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

Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
trunk/src/rnemd/RNEMD.cpp (file contents), Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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 62 | Line 68 | namespace OpenMD {
68		using namespace std;
69		namespace OpenMD {
70
71	<	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	<	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
71	>	RNEMD::RNEMD(SimInfo* info) : info_(info),
72	>	evaluator_(info_), seleMan_(info_),
73	>	evaluatorA_(info_), seleManA_(info_),
74	>	evaluatorB_(info_), seleManB_(info_),
75	>	commonA_(info_), commonB_(info_),
76	>	usePeriodicBoundaryConditions_(info_->getSimParams()->getUsePeriodicBoundaryConditions()),
77	>	hasDividingArea_(false),
78	>	hasData_(false) {
79
80	+	trialCount_ = 0;
81		failTrialCount_ = 0;
82		failRootCount_ = 0;
83
84	<	int seedValue;
85	<	Globals * simParams = info->getSimParams();
84	>	Globals* simParams = info->getSimParams();
85	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
86
87	<	stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
88	<	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;
87	>	doRNEMD_ = rnemdParams->getUseRNEMD();
88	>	if (!doRNEMD_) return;
89
90	<	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
91	<	evaluator_.loadScriptString(rnemdObjectSelection_);
92	<	seleMan_.setSelectionSet(evaluator_.evaluate());
90	>	stringToMethod_["Swap"]  = rnemdSwap;
91	>	stringToMethod_["NIVS"]  = rnemdNIVS;
92	>	stringToMethod_["VSS"]   = rnemdVSS;
93
94	<	// do some sanity checking
94	>	stringToFluxType_["KE"]  = rnemdKE;
95	>	stringToFluxType_["Px"]  = rnemdPx;
96	>	stringToFluxType_["Py"]  = rnemdPy;
97	>	stringToFluxType_["Pz"]  = rnemdPz;
98	>	stringToFluxType_["Pvector"]  = rnemdPvector;
99	>	stringToFluxType_["Lx"]  = rnemdLx;
100	>	stringToFluxType_["Ly"]  = rnemdLy;
101	>	stringToFluxType_["Lz"]  = rnemdLz;
102	>	stringToFluxType_["Lvector"]  = rnemdLvector;
103	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
104	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
105	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
106	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
107	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
108	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
109	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
110
111	<	int selectionCount = seleMan_.getSelectionCount();
112	<	int nIntegrable = info->getNGlobalIntegrableObjects();
111	>	runTime_ = simParams->getRunTime();
112	>	statusTime_ = simParams->getStatusTime();
113
114	<	if (selectionCount > nIntegrable) {
114	>	const string methStr = rnemdParams->getMethod();
115	>	bool hasFluxType = rnemdParams->haveFluxType();
116	>
117	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
118	>
119	>	string fluxStr;
120	>	if (hasFluxType) {
121	>	fluxStr = rnemdParams->getFluxType();
122	>	} else {
123		sprintf(painCave.errMsg,
124	<	"RNEMD: The current RNEMD_objectSelection,\n"
125	<	"\t\t%s\n"
126	<	"\thas resulted in %d selected objects.  However,\n"
127	<	"\tthe total number of integrable objects in the system\n"
128	<	"\tis only %d.  This is almost certainly not what you want\n"
129	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
130	<	"\tselector in the selection script!\n",
106	<	rnemdObjectSelection_.c_str(),
107	<	selectionCount, nIntegrable);
108	<	painCave.isFatal = 0;
109	<	painCave.severity = OPENMD_WARNING;
124	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
125	>	"\twhich must be one of the following values:\n"
126	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
127	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
128	>	"\tmust be set to use RNEMD\n");
129	>	painCave.isFatal = 1;
130	>	painCave.severity = OPENMD_ERROR;
131		simError();
132		}
133	+
134	+	bool hasKineticFlux = rnemdParams->haveKineticFlux();
135	+	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
136	+	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
137	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
138	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
139	+	hasSelectionA_ = rnemdParams->haveSelectionA();
140	+	hasSelectionB_ = rnemdParams->haveSelectionB();
141	+	bool hasSlabWidth = rnemdParams->haveSlabWidth();
142	+	bool hasSlabACenter = rnemdParams->haveSlabACenter();
143	+	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
144	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
145	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
146	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
147	+	bool hasOutputFileName = rnemdParams->haveOutputFileName();
148	+	bool hasOutputFields = rnemdParams->haveOutputFields();
149
150	<	const string st = simParams->getRNEMD_exchangeType();
150	>	map<string, RNEMDMethod>::iterator i;
151	>	i = stringToMethod_.find(methStr);
152	>	if (i != stringToMethod_.end())
153	>	rnemdMethod_ = i->second;
154	>	else {
155	>	sprintf(painCave.errMsg,
156	>	"RNEMD: The current method,\n"
157	>	"\t\t%s is not one of the recognized\n"
158	>	"\texchange methods: Swap, NIVS, or VSS\n",
159	>	methStr.c_str());
160	>	painCave.isFatal = 1;
161	>	painCave.severity = OPENMD_ERROR;
162	>	simError();
163	>	}
164
165	<	map<string, RNEMDTypeEnum>::iterator i;
166	<	i = stringToEnumMap_.find(st);
167	<	rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
168	<	if (rnemdType_ == rnemdUnknown) {
165	>	map<string, RNEMDFluxType>::iterator j;
166	>	j = stringToFluxType_.find(fluxStr);
167	>	if (j != stringToFluxType_.end())
168	>	rnemdFluxType_ = j->second;
169	>	else {
170		sprintf(painCave.errMsg,
171	<	"RNEMD: The current RNEMD_exchangeType,\n"
171	>	"RNEMD: The current fluxType,\n"
172		"\t\t%s\n"
173	<	"\tis not one of the recognized exchange types.\n",
174	<	st.c_str());
173	>	"\tis not one of the recognized flux types.\n",
174	>	fluxStr.c_str());
175		painCave.isFatal = 1;
176		painCave.severity = OPENMD_ERROR;
177		simError();
178		}
128	–
129	–	outputTemp_ = false;
130	–	if (simParams->haveRNEMD_outputTemperature()) {
131	–	outputTemp_ = simParams->getRNEMD_outputTemperature();
132	–	} else if ((rnemdType_ == rnemdKineticSwap) ||
133	–	(rnemdType_ == rnemdKineticScale) ||
134	–	(rnemdType_ == rnemdKineticScaleVAM) ||
135	–	(rnemdType_ == rnemdKineticScaleAM)) {
136	–	outputTemp_ = true;
137	–	}
138	–	outputVx_ = false;
139	–	if (simParams->haveRNEMD_outputVx()) {
140	–	outputVx_ = simParams->getRNEMD_outputVx();
141	–	} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
142	–	outputVx_ = true;
143	–	}
144	–	outputVy_ = false;
145	–	if (simParams->haveRNEMD_outputVy()) {
146	–	outputVy_ = simParams->getRNEMD_outputVy();
147	–	} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
148	–	outputVy_ = true;
149	–	}
150	–	output3DTemp_ = false;
151	–	if (simParams->haveRNEMD_outputXyzTemperature()) {
152	–	output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
153	–	}
154	–	outputRotTemp_ = false;
155	–	if (simParams->haveRNEMD_outputRotTemperature()) {
156	–	outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
157	–	}
179
180	<	#ifdef IS_MPI
181	<	if (worldRank == 0) {
182	<	#endif
183	<
184	<	//may have rnemdWriter separately
185	<	string rnemdFileName;
186	<
187	<	if (outputTemp_) {
188	<	rnemdFileName = "temperature.log";
189	<	tempLog_.open(rnemdFileName.c_str());
180	>	bool methodFluxMismatch = false;
181	>	bool hasCorrectFlux = false;
182	>	switch(rnemdMethod_) {
183	>	case rnemdSwap:
184	>	switch (rnemdFluxType_) {
185	>	case rnemdKE:
186	>	hasCorrectFlux = hasKineticFlux;
187	>	break;
188	>	case rnemdPx:
189	>	case rnemdPy:
190	>	case rnemdPz:
191	>	hasCorrectFlux = hasMomentumFlux;
192	>	break;
193	>	default :
194	>	methodFluxMismatch = true;
195	>	break;
196		}
197	<	if (outputVx_) {
198	<	rnemdFileName = "velocityX.log";
199	<	vxzLog_.open(rnemdFileName.c_str());
197	>	break;
198	>	case rnemdNIVS:
199	>	switch (rnemdFluxType_) {
200	>	case rnemdKE:
201	>	case rnemdRotKE:
202	>	case rnemdFullKE:
203	>	hasCorrectFlux = hasKineticFlux;
204	>	break;
205	>	case rnemdPx:
206	>	case rnemdPy:
207	>	case rnemdPz:
208	>	hasCorrectFlux = hasMomentumFlux;
209	>	break;
210	>	case rnemdKePx:
211	>	case rnemdKePy:
212	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
213	>	break;
214	>	default:
215	>	methodFluxMismatch = true;
216	>	break;
217		}
218	<	if (outputVy_) {
219	<	rnemdFileName = "velocityY.log";
220	<	vyzLog_.open(rnemdFileName.c_str());
221	<	}
222	<
223	<	if (output3DTemp_) {
224	<	rnemdFileName = "temperatureX.log";
225	<	xTempLog_.open(rnemdFileName.c_str());
226	<	rnemdFileName = "temperatureY.log";
227	<	yTempLog_.open(rnemdFileName.c_str());
228	<	rnemdFileName = "temperatureZ.log";
229	<	zTempLog_.open(rnemdFileName.c_str());
230	<	}
231	<	if (outputRotTemp_) {
232	<	rnemdFileName = "temperatureR.log";
233	<	rotTempLog_.open(rnemdFileName.c_str());
234	<	}
235	<
236	<	#ifdef IS_MPI
237	<	}
238	<	#endif
239	<
240	<	set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
241	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
242	<	midBin_ = nBins_ / 2;
243	<	if (simParams->haveRNEMD_binShift()) {
244	<	if (simParams->getRNEMD_binShift()) {
245	<	zShift_ = 0.5 / (RealType)(nBins_);
246	<	} else {
247	<	zShift_ = 0.0;
218	>	break;
219	>	case rnemdVSS:
220	>	switch (rnemdFluxType_) {
221	>	case rnemdKE:
222	>	case rnemdRotKE:
223	>	case rnemdFullKE:
224	>	hasCorrectFlux = hasKineticFlux;
225	>	break;
226	>	case rnemdPx:
227	>	case rnemdPy:
228	>	case rnemdPz:
229	>	hasCorrectFlux = hasMomentumFlux;
230	>	break;
231	>	case rnemdLx:
232	>	case rnemdLy:
233	>	case rnemdLz:
234	>	hasCorrectFlux = hasAngularMomentumFlux;
235	>	break;
236	>	case rnemdPvector:
237	>	hasCorrectFlux = hasMomentumFluxVector;
238	>	break;
239	>	case rnemdLvector:
240	>	hasCorrectFlux = hasAngularMomentumFluxVector;
241	>	break;
242	>	case rnemdKePx:
243	>	case rnemdKePy:
244	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
245	>	break;
246	>	case rnemdKeLx:
247	>	case rnemdKeLy:
248	>	case rnemdKeLz:
249	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
250	>	break;
251	>	case rnemdKePvector:
252	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
253	>	break;
254	>	case rnemdKeLvector:
255	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
256	>	break;
257	>	default:
258	>	methodFluxMismatch = true;
259	>	break;
260		}
261	<	} else {
262	<	zShift_ = 0.0;
261	>	default:
262	>	break;
263		}
208	–	//cerr << "I shift slabs by " << zShift_ << " Lz\n";
209	–	//shift slabs by half slab width, maybe useful in heterogeneous systems
210	–	//set to 0.0 if not using it; N/A in status output yet
211	–	if (simParams->haveRNEMD_logWidth()) {
212	–	set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
213	–	/*arbitary rnemdLogWidth_, no checking;
214	–	if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
215	–	cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
216	–	cerr << "Automaically set back to default.\n";
217	–	rnemdLogWidth_ = nBins_;
218	–	}*/
219	–	} else {
220	–	set_RNEMD_logWidth(nBins_);
221	–	}
222	–	tempHist_.resize(rnemdLogWidth_, 0.0);
223	–	tempCount_.resize(rnemdLogWidth_, 0);
224	–	pxzHist_.resize(rnemdLogWidth_, 0.0);
225	–	//vxzCount_.resize(rnemdLogWidth_, 0);
226	–	pyzHist_.resize(rnemdLogWidth_, 0.0);
227	–	//vyzCount_.resize(rnemdLogWidth_, 0);
264
265	<	mHist_.resize(rnemdLogWidth_, 0.0);
266	<	xTempHist_.resize(rnemdLogWidth_, 0.0);
267	<	yTempHist_.resize(rnemdLogWidth_, 0.0);
268	<	zTempHist_.resize(rnemdLogWidth_, 0.0);
269	<	xyzTempCount_.resize(rnemdLogWidth_, 0);
270	<	rotTempHist_.resize(rnemdLogWidth_, 0.0);
271	<	rotTempCount_.resize(rnemdLogWidth_, 0);
265	>	if (methodFluxMismatch) {
266	>	sprintf(painCave.errMsg,
267	>	"RNEMD: The current method,\n"
268	>	"\t\t%s\n"
269	>	"\tcannot be used with the current flux type, %s\n",
270	>	methStr.c_str(), fluxStr.c_str());
271	>	painCave.isFatal = 1;
272	>	painCave.severity = OPENMD_ERROR;
273	>	simError();
274	>	}
275	>	if (!hasCorrectFlux) {
276	>	sprintf(painCave.errMsg,
277	>	"RNEMD: The current method, %s, and flux type, %s,\n"
278	>	"\tdid not have the correct flux value specified. Options\n"
279	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
280	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
281	>	methStr.c_str(), fluxStr.c_str());
282	>	painCave.isFatal = 1;
283	>	painCave.severity = OPENMD_ERROR;
284	>	simError();
285	>	}
286
287	<	set_RNEMD_exchange_total(0.0);
288	<	if (simParams->haveRNEMD_targetFlux()) {
289	<	set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
287	>	if (hasKineticFlux) {
288	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
289	>	// into  amu / fs^3:
290	>	kineticFlux_ = rnemdParams->getKineticFlux()
291	>	* PhysicalConstants::energyConvert;
292		} else {
293	<	set_RNEMD_target_flux(0.0);
293	>	kineticFlux_ = 0.0;
294		}
295	<	if (simParams->haveRNEMD_targetJzKE()) {
296	<	set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
295	>	if (hasMomentumFluxVector) {
296	>	std::vector<RealType> mf = rnemdParams->getMomentumFluxVector();
297	>	if (mf.size() != 3) {
298	>	sprintf(painCave.errMsg,
299	>	"RNEMD: Incorrect number of parameters specified for momentumFluxVector.\n"
300	>	"\tthere should be 3 parameters, but %lu were specified.\n",
301	>	mf.size());
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>	momentumFluxVector_.x() = mf[0];
306	>	momentumFluxVector_.y() = mf[1];
307	>	momentumFluxVector_.z() = mf[2];
308		} else {
309	<	set_RNEMD_target_JzKE(0.0);
309	>	momentumFluxVector_ = V3Zero;
310	>	if (hasMomentumFlux) {
311	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
312	>	switch (rnemdFluxType_) {
313	>	case rnemdPx:
314	>	momentumFluxVector_.x() = momentumFlux;
315	>	break;
316	>	case rnemdPy:
317	>	momentumFluxVector_.y() = momentumFlux;
318	>	break;
319	>	case rnemdPz:
320	>	momentumFluxVector_.z() = momentumFlux;
321	>	break;
322	>	case rnemdKePx:
323	>	momentumFluxVector_.x() = momentumFlux;
324	>	break;
325	>	case rnemdKePy:
326	>	momentumFluxVector_.y() = momentumFlux;
327	>	break;
328	>	default:
329	>	break;
330	>	}
331	>	}
332		}
333	<	if (simParams->haveRNEMD_targetJzpx()) {
334	<	set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
333	>	if (hasAngularMomentumFluxVector) {
334	>	std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
335	>	if (amf.size() != 3) {
336	>	sprintf(painCave.errMsg,
337	>	"RNEMD: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
338	>	"\tthere should be 3 parameters, but %lu were specified.\n",
339	>	amf.size());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343	>	angularMomentumFluxVector_.x() = amf[0];
344	>	angularMomentumFluxVector_.y() = amf[1];
345	>	angularMomentumFluxVector_.z() = amf[2];
346		} else {
347	<	set_RNEMD_target_jzpx(0.0);
347	>	angularMomentumFluxVector_ = V3Zero;
348	>	if (hasAngularMomentumFlux) {
349	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
350	>	switch (rnemdFluxType_) {
351	>	case rnemdLx:
352	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
353	>	break;
354	>	case rnemdLy:
355	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
356	>	break;
357	>	case rnemdLz:
358	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
359	>	break;
360	>	case rnemdKeLx:
361	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
362	>	break;
363	>	case rnemdKeLy:
364	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
365	>	break;
366	>	case rnemdKeLz:
367	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
368	>	break;
369	>	default:
370	>	break;
371	>	}
372	>	}
373		}
374	<	jzp_.x() = targetJzpx_;
375	<	njzp_.x() = -targetJzpx_;
376	<	if (simParams->haveRNEMD_targetJzpy()) {
377	<	set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
374	>
375	>	if (hasCoordinateOrigin) {
376	>	std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
377	>	if (co.size() != 3) {
378	>	sprintf(painCave.errMsg,
379	>	"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
380	>	"\tthere should be 3 parameters, but %lu were specified.\n",
381	>	co.size());
382	>	painCave.isFatal = 1;
383	>	simError();
384	>	}
385	>	coordinateOrigin_.x() = co[0];
386	>	coordinateOrigin_.y() = co[1];
387	>	coordinateOrigin_.z() = co[2];
388		} else {
389	<	set_RNEMD_target_jzpy(0.0);
389	>	coordinateOrigin_ = V3Zero;
390		}
391	<	jzp_.y() = targetJzpy_;
392	<	njzp_.y() = -targetJzpy_;
393	<	if (simParams->haveRNEMD_targetJzpz()) {
394	<	set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
395	<	} else {
396	<	set_RNEMD_target_jzpz(0.0);
391	>
392	>	// do some sanity checking
393	>
394	>	int selectionCount = seleMan_.getSelectionCount();
395	>	int nIntegrable = info->getNGlobalIntegrableObjects();
396	>	if (selectionCount > nIntegrable) {
397	>	sprintf(painCave.errMsg,
398	>	"RNEMD: The current objectSelection,\n"
399	>	"\t\t%s\n"
400	>	"\thas resulted in %d selected objects.  However,\n"
401	>	"\tthe total number of integrable objects in the system\n"
402	>	"\tis only %d.  This is almost certainly not what you want\n"
403	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
404	>	"\tselector in the selection script!\n",
405	>	rnemdObjectSelection_.c_str(),
406	>	selectionCount, nIntegrable);
407	>	painCave.isFatal = 0;
408	>	painCave.severity = OPENMD_WARNING;
409	>	simError();
410	>	}
411	>
412	>	areaAccumulator_ = new Accumulator();
413	>
414	>	nBins_ = rnemdParams->getOutputBins();
415	>	binWidth_ = rnemdParams->getOutputBinWidth();
416	>
417	>	data_.resize(RNEMD::ENDINDEX);
418	>	OutputData z;
419	>	z.units =  "Angstroms";
420	>	z.title =  "Z";
421	>	z.dataType = "RealType";
422	>	z.accumulator.reserve(nBins_);
423	>	for (int i = 0; i < nBins_; i++)
424	>	z.accumulator.push_back( new Accumulator() );
425	>	data_[Z] = z;
426	>	outputMap_["Z"] =  Z;
427	>
428	>	OutputData r;
429	>	r.units =  "Angstroms";
430	>	r.title =  "R";
431	>	r.dataType = "RealType";
432	>	r.accumulator.reserve(nBins_);
433	>	for (int i = 0; i < nBins_; i++)
434	>	r.accumulator.push_back( new Accumulator() );
435	>	data_[R] = r;
436	>	outputMap_["R"] =  R;
437	>
438	>	OutputData temperature;
439	>	temperature.units =  "K";
440	>	temperature.title =  "Temperature";
441	>	temperature.dataType = "RealType";
442	>	temperature.accumulator.reserve(nBins_);
443	>	for (int i = 0; i < nBins_; i++)
444	>	temperature.accumulator.push_back( new Accumulator() );
445	>	data_[TEMPERATURE] = temperature;
446	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
447	>
448	>	OutputData velocity;
449	>	velocity.units = "angstroms/fs";
450	>	velocity.title =  "Velocity";
451	>	velocity.dataType = "Vector3d";
452	>	velocity.accumulator.reserve(nBins_);
453	>	for (int i = 0; i < nBins_; i++)
454	>	velocity.accumulator.push_back( new VectorAccumulator() );
455	>	data_[VELOCITY] = velocity;
456	>	outputMap_["VELOCITY"] = VELOCITY;
457	>
458	>	OutputData angularVelocity;
459	>	angularVelocity.units = "angstroms^2/fs";
460	>	angularVelocity.title =  "AngularVelocity";
461	>	angularVelocity.dataType = "Vector3d";
462	>	angularVelocity.accumulator.reserve(nBins_);
463	>	for (int i = 0; i < nBins_; i++)
464	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
465	>	data_[ANGULARVELOCITY] = angularVelocity;
466	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
467	>
468	>	OutputData density;
469	>	density.units =  "g cm^-3";
470	>	density.title =  "Density";
471	>	density.dataType = "RealType";
472	>	density.accumulator.reserve(nBins_);
473	>	for (int i = 0; i < nBins_; i++)
474	>	density.accumulator.push_back( new Accumulator() );
475	>	data_[DENSITY] = density;
476	>	outputMap_["DENSITY"] =  DENSITY;
477	>
478	>	if (hasOutputFields) {
479	>	parseOutputFileFormat(rnemdParams->getOutputFields());
480	>	} else {
481	>	if (usePeriodicBoundaryConditions_)
482	>	outputMask_.set(Z);
483	>	else
484	>	outputMask_.set(R);
485	>	switch (rnemdFluxType_) {
486	>	case rnemdKE:
487	>	case rnemdRotKE:
488	>	case rnemdFullKE:
489	>	outputMask_.set(TEMPERATURE);
490	>	break;
491	>	case rnemdPx:
492	>	case rnemdPy:
493	>	outputMask_.set(VELOCITY);
494	>	break;
495	>	case rnemdPz:
496	>	case rnemdPvector:
497	>	outputMask_.set(VELOCITY);
498	>	outputMask_.set(DENSITY);
499	>	break;
500	>	case rnemdLx:
501	>	case rnemdLy:
502	>	case rnemdLz:
503	>	case rnemdLvector:
504	>	outputMask_.set(ANGULARVELOCITY);
505	>	break;
506	>	case rnemdKeLx:
507	>	case rnemdKeLy:
508	>	case rnemdKeLz:
509	>	case rnemdKeLvector:
510	>	outputMask_.set(TEMPERATURE);
511	>	outputMask_.set(ANGULARVELOCITY);
512	>	break;
513	>	case rnemdKePx:
514	>	case rnemdKePy:
515	>	outputMask_.set(TEMPERATURE);
516	>	outputMask_.set(VELOCITY);
517	>	break;
518	>	case rnemdKePvector:
519	>	outputMask_.set(TEMPERATURE);
520	>	outputMask_.set(VELOCITY);
521	>	outputMask_.set(DENSITY);
522	>	break;
523	>	default:
524	>	break;
525	>	}
526		}
527	<	jzp_.z() = targetJzpz_;
528	<	njzp_.z() = -targetJzpz_;
529	<
530	<	#ifndef IS_MPI
531	<	if (simParams->haveSeed()) {
532	<	seedValue = simParams->getSeed();
533	<	randNumGen_ = new SeqRandNumGen(seedValue);
534	<	}else {
535	<	randNumGen_ = new SeqRandNumGen();
536	<	}
537	<	#else
538	<	if (simParams->haveSeed()) {
539	<	seedValue = simParams->getSeed();
540	<	randNumGen_ = new ParallelRandNumGen(seedValue);
541	<	}else {
542	<	randNumGen_ = new ParallelRandNumGen();
543	<	}
544	<	#endif
527	>
528	>	if (hasOutputFileName) {
529	>	rnemdFileName_ = rnemdParams->getOutputFileName();
530	>	} else {
531	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
532	>	}
533	>
534	>	exchangeTime_ = rnemdParams->getExchangeTime();
535	>
536	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
537	>	// total exchange sums are zeroed out at the beginning:
538	>
539	>	kineticExchange_ = 0.0;
540	>	momentumExchange_ = V3Zero;
541	>	angularMomentumExchange_ = V3Zero;
542	>
543	>	std::ostringstream selectionAstream;
544	>	std::ostringstream selectionBstream;
545	>
546	>	if (hasSelectionA_) {
547	>	selectionA_ = rnemdParams->getSelectionA();
548	>	} else {
549	>	if (usePeriodicBoundaryConditions_) {
550	>	Mat3x3d hmat = currentSnap_->getHmat();
551	>
552	>	if (hasSlabWidth)
553	>	slabWidth_ = rnemdParams->getSlabWidth();
554	>	else
555	>	slabWidth_ = hmat(2,2) / 10.0;
556	>
557	>	if (hasSlabACenter)
558	>	slabACenter_ = rnemdParams->getSlabACenter();
559	>	else
560	>	slabACenter_ = 0.0;
561	>
562	>	selectionAstream << "select wrappedz > "
563	>	<< slabACenter_ - 0.5*slabWidth_
564	>	<<  " && wrappedz < "
565	>	<< slabACenter_ + 0.5*slabWidth_;
566	>	selectionA_ = selectionAstream.str();
567	>	} else {
568	>	if (hasSphereARadius)
569	>	sphereARadius_ = rnemdParams->getSphereARadius();
570	>	else {
571	>	// use an initial guess to the size of the inner slab to be 1/10 the
572	>	// radius of an approximately spherical hull:
573	>	Thermo thermo(info);
574	>	RealType hVol = thermo.getHullVolume();
575	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
576	>	}
577	>	selectionAstream << "select r < " << sphereARadius_;
578	>	selectionA_ = selectionAstream.str();
579	>	}
580	>	}
581	>
582	>	if (hasSelectionB_) {
583	>	selectionB_ = rnemdParams->getSelectionB();
584	>
585	>	} else {
586	>	if (usePeriodicBoundaryConditions_) {
587	>	Mat3x3d hmat = currentSnap_->getHmat();
588	>
589	>	if (hasSlabWidth)
590	>	slabWidth_ = rnemdParams->getSlabWidth();
591	>	else
592	>	slabWidth_ = hmat(2,2) / 10.0;
593	>
594	>	if (hasSlabBCenter)
595	>	slabBCenter_ = rnemdParams->getSlabBCenter();
596	>	else
597	>	slabBCenter_ = hmat(2,2) / 2.0;
598	>
599	>	selectionBstream << "select wrappedz > "
600	>	<< slabBCenter_ - 0.5*slabWidth_
601	>	<<  " && wrappedz < "
602	>	<< slabBCenter_ + 0.5*slabWidth_;
603	>	selectionB_ = selectionBstream.str();
604	>	} else {
605	>	if (hasSphereBRadius_) {
606	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
607	>	selectionBstream << "select r > " << sphereBRadius_;
608	>	selectionB_ = selectionBstream.str();
609	>	} else {
610	>	selectionB_ = "select hull";
611	>	BisHull_ = true;
612	>	hasSelectionB_ = true;
613	>	}
614	>	}
615	>	}
616	>
617	>
618	>	// object evaluator:
619	>	evaluator_.loadScriptString(rnemdObjectSelection_);
620	>	seleMan_.setSelectionSet(evaluator_.evaluate());
621	>	evaluatorA_.loadScriptString(selectionA_);
622	>	evaluatorB_.loadScriptString(selectionB_);
623	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
624	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
625	>	commonA_ = seleManA_ & seleMan_;
626	>	commonB_ = seleManB_ & seleMan_;
627		}
628
287	–	RNEMD::~RNEMD() {
288	–	delete randNumGen_;
629
630	+	RNEMD::~RNEMD() {
631	+	if (!doRNEMD_) return;
632		#ifdef IS_MPI
633		if (worldRank == 0) {
634		#endif
293	–
294	–	sprintf(painCave.errMsg,
295	–	"RNEMD: total failed trials: %d\n",
296	–	failTrialCount_);
297	–	painCave.isFatal = 0;
298	–	painCave.severity = OPENMD_INFO;
299	–	simError();
635
636	<	if (outputTemp_) tempLog_.close();
302	<	if (outputVx_)   vxzLog_.close();
303	<	if (outputVy_)   vyzLog_.close();
636	>	writeOutputFile();
637
638	<	if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale ||
639	<	rnemdType_ == rnemdPyScale) {
307	<	sprintf(painCave.errMsg,
308	<	"RNEMD: total root-checking warnings: %d\n",
309	<	failRootCount_);
310	<	painCave.isFatal = 0;
311	<	painCave.severity = OPENMD_INFO;
312	<	simError();
313	<	}
314	<	if (output3DTemp_) {
315	<	xTempLog_.close();
316	<	yTempLog_.close();
317	<	zTempLog_.close();
318	<	}
319	<	if (outputRotTemp_) rotTempLog_.close();
320	<
638	>	rnemdFile_.close();
639	>
640		#ifdef IS_MPI
641		}
642		#endif
643	+
644	+	// delete all of the objects we created:
645	+	delete areaAccumulator_;
646	+	data_.clear();
647		}
648	+
649	+	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
650	+	if (!doRNEMD_) return;
651	+	int selei;
652	+	int selej;
653
326	–	void RNEMD::doSwap() {
327	–
654		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
655		Mat3x3d hmat = currentSnap_->getHmat();
656
331	–	seleMan_.setSelectionSet(evaluator_.evaluate());
332	–
333	–	int selei;
657		StuntDouble* sd;
335	–	int idx;
658
659	<	RealType min_val;
660	<	bool min_found = false;
661	<	StuntDouble* min_sd;
659	>	RealType min_val(0.0);
660	>	int min_found = 0;
661	>	StuntDouble* min_sd = NULL;
662
663	<	RealType max_val;
664	<	bool max_found = false;
665	<	StuntDouble* max_sd;
344	<
345	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
346	<	sd = seleMan_.nextSelected(selei)) {
663	>	RealType max_val(0.0);
664	>	int max_found = 0;
665	>	StuntDouble* max_sd = NULL;
666
667	<	idx = sd->getLocalIndex();
667	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
668	>	sd = seleManA_.nextSelected(selei)) {
669
670		Vector3d pos = sd->getPos();
671	<
671	>
672		// wrap the stuntdouble's position back into the box:
673	<
673	>
674		if (usePeriodicBoundaryConditions_)
675		currentSnap_->wrapVector(pos);
676	<
677	<	// which bin is this stuntdouble in?
678	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
679	<
680	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
681	<
682	<
363	<	// if we're in bin 0 or the middleBin
364	<	if (binNo == 0 || binNo == midBin_) {
676	>
677	>	RealType mass = sd->getMass();
678	>	Vector3d vel = sd->getVel();
679	>	RealType value(0.0);
680	>
681	>	switch(rnemdFluxType_) {
682	>	case rnemdKE :
683
684	<	RealType mass = sd->getMass();
685	<	Vector3d vel = sd->getVel();
686	<	RealType value;
687	<
688	<	switch(rnemdType_) {
371	<	case rnemdKineticSwap :
684	>	value = mass * vel.lengthSquare();
685	>
686	>	if (sd->isDirectional()) {
687	>	Vector3d angMom = sd->getJ();
688	>	Mat3x3d I = sd->getI();
689
690	<	value = mass * vel.lengthSquare();
691	<
692	<	if (sd->isDirectional()) {
693	<	Vector3d angMom = sd->getJ();
694	<	Mat3x3d I = sd->getI();
695	<
696	<	if (sd->isLinear()) {
697	<	int i = sd->linearAxis();
698	<	int j = (i + 1) % 3;
699	<	int k = (i + 2) % 3;
700	<	value += angMom[j] * angMom[j] / I(j, j) +
701	<	angMom[k] * angMom[k] / I(k, k);
702	<	} else {
703	<	value += angMom[0]*angMom[0]/I(0, 0)
704	<	+ angMom[1]*angMom[1]/I(1, 1)
705	<	+ angMom[2]*angMom[2]/I(2, 2);
706	<	}
707	<	} //angular momenta exchange enabled
708	<	//energyConvert temporarily disabled
709	<	//make exchangeSum_ comparable between swap & scale
710	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
711	<	value *= 0.5;
712	<	break;
713	<	case rnemdPx :
714	<	value = mass * vel[0];
715	<	break;
716	<	case rnemdPy :
717	<	value = mass * vel[1];
718	<	break;
719	<	case rnemdPz :
720	<	value = mass * vel[2];
721	<	break;
722	<	default :
723	<	break;
690	>	if (sd->isLinear()) {
691	>	int i = sd->linearAxis();
692	>	int j = (i + 1) % 3;
693	>	int k = (i + 2) % 3;
694	>	value += angMom[j] * angMom[j] / I(j, j) +
695	>	angMom[k] * angMom[k] / I(k, k);
696	>	} else {
697	>	value += angMom[0]*angMom[0]/I(0, 0)
698	>	+ angMom[1]*angMom[1]/I(1, 1)
699	>	+ angMom[2]*angMom[2]/I(2, 2);
700	>	}
701	>	} //angular momenta exchange enabled
702	>	value *= 0.5;
703	>	break;
704	>	case rnemdPx :
705	>	value = mass * vel[0];
706	>	break;
707	>	case rnemdPy :
708	>	value = mass * vel[1];
709	>	break;
710	>	case rnemdPz :
711	>	value = mass * vel[2];
712	>	break;
713	>	default :
714	>	break;
715	>	}
716	>	if (!max_found) {
717	>	max_val = value;
718	>	max_sd = sd;
719	>	max_found = 1;
720	>	} else {
721	>	if (max_val < value) {
722	>	max_val = value;
723	>	max_sd = sd;
724		}
725	+	}
726	+	}
727
728	<	if (binNo == 0) {
729	<	if (!min_found) {
730	<	min_val = value;
731	<	min_sd = sd;
732	<	min_found = true;
733	<	} else {
734	<	if (min_val > value) {
735	<	min_val = value;
736	<	min_sd = sd;
737	<	}
738	<	}
739	<	} else { //midBin_
740	<	if (!max_found) {
741	<	max_val = value;
742	<	max_sd = sd;
743	<	max_found = true;
744	<	} else {
745	<	if (max_val < value) {
746	<	max_val = value;
747	<	max_sd = sd;
748	<	}
749	<	}
750	<	}
728	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
729	>	sd = seleManB_.nextSelected(selej)) {
730	>
731	>	Vector3d pos = sd->getPos();
732	>
733	>	// wrap the stuntdouble's position back into the box:
734	>
735	>	if (usePeriodicBoundaryConditions_)
736	>	currentSnap_->wrapVector(pos);
737	>
738	>	RealType mass = sd->getMass();
739	>	Vector3d vel = sd->getVel();
740	>	RealType value(0.0);
741	>
742	>	switch(rnemdFluxType_) {
743	>	case rnemdKE :
744	>
745	>	value = mass * vel.lengthSquare();
746	>
747	>	if (sd->isDirectional()) {
748	>	Vector3d angMom = sd->getJ();
749	>	Mat3x3d I = sd->getI();
750	>
751	>	if (sd->isLinear()) {
752	>	int i = sd->linearAxis();
753	>	int j = (i + 1) % 3;
754	>	int k = (i + 2) % 3;
755	>	value += angMom[j] * angMom[j] / I(j, j) +
756	>	angMom[k] * angMom[k] / I(k, k);
757	>	} else {
758	>	value += angMom[0]*angMom[0]/I(0, 0)
759	>	+ angMom[1]*angMom[1]/I(1, 1)
760	>	+ angMom[2]*angMom[2]/I(2, 2);
761	>	}
762	>	} //angular momenta exchange enabled
763	>	value *= 0.5;
764	>	break;
765	>	case rnemdPx :
766	>	value = mass * vel[0];
767	>	break;
768	>	case rnemdPy :
769	>	value = mass * vel[1];
770	>	break;
771	>	case rnemdPz :
772	>	value = mass * vel[2];
773	>	break;
774	>	default :
775	>	break;
776		}
777	+
778	+	if (!min_found) {
779	+	min_val = value;
780	+	min_sd = sd;
781	+	min_found = 1;
782	+	} else {
783	+	if (min_val > value) {
784	+	min_val = value;
785	+	min_sd = sd;
786	+	}
787	+	}
788		}
789	+
790	+	#ifdef IS_MPI
791	+	int worldRank;
792	+	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
793	+
794	+	int my_min_found = min_found;
795	+	int my_max_found = max_found;
796
435	–	#ifdef IS_MPI
436	–	int nProc, worldRank;
437	–
438	–	nProc = MPI::COMM_WORLD.Get_size();
439	–	worldRank = MPI::COMM_WORLD.Get_rank();
440	–
441	–	bool my_min_found = min_found;
442	–	bool my_max_found = max_found;
443	–
797		// Even if we didn't find a minimum, did someone else?
798	<	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
798	>	MPI_Allreduce(&my_min_found, &min_found, 1, MPI_INT, MPI_LOR,
799	>	MPI_COMM_WORLD);
800		// Even if we didn't find a maximum, did someone else?
801	<	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
801	>	MPI_Allreduce(&my_max_found, &max_found, 1, MPI_INT, MPI_LOR,
802	>	MPI_COMM_WORLD);
803		#endif
804
805		if (max_found && min_found) {
#	Line 454 | Line 809 | namespace OpenMD {
809		RealType val;
810		int rank;
811		} max_vals, min_vals;
812	<
812	>
813		if (my_min_found) {
814		min_vals.val = min_val;
815		} else {
#	Line 463 | Line 818 | namespace OpenMD {
818		min_vals.rank = worldRank;
819
820		// Who had the minimum?
821	<	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
822	<	1, MPI::REALTYPE_INT, MPI::MINLOC);
821	>	MPI_Allreduce(&min_vals, &min_vals,
822	>	1, MPI_REALTYPE_INT, MPI_MINLOC, MPI_COMM_WORLD);
823		min_val = min_vals.val;
824
825		if (my_max_found) {
#	Line 475 | Line 830 | namespace OpenMD {
830		max_vals.rank = worldRank;
831
832		// Who had the maximum?
833	<	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
834	<	1, MPI::REALTYPE_INT, MPI::MAXLOC);
833	>	MPI_Allreduce(&max_vals, &max_vals,
834	>	1, MPI_REALTYPE_INT, MPI_MAXLOC, MPI_COMM_WORLD);
835		max_val = max_vals.val;
836		#endif
837
#	Line 492 | Line 847 | namespace OpenMD {
847		Vector3d max_vel = max_sd->getVel();
848		RealType temp_vel;
849
850	<	switch(rnemdType_) {
851	<	case rnemdKineticSwap :
850	>	switch(rnemdFluxType_) {
851	>	case rnemdKE :
852		min_sd->setVel(max_vel);
853		max_sd->setVel(min_vel);
854		if (min_sd->isDirectional() && max_sd->isDirectional()) {
#	Line 536 | Line 891 | namespace OpenMD {
891
892		Vector3d min_vel;
893		Vector3d max_vel = max_sd->getVel();
894	<	MPI::Status status;
894	>	MPI_Status status;
895
896		// point-to-point swap of the velocity vector
897	<	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
898	<	min_vals.rank, 0,
899	<	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
900	<	min_vals.rank, 0, status);
897	>	MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
898	>	min_vals.rank, 0,
899	>	min_vel.getArrayPointer(), 3, MPI_REALTYPE,
900	>	min_vals.rank, 0, MPI_COMM_WORLD, &status);
901
902	<	switch(rnemdType_) {
903	<	case rnemdKineticSwap :
902	>	switch(rnemdFluxType_) {
903	>	case rnemdKE :
904		max_sd->setVel(min_vel);
905		//angular momenta exchange enabled
906		if (max_sd->isDirectional()) {
#	Line 553 | Line 908 | namespace OpenMD {
908		Vector3d max_angMom = max_sd->getJ();
909
910		// point-to-point swap of the angular momentum vector
911	<	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
912	<	MPI::REALTYPE, min_vals.rank, 1,
913	<	min_angMom.getArrayPointer(), 3,
914	<	MPI::REALTYPE, min_vals.rank, 1,
915	<	status);
911	>	MPI_Sendrecv(max_angMom.getArrayPointer(), 3,
912	>	MPI_REALTYPE, min_vals.rank, 1,
913	>	min_angMom.getArrayPointer(), 3,
914	>	MPI_REALTYPE, min_vals.rank, 1,
915	>	MPI_COMM_WORLD, &status);
916
917		max_sd->setJ(min_angMom);
918		}
#	Line 582 | Line 937 | namespace OpenMD {
937
938		Vector3d max_vel;
939		Vector3d min_vel = min_sd->getVel();
940	<	MPI::Status status;
940	>	MPI_Status status;
941
942		// point-to-point swap of the velocity vector
943	<	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
944	<	max_vals.rank, 0,
945	<	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
946	<	max_vals.rank, 0, status);
943	>	MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
944	>	max_vals.rank, 0,
945	>	max_vel.getArrayPointer(), 3, MPI_REALTYPE,
946	>	max_vals.rank, 0, MPI_COMM_WORLD, &status);
947
948	<	switch(rnemdType_) {
949	<	case rnemdKineticSwap :
948	>	switch(rnemdFluxType_) {
949	>	case rnemdKE :
950		min_sd->setVel(max_vel);
951		//angular momenta exchange enabled
952		if (min_sd->isDirectional()) {
#	Line 599 | Line 954 | namespace OpenMD {
954		Vector3d max_angMom;
955
956		// point-to-point swap of the angular momentum vector
957	<	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
958	<	MPI::REALTYPE, max_vals.rank, 1,
959	<	max_angMom.getArrayPointer(), 3,
960	<	MPI::REALTYPE, max_vals.rank, 1,
961	<	status);
957	>	MPI_Sendrecv(min_angMom.getArrayPointer(), 3,
958	>	MPI_REALTYPE, max_vals.rank, 1,
959	>	max_angMom.getArrayPointer(), 3,
960	>	MPI_REALTYPE, max_vals.rank, 1,
961	>	MPI_COMM_WORLD, &status);
962
963		min_sd->setJ(max_angMom);
964		}
#	Line 625 | Line 980 | namespace OpenMD {
980		}
981		}
982		#endif
983	<	exchangeSum_ += max_val - min_val;
983	>
984	>	switch(rnemdFluxType_) {
985	>	case rnemdKE:
986	>	kineticExchange_ += max_val - min_val;
987	>	break;
988	>	case rnemdPx:
989	>	momentumExchange_.x() += max_val - min_val;
990	>	break;
991	>	case rnemdPy:
992	>	momentumExchange_.y() += max_val - min_val;
993	>	break;
994	>	case rnemdPz:
995	>	momentumExchange_.z() += max_val - min_val;
996	>	break;
997	>	default:
998	>	break;
999	>	}
1000		} else {
1001		sprintf(painCave.errMsg,
1002	<	"RNEMD: exchange NOT performed because min_val > max_val\n");
1002	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
1003		painCave.isFatal = 0;
1004		painCave.severity = OPENMD_INFO;
1005		simError();
#	Line 636 | Line 1007 | namespace OpenMD {
1007		}
1008		} else {
1009		sprintf(painCave.errMsg,
1010	<	"RNEMD: exchange NOT performed because selected object\n"
1011	<	"\tnot present in at least one of the two slabs.\n");
1010	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
1011	>	"\twas not present in at least one of the two slabs.\n");
1012		painCave.isFatal = 0;
1013		painCave.severity = OPENMD_INFO;
1014		simError();
1015		failTrialCount_++;
1016	<	}
646	<
1016	>	}
1017		}
1018
1019	<	void RNEMD::doScale() {
1019	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
1020	>	if (!doRNEMD_) return;
1021	>	int selei;
1022	>	int selej;
1023
1024		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1025		Mat3x3d hmat = currentSnap_->getHmat();
1026
654	–	seleMan_.setSelectionSet(evaluator_.evaluate());
655	–
656	–	int selei;
1027		StuntDouble* sd;
658	–	int idx;
1028
1029		vector<StuntDouble*> hotBin, coldBin;
1030
#	Line 674 | Line 1043 | namespace OpenMD {
1043		RealType Kcz = 0.0;
1044		RealType Kcw = 0.0;
1045
1046	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1047	<	sd = seleMan_.nextSelected(selei)) {
1046	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1047	>	sd = smanA.nextSelected(selei)) {
1048
680	–	idx = sd->getLocalIndex();
681	–
1049		Vector3d pos = sd->getPos();
1050	<
1050	>
1051		// wrap the stuntdouble's position back into the box:
1052	<
1052	>
1053		if (usePeriodicBoundaryConditions_)
1054		currentSnap_->wrapVector(pos);
1055	+
1056	+
1057	+	RealType mass = sd->getMass();
1058	+	Vector3d vel = sd->getVel();
1059	+
1060	+	hotBin.push_back(sd);
1061	+	Phx += mass * vel.x();
1062	+	Phy += mass * vel.y();
1063	+	Phz += mass * vel.z();
1064	+	Khx += mass * vel.x() * vel.x();
1065	+	Khy += mass * vel.y() * vel.y();
1066	+	Khz += mass * vel.z() * vel.z();
1067	+	if (sd->isDirectional()) {
1068	+	Vector3d angMom = sd->getJ();
1069	+	Mat3x3d I = sd->getI();
1070	+	if (sd->isLinear()) {
1071	+	int i = sd->linearAxis();
1072	+	int j = (i + 1) % 3;
1073	+	int k = (i + 2) % 3;
1074	+	Khw += angMom[j] * angMom[j] / I(j, j) +
1075	+	angMom[k] * angMom[k] / I(k, k);
1076	+	} else {
1077	+	Khw += angMom[0]*angMom[0]/I(0, 0)
1078	+	+ angMom[1]*angMom[1]/I(1, 1)
1079	+	+ angMom[2]*angMom[2]/I(2, 2);
1080	+	}
1081	+	}
1082	+	}
1083	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1084	+	sd = smanB.nextSelected(selej)) {
1085	+	Vector3d pos = sd->getPos();
1086	+
1087	+	// wrap the stuntdouble's position back into the box:
1088	+
1089	+	if (usePeriodicBoundaryConditions_)
1090	+	currentSnap_->wrapVector(pos);
1091	+
1092	+	RealType mass = sd->getMass();
1093	+	Vector3d vel = sd->getVel();
1094
1095	<	// which bin is this stuntdouble in?
1096	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1097	<
1098	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1099	<
1100	<	// if we're in bin 0 or the middleBin
1101	<	if (binNo == 0 || binNo == midBin_) {
1102	<
1103	<	RealType mass = sd->getMass();
1104	<	Vector3d vel = sd->getVel();
1105	<
1106	<	if (binNo == 0) {
1107	<	hotBin.push_back(sd);
1108	<	Phx += mass * vel.x();
1109	<	Phy += mass * vel.y();
1110	<	Phz += mass * vel.z();
1111	<	Khx += mass * vel.x() * vel.x();
1112	<	Khy += mass * vel.y() * vel.y();
1113	<	Khz += mass * vel.z() * vel.z();
1114	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
1115	<	if (sd->isDirectional()) {
710	<	Vector3d angMom = sd->getJ();
711	<	Mat3x3d I = sd->getI();
712	<	if (sd->isLinear()) {
713	<	int i = sd->linearAxis();
714	<	int j = (i + 1) % 3;
715	<	int k = (i + 2) % 3;
716	<	Khw += angMom[j] * angMom[j] / I(j, j) +
717	<	angMom[k] * angMom[k] / I(k, k);
718	<	} else {
719	<	Khw += angMom[0]*angMom[0]/I(0, 0)
720	<	+ angMom[1]*angMom[1]/I(1, 1)
721	<	+ angMom[2]*angMom[2]/I(2, 2);
722	<	}
723	<	}
724	<	//}
725	<	} else { //midBin_
726	<	coldBin.push_back(sd);
727	<	Pcx += mass * vel.x();
728	<	Pcy += mass * vel.y();
729	<	Pcz += mass * vel.z();
730	<	Kcx += mass * vel.x() * vel.x();
731	<	Kcy += mass * vel.y() * vel.y();
732	<	Kcz += mass * vel.z() * vel.z();
733	<	//if (rnemdType_ == rnemdKineticScaleVAM) {
734	<	if (sd->isDirectional()) {
735	<	Vector3d angMom = sd->getJ();
736	<	Mat3x3d I = sd->getI();
737	<	if (sd->isLinear()) {
738	<	int i = sd->linearAxis();
739	<	int j = (i + 1) % 3;
740	<	int k = (i + 2) % 3;
741	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
742	<	angMom[k] * angMom[k] / I(k, k);
743	<	} else {
744	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
745	<	+ angMom[1]*angMom[1]/I(1, 1)
746	<	+ angMom[2]*angMom[2]/I(2, 2);
747	<	}
748	<	}
749	<	//}
750	<	}
1095	>	coldBin.push_back(sd);
1096	>	Pcx += mass * vel.x();
1097	>	Pcy += mass * vel.y();
1098	>	Pcz += mass * vel.z();
1099	>	Kcx += mass * vel.x() * vel.x();
1100	>	Kcy += mass * vel.y() * vel.y();
1101	>	Kcz += mass * vel.z() * vel.z();
1102	>	if (sd->isDirectional()) {
1103	>	Vector3d angMom = sd->getJ();
1104	>	Mat3x3d I = sd->getI();
1105	>	if (sd->isLinear()) {
1106	>	int i = sd->linearAxis();
1107	>	int j = (i + 1) % 3;
1108	>	int k = (i + 2) % 3;
1109	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1110	>	angMom[k] * angMom[k] / I(k, k);
1111	>	} else {
1112	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1113	>	+ angMom[1]*angMom[1]/I(1, 1)
1114	>	+ angMom[2]*angMom[2]/I(2, 2);
1115	>	}
1116		}
1117		}
1118
#	Line 760 | Line 1125 | namespace OpenMD {
1125		Kcz *= 0.5;
1126		Kcw *= 0.5;
1127
763	–	std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz
764	–	<< "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy
765	–	<< "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n";
766	–	std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz
767	–	<< "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n";
768	–
1128		#ifdef IS_MPI
1129	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1130	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1131	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1132	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1133	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1134	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1129	>	MPI_Allreduce(MPI_IN_PLACE, &Phx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1130	>	MPI_Allreduce(MPI_IN_PLACE, &Phy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1131	>	MPI_Allreduce(MPI_IN_PLACE, &Phz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1132	>	MPI_Allreduce(MPI_IN_PLACE, &Pcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1133	>	MPI_Allreduce(MPI_IN_PLACE, &Pcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1134	>	MPI_Allreduce(MPI_IN_PLACE, &Pcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1135
1136	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1137	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1138	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1139	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1136	>	MPI_Allreduce(MPI_IN_PLACE, &Khx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1137	>	MPI_Allreduce(MPI_IN_PLACE, &Khy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1138	>	MPI_Allreduce(MPI_IN_PLACE, &Khz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1139	>	MPI_Allreduce(MPI_IN_PLACE, &Khw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1140
1141	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1142	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1143	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1144	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1141	>	MPI_Allreduce(MPI_IN_PLACE, &Kcx, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1142	>	MPI_Allreduce(MPI_IN_PLACE, &Kcy, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1143	>	MPI_Allreduce(MPI_IN_PLACE, &Kcz, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1144	>	MPI_Allreduce(MPI_IN_PLACE, &Kcw, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1145		#endif
1146
1147		//solve coldBin coeff's first
1148		RealType px = Pcx / Phx;
1149		RealType py = Pcy / Phy;
1150		RealType pz = Pcz / Phz;
1151	<	RealType c, x, y, z;
1151	>	RealType c(0.0), x(0.0), y(0.0), z(0.0);
1152		bool successfulScale = false;
1153	<	if ((rnemdType_ == rnemdKineticScaleVAM) ||
1154	<	(rnemdType_ == rnemdKineticScaleAM)) {
1153	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1154	>	(rnemdFluxType_ == rnemdRotKE)) {
1155		//may need sanity check Khw & Kcw > 0
1156
1157	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1158	<	c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw);
1157	>	if (rnemdFluxType_ == rnemdFullKE) {
1158	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1159		} else {
1160	<	c = 1.0 - targetFlux_ / Kcw;
1160	>	c = 1.0 - kineticTarget_ / Kcw;
1161		}
1162
1163		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1164		c = sqrt(c);
1165	<	std::cerr << "cold slab scaling coefficient: " << c << endl;
807	<	//now convert to hotBin coefficient
1165	>
1166		RealType w = 0.0;
1167	<	if (rnemdType_ ==  rnemdKineticScaleVAM) {
1167	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1168		x = 1.0 + px * (1.0 - c);
1169		y = 1.0 + py * (1.0 - c);
1170		z = 1.0 + pz * (1.0 - c);
#	Line 820 | Line 1178 | namespace OpenMD {
1178		*/
1179		if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1180		(fabs(z - 1.0) < 0.1)) {
1181	<	w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1181	>	w = 1.0 + (kineticTarget_
1182	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1183		+ Khz * (1.0 - z * z)) / Khw;
1184		}//no need to calculate w if x, y or z is out of range
1185		} else {
1186	<	w = 1.0 + targetFlux_ / Khw;
1186	>	w = 1.0 + kineticTarget_ / Khw;
1187		}
1188		if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1189		//if w is in the right range, so should be x, y, z.
1190		vector<StuntDouble*>::iterator sdi;
1191		Vector3d vel;
1192	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1193	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1192	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1193	>	if (rnemdFluxType_ == rnemdFullKE) {
1194		vel = (*sdi)->getVel() * c;
836	–	//vel.x() *= c;
837	–	//vel.y() *= c;
838	–	//vel.z() *= c;
1195		(*sdi)->setVel(vel);
1196		}
1197		if ((*sdi)->isDirectional()) {
1198		Vector3d angMom = (*sdi)->getJ() * c;
843	–	//angMom[0] *= c;
844	–	//angMom[1] *= c;
845	–	//angMom[2] *= c;
1199		(*sdi)->setJ(angMom);
1200		}
1201		}
1202		w = sqrt(w);
1203	<	std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
1204	<	<< "\twh= " << w << endl;
852	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
853	<	if (rnemdType_ == rnemdKineticScaleVAM) {
1203	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1204	>	if (rnemdFluxType_ == rnemdFullKE) {
1205		vel = (*sdi)->getVel();
1206		vel.x() *= x;
1207		vel.y() *= y;
#	Line 859 | Line 1210 | namespace OpenMD {
1210		}
1211		if ((*sdi)->isDirectional()) {
1212		Vector3d angMom = (*sdi)->getJ() * w;
862	–	//angMom[0] *= w;
863	–	//angMom[1] *= w;
864	–	//angMom[2] *= w;
1213		(*sdi)->setJ(angMom);
1214		}
1215		}
1216		successfulScale = true;
1217	<	exchangeSum_ += targetFlux_;
1217	>	kineticExchange_ += kineticTarget_;
1218		}
1219		}
1220		} else {
1221	<	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1222	<	switch(rnemdType_) {
1223	<	case rnemdKineticScale :
1221	>	RealType a000(0.0), a110(0.0), c0(0.0);
1222	>	RealType a001(0.0), a111(0.0), b01(0.0), b11(0.0), c1(0.0);
1223	>	switch(rnemdFluxType_) {
1224	>	case rnemdKE :
1225		/* used hotBin coeff's & only scale x & y dimensions
1226		RealType px = Phx / Pcx;
1227		RealType py = Phy / Pcy;
1228		a110 = Khy;
1229	<	c0 = - Khx - Khy - targetFlux_;
1229	>	c0 = - Khx - Khy - kineticTarget_;
1230		a000 = Khx;
1231		a111 = Kcy * py * py;
1232		b11 = -2.0 * Kcy * py * (1.0 + py);
1233	<	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_;
1233	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1234		b01 = -2.0 * Kcx * px * (1.0 + px);
1235		a001 = Kcx * px * px;
1236		*/
1237		//scale all three dimensions, let c_x = c_y
1238		a000 = Kcx + Kcy;
1239		a110 = Kcz;
1240	<	c0 = targetFlux_ - Kcx - Kcy - Kcz;
1240	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1241		a001 = Khx * px * px + Khy * py * py;
1242		a111 = Khz * pz * pz;
1243		b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1244		b11 = -2.0 * Khz * pz * (1.0 + pz);
1245		c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1246	<	+ Khz * pz * (2.0 + pz) - targetFlux_;
1246	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1247		break;
1248	<	case rnemdPxScale :
1249	<	c = 1 - targetFlux_ / Pcx;
1248	>	case rnemdPx :
1249	>	c = 1 - momentumTarget_.x() / Pcx;
1250		a000 = Kcy;
1251		a110 = Kcz;
1252		c0 = Kcx * c * c - Kcx - Kcy - Kcz;
#	Line 908 | Line 1257 | namespace OpenMD {
1257		c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1258		+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1259		break;
1260	<	case rnemdPyScale :
1261	<	c = 1 - targetFlux_ / Pcy;
1260	>	case rnemdPy :
1261	>	c = 1 - momentumTarget_.y() / Pcy;
1262		a000 = Kcx;
1263		a110 = Kcz;
1264		c0 = Kcy * c * c - Kcx - Kcy - Kcz;
#	Line 920 | Line 1269 | namespace OpenMD {
1269		c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1270		+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1271		break;
1272	<	case rnemdPzScale ://we don't really do this, do we?
1273	<	c = 1 - targetFlux_ / Pcz;
1272	>	case rnemdPz ://we don't really do this, do we?
1273	>	c = 1 - momentumTarget_.z() / Pcz;
1274		a000 = Kcx;
1275		a110 = Kcy;
1276		c0 = Kcz * c * c - Kcx - Kcy - Kcz;
#	Line 971 | Line 1320 | namespace OpenMD {
1320		vector<RealType>::iterator ri;
1321		RealType r1, r2, alpha0;
1322		vector<pair<RealType,RealType> > rps;
1323	<	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1323	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
1324		r2 = *ri;
1325	<	//check if FindRealRoots() give the right answer
1325	>	// Check to see if FindRealRoots() gave the right answer:
1326		if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1327		sprintf(painCave.errMsg,
1328		"RNEMD Warning: polynomial solve seems to have an error!");
#	Line 981 | Line 1330 | namespace OpenMD {
1330		simError();
1331		failRootCount_++;
1332		}
1333	<	//might not be useful w/o rescaling coefficients
1333	>	// Might not be useful w/o rescaling coefficients
1334		alpha0 = -c0 - a110 * r2 * r2;
1335		if (alpha0 >= 0.0) {
1336		r1 = sqrt(alpha0 / a000);
#	Line 996 | Line 1345 | namespace OpenMD {
1345		}
1346		}
1347		}
1348	<	// Consider combining together the solving pair part w/ the searching
1349	<	// best solution part so that we don't need the pairs vector
1348	>	// Consider combining together the part for solving for the pair
1349	>	// w/ the searching for the best solution part so that we don't
1350	>	// need the pairs vector:
1351		if (!rps.empty()) {
1352		RealType smallestDiff = HONKING_LARGE_VALUE;
1353	<	RealType diff;
1354	<	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1355	<	vector<pair<RealType,RealType> >::iterator rpi;
1356	<	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1353	>	RealType diff(0.0);
1354	>	std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0);
1355	>	std::vector<std::pair<RealType,RealType> >::iterator rpi;
1356	>	for (rpi = rps.begin(); rpi != rps.end(); ++rpi) {
1357		r1 = (*rpi).first;
1358		r2 = (*rpi).second;
1359	<	switch(rnemdType_) {
1360	<	case rnemdKineticScale :
1359	>	switch(rnemdFluxType_) {
1360	>	case rnemdKE :
1361		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1362		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1363		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1364		break;
1365	<	case rnemdPxScale :
1365	>	case rnemdPx :
1366		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1367		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1368		break;
1369	<	case rnemdPyScale :
1369	>	case rnemdPy :
1370		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1371		+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1372		break;
1373	<	case rnemdPzScale :
1373	>	case rnemdPz :
1374		diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1375		+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1376		default :
#	Line 1034 | Line 1384 | namespace OpenMD {
1384		#ifdef IS_MPI
1385		if (worldRank == 0) {
1386		#endif
1387	<	sprintf(painCave.errMsg,
1388	<	"RNEMD: roots r1= %lf\tr2 = %lf\n",
1389	<	bestPair.first, bestPair.second);
1390	<	painCave.isFatal = 0;
1391	<	painCave.severity = OPENMD_INFO;
1392	<	simError();
1387	>	// sprintf(painCave.errMsg,
1388	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1389	>	//         bestPair.first, bestPair.second);
1390	>	// painCave.isFatal = 0;
1391	>	// painCave.severity = OPENMD_INFO;
1392	>	// simError();
1393		#ifdef IS_MPI
1394		}
1395		#endif
1396
1397	<	switch(rnemdType_) {
1398	<	case rnemdKineticScale :
1397	>	switch(rnemdFluxType_) {
1398	>	case rnemdKE :
1399		x = bestPair.first;
1400		y = bestPair.first;
1401		z = bestPair.second;
1402		break;
1403	<	case rnemdPxScale :
1403	>	case rnemdPx :
1404		x = c;
1405		y = bestPair.first;
1406		z = bestPair.second;
1407		break;
1408	<	case rnemdPyScale :
1408	>	case rnemdPy :
1409		x = bestPair.first;
1410		y = c;
1411		z = bestPair.second;
1412		break;
1413	<	case rnemdPzScale :
1413	>	case rnemdPz :
1414		x = bestPair.first;
1415		y = bestPair.second;
1416		z = c;
#	Line 1070 | Line 1420 | namespace OpenMD {
1420		}
1421		vector<StuntDouble*>::iterator sdi;
1422		Vector3d vel;
1423	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1423	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1424		vel = (*sdi)->getVel();
1425		vel.x() *= x;
1426		vel.y() *= y;
#	Line 1081 | Line 1431 | namespace OpenMD {
1431		x = 1.0 + px * (1.0 - x);
1432		y = 1.0 + py * (1.0 - y);
1433		z = 1.0 + pz * (1.0 - z);
1434	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1434	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1435		vel = (*sdi)->getVel();
1436		vel.x() *= x;
1437		vel.y() *= y;
#	Line 1089 | Line 1439 | namespace OpenMD {
1439		(*sdi)->setVel(vel);
1440		}
1441		successfulScale = true;
1442	<	exchangeSum_ += targetFlux_;
1442	>	switch(rnemdFluxType_) {
1443	>	case rnemdKE :
1444	>	kineticExchange_ += kineticTarget_;
1445	>	break;
1446	>	case rnemdPx :
1447	>	case rnemdPy :
1448	>	case rnemdPz :
1449	>	momentumExchange_ += momentumTarget_;
1450	>	break;
1451	>	default :
1452	>	break;
1453	>	}
1454		}
1455		}
1456		if (successfulScale != true) {
1457		sprintf(painCave.errMsg,
1458	<	"RNEMD: exchange NOT performed!\n");
1458	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1459	>	"\tthe constraint equations may not exist or there may be\n"
1460	>	"\tno selected objects in one or both slabs.\n");
1461		painCave.isFatal = 0;
1462		painCave.severity = OPENMD_INFO;
1463		simError();
1464		failTrialCount_++;
1465		}
1466		}
1467	+
1468	+	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1469	+	if (!doRNEMD_) return;
1470	+	int selei;
1471	+	int selej;
1472
1105	–	void RNEMD::doShiftScale() {
1106	–
1473		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1474		Mat3x3d hmat = currentSnap_->getHmat();
1475
1110	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1111	–
1112	–	int selei;
1476		StuntDouble* sd;
1114	–	int idx;
1477
1478		vector<StuntDouble*> hotBin, coldBin;
1479
1480		Vector3d Ph(V3Zero);
1481	+	Vector3d Lh(V3Zero);
1482		RealType Mh = 0.0;
1483	+	Mat3x3d Ih(0.0);
1484		RealType Kh = 0.0;
1485		Vector3d Pc(V3Zero);
1486	+	Vector3d Lc(V3Zero);
1487		RealType Mc = 0.0;
1488	+	Mat3x3d Ic(0.0);
1489		RealType Kc = 0.0;
1490
1491	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1492	<	sd = seleMan_.nextSelected(selei)) {
1491	>	// Constraints can be on only the linear or angular momentum, but
1492	>	// not both.  Usually, the user will specify which they want, but
1493	>	// in case they don't, the use of periodic boundaries should make
1494	>	// the choice for us.
1495	>	bool doLinearPart = false;
1496	>	bool doAngularPart = false;
1497
1498	<	idx = sd->getLocalIndex();
1498	>	switch (rnemdFluxType_) {
1499	>	case rnemdPx:
1500	>	case rnemdPy:
1501	>	case rnemdPz:
1502	>	case rnemdPvector:
1503	>	case rnemdKePx:
1504	>	case rnemdKePy:
1505	>	case rnemdKePvector:
1506	>	doLinearPart = true;
1507	>	break;
1508	>	case rnemdLx:
1509	>	case rnemdLy:
1510	>	case rnemdLz:
1511	>	case rnemdLvector:
1512	>	case rnemdKeLx:
1513	>	case rnemdKeLy:
1514	>	case rnemdKeLz:
1515	>	case rnemdKeLvector:
1516	>	doAngularPart = true;
1517	>	break;
1518	>	case rnemdKE:
1519	>	case rnemdRotKE:
1520	>	case rnemdFullKE:
1521	>	default:
1522	>	if (usePeriodicBoundaryConditions_)
1523	>	doLinearPart = true;
1524	>	else
1525	>	doAngularPart = true;
1526	>	break;
1527	>	}
1528	>
1529	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1530	>	sd = smanA.nextSelected(selei)) {
1531
1532		Vector3d pos = sd->getPos();
1533
1534		// wrap the stuntdouble's position back into the box:
1535	+
1536	+	if (usePeriodicBoundaryConditions_)
1537	+	currentSnap_->wrapVector(pos);
1538	+
1539	+	RealType mass = sd->getMass();
1540	+	Vector3d vel = sd->getVel();
1541	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1542	+	RealType r2;
1543	+
1544	+	hotBin.push_back(sd);
1545	+	Ph += mass * vel;
1546	+	Mh += mass;
1547	+	Kh += mass * vel.lengthSquare();
1548	+	Lh += mass * cross(rPos, vel);
1549	+	Ih -= outProduct(rPos, rPos) * mass;
1550	+	r2 = rPos.lengthSquare();
1551	+	Ih(0, 0) += mass * r2;
1552	+	Ih(1, 1) += mass * r2;
1553	+	Ih(2, 2) += mass * r2;
1554	+
1555	+	if (rnemdFluxType_ == rnemdFullKE) {
1556	+	if (sd->isDirectional()) {
1557	+	Vector3d angMom = sd->getJ();
1558	+	Mat3x3d I = sd->getI();
1559	+	if (sd->isLinear()) {
1560	+	int i = sd->linearAxis();
1561	+	int j = (i + 1) % 3;
1562	+	int k = (i + 2) % 3;
1563	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1564	+	angMom[k] * angMom[k] / I(k, k);
1565	+	} else {
1566	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1567	+	angMom[1] * angMom[1] / I(1, 1) +
1568	+	angMom[2] * angMom[2] / I(2, 2);
1569	+	}
1570	+	}
1571	+	}
1572	+	}
1573	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1574	+	sd = smanB.nextSelected(selej)) {
1575
1576	+	Vector3d pos = sd->getPos();
1577	+
1578	+	// wrap the stuntdouble's position back into the box:
1579	+
1580		if (usePeriodicBoundaryConditions_)
1581		currentSnap_->wrapVector(pos);
1582	+
1583	+	RealType mass = sd->getMass();
1584	+	Vector3d vel = sd->getVel();
1585	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1586	+	RealType r2;
1587
1588	<	// which bin is this stuntdouble in?
1589	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1590	<
1591	<	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_;
1592	<
1593	<	// if we're in bin 0 or the middleBin
1594	<	if (binNo == 0 || binNo == midBin_) {
1595	<
1596	<	RealType mass = sd->getMass();
1597	<	Vector3d vel = sd->getVel();
1598	<
1599	<	if (binNo == 0) {
1600	<	hotBin.push_back(sd);
1601	<	//std::cerr << "before, velocity = " << vel << endl;
1602	<	Ph += mass * vel;
1603	<	//std::cerr << "after, velocity = " << vel << endl;
1604	<	Mh += mass;
1605	<	Kh += mass * vel.lengthSquare();
1606	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1607	<	if (sd->isDirectional()) {
1608	<	Vector3d angMom = sd->getJ();
1609	<	Mat3x3d I = sd->getI();
1610	<	if (sd->isLinear()) {
1611	<	int i = sd->linearAxis();
1612	<	int j = (i + 1) % 3;
1613	<	int k = (i + 2) % 3;
1614	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1164	<	angMom[k] * angMom[k] / I(k, k);
1165	<	} else {
1166	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1167	<	angMom[1] * angMom[1] / I(1, 1) +
1168	<	angMom[2] * angMom[2] / I(2, 2);
1169	<	}
1170	<	}
1171	<	}
1172	<	} else { //midBin_
1173	<	coldBin.push_back(sd);
1174	<	Pc += mass * vel;
1175	<	Mc += mass;
1176	<	Kc += mass * vel.lengthSquare();
1177	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1178	<	if (sd->isDirectional()) {
1179	<	Vector3d angMom = sd->getJ();
1180	<	Mat3x3d I = sd->getI();
1181	<	if (sd->isLinear()) {
1182	<	int i = sd->linearAxis();
1183	<	int j = (i + 1) % 3;
1184	<	int k = (i + 2) % 3;
1185	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1186	<	angMom[k] * angMom[k] / I(k, k);
1187	<	} else {
1188	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1189	<	angMom[1] * angMom[1] / I(1, 1) +
1190	<	angMom[2] * angMom[2] / I(2, 2);
1191	<	}
1192	<	}
1193	<	}
1194	<	}
1588	>	coldBin.push_back(sd);
1589	>	Pc += mass * vel;
1590	>	Mc += mass;
1591	>	Kc += mass * vel.lengthSquare();
1592	>	Lc += mass * cross(rPos, vel);
1593	>	Ic -= outProduct(rPos, rPos) * mass;
1594	>	r2 = rPos.lengthSquare();
1595	>	Ic(0, 0) += mass * r2;
1596	>	Ic(1, 1) += mass * r2;
1597	>	Ic(2, 2) += mass * r2;
1598	>
1599	>	if (rnemdFluxType_ == rnemdFullKE) {
1600	>	if (sd->isDirectional()) {
1601	>	Vector3d angMom = sd->getJ();
1602	>	Mat3x3d I = sd->getI();
1603	>	if (sd->isLinear()) {
1604	>	int i = sd->linearAxis();
1605	>	int j = (i + 1) % 3;
1606	>	int k = (i + 2) % 3;
1607	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1608	>	angMom[k] * angMom[k] / I(k, k);
1609	>	} else {
1610	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1611	>	angMom[1] * angMom[1] / I(1, 1) +
1612	>	angMom[2] * angMom[2] / I(2, 2);
1613	>	}
1614	>	}
1615		}
1616		}
1617
1618		Kh *= 0.5;
1619		Kc *= 0.5;
1620	<
1201	<	std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1202	<	<< "\tKc= " << Kc << endl;
1203	<	std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1204	<
1620	>
1621		#ifdef IS_MPI
1622	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1623	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1624	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1625	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1626	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1627	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1622	>	MPI_Allreduce(MPI_IN_PLACE, &Ph[0], 3, MPI_REALTYPE, MPI_SUM,
1623	>	MPI_COMM_WORLD);
1624	>	MPI_Allreduce(MPI_IN_PLACE, &Pc[0], 3, MPI_REALTYPE, MPI_SUM,
1625	>	MPI_COMM_WORLD);
1626	>	MPI_Allreduce(MPI_IN_PLACE, &Lh[0], 3, MPI_REALTYPE, MPI_SUM,
1627	>	MPI_COMM_WORLD);
1628	>	MPI_Allreduce(MPI_IN_PLACE, &Lc[0], 3, MPI_REALTYPE, MPI_SUM,
1629	>	MPI_COMM_WORLD);
1630	>	MPI_Allreduce(MPI_IN_PLACE, &Mh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1631	>	MPI_Allreduce(MPI_IN_PLACE, &Kh, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1632	>	MPI_Allreduce(MPI_IN_PLACE, &Mc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1633	>	MPI_Allreduce(MPI_IN_PLACE, &Kc, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1634	>	MPI_Allreduce(MPI_IN_PLACE, Ih.getArrayPointer(), 9,
1635	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1636	>	MPI_Allreduce(MPI_IN_PLACE, Ic.getArrayPointer(), 9,
1637	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1638		#endif
1639	+
1640
1641	+	Vector3d ac, acrec, bc, bcrec;
1642	+	Vector3d ah, ahrec, bh, bhrec;
1643	+
1644		bool successfulExchange = false;
1645		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1646		Vector3d vc = Pc / Mc;
1647	<	Vector3d ac = njzp_ / Mc + vc;
1648	<	RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare();
1647	>	ac = -momentumTarget_ / Mc + vc;
1648	>	acrec = -momentumTarget_ / Mc;
1649	>
1650	>	// We now need the inverse of the inertia tensor to calculate the
1651	>	// angular velocity of the cold slab;
1652	>	Mat3x3d Ici = Ic.inverse();
1653	>	Vector3d omegac = Ici * Lc;
1654	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1655	>	bcrec = bc - omegac;
1656	>
1657	>	RealType cNumerator = Kc - kineticTarget_;
1658	>	if (doLinearPart)
1659	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1660	>
1661	>	if (doAngularPart)
1662	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1663	>
1664		if (cNumerator > 0.0) {
1665	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1665	>
1666	>	RealType cDenominator = Kc;
1667	>
1668	>	if (doLinearPart)
1669	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1670	>
1671	>	if (doAngularPart)
1672	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1673	>
1674		if (cDenominator > 0.0) {
1675		RealType c = sqrt(cNumerator / cDenominator);
1676		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1677	+
1678		Vector3d vh = Ph / Mh;
1679	<	Vector3d ah = jzp_ / Mh + vh;
1680	<	RealType hNumerator = Kh + targetJzKE_
1681	<	- 0.5 * Mh * ah.lengthSquare();
1682	<	if (hNumerator > 0.0) {
1683	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1679	>	ah = momentumTarget_ / Mh + vh;
1680	>	ahrec = momentumTarget_ / Mh;
1681	>
1682	>	// We now need the inverse of the inertia tensor to
1683	>	// calculate the angular velocity of the hot slab;
1684	>	Mat3x3d Ihi = Ih.inverse();
1685	>	Vector3d omegah = Ihi * Lh;
1686	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1687	>	bhrec = bh - omegah;
1688	>
1689	>	RealType hNumerator = Kh + kineticTarget_;
1690	>	if (doLinearPart)
1691	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1692	>
1693	>	if (doAngularPart)
1694	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1695	>
1696	>	if (hNumerator > 0.0) {
1697	>
1698	>	RealType hDenominator = Kh;
1699	>	if (doLinearPart)
1700	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1701	>	if (doAngularPart)
1702	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1703	>
1704		if (hDenominator > 0.0) {
1705		RealType h = sqrt(hNumerator / hDenominator);
1706		if ((h > 0.9) && (h < 1.1)) {
1707	<	std::cerr << "cold slab scaling coefficient: " << c << "\n";
1234	<	std::cerr << "hot slab scaling coefficient: " << h << "\n";
1707	>
1708		vector<StuntDouble*>::iterator sdi;
1709		Vector3d vel;
1710	<	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1710	>	Vector3d rPos;
1711	>
1712	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) {
1713		//vel = (*sdi)->getVel();
1714	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1714	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1715	>	if (doLinearPart)
1716	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1717	>	if (doAngularPart)
1718	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1719	>
1720		(*sdi)->setVel(vel);
1721	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1721	>	if (rnemdFluxType_ == rnemdFullKE) {
1722		if ((*sdi)->isDirectional()) {
1723		Vector3d angMom = (*sdi)->getJ() * c;
1724		(*sdi)->setJ(angMom);
1725		}
1726		}
1727		}
1728	<	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1728	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) {
1729		//vel = (*sdi)->getVel();
1730	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1730	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1731	>	if (doLinearPart)
1732	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1733	>	if (doAngularPart)
1734	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1735	>
1736		(*sdi)->setVel(vel);
1737	<	if (rnemdType_ == rnemdShiftScaleVAM) {
1737	>	if (rnemdFluxType_ == rnemdFullKE) {
1738		if ((*sdi)->isDirectional()) {
1739		Vector3d angMom = (*sdi)->getJ() * h;
1740		(*sdi)->setJ(angMom);
#	Line 1257 | Line 1742 | namespace OpenMD {
1742		}
1743		}
1744		successfulExchange = true;
1745	<	exchangeSum_ += targetFlux_;
1746	<	// this is a redundant variable for doShiftScale() so that
1747	<	// RNEMD can output one exchange quantity needed in a job.
1263	<	// need a better way to do this.
1745	>	kineticExchange_ += kineticTarget_;
1746	>	momentumExchange_ += momentumTarget_;
1747	>	angularMomentumExchange_ += angularMomentumTarget_;
1748		}
1749		}
1750		}
#	Line 1270 | Line 1754 | namespace OpenMD {
1754		}
1755		if (successfulExchange != true) {
1756		sprintf(painCave.errMsg,
1757	<	"RNEMD: exchange NOT performed!\n");
1757	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1758	>	"\tthe constraint equations may not exist or there may be\n"
1759	>	"\tno selected objects in one or both slabs.\n");
1760		painCave.isFatal = 0;
1761		painCave.severity = OPENMD_INFO;
1762		simError();
#	Line 1278 | Line 1764 | namespace OpenMD {
1764		}
1765		}
1766
1767	<	void RNEMD::doRNEMD() {
1767	>	RealType RNEMD::getDividingArea() {
1768
1769	<	switch(rnemdType_) {
1770	<	case rnemdKineticScale :
1771	<	case rnemdKineticScaleVAM :
1772	<	case rnemdKineticScaleAM :
1773	<	case rnemdPxScale :
1774	<	case rnemdPyScale :
1775	<	case rnemdPzScale :
1776	<	doScale();
1777	<	break;
1778	<	case rnemdKineticSwap :
1779	<	case rnemdPx :
1780	<	case rnemdPy :
1781	<	case rnemdPz :
1782	<	doSwap();
1783	<	break;
1784	<	case rnemdShiftScaleV :
1785	<	case rnemdShiftScaleVAM :
1786	<	doShiftScale();
1769	>	if (hasDividingArea_) return dividingArea_;
1770	>
1771	>	RealType areaA, areaB;
1772	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1773	>
1774	>	if (hasSelectionA_) {
1775	>
1776	>	if (evaluatorA_.hasSurfaceArea())
1777	>	areaA = evaluatorA_.getSurfaceArea();
1778	>	else {
1779	>
1780	>	int isd;
1781	>	StuntDouble* sd;
1782	>	vector<StuntDouble*> aSites;
1783	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1784	>	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1785	>	sd = seleManA_.nextSelected(isd)) {
1786	>	aSites.push_back(sd);
1787	>	}
1788	>	#if defined(HAVE_QHULL)
1789	>	ConvexHull* surfaceMeshA = new ConvexHull();
1790	>	surfaceMeshA->computeHull(aSites);
1791	>	areaA = surfaceMeshA->getArea();
1792	>	delete surfaceMeshA;
1793	>	#else
1794	>	sprintf( painCave.errMsg,
1795	>	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1796	>	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1797	>	painCave.severity = OPENMD_ERROR;
1798	>	painCave.isFatal = 1;
1799	>	simError();
1800	>	#endif
1801	>	}
1802	>
1803	>	} else {
1804	>	if (usePeriodicBoundaryConditions_) {
1805	>	// in periodic boundaries, the surface area is twice the x-y
1806	>	// area of the current box:
1807	>	areaA = 2.0 * snap->getXYarea();
1808	>	} else {
1809	>	// in non-periodic simulations, without explicitly setting
1810	>	// selections, the sphere radius sets the surface area of the
1811	>	// dividing surface:
1812	>	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1813	>	}
1814	>	}
1815	>
1816	>	if (hasSelectionB_) {
1817	>	if (evaluatorB_.hasSurfaceArea()) {
1818	>	areaB = evaluatorB_.getSurfaceArea();
1819	>	} else {
1820	>
1821	>	int isd;
1822	>	StuntDouble* sd;
1823	>	vector<StuntDouble*> bSites;
1824	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1825	>	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1826	>	sd = seleManB_.nextSelected(isd)) {
1827	>	bSites.push_back(sd);
1828	>	}
1829	>
1830	>	#if defined(HAVE_QHULL)
1831	>	ConvexHull* surfaceMeshB = new ConvexHull();
1832	>	surfaceMeshB->computeHull(bSites);
1833	>	areaB = surfaceMeshB->getArea();
1834	>	delete surfaceMeshB;
1835	>	#else
1836	>	sprintf( painCave.errMsg,
1837	>	"RNEMD::getDividingArea : Hull calculation is not possible\n"
1838	>	"\twithout libqhull. Please rebuild OpenMD with qhull enabled.");
1839	>	painCave.severity = OPENMD_ERROR;
1840	>	painCave.isFatal = 1;
1841	>	simError();
1842	>	#endif
1843	>	}
1844	>
1845	>	} else {
1846	>	if (usePeriodicBoundaryConditions_) {
1847	>	// in periodic boundaries, the surface area is twice the x-y
1848	>	// area of the current box:
1849	>	areaB = 2.0 * snap->getXYarea();
1850	>	} else {
1851	>	// in non-periodic simulations, without explicitly setting
1852	>	// selections, but if a sphereBradius has been set, just use that:
1853	>	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1854	>	}
1855	>	}
1856	>
1857	>	dividingArea_ = min(areaA, areaB);
1858	>	hasDividingArea_ = true;
1859	>	return dividingArea_;
1860	>	}
1861	>
1862	>	void RNEMD::doRNEMD() {
1863	>	if (!doRNEMD_) return;
1864	>	trialCount_++;
1865	>
1866	>	// object evaluator:
1867	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1868	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1869	>
1870	>	evaluatorA_.loadScriptString(selectionA_);
1871	>	evaluatorB_.loadScriptString(selectionB_);
1872	>
1873	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1874	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1875	>
1876	>	commonA_ = seleManA_ & seleMan_;
1877	>	commonB_ = seleManB_ & seleMan_;
1878	>
1879	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1880	>	// dt = exchange time interval
1881	>	// flux = target flux
1882	>	// dividingArea = smallest dividing surface between the two regions
1883	>
1884	>	hasDividingArea_ = false;
1885	>	RealType area = getDividingArea();
1886	>
1887	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1888	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1889	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1890	>
1891	>	switch(rnemdMethod_) {
1892	>	case rnemdSwap:
1893	>	doSwap(commonA_, commonB_);
1894		break;
1895	<	case rnemdUnknown :
1895	>	case rnemdNIVS:
1896	>	doNIVS(commonA_, commonB_);
1897	>	break;
1898	>	case rnemdVSS:
1899	>	doVSS(commonA_, commonB_);
1900	>	break;
1901	>	case rnemdUnkownMethod:
1902		default :
1903		break;
1904		}
1905		}
1906
1907		void RNEMD::collectData() {
1908	<
1908	>	if (!doRNEMD_) return;
1909		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1910	+
1911	+	// collectData can be called more frequently than the doRNEMD, so use the
1912	+	// computed area from the last exchange time:
1913	+	RealType area = getDividingArea();
1914	+	areaAccumulator_->add(area);
1915		Mat3x3d hmat = currentSnap_->getHmat();
1916	+	Vector3d u = angularMomentumFluxVector_;
1917	+	u.normalize();
1918
1919		seleMan_.setSelectionSet(evaluator_.evaluate());
1920
1921	<	int selei;
1921	>	int selei(0);
1922		StuntDouble* sd;
1923	<	int idx;
1923	>	int binNo;
1924	>	RealType mass;
1925	>	Vector3d vel;
1926	>	Vector3d rPos;
1927	>	RealType KE;
1928	>	Vector3d L;
1929	>	Mat3x3d I;
1930	>	RealType r2;
1931
1932	+	vector<RealType> binMass(nBins_, 0.0);
1933	+	vector<Vector3d> binP(nBins_, V3Zero);
1934	+	vector<RealType> binOmega(nBins_, 0.0);
1935	+	vector<Vector3d> binL(nBins_, V3Zero);
1936	+	vector<Mat3x3d>  binI(nBins_);
1937	+	vector<RealType> binKE(nBins_, 0.0);
1938	+	vector<int> binDOF(nBins_, 0);
1939	+	vector<int> binCount(nBins_, 0);
1940	+
1941		// alternative approach, track all molecules instead of only those
1942		// selected for scaling/swapping:
1943		/*
1944	<	SimInfo::MoleculeIterator miter;
1945	<	vector<StuntDouble*>::iterator iiter;
1946	<	Molecule* mol;
1947	<	StuntDouble* integrableObject;
1948	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1949	<	mol = info_->nextMolecule(miter))
1950	<	integrableObject is essentially sd
1951	<	for (integrableObject = mol->beginIntegrableObject(iiter);
1952	<	integrableObject != NULL;
1953	<	integrableObject = mol->nextIntegrableObject(iiter))
1944	>	SimInfo::MoleculeIterator miter;
1945	>	vector<StuntDouble*>::iterator iiter;
1946	>	Molecule* mol;
1947	>	StuntDouble* sd;
1948	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1949	>	mol = info_->nextMolecule(miter))
1950	>	sd is essentially sd
1951	>	for (sd = mol->beginIntegrableObject(iiter);
1952	>	sd != NULL;
1953	>	sd = mol->nextIntegrableObject(iiter))
1954		*/
1955	+
1956		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1957	<	sd = seleMan_.nextSelected(selei)) {
1958	<
1336	<	idx = sd->getLocalIndex();
1337	<
1957	>	sd = seleMan_.nextSelected(selei)) {
1958	>
1959		Vector3d pos = sd->getPos();
1960
1961		// wrap the stuntdouble's position back into the box:
1962
1963	<	if (usePeriodicBoundaryConditions_)
1963	>	if (usePeriodicBoundaryConditions_) {
1964		currentSnap_->wrapVector(pos);
1965	<
1966	<	// which bin is this stuntdouble in?
1967	<	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1968	<
1969	<	int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) %
1970	<	rnemdLogWidth_;
1971	<	// no symmetrization allowed due to arbitary rnemdLogWidth_
1972	<	/*
1973	<	if (rnemdLogWidth_ == midBin_ + 1)
1974	<	if (binNo > midBin_)
1354	<	binNo = nBins_ - binNo;
1355	<	*/
1356	<	RealType mass = sd->getMass();
1357	<	mHist_[binNo] += mass;
1358	<	Vector3d vel = sd->getVel();
1359	<	RealType value;
1360	<	//RealType xVal, yVal, zVal;
1965	>	// which bin is this stuntdouble in?
1966	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1967	>	// Shift molecules by half a box to have bins start at 0
1968	>	// The modulo operator is used to wrap the case when we are
1969	>	// beyond the end of the bins back to the beginning.
1970	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1971	>	} else {
1972	>	Vector3d rPos = pos - coordinateOrigin_;
1973	>	binNo = int(rPos.length() / binWidth_);
1974	>	}
1975
1976	<	if (outputTemp_) {
1977	<	value = mass * vel.lengthSquare();
1978	<	tempCount_[binNo] += 3;
1979	<	if (sd->isDirectional()) {
1980	<	Vector3d angMom = sd->getJ();
1981	<	Mat3x3d I = sd->getI();
1982	<	if (sd->isLinear()) {
1983	<	int i = sd->linearAxis();
1984	<	int j = (i + 1) % 3;
1985	<	int k = (i + 2) % 3;
1986	<	value += angMom[j] * angMom[j] / I(j, j) +
1987	<	angMom[k] * angMom[k] / I(k, k);
1988	<	tempCount_[binNo] +=2;
1989	<	} else {
1990	<	value += angMom[0] * angMom[0] / I(0, 0) +
1991	<	angMom[1]*angMom[1]/I(1, 1) +
1992	<	angMom[2]*angMom[2]/I(2, 2);
1993	<	tempCount_[binNo] +=3;
1994	<	}
1995	<	}
1996	<	value = value / PhysicalConstants::energyConvert
1997	<	/ PhysicalConstants::kb;//may move to getStatus()
1998	<	tempHist_[binNo] += value;
1976	>	mass = sd->getMass();
1977	>	vel = sd->getVel();
1978	>	rPos = sd->getPos() - coordinateOrigin_;
1979	>	KE = 0.5 * mass * vel.lengthSquare();
1980	>	L = mass * cross(rPos, vel);
1981	>	I = outProduct(rPos, rPos) * mass;
1982	>	r2 = rPos.lengthSquare();
1983	>	I(0, 0) += mass * r2;
1984	>	I(1, 1) += mass * r2;
1985	>	I(2, 2) += mass * r2;
1986	>
1987	>	// Project the relative position onto a plane perpendicular to
1988	>	// the angularMomentumFluxVector:
1989	>	// Vector3d rProj = rPos - dot(rPos, u) * u;
1990	>	// Project the velocity onto a plane perpendicular to the
1991	>	// angularMomentumFluxVector:
1992	>	// Vector3d vProj = vel  - dot(vel, u) * u;
1993	>	// Compute angular velocity vector (should be nearly parallel to
1994	>	// angularMomentumFluxVector
1995	>	// Vector3d aVel = cross(rProj, vProj);
1996	>
1997	>	if (binNo >= 0 && binNo < nBins_)  {
1998	>	binCount[binNo]++;
1999	>	binMass[binNo] += mass;
2000	>	binP[binNo] += mass*vel;
2001	>	binKE[binNo] += KE;
2002	>	binI[binNo] += I;
2003	>	binL[binNo] += L;
2004	>	binDOF[binNo] += 3;
2005	>
2006	>	if (sd->isDirectional()) {
2007	>	Vector3d angMom = sd->getJ();
2008	>	Mat3x3d Ia = sd->getI();
2009	>	if (sd->isLinear()) {
2010	>	int i = sd->linearAxis();
2011	>	int j = (i + 1) % 3;
2012	>	int k = (i + 2) % 3;
2013	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
2014	>	angMom[k] * angMom[k] / Ia(k, k));
2015	>	binDOF[binNo] += 2;
2016	>	} else {
2017	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
2018	>	angMom[1] * angMom[1] / Ia(1, 1) +
2019	>	angMom[2] * angMom[2] / Ia(2, 2));
2020	>	binDOF[binNo] += 3;
2021	>	}
2022	>	}
2023		}
2024	<	if (outputVx_) {
1387	<	value = mass * vel[0];
1388	<	//vxzCount_[binNo]++;
1389	<	pxzHist_[binNo] += value;
1390	<	}
1391	<	if (outputVy_) {
1392	<	value = mass * vel[1];
1393	<	//vyzCount_[binNo]++;
1394	<	pyzHist_[binNo] += value;
1395	<	}
2024	>	}
2025
2026	<	if (output3DTemp_) {
2027	<	value = mass * vel.x() * vel.x();
2028	<	xTempHist_[binNo] += value;
2029	<	value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
2030	<	/ PhysicalConstants::kb;
2031	<	yTempHist_[binNo] += value;
2032	<	value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
2033	<	/ PhysicalConstants::kb;
2034	<	zTempHist_[binNo] += value;
2035	<	xyzTempCount_[binNo]++;
2026	>	#ifdef IS_MPI
2027	>
2028	>	for (int i = 0; i < nBins_; i++) {
2029	>
2030	>	MPI_Allreduce(MPI_IN_PLACE, &binCount[i],
2031	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2032	>	MPI_Allreduce(MPI_IN_PLACE, &binMass[i],
2033	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2034	>	MPI_Allreduce(MPI_IN_PLACE, binP[i].getArrayPointer(),
2035	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2036	>	MPI_Allreduce(MPI_IN_PLACE, binL[i].getArrayPointer(),
2037	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2038	>	MPI_Allreduce(MPI_IN_PLACE, binI[i].getArrayPointer(),
2039	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2040	>	MPI_Allreduce(MPI_IN_PLACE, &binKE[i],
2041	>	1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2042	>	MPI_Allreduce(MPI_IN_PLACE, &binDOF[i],
2043	>	1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
2044	>	//MPI_Allreduce(MPI_IN_PLACE, &binOmega[i],
2045	>	//                          1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
2046	>	}
2047	>
2048	>	#endif
2049	>
2050	>	Vector3d omega;
2051	>	RealType den;
2052	>	RealType temp;
2053	>	RealType z;
2054	>	RealType r;
2055	>	for (int i = 0; i < nBins_; i++) {
2056	>	if (usePeriodicBoundaryConditions_) {
2057	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
2058	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
2059	>	/ currentSnap_->getVolume() ;
2060	>	} else {
2061	>	r = (((RealType)i + 0.5) * binWidth_);
2062	>	RealType rinner = (RealType)i * binWidth_;
2063	>	RealType router = (RealType)(i+1) * binWidth_;
2064	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
2065	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
2066		}
2067	<	if (outputRotTemp_) {
1409	<	if (sd->isDirectional()) {
1410	<	Vector3d angMom = sd->getJ();
1411	<	Mat3x3d I = sd->getI();
1412	<	if (sd->isLinear()) {
1413	<	int i = sd->linearAxis();
1414	<	int j = (i + 1) % 3;
1415	<	int k = (i + 2) % 3;
1416	<	value = angMom[j] * angMom[j] / I(j, j) +
1417	<	angMom[k] * angMom[k] / I(k, k);
1418	<	rotTempCount_[binNo] +=2;
1419	<	} else {
1420	<	value = angMom[0] * angMom[0] / I(0, 0) +
1421	<	angMom[1] * angMom[1] / I(1, 1) +
1422	<	angMom[2] * angMom[2] / I(2, 2);
1423	<	rotTempCount_[binNo] +=3;
1424	<	}
1425	<	}
1426	<	value = value / PhysicalConstants::energyConvert
1427	<	/ PhysicalConstants::kb;//may move to getStatus()
1428	<	rotTempHist_[binNo] += value;
1429	<	}
2067	>	vel = binP[i] / binMass[i];
2068
2069	+	omega = binI[i].inverse() * binL[i];
2070	+
2071	+	// omega = binOmega[i] / binCount[i];
2072	+
2073	+	if (binCount[i] > 0) {
2074	+	// only add values if there are things to add
2075	+	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
2076	+	PhysicalConstants::energyConvert);
2077	+
2078	+	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
2079	+	if(outputMask_[j]) {
2080	+	switch(j) {
2081	+	case Z:
2082	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
2083	+	break;
2084	+	case R:
2085	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
2086	+	break;
2087	+	case TEMPERATURE:
2088	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
2089	+	break;
2090	+	case VELOCITY:
2091	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
2092	+	break;
2093	+	case ANGULARVELOCITY:
2094	+	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(omega);
2095	+	break;
2096	+	case DENSITY:
2097	+	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2098	+	break;
2099	+	}
2100	+	}
2101	+	}
2102	+	}
2103		}
2104	+	hasData_ = true;
2105		}
2106
2107		void RNEMD::getStarted() {
2108	+	if (!doRNEMD_) return;
2109	+	hasDividingArea_ = false;
2110		collectData();
2111	<	/*now can output profile in step 0, but might not be useful;
1437	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1438	<	Stats& stat = currentSnap_->statData;
1439	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
1440	<	*/
1441	<	//may output a header for the log file here
1442	<	getStatus();
2111	>	writeOutputFile();
2112		}
2113
2114	<	void RNEMD::getStatus() {
2115	<
2116	<	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2117	<	Stats& stat = currentSnap_->statData;
2118	<	RealType time = currentSnap_->getTime();
2119	<
2120	<	stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_;
2121	<	//or to be more meaningful, define another item as exchangeSum_ / time
2122	<	int j;
2123	<
2124	<	#ifdef IS_MPI
2125	<
2126	<	// all processors have the same number of bins, and STL vectors pack their
2127	<	// arrays, so in theory, this should be safe:
2128	<
2129	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0],
2130	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
2131	<	if (outputTemp_) {
1463	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0],
1464	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1465	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0],
1466	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1467	<	}
1468	<	if (outputVx_) {
1469	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0],
1470	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1471	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0],
1472	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
2114	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
2115	>	if (!doRNEMD_) return;
2116	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
2117	>
2118	>	while(tokenizer.hasMoreTokens()) {
2119	>	std::string token(tokenizer.nextToken());
2120	>	toUpper(token);
2121	>	OutputMapType::iterator i = outputMap_.find(token);
2122	>	if (i != outputMap_.end()) {
2123	>	outputMask_.set(i->second);
2124	>	} else {
2125	>	sprintf( painCave.errMsg,
2126	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
2127	>	"\toutputFileFormat keyword.\n", token.c_str() );
2128	>	painCave.isFatal = 0;
2129	>	painCave.severity = OPENMD_ERROR;
2130	>	simError();
2131	>	}
2132		}
2133	<	if (outputVy_) {
2134	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0],
2135	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
2136	<	//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0],
2137	<	//                        rnemdLogWidth_, MPI::INT, MPI::SUM);
2138	<	}
2139	<	if (output3DTemp_) {
1481	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0],
1482	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1483	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0],
1484	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1485	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0],
1486	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1487	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0],
1488	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1489	<	}
1490	<	if (outputRotTemp_) {
1491	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0],
1492	<	rnemdLogWidth_, MPI::REALTYPE, MPI::SUM);
1493	<	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0],
1494	<	rnemdLogWidth_, MPI::INT, MPI::SUM);
1495	<	}
1496	<
2133	>	}
2134	>
2135	>	void RNEMD::writeOutputFile() {
2136	>	if (!doRNEMD_) return;
2137	>	if (!hasData_) return;
2138	>
2139	>	#ifdef IS_MPI
2140		// If we're the root node, should we print out the results
2141	<	int worldRank = MPI::COMM_WORLD.Get_rank();
2141	>	int worldRank;
2142	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
2143	>
2144		if (worldRank == 0) {
2145		#endif
2146	+	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
2147	+
2148	+	if( !rnemdFile_ ){
2149	+	sprintf( painCave.errMsg,
2150	+	"Could not open \"%s\" for RNEMD output.\n",
2151	+	rnemdFileName_.c_str());
2152	+	painCave.isFatal = 1;
2153	+	simError();
2154	+	}
2155
2156	<	if (outputTemp_) {
2157	<	tempLog_ << time;
2158	<	for (j = 0; j < rnemdLogWidth_; j++) {
2159	<	tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j];
2160	<	}
2161	<	tempLog_ << endl;
2156	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2157	>
2158	>	RealType time = currentSnap_->getTime();
2159	>	RealType avgArea;
2160	>	areaAccumulator_->getAverage(avgArea);
2161	>
2162	>	RealType Jz(0.0);
2163	>	Vector3d JzP(V3Zero);
2164	>	Vector3d JzL(V3Zero);
2165	>	if (time >= info_->getSimParams()->getDt()) {
2166	>	Jz = kineticExchange_ / (time * avgArea)
2167	>	/ PhysicalConstants::energyConvert;
2168	>	JzP = momentumExchange_ / (time * avgArea);
2169	>	JzL = angularMomentumExchange_ / (time * avgArea);
2170		}
2171	<	if (outputVx_) {
2172	<	vxzLog_ << time;
2173	<	for (j = 0; j < rnemdLogWidth_; j++) {
2174	<	vxzLog_ << "\t" << pxzHist_[j] / mHist_[j];
2175	<	}
2176	<	vxzLog_ << endl;
2171	>
2172	>	rnemdFile_ << "#######################################################\n";
2173	>	rnemdFile_ << "# RNEMD {\n";
2174	>
2175	>	map<string, RNEMDMethod>::iterator mi;
2176	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2177	>	if ( (*mi).second == rnemdMethod_)
2178	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2179		}
2180	<	if (outputVy_) {
2181	<	vyzLog_ << time;
2182	<	for (j = 0; j < rnemdLogWidth_; j++) {
2183	<	vyzLog_ << "\t" << pyzHist_[j] / mHist_[j];
1520	<	}
1521	<	vyzLog_ << endl;
2180	>	map<string, RNEMDFluxType>::iterator fi;
2181	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2182	>	if ( (*fi).second == rnemdFluxType_)
2183	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2184		}
2185	+
2186	+	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2187
2188	<	if (output3DTemp_) {
2189	<	RealType temp;
2190	<	xTempLog_ << time;
2191	<	for (j = 0; j < rnemdLogWidth_; j++) {
2192	<	if (outputVx_)
2193	<	xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j];
2194	<	temp = xTempHist_[j] / (RealType)xyzTempCount_[j]
2195	<	/ PhysicalConstants::energyConvert / PhysicalConstants::kb;
2196	<	xTempLog_ << "\t" << temp;
2188	>	rnemdFile_ << "#    objectSelection = \""
2189	>	<< rnemdObjectSelection_ << "\";\n";
2190	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2191	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2192	>	rnemdFile_ << "# }\n";
2193	>	rnemdFile_ << "#######################################################\n";
2194	>	rnemdFile_ << "# RNEMD report:\n";
2195	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2196	>	rnemdFile_ << "# Target flux:\n";
2197	>	rnemdFile_ << "#           kinetic = "
2198	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2199	>	<< " (kcal/mol/A^2/fs)\n";
2200	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2201	>	<< " (amu/A/fs^2)\n";
2202	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2203	>	<< " (amu/A^2/fs^2)\n";
2204	>	rnemdFile_ << "# Target one-time exchanges:\n";
2205	>	rnemdFile_ << "#          kinetic = "
2206	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2207	>	<< " (kcal/mol)\n";
2208	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2209	>	<< " (amu*A/fs)\n";
2210	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2211	>	<< " (amu*A^2/fs)\n";
2212	>	rnemdFile_ << "# Actual exchange totals:\n";
2213	>	rnemdFile_ << "#          kinetic = "
2214	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2215	>	<< " (kcal/mol)\n";
2216	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2217	>	<< " (amu*A/fs)\n";
2218	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2219	>	<< " (amu*A^2/fs)\n";
2220	>	rnemdFile_ << "# Actual flux:\n";
2221	>	rnemdFile_ << "#          kinetic = " << Jz
2222	>	<< " (kcal/mol/A^2/fs)\n";
2223	>	rnemdFile_ << "#          momentum = " << JzP
2224	>	<< " (amu/A/fs^2)\n";
2225	>	rnemdFile_ << "#  angular momentum = " << JzL
2226	>	<< " (amu/A^2/fs^2)\n";
2227	>	rnemdFile_ << "# Exchange statistics:\n";
2228	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2229	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2230	>	if (rnemdMethod_ == rnemdNIVS) {
2231	>	rnemdFile_ << "#  NIVS root-check errors = "
2232	>	<< failRootCount_ << "\n";
2233	>	}
2234	>	rnemdFile_ << "#######################################################\n";
2235	>
2236	>
2237	>
2238	>	//write title
2239	>	rnemdFile_ << "#";
2240	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2241	>	if (outputMask_[i]) {
2242	>	rnemdFile_ << "\t" << data_[i].title <<
2243	>	"(" << data_[i].units << ")";
2244	>	// add some extra tabs for column alignment
2245	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2246		}
1534	–	xTempLog_ << endl;
1535	–	yTempLog_ << time;
1536	–	for (j = 0; j < rnemdLogWidth_; j++) {
1537	–	yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j];
1538	–	}
1539	–	yTempLog_ << endl;
1540	–	zTempLog_ << time;
1541	–	for (j = 0; j < rnemdLogWidth_; j++) {
1542	–	zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j];
1543	–	}
1544	–	zTempLog_ << endl;
2247		}
2248	<	if (outputRotTemp_) {
2249	<	rotTempLog_ << time;
2250	<	for (j = 0; j < rnemdLogWidth_; j++) {
2251	<	rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j];
2252	<	}
2253	<	rotTempLog_ << endl;
2254	<	}
2248	>	rnemdFile_ << std::endl;
2249	>
2250	>	rnemdFile_.precision(8);
2251	>
2252	>	for (int j = 0; j < nBins_; j++) {
2253	>
2254	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2255	>	if (outputMask_[i]) {
2256	>	if (data_[i].dataType == "RealType")
2257	>	writeReal(i,j);
2258	>	else if (data_[i].dataType == "Vector3d")
2259	>	writeVector(i,j);
2260	>	else {
2261	>	sprintf( painCave.errMsg,
2262	>	"RNEMD found an unknown data type for: %s ",
2263	>	data_[i].title.c_str());
2264	>	painCave.isFatal = 1;
2265	>	simError();
2266	>	}
2267	>	}
2268	>	}
2269	>	rnemdFile_ << std::endl;
2270	>
2271	>	}
2272
2273	+	rnemdFile_ << "#######################################################\n";
2274	+	rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2275	+	rnemdFile_ << "#######################################################\n";
2276	+
2277	+
2278	+	for (int j = 0; j < nBins_; j++) {
2279	+	rnemdFile_ << "#";
2280	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2281	+	if (outputMask_[i]) {
2282	+	if (data_[i].dataType == "RealType")
2283	+	writeRealErrorBars(i,j);
2284	+	else if (data_[i].dataType == "Vector3d")
2285	+	writeVectorErrorBars(i,j);
2286	+	else {
2287	+	sprintf( painCave.errMsg,
2288	+	"RNEMD found an unknown data type for: %s ",
2289	+	data_[i].title.c_str());
2290	+	painCave.isFatal = 1;
2291	+	simError();
2292	+	}
2293	+	}
2294	+	}
2295	+	rnemdFile_ << std::endl;
2296	+
2297	+	}
2298	+
2299	+	rnemdFile_.flush();
2300	+	rnemdFile_.close();
2301	+
2302		#ifdef IS_MPI
2303		}
2304		#endif
2305	+
2306	+	}
2307	+
2308	+	void RNEMD::writeReal(int index, unsigned int bin) {
2309	+	if (!doRNEMD_) return;
2310	+	assert(index >=0 && index < ENDINDEX);
2311	+	assert(int(bin) < nBins_);
2312	+	RealType s;
2313	+	int count;
2314	+
2315	+	count = data_[index].accumulator[bin]->count();
2316	+	if (count == 0) return;
2317	+
2318	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2319	+
2320	+	if (! isinf(s) && ! isnan(s)) {
2321	+	rnemdFile_ << "\t" << s;
2322	+	} else{
2323	+	sprintf( painCave.errMsg,
2324	+	"RNEMD detected a numerical error writing: %s for bin %u",
2325	+	data_[index].title.c_str(), bin);
2326	+	painCave.isFatal = 1;
2327	+	simError();
2328	+	}
2329	+	}
2330	+
2331	+	void RNEMD::writeVector(int index, unsigned int bin) {
2332	+	if (!doRNEMD_) return;
2333	+	assert(index >=0 && index < ENDINDEX);
2334	+	assert(int(bin) < nBins_);
2335	+	Vector3d s;
2336	+	int count;
2337	+
2338	+	count = data_[index].accumulator[bin]->count();
2339
2340	<	for (j = 0; j < rnemdLogWidth_; j++) {
2341	<	mHist_[j] = 0.0;
2340	>	if (count == 0) return;
2341	>
2342	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2343	>	if (isinf(s[0]) || isnan(s[0]) ||
2344	>	isinf(s[1]) || isnan(s[1]) ||
2345	>	isinf(s[2]) || isnan(s[2]) ) {
2346	>	sprintf( painCave.errMsg,
2347	>	"RNEMD detected a numerical error writing: %s for bin %u",
2348	>	data_[index].title.c_str(), bin);
2349	>	painCave.isFatal = 1;
2350	>	simError();
2351	>	} else {
2352	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2353		}
2354	<	if (outputTemp_)
1562	<	for (j = 0; j < rnemdLogWidth_; j++) {
1563	<	tempCount_[j] = 0;
1564	<	tempHist_[j] = 0.0;
1565	<	}
1566	<	if (outputVx_)
1567	<	for (j = 0; j < rnemdLogWidth_; j++) {
1568	<	//pxzCount_[j] = 0;
1569	<	pxzHist_[j] = 0.0;
1570	<	}
1571	<	if (outputVy_)
1572	<	for (j = 0; j < rnemdLogWidth_; j++) {
1573	<	//pyzCount_[j] = 0;
1574	<	pyzHist_[j] = 0.0;
1575	<	}
2354	>	}
2355
2356	<	if (output3DTemp_)
2357	<	for (j = 0; j < rnemdLogWidth_; j++) {
2358	<	xTempHist_[j] = 0.0;
2359	<	yTempHist_[j] = 0.0;
2360	<	zTempHist_[j] = 0.0;
2361	<	xyzTempCount_[j] = 0;
2362	<	}
2363	<	if (outputRotTemp_)
2364	<	for (j = 0; j < rnemdLogWidth_; j++) {
2365	<	rotTempCount_[j] = 0;
2366	<	rotTempHist_[j] = 0.0;
2367	<	}
2356	>	void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2357	>	if (!doRNEMD_) return;
2358	>	assert(index >=0 && index < ENDINDEX);
2359	>	assert(int(bin) < nBins_);
2360	>	RealType s;
2361	>	int count;
2362	>
2363	>	count = data_[index].accumulator[bin]->count();
2364	>	if (count == 0) return;
2365	>
2366	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2367	>
2368	>	if (! isinf(s) && ! isnan(s)) {
2369	>	rnemdFile_ << "\t" << s;
2370	>	} else{
2371	>	sprintf( painCave.errMsg,
2372	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2373	>	data_[index].title.c_str(), bin);
2374	>	painCave.isFatal = 1;
2375	>	simError();
2376	>	}
2377		}
2378	+
2379	+	void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2380	+	if (!doRNEMD_) return;
2381	+	assert(index >=0 && index < ENDINDEX);
2382	+	assert(int(bin) < nBins_);
2383	+	Vector3d s;
2384	+	int count;
2385	+
2386	+	count = data_[index].accumulator[bin]->count();
2387	+	if (count == 0) return;
2388	+
2389	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2390	+	if (isinf(s[0]) || isnan(s[0]) ||
2391	+	isinf(s[1]) || isnan(s[1]) ||
2392	+	isinf(s[2]) || isnan(s[2]) ) {
2393	+	sprintf( painCave.errMsg,
2394	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %u",
2395	+	data_[index].title.c_str(), bin);
2396	+	painCave.isFatal = 1;
2397	+	simError();
2398	+	} else {
2399	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2400	+	}
2401	+	}
2402		}
2403

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