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root/OpenMD/trunk/src/rnemd/RNEMD.cpp

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1946 by gezelter, Tue Nov 12 02:18:35 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	+	#ifdef IS_MPI
42	+	#include <mpi.h>
43	+	#endif
44
45		#include <cmath>
46	<	#include "integrators/RNEMD.hpp"
46	>	#include <sstream>
47	>	#include <string>
48	>
49	>	#include "rnemd/RNEMD.hpp"
50		#include "math/Vector3.hpp"
51		#include "math/Vector.hpp"
52		#include "math/SquareMatrix3.hpp"
#	Line 49 | Line 55
55		#include "primitives/StuntDouble.hpp"
56		#include "utils/PhysicalConstants.hpp"
57		#include "utils/Tuple.hpp"
58	+	#include "brains/Thermo.hpp"
59	+	#include "math/ConvexHull.hpp"
60
61	<	#ifndef IS_MPI
62	<	#include "math/SeqRandNumGen.hpp"
63	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
57	<	#include <mpi.h>
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
#	Line 63 | Line 69 | namespace OpenMD {
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	+	hasData_(false), hasDividingArea_(false),
76		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
77
78	+	trialCount_ = 0;
79		failTrialCount_ = 0;
80		failRootCount_ = 0;
81
82	<	int seedValue;
83	<	Globals * simParams = info->getSimParams();
82	>	Globals* simParams = info->getSimParams();
83	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84
85	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
86	<	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;
85	>	doRNEMD_ = rnemdParams->getUseRNEMD();
86	>	if (!doRNEMD_) return;
87
88	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
89	<	evaluator_.loadScriptString(rnemdObjectSelection_);
90	<	seleMan_.setSelectionSet(evaluator_.evaluate());
88	>	stringToMethod_["Swap"]  = rnemdSwap;
89	>	stringToMethod_["NIVS"]  = rnemdNIVS;
90	>	stringToMethod_["VSS"]   = rnemdVSS;
91
92	<	// do some sanity checking
92	>	stringToFluxType_["KE"]  = rnemdKE;
93	>	stringToFluxType_["Px"]  = rnemdPx;
94	>	stringToFluxType_["Py"]  = rnemdPy;
95	>	stringToFluxType_["Pz"]  = rnemdPz;
96	>	stringToFluxType_["Pvector"]  = rnemdPvector;
97	>	stringToFluxType_["Lx"]  = rnemdLx;
98	>	stringToFluxType_["Ly"]  = rnemdLy;
99	>	stringToFluxType_["Lz"]  = rnemdLz;
100	>	stringToFluxType_["Lvector"]  = rnemdLvector;
101	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
102	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
103	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
104	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
105	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
106	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
107	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
108
109	<	int selectionCount = seleMan_.getSelectionCount();
110	<	int nIntegrable = info->getNGlobalIntegrableObjects();
109	>	runTime_ = simParams->getRunTime();
110	>	statusTime_ = simParams->getStatusTime();
111
112	<	if (selectionCount > nIntegrable) {
112	>	const string methStr = rnemdParams->getMethod();
113	>	bool hasFluxType = rnemdParams->haveFluxType();
114	>
115	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
116	>
117	>	string fluxStr;
118	>	if (hasFluxType) {
119	>	fluxStr = rnemdParams->getFluxType();
120	>	} else {
121		sprintf(painCave.errMsg,
122	<	"RNEMD: The current RNEMD_objectSelection,\n"
123	<	"\t\t%s\n"
124	<	"\thas resulted in %d selected objects.  However,\n"
125	<	"\tthe total number of integrable objects in the system\n"
126	<	"\tis only %d.  This is almost certainly not what you want\n"
127	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
128	<	"\tselector in the selection script!\n",
106	<	rnemdObjectSelection_.c_str(),
107	<	selectionCount, nIntegrable);
108	<	painCave.isFatal = 0;
109	<	painCave.severity = OPENMD_WARNING;
122	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
123	>	"\twhich must be one of the following values:\n"
124	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
125	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
126	>	"\tmust be set to use RNEMD\n");
127	>	painCave.isFatal = 1;
128	>	painCave.severity = OPENMD_ERROR;
129		simError();
130		}
131	+
132	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
133	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
134	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
135	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
136	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
137	+	hasSelectionA_ = rnemdParams->haveSelectionA();
138	+	hasSelectionB_ = rnemdParams->haveSelectionB();
139	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
140	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
141	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
142	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
143	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
144	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
145	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
146	+	bool hasOutputFields = rnemdParams->haveOutputFields();
147
148	<	const string st = simParams->getRNEMD_exchangeType();
148	>	map<string, RNEMDMethod>::iterator i;
149	>	i = stringToMethod_.find(methStr);
150	>	if (i != stringToMethod_.end())
151	>	rnemdMethod_ = i->second;
152	>	else {
153	>	sprintf(painCave.errMsg,
154	>	"RNEMD: The current method,\n"
155	>	"\t\t%s is not one of the recognized\n"
156	>	"\texchange methods: Swap, NIVS, or VSS\n",
157	>	methStr.c_str());
158	>	painCave.isFatal = 1;
159	>	painCave.severity = OPENMD_ERROR;
160	>	simError();
161	>	}
162
163	<	map<string, RNEMDTypeEnum>::iterator i;
164	<	i = stringToEnumMap_.find(st);
165	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
166	<	if (rnemdType_ == rnemdUnknown) {
163	>	map<string, RNEMDFluxType>::iterator j;
164	>	j = stringToFluxType_.find(fluxStr);
165	>	if (j != stringToFluxType_.end())
166	>	rnemdFluxType_ = j->second;
167	>	else {
168		sprintf(painCave.errMsg,
169	<	"RNEMD: The current RNEMD_exchangeType,\n"
169	>	"RNEMD: The current fluxType,\n"
170		"\t\t%s\n"
171	<	"\tis not one of the recognized exchange types.\n",
172	<	st.c_str());
171	>	"\tis not one of the recognized flux types.\n",
172	>	fluxStr.c_str());
173		painCave.isFatal = 1;
174		painCave.severity = OPENMD_ERROR;
175		simError();
176		}
128	–
129	–	outputTemp_ = false;
130	–	if (simParams->haveRNEMD_outputTemperature()) {
131	–	outputTemp_ = simParams->getRNEMD_outputTemperature();
132	–	} else if ((rnemdType_ == rnemdKineticSwap) ||
133	–	(rnemdType_ == rnemdKineticScale) ||
134	–	(rnemdType_ == rnemdKineticScaleVAM) ||
135	–	(rnemdType_ == rnemdKineticScaleAM)) {
136	–	outputTemp_ = true;
137	–	}
138	–	outputVx_ = false;
139	–	if (simParams->haveRNEMD_outputVx()) {
140	–	outputVx_ = simParams->getRNEMD_outputVx();
141	–	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
142	–	outputVx_ = true;
143	–	}
144	–	outputVy_ = false;
145	–	if (simParams->haveRNEMD_outputVy()) {
146	–	outputVy_ = simParams->getRNEMD_outputVy();
147	–	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
148	–	outputVy_ = true;
149	–	}
150	–	output3DTemp_ = false;
151	–	if (simParams->haveRNEMD_outputXyzTemperature()) {
152	–	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
153	–	}
154	–	outputRotTemp_ = false;
155	–	if (simParams->haveRNEMD_outputRotTemperature()) {
156	–	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
157	–	}
177
178	<	#ifdef IS_MPI
179	<	if (worldRank == 0) {
180	<	#endif
181	<
182	<	//may have rnemdWriter separately
183	<	string rnemdFileName;
184	<
185	<	if (outputTemp_) {
186	<	rnemdFileName = "temperature.log";
187	<	tempLog_.open(rnemdFileName.c_str());
178	>	bool methodFluxMismatch = false;
179	>	bool hasCorrectFlux = false;
180	>	switch(rnemdMethod_) {
181	>	case rnemdSwap:
182	>	switch (rnemdFluxType_) {
183	>	case rnemdKE:
184	>	hasCorrectFlux = hasKineticFlux;
185	>	break;
186	>	case rnemdPx:
187	>	case rnemdPy:
188	>	case rnemdPz:
189	>	hasCorrectFlux = hasMomentumFlux;
190	>	break;
191	>	default :
192	>	methodFluxMismatch = true;
193	>	break;
194		}
195	<	if (outputVx_) {
196	<	rnemdFileName = "velocityX.log";
197	<	vxzLog_.open(rnemdFileName.c_str());
195	>	break;
196	>	case rnemdNIVS:
197	>	switch (rnemdFluxType_) {
198	>	case rnemdKE:
199	>	case rnemdRotKE:
200	>	case rnemdFullKE:
201	>	hasCorrectFlux = hasKineticFlux;
202	>	break;
203	>	case rnemdPx:
204	>	case rnemdPy:
205	>	case rnemdPz:
206	>	hasCorrectFlux = hasMomentumFlux;
207	>	break;
208	>	case rnemdKePx:
209	>	case rnemdKePy:
210	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
211	>	break;
212	>	default:
213	>	methodFluxMismatch = true;
214	>	break;
215		}
216	<	if (outputVy_) {
217	<	rnemdFileName = "velocityY.log";
218	<	vyzLog_.open(rnemdFileName.c_str());
216	>	break;
217	>	case rnemdVSS:
218	>	switch (rnemdFluxType_) {
219	>	case rnemdKE:
220	>	case rnemdRotKE:
221	>	case rnemdFullKE:
222	>	hasCorrectFlux = hasKineticFlux;
223	>	break;
224	>	case rnemdPx:
225	>	case rnemdPy:
226	>	case rnemdPz:
227	>	hasCorrectFlux = hasMomentumFlux;
228	>	break;
229	>	case rnemdLx:
230	>	case rnemdLy:
231	>	case rnemdLz:
232	>	hasCorrectFlux = hasAngularMomentumFlux;
233	>	break;
234	>	case rnemdPvector:
235	>	hasCorrectFlux = hasMomentumFluxVector;
236	>	break;
237	>	case rnemdLvector:
238	>	hasCorrectFlux = hasAngularMomentumFluxVector;
239	>	break;
240	>	case rnemdKePx:
241	>	case rnemdKePy:
242	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
243	>	break;
244	>	case rnemdKeLx:
245	>	case rnemdKeLy:
246	>	case rnemdKeLz:
247	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
248	>	break;
249	>	case rnemdKePvector:
250	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
251	>	break;
252	>	case rnemdKeLvector:
253	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
254	>	break;
255	>	default:
256	>	methodFluxMismatch = true;
257	>	break;
258		}
259	+	default:
260	+	break;
261	+	}
262
263	<	if (output3DTemp_) {
264	<	rnemdFileName = "temperatureX.log";
265	<	xTempLog_.open(rnemdFileName.c_str());
266	<	rnemdFileName = "temperatureY.log";
267	<	yTempLog_.open(rnemdFileName.c_str());
268	<	rnemdFileName = "temperatureZ.log";
269	<	zTempLog_.open(rnemdFileName.c_str());
263	>	if (methodFluxMismatch) {
264	>	sprintf(painCave.errMsg,
265	>	"RNEMD: The current method,\n"
266	>	"\t\t%s\n"
267	>	"\tcannot be used with the current flux type, %s\n",
268	>	methStr.c_str(), fluxStr.c_str());
269	>	painCave.isFatal = 1;
270	>	painCave.severity = OPENMD_ERROR;
271	>	simError();
272	>	}
273	>	if (!hasCorrectFlux) {
274	>	sprintf(painCave.errMsg,
275	>	"RNEMD: The current method, %s, and flux type, %s,\n"
276	>	"\tdid not have the correct flux value specified. Options\n"
277	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
278	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
279	>	methStr.c_str(), fluxStr.c_str());
280	>	painCave.isFatal = 1;
281	>	painCave.severity = OPENMD_ERROR;
282	>	simError();
283	>	}
284	>
285	>	if (hasKineticFlux) {
286	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
287	>	// into  amu / fs^3:
288	>	kineticFlux_ = rnemdParams->getKineticFlux()
289	>	* PhysicalConstants::energyConvert;
290	>	} else {
291	>	kineticFlux_ = 0.0;
292	>	}
293	>	if (hasMomentumFluxVector) {
294	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
295	>	} else {
296	>	momentumFluxVector_ = V3Zero;
297	>	if (hasMomentumFlux) {
298	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
299	>	switch (rnemdFluxType_) {
300	>	case rnemdPx:
301	>	momentumFluxVector_.x() = momentumFlux;
302	>	break;
303	>	case rnemdPy:
304	>	momentumFluxVector_.y() = momentumFlux;
305	>	break;
306	>	case rnemdPz:
307	>	momentumFluxVector_.z() = momentumFlux;
308	>	break;
309	>	case rnemdKePx:
310	>	momentumFluxVector_.x() = momentumFlux;
311	>	break;
312	>	case rnemdKePy:
313	>	momentumFluxVector_.y() = momentumFlux;
314	>	break;
315	>	default:
316	>	break;
317	>	}
318		}
319	<	if (outputRotTemp_) {
320	<	rnemdFileName = "temperatureR.log";
321	<	rotTempLog_.open(rnemdFileName.c_str());
319	>	if (hasAngularMomentumFluxVector) {
320	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
321	>	} else {
322	>	angularMomentumFluxVector_ = V3Zero;
323	>	if (hasAngularMomentumFlux) {
324	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
325	>	switch (rnemdFluxType_) {
326	>	case rnemdLx:
327	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
328	>	break;
329	>	case rnemdLy:
330	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
331	>	break;
332	>	case rnemdLz:
333	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
334	>	break;
335	>	case rnemdKeLx:
336	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
337	>	break;
338	>	case rnemdKeLy:
339	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
340	>	break;
341	>	case rnemdKeLz:
342	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
343	>	break;
344	>	default:
345	>	break;
346	>	}
347	>	}
348		}
349
350	<	#ifdef IS_MPI
351	<	}
194	<	#endif
195	<
196	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
197	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
198	<	midBin_ = nBins_ / 2;
199	<	if (simParams->haveRNEMD_binShift()) {
200	<	if (simParams->getRNEMD_binShift()) {
201	<	zShift_ = 0.5 / (RealType)(nBins_);
350	>	if (hasCoordinateOrigin) {
351	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
352		} else {
353	<	zShift_ = 0.0;
353	>	coordinateOrigin_ = V3Zero;
354		}
205	–	} else {
206	–	zShift_ = 0.0;
207	–	}
208	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
209	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
210	–	//set to 0.0 if not using it; N/A in status output yet
211	–	if (simParams->haveRNEMD_logWidth()) {
212	–	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
213	–	/*arbitary rnemdLogWidth_, no checking;
214	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
215	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
216	–	cerr << "Automaically set back to default.\n";
217	–	rnemdLogWidth_ = nBins_;
218	–	}*/
219	–	} else {
220	–	set_RNEMD_logWidth(nBins_);
221	–	}
222	–	tempHist_.resize(rnemdLogWidth_, 0.0);
223	–	tempCount_.resize(rnemdLogWidth_, 0);
224	–	pxzHist_.resize(rnemdLogWidth_, 0.0);
225	–	//vxzCount_.resize(rnemdLogWidth_, 0);
226	–	pyzHist_.resize(rnemdLogWidth_, 0.0);
227	–	//vyzCount_.resize(rnemdLogWidth_, 0);
355
356	<	mHist_.resize(rnemdLogWidth_, 0.0);
230	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
231	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
232	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
233	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
234	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
235	<	rotTempCount_.resize(rnemdLogWidth_, 0);
356	>	// do some sanity checking
357
358	<	set_RNEMD_exchange_total(0.0);
238	<	if (simParams->haveRNEMD_targetFlux()) {
239	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
240	<	} else {
241	<	set_RNEMD_target_flux(0.0);
242	<	}
243	<	if (simParams->haveRNEMD_targetJzKE()) {
244	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
245	<	} else {
246	<	set_RNEMD_target_JzKE(0.0);
247	<	}
248	<	if (simParams->haveRNEMD_targetJzpx()) {
249	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
250	<	} else {
251	<	set_RNEMD_target_jzpx(0.0);
252	<	}
253	<	jzp_.x() = targetJzpx_;
254	<	njzp_.x() = -targetJzpx_;
255	<	if (simParams->haveRNEMD_targetJzpy()) {
256	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
257	<	} else {
258	<	set_RNEMD_target_jzpy(0.0);
259	<	}
260	<	jzp_.y() = targetJzpy_;
261	<	njzp_.y() = -targetJzpy_;
262	<	if (simParams->haveRNEMD_targetJzpz()) {
263	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
264	<	} else {
265	<	set_RNEMD_target_jzpz(0.0);
266	<	}
267	<	jzp_.z() = targetJzpz_;
268	<	njzp_.z() = -targetJzpz_;
358	>	int selectionCount = seleMan_.getSelectionCount();
359
360	<	#ifndef IS_MPI
361	<	if (simParams->haveSeed()) {
362	<	seedValue = simParams->getSeed();
363	<	randNumGen_ = new SeqRandNumGen(seedValue);
364	<	}else {
365	<	randNumGen_ = new SeqRandNumGen();
366	<	}
367	<	#else
368	<	if (simParams->haveSeed()) {
369	<	seedValue = simParams->getSeed();
370	<	randNumGen_ = new ParallelRandNumGen(seedValue);
371	<	}else {
372	<	randNumGen_ = new ParallelRandNumGen();
373	<	}
374	<	#endif
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361	>
362	>	if (selectionCount > nIntegrable) {
363	>	sprintf(painCave.errMsg,
364	>	"RNEMD: The current objectSelection,\n"
365	>	"\t\t%s\n"
366	>	"\thas resulted in %d selected objects.  However,\n"
367	>	"\tthe total number of integrable objects in the system\n"
368	>	"\tis only %d.  This is almost certainly not what you want\n"
369	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
370	>	"\tselector in the selection script!\n",
371	>	rnemdObjectSelection_.c_str(),
372	>	selectionCount, nIntegrable);
373	>	painCave.isFatal = 0;
374	>	painCave.severity = OPENMD_WARNING;
375	>	simError();
376	>	}
377	>
378	>	areaAccumulator_ = new Accumulator();
379	>
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382	>
383	>	data_.resize(RNEMD::ENDINDEX);
384	>	OutputData z;
385	>	z.units =  "Angstroms";
386	>	z.title =  "Z";
387	>	z.dataType = "RealType";
388	>	z.accumulator.reserve(nBins_);
389	>	for (int i = 0; i < nBins_; i++)
390	>	z.accumulator.push_back( new Accumulator() );
391	>	data_[Z] = z;
392	>	outputMap_["Z"] =  Z;
393	>
394	>	OutputData r;
395	>	r.units =  "Angstroms";
396	>	r.title =  "R";
397	>	r.dataType = "RealType";
398	>	r.accumulator.reserve(nBins_);
399	>	for (int i = 0; i < nBins_; i++)
400	>	r.accumulator.push_back( new Accumulator() );
401	>	data_[R] = r;
402	>	outputMap_["R"] =  R;
403	>
404	>	OutputData temperature;
405	>	temperature.units =  "K";
406	>	temperature.title =  "Temperature";
407	>	temperature.dataType = "RealType";
408	>	temperature.accumulator.reserve(nBins_);
409	>	for (int i = 0; i < nBins_; i++)
410	>	temperature.accumulator.push_back( new Accumulator() );
411	>	data_[TEMPERATURE] = temperature;
412	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
413	>
414	>	OutputData velocity;
415	>	velocity.units = "angstroms/fs";
416	>	velocity.title =  "Velocity";
417	>	velocity.dataType = "Vector3d";
418	>	velocity.accumulator.reserve(nBins_);
419	>	for (int i = 0; i < nBins_; i++)
420	>	velocity.accumulator.push_back( new VectorAccumulator() );
421	>	data_[VELOCITY] = velocity;
422	>	outputMap_["VELOCITY"] = VELOCITY;
423	>
424	>	OutputData angularVelocity;
425	>	angularVelocity.units = "angstroms^2/fs";
426	>	angularVelocity.title =  "AngularVelocity";
427	>	angularVelocity.dataType = "Vector3d";
428	>	angularVelocity.accumulator.reserve(nBins_);
429	>	for (int i = 0; i < nBins_; i++)
430	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
431	>	data_[ANGULARVELOCITY] = angularVelocity;
432	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
433	>
434	>	OutputData density;
435	>	density.units =  "g cm^-3";
436	>	density.title =  "Density";
437	>	density.dataType = "RealType";
438	>	density.accumulator.reserve(nBins_);
439	>	for (int i = 0; i < nBins_; i++)
440	>	density.accumulator.push_back( new Accumulator() );
441	>	data_[DENSITY] = density;
442	>	outputMap_["DENSITY"] =  DENSITY;
443	>
444	>	if (hasOutputFields) {
445	>	parseOutputFileFormat(rnemdParams->getOutputFields());
446	>	} else {
447	>	if (usePeriodicBoundaryConditions_)
448	>	outputMask_.set(Z);
449	>	else
450	>	outputMask_.set(R);
451	>	switch (rnemdFluxType_) {
452	>	case rnemdKE:
453	>	case rnemdRotKE:
454	>	case rnemdFullKE:
455	>	outputMask_.set(TEMPERATURE);
456	>	break;
457	>	case rnemdPx:
458	>	case rnemdPy:
459	>	outputMask_.set(VELOCITY);
460	>	break;
461	>	case rnemdPz:
462	>	case rnemdPvector:
463	>	outputMask_.set(VELOCITY);
464	>	outputMask_.set(DENSITY);
465	>	break;
466	>	case rnemdLx:
467	>	case rnemdLy:
468	>	case rnemdLz:
469	>	case rnemdLvector:
470	>	outputMask_.set(ANGULARVELOCITY);
471	>	break;
472	>	case rnemdKeLx:
473	>	case rnemdKeLy:
474	>	case rnemdKeLz:
475	>	case rnemdKeLvector:
476	>	outputMask_.set(TEMPERATURE);
477	>	outputMask_.set(ANGULARVELOCITY);
478	>	break;
479	>	case rnemdKePx:
480	>	case rnemdKePy:
481	>	outputMask_.set(TEMPERATURE);
482	>	outputMask_.set(VELOCITY);
483	>	break;
484	>	case rnemdKePvector:
485	>	outputMask_.set(TEMPERATURE);
486	>	outputMask_.set(VELOCITY);
487	>	outputMask_.set(DENSITY);
488	>	break;
489	>	default:
490	>	break;
491	>	}
492	>	}
493	>
494	>	if (hasOutputFileName) {
495	>	rnemdFileName_ = rnemdParams->getOutputFileName();
496	>	} else {
497	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	>	}
499	>
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501	>
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504	>
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508	>
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511	>
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547	>
548	>	if (hasSelectionB_) {
549	>	selectionB_ = rnemdParams->getSelectionB();
550	>
551	>	} else {
552	>	if (usePeriodicBoundaryConditions_) {
553	>	Mat3x3d hmat = currentSnap_->getHmat();
554	>
555	>	if (hasSlabWidth)
556	>	slabWidth_ = rnemdParams->getSlabWidth();
557	>	else
558	>	slabWidth_ = hmat(2,2) / 10.0;
559	>
560	>	if (hasSlabBCenter)
561	>	slabBCenter_ = rnemdParams->getSlabBCenter();
562	>	else
563	>	slabBCenter_ = hmat(2,2) / 2.0;
564	>
565	>	selectionBstream << "select wrappedz > "
566	>	<< slabBCenter_ - 0.5*slabWidth_
567	>	<<  " && wrappedz < "
568	>	<< slabBCenter_ + 0.5*slabWidth_;
569	>	selectionB_ = selectionBstream.str();
570	>	} else {
571	>	if (hasSphereBRadius_) {
572	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
573	>	selectionBstream << "select r > " << sphereBRadius_;
574	>	selectionB_ = selectionBstream.str();
575	>	} else {
576	>	selectionB_ = "select hull";
577	>	BisHull_ = true;
578	>	hasSelectionB_ = true;
579	>	}
580	>	}
581	>	}
582	>	}
583	>
584	>	// object evaluator:
585	>	evaluator_.loadScriptString(rnemdObjectSelection_);
586	>	seleMan_.setSelectionSet(evaluator_.evaluate());
587	>	evaluatorA_.loadScriptString(selectionA_);
588	>	evaluatorB_.loadScriptString(selectionB_);
589	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
590	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
591	>	commonA_ = seleManA_ & seleMan_;
592	>	commonB_ = seleManB_ & seleMan_;
593		}
594
287	–	RNEMD::~RNEMD() {
288	–	delete randNumGen_;
595
596	+	RNEMD::~RNEMD() {
597	+	if (!doRNEMD_) return;
598		#ifdef IS_MPI
599		if (worldRank == 0) {
600		#endif
293	–
294	–	sprintf(painCave.errMsg,
295	–	"RNEMD: total failed trials: %d\n",
296	–	failTrialCount_);
297	–	painCave.isFatal = 0;
298	–	painCave.severity = OPENMD_INFO;
299	–	simError();
601
602	<	if (outputTemp_) tempLog_.close();
302	<	if (outputVx_)   vxzLog_.close();
303	<	if (outputVy_)   vyzLog_.close();
602	>	writeOutputFile();
603
604	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
605	<	rnemdType_ == rnemdPyScale) {
307	<	sprintf(painCave.errMsg,
308	<	"RNEMD: total root-checking warnings: %d\n",
309	<	failRootCount_);
310	<	painCave.isFatal = 0;
311	<	painCave.severity = OPENMD_INFO;
312	<	simError();
313	<	}
314	<	if (output3DTemp_) {
315	<	xTempLog_.close();
316	<	yTempLog_.close();
317	<	zTempLog_.close();
318	<	}
319	<	if (outputRotTemp_) rotTempLog_.close();
320	<
604	>	rnemdFile_.close();
605	>
606		#ifdef IS_MPI
607		}
608		#endif
609	+
610	+	// delete all of the objects we created:
611	+	delete areaAccumulator_;
612	+	data_.clear();
613		}
614	+
615	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
616	+	if (!doRNEMD_) return;
617	+	int selei;
618	+	int selej;
619
326	–	void RNEMD::doSwap() {
327	–
620		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
621		Mat3x3d hmat = currentSnap_->getHmat();
622
331	–	seleMan_.setSelectionSet(evaluator_.evaluate());
332	–
333	–	int selei;
623		StuntDouble* sd;
335	–	int idx;
624
625		RealType min_val;
626		bool min_found = false;
#	Line 342 | Line 630 | namespace OpenMD {
630		bool max_found = false;
631		StuntDouble* max_sd;
632
633	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
634	<	sd = seleMan_.nextSelected(selei)) {
633	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
634	>	sd = seleManA_.nextSelected(selei)) {
635
348	–	idx = sd->getLocalIndex();
349	–
636		Vector3d pos = sd->getPos();
637	<
637	>
638		// wrap the stuntdouble's position back into the box:
639	<
639	>
640		if (usePeriodicBoundaryConditions_)
641		currentSnap_->wrapVector(pos);
642	<
643	<	// which bin is this stuntdouble in?
644	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
645	<
646	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
647	<
648	<
363	<	// if we're in bin 0 or the middleBin
364	<	if (binNo == 0 || binNo == midBin_) {
642	>
643	>	RealType mass = sd->getMass();
644	>	Vector3d vel = sd->getVel();
645	>	RealType value;
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649
650	<	RealType mass = sd->getMass();
651	<	Vector3d vel = sd->getVel();
652	<	RealType value;
653	<
654	<	switch(rnemdType_) {
371	<	case rnemdKineticSwap :
650	>	value = mass * vel.lengthSquare();
651	>
652	>	if (sd->isDirectional()) {
653	>	Vector3d angMom = sd->getJ();
654	>	Mat3x3d I = sd->getI();
655
656	<	value = mass * vel.lengthSquare();
657	<
658	<	if (sd->isDirectional()) {
659	<	Vector3d angMom = sd->getJ();
660	<	Mat3x3d I = sd->getI();
661	<
662	<	if (sd->isLinear()) {
663	<	int i = sd->linearAxis();
664	<	int j = (i + 1) % 3;
665	<	int k = (i + 2) % 3;
666	<	value += angMom[j] * angMom[j] / I(j, j) +
667	<	angMom[k] * angMom[k] / I(k, k);
668	<	} else {
669	<	value += angMom[0]*angMom[0]/I(0, 0)
670	<	+ angMom[1]*angMom[1]/I(1, 1)
671	<	+ angMom[2]*angMom[2]/I(2, 2);
672	<	}
673	<	} //angular momenta exchange enabled
674	<	//energyConvert temporarily disabled
675	<	//make exchangeSum_ comparable between swap & scale
676	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
677	<	value *= 0.5;
678	<	break;
679	<	case rnemdPx :
680	<	value = mass * vel[0];
681	<	break;
682	<	case rnemdPy :
683	<	value = mass * vel[1];
684	<	break;
685	<	case rnemdPz :
686	<	value = mass * vel[2];
687	<	break;
688	<	default :
689	<	break;
656	>	if (sd->isLinear()) {
657	>	int i = sd->linearAxis();
658	>	int j = (i + 1) % 3;
659	>	int k = (i + 2) % 3;
660	>	value += angMom[j] * angMom[j] / I(j, j) +
661	>	angMom[k] * angMom[k] / I(k, k);
662	>	} else {
663	>	value += angMom[0]*angMom[0]/I(0, 0)
664	>	+ angMom[1]*angMom[1]/I(1, 1)
665	>	+ angMom[2]*angMom[2]/I(2, 2);
666	>	}
667	>	} //angular momenta exchange enabled
668	>	value *= 0.5;
669	>	break;
670	>	case rnemdPx :
671	>	value = mass * vel[0];
672	>	break;
673	>	case rnemdPy :
674	>	value = mass * vel[1];
675	>	break;
676	>	case rnemdPz :
677	>	value = mass * vel[2];
678	>	break;
679	>	default :
680	>	break;
681	>	}
682	>	if (!max_found) {
683	>	max_val = value;
684	>	max_sd = sd;
685	>	max_found = true;
686	>	} else {
687	>	if (max_val < value) {
688	>	max_val = value;
689	>	max_sd = sd;
690		}
691	+	}
692	+	}
693
694	<	if (binNo == 0) {
695	<	if (!min_found) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	min_found = true;
699	<	} else {
700	<	if (min_val > value) {
701	<	min_val = value;
702	<	min_sd = sd;
703	<	}
704	<	}
705	<	} else { //midBin_
706	<	if (!max_found) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	max_found = true;
710	<	} else {
711	<	if (max_val < value) {
712	<	max_val = value;
713	<	max_sd = sd;
714	<	}
715	<	}
716	<	}
694	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
695	>	sd = seleManB_.nextSelected(selej)) {
696	>
697	>	Vector3d pos = sd->getPos();
698	>
699	>	// wrap the stuntdouble's position back into the box:
700	>
701	>	if (usePeriodicBoundaryConditions_)
702	>	currentSnap_->wrapVector(pos);
703	>
704	>	RealType mass = sd->getMass();
705	>	Vector3d vel = sd->getVel();
706	>	RealType value;
707	>
708	>	switch(rnemdFluxType_) {
709	>	case rnemdKE :
710	>
711	>	value = mass * vel.lengthSquare();
712	>
713	>	if (sd->isDirectional()) {
714	>	Vector3d angMom = sd->getJ();
715	>	Mat3x3d I = sd->getI();
716	>
717	>	if (sd->isLinear()) {
718	>	int i = sd->linearAxis();
719	>	int j = (i + 1) % 3;
720	>	int k = (i + 2) % 3;
721	>	value += angMom[j] * angMom[j] / I(j, j) +
722	>	angMom[k] * angMom[k] / I(k, k);
723	>	} else {
724	>	value += angMom[0]*angMom[0]/I(0, 0)
725	>	+ angMom[1]*angMom[1]/I(1, 1)
726	>	+ angMom[2]*angMom[2]/I(2, 2);
727	>	}
728	>	} //angular momenta exchange enabled
729	>	value *= 0.5;
730	>	break;
731	>	case rnemdPx :
732	>	value = mass * vel[0];
733	>	break;
734	>	case rnemdPy :
735	>	value = mass * vel[1];
736	>	break;
737	>	case rnemdPz :
738	>	value = mass * vel[2];
739	>	break;
740	>	default :
741	>	break;
742		}
743	+
744	+	if (!min_found) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	min_found = true;
748	+	} else {
749	+	if (min_val > value) {
750	+	min_val = value;
751	+	min_sd = sd;
752	+	}
753	+	}
754		}
755	<
756	<	#ifdef IS_MPI
757	<	int nProc, worldRank;
758	<
438	<	nProc = MPI::COMM_WORLD.Get_size();
439	<	worldRank = MPI::COMM_WORLD.Get_rank();
440	<
755	>
756	>	#ifdef IS_MPI
757	>	int worldRank = MPI::COMM_WORLD.Get_rank();
758	>
759		bool my_min_found = min_found;
760		bool my_max_found = max_found;
761
#	Line 454 | Line 772 | namespace OpenMD {
772		RealType val;
773		int rank;
774		} max_vals, min_vals;
775	<
775	>
776		if (my_min_found) {
777		min_vals.val = min_val;
778		} else {
#	Line 492 | Line 810 | namespace OpenMD {
810		Vector3d max_vel = max_sd->getVel();
811		RealType temp_vel;
812
813	<	switch(rnemdType_) {
814	<	case rnemdKineticSwap :
813	>	switch(rnemdFluxType_) {
814	>	case rnemdKE :
815		min_sd->setVel(max_vel);
816		max_sd->setVel(min_vel);
817		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 544 | Line 862 | namespace OpenMD {
862		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
863		min_vals.rank, 0, status);
864
865	<	switch(rnemdType_) {
866	<	case rnemdKineticSwap :
865	>	switch(rnemdFluxType_) {
866	>	case rnemdKE :
867		max_sd->setVel(min_vel);
868		//angular momenta exchange enabled
869		if (max_sd->isDirectional()) {
#	Line 590 | Line 908 | namespace OpenMD {
908		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
909		max_vals.rank, 0, status);
910
911	<	switch(rnemdType_) {
912	<	case rnemdKineticSwap :
911	>	switch(rnemdFluxType_) {
912	>	case rnemdKE :
913		min_sd->setVel(max_vel);
914		//angular momenta exchange enabled
915		if (min_sd->isDirectional()) {
#	Line 625 | Line 943 | namespace OpenMD {
943		}
944		}
945		#endif
946	<	exchangeSum_ += max_val - min_val;
946	>
947	>	switch(rnemdFluxType_) {
948	>	case rnemdKE:
949	>	kineticExchange_ += max_val - min_val;
950	>	break;
951	>	case rnemdPx:
952	>	momentumExchange_.x() += max_val - min_val;
953	>	break;
954	>	case rnemdPy:
955	>	momentumExchange_.y() += max_val - min_val;
956	>	break;
957	>	case rnemdPz:
958	>	momentumExchange_.z() += max_val - min_val;
959	>	break;
960	>	default:
961	>	break;
962	>	}
963		} else {
964		sprintf(painCave.errMsg,
965	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
965	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
966		painCave.isFatal = 0;
967		painCave.severity = OPENMD_INFO;
968		simError();
#	Line 636 | Line 970 | namespace OpenMD {
970		}
971		} else {
972		sprintf(painCave.errMsg,
973	<	"RNEMD: exchange NOT performed because selected object\n"
974	<	"\tnot present in at least one of the two slabs.\n");
973	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
974	>	"\twas not present in at least one of the two slabs.\n");
975		painCave.isFatal = 0;
976		painCave.severity = OPENMD_INFO;
977		simError();
978		failTrialCount_++;
979	<	}
646	<
979	>	}
980		}
981
982	<	void RNEMD::doScale() {
982	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
983	>	if (!doRNEMD_) return;
984	>	int selei;
985	>	int selej;
986
987		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
988	+	RealType time = currentSnap_->getTime();
989		Mat3x3d hmat = currentSnap_->getHmat();
990
654	–	seleMan_.setSelectionSet(evaluator_.evaluate());
655	–
656	–	int selei;
991		StuntDouble* sd;
658	–	int idx;
992
993		vector<StuntDouble*> hotBin, coldBin;
994
#	Line 674 | Line 1007 | namespace OpenMD {
1007		RealType Kcz = 0.0;
1008		RealType Kcw = 0.0;
1009
1010	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1011	<	sd = seleMan_.nextSelected(selei)) {
1010	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1011	>	sd = smanA.nextSelected(selei)) {
1012
680	–	idx = sd->getLocalIndex();
681	–
1013		Vector3d pos = sd->getPos();
1014	<
1014	>
1015		// wrap the stuntdouble's position back into the box:
1016	<
1016	>
1017		if (usePeriodicBoundaryConditions_)
1018		currentSnap_->wrapVector(pos);
1019	<
1020	<	// which bin is this stuntdouble in?
1021	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1022	<
1023	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1024	<
1025	<	// if we're in bin 0 or the middleBin
1026	<	if (binNo == 0 || binNo == midBin_) {
1027	<
1028	<	RealType mass = sd->getMass();
1029	<	Vector3d vel = sd->getVel();
1030	<
1031	<	if (binNo == 0) {
1032	<	hotBin.push_back(sd);
1033	<	Phx += mass * vel.x();
1034	<	Phy += mass * vel.y();
1035	<	Phz += mass * vel.z();
1036	<	Khx += mass * vel.x() * vel.x();
1037	<	Khy += mass * vel.y() * vel.y();
1038	<	Khz += mass * vel.z() * vel.z();
1039	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1040	<	if (sd->isDirectional()) {
1041	<	Vector3d angMom = sd->getJ();
1042	<	Mat3x3d I = sd->getI();
1043	<	if (sd->isLinear()) {
1044	<	int i = sd->linearAxis();
714	<	int j = (i + 1) % 3;
715	<	int k = (i + 2) % 3;
716	<	Khw += angMom[j] * angMom[j] / I(j, j) +
717	<	angMom[k] * angMom[k] / I(k, k);
718	<	} else {
719	<	Khw += angMom[0]*angMom[0]/I(0, 0)
720	<	+ angMom[1]*angMom[1]/I(1, 1)
721	<	+ angMom[2]*angMom[2]/I(2, 2);
722	<	}
723	<	}
724	<	//}
725	<	} else { //midBin_
726	<	coldBin.push_back(sd);
727	<	Pcx += mass * vel.x();
728	<	Pcy += mass * vel.y();
729	<	Pcz += mass * vel.z();
730	<	Kcx += mass * vel.x() * vel.x();
731	<	Kcy += mass * vel.y() * vel.y();
732	<	Kcz += mass * vel.z() * vel.z();
733	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
734	<	if (sd->isDirectional()) {
735	<	Vector3d angMom = sd->getJ();
736	<	Mat3x3d I = sd->getI();
737	<	if (sd->isLinear()) {
738	<	int i = sd->linearAxis();
739	<	int j = (i + 1) % 3;
740	<	int k = (i + 2) % 3;
741	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
742	<	angMom[k] * angMom[k] / I(k, k);
743	<	} else {
744	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
745	<	+ angMom[1]*angMom[1]/I(1, 1)
746	<	+ angMom[2]*angMom[2]/I(2, 2);
747	<	}
748	<	}
749	<	//}
750	<	}
1019	>
1020	>
1021	>	RealType mass = sd->getMass();
1022	>	Vector3d vel = sd->getVel();
1023	>
1024	>	hotBin.push_back(sd);
1025	>	Phx += mass * vel.x();
1026	>	Phy += mass * vel.y();
1027	>	Phz += mass * vel.z();
1028	>	Khx += mass * vel.x() * vel.x();
1029	>	Khy += mass * vel.y() * vel.y();
1030	>	Khz += mass * vel.z() * vel.z();
1031	>	if (sd->isDirectional()) {
1032	>	Vector3d angMom = sd->getJ();
1033	>	Mat3x3d I = sd->getI();
1034	>	if (sd->isLinear()) {
1035	>	int i = sd->linearAxis();
1036	>	int j = (i + 1) % 3;
1037	>	int k = (i + 2) % 3;
1038	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1039	>	angMom[k] * angMom[k] / I(k, k);
1040	>	} else {
1041	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1042	>	+ angMom[1]*angMom[1]/I(1, 1)
1043	>	+ angMom[2]*angMom[2]/I(2, 2);
1044	>	}
1045		}
1046		}
1047	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1048	+	sd = smanB.nextSelected(selej)) {
1049	+	Vector3d pos = sd->getPos();
1050	+
1051	+	// wrap the stuntdouble's position back into the box:
1052	+
1053	+	if (usePeriodicBoundaryConditions_)
1054	+	currentSnap_->wrapVector(pos);
1055	+
1056	+	RealType mass = sd->getMass();
1057	+	Vector3d vel = sd->getVel();
1058	+
1059	+	coldBin.push_back(sd);
1060	+	Pcx += mass * vel.x();
1061	+	Pcy += mass * vel.y();
1062	+	Pcz += mass * vel.z();
1063	+	Kcx += mass * vel.x() * vel.x();
1064	+	Kcy += mass * vel.y() * vel.y();
1065	+	Kcz += mass * vel.z() * vel.z();
1066	+	if (sd->isDirectional()) {
1067	+	Vector3d angMom = sd->getJ();
1068	+	Mat3x3d I = sd->getI();
1069	+	if (sd->isLinear()) {
1070	+	int i = sd->linearAxis();
1071	+	int j = (i + 1) % 3;
1072	+	int k = (i + 2) % 3;
1073	+	Kcw += angMom[j] * angMom[j] / I(j, j) +
1074	+	angMom[k] * angMom[k] / I(k, k);
1075	+	} else {
1076	+	Kcw += angMom[0]*angMom[0]/I(0, 0)
1077	+	+ angMom[1]*angMom[1]/I(1, 1)
1078	+	+ angMom[2]*angMom[2]/I(2, 2);
1079	+	}
1080	+	}
1081	+	}
1082
1083		Khx *= 0.5;
1084		Khy *= 0.5;
#	Line 760 | Line 1089 | namespace OpenMD {
1089		Kcz *= 0.5;
1090		Kcw *= 0.5;
1091
763	–	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
764	–	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
765	–	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
766	–	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
767	–	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
768	–
1092		#ifdef IS_MPI
1093		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1094		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 791 | Line 1114 | namespace OpenMD {
1114		RealType pz = Pcz / Phz;
1115		RealType c, x, y, z;
1116		bool successfulScale = false;
1117	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1118	<	(rnemdType_ == rnemdKineticScaleAM)) {
1117	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1118	>	(rnemdFluxType_ == rnemdRotKE)) {
1119		//may need sanity check Khw & Kcw > 0
1120
1121	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1122	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1121	>	if (rnemdFluxType_ == rnemdFullKE) {
1122	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1123		} else {
1124	<	c = 1.0 - targetFlux_ / Kcw;
1124	>	c = 1.0 - kineticTarget_ / Kcw;
1125		}
1126
1127		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1128		c = sqrt(c);
1129	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
807	<	//now convert to hotBin coefficient
1129	>
1130		RealType w = 0.0;
1131	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1131	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1132		x = 1.0 + px * (1.0 - c);
1133		y = 1.0 + py * (1.0 - c);
1134		z = 1.0 + pz * (1.0 - c);
#	Line 820 | Line 1142 | namespace OpenMD {
1142		*/
1143		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1144		(fabs(z - 1.0) < 0.1)) {
1145	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1145	>	w = 1.0 + (kineticTarget_
1146	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1147		+ Khz * (1.0 - z * z)) / Khw;
1148		}//no need to calculate w if x, y or z is out of range
1149		} else {
1150	<	w = 1.0 + targetFlux_ / Khw;
1150	>	w = 1.0 + kineticTarget_ / Khw;
1151		}
1152		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1153		//if w is in the right range, so should be x, y, z.
1154		vector<StuntDouble*>::iterator sdi;
1155		Vector3d vel;
1156	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1157	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1156	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1157	>	if (rnemdFluxType_ == rnemdFullKE) {
1158		vel = (*sdi)->getVel() * c;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
1159		(*sdi)->setVel(vel);
1160		}
1161		if ((*sdi)->isDirectional()) {
1162		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//angMom[2] *= c;
1163		(*sdi)->setJ(angMom);
1164		}
1165		}
1166		w = sqrt(w);
1167	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
1168	<	<< "\twh= " << w << endl;
852	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
853	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1167	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1168	>	if (rnemdFluxType_ == rnemdFullKE) {
1169		vel = (*sdi)->getVel();
1170		vel.x() *= x;
1171		vel.y() *= y;
#	Line 859 | Line 1174 | namespace OpenMD {
1174		}
1175		if ((*sdi)->isDirectional()) {
1176		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//angMom[2] *= w;
1177		(*sdi)->setJ(angMom);
1178		}
1179		}
1180		successfulScale = true;
1181	<	exchangeSum_ += targetFlux_;
1181	>	kineticExchange_ += kineticTarget_;
1182		}
1183		}
1184		} else {
1185		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1186	<	switch(rnemdType_) {
1187	<	case rnemdKineticScale :
1186	>	switch(rnemdFluxType_) {
1187	>	case rnemdKE :
1188		/* used hotBin coeff's & only scale x & y dimensions
1189		RealType px = Phx / Pcx;
1190		RealType py = Phy / Pcy;
1191		a110 = Khy;
1192	<	c0 = - Khx - Khy - targetFlux_;
1192	>	c0 = - Khx - Khy - kineticTarget_;
1193		a000 = Khx;
1194		a111 = Kcy * py * py;
1195		b11 = -2.0 * Kcy * py * (1.0 + py);
1196	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1196	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1197		b01 = -2.0 * Kcx * px * (1.0 + px);
1198		a001 = Kcx * px * px;
1199		*/
1200		//scale all three dimensions, let c_x = c_y
1201		a000 = Kcx + Kcy;
1202		a110 = Kcz;
1203	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1203	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1204		a001 = Khx * px * px + Khy * py * py;
1205		a111 = Khz * pz * pz;
1206		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1207		b11 = -2.0 * Khz * pz * (1.0 + pz);
1208		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1209	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1209	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1210		break;
1211	<	case rnemdPxScale :
1212	<	c = 1 - targetFlux_ / Pcx;
1211	>	case rnemdPx :
1212	>	c = 1 - momentumTarget_.x() / Pcx;
1213		a000 = Kcy;
1214		a110 = Kcz;
1215		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 908 | Line 1220 | namespace OpenMD {
1220		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1221		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1222		break;
1223	<	case rnemdPyScale :
1224	<	c = 1 - targetFlux_ / Pcy;
1223	>	case rnemdPy :
1224	>	c = 1 - momentumTarget_.y() / Pcy;
1225		a000 = Kcx;
1226		a110 = Kcz;
1227		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 920 | Line 1232 | namespace OpenMD {
1232		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1233		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1234		break;
1235	<	case rnemdPzScale ://we don't really do this, do we?
1236	<	c = 1 - targetFlux_ / Pcz;
1235	>	case rnemdPz ://we don't really do this, do we?
1236	>	c = 1 - momentumTarget_.z() / Pcz;
1237		a000 = Kcx;
1238		a110 = Kcy;
1239		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 971 | Line 1283 | namespace OpenMD {
1283		vector<RealType>::iterator ri;
1284		RealType r1, r2, alpha0;
1285		vector<pair<RealType,RealType> > rps;
1286	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1286	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1287		r2 = *ri;
1288		//check if FindRealRoots() give the right answer
1289		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1003 | Line 1315 | namespace OpenMD {
1315		RealType diff;
1316		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1317		vector<pair<RealType,RealType> >::iterator rpi;
1318	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1318	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1319		r1 = (*rpi).first;
1320		r2 = (*rpi).second;
1321	<	switch(rnemdType_) {
1322	<	case rnemdKineticScale :
1321	>	switch(rnemdFluxType_) {
1322	>	case rnemdKE :
1323		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1324		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1325		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1326		break;
1327	<	case rnemdPxScale :
1327	>	case rnemdPx :
1328		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1329		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1330		break;
1331	<	case rnemdPyScale :
1331	>	case rnemdPy :
1332		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1333		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1334		break;
1335	<	case rnemdPzScale :
1335	>	case rnemdPz :
1336		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1337		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1338		default :
#	Line 1034 | Line 1346 | namespace OpenMD {
1346		#ifdef IS_MPI
1347		if (worldRank == 0) {
1348		#endif
1349	<	sprintf(painCave.errMsg,
1350	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1351	<	bestPair.first, bestPair.second);
1352	<	painCave.isFatal = 0;
1353	<	painCave.severity = OPENMD_INFO;
1354	<	simError();
1349	>	// sprintf(painCave.errMsg,
1350	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1351	>	//         bestPair.first, bestPair.second);
1352	>	// painCave.isFatal = 0;
1353	>	// painCave.severity = OPENMD_INFO;
1354	>	// simError();
1355		#ifdef IS_MPI
1356		}
1357		#endif
1358
1359	<	switch(rnemdType_) {
1360	<	case rnemdKineticScale :
1359	>	switch(rnemdFluxType_) {
1360	>	case rnemdKE :
1361		x = bestPair.first;
1362		y = bestPair.first;
1363		z = bestPair.second;
1364		break;
1365	<	case rnemdPxScale :
1365	>	case rnemdPx :
1366		x = c;
1367		y = bestPair.first;
1368		z = bestPair.second;
1369		break;
1370	<	case rnemdPyScale :
1370	>	case rnemdPy :
1371		x = bestPair.first;
1372		y = c;
1373		z = bestPair.second;
1374		break;
1375	<	case rnemdPzScale :
1375	>	case rnemdPz :
1376		x = bestPair.first;
1377		y = bestPair.second;
1378		z = c;
#	Line 1070 | Line 1382 | namespace OpenMD {
1382		}
1383		vector<StuntDouble*>::iterator sdi;
1384		Vector3d vel;
1385	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1385	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1386		vel = (*sdi)->getVel();
1387		vel.x() *= x;
1388		vel.y() *= y;
#	Line 1081 | Line 1393 | namespace OpenMD {
1393		x = 1.0 + px * (1.0 - x);
1394		y = 1.0 + py * (1.0 - y);
1395		z = 1.0 + pz * (1.0 - z);
1396	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1396	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1397		vel = (*sdi)->getVel();
1398		vel.x() *= x;
1399		vel.y() *= y;
#	Line 1089 | Line 1401 | namespace OpenMD {
1401		(*sdi)->setVel(vel);
1402		}
1403		successfulScale = true;
1404	<	exchangeSum_ += targetFlux_;
1404	>	switch(rnemdFluxType_) {
1405	>	case rnemdKE :
1406	>	kineticExchange_ += kineticTarget_;
1407	>	break;
1408	>	case rnemdPx :
1409	>	case rnemdPy :
1410	>	case rnemdPz :
1411	>	momentumExchange_ += momentumTarget_;
1412	>	break;
1413	>	default :
1414	>	break;
1415	>	}
1416		}
1417		}
1418		if (successfulScale != true) {
1419		sprintf(painCave.errMsg,
1420	<	"RNEMD: exchange NOT performed!\n");
1420	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1421	>	"\tthe constraint equations may not exist or there may be\n"
1422	>	"\tno selected objects in one or both slabs.\n");
1423		painCave.isFatal = 0;
1424		painCave.severity = OPENMD_INFO;
1425		simError();
1426		failTrialCount_++;
1427		}
1428		}
1429	+
1430	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1431	+	if (!doRNEMD_) return;
1432	+	int selei;
1433	+	int selej;
1434
1105	–	void RNEMD::doShiftScale() {
1106	–
1435		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1436	+	RealType time = currentSnap_->getTime();
1437		Mat3x3d hmat = currentSnap_->getHmat();
1438
1110	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1111	–
1112	–	int selei;
1439		StuntDouble* sd;
1114	–	int idx;
1440
1441		vector<StuntDouble*> hotBin, coldBin;
1442
1443		Vector3d Ph(V3Zero);
1444	+	Vector3d Lh(V3Zero);
1445		RealType Mh = 0.0;
1446	+	Mat3x3d Ih(0.0);
1447		RealType Kh = 0.0;
1448		Vector3d Pc(V3Zero);
1449	+	Vector3d Lc(V3Zero);
1450		RealType Mc = 0.0;
1451	+	Mat3x3d Ic(0.0);
1452		RealType Kc = 0.0;
1453
1454	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1455	<	sd = seleMan_.nextSelected(selei)) {
1454	>	// Constraints can be on only the linear or angular momentum, but
1455	>	// not both.  Usually, the user will specify which they want, but
1456	>	// in case they don't, the use of periodic boundaries should make
1457	>	// the choice for us.
1458	>	bool doLinearPart = false;
1459	>	bool doAngularPart = false;
1460
1461	<	idx = sd->getLocalIndex();
1461	>	switch (rnemdFluxType_) {
1462	>	case rnemdPx:
1463	>	case rnemdPy:
1464	>	case rnemdPz:
1465	>	case rnemdPvector:
1466	>	case rnemdKePx:
1467	>	case rnemdKePy:
1468	>	case rnemdKePvector:
1469	>	doLinearPart = true;
1470	>	break;
1471	>	case rnemdLx:
1472	>	case rnemdLy:
1473	>	case rnemdLz:
1474	>	case rnemdLvector:
1475	>	case rnemdKeLx:
1476	>	case rnemdKeLy:
1477	>	case rnemdKeLz:
1478	>	case rnemdKeLvector:
1479	>	doAngularPart = true;
1480	>	break;
1481	>	case rnemdKE:
1482	>	case rnemdRotKE:
1483	>	case rnemdFullKE:
1484	>	default:
1485	>	if (usePeriodicBoundaryConditions_)
1486	>	doLinearPart = true;
1487	>	else
1488	>	doAngularPart = true;
1489	>	break;
1490	>	}
1491	>
1492	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1493	>	sd = smanA.nextSelected(selei)) {
1494
1495		Vector3d pos = sd->getPos();
1496
1497		// wrap the stuntdouble's position back into the box:
1498	+
1499	+	if (usePeriodicBoundaryConditions_)
1500	+	currentSnap_->wrapVector(pos);
1501	+
1502	+	RealType mass = sd->getMass();
1503	+	Vector3d vel = sd->getVel();
1504	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1505	+	RealType r2;
1506	+
1507	+	hotBin.push_back(sd);
1508	+	Ph += mass * vel;
1509	+	Mh += mass;
1510	+	Kh += mass * vel.lengthSquare();
1511	+	Lh += mass * cross(rPos, vel);
1512	+	Ih -= outProduct(rPos, rPos) * mass;
1513	+	r2 = rPos.lengthSquare();
1514	+	Ih(0, 0) += mass * r2;
1515	+	Ih(1, 1) += mass * r2;
1516	+	Ih(2, 2) += mass * r2;
1517	+
1518	+	if (rnemdFluxType_ == rnemdFullKE) {
1519	+	if (sd->isDirectional()) {
1520	+	Vector3d angMom = sd->getJ();
1521	+	Mat3x3d I = sd->getI();
1522	+	if (sd->isLinear()) {
1523	+	int i = sd->linearAxis();
1524	+	int j = (i + 1) % 3;
1525	+	int k = (i + 2) % 3;
1526	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1527	+	angMom[k] * angMom[k] / I(k, k);
1528	+	} else {
1529	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1530	+	angMom[1] * angMom[1] / I(1, 1) +
1531	+	angMom[2] * angMom[2] / I(2, 2);
1532	+	}
1533	+	}
1534	+	}
1535	+	}
1536	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1537	+	sd = smanB.nextSelected(selej)) {
1538
1539	+	Vector3d pos = sd->getPos();
1540	+
1541	+	// wrap the stuntdouble's position back into the box:
1542	+
1543		if (usePeriodicBoundaryConditions_)
1544		currentSnap_->wrapVector(pos);
1545	+
1546	+	RealType mass = sd->getMass();
1547	+	Vector3d vel = sd->getVel();
1548	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1549	+	RealType r2;
1550
1551	<	// which bin is this stuntdouble in?
1552	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1553	<
1554	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1555	<
1556	<	// if we're in bin 0 or the middleBin
1557	<	if (binNo == 0 || binNo == midBin_) {
1558	<
1559	<	RealType mass = sd->getMass();
1560	<	Vector3d vel = sd->getVel();
1561	<
1562	<	if (binNo == 0) {
1563	<	hotBin.push_back(sd);
1564	<	//std::cerr << "before, velocity = " << vel << endl;
1565	<	Ph += mass * vel;
1566	<	//std::cerr << "after, velocity = " << vel << endl;
1567	<	Mh += mass;
1568	<	Kh += mass * vel.lengthSquare();
1569	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1570	<	if (sd->isDirectional()) {
1571	<	Vector3d angMom = sd->getJ();
1572	<	Mat3x3d I = sd->getI();
1573	<	if (sd->isLinear()) {
1574	<	int i = sd->linearAxis();
1575	<	int j = (i + 1) % 3;
1576	<	int k = (i + 2) % 3;
1577	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1164	<	angMom[k] * angMom[k] / I(k, k);
1165	<	} else {
1166	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1167	<	angMom[1] * angMom[1] / I(1, 1) +
1168	<	angMom[2] * angMom[2] / I(2, 2);
1169	<	}
1170	<	}
1171	<	}
1172	<	} else { //midBin_
1173	<	coldBin.push_back(sd);
1174	<	Pc += mass * vel;
1175	<	Mc += mass;
1176	<	Kc += mass * vel.lengthSquare();
1177	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1178	<	if (sd->isDirectional()) {
1179	<	Vector3d angMom = sd->getJ();
1180	<	Mat3x3d I = sd->getI();
1181	<	if (sd->isLinear()) {
1182	<	int i = sd->linearAxis();
1183	<	int j = (i + 1) % 3;
1184	<	int k = (i + 2) % 3;
1185	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1186	<	angMom[k] * angMom[k] / I(k, k);
1187	<	} else {
1188	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1189	<	angMom[1] * angMom[1] / I(1, 1) +
1190	<	angMom[2] * angMom[2] / I(2, 2);
1191	<	}
1192	<	}
1193	<	}
1194	<	}
1551	>	coldBin.push_back(sd);
1552	>	Pc += mass * vel;
1553	>	Mc += mass;
1554	>	Kc += mass * vel.lengthSquare();
1555	>	Lc += mass * cross(rPos, vel);
1556	>	Ic -= outProduct(rPos, rPos) * mass;
1557	>	r2 = rPos.lengthSquare();
1558	>	Ic(0, 0) += mass * r2;
1559	>	Ic(1, 1) += mass * r2;
1560	>	Ic(2, 2) += mass * r2;
1561	>
1562	>	if (rnemdFluxType_ == rnemdFullKE) {
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	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1571	>	angMom[k] * angMom[k] / I(k, k);
1572	>	} else {
1573	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1574	>	angMom[1] * angMom[1] / I(1, 1) +
1575	>	angMom[2] * angMom[2] / I(2, 2);
1576	>	}
1577	>	}
1578		}
1579		}
1580
1581		Kh *= 0.5;
1582		Kc *= 0.5;
1583	<
1201	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	<	<< "\tKc= " << Kc << endl;
1203	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	<
1583	>
1584		#ifdef IS_MPI
1585		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1586		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1587	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1589		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1590		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1591		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1592		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1596	+	MPI::REALTYPE, MPI::SUM);
1597		#endif
1598	+
1599
1600	+	Vector3d ac, acrec, bc, bcrec;
1601	+	Vector3d ah, ahrec, bh, bhrec;
1602	+
1603		bool successfulExchange = false;
1604		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1605		Vector3d vc = Pc / Mc;
1606	<	Vector3d ac = njzp_ / Mc + vc;
1607	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1606	>	ac = -momentumTarget_ / Mc + vc;
1607	>	acrec = -momentumTarget_ / Mc;
1608	>
1609	>	// We now need the inverse of the inertia tensor to calculate the
1610	>	// angular velocity of the cold slab;
1611	>	Mat3x3d Ici = Ic.inverse();
1612	>	Vector3d omegac = Ici * Lc;
1613	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1614	>	bcrec = bc - omegac;
1615	>
1616	>	RealType cNumerator = Kc - kineticTarget_;
1617	>	if (doLinearPart)
1618	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1619	>
1620	>	if (doAngularPart)
1621	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1622	>
1623		if (cNumerator > 0.0) {
1624	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1624	>
1625	>	RealType cDenominator = Kc;
1626	>
1627	>	if (doLinearPart)
1628	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1629	>
1630	>	if (doAngularPart)
1631	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1632	>
1633		if (cDenominator > 0.0) {
1634		RealType c = sqrt(cNumerator / cDenominator);
1635		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1636	+
1637		Vector3d vh = Ph / Mh;
1638	<	Vector3d ah = jzp_ / Mh + vh;
1639	<	RealType hNumerator = Kh + targetJzKE_
1640	<	- 0.5 * Mh * ah.lengthSquare();
1641	<	if (hNumerator > 0.0) {
1642	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1638	>	ah = momentumTarget_ / Mh + vh;
1639	>	ahrec = momentumTarget_ / Mh;
1640	>
1641	>	// We now need the inverse of the inertia tensor to
1642	>	// calculate the angular velocity of the hot slab;
1643	>	Mat3x3d Ihi = Ih.inverse();
1644	>	Vector3d omegah = Ihi * Lh;
1645	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1646	>	bhrec = bh - omegah;
1647	>
1648	>	RealType hNumerator = Kh + kineticTarget_;
1649	>	if (doLinearPart)
1650	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1651	>
1652	>	if (doAngularPart)
1653	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1654	>
1655	>	if (hNumerator > 0.0) {
1656	>
1657	>	RealType hDenominator = Kh;
1658	>	if (doLinearPart)
1659	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1660	>	if (doAngularPart)
1661	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1662	>
1663		if (hDenominator > 0.0) {
1664		RealType h = sqrt(hNumerator / hDenominator);
1665		if ((h > 0.9) && (h < 1.1)) {
1666	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1666	>
1667		vector<StuntDouble*>::iterator sdi;
1668		Vector3d vel;
1669	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1669	>	Vector3d rPos;
1670	>
1671	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1672		//vel = (*sdi)->getVel();
1673	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1673	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1674	>	if (doLinearPart)
1675	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1676	>	if (doAngularPart)
1677	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1678	>
1679		(*sdi)->setVel(vel);
1680	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1680	>	if (rnemdFluxType_ == rnemdFullKE) {
1681		if ((*sdi)->isDirectional()) {
1682		Vector3d angMom = (*sdi)->getJ() * c;
1683		(*sdi)->setJ(angMom);
1684		}
1685		}
1686		}
1687	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1687	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1688		//vel = (*sdi)->getVel();
1689	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1689	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1690	>	if (doLinearPart)
1691	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1692	>	if (doAngularPart)
1693	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1694	>
1695		(*sdi)->setVel(vel);
1696	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1696	>	if (rnemdFluxType_ == rnemdFullKE) {
1697		if ((*sdi)->isDirectional()) {
1698		Vector3d angMom = (*sdi)->getJ() * h;
1699		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1701 | namespace OpenMD {
1701		}
1702		}
1703		successfulExchange = true;
1704	<	exchangeSum_ += targetFlux_;
1705	<	// this is a redundant variable for doShiftScale() so that
1706	<	// RNEMD can output one exchange quantity needed in a job.
1263	<	// need a better way to do this.
1704	>	kineticExchange_ += kineticTarget_;
1705	>	momentumExchange_ += momentumTarget_;
1706	>	angularMomentumExchange_ += angularMomentumTarget_;
1707		}
1708		}
1709		}
#	Line 1270 | Line 1713 | namespace OpenMD {
1713		}
1714		if (successfulExchange != true) {
1715		sprintf(painCave.errMsg,
1716	<	"RNEMD: exchange NOT performed!\n");
1716	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1717	>	"\tthe constraint equations may not exist or there may be\n"
1718	>	"\tno selected objects in one or both slabs.\n");
1719		painCave.isFatal = 0;
1720		painCave.severity = OPENMD_INFO;
1721		simError();
#	Line 1278 | Line 1723 | namespace OpenMD {
1723		}
1724		}
1725
1726	+	RealType RNEMD::getDividingArea() {
1727	+
1728	+	if (hasDividingArea_) return dividingArea_;
1729	+
1730	+	RealType areaA, areaB;
1731	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1732	+
1733	+	if (hasSelectionA_) {
1734	+
1735	+	if (evaluatorA_.hasSurfaceArea())
1736	+	areaA = evaluatorA_.getSurfaceArea();
1737	+	else {
1738	+
1739	+	cerr << "selection A did not have surface area, recomputing\n";
1740	+	int isd;
1741	+	StuntDouble* sd;
1742	+	vector<StuntDouble*> aSites;
1743	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1744	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1745	+	sd = seleManA_.nextSelected(isd)) {
1746	+	aSites.push_back(sd);
1747	+	}
1748	+	#if defined(HAVE_QHULL)
1749	+	ConvexHull* surfaceMeshA = new ConvexHull();
1750	+	surfaceMeshA->computeHull(aSites);
1751	+	areaA = surfaceMeshA->getArea();
1752	+	delete surfaceMeshA;
1753	+	#else
1754	+	sprintf( painCave.errMsg,
1755	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1756	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1757	+	painCave.severity = OPENMD_ERROR;
1758	+	painCave.isFatal = 1;
1759	+	simError();
1760	+	#endif
1761	+	}
1762	+
1763	+	} else {
1764	+	if (usePeriodicBoundaryConditions_) {
1765	+	// in periodic boundaries, the surface area is twice the x-y
1766	+	// area of the current box:
1767	+	areaA = 2.0 * snap->getXYarea();
1768	+	} else {
1769	+	// in non-periodic simulations, without explicitly setting
1770	+	// selections, the sphere radius sets the surface area of the
1771	+	// dividing surface:
1772	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1773	+	}
1774	+	}
1775	+
1776	+	if (hasSelectionB_) {
1777	+	if (evaluatorB_.hasSurfaceArea())
1778	+	areaB = evaluatorB_.getSurfaceArea();
1779	+	else {
1780	+	cerr << "selection B did not have surface area, recomputing\n";
1781	+
1782	+	int isd;
1783	+	StuntDouble* sd;
1784	+	vector<StuntDouble*> bSites;
1785	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1786	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1787	+	sd = seleManB_.nextSelected(isd)) {
1788	+	bSites.push_back(sd);
1789	+	}
1790	+
1791	+	#if defined(HAVE_QHULL)
1792	+	ConvexHull* surfaceMeshB = new ConvexHull();
1793	+	surfaceMeshB->computeHull(bSites);
1794	+	areaB = surfaceMeshB->getArea();
1795	+	delete surfaceMeshB;
1796	+	#else
1797	+	sprintf( painCave.errMsg,
1798	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1799	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1800	+	painCave.severity = OPENMD_ERROR;
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	#endif
1804	+	}
1805	+
1806	+	} else {
1807	+	if (usePeriodicBoundaryConditions_) {
1808	+	// in periodic boundaries, the surface area is twice the x-y
1809	+	// area of the current box:
1810	+	areaB = 2.0 * snap->getXYarea();
1811	+	} else {
1812	+	// in non-periodic simulations, without explicitly setting
1813	+	// selections, but if a sphereBradius has been set, just use that:
1814	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1815	+	}
1816	+	}
1817	+
1818	+	dividingArea_ = min(areaA, areaB);
1819	+	hasDividingArea_ = true;
1820	+	return dividingArea_;
1821	+	}
1822	+
1823		void RNEMD::doRNEMD() {
1824	+	if (!doRNEMD_) return;
1825	+	trialCount_++;
1826
1827	<	switch(rnemdType_) {
1828	<	case rnemdKineticScale :
1829	<	case rnemdKineticScaleVAM :
1830	<	case rnemdKineticScaleAM :
1831	<	case rnemdPxScale :
1832	<	case rnemdPyScale :
1833	<	case rnemdPzScale :
1834	<	doScale();
1827	>	// object evaluator:
1828	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1829	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1830	>
1831	>	evaluatorA_.loadScriptString(selectionA_);
1832	>	evaluatorB_.loadScriptString(selectionB_);
1833	>
1834	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1835	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1836	>
1837	>	commonA_ = seleManA_ & seleMan_;
1838	>	commonB_ = seleManB_ & seleMan_;
1839	>
1840	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1841	>	// dt = exchange time interval
1842	>	// flux = target flux
1843	>	// dividingArea = smallest dividing surface between the two regions
1844	>
1845	>	hasDividingArea_ = false;
1846	>	RealType area = getDividingArea();
1847	>
1848	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1849	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1850	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1851	>
1852	>	switch(rnemdMethod_) {
1853	>	case rnemdSwap:
1854	>	doSwap(commonA_, commonB_);
1855		break;
1856	<	case rnemdKineticSwap :
1857	<	case rnemdPx :
1294	<	case rnemdPy :
1295	<	case rnemdPz :
1296	<	doSwap();
1856	>	case rnemdNIVS:
1857	>	doNIVS(commonA_, commonB_);
1858		break;
1859	<	case rnemdShiftScaleV :
1860	<	case rnemdShiftScaleVAM :
1300	<	doShiftScale();
1859	>	case rnemdVSS:
1860	>	doVSS(commonA_, commonB_);
1861		break;
1862	<	case rnemdUnknown :
1862	>	case rnemdUnkownMethod:
1863		default :
1864		break;
1865		}
1866		}
1867
1868		void RNEMD::collectData() {
1869	<
1869	>	if (!doRNEMD_) return;
1870		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1871	+
1872	+	// collectData can be called more frequently than the doRNEMD, so use the
1873	+	// computed area from the last exchange time:
1874	+	RealType area = getDividingArea();
1875	+	areaAccumulator_->add(area);
1876		Mat3x3d hmat = currentSnap_->getHmat();
1877	+	Vector3d u = angularMomentumFluxVector_;
1878	+	u.normalize();
1879
1880		seleMan_.setSelectionSet(evaluator_.evaluate());
1881
1882	<	int selei;
1882	>	int selei(0);
1883		StuntDouble* sd;
1884	<	int idx;
1884	>	int binNo;
1885	>	RealType mass;
1886	>	Vector3d vel;
1887	>	Vector3d rPos;
1888	>	RealType KE;
1889	>	Vector3d L;
1890	>	Mat3x3d I;
1891	>	RealType r2;
1892
1893	+	vector<RealType> binMass(nBins_, 0.0);
1894	+	vector<Vector3d> binP(nBins_, V3Zero);
1895	+	vector<RealType> binOmega(nBins_, 0.0);
1896	+	vector<Vector3d> binL(nBins_, V3Zero);
1897	+	vector<Mat3x3d>  binI(nBins_);
1898	+	vector<RealType> binKE(nBins_, 0.0);
1899	+	vector<int> binDOF(nBins_, 0);
1900	+	vector<int> binCount(nBins_, 0);
1901	+
1902		// alternative approach, track all molecules instead of only those
1903		// selected for scaling/swapping:
1904		/*
1905	<	SimInfo::MoleculeIterator miter;
1906	<	vector<StuntDouble*>::iterator iiter;
1907	<	Molecule* mol;
1908	<	StuntDouble* integrableObject;
1909	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1910	<	mol = info_->nextMolecule(miter))
1911	<	integrableObject is essentially sd
1912	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1913	<	integrableObject != NULL;
1914	<	integrableObject = mol->nextIntegrableObject(iiter))
1905	>	SimInfo::MoleculeIterator miter;
1906	>	vector<StuntDouble*>::iterator iiter;
1907	>	Molecule* mol;
1908	>	StuntDouble* sd;
1909	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1910	>	mol = info_->nextMolecule(miter))
1911	>	sd is essentially sd
1912	>	for (sd = mol->beginIntegrableObject(iiter);
1913	>	sd != NULL;
1914	>	sd = mol->nextIntegrableObject(iiter))
1915		*/
1916	+
1917		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1918	<	sd = seleMan_.nextSelected(selei)) {
1919	<
1336	<	idx = sd->getLocalIndex();
1337	<
1918	>	sd = seleMan_.nextSelected(selei)) {
1919	>
1920		Vector3d pos = sd->getPos();
1921
1922		// wrap the stuntdouble's position back into the box:
1923
1924	<	if (usePeriodicBoundaryConditions_)
1924	>	if (usePeriodicBoundaryConditions_) {
1925		currentSnap_->wrapVector(pos);
1926	<
1927	<	// which bin is this stuntdouble in?
1928	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1929	<
1930	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1931	<	rnemdLogWidth_;
1932	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1933	<	/*
1934	<	if (rnemdLogWidth_ == midBin_ + 1)
1935	<	if (binNo > midBin_)
1354	<	binNo = nBins_ - binNo;
1355	<	*/
1356	<	RealType mass = sd->getMass();
1357	<	mHist_[binNo] += mass;
1358	<	Vector3d vel = sd->getVel();
1359	<	RealType value;
1360	<	//RealType xVal, yVal, zVal;
1926	>	// which bin is this stuntdouble in?
1927	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1928	>	// Shift molecules by half a box to have bins start at 0
1929	>	// The modulo operator is used to wrap the case when we are
1930	>	// beyond the end of the bins back to the beginning.
1931	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1932	>	} else {
1933	>	Vector3d rPos = pos - coordinateOrigin_;
1934	>	binNo = int(rPos.length() / binWidth_);
1935	>	}
1936
1937	<	if (outputTemp_) {
1938	<	value = mass * vel.lengthSquare();
1939	<	tempCount_[binNo] += 3;
1940	<	if (sd->isDirectional()) {
1941	<	Vector3d angMom = sd->getJ();
1942	<	Mat3x3d I = sd->getI();
1943	<	if (sd->isLinear()) {
1944	<	int i = sd->linearAxis();
1945	<	int j = (i + 1) % 3;
1946	<	int k = (i + 2) % 3;
1947	<	value += angMom[j] * angMom[j] / I(j, j) +
1948	<	angMom[k] * angMom[k] / I(k, k);
1949	<	tempCount_[binNo] +=2;
1950	<	} else {
1951	<	value += angMom[0] * angMom[0] / I(0, 0) +
1952	<	angMom[1]*angMom[1]/I(1, 1) +
1953	<	angMom[2]*angMom[2]/I(2, 2);
1954	<	tempCount_[binNo] +=3;
1955	<	}
1956	<	}
1957	<	value = value / PhysicalConstants::energyConvert
1958	<	/ PhysicalConstants::kb;//may move to getStatus()
1959	<	tempHist_[binNo] += value;
1937	>	mass = sd->getMass();
1938	>	vel = sd->getVel();
1939	>	rPos = sd->getPos() - coordinateOrigin_;
1940	>	KE = 0.5 * mass * vel.lengthSquare();
1941	>	L = mass * cross(rPos, vel);
1942	>	I = outProduct(rPos, rPos) * mass;
1943	>	r2 = rPos.lengthSquare();
1944	>	I(0, 0) += mass * r2;
1945	>	I(1, 1) += mass * r2;
1946	>	I(2, 2) += mass * r2;
1947	>
1948	>	// Project the relative position onto a plane perpendicular to
1949	>	// the angularMomentumFluxVector:
1950	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1951	>	// Project the velocity onto a plane perpendicular to the
1952	>	// angularMomentumFluxVector:
1953	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1954	>	// Compute angular velocity vector (should be nearly parallel to
1955	>	// angularMomentumFluxVector
1956	>	// Vector3d aVel = cross(rProj, vProj);
1957	>
1958	>	if (binNo >= 0 && binNo < nBins_)  {
1959	>	binCount[binNo]++;
1960	>	binMass[binNo] += mass;
1961	>	binP[binNo] += mass*vel;
1962	>	binKE[binNo] += KE;
1963	>	binI[binNo] += I;
1964	>	binL[binNo] += L;
1965	>	binDOF[binNo] += 3;
1966	>
1967	>	if (sd->isDirectional()) {
1968	>	Vector3d angMom = sd->getJ();
1969	>	Mat3x3d Ia = sd->getI();
1970	>	if (sd->isLinear()) {
1971	>	int i = sd->linearAxis();
1972	>	int j = (i + 1) % 3;
1973	>	int k = (i + 2) % 3;
1974	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
1975	>	angMom[k] * angMom[k] / Ia(k, k));
1976	>	binDOF[binNo] += 2;
1977	>	} else {
1978	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
1979	>	angMom[1] * angMom[1] / Ia(1, 1) +
1980	>	angMom[2] * angMom[2] / Ia(2, 2));
1981	>	binDOF[binNo] += 3;
1982	>	}
1983	>	}
1984		}
1985	<	if (outputVx_) {
1986	<	value = mass * vel[0];
1987	<	//vxzCount_[binNo]++;
1389	<	pxzHist_[binNo] += value;
1390	<	}
1391	<	if (outputVy_) {
1392	<	value = mass * vel[1];
1393	<	//vyzCount_[binNo]++;
1394	<	pyzHist_[binNo] += value;
1395	<	}
1985	>	}
1986	>
1987	>	#ifdef IS_MPI
1988
1989	<	if (output3DTemp_) {
1990	<	value = mass * vel.x() * vel.x();
1991	<	xTempHist_[binNo] += value;
1992	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1993	<	/ PhysicalConstants::kb;
1994	<	yTempHist_[binNo] += value;
1995	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1996	<	/ PhysicalConstants::kb;
1997	<	zTempHist_[binNo] += value;
1998	<	xyzTempCount_[binNo]++;
1989	>	for (int i = 0; i < nBins_; i++) {
1990	>
1991	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[i],
1992	>	1, MPI::INT, MPI::SUM);
1993	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[i],
1994	>	1, MPI::REALTYPE, MPI::SUM);
1995	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binP[i],
1996	>	3, MPI::REALTYPE, MPI::SUM);
1997	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binL[i],
1998	>	3, MPI::REALTYPE, MPI::SUM);
1999	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binI[i],
2000	>	9, MPI::REALTYPE, MPI::SUM);
2001	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[i],
2002	>	1, MPI::REALTYPE, MPI::SUM);
2003	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[i],
2004	>	1, MPI::INT, MPI::SUM);
2005	>	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmega[i],
2006	>	//                          1, MPI::REALTYPE, MPI::SUM);
2007	>	}
2008	>
2009	>	#endif
2010	>
2011	>	Vector3d omega;
2012	>	RealType den;
2013	>	RealType temp;
2014	>	RealType z;
2015	>	RealType r;
2016	>	for (int i = 0; i < nBins_; i++) {
2017	>	if (usePeriodicBoundaryConditions_) {
2018	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2019	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2020	>	/ currentSnap_->getVolume() ;
2021	>	} else {
2022	>	r = (((RealType)i + 0.5) * binWidth_);
2023	>	RealType rinner = (RealType)i * binWidth_;
2024	>	RealType router = (RealType)(i+1) * binWidth_;
2025	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2026	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2027		}
2028	<	if (outputRotTemp_) {
1409	<	if (sd->isDirectional()) {
1410	<	Vector3d angMom = sd->getJ();
1411	<	Mat3x3d I = sd->getI();
1412	<	if (sd->isLinear()) {
1413	<	int i = sd->linearAxis();
1414	<	int j = (i + 1) % 3;
1415	<	int k = (i + 2) % 3;
1416	<	value = angMom[j] * angMom[j] / I(j, j) +
1417	<	angMom[k] * angMom[k] / I(k, k);
1418	<	rotTempCount_[binNo] +=2;
1419	<	} else {
1420	<	value = angMom[0] * angMom[0] / I(0, 0) +
1421	<	angMom[1] * angMom[1] / I(1, 1) +
1422	<	angMom[2] * angMom[2] / I(2, 2);
1423	<	rotTempCount_[binNo] +=3;
1424	<	}
1425	<	}
1426	<	value = value / PhysicalConstants::energyConvert
1427	<	/ PhysicalConstants::kb;//may move to getStatus()
1428	<	rotTempHist_[binNo] += value;
1429	<	}
2028	>	vel = binP[i] / binMass[i];
2029
2030	+	omega = binI[i].inverse() * binL[i];
2031	+
2032	+	// omega = binOmega[i] / binCount[i];
2033	+
2034	+	if (binCount[i] > 0) {
2035	+	// only add values if there are things to add
2036	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2037	+	PhysicalConstants::energyConvert);
2038	+
2039	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2040	+	if(outputMask_[j]) {
2041	+	switch(j) {
2042	+	case Z:
2043	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2044	+	break;
2045	+	case R:
2046	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2047	+	break;
2048	+	case TEMPERATURE:
2049	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2050	+	break;
2051	+	case VELOCITY:
2052	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2053	+	break;
2054	+	case ANGULARVELOCITY:
2055	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2056	+	break;
2057	+	case DENSITY:
2058	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2059	+	break;
2060	+	}
2061	+	}
2062	+	}
2063	+	}
2064		}
2065	+	hasData_ = true;
2066		}
2067
2068		void RNEMD::getStarted() {
2069	+	if (!doRNEMD_) return;
2070	+	hasDividingArea_ = false;
2071		collectData();
2072	<	/*now can output profile in step 0, but might not be useful;
1437	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	<	Stats& stat = currentSnap_->statData;
1439	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1440	<	*/
1441	<	//may output a header for the log file here
1442	<	getStatus();
2072	>	writeOutputFile();
2073		}
2074
2075	<	void RNEMD::getStatus() {
2076	<
2077	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2078	<	Stats& stat = currentSnap_->statData;
2079	<	RealType time = currentSnap_->getTime();
2080	<
2081	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2082	<	//or to be more meaningful, define another item as exchangeSum_ / time
2083	<	int j;
2084	<
2075	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2076	>	if (!doRNEMD_) return;
2077	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2078	>
2079	>	while(tokenizer.hasMoreTokens()) {
2080	>	std::string token(tokenizer.nextToken());
2081	>	toUpper(token);
2082	>	OutputMapType::iterator i = outputMap_.find(token);
2083	>	if (i != outputMap_.end()) {
2084	>	outputMask_.set(i->second);
2085	>	} else {
2086	>	sprintf( painCave.errMsg,
2087	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2088	>	"\toutputFileFormat keyword.\n", token.c_str() );
2089	>	painCave.isFatal = 0;
2090	>	painCave.severity = OPENMD_ERROR;
2091	>	simError();
2092	>	}
2093	>	}
2094	>	}
2095	>
2096	>	void RNEMD::writeOutputFile() {
2097	>	if (!doRNEMD_) return;
2098	>	if (!hasData_) return;
2099	>
2100		#ifdef IS_MPI
1456	–
1457	–	// all processors have the same number of bins, and STL vectors pack their
1458	–	// arrays, so in theory, this should be safe:
1459	–
1460	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1461	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1462	–	if (outputTemp_) {
1463	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1464	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1465	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1466	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1467	–	}
1468	–	if (outputVx_) {
1469	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1470	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1471	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1472	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1473	–	}
1474	–	if (outputVy_) {
1475	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1476	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1477	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1478	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1479	–	}
1480	–	if (output3DTemp_) {
1481	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1482	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1483	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1484	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1485	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1486	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1487	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1488	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1489	–	}
1490	–	if (outputRotTemp_) {
1491	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1492	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1493	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1494	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1495	–	}
1496	–
2101		// If we're the root node, should we print out the results
2102		int worldRank = MPI::COMM_WORLD.Get_rank();
2103		if (worldRank == 0) {
2104		#endif
2105	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2106	+
2107	+	if( !rnemdFile_ ){
2108	+	sprintf( painCave.errMsg,
2109	+	"Could not open \"%s\" for RNEMD output.\n",
2110	+	rnemdFileName_.c_str());
2111	+	painCave.isFatal = 1;
2112	+	simError();
2113	+	}
2114
2115	<	if (outputTemp_) {
2116	<	tempLog_ << time;
2117	<	for (j = 0; j < rnemdLogWidth_; j++) {
2118	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
2119	<	}
2120	<	tempLog_ << endl;
2115	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2116	>
2117	>	RealType time = currentSnap_->getTime();
2118	>	RealType avgArea;
2119	>	areaAccumulator_->getAverage(avgArea);
2120	>
2121	>	RealType Jz(0.0);
2122	>	Vector3d JzP(V3Zero);
2123	>	Vector3d JzL(V3Zero);
2124	>	if (time >= info_->getSimParams()->getDt()) {
2125	>	Jz = kineticExchange_ / (time * avgArea)
2126	>	/ PhysicalConstants::energyConvert;
2127	>	JzP = momentumExchange_ / (time * avgArea);
2128	>	JzL = angularMomentumExchange_ / (time * avgArea);
2129		}
2130	<	if (outputVx_) {
2131	<	vxzLog_ << time;
2132	<	for (j = 0; j < rnemdLogWidth_; j++) {
2133	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
2134	<	}
2135	<	vxzLog_ << endl;
2130	>
2131	>	rnemdFile_ << "#######################################################\n";
2132	>	rnemdFile_ << "# RNEMD {\n";
2133	>
2134	>	map<string, RNEMDMethod>::iterator mi;
2135	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2136	>	if ( (*mi).second == rnemdMethod_)
2137	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2138		}
2139	<	if (outputVy_) {
2140	<	vyzLog_ << time;
2141	<	for (j = 0; j < rnemdLogWidth_; j++) {
2142	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
2139	>	map<string, RNEMDFluxType>::iterator fi;
2140	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2141	>	if ( (*fi).second == rnemdFluxType_)
2142	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2143		}
2144	+
2145	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2146
2147	<	if (output3DTemp_) {
2148	<	RealType temp;
2149	<	xTempLog_ << time;
2150	<	for (j = 0; j < rnemdLogWidth_; j++) {
2151	<	if (outputVx_)
2152	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2153	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2154	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2155	<	xTempLog_ << "\t" << temp;
2147	>	rnemdFile_ << "#    objectSelection = \""
2148	>	<< rnemdObjectSelection_ << "\";\n";
2149	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2150	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2151	>	rnemdFile_ << "# }\n";
2152	>	rnemdFile_ << "#######################################################\n";
2153	>	rnemdFile_ << "# RNEMD report:\n";
2154	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2155	>	rnemdFile_ << "# Target flux:\n";
2156	>	rnemdFile_ << "#           kinetic = "
2157	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2158	>	<< " (kcal/mol/A^2/fs)\n";
2159	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2160	>	<< " (amu/A/fs^2)\n";
2161	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2162	>	<< " (amu/A^2/fs^2)\n";
2163	>	rnemdFile_ << "# Target one-time exchanges:\n";
2164	>	rnemdFile_ << "#          kinetic = "
2165	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2166	>	<< " (kcal/mol)\n";
2167	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2168	>	<< " (amu*A/fs)\n";
2169	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2170	>	<< " (amu*A^2/fs)\n";
2171	>	rnemdFile_ << "# Actual exchange totals:\n";
2172	>	rnemdFile_ << "#          kinetic = "
2173	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2174	>	<< " (kcal/mol)\n";
2175	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2176	>	<< " (amu*A/fs)\n";
2177	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2178	>	<< " (amu*A^2/fs)\n";
2179	>	rnemdFile_ << "# Actual flux:\n";
2180	>	rnemdFile_ << "#          kinetic = " << Jz
2181	>	<< " (kcal/mol/A^2/fs)\n";
2182	>	rnemdFile_ << "#          momentum = " << JzP
2183	>	<< " (amu/A/fs^2)\n";
2184	>	rnemdFile_ << "#  angular momentum = " << JzL
2185	>	<< " (amu/A^2/fs^2)\n";
2186	>	rnemdFile_ << "# Exchange statistics:\n";
2187	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2188	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2189	>	if (rnemdMethod_ == rnemdNIVS) {
2190	>	rnemdFile_ << "#  NIVS root-check errors = "
2191	>	<< failRootCount_ << "\n";
2192	>	}
2193	>	rnemdFile_ << "#######################################################\n";
2194	>
2195	>
2196	>
2197	>	//write title
2198	>	rnemdFile_ << "#";
2199	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2200	>	if (outputMask_[i]) {
2201	>	rnemdFile_ << "\t" << data_[i].title <<
2202	>	"(" << data_[i].units << ")";
2203	>	// add some extra tabs for column alignment
2204	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2205		}
1534	–	xTempLog_ << endl;
1535	–	yTempLog_ << time;
1536	–	for (j = 0; j < rnemdLogWidth_; j++) {
1537	–	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1538	–	}
1539	–	yTempLog_ << endl;
1540	–	zTempLog_ << time;
1541	–	for (j = 0; j < rnemdLogWidth_; j++) {
1542	–	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1543	–	}
1544	–	zTempLog_ << endl;
2206		}
2207	<	if (outputRotTemp_) {
2208	<	rotTempLog_ << time;
2209	<	for (j = 0; j < rnemdLogWidth_; j++) {
2210	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2211	<	}
2212	<	rotTempLog_ << endl;
2213	<	}
2207	>	rnemdFile_ << std::endl;
2208	>
2209	>	rnemdFile_.precision(8);
2210	>
2211	>	for (int j = 0; j < nBins_; j++) {
2212	>
2213	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2214	>	if (outputMask_[i]) {
2215	>	if (data_[i].dataType == "RealType")
2216	>	writeReal(i,j);
2217	>	else if (data_[i].dataType == "Vector3d")
2218	>	writeVector(i,j);
2219	>	else {
2220	>	sprintf( painCave.errMsg,
2221	>	"RNEMD found an unknown data type for: %s ",
2222	>	data_[i].title.c_str());
2223	>	painCave.isFatal = 1;
2224	>	simError();
2225	>	}
2226	>	}
2227	>	}
2228	>	rnemdFile_ << std::endl;
2229	>
2230	>	}
2231
2232	+	rnemdFile_ << "#######################################################\n";
2233	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2234	+	rnemdFile_ << "#######################################################\n";
2235	+
2236	+
2237	+	for (int j = 0; j < nBins_; j++) {
2238	+	rnemdFile_ << "#";
2239	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2240	+	if (outputMask_[i]) {
2241	+	if (data_[i].dataType == "RealType")
2242	+	writeRealStdDev(i,j);
2243	+	else if (data_[i].dataType == "Vector3d")
2244	+	writeVectorStdDev(i,j);
2245	+	else {
2246	+	sprintf( painCave.errMsg,
2247	+	"RNEMD found an unknown data type for: %s ",
2248	+	data_[i].title.c_str());
2249	+	painCave.isFatal = 1;
2250	+	simError();
2251	+	}
2252	+	}
2253	+	}
2254	+	rnemdFile_ << std::endl;
2255	+
2256	+	}
2257	+
2258	+	rnemdFile_.flush();
2259	+	rnemdFile_.close();
2260	+
2261		#ifdef IS_MPI
2262		}
2263		#endif
2264	+
2265	+	}
2266	+
2267	+	void RNEMD::writeReal(int index, unsigned int bin) {
2268	+	if (!doRNEMD_) return;
2269	+	assert(index >=0 && index < ENDINDEX);
2270	+	assert(int(bin) < nBins_);
2271	+	RealType s;
2272	+	int count;
2273	+
2274	+	count = data_[index].accumulator[bin]->count();
2275	+	if (count == 0) return;
2276	+
2277	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2278	+
2279	+	if (! isinf(s) && ! isnan(s)) {
2280	+	rnemdFile_ << "\t" << s;
2281	+	} else{
2282	+	sprintf( painCave.errMsg,
2283	+	"RNEMD detected a numerical error writing: %s for bin %u",
2284	+	data_[index].title.c_str(), bin);
2285	+	painCave.isFatal = 1;
2286	+	simError();
2287	+	}
2288	+	}
2289	+
2290	+	void RNEMD::writeVector(int index, unsigned int bin) {
2291	+	if (!doRNEMD_) return;
2292	+	assert(index >=0 && index < ENDINDEX);
2293	+	assert(int(bin) < nBins_);
2294	+	Vector3d s;
2295	+	int count;
2296	+
2297	+	count = data_[index].accumulator[bin]->count();
2298
2299	<	for (j = 0; j < rnemdLogWidth_; j++) {
2300	<	mHist_[j] = 0.0;
2299	>	if (count == 0) return;
2300	>
2301	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2302	>	if (isinf(s[0]) || isnan(s[0]) ||
2303	>	isinf(s[1]) || isnan(s[1]) ||
2304	>	isinf(s[2]) || isnan(s[2]) ) {
2305	>	sprintf( painCave.errMsg,
2306	>	"RNEMD detected a numerical error writing: %s for bin %u",
2307	>	data_[index].title.c_str(), bin);
2308	>	painCave.isFatal = 1;
2309	>	simError();
2310	>	} else {
2311	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2312		}
2313	<	if (outputTemp_)
1562	<	for (j = 0; j < rnemdLogWidth_; j++) {
1563	<	tempCount_[j] = 0;
1564	<	tempHist_[j] = 0.0;
1565	<	}
1566	<	if (outputVx_)
1567	<	for (j = 0; j < rnemdLogWidth_; j++) {
1568	<	//pxzCount_[j] = 0;
1569	<	pxzHist_[j] = 0.0;
1570	<	}
1571	<	if (outputVy_)
1572	<	for (j = 0; j < rnemdLogWidth_; j++) {
1573	<	//pyzCount_[j] = 0;
1574	<	pyzHist_[j] = 0.0;
1575	<	}
2313	>	}
2314
2315	<	if (output3DTemp_)
2316	<	for (j = 0; j < rnemdLogWidth_; j++) {
2317	<	xTempHist_[j] = 0.0;
2318	<	yTempHist_[j] = 0.0;
2319	<	zTempHist_[j] = 0.0;
2320	<	xyzTempCount_[j] = 0;
2321	<	}
2322	<	if (outputRotTemp_)
2323	<	for (j = 0; j < rnemdLogWidth_; j++) {
2324	<	rotTempCount_[j] = 0;
2325	<	rotTempHist_[j] = 0.0;
2326	<	}
2315	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2316	>	if (!doRNEMD_) return;
2317	>	assert(index >=0 && index < ENDINDEX);
2318	>	assert(int(bin) < nBins_);
2319	>	RealType s;
2320	>	int count;
2321	>
2322	>	count = data_[index].accumulator[bin]->count();
2323	>	if (count == 0) return;
2324	>
2325	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2326	>
2327	>	if (! isinf(s) && ! isnan(s)) {
2328	>	rnemdFile_ << "\t" << s;
2329	>	} else{
2330	>	sprintf( painCave.errMsg,
2331	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2332	>	data_[index].title.c_str(), bin);
2333	>	painCave.isFatal = 1;
2334	>	simError();
2335	>	}
2336		}
2337	+
2338	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2339	+	if (!doRNEMD_) return;
2340	+	assert(index >=0 && index < ENDINDEX);
2341	+	assert(int(bin) < nBins_);
2342	+	Vector3d s;
2343	+	int count;
2344	+
2345	+	count = data_[index].accumulator[bin]->count();
2346	+	if (count == 0) return;
2347	+
2348	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2349	+	if (isinf(s[0]) || isnan(s[0]) ||
2350	+	isinf(s[1]) || isnan(s[1]) ||
2351	+	isinf(s[2]) || isnan(s[2]) ) {
2352	+	sprintf( painCave.errMsg,
2353	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2354	+	data_[index].title.c_str(), bin);
2355	+	painCave.isFatal = 1;
2356	+	simError();
2357	+	} else {
2358	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2359	+	}
2360	+	}
2361		}
2362

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