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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1728 by jmarr, Wed May 30 16:07:03 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+	#ifdef IS_MPI
42	+	#include <mpi.h>
43	+	#endif
44
45		#include <cmath>
46	<	#include "integrators/RNEMD.hpp"
46	>	#include <sstream>
47	>	#include <string>
48	>
49	>	#include "rnemd/RNEMD.hpp"
50		#include "math/Vector3.hpp"
51		#include "math/Vector.hpp"
52		#include "math/SquareMatrix3.hpp"
#	Line 49 | Line 55
55		#include "primitives/StuntDouble.hpp"
56		#include "utils/PhysicalConstants.hpp"
57		#include "utils/Tuple.hpp"
58	+	#include "brains/Thermo.hpp"
59	+	#include "math/ConvexHull.hpp"
60
61	<	#ifndef IS_MPI
62	<	#include "math/SeqRandNumGen.hpp"
63	<	#else
56	<	#include "math/ParallelRandNumGen.hpp"
57	<	#include <mpi.h>
61	>	#ifdef _MSC_VER
62	>	#define isnan(x) _isnan((x))
63	>	#define isinf(x) (!_finite(x) && !_isnan(x))
64		#endif
65
66		#define HONKING_LARGE_VALUE 1.0e10
#	Line 63 | Line 69 | namespace OpenMD {
69		namespace OpenMD {
70
71		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75	+	hasData_(false), hasDividingArea_(false),
76		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
77
78	+	trialCount_ = 0;
79		failTrialCount_ = 0;
80		failRootCount_ = 0;
81
82	<	int seedValue;
83	<	Globals * simParams = info->getSimParams();
82	>	Globals* simParams = info->getSimParams();
83	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
84
85	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
86	<	stringToEnumMap_["KineticScale"] = rnemdKineticScale;
76	<	stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM;
77	<	stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM;
78	<	stringToEnumMap_["PxScale"] = rnemdPxScale;
79	<	stringToEnumMap_["PyScale"] = rnemdPyScale;
80	<	stringToEnumMap_["PzScale"] = rnemdPzScale;
81	<	stringToEnumMap_["Px"] = rnemdPx;
82	<	stringToEnumMap_["Py"] = rnemdPy;
83	<	stringToEnumMap_["Pz"] = rnemdPz;
84	<	stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV;
85	<	stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM;
86	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
85	>	doRNEMD_ = rnemdParams->getUseRNEMD();
86	>	if (!doRNEMD_) return;
87
88	+	stringToMethod_["Swap"]  = rnemdSwap;
89	+	stringToMethod_["NIVS"]  = rnemdNIVS;
90	+	stringToMethod_["VSS"]   = rnemdVSS;
91	+
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		runTime_ = simParams->getRunTime();
110		statusTime_ = simParams->getStatusTime();
111
112	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
113	<	evaluator_.loadScriptString(rnemdObjectSelection_);
93	<	seleMan_.setSelectionSet(evaluator_.evaluate());
112	>	const string methStr = rnemdParams->getMethod();
113	>	bool hasFluxType = rnemdParams->haveFluxType();
114
115	<	// do some sanity checking
115	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
116
117	<	int selectionCount = seleMan_.getSelectionCount();
118	<	int nIntegrable = info->getNGlobalIntegrableObjects();
119	<
120	<	if (selectionCount > nIntegrable) {
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",
109	<	rnemdObjectSelection_.c_str(),
110	<	selectionCount, nIntegrable);
111	<	painCave.isFatal = 0;
112	<	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		}
131	–
132	–	outputTemp_ = false;
133	–	if (simParams->haveRNEMD_outputTemperature()) {
134	–	outputTemp_ = simParams->getRNEMD_outputTemperature();
135	–	} else if ((rnemdType_ == rnemdKineticSwap) ||
136	–	(rnemdType_ == rnemdKineticScale) ||
137	–	(rnemdType_ == rnemdKineticScaleVAM) ||
138	–	(rnemdType_ == rnemdKineticScaleAM)) {
139	–	outputTemp_ = true;
140	–	}
141	–	outputVx_ = false;
142	–	if (simParams->haveRNEMD_outputVx()) {
143	–	outputVx_ = simParams->getRNEMD_outputVx();
144	–	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
145	–	outputVx_ = true;
146	–	}
147	–	outputVy_ = false;
148	–	if (simParams->haveRNEMD_outputVy()) {
149	–	outputVy_ = simParams->getRNEMD_outputVy();
150	–	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
151	–	outputVy_ = true;
152	–	}
153	–	output3DTemp_ = false;
154	–	if (simParams->haveRNEMD_outputXyzTemperature()) {
155	–	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
156	–	}
157	–	outputRotTemp_ = false;
158	–	if (simParams->haveRNEMD_outputRotTemperature()) {
159	–	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
160	–	}
161	–	// James put this in.
162	–	outputDen_ = false;
163	–	if (simParams->haveRNEMD_outputDen()) {
164	–	outputDen_ = simParams->getRNEMD_outputDen();
165	–	}
166	–	outputAh_ = false;
167	–	if (simParams->haveRNEMD_outputAh()) {
168	–	outputAh_ = simParams->getRNEMD_outputAh();
169	–	}
170	–	outputVz_ = false;
171	–	if (simParams->haveRNEMD_outputVz()) {
172	–	outputVz_ = simParams->getRNEMD_outputVz();
173	–	} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
174	–	outputVz_ = true;
175	–	}
176	–
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		}
210	–
211	–	//James put this in
212	–	if (outputDen_) {
213	–	rnemdFileName = "Density.log";
214	–	denLog_.open(rnemdFileName.c_str());
215	–	}
216	–	if (outputAh_) {
217	–	rnemdFileName = "Ah.log";
218	–	AhLog_.open(rnemdFileName.c_str());
219	–	}
220	–	if (outputVz_) {
221	–	rnemdFileName = "velocityZ.log";
222	–	vzzLog_.open(rnemdFileName.c_str());
223	–	}
224	–	logFrameCount_ = 0;
225	–	#ifdef IS_MPI
226	–	}
227	–	#endif
349
350	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
351	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
231	<	midBin_ = nBins_ / 2;
232	<	if (simParams->haveRNEMD_binShift()) {
233	<	if (simParams->getRNEMD_binShift()) {
234	<	zShift_ = 0.5 / (RealType)(nBins_);
350	>	if (hasCoordinateOrigin) {
351	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
352		} else {
353	<	zShift_ = 0.0;
353	>	coordinateOrigin_ = V3Zero;
354		}
238	–	} else {
239	–	zShift_ = 0.0;
240	–	}
241	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
242	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
243	–	//set to 0.0 if not using it; N/A in status output yet
244	–	if (simParams->haveRNEMD_logWidth()) {
245	–	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
246	–	/*arbitary rnemdLogWidth_, no checking;
247	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
248	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
249	–	cerr << "Automaically set back to default.\n";
250	–	rnemdLogWidth_ = nBins_;
251	–	}*/
252	–	} else {
253	–	set_RNEMD_logWidth(nBins_);
254	–	}
255	–	tempHist_.resize(rnemdLogWidth_, 0.0);
256	–	tempCount_.resize(rnemdLogWidth_, 0);
257	–	pxzHist_.resize(rnemdLogWidth_, 0.0);
258	–	//vxzCount_.resize(rnemdLogWidth_, 0);
259	–	pyzHist_.resize(rnemdLogWidth_, 0.0);
260	–	//vyzCount_.resize(rnemdLogWidth_, 0);
355
356	<	mHist_.resize(rnemdLogWidth_, 0.0);
263	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
264	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
265	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
266	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
267	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
268	<	rotTempCount_.resize(rnemdLogWidth_, 0);
269	<	// James put this in
270	<	DenHist_.resize(rnemdLogWidth_, 0.0);
271	<	pzzHist_.resize(rnemdLogWidth_, 0.0);
356	>	// do some sanity checking
357
358	<	set_RNEMD_exchange_total(0.0);
274	<	if (simParams->haveRNEMD_targetFlux()) {
275	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
276	<	} else {
277	<	set_RNEMD_target_flux(0.0);
278	<	}
279	<	if (simParams->haveRNEMD_targetJzKE()) {
280	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
281	<	} else {
282	<	set_RNEMD_target_JzKE(0.0);
283	<	}
284	<	if (simParams->haveRNEMD_targetJzpx()) {
285	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
286	<	} else {
287	<	set_RNEMD_target_jzpx(0.0);
288	<	}
289	<	jzp_.x() = targetJzpx_;
290	<	njzp_.x() = -targetJzpx_;
291	<	if (simParams->haveRNEMD_targetJzpy()) {
292	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
293	<	} else {
294	<	set_RNEMD_target_jzpy(0.0);
295	<	}
296	<	jzp_.y() = targetJzpy_;
297	<	njzp_.y() = -targetJzpy_;
298	<	if (simParams->haveRNEMD_targetJzpz()) {
299	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
300	<	} else {
301	<	set_RNEMD_target_jzpz(0.0);
302	<	}
303	<	jzp_.z() = targetJzpz_;
304	<	njzp_.z() = -targetJzpz_;
358	>	int selectionCount = seleMan_.getSelectionCount();
359
360	<	#ifndef IS_MPI
361	<	if (simParams->haveSeed()) {
362	<	seedValue = simParams->getSeed();
363	<	randNumGen_ = new SeqRandNumGen(seedValue);
364	<	}else {
365	<	randNumGen_ = new SeqRandNumGen();
366	<	}
367	<	#else
368	<	if (simParams->haveSeed()) {
369	<	seedValue = simParams->getSeed();
370	<	randNumGen_ = new ParallelRandNumGen(seedValue);
371	<	}else {
372	<	randNumGen_ = new ParallelRandNumGen();
373	<	}
374	<	#endif
360	>	int nIntegrable = info->getNGlobalIntegrableObjects();
361	>
362	>	if (selectionCount > nIntegrable) {
363	>	sprintf(painCave.errMsg,
364	>	"RNEMD: The current objectSelection,\n"
365	>	"\t\t%s\n"
366	>	"\thas resulted in %d selected objects.  However,\n"
367	>	"\tthe total number of integrable objects in the system\n"
368	>	"\tis only %d.  This is almost certainly not what you want\n"
369	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
370	>	"\tselector in the selection script!\n",
371	>	rnemdObjectSelection_.c_str(),
372	>	selectionCount, nIntegrable);
373	>	painCave.isFatal = 0;
374	>	painCave.severity = OPENMD_WARNING;
375	>	simError();
376	>	}
377	>
378	>	areaAccumulator_ = new Accumulator();
379	>
380	>	nBins_ = rnemdParams->getOutputBins();
381	>	binWidth_ = rnemdParams->getOutputBinWidth();
382	>
383	>	data_.resize(RNEMD::ENDINDEX);
384	>	OutputData z;
385	>	z.units =  "Angstroms";
386	>	z.title =  "Z";
387	>	z.dataType = "RealType";
388	>	z.accumulator.reserve(nBins_);
389	>	for (int i = 0; i < nBins_; i++)
390	>	z.accumulator.push_back( new Accumulator() );
391	>	data_[Z] = z;
392	>	outputMap_["Z"] =  Z;
393	>
394	>	OutputData r;
395	>	r.units =  "Angstroms";
396	>	r.title =  "R";
397	>	r.dataType = "RealType";
398	>	r.accumulator.reserve(nBins_);
399	>	for (int i = 0; i < nBins_; i++)
400	>	r.accumulator.push_back( new Accumulator() );
401	>	data_[R] = r;
402	>	outputMap_["R"] =  R;
403	>
404	>	OutputData temperature;
405	>	temperature.units =  "K";
406	>	temperature.title =  "Temperature";
407	>	temperature.dataType = "RealType";
408	>	temperature.accumulator.reserve(nBins_);
409	>	for (int i = 0; i < nBins_; i++)
410	>	temperature.accumulator.push_back( new Accumulator() );
411	>	data_[TEMPERATURE] = temperature;
412	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
413	>
414	>	OutputData velocity;
415	>	velocity.units = "angstroms/fs";
416	>	velocity.title =  "Velocity";
417	>	velocity.dataType = "Vector3d";
418	>	velocity.accumulator.reserve(nBins_);
419	>	for (int i = 0; i < nBins_; i++)
420	>	velocity.accumulator.push_back( new VectorAccumulator() );
421	>	data_[VELOCITY] = velocity;
422	>	outputMap_["VELOCITY"] = VELOCITY;
423	>
424	>	OutputData angularVelocity;
425	>	angularVelocity.units = "angstroms^2/fs";
426	>	angularVelocity.title =  "AngularVelocity";
427	>	angularVelocity.dataType = "Vector3d";
428	>	angularVelocity.accumulator.reserve(nBins_);
429	>	for (int i = 0; i < nBins_; i++)
430	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
431	>	data_[ANGULARVELOCITY] = angularVelocity;
432	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
433	>
434	>	OutputData density;
435	>	density.units =  "g cm^-3";
436	>	density.title =  "Density";
437	>	density.dataType = "RealType";
438	>	density.accumulator.reserve(nBins_);
439	>	for (int i = 0; i < nBins_; i++)
440	>	density.accumulator.push_back( new Accumulator() );
441	>	data_[DENSITY] = density;
442	>	outputMap_["DENSITY"] =  DENSITY;
443	>
444	>	if (hasOutputFields) {
445	>	parseOutputFileFormat(rnemdParams->getOutputFields());
446	>	} else {
447	>	if (usePeriodicBoundaryConditions_)
448	>	outputMask_.set(Z);
449	>	else
450	>	outputMask_.set(R);
451	>	switch (rnemdFluxType_) {
452	>	case rnemdKE:
453	>	case rnemdRotKE:
454	>	case rnemdFullKE:
455	>	outputMask_.set(TEMPERATURE);
456	>	break;
457	>	case rnemdPx:
458	>	case rnemdPy:
459	>	outputMask_.set(VELOCITY);
460	>	break;
461	>	case rnemdPz:
462	>	case rnemdPvector:
463	>	outputMask_.set(VELOCITY);
464	>	outputMask_.set(DENSITY);
465	>	break;
466	>	case rnemdLx:
467	>	case rnemdLy:
468	>	case rnemdLz:
469	>	case rnemdLvector:
470	>	outputMask_.set(ANGULARVELOCITY);
471	>	break;
472	>	case rnemdKeLx:
473	>	case rnemdKeLy:
474	>	case rnemdKeLz:
475	>	case rnemdKeLvector:
476	>	outputMask_.set(TEMPERATURE);
477	>	outputMask_.set(ANGULARVELOCITY);
478	>	break;
479	>	case rnemdKePx:
480	>	case rnemdKePy:
481	>	outputMask_.set(TEMPERATURE);
482	>	outputMask_.set(VELOCITY);
483	>	break;
484	>	case rnemdKePvector:
485	>	outputMask_.set(TEMPERATURE);
486	>	outputMask_.set(VELOCITY);
487	>	outputMask_.set(DENSITY);
488	>	break;
489	>	default:
490	>	break;
491	>	}
492	>	}
493	>
494	>	if (hasOutputFileName) {
495	>	rnemdFileName_ = rnemdParams->getOutputFileName();
496	>	} else {
497	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
498	>	}
499	>
500	>	exchangeTime_ = rnemdParams->getExchangeTime();
501	>
502	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
503	>	// total exchange sums are zeroed out at the beginning:
504	>
505	>	kineticExchange_ = 0.0;
506	>	momentumExchange_ = V3Zero;
507	>	angularMomentumExchange_ = V3Zero;
508	>
509	>	std::ostringstream selectionAstream;
510	>	std::ostringstream selectionBstream;
511	>
512	>	if (hasSelectionA_) {
513	>	selectionA_ = rnemdParams->getSelectionA();
514	>	} else {
515	>	if (usePeriodicBoundaryConditions_) {
516	>	Mat3x3d hmat = currentSnap_->getHmat();
517	>
518	>	if (hasSlabWidth)
519	>	slabWidth_ = rnemdParams->getSlabWidth();
520	>	else
521	>	slabWidth_ = hmat(2,2) / 10.0;
522	>
523	>	if (hasSlabACenter)
524	>	slabACenter_ = rnemdParams->getSlabACenter();
525	>	else
526	>	slabACenter_ = 0.0;
527	>
528	>	selectionAstream << "select wrappedz > "
529	>	<< slabACenter_ - 0.5*slabWidth_
530	>	<<  " && wrappedz < "
531	>	<< slabACenter_ + 0.5*slabWidth_;
532	>	selectionA_ = selectionAstream.str();
533	>	} else {
534	>	if (hasSphereARadius)
535	>	sphereARadius_ = rnemdParams->getSphereARadius();
536	>	else {
537	>	// use an initial guess to the size of the inner slab to be 1/10 the
538	>	// radius of an approximately spherical hull:
539	>	Thermo thermo(info);
540	>	RealType hVol = thermo.getHullVolume();
541	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
542	>	}
543	>	selectionAstream << "select r < " << sphereARadius_;
544	>	selectionA_ = selectionAstream.str();
545	>	}
546	>	}
547	>
548	>	if (hasSelectionB_) {
549	>	selectionB_ = rnemdParams->getSelectionB();
550	>
551	>	} else {
552	>	if (usePeriodicBoundaryConditions_) {
553	>	Mat3x3d hmat = currentSnap_->getHmat();
554	>
555	>	if (hasSlabWidth)
556	>	slabWidth_ = rnemdParams->getSlabWidth();
557	>	else
558	>	slabWidth_ = hmat(2,2) / 10.0;
559	>
560	>	if (hasSlabBCenter)
561	>	slabBCenter_ = rnemdParams->getSlabBCenter();
562	>	else
563	>	slabBCenter_ = hmat(2,2) / 2.0;
564	>
565	>	selectionBstream << "select wrappedz > "
566	>	<< slabBCenter_ - 0.5*slabWidth_
567	>	<<  " && wrappedz < "
568	>	<< slabBCenter_ + 0.5*slabWidth_;
569	>	selectionB_ = selectionBstream.str();
570	>	} else {
571	>	if (hasSphereBRadius_) {
572	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
573	>	selectionBstream << "select r > " << sphereBRadius_;
574	>	selectionB_ = selectionBstream.str();
575	>	} else {
576	>	selectionB_ = "select hull";
577	>	BisHull_ = true;
578	>	hasSelectionB_ = true;
579	>	}
580	>	}
581	>	}
582	>	}
583	>
584	>	// object evaluator:
585	>	evaluator_.loadScriptString(rnemdObjectSelection_);
586	>	seleMan_.setSelectionSet(evaluator_.evaluate());
587	>	evaluatorA_.loadScriptString(selectionA_);
588	>	evaluatorB_.loadScriptString(selectionB_);
589	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
590	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
591	>	commonA_ = seleManA_ & seleMan_;
592	>	commonB_ = seleManB_ & seleMan_;
593		}
594
323	–	RNEMD::~RNEMD() {
324	–	delete randNumGen_;
595
596	+	RNEMD::~RNEMD() {
597	+	if (!doRNEMD_) return;
598		#ifdef IS_MPI
599		if (worldRank == 0) {
600		#endif
329	–
330	–	sprintf(painCave.errMsg,
331	–	"RNEMD: total failed trials: %d\n",
332	–	failTrialCount_);
333	–	painCave.isFatal = 0;
334	–	painCave.severity = OPENMD_INFO;
335	–	simError();
336	–
337	–	if (outputTemp_) tempLog_.close();
338	–	if (outputVx_)   vxzLog_.close();
339	–	if (outputVy_)   vyzLog_.close();
601
602	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
603	<	rnemdType_ == rnemdPyScale) {
604	<	sprintf(painCave.errMsg,
344	<	"RNEMD: total root-checking warnings: %d\n",
345	<	failRootCount_);
346	<	painCave.isFatal = 0;
347	<	painCave.severity = OPENMD_INFO;
348	<	simError();
349	<	}
350	<	if (output3DTemp_) {
351	<	xTempLog_.close();
352	<	yTempLog_.close();
353	<	zTempLog_.close();
354	<	}
355	<	if (outputRotTemp_) rotTempLog_.close();
356	<	// James put this in
357	<	if (outputDen_) denLog_.close();
358	<	if (outputAh_)  AhLog_.close();
359	<	if (outputVz_)  vzzLog_.close();
602	>	writeOutputFile();
603	>
604	>	rnemdFile_.close();
605
606		#ifdef IS_MPI
607		}
608		#endif
609	+
610	+	// delete all of the objects we created:
611	+	delete areaAccumulator_;
612	+	data_.clear();
613		}
614	+
615	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
616	+	if (!doRNEMD_) return;
617	+	int selei;
618	+	int selej;
619
366	–	void RNEMD::doSwap() {
367	–
620		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
621		Mat3x3d hmat = currentSnap_->getHmat();
622
371	–	seleMan_.setSelectionSet(evaluator_.evaluate());
372	–
373	–	int selei;
623		StuntDouble* sd;
375	–	int idx;
624
625		RealType min_val;
626		bool min_found = false;
#	Line 382 | Line 630 | namespace OpenMD {
630		bool max_found = false;
631		StuntDouble* max_sd;
632
633	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
634	<	sd = seleMan_.nextSelected(selei)) {
387	<
388	<	idx = sd->getLocalIndex();
633	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
634	>	sd = seleManA_.nextSelected(selei)) {
635
636		Vector3d pos = sd->getPos();
637	<
637	>
638		// wrap the stuntdouble's position back into the box:
639	<
639	>
640		if (usePeriodicBoundaryConditions_)
641		currentSnap_->wrapVector(pos);
642	<
643	<	// which bin is this stuntdouble in?
644	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
645	<
646	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
647	<
648	<
403	<	// if we're in bin 0 or the middleBin
404	<	if (binNo == 0 || binNo == midBin_) {
642	>
643	>	RealType mass = sd->getMass();
644	>	Vector3d vel = sd->getVel();
645	>	RealType value;
646	>
647	>	switch(rnemdFluxType_) {
648	>	case rnemdKE :
649
650	<	RealType mass = sd->getMass();
651	<	Vector3d vel = sd->getVel();
652	<	RealType value;
653	<
654	<	switch(rnemdType_) {
411	<	case rnemdKineticSwap :
650	>	value = mass * vel.lengthSquare();
651	>
652	>	if (sd->isDirectional()) {
653	>	Vector3d angMom = sd->getJ();
654	>	Mat3x3d I = sd->getI();
655
656	<	value = mass * vel.lengthSquare();
657	<
658	<	if (sd->isDirectional()) {
659	<	Vector3d angMom = sd->getJ();
660	<	Mat3x3d I = sd->getI();
661	<
662	<	if (sd->isLinear()) {
663	<	int i = sd->linearAxis();
664	<	int j = (i + 1) % 3;
665	<	int k = (i + 2) % 3;
666	<	value += angMom[j] * angMom[j] / I(j, j) +
667	<	angMom[k] * angMom[k] / I(k, k);
668	<	} else {
669	<	value += angMom[0]*angMom[0]/I(0, 0)
670	<	+ angMom[1]*angMom[1]/I(1, 1)
671	<	+ angMom[2]*angMom[2]/I(2, 2);
672	<	}
673	<	} //angular momenta exchange enabled
674	<	//energyConvert temporarily disabled
675	<	//make exchangeSum_ comparable between swap & scale
676	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
677	<	value *= 0.5;
678	<	break;
679	<	case rnemdPx :
680	<	value = mass * vel[0];
681	<	break;
682	<	case rnemdPy :
683	<	value = mass * vel[1];
684	<	break;
685	<	case rnemdPz :
686	<	value = mass * vel[2];
687	<	break;
688	<	default :
689	<	break;
656	>	if (sd->isLinear()) {
657	>	int i = sd->linearAxis();
658	>	int j = (i + 1) % 3;
659	>	int k = (i + 2) % 3;
660	>	value += angMom[j] * angMom[j] / I(j, j) +
661	>	angMom[k] * angMom[k] / I(k, k);
662	>	} else {
663	>	value += angMom[0]*angMom[0]/I(0, 0)
664	>	+ angMom[1]*angMom[1]/I(1, 1)
665	>	+ angMom[2]*angMom[2]/I(2, 2);
666	>	}
667	>	} //angular momenta exchange enabled
668	>	value *= 0.5;
669	>	break;
670	>	case rnemdPx :
671	>	value = mass * vel[0];
672	>	break;
673	>	case rnemdPy :
674	>	value = mass * vel[1];
675	>	break;
676	>	case rnemdPz :
677	>	value = mass * vel[2];
678	>	break;
679	>	default :
680	>	break;
681	>	}
682	>	if (!max_found) {
683	>	max_val = value;
684	>	max_sd = sd;
685	>	max_found = true;
686	>	} else {
687	>	if (max_val < value) {
688	>	max_val = value;
689	>	max_sd = sd;
690		}
691	+	}
692	+	}
693
694	<	if (binNo == 0) {
695	<	if (!min_found) {
696	<	min_val = value;
697	<	min_sd = sd;
698	<	min_found = true;
699	<	} else {
700	<	if (min_val > value) {
701	<	min_val = value;
702	<	min_sd = sd;
703	<	}
704	<	}
705	<	} else { //midBin_
706	<	if (!max_found) {
707	<	max_val = value;
708	<	max_sd = sd;
709	<	max_found = true;
710	<	} else {
711	<	if (max_val < value) {
712	<	max_val = value;
713	<	max_sd = sd;
714	<	}
715	<	}
716	<	}
694	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
695	>	sd = seleManB_.nextSelected(selej)) {
696	>
697	>	Vector3d pos = sd->getPos();
698	>
699	>	// wrap the stuntdouble's position back into the box:
700	>
701	>	if (usePeriodicBoundaryConditions_)
702	>	currentSnap_->wrapVector(pos);
703	>
704	>	RealType mass = sd->getMass();
705	>	Vector3d vel = sd->getVel();
706	>	RealType value;
707	>
708	>	switch(rnemdFluxType_) {
709	>	case rnemdKE :
710	>
711	>	value = mass * vel.lengthSquare();
712	>
713	>	if (sd->isDirectional()) {
714	>	Vector3d angMom = sd->getJ();
715	>	Mat3x3d I = sd->getI();
716	>
717	>	if (sd->isLinear()) {
718	>	int i = sd->linearAxis();
719	>	int j = (i + 1) % 3;
720	>	int k = (i + 2) % 3;
721	>	value += angMom[j] * angMom[j] / I(j, j) +
722	>	angMom[k] * angMom[k] / I(k, k);
723	>	} else {
724	>	value += angMom[0]*angMom[0]/I(0, 0)
725	>	+ angMom[1]*angMom[1]/I(1, 1)
726	>	+ angMom[2]*angMom[2]/I(2, 2);
727	>	}
728	>	} //angular momenta exchange enabled
729	>	value *= 0.5;
730	>	break;
731	>	case rnemdPx :
732	>	value = mass * vel[0];
733	>	break;
734	>	case rnemdPy :
735	>	value = mass * vel[1];
736	>	break;
737	>	case rnemdPz :
738	>	value = mass * vel[2];
739	>	break;
740	>	default :
741	>	break;
742		}
743	+
744	+	if (!min_found) {
745	+	min_val = value;
746	+	min_sd = sd;
747	+	min_found = true;
748	+	} else {
749	+	if (min_val > value) {
750	+	min_val = value;
751	+	min_sd = sd;
752	+	}
753	+	}
754		}
755	+
756	+	#ifdef IS_MPI
757	+	int worldRank;
758	+	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
759	+
760	+	int my_min_found = min_found;
761	+	int my_max_found = max_found;
762
475	–	#ifdef IS_MPI
476	–	int nProc, worldRank;
477	–
478	–	nProc = MPI::COMM_WORLD.Get_size();
479	–	worldRank = MPI::COMM_WORLD.Get_rank();
480	–
481	–	bool my_min_found = min_found;
482	–	bool my_max_found = max_found;
483	–
763		// Even if we didn't find a minimum, did someone else?
764	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
764	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
765	>	MPI_COMM_WORLD);
766		// Even if we didn't find a maximum, did someone else?
767	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
767	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
768	>	MPI_COMM_WORLD);
769		#endif
770
771		if (max_found && min_found) {
#	Line 503 | Line 784 | namespace OpenMD {
784		min_vals.rank = worldRank;
785
786		// Who had the minimum?
787	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
788	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
787	>	MPI_Allreduce(&min_vals, &min_vals,
788	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
789		min_val = min_vals.val;
790
791		if (my_max_found) {
#	Line 515 | Line 796 | namespace OpenMD {
796		max_vals.rank = worldRank;
797
798		// Who had the maximum?
799	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
800	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
799	>	MPI_Allreduce(&max_vals, &max_vals,
800	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
801		max_val = max_vals.val;
802		#endif
803
#	Line 532 | Line 813 | namespace OpenMD {
813		Vector3d max_vel = max_sd->getVel();
814		RealType temp_vel;
815
816	<	switch(rnemdType_) {
817	<	case rnemdKineticSwap :
816	>	switch(rnemdFluxType_) {
817	>	case rnemdKE :
818		min_sd->setVel(max_vel);
819		max_sd->setVel(min_vel);
820		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 576 | Line 857 | namespace OpenMD {
857
858		Vector3d min_vel;
859		Vector3d max_vel = max_sd->getVel();
860	<	MPI::Status status;
860	>	MPI_Status* status;
861
862		// point-to-point swap of the velocity vector
863	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
864	<	min_vals.rank, 0,
865	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
866	<	min_vals.rank, 0, status);
863	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
864	>	min_vals.rank, 0,
865	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
866	>	min_vals.rank, 0, MPI_COMM_WORLD, status);
867
868	<	switch(rnemdType_) {
869	<	case rnemdKineticSwap :
868	>	switch(rnemdFluxType_) {
869	>	case rnemdKE :
870		max_sd->setVel(min_vel);
871		//angular momenta exchange enabled
872		if (max_sd->isDirectional()) {
#	Line 593 | Line 874 | namespace OpenMD {
874		Vector3d max_angMom = max_sd->getJ();
875
876		// point-to-point swap of the angular momentum vector
877	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
878	<	MPI::REALTYPE, min_vals.rank, 1,
879	<	min_angMom.getArrayPointer(), 3,
880	<	MPI::REALTYPE, min_vals.rank, 1,
881	<	status);
877	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
878	>	MPI_REALTYPE, min_vals.rank, 1,
879	>	min_angMom.getArrayPointer(), 3,
880	>	MPI_REALTYPE, min_vals.rank, 1,
881	>	MPI_COMM_WORLD, status);
882
883		max_sd->setJ(min_angMom);
884		}
#	Line 622 | Line 903 | namespace OpenMD {
903
904		Vector3d max_vel;
905		Vector3d min_vel = min_sd->getVel();
906	<	MPI::Status status;
906	>	MPI_Status* status;
907
908		// point-to-point swap of the velocity vector
909	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
910	<	max_vals.rank, 0,
911	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
912	<	max_vals.rank, 0, status);
913	<
914	<	switch(rnemdType_) {
915	<	case rnemdKineticSwap :
909	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
910	>	max_vals.rank, 0,
911	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
912	>	max_vals.rank, 0, MPI_COMM_WORLD, status);
913	>
914	>	switch(rnemdFluxType_) {
915	>	case rnemdKE :
916		min_sd->setVel(max_vel);
917		//angular momenta exchange enabled
918		if (min_sd->isDirectional()) {
#	Line 639 | Line 920 | namespace OpenMD {
920		Vector3d max_angMom;
921
922		// point-to-point swap of the angular momentum vector
923	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
924	<	MPI::REALTYPE, max_vals.rank, 1,
925	<	max_angMom.getArrayPointer(), 3,
926	<	MPI::REALTYPE, max_vals.rank, 1,
927	<	status);
923	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
924	>	MPI_REALTYPE, max_vals.rank, 1,
925	>	max_angMom.getArrayPointer(), 3,
926	>	MPI_REALTYPE, max_vals.rank, 1,
927	>	MPI_COMM_WORLD, status);
928
929		min_sd->setJ(max_angMom);
930		}
#	Line 665 | Line 946 | namespace OpenMD {
946		}
947		}
948		#endif
949	<	exchangeSum_ += max_val - min_val;
949	>
950	>	switch(rnemdFluxType_) {
951	>	case rnemdKE:
952	>	kineticExchange_ += max_val - min_val;
953	>	break;
954	>	case rnemdPx:
955	>	momentumExchange_.x() += max_val - min_val;
956	>	break;
957	>	case rnemdPy:
958	>	momentumExchange_.y() += max_val - min_val;
959	>	break;
960	>	case rnemdPz:
961	>	momentumExchange_.z() += max_val - min_val;
962	>	break;
963	>	default:
964	>	break;
965	>	}
966		} else {
967		sprintf(painCave.errMsg,
968	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
968	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
969		painCave.isFatal = 0;
970		painCave.severity = OPENMD_INFO;
971		simError();
#	Line 676 | Line 973 | namespace OpenMD {
973		}
974		} else {
975		sprintf(painCave.errMsg,
976	<	"RNEMD: exchange NOT performed because selected object\n"
977	<	"\tnot present in at least one of the two slabs.\n");
976	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
977	>	"\twas not present in at least one of the two slabs.\n");
978		painCave.isFatal = 0;
979		painCave.severity = OPENMD_INFO;
980		simError();
981		failTrialCount_++;
982	<	}
686	<
982	>	}
983		}
984
985	<	void RNEMD::doScale() {
985	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
986	>	if (!doRNEMD_) return;
987	>	int selei;
988	>	int selej;
989
990		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
991	+	RealType time = currentSnap_->getTime();
992		Mat3x3d hmat = currentSnap_->getHmat();
993
694	–	seleMan_.setSelectionSet(evaluator_.evaluate());
695	–
696	–	int selei;
994		StuntDouble* sd;
698	–	int idx;
995
996		vector<StuntDouble*> hotBin, coldBin;
997
#	Line 714 | Line 1010 | namespace OpenMD {
1010		RealType Kcz = 0.0;
1011		RealType Kcw = 0.0;
1012
1013	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1014	<	sd = seleMan_.nextSelected(selei)) {
1013	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1014	>	sd = smanA.nextSelected(selei)) {
1015
720	–	idx = sd->getLocalIndex();
721	–
1016		Vector3d pos = sd->getPos();
1017	<
1017	>
1018		// wrap the stuntdouble's position back into the box:
1019	<
1019	>
1020		if (usePeriodicBoundaryConditions_)
1021		currentSnap_->wrapVector(pos);
1022	+
1023	+
1024	+	RealType mass = sd->getMass();
1025	+	Vector3d vel = sd->getVel();
1026	+
1027	+	hotBin.push_back(sd);
1028	+	Phx += mass * vel.x();
1029	+	Phy += mass * vel.y();
1030	+	Phz += mass * vel.z();
1031	+	Khx += mass * vel.x() * vel.x();
1032	+	Khy += mass * vel.y() * vel.y();
1033	+	Khz += mass * vel.z() * vel.z();
1034	+	if (sd->isDirectional()) {
1035	+	Vector3d angMom = sd->getJ();
1036	+	Mat3x3d I = sd->getI();
1037	+	if (sd->isLinear()) {
1038	+	int i = sd->linearAxis();
1039	+	int j = (i + 1) % 3;
1040	+	int k = (i + 2) % 3;
1041	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1042	+	angMom[k] * angMom[k] / I(k, k);
1043	+	} else {
1044	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1045	+	+ angMom[1]*angMom[1]/I(1, 1)
1046	+	+ angMom[2]*angMom[2]/I(2, 2);
1047	+	}
1048	+	}
1049	+	}
1050	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1051	+	sd = smanB.nextSelected(selej)) {
1052	+	Vector3d pos = sd->getPos();
1053	+
1054	+	// wrap the stuntdouble's position back into the box:
1055	+
1056	+	if (usePeriodicBoundaryConditions_)
1057	+	currentSnap_->wrapVector(pos);
1058	+
1059	+	RealType mass = sd->getMass();
1060	+	Vector3d vel = sd->getVel();
1061
1062	<	// which bin is this stuntdouble in?
1063	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1064	<
1065	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1066	<
1067	<	// if we're in bin 0 or the middleBin
1068	<	if (binNo == 0 || binNo == midBin_) {
1069	<
1070	<	RealType mass = sd->getMass();
1071	<	Vector3d vel = sd->getVel();
1072	<
1073	<	if (binNo == 0) {
1074	<	hotBin.push_back(sd);
1075	<	Phx += mass * vel.x();
1076	<	Phy += mass * vel.y();
1077	<	Phz += mass * vel.z();
1078	<	Khx += mass * vel.x() * vel.x();
1079	<	Khy += mass * vel.y() * vel.y();
1080	<	Khz += mass * vel.z() * vel.z();
1081	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1082	<	if (sd->isDirectional()) {
750	<	Vector3d angMom = sd->getJ();
751	<	Mat3x3d I = sd->getI();
752	<	if (sd->isLinear()) {
753	<	int i = sd->linearAxis();
754	<	int j = (i + 1) % 3;
755	<	int k = (i + 2) % 3;
756	<	Khw += angMom[j] * angMom[j] / I(j, j) +
757	<	angMom[k] * angMom[k] / I(k, k);
758	<	} else {
759	<	Khw += angMom[0]*angMom[0]/I(0, 0)
760	<	+ angMom[1]*angMom[1]/I(1, 1)
761	<	+ angMom[2]*angMom[2]/I(2, 2);
762	<	}
763	<	}
764	<	//}
765	<	} else { //midBin_
766	<	coldBin.push_back(sd);
767	<	Pcx += mass * vel.x();
768	<	Pcy += mass * vel.y();
769	<	Pcz += mass * vel.z();
770	<	Kcx += mass * vel.x() * vel.x();
771	<	Kcy += mass * vel.y() * vel.y();
772	<	Kcz += mass * vel.z() * vel.z();
773	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
774	<	if (sd->isDirectional()) {
775	<	Vector3d angMom = sd->getJ();
776	<	Mat3x3d I = sd->getI();
777	<	if (sd->isLinear()) {
778	<	int i = sd->linearAxis();
779	<	int j = (i + 1) % 3;
780	<	int k = (i + 2) % 3;
781	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
782	<	angMom[k] * angMom[k] / I(k, k);
783	<	} else {
784	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
785	<	+ angMom[1]*angMom[1]/I(1, 1)
786	<	+ angMom[2]*angMom[2]/I(2, 2);
787	<	}
788	<	}
789	<	//}
790	<	}
1062	>	coldBin.push_back(sd);
1063	>	Pcx += mass * vel.x();
1064	>	Pcy += mass * vel.y();
1065	>	Pcz += mass * vel.z();
1066	>	Kcx += mass * vel.x() * vel.x();
1067	>	Kcy += mass * vel.y() * vel.y();
1068	>	Kcz += mass * vel.z() * vel.z();
1069	>	if (sd->isDirectional()) {
1070	>	Vector3d angMom = sd->getJ();
1071	>	Mat3x3d I = sd->getI();
1072	>	if (sd->isLinear()) {
1073	>	int i = sd->linearAxis();
1074	>	int j = (i + 1) % 3;
1075	>	int k = (i + 2) % 3;
1076	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1077	>	angMom[k] * angMom[k] / I(k, k);
1078	>	} else {
1079	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1080	>	+ angMom[1]*angMom[1]/I(1, 1)
1081	>	+ angMom[2]*angMom[2]/I(2, 2);
1082	>	}
1083		}
1084		}
1085
#	Line 800 | Line 1092 | namespace OpenMD {
1092		Kcz *= 0.5;
1093		Kcw *= 0.5;
1094
803	–	// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
804	–	//        << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
805	–	//        << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
806	–	// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
807	–	//        << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
808	–
1095		#ifdef IS_MPI
1096	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1097	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1098	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1099	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1100	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1101	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
816	<
817	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
818	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
819	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
820	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1096	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1097	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1098	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1099	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1100	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1101	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1102
1103	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1104	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1105	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1106	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1103	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1104	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1105	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1106	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1107	>
1108	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1109	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1110	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1111	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1112		#endif
1113
1114		//solve coldBin coeff's first
#	Line 831 | Line 1117 | namespace OpenMD {
1117		RealType pz = Pcz / Phz;
1118		RealType c, x, y, z;
1119		bool successfulScale = false;
1120	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1121	<	(rnemdType_ == rnemdKineticScaleAM)) {
1120	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1121	>	(rnemdFluxType_ == rnemdRotKE)) {
1122		//may need sanity check Khw & Kcw > 0
1123
1124	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1125	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1124	>	if (rnemdFluxType_ == rnemdFullKE) {
1125	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1126		} else {
1127	<	c = 1.0 - targetFlux_ / Kcw;
1127	>	c = 1.0 - kineticTarget_ / Kcw;
1128		}
1129
1130		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1131		c = sqrt(c);
1132	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
847	<	//now convert to hotBin coefficient
1132	>
1133		RealType w = 0.0;
1134	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1134	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1135		x = 1.0 + px * (1.0 - c);
1136		y = 1.0 + py * (1.0 - c);
1137		z = 1.0 + pz * (1.0 - c);
#	Line 860 | Line 1145 | namespace OpenMD {
1145		*/
1146		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1147		(fabs(z - 1.0) < 0.1)) {
1148	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1148	>	w = 1.0 + (kineticTarget_
1149	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1150		+ Khz * (1.0 - z * z)) / Khw;
1151		}//no need to calculate w if x, y or z is out of range
1152		} else {
1153	<	w = 1.0 + targetFlux_ / Khw;
1153	>	w = 1.0 + kineticTarget_ / Khw;
1154		}
1155		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1156		//if w is in the right range, so should be x, y, z.
1157		vector<StuntDouble*>::iterator sdi;
1158		Vector3d vel;
1159	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1160	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1159	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1160	>	if (rnemdFluxType_ == rnemdFullKE) {
1161		vel = (*sdi)->getVel() * c;
876	–	//vel.x() *= c;
877	–	//vel.y() *= c;
878	–	//vel.z() *= c;
1162		(*sdi)->setVel(vel);
1163		}
1164		if ((*sdi)->isDirectional()) {
1165		Vector3d angMom = (*sdi)->getJ() * c;
883	–	//angMom[0] *= c;
884	–	//angMom[1] *= c;
885	–	//angMom[2] *= c;
1166		(*sdi)->setJ(angMom);
1167		}
1168		}
1169		w = sqrt(w);
1170	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
1171	<	<< "\twh= " << w << endl;
892	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
893	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1170	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1171	>	if (rnemdFluxType_ == rnemdFullKE) {
1172		vel = (*sdi)->getVel();
1173		vel.x() *= x;
1174		vel.y() *= y;
#	Line 899 | Line 1177 | namespace OpenMD {
1177		}
1178		if ((*sdi)->isDirectional()) {
1179		Vector3d angMom = (*sdi)->getJ() * w;
902	–	//angMom[0] *= w;
903	–	//angMom[1] *= w;
904	–	//angMom[2] *= w;
1180		(*sdi)->setJ(angMom);
1181		}
1182		}
1183		successfulScale = true;
1184	<	exchangeSum_ += targetFlux_;
1184	>	kineticExchange_ += kineticTarget_;
1185		}
1186		}
1187		} else {
1188		RealType a000, a110, c0, a001, a111, b01, b11, c1;
1189	<	switch(rnemdType_) {
1190	<	case rnemdKineticScale :
1189	>	switch(rnemdFluxType_) {
1190	>	case rnemdKE :
1191		/* used hotBin coeff's & only scale x & y dimensions
1192		RealType px = Phx / Pcx;
1193		RealType py = Phy / Pcy;
1194		a110 = Khy;
1195	<	c0 = - Khx - Khy - targetFlux_;
1195	>	c0 = - Khx - Khy - kineticTarget_;
1196		a000 = Khx;
1197		a111 = Kcy * py * py;
1198		b11 = -2.0 * Kcy * py * (1.0 + py);
1199	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1199	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1200		b01 = -2.0 * Kcx * px * (1.0 + px);
1201		a001 = Kcx * px * px;
1202		*/
1203		//scale all three dimensions, let c_x = c_y
1204		a000 = Kcx + Kcy;
1205		a110 = Kcz;
1206	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1206	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1207		a001 = Khx * px * px + Khy * py * py;
1208		a111 = Khz * pz * pz;
1209		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1210		b11 = -2.0 * Khz * pz * (1.0 + pz);
1211		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1212	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1212	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1213		break;
1214	<	case rnemdPxScale :
1215	<	c = 1 - targetFlux_ / Pcx;
1214	>	case rnemdPx :
1215	>	c = 1 - momentumTarget_.x() / Pcx;
1216		a000 = Kcy;
1217		a110 = Kcz;
1218		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 948 | Line 1223 | namespace OpenMD {
1223		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1224		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1225		break;
1226	<	case rnemdPyScale :
1227	<	c = 1 - targetFlux_ / Pcy;
1226	>	case rnemdPy :
1227	>	c = 1 - momentumTarget_.y() / Pcy;
1228		a000 = Kcx;
1229		a110 = Kcz;
1230		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 960 | Line 1235 | namespace OpenMD {
1235		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1236		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1237		break;
1238	<	case rnemdPzScale ://we don't really do this, do we?
1239	<	c = 1 - targetFlux_ / Pcz;
1238	>	case rnemdPz ://we don't really do this, do we?
1239	>	c = 1 - momentumTarget_.z() / Pcz;
1240		a000 = Kcx;
1241		a110 = Kcy;
1242		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 1011 | Line 1286 | namespace OpenMD {
1286		vector<RealType>::iterator ri;
1287		RealType r1, r2, alpha0;
1288		vector<pair<RealType,RealType> > rps;
1289	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1289	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1290		r2 = *ri;
1291		//check if FindRealRoots() give the right answer
1292		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
#	Line 1043 | Line 1318 | namespace OpenMD {
1318		RealType diff;
1319		pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1320		vector<pair<RealType,RealType> >::iterator rpi;
1321	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1321	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1322		r1 = (*rpi).first;
1323		r2 = (*rpi).second;
1324	<	switch(rnemdType_) {
1325	<	case rnemdKineticScale :
1324	>	switch(rnemdFluxType_) {
1325	>	case rnemdKE :
1326		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1327		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1328		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1329		break;
1330	<	case rnemdPxScale :
1330	>	case rnemdPx :
1331		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1332		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1333		break;
1334	<	case rnemdPyScale :
1334	>	case rnemdPy :
1335		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1336		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1337		break;
1338	<	case rnemdPzScale :
1338	>	case rnemdPz :
1339		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1340		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1341		default :
#	Line 1074 | Line 1349 | namespace OpenMD {
1349		#ifdef IS_MPI
1350		if (worldRank == 0) {
1351		#endif
1352	<	sprintf(painCave.errMsg,
1353	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1354	<	bestPair.first, bestPair.second);
1355	<	painCave.isFatal = 0;
1356	<	painCave.severity = OPENMD_INFO;
1357	<	simError();
1352	>	// sprintf(painCave.errMsg,
1353	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1354	>	//         bestPair.first, bestPair.second);
1355	>	// painCave.isFatal = 0;
1356	>	// painCave.severity = OPENMD_INFO;
1357	>	// simError();
1358		#ifdef IS_MPI
1359		}
1360		#endif
1361
1362	<	switch(rnemdType_) {
1363	<	case rnemdKineticScale :
1362	>	switch(rnemdFluxType_) {
1363	>	case rnemdKE :
1364		x = bestPair.first;
1365		y = bestPair.first;
1366		z = bestPair.second;
1367		break;
1368	<	case rnemdPxScale :
1368	>	case rnemdPx :
1369		x = c;
1370		y = bestPair.first;
1371		z = bestPair.second;
1372		break;
1373	<	case rnemdPyScale :
1373	>	case rnemdPy :
1374		x = bestPair.first;
1375		y = c;
1376		z = bestPair.second;
1377		break;
1378	<	case rnemdPzScale :
1378	>	case rnemdPz :
1379		x = bestPair.first;
1380		y = bestPair.second;
1381		z = c;
#	Line 1110 | Line 1385 | namespace OpenMD {
1385		}
1386		vector<StuntDouble*>::iterator sdi;
1387		Vector3d vel;
1388	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1388	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1389		vel = (*sdi)->getVel();
1390		vel.x() *= x;
1391		vel.y() *= y;
#	Line 1121 | Line 1396 | namespace OpenMD {
1396		x = 1.0 + px * (1.0 - x);
1397		y = 1.0 + py * (1.0 - y);
1398		z = 1.0 + pz * (1.0 - z);
1399	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1399	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1400		vel = (*sdi)->getVel();
1401		vel.x() *= x;
1402		vel.y() *= y;
#	Line 1129 | Line 1404 | namespace OpenMD {
1404		(*sdi)->setVel(vel);
1405		}
1406		successfulScale = true;
1407	<	exchangeSum_ += targetFlux_;
1407	>	switch(rnemdFluxType_) {
1408	>	case rnemdKE :
1409	>	kineticExchange_ += kineticTarget_;
1410	>	break;
1411	>	case rnemdPx :
1412	>	case rnemdPy :
1413	>	case rnemdPz :
1414	>	momentumExchange_ += momentumTarget_;
1415	>	break;
1416	>	default :
1417	>	break;
1418	>	}
1419		}
1420		}
1421		if (successfulScale != true) {
1422		sprintf(painCave.errMsg,
1423	<	"RNEMD: exchange NOT performed!\n");
1423	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1424	>	"\tthe constraint equations may not exist or there may be\n"
1425	>	"\tno selected objects in one or both slabs.\n");
1426		painCave.isFatal = 0;
1427		painCave.severity = OPENMD_INFO;
1428		simError();
1429		failTrialCount_++;
1430		}
1431		}
1432	+
1433	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1434	+	if (!doRNEMD_) return;
1435	+	int selei;
1436	+	int selej;
1437
1145	–	void RNEMD::doShiftScale() {
1146	–
1438		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1439		RealType time = currentSnap_->getTime();
1440		Mat3x3d hmat = currentSnap_->getHmat();
1441
1151	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1152	–
1153	–	int selei;
1442		StuntDouble* sd;
1155	–	int idx;
1443
1444		vector<StuntDouble*> hotBin, coldBin;
1445
1446		Vector3d Ph(V3Zero);
1447	+	Vector3d Lh(V3Zero);
1448		RealType Mh = 0.0;
1449	+	Mat3x3d Ih(0.0);
1450		RealType Kh = 0.0;
1451		Vector3d Pc(V3Zero);
1452	+	Vector3d Lc(V3Zero);
1453		RealType Mc = 0.0;
1454	+	Mat3x3d Ic(0.0);
1455		RealType Kc = 0.0;
1165	–
1456
1457	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1458	<	sd = seleMan_.nextSelected(selei)) {
1457	>	// Constraints can be on only the linear or angular momentum, but
1458	>	// not both.  Usually, the user will specify which they want, but
1459	>	// in case they don't, the use of periodic boundaries should make
1460	>	// the choice for us.
1461	>	bool doLinearPart = false;
1462	>	bool doAngularPart = false;
1463
1464	<	idx = sd->getLocalIndex();
1464	>	switch (rnemdFluxType_) {
1465	>	case rnemdPx:
1466	>	case rnemdPy:
1467	>	case rnemdPz:
1468	>	case rnemdPvector:
1469	>	case rnemdKePx:
1470	>	case rnemdKePy:
1471	>	case rnemdKePvector:
1472	>	doLinearPart = true;
1473	>	break;
1474	>	case rnemdLx:
1475	>	case rnemdLy:
1476	>	case rnemdLz:
1477	>	case rnemdLvector:
1478	>	case rnemdKeLx:
1479	>	case rnemdKeLy:
1480	>	case rnemdKeLz:
1481	>	case rnemdKeLvector:
1482	>	doAngularPart = true;
1483	>	break;
1484	>	case rnemdKE:
1485	>	case rnemdRotKE:
1486	>	case rnemdFullKE:
1487	>	default:
1488	>	if (usePeriodicBoundaryConditions_)
1489	>	doLinearPart = true;
1490	>	else
1491	>	doAngularPart = true;
1492	>	break;
1493	>	}
1494	>
1495	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1496	>	sd = smanA.nextSelected(selei)) {
1497
1498		Vector3d pos = sd->getPos();
1499
1500		// wrap the stuntdouble's position back into the box:
1501	+
1502	+	if (usePeriodicBoundaryConditions_)
1503	+	currentSnap_->wrapVector(pos);
1504	+
1505	+	RealType mass = sd->getMass();
1506	+	Vector3d vel = sd->getVel();
1507	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1508	+	RealType r2;
1509	+
1510	+	hotBin.push_back(sd);
1511	+	Ph += mass * vel;
1512	+	Mh += mass;
1513	+	Kh += mass * vel.lengthSquare();
1514	+	Lh += mass * cross(rPos, vel);
1515	+	Ih -= outProduct(rPos, rPos) * mass;
1516	+	r2 = rPos.lengthSquare();
1517	+	Ih(0, 0) += mass * r2;
1518	+	Ih(1, 1) += mass * r2;
1519	+	Ih(2, 2) += mass * r2;
1520	+
1521	+	if (rnemdFluxType_ == rnemdFullKE) {
1522	+	if (sd->isDirectional()) {
1523	+	Vector3d angMom = sd->getJ();
1524	+	Mat3x3d I = sd->getI();
1525	+	if (sd->isLinear()) {
1526	+	int i = sd->linearAxis();
1527	+	int j = (i + 1) % 3;
1528	+	int k = (i + 2) % 3;
1529	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1530	+	angMom[k] * angMom[k] / I(k, k);
1531	+	} else {
1532	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1533	+	angMom[1] * angMom[1] / I(1, 1) +
1534	+	angMom[2] * angMom[2] / I(2, 2);
1535	+	}
1536	+	}
1537	+	}
1538	+	}
1539	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1540	+	sd = smanB.nextSelected(selej)) {
1541
1542	+	Vector3d pos = sd->getPos();
1543	+
1544	+	// wrap the stuntdouble's position back into the box:
1545	+
1546		if (usePeriodicBoundaryConditions_)
1547		currentSnap_->wrapVector(pos);
1548	+
1549	+	RealType mass = sd->getMass();
1550	+	Vector3d vel = sd->getVel();
1551	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1552	+	RealType r2;
1553
1554	<	// which bin is this stuntdouble in?
1555	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1556	<
1557	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1558	<
1559	<	// if we're in bin 0 or the middleBin
1560	<	if (binNo == 0 || binNo == midBin_) {
1561	<
1562	<	RealType mass = sd->getMass();
1563	<	Vector3d vel = sd->getVel();
1564	<
1565	<	if (binNo == 0) {
1566	<	hotBin.push_back(sd);
1567	<	//std::cerr << "before, velocity = " << vel << endl;
1568	<	Ph += mass * vel;
1569	<	//std::cerr << "after, velocity = " << vel << endl;
1570	<	Mh += mass;
1571	<	Kh += mass * vel.lengthSquare();
1572	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1573	<	if (sd->isDirectional()) {
1574	<	Vector3d angMom = sd->getJ();
1575	<	Mat3x3d I = sd->getI();
1576	<	if (sd->isLinear()) {
1577	<	int i = sd->linearAxis();
1578	<	int j = (i + 1) % 3;
1579	<	int k = (i + 2) % 3;
1580	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1206	<	angMom[k] * angMom[k] / I(k, k);
1207	<	} else {
1208	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1209	<	angMom[1] * angMom[1] / I(1, 1) +
1210	<	angMom[2] * angMom[2] / I(2, 2);
1211	<	}
1212	<	}
1213	<	}
1214	<	} else { //midBin_
1215	<	coldBin.push_back(sd);
1216	<	Pc += mass * vel;
1217	<	Mc += mass;
1218	<	Kc += mass * vel.lengthSquare();
1219	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1220	<	if (sd->isDirectional()) {
1221	<	Vector3d angMom = sd->getJ();
1222	<	Mat3x3d I = sd->getI();
1223	<	if (sd->isLinear()) {
1224	<	int i = sd->linearAxis();
1225	<	int j = (i + 1) % 3;
1226	<	int k = (i + 2) % 3;
1227	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1228	<	angMom[k] * angMom[k] / I(k, k);
1229	<	} else {
1230	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1231	<	angMom[1] * angMom[1] / I(1, 1) +
1232	<	angMom[2] * angMom[2] / I(2, 2);
1233	<	}
1234	<	}
1235	<	}
1236	<	}
1554	>	coldBin.push_back(sd);
1555	>	Pc += mass * vel;
1556	>	Mc += mass;
1557	>	Kc += mass * vel.lengthSquare();
1558	>	Lc += mass * cross(rPos, vel);
1559	>	Ic -= outProduct(rPos, rPos) * mass;
1560	>	r2 = rPos.lengthSquare();
1561	>	Ic(0, 0) += mass * r2;
1562	>	Ic(1, 1) += mass * r2;
1563	>	Ic(2, 2) += mass * r2;
1564	>
1565	>	if (rnemdFluxType_ == rnemdFullKE) {
1566	>	if (sd->isDirectional()) {
1567	>	Vector3d angMom = sd->getJ();
1568	>	Mat3x3d I = sd->getI();
1569	>	if (sd->isLinear()) {
1570	>	int i = sd->linearAxis();
1571	>	int j = (i + 1) % 3;
1572	>	int k = (i + 2) % 3;
1573	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1574	>	angMom[k] * angMom[k] / I(k, k);
1575	>	} else {
1576	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1577	>	angMom[1] * angMom[1] / I(1, 1) +
1578	>	angMom[2] * angMom[2] / I(2, 2);
1579	>	}
1580	>	}
1581		}
1582		}
1583
1584		Kh *= 0.5;
1585		Kc *= 0.5;
1242	–
1243	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1244	–	//        << "\tKc= " << Kc << endl;
1245	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1586
1587		#ifdef IS_MPI
1588	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1589	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1590	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1591	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1592	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1593	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1588	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1589	>	MPI_COMM_WORLD);
1590	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1591	>	MPI_COMM_WORLD);
1592	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1593	>	MPI_COMM_WORLD);
1594	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1595	>	MPI_COMM_WORLD);
1596	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1597	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1598	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1599	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1600	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1601	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1602	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1603	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1604		#endif
1605	+
1606
1607	+	Vector3d ac, acrec, bc, bcrec;
1608	+	Vector3d ah, ahrec, bh, bhrec;
1609	+
1610		bool successfulExchange = false;
1611		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1612		Vector3d vc = Pc / Mc;
1613	<	Vector3d ac = njzp_ / Mc + vc;
1614	<	Vector3d acrec = njzp_ / Mc;
1615	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1613	>	ac = -momentumTarget_ / Mc + vc;
1614	>	acrec = -momentumTarget_ / Mc;
1615	>
1616	>	// We now need the inverse of the inertia tensor to calculate the
1617	>	// angular velocity of the cold slab;
1618	>	Mat3x3d Ici = Ic.inverse();
1619	>	Vector3d omegac = Ici * Lc;
1620	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1621	>	bcrec = bc - omegac;
1622	>
1623	>	RealType cNumerator = Kc - kineticTarget_;
1624	>	if (doLinearPart)
1625	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1626	>
1627	>	if (doAngularPart)
1628	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1629	>
1630		if (cNumerator > 0.0) {
1631	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1631	>
1632	>	RealType cDenominator = Kc;
1633	>
1634	>	if (doLinearPart)
1635	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1636	>
1637	>	if (doAngularPart)
1638	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1639	>
1640		if (cDenominator > 0.0) {
1641		RealType c = sqrt(cNumerator / cDenominator);
1642		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1643	+
1644		Vector3d vh = Ph / Mh;
1645	<	Vector3d ah = jzp_ / Mh + vh;
1646	<	Vector3d ahrec = jzp_ / Mh;
1647	<	RealType hNumerator = Kh + targetJzKE_
1648	<	- 0.5 * Mh * ah.lengthSquare();
1649	<	if (hNumerator > 0.0) {
1650	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1645	>	ah = momentumTarget_ / Mh + vh;
1646	>	ahrec = momentumTarget_ / Mh;
1647	>
1648	>	// We now need the inverse of the inertia tensor to
1649	>	// calculate the angular velocity of the hot slab;
1650	>	Mat3x3d Ihi = Ih.inverse();
1651	>	Vector3d omegah = Ihi * Lh;
1652	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1653	>	bhrec = bh - omegah;
1654	>
1655	>	RealType hNumerator = Kh + kineticTarget_;
1656	>	if (doLinearPart)
1657	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1658	>
1659	>	if (doAngularPart)
1660	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1661	>
1662	>	if (hNumerator > 0.0) {
1663	>
1664	>	RealType hDenominator = Kh;
1665	>	if (doLinearPart)
1666	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1667	>	if (doAngularPart)
1668	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1669	>
1670		if (hDenominator > 0.0) {
1671		RealType h = sqrt(hNumerator / hDenominator);
1672		if ((h > 0.9) && (h < 1.1)) {
1673	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1278	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1673	>
1674		vector<StuntDouble*>::iterator sdi;
1675		Vector3d vel;
1676	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1676	>	Vector3d rPos;
1677	>
1678	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1679		//vel = (*sdi)->getVel();
1680	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1680	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1681	>	if (doLinearPart)
1682	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1683	>	if (doAngularPart)
1684	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1685	>
1686		(*sdi)->setVel(vel);
1687	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1687	>	if (rnemdFluxType_ == rnemdFullKE) {
1688		if ((*sdi)->isDirectional()) {
1689		Vector3d angMom = (*sdi)->getJ() * c;
1690		(*sdi)->setJ(angMom);
1691		}
1692		}
1693		}
1694	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1694	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1695		//vel = (*sdi)->getVel();
1696	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1696	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1697	>	if (doLinearPart)
1698	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1699	>	if (doAngularPart)
1700	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1701	>
1702		(*sdi)->setVel(vel);
1703	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1703	>	if (rnemdFluxType_ == rnemdFullKE) {
1704		if ((*sdi)->isDirectional()) {
1705		Vector3d angMom = (*sdi)->getJ() * h;
1706		(*sdi)->setJ(angMom);
#	Line 1301 | Line 1708 | namespace OpenMD {
1708		}
1709		}
1710		successfulExchange = true;
1711	<	exchangeSum_ += targetFlux_;
1712	<	// this is a redundant variable for doShiftScale() so that
1713	<	// RNEMD can output one exchange quantity needed in a job.
1307	<	// need a better way to do this.
1308	<	//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n';
1309	<	//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n';
1310	<	//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n';
1311	<	Asum_ += (ahrec.z() - acrec.z());
1312	<	Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc)));
1313	<	AhCount_ = ahrec.z();
1314	<	if (outputAh_) {
1315	<	AhLog_ << time << "   ";
1316	<	AhLog_ << AhCount_;
1317	<	AhLog_ << endl;
1318	<	}
1711	>	kineticExchange_ += kineticTarget_;
1712	>	momentumExchange_ += momentumTarget_;
1713	>	angularMomentumExchange_ += angularMomentumTarget_;
1714		}
1715		}
1716		}
#	Line 1324 | Line 1719 | namespace OpenMD {
1719		}
1720		}
1721		if (successfulExchange != true) {
1722	<	//   sprintf(painCave.errMsg,
1723	<	//              "RNEMD: exchange NOT performed!\n");
1724	<	//   painCave.isFatal = 0;
1725	<	//   painCave.severity = OPENMD_INFO;
1726	<	//   simError();
1722	>	sprintf(painCave.errMsg,
1723	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1724	>	"\tthe constraint equations may not exist or there may be\n"
1725	>	"\tno selected objects in one or both slabs.\n");
1726	>	painCave.isFatal = 0;
1727	>	painCave.severity = OPENMD_INFO;
1728	>	simError();
1729		failTrialCount_++;
1730		}
1731		}
1732
1733	+	RealType RNEMD::getDividingArea() {
1734	+
1735	+	if (hasDividingArea_) return dividingArea_;
1736	+
1737	+	RealType areaA, areaB;
1738	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1739	+
1740	+	if (hasSelectionA_) {
1741	+
1742	+	if (evaluatorA_.hasSurfaceArea())
1743	+	areaA = evaluatorA_.getSurfaceArea();
1744	+	else {
1745	+
1746	+	cerr << "selection A did not have surface area, recomputing\n";
1747	+	int isd;
1748	+	StuntDouble* sd;
1749	+	vector<StuntDouble*> aSites;
1750	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1751	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1752	+	sd = seleManA_.nextSelected(isd)) {
1753	+	aSites.push_back(sd);
1754	+	}
1755	+	#if defined(HAVE_QHULL)
1756	+	ConvexHull* surfaceMeshA = new ConvexHull();
1757	+	surfaceMeshA->computeHull(aSites);
1758	+	areaA = surfaceMeshA->getArea();
1759	+	delete surfaceMeshA;
1760	+	#else
1761	+	sprintf( painCave.errMsg,
1762	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1763	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1764	+	painCave.severity = OPENMD_ERROR;
1765	+	painCave.isFatal = 1;
1766	+	simError();
1767	+	#endif
1768	+	}
1769	+
1770	+	} else {
1771	+	if (usePeriodicBoundaryConditions_) {
1772	+	// in periodic boundaries, the surface area is twice the x-y
1773	+	// area of the current box:
1774	+	areaA = 2.0 * snap->getXYarea();
1775	+	} else {
1776	+	// in non-periodic simulations, without explicitly setting
1777	+	// selections, the sphere radius sets the surface area of the
1778	+	// dividing surface:
1779	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1780	+	}
1781	+	}
1782	+
1783	+	if (hasSelectionB_) {
1784	+	if (evaluatorB_.hasSurfaceArea())
1785	+	areaB = evaluatorB_.getSurfaceArea();
1786	+	else {
1787	+	cerr << "selection B did not have surface area, recomputing\n";
1788	+
1789	+	int isd;
1790	+	StuntDouble* sd;
1791	+	vector<StuntDouble*> bSites;
1792	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1793	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1794	+	sd = seleManB_.nextSelected(isd)) {
1795	+	bSites.push_back(sd);
1796	+	}
1797	+
1798	+	#if defined(HAVE_QHULL)
1799	+	ConvexHull* surfaceMeshB = new ConvexHull();
1800	+	surfaceMeshB->computeHull(bSites);
1801	+	areaB = surfaceMeshB->getArea();
1802	+	delete surfaceMeshB;
1803	+	#else
1804	+	sprintf( painCave.errMsg,
1805	+	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1806	+	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1807	+	painCave.severity = OPENMD_ERROR;
1808	+	painCave.isFatal = 1;
1809	+	simError();
1810	+	#endif
1811	+	}
1812	+
1813	+	} else {
1814	+	if (usePeriodicBoundaryConditions_) {
1815	+	// in periodic boundaries, the surface area is twice the x-y
1816	+	// area of the current box:
1817	+	areaB = 2.0 * snap->getXYarea();
1818	+	} else {
1819	+	// in non-periodic simulations, without explicitly setting
1820	+	// selections, but if a sphereBradius has been set, just use that:
1821	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1822	+	}
1823	+	}
1824	+
1825	+	dividingArea_ = min(areaA, areaB);
1826	+	hasDividingArea_ = true;
1827	+	return dividingArea_;
1828	+	}
1829	+
1830		void RNEMD::doRNEMD() {
1831	+	if (!doRNEMD_) return;
1832	+	trialCount_++;
1833
1834	<	switch(rnemdType_) {
1835	<	case rnemdKineticScale :
1836	<	case rnemdKineticScaleVAM :
1837	<	case rnemdKineticScaleAM :
1838	<	case rnemdPxScale :
1839	<	case rnemdPyScale :
1840	<	case rnemdPzScale :
1841	<	doScale();
1842	<	break;
1843	<	case rnemdKineticSwap :
1844	<	case rnemdPx :
1845	<	case rnemdPy :
1846	<	case rnemdPz :
1847	<	doSwap();
1848	<	break;
1849	<	case rnemdShiftScaleV :
1850	<	case rnemdShiftScaleVAM :
1851	<	doShiftScale();
1834	>	// object evaluator:
1835	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1836	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1837	>
1838	>	evaluatorA_.loadScriptString(selectionA_);
1839	>	evaluatorB_.loadScriptString(selectionB_);
1840	>
1841	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1842	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1843	>
1844	>	commonA_ = seleManA_ & seleMan_;
1845	>	commonB_ = seleManB_ & seleMan_;
1846	>
1847	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1848	>	// dt = exchange time interval
1849	>	// flux = target flux
1850	>	// dividingArea = smallest dividing surface between the two regions
1851	>
1852	>	hasDividingArea_ = false;
1853	>	RealType area = getDividingArea();
1854	>
1855	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1856	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1857	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1858	>
1859	>	switch(rnemdMethod_) {
1860	>	case rnemdSwap:
1861	>	doSwap(commonA_, commonB_);
1862		break;
1863	<	case rnemdUnknown :
1863	>	case rnemdNIVS:
1864	>	doNIVS(commonA_, commonB_);
1865	>	break;
1866	>	case rnemdVSS:
1867	>	doVSS(commonA_, commonB_);
1868	>	break;
1869	>	case rnemdUnkownMethod:
1870		default :
1871		break;
1872		}
1873		}
1874
1875		void RNEMD::collectData() {
1876	<
1876	>	if (!doRNEMD_) return;
1877		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1878	+
1879	+	// collectData can be called more frequently than the doRNEMD, so use the
1880	+	// computed area from the last exchange time:
1881	+	RealType area = getDividingArea();
1882	+	areaAccumulator_->add(area);
1883		Mat3x3d hmat = currentSnap_->getHmat();
1884	+	Vector3d u = angularMomentumFluxVector_;
1885	+	u.normalize();
1886
1887		seleMan_.setSelectionSet(evaluator_.evaluate());
1888
1889	<	int selei;
1889	>	int selei(0);
1890		StuntDouble* sd;
1891	<	int idx;
1891	>	int binNo;
1892	>	RealType mass;
1893	>	Vector3d vel;
1894	>	Vector3d rPos;
1895	>	RealType KE;
1896	>	Vector3d L;
1897	>	Mat3x3d I;
1898	>	RealType r2;
1899
1900	<	logFrameCount_++;
1900	>	vector<RealType> binMass(nBins_, 0.0);
1901	>	vector<Vector3d> binP(nBins_, V3Zero);
1902	>	vector<RealType> binOmega(nBins_, 0.0);
1903	>	vector<Vector3d> binL(nBins_, V3Zero);
1904	>	vector<Mat3x3d>  binI(nBins_);
1905	>	vector<RealType> binKE(nBins_, 0.0);
1906	>	vector<int> binDOF(nBins_, 0);
1907	>	vector<int> binCount(nBins_, 0);
1908
1909		// alternative approach, track all molecules instead of only those
1910		// selected for scaling/swapping:
1911		/*
1912	<	SimInfo::MoleculeIterator miter;
1913	<	vector<StuntDouble*>::iterator iiter;
1914	<	Molecule* mol;
1915	<	StuntDouble* integrableObject;
1916	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1912	>	SimInfo::MoleculeIterator miter;
1913	>	vector<StuntDouble*>::iterator iiter;
1914	>	Molecule* mol;
1915	>	StuntDouble* sd;
1916	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1917		mol = info_->nextMolecule(miter))
1918	<	integrableObject is essentially sd
1919	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1920	<	integrableObject != NULL;
1921	<	integrableObject = mol->nextIntegrableObject(iiter))
1918	>	sd is essentially sd
1919	>	for (sd = mol->beginIntegrableObject(iiter);
1920	>	sd != NULL;
1921	>	sd = mol->nextIntegrableObject(iiter))
1922		*/
1923	+
1924		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1925	<	sd = seleMan_.nextSelected(selei)) {
1926	<
1393	<	idx = sd->getLocalIndex();
1394	<
1925	>	sd = seleMan_.nextSelected(selei)) {
1926	>
1927		Vector3d pos = sd->getPos();
1928
1929		// wrap the stuntdouble's position back into the box:
1930
1931	<	if (usePeriodicBoundaryConditions_)
1931	>	if (usePeriodicBoundaryConditions_) {
1932		currentSnap_->wrapVector(pos);
1933	+	// which bin is this stuntdouble in?
1934	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1935	+	// Shift molecules by half a box to have bins start at 0
1936	+	// The modulo operator is used to wrap the case when we are
1937	+	// beyond the end of the bins back to the beginning.
1938	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1939	+	} else {
1940	+	Vector3d rPos = pos - coordinateOrigin_;
1941	+	binNo = int(rPos.length() / binWidth_);
1942	+	}
1943	+
1944	+	mass = sd->getMass();
1945	+	vel = sd->getVel();
1946	+	rPos = sd->getPos() - coordinateOrigin_;
1947	+	KE = 0.5 * mass * vel.lengthSquare();
1948	+	L = mass * cross(rPos, vel);
1949	+	I = outProduct(rPos, rPos) * mass;
1950	+	r2 = rPos.lengthSquare();
1951	+	I(0, 0) += mass * r2;
1952	+	I(1, 1) += mass * r2;
1953	+	I(2, 2) += mass * r2;
1954	+
1955	+	// Project the relative position onto a plane perpendicular to
1956	+	// the angularMomentumFluxVector:
1957	+	// Vector3d rProj = rPos - dot(rPos, u) * u;
1958	+	// Project the velocity onto a plane perpendicular to the
1959	+	// angularMomentumFluxVector:
1960	+	// Vector3d vProj = vel  - dot(vel, u) * u;
1961	+	// Compute angular velocity vector (should be nearly parallel to
1962	+	// angularMomentumFluxVector
1963	+	// Vector3d aVel = cross(rProj, vProj);
1964	+
1965	+	if (binNo >= 0 && binNo < nBins_)  {
1966	+	binCount[binNo]++;
1967	+	binMass[binNo] += mass;
1968	+	binP[binNo] += mass*vel;
1969	+	binKE[binNo] += KE;
1970	+	binI[binNo] += I;
1971	+	binL[binNo] += L;
1972	+	binDOF[binNo] += 3;
1973	+
1974	+	if (sd->isDirectional()) {
1975	+	Vector3d angMom = sd->getJ();
1976	+	Mat3x3d Ia = sd->getI();
1977	+	if (sd->isLinear()) {
1978	+	int i = sd->linearAxis();
1979	+	int j = (i + 1) % 3;
1980	+	int k = (i + 2) % 3;
1981	+	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
1982	+	angMom[k] * angMom[k] / Ia(k, k));
1983	+	binDOF[binNo] += 2;
1984	+	} else {
1985	+	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
1986	+	angMom[1] * angMom[1] / Ia(1, 1) +
1987	+	angMom[2] * angMom[2] / Ia(2, 2));
1988	+	binDOF[binNo] += 3;
1989	+	}
1990	+	}
1991	+	}
1992	+	}
1993	+
1994	+	#ifdef IS_MPI
1995	+
1996	+	for (int i = 0; i < nBins_; i++) {
1997
1998	<	// which bin is this stuntdouble in?
1999	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
2000	<
2001	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
2002	<	rnemdLogWidth_;
2003	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
2004	<	/*
2005	<	if (rnemdLogWidth_ == midBin_ + 1)
2006	<	if (binNo > midBin_)
2007	<	binNo = nBins_ - binNo;
2008	<	*/
2009	<	RealType mass = sd->getMass();
2010	<	mHist_[binNo] += mass;
2011	<	Vector3d vel = sd->getVel();
2012	<	RealType value;
2013	<	//RealType xVal, yVal, zVal;
1998	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
1999	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2000	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2001	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2002	>	MPI_Allreduce(MPI_IN_PLACE, &binP[i],
2003	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2004	>	MPI_Allreduce(MPI_IN_PLACE, &binL[i],
2005	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2006	>	MPI_Allreduce(MPI_IN_PLACE, &binI[i],
2007	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2008	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2009	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2010	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2011	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2012	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2013	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2014	>	}
2015	>
2016	>	#endif
2017
2018	<	if (outputTemp_) {
2019	<	value = mass * vel.lengthSquare();
2020	<	tempCount_[binNo] += 3;
2021	<	if (sd->isDirectional()) {
2022	<	Vector3d angMom = sd->getJ();
2023	<	Mat3x3d I = sd->getI();
2024	<	if (sd->isLinear()) {
2025	<	int i = sd->linearAxis();
2026	<	int j = (i + 1) % 3;
2027	<	int k = (i + 2) % 3;
2028	<	value += angMom[j] * angMom[j] / I(j, j) +
2029	<	angMom[k] * angMom[k] / I(k, k);
2030	<	tempCount_[binNo] +=2;
2031	<	} else {
2032	<	value += angMom[0] * angMom[0] / I(0, 0) +
2033	<	angMom[1]*angMom[1]/I(1, 1) +
1435	<	angMom[2]*angMom[2]/I(2, 2);
1436	<	tempCount_[binNo] +=3;
1437	<	}
1438	<	}
1439	<	value = value / PhysicalConstants::energyConvert
1440	<	/ PhysicalConstants::kb;//may move to getStatus()
1441	<	tempHist_[binNo] += value;
2018	>	Vector3d omega;
2019	>	RealType den;
2020	>	RealType temp;
2021	>	RealType z;
2022	>	RealType r;
2023	>	for (int i = 0; i < nBins_; i++) {
2024	>	if (usePeriodicBoundaryConditions_) {
2025	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2026	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2027	>	/ currentSnap_->getVolume() ;
2028	>	} else {
2029	>	r = (((RealType)i + 0.5) * binWidth_);
2030	>	RealType rinner = (RealType)i * binWidth_;
2031	>	RealType router = (RealType)(i+1) * binWidth_;
2032	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2033	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2034		}
2035	<	if (outputVx_) {
1444	<	value = mass * vel[0];
1445	<	//vxzCount_[binNo]++;
1446	<	pxzHist_[binNo] += value;
1447	<	}
1448	<	if (outputVy_) {
1449	<	value = mass * vel[1];
1450	<	//vyzCount_[binNo]++;
1451	<	pyzHist_[binNo] += value;
1452	<	}
2035	>	vel = binP[i] / binMass[i];
2036
2037	<	if (output3DTemp_) {
2038	<	value = mass * vel.x() * vel.x();
2039	<	xTempHist_[binNo] += value;
2040	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
2041	<	/ PhysicalConstants::kb;
2042	<	yTempHist_[binNo] += value;
2043	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
2044	<	/ PhysicalConstants::kb;
2045	<	zTempHist_[binNo] += value;
2046	<	xyzTempCount_[binNo]++;
2037	>	omega = binI[i].inverse() * binL[i];
2038	>
2039	>	// omega = binOmega[i] / binCount[i];
2040	>
2041	>	if (binCount[i] > 0) {
2042	>	// only add values if there are things to add
2043	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2044	>	PhysicalConstants::energyConvert);
2045	>
2046	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2047	>	if(outputMask_[j]) {
2048	>	switch(j) {
2049	>	case Z:
2050	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2051	>	break;
2052	>	case R:
2053	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2054	>	break;
2055	>	case TEMPERATURE:
2056	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2057	>	break;
2058	>	case VELOCITY:
2059	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2060	>	break;
2061	>	case ANGULARVELOCITY:
2062	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2063	>	break;
2064	>	case DENSITY:
2065	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2066	>	break;
2067	>	}
2068	>	}
2069	>	}
2070		}
1465	–	if (outputRotTemp_) {
1466	–	if (sd->isDirectional()) {
1467	–	Vector3d angMom = sd->getJ();
1468	–	Mat3x3d I = sd->getI();
1469	–	if (sd->isLinear()) {
1470	–	int i = sd->linearAxis();
1471	–	int j = (i + 1) % 3;
1472	–	int k = (i + 2) % 3;
1473	–	value = angMom[j] * angMom[j] / I(j, j) +
1474	–	angMom[k] * angMom[k] / I(k, k);
1475	–	rotTempCount_[binNo] +=2;
1476	–	} else {
1477	–	value = angMom[0] * angMom[0] / I(0, 0) +
1478	–	angMom[1] * angMom[1] / I(1, 1) +
1479	–	angMom[2] * angMom[2] / I(2, 2);
1480	–	rotTempCount_[binNo] +=3;
1481	–	}
1482	–	}
1483	–	value = value / PhysicalConstants::energyConvert
1484	–	/ PhysicalConstants::kb;//may move to getStatus()
1485	–	rotTempHist_[binNo] += value;
1486	–	}
1487	–	// James put this in.
1488	–	if (outputDen_) {
1489	–	//value = 1.0;
1490	–	DenHist_[binNo] += 1;
1491	–	}
1492	–	if (outputVz_) {
1493	–	value = mass * vel[2];
1494	–	//vyzCount_[binNo]++;
1495	–	pzzHist_[binNo] += value;
1496	–	}
2071		}
2072	+	hasData_ = true;
2073		}
2074
2075		void RNEMD::getStarted() {
2076	+	if (!doRNEMD_) return;
2077	+	hasDividingArea_ = false;
2078		collectData();
2079	<	/*now can output profile in step 0, but might not be useful;
1503	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1504	<	Stats& stat = currentSnap_->statData;
1505	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1506	<	*/
1507	<	//may output a header for the log file here
1508	<	getStatus();
2079	>	writeOutputFile();
2080		}
2081
2082	<	void RNEMD::getStatus() {
2083	<
2084	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2085	<	Stats& stat = currentSnap_->statData;
2086	<	RealType time = currentSnap_->getTime();
2087	<
2088	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2089	<	//or to be more meaningful, define another item as exchangeSum_ / time
2090	<	int j;
2091	<
2092	<	#ifdef IS_MPI
2093	<
2094	<	// all processors have the same number of bins, and STL vectors pack their
2095	<	// arrays, so in theory, this should be safe:
2096	<
2097	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
2098	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
2099	<	if (outputTemp_) {
2100	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
2101	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
2102	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
2103	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
2104	<	}
2105	<	if (outputVx_) {
1535	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1536	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1537	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1538	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1539	<	}
1540	<	if (outputVy_) {
1541	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
1542	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1543	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
1544	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
1545	<	}
1546	<	if (output3DTemp_) {
1547	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1548	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1549	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1550	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1551	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1552	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1553	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1554	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1555	<	}
1556	<	if (outputRotTemp_) {
1557	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1558	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1559	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1560	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1561	<	}
1562	<	// James put this in
1563	<	if (outputDen_) {
1564	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0],
1565	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1566	<	}
1567	<	if (outputAh_) {
1568	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_,
1569	<	1, MPI::REALTYPE, MPI::SUM);
1570	<	}
1571	<	if (outputVz_) {
1572	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0],
1573	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1574	<	}
2082	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2083	>	if (!doRNEMD_) return;
2084	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2085	>
2086	>	while(tokenizer.hasMoreTokens()) {
2087	>	std::string token(tokenizer.nextToken());
2088	>	toUpper(token);
2089	>	OutputMapType::iterator i = outputMap_.find(token);
2090	>	if (i != outputMap_.end()) {
2091	>	outputMask_.set(i->second);
2092	>	} else {
2093	>	sprintf( painCave.errMsg,
2094	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2095	>	"\toutputFileFormat keyword.\n", token.c_str() );
2096	>	painCave.isFatal = 0;
2097	>	painCave.severity = OPENMD_ERROR;
2098	>	simError();
2099	>	}
2100	>	}
2101	>	}
2102	>
2103	>	void RNEMD::writeOutputFile() {
2104	>	if (!doRNEMD_) return;
2105	>	if (!hasData_) return;
2106
2107	+	#ifdef IS_MPI
2108		// If we're the root node, should we print out the results
2109	<	int worldRank = MPI::COMM_WORLD.Get_rank();
2109	>	int worldRank;
2110	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2111	>
2112		if (worldRank == 0) {
2113		#endif
2114	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2115	+
2116	+	if( !rnemdFile_ ){
2117	+	sprintf( painCave.errMsg,
2118	+	"Could not open \"%s\" for RNEMD output.\n",
2119	+	rnemdFileName_.c_str());
2120	+	painCave.isFatal = 1;
2121	+	simError();
2122	+	}
2123
2124	<	if (outputTemp_) {
2125	<	tempLog_ << time;
2126	<	for (j = 0; j < rnemdLogWidth_; j++) {
2127	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
2128	<	}
2129	<	tempLog_ << endl;
2124	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2125	>
2126	>	RealType time = currentSnap_->getTime();
2127	>	RealType avgArea;
2128	>	areaAccumulator_->getAverage(avgArea);
2129	>
2130	>	RealType Jz(0.0);
2131	>	Vector3d JzP(V3Zero);
2132	>	Vector3d JzL(V3Zero);
2133	>	if (time >= info_->getSimParams()->getDt()) {
2134	>	Jz = kineticExchange_ / (time * avgArea)
2135	>	/ PhysicalConstants::energyConvert;
2136	>	JzP = momentumExchange_ / (time * avgArea);
2137	>	JzL = angularMomentumExchange_ / (time * avgArea);
2138		}
2139	<	if (outputVx_) {
2140	<	vxzLog_ << time;
2141	<	for (j = 0; j < rnemdLogWidth_; j++) {
2142	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
2143	<	}
2144	<	vxzLog_ << endl;
2139	>
2140	>	rnemdFile_ << "#######################################################\n";
2141	>	rnemdFile_ << "# RNEMD {\n";
2142	>
2143	>	map<string, RNEMDMethod>::iterator mi;
2144	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2145	>	if ( (*mi).second == rnemdMethod_)
2146	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2147		}
2148	<	if (outputVy_) {
2149	<	vyzLog_ << time;
2150	<	for (j = 0; j < rnemdLogWidth_; j++) {
2151	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1599	<	}
1600	<	vyzLog_ << endl;
2148	>	map<string, RNEMDFluxType>::iterator fi;
2149	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2150	>	if ( (*fi).second == rnemdFluxType_)
2151	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2152		}
2153	+
2154	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2155
2156	<	if (output3DTemp_) {
2157	<	RealType temp;
2158	<	xTempLog_ << time;
2159	<	for (j = 0; j < rnemdLogWidth_; j++) {
2160	<	if (outputVx_)
2161	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2162	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2163	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2164	<	xTempLog_ << "\t" << temp;
2156	>	rnemdFile_ << "#    objectSelection = \""
2157	>	<< rnemdObjectSelection_ << "\";\n";
2158	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2159	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2160	>	rnemdFile_ << "# }\n";
2161	>	rnemdFile_ << "#######################################################\n";
2162	>	rnemdFile_ << "# RNEMD report:\n";
2163	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2164	>	rnemdFile_ << "# Target flux:\n";
2165	>	rnemdFile_ << "#           kinetic = "
2166	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2167	>	<< " (kcal/mol/A^2/fs)\n";
2168	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2169	>	<< " (amu/A/fs^2)\n";
2170	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2171	>	<< " (amu/A^2/fs^2)\n";
2172	>	rnemdFile_ << "# Target one-time exchanges:\n";
2173	>	rnemdFile_ << "#          kinetic = "
2174	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2175	>	<< " (kcal/mol)\n";
2176	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2177	>	<< " (amu*A/fs)\n";
2178	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2179	>	<< " (amu*A^2/fs)\n";
2180	>	rnemdFile_ << "# Actual exchange totals:\n";
2181	>	rnemdFile_ << "#          kinetic = "
2182	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2183	>	<< " (kcal/mol)\n";
2184	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2185	>	<< " (amu*A/fs)\n";
2186	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2187	>	<< " (amu*A^2/fs)\n";
2188	>	rnemdFile_ << "# Actual flux:\n";
2189	>	rnemdFile_ << "#          kinetic = " << Jz
2190	>	<< " (kcal/mol/A^2/fs)\n";
2191	>	rnemdFile_ << "#          momentum = " << JzP
2192	>	<< " (amu/A/fs^2)\n";
2193	>	rnemdFile_ << "#  angular momentum = " << JzL
2194	>	<< " (amu/A^2/fs^2)\n";
2195	>	rnemdFile_ << "# Exchange statistics:\n";
2196	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2197	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2198	>	if (rnemdMethod_ == rnemdNIVS) {
2199	>	rnemdFile_ << "#  NIVS root-check errors = "
2200	>	<< failRootCount_ << "\n";
2201	>	}
2202	>	rnemdFile_ << "#######################################################\n";
2203	>
2204	>
2205	>
2206	>	//write title
2207	>	rnemdFile_ << "#";
2208	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2209	>	if (outputMask_[i]) {
2210	>	rnemdFile_ << "\t" << data_[i].title <<
2211	>	"(" << data_[i].units << ")";
2212	>	// add some extra tabs for column alignment
2213	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2214		}
2215	<	xTempLog_ << endl;
2216	<	yTempLog_ << time;
2217	<	for (j = 0; j < rnemdLogWidth_; j++) {
2218	<	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
2215	>	}
2216	>	rnemdFile_ << std::endl;
2217	>
2218	>	rnemdFile_.precision(8);
2219	>
2220	>	for (int j = 0; j < nBins_; j++) {
2221	>
2222	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2223	>	if (outputMask_[i]) {
2224	>	if (data_[i].dataType == "RealType")
2225	>	writeReal(i,j);
2226	>	else if (data_[i].dataType == "Vector3d")
2227	>	writeVector(i,j);
2228	>	else {
2229	>	sprintf( painCave.errMsg,
2230	>	"RNEMD found an unknown data type for: %s ",
2231	>	data_[i].title.c_str());
2232	>	painCave.isFatal = 1;
2233	>	simError();
2234	>	}
2235	>	}
2236		}
2237	<	yTempLog_ << endl;
2238	<	zTempLog_ << time;
2239	<	for (j = 0; j < rnemdLogWidth_; j++) {
2240	<	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
2237	>	rnemdFile_ << std::endl;
2238	>
2239	>	}
2240	>
2241	>	rnemdFile_ << "#######################################################\n";
2242	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2243	>	rnemdFile_ << "#######################################################\n";
2244	>
2245	>
2246	>	for (int j = 0; j < nBins_; j++) {
2247	>	rnemdFile_ << "#";
2248	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2249	>	if (outputMask_[i]) {
2250	>	if (data_[i].dataType == "RealType")
2251	>	writeRealStdDev(i,j);
2252	>	else if (data_[i].dataType == "Vector3d")
2253	>	writeVectorStdDev(i,j);
2254	>	else {
2255	>	sprintf( painCave.errMsg,
2256	>	"RNEMD found an unknown data type for: %s ",
2257	>	data_[i].title.c_str());
2258	>	painCave.isFatal = 1;
2259	>	simError();
2260	>	}
2261	>	}
2262		}
2263	<	zTempLog_ << endl;
2264	<	}
2265	<	if (outputRotTemp_) {
2266	<	rotTempLog_ << time;
2267	<	for (j = 0; j < rnemdLogWidth_; j++) {
2268	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2269	<	}
1630	<	rotTempLog_ << endl;
1631	<	}
1632	<	// James put this in.
1633	<	Mat3x3d hmat = currentSnap_->getHmat();
1634	<	if (outputDen_) {
1635	<	denLog_ << time;
1636	<	for (j = 0; j < rnemdLogWidth_; j++) {
1637	<
1638	<	RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_));
1639	<	denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol);
1640	<	}
1641	<	denLog_ << endl;
1642	<	}
1643	<	if (outputVz_) {
1644	<	vzzLog_ << time;
1645	<	for (j = 0; j < rnemdLogWidth_; j++) {
1646	<	vzzLog_ << "\t" << pzzHist_[j] / mHist_[j];
1647	<	}
1648	<	vzzLog_ << endl;
1649	<	}
2263	>	rnemdFile_ << std::endl;
2264	>
2265	>	}
2266	>
2267	>	rnemdFile_.flush();
2268	>	rnemdFile_.close();
2269	>
2270		#ifdef IS_MPI
2271		}
2272		#endif
2273	+
2274	+	}
2275	+
2276	+	void RNEMD::writeReal(int index, unsigned int bin) {
2277	+	if (!doRNEMD_) return;
2278	+	assert(index >=0 && index < ENDINDEX);
2279	+	assert(int(bin) < nBins_);
2280	+	RealType s;
2281	+	int count;
2282	+
2283	+	count = data_[index].accumulator[bin]->count();
2284	+	if (count == 0) return;
2285	+
2286	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2287	+
2288	+	if (! isinf(s) && ! isnan(s)) {
2289	+	rnemdFile_ << "\t" << s;
2290	+	} else{
2291	+	sprintf( painCave.errMsg,
2292	+	"RNEMD detected a numerical error writing: %s for bin %u",
2293	+	data_[index].title.c_str(), bin);
2294	+	painCave.isFatal = 1;
2295	+	simError();
2296	+	}
2297	+	}
2298	+
2299	+	void RNEMD::writeVector(int index, unsigned int bin) {
2300	+	if (!doRNEMD_) return;
2301	+	assert(index >=0 && index < ENDINDEX);
2302	+	assert(int(bin) < nBins_);
2303	+	Vector3d s;
2304	+	int count;
2305	+
2306	+	count = data_[index].accumulator[bin]->count();
2307
2308	<	for (j = 0; j < rnemdLogWidth_; j++) {
2309	<	mHist_[j] = 0.0;
2308	>	if (count == 0) return;
2309	>
2310	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2311	>	if (isinf(s[0]) || isnan(s[0]) ||
2312	>	isinf(s[1]) || isnan(s[1]) ||
2313	>	isinf(s[2]) || isnan(s[2]) ) {
2314	>	sprintf( painCave.errMsg,
2315	>	"RNEMD detected a numerical error writing: %s for bin %u",
2316	>	data_[index].title.c_str(), bin);
2317	>	painCave.isFatal = 1;
2318	>	simError();
2319	>	} else {
2320	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2321		}
2322	<	if (outputTemp_)
1658	<	for (j = 0; j < rnemdLogWidth_; j++) {
1659	<	tempCount_[j] = 0;
1660	<	tempHist_[j] = 0.0;
1661	<	}
1662	<	if (outputVx_)
1663	<	for (j = 0; j < rnemdLogWidth_; j++) {
1664	<	//pxzCount_[j] = 0;
1665	<	pxzHist_[j] = 0.0;
1666	<	}
1667	<	if (outputVy_)
1668	<	for (j = 0; j < rnemdLogWidth_; j++) {
1669	<	//pyzCount_[j] = 0;
1670	<	pyzHist_[j] = 0.0;
1671	<	}
2322	>	}
2323
2324	<	if (output3DTemp_)
2325	<	for (j = 0; j < rnemdLogWidth_; j++) {
2326	<	xTempHist_[j] = 0.0;
2327	<	yTempHist_[j] = 0.0;
2328	<	zTempHist_[j] = 0.0;
2329	<	xyzTempCount_[j] = 0;
1679	<	}
1680	<	if (outputRotTemp_)
1681	<	for (j = 0; j < rnemdLogWidth_; j++) {
1682	<	rotTempCount_[j] = 0;
1683	<	rotTempHist_[j] = 0.0;
1684	<	}
1685	<	// James put this in
1686	<	if (outputDen_)
1687	<	for (j = 0; j < rnemdLogWidth_; j++) {
1688	<	//pyzCount_[j] = 0;
1689	<	DenHist_[j] = 0.0;
1690	<	}
1691	<	if (outputVz_)
1692	<	for (j = 0; j < rnemdLogWidth_; j++) {
1693	<	//pyzCount_[j] = 0;
1694	<	pzzHist_[j] = 0.0;
1695	<	}
1696	<	// reset the counter
1697	<
1698	<	Numcount_++;
1699	<	if (Numcount_ > int(runTime_/statusTime_))
1700	<	cerr << "time =" << time << "  Asum =" << Asum_ << '\n';
1701	<	if (Numcount_ > int(runTime_/statusTime_))
1702	<	cerr << "time =" << time << "  Jsum =" << Jsum_ << '\n';
2324	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2325	>	if (!doRNEMD_) return;
2326	>	assert(index >=0 && index < ENDINDEX);
2327	>	assert(int(bin) < nBins_);
2328	>	RealType s;
2329	>	int count;
2330
2331	<	logFrameCount_ = 0;
2331	>	count = data_[index].accumulator[bin]->count();
2332	>	if (count == 0) return;
2333	>
2334	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2335	>
2336	>	if (! isinf(s) && ! isnan(s)) {
2337	>	rnemdFile_ << "\t" << s;
2338	>	} else{
2339	>	sprintf( painCave.errMsg,
2340	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2341	>	data_[index].title.c_str(), bin);
2342	>	painCave.isFatal = 1;
2343	>	simError();
2344	>	}
2345		}
2346	+
2347	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2348	+	if (!doRNEMD_) return;
2349	+	assert(index >=0 && index < ENDINDEX);
2350	+	assert(int(bin) < nBins_);
2351	+	Vector3d s;
2352	+	int count;
2353	+
2354	+	count = data_[index].accumulator[bin]->count();
2355	+	if (count == 0) return;
2356	+
2357	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2358	+	if (isinf(s[0]) || isnan(s[0]) ||
2359	+	isinf(s[1]) || isnan(s[1]) ||
2360	+	isinf(s[2]) || isnan(s[2]) ) {
2361	+	sprintf( painCave.errMsg,
2362	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2363	+	data_[index].title.c_str(), bin);
2364	+	painCave.isFatal = 1;
2365	+	simError();
2366	+	} else {
2367	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2368	+	}
2369	+	}
2370		}
2371

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