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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1876 by gezelter, Fri May 17 17:10:11 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <cmath>
43	<	#include "integrators/RNEMD.hpp"
43	>	#include <sstream>
44	>	#include <string>
45	>
46	>	#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48		#include "math/Vector.hpp"
49		#include "math/SquareMatrix3.hpp"
#	Line 49 | Line 52
52		#include "primitives/StuntDouble.hpp"
53		#include "utils/PhysicalConstants.hpp"
54		#include "utils/Tuple.hpp"
55	<
56	<	#ifndef IS_MPI
57	<	#include "math/SeqRandNumGen.hpp"
55	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
55	>	#include "brains/Thermo.hpp"
56	>	#include "math/ConvexHull.hpp"
57	>	#ifdef IS_MPI
58		#include <mpi.h>
59		#endif
60
61	+	#ifdef _MSC_VER
62	+	#define isnan(x) _isnan((x))
63	+	#define isinf(x) (!_finite(x) && !_isnan(x))
64	+	#endif
65	+
66		#define HONKING_LARGE_VALUE 1.0e10
67
68		using namespace std;
69		namespace OpenMD {
70
71		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75	+	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	>	} else {
551	>	if (usePeriodicBoundaryConditions_) {
552	>	Mat3x3d hmat = currentSnap_->getHmat();
553	>
554	>	if (hasSlabWidth)
555	>	slabWidth_ = rnemdParams->getSlabWidth();
556	>	else
557	>	slabWidth_ = hmat(2,2) / 10.0;
558	>
559	>	if (hasSlabBCenter)
560	>	slabBCenter_ = rnemdParams->getSlabBCenter();
561	>	else
562	>	slabBCenter_ = hmat(2,2) / 2.0;
563	>
564	>	selectionBstream << "select wrappedz > "
565	>	<< slabBCenter_ - 0.5*slabWidth_
566	>	<<  " && wrappedz < "
567	>	<< slabBCenter_ + 0.5*slabWidth_;
568	>	selectionB_ = selectionBstream.str();
569	>	} else {
570	>	if (hasSphereBRadius_) {
571	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
572	>	selectionBstream << "select r > " << sphereBRadius_;
573	>	selectionB_ = selectionBstream.str();
574	>	} else {
575	>	selectionB_ = "select hull";
576	>	hasSelectionB_ = true;
577	>	}
578	>	}
579	>	}
580	>	}
581	>
582	>	// object evaluator:
583	>	evaluator_.loadScriptString(rnemdObjectSelection_);
584	>	seleMan_.setSelectionSet(evaluator_.evaluate());
585	>	evaluatorA_.loadScriptString(selectionA_);
586	>	evaluatorB_.loadScriptString(selectionB_);
587	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
588	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
589	>	commonA_ = seleManA_ & seleMan_;
590	>	commonB_ = seleManB_ & seleMan_;
591		}
592
287	–	RNEMD::~RNEMD() {
288	–	delete randNumGen_;
593
594	+	RNEMD::~RNEMD() {
595	+	if (!doRNEMD_) return;
596		#ifdef IS_MPI
597		if (worldRank == 0) {
598		#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();
599
600	<	if (outputTemp_) tempLog_.close();
302	<	if (outputVx_)   vxzLog_.close();
303	<	if (outputVy_)   vyzLog_.close();
600	>	writeOutputFile();
601
602	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
603	<	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	<
602	>	rnemdFile_.close();
603	>
604		#ifdef IS_MPI
605		}
606		#endif
607	+
608	+	// delete all of the objects we created:
609	+	delete areaAccumulator_;
610	+	data_.clear();
611		}
612	+
613	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
614	+	if (!doRNEMD_) return;
615	+	int selei;
616	+	int selej;
617
326	–	void RNEMD::doSwap() {
327	–
618		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
619		Mat3x3d hmat = currentSnap_->getHmat();
620
331	–	seleMan_.setSelectionSet(evaluator_.evaluate());
332	–
333	–	int selei;
621		StuntDouble* sd;
335	–	int idx;
622
623		RealType min_val;
624		bool min_found = false;
#	Line 342 | Line 628 | namespace OpenMD {
628		bool max_found = false;
629		StuntDouble* max_sd;
630
631	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
632	<	sd = seleMan_.nextSelected(selei)) {
631	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
632	>	sd = seleManA_.nextSelected(selei)) {
633
348	–	idx = sd->getLocalIndex();
349	–
634		Vector3d pos = sd->getPos();
635	<
635	>
636		// wrap the stuntdouble's position back into the box:
637	<
637	>
638		if (usePeriodicBoundaryConditions_)
639		currentSnap_->wrapVector(pos);
640	<
641	<	// which bin is this stuntdouble in?
642	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
643	<
644	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
645	<
646	<
363	<	// if we're in bin 0 or the middleBin
364	<	if (binNo == 0 || binNo == midBin_) {
640	>
641	>	RealType mass = sd->getMass();
642	>	Vector3d vel = sd->getVel();
643	>	RealType value;
644	>
645	>	switch(rnemdFluxType_) {
646	>	case rnemdKE :
647
648	<	RealType mass = sd->getMass();
649	<	Vector3d vel = sd->getVel();
650	<	RealType value;
651	<
652	<	switch(rnemdType_) {
371	<	case rnemdKineticSwap :
648	>	value = mass * vel.lengthSquare();
649	>
650	>	if (sd->isDirectional()) {
651	>	Vector3d angMom = sd->getJ();
652	>	Mat3x3d I = sd->getI();
653
654	<	value = mass * vel.lengthSquare();
655	<
656	<	if (sd->isDirectional()) {
657	<	Vector3d angMom = sd->getJ();
658	<	Mat3x3d I = sd->getI();
659	<
660	<	if (sd->isLinear()) {
661	<	int i = sd->linearAxis();
662	<	int j = (i + 1) % 3;
663	<	int k = (i + 2) % 3;
664	<	value += angMom[j] * angMom[j] / I(j, j) +
665	<	angMom[k] * angMom[k] / I(k, k);
666	<	} else {
667	<	value += angMom[0]*angMom[0]/I(0, 0)
668	<	+ angMom[1]*angMom[1]/I(1, 1)
669	<	+ angMom[2]*angMom[2]/I(2, 2);
670	<	}
671	<	} //angular momenta exchange enabled
672	<	//energyConvert temporarily disabled
673	<	//make exchangeSum_ comparable between swap & scale
674	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
675	<	value *= 0.5;
676	<	break;
677	<	case rnemdPx :
678	<	value = mass * vel[0];
679	<	break;
680	<	case rnemdPy :
681	<	value = mass * vel[1];
682	<	break;
683	<	case rnemdPz :
684	<	value = mass * vel[2];
685	<	break;
686	<	default :
687	<	break;
654	>	if (sd->isLinear()) {
655	>	int i = sd->linearAxis();
656	>	int j = (i + 1) % 3;
657	>	int k = (i + 2) % 3;
658	>	value += angMom[j] * angMom[j] / I(j, j) +
659	>	angMom[k] * angMom[k] / I(k, k);
660	>	} else {
661	>	value += angMom[0]*angMom[0]/I(0, 0)
662	>	+ angMom[1]*angMom[1]/I(1, 1)
663	>	+ angMom[2]*angMom[2]/I(2, 2);
664	>	}
665	>	} //angular momenta exchange enabled
666	>	value *= 0.5;
667	>	break;
668	>	case rnemdPx :
669	>	value = mass * vel[0];
670	>	break;
671	>	case rnemdPy :
672	>	value = mass * vel[1];
673	>	break;
674	>	case rnemdPz :
675	>	value = mass * vel[2];
676	>	break;
677	>	default :
678	>	break;
679	>	}
680	>	if (!max_found) {
681	>	max_val = value;
682	>	max_sd = sd;
683	>	max_found = true;
684	>	} else {
685	>	if (max_val < value) {
686	>	max_val = value;
687	>	max_sd = sd;
688		}
689	+	}
690	+	}
691
692	<	if (binNo == 0) {
693	<	if (!min_found) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	min_found = true;
697	<	} else {
698	<	if (min_val > value) {
699	<	min_val = value;
700	<	min_sd = sd;
701	<	}
702	<	}
703	<	} else { //midBin_
704	<	if (!max_found) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	max_found = true;
708	<	} else {
709	<	if (max_val < value) {
710	<	max_val = value;
711	<	max_sd = sd;
712	<	}
713	<	}
714	<	}
692	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
693	>	sd = seleManB_.nextSelected(selej)) {
694	>
695	>	Vector3d pos = sd->getPos();
696	>
697	>	// wrap the stuntdouble's position back into the box:
698	>
699	>	if (usePeriodicBoundaryConditions_)
700	>	currentSnap_->wrapVector(pos);
701	>
702	>	RealType mass = sd->getMass();
703	>	Vector3d vel = sd->getVel();
704	>	RealType value;
705	>
706	>	switch(rnemdFluxType_) {
707	>	case rnemdKE :
708	>
709	>	value = mass * vel.lengthSquare();
710	>
711	>	if (sd->isDirectional()) {
712	>	Vector3d angMom = sd->getJ();
713	>	Mat3x3d I = sd->getI();
714	>
715	>	if (sd->isLinear()) {
716	>	int i = sd->linearAxis();
717	>	int j = (i + 1) % 3;
718	>	int k = (i + 2) % 3;
719	>	value += angMom[j] * angMom[j] / I(j, j) +
720	>	angMom[k] * angMom[k] / I(k, k);
721	>	} else {
722	>	value += angMom[0]*angMom[0]/I(0, 0)
723	>	+ angMom[1]*angMom[1]/I(1, 1)
724	>	+ angMom[2]*angMom[2]/I(2, 2);
725	>	}
726	>	} //angular momenta exchange enabled
727	>	value *= 0.5;
728	>	break;
729	>	case rnemdPx :
730	>	value = mass * vel[0];
731	>	break;
732	>	case rnemdPy :
733	>	value = mass * vel[1];
734	>	break;
735	>	case rnemdPz :
736	>	value = mass * vel[2];
737	>	break;
738	>	default :
739	>	break;
740		}
741	+
742	+	if (!min_found) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	min_found = true;
746	+	} else {
747	+	if (min_val > value) {
748	+	min_val = value;
749	+	min_sd = sd;
750	+	}
751	+	}
752		}
753	<
754	<	#ifdef IS_MPI
755	<	int nProc, worldRank;
756	<
438	<	nProc = MPI::COMM_WORLD.Get_size();
439	<	worldRank = MPI::COMM_WORLD.Get_rank();
440	<
753	>
754	>	#ifdef IS_MPI
755	>	int worldRank = MPI::COMM_WORLD.Get_rank();
756	>
757		bool my_min_found = min_found;
758		bool my_max_found = max_found;
759
#	Line 454 | Line 770 | namespace OpenMD {
770		RealType val;
771		int rank;
772		} max_vals, min_vals;
773	<
773	>
774		if (my_min_found) {
775		min_vals.val = min_val;
776		} else {
#	Line 492 | Line 808 | namespace OpenMD {
808		Vector3d max_vel = max_sd->getVel();
809		RealType temp_vel;
810
811	<	switch(rnemdType_) {
812	<	case rnemdKineticSwap :
811	>	switch(rnemdFluxType_) {
812	>	case rnemdKE :
813		min_sd->setVel(max_vel);
814		max_sd->setVel(min_vel);
815		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 544 | Line 860 | namespace OpenMD {
860		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
861		min_vals.rank, 0, status);
862
863	<	switch(rnemdType_) {
864	<	case rnemdKineticSwap :
863	>	switch(rnemdFluxType_) {
864	>	case rnemdKE :
865		max_sd->setVel(min_vel);
866		//angular momenta exchange enabled
867		if (max_sd->isDirectional()) {
#	Line 590 | Line 906 | namespace OpenMD {
906		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
907		max_vals.rank, 0, status);
908
909	<	switch(rnemdType_) {
910	<	case rnemdKineticSwap :
909	>	switch(rnemdFluxType_) {
910	>	case rnemdKE :
911		min_sd->setVel(max_vel);
912		//angular momenta exchange enabled
913		if (min_sd->isDirectional()) {
#	Line 625 | Line 941 | namespace OpenMD {
941		}
942		}
943		#endif
944	<	exchangeSum_ += max_val - min_val;
944	>
945	>	switch(rnemdFluxType_) {
946	>	case rnemdKE:
947	>	kineticExchange_ += max_val - min_val;
948	>	break;
949	>	case rnemdPx:
950	>	momentumExchange_.x() += max_val - min_val;
951	>	break;
952	>	case rnemdPy:
953	>	momentumExchange_.y() += max_val - min_val;
954	>	break;
955	>	case rnemdPz:
956	>	momentumExchange_.z() += max_val - min_val;
957	>	break;
958	>	default:
959	>	break;
960	>	}
961		} else {
962		sprintf(painCave.errMsg,
963	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
963	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
964		painCave.isFatal = 0;
965		painCave.severity = OPENMD_INFO;
966		simError();
#	Line 636 | Line 968 | namespace OpenMD {
968		}
969		} else {
970		sprintf(painCave.errMsg,
971	<	"RNEMD: exchange NOT performed because selected object\n"
972	<	"\tnot present in at least one of the two slabs.\n");
971	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
972	>	"\twas not present in at least one of the two slabs.\n");
973		painCave.isFatal = 0;
974		painCave.severity = OPENMD_INFO;
975		simError();
976		failTrialCount_++;
977	<	}
646	<
977	>	}
978		}
979
980	<	void RNEMD::doScale() {
980	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
981	>	if (!doRNEMD_) return;
982	>	int selei;
983	>	int selej;
984
985		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
986	+	RealType time = currentSnap_->getTime();
987		Mat3x3d hmat = currentSnap_->getHmat();
988
654	–	seleMan_.setSelectionSet(evaluator_.evaluate());
655	–
656	–	int selei;
989		StuntDouble* sd;
658	–	int idx;
990
991		vector<StuntDouble*> hotBin, coldBin;
992
#	Line 674 | Line 1005 | namespace OpenMD {
1005		RealType Kcz = 0.0;
1006		RealType Kcw = 0.0;
1007
1008	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1009	<	sd = seleMan_.nextSelected(selei)) {
1008	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1009	>	sd = smanA.nextSelected(selei)) {
1010
680	–	idx = sd->getLocalIndex();
681	–
1011		Vector3d pos = sd->getPos();
1012	<
1012	>
1013		// wrap the stuntdouble's position back into the box:
1014	<
1014	>
1015		if (usePeriodicBoundaryConditions_)
1016		currentSnap_->wrapVector(pos);
1017	<
1018	<	// which bin is this stuntdouble in?
1019	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1020	<
1021	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1022	<
1023	<	// if we're in bin 0 or the middleBin
1024	<	if (binNo == 0 || binNo == midBin_) {
1025	<
1026	<	RealType mass = sd->getMass();
1027	<	Vector3d vel = sd->getVel();
1028	<
1029	<	if (binNo == 0) {
1030	<	hotBin.push_back(sd);
1031	<	Phx += mass * vel.x();
1032	<	Phy += mass * vel.y();
1033	<	Phz += mass * vel.z();
1034	<	Khx += mass * vel.x() * vel.x();
1035	<	Khy += mass * vel.y() * vel.y();
1036	<	Khz += mass * vel.z() * vel.z();
1037	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1038	<	if (sd->isDirectional()) {
1039	<	Vector3d angMom = sd->getJ();
1040	<	Mat3x3d I = sd->getI();
1041	<	if (sd->isLinear()) {
1042	<	int i = sd->linearAxis();
1043	<	int j = (i + 1) % 3;
1044	<	int k = (i + 2) % 3;
1045	<	Khw += angMom[j] * angMom[j] / I(j, j) +
1046	<	angMom[k] * angMom[k] / I(k, k);
1047	<	} else {
1048	<	Khw += angMom[0]*angMom[0]/I(0, 0)
1049	<	+ angMom[1]*angMom[1]/I(1, 1)
1050	<	+ angMom[2]*angMom[2]/I(2, 2);
1051	<	}
1052	<	}
1053	<	//}
1054	<	} else { //midBin_
1055	<	coldBin.push_back(sd);
1056	<	Pcx += mass * vel.x();
1057	<	Pcy += mass * vel.y();
1058	<	Pcz += mass * vel.z();
1059	<	Kcx += mass * vel.x() * vel.x();
1060	<	Kcy += mass * vel.y() * vel.y();
1061	<	Kcz += mass * vel.z() * vel.z();
1062	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1063	<	if (sd->isDirectional()) {
1064	<	Vector3d angMom = sd->getJ();
1065	<	Mat3x3d I = sd->getI();
1066	<	if (sd->isLinear()) {
1067	<	int i = sd->linearAxis();
1068	<	int j = (i + 1) % 3;
1069	<	int k = (i + 2) % 3;
1070	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
1071	<	angMom[k] * angMom[k] / I(k, k);
1072	<	} else {
1073	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
1074	<	+ angMom[1]*angMom[1]/I(1, 1)
1075	<	+ angMom[2]*angMom[2]/I(2, 2);
1076	<	}
1077	<	}
749	<	//}
750	<	}
1017	>
1018	>
1019	>	RealType mass = sd->getMass();
1020	>	Vector3d vel = sd->getVel();
1021	>
1022	>	hotBin.push_back(sd);
1023	>	Phx += mass * vel.x();
1024	>	Phy += mass * vel.y();
1025	>	Phz += mass * vel.z();
1026	>	Khx += mass * vel.x() * vel.x();
1027	>	Khy += mass * vel.y() * vel.y();
1028	>	Khz += mass * vel.z() * vel.z();
1029	>	if (sd->isDirectional()) {
1030	>	Vector3d angMom = sd->getJ();
1031	>	Mat3x3d I = sd->getI();
1032	>	if (sd->isLinear()) {
1033	>	int i = sd->linearAxis();
1034	>	int j = (i + 1) % 3;
1035	>	int k = (i + 2) % 3;
1036	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1037	>	angMom[k] * angMom[k] / I(k, k);
1038	>	} else {
1039	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1040	>	+ angMom[1]*angMom[1]/I(1, 1)
1041	>	+ angMom[2]*angMom[2]/I(2, 2);
1042	>	}
1043	>	}
1044	>	}
1045	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1046	>	sd = smanB.nextSelected(selej)) {
1047	>	Vector3d pos = sd->getPos();
1048	>
1049	>	// wrap the stuntdouble's position back into the box:
1050	>
1051	>	if (usePeriodicBoundaryConditions_)
1052	>	currentSnap_->wrapVector(pos);
1053	>
1054	>	RealType mass = sd->getMass();
1055	>	Vector3d vel = sd->getVel();
1056	>
1057	>	coldBin.push_back(sd);
1058	>	Pcx += mass * vel.x();
1059	>	Pcy += mass * vel.y();
1060	>	Pcz += mass * vel.z();
1061	>	Kcx += mass * vel.x() * vel.x();
1062	>	Kcy += mass * vel.y() * vel.y();
1063	>	Kcz += mass * vel.z() * vel.z();
1064	>	if (sd->isDirectional()) {
1065	>	Vector3d angMom = sd->getJ();
1066	>	Mat3x3d I = sd->getI();
1067	>	if (sd->isLinear()) {
1068	>	int i = sd->linearAxis();
1069	>	int j = (i + 1) % 3;
1070	>	int k = (i + 2) % 3;
1071	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1072	>	angMom[k] * angMom[k] / I(k, k);
1073	>	} else {
1074	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1075	>	+ angMom[1]*angMom[1]/I(1, 1)
1076	>	+ angMom[2]*angMom[2]/I(2, 2);
1077	>	}
1078		}
1079		}
1080
#	Line 760 | Line 1087 | namespace OpenMD {
1087		Kcz *= 0.5;
1088		Kcw *= 0.5;
1089
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	–
1090		#ifdef IS_MPI
1091		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1092		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
#	Line 791 | Line 1112 | namespace OpenMD {
1112		RealType pz = Pcz / Phz;
1113		RealType c, x, y, z;
1114		bool successfulScale = false;
1115	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1116	<	(rnemdType_ == rnemdKineticScaleAM)) {
1115	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1116	>	(rnemdFluxType_ == rnemdRotKE)) {
1117		//may need sanity check Khw & Kcw > 0
1118
1119	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1120	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1119	>	if (rnemdFluxType_ == rnemdFullKE) {
1120	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1121		} else {
1122	<	c = 1.0 - targetFlux_ / Kcw;
1122	>	c = 1.0 - kineticTarget_ / Kcw;
1123		}
1124
1125		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1126		c = sqrt(c);
1127	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
807	<	//now convert to hotBin coefficient
1127	>
1128		RealType w = 0.0;
1129	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1129	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1130		x = 1.0 + px * (1.0 - c);
1131		y = 1.0 + py * (1.0 - c);
1132		z = 1.0 + pz * (1.0 - c);
#	Line 820 | Line 1140 | namespace OpenMD {
1140		*/
1141		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1142		(fabs(z - 1.0) < 0.1)) {
1143	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1143	>	w = 1.0 + (kineticTarget_
1144	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1145		+ Khz * (1.0 - z * z)) / Khw;
1146		}//no need to calculate w if x, y or z is out of range
1147		} else {
1148	<	w = 1.0 + targetFlux_ / Khw;
1148	>	w = 1.0 + kineticTarget_ / Khw;
1149		}
1150		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1151		//if w is in the right range, so should be x, y, z.
1152		vector<StuntDouble*>::iterator sdi;
1153		Vector3d vel;
1154	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1155	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1154	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1155	>	if (rnemdFluxType_ == rnemdFullKE) {
1156		vel = (*sdi)->getVel() * c;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
1157		(*sdi)->setVel(vel);
1158		}
1159		if ((*sdi)->isDirectional()) {
1160		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//angMom[2] *= c;
1161		(*sdi)->setJ(angMom);
1162		}
1163		}
1164		w = sqrt(w);
1165	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
1166	<	<< "\twh= " << w << endl;
852	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
853	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1165	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1166	>	if (rnemdFluxType_ == rnemdFullKE) {
1167		vel = (*sdi)->getVel();
1168		vel.x() *= x;
1169		vel.y() *= y;
#	Line 859 | Line 1172 | namespace OpenMD {
1172		}
1173		if ((*sdi)->isDirectional()) {
1174		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//angMom[2] *= w;
1175		(*sdi)->setJ(angMom);
1176		}
1177		}
1178		successfulScale = true;
1179	<	exchangeSum_ += targetFlux_;
1179	>	kineticExchange_ += kineticTarget_;
1180		}
1181		}
1182		} else {
1183		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1184	<	switch(rnemdType_) {
1185	<	case rnemdKineticScale :
1184	>	switch(rnemdFluxType_) {
1185	>	case rnemdKE :
1186		/* used hotBin coeff's & only scale x & y dimensions
1187		RealType px = Phx / Pcx;
1188		RealType py = Phy / Pcy;
1189		a110 = Khy;
1190	<	c0 = - Khx - Khy - targetFlux_;
1190	>	c0 = - Khx - Khy - kineticTarget_;
1191		a000 = Khx;
1192		a111 = Kcy * py * py;
1193		b11 = -2.0 * Kcy * py * (1.0 + py);
1194	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1194	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1195		b01 = -2.0 * Kcx * px * (1.0 + px);
1196		a001 = Kcx * px * px;
1197		*/
1198		//scale all three dimensions, let c_x = c_y
1199		a000 = Kcx + Kcy;
1200		a110 = Kcz;
1201	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1201	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1202		a001 = Khx * px * px + Khy * py * py;
1203		a111 = Khz * pz * pz;
1204		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1205		b11 = -2.0 * Khz * pz * (1.0 + pz);
1206		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1207	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1207	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1208		break;
1209	<	case rnemdPxScale :
1210	<	c = 1 - targetFlux_ / Pcx;
1209	>	case rnemdPx :
1210	>	c = 1 - momentumTarget_.x() / Pcx;
1211		a000 = Kcy;
1212		a110 = Kcz;
1213		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 908 | Line 1218 | namespace OpenMD {
1218		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1219		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1220		break;
1221	<	case rnemdPyScale :
1222	<	c = 1 - targetFlux_ / Pcy;
1221	>	case rnemdPy :
1222	>	c = 1 - momentumTarget_.y() / Pcy;
1223		a000 = Kcx;
1224		a110 = Kcz;
1225		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 920 | Line 1230 | namespace OpenMD {
1230		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1231		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1232		break;
1233	<	case rnemdPzScale ://we don't really do this, do we?
1234	<	c = 1 - targetFlux_ / Pcz;
1233	>	case rnemdPz ://we don't really do this, do we?
1234	>	c = 1 - momentumTarget_.z() / Pcz;
1235		a000 = Kcx;
1236		a110 = Kcy;
1237		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 971 | Line 1281 | namespace OpenMD {
1281		vector<RealType>::iterator ri;
1282		RealType r1, r2, alpha0;
1283		vector<pair<RealType,RealType> > rps;
1284	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1284	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1285		r2 = *ri;
1286		//check if FindRealRoots() give the right answer
1287		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1003 | Line 1313 | namespace OpenMD {
1313		RealType diff;
1314		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1315		vector<pair<RealType,RealType> >::iterator rpi;
1316	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1316	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1317		r1 = (*rpi).first;
1318		r2 = (*rpi).second;
1319	<	switch(rnemdType_) {
1320	<	case rnemdKineticScale :
1319	>	switch(rnemdFluxType_) {
1320	>	case rnemdKE :
1321		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1323		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1324		break;
1325	<	case rnemdPxScale :
1325	>	case rnemdPx :
1326		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1327		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1328		break;
1329	<	case rnemdPyScale :
1329	>	case rnemdPy :
1330		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1331		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1332		break;
1333	<	case rnemdPzScale :
1333	>	case rnemdPz :
1334		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1335		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1336		default :
#	Line 1034 | Line 1344 | namespace OpenMD {
1344		#ifdef IS_MPI
1345		if (worldRank == 0) {
1346		#endif
1347	<	sprintf(painCave.errMsg,
1348	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1349	<	bestPair.first, bestPair.second);
1350	<	painCave.isFatal = 0;
1351	<	painCave.severity = OPENMD_INFO;
1352	<	simError();
1347	>	// sprintf(painCave.errMsg,
1348	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1349	>	//         bestPair.first, bestPair.second);
1350	>	// painCave.isFatal = 0;
1351	>	// painCave.severity = OPENMD_INFO;
1352	>	// simError();
1353		#ifdef IS_MPI
1354		}
1355		#endif
1356
1357	<	switch(rnemdType_) {
1358	<	case rnemdKineticScale :
1357	>	switch(rnemdFluxType_) {
1358	>	case rnemdKE :
1359		x = bestPair.first;
1360		y = bestPair.first;
1361		z = bestPair.second;
1362		break;
1363	<	case rnemdPxScale :
1363	>	case rnemdPx :
1364		x = c;
1365		y = bestPair.first;
1366		z = bestPair.second;
1367		break;
1368	<	case rnemdPyScale :
1368	>	case rnemdPy :
1369		x = bestPair.first;
1370		y = c;
1371		z = bestPair.second;
1372		break;
1373	<	case rnemdPzScale :
1373	>	case rnemdPz :
1374		x = bestPair.first;
1375		y = bestPair.second;
1376		z = c;
#	Line 1070 | Line 1380 | namespace OpenMD {
1380		}
1381		vector<StuntDouble*>::iterator sdi;
1382		Vector3d vel;
1383	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1383	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1384		vel = (*sdi)->getVel();
1385		vel.x() *= x;
1386		vel.y() *= y;
#	Line 1081 | Line 1391 | namespace OpenMD {
1391		x = 1.0 + px * (1.0 - x);
1392		y = 1.0 + py * (1.0 - y);
1393		z = 1.0 + pz * (1.0 - z);
1394	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1394	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1395		vel = (*sdi)->getVel();
1396		vel.x() *= x;
1397		vel.y() *= y;
#	Line 1089 | Line 1399 | namespace OpenMD {
1399		(*sdi)->setVel(vel);
1400		}
1401		successfulScale = true;
1402	<	exchangeSum_ += targetFlux_;
1402	>	switch(rnemdFluxType_) {
1403	>	case rnemdKE :
1404	>	kineticExchange_ += kineticTarget_;
1405	>	break;
1406	>	case rnemdPx :
1407	>	case rnemdPy :
1408	>	case rnemdPz :
1409	>	momentumExchange_ += momentumTarget_;
1410	>	break;
1411	>	default :
1412	>	break;
1413	>	}
1414		}
1415		}
1416		if (successfulScale != true) {
1417		sprintf(painCave.errMsg,
1418	<	"RNEMD: exchange NOT performed!\n");
1418	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1419	>	"\tthe constraint equations may not exist or there may be\n"
1420	>	"\tno selected objects in one or both slabs.\n");
1421		painCave.isFatal = 0;
1422		painCave.severity = OPENMD_INFO;
1423		simError();
1424		failTrialCount_++;
1425		}
1426		}
1427	+
1428	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1429	+	if (!doRNEMD_) return;
1430	+	int selei;
1431	+	int selej;
1432
1105	–	void RNEMD::doShiftScale() {
1106	–
1433		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1434	+	RealType time = currentSnap_->getTime();
1435		Mat3x3d hmat = currentSnap_->getHmat();
1436
1110	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1111	–
1112	–	int selei;
1437		StuntDouble* sd;
1114	–	int idx;
1438
1439		vector<StuntDouble*> hotBin, coldBin;
1440
1441		Vector3d Ph(V3Zero);
1442	+	Vector3d Lh(V3Zero);
1443		RealType Mh = 0.0;
1444	+	Mat3x3d Ih(0.0);
1445		RealType Kh = 0.0;
1446		Vector3d Pc(V3Zero);
1447	+	Vector3d Lc(V3Zero);
1448		RealType Mc = 0.0;
1449	+	Mat3x3d Ic(0.0);
1450		RealType Kc = 0.0;
1451
1452	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1453	<	sd = seleMan_.nextSelected(selei)) {
1452	>	// Constraints can be on only the linear or angular momentum, but
1453	>	// not both.  Usually, the user will specify which they want, but
1454	>	// in case they don't, the use of periodic boundaries should make
1455	>	// the choice for us.
1456	>	bool doLinearPart = false;
1457	>	bool doAngularPart = false;
1458
1459	<	idx = sd->getLocalIndex();
1459	>	switch (rnemdFluxType_) {
1460	>	case rnemdPx:
1461	>	case rnemdPy:
1462	>	case rnemdPz:
1463	>	case rnemdPvector:
1464	>	case rnemdKePx:
1465	>	case rnemdKePy:
1466	>	case rnemdKePvector:
1467	>	doLinearPart = true;
1468	>	break;
1469	>	case rnemdLx:
1470	>	case rnemdLy:
1471	>	case rnemdLz:
1472	>	case rnemdLvector:
1473	>	case rnemdKeLx:
1474	>	case rnemdKeLy:
1475	>	case rnemdKeLz:
1476	>	case rnemdKeLvector:
1477	>	doAngularPart = true;
1478	>	break;
1479	>	case rnemdKE:
1480	>	case rnemdRotKE:
1481	>	case rnemdFullKE:
1482	>	default:
1483	>	if (usePeriodicBoundaryConditions_)
1484	>	doLinearPart = true;
1485	>	else
1486	>	doAngularPart = true;
1487	>	break;
1488	>	}
1489	>
1490	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1491	>	sd = smanA.nextSelected(selei)) {
1492
1493		Vector3d pos = sd->getPos();
1494
1495		// wrap the stuntdouble's position back into the box:
1496	+
1497	+	if (usePeriodicBoundaryConditions_)
1498	+	currentSnap_->wrapVector(pos);
1499	+
1500	+	RealType mass = sd->getMass();
1501	+	Vector3d vel = sd->getVel();
1502	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1503	+	RealType r2;
1504	+
1505	+	hotBin.push_back(sd);
1506	+	Ph += mass * vel;
1507	+	Mh += mass;
1508	+	Kh += mass * vel.lengthSquare();
1509	+	Lh += mass * cross(rPos, vel);
1510	+	Ih -= outProduct(rPos, rPos) * mass;
1511	+	r2 = rPos.lengthSquare();
1512	+	Ih(0, 0) += mass * r2;
1513	+	Ih(1, 1) += mass * r2;
1514	+	Ih(2, 2) += mass * r2;
1515	+
1516	+	if (rnemdFluxType_ == rnemdFullKE) {
1517	+	if (sd->isDirectional()) {
1518	+	Vector3d angMom = sd->getJ();
1519	+	Mat3x3d I = sd->getI();
1520	+	if (sd->isLinear()) {
1521	+	int i = sd->linearAxis();
1522	+	int j = (i + 1) % 3;
1523	+	int k = (i + 2) % 3;
1524	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1525	+	angMom[k] * angMom[k] / I(k, k);
1526	+	} else {
1527	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1528	+	angMom[1] * angMom[1] / I(1, 1) +
1529	+	angMom[2] * angMom[2] / I(2, 2);
1530	+	}
1531	+	}
1532	+	}
1533	+	}
1534	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1535	+	sd = smanB.nextSelected(selej)) {
1536
1537	+	Vector3d pos = sd->getPos();
1538	+
1539	+	// wrap the stuntdouble's position back into the box:
1540	+
1541		if (usePeriodicBoundaryConditions_)
1542		currentSnap_->wrapVector(pos);
1543	+
1544	+	RealType mass = sd->getMass();
1545	+	Vector3d vel = sd->getVel();
1546	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1547	+	RealType r2;
1548
1549	<	// which bin is this stuntdouble in?
1550	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1551	<
1552	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1553	<
1554	<	// if we're in bin 0 or the middleBin
1555	<	if (binNo == 0 || binNo == midBin_) {
1556	<
1557	<	RealType mass = sd->getMass();
1558	<	Vector3d vel = sd->getVel();
1559	<
1560	<	if (binNo == 0) {
1561	<	hotBin.push_back(sd);
1562	<	//std::cerr << "before, velocity = " << vel << endl;
1563	<	Ph += mass * vel;
1564	<	//std::cerr << "after, velocity = " << vel << endl;
1565	<	Mh += mass;
1566	<	Kh += mass * vel.lengthSquare();
1567	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1568	<	if (sd->isDirectional()) {
1569	<	Vector3d angMom = sd->getJ();
1570	<	Mat3x3d I = sd->getI();
1571	<	if (sd->isLinear()) {
1572	<	int i = sd->linearAxis();
1573	<	int j = (i + 1) % 3;
1574	<	int k = (i + 2) % 3;
1575	<	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	<	}
1549	>	coldBin.push_back(sd);
1550	>	Pc += mass * vel;
1551	>	Mc += mass;
1552	>	Kc += mass * vel.lengthSquare();
1553	>	Lc += mass * cross(rPos, vel);
1554	>	Ic -= outProduct(rPos, rPos) * mass;
1555	>	r2 = rPos.lengthSquare();
1556	>	Ic(0, 0) += mass * r2;
1557	>	Ic(1, 1) += mass * r2;
1558	>	Ic(2, 2) += mass * r2;
1559	>
1560	>	if (rnemdFluxType_ == rnemdFullKE) {
1561	>	if (sd->isDirectional()) {
1562	>	Vector3d angMom = sd->getJ();
1563	>	Mat3x3d I = sd->getI();
1564	>	if (sd->isLinear()) {
1565	>	int i = sd->linearAxis();
1566	>	int j = (i + 1) % 3;
1567	>	int k = (i + 2) % 3;
1568	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1569	>	angMom[k] * angMom[k] / I(k, k);
1570	>	} else {
1571	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1572	>	angMom[1] * angMom[1] / I(1, 1) +
1573	>	angMom[2] * angMom[2] / I(2, 2);
1574	>	}
1575	>	}
1576		}
1577		}
1578
1579		Kh *= 0.5;
1580		Kc *= 0.5;
1581	<
1201	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	<	<< "\tKc= " << Kc << endl;
1203	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	<
1581	>
1582		#ifdef IS_MPI
1583		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1585	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1587		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1588		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1589		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1590		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1591	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1592	+	MPI::REALTYPE, MPI::SUM);
1593	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1594	+	MPI::REALTYPE, MPI::SUM);
1595		#endif
1596	+
1597
1598	+	Vector3d ac, acrec, bc, bcrec;
1599	+	Vector3d ah, ahrec, bh, bhrec;
1600	+
1601		bool successfulExchange = false;
1602		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1603		Vector3d vc = Pc / Mc;
1604	<	Vector3d ac = njzp_ / Mc + vc;
1605	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1604	>	ac = -momentumTarget_ / Mc + vc;
1605	>	acrec = -momentumTarget_ / Mc;
1606	>
1607	>	// We now need the inverse of the inertia tensor to calculate the
1608	>	// angular velocity of the cold slab;
1609	>	Mat3x3d Ici = Ic.inverse();
1610	>	Vector3d omegac = Ici * Lc;
1611	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1612	>	bcrec = bc - omegac;
1613	>
1614	>	RealType cNumerator = Kc - kineticTarget_;
1615	>	if (doLinearPart)
1616	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1617	>
1618	>	if (doAngularPart)
1619	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1620	>
1621		if (cNumerator > 0.0) {
1622	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1622	>
1623	>	RealType cDenominator = Kc;
1624	>
1625	>	if (doLinearPart)
1626	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1627	>
1628	>	if (doAngularPart)
1629	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1630	>
1631		if (cDenominator > 0.0) {
1632		RealType c = sqrt(cNumerator / cDenominator);
1633		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1634	+
1635		Vector3d vh = Ph / Mh;
1636	<	Vector3d ah = jzp_ / Mh + vh;
1637	<	RealType hNumerator = Kh + targetJzKE_
1638	<	- 0.5 * Mh * ah.lengthSquare();
1639	<	if (hNumerator > 0.0) {
1640	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1636	>	ah = momentumTarget_ / Mh + vh;
1637	>	ahrec = momentumTarget_ / Mh;
1638	>
1639	>	// We now need the inverse of the inertia tensor to
1640	>	// calculate the angular velocity of the hot slab;
1641	>	Mat3x3d Ihi = Ih.inverse();
1642	>	Vector3d omegah = Ihi * Lh;
1643	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1644	>	bhrec = bh - omegah;
1645	>
1646	>	RealType hNumerator = Kh + kineticTarget_;
1647	>	if (doLinearPart)
1648	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1649	>
1650	>	if (doAngularPart)
1651	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1652	>
1653	>	if (hNumerator > 0.0) {
1654	>
1655	>	RealType hDenominator = Kh;
1656	>	if (doLinearPart)
1657	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1658	>	if (doAngularPart)
1659	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1660	>
1661		if (hDenominator > 0.0) {
1662		RealType h = sqrt(hNumerator / hDenominator);
1663		if ((h > 0.9) && (h < 1.1)) {
1664	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1664	>
1665		vector<StuntDouble*>::iterator sdi;
1666		Vector3d vel;
1667	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1667	>	Vector3d rPos;
1668	>
1669	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1670		//vel = (*sdi)->getVel();
1671	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1671	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1672	>	if (doLinearPart)
1673	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1674	>	if (doAngularPart)
1675	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1676	>
1677		(*sdi)->setVel(vel);
1678	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1678	>	if (rnemdFluxType_ == rnemdFullKE) {
1679		if ((*sdi)->isDirectional()) {
1680		Vector3d angMom = (*sdi)->getJ() * c;
1681		(*sdi)->setJ(angMom);
1682		}
1683		}
1684		}
1685	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1685	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1686		//vel = (*sdi)->getVel();
1687	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1687	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1688	>	if (doLinearPart)
1689	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1690	>	if (doAngularPart)
1691	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1692	>
1693		(*sdi)->setVel(vel);
1694	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1694	>	if (rnemdFluxType_ == rnemdFullKE) {
1695		if ((*sdi)->isDirectional()) {
1696		Vector3d angMom = (*sdi)->getJ() * h;
1697		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1699 | namespace OpenMD {
1699		}
1700		}
1701		successfulExchange = true;
1702	<	exchangeSum_ += targetFlux_;
1703	<	// this is a redundant variable for doShiftScale() so that
1704	<	// RNEMD can output one exchange quantity needed in a job.
1263	<	// need a better way to do this.
1702	>	kineticExchange_ += kineticTarget_;
1703	>	momentumExchange_ += momentumTarget_;
1704	>	angularMomentumExchange_ += angularMomentumTarget_;
1705		}
1706		}
1707		}
#	Line 1270 | Line 1711 | namespace OpenMD {
1711		}
1712		if (successfulExchange != true) {
1713		sprintf(painCave.errMsg,
1714	<	"RNEMD: exchange NOT performed!\n");
1714	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1715	>	"\tthe constraint equations may not exist or there may be\n"
1716	>	"\tno selected objects in one or both slabs.\n");
1717		painCave.isFatal = 0;
1718		painCave.severity = OPENMD_INFO;
1719		simError();
#	Line 1278 | Line 1721 | namespace OpenMD {
1721		}
1722		}
1723
1724	+	RealType RNEMD::getDividingArea() {
1725	+
1726	+	if (hasDividingArea_) return dividingArea_;
1727	+
1728	+	RealType areaA, areaB;
1729	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1730	+
1731	+	if (hasSelectionA_) {
1732	+	int isd;
1733	+	StuntDouble* sd;
1734	+	vector<StuntDouble*> aSites;
1735	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1736	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1737	+	sd = seleManA_.nextSelected(isd)) {
1738	+	aSites.push_back(sd);
1739	+	}
1740	+	#if defined(HAVE_QHULL)
1741	+	ConvexHull* surfaceMeshA = new ConvexHull();
1742	+	surfaceMeshA->computeHull(aSites);
1743	+	areaA = surfaceMeshA->getArea();
1744	+	delete surfaceMeshA;
1745	+	#else
1746	+	sprintf( painCave.errMsg,
1747	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1748	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1749	+	painCave.severity = OPENMD_ERROR;
1750	+	painCave.isFatal = 1;
1751	+	simError();
1752	+	#endif
1753	+
1754	+	} else {
1755	+	if (usePeriodicBoundaryConditions_) {
1756	+	// in periodic boundaries, the surface area is twice the x-y
1757	+	// area of the current box:
1758	+	areaA = 2.0 * snap->getXYarea();
1759	+	} else {
1760	+	// in non-periodic simulations, without explicitly setting
1761	+	// selections, the sphere radius sets the surface area of the
1762	+	// dividing surface:
1763	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1764	+	}
1765	+	}
1766	+
1767	+	if (hasSelectionB_) {
1768	+	int isd;
1769	+	StuntDouble* sd;
1770	+	vector<StuntDouble*> bSites;
1771	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1772	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1773	+	sd = seleManB_.nextSelected(isd)) {
1774	+	bSites.push_back(sd);
1775	+	}
1776	+
1777	+	#if defined(HAVE_QHULL)
1778	+	ConvexHull* surfaceMeshB = new ConvexHull();
1779	+	surfaceMeshB->computeHull(bSites);
1780	+	areaB = surfaceMeshB->getArea();
1781	+	delete surfaceMeshB;
1782	+	#else
1783	+	sprintf( painCave.errMsg,
1784	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1785	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1786	+	painCave.severity = OPENMD_ERROR;
1787	+	painCave.isFatal = 1;
1788	+	simError();
1789	+	#endif
1790	+
1791	+
1792	+	} else {
1793	+	if (usePeriodicBoundaryConditions_) {
1794	+	// in periodic boundaries, the surface area is twice the x-y
1795	+	// area of the current box:
1796	+	areaB = 2.0 * snap->getXYarea();
1797	+	} else {
1798	+	// in non-periodic simulations, without explicitly setting
1799	+	// selections, but if a sphereBradius has been set, just use that:
1800	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1801	+	}
1802	+	}
1803	+
1804	+	dividingArea_ = min(areaA, areaB);
1805	+	hasDividingArea_ = true;
1806	+	return dividingArea_;
1807	+	}
1808	+
1809		void RNEMD::doRNEMD() {
1810	+	if (!doRNEMD_) return;
1811	+	trialCount_++;
1812
1813	<	switch(rnemdType_) {
1814	<	case rnemdKineticScale :
1815	<	case rnemdKineticScaleVAM :
1816	<	case rnemdKineticScaleAM :
1817	<	case rnemdPxScale :
1818	<	case rnemdPyScale :
1819	<	case rnemdPzScale :
1820	<	doScale();
1813	>	// object evaluator:
1814	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1815	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1816	>
1817	>	evaluatorA_.loadScriptString(selectionA_);
1818	>	evaluatorB_.loadScriptString(selectionB_);
1819	>
1820	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1821	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1822	>
1823	>	commonA_ = seleManA_ & seleMan_;
1824	>	commonB_ = seleManB_ & seleMan_;
1825	>
1826	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1827	>	// dt = exchange time interval
1828	>	// flux = target flux
1829	>	// dividingArea = smallest dividing surface between the two regions
1830	>
1831	>	hasDividingArea_ = false;
1832	>	RealType area = getDividingArea();
1833	>
1834	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1835	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1836	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1837	>
1838	>	switch(rnemdMethod_) {
1839	>	case rnemdSwap:
1840	>	doSwap(commonA_, commonB_);
1841		break;
1842	<	case rnemdKineticSwap :
1843	<	case rnemdPx :
1294	<	case rnemdPy :
1295	<	case rnemdPz :
1296	<	doSwap();
1842	>	case rnemdNIVS:
1843	>	doNIVS(commonA_, commonB_);
1844		break;
1845	<	case rnemdShiftScaleV :
1846	<	case rnemdShiftScaleVAM :
1300	<	doShiftScale();
1845	>	case rnemdVSS:
1846	>	doVSS(commonA_, commonB_);
1847		break;
1848	<	case rnemdUnknown :
1848	>	case rnemdUnkownMethod:
1849		default :
1850		break;
1851		}
1852		}
1853
1854		void RNEMD::collectData() {
1855	<
1855	>	if (!doRNEMD_) return;
1856		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1857	+
1858	+	// collectData can be called more frequently than the doRNEMD, so use the
1859	+	// computed area from the last exchange time:
1860	+	RealType area = getDividingArea();
1861	+	areaAccumulator_->add(area);
1862		Mat3x3d hmat = currentSnap_->getHmat();
1312	–
1863		seleMan_.setSelectionSet(evaluator_.evaluate());
1864
1865	<	int selei;
1865	>	int selei(0);
1866		StuntDouble* sd;
1867	<	int idx;
1867	>	int binNo;
1868
1869	+	vector<RealType> binMass(nBins_, 0.0);
1870	+	vector<RealType> binPx(nBins_, 0.0);
1871	+	vector<RealType> binPy(nBins_, 0.0);
1872	+	vector<RealType> binPz(nBins_, 0.0);
1873	+	vector<RealType> binOmegax(nBins_, 0.0);
1874	+	vector<RealType> binOmegay(nBins_, 0.0);
1875	+	vector<RealType> binOmegaz(nBins_, 0.0);
1876	+	vector<RealType> binKE(nBins_, 0.0);
1877	+	vector<int> binDOF(nBins_, 0);
1878	+	vector<int> binCount(nBins_, 0);
1879	+
1880		// alternative approach, track all molecules instead of only those
1881		// selected for scaling/swapping:
1882		/*
1883	<	SimInfo::MoleculeIterator miter;
1884	<	vector<StuntDouble*>::iterator iiter;
1885	<	Molecule* mol;
1886	<	StuntDouble* integrableObject;
1887	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1888	<	mol = info_->nextMolecule(miter))
1889	<	integrableObject is essentially sd
1890	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1891	<	integrableObject != NULL;
1892	<	integrableObject = mol->nextIntegrableObject(iiter))
1883	>	SimInfo::MoleculeIterator miter;
1884	>	vector<StuntDouble*>::iterator iiter;
1885	>	Molecule* mol;
1886	>	StuntDouble* sd;
1887	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1888	>	mol = info_->nextMolecule(miter))
1889	>	sd is essentially sd
1890	>	for (sd = mol->beginIntegrableObject(iiter);
1891	>	sd != NULL;
1892	>	sd = mol->nextIntegrableObject(iiter))
1893		*/
1894	+
1895		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1896	<	sd = seleMan_.nextSelected(selei)) {
1897	<
1336	<	idx = sd->getLocalIndex();
1337	<
1896	>	sd = seleMan_.nextSelected(selei)) {
1897	>
1898		Vector3d pos = sd->getPos();
1899
1900		// wrap the stuntdouble's position back into the box:
1901
1902	<	if (usePeriodicBoundaryConditions_)
1902	>	if (usePeriodicBoundaryConditions_) {
1903		currentSnap_->wrapVector(pos);
1904	<
1905	<	// which bin is this stuntdouble in?
1906	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1907	<
1908	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1909	<	rnemdLogWidth_;
1910	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1911	<	/*
1912	<	if (rnemdLogWidth_ == midBin_ + 1)
1913	<	if (binNo > midBin_)
1914	<	binNo = nBins_ - binNo;
1355	<	*/
1904	>	// which bin is this stuntdouble in?
1905	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1906	>	// Shift molecules by half a box to have bins start at 0
1907	>	// The modulo operator is used to wrap the case when we are
1908	>	// beyond the end of the bins back to the beginning.
1909	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1910	>	} else {
1911	>	Vector3d rPos = pos - coordinateOrigin_;
1912	>	binNo = int(rPos.length() / binWidth_);
1913	>	}
1914	>
1915		RealType mass = sd->getMass();
1357	–	mHist_[binNo] += mass;
1916		Vector3d vel = sd->getVel();
1917	<	RealType value;
1918	<	//RealType xVal, yVal, zVal;
1919	<
1920	<	if (outputTemp_) {
1921	<	value = mass * vel.lengthSquare();
1922	<	tempCount_[binNo] += 3;
1923	<	if (sd->isDirectional()) {
1924	<	Vector3d angMom = sd->getJ();
1925	<	Mat3x3d I = sd->getI();
1926	<	if (sd->isLinear()) {
1927	<	int i = sd->linearAxis();
1928	<	int j = (i + 1) % 3;
1929	<	int k = (i + 2) % 3;
1930	<	value += angMom[j] * angMom[j] / I(j, j) +
1931	<	angMom[k] * angMom[k] / I(k, k);
1932	<	tempCount_[binNo] +=2;
1933	<	} else {
1934	<	value += angMom[0] * angMom[0] / I(0, 0) +
1935	<	angMom[1]*angMom[1]/I(1, 1) +
1936	<	angMom[2]*angMom[2]/I(2, 2);
1937	<	tempCount_[binNo] +=3;
1938	<	}
1939	<	}
1940	<	value = value / PhysicalConstants::energyConvert
1941	<	/ PhysicalConstants::kb;//may move to getStatus()
1942	<	tempHist_[binNo] += value;
1917	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1918	>	Vector3d aVel = cross(rPos, vel);
1919	>
1920	>	if (binNo >= 0 && binNo < nBins_)  {
1921	>	binCount[binNo]++;
1922	>	binMass[binNo] += mass;
1923	>	binPx[binNo] += mass*vel.x();
1924	>	binPy[binNo] += mass*vel.y();
1925	>	binPz[binNo] += mass*vel.z();
1926	>	binOmegax[binNo] += aVel.x();
1927	>	binOmegay[binNo] += aVel.y();
1928	>	binOmegaz[binNo] += aVel.z();
1929	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1930	>	binDOF[binNo] += 3;
1931	>
1932	>	if (sd->isDirectional()) {
1933	>	Vector3d angMom = sd->getJ();
1934	>	Mat3x3d I = sd->getI();
1935	>	if (sd->isLinear()) {
1936	>	int i = sd->linearAxis();
1937	>	int j = (i + 1) % 3;
1938	>	int k = (i + 2) % 3;
1939	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1940	>	angMom[k] * angMom[k] / I(k, k));
1941	>	binDOF[binNo] += 2;
1942	>	} else {
1943	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1944	>	angMom[1] * angMom[1] / I(1, 1) +
1945	>	angMom[2] * angMom[2] / I(2, 2));
1946	>	binDOF[binNo] += 3;
1947	>	}
1948	>	}
1949		}
1950	<	if (outputVx_) {
1951	<	value = mass * vel[0];
1952	<	//vxzCount_[binNo]++;
1953	<	pxzHist_[binNo] += value;
1954	<	}
1955	<	if (outputVy_) {
1956	<	value = mass * vel[1];
1957	<	//vyzCount_[binNo]++;
1958	<	pyzHist_[binNo] += value;
1959	<	}
1950	>	}
1951	>
1952	>	#ifdef IS_MPI
1953	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1954	>	nBins_, MPI::INT, MPI::SUM);
1955	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1956	>	nBins_, MPI::REALTYPE, MPI::SUM);
1957	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1958	>	nBins_, MPI::REALTYPE, MPI::SUM);
1959	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1960	>	nBins_, MPI::REALTYPE, MPI::SUM);
1961	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1962	>	nBins_, MPI::REALTYPE, MPI::SUM);
1963	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1964	>	nBins_, MPI::REALTYPE, MPI::SUM);
1965	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1966	>	nBins_, MPI::REALTYPE, MPI::SUM);
1967	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1968	>	nBins_, MPI::REALTYPE, MPI::SUM);
1969	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1970	>	nBins_, MPI::REALTYPE, MPI::SUM);
1971	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1972	>	nBins_, MPI::INT, MPI::SUM);
1973	>	#endif
1974
1975	<	if (output3DTemp_) {
1976	<	value = mass * vel.x() * vel.x();
1977	<	xTempHist_[binNo] += value;
1978	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1979	<	/ PhysicalConstants::kb;
1980	<	yTempHist_[binNo] += value;
1981	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1982	<	/ PhysicalConstants::kb;
1983	<	zTempHist_[binNo] += value;
1984	<	xyzTempCount_[binNo]++;
1975	>	Vector3d vel;
1976	>	Vector3d aVel;
1977	>	RealType den;
1978	>	RealType temp;
1979	>	RealType z;
1980	>	RealType r;
1981	>	for (int i = 0; i < nBins_; i++) {
1982	>	if (usePeriodicBoundaryConditions_) {
1983	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1984	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1985	>	/ currentSnap_->getVolume() ;
1986	>	} else {
1987	>	r = (((RealType)i + 0.5) * binWidth_);
1988	>	RealType rinner = (RealType)i * binWidth_;
1989	>	RealType router = (RealType)(i+1) * binWidth_;
1990	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1991	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1992		}
1993	<	if (outputRotTemp_) {
1994	<	if (sd->isDirectional()) {
1995	<	Vector3d angMom = sd->getJ();
1996	<	Mat3x3d I = sd->getI();
1997	<	if (sd->isLinear()) {
1998	<	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	<	}
1993	>	vel.x() = binPx[i] / binMass[i];
1994	>	vel.y() = binPy[i] / binMass[i];
1995	>	vel.z() = binPz[i] / binMass[i];
1996	>	aVel.x() = binOmegax[i] / binCount[i];
1997	>	aVel.y() = binOmegay[i] / binCount[i];
1998	>	aVel.z() = binOmegaz[i] / binCount[i];
1999
2000	+	if (binCount[i] > 0) {
2001	+	// only add values if there are things to add
2002	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2003	+	PhysicalConstants::energyConvert);
2004	+
2005	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2006	+	if(outputMask_[j]) {
2007	+	switch(j) {
2008	+	case Z:
2009	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2010	+	break;
2011	+	case R:
2012	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2013	+	break;
2014	+	case TEMPERATURE:
2015	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2016	+	break;
2017	+	case VELOCITY:
2018	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2019	+	break;
2020	+	case ANGULARVELOCITY:
2021	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2022	+	break;
2023	+	case DENSITY:
2024	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2025	+	break;
2026	+	}
2027	+	}
2028	+	}
2029	+	}
2030		}
2031	+	hasData_ = true;
2032		}
2033
2034		void RNEMD::getStarted() {
2035	+	if (!doRNEMD_) return;
2036	+	hasDividingArea_ = false;
2037		collectData();
2038	<	/*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();
2038	>	writeOutputFile();
2039		}
2040
2041	<	void RNEMD::getStatus() {
2042	<
2043	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2044	<	Stats& stat = currentSnap_->statData;
2045	<	RealType time = currentSnap_->getTime();
2046	<
2047	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2048	<	//or to be more meaningful, define another item as exchangeSum_ / time
2049	<	int j;
2050	<
2041	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2042	>	if (!doRNEMD_) return;
2043	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2044	>
2045	>	while(tokenizer.hasMoreTokens()) {
2046	>	std::string token(tokenizer.nextToken());
2047	>	toUpper(token);
2048	>	OutputMapType::iterator i = outputMap_.find(token);
2049	>	if (i != outputMap_.end()) {
2050	>	outputMask_.set(i->second);
2051	>	} else {
2052	>	sprintf( painCave.errMsg,
2053	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2054	>	"\toutputFileFormat keyword.\n", token.c_str() );
2055	>	painCave.isFatal = 0;
2056	>	painCave.severity = OPENMD_ERROR;
2057	>	simError();
2058	>	}
2059	>	}
2060	>	}
2061	>
2062	>	void RNEMD::writeOutputFile() {
2063	>	if (!doRNEMD_) return;
2064	>	if (!hasData_) return;
2065	>
2066		#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	–
2067		// If we're the root node, should we print out the results
2068		int worldRank = MPI::COMM_WORLD.Get_rank();
2069		if (worldRank == 0) {
2070		#endif
2071	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2072	+
2073	+	if( !rnemdFile_ ){
2074	+	sprintf( painCave.errMsg,
2075	+	"Could not open \"%s\" for RNEMD output.\n",
2076	+	rnemdFileName_.c_str());
2077	+	painCave.isFatal = 1;
2078	+	simError();
2079	+	}
2080
2081	<	if (outputTemp_) {
2082	<	tempLog_ << time;
2083	<	for (j = 0; j < rnemdLogWidth_; j++) {
2084	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
2085	<	}
2086	<	tempLog_ << endl;
2081	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2082	>
2083	>	RealType time = currentSnap_->getTime();
2084	>	RealType avgArea;
2085	>	areaAccumulator_->getAverage(avgArea);
2086	>
2087	>	RealType Jz(0.0);
2088	>	Vector3d JzP(V3Zero);
2089	>	Vector3d JzL(V3Zero);
2090	>	if (time >= info_->getSimParams()->getDt()) {
2091	>	Jz = kineticExchange_ / (time * avgArea)
2092	>	/ PhysicalConstants::energyConvert;
2093	>	JzP = momentumExchange_ / (time * avgArea);
2094	>	JzL = angularMomentumExchange_ / (time * avgArea);
2095		}
2096	<	if (outputVx_) {
2097	<	vxzLog_ << time;
2098	<	for (j = 0; j < rnemdLogWidth_; j++) {
2099	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
2100	<	}
2101	<	vxzLog_ << endl;
2096	>
2097	>	rnemdFile_ << "#######################################################\n";
2098	>	rnemdFile_ << "# RNEMD {\n";
2099	>
2100	>	map<string, RNEMDMethod>::iterator mi;
2101	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2102	>	if ( (*mi).second == rnemdMethod_)
2103	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2104		}
2105	<	if (outputVy_) {
2106	<	vyzLog_ << time;
2107	<	for (j = 0; j < rnemdLogWidth_; j++) {
2108	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
2105	>	map<string, RNEMDFluxType>::iterator fi;
2106	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2107	>	if ( (*fi).second == rnemdFluxType_)
2108	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2109		}
2110	+
2111	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2112
2113	<	if (output3DTemp_) {
2114	<	RealType temp;
2115	<	xTempLog_ << time;
2116	<	for (j = 0; j < rnemdLogWidth_; j++) {
2117	<	if (outputVx_)
2118	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2119	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2120	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2121	<	xTempLog_ << "\t" << temp;
2113	>	rnemdFile_ << "#    objectSelection = \""
2114	>	<< rnemdObjectSelection_ << "\";\n";
2115	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2116	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2117	>	rnemdFile_ << "# }\n";
2118	>	rnemdFile_ << "#######################################################\n";
2119	>	rnemdFile_ << "# RNEMD report:\n";
2120	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2121	>	rnemdFile_ << "# Target flux:\n";
2122	>	rnemdFile_ << "#           kinetic = "
2123	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2124	>	<< " (kcal/mol/A^2/fs)\n";
2125	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2126	>	<< " (amu/A/fs^2)\n";
2127	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2128	>	<< " (amu/A^2/fs^2)\n";
2129	>	rnemdFile_ << "# Target one-time exchanges:\n";
2130	>	rnemdFile_ << "#          kinetic = "
2131	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2132	>	<< " (kcal/mol)\n";
2133	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2134	>	<< " (amu*A/fs)\n";
2135	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2136	>	<< " (amu*A^2/fs)\n";
2137	>	rnemdFile_ << "# Actual exchange totals:\n";
2138	>	rnemdFile_ << "#          kinetic = "
2139	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2140	>	<< " (kcal/mol)\n";
2141	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2142	>	<< " (amu*A/fs)\n";
2143	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2144	>	<< " (amu*A^2/fs)\n";
2145	>	rnemdFile_ << "# Actual flux:\n";
2146	>	rnemdFile_ << "#          kinetic = " << Jz
2147	>	<< " (kcal/mol/A^2/fs)\n";
2148	>	rnemdFile_ << "#          momentum = " << JzP
2149	>	<< " (amu/A/fs^2)\n";
2150	>	rnemdFile_ << "#  angular momentum = " << JzL
2151	>	<< " (amu/A^2/fs^2)\n";
2152	>	rnemdFile_ << "# Exchange statistics:\n";
2153	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2154	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2155	>	if (rnemdMethod_ == rnemdNIVS) {
2156	>	rnemdFile_ << "#  NIVS root-check errors = "
2157	>	<< failRootCount_ << "\n";
2158	>	}
2159	>	rnemdFile_ << "#######################################################\n";
2160	>
2161	>
2162	>
2163	>	//write title
2164	>	rnemdFile_ << "#";
2165	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2166	>	if (outputMask_[i]) {
2167	>	rnemdFile_ << "\t" << data_[i].title <<
2168	>	"(" << data_[i].units << ")";
2169	>	// add some extra tabs for column alignment
2170	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2171		}
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;
2172		}
2173	<	if (outputRotTemp_) {
2174	<	rotTempLog_ << time;
2175	<	for (j = 0; j < rnemdLogWidth_; j++) {
2176	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2177	<	}
2178	<	rotTempLog_ << endl;
2179	<	}
2173	>	rnemdFile_ << std::endl;
2174	>
2175	>	rnemdFile_.precision(8);
2176	>
2177	>	for (int j = 0; j < nBins_; j++) {
2178	>
2179	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2180	>	if (outputMask_[i]) {
2181	>	if (data_[i].dataType == "RealType")
2182	>	writeReal(i,j);
2183	>	else if (data_[i].dataType == "Vector3d")
2184	>	writeVector(i,j);
2185	>	else {
2186	>	sprintf( painCave.errMsg,
2187	>	"RNEMD found an unknown data type for: %s ",
2188	>	data_[i].title.c_str());
2189	>	painCave.isFatal = 1;
2190	>	simError();
2191	>	}
2192	>	}
2193	>	}
2194	>	rnemdFile_ << std::endl;
2195	>
2196	>	}
2197
2198	+	rnemdFile_ << "#######################################################\n";
2199	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2200	+	rnemdFile_ << "#######################################################\n";
2201	+
2202	+
2203	+	for (int j = 0; j < nBins_; j++) {
2204	+	rnemdFile_ << "#";
2205	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2206	+	if (outputMask_[i]) {
2207	+	if (data_[i].dataType == "RealType")
2208	+	writeRealStdDev(i,j);
2209	+	else if (data_[i].dataType == "Vector3d")
2210	+	writeVectorStdDev(i,j);
2211	+	else {
2212	+	sprintf( painCave.errMsg,
2213	+	"RNEMD found an unknown data type for: %s ",
2214	+	data_[i].title.c_str());
2215	+	painCave.isFatal = 1;
2216	+	simError();
2217	+	}
2218	+	}
2219	+	}
2220	+	rnemdFile_ << std::endl;
2221	+
2222	+	}
2223	+
2224	+	rnemdFile_.flush();
2225	+	rnemdFile_.close();
2226	+
2227		#ifdef IS_MPI
2228		}
2229		#endif
2230	+
2231	+	}
2232	+
2233	+	void RNEMD::writeReal(int index, unsigned int bin) {
2234	+	if (!doRNEMD_) return;
2235	+	assert(index >=0 && index < ENDINDEX);
2236	+	assert(int(bin) < nBins_);
2237	+	RealType s;
2238	+	int count;
2239	+
2240	+	count = data_[index].accumulator[bin]->count();
2241	+	if (count == 0) return;
2242	+
2243	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2244	+
2245	+	if (! isinf(s) && ! isnan(s)) {
2246	+	rnemdFile_ << "\t" << s;
2247	+	} else{
2248	+	sprintf( painCave.errMsg,
2249	+	"RNEMD detected a numerical error writing: %s for bin %u",
2250	+	data_[index].title.c_str(), bin);
2251	+	painCave.isFatal = 1;
2252	+	simError();
2253	+	}
2254	+	}
2255	+
2256	+	void RNEMD::writeVector(int index, unsigned int bin) {
2257	+	if (!doRNEMD_) return;
2258	+	assert(index >=0 && index < ENDINDEX);
2259	+	assert(int(bin) < nBins_);
2260	+	Vector3d s;
2261	+	int count;
2262	+
2263	+	count = data_[index].accumulator[bin]->count();
2264
2265	<	for (j = 0; j < rnemdLogWidth_; j++) {
2266	<	mHist_[j] = 0.0;
2265	>	if (count == 0) return;
2266	>
2267	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2268	>	if (isinf(s[0]) || isnan(s[0]) ||
2269	>	isinf(s[1]) || isnan(s[1]) ||
2270	>	isinf(s[2]) || isnan(s[2]) ) {
2271	>	sprintf( painCave.errMsg,
2272	>	"RNEMD detected a numerical error writing: %s for bin %u",
2273	>	data_[index].title.c_str(), bin);
2274	>	painCave.isFatal = 1;
2275	>	simError();
2276	>	} else {
2277	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2278		}
2279	<	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	<	}
2279	>	}
2280
2281	<	if (output3DTemp_)
2282	<	for (j = 0; j < rnemdLogWidth_; j++) {
2283	<	xTempHist_[j] = 0.0;
2284	<	yTempHist_[j] = 0.0;
2285	<	zTempHist_[j] = 0.0;
2286	<	xyzTempCount_[j] = 0;
2287	<	}
2288	<	if (outputRotTemp_)
2289	<	for (j = 0; j < rnemdLogWidth_; j++) {
2290	<	rotTempCount_[j] = 0;
2291	<	rotTempHist_[j] = 0.0;
2292	<	}
2281	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2282	>	if (!doRNEMD_) return;
2283	>	assert(index >=0 && index < ENDINDEX);
2284	>	assert(int(bin) < nBins_);
2285	>	RealType s;
2286	>	int count;
2287	>
2288	>	count = data_[index].accumulator[bin]->count();
2289	>	if (count == 0) return;
2290	>
2291	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2292	>
2293	>	if (! isinf(s) && ! isnan(s)) {
2294	>	rnemdFile_ << "\t" << s;
2295	>	} else{
2296	>	sprintf( painCave.errMsg,
2297	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2298	>	data_[index].title.c_str(), bin);
2299	>	painCave.isFatal = 1;
2300	>	simError();
2301	>	}
2302		}
2303	+
2304	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2305	+	if (!doRNEMD_) return;
2306	+	assert(index >=0 && index < ENDINDEX);
2307	+	assert(int(bin) < nBins_);
2308	+	Vector3d s;
2309	+	int count;
2310	+
2311	+	count = data_[index].accumulator[bin]->count();
2312	+	if (count == 0) return;
2313	+
2314	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2315	+	if (isinf(s[0]) || isnan(s[0]) ||
2316	+	isinf(s[1]) || isnan(s[1]) ||
2317	+	isinf(s[2]) || isnan(s[2]) ) {
2318	+	sprintf( painCave.errMsg,
2319	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2320	+	data_[index].title.c_str(), bin);
2321	+	painCave.isFatal = 1;
2322	+	simError();
2323	+	} else {
2324	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2325	+	}
2326	+	}
2327		}
2328

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