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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1722 by gezelter, Thu May 24 14:23:40 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1854 by gezelter, Thu Mar 28 20:54:06 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	+	#include "brains/Thermo.hpp"
56	+	#include "math/ConvexHull.hpp"
57	+	#ifdef IS_MPI
58	+	#include <mpi.h>
59	+	#endif
60
61	<	#ifndef IS_MPI
62	<	#include "math/SeqRandNumGen.hpp"
63	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
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 62 | 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		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
76
77	+	trialCount_ = 0;
78		failTrialCount_ = 0;
79		failRootCount_ = 0;
80
81	<	int seedValue;
82	<	Globals * simParams = info->getSimParams();
81	>	Globals* simParams = info->getSimParams();
82	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83
84	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
85	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
75	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
76	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
77	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
78	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
79	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
80	<	stringToEnumMap_["Px"] = rnemdPx;
81	<	stringToEnumMap_["Py"] = rnemdPy;
82	<	stringToEnumMap_["Pz"] = rnemdPz;
83	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
84	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
85	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
84	>	doRNEMD_ = rnemdParams->getUseRNEMD();
85	>	if (!doRNEMD_) return;
86
87	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
88	<	evaluator_.loadScriptString(rnemdObjectSelection_);
89	<	seleMan_.setSelectionSet(evaluator_.evaluate());
87	>	stringToMethod_["Swap"]  = rnemdSwap;
88	>	stringToMethod_["NIVS"]  = rnemdNIVS;
89	>	stringToMethod_["VSS"]   = rnemdVSS;
90
91	<	// do some sanity checking
91	>	stringToFluxType_["KE"]  = rnemdKE;
92	>	stringToFluxType_["Px"]  = rnemdPx;
93	>	stringToFluxType_["Py"]  = rnemdPy;
94	>	stringToFluxType_["Pz"]  = rnemdPz;
95	>	stringToFluxType_["Pvector"]  = rnemdPvector;
96	>	stringToFluxType_["Lx"]  = rnemdLx;
97	>	stringToFluxType_["Ly"]  = rnemdLy;
98	>	stringToFluxType_["Lz"]  = rnemdLz;
99	>	stringToFluxType_["Lvector"]  = rnemdLvector;
100	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
101	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
102	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
103	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
104	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
105	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
106	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
107
108	<	int selectionCount = seleMan_.getSelectionCount();
109	<	int nIntegrable = info->getNGlobalIntegrableObjects();
108	>	runTime_ = simParams->getRunTime();
109	>	statusTime_ = simParams->getStatusTime();
110
111	<	if (selectionCount > nIntegrable) {
111	>	const string methStr = rnemdParams->getMethod();
112	>	bool hasFluxType = rnemdParams->haveFluxType();
113	>
114	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115	>
116	>	string fluxStr;
117	>	if (hasFluxType) {
118	>	fluxStr = rnemdParams->getFluxType();
119	>	} else {
120		sprintf(painCave.errMsg,
121	<	"RNEMD: The current RNEMD_objectSelection,\n"
122	<	"\t\t%s\n"
123	<	"\thas resulted in %d selected objects.  However,\n"
124	<	"\tthe total number of integrable objects in the system\n"
125	<	"\tis only %d.  This is almost certainly not what you want\n"
126	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
127	<	"\tselector in the selection script!\n",
105	<	rnemdObjectSelection_.c_str(),
106	<	selectionCount, nIntegrable);
107	<	painCave.isFatal = 0;
108	<	painCave.severity = OPENMD_WARNING;
121	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
122	>	"\twhich must be one of the following values:\n"
123	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
124	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
125	>	"\tmust be set to use RNEMD\n");
126	>	painCave.isFatal = 1;
127	>	painCave.severity = OPENMD_ERROR;
128		simError();
129		}
130	+
131	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
132	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
133	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
134	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
135	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
136	+	hasSelectionA_ = rnemdParams->haveSelectionA();
137	+	hasSelectionB_ = rnemdParams->haveSelectionB();
138	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
139	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
140	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
141	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
142	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
143	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
144	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
145	+	bool hasOutputFields = rnemdParams->haveOutputFields();
146
147	<	const string st = simParams->getRNEMD_exchangeType();
147	>	map<string, RNEMDMethod>::iterator i;
148	>	i = stringToMethod_.find(methStr);
149	>	if (i != stringToMethod_.end())
150	>	rnemdMethod_ = i->second;
151	>	else {
152	>	sprintf(painCave.errMsg,
153	>	"RNEMD: The current method,\n"
154	>	"\t\t%s is not one of the recognized\n"
155	>	"\texchange methods: Swap, NIVS, or VSS\n",
156	>	methStr.c_str());
157	>	painCave.isFatal = 1;
158	>	painCave.severity = OPENMD_ERROR;
159	>	simError();
160	>	}
161
162	<	map<string, RNEMDTypeEnum>::iterator i;
163	<	i = stringToEnumMap_.find(st);
164	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
165	<	if (rnemdType_ == rnemdUnknown) {
162	>	map<string, RNEMDFluxType>::iterator j;
163	>	j = stringToFluxType_.find(fluxStr);
164	>	if (j != stringToFluxType_.end())
165	>	rnemdFluxType_ = j->second;
166	>	else {
167		sprintf(painCave.errMsg,
168	<	"RNEMD: The current RNEMD_exchangeType,\n"
168	>	"RNEMD: The current fluxType,\n"
169		"\t\t%s\n"
170	<	"\tis not one of the recognized exchange types.\n",
171	<	st.c_str());
170	>	"\tis not one of the recognized flux types.\n",
171	>	fluxStr.c_str());
172		painCave.isFatal = 1;
173		painCave.severity = OPENMD_ERROR;
174		simError();
175		}
127	–
128	–	outputTemp_ = false;
129	–	if (simParams->haveRNEMD_outputTemperature()) {
130	–	outputTemp_ = simParams->getRNEMD_outputTemperature();
131	–	} else if ((rnemdType_ == rnemdKineticSwap) ||
132	–	(rnemdType_ == rnemdKineticScale) ||
133	–	(rnemdType_ == rnemdKineticScaleVAM) ||
134	–	(rnemdType_ == rnemdKineticScaleAM)) {
135	–	outputTemp_ = true;
136	–	}
137	–	outputVx_ = false;
138	–	if (simParams->haveRNEMD_outputVx()) {
139	–	outputVx_ = simParams->getRNEMD_outputVx();
140	–	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
141	–	outputVx_ = true;
142	–	}
143	–	outputVy_ = false;
144	–	if (simParams->haveRNEMD_outputVy()) {
145	–	outputVy_ = simParams->getRNEMD_outputVy();
146	–	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
147	–	outputVy_ = true;
148	–	}
149	–	output3DTemp_ = false;
150	–	if (simParams->haveRNEMD_outputXyzTemperature()) {
151	–	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
152	–	}
153	–	outputRotTemp_ = false;
154	–	if (simParams->haveRNEMD_outputRotTemperature()) {
155	–	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
156	–	}
176
177	<	#ifdef IS_MPI
178	<	if (worldRank == 0) {
179	<	#endif
180	<
181	<	//may have rnemdWriter separately
182	<	string rnemdFileName;
183	<
184	<	if (outputTemp_) {
185	<	rnemdFileName = "temperature.log";
186	<	tempLog_.open(rnemdFileName.c_str());
177	>	bool methodFluxMismatch = false;
178	>	bool hasCorrectFlux = false;
179	>	switch(rnemdMethod_) {
180	>	case rnemdSwap:
181	>	switch (rnemdFluxType_) {
182	>	case rnemdKE:
183	>	hasCorrectFlux = hasKineticFlux;
184	>	break;
185	>	case rnemdPx:
186	>	case rnemdPy:
187	>	case rnemdPz:
188	>	hasCorrectFlux = hasMomentumFlux;
189	>	break;
190	>	default :
191	>	methodFluxMismatch = true;
192	>	break;
193		}
194	<	if (outputVx_) {
195	<	rnemdFileName = "velocityX.log";
196	<	vxzLog_.open(rnemdFileName.c_str());
194	>	break;
195	>	case rnemdNIVS:
196	>	switch (rnemdFluxType_) {
197	>	case rnemdKE:
198	>	case rnemdRotKE:
199	>	case rnemdFullKE:
200	>	hasCorrectFlux = hasKineticFlux;
201	>	break;
202	>	case rnemdPx:
203	>	case rnemdPy:
204	>	case rnemdPz:
205	>	hasCorrectFlux = hasMomentumFlux;
206	>	break;
207	>	case rnemdKePx:
208	>	case rnemdKePy:
209	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
210	>	break;
211	>	default:
212	>	methodFluxMismatch = true;
213	>	break;
214		}
215	<	if (outputVy_) {
216	<	rnemdFileName = "velocityY.log";
217	<	vyzLog_.open(rnemdFileName.c_str());
215	>	break;
216	>	case rnemdVSS:
217	>	switch (rnemdFluxType_) {
218	>	case rnemdKE:
219	>	case rnemdRotKE:
220	>	case rnemdFullKE:
221	>	hasCorrectFlux = hasKineticFlux;
222	>	break;
223	>	case rnemdPx:
224	>	case rnemdPy:
225	>	case rnemdPz:
226	>	hasCorrectFlux = hasMomentumFlux;
227	>	break;
228	>	case rnemdLx:
229	>	case rnemdLy:
230	>	case rnemdLz:
231	>	hasCorrectFlux = hasAngularMomentumFlux;
232	>	break;
233	>	case rnemdPvector:
234	>	hasCorrectFlux = hasMomentumFluxVector;
235	>	break;
236	>	case rnemdLvector:
237	>	hasCorrectFlux = hasAngularMomentumFluxVector;
238	>	break;
239	>	case rnemdKePx:
240	>	case rnemdKePy:
241	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
242	>	break;
243	>	case rnemdKeLx:
244	>	case rnemdKeLy:
245	>	case rnemdKeLz:
246	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
247	>	break;
248	>	case rnemdKePvector:
249	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
250	>	break;
251	>	case rnemdKeLvector:
252	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
253	>	break;
254	>	default:
255	>	methodFluxMismatch = true;
256	>	break;
257		}
258	+	default:
259	+	break;
260	+	}
261
262	<	if (output3DTemp_) {
263	<	rnemdFileName = "temperatureX.log";
264	<	xTempLog_.open(rnemdFileName.c_str());
265	<	rnemdFileName = "temperatureY.log";
266	<	yTempLog_.open(rnemdFileName.c_str());
267	<	rnemdFileName = "temperatureZ.log";
268	<	zTempLog_.open(rnemdFileName.c_str());
262	>	if (methodFluxMismatch) {
263	>	sprintf(painCave.errMsg,
264	>	"RNEMD: The current method,\n"
265	>	"\t\t%s\n"
266	>	"\tcannot be used with the current flux type, %s\n",
267	>	methStr.c_str(), fluxStr.c_str());
268	>	painCave.isFatal = 1;
269	>	painCave.severity = OPENMD_ERROR;
270	>	simError();
271	>	}
272	>	if (!hasCorrectFlux) {
273	>	sprintf(painCave.errMsg,
274	>	"RNEMD: The current method, %s, and flux type, %s,\n"
275	>	"\tdid not have the correct flux value specified. Options\n"
276	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
277	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
278	>	methStr.c_str(), fluxStr.c_str());
279	>	painCave.isFatal = 1;
280	>	painCave.severity = OPENMD_ERROR;
281	>	simError();
282	>	}
283	>
284	>	if (hasKineticFlux) {
285	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
286	>	// into  amu / fs^3:
287	>	kineticFlux_ = rnemdParams->getKineticFlux()
288	>	* PhysicalConstants::energyConvert;
289	>	} else {
290	>	kineticFlux_ = 0.0;
291	>	}
292	>	if (hasMomentumFluxVector) {
293	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
294	>	} else {
295	>	momentumFluxVector_ = V3Zero;
296	>	if (hasMomentumFlux) {
297	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
298	>	switch (rnemdFluxType_) {
299	>	case rnemdPx:
300	>	momentumFluxVector_.x() = momentumFlux;
301	>	break;
302	>	case rnemdPy:
303	>	momentumFluxVector_.y() = momentumFlux;
304	>	break;
305	>	case rnemdPz:
306	>	momentumFluxVector_.z() = momentumFlux;
307	>	break;
308	>	case rnemdKePx:
309	>	momentumFluxVector_.x() = momentumFlux;
310	>	break;
311	>	case rnemdKePy:
312	>	momentumFluxVector_.y() = momentumFlux;
313	>	break;
314	>	default:
315	>	break;
316	>	}
317		}
318	<	if (outputRotTemp_) {
319	<	rnemdFileName = "temperatureR.log";
320	<	rotTempLog_.open(rnemdFileName.c_str());
318	>	if (hasAngularMomentumFluxVector) {
319	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
320	>	} else {
321	>	angularMomentumFluxVector_ = V3Zero;
322	>	if (hasAngularMomentumFlux) {
323	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
324	>	switch (rnemdFluxType_) {
325	>	case rnemdLx:
326	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
327	>	break;
328	>	case rnemdLy:
329	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
330	>	break;
331	>	case rnemdLz:
332	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
333	>	break;
334	>	case rnemdKeLx:
335	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
336	>	break;
337	>	case rnemdKeLy:
338	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
339	>	break;
340	>	case rnemdKeLz:
341	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
342	>	break;
343	>	default:
344	>	break;
345	>	}
346	>	}
347		}
348
349	<	#ifdef IS_MPI
350	<	}
193	<	#endif
194	<
195	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
196	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
197	<	midBin_ = nBins_ / 2;
198	<	if (simParams->haveRNEMD_binShift()) {
199	<	if (simParams->getRNEMD_binShift()) {
200	<	zShift_ = 0.5 / (RealType)(nBins_);
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351		} else {
352	<	zShift_ = 0.0;
352	>	coordinateOrigin_ = V3Zero;
353		}
204	–	} else {
205	–	zShift_ = 0.0;
206	–	}
207	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
208	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
209	–	//set to 0.0 if not using it; N/A in status output yet
210	–	if (simParams->haveRNEMD_logWidth()) {
211	–	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
212	–	/*arbitary rnemdLogWidth_, no checking;
213	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
214	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
215	–	cerr << "Automaically set back to default.\n";
216	–	rnemdLogWidth_ = nBins_;
217	–	}*/
218	–	} else {
219	–	set_RNEMD_logWidth(nBins_);
220	–	}
221	–	tempHist_.resize(rnemdLogWidth_, 0.0);
222	–	tempCount_.resize(rnemdLogWidth_, 0);
223	–	pxzHist_.resize(rnemdLogWidth_, 0.0);
224	–	//vxzCount_.resize(rnemdLogWidth_, 0);
225	–	pyzHist_.resize(rnemdLogWidth_, 0.0);
226	–	//vyzCount_.resize(rnemdLogWidth_, 0);
354
355	<	mHist_.resize(rnemdLogWidth_, 0.0);
229	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
230	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
231	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
232	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
233	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
234	<	rotTempCount_.resize(rnemdLogWidth_, 0);
355	>	// do some sanity checking
356
357	<	set_RNEMD_exchange_total(0.0);
237	<	if (simParams->haveRNEMD_targetFlux()) {
238	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
239	<	} else {
240	<	set_RNEMD_target_flux(0.0);
241	<	}
242	<	if (simParams->haveRNEMD_targetJzKE()) {
243	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
244	<	} else {
245	<	set_RNEMD_target_JzKE(0.0);
246	<	}
247	<	if (simParams->haveRNEMD_targetJzpx()) {
248	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
249	<	} else {
250	<	set_RNEMD_target_jzpx(0.0);
251	<	}
252	<	jzp_.x() = targetJzpx_;
253	<	njzp_.x() = -targetJzpx_;
254	<	if (simParams->haveRNEMD_targetJzpy()) {
255	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
256	<	} else {
257	<	set_RNEMD_target_jzpy(0.0);
258	<	}
259	<	jzp_.y() = targetJzpy_;
260	<	njzp_.y() = -targetJzpy_;
261	<	if (simParams->haveRNEMD_targetJzpz()) {
262	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
263	<	} else {
264	<	set_RNEMD_target_jzpz(0.0);
265	<	}
266	<	jzp_.z() = targetJzpz_;
267	<	njzp_.z() = -targetJzpz_;
357	>	int selectionCount = seleMan_.getSelectionCount();
358
359	<	#ifndef IS_MPI
360	<	if (simParams->haveSeed()) {
361	<	seedValue = simParams->getSeed();
362	<	randNumGen_ = new SeqRandNumGen(seedValue);
363	<	}else {
364	<	randNumGen_ = new SeqRandNumGen();
365	<	}
366	<	#else
367	<	if (simParams->haveSeed()) {
368	<	seedValue = simParams->getSeed();
369	<	randNumGen_ = new ParallelRandNumGen(seedValue);
370	<	}else {
371	<	randNumGen_ = new ParallelRandNumGen();
372	<	}
373	<	#endif
359	>	int nIntegrable = info->getNGlobalIntegrableObjects();
360	>
361	>	if (selectionCount > nIntegrable) {
362	>	sprintf(painCave.errMsg,
363	>	"RNEMD: The current objectSelection,\n"
364	>	"\t\t%s\n"
365	>	"\thas resulted in %d selected objects.  However,\n"
366	>	"\tthe total number of integrable objects in the system\n"
367	>	"\tis only %d.  This is almost certainly not what you want\n"
368	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
369	>	"\tselector in the selection script!\n",
370	>	rnemdObjectSelection_.c_str(),
371	>	selectionCount, nIntegrable);
372	>	painCave.isFatal = 0;
373	>	painCave.severity = OPENMD_WARNING;
374	>	simError();
375	>	}
376	>
377	>	areaAccumulator_ = new Accumulator();
378	>
379	>	nBins_ = rnemdParams->getOutputBins();
380	>	binWidth_ = rnemdParams->getOutputBinWidth();
381	>
382	>	data_.resize(RNEMD::ENDINDEX);
383	>	OutputData z;
384	>	z.units =  "Angstroms";
385	>	z.title =  "Z";
386	>	z.dataType = "RealType";
387	>	z.accumulator.reserve(nBins_);
388	>	for (int i = 0; i < nBins_; i++)
389	>	z.accumulator.push_back( new Accumulator() );
390	>	data_[Z] = z;
391	>	outputMap_["Z"] =  Z;
392	>
393	>	OutputData r;
394	>	r.units =  "Angstroms";
395	>	r.title =  "R";
396	>	r.dataType = "RealType";
397	>	r.accumulator.reserve(nBins_);
398	>	for (int i = 0; i < nBins_; i++)
399	>	r.accumulator.push_back( new Accumulator() );
400	>	data_[R] = r;
401	>	outputMap_["R"] =  R;
402	>
403	>	OutputData temperature;
404	>	temperature.units =  "K";
405	>	temperature.title =  "Temperature";
406	>	temperature.dataType = "RealType";
407	>	temperature.accumulator.reserve(nBins_);
408	>	for (int i = 0; i < nBins_; i++)
409	>	temperature.accumulator.push_back( new Accumulator() );
410	>	data_[TEMPERATURE] = temperature;
411	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
412	>
413	>	OutputData velocity;
414	>	velocity.units = "angstroms/fs";
415	>	velocity.title =  "Velocity";
416	>	velocity.dataType = "Vector3d";
417	>	velocity.accumulator.reserve(nBins_);
418	>	for (int i = 0; i < nBins_; i++)
419	>	velocity.accumulator.push_back( new VectorAccumulator() );
420	>	data_[VELOCITY] = velocity;
421	>	outputMap_["VELOCITY"] = VELOCITY;
422	>
423	>	OutputData density;
424	>	density.units =  "g cm^-3";
425	>	density.title =  "Density";
426	>	density.dataType = "RealType";
427	>	density.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	density.accumulator.push_back( new Accumulator() );
430	>	data_[DENSITY] = density;
431	>	outputMap_["DENSITY"] =  DENSITY;
432	>
433	>	if (hasOutputFields) {
434	>	parseOutputFileFormat(rnemdParams->getOutputFields());
435	>	} else {
436	>	if (usePeriodicBoundaryConditions_)
437	>	outputMask_.set(Z);
438	>	else
439	>	outputMask_.set(R);
440	>	switch (rnemdFluxType_) {
441	>	case rnemdKE:
442	>	case rnemdRotKE:
443	>	case rnemdFullKE:
444	>	outputMask_.set(TEMPERATURE);
445	>	break;
446	>	case rnemdPx:
447	>	case rnemdPy:
448	>	outputMask_.set(VELOCITY);
449	>	break;
450	>	case rnemdPz:
451	>	case rnemdPvector:
452	>	outputMask_.set(VELOCITY);
453	>	outputMask_.set(DENSITY);
454	>	break;
455	>	case rnemdLx:
456	>	case rnemdLy:
457	>	case rnemdLz:
458	>	case rnemdLvector:
459	>	outputMask_.set(ANGULARVELOCITY);
460	>	break;
461	>	case rnemdKeLx:
462	>	case rnemdKeLy:
463	>	case rnemdKeLz:
464	>	case rnemdKeLvector:
465	>	outputMask_.set(TEMPERATURE);
466	>	outputMask_.set(ANGULARVELOCITY);
467	>	break;
468	>	case rnemdKePx:
469	>	case rnemdKePy:
470	>	outputMask_.set(TEMPERATURE);
471	>	outputMask_.set(VELOCITY);
472	>	break;
473	>	case rnemdKePvector:
474	>	outputMask_.set(TEMPERATURE);
475	>	outputMask_.set(VELOCITY);
476	>	outputMask_.set(DENSITY);
477	>	break;
478	>	default:
479	>	break;
480	>	}
481	>	}
482	>
483	>	if (hasOutputFileName) {
484	>	rnemdFileName_ = rnemdParams->getOutputFileName();
485	>	} else {
486	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
487	>	}
488	>
489	>	exchangeTime_ = rnemdParams->getExchangeTime();
490	>
491	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
492	>	// total exchange sums are zeroed out at the beginning:
493	>
494	>	kineticExchange_ = 0.0;
495	>	momentumExchange_ = V3Zero;
496	>	angularMomentumExchange_ = V3Zero;
497	>
498	>	std::ostringstream selectionAstream;
499	>	std::ostringstream selectionBstream;
500	>
501	>	if (hasSelectionA_) {
502	>	selectionA_ = rnemdParams->getSelectionA();
503	>	} else {
504	>	if (usePeriodicBoundaryConditions_) {
505	>	Mat3x3d hmat = currentSnap_->getHmat();
506	>
507	>	if (hasSlabWidth)
508	>	slabWidth_ = rnemdParams->getSlabWidth();
509	>	else
510	>	slabWidth_ = hmat(2,2) / 10.0;
511	>
512	>	if (hasSlabACenter)
513	>	slabACenter_ = rnemdParams->getSlabACenter();
514	>	else
515	>	slabACenter_ = 0.0;
516	>
517	>	selectionAstream << "select wrappedz > "
518	>	<< slabACenter_ - 0.5*slabWidth_
519	>	<<  " && wrappedz < "
520	>	<< slabACenter_ + 0.5*slabWidth_;
521	>	selectionA_ = selectionAstream.str();
522	>	} else {
523	>	if (hasSphereARadius)
524	>	sphereARadius_ = rnemdParams->getSphereARadius();
525	>	else {
526	>	// use an initial guess to the size of the inner slab to be 1/10 the
527	>	// radius of an approximately spherical hull:
528	>	Thermo thermo(info);
529	>	RealType hVol = thermo.getHullVolume();
530	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
531	>	}
532	>	selectionAstream << "select r < " << sphereARadius_;
533	>	selectionA_ = selectionAstream.str();
534	>	}
535	>	}
536	>
537	>	if (hasSelectionB_) {
538	>	selectionB_ = rnemdParams->getSelectionB();
539	>	} else {
540	>	if (usePeriodicBoundaryConditions_) {
541	>	Mat3x3d hmat = currentSnap_->getHmat();
542	>
543	>	if (hasSlabWidth)
544	>	slabWidth_ = rnemdParams->getSlabWidth();
545	>	else
546	>	slabWidth_ = hmat(2,2) / 10.0;
547	>
548	>	if (hasSlabBCenter)
549	>	slabBCenter_ = rnemdParams->getSlabACenter();
550	>	else
551	>	slabBCenter_ = hmat(2,2) / 2.0;
552	>
553	>	selectionBstream << "select wrappedz > "
554	>	<< slabBCenter_ - 0.5*slabWidth_
555	>	<<  " && wrappedz < "
556	>	<< slabBCenter_ + 0.5*slabWidth_;
557	>	selectionB_ = selectionBstream.str();
558	>	} else {
559	>	if (hasSphereBRadius_) {
560	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
561	>	selectionBstream << "select r > " << sphereBRadius_;
562	>	selectionB_ = selectionBstream.str();
563	>	} else {
564	>	selectionB_ = "select hull";
565	>	hasSelectionB_ = true;
566	>	}
567	>	}
568	>	}
569	>	}
570	>	// object evaluator:
571	>	evaluator_.loadScriptString(rnemdObjectSelection_);
572	>	seleMan_.setSelectionSet(evaluator_.evaluate());
573	>
574	>	evaluatorA_.loadScriptString(selectionA_);
575	>	evaluatorB_.loadScriptString(selectionB_);
576	>
577	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
578	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
579	>
580	>	commonA_ = seleManA_ & seleMan_;
581	>	commonB_ = seleManB_ & seleMan_;
582		}
583
286	–	RNEMD::~RNEMD() {
287	–	delete randNumGen_;
584
585	+	RNEMD::~RNEMD() {
586	+	if (!doRNEMD_) return;
587		#ifdef IS_MPI
588		if (worldRank == 0) {
589		#endif
292	–
293	–	sprintf(painCave.errMsg,
294	–	"RNEMD: total failed trials: %d\n",
295	–	failTrialCount_);
296	–	painCave.isFatal = 0;
297	–	painCave.severity = OPENMD_INFO;
298	–	simError();
590
591	<	if (outputTemp_) tempLog_.close();
301	<	if (outputVx_)   vxzLog_.close();
302	<	if (outputVy_)   vyzLog_.close();
591	>	writeOutputFile();
592
593	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
594	<	rnemdType_ == rnemdPyScale) {
306	<	sprintf(painCave.errMsg,
307	<	"RNEMD: total root-checking warnings: %d\n",
308	<	failRootCount_);
309	<	painCave.isFatal = 0;
310	<	painCave.severity = OPENMD_INFO;
311	<	simError();
312	<	}
313	<	if (output3DTemp_) {
314	<	xTempLog_.close();
315	<	yTempLog_.close();
316	<	zTempLog_.close();
317	<	}
318	<	if (outputRotTemp_) rotTempLog_.close();
319	<
593	>	rnemdFile_.close();
594	>
595		#ifdef IS_MPI
596		}
597		#endif
598		}
599	+
600	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
601	+	if (!doRNEMD_) return;
602	+	int selei;
603	+	int selej;
604
325	–	void RNEMD::doSwap() {
326	–
605		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
606		Mat3x3d hmat = currentSnap_->getHmat();
607
330	–	seleMan_.setSelectionSet(evaluator_.evaluate());
331	–
332	–	int selei;
608		StuntDouble* sd;
334	–	int idx;
609
610		RealType min_val;
611		bool min_found = false;
#	Line 341 | Line 615 | namespace OpenMD {
615		bool max_found = false;
616		StuntDouble* max_sd;
617
618	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
619	<	sd = seleMan_.nextSelected(selei)) {
618	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
619	>	sd = seleManA_.nextSelected(selei)) {
620
347	–	idx = sd->getLocalIndex();
348	–
621		Vector3d pos = sd->getPos();
622	<
622	>
623		// wrap the stuntdouble's position back into the box:
624	<
624	>
625		if (usePeriodicBoundaryConditions_)
626		currentSnap_->wrapVector(pos);
627	<
628	<	// which bin is this stuntdouble in?
629	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
630	<
631	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
632	<
633	<
362	<	// if we're in bin 0 or the middleBin
363	<	if (binNo == 0 || binNo == midBin_) {
627	>
628	>	RealType mass = sd->getMass();
629	>	Vector3d vel = sd->getVel();
630	>	RealType value;
631	>
632	>	switch(rnemdFluxType_) {
633	>	case rnemdKE :
634
635	<	RealType mass = sd->getMass();
636	<	Vector3d vel = sd->getVel();
637	<	RealType value;
638	<
639	<	switch(rnemdType_) {
370	<	case rnemdKineticSwap :
635	>	value = mass * vel.lengthSquare();
636	>
637	>	if (sd->isDirectional()) {
638	>	Vector3d angMom = sd->getJ();
639	>	Mat3x3d I = sd->getI();
640
641	<	value = mass * vel.lengthSquare();
642	<
643	<	if (sd->isDirectional()) {
644	<	Vector3d angMom = sd->getJ();
645	<	Mat3x3d I = sd->getI();
646	<
647	<	if (sd->isLinear()) {
648	<	int i = sd->linearAxis();
649	<	int j = (i + 1) % 3;
650	<	int k = (i + 2) % 3;
651	<	value += angMom[j] * angMom[j] / I(j, j) +
652	<	angMom[k] * angMom[k] / I(k, k);
653	<	} else {
654	<	value += angMom[0]*angMom[0]/I(0, 0)
655	<	+ angMom[1]*angMom[1]/I(1, 1)
656	<	+ angMom[2]*angMom[2]/I(2, 2);
657	<	}
658	<	} //angular momenta exchange enabled
659	<	//energyConvert temporarily disabled
660	<	//make exchangeSum_ comparable between swap & scale
661	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
662	<	value *= 0.5;
663	<	break;
664	<	case rnemdPx :
665	<	value = mass * vel[0];
666	<	break;
667	<	case rnemdPy :
668	<	value = mass * vel[1];
669	<	break;
670	<	case rnemdPz :
671	<	value = mass * vel[2];
672	<	break;
673	<	default :
674	<	break;
641	>	if (sd->isLinear()) {
642	>	int i = sd->linearAxis();
643	>	int j = (i + 1) % 3;
644	>	int k = (i + 2) % 3;
645	>	value += angMom[j] * angMom[j] / I(j, j) +
646	>	angMom[k] * angMom[k] / I(k, k);
647	>	} else {
648	>	value += angMom[0]*angMom[0]/I(0, 0)
649	>	+ angMom[1]*angMom[1]/I(1, 1)
650	>	+ angMom[2]*angMom[2]/I(2, 2);
651	>	}
652	>	} //angular momenta exchange enabled
653	>	value *= 0.5;
654	>	break;
655	>	case rnemdPx :
656	>	value = mass * vel[0];
657	>	break;
658	>	case rnemdPy :
659	>	value = mass * vel[1];
660	>	break;
661	>	case rnemdPz :
662	>	value = mass * vel[2];
663	>	break;
664	>	default :
665	>	break;
666	>	}
667	>	if (!max_found) {
668	>	max_val = value;
669	>	max_sd = sd;
670	>	max_found = true;
671	>	} else {
672	>	if (max_val < value) {
673	>	max_val = value;
674	>	max_sd = sd;
675		}
676	+	}
677	+	}
678
679	<	if (binNo == 0) {
680	<	if (!min_found) {
681	<	min_val = value;
682	<	min_sd = sd;
683	<	min_found = true;
684	<	} else {
685	<	if (min_val > value) {
686	<	min_val = value;
687	<	min_sd = sd;
688	<	}
689	<	}
690	<	} else { //midBin_
691	<	if (!max_found) {
692	<	max_val = value;
693	<	max_sd = sd;
694	<	max_found = true;
695	<	} else {
696	<	if (max_val < value) {
697	<	max_val = value;
698	<	max_sd = sd;
699	<	}
700	<	}
701	<	}
679	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
680	>	sd = seleManB_.nextSelected(selej)) {
681	>
682	>	Vector3d pos = sd->getPos();
683	>
684	>	// wrap the stuntdouble's position back into the box:
685	>
686	>	if (usePeriodicBoundaryConditions_)
687	>	currentSnap_->wrapVector(pos);
688	>
689	>	RealType mass = sd->getMass();
690	>	Vector3d vel = sd->getVel();
691	>	RealType value;
692	>
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695	>
696	>	value = mass * vel.lengthSquare();
697	>
698	>	if (sd->isDirectional()) {
699	>	Vector3d angMom = sd->getJ();
700	>	Mat3x3d I = sd->getI();
701	>
702	>	if (sd->isLinear()) {
703	>	int i = sd->linearAxis();
704	>	int j = (i + 1) % 3;
705	>	int k = (i + 2) % 3;
706	>	value += angMom[j] * angMom[j] / I(j, j) +
707	>	angMom[k] * angMom[k] / I(k, k);
708	>	} else {
709	>	value += angMom[0]*angMom[0]/I(0, 0)
710	>	+ angMom[1]*angMom[1]/I(1, 1)
711	>	+ angMom[2]*angMom[2]/I(2, 2);
712	>	}
713	>	} //angular momenta exchange enabled
714	>	value *= 0.5;
715	>	break;
716	>	case rnemdPx :
717	>	value = mass * vel[0];
718	>	break;
719	>	case rnemdPy :
720	>	value = mass * vel[1];
721	>	break;
722	>	case rnemdPz :
723	>	value = mass * vel[2];
724	>	break;
725	>	default :
726	>	break;
727	>	}
728	>
729	>	if (!min_found) {
730	>	min_val = value;
731	>	min_sd = sd;
732	>	min_found = true;
733	>	} else {
734	>	if (min_val > value) {
735	>	min_val = value;
736	>	min_sd = sd;
737	>	}
738		}
739		}
740	<
741	<	#ifdef IS_MPI
742	<	int nProc, worldRank;
743	<
437	<	nProc = MPI::COMM_WORLD.Get_size();
438	<	worldRank = MPI::COMM_WORLD.Get_rank();
439	<
740	>
741	>	#ifdef IS_MPI
742	>	int worldRank = MPI::COMM_WORLD.Get_rank();
743	>
744		bool my_min_found = min_found;
745		bool my_max_found = max_found;
746
#	Line 453 | Line 757 | namespace OpenMD {
757		RealType val;
758		int rank;
759		} max_vals, min_vals;
760	<
760	>
761		if (my_min_found) {
762		min_vals.val = min_val;
763		} else {
#	Line 491 | Line 795 | namespace OpenMD {
795		Vector3d max_vel = max_sd->getVel();
796		RealType temp_vel;
797
798	<	switch(rnemdType_) {
799	<	case rnemdKineticSwap :
798	>	switch(rnemdFluxType_) {
799	>	case rnemdKE :
800		min_sd->setVel(max_vel);
801		max_sd->setVel(min_vel);
802		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 543 | Line 847 | namespace OpenMD {
847		min_vel.getArrayPointer(), 3, MPI::REALTYPE,
848		min_vals.rank, 0, status);
849
850	<	switch(rnemdType_) {
851	<	case rnemdKineticSwap :
850	>	switch(rnemdFluxType_) {
851	>	case rnemdKE :
852		max_sd->setVel(min_vel);
853		//angular momenta exchange enabled
854		if (max_sd->isDirectional()) {
#	Line 589 | Line 893 | namespace OpenMD {
893		max_vel.getArrayPointer(), 3, MPI::REALTYPE,
894		max_vals.rank, 0, status);
895
896	<	switch(rnemdType_) {
897	<	case rnemdKineticSwap :
896	>	switch(rnemdFluxType_) {
897	>	case rnemdKE :
898		min_sd->setVel(max_vel);
899		//angular momenta exchange enabled
900		if (min_sd->isDirectional()) {
#	Line 624 | Line 928 | namespace OpenMD {
928		}
929		}
930		#endif
931	<	exchangeSum_ += max_val - min_val;
931	>
932	>	switch(rnemdFluxType_) {
933	>	case rnemdKE:
934	>	kineticExchange_ += max_val - min_val;
935	>	break;
936	>	case rnemdPx:
937	>	momentumExchange_.x() += max_val - min_val;
938	>	break;
939	>	case rnemdPy:
940	>	momentumExchange_.y() += max_val - min_val;
941	>	break;
942	>	case rnemdPz:
943	>	momentumExchange_.z() += max_val - min_val;
944	>	break;
945	>	default:
946	>	break;
947	>	}
948		} else {
949		sprintf(painCave.errMsg,
950	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
950	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
951		painCave.isFatal = 0;
952		painCave.severity = OPENMD_INFO;
953		simError();
#	Line 635 | Line 955 | namespace OpenMD {
955		}
956		} else {
957		sprintf(painCave.errMsg,
958	<	"RNEMD: exchange NOT performed because selected object\n"
959	<	"\tnot present in at least one of the two slabs.\n");
958	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
959	>	"\twas not present in at least one of the two slabs.\n");
960		painCave.isFatal = 0;
961		painCave.severity = OPENMD_INFO;
962		simError();
963		failTrialCount_++;
964	<	}
645	<
964	>	}
965		}
966
967	<	void RNEMD::doScale() {
967	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
968	>	if (!doRNEMD_) return;
969	>	int selei;
970	>	int selej;
971
972		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
973	+	RealType time = currentSnap_->getTime();
974		Mat3x3d hmat = currentSnap_->getHmat();
975
653	–	seleMan_.setSelectionSet(evaluator_.evaluate());
654	–
655	–	int selei;
976		StuntDouble* sd;
657	–	int idx;
977
978		vector<StuntDouble*> hotBin, coldBin;
979
#	Line 673 | Line 992 | namespace OpenMD {
992		RealType Kcz = 0.0;
993		RealType Kcw = 0.0;
994
995	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
996	<	sd = seleMan_.nextSelected(selei)) {
995	>	for (sd = smanA.beginSelected(selei); sd != NULL;
996	>	sd = smanA.nextSelected(selei)) {
997
679	–	idx = sd->getLocalIndex();
680	–
998		Vector3d pos = sd->getPos();
999	<
999	>
1000		// wrap the stuntdouble's position back into the box:
1001	<
1001	>
1002		if (usePeriodicBoundaryConditions_)
1003		currentSnap_->wrapVector(pos);
1004	+
1005	+
1006	+	RealType mass = sd->getMass();
1007	+	Vector3d vel = sd->getVel();
1008	+
1009	+	hotBin.push_back(sd);
1010	+	Phx += mass * vel.x();
1011	+	Phy += mass * vel.y();
1012	+	Phz += mass * vel.z();
1013	+	Khx += mass * vel.x() * vel.x();
1014	+	Khy += mass * vel.y() * vel.y();
1015	+	Khz += mass * vel.z() * vel.z();
1016	+	if (sd->isDirectional()) {
1017	+	Vector3d angMom = sd->getJ();
1018	+	Mat3x3d I = sd->getI();
1019	+	if (sd->isLinear()) {
1020	+	int i = sd->linearAxis();
1021	+	int j = (i + 1) % 3;
1022	+	int k = (i + 2) % 3;
1023	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1024	+	angMom[k] * angMom[k] / I(k, k);
1025	+	} else {
1026	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1027	+	+ angMom[1]*angMom[1]/I(1, 1)
1028	+	+ angMom[2]*angMom[2]/I(2, 2);
1029	+	}
1030	+	}
1031	+	}
1032	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1033	+	sd = smanB.nextSelected(selej)) {
1034	+	Vector3d pos = sd->getPos();
1035	+
1036	+	// wrap the stuntdouble's position back into the box:
1037	+
1038	+	if (usePeriodicBoundaryConditions_)
1039	+	currentSnap_->wrapVector(pos);
1040	+
1041	+	RealType mass = sd->getMass();
1042	+	Vector3d vel = sd->getVel();
1043
1044	<	// which bin is this stuntdouble in?
1045	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1046	<
1047	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1048	<
1049	<	// if we're in bin 0 or the middleBin
1050	<	if (binNo == 0 || binNo == midBin_) {
1051	<
1052	<	RealType mass = sd->getMass();
1053	<	Vector3d vel = sd->getVel();
1054	<
1055	<	if (binNo == 0) {
1056	<	hotBin.push_back(sd);
1057	<	Phx += mass * vel.x();
1058	<	Phy += mass * vel.y();
1059	<	Phz += mass * vel.z();
1060	<	Khx += mass * vel.x() * vel.x();
1061	<	Khy += mass * vel.y() * vel.y();
1062	<	Khz += mass * vel.z() * vel.z();
1063	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1064	<	if (sd->isDirectional()) {
709	<	Vector3d angMom = sd->getJ();
710	<	Mat3x3d I = sd->getI();
711	<	if (sd->isLinear()) {
712	<	int i = sd->linearAxis();
713	<	int j = (i + 1) % 3;
714	<	int k = (i + 2) % 3;
715	<	Khw += angMom[j] * angMom[j] / I(j, j) +
716	<	angMom[k] * angMom[k] / I(k, k);
717	<	} else {
718	<	Khw += angMom[0]*angMom[0]/I(0, 0)
719	<	+ angMom[1]*angMom[1]/I(1, 1)
720	<	+ angMom[2]*angMom[2]/I(2, 2);
721	<	}
722	<	}
723	<	//}
724	<	} else { //midBin_
725	<	coldBin.push_back(sd);
726	<	Pcx += mass * vel.x();
727	<	Pcy += mass * vel.y();
728	<	Pcz += mass * vel.z();
729	<	Kcx += mass * vel.x() * vel.x();
730	<	Kcy += mass * vel.y() * vel.y();
731	<	Kcz += mass * vel.z() * vel.z();
732	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
733	<	if (sd->isDirectional()) {
734	<	Vector3d angMom = sd->getJ();
735	<	Mat3x3d I = sd->getI();
736	<	if (sd->isLinear()) {
737	<	int i = sd->linearAxis();
738	<	int j = (i + 1) % 3;
739	<	int k = (i + 2) % 3;
740	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
741	<	angMom[k] * angMom[k] / I(k, k);
742	<	} else {
743	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
744	<	+ angMom[1]*angMom[1]/I(1, 1)
745	<	+ angMom[2]*angMom[2]/I(2, 2);
746	<	}
747	<	}
748	<	//}
749	<	}
1044	>	coldBin.push_back(sd);
1045	>	Pcx += mass * vel.x();
1046	>	Pcy += mass * vel.y();
1047	>	Pcz += mass * vel.z();
1048	>	Kcx += mass * vel.x() * vel.x();
1049	>	Kcy += mass * vel.y() * vel.y();
1050	>	Kcz += mass * vel.z() * vel.z();
1051	>	if (sd->isDirectional()) {
1052	>	Vector3d angMom = sd->getJ();
1053	>	Mat3x3d I = sd->getI();
1054	>	if (sd->isLinear()) {
1055	>	int i = sd->linearAxis();
1056	>	int j = (i + 1) % 3;
1057	>	int k = (i + 2) % 3;
1058	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1059	>	angMom[k] * angMom[k] / I(k, k);
1060	>	} else {
1061	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1062	>	+ angMom[1]*angMom[1]/I(1, 1)
1063	>	+ angMom[2]*angMom[2]/I(2, 2);
1064	>	}
1065		}
1066		}
1067
#	Line 758 | Line 1073 | namespace OpenMD {
1073		Kcy *= 0.5;
1074		Kcz *= 0.5;
1075		Kcw *= 0.5;
761	–
762	–	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
763	–	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
764	–	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
765	–	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
766	–	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
1076
1077		#ifdef IS_MPI
1078		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
#	Line 790 | Line 1099 | namespace OpenMD {
1099		RealType pz = Pcz / Phz;
1100		RealType c, x, y, z;
1101		bool successfulScale = false;
1102	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1103	<	(rnemdType_ == rnemdKineticScaleAM)) {
1102	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1103	>	(rnemdFluxType_ == rnemdRotKE)) {
1104		//may need sanity check Khw & Kcw > 0
1105
1106	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1107	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1106	>	if (rnemdFluxType_ == rnemdFullKE) {
1107	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1108		} else {
1109	<	c = 1.0 - targetFlux_ / Kcw;
1109	>	c = 1.0 - kineticTarget_ / Kcw;
1110		}
1111
1112		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1113		c = sqrt(c);
1114	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
806	<	//now convert to hotBin coefficient
1114	>
1115		RealType w = 0.0;
1116	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1116	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1117		x = 1.0 + px * (1.0 - c);
1118		y = 1.0 + py * (1.0 - c);
1119		z = 1.0 + pz * (1.0 - c);
#	Line 819 | Line 1127 | namespace OpenMD {
1127		*/
1128		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1129		(fabs(z - 1.0) < 0.1)) {
1130	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1130	>	w = 1.0 + (kineticTarget_
1131	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1132		+ Khz * (1.0 - z * z)) / Khw;
1133		}//no need to calculate w if x, y or z is out of range
1134		} else {
1135	<	w = 1.0 + targetFlux_ / Khw;
1135	>	w = 1.0 + kineticTarget_ / Khw;
1136		}
1137		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1138		//if w is in the right range, so should be x, y, z.
1139		vector<StuntDouble*>::iterator sdi;
1140		Vector3d vel;
1141		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1142	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1142	>	if (rnemdFluxType_ == rnemdFullKE) {
1143		vel = (*sdi)->getVel() * c;
835	–	//vel.x() *= c;
836	–	//vel.y() *= c;
837	–	//vel.z() *= c;
1144		(*sdi)->setVel(vel);
1145		}
1146		if ((*sdi)->isDirectional()) {
1147		Vector3d angMom = (*sdi)->getJ() * c;
842	–	//angMom[0] *= c;
843	–	//angMom[1] *= c;
844	–	//angMom[2] *= c;
1148		(*sdi)->setJ(angMom);
1149		}
1150		}
1151		w = sqrt(w);
849	–	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
850	–	<< "\twh= " << w << endl;
1152		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1153	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1153	>	if (rnemdFluxType_ == rnemdFullKE) {
1154		vel = (*sdi)->getVel();
1155		vel.x() *= x;
1156		vel.y() *= y;
#	Line 858 | Line 1159 | namespace OpenMD {
1159		}
1160		if ((*sdi)->isDirectional()) {
1161		Vector3d angMom = (*sdi)->getJ() * w;
861	–	//angMom[0] *= w;
862	–	//angMom[1] *= w;
863	–	//angMom[2] *= w;
1162		(*sdi)->setJ(angMom);
1163		}
1164		}
1165		successfulScale = true;
1166	<	exchangeSum_ += targetFlux_;
1166	>	kineticExchange_ += kineticTarget_;
1167		}
1168		}
1169		} else {
1170		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1171	<	switch(rnemdType_) {
1172	<	case rnemdKineticScale :
1171	>	switch(rnemdFluxType_) {
1172	>	case rnemdKE :
1173		/* used hotBin coeff's & only scale x & y dimensions
1174		RealType px = Phx / Pcx;
1175		RealType py = Phy / Pcy;
1176		a110 = Khy;
1177	<	c0 = - Khx - Khy - targetFlux_;
1177	>	c0 = - Khx - Khy - kineticTarget_;
1178		a000 = Khx;
1179		a111 = Kcy * py * py;
1180		b11 = -2.0 * Kcy * py * (1.0 + py);
1181	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1181	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1182		b01 = -2.0 * Kcx * px * (1.0 + px);
1183		a001 = Kcx * px * px;
1184		*/
1185		//scale all three dimensions, let c_x = c_y
1186		a000 = Kcx + Kcy;
1187		a110 = Kcz;
1188	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1188	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1189		a001 = Khx * px * px + Khy * py * py;
1190		a111 = Khz * pz * pz;
1191		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1192		b11 = -2.0 * Khz * pz * (1.0 + pz);
1193		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1194	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1194	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1195		break;
1196	<	case rnemdPxScale :
1197	<	c = 1 - targetFlux_ / Pcx;
1196	>	case rnemdPx :
1197	>	c = 1 - momentumTarget_.x() / Pcx;
1198		a000 = Kcy;
1199		a110 = Kcz;
1200		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 907 | Line 1205 | namespace OpenMD {
1205		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1206		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1207		break;
1208	<	case rnemdPyScale :
1209	<	c = 1 - targetFlux_ / Pcy;
1208	>	case rnemdPy :
1209	>	c = 1 - momentumTarget_.y() / Pcy;
1210		a000 = Kcx;
1211		a110 = Kcz;
1212		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 919 | Line 1217 | namespace OpenMD {
1217		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1218		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1219		break;
1220	<	case rnemdPzScale ://we don't really do this, do we?
1221	<	c = 1 - targetFlux_ / Pcz;
1220	>	case rnemdPz ://we don't really do this, do we?
1221	>	c = 1 - momentumTarget_.z() / Pcz;
1222		a000 = Kcx;
1223		a110 = Kcy;
1224		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1005 | Line 1303 | namespace OpenMD {
1303		for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1304		r1 = (*rpi).first;
1305		r2 = (*rpi).second;
1306	<	switch(rnemdType_) {
1307	<	case rnemdKineticScale :
1306	>	switch(rnemdFluxType_) {
1307	>	case rnemdKE :
1308		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1309		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1310		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1311		break;
1312	<	case rnemdPxScale :
1312	>	case rnemdPx :
1313		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1314		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1315		break;
1316	<	case rnemdPyScale :
1316	>	case rnemdPy :
1317		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1318		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1319		break;
1320	<	case rnemdPzScale :
1320	>	case rnemdPz :
1321		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1323		default :
#	Line 1033 | Line 1331 | namespace OpenMD {
1331		#ifdef IS_MPI
1332		if (worldRank == 0) {
1333		#endif
1334	<	sprintf(painCave.errMsg,
1335	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1336	<	bestPair.first, bestPair.second);
1337	<	painCave.isFatal = 0;
1338	<	painCave.severity = OPENMD_INFO;
1339	<	simError();
1334	>	// sprintf(painCave.errMsg,
1335	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1336	>	//         bestPair.first, bestPair.second);
1337	>	// painCave.isFatal = 0;
1338	>	// painCave.severity = OPENMD_INFO;
1339	>	// simError();
1340		#ifdef IS_MPI
1341		}
1342		#endif
1343
1344	<	switch(rnemdType_) {
1345	<	case rnemdKineticScale :
1344	>	switch(rnemdFluxType_) {
1345	>	case rnemdKE :
1346		x = bestPair.first;
1347		y = bestPair.first;
1348		z = bestPair.second;
1349		break;
1350	<	case rnemdPxScale :
1350	>	case rnemdPx :
1351		x = c;
1352		y = bestPair.first;
1353		z = bestPair.second;
1354		break;
1355	<	case rnemdPyScale :
1355	>	case rnemdPy :
1356		x = bestPair.first;
1357		y = c;
1358		z = bestPair.second;
1359		break;
1360	<	case rnemdPzScale :
1360	>	case rnemdPz :
1361		x = bestPair.first;
1362		y = bestPair.second;
1363		z = c;
#	Line 1088 | Line 1386 | namespace OpenMD {
1386		(*sdi)->setVel(vel);
1387		}
1388		successfulScale = true;
1389	<	exchangeSum_ += targetFlux_;
1389	>	switch(rnemdFluxType_) {
1390	>	case rnemdKE :
1391	>	kineticExchange_ += kineticTarget_;
1392	>	break;
1393	>	case rnemdPx :
1394	>	case rnemdPy :
1395	>	case rnemdPz :
1396	>	momentumExchange_ += momentumTarget_;
1397	>	break;
1398	>	default :
1399	>	break;
1400	>	}
1401		}
1402		}
1403		if (successfulScale != true) {
1404		sprintf(painCave.errMsg,
1405	<	"RNEMD: exchange NOT performed!\n");
1405	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1406	>	"\tthe constraint equations may not exist or there may be\n"
1407	>	"\tno selected objects in one or both slabs.\n");
1408		painCave.isFatal = 0;
1409		painCave.severity = OPENMD_INFO;
1410		simError();
1411		failTrialCount_++;
1412		}
1413		}
1414	+
1415	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1416	+	if (!doRNEMD_) return;
1417	+	int selei;
1418	+	int selej;
1419
1104	–	void RNEMD::doShiftScale() {
1105	–
1420		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1421	+	RealType time = currentSnap_->getTime();
1422		Mat3x3d hmat = currentSnap_->getHmat();
1423
1109	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1110	–
1111	–	int selei;
1424		StuntDouble* sd;
1113	–	int idx;
1425
1426		vector<StuntDouble*> hotBin, coldBin;
1427
1428		Vector3d Ph(V3Zero);
1429	+	Vector3d Lh(V3Zero);
1430		RealType Mh = 0.0;
1431	+	Mat3x3d Ih(0.0);
1432		RealType Kh = 0.0;
1433		Vector3d Pc(V3Zero);
1434	+	Vector3d Lc(V3Zero);
1435		RealType Mc = 0.0;
1436	+	Mat3x3d Ic(0.0);
1437		RealType Kc = 0.0;
1438	+
1439	+	for (sd = smanA.beginSelected(selei); sd != NULL;
1440	+	sd = smanA.nextSelected(selei)) {
1441
1124	–	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1125	–	sd = seleMan_.nextSelected(selei)) {
1126	–
1127	–	idx = sd->getLocalIndex();
1128	–
1442		Vector3d pos = sd->getPos();
1443
1444		// wrap the stuntdouble's position back into the box:
1445	+
1446	+	if (usePeriodicBoundaryConditions_)
1447	+	currentSnap_->wrapVector(pos);
1448	+
1449	+	RealType mass = sd->getMass();
1450	+	Vector3d vel = sd->getVel();
1451	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1452	+	RealType r2;
1453	+
1454	+	hotBin.push_back(sd);
1455	+	Ph += mass * vel;
1456	+	Mh += mass;
1457	+	Kh += mass * vel.lengthSquare();
1458	+	Lh += mass * cross(rPos, vel);
1459	+	Ih -= outProduct(rPos, rPos) * mass;
1460	+	r2 = rPos.lengthSquare();
1461	+	Ih(0, 0) += mass * r2;
1462	+	Ih(1, 1) += mass * r2;
1463	+	Ih(2, 2) += mass * r2;
1464	+
1465	+	if (rnemdFluxType_ == rnemdFullKE) {
1466	+	if (sd->isDirectional()) {
1467	+	Vector3d angMom = sd->getJ();
1468	+	Mat3x3d I = sd->getI();
1469	+	if (sd->isLinear()) {
1470	+	int i = sd->linearAxis();
1471	+	int j = (i + 1) % 3;
1472	+	int k = (i + 2) % 3;
1473	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1474	+	angMom[k] * angMom[k] / I(k, k);
1475	+	} else {
1476	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1477	+	angMom[1] * angMom[1] / I(1, 1) +
1478	+	angMom[2] * angMom[2] / I(2, 2);
1479	+	}
1480	+	}
1481	+	}
1482	+	}
1483	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1484	+	sd = smanB.nextSelected(selej)) {
1485
1486	+	Vector3d pos = sd->getPos();
1487	+
1488	+	// wrap the stuntdouble's position back into the box:
1489	+
1490		if (usePeriodicBoundaryConditions_)
1491		currentSnap_->wrapVector(pos);
1492	+
1493	+	RealType mass = sd->getMass();
1494	+	Vector3d vel = sd->getVel();
1495	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1496	+	RealType r2;
1497
1498	<	// which bin is this stuntdouble in?
1499	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1500	<
1501	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1502	<
1503	<	// if we're in bin 0 or the middleBin
1504	<	if (binNo == 0 || binNo == midBin_) {
1505	<
1506	<	RealType mass = sd->getMass();
1507	<	Vector3d vel = sd->getVel();
1508	<
1509	<	if (binNo == 0) {
1510	<	hotBin.push_back(sd);
1511	<	//std::cerr << "before, velocity = " << vel << endl;
1512	<	Ph += mass * vel;
1513	<	//std::cerr << "after, velocity = " << vel << endl;
1514	<	Mh += mass;
1515	<	Kh += mass * vel.lengthSquare();
1516	<	if (rnemdType_ == rnemdShiftScaleVAM) {
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) +
1163	<	angMom[k] * angMom[k] / I(k, k);
1164	<	} else {
1165	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1166	<	angMom[1] * angMom[1] / I(1, 1) +
1167	<	angMom[2] * angMom[2] / I(2, 2);
1168	<	}
1169	<	}
1170	<	}
1171	<	} else { //midBin_
1172	<	coldBin.push_back(sd);
1173	<	Pc += mass * vel;
1174	<	Mc += mass;
1175	<	Kc += mass * vel.lengthSquare();
1176	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1177	<	if (sd->isDirectional()) {
1178	<	Vector3d angMom = sd->getJ();
1179	<	Mat3x3d I = sd->getI();
1180	<	if (sd->isLinear()) {
1181	<	int i = sd->linearAxis();
1182	<	int j = (i + 1) % 3;
1183	<	int k = (i + 2) % 3;
1184	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1185	<	angMom[k] * angMom[k] / I(k, k);
1186	<	} else {
1187	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1188	<	angMom[1] * angMom[1] / I(1, 1) +
1189	<	angMom[2] * angMom[2] / I(2, 2);
1190	<	}
1191	<	}
1192	<	}
1193	<	}
1498	>	coldBin.push_back(sd);
1499	>	Pc += mass * vel;
1500	>	Mc += mass;
1501	>	Kc += mass * vel.lengthSquare();
1502	>	Lc += mass * cross(rPos, vel);
1503	>	Ic -= outProduct(rPos, rPos) * mass;
1504	>	r2 = rPos.lengthSquare();
1505	>	Ic(0, 0) += mass * r2;
1506	>	Ic(1, 1) += mass * r2;
1507	>	Ic(2, 2) += mass * r2;
1508	>
1509	>	if (rnemdFluxType_ == rnemdFullKE) {
1510	>	if (sd->isDirectional()) {
1511	>	Vector3d angMom = sd->getJ();
1512	>	Mat3x3d I = sd->getI();
1513	>	if (sd->isLinear()) {
1514	>	int i = sd->linearAxis();
1515	>	int j = (i + 1) % 3;
1516	>	int k = (i + 2) % 3;
1517	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1518	>	angMom[k] * angMom[k] / I(k, k);
1519	>	} else {
1520	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1521	>	angMom[1] * angMom[1] / I(1, 1) +
1522	>	angMom[2] * angMom[2] / I(2, 2);
1523	>	}
1524	>	}
1525		}
1526		}
1527
1528		Kh *= 0.5;
1529		Kc *= 0.5;
1530	<
1200	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1201	<	<< "\tKc= " << Kc << endl;
1202	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1203	<
1530	>
1531		#ifdef IS_MPI
1532		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1533		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1534	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1535	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1536		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1537		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1538		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1539		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1540	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1541	+	MPI::REALTYPE, MPI::SUM);
1542	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1543	+	MPI::REALTYPE, MPI::SUM);
1544		#endif
1545	<
1545	>
1546		bool successfulExchange = false;
1547		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1548		Vector3d vc = Pc / Mc;
1549	<	Vector3d ac = njzp_ / Mc + vc;
1550	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1549	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1550	>	Vector3d acrec = -momentumTarget_ / Mc;
1551	>
1552	>	// We now need the inverse of the inertia tensor to calculate the
1553	>	// angular velocity of the cold slab;
1554	>	Mat3x3d Ici = Ic.inverse();
1555	>	Vector3d omegac = Ici * Lc;
1556	>	Vector3d bc  = -(Ici * angularMomentumTarget_) + omegac;
1557	>	Vector3d bcrec = bc - omegac;
1558	>
1559	>	RealType cNumerator = Kc - kineticTarget_
1560	>	- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc));
1561		if (cNumerator > 0.0) {
1562	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1562	>
1563	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare()
1564	>	- 0.5*(dot(omegac, Ic * omegac));
1565	>
1566		if (cDenominator > 0.0) {
1567		RealType c = sqrt(cNumerator / cDenominator);
1568		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1569	+
1570		Vector3d vh = Ph / Mh;
1571	<	Vector3d ah = jzp_ / Mh + vh;
1572	<	RealType hNumerator = Kh + targetJzKE_
1573	<	- 0.5 * Mh * ah.lengthSquare();
1574	<	if (hNumerator > 0.0) {
1575	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1571	>	Vector3d ah = momentumTarget_ / Mh + vh;
1572	>	Vector3d ahrec = momentumTarget_ / Mh;
1573	>
1574	>	// We now need the inverse of the inertia tensor to
1575	>	// calculate the angular velocity of the hot slab;
1576	>	Mat3x3d Ihi = Ih.inverse();
1577	>	Vector3d omegah = Ihi * Lh;
1578	>	Vector3d bh  = (Ihi * angularMomentumTarget_) + omegah;
1579	>	Vector3d bhrec = bh - omegah;
1580	>
1581	>	RealType hNumerator = Kh + kineticTarget_
1582	>	- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));;
1583	>	if (hNumerator > 0.0) {
1584	>
1585	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare()
1586	>	- 0.5*(dot(omegah, Ih * omegah));
1587	>
1588		if (hDenominator > 0.0) {
1589		RealType h = sqrt(hNumerator / hDenominator);
1590		if ((h > 0.9) && (h < 1.1)) {
1591	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1233	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1591	>
1592		vector<StuntDouble*>::iterator sdi;
1593		Vector3d vel;
1594	+	Vector3d rPos;
1595	+
1596		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1597		//vel = (*sdi)->getVel();
1598	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1598	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1599	>	vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c
1600	>	+ ac + cross(bc, rPos);
1601		(*sdi)->setVel(vel);
1602	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1602	>	if (rnemdFluxType_ == rnemdFullKE) {
1603		if ((*sdi)->isDirectional()) {
1604		Vector3d angMom = (*sdi)->getJ() * c;
1605		(*sdi)->setJ(angMom);
#	Line 1246 | Line 1608 | namespace OpenMD {
1608		}
1609		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1610		//vel = (*sdi)->getVel();
1611	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1611	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1612	>	vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1613	>	+ ah + cross(bh, rPos);
1614		(*sdi)->setVel(vel);
1615	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1615	>	if (rnemdFluxType_ == rnemdFullKE) {
1616		if ((*sdi)->isDirectional()) {
1617		Vector3d angMom = (*sdi)->getJ() * h;
1618		(*sdi)->setJ(angMom);
#	Line 1256 | Line 1620 | namespace OpenMD {
1620		}
1621		}
1622		successfulExchange = true;
1623	<	exchangeSum_ += targetFlux_;
1624	<	// this is a redundant variable for doShiftScale() so that
1625	<	// RNEMD can output one exchange quantity needed in a job.
1262	<	// need a better way to do this.
1623	>	kineticExchange_ += kineticTarget_;
1624	>	momentumExchange_ += momentumTarget_;
1625	>	angularMomentumExchange_ += angularMomentumTarget_;
1626		}
1627		}
1628		}
#	Line 1269 | Line 1632 | namespace OpenMD {
1632		}
1633		if (successfulExchange != true) {
1634		sprintf(painCave.errMsg,
1635	<	"RNEMD: exchange NOT performed!\n");
1635	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1636	>	"\tthe constraint equations may not exist or there may be\n"
1637	>	"\tno selected objects in one or both slabs.\n");
1638		painCave.isFatal = 0;
1639		painCave.severity = OPENMD_INFO;
1640		simError();
#	Line 1277 | Line 1642 | namespace OpenMD {
1642		}
1643		}
1644
1645	+	RealType RNEMD::getDividingArea() {
1646	+
1647	+	if (hasDividingArea_) return dividingArea_;
1648	+
1649	+	RealType areaA, areaB;
1650	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1651	+
1652	+	if (hasSelectionA_) {
1653	+	int isd;
1654	+	StuntDouble* sd;
1655	+	vector<StuntDouble*> aSites;
1656	+	ConvexHull* surfaceMeshA = new ConvexHull();
1657	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1658	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1659	+	sd = seleManA_.nextSelected(isd)) {
1660	+	aSites.push_back(sd);
1661	+	}
1662	+	surfaceMeshA->computeHull(aSites);
1663	+	areaA = surfaceMeshA->getArea();
1664	+	} else {
1665	+	if (usePeriodicBoundaryConditions_) {
1666	+	// in periodic boundaries, the surface area is twice the x-y
1667	+	// area of the current box:
1668	+	areaA = 2.0 * snap->getXYarea();
1669	+	} else {
1670	+	// in non-periodic simulations, without explicitly setting
1671	+	// selections, the sphere radius sets the surface area of the
1672	+	// dividing surface:
1673	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1674	+	}
1675	+	}
1676	+
1677	+	if (hasSelectionB_) {
1678	+	int isd;
1679	+	StuntDouble* sd;
1680	+	vector<StuntDouble*> bSites;
1681	+	ConvexHull* surfaceMeshB = new ConvexHull();
1682	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1683	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1684	+	sd = seleManB_.nextSelected(isd)) {
1685	+	bSites.push_back(sd);
1686	+	}
1687	+	surfaceMeshB->computeHull(bSites);
1688	+	areaB = surfaceMeshB->getArea();
1689	+	} else {
1690	+	if (usePeriodicBoundaryConditions_) {
1691	+	// in periodic boundaries, the surface area is twice the x-y
1692	+	// area of the current box:
1693	+	areaB = 2.0 * snap->getXYarea();
1694	+	} else {
1695	+	// in non-periodic simulations, without explicitly setting
1696	+	// selections, but if a sphereBradius has been set, just use that:
1697	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1698	+	}
1699	+	}
1700	+
1701	+	dividingArea_ = min(areaA, areaB);
1702	+	hasDividingArea_ = true;
1703	+	return dividingArea_;
1704	+	}
1705	+
1706		void RNEMD::doRNEMD() {
1707	+	if (!doRNEMD_) return;
1708	+	trialCount_++;
1709
1710	<	switch(rnemdType_) {
1711	<	case rnemdKineticScale :
1712	<	case rnemdKineticScaleVAM :
1713	<	case rnemdKineticScaleAM :
1714	<	case rnemdPxScale :
1715	<	case rnemdPyScale :
1716	<	case rnemdPzScale :
1717	<	doScale();
1710	>	// object evaluator:
1711	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1712	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1713	>
1714	>	evaluatorA_.loadScriptString(selectionA_);
1715	>	evaluatorB_.loadScriptString(selectionB_);
1716	>
1717	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1718	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1719	>
1720	>	commonA_ = seleManA_ & seleMan_;
1721	>	commonB_ = seleManB_ & seleMan_;
1722	>
1723	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1724	>	// dt = exchange time interval
1725	>	// flux = target flux
1726	>	// dividingArea = smallest dividing surface between the two regions
1727	>
1728	>	hasDividingArea_ = false;
1729	>	RealType area = getDividingArea();
1730	>
1731	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1732	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1733	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1734	>
1735	>	switch(rnemdMethod_) {
1736	>	case rnemdSwap:
1737	>	doSwap(commonA_, commonB_);
1738		break;
1739	<	case rnemdKineticSwap :
1740	<	case rnemdPx :
1293	<	case rnemdPy :
1294	<	case rnemdPz :
1295	<	doSwap();
1739	>	case rnemdNIVS:
1740	>	doNIVS(commonA_, commonB_);
1741		break;
1742	<	case rnemdShiftScaleV :
1743	<	case rnemdShiftScaleVAM :
1299	<	doShiftScale();
1742	>	case rnemdVSS:
1743	>	doVSS(commonA_, commonB_);
1744		break;
1745	<	case rnemdUnknown :
1745	>	case rnemdUnkownMethod:
1746		default :
1747		break;
1748		}
1749		}
1750
1751		void RNEMD::collectData() {
1752	<
1752	>	if (!doRNEMD_) return;
1753		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1310	–	Mat3x3d hmat = currentSnap_->getHmat();
1754
1755	+	// collectData can be called more frequently than the doRNEMD, so use the
1756	+	// computed area from the last exchange time:
1757	+
1758	+	areaAccumulator_->add(getDividingArea());
1759	+	Mat3x3d hmat = currentSnap_->getHmat();
1760		seleMan_.setSelectionSet(evaluator_.evaluate());
1761
1762	<	int selei;
1762	>	int selei(0);
1763		StuntDouble* sd;
1764	<	int idx;
1764	>	int binNo;
1765
1766	+	vector<RealType> binMass(nBins_, 0.0);
1767	+	vector<RealType> binPx(nBins_, 0.0);
1768	+	vector<RealType> binPy(nBins_, 0.0);
1769	+	vector<RealType> binPz(nBins_, 0.0);
1770	+	vector<RealType> binOmegax(nBins_, 0.0);
1771	+	vector<RealType> binOmegay(nBins_, 0.0);
1772	+	vector<RealType> binOmegaz(nBins_, 0.0);
1773	+	vector<RealType> binKE(nBins_, 0.0);
1774	+	vector<int> binDOF(nBins_, 0);
1775	+	vector<int> binCount(nBins_, 0);
1776	+
1777		// alternative approach, track all molecules instead of only those
1778		// selected for scaling/swapping:
1779		/*
1780	<	SimInfo::MoleculeIterator miter;
1781	<	vector<StuntDouble*>::iterator iiter;
1782	<	Molecule* mol;
1783	<	StuntDouble* integrableObject;
1784	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1785	<	mol = info_->nextMolecule(miter))
1786	<	integrableObject is essentially sd
1787	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1788	<	integrableObject != NULL;
1789	<	integrableObject = mol->nextIntegrableObject(iiter))
1780	>	SimInfo::MoleculeIterator miter;
1781	>	vector<StuntDouble*>::iterator iiter;
1782	>	Molecule* mol;
1783	>	StuntDouble* sd;
1784	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1785	>	mol = info_->nextMolecule(miter))
1786	>	sd is essentially sd
1787	>	for (sd = mol->beginIntegrableObject(iiter);
1788	>	sd != NULL;
1789	>	sd = mol->nextIntegrableObject(iiter))
1790		*/
1791	+
1792		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1793	<	sd = seleMan_.nextSelected(selei)) {
1794	<
1335	<	idx = sd->getLocalIndex();
1336	<
1793	>	sd = seleMan_.nextSelected(selei)) {
1794	>
1795		Vector3d pos = sd->getPos();
1796
1797		// wrap the stuntdouble's position back into the box:
1798
1799	<	if (usePeriodicBoundaryConditions_)
1799	>	if (usePeriodicBoundaryConditions_) {
1800		currentSnap_->wrapVector(pos);
1801	<
1802	<	// which bin is this stuntdouble in?
1803	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1804	<
1805	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1806	<	rnemdLogWidth_;
1807	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1808	<	/*
1809	<	if (rnemdLogWidth_ == midBin_ + 1)
1810	<	if (binNo > midBin_)
1811	<	binNo = nBins_ - binNo;
1354	<	*/
1801	>	// which bin is this stuntdouble in?
1802	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1803	>	// Shift molecules by half a box to have bins start at 0
1804	>	// The modulo operator is used to wrap the case when we are
1805	>	// beyond the end of the bins back to the beginning.
1806	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1807	>	} else {
1808	>	Vector3d rPos = pos - coordinateOrigin_;
1809	>	binNo = int(rPos.length() / binWidth_);
1810	>	}
1811	>
1812		RealType mass = sd->getMass();
1356	–	mHist_[binNo] += mass;
1813		Vector3d vel = sd->getVel();
1814	<	RealType value;
1815	<	//RealType xVal, yVal, zVal;
1816	<
1817	<	if (outputTemp_) {
1818	<	value = mass * vel.lengthSquare();
1819	<	tempCount_[binNo] += 3;
1820	<	if (sd->isDirectional()) {
1821	<	Vector3d angMom = sd->getJ();
1822	<	Mat3x3d I = sd->getI();
1823	<	if (sd->isLinear()) {
1824	<	int i = sd->linearAxis();
1825	<	int j = (i + 1) % 3;
1826	<	int k = (i + 2) % 3;
1827	<	value += angMom[j] * angMom[j] / I(j, j) +
1828	<	angMom[k] * angMom[k] / I(k, k);
1829	<	tempCount_[binNo] +=2;
1830	<	} else {
1831	<	value += angMom[0] * angMom[0] / I(0, 0) +
1832	<	angMom[1]*angMom[1]/I(1, 1) +
1833	<	angMom[2]*angMom[2]/I(2, 2);
1834	<	tempCount_[binNo] +=3;
1835	<	}
1836	<	}
1837	<	value = value / PhysicalConstants::energyConvert
1838	<	/ PhysicalConstants::kb;//may move to getStatus()
1839	<	tempHist_[binNo] += value;
1814	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1815	>	Vector3d aVel = cross(rPos, vel);
1816	>
1817	>	if (binNo < nBins_)  {
1818	>	binCount[binNo]++;
1819	>	binMass[binNo] += mass;
1820	>	binPx[binNo] += mass*vel.x();
1821	>	binPy[binNo] += mass*vel.y();
1822	>	binPz[binNo] += mass*vel.z();
1823	>	binOmegax[binNo] += aVel.x();
1824	>	binOmegay[binNo] += aVel.y();
1825	>	binOmegaz[binNo] += aVel.z();
1826	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1827	>	binDOF[binNo] += 3;
1828	>
1829	>	if (sd->isDirectional()) {
1830	>	Vector3d angMom = sd->getJ();
1831	>	Mat3x3d I = sd->getI();
1832	>	if (sd->isLinear()) {
1833	>	int i = sd->linearAxis();
1834	>	int j = (i + 1) % 3;
1835	>	int k = (i + 2) % 3;
1836	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1837	>	angMom[k] * angMom[k] / I(k, k));
1838	>	binDOF[binNo] += 2;
1839	>	} else {
1840	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1841	>	angMom[1] * angMom[1] / I(1, 1) +
1842	>	angMom[2] * angMom[2] / I(2, 2));
1843	>	binDOF[binNo] += 3;
1844	>	}
1845	>	}
1846		}
1847	<	if (outputVx_) {
1848	<	value = mass * vel[0];
1849	<	//vxzCount_[binNo]++;
1850	<	pxzHist_[binNo] += value;
1851	<	}
1852	<	if (outputVy_) {
1853	<	value = mass * vel[1];
1854	<	//vyzCount_[binNo]++;
1855	<	pyzHist_[binNo] += value;
1856	<	}
1847	>	}
1848	>
1849	>	#ifdef IS_MPI
1850	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1851	>	nBins_, MPI::INT, MPI::SUM);
1852	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1853	>	nBins_, MPI::REALTYPE, MPI::SUM);
1854	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1855	>	nBins_, MPI::REALTYPE, MPI::SUM);
1856	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1857	>	nBins_, MPI::REALTYPE, MPI::SUM);
1858	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1859	>	nBins_, MPI::REALTYPE, MPI::SUM);
1860	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1861	>	nBins_, MPI::REALTYPE, MPI::SUM);
1862	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1863	>	nBins_, MPI::REALTYPE, MPI::SUM);
1864	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1865	>	nBins_, MPI::REALTYPE, MPI::SUM);
1866	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1867	>	nBins_, MPI::REALTYPE, MPI::SUM);
1868	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1869	>	nBins_, MPI::INT, MPI::SUM);
1870	>	#endif
1871
1872	<	if (output3DTemp_) {
1873	<	value = mass * vel.x() * vel.x();
1874	<	xTempHist_[binNo] += value;
1875	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
1876	<	/ PhysicalConstants::kb;
1877	<	yTempHist_[binNo] += value;
1878	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
1879	<	/ PhysicalConstants::kb;
1880	<	zTempHist_[binNo] += value;
1881	<	xyzTempCount_[binNo]++;
1872	>	Vector3d vel;
1873	>	Vector3d aVel;
1874	>	RealType den;
1875	>	RealType temp;
1876	>	RealType z;
1877	>	RealType r;
1878	>	for (int i = 0; i < nBins_; i++) {
1879	>	if (usePeriodicBoundaryConditions_) {
1880	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1881	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1882	>	/ currentSnap_->getVolume() ;
1883	>	} else {
1884	>	r = (((RealType)i + 0.5) * binWidth_);
1885	>	RealType rinner = (RealType)i * binWidth_;
1886	>	RealType router = (RealType)(i+1) * binWidth_;
1887	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1888	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1889		}
1890	<	if (outputRotTemp_) {
1891	<	if (sd->isDirectional()) {
1892	<	Vector3d angMom = sd->getJ();
1893	<	Mat3x3d I = sd->getI();
1894	<	if (sd->isLinear()) {
1895	<	int i = sd->linearAxis();
1413	<	int j = (i + 1) % 3;
1414	<	int k = (i + 2) % 3;
1415	<	value = angMom[j] * angMom[j] / I(j, j) +
1416	<	angMom[k] * angMom[k] / I(k, k);
1417	<	rotTempCount_[binNo] +=2;
1418	<	} else {
1419	<	value = angMom[0] * angMom[0] / I(0, 0) +
1420	<	angMom[1] * angMom[1] / I(1, 1) +
1421	<	angMom[2] * angMom[2] / I(2, 2);
1422	<	rotTempCount_[binNo] +=3;
1423	<	}
1424	<	}
1425	<	value = value / PhysicalConstants::energyConvert
1426	<	/ PhysicalConstants::kb;//may move to getStatus()
1427	<	rotTempHist_[binNo] += value;
1428	<	}
1890	>	vel.x() = binPx[i] / binMass[i];
1891	>	vel.y() = binPy[i] / binMass[i];
1892	>	vel.z() = binPz[i] / binMass[i];
1893	>	aVel.x() = binOmegax[i];
1894	>	aVel.y() = binOmegay[i];
1895	>	aVel.z() = binOmegaz[i];
1896
1897	+	if (binCount[i] > 0) {
1898	+	// only add values if there are things to add
1899	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1900	+	PhysicalConstants::energyConvert);
1901	+
1902	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1903	+	if(outputMask_[j]) {
1904	+	switch(j) {
1905	+	case Z:
1906	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1907	+	break;
1908	+	case R:
1909	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1910	+	break;
1911	+	case TEMPERATURE:
1912	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1913	+	break;
1914	+	case VELOCITY:
1915	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1916	+	break;
1917	+	case ANGULARVELOCITY:
1918	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1919	+	break;
1920	+	case DENSITY:
1921	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1922	+	break;
1923	+	}
1924	+	}
1925	+	}
1926	+	}
1927		}
1928		}
1929
1930		void RNEMD::getStarted() {
1931	+	if (!doRNEMD_) return;
1932	+	hasDividingArea_ = false;
1933		collectData();
1934	<	/*now can output profile in step 0, but might not be useful;
1436	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1437	<	Stats& stat = currentSnap_->statData;
1438	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1439	<	*/
1440	<	//may output a header for the log file here
1441	<	getStatus();
1934	>	writeOutputFile();
1935		}
1936
1937	<	void RNEMD::getStatus() {
1938	<
1939	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1940	<	Stats& stat = currentSnap_->statData;
1941	<	RealType time = currentSnap_->getTime();
1942	<
1943	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1944	<	//or to be more meaningful, define another item as exchangeSum_ / time
1945	<	int j;
1946	<
1937	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1938	>	if (!doRNEMD_) return;
1939	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1940	>
1941	>	while(tokenizer.hasMoreTokens()) {
1942	>	std::string token(tokenizer.nextToken());
1943	>	toUpper(token);
1944	>	OutputMapType::iterator i = outputMap_.find(token);
1945	>	if (i != outputMap_.end()) {
1946	>	outputMask_.set(i->second);
1947	>	} else {
1948	>	sprintf( painCave.errMsg,
1949	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1950	>	"\toutputFileFormat keyword.\n", token.c_str() );
1951	>	painCave.isFatal = 0;
1952	>	painCave.severity = OPENMD_ERROR;
1953	>	simError();
1954	>	}
1955	>	}
1956	>	}
1957	>
1958	>	void RNEMD::writeOutputFile() {
1959	>	if (!doRNEMD_) return;
1960	>
1961		#ifdef IS_MPI
1455	–
1456	–	// all processors have the same number of bins, and STL vectors pack their
1457	–	// arrays, so in theory, this should be safe:
1458	–
1459	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
1460	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1461	–	if (outputTemp_) {
1462	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1463	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1464	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1465	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1466	–	}
1467	–	if (outputVx_) {
1468	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1469	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1470	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1471	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1472	–	}
1473	–	if (outputVy_) {
1474	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1475	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1476	–	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1477	–	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1478	–	}
1479	–	if (output3DTemp_) {
1480	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1481	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1482	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1483	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1484	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1485	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1486	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1487	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1488	–	}
1489	–	if (outputRotTemp_) {
1490	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1491	–	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1492	–	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1493	–	rnemdLogWidth_, MPI::INT, MPI::SUM);
1494	–	}
1495	–
1962		// If we're the root node, should we print out the results
1963		int worldRank = MPI::COMM_WORLD.Get_rank();
1964		if (worldRank == 0) {
1965		#endif
1966	<
1967	<	if (outputTemp_) {
1968	<	tempLog_ << time;
1969	<	for (j = 0; j < rnemdLogWidth_; j++) {
1970	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
1971	<	}
1972	<	tempLog_ << endl;
1973	<	}
1508	<	if (outputVx_) {
1509	<	vxzLog_ << time;
1510	<	for (j = 0; j < rnemdLogWidth_; j++) {
1511	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
1512	<	}
1513	<	vxzLog_ << endl;
1514	<	}
1515	<	if (outputVy_) {
1516	<	vyzLog_ << time;
1517	<	for (j = 0; j < rnemdLogWidth_; j++) {
1518	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1519	<	}
1520	<	vyzLog_ << endl;
1966	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1967	>
1968	>	if( !rnemdFile_ ){
1969	>	sprintf( painCave.errMsg,
1970	>	"Could not open \"%s\" for RNEMD output.\n",
1971	>	rnemdFileName_.c_str());
1972	>	painCave.isFatal = 1;
1973	>	simError();
1974		}
1975
1976	<	if (output3DTemp_) {
1977	<	RealType temp;
1978	<	xTempLog_ << time;
1979	<	for (j = 0; j < rnemdLogWidth_; j++) {
1980	<	if (outputVx_)
1981	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
1982	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
1983	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
1984	<	xTempLog_ << "\t" << temp;
1985	<	}
1986	<	xTempLog_ << endl;
1987	<	yTempLog_ << time;
1988	<	for (j = 0; j < rnemdLogWidth_; j++) {
1989	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1990	<	}
1991	<	yTempLog_ << endl;
1992	<	zTempLog_ << time;
1540	<	for (j = 0; j < rnemdLogWidth_; j++) {
1541	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1542	<	}
1543	<	zTempLog_ << endl;
1976	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1977	>
1978	>	RealType time = currentSnap_->getTime();
1979	>	RealType avgArea;
1980	>	areaAccumulator_->getAverage(avgArea);
1981	>	RealType Jz = kineticExchange_ / (time * avgArea)
1982	>	/ PhysicalConstants::energyConvert;
1983	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
1984	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
1985	>
1986	>	rnemdFile_ << "#######################################################\n";
1987	>	rnemdFile_ << "# RNEMD {\n";
1988	>
1989	>	map<string, RNEMDMethod>::iterator mi;
1990	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1991	>	if ( (*mi).second == rnemdMethod_)
1992	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1993		}
1994	<	if (outputRotTemp_) {
1995	<	rotTempLog_ << time;
1996	<	for (j = 0; j < rnemdLogWidth_; j++) {
1997	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
1549	<	}
1550	<	rotTempLog_ << endl;
1994	>	map<string, RNEMDFluxType>::iterator fi;
1995	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1996	>	if ( (*fi).second == rnemdFluxType_)
1997	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1998		}
1999	+
2000	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2001
2002	+	rnemdFile_ << "#    objectSelection = \""
2003	+	<< rnemdObjectSelection_ << "\";\n";
2004	+	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2005	+	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2006	+	rnemdFile_ << "# }\n";
2007	+	rnemdFile_ << "#######################################################\n";
2008	+	rnemdFile_ << "# RNEMD report:\n";
2009	+	rnemdFile_ << "#      running time = " << time << " fs\n";
2010	+	rnemdFile_ << "# Target flux:\n";
2011	+	rnemdFile_ << "#           kinetic = "
2012	+	<< kineticFlux_ / PhysicalConstants::energyConvert
2013	+	<< " (kcal/mol/A^2/fs)\n";
2014	+	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2015	+	<< " (amu/A/fs^2)\n";
2016	+	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2017	+	<< " (amu/A^2/fs^2)\n";
2018	+	rnemdFile_ << "# Target one-time exchanges:\n";
2019	+	rnemdFile_ << "#          kinetic = "
2020	+	<< kineticTarget_ / PhysicalConstants::energyConvert
2021	+	<< " (kcal/mol)\n";
2022	+	rnemdFile_ << "#          momentum = " << momentumTarget_
2023	+	<< " (amu*A/fs)\n";
2024	+	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2025	+	<< " (amu*A^2/fs)\n";
2026	+	rnemdFile_ << "# Actual exchange totals:\n";
2027	+	rnemdFile_ << "#          kinetic = "
2028	+	<< kineticExchange_ / PhysicalConstants::energyConvert
2029	+	<< " (kcal/mol)\n";
2030	+	rnemdFile_ << "#          momentum = " << momentumExchange_
2031	+	<< " (amu*A/fs)\n";
2032	+	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2033	+	<< " (amu*A^2/fs)\n";
2034	+	rnemdFile_ << "# Actual flux:\n";
2035	+	rnemdFile_ << "#          kinetic = " << Jz
2036	+	<< " (kcal/mol/A^2/fs)\n";
2037	+	rnemdFile_ << "#          momentum = " << JzP
2038	+	<< " (amu/A/fs^2)\n";
2039	+	rnemdFile_ << "#  angular momentum = " << JzL
2040	+	<< " (amu/A^2/fs^2)\n";
2041	+	rnemdFile_ << "# Exchange statistics:\n";
2042	+	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2043	+	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2044	+	if (rnemdMethod_ == rnemdNIVS) {
2045	+	rnemdFile_ << "#  NIVS root-check errors = "
2046	+	<< failRootCount_ << "\n";
2047	+	}
2048	+	rnemdFile_ << "#######################################################\n";
2049	+
2050	+
2051	+
2052	+	//write title
2053	+	rnemdFile_ << "#";
2054	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2055	+	if (outputMask_[i]) {
2056	+	rnemdFile_ << "\t" << data_[i].title <<
2057	+	"(" << data_[i].units << ")";
2058	+	// add some extra tabs for column alignment
2059	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2060	+	}
2061	+	}
2062	+	rnemdFile_ << std::endl;
2063	+
2064	+	rnemdFile_.precision(8);
2065	+
2066	+	for (int j = 0; j < nBins_; j++) {
2067	+
2068	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2069	+	if (outputMask_[i]) {
2070	+	if (data_[i].dataType == "RealType")
2071	+	writeReal(i,j);
2072	+	else if (data_[i].dataType == "Vector3d")
2073	+	writeVector(i,j);
2074	+	else {
2075	+	sprintf( painCave.errMsg,
2076	+	"RNEMD found an unknown data type for: %s ",
2077	+	data_[i].title.c_str());
2078	+	painCave.isFatal = 1;
2079	+	simError();
2080	+	}
2081	+	}
2082	+	}
2083	+	rnemdFile_ << std::endl;
2084	+
2085	+	}
2086	+
2087	+	rnemdFile_ << "#######################################################\n";
2088	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2089	+	rnemdFile_ << "#######################################################\n";
2090	+
2091	+
2092	+	for (int j = 0; j < nBins_; j++) {
2093	+	rnemdFile_ << "#";
2094	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2095	+	if (outputMask_[i]) {
2096	+	if (data_[i].dataType == "RealType")
2097	+	writeRealStdDev(i,j);
2098	+	else if (data_[i].dataType == "Vector3d")
2099	+	writeVectorStdDev(i,j);
2100	+	else {
2101	+	sprintf( painCave.errMsg,
2102	+	"RNEMD found an unknown data type for: %s ",
2103	+	data_[i].title.c_str());
2104	+	painCave.isFatal = 1;
2105	+	simError();
2106	+	}
2107	+	}
2108	+	}
2109	+	rnemdFile_ << std::endl;
2110	+
2111	+	}
2112	+
2113	+	rnemdFile_.flush();
2114	+	rnemdFile_.close();
2115	+
2116		#ifdef IS_MPI
2117		}
2118		#endif
2119	+
2120	+	}
2121	+
2122	+	void RNEMD::writeReal(int index, unsigned int bin) {
2123	+	if (!doRNEMD_) return;
2124	+	assert(index >=0 && index < ENDINDEX);
2125	+	assert(int(bin) < nBins_);
2126	+	RealType s;
2127	+	int count;
2128	+
2129	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2130	+	if (count == 0) return;
2131	+
2132	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2133	+
2134	+	if (! isinf(s) && ! isnan(s)) {
2135	+	rnemdFile_ << "\t" << s;
2136	+	} else{
2137	+	sprintf( painCave.errMsg,
2138	+	"RNEMD detected a numerical error writing: %s for bin %d",
2139	+	data_[index].title.c_str(), bin);
2140	+	painCave.isFatal = 1;
2141	+	simError();
2142	+	}
2143	+	}
2144	+
2145	+	void RNEMD::writeVector(int index, unsigned int bin) {
2146	+	if (!doRNEMD_) return;
2147	+	assert(index >=0 && index < ENDINDEX);
2148	+	assert(int(bin) < nBins_);
2149	+	Vector3d s;
2150	+	int count;
2151	+
2152	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2153	+	if (count == 0) return;
2154
2155	<	for (j = 0; j < rnemdLogWidth_; j++) {
2156	<	mHist_[j] = 0.0;
2155	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2156	>	if (isinf(s[0]) || isnan(s[0]) ||
2157	>	isinf(s[1]) || isnan(s[1]) ||
2158	>	isinf(s[2]) || isnan(s[2]) ) {
2159	>	sprintf( painCave.errMsg,
2160	>	"RNEMD detected a numerical error writing: %s for bin %d",
2161	>	data_[index].title.c_str(), bin);
2162	>	painCave.isFatal = 1;
2163	>	simError();
2164	>	} else {
2165	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2166		}
2167	<	if (outputTemp_)
1561	<	for (j = 0; j < rnemdLogWidth_; j++) {
1562	<	tempCount_[j] = 0;
1563	<	tempHist_[j] = 0.0;
1564	<	}
1565	<	if (outputVx_)
1566	<	for (j = 0; j < rnemdLogWidth_; j++) {
1567	<	//pxzCount_[j] = 0;
1568	<	pxzHist_[j] = 0.0;
1569	<	}
1570	<	if (outputVy_)
1571	<	for (j = 0; j < rnemdLogWidth_; j++) {
1572	<	//pyzCount_[j] = 0;
1573	<	pyzHist_[j] = 0.0;
1574	<	}
2167	>	}
2168
2169	<	if (output3DTemp_)
2170	<	for (j = 0; j < rnemdLogWidth_; j++) {
2171	<	xTempHist_[j] = 0.0;
2172	<	yTempHist_[j] = 0.0;
2173	<	zTempHist_[j] = 0.0;
2174	<	xyzTempCount_[j] = 0;
2175	<	}
2176	<	if (outputRotTemp_)
2177	<	for (j = 0; j < rnemdLogWidth_; j++) {
2178	<	rotTempCount_[j] = 0;
2179	<	rotTempHist_[j] = 0.0;
2180	<	}
2169	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2170	>	if (!doRNEMD_) return;
2171	>	assert(index >=0 && index < ENDINDEX);
2172	>	assert(int(bin) < nBins_);
2173	>	RealType s;
2174	>	int count;
2175	>
2176	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2177	>	if (count == 0) return;
2178	>
2179	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2180	>
2181	>	if (! isinf(s) && ! isnan(s)) {
2182	>	rnemdFile_ << "\t" << s;
2183	>	} else{
2184	>	sprintf( painCave.errMsg,
2185	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2186	>	data_[index].title.c_str(), bin);
2187	>	painCave.isFatal = 1;
2188	>	simError();
2189	>	}
2190		}
2191	+
2192	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2193	+	if (!doRNEMD_) return;
2194	+	assert(index >=0 && index < ENDINDEX);
2195	+	assert(int(bin) < nBins_);
2196	+	Vector3d s;
2197	+	int count;
2198	+
2199	+	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2200	+	if (count == 0) return;
2201	+
2202	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2203	+	if (isinf(s[0]) || isnan(s[0]) ||
2204	+	isinf(s[1]) || isnan(s[1]) ||
2205	+	isinf(s[2]) || isnan(s[2]) ) {
2206	+	sprintf( painCave.errMsg,
2207	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2208	+	data_[index].title.c_str(), bin);
2209	+	painCave.isFatal = 1;
2210	+	simError();
2211	+	} else {
2212	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2213	+	}
2214	+	}
2215		}
2216

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