	>	doAngularPart = true;
1484	>	break;
1485	>	}
1486	>
1487	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1488	>	sd = smanA.nextSelected(selei)) {
1489
1490		Vector3d pos = sd->getPos();
1491
1492		// wrap the stuntdouble's position back into the box:
1493	+
1494	+	if (usePeriodicBoundaryConditions_)
1495	+	currentSnap_->wrapVector(pos);
1496	+
1497	+	RealType mass = sd->getMass();
1498	+	Vector3d vel = sd->getVel();
1499	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1500	+	RealType r2;
1501	+
1502	+	hotBin.push_back(sd);
1503	+	Ph += mass * vel;
1504	+	Mh += mass;
1505	+	Kh += mass * vel.lengthSquare();
1506	+	Lh += mass * cross(rPos, vel);
1507	+	Ih -= outProduct(rPos, rPos) * mass;
1508	+	r2 = rPos.lengthSquare();
1509	+	Ih(0, 0) += mass * r2;
1510	+	Ih(1, 1) += mass * r2;
1511	+	Ih(2, 2) += mass * r2;
1512	+
1513	+	if (rnemdFluxType_ == rnemdFullKE) {
1514	+	if (sd->isDirectional()) {
1515	+	Vector3d angMom = sd->getJ();
1516	+	Mat3x3d I = sd->getI();
1517	+	if (sd->isLinear()) {
1518	+	int i = sd->linearAxis();
1519	+	int j = (i + 1) % 3;
1520	+	int k = (i + 2) % 3;
1521	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1522	+	angMom[k] * angMom[k] / I(k, k);
1523	+	} else {
1524	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1525	+	angMom[1] * angMom[1] / I(1, 1) +
1526	+	angMom[2] * angMom[2] / I(2, 2);
1527	+	}
1528	+	}
1529	+	}
1530	+	}
1531	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1532	+	sd = smanB.nextSelected(selej)) {
1533
1534	+	Vector3d pos = sd->getPos();
1535	+
1536	+	// wrap the stuntdouble's position back into the box:
1537	+
1538		if (usePeriodicBoundaryConditions_)
1539		currentSnap_->wrapVector(pos);
1540	+
1541	+	RealType mass = sd->getMass();
1542	+	Vector3d vel = sd->getVel();
1543	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1544	+	RealType r2;
1545
1546	<	// which bin is this stuntdouble in?
1547	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1548	<
1549	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1550	<
1551	<	// if we're in bin 0 or the middleBin
1552	<	if (binNo == 0 || binNo == midBin_) {
1553	<
1554	<	RealType mass = sd->getMass();
1555	<	Vector3d vel = sd->getVel();
1556	<
1557	<	if (binNo == 0) {
1558	<	hotBin.push_back(sd);
1559	<	//std::cerr << "before, velocity = " << vel << endl;
1560	<	Ph += mass * vel;
1561	<	//std::cerr << "after, velocity = " << vel << endl;
1562	<	Mh += mass;
1563	<	Kh += mass * vel.lengthSquare();
1564	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1565	<	if (sd->isDirectional()) {
1566	<	Vector3d angMom = sd->getJ();
1567	<	Mat3x3d I = sd->getI();
1568	<	if (sd->isLinear()) {
1569	<	int i = sd->linearAxis();
1570	<	int j = (i + 1) % 3;
1571	<	int k = (i + 2) % 3;
1572	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1164	<	angMom[k] * angMom[k] / I(k, k);
1165	<	} else {
1166	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1167	<	angMom[1] * angMom[1] / I(1, 1) +
1168	<	angMom[2] * angMom[2] / I(2, 2);
1169	<	}
1170	<	}
1171	<	}
1172	<	} else { //midBin_
1173	<	coldBin.push_back(sd);
1174	<	Pc += mass * vel;
1175	<	Mc += mass;
1176	<	Kc += mass * vel.lengthSquare();
1177	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1178	<	if (sd->isDirectional()) {
1179	<	Vector3d angMom = sd->getJ();
1180	<	Mat3x3d I = sd->getI();
1181	<	if (sd->isLinear()) {
1182	<	int i = sd->linearAxis();
1183	<	int j = (i + 1) % 3;
1184	<	int k = (i + 2) % 3;
1185	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1186	<	angMom[k] * angMom[k] / I(k, k);
1187	<	} else {
1188	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1189	<	angMom[1] * angMom[1] / I(1, 1) +
1190	<	angMom[2] * angMom[2] / I(2, 2);
1191	<	}
1192	<	}
1193	<	}
1194	<	}
1546	>	coldBin.push_back(sd);
1547	>	Pc += mass * vel;
1548	>	Mc += mass;
1549	>	Kc += mass * vel.lengthSquare();
1550	>	Lc += mass * cross(rPos, vel);
1551	>	Ic -= outProduct(rPos, rPos) * mass;
1552	>	r2 = rPos.lengthSquare();
1553	>	Ic(0, 0) += mass * r2;
1554	>	Ic(1, 1) += mass * r2;
1555	>	Ic(2, 2) += mass * r2;
1556	>
1557	>	if (rnemdFluxType_ == rnemdFullKE) {
1558	>	if (sd->isDirectional()) {
1559	>	Vector3d angMom = sd->getJ();
1560	>	Mat3x3d I = sd->getI();
1561	>	if (sd->isLinear()) {
1562	>	int i = sd->linearAxis();
1563	>	int j = (i + 1) % 3;
1564	>	int k = (i + 2) % 3;
1565	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1566	>	angMom[k] * angMom[k] / I(k, k);
1567	>	} else {
1568	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1569	>	angMom[1] * angMom[1] / I(1, 1) +
1570	>	angMom[2] * angMom[2] / I(2, 2);
1571	>	}
1572	>	}
1573		}
1574		}
1575
1576		Kh *= 0.5;
1577		Kc *= 0.5;
1578	<
1201	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	<	<< "\tKc= " << Kc << endl;
1203	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	<
1578	>
1579		#ifdef IS_MPI
1580		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1581		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1582	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1583	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1585		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1586		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1587		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1589	+	MPI::REALTYPE, MPI::SUM);
1590	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1591	+	MPI::REALTYPE, MPI::SUM);
1592		#endif
1593	+
1594
1595	+	Vector3d ac, acrec, bc, bcrec;
1596	+	Vector3d ah, ahrec, bh, bhrec;
1597	+	RealType cNumerator, cDenominator;
1598	+	RealType hNumerator, hDenominator;
1599	+
1600	+
1601		bool successfulExchange = false;
1602		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1603		Vector3d vc = Pc / Mc;
1604	<	Vector3d ac = njzp_ / Mc + vc;
1605	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1604	>	ac = -momentumTarget_ / Mc + vc;
1605	>	acrec = -momentumTarget_ / Mc;
1606	>
1607	>	// We now need the inverse of the inertia tensor to calculate the
1608	>	// angular velocity of the cold slab;
1609	>	Mat3x3d Ici = Ic.inverse();
1610	>	Vector3d omegac = Ici * Lc;
1611	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1612	>	bcrec = bc - omegac;
1613	>
1614	>	cNumerator = Kc - kineticTarget_;
1615	>	if (doLinearPart)
1616	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1617	>
1618	>	if (doAngularPart)
1619	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1620	>
1621		if (cNumerator > 0.0) {
1622	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1622	>
1623	>	cDenominator = Kc;
1624	>
1625	>	if (doLinearPart)
1626	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1627	>
1628	>	if (doAngularPart)
1629	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1630	>
1631		if (cDenominator > 0.0) {
1632		RealType c = sqrt(cNumerator / cDenominator);
1633		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1634	+
1635		Vector3d vh = Ph / Mh;
1636	<	Vector3d ah = jzp_ / Mh + vh;
1637	<	RealType hNumerator = Kh + targetJzKE_
1638	<	- 0.5 * Mh * ah.lengthSquare();
1639	<	if (hNumerator > 0.0) {
1640	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1636	>	ah = momentumTarget_ / Mh + vh;
1637	>	ahrec = momentumTarget_ / Mh;
1638	>
1639	>	// We now need the inverse of the inertia tensor to
1640	>	// calculate the angular velocity of the hot slab;
1641	>	Mat3x3d Ihi = Ih.inverse();
1642	>	Vector3d omegah = Ihi * Lh;
1643	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1644	>	bhrec = bh - omegah;
1645	>
1646	>	hNumerator = Kh + kineticTarget_;
1647	>	if (doLinearPart)
1648	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1649	>
1650	>	if (doAngularPart)
1651	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1652	>
1653	>	if (hNumerator > 0.0) {
1654	>
1655	>	hDenominator = Kh;
1656	>	if (doLinearPart)
1657	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1658	>	if (doAngularPart)
1659	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1660	>
1661		if (hDenominator > 0.0) {
1662		RealType h = sqrt(hNumerator / hDenominator);
1663		if ((h > 0.9) && (h < 1.1)) {
1664	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1664	>
1665		vector<StuntDouble*>::iterator sdi;
1666		Vector3d vel;
1667	+	Vector3d rPos;
1668	+
1669		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1670		//vel = (*sdi)->getVel();
1671	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1671	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1672	>	if (doLinearPart)
1673	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1674	>	if (doAngularPart)
1675	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1676	>
1677		(*sdi)->setVel(vel);
1678	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1678	>	if (rnemdFluxType_ == rnemdFullKE) {
1679		if ((*sdi)->isDirectional()) {
1680		Vector3d angMom = (*sdi)->getJ() * c;
1681		(*sdi)->setJ(angMom);
#	Line 1247 | Line 1684 | namespace OpenMD {
1684		}
1685		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1686		//vel = (*sdi)->getVel();
1687	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1687	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1688	>	if (doLinearPart)
1689	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1690	>	if (doAngularPart)
1691	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1692	>
1693		(*sdi)->setVel(vel);
1694	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1694	>	if (rnemdFluxType_ == rnemdFullKE) {
1695		if ((*sdi)->isDirectional()) {
1696		Vector3d angMom = (*sdi)->getJ() * h;
1697		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1699 | namespace OpenMD {
1699		}
1700		}
1701		successfulExchange = true;
1702	<	exchangeSum_ += targetFlux_;
1703	<	// this is a redundant variable for doShiftScale() so that
1704	<	// RNEMD can output one exchange quantity needed in a job.
1263	<	// need a better way to do this.
1702	>	kineticExchange_ += kineticTarget_;
1703	>	momentumExchange_ += momentumTarget_;
1704	>	angularMomentumExchange_ += angularMomentumTarget_;
1705		}
1706		}
1707		}
#	Line 1270 | Line 1711 | namespace OpenMD {
1711		}
1712		if (successfulExchange != true) {
1713		sprintf(painCave.errMsg,
1714	<	"RNEMD: exchange NOT performed!\n");
1714	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1715	>	"\tthe constraint equations may not exist or there may be\n"
1716	>	"\tno selected objects in one or both slabs.\n");
1717		painCave.isFatal = 0;
1718		painCave.severity = OPENMD_INFO;
1719		simError();
#	Line 1278 | Line 1721 | namespace OpenMD {
1721		}
1722		}
1723
1724	+	RealType RNEMD::getDividingArea() {
1725	+
1726	+	if (hasDividingArea_) return dividingArea_;
1727	+
1728	+	RealType areaA, areaB;
1729	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1730	+
1731	+	if (hasSelectionA_) {
1732	+	int isd;
1733	+	StuntDouble* sd;
1734	+	vector<StuntDouble*> aSites;
1735	+	ConvexHull* surfaceMeshA = new ConvexHull();
1736	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1737	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1738	+	sd = seleManA_.nextSelected(isd)) {
1739	+	aSites.push_back(sd);
1740	+	}
1741	+	surfaceMeshA->computeHull(aSites);
1742	+	areaA = surfaceMeshA->getArea();
1743	+	} else {
1744	+	if (usePeriodicBoundaryConditions_) {
1745	+	// in periodic boundaries, the surface area is twice the x-y
1746	+	// area of the current box:
1747	+	areaA = 2.0 * snap->getXYarea();
1748	+	} else {
1749	+	// in non-periodic simulations, without explicitly setting
1750	+	// selections, the sphere radius sets the surface area of the
1751	+	// dividing surface:
1752	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1753	+	}
1754	+	}
1755	+
1756	+	if (hasSelectionB_) {
1757	+	int isd;
1758	+	StuntDouble* sd;
1759	+	vector<StuntDouble*> bSites;
1760	+	ConvexHull* surfaceMeshB = new ConvexHull();
1761	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1762	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1763	+	sd = seleManB_.nextSelected(isd)) {
1764	+	bSites.push_back(sd);
1765	+	}
1766	+	surfaceMeshB->computeHull(bSites);
1767	+	areaB = surfaceMeshB->getArea();
1768	+	} else {
1769	+	if (usePeriodicBoundaryConditions_) {
1770	+	// in periodic boundaries, the surface area is twice the x-y
1771	+	// area of the current box:
1772	+	areaB = 2.0 * snap->getXYarea();
1773	+	} else {
1774	+	// in non-periodic simulations, without explicitly setting
1775	+	// selections, but if a sphereBradius has been set, just use that:
1776	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1777	+	}
1778	+	}
1779	+
1780	+	dividingArea_ = min(areaA, areaB);
1781	+	hasDividingArea_ = true;
1782	+	return dividingArea_;
1783	+	}
1784	+
1785		void RNEMD::doRNEMD() {
1786	+	if (!doRNEMD_) return;
1787	+	trialCount_++;
1788
1789	<	switch(rnemdType_) {
1790	<	case rnemdKineticScale :
1791	<	case rnemdKineticScaleVAM :
1792	<	case rnemdKineticScaleAM :
1793	<	case rnemdPxScale :
1794	<	case rnemdPyScale :
1795	<	case rnemdPzScale :
1796	<	doScale();
1789	>	// object evaluator:
1790	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1791	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1792	>
1793	>	evaluatorA_.loadScriptString(selectionA_);
1794	>	evaluatorB_.loadScriptString(selectionB_);
1795	>
1796	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1797	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1798	>
1799	>	commonA_ = seleManA_ & seleMan_;
1800	>	commonB_ = seleManB_ & seleMan_;
1801	>
1802	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1803	>	// dt = exchange time interval
1804	>	// flux = target flux
1805	>	// dividingArea = smallest dividing surface between the two regions
1806	>
1807	>	hasDividingArea_ = false;
1808	>	RealType area = getDividingArea();
1809	>
1810	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1811	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1812	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1813	>
1814	>	switch(rnemdMethod_) {
1815	>	case rnemdSwap:
1816	>	doSwap(commonA_, commonB_);
1817		break;
1818	<	case rnemdKineticSwap :
1819	<	case rnemdPx :
1294	<	case rnemdPy :
1295	<	case rnemdPz :
1296	<	doSwap();
1818	>	case rnemdNIVS:
1819	>	doNIVS(commonA_, commonB_);
1820		break;
1821	<	case rnemdShiftScaleV :
1822	<	case rnemdShiftScaleVAM :
1300	<	doShiftScale();
1821	>	case rnemdVSS:
1822	>	doVSS(commonA_, commonB_);
1823		break;
1824	<	case rnemdUnknown :
1824	>	case rnemdUnkownMethod:
1825		default :
1826		break;
1827		}
1828		}
1829
1830		void RNEMD::collectData() {
1831	<
1831	>	if (!doRNEMD_) return;
1832		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1833	+
1834	+	// collectData can be called more frequently than the doRNEMD, so use the
1835	+	// computed area from the last exchange time:
1836	+	RealType area = getDividingArea();
1837	+	areaAccumulator_->add(area);
1838		Mat3x3d hmat = currentSnap_->getHmat();
1312	–
1839		seleMan_.setSelectionSet(evaluator_.evaluate());
1840
1841	<	int selei;
1841	>	int selei(0);
1842		StuntDouble* sd;
1843	<	int idx;
1843	>	int binNo;
1844
1845	+	vector<RealType> binMass(nBins_, 0.0);
1846	+	vector<RealType> binPx(nBins_, 0.0);
1847	+	vector<RealType> binPy(nBins_, 0.0);
1848	+	vector<RealType> binPz(nBins_, 0.0);
1849	+	vector<RealType> binOmegax(nBins_, 0.0);
1850	+	vector<RealType> binOmegay(nBins_, 0.0);
1851	+	vector<RealType> binOmegaz(nBins_, 0.0);
1852	+	vector<RealType> binKE(nBins_, 0.0);
1853	+	vector<int> binDOF(nBins_, 0);
1854	+	vector<int> binCount(nBins_, 0);
1855	+
1856		// alternative approach, track all molecules instead of only those
1857		// selected for scaling/swapping:
1858		/*
1859	<	SimInfo::MoleculeIterator miter;
1860	<	vector<StuntDouble*>::iterator iiter;
1861	<	Molecule* mol;
1862	<	StuntDouble* integrableObject;
1863	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1864	<	mol = info_->nextMolecule(miter))
1865	<	integrableObject is essentially sd
1866	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1867	<	integrableObject != NULL;
1868	<	integrableObject = mol->nextIntegrableObject(iiter))
1859	>	SimInfo::MoleculeIterator miter;
1860	>	vector<StuntDouble*>::iterator iiter;
1861	>	Molecule* mol;
1862	>	StuntDouble* sd;
1863	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1864	>	mol = info_->nextMolecule(miter))
1865	>	sd is essentially sd
1866	>	for (sd = mol->beginIntegrableObject(iiter);
1867	>	sd != NULL;
1868	>	sd = mol->nextIntegrableObject(iiter))
1869		*/
1870	+
1871		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1872	<	sd = seleMan_.nextSelected(selei)) {
1873	<
1336	<	idx = sd->getLocalIndex();
1337	<
1872	>	sd = seleMan_.nextSelected(selei)) {
1873	>
1874		Vector3d pos = sd->getPos();
1875
1876		// wrap the stuntdouble's position back into the box:
1877
1878	<	if (usePeriodicBoundaryConditions_)
1878	>	if (usePeriodicBoundaryConditions_) {
1879		currentSnap_->wrapVector(pos);
1880	<
1881	<	// which bin is this stuntdouble in?
1882	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1883	<
1884	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1885	<	rnemdLogWidth_;
1886	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1887	<	/*
1888	<	if (rnemdLogWidth_ == midBin_ + 1)
1889	<	if (binNo > midBin_)
1890	<	binNo = nBins_ - binNo;
1355	<	*/
1880	>	// which bin is this stuntdouble in?
1881	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1882	>	// Shift molecules by half a box to have bins start at 0
1883	>	// The modulo operator is used to wrap the case when we are
1884	>	// beyond the end of the bins back to the beginning.
1885	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1886	>	} else {
1887	>	Vector3d rPos = pos - coordinateOrigin_;
1888	>	binNo = int(rPos.length() / binWidth_);
1889	>	}
1890	>
1891		RealType mass = sd->getMass();
1357	–	mHist_[binNo] += mass;
1892		Vector3d vel = sd->getVel();
1893	<	RealType value;
1894	<	//RealType xVal, yVal, zVal;
1895	<
1896	<	if (outputTemp_) {
1897	<	value = mass * vel.lengthSquare();
1898	<	tempCount_[binNo] += 3;
1899	<	if (sd->isDirectional()) {
1900	<	Vector3d angMom = sd->getJ();
1901	<	Mat3x3d I = sd->getI();
1902	<	if (sd->isLinear()) {
1903	<	int i = sd->linearAxis();
1904	<	int j = (i + 1) % 3;
1905	<	int k = (i + 2) % 3;
1906	<	value += angMom[j] * angMom[j] / I(j, j) +
1907	<	angMom[k] * angMom[k] / I(k, k);
1908	<	tempCount_[binNo] +=2;
1909	<	} else {
1910	<	value += angMom[0] * angMom[0] / I(0, 0) +
1911	<	angMom[1]*angMom[1]/I(1, 1) +
1912	<	angMom[2]*angMom[2]/I(2, 2);
1913	<	tempCount_[binNo] +=3;
1914	<	}
1915	<	}
1916	<	value = value / PhysicalConstants::energyConvert
1917	<	/ PhysicalConstants::kb;//may move to getStatus()
1918	<	tempHist_[binNo] += value;
1893	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1894	>	Vector3d aVel = cross(rPos, vel);
1895	>
1896	>	if (binNo >= 0 && binNo < nBins_)  {
1897	>	binCount[binNo]++;
1898	>	binMass[binNo] += mass;
1899	>	binPx[binNo] += mass*vel.x();
1900	>	binPy[binNo] += mass*vel.y();
1901	>	binPz[binNo] += mass*vel.z();
1902	>	binOmegax[binNo] += aVel.x();
1903	>	binOmegay[binNo] += aVel.y();
1904	>	binOmegaz[binNo] += aVel.z();
1905	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1906	>	binDOF[binNo] += 3;
1907	>
1908	>	if (sd->isDirectional()) {
1909	>	Vector3d angMom = sd->getJ();
1910	>	Mat3x3d I = sd->getI();
1911	>	if (sd->isLinear()) {
1912	>	int i = sd->linearAxis();
1913	>	int j = (i + 1) % 3;
1914	>	int k = (i + 2) % 3;
1915	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1916	>	angMom[k] * angMom[k] / I(k, k));
1917	>	binDOF[binNo] += 2;
1918	>	} else {
1919	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1920	>	angMom[1] * angMom[1] / I(1, 1) +
1921	>	angMom[2] * angMom[2] / I(2, 2));
1922	>	binDOF[binNo] += 3;
1923	>	}
1924	>	}
1925		}
1926	<	if (outputVx_) {
1927	<	value = mass * vel[0];
1928	<	//vxzCount_[binNo]++;
1929	<	pxzHist_[binNo] += value;
1930	<	}
1931	<	if (outputVy_) {
1932	<	value = mass * vel[1];
1933	<	//vyzCount_[binNo]++;
1934	<	pyzHist_[binNo] += value;
1935	<	}
1926	>	}
1927	>
1928	>	#ifdef IS_MPI
1929	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1930	>	nBins_, MPI::INT, MPI::SUM);
1931	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1932	>	nBins_, MPI::REALTYPE, MPI::SUM);
1933	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1934	>	nBins_, MPI::REALTYPE, MPI::SUM);
1935	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1936	>	nBins_, MPI::REALTYPE, MPI::SUM);
1937	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1938	>	nBins_, MPI::REALTYPE, MPI::SUM);
1939	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1940	>	nBins_, MPI::REALTYPE, MPI::SUM);
1941	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1942	>	nBins_, MPI::REALTYPE, MPI::SUM);
1943	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1944	>	nBins_, MPI::REALTYPE, MPI::SUM);
1945	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1946	>	nBins_, MPI::REALTYPE, MPI::SUM);
1947	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1948	>	nBins_, MPI::INT, MPI::SUM);
1949	>	#endif
1950
1951	<	if (output3DTemp_) {
1952	<	value = mass * vel.x() * vel.x();
1953	<	xTempHist_[binNo] += value;
1954	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1955	<	/ PhysicalConstants::kb;
1956	<	yTempHist_[binNo] += value;
1957	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1958	<	/ PhysicalConstants::kb;
1959	<	zTempHist_[binNo] += value;
1960	<	xyzTempCount_[binNo]++;
1951	>	Vector3d vel;
1952	>	Vector3d aVel;
1953	>	RealType den;
1954	>	RealType temp;
1955	>	RealType z;
1956	>	RealType r;
1957	>	for (int i = 0; i < nBins_; i++) {
1958	>	if (usePeriodicBoundaryConditions_) {
1959	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1960	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1961	>	/ currentSnap_->getVolume() ;
1962	>	} else {
1963	>	r = (((RealType)i + 0.5) * binWidth_);
1964	>	RealType rinner = (RealType)i * binWidth_;
1965	>	RealType router = (RealType)(i+1) * binWidth_;
1966	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1967	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1968		}
1969	<	if (outputRotTemp_) {
1970	<	if (sd->isDirectional()) {
1971	<	Vector3d angMom = sd->getJ();
1972	<	Mat3x3d I = sd->getI();
1973	<	if (sd->isLinear()) {
1974	<	int i = sd->linearAxis();
1414	<	int j = (i + 1) % 3;
1415	<	int k = (i + 2) % 3;
1416	<	value = angMom[j] * angMom[j] / I(j, j) +
1417	<	angMom[k] * angMom[k] / I(k, k);
1418	<	rotTempCount_[binNo] +=2;
1419	<	} else {
1420	<	value = angMom[0] * angMom[0] / I(0, 0) +
1421	<	angMom[1] * angMom[1] / I(1, 1) +
1422	<	angMom[2] * angMom[2] / I(2, 2);
1423	<	rotTempCount_[binNo] +=3;
1424	<	}
1425	<	}
1426	<	value = value / PhysicalConstants::energyConvert
1427	<	/ PhysicalConstants::kb;//may move to getStatus()
1428	<	rotTempHist_[binNo] += value;
1429	<	}
1969	>	vel.x() = binPx[i] / binMass[i];
1970	>	vel.y() = binPy[i] / binMass[i];
1971	>	vel.z() = binPz[i] / binMass[i];
1972	>	aVel.x() = binOmegax[i] / binCount[i];
1973	>	aVel.y() = binOmegay[i] / binCount[i];
1974	>	aVel.z() = binOmegaz[i] / binCount[i];
1975
1976	+	if (binCount[i] > 0) {
1977	+	// only add values if there are things to add
1978	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1979	+	PhysicalConstants::energyConvert);
1980	+
1981	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1982	+	if(outputMask_[j]) {
1983	+	switch(j) {
1984	+	case Z:
1985	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1986	+	break;
1987	+	case R:
1988	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1989	+	break;
1990	+	case TEMPERATURE:
1991	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1992	+	break;
1993	+	case VELOCITY:
1994	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1995	+	break;
1996	+	case ANGULARVELOCITY:
1997	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1998	+	break;
1999	+	case DENSITY:
2000	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2001	+	break;
2002	+	}
2003	+	}
2004	+	}
2005	+	}
2006		}
2007		}
2008
2009		void RNEMD::getStarted() {
2010	+	if (!doRNEMD_) return;
2011	+	hasDividingArea_ = false;
2012		collectData();
2013	<	/*now can output profile in step 0, but might not be useful;
1437	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	<	Stats& stat = currentSnap_->statData;
1439	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1440	<	*/
1441	<	//may output a header for the log file here
1442	<	getStatus();
2013	>	writeOutputFile();
2014		}
2015
2016	<	void RNEMD::getStatus() {
2017	<
2018	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2019	<	Stats& stat = currentSnap_->statData;
2020	<	RealType time = currentSnap_->getTime();
2021	<
2022	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2023	<	//or to be more meaningful, define another item as exchangeSum_ / time
2024	<	int j;
2025	<
2016	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2017	>	if (!doRNEMD_) return;
2018	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2019	>
2020	>	while(tokenizer.hasMoreTokens()) {
2021	>	std::string token(tokenizer.nextToken());
2022	>	toUpper(token);
2023	>	OutputMapType::iterator i = outputMap_.find(token);
2024	>	if (i != outputMap_.end()) {
2025	>	outputMask_.set(i->second);
2026	>	} else {
2027	>	sprintf( painCave.errMsg,
2028	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2029	>	"\toutputFileFormat keyword.\n", token.c_str() );
2030	>	painCave.isFatal = 0;
2031	>	painCave.severity = OPENMD_ERROR;
2032	>	simError();
2033	>	}
2034	>	}
2035	>	}
2036	>
2037	>	void RNEMD::writeOutputFile() {
2038	>	if (!doRNEMD_) return;
2039	>
2040		#ifdef IS_MPI
1456	–
1457	–	// all processors have the same number of bins, and STL vectors pack their
1458	–	// arrays, so in theory, this should be safe:
1459	–
1460	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1461	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1462	–	if (outputTemp_) {
1463	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1464	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1465	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1466	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1467	–	}
1468	–	if (outputVx_) {
1469	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1470	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1471	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1472	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1473	–	}
1474	–	if (outputVy_) {
1475	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1476	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1477	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1478	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1479	–	}
1480	–	if (output3DTemp_) {
1481	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1482	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1483	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1484	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1485	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1486	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1487	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1488	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1489	–	}
1490	–	if (outputRotTemp_) {
1491	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1492	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1493	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1494	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1495	–	}
1496	–
2041		// If we're the root node, should we print out the results
2042		int worldRank = MPI::COMM_WORLD.Get_rank();
2043		if (worldRank == 0) {
2044		#endif
2045	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2046	+
2047	+	if( !rnemdFile_ ){
2048	+	sprintf( painCave.errMsg,
2049	+	"Could not open \"%s\" for RNEMD output.\n",
2050	+	rnemdFileName_.c_str());
2051	+	painCave.isFatal = 1;
2052	+	simError();
2053	+	}
2054
2055	<	if (outputTemp_) {
2056	<	tempLog_ << time;
2057	<	for (j = 0; j < rnemdLogWidth_; j++) {
2058	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
2059	<	}
2060	<	tempLog_ << endl;
2055	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2056	>
2057	>	RealType time = currentSnap_->getTime();
2058	>	RealType avgArea;
2059	>	areaAccumulator_->getAverage(avgArea);
2060	>	RealType Jz = kineticExchange_ / (time * avgArea)
2061	>	/ PhysicalConstants::energyConvert;
2062	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
2063	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
2064	>
2065	>	rnemdFile_ << "#######################################################\n";
2066	>	rnemdFile_ << "# RNEMD {\n";
2067	>
2068	>	map<string, RNEMDMethod>::iterator mi;
2069	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2070	>	if ( (*mi).second == rnemdMethod_)
2071	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2072		}
2073	<	if (outputVx_) {
2074	<	vxzLog_ << time;
2075	<	for (j = 0; j < rnemdLogWidth_; j++) {
2076	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1513	<	}
1514	<	vxzLog_ << endl;
2073	>	map<string, RNEMDFluxType>::iterator fi;
2074	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2075	>	if ( (*fi).second == rnemdFluxType_)
2076	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2077		}
2078	<	if (outputVy_) {
2079	<	vyzLog_ << time;
1518	<	for (j = 0; j < rnemdLogWidth_; j++) {
1519	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
1522	<	}
2078	>
2079	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2080
2081	<	if (output3DTemp_) {
2082	<	RealType temp;
2083	<	xTempLog_ << time;
2084	<	for (j = 0; j < rnemdLogWidth_; j++) {
2085	<	if (outputVx_)
2086	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2087	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2088	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2089	<	xTempLog_ << "\t" << temp;
2081	>	rnemdFile_ << "#    objectSelection = \""
2082	>	<< rnemdObjectSelection_ << "\";\n";
2083	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2084	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2085	>	rnemdFile_ << "# }\n";
2086	>	rnemdFile_ << "#######################################################\n";
2087	>	rnemdFile_ << "# RNEMD report:\n";
2088	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2089	>	rnemdFile_ << "# Target flux:\n";
2090	>	rnemdFile_ << "#           kinetic = "
2091	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2092	>	<< " (kcal/mol/A^2/fs)\n";
2093	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2094	>	<< " (amu/A/fs^2)\n";
2095	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2096	>	<< " (amu/A^2/fs^2)\n";
2097	>	rnemdFile_ << "# Target one-time exchanges:\n";
2098	>	rnemdFile_ << "#          kinetic = "
2099	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2100	>	<< " (kcal/mol)\n";
2101	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2102	>	<< " (amu*A/fs)\n";
2103	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2104	>	<< " (amu*A^2/fs)\n";
2105	>	rnemdFile_ << "# Actual exchange totals:\n";
2106	>	rnemdFile_ << "#          kinetic = "
2107	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2108	>	<< " (kcal/mol)\n";
2109	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2110	>	<< " (amu*A/fs)\n";
2111	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2112	>	<< " (amu*A^2/fs)\n";
2113	>	rnemdFile_ << "# Actual flux:\n";
2114	>	rnemdFile_ << "#          kinetic = " << Jz
2115	>	<< " (kcal/mol/A^2/fs)\n";
2116	>	rnemdFile_ << "#          momentum = " << JzP
2117	>	<< " (amu/A/fs^2)\n";
2118	>	rnemdFile_ << "#  angular momentum = " << JzL
2119	>	<< " (amu/A^2/fs^2)\n";
2120	>	rnemdFile_ << "# Exchange statistics:\n";
2121	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2122	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2123	>	if (rnemdMethod_ == rnemdNIVS) {
2124	>	rnemdFile_ << "#  NIVS root-check errors = "
2125	>	<< failRootCount_ << "\n";
2126	>	}
2127	>	rnemdFile_ << "#######################################################\n";
2128	>
2129	>
2130	>
2131	>	//write title
2132	>	rnemdFile_ << "#";
2133	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2134	>	if (outputMask_[i]) {
2135	>	rnemdFile_ << "\t" << data_[i].title <<
2136	>	"(" << data_[i].units << ")";
2137	>	// add some extra tabs for column alignment
2138	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2139		}
1534	–	xTempLog_ << endl;
1535	–	yTempLog_ << time;
1536	–	for (j = 0; j < rnemdLogWidth_; j++) {
1537	–	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1538	–	}
1539	–	yTempLog_ << endl;
1540	–	zTempLog_ << time;
1541	–	for (j = 0; j < rnemdLogWidth_; j++) {
1542	–	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1543	–	}
1544	–	zTempLog_ << endl;
2140		}
2141	<	if (outputRotTemp_) {
2142	<	rotTempLog_ << time;
2143	<	for (j = 0; j < rnemdLogWidth_; j++) {
2144	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2145	<	}
2146	<	rotTempLog_ << endl;
2147	<	}
2141	>	rnemdFile_ << std::endl;
2142	>
2143	>	rnemdFile_.precision(8);
2144	>
2145	>	for (int j = 0; j < nBins_; j++) {
2146	>
2147	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2148	>	if (outputMask_[i]) {
2149	>	if (data_[i].dataType == "RealType")
2150	>	writeReal(i,j);
2151	>	else if (data_[i].dataType == "Vector3d")
2152	>	writeVector(i,j);
2153	>	else {
2154	>	sprintf( painCave.errMsg,
2155	>	"RNEMD found an unknown data type for: %s ",
2156	>	data_[i].title.c_str());
2157	>	painCave.isFatal = 1;
2158	>	simError();
2159	>	}
2160	>	}
2161	>	}
2162	>	rnemdFile_ << std::endl;
2163	>
2164	>	}
2165
2166	+	rnemdFile_ << "#######################################################\n";
2167	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2168	+	rnemdFile_ << "#######################################################\n";
2169	+
2170	+
2171	+	for (int j = 0; j < nBins_; j++) {
2172	+	rnemdFile_ << "#";
2173	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2174	+	if (outputMask_[i]) {
2175	+	if (data_[i].dataType == "RealType")
2176	+	writeRealStdDev(i,j);
2177	+	else if (data_[i].dataType == "Vector3d")
2178	+	writeVectorStdDev(i,j);
2179	+	else {
2180	+	sprintf( painCave.errMsg,
2181	+	"RNEMD found an unknown data type for: %s ",
2182	+	data_[i].title.c_str());
2183	+	painCave.isFatal = 1;
2184	+	simError();
2185	+	}
2186	+	}
2187	+	}
2188	+	rnemdFile_ << std::endl;
2189	+
2190	+	}
2191	+
2192	+	rnemdFile_.flush();
2193	+	rnemdFile_.close();
2194	+
2195		#ifdef IS_MPI
2196		}
2197		#endif
2198	+
2199	+	}
2200	+
2201	+	void RNEMD::writeReal(int index, unsigned int bin) {
2202	+	if (!doRNEMD_) return;
2203	+	assert(index >=0 && index < ENDINDEX);
2204	+	assert(int(bin) < nBins_);
2205	+	RealType s;
2206	+	int count;
2207	+
2208	+	count = data_[index].accumulator[bin]->count();
2209	+	if (count == 0) return;
2210	+
2211	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2212	+
2213	+	if (! isinf(s) && ! isnan(s)) {
2214	+	rnemdFile_ << "\t" << s;
2215	+	} else{
2216	+	sprintf( painCave.errMsg,
2217	+	"RNEMD detected a numerical error writing: %s for bin %d",
2218	+	data_[index].title.c_str(), bin);
2219	+	painCave.isFatal = 1;
2220	+	simError();
2221	+	}
2222	+	}
2223	+
2224	+	void RNEMD::writeVector(int index, unsigned int bin) {
2225	+	if (!doRNEMD_) return;
2226	+	assert(index >=0 && index < ENDINDEX);
2227	+	assert(int(bin) < nBins_);
2228	+	Vector3d s;
2229	+	int count;
2230	+
2231	+	count = data_[index].accumulator[bin]->count();
2232
2233	<	for (j = 0; j < rnemdLogWidth_; j++) {
2234	<	mHist_[j] = 0.0;
2233	>	if (count == 0) return;
2234	>
2235	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2236	>	if (isinf(s[0]) || isnan(s[0]) ||
2237	>	isinf(s[1]) || isnan(s[1]) ||
2238	>	isinf(s[2]) || isnan(s[2]) ) {
2239	>	sprintf( painCave.errMsg,
2240	>	"RNEMD detected a numerical error writing: %s for bin %d",
2241	>	data_[index].title.c_str(), bin);
2242	>	painCave.isFatal = 1;
2243	>	simError();
2244	>	} else {
2245	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2246		}
2247	<	if (outputTemp_)
1562	<	for (j = 0; j < rnemdLogWidth_; j++) {
1563	<	tempCount_[j] = 0;
1564	<	tempHist_[j] = 0.0;
1565	<	}
1566	<	if (outputVx_)
1567	<	for (j = 0; j < rnemdLogWidth_; j++) {
1568	<	//pxzCount_[j] = 0;
1569	<	pxzHist_[j] = 0.0;
1570	<	}
1571	<	if (outputVy_)
1572	<	for (j = 0; j < rnemdLogWidth_; j++) {
1573	<	//pyzCount_[j] = 0;
1574	<	pyzHist_[j] = 0.0;
1575	<	}
2247	>	}
2248
2249	<	if (output3DTemp_)
2250	<	for (j = 0; j < rnemdLogWidth_; j++) {
2251	<	xTempHist_[j] = 0.0;
2252	<	yTempHist_[j] = 0.0;
2253	<	zTempHist_[j] = 0.0;
2254	<	xyzTempCount_[j] = 0;
2255	<	}
2256	<	if (outputRotTemp_)
2257	<	for (j = 0; j < rnemdLogWidth_; j++) {
2258	<	rotTempCount_[j] = 0;
2259	<	rotTempHist_[j] = 0.0;
2260	<	}
2249	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2250	>	if (!doRNEMD_) return;
2251	>	assert(index >=0 && index < ENDINDEX);
2252	>	assert(int(bin) < nBins_);
2253	>	RealType s;
2254	>	int count;
2255	>
2256	>	count = data_[index].accumulator[bin]->count();
2257	>	if (count == 0) return;
2258	>
2259	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2260	>
2261	>	if (! isinf(s) && ! isnan(s)) {
2262	>	rnemdFile_ << "\t" << s;
2263	>	} else{
2264	>	sprintf( painCave.errMsg,
2265	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2266	>	data_[index].title.c_str(), bin);
2267	>	painCave.isFatal = 1;
2268	>	simError();
2269	>	}
2270		}
2271	+
2272	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2273	+	if (!doRNEMD_) return;
2274	+	assert(index >=0 && index < ENDINDEX);
2275	+	assert(int(bin) < nBins_);
2276	+	Vector3d s;
2277	+	int count;
2278	+
2279	+	count = data_[index].accumulator[bin]->count();
2280	+	if (count == 0) return;
2281	+
2282	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2283	+	if (isinf(s[0]) || isnan(s[0]) ||
2284	+	isinf(s[1]) || isnan(s[1]) ||
2285	+	isinf(s[2]) || isnan(s[2]) ) {
2286	+	sprintf( painCave.errMsg,
2287	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2288	+	data_[index].title.c_str(), bin);
2289	+	painCave.isFatal = 1;
2290	+	simError();
2291	+	} else {
2292	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2293	+	}
2294	+	}
2295		}
2296

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