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root/OpenMD/trunk/src/nonbonded/Electrostatic.cpp

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branches/development/src/nonbonded/Electrostatic.cpp (file contents), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
trunk/src/nonbonded/Electrostatic.cpp (file contents), Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

#	Line 34 | Line 34
34		* work.  Good starting points are:
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).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#ifdef IS_MPI
44	+	#include <mpi.h>
45	+	#endif
46	+
47		#include <stdio.h>
48		#include <string.h>
49
50		#include <cmath>
51	+	#include <numeric>
52		#include "nonbonded/Electrostatic.hpp"
53		#include "utils/simError.h"
54		#include "types/NonBondedInteractionType.hpp"
55	<	#include "types/DirectionalAtomType.hpp"
55	>	#include "types/FixedChargeAdapter.hpp"
56	>	#include "types/FluctuatingChargeAdapter.hpp"
57	>	#include "types/MultipoleAdapter.hpp"
58		#include "io/Globals.hpp"
59	+	#include "nonbonded/SlaterIntegrals.hpp"
60	+	#include "utils/PhysicalConstants.hpp"
61	+	#include "math/erfc.hpp"
62	+	#include "math/SquareMatrix.hpp"
63	+	#include "primitives/Molecule.hpp"
64
65		namespace OpenMD {
66
67		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
68	<	forceField_(NULL) {}
68	>	forceField_(NULL), info_(NULL),
69	>	haveCutoffRadius_(false),
70	>	haveDampingAlpha_(false),
71	>	haveDielectric_(false),
72	>	haveElectroSplines_(false)
73	>	{}
74
75		void Electrostatic::initialize() {
76	+
77	+	Globals* simParams_ = info_->getSimParams();
78
59	–	Globals* simParams_;
60	–
79		summationMap_["HARD"]               = esm_HARD;
80	+	summationMap_["NONE"]               = esm_HARD;
81		summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
82		summationMap_["SHIFTED_POTENTIAL"]  = esm_SHIFTED_POTENTIAL;
83		summationMap_["SHIFTED_FORCE"]      = esm_SHIFTED_FORCE;
84	+	summationMap_["TAYLOR_SHIFTED"]     = esm_TAYLOR_SHIFTED;
85		summationMap_["REACTION_FIELD"]     = esm_REACTION_FIELD;
86		summationMap_["EWALD_FULL"]         = esm_EWALD_FULL;
87		summationMap_["EWALD_PME"]          = esm_EWALD_PME;
#	Line 76 | Line 96 | namespace OpenMD {
96		// Charge-Dipole, assuming charges are measured in electrons, and
97		// dipoles are measured in debyes
98		pre12_ = 69.13373;
99	<	// Dipole-Dipole, assuming dipoles are measured in debyes
99	>	// Dipole-Dipole, assuming dipoles are measured in Debye
100		pre22_ = 14.39325;
101		// Charge-Quadrupole, assuming charges are measured in electrons, and
102		// quadrupoles are measured in 10^-26 esu cm^2
103	<	// This unit is also known affectionately as an esu centi-barn.
103	>	// This unit is also known affectionately as an esu centibarn.
104		pre14_ = 69.13373;
105	<
105	>	// Dipole-Quadrupole, assuming dipoles are measured in debyes and
106	>	// quadrupoles in esu centibarns:
107	>	pre24_ = 14.39325;
108	>	// Quadrupole-Quadrupole, assuming esu centibarns:
109	>	pre44_ = 14.39325;
110	>
111		// conversions for the simulation box dipole moment
112		chargeToC_ = 1.60217733e-19;
113		angstromToM_ = 1.0e-10;
114		debyeToCm_ = 3.33564095198e-30;
115
116	<	// number of points for electrostatic splines
116	>	// Default number of points for electrostatic splines
117		np_ = 100;
118
119		// variables to handle different summation methods for long-range
#	Line 96 | Line 121 | namespace OpenMD {
121		summationMethod_ = esm_HARD;
122		screeningMethod_ = UNDAMPED;
123		dielectric_ = 1.0;
99	–	one_third_ = 1.0 / 3.0;
100	–	haveCutoffRadius_ = false;
101	–	haveDampingAlpha_ = false;
102	–	haveDielectric_ = false;
103	–	haveElectroSpline_ = false;
124
125		// check the summation method:
126		if (simParams_->haveElectrostaticSummationMethod()) {
#	Line 113 | Line 133 | namespace OpenMD {
133		} else {
134		// throw error
135		sprintf( painCave.errMsg,
136	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
136	>	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
137		"\t(Input file specified %s .)\n"
138	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
139	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
140	<	"\t\"reaction_field\".\n", myMethod.c_str() );
138	>	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
139	>	"\t\"shifted_potential\", \"shifted_force\",\n"
140	>	"\t\"taylor_shifted\", or \"reaction_field\".\n",
141	>	myMethod.c_str() );
142		painCave.isFatal = 1;
143		simError();
144		}
#	Line 176 | Line 197 | namespace OpenMD {
197		simError();
198		}
199
200	<	if (screeningMethod_ == DAMPED) {
200	>	if (screeningMethod_ == DAMPED || summationMethod_ == esm_EWALD_FULL) {
201		if (!simParams_->haveDampingAlpha()) {
202		// first set a cutoff dependent alpha value
203		// we assume alpha depends linearly with rcut from 0 to 20.5 ang
204		dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
205	<	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
185	<
205	>	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
206		// throw warning
207		sprintf( painCave.errMsg,
208	<	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
209	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
208	>	"Electrostatic::initialize: dampingAlpha was not specified in the\n"
209	>	"\tinput file.  A default value of %f (1/ang) will be used for the\n"
210	>	"\tcutoff of %f (ang).\n",
211		dampingAlpha_, cutoffRadius_);
212		painCave.severity = OPENMD_INFO;
213		painCave.isFatal = 0;
#	Line 197 | Line 218 | namespace OpenMD {
218		haveDampingAlpha_ = true;
219		}
220
200	–	// find all of the Electrostatic atom Types:
201	–	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
202	–	ForceField::AtomTypeContainer::MapTypeIterator i;
203	–	AtomType* at;
204	–
205	–	for (at = atomTypes->beginType(i); at != NULL;
206	–	at = atomTypes->nextType(i)) {
207	–
208	–	if (at->isElectrostatic())
209	–	addType(at);
210	–	}
211	–
221
222	<	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
223	<	rcuti_ = 1.0 / cutoffRadius_;
224	<	rcuti2_ = rcuti_ * rcuti_;
225	<	rcuti3_ = rcuti2_ * rcuti_;
226	<	rcuti4_ = rcuti2_ * rcuti2_;
222	>	Etypes.clear();
223	>	Etids.clear();
224	>	FQtypes.clear();
225	>	FQtids.clear();
226	>	ElectrostaticMap.clear();
227	>	Jij.clear();
228	>	nElectro_ = 0;
229	>	nFlucq_ = 0;
230
231	<	if (screeningMethod_ == DAMPED) {
232	<
221	<	alpha2_ = dampingAlpha_ * dampingAlpha_;
222	<	alpha4_ = alpha2_ * alpha2_;
223	<	alpha6_ = alpha4_ * alpha2_;
224	<	alpha8_ = alpha4_ * alpha4_;
225	<
226	<	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
227	<	invRootPi_ = 0.56418958354775628695;
228	<	alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
231	>	Etids.resize( forceField_->getNAtomType(), -1);
232	>	FQtids.resize( forceField_->getNAtomType(), -1);
233
234	<	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
235	<	c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
236	<	c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
237	<	c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
234	<	c5c_ = 8.0 * alphaPi_ * alpha6_ + 7.0 * c4c_ * rcuti2_;
235	<	c6c_ = 16.0 * alphaPi_ * alpha8_ + 9.0 * c5c_ * rcuti2_;
236	<	} else {
237	<	c1c_ = rcuti_;
238	<	c2c_ = c1c_ * rcuti_;
239	<	c3c_ = 3.0 * c2c_ * rcuti_;
240	<	c4c_ = 5.0 * c3c_ * rcuti2_;
241	<	c5c_ = 7.0 * c4c_ * rcuti2_;
242	<	c6c_ = 9.0 * c5c_ * rcuti2_;
234	>	set<AtomType*>::iterator at;
235	>	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
236	>	if ((*at)->isElectrostatic()) nElectro_++;
237	>	if ((*at)->isFluctuatingCharge()) nFlucq_++;
238		}
239	<
239	>
240	>	Jij.resize(nFlucq_);
241	>
242	>	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
243	>	if ((*at)->isElectrostatic()) addType(*at);
244	>	}
245	>
246		if (summationMethod_ == esm_REACTION_FIELD) {
247		preRF_ = (dielectric_ - 1.0) /
248	<	((2.0 * dielectric_ + 1.0) * cutoffRadius2_ * cutoffRadius_);
248	<	preRF2_ = 2.0 * preRF_;
248	>	((2.0 * dielectric_ + 1.0) * pow(cutoffRadius_,3) );
249		}
250
251	<	RealType dx = cutoffRadius_ / RealType(np_ - 1);
252	<	RealType rval;
253	<	vector<RealType> rvals;
254	<	vector<RealType> yvals;
255	<	for (int i = 0; i < np_; i++) {
256	<	rval = RealType(i) * dx;
257	<	rvals.push_back(rval);
258	<	yvals.push_back(erfc(dampingAlpha_ * rval));
251	>	RealType b0c, b1c, b2c, b3c, b4c, b5c;
252	>	RealType db0c_1, db0c_2, db0c_3, db0c_4, db0c_5;
253	>	RealType a2, expTerm, invArootPi;
254	>
255	>	RealType r = cutoffRadius_;
256	>	RealType r2 = r * r;
257	>	RealType ric = 1.0 / r;
258	>	RealType ric2 = ric * ric;
259	>
260	>	if (screeningMethod_ == DAMPED) {
261	>	a2 = dampingAlpha_ * dampingAlpha_;
262	>	invArootPi = 1.0 / (dampingAlpha_ * sqrt(M_PI));
263	>	expTerm = exp(-a2 * r2);
264	>	// values of Smith's B_l functions at the cutoff radius:
265	>	b0c = erfc(dampingAlpha_ * r) / r;
266	>	b1c = (      b0c     + 2.0*a2     * expTerm * invArootPi) / r2;
267	>	b2c = (3.0 * b1c + pow(2.0*a2, 2) * expTerm * invArootPi) / r2;
268	>	b3c = (5.0 * b2c + pow(2.0*a2, 3) * expTerm * invArootPi) / r2;
269	>	b4c = (7.0 * b3c + pow(2.0*a2, 4) * expTerm * invArootPi) / r2;
270	>	b5c = (9.0 * b4c + pow(2.0*a2, 5) * expTerm * invArootPi) / r2;
271	>	// Half the Smith self piece:
272	>	selfMult1_ = - a2 * invArootPi;
273	>	selfMult2_ = - 2.0 * a2 * a2 * invArootPi / 3.0;
274	>	selfMult4_ = - 4.0 * a2 * a2 * a2 * invArootPi / 5.0;
275	>	} else {
276	>	a2 = 0.0;
277	>	b0c = 1.0 / r;
278	>	b1c = (      b0c) / r2;
279	>	b2c = (3.0 * b1c) / r2;
280	>	b3c = (5.0 * b2c) / r2;
281	>	b4c = (7.0 * b3c) / r2;
282	>	b5c = (9.0 * b4c) / r2;
283	>	selfMult1_ = 0.0;
284	>	selfMult2_ = 0.0;
285	>	selfMult4_ = 0.0;
286		}
260	–	erfcSpline_ = new CubicSpline();
261	–	erfcSpline_->addPoints(rvals, yvals);
262	–	haveElectroSpline_ = true;
287
288	<	initialized_ = true;
289	<	}
290	<
291	<	void Electrostatic::addType(AtomType* atomType){
288	>	// higher derivatives of B_0 at the cutoff radius:
289	>	db0c_1 = -r * b1c;
290	>	db0c_2 =     -b1c + r2 * b2c;
291	>	db0c_3 =          3.0*r*b2c  - r2*r*b3c;
292	>	db0c_4 =          3.0*b2c  - 6.0*r2*b3c     + r2*r2*b4c;
293	>	db0c_5 =                    -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c;
294
295	<	ElectrostaticAtomData electrostaticAtomData;
296	<	electrostaticAtomData.is_Charge = false;
297	<	electrostaticAtomData.is_Dipole = false;
298	<	electrostaticAtomData.is_SplitDipole = false;
299	<	electrostaticAtomData.is_Quadrupole = false;
295	>	if (summationMethod_ != esm_EWALD_FULL) {
296	>	selfMult1_ -= b0c;
297	>	selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) /  3.0;
298	>	selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0;
299	>	}
300
301	<	if (atomType->isCharge()) {
302	<	GenericData* data = atomType->getPropertyByName("Charge");
301	>	// working variables for the splines:
302	>	RealType ri, ri2;
303	>	RealType b0, b1, b2, b3, b4, b5;
304	>	RealType db0_1, db0_2, db0_3, db0_4, db0_5;
305	>	RealType f, fc, f0;
306	>	RealType g, gc, g0, g1, g2, g3, g4;
307	>	RealType h, hc, h1, h2, h3, h4;
308	>	RealType s, sc, s2, s3, s4;
309	>	RealType t, tc, t3, t4;
310	>	RealType u, uc, u4;
311
312	<	if (data == NULL) {
313	<	sprintf( painCave.errMsg, "Electrostatic::addType could not find "
280	<	"Charge\n"
281	<	"\tparameters for atomType %s.\n",
282	<	atomType->getName().c_str());
283	<	painCave.severity = OPENMD_ERROR;
284	<	painCave.isFatal = 1;
285	<	simError();
286	<	}
287	<
288	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
289	<	if (doubleData == NULL) {
290	<	sprintf( painCave.errMsg,
291	<	"Electrostatic::addType could not convert GenericData to "
292	<	"Charge for\n"
293	<	"\tatom type %s\n", atomType->getName().c_str());
294	<	painCave.severity = OPENMD_ERROR;
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<	electrostaticAtomData.is_Charge = true;
299	<	electrostaticAtomData.charge = doubleData->getData();
300	<	}
312	>	// working variables for Taylor expansion:
313	>	RealType rmRc, rmRc2, rmRc3, rmRc4;
314
315	<	if (atomType->isDirectional()) {
316	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
317	<
318	<	if (daType->isDipole()) {
319	<	GenericData* data = daType->getPropertyByName("Dipole");
320	<
321	<	if (data == NULL) {
322	<	sprintf( painCave.errMsg,
323	<	"Electrostatic::addType could not find Dipole\n"
324	<	"\tparameters for atomType %s.\n",
325	<	daType->getName().c_str());
326	<	painCave.severity = OPENMD_ERROR;
327	<	painCave.isFatal = 1;
328	<	simError();
329	<	}
330	<
331	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
332	<	if (doubleData == NULL) {
333	<	sprintf( painCave.errMsg,
334	<	"Electrostatic::addType could not convert GenericData to "
335	<	"Dipole Moment\n"
336	<	"\tfor atom type %s\n", daType->getName().c_str());
337	<	painCave.severity = OPENMD_ERROR;
338	<	painCave.isFatal = 1;
339	<	simError();
340	<	}
341	<	electrostaticAtomData.is_Dipole = true;
342	<	electrostaticAtomData.dipole_moment = doubleData->getData();
315	>	// Approximate using splines using a maximum of 0.1 Angstroms
316	>	// between points.
317	>	int nptest = int((cutoffRadius_ + 2.0) / 0.1);
318	>	np_ = (np_ > nptest) ? np_ : nptest;
319	>
320	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
321	>	// have charged atoms longer than the cutoffRadius away from each
322	>	// other.  Splining is almost certainly the best choice here.
323	>	// Direct calls to erfc would be preferrable if it is a very fast
324	>	// implementation.
325	>
326	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_);
327	>
328	>	// Storage vectors for the computed functions
329	>	vector<RealType> rv;
330	>	vector<RealType> v01v;
331	>	vector<RealType> v11v;
332	>	vector<RealType> v21v, v22v;
333	>	vector<RealType> v31v, v32v;
334	>	vector<RealType> v41v, v42v, v43v;
335	>
336	>	for (int i = 1; i < np_ + 1; i++) {
337	>	r = RealType(i) * dx;
338	>	rv.push_back(r);
339	>
340	>	ri = 1.0 / r;
341	>	ri2 = ri * ri;
342	>
343	>	r2 = r * r;
344	>	expTerm = exp(-a2 * r2);
345	>
346	>	// Taylor expansion factors (no need for factorials this way):
347	>	rmRc = r - cutoffRadius_;
348	>	rmRc2 = rmRc  * rmRc / 2.0;
349	>	rmRc3 = rmRc2 * rmRc / 3.0;
350	>	rmRc4 = rmRc3 * rmRc / 4.0;
351	>
352	>	// values of Smith's B_l functions at r:
353	>	if (screeningMethod_ == DAMPED) {
354	>	b0 = erfc(dampingAlpha_ * r) * ri;
355	>	b1 = (      b0 +     2.0*a2     * expTerm * invArootPi) * ri2;
356	>	b2 = (3.0 * b1 + pow(2.0*a2, 2) * expTerm * invArootPi) * ri2;
357	>	b3 = (5.0 * b2 + pow(2.0*a2, 3) * expTerm * invArootPi) * ri2;
358	>	b4 = (7.0 * b3 + pow(2.0*a2, 4) * expTerm * invArootPi) * ri2;
359	>	b5 = (9.0 * b4 + pow(2.0*a2, 5) * expTerm * invArootPi) * ri2;
360	>	} else {
361	>	b0 = ri;
362	>	b1 = (      b0) * ri2;
363	>	b2 = (3.0 * b1) * ri2;
364	>	b3 = (5.0 * b2) * ri2;
365	>	b4 = (7.0 * b3) * ri2;
366	>	b5 = (9.0 * b4) * ri2;
367		}
368	+
369	+	// higher derivatives of B_0 at r:
370	+	db0_1 = -r * b1;
371	+	db0_2 =     -b1 + r2 * b2;
372	+	db0_3 =          3.0*r*b2   - r2*r*b3;
373	+	db0_4 =          3.0*b2   - 6.0*r2*b3     + r2*r2*b4;
374	+	db0_5 =                    -15.0*r*b3 + 10.0*r2*r*b4 - r2*r2*r*b5;
375
376	<	if (daType->isSplitDipole()) {
377	<	GenericData* data = daType->getPropertyByName("SplitDipoleDistance");
378	<
379	<	if (data == NULL) {
380	<	sprintf(painCave.errMsg,
381	<	"Electrostatic::addType could not find SplitDipoleDistance\n"
382	<	"\tparameter for atomType %s.\n",
383	<	daType->getName().c_str());
384	<	painCave.severity = OPENMD_ERROR;
385	<	painCave.isFatal = 1;
386	<	simError();
387	<	}
376	>	f = b0;
377	>	fc = b0c;
378	>	f0 = f - fc - rmRc*db0c_1;
379	>
380	>	g = db0_1;
381	>	gc = db0c_1;
382	>	g0 = g - gc;
383	>	g1 = g0 - rmRc *db0c_2;
384	>	g2 = g1 - rmRc2*db0c_3;
385	>	g3 = g2 - rmRc3*db0c_4;
386	>	g4 = g3 - rmRc4*db0c_5;
387	>
388	>	h = db0_2;
389	>	hc = db0c_2;
390	>	h1 = h - hc;
391	>	h2 = h1 - rmRc *db0c_3;
392	>	h3 = h2 - rmRc2*db0c_4;
393	>	h4 = h3 - rmRc3*db0c_5;
394	>
395	>	s = db0_3;
396	>	sc = db0c_3;
397	>	s2 = s - sc;
398	>	s3 = s2 - rmRc *db0c_4;
399	>	s4 = s3 - rmRc2*db0c_5;
400	>
401	>	t = db0_4;
402	>	tc = db0c_4;
403	>	t3 = t - tc;
404	>	t4 = t3 - rmRc *db0c_5;
405
406	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
407	<	if (doubleData == NULL) {
408	<	sprintf( painCave.errMsg,
348	<	"Electrostatic::addType could not convert GenericData to "
349	<	"SplitDipoleDistance for\n"
350	<	"\tatom type %s\n", daType->getName().c_str());
351	<	painCave.severity = OPENMD_ERROR;
352	<	painCave.isFatal = 1;
353	<	simError();
354	<	}
355	<	electrostaticAtomData.is_SplitDipole = true;
356	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
357	<	}
406	>	u = db0_5;
407	>	uc = db0c_5;
408	>	u4 = u - uc;
409
410	<	if (daType->isQuadrupole()) {
411	<	GenericData* data = daType->getPropertyByName("QuadrupoleMoments");
410	>	// in what follows below, the various v functions are used for
411	>	// potentials and torques, while the w functions show up in the
412	>	// forces.
413	>
414	>	switch (summationMethod_) {
415	>	case esm_SHIFTED_FORCE:
416	>
417	>	v01 = f - fc - rmRc*gc;
418	>	v11 = g - gc - rmRc*hc;
419	>	v21 = g*ri - gc*ric - rmRc*(hc - gc*ric)*ric;
420	>	v22 = h - g*ri - (hc - gc*ric) - rmRc*(sc - (hc - gc*ric)*ric);
421	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric - rmRc*(sc-2.0*(hc-gc*ric)*ric)*ric;
422	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric)
423	>	- rmRc*(tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric);
424	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2
425	>	- rmRc*(sc - 3.0*(hc-gc*ric)*ric)*ric2;
426	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric
427	>	- rmRc*(tc - (4.0*sc - 9.0*(hc - gc*ric)*ric)*ric)*ric;
428
429	<	if (data == NULL) {
430	<	sprintf( painCave.errMsg,
431	<	"Electrostatic::addType could not find QuadrupoleMoments\n"
432	<	"\tparameter for atomType %s.\n",
433	<	daType->getName().c_str());
434	<	painCave.severity = OPENMD_ERROR;
435	<	painCave.isFatal = 1;
436	<	simError();
437	<	}
429	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
430	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric)
431	>	- rmRc*(uc-3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric);
432	>
433	>	dv01 = g - gc;
434	>	dv11 = h - hc;
435	>	dv21 = (h - g*ri)*ri - (hc - gc*ric)*ric;
436	>	dv22 = (s - (h - g*ri)*ri) - (sc - (hc - gc*ric)*ric);
437	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri - (sc - 2.0*(hc-gc*ric)*ric)*ric;
438	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri)
439	>	- (tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric);
440	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2 - (sc - 3.0*(hc - gc*ric)*ric)*ric2;
441	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri
442	>	- (tc - (4.0*sc - 9.0*(hc-gc*ric)*ric)*ric)*ric;
443	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri)
444	>	- (uc - 3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric);
445
446	<	// Quadrupoles in OpenMD are set as the diagonal elements
373	<	// of the diagonalized traceless quadrupole moment tensor.
374	<	// The column vectors of the unitary matrix that diagonalizes
375	<	// the quadrupole moment tensor become the eFrame (or the
376	<	// electrostatic version of the body-fixed frame.
446	>	break;
447
448	<	Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
449	<	if (v3dData == NULL) {
450	<	sprintf( painCave.errMsg,
451	<	"Electrostatic::addType could not convert GenericData to "
452	<	"Quadrupole Moments for\n"
453	<	"\tatom type %s\n", daType->getName().c_str());
454	<	painCave.severity = OPENMD_ERROR;
455	<	painCave.isFatal = 1;
456	<	simError();
448	>	case esm_TAYLOR_SHIFTED:
449	>
450	>	v01 = f0;
451	>	v11 = g1;
452	>	v21 = g2 * ri;
453	>	v22 = h2 - v21;
454	>	v31 = (h3 - g3 * ri) * ri;
455	>	v32 = s3 - 3.0*v31;
456	>	v41 = (h4 - g4 * ri) * ri2;
457	>	v42 = s4 * ri - 3.0*v41;
458	>	v43 = t4 - 6.0*v42 - 3.0*v41;
459	>
460	>	dv01 = g0;
461	>	dv11 = h1;
462	>	dv21 = (h2 - g2*ri)*ri;
463	>	dv22 = (s2 - (h2 - g2*ri)*ri);
464	>	dv31 = (s3 - 2.0*(h3-g3*ri)*ri)*ri;
465	>	dv32 = (t3 - 3.0*(s3-2.0*(h3-g3*ri)*ri)*ri);
466	>	dv41 = (s4 - 3.0*(h4 - g4*ri)*ri)*ri2;
467	>	dv42 = (t4 - (4.0*s4 - 9.0*(h4-g4*ri)*ri)*ri)*ri;
468	>	dv43 = (u4 - 3.0*(2.0*t4 - (7.0*s4 - 15.0*(h4 - g4*ri)*ri)*ri)*ri);
469	>
470	>	break;
471	>
472	>	case esm_SHIFTED_POTENTIAL:
473	>
474	>	v01 = f - fc;
475	>	v11 = g - gc;
476	>	v21 = g*ri - gc*ric;
477	>	v22 = h - g*ri - (hc - gc*ric);
478	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric;
479	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric);
480	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2;
481	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric;
482	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
483	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric);
484	>
485	>	dv01 = g;
486	>	dv11 = h;
487	>	dv21 = (h - g*ri)*ri;
488	>	dv22 = (s - (h - g*ri)*ri);
489	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
490	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
491	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
492	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
493	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
494	>
495	>	break;
496	>
497	>	case esm_SWITCHING_FUNCTION:
498	>	case esm_HARD:
499	>	case esm_EWALD_FULL:
500	>
501	>	v01 = f;
502	>	v11 = g;
503	>	v21 = g*ri;
504	>	v22 = h - g*ri;
505	>	v31 = (h-g*ri)*ri;
506	>	v32 = (s - 3.0*(h-g*ri)*ri);
507	>	v41 = (h - g*ri)*ri2;
508	>	v42 = (s-3.0*(h-g*ri)*ri)*ri;
509	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri);
510	>
511	>	dv01 = g;
512	>	dv11 = h;
513	>	dv21 = (h - g*ri)*ri;
514	>	dv22 = (s - (h - g*ri)*ri);
515	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
516	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
517	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
518	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
519	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
520	>
521	>	break;
522	>
523	>	case esm_REACTION_FIELD:
524	>
525	>	// following DL_POLY's lead for shifting the image charge potential:
526	>	f = b0 + preRF_ * r2;
527	>	fc = b0c + preRF_ * cutoffRadius_ * cutoffRadius_;
528	>
529	>	g = db0_1 + preRF_ * 2.0 * r;
530	>	gc = db0c_1 + preRF_ * 2.0 * cutoffRadius_;
531	>
532	>	h = db0_2 + preRF_ * 2.0;
533	>	hc = db0c_2 + preRF_ * 2.0;
534	>
535	>	v01 = f - fc;
536	>	v11 = g - gc;
537	>	v21 = g*ri - gc*ric;
538	>	v22 = h - g*ri - (hc - gc*ric);
539	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric;
540	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric);
541	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2;
542	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric;
543	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
544	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric);
545	>
546	>	dv01 = g;
547	>	dv11 = h;
548	>	dv21 = (h - g*ri)*ri;
549	>	dv22 = (s - (h - g*ri)*ri);
550	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
551	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
552	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
553	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
554	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
555	>
556	>	break;
557	>
558	>	case esm_EWALD_PME:
559	>	case esm_EWALD_SPME:
560	>	default :
561	>	map<string, ElectrostaticSummationMethod>::iterator i;
562	>	std::string meth;
563	>	for (i = summationMap_.begin(); i != summationMap_.end(); ++i) {
564	>	if ((*i).second == summationMethod_) meth = (*i).first;
565		}
566	+	sprintf( painCave.errMsg,
567	+	"Electrostatic::initialize: electrostaticSummationMethod %s \n"
568	+	"\thas not been implemented yet. Please select one of:\n"
569	+	"\t\"hard\", \"shifted_potential\", or \"shifted_force\"\n",
570	+	meth.c_str() );
571	+	painCave.isFatal = 1;
572	+	simError();
573	+	break;
574	+	}
575	+
576	+	// Add these computed values to the storage vectors for spline creation:
577	+	v01v.push_back(v01);
578	+	v11v.push_back(v11);
579	+	v21v.push_back(v21);
580	+	v22v.push_back(v22);
581	+	v31v.push_back(v31);
582	+	v32v.push_back(v32);
583	+	v41v.push_back(v41);
584	+	v42v.push_back(v42);
585	+	v43v.push_back(v43);
586	+	}
587	+
588	+	// construct the spline structures and fill them with the values we've
589	+	// computed:
590	+
591	+	v01s = new CubicSpline();
592	+	v01s->addPoints(rv, v01v);
593	+	v11s = new CubicSpline();
594	+	v11s->addPoints(rv, v11v);
595	+	v21s = new CubicSpline();
596	+	v21s->addPoints(rv, v21v);
597	+	v22s = new CubicSpline();
598	+	v22s->addPoints(rv, v22v);
599	+	v31s = new CubicSpline();
600	+	v31s->addPoints(rv, v31v);
601	+	v32s = new CubicSpline();
602	+	v32s->addPoints(rv, v32v);
603	+	v41s = new CubicSpline();
604	+	v41s->addPoints(rv, v41v);
605	+	v42s = new CubicSpline();
606	+	v42s->addPoints(rv, v42v);
607	+	v43s = new CubicSpline();
608	+	v43s->addPoints(rv, v43v);
609	+
610	+	haveElectroSplines_ = true;
611	+
612	+	initialized_ = true;
613	+	}
614	+
615	+	void Electrostatic::addType(AtomType* atomType){
616	+
617	+	ElectrostaticAtomData electrostaticAtomData;
618	+	electrostaticAtomData.is_Charge = false;
619	+	electrostaticAtomData.is_Dipole = false;
620	+	electrostaticAtomData.is_Quadrupole = false;
621	+	electrostaticAtomData.is_Fluctuating = false;
622	+
623	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
624	+
625	+	if (fca.isFixedCharge()) {
626	+	electrostaticAtomData.is_Charge = true;
627	+	electrostaticAtomData.fixedCharge = fca.getCharge();
628	+	}
629	+
630	+	MultipoleAdapter ma = MultipoleAdapter(atomType);
631	+	if (ma.isMultipole()) {
632	+	if (ma.isDipole()) {
633	+	electrostaticAtomData.is_Dipole = true;
634	+	electrostaticAtomData.dipole = ma.getDipole();
635	+	}
636	+	if (ma.isQuadrupole()) {
637		electrostaticAtomData.is_Quadrupole = true;
638	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
638	>	electrostaticAtomData.quadrupole = ma.getQuadrupole();
639		}
640		}
641
642	<	AtomTypeProperties atp = atomType->getATP();
642	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
643
644	<	pair<map<int,AtomType*>::iterator,bool> ret;
645	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
644	>	if (fqa.isFluctuatingCharge()) {
645	>	electrostaticAtomData.is_Fluctuating = true;
646	>	electrostaticAtomData.electronegativity = fqa.getElectronegativity();
647	>	electrostaticAtomData.hardness = fqa.getHardness();
648	>	electrostaticAtomData.slaterN = fqa.getSlaterN();
649	>	electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
650	>	}
651	>
652	>	int atid = atomType->getIdent();
653	>	int etid = Etypes.size();
654	>	int fqtid = FQtypes.size();
655	>
656	>	pair<set<int>::iterator,bool> ret;
657	>	ret = Etypes.insert( atid );
658		if (ret.second == false) {
659		sprintf( painCave.errMsg,
660		"Electrostatic already had a previous entry with ident %d\n",
661	<	atp.ident);
661	>	atid);
662		painCave.severity = OPENMD_INFO;
663		painCave.isFatal = 0;
664		simError();
665		}
666
667	<	ElectrostaticMap[atomType] = electrostaticAtomData;
667	>	Etids[ atid ] = etid;
668	>	ElectrostaticMap.push_back(electrostaticAtomData);
669	>
670	>	if (electrostaticAtomData.is_Fluctuating) {
671	>	ret = FQtypes.insert( atid );
672	>	if (ret.second == false) {
673	>	sprintf( painCave.errMsg,
674	>	"Electrostatic already had a previous fluctuating charge entry with ident %d\n",
675	>	atid );
676	>	painCave.severity = OPENMD_INFO;
677	>	painCave.isFatal = 0;
678	>	simError();
679	>	}
680	>	FQtids[atid] = fqtid;
681	>	Jij[fqtid].resize(nFlucq_);
682	>
683	>	// Now, iterate over all known fluctuating and add to the
684	>	// coulomb integral map:
685	>
686	>	std::set<int>::iterator it;
687	>	for( it = FQtypes.begin(); it != FQtypes.end(); ++it) {
688	>	int etid2 = Etids[ (*it) ];
689	>	int fqtid2 = FQtids[ (*it) ];
690	>	ElectrostaticAtomData eaData2 = ElectrostaticMap[ etid2 ];
691	>	RealType a = electrostaticAtomData.slaterZeta;
692	>	RealType b = eaData2.slaterZeta;
693	>	int m = electrostaticAtomData.slaterN;
694	>	int n = eaData2.slaterN;
695	>
696	>	// Create the spline of the coulombic integral for s-type
697	>	// Slater orbitals.  Add a 2 angstrom safety window to deal
698	>	// with cutoffGroups that have charged atoms longer than the
699	>	// cutoffRadius away from each other.
700	>
701	>	RealType rval;
702	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
703	>	vector<RealType> rvals;
704	>	vector<RealType> Jvals;
705	>	// don't start at i = 0, as rval = 0 is undefined for the
706	>	// slater overlap integrals.
707	>	for (int i = 1; i < np_+1; i++) {
708	>	rval = RealType(i) * dr;
709	>	rvals.push_back(rval);
710	>	Jvals.push_back(sSTOCoulInt( a, b, m, n, rval *
711	>	PhysicalConstants::angstromToBohr ) *
712	>	PhysicalConstants::hartreeToKcal );
713	>	}
714	>
715	>	CubicSpline* J = new CubicSpline();
716	>	J->addPoints(rvals, Jvals);
717	>	Jij[fqtid][fqtid2] = J;
718	>	Jij[fqtid2].resize( nFlucq_ );
719	>	Jij[fqtid2][fqtid] = J;
720	>	}
721	>	}
722		return;
723		}
724
725	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
726	<	RealType theRSW ) {
412	<	cutoffRadius_ = theECR;
413	<	rrf_ = cutoffRadius_;
414	<	rt_ = theRSW;
725	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
726	>	cutoffRadius_ = rCut;
727		haveCutoffRadius_ = true;
728		}
729	+
730		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
731		summationMethod_ = esm;
732		}
#	Line 429 | Line 742 | namespace OpenMD {
742		haveDielectric_ = true;
743		}
744
745	<	void Electrostatic::calcForce(InteractionData idat) {
745	>	void Electrostatic::calcForce(InteractionData &idat) {
746
434	–	// utility variables.  Should clean these up and use the Vector3d and
435	–	// Mat3x3d to replace as many as we can in future versions:
436	–
437	–	RealType q_i, q_j, mu_i, mu_j, d_i, d_j;
438	–	RealType qxx_i, qyy_i, qzz_i;
439	–	RealType qxx_j, qyy_j, qzz_j;
440	–	RealType cx_i, cy_i, cz_i;
441	–	RealType cx_j, cy_j, cz_j;
442	–	RealType cx2, cy2, cz2;
443	–	RealType ct_i, ct_j, ct_ij, a1;
444	–	RealType riji, ri, ri2, ri3, ri4;
445	–	RealType pref, vterm, epot, dudr;
446	–	RealType scale, sc2;
447	–	RealType pot_term, preVal, rfVal;
448	–	RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
449	–	RealType preSw, preSwSc;
450	–	RealType c1, c2, c3, c4;
451	–	RealType erfcVal, derfcVal;
452	–	RealType BigR;
453	–
454	–	Vector3d Q_i, Q_j;
455	–	Vector3d ux_i, uy_i, uz_i;
456	–	Vector3d ux_j, uy_j, uz_j;
457	–	Vector3d dudux_i, duduy_i, duduz_i;
458	–	Vector3d dudux_j, duduy_j, duduz_j;
459	–	Vector3d rhatdot2, rhatc4;
460	–	Vector3d dVdr;
461	–
462	–	pair<RealType, RealType> res;
463	–
747		if (!initialized_) initialize();
748
749	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
750	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
749	>	data1 = ElectrostaticMap[Etids[idat.atid1]];
750	>	data2 = ElectrostaticMap[Etids[idat.atid2]];
751	>
752	>	U = 0.0;  // Potential
753	>	F.zero();  // Force
754	>	Ta.zero(); // Torque on site a
755	>	Tb.zero(); // Torque on site b
756	>	Ea.zero(); // Electric field at site a
757	>	Eb.zero(); // Electric field at site b
758	>	dUdCa = 0.0; // fluctuating charge force at site a
759	>	dUdCb = 0.0; // fluctuating charge force at site a
760
761	<	// some variables we'll need independent of electrostatic type:
761	>	// Indirect interactions mediated by the reaction field.
762	>	indirect_Pot = 0.0;   // Potential
763	>	indirect_F.zero();    // Force
764	>	indirect_Ta.zero();   // Torque on site a
765	>	indirect_Tb.zero();   // Torque on site b
766
767	<	riji = 1.0 / idat.rij;
768	<	Vector3d rhat = idat.d  * riji;
767	>	// Excluded potential that is still computed for fluctuating charges
768	>	excluded_Pot= 0.0;
769
770	<	// logicals
770	>	// some variables we'll need independent of electrostatic type:
771
772	<	bool i_is_Charge = data1.is_Charge;
773	<	bool i_is_Dipole = data1.is_Dipole;
478	<	bool i_is_SplitDipole = data1.is_SplitDipole;
479	<	bool i_is_Quadrupole = data1.is_Quadrupole;
480	<
481	<	bool j_is_Charge = data2.is_Charge;
482	<	bool j_is_Dipole = data2.is_Dipole;
483	<	bool j_is_SplitDipole = data2.is_SplitDipole;
484	<	bool j_is_Quadrupole = data2.is_Quadrupole;
485	<
486	<	if (i_is_Charge)
487	<	q_i = data1.charge;
488	<
489	<	if (i_is_Dipole) {
490	<	mu_i = data1.dipole_moment;
491	<	uz_i = idat.eFrame1.getColumn(2);
772	>	ri = 1.0 /  *(idat.rij);
773	>	rhat =  *(idat.d)  * ri;
774
775	<	ct_i = dot(uz_i, rhat);
775	>	// logicals
776
777	<	if (i_is_SplitDipole)
778	<	d_i = data1.split_dipole_distance;
779	<
780	<	duduz_i = V3Zero;
499	<	}
500	<
501	<	if (i_is_Quadrupole) {
502	<	Q_i = data1.quadrupole_moments;
503	<	qxx_i = Q_i.x();
504	<	qyy_i = Q_i.y();
505	<	qzz_i = Q_i.z();
506	<
507	<	ux_i = idat.eFrame1.getColumn(0);
508	<	uy_i = idat.eFrame1.getColumn(1);
509	<	uz_i = idat.eFrame1.getColumn(2);
777	>	a_is_Charge = data1.is_Charge;
778	>	a_is_Dipole = data1.is_Dipole;
779	>	a_is_Quadrupole = data1.is_Quadrupole;
780	>	a_is_Fluctuating = data1.is_Fluctuating;
781
782	<	cx_i = dot(ux_i, rhat);
783	<	cy_i = dot(uy_i, rhat);
784	<	cz_i = dot(uz_i, rhat);
782	>	b_is_Charge = data2.is_Charge;
783	>	b_is_Dipole = data2.is_Dipole;
784	>	b_is_Quadrupole = data2.is_Quadrupole;
785	>	b_is_Fluctuating = data2.is_Fluctuating;
786
787	<	dudux_i = V3Zero;
788	<	duduy_i = V3Zero;
789	<	duduz_i = V3Zero;
787	>	// Obtain all of the required radial function values from the
788	>	// spline structures:
789	>
790	>	// needed for fields (and forces):
791	>	if (a_is_Charge || b_is_Charge) {
792	>	v01s->getValueAndDerivativeAt( *(idat.rij), v01, dv01);
793		}
794	+	if (a_is_Dipole || b_is_Dipole) {
795	+	v11s->getValueAndDerivativeAt( *(idat.rij), v11, dv11);
796	+	v11or = ri * v11;
797	+	}
798	+	if (a_is_Quadrupole || b_is_Quadrupole ||  (a_is_Dipole && b_is_Dipole)) {
799	+	v21s->getValueAndDerivativeAt( *(idat.rij), v21, dv21);
800	+	v22s->getValueAndDerivativeAt( *(idat.rij), v22, dv22);
801	+	v22or = ri * v22;
802	+	}
803
804	<	if (j_is_Charge)
805	<	q_j = data2.charge;
804	>	// needed for potentials (and forces and torques):
805	>	if ((a_is_Dipole && b_is_Quadrupole) ||
806	>	(b_is_Dipole && a_is_Quadrupole)) {
807	>	v31s->getValueAndDerivativeAt( *(idat.rij), v31, dv31);
808	>	v32s->getValueAndDerivativeAt( *(idat.rij), v32, dv32);
809	>	v31or = v31 * ri;
810	>	v32or = v32 * ri;
811	>	}
812	>	if (a_is_Quadrupole && b_is_Quadrupole) {
813	>	v41s->getValueAndDerivativeAt( *(idat.rij), v41, dv41);
814	>	v42s->getValueAndDerivativeAt( *(idat.rij), v42, dv42);
815	>	v43s->getValueAndDerivativeAt( *(idat.rij), v43, dv43);
816	>	v42or = v42 * ri;
817	>	v43or = v43 * ri;
818	>	}
819
820	<	if (j_is_Dipole) {
821	<	mu_j = data2.dipole_moment;
822	<	uz_j = idat.eFrame2.getColumn(2);
820	>	// calculate the single-site contributions (fields, etc).
821	>
822	>	if (a_is_Charge) {
823	>	C_a = data1.fixedCharge;
824
825	<	ct_j = dot(uz_j, rhat);
826	<
827	<	if (j_is_SplitDipole)
530	<	d_j = data2.split_dipole_distance;
825	>	if (a_is_Fluctuating) {
826	>	C_a += *(idat.flucQ1);
827	>	}
828
829	<	duduz_j = V3Zero;
829	>	if (idat.excluded) {
830	>	*(idat.skippedCharge2) += C_a;
831	>	} else {
832	>	// only do the field if we're not excluded:
833	>	Eb -= C_a *  pre11_ * dv01 * rhat;
834	>	}
835		}
836
837	<	if (j_is_Quadrupole) {
838	<	Q_j = data2.quadrupole_moments;
839	<	qxx_j = Q_j.x();
840	<	qyy_j = Q_j.y();
841	<	qzz_j = Q_j.z();
837	>	if (a_is_Dipole) {
838	>	D_a = *(idat.dipole1);
839	>	rdDa = dot(rhat, D_a);
840	>	rxDa = cross(rhat, D_a);
841	>	if (!idat.excluded)
842	>	Eb -=  pre12_ * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
843	>	}
844	>
845	>	if (a_is_Quadrupole) {
846	>	Q_a = *(idat.quadrupole1);
847	>	trQa =  Q_a.trace();
848	>	Qar =   Q_a * rhat;
849	>	rQa = rhat * Q_a;
850	>	rdQar = dot(rhat, Qar);
851	>	rxQar = cross(rhat, Qar);
852	>	if (!idat.excluded)
853	>	Eb -= pre14_ * (trQa * rhat * dv21 + 2.0 * Qar * v22or
854	>	+ rdQar * rhat * (dv22 - 2.0*v22or));
855	>	}
856	>
857	>	if (b_is_Charge) {
858	>	C_b = data2.fixedCharge;
859
860	<	ux_j = idat.eFrame2.getColumn(0);
861	<	uy_j = idat.eFrame2.getColumn(1);
862	<	uz_j = idat.eFrame2.getColumn(2);
863	<
864	<	cx_j = dot(ux_j, rhat);
865	<	cy_j = dot(uy_j, rhat);
866	<	cz_j = dot(uz_j, rhat);
867	<
868	<	dudux_j = V3Zero;
550	<	duduy_j = V3Zero;
551	<	duduz_j = V3Zero;
860	>	if (b_is_Fluctuating)
861	>	C_b += *(idat.flucQ2);
862	>
863	>	if (idat.excluded) {
864	>	*(idat.skippedCharge1) += C_b;
865	>	} else {
866	>	// only do the field if we're not excluded:
867	>	Ea += C_b *  pre11_ * dv01 * rhat;
868	>	}
869		}
870
871	<	epot = 0.0;
872	<	dVdr = V3Zero;
871	>	if (b_is_Dipole) {
872	>	D_b = *(idat.dipole2);
873	>	rdDb = dot(rhat, D_b);
874	>	rxDb = cross(rhat, D_b);
875	>	if (!idat.excluded)
876	>	Ea += pre12_ * ((dv11-v11or) * rdDb * rhat + v11or * D_b);
877	>	}
878
879	<	if (i_is_Charge) {
879	>	if (b_is_Quadrupole) {
880	>	Q_b = *(idat.quadrupole2);
881	>	trQb =  Q_b.trace();
882	>	Qbr =   Q_b * rhat;
883	>	rQb = rhat * Q_b;
884	>	rdQbr = dot(rhat, Qbr);
885	>	rxQbr = cross(rhat, Qbr);
886	>	if (!idat.excluded)
887	>	Ea += pre14_ * (trQb * rhat * dv21 + 2.0 * Qbr * v22or
888	>	+ rdQbr * rhat * (dv22 - 2.0*v22or));
889	>	}
890	>
891	>
892	>	if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) {
893	>	J = Jij[FQtids[idat.atid1]][FQtids[idat.atid2]];
894	>	}
895	>
896	>	if (a_is_Charge) {
897
898	<	if (j_is_Charge) {
899	<	if (screeningMethod_ == DAMPED) {
900	<	// assemble the damping variables
901	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
563	<	erfcVal = res.first;
564	<	derfcVal = res.second;
565	<	c1 = erfcVal * riji;
566	<	c2 = (-derfcVal + c1) * riji;
567	<	} else {
568	<	c1 = riji;
569	<	c2 = c1 * riji;
570	<	}
898	>	if (b_is_Charge) {
899	>	pref =  pre11_ * *(idat.electroMult);
900	>	U  += C_a * C_b * pref * v01;
901	>	F  += C_a * C_b * pref * dv01 * rhat;
902
903	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
904	<
574	<	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
575	<	vterm = preVal * (c1 - c1c_);
576	<	dudr  = -idat.sw * preVal * c2;
903	>	// If this is an excluded pair, there are still indirect
904	>	// interactions via the reaction field we must worry about:
905
906	<	} else if (summationMethod_ == esm_SHIFTED_FORCE)  {
907	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - cutoffRadius_) );
908	<	dudr  = idat.sw * preVal * (c2c_ - c2);
906	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
907	>	rfContrib = preRF_ * pref * C_a * C_b * *(idat.r2);
908	>	indirect_Pot += rfContrib;
909	>	indirect_F   += rfContrib * 2.0 * ri * rhat;
910	>	}
911
912	<	} else if (summationMethod_ == esm_REACTION_FIELD) {
913	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
914	<	vterm = preVal * ( riji + rfVal );
585	<	dudr  = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
912	>	// Fluctuating charge forces are handled via Coulomb integrals
913	>	// for excluded pairs (i.e. those connected via bonds) and
914	>	// with the standard charge-charge interaction otherwise.
915
916	+	if (idat.excluded) {
917	+	if (a_is_Fluctuating || b_is_Fluctuating) {
918	+	coulInt = J->getValueAt( *(idat.rij) );
919	+	if (a_is_Fluctuating) dUdCa += C_b * coulInt;
920	+	if (b_is_Fluctuating) dUdCb += C_a * coulInt;
921	+	}
922		} else {
923	<	vterm = preVal * riji * erfcVal;
923	>	if (a_is_Fluctuating) dUdCa += C_b * pref * v01;
924	>	if (b_is_Fluctuating) dUdCb += C_a * pref * v01;
925	>	}
926	>	}
927
928	<	dudr  = - idat.sw * preVal * c2;
928	>	if (b_is_Dipole) {
929	>	pref =  pre12_ * *(idat.electroMult);
930	>	U  += C_a * pref * v11 * rdDb;
931	>	F  += C_a * pref * ((dv11 - v11or) * rdDb * rhat + v11or * D_b);
932	>	Tb += C_a * pref * v11 * rxDb;
933
934	<	}
593	<
594	<	idat.vpair += vterm;
595	<	epot += idat.sw * vterm;
934	>	if (a_is_Fluctuating) dUdCa += pref * v11 * rdDb;
935
936	<	dVdr += dudr * rhat;
937	<	}
936	>	// Even if we excluded this pair from direct interactions, we
937	>	// still have the reaction-field-mediated charge-dipole
938	>	// interaction:
939
940	<	if (j_is_Dipole) {
941	<	// pref is used by all the possible methods
942	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
943	<	preSw = idat.sw * pref;
940	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
941	>	rfContrib = C_a * pref * preRF_ * 2.0 * *(idat.rij);
942	>	indirect_Pot += rfContrib * rdDb;
943	>	indirect_F   += rfContrib * D_b / (*idat.rij);
944	>	indirect_Tb  += C_a * pref * preRF_ * rxDb;
945	>	}
946	>	}
947
948	<	if (summationMethod_ == esm_REACTION_FIELD) {
949	<	ri2 = riji * riji;
950	<	ri3 = ri2 * riji;
951	<
952	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
953	<	idat.vpair += vterm;
611	<	epot += idat.sw * vterm;
948	>	if (b_is_Quadrupole) {
949	>	pref = pre14_ * *(idat.electroMult);
950	>	U  +=  C_a * pref * (v21 * trQb + v22 * rdQbr);
951	>	F  +=  C_a * pref * (trQb * dv21 * rhat + 2.0 * Qbr * v22or);
952	>	F  +=  C_a * pref * rdQbr * rhat * (dv22 - 2.0*v22or);
953	>	Tb +=  C_a * pref * 2.0 * rxQbr * v22;
954
955	<	dVdr +=  -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
956	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
955	>	if (a_is_Fluctuating) dUdCa += pref * (v21 * trQb + v22 * rdQbr);
956	>	}
957	>	}
958
959	<	} else {
617	<	// determine the inverse r used if we have split dipoles
618	<	if (j_is_SplitDipole) {
619	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
620	<	ri = 1.0 / BigR;
621	<	scale = idat.rij * ri;
622	<	} else {
623	<	ri = riji;
624	<	scale = 1.0;
625	<	}
626	<
627	<	sc2 = scale * scale;
959	>	if (a_is_Dipole) {
960
961	<	if (screeningMethod_ == DAMPED) {
962	<	// assemble the damping variables
631	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
632	<	erfcVal = res.first;
633	<	derfcVal = res.second;
634	<	c1 = erfcVal * ri;
635	<	c2 = (-derfcVal + c1) * ri;
636	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
637	<	} else {
638	<	c1 = ri;
639	<	c2 = c1 * ri;
640	<	c3 = 3.0 * c2 * ri;
641	<	}
642	<
643	<	c2ri = c2 * ri;
961	>	if (b_is_Charge) {
962	>	pref = pre12_ * *(idat.electroMult);
963
964	<	// calculate the potential
965	<	pot_term =  scale * c2;
966	<	vterm = -pref * ct_j * pot_term;
648	<	idat.vpair += vterm;
649	<	epot += idat.sw * vterm;
650	<
651	<	// calculate derivatives for forces and torques
964	>	U  -= C_b * pref * v11 * rdDa;
965	>	F  -= C_b * pref * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
966	>	Ta -= C_b * pref * v11 * rxDa;
967
968	<	dVdr += -preSw * (uz_j * c2ri - ct_j * rhat * sc2 * c3);
654	<	duduz_j += -preSw * pot_term * rhat;
968	>	if (b_is_Fluctuating) dUdCb -= pref * v11 * rdDa;
969
970	+	// Even if we excluded this pair from direct interactions,
971	+	// we still have the reaction-field-mediated charge-dipole
972	+	// interaction:
973	+	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
974	+	rfContrib = C_b * pref * preRF_ * 2.0 * *(idat.rij);
975	+	indirect_Pot -= rfContrib * rdDa;
976	+	indirect_F   -= rfContrib * D_a / (*idat.rij);
977	+	indirect_Ta  -= C_b * pref * preRF_ * rxDa;
978		}
979		}
980
981	<	if (j_is_Quadrupole) {
982	<	// first precalculate some necessary variables
983	<	cx2 = cx_j * cx_j;
984	<	cy2 = cy_j * cy_j;
985	<	cz2 = cz_j * cz_j;
986	<	pref =  idat.electroMult * pre14_ * q_i * one_third_;
987	<
988	<	if (screeningMethod_ == DAMPED) {
989	<	// assemble the damping variables
990	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
991	<	erfcVal = res.first;
992	<	derfcVal = res.second;
993	<	c1 = erfcVal * riji;
994	<	c2 = (-derfcVal + c1) * riji;
995	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
996	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
997	<	} else {
998	<	c1 = riji;
677	<	c2 = c1 * riji;
678	<	c3 = 3.0 * c2 * riji;
679	<	c4 = 5.0 * c3 * riji * riji;
981	>	if (b_is_Dipole) {
982	>	pref = pre22_ * *(idat.electroMult);
983	>	DadDb = dot(D_a, D_b);
984	>	DaxDb = cross(D_a, D_b);
985	>
986	>	U  -= pref * (DadDb * v21 + rdDa * rdDb * v22);
987	>	F  -= pref * (dv21 * DadDb * rhat + v22or * (rdDb * D_a + rdDa * D_b));
988	>	F  -= pref * (rdDa * rdDb) * (dv22 - 2.0*v22or) * rhat;
989	>	Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa);
990	>	Tb += pref * (-v21 * DaxDb - v22 * rdDa * rxDb);
991	>	// Even if we excluded this pair from direct interactions, we
992	>	// still have the reaction-field-mediated dipole-dipole
993	>	// interaction:
994	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
995	>	rfContrib = -pref * preRF_ * 2.0;
996	>	indirect_Pot += rfContrib * DadDb;
997	>	indirect_Ta  += rfContrib * DaxDb;
998	>	indirect_Tb  -= rfContrib * DaxDb;
999		}
1000	+	}
1001
1002	<	// precompute variables for convenience
1003	<	preSw = idat.sw * pref;
1004	<	c2ri = c2 * riji;
1005	<	c3ri = c3 * riji;
1006	<	c4rij = c4 * idat.rij;
687	<	rhatdot2 = 2.0 * rhat * c3;
688	<	rhatc4 = rhat * c4rij;
1002	>	if (b_is_Quadrupole) {
1003	>	pref = pre24_ * *(idat.electroMult);
1004	>	DadQb = D_a * Q_b;
1005	>	DadQbr = dot(D_a, Qbr);
1006	>	DaxQbr = cross(D_a, Qbr);
1007
1008	<	// calculate the potential
1009	<	pot_term = ( qxx_j * (cx2*c3 - c2ri) +
1010	<	qyy_j * (cy2*c3 - c2ri) +
1011	<	qzz_j * (cz2*c3 - c2ri) );
1012	<	vterm = pref * pot_term;
1013	<	idat.vpair += vterm;
1014	<	epot += idat.sw * vterm;
1015	<
698	<	// calculate derivatives for the forces and torques
699	<
700	<	dVdr += -preSw * ( qxx_j* (cx2*rhatc4 - (2.0*cx_j*ux_j + rhat)*c3ri) +
701	<	qyy_j* (cy2*rhatc4 - (2.0*cy_j*uy_j + rhat)*c3ri) +
702	<	qzz_j* (cz2*rhatc4 - (2.0*cz_j*uz_j + rhat)*c3ri));
703	<
704	<	dudux_j += preSw * qxx_j * cx_j * rhatdot2;
705	<	duduy_j += preSw * qyy_j * cy_j * rhatdot2;
706	<	duduz_j += preSw * qzz_j * cz_j * rhatdot2;
1008	>	U  -= pref * ((trQb*rdDa + 2.0*DadQbr)*v31 + rdDa*rdQbr*v32);
1009	>	F  -= pref * (trQb*D_a + 2.0*DadQb) * v31or;
1010	>	F  -= pref * (trQb*rdDa + 2.0*DadQbr) * (dv31-v31or) * rhat;
1011	>	F  -= pref * (D_a*rdQbr + 2.0*rdDa*rQb) * v32or;
1012	>	F  -= pref * (rdDa * rdQbr * rhat * (dv32-3.0*v32or));
1013	>	Ta += pref * ((-trQb*rxDa + 2.0 * DaxQbr)*v31 - rxDa*rdQbr*v32);
1014	>	Tb += pref * ((2.0*cross(DadQb, rhat) - 2.0*DaxQbr)*v31
1015	>	- 2.0*rdDa*rxQbr*v32);
1016		}
1017		}
709	–
710	–	if (i_is_Dipole) {
1018
1019	<	if (j_is_Charge) {
1020	<	// variables used by all the methods
1021	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
1022	<	preSw = idat.sw * pref;
1019	>	if (a_is_Quadrupole) {
1020	>	if (b_is_Charge) {
1021	>	pref = pre14_ * *(idat.electroMult);
1022	>	U  += C_b * pref * (v21 * trQa + v22 * rdQar);
1023	>	F  += C_b * pref * (trQa * rhat * dv21 + 2.0 * Qar * v22or);
1024	>	F  += C_b * pref * rdQar * rhat * (dv22 - 2.0*v22or);
1025	>	Ta += C_b * pref * 2.0 * rxQar * v22;
1026
1027	<	if (summationMethod_ == esm_REACTION_FIELD) {
1027	>	if (b_is_Fluctuating) dUdCb += pref * (v21 * trQa + v22 * rdQar);
1028	>	}
1029	>	if (b_is_Dipole) {
1030	>	pref = pre24_ * *(idat.electroMult);
1031	>	DbdQa = D_b * Q_a;
1032	>	DbdQar = dot(D_b, Qar);
1033	>	DbxQar = cross(D_b, Qar);
1034
1035	<	ri2 = riji * riji;
1036	<	ri3 = ri2 * riji;
1035	>	U  += pref * ((trQa*rdDb + 2.0*DbdQar)*v31 + rdDb*rdQar*v32);
1036	>	F  += pref * (trQa*D_b + 2.0*DbdQa) * v31or;
1037	>	F  += pref * (trQa*rdDb + 2.0*DbdQar) * (dv31-v31or) * rhat;
1038	>	F  += pref * (D_b*rdQar + 2.0*rdDb*rQa) * v32or;
1039	>	F  += pref * (rdDb * rdQar * rhat * (dv32-3.0*v32or));
1040	>	Ta += pref * ((-2.0*cross(DbdQa, rhat) + 2.0*DbxQar)*v31
1041	>	+ 2.0*rdDb*rxQar*v32);
1042	>	Tb += pref * ((trQa*rxDb - 2.0 * DbxQar)*v31 + rxDb*rdQar*v32);
1043	>	}
1044	>	if (b_is_Quadrupole) {
1045	>	pref = pre44_ * *(idat.electroMult);  // yes
1046	>	QaQb = Q_a * Q_b;
1047	>	trQaQb = QaQb.trace();
1048	>	rQaQb = rhat * QaQb;
1049	>	QaQbr = QaQb * rhat;
1050	>	QaxQb = mCross(Q_a, Q_b);
1051	>	rQaQbr = dot(rQa, Qbr);
1052	>	rQaxQbr = cross(rQa, Qbr);
1053	>
1054	>	U  += pref * (trQa * trQb + 2.0 * trQaQb) * v41;
1055	>	U  += pref * (trQa * rdQbr + trQb * rdQar  + 4.0 * rQaQbr) * v42;
1056	>	U  += pref * (rdQar * rdQbr) * v43;
1057
1058	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
1059	<	idat.vpair += vterm;
1060	<	epot += idat.sw * vterm;
725	<
726	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
727	<
728	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
729	<
730	<	} else {
731	<
732	<	// determine inverse r if we are using split dipoles
733	<	if (i_is_SplitDipole) {
734	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
735	<	ri = 1.0 / BigR;
736	<	scale = idat.rij * ri;
737	<	} else {
738	<	ri = riji;
739	<	scale = 1.0;
740	<	}
741	<
742	<	sc2 = scale * scale;
743	<
744	<	if (screeningMethod_ == DAMPED) {
745	<	// assemble the damping variables
746	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
747	<	erfcVal = res.first;
748	<	derfcVal = res.second;
749	<	c1 = erfcVal * ri;
750	<	c2 = (-derfcVal + c1) * ri;
751	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
752	<	} else {
753	<	c1 = ri;
754	<	c2 = c1 * ri;
755	<	c3 = 3.0 * c2 * ri;
756	<	}
757	<
758	<	c2ri = c2 * ri;
759	<
760	<	// calculate the potential
761	<	pot_term = c2 * scale;
762	<	vterm = pref * ct_i * pot_term;
763	<	idat.vpair += vterm;
764	<	epot += idat.sw * vterm;
1058	>	F  += pref * rhat * (trQa * trQb + 2.0 * trQaQb)*dv41;
1059	>	F  += pref*rhat*(trQa*rdQbr + trQb*rdQar + 4.0*rQaQbr)*(dv42-2.0*v42or);
1060	>	F  += pref * rhat * (rdQar * rdQbr)*(dv43 - 4.0*v43or);
1061
1062	<	// calculate derivatives for the forces and torques
1063	<	dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
1064	<	duduz_i += preSw * pot_term * rhat;
769	<	}
770	<	}
1062	>	F  += pref * 2.0 * (trQb*rQa + trQa*rQb) * v42or;
1063	>	F  += pref * 4.0 * (rQaQb + QaQbr) * v42or;
1064	>	F  += pref * 2.0 * (rQa*rdQbr + rdQar*rQb) * v43or;
1065
1066	<	if (j_is_Dipole) {
1067	<	// variables used by all methods
1068	<	ct_ij = dot(uz_i, uz_j);
1066	>	Ta += pref * (- 4.0 * QaxQb * v41);
1067	>	Ta += pref * (- 2.0 * trQb * cross(rQa, rhat)
1068	>	+ 4.0 * cross(rhat, QaQbr)
1069	>	- 4.0 * rQaxQbr) * v42;
1070	>	Ta += pref * 2.0 * cross(rhat,Qar) * rdQbr * v43;
1071
776	–	pref = idat.electroMult * pre22_ * mu_i * mu_j;
777	–	preSw = idat.sw * pref;
1072
1073	<	if (summationMethod_ == esm_REACTION_FIELD) {
1074	<	ri2 = riji * riji;
1075	<	ri3 = ri2 * riji;
1076	<	ri4 = ri2 * ri2;
1073	>	Tb += pref * (+ 4.0 * QaxQb * v41);
1074	>	Tb += pref * (- 2.0 * trQa * cross(rQb, rhat)
1075	>	- 4.0 * cross(rQaQb, rhat)
1076	>	+ 4.0 * rQaxQbr) * v42;
1077	>	// Possible replacement for line 2 above:
1078	>	//             + 4.0 * cross(rhat, QbQar)
1079
1080	<	vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
785	<	preRF2_ * ct_ij );
786	<	idat.vpair += vterm;
787	<	epot += idat.sw * vterm;
788	<
789	<	a1 = 5.0 * ct_i * ct_j - ct_ij;
790	<
791	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
792	<
793	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
794	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
795	<
796	<	} else {
797	<
798	<	if (i_is_SplitDipole) {
799	<	if (j_is_SplitDipole) {
800	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
801	<	} else {
802	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
803	<	}
804	<	ri = 1.0 / BigR;
805	<	scale = idat.rij * ri;
806	<	} else {
807	<	if (j_is_SplitDipole) {
808	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
809	<	ri = 1.0 / BigR;
810	<	scale = idat.rij * ri;
811	<	} else {
812	<	ri = riji;
813	<	scale = 1.0;
814	<	}
815	<	}
816	<	if (screeningMethod_ == DAMPED) {
817	<	// assemble damping variables
818	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
819	<	erfcVal = res.first;
820	<	derfcVal = res.second;
821	<	c1 = erfcVal * ri;
822	<	c2 = (-derfcVal + c1) * ri;
823	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
824	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * ri * ri;
825	<	} else {
826	<	c1 = ri;
827	<	c2 = c1 * ri;
828	<	c3 = 3.0 * c2 * ri;
829	<	c4 = 5.0 * c3 * ri * ri;
830	<	}
831	<
832	<	// precompute variables for convenience
833	<	sc2 = scale * scale;
834	<	cti3 = ct_i * sc2 * c3;
835	<	ctj3 = ct_j * sc2 * c3;
836	<	ctidotj = ct_i * ct_j * sc2;
837	<	preSwSc = preSw * scale;
838	<	c2ri = c2 * ri;
839	<	c3ri = c3 * ri;
840	<	c4rij = c4 * idat.rij;
841	<
842	<	// calculate the potential
843	<	pot_term = (ct_ij * c2ri - ctidotj * c3);
844	<	vterm = pref * pot_term;
845	<	idat.vpair += vterm;
846	<	epot += idat.sw * vterm;
847	<
848	<	// calculate derivatives for the forces and torques
849	<	dVdr += preSwSc * ( ctidotj * rhat * c4rij  -
850	<	(ct_i*uz_j + ct_j*uz_i + ct_ij*rhat) * c3ri);
851	<
852	<	duduz_i += preSw * (uz_j * c2ri - ctj3 * rhat);
853	<	duduz_j += preSw * (uz_i * c2ri - cti3 * rhat);
854	<	}
1080	>	Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43;
1081		}
1082		}
1083
1084	<	if (i_is_Quadrupole) {
1085	<	if (j_is_Charge) {
1086	<	// precompute some necessary variables
1087	<	cx2 = cx_i * cx_i;
862	<	cy2 = cy_i * cy_i;
863	<	cz2 = cz_i * cz_i;
1084	>	if (idat.doElectricField) {
1085	>	*(idat.eField1) += Ea * *(idat.electroMult);
1086	>	*(idat.eField2) += Eb * *(idat.electroMult);
1087	>	}
1088
1089	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
1089	>	if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw);
1090	>	if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw);
1091
1092	<	if (screeningMethod_ == DAMPED) {
1093	<	// assemble the damping variables
1094	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
1095	<	erfcVal = res.first;
1096	<	derfcVal = res.second;
1097	<	c1 = erfcVal * riji;
1098	<	c2 = (-derfcVal + c1) * riji;
1099	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
875	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
876	<	} else {
877	<	c1 = riji;
878	<	c2 = c1 * riji;
879	<	c3 = 3.0 * c2 * riji;
880	<	c4 = 5.0 * c3 * riji * riji;
881	<	}
882	<
883	<	// precompute some variables for convenience
884	<	preSw = idat.sw * pref;
885	<	c2ri = c2 * riji;
886	<	c3ri = c3 * riji;
887	<	c4rij = c4 * idat.rij;
888	<	rhatdot2 = 2.0 * rhat * c3;
889	<	rhatc4 = rhat * c4rij;
1092	>	if (!idat.excluded) {
1093	>
1094	>	*(idat.vpair) += U;
1095	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += U * *(idat.sw);
1096	>	*(idat.f1) += F * *(idat.sw);
1097	>
1098	>	if (a_is_Dipole || a_is_Quadrupole)
1099	>	*(idat.t1) += Ta * *(idat.sw);
1100
1101	<	// calculate the potential
1102	<	pot_term = ( qxx_i * (cx2 * c3 - c2ri) +
1103	<	qyy_i * (cy2 * c3 - c2ri) +
1104	<	qzz_i * (cz2 * c3 - c2ri) );
895	<
896	<	vterm = pref * pot_term;
897	<	idat.vpair += vterm;
898	<	epot += idat.sw * vterm;
1101	>	if (b_is_Dipole || b_is_Quadrupole)
1102	>	*(idat.t2) += Tb * *(idat.sw);
1103	>
1104	>	} else {
1105
1106	<	// calculate the derivatives for the forces and torques
1106	>	// only accumulate the forces and torques resulting from the
1107	>	// indirect reaction field terms.
1108
1109	<	dVdr += -preSw * (qxx_i* (cx2*rhatc4 - (2.0*cx_i*ux_i + rhat)*c3ri) +
1110	<	qyy_i* (cy2*rhatc4 - (2.0*cy_i*uy_i + rhat)*c3ri) +
1111	<	qzz_i* (cz2*rhatc4 - (2.0*cz_i*uz_i + rhat)*c3ri));
1112	<
1113	<	dudux_i += preSw * qxx_i * cx_i *  rhatdot2;
1114	<	duduy_i += preSw * qyy_i * cy_i *  rhatdot2;
1115	<	duduz_i += preSw * qzz_i * cz_i *  rhatdot2;
1116	<	}
1109	>	*(idat.vpair) += indirect_Pot;
1110	>	(*(idat.excludedPot))[ELECTROSTATIC_FAMILY] +=  excluded_Pot;
1111	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += *(idat.sw) * indirect_Pot;
1112	>	*(idat.f1) += *(idat.sw) * indirect_F;
1113	>
1114	>	if (a_is_Dipole || a_is_Quadrupole)
1115	>	*(idat.t1) += *(idat.sw) * indirect_Ta;
1116	>
1117	>	if (b_is_Dipole || b_is_Quadrupole)
1118	>	*(idat.t2) += *(idat.sw) * indirect_Tb;
1119		}
911	–
912	–	idat.pot += epot;
913	–	idat.f1 += dVdr;
914	–
915	–	if (i_is_Dipole || i_is_Quadrupole)
916	–	idat.t1 -= cross(uz_i, duduz_i);
917	–	if (i_is_Quadrupole) {
918	–	idat.t1 -= cross(ux_i, dudux_i);
919	–	idat.t1 -= cross(uy_i, duduy_i);
920	–	}
921	–
922	–	if (j_is_Dipole || j_is_Quadrupole)
923	–	idat.t2 -= cross(uz_j, duduz_j);
924	–	if (j_is_Quadrupole) {
925	–	idat.t2 -= cross(uz_j, dudux_j);
926	–	idat.t2 -= cross(uz_j, duduy_j);
927	–	}
928	–
1120		return;
1121	<	}
1121	>	}
1122	>
1123	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1124
932	–	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
933	–
1125		if (!initialized_) initialize();
1126	+
1127	+	ElectrostaticAtomData data = ElectrostaticMap[Etids[sdat.atid]];
1128
936	–	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
937	–	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
938	–
1129		// logicals
1130	+	bool i_is_Charge = data.is_Charge;
1131	+	bool i_is_Dipole = data.is_Dipole;
1132	+	bool i_is_Quadrupole = data.is_Quadrupole;
1133	+	bool i_is_Fluctuating = data.is_Fluctuating;
1134	+	RealType C_a = data.fixedCharge;
1135	+	RealType self(0.0), preVal, DdD, trQ, trQQ;
1136
1137	<	bool i_is_Charge = data1.is_Charge;
1138	<	bool i_is_Dipole = data1.is_Dipole;
943	<
944	<	bool j_is_Charge = data2.is_Charge;
945	<	bool j_is_Dipole = data2.is_Dipole;
946	<
947	<	RealType q_i, q_j;
948	<
949	<	// The skippedCharge computation is needed by the real-space cutoff methods
950	<	// (i.e. shifted force and shifted potential)
951	<
952	<	if (i_is_Charge) {
953	<	q_i = data1.charge;
954	<	skdat.skippedCharge2 += q_i;
1137	>	if (i_is_Dipole) {
1138	>	DdD = data.dipole.lengthSquare();
1139		}
1140	<
1141	<	if (j_is_Charge) {
1142	<	q_j = data2.charge;
1143	<	skdat.skippedCharge1 += q_j;
1140	>
1141	>	if (i_is_Fluctuating) {
1142	>	C_a += *(sdat.flucQ);
1143	>	*(sdat.flucQfrc) -=  *(sdat.flucQ) * data.hardness + data.electronegativity;
1144	>	(*(sdat.excludedPot))[ELECTROSTATIC_FAMILY] += (*sdat.flucQ) *
1145	>	(*(sdat.flucQ) * data.hardness * 0.5 + data.electronegativity);
1146		}
1147
1148	<	// the rest of this function should only be necessary for reaction field.
1149	<
964	<	if (summationMethod_ == esm_REACTION_FIELD) {
965	<	RealType riji, ri2, ri3;
966	<	RealType q_i, mu_i, ct_i;
967	<	RealType q_j, mu_j, ct_j;
968	<	RealType preVal, rfVal, vterm, dudr, pref, myPot;
969	<	Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat;
970	<
971	<	// some variables we'll need independent of electrostatic type:
1148	>	switch (summationMethod_) {
1149	>	case esm_REACTION_FIELD:
1150
973	–	riji = 1.0 / skdat.rij;
974	–	rhat = skdat.d  * riji;
975	–
976	–	if (i_is_Dipole) {
977	–	mu_i = data1.dipole_moment;
978	–	uz_i = skdat.eFrame1.getColumn(2);
979	–	ct_i = dot(uz_i, rhat);
980	–	duduz_i = V3Zero;
981	–	}
982	–
983	–	if (j_is_Dipole) {
984	–	mu_j = data2.dipole_moment;
985	–	uz_j = skdat.eFrame2.getColumn(2);
986	–	ct_j = dot(uz_j, rhat);
987	–	duduz_j = V3Zero;
988	–	}
989	–
1151		if (i_is_Charge) {
1152	<	if (j_is_Charge) {
1153	<	preVal = skdat.electroMult * pre11_ * q_i * q_j;
1154	<	rfVal = preRF_ * skdat.rij * skdat.rij;
1155	<	vterm = preVal * rfVal;
1156	<	myPot += skdat.sw * vterm;
996	<	dudr  = skdat.sw * preVal * 2.0 * rfVal * riji;
997	<	dVdr += dudr * rhat;
998	<	}
999	<
1000	<	if (j_is_Dipole) {
1001	<	ri2 = riji * riji;
1002	<	ri3 = ri2 * riji;
1003	<	pref = skdat.electroMult * pre12_ * q_i * mu_j;
1004	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * skdat.rij );
1005	<	myPot += skdat.sw * vterm;
1006	<	dVdr += -skdat.sw * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j);
1007	<	duduz_j += -skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
1008	<	}
1152	>	// Self potential [see Wang and Hermans, "Reaction Field
1153	>	// Molecular Dynamics Simulation with Friedman’s Image Charge
1154	>	// Method," J. Phys. Chem. 99, 12001-12007 (1995).]
1155	>	preVal = pre11_ * preRF_ * C_a * C_a;
1156	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 * preVal / cutoffRadius_;
1157		}
1158	+
1159		if (i_is_Dipole) {
1160	<	if (j_is_Charge) {
1012	<	ri2 = riji * riji;
1013	<	ri3 = ri2 * riji;
1014	<	pref = skdat.electroMult * pre12_ * q_j * mu_i;
1015	<	vterm = - pref * ct_i * ( ri2 - preRF2_ * skdat.rij );
1016	<	myPot += skdat.sw * vterm;
1017	<	dVdr += skdat.sw * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
1018	<	duduz_i += skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
1019	<	}
1160	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DdD;
1161		}
1162
1163	<	// accumulate the forces and torques resulting from the self term
1023	<	skdat.pot += myPot;
1024	<	skdat.f1 += dVdr;
1163	>	break;
1164
1165	+	case esm_SHIFTED_FORCE:
1166	+	case esm_SHIFTED_POTENTIAL:
1167	+	case esm_TAYLOR_SHIFTED:
1168	+	case esm_EWALD_FULL:
1169	+	if (i_is_Charge)
1170	+	self += selfMult1_ * pre11_ * C_a * (C_a + *(sdat.skippedCharge));
1171		if (i_is_Dipole)
1172	<	skdat.t1 -= cross(uz_i, duduz_i);
1173	<	if (j_is_Dipole)
1174	<	skdat.t2 -= cross(uz_j, duduz_j);
1172	>	self += selfMult2_ * pre22_ * DdD;
1173	>	if (i_is_Quadrupole) {
1174	>	trQ = data.quadrupole.trace();
1175	>	trQQ = (data.quadrupole * data.quadrupole).trace();
1176	>	self += selfMult4_ * pre44_ * (2.0*trQQ + trQ*trQ);
1177	>	if (i_is_Charge)
1178	>	self -= selfMult2_ * pre14_ * 2.0 * C_a * trQ;
1179	>	}
1180	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1181	>	break;
1182	>	default:
1183	>	break;
1184		}
1185		}
1186	+
1187	+	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
1188	+	// This seems to work moderately well as a default.  There's no
1189	+	// inherent scale for 1/r interactions that we can standardize.
1190	+	// 12 angstroms seems to be a reasonably good guess for most
1191	+	// cases.
1192	+	return 12.0;
1193	+	}
1194	+
1195	+
1196	+	void Electrostatic::ReciprocalSpaceSum(RealType& pot) {
1197
1198	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1199	<	RealType mu1, preVal, chg1, self;
1198	>	RealType kPot = 0.0;
1199	>	RealType kVir = 0.0;
1200
1201	<	if (!initialized_) initialize();
1201	>	const RealType mPoleConverter = 0.20819434; // converts from the
1202	>	// internal units of
1203	>	// Debye (for dipoles)
1204	>	// or Debye-angstroms
1205	>	// (for quadrupoles) to
1206	>	// electron angstroms or
1207	>	// electron-angstroms^2
1208
1209	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1210	<
1211	<	// logicals
1209	>	const RealType eConverter = 332.0637778; // convert the
1210	>	// Charge-Charge
1211	>	// electrostatic
1212	>	// interactions into kcal /
1213	>	// mol assuming distances
1214	>	// are measured in
1215	>	// angstroms.
1216
1217	<	bool i_is_Charge = data.is_Charge;
1218	<	bool i_is_Dipole = data.is_Dipole;
1217	>	Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
1218	>	Vector3d box = hmat.diagonals();
1219	>	RealType boxMax = box.max();
1220	>
1221	>	//int kMax = int(2.0 * M_PI / (pow(dampingAlpha_,2)*cutoffRadius_ * boxMax) );
1222	>	int kMax = 7;
1223	>	int kSqMax = kMax*kMax + 2;
1224	>
1225	>	int kLimit = kMax+1;
1226	>	int kLim2 = 2*kMax+1;
1227	>	int kSqLim = kSqMax;
1228	>
1229	>	vector<RealType> AK(kSqLim+1, 0.0);
1230	>	RealType xcl = 2.0 * M_PI / box.x();
1231	>	RealType ycl = 2.0 * M_PI / box.y();
1232	>	RealType zcl = 2.0 * M_PI / box.z();
1233	>	RealType rcl = 2.0 * M_PI / boxMax;
1234	>	RealType rvol = 2.0 * M_PI /(box.x() * box.y() * box.z());
1235	>
1236	>	if(dampingAlpha_ < 1.0e-12) return;
1237	>
1238	>	RealType ralph = -0.25/pow(dampingAlpha_,2);
1239	>
1240	>	// Calculate and store exponential factors
1241	>
1242	>	vector<vector<RealType> > elc;
1243	>	vector<vector<RealType> > emc;
1244	>	vector<vector<RealType> > enc;
1245	>	vector<vector<RealType> > els;
1246	>	vector<vector<RealType> > ems;
1247	>	vector<vector<RealType> > ens;
1248
1249	<	if (summationMethod_ == esm_REACTION_FIELD) {
1250	<	if (i_is_Dipole) {
1251	<	mu1 = data.dipole_moment;
1252	<	preVal = pre22_ * preRF2_ * mu1 * mu1;
1253	<	scdat.pot -= 0.5 * preVal;
1249	>
1250	>	int nMax = info_->getNAtoms();
1251	>
1252	>	elc.resize(kLimit+1);
1253	>	emc.resize(kLimit+1);
1254	>	enc.resize(kLimit+1);
1255	>	els.resize(kLimit+1);
1256	>	ems.resize(kLimit+1);
1257	>	ens.resize(kLimit+1);
1258	>
1259	>	for (int j = 0; j < kLimit+1; j++) {
1260	>	elc[j].resize(nMax);
1261	>	emc[j].resize(nMax);
1262	>	enc[j].resize(nMax);
1263	>	els[j].resize(nMax);
1264	>	ems[j].resize(nMax);
1265	>	ens[j].resize(nMax);
1266	>	}
1267	>
1268	>	Vector3d t( 2.0 * M_PI );
1269	>	t.Vdiv(t, box);
1270	>
1271	>
1272	>	SimInfo::MoleculeIterator mi;
1273	>	Molecule::AtomIterator ai;
1274	>	int i;
1275	>	Vector3d r;
1276	>	Vector3d tt;
1277	>
1278	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1279	>	mol = info_->nextMolecule(mi)) {
1280	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1281	>	atom = mol->nextAtom(ai)) {
1282
1283	<	// The self-correction term adds into the reaction field vector
1284	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1285	<	Vector3d ei = preVal * uz_i;
1283	>	i = atom->getLocalIndex();
1284	>	r = atom->getPos();
1285	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(r);
1286	>
1287	>	tt.Vmul(t, r);
1288
1289	<	// This looks very wrong.  A vector crossed with itself is zero.
1290	<	scdat.t -= cross(uz_i, ei);
1289	>	elc[1][i] = 1.0;
1290	>	emc[1][i] = 1.0;
1291	>	enc[1][i] = 1.0;
1292	>	els[1][i] = 0.0;
1293	>	ems[1][i] = 0.0;
1294	>	ens[1][i] = 0.0;
1295	>
1296	>	elc[2][i] = cos(tt.x());
1297	>	emc[2][i] = cos(tt.y());
1298	>	enc[2][i] = cos(tt.z());
1299	>	els[2][i] = sin(tt.x());
1300	>	ems[2][i] = sin(tt.y());
1301	>	ens[2][i] = sin(tt.z());
1302	>
1303	>	for(int l = 3; l <= kLimit; l++) {
1304	>	elc[l][i]=elc[l-1][i]*elc[2][i]-els[l-1][i]*els[2][i];
1305	>	emc[l][i]=emc[l-1][i]*emc[2][i]-ems[l-1][i]*ems[2][i];
1306	>	enc[l][i]=enc[l-1][i]*enc[2][i]-ens[l-1][i]*ens[2][i];
1307	>	els[l][i]=els[l-1][i]*elc[2][i]+elc[l-1][i]*els[2][i];
1308	>	ems[l][i]=ems[l-1][i]*emc[2][i]+emc[l-1][i]*ems[2][i];
1309	>	ens[l][i]=ens[l-1][i]*enc[2][i]+enc[l-1][i]*ens[2][i];
1310	>	}
1311		}
1312	<	} else if (summationMethod_ == esm_SHIFTED_FORCE || summationMethod_ == esm_SHIFTED_POTENTIAL) {
1313	<	if (i_is_Charge) {
1314	<	chg1 = data.charge;
1315	<	if (screeningMethod_ == DAMPED) {
1316	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1317	<	} else {
1318	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1312	>	}
1313	>
1314	>	// Calculate and store AK coefficients:
1315	>
1316	>	RealType eksq = 1.0;
1317	>	RealType expf = 0.0;
1318	>	if (ralph < 0.0) expf = exp(ralph*rcl*rcl);
1319	>	for (i = 1; i <= kSqLim; i++) {
1320	>	RealType rksq = float(i)*rcl*rcl;
1321	>	eksq = expf*eksq;
1322	>	AK[i] = eConverter * eksq/rksq;
1323	>	}
1324	>
1325	>	/*
1326	>	* Loop over all k vectors k = 2 pi (ll/Lx, mm/Ly, nn/Lz)
1327	>	* the values of ll, mm and nn are selected so that the symmetry of
1328	>	* reciprocal lattice is taken into account i.e. the following
1329	>	* rules apply.
1330	>	*
1331	>	* ll ranges over the values 0 to kMax only.
1332	>	*
1333	>	* mm ranges over 0 to kMax when ll=0 and over
1334	>	*            -kMax to kMax otherwise.
1335	>	* nn ranges over 1 to kMax when ll=mm=0 and over
1336	>	*            -kMax to kMax otherwise.
1337	>	*
1338	>	* Hence the result of the summation must be doubled at the end.
1339	>	*/
1340	>
1341	>	std::vector<RealType> clm(nMax, 0.0);
1342	>	std::vector<RealType> slm(nMax, 0.0);
1343	>	std::vector<RealType> ckr(nMax, 0.0);
1344	>	std::vector<RealType> skr(nMax, 0.0);
1345	>	std::vector<RealType> ckc(nMax, 0.0);
1346	>	std::vector<RealType> cks(nMax, 0.0);
1347	>	std::vector<RealType> dkc(nMax, 0.0);
1348	>	std::vector<RealType> dks(nMax, 0.0);
1349	>	std::vector<RealType> qkc(nMax, 0.0);
1350	>	std::vector<RealType> qks(nMax, 0.0);
1351	>	std::vector<Vector3d> dxk(nMax, V3Zero);
1352	>	std::vector<Vector3d> qxk(nMax, V3Zero);
1353	>	RealType rl, rm, rn;
1354	>	Vector3d kVec;
1355	>	Vector3d Qk;
1356	>	Mat3x3d k2;
1357	>	RealType ckcs, ckss, dkcs, dkss, qkcs, qkss;
1358	>	int atid;
1359	>	ElectrostaticAtomData data;
1360	>	RealType C, dk, qk;
1361	>	Vector3d D;
1362	>	Mat3x3d  Q;
1363	>
1364	>	int mMin = kLimit;
1365	>	int nMin = kLimit + 1;
1366	>	for (int l = 1; l <= kLimit; l++) {
1367	>	int ll = l - 1;
1368	>	rl = xcl * float(ll);
1369	>	for (int mmm = mMin; mmm <= kLim2; mmm++) {
1370	>	int mm = mmm - kLimit;
1371	>	int m = abs(mm) + 1;
1372	>	rm = ycl * float(mm);
1373	>	// Set temporary products of exponential terms
1374	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1375	>	mol = info_->nextMolecule(mi)) {
1376	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1377	>	atom = mol->nextAtom(ai)) {
1378	>
1379	>	i = atom->getLocalIndex();
1380	>	if(mm < 0) {
1381	>	clm[i]=elc[l][i]*emc[m][i]+els[l][i]*ems[m][i];
1382	>	slm[i]=els[l][i]*emc[m][i]-ems[m][i]*elc[l][i];
1383	>	} else {
1384	>	clm[i]=elc[l][i]*emc[m][i]-els[l][i]*ems[m][i];
1385	>	slm[i]=els[l][i]*emc[m][i]+ems[m][i]*elc[l][i];
1386	>	}
1387	>	}
1388		}
1389	<	scdat.pot += self;
1389	>	for (int nnn = nMin; nnn <= kLim2; nnn++) {
1390	>	int nn = nnn - kLimit;
1391	>	int n = abs(nn) + 1;
1392	>	rn = zcl * float(nn);
1393	>	// Test on magnitude of k vector:
1394	>	int kk=ll*ll + mm*mm + nn*nn;
1395	>	if(kk <= kSqLim) {
1396	>	kVec = Vector3d(rl, rm, rn);
1397	>	k2 = outProduct(kVec, kVec);
1398	>	// Calculate exp(ikr) terms
1399	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1400	>	mol = info_->nextMolecule(mi)) {
1401	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1402	>	atom = mol->nextAtom(ai)) {
1403	>	i = atom->getLocalIndex();
1404	>
1405	>	if (nn < 0) {
1406	>	ckr[i]=clm[i]*enc[n][i]+slm[i]*ens[n][i];
1407	>	skr[i]=slm[i]*enc[n][i]-clm[i]*ens[n][i];
1408	>
1409	>	} else {
1410	>	ckr[i]=clm[i]*enc[n][i]-slm[i]*ens[n][i];
1411	>	skr[i]=slm[i]*enc[n][i]+clm[i]*ens[n][i];
1412	>	}
1413	>	}
1414	>	}
1415	>
1416	>	// Calculate scalar and vector products for each site:
1417	>
1418	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1419	>	mol = info_->nextMolecule(mi)) {
1420	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1421	>	atom = mol->nextAtom(ai)) {
1422	>	i = atom->getLocalIndex();
1423	>	int atid = atom->getAtomType()->getIdent();
1424	>	data = ElectrostaticMap[Etids[atid]];
1425	>
1426	>	if (data.is_Charge) {
1427	>	C = data.fixedCharge;
1428	>	if (atom->isFluctuatingCharge()) C += atom->getFlucQPos();
1429	>	ckc[i] = C * ckr[i];
1430	>	cks[i] = C * skr[i];
1431	>	}
1432	>
1433	>	if (data.is_Dipole) {
1434	>	D = atom->getDipole() * mPoleConverter;
1435	>	dk = dot(D, kVec);
1436	>	dxk[i] = cross(D, kVec);
1437	>	dkc[i] = dk * ckr[i];
1438	>	dks[i] = dk * skr[i];
1439	>	}
1440	>	if (data.is_Quadrupole) {
1441	>	Q = atom->getQuadrupole() * mPoleConverter;
1442	>	Qk = Q * kVec;
1443	>	qk = dot(kVec, Qk);
1444	>	qxk[i] = -cross(kVec, Qk);
1445	>	qkc[i] = qk * ckr[i];
1446	>	qks[i] = qk * skr[i];
1447	>	}
1448	>	}
1449	>	}
1450	>
1451	>	// calculate vector sums
1452	>
1453	>	ckcs = std::accumulate(ckc.begin(),ckc.end(),0.0);
1454	>	ckss = std::accumulate(cks.begin(),cks.end(),0.0);
1455	>	dkcs = std::accumulate(dkc.begin(),dkc.end(),0.0);
1456	>	dkss = std::accumulate(dks.begin(),dks.end(),0.0);
1457	>	qkcs = std::accumulate(qkc.begin(),qkc.end(),0.0);
1458	>	qkss = std::accumulate(qks.begin(),qks.end(),0.0);
1459	>
1460	>	#ifdef IS_MPI
1461	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckcs, 1, MPI::REALTYPE,
1462	>	MPI::SUM);
1463	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckss, 1, MPI::REALTYPE,
1464	>	MPI::SUM);
1465	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkcs, 1, MPI::REALTYPE,
1466	>	MPI::SUM);
1467	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkss, 1, MPI::REALTYPE,
1468	>	MPI::SUM);
1469	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkcs, 1, MPI::REALTYPE,
1470	>	MPI::SUM);
1471	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkss, 1, MPI::REALTYPE,
1472	>	MPI::SUM);
1473	>	#endif
1474	>
1475	>	// Accumulate potential energy and virial contribution:
1476	>
1477	>	kPot += 2.0 * rvol * AK[kk]*((ckss+dkcs-qkss)*(ckss+dkcs-qkss)
1478	>	+ (ckcs-dkss-qkcs)*(ckcs-dkss-qkcs));
1479	>
1480	>	kVir += 2.0 * rvol  * AK[kk]*(ckcs*ckcs+ckss*ckss
1481	>	+4.0*(ckss*dkcs-ckcs*dkss)
1482	>	+3.0*(dkcs*dkcs+dkss*dkss)
1483	>	-6.0*(ckss*qkss+ckcs*qkcs)
1484	>	+8.0*(dkss*qkcs-dkcs*qkss)
1485	>	+5.0*(qkss*qkss+qkcs*qkcs));
1486	>
1487	>	// Calculate force and torque for each site:
1488	>
1489	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1490	>	mol = info_->nextMolecule(mi)) {
1491	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1492	>	atom = mol->nextAtom(ai)) {
1493	>
1494	>	i = atom->getLocalIndex();
1495	>	atid = atom->getAtomType()->getIdent();
1496	>	data = ElectrostaticMap[Etids[atid]];
1497	>
1498	>	RealType qfrc = AK[kk]*((cks[i]+dkc[i]-qks[i])*(ckcs-dkss-qkcs)
1499	>	- (ckc[i]-dks[i]-qkc[i])*(ckss+dkcs-qkss));
1500	>	RealType qtrq1 = AK[kk]*(skr[i]*(ckcs-dkss-qkcs)
1501	>	-ckr[i]*(ckss+dkcs-qkss));
1502	>	RealType qtrq2 = 2.0*AK[kk]*(ckr[i]*(ckcs-dkss-qkcs)
1503	>	+skr[i]*(ckss+dkcs-qkss));
1504	>
1505	>	atom->addFrc( 4.0 * rvol * qfrc * kVec );
1506	>
1507	>	if (data.is_Dipole) {
1508	>	atom->addTrq( 4.0 * rvol * qtrq1 * dxk[i] );
1509	>	}
1510	>	if (data.is_Quadrupole) {
1511	>	atom->addTrq( 4.0 * rvol * qtrq2 * qxk[i] );
1512	>	}
1513	>	}
1514	>	}
1515	>	}
1516	>	}
1517	>	nMin = 1;
1518		}
1519	+	mMin = 1;
1520		}
1521	+	pot += kPot;
1522		}
1070	–
1071	–	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
1072	–	// This seems to work moderately well as a default.  There's no
1073	–	// inherent scale for 1/r interactions that we can standardize.
1074	–	// 12 angstroms seems to be a reasonably good guess for most
1075	–	// cases.
1076	–	return 12.0;
1077	–	}
1523		}

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