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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 1867 by gezelter, Mon Apr 29 17:53:48 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->getSlabBCenter();
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	>
581	>	// object evaluator:
582	>	evaluator_.loadScriptString(rnemdObjectSelection_);
583	>	seleMan_.setSelectionSet(evaluator_.evaluate());
584	>	evaluatorA_.loadScriptString(selectionA_);
585	>	evaluatorB_.loadScriptString(selectionB_);
586	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
587	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
588	>	commonA_ = seleManA_ & seleMan_;
589	>	commonB_ = seleManB_ & seleMan_;
590		}
591
323	–	RNEMD::~RNEMD() {
324	–	delete randNumGen_;
592
593	+	RNEMD::~RNEMD() {
594	+	if (!doRNEMD_) return;
595		#ifdef IS_MPI
596		if (worldRank == 0) {
597		#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();
598
599	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
600	<	rnemdType_ == rnemdPyScale) {
601	<	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();
599	>	writeOutputFile();
600	>
601	>	rnemdFile_.close();
602
603		#ifdef IS_MPI
604		}
605		#endif
606		}
607	+
608	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
609	+	if (!doRNEMD_) return;
610	+	int selei;
611	+	int selej;
612
366	–	void RNEMD::doSwap() {
367	–
613		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
614		Mat3x3d hmat = currentSnap_->getHmat();
615
371	–	seleMan_.setSelectionSet(evaluator_.evaluate());
372	–
373	–	int selei;
616		StuntDouble* sd;
375	–	int idx;
617
618		RealType min_val;
619		bool min_found = false;
#	Line 382 | Line 623 | namespace OpenMD {
623		bool max_found = false;
624		StuntDouble* max_sd;
625
626	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
627	<	sd = seleMan_.nextSelected(selei)) {
626	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
627	>	sd = seleManA_.nextSelected(selei)) {
628
388	–	idx = sd->getLocalIndex();
389	–
629		Vector3d pos = sd->getPos();
630	<
630	>
631		// wrap the stuntdouble's position back into the box:
632	<
632	>
633		if (usePeriodicBoundaryConditions_)
634		currentSnap_->wrapVector(pos);
635	<
636	<	// which bin is this stuntdouble in?
637	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
638	<
639	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
640	<
641	<
403	<	// if we're in bin 0 or the middleBin
404	<	if (binNo == 0 || binNo == midBin_) {
635	>
636	>	RealType mass = sd->getMass();
637	>	Vector3d vel = sd->getVel();
638	>	RealType value;
639	>
640	>	switch(rnemdFluxType_) {
641	>	case rnemdKE :
642
643	<	RealType mass = sd->getMass();
644	<	Vector3d vel = sd->getVel();
645	<	RealType value;
646	<
647	<	switch(rnemdType_) {
411	<	case rnemdKineticSwap :
643	>	value = mass * vel.lengthSquare();
644	>
645	>	if (sd->isDirectional()) {
646	>	Vector3d angMom = sd->getJ();
647	>	Mat3x3d I = sd->getI();
648
649	<	value = mass * vel.lengthSquare();
650	<
651	<	if (sd->isDirectional()) {
652	<	Vector3d angMom = sd->getJ();
653	<	Mat3x3d I = sd->getI();
654	<
655	<	if (sd->isLinear()) {
656	<	int i = sd->linearAxis();
657	<	int j = (i + 1) % 3;
658	<	int k = (i + 2) % 3;
659	<	value += angMom[j] * angMom[j] / I(j, j) +
660	<	angMom[k] * angMom[k] / I(k, k);
661	<	} else {
662	<	value += angMom[0]*angMom[0]/I(0, 0)
663	<	+ angMom[1]*angMom[1]/I(1, 1)
664	<	+ angMom[2]*angMom[2]/I(2, 2);
665	<	}
666	<	} //angular momenta exchange enabled
667	<	//energyConvert temporarily disabled
668	<	//make exchangeSum_ comparable between swap & scale
669	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
670	<	value *= 0.5;
671	<	break;
672	<	case rnemdPx :
673	<	value = mass * vel[0];
674	<	break;
675	<	case rnemdPy :
676	<	value = mass * vel[1];
677	<	break;
678	<	case rnemdPz :
679	<	value = mass * vel[2];
680	<	break;
681	<	default :
682	<	break;
649	>	if (sd->isLinear()) {
650	>	int i = sd->linearAxis();
651	>	int j = (i + 1) % 3;
652	>	int k = (i + 2) % 3;
653	>	value += angMom[j] * angMom[j] / I(j, j) +
654	>	angMom[k] * angMom[k] / I(k, k);
655	>	} else {
656	>	value += angMom[0]*angMom[0]/I(0, 0)
657	>	+ angMom[1]*angMom[1]/I(1, 1)
658	>	+ angMom[2]*angMom[2]/I(2, 2);
659	>	}
660	>	} //angular momenta exchange enabled
661	>	value *= 0.5;
662	>	break;
663	>	case rnemdPx :
664	>	value = mass * vel[0];
665	>	break;
666	>	case rnemdPy :
667	>	value = mass * vel[1];
668	>	break;
669	>	case rnemdPz :
670	>	value = mass * vel[2];
671	>	break;
672	>	default :
673	>	break;
674	>	}
675	>	if (!max_found) {
676	>	max_val = value;
677	>	max_sd = sd;
678	>	max_found = true;
679	>	} else {
680	>	if (max_val < value) {
681	>	max_val = value;
682	>	max_sd = sd;
683		}
684	+	}
685	+	}
686
687	<	if (binNo == 0) {
688	<	if (!min_found) {
689	<	min_val = value;
690	<	min_sd = sd;
691	<	min_found = true;
692	<	} else {
693	<	if (min_val > value) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	}
697	<	}
698	<	} else { //midBin_
699	<	if (!max_found) {
700	<	max_val = value;
701	<	max_sd = sd;
702	<	max_found = true;
703	<	} else {
704	<	if (max_val < value) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	}
708	<	}
709	<	}
687	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
688	>	sd = seleManB_.nextSelected(selej)) {
689	>
690	>	Vector3d pos = sd->getPos();
691	>
692	>	// wrap the stuntdouble's position back into the box:
693	>
694	>	if (usePeriodicBoundaryConditions_)
695	>	currentSnap_->wrapVector(pos);
696	>
697	>	RealType mass = sd->getMass();
698	>	Vector3d vel = sd->getVel();
699	>	RealType value;
700	>
701	>	switch(rnemdFluxType_) {
702	>	case rnemdKE :
703	>
704	>	value = mass * vel.lengthSquare();
705	>
706	>	if (sd->isDirectional()) {
707	>	Vector3d angMom = sd->getJ();
708	>	Mat3x3d I = sd->getI();
709	>
710	>	if (sd->isLinear()) {
711	>	int i = sd->linearAxis();
712	>	int j = (i + 1) % 3;
713	>	int k = (i + 2) % 3;
714	>	value += angMom[j] * angMom[j] / I(j, j) +
715	>	angMom[k] * angMom[k] / I(k, k);
716	>	} else {
717	>	value += angMom[0]*angMom[0]/I(0, 0)
718	>	+ angMom[1]*angMom[1]/I(1, 1)
719	>	+ angMom[2]*angMom[2]/I(2, 2);
720	>	}
721	>	} //angular momenta exchange enabled
722	>	value *= 0.5;
723	>	break;
724	>	case rnemdPx :
725	>	value = mass * vel[0];
726	>	break;
727	>	case rnemdPy :
728	>	value = mass * vel[1];
729	>	break;
730	>	case rnemdPz :
731	>	value = mass * vel[2];
732	>	break;
733	>	default :
734	>	break;
735		}
736	+
737	+	if (!min_found) {
738	+	min_val = value;
739	+	min_sd = sd;
740	+	min_found = true;
741	+	} else {
742	+	if (min_val > value) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	}
746	+	}
747		}
748	<
749	<	#ifdef IS_MPI
750	<	int nProc, worldRank;
751	<
478	<	nProc = MPI::COMM_WORLD.Get_size();
479	<	worldRank = MPI::COMM_WORLD.Get_rank();
480	<
748	>
749	>	#ifdef IS_MPI
750	>	int worldRank = MPI::COMM_WORLD.Get_rank();
751	>
752		bool my_min_found = min_found;
753		bool my_max_found = max_found;
754
#	Line 532 | Line 803 | namespace OpenMD {
803		Vector3d max_vel = max_sd->getVel();
804		RealType temp_vel;
805
806	<	switch(rnemdType_) {
807	<	case rnemdKineticSwap :
806	>	switch(rnemdFluxType_) {
807	>	case rnemdKE :
808		min_sd->setVel(max_vel);
809		max_sd->setVel(min_vel);
810		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 584 | Line 855 | namespace OpenMD {
855		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
856		min_vals.rank, 0, status);
857
858	<	switch(rnemdType_) {
859	<	case rnemdKineticSwap :
858	>	switch(rnemdFluxType_) {
859	>	case rnemdKE :
860		max_sd->setVel(min_vel);
861		//angular momenta exchange enabled
862		if (max_sd->isDirectional()) {
#	Line 630 | Line 901 | namespace OpenMD {
901		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
902		max_vals.rank, 0, status);
903
904	<	switch(rnemdType_) {
905	<	case rnemdKineticSwap :
904	>	switch(rnemdFluxType_) {
905	>	case rnemdKE :
906		min_sd->setVel(max_vel);
907		//angular momenta exchange enabled
908		if (min_sd->isDirectional()) {
#	Line 665 | Line 936 | namespace OpenMD {
936		}
937		}
938		#endif
939	<	exchangeSum_ += max_val - min_val;
939	>
940	>	switch(rnemdFluxType_) {
941	>	case rnemdKE:
942	>	kineticExchange_ += max_val - min_val;
943	>	break;
944	>	case rnemdPx:
945	>	momentumExchange_.x() += max_val - min_val;
946	>	break;
947	>	case rnemdPy:
948	>	momentumExchange_.y() += max_val - min_val;
949	>	break;
950	>	case rnemdPz:
951	>	momentumExchange_.z() += max_val - min_val;
952	>	break;
953	>	default:
954	>	break;
955	>	}
956		} else {
957		sprintf(painCave.errMsg,
958	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
958	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
959		painCave.isFatal = 0;
960		painCave.severity = OPENMD_INFO;
961		simError();
#	Line 676 | Line 963 | namespace OpenMD {
963		}
964		} else {
965		sprintf(painCave.errMsg,
966	<	"RNEMD: exchange NOT performed because selected object\n"
967	<	"\tnot present in at least one of the two slabs.\n");
966	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
967	>	"\twas not present in at least one of the two slabs.\n");
968		painCave.isFatal = 0;
969		painCave.severity = OPENMD_INFO;
970		simError();
971		failTrialCount_++;
972	<	}
686	<
972	>	}
973		}
974
975	<	void RNEMD::doScale() {
975	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
976	>	if (!doRNEMD_) return;
977	>	int selei;
978	>	int selej;
979
980		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
981	+	RealType time = currentSnap_->getTime();
982		Mat3x3d hmat = currentSnap_->getHmat();
983
694	–	seleMan_.setSelectionSet(evaluator_.evaluate());
695	–
696	–	int selei;
984		StuntDouble* sd;
698	–	int idx;
985
986		vector<StuntDouble*> hotBin, coldBin;
987
#	Line 714 | Line 1000 | namespace OpenMD {
1000		RealType Kcz = 0.0;
1001		RealType Kcw = 0.0;
1002
1003	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1004	<	sd = seleMan_.nextSelected(selei)) {
1003	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1004	>	sd = smanA.nextSelected(selei)) {
1005
720	–	idx = sd->getLocalIndex();
721	–
1006		Vector3d pos = sd->getPos();
1007	<
1007	>
1008		// wrap the stuntdouble's position back into the box:
1009	<
1009	>
1010		if (usePeriodicBoundaryConditions_)
1011		currentSnap_->wrapVector(pos);
1012	<
1013	<	// which bin is this stuntdouble in?
1014	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1012	>
1013	>
1014	>	RealType mass = sd->getMass();
1015	>	Vector3d vel = sd->getVel();
1016	>
1017	>	hotBin.push_back(sd);
1018	>	Phx += mass * vel.x();
1019	>	Phy += mass * vel.y();
1020	>	Phz += mass * vel.z();
1021	>	Khx += mass * vel.x() * vel.x();
1022	>	Khy += mass * vel.y() * vel.y();
1023	>	Khz += mass * vel.z() * vel.z();
1024	>	if (sd->isDirectional()) {
1025	>	Vector3d angMom = sd->getJ();
1026	>	Mat3x3d I = sd->getI();
1027	>	if (sd->isLinear()) {
1028	>	int i = sd->linearAxis();
1029	>	int j = (i + 1) % 3;
1030	>	int k = (i + 2) % 3;
1031	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1032	>	angMom[k] * angMom[k] / I(k, k);
1033	>	} else {
1034	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1035	>	+ angMom[1]*angMom[1]/I(1, 1)
1036	>	+ angMom[2]*angMom[2]/I(2, 2);
1037	>	}
1038	>	}
1039	>	}
1040	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1041	>	sd = smanB.nextSelected(selej)) {
1042	>	Vector3d pos = sd->getPos();
1043	>
1044	>	// wrap the stuntdouble's position back into the box:
1045	>
1046	>	if (usePeriodicBoundaryConditions_)
1047	>	currentSnap_->wrapVector(pos);
1048	>
1049	>	RealType mass = sd->getMass();
1050	>	Vector3d vel = sd->getVel();
1051
1052	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1053	<
1054	<	// if we're in bin 0 or the middleBin
1055	<	if (binNo == 0 || binNo == midBin_) {
1056	<
1057	<	RealType mass = sd->getMass();
1058	<	Vector3d vel = sd->getVel();
1059	<
1060	<	if (binNo == 0) {
1061	<	hotBin.push_back(sd);
1062	<	Phx += mass * vel.x();
1063	<	Phy += mass * vel.y();
1064	<	Phz += mass * vel.z();
1065	<	Khx += mass * vel.x() * vel.x();
1066	<	Khy += mass * vel.y() * vel.y();
1067	<	Khz += mass * vel.z() * vel.z();
1068	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1069	<	if (sd->isDirectional()) {
1070	<	Vector3d angMom = sd->getJ();
1071	<	Mat3x3d I = sd->getI();
1072	<	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	<	}
1052	>	coldBin.push_back(sd);
1053	>	Pcx += mass * vel.x();
1054	>	Pcy += mass * vel.y();
1055	>	Pcz += mass * vel.z();
1056	>	Kcx += mass * vel.x() * vel.x();
1057	>	Kcy += mass * vel.y() * vel.y();
1058	>	Kcz += mass * vel.z() * vel.z();
1059	>	if (sd->isDirectional()) {
1060	>	Vector3d angMom = sd->getJ();
1061	>	Mat3x3d I = sd->getI();
1062	>	if (sd->isLinear()) {
1063	>	int i = sd->linearAxis();
1064	>	int j = (i + 1) % 3;
1065	>	int k = (i + 2) % 3;
1066	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1067	>	angMom[k] * angMom[k] / I(k, k);
1068	>	} else {
1069	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1070	>	+ angMom[1]*angMom[1]/I(1, 1)
1071	>	+ angMom[2]*angMom[2]/I(2, 2);
1072	>	}
1073		}
1074		}
1075
#	Line 800 | Line 1082 | namespace OpenMD {
1082		Kcz *= 0.5;
1083		Kcw *= 0.5;
1084
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	–
1085		#ifdef IS_MPI
1086		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1087		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 831 | Line 1107 | namespace OpenMD {
1107		RealType pz = Pcz / Phz;
1108		RealType c, x, y, z;
1109		bool successfulScale = false;
1110	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1111	<	(rnemdType_ == rnemdKineticScaleAM)) {
1110	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1111	>	(rnemdFluxType_ == rnemdRotKE)) {
1112		//may need sanity check Khw & Kcw > 0
1113
1114	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1115	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1114	>	if (rnemdFluxType_ == rnemdFullKE) {
1115	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1116		} else {
1117	<	c = 1.0 - targetFlux_ / Kcw;
1117	>	c = 1.0 - kineticTarget_ / Kcw;
1118		}
1119
1120		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1121		c = sqrt(c);
1122	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
847	<	//now convert to hotBin coefficient
1122	>
1123		RealType w = 0.0;
1124	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1124	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1125		x = 1.0 + px * (1.0 - c);
1126		y = 1.0 + py * (1.0 - c);
1127		z = 1.0 + pz * (1.0 - c);
#	Line 860 | Line 1135 | namespace OpenMD {
1135		*/
1136		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1137		(fabs(z - 1.0) < 0.1)) {
1138	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1138	>	w = 1.0 + (kineticTarget_
1139	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1140		+ Khz * (1.0 - z * z)) / Khw;
1141		}//no need to calculate w if x, y or z is out of range
1142		} else {
1143	<	w = 1.0 + targetFlux_ / Khw;
1143	>	w = 1.0 + kineticTarget_ / Khw;
1144		}
1145		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1146		//if w is in the right range, so should be x, y, z.
1147		vector<StuntDouble*>::iterator sdi;
1148		Vector3d vel;
1149		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1150	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1150	>	if (rnemdFluxType_ == rnemdFullKE) {
1151		vel = (*sdi)->getVel() * c;
876	–	//vel.x() *= c;
877	–	//vel.y() *= c;
878	–	//vel.z() *= c;
1152		(*sdi)->setVel(vel);
1153		}
1154		if ((*sdi)->isDirectional()) {
1155		Vector3d angMom = (*sdi)->getJ() * c;
883	–	//angMom[0] *= c;
884	–	//angMom[1] *= c;
885	–	//angMom[2] *= c;
1156		(*sdi)->setJ(angMom);
1157		}
1158		}
1159		w = sqrt(w);
890	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
891	–	<< "\twh= " << w << endl;
1160		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1161	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1161	>	if (rnemdFluxType_ == rnemdFullKE) {
1162		vel = (*sdi)->getVel();
1163		vel.x() *= x;
1164		vel.y() *= y;
#	Line 899 | Line 1167 | namespace OpenMD {
1167		}
1168		if ((*sdi)->isDirectional()) {
1169		Vector3d angMom = (*sdi)->getJ() * w;
902	–	//angMom[0] *= w;
903	–	//angMom[1] *= w;
904	–	//angMom[2] *= w;
1170		(*sdi)->setJ(angMom);
1171		}
1172		}
1173		successfulScale = true;
1174	<	exchangeSum_ += targetFlux_;
1174	>	kineticExchange_ += kineticTarget_;
1175		}
1176		}
1177		} else {
1178		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1179	<	switch(rnemdType_) {
1180	<	case rnemdKineticScale :
1179	>	switch(rnemdFluxType_) {
1180	>	case rnemdKE :
1181		/* used hotBin coeff's & only scale x & y dimensions
1182		RealType px = Phx / Pcx;
1183		RealType py = Phy / Pcy;
1184		a110 = Khy;
1185	<	c0 = - Khx - Khy - targetFlux_;
1185	>	c0 = - Khx - Khy - kineticTarget_;
1186		a000 = Khx;
1187		a111 = Kcy * py * py;
1188		b11 = -2.0 * Kcy * py * (1.0 + py);
1189	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1189	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1190		b01 = -2.0 * Kcx * px * (1.0 + px);
1191		a001 = Kcx * px * px;
1192		*/
1193		//scale all three dimensions, let c_x = c_y
1194		a000 = Kcx + Kcy;
1195		a110 = Kcz;
1196	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1196	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1197		a001 = Khx * px * px + Khy * py * py;
1198		a111 = Khz * pz * pz;
1199		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1200		b11 = -2.0 * Khz * pz * (1.0 + pz);
1201		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1202	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1202	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1203		break;
1204	<	case rnemdPxScale :
1205	<	c = 1 - targetFlux_ / Pcx;
1204	>	case rnemdPx :
1205	>	c = 1 - momentumTarget_.x() / Pcx;
1206		a000 = Kcy;
1207		a110 = Kcz;
1208		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 948 | Line 1213 | namespace OpenMD {
1213		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1214		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1215		break;
1216	<	case rnemdPyScale :
1217	<	c = 1 - targetFlux_ / Pcy;
1216	>	case rnemdPy :
1217	>	c = 1 - momentumTarget_.y() / Pcy;
1218		a000 = Kcx;
1219		a110 = Kcz;
1220		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 960 | Line 1225 | namespace OpenMD {
1225		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1226		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1227		break;
1228	<	case rnemdPzScale ://we don't really do this, do we?
1229	<	c = 1 - targetFlux_ / Pcz;
1228	>	case rnemdPz ://we don't really do this, do we?
1229	>	c = 1 - momentumTarget_.z() / Pcz;
1230		a000 = Kcx;
1231		a110 = Kcy;
1232		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1046 | Line 1311 | namespace OpenMD {
1311		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1312		r1 = (*rpi).first;
1313		r2 = (*rpi).second;
1314	<	switch(rnemdType_) {
1315	<	case rnemdKineticScale :
1314	>	switch(rnemdFluxType_) {
1315	>	case rnemdKE :
1316		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1317		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1318		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1319		break;
1320	<	case rnemdPxScale :
1320	>	case rnemdPx :
1321		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1323		break;
1324	<	case rnemdPyScale :
1324	>	case rnemdPy :
1325		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1326		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1327		break;
1328	<	case rnemdPzScale :
1328	>	case rnemdPz :
1329		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1330		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1331		default :
#	Line 1074 | Line 1339 | namespace OpenMD {
1339		#ifdef IS_MPI
1340		if (worldRank == 0) {
1341		#endif
1342	<	sprintf(painCave.errMsg,
1343	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1344	<	bestPair.first, bestPair.second);
1345	<	painCave.isFatal = 0;
1346	<	painCave.severity = OPENMD_INFO;
1347	<	simError();
1342	>	// sprintf(painCave.errMsg,
1343	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1344	>	//         bestPair.first, bestPair.second);
1345	>	// painCave.isFatal = 0;
1346	>	// painCave.severity = OPENMD_INFO;
1347	>	// simError();
1348		#ifdef IS_MPI
1349		}
1350		#endif
1351
1352	<	switch(rnemdType_) {
1353	<	case rnemdKineticScale :
1352	>	switch(rnemdFluxType_) {
1353	>	case rnemdKE :
1354		x = bestPair.first;
1355		y = bestPair.first;
1356		z = bestPair.second;
1357		break;
1358	<	case rnemdPxScale :
1358	>	case rnemdPx :
1359		x = c;
1360		y = bestPair.first;
1361		z = bestPair.second;
1362		break;
1363	<	case rnemdPyScale :
1363	>	case rnemdPy :
1364		x = bestPair.first;
1365		y = c;
1366		z = bestPair.second;
1367		break;
1368	<	case rnemdPzScale :
1368	>	case rnemdPz :
1369		x = bestPair.first;
1370		y = bestPair.second;
1371		z = c;
#	Line 1129 | Line 1394 | namespace OpenMD {
1394		(*sdi)->setVel(vel);
1395		}
1396		successfulScale = true;
1397	<	exchangeSum_ += targetFlux_;
1397	>	switch(rnemdFluxType_) {
1398	>	case rnemdKE :
1399	>	kineticExchange_ += kineticTarget_;
1400	>	break;
1401	>	case rnemdPx :
1402	>	case rnemdPy :
1403	>	case rnemdPz :
1404	>	momentumExchange_ += momentumTarget_;
1405	>	break;
1406	>	default :
1407	>	break;
1408	>	}
1409		}
1410		}
1411		if (successfulScale != true) {
1412		sprintf(painCave.errMsg,
1413	<	"RNEMD: exchange NOT performed!\n");
1413	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1414	>	"\tthe constraint equations may not exist or there may be\n"
1415	>	"\tno selected objects in one or both slabs.\n");
1416		painCave.isFatal = 0;
1417		painCave.severity = OPENMD_INFO;
1418		simError();
1419		failTrialCount_++;
1420		}
1421		}
1422	+
1423	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1424	+	if (!doRNEMD_) return;
1425	+	int selei;
1426	+	int selej;
1427
1145	–	void RNEMD::doShiftScale() {
1146	–
1428		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1429		RealType time = currentSnap_->getTime();
1430		Mat3x3d hmat = currentSnap_->getHmat();
1431
1151	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1152	–
1153	–	int selei;
1432		StuntDouble* sd;
1155	–	int idx;
1433
1434		vector<StuntDouble*> hotBin, coldBin;
1435
1436		Vector3d Ph(V3Zero);
1437	+	Vector3d Lh(V3Zero);
1438		RealType Mh = 0.0;
1439	+	Mat3x3d Ih(0.0);
1440		RealType Kh = 0.0;
1441		Vector3d Pc(V3Zero);
1442	+	Vector3d Lc(V3Zero);
1443		RealType Mc = 0.0;
1444	+	Mat3x3d Ic(0.0);
1445		RealType Kc = 0.0;
1165	–
1446
1447	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1448	<	sd = seleMan_.nextSelected(selei)) {
1447	>	// Constraints can be on only the linear or angular momentum, but
1448	>	// not both.  Usually, the user will specify which they want, but
1449	>	// in case they don't, the use of periodic boundaries should make
1450	>	// the choice for us.
1451	>	bool doLinearPart = false;
1452	>	bool doAngularPart = false;
1453
1454	<	idx = sd->getLocalIndex();
1454	>	switch (rnemdFluxType_) {
1455	>	case rnemdPx:
1456	>	case rnemdPy:
1457	>	case rnemdPz:
1458	>	case rnemdPvector:
1459	>	case rnemdKePx:
1460	>	case rnemdKePy:
1461	>	case rnemdKePvector:
1462	>	doLinearPart = true;
1463	>	break;
1464	>	case rnemdLx:
1465	>	case rnemdLy:
1466	>	case rnemdLz:
1467	>	case rnemdLvector:
1468	>	case rnemdKeLx:
1469	>	case rnemdKeLy:
1470	>	case rnemdKeLz:
1471	>	case rnemdKeLvector:
1472	>	doAngularPart = true;
1473	>	break;
1474	>	case rnemdKE:
1475	>	case rnemdRotKE:
1476	>	case rnemdFullKE:
1477	>	default:
1478	>	if (usePeriodicBoundaryConditions_)
1479	>	doLinearPart = true;
1480	>	else
1481	>	doAngularPart = true;
1482	>	break;
1483	>	}
1484	>
1485	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1486	>	sd = smanA.nextSelected(selei)) {
1487
1488		Vector3d pos = sd->getPos();
1489
1490		// wrap the stuntdouble's position back into the box:
1491	+
1492	+	if (usePeriodicBoundaryConditions_)
1493	+	currentSnap_->wrapVector(pos);
1494	+
1495	+	RealType mass = sd->getMass();
1496	+	Vector3d vel = sd->getVel();
1497	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1498	+	RealType r2;
1499	+
1500	+	hotBin.push_back(sd);
1501	+	Ph += mass * vel;
1502	+	Mh += mass;
1503	+	Kh += mass * vel.lengthSquare();
1504	+	Lh += mass * cross(rPos, vel);
1505	+	Ih -= outProduct(rPos, rPos) * mass;
1506	+	r2 = rPos.lengthSquare();
1507	+	Ih(0, 0) += mass * r2;
1508	+	Ih(1, 1) += mass * r2;
1509	+	Ih(2, 2) += mass * r2;
1510	+
1511	+	if (rnemdFluxType_ == rnemdFullKE) {
1512	+	if (sd->isDirectional()) {
1513	+	Vector3d angMom = sd->getJ();
1514	+	Mat3x3d I = sd->getI();
1515	+	if (sd->isLinear()) {
1516	+	int i = sd->linearAxis();
1517	+	int j = (i + 1) % 3;
1518	+	int k = (i + 2) % 3;
1519	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1520	+	angMom[k] * angMom[k] / I(k, k);
1521	+	} else {
1522	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1523	+	angMom[1] * angMom[1] / I(1, 1) +
1524	+	angMom[2] * angMom[2] / I(2, 2);
1525	+	}
1526	+	}
1527	+	}
1528	+	}
1529	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1530	+	sd = smanB.nextSelected(selej)) {
1531
1532	+	Vector3d pos = sd->getPos();
1533	+
1534	+	// wrap the stuntdouble's position back into the box:
1535	+
1536		if (usePeriodicBoundaryConditions_)
1537		currentSnap_->wrapVector(pos);
1538	+
1539	+	RealType mass = sd->getMass();
1540	+	Vector3d vel = sd->getVel();
1541	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1542	+	RealType r2;
1543
1544	<	// which bin is this stuntdouble in?
1545	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1546	<
1547	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1548	<
1549	<	// if we're in bin 0 or the middleBin
1550	<	if (binNo == 0 || binNo == midBin_) {
1551	<
1552	<	RealType mass = sd->getMass();
1553	<	Vector3d vel = sd->getVel();
1554	<
1555	<	if (binNo == 0) {
1556	<	hotBin.push_back(sd);
1557	<	//std::cerr << "before, velocity = " << vel << endl;
1558	<	Ph += mass * vel;
1559	<	//std::cerr << "after, velocity = " << vel << endl;
1560	<	Mh += mass;
1561	<	Kh += mass * vel.lengthSquare();
1562	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1563	<	if (sd->isDirectional()) {
1564	<	Vector3d angMom = sd->getJ();
1565	<	Mat3x3d I = sd->getI();
1566	<	if (sd->isLinear()) {
1567	<	int i = sd->linearAxis();
1568	<	int j = (i + 1) % 3;
1569	<	int k = (i + 2) % 3;
1570	<	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	<	}
1544	>	coldBin.push_back(sd);
1545	>	Pc += mass * vel;
1546	>	Mc += mass;
1547	>	Kc += mass * vel.lengthSquare();
1548	>	Lc += mass * cross(rPos, vel);
1549	>	Ic -= outProduct(rPos, rPos) * mass;
1550	>	r2 = rPos.lengthSquare();
1551	>	Ic(0, 0) += mass * r2;
1552	>	Ic(1, 1) += mass * r2;
1553	>	Ic(2, 2) += mass * r2;
1554	>
1555	>	if (rnemdFluxType_ == rnemdFullKE) {
1556	>	if (sd->isDirectional()) {
1557	>	Vector3d angMom = sd->getJ();
1558	>	Mat3x3d I = sd->getI();
1559	>	if (sd->isLinear()) {
1560	>	int i = sd->linearAxis();
1561	>	int j = (i + 1) % 3;
1562	>	int k = (i + 2) % 3;
1563	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1564	>	angMom[k] * angMom[k] / I(k, k);
1565	>	} else {
1566	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1567	>	angMom[1] * angMom[1] / I(1, 1) +
1568	>	angMom[2] * angMom[2] / I(2, 2);
1569	>	}
1570	>	}
1571		}
1572		}
1573
1574		Kh *= 0.5;
1575		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;
1576
1577		#ifdef IS_MPI
1578		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1579		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1580	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1581	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1582		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1583		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1585		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1587	+	MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1589	+	MPI::REALTYPE, MPI::SUM);
1590		#endif
1591	+
1592
1593	+	Vector3d ac, acrec, bc, bcrec;
1594	+	Vector3d ah, ahrec, bh, bhrec;
1595	+	RealType cNumerator, cDenominator;
1596	+	RealType hNumerator, hDenominator;
1597	+
1598	+
1599		bool successfulExchange = false;
1600		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1601		Vector3d vc = Pc / Mc;
1602	<	Vector3d ac = njzp_ / Mc + vc;
1603	<	Vector3d acrec = njzp_ / Mc;
1604	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1602	>	ac = -momentumTarget_ / Mc + vc;
1603	>	acrec = -momentumTarget_ / Mc;
1604	>
1605	>	// We now need the inverse of the inertia tensor to calculate the
1606	>	// angular velocity of the cold slab;
1607	>	Mat3x3d Ici = Ic.inverse();
1608	>	Vector3d omegac = Ici * Lc;
1609	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1610	>	bcrec = bc - omegac;
1611	>
1612	>	cNumerator = Kc - kineticTarget_;
1613	>	if (doLinearPart)
1614	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1615	>
1616	>	if (doAngularPart)
1617	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1618	>
1619		if (cNumerator > 0.0) {
1620	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1620	>
1621	>	cDenominator = Kc;
1622	>
1623	>	if (doLinearPart)
1624	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1625	>
1626	>	if (doAngularPart)
1627	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1628	>
1629		if (cDenominator > 0.0) {
1630		RealType c = sqrt(cNumerator / cDenominator);
1631		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1632	+
1633		Vector3d vh = Ph / Mh;
1634	<	Vector3d ah = jzp_ / Mh + vh;
1635	<	Vector3d ahrec = jzp_ / Mh;
1636	<	RealType hNumerator = Kh + targetJzKE_
1637	<	- 0.5 * Mh * ah.lengthSquare();
1638	<	if (hNumerator > 0.0) {
1639	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1634	>	ah = momentumTarget_ / Mh + vh;
1635	>	ahrec = momentumTarget_ / Mh;
1636	>
1637	>	// We now need the inverse of the inertia tensor to
1638	>	// calculate the angular velocity of the hot slab;
1639	>	Mat3x3d Ihi = Ih.inverse();
1640	>	Vector3d omegah = Ihi * Lh;
1641	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1642	>	bhrec = bh - omegah;
1643	>
1644	>	hNumerator = Kh + kineticTarget_;
1645	>	if (doLinearPart)
1646	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1647	>
1648	>	if (doAngularPart)
1649	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1650	>
1651	>	if (hNumerator > 0.0) {
1652	>
1653	>	hDenominator = Kh;
1654	>	if (doLinearPart)
1655	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1656	>	if (doAngularPart)
1657	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1658	>
1659		if (hDenominator > 0.0) {
1660		RealType h = sqrt(hNumerator / hDenominator);
1661		if ((h > 0.9) && (h < 1.1)) {
1662	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1278	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1662	>
1663		vector<StuntDouble*>::iterator sdi;
1664		Vector3d vel;
1665	+	Vector3d rPos;
1666	+
1667		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1668		//vel = (*sdi)->getVel();
1669	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1669	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1670	>	if (doLinearPart)
1671	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1672	>	if (doAngularPart)
1673	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1674	>
1675		(*sdi)->setVel(vel);
1676	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1676	>	if (rnemdFluxType_ == rnemdFullKE) {
1677		if ((*sdi)->isDirectional()) {
1678		Vector3d angMom = (*sdi)->getJ() * c;
1679		(*sdi)->setJ(angMom);
#	Line 1291 | Line 1682 | namespace OpenMD {
1682		}
1683		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1684		//vel = (*sdi)->getVel();
1685	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1685	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1686	>	if (doLinearPart)
1687	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1688	>	if (doAngularPart)
1689	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1690	>
1691		(*sdi)->setVel(vel);
1692	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1692	>	if (rnemdFluxType_ == rnemdFullKE) {
1693		if ((*sdi)->isDirectional()) {
1694		Vector3d angMom = (*sdi)->getJ() * h;
1695		(*sdi)->setJ(angMom);
#	Line 1301 | Line 1697 | namespace OpenMD {
1697		}
1698		}
1699		successfulExchange = true;
1700	<	exchangeSum_ += targetFlux_;
1701	<	// this is a redundant variable for doShiftScale() so that
1702	<	// 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	<	}
1700	>	kineticExchange_ += kineticTarget_;
1701	>	momentumExchange_ += momentumTarget_;
1702	>	angularMomentumExchange_ += angularMomentumTarget_;
1703		}
1704		}
1705		}
#	Line 1324 | Line 1708 | namespace OpenMD {
1708		}
1709		}
1710		if (successfulExchange != true) {
1711	<	//   sprintf(painCave.errMsg,
1712	<	//              "RNEMD: exchange NOT performed!\n");
1713	<	//   painCave.isFatal = 0;
1714	<	//   painCave.severity = OPENMD_INFO;
1715	<	//   simError();
1711	>	sprintf(painCave.errMsg,
1712	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1713	>	"\tthe constraint equations may not exist or there may be\n"
1714	>	"\tno selected objects in one or both slabs.\n");
1715	>	painCave.isFatal = 0;
1716	>	painCave.severity = OPENMD_INFO;
1717	>	simError();
1718		failTrialCount_++;
1719		}
1720		}
1721
1722	+	RealType RNEMD::getDividingArea() {
1723	+
1724	+	if (hasDividingArea_) return dividingArea_;
1725	+
1726	+	RealType areaA, areaB;
1727	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1728	+
1729	+	if (hasSelectionA_) {
1730	+	int isd;
1731	+	StuntDouble* sd;
1732	+	vector<StuntDouble*> aSites;
1733	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1734	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1735	+	sd = seleManA_.nextSelected(isd)) {
1736	+	aSites.push_back(sd);
1737	+	}
1738	+	ConvexHull* surfaceMeshA = new ConvexHull();
1739	+	surfaceMeshA->computeHull(aSites);
1740	+	areaA = surfaceMeshA->getArea();
1741	+	delete surfaceMeshA;
1742	+
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	+
1757	+
1758	+	if (hasSelectionB_) {
1759	+	int isd;
1760	+	StuntDouble* sd;
1761	+	vector<StuntDouble*> bSites;
1762	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1763	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1764	+	sd = seleManB_.nextSelected(isd)) {
1765	+	bSites.push_back(sd);
1766	+	}
1767	+	ConvexHull* surfaceMeshB = new ConvexHull();
1768	+	surfaceMeshB->computeHull(bSites);
1769	+	areaB = surfaceMeshB->getArea();
1770	+	delete surfaceMeshB;
1771	+
1772	+	} else {
1773	+	if (usePeriodicBoundaryConditions_) {
1774	+	// in periodic boundaries, the surface area is twice the x-y
1775	+	// area of the current box:
1776	+	areaB = 2.0 * snap->getXYarea();
1777	+	} else {
1778	+	// in non-periodic simulations, without explicitly setting
1779	+	// selections, but if a sphereBradius has been set, just use that:
1780	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1781	+	}
1782	+	}
1783	+
1784	+	dividingArea_ = min(areaA, areaB);
1785	+	hasDividingArea_ = true;
1786	+	return dividingArea_;
1787	+	}
1788	+
1789		void RNEMD::doRNEMD() {
1790	+	if (!doRNEMD_) return;
1791	+	trialCount_++;
1792
1793	<	switch(rnemdType_) {
1794	<	case rnemdKineticScale :
1795	<	case rnemdKineticScaleVAM :
1796	<	case rnemdKineticScaleAM :
1797	<	case rnemdPxScale :
1798	<	case rnemdPyScale :
1799	<	case rnemdPzScale :
1800	<	doScale();
1793	>	// object evaluator:
1794	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1795	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1796	>
1797	>	evaluatorA_.loadScriptString(selectionA_);
1798	>	evaluatorB_.loadScriptString(selectionB_);
1799	>
1800	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1801	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1802	>
1803	>	commonA_ = seleManA_ & seleMan_;
1804	>	commonB_ = seleManB_ & seleMan_;
1805	>
1806	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1807	>	// dt = exchange time interval
1808	>	// flux = target flux
1809	>	// dividingArea = smallest dividing surface between the two regions
1810	>
1811	>	hasDividingArea_ = false;
1812	>	RealType area = getDividingArea();
1813	>
1814	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1815	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1816	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1817	>
1818	>	switch(rnemdMethod_) {
1819	>	case rnemdSwap:
1820	>	doSwap(commonA_, commonB_);
1821		break;
1822	<	case rnemdKineticSwap :
1823	<	case rnemdPx :
1349	<	case rnemdPy :
1350	<	case rnemdPz :
1351	<	doSwap();
1822	>	case rnemdNIVS:
1823	>	doNIVS(commonA_, commonB_);
1824		break;
1825	<	case rnemdShiftScaleV :
1826	<	case rnemdShiftScaleVAM :
1355	<	doShiftScale();
1825	>	case rnemdVSS:
1826	>	doVSS(commonA_, commonB_);
1827		break;
1828	<	case rnemdUnknown :
1828	>	case rnemdUnkownMethod:
1829		default :
1830		break;
1831		}
1832		}
1833
1834		void RNEMD::collectData() {
1835	<
1835	>	if (!doRNEMD_) return;
1836		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1837	+
1838	+	// collectData can be called more frequently than the doRNEMD, so use the
1839	+	// computed area from the last exchange time:
1840	+	RealType area = getDividingArea();
1841	+	areaAccumulator_->add(area);
1842		Mat3x3d hmat = currentSnap_->getHmat();
1367	–
1843		seleMan_.setSelectionSet(evaluator_.evaluate());
1844
1845	<	int selei;
1845	>	int selei(0);
1846		StuntDouble* sd;
1847	<	int idx;
1847	>	int binNo;
1848
1849	<	logFrameCount_++;
1849	>	vector<RealType> binMass(nBins_, 0.0);
1850	>	vector<RealType> binPx(nBins_, 0.0);
1851	>	vector<RealType> binPy(nBins_, 0.0);
1852	>	vector<RealType> binPz(nBins_, 0.0);
1853	>	vector<RealType> binOmegax(nBins_, 0.0);
1854	>	vector<RealType> binOmegay(nBins_, 0.0);
1855	>	vector<RealType> binOmegaz(nBins_, 0.0);
1856	>	vector<RealType> binKE(nBins_, 0.0);
1857	>	vector<int> binDOF(nBins_, 0);
1858	>	vector<int> binCount(nBins_, 0);
1859
1860		// alternative approach, track all molecules instead of only those
1861		// selected for scaling/swapping:
1862		/*
1863	<	SimInfo::MoleculeIterator miter;
1864	<	vector<StuntDouble*>::iterator iiter;
1865	<	Molecule* mol;
1866	<	StuntDouble* integrableObject;
1867	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1863	>	SimInfo::MoleculeIterator miter;
1864	>	vector<StuntDouble*>::iterator iiter;
1865	>	Molecule* mol;
1866	>	StuntDouble* sd;
1867	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1868		mol = info_->nextMolecule(miter))
1869	<	integrableObject is essentially sd
1870	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1871	<	integrableObject != NULL;
1872	<	integrableObject = mol->nextIntegrableObject(iiter))
1869	>	sd is essentially sd
1870	>	for (sd = mol->beginIntegrableObject(iiter);
1871	>	sd != NULL;
1872	>	sd = mol->nextIntegrableObject(iiter))
1873		*/
1874	+
1875		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1876	<	sd = seleMan_.nextSelected(selei)) {
1877	<
1393	<	idx = sd->getLocalIndex();
1394	<
1876	>	sd = seleMan_.nextSelected(selei)) {
1877	>
1878		Vector3d pos = sd->getPos();
1879
1880		// wrap the stuntdouble's position back into the box:
1881
1882	<	if (usePeriodicBoundaryConditions_)
1882	>	if (usePeriodicBoundaryConditions_) {
1883		currentSnap_->wrapVector(pos);
1884	<
1885	<	// which bin is this stuntdouble in?
1886	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1887	<
1888	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1889	<	rnemdLogWidth_;
1890	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1891	<	/*
1892	<	if (rnemdLogWidth_ == midBin_ + 1)
1893	<	if (binNo > midBin_)
1894	<	binNo = nBins_ - binNo;
1412	<	*/
1884	>	// which bin is this stuntdouble in?
1885	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1886	>	// Shift molecules by half a box to have bins start at 0
1887	>	// The modulo operator is used to wrap the case when we are
1888	>	// beyond the end of the bins back to the beginning.
1889	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1890	>	} else {
1891	>	Vector3d rPos = pos - coordinateOrigin_;
1892	>	binNo = int(rPos.length() / binWidth_);
1893	>	}
1894	>
1895		RealType mass = sd->getMass();
1414	–	mHist_[binNo] += mass;
1896		Vector3d vel = sd->getVel();
1897	<	RealType value;
1898	<	//RealType xVal, yVal, zVal;
1897	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1898	>	Vector3d aVel = cross(rPos, vel);
1899	>
1900	>	if (binNo >= 0 && binNo < nBins_)  {
1901	>	binCount[binNo]++;
1902	>	binMass[binNo] += mass;
1903	>	binPx[binNo] += mass*vel.x();
1904	>	binPy[binNo] += mass*vel.y();
1905	>	binPz[binNo] += mass*vel.z();
1906	>	binOmegax[binNo] += aVel.x();
1907	>	binOmegay[binNo] += aVel.y();
1908	>	binOmegaz[binNo] += aVel.z();
1909	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1910	>	binDOF[binNo] += 3;
1911	>
1912	>	if (sd->isDirectional()) {
1913	>	Vector3d angMom = sd->getJ();
1914	>	Mat3x3d I = sd->getI();
1915	>	if (sd->isLinear()) {
1916	>	int i = sd->linearAxis();
1917	>	int j = (i + 1) % 3;
1918	>	int k = (i + 2) % 3;
1919	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1920	>	angMom[k] * angMom[k] / I(k, k));
1921	>	binDOF[binNo] += 2;
1922	>	} else {
1923	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1924	>	angMom[1] * angMom[1] / I(1, 1) +
1925	>	angMom[2] * angMom[2] / I(2, 2));
1926	>	binDOF[binNo] += 3;
1927	>	}
1928	>	}
1929	>	}
1930	>	}
1931	>
1932	>	#ifdef IS_MPI
1933	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1934	>	nBins_, MPI::INT, MPI::SUM);
1935	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1936	>	nBins_, MPI::REALTYPE, MPI::SUM);
1937	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1938	>	nBins_, MPI::REALTYPE, MPI::SUM);
1939	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1940	>	nBins_, MPI::REALTYPE, MPI::SUM);
1941	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1942	>	nBins_, MPI::REALTYPE, MPI::SUM);
1943	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1944	>	nBins_, MPI::REALTYPE, MPI::SUM);
1945	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1946	>	nBins_, MPI::REALTYPE, MPI::SUM);
1947	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1948	>	nBins_, MPI::REALTYPE, MPI::SUM);
1949	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1950	>	nBins_, MPI::REALTYPE, MPI::SUM);
1951	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1952	>	nBins_, MPI::INT, MPI::SUM);
1953	>	#endif
1954
1955	<	if (outputTemp_) {
1956	<	value = mass * vel.lengthSquare();
1957	<	tempCount_[binNo] += 3;
1958	<	if (sd->isDirectional()) {
1959	<	Vector3d angMom = sd->getJ();
1960	<	Mat3x3d I = sd->getI();
1961	<	if (sd->isLinear()) {
1962	<	int i = sd->linearAxis();
1963	<	int j = (i + 1) % 3;
1964	<	int k = (i + 2) % 3;
1965	<	value += angMom[j] * angMom[j] / I(j, j) +
1966	<	angMom[k] * angMom[k] / I(k, k);
1967	<	tempCount_[binNo] +=2;
1968	<	} else {
1969	<	value += angMom[0] * angMom[0] / I(0, 0) +
1970	<	angMom[1]*angMom[1]/I(1, 1) +
1971	<	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;
1955	>	Vector3d vel;
1956	>	Vector3d aVel;
1957	>	RealType den;
1958	>	RealType temp;
1959	>	RealType z;
1960	>	RealType r;
1961	>	for (int i = 0; i < nBins_; i++) {
1962	>	if (usePeriodicBoundaryConditions_) {
1963	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1964	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1965	>	/ currentSnap_->getVolume() ;
1966	>	} else {
1967	>	r = (((RealType)i + 0.5) * binWidth_);
1968	>	RealType rinner = (RealType)i * binWidth_;
1969	>	RealType router = (RealType)(i+1) * binWidth_;
1970	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1971	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1972		}
1973	<	if (outputVx_) {
1974	<	value = mass * vel[0];
1975	<	//vxzCount_[binNo]++;
1976	<	pxzHist_[binNo] += value;
1977	<	}
1978	<	if (outputVy_) {
1449	<	value = mass * vel[1];
1450	<	//vyzCount_[binNo]++;
1451	<	pyzHist_[binNo] += value;
1452	<	}
1973	>	vel.x() = binPx[i] / binMass[i];
1974	>	vel.y() = binPy[i] / binMass[i];
1975	>	vel.z() = binPz[i] / binMass[i];
1976	>	aVel.x() = binOmegax[i] / binCount[i];
1977	>	aVel.y() = binOmegay[i] / binCount[i];
1978	>	aVel.z() = binOmegaz[i] / binCount[i];
1979
1980	<	if (output3DTemp_) {
1981	<	value = mass * vel.x() * vel.x();
1982	<	xTempHist_[binNo] += value;
1983	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1984	<	/ PhysicalConstants::kb;
1985	<	yTempHist_[binNo] += value;
1986	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1987	<	/ PhysicalConstants::kb;
1988	<	zTempHist_[binNo] += value;
1989	<	xyzTempCount_[binNo]++;
1980	>	if (binCount[i] > 0) {
1981	>	// only add values if there are things to add
1982	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1983	>	PhysicalConstants::energyConvert);
1984	>
1985	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1986	>	if(outputMask_[j]) {
1987	>	switch(j) {
1988	>	case Z:
1989	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1990	>	break;
1991	>	case R:
1992	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1993	>	break;
1994	>	case TEMPERATURE:
1995	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1996	>	break;
1997	>	case VELOCITY:
1998	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1999	>	break;
2000	>	case ANGULARVELOCITY:
2001	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2002	>	break;
2003	>	case DENSITY:
2004	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2005	>	break;
2006	>	}
2007	>	}
2008	>	}
2009		}
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	–	}
2010		}
2011		}
2012
2013		void RNEMD::getStarted() {
2014	+	if (!doRNEMD_) return;
2015	+	hasDividingArea_ = false;
2016		collectData();
2017	<	/*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();
2017	>	writeOutputFile();
2018		}
2019
2020	<	void RNEMD::getStatus() {
2021	<
2022	<	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	<	}
2020	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2021	>	if (!doRNEMD_) return;
2022	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2023
2024	+	while(tokenizer.hasMoreTokens()) {
2025	+	std::string token(tokenizer.nextToken());
2026	+	toUpper(token);
2027	+	OutputMapType::iterator i = outputMap_.find(token);
2028	+	if (i != outputMap_.end()) {
2029	+	outputMask_.set(i->second);
2030	+	} else {
2031	+	sprintf( painCave.errMsg,
2032	+	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2033	+	"\toutputFileFormat keyword.\n", token.c_str() );
2034	+	painCave.isFatal = 0;
2035	+	painCave.severity = OPENMD_ERROR;
2036	+	simError();
2037	+	}
2038	+	}
2039	+	}
2040	+
2041	+	void RNEMD::writeOutputFile() {
2042	+	if (!doRNEMD_) return;
2043	+
2044	+	#ifdef IS_MPI
2045		// If we're the root node, should we print out the results
2046		int worldRank = MPI::COMM_WORLD.Get_rank();
2047		if (worldRank == 0) {
2048		#endif
2049	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2050	+
2051	+	if( !rnemdFile_ ){
2052	+	sprintf( painCave.errMsg,
2053	+	"Could not open \"%s\" for RNEMD output.\n",
2054	+	rnemdFileName_.c_str());
2055	+	painCave.isFatal = 1;
2056	+	simError();
2057	+	}
2058
2059	<	if (outputTemp_) {
2060	<	tempLog_ << time;
2061	<	for (j = 0; j < rnemdLogWidth_; j++) {
2062	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
2063	<	}
2064	<	tempLog_ << endl;
2059	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2060	>
2061	>	RealType time = currentSnap_->getTime();
2062	>	RealType avgArea;
2063	>	areaAccumulator_->getAverage(avgArea);
2064	>	RealType Jz = kineticExchange_ / (time * avgArea)
2065	>	/ PhysicalConstants::energyConvert;
2066	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
2067	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
2068	>
2069	>	rnemdFile_ << "#######################################################\n";
2070	>	rnemdFile_ << "# RNEMD {\n";
2071	>
2072	>	map<string, RNEMDMethod>::iterator mi;
2073	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2074	>	if ( (*mi).second == rnemdMethod_)
2075	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2076		}
2077	<	if (outputVx_) {
2078	<	vxzLog_ << time;
2079	<	for (j = 0; j < rnemdLogWidth_; j++) {
2080	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1592	<	}
1593	<	vxzLog_ << endl;
2077	>	map<string, RNEMDFluxType>::iterator fi;
2078	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2079	>	if ( (*fi).second == rnemdFluxType_)
2080	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2081		}
2082	<	if (outputVy_) {
2083	<	vyzLog_ << time;
1597	<	for (j = 0; j < rnemdLogWidth_; j++) {
1598	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	<	}
1600	<	vyzLog_ << endl;
1601	<	}
2082	>
2083	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2084
2085	<	if (output3DTemp_) {
2086	<	RealType temp;
2087	<	xTempLog_ << time;
2088	<	for (j = 0; j < rnemdLogWidth_; j++) {
2089	<	if (outputVx_)
2090	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2091	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2092	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2093	<	xTempLog_ << "\t" << temp;
2085	>	rnemdFile_ << "#    objectSelection = \""
2086	>	<< rnemdObjectSelection_ << "\";\n";
2087	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2088	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2089	>	rnemdFile_ << "# }\n";
2090	>	rnemdFile_ << "#######################################################\n";
2091	>	rnemdFile_ << "# RNEMD report:\n";
2092	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2093	>	rnemdFile_ << "# Target flux:\n";
2094	>	rnemdFile_ << "#           kinetic = "
2095	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2096	>	<< " (kcal/mol/A^2/fs)\n";
2097	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2098	>	<< " (amu/A/fs^2)\n";
2099	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2100	>	<< " (amu/A^2/fs^2)\n";
2101	>	rnemdFile_ << "# Target one-time exchanges:\n";
2102	>	rnemdFile_ << "#          kinetic = "
2103	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2104	>	<< " (kcal/mol)\n";
2105	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2106	>	<< " (amu*A/fs)\n";
2107	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2108	>	<< " (amu*A^2/fs)\n";
2109	>	rnemdFile_ << "# Actual exchange totals:\n";
2110	>	rnemdFile_ << "#          kinetic = "
2111	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2112	>	<< " (kcal/mol)\n";
2113	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2114	>	<< " (amu*A/fs)\n";
2115	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2116	>	<< " (amu*A^2/fs)\n";
2117	>	rnemdFile_ << "# Actual flux:\n";
2118	>	rnemdFile_ << "#          kinetic = " << Jz
2119	>	<< " (kcal/mol/A^2/fs)\n";
2120	>	rnemdFile_ << "#          momentum = " << JzP
2121	>	<< " (amu/A/fs^2)\n";
2122	>	rnemdFile_ << "#  angular momentum = " << JzL
2123	>	<< " (amu/A^2/fs^2)\n";
2124	>	rnemdFile_ << "# Exchange statistics:\n";
2125	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2126	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2127	>	if (rnemdMethod_ == rnemdNIVS) {
2128	>	rnemdFile_ << "#  NIVS root-check errors = "
2129	>	<< failRootCount_ << "\n";
2130	>	}
2131	>	rnemdFile_ << "#######################################################\n";
2132	>
2133	>
2134	>
2135	>	//write title
2136	>	rnemdFile_ << "#";
2137	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2138	>	if (outputMask_[i]) {
2139	>	rnemdFile_ << "\t" << data_[i].title <<
2140	>	"(" << data_[i].units << ")";
2141	>	// add some extra tabs for column alignment
2142	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2143		}
2144	<	xTempLog_ << endl;
2145	<	yTempLog_ << time;
2146	<	for (j = 0; j < rnemdLogWidth_; j++) {
2147	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
2144	>	}
2145	>	rnemdFile_ << std::endl;
2146	>
2147	>	rnemdFile_.precision(8);
2148	>
2149	>	for (int j = 0; j < nBins_; j++) {
2150	>
2151	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2152	>	if (outputMask_[i]) {
2153	>	if (data_[i].dataType == "RealType")
2154	>	writeReal(i,j);
2155	>	else if (data_[i].dataType == "Vector3d")
2156	>	writeVector(i,j);
2157	>	else {
2158	>	sprintf( painCave.errMsg,
2159	>	"RNEMD found an unknown data type for: %s ",
2160	>	data_[i].title.c_str());
2161	>	painCave.isFatal = 1;
2162	>	simError();
2163	>	}
2164	>	}
2165		}
2166	<	yTempLog_ << endl;
2167	<	zTempLog_ << time;
2168	<	for (j = 0; j < rnemdLogWidth_; j++) {
2169	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
2166	>	rnemdFile_ << std::endl;
2167	>
2168	>	}
2169	>
2170	>	rnemdFile_ << "#######################################################\n";
2171	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2172	>	rnemdFile_ << "#######################################################\n";
2173	>
2174	>
2175	>	for (int j = 0; j < nBins_; j++) {
2176	>	rnemdFile_ << "#";
2177	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2178	>	if (outputMask_[i]) {
2179	>	if (data_[i].dataType == "RealType")
2180	>	writeRealStdDev(i,j);
2181	>	else if (data_[i].dataType == "Vector3d")
2182	>	writeVectorStdDev(i,j);
2183	>	else {
2184	>	sprintf( painCave.errMsg,
2185	>	"RNEMD found an unknown data type for: %s ",
2186	>	data_[i].title.c_str());
2187	>	painCave.isFatal = 1;
2188	>	simError();
2189	>	}
2190	>	}
2191		}
2192	<	zTempLog_ << endl;
2193	<	}
2194	<	if (outputRotTemp_) {
2195	<	rotTempLog_ << time;
2196	<	for (j = 0; j < rnemdLogWidth_; j++) {
2197	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2198	<	}
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	<	}
2192	>	rnemdFile_ << std::endl;
2193	>
2194	>	}
2195	>
2196	>	rnemdFile_.flush();
2197	>	rnemdFile_.close();
2198	>
2199		#ifdef IS_MPI
2200		}
2201		#endif
2202	+
2203	+	}
2204	+
2205	+	void RNEMD::writeReal(int index, unsigned int bin) {
2206	+	if (!doRNEMD_) return;
2207	+	assert(index >=0 && index < ENDINDEX);
2208	+	assert(int(bin) < nBins_);
2209	+	RealType s;
2210	+	int count;
2211	+
2212	+	count = data_[index].accumulator[bin]->count();
2213	+	if (count == 0) return;
2214	+
2215	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2216	+
2217	+	if (! isinf(s) && ! isnan(s)) {
2218	+	rnemdFile_ << "\t" << s;
2219	+	} else{
2220	+	sprintf( painCave.errMsg,
2221	+	"RNEMD detected a numerical error writing: %s for bin %d",
2222	+	data_[index].title.c_str(), bin);
2223	+	painCave.isFatal = 1;
2224	+	simError();
2225	+	}
2226	+	}
2227	+
2228	+	void RNEMD::writeVector(int index, unsigned int bin) {
2229	+	if (!doRNEMD_) return;
2230	+	assert(index >=0 && index < ENDINDEX);
2231	+	assert(int(bin) < nBins_);
2232	+	Vector3d s;
2233	+	int count;
2234	+
2235	+	count = data_[index].accumulator[bin]->count();
2236
2237	<	for (j = 0; j < rnemdLogWidth_; j++) {
2238	<	mHist_[j] = 0.0;
2237	>	if (count == 0) return;
2238	>
2239	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2240	>	if (isinf(s[0]) || isnan(s[0]) ||
2241	>	isinf(s[1]) || isnan(s[1]) ||
2242	>	isinf(s[2]) || isnan(s[2]) ) {
2243	>	sprintf( painCave.errMsg,
2244	>	"RNEMD detected a numerical error writing: %s for bin %d",
2245	>	data_[index].title.c_str(), bin);
2246	>	painCave.isFatal = 1;
2247	>	simError();
2248	>	} else {
2249	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2250		}
2251	<	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	<	}
2251	>	}
2252
2253	<	if (output3DTemp_)
2254	<	for (j = 0; j < rnemdLogWidth_; j++) {
2255	<	xTempHist_[j] = 0.0;
2256	<	yTempHist_[j] = 0.0;
2257	<	zTempHist_[j] = 0.0;
2258	<	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';
2253	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2254	>	if (!doRNEMD_) return;
2255	>	assert(index >=0 && index < ENDINDEX);
2256	>	assert(int(bin) < nBins_);
2257	>	RealType s;
2258	>	int count;
2259
2260	<	logFrameCount_ = 0;
2260	>	count = data_[index].accumulator[bin]->count();
2261	>	if (count == 0) return;
2262	>
2263	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2264	>
2265	>	if (! isinf(s) && ! isnan(s)) {
2266	>	rnemdFile_ << "\t" << s;
2267	>	} else{
2268	>	sprintf( painCave.errMsg,
2269	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2270	>	data_[index].title.c_str(), bin);
2271	>	painCave.isFatal = 1;
2272	>	simError();
2273	>	}
2274		}
2275	+
2276	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2277	+	if (!doRNEMD_) return;
2278	+	assert(index >=0 && index < ENDINDEX);
2279	+	assert(int(bin) < nBins_);
2280	+	Vector3d s;
2281	+	int count;
2282	+
2283	+	count = data_[index].accumulator[bin]->count();
2284	+	if (count == 0) return;
2285	+
2286	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2287	+	if (isinf(s[0]) || isnan(s[0]) ||
2288	+	isinf(s[1]) || isnan(s[1]) ||
2289	+	isinf(s[2]) || isnan(s[2]) ) {
2290	+	sprintf( painCave.errMsg,
2291	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2292	+	data_[index].title.c_str(), bin);
2293	+	painCave.isFatal = 1;
2294	+	simError();
2295	+	} else {
2296	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2297	+	}
2298	+	}
2299		}
2300

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